Transcript GO tools
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.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 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.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