BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks...

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BioPathways SIG, July.29.2004

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Transcript of BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks...

Page 1: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

BioPathways SIG, July.29.2004

Page 2: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 3: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 4: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

Network Visualization Tools• Pajek - Slovenia

• Osprey - SLRI, Toronto

• VisANT - BU

• Biolayout - EBI

• GraphViz

• PowerPoint

• Others

• Cytoscape (only open-source biology)

Page 5: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 6: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.
Page 7: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 8: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Proteasome 26S

Proteasome 20S

Ribosome

RNA Pol core

RNA Splicing

Page 9: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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)

Page 10: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

Layout

• 16 algorithms available through plugins

• Zooming, hide/show, alignment

Page 11: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

yFiles Organic

Page 12: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

yFiles Circular

Page 13: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.
Page 14: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 15: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Visual Styles

Load “Your Favorite Network”

Page 16: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Visual Styles

Load “Your Favorite Expression”Dataset

Page 17: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Visual Styles

Map expression valuesto node colors using acontinuous mapper

Page 18: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Visual Styles

Expression data mappedto node colors

Page 19: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 20: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.
Page 21: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

Filters• Multiple different filters are available

• Arbitrary Boolean combinations

Page 22: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 23: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 24: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

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

Page 25: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Active Modules(UCSD)

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

Page 26: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Active Modules

Page 27: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Biomodules (ISB)

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

Page 28: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

cPath (MSKCC)

Page 29: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

Extensible• Architecture: 100% open source Java

– Core + plugin API– Plugins are independently licensed

• “Just need to write the algorithm”

• Template code samples

Plugin

Page 30: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

Community

• Mailing lists• [email protected]• [email protected]

• http://www.cytoscape.org

• 100% open source• Contributions are encouraged

Page 31: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

MSK’s caBIG Pathway Plan• High-quality, non-redundant human pathways

• Pathways (BioPAX)cPathCytoscape

• 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

Page 32: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

MSK’s caBIG Pathway Plan• High-quality, non-redundant human pathways

• Pathways (BioPAX)cPathCytoscape

• 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

Page 33: BioPathways SIG, July.29.2004. Networks in Biology Molecular interaction and similarity networks are vital for understanding gene function.

www.cytoscape.org

Cytoscape Team

Trey IdekerNada AminRyan KelleyDan RamageJonathan WangChris Workman

Benno SchwikowskiHamid BolouriRowan ChristmasIliana Avila-CampilloLarissa KamenkovichAndrew MarkielPaul Shannon

Chris SanderGary BaderEthan CeramiRob Sheridan


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