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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
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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
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 • can search by GO Term or by UniProt ID • 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
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.
Filtering Results Displays all annotations to the search term and its child terms
Filtering Results use to filter results use to filter results
The AmiGO Browser http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
1. Searching by Gene Product Note: does not search for multiple IDs
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.
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
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.