<p><em>presented in:Keystone Symposia: Omics Meets Cell Biology: Applications to Human Health and Disease in Taos, New Mexico, 2014</em></p>
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<p>Quantitative and qualitative protein characteristics differ between individuals and are regulated at genomic, transcriptomic and post-transcriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 12,989 rat liver proteins, including 792 novel gene predictions, 337 novel splice events, 112 non-synonymous variants, and 54 RNA editing sites. Respectively, quantitative RNA-Seq and proteomics data correlate highly between strains, but poorly when two data types are compared within a strain, indicating extensive non-genetic regulation. Our multi-level analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in GWAS for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.</p
