1. Getting GO annotation for your dataset
Fiona McCarthy, Shane Burgess, Susan Bridges
The AgBase Databases, Institute of Digital Biology, Mississippi State University

2. Getting GO:
Primary sources of GO: from the GO Consortium (GOC) & GOC members
most up to date
most comprehensive
Secondary sources: other resources that use GO provided by GOC members
public databases (eg. NCBI, UniProtKB)
genome browsers (eg. Ensembl)
array vendors (eg. Affymetrix)
GO expression analysis tools

3. GO Browsers

4. 1.1 GO Browsers QuickGO Browser (EBI GOA Project)
can search by GO Term or by UniProt ID
includes IEA annotations
beta version in testing: will expand functionality
AmiGO Browser (GO Consortium Project)
does not include IEA annotations

5. GO Browser demonstration
AIM: To demonstrate the QuickGO & AmiGO browsers and how they can be used to find GO, find GO terms

6. The QuickGO Browser (EBI-GOA)

7.
This site is under development - feedback is being requested to make this resource useful to you.
Coming soon: download GO annotations for your dataset.

8. 1. Searching by Protein
Multiple protein IDs can be separated by a space or a comma.

11. Click on “Home” to start a new search.

12. Search for a GO Term

16. Filtering Results
Displays all annotations to the search term and its child terms

17. Filtering Results
use to filter results
use to filter results

18. Filter by database.

19. Filter by GO Terms

20. Filter by GO evidence code.

21. Filter by taxon.

22. Click on “Home” to start a new search.

23. The AmiGO Browser

24. Note: does not search for multiple IDs
1. Searching by Gene Product
Note: does not search for multiple IDs

26. Information about the gene product.

27. Links to GO annotations.

28. Download gene GO annotations.

29. 2. Searching by GO Term

30. Results can be filtered by ontology.

31. Find term details by clicking on the term name.

32. See how the term fits in the ontology by selecting Term Lineage.

35. Select ‘gene product associations’ to display the GO annotations for your search results.

36. 3. Filtering Results
Annotations can be filtered using drop down windows & selecting “set filters”.

38. Filtered results can be selected & downloaded as a gene association file.

39. Downloading ga files

40. 1.2 Gene Association files
The gene association (ga) file is used by GO groups to link GO function to gene products
tab-delimited file (smaller files can be viewed by opening in Excel)
15 columns (‘fields’)
GO Annotation File Format Guide explains data in each column:

41. Gene Association files
The gene association (ga) file is used by GO groups to link function (GO) to gene products
tab-delimited file (smaller files can be viewed by opening in Excel)
15 columns (‘fields’)
GO Annotation File Format Guide explains data in each column:

44. GOC: submitted to GO Consortium via EBI-GOA
Community: includes annotations not yet submitted, not supported (have QC)

45. B. Gene Association file Demonstration
AIM: To show how to download gene association files.

46.
Select “Downloads & Statistics link.

47. Click on “Download” link and choose “Save to disk” option.

48. Find file on desktop.

49. Unzip using Winzip.

50. Open extracted file in Excel.

51. WARNING: some files are too large to open in Excel.

52. 2. Secondary sources of GO annotation

53. Secondary Sources of GO annotation
EXAMPLES:
public databases (eg. NCBI, UniProtKB)
genome browsers (eg. Ensembl)
array vendors (eg. Affymetrix)
CONSIDERATIONS:
What is the original source?
When was it last updated?
Are evidence codes displayed?

54. C. Obtaining GO annotations from Secondary Sources
AIM: Look at how different public resources and tools display GO.

55. GO annotation obtained for chick GAPDH (P00356) from different sources:
QuickGO (primary source)
UniProtKB database
NCBI Entrez Gene page
Ensembl browser
Affymetrix chick array
g:profiler gene expression analysis tool

56. QuickGO

57. 1.

58. 2.

64. Comparison of Chicken GAPDH GO annotation
obtained from different sources.
GO evidence codes not reported.