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 user interface, ErmineJ has a 
command line interface and an application programming interface that can be used 
to automate analyses. The graphical user interface includes tools for creating 
and modifying gene sets, visualizing the Gene Ontology as a table or tree, and 
visualizing gene expression data. ErmineJ comes with a complete user manual, and 
is open-source software licensed under the Gnu Public License.
CONCLUSION: The availability of multiple analysis algorithms, together with a 
rich feature set and simple graphical interface, should make ErmineJ a useful 
addition to the biologist's informatics toolbox. ErmineJ is available from 
http://microarray.cu.genome.org.