Question: topGO approach for a list a genes without expression
1
gravatar for serpalma.v
4.9 years ago by
serpalma.v20
Germany
serpalma.v20 wrote:

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

 

 

mirna go bioconductor R • 3.8k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by serpalma.v20
0
gravatar for Sudeep
4.9 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

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

ADD COMMENTlink written 4.9 years ago by Sudeep1.6k

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 apporach?

Cheers!

ADD REPLYlink written 4.9 years ago by serpalma.v20
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