Journal
GENOME BIOLOGY
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-015-0851-6
Keywords
ChIA-PET; Chromatin interactions; Co-factors; Hierarchical Dirichlet process
Funding
- National Basic Research Program of China [2012CB316503]
- National High Technology Research and Development Program of China [2012AA020401]
- National Nature Science Foundation of China [91019016, 31361163004, 31301044]
- Tsinghua National Laboratory for Information Science and Technology Cross-discipline Foundation
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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.
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