ArticleNature genetics2015
Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.
Erratum issuedOpen access · greenAbstract read
In one paragraph
Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 130 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
130citing papers in PubMed, 2 pooled it
22.5field-weighted citation impact, top 1% of its field
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
130 citing papers in PubMed, 2 syntheses or guidelines pooled it, 233 citations in OpenAlex.
- Pooled it
- A meta-analysis of gene expression quantitative trait loci in brain.Translational psychiatry · 2014Pooled it
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Autosomal allelic inactivation at loci with variable replication timing and dosage sensitivity.eLife · 2026Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- Gene and allele-specific expression during electric organ ontogeny in African weakly electric fish (Campylomormyrus).Communications biology · 2026Article
- Allele-specific gene expression in F1 hybrid mice reveals structural variants affecting macrophage characteristics.Scientific reports · 2025Article
- A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.Animals : an open access journal from MDPI · 2025Article
- The regulatory architecture of gene expression variation in Caenorhabditis elegans revealed by multi-strain allele-specific analysis.Genetics · 2025Article
- Sequence and parent-of-origin dependent mThe EMBO journal · 2025Article
- The regulatory architecture of gene expression variation inbioRxiv : the preprint server for biology · 2025Article
- Cell-cell communication-mediated cell-type-specific parent-of-origin effects in mammals.Nature communications · 2025Article
- Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms.Journal of advanced research · 2025Article
- Enhancing the neural differentiation capabilities of genetically asymmetric mouse F1 hybrid embryonic stem cell lines.Experimental animals · 2025Article
- An Integrated Database for Exploring Alternative Promoters in Animals.Scientific data · 2025Article
- The X chromosome's influences on the human brain.Science advances · 2025Article
- A comprehensive analysis of allele-specific expression and transcriptomic profiling in pig limbic and endocrine tissues.Frontiers in molecular neuroscience · 2025Article
- Cis-regulatory Variation in Relation to Sex and Sexual Dimorphism in Drosophila melanogaster.Genome biology and evolution · 2024Article
- Inter-subspecies mouse F1 hybrid embryonic stem cell lines newly established for studies of allelic imbalance in gene expression.Experimental animals · 2024Article
70 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
41 authors at 2 institutions in 1 country.
James J CrowleyDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Vasyl ZhabotynskyDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Wei Sun1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Shunping HuangDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Isa Kemal PakatciDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Yunjung KimDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.ORCID 0000000190804739
Jeremy R WangDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Andrew P Morgan1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
John D Calaway1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
David L AylorDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Zaining YunDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Timothy A Bell1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Ryan J Buus1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Mark E Calaway1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
John P Didion1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Terry J Gooch1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Stephanie D Hansen1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Nashiya N Robinson1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Ginger D Shaw1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Jason S SpenceDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Corey R QuackenbushDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Cordelia J BarrickDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Randal J NonnemanDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Kyungsu KimDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
James XenakisDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Yuying XieDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
William Valdar1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.ORCID 0000000224190430
Alan B LenarcicDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Wei WangDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Catherine E WelshDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Chen-Ping FuDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Zhaojun ZhangDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
James HoltDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Zhishan GuoDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
David W ThreadgillDepartment of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, USA.
Lisa M TarantinoDepartment of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Darla R Miller1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Fei ZouDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Leonard McMillanDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Patrick F Sullivan1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [4] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.ORCID 000000026619873X
Fernando Pardo-Manuel de Villena1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
University of North Carolina at Chapel Hill · USTexas A&M Health Science Center · US
Funding
Preclinical CoreU54HD079124 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI LI, YUN · 2013 to 2019
$8.0MAn Interdisciplinary program for systems genomics of complex behaviorsP50MH090338 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PARDO-MANUEL DE VILLENA, FERNANDO · 2009 to 2010
$6.0MBiostatistics for Research in Genomics and CancerT32CA106209 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI JOSEPH G IBRAHIM, Naim Ur Rashid · 2004 to 2026
$4.8MStatistical Methods for RNA-seq Data AnalysisR01GM105785 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Wei Sun · 2014 to 2026
$4.6MAn Interdisciplinary program for systems genomics of complex behaviorsP50HG006582 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PARDO-MANUEL DE VILLENA, FERNANDO · 2011 to 2013
$2.6MRobust Methods for Complex Trait Mapping with Collaborative CrossR01GM074175 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ZOU, FEI · 2006 to 2014
$1.7MSystems Genetics of Fluoxetine-Induced Neurogenesis and Antidepressant ResponseK01MH094406 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CROWLEY, JAMES JOSEPH · 2012 to 2015
$588kEpigenetics, environmental exposure, and reproduction in the Collaborative CrossK99ES021535 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI AYLOR, DAVID LAWRENCE · 2012 to 2013
$176kEffects of advanced paternal age on germline genome stabilityF30MH103925 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI MORGAN, ANDREW PARKER · 2014 to 2017
$151kNCI NIH HHS T32 CA106209NHGRI NIH HHS P50 HG006582NHGRI NIH HHS P50HG006582NICHD NIH HHS U54 HD079124NIEHS NIH HHS K99 ES021535NIGMS NIH HHS R01 GM074175NIGMS NIH HHS R01GM074175NIMH NIH HHS F30 MH103925NIMH NIH HHS K01 MH094406NIMH NIH HHS K01MH094406NIMH NIH HHS P50 MH090338NIMH NIH HHS P50MH090338
Abstract
Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.
Indexed as
AllelesCrosses, GeneticGene ExpressionGenetic SpeciationAllelic ImbalanceAnimalsDosage Compensation, GeneticFemaleHumansMaleMiceMice, KnockoutPhylogenyPolymorphism, Single Nucleotide
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