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ExpressionDB: An open source platform for distributing genome-scale datasets.

Laura D Hughes1, Scott A Lewis1, Michael E Hughes1

  • 1Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.

Plos One
|November 3, 2017
PubMed
Summary
This summary is machine-generated.

ExpressionDB is a new, open-source platform that simplifies gene expression data visualization for RNA-sequencing (RNA-seq) and microarrays. It empowers small labs to easily share functional genomics data, overcoming bioinformatics barriers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • RNA-sequencing (RNA-seq) and microarrays are essential for transcriptome-wide gene expression analysis.
  • Advances have made these techniques accessible, yet bioinformatics expertise remains a barrier for many labs.
  • Sharing analyzed functional genomics data is crucial for research reproducibility and community resource building.

Purpose of the Study:

  • To introduce ExpressionDB, an open-source platform designed to facilitate the visualization and sharing of RNA-seq and microarray data.
  • To lower the technical barriers for small laboratories to utilize and share gene expression data.
  • To provide a user-friendly tool for researchers with limited bioinformatics experience.

Main Methods:

  • ExpressionDB is built on Shiny, a web application framework using R for customizable data visualization.
  • The platform supports virtually any number of samples and allows intuitive searching by gene symbols, descriptions, or Gene Ontology (GO) terms.
  • Dynamic filtering based on expression levels, fold change, and false-discovery rates, along with built-in visualizations like heatmaps and principal component analysis, are incorporated.

Main Results:

  • ExpressionDB enables intuitive searching and dynamic filtering of gene expression data.
  • Integrated visualization tools (heatmaps, volcano plots, PCA) ensure consistent data presentation.
  • The platform is open-source, freely available on GitHub, and customizable under a Creative Commons license.
  • A demo database can be created in under an hour with minimal programming experience, and a full database can be deployed online in less than a day.

Conclusions:

  • ExpressionDB effectively addresses the need for accessible gene expression data visualization and sharing.
  • The platform empowers smaller research labs to contribute analyzed functional genomics data to the wider scientific community.
  • ExpressionDB promotes data sharing and reproducibility in genomics research by simplifying complex analyses.