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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.

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Go tools

GO tools

Rama Balakrishnan

Saccharomyces Genome Database

Stanford University


How can go data be useful
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
List of tools available at GOhttp://www.geneontology.org/GO.tools.shtml


Tools available at sgd
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
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




Go slim mapper tool at sgd
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





Generic go slim mapper http go princeton edu cgi bin gotermmapper
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
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/





Generic go term finder http go princeton edu cgi bin gotermfinder gotermfinder
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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