We studied saline vs ethanol S-score expression data, as well as individual saline- and ethanol-treatment RMA expression data, using a graph theoretical algorithm that identified discreet paracliques within each dataset [32]. As described in Methods, the resulting paracliques, referred to as networks henceforth, represent densely intercorrelated groups of genes that likely share functional and regulatory homology. In the saline and ethanol networks formed with RMA expression datasets, inter-gene correlations represented the admixture of treatment variation superimposed on basal steady-state mRNA levels. In the context of the S-score networks, the correlations strictly reflect coordinated changes in expression induced by acute ethanol. The size of these networks ranged from 710 to 11 probe-sets (Figure 3a; Table S3).
