1. Rama Balakrishnan Saccharomyces Genome Database Stanford University
GO tools
Rama Balakrishnan
Saccharomyces Genome Database
Stanford University

2. How can GO data be useful?
Dealing with large data sets
genomic data
Microarray analysis
Grouping genes into broad categories

3. List of tools available at GO http://www. geneontology. org/GO. tools

4. 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.

5. 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

6. 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.

7. How do you access the GO Slim Mapper tool? http://www.yeastgenome.org

8. 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

9. Features of GO Slim Mapper tool

10. Results of GO Slim Mapper

11. Distribution of Gene products in Biological Process

12. 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

13. 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

14. How do you access the GO term finder at SGD?

15. Features of GO Term Finder

16. Term Finder Results

17. 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