Outdated GO terms for enrichment analysis

[mgalland]

Apparently, the GO terms in the org.At.tair.db Bioconductor package (release 3.10) are outdated.

In this package, there are 27,416 Arabidopsis genes for a total of 4837 GO terms.

columns(org.At.tair.db)
 [1] "ARACYC"       "ARACYCENZYME" "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL" 
 [7] "GENENAME"     "GO"           "GOALL"        "ONTOLOGY"     "ONTOLOGYALL"  "PATH"        
[13] "PMID"         "REFSEQ"       "SYMBOL"       "TAIR"        

length(keys(org.At.tair.db, keytype = 'TAIR'))
[1] 27416

length(keys(org.At.tair.db, keytype = 'GO'))
[1] 4837

One solution would perhaps to use the official most up to date GO terms (available here) and perform the enrichment analysis manually.

[mgalland]

Useful links:
https://davetang.org/muse/2017/08/08/getting-started-arabidopsis-thaliana-genomics/
https://davetang.org/muse/2010/11/10/gene-ontology-enrichment-analysis/