Kegg Pathways In Text?

Question

[Avoks]

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.

[Joachim]

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.

[Avoks]

Thanks Joachim.

Answer 1

[Neilfws]

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.

[Avoks]

Thanks. I will try gene2pathway.

[Neilfws]

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

Answer 2

[Casey Bergman]

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

• http://www.myexperiment.org/workflows/786.html
• http://www.myexperiment.org/workflows/15.html

[Avoks]

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