Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)
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![Table Browser
Local Column
Table Tabs
List Data
(Values in [ ])
Shared Column](https://image.slidesharecdn.com/bioinformaticssummittutorial1-140411191733-phpapp01/75/cytoscape-tutorial-session-1-at-utkbrin-bioinformatics-summit-2014-4112014-24-2048.jpg?cb=1666720440)
Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)
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Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)
- 1. Keiichiro Ono UC, San Diego Bioinformatics Summit 2014 4/11/2014 Cytoscape Tutorial 1: Introduction to Biological Data Analysis and Visualization with Cytoscape
- 2. Welcome Back! - Scope of Tutorial Session - Part1: Basic Concepts - Overview of Core Features - Part2: Advanced Topics - Effective Visualization Techniques - External Tools
- 3. Welcome Back! - Scope of 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
- 7. Cytoscape is for... - Data integration - Join networks and annotation tables - Network data analysis - Visualization
- 9. Data Types - There are 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 1 3 4 3 Network Representation
- 12. PPARG EP300! PPARG PRNP! PPARG MAP4K4! … EP300 PPARG SMARCD3 STMN1 SMARCA4 OPTN ATP6V1C1 PSMD1 HTT PRNP HNRNPUL1 CCDC88A CLU HSP90AB1 SMARCD3 MAP4K4 MIF4GD USP11 MARCH6TUBB EDF1 CHD8
- 13. PPARG two hybrid MIF4DG! 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 about nodes, edges, and networks.
- 15. Summary - There are two types of data - Networks - Attributes - You need integrated, or annotated, network before analyze / visualize your data
- 16. Before actual data analysis… - 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 Right Tool
- 18. Choose a Right Tool 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
- 21. https://github.com/ keiono/cytoscape- workshop-materials Example files are available here: tutorialYeast.cys And there are many sample files in “Samples” directory in Cytoscape application folder
- 22. Goal of This Lesson - 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 Network Panel Bird’s Eve View Table Browser Network Views
- 24. Table Browser Local Column Table Tabs List Data (Values in [ ]) Shared Column
- 25. Session File - Snapshot of 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 of Nodes CTR+6
- 30. Create New Sub-Network From Selection CTR+N
- 31. - CTR (Command on Mac) + G
- 32. Show Graphics Details - View → Show Graphics Details
- 33. Lesson 1 Demo
- 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. 2. Data Import
- 36. Data Integration - Loading networks 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 pp YOR167C 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 & Mapping Tables - In most cases you need to import them from tables - e.g. Expression matrix saved as Excel workbook
- 42. Mapping Key in the Network Mapping Key in the Table
- 43. Load Network from Table - Simple list of binary interactions can be loaded as networks ! - Source - Interaction Type - Target - Or, Source - Target
- 45. Small Network Data - Send query to database - List of genes - Keywords
- 46. Import from Public Database
- 47. Large Network Data (Interactome) - Start from an Interactome - Filter and extract smaller modules
- 50. Large Network Data (Interactome) - Download Database Dump - Extract compressed data - Import as table - Filter - Visualize
- 51. Lesson 2 Demo
- 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
- 54. Goal of This Section - 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
- 57. Network Analyzer - Provides basic statistics of networks - Degree - Centrality - Shortest Pass Length Distribution - etc.
- 58. Filtering by Network Statistics - NetworkAnalyzer provides all results as regular attributes - Can be used for filtering
- 59. Search
- 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. Lesson 3 Demo
- 62. 4. Visualization
- 63. Layouts
- 64. Automatic Layout - Choose proper algorithm - Tree-like data - Hierarchical Layout - Scale-Free Network - Force-directed - Circular process - Circular Layout - Tweak parameters if necessary
- 65. Manual Layout - Tweak result from automatic layout - Scale - Align - Rotate
- 66. Visual Style - Collection of 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. Data Controls The View
- 69. Discrete Mapping Editor Continuous Mapping Editor
- 70. Demo
- 71. Summary
- 72. Original
- 75. Visualization Techniques will be discussed in Part 2
- 76. Apps
- 77. Apps - Adding new features 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. To be Continued…
- 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 !