Question: How can I do GO enrichment analysis for bacteria genome? (biomaRt is not support bacteria anymore)
1
gravatar for wm
5.4 years ago by
wm450
China
wm450 wrote:

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: the 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 works 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")
rna-seq genome • 5.9k views
ADD COMMENTlink modified 5.4 years ago by dago2.6k • written 5.4 years ago by wm450
4
gravatar for dago
5.4 years ago by
dago2.6k
Germany
dago2.6k wrote:

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

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

Look also the many previouse question on the topic:

GO enrichment in non-model organism

A: Go Enrichment From Protein Id

Gene Ontology Enrichment Of Non-Model Bacterial Genome

 

ADD COMMENTlink written 5.4 years ago by dago2.6k

Thanks dago,

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

ADD REPLYlink written 5.4 years ago by wm450
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