Abstract B1-28: GEO2Enrichr: A Google Chrome extension to extract gene sets from the Gene Expression Omnibus and analyze these lists for common biological functions
Authors: Gundersen Gregory W. , Jones Matthew R. , Ma'ayan Avi 
Published: May 2016

Background: Identification of differentially expressed genes from gene expression profiling studies is a necessary and important step in the analysis of microarray and RNA-seq data. Such data is deposited into the Gene Expression Omnibus (GEO). However, currently, to extract and analyze differentially expressed genes from GEO requires significant computational expertise.

Methodology: GEO2Enrichr has a front-end browser extension and back-end server application. The back-end is written in Python and uses the Flask framework for the web application server. The server exposes three API endpoints to: (1) query GEO; (2) identify the differentially expressed genes; and (3) query Enrichr. The API endpoints are chained into a useful data pipeline. The front-end is a Google Chrome Extension written in JavaScript and CSS and programmatically inserts HTML elements into the native GEO interface. The Chrome web browser loads the extension whenever the user navigates to an NCBI GEO webpage. GEO2Enrichr unobtrusively inserts itself onto the page as a single button and checkboxes for easy sample selection. The button opens a modal box that allows users to edit their selected data, choose settings for differential expression identification, insert metadata about the experiments, download their resultant gene lists, and submit their gene lists to Enrichr for further analysis. Differential expression analysis has five options: Characteristic Direction1, T-test, limma, SAM, and fold-change. Other options are available to control for the size of the resultant differentially expressed gene lists by setting p-value and FDR cutoffs.

Results: GEO2Enrichr is a Google Chrome Extension and Python-based API that adds functionality to GEO by allowing users to pipe Simple Omnibus Format in Text (SOFT) files to a differential expression analysis tool and then pipe the differentially expressed genes for analysis to Enrichr2, a popular gene list enrichment analysis web application. GEO2Enrichr addresses a need for improved functionality of GEO by embedding new features into the existing GEO pages, allowing researchers to easily select samples and process them for differential expression by various methods and perform enrichment analyses. GEO2Enrichr is free and available for installation at the Chrome Web Store.

Conclusions: GEO2Enrichr can facilitate the more broad reusability of the GEO resource by lowering the point of entry to biologists without computational expertise. The systematic use of GEO2Enrichr can generate a new useful searchable resource. Overall, GEO2Enrichr can lead to improved extraction of knowledge from data3.

[1] http://maayanlab.net/CD

[2] http://amp.pharm.mssm.edu/Enrichr

[3] http://bd2k.nih.gov

Citation Format: Gregory W. Gundersen, Matthew R. Jones, Avi Ma'ayan. GEO2Enrichr: A Google Chrome extension to extract gene sets from the Gene Expression Omnibus and analyze these lists for common biological functions. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-28.