ReMap
Names
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ReMap
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
inserm-remap
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
Names
More detailed information about this field from each metasource.
ReMap
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
inserm-remap
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
Names
More detailed information about this field from each metasource.
ReMap
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
inserm-remap
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
This source may no longer be available. No known URL could be resolved successfully.
ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs). The data is available to browse or download either for a given transcription factor or for the entire dataset.
Description
More detailed information about this field from each metasource.
ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs). The data is available to browse or download either for a given transcription factor or for the entire dataset.
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Integrative analysis of transcription factor ChIP-seq experiments publicly available merged with the Encode dataset. We propose an extensive regulatory catalogue of 8 million transcription factor binding sites from 237 transcription factors (TFs). Among those factors 50 TFs are common with Encode, 82 TFs are Public specific and 105 Encode specific. The results of this analysis are available to browse or download either for a given transcription factor or for the entire dataset.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
Webpage:
http://tagc.univ-mrs.fr/remap/Webpage
More detailed information about this field from each metasource.
http://tagc.univ-mrs.fr/remap/
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://remap.cisreg.eu
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://tagc.univ-mrs.fr/remap/index.php
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
Publications:
Publications
More detailed information about this field from each metasource.
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
PMID: 25477382
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
http://dx.doi.org/10.1093/nar/gkx1092
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
PMID: 25477382
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
http://dx.doi.org/10.1093/nar/gkx1092
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
PubMed citations: 72.
72 articles citing: Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function. PMID:34980917
Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. PMID:34796338
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. PMID:34751401
Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells. PMID:34721373
SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits. PMID:34493297
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. PMID:34331449
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. PMID:33268804
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL. PMID:33186463
A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer. PMID:32859160
Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. PMID:32737375
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. PMID:32718321
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. PMID:32039697
Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy. PMID:31919106
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. PMID:31818883
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. PMID:31665499
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. PMID:31504167
Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. PMID:31477735
TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes. PMID:31045203
Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. PMID:31039056
Mechanism of Action for HDAC Inhibitors-Insights from Omics Approaches. PMID:30939743
RECAP reveals the true statistical significance of ChIP-seq peak calls. PMID:30824903
Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci. PMID:30807572
Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study. PMID:30639570
ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis. PMID:30478421
TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data. PMID:30416387
Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. PMID:30090644
Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. PMID:29895819
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. PMID:29878235
Japanese GWAS identifies variants for bust-size, dysmenorrhea, and menstrual fever that are eQTLs for relevant protein-coding or long non-coding RNAs. PMID:29855537
Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration. PMID:29808619
Nasal DNA methylation is associated with childhood asthma. PMID:29692198
Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. PMID:29662164
Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. PMID:29348432
Systematic target function annotation of human transcription factors. PMID:29325558
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285
DNA methylation at enhancers identifies distinct breast cancer lineages. PMID:29123100
Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. PMID:29121672
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. PMID:29106441
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach. PMID:29033978
Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. PMID:28946896
Identification of a p53-repressed gene module in breast cancer cells. PMID:28915555
Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. PMID:28877031
Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. PMID:28819152
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. PMID:28765546
Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population. PMID:28703132
A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease. PMID:28628103
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. PMID:28569135
DNA methylation at the mu-1 opioid receptor gene (OPRM1) promoter predicts preoperative, acute, and chronic postsurgical pain after spine fusion. PMID:28533693
Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis. PMID:28484236
CHD1 regulates cell fate determination by activation of differentiation-induced genes. PMID:28475736
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017. PMID:28472390
Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. PMID:28408400
Histone deacetylase class-I inhibition promotes epithelial gene expression in pancreatic cancer cells in a BRD4- and MYC-dependent manner. PMID:28369619
Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics. PMID:28171547
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PMID:28103241
Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. PMID:28068916
Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. PMID:27782208
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. PMID:27716038
Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. PMID:27677335
BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire. PMID:27651452
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). PMID:27585267
A microRNA-328 binding site in PAX6 is associated with centrotemporal spikes of rolandic epilepsy. PMID:27386500
Goldmine integrates information placing genomic ranges into meaningful biological contexts. PMID:27257071
Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. PMID:27127234
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. PMID:26979602
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. PMID:26973327
The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney. PMID:26678048
Modeling co-occupancy of transcription factors using chromatin features. PMID:26590261
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. PMID:26508757
Androgen receptor profiling predicts prostate cancer outcome. PMID:26412853
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389 - http://dx.doi.org/10.1093/nar/gkx1092
Tags:
Tags
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cancer
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
cell line
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
functional genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
epigenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:00.047861
Tags
More detailed information about this field from each metasource.
cancer
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
cell line
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: ReMap; ReMap; DOI: https://doi.org/10.25504/FAIRsharing.c8dxsv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
functional genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
mapping
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
epigenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:00.047861
cancer cell line chromatin immunoprecipitation - dna sequencing transcription functional genomics mapping epigenomics
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