ENCODE whole-genome data in the UCSC genome browser (2011 update)

Abstract

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.

Figure 1.

Constitutive and tissue-specific gene regulation under the ENCODE Integrated Regulation tracks. These tracks compare transcription, promoter marks and enhancer marks across the ENCODE Tier 1 and Tier 2 cell lines. Each cell line is rendered in one color, and darker regions indicate signals present in many cell types. ATP2B4 (left) is expressed constitutively, with the strongest expression in NHEK (lilac). Consistent with this, its leftmost promoter appears poised for activity in many tissues (indicated by the black signal in the Promoter H3K4Me3 track). Txn Factor ChIP shows abundant transcription factor binding at the promoter, and Enhancer H3K27Ac and Enhancer H3K4Me1 both show marks suggesting enhancer activity in many cell types. For contrast, LAX1 (right) shows expression only in GM12878 (orange). At the first promoter (shown in the upper isoforms), Promoter H3K4Me3 and Enhancer H3K27Ac show marks only in GM12878. At the second promoter (shown in the bottom isoform), Enhancer H3K27Ac appears active in NHEK (lilac), but Promoter H3K4Me3 does not appear to be active, suggesting that a transcriptional enhancer may be poised for activity but the promoter is not.