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GESBAP specifications

Information


Unique identifier OMICS_04387
Name GESBAP
Alternative name Gene Set-based Analysis of Polymorphisms
Interface Web user interface
Restrictions to use None
Input data GeSBAP inputs lists of SNP or CNV identifiers arranged according to a parameter accounting for the association (P-value).
Output data It returns a collection of biological processes significantly associated to the trait studied.
Programming languages C++, Java
Computer skills Basic
Stability No
Maintained No

Publication for Gene Set-based Analysis of Polymorphisms

GESBAP citations

 (6)
library_books

Multiple analyses of large scale genome wide association study highlight new risk pathways in lumbar spine bone mineral density

2016
Oncotarget
PMCID: 5058768
PMID: 27119226
DOI: 10.18632/oncotarget.8948

[…] including SNP ratio test [], GenGen [], GRASS [], accept raw genotype datasets as input data. Other tools including ProxyGeneLD [], ALIGATOR [], i-GSEA4GWAS [], and PLINK set-test [], MAGENTA [], and GESBAP [] accept the summary results to subsequent pathway analysis. Here, we selected ProxyGeneLD and PLINK for gene-based test, as we did not have access to raw BMD genotype data. Both the ProxyGene […]

library_books

Pathway analysis of body mass index genome wide association study highlights risk pathways in cardiovascular disease

2015
Sci Rep
PMCID: 4533004
PMID: 26264282
DOI: 10.1038/srep13025

[…] nalysis of GWAS data. Some tools including SNP ratio test, GenGen, GRASS, and PLINK set-test, accept raw genotype datasets as input data. Other tools including ProxyGeneLD, ALIGATOR, i-GSEA4GWAS, and GESBAP accept the summary results to subsequent pathway analysis. Here, we selected ProxyGeneLD for gene-based test because we did not have access to raw CRC genotype data. This software adjusts for g […]

library_books

Pathways systematically associated to Hirschsprung’s disease

2013
Orphanet J Rare Dis
PMCID: 3879038
PMID: 24289864
DOI: 10.1186/1750-1172-8-187

[…] in the PLINK [] software for the different sets of trios analyzed (see Figure ).The SNPs were ranked according to their p-values obtained in the TDT test and then a PBA test [], as implemented in the GESBAP [] module of the Babelomics [] software, was conducted. PBA seeks for gene sets (GO terms in this study) associated to low p-values. This association is found significant when a number of genes […]

library_books

Four new loci associations discovered by pathway based and network analyses of the genome wide variability profile of Hirschsprung’s disease

2012
Orphanet J Rare Dis
PMCID: 3575329
PMID: 23270508
DOI: 10.1186/1750-1172-7-103

[…] The SNPs were ranked according to their p-values obtained in the TDT test and a PBA test [], as implemented in the GESBAP [] module of the Babelomics software [,], was conducted. Briefly, PBA tests make only use of SNPs mapping within genes or in the neighborhood (here defined as 500 bps up-and downstream of the g […]

library_books

Performance Comparison of Two Gene Set Analysis Methods for Genome wide Association Study Results: GSA SNP vs i GSEA4GWAS

2012
PMCID: 3480679
PMID: 23105940
DOI: 10.5808/GI.2012.10.2.123

[…] eases as an approach for the secondary analysis of a genome-wide association study (GWAS) result [-]. Currently, several software tools for GSA are available: GSA-SNP [], i-GSEA4GWAS [], GSEA-SNP [], GeSBAP [], and so on.GSA-SNP is useful only when p-values of the single nucleotide polymorphism (SNP) markers are available. While GSA-SNP has implemented several options for estimating the significan […]

library_books

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

2010
Nucleic Acids Res
PMCID: 2896184
PMID: 20478823
DOI: 10.1093/nar/gkq388

[…] enecodis method () that finds concurrent annotations in ranked lists of genes is one of the new methods included. It is also possible to carry our PBA in GWAS experiments by means of the novel module Gesbap (). Gene modules defined using text-mining derived functional annotations related to medical terms and chemical compounds can also be used for gene-set analysis (GSA) (). Also another module us […]

Citations

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GESBAP institution(s)
Department of Bioinformatics and Genomics, CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain
GESBAP funding source(s)
Spanish Ministry of Science and Innovation (grant BIO2008-04212)

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