go tools 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 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