GSEA-SNP statistics

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Associated diseases

Associated diseases

GSEA-SNP specifications

Information


Unique identifier OMICS_04389
Name GSEA-SNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Raw genotypes
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for GSEA-SNP

GSEA-SNP in publications

 (9)
PMCID: 5724891
PMID: 29228019
DOI: 10.1371/journal.pone.0188997

[…] analysis (gwaa) was conducted comparing 30 high fertility heifers with 100% success in establishing pregnancy to 55 subfertile heifers with 25% or less success. a gene set enrichment analysis snp (gsea-snp) was performed to identify gene sets and leading edge genes influencing pregnancy loss. the gwaa identified 22 qtl (p < 1 x 10−5), and gsea-snp identified 9 gene sets (normalized […]

PMCID: 5471232
PMID: 28615668
DOI: 10.1038/s41598-017-03826-2

[…] the methods for pathway analysis on gwas data are mainly divided into two classes according to the type of input data. the first class works with an input of raw genotype data, such as fpca and gsea-snp, . their applications are limited because raw data is not always available (especially with the shift towards meta-analysis of gwas summary statistics). in contrast, the other class requires […]

PMCID: 5068862
PMID: 27489002
DOI: 10.1534/genetics.116.188391

[…] are assigned to gene scores observed in an annotated pathway. second, we describe tests for enrichment in related annotations among genes in a predetermined list (e.g., grail, magenta, david, and gsea-snp) (; ; ; ). to conduct these tests, the investigator must compute a gene score and, in some cases, determine a threshold for extreme gene scores to generate a list of genes associated […]

PMCID: 4391470
PMID: 25887572
DOI: 10.1186/s12863-015-0191-2

[…] within genes with five causal snps, vegas’s sensitivity increased to 40% from the original overall 28.57%., a total of 10 pathway-level programs were evaluated: aligator, gengen, gsa-snp, gsea-snp, magenta, modified generalized fisher method (mgfm), snp ratio test (srt), grass, hyst, and plink set test (pst). only the 20 pathways that were simulated to be associated were evaluated […]

PMCID: 4324474
PMID: 25972728
DOI: 10.4137/CIN.S14069

[…] holden et al combined single-nucleotide polymorphism (snp) association analysis with the pathway-driven gsea, to facilitate handling of genome-wide gene expression data. the method they developed, gsea-snp, may facilitate the identification of disease-associated snps and pathways, as well as the understanding of the underlying biological mechanisms., therefore, we presented an approach […]


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GSEA-SNP institution(s)
Norwegian Computing Center, Oslo, Norway; Department of Pharmacology, University of Mainz, Mainz, Germany

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