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

2. Saccharomyces Genome Database (SGD) The Yeast Model Organism Database for Saccharomyces cerevisiae Materials prepared by: Dorothy S. Reilly, Ph.D. Jennifer M. Williams, Ph.D. www.openhelix.com Updated: Q2 2011 Version 3

3. Copyright OpenHelix. No use or reproduction without express written consent3 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction to SGD Saccharomyces Genome Database: http://www.yeastgenome.org/ “SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.” Vast collection of well-organized yeast information! Official nomenclature arbiter

5. http://genome-www.stanford.edu/usage/sgd/ Copyright OpenHelix. No use or reproduction without express written consent5 History of SGD http://www.yeastgenome.org/newsletters/ History & Growth Newsletter Archive

6. Homepage “Publications” link Copyright OpenHelix. No use or reproduction without express written consent6 SGD Publications Citing SGD: http://www.yeastgenome.org/cite.shtml

7. Copyright OpenHelix. No use or reproduction without express written consent7 SGD Acknowledgements & Funding http://www.yeastgenome.org/AboutContents.shtml SGD Suggestions and Questions On most pages

8. Copyright OpenHelix. No use or reproduction without express written consent8 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

9. Copyright OpenHelix. No use or reproduction without express written consent9 SGD Organization & Navigation Click Saccharomyces Genome Database: http://www.yeastgenome.org/

10. Copyright OpenHelix. No use or reproduction without express written consent10 SGD Help Resources SGD web form or yeast-curator@genome.stanford.edu Click

11. Copyright OpenHelix. No use or reproduction without express written consent11 SGD Site Map

12. Copyright OpenHelix. No use or reproduction without express written consent12 Site Map Help

13. SGD Site Navigation Saccharomyces Genome Database: http://www.yeastgenome.org/ Contact SGD SGD web form or yeast-curator@genome.stanford.edu search help

14. Copyright OpenHelix. No use or reproduction without express written consent14 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

15. Copyright OpenHelix. No use or reproduction without express written consent15 drug Basic Search & Display Gene & Protein Information Functional Information Colleagues & Authors IDs at External Resources

16. Copyright OpenHelix. No use or reproduction without express written consent16 SGD Locus Summary ERG5 Locus Summary Page Basic information ERG5 resources Pulldown menus References for this page Gene summary paragraph Subject tabs Subject tabs, pulldown menus, and links to additional information Additional information

17. Copyright OpenHelix. No use or reproduction without express written consent17 ERG5 Basic Info, Top Names, Aliases & Feature Type Yeast Systematic Names: YMR015C Y = “Yeast” M = letter representing chromosome number (1=A) R = Right or Left arm of chromosome 015 = relative position of ORF from centromere C = Watson or Crick strand Gene Ontology & Pathway Annotations

18. Phenotypes ERG5 Basic Info, Middle Interactions Copyright OpenHelix. No use or reproduction without express written consent18

19. Copyright OpenHelix. No use or reproduction without express written consent19 ERG5 Basic Info, Bottom Sequences

20. Copyright OpenHelix. No use or reproduction without express written consent20 ERG5 Locus Summary, Lower References Cited

21. Copyright OpenHelix. No use or reproduction without express written consent21 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

22. Copyright OpenHelix. No use or reproduction without express written consent22 ERG5 Locus Summary, Right Panel SGD ORF map & GBrowse access to many resources from pulldown menus Expression Summary histogram

23. Copyright OpenHelix. No use or reproduction without express written consent23 Locus Page Pull-Down Menus

24. Copyright OpenHelix. No use or reproduction without express written consent24 SGD Locus Page Tabs Summary Locus History Literature Gene Ontology Phenotype Interactions Expression Protein Wiki

25. 25 Locus Tabs: Locus History, Literature, GO Curation Types: Manual High-throughput Computational Molecular Function Biological Process Cellular Component Copyright OpenHelix. No use or reproduction without express written consent

26. 26 Locus Tabs: Mutant Phenotypes, Interactions Add data filter Scroll to:

27. Copyright OpenHelix. No use or reproduction without express written consent Locus Tabs: Expression, Protein, Wiki 27 Log in or create an account

28. Copyright OpenHelix. No use or reproduction without express written consent28 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

29. Copyright OpenHelix. No use or reproduction without express written consent29 SGD Search Options Every search option is different If you want it, it’s probably there! Advanced & SGD web page searches Search Yeast Literature Search Gene Function Info Search Protein Info Search Colleague Info Basic Search Gene & Sequence Searches

30. Copyright OpenHelix. No use or reproduction without express written consent30 Basic Search Advanced Search Link Google Search Advanced Search 1) Chromosomal Feature 2) Property Filters: Annotation/sequence Protein Phenotype Interaction GO Annotations Large-scale

31. Copyright OpenHelix. No use or reproduction without express written consent31 YeastMine A project with InterMine, RGD, & ZFIN Allows interoperability between MODs Powerful & flexible search interface Quick Search, Templates, QueryBuilder Homepage left menu FAQs Help Quick Search

32. Copyright OpenHelix. No use or reproduction without express written consent32 YeastMine – Lists Example click rad51; rad52; rad53; ddc1; rad55; rad57; spo11; dmc1; rad17; rad9; rad24; msh1; msh5; mre11; xrs2; ndt80; tid1; ssb1; pre3; acr1; doa3; rad54; ssf1 upload Example list of 23 yeast gene names

33. Copyright OpenHelix. No use or reproduction without express written consent33 YeastMine – Confirm List add click

34. Copyright OpenHelix. No use or reproduction without express written consent34 YeastMine –List Analysis List Summary Information Widgets List Template Queries Log in to save Lists, query results, etc.

35. Biochemical Pathway Search allantoin Copyright OpenHelix. No use or reproduction without express written consent35

36. Copyright OpenHelix. No use or reproduction without express written consent36 Global Gene Hunter Databases searched: SGD, PubMed, Entrez Nucleotide, PDB, PIR, etc. Gene Name Additional Filters

37. Copyright OpenHelix. No use or reproduction without express written consent37 Textpresso Literature Search drug resistance Enter term Reference Information Abstract Matching Sentences Supplemental Info

38. Copyright OpenHelix. No use or reproduction without express written consent38 Advanced Search Summary Many search types, lots of information to find!

39. Copyright OpenHelix. No use or reproduction without express written consent39 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

40. Copyright OpenHelix. No use or reproduction without express written consent40 GO Resources - GO Slim Mapper Homepage left menu

41. Copyright OpenHelix. No use or reproduction without express written consent41 Submit Data Homepage left menu

42. Homepage left menu Copyright OpenHelix. No use or reproduction without express written consent42 Download Data

43. Copyright OpenHelix. No use or reproduction without express written consent43 Yeast Genome Wiki Wiki Background Information includes: General S. cerevisiae information Educational resources S. pombe information Candida albicans information Links to other fungal information Fungal genome sequencing projects Fungal genome database projects http://wiki.yeastgenome.org/index.php/General_Topics

44. Copyright OpenHelix. No use or reproduction without express written consent44 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

45. Copyright OpenHelix. No use or reproduction without express written consent45 Summary Extensive collection of data & tools Model organism specific focus If you want it, it’s probably there! http://www.yeastgenome.org/ You’ll receive a prompt reply! Contact SGD

46. SGD - Extensive Data & Tools Available SGD: So Much to Offer! Copyright OpenHelix. No use or reproduction without express written consent46

47. Copyright OpenHelix. No use or reproduction without express written consent47 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database: http://www.yeastgenome.org/

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