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Data management of protein interaction networks / Mario Cannataro, Pietro Hiram Guzzi. -- Hoboken, NY : Wiley, 2012. -- (58.17421056 /C224) |
Contents
Table Of Contents:
List of Figures xiii
List of Tables xix
Foreword xxi
Preface xxiii
Acknowledgments xxix
Introduction xxxi
Acronyms xxxiii
1 Interactomics 1(12)
1.1 Interactomics and Omics Sciences 1(3)
1.2 Genomics and Proteomics 4(1)
1.3 Representation and Management of Protein Interaction Data 5(1)
1.4 Analysis of Protein Interaction Networks 5(1)
1.5 Visualization of Protein Interaction Networks 6(1)
1.6 Models for Biological Networks 7(1)
1.7 Flow of Information in Interactomics 8(2)
1.8 Applications of Interactomics in Biology and Medicine 10(1)
1.9 Summary 11(2)
2 Technologies for Discovering Protein Interactions 13(8)
2.1 Introduction 13(1)
2.2 Techniques Investigating Physical Interactions 14(3)
2.3 Technologies Investigating Kinetic Dynamics 17(1)
2.4 Summary 18(3)
3 Graph Theory and Applications 21(12)
3.1 Introduction 21(1)
3.2 Graph Data Structures 22(6)
3.3 Graph-Based Problems and Algorithms 28(3)
3.4 Summary 31(2)
4 Protein-To-Protein Interaction Data 33(10)
4.1 Introduction 33(1)
4.2 HUPO PSI-MI 34(7)
4.3 Summary 41(2)
5 Protein-To-Protein Interaction Databases 43(28)
5.1 Introduction 43(2)
5.2 Databases of Experimentally Determined Interactions 45(10)
5.3 Databases of Predicted Interactions 55(7)
5.4 Metadatabases: Integration of PPI Databases 62(8)
5.5 Summary 70(1)
6 Models for Protein Interaction Networks 71(8)
6.1 Introduction 71(1)
6.2 Random Graph Model 72(1)
6.3 Scale-Free Model 73(1)
6.4 Geometric Random Graph Model 73(1)
6.5 Stickiness Index (STICKY) Model 74(1)
6.6 Degree-Weighted Model 74(1)
6.7 Network Scoring Models 75(1)
6.8 Summary 76(3)
7 Algorithms Analyzing Features of Protein Interaction Networks 79(22)
7.1 Introduction 79(1)
7.2 Analysis of Protein Interaction Networks through Centrality Measures 80(1)
7.3 Extraction of Network Motifs 81(7)
7.4 Individuation of Protein Complexes 88(11)
7.5 Summary 99(2)
8 Algorithms Comparing Protein Interaction Networks 101(12)
8.1 Introduction 101(3)
8.2 Local Alignment Algorithms 104(5)
8.3 Global Alignment Algorithms 109(2)
8.4 Summary 111(2)
9 Ontology-Based Analysis of Protein Interaction Networks 113(12)
9.1 Definition of Ontology 113(2)
9.2 Languages for Modeling Ontologies 115(1)
9.3 Biomedical Ontologies 116(1)
9.4 Ontology-Based Analysis of Protein Interaction Data 117(3)
9.5 Semantic Similarity Measures of Proteins 120(2)
9.6 The Gene Ontology Annotation Database (GOA) 122(1)
9.7 FussiMeg and ProteinOn 123(1)
9.8 Summary 123(2)
10 Visualization of Protein Interaction Networks 125(16)
10.1 Introduction 125(1)
10.2 Cytoscape 126(1)
10.3 CytoMCL 127(1)
10.4 NAViGaTOR 128(2)
10.5 BioLayout Express3D 130(1)
10.6 Medusa 130(1)
10.7 ProViz 131(1)
10.8 Ondex 132(1)
10.9 PIVOT 132(1)
10.10 Pajek 133(1)
10.11 Graphviz 134(1)
10.12 GraphCrunch 134(1)
10.13 VisANT 135(1)
10.14 PIANA 136(1)
10.15 Osprey 136(1)
10.16 cPATH 137(1)
10.17 PATIKA 138(1)
10.18 Summary 139(2)
11 Case Studies in Biology and Bioinformatics 141(10)
11.1 Analysis of an Interaction Network from Proteomic Data 141(2)
11.2 Experimental Comparison of Two Interaction Networks 143(2)
11.3 Ontology-Based Management of PIN (OntoPIN) 145(4)
11.4 Ontology-Based Prediction of Protein Complexes 149(2)
12 Future Trends 151(6)
References 157(20)
Index 177
