Question

topGO: how to visualize gene in GO enriched categories?

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artur ▴ 80

@artur-6730

Last seen 8.9 years ago

Germany

Hi All, I am using 'topGO package for GO enrichment analysis in non model organisms. I found the tool really intuitive and versatile as far as the statistical test are concerning. However, I was wondering if there is a way to display/list the genes belongig to each GO enriched categories. Thanks in advance. [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.3 years ago by Bernd Klaus ▴ 610 • written 10.3 years ago by artur ▴ 80

Martin Morgan · Answer 1 · 2014-09-18

Dear stefano,

check out the "print genes" function: If tab contains the results of GenTable call,

tab <- GenTable(...)

Then just say:

res <- printGenes(tgd, whichTerms = tab$GO.ID ,chip = "mogene20sttranscriptcluster.db", geneCutOff = 1000)

where the chip argument specifies the micrarray annotation database from Bioconductor and geneCutOff specifies how many genes per term to return maximum.

If you did not perform a microarray analysis, you probably have to use biomaRt or other annotation resources to get the genes for a GO term. See:

http://bioconductor.org/help/workflows/annotation/annotation/

Best wishes,

Bernd