Question: Getting a list of up and down regulated genes in a pathway
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gravatar for A
9 months ago by
A3.7k
A3.7k 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 • 253 views
ADD COMMENTlink modified 9 months ago by Gabriel60 • written 9 months ago by A3.7k
2
gravatar for Gabriel
9 months ago by
Gabriel60
Paris
Gabriel60 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 9 months ago by Gabriel60

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 9 months ago by A3.7k

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

ADD REPLYlink written 9 months ago by Gabriel60

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

ADD REPLYlink written 9 months ago by A3.7k
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