Circadian rhythms exist in almost all organisms to anticipate the daily changes in the environment and to temporally coordinate biological processes. Although much progress has been made to identify the components of the mammalian clock and the mechanisms by which it controls physiology, the knowledge base is by no means complete. We propose to further elucidate the architecture of the liver clock and its relationship with metabolism by generating and integrating divergent types of large-scale data, followed by validation of these data in vivo. In order to isolate and study the cell-autonomous clock, we have identified a unique cell line, Met Murine Hepatocyte-Day 3 (MMH-D3) that retains many metabolic functions and exhibits robust circadian rhythms. Thus we will be able to interrogate both the clock and metabolic pathways and study their interactions. We have already obtained transcriptomic and metabolomic data for MMH-D3 time-courses (every 2-hours for 48-hours) to identify cycling entities. Furthermore, we will perform chromatin immunoprecipitation followed by sequencing (ChIP-seq) for REV-ERB1, a nuclear hormone receptor that is part of the clock and a regulator of lipid metabolism, to explore one of the mechanisms of how the clock controls metabolism. To identify novel proteins that act as systemic cues for the liver clock, we will perform high- throughput screening of an invaluable library of over 6,000 secreted proteins. To our knowledge, this is one of the broadest and diverse data sets collected for the analysis of the circadian clock. To generate the most comprehensive model of the clock, these data sets will not only be evaluated individually, but will be integrated to reconstruct biological networks using methods based on vector auto-regression. Such networks have the ability to predict regulation and interaction within and between the different layers, as well as their associations with metabolic pathways. The hypotheses generated by the network model will be verified using adenovirus techniques in vivo, which will also enable us to differentiate between cell-autonomous and systemic signals governing the liver clock. The clock clearly has an influence on proper physiological function, thus a better understanding of circadian clockwork will improve our understanding of the mechanisms that underlie human disease; this will refine diagnostic and therapeutic strategies.