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Online Journal of Bioinformatics ©
Volume 11 (2): 177-218, 2010.
Inferring the kinetic constants of cyclin-triggered expression of Cdc20 gene in eukaryotic cell cycle
Paola Lecca, Alida Palmisano and Ihekwaba AEC
The Microsoft Research - University of Trento Centre for Computational and Systems Biology, 38123 Povo (Trento), Italy
Lecca P, Palmisano A Inferring the kinetic constants of cyclin-triggered expression of Cdc20 gene in eukaryotic cell cycle, Onl J Bioinform, 11(2) 177-218, 2010. A method of parameter identification for the rate equations and the computation of confidence intervals for the parameter estimates recently developed by the authors is described .The software KInfer implementing this method is applied to infer the model parameters regarding the genetic regulation of gene Cdc20 (cell division cycle 20) in the eukaryotic cell cycle control network. The focus on Cdc20 is motivated by the fact that Cdc20 is an essential regulator of cell division. Its main function is to activate the anaphase promoting complex, a large 11-13 subunit complex that initiates chromatid separation and entrance into anaphase. The transcription of the gene Cdc20 has been modeled as a cyclin/Cdk - triggered process on the ground of recent theoretical and experimental studies, and has been incorporated in an existing well established model of the cell cycle control protein network. In this study the model of Cdc20 transcription is realized by a linear function of cyclin/CDK concentration and the model parameter optimization has been performed by KInfer to fit experimental micro-array data of the Cdc20 expression level. Six different time-series of micro-array data of mRNA Cdc20 level obtained in six different experiments available in public online databases have been used to optimize the parameters and to establish the appropriateness of the proposed model variant.