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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 citations

 (9)
library_books

Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle

2017
PLoS One
PMCID: 5724891
PMID: 29228019
DOI: 10.1371/journal.pone.0188997

[…] lassified heifers to identify loci, genes, gene pathways and regulators associated with uterine capacity for pregnancy using genome-wide association analysis (GWAA), gene set enrichment analysis-SNP (GSEA-SNP), and gene network analysis of SNP data. This approach identified genetic factors associated with early pregnancy loss in beef cattle and provides important predictors of fertility for genomi […]

library_books

Improving the detection of pathways in genome wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

2017
Sci Rep
PMCID: 5471232
PMID: 28615668
DOI: 10.1038/s41598-017-03826-2

[…] ntly, 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 […]

call_split

Relative performance of gene and pathway level methods as secondary analyses for genome wide association studies

2015
BMC Genet
PMCID: 4391470
PMID: 25887572
DOI: 10.1186/s12863-015-0191-2
call_split See protocol

[…] 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 (Add […]

library_books

Pathway based Biomarkers for Breast Cancer in Proteomics

2015
Cancer Inform
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 that combi […]

call_split

The Associations between Immunity Related Genes and Breast Cancer Prognosis in South Korean Women

2014
PLoS One
PMCID: 4116221
PMID: 25075970
DOI: 10.1371/journal.pone.0103593
call_split See protocol

[…] estimated based on those SNPs in validation set. The cross-validation process was then repeated 4 times. The summary of these 4 Harrell’s indices was assessed by fixed-effect model meta-analysis.The GSEA-SNP method was used to reveal the biological function of the SNPs which were significantly related to breast cancer prognosis . Pathway information was obtained from the Molecular Signatures Data […]

library_books

Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data

2012
BMC Syst Biol
PMCID: 3524014
PMID: 23281810
DOI: 10.1186/1752-0509-6-S3-S15

[…] to be efficient enough for an exhaustive search of GWAS data in a relatively short time [,]. An alternative approach to probing the effects of multiple genes is gene set enrichment analysis (such as GSEA-SNP and others [,]), which can serve to identify pathways that are implicated in disease. However, this approach considers all the genes in the pathway as equal, and cannot reveal the discrete st […]

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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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