Selective transcriptional profiling and data analysis strategies for expression quantitative trait loci mapping in outbred F2 populations.

PubWeight™: 0.79‹?›

🔗 View Article (PMC 2581967)

Published in Genetics on September 14, 2008

Authors

Fernando F Cardoso1, Guilherme J M Rosa, Juan P Steibel, Catherine W Ernst, Ronald O Bates, Robert J Tempelman

Author Affiliations

1: Embrapa Pecuária Sul (Brazilian Agricultural Research Corporation South-Cattle and Sheep Center), Bagé, RS, Brazil. fcardoso@cppsul.embrapa.br

Articles cited by this

Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet (1980) 75.25

Genetic dissection of transcriptional regulation in budding yeast. Science (2002) 25.01

Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17

Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet (2003) 11.84

Genetical genomics: the added value from segregation. Trends Genet (2001) 8.23

Genetics of global gene expression. Nat Rev Genet (2006) 6.80

Experimental strategies for the genetic dissection of complex traits in animal models. Nat Genet (1998) 4.12

The quantitative genetics of transcription. Trends Genet (2005) 2.62

Controlling the proportion of false positives in multiple dependent tests. Genetics (2004) 2.46

Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics (2004) 1.68

Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits. J Anim Sci (2007) 1.46

Selective phenotyping for increased efficiency in genetic mapping studies. Genetics (2004) 1.34

Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics (2005) 1.25

Quantitative trait locus mapping for meat quality traits in an Iberian x Landrace F2 pig population. J Anim Sci (2002) 1.18

Optimal design and analysis of genetic studies on gene expression. Genetics (2005) 1.17

Review of microarray experimental design strategies for genetical genomics studies. Physiol Genomics (2006) 1.17

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genet Res (2002) 1.08

Quantitative trait loci mapping in an F2 Duroc x Pietrain resource population: I. Growth traits. J Anim Sci (2007) 1.07

Detection and characterization of quantitative trait loci for meat quality traits in pigs. J Anim Sci (2001) 1.04

A comparison of bivariate and univariate QTL mapping in livestock populations. Genet Sel Evol (2003) 1.01

Design of microarray experiments for genetical genomics studies. Genetics (2006) 0.94

Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling. Biometrics (2006) 0.80

Selective transcriptional profiling for trait-based eQTL mapping. Anim Genet (2006) 0.80

Articles by these authors

Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods. Genet Res (Camb) (2010) 2.96

Nonparametric methods for incorporating genomic information into genetic evaluations: an application to mortality in broilers. Genetics (2008) 2.32

The transcriptome of human oocytes. Proc Natl Acad Sci U S A (2006) 1.70

Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics (2012) 1.50

A Bayesian antedependence model for whole genome prediction. Genetics (2011) 1.45

Radial basis function regression methods for predicting quantitative traits using SNP markers. Genet Res (Camb) (2010) 1.28

Sexual differentiation of the zebra finch song system: potential roles for sex chromosome genes. BMC Neurosci (2009) 1.23

A powerful and flexible linear mixed model framework for the analysis of relative quantification RT-PCR data. Genomics (2009) 1.22

A comprehensive genetic approach for improving prediction of skin cancer risk in humans. Genetics (2012) 1.20

One hundred years of statistical developments in animal breeding. Annu Rev Anim Biosci (2014) 1.18

Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics (2008) 1.13

A cDNA microarray from the telencephalon of juvenile male and female zebra finches. J Neurosci Methods (2004) 1.08

An ensemble-based approach to imputation of moderate-density genotypes for genomic selection with application to Angus cattle. Genet Res (Camb) (2012) 1.07

Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS One (2011) 1.05

A general approach to mixed effects modeling of residual variances in generalized linear mixed models. Genet Sel Evol (2004) 1.05

Evidence for a novel gene expression program in peripheral blood mononuclear cells from Mycobacterium avium subsp. paratuberculosis-infected cattle. Infect Immun (2003) 1.05

Searching for recursive causal structures in multivariate quantitative genetics mixed models. Genetics (2010) 1.03

Reassessing design and analysis of two-colour microarray experiments using mixed effects models. Comp Funct Genomics (2005) 1.02

Marker-assisted prediction of non-additive genetic values. Genetica (2011) 1.02

Modeling relationships between calving traits: a comparison between standard and recursive mixed models. Genet Sel Evol (2010) 1.02

Evaluating statistical analysis models for RNA sequencing experiments. Front Genet (2013) 1.01

A large-scale study of differential gene expression in monocyte-derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis. Brief Funct Genomics (2010) 0.99

Enhanced gene expression in the forebrain of hatchling and juvenile male zebra finches. J Neurobiol (2005) 0.99

Application of support vector regression to genome-assisted prediction of quantitative traits. Theor Appl Genet (2011) 0.97

Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels. BMC Genet (2013) 0.96

Predicting complex traits using a diffusion kernel on genetic markers with an application to dairy cattle and wheat data. Genet Sel Evol (2013) 0.94

Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts. Physiol Genomics (2003) 0.94

Design of microarray experiments for genetical genomics studies. Genetics (2006) 0.94

A primer on high-throughput computing for genomic selection. Front Genet (2011) 0.94

Methods of tagSNP selection and other variables affecting imputation accuracy in swine. BMC Genet (2013) 0.93

Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study. Front Genet (2013) 0.92

Identification of small molecules from human embryonic stem cells using metabolomics. Stem Cells Dev (2007) 0.91

Accuracy of Genome-Enabled Prediction in a Dairy Cattle Population using Different Cross-Validation Layouts. Front Genet (2012) 0.90

Transcriptome of local innate and adaptive immunity during early phase of infectious bronchitis viral infection. Viral Immunol (2006) 0.89

Identification of a novel gene set in human cumulus cells predictive of an oocyte's pregnancy potential. Fertil Steril (2012) 0.88

Energy balance modulates colon tumor growth: Interactive roles of insulin and estrogen. Mol Carcinog (2010) 0.87

Is structural equation modeling advantageous for the genetic improvement of multiple traits? Genetics (2013) 0.87

Molecular advances in QTL discovery and application in pig breeding. Trends Genet (2013) 0.86

Characterizing differential individual response to porcine reproductive and respiratory syndrome virus infection through statistical and functional analysis of gene expression. Front Genet (2013) 0.86

Glucocorticoid modulation of Bcl-2 family members A1 and Bak during delayed spontaneous apoptosis of bovine blood neutrophils. Endocrinology (2006) 0.86

Bayesian inference on genetic merit under uncertain paternity. Genet Sel Evol (2003) 0.85

Development of an adjuvant-free cashew nut allergy mouse model. Int Arch Allergy Immunol (2009) 0.85

Accuracy of estimation of genomic breeding values in pigs using low-density genotypes and imputation. G3 (Bethesda) (2014) 0.85

L2-Boosting algorithm applied to high-dimensional problems in genomic selection. Genet Res (Camb) (2010) 0.85

Gene expression profiling of peripheral blood mononuclear cells (PBMC) from Mycobacterium bovis infected cattle after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD). Vet Immunol Immunopathol (2006) 0.85

On reference designs for microarray experiments. Stat Appl Genet Mol Biol (2005) 0.85

Cumulative t-link threshold models for the genetic analysis of calving ease scores. Genet Sel Evol (2003) 0.85

Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Anim Biotechnol (2002) 0.84

Identification of Carcass and Meat Quality QTL in an F(2) Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models. Front Genet (2011) 0.84

Development and testing of a high-density cDNA microarray resource for cattle. Physiol Genomics (2003) 0.83

Predicting expected progeny difference for marbling score in Angus cattle using artificial neural networks and Bayesian regression models. Genet Sel Evol (2013) 0.83

Pharmacological zinc and phytase supplementation enhance metallothionein mRNA abundance and protein concentration in newly weaned pigs. J Nutr (2004) 0.82

Gene expression profiling of peripheral mononuclear cells in lame dairy cows with foot lesions. Vet Immunol Immunopathol (2007) 0.82

Evaluation of QTL for carcass merit and meat quality traits in a US commercial Duroc population. Meat Sci (2012) 0.82

Hierarchical Bayesian modeling of random and residual variance-covariance matrices in bivariate mixed effects models. Biom J (2010) 0.80

Postnatal development of canine axial globe length measured by B-scan ultrasonography. Vet Ophthalmol (2007) 0.80

Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population. BMC Genet (2010) 0.80

Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets. BMC Genomics (2008) 0.79

Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiol Genomics (2004) 0.79

Long-term impacts of genome-enabled selection. J Appl Genet (2011) 0.79

Hierarchical Bayesian modeling of heterogeneous cluster- and subject-level associations between continuous and binary outcomes in dairy production. Biom J (2012) 0.79

Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. BMC Bioinformatics (2014) 0.79

Searching for phenotypic causal networks involving complex traits: an application to European quail. Genet Sel Evol (2011) 0.78

Comparison of classification methods for detecting associations between SNPs and chick mortality. Genet Sel Evol (2009) 0.78

Upregulation of imprinted genes in mice: an insight into the intensity of gene expression and the evolution of genomic imprinting. Epigenetics (2010) 0.77

Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle. BMC Genomics (2011) 0.77

Liver functional genomics in beef cows on grazing systems: novel genes and pathways revealed. Physiol Genomics (2013) 0.77

Differential gene expression segregates cattle confirmed positive for bovine tuberculosis from antemortem tuberculosis test-false positive cattle originating from herds free of bovine tuberculosis. Vet Med Int (2012) 0.77

A comparative evaluation of the protective efficacy of rMd5deltaMeq and CVI988/ Rispens against a vv+ strain of Marek's disease virus infection in a series of recombinant congenic strains of White Leghorn chickens. Avian Dis (2011) 0.76

Exploring causal networks of bovine milk fatty acids in a multivariate mixed model context. Genet Sel Evol (2014) 0.76

Estradiol and progesterone exhibit similar patterns of hepatic gene expression regulation in the bovine model. PLoS One (2013) 0.76

Humble Thanks to a Gentle Giant (an Obituary for James F. Crow). Front Genet (2012) 0.75

Developmental changes in the fetal pig transcriptome. Physiol Genomics (2004) 0.75

Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population. Genet Mol Biol (2011) 0.75