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Old 11-14-2017, 05:42 AM   #1
BioLion
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Location: France

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

Hello,
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.

Code:
head(foldchanges)
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:

Code:
kegg.ath=kegg.gsets("ath",id.type="entrez")
kegg.ath.sigmet=kegg.ath$kg.sets[kegg.ath$sigmet.idx]
keggres=gage(foldchanges, gsets=kegg.ath.sigmet, same.dir=TRUE)
But I get this kind of results:

$greater
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…
Code:
data(kegg.sets.hs)
data(sigmet.idx.hs)
kegg.sets.hs=kegg.sets.hs[sigmet.idx.hs]
keggres=gage(foldchanges, gsets=kegg.sets.hs, same.dir=TRUE)
$greater
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
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enrichment analysis, gage, kegg, rna-seq

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