ArticleGenome biology2026
Mapping the landscape of allele-specific expression in porcine genomes.
Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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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
3 citing papers in PubMed.
- Genome-wide DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.BMC genomics · 2026Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs.BMC biology · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundAllele-specific expression (ASE) is the imbalanced expression of two alleles of the same locus. It is quite pervasive among many species and is associated with health and economically relevant traits. ASE is often used to support the identification of variants related to gene expression (cis-eQTL). Thus, profiling allele-specific expression represents a significant step in elucidating the mechanism underlying gene expression regulation.
resultIn this study, we developed an ASE pipeline using publicly available RNA-seq data and open-source software. Using this pipeline, we are able to profile pervasive allelic imbalance across 42 tissues and 34 breeds from the Farm-GTEx-pig consortium at both SNP and gene levels without the need for parental genotypes or whole genome sequence data. We find that ASE is widely, but not evenly, spread across the genome. We also observe considerable variation in ASE profiles across various tissues, where the site fraction ranged from 1.3% to 54.1%. ASE tends to be highly tissue-specific, with limited overlap across tissues. The functional analysis of tissue-specific ASE sites indicates that they are involved in important biological functions of these tissues. Our ASE pipeline can be readily applied to other RNA-seq datasets for livestock and other species, thereby expanding its potential utility.
conclusionsThe wealth of available ASE resources provides a solid foundation for identifying regulatory elements within the genome that drive complex traits in livestock, making our pipeline and results valuable resources for researchers in this field.
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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 Socratic graph.