Canadian Bioinformatics Workshops

2Module #: Title of Module

Module 3 Pathway and Network Analysis

Module 3: Pathway and Network Analysis bioinformatics.ca Network Visualization Outline Automatic network layout Visual features Visually interpreting a network

Module 3: Pathway and Network Analysis bioinformatics.ca Automatic network layout

Module 3: Pathway and Network Analysis bioinformatics.ca Automatic network layout Force-directed: nodes repel and edges pull Good for up to 500 nodes – Bigger networks give hairballs - Reduce number of edges Advice: try force directed first, or hierarchical for tree-like networks Tips for better looking networks – Manually adjust layout – Load network into a drawing program (e.g. Illustrator) and adjust labels

Focus Overview Zoom PKC Cell Wall Integrity

Module 3: Pathway and Network Analysis bioinformatics.ca Visual Features Node and edge attributes – String, integer, float, Boolean, list – E.g. represent gene, interaction attributes Visual attributes – Node, edge visual properties – Colour, shape, size, borders, opacity...

Module 3: Pathway and Network Analysis bioinformatics.ca Visual Features Guilt-by-association Dense clusters Global relationships

Module 3: Pathway and Network Analysis bioinformatics.ca Network Representations

Module 3: Pathway and Network Analysis bioinformatics.ca What Have We Learned? Automatic layout is required to visualize networks Networks help you visualize interesting relationships in your data Avoid hairballs by focusing analysis Visual attributes enable multiple types of data to be shown at once – useful to see their relationships

Module 3: Pathway and Network Analysis bioinformatics.ca Network Visualization/Analysis using Cytoscape Network visualization and analysis using Cytoscape software Cytoscape basics Cytoscape network analysis examples

Network visualization and analysis UCSD, ISB, Agilent, MSKCC, Pasteur, UCSF, Unilever, UToronto, U Texas Pathway comparison Literature mining Gene Ontology analysis Active modules Complex detection Network motif search

Network Analysis using Cytoscape Databases Literature Expert knowledge Experimental Data Find biological processes underlying a phenotype Network Information Network Analysis

Manipulate NetworksFilter/Query Automatic Layout Interaction Database Search

Module 3: Pathway and Network Analysis bioinformatics.ca Active Community Help – 8 tutorials, >10 case studies – Mailing lists for discussion – Documentation, data sets Annual Conference: Ann Arbor July 18-20, ,000s users, 2500 downloads/month >60 Plugins Extend Functionality – Build your own, requires programming Cline MS et al. Integration of biological networks and gene expression data using Cytoscape Nat Protoc. 2007;2(10):

Module 3: Pathway and Network Analysis bioinformatics.ca What Have We Learned? Cytoscape is a useful, free software tool for network visualization and analysis Provides basic network manipulation features Plugins are available to extend the functionality

Cytoscape Demo Version

Desktop Canvas Network overview Network manager Attribute browser CytoPanels FYI

yFiles Organic FYI

yFiles Circular FYI

Module 3: Pathway and Network Analysis bioinformatics.ca Network Layout 15 algorithms available through plugins Demo: Move, zoom/pan, rotate, scale, align FYI

Create Subnetwork FYI

Create Subnetwork FYI

Module 3: Pathway and Network Analysis bioinformatics.ca Visual Style Customized views of experimental data in a network context Network has node and edge attributes E.g. expression data, GO function, interaction type Mapped to visual attributes E.g. node/edge size, shape, colour… E.g. Visualize gene expression data as node colour gradient on the network FYI

Visual Style Load “Your Favorite Network” FYI

Visual Style Load “Your Favorite Expression” Dataset FYI

Visual Style Map expression values to node colours using a continuous mapper FYI

Visual Style Expression data mapped to node colours FYI

Module 3: Pathway and Network Analysis bioinformatics.ca Network Filtering FYI

Interaction Database Search FYI

Module 3: Pathway and Network Analysis bioinformatics.ca FYI

Module 3: Pathway and Network Analysis bioinformatics.ca FYI

Module 3: Pathway and Network Analysis bioinformatics.ca VistaClara Visualization for gene expression data Heat maps, sorting, animation

Module 3: Pathway and Network Analysis bioinformatics.ca Lab – Until 12:30pm Cytoscape – expression data visualization – Load the sample network file: galFiltered.sif – Lay it out – try different layouts – Load expression data - galExpData.pvals Use File->Import->Attribute from Table – Examine node attributes – Visualize gene expression data using the Visual Mapper – Install the VistaClara plugin from the plugin manager – Play the expression data as a movie

Module 3: Pathway and Network Analysis bioinformatics.ca Cytoscape 2.7, 2.8 Cytosape 2.7 is out now – Nested networks – Command line scripting Cytoscape 2.8 coming soon – Equations in attributes – Custom graphics

Module 3: Pathway and Network Analysis bioinformatics.ca We are on a Coffee Break & Networking Session