1. Tutorial session 1 Network generation Exploring PPI networks using Cytoscape EMBO Practical Course Session 8 Nadezhda Doncheva and Piet Molenaar

2. Overview  Focus: Network generation  Importing pre-formatted networks  Generating new networks  Visualizing networks  Saving and exporting network data  Concepts  Layouts  Data  Drosophila protein network 11/24/20152

3. Let’s start: GUI basics (Demo) 11/24/20153

4. 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…) 11/24/20154

5. Loading networks (Demo) 11/24/20155

6. 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  … 11/24/20156

7. Layouts (Demo) 11/24/20157

8. 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 11/24/20158

9. 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 11/24/20159

10. 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 11/24/201510

11. Assignment 1.1 results 1. Creating the network 2. Testing layouts: take the edge weight in consideration; best bet: edge weighted spring embedded 11/24/201511

12. 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) 11/24/201512

13. Generating networks (Demo) 11/24/201513

14. 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 11/24/201514

15. Assignment 1.2 results 1. Look for the denser regions 11/24/201515

16. Assignment 1.2 results 1. Look for the denser regions 2. PathwayCommons: Reactome interactions: 2 Complexes 11/24/201516

17. 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 11/24/201517

18. 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) 11/24/201518

19. Exporting & saving data (Demo) 11/24/201519

20. 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 11/24/201520

21. 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! 11/24/201521

22. 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 11/24/201522

23. Assignment 1.3 results 1. Exporting figures 1. Mind the settings 2. Achieve high resolution by toying with zoom and dpi 2. Best export format 1. usually *.xgmml: maintains most (or even better; whole session) 2. For use in other tools; attribute files can be easily converted to tab separated 3. Also the data attributes panel can be used to exported as table 3. Saving sessions is always a good plan! 1. Avoids cluttering of attributes 11/24/201523

24. Cytoscape extended functionality 11/24/201524  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

25. Cytoscape Plugin Manager (Demo) 11/24/201525

26. Use case: Assignment 1.4 1. Explore available plugins for PPi relevance http://cytoscape.org/manual/Cytoscape2_8Manual.html#Plugins and the Plugin Manager 11/24/201526

27. Assignment 1.4 results  Use the app store via cytoscape.org  Interaction databases  Genemania, Bisogenet, Mimi, Cpath  Structural information  StructureViz,  Note: not all apps/plugins available through the plugin manager; exploring PubMed using Cytoscape citation will reveal more… 11/24/201527

28. 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 11/24/201528