Discussion summary Cytoscape introduction. 27803::Systems Biology2CBS, Department of Systems Biology.

Discussion summaryCytoscape introduction

27803::Systems Biology2 CBS, Department of Systems Biology

27803::Systems Biology3 CBS, Department of Systems Biology

Sub-cellular localization coverage

27803::Systems Biology4 CBS, Department of Systems Biology

Co-localization of interacting proteins

27803::Systems Biology5 CBS, Department of Systems Biology

Tendency to interact with your cousin

27803::Systems Biology6 CBS, Department of Systems Biology

Over-representation of highly abundant proteins

27803::Systems Biology7 CBS, Department of Systems Biology

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

27803::Systems Biology9 CBS, Department of Systems Biology

Outline• Visualization

• Why Cytoscape?

• Getting started

• Attributes for nodes and edges

• Examples

27803::Systems Biology10 CBS, Department of Systems Biology

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

27803::Systems Biology12 CBS, Department of Systems Biology

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

27803::Systems Biology13 CBS, Department of Systems Biology

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

27803::Systems Biology14 CBS, Department of Systems Biology

GML – node example

node[id 37label "37"graphics

[x 411.0y 395.0h 34.0w 122.0fill "#ccccff"type "rectangle"]

]

27803::Systems Biology17 CBS, Department of Systems Biology

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

27803::Systems Biology18 CBS, Department of Systems Biology

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

...

...

...

27803::Systems Biology19 CBS, Department of Systems Biology

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

27803::Systems Biology21 CBS, Department of Systems Biology

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