GAGE - eg2sym (ID conversion)

Question

[mbk0asis]

Hello.

I'm trying to run the KEGG pathway analysis using "GAGE" and having trouble of running it because ID conversion isn't working for me.

First of all, I'm dealing with "cow" RNA-seq data.

Here's the R code I used...

kg.bta=kegg.gsets("bta")
kegg.gs=kg.bta$kg.sets[kg.bta$sigmet.idx]
kegg.gs.sym <- lapplykegg.gs,eg2sym)
lapply(kegg.gs.sym[1:3],head)

and the results are...

$`bta00970 Aminoacyl-tRNA biosynthesis`
[1] NA NA NA NA NA NA

$`bta02010 ABC transporters`
[1] NA NA NA NA NA NA

$`bta03008 Ribosome biogenesis in eukaryotes`
[1] NA NA NA NA NA NA

I guess the "eg2sym" only works for "human".

I know I could also convert IDs on my RNA-seq data to Entrez, but I experienced a loss of about 5000 genes after conversion. And I'm worrying the loss of genes might distort the results.

So, I wonder if I can use "eg2sym" on cow data, and if not, how I can do it.

Thank you!

Answer 1

[bigmawen]

You used eg2sym function, which only works for human data. Pathview package provides a set of more general gene ID conversion functions, i.e. eg2id, id2eg, geneannot.map etc. these functions work for 19 major research species. For more details:

library(pathview)
?eg2id

The following code would work for you.

kegg.gs.sym <- lapplykegg.gs,function(x){
syms=eg2id(x, org="Bt", category =”symbol”)
return(syms[,2])
})

Result shown:

> lapply(kegg.gs.sym[1:3],head)
$`bta00970 Aminoacyl-tRNA biosynthesis`
[1] "EARS2" "VARS2" "SARS"  "WARS"  "YARS"  "SARS2"

$`bta02010 ABC transporters`
[1] "LOC100296627" "ABCA2"        "ABCC9"        "ABCB4"        "ABCC6"       
[6] "LOC101909228"

$`bta03008 Ribosome biogenesis in eukaryotes`
[1] "RMRP"    "SPATA5"  "RN28S1"  "RN5-8S1" "AK6"     NA

[mbk0asis]

Thank you! It works perfectly.

Answer 2

[Guangchuang Yu]

bitr in clusterProfiler is another choice for you.

> require(org.Bt.eg.db)
> sample_eg = sample(keys(org.Bt.eg.db), 100)
> head(sample_eg)
[1] "104971204" "107131358" "107131847" "788587"    "789592"    "519105"
> require(clusterProfiler)
> eg2sym = bitr(sample_eg, fromType='ENTREZID', toType="SYMBOL", OrgDb=org.Bt.eg.db)
> head(eg2sym)
   ENTREZID       SYMBOL
1 104971204 LOC104971204
2 107131358 LOC107131358
3 107131847 LOC107131847
4    788587    LOC788587
5    789592    LOC789592
6    519105    LOC519105
> tail(eg2sym)
     ENTREZID       SYMBOL
95  104977419       CALEST
96  104974952 LOC104974952
97  107080383       INSINT
98  100336249 LOC100336249
99     504224  C15H11orf16
100    529919    LOC529919

Answer 3

[EagleEye]

Have you tried GeneSCF.

Here is the example for retrieving sheep and cow KEGG as simple text file,

A: Gene ontology in sheep

For enrichment analysis use,

./geneSCF -m=update -i=INPUTgene.list -t=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=bta --plot=yes --background=#NumberOfBackgroundGenes

For complete information check,

Gene Set Clustering based on Functional annotation (GeneSCF)