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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


Relationship between whole ontology and a go slim

Relationship between whole ontology and a GO-Slim


How do you access the go slim mapper tool http www yeastgenome org

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


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


Features of go slim mapper tool

Features of GO Slim Mapper tool


Results of go slim mapper

Results of GO Slim Mapper


Distribution of gene products in biological process

Distribution of Gene products in Biological Process


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/


How do you access the go term finder at sgd

How do you access the GO term finder at SGD?


Features of go term finder

Features of GO Term Finder


Term finder results

Term Finder Results


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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