Enrichment Analysis with KEGG pathways

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Sarah Pohl

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May 26, 2014, 3:28:20 AM5/26/14
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Hello,

I am trying to do an enrichment analysis on my human gene expression data. I have no problems loading my file and I can see the heat map showing the data for all the different genes. When I do the analysis with the human KEGG pathway files I downloaded, though, I can't see anything in the resulting heat map.
The only gene IDs I have are the gene symbols (e.g. ABCD1), could that be a problem?

Best,
Sarah

Michael P Schroeder

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May 26, 2014, 3:57:08 AM5/26/14
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Hi

It doesn't matter which gene id you are using as long you use the same in the data file as well as the mapping file, which would be the gene to kegg pathway mapping. Is that the case?

If not, you can go to the menu Download->Modules->Kegg patwhays and shoose the correct identifier in the Select Identifiers step. I reckon in your case it would be HGNC symbol

Best,
Michael


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Sarah Pohl

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May 26, 2014, 4:08:37 AM5/26/14
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I see, thank you!
I downloaded the pathway two weeks ago when I had the work laptop outside our workplace network, because I can't connect to the server from here. Maybe I chose the wrong identifiers back then.
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