GO annotation with entrez gene id for non-model organism
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4.2 years ago
bifStudent • 0

Hi everybody,

I am working on a shiny project which supports users lacking programming skills to perform GO enrichment analysis. Unfortunately I am struggling to enable the user to use entrez gene IDs of a non-model organism (institution is working with plant organisms and also doing microbiome analysis).

My first attempt was to convert IDs to ensembl IDs and get GO terms via biomaRt. But it seems, that resulting table is not complete and there are a lot of ensembl ids with GO terms and without entrez gene ID. I also want to avoid the use of rentrez::entrez_search, because without API-key it takes to long.

Another idea would be to use homolog of model-organism e.g. Arabidopsis thaliana for plants (didn't try that so far) but I hope for a better solution.

Thanks in advance for any help/suggestions!

R GO non-model organism entrez gene id • 1.8k views
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4.2 years ago
ashish ▴ 680

Usually one would BLAST the sequences and then use those results to retrieve GO terms. BLAST2GO uses this approach but the BLAST part of it is very slow and I am not sure if there is a way to access BLAST2GO using R. You can create your own annotation package for any organism using the AnnotationForge package from bioconductor. See James's answer in this thread for an example.

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Thanks a lot for the suggestion of AnnotationForge. It looks like this is the solution to my problem and I am trying to integrate this. It also seems to take a long time, but I guess this is the price for it.

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