title: 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process.
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.
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. nde12@mails.tsinghua.edu.cn.
authors.forename: Mohamed Nadhir
authors.initials: MN
authors.lastname: Djekidel
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. liangzy12@mails.tsinghua.edu.cn.
authors.forename: Zhengyu
authors.initials: Z
authors.lastname: Liang
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. wqwq_945@163.com.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. xyz111131@gmail.com.
authors.forename: Zhirui
authors.initials: Z
authors.lastname: Hu
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. ligp12@mails.tsinghua.edu.cn.
authors.forename: Guipeng
authors.initials: G
authors.lastname: Li
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. yc@tsinghua.edu.cn.
authors.forename: Yang
authors.initials: Y
authors.lastname: Chen
authors.affiliation: MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. michaelzhang@tsinghua.edu.cn.|Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas, Dallas, 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA. michaelzhang@tsinghua.edu.cn.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D014157:Transcription Factors