From gene-expressions to pathways

Abstract

Rapid advancements in experimental techniques have benefited molecular biology in many ways. The experiments once considered impossible due to the lack of resources can now be performed with relative ease in an acceptable time-span; monitoring simultaneous expressions of thousands of genes at a given time point is one of them. Microarray technology is the most popular method in biological sciences to observe the simultaneous expression levels of a large number of genes. The large amount of data produced by a microarray experiment requires considerable computational analysis before some biologically meaningful hypothesis can be drawn. In contrast to a single time-point microarray experiment, the temporal microarray experiments enable us to understand the dynamics of the underlying system. Such information, if properly utilized, can provide vital clues about the structure and functioning of the system under study. This dissertation introduces some new computational techniques to process temporal microarray data. We focus on three broad stages of microarray data analysis - normalization, clustering and inference of gene-regulatory networks. We explain our methods using various synthesized datasets and a real biological dataset, produced in-house, to monitor the leaf senescence process in Arabidopsis thaliana