ArticleBMC genomics2017
Tissue resolved, gene structure refined equine transcriptome.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A missense mutation in the KCNE4 gene is not predictive of equine anhidrosis.Animal genetics · 2025Article
- Functional annotation of the animal genomes: An integrated annotation resource for the horse.PLoS genetics · 2023Review
- Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy.Journal of genetic mutation disorders · 2022Article
- "Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare.Frontiers in genetics · 2021Article
- Adding exogenous biglycan or decorin improves tendon formation for equine peritenon and tendon proper cells in vitro.BMC musculoskeletal disorders · 2020Article
- Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules.Animals : an open access journal from MDPI · 2020Article
- Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds.Animals : an open access journal from MDPI · 2020Article
- Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.Animal genetics · 2019Review
- Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.GigaScience · 2019Article
- A missense mutation in MYH1 is associated with susceptibility to immune-mediated myositis in Quarter Horses.Skeletal muscle · 2018Article
- Transcriptome analysis of immune genes in peripheral blood mononuclear cells of young foals and adult horses.PloS one · 2018Article
- Variation in MUTYH expression in Arabian horses with Cerebellar Abiotrophy.Brain research · 2018Article
- A high resolution atlas of gene expression in the domestic sheep (Ovis aries).PLoS genetics · 2017Article
- Identification of long non-coding RNA in the horse transcriptome.BMC genomics · 2017Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.
resultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.
conclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.
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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.