ArticleGenetics2008
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
88 citing papers in PubMed, 159 citations in OpenAlex.
- Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations.Cell genomics · 2025Article
- Genome-wide association studies for conformation traits in the Turkish Holstein cattle population.Iranian journal of veterinary research · 2025Article
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- Transcriptome-wide association study of the plasma proteome reveals cis and trans regulatory mechanisms underlying complex traits.American journal of human genetics · 2024Article
- Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis.BioData mining · 2024Article
- Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder.Nature genetics · 2023Article
- Pancan-MNVQTLdb: systematic identification of multi-nucleotide variant quantitative trait loci in 33 cancer types.NAR cancer · 2022Article
- Accurate modeling of replication rates in genome-wide association studies by accounting for Winner's Curse and study-specific heterogeneity.G3 (Bethesda, Md.) · 2022Article
- Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders.G3 (Bethesda, Md.) · 2022Article
- Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat.Plant biotechnology journal · 2021Article
- UNIFYING AND GENERALIZING METHODS FOR REMOVING UNWANTED VARIATION BASED ON NEGATIVE CONTROLS.Statistica Sinica · 2021Article
- Article
- An approach for normalization and quality control for NanoString RNA expression data.Briefings in bioinformatics · 2021Article
- DataRemix: a universal data transformation for optimal inference from gene expression datasets.Bioinformatics (Oxford, England) · 2021Article
- Fully automated web-based tool for identifying regulatory hotspots.BMC genomics · 2020Article
- GBAT: a gene-based association test for robust detection of trans-gene regulation.Genome biology · 2020Article
- Data-based RNA-seq simulations by binomial thinning.BMC bioinformatics · 2020Article
- ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types.Nucleic acids research · 2020Article
- Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives.Genetics · 2019Article
- BAYESIAN LATENT HIERARCHICAL MODEL FOR TRANSCRIPTOMIC META-ANALYSIS TO DETECT BIOMARKERS WITH CLUSTERED META-PATTERNS OF DIFFERENTIAL EXPRESSION SIGNALS.The annals of applied statistics · 2019Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
In genomewide mapping of expression quantitative trait loci (eQTL), it is widely believed that thousands of genes are trans-regulated by a small number of genomic regions called "regulatory hotspots," resulting in "trans-regulatory bands" in an eQTL map. As several recent studies have demonstrated, technical confounding factors such as batch effects can complicate eQTL analysis by causing many spurious associations including spurious regulatory hotspots. Yet little is understood about how these technical confounding factors affect eQTL analyses and how to correct for these factors. Our analysis of data sets with biological replicates suggests that it is this intersample correlation structure inherent in expression data that leads to spurious associations between genetic loci and a large number of transcripts inducing spurious regulatory hotspots. We propose a statistical method that corrects for the spurious associations caused by complex intersample correlation of expression measurements in eQTL mapping. Applying our intersample correlation emended (ICE) eQTL mapping method to mouse, yeast, and human identifies many more cis associations while eliminating most of the spurious trans associations. The concordances of cis and trans associations have consistently increased between different replicates, tissues, and populations, demonstrating the higher accuracy of our method to identify real genetic effects.
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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.