Upcoming SlideShare
×

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

8,991 views

Published on

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

Published in: Technology, Education
8 Likes
Statistics
Notes
• Full Name
Comment goes here.

Are you sure you want to Yes No
Your message goes here
• Be the first to comment

Views
Total views
8,991
On SlideShare
0
From Embeds
0
Number of Embeds
116
Actions
Shares
0
958
0
Likes
8
Embeds 0
No embeds

No notes for slide

### 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
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