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

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Genome Biol. 2016 Apr 30;17:82


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


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