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Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)
This document outlines a tutorial on biological data analysis and visualization using Cytoscape. The tutorial covers basic concepts like networks and tables in Cytoscape, data import, network analysis features, and visualization techniques. It discusses loading sample network data, calculating network statistics, filtering networks, basic search functionality, and applying visual styles. The tutorial is intended to provide a practical introduction to Cytoscape's core features through examples and demos.
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Introduction to the tutorial on Biological Data Analysis using Cytoscape, covering basic concepts, core features, and advanced topics.
Discusses basic concepts and core features of Cytoscape, including network data browsing, visualization, and data integration.
Tips on preparing data for analysis in Cytoscape, focusing on file types and using concrete ID sets.
Guides on navigating the Cytoscape interface, including the toolbar, network panel, and table browser.
Details on session file management, workspace snapshots, navigation techniques, and creating subnetworks.
Methods for importing data into Cytoscape, including network data formats and importance of data preparation.
Introduction to basic analysis features, including network statistics and filtering using the Network Analyzer.Overview of visualization methods, including layout options, visual styles, and application of visualization techniques.
Discusses how to extend Cytoscape's capabilities using apps, including installation and available features.
References for additional reading on network biology, Cytoscape apps, and tutorials for further learning.
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Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)
- 1. Keiichiro Ono UC, SanDiego Bioinformatics Summit 2014 4/11/2014 Cytoscape Tutorial 1: Introduction to Biological Data Analysis and Visualization with Cytoscape
- 2. Welcome Back! - Scopeof Tutorial Session - Part1: Basic Concepts - Overview of Core Features - Part2: Advanced Topics - Effective Visualization Techniques - External Tools
- 3. Welcome Back! - Scopeof Tutorial Session - Part1: Basic Concepts - Overview of Core Features - Part2: Advanced Topics - Effective Visualization Techniques - External Tools
- 4. Part 1: Agenda -Basic Concepts - Browsing Network Data - Networks and Tables - Visualization - Basic Analysis
- 5. About This Section… -Lecture Style - Practical introduction to specific features - You can play with the examples during this session, but it’s not required - I’ll upload all slides to the web, and you can try it later
- 6.
- 7. Cytoscape is for... -Data integration - Join networks and annotation tables - Network data analysis - Visualization
- 8.
- 9. Data Types - Thereare two data types in Cytoscape: - Network - Table
- 10. - Mathematical Graph -G = (V, E) - Nodes - Any objects - Edges - Relationships between objects Network
- 11. 1 2 2 3 13 4 3 Network Representation
- 12. PPARG EP300! PPARG PRNP! PPARGMAP4K4! … EP300 PPARG SMARCD3 STMN1 SMARCA4 OPTN ATP6V1C1 PSMD1 HTT PRNP HNRNPUL1 CCDC88A CLU HSP90AB1 SMARCD3 MAP4K4 MIF4GD USP11 MARCH6TUBB EDF1 CHD8
- 13. PPARG two hybridMIF4DG! PPARG pull down SMARCD3 … pull down display technology display technology display technology display technology display technology two hybrid display technology display technology display technology two hybrid display technology anti bait coimmunoprecipitation pull down display technology pull down display technology display technology two hybrid display technology display technology STMN1 PPARG P6V1C1 SMARCD3 SMARCA4 OPTN PSMD1 HTT SMARCD3 CCDC88A CLU HNRNPUL1 PRNP HSP90AB1 EDF1 CHD8 P11 MIF4GD
- 14. Table Any data aboutnodes, edges, and networks.
- 15. Summary - There aretwo types of data - Networks - Attributes - You need integrated, or annotated, network before analyze / visualize your data
- 16. Before actual dataanalysis… - There is no silver bullet! - You cannot do everything with a single program - Understand Cytoscape Core Features - Research available Apps - Data pre-processing/post-processing may be required - Excel, R / Bioconductor, Scripts, Web Tools
- 17. Choose a RightTool
- 18. Choose a RightTool Analysis VisualizationData Preparation
- 19. Data Preparation Tips -Prepare machine-friendly file - CSV, TSV, XML - Use concrete, widely-used ID sets - NCBI Gene ID - Ensemble Gene ID
- 20.
- 21. https://github.com/ keiono/cytoscape- workshop-materials Example files areavailable here: tutorialYeast.cys And there are many sample files in “Samples” directory in Cytoscape application folder
- 22. Goal of ThisLesson - Understand Basic UI - Loading a sample Session file - Learn how to browse the network and attributes - Know useful basic shortcuts/commands
- 23. Cytoscape 3.1 Desktop Toolbar NetworkPanel Bird’s Eve View Table Browser Network Views
- 24. Table Browser Local Column TableTabs List Data (Values in [ ]) Shared Column
- 25. Session File - Snapshotof your workspace - Networks - Attributes - Visual Styles - System Properties
- 26. Saving & Opening -In Cytoscape, Save means saving your workspace states into a Session File - Open means loading a Session file - You can open only one session at a time - Merge Session feature will be implemented in the future version of Cytoscape 3.x
- 27. Open a Session -Click folder icon - Or, File → Open
- 28. Navigation - Pan: Middle-Click+ Drag or Command + Left-Click + Drag on Mac - Zoom - IN: Mouse Wheel UP - OUT: Mouse Wheel DOWN - Selection: Left-Click and Drag - Fit to Window - Selected region - Entire network
- 29. First Neighbor ofNodes CTR+6
- 30. Create New Sub-NetworkFrom Selection CTR+N
- 31. - CTR (Commandon Mac) + G
- 32. Show Graphics Details -View → Show Graphics Details
- 33.
- 34. Lesson 1: Summary -Session File is a snapshot of your workspace - Creating subnetworks from selection is easy - Attribute browser is a spreadsheet-like viewer for your attributes
- 35.
- 36. Data Integration - Loadingnetworks and mapping attributes onto them - Cytoscape provides: - Data import from files - Direct access to remote data sources
- 37. Import & Export -Import - Load any type of data - Network, Attributes, Visual Styles, etc. - Export - as network files, tables, or images
- 38. Network Import - Usually,imported from pre-formatted data file - Or, use Table Import feature to select columns to be used as edges
- 39. SIF File YJR022W ppYOR167C YJR022W pp YLR264W YJR022W pp YNR053C YER116C pp YDL013W YNL307C pp YAL038W YNL216W pd YCR012W YNL216W pd YGR254W YNL216W pd YHR174W YNL216W pd YIL133C YNL216W pd YLR044C YNL216W pd YOL120C YNL216W pd YNL301C YNL216W pd YCL030C
- 40. Loading & MappingTables - In most cases you need to import them from tables - e.g. Expression matrix saved as Excel workbook
- 42. Mapping Key in theNetwork Mapping Key in the Table
- 43. Load Network fromTable - Simple list of binary interactions can be loaded as networks ! - Source - Interaction Type - Target - Or, Source - Target
- 44.
- 45. Small Network Data -Send query to database - List of genes - Keywords
- 46. Import from PublicDatabase
- 47. Large Network Data(Interactome) - Start from an Interactome - Filter and extract smaller modules
- 48.
- 50. Large Network Data (Interactome) -Download Database Dump - Extract compressed data - Import as table - Filter - Visualize
- 51.
- 52. Lesson 2: Summary -Cytoscape supports many standard network data formats - Any table data can be imported to Cytoscape by Table Import function - Preparing your table data with widely-used ID is important for easy mapping
- 53.
- 54. Goal of ThisSection - Calculate network statistics by Network Analyzer - Filtering based on statistics - Basic search by EnhancedSearch Plugin - Try some more realistic example (requires faster machine!)
- 55. Core Analysis Features -Network Statistics - Search - Filtering
- 56.
- 57. Network Analyzer - Providesbasic statistics of networks - Degree - Centrality - Shortest Pass Length Distribution - etc.
- 58. Filtering by NetworkStatistics - NetworkAnalyzer provides all results as regular attributes - Can be used for filtering
- 59.
- 60. Query Syntax Cytoscape ESP:simple search of complex biological networks ! Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States ! Bioinformatics. 2008 June 15; 24(12): 1465–1466. Published online 2008 April 28. doi: 10.1093/bioinformatics/btn208 PMCID: PMC2427162
- 61.
- 62.
- 63.
- 64. Automatic Layout - Chooseproper algorithm - Tree-like data - Hierarchical Layout - Scale-Free Network - Force-directed - Circular process - Circular Layout - Tweak parameters if necessary
- 65. Manual Layout - Tweakresult from automatic layout - Scale - Align - Rotate
- 66. Visual Style - Collectionof mappings from Attributes to Visual Properties
- 67. Visual Styles - Defaults+ Mappings - Expression values to node color - Gene function to node shape - Interaction detection method to edge line type - Confidence score to edge width
- 68.
- 69. Discrete Mapping Editor ContinuousMapping Editor
- 70.
- 71.
- 72.
- 73.
- 74.
- 75. Visualization Techniques will bediscussed in Part 2
- 76.
- 77. Apps - Adding newfeatures to Cytoscape - Lots of categories - (Almost) all of them are free, so just play with it to learn what’s possible
- 78. Installing Apps - Easy- Just install from App manager. - For browsing, just visit App Store - http://apps.cytoscape.org/
- 79.
- 80. Further Readings 1 -Introduction to Network Biology - Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases. PLoS Comput Biol 3(3): e42.doi:10.1371/journal.pcbi.0030042 - Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. PLoS Comput Biol 3(4): e43. doi:10.1371/ journal.pcbi.0030043
- 81. Further Readings 2 -Overview of Cytoscape Apps (Plugins) - A travel guide to Cytoscape plugins Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012) Nature Methods 9 (11) p. 1069-1076 - Sample Protocol (based on 2.x) − Integration of biological networks and gene expression data using Cytoscape Cline, et al. Nature Protocols, 2, 2366-2382 (2007).
- 82. Further Readings 3 -Cytoscape Tutorial Booklet: Analysis and Visualization of Biological Networks with Cytoscape - http://www.rbvi.ucsf.edu/Outreach/Workshops/ISMBTutorial.pdf !
- 83.