Data Management of Protein Interaction Networks

213 Pages·2011·2.237 MB·English

by  Mario Cannataro, Pietro Hiram Guzzi(auth.), Yi Pan, Albert Y. Zomaya(eds.)

DATA MANAGEMENT OF
PROTEIN INTERACTION
NETWORKS
Wiley Series on
Bioinformatics: Computational Techniques and Engineering
Bioinformatics and computational biology involve the comprehensive
application of mathematics, statistics, science, and computer science to the
understanding of living systems. Research and development in these areas
require cooperation among specialists from the fi elds of biology,
computer science, mathematics, statistics, physics, and related sciences.
The objective of this book series is to provide timely treatments of the
different aspects of bioinformatics spanning theory, new and established
techniques, technologies and tools, and application domains. This series
emphasizes algorithmic, mathematical, statistical, and computational
methods that are central in bioinformatics and computational biology.
Series Editors: P rofessor Yi Pan Professor Albert Y. Zomaya
[email protected] [email protected]
Knowledge Discovery in Bioinformatics: Techniques, Methods and
Applications / Xiaohua Hu & Yi Pan
Grid Computing for Bioinformatics and Computational Biology / Albert
Zomaya & El - Ghazali Talbi
Analysis of Biological Networks / Bj ö rn H. Junker & Falk Schreiber
Bioinformatics Algorithms: Techniques and Applications / Ion Mandoiu
& Alexander Zelikovsky
Machine Learning in Bioinformatics / Yanqing Zhang & Jagath C.
Rajapakse
Biomolecular Networks / Luonan Chen, Rui - Sheng Wang, & Xiang - Sun
Zhang
Computational Systems Biology / Huma Lodhi
Computational Intelligence and Pattern Analysis in Biology Informatics /
Ujjwal Maulik, Sanghamitra Bandyopadhyay, & Jason T. Wang
Mathematics of Bioinformatics: Theory, Practice, and Applications /
Matthew He & Sergey Petoukhov
Introduction to Protein Structure Prediction: Methods and Algorithms /
Huzefa Rangwala & George Karypis
Data Management of Protein Interaction Networks / Mario Cannataro &
Pietro Hiram Guzzi
DATA MANAGEMENT OF
PROTEIN INTERACTION
NETWORKS
MARIO CANNATARO
PIETRO HIRAM GUZZI
Department of Experimental Medicine and Clinic
University Magna Graecia of Catanzaro
A JOHN WILEY & SONS, INC., PUBLICATION
Copyright © 2011 by John Wiley & Sons, Inc. All rights reserved
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Library of Congress Cataloging-in-Publication Data:
Cannataro, Mario, 1964-
Data management of protein interaction networks / Mario Cannataro, Pietro
Hiram Guzzi.
p. cm. – (Wiley series in bioinformatics ; 17)
ISBN 978-0-470-77040-5 (hardback)
1. Protein-protein interaction–Information resources. 2. Information
resources management. I. Guzzi, Pietro Hiram, 1980- II. Title.
QP551.C346 2012
025.06'572644–dc22
2011010581
Printed in the United States of America
eISBN: 9781118103715
oISBN: 9781118103746
ePub: 9781118103739
MOBI: 9781118103722
10 9 8 7 6 5 4 3 2 1
To Angela, Francesco,
and Matteo.
M.C.
To my sister, my mother,
my father, and those
who are close to me.
P.H.G.
CONTENTS
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
vii
viii CONTENTS
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
CONTENTS ix
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
x CONTENTS
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
CONTENTS xi
11.4 Ontology-Based Prediction of
Protein Complexes / 149
12 FUTURE TRENDS 151
REFERENCES 157
INDEX 177