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 mainta...

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Detalles Bibliográficos
Autores principales: Djekidel, Mohamed Nadhir, Liang, Zhengyu, Wang, Qi, Hu, Zhirui, Li, Guipeng, Chen, Yang, Zhang, Michael Q.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716632/
https://www.ncbi.nlm.nih.gov/pubmed/26694485
http://dx.doi.org/10.1186/s13059-015-0851-6
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author Djekidel, Mohamed Nadhir
Liang, Zhengyu
Wang, Qi
Hu, Zhirui
Li, Guipeng
Chen, Yang
Zhang, Michael Q.
author_facet Djekidel, Mohamed Nadhir
Liang, Zhengyu
Wang, Qi
Hu, Zhirui
Li, Guipeng
Chen, Yang
Zhang, Michael Q.
author_sort Djekidel, Mohamed Nadhir
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0851-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-47166322016-01-19 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process Djekidel, Mohamed Nadhir Liang, Zhengyu Wang, Qi Hu, Zhirui Li, Guipeng Chen, Yang Zhang, Michael Q. Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0851-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-22 /pmc/articles/PMC4716632/ /pubmed/26694485 http://dx.doi.org/10.1186/s13059-015-0851-6 Text en © Djekidel et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Djekidel, Mohamed Nadhir
Liang, Zhengyu
Wang, Qi
Hu, Zhirui
Li, Guipeng
Chen, Yang
Zhang, Michael Q.
3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title_full 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title_fullStr 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title_full_unstemmed 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title_short 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
title_sort 3cpet: finding co-factor complexes from chia-pet data using a hierarchical dirichlet process
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716632/
https://www.ncbi.nlm.nih.gov/pubmed/26694485
http://dx.doi.org/10.1186/s13059-015-0851-6
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