Question: KEGG enrichment for non-model
1
gravatar for bekah
12 months ago by
bekah20
bekah20 wrote:

Hi,
Not sure if I have mis-understood. It looks like GAGE can be used for non-model organisms using KO?
I have a set of data - gene IDs with associated kegg Ids from using KAAS for my genome.
geneID           keggID
gene30651     K01416 ……...

I used this to match keggIDs with my set of differentially expressed genes I previously identified with their average fold change between control and treatment groups for each gene.
Is it possible to use this list of differentially expressed KEGG Ids to do pathway enrichment using GAGE and KO db?

geneID          keggID     FC
gene40167     k00236    43  …………….

Best wishes,

bekah

ADD COMMENTlink modified 12 months ago by Luo Weijun1.4k • written 12 months ago by bekah20

Have followed this tutorial for anyone else having the same problem:

http://genviz.org/module%204/0004/03/01/pathwayAnalysis/

ADD REPLYlink written 12 months ago by bekah20
Answer: KEGG enrichment for non-model
0
gravatar for Luo Weijun
12 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

GAGE will work with your data if you:

-change the rowname of your data matrix or the names of your data vector to ko gene ID (keggID in your example)

-if the data is fold change already, set both ref and samp to NULL when calling gage function.

-follow/understand the tutorial and package documentation accurately

 

We have developed a web server for user with less programming skills, which can do both pathway/gage analysis and visualization:

https://pathview.uncc.edu/

HTHs,

ADD COMMENTlink written 12 months ago by Luo Weijun1.4k

cheers - I managed to work it out so no need for the web server :) thanks again

ADD REPLYlink written 11 months ago by bekah20

I realised that GAGE is not suitable for my data - as I am using KO so, multiple genes that are similar have been given the same k number which makes assigning the correct LFC difficult. What I was wanting was a software that used enrichment test on keggIDs rather than expression data - so I have used enrichKEGG in ClusterProfiler and then will use pathview to visualise the significantly enriched pathways!

ADD REPLYlink written 11 months ago by bekah20
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