The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched.
Interaction data,
- DIP http://dip.doe-mbi.ucla.edu/ (Registration is required. Pairwise data is provided)
* MPact @ MIPS and FTP site
- BIND
- genetic interactions:
- By double-deletion assay, Costanzo 2010 Science
- http://www.yeastnet.org/ , predicted network
- pixie at Princeton, predicted network
- protein half lives:
Archana Belle etal PNAS 2006
- protein abundance
S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature, 2003, 425, 737–741.
- protein expression noise
Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840–846
- protein localization
Nature. 2003 Oct 16;425(6959):686-91. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK.
Botstein lab.
http://www.genomics.princeton.edu/~nslavov/ymc/metabolites.html
http://genomics.princeton.edu/~nslavov/grr_html/transcripts.html
- growth curves
- Yeast deletion project, fitness data
http://www-deletion.stanford.edu/YDPM/YDPM_index.html
http://fitdb.stanford.edu/
multiple sources. Austria.
- Yeast morphology database (SCMD)
http://yeast.gi.k.u-tokyo.ac.jp/datamine/
http://chemogenomics.stanford.edu:16080/supplements/global/download.html
Supplementary information From the following article Quantification of the yeast transcriptome by single-molecule sequencing Doron Lipson, Tal Raz, Alix Kieu, Daniel R Jones, Eldar Giladi, Edward Thayer, John F Thompson, Stan Letovsky, Patrice Milos & M
Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis
David C Hess, Chad L Myers, Curtis Huttenhower, Matthew A Hibbs, Alicia P Hayes, Jadine Paw, John J Clore, Rosa M Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G Troyanskaya, Amy A Caudy (2009), PLoS Genetics 5 (3) p. 16
Mol Biol Cell. 2011 Apr;22(7):988-98. Epub 2011 Feb 2.
The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures.
Davidson GS, Joe RM, Roy S, Meirelles O, Allen CP, Wilson MR, Tapia PH, Manzanilla EE, Dodson AE, Chakraborty S, Carter M, Young S, Edwards B, Sklar L, Werner-Washburne M.
http://www.ncbi.nlm.nih.gov/pubmed/21289090
Evidence for widespread adaptive evolution of gene expression in budding yeast
Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc, PNAS
Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiaew
Sukhraj Pal Singh Dhami,a Nitish Mittal,ab Sarath Chandra Jangab and Nilanjan Roy
Molecular Biology of the Cell Vol. 16, 5410–5417, November 2005
Role of Essential Genes in Mitochondrial Morphogenesis in Saccharomyces cerevisiae□D
Katrin Altmann* and Benedikt Westermann
Molecular Systems Biology 4; Article number 179; doi:10.1038/msb.2008.16
The role of disorder in interaction networks: a structural analysis
Philip M Kim1,5,*, Andrea Sboner1,5, Yu Xia2 and Mark Gerstein1,3,4,*
Complex data
Nature 440, 637-643 (30 March 2006)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
http://www.nature.com/nature/journal/v440/n7084/full/nature04670.html
Positive selection for elevated gene expression noise in yeast, George Zhang's lab
Reviews
[[http://www.ncbi.nlm.nih.gov/pubmed/19743424 | Proteomics. 2009 Oct;9(20):4731-43.
Recent advances in yeast organelle and membrane proteomics. Premsler T, Zahedi RP, Lewandrowski U, Sickmann A.]]
Labs to follow
- Boone lab
- Botstein lab
- Oshea lab
- Weismann lab
- Sherlock lab
- Siegal lab
- Fay lab