GO analysis using topGO Arabidopsis

Question

[Sreeraj Thamban]

Hi, I have a list differentially expressed genes and I wanted to do GO enrichment analysis using topGO. I am having trouble making a geneID2GO annotation file, I extracted GO terms corresponding to each gene ID using the following script. How to make the 'geneID2GO' object from the following script compatible with topGO? Thanks.

library("biomaRt")
#collect gene names from biomart
mart <- biomaRt::useMart(biomart = "plants_mart",
                         dataset = "athaliana_eg_gene",
                         host = 'plants.ensembl.org')
# Get ensembl gene ids and GO terms
GTOGO <- biomaRt::getBM(attributes = c( "ensembl_gene_id",
                                     "go_id"), mart = mart)
#examine result
head (GTOGO)
#Remove blank entries
GTOGO <- GTOGO[GTOGO$go_id != '',]
# convert from table format to list format
geneID2GO <- by(GTOGO$go_id,
                GTOGO$ensembl_gene_id,
                function(x) as.character(x))
#examine result
head (geneID2GO)

Answer 1

[e.rempel]

Hi Sreeraj,

you can create 'topGOdata' object by calling

go.obj = new("topGOdata", ontology='BP'
, allGenes = int.genes
, annot = annFUN.gene2GO
, gene2GO = geneID2GO)

where int.genes is a factor containing the information which genes are interesting (in your case, differentially expressed).

Here a small working example (run after your lines):

all.genes <- sort(unique(as.character(GTOGO$ensembl_gene_id)))
int.genes <- sample(x = all.genes, size = 200) # some random genes 
int.genes <- factor(as.integer(all.genes %in% int.genes))
names(int.genes) = all.genes

go.obj <- new("topGOdata", ontology='BP'
                 , allGenes = int.genes
                 , annot = annFUN.gene2GO
                 , gene2GO = geneID2GO
                 )

results <- runTest(go.obj, algorithm = "elim", statistic = "fisher")

results.tab <- GenTable(object = go.obj, elimFisher = results)

The results.tab contains the table of enriched GO terms.

HTH

[Sreeraj Thamban]

Thank you so much, it worked.