Question: Getting a list of up and down regulated genes in a pathway
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gravatar for F
17 days ago by
F3.4k
Iran
F3.4k wrote:

Hi

I need a list of up and down regulated genes in EGFR pathway

In googling I found 2 things one is not downloadable one is not with gene symbol

https://www.jneurosci.org/content/jneuro/suppl/2006/07/12/26.28.7532.DC1/liu-Table_S3.pdf

http://amp.pharm.mssm.edu/Harmonizome/gene_set/EGF$slash$EGFR+Signaling+Pathway(Homo+sapiens)/Wikipathways+Pathways

any suggestion please?

pathway gene • 116 views
ADD COMMENTlink modified 17 days ago by Gabriel50 • written 17 days ago by F3.4k
2
gravatar for Gabriel
17 days ago by
Gabriel50
Paris
Gabriel50 wrote:

Download the WIKIPATHWAYS gmt files, load them into R, then select the genes from said pathway, and find the differentially expressed genes from said gene vector

ADD COMMENTlink written 17 days ago by Gabriel50

Sorry in wp2gene I found 164 genes for EGFR signaling pathway but in REACTOME I found 3000 genes, how is it possible?

https://reactome.org/PathwayBrowser/#/R-HSA-177929&DTAB=MT

ADD REPLYlink written 17 days ago by F3.4k

What? In the link you sent it says there are 50 proteins in the geneset

ADD REPLYlink written 17 days ago by Gabriel50

Sorry you know how from a list of genes in a pathway which one is activator and which one is inhibitor?

ADD REPLYlink written 16 days ago by F3.4k
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