Question: focus on specific pathway
0
gravatar for Learner
2.6 years ago by
Learner 110
Learner 110 wrote:

Hello,

I would like to know if there is any way to get a targeted pathway (lets say Receptor tyrosine kinase) then check for a gene list if any is elevated

cancer pathway analysis gene • 1.2k views
ADD COMMENTlink modified 2.6 years ago by EagleEye6.0k • written 2.6 years ago by Learner 110
2
gravatar for EagleEye
2.6 years ago by
EagleEye6.0k
Sweden
EagleEye6.0k wrote:

Do you need the list of genes to a particular pathway ??

If it is so,

In GeneSCF there is command where you can extract all pathways and the corresponding genes list (tab-separated tabular format) using this module,

./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -org=[see,org_codes_help]

The pathways and the genes can be found in the following directory in the tool,

geneSCF-master_xxx/class/lib/db/[org]/

Download GeneSCF from http://genescf.kandurilab.org/

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by EagleEye6.0k

@EagleEye is it possible to get the database in another platform like Mac ?

ADD REPLYlink written 2.6 years ago by Learner 110

Right now GeneSCF does not support platforms other than Linux. But you can still try using unix-like virtual terminals which supports all commands from Linux (Example, mobaxterm, but I am not sure that it will work).

ADD REPLYlink written 2.6 years ago by EagleEye6.0k
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