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ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data.

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  • معلومة اضافية
    • المصدر:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
    • بيانات النشر:
      Publication: 1992- : Oxford : Oxford University Press
      Original Publication: London, Information Retrieval ltd.
    • الموضوع:
      Chromatin Immunoprecipitation Sequencing* ; Epigenomics*/methods; Animals ; Humans ; Data Mining ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Models, Animal ; Atlases as Topic ; Databases as Topic
    • نبذة مختصرة :
      ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape. ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein-genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.
      (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
    • الموضوع:
      Date Created: 20220324 Date Completed: 20230410 Latest Revision: 20230412
    • الموضوع:
      20250114
    • الرقم المعرف:
      PMC9252733
    • الرقم المعرف:
      10.1093/nar/gkac199
    • الرقم المعرف:
      35325188