Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat.

PubWeight™: 1.01‹?› | Rank: Top 15%

🔗 View Article (PMID 17364174)

Published in Funct Integr Genomics on March 16, 2007

Authors

Rebecca Poole1, Gary Barker, Ian D Wilson, Jane A Coghill, Keith J Edwards

Author Affiliations

1: School of Biological Sciences, University of Bristol, Bristol, UK. R.L.Poole@bristol.ac.uk

Articles citing this

Transcriptome analysis of grain development in hexaploid wheat. BMC Genomics (2008) 1.92

Wheat genomics: present status and future prospects. Int J Plant Genomics (2008) 1.83

Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc Natl Acad Sci U S A (2008) 1.38

Identification of suitable reference genes for normalization of qPCR data in comparative transcriptomics analyses in the Triticeae. Planta (2010) 1.28

Comparative transcriptomics in the Triticeae. BMC Genomics (2009) 1.19

Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics (2010) 1.18

Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays. PLoS One (2009) 1.02

wDBTF: an integrated database resource for studying wheat transcription factor families. BMC Genomics (2010) 0.90

Gene expression in a starch synthase IIa mutant of barley: changes in the level of gene transcription and grain composition. Funct Integr Genomics (2008) 0.89

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics (2008) 0.88

Single-species microarrays and comparative transcriptomics. PLoS One (2008) 0.86

Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat. Funct Integr Genomics (2010) 0.85

MicroRNA expression profiles in conventional and micropropagated strawberry (Fragaria x ananassa Duch.) plants. Plant Cell Rep (2009) 0.79

The genetic study utility of a hexaploid wheat DH population with non-recombinant A- and B-genomes. Springerplus (2013) 0.75

High Transferability of Homoeolog-Specific Markers between Bread Wheat and Newly Synthesized Hexaploid Wheat Lines. PLoS One (2016) 0.75

Association of gene expression with biomass content and composition in sugarcane. PLoS One (2017) 0.75

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48

Serial analysis of gene expression. Science (1995) 60.15

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol (2000) 15.79

Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08

Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (2002) 7.07

Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res (2000) 6.20

Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A (1997) 4.82

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res (2004) 4.43

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41

Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics (2005) 3.66

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23

Are data from different gene expression microarray platforms comparable? Genomics (2004) 3.13

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics (2003) 3.11

Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res (2005) 2.66

The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res (2003) 2.62

Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci (2002) 2.61

Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40

Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics (2003) 2.20

Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr Biol (2006) 2.16

Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines. Mol Vis (2003) 1.77

Focused microarray analysis. Methods (2003) 1.73

A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech (2004) 1.73

Microarray expression profiling resources for plant genomics. Trends Plant Sci (2005) 1.65

Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics (2004) 1.53

Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res (2005) 1.42

Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol (2006) 1.33

Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J (2006) 1.12

A transcriptomics resource for wheat functional genomics. Plant Biotechnol J (2004) 1.08

Alteration of the embryo transcriptome of hexaploid winter wheat (Triticum aestivum cv. Mercia) during maturation and germination. Funct Integr Genomics (2005) 1.03

Isolation and analysis of a cDNA clone encoding the small subunit of ADP-glucose pyrophosphorylase from wheat. Plant Mol Biol (1993) 1.01

Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol J (2006) 0.98

A microarray-based comparative analysis of gene expression profiles during grain development in transgenic and wild type wheat. Transgenic Res (2005) 0.98

Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray. Funct Integr Genomics (2005) 0.95

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays. Funct Integr Genomics (2005) 0.93

Differentially expressed genes in sporadic amyotrophic lateral sclerosis spinal cords--screening by molecular indexing and subsequent cDNA microarray analysis. FEBS Lett (2002) 0.90

Comparison of transcript profiling on Arabidopsis microarray platform technologies. Plant Mol Biol (2005) 0.87

Large-scale gene expression studies of the endometrium: what have we learnt? Reproduction (2006) 0.85

Serial Analysis of Gene Expression: Applications in Human Studies. J Biomed Biotechnol (2004) 0.81

Toward a global picture of development: lessons from genome-scale analysis in Caenorhabditis elegans embryonic development. Dev Dyn (2006) 0.77

Articles by these authors

The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol (2005) 5.35

Opinion: understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov (2003) 4.46

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc (2011) 4.13

Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J (2014) 4.02

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat (2012) 3.60

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics (2003) 3.11

Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol (2005) 2.90

Metabolic phenotyping in health and disease. Cell (2008) 2.80

Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A (2010) 2.52

Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc (2010) 2.18

UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom (2006) 2.17

Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr Biol (2006) 2.16

Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice. PLoS One (2010) 2.14

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J (2011) 2.13

Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal Chem (2009) 2.06

Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol (2003) 2.05

The challenges of modeling mammalian biocomplexity. Nat Biotechnol (2004) 2.03

Analytical strategies in metabonomics. J Proteome Res (2007) 2.00

Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res (2007) 1.99

Transcriptome analysis of grain development in hexaploid wheat. BMC Genomics (2008) 1.92

Challenging and changing gender attitudes among young men in Mumbai, India. Reprod Health Matters (2006) 1.77

Within-day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine. J Proteome Res (2007) 1.74

Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell (2006) 1.72

CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics (2012) 1.69

Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J Proteome Res (2008) 1.67

Plant responses to cold: Transcriptome analysis of wheat. Plant Biotechnol J (2010) 1.61

Systems biology tools for toxicology. Arch Toxicol (2012) 1.58

Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents. J Proteome Res (2009) 1.57

Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics (2004) 1.54

A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabonomic analysis. Analyst (2006) 1.49

Managing the challenge of chemically reactive metabolites in drug development. Nat Rev Drug Discov (2011) 1.45

TreeVector: scalable, interactive, phylogenetic trees for the web. PLoS One (2010) 1.45

SNPServer: a real-time SNP discovery tool. Nucleic Acids Res (2005) 1.42

Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol (2005) 1.40

Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J (2012) 1.35

Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet (2006) 1.32

An integrated metabonomic investigation of acetaminophen toxicity in the mouse using NMR spectroscopy. Chem Res Toxicol (2003) 1.30

The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. Bioanalysis (2012) 1.29

Liquid chromatography-mass spectrometry based global metabolite profiling: a review. Anal Chim Acta (2011) 1.29

De novo derivation of proteomes from transcriptomes for transcript and protein identification. Nat Methods (2012) 1.26

Gut microbiome modulates the toxicity of hydrazine: a metabonomic study. Mol Biosyst (2009) 1.24

Mass spectrometry-based holistic analytical approaches for metabolite profiling in systems biology studies. Mass Spectrom Rev (2011) 1.23

Evaluation of the repeatability of ultra-performance liquid chromatography-TOF-MS for global metabolic profiling of human urine samples. J Chromatogr B Analyt Technol Biomed Life Sci (2008) 1.22

Cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth. BMC Plant Biol (2009) 1.21

Hydrogen sulfide: environmental factor or signalling molecule? Plant Cell Environ (2013) 1.19

Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats. J Proteome Res (2011) 1.13

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. Philos Trans R Soc Lond B Biol Sci (2008) 1.13

Global metabolic profiling of animal and human tissues via UPLC-MS. Nat Protoc (2012) 1.13

Liquid chromatography and ultra-performance liquid chromatography-mass spectrometry fingerprinting of human urine: sample stability under different handling and storage conditions for metabonomics studies. J Chromatogr A (2007) 1.12

HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. Anal Chem (2010) 1.12

Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J (2006) 1.12

A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops. Plant Biotechnol J (2009) 1.11

Photophysiology and albedo-changing potential of the ice algal community on the surface of the Greenland ice sheet. ISME J (2012) 1.11

Metabonomic analysis of mouse urine by liquid-chromatography-time of flight mass spectrometry (LC-TOFMS): detection of strain, diurnal and gender differences. Analyst (2003) 1.09

A transcriptomics resource for wheat functional genomics. Plant Biotechnol J (2004) 1.08

Current practice of liquid chromatography-mass spectrometry in metabolomics and metabonomics. J Pharm Biomed Anal (2013) 1.08

Pharmacometabonomics as an effector for personalized medicine. Pharmacogenomics (2011) 1.07

Exceptionally high levels of multiple mating in an army ant. Naturwissenschaften (2004) 1.06

Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). Mol Ecol (2010) 1.05

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol J (2012) 1.05

Hippurate: the natural history of a mammalian-microbial cometabolite. J Proteome Res (2013) 1.04

Alteration of the embryo transcriptome of hexaploid winter wheat (Triticum aestivum cv. Mercia) during maturation and germination. Funct Integr Genomics (2005) 1.03

Metabolic phenotyping of nude and normal (Alpk:ApfCD, C57BL10J) mice. J Proteome Res (2006) 1.03

Hydrophilic interaction chromatography coupled to MS for metabonomic/metabolomic studies. J Sep Sci (2010) 1.03

Direct analysis of pharmaceutical drug formulations using ion mobility spectrometry/quadrupole-time-of-flight mass spectrometry combined with desorption electrospray ionization. Anal Chem (2005) 1.02

Integrated application of transcriptomics and metabonomics yields new insight into the toxicity due to paracetamol in the mouse. J Pharm Biomed Anal (2004) 1.02

A rapid screening approach to metabonomics using UPLC and oa-TOF mass spectrometry: application to age, gender and diurnal variation in normal/Zucker obese rats and black, white and nude mice. Analyst (2005) 1.00

Differential requirement for NO during ABA-induced stomatal closure in turgid and wilted leaves. Plant Cell Environ (2008) 1.00

Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenesis in a protease gene. New Phytol (2007) 0.99

A reassessment of the mating system characteristics of the army ant Eciton burchellii. Naturwissenschaften (2006) 0.97

Hydrophilic interaction and reversed-phase ultra-performance liquid chromatography TOF-MS for metabonomic analysis of Zucker rat urine. J Sep Sci (2008) 0.96

A combined (1)H NMR and HPLC-MS-based metabonomic study of urine from obese (fa/fa) Zucker and normal Wistar-derived rats. J Pharm Biomed Anal (2005) 0.95

Extreme changes to gene expression associated with homoploid hybrid speciation. Mol Ecol (2009) 0.94

Hydrogen sulfide effects on stomatal apertures. Plant Signal Behav (2011) 0.93

Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem (2007) 0.93

Brassica ASTRA: an integrated database for Brassica genomic research. Nucleic Acids Res (2005) 0.93

Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower. Genome (2002) 0.93

A metabonomic analysis of plasma from Zucker rat strains using gas chromatography/mass spectrometry and pattern recognition. Rapid Commun Mass Spectrom (2006) 0.92

Generation of ultrahigh peak capacity LC separations via elevated temperatures and high linear mobile-phase velocities. Anal Chem (2006) 0.92

Methodological considerations in the development of HPLC-MS methods for the analysis of rodent plasma for metabonomic studies. Mol Biosyst (2009) 0.91

A joint transcriptomic, proteomic and metabolic analysis of maize endosperm development and starch filling. Plant Biotechnol J (2008) 0.91

Metabolic profiling of transgenic adenocarcinoma of mouse prostate (TRAMP) tissue by 1H-NMR analysis: evidence for unusual phospholipid metabolism. Prostate (2008) 0.90

Multiplex single nucleotide polymorphism (SNP)-based genotyping in allohexaploid wheat using padlock probes. Plant Biotechnol J (2009) 0.89

High temperature-ultra performance liquid chromatography-mass spectrometry for the metabonomic analysis of Zucker rat urine. J Chromatogr B Analyt Technol Biomed Life Sci (2008) 0.89