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Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways

Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects exp...

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Autores principales: Feng, Chenchen, Zhang, Jian, Li, Xuecang, Ai, Bo, Han, Junwei, Wang, Qiuyu, Wei, Taiming, Xu, Yong, Li, Meng, Li, Shang, Song, Chao, Li, Chunquan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021946/
https://www.ncbi.nlm.nih.gov/pubmed/27625019
http://dx.doi.org/10.1038/srep33262
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author Feng, Chenchen
Zhang, Jian
Li, Xuecang
Ai, Bo
Han, Junwei
Wang, Qiuyu
Wei, Taiming
Xu, Yong
Li, Meng
Li, Shang
Song, Chao
Li, Chunquan
author_facet Feng, Chenchen
Zhang, Jian
Li, Xuecang
Ai, Bo
Han, Junwei
Wang, Qiuyu
Wei, Taiming
Xu, Yong
Li, Meng
Li, Shang
Song, Chao
Li, Chunquan
author_sort Feng, Chenchen
collection PubMed
description Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects expression correlations or topological features embedded in the pathways. In this study, we propose a powerful method, Subpathway-CorSP, for identifying metabolic subpathway regions. This method improved on original pathway identification methods by using a subpathway identification strategy and emphasizing expression correlations between metabolites and genes of interest based on topological features within the metabolic pathways. We analyzed a prostate cancer data set and its metastatic sub-group data set with detailed comparison of Subpathway-CorSP with four traditional pathway identification methods. Subpathway-CorSP was able to identify multiple subpathway regions whose entire corresponding pathways were not detected by traditional pathway identification methods. Further evidences indicated that Subpathway-CorSP provided a robust and efficient way of reliably recalling cancer-related subpathways and locating novel subpathways by the combined effect of metabolites and genes. This was a novel subpathway strategy based on systematically considering expression correlations and topological features between metabolites and genes of interest within given pathways.
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spelling pubmed-50219462016-09-20 Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways Feng, Chenchen Zhang, Jian Li, Xuecang Ai, Bo Han, Junwei Wang, Qiuyu Wei, Taiming Xu, Yong Li, Meng Li, Shang Song, Chao Li, Chunquan Sci Rep Article Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects expression correlations or topological features embedded in the pathways. In this study, we propose a powerful method, Subpathway-CorSP, for identifying metabolic subpathway regions. This method improved on original pathway identification methods by using a subpathway identification strategy and emphasizing expression correlations between metabolites and genes of interest based on topological features within the metabolic pathways. We analyzed a prostate cancer data set and its metastatic sub-group data set with detailed comparison of Subpathway-CorSP with four traditional pathway identification methods. Subpathway-CorSP was able to identify multiple subpathway regions whose entire corresponding pathways were not detected by traditional pathway identification methods. Further evidences indicated that Subpathway-CorSP provided a robust and efficient way of reliably recalling cancer-related subpathways and locating novel subpathways by the combined effect of metabolites and genes. This was a novel subpathway strategy based on systematically considering expression correlations and topological features between metabolites and genes of interest within given pathways. Nature Publishing Group 2016-09-14 /pmc/articles/PMC5021946/ /pubmed/27625019 http://dx.doi.org/10.1038/srep33262 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Feng, Chenchen
Zhang, Jian
Li, Xuecang
Ai, Bo
Han, Junwei
Wang, Qiuyu
Wei, Taiming
Xu, Yong
Li, Meng
Li, Shang
Song, Chao
Li, Chunquan
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title_full Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title_fullStr Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title_full_unstemmed Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title_short Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
title_sort subpathway-corsp: identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021946/
https://www.ncbi.nlm.nih.gov/pubmed/27625019
http://dx.doi.org/10.1038/srep33262
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