KEGG Pathway visualization using Cytoscape

[Nikos P.]

Hi all,

This is not an actual question, but more like a proposed workflow that can hopefully be useful for some, when analyzing your datasets.

I was trying to find a way to visualize my PICRUSt predictions in a comprehensive manner outside of the KEGG platform (due to its commercial nature) and , more specifically, map my K# 's on the KEGG reference pathways. So, I came across the KEGGscape app in Cytoscape (package details: https://github.com/idekerlab/KEGGscape/wiki , and its publication http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141640/ , all credits to these people).

Suppose you have run all your analyses and statistics on your PICRUSt dataset and you have narrowed it down to some specific pathways that are potentially interesting for your question at hand. By using this tool (and some data preprocessing) you can map your K# 's on a specific pathway (e.g. Nitrogen metabolism, reference or organism specific) along with any other information (e.g. differentially abundant  K# 's in your samples/groups with p-values) and produce some nice images with Cytoscape's functionality.

This is a rough outline of what I have done for my data and works pretty well.

Of course, for some datasets this might be prove to be more tricky than for others, but I just wanted to share it with all of you. :)

Kind regards,

Nikos P.

[Jesse Zaneveld]

Thanks Nikos! Sounds like a neat approach.

Best,
Jesse

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