Automatic reconstruction of molecular and genetic networks from discrete time series data.
We apply a mathematical algorithm which processes discrete time series data to generate a complete list of Petri net structures containing the minimal number of nodes required to reproduce the data set. The completeness of the list as guaranteed by a mathematical proof allows to define a minimal set of experiments required to discriminate between alternative network structures. This in principle allows to prove all possible minimal network structures by disproving all alternative candidate structures. The dynamic behaviour of the networks in terms of a switching rule for the transitions of the Petri net is part of the result. In addition to network reconstruction, the algorithm can be used to determine how many yet undetected components at least must be involved in a certain process. The algorithm also reveals all alternative structural modifications of a network that are required to generate a predefined behaviour.
Magdeburg Centre for Systems Biology, Otto-von-Guericke-Universität Magdeburg, Magdeburg, Germany.
Markus
M
Durzinsky
Annegret
A
Wagler
Robert
R
Weismantel
Wolfgang
W
Marwan
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D053263:Gene Regulatory Networks; D019617:Halobacterium salinarum / Q000378:metabolism / Q000528:radiation effects; D007700:Kinetics; D008954:Models, Biological; D020283:Photoreceptors, Microbial / Q000378:metabolism; D016839:Physarum polycephalum / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D012243:Rhodopsin / Q000378:metabolism; D015398:Signal Transduction / Q000528:radiation effects; D013997:Time Factors
D020283:Photoreceptors, Microbial; D012243:Rhodopsin