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

2. DAVID Database for Annotation, Visualization and Integrated Discovery Materials prepared by: Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q2 2010 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

4. Homepage access: Copyright OpenHelix. No use or reproduction without express written consent4 Introduction DAVID Database of Annotation, Visualization, and Integrated Discovery free, web-based bioinformatics tool extracts biological meaning from genes covers all species developed by Lempicki & colleagues (NIAID) 2003 2009 http://www.ncbi.nlm.nih.gov/pubmed/19131956?dopt=Abstract http://www.ncbi.nlm.nih.gov/pubmed/12734009?dopt=Abstract

5. Copyright OpenHelix. No use or reproduction without express written consent5 Making Sense of Large Gene Lists 1456 genes upregulated 2846 genes downregulated microarray but what does it all mean? secreted proteins defensive response involved in

6. Copyright OpenHelix. No use or reproduction without express written consent6 DAVID Gene Concept UniProt: P84215 UniProt: Q73415 SwissProt: ABC UniProt PIR RefSeq: NM_2355 UniProt: N66532 GenPep: AA63554 Entrez-Gene Gene: ABC1 SwissProt: ABC GO: cytoplasm GO: limb development GO: kinase UniProt: 58896 RefSeq: NM_500456 RefSeq: NM_2355 DAVID gene UniProt: P84215 UniProt: Q73415 Gene: ABC1 SwissProt: ABC GO: cytoplasm GO: limb development GO: kinase UniProt: 58896 RefSeq: NM_500456 RefSeq: NM_2355 UniProt: N66532 GenPep: AA63554 Most complete set of annotations

7. Copyright OpenHelix. No use or reproduction without express written consent7 90 Million Annotations! Taken from: Sherman et al., BMC Bioinformatics (2007) 8: 426 40 million from Ontologies, such as GO

8. Copyright OpenHelix. No use or reproduction without express written consent8 DAVID Homepage http://david.abcc.ncifcrf.gov/

9. Copyright OpenHelix. No use or reproduction without express written consent9 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

10. Copyright OpenHelix. No use or reproduction without express written consent10 Starting DAVID http://david.abcc.ncifcrf.gov/

11. Copyright OpenHelix. No use or reproduction without express written consent11 Upload a Gene List Tab delimited text file how to make a file “Save As...”

12. Copyright OpenHelix. No use or reproduction without express written consent12 Upload a Gene List, continued numerous gene ID options or “Not Sure” or official gene symbols

13. Copyright OpenHelix. No use or reproduction without express written consent13 Pre-Loaded Affymetrix Background Lists Background Chip Options Scroll to:

14. Copyright OpenHelix. No use or reproduction without express written consent14 Resveratrol Example >300 genes tab-delimited text file (.txt) www.ctd.mdibl.org

15. Copyright OpenHelix. No use or reproduction without express written consent15 Selecting Species and Renaming the File

16. Copyright OpenHelix. No use or reproduction without express written consent16 Show Gene List detailed gene report functionally related genes

17. Copyright OpenHelix. No use or reproduction without express written consent17 Which Tool?

18. Copyright OpenHelix. No use or reproduction without express written consent18 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

19. Copyright OpenHelix. No use or reproduction without express written consent19 click Annotation Categories Disease General Literature Pathways Protein Domains Protein Interactions

20. Copyright OpenHelix. No use or reproduction without express written consent20 Functional Annotation Tool default Click here

21. Copyright OpenHelix. No use or reproduction without express written consent21 GO Category Details 314 325 = 96.6% OPTION : select different levels of GO BP_4 BP_3 BP_2 BP_1 GO-BP Levels

22. Copyright OpenHelix. No use or reproduction without express written consent22 GO Category Details, part 2 list of all 314 genes

23. Copyright OpenHelix. No use or reproduction without express written consent23 Functional Annotation Chart (for a Category) Related Terms Genes that have this GO-BP annotation

24. Copyright OpenHelix. No use or reproduction without express written consent24 Functional Annotation Options at least 2 genes must be annotated to the term range = 0 - 1 (lower = more enriched) additional statistical display options

25. Copyright OpenHelix. No use or reproduction without express written consent25 Show Me All the Annotations! lists all annotations from every selected category

26. Copyright OpenHelix. No use or reproduction without express written consent26 Functional Annotation Chart (Total) Page 1...... Page 2 > 1,600 annotations

27. Copyright OpenHelix. No use or reproduction without express written consent27 Functional Annotation Clustering

28. Copyright OpenHelix. No use or reproduction without express written consent28 Functional Annotation Clustering Results Enrichment Scores “apoptosis” annotations clustered into functional groups

29. Copyright OpenHelix. No use or reproduction without express written consent29 Functional Annotation Clustering Details Genes associated with term Genes associated with Cluster 1

30. Copyright OpenHelix. No use or reproduction without express written consent30 Functional Annotation Clustering Options edit threshold levels to change stringency and clustering parameters

31. Copyright OpenHelix. No use or reproduction without express written consent31 Heat Maps 6 annotations15 genes click

32. Copyright OpenHelix. No use or reproduction without express written consent32 Heat Map Display 15 genes 6 annotations

33. Copyright OpenHelix. No use or reproduction without express written consent33 Making Biological Sense resveratrol >300 genes DAVID

34. Copyright OpenHelix. No use or reproduction without express written consent34 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

35. Copyright OpenHelix. No use or reproduction without express written consent35 Gene Functional Classification Tool click

36. Copyright OpenHelix. No use or reproduction without express written consent36 Gene Functional Classification Results clusters genes into functional groups edit threshold levels to change stringency and clustering parameters

37. Copyright OpenHelix. No use or reproduction without express written consent37 Gene Functional Classification Icons Gene Report heat map Related Genes Term Report

38. Copyright OpenHelix. No use or reproduction without express written consent38 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

39. Copyright OpenHelix. No use or reproduction without express written consent 39 Create a Sublist new sublist

40. Copyright OpenHelix. No use or reproduction without express written consent40 Gene ID Conversion Tool click

41. Copyright OpenHelix. No use or reproduction without express written consent41 Gene ID Conversion Results inputoutput

42. Copyright OpenHelix. No use or reproduction without express written consent42 Gene Name Batch Viewer

43. Copyright OpenHelix. No use or reproduction without express written consent43 Gene Name Batch Viewer Gene List upload list

44. Copyright OpenHelix. No use or reproduction without express written consent44 Gene Name Batch Viewer Results

45. Copyright OpenHelix. No use or reproduction without express written consent45 Pathway Viewer = genes in your list

46. Copyright OpenHelix. No use or reproduction without express written consent46 Disease Analysis GAD OMIM GAD_CLASS

47. Copyright OpenHelix. No use or reproduction without express written consent47 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

48. Copyright OpenHelix. No use or reproduction without express written consent48 DAVID: Gene Lists --> Annotations Extracts Annotations Annotations http://david.abcc.ncifcrf.gov/

49. Copyright OpenHelix. No use or reproduction without express written consent49 DAVID: Discover the Biology > 1600 Annotations > 100 Functional Clusters Group Annotations into Functional Clusters apoptosis cell cycle development

50. Copyright OpenHelix. No use or reproduction without express written consent50 DAVID: Convert IDs --> Symbols --> Clusters 120 Gene Symbols Convert IDs into Symbols 3 Gene Clusters Gene Lists into Gene Clusters

51. Genes Copyright OpenHelix. No use or reproduction without express written consent51 DAVID: Integrated Data, Seamless Navigation

52. Copyright OpenHelix. No use or reproduction without express written consent52 DAVID: Visualize Data in a New Way Heat Maps Pathway Maps

53. Copyright OpenHelix. No use or reproduction without express written consent53 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID: http://david.abcc.ncifcrf.gov/

54. Copyright OpenHelix. No use or reproduction without express written consent54