3CPET: Finding Co-Factor Complexes from ChIA-Pet Data Using a Hierarchical Dirichlet Process



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.



Chromatin, Breast--Cancer, beta-Globins, Gene expression, Cohesins, Biotechnology, Genetics, Microbiology


This work is supported by the National Basic Research Program of China (2012CB316503), the National High Technology Research and Development Program of China (2012AA020401), the National Nature Science Foundation of China (91019016, 31361163004, and 31301044), and Tsinghua National Laboratory for Information Science and Technology Cross-discipline Foundation.


CC BY 4.0 (Attribution), ©2015 The Authors