ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach
| dc.contributor.author | Chen, Xi | en |
| dc.contributor.author | Shi, Xu | en |
| dc.contributor.author | Neuwald, Andrew F. | en |
| dc.contributor.author | Hilakivi-Clarke, Leena | en |
| dc.contributor.author | Clarke, Robert | en |
| dc.contributor.author | Xuan, Jianhua | en |
| dc.contributor.department | Electrical and Computer Engineering | en |
| dc.date.accessioned | 2021-04-19T11:41:53Z | en |
| dc.date.available | 2021-04-19T11:41:53Z | en |
| dc.date.issued | 2021-04-15 | en |
| dc.date.updated | 2021-04-18T03:13:51Z | en |
| dc.description.abstract | Background 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.description.version | Published version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.citation | BMC Bioinformatics. 2021 Apr 15;22(1):193 | en |
| dc.identifier.doi | https://doi.org/10.1186/s12859-021-04108-5 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/103056 | en |
| dc.language.iso | en | en |
| dc.rights | Creative Commons Attribution 4.0 International | en |
| dc.rights.holder | The Author(s) | en |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en |
| dc.title | ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach | en |
| dc.title.serial | BMC Bioinformatics | en |
| dc.type | Article - Refereed | en |
| dc.type.dcmitype | Text | en |
| dc.type.dcmitype | StillImage | en |