title: Analysis of SNP-expression association matrices.
abstract: 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 transcript-SNP associations in this data, and pinpoint SNPs that are potential master regulators of transcription. We also identify several statistically significant transcript-subsets with common putative regulators that fall into well-defined functional categories.
authors.affiliation: Agilent Technologies, 3500 Deer Creek Road, Palo Alto, CA 94304, USA. anya_tsalenko@agilent.com
authors.forename: Anya
authors.initials: A
authors.lastname: Tsalenko
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
authors.forename: Hege
authors.initials: H
authors.lastname: Edvardsen
authors.forename: Vessela
authors.initials: V
authors.lastname: Kristensen
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.forename: Amir
authors.initials: A
authors.lastname: Ben-Dor
authors.forename: Zohar
authors.initials: Z
authors.lastname: Yakhini
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D015870:Gene Expression / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D009363:Neoplasm Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins