Studies conducted on genes expression through the sleep-wake cycle and after sleep deprivation have revealed a number of genes that are more active during wakefulness/prolonged wakefulness than sleep, but also a few genes that are more active during sleep than wakefulness. Gene expression profiles during a specific vigilance state can be effectively monitored using microarrays, and when comparing profiles under different vigilance states, state-specific gene expression patterns can be precipitated. As such approach is random, and does not include any assumptions as to which genes would be expressed, it offers a non-biased view on the participation of different factors in the regulation of vigilance states. Combining results from different species offers a powerful tool for the analysis of genes that are involved in sleep-wake cycle regulation. The results of such assays are dependent on what area the tissue for the analysis is collected and the time point of the collection in respect to the duration of the specific vigilance state.