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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8479658 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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