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. 1998 Jan 1;26(1):68–72. doi: 10.1093/nar/26.1.68

The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae.

P E Hodges 1, W E Payne 1, J I Garrels 1
PMCID: PMC147175  PMID: 9399803

Abstract

The Yeast Protein Database (YPD) is a curated database for the proteome of Saccharomyces cerevisiae . It consists of approximately 6000 Yeast Protein Reports, one for each of the known or predicted yeast proteins. Each Yeast Protein Report is a one-page presentation of protein properties, annotation lines that summarize findings from the literature, and references. In the past year, the number of annotation lines has grown from 25 000 to approximately 35 000, and the number of articles curated has grown from approximately 3500 to >5000. Recently, new data types have been included in YPD: protein-protein interactions, genetic interactions, and regulators of gene expression. Finally, a new layer of information, the YPD Protein Minireviews, has recently been introduced. The Yeast Protein Database can be found on the Web at http://www.proteome.com/YPDhome. html

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Selected References

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  1. Burns N., Grimwade B., Ross-Macdonald P. B., Choi E. Y., Finberg K., Roeder G. S., Snyder M. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 1994 May 1;8(9):1087–1105. doi: 10.1101/gad.8.9.1087. [DOI] [PubMed] [Google Scholar]
  2. Fromont-Racine M., Rain J. C., Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genet. 1997 Jul;16(3):277–282. doi: 10.1038/ng0797-277. [DOI] [PubMed] [Google Scholar]
  3. Garrels J. I., McLaughlin C. S., Warner J. R., Futcher B., Latter G. I., Kobayashi R., Schwender B., Volpe T., Anderson D. S., Mesquita-Fuentes R. Proteome studies of Saccharomyces cerevisiae: identification and characterization of abundant proteins. Electrophoresis. 1997 Aug;18(8):1347–1360. doi: 10.1002/elps.1150180810. [DOI] [PubMed] [Google Scholar]
  4. Garrels J. I. YPD-A database for the proteins of Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Jan 1;24(1):46–49. doi: 10.1093/nar/24.1.46. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Goffeau A., Barrell B. G., Bussey H., Davis R. W., Dujon B., Feldmann H., Galibert F., Hoheisel J. D., Jacq C., Johnston M. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546, 563-7. doi: 10.1126/science.274.5287.546. [DOI] [PubMed] [Google Scholar]
  6. Hunter T., Plowman G. D. The protein kinases of budding yeast: six score and more. Trends Biochem Sci. 1997 Jan;22(1):18–22. doi: 10.1016/s0968-0004(96)10068-2. [DOI] [PubMed] [Google Scholar]
  7. Niedenthal R. K., Riles L., Johnston M., Hegemann J. H. Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast. Yeast. 1996 Jun 30;12(8):773–786. doi: 10.1002/(SICI)1097-0061(19960630)12:8%3C773::AID-YEA972%3E3.0.CO;2-L. [DOI] [PubMed] [Google Scholar]
  8. Payne W. E., Garrels J. I. Yeast Protein database (YPD): a database for the complete proteome of Saccharomyces cerevisiae. Nucleic Acids Res. 1997 Jan 1;25(1):57–62. doi: 10.1093/nar/25.1.57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Shevchenko A., Jensen O. N., Podtelejnikov A. V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., Mann M. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14440–14445. doi: 10.1073/pnas.93.25.14440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Shoemaker D. D., Lashkari D. A., Morris D., Mittmann M., Davis R. W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet. 1996 Dec;14(4):450–456. doi: 10.1038/ng1296-450. [DOI] [PubMed] [Google Scholar]
  11. Smith V., Chou K. N., Lashkari D., Botstein D., Brown P. O. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science. 1996 Dec 20;274(5295):2069–2074. doi: 10.1126/science.274.5295.2069. [DOI] [PubMed] [Google Scholar]
  12. Velculescu V. E., Zhang L., Zhou W., Vogelstein J., Basrai M. A., Bassett D. E., Jr, Hieter P., Vogelstein B., Kinzler K. W. Characterization of the yeast transcriptome. Cell. 1997 Jan 24;88(2):243–251. doi: 10.1016/s0092-8674(00)81845-0. [DOI] [PubMed] [Google Scholar]

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