ArticleGenomics2009
Single nucleotide polymorphisms affect both cis- and trans-eQTLs.
Article in Genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Genomic-Analysis-Oriented Drug Repurposing in the Search for Novel Antidepressants.Biomedicines · 2022Article
- Effective SNP ranking improves the performance of eQTL mapping.Genetic epidemiology · 2020Article
- Dissecting Brain Networks Underlying Alcohol Binge Drinking Using a Systems Genomics Approach.Molecular neurobiology · 2019Article
- The emerging landscape of dynamic DNA methylation in early childhood.BMC genomics · 2017Article
- Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population.Frontiers in genetics · 2017Article
- PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs.Scientific reports · 2015Article
- Variation in Drosophila melanogaster central metabolic genes appears driven by natural selection both within and between populations.Proceedings. Biological sciences · 2015Article
- A small system--high-resolution study of metabolic adaptation in the central metabolic pathway to temperate climates in Drosophila melanogaster.Molecular biology and evolution · 2014Article
- Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.PLoS genetics · 2014Article
- Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics.BMC genomics · 2014Article
- 'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences.BMC bioinformatics · 2012Article
- Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG.PloS one · 2012Article
- Ethanol modulation of gene networks: implications for alcoholism.Neurobiology of disease · 2012Review
- Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis.PLoS genetics · 2011Article
- QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments.BMC genomics · 2011Article
- Modeling expression quantitative trait loci in data combining ethnic populations.BMC bioinformatics · 2010Article
- Detection, validation, and downstream analysis of allelic variation in gene expression.Genetics · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Single nucleotide polymorphisms (SNPs) between microarray probes and RNA targets can affect the performance of expression array by weakening the hybridization. In this paper, we examined the effect of the SNPs on Affymetrix GeneChip probe set summaries and the expression quantitative trait loci (eQTL) mapping results in two eQTL datasets, one from mouse and one from human. We showed that removing SNP-containing probes significantly changed the probe set summaries and the more SNP-containing probes we removed the greater the change. Comparison of the eQTL mapping results between with and without SNP-containing probes showed that less than 70% of the significant eQTL peaks were concordant regardless of the significance threshold. These results indicate that SNPs do affect both probe set summaries and eQTLs (both cis and trans), thus SNP-containing probes should be filtered out to improve the performance of eQTL mapping.
Indexed as
Identifiers
What OpenQuestion holds
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.