Download - Discussion summary Cytoscape introduction. 27803::Systems Biology2CBS, Department of Systems Biology
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Discussion summaryCytoscape introduction
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27803::Systems Biology2 CBS, Department of Systems Biology
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Sub-cellular localization coverage
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Co-localization of interacting proteins
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Tendency to interact with your cousin
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Over-representation of highly abundant proteins
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Coverage versus Accuracy
say a lot, of which most is wrong
say a lot, of which most is right
say little, of which most is wrong
say little, of which most is right
Specificity
Sensitivity
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Visualizing protein relationships A short introduction to Cytoscape
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Outline• Visualization
• Why Cytoscape?
• Getting started
• Attributes for nodes and edges
• Examples
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Visualization• Systems Biology - looking at a system
– a collection of units (gene/proteins) in a context
• Massive amounts of protein/gene relationships– a lot of undiscovered biology is hiding in that data– impossible to get an overview if investigated by hand
• Integrate many types of relationships– the data is available in the CBS data warehouse
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Why Cytoscape?• www.cytoscape.org
– can visualize relationships– is easy to use– has an advanced color coding scheme– allows for custom made plug-ins– has a strong community– is free for academia
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Getting started• Types of input formats
– Tables of interactions (tab-delimited)– GML: a graphical markup language– SIF: a simple input format
• Nodes (genes/proteins) and relationships are specified in one file
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GML – node example
node[id 37label "37"graphics
[x 411.0y 395.0h 34.0w 122.0fill "#ccccff"type "rectangle"]
]
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SIF example PPI in yeast
YDL224C pp YER059W
YDL224C pp YIL050W
YDL224C pp YML064C
YDL224C pp YNL189W
YDR386W pp YBR009C
YDR386W pp YBR098W
YDR386W pp YCL032W
YDR386W pp YDL043C
YDR386W pp YDL208W
YDR386W pp YDR363W
YDR386W pp YDR381W
YDR386W pp YER006W
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Node and edge attributes• Coloring based on attributes
– Nodes; cell cycle regulated, tissue type, etc.– Edges; ppi, protein-DNA, etc.
• Expression data
Node_idexp1 exp2 exp3 exp4
...
...
...
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Node annotation
YeastCompartment
YAL001C = transcription factor TFIIIC complex
YAL002W = membrane fraction
YAL003W = ribosome
YAL005C = cytoplasm*
YAL007C = COPII-coated vesicle
YAL008W = mitochondrion
YAL009W = integral to membrane*
YAL010C = mitochondrial outer membrane
YAL011W = nucleus
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Edge annotation
ActivationRepression
MBF (pd) YER059W = 1
MBF (pd) YIL050W = 0
MBF (pd) YML064C = 1
YML064C (pd) YNL189W = 0
YML064C (pd) YER059W = 0
YML064C (pd) YBR098W = 1
YBR098W (pd) YCL032W = 0
YBR098W (pd) YDL043C = 1
YDL043C (pd) YDL208W = 1
YDL043C (pd) YDR363W = 1
YDL208W (pd) YDR381W = 1
YDL208W (pd) YML064C = 0