Genetic dissection of acute ethanol responsive gene networks in prefrontal cortex: functional and mechanistic implications.

Transcriptional response to acute-ethanol within 3 regions of mesocorticolimbic reward circuit across the BXD family.(A) Number of genes found to be significantly ethanol-responsive in the prefrontal cortex (PFC, n = 29), nucleus accumbens (NAc, n = 37) and ventral midbrain (VMB, n = 37) by analysis of saline vs ethanol S-scores across BXD, B6 and D2 samples. (B) Venn-diagram depicting which subsets of ethanol-responsive genes are region specific (blue), overlap across two regions (grey) or common to all three regions (red). All three pairwise overlap combinations were statistically significant as determined by Fisher's Exact Test for count data. Odds ratios from this analysis are depicted in word bubbles.

Acute ethanol transcriptional response profiles.(A) Strain frequency distributions of gene transcriptional-response classes based on PFC S-score analysis. S-scores >2 indicate a gene was up-regulated by acute ethanol, S-scores <2 indicate down-regulation and S-scores between these thresholds were considered unchanged. (B) S-score strain distributions for three significantly ethanol responsive genes that each represent a different class of ethanol response profile.

Saline vs ethanol S-score paraclique networks.(A) Distribution of S-score network sizes based on the number of genes assigned to each. Significantly ethanol-responsive genes were over-represented in a subset of these networks (red bars). (B) These 16 paracliques were considered ethanol-responsive gene-enriched networks (ErGeNs). (C) Network-based clustering of the 1,246 significantly ethanol-responsive genes in the PFC revealed distinct modules largely corresponding to the ErGeNs depicted in B.

Relationship between ErGeNs and counterpart networks in RMA expression data.Both S-score networks, ErGeN1 and ErGeN2, had counterpart networks in the basal saline and post-ethanol expression data: ErGeN1 significantly overlapped with saline network 1 and ethanol network 1; ErGeN3 significantly overlapped with saline network 4 and ethanol network 2 (Figure S3). Each point represents a gene that belongs to a given ErGeN's counterpart saline network (blue), ethanol network (red) or both (green). Filled-in points indicate the gene also belongs to the overlapping ErGeN. The X- and Y-axes measure gene connectivity (|Pearson correlation coefficient|≥0.7) within the saline and ethanol expression datasets, respectively.

Genetic regulatory architecture of major ErGeNs.Histogram of saline vs ethanol S-score eQTL (genome-wide p-value<0.63) frequencies across the genome divided into 10 megabase (Mb) bins.

Hub genes within ErGeN3.Network visualization of all genes comprising ErGeN3 that share at least one adjacent edge at a correlation threshold of >|0.9|. Node color indicates the magnitude of a gene's transcriptional response to ethanol, quantified using Fisher's combined p-values. Grey nodes were not altered by ethanol. Node size represents a genes degree of connectivity.

ErGeN trans-bands have distinct phenotypic correlations.Correlations between principal component traits of ErGeN trans-bands and BXD phenotypes (p-value<0.01). Edge thickness indicates strength of network/phenotype association and dashed lines indicate a negative correlation. Each phenotype node is labeled with a trait ID that can be queried on GeneNetwork.