Deﬁne Your Goal - You need to deﬁne your goal.Attributes - Analysis and visualization will be performed for the integrated data (networks+attributes) Summary - There are two types of data - Networks.Network Attributes - Experiment details - Pathway Metadata - Description.Interaction Type - Physical, genetic, predicted - Publication ID Edge Attributes - Interaction Detection Methods - Y2H, NMR, afﬁnityĬhromatography, etc.Node Attributes - Gene Expression Data - Human-readable gene names.BRCA1 NCBI Gene ID 672 On Chromosome 17 GO Terms:ĭNA Repair Cell Cycle DNA Binding Ensemble ID ENSG00000012048.BRCA1 NCBI Gene ID 672 On Chromosome 17.Attributes - Any data about nodes, edges, and networks.Network Data Annotated Networks Attributes Analyzed Data Apps.Network Data Annotated Networks Attributes Apps.Network Data Annotated Networks Attributes.“Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, 2366-2382 (2007). Networks)‏ 3.Analyze and Visualize Networks 4.Prepare for Publication - A speciﬁc example of this workﬂow: − Cline, et al.

Networks)‏ 3.Analyze and Visualize Networks 4.Prepare for Publication - A speciﬁc example of this workﬂow: Cytoscape Workﬂow Networks)‏ 3.Analyze and Visualize Networks 4.Prepare for Publication Cytoscape Workﬂow Networks)‏ 3.Analyze and Visualize Networks Cytoscape Workﬂow

1.Load Networks (Get network data)‏ 2.Load Attributes (Get data about.

1.Load Networks (Get network data)‏ Cytoscape Workﬂow.

Data integration - Join networks andĪttributes - Network data analysis - Visualization

Human Interactome data from BioGRID visualized by Cytoscape.

Information, or modules, out of large biological networks

Basic Scope - Cytoscape is a tool for extracting meaningful.

Nodes - Any objects - Edges - Relationships between objects

Network - Mathematical Graph - G = (V, E).

Data Types in Cytoscape - There are two types ofĭata in Cytoscape - Network - Attribute (Data Table).

Machine Requirement - Faster, larger is better! - Cytoscape isĪ Java application, and it uses lots of memory - 4+ GB of memory is recommended for large network analysis / visualization.

V 0.31 - KGMLReader v 0.15 - ClusterMaker v1.10 - MCODE v1.32

Other Recommended Apps - Shortest Path v1.1 - PSICQUIC Client.

Differences between 3.x and 2.x will be discussed Cytoscape 3.0.0 release is available, but at this point, it is for power users due to missing plugins.

Prerequisites - Cytoscape 2.8.3 and EnhancedSearch Plugin should be installed.

Networks and Attributes - Visualization Techniques - Basic Analysis - Expression Data Analysis - Advanced Topics

Today’s Agenda - Basic Concepts - Browsing Network Data.Please Ask Questions! - Anytime you can atop me and.Area of Interest: Data Integration & Visualization - University of California, San Diego Trey Ideker Lab - This presentation ﬁle is available on my Speaker Deck account - /keiono Welcome! - Keiichiro Ono - Cytoscape Core Developer since 2005.25, 2013 University of Tokyo HGC Keiichiro Ono Cytoscape Core Developer Team University of California, San Diego Trey Ideker Lab Cytoscape Hands-On: Introduction to Biological Network Analysis and Visualization withĬytoscape Feb.

Cytoscape 3 tutorial