topGO: how to visualize gene in GO enriched categories?
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artur ▴ 80
@artur-6730
Last seen 5.5 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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Bernd Klaus ▴ 600
@bernd-klaus-6281
Last seen 2.8 years ago
Germany

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

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