Model-Based Inference of Transcriptional Regulatory Mechanisms from DNA Microarray Data

摘要: The development of DNA microarray technology has made it possible to monitor the mRNA abundance all genes simultaneously (the transcriptome) for a variety cellular conditions. In addition, microarray-based genomewide measurements promoter occupancy occupome) are now available an increasing number transcription factors. With this data and complete genome sequence many important organisms, is becoming quantitatively model molecular computation performed at each promoter, which as input nuclear concentration active form various regulatory proteins regulome) output rate, in turn determines abundance. chapter, we describe how our group used multivariate linear regression methods to: (i) discover cis-regulatory elements upstream regions unbiased manner; (ii) infer activity profile across conditions factor; (iii) determine whether expression level gene whose occupied by particular factor truly regulated that factor, through integrated modeling data. Together, these results show model-based analysis functional genomics be versatile conceptual practical framework elucidation circuitry, powerful alternative currently prevalent clustering-based methods.