New GeneMANIA data release.

[Gary Bader]

Hello,

We are pleased to announce a new GeneMANIA data release. The major changes are:

1. We have added iRefIndex as a replacement to Pathway Commons data source for physical interactions. This solves an issue where some protein interactions derived from large-scale proteomics studies were too highly connected to each other. iRefIndex compiles physical interactions from the same sources as Pathway Commons (and more). However, some of the interaction numbers may change slightly compared to our previous version of GeneMANIA due to differences in data processing between data sources. Pathway Commons is still used for Pathway information from Reactome, NCI/Nature PID, HumanCyc, IMID and the MSKCC Cancer Cell Map.

2. We have updated our databases to the following versions:
GEO: December 10, 2011
PathwayCommons: October 26, 2011
iRefIndex release 8.0

3. More gene names are recognized after an update to the Ensembl database we use (version 62, 60 for Ensembl Plants), including Oct4 and TNF.

4. We have changed the way we infer co-expression interactions. Now we require every inferred co-expression interaction to be supported by co-expression in another dataset or another source of interaction data. This change greatly reduces the number of interactions in our database but does not impact the precision of our gene function predictions.

Thanks for using GeneMANIA!

The GeneMANIA team

[Jason Montojo]

Hi folks,

This data release is now available for the GeneMANIA Cytoscape plugin.  You can select either "Choose Another Data Set" or "Check for Data Updates" from the menu to install it.  Command line users can do the same through the Data Admin tool.

Thanks,

Jason

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