Download Protein Protein interactions (PPI)

Tutorial 12
Biological networks
Biological networks
• Protein-Protein interactions
– STRING
• Protein and genetic interactions
– BioGRID
• Signaling pathways
– SPIKE
• Network visualization
– Cytoscape
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Can also show regulatory
relations
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Protein Protein interactions (PPI)
Protein and genetic interactions
Protein and genetic interactions
Signaling pathway networks
Signaling pathway networks
Signaling pathways
Hearing and vision map
Network visualization - Cytoscape
Network visualization - Cytoscape
Number
of nodes
Number
of edges
node edge
Network visualization - Cytoscape
Analyzing the network
Network visualization - Cytoscape
“Know your network type”
Directed – for regulatory networks
Undirected – for protein-protein networks
Network visualization - Cytoscape
NetworkAnalyzer plug-in
Network visualization - Cytoscape
Degree: the number of edges that a node has.
The node with the highest degree in the graph
Network visualization - Cytoscape
Closeness: measure how close a node to all other nodes in the network.
The nodes with the highest closeness
Network visualization - Cytoscape
Betweenness: quantify the number of all shortest paths that pass through a node.
The node with the highest betweenness
Network visualization - Cytoscape
Network visualization - Cytoscape
Network visualization - Cytoscape
Highest degree = big
Highest betweens = red
Network visualization - Cytoscape
Network visualization - Cytoscape
Mcode plug-in
Network visualization - Cytoscape
Network visualization - Cytoscape
Cytoscape has 140 (!) plug-ins