GSA-SNP statistics

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GSA-SNP specifications


Unique identifier OMICS_04385
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some marker association and gene sets.
Output data A list of significantly associated gene sets with P-values, corrected P-values, and their members that are sorted according their association strength by descending order.
Output format CSV
Operating system Unix/Linux, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Sangsoo Kim

Publication for GSA-SNP

GSA-SNP citations


Real life helping behaviours in North America: A genome wide association approach

PLoS One
PMCID: 5764334
PMID: 29324852
DOI: 10.1371/journal.pone.0190950

[…] We applied the gene set analysis (GSA) approach developed by Nam et al [] implementing in the Java application “GSA SNP” ( on the present GWAS results (SNP with its P value from the GWAS). GSA assigns SNPs to a gene that encompasses the SNP with some […]


Genome wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia

PMCID: 5537640
PMID: 28632202
DOI: 10.1038/tp.2017.115

[…] tal, 674 gene sets were tested. The results were adjusted for multiple testing using false discovery rate (FDR). To validate the significant finding, the respective gene set was investigated with (i) GSA-SNP, using the P-value of the second-best SNP in each gene ( and (ii) MAGMA using summary data and a nominal P-value threshold of P<0.05. […]


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

Sci Rep
PMCID: 5471232
PMID: 28615668
DOI: 10.1038/s41598-017-03826-2
call_split See protocol

[…] We downloaded KGG from, GSA-SNP from, MAGMA (MAGMA-pval-1k version) from, PARIS from, and Genomi […]


Meta analysis of lipid traits in Hispanics identifies novel loci, population specific effects, and tissue specific enrichment of eQTLs

Sci Rep
PMCID: 4726092
PMID: 26780889
DOI: 10.1038/srep19429

[…] eport only pathways that are significant using the HYST test and also a hypergeometric test enrolling genes with a p-value of 0.001. We also performed a pathway analysis using an alternative program, GSA-SNP, using the PAGE (parametric analysis of gene set enrichment) method. When using GSA-SNP, we selected the SNP with the 2nd lowest p-value to define the gene p-values, and used a padding window […]


Pathway Based Genome wide Association Studies Reveal That the Rac1 Pathway Is Associated with Plasma Adiponectin Levels

Sci Rep
PMCID: 4642532
PMID: 26299439
DOI: 10.1038/srep13422

[…] iated with body weight related phenotypes.We further replicated our results in the ADIPOGen Consortium. Using SNP specific P values from the ADIPOGen GWAS, we performed pathway association studies by GSA-SNP. A key pathway found in our study, GO0032990 (centered by the Rac-1 pathway and the CDH13 gene) was among the top associations (corrected P  = 1.06 × 10−13, FDR = 0) in the ADIPOGen data ().Si […]


JAG: A Computational Tool to Evaluate the Role of Gene Sets in Complex Traits

PMCID: 4488663
PMID: 26110313
DOI: 10.3390/genes6020238

[…] whether at least one genetic variant in the gene-set is associated with the trait (e.g., GATES and GENGEN), or whether N best p-values of genetic variants per gene in a gene-set are associated (e.g., GSA-SNP []). Some tools test whether there is an enrichment of genetic variants with a p-value below a certain threshold within the gene-set (e.g., ALIGATOR) or the other way around: tests whether the […]


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GSA-SNP institution(s)
School of Nano-Biotech and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea; School of Computer Science and Engineering, Seoul National University, Seoul, South Korea; Medical Genomics Research Center, Korea Research Institute for Bioscience and Biotechnology, Daejeon, South Korea; Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
GSA-SNP funding source(s)
Supported by the National Institute for Mathematical Sciences, Daejeon, Korea (NIMS); the Basic Science Research Program through the National Research Foundation of Korea (NRF) (grant no. 2010-0016668); the MEST, and NRF (grant R11-2008-0062293).

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