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
Descripción
Sumario: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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