Sleep is an animal behavior shared by a wide range of species, suggesting that it must serve fundamental functions. However, the functions and molecular mechanisms underlying sleep are largely unknown. Through a meta-analysis of all available short-term sleep deprivation (SD) microarray data in mouse brain, we identified 91 key mouse SD-affected genes and two RBM3 isoforms showing opposite changes of expression during SD. Although most of the key SD-affected genes showed consistent changes of expression during SD across brain subregions despite their heterogeneous basal expression levels, we also identified the genes whose SD responses strongly depend upon the brain subregion. A gene regulatory network was also constructed for these genes showing that cAMP-responsive element (CRE) is one of the key cis-regulatory elements controlling SD-affected genes. We observed that SD during an animal's normal sleeping time could significantly disturb the circadian oscillation of clock genes. Surprisingly, synaptogenesis markers were significantly underexpressed in SD mice, differing from the previous findings in rat and fly. Comparing SD microarray data in mouse, rat, sparrow, and fly, we identified Egr and Nr4a gene families as conserved SD-affected genes, thus shedding new light on the origin of sleep in animals.