How can I do GO enrichment analysis for bacteria genome? (biomaRt is not support bacteria anymore)

Question

[wm]

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")

Answer 1

[dago]

You can try to annotate your gene using blast2GO or retrieve the GO annotation in quickGO if the genome of your organism is present.

After having the GO annotation you can do the enrichment with the R package you prefer.

Look also the many previous questions on the topic:

• GO enrichment in non-model organism
• Go Enrichment From Protein Id
• Gene Ontology Enrichment Of Non-Model Bacterial Genome

[wm]

Thanks dago,

I am trying quickGO to retrieve the GO annoataion of the genes, then use the R packages for the GO enrichment analysis.