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EXPath 2.0: An Updated Database for Integrating High-Throughput Gene Expression Data with Biological Pathways.

Kuan-Chieh Tseng1, Guan-Zhen Li2, Yu-Cheng Hung2

  • 1Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.

Plant & Cell Physiology
|September 8, 2020
PubMed
Summary
This summary is machine-generated.

EXPath 2.0 enhances plant gene expression analysis by integrating co-expressed genes, metabolic pathways, and regulatory transcription factors (TFs). This updated database aids researchers in understanding plant biological processes and gene regulation.

Keywords:
Comparative gene expression analysisGene regulationMetabolic pathwaysPromoter analysisTranscription factors

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Area of Science:

  • Plant molecular biology
  • Bioinformatics
  • Systems biology

Background:

  • Co-expressed genes often share regulatory relationships and biological functions.
  • Gene correlation networks are valuable for studying transcriptional regulation and metabolic pathways.
  • Identifying regulatory transcription factors (TFs) for co-expressed genes is crucial but often challenging.

Purpose of the Study:

  • To introduce EXPath 2.0, an updated database for investigating regulatory mechanisms in plant metabolic pathways.
  • To provide a comprehensive platform for analyzing gene expression profiles and identifying regulatory TFs.
  • To facilitate research on plant biological processes and gene regulation.

Main Methods:

  • Expanded species coverage to six plants (Arabidopsis, rice, maize, Medicago, soybean, tomato).
  • Incorporated gene expression data across various developmental stages.
  • Enabled construction of gene correlation networks and promoter analysis.
  • Added hierarchical Gene Ontology (GO) term visualization.
  • Allowed user data upload for custom analysis.

Main Results:

  • EXPath 2.0 integrates 1,881 microarray and 978 RNA-seq samples.
  • The database now supports a wider range of plant species and developmental stages.
  • New features facilitate network construction, promoter analysis, and GO term enrichment visualization.
  • Users can upload their own expression data for in-depth analysis.

Conclusions:

  • EXPath 2.0 is a significantly enhanced platform for exploring plant gene expression and metabolic pathways.
  • The database provides powerful tools for identifying regulatory TFs and understanding gene regulatory networks.
  • It serves as a valuable resource for plant biologists studying gene regulation and biological processes.