Abstract 5292: An online tool for biomarker analysis in Gene Expression Omnibus (GEO) datasets

Abstract

Abstract The Gene Expression Omnibus (GEO) is a public repository of gene expression and sequence-based datasets, that currently includes >42,000 datasets with gene expression profiles obtained by microarray, and >12,000 datasets containing the keyword “cancer”. Although GEO has its own analysis tool (GEO2R) for identifying differentially expressed genes, evaluation of a single gene is not straightforward, and GEO2R was not designed to identify prognostic biomarkers based on survival analyses. In this work, we describe an online, easy-to-use tool for biomarker analysis in GEO datasets. shinyGEO is a web-based tool that allows a user to download the expression and sample data from a GEO dataset, select a gene of interest, and perform a survival or differential expression analysis in order to evaluate gene expression diagnostic or prognostic biomarkers. For both analyses, shinyGEO produces publication-ready graphics and generates R code ensuring that all analyses are reproducible. The tool is developed using shiny, a web application framework for R, a language for statistical computing and graphics. The web application and source code is available at the following link: http://bioinformatics.easternct.edu/shinyGEO/ Citation Format: Jasmine Dumas, Michael Gargano, Garrett M. Dancik. An online tool for biomarker analysis in Gene Expression Omnibus (GEO) datasets. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5292.