2. Outline
• Introduc4on to Interac4on Networks
• Basic components of an interac4on network
• Types of interac4on networks
• Predic4ng Protein‐Protein Interac4on Networks
• Methods
» Logic and concept
• Available Interac4on data
• Integrated protein‐protein interac4on databases
• Searching for interac4on data
• Network Visualiza4on and Analysis tools
• Popular visualiza4on tools
• Network analysis
• Demonstra4on
• Predic4on of interac4on (PPI…?) network from microarray (ARACNE)
• Visualiza4on and analysis of the predicted network (Cytoscape)
3. • Nodes
– DNA/RNA/Protein/Metabolite
• Edges
Directed
– Dis4nc4on between source and target
» Ac4va4on (direct/indirect)
» Repression (direct/indirect)
Undirected
– No dis4nc4on between source and target
» Co‐expression (indirect)
» Binding (direct)
Interac-on Networks – Basic Components
7. Single gene
– Regulators/Co‐regulators
– Upstream/Downstream elements in the network
– Global connec4vity/interconnec4vity
– Func4onal features
– Differen4ally expressed subnetworks
– One gene – one disease : bunch of genes – pathways
– Nextgen sequencing data
List of genes
Why Build/Analyze Interac-on Networks ?
8. Outline
• Introduc4on to Interac4on Networks
• Basic components of an interac4on network
• Types of interac4on networks
• Predic4ng Protein‐Protein Interac4on Networks
• Methods
» Logic and concept
• Available Interac4on data
• Integrated protein‐protein interac4on databases
• Searching for interac4on data
• Network Visualiza4on and Analysis tools
• Popular visualiza4on tools
• Network analysis
• Demonstra4on
• Predic4on of interac4on (PPI…?) network from microarray (ARACNE)
• Visualiza4on and analysis of the predicted network (Cytoscape)
12. Outline
• Introduc4on to Interac4on Networks
• Basic components of an interac4on network
• Types of interac4on networks
• Predic4ng Protein‐Protein Interac4on Networks
• Methods
» Logic and concept
• Available Interac4on data
• Integrated protein‐protein interac4on databases
• Searching for interac4on data
• Network Visualiza4on and Analysis tools
• Popular visualiza4on tools
• Network analysis
• Demonstra4on
• Predic4on of interac4on (PPI…?) network from microarray (ARACNE)
• Visualiza4on and analysis of the predicted network (Cytoscape)
32. Outline
• Introduc4on to Interac4on Networks
• Basic components of an interac4on network
• Types of interac4on networks
• Predic4ng Protein‐Protein Interac4on Networks
• Methods
» Logic and concept
• Available Interac4on data
• Integrated protein‐protein interac4on databases
• Searching for interac4on data
• Network Visualiza4on and Analysis tools
• Popular visualiza4on tools
• Network analysis
• Demonstra4on
• Predic4on of interac4on (PPI…?) network from microarray (ARACNE)
• Visualiza4on and analysis of the predicted network (Cytoscape)
44. Outline
• Introduc4on to Interac4on Networks
• Basic components of an interac4on network
• Types of interac4on networks
• Predic4ng Protein‐Protein Interac4on Networks
• Methods
» Logic and concept
• Available Interac4on data
• Integrated protein‐protein interac4on databases
• Searching for interac4on data
• Network Visualiza4on and Analysis tools
• Popular visualiza4on tools
• Network analysis
• Demonstra4on
• Predic4on of interac4on (PPI…?) network from microarray (ARACNE)
• Visualiza4on and analysis of the predicted network (Cytoscape)
45. PPI Predic-on Using Microarray Data
• Co‐expression concept
• Correla4on Coefficient
» SIMoNE (Sta4s4cal Inference for Modular Networks) ‐ R
• Mutual Informa4on
» Reference Networks
» ARACNE (Algorithm for Reconstruc4on of Accurate Cellular
Networks) – R, geWorkbench
» CLR (Context Likelihood of Relatedness) – R
» MRNET (Maximum Relevance/Minimum Redundancy) – R
» MONET (Modularized NETwork Learning) ‐ Cytoscape
• Bayesian Network