The major public microarray repositories Gene Expression Omnibus and ArrayExpress are growing rapidly. This enables meta-analysis studies, in which expression data from multiple individual studies are combined. To facilitate these types of studies, we developed Microarray Retriever for searching and retrieval of data from GEO and ArrayExpress. The tool allows access to the two repositories simultaneously, to search in the repositories using complex queries, to retrieve microarray data for published articles and to download data in one structured archive. The tool is available on the web at: http://www.lgtc.nl/MaRe/
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| http://dx.doi.org/10.1093/nar/gkn213 | DOI Listing |
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Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study.
View Article and Find Full Text PDFAccuracy of genotype imputation in Labrador Retrievers.
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Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs.
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Metabolites
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Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599-7525, USA.
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