Comparison mESC-Specific and Test Network Connectivity.

Notes: The percentage of strongly connected gene hubs (those with a mean degree greater than 0.2 out of a total of 21,291 protein coding genes) is markedly higher in the mESC-specific network as compared to the superset or negative control networks. Degree is a measure that reflects the number of genes within the network that are predicted to be functionally linked to a given gene. In these networks, which were trained using a gold standard focused on mESC self-renewal, a higher mean degree indicated that the given gene is more likely to interact with multiple other genes, and tended to be enriched for mESC-specific self-renewal processes. Highly connected genes in the negative control network were predominantly annotated to biological processes related to self-renewal functions that are active in all cell types, such as transcriptional regulation, cell proliferation, as well as developmental processes associated with multiple cell types, such as embryonic morphogenesis.