Cluster of genes - cellular pathways

Question

[Kizuna]

Hi all,

I obtained from a BacTRAP experiment a list of genes which are differentially expressed between 2 genotypes (a control and an experimental one) and in 2 tissue preparations. I would like to cluster these genes according to different parameters, to see I can obtain some indication of cellular pathways, functions which might be affected in the experimental group.

The problem does not seem too complicated, but I do not have experience on these kind of things, and I was wondering if you with your background in bioinformatics, you could give me some online tools? any R libraries? or the best way to proceed?

Many thanks in advance

Answer 1

[EagleEye]

If you are new to this start with online tool DAVID, http://david.abcc.ncifcrf.gov

Otherwise if you are familiar with Unix/Linux, I have integrated different available databases like geneontology, KEGG, reactome in commandline tool GeneSCF, Gene Set Clustering based on Functional annotation (GeneSCF)

Please let me know, if you need any help in using GeneSCF.

Note: Rightnow GeneSCF only supports for human genes (gene symbols or Entrez GeneID).

Update GeneSCF v1.1: Support for more organisms and for information please follow http://genescf.kandurilab.org/

[Kizuna]

Thank you Santhilal Subhash!

I will check both softwares and get back to you ..

Kiz