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An introduction to using the AmiGO Gene Ontology tool

An introduction to using the AmiGO Gene Ontology tool. Gene Ontology (GO) HTML based application Used to browse, query and visualise GO data Can be installed locally freely available from GO website. GO to the geneDB S. pombe web page: http://www.genedb.org/genedb/pombe/index.jsp

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An introduction to using the AmiGO Gene Ontology tool

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  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’

  4. browsable GO tree

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

  6. search functions

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

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

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

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

  11. node ‘physiological process’ also open indicates that a term has no children number of genes annotated to term, and its children

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

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

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

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

  16. GO terms matching search string

  17. GO term numerical identifier

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

  19. text definition for the term

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

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

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

  23. term details

  24. all parent terms of term

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

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

  27. number of genes annotated to term

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

  29. gene description

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

  31. links to gene page in S. pombe database

  32. evidence for annotation - mouseover for full name

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

  34. filters for setting which data displayed.

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

  36. now 31 results

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

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

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

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

  41. gene matching search string

  42. other GO annotations for gene

  43. click AmiGO icon to return to main tree page

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

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

  46. 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

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