Data Management of Protein Interaction Networks

by Cannataro, Mario; Guzzi, Pietro H.

• ISBN13: 9780470770405
• ISBN10: 0470770406
• Format: Hardcover
• Copyright: 2011-11-22
• Publisher: IEEE Computer Society

Summary

Current PPI databases do not offer sophisticated querying interfaces and especially do not integrate existing information about proteins. Current algorithms for PIN analysis use only topological information, while emerging approaches attempt to exploit the biological knowledge related to proteins and kinds of interaction, e.g. protein function, localization, structure, described in Gene Ontology or PDB. The book discusses technologies, standards and databases for, respectively, generating, representing and storing PPI data. It also describes main algorithms and tools for the analysis, comparison and knowledge extraction from PINs. Moreover, some case studies and applications of PINs are also discussed.

Author Biography

Marro Cannataro PhD is Associate Professor of Computer Engineering at the Magna Grcia University of Catanzaro. His research explores bio informatics, computational proteomics and genomics, medical informatics, grid and parallel computing, and adaptive web systems. Dr. Cannataro has published three books and more than 150 papers in international journals and conference proceedings. Pietro Hiram Guzzi PhD, is Assistant Professor of Computer Engineering at the Magna Grcia University of Catanzaro. His research focuses on the analysis of protein interaction networks and the use of biological knowledge encoded in ontologies for modeling, querying, and analyzing protein interaction networks.

Table of Contents

List Of Figures	p. xiii
List Of Tables	p. xix
Foreword	p. xxi
Preface	p. xxiii
Acknowledgments	p. xxix
Introduction	p. xxxi
Acronyms	p. xxxiii
Interactomics	p. 1
Interactomics and Omics Sciences	p. 1
Genomics and Proteomics	p. 4
Representation and Management of Protein Interaction Data	p. 5
Analysis of Protein Interaction Networks	p. 5
Visualization of Protein Interaction Networks	p. 6
Models for Biological Networks	p. 7
Flow of Information in Interactomics	p. 8
Applications of Interactomics in Biology and Medicine	p. 10
Summary	p. 11
Technologies For Discovering Protein Interactions	p. 13
Introduction	p. 13
Techniques Investigating Physical Interactions	p. 14
Technologies Investigating Kinetic Dynamics	p. 17
Summary	p. 18
Graph Theory And Applications	p. 21
Introduction	p. 21
Graph Data Structures	p. 22
tGraph-Based Problems and Algorithms	p. 28
Summary	p. 31
Protein-To-Protein Interaction Data	p. 33
Introduction	p. 33
HUPO PSI-MI	p. 34
Summary	p. 41
Protein-To-Protein Interaction Databases	p. 43
Introduction	p. 43
Databases of Experimentally Determined Interactions	p. 45
Databases of Predicted Interactions	p. 55
Metadatabases: Integration of PPI Databases	p. 62
Summary	p. 70
Models For Protein Interaction Networks	p. 71
Introduction	p. 71
Random Graph Model	p. 72
Scale-Free Model	p. 73
Geometric Random Graph Model	p. 73
Stickiness Index (STICKY) Model	p. 74
Degree-Weighted Model	p. 74
Network Scoring Models	p. 75
Summary	p. 76
Algorithms Analyzing Features Of Protein Interaction Networks	p. 79
Introduction	p. 79
Analysis of Protein Interaction Networks through Centrality Measures	p. 80
Extraction of Network Motifs	p. 81
Individuation of Protein Complexes	p. 88
Summary	p. 99
Algorithms Comparing Protein Interaction Networks	p. 101
Introduction	p. 101
Local Alignment Algorithms	p. 104
Global Alignment Algorithms	p. 109
Summary	p. 111
Ontology-Based Analysis Of Protein Interaction Networks	p. 113
Definition of Ontology	p. 113
Languages for Modeling Ontologies	p. 115
Biomedical Ontologies	p. 116
Ontology-Based Analysis of Protein Interaction Data	p. 117
Semantic Similarity Measures of Proteins	p. 120
The Gene Ontology Annotation Database (GOA)	p. 122
FussiMeg and ProteinOn	p. 123
Summary	p. 123
Visualization Of Protein Interaction Networks	p. 125
Introduction	p. 125
Cytoscape	p. 126
CytoMCL	p. 127
NAViGaTOR	p. 128
BioLayout Express	p. 130
Medusa	p. 130
ProViz	p. 131
Ondex	p. 132
PIVOT	p. 132
Pajek	p. 133
Graphviz	p. 134
GraphCrunch	p. 134
VisANT	p. 135
PIANA	p. 136
Osprey	p. 136
cPATH	p. 137
PATIKA	p. 138
Summary	p. 139
Case Studies In Biology And Bioinformatics	p. 141
Analysis of an Interaction Network from Proteomic Data	p. 141
Experimental Comparison of Two Interaction Networks	p. 143
Ontology-Based Management of PIN (OntoPIN)	p. 145
Ontology-Based Prediction of Protein Complexes	p. 149
Future Trends	p. 151
References	p. 157
Index	p. 177
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