Allele-specific expression analysis methods for high-density SNP microarray data

Allele-specific expression analysis methods for high-density SNP microarray data

MOTIVATION In the past decade, a number of technologies to quantify allele-specific expression (ASE) in a genome-wide manner have become available to researchers. We investigate the application of single-nucleotide polymorphism (SNP) microarrays to this task, exploring data obtained from both cell lines and primary tissue for which both RNA and DNA profiles are available. RESULTS We analyze d...

SNP-specific array-based allele-specific expression analysis.

We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39-49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE...

Multiplex Snp Analysis Microdevice Using Allele-specific Polymerase Chain Reaction-microarray

In this study, we developed an allele-specific polymerase chain reaction-microarray (AS PCR-microarray) chip to perform the allele-specific gene amplification and microarray-based detection on a single wafer to identify Korean indigenous beef cattle, called Hanwoo. For allele-specific discrimination and amplification, Hanwoo-specific ten homozygous single nucleotide polymorphism (SNP) sites wer...

Methods for regression analysis in high-dimensional data

By evolving science, knowledge and technology, new and precise methods for measuring, collecting and recording information have been innovated, which have resulted in the appearance and development of high-dimensional data. The high-dimensional data set, i.e., a data set in which the number of explanatory variables is much larger than the number of observations, cannot be easily analyzed by ...

Analysis of High-density Snp Data from Complex Populations