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PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida.

Eugene Koh1, William Goh1, Irene Julca1

  • 1School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.

The Plant Journal : for Cell and Molecular Biology
|December 5, 2023
PubMed
Summary

The Plant Expression Omnibus (PEO) is a powerful web tool for plant biology research, offering gene expression data across thousands of RNA-seq samples for over 100 species. It aids in discovering gene functions and pathways.

Keywords:
RNA-sequencingcoexpressioncomparativedatabasegene familiespathway

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Area of Science:

  • Plant Biology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression analysis is crucial for understanding plant development and function.
  • Access to comprehensive, manually curated expression data across diverse plant species is limited.
  • Existing resources often lack integrated functional annotation and comparative analysis capabilities.

Purpose of the Study:

  • To introduce the Plant Expression Omnibus (PEO), a novel web application for plant gene expression analysis.
  • To provide a centralized resource for exploring gene expression patterns, identifying organ-specific genes, and discovering co-expressed genes.
  • To facilitate kingdom-wide comparative gene expression studies and functional genomics research in plants.

Main Methods:

  • Development of a web application integrating ~60,000 manually annotated RNA-seq samples from over 100 plant species.
  • Implementation of tools for exploring gene expression across organs, identifying co-expressed genes, and retrieving functional annotations.
  • Utilizing curated data to enable comparative analysis and pathway identification.

Main Results:

  • PEO offers access to expression data for over 4 million genes across numerous plant species.
  • Users can identify organ-specific genes and top co-expressed genes for any gene of interest.
  • Functional annotations facilitate the discovery of genetic modules and pathways, demonstrated via case studies in Arabidopsis and Capsicum annuum.

Conclusions:

  • PEO serves as a valuable, freely accessible resource for plant biology research.
  • The tool empowers researchers to conduct in-depth gene expression analysis and functional genomics studies.
  • Case studies highlight PEO's utility in identifying candidate genes for specific biological processes.