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BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data

SUMMARY: Identification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present...

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Detalles Bibliográficos
Autores principales: Wang, Zhenjia, Zhang, Yifan, Zang, Chongzhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479658/
https://www.ncbi.nlm.nih.gov/pubmed/33720325
http://dx.doi.org/10.1093/bioinformatics/btab173
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author Wang, Zhenjia
Zhang, Yifan
Zang, Chongzhi
author_facet Wang, Zhenjia
Zhang, Yifan
Zang, Chongzhi
author_sort Wang, Zhenjia
collection PubMed
description SUMMARY: Identification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present BART3D, a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, leveraging public ChIP-seq data for human and mouse. We demonstrate that BART3D can detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation. BART3D can be a useful tool in 3D genome data analysis and functional genomics research. AVAILABILITY AND IMPLEMENTATION: BART3D is implemented in Python and the source code is available at https://github.com/zanglab/bart3d. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-84796582021-09-30 BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data Wang, Zhenjia Zhang, Yifan Zang, Chongzhi Bioinformatics Applications Notes SUMMARY: Identification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present BART3D, a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, leveraging public ChIP-seq data for human and mouse. We demonstrate that BART3D can detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation. BART3D can be a useful tool in 3D genome data analysis and functional genomics research. AVAILABILITY AND IMPLEMENTATION: BART3D is implemented in Python and the source code is available at https://github.com/zanglab/bart3d. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-03-15 /pmc/articles/PMC8479658/ /pubmed/33720325 http://dx.doi.org/10.1093/bioinformatics/btab173 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Wang, Zhenjia
Zhang, Yifan
Zang, Chongzhi
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title_full BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title_fullStr BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title_full_unstemmed BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title_short BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
title_sort bart3d: inferring transcriptional regulators associated with differential chromatin interactions from hi-c data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479658/
https://www.ncbi.nlm.nih.gov/pubmed/33720325
http://dx.doi.org/10.1093/bioinformatics/btab173
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AT zangchongzhi bart3dinferringtranscriptionalregulatorsassociatedwithdifferentialchromatininteractionsfromhicdata