System biology top down key words

Question 1

Degree of a network(connectivty)

Answer 1

The degree of a node in a network (sometimes referred to incorrectly as the connectivity) is the number of connections or edges the node has to other nodes. If a network is directed, meaning that edges point in one direction from one node to another node, then nodes have two different degrees, the in-degree, which is the number of incoming edges, and the out-degree, which is the number of outgoing edges.

Question 2

Degree distribution

Answer 2

The degree distribution P(k) of a network is then defined to be the fraction of nodes in the network with degree k. So you divide the the degree of the network with the total number of nodes.

Question 3

Centrality

Answer 3

Indicators of centrality assign numbers or rankings to nodes within a graph corresponding to their network position.

Question 4

Diamond

Answer 4

A DIseAse MOdule Detection (DIAMOnD) is an algorithm that is used to analyze the connectivity

Question 5

Adjacency matrix

Answer 5

Adjacency matrix is a square matrix used to represent a finite graph. The elements of the matrix indicate whether pairs of vertices are adjacent or not in the graph.

Question 6

Protein–protein interaction networks

Answer 6

Protein-protein interaction networks (PINs) represent the physical relationship among proteins present in a cell, where proteins are nodes, and their interactions are undirected edges.

Recent studies have indicated the conservation of molecular networks through deep evolutionary time.[11] Moreover, it has been discovered that proteins with high degrees of connectedness are more likely to be essential for survival than proteins with lesser degrees.[12] This observation suggests that the overall composition of the network (not simply interactions between protein pairs) is vital for an organism’s overall functioning.

Question 7

Gene regulatory networks (DNA–protein interaction networks)

Answer 7

The complete set of gene products and the interactions among them constitutes gene regulatory networks (GRN).

GRNs are represented with genes and transcriptional factors as nodes and the relationship between them as edges. These edges are directional, representing the regulatory relationship between the two ends of the edge. For example., the directed edge from gene A to gene B indicates that A regulates the expression of B. Thus, these directional edges can not only represent the promotion of gene regulation but also its inhibition.