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vahuynh / GENIE3

Machine learning-based approach for the inference of gene regulatory networks from expression data.

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The application of GENIE3 to pathway score matrix

DrZhaoJie opened this issue · comments

commented

Hi, I really enjoy your package GENIE3. I had an idea. May I apply the method to a pathway score matrix (calculated from GSVA) to find the co-interaction of the pathways? And then find hub-pathway by Cytoscape?
Was this reasonable? Thank you very much!

commented

Hi,

Well, if you think that it makes sense to try to predict the score of a pathway from the scores of other pathways, then yes you can use GENIE3 to identify the interactions between pathways. GENIE3 is very generic, and hence can potentially be used to find interactions between nodes of a graph, whatever the type of the nodes.

Best,
Vân Anh