A systems biology design and implementation of novel bioinformatics software tools for high throughput gene expression analysis

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Microarray technology has revolutionized the field of molecular biology by offering an efficient and cost effective platform for the simultaneous quantification of thousands of genes or even entire genomes in a single experiment. Unlike southern blotting, which is restricted to the measurement of one gene at-a-time, microarrays offer biologists with the opportunity to carry out genome-wide experiments in order to help them gain a systems level understanding of cell regulation and control. The application of bioinformatics in the milieu of gene expression analysis has attracted a great deal of attention in the recent past due to specific algorithms and software solutions that attempt to illustrate complex multidimensional microarray data in a biologically coherent fashion so that it can be understood by the biologist. This has given rise to some exciting prospects for deciphering microarray data, by helping us refine our comprehension pertinent to the underlying physiological dynamics of disease. Although much progress is being made in the development of specialized bioinformatics software pipelines with the purpose of decoding large volumes of gene expression data in the context of systems biology, several loopholes exist. Perhaps most notable of these loopholes is the fact that there is an increasing demand for software solutions that specialize in automating the comparison of multiple gene expression profiles, derived from microarray experiments sharing a common biological theme. This is no doubt an important challenge, since common genes across different biological conditions having similar expression patterns are likely to be involved in the same biological process and hence, may share the same regulatory signatures. The potential benefits of this in refining our understanding of the physiology of disease are undeniable. The research presented in this thesis provides a systematic walkthrough of a series of software pipelines developed for the purpose of streamlining gene expression analysis in a systems biology context. Firstly, we present BiSAn, a software tool that deciphers expression data from the perspective of transcriptional regulation. Following this, we present Genome Interaction Analyzer (GIA), which analyzes microarray data in the integrative framework of transcription factor binding sites, protein-protein interactions and molecular pathways. The final contribution is a software pipeline called MicroPath, which analyzes multiple sets of gene expression profiles and attempts to extract common regulatory signatures that may be implicating the biological question