EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data

Han Qin Zheng, Nai Yun Wu, Chi Nga Chow, Kuan Chieh Tseng, Chia Hung Chien, Yu Cheng Hung, Guan Zhen Li, Wen Chi Chang

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)371-375
Number of pages5
JournalDNA Research
Volume24
Issue number4
DOIs
Publication statusPublished - 2017 Aug 1

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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