I have a network of miRNAs and genes that correlate in my experiment (based on expression levels). The edges link each miRNA to the gene that it correlates with. None of these miRNAs and genes have any known direct interactions according several databases of experimentally validated gene miRNA interactions. It is possible that these correlations exist because of genes which were not measured in my experiment E.g.  miR-1 interacts with geneX (not measured in my experiment) which interacts with geneY(measured) leading to a correlation between miR-1 and gene-Y in my network.

I want to create a new network that tries to link  (e.g. through gene-gene interactions, perhaps even transcription factors) each miRNA with its correlating gene.

I thought cytoscape may be able to help but I have never used it before and am struggling to find a plug-in which does what I want.

I have a list of experimentally validated gene miRNA interactions and I presume it is possible to get a list of gene-gene interactions e.g. from an interactome database. Does anyone have any ideas on how can I integrate this information with my network so that I can link each miRNA with its correlating gene?

Many thanks
Greetings, and welcome to Cytoscape.  I think there are a couple of plugins that might be useful.  What I would suggest is to use your list of genes and then probe one of the databases to explore how those genes might be related.  For example, you could use the stringApp, add your list of genes, but then also add a number of high confidence edges that might bring in interacting genes that links them.  If you want to view your miRNA interactions in the same network, Cytoscape has an excellent "merge networks" tool that will allow you to merge your original network with the STRING network.  You might also want to look at the new IntActApp as an alternative using the IntAct database in lieu of the STRING database.

-- scooter