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ErmineJ is a handy, easy to use tool designed to help you perform analysis of gene sets in expression micro-array data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background.ErmineJ main features:Implementation of multiple methods for gene set analysis:Over-representation analysisA resampling-based method that uses gene scoresA rank-based method that uses gene scoresA resampling-based method that uses correlation between gene expression profiles (a type of "cluster-enrichment" analysis).Gene sets receive statistical scores (p-values), and multiple test correction is supported.Support of the Gene Ontology terminology; users can choose which aspects to analyze.User files use simple text formats.Users can modify gene sets or create new ones.The results can be visualized within the software.It is simple to compare multiple analyses of the same data set with different settings.User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results.For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code
