Question: Evaluate Cluster with GO Terms enrichment
gravatar for Benni
2.9 years ago by
Benni30 wrote:

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?

ontology go cluster • 1.5k views
ADD COMMENTlink modified 2.9 years ago by EagleEye6.4k • written 2.9 years ago by Benni30

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


ADD REPLYlink written 2.9 years ago by Khader Shameer18k
gravatar for Guangchuang Yu
2.9 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

maybe clusterProfiler.

ADD COMMENTlink written 2.9 years ago by Guangchuang Yu2.2k
gravatar for EagleEye
2.9 years ago by
EagleEye6.4k wrote:

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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by EagleEye6.4k
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