ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.

150 150 Penn Lab
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Journal:

Genome Biol. 2016 Apr 30;17:82

Authors:

Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI.

Abstract:

A cell’s epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.

Link: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0925-0