ENCODE whole-genome data in the UCSC Genome Browser: update 2012

Abstract

The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets.

Figure 1.

ENCODE data displayed in the UCSC Genome Browser together with two annotations from the Roadmap Epigenomics Release III data hub. The genomic region contains two protein coding genes, plasma membrane calcium ATPase 4a (ATP2B4) and lymphocyte transmembrane adaptor 1 isoform a (LAX1). The GENCODE Genes track shows multiple variant transcripts for both genes as well as a snoRNA in the region. The Epigenomics Roadmap tracks just below the GENCODE track show H3K4me3, a histone mark associated with promoters, in two cell lines not assayed by the ENCODE project. These tracks show support for the short, non-coding form of LAX1 in mesenchymal stem cells, and support for the longer isoform in CD34 cells, based on peaks at likely promoter regions. The next three tracks are transparent overlays from seven cell lines assayed by the ENCODE project showing the H3K4me3 mark again, the H3K27Ac mark associated with active regulatory regions, and a log plot of transcription levels in the same cell lines. The histone marks and pattern of transcription show coordinated, cell-type-specific activity; the ATP2B4 gene is most active in NHEK (purple) and K562 (blue) cells, while LAX1 is most active in GM12878 (orange) cells. The DNAse and Transcription Factor ChIP-seq clusters shown in the last two tracks summarize data from a much wider range of cell lines and indicate a large number of regulatory regions. Additional details for these annotations are available on click-through.

Figure 2.

Data matrix display and selection of files for download. This feature will be linked to the ENCODE portal, and will navigate to the Advanced Search features of File and Track Search.