GO enrichment of DEGs - DeNovo RNAseq

Question

[Sowmya Pulapet]

Hi,

I did the DeNovo assembly of a few RNAseq samples using Trinity. After that, I mapped the raw data to the DeNovo assembly and did quantification and DEG analysis. The annotation of the DeNovo assembly was done using Trinotate. The GO IDs, gene descriptions, KEGG IDs, etc. were assigned to the DEGs using the annotation data from Trinotate.

Now I want to do GO and KEGG enrichment, but since the gene IDs I have are from different organisms I am not able to use several of the R packages and tools. Moreover, a single gene ID has multiple GO IDs assigned to it.

How can I create an enrichment plot using the data I have? I hope someone will help me.

Thank you.

Answer 1

[geneontologyhelp]

a single gene ID is having multiple GO IDs assigned to it

This is common and not unexpected for GO. As explained in our FAQ, these may be terms from each of the aspects (Cellular Component, Molecular Function, Biological Process) or even represent multiple activities/functions for the same gene product.

As far as tool recommendations, if you provide the organisms someone may be familiar with a package that would work for you. While the GO's tool, PANTHER, would have to be repeated on each organism, there are other tools like GeneWeaver that work on a limited group of organisms.

[Sowmya Pulapet]

Since I have done DeNovo transcriptome assembly of a particular plant, I can't pinpoint to say that the GO obtained is for a single organism. The GO results were obtained from the tool Trinotate used for the annotation of DeNovo transcriptome assembly.