Analyzing allele specific RNA expression using mixture models.

ABSTRACT:

Background

Measuring allele-specific RNA expression provides valuable insights into cis-acting genetic and epigenetic regulation of gene expression. Widespread adoption of high-throughput sequencing technologies for studying RNA expression (RNA-Seq) permits measurement of allelic RNA expression imbalance (AEI) at heterozygous single nucleotide polymorphisms (SNPs) across the entire transcriptome, and this approach has become especially popular with the emergence of large databases, such as GTEx. However, the existing binomial-type methods used to model allelic expression from RNA-seq assume a strong negative correlation between reference and variant allele reads, which may not be reasonable biologically.

Results

Here we propose a new strategy for AEI analysis using RNA-seq d

SUBMITTER: Lu R 

PROVIDER: S-EPMC4521363 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature