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Genomic analysis of allele-specific expression in the mouse liver

https://doi.org/10.1101/024588
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay
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Increased nicotinamide nucleotide transhydrogenase levels predispose to insulin hypersecretion in a mouse strain susceptible to diabetes
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Genetics of Gene Expression in CNS
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Nonsense-mediated mRNA decay: terminating erroneous gene expression
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Distinct Role of Long 3′ UTR BDNF mRNA in Spine Morphology and Synaptic Plasticity in Hippocampal Neurons
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Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits
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Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population
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Correlation of mRNA and protein in complex biological samples
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Carbonic anhydrase III regulates peroxisome proliferator-activated receptor-γ2
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A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
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Genetic architecture of the mouse hippocampus: identification of gene loci with selective regional effects
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CANALIZATION OF DEVELOPMENT AND THE INHERITANCE OF ACQUIRED CHARACTERS
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AlleleSeq: analysis of allele‐specific expression and binding in a network framework
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Genetics of gene expression surveyed in maize, mouse and man
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Global quantification of mammalian gene expression control
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Mouse genomic variation and its effect on phenotypes and gene regulation
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Transcriptome and genome sequencing uncovers functional variation in humans
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Genetics of single-cell protein abundance variation in large yeast populations
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Interpreting noncoding genetic variation in complex traits and human disease
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The Genotype-Tissue Expression (GTEx) project
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System-wide molecular evidence for phenotypic buffering in Arabidopsis
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Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
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Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
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A promoter polymorphism in the Per3 gene is associated with alcohol and stress response
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Metabolomic analysis of liver and skeletal muscle tissues in C57BL/6J and DBA/2J mice exposed to 2,3,7,8-tetrachlorodibenzo- p -dioxin
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Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes
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Neural-specific elongation of 3′ UTRs during Drosophila development
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Fast and accurate short read alignment with Burrows–Wheeler transform
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The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp579openalex-snapshot
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
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Copy number variant detection in inbred strains from short read sequence data
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Fast and accurate long-read alignment with Burrows–Wheeler transform
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MamPhEA: a web tool for mammalian phenotype enrichment analysis
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STAR: ultrafast universal RNA-seq aligner
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RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations
inferredcites →https://doi.org/10.1093/genetics/136.3.1195openalex-snapshot
Mapping quantitative trait loci in crosses between outbred lines using least squares.
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Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression.
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Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes
inferredcites →https://doi.org/10.1093/nar/gkn886openalex-snapshot
The Mouse Genome Database genotypes::phenotypes
inferredcites →https://doi.org/10.1093/nar/gkp265openalex-snapshot
BioMart Central Portal—unified access to biological data
inferredcites →https://doi.org/10.1093/nar/gks425openalex-snapshot
A new strategy to reduce allelic bias in RNA-Seq readmapping
inferredcites →https://doi.org/10.1101/gad.9.24.3097openalex-snapshot
Allele-specific expression and total expression levels of imprinted genes during early mouse development: implications for imprinting mechanisms.
inferredcites →https://doi.org/10.1101/gr.073585.107openalex-snapshot
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
inferredcites →https://doi.org/10.1101/gr.102491.109openalex-snapshot
Regulatory divergence in Drosophila revealed by mRNA-seq
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.124321.111openalex-snapshot
Differential expression in RNA-seq: A matter of depth
inferredcites →https://doi.org/10.1101/gr.146886.112openalex-snapshot
Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
inferredcites →https://doi.org/10.1101/gr.155762.113openalex-snapshot
Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1101/gr.3577405openalex-snapshot
Distribution and intensity of constraint in mammalian genomic sequence
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.1069516openalex-snapshot
Genetic Dissection of Transcriptional Regulation in Budding Yeast
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1152/ajprenal.90318.2008openalex-snapshot
Potassium restriction, high protein intake, and metabolic acidosis increase expression of the glutamine transporter SNAT3 (Slc38a3) in mouse kidney
inferredcites →https://doi.org/10.1159/000363024openalex-snapshot
Dysregulation of the Glutamine Transporter Slc38a3 (SNAT3) and Ammoniagenic Enzymes in Obese, Glucose-Intolerant Mice
inferredcites →https://doi.org/10.1186/1471-2105-11-s4-o7openalex-snapshot
High-throughput sequencing of the DBA/2J mouse genome
inferredcites →https://doi.org/10.1186/1471-2105-12-495openalex-snapshot
MotifMap: integrative genome-wide maps of regulatory motif sites for model species
inferredcites →https://doi.org/10.1186/1471-2164-10-269openalex-snapshot
Definition, conservation and epigenetics of housekeeping and tissue-enriched genes
inferredcites →https://doi.org/10.1186/1471-2164-11-473openalex-snapshot
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
inferredcites →https://doi.org/10.1186/1471-2164-15-471openalex-snapshot
Allele-specific expression and eQTL analysis in mouse adipose tissue
inferredcites →https://doi.org/10.1186/1741-7007-7-23openalex-snapshot
Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay
inferredcites →https://doi.org/10.1186/gb-2005-6-4-r31openalex-snapshot
Conservation of tandem stop codons in yeasts
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r90openalex-snapshot
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
inferredcites →https://doi.org/10.1186/gb-2012-13-8-418openalex-snapshot
An encyclopedia of mouse DNA elements (Mouse ENCODE)
inferredcites →https://doi.org/10.1371/journal.pcbi.1001025openalex-snapshot
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
inferredcites →https://doi.org/10.1371/journal.pgen.1001393openalex-snapshot
Comparative Analysis of Proteome and Transcriptome Variation in Mouse
inferredcites →https://doi.org/10.1371/journal.pgen.1002600openalex-snapshot
Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective
inferredcites →https://doi.org/10.1371/journal.pgen.1004673openalex-snapshot
An Evolutionarily Conserved Role for the Aryl Hydrocarbon Receptor in the Regulation of Movement
inferredcites →https://doi.org/10.1371/journal.pone.0003839openalex-snapshot
Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain
inferredcites →https://doi.org/10.1371/journal.pone.0012181openalex-snapshot
A Transposon in Comt Generates mRNA Variants and Causes Widespread Expression and Behavioral Differences among Mice
inferredcites →https://doi.org/10.1534/genetics.109.107474openalex-snapshot
Detection, Validation, and Downstream Analysis of Allelic Variation in Gene Expression
inferredcites →https://doi.org/10.1534/genetics.113.153882openalex-snapshot
Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage
inferredcites →https://doi.org/10.3109/07357907.2012.732160openalex-snapshot
TXNDC9 Expression in Colorectal Cancer Cells and Its Influence on Colorectal Cancer Prognosis
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Role of Glyoxalase 1 (Glo1) and methylglyoxal (MG) in behavior: recent advances and mechanistic insights
inferredcites →https://doi.org/10.3389/fnins.2012.00063openalex-snapshot
Sex-Specific Modulation of Gene Expression Networks in Murine Hypothalamus
inferredcites →https://doi.org/10.3390/jpm5010022openalex-snapshot
The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2025.10.09.681373openalex-snapshot
Tissue-Specific Regulatory and Expression Patterns of CDG-causative genes account to Phenotypic Variability
inferred← citeshttps://doi.org/10.1101/225714openalex-snapshot
Systems genetics identifies modifiers of Alzheimer’s disease risk and resilience
inferred← citeshttps://doi.org/10.1186/s12864-021-08168-yopenalex-snapshot
Genetic architecture of protein expression and its regulation in the mouse brain
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