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

2. GoMiner Biological Interpretation of Genomic & Proteomic Data Materials prepared by: Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q3 2010 Version 1

3. Copyright OpenHelix. No use or reproduction without express written consent3 GoMiner Agenda Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises GoMiner: http://discover.nci.nih.gov/gominer/

4. Copyright OpenHelix. No use or reproduction without express written consent4 GoMiner Homepage Functional annotation by GO terms Two main tools Original GUI GoMiner must be downloaded High- Throughput GoMiner is web- based Command-line options, visualization tools Statistical analysis, links http://discover.nci.nih.gov/gominer/ Results in tree & DAG formats Statistical analysis & links High-Throughput GoMiner access

5. Copyright OpenHelix. No use or reproduction without express written consent5 High-Throughput GoMiner Homepage Click here A Clustered Image Map (CIM) using CIMminer Shows genes with altered expression vs. GO categories See a “molecular phenotype”

6. Copyright OpenHelix. No use or reproduction without express written consent6 Original & High-Throughput GoMiner High-throughput GoMiner is a companion to the original version Web-based High-Throughput GoMiner may offer some advantages Original version More advances here: batch processing rank-ordering, CIMs, FDR calculations, transcription factor binding sites http://discover.nci.nih.gov/gominer/relationship.jsp

7. Copyright OpenHelix. No use or reproduction without express written consent7 GoMiner Provides Detailed Data Links, statistics, rank-ordered, can get in Excel One of many types of data made available to you Links to AmiGO & Entrez Gene Rank-ordered & statistical analysis

8. Copyright OpenHelix. No use or reproduction without express written consent8 Graphical Process Overview of Web-based GoMiner 1. Configuration 2. Quality assurance 3. GoMiner execution 4. Random-gene file generation 5. Mapping genes to GO categories 6. Result integration 7. Email notification of results

9. Copyright OpenHelix. No use or reproduction without express written consent9 GoMiner Team & Contact Information Email Original developers

10. Copyright OpenHelix. No use or reproduction without express written consent10 GoMiner Citations

11. Copyright OpenHelix. No use or reproduction without express written consent11 GoMiner Agenda Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Custered Image Maps Summary Exercises GoMiner: http://discover.nci.nih.gov/gominer/

12. Copyright OpenHelix. No use or reproduction without express written consent12 Differential Gene Expression Studies 225 genes up-regulated 46 genes down-regulated vs. “normal” 300 genes up-regulated 24 genes down-regulated vs. “normal” Normal Heart Heart Failure Type 1 Heart Failure Type 2 Differential gene expression results:

13. Copyright OpenHelix. No use or reproduction without express written consent13 Biological Significance of Results What does it all mean biologically? No need for a gene by gene analysis! Treatment X Treatment Y 50 genes up-regulated 32 genes down-regulated by treatment X 38 genes up-regulated 84 genes down-regulated by treatment Y 4X more Treatment X Serial analysis of expression Heart Failure Type 1 Differential gene expression results:

14. Copyright OpenHelix. No use or reproduction without express written consent14 Limitless Experimental Applications of GoMiner Examples include growth, diseases, toxicology, temporal & spatial profiles, mutants, RNA interference and more!  Ascribe functional significance to your results  Use with ANY list of “interesting” genes you choose

15. Copyright OpenHelix. No use or reproduction without express written consent15 The Importance of Gene Ontology Annotation To access GO http://www.geneontology.org/ AmiGO is GO browser Read more

16. Copyright OpenHelix. No use or reproduction without express written consent16 There Are Three GO Vocabularies

17. Terms not included in GO hierarchy Functions outside of GO’s mission Copyright OpenHelix. No use or reproduction without express written consent17 What Go is NOT

18. Copyright OpenHelix. No use or reproduction without express written consent18 Ontologies Are Hierarchical Relationships  Clicking on “+” expands tree  More specialized terms-“child”  Less specialized terms-“parent”  Terms can have more than one “parent” More specific A “child” More specific Less specific http://bioportal.bioontology.org/

19. Copyright OpenHelix. No use or reproduction without express written consent19 GoMiner Data is Organized Similarly More specific GoMiner provides color- coded results and statistics

20. Copyright OpenHelix. No use or reproduction without express written consent20 Annotate and Cluster Afflicted Genes by GO Normal Heart Heart Failure GoMiner results may show: Overexpressed genes control cell calcium Important biological questions GoMiner Analysis += Answers! + GO Annotation What Genes Differ? Underexpressed genes regulate apoptosis

21. Copyright OpenHelix. No use or reproduction without express written consent21 GoMiner Agenda Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises GoMiner: http://discover.nci.nih.gov/gominer/

22. Copyright OpenHelix. No use or reproduction without express written consent22 Understanding & Utilizing Navigation Menus GoMiner navigation bar High-Throughput GoMiner navigation bar includes a second row of options This is the section we will focus on to get started Some of this information should be explored, depending on your needs Click here

23. Copyright OpenHelix. No use or reproduction without express written consent23 Choosing Your GoMiner Tool  Many requirements are similar between the two Original GoMiner, must download Web-based High- Throughput GoMiner Both have command -line interfaces

24. Windows 98 or Mac OS X or above We will show Windows XP Copyright OpenHelix. No use or reproduction without express written consent24 System Requirements Links to help you set up

25. Copyright OpenHelix. No use or reproduction without express written consent25 Input File Format Generally, need a total gene file and one or more changed gene files (but auto-generation option to produce a total gene file) Can upload a zip archive of multiple changed gene files Use.txt (single files) or.zip (zip archives), order does matter Click here for examples of input files

26. Copyright OpenHelix. No use or reproduction without express written consent26 Examples of Input Files For changed gene files you can use “-1” or “1” for expression changes All genesChanged genes

27. Copyright OpenHelix. No use or reproduction without express written consent27 MatchMiner Can Translate Gene IDs http://discover.nci.nih.gov/matchminer/index.jsp GoMiner can take input identifiers other than gene names Works with all included in GO Consortium database Lookup options in search form MatchMiner can translate gene IDs

28. Copyright OpenHelix. No use or reproduction without express written consent28 GoMiner Agenda GoMiner: http://discover.nci.nih.gov/gominer/ Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises

29. Copyright OpenHelix. No use or reproduction without express written consent29 Original GUI GoMiner http://discover.nci.nih.gov/gominer/ Click to download

30. Copyright OpenHelix. No use or reproduction without express written consent30 Beginning to Use GUI GoMiner Start Up Panel will appear when you open to help you

31. Copyright OpenHelix. No use or reproduction without express written consent31 Opening GUI GoMiner Click here Use to generate a list of genes status bar

32. Copyright OpenHelix. No use or reproduction without express written consent32 Results-Input Summary & Genes Mapped on GO Key Options Underexpressed Overexpressed Unchanged Total genes/category, relative enrichment, color-coded, statistics ↔ ↔

33. Copyright OpenHelix. No use or reproduction without express written consent33 Results Summary ↔ False Discovery Rate statistics- ranked by most enriched GO categories Most Enriched

34. Copyright OpenHelix. No use or reproduction without express written consent34 Link Out to Many Resources Click on a gene to link out Expanded view

35. Copyright OpenHelix. No use or reproduction without express written consent35 Selected Gene View & Additional Options

36. Copyright OpenHelix. No use or reproduction without express written consent36 Exporting your Data, Maps & Visualization Tools Click to highlight, right click for menu

37. Copyright OpenHelix. No use or reproduction without express written consent37 Original GUI GoMiner: Tip Double click to run Right click here Type Save and close RenameRight click gominer.jar space –Xmx900m

38. Copyright OpenHelix. No use or reproduction without express written consent38 GoMiner Agenda GoMiner: http://discover.nci.nih.gov/gominer/ Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises

39. Copyright OpenHelix. No use or reproduction without express written consent39 Submitting Your Data Select Web Interface from High-Throughput navigation bar Have your files prepared to upload GoMiner has set defaults applicable for most users Top: upload files; select data source; organism; evidence code Bottom: lookup settings; statistical parameters; email address Select High-Throughput Go to “Web Interface” for this input form

40. Copyright OpenHelix. No use or reproduction without express written consent40 Selecting Your Total Gene File Let’s take a closer look at the Auto-Generate option Total file selection

41. Copyright OpenHelix. No use or reproduction without express written consent41 Auto-Generate Function for a Total Genes Files Not needed: total genes represented in the genome Needed: only a list of “interesting” genes, for example Needed: arrays skewed towards a particular GO category (onco-chip with excessive representation of signal transduction genes) Auto-generation of a total genes list can be useful

42. Copyright OpenHelix. No use or reproduction without express written consent42 Steps 2, 3 & 4 Changed gene file Data Source & Organism

43. Copyright OpenHelix. No use or reproduction without express written consent43 Evidence Codes Evidence Levels IDA NAS

44. Copyright OpenHelix. No use or reproduction without express written consent44 Lookup Settings Even more info in FAQs Lookup Settings

45. Copyright OpenHelix. No use or reproduction without express written consent45 Statistical Selections, FDRs & P Values Statistical Selections Find info in FAQs and manuscripts

46. Copyright OpenHelix. No use or reproduction without express written consent46 CIM, Root Category, TF Binding & Submission CIMs Root Category TF Binding Your Email Submit

47. Copyright OpenHelix. No use or reproduction without express written consent47 Results Sent Back by Email NOTE: Results deleted in three days 954403031

48. Copyright OpenHelix. No use or reproduction without express written consent48 GoMiner HTML Display of Results Analysis Input Summary Link to zip files Result Summaries Link to result displays

49. Copyright OpenHelix. No use or reproduction without express written consent49 Access to Individual Result Displays

50. Copyright OpenHelix. No use or reproduction without express written consent50 Detailed Output Descriptions Access output details in High- Throughput navigation bar under Output Files The top gives you general output information Debug information at bottom Then select Output Files General output info Debug info Select High-Throughput

51. Copyright OpenHelix. No use or reproduction without express written consent51 GoMiner Agenda GoMiner: http://discover.nci.nih.gov/gominer/ Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises

52. Copyright OpenHelix. No use or reproduction without express written consent52 Clustered Image Maps You can access CIM image tool from GoMiner homepage Select “High-Throughput” and then “Using CIMminer” Enter data here or click to CIMminer’s homepage Enter your data here or at CIMminer’s homepage

53. Copyright OpenHelix. No use or reproduction without express written consent53 Generate Clustered Image Maps Using CIMminer CIMminer is a complimentary tool developed by same group Let’s try an example using the One Matrix CIM http://discover.nci.nih.gov/cimminer/ Click here

54. Copyright OpenHelix. No use or reproduction without express written consent54 Submitting Your Data to CIMminer Our example will use the One Matrix CIM and their sample file option Select input, enter address, choose algorithm and click on Submit Click here Enter Email Click here Help scientist@openhelix.com

55. Copyright OpenHelix. No use or reproduction without express written consent55 CIMminer Results Results Emailed Click here Image controls

56. Copyright OpenHelix. No use or reproduction without express written consent56 GoMiner Agenda GoMiner: http://discover.nci.nih.gov/gominer/ Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises

57. Copyright OpenHelix. No use or reproduction without express written consent57 Summary Ascribe biological significance to ANY list of genes by adding GO annotation http://discover.nci.nih.gov/gominer/

58. Copyright OpenHelix. No use or reproduction without express written consent58 Tools To Meet Your Needs Classic GoMiner: downloadable GUI version High-Throughput GoMiner: large datasets; serial analysis; CIMs

59. Copyright OpenHelix. No use or reproduction without express written consent59 GoMiner Agenda GoMiner: http://discover.nci.nih.gov/gominer/ Introduction and Credits Biological Significance Getting Started GUI GoMiner High-Throughput GoMiner Clustered Image Maps Summary Exercises

60. Copyright OpenHelix. No use or reproduction without express written consent60