Question: Output from KEGG pathway analysis: multiple genes correspond to the same enzyme
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gravatar for abbeysj20
8 weeks ago by
abbeysj200
abbeysj200 wrote:

Hello,

I am performing a transcriptomic analysis between control and treatment group. Using BLAST2GO, I have downloaded all KEGG pathways that my DE genes are involved in. However, I have multiple genes that then correspond to the same enzyme. For example, I have 10 different genes that all have ATPase activity within the purine metabolism pathway. Some of these genes are upregulated in my treatment group and some are downregulated, so I'm not sure how this then affects the overall enzymatic activity within the pathway. Does anyone have experience with this issue? I do not have access to expensive pathway analysis software such as IPA.

Thanks in advance for any advice!

enzyme rna-seq kegg pathway • 159 views
ADD COMMENTlink modified 12 days ago by Biostar ♦♦ 20 • written 8 weeks ago by abbeysj200
2

I am assuming you're actually interested in doing some sort of enrichment analysis, i.e. whether your DE genes are enriched for certain types of pathway. There are many solutions out there (BLAST2GO not necessarily being one of them), such as GSEA or Enrichr. A starting point to familiarize yourself with some of the concepts could be these papers: Mathur 2018, Chen 2013, Hung2012.

ADD REPLYlink written 8 weeks ago by Friederike3.6k
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