New weakly expressed cell cycle-regulated genes in yeast

Yeast

Volumn 22, Issue 15, 2005, Pages 1191-1201

  de Lichtenberg, Ulrik ^a   Wernersson, Rasmus ^a   Jensen, Thomas Skøt ^a   Nielsen, Henrik Bjørn ^a   Fausbøll, Anders ^a   Schmidt, Peer ^b   Hansen, Fleming Bryde ^a   Knudsen, Steen ^a   Brunak, Søren ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Febit AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BIOINFORMATICS; CELL CYCLE; CELL SIZE; CONTROLLED STUDY; DNA REPAIR; GENETIC TRANSCRIPTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION; VALIDATION PROCESS; YEAST CELL;

CELL CYCLE PROTEINS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, CDC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

HOMO SAPIENS; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 28844455307     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.1302     Document Type: Article

References (42)

1. Banerjee N, Zhang MQ. 2003. Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23): 7024-7031.
2. Baum M, Bielau S, Rittner N, et al. 2003. Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res 31(23): e151-e151.
3. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodol) 57(1): 289-300.
4. Brazma A, Parkinson H, Sarkans U, et al. 2003. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31(1): 68-71.
5. Breeden LL. 2003. Periodic transcription: a cycle within a cycle. Curr Biol 13: R31-R38.
6. Cho R, Campbell M, Winzeler E, et al. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2: 65-73.
7. Coghlan A, Wolfe KH. 2000. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16(12): 1131-1145.
8. Cooper S. 2004a. Is whole-culture synchronization biology's 'perpetual-motion machine'? Trends Biotechnol 22(6): 266-269.
9. Cooper S. 2004b. Rejoinder: whole-culture synchronization cannot, and does not, synchronize cells. Trends Biotechnol 22(6): 274-276.
10. de Lichtenberg U, Jensen LJ, Brunak S, Bork P. 2005a. Dynamic complex formation during the yeast cell cycle. Science 307(5710): 724-727.
11. de Lichtenberg U, Jensen LJ, Fausbøll A, et al. 2005b. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21(7): 1164-1171. DOI:10.1093/bioinformatics/bti093.
12. de Lichtenberg U, Jensen T, Jensen L, Brunak S. 2003. Protein feature based identification of cell cycle-regulated proteins in yeast. J Mol Biol 329(1): 663-674.
13. Dolinski K, Balakrishnan R, Christie K, et al. Saccharomyces genome database; accessed 1 December 2003: ftp://ftp.yeastgenome.org/yeast/
14. Futcher B. 1999. Cell cycle synchronization. Methods Cell Sci 21(2-3): 79-86.
15. 1 cyclin cln3 to modulate cell fate in budding yeast. Genes Dev 15(21): 2803-2808.
16. Gautier L, Cope L, Bolstad BM, Irizarry RA. 2004. Affy-analysis of Affymetrix genechip data at the probe level. Bioinformatics 20(3): 307-315.
17. Gray NS, Wodicka L, Thunnissen AMWH, et al. 1998. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science 281: 533-538.
18. Holstege FC, Jennings EG, Wyrick JJ, et al. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95(5): 717-728.
19. 1/S transition in Saccharomyces cerevisiae. Genes Dev 16: 3017-3033.
20. Iyer V, Horak C, Scafe C, et al. 2001. Genomics binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
21. Johansson D, Lindgren P, Berglund A. 2003. A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. Bioinformatics 19(4): 467-473.
22. Lee T, Rinaldi N, Robert F, et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
23. Li C, Wong W. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98(1): 31-36.
24. Lu X, Zhang W, Qin ZS, et al. 2004. Statistical resyncronization and Bayesian detection of periodically expressed genes. Nucleic Acids Res 32: 447-455.
25. Luan Y, Li H. 2004. Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. Bioinformatics 20(3): 332-339.
26. Nielsen H, Wernersson R, Knudsen S. 2003. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31(13): 3491-3496.
27. Reiner A, Yekutieli D, Benjamini Y. 2003. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19(3): 368-375.
28. Rustici G, Mata J, Kivinen K, et al. 2004. Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36(8): 809-817.
29. Schmitt M, Brown T, Trumpower B. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18: 3091-3092.
30. Shedden K, Cooper S. 2002. Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucleic Acids Res 30(13): 2920-2929.
31. Shimizu M, Li W, Covitz PA, et al. 1998. Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator Ime1. Nucleic Acids Res 26: 2329-2336.
32. Simon I, Barnett J, Hannett N, et al. 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106: 697-708.
33. Spellman P, Sherlock G, Zhang M, et al. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast S. cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
34. Spellman PT, Sherlock G. 2004a. Final words: cell age and cell cycle are unlinked. Trends Biotechnol 22(6): 277-278.
35. Spellman PT, Sherlock G. 2004b. Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends Biotechnol 22(6): 270-273.
36. Tyers M, Jorgensen P. 2000. Proteolysis and the cell cycle: with this RING I thee destroy. Curr Opin Genet Dev 10: 54-64.
37. Übersax JA, Woodbury EL, Quang PN, et al. 2003. Targets of the cyclin-dependent kinase cdk1. Nature 425(6960): 859-864.
38. Verduyn C, Postma E, Scheffers W, Van Dijken J. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8(7): 501-517.
39. Whitfield ML, Sherlock G, Saldanha AJ, et al. 2002. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13: 1977-2000.
40. Wichert S, Fokianos K, Strimmer K. 2004. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 20(1): 5-20.
41. Workman C, Jensen L, Jarmer H, et al. 2002. A new non-linear normalization method to reduce variability in DNA microarray experiments. Genome Biol 3(9): research0048.1-0048.16.
42. Zhao L, Prentice R, Breeden L. 2001. Statistical modeling of large microarray datasets to identify stimulus-response profiles. Proc Natl Acad Sci USA 98: 5631-5636.