METABOLOMICS: METABOLITES, METABONOMICS, AND ANALYTICAL TECHNOLOGIES -- METABOLOMICS: METABOLITES, METABONOMICS, AND ANALYTICAL TECHNOLOGIES -- LIBRARY OF CONGRESS CATALOGING-IN-PUBLICATION DATA -- CONTENTS -- PREFACE -- Chapter 1 CORRELATIONS- AND DISTANCES-BASED APPROACHES TO STATIC ANALYSIS OF THE VARIABILITY IN METABOLOMIC DATASETS. APPLICATIONS AND COMPARISONS WITH OTHER STATIC AND KINETIC APPROACHES -- Abstract -- I. Introduction -- II. Diversity and Intrinsic Variability of Metabolomic Datasets -- II.1. Presentation of Metabolomic Datasets -- II.2. Repeated Experiments for Highlighting of Metabolic States -- III. General presentation of Different Metabolomic Approaches and Parameters -- III.1. Classification of Metabolomic Approaches Based on Different Criteria -- III.2. Boolean Matrix Based Approaches -- III.3. Transition Matrix Based Approaches -- III.4. Stoichiometric Matrix Based Approaches -- III.5. Jacobian Matrix Based Approach -- III.6. Scheffe Matrix Based Approach -- IV. Metabolomic Approaches Based on Distance and Correlation Matrices -- IV.1. Correlation Based Approaches -- IV.1.1. Graphical Identification of Correlation Models -- IV.1.2. Data Transformation to Application of Linear Model -- IV.1.3. Correlation Coefficient Computation -- IV.1.3.1. Pearson Correlation Computation -- IV.1.3.2. Matrix Correlation Computation -- IV.1.3.3. Spearman Correlation Calculation -- IV.1.4. Origins and Interpretation of Correlations in Metabolic Systems -- IV.1.4.1. Chemical Equilibrium -- IV.1.4.2. Mass Conservation -- IV.1.4.3. Assymetric Control -- IV.1.4.4. Unusually High Variance in the Expression of a Single Gene -- IV.1.5. Scale-Dependent Interpretations of Correlations -- IV.1.6. Multidimensional Correlation Screening by Means of Principle Component Analysis -- IV.1.6.1. Aim -- IV.1.6.2. General Principle of PCA.

IV.1.6.3. Computation of Eigenvalues, Eigenvectors and Principle Components -- IV.1.6.4. Graphical Interpretation of Factorial Plans -- IV.1.6.5. Different Types of PCA -- IV.1.6.6. Numerical Application and Interpretation of Standardized PCA -- IV.2. Distance Matrix-Based Approach: Cluster Analysis -- IV.2.1. Introduction -- IV.2.2 Goal of Cluster Analysis -- IV.2.3. General Protocols in Hierarchical Cluster Analysis (HCA) -- IV.2.4. Dissimilarity Measures -- IV.2.4.1. Continuous Data and Distance Computation -- IV.2.4.1.1. Euclidean Distance -- IV.2.4.1.2. Chi-Square Distance -- IV.2.4.2. Qualitative Variables and Similarity Indices -- IV.2.5. Clustering Techniques -- IV.2.5.1. Single Link-Based Clustering -- IV.2.5.2. Complete Link-Based Clustering -- IV.2.5.3. Centroid Link-Based Clustering -- IV.2.5.4. Average Link-Based Clustering -- IV.2.5.5. Variance Criterion Clustering: Ward Method -- IV.2.6. Identification and Interpretation of Clusters from Dendrogram -- V. Outlier Analyses -- V.1. Introduction -- V.2. Different Types of Outliers -- V.3. Statistical Criteria for Identification of Outliers -- V.4. Graphical Identification of Univariate Outliers -- V.5. Graphical Identification of Bivariate Outliers -- V.6. Identification of Multivariate Outliers Based on Distance Computations -- V.6.1. Standard Mahalanobis Distance Computation -- V.6.2. Jackknifed Mahalanobis Distance Computation -- V.6.3. Outlier Screening from Correspondence Analysis -- V.6.3.1. General Concepts of Correspondence Analysis -- V.6.3.2 Basic Computations in Correspondence Analysis -- V.6.3.3. Graphical Interpretation of CA Results and Outlier Diagnostic -- V.6.4. Outlier Diagnostic Based on Andrews Curves -- V.6.4.1. General Concepts -- V.6.4.2. Computation of Andrews Curves -- V.6.4.3. Graphical Outlier Diagnostic Based on Andrews Curves -- References.

Chapter 2 METABOLOMIC PROFILE AND FRACTAL DIMENSIONS IN BREAST CANCER CELLS -- Abstract -- Introduction -- Metabolomics and Cancer -- Cancer Metabolism -- Metabolism and Cancer: Cause or Epiphenomenon? -- Phenotype Metabolism, Cell Shape and Microenvironment -- Cancer Cell Shape -- Cell Shape and Metabolic Phenotype -- Conclusion -- References -- Chapter 3 FROM METABOLIC PROFILING TO METABOLOMICS: FIFTY YEARS OF INSTRUMENTAL AND METHODOLOGICAL IMPROVEMENTS -- Abstract -- Introduction -- Origins and Development: Looking Back -- Chromatographic Separation Techniques - Mass Spectrometry -- GC-MS -- Sample Preparation -- GC-MS Analysis -- LC-MS -- Sample Preparation -- LC-MS Analysis -- Direct Infusion MS and MS/MS -- Desorption and Imaging MS -- Data Handling -- Future Perspectives -- References -- Chapter 4 PLANT ENVIRONMENTAL METABOLOMICS -- Introduction -- Environment - Abiotic Interactions -- Nitrogen Deposition -- Nutrient Deficiency -- Salinity -- Drought -- Metals and Soil Pollution -- Atmospheric Carbon Dioxide (CO2) -- Ozone -- Photoperiod -- UltraViolet Radiation -- Temperature -- Ecology -- Herbivory -- Competition -- Floral Scents -- Populations, Evolution and Genetics -- Genetic versus Environmental Influences on the Metabolome -- Populations -- Conclusion -- Abbreviations -- References -- Chapter 5 MICROBIAL METAGENOMICS: CONCEPT, METHODOLOGY AND PROSPECTS FOR NOVEL BIOCATALYSTS AND THERAPEUTICS FROM THE MAMMALIAN GUT MICROBIOME -- Abstract -- Introduction -- The Concept of Genomics in Microbial Ecology -- What is Metagenomics? -- Microbial Metagenomics: Major Procedural Steps -- Sampling and Microbial Nucleic Acids Extraction -- Microbial Genome- and Gene-Enrichment -- Metagenome Cloning and Targeting -- Screening and Analysis of Metagenomic Libraries -- The Function-Driven Analysis -- The Sequence-Driven Analysis.

Genomics in Mammalian Gut Microbial Diversity -- Metagenomics in Rumen Microbiome-Motives and Applications -- 1. Rumen Microbes as Sources of Valuable Hydrolytic Enzymes -- 2. Direct Fed Microbials (DFM) from the Rumen -- 3. Rumen-Originated Antimicrobial Products -- 4. Lowering Methane Emissions -- 5. Determining the Protozoal Ecology of the Rumen -- 6. Genes and Genetic Engineering Tools from Rumen Microbiome -- Bottlenecks of the Technology -- Conclusion -- References -- Chapter 6 NUTRIGENOMICS, METABOLOMICS AND METABONOMICS: EMERGING FACES OF MOLECULAR GENOMICS AND NUTRITION -- Abstract -- Introduction -- Nutrigenomics Concept -- Nutrient-Gene Interaction -- Nutrigenomics in Livestock Perspective -- What is Metabolomics? -- Techniques and Data Analysis in Metabolomics -- What Is Metabonomics? -- Sample Analysis and Data Processing in Metabonomics -- Conclusion -- References -- Chapter7MACHINERECONSTRUCTIONOFMETABOLICNETWORKSFROMMETABOLOMICDATATHROUGHSYMBOLIC-STATISTICALLEARNING -- Abstract -- 1.Introduction -- 2.MetabolicPathways -- 3.TheSymbolic-StatisticalFrameworkPRISM -- 4.ModelingBisphenolADegradationPathwayinPRISM -- 5.ReconstructingPathwaysfromSequencesofReactions -- 6.RelatedWork -- 7.ConclusionandFutureWork -- References -- Chapter 8 METABOLOMICS -- Introduction to Metabolomics -- A. General Information on Metabolomics -- B. Database and Tool in Metabolomics -- MSFACTs [13] -- HybGFS [14] -- HMDB [15] -- aMAZE LightBench [16] -- BioSilico [17] -- Eco Cyc [18 - 21] -- Patikaweb [22] -- PathAligner [23] -- MetaCys [24 - 26] -- Golm Metabolome Database [27] -- C. Application of Metabolomics -- 1. Application in Oncology -- 2. Application in Pharmacology -- 3. Application in Genetics -- Pathway and Metabolism -- A. What is Metabolism? -- B. Pathway Drawing -- 1. PathFinder [42] -- 2. MetaViz [43].

3. FluxAnalyzer [44] -- 4. ePath3D -- C. Usefulness of Pathway Analysis -- D. Pathway Analysis Tool -- 1. Pathway Miner [53] -- 2. WholePathwayScope [54] -- 3. ArrayxPath [55] -- 4. Genome Expression Pathway Analysis Tool [56] -- Introduction to Metabolonics -- References -- Chapter 9 THE ROLE OF SPECIFIC ESTROGEN METABOLITES IN THE INITIATION OF BREAST AND OTHER HUMAN CANCERS -- Introduction -- Catechol Estrogen Quinones as Mutagens Initiating Breast, Prostate and Other Human Cancers -- Imbalance in Estrogen Homeostasis -- The Kidney of Syrian Golden Hamsters -- The Mammary Gland of ERKO/Wnt-1 Mice -- The Prostate of Noble Rats -- The Breast of Women with Breast Carcinoma -- Estrogen-Induced Mutations and Cell Transformation -- Conclusions -- Acknowledgments -- References -- INDEX.