Skip Navigation

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (111K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (32)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ball, C. A.
Right arrow Articles by Cherry, J. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ball, C. A.
Right arrow Articles by Cherry, J. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 1 80-81
© 2001 Oxford University Press

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

Catherine A. Ball, Heng Jin, Gavin Sherlock, Shuai Weng, John C. Matese, Rey Andrada, Gail Binkley, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Mark Schroeder, David Botstein and J. Michael Cherry*

Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120, USA

Received October 2, 2000; Accepted October 11, 2000.


   ABSTRACT
TOP
 ABSTRACT
FUNCTION JUNCTION
 EXPRESSION CONNECTION
 CONCLUSIONS
 REFERENCES
 
Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford.edu/Saccharomyces/.


   FUNCTION JUNCTION
TOP
 ABSTRACT
 FUNCTION JUNCTION
EXPRESSION CONNECTION
 CONCLUSIONS
 REFERENCES
 
The Function Junction resource allows a Saccharomyces Genome Database (SGD) (1–3) user to simultaneously retrieve genome-wide functional analysis information from a variety of online sources for a selected gene name. The various sites surveyed by Function Junction use a wide assortment of techniques to assay or predict information about a gene product. SGD users can query all sites, or specify an interesting subset. Function Junction, which can be accessed by entering a gene or ORF name at genome-www.stanford.edu/cgi-bin/SGD/functionJunction, currently searches the following sites:

• Portal PathCalling provides data from Uetz et al. (4), investigation of protein–protein interactions and is accessible at: portal.curagen.com/extpc/com.curagen.portal.servlet.Yeast.

• UCLA Function Assignment provides the results of several different gene function prediction methods, including phylogenetic profiling, protein interactions and shared expression patterns (5–7) and can be accessed at www.doe-mbi.ucla.edu/people/marcotte/yeast.html.

• Worm–Yeast Comparison reports potential homologs identified by the Chervitz et al. sequence comparison (8) and can be found at genome-www.stanford.edu/Saccharomyces/worm/.

• Serial Analysis of Gene Expression (SAGE) provides data from the Velculescu et al. study of gene expression (9) and is available at an SGD website, genome-www.stanford.edu/Saccharomyces/SAGE/AdvancedQuery.html.

• Triples Database reports the results of transposon muta­genesis studies (10) providing data about phenotype, expression and localization and is available at ygac.med.yale.edu/triples/triples.htm.


   EXPRESSION CONNECTION
TOP
 ABSTRACT
 FUNCTION JUNCTION
 EXPRESSION CONNECTION
CONCLUSIONS
 REFERENCES
 
Expression Connection is similar to Function Junction in concept, but it queries only microarray expression data (see Fig. 1 for an example). Using software developed at SGD, downloaded data from several microarray studies are queried to display the expression pattern of a gene and its most similarly expressed neighbors. For serial experiments, a graph showing the expression pattern over the course of the experiment is available. The datasets currently queried by Expression Connection include results of a diauxic shift timecourse (11), a sporulation time series (12), two studies of cell-cycle synchronization (13,14), a study of evolution under glucose limitation (15), a histone depletion timecourse (16), an analysis of gene expression perturbation caused by mutations in the yeast transcriptional machinery (17), an {alpha}-factor concentration series and an {alpha}-factor treatment timecourse (18). To use Expression Connection, enter a gene or ORF name at the following URL: genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl.



View larger version (19K):
[in this window]
[in a new window]
  		Figure 1. Expression Connection. For any gene, users may display several sets of microarray data. (A) For each set of serial data, a graphic representation of the gene’s expression pattern is rendered. (B) Two color representations of the expression data are presented, showing the gene’s expression pattern along with the 20 loci whose expression patterns are most similar. The two color representations are accompanied by annotation of gene names, molecular function and biological processes.

 

   CONCLUSIONS
TOP
 ABSTRACT
 FUNCTION JUNCTION
 EXPRESSION CONNECTION
 CONCLUSIONS
REFERENCES
 
Together, Function Junction and Expression Connection will serve as a central resource on the World Wide Web for quickly retrieving information generated by comprehensive analyses of the yeast genome. As more large-scale datasets are published, SGD will include them on the list of sites queried by these software packages. In this manner, SGD will enable online researchers to benefit from the accumulation of genome-wide studies of Saccharomyces cerevisiae.


   ACKNOWLEDGEMENT
 
S.G.D. is supported by a P41, National Resources, grant from the National Genome Research Institute at the US National Institutes of Health.


   FOOTNOTES
 
* To whom correspondence should be addressed. Tel: +1 650 723 7541; Fax: +1 650 723 7016; Email: cherry{at}genome.stanford.edu Back


   REFERENCES
TOP
 ABSTRACT
 FUNCTION JUNCTION
 EXPRESSION CONNECTION
 CONCLUSIONS
 REFERENCES
 

    1 Cherry,J.M., Adler,C., Ball,C., Chervitz,S.A., Dwight,S.S., Hester,E.T., Jia,Y., Juvik,G., Roe,T., Schroeder,M., Weng,S. and Botstein,D. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res., 26, 73–79.[Abstract/Free Full Text]

    2 Chervitz,S.A., Hester,E.T., Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Juvik,G., Malekian,A., Roberts,S., Roe,T., Scafe,C., Schroeder,M., Sherlock,G., Weng,S., Zhu,Y., Cherry,J.M. and Botstein,D. (1999) Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res., 27, 74–78.[Abstract/Free Full Text]

    3 Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H., Kaloper,M., Orr,S.D., Schroeder,M., Weng,S., Zhu,Y., Botstein,D. and Cherry,J.M. (2000) Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res., 28, 77–80.[Abstract/Free Full Text]

    4 Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P., Qureshi-Emili,A., Li,Y., Godwin,B., Conover,D., Kalbfleisch,T., Vijayadamodar,G., Yang,M., Johnston,M., Fields,S. and Rothberg,J.M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623–627.[Medline]

    5 Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T.O. and Eisenberg,D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83–86.[Medline]

    6 Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751–753.[Abstract/Free Full Text]

    7 Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285–4288.[Abstract/Free Full Text]

    8 Chervitz,S.A., Aravind,L., Sherlock,G., Ball,C.A., Koonin,E.V., Dwight,S.S., Harris,M.A., Dolinski,K., Mohr,S., Smith,T., Weng,S., Cherry,J.M. and Botstein,D. (1998) Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science, 282, 2022–2028.[Abstract/Free Full Text]

    9 Velculescu,V.E., Zhang,L., Zhou,W., Vogelstein,J., Basrai,M.A., Bassett,D.E.,Jr, Hieter,P., Vogelstein,B. and Kinzler,K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243–251.[Web of Science][Medline]

    10 Ross-Macdonald,P., Coelho,P.S., Roemer,T., Agarwal,S., Kumar,A., Jansen,R., Cheung,K.H., Sheehan,A., Symoniatis,D., Umansky,L., Heidtman,M., Nelson,F.K., Iwasaki,H., Hager,K., Gerstein,M., Miller,P., Roeder,G.S. and Snyder,M. (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption [see comments]. Nature, 402, 413–418.[Medline]

    11 DeRisi,J.L., Iyer,V.R. and Brown,P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680–686.[Abstract/Free Full Text]

    12 Chu,S., DeRisi,J., Eisen,M., Mulholland,J., Botstein,D., Brown,P.O. and Herskowitz,I. (1998) The transcriptional program of sporulation in budding yeast [published erratum appears in Science (1998) 20, 1421]. Science, 282, 699–705.

    13 Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273–3297.[Abstract/Free Full Text]

    14 Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. and Davis,R.W. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65–73.[Web of Science][Medline]

    15 Ferea,T.L., Botstein,D., Brown,P.O. and Rosenzweig,R.F. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl Acad. Sci. USA, 96, 9721–9726.[Abstract/Free Full Text]

    16 Wyrick,J.J., Holstege,F.C., Jennings,E.G., Causton,H.C., Shore,D., Grunstein,M., Lander,E.S. and Young,R.A. (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature, 402, 418–421.[Medline]

    17 Holstege,F.C., Jennings,E.G., Wyrick,J.J., Lee,T.I., Hengartner,C.J., Green,M.R., Golub,T.R., Lander,E.S. and Young,R.A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95, 717–728.[Web of Science][Medline]

    18 Roberts,C.J., Nelson,B., Marton,M.J., Stoughton,R., Meyer,M.R., Bennett,H.A., He,Y.D., Dai,H., Walker,W.L., Hughes,T.R., Tyers,M., Boone,C. and Friend,S.H. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science, 287, 873–880.[Abstract/Free Full Text]


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Baitaluk, M. Sedova, A. Ray, and A. Gupta
BiologicalNetworks: visualization and analysis tool for systems biology.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W466 - W471.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. Dolinski and D. Botstein
Changing perspectives in yeast research nearly a decade after the genome sequence
Genome Res., December 1, 2005; 15(12): 1611 - 1619.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
B. C. Meyers, S. S. Tej, T. H. Vu, C. D. Haudenschild, V. Agrawal, S. B. Edberg, H. Ghazal, and S. Decola
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
Genome Res., August 1, 2004; 14(8): 1641 - 1653.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. W. Van Dyke, L. D. Nelson, R. G. Weilbaecher, and D. V. Mehta
Stm1p, a G4 Quadruplex and Purine Motif Triplex Nucleic Acid-binding Protein, Interacts with Ribosomes and Subtelomeric Y' DNA in Saccharomyces cerevisiae
J. Biol. Chem., June 4, 2004; 279(23): 24323 - 24333.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. C. Meyers, D. K. Lee, T. H. Vu, S. S. Tej, S. B. Edberg, M. Matvienko, and L. D. Tindell
Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis
Plant Physiology, June 1, 2004; 135(2): 801 - 813.
[Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Daran-Lapujade, M. L. A. Jansen, J.-M. Daran, W. van Gulik, J. H. de Winde, and J. T. Pronk
Role of Transcriptional Regulation in Controlling Fluxes in Central Carbon Metabolism of Saccharomyces cerevisiae: A CHEMOSTAT CULTURE STUDY
J. Biol. Chem., March 5, 2004; 279(10): 9125 - 9138.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. L. Saito, M. Ohtani, H. Sawai, F. Sano, A. Saka, D. Watanabe, M. Yukawa, Y. Ohya, and S. Morishita
SCMD: Saccharomyces cerevisiae Morphological Database
Nucleic Acids Res., January 1, 2004; 32(90001): D319 - 322.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
T. Schlitt, K. Palin, J. Rung, S. Dietmann, M. Lappe, E. Ukkonen, and A. Brazma
From Gene Networks to Gene Function
Genome Res., December 1, 2003; 13(12): 2568 - 2576.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Shedden and S. Cooper
Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods
Nucleic Acids Res., July 1, 2002; 30(13): 2920 - 2929.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
P. Grosu, J. P. Townsend, D. L. Hartl, and D. Cavalieri
Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks
Genome Res., July 1, 2002; 12(7): 1121 - 1126.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. S. Dwight, M. A. Harris, K. Dolinski, C. A. Ball, G. Binkley, K. R. Christie, D. G. Fisk, L. Issel-Tarver, M. Schroeder, G. Sherlock, et al.
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
Nucleic Acids Res., January 1, 2002; 30(1): 69 - 72.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Kumar, K.-H. Cheung, N. Tosches, P. Masiar, Y. Liu, P. Miller, and M. Snyder
The TRIPLES database: a community resource for yeast molecular biology
Nucleic Acids Res., January 1, 2002; 30(1): 73 - 75.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Le Crom, F. Devaux, C. Jacq, and P. Marc
yMGV: helping biologists with yeast microarray data mining
Nucleic Acids Res., January 1, 2002; 30(1): 76 - 79.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. Pal, B. Papp, and L. D. Hurst
Does the Recombination Rate Affect the Efficiency of Purifying Selection? The Yeast Genome Provides a Partial Answer
Mol. Biol. Evol., December 1, 2001; 18(12): 2323 - 2326.
[Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Marc, F. Devaux, and C. Jacq
yMGV: a database for visualization and data mining of published genome-wide yeast expression data
Nucleic Acids Res., July 1, 2001; 29(13): e63 - e63.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (111K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (32)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ball, C. A.
Right arrow Articles by Cherry, J. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ball, C. A.
Right arrow Articles by Cherry, J. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?