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

6. Core Concepts

7. Cytoscape is for...
- Data integration
- Join networks and annotation tables
- Network data analysis
- Visualization

8. Module 1
Module 2

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

20. 1. Understand
Cytoscape Desktop

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

44. Import Public Data

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

48. Download Zipped Archives

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

53. 3. Basic Analysis

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

56. Network Statistics

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

73. Visual Style Applied

74. Final Visualization

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
!

83. 2014 Keiichiro Ono
kono@ucsd.edu