Cytoscape User Manual Table of Contents Cytoscape User Manual ........................................................................................................ 3 Introduction ...................................................................................................................... 48 Development .............................................................................................................. 4 License ...................................................................................................................... 4 What’s New in 2.7 ....................................................................................................... 4 Please Cite Cytoscape! ................................................................................................. 7 Launching Cytoscape ........................................................................................................... 8 System requirements .................................................................................................... 8 Getting Started .......................................................................................................... 56 Quick Tour of Cytoscape ..................................................................................................... 12 The Menus ............................................................................................................... 15 Network Management ................................................................................................. 18 The Network Overview Window ................................................................................... 20 Command Line Arguments .................................................................................................. 21 Cytoscape Preferences ........................................................................................................ 22 Managing Properties ................................................................................................... 22 Managing Bookmarks ................................................................................................. 24 Managing Proxy Servers ............................................................................................. 24 Creating Networks ............................................................................................................. 24 Import Fixed-Format Network Files ............................................................................... 25 Import Free-Format Table Files ..................................................................................... 26 Import Networks from Web Services ............................................................................. 30 Edit a New Network ................................................................................................... 30 Supported Network File Formats ........................................................................................... 31 SIF Format ............................................................................................................... 31 NNF ........................................................................................................................ 33 GML Format ............................................................................................................. 38 XGMML Format ....................................................................................................... 38 SBML (Systems Biology Markup Language) Format ........................................................ 39 BioPAX (Biological PAthways eXchange) Format ............................................................ 39 PSI-MI Format .......................................................................................................... 39 Delimited Text Table and Excel Workbook ...................................................................... 39 Node Naming Issues in Cytoscape ................................................................................. 40 Node and Edge Attributes .................................................................................................... 41 Cytoscape Attribute File Format .................................................................................... 41 Import Attribute Table Files ......................................................................................... 44 Attribute Functions and Equations ......................................................................................... 48 Attribute Formulas ..................................................................................................... 48 Loading Gene Expression (Attribute Matrix) Data .................................................................... 52 Data File Format ........................................................................................................ 52 General Procedure ...................................................................................................... 53 Worked Example ....................................................................................................... 53 Detailed file format (Advanced users) ............................................................................ 54 Importing Networks and Attributes from External Databases ...................................................... 55 Web Service Client Manager ........................................................................................ 55 Getting Started .......................................................................................................... 56 1 Cytoscape User Manual Example #1: Retrieving Protein-Protein Interaction Networks from IntAct ............................ 56 Example #2: Retrieving Protein-Protein Interaction Networks from NCBI Entrez Gene ........... 57 Example #3: Retrieving Pathways and Networks from Pathway Commons ............................ 58 Future Directions ....................................................................................................... 61 Import Attributes from External Database ....................................................................... 61 Use Multiple Services in a Workflow ............................................................................. 64 Navigation and Layout ........................................................................................................ 66 Basic Network Navigation ........................................................................................... 66 Other Mouse Behaviors ............................................................................................... 67 Automatic Layout Algorithms ...................................................................................... 68 Manual Layout .......................................................................................................... 77 Node Movement and Placement .................................................................................... 81 Visual Styles ..................................................................................................................... 81 What is a Visual Style? ................................................................................................ 81 Introduction to the VizMapper User Interface .................................................................. 96 Introduction to Visual Styles ........................................................................................ 97 Visual Attributes, Graph Attributes and Visual Mappers ..................................................... 99 Custom Graphics Manager ......................................................................................... 107 Visual Styles Tutorials ............................................................................................... 111 Advanced Topics ...................................................................................................... 126 Managing Visual Styles ............................................................................................. 131 Bypassing Visual Styles ............................................................................................. 131 Finding and Filtering Nodes and Edges ................................................................................. 132 QuickFind ............................................................................................................... 132 Filters .................................................................................................................... 136 Using New Filters .................................................................................................... 137 Using Old Filters ...................................................................................................... 141 The Select Menu ...................................................................................................... 145 Editing Networks ............................................................................................................. 146 Add Interactions (SIF Style) ....................................................................................... 147 Nested Networks .............................................................................................................. 148 Introducing Nested Networks ..................................................................................... 148 Creating Nested Networks .........................................................................................