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

Bioinformatics
Ruijie LiuMatthew E Ritchie

Abstract

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. We analyze data from two experiments that make use of high-density Illumina Infinium II genotyping arrays to measure ASE. We first preprocess each data set, which involves removal of outlier samples, careful normalization and a two-step filtering procedure to remove SNPs that show no evidence of expression in the samples being analyzed and calls that are clear genotyping errors. We then compare three different tests for detecting ASE, one of which has been previously published and two novel approaches. These tests vary at the level at which they operate (per SNP per individual or per SNP) and in the input data they require. Using SNPs from imprinted genes as true positives for ASE, we observe varying sensitivity for the different testing procedures that improves with increasing sample size. Methods that rely on RNA signal alone were found to perform best across a range o...Continue Reading

References

Aug 7, 2003·Genome Research·H Shuen LoMaxwell P Lee
Mar 31, 2004·Trends in Genetics : TIG·Julia C Knight
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 22, 2005·Nature Methods·Frank J SteemersKevin L Gunderson
Feb 10, 2006·Genome Research·P V Krishna PantKelly A Frazer
Oct 19, 2007·Nature·UNKNOWN International HapMap ConsortiumJohn Stewart
Nov 17, 2007·Science·Alexander GimelbrantAndrew Chess
Mar 29, 2008·Genome Research·Hans T BjornssonAndrew P Feinberg
May 9, 2008·PLoS Biology·Kerstin B MeyerBruce A J Ponder
Aug 2, 2008·BMC Genomics·Joëlle MichaudHamish S Scott
Aug 8, 2009·Bioinformatics·Matthew E RitchieRafael A Irizarry
Dec 17, 2009·Breast Cancer Research : BCR·Ana-Teresa MaiaBruce A J Ponder
May 28, 2010·BMC Bioinformatics·Matthew E RitchieSimon Tavaré
Jul 16, 2010·PLoS Computational Biology·James R WagnerMathieu Blanchette
Mar 23, 2011·Genome Biology·Lisanne MorcosTomi Pastinen

❮ Previous
Next ❯

Citations

Apr 24, 2013·Journal of Applied Genetics·Uma GaurGuisheng Liu
Aug 24, 2013·BMC Genomics·Ryan M SmithWolfgang Sadee
Mar 5, 2020·NPJ Genomic Medicine·Ana Jacinta-FernandesAna-Teresa Maia
Feb 13, 2021·NPJ Genomic Medicine·Ana Jacinta-FernandesAna-Teresa Maia

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.