ArticleGenetics2006
Optimal design and analysis of genetic studies on gene expression.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.Plant physiology · 2016Article
- Genetic dissection of leaf development in Brassica rapa using a genetical genomics approach.Plant physiology · 2014Article
- Regulatory network of secondary metabolism in Brassica rapa: insight into the glucosinolate pathway.PloS one · 2014Article
- The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks.Journal of experimental botany · 2013Article
- Genetical Genomics Reveals Large Scale Genotype-By-Environment Interactions in Arabidopsis thaliana.Frontiers in genetics · 2012Article
- Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce.PloS one · 2012Article
- Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway.BMC genomics · 2011Article
- Article
- designGG: an R-package and web tool for the optimal design of genetical genomics experiments.BMC bioinformatics · 2009Article
- Article
- Optimal design of genetic studies of gene expression with two-color microarrays in outbred crosses.Genetics · 2008Article
- Article
- Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data.Genetics · 2007Article
- Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.PLoS genetics · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome profiling of gene expression in a segregating population has the potential to identify the regulatory consequences of natural allelic variation. Costs of such studies are high and require that resources--microarrays and population--are used as efficiently as possible. We show that current studies can be improved significantly by a new design for two-color microarrays. Our "distant pair design" profiles twice as many individuals as there are arrays, cohybridizes individuals with dissimilar genomes, gives more weight to known regulatory loci if wished, and therewith maximizes the power for decomposing expression variation into regulatory factors. It can also exploit a large population (larger than twice the number of available microarrays) as a useful resource to select the most dissimilar pairs of individuals from. Our approach identifies more regulatory factors than alternative strategies do in computer simulations for realistic genome sizes, and similar promising results are obtained in an application on Arabidopsis thaliana. Our results will aid the design and analysis of future studies on gene expression and will help to shed more light on gene regulatory networks.
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Registered trials
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