ArticleGenetics2009
Expression quantitative trait loci mapping with multivariate sparse partial least squares regression.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Integrative Analysis of Multimodal Omics Data.Annual review of statistics and its application · 2026Article
- The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest.Microorganisms · 2022Article
- Integrative sparse partial least squares.Statistics in medicine · 2021Article
- LORSEN: Fast and Efficient eQTL Mapping With Low Rank Penalized Regression.Frontiers in genetics · 2021Article
- Predicting soft tissue changes after orthognathic surgery:The Angle orthodontist · 2019Article
- Statistical Workflow for Feature Selection in Human Metabolomics Data.Metabolites · 2019Review
- Comprehensive functional genomic resource and integrative model for the human brain.Science (New York, N.Y.) · 2018Article
- A multivariate approach to investigate the combined biological effects of multiple exposures.Journal of epidemiology and community health · 2018Article
- Structural cerebellar correlates of cognitive and motor dysfunctions in cerebellar degeneration.Brain : a journal of neurology · 2017Article
- A block mixture model to map eQTLs for gene clustering and networking.Scientific reports · 2016Article
- Fast eQTL Analysis for Twin Studies.Genetic epidemiology · 2015Article
- Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data.Cancer informatics · 2015Article
- Bayesian Partition Models for Identifying Expression Quantitative Trait Loci.Journal of the American Statistical Association · 2015Article
- Article
- Mapping eQTL networks with mixed graphical Markov models.Genetics · 2014Article
- Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix.Heredity · 2014Article
- Identification of genetic variants associated with alternative splicing using sQTLseekeR.Nature communications · 2014Article
- Causal inference of gene regulation with subnetwork assembly from genetical genomics data.Nucleic acids research · 2014Article
- The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Review
- MicroRNAs MiR-218, MiR-125b, and Let-7g predict prognosis in patients with oral cavity squamous cell carcinoma.PloS one · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Expression quantitative trait loci (eQTL) mapping concerns finding genomic variation to elucidate variation of expression traits. This problem poses significant challenges due to high dimensionality of both the gene expression and the genomic marker data. We propose a multivariate response regression approach with simultaneous variable selection and dimension reduction for the eQTL mapping problem. Transcripts with similar expression are clustered into groups, and their expression profiles are viewed as a multivariate response. Then, we employ our recently developed sparse partial least-squares regression methodology to select markers associated with each cluster of genes. We demonstrate with extensive simulations that our eQTL mapping with multivariate response sparse partial least-squares regression (M-SPLS eQTL) method overcomes the issue of multiple transcript- or marker-specific analyses, thereby avoiding potential elevation of type I error. Additionally, joint analysis of multiple transcripts by multivariate response regression increases power for detecting weak linkages. We illustrate that M-SPLS eQTL compares competitively with other approaches and has a number of significant advantages, including the ability to handle highly correlated genotype data and computational efficiency. We provide an application of this methodology to a mouse data set concerning obesity and diabetes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.