Transcript Some Examples of Networks in Cytoscape

Some Examples of Networks
in Cytoscape
Institute for Systems Biology
& Bellevue School District
Networks in Ecology:
Food Webs
http://staff.harrisonburg.k12.va.us/~gharper/bay/weboflifepage/foodweb.jpg
Put this food web into cytoscape:
An Ocean Food Web
Nodes = organisms
Edges/arrows = flow of energy
A Food Web:
Salmon
Nodes = organisms
Arrows represent
flow of energy
Cell Phone Network
Nodes = people/phones
Edges = can call
Here we track
the flow of
information
analogous to the
flow of energy
in a food web
Gene Networks, etc
Nodes can represent
genes, proteins, etc…
Edges can represent
interaction between stimuli
(such as presence of light
or sugar) and a receptor,
promoter, etc…
Network Model = helpful for large systems,
lots of information
Figure 3 Screening DNA-damage phenotypes against a scaffold of molecular
interactions. A large molecular interaction network was integrated with 1615 yeast
deletion phenotypes gathered systematically in response to MMS exposure.
http://www.genome.org/cgi/content/full/13/11/2498