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EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737374/ https://www.ncbi.nlm.nih.gov/pubmed/28338930 http://dx.doi.org/10.1093/dnares/dsx009 |
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author | Zheng, Han-Qin Wu, Nai-Yun Chow, Chi-Nga Tseng, Kuan-Chieh Chien, Chia-Hung Hung, Yu-Cheng Li, Guan-Zhen Chang, Wen-Chi |
author_facet | Zheng, Han-Qin Wu, Nai-Yun Chow, Chi-Nga Tseng, Kuan-Chieh Chien, Chia-Hung Hung, Yu-Cheng Li, Guan-Zhen Chang, Wen-Chi |
author_sort | Zheng, Han-Qin |
collection | PubMed |
description | Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data. EXPath Tool (available at: http://expathtool.itps.ncku.edu.tw/) was developed for the pathway annotation and comparative analysis of user-customized gene expression profiles derived from microarray or NGS platforms under various conditions to infer metabolic pathways for all organisms in the KEGG database. EXPath Tool contains several functions: access the gene expression patterns and the candidates of co-expression genes; dissect differentially expressed genes (DEGs) between two conditions (DEGs search), functional grouping with pathway and GO (Pathway/GO enrichment analysis), and correlation networks (co-expression analysis), and view the expression patterns of genes involved in specific pathways to infer the effects of the treatment. Additionally, the effectively of EXPath Tool has been performed by a case study on IAA-responsive genes. The results demonstrated that critical hub genes under IAA treatment could be efficiently identified. |
format | Online Article Text |
id | pubmed-5737374 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57373742018-01-08 EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data Zheng, Han-Qin Wu, Nai-Yun Chow, Chi-Nga Tseng, Kuan-Chieh Chien, Chia-Hung Hung, Yu-Cheng Li, Guan-Zhen Chang, Wen-Chi DNA Res Full Papers Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data. EXPath Tool (available at: http://expathtool.itps.ncku.edu.tw/) was developed for the pathway annotation and comparative analysis of user-customized gene expression profiles derived from microarray or NGS platforms under various conditions to infer metabolic pathways for all organisms in the KEGG database. EXPath Tool contains several functions: access the gene expression patterns and the candidates of co-expression genes; dissect differentially expressed genes (DEGs) between two conditions (DEGs search), functional grouping with pathway and GO (Pathway/GO enrichment analysis), and correlation networks (co-expression analysis), and view the expression patterns of genes involved in specific pathways to infer the effects of the treatment. Additionally, the effectively of EXPath Tool has been performed by a case study on IAA-responsive genes. The results demonstrated that critical hub genes under IAA treatment could be efficiently identified. Oxford University Press 2017-08 2017-03-13 /pmc/articles/PMC5737374/ /pubmed/28338930 http://dx.doi.org/10.1093/dnares/dsx009 Text en © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Full Papers Zheng, Han-Qin Wu, Nai-Yun Chow, Chi-Nga Tseng, Kuan-Chieh Chien, Chia-Hung Hung, Yu-Cheng Li, Guan-Zhen Chang, Wen-Chi EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title | EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title_full | EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title_fullStr | EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title_full_unstemmed | EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title_short | EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
title_sort | expath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737374/ https://www.ncbi.nlm.nih.gov/pubmed/28338930 http://dx.doi.org/10.1093/dnares/dsx009 |
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