High throughput expression profiling enables the global study about gene activities. It is known that co-expressed genes are likely to be functionally related. However, because cellular processes are interlocked and many proteins have multiple functions, co-regulated genes may disassociate as the intrinsic cellular state changes. For depicting such complex physiology, a theory of co-expression dynamics is presented. In one application, SCH9 is found to scout the co-expression activity between ARG1 and ARG2, linking yeast longevity to efficient expression of urea cycle. Other examples include mitochondrial electron transport, calmodulin, and two genes ECM1, YNL101W whose functions are newly revealed.