Show simple item record

dc.contributor.authorChen, Xien
dc.contributor.authorShi, Xuen
dc.contributor.authorNeuwald, Andrew F.en
dc.contributor.authorHilakivi-Clarke, Leenaen
dc.contributor.authorClarke, Roberten
dc.contributor.authorXuan, Jianhuaen
dc.date.accessioned2021-04-19T11:41:53Zen
dc.date.available2021-04-19T11:41:53Zen
dc.date.issued2021-04-15en
dc.identifier.citationBMC Bioinformatics. 2021 Apr 15;22(1):193en
dc.identifier.urihttp://hdl.handle.net/10919/103056en
dc.description.abstractBackground ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs. Results ChIP-BIT2 ( http://sourceforge.net/projects/chipbitc/) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability. Conclusion ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.en
dc.format.mimetypeapplication/pdfen
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approachen
dc.typeArticle - Refereeden
dc.date.updated2021-04-18T03:13:51Zen
dc.rights.holderThe Author(s)en
dc.contributor.departmentElectrical and Computer Engineeringen
dc.title.serialBMC Bioinformaticsen
dc.identifier.doihttps://doi.org/10.1186/s12859-021-04108-5en
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International