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

2. MINT MINT: providing a collection of databases to analyze and display molecular interaction data Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q2 2011 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

4. Copyright OpenHelix. No use or reproduction without express written consent4 A collection of molecular interaction databases: MINT Focus: Molecular Interaction Data HomoMINT Inferred network Domino Domain Interactions SH3 P-X-X-P VirusMINT Viral Interactions A B Protein-Protein MINT C MINT homepage: http://mint.bio.uniroma2.it/mint

5. Copyright OpenHelix. No use or reproduction without express written consent5 MINT Content & Organization MINT captures curated protein interaction information from literature & direct user submission Uses the IntAct database relational data model Allows for tool compatibility with IntAct Shared curation efforts

6. Copyright OpenHelix. No use or reproduction without express written consent6 Interactions Represented Graphically runs as a JAVA applet, may require download of JAVA 2, Mac users should use Safari browser for better compatibility Center node represents selected protein, interconnecting lines show interactions to other proteins Interconnecting Line Interactor

7. Copyright OpenHelix. No use or reproduction without express written consent7 MINT Homepage Navigation & Features Search page MINT homepage: http://mint.bio.uniroma2.it/mint Curation Statistics Download News, RSS feed Links Member organizations Navigation

8. Copyright OpenHelix. No use or reproduction without express written consent8 Additional Features Open Source software system hosted on SourceForge Data downloading in PSI-MI formats, flat file, & Osprey Choose format Download

9. Copyright OpenHelix. No use or reproduction without express written consent9 Credits & Publication Information The MINTers : Contact/Links/Linking Citation : Citation http://nar.oxfordjournals.org/content/38/suppl_1/D532.long

10. Copyright OpenHelix. No use or reproduction without express written consent10 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

11. MINT homepage: http://mint.bio.uniroma2.it/mint Copyright OpenHelix. No use or reproduction without express written consent11 MINT Search & Results Click here

12. Copyright OpenHelix. No use or reproduction without express written consent12 MINT Search Page Accepts UniProt, Ensembl, FlyBase, SGD, WormBase, OMIM, HUGE & Reactome accession numbers Gja1 MINT/IMEx ID search Click here

13. Copyright OpenHelix. No use or reproduction without express written consent13 MINT Protein Name Search Click here Or here List of all proteins with that gene name Toggle open

14. Copyright OpenHelix. No use or reproduction without express written consent14 MINT Search Results Protein Details Domains 2 interaction partners Interaction given a score GO terms Other accessions Keywords Domain prediction Protein orthologs Scroll to Table Key Disease link

15. Copyright OpenHelix. No use or reproduction without express written consent15 Publication Search Only shows curated references 17318185 Click here

16. Copyright OpenHelix. No use or reproduction without express written consent16 PubMed ID Search Results Reference details # of Experiments Detection methods MINT interaction #

17. Copyright OpenHelix. No use or reproduction without express written consent17 Additional Search Features Search for interaction with list of proteins Input sequence & Blast against proteins present in MINT Search for an interaction involving a list of proteins (100 or less) Input sequence & Blast against MINT database proteins

18. Copyright OpenHelix. No use or reproduction without express written consent18 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

19. Copyright OpenHelix. No use or reproduction without express written consent19 Accessing MINT Viewer Click here

20. Copyright OpenHelix. No use or reproduction without express written consent20 Mint Viewer New window on right shows graphical representation of interaction network Only interaction partners shown

21. Copyright OpenHelix. No use or reproduction without express written consent21 MINT Viewer Window Move bar to move proteins out away from each other Red = center, - circle indicates expanded node Number of times that interaction has been recorded Move bar to make circles around protein names larger or smaller Click for score calculation info + circle indicates node not fully expanded Move bar to see only interactions that meet set threshold

22. Copyright OpenHelix. No use or reproduction without express written consent22 MINT Viewer Tool Bar Opens score window for interaction To download visible interactions in flat file or PSI Freeze/Unfreeze a proteinHelp window

23. Copyright OpenHelix. No use or reproduction without express written consent23 MINT Viewer Options Click to change protein at center of the network Right click to delete protein Get deleted proteins back by clicking on +

24. Copyright OpenHelix. No use or reproduction without express written consent24 MINT Viewer Options - Connect Click on connect A “connected” network of interactions Click on +

25. Copyright OpenHelix. No use or reproduction without express written consent25 Expanding Interaction Network Expanded network by clicking on + Proteins can be moved by clicking & dragging mouse Click on - to shrink network back again Key to color-coding in Help

26. Copyright OpenHelix. No use or reproduction without express written consent26 Show Protein Information Window opens for selected protein Show interaction info by clicking on circle on line Click on protein

27. Copyright OpenHelix. No use or reproduction without express written consent27 Show Interaction Details Lists interaction type, methods & PubMed ID Window opens with interaction details

28. Copyright OpenHelix. No use or reproduction without express written consent28 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

29. MINT homepage: http://mint.bio.uniroma2.it/mint Copyright OpenHelix. No use or reproduction without express written consent29 HomoMINT Access Click here

30. Copyright OpenHelix. No use or reproduction without express written consent30 HomoMINT Homepage Search for inferred human network from verified model organism networks Download text file of HomoMINT datasets Download Search

31. Copyright OpenHelix. No use or reproduction without express written consent31 HomoMINT Search Enter human protein or gene name Accepts UniProtKB, Ensembl, OMIM, HUGE, Reactome accession numbers SNAP25 Click here

32. Copyright OpenHelix. No use or reproduction without express written consent32 HomoMINT Search Results Lists proteins with SNAP25 in protein name or gene name Toggle open for more details Click here

33. Copyright OpenHelix. No use or reproduction without express written consent33 HomoMINT Protein Details Protein details window Interaction details window Click here Evidence/ Inference Scroll to Table Key

34. SNAP25 interaction graphic Copyright OpenHelix. No use or reproduction without express written consent34 HomoMINT Viewer

35. Copyright OpenHelix. No use or reproduction without express written consent35 HomoMINT Viewer Options Allows user to view inferences from selected species or taxonomic groups Note: other functions are the same as in the MINT database Now fewer interaction partners Uncheck

36. Copyright OpenHelix. No use or reproduction without express written consent36 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

37. Copyright OpenHelix. No use or reproduction without express written consent37 Domino Access Click here MINT homepage: http://mint.bio.uniroma2.it/mint

38. Copyright OpenHelix. No use or reproduction without express written consent38 Domino Homepage Database contains interaction information for peptide domains of proteins Database focuses on these domains Domain list Species Yes1 Protein name

39. Copyright OpenHelix. No use or reproduction without express written consent39 Domino Search Results Protein infoDomain info Use to exclude or show interactions mediated by selected domain Check to select whole protein Use to consider or exclude a selected detection method Check to select domain check Click here

40. Copyright OpenHelix. No use or reproduction without express written consent40 Domino Interaction Results Domain graphic Protein title Score Experimental method Domain name

41. Copyright OpenHelix. No use or reproduction without express written consent41 Domino Interaction Results, cont. hide

42. Copyright OpenHelix. No use or reproduction without express written consent42 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

43. MINT homepage: http://mint.bio.uniroma2.it/mint Copyright OpenHelix. No use or reproduction without express written consent43 VirusMINT Access Click here

44. VirusMINT homepage: http://mint.bio.uniroma2.it/virusmint/Welcome.do Copyright OpenHelix. No use or reproduction without express written consent44 VirusMINT Homepage Description of VirusMINT Click

45. Copyright OpenHelix. No use or reproduction without express written consent45 Viral Interactomes Click MCM3 Click PB2

46. Copyright OpenHelix. No use or reproduction without express written consent46 Viral Interactomes, cont. Fewer connections

47. Copyright OpenHelix. No use or reproduction without express written consent47 ViralMINT Advanced Search PubMed Search Search by protein name or ID click Our example: “ICP0” in all species ICP0 Select species

48. Copyright OpenHelix. No use or reproduction without express written consent48 ViralMINT Search Results Human Virus Click

49. Copyright OpenHelix. No use or reproduction without express written consent49 ViralMINT Viewer Click “+” Click

50. Copyright OpenHelix. No use or reproduction without express written consent50 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

51. Copyright OpenHelix. No use or reproduction without express written consent51 MINT Database IMEx Molecular INTeraction (MINT) Database Conforms to IMEx, PSI-ME and MIMIex standards

52. Copyright OpenHelix. No use or reproduction without express written consent52 MINT Data and Displays High quality data, interactive displays

53. Copyright OpenHelix. No use or reproduction without express written consent53 MINT Sister Databases Each uses MINT viewer to display interaction networks Allows easy manipulation of proteins and network A virus protein interactions database An inferred human network A domain peptide interactions database

54. Copyright OpenHelix. No use or reproduction without express written consent54 MINT Agenda Introduction & Credits MINT Search & Results MINT Viewer HomoMINT Domino VirusMINT Summary Exercises MINT: http://mint.bio.uniroma2.it/mint

55. Copyright OpenHelix. No use or reproduction without express written consent55