1. CSC, Dec.15-16,2005

2. Cytoscape Team Trey Ideker Mark Anderson Nerius Landys Ryan Kelley Chris Workman Past contributors: Nada Amin Owen Ozier Jonathan Wang Benno Schwikowski Melissa Cline Andrea Splendiadi Lee Hood Richard Bonneau Rowan Christmas Iliana Avila-Campillo Past contributors: Larissa Kamenkovich Andrew Markiel Paul Shannon Chris Sander Gary Bader Ethan Cerami Rob Sheridan Agilent Annette Adler Allan Kuchinsky Aditya Vailaya Mike Creech

3. Logistics  Four units per day  1/2 hour lecture  45 minute hands-on exercises  Lecture  Background for the hands-on exercises  Questions and comments encouraged  Hands-on exercises  Mostly Cytoscape 2.2, a little Cytoscape 2.1.  Teamwork encouraged  Proceed at own pace

4. Schedule  Thursday am: getting started  Introduction  Coffee break  Biological network data  Lunch  Thursday pm: companion resources for network analysis  Text mining  Coffee break  Gene Ontology  Leave  Friday am: mRNA Expression  Expression basics  Coffee break  Expression & text mining & GO  Lunch  Friday pm: advanced topics in network topology  Modules and complexes  Coffee break  Protein domain networks, future directions, feedback.

5. Overview  Introduction  What is Cytoscape?  Resources for getting help  Basic functionality

6. Biological networks Motivation: most biological processes are not performed by a single, independent macromolecule

7. Cytoscape.org Cytoscape is a freely-available (open-source, java-based) bioinformatics software platform for visualizing biological networks (e.g. molecular interaction networks) and analyzing networks with gene expression profiles and other state data. Additional features are available as plugins. jActiveModules: identify significant “active” subnetworks Expression Correlation Network: cluster expression data Agilent Literature Search: build networks by extracting interactions from scientific literature. MCODE: finds clusters of highly interconnected regions in networks cPath: query, retrieve and visualize interactions from the MSKCC Cancer Pathway database BiNGO: determine which Gene Ontology (GO) categories are statistically over-represented in a set of genes Motif Finder: runs a Gibbs sampling motif detector on sequences for nodes in a Cytoscape network. CytoTalk: Interact with Cytoscape from Perl, Python, R, shell scripts or C or C++ programs. Core Features Customize network data display using visual styles Powerful graph layout tools Easily organize multiple networks Easily navigate large networks Filter the network Plugin API Input/Output Protein protein interactions from BIND, TRANSFAC databases Gene functional annotations from Gene Ontology (GO) and KEGG databases Biological models from Systems Biology Markup Language (SBML) cPath: Cancer Pathway database Proteomics Standards Initiative Molecular Interaction (PSI-MI) or Biopathway Exchange Language (BioPAX) formats Oracle Spatial Network data model

8. Use Case 1: Atherosclerosis  King et. al., Physiol Genomics. 2005 Sep 21;23(1):103-18.

9. Use Case 2: Hepatitis C virus infection  Reiss et. al., BMC Bioinformatics 2005, 6:154

13. Hands-on Session 1  Navigating the Cytoscape panels  Loading, editing, and saving a network  Graph layout methods  Setting visual properties

14. Checkpoint question: how can you get help on Cytoscape?