Question: Retrieving the gene list related to all GO ID
0
gravatar for Sreeraj Thamban
22 months ago by
Indian Institute of Science Education and Research
Sreeraj Thamban120 wrote:

Hi Biostars, I used topGO to do GO enrichment analysis for my list of interesting genes. After the run, I used the following script to retrieve significant genes for each GO ID. Can anyone help me to automate this process in such a way that I will get a table with all enriched GO IDs with corresponding significant genes? Thank you

# retrieving the gene list related to a GO ID 
# retrieve genes2GO list from the "expanded" annotation in GOdata
allGO <- genesInTerm(topGOobject)
#Getting all annotated genes for a GO ID
allGO["GO:123456"]
RetrivedGenes <- lapply(allGO,function(x) x[x %in% INT.GENES$V1] ) # where INT.GENES$V1 is my list of interesting genes
# Your significant genes for GO:123456
RetrivedGenes[["GO:123456"]]
rna-seq topgo gene ontology R • 1.3k views
ADD COMMENTlink modified 22 months ago by e.rempel740 • written 22 months ago by Sreeraj Thamban120
1
gravatar for EagleEye
22 months ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Give a try with GeneSCF (simple to use),

Here is an example to download complete Gene Ontology as simple table with corresponding genes

ADD COMMENTlink modified 22 months ago • written 22 months ago by EagleEye6.2k

Hi EagleEye, I checked GeneSCF , but we have been using topGO in our pipeline for long and repeating all the analysis using GeneSCF is not feasible at this point of time. It will be great if you can suggest any modification in the above script. Thank you

ADD REPLYlink written 22 months ago by Sreeraj Thamban120
1
gravatar for Chirag Parsania
22 months ago by
Chirag Parsania1.4k
University of Macau
Chirag Parsania1.4k wrote:

Hi,

I have automated the package for species of my interest. Use below github link for automated script of topGO. Input format provided in the sample data folder.

https://github.com/cparsania/topGO_Customized

~Chirag.

ADD COMMENTlink modified 22 months ago • written 22 months ago by Chirag Parsania1.4k
1
gravatar for e.rempel
22 months ago by
e.rempel740
Germany, Heidelberg, COS
e.rempel740 wrote:

Hi,

I encountered the same issue and solved it this way:

results <- runTest(topGOobject, algorithm = "elim", statistic = "fisher") 
results.tab <- GenTable(object = topGOobject, elimFisher = results)  # results.tab is the table with enriched GO
AnnotatedGenes = lapply(results.tab$GO.ID, function(x) as.character(unlist(genesInTerm(object = topGOobject, whichGO = x)))) # list containg genes annotated to significant GO terms
SignificantGenes = lapply(AnnotatedGenes, function(x) intersect(x, INT.GENES$V1)) # where INT.GENES$V1 is your list of interesting genes

HTH

ADD COMMENTlink written 22 months ago by e.rempel740
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