Version 3.0

Version 3.0 –  (June 2013) Many major and minor new features, numerous bug fixes, and major code rewrites.

Note that this version of ErmineJ is not completely backwards-compatible with previous versions. Your old results files may not load properly, and old settings ( may not be read in completely. Also not that version 3.x files will not work with version 2.x.

  • Application package for Mac OSX
  • New feature: Overhaul of management of user-defined (non-GO) gene groups. This simplifies the use of schemes such as KEGG. See the help pages for more information. We removed some rarely used (and confusing) features such as the ability to redefine GO groups.
  • New feature: Introduction of “gene multifunctionality” features, a unique new feature of ErmineJ. See the documentation for details.
  • New feature: Introduction of a new gene set scoring method based on precision-recall.
  • New feature: Allow the creation of “projects” that store information on the annotations that were used as well as the data and analysis results (in addition to the existing “save/load results”). This means it is now possible to switch the annotation file without restarting ErmineJ.
  • New feature: ‘Quick list’ makes it easy to test over-representation in a list of genes. See the documentation for details.
  • The search utilities have been fixed and streamlined.
  • Algorithm clarification: Gene that are not in any group are removed from analysis. This should help ameliorate the effects of multifunctionality, since genes that are completely unannotated are less likely to be “discovered” in a assay, and don’t contribute to the analysis in any positive way. This affects the computation of null distributions.
  • Tree view enhancements: You can now hide nodes in the GO hierarchy based on significance, making it easier to browser your results. See the documentation for details. You can also hide terms that are empty.
  • Algorithm improvement: In previous versions of ErmineJ, groups that were completely redundant with others (containing the same genes) were identified but not handled particularly well. Now redundant groups are exhaustively identified. While these groups are included in the analysis (to avoid confusion and other problems), they are considered as one in multiple testing correction.
  • Table view enhancements: You can hide rows in the table to remove clutter due to empty gene sets.
  • Improvement: A major cleanup of the way ErmineJ handles gene annotations. A number of lurking problems were flushed out. Perhaps the most serious was that it is not clear whether redundant gene sets were being excluded from analyses (as they should). It is now much easier to find out how many gene sets there are, how many have genes, and how many are redundant.
  • Output file format changes: The output is more informative so settings which were not used are not listed. The output also now includes additional columns on multifunctionality.
  • Bug fix: Error handling is improved, so mysterious stoppages of analyses should be easier to diagnose.
  • Bug fix: Command line tool didn’t correctly deal with correlation method when no score file was supplied.
  • Bug fix: Command line tool assumed gene scores were p-value like when validating the “threshold” option.
  • Bug fix: Replacing gene URL patterns in Gene Set Details was broken.
  • Bug fix: Switching gene score files was probably broken.
  • Bug fix: “Obsolete” GO terms no longer displayed in tree or table.
  • Bug fix: Affymetrix CSV files work again (NetAffx format changed)
  • Bug fix: Webstart startup dialog was not working consistently. This was fixed for good by making the startup dialog part of the main application window.
  • Bug fix: Problems with hangs and (related to this) missing log files should be fixed for Windows users.
  • Bug fix: MacOSX and Linux graphical interface problems have been ameliorated.
  • Numerous documentation updates. Added documentation of how to deal with “down-regulated” vs. “up-regulated” genes ( FAQ). There are quite a few updates to the manual.
  • (Behind the scenes) Large parts of ErmineJ’s code has been rewritten to improve future maintainability and modularity. A wide range of other minor bugs have been fixed.