Hi, I am interested in using Cytoscape to analyze molecular relationships between genes, and I have been reading the tutorials on the Cytoscape website, but am unsure how to use Cytoscape for "one-to-many" comparisons.
For example, each gene is typically assigned as a "node", with "edges" that correspond interactions with other genes. Cytoscape used "Attributes" to map node or edge names to specific data values. In a simple "one-to-one" comparison, you might have a list of 10 genes with their expression values, such that the attribute for each gene would be 1) the name of the gene and 2) the expression value. It looks clear how Cytoscape would use these types of data to construct the interaction network.
However, I have multiple data values for each gene (node), e.g. for Gene X, I will have data values that indicate the predicted interactions between Gene X and all other genes in the analysis. It isn't clear to me how to use attributes or other Cytoscape features to translate this type of "one-to-many" data set into the format that Cytoscape can read.
My goal is to have a certain number of genes as the nodes, with edges connecting each gene to any other gene that it is predicted to interact with, just like the canonical gene interaction analysis plots that Cytoscape and similar software produce.
Please let me know if anyone has advice on how to properly use "one-to-many" data as input for Cytoscape.