Preface. Contributors

Transcription

1 CONTENTS Foreword Preface Contributors PART I INTRODUCTION 1 1 Networks in Biology 3 Björn H. Junker 1.1 Introduction Biology Biochemistry and Molecular Biology Cell Biology Ecology and Evolution Systems Biology Properties of Biological Networks Networks on a Microscopic Scale Networks on a Macroscopic Scale Other Biological Networks Summary Exercises 12 References 12 COPYRIGHTED MATERIAL xiii xv xix v

2 vi CONTENTS 2 Graph Theory 15 Falk Schreiber 2.1 Introduction Basic Notation Sets Graphs Graph Attributes Special Graphs Undirected, Directed, Mixed, and Multigraphs Hypergraphs and Bipartite Graphs Trees Graph Representation Adjacency Matrix Adjacency List Graph Algorithms Running Times of Algorithms Traversal Summary Exercises 27 References 28 PART II NETWORK ANALYSIS 29 3 Global Network Properties 31 Ralf Steuer and Gorka Zamora López 3.1 Introduction Global Properties of Complex Networks Distance, Average Path Length, and Diameter Six Degrees of Separation: Concepts of a Small World The Degree Distribution Assortative Mixing and Degree Correlations The Clustering Coefficient The Matching Index Network Centralities Eigenvalues and Spectral Properties of Networks Models of Complex Networks The Erdös Rényi Model The Watts Strogatz Model The Barabási Albert Model Extensions of the BA Model Additional Properties of Complex Networks Structural Robustness and Attack Tolerance 49

3 CONTENTS vii Modularity, Community Structures and Hierarchies Subgraphs and Motifs in Networks Statistical Testing of Network Properties Generating Networks and Null Models The Conceptualization of Cellular Networks Bipartite Graphs Correlation Networks Summary Exercises 58 References 59 4 Network Centralities 65 Dirk Koschützki 4.1 Introduction Centrality Definition and Fundamental Properties Comparison of Centrality Values Disconnected Networks Degree and Shortest Path-Based Centralities Degree Centrality Eccentricity Centrality Closeness Centrality Shortest Path Betweenness Centrality Algorithms Example Feedback-Based Centralities Katz s Status Index Bonacich s Eigenvector Centrality PageRank Tools Summary Exercises 81 References 81 5 Network Motifs 85 Henning Schwöbbermeyer 5.1 Introduction Definitions and Basic Concepts Definitions Modeling of Biological Networks Concepts of Motif Frequency Motif Statistics and Motif-Based Network Distance Determination of Statistical Significance of Network Motifs 89

4 viii CONTENTS Randomization Algorithm for Generation of Null Model Networks Influence of the Null Model on Motif Significance Limitations of the Null Model on Motif Detection Measures of Motif Significance and for Network Comparison Complexity of Network Motif Detection Aspects Affecting the Complexity of Network Motif Detection Frequency Estimation by Motif Sampling Methods and Tools for Network Motif Analysis Pajek Mfinder MAVisto FANMOD Analyses and Applications of Network Motifs Network Motifs in Complex Networks Dynamic Properties of Network Motifs Higher Order Structures Formed by Network Motifs Network Comparison Based on Network Motifs Evolutionary Origin of Network Motifs Summary Exercises 108 References Network Clustering 113 Balabhaskar Balasundaram and Sergiy Butenko 6.1 Introduction Notations and Definitions Network Clustering Problem Clique-Based Clustering Minimum Clique Partitioning Min Max k-clustering Center-Based Clustering Clustering with Dominating Sets k-center Clustering Conclusion Summary Exercises 133 References Petri Nets 139 Ina Koch and Monika Heiner 7.1 Introduction 139

5 CONTENTS ix 7.2 Qualitative Modeling The Model The Behavioral Properties Qualitative Analysis Structural Analysis Invariant Analysis MCT-Sets Dynamic Analysis of General Properties Dynamic Analysis of Special Properties Model Validation Criteria Quantitative Modeling and Analysis Tool Support Case Studies Summary Exercises 175 References 177 PART III BIOLOGICAL NETWORKS Signal Transduction and Gene Regulation Networks 183 Anatolij P. Potapov 8.1 Introduction Decisive Role of Regulatory Networks in the Evolution and Existence of Organisms Gene Regulatory Network as a System of Many Subnetworks Databases on Gene Regulation and Software Tools for Network Analysis Peculiarities of Signal Transduction Networks Topology of Signal Transduction Networks Topology of Transcription Networks Intercellular Molecular Regulatory Networks Summary Exercises 201 References Protein Interaction Networks 207 Frederik Börnke 9.1 Introduction Detecting Protein Interactions The Yeast Two-Hybrid System Affinity Capture of Protein Complexes Computational Methods to Predict Protein Interactions 218

6 x CONTENTS Other Ways to Identify Protein Interactions Establishing Protein Interaction Networks Data Storage and Network Generation Benchmarking High-Throughput Interaction Data Analyzing Protein Interaction Networks Network Topology and Functional Implications Functional Modules in Protein Interaction Networks Evolution of Protein Interaction Networks Comparative Interactomics Summary Exercises 226 References Metabolic Networks 233 Márcio Rosa da Silva, Jibin Sun, Hongwu Ma, Feng He, and An-Ping Zeng 10.1 Introduction Visualization and Graph Representation Reconstruction of Genome-Scale Metabolic Networks Connectivity and Centrality in Metabolic Networks Modularity and Decomposition of Metabolic Networks Modularity Coefficient Modularity-Based Decomposition Elementary Flux Modes and Extreme Pathways Summary Exercises 249 References Phylogenetic Networks 255 Birgit Gemeinholzer 11.1 Introduction Character Selection, Character Coding, and Matrices for Phylogenetic Reconstruction Tree Reconstruction Methodologies Phylogenetic Networks Galled Trees Statistical Parsimony Median Network Median-Joining Networks Pyramids Example of a Pyramidal Clustering Model Split Decomposition 274

7 CONTENTS xi 11.5 Summary Exercises 276 References Ecological Networks 283 Ursula Gaedke 12.1 Introduction Binary Food Webs Introduction and Definitions Descriptors of the Network Operational Problems Aims and Results Conclusion Quantitative Trophic Food Webs Introduction, Definitions, and Database Multiple Commodities Descriptors of the Network and Information to be Gained Conclusion Ecological Information Networks Summary Exercises 301 References Correlation Networks 305 Dirk Steinhauser, Leonard Krall, Carsten Müssig, Dirk Büssis, and Björn Usadel 13.1 Introduction General Remarks Basic Notation Data, Unit, Variable, and Observation Sample, Profiles, and Replica Set Measures of Association Simple Correlation Measures Complex Correlation and Association Measures Probability, Confidence, and Power Matrices Construction and Analyses of Correlation Networks Data and Profiles Data Set and Matrix Correlation Matrix Network Matrix Correlation Network Analysis 319

8 xii CONTENTS Interpretation and Validation Biological Use of Correlation Networks The Global Analysis Approach The Guide Gene Approach A Simple Coregulation Test: Photosynthesis A Complex Coregulation Test: Brassinosteroids Summary Exercises 329 References 330 Index 335