Description

This track displays associations among gene expression data from the 60 unrelated Centre d'Etude du Polymorphisme Humain (CEPH) individuals of the International HapMap Project with SNPs genotyped by HapMap. The CEPH population is composed of Utah residents with ancestry from northern and western Europe. The expression data were generated with the Illumina platform at the Wellcome Trust Sanger Institute.

Display Conventions and Configuration

In the graphical display, an association is displayed as a block drawn at the location of the associated SNP. In pack or full modes, the name of the associated gene is drawn to the left of the block. The shading of the block indicates the strength of the association: light gray indicates a (-log₁₀) P-value close to 0 and black indicates a P-value of 2 or more.

Methods

An association analysis was performed for each ENCODE RefSeq gene with the genotypes of SNPs in the same ENCODE region (cis). Expression values were initially log₂ transformed and subsequently normalized with quantile normalization to ensure homogeneous levels between arrays. Analysis of variance (ANOVA) was then performed with 1 or 2 degrees of freedom (depending on whether only two or all three genotypes in the population were available), using the genotype as a categorical variable and the normalized/transformed expression values as the response. The values presented here are the -log₁₀ P-value.

Verification

There were six technical replicates for each sample; the average values from these were used for the ANOVA.

Credits

The following people contributed to this analysis: Barbara Stranger, Matthew Forrest, Panos Deloukas, and Manolis Dermitzakis from Wellcome Trust Sanger Institute and Simon Tavare from Cambridge University.

References

Dausset, J., Cann, H., Cohen, D., Lathrop, M., Lalouel, J.M. and White, R. Centre d'Etude du Polymorphisme Humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6(3), 575-7 (1990).