3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Djekidel, Mohamed; Liang, Zhengyu; Wang, Qi; Hu, Zhirui; Li, Guipeng; Chen, Yang; Zhang, Michael
• Is Part Of: Genome biology. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 16
• Publication Date: 2015-12
• Subjects: ChIA-PET -- Chromatin interactions -- Co-factors -- Hierarchical Dirichlet process; Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-015-0851-6
• Languages: English
• ISSNs: 1474-760X

Abstract

Abstract Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies. 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interactions. 3CPET results show biologically significant and accurate predictions when validated against experimental and simulation data.