for Biological Network Analysis and Visualization 2/22/2013 @University of Tokyo HGC Keiichiro Ono Cytoscape Core Developer Team University of California, San Diego Trey Ideker Lab
Thanks for Attending! - Keiichiro Ono - Cytoscape Core Developer since 2005 - Core modules design & implementation - Release management - Area of Interest: Data Integration & Visualization - University of California, San Diego Trey Ideker Lab
Outline - What is Cytoscape? - How Cytoscape helps your research projects - Cytoscape Ecosystem
What is Cytoscape?
Cytoscape - Open source platform for biological network data integration, analysis, and visualization
- Free! (open source, LGPL) - Developed and maintained by universities, companies, and research institutions - De-facto standard software in biological network research community - Expandable by Apps
Nodes and Edges in Biology Node - Protein - Protein - Protein - DNA Node - Genetic (Epistasis) Edge - Synthetic lethality - Biochemical Reactions - Compound - Enzyme - Compound Cartoon representation of a complex between DNA and the protein p53
Human-Curated Pathways KEGG Pathway Visualized by Cytoscape
Undirected Network - Protein - Protein Interaction
Directed Network KEGG Pathway (TCA Cycle) visualized by Cytoscape KGMLReader
Biological Networks - Tell us anything by themselves - Big hairball (or small galaxy...)
Tool for Hacking Hairballs - Biologists need a tool to extract meaningful biological modules from the huge hairballs - Cytoscape is focussing that area of problem
In Other Words...
Genes of Interest
List of Drug Targets Other knowledge
Cytoscape Core is NOT a... - Simulator - Pathway diagram (SBGN) editor - Statistical network analysis tool suite - Still, you can implement these as Apps though
Large-Scale Network Analysis and Visualization Human Interactome data from BioGRID visualized by Cytoscape
How Big? - Protein-Protein: ~10k nodes/ ~20k edges - Genetic: ~Millions - And more flood of data is coming - Microbiomes - Co-expression of SNPs - ...
Pick a Right Tool NetworkX
Advantages of Open Platform - Write a bridge App and use other applications‘ features - Web Service API, etc... - Cytoscape as a part of your workflow
Summary - Cytoscape is a platform for: - Data integration: networks & known annotations, experimental/clinical data - Analysis: filter/search/module extraction - Visualization: Helps you to understand the data
Introduction to Biological Network Analysis Using Cytoscape
Cytoscape Workflow 1.Load Networks (Get network data) 2.Load Attributes (Get data about networks) 3.Analyze and Visualize Networks 4.Prepare for Publication - A specific example of this workflow: − Cline, et al. “Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, 2366-2382 (2007).
Network Data Attributes Annotated Apps Networks Analyzed Data
I Don’t Have a Network! - Don’t worry - There are tons of public interaction data sets - Cytoscape can import those public data sets directly via Internet.
Which Database? - Protein - Protein - STRING, IntAct - Genetic - BioGRID - Protein - Compound - ChEMBL - Human-Curated Pathways - KEGG, Reactome, PathwayCommons
PSICQUIC - Standardized mechanism to access public interaction data sets - In short, you can search multiple databases at once
What are Attributes? - Any data that describes or provides details about nodes, edges, and networks.
GO Terms: DNA Repair NCBI Gene ID 672 Cell Cycle DNA Binding BRCA1 Ensemble ID On Chromosome 17 ENSG00000012048
Why we need attributes? - Analysis - It is hard to get biologically meaningful analysis result only from network topology (= structure) - Meaningful Visualization - Expression values - Node Color - Gene Function - Node Shape - etc.
Public Data Source - Access directly from Cytoscape, or - Import as Table (Text/Excel)
Your Data Sets - Anything saved as a table cam be loaded into Cytoscape - Excel - Tab Delimited Document - CSV - As long as proper mapping key is available, Cytoscape can map them to your networks.
Mapping Key in the Network Mapping Key in the Table
Network Analysis - Filtering - Calculate network statistics by Network Analyzer - Degree distribution,centrality, etc. - Advanced analysis by Apps
Filtering - Find nodes and edges with specific conditions - Pick nodes with degree > 5 - Select edges extracted from publication X - Find nodes annotated by GO term ID Y
Biological Data Visualization - Help others to understand your data - Emphasize what you want to tell by the image - Use color, shape, size of objects effectively! - Excellent resource for data visualization - Tamara Munzner’s Web Site: http://www.cs.ubc.ca/~tmm/
Visualization Core Idea - Map values to visual properties - Expression Value to Node Color - Edge Weight to Width - Degree to Node Size - Node Type to Shape
Map Attributes to Visual Properties
Visual Style - Collection of mappings from Attributes to Visual Properties
A Must Read 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
Rintaro Saito et al: a travel guide to cytoscape plugins Nature Methods 9 (11) p. 1069-1076
Cytoscape Family - Version 2.x - Production version - Version 3.x - Next generation - 3.0.x - Maintenance - 3.1.x - Next release with new features - cytoscape.js - Library for web applications
What’s New in 3? - New Visualization features - Edge Bend, Background Images - Server-side applications - Headless Mode (Command-line) - More advanced visualization by new rendering engines - For developers: Cleaner API
Release Schedule - 3.0.0 is (finally) available! - For more information, please visit: http://www.cytoscape.org/cy3.html - 3.0.1 will be available shortly - We will release more frequently
Collaboration - National Resources for Network Biology (NRNB) - Always open for new collaboration! - Scientific Research - Application / Tool Development - nrnb.org
Where is Japan...? Countries of origin for each App based on contact e-mail addresses and affiliations
Where to Start? - Cytoscape Web Site - cytoscape.org - Open Tutorials - opentutorials.cgl.ucsf.edu/ index.php/Main_Page
Getting Help - Two Google Groups - email@example.com - firstname.lastname@example.org - ANY question is OK!