I used to do the GO analysis using these R bioconductor packages: biomaRt, clusterProfiler

First, I need to build the GO map of the bacteria genome.

Then, use the clusterProfiler to finish the enrichment analysis. (GO enrichment, KEGG enrichment ...)

My problem is: biomaRt does not support bacteria genomes anymore. so that I can not get the GO db for the rest analysis.

The following are my * R scripts** that worked in 2012.

R code:

# load libraries
library(clusterProfiler)

# Build specific GO map using GFF file
library(biomaRt)
Gff2GeneTable("NC_000962.gff")
load("geneTable.rda")
Mtb <- useMart(biomart="bacteria_mart_16",
               dataset="myc_30_gene")
gomap <- getBM(attributes=c("entrezgene", "go_accession"),
               filters="entrezgene",
               values=geneTable$GeneID,
               mart=Mtb)
#dim(gomap)
#head(gomap)
buildGOmap(gomap)

# Load the genes (differentially expressed, or other)
input_genes <- read.table("input_list.txt") # geneName geneID
input_IDS <- as.character(input_genes$geneID)

GOe <- enrichGO(input_IDs, organism = "H37Rv", ont = "BP",
pvalueCutoff = 0.05, qvalue = 0.1, readable = TRUE)

# make a plot
p1 <- plot(GOe, type = "bar", order = TRUE, showCategory = 15)
print(p1)

# write the results to a file
write.table(summary(GOe), file = "out_GOenrichment.txt", sep = "\t")