How to do the gene ontology analysis for the list of genes

Question

[luckysardar171]

Hello I have list of ensembl IDs for this list of gene IDs i wanted to the gene ontology analysis. any suggestions for the tools

Thank you

[camillab.]

you can use clusterProfiler package in R gsea clusterprofiler

[luckysardar171]

tried This but we need to give fold chain info that I don't have. only gene IDs I have

[Friederike]

You want to look at Chapter 5 (GO Analysis) of the clusterProfiler book.

This paper by Khatri et al. is a great starting point to understand the differences between enrichment analyses and overrepresentation analyses and the corresponding tools.

EDIT: If you only want to retrieve the GO terms associated with each gene ID (not any type of enrichment/overrepresentation analysis), you can check out the getgo() function from the goseq package.

Answer 1

[lieven.sterck]

If you got those IDs from ensembl it should be possible to also get the orthologs based on those IDs. I look around on the Ensembl portal , especially the compara subsection (https://www.ensembl.org/info/genome/compara/index.html)

EDIT: misread the question, it's not about orthology but about ontology.

[luckysardar171]

I did not get how this relevant to my question?

[lieven.sterck]

well, that you do not need any tools to get the orthologs. You can get the orthologs directly from the ensembl website (given that the species you work with are in ensembl?).

If I misread your question, do correct me.

[luckysardar171]

Yes its mouse ensemble IDs which are not DE genes, for my objective I need the GO info from the list of IDs is it possible get GO info only with IDs

[lieven.sterck]

ok, so I did misread your question somewhat, my bad.

but yes, you can also get the GO info from the ensembl website.

(what do you mean with mouse RNAseq IDs ?)

[luckysardar171]

sorry for typo I have edited. can you provide me the link