Evaluate Cluster with GO Terms enrichment

Question

[Benni]

I clustered proteins (and their corresponding genes) from an Matrix with Protein expression changes in different experimental settings from E.Coli. Proteins, that correspond in their expression changes should be together in a cluster.

I want to evaluate the clusters/gen lists using a functional enrichment analysis / GO analysis / Pathway analysis / KEGG and so on.... So I enter my gen list, all genes detected in the experiment and a GO-Term list or another functional list. The result would be a score, which category is enriched in the set. (Which would give a hint about the cluster quality)

DAVID has all the function I need, but I read, that it is no longer up to date. Also I want to check many sets in an automated way. And I want to be able to plot my results. So I think an Python or R implementation would be better (I prefer Python). Is there maybe a module, that can do the same analysis as DAVID?

[Khader Shameer]

DAVID is back and uptodate with 2016 annotations DAVID 6.8 (current beta release) May. 2016

See: https://david.ncifcrf.gov/content.jsp?file=release.html

Answer 1

[Guangchuang Yu]

maybe clusterProfiler.

Answer 2

[EagleEye]

There is Perl implementation, GeneSCF (linux-based tool). It uses KEGG and Gene Ontology directly from the source database in real-time while performing enrichment analysis. You can also perform enrichment analysis on multiple gene lists simultaneously.

Gene Set Clustering based on Functional annotation (GeneSCF)

More discussions about GeneSCF on biostars