Book contents
- Frontmatter
- Contents
- List of contributors
- Introduction
- 1 Network views of the cell
- 2 Transcriptional regulatory networks
- 3 Transcription factors and gene regulatory networks
- 4 Experimental methods for protein interaction identification
- 5 Modeling protein interaction networks
- 6 Dynamics and evolution of metabolic networks
- 7 Hierarchical modularity in biological networks: the case of metabolic networks
- 8 Signalling networks
- 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
Appendix A - Complex networks: from local to global properties
Published online by Cambridge University Press: 05 June 2012
- Frontmatter
- Contents
- List of contributors
- Introduction
- 1 Network views of the cell
- 2 Transcriptional regulatory networks
- 3 Transcription factors and gene regulatory networks
- 4 Experimental methods for protein interaction identification
- 5 Modeling protein interaction networks
- 6 Dynamics and evolution of metabolic networks
- 7 Hierarchical modularity in biological networks: the case of metabolic networks
- 8 Signalling networks
- 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
Summary
Introduction
In this appendix we provide basic concepts aimed at introducing the formalism of networks. We first introduce graphs and make simple examples, and then discuss the topological properties of networks. Other general presentations of network structure can be found in review articles and books.
A network (or graph in a more mathematical language) is defined as a set of Nvertices (or nodes) connected by links (or edges). Links, and consequently the whole graph, can be either directed (oriented), if a direction is specified as in Fig. A.1a, or undirected (not oriented), if no direction is specified as in Fig. A.1b. More precisely, undirected links are rather bidirectional ones, since they can be traversed in both directions. For this reason an undirected graph can always be thought of as a directed one where each undirected link is replaced by two directed links pointing in opposite directions (see Fig. A.1c). A link in a directed network is said to be reciprocated if another link between the same pair of vertices, but with opposite direction, is there. Therefore, an undirected network can be regarded as a special case of a directed network where all links are reciprocated. The links of a network may also carry a number, referred to as the weight of the edge, representing the strength of the corresponding interaction. In such a case one speaks of a weighted network. In the present appendix we do not consider weighted networks explicitly.
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- Information
- Networks in Cell Biology , pp. 170 - 187Publisher: Cambridge University PressPrint publication year: 2010