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Identification of Novel Genes in Arabidopsis Involved in Secondary Cell Wall Formation Using Expression Profiling and Reverse Genetics
Microarray data have been generated from tissue undergoingsecondary cell wall formation and used to identify genes that exhibit a similar expression pattern to the secondary cell wall–specific cellulose synthase genes IRREGULAR XYLEM1 (IRX1) and IRX3, which resulted in the selection of 16 genes for reverse genetic analysis. Expand
Proposed minimum reporting standards for chemical analysis
This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. Expand
Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis.
The cell-wall phenotype of irx7, irx8 and irx9, three previously described irregular xylem (irx) mutants, and irX14 and parvus-3 are shown to be secondary cell- wall mutants, which have mutations in genes encoding putative glycosyltransferases and exhibited large decreases in xylan. Expand
Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
The experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years is described. Expand
Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy.
An introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided and the applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. Expand
Metabolomics by numbers: acquiring and understanding global metabolite data.
Abstract In this postgenomic era, there is a specific need to assign function to orphan genes in order to validate potential targets for drug therapy and to discover new biomarkers of disease.Expand
A tutorial review: Metabolomics and partial least squares-discriminant analysis--a marriage of convenience or a shotgun wedding.
This tutorial review aims to provide an introductory overview to several straightforward statistical methods such as principal component-discriminant function analysis (PC-DFA), support vector machines (SVM) and random forests (RF), which could very easily be used either to augment PLS or as alternative supervised learning methods to PLS-DA. Expand
Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites.
Standard operating procedures for quenching and efficient extraction of metabolites from Escherichia coli are developed and validated and it is indicated that 60% cold (-48 degrees C) methanol solution is the most appropriate method to quench metabolism. Expand
Proposed minimum reporting standards for data analysis in metabolomics
The goal of this group is to define the reporting requirements associated with the statistical analysis of metabolite data with respect to other measured/collected experimental data (often called meta-data). Expand
Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy.
This review focuses on a selective number of recent studies where metabolic fingerprinting has been forwarded as a potential tool for disease diagnosis using infrared and Raman spectroscopies. Expand