ENCODE Project
Names
More detailed information about this field from each metasource.
ENCODE Project
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ENCODE
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 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: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE Encyclopedia
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
Encyclopedia of DNA Elements
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE DCC
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
encode_dcc
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
Names
More detailed information about this field from each metasource.
ENCODE Project
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ENCODE
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 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: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE Encyclopedia
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
Encyclopedia of DNA Elements
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE DCC
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
encode_dcc
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
Other names: ENCODE, ENCODE Encyclopedia, Encyclopedia of DNA Elements, ENCODE DCC, encode_dcc
Names
More detailed information about this field from each metasource.
ENCODE Project
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ENCODE
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 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: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE Encyclopedia
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
Encyclopedia of DNA Elements
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
ENCODE DCC
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
encode_dcc
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
Description
More detailed information about this field from each metasource.
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
It has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
Webpage:
https://www.encodeproject.org/Webpage
More detailed information about this field from each metasource.
https://www.encodeproject.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 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: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
http://encodeproject.org/ENCODE/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
Licence:
Name: CopyrightsLicence name
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Copyrights
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://www.encodeproject.org/help/citing-encode/
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
Publications:
(7)
Publications
More detailed information about this field from each metasource.
ENCODE data at the ENCODE portal
PMID: 26527727
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ENCODE whole-genome data in the UCSC Genome Browser
PMID: 19920125
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
ENCODE whole-genome data in the UCSC genome browser (2011 update)
PMID: 21037257
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
Ontology application and use at the ENCODE DCC
PMID: 25776021
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Principles of metadata organization at the ENCODE data coordination center
PMID: 26980513
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
PMID: 31713622
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
http://dx.doi.org/10.1093/nar/gkx1081
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.
ENCODE data at the ENCODE portal
PMID: 26527727
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ENCODE whole-genome data in the UCSC Genome Browser
PMID: 19920125
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
ENCODE whole-genome data in the UCSC genome browser (2011 update)
PMID: 21037257
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
Ontology application and use at the ENCODE DCC
PMID: 25776021
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Principles of metadata organization at the ENCODE data coordination center
PMID: 26980513
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
PMID: 31713622
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
http://dx.doi.org/10.1093/nar/gkx1081
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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ENCODE data at the ENCODE portal
PubMed citations: 208.
208 articles citing: ENCODE data at the ENCODE portal
Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination. PMID:35927700
CCDC65, a Gene Knockout that leads to Early Death of Mice, acts as a potentially Novel Tumor Suppressor in Lung Adenocarcinoma. PMID:35844805
Single-cell specific and interpretable machine learning models for sparse scChIP-seq data imputation. PMID:35776722
TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma. PMID:35694846
ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. PMID:35672450
3D genome organization in the epithelial-mesenchymal transition spectrum. PMID:35637517
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. PMID:35551305
Multiple sclerosis genetic and non-genetic factors interact through the transient transcriptome. PMID:35534508
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. PMID:35501320
CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. PMID:35396392
Regulation of chromatin accessibility by hypoxia and HIF. PMID:35258521
HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation. PMID:35202091
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. PMID:35042549
Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN. PMID:34965941
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. PMID:34928370
Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation. PMID:34922480
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. PMID:34898596
A Transcriptional Signature of IL-2 Expanded Natural Killer Cells Predicts More Favorable Prognosis in Bladder Cancer. PMID:34858395
Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer. PMID:34730999
DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity. PMID:34706222
Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age. PMID:34687484
Deficiencies in the DNA Binding Protein ARID3a Alter Chromatin Structures Important for Early Human Erythropoiesis. PMID:34663594
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. PMID:34663425
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. PMID:34662402
Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. PMID:34634799
Metabolic gene regulation by Drosophila GATA transcription factor Grain. PMID:34634038
Identification and Functional Characterization of Two Noncoding RNAs Transcribed from Putative Active Enhancers in Hepatocellular Carcinoma. PMID:34588321
High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. PMID:34579770
A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma. PMID:34539622
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor. PMID:34406415
m6Am-seq reveals the dynamic m6Am methylation in the human transcriptome. PMID:34362929
Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. PMID:34256850
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. PMID:34244796
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. PMID:34216543
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization. PMID:34034791
Regulatory rare variants of the dopaminergic gene ANKK1 as potential risk factors for Parkinson's disease. PMID:33972609
Chromatin remodeller CHD7 is required for GABAergic neuron development by promoting PAQR3 expression. PMID:33900016
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms. PMID:33852859
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PMID:33826604
A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation. PMID:33823549
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. PMID:33789096
Effects of sheared chromatin length on ChIP-seq quality and sensitivity. PMID:33788948
Cell type-specific chromatin accessibility analysis in the mouse and human brain. PMID:33775205
Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. PMID:33693641
Reactive astrocytes in ALS display diminished intron retention. PMID:33684213
Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome. PMID:33664286
Annotation of chromatin states in 66 complete mouse epigenomes during development. PMID:33619351
A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer. PMID:33517887
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. PMID:33482885
Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing. PMID:33462199
Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq. PMID:33441968
First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach. PMID:33413117
Bipartite regulation of cellular communication network factor 2 and fibroblast growth factor 1 genes by fibroblast growth factor 1 through histone deacetylase 1 and fork head box protein A1. PMID:33398720
Evaluation of Male Fertility-Associated Loci in a European Population of Patients with Severe Spermatogenic Impairment. PMID:33383876
CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology. PMID:33364592
Improving CLIP-seq data analysis by incorporating transcript information. PMID:33334306
Identifying chromatin features that regulate gene expression distribution. PMID:33239733
Genetic associations of in vivo pathology influence Alzheimer's disease susceptibility. PMID:33213512
Dedifferentiation and neuronal repression define familial Alzheimer's disease. PMID:33188013
FOXL1 Regulates Lung Fibroblast Function via Multiple Mechanisms. PMID:32946266
Alteration of genome folding via contact domain boundary insertion. PMID:32868908
A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis. PMID:32859762
Single-Cell Sequencing of Mouse Thymocytes Reveals Mutational Landscape Shaped by Replication Errors, Mismatch Repair, and H3K36me3. PMID:32858340
The ubiquitin ligase Cullin-1 associates with chromatin and regulates transcription of specific c-MYC target genes. PMID:32811853
Expanded encyclopaedias of DNA elements in the human and mouse genomes. PMID:32728249
An atlas of dynamic chromatin landscapes in mouse fetal development. PMID:32728240
Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. PMID:32710817
NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli. PMID:32683448
Overexpression of Gjb4 impairs cell proliferation and insulin secretion in primary islet cells. PMID:32565358
Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver. PMID:32527045
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes. PMID:32469866
UAP56/DDX39B is a major cotranscriptional RNA-DNA helicase that unwinds harmful R loops genome-wide. PMID:32439635
Analysis of Putative Epigenetic Regulatory Elements in the FXN Genomic Locus. PMID:32408537
CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection. PMID:32404971
HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6. PMID:32344511
Phenotypic and functional translation of IL1RL1 locus polymorphisms in lung tissue and asthmatic airway epithelium. PMID:32324168
Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. PMID:32296450
Transcriptional Patterning of the Ventricular Cardiac Conduction System. PMID:32290757
LARP1 isoform expression in human cancer cell lines. PMID:32286153
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. PMID:32213349
Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. PMID:32211031
An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. PMID:32179771
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells. PMID:32168782
Reprogramming of macrophages employing gene regulatory and metabolic network models. PMID:32097424
Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses. PMID:32060051
pyBedGraph: a python package for fast operations on 1D genomic signal tracks. PMID:32044918
EHMT2 Inhibition Induces Cell Death in Human Non-Small Cell Lung Cancer by Altering the Cholesterol Biosynthesis Pathway. PMID:32028644
Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer. PMID:32012149
VISTA is a checkpoint regulator for naïve T cell quiescence and peripheral tolerance. PMID:31949051
ASCOT identifies key regulators of neuronal subtype-specific splicing. PMID:31919425
Integrative network analysis identifies cell-specific trans regulators of m6A. PMID:31912146
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. PMID:31911677
The epigenomic landscape of transposable elements across normal human development and anatomy. PMID:31822674
MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation. PMID:31784360
LncRNA SNHG15: A new budding star in human cancers. PMID:31774607
Optimization of Ligands Using Focused DNA-Encoded Libraries To Develop a Selective, Cell-Permeable CBX8 Chromodomain Inhibitor. PMID:31755685
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. PMID:31636457
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs. PMID:31570000
SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome. PMID:31494246
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
A de novo evolved gene in the house mouse regulates female pregnancy cycles. PMID:31436535
Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma. PMID:31159876
Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. PMID:31155493
ImmuneRegulation: a web-based tool for identifying human immune regulatory elements. PMID:31114925
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants. PMID:31106382
Radiogenomics Consortium Genome-Wide Association Study Meta-Analysis of Late Toxicity After Prostate Cancer Radiotherapy. PMID:31095341
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. PMID:31053165
scMatch: a single-cell gene expression profile annotation tool using reference datasets. PMID:31028376
LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data. PMID:31014252
Applications of ENCODE data to Systematic Analyses via Data Integration. PMID:31011690
Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study. PMID:31009952
Clinical application of next-generation sequencing to the practice of neurology. PMID:30981321
Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle. PMID:30967894
The long noncoding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration. PMID:30923168
AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks. PMID:30918970
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. PMID:30916337
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
EZH2 Inhibition in Ewing Sarcoma Upregulates GD2 Expression for Targeting with Gene-Modified T Cells. PMID:30879952
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. PMID:30864654
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling. PMID:30791920
Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. PMID:30765617
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. PMID:30737237
Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. PMID:30736359
Probing transcription factor combinatorics in different promoter classes and in enhancers. PMID:30709337
Role of Segregation for Variant Discovery in Multiplex Families Ascertained by Probands With Left Sided Cardiovascular Malformations. PMID:30687393
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. PMID:30668832
Engagement of DNA and H3K27me3 by the CBX8 chromodomain drives chromatin association. PMID:30597065
TICA: Transcriptional Interaction and Coregulation Analyzer. PMID:30578913
Human genome-wide measurement of drug-responsive regulatory activity. PMID:30575722
Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. PMID:30496478
RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. PMID:30445601
Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins. PMID:30445574
The UCSC Genome Browser database: 2019 update. PMID:30407534
Humanization of the Blood-Brain Barrier Transporter ABCB1 in Mice Disrupts Genomic Locus - Lessons from Three Unsuccessful Approaches. PMID:30345087
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation. PMID:30343898
CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. PMID:30296942
A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains. PMID:30266094
Identification of a functional antioxidant response element at the HIF1A locus. PMID:30241031
Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. PMID:30183087
Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci. PMID:30146127
Association of internal smoking dose with blood DNA methylation in three racial/ethnic populations. PMID:30139389
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. PMID:30078707
Tracing human stem cell lineage during development using DNA methylation. PMID:30072366
Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteoporosis and fracture. PMID:30048462
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids. PMID:29983891
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. PMID:29912475
Comprehensive comparative analysis of 5'-end RNA-sequencing methods. PMID:29867192
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. PMID:29789581
SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression. PMID:29784889
REGGAE: a novel approach for the identification of key transcriptional regulators. PMID:29741575
SPAR: small RNA-seq portal for analysis of sequencing experiments. PMID:29733404
Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. PMID:29695722
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. PMID:29684008
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. PMID:29618048
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
A computational biology approach of a genome-wide screen connected miRNAs to obesity and type 2 diabetes. PMID:29605715
HnRNP L represses cryptic exons. PMID:29581412
Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes. PMID:29561703
STAT3 precedes HIF1α transcriptional responses to oxygen and oxygen and glucose deprivation in human brain pericytes. PMID:29518129
Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. PMID:29441061
ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters. PMID:29429977
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. PMID:29284540
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PMID:29267285
A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons. PMID:29158107
rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks. PMID:29140525
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder. PMID:29100085
Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin. PMID:29089515
Loci associated with skin pigmentation identified in African populations. PMID:29025994
Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity. PMID:28985297
Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein. PMID:28934014
Next-Generation Sequencing: The Translational Medicine Approach from "Bench to Bedside to Population". PMID:28930123
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. PMID:28855260
microRNA dysregulation in polyglutamine toxicity of TATA-box binding protein is mediated through STAT1 in mouse neuronal cells. PMID:28774347
A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease. PMID:28628103
DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis. PMID:28592290
Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. PMID:28583252
The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. PMID:28580133
The microprotein Minion controls cell fusion and muscle formation. PMID:28569745
Transcriptomics technologies. PMID:28545146
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. PMID:28379566
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome. PMID:28180283
An Improved Method for Identifying Specific DNA-Protein-Binding Sites In Vitro. PMID:28132389
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. PMID:28112740
The UCSC Genome Browser database: 2017 update. PMID:27899642
Using GWAS to identify novel therapeutic targets for osteoporosis. PMID:27837649
A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. PMID:27831498
Exploration and detection of potential regulatory variants in refractive error GWAS. PMID:27604318
Genetic Susceptibility to Bortezomib-Induced Peripheral Neuroropathy: Replication of the Reported Candidate Susceptibility Loci. PMID:27422265
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs. PMID:27125735
Resources for the Comprehensive Discovery of Functional RNA Elements. PMID:26990993
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513 -
ENCODE whole-genome data in the UCSC Genome Browser
PubMed citations: 158.
158 articles citing: ENCODE whole-genome data in the UCSC Genome Browser
BPIFB1 inhibits vasculogenic mimicry via downregulation of GLUT1-mediated H3K27 acetylation in nasopharyngeal carcinoma. PMID:34725462
The oncogenic role of the cerebral endothelial cell adhesion molecule (CERCAM) in bladder cancer cells in vitro and in vivo. PMID:34105305
Inducible expression quantitative trait locus analysis of the MUC5AC gene in asthma in urban populations of children. PMID:34019912
Immunogenetic determinants of heterosexual HIV-1 transmission: key findings and lessons from two distinct African cohorts. PMID:33934119
Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. PMID:33148170
Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. PMID:32051932
Genomics of neonatal sepsis: has-miR-150 targeting BCL11B functions in disease progression. PMID:30497506
RNA Sequencing and Pathway Analysis Identify Important Pathways Involved in Hypertrichosis and Intellectual Disability in Patients with Wiedemann-Steiner Syndrome. PMID:30014449
LSCC SNP variant regulates SOX2 modulation of VDAC3. PMID:29854282
Alternative utrophin mRNAs contribute to phenotypic differences between dystrophin-deficient mice and Duchenne muscular dystrophy. PMID:29772070
Soluble TREM2 and biomarkers of central and peripheral inflammation in neurodegenerative disease. PMID:29685286
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. PMID:29458327
Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. PMID:29440389
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. PMID:29361190
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites. PMID:29081688
Genome-wide Association Study of Susceptibility to Particulate Matter-Associated QT Prolongation. PMID:28749367
Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer. PMID:28415573
Genetic Variants of Cytochrome b-245, Alpha Polypeptide Gene and Premature Acute Myocardial Infarction Risk in an Iranian Population. PMID:28356848
Opportunities and challenges of whole-genome and -exome sequencing. PMID:28193154
Dynamics and Correlates of CD8 T-Cell Counts in Africans with Primary Human Immunodeficiency Virus Type 1 Infection. PMID:27630231
Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2. PMID:27490946
The BRG1 chromatin remodeling enzyme links cancer cell metabolism and proliferation. PMID:27223259
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Targeting the chromatin remodeling enzyme BRG1 increases the efficacy of chemotherapy drugs in breast cancer cells. PMID:27029062
Time course analysis based on gene expression profile and identification of target molecules for colorectal cancer. PMID:27013928
Bioinformatics analysis of hepatitis C virus genotype 2a-induced human hepatocellular carcinoma in Huh7 cells. PMID:26811688
Rare variants analysis using penalization methods for whole genome sequence data. PMID:26637205
Bioinformatics Analysis of Estrogen-Responsive Genes. PMID:26585125
ENCODE data at the ENCODE portal. PMID:26527727
Distinct Transcriptional Programs Underlie Sox9 Regulation of the Mammalian Chondrocyte. PMID:26146088
Targeted inhibition of genome-wide DNA methylation analysis in epigenetically modulated phenotypes in lung cancer. PMID:25926333
Cerebrospinal fluid Aβ42 levels and APP processing pathway genes in Parkinson's disease. PMID:25808939
Non-coding genomic regions possessing enhancer and silencer potential are associated with healthy aging and exceptional survival. PMID:25682868
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PMID:25634236
Immunogenetic influences on acquisition of HIV-1 infection: consensus findings from two African cohorts point to an enhancer element in IL19 (1q32.2). PMID:25633979
Identification and computational analysis of gene regulatory elements. PMID:25561628
Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms. PMID:25375159
Association of common variants in TCF4 and PTPRG with Fuchs' corneal dystrophy: a systematic review and meta-analysis. PMID:25299301
H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. PMID:25271306
Comparative assembly hubs: web-accessible browsers for comparative genomics. PMID:25138168
In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. PMID:25011554
Host genetics and viral load in primary HIV-1 infection: clear evidence for gene by sex interactions. PMID:24969460
Ancient evolutionary origins of epigenetic regulation associated with posttraumatic stress disorder. PMID:24860472
Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms. PMID:24832652
Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress. PMID:24823795
Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. PMID:24784026
Nucleosome regulatory dynamics in response to TGFβ. PMID:24771338
Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells. PMID:24555823
Epigenetic regulation and functional characterization of microRNA-142 in mesenchymal cells. PMID:24236112
GSTCD and INTS12 regulation and expression in the human lung. PMID:24058608
MEF2 is a converging hub for histone deacetylase 4 and phosphatidylinositol 3-kinase/Akt-induced transformation. PMID:24043307
Association of cerebrospinal fluid Aβ42 with A2M gene in cognitively normal subjects. PMID:24011543
GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. PMID:23868195
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. PMID:23755361
Conserved expression of natural antisense transcripts in mammals. PMID:23577827
DISC1 genetics, biology and psychiatric illness. PMID:23550053
The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells. PMID:23549118
Genome-wide analysis of DNA methylation in human amnion. PMID:23533356
Fatty acid binding protein 3 (fabp3) is associated with insulin, lipids and cardiovascular phenotypes of the metabolic syndrome through epigenetic modifications in a Northern European family population. PMID:23510163
GATA2 haploinsufficiency caused by mutations in a conserved intronic element leads to MonoMAC syndrome. PMID:23502222
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. PMID:23482648
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. PMID:23325852
Coordinate regulation of the gel-forming mucin genes at chromosome 11p15.5. PMID:23303185
Hedgehog signaling regulates MyoD expression and activity. PMID:23266826
Searching for transcription factor binding sites in vector spaces. PMID:23244338
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. PMID:23166687
Intra-familial tests of association between familial idiopathic scoliosis and linked regions on 9q31.3-q34.3 and 16p12.3-q22.2. PMID:23154503
Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. PMID:23125224
Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers. PMID:23070629
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. PMID:23064413
Cell type-specific termination of transcription by transposable element sequences. PMID:23020800
Decoding the human genome. PMID:22955971
Genome-wide in silico prediction of gene expression. PMID:22954627
Functional analysis of transcription factor binding sites in human promoters. PMID:22951020
Regulation of SOD2 in cancer by histone modifications and CpG methylation: closing the loop between redox biology and epigenetics. PMID:22946823
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. PMID:22936659
Tau phosphorylation pathway genes and cerebrospinal fluid tau levels in Alzheimer's disease. PMID:22927204
Why is DNA methylation of Igf2 CpG island shore affected during ageing? PMID:22879347
ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PMID:22870189
Tristetraprolin impairs myc-induced lymphoma and abolishes the malignant state. PMID:22863009
Evidence for sequence biases associated with patterns of histone methylation. PMID:22857523
PACSIN2 polymorphism influences TPMT activity and mercaptopurine-related gastrointestinal toxicity. PMID:22846425
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. PMID:22824656
p53, a target of estrogen receptor (ER) α, modulates DNA damage-induced growth suppression in ER-positive breast cancer cells. PMID:22787161
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. PMID:22784574
Finding combinatorial histone code by semi-supervised biclustering. PMID:22759587
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
The NIH Roadmap Epigenomics Program data resource. PMID:22690667
At the crossroads: EGFR and PTHrP signaling in cancer-mediated diseases of bone. PMID:22684584
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. PMID:22675074
Regulated Expression of Chromobox Homolog 5 Revealed in Tumors of Apc(Min) (/+) ROSA11 Gene Trap Mice. PMID:22670227
The MTAP-CDKN2A locus confers susceptibility to a naturally occurring canine cancer. PMID:22623710
A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci. PMID:22607690
The 1000 Genomes Project: data management and community access. PMID:22543379
A novel ChREBP isoform in adipose tissue regulates systemic glucose metabolism. PMID:22466288
Evolutionary forces shaping genomic islands of population differentiation in humans. PMID:22439654
Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain. PMID:22396734
Epigenetic regulation of human cis-natural antisense transcripts. PMID:22371288
Clusters of adaptive evolution in the human genome. PMID:22303346
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. PMID:22248020
Joint ancestry and association testing in admixed individuals. PMID:22216000
Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation. PMID:22158964
The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene. PMID:22150271
Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. PMID:22102577
Functional analysis of APOE locus genetic variation implicates regional enhancers in the regulation of both TOMM40 and APOE. PMID:22089642
Prediction of transposable element derived enhancers using chromatin modification profiles. PMID:22087331
Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. PMID:22087219
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
A role for insulator elements in the regulation of gene expression response to hypoxia. PMID:22067454
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. PMID:22047616
Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation. PMID:22039435
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. PMID:22036566
Transcriptional regulation of co-expressed microRNA target genes. PMID:22002038
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PMID:21852959
Methionine adenosyltransferase 2A/2B and methylation: gene sequence variation and functional genomics. PMID:21813468
The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. PMID:21813016
Enhancers regulate progression of development in mammalian cells. PMID:21785139
From oncoproteins/tumor suppressors to microRNAs, the newest therapeutic targets for pulmonary arterial hypertension. PMID:21761156
Meta-analysis of new genome-wide association studies of colorectal cancer risk. PMID:21761138
An integrated ChIP-seq analysis platform with customizable workflows. PMID:21736739
Extensive relationship between antisense transcription and alternative splicing in the human genome. PMID:21719572
Long conserved fragments upstream of Mammalian polyadenylation sites. PMID:21705472
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny. PMID:21663614
Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. PMID:21653641
Genome-scale analysis of replication timing: from bench to bioinformatics. PMID:21637205
Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. PMID:21627829
LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. PMID:21602794
RNA-sequence analysis of human B-cells. PMID:21536721
Replication of TCF4 through association and linkage studies in late-onset Fuchs endothelial corneal dystrophy. PMID:21533127
Multiple Wnt/ß-catenin responsive enhancers align with the MYC promoter through long-range chromatin loops. PMID:21533051
A user's guide to the encyclopedia of DNA elements (ENCODE). PMID:21526222
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. PMID:21450710
Individual variability in the detoxification of carcinogenic arylhydroxylamines in human breast. PMID:21447608
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. PMID:21423168
A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression. PMID:21385855
Signal transducers and activators of transcription-3/pim1 axis plays a critical role in the pathogenesis of human pulmonary arterial hypertension. PMID:21382889
Neutral evolution of robustness in Drosophila microRNA precursors. PMID:21285032
High-resolution genome-wide mapping of the primary structure of chromatin. PMID:21241889
MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. PMID:21205891
Amyloid precursor protein (APP) processing genes and cerebrospinal fluid APP cleavage product levels in Alzheimer's disease. PMID:21196064
Mugsy: fast multiple alignment of closely related whole genomes. PMID:21148543
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. PMID:21075797
Ensembl 2011. PMID:21045057
ENCODE whole-genome data in the UCSC genome browser (2011 update). PMID:21037257
The UCSC Genome Browser database: update 2011. PMID:20959295
Putting epigenome comparison into practice. PMID:20944597
p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins. PMID:20833636
Next generation tools for genomic data generation, distribution, and visualization. PMID:20828407
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. PMID:20736230
Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PMID:20661439
Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. PMID:20587588
Next-generation genomics: an integrative approach. PMID:20531367
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. PMID:20430782
Using galaxy to perform large-scale interactive data analyses. PMID:18428782 -
ENCODE whole-genome data in the UCSC genome browser (2011 update)
PubMed citations: 119.
119 articles citing: ENCODE whole-genome data in the UCSC genome browser (2011 update)
Genetic data sharing and artificial intelligence in the era of personalized medicine based on a cross-sectional analysis of the Saudi human genome program. PMID:35082362
DNA hypomethylation drives changes in MAGE-A gene expression resulting in alteration of proliferative status of cells. PMID:32760472
ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells. PMID:32061921
LncRNA SNHG15: A new budding star in human cancers. PMID:31774607
LIN28-let-7 axis regulates genes in immortalized human trophoblast cells by targeting the ARID3B-complex. PMID:31415216
Identification of ESM1 overexpressed in head and neck squamous cell carcinoma. PMID:31073279
Identification of Potential Molecular Mechanisms and Candidate Genes Involved in The Acute Phase of Myocardial Infarction. PMID:29845799
A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics. PMID:29727690
Chemical genomics reveals inhibition of breast cancer lung metastasis by Ponatinib via c-Jun. PMID:29667003
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. PMID:29458327
Identification of key genes implicated in the suppressive function of human FOXP3+CD25+CD4+ regulatory T cells through the analysis of time‑series data. PMID:29286140
Variant Ranker: a web-tool to rank genomic data according to functional significance. PMID:28716001
Stat3 regulates desmoglein 3 transcription in epithelial keratinocytes. PMID:28469076
Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. PMID:28455512
Investigation of candidate genes for osteoarthritis based on gene expression profiles. PMID:27866912
Potential molecular characteristics in situ in response to repetitive UVB irradiation. PMID:27829444
Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells. PMID:27716259
Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. PMID:27132591
Interferon-α signaling promotes embryonic HSC maturation. PMID:27095787
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. PMID:26961139
NEAT: a framework for building fully automated NGS pipelines and analyses. PMID:26830846
Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. PMID:26673693
Regulatory single nucleotide polymorphisms at the beginning of intron 2 of the human KRAS gene. PMID:26648033
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. PMID:26631489
Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene. PMID:26559844
ENCODE data at the ENCODE portal. PMID:26527727
APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions. PMID:26527001
Neurodevelopmental LincRNA Microsyteny Conservation and Mammalian Brain Size Evolution. PMID:26134977
ARID3B Directly Regulates Ovarian Cancer Promoting Genes. PMID:26121572
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures. PMID:26099518
Prediction of promoters and enhancers using multiple DNA methylation-associated features. PMID:26099324
The short and long of noncoding sequences in the control of vascular cell phenotypes. PMID:26022065
The role of epigenetics in the endothelial cell shear stress response and atherosclerosis. PMID:25979369
HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes. PMID:25941940
Flow-induced protein kinase A-CREB pathway acts via BMP signaling to promote HSC emergence. PMID:25870201
Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. PMID:25860294
Computational methodology for ChIP-seq analysis. PMID:25741452
Epigenetic Regulation of Placenta-Specific 8 Contributes to Altered Function of Endothelial Colony-Forming Cells Exposed to Intrauterine Gestational Diabetes Mellitus. PMID:25720387
The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues. PMID:25634226
Salinomycin inhibits hepatocellular carcinoma cell invasion and migration through JNK/JunD pathway-mediated MMP9 expression. PMID:25522777
Interplay of microRNA and epigenetic regulation in the human regulatory network. PMID:25339974
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation. PMID:25183525
Disease mechanisms in rheumatology--tools and pathways: defining functional genetic variants in autoimmune diseases. PMID:25132667
Integrin αvβ3 drives slug activation and stemness in the pregnant and neoplastic mammary gland. PMID:25117682
4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. PMID:24887486
Elastic network models capture the motions apparent within ensembles of RNA structures. PMID:24759093
Vascular histone deacetylation by pharmacological HDAC inhibition. PMID:24732587
Inflammation-induced NFATc1-STAT3 transcription complex promotes pancreatic cancer initiation by KrasG12D. PMID:24694735
CRY1 circadian gene variant interacts with carbohydrate intake for insulin resistance in two independent populations: Mediterranean and North American. PMID:24548145
Topiramate treatment for heavy drinkers: moderation by a GRIK1 polymorphism. PMID:24525690
bwtool: a tool for bigWig files. PMID:24489365
DNA hypermethylation in prostate cancer is a consequence of aberrant epithelial differentiation and hyperproliferation. PMID:24464224
Peroxisome proliferator-activated receptor γ regulates genes involved in insulin/insulin-like growth factor signaling and lipid metabolism during adipogenesis through functionally distinct enhancer classes. PMID:24288131
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. PMID:24174536
Regulation of the F11, Klkb1, Cyp4v3 gene cluster in livers of metabolically challenged mice. PMID:24066149
An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. PMID:24053169
Common DNA methylation alterations in multiple brain regions in autism. PMID:23999529
Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches. PMID:23785426
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. PMID:23761436
Scalable web services for the PSIPRED Protein Analysis Workbench. PMID:23748958
Association of the BRCA1 promoter polymorphism rs11655505 with the risk of familial breast and/or ovarian cancer. PMID:23657760
Fundamental differences in endoreplication in mammals and Drosophila revealed by analysis of endocycling and endomitotic cells. PMID:23613587
High-throughput identification of long-range regulatory elements and their target promoters in the human genome. PMID:23525463
The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination. PMID:23438597
A survey of tools for variant analysis of next-generation genome sequencing data. PMID:23341494
Genome-wide significant locus of beta-trace protein, a novel kidney function biomarker, identified in European and African Americans. PMID:23328707
Dynamic DNA methylation across diverse human cell lines and tissues. PMID:23325432
Space exploration by the promoter of a long human gene during one transcription cycle. PMID:23303786
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. PMID:23281809
Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization. PMID:23236496
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes. PMID:23165207
Soluble CD14: genomewide association analysis and relationship to cardiovascular risk and mortality in older adults. PMID:23162014
A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. PMID:23110100
Surveying the epigenomic landscape, one base at a time. PMID:23088423
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. PMID:23064413
EpiExplorer: live exploration and global analysis of large epigenomic datasets. PMID:23034089
Cell type-specific termination of transcription by transposable element sequences. PMID:23020800
The chromatin fingerprint of gene enhancer elements. PMID:22952241
Corepressors (NCoR and SMRT) as well as coactivators are recruited to positively regulated 1α,25-dihydroxyvitamin D3-responsive genes. PMID:22944139
The UCSC genome browser and associated tools. PMID:22908213
An encyclopedia of mouse DNA elements (Mouse ENCODE). PMID:22889292
Human developmental enhancers conserved between deuterostomes and protostomes. PMID:22876195
Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy. PMID:22846883
PACSIN2 polymorphism influences TPMT activity and mercaptopurine-related gastrointestinal toxicity. PMID:22846425
Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PMID:22829947
wANNOVAR: annotating genetic variants for personal genomes via the web. PMID:22717648
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
Genome-wide copy number analysis uncovers a new HSCR gene: NRG3. PMID:22589734
Shape-based alignment of genomic landscapes in multi-scale resolution. PMID:22561376
GeSICA: genome segmentation from intra-chromosomal associations. PMID:22559164
Evolution of vertebrate interferon inducible transmembrane proteins. PMID:22537233
Resolving the variable genome and epigenome in human disease. PMID:22443201
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. PMID:22426492
Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. PMID:22416122
Conservation of the relative tRNA composition in healthy and cancerous tissues. PMID:22357911
Interaction between genetic and epigenetic variation defines gene expression patterns at the asthma-associated locus 17q12-q21 in lymphoblastoid cell lines. PMID:22271045
A genome-wide association study of gestational diabetes mellitus in Korean women. PMID:22233651
p63-microRNA feedback in keratinocyte senescence. PMID:22228303
Early progress in epigenetic regulation of endothelin pathway genes. PMID:22220553
Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites. PMID:22158963
Polycomb-repressed genes have permissive enhancers that initiate reprogramming. PMID:22153073
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. PMID:22102592
Blood pressure loci identified with a gene-centric array. PMID:22100073
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. PMID:22036566
Genomes, proteomes, and the central dogma. PMID:22010165
Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. PMID:21989056
The UCSC Genome Browser. PMID:21975940
RNA splicing in regulation of nitric oxide receptor soluble guanylyl cyclase. PMID:21867767
Ensembl BioMarts: a hub for data retrieval across taxonomic space. PMID:21785142
Identifying functional single nucleotide polymorphisms in the human CArGome. PMID:21771879
Epigenetically coordinated GATA2 binding is necessary for endothelium-specific endomucin expression. PMID:21666600
Reconstructing regulatory network transitions. PMID:21632251
Emerging patterns of epigenomic variation. PMID:21507501
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
Using galaxy to perform large-scale interactive data analyses. PMID:18428782 -
Ontology application and use at the ENCODE DCC
PubMed citations: 25.
25 articles citing: Ontology application and use at the ENCODE DCC
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. PMID:34890448
Leveraging the Cell Ontology to classify unseen cell types. PMID:34548483
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging. PMID:33068112
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Annot: a Django-based sample, reagent, and experiment metadata tracking system. PMID:31675914
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. PMID:30540547
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Cell type discovery and representation in the era of high-content single cell phenotyping. PMID:29322913
Challenges and recommendations for epigenomics in precision health. PMID:29220033
Evaluation of the role of downregulation of SNF5/INI1 core subunit of SWI/SNF complex in clear cell renal cell carcinoma development. PMID:29218250
Long noncoding RNA NBAT1 negatively modulates growth and metastasis of osteosarcoma cells through suppression of miR-21. PMID:29119050
Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. PMID:29061976
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
Are Randomized Controlled Trials the (G)old Standard? From Clinical Intelligence to Prescriptive Analytics. PMID:27383622
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. PMID:27042287
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
ENCODE data at the ENCODE portal. PMID:26527727
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381 -
Principles of metadata organization at the ENCODE data coordination center
PubMed citations: 22.
22 articles citing: Principles of metadata organization at the ENCODE data coordination center
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. PMID:35134925
MVIP: multi-omics portal of viral infection. PMID:34718748
CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin. PMID:34694145
Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. PMID:34449663
Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. PMID:33846360
Resources and challenges for integrative analysis of nuclear architecture data. PMID:33450522
Ten simple rules for annotating sequencing experiments. PMID:33017400
Ten simple rules for providing effective bioinformatics research support. PMID:32214318
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. PMID:31597973
VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. PMID:31084623
Meffil: efficient normalization and analysis of very large DNA methylation datasets. PMID:29931280
Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. PMID:29807547
An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. PMID:29744254
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques. PMID:29363555
circlncRNAnet: an integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs. PMID:29194536
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups. PMID:28584254
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. PMID:27255077 -
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
PubMed citations: 15.
15 articles citing: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Common Variation in the PIN1 Locus Increases the Genetic Risk to Suffer from Sertoli Cell-Only Syndrome. PMID:35743717
Nuclear mechanoprotection: From tissue atlases as blueprints to distinctive regulation of nuclear lamins. PMID:35719698
Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self. PMID:35430876
Monitoring the Levels of Cellular NF-κB Activation States. PMID:34771516
Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PMID:34685799
Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma. PMID:34399838
Long noncoding RNA IL6-AS1 is highly expressed in chronic obstructive pulmonary disease and is associated with interleukin 6 by targeting miR-149-5p and early B-cell factor 1. PMID:34323408
The Role of Epigenomic Regulatory Pathways in the Gut-Brain Axis and Visceral Hyperalgesia. PMID:34057682
Modeling regulatory network topology improves genome-wide analyses of complex human traits. PMID:33990562
Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research. PMID:33827270
GTRD: an integrated view of transcription regulation. PMID:33231677
LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements. PMID:33219661
HeRA: an atlas of enhancer RNAs across human tissues. PMID:33119754
Analysis of Putative Epigenetic Regulatory Elements in the FXN Genomic Locus. PMID:32408537
Regulation of gene expression by growth hormone. PMID:32151566 - http://dx.doi.org/10.1093/nar/gkx1081
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chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
methylation
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcript
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
dna
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
epigenetics
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
epigenomics
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
gwas
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
genome-wide association studies
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
rna
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
cres
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
candidate regulatory elements
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
chromatin
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
rdhss
metasource: re3data.org
version: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
chip-seq
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
rna-seq
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
Tags
More detailed information about this field from each metasource.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
methylation
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcript
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; ENCODE Project ; DOI: https://doi.org/10.25504/FAIRsharing.7ykpy5; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
dna
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
epigenetics
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122
epigenomics
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
gwas
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
genome-wide association studies
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
rna
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
cres
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
candidate regulatory elements
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
chromatin
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
rdhss
metasource: re3data.orgversion: re3data.org: ENCODE; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMKB last accessed: 2022-11-04
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
chip-seq
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
rna-seq
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:26.733122
chromatin immunoprecipitation - dna sequencing methylation transcript transcription dna epigenetics epigenomics gwas genome-wide association studies rna cres candidate regulatory elements chromatin rdhss gene expression chip-seq rna sequence
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