GEO2R: a new interactive web-tool for analyzing GEO data

Tuesday, October 09, 2012 — Poster Session I
1:00 p.m. – 3:00 p.m	Natcher Conference Center, Building 45	NLM	BIOINFO-8

Authors

• M Holko
• C Evangelista
• I Kim
• P Ledoux
• H Lee
• K Marshall
• K Phillippy
• N Serova
• P.M. Sherman
• A Soboleva
• M Tomashevsky
• S.E. Wilhite
• A Yefanov
• N Zhang
• T Barrett

Abstract

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the world's largest open repository and distribution hub for functional genomic data generated by microarray and next-generation sequencing technologies. It currently holds over 30,000 studies encompassing three-quarter of a million samples, spanning almost 2,000 organisms, and addressing a huge variety of biological phenomena. To facilitate re-use of these data by the research community, we recently developed GEO2R, an interactive web tool that allows users to compare two or more groups of Samples in a GEO microarray Series in order to identify genes that are differentially expressed across experimental conditions for a wide range of experimental designs and data types. GEO2R utilizes R-based Bioconductor project packages, including GEOquery and limma, and applies multiple-testing corrections on P-values to help correct for the occurrence of false positives. Unlike GEO's other analysis tools, GEO2R does not rely on curated DataSets and interrogates the original Series Matrix data file directly. Thus, GEO2R allows a greater proportion of data to be analyzed in a timely manner, and further promotes accessibility and discovery using public GEO data. GEO2R is available at http://www.ncbi.nlm.nih.gov/geo/geo2r/.

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