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Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis
Key messageThis study provided important insights into the genetic architecture of variations in
A. thaliana leaf ionome in a cell-type-specific...
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Control of false discoveries in grouped hypothesis testing for eQTL data
BackgroundExpression quantitative trait locus (eQTL) analysis aims to detect the genetic variants that influence the expression of one or more genes....
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Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses
Using latent variables in gene expression data can help correct unobserved confounders and increase statistical power for expression quantitative...
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Genome-wide QTL and eQTL map** reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei)
BackgroundGrowth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model...
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Integrative analysis of summary data from GWAS and eQTL studies implicates genes differentially expressed in Alzheimer’s disease
BackgroundAlthough genome-wide association studies (GWAS) have successfully located various genetic variants susceptible to Alzheimer’s Disease (AD),...
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The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle
BackgroundA detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit...
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A pipeline for RNA-seq based eQTL analysis with automated quality control procedures
BackgroundAdvances in the expression quantitative trait loci (eQTL) studies have provided valuable insights into the mechanism of diseases and...
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eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants
We developed a combinatorial next generation sequencing (NGS)-based high-throughput expression QTL-seq (eQTL-seq) strategy for rapid elucidation of...
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Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat
BackgroundIntramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is...
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eQTL Analysis Methods and Protocols
This volume details state-of-art eQTL analysis, where interdisciplinary researchers are provided both theoretical and practical guidance to eQTL...
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eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
BackgroundGenomic studies increasingly integrate expression quantitative trait loci (eQTL) information into their analysis pipelines, but few tools...
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Comparative transcriptomics and eQTL map** of response to Melampsora americana in selected Salix purpurea F2 progeny
BackgroundMelampsora spp. rusts are the greatest pathogen threat to shrub willow ( Salix spp.) bioenergy crops. Genetic resistance is key to limit...
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PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs
Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on...
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Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis
Expression quantitative trait loci (eQTL) map** studies identify genetic loci that regulate gene expression. eQTL map** studies can capture gene...
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Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits
BackgroundGenetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic...
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Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
BackgroundPopulation structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious...
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Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
BackgroundThe discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human...
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Expression Quantitative Trait Loci (eQTL) Analysis in Cancer
Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. Analyzing both cis- and trans-eQTLs from...
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Statistical and Machine Learning Methods for eQTL Analysis
An immense amount of observable diversity exists for all traits and across global populations. In the post-genomic era, equipped with efficient...