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
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library


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

PDF or HTML at Wiley Online Library

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
PDF or HTML at Wiley Online Library


PDF or HTML at Wiley Online Library



Literature Cited

Literature Cited
   Arnaud, M.B., Chibucos, M.C., Costanzo, M.C., Crabtree, J., Inglis, D.O., Lotia, A., Orvis, J., Shah, P., Skrzypek, M.S., Binkley, G., Miyasato, S.R., Wortman, J.R., and Sherlock, G. 2010. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res. 38:D420‐D427.
   Cherry, J.M., Ball, C., Weng, S., Juvik, G., Schmidt, R., Adler, C., Dunn, B., Dwight, S., Riles, L., Mortimer, R.K., and Botstein, D. 1997. Genetic and physical maps of Saccharomyces cerevisiae. Nature 387:67‐73.
   Costanzo, M.C., Skrzypek, M.S., Nash, R., Wong, E., Binkley, G., Engel, S.R., Hitz, B., Hong, E.L., Cherry, J.M., and the Saccharomyces Genome Database Project. 2009. New mutant phenotype data curation system in the Saccharomyces Genome Database. Database (Oxford) 2009:bap001.
   Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., and Ashburner, M. 2008. ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36:D344‐D350.
   Dwight, S.S., Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., Engel, S.R., Feierbach, B., Fisk, D.G., Hirschman, J., Hong, E.L., Issel‐Tarver, L., Nash, R.S., Sethuraman, A., Starr, B., Theesfeld, C.L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Weng, S., Botstein, D., and Cherry, J.M. 2004. Saccharomyces Genome Database: Underlying principles and organisation. Brief. Bioinform. 5:9‐22.
   Engel, S.R., Balakrishnan, R., Binkley, G., Christie, K.R., Costanzo, M.C., Dwight, S.S., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Hong, E.L., Krieger, C.J., Livstone, M.S., Miyasato, S.R., Nash, R., Oughtred, R., Park, J., Skrzypek, M.S., Weng, S., Wong, E.D., Dolinski, K., Botstein, D., and Cherry, J.M. 2010. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 38:D433‐D436.
   Fey, P., Gaudet, P., Curk, T., Zupan, B., Just, E.M., Basu, S., Merchant, S.N., Bushmanova, Y.A., Shaulsky, G., Kibbe, W.A., and Chisholm, R.L. 2009. dictyBase: A Dictyostelium bioinformatics resource update. Nucleic Acids Res. 37:D515‐D519.
   Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S.G. 1996. Life with 6000 genes. Science 274:546‐567.
   Harris, M. and the Gene Ontology Consortium. 2008. The Gene Ontology project in 2008. Nucleic Acids Res. 36:440‐444.
   Hibbs, M.A., Hess, D.C., Myers, C.L., Huttenhower, C., Li, K., and Troyanskaya, O.G. 2007. Exploring the functional landscape of gene expression: Directed search of large microarray compendia. Bioinformatics 23:2692‐2699.
   Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H., and Yeats, C. 2009. InterPro: The integrative protein signature database. Nucleic Acids Res. 37:D224‐D228.
   Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., Mclaren, P., North, P., Rana, D., Riley, T., Sullivan, J., Watkins, X., Woodbridge, M., Lilley, K., Russell, S., Ashburner, M., Mizuguchi, K., and Micklem, G. 2007. FlyMine: An integrated database for Drosophila and Anopheles genomics. Genome Biol. 8:R129.
   MacIsaac, K.D., Wang, T., Gordon, D.B., Gifford, D.K., Stormo, G.D., and Fraenkel, E. 2006. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7:113.
   Mancera, E., Bourgon, R., Brozzi, A., Huber, W., and Steinmetz, L.M. 2008. High‐resolution mapping of meiotic crossovers and non‐crossovers in yeast. Nature 454:479‐485.
   Miura, H., Tomaru, Y., and Hayashizaki, Y. 2006. Innovation of transcriptome analysis. Tanpakushitsu Kakusan Koso 51:2413‐2419.
   Skrzypek, M.S., Arnaud, M.B., Costanzo, M.C., Inglis, D.O., Shah, P., Binkley, G., Miyasato, S.R., and Sherlock, G. 2010. New tools at the Candida Genome Database: Biochemical pathways and full‐text literature search. Nucleic Acids Res. 38:D428‐D432.
   Stark, C., Su, T.C., Breitkreutz, A., Lourenco, P., Dahabieh, M., Breitkreutz, B.J., Tyers, M., and Sadowski, I. 2010. PhosphoGRID: A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) 2010:bap026.
   Stark, C., Breitkreutz, B.J., Chatr‐Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M.S., Nixon, J., Van Auken, K., Wang, X., Shi, X., Reguly, T., Rust, J.M., Winter, A., Dolinski, K., and Tyers, M. 2011. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 39:D698‐D704.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
   Steinmetz, E.J., Warren, C.L., Kuehner, J.N., Panbehi, B., Ansari, A.Z, and Brow, D.A. 2006. Genome‐wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Molecular Cell 24:735‐746.
   Stover, N.A., Krieger, C.J., Binkley, G., Dong, Q., Fisk, D.G., Nash, R., Sethuraman, A., Weng, S., and Cherry, J.M. 2006. Tetrahymena Genome Database (TGD): A new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res. 34:D500‐D503.
   Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder‐Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W., and Steinmetz, L.M. 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457:1033‐1037.
   Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A., Nusbaum, C., Thompson, D.A., Friedman, N., and Regev, A. 2009. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 106:3264‐3269.
PDF or HTML at Wiley Online Library