multi-omics analysis

[Hashan Jayarathne]

Hi,

I have bulk RNA seq data, proteomics data and metabolomics data. I would like to do a multi-omics analysis. How can I do this in cytoscape?

Thank you.

[Christopher Churas]

Hi,

I'm sure others will have a better answer, but I'd suggest taking a look at our tutorials 

under Network Analysis: 

https://github.com/cytoscape/cytoscape-tutorials/wiki#network-analysis

There are also several apps that can help:

https://apps.cytoscape.org/search?q=metabolomics

https://apps.cytoscape.org/search?q=proteomics

https://apps.cytoscape.org/search?q=RNA

chris

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[Scooter Morris]

Typically, the way I would approach this is by importing all of the data and then doing some simple visualizations.  For example, you could map the fold change for each data type as a ring around the nodes in an interaction network.   You could normalize the data across all channels and then do a correlation network, but I frankly think that may not be as interesting as looking for differential perturbation within the context of an interaction network.  At the end of the day, the answer really depends on what you are hoping to acheive with your analysis -- what is your biological question?

-- scooter