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Allele Specific Expression in Human – Genomic Makeup and Phenotypic Implications

https://doi.org/10.1101/757997
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What this work says

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

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Quantifying the effect of sequence variation on regulatory interactions
inferredcites →https://doi.org/10.1006/geno.2000.6406openalex-snapshot
The Cluster of BTN Genes in the Extended Major Histocompatibility Complex
inferredcites →https://doi.org/10.1007/978-1-4939-7868-7_7openalex-snapshot
Gene-Gene and Gene-Environment Interactions
inferredcites →https://doi.org/10.1007/pl00006194openalex-snapshot
The major histocompatability complex (MHC) contains conserved polymorphic genomic sequences that are shuffled by recombination to form ethnic-specific haplotypes
inferredcites →https://doi.org/10.1007/s00251-003-0630-5openalex-snapshot
MHC polymorphism under host-pathogen coevolution
inferredcites →https://doi.org/10.1016/j.ajhg.2017.01.028openalex-snapshot
Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression
inferredcites →https://doi.org/10.1016/j.ceb.2012.10.007openalex-snapshot
Recent advances in X-chromosome inactivation research
inferredcites →https://doi.org/10.1016/j.cell.2013.02.016openalex-snapshot
X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease
inferredcites →https://doi.org/10.1016/j.cell.2017.05.038openalex-snapshot
An Expanded View of Complex Traits: From Polygenic to Omnigenic
inferredcites →https://doi.org/10.1016/j.cell.2018.10.022openalex-snapshot
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression
inferredcites →https://doi.org/10.1016/j.gde.2015.04.002openalex-snapshot
X-chromosome inactivation: new insights into cis and trans regulation
inferredcites →https://doi.org/10.1016/j.humimm.2018.10.002openalex-snapshot
The MHC in the era of next-generation sequencing: Implications for bridging structure with function
inferredcites →https://doi.org/10.1016/j.neuron.2017.01.033openalex-snapshot
Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain
inferredcites →https://doi.org/10.1016/j.tig.2008.06.001openalex-snapshot
Revealing the architecture of gene regulation: the promise of eQTL studies
inferredcites →https://doi.org/10.1016/s0140-6736(16)30582-7openalex-snapshot
Genetic risk factors for type 1 diabetes
inferredcites →https://doi.org/10.1023/a:1026494212540openalex-snapshot
Balancing selection and MHC
inferredcites →https://doi.org/10.1038/35047580openalex-snapshot
X-chromosome inactivation: counting, choice and initiation
inferredcites →https://doi.org/10.1038/jhg.2015.64openalex-snapshot
Functional and genetic diversity of leukocyte immunoglobulin-like receptor and implication for disease associations
inferredcites →https://doi.org/10.1038/msb.2011.54openalex-snapshot
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
inferredcites →https://doi.org/10.1038/nature10659openalex-snapshot
New gene functions in megakaryopoiesis and platelet formation
inferredcites →https://doi.org/10.1038/nature24277openalex-snapshot
Genetic effects on gene expression across human tissues
inferredcites →https://doi.org/10.1038/ncomms11101openalex-snapshot
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals
inferredcites →https://doi.org/10.1038/ncomms9687openalex-snapshot
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression
inferredcites →https://doi.org/10.1038/ng.3162openalex-snapshot
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
inferredcites →https://doi.org/10.1038/ng.3222openalex-snapshot
Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
inferredcites →https://doi.org/10.1038/ng.3274openalex-snapshot
Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse
inferredcites →https://doi.org/10.1038/ng.3432openalex-snapshot
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
inferredcites →https://doi.org/10.1038/ng.3721openalex-snapshot
Disease variants alter transcription factor levels and methylation of their binding sites
inferredcites →https://doi.org/10.1038/ni0901-802openalex-snapshot
The genetics of complex autoimmune diseases: non-MHC susceptibility genes
inferredcites →https://doi.org/10.1038/nm.2731openalex-snapshot
Innate and adaptive immune responses in asthma
inferredcites →https://doi.org/10.1038/nm1599openalex-snapshot
Fen1 mutations result in autoimmunity, chronic inflammation and cancers
inferredcites →https://doi.org/10.1038/nmeth.1357openalex-snapshot
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
inferredcites →https://doi.org/10.1038/nmeth.2772openalex-snapshot
Quantitative single-cell RNA-seq with unique molecular identifiers
inferredcites →https://doi.org/10.1038/nrg.2015.33openalex-snapshot
Autoimmune diseases — connecting risk alleles with molecular traits of the immune system
inferredcites →https://doi.org/10.1038/nrg3888openalex-snapshot
Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
inferredcites →https://doi.org/10.1038/onc.2009.194openalex-snapshot
Genetic predisposition to human disease: allele-specific expression and low-penetrance regulatory loci
inferredcites →https://doi.org/10.1038/s41586-018-0836-1openalex-snapshot
Genomic encoding of transcriptional burst kinetics
inferredcites →https://doi.org/10.1038/s41598-017-07514-zopenalex-snapshot
Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
inferredcites →https://doi.org/10.1038/srep21134openalex-snapshot
GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information
inferredcites →https://doi.org/10.1073/pnas.1219099110openalex-snapshot
Systematic functional regulatory assessment of disease-associated variants
inferredcites →https://doi.org/10.1073/pnas.1708597115openalex-snapshot
Immunogenetic novelty confers a selective advantage in host–pathogen coevolution
inferredcites →https://doi.org/10.1073/pnas.1717421114openalex-snapshot
High-resolution mapping of cis -regulatory variation in budding yeast
inferredcites →https://doi.org/10.1080/01621459.2015.1038449openalex-snapshot
Proper Use of Allele-Specific Expression Improves Statistical Power for cis -eQTL Mapping with RNA-Seq Data
inferredcites →https://doi.org/10.1093/bioinformatics/btp579openalex-snapshot
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
inferredcites →https://doi.org/10.1093/brain/awz054openalex-snapshot
Outcome prediction models in AQP4-IgG positive neuromyelitis optica spectrum disorders
inferredcites →https://doi.org/10.1093/gbe/evx080openalex-snapshot
Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
inferredcites →https://doi.org/10.1093/hmg/ddp473openalex-snapshot
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing
inferredcites →https://doi.org/10.1093/hmg/ddx036openalex-snapshot
GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci
inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
inferredcites →https://doi.org/10.1093/nar/gky1120openalex-snapshot
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019
inferredcites →https://doi.org/10.1101/166298openalex-snapshot
Genome-wide genetic data on ~500,000 UK Biobank participants
inferredcites →https://doi.org/10.1101/531210openalex-snapshot
The mutational constraint spectrum quantified from variation in 141,456 humans
inferredcites →https://doi.org/10.1101/gr.119784.110openalex-snapshot
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
inferredcites →https://doi.org/10.1101/gr.137323.112openalex-snapshot
Annotation of functional variation in personal genomes using RegulomeDB
inferredcites →https://doi.org/10.1101/gr.192278.115openalex-snapshot
The landscape of genomic imprinting across diverse adult human tissues
inferredcites →https://doi.org/10.1101/gr.209759.116openalex-snapshot
High-throughput allele-specific expression across 250 environmental conditions
inferredcites →https://doi.org/10.1101/gr.213538.116openalex-snapshot
Sequences of 95 humanMHChaplotypes reveal extreme coding variation in genes other than highly polymorphicHLA class IandII
inferredcites →https://doi.org/10.1111/1755-0998.12110openalex-snapshot
Allelic imbalance metre ( A llim), a new tool for measuring allele‐specific gene expression with RNA ‐seq data
inferredcites →https://doi.org/10.1126/science.1148910openalex-snapshot
Widespread Monoallelic Expression on Human Autosomes
inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
inferredcites →https://doi.org/10.1158/1538-7445.sabcs18-1584openalex-snapshot
Abstract 1584: Transcriptome analysis links immune genes allelic expression imbalances to lung cancer
inferredcites →https://doi.org/10.1186/1471-2105-10-48openalex-snapshot
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
inferredcites →https://doi.org/10.1186/1471-2164-14-536openalex-snapshot
Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome
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/s12859-016-1238-8openalex-snapshot
A haplotype-based normalization technique for the analysis and detection of allele specific expression
inferredcites →https://doi.org/10.1186/s12859-018-2533-3openalex-snapshot
GOnet: a tool for interactive Gene Ontology analysis
inferredcites →https://doi.org/10.1186/s12864-015-2174-0openalex-snapshot
Extensive variation between tissues in allele specific expression in an outbred mammal
inferredcites →https://doi.org/10.1186/s13059-014-0467-2openalex-snapshot
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies
inferredcites →https://doi.org/10.1186/s13059-016-0881-8openalex-snapshot
A survey of best practices for RNA-seq data analysis
inferredcites →https://doi.org/10.1186/s13059-017-1212-4openalex-snapshot
The impact of rare and low-frequency genetic variants in common disease
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.pmed.1001779openalex-snapshot
UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age
inferredcites →https://doi.org/10.1371/journal.pone.0044008openalex-snapshot
Genome-Wide Association Studies of Asthma in Population-Based Cohorts Confirm Known and Suggested Loci and Identify an Additional Association near HLA
inferredcites →https://doi.org/10.1371/journal.pone.0085093openalex-snapshot
Random or Stochastic Monoallelic Expressed Genes Are Enriched for Neurodevelopmental Disorder Candidate Genes
inferredcites →https://doi.org/10.2337/diabetes.54.5.1588openalex-snapshot
OAS1 Splice Site Polymorphism Controlling Antiviral Enzyme Activity Influences Susceptibility to Type 1 Diabetes
inferredcites →https://doi.org/10.3390/cells8090944openalex-snapshot
MHC Genomics and Disease: Looking Back to Go Forward
inferredcites →https://doi.org/10.34944/dspace/4648openalex-snapshot
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

What points at this work

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

inferred← citeshttps://doi.org/10.1186/s13059-026-04174-zopenalex-snapshot
Mapping the landscape of allele-specific expression in porcine genomes
inferred← citeshttps://doi.org/10.7554/elife.71348openalex-snapshot
Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)
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