BICORN: An R package for integrative inference of de novo cisregulatory modules

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dc.contributor.authorChen, Xien
dc.contributor.authorGu, Jinghuaen
dc.contributor.authorNeuwald, Andrew F.en
dc.contributor.authorHilakivi-Clarke, Leenaen
dc.contributor.authorClarke, Roberten
dc.contributor.authorXuan, Jianhuaen
dc.contributor.departmentElectrical and Computer Engineeringen
dc.date.accessioned2020-08-06T17:58:58Zen
dc.date.available2020-08-06T17:58:58Zen
dc.date.issued2020-05-14en
dc.description.abstractGenome-wide transcription factor (TF) binding signal analyses reveal co-localization of TF binding sites based on inferred cis-regulatory modules (CRMs). CRMs play a key role in understanding the cooperation of multiple TFs under specific conditions. However, the functions of CRMs and their effects on nearby gene transcription are highly dynamic and context-specific and therefore are challenging to characterize. BICORN (Bayesian Inference of COoperative Regulatory Network) builds a hierarchical Bayesian model and infers context-specific CRMs based on TF-gene binding events and gene expression data for a particular cell type. BICORN automatically searches for a list of candidate CRMs based on the input TF bindings at regulatory regions associated with genes of interest. Applying Gibbs sampling, BICORN iteratively estimates model parameters of CRMs, TF activities, and corresponding regulation on gene transcription, which it models as a sparse network of functional CRMs regulating target genes. The BICORN package is implemented in R (version 3.4 or later) and is publicly available on the CRAN server at https://cran.r-project.org/web/packages/BICORN/index.html.en
dc.format.extent10 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41598-020-63043-2en
dc.identifier.urihttp://hdl.handle.net/10919/99596en
dc.identifier.volume10en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleBICORN: An R package for integrative inference of de novo cisregulatory modulesen
dc.title.serialScientific Reportsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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