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Incomplete pathway visualisation on Cytoscape

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

cytoscape kegg wikipathway pathwayvisualisation
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updated by scooter scooter • written by sma180055 • sma180055

1 answer

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

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written by scooter scooter

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

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written by sma180055 • sma180055

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