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VisANT VisANT: Integrative Visual Analysis Tool for Biological Networks and Pathways Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q3 2009 Version 1.0_0809 Copyright OpenHelix. No use or reproduction without express written consent 1 VisANT Agenda VisANT Introduction GFAP and TFAP2 Interaction Network Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 3 Biomolecular interaction tool Web-based, open-source Uses metagraph data structure Supports analysis of large networks Integrative Data mining Copyright OpenHelix. No use or reproduction without express written consent 4 1 VisANT Data Model Node: Represents a Protein or gene Metanode Expanded Edge: Represents an interaction Double Click Data represented as a metagraph with nodes, edges and subnetworks in a nested structure Structure allows for one node to have multiple instances and allows a metanode in a metagraph to share nodes Copyright OpenHelix. No use or reproduction without express written consent 5 Databases Copyright OpenHelix. No use or reproduction without express written consent 6 VisANT Homepage Predictome: a database of predicted functional associations among genes and proteins http://cagt.bu.edu/page/Predictome Main Tool Bar Search Quick Links News Tool Features BIND, MIPS, HPRD etc.: provide experimentally determined association data GenBank, SGD, FlyBase, KEGG, GO, HUGO etc. : provide name normalization and linkout functions Copyright OpenHelix. No use or reproduction without express written consent Ref. Links VisANT: http://visant.bu.edu/ 7 Copyright OpenHelix. No use or reproduction without express written consent 8 2 Credits Collaborators Documents Homepage Advisory Board D Development l tT Team Funded partially by grants from the National Institutes of Health (1R01RR02297 1-01A1) http://bib.oxfordjournals.org/cgi/reprint/9/4/317 Joint Developers Document Links Publications Veteran Members http://nar.oxfordjournals.org/cgi/screenpdf/gkm295v1 Copyright OpenHelix. No use or reproduction without express written consent 9 VisANT Agenda Copyright OpenHelix. No use or reproduction without express written consent 10 Running VisANT Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises Four run modes for VisANT All versions require Java: Must install latest version of Java (http://www.java. com/en/) Choose run mode based on needed features Description of Run Modes VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 11 Copyright OpenHelix. No use or reproduction without express written consent 12 3 Summary of Run Modes Advantages Online Java Applet Run latest version, easy access with internet User Registration Disadvantages http://visant bu edu:8080/test/register jsp http://visant.bu.edu:8080/test/register.jsp Java Web Application Access to latest version and all features, create shortcut Local Application Access to all features, local copy of VisANT, allows plug-in development, share networks online Requires manual download of latest software version Batch Mode Automated processing of time consuming tasks and large networks No user interaction, not all functions available as commands Requires Java Web start Copyright OpenHelix. No use or reproduction without express written consent User Registration Section of User Manual Registration Page 13 Starting Java Web Application Tutorial will use Java Web application mode Demonstrate full range of features Copyright OpenHelix. No use or reproduction without express written consent 14 VisANT User Interface Online mode Documents => user manual Lack of access to Save/Load and printing features Main Tool Bar Control Panel Click here Interaction Network graph Copyright OpenHelix. No use or reproduction without express written consent 15 Copyright OpenHelix. No use or reproduction without express written consent 16 4 Main Menu Bar: File, Edit & View Main Menu Bar: Filters, Layout, Node, Edge File: Export Files, Open, Save, Exit Edit: Invert node or edge selection, Select, Deselect, Delete View: methods table, statistics report, Toolbar Copyright OpenHelix. No use or reproduction without express written consent 17 Main Menu Bar, cont. Filters: Choose different filtering methods Layout: change network layout, select algorithm for layout Node(s): when node selected enables functions for node manipulation Edge(s): when edge selected enables functions for edge manipulation Copyright OpenHelix. No use or reproduction without express written consent Main Menu Bar, Additional Tools Change Expression Experiment MetaGraph: meta- nodes and edges, grouping, duplication, manipulation Topology: graph statistics, statistics shortest path path, motif detection Options: turn on or off pop-up features, visualization features Expression: loading expression data Plugins: loading plugins into VisANT Help: opens up user manual Copyright OpenHelix. No use or reproduction without express written consent 18 19 View Expression Plot Weight Cutoff – allows you to choose a range of edge weights from 0 to 1.0 for the edges Edge Optimization- optimizes the edge distribution. When selected, nodes within the Meta-node have the higher priority to own the edge. Note: Pre-release function, use with caution Expression – use slider to change expression experiment, and check Expression plot to view an expression plot graph for each node Copyright OpenHelix. No use or reproduction without express written consent 20 5 Control Panel GO Explorer Labels: turn on/off node labels Auto Fit: when checked network will fit to size of panel Quick Tip: quickly gain detailed annotation with mouse over Zoom In/out and Pane Clear graph pane Mouse Over Window Search Expand Login GO annotation is now available for 13 species: Saccharomyces cerevisiae, Arabidopsis thaliana, Bos taurus, taurus Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Gallus gallus, Homo sapiens, Magnaporthe grisea, Mus musculus, Oryza sativa, Plasmodium falciparum, and Rattus norvegicus Data options Copyright OpenHelix. No use or reproduction without express written consent 21 GO Explorer Tools Check To link GO and Network Copyright OpenHelix. No use or reproduction without express written consent Copyright OpenHelix. No use or reproduction without express written consent 22 Copyright OpenHelix. No use or reproduction without express written consent 24 Graph Panel Search using Use to Hide/Show GO ID or keyword Configurations Choose Cutoff for Informative Terms and Number of genes GO annotations will be available as node description if they are available 23 Move mouse over node or edge to see label and information Click on node to select Right click mouse to open pop up menu 6 VisANT Agenda Clear Graph Panel Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises First Clear graph pane Click Clear VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 25 Log In To VisANT Copyright OpenHelix. No use or reproduction without express written consent 26 Logged In User Interface your email password Click here Click here Logged In Copyright OpenHelix. No use or reproduction without express written consent 27 Copyright OpenHelix. No use or reproduction without express written consent 28 7 Input Search Term Search Results Select Labels, Autofit, and Quick Tip Click Search Akap12 Input Search Term here Choose Species Edges have more than one color = More than one experimental method Search term: gene, protein can use name/ORF/GI number For KEGG pathway search entry must started with "map" followed by KEGG ID Multiple entries can be separated by either ',' or space/tab Copyright OpenHelix. No use or reproduction without express written consent 29 Expand Network Copyright OpenHelix. No use or reproduction without express written consent 30 Quick Search Click here Copyright OpenHelix. No use or reproduction without express written consent 31 Opens in online java applet version of VisANT Copyright OpenHelix. No use or reproduction without express written consent 32 8 Browse KEGG Pathways KEGG Pathways Click here Scroll Down Copyright OpenHelix. No use or reproduction without express written consent 33 Cell Communication Pathway Copyright OpenHelix. No use or reproduction without express written consent Search KEGG Pathway map04540 Copyright OpenHelix. No use or reproduction without express written consent 34 35 Input KEGG Search term Input Species Search term “map” and KEGG ID number Species must match Copyright OpenHelix. No use or reproduction without express written consent 36 9 KEGG Gap Junction Pathway VisANT Agenda Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 37 Loading Data Copyright OpenHelix. No use or reproduction without express written consent Method Based Data Loading For large scale analysis of interactions based on method Check Methods Load Data here 38 Function is only available after users login Data format: Column 1 Column 2 Column3 Starting node Ending node Direction Only Column 1 required Column4 Method Copyright OpenHelix. No use or reproduction without express written consent Select all 39 Add Method Copyright OpenHelix. No use or reproduction without express written consent Close 40 10 Use of Methods Table Saving Data GNA11 With all Methods Selected Click here GNA11 With only Two-hybrid Selected Click here Copyright OpenHelix. No use or reproduction without express written consent 41 Available Files Must be logged in as a registered user Copyright OpenHelix. No use or reproduction without express written consent 42 VisANT Agenda File Now Available Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 43 Copyright OpenHelix. No use or reproduction without express written consent 44 11 Advanced Techniques Select Multiple Nodes Curved Line Indicates “self loop” Put Rectangle Around Nodes All Nodes Now Selected A connection to the node itself is called a “self loop” Copyright OpenHelix. No use or reproduction without express written consent 45 Find Connections Once selected, click and drag on node or edge to move as a group Copyright OpenHelix. No use or reproduction without express written consent 46 Add GO Annotation Select Interaction Network Click Add Add Data Find connections between a set of proteins Copyright OpenHelix. No use or reproduction without express written consent 47 Copyright OpenHelix. No use or reproduction without express written consent 48 12 VisANT Agenda Integration of Interactome Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 49 Filter by Multiple Methods Copyright OpenHelix. No use or reproduction without express written consent 50 Invert Selection Select Select Copyright OpenHelix. No use or reproduction without express written consent Find only those interactions with multiple methods 51 Copyright OpenHelix. No use or reproduction without express written consent 52 13 Delete Selected Nodes Interactions with Multiple Methods All Interactions Show Multiple Methods Select Copyright OpenHelix. No use or reproduction without express written consent 53 Integration of Expression Profile Copyright OpenHelix. No use or reproduction without express written consent 54 Loaded Expression Data Select Expression menu can only be run with Java Web start version or Local Application Copyright OpenHelix. No use or reproduction without express written consent 55 Copyright OpenHelix. No use or reproduction without express written consent 56 14 Change Expression Experiment Expression Plot Value Copyright OpenHelix. No use or reproduction without express written consent 57 Integration with Other Annotation Copyright OpenHelix. No use or reproduction without express written consent 58 VisANT Agenda Select Select Select Se ec Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 59 Copyright OpenHelix. No use or reproduction without express written consent 60 15 VisANT Search for Interactions Main Tool B Bar Control C t l Panel Search Window Save, Open, p , Share Files Interaction Network graph Copyright OpenHelix. No use or reproduction without express written consent Add Data 61 Search for KEGG Pathways Input KEGG Search term Copyright OpenHelix. No use or reproduction without express written consent 62 Find Connections Only Internal Connections Shown Map04540 Copyright OpenHelix. No use or reproduction without express written consent 63 Copyright OpenHelix. No use or reproduction without express written consent 64 16 Data Integration Integrate data on GO annotations Link to GenBank, OMIM, Entrez Gene, HUGO, and KEGG Integrate Expression data Sample Files Load Files Load these files directly into VisANT Load Networks Expression Visualization Copyright OpenHelix. No use or reproduction without express written consent 65 VisANT Summary Copyright OpenHelix. No use or reproduction without express written consent 66 VisANT Agenda Introduction and Credits Starting g VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/ Copyright OpenHelix. No use or reproduction without express written consent 67 Copyright OpenHelix. No use or reproduction without express written consent 68 17 Copyright OpenHelix. No use or reproduction without express written consent 69 18
