Data Management of Protein Interaction Networks

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 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