ArticleMammalian genome : official journal of the International Mammalian Genome Society2010
GSEA-SNP identifies genes associated with Johne's disease in cattle.
Article in Mammalian genome : official journal of the International Mammalian Genome Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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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
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
- Pooled it
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- The Paratuberculosis Paradigm Examined: A Review of Host Genetic Resistance and Innate Immune Fitness inFrontiers in veterinary science · 2021Review
- Functional Variants Surrounding Endothelin 2 Are Associated WithFrontiers in veterinary science · 2021Article
- Selection signatures of Fuzhong Buffalo based on whole-genome sequences.BMC genomics · 2020Article
- The EDN2 rs110287192 gene polymorphism is associated with paratuberculosis susceptibility in multibreed cattle population.PloS one · 2020Article
- Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP.Mammalian genome : official journal of the International Mammalian Genome Society · 2018Article
- Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Which phenotypic traits of resistance should be improved in cattle to control paratuberculosis dynamics in a dairy herd: a modelling approach.Veterinary research · 2017Article
- Genomic Tools and Animal Health.Veterinary sciences · 2016Review
- Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.Nucleic acids research · 2016Article
- Genome-wide association study of susceptibility to infection by Mycobacterium avium subspecies paratuberculosis in Holstein cattle.PloS one · 2014Article
- Genomics of complex traits.Annals of the New York Academy of Sciences · 2012Review
- Evolution of the bovine TLR gene family and member associations with Mycobacterium avium subspecies paratuberculosis infection.PloS one · 2011Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SNP-based gene-set enrichment analysis from single nucleotide polymorphisms, or GSEA-SNP, is a tool to identify candidate genes based on enrichment analysis of sets of genes rather than single SNP associations. The objective of this study was to identify modest-effect genes associated with Mycobacterium avium subsp. paratuberculosis (Map) tissue infection or fecal shedding using GSEA-SNP applied to KEGG pathways or Gene Ontology (GO) gene sets. The Illumina Bovine SNP50 BeadChip was used to genotype 209 Holstein cows for the GSEA-SNP analyses. For each of 13,744 annotated genes genome-wide located within 50 kb of a Bovine SNP50 SNP, the single SNP with the highest Cochran-Armitage Max statistic was used as a proxy statistic for that gene's strength of affiliation with Map. Gene-set enrichment was tested using a weighted Kolmogorov-Smirnov-like running sum statistic with data permutation to adjust for multiple testing. For tissue infection and fecal shedding, no gene sets in KEGG pathways or in GO sets for molecular function or cellular component were enriched for signal. The GO biological process gene set for positive regulation of cell motion (GO:0051272, q = 0.039, 5/11 genes contributing to the core enrichment) was enriched for Map tissue infection, while no GO biological process gene sets were enriched for fecal shedding. GSEA-SNP complements traditional SNP association approaches to identify genes of modest effects as well as genes with larger effects as demonstrated by the identification of one locus that we previously found to be associated with Map tissue infection using a SNP-by-SNP genome-wide association study.
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Registered trials
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