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GO tools
Rama Balakrishnan
Saccharomyces Genome Database
Stanford University
How can GO data be useful?
• Dealing with large data sets– genomic data– Microarray analysis
• Grouping genes into broad categories
List of tools available at GOhttp://www.geneontology.org/GO.tools.shtml
Tools available at SGD
• GO Slim Mapper- maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms.
• GO term finder- searches for significant shared GO terms, or parents of the GO terms, used to annotate gene products in a given list.
What is GO Slim?• High level view of GO• Allows users to group genes into broader categories• Useful for large scale, genome wide analyses• Different Annotation groups have come up with specifc
GO_Slims• Different GO_Slims are available at GO’s FTP site
Relationship between whole ontology and a GO-Slim
How do you access the GO Slim Mapper tool?http://www.yeastgenome.org
GO Slim Mapper tool at SGD
• Genes annotated to granular terms are mapped to higher level terms
• Offers three GO Slim sets• Yeast GO Slim• Super GO Slim• Macromolecular complex terms
Features of GO Slim Mapper tool
Results of GO Slim Mapper
Distribution of Gene products in Biological Process
Generic GO Slim Mapperhttp://go.princeton.edu/cgi-bin/GOTermMapper
• Available at Princeton University
• Can be used with any available GOC gene_associations file
• Can upload your own files (1 or many)– GO Slim– gene_associations file
GO Term Finder
• finds significant GO terms shared among a list of genes
• discover what these genes may have in common
• Software downloadable from CPAN– http://search.cpan.org/dist/GO-TermFinder/
How do you access the GO term finder at SGD?
Features of GO Term Finder
Term Finder Results
Generic GO Term Finderhttp://go.princeton.edu/cgi-bin/GOTermFinder/GOTermFinder
• Available at Princeton University
• Uses the same algorithm as SGD’s tool
• Customizable
• Can upload your own gene_associations file
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