Rat CNS Interactome (Signalling Molecules)

To construct the CNS Signaling Molecule 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).

Signaling Molecules (Sigs), were defined as rat genes annotated in the GO Biological Process database as: ‘signal transduction’ and in the GO Cellular Component database as GO:0005622 – ‘intracellular’ or GO:0005886 – ‘plasma membrane’. This produced a final list of 2,842 genes from which 1,101 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 the adaptive partitioning algorithm (MI ≥ 0.43795) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs, and the resulting CNS signaling molecule interactome contained 154,785 statistically significant MIs between 7,018 genes.