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Database Commons - NCBI Epigenomics

NCBI Epigenomics

Citations: 51

z-index 1.46

Short name NCBI Epigenomics
Full name NCBI Epigenomics
Description Explore,view,and download genome-wide maps of DNA and histone modifications from our diverse collection of epigenomic data sets
URL http://www.ncbi.nlm.nih.gov/epigenomics
Year founded 2010
Last update & version 2012-11-26    
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address 45 Center Drive,Bethesda,MD 20892,USA
City Bethesda
Province/State MD
Country/Region United States
Contact name Ian M. Fingerman
Contact email fingerma@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • DNA and histone modification
  • epigenomics
Publication(s)
  • NCBI Epigenomics: what's new for 2013. [PMID: 23193265]

    Ian M Fingerman, Xuan Zhang, Walter Ratzat, Nora Husain, Robert F Cohen, Gregory D Schuler
    Nucleic acids research 2013:41(Database issue)
    12 Citations (Google Scholar as of 2016-05-08)

    Abstract: The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.

  • NCBI Epigenomics: a new public resource for exploring epigenomic data sets. [PMID: 21075792]

    Ian M Fingerman, Lee McDaniel, Xuan Zhang, Walter Ratzat, Tarek Hassan, Zhifang Jiang, Robert F Cohen, Gregory D Schuler
    Nucleic acids research 2011:39(Database issue)
    39 Citations (Google Scholar as of 2016-05-08)

    Abstract: The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.

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Tags

DNA Phenotype Protein
Arabidopsis thaliana Caenorhabditis elegans Drosophila melanogaster Homo sapiens Mus musculus
DNA and histone modification epigenomics

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-04-11]
    • Lin Liu [2016-03-27]
    • Li Yang [2015-11-24]
    • Zhang Zhang [2015-06-27]
    • Li Yang [2015-06-26]
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