NCBI Epigenomics: what's new for 2013

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.

Figure 1.

Track data in the NCBI Epigenomics resource over time. Holdings have increased by >3-fold in the time period spanning from 2010 to 2012. Currently there are 3708 tracks available.

Figure 2.

Composition of track holdings in the NCBI Epigenomics resource. (A) Percentage of holdings by species. Species include Homo sapiens (H. sapiens), Mus musculus (M. musculus), Arabidopsis thaliana (A. thaliana), Drosophila melanogaster (D. melanogaster) and Caenorhabditis elegans (C. elegans). (B) Percentage of holdings by assay type. Assay types include histone modifications, DNA methylation, chromatin accessibility, various chromatin-associated factors (including RNA polymerase, transcription factors and various histone-modifying enzymes) and small RNA and gene expression.