etd - Abstract ZOU WEI Transcriptional Regulatory Patterns...

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Abstract ZOU, WEI. Transcriptional Regulatory Patterns in Yeast Revealed through Expres- sion Quantitative Trait Locus Mapping. (Under the direction of Dr. Zhao-Bang Zeng.) Expression Quantitative Trait Locus (eQTL) mapping combines large scale mRNA expression analysis and classical quantitative genetics methods to find the correlated variation between genome and transcriptome. We applied a sequential genome scan method to build genetic architectures for expression traits in a published yeast eQTL mapping data set. We compared mapping results from several variants of the method. We used the threshold controlling the genome-wise type I error rate to declare eQTLs, and used False Discovery Rate (FDR) to assess the overall error rate in the whole mapping study. In this mapping population, expression traits tend to be mapped onto its own sequence and avoid being mapped onto their transcriptional factors. Sequence variations around transcriptional factors are not preferentially associated with transcript abundance variation of their regulatory target genes, though the ex- pression traits of transcriptional factors and their targets tend to have overlapping eQTL regions. Indirect trans-regulation mechanisms play a significant role in order to connect trans-acting eQTLs with certain biological pathways. We have developed a graphical tool to visualize the myriad relationships suggested by eQTL analysis. The tool allows dynamical superimposition of biological annotation onto declared eQTLs to find the matching cases between statistical patterns inferred from this mapping population and results of biological investigation on this organism. Finally, we pro- posed a probabilistic way of combining statistical patterns with biological annotations based on Bayes’ Theorem. The resulting posterior probability that a gene in an eQTL causes the trait variation can be used to prioritize genes in an eQTL.
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Transcriptional Regulatory Patterns in Yeast Revealed through Expression Quantitative Trait Locus Mapping by Wei Zou a dissertation submitted to the graduate faculty of north carolina state university in partial fulfillment of the requirements for the degree of doctor of philosophy bioinformatics raleigh 2006 approved by: Trudy F.C. Mackay Sujit K. Ghosh Zhao-Bang Zeng Bruce S. Weir chair of advisory committee
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To my parents ii
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Biography Wei Zou was born as the only child to his parents Heng Zou and Lipin Shen in Simao, Yunnan Province, China in October 1976. He was admitted to a bio-medical program jointly offered by Fudan University and Shanghai Second Medical University in 1994 and received a Bachelor of Medicine degree in July 1999. He then studied Human Genetics in the graduate school of Fudan University. In August 2002, Wei came to North Carolina State University (NCSU) to pursue a PhD degree in Bioin- formatics. Under the direction of Dr. Zhao-Bang Zeng, Wei studied Quantitative Trait Locus Mapping.
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