# Presentation: 692178

## BioPathways SIG, July.29.2004 

**BioPathways SIG, July.29.2004 **

## Networks in Biology

- Molecular interaction and similarity networks are vital for understanding gene function in biology
- How does my gene of unknown function relate to a known gene?
- Many biological questions can be answered by mapping the problem to a network problem

## Lots of Data to Analyze

- Network data is accumulating
- Protein-protein interactions, genetic pathways, metabolic networks, cell signals, gene regulations, similarity relationships, literature-based links
- Software to view and query this information is required to efficiently answer scientific questions

## Network Visualization Tools

- Pajek - Slovenia
- Osprey - SLRI, Toronto
- VisANT - BU
- Biolayout - EBI
- GraphViz
- PowerPoint
- Others
- Cytoscape (only open-source biology)

## What is Cytoscape?

- Cytoscape is a network visualization and analysis tool
- An extensible platform for bioinformatics software development
- New! 100% Open-source Java
- GINY Graph Library
- Version 2.0 released this week:www.cytoscape.org

## Slide 6

## Example: Network Clustering

- Clusters in a protein-protein interaction network have been shown to represent protein complexes and parts of pathways
- Clusters in a protein similarity network represent protein families
- Network clustering is available through the MCODE Cytoscape plugin

## Slide 8

## Cytoscape Core Features

- Visualize and lay out networks
- Display network data using visual styles
- Easily organize multiple networks
- Bird’s eye view navigation of large networks
- Supports SIF and GML, molecular profiling formats, node/edge attributes
- Functional annotation from GO + KEGG
- Metanodes (hyper graph / compound graph)
- Extensible through plugins (20 developed)

## Layout

- 16 algorithms available through plugins
- Zooming, hide/show, alignment

## yFiles Organic

## yFiles Circular

## Slide 13

## Visual Styles

- Map graph attributes to visual attributes
- Define visual styles for later use
- Graph has node and edge attributes
- E.g. expression data, interaction type, GO function
- Mapped to visual attributes
- E.g. node/edge size, shape, color, font...
- Take continuous gene expression data and visualize it as continuous node colors

## Visual Styles

**Load “Your Favorite Network”**

## Visual Styles

**Load “Your Favorite Expression”**
**Dataset**

## Visual Styles

**Map expression values**
**to node colors using a**
**continuous mapper**

## Visual Styles

**Expression data mapped**
**to node colors**

## Visual Styles

- Node attributes: node color, border color, border type, node shape, size, label, font
- Edge attributes: edge color, line types, arrows, label, font
- Multidimensional visual attribute mapping soon

## Slide 20

## Filters

- Multiple different filters are available
- Arbitrary Boolean combinations

## What can you use it for?

- Network visualization - multi-dimensional
- Network-based molecular profiling analysis
- Transcriptionally active network modules
- Network clustering
- Module and cluster detection
- Network comparison
- PathBLAST

## Network Analysis

- Plugins for:
- Networks and Transcriptional Profiling
- Active Modules (UCSD)
- Activity Centers (MSKCC)
- Expression Data Viewers (ISB)
- BioModules (ISB)
- General network analysis
- MCODE: network clustering (MSKCC)
- PathBLAST (UCSD)
- 10 published papers
- >10 in development

## Data Access

- Plugins for:
- cPath / data services plugin (MSKCC)
- Poster at main meeting
- Recently available:
- Control from Perl, Python, R (Cytotalk)
- Data Cube Browser
- BIND, PreBIND, HPRD access
- Open architecture for plugin development

## Active Modules

**Active Modules**
**(UCSD)**

**Ideker T, Ozier O, Schwikowski B, Siegel AF**
- Bioinformatics. 2002;18 Suppl 1:S233-40

## Active Modules

**Active Modules**

## Biomodules (ISB)

**Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A,**
**Dimitrov K, Siegel AF, and Galitski T**
- Genome Res. 2004 14: 380-390

## cPath (MSKCC)

## Extensible

- Architecture: 100% open source Java
- Core + plugin API
- Plugins are independently licensed
- “Just need to write the algorithm”
- Template code samples

**Plugin**

## Community

- Mailing lists
- cytoscape-announce@googlegroups.com
- cytoscape-discuss@googlegroups.com
- http://www.cytoscape.org
- 100% open source
- Contributions are encouraged

## MSK’s caBIG Pathway Plan

- High-quality, non-redundant **human** pathways
- Pathways (BioPAX)cPathCytoscape
- BioPAX/PSI-MI represent pathway data
- Pathway DBs + curation support standards
- cPath merges BioPAX/PSI-MI datasets
- Cytoscape analyses pathway datasets in context with other data e.g. gene expression
- Query/retrieve caCORE information via plugin
- Link with other caBIG groups/tools

## MSK’s caBIG Pathway Plan

- High-quality, non-redundant **human** pathways
- Pathways (BioPAX)cPathCytoscape
- BioPAX/PSI-MI represent pathway data
- Pathway DBs + curation support standards
- cPath merges BioPAX/PSI-MI datasets
- Cytoscape analyses pathway datasets in context with other data e.g. gene expression
- Query/retrieve caCORE information via plugin
- Link with other caBIG groups/tools

## Cytoscape Team

**Trey Ideker**
- Nada Amin
- Ryan Kelley
- Dan Ramage
- Jonathan Wang
- Chris Workman

**Benno Schwikowski**
**Hamid Bolouri**
- Rowan Christmas
- Iliana Avila-Campillo
- Larissa Kamenkovich
- Andrew Markiel
- Paul Shannon

**Chris Sander**
- Gary Bader
- Ethan Cerami
- Rob Sheridan