ErmineJ: Tool for functional analysis of gene expression data sets

Background: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. Results: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical us...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Homin K. Lee, William Braynen, Kiran Keshav, Paul Pavlidis
• Keywords: BMCBI 2005, Gene, Gene Expression, Gene Expression Data