Using the Saccharomyces Genome Database (SGD) for analysis of genomic information.

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.

[1]  Blaz Zupan,et al.  dictyBase—a Dictyostelium bioinformatics resource update , 2008, Nucleic Acids Res..

[2]  Marek S. Skrzypek,et al.  New tools at the Candida Genome Database: biochemical pathways and full-text literature search , 2009, Nucleic Acids Res..

[3]  Kara Dolinski,et al.  The BioGRID Interaction Database: 2011 update , 2010, Nucleic Acids Res..

[4]  Ting Wang,et al.  An improved map of conserved regulatory sites for Saccharomyces cerevisiae , 2006, BMC Bioinformatics.

[5]  Kara Dolinski,et al.  Saccharomyces Genome Database provides mutant phenotype data , 2009, Nucleic Acids Res..

[6]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[7]  Kara Dolinski,et al.  Saccharomyces genome database: Underlying principles and organisation , 2004, Briefings Bioinform..

[8]  Giorgio Valle,et al.  The Gene Ontology project in 2008 , 2007, Nucleic Acids Res..

[9]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[10]  L. Steinmetz,et al.  High-resolution mapping of meiotic crossovers and non-crossovers in yeast , 2008, Nature.

[11]  Julie M. Sullivan,et al.  FlyMine: an integrated database for Drosophila and Anopheles genomics , 2007, Genome Biology.

[12]  Shuai Weng,et al.  Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research , 2005, Nucleic Acids Res..

[13]  Edith D. Wong,et al.  New mutant phenotype data curation system in the Saccharomyces Genome Database , 2009, Database J. Biol. Databases Curation.

[14]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[15]  Christopher L. Warren,et al.  Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. , 2006, Molecular cell.

[16]  Kai Li,et al.  Exploring the functional landscape of gene expression: directed search of large microarray compendia , 2007, Bioinform..

[17]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[18]  Michael Cherry,et al.  South African museums' status ‘at risk’ , 1997, Nature.

[19]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[20]  Hunter B. Fraser,et al.  Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing , 2009, Proceedings of the National Academy of Sciences.

[21]  Marcus C. Chibucos,et al.  The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community , 2009, Nucleic Acids Res..

[22]  Mike Tyers,et al.  PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae , 2010, Database J. Biol. Databases Curation.