eadgene and sabre post-analyses workshop 12-14th november 2008, lelystad, netherlands 1 françois...
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EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands1
François MoreewsSIGENAE, INRA, Rennes
Cytoscape and microarray annotations
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands2
http://www.sigenae.org/index.php?id=171
Training course web page
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands3
• Context
• Software presentation
• History
• Functionalities
• User Interface
• User cases for biologists
• Exercises
Cytoscape : presentation
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands4
• Biologists store their annotation data in table formats (Excel…)
• These formats are suited to store simple annotations like blast best hit, IDS...
• But are inappropriate with lists (hit lists…).Many tables are needed.
• Pathways and biological networks can’t be represented in Excel because they are based on graph structures
Why to choose Cytoscape ?
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands5
Graph structures in biologytree
undirected graph
directed graph
ontologies
biological interaction networksa graph pathway
nodes =biological entities (genes, proteins…)
edges = interactions
(genetic regulation, protein/protein…)
node
edge
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands6
biological interaction networks
nodes =biological entities (genes, proteins…)
edges = interactions
(genetic regulation, protein/protein…)
+ nodes and edges attributes
Cytoscape : a tool to work with graph structures
CYTOSCAPE
IDs,expression values, cluster name, GO, xref,,sequence…
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands7
What is Cytoscape?
• Cytoscape was initially made public in July, 2002• Cytoscape is open source and community driven • Plugins may be developed by anyone using the Cytoscape open API
based on Java™ technology
Cytoscape is a software that allows to
•visualize molecular interaction network and metabolic pathways,
•with there annotations, expression profiles or other associated attributes.
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands8
Is Cytoscape used by biologists ?
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publications
PubMed Central publications related to Cytoscape
295 citations (evaluated on november 2008)
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands9
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Example:
Stefano Campanaro et al , BMC genomics 2007
Is Cytoscape used by biologists ?
BMC Genomics, Genome Res, Genome Biol, Nat Protoc, Plant Physiol…
journals
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands10
• the Cytoscape core distribution contains the basic tools for data integration and visualization.
• The Advanced functionalities are available as plugins developed by the community:
More than 65 plugins available
• Analysis -- analyzing existing networks• Network and Attribute I/O -- importing networks and attributes • Network Inference -- inferring new networks • Functional Enrichment -- functional enrichment of networks• Communication/Scripting and Other
Advanced functionalities: plugins
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands11
Embedded connectors to online data ( Pathway Commons, Biomart… ) give
a quick access to interactions data sources.
Data source connectors
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands12
Navigator view
file management
Zoom
search and indexation
Data panel
Networks management
Graphic style editor and manager « VizMapper »
Graph editor
Explore and visualize
annotations data import
Visualize and explore graphs
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands13
• Illustrate a publication (GO summary, interactions graph, metabolic schema)
• Explore the literature from the neighbourhood of a target gene list.
• Capture from experiments and literature my own interaction model, used to summarize the available knowledge on a subject
What can I do with Cytoscape ?
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands14
• Give meaning to a group of co-expressed genes by finding common regulations
• Check the coherence of a network and experimental data
• Model genetic and metabolic regulations …
What can I do with Cytoscape ?
EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands15
Cytoscape exercises
• Cytoscape User Interface presentation• Using networks with microarray probes
annotations– Co expression Clusters– Hugo gene name annotation and expression values– KEGG annotations
• Advanced features with plugins
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How to run Cytoscape
• Java Web Start (from http://www.pathwaycommons.org)
• or download
• test your Java Installation now (for MS windows : start, execute, cmd, JAVA –version)