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snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets
Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262737/ https://www.ncbi.nlm.nih.gov/pubmed/34048563 http://dx.doi.org/10.1093/nar/gkab410 |
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author | Tesi, Niccolo van der Lee, Sven Hulsman, Marc Holstege, Henne Reinders, Marcel J T |
author_facet | Tesi, Niccolo van der Lee, Sven Hulsman, Marc Holstege, Henne Reinders, Marcel J T |
author_sort | Tesi, Niccolo |
collection | PubMed |
description | Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer. |
format | Online Article Text |
id | pubmed-8262737 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-82627372021-07-08 snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets Tesi, Niccolo van der Lee, Sven Hulsman, Marc Holstege, Henne Reinders, Marcel J T Nucleic Acids Res Web Server Issue Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer. Oxford University Press 2021-05-28 /pmc/articles/PMC8262737/ /pubmed/34048563 http://dx.doi.org/10.1093/nar/gkab410 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Tesi, Niccolo van der Lee, Sven Hulsman, Marc Holstege, Henne Reinders, Marcel J T snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title | snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title_full | snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title_fullStr | snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title_full_unstemmed | snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title_short | snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets |
title_sort | snpxplorer: a web application to explore human snp-associations and annotate snp-sets |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262737/ https://www.ncbi.nlm.nih.gov/pubmed/34048563 http://dx.doi.org/10.1093/nar/gkab410 |
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