Map PPi databases like I2D to microarray gene co-expression network.
Hello.
Let's say that we have created a gene-coexpression matrix out of microarray data but we want to keep only those gene-pairs that have been annotated in protein-protein interactions databases like I2D. Is there any automatic way, through an R package to do such a job?
What do you do, you on such occasions?
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For such things, I don't use a package. I just write a script to filter my experimental gene pairs to only keep those with interacting proteins. Representing both co-expression data and protein interactions as graphs with genes as nodes (maybe using the igraph package in R), this is just a matter of finding the edges of the co-expression graph that are also in the interaction graph.