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

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

GO Browsers

1.1 GO Browsers QuickGO Browser (EBI GOA Project) http://www.ebi.ac.uk/ego/ can search by GO Term or by UniProt ID includes IEA annotations beta version in testing: will expand functionality AmiGO Browser (GO Consortium Project) http://amigo.geneontology.org/cgi-bin/amigo/go.cgi does not include IEA annotations

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

The QuickGO Browser (EBI-GOA)

http://www.ebi.ac.uk/ego/ This site is under development - feedback is being requested to make this resource useful to you. Coming soon: download GO annotations for your dataset.

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

Click on “Home” to start a new search.

Search for a GO Term

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

Filtering Results use to filter results use to filter results

Filter by database.

Filter by GO Terms

Filter by GO evidence code.

Filter by taxon.

Click on “Home” to start a new search.

The AmiGO Browser http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

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

Information about the gene product.

Links to GO annotations.

Download gene GO annotations.

2. Searching by GO Term

Results can be filtered by ontology.

Find term details by clicking on the term name.

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

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

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

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

Downloading ga files

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: http://www.geneontology.org/GO.format.annotation.shtml

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: http://www.geneontology.org/GO.format.annotation.shtml

http://www.geneontology.org/GO.current.annotations.shtml

http://www.ebi.ac.uk/GOA/downloads.html

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

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

http://www.agbase.msstate.edu/ Select “Downloads & Statistics link.

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

Find file on desktop.

Unzip using Winzip.

Open extracted file in Excel.

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

2. Secondary sources of GO annotation

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?

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

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

QuickGO

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