CytoKEGG on the KEGG reference pathway

[Kristin Kaiser]

Hey guys.

I'm exploring some data with CytoKEGG and find it really nice. However, I do not have organismal data, I have metagenomic data. My question therefore would be: Is there any way, to get the genereal reference Pathways from KEGG as a template? And not the Pathway from an organism?
For example: I want to visualize all the nitrogen metabolism-related genes from my dataset. I already played around with Bacillus reference pathway, and a Nitrosomonas pathway. This is nice and give me results, however, these organisms contain different subsets of genes involved in nitrogen metabolism. Therefore, I can only visualize a subset of my data.

Using the Repository, I can only import the pathways for individual organisms. So is there a chance to get the general pathways here?
This would be really helpful.

Thank you very much in advance.

Sincerely, Kristin

[Keiichiro Ono]

Hi.

I'm not sure about CytoKEGG, but you can download reference pathways
in KGML and import it with KEGGScape App.

For example, this:

http://www.genome.jp/kegg-bin/show_pathway?org_name=ec&mapno=00910&mapscale=&show_description=hide

Will be visualized like the attached picture if you use it. You may
need to do some ID mapping, but it depends on your data files.


Kei

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Keiichiro Ono
http://keiono.github.io/

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[Kristin Kaiser]

Hey Kei,

this is EXTREMELY helpful, I was not aware of this App.
This is really great and will definitely save some time :) I will try it, may I refer back to you, if I got some questions?

Best, Kristin

[Kristin Kaiser]

Actually, I can only download reference pathways of certain organisms as KGML. Not the GENERAL reference pathway :(