Encyclopedia of DNA Elements at UCSC
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Encyclopedia of DNA Elements at UCSC
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE Project at UCSC
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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Encyclopedia of DNA Elements at UCSC
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE Project at UCSC
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: ENCODE, ENCODE Project at UCSC
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Encyclopedia of DNA Elements at UCSC
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE Project at UCSC
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Encyclopedia of DNA Elements (ENCODE) has created 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. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.
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Encyclopedia of DNA Elements (ENCODE) has created 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. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. Initially a pilot project focused on 1% of the human genome sequence, ENCODE was scaled up in September 2007 to cover the entire genome. The ENCODE Data Coordination Center (DCC) at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). To support the breadth and volume of ENCODE data, new features for organizing and selecting datasets have been added to the browser. Additionally, metadata describing the experiments is now captured more formally via controlled vocabularies which are associated with browser tracks and download files. The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. As of September 2009, the ENCODE investigators have completed four production-level data freezes, consisting of 341 experiments submitted to the ENCODE DCC, with 207 of these released in a total of 18 tracks on the UCSC Genome Browser. These experiments represent a major methodology shift from microarray to high-throughput sequencing assays, and include a broad range of experiment types (e.g. ChIP-seq, RNA-seq, Methyl-seq) in 7 designated common cell types, and 51 additional human cell lines and tissues.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://genome.ucsc.edu/ENCODE/Webpage
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http://genome.ucsc.edu/ENCODE/
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://genome.ucsc.edu/ENCODE
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: ENCODE Data has usage restrictions for 9 months after public availabilityLicence name
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ENCODE Data has usage restrictions for 9 months after public availability
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
Licence URL
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http://genome.ucsc.edu/ENCODE/
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
Publications:
(6)
Publications
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ENCODE data in the UCSC Genome Browser: year 5 update
PMID: 23193274
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC Genome Browser
PMID: 19920125
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
PMID: 22075998
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC genome browser (2011 update)
PMID: 21037257
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
The ENCODE Project at UC Santa Cruz
PMID: 17166863
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1172
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 in the UCSC Genome Browser: year 5 update
PMID: 23193274
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC Genome Browser
PMID: 19920125
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
PMID: 22075998
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
ENCODE whole-genome data in the UCSC genome browser (2011 update)
PMID: 21037257
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
The ENCODE Project at UC Santa Cruz
PMID: 17166863
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1172
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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ENCODE data in the UCSC Genome Browser: year 5 update
PubMed citations: 479.
479 articles citing: ENCODE data in the UCSC Genome Browser: year 5 update
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
Nuclear mechanoprotection: From tissue atlases as blueprints to distinctive regulation of nuclear lamins. PMID:35719698
An alternative CYB5A transcript is expressed in aneuploid ALL and enriched in relapse. PMID:35436854
Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia. PMID:35294436
Methylome and Transcriptome-Based Integration Analysis Identified Molecular Signatures Associated With Meningitis Induced by Glaesserella parasuis. PMID:35281072
SUMOylation inhibition enhances dexamethasone sensitivity in multiple myeloma. PMID:34983615
Association of IL33, IL1RL1, IL1RAP Polymorphisms and Asthma in Chinese Han Children. PMID:34977013
Epigenetic Dysregulation of KCNK9 Imprinting and Triple-Negative Breast Cancer. PMID:34885139
Loss of Integrin α9β1 on Tumor Keratinocytes Enhances the Stromal Vasculature and Growth of Cutaneous Tumors. PMID:34843681
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. PMID:34737427
Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation. PMID:34717534
Epigenetic DNA Modifications Upregulate SPRY2 in Human Colorectal Cancers. PMID:34685612
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. PMID:34649537
Myogenin controls via AKAP6 non-centrosomal microtubule-organizing center formation at the nuclear envelope. PMID:34605406
Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis. PMID:34599306
Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells. PMID:34575842
The Emerging Landscapes of Long Noncoding RNA in Thyroid Carcinoma: Biological Functions and Clinical Significance. PMID:34447696
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Assessing acute myeloid leukemia susceptibility in rearrangement-driven patients by DNA breakage at topoisomerase II and CCCTC-binding factor/cohesin binding sites. PMID:34405474
Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. PMID:34289059
New susceptible locus, rs9428555, is associated with pediatric-onset immunoglobulin A nephropathy and immunoglobulin A vasculitis in Koreans. PMID:34146253
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. PMID:34140314
A Functional Indel Polymorphism Within MIR155HG Is Associated With Sudden Cardiac Death Risk in a Chinese Population. PMID:34136547
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. PMID:34093998
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization. PMID:34034791
Genetic predisposition in the 2'-5'A pathway in the development of type 1 diabetes: potential contribution to dysregulation of innate antiviral immunity. PMID:33973017
Identification of novel functional CpG-SNPs associated with Type 2 diabetes and birth weight. PMID:33835050
Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial. PMID:33821793
Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. PMID:33818294
The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. PMID:33799353
Associations between childhood family emotional health, fronto-limbic grey matter volume, and saliva 5mC in young adulthood. PMID:33789736
Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations. PMID:33757590
Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. PMID:33686085
Identification of a novel genetic locus associated with immune-mediated thrombotic thrombocytopenic purpura. PMID:33596643
Genetics of Polycystic Ovary Syndrome: What is New? PMID:33518187
Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. PMID:33504799
Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. PMID:33482747
CTCF and EGR1 suppress breast cancer cell migration through transcriptional control of Nm23-H1. PMID:33436746
MassArray analysis of genomic susceptibility variants in ovarian cancer. PMID:33273524
SNP-SNP Interaction in Genes Encoding PD-1/PD-L1 Axis as a Potential Risk Factor for Clear Cell Renal Cell Carcinoma. PMID:33255938
Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. PMID:33248247
Allele-specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (TERT) associates with TERT expression in multiple cancers. PMID:33245585
Genetic Predictors of Severe Skin Toxicity in Patients with Stage III Colon Cancer Treated with Cetuximab: NCCTG N0147 (Alliance). PMID:33203692
Transfer learning enables prediction of CYP2D6 haplotype function. PMID:33137098
Effects of NT5C2 Germline Variants on 6-Mecaptopurine Metabolism in Children With Acute Lymphoblastic Leukemia. PMID:33124053
Association of Common Variants of TNFSF13 and TNFRSF13B Genes with CLL Risk and Clinical Picture, as Well as Expression of Their Products-APRIL and TACI Molecules. PMID:33036273
Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development. PMID:32993798
Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions. PMID:32962511
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. PMID:32938926
Transcription factor POU3F2 regulates TRIM8 expression contributing to cellular functions implicated in schizophrenia. PMID:32929213
Frequency of Mia (MNS7) and Classification of Mia-Positive Hybrid Glycophorins in an Australian Blood Donor Population. PMID:32884500
Cancer SLC43A2 alters T cell methionine metabolism and histone methylation. PMID:32879489
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. PMID:32832596
SUMOylation of E2F1 Regulates Expression of EZH2. PMID:32816857
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model. PMID:32793490
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. PMID:32689928
Global translation during early development depends on the essential transcription factor PRDM10. PMID:32681107
H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts. PMID:32664951
Wnt-driven LARGE2 mediates laminin-adhesive O-glycosylation in human colonic epithelial cells and colorectal cancer. PMID:32586342
Association of variants in selected genes mediating host immune response with duration of Staphylococcus aureus bacteremia. PMID:32507857
Diacylglycerol Kinase Alpha in Radiation-Induced Fibrosis: Potential as a Predictive Marker or Therapeutic Target. PMID:32477950
Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. PMID:32341350
Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China. PMID:32324877
Gene-Specific Control of tRNA Expression by RNA Polymerase II. PMID:32298650
DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels. PMID:32237968
Epigenetic Regulation of WNT3A Enhancer during Regeneration of Injured Cortical Neurons. PMID:32164275
Identification of novel functional CpG-SNPs associated with type 2 diabetes and coronary artery disease. PMID:32162118
Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but not Decreased Promoter Methylation in Colorectal Cancer. PMID:32110952
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. PMID:32084333
Transcriptional corepressor SIN3A regulates hippocampal synaptic plasticity via Homer1/mGluR5 signaling. PMID:32069266
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. PMID:32039697
Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks. PMID:32029477
Combined burden and functional impact tests for cancer driver discovery using DriverPower. PMID:32024818
Prediction of short-term neonatal complications in preterm infants using exome-wide genetic variation and gestational age: a pilot study. PMID:32023625
Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. PMID:31988093
Enhancer jungles establish robust tissue-specific regulatory control in the human genome. PMID:31887344
SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. PMID:31866047
Multivariable regulation of gene expression plasticity in metazoans. PMID:31795914
Gene expression and DNA methylation changes in BeWo cells dependent on tumor necrosis factor-α and insulin-like growth factor-I. PMID:31724103
A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. PMID:31691800
Two novel ligand-independent variants of the VEGFR-1 receptor are expressed in human testis and spermatozoa, one of them with the ability to activate SRC proto-oncogene tyrosine kinases. PMID:31645906
Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes. PMID:31639821
Repression of eEF2K transcription by NF-κB tunes translation elongation to inflammation and dsDNA-sensing. PMID:31636182
Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. PMID:31599933
A variant of the castor zinc finger 1 (CASZ1) gene is differentially associated with the clinical classification of chronic venous disease. PMID:31570750
DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load. PMID:31537801
Developmentally regulated Shh expression is robust to TAD perturbations. PMID:31511252
Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction. PMID:31434962
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. PMID:31362726
Differentially methylated regions in bipolar disorder and suicide. PMID:31350827
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation. PMID:31307522
Chronic activation of FXR-induced liver growth with tissue-specific targeting Cyclin D1. PMID:31223053
Nanofiber-expanded human CD34+ cells heal cutaneous wounds in streptozotocin-induced diabetic mice. PMID:31182750
Haplotype-aware diplotyping from noisy long reads. PMID:31159868
Genetic variants in the circadian rhythm pathway as indicators of prostate cancer progression. PMID:30996687
In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression. PMID:30985765
Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability. PMID:30874922
Decreased Nuclear Ascorbate Accumulation Accompanied with Altered Genomic Methylation Pattern in Fibroblasts from Arterial Tortuosity Syndrome Patients. PMID:30800210
Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. PMID:30636336
A novel form of JARID2 is required for differentiation in lineage-committed cells. PMID:30573669
Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1. PMID:30557369
Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals. PMID:30545422
Glucocorticoid Receptor Binding Inhibits an Intronic IL33 Enhancer and is Disrupted by rs4742170 (T) Allele Associated with Specific Wheezing Phenotype in Early Childhood. PMID:30544846
HDAC is indispensable for IFN-γ-induced B7-H1 expression in gastric cancer. PMID:30537988
ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. PMID:30519505
Antiviral activity of bone morphogenetic proteins and activins. PMID:30510168
Molecular analysis of NPAS3 functional domains and variants. PMID:30509165
A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. PMID:30499775
ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients. PMID:30413149
Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females. PMID:30410588
The UCSC Genome Browser database: 2019 update. PMID:30407534
Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. PMID:30276537
Topological alternate centrality measure capturing drug targets in the network of MAPK pathways. PMID:30259868
Histone H2A.Z Suppression of Interferon-Stimulated Transcription and Antiviral Immunity Is Modulated by GCN5 and BRD2. PMID:30240626
Genome-wide association analysis of common genetic variants of resistant hypertension. PMID:30237584
Reduced monocyte and macrophage TNFSF15/TL1A expression is associated with susceptibility to inflammatory bowel disease. PMID:30199539
MiR-9, miR-153 and miR-124 are down-regulated by acute exposure to cocaine in a dopaminergic cell model and may contribute to cocaine dependence. PMID:30166527
A tale of two cities: The genetic mechanisms governing calvarial bone development. PMID:30155972
Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study. PMID:30107520
Non-coding genetic variation shaping mental health. PMID:30099302
Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. PMID:30096381
Tracing human stem cell lineage during development using DNA methylation. PMID:30072366
Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. PMID:30031967
Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. PMID:30001206
Nuclear respiratory factor 1 promotes spheroid survival and mesenchymal transition in mammary epithelial cells. PMID:29995872
Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. PMID:29956121
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. PMID:29936186
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. PMID:29912475
Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). PMID:29845286
Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes. PMID:29771307
UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. PMID:29743725
Towards a map of cis-regulatory sequences in the human genome. PMID:29733395
LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data. PMID:29697370
The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. PMID:29695719
Abnormal islet sphingolipid metabolism in type 1 diabetes. PMID:29671030
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. PMID:29648536
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. PMID:29618487
Tissue-specific impact of FADS cluster variants on FADS1 and FADS2 gene expression. PMID:29590160
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. PMID:29579309
miR-181a regulates erythroid enucleation via the regulation of Xpo7 expression. PMID:29567782
Demethylator phenotypes in acute myeloid leukemia. PMID:29556023
A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia. PMID:29547969
Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. PMID:29335803
Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. PMID:29335020
Meta-analysis of epigenome-wide association studies of cognitive abilities. PMID:29311653
Identification of specific feed-forward apoptosis mechanisms and associated higher survival rates for low grade glioma and lung squamous cell carcinoma. PMID:29305708
Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. PMID:29281820
"DNA Methylation signatures in panic disorder". PMID:29249830
MicroRNA-transcription factor interactions and their combined effect on target gene expression in colon cancer cases. PMID:29226599
Hypoxic Induction of Vasorin Regulates Notch1 Turnover to Maintain Glioma Stem-like Cells. PMID:29198941
MAX Mutations in Endometrial Cancer: Clinicopathologic Associations and Recurrent MAX p.His28Arg Functional Characterization. PMID:29155953
Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. PMID:29141961
Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. PMID:29121672
Chromatin-state discovery and genome annotation with ChromHMM. PMID:29120462
The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. PMID:29112714
Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics. PMID:29095815
Forkhead Box Transcription Factors of the FOXA Class Are Required for Basal Transcription of Angiotensin-Converting Enzyme 2. PMID:29082356
HEDD: Human Enhancer Disease Database. PMID:29077884
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. PMID:29059365
Induction of anti-VEGF therapy resistance by upregulated expression of microseminoprotein (MSMP). PMID:29059175
A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers. PMID:29042628
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. PMID:29021290
Computational characterization of chromatin domain boundary-associated genomic elements. PMID:28977568
Systems biology analysis of longitudinal functional response of endothelial cells to shear stress. PMID:28973892
EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PMID:28968461
miRNA-122 Protects Mice and Human Hepatocytes from Acetaminophen Toxicity by Regulating Cytochrome P450 Family 1 Subfamily A Member 2 and Family 2 Subfamily E Member 1 Expression. PMID:28963035
Coordinated increase of nuclear tension and lamin-A with matrix stiffness outcompetes lamin-B receptor that favors soft tissue phenotypes. PMID:28931598
C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. PMID:28915724
MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer. PMID:28888037
Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. PMID:28855511
Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers. PMID:28854564
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells. PMID:28818098
Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1. PMID:28813576
Association between Promoter Methylation of Gene ERCC3 and Benzene Hematotoxicity. PMID:28813025
Biogenesis of Pro-senescent Microparticles by Endothelial Colony Forming Cells from Premature Neonates is driven by SIRT1-Dependent Epigenetic Regulation of MKK6. PMID:28811647
Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PMID:28797094
Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing. PMID:28762674
Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. PMID:28759043
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. PMID:28750606
miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. PMID:28748534
Selectivity and Kinetic Requirements of HDAC Inhibitors as Progranulin Enhancers for Treating Frontotemporal Dementia. PMID:28712747
GWAS follow-up study of esophageal squamous cell carcinoma identifies potential genetic loci associated with family history of upper gastrointestinal cancer. PMID:28680059
Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. PMID:28674729
Transcription factor-microRNA associations and their impact on colorectal cancer survival. PMID:28667784
Kaiso differentially regulates components of the Notch signaling pathway in intestinal cells. PMID:28637464
Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. PMID:28583252
Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PMID:28549066
A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. PMID:28531272
The microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection. PMID:28530712
In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants. PMID:28506205
Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes. PMID:28505376
Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes. PMID:28490592
DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. PMID:28473707
Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects. PMID:28468790
A comprehensive analysis of cancer-driving mutations and genes in kidney cancer. PMID:28454375
LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes. PMID:28440307
Predictive long-range allele-specific mapping of regulatory variants and target transcripts. PMID:28406955
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. PMID:28351423
A null variant in the apolipoprotein L3 gene is associated with non-diabetic nephropathy. PMID:28339911
PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. PMID:28332630
Age-associated DNA methylation changes in naive CD4+ T cells suggest an evolving autoimmune epigenotype in aging T cells. PMID:28322571
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. PMID:28317029
Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis. PMID:28272906
Epigenetic Regulation of BDNF Gene during Development and Diseases. PMID:28272318
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. PMID:28169395
Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus. PMID:28150878
Targeted Sequencing of Lung Function Loci in Chronic Obstructive Pulmonary Disease Cases and Controls. PMID:28114305
Constitutively active RAS signaling reduces 1,25 dihydroxyvitamin D-mediated gene transcription in intestinal epithelial cells by reducing vitamin D receptor expression. PMID:28104492
Sox17 drives functional engraftment of endothelium converted from non-vascular cells. PMID:28091527
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Regulatory region genetic variation is associated with FYN expression in Alzheimer's disease. PMID:28033507
Genome-Wide Association Study for Anthracycline-Induced Congestive Heart Failure. PMID:27993963
Discovering Genome-Wide Tag SNPs Based on the Mutual Information of the Variants. PMID:27992465
Transcriptional programs that control expression of the autoimmune regulator gene Aire. PMID:27941786
Integrative genomic analysis identifies ancestry-related expression quantitative trait loci on DNA polymerase β and supports the association of genetic ancestry with survival disparities in head and neck squamous cell carcinoma. PMID:27906459
Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. PMID:27903900
Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP. PMID:27903646
Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). PMID:27903268
The UCSC Genome Browser database: 2017 update. PMID:27899642
Prioritization of non-coding disease-causing variants and long non-coding RNAs in liver cancer. PMID:27895760
IL1A rs1800587 associates with chronic noncrisis pain in sickle cell disease. PMID:27883292
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. PMID:27876760
High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients. PMID:27858503
JUN is a key transcriptional regulator of the unfolded protein response in acute myeloid leukemia. PMID:27840425
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PMID:27798693
Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis. PMID:27701424
An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile. PMID:27661099
Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. PMID:27652892
Dysferlin-mediated phosphatidylserine sorting engages macrophages in sarcolemma repair. PMID:27641898
Genetic Factors of the Disease Course after Sepsis: A Genome-Wide Study for 28Day Mortality. PMID:27639821
Mouse models of Down syndrome: gene content and consequences. PMID:27538963
In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. PMID:27524623
A 1.35 Mb DNA fragment is inserted into the DHMN1 locus on chromosome 7q34-q36.2. PMID:27487800
Specific detection of interferon regulatory factor 5 (IRF5): A case of antibody inequality. PMID:27481535
Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk. PMID:27465306
Novel variation at chr11p13 associated with cystic fibrosis lung disease severity. PMID:27408752
Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. PMID:27378782
Genetic influences on nicotinic α5 receptor (CHRNA5) CpG methylation and mRNA expression in brain and adipose tissue. PMID:27350810
Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation. PMID:27349968
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PMID:27309962
A calcium- and calpain-dependent pathway determines the response to lenalidomide in myelodysplastic syndromes. PMID:27294874
A catalog of hemizygous variation in 127 22q11 deletion patients. PMID:27274857
Defining the identity of mouse embryonic dermal fibroblasts. PMID:27265328
The Third Intron of the Interferon Regulatory Factor-8 Is an Initiator of Repressed Chromatin Restricting Its Expression in Non-Immune Cells. PMID:27257682
Intragenic Locus in Human PIWIL2 Gene Shares Promoter and Enhancer Functions. PMID:27248499
Bioinformatic Studies to Predict MicroRNAs with the Potential of Uncoupling RECK Expression from Epithelial-Mesenchymal Transition in Cancer Cells. PMID:27226706
Pan-cancer analyses of the nuclear receptor superfamily. PMID:27200367
Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1. PMID:27187934
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets. PMID:27153607
Inhibition of REST Suppresses Proliferation and Migration in Glioblastoma Cells. PMID:27153061
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. PMID:27139377
Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function. PMID:27129775
Epigenomic elements analyses for promoters identify ESRRG as a new susceptibility gene for obesity-related traits. PMID:27113491
Epigenetic Reprogramming in Naive CD4+ T Cells Favoring T Cell Activation and Non-Th1 Effector T Cell Immune Response as an Early Event in Lupus Flares. PMID:27111767
PDGF induces SphK1 expression via Egr-1 to promote pulmonary artery smooth muscle cell proliferation. PMID:27099350
Tissue-specific DNA demethylation is required for proper B-cell differentiation and function. PMID:27091986
Nuclear RNA-seq of single neurons reveals molecular signatures of activation. PMID:27090946
Novel rare variations of the oxytocin receptor (OXTR) gene in autism spectrum disorder individuals. PMID:27081536
Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease. PMID:27077110
ST8SIA4-Dependent Polysialylation is Part of a Developmental Program Required for Germ Layer Formation from Human Pluripotent Stem Cells. PMID:27074314
Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. PMID:27056836
Downregulation of ATOH8 induced by EBV-encoded LMP1 contributes to the malignant phenotype of nasopharyngeal carcinoma. PMID:27049918
System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PMID:27031986
Methylomic predictors demonstrate the role of NF-κB in old-age mortality and are unrelated to the aging-associated epigenetic drift. PMID:27015559
Searching the Human Genome for Snail and Slug With DNA@Home. PMID:26998498
Genome-wide analysis of DNA methylation and gene expression defines molecular characteristics of Crohn's disease-associated fibrosis. PMID:26973718
Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing. PMID:26957605
Genetic contribution of CYP1A1 variant on treatment outcome in epilepsy patients: a functional and interethnic perspective. PMID:26951882
A PWWP Domain of Histone-Lysine N-Methyltransferase NSD2 Binds to Dimethylated Lys-36 of Histone H3 and Regulates NSD2 Function at Chromatin. PMID:26912663
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. PMID:26907635
Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma. PMID:26905591
Genetic variants in ultraconserved regions associate with prostate cancer recurrence and survival. PMID:26902966
Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1. PMID:26877820
Mutation pattern is an influential factor on functional mutation rates in cancer. PMID:26865835
Enhancer RNA-driven looping enhances the transcription of the long noncoding RNA DHRS4-AS1, a controller of the DHRS4 gene cluster. PMID:26864944
Serotonin 2A Receptor SNP rs7330461 Association with Treatment Response to Pomaglumetad Methionil in Patients with Schizophrenia. PMID:26861400
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. PMID:26846207
A maximum-likelihood approach for building cell-type trees by lifting. PMID:26819094
RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PMID:26808730
The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. PMID:26808208
DNA methylation in a Scottish family multiply affected by bipolar disorder and major depressive disorder. PMID:26798408
Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus. PMID:26795348
Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. PMID:26748710
Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. PMID:26725182
Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins. PMID:26724866
Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. PMID:26721890
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. PMID:26699738
Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. PMID:26673704
Pathway, in silico and tissue-specific expression quantitative analyses of oesophageal squamous cell carcinoma genome-wide association studies data. PMID:26635288
Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. PMID:26635082
The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster. PMID:26615201
The UCSC Genome Browser database: 2016 update. PMID:26590259
A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events. PMID:26588488
Brain-specific epigenetic markers of schizophrenia. PMID:26575221
Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. PMID:26562774
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
ENCODE data at the ENCODE portal. PMID:26527727
Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes. PMID:26517682
Association study of androgen signaling pathway genes in polycystic ovary syndrome. PMID:26493122
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. PMID:26428292
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. PMID:26423047
Epigenome-wide association study suggests that SNPs in the promoter region of RETN influence plasma resistin level via effects on DNA methylation at neighbouring sites. PMID:26404063
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. PMID:26388941
Using mixtures of biological samples as process controls for RNA-sequencing experiments. PMID:26383878
A newly identified susceptibility locus near FOXP1 modifies the association of gastroesophageal reflux with Barrett's esophagus. PMID:26377193
Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. PMID:26366553
Genetic variants of the autophagy pathway as prognostic indicators for prostate cancer. PMID:26365175
MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. PMID:26351698
DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical Atherosclerosis. PMID:26307030
Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity. PMID:26305227
Genome-Wide Mapping and Interrogation of the Nmp4 Antianabolic Bone Axis. PMID:26244796
Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. PMID:26204995
Genome-Wide Association Study of Down Syndrome-Associated Atrioventricular Septal Defects. PMID:26194203
Characterization of CpG sites that escape methylation on the inactive human X-chromosome. PMID:26178744
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks. PMID:26163319
Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. PMID:26153245
Proteotoxic stress reprograms the chromatin landscape of SUMO modification. PMID:26152697
Dynamic aberrant NF-κB spurs tumorigenesis: a new model encompassing the microenvironment. PMID:26119834
Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity. PMID:26117541
Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs). PMID:26111110
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Exonic Re-Sequencing of the Chromosome 2q24.3 Parkinson's Disease Locus. PMID:26090850
PAX8 expression in ovarian surface epithelial cells. PMID:26079312
Regulation of cholesteryl ester transfer protein expression by upstream polymorphisms: reduced expression associated with rs247616. PMID:26061659
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. PMID:26025802
βA3/A1-crystallin and persistent fetal vasculature (PFV) disease of the eye. PMID:26022148
The pluripotency factor NANOG promotes the formation of squamous cell carcinomas. PMID:25988972
BAG2 Is Repressed by NF-κB Signaling, and Its Overexpression Is Sufficient to Shift Aβ1-42 from Neurotrophic to Neurotoxic in Undifferentiated SH-SY5Y Neuroblastoma. PMID:25985852
Genome-wide Survey of Runs of Homozygosity Identifies Recessive Loci for Bone Mineral Density in Caucasian and Chinese Populations. PMID:25983029
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. PMID:25972927
PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond. PMID:25970601
Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up. PMID:25963972
Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. PMID:25956794
Improved integrative framework combining association data with gene expression features to prioritize Crohn's disease genes. PMID:25935003
Gender-specific postnatal demethylation and establishment of epigenetic memory. PMID:25934504
Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions. PMID:25927889
Common genetic variants in epigenetic machinery genes and risk of upper gastrointestinal cancers. PMID:25921222
Rapid transient isoform-specific neuregulin1 transcription in motor neurons is regulated by neurotrophic factors and axon-target interactions. PMID:25913151
ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PMID:25879845
Roles of progesterone receptor A and B isoforms during human endometrial decidualization. PMID:25875046
Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression. PMID:25865496
The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. PMID:25857663
An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development. PMID:25847946
Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer. PMID:25779658
Involvement of RNA Polymerase III in Immune Responses. PMID:25776554
Ontology application and use at the ENCODE DCC. PMID:25776021
Transcriptional regulation of microRNA-100, -146a, and -150 genes by p53 and NFκB p65/RelA in mouse striatal STHdh(Q7)/ Hdh(Q7) cells and human cervical carcinoma HeLa cells. PMID:25757558
HERV-K(HML-2) rec and np9 transcripts not restricted to disease but present in many normal human tissues. PMID:25750667
LocusTrack: Integrated visualization of GWAS results and genomic annotation. PMID:25750659
Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. PMID:25739401
βA3/A1-crystallin is a critical mediator of STAT3 signaling in optic nerve astrocytes. PMID:25736717
Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. PMID:25716334
Genetic variants in the Hippo pathway predict biochemical recurrence after radical prostatectomy for localized prostate cancer. PMID:25707771
Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. PMID:25704602
APP intracellular domain acts as a transcriptional regulator of miR-663 suppressing neuronal differentiation. PMID:25695604
Genetic interaction analysis of TCF7L2 for biochemical recurrence after radical prostatectomy in localized prostate cancer. PMID:25678841
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. PMID:25668385
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility. PMID:25631608
ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. PMID:25605800
DCLK1 is a broadly dysregulated target against epithelial-mesenchymal transition, focal adhesion, and stemness in clear cell renal carcinoma. PMID:25605241
Genetic associations of the interleukin locus at 1q32.1 with clinical outcomes of cutaneous melanoma. PMID:25604082
The landscape of long noncoding RNAs in the human transcriptome. PMID:25599403
Variation in PPARG is associated with longitudinal change in insulin resistance in Mexican Americans at risk for type 2 diabetes. PMID:25584717
Smoking-Associated Site-Specific Differential Methylation in Buccal Mucosa in the COPDGene Study. PMID:25517428
Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. PMID:25488688
Molecular signatures of mood stabilisers highlight the role of the transcription factor REST/NRSF. PMID:25451397
The UCSC Genome Browser database: 2015 update. PMID:25428374
Prostate cancer epigenome. PMID:25421658
Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit. PMID:25406515
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PMID:25405470
Age-related variations in the methylome associated with gene expression in human monocytes and T cells. PMID:25404168
Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes. PMID:25384072
Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding. PMID:25369454
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. PMID:25348400
Navigating protected genomics data with UCSC Genome Browser in a Box. PMID:25348212
Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. PMID:25343476
Interplay of microRNA and epigenetic regulation in the human regulatory network. PMID:25339974
Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation. PMID:25336616
Vitamin D receptor and RXR in the post-genomic era. PMID:25335912
Genetic modifiers of neurofibromatosis type 1-associated café-au-lait macule count identified using multi-platform analysis. PMID:25329635
R-loops induce repressive chromatin marks over mammalian gene terminators. PMID:25296254
Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate. PMID:25290263
Functional annotation of putative regulatory elements at cancer susceptibility Loci. PMID:25288875
Sexually-motivated song is predicted by androgen-and opioid-related gene expression in the medial preoptic nucleus of male European starlings (Sturnus vulgaris). PMID:25264575
Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. PMID:25239644
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. PMID:25236618
circBase: a database for circular RNAs. PMID:25234927
Morphological and population genomic evidence that human faces have evolved to signal individual identity. PMID:25226282
Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding. PMID:25200388
Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network. PMID:25199827
Epigenome-wide DNA methylation in hearing ability: new mechanisms for an old problem. PMID:25184702
microRNA-29 negatively regulates EMT regulator N-myc interactor in breast cancer. PMID:25174825
Ankylosing spondylitis is associated with the anthrax toxin receptor 2 gene (ANTXR2). PMID:25169729
Characterization of a REST-Regulated Internal Promoter in the Schizophrenia Genome-Wide Associated Gene MIR137. PMID:25154622
Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PMID:25133550
Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma. PMID:25114248
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Study of cell differentiation by phylogenetic analysis using histone modification data. PMID:25104072
Innate immunity pathways regulate the nephropathy gene Apolipoprotein L1. PMID:25100047
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. PMID:25070602
Characterization of T gene sequence variants and germline duplications in familial and sporadic chordoma. PMID:24990759
Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. PMID:24990743
The UCSC Genome Browser: What Every Molecular Biologist Should Know. PMID:24984850
Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. PMID:24939938
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. PMID:24927817
Distinct and separable roles for EZH2 in neurogenic astroglia. PMID:24867641
Vitamin D and the RNA transcriptome: more than mRNA regulation. PMID:24860511
Motif enrichment tool. PMID:24860165
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. PMID:24838573
LKB1 Loss induces characteristic patterns of gene expression in human tumors associated with NRF2 activation and attenuation of PI3K-AKT. PMID:24828662
C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD. PMID:24806409
Engineered zinc-finger transcription factors activate OCT4 (POU5F1), SOX2, KLF4, c-MYC (MYC) and miR302/367. PMID:24792165
Apoptosis-Related Single Nucleotide Polymorphisms and the Risk of Non-Small Cell Lung Cancer in Women. PMID:24790730
MYC regulation of cell growth through control of transcription by RNA polymerases I and III. PMID:24789877
Natural selection and infectious disease in human populations. PMID:24776769
Genetic interactions affecting human gene expression identified by variance association mapping. PMID:24771767
Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. PMID:24743992
Genome-wide diet-gene interaction analyses for risk of colorectal cancer. PMID:24743840
Severe osteoarthritis of the hand associates with common variants within the ALDH1A2 gene and with rare variants at 1p31. PMID:24728293
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
A chromatin structure-based model accurately predicts DNA replication timing in human cells. PMID:24682507
Prolyl-hydroxylase 3: Evolving Roles for an Ancient Signaling Protein. PMID:24672806
Characterisation of genetic variation in ST8SIA2 and its interaction region in NCAM1 in patients with bipolar disorder. PMID:24651862
Genetics of PICALM expression and Alzheimer's disease. PMID:24618820
Genome-wide DNA methylation analysis predicts an epigenetic switch for GATA factor expression in endometriosis. PMID:24603652
Transcriptional divergence and conservation of human and mouse erythropoiesis. PMID:24591581
Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival. PMID:24567359
Inherited variation in the PARP1 gene and survival from melanoma. PMID:24535833
Meta-analysis of loci associated with age at natural menopause in African-American women. PMID:24493794
Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. PMID:24443471
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. PMID:24413736
Deficiency of MIWI2 (Piwil4) induces mouse erythroleukemia cell differentiation, but has no effect on hematopoiesis in vivo. PMID:24376547
SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes. PMID:24369422
Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. PMID:24316981
Ensembl 2014. PMID:24316576
rSNPBase: a database for curated regulatory SNPs. PMID:24285297
The UCSC Genome Browser database: 2014 update. PMID:24270787
Systematic classification of non-coding RNAs by epigenomic similarity. PMID:24267974
RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PMID:24244175
Genotype to phenotype via network analysis. PMID:24238873
Four Promoters of IRF5 Respond Distinctly to Stimuli and are Affected by Autoimmune-Risk Polymorphisms. PMID:24223576
Many human accelerated regions are developmental enhancers. PMID:24218637
Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. PMID:24213554
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. PMID:24137000
Bridging the gap between genetic associations and molecular mechanisms for type 2 diabetes. PMID:24127137
Interactions between GSK3β and amyloid genes explain variance in amyloid burden. PMID:24112793
Replication of a GWAS signal in a Caucasian population implicates ADD3 in susceptibility to biliary atresia. PMID:24104524
The transcription factor HNF1α induces expression of angiotensin-converting enzyme 2 (ACE2) in pancreatic islets from evolutionarily conserved promoter motifs. PMID:24100303
Germline variants in MRE11/RAD50/NBN complex genes in childhood leukemia. PMID:24093751
Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. PMID:24071585
Transcriptional regulation by STAT1 and STAT2 in the interferon JAK-STAT pathway. PMID:24069549
Identification and characterization of regulatory elements in the promoter of ACVR1, the gene mutated in Fibrodysplasia Ossificans Progressiva. PMID:24047559
A mouse model for inducible overexpression of Prdm14 results in rapid-onset and highly penetrant T-cell acute lymphoblastic leukemia (T-ALL). PMID:24046360
Emerging patterns of somatic mutations in cancer. PMID:24022702
Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. PMID:24004852
HIV latency and integration site placement in five cell-based models. PMID:23953889
Methylomics of gene expression in human monocytes. PMID:23900078
Genetic variants predicting left ventricular hypertrophy in a diabetic population: a Go-DARTS study including meta-analysis. PMID:23879873
Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. PMID:23819581
Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. PMID:23793816
RAP1 protects from obesity through its extratelomeric role regulating gene expression. PMID:23791526
GAT: a simulation framework for testing the association of genomic intervals. PMID:23782611
Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken. PMID:23762306
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. PMID:23748563
Gene regulation by the act of long non-coding RNA transcription. PMID:23721193
Rab3Gap1 mediates exocytosis of Claudin-1 and tight junction formation during epidermal barrier acquisition. PMID:23685254
Prolactin receptor gene polymorphisms are associated with gestational diabetes. PMID:23651351
PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. PMID:23620286
Peppy: proteogenomic search software. PMID:23614390
Microarray analyses of glucocorticoid and vitamin D3 target genes in differentiating cultured human podocytes. PMID:23593176
Widespread and extensive lengthening of 3' UTRs in the mammalian brain. PMID:23520388
Whole-exome sequencing identifies mutated c12orf57 in recessive corpus callosum hypoplasia. PMID:23453666
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
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: update 2012
PubMed citations: 148.
148 articles citing: ENCODE whole-genome data in the UCSC Genome Browser: update 2012
Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma. PMID:35887228
Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration. PMID:35102202
MicroRNA-Related Strategies to Improve Cardiac Function in Heart Failure. PMID:34869689
Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis. PMID:34539736
Epigenetic Regulation of the N-Terminal Truncated Isoform of Matrix Metalloproteinase-2 (NTT-MMP-2) and Its Presence in Renal and Cardiac Diseases. PMID:33732288
ANKLE1 as New Hotspot Mutation for Breast Cancer in Indian Population and Has a Role in DNA Damage and Repair in Mammalian Cells. PMID:33584808
Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer. PMID:33177242
Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development. PMID:32993798
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. PMID:32404186
The role of long noncoding RNAs in hepatocellular carcinoma. PMID:32295598
Identifying lncRNA-miRNA-mRNA networks to investigate Alzheimer's disease pathogenesis and therapy strategy. PMID:32035423
Ultraconserved long non-coding RNA uc.112 is highly expressed in childhood T versus B-cell acute lymphoblastic leukemia. PMID:32014474
Epistatic interaction between PKD2 and ABCG2 influences the pathogenesis of hyperuricemia and gout. PMID:32000861
Epigenetic regulation of human papillomavirus transcription in the productive virus life cycle. PMID:31919577
The landscape of tiered regulation of breast cancer cell metabolism. PMID:31780802
Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases. PMID:31527394
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
Expression of Micro-RNA-492 (MiR-492) in Human Cervical Cancer Cell Lines is Upregulated by Transfection with Wild-Type P53, Irradiation, and 5-Fluorouracil Treatment In Vitro. PMID:30374014
Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. PMID:30344479
Regulatory variants: from detection to predicting impact. PMID:29893792
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
A functional SNP upstream of the ADRB2 gene is associated with COPD. PMID:29588580
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. PMID:29458327
Non-coding RNAs in hepatocellular carcinoma: molecular functions and pathological implications. PMID:29317776
Roles of alternative splicing in modulating transcriptional regulation. PMID:28984199
Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1. PMID:28439269
BCL9L Dysfunction Impairs Caspase-2 Expression Permitting Aneuploidy Tolerance in Colorectal Cancer. PMID:28073006
Genomic approaches to the assessment of human spina bifida risk. PMID:27883265
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. PMID:27857184
Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. PMID:27821551
Epigenetic regulation of long noncoding RNA UCA1 by SATB1 in breast cancer. PMID:27697109
Cross-species Conservation of context-specific networks. PMID:27531214
S100A6 Regulates Endothelial Cell Cycle Progression by Attenuating Antiproliferative Signal Transducers and Activators of Transcription 1 Signaling. PMID:27386938
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Transcriptional gene silencing in humans. PMID:27060137
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes. PMID:26924971
Metagenomics: Retrospect and Prospects in High Throughput Age. PMID:26664751
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. PMID:26607552
Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. PMID:26596347
ENCODE data at the ENCODE portal. PMID:26527727
Repression of Esophageal Neoplasia and Inflammatory Signaling by Anti-miR-31 Delivery In Vivo. PMID:26286729
Correlation of the osteoarthritis susceptibility variants that map to chromosome 20q13 with an expression quantitative trait locus operating on NCOA3 and with functional variation at the polymorphism rs116855380. PMID:26211391
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PMID:26208222
Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. PMID:26185457
swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing. PMID:26176536
Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. PMID:26046465
Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation. PMID:25986534
Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. PMID:25918715
Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. PMID:25877919
Ontology application and use at the ENCODE DCC. PMID:25776021
Molecular characterization of LASP-1 expression reveals vimentin as its new partner in human hepatocellular carcinoma cells. PMID:25760690
Neighboring Genes Show Correlated Evolution in Gene Expression. PMID:25743543
The theory of RNA-mediated gene evolution. PMID:25581873
Heterozygous triplication of upstream regulatory sequences leads to dysregulation of matrix metalloproteinase 19 in patients with cavitary optic disc anomaly. PMID:25581579
Identification and computational analysis of gene regulatory elements. PMID:25561628
Identification of epidermal growth factor receptor (EGFR) genetic variants that modify risk for head and neck squamous cell carcinoma. PMID:25511740
Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. PMID:25286960
H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. PMID:25271306
Determination and inference of eukaryotic transcription factor sequence specificity. PMID:25215497
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels. PMID:25080503
Transcriptional landscape of repetitive elements in normal and cancer human cells. PMID:25012247
In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. PMID:25011554
Diabetic nephropathy--emerging epigenetic mechanisms. PMID:25003613
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Sequence variation in TMEM18 in association with body mass index: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. PMID:24951660
On the identification of potential regulatory variants within genome wide association candidate SNP sets. PMID:24920305
Genetic variation in prostaglandin synthesis and related pathways, NSAID use and colorectal cancer risk in the Colon Cancer Family Registry. PMID:24908683
A multivariate approach to the integration of multi-omics datasets. PMID:24884486
Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription. PMID:24860841
Convergent and divergent cellular responses by ErbB4 isoforms in mammary epithelial cells. PMID:24829397
Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid. PMID:24821702
The rise of regulatory RNA. PMID:24776770
Recurrent epimutations activate gene body promoters in primary glioblastoma. PMID:24709822
Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. PMID:24705081
Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis. PMID:24695009
Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PMID:24586184
An HIV-encoded antisense long noncoding RNA epigenetically regulates viral transcription. PMID:24576854
The de novo sequence origin of two long non-coding genes from an inter-genic region. PMID:24564579
Target gene abundance contributes to the efficiency of siRNA-mediated gene silencing. PMID:24527979
Assessment of common variability and expression quantitative trait loci for genome-wide associations for progressive supranuclear palsy. PMID:24503276
Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PMID:24489775
A general framework for estimating the relative pathogenicity of human genetic variants. PMID:24487276
MLV integration site selection is driven by strong enhancers and active promoters. PMID:24464997
Chromatin remodeling mediated by the FOXA1/A2 transcription factors activates CFTR expression in intestinal epithelial cells. PMID:24440874
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. PMID:24330828
Genetic associations with 25-hydroxyvitamin D deficiency in HIV-1-infected youth: fine-mapping for the GC/DBP gene that encodes the vitamin D-binding protein. PMID:24294218
Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch. PMID:24234445
RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing. PMID:24234443
Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. PMID:24158853
Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines. PMID:24149212
Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy. PMID:24134860
Germline variants in MRE11/RAD50/NBN complex genes in childhood leukemia. PMID:24093751
Genome-wide association study implicates a novel RNA gene, the lincRNA AC068718.1, as a risk factor for post-traumatic stress disorder in women. PMID:24080187
Epigenetic modifications in the pathogenesis of diabetic nephropathy. PMID:24011576
Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. PMID:24009515
A genome-wide association study of chronic otitis media with effusion and recurrent otitis media identifies a novel susceptibility locus on chromosome 2. PMID:23974705
Elucidation of how cancer cells avoid acidosis through comparative transcriptomic data analysis. PMID:23967163
Epigenetics of human papillomaviruses. PMID:23953230
HTR4 gene structure and altered expression in the developing lung. PMID:23890215
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. PMID:23865674
Heterogeneous nuclear ribonucleoprotein (HnRNP) K genome-wide binding survey reveals its role in regulating 3'-end RNA processing and transcription termination at the early growth response 1 (EGR1) gene through XRN2 exonuclease. PMID:23857582
Positive effects of methylphenidate on hyperactivity are moderated by monoaminergic gene variants in children with autism spectrum disorders. PMID:23856854
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. PMID:23827707
PCSK6 VNTR Polymorphism Is Associated with Degree of Handedness but Not Direction of Handedness. PMID:23826248
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. PMID:23804400
Moderation of antipsychotic-induced weight gain by energy balance gene variants in the RUPP autism network risperidone studies. PMID:23799528
Network2Canvas: network visualization on a canvas with enrichment analysis. PMID:23749960
Comprehensive functional annotation of seventy-one breast cancer risk Loci. PMID:23717510
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. PMID:23708189
Role of the human endogenous retrovirus HERV-K18 in autoimmune disease susceptibility: study in the Spanish population and meta-analysis. PMID:23634223
A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation. PMID:23628382
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
SEC24A deficiency lowers plasma cholesterol through reduced PCSK9 secretion. PMID:23580231
Identification of seven loci affecting mean telomere length and their association with disease. PMID:23535734
Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. PMID:23535731
High-throughput identification of long-range regulatory elements and their target promoters in the human genome. PMID:23525463
Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation. PMID:23516500
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
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. PMID:23446634
YY1TargetDB: an integral information resource for Yin Yang 1 target loci. PMID:23411719
Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11. PMID:23408857
Robust, synergistic regulation of human gene expression using TALE activators. PMID:23396285
Early growth response genes signaling supports strong paracrine capability of mesenchymal stem cells. PMID:23304166
A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. PMID:23291588
GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. PMID:23268441
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
The UCSC Genome Browser database: extensions and updates 2013. PMID:23155063
From cells to chromatin: capturing snapshots of genome organization with 5C technology. PMID:23137922
A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. PMID:23110100
Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells. PMID:22992673
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. PMID:22955991
A high-coverage genome sequence from an archaic Denisovan individual. PMID:22936568
Mutant p53 is a transcriptional co-factor that binds to G-rich regulatory regions of active genes and generates transcriptional plasticity. PMID:22894900
Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. PMID:22840920
Mechanism of generation of therapy related leukemia in response to anti-topoisomerase II agents. PMID:22829791
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. PMID:22706305
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. PMID:22669907
Lineage-specific adjacent IFNG and IL26 genes share a common distal enhancer element. PMID:22622197
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
ADAM10 expression and promoter haplotype in Alzheimer's disease. PMID:22572541
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. PMID:22517426
Thematic minireview series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome. PMID:22451669
Coding exons function as tissue-specific enhancers of nearby genes. PMID:22442009 -
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 -
The ENCODE Project at UC Santa Cruz
PubMed citations: 50.
50 articles citing: The ENCODE Project at UC Santa Cruz
Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks. PMID:35249174
Analysis of Putative Epigenetic Regulatory Elements in the FXN Genomic Locus. PMID:32408537
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. PMID:31373611
Trafficking of the human ether-a-go-go-related gene (hERG) potassium channel is regulated by the ubiquitin ligase rififylin (RFFL). PMID:30401747
Alternative splicing links histone modifications to stem cell fate decision. PMID:30217220
Diminished PRRX1 Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential. PMID:28974514
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. PMID:28929968
Identification of key genes induced by platelet-rich plasma in human dermal papilla cells using bioinformatics methods. PMID:27922680
A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a. PMID:27866707
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Regulation of functional KCNQ1OT1 lncRNA by β-catenin. PMID:26868975
Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. PMID:26749308
MIR retrotransposon sequences provide insulators to the human genome. PMID:26216945
LncRNA HOTAIR: A master regulator of chromatin dynamics and cancer. PMID:26208723
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. PMID:25682068
Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis. PMID:25526687
The common marmoset genome provides insight into primate biology and evolution. PMID:25038751
Regulation of metabolism by long, non-coding RNAs. PMID:24723937
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information. PMID:24608116
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
Tissue-specific differences in the regulation of KIBRA gene expression involve transcription factor TCF7L2 and a complex alternative promoter system. PMID:24072042
PAVIS: a tool for Peak Annotation and Visualization. PMID:24008416
Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. PMID:23248761
Integrating many co-splicing networks to reconstruct splicing regulatory modules. PMID:23046974
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. PMID:22863767
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. PMID:22697243
On the presence and role of human gene-body DNA methylation. PMID:22577155
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. PMID:22362738
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
Tissue-specific prediction of directly regulated genes. PMID:21724591
Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease. PMID:21712996
Integrative analysis of many weighted co-expression networks using tensor computation. PMID:21698123
SNPTransformer: a lightweight toolkit for genome-wide association studies. PMID:21382596
Bacterial artificial chromosomes as analytical basis for gene transcriptional machineries. PMID:21132362
The UCSC Genome Browser database: update 2011. PMID:20959295
Most transcription factor binding sites are in a few mosaic classes of the human genome. PMID:20459624
Genomic screening with RNAi: results and challenges. PMID:20367032
The UCSC Genome Browser. PMID:19957273
ENCODE whole-genome data in the UCSC Genome Browser. PMID:19920125
The UCSC Genome Browser database: update 2010. PMID:19906737
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. PMID:19374775
Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time. PMID:19308935
PcG proteins, DNA methylation, and gene repression by chromatin looping. PMID:19053175
The UCSC Genome Browser Database: 2008 update. PMID:18086701
The genome browser at UCSC for locating genes, and much more! PMID:18058261
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. PMID:18053139
Statistical power of phylo-HMM for evolutionarily conserved element detection. PMID:17919331
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. PMID:17567996
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. PMID:17567995
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. PMID:17498294
Tags:
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More detailed information about this field from each metasource.
cap analysis gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin interaction analysis by paired-end tag sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin binding
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
dna methylation
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
transcript analysis by paired-end tag sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
human genome databases, maps and viewers
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
human orfs
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
cap analysis gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin interaction analysis by paired-end tag sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin binding
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
dna methylation
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
genome annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
rna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
transcript analysis by paired-end tag sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: ENCODE; Encyclopedia of DNA Elements at UCSC; DOI: https://doi.org/10.25504/FAIRsharing.v0hbjs; Last edited: April 26, 2021, 8:18 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
human genome databases, maps and viewers
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
human orfs
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
cap analysis gene expression chromatin interaction analysis by paired-end tag sequencing chromatin binding chromatin immunoprecipitation - dna sequencing dna methylation genome annotation rna sequence transcript analysis by paired-end tag sequencing transcription human and other vertebrate genomes human genome, maps and viewers human orfs
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