lecture05.pdf

NETWORKS NETWORK TERMS Parts of the network Nodes Edges Leaves Weighted vs Unweighted  0 1 1 0 0 UNWEIGHTED GRAPH 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1...

NETWORKS NETWORK TERMS Parts of the network Nodes Edges Leaves Weighted vs Unweighted  0 1 1 0 0 UNWEIGHTED GRAPH 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 B 0 0 0 1 0 A D E C  0 1.5 5 0 0 WEIGHTED GRAPH 0 0 0 0.25 0 0 0 0 0 0 0 0 0 0 2 B 0 0 0 2 0 A D E C A CYCLE IN A DIRECTED NETWORK B A D C AN ACYCLIC DIRECTED NETWORK B A D C TREES A B C D E MULTILAYER AND MULTIPLEX NETWORKS B Multilayer – Different networks D E A that connected by edges between the subnetworks Multiplex – Nodes are the same, C but the edges are different in the B subnetworks D A E C DEGREE OF A NODE The degree of a node is the number of edges connected to it B A=2 A D E B=2 E=1 C WALKS AND PATHS Walks – A sequence of nodes that every consecutive pair of nodes in the sequence is connected by an edge Self-avoiding walks Length – The number of edges transversed, not the number of nodes Paths – Walks that do not intersect themselves There are many algorithms to identify the shortest path PHYLOGENETIC TREES A B C D E  0 1.5 5 0 0 GENE REGULATORY NETWORKS 0 0 0 0.25 0 0 -0.5 0 0 0 0 0 0 0 2 B 0 0 0 2 0 A D E C HOW TO DETERMINE THE GRNS Transcriptomic studies Knockout Knockin Drugs REMEMBER THE MULTIPLEX NETWORKS B Different cell types D E A Different conditions C B A D E C PROTEIN – PROTEIN INTERACTIONS WARNING: USE FIGURES THAT YOU CAN CLEARLY EXPLAIN