Figure 1.

Overview of the discovery, enrichment, and comparative analyses. In the discovery phase, membrane and mitochondrial enriched protein fractions were collected from the striatum (dorsal and ventral) of four males from the B6 and D2 inbred mouse strains. For the enrichment analysis, all detected proteins were first queried for enrichment of functional terms using the ENRICHR web service. This resulted in detection of 339 mitochondrial genes. The remaining proteins were found to be enriched for synaptic signaling pathways (summarized in Figure 2). In the last phase of enrichment analysis, 369 differentially expressed (DE) proteins were divided into two groups for additional enrichment analysis based on higher expression in the B6 or D2 strain. The results of this analysis can be found in Figure 3. For comparative and genetic analysis the top 160 DE proteins based on a 10% FDR were compared against two related data sets. The first data set consisted of striatal gene expression profiled in male B6 and D2 mice by RNA-seq. The second data set included expression quantitative trait loci (eQTL) mapping in three different striatal expression data sets from a recombinant inbred progeny—the BXD population—derived from the B6 and D2 strains. The final list of 26 proteins with differential mRNA expression and evidence of genetic regulation of gene expression in the BXD panel is shown above (blue, red, and black text indicates higher expression of the B6 allele, D2 allele, or a mixture of both across the three data sets, respectively). A summary of the overlap analysis can be found in Supplementary Table S3.