DSGeo: Software tools for cross-platform analysis of gene expression data in GEO

The Gene Expression Omnibus (GEO) is the largest resource of public gene expression data. While GEO enables data browsing, query and retrieval, additional tools can help realize its potential for aggregating and comparing data across multiple studies and platforms. This paper describes DSGeo—a collection of valuable tools that were developed for annotating, aggregating, integrating, and analyzing data deposited in GEO. The core set of tools include a Relational Database, a Data Loader, a Data Browser, and an Expression Combiner and Analyzer.The application enables querying for specific sample characteristics and identifying studies containing samples that match the query. The Expression Combiner application enables normalization and aggregation of data from these samples and returns these data to the user after filtering, according to the user’s preferences. The Expression Analyzer allows simple statistical comparisons between groups of data. This seamless integration makes annotated cross-platform data directly available for analysis.