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

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

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title 3CPET: Finding Co-Factor Complexes from ChIA-Pet Data Using a Hierarchical Dirichlet Process
contributor.author Djekidel, Mohamed Nadhir
contributor.author Liang, Zhengyu
contributor.author Wang, Qi
contributor.author Hu, Zhirui
contributor.author Li, Guipeng
contributor.author Chen, Yang
contributor.author Zhang, Michael Q. (UT Dallas)
contributor.ISNI 0000 0001 1707 1372 (Zhang, MQ)
description.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.
description.sponsorship 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.
identifier.issn 1465-6906
identifier.uri http://hdl.handle.net/10735.1/4953
identifier.uri http://dx.doi.org/10.1186/s13059-015-0851-6
identifier.bibliographicCitation Djekidel, Mohamed Nadhir, Zhengyu Liang, Qi Wang, Zhirui Hu, et al. 2015. "3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process." Genome Biology 2015(16), doi:10.1186/s13059-015-0851-610.1186/s13059-015-0851-6.
identifier.volume 16
subject Chromatin
subject Breast--Cancer
subject beta-Globins
subject Gene expression
subject Cohesins
subject Biotechnology
subject Genetics
subject Microbiology
date.issued 2015-12-22
publisher BioMed Central Ltd
rights CC BY 4.0 (Attribution) License
rights ©2015 The Authors
rights.uri http://creativecommons.org/licenses/by/4.0/
language.iso en
source.journal Genome Biology

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