Gene Ontology - How to do Transcript Ontology?
Entering edit mode
11 weeks ago

Hi all,

I am very new and I apologize if I ask very basic and stupid questions. I've been kind of thrown into doing transcriptomics and there isn't anyone in my lab who can teach/help me with this.

I have run through DESeq analysis (samples are Mus musculus) in R, and have the significant differentially expressed transcripts which I'd like to now run Gene Ontology for. But, I'm having trouble doing this using the transcripts. I see others using Ensemble_IDs or Entrez_IDs, but from my understanding those are not particular to the transcript?

Am I able to run moreso "Transcript Ontology"? I am attempting to implement this using the enrichGO function of ClusterProfiler.

Thank you so very much for any help!

gene-ontology GO transcripts • 368 views
Entering edit mode

What format/type are your current IDs? Ensembl has IDs for both genes and transcripts. You can use the biomaRt library in R to request transcript ID to GO ID associations that you could hand to the topGO library, for instance. Entrez IDs are also available via that route. You might take a look at other discussions of this topic.

Entering edit mode

Thank you for your help! My current ID format is Transcript ID or Accession ID for the transcripts. It looks like this: NM_007377 Are there any differences in using different packages/libraries for GO analysis in regards to results?

Thank you very much again, I will check out the discussions you recommended.


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