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OJBTM
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
ABSTRACT
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.
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