Question: Cluster of genes - cellular pathways
0
gravatar for Kizuna
4.4 years ago by
Kizuna760
France, Paris
Kizuna760 wrote:

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  

microarray rna R gene • 1.6k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Kizuna760
2
gravatar for EagleEye
4.4 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

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/

ADD COMMENTlink modified 2.9 years ago • written 4.4 years ago by EagleEye6.2k

Thank you  Santhilal Subhash !

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

Kiz

 

ADD REPLYlink written 4.4 years ago by Kizuna760
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1091 users visited in the last hour