TRANSFAC

Names
More detailed information about this field from each metasource.

TRANSFAC
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

transfac
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

Other names: transfac

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

Webpage:

http://www.gene-regulation.com/pub/databases.html#transfac

Publications: (7)

Publications
More detailed information about this field from each metasource.

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
PMID: 16381825
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

TRANSFAC: transcriptional regulation, from patterns to profiles
PMID: 12520026
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

TRANSFAC: an integrated system for gene expression regulation
PMID: 10592259
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

TRANSFAC: a database on transcription factors and their DNA binding sites
PMID: 8594589
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

The TRANSFAC system on gene expression regulation
PMID: 11125113
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
PMID: 18436575
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
PMID: 9847216
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes PubMed citations: 1174.

1174 articles citing: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls. PMID:35356752
Overexpression of the Hsa21 Transcription Factor RUNX1 Modulates the Extracellular Matrix in Trisomy 21 Cells. PMID:35356434
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. PMID:35269428
The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling. PMID:35177770
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. PMID:35140205
Histone acetylome-wide associations in immune cells from individuals with active Mycobacterium tuberculosis infection. PMID:35102304
Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity. PMID:35098922
Polympact: exploring functional relations among common human genetic variants. PMID:35061909
GCN5 maintains muscle integrity by acetylating YY1 to promote dystrophin expression. PMID:35024765
Molecular Pathways Modulating Sensory Hair Cell Regeneration in Adult Mammalian Cochleae: Progress and Perspectives. PMID:35008497
Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. PMID:34947998
KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma. PMID:34893606
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502
Mutant IDH Inhibits IFNγ-TET2 Signaling to Promote Immunoevasion and Tumor Maintenance in Cholangiocarcinoma. PMID:34848557
Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis. PMID:34829754
Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization. PMID:34795444
Regulatory network of miRNA, lncRNA, transcription factor and target immune response genes in bovine mastitis. PMID:34753991
Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines. PMID:34742908
Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform. PMID:34712617
Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer. PMID:34686186
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. PMID:34664074
Identification and Characterisation of cis-Regulatory Elements Upstream of the Human Receptor Tyrosine Kinase Gene MERTK. PMID:34631417
Heme Oxygenase-1 at the Nexus of Endothelial Cell Fate Decision Under Oxidative Stress. PMID:34595164
Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease. PMID:34494552
Acute depletion of CTCF rewires genome-wide chromatin accessibility. PMID:34429148
Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function. PMID:34425299
Patients with PWS and related syndromes display differentially methylated regions involved in neurodevelopmental and nutritional trajectory. PMID:34389046
ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells. PMID:34381375
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. PMID:34331449
Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells. PMID:34285924
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. PMID:34208629
Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation. PMID:34207065
Identification of hub genes associated with prognosis, diagnosis, immune infiltration and therapeutic drug in liver cancer by integrated analysis. PMID:34187556
G-quadruplex binders as cytostatic modulators of innate immune genes in cancer cells. PMID:34139015
DNA methylation profile of liver of mice conceived by in vitro fertilization. PMID:34121654
Involvement of Scratch2 in GalR1-mediated depression-like behaviors in the rat ventral periaqueductal gray. PMID:34108238
Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. PMID:34104955
High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. PMID:34099689
Skeletal Muscle Gene Expression Profile in Response to Caloric Restriction and Aging: A Role for SirT1. PMID:34063079
Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host-gene. PMID:34045480
Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression. PMID:34034800
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. PMID:34034647
Dysregulation of PI3K and Hippo signaling pathways synergistically induces chronic pancreatitis via CTGF upregulation. PMID:34032634
A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression. PMID:34025935
Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PMID:34015058
Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation. PMID:34000990
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. PMID:33929018
A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures. PMID:33849996
NREM delta power and AD-relevant tauopathy are associated with shared cortical gene networks. PMID:33833255
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. PMID:33748705
Molecular and computational approaches to map regulatory elements in 3D chromatin structure. PMID:33741028
DNA methylation predicts age and provides insight into exceptional longevity of bats. PMID:33712580
An Early Stage Researcher's Primer on Systems Medicine Terminology. PMID:33659919
The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation. PMID:33608456
Loss of the orphan nuclear receptor NR2F6 enhances CD8+ T-cell memory via IFN-γ. PMID:33589606
Genome-Wide Reduction in Chromatin Accessibility and Unique Transcription Factor Footprints in Endothelial Cells and Fibroblasts in Scleroderma Skin. PMID:33586346
Multiomics-Identified Intervention to Restore Ethanol-Induced Dysregulated Proteostasis and Secondary Sarcopenia in Alcoholic Liver Disease. PMID:33543862
Phospholipase iPLA2β averts ferroptosis by eliminating a redox lipid death signal. PMID:33542532
Gene networks and transcriptional regulators associated with liver cancer development and progression. PMID:33541355
A machine learning-based framework for modeling transcription elongation. PMID:33526657
Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity. PMID:33521702
Evolutionary conservation and divergence of the human brain transcriptome. PMID:33514394
Dbx2 regulation in limbs suggests interTAD sharing of enhancers. PMID:33497014
Abiraterone Acetate Induces CREB1 Phosphorylation and Enhances the Function of the CBP-p300 Complex, Leading to Resistance in Prostate Cancer Cells. PMID:33495313
Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice. PMID:33471342
Common Transcriptional Program of Liver Fibrosis in Mouse Genetic Models and Humans. PMID:33467660
CTCF and EGR1 suppress breast cancer cell migration through transcriptional control of Nm23-H1. PMID:33436746
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. PMID:33432199
Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients. PMID:33398088
Genetic information from discordant sibling pairs points to ESRP2 as a candidate trans-acting regulator of the CF modifier gene SCNN1B. PMID:33384439
GATA4 regulates mesenchymal stem cells via direct transcriptional regulation of the WNT signalosome. PMID:33338666
GNG5 Controls the Number of Apical and Basal Progenitors and Alters Neuronal Migration During Cortical Development. PMID:33330619
Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells. PMID:33324639
DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. PMID:33301553
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. PMID:33259802
A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development. PMID:33234712
GTRD: an integrated view of transcription regulation. PMID:33231677
The APOE gene cluster responds to air pollution factors in mice with coordinated expression of genes that differs by age in humans. PMID:33215813
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL. PMID:33186463
Chronic Disruption of the Late Cholesterol Synthesis Leads to Female-Prevalent Liver Cancer. PMID:33182326
Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes. PMID:33083727
Integrative Analysis of Regulatory Module Reveals Associations of Microgravity with Dysfunctions of Multi-body Systems and Tumorigenesis. PMID:33066530
Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF. PMID:33010164
Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. PMID:32946763
High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. PMID:32926651
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. PMID:32858223
Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity. PMID:32847508
Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development. PMID:32822378
Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. PMID:32816922
A framework for pathway knowledge driven prioritization in genome-wide association studies. PMID:32779262
Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. PMID:32760422
FK506 induces lung lymphatic endothelial cell senescence and downregulates LYVE-1 expression, with associated decreased hyaluronan uptake. PMID:32736525
Yin Yang 1 is critical for mid-hindbrain neuroepithelium development and involved in cerebellar agenesis. PMID:32703236
Footprint-based functional analysis of multiomic data. PMID:32685770
Inherited variant in NFκB-1 promoter is associated with increased risk of IBD in an Algerian population and modulates SOX9 binding. PMID:32671985
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. PMID:32657363
Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins. PMID:32650431
Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity. PMID:32647371
Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours. PMID:32615059
Exercise rejuvenates quiescent skeletal muscle stem cells in old mice through restoration of Cyclin D1. PMID:32601609
Growth hormone increases regulator of calcineurin 1-4 (Rcan1-4) mRNA through c-JUN in rat liver. PMID:32589657
H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. PMID:32585626
Cell stemness is maintained upon concurrent expression of RB and the mitochondrial ribosomal protein S18-2. PMID:32571933
Folding Keratin Gene Clusters during Skin Regional Specification. PMID:32516596
A transcriptome-based approach to identify functional modules within and across primary human immune cells. PMID:32469933
Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC. PMID:32460441
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome. PMID:32450911
Dysregulation of FOXO1 (Forkhead Box O1 Protein) Drives Calcification in Arterial Calcification due to Deficiency of CD73 and Is Present in Peripheral Artery Disease. PMID:32375544
Epigenetic regulation of neuronal cell specification inferred with single cell "Omics" data. PMID:32368329
Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. PMID:32362655
A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter. PMID:32343731
Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First? PMID:32295185
Context-Specific Coordinately Regulatory Network Prioritize Breast Cancer Genetic Risk Factors. PMID:32273883
Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties. PMID:32264855
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
Neuronal Calcium Sensor 1 is up-regulated in response to stress to promote cell survival and motility in cancer cells. PMID:32239615
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. PMID:32184350
Investigation of the Possible Role of Tie2 Pathway and TEK Gene in Asthma and Allergic Conjunctivitis. PMID:32180797
Prediction of Alzheimer's disease using blood gene expression data. PMID:32103140
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. PMID:32014034
Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis. PMID:32012706
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. PMID:31995498
GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. PMID:31989924
A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. PMID:31968263
MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. PMID:31965022
Progesterone and estrogen regulate NALCN expression in human myometrial smooth muscle cells. PMID:31935111
Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism. PMID:31921306
Are We Meeting the Promise of Endotypes and Precision Medicine in Asthma? PMID:31917651
Upregulation of β3-adrenoceptors-a general marker of and protective mechanism against hypoxia? PMID:31853614
Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46. PMID:31840818
1q21.1 deletion and a rare functional polymorphism in siblings with thrombocytopenia-absent radius-like phenotypes. PMID:31836590
Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. PMID:31825311
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523
Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington's disease. PMID:31744868
Improved linking of motifs to their TFs using domain information. PMID:31742324
Identification of loci associated with conception rate in primiparous Holstein cows. PMID:31718557
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. PMID:31659113
Meta-analysis of blood genome-wide expression profiling studies in pulmonary arterial hypertension. PMID:31617731
IRF2 is a master regulator of human keratinocyte stem cell fate. PMID:31611556
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. PMID:31589286
UHRF1-KAT7-mediated regulation of TUSC3 expression via histone methylation/acetylation is critical for the proliferation of colon cancer cells. PMID:31582837
Enhancer activation by FGF signalling during otic induction. PMID:31539539
The circadian clock of CD8 T cells modulates their early response to vaccination and the rhythmicity of related signaling pathways. PMID:31527231
Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis. PMID:31523389
Orphan Nuclear Receptor NR2F6 Suppresses T Follicular Helper Cell Accumulation through Regulation of IL-21. PMID:31509749
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. PMID:31507631
CiiiDER: A tool for predicting and analysing transcription factor binding sites. PMID:31483836
SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. PMID:31477007
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
PAX8 activates metabolic genes via enhancer elements in Renal Cell Carcinoma. PMID:31431624
Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport. PMID:31426446
Integrated systems-genetic analyses reveal a network target for delaying glioma progression. PMID:31420939
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code. PMID:31356126
Identification and Application of Gene Expression Signatures Associated with Lifespan Extension. PMID:31353263
Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network. PMID:31336830
Shiny-Seq: advanced guided transcriptome analysis. PMID:31319888
Structural Features of Transcription Factors Associating with Nucleosome Binding. PMID:31303471
Identification of Novel Biomarkers for Drug Hypersensitivity After Sequencing of the Promoter Area in 16 Genes of the Vitamin D Pathway and the High-Affinity IgE Receptor. PMID:31293618
Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. PMID:31286320
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Predicting functional variants in enhancer and promoter elements using RegulomeDB. PMID:31228310
A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA. PMID:31221127
Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. PMID:31175293
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning. PMID:31161194
Cmah deficiency may lead to age-related hearing loss by influencing miRNA-PPAR mediated signaling pathway. PMID:31149396
Deregulated expression of NKL homeobox genes in T-cell lymphomas. PMID:31143370
Increased 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 activity in response to EGFR signaling contributes to non-small cell lung cancer cell survival. PMID:31126985
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. PMID:31114870
Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. PMID:31085178
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. PMID:31061989
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions. PMID:31008453
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. PMID:30999858
Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma. PMID:30948495
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
Transcriptome Analysis of the Human Tibial Nerve Identifies Sexually Dimorphic Expression of Genes Involved in Pain, Inflammation, and Neuro-Immunity. PMID:30890918
Collective influencers in protein interaction networks. PMID:30850642
Hepatic IFN-Induced Protein with Tetratricopeptide Repeats Regulation of HCV Infection. PMID:30844328
Oxidative stress and the presence of bacteria increase gene expression of the antimicrobial peptide aclasin, a fungal CSαβ defensin in Aspergillus clavatus. PMID:30828484
Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma. PMID:30827930
The biological characteristics of transcription factors AP-2α and AP-2γ and their importance in various types of cancers. PMID:30824562
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers. PMID:30814546
Identification of transcription factor binding sites using ATAC-seq. PMID:30808370
Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci. PMID:30760496
Network-based identification of critical regulators as putative drivers of human cleft lip. PMID:30704473
Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. PMID:30673601
Rapid Communication: Genome-wide association analyses identify loci associated with colostrum production in Jersey cattle1. PMID:30576450
MicroRNA-31 Reduces the Motility of Proinflammatory T Helper 1 Lymphocytes. PMID:30574141
Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders. PMID:30537354
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. PMID:30524706
Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. PMID:30503705
TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences. PMID:30496469
Investigating the Role of MicroRNA and Transcription Factor Co-regulatory Networks in Multiple Sclerosis Pathogenesis. PMID:30463275
Enhancer deletion and allelic effects define a regulatory molecular mechanism at the VLDLR cholesterol GWAS locus. PMID:30445632
Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer's Disease. PMID:30415998
Inferring Novel Autophagy Regulators Based on Transcription Factors and Non-Coding RNAs Coordinated Regulatory Network. PMID:30400235
Unraveling the transcriptional regulation of TWIST1 in limb development. PMID:30372441
SEdb: a comprehensive human super-enhancer database. PMID:30371817
Identification of the Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer. PMID:30314329
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Multiple inputs into a posterior-specific regulatory network in the Ciona notochord. PMID:30287118
Targeting nuclear receptor NR4A1-dependent adipocyte progenitor quiescence promotes metabolic adaptation to obesity. PMID:30277475
Bioinformatics analysis to identify action targets in NCI-N87 gastric cancer cells exposed to quercetin. PMID:30266078
REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species. PMID:30256993
Comprehensive analysis of gene expression profiles associated with proliferative diabetic retinopathy. PMID:30250524
Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. PMID:30143559
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PMID:30142147
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. PMID:30137416
Genome-wide association study of cognitive flexibility assessed by the Wisconsin Card Sorting Test. PMID:30134085
Altered leukocyte gene expression after traumatic spinal cord injury: clinical implications. PMID:30127106
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Chemotherapy-induced peripheral neuropathy: evidence from genome-wide association studies and replication within multiple myeloma patients. PMID:30111286
The landscape of the A-to-I RNA editome from 462 human genomes. PMID:30104667
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. PMID:30011030
ER stress regulating protein phosphatase 2A-B56γ, targeted by hepatitis B virus X protein, induces cell cycle arrest and apoptosis of hepatocytes. PMID:29988038
Positional specificity of different transcription factor classes within enhancers. PMID:29987030
Strand-Specific Dual RNA Sequencing of Bronchial Epithelial Cells Infected with Influenza A/H3N2 Viruses Reveals Splicing of Gene Segment 6 and Novel Host-Virus Interactions. PMID:29976658
A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells. PMID:29970458
Novel lymphoid enhancer-binding factor 1-cytoglobin axis promotes extravasation of osteosarcoma cells into the lungs. PMID:29927026
Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data. PMID:29900118
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files. PMID:29850891
Systematic pan-cancer analysis of somatic allele frequency. PMID:29769535
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. PMID:29764390
Detecting Differential Transcription Factor Activity from ATAC-Seq Data. PMID:29748466
Aberrant activity of NKL homeobox gene NKX3-2 in a T-ALL subset. PMID:29746601
Diverse reprogramming codes for neuronal identity. PMID:29743677
Mycoplasma hyorhinis reduces sensitivity of human lung carcinoma cells to Nutlin-3 and promotes their malignant phenotype. PMID:29737431
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3. PMID:29730990
Development of a computational promoter with highly efficient expression in tumors. PMID:29703163
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs. PMID:29643333
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. PMID:29617668
Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. PMID:29608725
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. PMID:29605182
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. PMID:29581148
Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity. PMID:29570050
Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines. PMID:29563587
Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells. PMID:29543748
A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human. PMID:29518216
Identification of potential genes and miRNAs associated with sepsis based on microarray analysis. PMID:29512785
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Dyslexia risk variant rs600753 is linked with dyslexia-specific differential allelic expression of DYX1C1. PMID:29473935
Identification and analysis of key genes in osteosarcoma using bioinformatics. PMID:29435005
Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084. PMID:29351903
Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. PMID:29344883
Differential tissue specific, temporal and spatial expression patterns of the Aggrecan gene is modulated by independent enhancer elements. PMID:29343853
Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis. PMID:29342503
Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study. PMID:29299133
Clinical Implications of the Autophagy Core Gene Variations in Advanced Lung Adenocarcinoma Treated with Gefitinib. PMID:29259263
Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. PMID:29258295
A Novel Heat Shock Element (HSE) in Entamoeba histolytica that Regulates the Transcriptional Activation of the EhPgp5 Gene in the Presence of Emetine Drug. PMID:29238701
Impact of regulatory variation across human iPSCs and differentiated cells. PMID:29208628
ATP2C2 and DYX1C1 are putative modulators of dyslexia-related MMR. PMID:29201552
Asymmetry between Activation and Deactivation during a Transcriptional Pulse. PMID:29153839
Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. PMID:29146583
STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation. PMID:29142074
Nucleotide patterns aiding in prediction of eukaryotic promoters. PMID:29141011
Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. PMID:29138457
PRODORIC2: the bacterial gene regulation database in 2018. PMID:29136200
A causal mediation model of ischemia reperfusion injury in the retina. PMID:29121052
Screening of potential therapy targets for prostate cancer using integrated analysis of two gene expression profiles. PMID:29113170
Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs. PMID:29087313
Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development. PMID:29085379
Nuclear Wiskott-Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells. PMID:29078804
Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. PMID:29045899
Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. PMID:29023490
CD169+ macrophages orchestrate innate immune responses by regulating bacterial localization in the spleen. PMID:28986418
GTSE1: a novel TEAD4-E2F1 target gene involved in cell protrusions formation in triple-negative breast cancer cell models. PMID:28978043
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. PMID:28977473
The SLC2A14 gene, encoding the novel glucose/dehydroascorbate transporter GLUT14, is associated with inflammatory bowel disease. PMID:28971850
SNPs near the cysteine proteinase cathepsin O gene (CTSO) determine tamoxifen sensitivity in ERα-positive breast cancer through regulation of BRCA1. PMID:28968398
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
Differential expression of genes and differentially perturbed pathways associated with very high evening fatigue in oncology patients receiving chemotherapy. PMID:28944404
Molecular mechanisms involved in the non-monotonic effect of bisphenol-a on ca2+ entry in mouse pancreatic β-cells. PMID:28924161
MYC-dependent recruitment of RUNX1 and GATA2 on the SET oncogene promoter enhances PP2A inactivation in acute myeloid leukemia. PMID:28903318
Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease. PMID:28899360
Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface. PMID:28879060
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. PMID:28865443
Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. PMID:28854641
Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. PMID:28811643
Challenging the Metallothionein (MT) Gene of Biomphalaria glabrata: Unexpected Response Patterns Due to Cadmium Exposure and Temperature Stress. PMID:28800079
Regulation of hypoxia-induced autophagy in glioblastoma involves ATG9A. PMID:28797031
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. PMID:28792927
Modelling the evolution of transcription factor binding preferences in complex eukaryotes. PMID:28790414
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. PMID:28784834
Nuclear orphan receptor NR2F6 as a safeguard against experimental murine colitis. PMID:28779026
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders. PMID:28761062
Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function. PMID:28747224
A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers. PMID:28733453
Choroidal γδ T cells in protection against retinal pigment epithelium and retinal injury. PMID:28729290
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. PMID:28691125
Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks. PMID:28675749
Ancestry-Adjusted Vitamin D Metabolite Concentrations in Association With Cytochrome P450 3A Polymorphisms. PMID:28673024
Inherited determinants of early recurrent somatic mutations in prostate cancer. PMID:28663546
Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. PMID:28659964
A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a. PMID:28642491
Truncating mutations in RBM12 are associated with psychosis. PMID:28628109
Identification of liver-specific enhancer-promoter activity in the 3' untranslated region of the wild-type AAV2 genome. PMID:28628105
SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development. PMID:28619820
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster. PMID:28584716
Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells. PMID:28584089
MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation. PMID:28575289
pathVar: a new method for pathway-based interpretation of gene expression variability. PMID:28560097
Regulatory Plasticity of Earthworm wMT-2 Gene Expression. PMID:28538660
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model. PMID:28497059
Intratumoural heterogeneity generated by Notch signalling promotes small-cell lung cancer. PMID:28489825
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017. PMID:28472390
MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets. PMID:28472340
Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PMID:28414715
CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region. PMID:28405742
Transcription factor-DNA binding: beyond binding site motifs. PMID:28359978
Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia. PMID:28302063
Mapping Gene Expression in Excitatory Neurons during Hippocampal Late-Phase Long-Term Potentiation. PMID:28275336
Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm. PMID:28255556
Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates. PMID:28251902
Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters. PMID:28223400
Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species. PMID:28185554
Alcohol and nicotine codependence-associated DNA methylation changes in promoter regions of addiction-related genes. PMID:28165486
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. PMID:28143596
Systematic dissection of genomic features determining transcription factor binding and enhancer function. PMID:28137873
The Long Noncoding RNA Landscape of the Ischemic Human Left Ventricle. PMID:28115490
Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence. PMID:28105936
Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. PMID:28103614
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PMID:28103241
c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine. PMID:28098247
Myofibril breakdown during atrophy is a delayed response requiring the transcription factor PAX4 and desmin depolymerization. PMID:28096335
RNA Binding to CBP Stimulates Histone Acetylation and Transcription. PMID:28086087
Alcohol-dose-dependent DNA methylation and expression in the nucleus accumbens identifies coordinated regulation of synaptic genes. PMID:28072409
Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. PMID:28055897
Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. PMID:27998931
iFORM: Incorporating Find Occurrence of Regulatory Motifs. PMID:27992540
Quantifying deleterious effects of regulatory variants. PMID:27980060
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. PMID:27924042
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. PMID:27924038
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. PMID:27924024
Clinical and Molecular Characterisation of Children with Pierre Robin Sequence and Additional Anomalies. PMID:27920635
Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. PMID:27911843
Brain transcriptome atlases: a computational perspective. PMID:27909802
mutLBSgeneDB: mutated ligand binding site gene DataBase. PMID:27907895
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. PMID:27899623
Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster. PMID:27871362
Genome-wide analysis of the nucleus accumbens identifies DNA methylation signals differentiating low/binge from heavy alcohol drinking. PMID:27866807
Evaluating tools for transcription factor binding site prediction. PMID:27806697
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
An Intronic Enhancer Element Regulates Angiotensin II Type 2 Receptor Expression during Satellite Cell Differentiation, and Its Activity Is Suppressed in Congestive Heart Failure. PMID:27756842
Evaluating the use of a CpG free promoter for long-term recombinant protein expression stability in Chinese hamster ovary cells. PMID:27756290
Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.). PMID:27738714
Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes. PMID:27738101
Genetic Networks in Mouse Retinal Ganglion Cells. PMID:27733864
ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PMID:27723773
In Vitro Functional Analyses of Infrequent Nucleotide Variants in the Lactase Enhancer Reveal Different Molecular Routes to Increased Lactase Promoter Activity and Lactase Persistence. PMID:27714771
A Meta-Path-Based Prediction Method for Human miRNA-Target Association. PMID:27703979
In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. PMID:27698666
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PMID:27690309
Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. PMID:27683156
Mineralocorticoid Receptor (MR) trans-Activation of Inflammatory AP-1 Signaling: DEPENDENCE ON DNA SEQUENCE, MR CONFORMATION, AND AP-1 FAMILY MEMBER EXPRESSION. PMID:27650495
Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells. PMID:27637333
SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. PMID:27637070
Genome-wide identification and characterisation of HOT regions in the human genome. PMID:27633377
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. PMID:27625390
Characterization of the Mouse and Human Monoacylglycerol O-Acyltransferase 1 (Mogat1) Promoter in Human Kidney Proximal Tubule and Rat Liver Cells. PMID:27611931
DLX1 acts as a crucial target of FOXM1 to promote ovarian cancer aggressiveness by enhancing TGF-β/SMAD4 signaling. PMID:27593933
Cross-species Conservation of context-specific networks. PMID:27531214
Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants. PMID:27503086
Disrupted cooperation between transcription factors across diverse cancer types. PMID:27496222
Epigenetic dynamics of monocyte-to-macrophage differentiation. PMID:27478504
Identification of differentially expressed genes in salivary adenoid cystic carcinoma cells associated with metastasis. PMID:27478471
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach. PMID:27466818
Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. PMID:27426982
Assembly PCR synthesis of optimally designed, compact, multi-responsive promoters suited to gene therapy application. PMID:27387837
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae. PMID:27362276
Establishing and validating regulatory regions for variant annotation and expression analysis. PMID:27357948
Characterization of the Rat GAL2R Promoter: Positive Role of ETS-1 in Regulation of the Rat GAL2R Gene in PC12 Cells. PMID:27349435
PEDLA: predicting enhancers with a deep learning-based algorithmic framework. PMID:27329130
GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis. PMID:27312530
MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. PMID:27302134
Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein. PMID:27302019
Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data. PMID:27295129
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. PMID:27288444
A systematic, large-scale comparison of transcription factor binding site models. PMID:27209209
Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots. PMID:27195960
Composing a Tumor Specific Bacterial Promoter. PMID:27171245
Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids. PMID:27166587
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. PMID:27124577
Positional distribution of transcription factor binding sites in Arabidopsis thaliana. PMID:27117388
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PMID:27096930
Altered oncomodules underlie chromatin regulatory factors driver mutations. PMID:27095575
A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. PMID:27078102
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Brg1 directly regulates Olig2 transcription and is required for oligodendrocyte progenitor cell specification. PMID:27067865
Data- and knowledge-based modeling of gene regulatory networks: an update. PMID:27047314
SM-TF: A structural database of small molecule-transcription factor complexes. PMID:27010673
Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains. PMID:27009150
Genetic Evidence of Human Adaptation to a Cooked Diet. PMID:26979798
Reconstruction of gene regulatory modules from RNA silencing of IFN-α modulators: experimental set-up and inference method. PMID:26969675
Constructing 3D interaction maps from 1D epigenomes. PMID:26960733
The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. PMID:26945717
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
Slow Muscle Precursors Lay Down a Collagen XV Matrix Fingerprint to Guide Motor Axon Navigation. PMID:26937007
The handedness-associated PCSK6 locus spans an intronic promoter regulating novel transcripts. PMID:26908617
Analysis of computational footprinting methods for DNase sequencing experiments. PMID:26901649
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PMID:26901046
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
The SOX11 transcription factor is a critical regulator of basal-like breast cancer growth, invasion, and basal-like gene expression. PMID:26894864
Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination. PMID:26884679
A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. PMID:26868379
Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. PMID:26868017
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PMID:26845687
Models of human core transcriptional regulatory circuitries. PMID:26843070
Prenatal β-catenin/Brn2/Tbr2 transcriptional cascade regulates adult social and stereotypic behaviors. PMID:26830142
Active medulloblastoma enhancers reveal subgroup-specific cellular origins. PMID:26814967
Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments. PMID:26797629
Exploration of nucleosome positioning patterns in transcription factor function. PMID:26790608
Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data. PMID:26779252
miRNA signature identification of retinoblastoma and the correlations between differentially expressed miRNAs during retinoblastoma progression. PMID:26730174
Origins of De Novo Genes in Human and Chimpanzee. PMID:26720152
PPIA rs6850: A > G single-nucleotide polymorphism is associated with raised plasma cyclophilin A levels in patients with coronary artery disease. PMID:26702934
Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. PMID:26655252
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237
Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype. PMID:26582133
Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain. PMID:26575220
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
The direction of cross affects [corrected] obesity after puberty in male but not female offspring. PMID:26546267
How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter. PMID:26516624
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. PMID:26502339
Zinc regulates a key transcriptional pathway for epileptogenesis via metal-regulatory transcription factor 1. PMID:26498180
A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. PMID:26494712
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle. PMID:26486459
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
RFX transcription factors are essential for hearing in mice. PMID:26469318
Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. PMID:26456756
Monocyte enhancers are highly altered in systemic lupus erythematosus. PMID:26442457
Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis. PMID:26438361
Regulatory variant in FZD6 gene contributes to nonsyndromic cleft lip and palate in an African-American family. PMID:26436110
Cell-Based Assay Design for High-Content Screening of Drug Candidates. PMID:26428732
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. PMID:26424082
High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. PMID:26399482
Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks. PMID:26393364
The Nuclear Orphan Receptor NR2F6 Is a Central Checkpoint for Cancer Immune Surveillance. PMID:26387951
Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system. PMID:26369791
Fungal biosynthesis of the bibenzoquinone oosporein to evade insect immunity. PMID:26305932
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors. PMID:26289072
RAGE Suppresses ABCG1-Mediated Macrophage Cholesterol Efflux in Diabetes. PMID:26253613
Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver. PMID:26218442
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. PMID:26217230
A microfluidic device for epigenomic profiling using 100 cells. PMID:26214128
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. PMID:26213851
Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. PMID:26209509
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PMID:26208222
Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence. PMID:26196144
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes. PMID:26158728
Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers. PMID:26156524
Conserved Noncoding Sequences Regulate lhx5 Expression in the Zebrafish Forebrain. PMID:26147098
Combined Whole Methylome and Genomewide Association Study Implicates CNTN4 in Alcohol Use. PMID:26146898
Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PMID:26134422
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PMID:26083494
Measuring information flow in cellular networks by the systems biology method through microarray data. PMID:26082788
Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. PMID:26073445
Recurrent somatic mutations in regulatory regions of human cancer genomes. PMID:26053494
Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems. PMID:26008846
Characterization of novel transcripts in pseudorabies virus. PMID:26008709
Gene and MicroRNA Expression Responses to Exercise; Relationship with Insulin Sensitivity. PMID:25984722
Flow-dependent regulation of genome-wide mRNA and microRNA expression in endothelial cells in vivo. PMID:25977794
Human Enhancers Are Fragile and Prone to Deactivating Mutations. PMID:25976354
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. PMID:25972927
Induction of anterior gradient 2 (AGR2) plays a key role in insulin-like growth factor-1 (IGF-1)-induced breast cancer cell proliferation and migration. PMID:25956506
PGMD: a comprehensive manually curated pharmacogenomic database. PMID:25939485
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. PMID:25927199
Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors. PMID:25918418
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
Regulatory networks in retinal ischemia-reperfusion injury. PMID:25902940
The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PMID:25894978
Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling. PMID:25887780
Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. PMID:25883770
Modeling the relationship of epigenetic modifications to transcription factor binding. PMID:25820421
Metallothionein gene activation in the earthworm (Lumbricus rubellus). PMID:25797623
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PMID:25790137
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. PMID:25779349
SOX11 identified by target gene evaluation of miRNAs differentially expressed in focal and non-focal brain tissue of therapy-resistant epilepsy patients. PMID:25766675
Nuclear p120-catenin regulates the anoikis resistance of mouse lobular breast cancer cells through Kaiso-dependent Wnt11 expression. PMID:25713299
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. PMID:25705211
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes. PMID:25699092
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. PMID:25682954
DEFA gene variants associated with IgA nephropathy in a Chinese population. PMID:25675412
The transcriptional repressor HDAC7 promotes apoptosis and c-Myc downregulation in particular types of leukemia and lymphoma. PMID:25675295
Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. PMID:25649046
New genetic variants of LATS1 detected in urinary bladder and colon cancer. PMID:25628642
Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. PMID:25609649
Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma. PMID:25607463
Identification and computational analysis of gene regulatory elements. PMID:25561628
The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. PMID:25539849
RNA-Seq identifies novel myocardial gene expression signatures of heart failure. PMID:25528681
TimeXNet: identifying active gene sub-networks using time-course gene expression profiles. PMID:25522063
Genome wide meta-analysis highlights the role of genetic variation in RARRES2 in the regulation of circulating serum chemerin. PMID:25521368
Identifying causal regulatory SNPs in ChIP-seq enhancers. PMID:25520196
Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. PMID:25503565
p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. PMID:25486198
The molecular signature of the stroma response in prostate cancer-induced osteoblastic bone metastasis highlights expansion of hematopoietic and prostate epithelial stem cell niches. PMID:25485970
Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. PMID:25484921
The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. PMID:25477386
HDAC2 deregulation in tumorigenesis is causally connected to repression of immune modulation and defense escape. PMID:25473896
Chromatin accessibility: a window into the genome. PMID:25473421
Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer. PMID:25447411
Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. PMID:25437555
A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors. PMID:25428913
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. PMID:25428367
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. PMID:25415054
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. PMID:25411453
Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PMID:25392756
Heat stress-induced Cup9-dependent transcriptional regulation of SIR2. PMID:25384977
DEEP: a general computational framework for predicting enhancers. PMID:25378307
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. PMID:25378249
Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development. PMID:25375179
Regulation of the orphan nuclear receptor Nr2f2 by the DFNA15 deafness gene Pou4f3. PMID:25372459
Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach. PMID:25366989
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. PMID:25362847
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome. PMID:25360157
Foxf genes integrate tbx5 and hedgehog pathways in the second heart field for cardiac septation. PMID:25356765
Single nucleotide polymorphisms in noncoding regions of Rad51C do not change the risk of unselected breast cancer but they modulate the level of oxidative stress and the DNA damage characteristics: a case-control study. PMID:25343521
Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PMID:25340400
Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation. PMID:25326829
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. PMID:25326687
A Follow-up Association Study of Genetic Variants for Bone Mineral Density in a Korean Population. PMID:25317110
Inferring protein modulation from gene expression data using conditional mutual information. PMID:25314274
Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy. PMID:25303361
RNase L attenuates mitogen-stimulated gene expression via transcriptional and post-transcriptional mechanisms to limit the proliferative response. PMID:25301952
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
The Prox1-Vegfr3 feedback loop maintains the identity and the number of lymphatic endothelial cell progenitors. PMID:25274728
NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis. PMID:25263595
Anomalies in network bridges involved in bile Acid metabolism predict outcomes of colorectal cancer patients. PMID:25259881
Large differences in global transcriptional regulatory programs of normal and tumor colon cells. PMID:25253512
Epigenetic dysregulation by nickel through repressive chromatin domain disruption. PMID:25246589
System analysis of LWDH related genes based on text mining in biological networks. PMID:25243143
Gene structure, regulatory control, and evolution of black widow venom latrotoxins. PMID:25217831
Determination and inference of eukaryotic transcription factor sequence specificity. PMID:25215497
Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network. PMID:25199827
Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PMID:25198066
Correcting transcription factor gene sets for copy number and promoter methylation variations. PMID:25195578
Comparative evaluation of DNase-seq footprint identification strategies. PMID:25177346
The expression profile and promoter analysis of ultraspiracle gene in the silkworm Bombyx mori. PMID:25175165
Sp6 and Sp8 transcription factors control AER formation and dorsal-ventral patterning in limb development. PMID:25166858
DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells. PMID:25161698
A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. PMID:25155555
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. PMID:25152886
The BCL9-2 proto-oncogene governs estrogen receptor alpha expression in breast tumorigenesis. PMID:25149534
A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. PMID:25148247
Network biology in medicine and beyond. PMID:25140061
The Babesia bovis gene and promoter model: an update from full-length EST analysis. PMID:25124460
Transcriptional regulation of the tumor suppressor FHL2 by p53 in human kidney and liver cells. PMID:25121502
TGFβ loss activates ADAMTS-1-mediated EGF-dependent invasion in a model of esophageal cell invasion. PMID:25064463
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes. PMID:25051172
GA binding protein augments autophagy via transcriptional activation of BECN1-PIK3C3 complex genes. PMID:25046113
Transcriptome analysis reveals a dynamic and differential transcriptional response to sulforaphane in normal and prostate cancer cells and suggests a role for Sp1 in chemoprevention. PMID:25044704
Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. PMID:25024357
Refined mapping of a hypertension susceptibility locus on rat chromosome 12. PMID:25001272
The role of melanogenesis in regulation of melanoma behavior: melanogenesis leads to stimulation of HIF-1α expression and HIF-dependent attendant pathways. PMID:24997364
TGA Transcription Factors Activate the Salicylic Acid-Suppressible Branch of the Ethylene-Induced Defense Program by Regulating ORA59 Expression. PMID:24989234
Transcriptional targets of the schizophrenia risk gene MIR137. PMID:24984191
The functional significance of common polymorphisms in zinc finger transcription factors. PMID:24970883
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. PMID:24965723
Altered translation of GATA1 in Diamond-Blackfan anemia. PMID:24952648
Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. PMID:24939938
Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics. PMID:24923803
Orphan nuclear receptor NR2F6 acts as an essential gatekeeper of Th17 CD4+ T cell effector functions. PMID:24919548
Genetic analysis of long-lived families reveals novel variants influencing high density-lipoprotein cholesterol. PMID:24917880
Genetic factors underlying discordance in chromatin accessibility between monozygotic twins. PMID:24887574
Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era. PMID:24885462
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. PMID:24885402
Human endometrial DNA methylome is cycle-dependent and is associated with gene expression regulation. PMID:24877562
COUGER--co-factors associated with uniquely-bound genomic regions. PMID:24861628
Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. PMID:24853077
Haplotype-specific modulation of a SOX10/CREB response element at the Charcot-Marie-Tooth disease type 4C locus SH3TC2. PMID:24833716
Global view of enhancer-promoter interactome in human cells. PMID:24821768
Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes. PMID:24802759
A comprehensive resequence-analysis of 250 kb region of 8q24.21 in men of African ancestry. PMID:24783269
Controllability in protein interaction networks. PMID:24778220
Genome-wide association study of sexual maturation in males and females highlights a role for body mass and menarche loci in male puberty. PMID:24770850
Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. PMID:24760461
An improved systematic approach to predicting transcription factor target genes using support vector machine. PMID:24743548
Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice. PMID:24735206
Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling. PMID:24725405
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. PMID:24682824
Transcriptional override: a regulatory network model of indirect responses to modulations in microRNA expression. PMID:24666724
Selection of higher order regression models in the analysis of multi-factorial transcription data. PMID:24658540
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. PMID:24658142
Specificity protein 1 (Sp1) maintains basal epithelial expression of the miR-200 family: implications for epithelial-mesenchymal transition. PMID:24627491
Dissecting the causal genetic mechanisms of coronary heart disease. PMID:24623178
Transcriptional enhancers: from properties to genome-wide predictions. PMID:24614317
The functional consequences of variation in transcription factor binding. PMID:24603674
A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. PMID:24596151
An α-smooth muscle actin (acta2/αsma) zebrafish transgenic line marking vascular mural cells and visceral smooth muscle cells. PMID:24594685
Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases. PMID:24504737
IL-15 prolongs CD154 expression on human CD4 T cells via STAT5 binding to the CD154 transcriptional promoter. PMID:24500400
Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PMID:24499934
Genome-wide analysis of functional and evolutionary features of tele-enhancers. PMID:24496725
The long non-coding RNA Paupar regulates the expression of both local and distal genes. PMID:24488179
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. PMID:24472686
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
Genome of the human hookworm Necator americanus. PMID:24441737
Determinants of expression variability. PMID:24435799
Expression analysis and RNA interference of BmCarE-10 gene from Bombyx mori. PMID:24415296
Reconstruction of transcriptional regulatory networks by stability-based network component analysis. PMID:24407294
Antenatal maternal long-term hypoxia: acclimatization responses with altered gene expression in ovine fetal carotid arteries. PMID:24367503
Whole blood gene expression profiles in insulin resistant Latinos with the metabolic syndrome. PMID:24358323
Wigwams: identifying gene modules co-regulated across multiple biological conditions. PMID:24351708
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. PMID:24349230
Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy. PMID:24345432
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. PMID:24317252
Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver. PMID:24288132
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. PMID:24271386
The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes. PMID:24265227
Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PMID:24260178
Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. PMID:24256810
Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PMID:24244133
Predicting tissue specific transcription factor binding sites. PMID:24238150
Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. PMID:24218641
Many human accelerated regions are developmental enhancers. PMID:24218637
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PMID:24205361
Fine-mapping an association of FSHR with preterm birth in a Finnish population. PMID:24205076
Putative role of HIF transcriptional activity in melanocytes and melanoma biology. PMID:24194964
FXR silencing in human colon cancer by DNA methylation and KRAS signaling. PMID:24177031
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival. PMID:24154670
Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. PMID:24129674
CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. PMID:24121688
Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element. PMID:24109594
Flanking sequence context-dependent transcription factor binding in early Drosophila development. PMID:24093548
Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. PMID:24084807
Gene Expression Under the Influence: Transcriptional Profiling of Ethanol in the Brain. PMID:24078902
Jaccard index based similarity measure to compare transcription factor binding site models. PMID:24074225
How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PMID:24009496
A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. PMID:24006278
The CRTC1-SIK1 pathway regulates entrainment of the circadian clock. PMID:23993098
Analysis of single nucleotide polymorphisms in the region of CLDN2-MORC4 in relation to inflammatory bowel disease. PMID:23946598
Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome. PMID:23936309
Transcription factor-pathway coexpression analysis reveals cooperation between SP1 and ESR1 on dysregulating cell cycle arrest in non-hyperdiploid multiple myeloma. PMID:23925045
MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters. PMID:23924163
Reverse differentiation as a gene filtering tool in genome expression profiling of adipogenesis for fat marker gene selection and their analysis. PMID:23922792
Induction of an inflammatory loop by interleukin-1β and tumor necrosis factor-α involves NF-kB and STAT-1 in differentiated human neuroprogenitor cells. PMID:23922745
Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients. PMID:23915137
Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. PMID:23887935
Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits. PMID:23882023
Runx transcription factors repress human and murine c-Myc expression in a DNA-binding and C-terminally dependent manner. PMID:23874874
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors. PMID:23867227
Decreased transcriptional activity of calcium-sensing receptor gene promoter 1 is associated with calcium nephrolithiasis. PMID:23864702
Purification and characterization of transcription factors. PMID:23832591
Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis. PMID:23832230
Integrative analysis of congenital muscular torticollis: from gene expression to clinical significance. PMID:23819832
DNA motif elucidation using belief propagation. PMID:23814189
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. PMID:23793028
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. PMID:23791644
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. PMID:23736530
Comprehensive functional annotation of seventy-one breast cancer risk Loci. PMID:23717510
PiDNA: Predicting protein-DNA interactions with structural models. PMID:23703214
The majority of primate-specific regulatory sequences are derived from transposable elements. PMID:23675311
The impact of trans-regulation on the evolutionary rates of metazoan proteins. PMID:23658220
Identification of transcriptional regulators in the mouse immune system. PMID:23624555
D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements. PMID:23617301
TherMos: Estimating protein-DNA binding energies from in vivo binding profiles. PMID:23595148
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. PMID:23578292
Under-dominance constrains the evolution of negative autoregulation in diploids. PMID:23555226
A discriminative approach for unsupervised clustering of DNA sequence motifs. PMID:23555204
HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. PMID:23539139
Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2. PMID:23527149
LASAGNA: a novel algorithm for transcription factor binding site alignment. PMID:23522376
Comparative annotation of functional regions in the human genome using epigenomic data. PMID:23482391
A temporal switch model for estimating transcriptional activity in gene expression. PMID:23479351
A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment. PMID:23471465
Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis. PMID:23441166
Salicylic acid suppresses jasmonic acid signaling downstream of SCFCOI1-JAZ by targeting GCC promoter motifs via transcription factor ORA59. PMID:23435661
Epigenomic model of cardiac enhancers with application to genome wide association studies. PMID:23424115
canEvolve: a web portal for integrative oncogenomics. PMID:23418540
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
A local genetic algorithm for the identification of condition-specific microRNA-gene modules. PMID:23401666
An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury. PMID:23387820
Robust shifts in S100a9 expression with aging: a novel mechanism for chronic inflammation. PMID:23386971
PRISM offers a comprehensive genomic approach to transcription factor function prediction. PMID:23382538
A high-resolution enhancer atlas of the developing telencephalon. PMID:23375746
A negative selection heuristic to predict new transcriptional targets. PMID:23368951
Quantitative, solution-phase profiling of multiple transcription factors in parallel. PMID:23361227
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. PMID:23355428
Sequencing ASMT identifies rare mutations in Chinese Han patients with autism. PMID:23349736
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. PMID:23331723
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. PMID:23323883
FOSL1 controls the assembly of endothelial cells into capillary tubes by direct repression of αv and β3 integrin transcription. PMID:23319049
Profiling of androgen response in rainbow trout pubertal testis: relevance to male gonad development and spermatogenesis. PMID:23301058
The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks. PMID:23300434
An integrative approach to inferring gene regulatory module networks. PMID:23285197
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. PMID:23282148
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. PMID:23282090
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. PMID:23280066
COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets. PMID:23272209
Genome-wide association analyses in East Asians identify new susceptibility loci for colorectal cancer. PMID:23263487
Cloning, molecular characterization, and mRNA expression of the thermostable family 3 β-glucosidase from the rare fungus Stachybotrys microspora. PMID:23242634
Complex modulation of the Aedes aegypti transcriptome in response to dengue virus infection. PMID:23209765
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PMID:23209563
TFClass: an expandable hierarchical classification of human transcription factors. PMID:23180794
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. PMID:23175603
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. PMID:23161675
Tumor suppressor maspin as a rheostat in HDAC regulation to achieve the fine-tuning of epithelial homeostasis. PMID:23140166
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. PMID:23110901
Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. PMID:23101584
Analyzing the promoters of two CYP9A genes in the silkworm Bombyx mori by dual-luciferase reporter assay. PMID:23090481
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. PMID:23090257
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. PMID:23089682
TSGene: a web resource for tumor suppressor genes. PMID:23066107
Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins. PMID:23050235
Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus. PMID:23045659
Three enhancements to the inference of statistical protein-DNA potentials. PMID:23042633
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. PMID:23034120
Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PMID:23029193
Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. PMID:23023172
Regulatory network operations in the Pathway Tools software. PMID:22998532
Annotation of functional variation in personal genomes using RegulomeDB. PMID:22955989
Predicting cell-type-specific gene expression from regions of open chromatin. PMID:22955983
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. PMID:22955979
Systematic localization of common disease-associated variation in regulatory DNA. PMID:22955828
An expansive human regulatory lexicon encoded in transcription factor footprints. PMID:22955618
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PMID:22952639
Increasing coverage of transcription factor position weight matrices through domain-level homology. PMID:22952610
Functional analysis of transcription factor binding sites in human promoters. PMID:22951020
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648
Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development. PMID:22931563
Regulatory elements of Caenorhabditis elegans ribosomal protein genes. PMID:22928635
Adiponectin regulates expression of hepatic genes critical for glucose and lipid metabolism. PMID:22904186
Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. PMID:22904091
Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns. PMID:22904079
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. PMID:22900683
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. PMID:22897887
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. PMID:22897824
Towards biological characters of interactions between transcription factors and their DNA targets in mammals. PMID:22888987
Human developmental enhancers conserved between deuterostomes and protostomes. PMID:22876195
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PMID:22829947
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PMID:22829753
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. PMID:22827163
Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape. PMID:22820642
Neuroplasticity, axonal guidance and micro-RNA genes are associated with morphine self-administration behavior. PMID:22804800
Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. PMID:22759862
Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures. PMID:22759573
Genes2FANs: connecting genes through functional association networks. PMID:22748121
Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PMID:22737085
Dynamical systems approach to endothelial heterogeneity. PMID:22723222
Cohesin proteins promote ribosomal RNA production and protein translation in yeast and human cells. PMID:22719263
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. PMID:22718975
wANNOVAR: annotating genetic variants for personal genomes via the web. PMID:22717648
Quercetin enhances ABCA1 expression and cholesterol efflux through a p38-dependent pathway in macrophages. PMID:22711909
Before It Gets Started: Regulating Translation at the 5' UTR. PMID:22693426
Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. PMID:22684279
Regulated Expression of Chromobox Homolog 5 Revealed in Tumors of Apc(Min) (/+) ROSA11 Gene Trap Mice. PMID:22670227
Mutations and binding sites of human transcription factors. PMID:22670148
Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. PMID:22634764
Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. PMID:22634755
Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PMID:22615549
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
Gene regulation is governed by a core network in hepatocellular carcinoma. PMID:22548756
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. PMID:22548745
Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. PMID:22513257
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. PMID:22510988
Improved models for transcription factor binding site identification using nonindependent interactions. PMID:22505627
Distinct cytoplasmic and nuclear functions of the stress induced protein DDIT3/CHOP/GADD153. PMID:22496745
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PMID:22479192
The transcription factor encyclopedia. PMID:22458515
Combinatorial activation and repression by seven transcription factors specify Drosophila odorant receptor expression. PMID:22427741
Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. PMID:22422841
CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. PMID:22422836
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PMID:22412381
Deriving transcriptional programs and functional processes from gene expression databases. PMID:22408194
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
A Whole-Chromosome Analysis of Meiotic Recombination in Drosophila melanogaster. PMID:22384403
Evolution of siglec-11 and siglec-16 genes in hominins. PMID:22383531
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Genome-level identification of targets of Hox protein Ultrabithorax in Drosophila: novel mechanisms for target selection. PMID:22355720
A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. PMID:22343619
A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PMID:22319554
Interleukin-1β modulates smooth muscle cell phenotype to a distinct inflammatory state relative to PDGF-DD via NF-κB-dependent mechanisms. PMID:22318995
Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. PMID:22313678
Predicting target DNA sequences of DNA-binding proteins based on unbound structures. PMID:22312425
Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase. PMID:22294689
DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. PMID:22293752
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. PMID:22278370
Tight regulation of wingless-type signaling in the articular cartilage - subchondral bone biomechanical unit: transcriptomics in Frzb-knockout mice. PMID:22264237
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
Ameloblastin upstream region contains structural elements regulating transcriptional activity in a stromal cell line derived from bone marrow. PMID:22243258
Use of ChIP-Seq data for the design of a multiple promoter-alignment method. PMID:22230796
CLARE: Cracking the LAnguage of Regulatory Elements. PMID:22199387
Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. PMID:22187154
Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. PMID:22165960
Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms. PMID:22151976
Etsrp/Etv2 is directly regulated by Foxc1a/b in the zebrafish angioblast. PMID:22135404
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. PMID:22121215
Common variation at 3p22.1 and 7p15.3 influences multiple myeloma risk. PMID:22120009
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. PMID:22102575
Lead, calcium uptake, and related genetic variants in association with renal cell carcinoma risk in a cohort of male Finnish smokers. PMID:22086884
Evolution of anterior Hox regulatory elements among chordates. PMID:22085760
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
Occupancy classification of position weight matrix-inferred transcription factor binding sites. PMID:22073148
FOG-1 and GATA-1 act sequentially to specify definitive megakaryocytic and erythroid progenitors. PMID:22068055
Network analysis of microRNAs and their regulation in human ovarian cancer. PMID:22050994
Automated protein-DNA interaction screening of Drosophila regulatory elements. PMID:22037703
PPARγ and NF-κB regulate the gene promoter activity of their shared repressor, TNIP1. PMID:22001530
Meta-analysis of high-throughput datasets reveals cellular responses following hemorrhagic fever virus infection. PMID:21994748
Assessing the effects of symmetry on motif discovery and modeling. PMID:21949783
Analysis of multiple polymorphisms in the bovine neuropeptide Y5 receptor gene and structural modelling of the encoded protein. PMID:21947839
Visualization and exploration of conserved regulatory modules using ReXSpecies 2. PMID:21942985
RXRα and LXR activate two promoters in placenta- and tumor-specific expression of PLAC1. PMID:21937108
Search for specific biomarkers of IFNβ bioactivity in patients with multiple sclerosis. PMID:21886806
Systems analysis of immune responses in Marek's disease virus-infected chickens identifies a gene involved in susceptibility and highlights a possible novel pathogenicity mechanism. PMID:21865384
Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. PMID:21862591
Cistrome: an integrative platform for transcriptional regulation studies. PMID:21859476
MIRTFnet: analysis of miRNA regulated transcription factors. PMID:21857930
The regulatory epicenter of miRNAs. PMID:21857109
Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat. PMID:21846806
Variants in genes that encode muscle contractile proteins influence risk for isolated clubfoot. PMID:21834041
AlleleSeq: analysis of allele-specific expression and binding in a network framework. PMID:21811232
Common variation at 10p12.31 near MLLT10 influences meningioma risk. PMID:21804547
ZEB1 limits adenoviral infectability by transcriptionally repressing the coxsackie virus and adenovirus receptor. PMID:21791114
Enhancers regulate progression of development in mammalian cells. PMID:21785139
CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute. PMID:21765476
DECOD: fast and accurate discriminative DNA motif finding. PMID:21752801
Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PMID:21750739
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
Characterisation of a desmosterol reductase involved in phytosterol dealkylation in the silkworm, Bombyx mori. PMID:21738635
Steroid hormone modulation of RET through two estrogen responsive enhancers in breast cancer. PMID:21737465
A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. PMID:21695229
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. PMID:21689477
Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. PMID:21685454
Sorting the nuclear proteome. PMID:21685104
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. PMID:21685098
An integrative clustering and modeling algorithm for dynamical gene expression data. PMID:21685097
RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples. PMID:21682879
SNPs occur in regions with less genomic sequence conservation. PMID:21674007
Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis. PMID:21673114
Global identification of SMAD2 target genes reveals a role for multiple co-regulatory factors in zebrafish early gastrulas. PMID:21669877
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
Inactivation of promoter 1B of APC causes partial gene silencing: evidence for a significant role of the promoter in regulation and causative of familial adenomatous polyposis. PMID:21643010
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PMID:21637758
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks. PMID:21619639
Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation. PMID:21615920
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. PMID:21602820
ConTra v2: a tool to identify transcription factor binding sites across species, update 2011. PMID:21576231
Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes. PMID:21562764
Estrogen-related receptor α regulates skeletal myocyte differentiation via modulation of the ERK MAP kinase pathway. PMID:21562305
Molecular signatures database (MSigDB) 3.0. PMID:21546393
DREME: motif discovery in transcription factor ChIP-seq data. PMID:21543442
GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge. PMID:21513505
What does biologically meaningful mean? A perspective on gene regulatory network validation. PMID:21489330
Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PMID:21464922
Studies in mice, hamsters, and rats demonstrate that repression of hepatic apoA-I expression by taurocholic acid in mice is not mediated by the farnesoid-X-receptor. PMID:21464203
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. PMID:21447789
Motif-guided sparse decomposition of gene expression data for regulatory module identification. PMID:21426557
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PMID:21408212
C/EBPβ regulates dexamethasone-induced muscle cell atrophy and expression of atrogin-1 and MuRF1. PMID:21381078
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. PMID:21372179
Mapping and functional characterization of the murine smoothelin-like 1 promoter. PMID:21352594
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PMID:21347314
An in vitro model that recapitulates the epithelial to mesenchymal transition (EMT) in human breast cancer. PMID:21347235
Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB. PMID:21331044
dPORE-miRNA: polymorphic regulation of microRNA genes. PMID:21326606
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. PMID:21310711
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. PMID:21276248
Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. PMID:21269450
Folate pathway and nonsyndromic cleft lip and palate. PMID:21254359
Smoking, the xenobiotic pathway, and clubfoot. PMID:21254355
Systematic characterization of protein-DNA interactions. PMID:21207099
Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling. PMID:21194568
BiologicalNetworks 2.0--an integrative view of genome biology data. PMID:21190573
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress. PMID:21182756
Arxes: retrotransposed genes required for adipogenesis. PMID:21177646
Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. PMID:21170361
Using bioinformatics to predict the functional impact of SNVs. PMID:21159622
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PMID:21124834
Computational biology for ageing. PMID:21115530
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. PMID:21106903
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. PMID:21097781
Cell-specific and hypoxia-dependent regulation of human HIF-3α: inhibition of the expression of HIF target genes in vascular cells. PMID:21069422
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. PMID:21059262
The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression. PMID:21059207
A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. PMID:21051460
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. PMID:21045055
A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3). PMID:21037568
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. PMID:21037262
RBPDB: a database of RNA-binding specificities. PMID:21036867
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
Statistical analysis strategies for association studies involving rare variants. PMID:20940738
Genetic and molecular functional characterization of variants within TNFSF13B, a positional candidate preeclampsia susceptibility gene on 13q. PMID:20927378
Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation. PMID:20923549
DDPC: Dragon Database of Genes associated with Prostate Cancer. PMID:20880996
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. PMID:20876297
A comprehensive statistical model for cell signaling. PMID:20855924
The BioPAX community standard for pathway data sharing. PMID:20829833
is-rSNP: a novel technique for in silico regulatory SNP detection. PMID:20823317
Androgen activation of the folate receptor α gene through partial tethering of the androgen receptor by C/EBPα. PMID:20817090
CRISPLD2 variants including a C471T silent mutation may contribute to nonsyndromic cleft lip with or without cleft palate. PMID:20815724
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. PMID:20731828
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. PMID:20724440
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. PMID:20705649
Protein kinase target discovery from genome-wide messenger RNA expression profiling. PMID:20687179
Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans. PMID:20686661
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
A systems approach to mapping transcriptional networks controlling surfactant homeostasis. PMID:20659319
Characterisation of a functional intronic polymorphism in the human growth hormone (GH1) gene. PMID:20650818
PriorsEditor: a tool for the creation and use of positional priors in motif discovery. PMID:20628076
Metamotifs--a generative model for building families of nucleotide position weight matrices. PMID:20579334
Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells. PMID:20574810
Stage-specific control of connective tissue growth factor (CTGF/CCN2) expression in chondrocytes by Sox9 and beta-catenin. PMID:20571031
Impact of methoxyacetic acid on mouse Leydig cell gene expression. PMID:20565877
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. PMID:20552250
JAMIE: joint analysis of multiple ChIP-chip experiments. PMID:20551135
Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PMID:20544005
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury. PMID:20534130
Discovering protein-DNA binding sequence patterns using association rule mining. PMID:20529874
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. PMID:20529327
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. PMID:20517297
TransFind--predicting transcriptional regulators for gene sets. PMID:20511592
Growth factor stimulation induces cell survival by c-Jun. ATF2-dependent activation of Bcl-XL. PMID:20507983
Sequence features that drive human promoter function and tissue specificity. PMID:20501695
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. PMID:20478823
DynaMod: dynamic functional modularity analysis. PMID:20460468
Targetfinder.org: a resource for systematic discovery of transcription factor target genes. PMID:20460454
Most transcription factor binding sites are in a few mosaic classes of the human genome. PMID:20459624
Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NF kappaB and microRNA network. PMID:20433755
Semantic integration of data on transcriptional regulation. PMID:20427517
The value of position-specific priors in motif discovery using MEME. PMID:20380693
The nuclear hormone receptor Coup-TFII is required for the initiation and early maintenance of Prox1 expression in lymphatic endothelial cells. PMID:20360386
A dictionary on microRNAs and their putative target pathways. PMID:20299343
Direct and coordinate regulation of ATP-binding cassette transporter genes by Myc factors generates specific transcription signatures that significantly affect the chemoresistance phenotype of cancer cells. PMID:20233711
Nucleosome dynamics define transcriptional enhancers. PMID:20208536
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
An effective model for natural selection in promoters. PMID:20194951
Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. PMID:20170488
Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. PMID:20134431
iMotifs: an integrated sequence motif visualization and analysis environment. PMID:20106815
Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. PMID:20100800
Genome-wide prediction of transcription factor binding sites using an integrated model. PMID:20096096
Identification of interacting transcription factors regulating tissue gene expression in human. PMID:20085649
Intergenic, gene terminal, and intragenic CpG islands in the human genome. PMID:20085634
Variable structure motifs for transcription factor binding sites. PMID:20074339
Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. PMID:20054984
Activation of Cdc6 by MyoD is associated with the expansion of quiescent myogenic satellite cells. PMID:20048262
Finding Occurrences of Relevant Functional Elements in Genomic Signatures. PMID:20046539
The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. PMID:20038494
Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure. PMID:20031553
GSK-3 represses growth factor-inducible genes by inhibiting NF-kappaB in quiescent cells. PMID:20018891
Integrated analysis of receptor activation and downstream signaling with EXTassays. PMID:20010833
Revealing global regulatory perturbations across human cancers. PMID:20005852
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. PMID:20003307
Insight into microRNA regulation by analyzing the characteristics of their targets in humans. PMID:20003303
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study. PMID:19997623
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. PMID:19955237
Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. PMID:19938081
Inducible male infertility by targeted cell ablation in zebrafish testis. PMID:19936986
Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair. PMID:19933264
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. PMID:19922652
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. PMID:19906716
Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data. PMID:19903850
Knowledge-based data analysis comes of age. PMID:19854753
Finding distal regulatory elements in the human genome. PMID:19854636
Regulation of miR-200 family microRNAs and ZEB transcription factors in ovarian cancer: evidence supporting a mesothelial-to-epithelial transition. PMID:19854497
Modeling tissue-specific structural patterns in human and mouse promoters. PMID:19850720
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. PMID:19843614
MicroRNAs regulate osteogenesis and chondrogenesis of mouse bone marrow stromal cells. PMID:19787082
3D-footprint: a database for the structural analysis of protein-DNA complexes. PMID:19767616
A c-Myc regulatory subnetwork from human transposable element sequences. PMID:19763338
Androgen-responsive gene database: integrated knowledge on androgen-responsive genes. PMID:19762544
Copper activation of NF-kappaB signaling in HepG2 cells. PMID:19747488
The complex spatio-temporal regulation of the Drosophila myoblast attractant gene duf/kirre. PMID:19742310
The smallest chemical reaction system with bistability. PMID:19737387
CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses. PMID:19736212
Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PMID:19707584
Control of chicken CR1 retrotransposons is independent of Dicer-mediated RNA interference pathway. PMID:19691826
A functional SNP in the regulatory region of the decay-accelerating factor gene associates with extraocular muscle pareses in myasthenia gravis. PMID:19675582
FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral. PMID:19615102
Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. PMID:19603121
Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome. PMID:19590981
A knowledge-based method to predict the cooperative relationship between transcription factors. PMID:19590970
Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19. PMID:19587786
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. PMID:19570198
PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells. PMID:19564417
A combinatorial mechanism for determining the specificity of E2F activation and repression. PMID:19543322
Transcriptional targets in adipocyte biology. PMID:19534570
Histone H2A.Z is essential for estrogen receptor signaling. PMID:19515975
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. PMID:19487240
VisHiC--hierarchical functional enrichment analysis of microarray data. PMID:19483095
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks. PMID:19454001
The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes. PMID:19450249
Curcumin decreases the expression of Pokemon by suppressing the binding activity of the Sp1 protein in human lung cancer cells. PMID:19444642
Diversity and complexity in DNA recognition by transcription factors. PMID:19443739
Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood. PMID:19429790
Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex-specific binding at low- but not high-affinity STAT5 sites. PMID:19423653
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. PMID:19417063
Foxa2-dependent hepatic gene regulatory networks depend on physiological state. PMID:19417011
Genetic and environmental pathways to complex diseases. PMID:19416532
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. PMID:19409082
Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts. PMID:19386601
Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PMID:19385720
Developmental programming of CpG island methylation profiles in the human genome. PMID:19377480
Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. PMID:19329064
p65/RelA modulates BECN1 transcription and autophagy. PMID:19289499
Statistical detection of cooperative transcription factors with similarity adjustment. PMID:19286833
COTRASIF: conservation-aided transcription-factor-binding site finder. PMID:19264796
Gene set-based module discovery in the breast cancer transcriptome. PMID:19243633
Massive transcriptional start site analysis of human genes in hypoxia cells. PMID:19237398
Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms. PMID:19220457
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. PMID:19208131
The expression of heparin-binding epidermal growth factor-like growth factor by regulatory macrophages. PMID:19201846
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
Egr-1 inhibits the expression of extracellular matrix genes in chondrocytes by TNFalpha-induced MEK/ERK signalling. PMID:19144181
Stress-related genes define essential steps in the response of maize seedlings to smoke-water. PMID:19139936
Prediction of Cis-Regulatory Elements Controlling Genes Differentially Expressed by Retinal and Choroidal Vascular Endothelial Cells. PMID:19122891
Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes. PMID:19074951
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. PMID:19074493
PASTAA: identifying transcription factors associated with sets of co-regulated genes. PMID:19073590
Compo: composite motif discovery using discrete models. PMID:19063744
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. PMID:19036138
Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae. PMID:19036124
Machine learning for regulatory analysis and transcription factor target prediction in yeast. PMID:19003435
INTERFEROME: the database of interferon regulated genes. PMID:18996892
Effect of elongation factor 1alpha promoter and SUMF1 over in vitro expression of N-acetylgalactosamine-6-sulfate sulfatase. PMID:18989752
Ex vivo promoter analysis of antiviral heat shock cognate 70B gene in Anopheles gambiae. PMID:18986525
An integrated software system for analyzing ChIP-chip and ChIP-seq data. PMID:18978777
Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PMID:18974838
ERRgamma mediates tamoxifen resistance in novel models of invasive lobular breast cancer. PMID:18974135
An optimized procedure for the design and evaluation of Ecotilling assays. PMID:18973671
Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions. PMID:18971640
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. PMID:18851746
Knowledge-guided multi-scale independent component analysis for biomarker identification. PMID:18837990
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. PMID:18823535
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. PMID:18815372
PCA-HPR: a principle component analysis model for human promoter recognition. PMID:18795109
Database for exploration of functional context of genes implicated in ovarian cancer. PMID:18790805
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation. PMID:18786246
Genome-wide analysis of natural selection on human cis-elements. PMID:18781197
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PMID:18769735
Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. PMID:18710571
Determining significance of pairwise co-occurrences of events in bursty sequences. PMID:18691400
A core paired-type and POU homeodomain-containing transcription factor program drives retinal bipolar cell gene expression. PMID:18667607
Histone methylation marks play important roles in predicting the methylation status of CpG islands. PMID:18656446
Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PMID:18654640
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. PMID:18590522
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. PMID:18586699
In silico regulatory analysis for exploring human disease progression. PMID:18564415
The genomic determinants of alcohol preference in mice. PMID:18563486
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. PMID:18554421
TiGER: a database for tissue-specific gene expression and regulation. PMID:18541026
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. PMID:18533028
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PMID:18523562
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. PMID:18515841
Classifying transcription factor targets and discovering relevant biological features. PMID:18513408
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. PMID:18490265
MADNet: microarray database network web server. PMID:18480121
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. PMID:18460544
c-Jun controls histone modifications, NF-kappaB recruitment, and RNA polymerase II function to activate the ccl2 gene. PMID:18443042
Studying the functional conservation of cis-regulatory modules and their transcriptional output. PMID:18442418
Discovering sequence motifs with arbitrary insertions and deletions. PMID:18437229
ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. PMID:18410675
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. PMID:18358809
Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells. PMID:18350142
Motif-directed network component analysis for regulatory network inference. PMID:18315853
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. PMID:18312685
MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters. PMID:18307768
Assessment of composite motif discovery methods. PMID:18302777
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. PMID:18294369
Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context. PMID:18291023
Asap: a framework for over-representation statistics for transcription factor binding sites. PMID:18286180
Text-mining assisted regulatory annotation. PMID:18271954
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation. PMID:18226260
Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NFkappaB transcription factors. PMID:18226221
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. PMID:18187510
Interferon regulatory factors are transcriptional regulators of adipogenesis. PMID:18177728
Sex differences in the recognition of and innate antiviral responses to Seoul virus in Norway rats. PMID:18053684
Prediction of synergistic transcription factors by function conservation. PMID:18053230
EndoNet: an information resource about regulatory networks of cell-to-cell communication. PMID:18045786
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. PMID:18042645
Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PMID:18030324
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes. PMID:18003658
Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. PMID:17986456
Inter- and intra-combinatorial regulation by transcription factors and microRNAs. PMID:17971223
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. PMID:17962303
Genomic organization and evolutionary conservation of plant D-type cyclins. PMID:17951462
ppdb: a plant promoter database. PMID:17947329
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. PMID:17947326
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. PMID:17945028
DBTSS: database of transcription start sites, progress report 2008. PMID:17942421
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. PMID:17937785
PlantTFDB: a comprehensive plant transcription factor database. PMID:17933783
DB-PABP: a database of polyanion-binding proteins. PMID:17916573
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. PMID:17916232
BNDB - the Biochemical Network Database. PMID:17910766
Computational analyses of eukaryotic promoters. PMID:17903284
In vivo validation of a computationally predicted conserved Ath5 target gene set. PMID:17892326
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. PMID:17784952
Computation of significance scores of unweighted Gene Set Enrichment Analyses. PMID:17683603
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
CRISPLD2: a novel NSCLP candidate gene. PMID:17616516
Sequence analysis of coding and 3' and 5' flanking regions of the epithelial sodium channel alpha, beta, and gamma genes in Dahl S versus R rats. PMID:17592634
Immediate-early and delayed primary response genes are distinct in function and genomic architecture. PMID:17575275
Construction of a genome-scale structural map at single-nucleotide resolution. PMID:17568010
Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. PMID:17567985
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. PMID:17565367
Decoding development in Xenopus tropicalis. PMID:17549727
GeneTrail--advanced gene set enrichment analysis. PMID:17526521
Enhancer responses to similarly distributed antagonistic gradients in development. PMID:17500585
Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis. PMID:17498287
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. PMID:17478515
Searching for tissue-specific expression pattern-linked nucleotides of UGT1A isoforms. PMID:17460763
Multiple non-collinear TF-map alignments of promoter regions. PMID:17456238
Regulatory circuit of human microRNA biogenesis. PMID:17447837
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
Characterization of three growth hormone-responsive transcription factors preferentially expressed in adult female liver. PMID:17412818
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs. PMID:17378935
Decoding transcriptional regulatory interactions. PMID:17364011
Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. PMID:17360609
A core transcriptional network for early mesoderm development in Drosophila melanogaster. PMID:17322403
Epigenetic control of the foxp3 locus in regulatory T cells. PMID:17298177
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. PMID:17286865
PlnTFDB: an integrative plant transcription factor database. PMID:17286856
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. PMID:17254313
Statistical significance of cis-regulatory modules. PMID:17241466
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. PMID:17239240
EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. PMID:17233892
Transcriptional regulation of protein complexes within and across species. PMID:17227853
DiscoverySpace: an interactive data analysis application. PMID:17210078
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
TRED: a transcriptional regulatory element database, new entries and other development. PMID:17202159
Multiple independent evolutionary solutions to core histone gene regulation. PMID:17184543
Beyond microarrays: find key transcription factors controlling signal transduction pathways. PMID:17118134
A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors. PMID:17090591
KBERG: KnowledgeBase for Estrogen Responsive Genes. PMID:17090589
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. PMID:16845074
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. PMID:16845066
POXO: a web-enabled tool series to discover transcription factor binding sites. PMID:16845065
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. PMID:16845041
Practical strategies for discovering regulatory DNA sequence motifs. PMID:16683017
TRANSFAC: transcriptional regulation, from patterns to profiles PubMed citations: 969.

969 articles citing: TRANSFAC: transcriptional regulation, from patterns to profiles

IMGT® Biocuration and Analysis of the Rhesus Monkey IG Loci. PMID:35335026
Cloning of the Human MORG1 Promoter: Differential Regulation by Hypoxia and Prolyl-Hydroxylase Inhibitors. PMID:35327980
Expression variations in ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in haplochromine cichlids. PMID:35272610
Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity. PMID:35098922
Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant. PMID:35052364
Computational modeling of chromatin accessibility identified important epigenomic regulators. PMID:34996354
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. PMID:34986601
Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. PMID:34947998
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). PMID:34927191
A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. PMID:34900134
Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection. PMID:34759955
Transcriptome Profiling Reveals Important Transcription Factors and Biological Processes in Skin Regeneration Mediated by Mechanical Stretch. PMID:34659370
Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. PMID:34634362
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. PMID:34607350
Evidence for a functional interaction of WNT10A and EBF1 in male-pattern baldness. PMID:34506541
SARS-CoV-2: Understanding the Transcriptional Regulation of ACE2 and TMPRSS2 and the Role of Single Nucleotide Polymorphism (SNP) at Codon 72 of p53 in the Innate Immune Response against Virus Infection. PMID:34445373
Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition. PMID:34436218
Metabolic preconditioning in CD4+ T cells restores inducible immune tolerance in lupus-prone mice. PMID:34403367
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. PMID:34377365
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain. PMID:34236575
Identification of hub genes associated with prognosis, diagnosis, immune infiltration and therapeutic drug in liver cancer by integrated analysis. PMID:34187556
Computational systems-biology approaches for modeling gene networks driving epithelial-mesenchymal transitions. PMID:34164628
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. PMID:34039271
DACH1 protects podocytes from experimental diabetic injury and modulates PTIP-H3K4Me3 activity. PMID:33998601
NREM delta power and AD-relevant tauopathy are associated with shared cortical gene networks. PMID:33833255
Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence. PMID:33796132
Epigenetics Involvement in Oxaliplatin-Induced Potassium Channel Transcriptional Downregulation and Hypersensitivity. PMID:33772465
Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. PMID:33763080
Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. PMID:33712615
Epigenetic Regulation of Processes Related to High Level of Fibroblast Growth Factor 21 in Obese Subjects. PMID:33670024
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PMID:33667222
GNG5 Controls the Number of Apical and Basal Progenitors and Alters Neuronal Migration During Cortical Development. PMID:33330619
A Multi-Source Data Fusion Framework for Revealing the Regulatory Mechanism of Breast Cancer Immune Evasion. PMID:33304391
Stem cell-intrinsic mechanisms regulating adult hair follicle homeostasis. PMID:33278851
HAHmiR.DB: a server platform for high-altitude human miRNA-gene coregulatory networks and associated regulatory circuits. PMID:33259604
What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? PMID:33256133
Investigating the human protein-host protein interactome of SARS-CoV-2 infection in the small intestine. PMID:33244381
New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy. PMID:33231937
nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. PMID:33209992
Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression. PMID:33207193
EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes. PMID:33024441
First Insight into the Modulation of Noncanonical NF-κB Signaling Components by Poxviruses in Established Immune-Derived Cell Lines: An In Vitro Model of Ectromelia Virus Infection. PMID:33020446
Unusual DNA-binding properties of the Arabidopsis thaliana WRKY50 transcription factor at target gene promoters. PMID:33006643
Glucagon-like peptide-1 receptor and sarcoglycan delta genetic variants can affect cardiovascular risk in chronic kidney disease patients under hemodialysis. PMID:32905248
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Systems Analysis of Biliary Atresia Through Integration of High-Throughput Biological Data. PMID:32848883
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network. PMID:32732921
Assessing and validating housekeeping genes in normal, cancerous, and polycystic human ovaries. PMID:32729067
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
SIRT1 accelerates the progression of activity-based anorexia. PMID:32499508
SCDb: an integrated database of stomach cancer. PMID:32487193
MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. PMID:32451429
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. PMID:32413319
Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval. PMID:32375685
Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. PMID:32362655
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. PMID:32268104
Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. PMID:32194972
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. PMID:32125007
Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer. PMID:32093698
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. PMID:32033573
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. PMID:31995498
Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15. PMID:31975641
Ligands, Receptors, and Transcription Factors that Mediate Inter-Cellular and Intra-Cellular Communication during Ovarian Follicle Development. PMID:31939199
RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome. PMID:31848596
Ribosome biogenesis restricts innate immune responses to virus infection and DNA. PMID:31841110
The landscape of tiered regulation of breast cancer cell metabolism. PMID:31780802
RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. PMID:31779641
The role of noncoding mutations in blood cancers. PMID:31771951
A Fruitful Decade Using Synthetic Promoters in the Improvement of Transgenic Plants. PMID:31737027
Characterization of cxorf21 Provides Molecular Insight Into Female-Bias Immune Response in SLE Pathogenesis. PMID:31695690
Characterizing binding sites of heat responsive microRNAs and their expression pattern in heat stressed PBMCs of native cattle, exotic cattle and riverine buffaloes. PMID:31637621
Architecture of population-differentiated polymorphisms in the human genome. PMID:31622447
Convolutional neural network model to predict causal risk factors that share complex regulatory features. PMID:31598692
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans. PMID:31491384
A Computational Analysis of Alternative Splicing across Mammalian Tissues Reveals Circadian and Ultradian Rhythms in Splicing Events. PMID:31443305
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
The orphan nuclear receptor NUR77 promotes trophoblast invasion at early pregnancy through paracrine placental growth factor. PMID:31312859
Identification of Novel Biomarkers for Drug Hypersensitivity After Sequencing of the Promoter Area in 16 Genes of the Vitamin D Pathway and the High-Affinity IgE Receptor. PMID:31293618
Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world. PMID:31238849
A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. PMID:31194899
Analysis of the role of DAMTC in lung adenocarcinoma cells based on the DNA microarrays. PMID:31186684
Transcriptome Changes of Skeletal Muscle RNA-Seq Speculates the Mechanism of Postprandial Hyperglycemia in Diabetic Goto-Kakizaki Rats During the Early Stage of T2D. PMID:31141985
Developing myelin specific promoters for schwannoma gene therapy. PMID:31125589
ZBTB12 DNA methylation is associated with coagulation- and inflammation-related blood cell parameters: findings from the Moli-family cohort. PMID:31077224
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. PMID:31061989
An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions. PMID:31008453
Intergenerational epigenetic inheritance of cancer susceptibility in mammals. PMID:30963999
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
Truncated, strong inducible promoter Pmcl1 from Metarhizium anisopliae. PMID:30800586
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845
A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. PMID:30660610
Peri-arterial specification of vascular mural cells from naïve mesenchyme requires Notch signaling. PMID:30642834
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. PMID:30577431
Performance evaluation for MOTIFSIM. PMID:30574025
Identification of novel candidate genes involved in the progression of emphysema by bioinformatic methods. PMID:30532529
Identification of Transcription Regulatory Relationships in Diabetic Nephropathy. PMID:30511699
IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation. PMID:30472158
A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts. PMID:30459414
Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure. PMID:30375404
MODSIDE: a motif discovery pipeline and similarity detector. PMID:30340511
Systematic identification and analysis of dysregulated miRNA and transcription factor feed-forward loops in hypertrophic cardiomyopathy. PMID:30338905
Identification of TRIM14 as a Type I IFN-Stimulated Gene Controlling Hepatitis B Virus Replication by Targeting HBx. PMID:30150992
Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. PMID:30143559
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex. PMID:30059966
Vitamin D Regulation of the Uridine Phosphorylase 1 Gene and Uridine-Induced DNA Damage in Colon in African Americans and European Americans. PMID:29964038
Fast sequence analysis based on diamond sampling. PMID:29953448
Towards a gene regulatory network shaping the fins of the Princess cichlid. PMID:29942008
A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks. PMID:29940845
Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato. PMID:29934298
Regulatory variants: from detection to predicting impact. PMID:29893792
Synthetic Promoters: Designing the cis Regulatory Modules for Controlled Gene Expression. PMID:29855997
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
REGGAE: a novel approach for the identification of key transcriptional regulators. PMID:29741575
High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. PMID:29738455
A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve. PMID:29716548
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
Measuring phenotype-phenotype similarity through the interactome. PMID:29671400
Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PMID:29659575
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction. PMID:29654070
Emerging applications of genome-editing technology to examine functionality of GWAS-associated variants for complex traits. PMID:29652634
ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. PMID:29636475
Identification of the key transcription factors in esophageal squamous cell carcinoma. PMID:29600044
A unified approach for quantifying and interpreting DNA shape readout by transcription factors. PMID:29472273
Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. PMID:29456552
Screening for key genes and transcription factors in ankylosing spondylitis by RNA-Seq. PMID:29434723
High-Resolution Mapping and Dynamics of the Transcriptome, Transcription Factors, and Transcription Co-Factor Networks in Classically and Alternatively Activated Macrophages. PMID:29403501
Identification of key genes associated with bladder cancer using gene expression profiles. PMID:29375713
Salicylic Acid Perturbs sRNA-Gibberellin Regulatory Network in Immune Response of Potato to Potato virus Y Infection. PMID:29312421
Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells. PMID:29233185
Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation. PMID:29158996
C/EBPβ mediates RNA polymerase III-driven transcription of oncomiR-138 in malignant gliomas. PMID:29136251
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines. PMID:29077896
Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma. PMID:28990066
Systems biology analysis of longitudinal functional response of endothelial cells to shear stress. PMID:28973892
In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PMID:28910327
TREM-1 SNP rs2234246 regulates TREM-1 protein and mRNA levels and is associated with plasma levels of L-selectin. PMID:28771614
Association analyses based on false discovery rate implicate new loci for coronary artery disease. PMID:28714975
Recurrent and functional regulatory mutations in breast cancer. PMID:28658208
The loss of Krüppel-like factor 15 in Foxd1+ stromal cells exacerbates kidney fibrosis. PMID:28651950
MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets. PMID:28632401
WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data. PMID:28607381
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. PMID:28591841
A comparison of nucleosome organization in Drosophila cell lines. PMID:28570602
Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). PMID:28560587
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
A computational approach for the functional classification of the epigenome. PMID:28515787
In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants. PMID:28506205
Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data. PMID:28496131
Gene Expression Profiling of the Optic Nerve Head of Patients with Primary Open-Angle Glaucoma. PMID:28484645
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
Identification of potential gene targets in systemic vasculitis using DNA microarray analysis. PMID:28440408
Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. PMID:28338730
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. PMID:28334916
Predicting the impact of non-coding variants on DNA methylation. PMID:28334830
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. PMID:28333948
Network perturbation by recurrent regulatory variants in cancer. PMID:28333928
Identification of lymph node metastasis-related microRNAs in lung adenocarcinoma and analysis of the underlying mechanisms using a bioinformatics approach. PMID:28299977
Analysis of Co-Associated Transcription Factors via Ordered Adjacency Differences on Motif Distribution. PMID:28240320
Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering. PMID:28220871
NF-κB1, c-Rel, and ELK1 inhibit miR-134 expression leading to TAB1 upregulation in paclitaxel-resistant human ovarian cancer. PMID:28206956
Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case. PMID:28196369
Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability. PMID:28180284
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. PMID:28155687
Global inference of disease-causing single nucleotide variants from exome sequencing data. PMID:28155632
A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species. PMID:28097057
Identification of Key Transcription Factors Associated with Lung Squamous Cell Carcinoma. PMID:28081052
Screening the key microRNAs and transcription factors in prostate cancer based on microRNA functional synergistic relationships. PMID:28072703
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PMID:28056026
MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression. PMID:28005952
Non-coding single nucleotide variants affecting estrogen receptor binding and activity. PMID:27964748
Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. PMID:27932399
Predicting the recurrence of noncoding regulatory mutations in cancer. PMID:27912731
Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells. PMID:27866206
PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets. PMID:27843946
Pattern analysis uncovers a chronic ethanol-induced disruption of the switch-like dynamics of C/EBP-β and C/EBP-α genome-wide binding during liver regeneration. PMID:27815535
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. PMID:27789693
Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PMID:27776185
Age-related changes in cerebellar and hypothalamic function accompany non-microglial immune gene expression, altered synapse organization, and excitatory amino acid neurotransmission deficits. PMID:27689748
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments. PMID:27655842
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network. PMID:27650546
An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures. PMID:27633916
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. PMID:27612563
Data sources for in vivo molecular profiling of human phenotypes. PMID:27599755
An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC). PMID:27556922
Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PMID:27500531
Modeling protein-DNA binding via high-throughput in vitro technologies. PMID:27497616
Context-specific functional module based drug efficacy prediction. PMID:27490093
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. PMID:27436282
Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types. PMID:27432226
Identification of candidate genes for myeloma-induced osteocyte death based on microarray data. PMID:27405725
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells. PMID:27367417
Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. PMID:27288011
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. PMID:27264734
MicroRNA-140-5p and SMURF1 regulate pulmonary arterial hypertension. PMID:27214554
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. PMID:27117414
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
The YY1/MMP2 axis promotes trophoblast invasion at the maternal-fetal interface. PMID:27071480
Network Biomarkers of Bladder Cancer Based on a Genome-Wide Genetic and Epigenetic Network Derived from Next-Generation Sequencing Data. PMID:27034531
A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program. PMID:26898779
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva. PMID:26896950
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages. PMID:26872335
Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study. PMID:26870257
A novel comparative pattern count analysis reveals a chronic ethanol-induced dynamic shift in immediate early NF-κB genome-wide promoter binding during liver regeneration. PMID:26847025
Network-based in silico drug efficacy screening. PMID:26831545
Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PMID:26799215
Nuclear hormone receptor DHR96 mediates the resistance to xenobiotics but not the increased lifespan of insulin-mutant Drosophila. PMID:26787908
Common variation in atrial fibrillation: navigating the path from genetic association to mechanism. PMID:26733238
Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. PMID:26721385
Role of NSC319726 in ovarian cancer based on the bioinformatics analyses. PMID:26719703
Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue. PMID:26688819
Discovery of Transcriptional Targets Regulated by Nuclear Receptors Using a Probabilistic Graphical Model. PMID:26643261
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing. PMID:26620638
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. PMID:26586797
A method for developing regulatory gene set networks to characterize complex biological systems. PMID:26576648
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. PMID:26552868
Construction and analysis of dynamic transcription factor regulatory networks in the progression of glioma. PMID:26526635
Further insight into molecular mechanism underlying thoracic spinal cord injury using bioinformatics methods. PMID:26497545
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
Association of the C-Reactive Protein Gene (CRP) rs1205 C>T Polymorphism with Aortic Valve Calcification in Patients with Aortic Stenosis. PMID:26473826
Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. PMID:26464005
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. PMID:26453433
How to Isolate a Plant's Hypomethylome in One Shot. PMID:26421293
The Role of ARF6 in Biliary Atresia. PMID:26379158
Genes related to inflammation and bone loss process in periodontitis suggested by bioinformatics methods. PMID:26334995
Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells. PMID:26314709
Network-Based Association Study of Obesity and Type 2 Diabetes with Gene Expression Profiles. PMID:26273637
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. PMID:26272204
MicroRNA and transcription factor mediated regulatory network analysis reveals critical regulators and regulatory modules in myocardial infarction. PMID:26258537
Wnt addiction of genetically defined cancers reversed by PORCN inhibition. PMID:26257057
Identification of the key genes connected with plasma cells of multiple myeloma using expression profiles. PMID:26229487
Effects of β-catenin on differentially expressed genes in multiple myeloma. PMID:26223925
Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses. PMID:26223639
Functional and Structural Characterization of FAU Gene/Protein from Marine Sponge Suberites domuncula. PMID:26198235
ROCK inhibition enhances microRNA function by promoting deadenylation of targeted mRNAs via increasing PAIP2 expression. PMID:26187994
Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. PMID:26185457
Beyond antioxidant genes in the ancient Nrf2 regulatory network. PMID:26163000
A widespread role of the motif environment in transcription factor binding across diverse protein families. PMID:26160164
Time-course gene profiling and networks in demethylated retinoblastoma cell line. PMID:26143641
A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PMID:26131856
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis. PMID:26100984
The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes. PMID:26100872
Inference of transcriptional regulation in cancers. PMID:26056275
Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. PMID:26046465
Combinations of Kinase Inhibitors Protecting Myoblasts against Hypoxia. PMID:26042811
Direct ChIP-Seq significance analysis improves target prediction. PMID:26040656
Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations. PMID:26029240
Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes. PMID:26001967
Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. PMID:25996148
A novel DNA sequence motif in human and mouse genomes. PMID:25990515
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. PMID:25972521
Identification of therapeutic targets for glioblastoma by network analysis. PMID:25961929
Determining minimum set of driver nodes in protein-protein interaction networks. PMID:25947063
Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock. PMID:25944781
TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. PMID:25943543
Variations in the Regulatory Region of Alpha S1-Casein Milk Protein Gene among Tropically Adapted Indian Native (Bos Indicus) Cattle. PMID:25937984
Bioinformatics analyses of significant prognostic risk markers for thyroid papillary carcinoma. PMID:25908172
A Sex-Specific MicroRNA-96/5-Hydroxytryptamine 1B Axis Influences Development of Pulmonary Hypertension. PMID:25871906
CDX2 homeoprotein is involved in the regulation of ST6GalNAc-I gene in intestinal metaplasia. PMID:25867765
NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma. PMID:25857630
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining. PMID:25844119
Alternative splicing of the androgen receptor in polycystic ovary syndrome. PMID:25825716
In silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of Strigolactones in plants. PMID:25815594
A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements. PMID:25796517
Selective coregulator function and restriction of steroid receptor chromatin occupancy by Hic-5. PMID:25763609
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Integrative analysis of 111 reference human epigenomes. PMID:25693563
Krüppel-like factor 6 regulates mitochondrial function in the kidney. PMID:25689250
Crucial microRNAs and genes of human primary breast cancer explored by microRNA-mRNA integrated analysis. PMID:25680412
Identification of genes and transcription factors associated with glucocorticoid response in lens epithelial cells. PMID:25672806
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. PMID:25627106
Identification of key genes associated with colorectal cancer based on the transcriptional network. PMID:25613817
Analysis of genetic variations across regulatory and coding regions of kappa-casein gene of Indian native cattle (Bos indicus) and buffalo (Bubalus bubalis). PMID:25606460
A hormone-responsive C1-domain-containing protein At5g17960 mediates stress response in Arabidopsis thaliana. PMID:25590629
Positive feedback regulation of type I interferon by the interferon-stimulated gene STING. PMID:25572843
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
DNA methylation profile and expression of surfactant protein A2 gene in lung cancer. PMID:25514367
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
ModuleBlast: identifying activated sub-networks within and across species. PMID:25428368
Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr. PMID:25419450
Learning dysregulated pathways in cancers from differential variability analysis. PMID:25392694
Text mining in cancer gene and pathway prioritization. PMID:25392685
Pathogenesis analysis of pituitary adenoma based on gene expression profiling. PMID:25360166
Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome. PMID:25360157
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. PMID:25348400
Inferring protein modulation from gene expression data using conditional mutual information. PMID:25314274
VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants. PMID:25306238
Subcellular localization of coagulation factor II receptor-like 1 in neurons governs angiogenesis. PMID:25216639
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Control of asymmetric Hopfield networks and application to cancer attractors. PMID:25170874
Characterization of a REST-Regulated Internal Promoter in the Schizophrenia Genome-Wide Associated Gene MIR137. PMID:25154622
Predicting and validating the pathway of Wnt3a-driven suppression of osteoclastogenesis. PMID:25038457
Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion. PMID:25028721
Using graphical adaptive lasso approach to construct transcription factor and microRNA's combinatorial regulatory network in breast cancer. PMID:25014375
Large-scale investigation of human TF-miRNA relations based on coexpression profiles. PMID:24995316
Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites. PMID:24992458
Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. PMID:24982665
Strategies to design and analyze targeted sequencing data: cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. PMID:24951659
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
Overexpression of histone deacetylases in cancer cells is controlled by interplay of transcription factors and epigenetic modulators. PMID:24948597
Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics. PMID:24923803
Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile. PMID:24894389
Dietary switch reveals fast coordinated gene expression changes in Drosophila melanogaster. PMID:24864304
Motif enrichment tool. PMID:24860165
Global microRNA depletion suppresses tumor angiogenesis. PMID:24788094
Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. PMID:24773781
Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders. PMID:24720851
An alternative transcription start site yields estrogen-unresponsive Kiss1 mRNA transcripts in the hypothalamus of prepubertal female rats. PMID:24686008
Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. PMID:24680932
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information. PMID:24608116
Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. PMID:24598577
RMaNI: Regulatory Module Network Inference framework. PMID:24564496
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. PMID:24555784
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. PMID:24515121
Genome-wide identification of Drosophila Hb9 targets reveals a pivotal role in directing the transcriptome within eight neuronal lineages, including activation of nitric oxide synthase and Fd59a/Fox-D. PMID:24512689
Cloning and Expression Analysis of a Gene Encoding for Ascorbate Peroxidase and Responsive to Salt Stress in Beet (Beta vulgaris). PMID:24465083
A common functional regulatory variant at a type 2 diabetes locus upregulates ARAP1 expression in the pancreatic beta cell. PMID:24439111
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
Fundamental diversity of human CpG islands at multiple biological levels. PMID:24419148
Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns. PMID:24395799
Vitamin D receptor, an important transcription factor associated with aldosterone-producing adenoma. PMID:24376526
Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy. PMID:24370116
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. PMID:24366875
Integrating human omics data to prioritize candidate genes. PMID:24344781
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant. PMID:24334606
Id4 dependent acetylation restores mutant-p53 transcriptional activity. PMID:24330748
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. PMID:24310002
Transcriptional regulatory network and protein-protein interaction to reveal the mechanism of pancreatic cancer. PMID:24307251
Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. PMID:24288374
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. PMID:24267887
Discovering transcription and splicing networks in myelodysplastic syndromes. PMID:24244432
Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis. PMID:24223768
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. PMID:24200043
Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA. PMID:24146751
MEF2 is an in vivo immune-metabolic switch. PMID:24075010
Cycles in spatial and temporal chromosomal organization driven by the circadian clock. PMID:24056944
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis. PMID:24053712
Integrative bioinformatics links HNF1B with clear cell carcinoma and tumor-associated thrombosis. PMID:24040285
Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PMID:24039560
HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts. PMID:24037088
PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation. PMID:24028770
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. PMID:23972209
Origin and functional diversification of an amphibian defense peptide arsenal. PMID:23935531
Genetic variants in IL1A and IL1B contribute to the susceptibility to 2009 pandemic H1N1 influenza A virus. PMID:23927441
A novel isoform of the B cell tyrosine kinase BTK protects breast cancer cells from apoptosis. PMID:23913792
An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. PMID:23907387
Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. PMID:23887936
Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PMID:23874175
Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups. PMID:23861666
Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes. PMID:23860795
Module-based breast cancer classification. PMID:23819260
Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms. PMID:23772952
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. PMID:23771147
DNA methylation data analysis and its application to cancer research. PMID:23750645
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. PMID:23748563
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. PMID:23734902
Mechanosensitive microRNAs-role in endothelial responses to shear stress and redox state. PMID:23727269
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. PMID:23700312
Identifying context-specific transcription factor targets from prior knowledge and gene expression data. PMID:23694699
Computational identification of active enhancers in model organisms. PMID:23685394
Twine: display and analysis of cis-regulatory modules. PMID:23658420
Sequence analysis and identification of new variations in the 5'-flanking region of αS2-casein gene in Indian zebu cattle. PMID:23657593
Nuclear factor κB-dependent histone acetylation is specifically involved in persistent forms of memory. PMID:23616565
Dynamic transcription factor networks in epithelial-mesenchymal transition in breast cancer models. PMID:23593114
Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood. PMID:23593028
NF-κB plays a key role in inducing CD274 expression in human monocytes after lipopolysaccharide treatment. PMID:23585913
Molecular cloning of doublesex genes of four cladocera (water flea) species. PMID:23575357
Multiple transcription factor binding sites predict AID targeting in non-Ig genes. PMID:23514741
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. PMID:23512712
Inferring microRNA and transcription factor regulatory networks in heterogeneous data. PMID:23497388
Identification of germ cell-specific genes in mammalian meiotic prophase. PMID:23445120
Identification of candidate transcription factor binding sites in the cattle genome. PMID:23433959
The role of bioactive nanofibers in enamel regeneration mediated through integrin signals acting upon C/EBPα and c-Jun. PMID:23398885
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. PMID:23393188
Identification of a genetic locus on chromosome 4q34-35 for type 2 diabetes with overweight. PMID:23392254
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. PMID:23369107
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Quantitative, solution-phase profiling of multiple transcription factors in parallel. PMID:23361227
Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. PMID:23355544
Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture. PMID:23335855
Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays. PMID:23327800
The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion. PMID:23320978
A structural-based strategy for recognition of transcription factor binding sites. PMID:23320072
Functional characterization of motif sequences under purifying selection. PMID:23303791
Regulation of GTP-binding protein (Gαs) expression in human myometrial cells: a role for tumor necrosis factor in modulating Gαs promoter acetylation by transcriptional complexes. PMID:23297421
Homocysteine induces inflammatory transcriptional signaling in monocytes. PMID:23276953
A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. PMID:23271069
The twilight zone of cis element alignments. PMID:23268451
Subset of genes targeted by transcription factor NF-κB in TNFα-stimulated human HeLa cells. PMID:23247759
Identifying grade/stage-related active modules in human co-regulatory networks: a case study for breast cancer. PMID:23215806
Microarray-based analysis of gene regulation by transcription factors and microRNAs in glioma. PMID:23212403
β-catenin regulates GnRH-induced FSHβ gene expression. PMID:23211523
On the contributions of topological features to transcriptional regulatory network robustness. PMID:23194062
The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. PMID:23190768
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. PMID:23180783
C/EBPγ deregulation results in differentiation arrest in acute myeloid leukemia. PMID:23160200
The DNA damage- and transcription-associated protein paxip1 controls thymocyte development and emigration. PMID:23159437
2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models. PMID:23153050
Distinct neurogenomic states in basal ganglia subregions relate differently to singing behavior in songbirds. PMID:23144607
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. PMID:23135404
Comparative genomics of neuroglobin reveals its early origins. PMID:23133533
Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. PMID:23124521
CDX2 is an amplified lineage-survival oncogene in colorectal cancer. PMID:23112155
Transcription factor networks in invasion-promoting breast carcinoma-associated fibroblasts. PMID:23090154
Genome-wide analysis of androgen receptor targets reveals COUP-TF1 as a novel player in human prostate cancer. PMID:23056316
Insights into the molecular mechanism of RGL2-mediated inhibition of seed germination in Arabidopsis thaliana. PMID:23035751
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PMID:23029415
Discovery and characterization of human exonic transcriptional regulatory elements. PMID:23029400
Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder. PMID:23020841
Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions. PMID:23019221
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. PMID:22955990
Personal and population genomics of human regulatory variation. PMID:22955981
Genome-wide in silico prediction of gene expression. PMID:22954627
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. PMID:22945787
Improved predictions of transcription factor binding sites using physicochemical features of DNA. PMID:22923524
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PMID:22912568
Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. PMID:22902740
Towards biological characters of interactions between transcription factors and their DNA targets in mammals. PMID:22888987
Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis. PMID:22875853
Phorbol esters enhance 1α,25-dihydroxyvitamin D3-regulated 25-hydroxyvitamin D-24-hydroxylase (CYP24A1) gene expression through ERK-mediated phosphorylation of specific protein 3 (Sp3) in Caco-2 cells. PMID:22871965
Cell-type specificity of ChIP-predicted transcription factor binding sites. PMID:22863112
Foxi2 is an animally localized maternal mRNA in Xenopus, and an activator of the zygotic ectoderm activator Foxi1e. PMID:22848601
Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. PMID:22844240
A common and functional mineralocorticoid receptor haplotype enhances optimism and protects against depression in females. PMID:22832354
The co-regulation mechanism of transcription factors in the human gene regulatory network. PMID:22798495
POWRS: position-sensitive motif discovery. PMID:22792292
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. PMID:22784574
Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PMID:22768038
Viral perturbations of host networks reflect disease etiology. PMID:22761553
Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. PMID:22759862
Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots. PMID:22759569
Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis. PMID:22744985
Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control. PMID:22740631
Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. PMID:22719926
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. PMID:22706305
Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PMID:22693540
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. PMID:22689766
Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. PMID:22672625
A computational profiling of changes in gene expression and transcription factors induced by vFLIP K13 in primary effusion lymphoma. PMID:22624040
Identification of a gene expression signature common to distinct cancer pathways. PMID:22619501
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. PMID:22573175
Inferring Genetic Interactions via a Data-Driven Second Order Model. PMID:22563331
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets. PMID:22548828
Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients. PMID:22545094
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. PMID:22540038
Cell cycle gene networks are associated with melanoma prognosis. PMID:22536322
Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. PMID:22534400
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
A flexible integrative approach based on random forest improves prediction of transcription factor binding sites. PMID:22492513
Analysis of Cryptococcus neoformans sexual development reveals rewiring of the pheromone-response network by a change in transcription factor identity. PMID:22466042
A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs. PMID:22454232
A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. PMID:22406746
DNA-protein interactions: methods for detection and analysis. PMID:22399265
Allele-specific differences in activity of a novel cannabinoid receptor 1 (CNR1) gene intronic enhancer in hypothalamus, dorsal root ganglia, and hippocampus. PMID:22362764
An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese. PMID:22355539
Modeling Equilibrium of microRNA Expression. PMID:22303331
Antipsychotics activate the TGFβ pathway effector SMAD3. PMID:22290122
Genome-wide progesterone receptor binding: cell type-specific and shared mechanisms in T47D breast cancer cells and primary leiomyoma cells. PMID:22272226
Ameloblastin upstream region contains structural elements regulating transcriptional activity in a stromal cell line derived from bone marrow. PMID:22243258
Statistical properties and robustness of biological controller-target networks. PMID:22235289
"Calling cards" for DNA-binding proteins in mammalian cells. PMID:22214611
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Promoter architecture of mouse olfactory receptor genes. PMID:22194471
A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene. PMID:22194342
Genomewide association study using a high-density single nucleotide polymorphism array and case-control design identifies a novel essential hypertension susceptibility locus in the promoter region of endothelial NO synthase. PMID:22184326
Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22. PMID:22180461
A computational pipeline for comparative ChIP-seq analyses. PMID:22179591
Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network. PMID:22176772
Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. PMID:22176622
Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks. PMID:22166063
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. PMID:22143240
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. PMID:22140105
GWASdb: a database for human genetic variants identified by genome-wide association studies. PMID:22139925
Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia. PMID:22093874
Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription. PMID:22086061
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. PMID:22080862
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. PMID:22064851
Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines. PMID:22051105
SOX10 regulates expression of the SH3-domain kinase binding protein 1 (Sh3kbp1) locus in Schwann cells via an alternative promoter. PMID:22037207
Master transcription factors determine cell-type-specific responses to TGF-β signaling. PMID:22036565
Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. PMID:21990380
Transcriptional networks in epithelial-mesenchymal transition. PMID:21980432
Express path analysis identifies a tyrosine kinase Src-centric network regulating divergent host responses to Mycobacterium tuberculosis infection. PMID:21953458
How yeast re-programmes its transcriptional profile in response to different nutrient impulses. PMID:21943358
AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses. PMID:21931761
Systems biology and the future of medicine. PMID:21928407
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. PMID:21923952
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. PMID:21917857
An iterative genetic and dynamical modelling approach identifies novel features of the gene regulatory network underlying melanocyte development. PMID:21909283
Inactivation of a single copy of Crebbp selectively alters pre-mRNA processing in mouse hematopoietic stem cells. PMID:21901164
Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state. PMID:21878914
Discriminative prediction of mammalian enhancers from DNA sequence. PMID:21875935
Characterization of two common 5' polymorphisms in PEX1 and correlation to survival in PEX1 peroxisome biogenesis disorder patients. PMID:21846392
Negative effect of glucose on ompA mRNA stability: a potential role of cyclic AMP in the repression of hfq in Escherichia coli. PMID:21840983
The Caenorhabditis elegans GATA factor ELT-1 works through the cell proliferation regulator BRO-1 and the Fusogen EFF-1 to maintain the seam stem-like fate. PMID:21829390
ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif. PMID:21764776
Integration of genome-wide computation DRE search, AhR ChIP-chip and gene expression analyses of TCDD-elicited responses in the mouse liver. PMID:21762485
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
The differential disease regulome. PMID:21736759
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. PMID:21708028
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. PMID:21694719
Functional pathway mapping analysis for hypoxia-inducible factors. PMID:21689478
Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis. PMID:21673114
Evolution of hsp70 gene expression: a role for changes in AT-richness within promoters. PMID:21655251
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Genome-wide association study for atopy and allergic rhinitis in a Singapore Chinese population. PMID:21625490
Kinetic profiling of the c-Myc transcriptome and bioinformatic analysis of repressed gene promoters. PMID:21623162
CENTDIST: discovery of co-associated factors by motif distribution. PMID:21602269
Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter. PMID:21596311
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. PMID:21586587
An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. PMID:21572177
Mechanisms of non-metastatic 2 (NME2)-mediated control of metastasis across tumor types. PMID:21556888
Preinvasive colorectal lesion transcriptomes correlate with endoscopic morphology (polypoid vs. nonpolypoid). PMID:21538994
Insights gained from the reverse engineering of gene networks in keloid fibroblasts. PMID:21535890
A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites. PMID:21533218
Using graph theory to analyze biological networks. PMID:21527005
NFIL3/E4BP4 controls type 2 T helper cell cytokine expression. PMID:21499227
Finding subtypes of transcription factor motif pairs with distinct regulatory roles. PMID:21486752
Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PMID:21483663
Development of transcriptional fusions to assess Leptospira interrogans promoter activity. PMID:21445252
Mapping and analysis of chromatin state dynamics in nine human cell types. PMID:21441907
Hepatitis B virus X protein regulates the mEZH2 promoter via the E2F1-binding site in AML12 cells. PMID:21439249
Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. PMID:21437642
An integrative approach to identifying cancer chemoresistance-associated pathways. PMID:21429228
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data. PMID:21422075
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PMID:21408212
Functional characterization of liver enhancers that regulate drug-associated transporters. PMID:21368754
Liver X receptor-retinoid X receptor (LXR-RXR) heterodimer cistrome reveals coordination of LXR and AP1 signaling in keratinocytes. PMID:21349840
Estrogen-dependent gene expression in the mouse ovary. PMID:21347412
Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models. PMID:21342559
Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes. PMID:21342535
Designer promoter: an artwork of cis engineering. PMID:21327513
G = MAT: linking transcription factor expression and DNA binding data. PMID:21297945
Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. PMID:21283670
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity. PMID:21272326
Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling. PMID:21194568
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. PMID:21183585
A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo. PMID:21179557
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. PMID:21177332
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
Inherited variants in the chemokine CCL2 gene and prostate cancer aggressiveness in a Caucasian cohort. PMID:21135144
A Bayesian search for transcriptional motifs. PMID:21124986
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. PMID:21118975
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. PMID:21113027
Regulation patterns in signaling networks of cancer. PMID:21110851
Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm. PMID:21079756
Aberrant estrogen regulation of PEMT results in choline deficiency-associated liver dysfunction. PMID:21059658
Combinatorial regulation of transcription factors and microRNAs. PMID:21059252
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PMID:21049040
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. PMID:21030438
Computational discovery of miR-TF regulatory modules in human genome. PMID:20975901
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. PMID:20959017
An integrated analysis of molecular aberrations in NCI-60 cell lines. PMID:20925909
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. PMID:20861161
Motif prediction to distinguish LPS-stimulated pro-inflammatory vs. antibacterial macrophage genes. PMID:20858252
The transcriptional control of female puberty. PMID:20851111
Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. PMID:20829281
Identification of cis-regulatory elements in the mammalian genome: the cREMaG database. PMID:20824209
Identification of a previously unrecognized promoter that drives expression of the UXP transcription unit in the human adenovirus type 5 genome. PMID:20739525
Apolipoprotein B genetic variants modify the response to fenofibrate: a GOLDN study. PMID:20724655
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. PMID:20709693
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. PMID:20685816
Comparative Membranome expression analysis in primary tumors and derived cell lines. PMID:20668533
Association between common variation in genes encoding sweet taste signaling components and human sucrose perception. PMID:20660057
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. PMID:20653936
Cloning and characterization of a sialidase from the filamentous fungus, Aspergillus fumigatus. PMID:20652740
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. PMID:20649980
Gene expression analysis of forskolin treated basilar papillae identifies microRNA181a as a mediator of proliferation. PMID:20634979
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. PMID:20615900
Research Resource: The androgen receptor modulates expression of genes with critical roles in muscle development and function. PMID:20610535
Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1. PMID:20600580
Effect of high intratesticular estrogen on global gene expression and testicular cell number in rats. PMID:20573204
Genome-wide association studies--data generation, storage, interpretation, and bioinformatics. PMID:20560038
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. PMID:20534127
TFM-Explorer: mining cis-regulatory regions in genomes. PMID:20522509
Genome-wide analysis of regions similar to promoters of histone genes. PMID:20522254
Characterization of a Novel DNA Motif in the Tctex1 and TCP10 Gene Complexes and its Prevalence in the Mouse Genome. PMID:20514145
A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PMID:20505756
Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. PMID:20479128
Discovering modulators of gene expression. PMID:20466809
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. PMID:20435683
Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. PMID:20435671
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
A cis-regulatory signature for chordate anterior neuroectodermal genes. PMID:20419150
PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. PMID:20398296
Growth delay of human bladder cancer cells by Prostate Stem Cell Antigen downregulation is associated with activation of immune signaling pathways. PMID:20374648
Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes. PMID:20369014
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. PMID:20363979
A systems biology approach to transcription factor binding site prediction. PMID:20360861
Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration. PMID:20358383
wDBTF: an integrated database resource for studying wheat transcription factor families. PMID:20298594
Coregulation mapping based on individual phenotypic variation in response to virus infection. PMID:20298589
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Integrating multiple evidence sources to predict transcription factor binding in the human genome. PMID:20219943
Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. PMID:20219939
Functional annotation of novel lineage-specific genes using co-expression and promoter analysis. PMID:20214810
Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. PMID:20176806
Antiviral response dictated by choreographed cascade of transcription factors. PMID:20164420
NETWORKS, BIOLOGY AND SYSTEMS ENGINEERING: A CASE STUDY IN INFLAMMATION. PMID:20161495
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PMID:20126523
Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. PMID:20100339
A novel alignment-free method for comparing transcription factor binding site motifs. PMID:20098703
Acute stress alters transcript expression pattern and reduces processing of proBDNF to mature BDNF in Dicentrarchus labrax. PMID:20074340
Binding sites for ETS family of transcription factors dominate the promoter regions of differentially expressed genes in abdominal aortic aneurysms. PMID:20031636
Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. PMID:19965633
Uncovering transcriptional interactions via an adaptive fuzzy logic approach. PMID:19961622
Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types. PMID:19949461
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. PMID:19941641
Genome-wide dynamics of chromatin binding of estrogen receptors alpha and beta: mutual restriction and competitive site selection. PMID:19897598
Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PMID:19893611
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. PMID:19853570
Protopia: a protein-protein interaction tool. PMID:19828077
Regulation of multiple renin-angiotensin system genes by Sry. PMID:19809364
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. PMID:19786498
MOODS: fast search for position weight matrix matches in DNA sequences. PMID:19773334
Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. PMID:19767611
A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes. PMID:19761575
D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs. PMID:19759861
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. PMID:19741643
A genome-wide screen for spatially restricted expression patterns identifies transcription factors that regulate glial development. PMID:19741146
Exhaustive search for over-represented DNA sequence motifs with CisFinder. PMID:19740934
A global survey identifies novel upstream components of the Ath5 neurogenic network. PMID:19735568
Polymorphisms in the hepatic lipase gene affect plasma HDL-cholesterol levels in a Turkish population. PMID:19734193
Prediction and experimental validation of novel STAT3 target genes in human cancer cells. PMID:19730699
Comparative analyses of plant transcription factor databases. PMID:19721806
Integrating multiple microarray data for cancer pathway analysis using bootstrapping K-S test. PMID:19704919
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. PMID:19704032
Integrative modeling of transcriptional regulation in response to antirheumatic therapy. PMID:19703281
Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. PMID:19678937
Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs. PMID:19654925
Host sequence motifs shared by HIV predict response to antiretroviral therapy. PMID:19627600
Transcriptional programs: modelling higher order structure in transcriptional control. PMID:19607663
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. PMID:19604364
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. PMID:19583839
Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. PMID:19568283
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation. PMID:19558665
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PMID:19543368
Internet Resources for Gene Expression Analysis in Arabidopsis thaliana. PMID:19506727
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. PMID:19483094
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. PMID:19451166
Systematic identification of transcription factors associated with patient survival in cancers. PMID:19442316
Analytical methods for inferring functional effects of single base pair substitutions in human cancers. PMID:19434427
An integrated approach to identifying cis-regulatory modules in the human genome. PMID:19434238
Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila. PMID:19409101
FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. PMID:19398761
The RhoU/Wrch1 Rho GTPase gene is a common transcriptional target of both the gp130/STAT3 and Wnt-1 pathways. PMID:19397496
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. PMID:19389732
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. PMID:19339991
Comparative expression pathway analysis of human and canine mammary tumors. PMID:19327144
Statistical detection of cooperative transcription factors with similarity adjustment. PMID:19286833
Biological convergence of cancer signatures. PMID:19229342
Integrating sequence, evolution and functional genomics in regulatory genomics. PMID:19226437
Environment-specific combinatorial cis-regulation in synthetic promoters. PMID:19225457
Involvement of FLIP in 2-methoxyestradiol-induced tumor regression in transgenic adenocarcinoma of mouse prostate model. PMID:19223508
Atypical X-chromosome inactivation in an X;1 translocation patient demonstrating Xq28 functional disomy. PMID:19215059
Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. PMID:19211936
A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data. PMID:19210737
Yin yang 1 modulates taxane response in epithelial ovarian cancer. PMID:19208743
A primer on regression methods for decoding cis-regulatory logic. PMID:19180174
Orientation, distance, regulation and function of neighbouring genes. PMID:19164091
Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter. PMID:19159624
High-resolution DNA-binding specificity analysis of yeast transcription factors. PMID:19158363
A transcription factor affinity-based code for mammalian transcription initiation. PMID:19141595
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. PMID:19118200
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. PMID:19105834
Ultraconserved elements in the Olig2 promoter. PMID:19079603
Temporal regulation of Ath5 gene expression during eye development. PMID:19059393
Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva. PMID:19055776
A survey of visualization tools for biological network analysis. PMID:19040716
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. PMID:19036135
Design and analysis of ChIP-seq experiments for DNA-binding proteins. PMID:19029915
Analysis of combinatorial cis-regulation in synthetic and genomic promoters. PMID:19029883
Predicting DNA recognition by Cys2His2 zinc finger proteins. PMID:19008249
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. PMID:19003267
Temporal and functional profile of the transcriptional regulatory network in the early regenerative response to partial hepatectomy in the rat. PMID:18990226
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. PMID:18981473
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PMID:18974828
Chromatin immunoprecipitation on microarray analysis of Smad2/3 binding sites reveals roles of ETS1 and TFAP2A in transforming growth factor beta signaling. PMID:18955504
Positional distribution of human transcription factor binding sites. PMID:18953043
An evolutionarily conserved intronic region controls the spatiotemporal expression of the transcription factor Sox10. PMID:18950534
An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome. PMID:18931920
Evolutionary computation for discovery of composite transcription factor binding sites. PMID:18927103
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. PMID:18842628
AthaMap, integrating transcriptional and post-transcriptional data. PMID:18842622
The role of positive selection in determining the molecular cause of species differences in disease. PMID:18837980
Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles. PMID:18822150
GBNet: deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. PMID:18811979
MicroRNA-155 is regulated by the transforming growth factor beta/Smad pathway and contributes to epithelial cell plasticity by targeting RhoA. PMID:18794355
Transcriptional autoregulatory loops are highly conserved in vertebrate evolution. PMID:18791639
Modeling ChIP sequencing in silico with applications. PMID:18725927
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. PMID:18722178
Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments. PMID:18721468
Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes. PMID:18715197
Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. PMID:18710571
Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium. PMID:18682805
Recent computational approaches to understand gene regulation: mining gene regulation in silico. PMID:18660846
Differentiating human multipotent mesenchymal stromal cells regulate microRNAs: prediction of microRNA regulation by PDGF during osteogenesis. PMID:18657893
Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. PMID:18631020
TRANSPATH--a high quality database focused on signal transduction. PMID:18629064
Interoperability of CABRI Services and Biochemical Pathways Databases. PMID:18629057
Bioinformatic tools for inferring functional information from plant microarray data II: Analysis beyond single gene. PMID:18615189
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. PMID:18606616
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. PMID:18585360
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. PMID:18585359
Exuberant expression of chemokine genes by adult human articular chondrocytes in response to IL-1beta. PMID:18565769
Extracting sequence features to predict protein-DNA interactions: a comparative study. PMID:18556756
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. PMID:18554421
Screening for PPAR Responsive Regulatory Modules in Cancer. PMID:18551184
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. PMID:18533028
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. PMID:18485226
Characterization of genome-wide p53-binding sites upon stress response. PMID:18474530
A novel Bayesian DNA motif comparison method for clustering and retrieval. PMID:18463706
Defensins and the convergent evolution of platypus and reptile venom genes. PMID:18463304
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. PMID:18453628
Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius. PMID:18434436
Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. PMID:18426580
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? PMID:18394174
Profiling the thermodynamic softness of adenoviral promoters. PMID:18390611
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. PMID:18387196
Identification of a calcitriol-regulated Sp-1 site in the promoter of human CD14 using a combined western blotting electrophoresis mobility shift assay (WEMSA). PMID:18385805
Statistical modeling of transcription factor binding affinities predicts regulatory interactions. PMID:18369429
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. PMID:18367472
An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. PMID:18366601
Substitution of DNA-contacting amino acids with functional variants in the Gata-1 zinc finger: a structurally and phylogenetically guided mutagenesis. PMID:18328814
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. PMID:18315851
ORMDL3 gene is associated with asthma in three ethnically diverse populations. PMID:18310477
MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters. PMID:18307768
An efficient method for statistical significance calculation of transcription factor binding sites. PMID:18305824
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. PMID:18294369
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. PMID:18291030
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. PMID:18269696
Molecular networks discriminating mouse bladder responses to intravesical bacillus Calmette-Guerin (BCG), LPS, and TNF-alpha. PMID:18267009
Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation. PMID:18263612
Prioritization of gene regulatory interactions from large-scale modules in yeast. PMID:18211684
In silico detection of sequence variations modifying transcriptional regulation. PMID:18208319
Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility. PMID:18190704
High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae. PMID:18171483
PPARGC1A variation associated with DNA damage, diabetes, and cardiovascular diseases: the Boston Puerto Rican Health Study. PMID:18162502
Investigation of miRNA biology by bioinformatic tools and impact of miRNAs in colorectal cancer--regulatory relationship of c-Myc and p53 with miRNAs. PMID:18079974
Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters. PMID:18078513
Chronic CD4+ T-cell activation and depletion in human immunodeficiency virus type 1 infection: type I interferon-mediated disruption of T-cell dynamics. PMID:18077723
A systematic approach to detecting transcription factors in response to environmental stresses. PMID:18067669
Motif module map reveals enforcement of aging by continual NF-kappaB activity. PMID:18055696
Prediction of synergistic transcription factors by function conservation. PMID:18053230
Expression microarray analysis implicates apoptosis and interferon-responsive mechanisms in susceptibility to experimental cerebral malaria. PMID:17991715
Comprehensive screening for reg1alpha gene rules out association with tropical calcific pancreatitis. PMID:17990360
Reliable prediction of regulator targets using 12 Drosophila genomes. PMID:17989251
Functional genomic delineation of TLR-induced transcriptional networks. PMID:17967192
Genomic analysis of human microRNA transcripts. PMID:17965236
Differential regulation of native estrogen receptor-regulatory elements by estradiol, tamoxifen, and raloxifene. PMID:17962382
fREDUCE: detection of degenerate regulatory elements using correlation with expression. PMID:17941998
Incorporating evolution of transcription factor binding sites into annotated alignments. PMID:17914226
Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. PMID:17884332
Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements. PMID:17849004
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. PMID:17785538
Cell- and gene-specific regulation of primary target genes by the androgen receptor. PMID:17699749
Inference of transcriptional regulation using gene expression data from the bovine and human genomes. PMID:17683551
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. PMID:17679089
BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences. PMID:17660203
Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PMID:17630826
Housekeeping genes tend to show reduced upstream sequence conservation. PMID:17626644
Evolutionary conservation of regulated longevity assurance mechanisms. PMID:17612391
A novel method combining linkage disequilibrium information and imputed functional knowledge for tagSNP selection. PMID:17587853
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. PMID:17584794
An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. PMID:17577400
Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach. PMID:17559886
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PMID:17559307
bZIPDB: a database of regulatory information for human bZIP transcription factors. PMID:17535445
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. PMID:17534450
Intrinsic promoter activities of primary DNA sequences in the human genome. PMID:17522093
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. PMID:17517777
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. PMID:17506886
STAMP: a web tool for exploring DNA-binding motif similarities. PMID:17478497
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. PMID:17463089
Systems biology of innate immunity. PMID:17433274
Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. PMID:17404513
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PMID:17397256
Context specific transcription factor prediction. PMID:17377845
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Size matters: network inference tackles the genome scale. PMID:17299414
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. PMID:17284674
Refinement and expansion of signaling pathways: the osmotic response network in yeast. PMID:17267811
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. PMID:17264128
Androgen responsive intronic non-coding RNAs. PMID:17263875
A single-nucleotide polymorphism in a half-binding site creates p53 and estrogen receptor control of vascular endothelial growth factor receptor 1. PMID:17242190
Tissue-specific regulatory elements in mammalian promoters. PMID:17224917
Chicken ovalbumin upstream promoter transcription factor II regulates uncoupling protein 3 gene transcription in Phodopus sungorus. PMID:17204145
A microRNA signature of hypoxia. PMID:17194750
AthaMap web tools for the analysis and identification of co-regulated genes. PMID:17148485
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. PMID:17148480
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. PMID:17137509
GeneSpeed: protein domain organization of the transcriptome. PMID:17132830
Inference of splicing regulatory activities by sequence neighborhood analysis. PMID:17121466
SMOTIF: efficient structured pattern and profile motif search. PMID:17118189
Using local gene expression similarities to discover regulatory binding site modules. PMID:17109764
BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. PMID:17078876
Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome. PMID:17075698
Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease. PMID:17058067
The evolution and genomic landscape of CGB1 and CGB2 genes. PMID:17055150
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. PMID:17041233
High expression of APOBEC3G in patients infected with hepatitis C virus. PMID:17036163
Design of a combinatorial DNA microarray for protein-DNA interaction studies. PMID:17018151
Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations. PMID:16978413
PhyloPat: phylogenetic pattern analysis of eukaryotic genes. PMID:16948844
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PMID:16933976
Fast index based algorithms and software for matching position specific scoring matrices. PMID:16930469
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. PMID:16880385
Identifying transcription factor functions and targets by phenotypic activation. PMID:16880382
Computational identification of transcriptional regulatory elements in DNA sequence. PMID:16855295
Acute myeloid leukemia-associated Mkl1 (Mrtf-a) is a key regulator of mammary gland function. PMID:16847333
CRSD: a comprehensive web server for composite regulatory signature discovery. PMID:16845073
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. PMID:16845071
CEAS: cis-regulatory element annotation system. PMID:16845068
Identification of a Hoxc8-regulated transcriptional network in mouse embryo fibroblast cells. PMID:16793922
Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling. PMID:16784547
Candidate genes and their regulatory elements: alcohol preference and tolerance. PMID:16783646
BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences. PMID:16756683
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. PMID:16749936
Transcription factor map alignment of promoter regions. PMID:16733547
Analysis of computational approaches for motif discovery. PMID:16722558
Causal inference of regulator-target pairs by gene mapping of expression phenotypes. PMID:16719927
Mice and men: their promoter properties. PMID:16683032
Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. PMID:16674813
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. PMID:16670430
Characterizing disease states from topological properties of transcriptional regulatory networks. PMID:16670008
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. PMID:16643658
A computational framework for the topological analysis and targeted disruption of signal transduction networks. PMID:16617070
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. PMID:16606849
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. PMID:16606704
RGS4 genotype is not associated with antipsychotic medication response in schizophrenia. PMID:16604300
Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events. PMID:16595861
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. PMID:16551355
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. PMID:16539733
Gene expression profiling of naïve sheep genetically resistant and susceptible to gastrointestinal nematodes. PMID:16515715
Determination of strongly overlapping signaling activity from microarray data. PMID:16507110
Characteristics and clustering of human ribosomal protein genes. PMID:16504170
Human RFP2 gene promoter: unique structure and unusual strength. PMID:16499869
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. PMID:16449500
The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa. PMID:16420690
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. PMID:16420668
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. PMID:16381983
HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites. PMID:16381982
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
The UCSC Genome Browser Database: update 2006. PMID:16381938
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. PMID:16381825
TiProD: the Tissue-specific Promoter Database. PMID:16381824
Deregulation of common genes by c-Myc and its direct target, MT-MC1. PMID:16365299
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. PMID:16356267
The design of transcription-factor binding sites is affected by combinatorial regulation. PMID:16356266
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. PMID:16301543
Pendrin is a novel in vivo downstream target gene of the TTF-1/Nkx-2.1 homeodomain transcription factor in differentiated thyroid cells. PMID:16260629
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function. PMID:16232321
Polymorphisms in the gene encoding adiponectin receptor 1 are associated with insulin resistance and high liver fat. PMID:16205883
Measuring similarities between transcription factor binding sites. PMID:16191190
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. PMID:16186128
Tandem machine learning for the identification of genes regulated by transcription factors. PMID:16115317
Glucocorticoid receptor-dependent gene regulatory networks. PMID:16110340
Transposable elements donate lineage-specific regulatory sequences to host genomes. PMID:16093685
From the Cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. PMID:16087863
Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. PMID:16079853
Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species. PMID:16027132
mSin3A corepressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival. PMID:15998811
Dcode.org anthology of comparative genomic tools. PMID:15980535
CONREAL web server: identification and visualization of conserved transcription factor binding sites. PMID:15980509
P-Match: transcription factor binding site search by combining patterns and weight matrices. PMID:15980505
AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. PMID:15980498
VisANT: data-integrating visual framework for biological networks and modules. PMID:15980487
Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. PMID:15962237
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. PMID:15961489
Exploring hepatic hormone actions using a compilation of gene expression profiles. PMID:15953391
Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. PMID:15892871
Ab initio identification of putative human transcription factor binding sites by comparative genomics. PMID:15865625
Identification of regulatory polymorphisms in the TNF-TNF receptor superfamily. PMID:15856221
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
A male-specific quantitative trait locus on 1p21 controlling human stature. PMID:15827092
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. PMID:15799782
A novel functional polymorphism (-336A/G) in the promoter of the partitioning-defective protein-6alpha gene is associated with increased glucose tolerance and lower concentrations of serum non-esterified fatty acids. PMID:15744531
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. PMID:15735639
GANN: genetic algorithm neural networks for the detection of conserved combinations of features in DNA. PMID:15725347
Comparative promoter region analysis powered by CORG. PMID:15723697
An initial blueprint for myogenic differentiation. PMID:15706034
Databases, models, and algorithms for functional genomics: a bioinformatics perspective. PMID:15699571
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. PMID:15693947
Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. PMID:15684073
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. PMID:15668401
Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays. PMID:15653641
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells. PMID:15647113
FESD: a Functional Element SNPs Database in human. PMID:15608252
CYGD: the Comprehensive Yeast Genome Database. PMID:15608217
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. PMID:15608156
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. PMID:15604458
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. PMID:15603590
A sugar beet chlorophyll a/b binding protein promoter void of G-box like elements confers strong and leaf specific reporter gene expression in transgenic sugar beet. PMID:15579211
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. PMID:15574824
Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. PMID:15535867
Mutations in SIN4 and RGR1 cause constitutive expression of MAL structural genes in Saccharomyces cerevisiae. PMID:15514050
The gut microbiota as an environmental factor that regulates fat storage. PMID:15505215
Whole-genome analysis of temporal gene expression during foregut development. PMID:15492775
An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. PMID:15489324
Decoding human regulatory circuits. PMID:15466295
In silico identification of transcriptional regulators associated with c-Myc. PMID:15388797
Transcriptional regulatory code of a eukaryotic genome. PMID:15343339
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. PMID:15317971
Discovery of sequence motifs related to coexpression of genes using evolutionary computation. PMID:15266008
Clustering of DNA sequences in human promoters. PMID:15256515
Target SNP selection in complex disease association studies. PMID:15248903
Caenorhabditis elegans lin-35/Rb, efl-1/E2F and other synthetic multivulva genes negatively regulate the anaphase-promoting complex gene mat-3/APC8. PMID:15238519
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. PMID:15215384
MSCAN: identification of functional clusters of transcription factor binding sites. PMID:15215379
Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. PMID:15148361
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs. PMID:15137914
A gene of the opsin family in the carotenoid gene cluster of Fusarium fujikuroi. PMID:15133714
A global view of the selection forces in the evolution of yeast cis-regulation. PMID:15123582
cis-Regulatory elements for mesophyll-specific gene expression in the C4 plant Flaveria trinervia, the promoter of the C4 phosphoenolpyruvate carboxylase gene. PMID:15100398
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. PMID:15053842
Identifying transcriptional regulatory sites in the human genome using an integrated system. PMID:15051813
Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. PMID:14968135
Statistical analysis of over-represented words in human promoter sequences. PMID:14963262
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. PMID:14762058
Computational prediction of transcription-factor binding site locations. PMID:14709165
The aMAZE LightBench: a web interface to a relational database of cellular processes. PMID:14681453
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. PMID:14681436
TrSDB: a proteome database of transcription factors. PMID:14681387
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. PMID:14681366
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. PMID:14681363
MIPS: analysis and annotation of proteins from whole genomes. PMID:14681354
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. PMID:14672977
Identification and characterization of multi-species conserved sequences. PMID:14656959
Impaired regulation of tumor suppressor p53 caused by mutations in the xeroderma pigmentosum DDB2 gene: mutual regulatory interactions between p48(DDB2) and p53. PMID:14560002
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. PMID:14530449
The inflammation-induced down-regulation of plasma Fetuin-A (alpha2HS-Glycoprotein) in liver results from the loss of interaction between long C/EBP isoforms at two neighbouring binding sites. PMID:14530444
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. PMID:12824386
PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. PMID:12824377
Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. PMID:12824376
Regulatory sequence analysis tools. PMID:12824373
SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences. PMID:12824368
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. PMID:12824365
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. PMID:12824357
GenePublisher: Automated analysis of DNA microarray data. PMID:12824347
A novel BDNF gene promoter directs expression to skeletal muscle. PMID:12812528
Identification of conserved regulatory elements by comparative genome analysis. PMID:12760745
TRANSFAC: an integrated system for gene expression regulation PubMed citations: 428.

428 articles citing: TRANSFAC: an integrated system for gene expression regulation

Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer. PMID:35222842
Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity. PMID:34567058
Long noncoding RNA#45 exerts broad inhibitory effect on influenza a virus replication via its stem ring arms. PMID:34517783
Evidence for a functional interaction of WNT10A and EBF1 in male-pattern baldness. PMID:34506541
FOXA2 inhibits doxorubicin-induced apoptosis via transcriptionally activating HBP rate-limiting enzyme GFPT1 in HCC cells. PMID:34291417
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories. PMID:33738135
Abiraterone Acetate Induces CREB1 Phosphorylation and Enhances the Function of the CBP-p300 Complex, Leading to Resistance in Prostate Cancer Cells. PMID:33495313
The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility. PMID:33407123
Endocan, a novel inflammatory marker, is upregulated in human chondrocytes stimulated with IL-1 beta. PMID:33398666
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event. PMID:32665861
Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval. PMID:32375685
Expanding Role of Ubiquitin in Translational Control. PMID:32050486
A Muscle Hybrid Promoter as a Novel Tool for Gene Therapy. PMID:31660418
A method for identifying allele-specific hydroxymethylation. PMID:31533538
A network-based analysis for mining the risk pathways in glioblastoma. PMID:31402957
Role of 4‑aminobutyrate aminotransferase (ABAT) and the lncRNA co‑expression network in the development of myelodysplastic syndrome. PMID:31173260
Exploring integument transcriptomes, cuticle ultrastructure, and cuticular hydrocarbons profiles in eusocial and solitary bee species displaying heterochronic adult cuticle maturation. PMID:30870522
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases. PMID:30804403
Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data. PMID:30740193
Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. PMID:30644396
Constructing tissue-specific transcriptional regulatory networks via a Markov random field. PMID:30598101
A new sequence logo plot to highlight enrichment and depletion. PMID:30526486
RAD9A promotes metastatic phenotypes through transcriptional regulation of anterior gradient 2 (AGR2). PMID:30295739
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
Burkitt lymphoma-associated network construction and important network motif analysis. PMID:30127896
Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice. PMID:30052469
BRCA1 and BRCA2 gene variants and nonsyndromic cleft lip/palate. PMID:29921024
Silencing of adaptor protein SH3BP2 reduces KIT/PDGFRA receptors expression and impairs gastrointestinal stromal tumors growth. PMID:29885053
Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. PMID:29748492
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
MiR-23a transcriptional activated by Runx2 increases metastatic potential of mouse hepatoma cell via directly targeting Mgat3. PMID:29743543
HPV-16 E7 expression up-regulates phospholipase D activity and promotes rapamycin resistance in a pRB-dependent manner. PMID:29703186
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates. PMID:29669733
Clinical and Functional Characterization of a Missense ELF2 Variant in a CANVAS Family. PMID:29628936
TACC3 transcriptionally upregulates E2F1 to promote cell growth and confer sensitivity to cisplatin in bladder cancer. PMID:29358577
MeDReaders: a database for transcription factors that bind to methylated DNA. PMID:29145608
GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif. PMID:29116820
Investigating transcription factor synergism in humans. PMID:29069301
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. PMID:29036684
NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program. PMID:28812581
Expression profiling of Tas2r genes reveals a complex pattern along the mouse GI tract and the presence of Tas2r131 in a subset of intestinal Paneth cells. PMID:28801754
Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. PMID:28775339
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. PMID:28750606
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells. PMID:28654683
Non-canonical Glucocorticoid Receptor Transactivation of gilz by Alcohol Suppresses Cell Inflammatory Response. PMID:28638383
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. PMID:28348391
Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy. PMID:28320388
Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case. PMID:28196369
Identifying key stage-specific genes and transcription factors for gastric cancer based on RNA-sequencing data. PMID:28121923
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PMID:28103241
Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line. PMID:28066512
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. PMID:28044063
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
HOP expression is regulated by p53 and RAS and characteristic of a cancer gene signature. PMID:27987076
Transcriptome and Metabolome Analyses in Exogenous FABP4- and FABP5-Treated Adipose-Derived Stem Cells. PMID:27936164
Transcriptional Regulation of Notch1 Expression by Nkx6.1 in Neural Stem/Progenitor Cells during Ventral Spinal Cord Development. PMID:27924849
In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. PMID:27856528
An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters. PMID:27812284
Positive selection of the TRIM family regulatory region in primate genomes. PMID:27733547
Impairment of DYRK2 augments stem-like traits by promoting KLF4 expression in breast cancer. PMID:27721402
Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer. PMID:27666291
Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells. PMID:27612989
Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. PMID:27511733
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Negative selection maintains transcription factor binding motifs in human cancer. PMID:27356864
RNA-Seq analysis reveals new evidence for inflammation-related changes in aged kidney. PMID:27153548
In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes. PMID:27038471
Transcription Factors Expressed in Mouse Cochlear Inner and Outer Hair Cells. PMID:26974322
PAX6 Isoforms, along with Reprogramming Factors, Differentially Regulate the Induction of Cornea-specific Genes. PMID:26899008
Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1. PMID:26877820
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships. PMID:26817421
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
E2F1 Transcription Factor Regulates O-linked N-acetylglucosamine (O-GlcNAc) Transferase and O-GlcNAcase Expression. PMID:26527687
Decreased MicroRNA-26a expression causes cisplatin resistance in human non-small cell lung cancer. PMID:26492332
Differences in the Early Development of Human and Mouse Embryonic Stem Cells. PMID:26473594
Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. PMID:26382291
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Methylation of the Gpat2 promoter regulates transient expression during mouse spermatogenesis. PMID:26268560
Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. PMID:26208504
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. PMID:26141830
Compound hierarchical correlated beta mixture with an application to cluster mouse transcription factor DNA binding data. PMID:25964663
Endothelial inflammatory transcriptional responses to an altered plasma exposome following inhalation of diesel emissions. PMID:25942053
A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data. PMID:25933378
Multiple functional variants in long-range enhancer elements contribute to the risk of SNP rs965513 in thyroid cancer. PMID:25918370
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. PMID:25887648
Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. PMID:25886852
Genome editing in plants via designed zinc finger nucleases. PMID:25774080
Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures. PMID:25708259
Inhibition of mutant EGFR in lung cancer cells triggers SOX2-FOXO6-dependent survival pathways. PMID:25686219
Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data. PMID:25653168
MicroRNA-130a can inhibit hepatitis B virus replication via targeting PGC1α and PPARγ. PMID:25595716
Using next-generation RNA sequencing to examine ischemic changes induced by cold blood cardioplegia on the human left ventricular myocardium transcriptome. PMID:25581909
Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype. PMID:25573853
Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. PMID:25537510
Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. PMID:25504138
The transcriptional repressor ZBTB4 regulates EZH2 through a MicroRNA-ZBTB4-specificity protein signaling axis. PMID:25499219
Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway. PMID:25474352
Regression analysis of combined gene expression regulation in acute myeloid leukemia. PMID:25340776
Reconstruction of the gene regulatory network involved in the sonic hedgehog pathway with a potential role in early development of the mouse brain. PMID:25299227
CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining. PMID:25268582
Reduced Krüppel-like factor 2 expression may aggravate the endothelial injury of diabetic nephropathy. PMID:25185079
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. PMID:25150839
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. PMID:25052024
Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. PMID:25006255
A novel nodal enhancer dependent on pluripotency factors and smad2/3 signaling conditions a regulatory switch during epiblast maturation. PMID:24960041
Conjugated bilirubin affects cytokine profiles in hepatitis A virus infection by modulating function of signal transducer and activator of transcription factors. PMID:24943111
Pathway and network analysis in proteomics. PMID:24911777
Genetic factors underlying discordance in chromatin accessibility between monozygotic twins. PMID:24887574
Molecular cloning, characterization and functional assessment of the myosin light polypeptide chain 2 (mylz2) promoter of farmed carp, Labeo rohita. PMID:24740361
Symbolic extensions applied to multiscale structure of genomes. PMID:24728912
Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells. PMID:24710559
Wnt-independent role of β-catenin in thyroid cell proliferation and differentiation. PMID:24645679
Importance of collection in gene set enrichment analysis of drug response in cancer cell lines. PMID:24522610
A comprehensive look at transcription factor gene expression changes in colorectal adenomas. PMID:24472434
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. PMID:24352427
Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data. PMID:24267147
Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA. PMID:24146751
ETS-1-mediated transcriptional up-regulation of CD44 is required for sphingosine-1-phosphate receptor subtype 3-stimulated chemotaxis. PMID:24064218
Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera. PMID:23981317
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. PMID:23813013
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. PMID:23775793
Ultra-rare mutation in long-range enhancer predisposes to thyroid carcinoma with high penetrance. PMID:23690926
The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations. PMID:23483893
Regulation of SIRT1 by oxidative stress-responsive miRNAs and a systematic approach to identify its role in the endothelium. PMID:23477488
Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish. PMID:23468616
Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. PMID:23439483
The Transcriptional Response of Neurotrophins and Their Tyrosine Kinase Receptors in Lumbar Sensorimotor Circuits to Spinal Cord Contusion is Affected by Injury Severity and Survival Time. PMID:23316162
Forkhead box M1 is regulated by heat shock factor 1 and promotes glioma cells survival under heat shock stress. PMID:23192351
Investigation of CD28 gene polymorphisms in patients with sporadic breast cancer in a Chinese Han population in Northeast China. PMID:23133541
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. PMID:23110901
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. PMID:23110343
MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data. PMID:23093591
Functional classification of skeletal muscle networks. I. Normal physiology. PMID:23085959
Itga2b regulation at the onset of definitive hematopoiesis and commitment to differentiation. PMID:22952660
Uncovering transcription factor modules using one- and three-dimensional analyses. PMID:22952238
A metabolic prosurvival role for PML in breast cancer. PMID:22886304
Network-enabled gene expression analysis. PMID:22799258
Effect of positional dependence and alignment strategy on modeling transcription factor binding sites. PMID:22748199
A defect in dystrophin causes a novel porcine stress syndrome. PMID:22691118
GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units. PMID:22662128
Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis. PMID:22549745
Population differences in transcript-regulator expression quantitative trait loci. PMID:22479588
Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene. PMID:22432041
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. PMID:22426492
pcaGoPromoter--an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data. PMID:22384239
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. PMID:22369687
Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling. PMID:22357628
Oct-1 cooperates with the TATA binding initiation complex to control rapid transcription of human iNOS. PMID:22349263
Meta-analysis identifies common variants associated with body mass index in east Asians. PMID:22344219
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. PMID:22178994
Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. PMID:22130890
Role of pharmacogenomics in the management of traditional and novel oral anticoagulants. PMID:22122181
Left ventricular remodeling in swine after myocardial infarction: a transcriptional genomics approach. PMID:22057716
A new methodology to associate SNPs with human diseases according to their pathway related context. PMID:22046267
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PMID:22028663
Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells. PMID:22011333
Endogenous myoglobin in breast cancer is hypoxia-inducible by alternative transcription and functions to impair mitochondrial activity: a role in tumor suppression? PMID:21930697
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
Activation of the glucocorticoid receptor is associated with poor prognosis in estrogen receptor-negative breast cancer. PMID:21868756
Characterization of two common 5' polymorphisms in PEX1 and correlation to survival in PEX1 peroxisome biogenesis disorder patients. PMID:21846392
A linear model for transcription factor binding affinity prediction in protein binding microarrays. PMID:21637853
Polymorphisms in promoter sequences of MDM2, p53, and p16 genes in normal Japanese individuals. PMID:21637567
BINOCh: binding inference from nucleosome occupancy changes. PMID:21551136
Improved similarity scores for comparing motifs. PMID:21543443
Multiple sequence-specific DNA-binding proteins mediate estrogen receptor signaling through a tethering pathway. PMID:21330404
Functional analysis of the DAT gene promoter using transient Catharanthus roseus and stable Nicotiana tabacum transformation systems. PMID:21308469
Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. PMID:21282644
The missing association: sequencing-based discovery of novel SNPs in VKORC1 and CYP2C9 that affect warfarin dose in African Americans. PMID:21270790
A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology. PMID:21203558
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PMID:21170338
Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. PMID:21167036
Assessing computational methods of cis-regulatory module prediction. PMID:21152003
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. PMID:21097781
Patterns of human gene expression variance show strong associations with signaling network hierarchy. PMID:21073694
Cloning and expression pattern of alkaline phosphatase during the development of Paralichthys olivaceus. PMID:20922565
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PMID:20808879
Transcriptional regulation by CHIP/LDB complexes. PMID:20730086
Bioinformatic identification and characterization of human endothelial cell-restricted genes. PMID:20509943
Molecular mechanisms underlying sex change in hermaphroditic groupers. PMID:20467860
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. PMID:20462429
Flanking region sequence information to refine microRNA target predictions. PMID:20413915
Estrogen receptor beta binds to and regulates three distinct classes of target genes. PMID:20404318
Appearance of the pituitary factor Pit-1 increases chromatin remodeling at hypersensitive site III in the human GH locus. PMID:20395397
The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones. PMID:20346164
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. PMID:20223837
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. PMID:20157479
Identification of common variants within KCNK17 in Chinese Han population. PMID:20155449
A potential tumor suppressor role for Hic1 in breast cancer through transcriptional repression of ephrin-A1. PMID:20154726
Expander: from expression microarrays to networks and functions. PMID:20134430
A map of open chromatin in human pancreatic islets. PMID:20118932
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. PMID:20065031
Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. PMID:19887448
Genetic variation in PARL influences mitochondrial content. PMID:19862556
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. PMID:19857274
A systematic approach to identify functional motifs within vertebrate developmental enhancers. PMID:19850031
HPD: an online integrated human pathway database enabling systems biology studies. PMID:19811689
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. PMID:19797408
Interaction of intestinal and pancreatic transcription factors in the regulation of CFTR gene expression. PMID:19782160
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. PMID:19737418
Computational design and application of endogenous promoters for transcriptionally targeted gene therapy for rheumatoid arthritis. PMID:19690516
Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia. PMID:19666576
Word-based characterization of promoters involved in human DNA repair pathways. PMID:19594877
Evaluation of gremlin 1 (GREM1) as a candidate susceptibility gene for albuminuria-related traits in Mexican Americans with type 2 diabetes mellitus. PMID:19577778
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. PMID:19555482
An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1. PMID:19549856
Functional assessment of time course microarray data. PMID:19534758
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. PMID:19487241
The transcriptional regulation and cell-specific expression of the MAPK-activated protein kinase MK5. PMID:19484198
DISCOVER: a feature-based discriminative method for motif search in complex genomes. PMID:19478006
Hypothesis: sarcoidosis is a STAT1-mediated disease. PMID:19464956
Cell survival from chemotherapy depends on NF-kappaB transcriptional up-regulation of coenzyme Q biosynthesis. PMID:19390650
Molecular cloning of rhamnose-binding lectin gene and its promoter region from snakehead Channa argus. PMID:19326250
A census of human transcription factors: function, expression and evolution. PMID:19274049
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. PMID:19265799
Identification of adjacent binding sites for the YY1 and E4BP4 transcription factors in the ovine PrP (Prion) gene promoter. PMID:19129193
Better estimation of protein-DNA interaction parameters improve prediction of functional sites. PMID:19105805
Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. PMID:19061489
A survey of visualization tools for biological network analysis. PMID:19040716
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. PMID:19036138
Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. PMID:18997859
A miRNA signature of prion induced neurodegeneration. PMID:18987751
STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. PMID:18841238
E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. PMID:18836037
Selective constraints in experimentally defined primate regulatory regions. PMID:18704158
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PMID:18654629
Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer. PMID:18631392
Combinatorial influence of environmental parameters on transcription factor activity. PMID:18586711
In silico promoters: modelling of cis-regulatory context facilitates target predictio. PMID:18505473
DiRE: identifying distant regulatory elements of co-expressed genes. PMID:18487623
Mating system and avpr1a promoter variation in primates. PMID:18430667
Identification of transcription factor contexts in literature using machine learning approaches. PMID:18426546
Probabilistic inference of transcription factor binding from multiple data sources. PMID:18364997
Slc11a1 (formerly Nramp1) and susceptibility to canine visceral leishmaniasis. PMID:18307968
Model-based comparative prediction of transcription-factor binding motifs in anabolic responses in bone. PMID:18267297
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Linking the ovarian cancer transcriptome and immunome. PMID:18173842
Efficient and accurate P-value computation for Position Weight Matrices. PMID:18072973
A systematic approach to detecting transcription factors in response to environmental stresses. PMID:18067669
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. PMID:18021416
Assessing and combining reliability of protein interaction sources. PMID:17990508
ADAM15 gene structure and differential alternative exon use in human tissues. PMID:17937806
A functional and regulatory map of asthma. PMID:17921359
Promoter- and cell-specific transcriptional transactivation by the Kaposi's sarcoma-associated herpesvirus ORF57/Mta protein. PMID:17913801
Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation. PMID:17893074
Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera. PMID:17577409
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. PMID:17567999
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. PMID:17567992
Role of a consensus AP-2 regulatory sequence within the Epstein-Barr virus LMP1 promoter in EBNA2 mediated transactivation. PMID:17546492
Unravelling the world of cis-regulatory elements. PMID:17541666
Direct interactions of Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 ORF50/Rta protein with the cellular protein octamer-1 and DNA are critical for specifying transactivation of a delayed-early promoter and stimulating viral reactivation. PMID:17537858
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. PMID:17478504
From genes to functional classes in the study of biological systems. PMID:17407596
Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME. PMID:17389643
A comparative genomics approach to identifying the plasticity transcriptome. PMID:17355637
Quantifying similarity between motifs. PMID:17324271
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. PMID:17302974
Localizing hotspots of antisense transcription. PMID:17284453
Boosting with stumps for predicting transcription start sites. PMID:17274821
Comparison of LTR enhancer elements in sheep beta retroviruses: insights into the basis for tissue-specific expression. PMID:17268841
The ubiquitous cellular transcriptional factor USF targets the varicella-zoster virus open reading frame 10 promoter and determines virulence in human skin xenografts in SCIDhu mice in vivo. PMID:17251302
Predicting tissue-specific enhancers in the human genome. PMID:17210927
DiscoverySpace: an interactive data analysis application. PMID:17210078
Klf4 and corticosteroids activate an overlapping set of transcriptional targets to accelerate in utero epidermal barrier acquisition. PMID:17130451
Lipid defect underlies selective skin barrier impairment of an epidermal-specific deletion of Gata-3. PMID:17116754
Patterns of sequence conservation in presynaptic neural genes. PMID:17096848
Global mapping of c-Myc binding sites and target gene networks in human B cells. PMID:17093053
Caste development and reproduction: a genome-wide analysis of hallmarks of insect eusociality. PMID:17069641
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. PMID:17053090
Coding limits on the number of transcription factors. PMID:16984633
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. PMID:16982645
Predicting transcription factor binding sites using local over-representation and comparative genomics. PMID:16945132
Artificial ants deposit pheromone to search for regulatory DNA elements. PMID:16942615
Survey and expression analysis of five new chitin synthase genes in the biotrophic rust fungus Puccinia graminis. PMID:16924501
MicroRNA promoter element discovery in Arabidopsis. PMID:16888323
Enhanced expression of selenocysteine lyase in acute glomerulonephritis and its regulation by AP-1. PMID:16874457
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians. PMID:16872505
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. PMID:16845085
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. PMID:16845052
Transcription factor STE12alpha has distinct roles in morphogenesis, virulence, and ecological fitness of the primary pathogenic yeast Cryptococcus gattii. PMID:16835451
Optimized mixed Markov models for motif identification. PMID:16749929
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. PMID:16740159
Global analysis of gene function in yeast by quantitative phenotypic profiling. PMID:16738548
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. PMID:16643658
Characterization of transcription factor binding to human papillomavirus type 16 DNA during cellular differentiation. PMID:16611894
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. PMID:16566817
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. PMID:16524982
Cooperation between MEF2 and PPARgamma in human intestinal beta,beta-carotene 15,15'-monooxygenase gene expression. PMID:16504037
Molecular characterization and expression of a granzyme of an ectothermic vertebrate with chymase-like activity expressed in the cytotoxic cells of Nile tilapia (Oreochromis niloticus). PMID:16467988
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. PMID:16464824
Identification and regulatory analysis of rainbow trout tapasin and tapasin-related genes. PMID:16447046
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. PMID:16381984
DBD: a transcription factor prediction database. PMID:16381970
In vivo and in vitro analysis of factor binding sites in Jaagsiekte sheep retrovirus long terminal repeat enhancer sequences: roles of HNF-3, NF-I, and C/EBP for activity in lung epithelial cells. PMID:16352558
A TNF-induced gene expression program under oscillatory NF-kappaB control. PMID:16191192
PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. PMID:16175503
Characterization of the mouse myeloid-associated differentiation marker (MYADM) gene: promoter analysis and protein localization. PMID:16172915
FAST DB: a website resource for the study of the expression regulation of human gene products. PMID:16052034
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. PMID:15980548
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. PMID:15980522
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. PMID:15980512
Identifying synonymous regulatory elements in vertebrate genomes. PMID:15980499
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. PMID:15980497
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. PMID:15967807
Discovering regulatory binding-site modules using rule-based learning. PMID:15930496
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. PMID:15882449
Isolation and characterization of the bovine Stearoyl-CoAdesaturase promoter and analysis of polymorphisms in the promoter region in dairy cows. PMID:15834635
Birth-and-death evolution of the Cecropin multigene family in Drosophila. PMID:15696364
Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions. PMID:15654088
Redefinition of the human kappa opioid receptor gene (OPRK1) structure and association of haplotypes with opiate addiction. PMID:15608558
Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. PMID:15608294
Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation. PMID:15574822
Characterization of the chicken inward rectifier K+ channel IRK1/Kir2.1 gene. PMID:15569391
Lineage-specific and ubiquitous biological roles of the mammalian transcription factor LSF. PMID:15563829
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. PMID:15543148
Polymorphisms in the sclerosteosis/van Buchem disease gene (SOST) region are associated with bone-mineral density in elderly whites. PMID:15514891
Sequence and expression of C-type lectin receptors in Atlantic salmon (Salmo salar). PMID:15490154
An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. PMID:15489324
Human cytomegalovirus DNA replication requires transcriptional activation via an IE2- and UL84-responsive bidirectional promoter element within oriLyt. PMID:15479808
The DNA element controlling expression of the varicella-zoster virus open reading frame 28 and 29 genes consists of two divergent unidirectional promoters which have a common USF site. PMID:15452214
Pattern of sequence variation across 213 environmental response genes. PMID:15364900
Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. PMID:15328365
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. PMID:15297614
Genomic characterization of a slow/low maedi visna virus. PMID:15284480
MotifPrototyper: a Bayesian profile model for motif families. PMID:15252200
Genomic structure, promoter activity, and developmental expression of the mouse homologue of the Machado-Joseph disease (MJD) gene. PMID:15233999
A GATA factor mediates cell type-restricted induction of HLA-E gene transcription by gamma interferon. PMID:15226423
CREME: Cis-Regulatory Module Explorer for the human genome. PMID:15215390
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. PMID:15215388
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. PMID:15215383
Common variants in the 5' region of the leptin gene are associated with body mass index in men from the National Heart, Lung, and Blood Institute Family Heart Study. PMID:15197684
Transcriptional regulation of protein complexes in yeast. PMID:15128447
Transcription factor binding element detection using functional clustering of mutant expression data. PMID:15115798
Analysis of the ERK1,2 transcriptome in mammary epithelial cells. PMID:15109307
A novel retinoic acid-responsive element regulates retinoic acid-induced BLR1 expression. PMID:14993281
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. PMID:14993210
Detection of functional DNA motifs via statistical over-representation. PMID:14988425
Polymorphisms in the taste receptor gene (Tas1r3) region are associated with saccharin preference in 30 mouse strains. PMID:14749438
Transcription of Drosophila troponin I gene is regulated by two conserved, functionally identical, synergistic elements. PMID:14718563
Finding functional sequence elements by multiple local alignment. PMID:14704356
Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. PMID:14704355
Genetic and biochemical analysis of cis regulatory elements within the keratinocyte enhancer region of the human papillomavirus type 31 upstream regulatory region during different stages of the viral life cycle. PMID:14694093
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. PMID:14681436
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. PMID:14681365
Calcium-dependent regulation of tumour necrosis factor-alpha receptor signalling by copine. PMID:14674885
Gata4 regulates testis expression of Dmrt1. PMID:14673170
HNF1alpha is involved in tissue-specific regulation of CFTR gene expression. PMID:14656222
In silico and in vivo analysis reveal a novel gene in Saccharomyces cerevisiae trehalose metabolism. PMID:14614785
Functional dissection of the mouse tyrosinase locus control region identifies a new putative boundary activity. PMID:14576318
LacZ expression in Fut2-LacZ reporter mice reveals estrogen-regulated endocervical glandular expression during estrous cycle, hormone replacement, and pregnancy. PMID:14576173
A novel AP-1 site is critical for maximal induction of the follicle-stimulating hormone beta gene by gonadotropin-releasing hormone. PMID:14570911
An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. PMID:14534330
SPAM1 (PH-20) protein and mRNA expression in the epididymides of humans and macaques: utilizing laser microdissection/RT-PCR. PMID:12932297
Hierarchical model of gene regulation by transforming growth factor beta. PMID:12930890
Molecular and cytogenetic organization of the 5S ribosomal DNA array in chicken (Gallus gallus). PMID:12906126
Evaluation of the microsomal glutathione S-transferase 3 (MGST3) locus on 1q23 as a Type 2 diabetes susceptibility gene in Pima Indians. PMID:12898215
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PMID:12857799
Characterisation, expression and promoter analysis of an interleukin 10 homologue in the puffer fish, Fugu rubripes. PMID:12845498
Cluster-Buster: Finding dense clusters of motifs in DNA sequences. PMID:12824389
PromH: Promoters identification using orthologous genomic sequences. PMID:12824362
INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. PMID:12824346
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. PMID:12820902
Evidence for an important role of perilipin in the regulation of human adipocyte lipolysis. PMID:12802495
Nuclear factor Y and steroidogenic factor 1 physically and functionally interact to contribute to cell-specific expression of the mouse Follicle-stimulating hormone-beta gene. PMID:12730328
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. PMID:12727897
Amylin gene promoter mutations predispose to Type 2 diabetes in New Zealand Maori. PMID:12679865
An approach to identify over-represented cis-elements in related sequences. PMID:12655017
Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. PMID:12654722
Somatic hypermutation of the B cell receptor genes B29 (Igbeta, CD79b) and mb1 (Igalpha, CD79a). PMID:12651942
Variation in the FABP2 promoter alters transcriptional activity and is associated with body composition and plasma lipid levels. PMID:12634920
Toucan: deciphering the cis-regulatory logic of coregulated genes. PMID:12626717
Cellular mobile genetic elements in the regulatory region of the pneumotropic mouse polyomavirus genome: structure and function in viral gene expression and DNA replication. PMID:12610123
Nucleotide and haplotypic diversity of the NOS2A promoter region and its relationship to cerebral malaria. PMID:12552317
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases. PMID:12537567
Heart-specific genes revealed by expressed sequence tag (EST) sampling. PMID:12537563
Identification and utilization of arbitrary correlations in models of recombination signal sequences. PMID:12537561
Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state. PMID:12537548
An automated method for finding molecular complexes in large protein interaction networks. PMID:12525261
TRANSFAC: transcriptional regulation, from patterns to profiles. PMID:12520026
Genome-wide coexpression dynamics: theory and application. PMID:12486219
The Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor has broad signaling effects in primary effusion lymphoma cells. PMID:12477810
Myeloid zinc finger (MZF)-like, Kruppel-like and Ets families of transcription factors determine the cell-specific expression of mouse extracellular superoxide dismutase. PMID:12374566
A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk. PMID:12218173
Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. PMID:12213778
Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs). PMID:12140328
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. PMID:12136103
Selective down-regulation of tyrosinase family gene TYRP1 by inhibition of the activity of melanocyte transcription factor, MITF. PMID:12136092
Functional interaction between TATA and upstream CACGTG elements regulates the temporally specific expression of Otx mRNAs during early embryogenesis of the sea urchin, Hemicentrotus pulcherrimus. PMID:12136085
A novel colonic repressor element regulates intestinal gene expression by interacting with Cux/CDP. PMID:12101240
Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease. PMID:12045141
Characterization of the human ephrin-A4 promoter. PMID:12030849
Dissection of a complex enhancer element: maintenance of keratinocyte specificity but loss of differentiation specificity. PMID:12024040
Combining chromatin immunoprecipitation and DNA footprinting: a novel method to analyze protein-DNA interactions in vivo. PMID:12000849
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. PMID:11997337
Genetic analysis of cis regulatory elements within the 5' region of the human papillomavirus type 31 upstream regulatory region during different stages of the viral life cycle. PMID:11967297
Transcriptional regulation of human 3'-phosphoadenosine 5'-phosphosulphate synthase 2. PMID:11931653
The human PER1 gene is inducible by interleukin-6. PMID:11931340
Transcription factor haploinsufficiency: when half a loaf is not enough. PMID:11854316
CDP binding to multiple sites in the mouse mammary tumor virus long terminal repeat suppresses basal and glucocorticoid-induced transcription. PMID:11836394
In silico prediction of scaffold/matrix attachment regions in large genomic sequences. PMID:11827955
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. PMID:11752327
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. PMID:11752326
The EMBL Nucleotide Sequence Database. PMID:11752244
Critical roles of PPAR beta/delta in keratinocyte response to inflammation. PMID:11751632
Negative regulation of phosphate starvation-induced genes. PMID:11743129
Identification of six putative novel human papillomaviruses (HPV) and characterization of candidate HPV type 87. PMID:11689676
Kilham polyomavirus: activation of gene expression and DNA replication in mouse fibroblast cells by an enhancer substitution. PMID:11581370
PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches. PMID:11574681
cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. PMID:11544201
Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. PMID:11454772
DNA binding by Kaposi's sarcoma-associated herpesvirus lytic switch protein is necessary for transcriptional activation of two viral delayed early promoters. PMID:11435557
Cloning and expression pattern of a gene encoding an alpha-xylosidase active against xyloglucan oligosaccharides from Arabidopsis. PMID:11402218
Identification of human ccn2 (connective tissue growth factor) promoter polymorphisms. PMID:11376134
Type B leukemogenic virus has a T-cell-specific enhancer that binds AML-1. PMID:11160721
Assessing clusters and motifs from gene expression data. PMID:11156620
Nerve growth factor, but not epidermal growth factor, increases Fra-2 expression and alters Fra-2/JunD binding to AP-1 and CREB binding elements in pheochromocytoma (PC12) cells. PMID:11150315
rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. PMID:11125123
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. PMID:11125114
The TRANSFAC system on gene expression regulation. PMID:11125113
Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names. PMID:11125066
The EMBL nucleotide sequence database. PMID:11125039
Alfresco--a workbench for comparative genomic sequence analysis. PMID:10958633
TRANSFAC: a database on transcription factors and their DNA binding sites PubMed citations: 411.

411 articles citing: TRANSFAC: a database on transcription factors and their DNA binding sites

abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. PMID:35240993
A Transcriptional Link between HER2, JAM-A and FOXA1 in Breast Cancer. PMID:35203384
Medial Arterial Calcification: A Significant and Independent Contributor of Peripheral Artery Disease. PMID:35081727
A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease. PMID:34782358
Investigating Pathogenetic Mechanisms of Alzheimer's Disease by Systems Biology Approaches for Drug Discovery. PMID:34681938
iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. PMID:34618085
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. PMID:34607350
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. PMID:34208629
Transcriptomic analysis of castration, chemo-resistant and metastatic prostate cancer elucidates complex genetic crosstalk leading to disease progression. PMID:34184132
Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection. PMID:34147086
Multiple-Molecule Drug Design Based on Systems Biology Approaches and Deep Neural Network to Mitigate Human Skin Aging. PMID:34073305
Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. PMID:33869630
Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model. PMID:33846515
The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation. PMID:33777260
Trim46 contributes to the midbrain development via Sonic Hedgehog signaling pathway in zebrafish embryos. PMID:33717417
Human Epidermal Growth Factor Receptor-3 Expression Is Regulated at Transcriptional Level in Breast Cancer Settings by Junctional Adhesion Molecule-A via a Pathway Involving Beta-Catenin and FOXA1. PMID:33669586
rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. PMID:33633225
TLR4 promoter rs1927914 variant contributes to the susceptibility of esophageal squamous cell carcinoma in the Chinese population. PMID:33585082
Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice. PMID:33475863
A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation. PMID:33425492
First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach. PMID:33413117
Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines. PMID:33126890
Beyond Trees: Regulons and Regulatory Motif Characterization. PMID:32854400
Relationship closeness buffers the effects of perceived stress on transcriptomic indicators of cellular stress and biological aging marker p16INK4a. PMID:32712602
Inhibition of ABL1 tyrosine kinase reduces HTLV-1 proviral loads in peripheral blood mononuclear cells from patients with HTLV-1-associated myelopathy/tropical spastic paraparesis. PMID:32667912
Expression Quantitative Trait Methylation Analysis Reveals Methylomic Associations With Gene Expression in Childhood Asthma. PMID:32569636
Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining study. PMID:32487076
Transcriptional Regulation of HMOX1 Gene in Hezuo Tibetan Pigs: Roles of WT1, Sp1, and C/EBPα. PMID:32224871
Identification of a functional human-unique 351-bp Alu insertion polymorphism associated with major depressive disorder in the 1p31.1 GWAS risk loci. PMID:32193514
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. PMID:32181813
BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs. PMID:32164557
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. PMID:32084333
Population-based RNA profiling in Add Health finds social disparities in inflammatory and antiviral gene regulation to emerge by young adulthood. PMID:32041883
Effects of Castration on miRNA, lncRNA, and mRNA Profiles in Mice Thymus. PMID:32019071
Identification and characterization of methylation-mediated transcriptional dysregulation dictate methylation roles in preeclampsia. PMID:32000849
Ligands, Receptors, and Transcription Factors that Mediate Inter-Cellular and Intra-Cellular Communication during Ovarian Follicle Development. PMID:31939199
Construction of a long non‑coding RNA‑mediated transcription factor and gene regulatory triplet network reveals global patterns and biomarkers for ischemic stroke. PMID:31894261
Ribosome biogenesis restricts innate immune responses to virus infection and DNA. PMID:31841110
Deepprune: Learning Efficient and Interpretable Convolutional Networks Through Weight Pruning for Predicting DNA-Protein Binding. PMID:31824562
Deep learning for inferring gene relationships from single-cell expression data. PMID:31822622
PNPLA3 I148M mediates the regulatory effect of NF-kB on inflammation in PA-treated HepG2 cells. PMID:31793207
Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding. PMID:31598637
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability. PMID:31595288
Novel interactions between ERα-36 and STAT3 mediate breast cancer cell migration. PMID:31409371
Whole genome and transcriptome sequencing of post-mortem cardiac tissues from sudden cardiac death victims identifies a gene regulatory variant in NEXN. PMID:31392414
A gene regulatory network explains RET-EDNRB epistasis in Hirschsprung disease. PMID:31313802
Multilevel regulation of the glass locus during Drosophila eye development. PMID:31299050
Estimation of Transcription Factor Activity in Knockdown Studies. PMID:31270369
Identification of long non‑coding RNA‑mediated transcriptional dysregulation triplets reveals global patterns and prognostic biomarkers for ER+/PR+, HER2‑ and triple negative breast cancer. PMID:31257479
Profiles of gene expression in maternal blood predict offspring birth weight in normal pregnancy. PMID:31204630
CREB-B acts as a key mediator of NPF/NO pathway involved in phase-related locomotor plasticity in locusts. PMID:31150381
Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping. PMID:31127282
Discovering Biomarkers and Pathways Shared by Alzheimer's Disease and Ischemic Stroke to Identify Novel Therapeutic Targets. PMID:31121943
ZBTB12 DNA methylation is associated with coagulation- and inflammation-related blood cell parameters: findings from the Moli-family cohort. PMID:31077224
Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data. PMID:31074374
MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites. PMID:31074373
DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer. PMID:31053176
Structural variants in 3000 rice genomes. PMID:30992303
Sterol Regulatory Element-Binding Protein (Sre1) Promotes the Synthesis of Carotenoids and Sterols in Xanthophyllomyces dendrorhous. PMID:30984134
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
Identification of Gene Expression Changes Associated With Uterine Receptivity in Mice. PMID:30890945
Glucose-Regulated HLP1 Acts as a Key Molecule in Governing Thermomemory. PMID:30890662
Probing transcription factor combinatorics in different promoter classes and in enhancers. PMID:30709337
POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33. PMID:30643196
A Novel Angiotensin II-Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells. PMID:30566058
NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. PMID:30528300
A distinct isoform of ZNF207 controls self-renewal and pluripotency of human embryonic stem cells. PMID:30349051
CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. PMID:30318302
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis. PMID:30261835
Comprehensive analysis of gene expression profiles associated with proliferative diabetic retinopathy. PMID:30250524
A novel mechanism of plasminogen activation in epithelial and mesenchymal cells. PMID:30237490
Omics for understanding the tolerant mechanism of Trichoderma asperellum TJ01 to organophosphorus pesticide dichlorvos. PMID:30089471
Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia. PMID:30024379
A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells. PMID:29970458
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files. PMID:29850891
From genome-wide associations to candidate causal variants by statistical fine-mapping. PMID:29844615
Analysis of pcC13-62 promoters predicts a link between cis-element variations and desiccation tolerance in Linderniaceae. PMID:29757404
A PAX5-OCT4-PRDM1 developmental switch specifies human primordial germ cells. PMID:29713018
Computational Methods for Assessing Chromatin Hierarchy. PMID:29686798
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. PMID:29579225
Integrating ChIP-seq with other functional genomics data. PMID:29579165
Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato. PMID:29551007
Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes. PMID:29363429
Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. PMID:29325176
Global mapping of transcription factor motifs in human aging. PMID:29293662
Targeting and silencing of rhodopsin by ectopic expression of the transcription factor KLF15. PMID:29263295
Hepatic Dysfunction Caused by Consumption of a High-Fat Diet. PMID:29241556
HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths. PMID:29192270
Multiple Copies of a Simple MYB-Binding Site Confers Trans-regulation by Specific Flavonoid-Related R2R3 MYBs in Diverse Species. PMID:29163590
Significance of functional disease-causal/susceptible variants identified by whole-genome analyses for the understanding of human diseases. PMID:29129848
Regulatory network involving miRNAs and genes in serous ovarian carcinoma. PMID:29113276
Cancer cell line specific co-factors modulate the FOXM1 cistrome. PMID:29100329
Identification of Gene Expression Changes in the Aorta of ApoE Null Mice Fed a High-Fat Diet. PMID:29064389
An improved compound Poisson model for the number of motif hits in DNA sequences. PMID:28961747
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis. PMID:28717181
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus. PMID:28684635
Transcriptional regulation of the Nkx3.1 gene in prostate luminal stem cell specification and cancer initiation via its 3' genomic region. PMID:28679531
Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis. PMID:28588209
Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits. PMID:28514657
Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data. PMID:28454466
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. PMID:28347313
Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice. PMID:28319609
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PMID:28316886
Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis. PMID:28282965
A study on the application of topic models to motif finding algorithms. PMID:28155646
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PMID:28103241
iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. PMID:28100260
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability. PMID:27766139
Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. PMID:27693352
Identification of rare variants in KCTD13 at the schizophrenia risk locus 16p11.2. PMID:27668412
Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression. PMID:27641356
Chum salmon egg extracts induce upregulation of collagen type I and exert antioxidative effects on human dermal fibroblast cultures. PMID:27621603
Hsa-miR-137, hsa-miR-520e and hsa-miR-590-3p perform crucial roles in Lynch syndrome. PMID:27602130
Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues. PMID:27470442
PATZ1 induces PP4R2 to form a negative feedback loop on IKK/NF-κB signaling in lung cancer. PMID:27391343
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis. PMID:27384774
Krüppel-like Factor 4 modulates interleukin-6 release in human dendritic cells after in vitro stimulation with Aspergillus fumigatus and Candida albicans. PMID:27346433
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. PMID:27294826
Alterations in leukocyte transcriptional control pathway activity associated with major depressive disorder and antidepressant treatment. PMID:27219347
Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. PMID:27184706
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data. PMID:27069368
Time course analysis based on gene expression profile and identification of target molecules for colorectal cancer. PMID:27013928
Identification of potential therapeutic targets for lung cancer by bioinformatics analysis. PMID:26739332
Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress. PMID:26669319
In search of underlying mechanisms and potential drugs of melphalan-induced vascular toxicity through retinal endothelial cells using bioinformatics approach. PMID:26662105
Identification and expression analyses of MYB and WRKY transcription factor genes in Papaver somniferum L. PMID:26600674
A Transcriptomic Study of Maternal Thyroid Adaptation to Pregnancy in Rats. PMID:26580608
Construction and analysis of dynamic transcription factor regulatory networks in the progression of glioma. PMID:26526635
An integrated functional genomic analysis identifies the antitumorigenic mechanism of action for PPARγ in lung cancer cells. PMID:26484153
Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions. PMID:26402252
Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer. PMID:26240829
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. PMID:26202972
Biochemical and Functional Characterization of RNF213 (Mysterin) R4810K, a Susceptibility Mutation of Moyamoya Disease, in Angiogenesis In Vitro and In Vivo. PMID:26126547
Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation. PMID:26099425
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. PMID:26016777
Classification and expression analyses of homeobox genes from Dictyostelium discoideum. PMID:25963254
Unraveling the 3D genome: genomics tools for multiscale exploration. PMID:25887733
Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining. PMID:25844119
Gene expression changes in human mesenchymal stem cells from patients with osteoporosis. PMID:25815782
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets. PMID:25583120
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
Conservation of trans-acting circuitry during mammalian regulatory evolution. PMID:25409825
Deregulation of Rb-E2F1 axis causes chromosomal instability by engaging the transactivation function of Cdc20-anaphase-promoting complex/cyclosome. PMID:25368385
Adiponectin influences progesterone production from MA-10 Leydig cells in a dose-dependent manner. PMID:25338202
Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation. PMID:25321476
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. PMID:25294834
The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. PMID:25205108
Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. PMID:25149281
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. PMID:25104437
Data integration in the era of omics: current and future challenges. PMID:25032990
Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder. PMID:24995881
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
Encoded expansion: an efficient algorithm to discover identical string motifs. PMID:24871320
Natural variation of histone modification and its impact on gene expression in the rat genome. PMID:24793478
A positive feedback mechanism that regulates expression of miR-9 during neurogenesis. PMID:24714615
An alternative transcription start site yields estrogen-unresponsive Kiss1 mRNA transcripts in the hypothalamus of prepubertal female rats. PMID:24686008
Resources for functional genomics studies in Drosophila melanogaster. PMID:24653003
Lsd1 restricts the number of germline stem cells by regulating multiple targets in escort cells. PMID:24625679
Long non-coding RNAs: new players in ocular neovascularization. PMID:24623407
Transcriptional regulation of proteoglycan 4 by 17β-estradiol in immortalized baboon temporomandibular joint disc cells. PMID:24621258
Functional characterization of a bidirectional plant promoter from cotton leaf curl Burewala virus using an Agrobacterium-mediated transient assay. PMID:24424501
Molecular evolution and diversity of Conus peptide toxins, as revealed by gene structure and intron sequence analyses. PMID:24349297
Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations. PMID:24322347
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach. PMID:24303025
Implications of adiponectin in linking metabolism to testicular function. PMID:24287788
Modular control of glutamatergic neuronal identity in C. elegans by distinct homeodomain proteins. PMID:24243022
Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. PMID:24217919
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. PMID:24204023
Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. PMID:24185839
Identification and visualization of stimulus-specific transcriptional activity in cardiac hypertrophy in mice. PMID:24162179
A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism. PMID:23981351
Oncogenic roles of PRL-3 in FLT3-ITD induced acute myeloid leukaemia. PMID:23929599
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. PMID:23849224
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. PMID:23805903
Uniform, optimal signal processing of mapped deep-sequencing data. PMID:23770639
Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems. PMID:23762209
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. PMID:23761436
Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis. PMID:23742070
Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq. PMID:23740999
Under-dominance constrains the evolution of negative autoregulation in diploids. PMID:23555226
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. PMID:23554463
SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. PMID:23437007
Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome. PMID:23416928
Reprogramming resistant genes: in-depth comparison of gene expressions among iPS, ES, and somatic cells. PMID:23386832
A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. PMID:23368633
A hybrid method for the exact planted (l, d) motif finding problem and its parallelization. PMID:23281969
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. PMID:23281809
Neuregulin 1-HER axis as a key mediator of hyperglycemic memory effects in breast cancer. PMID:23213231
Complex effects of nucleotide variants in a mammalian cis-regulatory element. PMID:23129659
Clinical implications of human population differences in genome-wide rates of functional genotypes. PMID:23125845
Alternative mRNA fates identified in microRNA-associated transcriptome analysis. PMID:23083446
P-value-based regulatory motif discovery using positional weight matrices. PMID:22990209
Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species. PMID:22984403
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. PMID:22964890
Circuitry and dynamics of human transcription factor regulatory networks. PMID:22959076
Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content. PMID:22937124
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. PMID:22915576
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. PMID:22824656
Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. PMID:22733202
Genetic and epigenetic regulation of AHR gene expression in MCF-7 breast cancer cells: role of the proximal promoter GC-rich region. PMID:22728919
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. PMID:22691419
regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. PMID:22611130
New cis-regulatory elements in the Rht-D1b locus region of wheat. PMID:22592657
The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR. PMID:22577947
Tbr2 is essential for hippocampal lineage progression from neural stem cells to intermediate progenitors and neurons. PMID:22553033
Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease. PMID:22543974
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. PMID:22537144
MicroRNA-22 can reduce parathymosin expression in transdifferentiated hepatocytes. PMID:22493679
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach. PMID:22185641
Transcription factor binding sites are highly enriched within microRNA precursor sequences. PMID:22136256
Evolutionary and functional analyses of cytochrome P4501A promoter polymorphisms in natural populations. PMID:22093087
Cognitive-behavioral stress management reverses anxiety-related leukocyte transcriptional dynamics. PMID:22088795
Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. PMID:22084422
Microevolution of cis-regulatory elements: an example from the pair-rule segmentation gene fushi tarazu in the Drosophila melanogaster subgroup. PMID:22073317
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. PMID:22051799
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. PMID:22039215
Epigenetic control of viral life-cycle by a DNA-methylation dependent transcription factor. PMID:22022468
E-box-independent regulation of transcription and differentiation by MYC. PMID:22020439
Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes. PMID:22011226
Transcriptional regulation of co-expressed microRNA target genes. PMID:22002038
Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction. PMID:21999673
Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood. PMID:21994764
High-throughput analysis of promoter occupancy reveals new targets for Arx, a gene mutated in mental retardation and interneuronopathies. PMID:21966449
Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: prediction and validation. PMID:21943362
Combination of two rare mutations causes β-thalassaemia in a Bangladeshi patient. PMID:21931510
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. PMID:21910886
Activation of the glucocorticoid receptor is associated with poor prognosis in estrogen receptor-negative breast cancer. PMID:21868756
The regulatory epicenter of miRNAs. PMID:21857109
Characterization of STAT6 target genes in human B cells and lung epithelial cells. PMID:21828071
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. PMID:21821659
Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. PMID:21803941
Intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. PMID:21775496
Polymorphisms of beta-lactoglobulin promoter region in three Sicilian goat breeds. PMID:21701825
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. PMID:21693013
Functional pathway mapping analysis for hypoxia-inducible factors. PMID:21689478
Fishing for function: zebrafish BAC transgenics for functional genomics. PMID:21647532
TAFFEL: Independent Enrichment Analysis of gene sets. PMID:21592412
Unraveling networks of co-regulated genes on the sole basis of genome sequences. PMID:21572103
Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other sheep breeds considered as ancestors. PMID:21567200
Using graph theory to analyze biological networks. PMID:21527005
Identification of common differentially expressed genes in urinary bladder cancer. PMID:21483740
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. PMID:21470963
Developmental origins of the adipocyte lineage: new insights from genetics and genomics studies. PMID:21365256
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PMID:21347314
G = MAT: linking transcription factor expression and DNA binding data. PMID:21297945
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. PMID:21232107
Systematic characterization of protein-DNA interactions. PMID:21207099
Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes. PMID:21136274
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. PMID:21106904
Small RING Finger Proteins RBX1 and RBX2 of SCF E3 Ubiquitin Ligases: The Role in Cancer and as Cancer Targets. PMID:21103004
Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. PMID:21045820
Systematic identification of conserved motif modules in the human genome. PMID:20946653
Dynamic transcriptomic profiles of zebrafish gills in response to zinc supplementation. PMID:20937081
Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion. PMID:20932299
Experimental strategies for studying transcription factor-DNA binding specificities. PMID:20864494
The transcriptional control of female puberty. PMID:20851111
Human dopamine β-hydroxylase promoter variant alters transcription in chromaffin cells, enzyme secretion, and blood pressure. PMID:20814407
Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. PMID:20678241
Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PMID:20668688
Evaluation of algorithm performance in ChIP-seq peak detection. PMID:20628599
Highly conserved transcriptional responses to mechanical ventilation of the lung. PMID:20460603
GOAL: a software tool for assessing biological significance of genes groups. PMID:20459620
The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome. PMID:20446088
Temporal changes in gene expression in the skin of patients treated with isotretinoin provide insight into its mechanism of action. PMID:20436886
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. PMID:20204374
Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs. PMID:20193056
Unifying generative and discriminative learning principles. PMID:20175896
An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments. PMID:20140066
Fast motif recognition via application of statistical thresholds. PMID:20122182
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. PMID:20085646
Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer. PMID:20081195
Genomics Portals: integrative web-platform for mining genomics data. PMID:20070909
GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data. PMID:20066124
Human dopamine beta-hydroxylase (DBH) regulatory polymorphism that influences enzymatic activity, autonomic function, and blood pressure. PMID:20009769
An integrated expression phenotype mapping approach defines common variants in LEP, ALOX15 and CAPNS1 associated with induction of IL-6. PMID:19942621
hPDI: a database of experimental human protein-DNA interactions. PMID:19900953
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. PMID:19879846
iTriplet, a rule-based nucleic acid sequence motif finder. PMID:19874606
The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina. PMID:19843539
An effective tri-clustering algorithm combining expression data with gene regulation information. PMID:19838334
MicroRNAs regulate osteogenesis and chondrogenesis of mouse bone marrow stromal cells. PMID:19787082
The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PMID:19727443
Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors. PMID:19689805
N(alpha)-tosyl-L-phenylalanine chloromethyl ketone induces caspase-dependent apoptosis in transformed human B cell lines with transcriptional down-regulation of anti-apoptotic HS1-associated protein X-1. PMID:19679660
Polymorphisms in the promoter region of bovine PRKAB1 gene. PMID:19609721
A knowledge-based method to predict the cooperative relationship between transcription factors. PMID:19590970
Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. PMID:19560204
Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks. PMID:19443447
Rule-based clustering for gene promoter structure discovery. PMID:19387502
Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PMID:19385720
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. PMID:19377474
Identification of a minimal cis-element and cognate trans-factor(s) required for induction of Rac2 gene expression during K562 cell differentiation. PMID:19376210
Biomedical discovery acceleration, with applications to craniofacial development. PMID:19325874
New scoring schema for finding motifs in DNA Sequences. PMID:19302709
The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. PMID:19267902
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. PMID:19222862
Early genomic responses to salicylic acid in Arabidopsis. PMID:19199050
Allegro: analyzing expression and sequence in concert to discover regulatory programs. PMID:19151090
G-protein coupled receptor signaling architecture of mammalian immune cells. PMID:19142232
A survey of visualization tools for biological network analysis. PMID:19040716
MotifMap: a human genome-wide map of candidate regulatory motif sites. PMID:19017655
MET and autism susceptibility: family and case-control studies. PMID:19002214
Genome-wide transcriptional profiling linked to social class in asthma. PMID:19001005
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. PMID:18945703
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. PMID:18927104
Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells. PMID:18831788
MTAP: the motif tool assessment platform. PMID:18793470
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. PMID:18790807
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast. PMID:18786274
Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis. PMID:18726591
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. PMID:18723883
Seeder: discriminative seeding DNA motif discovery. PMID:18718942
Low nucleosome occupancy is encoded around functional human transcription factor binding sites. PMID:18627598
Computational identification of transcription frameworks of early committed spermatogenic cells. PMID:18615256
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. PMID:18606616
Depression, social support, and beta-adrenergic transcription control in human ovarian cancer. PMID:18550328
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PMID:18523562
Identification and characterization of the human inhibitor of caspase-activated DNase gene promoter. PMID:18500556
A functional genomic fingerprint of chronic stress in humans: blunted glucocorticoid and increased NF-kappaB signaling. PMID:18440494
In vitro analysis of promoter activity in Müller cells. PMID:18437242
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. PMID:18411406
Progesterone induction of the 11beta-hydroxysteroid dehydrogenase type 2 promoter in breast cancer cells involves coordinated recruitment of STAT5A and progesterone receptor to a distal enhancer and polymerase tracking. PMID:18378698
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PMID:18369420
The Innate Immune Database (IIDB). PMID:18321385
Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor. PMID:18245447
High-resolution mapping and characterization of open chromatin across the genome. PMID:18243105
Functional evolution of the p53 regulatory network through its target response elements. PMID:18187580
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. PMID:18176569
A survey of DNA motif finding algorithms. PMID:18047721
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. PMID:18028544
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. PMID:18005433
Mulan: multiple-sequence alignment to predict functional elements in genomic sequences. PMID:17993678
Regulatory pathway analysis by high-throughput in situ hybridization. PMID:17953485
Social regulation of gene expression in human leukocytes. PMID:17854483
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. PMID:17785538
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. PMID:17784952
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PMID:17708682
rMotifGen: random motif generator for DNA and protein sequences. PMID:17683637
PMA stimulates MUC5B gene expression through an Sp1-based mechanism in airway epithelial cells. PMID:17600309
Transcription factor binding and modified histones in human bidirectional promoters. PMID:17568000
Improved benchmarks for computational motif discovery. PMID:17559676
MATLIGN: a motif clustering, comparison and matching tool. PMID:17559640
A search engine to identify pathway genes from expression data on multiple organisms. PMID:17477880
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. PMID:17452354
Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. PMID:17411336
Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms. PMID:17359522
SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146
Retinoic acid-inducible gene I mediates early antiviral response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells. PMID:17108032
Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT. PMID:17064417
A combinatorial optimization approach for diverse motif finding applications. PMID:16916460
Heterotachy in mammalian promoter evolution. PMID:16683025
K-SPMM: a database of murine spermatogenic promoters modules & motifs. PMID:16670029
Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. PMID:16547164
Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis. PMID:16307367
Principal component analysis for predicting transcription-factor binding motifs from array-derived data. PMID:16297243
Reliable prediction of transcription factor binding sites by phylogenetic verification. PMID:16286651
beta-Adrenoreceptors reactivate Kaposi's sarcoma-associated herpesvirus lytic replication via PKA-dependent control of viral RTA. PMID:16227274
Detecting seeded motifs in DNA sequences. PMID:16141193
Sampling motifs on phylogenetic trees. PMID:15983378
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. PMID:15933209
A multistep bioinformatic approach detects putative regulatory elements in gene promoters. PMID:15904489
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. PMID:15590941
Estrogen receptor (ER)beta isoforms rather than ERalpha regulate corticotropin-releasing hormone promoter activity through an alternate pathway. PMID:15564578
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. PMID:15511292
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. PMID:15256513
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. PMID:15215395
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions. PMID:15215391
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. PMID:15215384
Quantitative high-throughput analysis of transcription factor binding specificities. PMID:14990752
Statistical analysis of over-represented words in human promoter sequences. PMID:14963262
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. PMID:14732688
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PMID:12857799
The phylogenetic diversity of eukaryotic transcription. PMID:12527774
TRANSFAC: transcriptional regulation, from patterns to profiles. PMID:12520026
Discovery of novel transcription factor binding sites by statistical overrepresentation. PMID:12490723
Predicting transcription factor synergism. PMID:12364607
Quantitative prediction of NF-kappa B DNA-protein interactions. PMID:12048232
Discovery of regulatory elements by a computational method for phylogenetic footprinting. PMID:11997340
A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. PMID:11809803
Differentiation-dependent chromatin rearrangement coincides with activation of human papillomavirus type 31 late gene expression. PMID:11559836
Protein-binding elements in the proximal parotid secretory protein gene enhancer essential for salivary-gland-specific expression. PMID:11439105
The TRANSFAC system on gene expression regulation. PMID:11125113
Structural study of the porcine Na+/H+ exchanger NHE1 gene and its 5'-flanking region. PMID:10976762
Zhangfei: a second cellular protein interacts with herpes simplex virus accessory factor HCF in a manner similar to Luman and VP16. PMID:10871379
Definition of a T-cell receptor beta gene core enhancer of V(D)J recombination by transgenic mapping. PMID:10594007
TRANSFAC: an integrated system for gene expression regulation. PMID:10592259
Peptide localization and gene structure of cryptdin 4, a differentially expressed mouse paneth cell alpha-defensin. PMID:10569786
Cloning and functional characterization of the 5'-flanking region of the human bone morphogenetic protein-2 gene. PMID:10024520
Predicting gene regulatory elements in silico on a genomic scale. PMID:9847082
DNase I-hypersensitive sites I and II of the human growth hormone locus control region are a major developmental activator of somatotrope gene expression. PMID:9724759
Novel salivary gland specific binding elements located in the PSP proximal enhancer core. PMID:9592166
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. PMID:9399875
PLACE: a database of plant cis-acting regulatory DNA elements. PMID:9399873
RegulonDB: a database on transcriptional regulation in Escherichia coli. PMID:9399800
Human cystathionine beta-synthase: gene organization and expression of different 5' alternative splicing. PMID:9383285
Luman, a new member of the CREB/ATF family, binds to herpes simplex virus VP16-associated host cellular factor. PMID:9271389
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. PMID:9016550
GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development. PMID:9016506
The TRANSFAC system on gene expression regulation PubMed citations: 213.

213 articles citing: The TRANSFAC system on gene expression regulation

Transcriptional Regulation of the Human IL5RA Gene through Alternative Promoter Usage during Eosinophil Development. PMID:34638583
In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio). PMID:34200177
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-κB. PMID:33542430
Enhancer Function of MicroRNA-3681 Derived from Long Terminal Repeats Represses the Activity of Variable Number Tandem Repeats in the 3' UTR of SHISA7. PMID:32655015
RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. PMID:32500918
Identifying Cattle Breed-Specific Partner Choice of Transcription Factors during the African Trypanosomiasis Disease Progression Using Bioinformatics Analysis. PMID:32456126
Systems Biology Analysis of the Antagonizing Effects of HIV-1 Tat Expression in the Brain over Transcriptional Changes Caused by Methamphetamine Sensitization. PMID:32283831
Polo-like kinase 3 inhibits glucose metabolism in colorectal cancer by targeting HSP90/STAT3/HK2 signaling. PMID:31655629
Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells. PMID:31462142
Novel interactions between ERα-36 and STAT3 mediate breast cancer cell migration. PMID:31409371
Temozolomide Treatment Induces lncRNA MALAT1 in an NF-κB and p53 Codependent Manner in Glioblastoma. PMID:30940658
Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus. PMID:30444878
Conserved Noncoding Sequences Boost ADR1 and SP1 Regulated Human Swiprosin-1 Promoter Activity. PMID:30405162
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3. PMID:29730990
Oncogenomics of c-Myc transgenic mice reveal novel regulators of extracellular signaling, angiogenesis and invasion with clinical significance for human lung adenocarcinoma. PMID:29254206
Functional polymorphism of the renalase gene is associated with cardiac hypertrophy in female patients with aortic stenosis. PMID:29065134
PHF14: an innate inhibitor against the progression of renal fibrosis following folic acid-induced kidney injury. PMID:28045076
Functional Profiling of Human MeCP2 by Automated Data Comparison Analysis and Computerized Expression Pathway Modeling. PMID:27200222
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
Monocyte enhancers are highly altered in systemic lupus erythematosus. PMID:26442457
Molecular aspects of zygotic embryogenesis in sunflower (Helianthus annuus L.): correlation of positive histone marks with HaWUS expression and putative link HaWUS/HaL1L. PMID:26377219
Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements. PMID:26142184
Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes. PMID:26108437
Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals. PMID:25944780
Endothelial inflammatory transcriptional responses to an altered plasma exposome following inhalation of diesel emissions. PMID:25942053
Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. PMID:25908307
Identification of transcription factor AML-1 binding site upstream of human cytomegalovirus UL111A gene. PMID:25658598
Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila. PMID:25609699
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Identification of genes associated with the differentiation potential of adipose-derived stem cells to osteocytes or myocytes. PMID:25385480
The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer. PMID:25333987
Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation. PMID:25321476
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. PMID:25150839
Apicidin F: characterization and genetic manipulation of a new secondary metabolite gene cluster in the rice pathogen Fusarium fujikuroi. PMID:25058475
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
REGNET: mining context-specific human transcription networks using composite genomic information. PMID:24912499
Genome-wide analysis of the bZIP transcription factors in cucumber. PMID:24760072
Genome-wide analysis of functional and evolutionary features of tele-enhancers. PMID:24496725
Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification. PMID:24496624
NFκB induces overexpression of bovine FcRn: a novel mechanism that further contributes to the enhanced immune response in genetically modified animals carrying extra copies of FcRn. PMID:24492342
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. PMID:24170807
MicroRNA-155 broadly orchestrates inflammation-induced changes of microRNA expression in breast cancer. PMID:24080728
Functional comparison between genes dysregulated in ulcerative colitis and colorectal carcinoma. PMID:23991021
High-power femtosecond-terahertz pulse induces a wound response in mouse skin. PMID:23907528
Hypoxamirs in Pulmonary Hypertension: Breathing New Life into Pulmonary Vascular Research. PMID:23745175
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites. PMID:23578135
Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell. PMID:23521829
A statistical thin-tail test of predicting regulatory regions in the Drosophila genome. PMID:23409927
A Relationship between Epithelial Maturation, Bronchopulmonary Dysplasia, and Chronic Obstructive Pulmonary Disease. PMID:23320163
One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses. PMID:23267010
Holding our breath: The emerging and anticipated roles of microRNA in pulmonary hypertension. PMID:23130098
Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. PMID:23101584
Increasing coverage of transcription factor position weight matrices through domain-level homology. PMID:22952610
A regulatory potential of the Xist gene promoter in vole M. rossiaemeridionalis. PMID:22606223
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). PMID:22544707
Population differences in transcript-regulator expression quantitative trait loci. PMID:22479588
Estrogen regulates JNK1 genomic localization to control gene expression and cell growth in breast cancer cells. PMID:22446103
DNA-protein interactions: methods for detection and analysis. PMID:22399265
Molecular analysis of a sunflower gene encoding an homologous of the B subunit of a CAAT binding factor. PMID:22359114
A novel miR-155/miR-143 cascade controls glycolysis by regulating hexokinase 2 in breast cancer cells. PMID:22354042
Discovery of functional gene variants associated with human longevity: opportunities and challenges. PMID:22156437
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites. PMID:22121218
Express path analysis identifies a tyrosine kinase Src-centric network regulating divergent host responses to Mycobacterium tuberculosis infection. PMID:21953458
The Arabidopsis AtbZIP1 transcription factor is a positive regulator of plant tolerance to salt, osmotic and drought stresses. PMID:21938515
Genotypes, haplotypes and diplotypes of IGF-II SNPs and their association with growth traits in largemouth bass (Micropterus salmoides). PMID:21894518
Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PMID:21750739
RSAT 2011: regulatory sequence analysis tools. PMID:21715389
Replacement of homologous mouse DNA sequence with pathogenic 6-base human CREB1 promoter sequence creates murine model of major depressive disorder. PMID:21598377
HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production. PMID:21411754
Multiple sequence-specific DNA-binding proteins mediate estrogen receptor signaling through a tethering pathway. PMID:21330404
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity. PMID:21272326
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. PMID:20972212
Molecular characterization, expression analysis, and role of ALDH3B1 in the cellular protection against oxidative stress. PMID:20699116
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. PMID:20494980
Ectopic Mitf in the embryonic chick retina by co-transfection of β-catenin and Otx2. PMID:20463321
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Predicting the protein-protein interactions using primary structures with predicted protein surface. PMID:20122202
Genome-wide discovery of human heart enhancers. PMID:20075146
Mechanisms of transcription factor selectivity. PMID:20074831
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. PMID:20003307
Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast. PMID:19761608
Asymmetric signal transduction through paralogs that comprise a genetic switch for sugar sensing in Saccharomyces cerevisiae. PMID:19720826
Super paramagnetic clustering of DNA sequences. PMID:19669432
CLEAN: CLustering Enrichment ANalysis. PMID:19640299
Synergistic induction of endothelin-1 by tumor necrosis factor alpha and interferon gamma is due to enhanced NF-kappaB binding and histone acetylation at specific kappaB sites. PMID:19592490
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. PMID:19555482
Identifying regulatory elements in eukaryotic genomes. PMID:19498043
Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks. PMID:19443447
The interplay between transcription factors and microRNAs in genome-scale regulatory networks. PMID:19274664
Different patterns of regulation for the copper and cadmium metallothioneins of the ectomycorrhizal fungus Hebeloma cylindrosporum. PMID:19233951
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. PMID:19098027
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. PMID:19074493
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. PMID:19015324
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. PMID:19014636
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools. PMID:18828907
Database for exploration of functional context of genes implicated in ovarian cancer. PMID:18790805
Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. PMID:18710571
The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PMID:18698409
Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: identification of the c-myc regulatory gene network. PMID:18498649
Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. PMID:18426580
CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. PMID:18411210
Systematic functional characterization of cis-regulatory motifs in human core promoters. PMID:18256240
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. PMID:18032429
Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. PMID:18024792
MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PMID:17997594
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. PMID:17996093
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. PMID:17683565
Interleukin-1 beta-induced Id2 gene expression is mediated by Egr-1 in vascular smooth muscle cells. PMID:17631285
The ZFHX1A gene is differentially autoregulated by its isoforms. PMID:17610840
Identification and characterization of suppressor of cytokine signaling 1 (SOCS-1) homologues in teleost fish. PMID:17569039
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. PMID:17537814
Progesterone derivatives increase expression of Krox-20 and Sox-10 in rat Schwann cells. PMID:17478888
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PMID:17447836
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes. PMID:17428321
Conservation of Toll-Like Receptor Signaling Pathways in Teleost Fish. PMID:17330145
Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells. PMID:17277356
Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. PMID:17204484
Experimental validation of predicted mammalian erythroid cis-regulatory modules. PMID:17038566
Genomic analysis of the hierarchical structure of regulatory networks. PMID:17003135
Common and divergent immune response signaling pathways discovered in peripheral blood mononuclear cell gene expression patterns in presymptomatic and clinically apparent malaria. PMID:16988231
Characterization of binding sites of eukaryotic transcription factors. PMID:16970547
Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes. PMID:16934159
Design principles of molecular networks revealed by global comparisons and composite motifs. PMID:16859507
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. PMID:16845064
Integrated assessment and prediction of transcription factor binding. PMID:16789814
Phylogeny based discovery of regulatory elements. PMID:16716228
A systems approach to mapping DNA damage response pathways. PMID:16709784
TF Target Mapper: a BLAST search tool for the identification of Transcription Factor target genes. PMID:16524462
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. PMID:16522199
NFATc1 regulation of the human beta3 integrin promoter in osteoclast differentiation. PMID:16513293
Transforming growth factor-beta1 upregulates transcription of alpha3 integrin gene in hepatocellular carcinoma cells via Ets-transcription factor-binding motif in the promoter region. PMID:16475024
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. PMID:16464824
Regulation of the human LAT gene by the Elf-1 transcription factor. PMID:16464244
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. PMID:16438730
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. PMID:16420670
Defining the sequence-recognition profile of DNA-binding molecules. PMID:16418267
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. PMID:16381908
TiProD: the Tissue-specific Promoter Database. PMID:16381824
Using hexamers to predict cis-regulatory motifs in Drosophila. PMID:16253142
Protein-DNA binding specificity predictions with structural models. PMID:16246914
Identification of a novel cis-element exhibiting cytokinin-dependent protein binding in vitro in the 5'-region of NADPH-protochlorophyllide oxidoreductase gene in cucumber. PMID:16244912
The distribution of SNPs in human gene regulatory regions. PMID:16209714
Web-based resources for comparative genomics. PMID:16197736
Targeted gene expression analysis in hemimegalencephaly: activation of beta-catenin signaling. PMID:16196383
Statistical methods for identifying yeast cell cycle transcription factors. PMID:16157877
Ab initio prediction of transcription factor targets using structural knowledge. PMID:16103898
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. PMID:16024817
Repression of c-kit and its downstream substrates by GATA-1 inhibits cell proliferation during erythroid maturation. PMID:16024808
Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. PMID:15998809
Signal transduction pathway profiling of individual tumor samples. PMID:15987529
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. PMID:15980550
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. PMID:15967807
Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. PMID:15939874
SNPs in the neural cell adhesion molecule 1 gene (NCAM1) may be associated with human neural tube defects. PMID:15883837
A target selection of somatic hypermutations is regulated similarly between T and B cells upon activation-induced cytidine deaminase expression. PMID:15767564
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. PMID:15608292
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. PMID:15608291
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. PMID:15608239
Polymorphisms in the sclerosteosis/van Buchem disease gene (SOST) region are associated with bone-mineral density in elderly whites. PMID:15514891
Characterization and phylogenetic epitope mapping of CD38 ADPR cyclase in the cynomolgus macaque. PMID:15383153
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. PMID:15371544
Patterns of gene divergence and VL promoter activity in immunoglobulin light chain clusters of the channel catfish. PMID:15349702
Identifying combinatorial regulation of transcription factors and binding motifs. PMID:15287978
Control of differentiation-induced calbindin-D9k gene expression in Caco-2 cells by cdx-2 and HNF-1alpha. PMID:15217781
POBO, transcription factor binding site verification with bootstrapping. PMID:15215385
Constitutive activation of the PDR16 promoter in a Candida albicans azole-resistant clinical isolate overexpressing CDR1 and CDR2. PMID:15215129
From sequence to structure and back again: approaches for predicting protein-DNA binding. PMID:15202939
The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication. PMID:15194764
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. PMID:15173116
Differential expression levels of MRP1, MRP4, and MRP5 in response to human immunodeficiency virus infection in human macrophages. PMID:15105153
Identifying transcriptional regulatory sites in the human genome using an integrated system. PMID:15051813
Universality and flexibility in gene expression from bacteria to human. PMID:14999098
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. PMID:14993211
Molecular analysis of the 5'-upstream region of a gibberellin-inducible cytosolic glutamine synthetase gene (GS1b) expressed in pine vascular tissue. PMID:14735362
A strategy for the integration of QTL, gene expression, and sequence analyses. PMID:14722723
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. PMID:14681436
Transcriptional regulation of protein complexes and biological pathways. PMID:14629111
A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. PMID:14614079
Cytoscape: a software environment for integrated models of biomolecular interaction networks. PMID:14597658
High prevalence of MMTV-like env gene sequences in gestational breast cancer. PMID:14514972
A non-parametric model for transcription factor binding sites. PMID:14500844
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis. PMID:12908878
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. PMID:12853624
Identification of novel tropomyosin 1 genes of pufferfish (Fugu rubripes) on genomic sequences and tissue distribution of their transcripts. PMID:12841578
MATCH: A tool for searching transcription factor binding sites in DNA sequences. PMID:12824369
Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence. PMID:12824356
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. PMID:12814519
GALA, a database for genomic sequence alignments and annotations. PMID:12671007
TRANSFAC: transcriptional regulation, from patterns to profiles. PMID:12520026
PRODORIC: prokaryotic database of gene regulation. PMID:12519998
PlantProm: a database of plant promoter sequences. PMID:12519961
TRANSPATH: an integrated database on signal transduction and a tool for array analysis. PMID:12519957
CORG: a database for COmparative Regulatory Genomics. PMID:12519946
EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites. PMID:12409480
Additivity in protein-DNA interactions: how good an approximation is it? PMID:12384591
Predicting transcription factor synergism. PMID:12364607
Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs). PMID:12140328
Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. PMID:12097338
Quantitative prediction of NF-kappa B DNA-protein interactions. PMID:12048232
rVista for comparative sequence-based discovery of functional transcription factor binding sites. PMID:11997350
Transcriptional regulation of human 3'-phosphoadenosine 5'-phosphosulphate synthase 2. PMID:11931653
Nucleoprotein structure of immediate-early promoters Zp and Rp and of oriLyt of latent Epstein-Barr virus genomes. PMID:11907252
tacg--a grep for DNA. PMID:11882250
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. PMID:11805330
GeneNet: a database on structure and functional organisation of gene networks. PMID:11752348
S/MARt DB: a database on scaffold/matrix attached regions. PMID:11752340
The Gene Resource Locator: gene locus maps for transcriptome analysis. PMID:11752299
The Celera Discovery System. PMID:11752274

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation PubMed citations: 205.

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms PubMed citations: 79.

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transcription factors and regulatory sites
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version: extracted_at: 2022-11-04T11:34:45.691111

gene expression
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version: extracted_at: 2022-11-04T11:34:45.691111

dna binding sites
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version: extracted_at: 2022-11-04T11:34:45.691111

molecular interactions, pathways and networks
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model organisms
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TRANSFAC

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TRANSFAC
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

transfac
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TRANSFAC®

RegPrecise

Drosophila DNase I footprint database

Saccharomyces cerevisiae Transcription Factor Database

rSNP_Guide

TRANSPATH®

SalMotifDB

PROkariotIC Database Of Gene-Regulation

TcoF-DB

Regulatory Element Database for Drosophila

PAZAR

Animal Transcription Factor Database

The Arabidopsis Gene Regulatory Information Server

Yeastract+

TRANSCompel®

Plant Transcription Factor Database

PlnTFDB

Yeast Searching for Transcriptional Regulators and Consensus Tracking

Fly Terminalia Database

FlyFactorSurvey

TRANSFAC Names More detailed information about this field from each metasource. × TRANSFAC metasource: bio.tools version: extracted_at: 2022-11-04T11:34:45.691111 transfac metasource: bio.tools version: extracted_at: 2022-11-04T11:34:45.691111 Close

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TRANSFAC®

RegPrecise

Drosophila DNase I footprint database

Saccharomyces cerevisiae Transcription Factor Database

rSNP_Guide

TRANSPATH®

SalMotifDB

PROkariotIC Database Of Gene-Regulation

TcoF-DB

Regulatory Element Database for Drosophila

PAZAR

Animal Transcription Factor Database

The Arabidopsis Gene Regulatory Information Server

Yeastract+

TRANSCompel®

Plant Transcription Factor Database

PlnTFDB

Yeast Searching for Transcriptional Regulators and Consensus Tracking

Fly Terminalia Database

FlyFactorSurvey

TRANSFAC

Names
More detailed information about this field from each metasource.

TRANSFAC
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111

transfac
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.691111