topGo custom Annotation table
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Aini • 0
@aini-24536
Last seen 1 hour ago

Hello, I am using topGo for customized background enrichment analysis. i made background file by names of genes and their corresponding GO IDs. I can do fisher's teat and every thing mentioned in the manual. I want my result table correspond to gene name not GO IDs. I found a code to find genes against GO ids

myterms = c("GO:0007610", "GO:0014070", "GO:0045910") mygenes <- genesInTerm(myGOdata, myterms)

for (i in 1:length(myterms)) { myterm <- myterms[i] mygenesforterm <- mygenes[myterm][[1]] mygenesforterm <- paste(mygenesforterm, collapse=',') print(paste("Term",myterm,"genes:",mygenesforterm)) }

i want opposite of it. From gene name to GO ids table. I am new to this. kindly help me.

thank you


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
customannotation enrichmentanalysis topGO • 70 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

Perhaps you can restate your goal? As it stands I am afraid it doesn't make any sense. In other words, my interpretation of your question is that you have a set of significant GO terms that you can output in a results table, but instead of GO terms you want each row to have a gene name.

But that doesn't make any sense! Each GO term is significant because there are multiple genes that are appended to that GO term, and which are significant in your analysis. So each row of the results table arose because of multiple genes, not one.

You might want to know which genes for each GO term were significant, and caused the term to be significant, which might be what the function you show does (alternatively probeSetSummary in GOstats does exactly that). But directly replacing the GO term with a Gene ID isn't really a thing.

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I have some experimental data of a non model organism. Usually for model organisms we use DAVID, Panther etc. We give gene name to the software and they find corresponding GO IDs with functions. This is usually the enrichment analysis for model organisms. I have gene names and Gene ID of a non model organism from an experiment. I made background data from whole genome of the organism using interpro scan. Now like DAVID and Panther software I want GO IDs against the Gene name or Gene IDs. I hope this will help clearing my goal.

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OK, so I am completely lost now. In your original post it seemed like you were able to run your GO analysis, but didn't like the output table. But now it seems like you might be stuck generating the list object required to do the GO analysis?

Have you looked at section 4.3 in the topGO vignette? What have you tried? Show code.

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