Rat CNS Interactome (TF and coTFs)

To construct the CNS Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA).

Transcription factors (TFs) were defined as rat genes annotated as “transcription factor activity” in Gene Ontology and the list of TFs from TRANSFAC. This produced a final list of 898 TFs, from which 898 were present on the Cleaner-mapped expression profile.

ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by ARACNe (MI >= 0.44068) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs. The resulting CNS Interactome contained 244,276 statistically significant MIs between the 6,716 genes.