ArticlePLoS genetics2018
Expression reflects population structure.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Genome research · 2024Article
- Multiset correlation and factor analysis enables exploration of multi-omics data.Cell genomics · 2023Article
- Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data.Frontiers in genetics · 2023Article
- Molecular Subtyping in Muscle-Invasive Bladder Cancer on Predicting Survival and Response of Treatment.Biomedicines · 2022Article
- Capturing discrete latent structures: choose LDs over PCs.Biostatistics (Oxford, England) · 2022Article
- Host genomic influence on bacterial composition in the switchgrass rhizosphere.Molecular ecology · 2022Article
- Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders.G3 (Bethesda, Md.) · 2022Article
- Consistency and overfitting of multi-omics methods on experimental data.Briefings in bioinformatics · 2020Article
- Article
- Transcriptional Basis for Differential Thermosensitivity of Seedlings of Various Tomato Genotypes.Genes · 2020Article
- Population-Specific Genetic and Expression Differentiation in Europeans.Genome biology and evolution · 2020Article
- Multimodal single-cell approaches shed light on T cell heterogeneity.Current opinion in immunology · 2019Review
- Coordination Analysis of Gene Expression Points to the Relative Impact of Different Regulators During Endoplasmic Reticulum Stress.DNA and cell biology · 2019Article
- CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets.Genome biology · 2019Article
- A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Population structure in genotype data has been extensively studied, and is revealed by looking at the principal components of the genotype matrix. However, no similar analysis of population structure in gene expression data has been conducted, in part because a naïve principal components analysis of the gene expression matrix does not cluster by population. We identify a linear projection that reveals population structure in gene expression data. Our approach relies on the coupling of the principal components of genotype to the principal components of gene expression via canonical correlation analysis. Our method is able to determine the significance of the variance in the canonical correlation projection explained by each gene. We identify 3,571 significant genes, only 837 of which had been previously reported to have an associated eQTL in the GEUVADIS results. We show that our projections are not primarily driven by differences in allele frequency at known cis-eQTLs and that similar projections can be recovered using only several hundred randomly selected genes and SNPs. Finally, we present preliminary work on the consequences for eQTL analysis. We observe that using our projection co-ordinates as covariates results in the discovery of slightly fewer genes with eQTLs, but that these genes replicate in GTEx matched tissue at a slightly higher rate.
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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.