3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process

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• 作者：Mohamed Nadhir Djekidel ; Zhengyu Liang ; Qi Wang ; Zhirui Hu ; Guipeng Li…
• 关键词：ChIA ; PET ; Chromatin interactions ; Co ; factors ; Hierarchical Dirichlet process
• 刊名：Genome Biology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：2,029 KB
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
• 出版者：BioMed Central
• ISSN：1465-6906

文摘

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.