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?