<title>Author Summary</title><sec id="st1"><title/><p>Prior studies have reported that ~15% of expressed genes show a circadian expression pattern in association with a specific function. A series of experimental and computational studies of gene expression in various murine tissues has led us to a different conclusion. By applying a new analysis strategy and a number of alternative algorithms, we identify baseline oscillation in almost 100% of all genes. While the phase and amplitude of oscillation vary between different tissues, circadian oscillation remains a fundamental property of every gene. Reanalysis of previously published data also reveals a greater number of oscillating genes than was previously reported. This suggests that circadian oscillation is a universal property of all mammalian genes, although phase and amplitude of oscillation are tissue-specific and remain associated with a gene's function. We hypothesize that the cell's metabolic respiratory cycle drives the oscillatory pattern of gene expression. These findings imply that biological pathways should be considered as dynamic systems of genes oscillating in coordination with each other.</p></sec>
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