Gene Ontology analysis for high-throughput data

Version 2.1.21

Overview

ErmineJ performs analyses 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. The software 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.

A description of ermineJ was published as: Lee H.K., Braynen W., Keshav K. and Pavlidis P. (2005) ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6:269. (Download a PDF or view the abstract).

While ErmineJ has a full user's manual, there is a Nature Protocols paper that contains many additional tips and a detailed walk-through.

ErmineJ can be downloaded here , or run ErmineJ right now using WebStart if you already have Java installed.

Major features include:

• 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

License information - ermineJ is free software.

There are some screen shots available, and more information is available in the manual.

News

Version 2.1.21 - (September 2010)

This release updates our GO parser to correct problems with the "Tree view". Thanks for Makio Tamura for pointing out the problem. Users should make sure they are using a recent "GO XML" file. See this page for details on how to get an updated GO file.

For more information see the full version history

Old news

Documentation

The software comes with on-line help. The manual is also available online (webstart users will have to use this option for now) or as a slightly out-dated PDF. If you are having problems with the software please read the FAQ. If your question isn't answered in the FAQ or in the manual, feel free to contact us

There is also a Nature Protocols paper describing how to use ErmineJ. It is meant to complement the users manual.

For more details about ermineJ and how it is used, see the publications list.

Mailing list

If you use ermineJ, we urge you to subscribe to the ermineJ users mailing list. This serves two purposes. First, it will allow you to automatically receive information on updates to ermineJ. Second, it helps us track how many people use ermineJ. This is especially important when we try to obtain support for ermineJ development.