ArticleScientific reports2016
GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 63 citations in OpenAlex.
- TIGER: The gene expression regulatory variation landscape of human pancreatic islets.Cell reports · 2021Pooled it
- Monoallelic expression characterizes a distinct molecular and clinical group of breast tumors.Research square · 2026Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications.GigaScience · 2025Article
- A comprehensive analysis of allele-specific expression and transcriptomic profiling in pig limbic and endocrine tissues.Frontiers in molecular neuroscience · 2025Article
- Ornaments for efficient allele-specific expression estimation with bias correction.American journal of human genetics · 2024Article
- Exploration of genotype-by-environment interactions affecting gene expression responses in porcine immune cells.Frontiers in genetics · 2023Article
- Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.Bioinformatics (Oxford, England) · 2022Article
- Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines.Frontiers in immunology · 2022Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality.Genome biology and evolution · 2021Article
- Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases.International journal of molecular sciences · 2021Review
- Replicate sequencing libraries are important for quantification of allelic imbalance.Nature communications · 2021Article
- Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data.PLoS genetics · 2021Article
- Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT.Scientific reports · 2021Article
- ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing.PLoS genetics · 2020Article
- Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross.Asian-Australasian journal of animal sciences · 2019Article
- A Mini-Atlas of Gene Expression for the Domestic Goat (Frontiers in genetics · 2019Article
- Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep.Frontiers in genetics · 2019Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.
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