Discussion summary Cytoscape introduction Thomas Skøt Jensen Center for Biological Sequence...
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Transcript of Discussion summary Cytoscape introduction Thomas Skøt Jensen Center for Biological Sequence...
Discussion summary
Cytoscape introduction
Thomas Skøt JensenCenter for Biological Sequence AnalysisThe Technical University of Denmark
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
Outline
• Visualization
• Why Cytoscape?
• Getting started
• Attributes for nodes and edges
• Examples
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
Why Cytoscape?
• 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
Getting started
• Two types of input formats– GML: a graphical markup language– SIF: a simple input format
• Nodes (genes/proteins) and relationships are specified in one file
GML - node• GML example:
node[id 37label "37"graphics
[x 411.0y 395.0h 34.0w 122.0fill "#ccccff"type "rectangle"]
]
GML - edge
• GML example:edge
[source 210target 92label "PPo"graphics
[width 1.0type "line"fill "#000000"]
]
SIF
• Very simple
node_1 edge_label node_2node_3 edge_label node_2node_4 edge_label node_2node_5 edge_label node_6node_7 edge_label node_1
SIF
YDL224C pp YER059WYDL224C pp YIL050WYDL224C pp YML064CYDL224C pp YNL189WYDR386W pp YBR009CYDR386W pp YBR098WYDR386W pp YCL032WYDR386W pp YDL043CYDR386W pp YDL208WYDR386W pp YDR363WYDR386W pp YDR381WYDR386W pp YER006W
SIF Example : protein-protein interactions in yeast
Node and edge attributes
• Coloring based on attributes– Nodes; cell cycle regulated, tissue type,
etc.– Edges; ppi, protein-DNA, etc.
• Expression dataNode_id exp1 exp2 exp3 exp4.........
Node annotation
YeastCompartmentYAL001C = transcription factor TFIIIC complexYAL002W = membrane fractionYAL003W = ribosomeYAL005C = cytoplasm*YAL007C = COPII-coated vesicleYAL008W = mitochondrionYAL009W = integral to membrane*YAL010C = mitochondrial outer membraneYAL011W = nucleus
Node annotation
CellCycleRegulatedYAL001C = 1YAL007C = 1YAL012W = 1YAL021C = 1YAL022C = 1YAL023C = 1YAL024C = 1YAL034W-A = 1YAL039C = 1YAL040C = 1YAL053W = 1YAL067C = 1
Edge annotation
Protein-DNA binding data
MBF pd YER059WMBF pd YIL050WMBF pd YML064CYML064C pd YNL189WYML064C pd YER059WYML064C pd YBR098WYBR098W pd YCL032WYBR098W pd YDL043CYDL043C pd YDL208WYDL043C pd YDR363WYDL208W pd YDR381WYDL208W pd YML064C
Edge annotation:
ActivationRepressionMBF (pd) YER059W = 1MBF (pd) YIL050W = 0MBF (pd) YML064C = 1YML064C (pd) YNL189W = 0YML064C (pd) YER059W = 0YML064C (pd) YBR098W = 1YBR098W (pd) YCL032W = 0YBR098W (pd) YDL043C = 1YDL043C (pd) YDL208W = 1YDL043C (pd) YDR363W = 1YDL208W (pd) YDR381W = 1YDL208W (pd) YML064C = 0