The identification of molecular biomarkers from expression data is a major objective in cancer research. It is clear that there is a benefit in pathway biomarkers (ie. measuring the activity of the pathway instead of individual genes). One easy way to analyze the transcriptional status of pathways (or other gene sets) is using Sample Level Enrichment Analysis (SLEA) in Gitools. This way you can assess the status of each pathway in each sample. This can be used to identify tumor subtypes and to correlate molecular features with clinical features.
As of now you can download the new version of Gitools – version 1.5.10 – which keeps up with the newest changes of the biological databases KEGG and Ensembl.
As some may have read or heard, KEGG has gone through some changes last year and so has the accessibility of its data. This change broke the functionality of the KEGG importer in Gitools. This is now fixed!
Additionally we also made an update for the Ensembl importer and added the new versions in the archive to make sure all data can be comfortably downloaded through Gitools.
That’s it for now, expect more news to come!