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CSC, Dec.15-16,2005
Cytoscape Team
Benno Schwikowski Trey Ideker
Melissa Cline
Mark Anderson
Andrea Splendiadi
Nerius Landys
Ryan Kelley
Lee Hood
Chris Workman
Richard Bonneau
Past contributors:
Rowan Christmas
Nada Amin
Iliana Avila-Campillo Owen Ozier
Past contributors:
Larissa Kamenkovich
Andrew Markiel
Paul Shannon
Jonathan Wang
Chris Sander
Gary Bader
Ethan Cerami
Rob Sheridan
Agilent
Annette Adler
Allan Kuchinsky
Aditya Vailaya
Mike Creech
Logistics
 Four units per day
 1/2 hour lecture
 45 minute hands-on exercises
 Lecture
 Background for the hands-on exercises
 Questions and comments encouraged
 Hands-on exercises
 Mostly Cytoscape 2.2, a little Cytoscape 2.1.
 Teamwork encouraged
 Proceed at own pace
Schedule
 Thursday am: getting
started




Introduction
Coffee break
Biological network data
Lunch
 Thursday pm: companion
resources for network
analysis




Text mining
Coffee break
Gene Ontology
Leave
 Friday am: mRNA Expression
 Expression basics
 Coffee break
 Expression & text mining &
GO
 Lunch
 Friday pm: advanced topics
in network topology
 Modules and complexes
 Coffee break
 Protein domain networks,
future directions,
feedback.
Overview
Introduction
What is Cytoscape?
Resources for getting help
Basic functionality
Biological networks
Motivation: most biological processes are not
performed by a single, independent
macromolecule
Core Features
• Customize network data
display using visual styles
• Powerful graph layout
tools
• Easily organize multiple
networks
• Easily navigate large
networks
• Filter the network
• Plugin API
Input/Output
• Protein protein interactions
from BIND, TRANSFAC
databases
• Gene functional annotations
from Gene Ontology (GO) and
KEGG databases
• Biological models from
Systems Biology Markup
Language (SBML)
• cPath: Cancer Pathway
database
• Proteomics Standards
Initiative Molecular Interaction
(PSI-MI) or Biopathway
Exchange Language (BioPAX)
formats
• Oracle Spatial Network data
model
Cytoscape.org
Cytoscape is a freely-available (open-source,
java-based) bioinformatics software platform for
visualizing biological networks (e.g. molecular
interaction networks) and
analyzing networks with gene expression
profiles and other state data.
Additional features
are available as
plugins.
• jActiveModules: identify
significant “active”
subnetworks
• Expression Correlation
Network: cluster expression
data
• Agilent Literature
Search: build networks by
extracting interactions from
scientific literature.
• MCODE: finds clusters of
highly interconnected
regions in networks
• cPath: query, retrieve and
visualize interactions from
the MSKCC Cancer
Pathway database
• BiNGO: determine which
Gene Ontology (GO)
categories are statistically
over-represented in a set of
genes
• Motif Finder: runs a Gibbs
sampling motif detector on
sequences for nodes in a
Cytoscape network.
• CytoTalk: Interact with
Cytoscape from Perl,
Python, R, shell scripts or C
or C++ programs.
Use Case 1: Atherosclerosis
 King et. al., Physiol Genomics. 2005 Sep 21;23(1):103-18.
Use Case 2: Hepatitis C virus
infection
 Reiss et. al., BMC Bioinformatics 2005, 6:154
Hands-on Session 1
 Navigating the Cytoscape panels
 Loading, editing, and saving a network
 Graph layout methods
 Setting visual properties