Expression profiling of genes involved in muscular activity and inactivity in hind legs of rats

In this study, gene expression profiles of rat hind limb (soleus) muscle in three different (suspension and loading) experiments was used to investigate the genes involved in muscular activity and atrophy. Duration of muscle activity and inactivity varied between experiments. In total, expression data were on 1184 genes profiled in 39 arrays from 3 different experiments. A set of nested linear models, nesting genes within treatments within experiments was defined in R package limma for analysis. Moderated t-statistics based on empirical Bayes methods was used to indicate mode of regulation and for gene ranking. Adjustment for multiple testing was by probability of false discovery rate (pFDR). At 5% pFDR, the number of differentially expressed (DE) genes ranged from 1 to 138 across experiments. Most genes were down regulated within experiments, compared to control groups (controlled state activity). A gene which encodes Glutathione-S-transferase showed differential expression pattern over all three experiments at 10% pFDR. As a comparative approach, the expression level of this gene was mapped to genomic locations using expression quantitative trait (eQTL) approach in mouse inbred lines; the results showed trans-eQTL regions on chromosomes 10 and 3. The different experiments affected genes which are mostly likely involved in ATP production and fatty acid synthesis. Hence, the implications of this result are that the supply of energy source are of great importance for longstanding work and exercise than protein and other mediator nutrient molecules. These results have significant impact on adaptive animal and human physiology.