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SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels

BACKGROUND: Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs) in the same individuals are publicly available. We aimed to generate a user-f...

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Autores principales: Holm, Kristian, Melum, Espen, Franke, Andre, Karlsen, Tom H
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022629/
https://www.ncbi.nlm.nih.gov/pubmed/21167019
http://dx.doi.org/10.1186/1471-2105-11-600
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author Holm, Kristian
Melum, Espen
Franke, Andre
Karlsen, Tom H
author_facet Holm, Kristian
Melum, Espen
Franke, Andre
Karlsen, Tom H
author_sort Holm, Kristian
collection PubMed
description BACKGROUND: Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs) in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL) analysis. RESULTS: SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results. CONCLUSIONS: SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.
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spelling pubmed-30226292011-01-19 SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels Holm, Kristian Melum, Espen Franke, Andre Karlsen, Tom H BMC Bioinformatics Software BACKGROUND: Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs) in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL) analysis. RESULTS: SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results. CONCLUSIONS: SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets. BioMed Central 2010-12-17 /pmc/articles/PMC3022629/ /pubmed/21167019 http://dx.doi.org/10.1186/1471-2105-11-600 Text en Copyright ©2010 Holm et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Holm, Kristian
Melum, Espen
Franke, Andre
Karlsen, Tom H
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title_full SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title_fullStr SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title_full_unstemmed SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title_short SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
title_sort snpexp - a web tool for calculating and visualizing correlation between hapmap genotypes and gene expression levels
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022629/
https://www.ncbi.nlm.nih.gov/pubmed/21167019
http://dx.doi.org/10.1186/1471-2105-11-600
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