The gene network was constructed and visualized using the Cytoscape utility through “Gene-set Cohesion Analysis Tool (GCAT)” (http://binf1.memphis.edu/gcat/index.py). The nodes in the network represent genes and the edge between two nodes represent cosine scores of Latent Semantic Indexing (LSI) determines if the functional coherence of gene sets is larger than 0.6. The significance of the functional cohesion is evaluated by the observed number of gene relationships above a cosine threshold of 0.6 in the LSI model. The literature p-value (LP) is calculated using Fisher’s exact test by comparing the cohesion of the given gene set to a random one [31].
