ArticleGenetics2010
Detection, validation, and downstream analysis of allelic variation in gene expression.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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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
40 citing papers in PubMed, 63 citations in OpenAlex.
- Rhes, a striatal enriched protein, regulates post-translational small-ubiquitin-like-modifier (SUMO) modification of nuclear proteins and alters gene expression.Cellular and molecular life sciences : CMLS · 2024Article
- Genetic dissection of glutathione S-transferase omega-1: identification of novel downstream targets and Alzheimer's disease pathways.Neural regeneration research · 2022Article
- Genetic architecture of protein expression and its regulation in the mouse brain.BMC genomics · 2021Article
- Exploring the involvement of Tac2 in the mouse hippocampal stress response through gene networking.Gene · 2019Article
- Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method.Scientific reports · 2019Article
- RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork.Molecular vision · 2019Article
- Post-genomic behavioral genetics: From revolution to routine.Genes, brain, and behavior · 2018Review
- Ethanol's Effect onFrontiers in genetics · 2018Article
- Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray.PloS one · 2018Article
- Genetic divergence in the transcriptional engram of chronic alcohol abuse: A laser-capture RNA-seq study of the mouse mesocorticolimbic system.Alcohol (Fayetteville, N.Y.) · 2017Article
- Analyses of differentially expressed genes after exposure to acute stress, acute ethanol, or a combination of both in mice.Alcohol (Fayetteville, N.Y.) · 2017Article
- The effect of alcohol on the differential expression of cluster of differentiation 14 gene, associated pathways, and genetic network.PloS one · 2017Article
- GeneNetwork: A Toolbox for Systems Genetics.Methods in molecular biology (Clifton, N.J.) · 2017Article
- RasGRP1 promotes amphetamine-induced motor behavior through a Rhes interaction network ("Rhesactome") in the striatum.Science signaling · 2016Article
- A novel heat shock protein alpha 8 (Hspa8) molecular network mediating responses to stress- and ethanol-related behaviors.Neurogenetics · 2016Article
- The Genetic Architecture of Murine Glutathione Transferases.PloS one · 2016Article
- Identification of candidate genes that underlie the QTL on chromosome 1 that mediates genetic differences in stress-ethanol interactions.Physiological genomics · 2015Article
- Equalizer reduces SNP bias in Affymetrix microarrays.BMC bioinformatics · 2015Article
- Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.PLoS genetics · 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
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 2 countries.
Funding
Abstract
Common sequence variants within a gene often generate important differences in expression of corresponding mRNAs. This high level of local (allelic) control-or cis modulation-rivals that produced by gene targeting, but expression is titrated finely over a range of levels. We are interested in exploiting this allelic variation to study gene function and downstream consequences of differences in expression dosage. We have used several bioinformatics and molecular approaches to estimate error rates in the discovery of cis modulation and to analyze some of the biological and technical confounds that contribute to the variation in gene expression profiling. Our analysis of SNPs and alternative transcripts, combined with eQTL maps and selective gene resequencing, revealed that between 17 and 25% of apparent cis modulation is caused by SNPs that overlap probes rather than by genuine quantitative differences in mRNA levels. This estimate climbs to 40-50% when qualitative differences between isoform variants are included. We have developed an analytical approach to filter differences in expression and improve the yield of genuine cis-modulated transcripts to approximately 80%. This improvement is important because the resulting variation can be successfully used to study downstream consequences of altered expression on higher-order phenotypes. Using a systems genetics approach we show that two validated cis-modulated genes, Stk25 and Rasd2, are likely to control expression of downstream targets and affect disease susceptibility.
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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.