Analysis of transcriptional regulatory circuitry

Abstract

The research in this thesis has focused on the analysis of data from two types of microarray technologies with the goal of improving understanding of transcriptional regulatory circuitry in yeast. These microarray technologies, expression analysis and location analysis (ChIP on CHIP), bring unique challenges for data analysis. I have adapted methods described previously and have developing new algorithms for addressing some of these challenges. I generated yeast transcription factor location data as part of a team effort to determine how a large set of transcriptional regulators occupy the yeast genome and to facilitate discovery of regulatory network structures. I also contributed to another team effort to deduce a portion of the yeast transcriptional regulatory code, the set of genomic DNA sequences recognized by transcriptional regulators to effect gene expression programs. Finally, I used these experimental and analytical methods to explore changes in gene expression circuitry that occur after exposure to oxidative stress in yeast.