Prioritizing transcriptional factors in gene regulatory networks with PageRank

Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating g...

Descripción completa

Detalles Bibliográficos
Autores principales: Ding, Hongxu, Yang, Ying, Xue, Yuanqing, Seninge, Lucas, Gong, Henry, Safavi, Rojin, Califano, Andrea, Stuart, Joshua M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809505/
https://www.ncbi.nlm.nih.gov/pubmed/33490923
http://dx.doi.org/10.1016/j.isci.2020.102017
_version_ 1783637136403070976
author Ding, Hongxu
Yang, Ying
Xue, Yuanqing
Seninge, Lucas
Gong, Henry
Safavi, Rojin
Califano, Andrea
Stuart, Joshua M.
author_facet Ding, Hongxu
Yang, Ying
Xue, Yuanqing
Seninge, Lucas
Gong, Henry
Safavi, Rojin
Califano, Andrea
Stuart, Joshua M.
author_sort Ding, Hongxu
collection PubMed
description Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating gene regulatory networks reverse engineered from multi-omics profiles, e.g. gene expression, chromatin accessibility, and chromosome conformation assays, using multiplex PageRank.
format Online
Article
Text
id pubmed-7809505
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-78095052021-01-22 Prioritizing transcriptional factors in gene regulatory networks with PageRank Ding, Hongxu Yang, Ying Xue, Yuanqing Seninge, Lucas Gong, Henry Safavi, Rojin Califano, Andrea Stuart, Joshua M. iScience Article Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating gene regulatory networks reverse engineered from multi-omics profiles, e.g. gene expression, chromatin accessibility, and chromosome conformation assays, using multiplex PageRank. Elsevier 2020-12-30 /pmc/articles/PMC7809505/ /pubmed/33490923 http://dx.doi.org/10.1016/j.isci.2020.102017 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Ding, Hongxu
Yang, Ying
Xue, Yuanqing
Seninge, Lucas
Gong, Henry
Safavi, Rojin
Califano, Andrea
Stuart, Joshua M.
Prioritizing transcriptional factors in gene regulatory networks with PageRank
title Prioritizing transcriptional factors in gene regulatory networks with PageRank
title_full Prioritizing transcriptional factors in gene regulatory networks with PageRank
title_fullStr Prioritizing transcriptional factors in gene regulatory networks with PageRank
title_full_unstemmed Prioritizing transcriptional factors in gene regulatory networks with PageRank
title_short Prioritizing transcriptional factors in gene regulatory networks with PageRank
title_sort prioritizing transcriptional factors in gene regulatory networks with pagerank
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809505/
https://www.ncbi.nlm.nih.gov/pubmed/33490923
http://dx.doi.org/10.1016/j.isci.2020.102017
work_keys_str_mv AT dinghongxu prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT yangying prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT xueyuanqing prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT seningelucas prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT gonghenry prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT safavirojin prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT califanoandrea prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank
AT stuartjoshuam prioritizingtranscriptionalfactorsingeneregulatorynetworkswithpagerank

Ejemplares similares