cytoscape
DESCRIPTION
Cytoscape. Mathieu Michaud [email protected]. A powerful bioinformatic tool. Plan. What is cytoscape ? Cytoscape’s core features Cytoscape 3.0. What is Cytoscape ?. An open source Java-based bioinformatics software platform developped by a team of developers. What is Cytoscape ?. - PowerPoint PPT PresentationTRANSCRIPT
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Plan
What is cytoscape ?
Cytoscape’s core features
Cytoscape 3.0
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What is Cytoscape ?
An open source Java-based bioinformatics software platform developped by a team of developers
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What is Cytoscape ?
Used to visualize molecular interaction networks and biological pathways
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What is Cytoscape ?
Integration of annotations, biological data( gene expression profiles)
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What is Cytoscape ?
Create a visual style based on data integrated with network information
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What is Cytoscape ?
History :July, 2002 : 1st release of 0.8
November, 2002 : 2nd release of 0.9
March 2003 : 1.0
Since then, multiple versions
Actual release : 2.7
3.0 is coming
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What is Cytoscape ?
A powerful tool that supports large networks of more than 100,000 nodes and edges
GalFiltered network
331 nodes362 edges
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What is Cytoscape ?
Or :
Human network 19905 nodes31704 edges(from Biomolecular Interaction Network
Database)
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What is Cytoscape ?
nodes can represent proteins, genes, molecules, metabolites, or enzymes
edges are the interactions
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What is Cytoscape ?
The core : provides basic set of functions to visualize networks and integrate data
network layouts
expression profile integration
linking network to databases
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What is Cytoscape ?
Additional features (Plugins) can be integrated in Cytoscape
add new layouts
more file format support
connection with databases
Plugins are developped using the Cytoscape API and are most freely available
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What is Cytoscape ?
Huge community of developpers (about 100 plugins are available in the plugin manager)
Download from the cytoscape website !
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Plan
What is cytoscape ?
Cytoscape’s core features
Cytoscape 3.0
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Cytoscape’s core featuresData integration :
networks, attributes, sessions, data files
Visual style :
Node/edges representation, layouts, browsing
attribute browser, vizmapper, image export
Analysis :
Filter, find Clusters/modules, ...
Others
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Cytoscape’s core features :Data integration
SIF : Simple Interaction Format
GML : Graph Modelling Language
BioPax : Biological Pathway eXchange
PSI-MI : Proteomics Standards Initiative - Molecular Interactions
...
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Data integration of files :
Expression profiles
Gene Ontology annotations
Interoperability :
insert cytoscape into a workflow to load data generated from another source (Igraph, Bioconductor)
Cytoscape’s core features :Data integration
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Session files :
.cys(CYtoscape Session)
save loaded networks
attributes of networks (for nodes, edges, networks)
desktop settings, data, plugins state...
Cytoscape’s core features :Data integration
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Web service client :
Cytoscape can connect to the external public databases and imports network and annotation data
Cytoscape’s core features :Data integration
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Vizmapper :
Cytoscape’s core features :Visualization
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Vizmapper :
Cytoscape’s core features :Visualization
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Vizmapper :
Map graph attributes to visual attributes
Customize visual styles for later use
Graph has node and edge attributes (expression data, interaction type, GO function)
Cytoscape’s core features :Visualization
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Mapped to visual attributes (node/edge size, shape, color, font,...)
Take continuous gene expression data and visualize it as continuous node colors
Cytoscape’s core features :Visualization
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Cytoscape’s core features :Visualization
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Layouts :
Layout networks in 2 dimensions.
Multiple available layouts : cyclic, tree, force-directed, edge-weight, and yFiles organic
Cytoscape’s core features :Visualization
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Cytoscape’s core features :Visualization
Circular Hierarchical
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Cytoscape’s core features :Visualization
Orthogonal Grid
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Browsing :
zoom in/out, pan for browsing network
With network manager : easiest way to organize multiple networks
Bird’s view to navigate large networks
Export your networks as image files :
PDF, EPS, SVG, PNG, JPEG, BMP files
Cytoscape’s core features :Visualization
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Network browserNetwork browser
Cytoscape canvasCytoscape canvas
ToolbarToolbar
Attribute browserAttribute browser
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Filter :
to select some nodes/interactions based on some loaded data.
Cytoscape’s core features :Analysis
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Filter :
exemple : select nodes involved in certain metabolic pathway, that share a particular GO annotation, or genes whose expression level changes due to p-values loaded from gene expression data...
Used to create subnetwork from filtered elements
Cytoscape’s core features :Analysis
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Find active subnetworks, pathway modules :
they can be highlighted by integrating gene expression data --> interaction subnetworks (genes with high level of different expression)
Cytoscape’s core features :Analysis
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Cytoscape’s core features :Analysis
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Find active subnetworks, pathway modules :
Provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes
Cytoscape’s core features :Analysis
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Find clusters (highly interconnected regions) from loaded networks
clusters may have different mean depending on the type of network :
in ppi : they have been shown to be protein complexes and part of pathways
in protein similarity network : they represent protein families
Cytoscape’s core features :Analysis
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Cytoscape’s core features :Analysis
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Multilingual, and Plugins !
jActiveModules
MCode
GOlorize
BinGO
Dynamic expression,...
Cytoscape’s core features :Other features
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Comparison of network analysis platforms
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Cytoscape 3.0Developped in a modular architecture.
Use of new technologies :
OSGi : Cytoscape made of independant modules (kind of plugins)
Spring : web technology to link the modules through “services”.
Maven : builder of application that loads the modules
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Cytoscape 3.0
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Cytoscape 3.0
Plugins are more easily integrated in the core using the OSGi technology
OSGi module --> Spring configuration file --> plugin integrated