Analyzing Output Files

Now you have a complete NetProphet 2.0 network!

The output is netprophet2_network.adjmtr. This network is in an adjacency matrix format. The rows represent regulators/TFs and the columns represent genes, i.e. the matrix dimension is # of regulators x # of target genes. Each entry Mij of matrix M is NetProphet predicted score for the potential of regulation from regulator Ri to target gene Tj. Higher edge scores present higher likelihood of direct, functional interactions.