A mathematical program to refine gene regulatory networks

Authors:
Guglielmo Lulli;Martin Romauch
Affiliations:
University of Milano "Bicocca", Department of Informatics, Systems and Communication, via Bicocca degli Arcimboldi 8, 20122 Milano, Italy;University of Vienna, Department of Business Administration, Brünner Straíe 72, A-1210 Vienna, Austria
Venue:
Discrete Applied Mathematics
Year:
2009

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Abstract

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.