Exploring PPI networks using Cytoscape

Introduction to Cytoscape

• Presentation slides: PDF, PPT
• Supplementary reading on analysis and visualization of biological networks with Cytoscape

Hands-on Cytoscape tutorials

• Tutorial 1: User Interface
• Tutorial 2: Networks, Data, Styles, Layouts and App Manager
• Tutorial 3: Filtering and Editing
• Example files: Cytoscape data

Application scenarios / Use cases

1. Given a list of genes or proteins, build an interaction network in Cytoscape
2. Integrate a protein interaction network with gene expression data
3. Annotate a set of genes or proteins with functional information (GO, pathways)
4. Identify putative protein complexes in a protein interaction network
5. Link protein interaction networks with protein structure visualization in UCSF Chimera
6. Your use case?