Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Q:Gage R package: kegg.gsets function algirdas Bioinformatics 3 10-02-2015 05:08 PM
GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14) bigmw Bioinformatics 0 04-18-2014 05:49 PM
Why could I not find "kegg.gsets" function in gage package? wmseq Bioinformatics 7 11-27-2013 02:28 PM
sus scrofa (pig) KEGG pathways: where to find... dietmar13 Bioinformatics 4 11-13-2013 10:55 AM
pathways API KEGG svl Bioinformatics 5 02-10-2011 01:37 PM

Thread Tools
Old 11-14-2017, 04:42 AM   #1
Junior Member
Location: France

Join Date: Apr 2014
Posts: 5
Default GAGE enrichment GO terms, KEGG pathways

I am currently trying to find the enriched pathways following a RNAseq analysis using DESeq2, in a plant species where there is no reference genome. However, it does not work as I expected.

I used the bioconductor package “mygene” in order to get entrez identifiers corresponding to my uniprot identifiers that I had in my genes list. I then constructed my fold changes table using the log2 fold change obtained by using DESeq2, and having for names the entrez identifiers.

111151 6920 100303206 24328 8668 20517
0.5957113 -0.4976848 0.4986454 -0.1833950 -0.3897194 0.5718210

However, then when I use the gage function, I have troubles finding the enriched pathways. My data actually comes from plants, so I thought of using the kegg’s pathways from Arabidopsis thaliana as such:

keggres=gage(foldchanges, gsets=kegg.ath.sigmet, same.dir=TRUE)
But I get this kind of results:

p.geomean stat.mean p.val q.val set.size exp1
ath00970 Aminoacyl-tRNA biosynthesis NA NaN NA NA 0 NA
ath02010 ABC transporters NA NaN NA NA 0 NA

However when I tried by curiosity to use the homo sapiens pathway with the following code, it seems to work better…
keggres=gage(foldchanges, gsets=kegg.sets.hs, same.dir=TRUE)
p.geomean stat.mean p.val q.val set.size exp1
hsa00010 Glycolysis / Gluconeogenesis 0.1426633 1.10118079 0.1426633 0.9257147 10 0.1426633
hsa00240 Pyrimidine metabolism 0.1566751 1.03046501 0.1566751 0.9257147 13 0.1566751

Can someone give me a clue about what is going on?

Best regards,
BioLion is offline   Reply With Quote

enrichment analysis, gage, kegg, rna-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:02 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO