Analysis of SNP-expression association matrices.
J Bioinform Comput Biol
; 4(2): 259-74, 2006 Apr.
Article
em En
| MEDLINE
| ID: mdl-16819783
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 50 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.
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Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Algoritmos
/
Neoplasias da Mama
/
Alinhamento de Sequência
/
Análise de Sequência de DNA
/
Polimorfismo de Nucleotídeo Único
/
Proteínas de Neoplasias
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2006
Tipo de documento:
Article