Question: Conversion sheep/mammal ID to human for GSEA
0
gravatar for VHahaut
3.7 years ago by
VHahaut1.1k
Belgium
VHahaut1.1k wrote:

Hello!

I have a list of ENSEMBL gene IDs from sheep and I would like to perform a GSEA analysis on them. From what I understand of GSEA, the easiest (best?) way to perform such analysis in my case is to transform my sheep IDs into orthologous human IDs.

I obtained the right translation using biomaRt but I am not completely satisfied by the result since only ~70% of my genes have an associated human gene ID. Moreover, I saw quite often duplications in the translation and don't know which human ID to choose in those cases:

ENSOARG000000011111 ==> ENSG000001234
ENSOARG000000011111 ==> ENSG000001235
ENSOARG000000011111 ==> ENSG000001236

Question 1: Is converting my sheep IDs like I'm doing the best way to conduct a GSEA analysis? Or can you propose me another method to analysis pathway/GO enrichment in my situation?

Question 2: What is the best way to obtain the most accurate translation of my sheep IDs in order to run a GSEA?

Can a blast analysis of my 400 Ovis Aries genes against a human database solves partially my problem or I should expect that it won't give me more information than the biomaRt query? 

 

Thanks in advance,

 

Radek

 

gsea orthology id • 1.3k views
ADD COMMENTlink modified 3.7 years ago by lelle800 • written 3.7 years ago by VHahaut1.1k
1
gravatar for lelle
3.7 years ago by
lelle800
Berlin
lelle800 wrote:

I don't know if this is the best way, but I would use the Annotation from http://www.ebi.ac.uk/QuickGO/GAnnotation

You can set a filter for the sheep taxon ID and add a Ensembl_GeneID mapping. Than you should get a table you can use.

Make sure to have a look at the Qualifier, Aspect and Evidence columns and set filters according to what you want.

ADD COMMENTlink written 3.7 years ago by lelle800
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