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

2. KEGG Version 2_0210 Kyoto Encyclopedia of Genes and Genomes Materials prepared by: Cynthia Perreault-Micale, Ph.D. Mary E. Mangan, Ph.D. www.openhelix.com Updated: Q1 2010

3. Copyright OpenHelix. No use or reproduction without express written consent3 3 KEGG Agenda Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises KEGG: http://www.kegg.jphttp://www.kegg.jp

4. Copyright OpenHelix. No use or reproduction without express written consent4 4 KEGG and Systems Biology KEGG has existed since 1995 High quality curated data on metabolic pathways Expanded to other data types Widely used at KEGG and in other genomics and systems biology tools www.kegg.org

5. Copyright OpenHelix. No use or reproduction without express written consent5 5 KEGG Credits Developed and maintained by the Kanehisa group Actively adding new data and software Freely available to academics Licensing provided by Pathway Solutions License: www.genome.jp/kegg/legal.html www.pathway.jp

6. Copyright OpenHelix. No use or reproduction without express written consent6 6 Foundations of KEGG Initially developed with a focus on metabolic pathways 80 pathway representations at the beginning; >100k now Human citric acid cycle (TCA cycle)

7. Copyright OpenHelix. No use or reproduction without express written consent7 7 KEGG Today 16 databases, highly integrated 13 curated “core” databases, 3 computationally derived Tools to add utility to the underlying data Systems Information KEGG PATHWAY KEGG BRITE KEGG MODULE KEGG DISEASE KEGG DRUG Chemical Information KEGG COMPOUND KEGG GLYCAN KEGG ENZYME KEGG REACTION KEGG RPAIR (reaction pairs) Genomic Information KEGG ORTHOLOGY KEGG GENOME KEGG GENES KEGG SSDB (seq similar) KEGG DGENES (draft) KEGG EGENES (ESTs)

8. Copyright OpenHelix. No use or reproduction without express written consent8 8 KEGG Objects and IDs Each database entry is a KEGG object IDs for specific data types Use in KEGG or even in Google!

9. Copyright OpenHelix. No use or reproduction without express written consent9 9 Homepage Project description Entry Points Help Documentation Associated tools GenomeNet DBGET Feedback http://www.kegg.jp Return to homepage

10. Copyright OpenHelix. No use or reproduction without express written consent10Copyright OpenHelix. No use or reproduction without express written consent10 Data Access Quick search Database-wide http://www.kegg.jp

11. Copyright OpenHelix. No use or reproduction without express written consent11Copyright OpenHelix. No use or reproduction without express written consent11 KEGG Table of Contents Access to KEGG data via “Entry Points” KEGG associated tools Analysis tools Software developers Systems information Genomic information Chemical information Specific organisms Web resources Computational tools Software development

12. Copyright OpenHelix. No use or reproduction without express written consent12Copyright OpenHelix. No use or reproduction without express written consent12 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

13. Copyright OpenHelix. No use or reproduction without express written consent13Copyright OpenHelix. No use or reproduction without express written consent13 General Table Features Search entire site from top menu Or focused searches from table

14. Copyright OpenHelix. No use or reproduction without express written consent14Copyright OpenHelix. No use or reproduction without express written consent14 General Search Options from the Table Systems, Genomic, Chemical Information table Query forms and browsing from Entry Points

15. Copyright OpenHelix. No use or reproduction without express written consent15Copyright OpenHelix. No use or reproduction without express written consent15 Systems - Pathway Overview Search options at the top Browse all of the pathways below search citrate cycle browse

16. Copyright OpenHelix. No use or reproduction without express written consent16Copyright OpenHelix. No use or reproduction without express written consent16 Pathway Search Example Compounds, References ID, Name Description, Class Pathway map Links Modules, Organism, Genes

17. Copyright OpenHelix. No use or reproduction without express written consent17 Human Citrate Cycle (TCA cycle) - Top Basic entry information Many links to explore BRITE hierarchy Many hits from many databases

18. Copyright OpenHelix. No use or reproduction without express written consent18 Human Citrate Cycle (TCA cycle) – Pathway Map Click on thumbnail or ID to view

19. Copyright OpenHelix. No use or reproduction without express written consent19Copyright OpenHelix. No use or reproduction without express written consent19 Human Citrate Cycle Pathway Map Features Options, Species For diagram codes Change size

20. Copyright OpenHelix. No use or reproduction without express written consent20Copyright OpenHelix. No use or reproduction without express written consent20 Pathway Features Help Diagram features have meanings: notations Color codes available Reference KO

21. Copyright OpenHelix. No use or reproduction without express written consent21Copyright OpenHelix. No use or reproduction without express written consent21 Metabolism Pathway Menu Options Menu to set map type: reference or species Underlying links will change to appropriate setting Options

22. Copyright OpenHelix. No use or reproduction without express written consent22 Human Citrate Cycle (TCA cycle) – Lower Section

23. Copyright OpenHelix. No use or reproduction without express written consent23Copyright OpenHelix. No use or reproduction without express written consent23 Genetic Information Processing Example Base excision repair Species settings Complexes available To Pathway entry – references & more

24. Copyright OpenHelix. No use or reproduction without express written consent24Copyright OpenHelix. No use or reproduction without express written consent24 Other Systems Information Entry Points Quick tour of other Systems Information Entry Points Including KEGG BRITE, Atlas, DISEASE, DRUG

25. Copyright OpenHelix. No use or reproduction without express written consent25Copyright OpenHelix. No use or reproduction without express written consent25 BRITE Entry Point BRITE: binary relationships and hierarchies browse search

26. Copyright OpenHelix. No use or reproduction without express written consent26Copyright OpenHelix. No use or reproduction without express written consent26 Atlas Entry Point KEGG Atlas: global maps, topic maps Learn more: Mouse over http://nar.oxfordjournals.org/cgi/content/full/36/suppl_2/W423

27. Copyright OpenHelix. No use or reproduction without express written consent27Copyright OpenHelix. No use or reproduction without express written consent27 DISEASE, DRUG Entry Points KEGG DISEASE & KEGG DRUG comprise KEGG MEDICUS Learn more: http://nar.oxfordjournals.org/cgi/reprint/38/suppl_1/D355

28. Copyright OpenHelix. No use or reproduction without express written consent28Copyright OpenHelix. No use or reproduction without express written consent28 DISEASE, DRUG Overview DISEASE Description & Human Diseases Disease Pathway Maps Disease Classification DRUG Drug Development Drugs in Japan Description & Nomenclature Drug Classification Target & Pathway Documents

29. Copyright OpenHelix. No use or reproduction without express written consent29Copyright OpenHelix. No use or reproduction without express written consent29 Table of Contents Options Ways to act on these components Search and color objects Sequence searches Other specialized functionality

30. Copyright OpenHelix. No use or reproduction without express written consent30Copyright OpenHelix. No use or reproduction without express written consent30 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

31. Copyright OpenHelix. No use or reproduction without express written consent31Copyright OpenHelix. No use or reproduction without express written consent31 Genomic & Chemical Information Entry Points Other entry points for Genomic & Chemical Information Quick tour of these additional resources

32. Copyright OpenHelix. No use or reproduction without express written consent32Copyright OpenHelix. No use or reproduction without express written consent32 Genomic Information Entry Point - ORTHOLOGY Ortholog groups corresponding to pathway & BRITE hierarchy nodes Ortholog Annotation - Details & Links Search & Browse

33. Copyright OpenHelix. No use or reproduction without express written consent33Copyright OpenHelix. No use or reproduction without express written consent33 Genomic Information Entry Point - GENES Gene Annotation KAAS & More ID xref Search & Browse syn:ssr3451

34. Copyright OpenHelix. No use or reproduction without express written consent34Copyright OpenHelix. No use or reproduction without express written consent34 Genomic Information Entry Point - Organisms Scroll to:

35. Copyright OpenHelix. No use or reproduction without express written consent35Copyright OpenHelix. No use or reproduction without express written consent35 Chemical Information Entry Points – LIGAND & GLYCAN Search & Browse Chemical Structure Search Computational Analysis Search LIGAND Relational DB Search & Browse Glycan Hierarchies, Pathways, Structures & More

36. Copyright OpenHelix. No use or reproduction without express written consent36Copyright OpenHelix. No use or reproduction without express written consent36 Chemical Information Entry Points – PLANT Overview map: Biosynthesis of plant secondary metabolites

37. Copyright OpenHelix. No use or reproduction without express written consent37Copyright OpenHelix. No use or reproduction without express written consent37 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

38. Copyright OpenHelix. No use or reproduction without express written consent38Copyright OpenHelix. No use or reproduction without express written consent38 KEGG Analysis Tools Some found in the Search & Compute group More specialized tools also available

39. Copyright OpenHelix. No use or reproduction without express written consent39Copyright OpenHelix. No use or reproduction without express written consent39 Search & Compute Features: Custom Colors Color objects in pathways & hierarchies

40. Copyright OpenHelix. No use or reproduction without express written consent40Copyright OpenHelix. No use or reproduction without express written consent40 Search & Compute Features: Similarities Sequence searches Similar compound searches Similar glycan chains http://www.genome.jp/ligand/kcam/kcam/tutorial.html

41. Copyright OpenHelix. No use or reproduction without express written consent41Copyright OpenHelix. No use or reproduction without express written consent41 Search & Compute Features: Reactions Reaction predictions Pathway computations

42. Copyright OpenHelix. No use or reproduction without express written consent42Copyright OpenHelix. No use or reproduction without express written consent42 KAAS KAAS: KEGG Automatic Annotation Server

43. Copyright OpenHelix. No use or reproduction without express written consent43Copyright OpenHelix. No use or reproduction without express written consent43 Expression Search the expression data in KEGG browse list search/download

44. Copyright OpenHelix. No use or reproduction without express written consent44Copyright OpenHelix. No use or reproduction without express written consent44 KEGG Desktop Applications Download, install and run KegHier for hierarchies KegArray for microarrays KegDraw for structures hierarchies microarrays compounds

45. Copyright OpenHelix. No use or reproduction without express written consent45Copyright OpenHelix. No use or reproduction without express written consent45 KegHier Explore hierarchies by browsing Add your own hierarchies

46. Copyright OpenHelix. No use or reproduction without express written consent46Copyright OpenHelix. No use or reproduction without express written consent46 KegArray Explore microarray data Analysis tools

47. Copyright OpenHelix. No use or reproduction without express written consent47Copyright OpenHelix. No use or reproduction without express written consent47 KegDraw Draw a structure with various tools Basic chemical structures C or glycans G Use that structure as a similarity search Chemical or Glycan options

48. Copyright OpenHelix. No use or reproduction without express written consent48Copyright OpenHelix. No use or reproduction without express written consent48 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

49. Copyright OpenHelix. No use or reproduction without express written consent49Copyright OpenHelix. No use or reproduction without express written consent49 KEGG for Software Development Instructions and documentation for KEGG aspects Information on KEGG Server

50. Copyright OpenHelix. No use or reproduction without express written consent50Copyright OpenHelix. No use or reproduction without express written consent50 KEGG FTP Free to academic users Others should contact Pathway Solutions www.pathway.jp

51. Copyright OpenHelix. No use or reproduction without express written consent51Copyright OpenHelix. No use or reproduction without express written consent51 KEGG is Widely Used in Other Tools Small survey of tools that use KEGG Understanding KEGG will help you to use other tools

52. Copyright OpenHelix. No use or reproduction without express written consent52Copyright OpenHelix. No use or reproduction without express written consent52 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

53. Copyright OpenHelix. No use or reproduction without express written consent53Copyright OpenHelix. No use or reproduction without express written consent53 KEGG for Systems Biology Extensive pathway information: Atlas and subsets Genes, disease, ligands, drugs, and more

54. Copyright OpenHelix. No use or reproduction without express written consent54Copyright OpenHelix. No use or reproduction without express written consent54 KEGG Additional Tools KEGG provides tools KEGG enables software developers Many other tools rely on KEGG

55. Copyright OpenHelix. No use or reproduction without express written consent55Copyright OpenHelix. No use or reproduction without express written consent55 KEGG Agenda KEGG: http://www.kegg.jphttp://www.kegg.jp Introduction & Credits Systems Information Genomic & Chemical Information Analysis Tools Software Development Tools Summary Exercises

56. Copyright OpenHelix. No use or reproduction without express written consent56Copyright OpenHelix. No use or reproduction without express written consent56