Data Management of Protein Interaction Networks (PDF)
(Sprache: Englisch)
Current PPI databases do not offer sophisticated queryinginterfaces and especially do not integrate existing informationabout proteins. Current algorithms for PIN analysis use onlytopological information, while emerging approaches attempt toexploit the...
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Current PPI databases do not offer sophisticated queryinginterfaces and especially do not integrate existing informationabout proteins. Current algorithms for PIN analysis use onlytopological information, while emerging approaches attempt toexploit the biological knowledge related to proteins and kinds ofinteraction, e.g. protein function, localization, structure,described in Gene Ontology or PDB. The book discussestechnologies, standards and databases for, respectively,generating, representing and storing PPI data. It also describesmain algorithms and tools for the analysis, comparison andknowledge extraction from PINs. Moreover, some case studies andapplications of PINs are also discussed.
Inhaltsverzeichnis zu „Data Management of Protein Interaction Networks (PDF)“
LIST OF FIGURES xiii LIST OF TABLES xix FOREWORD xxi PREFACE xxiii ACKNOWLEDGMENTS xxix INTRODUCTION xxxi ACRONYMS xxxiii 1 INTERACTOMICS 1 1.1 Interactomics and Omics Sciences / 1 1.2 Genomics and Proteomics / 4 1.3 Representation and Management of Protein Interaction Data / 5 1.4 Analysis of Protein Interaction Networks / 5 1.5 Visualization of Protein Interaction Networks / 6 1.6 Models for Biological Networks / 7 1.7 Flow of Information in Interactomics / 8 1.8 Applications of Interactomics in Biology and Medicine / 10 1.9 Summary / 11 2 TECHNOLOGIES FOR DISCOVERING PROTEIN INTERACTIONS 13 2.1 Introduction / 13 2.2 Techniques Investigating Physical Interactions / 14 2.3 Technologies Investigating Kinetic Dynamics / 17 2.4 Summary / 18 3 GRAPH THEORY AND APPLICATIONS 21 3.1 Introduction / 21 3.2 Graph Data Structures / 22 3.3 Graph-Based Problems and Algorithms / 28 3.4 Summary / 31 4 PROTEIN-TO-PROTEIN INTERACTION DATA 33 4.1 Introduction / 33 4.2 HUPO PSI-MI / 34 4.3 Summary / 41 5 PROTEIN-TO-PROTEIN INTERACTION DATABASES 43 5.1 Introduction / 43 5.2 Databases of Experimentally Determined Interactions / 45 5.3 Databases of Predicted Interactions / 55 5.4 Metadatabases: Integration of PPI Databases / 62 5.5 Summary / 70 6 MODELS FOR PROTEIN INTERACTION NETWORKS 71 6.1 Introduction / 71 6.2 Random Graph Model / 72 6.3 Scale-Free Model / 73 6.4 Geometric Random Graph Model / 73 6.5 Stickiness Index (STICKY) Model / 74 6.6 Degree-Weighted Model / 74 6.7 Network Scoring Models / 75 6.8 Summary / 76 7 ALGORITHMS ANALYZING FEATURES OF PROTEIN INTERACTION NETWORKS 79 7.1 Introduction / 79 7.2 Analysis of Protein Interaction Networks through Centrality Measures / 80 7.3 Extraction of Network Motifs / 81 7.4 Individuation of Protein Complexes / 88 7.5 Summary / 99 8 ALGORITHMS COMPARING PROTEIN INTERACTION NETWORKS 101 8.1 Introduction / 101 8.2 Local Alignment Algorithms / 104 8.3 Global Alignment Algorithms / 109 8.4 Summary / 111 9 ONTOLOGY-BASED ANALYSIS OF PROTEIN
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INTERACTION NETWORKS 113 9.1 Definition of Ontology / 113 9.2 Languages for Modeling Ontologies / 115 9.3 Biomedical Ontologies / 116 9.4 Ontology-Based Analysis of Protein Interaction Data / 117 9.5 Semantic Similarity Measures of Proteins / 120 9.6 The Gene Ontology Annotation Database (GOA) / 122 9.7 FussiMeg and ProteinOn / 123 9.8 Summary / 123 10 VISUALIZATION OF PROTEIN INTERACTION NETWORKS 125 10.1 Introduction / 125 10.2 Cytoscape / 126 10.3 CytoMCL / 127 10.4 NAViGaTOR / 128 10.5 BioLayout Express3D / 130 10.6 Medusa / 130 10.7 ProViz / 131 10.8 Ondex / 132 10.9 PIVOT / 132 10.10 Pajek / 133 10.11 Graphviz / 134 10.12 GraphCrunch / 134 10.13 VisANT / 135 10.14 PIANA / 136 10.15 Osprey / 136 10.16 cPATH / 137 10.17 PATIKA / 138 10.18 Summary / 139 11 CASE STUDIES IN BIOLOGY AND BIOINFORMATICS 141 11.1 Analysis of an Interaction Network from Proteomic Data / 141 11.2 Experimental Comparison of Two Interaction Networks / 143 11.3 Ontology-Based Management of PIN (OntoPIN) / 145 11.4 Ontology-Based Prediction of Protein Complexes / 149 12 FUTURE TRENDS 151 REFERENCES 157 INDEX 177
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Autoren-Porträt von Mario Cannataro, Pietro H. Guzzi
MARIO CANNATARO, PhD, is Associate Professor of ComputerEngineering at the Magna Græcia University of Catanzaro. Hisresearch explores bioinformatics, computational proteomics andgenomics, medical informatics, grid and parallel computing, andadaptive web systems. Dr. Cannataro has published three books andmore than 150 papers in international journals and conferenceproceedings.PIETRO HIRAM GUZZI, PhD, is Assistant Professor ofComputer Engineering at the Magna Græcia University ofCatanzaro. His research focuses on the analysis of proteininteraction networks and the use of biological knowledge encoded inontologies for modeling, querying, and analyzing proteininteraction networks.
Bibliographische Angaben
- Autoren: Mario Cannataro , Pietro H. Guzzi
- 2012, 1. Auflage, 300 Seiten, Englisch
- Verlag: John Wiley & Sons
- ISBN-10: 1118103718
- ISBN-13: 9781118103715
- Erscheinungsdatum: 03.02.2012
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