Question: Appropriate gene IDs for enrichment analysis (with clusterProfiler)
0
gravatar for ayatrience
16 days ago by
ayatrience0
ayatrience0 wrote:

Hi, I am trying to do GO&KEGG enrichment analysis using R package, clusterProfiler. I changed gene IDs (ENSEMBL→uniprot) by "bitr" functions for KEGG enrichment analysis. However, "bitr" returned the multiple IDs from single gene sometimes (I changed into ENTREZ id at the same time). I should pick up one ID from multiple IDs returned from single gene, for enrichment analysis, I thought. So my question is ②How people select the appropriate IDs from multiple returns. I need to do it manually by confirming each returned IDs using uniprot website ? (Ex. judging from the annotation score) but this is so hard working. How everyone deal with this problem ?? (Or we don't need to pick up one from single gene in the first place ...?)

ADD COMMENTlink modified 15 days ago • written 16 days ago by ayatrience0

It seems very nice to pick up one. If I want to refer the uniprot annotation score, we also can write down another script using function in "multiVal". I will follow your script and workflow. Thank you very much !!

ADD REPLYlink written 15 days ago by ayatrience0
2
gravatar for b.d237
15 days ago by
b.d237160
National University of Ireland, Galway
b.d237160 wrote:

Follow the detailed workflow here : https://github.com/twbattaglia/RNAseq-workflow :

# Add ENTREZ ID
results$entrez <- mapIds(x = org.Mm.eg.db,
                     keys = row.names(results),
                     column = "ENTREZID",
                     keytype = "SYMBOL",
                     multiVals = "first")

For starters, don't bother using ENSEMBL to UniProt. In the guide, the user has set

multiVals = "first'

Which means: "This value means that when there are multiple matches only the 1st thing that comes back will be returned. This is the default behavior." I have seen this used quite a lot in workflows, so assumed it is ok. If you want to set it to something else, check out the MultiVals argument here: https://www.rdocumentation.org/packages/AnnotationDbi/versions/1.30.1/topics/AnnotationDb-objects

(EDIT): When you get a handle of that workflow, move to this one: https://yulab-smu.github.io/clusterProfiler-book/chapter12.html

ADD COMMENTlink modified 15 days ago • written 15 days ago by b.d237160

It seems very nice to pick up one. If I want to refer the uniprot annotation score, we also can write down another script using function in "multiVal". I will follow your script and workflow. Thank you very much !!

ADD REPLYlink written 15 days ago by ayatrience0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1443 users visited in the last hour