Rama Balakrishnan Saccharomyces Genome Database Stanford University 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 GO http://www. geneontology. org/GO. tools

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 Updated/kept current, available in OBO format

Relationship between whole ontology and a GO-Slim So the graphical view from the GO term finder gave you an idea of how complicated the ontology can get. What if you are only interested in what general categories a group of genes is involved in? If this is a stylized view of the ontology and all the different relationships between terms, you can only look at a slice of the ontology by selecting general terms. This is called a GO-Slim. You are only taking a look at the major branches of the ontology. And because of the DAG structure, you can map all the terms to a general parent and it will still be true. So this next tool at SGD takes advantage of the GO Slim in order to find what major branches a gene has been annotated to.

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 Mapper http://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 Finder http://go. princeton Available at Princeton University Uses the same algorithm as SGD’s tool Customizable Can upload your own gene_associations file