Discussion summaryCytoscape introduction

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

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

27803::Systems Biology11 CBS, Department of Systems Biology

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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