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GO Tools for Genome Analysis: Utilizing GO Slim Mapper and Term Finder

Discover how to effectively analyze genomic data using GO (Gene Ontology) tools such as the GO Slim Mapper and Term Finder. These tools help in grouping genes into broad categories, dealing with large datasets, and conducting microarray analysis on the Saccharomyces Genome Database. Explore the relationship between the ontology and GO-Slim, access the tools at SGD and Princeton University, and learn how to find significant shared GO terms. Enhance your genome-wide analyses and understand the distribution of gene products in biological processes by utilizing these powerful tools.

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GO Tools for Genome Analysis: Utilizing GO Slim Mapper and Term Finder

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  1. 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 GOhttp://www.geneontology.org/GO.tools.shtml

  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

  6. Relationship between whole ontology and a GO-Slim

  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 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

  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 • http://search.cpan.org/dist/GO-TermFinder/

  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 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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