GO enrichment analysis in R on Solanum lycopersicum proteomics dataset

Question

[Alb]

Hello people! I am analyzing a proteomic dataset of Solanum lycopersicum that is organized as following: Treated vs Control in a time series: TP1; TP2; TP3... On this dataset I need to perform a GeneOntology enrichment analysis in R, and I was planning to do it with the

library(clusterProfiler)

I want to perform both ORA, (enrichment analysis on over represented tomato proteins in treated vs control on each time point) and GESA (Gene set enrichment analysis, that in this case would be the whole proteome set for each time point). Now I have two problems that are related to each other. 1) Solanum lycopersicum is not among the org.db model organism supported by clusterprofiler. I tried to import the AnnotationHub Solanum as following but it doesn't seem to work with clusterprofiler

hub <- AnnotationHub()
query(hub, c("Solanum"))
org.Sl.eg.db <- hub[["AH80808"]]

and also seems not appropriate for my aim because it doesn't contain UNIPROT-IDs either.

AnnotationDbi::keytypes(org.Sl.eg.db)
[1] "ACCNUM"      "ALIAS"       "ENTREZID"    "EVIDENCE"    "EVIDENCEALL" "GENENAME"    "GID"         "GO"          "GOALL"      
[10] "ONTOLOGY"    "ONTOLOGYALL" "PMID"        "REFSEQ"      "SYMBOL"      "UNIGENE"

2) I downloaded all the GO terms associated to each UNIPROT ID for each timepoint, so I was wondering, if there is a way to start my analysis direclty from this tipe of dataset

UNIPROTID    GO     ONTOLOGY

I hope I was clear and that you people can give me a help Cheers

[Dunois]

Take a look at goseq.

Answer 1

[Guangchuang Yu]

yes, it is supported by clusterProfiler.

pls refer to the Universal Interface for Biomedical Gene Sets session in https://doi.org/10.1016/j.xinn.2021.100141.