网络模型基础.pdfVIP

系统生物学 (Systems Biology) 马彬广 网络模型基础 （第三讲） M ∂ 蛋白互作网络与基因调控网络 ∑ (a) Network of protein–protein interactions in yeast. From Jeong et al. (b) Regulatory interactions between E. coli genes. Courtesy of S. Ortiz, L. Rico, and A. Valencia. M ∂ 代谢网络 ∑ M ∂ 图论 ∑ 格尼斯堡七桥问题 Taken from the book “analysis of biological networks” M ∂ ∑ Mathematical Graph (a) Directed graph with 6 nodes and 9 edges. (b) An undirected graph with similar topology. (c) By rewiring, we can obtain a new graph without changing the degrees k . i M ∂ Basic Notions for Graph and Network ∑  Graph: G = {V, E}, V, a set of vertices (nodes), E, a set of edges. (used in Math Theory)  Network: directed graph with weights for edges. (used in practice)  Usually: the two concepts Graph and Network are used interchangeably.  Directed or Undirected: a edge is a ordered or order-less pair of nodes.  Neighbors: the nodes directly connected to the current node.  Order and Size: the number of nodes and the number of edges.  Degree: for undirected, the degree for a node is the number its edges; for directed graph, two kinds of degree, the incoming degree is the number of edges from other nodes, the outgoing degree is the number of edges to other nodes. M ∂ Basic Notions for Graph and Network ∑  Loop: an edge start from and end with the same node.  Path: a sequence of edges leads one node to another node.  Acyclic graph: a directed graph without cycles (a path starting and ending at the same node). M ∂ 图的两种表示方法 ∑ 例图：