GO enrichment analysis with clusterProfiler

Question

[el97004]

Hi!

I'm trying to use the enrichGO function in the clusterProfiler package to get significant GO categories for a list of genes from my fungi species. One of the things the function needs is an "OrgDb". When I go to the list of OrgDbs here, I cannot find anything for fungi. Anyone know what I can use for this?

thank you.

Answer 1

[cfos4698]

If user have GO annotation data (in data.frame format with first column of gene ID and second column of GO ID), they can use enricher() and gseGO() functions to perform over-representation test and gene set enrichment analysis.

https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html#clusterProfiler-go-supported-organisms

So, for your case, use the enricher() function rather than enrichGO. You will need to get two data frames ready with annotation information:

• TERM2GENE: user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene

• TERM2NAME: user input of TERM TO NAME mapping, a data.frame of 2 column with term and name

https://rdrr.io/bioc/clusterProfiler/man/enricher.html

[el97004]

Hi, thanks for your suggestion. I don’t currently have GO annotations though, just a list of genes. Is there a way to directly run gene set enrichment analysis on non supported organisms?

[cfos4698]

If you organism isn't in the list of supported organisms, you can't directly use just a gene list. The program would normally internally map gene IDs to GO annotations based on annotation databases for supported organisms, but this can't be done in your case. You'll need to somehow get some form of GO annotations by homology comparisons with as closely related organisms as possible. Consider using something like Trinotate: https://github.com/Trinotate/Trinotate.github.io/wiki

[el97004]

Got it. I will check Trinotate out, thanks for the suggestion!