Stochastic models for inferring genetic regulation from microarray gene expression data

Bio Systems
Tianhai Tian

Abstract

Microarray expression profiles are inherently noisy and many different sources of variation exist in microarray experiments. It is still a significant challenge to develop stochastic models to realize noise in microarray expression profiles, which has profound influence on the reverse engineering of genetic regulation. Using the target genes of the tumour suppressor gene p53 as the test problem, we developed stochastic differential equation models and established the relationship between the noise strength of stochastic models and parameters of an error model for describing the distribution of the microarray measurements. Numerical results indicate that the simulated variance from stochastic models with a stochastic degradation process can be represented by a monomial in terms of the hybridization intensity and the order of the monomial depends on the type of stochastic process. The developed stochastic models with multiple stochastic processes generated simulations whose variance is consistent with the prediction of the error model. This work also established a general method to develop stochastic models from experimental information.

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Citations

Sep 14, 2011·EURASIP Journal on Bioinformatics & Systems Biology·Elena S DimitrovaAbdul Salam Jarrah
Aug 21, 2012·PloS One·Tianhai Tian, Jiangning Song
Sep 18, 2015·Cognitive Neurodynamics·Ahsan Raja ChowdhuryRob Evans
Aug 16, 2016·Methods : a Companion to Methods in Enzymology·Junbai WangTianhai Tian
Aug 16, 2012·European Journal of Human Genetics : EJHG·David M AlvaradoChristina A Gurnett
Apr 9, 2019·Journal of the Royal Society, Interface·David J WarneMatthew J Simpson
Jul 25, 2020·Journal of Bioinformatics and Computational Biology·O ChatrabgounA Daneshkhah

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