We examined in detail how the two major networks comprising the PFC transcriptional response to ethanol, ErGeN1 and ErGeN3, related to their respective counterparts in the saline and ethanol RMA expression data, in order to determine what additional information is provided by the S-score networks. ErGeN1 was significantly enriched for members of saline network 1 and ethanol network 1. Likewise, the gene members of saline network 1 and ethanol network 1 significantly overlapped each other, with 215 genes in common. The overlapping components of these three networks were frequently the mostly highly connected nodes (Figure 4, ErGeN1 panel). ErGeN3 exhibited a similar relationship with saline network 4 and ethanol network (Figure 4, ErGeN3 panel). Therefore, these S-score networks largely comprise the robustly inter-connected hubs of existing networks. However, missing from Figure 4 are the 439 and 143 probe-sets that belong to ErGeN1 and ErGeN3, respectively, but not their counterpart networks in the saline or ethanol RMA expression data. These network facets unique to the ErGeNs represent a form of genetic co-regulation that would have gone undetected without the use of S-score data.
