If you use ErmineJ in your published work please cite:
- Ballouz S., Pavlidis P., Gillis J. Using predictive specificity to determine when gene set analysis is biologically meaningful (2016) Nucleic Acids Research (full text).
- Gillis J., Mistry M., Pavlidis P. (2010) Gene function analysis in complex data sets using ErmineJ. Nature Protocols 5: 1148 – 1159 (abstract)
- 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).
The original work that led to the development of ermineJ is described here:
- Pavlidis, Lewis and Noble, Proceedings of the Pacific Symposium on Biocomputing 7. pp 474-485, 2002. (pubmed; PDF).
Gene multifunctionality is defined and described in the following paper, which also raises the issue of the potential impact on GO analysis.
- Gillis and Pavlidis (2011) The Impact of Multifunctional Genes on “Guilt by Association” Analysis PLoS ONE 6(2): e17258 (abstract)
Before reporting a problem:
- Check that your input files are in the right format. This is the cause of most problems.
- Please confirm that you are using the latest version of ermineJ. If you found a bug, it might already have been fixed and updated.
- Read the FAQ and the manual, your question may already be addressed.
When writing us with questions about ermineJ, please:
- Most important: include the contents of your ermineJ log file (found using “Help→View log” menu item, or look in your ermineJ.data directory; it’s called erminej.log).
- Specify the version of ermineJ you are using (found using the “Help→About ermineJ” menu item).
- Tell us your operating system and amount of memory (e.g. “Windows 8 with 4Gb RAM”)
- Mention the version of java you are running, if you can figure it out (it’s usually not that important unless the software is not working at all). Under Windows this can usually be found in the Control Panel called “Java” by clicking on “About” in the “General” tab, or by typing
java -versionat a command line. On MacOSX you may find the Java version under System Preferences.
In some situations sending the results of a saved analysis or your input data files will be helpful, but don’t send those items unless we ask for them or your question is about those files in particular.
If you use ermineJ, we urge you to subscribe to the ermineJ announcement 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.
The software was written by Paul Pavlidis, Homin Lee, William Braynen, Kiran Keshav and Kelsey Hamer. Some code is based on an earlier version of the software written by Shahmil Merchant and Edward Chen, based in turn on a Perl implementation by Paul Pavlidis. Gene Ontology information is obtained through the Gene Ontology Consortium. We are grateful for the efforts of curators and ontology developers.
We also thank users who reported bugs, made suggestions, or just wrote to say they like ErmineJ.