Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
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ju.ry • 0
@b38c26b5
Last seen 6 weeks ago
Germany

Hey guys,

I'm trying to perform a GO enrichment analysis using clusterProfiler. I've done this before for model organisms like human or A. thaliana for which there are annotation packages available.

Now I'm struggling to do this for tomato, since I can't find a way to translate my gene IDs to ENTREZIDs. I have the gene IDs in the following format: Solyc01g005000.3 (which are ITAG IDs, right?). In AnnotationHub I can't find a package containing the needed keytype and I wasn't able to find a translation table either.

Did somebody face this issue before and found a way to solve this? (I know there are a lot of posts related to this topic but I couldn't find one solving my problem. However, if this has already been answered, please refer me to the post :) )

Thanks a lot for helping!

Regards,

Judith

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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 4 hours ago
Wageningen University, Wageningen, the …

Please note that for clusterProfiler you do NOT necessarily need an OrgDb package, or a mapping to ENTREZIDs. What you obviously do need is a mapping file that connects your gene ID to a GO ID. This mapping file can then be used directly by clusterProfiler. I am not really an expert on tomato, but to me it seems that you may get this mapping info from e.g. Ensembl-Plants, or PLAZA, or... ??? But why not ask the plant biologist you are presumably collaborating with for this info? Finally, I had a similar research question, while having Uniprot IDs. I got clusterProfiler working using the code that I posted here.

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I (and my colleagues) am quite new to Bionconductor and clusterProfiler, so I didn't know that. Thanks for clarifying! I got the GO IDs from Ensembl Plants and, as you said, they worked with clusterProfiler. Thanks a lot!