Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array dataJean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
PLoS ONE 7:e30629. 2012
..Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation...
- Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits
Sarah Danan
Institut National de la Recherche Agronomique, UR 1052 Génétique et Amélioration des Fruits et Légumes, BP94, 84140 Montfavet, France
BMC Plant Biol 11:16. 2011
..Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits...
- High-resolution mapping of expression-QTLs yields insight into human gene regulation
Jean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
PLoS Genet 4:e1000214. 2008
..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
- The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
Athma A Pai
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
PLoS Genet 8:e1003000. 2012
..By analyzing our data within the context of known steady-state eQTLs, we estimate that a substantial fraction of eQTLs are associated with inter-individual variation in mRNA decay rates...
- Dissecting the regulatory architecture of gene expression QTLs
Daniel J Gaffney
Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
Genome Biol 13:R7. 2012
..Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb...
- Understanding mechanisms underlying human gene expression variation with RNA sequencing
Joseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago 60637, USA
Nature 464:768-72. 2010
..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals...
- DNase I sensitivity QTLs are a major determinant of human expression variation
Jacob F Degner
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Nature 482:390-4. 2012
..Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation...
- Gene expression levels are a target of recent natural selection in the human genome
Sridhar Kudaravalli
Department of Human Genetics, The University of Chicago, USA
Mol Biol Evol 26:649-58. 2009
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- Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information
Sébastien Ducrocq
UMR de Genetique Vegetale, Institut National de la Recherche Agronomique, Universite Paris Sud, Centre National de la Recherche Scientifique, AgroParisTech, Ferme du Moulon, 91190 Gif sur Yvette, France
Genetics 178:2433-7. 2008
..Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation...
- MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments
Jean Baptiste Veyrieras
UMR, INRA UPS XI INAPG CNRS Génétique Végétale, Ferme du Moulon, 91190 Gif sur Yvette, France
BMC Bioinformatics 8:49. 2007
..Presently, the few computational and statistical frameworks to do so are mainly based on empirical methods (e.g. consensus genetic maps are generally built by iterative projection)...
- GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
Delphine Samson
Génoplante Info, Unité de Recherche Génomique Info, INRA, Infobiogen, 523 Place des Terrasses, F 91000 Evry, France
Nucleic Acids Res 31:179-82. 2003
..This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/...
