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The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data
Open accessAbstract
The Yeast Proteome Database (YPD) is a model for the organization and presentation of comprehensive protein information. Based on the detailed curation of the scientific literature for the yeast Saccharomyces cerevisiae, YPD contains more than 50 000 annotations lines derived from the review of 8500 research publications. The information concerning each of the approximately 6100 yeast proteins is structured around a convenient one-page format, the Yeast Protein Report, with additional information provided as pop-up windows. Protein classification schema have been revised this year, defining each protein's cellular role, function and pathway, and adding a Functional to the Yeast Protein Report. These changes provide the user with a succinct summary of the protein's function and its place in the biology of the cell, and they enhance the power of YPD Search functions. Precalculated sequence alignments have been added, to provide a crossover point for comparative genomics. The first transcript profiling data has been integrated into the YPD Protein Reports, providing the framework for the presentation of genome-wide functional data. The Yeast Proteome Database can be accessed on the Web at http://www.proteome.com/YPDhome.html
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Cited by
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683
DIP: the Database of Interacting Proteins
Xenarios, I. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.289 · Cited by 1,123
Yu, H., Kim, P. M., Sprecher, E., Trifonov, V., & Gerstein, M. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030059 · Cited by 1,014
Dosage sensitivity and the evolution of gene families in yeast
Papp, B., Pál, C., & Hurst, L. D. (2003) · Nature · doi:10.1038/nature01771 · Cited by 753
Metadata
- Authors
- Hodges, P. E., McKee, A. H. Z., Davis, B. P., Payne, W. E., & Garrels, J. I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-01-01
- Volume
- 27
- Issue
- 1
- Pages
- 69-73
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2149887408
- Cited by
- 215
- References
- 0
- FWCI
- 11.74
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Hodges, P. E., McKee, A. H. Z., Davis, B. P., Payne, W. E., & Garrels, J. I. (1999). The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Research. https://doi.org/10.1093/nar/27.1.69
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