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BMCBI
2005

ErmineJ: Tool for functional analysis of gene expression data sets

9 years 10 months ago
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...
Homin K. Lee, William Braynen, Kiran Keshav, Paul
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2005
Where BMCBI
Authors Homin K. Lee, William Braynen, Kiran Keshav, Paul Pavlidis
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