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-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 t...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Kristian Holm, Espen Melum, Andre Franke, Tom H. Karlsen
• Keywords: BMCBI 2010, Business, Expression Levels, Genotypes, Single Nucleotide Polymorphisms