Evidence map›Paper›PMID 39885415›Full record

ArticleBMC genomics2025

A comprehensive allele specific expression resource for the equine transcriptome.

Harrison D Heath, Sichong Peng, Tomasz Szmatola, Stephanie Ryan, Rebecca R Bellone, Theodore Kalbfleisch, Jessica L Petersen, Carrie J Finno

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Harrison D HeathDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Sichong PengDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Tomasz SzmatolaDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Stephanie RyanDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Rebecca R BelloneDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Theodore KalbfleischMaxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA.
Jessica L PetersenDepartment of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
Carrie J FinnoDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA. cjfinno@ucdavis.edu.

Funding

UC Davis Comparative Oncology Training ProgramT32CA251007 · NCI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Robert J. Canter, Xinbin Chen · 2020 to 2026
$1.8M
National Institute of Food and Agriculture 2019-67015-29340NCATS NIH HHS L40 TR001136NCI NIH HHS T32 CA251007UC Davis Center for Equine Health 21-04
6 · The paper itself

Abstract

backgroundAllele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression.

resultsAn equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were located in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE.

conclusionsThis valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.

Indexed as

AllelesGene Expression ProfilingTranscriptomeAnimalsHaplotypesHorsesLiverEpigeneticsFAANGHaplotypeHorseRNA-sequencing

Identifiers

PMID39885415
PMCPMC11780778

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.