Hello,

I am running TopGO over a genome that was sequenced, assembled and annotated by my group so I supply my own GO annotation. I am interested to see if there are enriched GO terms in sub-group of genes of this genome and am little confused with TopGo results - because the first 6 best results include GO terms that are not even annotated for this genome, not to mention in the subgroup of genes in this genome. I am using Fisher, classic algorithm. Does TopGO look for enriched GO terms that are not in the list, finding them using GO graph topography?

My Code:

library(topGO)

setwd("C:\\pnina\\Studies\\GOSnIPRE")

geneID2GO <- readMappings (file = "my_M1.SINV.gene_GO",sep = "\t", IDsep = ",")

geneUniverse <- names(geneID2GO)

genesOfInterest <- read.table("interestinggenes.txt",header=FALSE)
genesOfInterest <- as.character(genesOfInterest$V1)
geneList <- factor(as.integer(geneUniverse %in% genesOfInterest),levels =c(0,1))

names(geneList) <- geneUniverse

plot(geneList)
#Creating the GO data
SnIPREGO <- new("topGOdata", description="SnIPRE GO", ontology="BP", allGenes=geneList,  annot = annFUN.gene2GO, gene2GO = geneID2GO)

#from here - analysis
resultFisher <- runTest(SnIPREGO, algorithm = "classic", statistic = "fisher")

showSigOfNodes(SnIPREGO, score(resultFisher), firstSigNodes = 6, useInfo = 'all')

Thank you,

Pnina