1. Copyright OpenHelix. No use or reproduction without express written consent1

2. 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

3. Copyright OpenHelix. No use or reproduction without express written consent3 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

4. Copyright OpenHelix. No use or reproduction without express written consent4 VisANT Introduction Biomolecular interaction tool Web-based, open-source Uses metagraph data structure Supports analysis of large networks Integrative Data mining GFAP and TFAP2 Interaction Network

5. Copyright OpenHelix. No use or reproduction without express written consent5 VisANT Data Model 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 Node: Represents a Protein or gene Edge: Represents an interaction

6. Copyright OpenHelix. No use or reproduction without express written consent6 Metanode Expanded Double Click

7. Copyright OpenHelix. No use or reproduction without express written consent7 Databases Predictome: a database of predicted functional associations among genes and proteins http://cagt.bu.edu/page/Predictome http://cagt.bu.edu/page/Predictome BIND, MIPS, HPRD etc.: provide experimentally determined association data GenBank, SGD, FlyBase, KEGG, GO, HUGO etc. : provide name normalization and linkout functions

8. Copyright OpenHelix. No use or reproduction without express written consent8 VisANT Homepage VisANT: http://visant.bu.edu/http://visant.bu.edu/ Main Tool Bar Tool Features Quick Links News Search Ref. Links

9. Copyright OpenHelix. No use or reproduction without express written consent9 Credits Funded partially by grants from the National Institutes of Health (1R01RR02297 1-01A1) Joint Developers Veteran Members Development Team Collaborators Advisory Board

10. Copyright OpenHelix. No use or reproduction without express written consent10 Documents Homepage Document Links Publications http://bib.oxfordjournals.org/cgi/reprint/9/4/317 http://nar.oxfordjournals.org/cgi/screenpdf/gkm295v1

11. Copyright OpenHelix. No use or reproduction without express written consent11 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

12. Copyright OpenHelix. No use or reproduction without express written consent12 Running VisANT Four run modes for VisANT All versions require Java: Must install latest version of Java (http://www.java. com/en/)http://www.java. com/en/ Choose run mode based on needed features Description of Run Modes

13. Copyright OpenHelix. No use or reproduction without express written consent13 Summary of Run Modes Online Java Applet Java Web Application Local Application Batch Mode AdvantagesDisadvantages Run latest version, easy access with internet Lack of access to Save/Load and printing features Access to latest version and all features, create shortcut Requires Java Web start Access to all features, local copy of VisANT, allows plug-in development, share networks online Requires manual download of latest software version Automated processing of time consuming tasks and large networks No user interaction, not all functions available as commands

14. Copyright OpenHelix. No use or reproduction without express written consent14 User Registration Documents => user manual http://visant.bu.edu:8080/test/register.jsp User Registration Section of User Manual Registration Page

15. Copyright OpenHelix. No use or reproduction without express written consent15 Starting Java Web Application Tutorial will use Java Web application mode Demonstrate full range of features Online mode Click here

16. Copyright OpenHelix. No use or reproduction without express written consent16 VisANT User Interface Interaction Network graph Main Tool Bar Control Panel

17. Copyright OpenHelix. No use or reproduction without express written consent17 Main Menu Bar: File, Edit & View File: Export Files, Open, Save, Exit Edit: Invert node or edge selection, Select, Deselect, Delete View: methods table, statistics report, Toolbar

18. Copyright OpenHelix. No use or reproduction without express written consent18 Main Menu Bar: Filters, Layout, Node, Edge 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

19. Copyright OpenHelix. No use or reproduction without express written consent19 Main Menu Bar, cont. MetaGraph: meta- nodes and edges, grouping, duplication, manipulation Topology: graph statistics, shortest 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

20. Copyright OpenHelix. No use or reproduction without express written consent20 Main Menu Bar, Additional Tools 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 Change Expression Experiment View Expression Plot

21. Copyright OpenHelix. No use or reproduction without express written consent21 Control Panel 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 Search Login Data options

22. Copyright OpenHelix. No use or reproduction without express written consent22 GO Explorer GO annotations will be available as node description if they are available Expand GO annotation is now available for 13 species: Saccharomyces cerevisiae, Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Gallus gallus, Homo sapiens, Magnaporthe grisea, Mus musculus, Oryza sativa, Plasmodium falciparum, and Rattus norvegicus Mouse Over Window

23. Copyright OpenHelix. No use or reproduction without express written consent23 GO Explorer Tools Search using GO ID or keyword Use to Hide/Show Configurations Choose Cutoff for Informative Terms and Number of genes Check To link GO and Network

24. Copyright OpenHelix. No use or reproduction without express written consent24 Graph Panel Move mouse over node or edge to see label and information Click on node to select Right click mouse to open pop up menu

25. Copyright OpenHelix. No use or reproduction without express written consent25 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

26. Copyright OpenHelix. No use or reproduction without express written consent26 Clear Graph Panel First Clear graph pane Click Clear

27. Copyright OpenHelix. No use or reproduction without express written consent27 Log In To VisANT Click here your email password

28. Copyright OpenHelix. No use or reproduction without express written consent28 Logged In User Interface Logged In

29. Copyright OpenHelix. No use or reproduction without express written consent29 Input Search Term 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 Akap12 Input Search Term here Choose Species Click Search Select Labels, Autofit, and Quick Tip

30. Copyright OpenHelix. No use or reproduction without express written consent30 Search Results Double Click Edges have more than one color = More than one experimental method

31. Copyright OpenHelix. No use or reproduction without express written consent31 Expand Network

32. Copyright OpenHelix. No use or reproduction without express written consent32 Quick Search Opens in online java applet version of VisANT Click here

33. Copyright OpenHelix. No use or reproduction without express written consent33 Browse KEGG Pathways Click here

34. Copyright OpenHelix. No use or reproduction without express written consent34 KEGG Pathways Scroll Down

35. Copyright OpenHelix. No use or reproduction without express written consent35 Cell Communication Pathway

36. Copyright OpenHelix. No use or reproduction without express written consent36 Search KEGG Pathway Search term “map” and KEGG ID number Species must match Input KEGG Search term map04540 Input Species

37. Copyright OpenHelix. No use or reproduction without express written consent37 KEGG Gap Junction Pathway

38. Copyright OpenHelix. No use or reproduction without express written consent38 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

39. Copyright OpenHelix. No use or reproduction without express written consent39 Loading Data Function is only available after users login Data format: Column 1 Column 2 Column3 Column4 Starting node Ending node Direction Method Only Column 1 required Load Data here

40. Copyright OpenHelix. No use or reproduction without express written consent40 Method Based Data Loading For large scale analysis of interactions based on method Check Methods Select allAdd MethodClose

41. Copyright OpenHelix. No use or reproduction without express written consent41 Use of Methods Table GNA11 With all Methods Selected GNA11 With only Two-hybrid Selected

42. Copyright OpenHelix. No use or reproduction without express written consent42 Saving Data Must be logged in as a registered user Click here

43. Copyright OpenHelix. No use or reproduction without express written consent43 Available Files File Now Available

44. Copyright OpenHelix. No use or reproduction without express written consent44 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

45. Copyright OpenHelix. No use or reproduction without express written consent45 Advanced Techniques A connection to the node itself is called a “self loop” Curved Line Indicates “self loop”

46. Copyright OpenHelix. No use or reproduction without express written consent46 Select Multiple Nodes Once selected, click and drag on node or edge to move as a group Put Rectangle Around Nodes All Nodes Now Selected

47. Copyright OpenHelix. No use or reproduction without express written consent47 Find Connections Find connections between a set of proteins Add Data Click Add Interaction Network

48. Copyright OpenHelix. No use or reproduction without express written consent48 Add GO Annotation Select

49. Copyright OpenHelix. No use or reproduction without express written consent49 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

50. Copyright OpenHelix. No use or reproduction without express written consent50 Integration of Interactome Find only those interactions with multiple methods

51. Copyright OpenHelix. No use or reproduction without express written consent51 Filter by Multiple Methods Select

52. Copyright OpenHelix. No use or reproduction without express written consent52 Invert Selection Select

53. Copyright OpenHelix. No use or reproduction without express written consent53 Delete Selected Nodes Select

54. Copyright OpenHelix. No use or reproduction without express written consent54 Interactions with Multiple Methods All Interactions Show Multiple Methods

55. Copyright OpenHelix. No use or reproduction without express written consent55 Integration of Expression Profile Expression menu can only be run with Java Web start version or Local Application Select

56. Copyright OpenHelix. No use or reproduction without express written consent56 Loaded Expression Data

57. Copyright OpenHelix. No use or reproduction without express written consent57 Change Expression Experiment

58. Copyright OpenHelix. No use or reproduction without express written consent58 Expression Plot Value

59. Copyright OpenHelix. No use or reproduction without express written consent59 Integration with Other Annotation Select

60. Copyright OpenHelix. No use or reproduction without express written consent60 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

61. Copyright OpenHelix. No use or reproduction without express written consent61 VisANT Main Tool Bar Control Panel Interaction Network graph

62. Copyright OpenHelix. No use or reproduction without express written consent62 Search for Interactions Search Window Add Data Save, Open, Share Files

63. Copyright OpenHelix. No use or reproduction without express written consent63 Search for KEGG Pathways Map04540 Input KEGG Search term

64. Copyright OpenHelix. No use or reproduction without express written consent64 Find Connections Only Internal Connections Shown

65. Copyright OpenHelix. No use or reproduction without express written consent65 Data Integration Integrate data on GO annotations Link to GenBank, OMIM, Entrez Gene, HUGO, and KEGG Integrate Expression data Expression Visualization

66. Copyright OpenHelix. No use or reproduction without express written consent66 Sample Files Load these files directly into VisANT Load Files Load Networks

67. Copyright OpenHelix. No use or reproduction without express written consent67 VisANT Summary

68. Copyright OpenHelix. No use or reproduction without express written consent68 VisANT Agenda Introduction and Credits Starting VisANT Basic Search and Navigation Loading/Saving Data Advanced Network Manipulation Integration of Data Summary Exercises VisANT: http://visant.bu.edu/http://visant.bu.edu/

69. Copyright OpenHelix. No use or reproduction without express written consent69