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Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)

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Slides for Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014.

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Cytoscape Tutorial Session 1 at UT-KBRIN Bioinformatics Summit 2014 (4/11/2014)

  1. 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. 2. Welcome Back! - Scope of Tutorial Session - Part1: Basic Concepts - Overview of Core Features - Part2: Advanced Topics - Effective Visualization Techniques - External Tools
  3. 3. Welcome Back! - Scope of Tutorial Session - Part1: Basic Concepts - Overview of Core Features - Part2: Advanced Topics - Effective Visualization Techniques - External Tools
  4. 4. Part 1: Agenda - Basic Concepts - Browsing Network Data - Networks and Tables - Visualization - Basic Analysis
  5. 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. 6. Core Concepts
  7. 7. Cytoscape is for... - Data integration - Join networks and annotation tables - Network data analysis - Visualization
  8. 8. Module 1 Module 2
  9. 9. Data Types - There are two data types in Cytoscape: - Network - Table
  10. 10. - Mathematical Graph - G = (V, E) - Nodes - Any objects - Edges - Relationships between objects Network
  11. 11. 1 2 2 3 1 3 4 3 Network Representation
  12. 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. 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. 14. Table Any data about nodes, edges, and networks.
  15. 15. Summary - There are two types of data - Networks - Attributes - You need integrated, or annotated, network before analyze / visualize your data
  16. 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. 17. Choose a Right Tool
  18. 18. Choose a Right Tool Analysis VisualizationData Preparation
  19. 19. Data Preparation Tips - Prepare machine-friendly file - CSV, TSV, XML - Use concrete, widely-used ID sets - NCBI Gene ID - Ensemble Gene ID
  20. 20. 1. Understand Cytoscape Desktop
  21. 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. 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. 23. Cytoscape 3.1 Desktop Toolbar Network Panel Bird’s Eve View Table Browser Network Views
  24. 24. Table Browser Local Column Table Tabs List Data
 (Values in [ ]) Shared Column
  25. 25. Session File - Snapshot of your workspace - Networks - Attributes - Visual Styles - System Properties
  26. 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. 27. Open a Session - Click folder icon - Or, File → Open
  28. 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. 29. First Neighbor of Nodes CTR+6
  30. 30. Create New Sub-Network From Selection CTR+N
  31. 31. - CTR (Command on Mac) + G
  32. 32. Show Graphics Details - View → Show Graphics Details
  33. 33. Lesson 1 Demo
  34. 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. 35. 2. Data Import
  36. 36. Data Integration - Loading networks and mapping attributes onto them - Cytoscape provides: - Data import from files - Direct access to remote data sources
  37. 37. Import & Export - Import - Load any type of data - Network, Attributes, Visual Styles, etc. - Export - as network files, tables, or images
  38. 38. Network Import - Usually, imported from pre-formatted data file - Or, use Table Import feature to select columns to be used as edges
  39. 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. 40. Loading & Mapping Tables - In most cases you need to import them from tables - e.g. Expression matrix saved as Excel workbook
  41. 41. Mapping Key in the Network Mapping Key in the Table
  42. 42. Load Network from Table - Simple list of binary interactions can be loaded as networks ! - Source - Interaction Type - Target - Or, Source - Target
  43. 43. Import Public Data
  44. 44. Small Network Data - Send query to database - List of genes - Keywords
  45. 45. Import from Public Database
  46. 46. Large Network Data (Interactome) - Start from an Interactome - Filter and extract smaller modules
  47. 47. Download Zipped Archives
  48. 48. Large Network Data (Interactome) - Download Database Dump - Extract compressed data - Import as table - Filter - Visualize
  49. 49. Lesson 2 Demo
  50. 50. 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
  51. 51. 3. Basic Analysis
  52. 52. 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!)
  53. 53. Core Analysis Features - Network Statistics - Search - Filtering
  54. 54. Network Statistics
  55. 55. Network Analyzer - Provides basic statistics of networks - Degree - Centrality - Shortest Pass Length Distribution - etc.
  56. 56. Filtering by Network Statistics - NetworkAnalyzer provides all results as regular attributes - Can be used for filtering
  57. 57. Search
  58. 58. 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
  59. 59. Lesson 3 Demo
  60. 60. 4. Visualization
  61. 61. Layouts
  62. 62. Automatic Layout - Choose proper algorithm - Tree-like data - Hierarchical Layout - Scale-Free Network - Force-directed - Circular process - Circular Layout - Tweak parameters if necessary
  63. 63. Manual Layout - Tweak result from automatic layout - Scale - Align - Rotate
  64. 64. Visual Style - Collection of mappings from Attributes to Visual Properties
  65. 65. 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
  66. 66. Data Controls The View
  67. 67. Discrete Mapping Editor Continuous Mapping Editor
  68. 68. Demo
  69. 69. Summary
  70. 70. Original
  71. 71. Visual Style Applied
  72. 72. Final Visualization
  73. 73. Visualization Techniques will be discussed in Part 2
  74. 74. Apps
  75. 75. 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
  76. 76. Installing Apps - Easy - Just install from App manager. - For browsing, just visit App Store - http://apps.cytoscape.org/
  77. 77. To be Continued…
  78. 78. 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
  79. 79. 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).
  80. 80. Further Readings 3 - Cytoscape Tutorial Booklet:
 
 Analysis and Visualization of Biological Networks with Cytoscape - http://www.rbvi.ucsf.edu/Outreach/Workshops/ISMBTutorial.pdf !
  81. 81. 2014 Keiichiro Ono kono@ucsd.edu

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