Using the Saccharomyces Genome Database (SGD) for Analysis of Genomic Information

Marek S. Skrzypek1, Jodi Hirschman1

1 Department of Genetics, Saccharomyces Genome Database, Stanford University, Palo Alto, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.20
DOI:  10.1002/0471250953.bi0120s35
Online Posting Date:  September, 2011
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Abstract

Analysis of genomic data requires access to software tools that place the sequence‐derived information in the context of biology. The Saccharomyces Genome Database (SGD) integrates functional information about budding yeast genes and their products with a set of analysis tools that facilitate exploring their biological details. This unit describes how the various types of functional data available at SGD can be searched, retrieved, and analyzed. Starting with the guided tour of the SGD Home page and Locus Summary page, this unit highlights how to retrieve data using YeastMine, how to visualize genomic information with GBrowse, how to explore gene expression patterns with SPELL, and how to use Gene Ontology tools to characterize large‐scale datasets. Curr. Protoc. Bioinform. 35:1.20.1‐1.20.23. © 2011 by John Wiley & Sons, Inc.

Keywords: genome database; gene expression; gene ontology; InterMine; SPELL; GBrowse; high‐throughput data

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Exploring the SGD Pages
  • Basic Protocol 2: Using YeastMine to Retrieve and Analyze Multiple Data Types for Sets of Genes
  • Basic Protocol 3: Exploring Genome Features with GBrowse
  • Basic Protocol 4: Using SPELL to Analyze Microarray Gene Expression Data
  • Basic Protocol 5: Using the GO Slim Mapper to Group Sets of Genes According to Their Function or Location in the Cell
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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