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BART: bioinformatics array research tool.

Maria Luisa Amaral1, Galina A Erikson1, Maxim N Shokhirev2

  • 1The Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA.

BMC Bioinformatics
|August 10, 2018
PubMed
Summary
This summary is machine-generated.

The Bioinformatics Array Research Tool (BART) simplifies microarray data analysis from the Gene Expression Omnibus (GEO). This web application automates downloads and analysis, making complex genomic data accessible to scientists without bioinformatics expertise.

Keywords:
Automated analysisDifferential expressionFunctional enrichment analysisGene expression omnibusGraphical user InterfaceMicroarray analysisOnline toolR

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Microarray experiments are prevalent in the Gene Expression Omnibus (GEO), constituting over half of all series.
  • Analyzing raw or semi-processed microarray data from GEO is challenging due to a lack of standardization and intuitive tools.
  • Existing methods require manual, error-prone analysis and a bioinformatics background for tasks like clustering, plotting, and differential expression testing.

Purpose of the Study:

  • To introduce the Bioinformatics Array Research Tool (BART), an R Shiny web application.
  • To automate the download and analysis of microarray data across diverse platforms from GEO.
  • To provide an intuitive interface for scientists lacking bioinformatics expertise.

Main Methods:

  • BART automatically downloads and parses data from GEO.
  • The tool suggests sample groupings for differential expression testing and performs batch effect correction.
  • It generates quality control plots, converts probe IDs, identifies differentially expressed genes, and conducts functional enrichment analysis.

Main Results:

  • BART enables comprehensive analysis of a wider range of GEO microarray datasets.
  • The tool's performance and comprehensiveness were compared favorably against four leading online microarray analysis tools.
  • BART successfully automates complex tasks, including data parsing, differential expression testing, and functional enrichment.

Conclusions:

  • BART empowers scientists without bioinformatics backgrounds to extract knowledge from their own or public microarray data.
  • The tool is more versatile and provides more in-depth analyses than existing microarray analysis solutions.
  • BART is accessible via a web interface (bart.salk.edu) and available for download, including a user tutorial.