ArticleGigaScience2022
Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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
15 citing papers in PubMed, 39 citations in OpenAlex.
- Multi-Layer Transcriptomic Comparison Across Human, Pig, and Mouse Informs Tissue- and Trait-Specific Animal Model Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds.Journal of animal science and biotechnology · 2026Article
- OmiGA for ultra-efficient molecular quantitative trait loci mapping.Nature communications · 2026Article
- Integrated analysis of GWAS and molQTLs reveals cell-specific genetic variants in the porcine immune system.Communications biology · 2026Article
- IPGCA: A Comprehensive Single Cell Atlas of 1 074 127 Porcine Intestinal Cells Revealing Cellular Dynamics, Genetic Regulation, and Cross-Species Conservation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genomic characterization and insights into the belted coat pattern of a local, reconstituted pig population.Animal biotechnology · 2025Article
- An updated Pig Haplotype Reference Panel (PHARP 4.0) comprising 13,298 haplotypes.Communications biology · 2025Article
- Exploring transcriptomic and genomic differences between susceptible and resistant fetal pigs to maternal PRRSV infection at late gestation.Veterinary research · 2025Article
- The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.Genetics, selection, evolution : GSE · 2025Article
- Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq.BMC genomics · 2025Article
- Genomic Insights into the Successful Invasion of the Avian Vampire Fly (Philornis downsi ) in the Galápagos Islands.Molecular biology and evolution · 2025Article
- The effects of runs-of-homozygosity on pig domestication and breeding.BMC genomics · 2025Article
- Unveiling regulatory variants in the blood transcriptome and their association with immunity traits in pigs.Frontiers in immunology · 2025Article
- Mutations on a conserved distal enhancer in the porcine C-reactive protein gene impair its expression in liver.Frontiers in immunology · 2023Article
- Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues.GigaScience · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundIn humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.
resultsMore than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.
conclusionsThe 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.
Indexed as
Identifiers
What OpenQuestion holds
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 OpenQuestion graph.