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bowang-lab / BIONIC

Biological Network Integration using Convolutions
MIT License
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Using differential expression and/or MOFA output as input #58

Closed ZainulArifin1 closed 11 months ago

ZainulArifin1 commented 11 months ago

Thank you for the tools. I currently have a resolved network (constructed from kinase and TF activity), coexpression network (one from transcriptomics, one from proteomics), and ground truth interactions from Omnipath. I also have output from MOFA (linear factorization integration method) and typical differential expression/abundance.

As we are interested to study the signaling of a specific gene and identify novel interaction in relation to that gene, can we also use the MOFA or DEG output as input for Bioinic?

Thank you.

duncster94 commented 11 months ago

Hi, thanks for your interest in BIONIC.

As long as you convert your inputs into networks (i.e. by computing pairwise similarity and thresholding to get edges), you can use these with BIONIC.

ZainulArifin1 commented 11 months ago

Noted. I think I can input these results into string and use string output as input. Many thanks for the prompt reply.