FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.435866

dbtss
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.435866

Other names: DBTSS, dbtss

This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.

Webpage:

http://dbtss.hgc.jp

Publications: (9)

Publications
More detailed information about this field from each metasource.

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
PMID: 11752328
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

DBTSS: database of transcription start sites, progress report 2008
PMID: 17942421
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
PMID: 14681363
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
PMID: 16381981
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites
PMID: 19910371
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.435866

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
PMID: 22086958
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.435866

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data
PMID: 25378318
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts
PMID: 24069199
metasource: Fairsharing.org
version: FAIRsharing.org: DBTSS; DataBase of Transcriptional Start Sites; DOI: https://doi.org/10.25504/FAIRsharing.f21e5v; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/gku1080
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs PubMed citations: 88.

88 articles citing: DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs

Host F-Box Protein 22 Enhances the Uptake of Brucella by Macrophages and Drives a Sustained Release of Proinflammatory Cytokines through Degradation of the Anti-Inflammatory Effector Proteins of Brucella. PMID:35420446
DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells. PMID:34205960
Synthetic Promoters: Designing the cis Regulatory Modules for Controlled Gene Expression. PMID:29855997
Chum salmon egg extracts induce upregulation of collagen type I and exert antioxidative effects on human dermal fibroblast cultures. PMID:27621603
Identification of a Novel C-Terminal Truncated WT1 Isoform with Antagonistic Effects against Major WT1 Isoforms. PMID:26090994
Evaluation of sgRNA target sites for CRISPR-mediated repression of TP53. PMID:25398078
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. PMID:25378343
Pax6 regulates the expression of Dkk3 in murine and human cell lines, and altered responses to Wnt signaling are shown in FlpIn-3T3 cells stably expressing either the Pax6 or the Pax6(5a) isoform. PMID:25029272
Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning. PMID:24531968
Identification and visualization of stimulus-specific transcriptional activity in cardiac hypertrophy in mice. PMID:24162179
Epigenetic regulation of organic anion transporting polypeptide 1B3 in cancer cell lines. PMID:23812637
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. PMID:23193273
Analysis of intron sequence features associated with transcriptional regulation in human genes. PMID:23082130
Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages. PMID:22784578
Contribution of microRNA-1275 to Claudin11 protein suppression via a polycomb-mediated silencing mechanism in human glioma stem-like cells. PMID:22736761
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. PMID:22086958
Functional characterization of human Kindlin-2 core promoter identifies a key role of SP1 in Kindlin-2 transcriptional regulation. PMID:21922223
Selective genomic targeting by FRA-2/FOSL2 transcription factor: regulation of the Rgs4 gene is mediated by a variant activator protein 1 (AP-1) promoter sequence/CREB-binding protein (CBP) mechanism. PMID:21367864
Ensemble approach combining multiple methods improves human transcription start site prediction. PMID:21118509
Genome-wide detection of a TFIID localization element from an initial human disease mutation. PMID:21071415
Retinoic acid induces expression of the thyroid hormone transporter, monocarboxylate transporter 8 (Mct8). PMID:20573951
Gene expression and transcription factor profiling reveal inhibition of transcription factor cAMP-response element-binding protein by gamma-herpesvirus replication and transcription activator. PMID:20516076
Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. PMID:20479128
Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. PMID:20226072
Repetitive DNA elements, nucleosome binding and human gene expression. PMID:19393174
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PMID:19287502
A transcription factor affinity-based code for mammalian transcription initiation. PMID:19141595
Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. PMID:19105848
Analysis of gene regulatory networks in the mammalian circadian rhythm. PMID:18846204
PCA-HPR: a principle component analysis model for human promoter recognition. PMID:18795109
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. PMID:18533028
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. PMID:18480124
Prediction for human transcription start site using diversity measure with quadratic discriminant. PMID:18478087
Genome-wide promoter analysis uncovers portions of the cancer methylome. PMID:18413733
Profiling the thermodynamic softness of adenoviral promoters. PMID:18390611
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. PMID:18367472
Asap: a framework for over-representation statistics for transcription factor binding sites. PMID:18286180
Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones. PMID:18053163
Promoter analysis of intestinal genes induced during iron-deprivation reveals enrichment of conserved SP1-like binding sites. PMID:18005439
Bioinformatic identification of novel putative photoreceptor specific cis-elements. PMID:17953763
Lithocholic acid induction of the FGF19 promoter in intestinal cells is mediated by PXR. PMID:17696253
A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. PMID:17522955
Transcription of the human cell cycle regulated BUB1B gene requires hStaf/ZNF143. PMID:17478512
Identification of N-acetyltransferase 2 (NAT2) transcription start sites and quantitation of NAT2-specific mRNA in human tissues. PMID:17287389
Tissue-specific regulatory elements in mammalian promoters. PMID:17224917
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. PMID:17210929
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. PMID:17053090
L1 antisense promoter drives tissue-specific transcription of human genes. PMID:16877819
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data. PMID:16817975
Periodicity of SNP distribution around transcription start sites. PMID:16579865
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. PMID:16381984
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. PMID:16381981
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. PMID:16344566
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function. PMID:16232321
The distribution of SNPs in human gene regulatory regions. PMID:16209714
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. PMID:16204454
Generalizations of Markov model to characterize biological sequences. PMID:16144548
Transposable elements donate lineage-specific regulatory sequences to host genomes. PMID:16093685
Genome-wide promoter extraction and analysis in human, mouse, and rat. PMID:16086854
Large-scale structural analysis of the core promoter in mammalian and plant genomes. PMID:16049029
Functional analysis of human and chimpanzee promoters. PMID:15998446
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. PMID:15980502
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. PMID:15967807
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. PMID:15933209
Begin at the beginning: predicting genes with 5' UTRs. PMID:15867435
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. PMID:15849315
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. PMID:15489325
Expression profiling of serum inducible genes identifies a subset of SRF target genes that are MKL dependent. PMID:15329155
Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. PMID:15328365
Clustering of DNA sequences in human promoters. PMID:15256515
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions. PMID:15215391
PromoSer: improvements to the algorithm, visualization and accessibility. PMID:15215378
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. PMID:15053842
Statistical analysis of over-represented words in human promoter sequences. PMID:14963262
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. PMID:14681365
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. PMID:14681364
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. PMID:14681363
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
Fugu ESTs: new resources for transcription analysis and genome annotation. PMID:14613980
Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. PMID:12869582
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. PMID:12824365
PromoSer: A large-scale mammalian promoter and transcription start site identification service. PMID:12824364
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. PMID:12824363
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. PMID:12808149
Identification and functional analysis of human transcriptional promoters. PMID:12566409
Distribution and characterization of regulatory elements in the human genome. PMID:12466286
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. PMID:12136103
DBTSS: database of transcription start sites, progress report 2008 PubMed citations: 73.

73 articles citing: DBTSS: database of transcription start sites, progress report 2008

Genome-Wide Profiling of Transcription Initiation with STRIPE-seq. PMID:35524109
Global approaches for profiling transcription initiation. PMID:34632443
Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. PMID:32660958
Diversification of CpG-Island Promoters Revealed by Comparative Analysis Between Human and Rhesus Monkey Genomes. PMID:32647942
Serum D-serine accumulation after proximal renal tubular damage involves neutral amino acid transporter Asc-1. PMID:31723194
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy. PMID:29540741
DNA structural features of eukaryotic TATA-containing and TATA-less promoters. PMID:28286728
Inducing gene expression by targeting promoter sequences using small activating RNAs. PMID:25839046
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. PMID:25426780
Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals. PMID:24792168
Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. PMID:23913413
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. PMID:23514374
Small RNA-Mediated Epigenetic Myostatin Silencing. PMID:23344003
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PMID:23056606
Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. PMID:22913572
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Aberrant DNA methylation and prostate cancer. PMID:22547956
Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile. PMID:22327645
A comparison study on feature selection of DNA structural properties for promoter prediction. PMID:22226192
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. PMID:22086958
Large-scale motif discovery using DNA Gray code and equiprobable oligomers. PMID:22057160
Characterization of STAT6 target genes in human B cells and lung epithelial cells. PMID:21828071
Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements. PMID:21826217
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. PMID:21372179
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. PMID:21172036
High sensitivity TSS prediction: estimates of locations where TSS cannot occur. PMID:21085627
Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing. PMID:21062826
Connections between alternative transcription and alternative splicing in mammals. PMID:20889654
A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. PMID:20699007
Mouse cytoplasmic dynein intermediate chains: identification of new isoforms, alternative splicing and tissue distribution of transcripts. PMID:20657784
Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens. PMID:20628623
Comparison of the chloroplast peroxidase system in the chlorophyte Chlamydomonas reinhardtii, the bryophyte Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana. PMID:20584316
Retinoic acid induces expression of the thyroid hormone transporter, monocarboxylate transporter 8 (Mct8). PMID:20573951
Sequence features that drive human promoter function and tissue specificity. PMID:20501695
Prediction of CpG-island function: CpG clustering vs. sliding-window methods. PMID:20500903
Effects of Alu elements on global nucleosome positioning in the human genome. PMID:20478020
Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes. PMID:20462404
Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer. PMID:20400770
Complex transcriptional control of the AZFa gene DDX3Y in human testis. PMID:20374305
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. PMID:20222994
Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PMID:20208995
High nucleosome occupancy is encoded at human regulatory sequences. PMID:20161746
A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells. PMID:20147304
Translog, a web browser for studying the expression divergence of homologous genes. PMID:20122234
Characteristics of the CArG-SRF binding context in mammalian genomes. PMID:19953255
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. PMID:19910371
Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. PMID:19898487
Modeling tissue-specific structural patterns in human and mouse promoters. PMID:19850720
An N- and C-terminal truncated isoform of zinc finger X-linked duplicated C protein represses MHC class II transcription. PMID:19777325
Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. PMID:19741000
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. PMID:19589141
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. PMID:19487241
Toward a gold standard for promoter prediction evaluation. PMID:19478005
Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. PMID:19476647
Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. PMID:19461583
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PMID:19390574
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. PMID:19374775
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. PMID:19374773
Massive transcriptional start site analysis of human genes in hypoxia cells. PMID:19237398
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. PMID:19151715
Papillomavirus E2 proteins and the host BRD4 protein associate with transcriptionally active cellular chromatin. PMID:19129460
High-resolution human core-promoter prediction with CoreBoost_HM. PMID:18997002
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. PMID:18987005
The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PMID:18941527
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PMID:18846210
Analysis of gene regulatory networks in the mammalian circadian rhythm. PMID:18846204
Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases. PMID:18842138
Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight. PMID:18817551
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. PMID:18815372
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. PMID:18586720
MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways. PMID:18367535
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004 PubMed citations: 70.

70 articles citing: DBTSS, DataBase of Transcriptional Start Sites: progress report 2004

Transcriptional Regulation of Selenoprotein F by Heat Shock Factor 1 during Selenium Supplementation and Stress Response. PMID:31109102
Landscape of transcriptional deregulations in the preeclamptic placenta. PMID:23785430
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PMID:22912590
A promoter polymorphism in the Per3 gene is associated with alcohol and stress response. PMID:22832735
Transcriptional protein Sp1 regulates LEDGF transcription by directly interacting with its cis-elements in GC-rich region of TATA-less gene promoter. PMID:22615874
Transcription factor binding sites and other features in human and Drosophila proximal promoters. PMID:21557085
Cis-acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium. PMID:20233728
IRF9 is a key factor for eliciting the antiproliferative activity of IFN-alpha. PMID:19752753
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. PMID:19667080
Promoter analysis: gene regulatory motif identification with A-GLAM. PMID:19378149
A composite intronic element directs dynamic binding of the progesterone receptor and GATA-2. PMID:19036901
Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites. PMID:19015127
Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes. PMID:18815892
Computational identification of transcription frameworks of early committed spermatogenic cells. PMID:18615256
Identification of the TFII-I family target genes in the vertebrate genome. PMID:18579769
Identification and characterization of the human inhibitor of caspase-activated DNase gene promoter. PMID:18500556
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. PMID:18480124
Prediction and analysis of nucleosome exclusion regions in the human genome. PMID:18430246
Genome-wide promoter analysis uncovers portions of the cancer methylome. PMID:18413733
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
An endosomally localized isoform of Eps15 interacts with Hrs to mediate degradation of epidermal growth factor receptor. PMID:18362181
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. PMID:18312685
Stress-induced expression of a novel variant of human fumarate hydratase (FH). PMID:18257390
Genomic sequence is highly predictive of local nucleosome depletion. PMID:18225943
A code for transcription initiation in mammalian genomes. PMID:18032727
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. PMID:17941982
Computational analyses of eukaryotic promoters. PMID:17903284
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PMID:17559307
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. PMID:17526516
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression. PMID:17504544
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. PMID:17452354
Mapping of transcription start sites of human retina expressed genes. PMID:17286855
Erythroid Krüppel-like factor directly activates the basic Krüppel-like factor gene in erythroid cells. PMID:17283065
Boosting with stumps for predicting transcription start sites. PMID:17274821
The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters. PMID:17210644
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. PMID:17123746
'Genome design' model and multicellular complexity: golden middle. PMID:17062620
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. PMID:16925837
Search for basonuclin target genes. PMID:16919236
Functional single nucleotide polymorphism-based association studies. PMID:16848977
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors. PMID:16845070
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PMID:16839196
Mice and men: their promoter properties. PMID:16683032
K-SPMM: a database of murine spermatogenic promoters modules & motifs. PMID:16670029
Periodicity of SNP distribution around transcription start sites. PMID:16579865
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. PMID:16556303
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. PMID:16522199
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. PMID:16381984
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. PMID:16381981
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. PMID:16381980
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. PMID:16381948
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
TiProD: the Tissue-specific Promoter Database. PMID:16381824
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. PMID:16344566
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. PMID:16344560
Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. PMID:16227614
ATG deserts define a novel core promoter subclass. PMID:16109972
Large-scale structural analysis of the core promoter in mammalian and plant genomes. PMID:16049029
GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region. PMID:16049025
Functional analysis of human and chimpanzee promoters. PMID:15998446
A high-resolution map of active promoters in the human genome. PMID:15988478
Direct isolation and identification of promoters in the human genome. PMID:15899964
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
Comparative promoter region analysis powered by CORG. PMID:15723697
5'SAGE: 5'-end Serial Analysis of Gene Expression database. PMID:15608259
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. PMID:15608156
Computational method for discovery of estrogen responsive genes. PMID:15576347
Comprehensive analysis of the base composition around the transcription start site in Metazoa. PMID:15171795
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 PubMed citations: 53.

53 articles citing: DBTSS: DataBase of Human Transcription Start Sites, progress report 2006

Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. PMID:28177284
IN-MACA-MCC: Integrated Multiple Attractor Cellular Automata with Modified Clonal Classifier for Human Protein Coding and Promoter Prediction. PMID:25132849
Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns. PMID:24465517
HIF-dependent regulation of AKAP12 (gravin) in the control of human vascular endothelial function. PMID:24029533
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. PMID:22369687
Profiling ascidian promoters as the primordial type of vertebrate promoter. PMID:22369359
A comparison study on feature selection of DNA structural properties for promoter prediction. PMID:22226192
Vasodilator phosphostimulated protein (VASP) protects endothelial barrier function during hypoxia. PMID:21607702
IFN-γ attenuates hypoxia-inducible factor (HIF) activity in intestinal epithelial cells through transcriptional repression of HIF-1β. PMID:21199896
Cross-species comparison of genomewide gene expression profiles reveals induction of hypoxia-inducible factor-responsive genes in iron-deprived intestinal epithelial cells. PMID:20702690
Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. PMID:20693610
Prediction of CpG-island function: CpG clustering vs. sliding-window methods. PMID:20500903
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. PMID:20494980
Inflammation-associated repression of vasodilator-stimulated phosphoprotein (VASP) reduces alveolar-capillary barrier function during acute lung injury. PMID:19690214
PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells. PMID:19564417
Growth controls connect: interactions between c-myc and the tuberous sclerosis complex-mTOR pathway. PMID:19342893
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PMID:19287502
Hypoxia-inducible factor-dependent induction of netrin-1 dampens inflammation caused by hypoxia. PMID:19122655
Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. PMID:19094208
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. PMID:18533028
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. PMID:18487259
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. PMID:18480124
Prediction for human transcription start site using diversity measure with quadratic discriminant. PMID:18478087
Profiling the thermodynamic softness of adenoviral promoters. PMID:18390611
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
Retrotransposition as a source of new promoters. PMID:18367464
DNA sequence and structural properties as predictors of human and mouse promoters. PMID:18234453
c-myc Repression of TSC2 contributes to control of translation initiation and Myc-induced transformation. PMID:18056446
Prediction of synergistic transcription factors by function conservation. PMID:18053230
A code for transcription initiation in mammalian genomes. PMID:18032727
DBTSS: database of transcription start sites, progress report 2008. PMID:17942421
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. PMID:17941982
Organismal complexity, cell differentiation and gene expression: human over mouse. PMID:17881362
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. PMID:17855401
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Transcription factor binding and modified histones in human bidirectional promoters. PMID:17568000
Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. PMID:17567985
Intrinsic promoter activities of primary DNA sequences in the human genome. PMID:17522093
Transcription of the human cell cycle regulated BUB1B gene requires hStaf/ZNF143. PMID:17478512
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PMID:17447839
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
Identification of vasodilator-stimulated phosphoprotein (VASP) as an HIF-regulated tissue permeability factor during hypoxia. PMID:17412998
Characterization and identification of microRNA core promoters in four model species. PMID:17352530
Identification of plant promoter constituents by analysis of local distribution of short sequences. PMID:17346352
Identification of N-acetyltransferase 2 (NAT2) transcription start sites and quantitation of NAT2-specific mRNA in human tissues. PMID:17287389
TRED: a transcriptional regulatory element database, new entries and other development. PMID:17202159
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. PMID:17151081
Beyond microarrays: find key transcription factors controlling signal transduction pathways. PMID:17118134
CpGcluster: a distance-based algorithm for CpG-island detection. PMID:17038168
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. PMID:16925837
Search for basonuclin target genes. PMID:16919236
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. PMID:16845074
Comparative genomics of Drosophila and human core promoters. PMID:16827941
DBTSS provides a tissue specific dynamic view of Transcription Start Sites PubMed citations: 35.

35 articles citing: DBTSS provides a tissue specific dynamic view of Transcription Start Sites

In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1. PMID:34156573
Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. PMID:33903630
Retinoic acid receptor-related orphan receptor α reduces lipid droplets by upregulating neutral cholesterol ester hydrolase 1 in macrophages. PMID:32321446
Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5' TOP motifs. PMID:32094190
Computational annotation of miRNA transcription start sites. PMID:32003428
Length and secondary structure of the 5' non-coding regions of mouse p53 mRNA transcripts - mouse as a model organism for p53 gene expression studies. PMID:30518296
Promoter-Associated RNAs Regulate HSPC152 Gene Expression in Malignant Melanoma. PMID:29657265
Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. PMID:28640837
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. PMID:27871221
Semaphorin 7A Aggravates Pulmonary Inflammation during Lung Injury. PMID:26752048
In silico discovery of novel transcription factors regulated by mTOR-pathway activities. PMID:25364730
Computational epigenetic profiling of CpG islets in MTHFR. PMID:25213548
Global transcriptome profiling of genes that are differentially regulated during differentiation of mouse embryonic neural stem cells into astrocytes. PMID:25104607
Local BMP-SMAD1 signaling increases LIF receptor-dependent STAT3 responsiveness and primed-to-naive mouse pluripotent stem cell conversion frequency. PMID:25068129
Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals. PMID:24792168
GJC2 promoter mutations causing Pelizaeus-Merzbacher-like disease. PMID:24374284
ToPS: a framework to manipulate probabilistic models of sequence data. PMID:24098098
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. PMID:23293005
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. PMID:23282148
Endothelial Semaphorin 7A promotes neutrophil migration during hypoxia. PMID:22891341
A unifying model for mTORC1-mediated regulation of mRNA translation. PMID:22552098
A novel intracellular isoform of matrix metalloproteinase-2 induced by oxidative stress activates innate immunity. PMID:22509276
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. PMID:22369889
Profiling ascidian promoters as the primordial type of vertebrate promoter. PMID:22369359
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. PMID:21821656
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. PMID:21806842
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. PMID:21555518
Predicting promoter activities of primary human DNA sequences. PMID:21486745
Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PMID:21464922
Connections between alternative transcription and alternative splicing in mammals. PMID:20889654
Minireview: Switching on progesterone receptor expression with duplex RNA. PMID:20592161
Identification and analysis of the promoter region of the human DHCR24 gene: involvement of DNA methylation and histone acetylation. PMID:20568014
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. PMID:20494980
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588