1. An introduction to using the AmiGO Gene Ontology tool

2. Gene Ontology (GO) HTML based application Used to browse, query and visualise GO data Can be installed locally –freely available from GO website

3. GO to the geneDB S. pombe web page: http://www.genedb.org/genedb/pombe/index.jsp click ‘AmiGO’

5. browsable GO tree

6. number of genes annotated to term (+ child terms)

7. search functions

8. functions for filtering what data is displayed in AmiGO - currently only S.pombe data is being shown

9. the tree can be expanded to show ‘child’ terms by clicking on the + symbol before the term

10. expanded node, can be closed again by clicking the - icon ‘child’ terms of biological process

11. number of genes annotated to term, and its children

12. node ‘physiological process’ also open indicates that a term has no children

13. number of genes annotated to term, and its children indicates relationship of term to its parent. P = part_of, I = is_a

14. Searching To find a specific term, it’s easiest to use the search facility in the top left of the screen

15. Searching select to search for GO terms select to search for annotated genes tick this box to search for only exactly matching strings search with extra options e.g. search only term names

16. Searching enter search string here and click ‘Submit Query’

17. GO terms matching search string

18. GO term numerical identifier

19. which of the three GO ontologies the term belongs to. P = biological process, F = molcular function and C = cellular component

20. text definition for the term

21. clicking on the tree icon takes you to the GO tree expanded at the term

22. view shows two different paths up the tree for term ‘1,3-beta- glucan synthase activity’

23. clicking a term name takes you to a detailed view of that term

24. term details

25. all parent terms of term

26. links between term and objects in other databases e.g EC numbers

27. genes annotated to term, with annotation information (scroll down window)

28. number of genes annotated to term

29. gene symbol/name. Links to page showing all annotations to gene

31. gene description

32. source of annotation i.e. the database that created the annotation

33. links to gene page in S. pombe database

34. evidence for annotation - mouseover for full name

35. reference for annotation - e.g. PubMed id for paper

36. filters for setting which data displayed.

37. selecting ‘All’ then clicking ‘Submit Query’ will show genes for all datasources annotated to term

38. now 31 results

39. genes from all databases annotated to term (more)

40. re-set to show only S. pombe data by selecting from the list, and clicking ‘Submit Query’

41. only S. pombe data now shown again. Filters stay set within a session.

42. Searching for genes enter gene to search for here, check the Gene Symbol/Name box and click ‘Submit Query’

43. gene matching search string

44. other GO annotations for gene

45. click AmiGO icon to return to main tree page

47. open nodes ‘biological process’ -> cellular process’ ->cellular physiological process

48. creates a pie-chart showing the distribution of genes annotated to terms in ‘cellular physiological process’ node

50. QuickGO is another GO browser, developed at EBI: http://www.ebi.ac.uk/ego/ GO terms only does not display annotations –can search on UniProt protein ids

52. select the field to search on e.g. GO id, UniProt identifier. Seaches name/synonym by defaut select ontology, i.e. biological process, molecular function, cellular component, to search. Seaches all by default.

53. enter search string and click ‘Search GO’

54. matches to search string

55. click term name to select

56. term details

57. (scroll down window) view of term location in tree alternative paths through tree

58. compare to different view of same information in AmiGO