ArticleFrontiers in genetics2020
epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A Multilayered Post-Genome-Wide Association Study Analysis Pipeline Defines Functional Variants and Target Genes for Systemic Lupus Erythematosus.Arthritis & rheumatology (Hoboken, N.J.) · 2024Article
- NAT10/ac4C/FOXP1 Promotes Malignant Progression and Facilitates Immunosuppression by Reprogramming Glycolytic Metabolism in Cervical Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Landscape of enhancer disruption and functional screen in melanoma cells.Genome biology · 2023Article
- An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping.Nature communications · 2023Article
- Cogito: automated and generic comparison of annotated genomic intervals.BMC bioinformatics · 2022Article
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- GenomicDistributions: fast analysis of genomic intervals with Bioconductor.BMC genomics · 2022Article
- Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.GigaScience · 2021Article
- Bedshift: perturbation of genomic interval sets.Genome biology · 2021Article
- Recommendations for the FAIRification of genomic track metadata.F1000Research · 2021Article
- The Vital Roles of LINC00662 in Human Cancers.Frontiers in cell and developmental biology · 2021Review
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Authors and funding
4 authors.
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Abstract
High-throughput genome-wide epigenomic assays, such as ChIP-seq, DNase-seq and ATAC-seq, have profiled a huge number of functional elements across numerous human tissues/cell types, which provide an unprecedented opportunity to interpret human genome and disease in context-dependent manner. Colocalization analysis determines whether genomic features are functionally related to a given search and will facilitate identifying the underlying biological functions characterizing intricate relationships with queries for genomic regions. Existing colocalization methods leveraged diverse assumptions and background models to assess the significance of enrichment, however, they only provided limited and predefined sets of epigenomic features. Here, we comprehensively collected and integrated over 44,385 bulk or single-cell epigenomic assays across 53 human tissues/cell types, such as transcription factor binding, histone modification, open chromatin and transcriptional event. By classifying these profiles into hierarchy of tissue/cell type, we developed a web portal, epiCOLOC (http://mulinlab.org/epicoloc or http://mulinlab.tmu.edu.cn/epicoloc), for users to perform context-dependent colocalization analysis in a convenient way.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.