4DGenome
Names
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4DGenome
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
Chromatin Interaction Database
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
Names
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4DGenome
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
Chromatin Interaction Database
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
Other names: Chromatin Interaction Database
Names
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4DGenome
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
Chromatin Interaction Database
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,248 interactions curated from both experimental studies (high throughput and individual studies) and computational predictions. It covers five organisms, Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
Description
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4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,248 interactions curated from both experimental studies (high throughput and individual studies) and computational predictions. It covers five organisms, Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
Curated database of chromatin interaction data covering five organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:34.616812
Webpage:
http://4dgenome.research.chop.edu/Webpage
More detailed information about this field from each metasource.
http://4dgenome.research.chop.edu/
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
https://4dgenome.research.chop.edu
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:34.616812
Licence:
Name: CCLicence name
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CC
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
CC-BY-NC-3.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:34.616812
Licence URL
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https://creativecommons.org/licenses/by/3.0/
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
Publications:
Publications
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4DGenome: a comprehensive database of chromatin interactions
PMID: 25788621
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
Publications
More detailed information about this field from each metasource.
4DGenome: a comprehensive database of chromatin interactions
PMID: 25788621
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
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4DGenome: a comprehensive database of chromatin interactions
PubMed citations: 59.
59 articles citing: 4DGenome: a comprehensive database of chromatin interactions
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer. PMID:35350772
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model. PMID:35300460
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
Epigenetic Silencing of HER2 Expression during Epithelial-Mesenchymal Transition Leads to Trastuzumab Resistance in Breast Cancer. PMID:34575017
Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility. PMID:34518541
Prioritization and functional analysis of GWAS risk loci for Barrett's esophagus and esophageal adenocarcinoma. PMID:34505128
Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. PMID:34316701
Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer. PMID:34135941
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer. PMID:33926515
EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2. PMID:33712565
Ultrasound May Suppress Tumor Growth, Inhibit Inflammation, and Establish Tolerogenesis by Remodeling Innatome via Pathways of ROS, Immune Checkpoints, Cytokines, and Trained Immunity/Tolerance. PMID:33628851
Iterative epigenomic analyses in the same single cell. PMID:33627472
CONQUER: an interactive toolbox to understand functional consequences of GWAS hits. PMID:33575630
Multi-omics analysis to identify susceptibility genes for colorectal cancer. PMID:33481017
An integrative multi-omics network-based approach identifies key regulators for breast cancer. PMID:33133424
Cancer and pH Dynamics: Transcriptional Regulation, Proteostasis, and the Need for New Molecular Tools. PMID:32992762
Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. PMID:32941995
regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data. PMID:32850739
Identification and Analysis of p53-Regulated Enhancers in Hepatic Carcinoma. PMID:32695760
Enhancer-Gene Interaction Analyses Identified the Epidermal Growth Factor Receptor as a Susceptibility Gene for Type 2 Diabetes Mellitus. PMID:32602275
GREG-studying transcriptional regulation using integrative graph databases. PMID:32055858
Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. PMID:31988093
Cardioinformatics: the nexus of bioinformatics and precision cardiology. PMID:31802103
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs. PMID:31797625
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. PMID:31740966
Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements. PMID:31484726
Identifying Putative Susceptibility Genes and Evaluating Their Associations with Somatic Mutations in Human Cancers. PMID:31402092
Experimental Data-Mining Analyses Reveal New Roles of Low-Intensity Ultrasound in Differentiating Cell Death Regulatome in Cancer and Non-cancer Cells via Potential Modulation of Chromatin Long-Range Interactions. PMID:31355136
Increased acetylation of H3K14 in the genomic regions that encode trained immunity enzymes in lysophosphatidylcholine-activated human aortic endothelial cells - Novel qualification markers for chronic disease risk factors and conditional DAMPs. PMID:31153039
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. PMID:31118277
Increasing Upstream Chromatin Long-Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells. PMID:31057422
Uncovering genetic mechanisms of kidney aging through transcriptomics, genomics, and epigenomics. PMID:30784661
Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females. PMID:30410588
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants. PMID:30359302
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation. PMID:30343898
De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. PMID:30256891
HACER: an atlas of human active enhancers to interpret regulatory variants. PMID:30247654
Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. PMID:30139328
Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line. PMID:29900125
MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. PMID:29871649
A Comprehensive cis-eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies. PMID:29727689
An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. PMID:29706346
Enhancing the Promise of Drug Repositioning through Genetics. PMID:29270124
EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases. PMID:29040751
Loci associated with skin pigmentation identified in African populations. PMID:29025994
Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. PMID:28874753
VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis. PMID:28453673
Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury. PMID:28271248
Software tools for visualizing Hi-C data. PMID:28159004
Statistical challenges in analyzing methylation and long-range chromosomal interaction data. PMID:28008337
Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3. PMID:27796716
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution. PMID:27563052
LOGIQA: a database dedicated to long-range genome interactions quality assessment. PMID:27185059
3CDB: a manually curated database of chromosome conformation capture data. PMID:27081154
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. PMID:26907635
Progress and challenges in bioinformatics approaches for enhancer identification. PMID:26634919
In the loop: promoter-enhancer interactions and bioinformatics. PMID:26586731
LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns. PMID:26485761
DENdb: database of integrated human enhancers. PMID:26342387
Tags:
Tags
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dna
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
drosophila melanogaster
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
homo sapiens
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
mus musculus
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
plasmodium falciparum
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
saccharomyces cerevisiae
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
chromosomes
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
epigenomics
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
gene expression
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
histone
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
systems bioloby
metasource: re3data.org
version: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
immunoprecipitation experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
Tags
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dna
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
drosophila melanogaster
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
homo sapiens
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
mus musculus
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
plasmodium falciparum
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
saccharomyces cerevisiae
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
chromosomes
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
epigenomics
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:34.616812
gene expression
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
histone
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
systems bioloby
metasource: re3data.orgversion: re3data.org: 4DGenome; editing status 2021-09-21; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SH37 last accessed: 2022-11-04
immunoprecipitation experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:34.616812
dna drosophila melanogaster homo sapiens mus musculus plasmodium falciparum saccharomyces cerevisiae chromosomes epigenomics gene expression histone systems bioloby immunoprecipitation experiment
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