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

2. GenMAPP Gene Map Annotator and Pathway Profiler Materials prepared by: Cynthia Foote, Ph.D. and Cath Waters, Ph.D. www.openhelix.com Updated: Q1 2011 Version 1.0_0310

3. Copyright OpenHelix. No use or reproduction without express written consent3 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP: Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

4. Copyright OpenHelix. No use or reproduction without express written consent4 Expression Levels Expression Values Introduction Microarray Data Researcher wants to visualize expression in terms of the Biological Pathway

5. Copyright OpenHelix. No use or reproduction without express written consent5 GenMAPP Annotator and Pathway Profiler Expression data visualized in terms of pathway Genes contain annotation data Contains platform for creating new pathway or importing from database

6. Copyright OpenHelix. No use or reproduction without express written consent6 GenMAPP Homepage Must register at “Download GenMAPP” to obtain GenMAPP software

7. Copyright OpenHelix. No use or reproduction without express written consent7 Credits Created in lab of Bruce Conklin at Gladstone Institutes, UCSF, California Funding from NIGMS, Agilent Foundation, and NHLBI

8. Copyright OpenHelix. No use or reproduction without express written consent8 Publications http://www.nature.com/ng/journal/v31/n1/full/ng0502-19.html http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151291/?tool=pubmed

9. Copyright OpenHelix. No use or reproduction without express written consent9 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

10. Copyright OpenHelix. No use or reproduction without express written consent10 GenMAPP Please make sure that your computer system meets the minimum requirements. http://www.genmapp.org/specs_genmapp_v2.html

11. Copyright OpenHelix. No use or reproduction without express written consent11 GenMAPP Registration Login

12. Copyright OpenHelix. No use or reproduction without express written consent12 GenMAPP Download Brief Description Of GenMAPP Getting Started Resources Trouble- shooting Download

13. Copyright OpenHelix. No use or reproduction without express written consent13 GenMAPP 2.1 Tool Pathway Shown Here Main Menu Bar Pathway Drawing Tools Loaded Expression set Zoom

14. Copyright OpenHelix. No use or reproduction without express written consent14 File Types GenMAPP maintains databases of genes and pathways. Three file types are associated with the GenMAPP application Expression data (.gex) Gene databases (.gdb) Pathways (.mapp)

15. Copyright OpenHelix. No use or reproduction without express written consent15 Downloading Gene Databases Before you start using GenMAPP a database of gene identifiers for an appropriate species must be downloaded From the DATA menu choose “Download data from GenMAPP.org”

16. Copyright OpenHelix. No use or reproduction without express written consent16 Data Acquisition Tool Click here To Start

17. Copyright OpenHelix. No use or reproduction without express written consent17 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

18. Copyright OpenHelix. No use or reproduction without express written consent18 Building a Pathway Use drafting tools to create a pathway Click on icon to add it to drafting window

19. Copyright OpenHelix. No use or reproduction without express written consent19 Drafting Icons -Gene object -a Label -draw a line -inhibition symbol -receptor symbol -ligand/receptor symbol -brace -rectangle -oval -arc symbol -Object toolbox icon

20. Copyright OpenHelix. No use or reproduction without express written consent20 Adding Graphics: Add Gene and Identify 2697 Enter label for gene Add gene ID and system Left Click and Drag to Create Gene Box Right click to add annotations

21. Copyright OpenHelix. No use or reproduction without express written consent21 Adding Graphics Double left click to open backpage annotations Gene now labeled & linked to annotation

22. Copyright OpenHelix. No use or reproduction without express written consent22 Connecting Genes To delete object, drag a box around an object then press delete key Save created MAPP in GenMAPP subfolder “mapps” Click here Click and drag

23. Copyright OpenHelix. No use or reproduction without express written consent23 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

24. Copyright OpenHelix. No use or reproduction without express written consent24 Formatting your Expression Dataset Gene ID System Public DatabasesSystem Code EnsemblEn UniProt/TrEMBLS Entrez GeneL RefSeqQ Gene ID System Model Organism DatabasesSystem Code WormBaseW FlyBaseF Mouse Genome Informatics (MGI)M Rat Genome Database (RGD)R Gene ID System Gene ArraysSystem Code Affymetrix Probe Set ID (Affy)X AgilentAg

25. Copyright OpenHelix. No use or reproduction without express written consent25 Expression Dataset Manager Click here

26. Copyright OpenHelix. No use or reproduction without express written consent26 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

27. Copyright OpenHelix. No use or reproduction without express written consent27 Pathway Visualization Need to set criteria for how expression data will be displayed Averages or Fold change Set Color coding of expression parameters Different time Points have different Expression levels

28. Copyright OpenHelix. No use or reproduction without express written consent28 Open GenMAPP Expression File Open expression (.gex file) to set visualization criteria

29. Copyright OpenHelix. No use or reproduction without express written consent29 Setting Visualization Criteria

30. Copyright OpenHelix. No use or reproduction without express written consent30 Criteria Builder

31. Copyright OpenHelix. No use or reproduction without express written consent31 Next Parameter

32. Copyright OpenHelix. No use or reproduction without express written consent32 Additional Parameters Follow same procedure to add additional parameters

33. Copyright OpenHelix. No use or reproduction without express written consent33 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

34. Copyright OpenHelix. No use or reproduction without express written consent34 Loading MAPP File Expression Dataset Loaded Legend Visible Open MAPP File Hs_Contributed_20070308 > cellular_process-GenMAPP > Hs_MAPK_Cascade.mapp

35. Copyright OpenHelix. No use or reproduction without express written consent35 Pathway Visualization colorset selection menu

36. Copyright OpenHelix. No use or reproduction without express written consent36 Exporting Data

37. Copyright OpenHelix. No use or reproduction without express written consent37 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

38. Copyright OpenHelix. No use or reproduction without express written consent38 MAPPFinder Click Specify data Analysis Settings

39. Copyright OpenHelix. No use or reproduction without express written consent39 MAPPFinder Results Yellow GO terms meet filter criteria Blue GO terms found via word or Gene ID search Green GO terms found in both (none shown)

40. Copyright OpenHelix. No use or reproduction without express written consent40 MAPPBuilder creates a MAPP file (.mapp) from list of genes, can be viewed and modified with theMAPP GenMAPP Program Click to Start Select Gene List File Created MAPP

41. Copyright OpenHelix. No use or reproduction without express written consent41 Additional Advanced Options Converting MAPP files between species WikiPathways & PathVisio http://www.wikipathways.org http://www.pathvisio.org/ Creating publication quality figures Human Mouse

42. Copyright OpenHelix. No use or reproduction without express written consent42 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

43. Copyright OpenHelix. No use or reproduction without express written consent43 GenMAPP: Pathway Visualization of Data Import existing pathway diagrams Create new pathway diagrams Add your expression data to a biological pathway Highlight genes of interest

44. Copyright OpenHelix. No use or reproduction without express written consent44 MAPPFinder Integrates Gene Ontology annotations with GenMAPP Are Searchable

45. Copyright OpenHelix. No use or reproduction without express written consent45 MAPPBuilder accessory application that automatically creates a MAPP file from a list of genes Created MAPP

46. Copyright OpenHelix. No use or reproduction without express written consent46 Medical Relevance Publications using GenMAPP to visualize expression data in human embryonic and adult tissues http://www.genmapp.org/showcase.html

47. Copyright OpenHelix. No use or reproduction without express written consent47 GenMAPP Introduction and Credits Downloading GenMAPP, databases and files Creating and Customizing MAPP files Creating a GenMAPP Expression Dataset Setting Visualization Criteria Visualizing Expression Data on Pathways Advanced Functions Summary Exercises GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org http://www.genmapp.org

48. Copyright OpenHelix. No use or reproduction without express written consent48