Periodicity in cellular processes is arguably the most underestimated phenomenon in molecular biology. We previously demonstrated the circadian oscillation of baseline expression in eukaryotic genes showing that cycling is a basic property of all genes and not a function of only a subset (10-15%). We further explore the periodicity of cellular processes in this study by asking the question of whether the circadian cascade of gene expression is reflected by a cascade of molecular functions. We do this by reanalyzing a set of time-course gene expression data from heart tissue of wild type and CLOCK-mutant mice. The analysis of sets of oscillating genes that peak at different times during the day, demonstrate that some molecular functions and processes are more active at certain times than others. Comparison between wild type and CLOCK-mutant tissue samples shows the difference not in the overall number of oscillating genes, but rather in coordination of molecular functions with time. These findings will impact the choice of background controls for future expression studies, and improve the models for biological pathways to name a few of its implications.


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