In this paper, we propose a methodology for making sense of large, multiple time-series data sets arising in expression analysis. Specifically, we present a mathematical model to release a reduced and coherent regulatory system given a putative regulatory network. We give two equivalent formulations of the problem and prove that the problem is NP-complete. For solving large scale instances we implemented an Ant Colony Optimization procedure. A computational analysis on randomly generated test instances validates the proposed algorithm and the computations on real data concerning Saccharomyces cerevisiae show the practicability of the proposed methodology.