Question: Gostats hypergeometric test for kegg enrichment pathway non model organism
gravatar for claire.morandin
5.4 years ago by
claire.morandin0 wrote:


I would like to run an hypergeometric testing on KEGG terms for non-model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes and it works really well.

However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and as a result I get the following error:
"Loading required package: KEGG.db
Failed with error:  ‘package ‘AnnotationDbi’ 1.24.0 is loaded, but >= 1.25.15 is required by ‘KEGG.db’’
In addition: Warning message:
package ‘KEGG.db’ was built under R version 3.1.0 
Error in .testKEGGFrame(x, organism) : 
 None of elements in the 1st column of your data.frame object are legitimate KEGG IDs."

Does anyone have any recommendations for Kegg enrichment analysis for non-model organism and /or how to do an hypergeometric test with R directly?

Thanks a lot for your help


rna-seq R • 3.9k views
ADD COMMENTlink modified 5.3 years ago by Arjun10 • written 5.4 years ago by claire.morandin0
gravatar for lkmklsmn
5.4 years ago by
United States
lkmklsmn920 wrote:

An intuitive approach to conducting enrichment analysis is done by using a two-by-two table of counts:  

  YESanno NOanno
YESgeneset X1 X2
NOgeneset Y1 Y2

, where X1 is the count of genes in your geneset AND in the annotation class (e.g. Goterm). X2 is the count of genes in your geneset AND NOT in the annotation class. Y1 is the count of genes NOT in your geneset (e.g. universe-geneset= background) AND in the annotation class. Y2 is the count of genes NOT in your geneset AND NOT in your annotation class.  

You can give this table to the R function fisher.test(). 

e.g. fisher.test(matrix(c(X1,X2,Y1,Y2),nrow=2,ncol=2,byrow=T))  

This function will give you the hypergeometric test for a given geneset and given annotation class.

ADD COMMENTlink written 5.4 years ago by lkmklsmn920

I agree with you, however if I want to report only the enriched pathways, with this method how do I know which ones are enriched?

ADD REPLYlink written 5.3 years ago by claire.morandin0

You can come up with you own criteria for enrichment. E.g. p-value < 0.05, odds ratio >1 etc...

ADD REPLYlink written 5.3 years ago by lkmklsmn920
gravatar for Arjun
5.3 years ago by
Ann Arbor, Michigan
Arjun10 wrote:

Hi Claire,


You can use iPathwayGuide for Go analysis as we use KEGG database.  iPathwayGuide is a pathway analysis application based on Impact Analysis approach that considers the role, function, interactions between the genes on each pathway.  As of now, you can work with human data in cuffdiff, DEseq and custom 3-column tab delimited file but in couple of weeks, you will also be able to work with mouse and rat data.  We are rapidly adding features and functionalities to our application and soon the choice of organism will also increase.

Currently iPathwayGuide application is free to use and you can register here.  Please feel free to reach out to me if I could be of further assistance.



Arjun Gupta

arjun (at) advaitacorporation (dot) com


ADD COMMENTlink written 5.3 years ago by Arjun10
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