ErmineJ: tool for functional analysis of gene expression data sets

Abstract

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.

Figure 1

A: The main panel of ErmineJ after several analyses have been performed. Gene sets selected at low FDR levels are indicated in color. B: The tree-view panel of ErmineJ, illustrating the ability to browse gene sets in the GO hierarchy. The icons at each node have specific meanings. For example, the yellow "bull's-eye" icon indicates a gene sets selected at an FDR of 0.05 or less. Purple diamonds indicate nodes that have "significant" sub-nodes.

Figure 2

A gene set details view. The controls at the top allow adjustment of the size and contrast of the heat map. The gene scores (in this case p-values) are shown in the second text column. The grey and blue graph, shown only for experiments using p-values, shows the expected (grey) and actual (blue) distribution of p-values in the gene set. This display is provided as an additional aid to evaluation of the results. The last two columns provide information about each gene. The targets of the hyperlinks are configurable by the user.

Figure 3

Examples of screens from ErmineJ Wizards. A: Analysis wizard. This illustrates options to set the range of gene set sizes to analyze, and the method of treating "replicates" of genes. See text for details of the latter. B: Gene set modification wizard. In this screen the user is selecting genes to delete from a gene set. The list of all probe available on the platform is available in the left panel. A "find" function simplifies the location of genes and probes.