ArticleBMC genomics2018
Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundWith the maturity of next generation sequencing technology, a huge amount of epigenomic data have been generated by several large consortia in the last decade. These plenty resources leave us the opportunity about sufficiently utilizing those data to explore biological problems.
resultsHere we developed an integrative and comparative method, CsreHMM, which is based on a hidden Markov model, to systematically reveal cell type-specific regulatory elements (CSREs) along the whole genome, and simultaneously recognize the histone codes (mark combinations) charactering them. This method also reveals the subclasses of CSREs and explicitly label those shared by a few cell types. We applied this method to a data set of 9 cell types and 9 chromatin marks to demonstrate its effectiveness and found that the revealed CSREs relates to different kinds of functional regulatory regions significantly. Their proximal genes have consistent expression and are likely to participate in cell type-specific biological functions.
conclusionsThese results suggest CsreHMM has the potential to help understand cell identity and the diverse mechanisms of gene regulation.
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