Question: is there anyway to investigate a specific pathway
0
gravatar for Learner
2.4 years ago by
Learner 100
Learner 100 wrote:

Hello,

I would like to know if there is any way that I check for a specific pathway using my gene list ?

I have a list of genes which are unregulated and I only want to check if a specific pathway is activated or not

Thanks

python pathway analysis R gene • 800 views
ADD COMMENTlink modified 24 months ago by Ron820 • written 2.4 years ago by Learner 100

Try http://www.reactome.org/ and "analyze data". If you just want to browse then http://pathwaycommons.org/

ADD REPLYlink written 2.4 years ago by genomax57k

You may find this thread useful! Kegg Pathway Analysis

ADD REPLYlink written 2.4 years ago by reza.jabal280

@reza.jabal DAVID is not the way to go, but thanks

ADD REPLYlink written 2.4 years ago by Learner 100
0
gravatar for EagleEye
2.4 years ago by
EagleEye5.7k
Sweden
EagleEye5.7k wrote:

Gene Set Clustering based on Functional annotation (GeneSCF)

try GeneSCF, simple command line tool accepts gene list and perform enrichment analysis in real-time (directly extract information from selected database). You can also choose between different database GO, KEGG, REACTOME.

http://genescf.kandurilab.org

ADD COMMENTlink modified 24 months ago • written 2.4 years ago by EagleEye5.7k
0
gravatar for Ron
24 months ago by
Ron820
United States
Ron820 wrote:

Use GSEA http://software.broadinstitute.org/gsea/index.jsp I am assuming the pathway and the list of genes is same. It will give enrichment results if your pathway is upregulated or down regulated with p-values. Also you can search for your own pathways,curate your own pathways to look for enrichments in your data.

ADD COMMENTlink written 24 months ago by Ron820
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