Incomplete pathway visualisation on Cytoscape

Question

[sma180055]

Hello,

I am trying to visualise multiple pathways onto Cytoscape - I load them individually before merging them. However, I encountered a problem whereby the pathway that I loaded through KEGGparser-web was not as complete as the one I viewed on KEGG's website.

I had also tried downloading the KGML file and load it onto Cytoscape and returned with the same result. Although WikiPathway gave a more comprehensive pathway visualisation, I would like to stick with KEGG since the upstream analysis was using KEGG.

An example of the pathway is HSA 00533 (Glycosaminoglycan synthesis - keratan sulfate). Could anyone please advise me how to best visualise the pathway as complete as the one on the KEGG website?

Thank you.

Kind regards, Als

Answer 1

[scooter]

Unfortunately, none of the apps I was able to find deduce the edges between the species in the KEGG pathway. I looked at the KGML and, as near as I can tell, the actual links aren't encoded in the file. That pathway has a list of gene, some relatively long labels for the genes (see the <graphics> tag) and the coordinates. I'm guessing that the "links" are meant to be deduced from the <graphics> tag type="line" attribute, but none of our existing tools seem to work with it. I would suggest dropping back to using wikipathways, unfortunately.

-- scooter

[sma180055]

Sorry for the delayed response and thank you for your reply!