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Tutorial session 1
Network generation
Exploring PPI networks using Cytoscape
EMBO Practical Course Session 8
Nadezhda Doncheva and Piet Molenaar
Overview
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Focus: Network generation
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Importing pre-formatted networks
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Generating new networks
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Visualizing networks
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Saving and exporting network data
Concepts
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Data
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Layouts
Drosophila protein network
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Let’s start: GUI basics (Demo)
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Loading networks
Import pre-formatted networks
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SIF
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GML, XGMML
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BioPAX
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PSI-MI 1 & 2.5
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SBML Level 2
Import your own data from a table
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Excel file
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Delimited text (tab, comma, etc…)
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Loading networks (Demo)
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Layouts
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Many algorithms available through plugins
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Simple: grid, not very informative
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Hierarchical: layout data as a tree or hierarchy (works best
when there are no loops)
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Circular (Radial): arrange nodes around a circle, could use
node attributes to govern position, e.g. degree sorted
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Force-Directed: simulate edges as springs (nodes repel and
edges pull), good for up to 500 nodes
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Multi-layer layouts: partition graph, layout each partition and
then layout partitions
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…
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Layouts (Demo)
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Tips & Tricks: Layouts
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Use layouts to convey the relationships between the
nodes
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Layout algorithms may need to be ”tuned” to fit your
network (Layouts  Settings ... menu)
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Consider laying out portions of your network
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Adjust the layout manually
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Load network into a drawing program (e.g. Illustrator)
and adjust labels
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Use case: Drosophila Protein network
Although from fly, serves as model for human
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Groundbreaking work now done in model systems
What did they do
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Bait-Protein interactions
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Statistical analysis; highly confident set
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Use case: Assignment 1.1
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Open the DrosophilaBasicSession.cys file
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Test several layouts; which one is informative?
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import Free-Format Table Files
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Automatic Layout Algorithms
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Generating networks
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Import network from web services supported by
Cytoscape
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Pathway commons (only well-studied organisms)
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PSICQUIC Universal Client (collection of many public
databases)
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MiMI (Michigan Molecular Interactions database)
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BisoGenet (SysBiomics database)
Generate a network using a Cytoscape plugin
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AgilentLiteratureSearch (based on text mining)
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Generating networks (Demo)
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Use case; Assignment 1.2
1.
Try to locate the protein complexes found in the article
in the network
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Lookup existing interactions for one of the MCM genes
in the PathwayCommons webservice
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Example #3: Retrieving
Pathways and Networks from Pathway Commons
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Tips & Tricks: Network view
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When you open a large network, you will not get a view
by default
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To improve interactive performance, Cytoscape has the
concept of ”Levels of Detail”
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Some visual attributes will only be apparent when you zoom in
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The level of detail for various attributes can be changed in the
preferences
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To see what things will look like at full detail: go to View 
Show Graphics Details
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Exporting & saving data
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Sessions save pretty much everything: Networks,
Properties,Visual styles, Screen sizes
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Export networks in different formats: SIF, GML, XGMML,
BioPAX, PSI-MI 1 & 2.5
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Publication quality graphics in several formats: PDF, EPS,
SVG, PNG, JPEG, and BMP
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Export Session to HTML for Web (SessionForWeb
plugin)
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Exporting & saving data (Demo)
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Tips & Tricks: Memory
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Cytoscape uses lots of it
Doesn’t like to let go of it
An occasional restart when working with large networks is a
good thing
Destroy views when you don’t need them
Java does not provide a good way to get the memory right at
start time
Cytoscape 2.7 and later releases do a much better job at
”guessing” good default memory sizes than previous versions
Increase Cytoscape’s default memory size:
http://cytoscape.wodaklab.org/wiki/How_to_increase_memor
y_for_Cytoscape
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Tips & Tricks: General
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By default, Cytoscape writes it’s logs to the Error Dialog: Help 
Error Dialog
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Change the ”logger.console” preference in Edit  Preferences 
Properties... to write it to the console
.cytoscape directory
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Your defaults and any plugins downloaded from the plugin manager will
go here
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Sometimes, if things get really messed up, deleting (or renaming) this
directory can give you a ”clean slate”
Plugin manager
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”Outdated” doesn’t necessarily mean ”won’t work”
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Plugin authors don’t always update their plugins immediately after new
releases
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Open source; sometimes bugs occur!
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Use case: Assignment 1.3
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Export the network view as figure
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Find out in which format you’d best save your network
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Save your session for later use
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Supported Network File
Formats
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Cytoscape extended functionality
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Cytoscape extends its functionality
with plugins
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Developed by third parties
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Listed at http://apps.cytoscape.org/
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Usually available through the Plugin
Manager
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Can be downloaded from the
plugins’s websites
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Cover many diverse areas of
application
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Cytoscape Plugin Manager (Demo)
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Use case: Assignment 1.4
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Explore available plugins for PPi relevance
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Plugins and the Plugin Manager
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To be continued…
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Build, visualize and analyze your own network with
Cytoscape
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Network generation
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Network annotation and visualization
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Loading and manipulating attributes
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Identifier mapping
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Mapping data onto the network
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Use visuals to convey data
Network analysis
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