ErmineJ is a free program that performs a analysis of gene sets in expression microarray 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.
ErmineJ is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ.
Here are some key features of "ErmineJ":
Implementation of multiple methods for gene set analysis:
· Over-representation analysis
· A resampling-based method that uses gene scores
· A rank-based method that uses gene scores
· A 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
Requirements:
· Java
What's New in This Release: [ read full changelog ]
· Another bug fix for ORA to correct the way duplicates genes are handled.
· Custom creation of gene sets through the GUI accepts lists of probes as well as genes.
· The analysis wizard allows you to preview the gene scores you are loading.
