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

2. IntAct IntAct: a database & analysis tools for protein interaction data Materials prepared by: Cynthia Foote, Ph.D. Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q3 2010 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

4. Copyright OpenHelix. No use or reproduction without express written consent4 Focus: protein interactions Interaction types: Valuable for cellular function & mapping signaling pathways IntAct Captures Protein Interaction Data A B Protein-Protein A Ca++ Protein-Small molecule Protein-Nucleic Acid A

5. Copyright OpenHelix. No use or reproduction without express written consent5 Sources & Organization of Interaction Data Curated interaction data from literature and direct user submissions Various experimental techniques used for determination The Data Model includes 3 levels of organization: Experiment Interaction Interactor

6. Copyright OpenHelix. No use or reproduction without express written consent6 IntAct Utilizes Controlled Vocabularies Controlled vocabularies ensure consistency and searchability For more details, see IntAct Help or OpenHelix introductory tutorials on Controlled Vocabularies or the Gene Ontology details

7. Static network views - Graph tab Copyright OpenHelix. No use or reproduction without express written consent7 View Protein Interactions Graphically Node Interconnecting lines Interactive network views - Cytoscape Control Panel Optional Network Panel Results Panel Data Panel - Attribute Browser Options Network View

8. Copyright OpenHelix. No use or reproduction without express written consent8 Many Homepage Features http://www.ebi.ac.uk/intact Highlighted data Tool bar open source software EMBL-EBI Introduction Statistics News examples

9. 9 Search Options, Tools & Help Basic search with help Copyright OpenHelix. No use or reproduction without express written consent

10. 10 Credits Developed by the Proteomics Services team at EBI, led by Henning Hermjakob Part of Protein and Nucleotide Database Group (PANDA), led by Rolf Apweiler and Ewan Birney Funding from a EU FELICS grant, other EU grants Collaborations: Shanghai Institutes for Biological Sciences AstraZeneca

11. Copyright OpenHelix. No use or reproduction without express written consent11 Publications & Citation Information http://nar.oxfordjournals.org/cgi/screenpdf/gkl958v1.pdf Homepage left tool bar http://nar.oxfordjournals.org/cgi/content/full/gkp878v1

12. Copyright OpenHelix. No use or reproduction without express written consent12 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

13. Copyright OpenHelix. No use or reproduction without express written consent13 IntAct Basic Search From Homepage Tpx2 http://www.ebi.ac.uk/intact More advanced searches can also be performed

14. Copyright OpenHelix. No use or reproduction without express written consent14 Basic Search Results Tabs Our query Query details Help for this view Options Click Magnifying glass for Interaction Details

15. Copyright OpenHelix. No use or reproduction without express written consent15 Basic Search Results - Interactions View Aliases Protein Names & Links Interaction Method & Accession Protein Species Publication Info. Expansion Method Molecule Type, i.e., protein Component, i.e., bait, prey, neutral Role, i.e., unspecified, inhibitor, ect.

16. Basic Search Results - Browsing Copyright OpenHelix. No use or reproduction without express written consent16 Click here

17. Basic Search Results - Lists View Copyright OpenHelix. No use or reproduction without express written consent17 Check all, one or several Choose an action for your selections Subtabs for molecule types

18. Copyright OpenHelix. No use or reproduction without express written consent18 Interaction Details Click Magnifying glass to reach Interaction Details Show all interactions Find similar interactions Experiment details Publication details Interaction details Click on any Dasty2 logo to reach Molecule View tab

19. Molecule View - Dasty2 Visualization Copyright OpenHelix. No use or reproduction without express written consent19 Mouse over Toggle open Protein features projected onto sequence & structure, if available BLAST

20. Copyright OpenHelix. No use or reproduction without express written consent20 Accessing Graphical Networks Click here to view graphical network Graph tab only active if less than 300 binary interactions Install Cytoscape locally to view a larger number of interactions (http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/ImportingNetworksFromWebServices)http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/ImportingNetworksFromWebServices

21. Copyright OpenHelix. No use or reproduction without express written consent21 Static Graphical Networks A static network view Click here to open interactive view with Cytoscape Click here to download Cytoscape

22. Copyright OpenHelix. No use or reproduction without express written consent22 Interactive Graphical Networks - Cytoscape ↔ Control Panel Optional Network Panel Network View Results Panel Data Panel - Attribute Browser ↔ Options Help

23. Cytoscape Help is Available Copyright OpenHelix. No use or reproduction without express written consent23 Cytoscape User Manual

24. Copyright OpenHelix. No use or reproduction without express written consent24 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

25. http://www.ebi.ac.uk/intact Copyright OpenHelix. No use or reproduction without express written consent25 Advanced Search Access Click here Or click here Select Advanced Search from homepage tool bar Or click the upper Search tab

26. Copyright OpenHelix. No use or reproduction without express written consent26 Advanced Search Query Page Brca2

27. Copyright OpenHelix. No use or reproduction without express written consent27 Many results An Advanced Search Example two hybrid Select Boolean Operator Select Field Enter term Click here Our new query Fewer & more specific results Add additional search terms Select Organism, Enter Human

28. Copyright OpenHelix. No use or reproduction without express written consent28 Additional Advanced Searching Methods Catalase activity # of matching interactions

29. Chemical Search Copyright OpenHelix. No use or reproduction without express written consent29 Combine search terms Search by Substructure, Similarity or Identity Draw your molecule or select a template link export

30. Copyright OpenHelix. No use or reproduction without express written consent30 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

31. Copyright OpenHelix. No use or reproduction without express written consent31 MiNe – Minimal Connecting Interaction Network Web-based application which computes the minimal connecting network for a given set of proteins, if possible Results are forwarded to Hierarch View to visualize Maximum number of proteins allowed is seven Click here Homepage left tool bar

32. Copyright OpenHelix. No use or reproduction without express written consent32 MiNe Homepage Introduction Application details Search phrases Enter search phrase EBI-1389, EBI-1765

33. Copyright OpenHelix. No use or reproduction without express written consent33 MiNe Results Results are displayed in the Hierarch View window Ontology window Don’t use

34. Copyright OpenHelix. No use or reproduction without express written consent34 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

35. Copyright OpenHelix. No use or reproduction without express written consent35 Additional Features 1. Downloading 2. Third party network visualization software http://www.psidev.info/index.php?q=node/31 3. Targets application

36. Copyright OpenHelix. No use or reproduction without express written consent36 Data Downloading PSI-MI is an XML format supported by the Human Proteome Organisation for storing and exchanging molecular interaction data Allows data to be held in multiple files which can be amalgamated On homepage Interactions view

37. Copyright OpenHelix. No use or reproduction without express written consent37 Data Download from Interactions View Open “Export to:” dropdown menu Select a format & click “Export”

38. Copyright OpenHelix. No use or reproduction without express written consent38 Data Download from Hierarch View - MiNe Tool From Hierarch View select PSI-MI TAB or PSI-MI 2.5 button on left side of window Click here

39. Copyright OpenHelix. No use or reproduction without express written consent39 PSI-MI 2.5 File XML file window opens Import into third party software

40. Copyright OpenHelix. No use or reproduction without express written consent40 Third Party Visualization Software Cytoscape- visualizes molecular interaction networks and integrates with gene expression data http://www.cytoscape.org/http://www.cytoscape.org/ PIMWalker- an interactive tool for displaying protein interaction networks http://pimr.hybrigenics.com/PIMRider/PIMRider- Categorie/PIMWALKER.html ProViz- allows for selecting of proteins by Gene Ontology Annotations but runs exclusively on the Linux operating system platform http://cbi.labri.fr/eng/proviz.htm http://cbi.labri.fr/eng/proviz.htm Access also directly from Graphs view Access also directly from Tools menu

41. Copyright OpenHelix. No use or reproduction without express written consent41 Targets Access Targets in Tools section of homepage An application to predict targets for pull-down experiments Click here Homepage left tool bar

42. Copyright OpenHelix. No use or reproduction without express written consent42 Predicting Targets for Pull-Down Experiments Click here

43. Copyright OpenHelix. No use or reproduction without express written consent43 Predicted Targets – Results RankedLinked

44. Copyright OpenHelix. No use or reproduction without express written consent44 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

45. http://www.ebi.ac.uk/intact Copyright OpenHelix. No use or reproduction without express written consent45 IntAct - A Protein Interaction Database System Tpx2 Catalase activity Basic & Advanced Search Tools

46. Copyright OpenHelix. No use or reproduction without express written consent46 Detailed Results & Access to Many Tools Help is easy to find & use Many additional tools available

47. Static network views - Graph tab Copyright OpenHelix. No use or reproduction without express written consent47 Visualize & Manipulate Protein Interaction Networks Node Interconnecting lines Customize your network view Interactive network views - Cytoscape A plethora of research applications

48. Copyright OpenHelix. No use or reproduction without express written consent48 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct: http://www.ebi.ac.uk/intact

49. Copyright OpenHelix. No use or reproduction without express written consent49