How To Use The Kegg Xml Files?

Question

[Panos]

I have used KAAS and assigned K numbers to my genes. I now want to use the xml files in order to see graphically, in certain pathways, what are the present enzymes.

Do you have any particular program or method (eg an 'svg-ish' approach) to suggest?

For example, I found KGML-ED. Has anyone tried it?

Answer 1

[Fred Fleche]

You can draw your KEGG pathways as SVG graphics. Then your pathways will become interactives

You will use the png file of the pathways as the background and in the foreground you will draw your genes as SVG objects. Each object will have an id that will be the Entrez Geneid of the Gene.

You can place the SVG objects at the right place thanks to the coordinates that are available in the KGML files.

Let's say that you have in the backend a database with the Entrez Geneid that are linked to Enzyme classification or whatever data then you will be able to hihlight the object (genes) that match a given criteria. I personnally use Ajax techniques to do it dynamically. See below two instances

The first one highlights ATPases in Cancer pathways:

The second one highlights Proteases in Cancer pathways:

[Fennan]

I am trying to do something similar and I believe that your suggestion would work just fine... Do you know where I can find more information about using the png file together with SVG objects?

Also, the instances cannot be seen. Could you post them again?

Thanks!

[Fred Fleche]

I will try to set up a tutorial during the next month and make it available on Bioinformatics.fr

[Fennan]

That would be GREAT! Thanks for that and the quick response.

My main problem right now is to obtain the SVG image from the XML obtained from KEGG... Do you know any guidelines I should follow?

Thanks again!

[Fennan]

Nevermind, I could do what I wanted following your indications :) Please, notify here when you have the tutorial ready. Thanks again!

[Husen]

Could you please elaborate on how you solved this issue? I have tried many tools for getting an SVG or a high quality image of a KEGG pathway (namely, hsa05200) but nothing seems to work.

[Giovanni M Dall'Olio]

Which tools did you try?

Answer 2

[Giovanni M Dall'Olio]

You can import KGML files into Cytoscape using the KGMLreader plugin, and then depending on what you want to do, you can color an arrange the network with cytoscape.

Another alternative is to use KeggGraph, a library for R to handle KEGG graphs.

I have never tried KGML-ED but it looks interesting, thanks.

[Panos]

Thanks for the answer giovanni! Just a note, however... I tried the KGMLreader plugin with Cytoscape 2.7.0 and it doesn't work. It works, though with Cytoscape 2.6.2!

[Panos]

Although the xml files are loaded ok, if I change the color of an item in the xml file (by changing the corresponding hex value), I have no difference in the network drawn in Cytoscape. KGML-ED, on the contrary, displays everything as I expect.

Any ideas?