focus on specific pathway

Question

[Learner]

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

Answer 1

[EagleEye]

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/

[Learner]

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

[EagleEye]

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).