Kegg Pathways In Text?
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9.8 years ago
Avoks ▴ 140

Hi all,

I have read through the related questions that popped up but I couldn't really find what I wanted. Here goes:

  • I run a list of genes through KEGG(Using postForm() in R)
  • I get a list of pathways back
  • I select my pathways of interest(is there a way to do this in R?)
  • I click on a pathway and get the graphics with the genes from my list in red
  • How do I get these images in a text format?
  • I'm trying to get neighboring genes/nodes to include in my gene list(is there a way to do this in R?)

I assume getting things in text is perhaps the first step, hence the initial question.

Thanks.

kegg r pathway text • 3.4k views
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Hi! Sorry, I don't want to be rude, but have you looked at http://www.genome.jp/kegg/soap/doc/keggapi_manual.html? It describes how to access KEGG via Perl/Ruby/Python/Java (no R) and it is quite a versatile interface to retrieve data associated with pathways and genes. However, I am not sure if you can get the network related information you are seeking via that interface.

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Thanks Joachim.

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9.8 years ago
Neilfws 49k

There are numerous tools in R Bioconductor for working with KEGG. Try searching at their website and see if any do what you want. Useful starting points are KEGG.db and gene2pathway.

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Thanks. I will try gene2pathway.

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You're welcome. Feel free to vote for answers you find useful :)

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9.8 years ago

If you are not committed to using R, maybe you could try adapting one of the Entrez/KEGG workflows from Taverna:

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Thanks Casey. I am committed to working with R at this point:~)

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