Analysis of allele-specific gene expression using a target-oriented tiling microarray assay.

@article{Zhang2013AnalysisOA,
  title={Analysis of allele-specific gene expression using a target-oriented tiling microarray assay.},
  author={Huiyong Zhang and Xing Wang Deng and Lei Li},
  journal={Methods in molecular biology},
  year={2013},
  volume={1067},
  pages={
          65-76
        }
}
Advances in molecular and computational biology in recent years have led to the development or the improvement of methods for analyzing global gene expression. In most of these efforts, it is assumed that alleles of different origins contribute equally to the transcript pool. However, accumulating evidence suggests that many genes are not equally expressed from the paternal and maternal chromosomes. In addition to imprinting, the phenomenon of imbalanced allelic expression is widespread in… 
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References

SHOWING 1-10 OF 49 REFERENCES

Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression.

Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.

In segregants from a cross between two unrelated strains of Saccharomyces cerevisiae, high-quality genotype data can also be obtained when mRNA is hybridized to an oligonucleotide-expression array, demonstrating how simultaneous genotyping and gene-expression profiling can reveal cis-regulatory variation.

Accurate quantitation of allele-specific expression patterns by analysis of DNA melting.

A novel procedure and algorithm to precisely and accurately quantitate the relative expression of each allele using the differential melting properties of DNAs differing at even a single base pair is presented.

Allelic variation in gene expression is common in the human genome.

It is demonstrated that variation of gene expression between alleles is common, and this variation may contribute to human variability, as shown by real-time quantitative PCR experiments.

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

It is concluded that microarray based minisequencing is an accurate and accessible tool for multiplexed screening for imbalanced allelic expression in multiple samples and tissues in parallel.

Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid Maize[W]

Comparisons provided evidence for tissue-specific cis-acting variation and for a slight maternal expression bias in ∼20% of genes in embryo tissue that contributes to biased allelic expression between genotypes and between tissues.

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

It is shown that allele-specific expression measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression.

Allele-specific gene expression differences in humans.

The evidence suggests that given a large enough population, most, if not all genes may have allele-specific expression differences in at least some individuals and finding the genetic origins of each of these and linking the former to a possible phenotype must be a major long term goal of the biomedical community.

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells

This study established a process for systematic screening for cis-acting rSNPs using experimental detection of AI as an initial approach and identified differential protein binding from a nuclear extract between the SNP alleles.

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.

This work developed a powerful and flexible hierarchical Bayesian model that combines information across loci to allow both global and locus-specific inferences about allele-specific expression (ASE) and provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes.