9.A Analysis of networks

1. 对无方向图的分析。node和edge
2. Scale free networks
3. Network topology of links and nodes
4. Small world networks
5. Network Properties:

Global:
Cyclic – Acyclic Presence or absence of loops …..important for regulatory motifs
Bipartite graphs …….important for understanding relationships between two non-
overlapping sets of nodes, e.g. drugs to drug targets in systems pharmacology Directed graphs …….important for understanding hierarchical interactions
Scale Free Distribution of edges/nodes follows power law
Robustness Resistance of the network to breakup after random node removal

Local:
Clustering coefficient how densely connected the region surrounding a node within a network is
Clique团： a fully connected region within a network

9.B 两篇文献举例说明怎样分析

Analysis of Networks from Differentially Expressed Genes
Fernald G.H et al (2007) J. Immunology 178: 5076

Analysis of Protein-protein Interaction Networks
de Chassey B et al ( 2008) Mol Sys Bio 4:230

10.A From Topology to Function: Directed Sign Specified Graphs I

1. Motifs in cell signaling networks
2. Boolean dynamics
3. Flux Balance Analysis for metabolic networks

10.B

1. 正反馈和负反馈回路