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

2. Pathway Interaction Database (PID) Materials prepared by: Karin Schinkmann, Ph.D. www.openhelix.com Updated: Q3 2010 Version 2

3. Copyright OpenHelix. No use or reproduction without express written consent3 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

4. Copyright OpenHelix. No use or reproduction without express written consent4 PID Overview  National Cancer Institute: http://www.cancer.gov/  Nature Publishing Group: http://www.nature.com/npghttp://www.nature.com/npg

5. Copyright OpenHelix. No use or reproduction without express written consent5 PID Introduction Summary Stats Searches Pathway Updates: Recently Added Highlights Primers E-alert & Feedback Navigation Bar: PID tools Updates About PID Help

6. Copyright OpenHelix. No use or reproduction without express written consent6 Navigation Menu http://pid.nci.nih.gov/PID/archive/2006/11/primer.shtml

7. Copyright OpenHelix. No use or reproduction without express written consent7 Navigation Menu, cont. E-alert – monthly RSS feed - frequently updated

8. Copyright OpenHelix. No use or reproduction without express written consent8 Links Related Links NCI Resources Nature Resources

9. Copyright OpenHelix. No use or reproduction without express written consent9 PID Data Content  NCI/Nature – curated data (ongoing) - reviewed by experts - annotated with UniProt identifiers, post-translational modifications, evidence codes, and references  BioCarta – imported data (June 2004) - not reviewed by experts - annotated with Entrez Gene Identifiers, no post- translational modifications, evidence codes, or references  Reactome-imported data (December 2007) - annotated with UniProt identifiers, post- translational modification, and references

10. Copyright OpenHelix. No use or reproduction without express written consent10 PID Credits and Citation http://pid.nci.nih.gov/PID/about.shtml#pid PID Team Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay & Kenneth H. Buetow. PID: The Pathway Interaction Database. Nucleic Acids Res. 37, D674-9 (2009) http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D674 Citing PID

11. Copyright OpenHelix. No use or reproduction without express written consent11 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

12. Copyright OpenHelix. No use or reproduction without express written consent12 Predefined Pathway Search Browse pathways by data source Insulin Pathway

13. Copyright OpenHelix. No use or reproduction without express written consent13 Predefined Pathway Search: Top Feedback Information Graphic Display Key to Icons

14. Copyright OpenHelix. No use or reproduction without express written consent14 Predefined Pathway Search: Top Molecule list Individual molecules Complexes of molecules References Links to PubMed

15. Copyright OpenHelix. No use or reproduction without express written consent15 PID Graphics: Output Two Graphic Formats  JPG (Joint Photographic Experts Group) - Default - Compatible with all browsers  SVG (Scalable Vector Graphics) - Easier to zoom and pan - Free Adobe plug-in is available: http://www.adobe.com/svg/viewer/install/main.html Two text formats  XML (Extensible Markup Language) - used to exchange data across different systems  BioPax (Biological Pathways exchange) - used to exchange data across different pathway databases

16. Copyright OpenHelix. No use or reproduction without express written consent16 Predefined Pathway Search: Key to Icons

17. Copyright OpenHelix. No use or reproduction without express written consent17 Predefined Pathway Search: Interactive Graphic Click for SVG view

18. Copyright OpenHelix. No use or reproduction without express written consent18 Predefined Pathway Search: Results Identifiers Participants Evidence Pathways Molecule Page Identifiers Complexes Roles Molecular Functions 18

19. Copyright OpenHelix. No use or reproduction without express written consent19 Basic Searches Summary  PID Basic Queries for pre-defined pathways result in a highly structured interactive pathway graphic.  On the graphic display you can identify - Components of pathways and complexes - Types of interaction a molecule participates in - Subcellular location - Determine the role of a molecule in an interaction  On the graphic display you can access - List of molecules and references - Interaction page - Molecule use page - Molecule page

20. Copyright OpenHelix. No use or reproduction without express written consent20 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

21. Copyright OpenHelix. No use or reproduction without express written consent21 PID Search Database: Identifiers Molecule Names and IDs: Any alias listed in Entrez Gene UniProt accession number HUGO gene symbol Entrez Gene ID CAS number Biological Process IDs: Gene Ontology terms GO identifiers (format: GO 0000000) NCI thesaurus terms and identifiers Simple Searches for molecule names and IDs and biological processes can be performed using the following identifiers :

22. Copyright OpenHelix. No use or reproduction without express written consent22 Database Search: Molecule Name/ID GO

23. Copyright OpenHelix. No use or reproduction without express written consent23 Search Result Summary Page Molecule Name/ID Search Results Data from BioCarta No Data from Reactome Data from NCI/Nature

24. Copyright OpenHelix. No use or reproduction without express written consent24 Search Result Summary Page Molecule Name/ID Search Results, cont. Output formats

25. Copyright OpenHelix. No use or reproduction without express written consent25 Database Search: Wildcards How to wildcard: -*integrins* - ras** * Enter wildcard GO

26. Copyright OpenHelix. No use or reproduction without express written consent26 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

27. Copyright OpenHelix. No use or reproduction without express written consent27 Advanced Search Page, Top

28. Copyright OpenHelix. No use or reproduction without express written consent28 Advanced Search Page, Lower

29. Copyright OpenHelix. No use or reproduction without express written consent29 Advanced Search Example Default p53 DNA repair Default SVG GO

30. Copyright OpenHelix. No use or reproduction without express written consent30 Advanced Search Results Molecule Use page Interaction page

31. Copyright OpenHelix. No use or reproduction without express written consent31 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

32. Copyright OpenHelix. No use or reproduction without express written consent32 Connected Molecules Search P53, MKK2 SVG GO NCI/Nature

33. Copyright OpenHelix. No use or reproduction without express written consent33 Connected Molecules Search Results Access to - interaction pages - molecule use pages - molecule pages

34. Copyright OpenHelix. No use or reproduction without express written consent34 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

35. Copyright OpenHelix. No use or reproduction without express written consent35 PID Batch Query 1: Search Page Go Select View Upload files Select Data Source

36. Copyright OpenHelix. No use or reproduction without express written consent36 Batch Query 1: Results P-value ranks pathways according to the probability that they include biomolecules from the query list. The lower the p-value the greater the probability that the query list is biased towards a given pathway. The pathway list is sorted by increasing P- values.

37. Copyright OpenHelix. No use or reproduction without express written consent37 Batch Query 1 Results, cont. Information Graphic Display Key to Icons Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

38. Copyright OpenHelix. No use or reproduction without express written consent38 Batch Query 2 Go Complete network map Upload files Select data source Complete network map

39. Copyright OpenHelix. No use or reproduction without express written consent39 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

40. Copyright OpenHelix. No use or reproduction without express written consent40 PID Download Data Download data Two download formats: PID XML and BioPAX NCI-Nature data PID XML

41. Copyright OpenHelix. No use or reproduction without express written consent41 Download Data, cont. 1. Save file 2. Open gz file 3. Extract data 4. View file

42. Copyright OpenHelix. No use or reproduction without express written consent42 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

43. Copyright OpenHelix. No use or reproduction without express written consent43 PID Summary Data sources: - NCI/Nature curated - BioCarta-imported - Reactome-imported

44. Copyright OpenHelix. No use or reproduction without express written consent44 PID Summary, Queries PID-supported queries: - pre-defined pathways - searches for molecule name/IDs, biological pathway name/IDs, and wildcards - advanced searches - connected molecule searches - batch queries

45. Copyright OpenHelix. No use or reproduction without express written consent45 PID Summary, Other Resources

46. Copyright OpenHelix. No use or reproduction without express written consent46 PID Agenda Introduction and Credits Basic Search Database Search Advanced Search Connected Molecule Search Batch Query Download Data Summary Exercises Pathway Interaction Database http://pid.nci.nih.gov/PID/index.shtml

47. Copyright OpenHelix. No use or reproduction without express written consent47