Multiple interval mapping for gene expression QTL analysis

Genetica
Wei Zou, Zhao-Bang Zeng

Abstract

To find the correlations between genome-wide gene expression variations and sequence polymorphisms in inbred cross populations, we developed a statistical method to claim expression quantitative trait loci (eQTL) in a genome. The method is based on multiple interval mapping (MIM), a model selection procedure, and uses false discovery rate (FDR) to measure the statistical significance of the large number of eQTL. We compared our method with a similar procedure proposed by Storey et al. and found that our method can be more powerful. We identified the features in the two methods that resulted in different statistical powers for eQTL detection, and confirmed them by simulation. We organized our computational procedure in an R package which can estimate FDR for positive findings from similar model selection procedures. The R package, MIM-eQTL, can be found at http://www.statgen.ncsu.edu/~wzou/MIM.eQTL.html .

References

Feb 26, 2000·Genetical Research·Z B ZengC J Basten
Dec 19, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R D WolfingerR S Paules
Feb 2, 2002·Nature Reviews. Genetics·N H Barton, P D Keightley
Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Mar 21, 2003·Nature·Eric E SchadtStephen H Friend
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Jan 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Rachel B Brem, Leonid Kruglyak
Mar 29, 2005·Nature Genetics·Jonathan MarchiniLon R Cardon
Jul 23, 2005·PLoS Biology·John D StoreyLeonid Kruglyak
Jul 13, 2006·Nature Genetics·William ValdarJonathan Flint

Citations

Sep 3, 2010·Genetica·Hong Li, Hongwen Deng
Sep 8, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Marcel E VisserBarbara Helm
Nov 26, 2010·Annals of Human Genetics·Yu ZhangJun S Liu
Jan 8, 2011·BMC Bioinformatics·Kyle C Chipman, Ambuj K Singh
Jan 22, 2010·PLoS Computational Biology·Wei ZhangJun S Liu
Feb 2, 2011·PLoS Genetics·Leopold PartsRichard Durbin
Dec 11, 2013·Nucleic Acids Research·Chien-Hua PengWen-Ping Hsieh

Related Concepts

Genome Mapping
In Silico
Yeasts
Gene Expression
Genomics
Quantitative Trait Loci
Gene Expression
Genome
Fluorescent stain
Quantitative Trait Loci

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