Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Zheng, Han-Qin, Wu, Nai-Yun, Chow, Chi-Nga, Tseng, Kuan-Chieh, Chien, Chia-Hung, Hung, Yu-Cheng, Li, Guan-Zhen, Chang, Wen-Chi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
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
_version_ 1783287507077562368
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
work_keys_str_mv AT zhenghanqin expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT wunaiyun expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT chowchinga expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT tsengkuanchieh expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT chienchiahung expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT hungyucheng expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT liguanzhen expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata
AT changwenchi expathtoolasystemforcomprehensivelyanalyzingregulatorypathwaysandcoexpressionnetworksfromhighthroughputtranscriptomedata