NCBI Epigenomics: a new public resource for exploring epigenomic data sets

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.

Figure 1.

The Sample Browser interface for navigating samples in the Epigenomics database. Samples can be filtered by free text by using the Term Filter. Additionally, three pre-set attribute filters based on species, cell type, or lab (submitting institution) are available. The samples panel displays samples with detailed biological attributes. This view is customizable and samples can be selected and sorted in this interface. The Sample Browser toolbar displays a series of icons that provide additional functionality for manipulating samples (from left to right): add record to clipboard, add record to a collection, remove record (applies to clipboard and collections), view sample information, view on genome, download track data/export browser data as table, and configure (allows column selection within the Sample Browser window).

Figure 2.

Visualization of epigenetic features in the vicinity of the NANOG gene locus using the NCBI sequence viewer. Epigenomic data tracks can be displayed allowing peaks at specific features to be visualized and compared across different samples. Epigenomic track data are displayed in the middle (blue) tracks. In this example, the track labels indicate we are comparing the epigenetic marks H3K4me3 and H3K27me3 at the NANOG gene locus in both H1 embryonic stem cells (top two tracks) and IMR90 fibroblasts (bottom two tracks). Peaks in the tracks indicate areas of the genome that are enriched for a particular epigenetic feature. The NANOG gene product participates in maintaining stem cell pluripotency. In H1 embryonic stem cells, where the NANOG gene is expressed, the genome tracks show an enrichment of H3K4me3 (a mark associated with actively transcribed genes), and a lack of H3K27me3 (a mark of repressed chromatin). Conversely, in IMR90 fibroblasts the NANOG gene is no longer expressed. In this instance, levels of H3K4me3 are reduced, and there is an enrichment of H3K27me3 at the NANOG locus.