topGO approach for a list a genes without expression
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Entering edit mode
7.3 years ago
serpalma.v ▴ 70

Hello,

I would like to know if this approach is correct. Briefly, I have a list of targets for a miR and I want to perform GO unsing topGO. TopGO needs a function (geneSel) telling it which genes to choose from the gene set, which is usually the differentially expressed ones. Since I have a list of genes (targets for the miR) I have no expression values and therefore, no sigincancies. So, this is what I did, but I am not sure if is correct:

  1. get all gene names:

    mart <- useDataset("hsapiens_gene_ensembl", mart=useMart("ensembl"))
    all_ensembl_gene_id <- getBM(attributes = "ensembl_gene_id",
                                 values = "*", mart = mart)
    
  2. Select the targets IDs and give them value of 1. The rest of IDs in the set are 0s.

    all <- factor(as.integer (all_ensembl_gene_id[,1] %in% targets))
    names(all) <- all_ensembl_gene_id[,1]
    
  3. Perform gene ontology, choosing only targets (1's)

    GOdata <- new("topGOdata",ontology = "CC",
               allGenes = all,
               geneSel=function(p) p == 1,
               description ="miR-targets",
               annot=annFUN.org, mapping="org.Hs.eg.db", ID="Ensembl")
    

Do you think this is a valid way to perform a GO. I am fairly new to this and I would appriciate your help very much.

Thanks

GO bioconductor R mirna • 5.0k views
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Entering edit mode
7.3 years ago
Sudeep ★ 1.7k

I do not see any problems as such with your R code, but instead of using the function, you can also use a vector of gene ids as inputs. Have a look at this topGO vignette esp. sections 4.4 through 4.6

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Thank you for replying.

The vector of gene ids would be my targets, right?

and, do you think that using all gene IDs as background is a valid approach?

Cheers!

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