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

2. CGAP from NCI The Cancer Genome Anatomy Project Materials prepared by: Cynthia Perreault-Micale, Ph.D. Dorothy S. Reilly, Ph.D. www.openhelix.com Updated: Q4 2010 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

4. Gene Expression in Normal & Cancerous Cells increase in gene expression decrease in gene expression altered protein product Normal cell:Cancerous cell: Relative gene expression: ?

5. Copyright OpenHelix. No use or reproduction without express written consent5 CGAP Data Sources SAGE Atomic Viewer mSAGE Expression Matrix

6. Copyright OpenHelix. No use or reproduction without express written consent6 CGAP Resources & Tools

7. Copyright OpenHelix. No use or reproduction without express written consent7 CGAP Credits Team Members

8. http://www.ncbi.nlm.nih.gov/CGAP/ Copyright OpenHelix. No use or reproduction without express written consent8 CGAP at NCBI & NCI Access to CGAP Visit CGCI The Cancer Genome Characterization Initiative

9. Copyright OpenHelix. No use or reproduction without express written consent9 Cancer Research 59:5403, 1999 http://cancerres.aacrjournals.org/cgi/content/full/59/21/5403 CGAP Publications Hum.Mol.Genet. 10:663, 2001 http://hmg.oxfordjournals.org/cgi/content/full/10/7/663 PNAS 99:11287, 2002 http://www.pnas.org/cgi/content/full/99/17/11287 NAR 33:W693, 2005 http://nar.oxfordjournals.org/cgi/content/full/33/suppl_2/W693 NAR 34:D617, 2006 http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D617

10. Copyright OpenHelix. No use or reproduction without express written consent10 Documentation & Help Links to Tutorials & Slide Shows See “Need help!” boxes for specific tools Contact NCICB Help Desk Access to NIH & NCI

11. Copyright OpenHelix. No use or reproduction without express written consent11 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

12. Copyright OpenHelix. No use or reproduction without express written consent12 Gene Searches & Tools Click here http://cgap.nci.nih.gov/cgap.html

13. Copyright OpenHelix. No use or reproduction without express written consent13 CGAP Gene Finder Search collagenase Help Specific searches General searches Enter Keyword & click Submit Query

14. Copyright OpenHelix. No use or reproduction without express written consent14 Gene Finder: Summary Gene Results Expression data

15. Copyright OpenHelix. No use or reproduction without express written consent15 Gene Finder: Summary Expression Array Cell type examined Gene searched & probe info Expression levels

16. Copyright OpenHelix. No use or reproduction without express written consent16 Gene Info Pages Provide Many Details Click here

17. Copyright OpenHelix. No use or reproduction without express written consent17 MMP1 Gene Info Page Overview An overview of the human matrix metallopeptidase 1 (MMP1) Gene Info page Many data types & links found here We will enlarge & examine each section in upcoming slides cytogenetic location species/name/symbol database links gene expression chromosomal position MGC clones protein motifs RefSeq & related seqs. homologs Gene Ontology pathways

18. Copyright OpenHelix. No use or reproduction without express written consent18 MMP1 General Info & Links Tutorial: Click here

19. Copyright OpenHelix. No use or reproduction without express written consent19 MMP1 & RNAi Short hairpin RNA shRNA Link to order clones RNAi targets mapped For more info

20. Copyright OpenHelix. No use or reproduction without express written consent20 MMP1 Gene Expression Data MMP1 gene expression: cDNA libraries 2-D array displays SAGE: Anatomic Viewer, Digital Northern, Virtual Northern Focus of next slides

21. Copyright OpenHelix. No use or reproduction without express written consent21 MMP1 SAGE Anatomic Viewer Key

22. Copyright OpenHelix. No use or reproduction without express written consent22 MMP1 SAGE Digital Northern

23. Copyright OpenHelix. No use or reproduction without express written consent23 MMP1 Virtual Northern Spot intensity reflects expression levels

24. Copyright OpenHelix. No use or reproduction without express written consent24 MMP1 Mapping Cytogenetic location Chromosomal position MGC clones Links to protein motif searches

25. Copyright OpenHelix. No use or reproduction without express written consent25 MMP1 Protein Information & Links

26. Copyright OpenHelix. No use or reproduction without express written consent26 MMP1 Homologs, GO & Pathways

27. Copyright OpenHelix. No use or reproduction without express written consent27 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

28. Copyright OpenHelix. No use or reproduction without express written consent28 Chromosome Search Tools Click here Click “Chromosomes” on homepage top navigation bar List of chromosome-related search tools http://cgap.nci.nih.gov/cgap.html

29. Copyright OpenHelix. No use or reproduction without express written consent29 Searches Help Citation Search tools Click here

30. Copyright OpenHelix. No use or reproduction without express written consent30 Chromosomes & Cancer Click here

31. Copyright OpenHelix. No use or reproduction without express written consent31 Chromosome Search Results

32. Copyright OpenHelix. No use or reproduction without express written consent32 SNP Searches - Several Types & Access Points Click Tools to Find SNPs Tools Click

33. Copyright OpenHelix. No use or reproduction without express written consent33 SNP500Cancer Data Merge to VariantGPS http://variantgps.nci.nih.gov/cgfseq/ Click Or here “Data merge: SNP500Cancer data have been merged to this website.”

34. Copyright OpenHelix. No use or reproduction without express written consent34 SNP500Cancer Search BCL10

35. Copyright OpenHelix. No use or reproduction without express written consent35 SNP Search Results

36. Copyright OpenHelix. No use or reproduction without express written consent36 Many Types of Searches chr1:85495906 Gene View Sequence View To Entrez Gene

37. Copyright OpenHelix. No use or reproduction without express written consent37 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/

38. Copyright OpenHelix. No use or reproduction without express written consent38 Searching Gene Expression Data Click “Tissues” on homepage top navigation bar List of tools for searching gene expression data Let’s focus on cDNA xProfiler next Click here http://cgap.nci.nih.gov/cgap.html

39. Copyright OpenHelix. No use or reproduction without express written consent39 cDNA xProfiler Leave defaults Use to compare gene expression in 2 pools of libraries Our example: Human, All EST Libraries, normal pancreas (Pool A) vs. cancerous pancreas (Pool B) Click on “Submit Query”

40. Copyright OpenHelix. No use or reproduction without express written consent40 cDNA xProfiler Results To CGAP Gene Info

41. Copyright OpenHelix. No use or reproduction without express written consent41 SAGE Genie Access by selecting “SAGE Genie” from homepage top navigation bar Description Human SAGE Genie Tools Mouse SAGE Genie Tools Help Collaborators

42. Mouse SAGE Genie Tools Copyright OpenHelix. No use or reproduction without express written consent42 Expression Matrix mSAGE Expression Matrix - visualize relative gene expression vs. developmental stages Also access via mouse Gene Info page

43. Copyright OpenHelix. No use or reproduction without express written consent43 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

44. Copyright OpenHelix. No use or reproduction without express written consent44 Sequence Search A modified Nucleotide BLAST tool Access from “Genes” or “Tools” menus

45. Copyright OpenHelix. No use or reproduction without express written consent45 CGAP Nucleotide BLAST Help Enter sequence Human FANCA NM_000135 Nucleotides 1- 900

46. Copyright OpenHelix. No use or reproduction without express written consent46 BLAST Search Results

47. Copyright OpenHelix. No use or reproduction without express written consent47 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

48. Copyright OpenHelix. No use or reproduction without express written consent48 Other Tools Select Tools http://cgap.nci.nih.gov/cgap.html

49. Copyright OpenHelix. No use or reproduction without express written consent49 Data Reports Large data sets for download Download from FTP site

50. Copyright OpenHelix. No use or reproduction without express written consent50 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

51. http://cgap.nci.nih.gov/cgap.html Copyright OpenHelix. No use or reproduction without express written consent51 Summary Focus: human & mouse Comparative gene expression

52. Copyright OpenHelix. No use or reproduction without express written consent52 Many Tools & Links Gene Info pages provide many details

53. Copyright OpenHelix. No use or reproduction without express written consent53 CGAP Agenda Introduction & Credits Gene Searches & Results Chromosome & SNP Searches Gene Expression Searches Sequence Searches Other Tools Summary Exercises CGAP: http://cgap.nci.nih.gov/cgap.html

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