focus on specific pathway
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5.1 years ago
Learner ▴ 240

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

pathway analysis gene cancer • 2.1k views
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5.1 years ago
EagleEye 7.0k

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/

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

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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).

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