Hi,

I conducted a GO enrichment analysis for some of my rice genes using the clusterProfiler and org.Osativa.eg.db packages in R. However, the analysis is not showing any enriched pathways for the genes I inputted, even though I am certain that these genes must have enriched pathways to display. I do not understand the reason for not providing any pathways.

I am including my script here to check with you if I am doing it correctly. Your help in solving this problem would be greatly appreciated.

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.18")

install.packages("https://github.com/xuzhougeng/org.Osativa.eg.db/releases/download/v0.01/org.Osativa.eg.db.tar.gz", 
                 repos = NULL, 
                 type="source")

library(org.Osativa.eg.db)
org <-org.Osativa.eg.db
library(clusterProfiler)
library(BiocManager)

gene_list <- read.csv("Mtest.csv")

result <- enrichGO(gene         = gene_list,
                   OrgDb       = org.Osativa.eg.db,
                   keyType     = "RAP",
                   ont         = "CC",
                   pAdjustMethod = "BH",
                   qvalueCutoff   = 0.05)

keytypes(org.Osativa.eg.db) 

#  result <- enrichGO(gene         = gene_list,
+                    OrgDb       = org.Osativa.eg.db,
+                    keyType     = "RAP",
+                    ont         = "CC",
+                    pAdjustMethod = "BH",
+                    qvalueCutoff   = 0.05)

#--> No gene can be mapped....
--> Expected input gene ID: Os11g0576100,Os04g0605900,Os08g0320100,Os05g0344400,Os06g0692800,Os01g0126900
--> return NULL...

sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

> head(keys(org.Osativa.eg.db))
[1] "LOC_Os01g01010" "LOC_Os01g01030"
[3] "LOC_Os01g01040" "LOC_Os01g01060"
[5] "LOC_Os01g01070" "LOC_Os01g01080"

For whatever reason all the IDs are prepended with LOC_. I suppose you could convert all the IDs you have for your data to have that prefix, or I believe you can supply the gene/GO mappings to enrichGO, but I don't use the package, so you will need to figure out how to do that if you prefer that route.