Keiichiro Ono UC, San Diego

Bioinformatics Summit 2014 4/11/2014

Cytoscape Tutorial 1: Introduction to Biological Data Analysis and Visualization with Cytoscape

Welcome Back!

- Scope of Tutorial Session - Part1: Basic Concepts

- Overview of Core Features

- Part2: Advanced Topics

- Effective Visualization Techniques

- External Tools

Welcome Back!

- Scope of Tutorial Session - Part1: Basic Concepts

- Overview of Core Features

- Part2: Advanced Topics

- Effective Visualization Techniques

- External Tools

Part 1: Agenda

- Basic Concepts - Browsing Network Data - Networks and Tables - Visualization - Basic Analysis

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

Core Concepts

Cytoscape is for...

- Data integration - Join networks and annotation tables

- Network data analysis - Visualization

Module 1

Module 2

Data Types

- There are two data types in Cytoscape: - Network

- Table

- Mathematical Graph - G = (V, E)

- Nodes - Any objects

- Edges - Relationships

between objects

Network

1 2 2 3 1 3 4 3

Network Representation

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EP300

PPARG

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PRNP

HNRNPUL1

CCDC88A

CLU

HSP90AB1

SMARCD3

MAP4K4

MIF4GDUSP11

MARCH6TUBB

EDF1 CHD8

PPARG two hybrid MIF4DG!PPARG pull down SMARCD3 !…

pull down

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EP300

STMN1PPARG

ATP6V1C1

SMARCD3

SMARCA4

OPTN

PSMD1

HTT

SMARCD3CCDC88A

MAP4K4

CLU

HNRNPUL1

PRNP

HSP90AB1

EDF1

TUBB

CHD8

MARCH6

USP11 MIF4GD

Table

Any data about nodes, edges, and networks.

Summary

- There are two types of data- Networks- Attributes

- You need integrated, or annotated, network before analyze / visualize your data

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

Choose a Right Tool

Choose a Right ToolAnalysis VisualizationData Preparation

Data Preparation Tips

- Prepare machine-friendly file- CSV, TSV, XML

- Use concrete, widely-used ID sets- NCBI Gene ID- Ensemble Gene ID

1. Understand Cytoscape Desktop

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

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

Cytoscape 3.1 Desktop

Toolbar

Network Panel

Bird’s Eve View

Table Browser

Network Views

Table Browser

Local Column

Table Tabs

List Data(Values in [ ])

Shared Column

Session File

- Snapshot of your workspace - Networks - Attributes - Visual Styles - System Properties

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

Open a Session

- Click folder icon - Or, File → Open

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

First Neighbor of Nodes

CTR+6

Create New Sub-Network From Selection

CTR+N

- CTR (Command on Mac) + G

Show Graphics Details- View → Show Graphics Details

Lesson 1 Demo

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

2. Data Import

Data Integration- Loading networks and mapping attributes

onto them - Cytoscape provides:

- Data import from files - Direct access to remote data sources

Import & Export

- Import - Load any type of data

- Network, Attributes, Visual Styles, etc. - Export

- as network files, tables, or images

Network Import

- Usually, imported from pre-formatted data file - Or, use Table Import feature to select

columns to be used as edges

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

Loading & Mapping Tables

- In most cases you need to import them from tables

- e.g. Expression matrix saved as Excel workbook

Mapping Key in the Network

Mapping Key in the Table

Load Network from Table

- Simple list of binary interactions can be loaded as networks !

- Source - Interaction Type - Target - Or, Source - Target

Import Public Data

Small Network Data

- Send query to database - List of genes - Keywords

Import from Public Database

Large Network Data (Interactome)

- Start from an Interactome - Filter and extract smaller

modules

Download Zipped Archives

Large Network Data (Interactome)

- Download Database Dump - Extract compressed data - Import as table

- Filter - Visualize

Lesson 2 Demo

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

3. Basic Analysis

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!)

Core Analysis Features

- Network Statistics - Search - Filtering

Network Statistics

Network Analyzer- Provides basic statistics

of networks - Degree - Centrality - Shortest Pass

Length Distribution - etc.

Filtering by Network Statistics

- NetworkAnalyzer provides all results as regular attributes

- Can be used for filtering

Search

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

Lesson 3 Demo

4. Visualization

Layouts

Automatic Layout

- Choose proper algorithm - Tree-like data - Hierarchical Layout - Scale-Free Network - Force-directed - Circular process - Circular Layout

- Tweak parameters if necessary

Manual Layout

- Tweak result from automatic layout - Scale - Align - Rotate

Visual Style

- Collection of mappings from Attributes to Visual Properties

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

Data Controls The View

Discrete Mapping Editor

Continuous Mapping Editor

Demo

Summary

Original

Visual Style Applied

Final Visualization

Visualization Techniques will be discussed in

Part 2

Apps

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

Installing Apps

- Easy - Just install from App manager.

- For browsing, just visit App Store

- http://apps.cytoscape.org/

To be Continued…

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

Further Readings 2- Overview of Cytoscape Apps (Plugins)

- A travel guide to Cytoscape pluginsRintaro 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 CytoscapeCline, et al. Nature Protocols, 2, 2366-2382 (2007).

Further Readings 3

- Cytoscape Tutorial Booklet: Analysis and Visualization of Biological Networks with Cytoscape

- http://www.rbvi.ucsf.edu/Outreach/Workshops/ISMBTutorial.pdf

!

2014 Keiichiro Ono kono@ucsd.edu