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Dynamic Modelling of Microarray Data

Dynamic Modelling of Microarray Data

This video was recorded at Workshop on Parameter Estimation in Systems Biology, Manchester 2007. We recently released rHVDM (Hidden Variable Dynamic Modelling), an R/Bioconductor package that predicts targets of a known transcription factor using time course microarray data. The key feature behind the algorithm is a simple ODE model of mRNA concentration. In the first stage of rHVDM, transcription factor activity (the hidden variable) is deduced from the expression time profile of a small number of known targets. This information is then used to screen other genes for dependency on that transcription factor. The accuracy of the technique has been demonstrated with Affymetrix microarray time course data and verified experimentally using siRNA knockdown of a targeted transcription factor... Show More


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