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Networks in cell biology / edited by M. Buchanan ... [et al.]. — Cambridge : Cambridge University Press, c2010. – (58.15/N476) |
Contents
Contents
List of contributors
Introduction
1 Network views of the cell
1.1 The network hypothesis
1.2 The central dogma and gene regulatory networks
1.3 Protein-protein interaction networks
1.4 Metabolic networks
1.5 Signaling networks
1.6 Networked networks and cell functionality
1.7 Concluding remarks
2 Transcriptional regulatory networks
2.1 Introduction
2.2 Transcriptional regulation in prokaryotes and eukaryotes
2.3 Structure of transcriptional regulatory networks
2.4 Evolution of transcriptional regulatory networks
2.5 Dynamics of transcriptional regulatory networks
2.6 Conclusions
3 Transcription factors and gene regulatory networks
3.1 Introduction
3.2 Promoters' complexity/eukaryotic gene promoters
3.3 Transcription factors
3.4 Bioinformatics of regulatory networks
4 Experimental methods for protein interaction identification
4.1 Introduction
4.2 Protein complementation techniques
4.3 Affinity purification methods
4.4 Protein complex purification and mass spectrometry
4.5 Protein and peptide chips
4.6 Other methods for interaction detection and functional analysis
4.7 Quality of large-scale interaction data
4.8 Comparison of methods
4.9 Conclusions
5 Modeling protein interaction networks
5.1 Introduction
5.2 Scaling laws and network topology
5.3 Predicting protein interactions
5.4 Towards models at an atomic level of resolution
5.5 Concluding remarks
6 Dynamics and evolution of metabolic networks
6.1 Introduction
6.2 Cellular metabolism and its regulation
6.3 Metabolism across disciplines
6.4 Dynamics of a metabolic system
6.5 Stoichiometric analysis
6.6 Constraint-based modeling: feasible states and optimality
6.7 Predicting genetic perturbations
6.8 Double perturbations and epistatic interactions
6.9 The ancient history of metabolism: from cell-scale to biosphere-scale
6.10 Conclusions
7 Hierarchical modularity in biological networks: the case of metabolic networks
7.1 Introduction
7.2 Modularity and hubs in biological networks
7.3 Scaling of the clustering coefficient: a signature of hierarchy
7.4 Method for finding network modules
7.5 A case study: the E. coli metabolic network
7.6 Hierarchy， fractality and the small world of networks
7.7 Conclusions
8 Signalling networks
8.1 Introduction
8.2 Chemical signalling: many pathways following a few general themes
8.3 Cross-talks among signal transduction pathways
8.4 Signalling networks， system organization and modelling
8.5 Conclusions and outlook
Appendix A Complex networks: from local to global properties
Appendix B Modelling the local structure of networks
Appendix C Higher-order topological properties
Appendix D Elementary mathematical concepts
References
Index
