Data Management of Protein Interaction NetworksISBN: 978-0-470-77040-5
Hardcover
216 pages
November 2011, Wiley-IEEE Computer Society Press
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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
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