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TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles

BACKGROUND: Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of ce...

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Autores principales: Patil, Ashwini, Nakai, Kenta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290689/
https://www.ncbi.nlm.nih.gov/pubmed/25522063
http://dx.doi.org/10.1186/1752-0509-8-S4-S2
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author Patil, Ashwini
Nakai, Kenta
author_facet Patil, Ashwini
Nakai, Kenta
author_sort Patil, Ashwini
collection PubMed
description BACKGROUND: Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. RESULTS: We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks in the mouse innate immune response and the yeast osmotic stress response. Compared to other similar methods, TimeXNet identified up to 50% more novel regulators from independent experimental datasets. It predicted paths within a greater number of known pathways with longer overlaps (up to 7 consecutive edges) within these pathways. TimeXNet was also shown to be robust in the presence of varying amounts of noise in the molecular interaction network. CONCLUSIONS: TimeXNet is a reliable tool that can be used to study cellular response to stimuli through the identification of time-dependent active gene sub-networks in diverse biological systems. It is significantly better than other similar tools. TimeXNet is implemented in Java as a stand-alone application and supported on Linux, MS Windows and Macintosh. The output of TimeXNet can be directly viewed in Cytoscape. TimeXNet is freely available for non-commercial users.
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spelling pubmed-42906892015-01-15 TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles Patil, Ashwini Nakai, Kenta BMC Syst Biol Research BACKGROUND: Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. RESULTS: We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks in the mouse innate immune response and the yeast osmotic stress response. Compared to other similar methods, TimeXNet identified up to 50% more novel regulators from independent experimental datasets. It predicted paths within a greater number of known pathways with longer overlaps (up to 7 consecutive edges) within these pathways. TimeXNet was also shown to be robust in the presence of varying amounts of noise in the molecular interaction network. CONCLUSIONS: TimeXNet is a reliable tool that can be used to study cellular response to stimuli through the identification of time-dependent active gene sub-networks in diverse biological systems. It is significantly better than other similar tools. TimeXNet is implemented in Java as a stand-alone application and supported on Linux, MS Windows and Macintosh. The output of TimeXNet can be directly viewed in Cytoscape. TimeXNet is freely available for non-commercial users. BioMed Central 2014-12-08 /pmc/articles/PMC4290689/ /pubmed/25522063 http://dx.doi.org/10.1186/1752-0509-8-S4-S2 Text en Copyright © 2014 Patil and Nakai; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 Research
Patil, Ashwini
Nakai, Kenta
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title_full TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title_fullStr TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title_full_unstemmed TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title_short TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
title_sort timexnet: identifying active gene sub-networks using time-course gene expression profiles
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290689/
https://www.ncbi.nlm.nih.gov/pubmed/25522063
http://dx.doi.org/10.1186/1752-0509-8-S4-S2
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