Analysis of SNP-Expression Association Matrices

High throughput expression profiling and genotyping technologies provide the means to study the genetic determinants of population variation in gene expression variation. In this paper we present a general statistical framework for the simultaneous analysis of gene expression data and SNP genotype data measured for the same cohort. The framework consists of methods to associate transcripts with SNPs affecting their expression, algorithms to detect subsets of transcripts that share significantly many associations with a subset of SNPs, and methods to visualize the identified relations. We apply our framework to SNP-expression data collected from 49 breast cancer patients. Our results demonstrate an overabundance of transcriptSNP associations in this data, and pinpoint SNPs that are potential master regulators of transcription. We also identify several statistically significant transcriptsubsets with common putative regulators that fall into well-defined functional categories.

• Type: Conference
• Year: 2005
• Where: CSB
• Authors: Anya Tsalenko, Roded Sharan, Hege Edvardsen, Vessela Kristensen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini
• Keywords: Bioinformatics, CSB 2005, Gene Expression, Gene Expression Data, Gene Expression Variation