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- Title
Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli.
- Authors
Mäkelä, Jarno; Huttunen, Heikki; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S.
- Abstract
Motivation: Production and degradation of RNA and proteins are stochastic processes, difficulting the distinction between spurious fluctuations in their numbers and changes in the dynamics of a genetic circuit. An accurate method of change detection is key to analyze plasticity and robustness of stochastic genetic circuits.Results: We use automatic change point detection methods to detect non-spurious changes in the dynamics of delayed stochastic models of gene networks at run time. We test the methods in detecting changes in mean and noise of protein numbers, and in the switching frequency of a genetic switch. We also detect changes, following genes' silencing, in the dynamics of a model of the core gene regulatory network of Saccharomyces cerevisiae with 328 genes. Finally, from images, we determine when RNA molecules tagged with fluorescent proteins are first produced in Escherichia coli. Provided prior knowledge on the time scale of the changes, the methods detect them accurately and are robust to fluctuations in protein and RNA levels.Availability: Simulator: www.cs.tut.fi/~sanchesr/SGN/SGNSim.htmlContact: andre.ribeiro@tut.fiSupplementary information:Supplementary data are available at Bioinformatics online.
- Subjects
BACTERIAL genetics; ESCHERICHIA coli; MOLECULAR dynamics; STOCHASTIC analysis; RNA; GENETICS; ROBUST control; GENE silencing
- Publication
Bioinformatics, 2011, Vol 27, Issue 19, p2714
- ISSN
1367-4803
- Publication type
Article