Transcriptome analysis and other high-throughput analyses of gene expression and proteomics technologies typically yield large lists of differentially expressed genes or proteins. These lists remain impenetrable without a second tier of analysis that subdivides them into functional categories ready for interpretation. Several methods have been developed to do this, the most widely used of which is Gene Set Analysis (GSA) [1
]. In GSA, the list of differentially expressed genes, called the test list, is compared to gene sets, which are lists of genes that have been classified into categories and deposited into accessible databases. Gene sets which are significantly over- or under-represented by genes in the test list are reported, with relevant statistical significance. This gives the researcher a starting point for functional genomics analysis and a more in-depth look at the gene expression profiles of the experiment.
The GSA approach was first applied to gene sets created from Gene Ontology (GO) classifications and was implemented in a large number of tools [3
]. Recently the approach was extended to include other gene sets such as KEGG pathways, chromosomal locations, cis-regulatory elements, and indeed any gene set category relevant to the experiment at hand. It is beyond the scope of this paper to list all the tools that have been developed in recent years for comparing test lists against gene sets, it suffices to state that 68 were recently reviewed [4
], and that the most commonly used of these tools are DAVID [5
] and GSEA [7
]. This paper is to introduce the GenSensor Suite as a customizable, user-friendly tool with additional functionalities not often found in a standard GSA tool.
From the point of view of a wet-lab researcher, the number one priority is to obtain an accurate answer as quickly as possible from a freely available tool that is ultra-user-friendly. Ideally this tool would also allow literature searching and pathway analysis. No such tool currently exists, and this was the motivation behind the GenSensor Suite.
Designed specifically for end user biologists, the GenSensor Suite was developed to meet the needs for a statistically valid over-/underrepresentation analysis tool that is easy and quick to use, allows searching of several different gene sets in one standardized format, allows literature searching and investigation of interaction data, and, in particular, allows users to input their own reference data set. The suite is made up of four tools, as detailed below.