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Tutorial session 1 Network generation Exploring PPI networks using Cytoscape EMBO Practical Course Session 8 Nadezhda Doncheva and Piet Molenaar
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Overview Focus: Network generation Importing pre-formatted networks Generating new networks Visualizing networks Saving and exporting network data Concepts Layouts Data Drosophila protein network 9/12/20152
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Let’s start: GUI basics (Demo) 9/12/20153
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Loading networks Import pre-formatted networks SIF GML, XGMML BioPAX PSI-MI 1 & 2.5 SBML Level 2 Import your own data from a table Excel file Delimited text (tab, comma, etc…) 9/12/20154
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Loading networks (Demo) 9/12/20155
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Layouts Many algorithms available through plugins Simple: grid, not very informative Hierarchical: layout data as a tree or hierarchy (works best when there are no loops) Circular (Radial): arrange nodes around a circle, could use node attributes to govern position, e.g. degree sorted Force-Directed: simulate edges as springs (nodes repel and edges pull), good for up to 500 nodes Multi-layer layouts: partition graph, layout each partition and then layout partitions … 9/12/20156
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Layouts (Demo) 9/12/20157
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Tips & Tricks: Layouts Use layouts to convey the relationships between the nodes Layout algorithms may need to be ”tuned” to fit your network (Layouts Settings... menu) Consider laying out portions of your network Adjust the layout manually Load network into a drawing program (e.g. Illustrator) and adjust labels 9/12/20158
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Use case: Drosophila Protein network Although from fly, serves as model for human Groundbreaking work now done in model systems What did they do Bait-Protein interactions Statistical analysis; highly confident set 9/12/20159
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Use case: Assignment 1.1 1. Open the DrosophilaBasicSession.cys file 2. 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 9/12/201510
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Generating networks Import network from web services supported by Cytoscape Pathway commons (only well-studied organisms) PSICQUIC Universal Client (collection of many public databases) MiMI (Michigan Molecular Interactions database) BisoGenet (SysBiomics database) Generate a network using a Cytoscape plugin AgilentLiteratureSearch (based on text mining) 9/12/201511
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Generating networks (Demo) 9/12/201512
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Use case; Assignment 1.2 1. Try to locate the protein complexes found in the article in the network 2. 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 9/12/201513
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Tips & Tricks: Network view When you open a large network, you will not get a view by default To improve interactive performance, Cytoscape has the concept of ”Levels of Detail” Some visual attributes will only be apparent when you zoom in The level of detail for various attributes can be changed in the preferences To see what things will look like at full detail: go to View Show Graphics Details 9/12/201514
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Exporting & saving data Sessions save pretty much everything: Networks, Properties, Visual styles, Screen sizes Export networks in different formats: SIF, GML, XGMML, BioPAX, PSI-MI 1 & 2.5 Publication quality graphics in several formats: PDF, EPS, SVG, PNG, JPEG, and BMP Export Session to HTML for Web (SessionForWeb plugin) 9/12/201515
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Exporting & saving data (Demo) 9/12/201516
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Tips & Tricks: Memory 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 9/12/201517
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Tips & Tricks: General By default, Cytoscape writes it’s logs to the Error Dialog: Help Error Dialog Change the ”logger.console” preference in Edit Preferences Properties... to write it to the console .cytoscape directory Your defaults and any plugins downloaded from the plugin manager will go here Sometimes, if things get really messed up, deleting (or renaming) this directory can give you a ”clean slate” Plugin manager ”Outdated” doesn’t necessarily mean ”won’t work” Plugin authors don’t always update their plugins immediately after new releases Open source; sometimes bugs occur! 9/12/201518
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Use case: Assignment 1.3 1. Export the network view as figure 2. Find out in which format you’d best save your network 3. Save your session for later use http://cytoscape.org/manual/Cytoscape2_8Manual.html#Supported Network File Formats 9/12/201519
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Cytoscape extended functionality 9/12/201520 Cytoscape extends its functionality with plugins Developed by third parties Listed at http://apps.cytoscape.org/ Usually available through the Plugin Manager Can be downloaded from the plugins’s websites Cover many diverse areas of application
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Cytoscape Plugin Manager (Demo) 9/12/201521
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Use case: Assignment 1.4 1. Explore available plugins for PPi relevance http://cytoscape.org/manual/Cytoscape2_8Manual.html#Plugins and the Plugin Manager 9/12/201522
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To be continued… Build, visualize and analyze your own network with Cytoscape Network generation Network annotation and visualization Loading and manipulating attributes Identifier mapping Mapping data onto the network Use visuals to convey data Network analysis 9/12/201523
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