Foundations of Computational Knowledge Discovery from cDNA Microarray Data

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Since the beginning of this research project, the cDNA microarrays have been intensively employed for measuring gene expressions in laboratories. Some projects on genome-wide gene expression analysis have planed where commercialized statistical analysis program packages and databases are employed as bioinformatics tools in an ad hoc way. However, foundations based on information science were not paid attentions so much while only software tools have been developed from the viewpoint of practice in Japan.This reseach project has contributed to the development of novel microarray data analysis technology. First, we have created a mathematical framework for gene network models from cDNA microarray data (Boolean network model, Bayesian network model, system of ordinary differential equations), then we have developed computational methods for inferring these models from cDNA microarray data. These methods were examined through real biological analyzes. The second contribution is a development of modeling and simulation technology for gene networks (an extention of hybrid Petri net and model simulation of various biopathways).With these research contributions, we have established a computational strategy for developing systems biology.