dbSUPER

Names
More detailed information about this field from each metasource.

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

dbsuper
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

Other names: dbsuper

dbSUPER is the first integrated and interactive database of super-enhancers, which contains 82234 super-enhancers in 102 human and 25 mouse tissue/cell types.

Webpage:

http://asntech.org/dbsuper/

Publications:

Publications
More detailed information about this field from each metasource.

dbSUPER: a database of super-enhancers in mouse and human genome
PMID: 26438538
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

http://dx.doi.org/10.1093/nar/gkv1002
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

dbSUPER: a database of super-enhancers in mouse and human genome PubMed citations: 165.

165 articles citing: dbSUPER: a database of super-enhancers in mouse and human genome

Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia. PMID:35301312
Epigenetics of Mitochondria-Associated Genes in Striated Muscle. PMID:35076500
Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells. PMID:35018885
Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. PMID:34968235
Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer. PMID:34910907
A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues. PMID:34899824
New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells. PMID:34884689
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
CircleBase: an integrated resource and analysis platform for human eccDNAs. PMID:34792166
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. PMID:34761274
A Core Response to the CDX2 Homeoprotein During Development and in Pathologies. PMID:34759958
Identification of cell states using super-enhancer RNA. PMID:34727867
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
FOXA1: A Pioneer of Nuclear Receptor Action in Breast Cancer. PMID:34680352
CircNCX1: the "Lord of the Ring" in the Heart - Insight into Its Sequence Characteristic, Expression, Molecular Mechanisms, and Clinical Application. PMID:34642871
Complex small-world regulatory networks emerge from the 3D organisation of the human genome. PMID:34599163
DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker. PMID:34538273
Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. PMID:34461601
Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. PMID:34454581
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. PMID:34410491
Genome-wide profiles of UV lesion susceptibility, repair, and mutagenic potential in melanoma. PMID:34333390
Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis. PMID:34320216
Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function. PMID:34312548
Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning. PMID:34257393
The histone H3.3 chaperone HIRA restrains erythroid-biased differentiation of adult hematopoietic stem cells. PMID:34242617
Integrative analysis of genomic and epigenomic data reveal underlying superenhancer-mediated microRNA regulatory network for human bone mineral density. PMID:34230965
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. PMID:34165568
Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. PMID:34162876
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Super-enhancer-mediated core regulatory circuitry in human cancer. PMID:34093993
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. PMID:34021236
Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. PMID:34011395
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. PMID:33960642
Super-enhancer-associated long noncoding RNA RP11-569A11.1 inhibited cell progression and metastasis by regulating IFIT2 in colorectal cancer. PMID:33942366
Employing core regulatory circuits to define cell identity. PMID:33934382
ZC3H4 restricts non-coding transcription in human cells. PMID:33913806
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. PMID:33770473
EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2. PMID:33712565
Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells. PMID:33679774
Fast searches of large collections of single-cell data using scfind. PMID:33649586
How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b. PMID:33625717
Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer. PMID:33622275
Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT. PMID:33538177
Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium. PMID:33362848
Super enhancers-Functional cores under the 3D genome. PMID:33336467
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. PMID:33245777
Genome-wide association study identifies 16 genomic regions associated with circulating cytokines at birth. PMID:33227023
Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. PMID:33193605
Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes. PMID:33182325
DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. PMID:33177077
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. PMID:33109274
Analyzing a putative enhancer of optic disc morphology. PMID:33092545
Bromodomain-containing protein 4 regulates interleukin-34 expression in mouse ovarian cancer cells. PMID:33072227
Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. PMID:33067454
Stress-induced RNA-chromatin interactions promote endothelial dysfunction. PMID:33060583
Inhibition of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells. PMID:33046784
SilencerDB: a comprehensive database of silencers. PMID:33045745
The emerging role of super enhancer-derived noncoding RNAs in human cancer. PMID:33042269
eRNAs and Superenhancer lncRNAs Are Functional in Human Prostate Cancer. PMID:33029258
Critical roles of super-enhancers in the pathogenesis of autoimmune diseases. PMID:32922569
Drivers underpinning the malignant transformation of giant cell tumour of bone. PMID:32866294
Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. PMID:32832663
Transcriptional regulators of the Golli/myelin basic protein locus integrate additive and stealth activities. PMID:32790717
Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis. PMID:32772801
Functions and Clinical Significance of Super-Enhancers in Bone-Related Diseases. PMID:32714929
HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. PMID:32665593
Core regulatory circuitries in defining cancer cell identity across the malignant spectrum. PMID:32634370
Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC. PMID:32460441
Super-enhancer function and its application in cancer targeted therapy. PMID:32128448
Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. PMID:32127534
Genomic footprints of activated telomere maintenance mechanisms in cancer. PMID:32024817
Super-Enhancer-Associated Hub Genes In Chronic Myeloid Leukemia Identified Using Weighted Gene Co-Expression Network Analysis. PMID:31920381
WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. PMID:31784729
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. PMID:31740966
Super-enhancers in transcriptional regulation and genome organization. PMID:31724731
Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. PMID:31696228
UCSC Genome Browser enters 20th year. PMID:31691824
A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. PMID:31691800
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive. PMID:31667506
ENdb: a manually curated database of experimentally supported enhancers for human and mouse. PMID:31665430
Single-nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4. PMID:31659808
Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 (CASZ1). PMID:31642367
Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51. PMID:31618627
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways. PMID:31614935
DNA sequence-dependent chromatin architecture and nuclear hubs formation. PMID:31601866
BET Proteins Are Required for Transcriptional Activation of the Senescent Islet Cell Secretome in Type 1 Diabetes. PMID:31561444
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration. PMID:31492853
Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. PMID:31417368
Heterozygous Mutations in SMARCA2 Reprogram the Enhancer Landscape by Global Retargeting of SMARCA4. PMID:31375262
Data showing atherosclerosis-associated differentially methylated regions are often at enhancers. PMID:31372457
Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers. PMID:31283468
BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity. PMID:31266503
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. PMID:31199868
Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility. PMID:31164884
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. PMID:31149037
Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. PMID:31053705
Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination. PMID:31033435
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways. PMID:30889380
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers. PMID:30814546
SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers. PMID:30806704
X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions. PMID:30691379
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845
Tissue-specific epigenetics of atherosclerosis-related ANGPT and ANGPTL genes. PMID:30688091
Integrative genomic analysis predicts novel functional enhancer-SNPs for bone mineral density. PMID:30656451
RAEdb: a database of enhancers identified by high-throughput reporter assays. PMID:30624654
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. PMID:30595451
Binding of HMGN proteins to cell specific enhancers stabilizes cell identity. PMID:30532006
Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers. PMID:30529831
The MYC Enhancer-ome: Long-Range Transcriptional Regulation of MYC in Cancer. PMID:30470303
Disruption of cardiac Med1 inhibits RNA polymerase II promoter occupancy and promotes chromatin remodeling. PMID:30461303
OncoBase: a platform for decoding regulatory somatic mutations in human cancers. PMID:30445567
SEdb: a comprehensive human super-enhancer database. PMID:30371817
High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies. PMID:30287550
HACER: an atlas of human active enhancers to interpret regulatory variants. PMID:30247654
Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours. PMID:30208958
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. PMID:30169995
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. PMID:30140277
Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family. PMID:30072699
Variants in genes encoding small GTPases and association with epithelial ovarian cancer susceptibility. PMID:29979793
Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients. PMID:29895674
Regulatory variants: from detection to predicting impact. PMID:29893792
MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. PMID:29871649
Postnatal DNA demethylation and its role in tissue maturation. PMID:29795194
Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. PMID:29695774
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. PMID:29514091
Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription. PMID:29498561
Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures. PMID:29429976
Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. PMID:29323272
Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers. PMID:29240919
DNA methylation at enhancers identifies distinct breast cancer lineages. PMID:29123100
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. PMID:29106441
HEDD: Human Enhancer Disease Database. PMID:29077884
DiseaseEnhancer: a resource of human disease-associated enhancer catalog. PMID:29059320
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. PMID:28977473
Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. PMID:28973462
Toward the human cellular microRNAome. PMID:28877962
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. PMID:28869592
Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation. PMID:28839111
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. PMID:28765546
Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. PMID:28683716
Genome-wide association study of heart rate and its variability in Hispanic/Latino cohorts. PMID:28610988
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. PMID:28569135
BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency. PMID:28530713
A computational approach for the functional classification of the epigenome. PMID:28515787
Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. PMID:28467369
Parkinson's disease-associated genetic variation is linked to quantitative expression of inflammatory genes. PMID:28407015
Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. PMID:28373299
Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. PMID:28359301
Common nonmutational NOTCH1 activation in chronic lymphocytic leukemia. PMID:28314854
Systematic analysis of telomere length and somatic alterations in 31 cancer types. PMID:28135248
DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression. PMID:28018137
Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. PMID:27911843
Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. PMID:27895109
Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. PMID:27668658
A generative model for the behavior of RNA polymerase. PMID:27663494
LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines. PMID:27662487
MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs. PMID:27490482
Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics. PMID:27097319
BET Inhibition Attenuates Helicobacter pylori-Induced Inflammatory Response by Suppressing Inflammatory Gene Transcription and Enhancer Activation. PMID:27084101
RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth. PMID:26883634
The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. PMID:26740669
SEA: a super-enhancer archive. PMID:26578594
http://dx.doi.org/10.1093/nar/gkv1002

Tags:

Tags
More detailed information about this field from each metasource.

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

transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

data acquisition
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

zoology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:45.890562

nucleic acid sequence transcription data acquisition genomics human zoology

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Super-Enhancer Archive

TTSMI

PRODORIC2

TrSDB

ENdb: a manually curated database of experimentally supported enhancers for human and mouse

Factorbook

YeTFaSCo

OnTheFly

EnhancerAtlas 2.0

PReMod

SNP2TFBS

MachiBase

DPRP

BloodChIP

HTPSELEX

CMGSDB

VISTA Enhancer Browser

TFBSbank

SCPD - Saccharomyces cerevisiae promoter database

Greglist