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).
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