A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

GWAS analysis of handgrip and lower body strength in older adults in the CHARGE consortium

“…First, we constructed haplotype blocks for GWAS most significant, or lead, SNPs and SNPs in high linkage disequilibrium (LD, r 2 > 0.8) with GWAS lead SNPs. Then, we identified regulatory elements including enhancers and promoters estimated by chromatin states in the haplotype blocks across 98 healthy human tissues/normal cell lines available in the ENCODE Project and the Epigenomics Roadmap Project (Encode and Consortium 2011; Chadwick, 2012). The regulatory elements were annotated by an algorithm named ChromHMM, and data were downloaded from HaploReg3 (Ernst & Kellis, 2012; Ward & Kellis, 2012).…”

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

“…To further characterize the set of high-confidence hypermethylated DMRs, publically available data sets on epigenetic marks in the human embryonic stem cells H1 from the ENCODE project were mined. 23 The correlations between support for hypermethylation and occupancy of H3K4me3, H3K27me3, H3K36me3, Pol2, CTCF and DNaseI hypersensitive sites were assessed (Fig. S9A).…”

Bioinformatic and Genomic Analyses of Cellular Reprogramming and Direct Lineage Conversion

“…Finally, downstream networks as assayed by direct protein/protein interactions could then be identified that coordinately regulate the pluripotent state [48,94]. The Encyclopedia of DNA Elements (ENCODE, http:// www.genome.gov/encode/) project is a multi-center consortium where many epigenetic modification and protein binding sites are mapped across the human genome, including human ES cells, and is a robust dataset for current and future bioinformatic studies of pluripotency [27].…”