The more the merrier: Comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast

Yeast

Volumn 23, Issue 4, 2006, Pages 261-277

  Marguerat, Samuel ^a   Jensen, Thomas S ^b   de Lichtenberg, Ulrik ^b   Wilhelm, Brian T ^a   Jensen, Lars J ^c   Bähler, Jürg ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Cell cycle; Cell division; Computational biology; Microarray; Periodic gene expression; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Transcription

Indexed keywords

ARTICLE; CELL CYCLE REGULATION; CELL SYNCHRONIZATION; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; FOLLOW UP; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; INTERNET; MICROARRAY ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; RELIABILITY; REPRODUCIBILITY; SCHIZOSACCHAROMYCES POMBE; TRANSCRIPTION REGULATION;

CELL CYCLE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, FUNGAL; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCHIZOSACCHAROMYCES;

SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 33645743420     PISSN: 0749503X     EISSN: 10970061     Source Type: Journal    
DOI: 10.1002/yea.1351     Document Type: Article

References (43)

1. Ahdesmäki M, Lahdesmäki H, Pearson R, Huttunen H, Yli-Harja O. 2005. Robust detection of periodic time series measured from biological systems. BMC Bioinf 6: 117.
2. Alonso-Nunez ML, An H, Martin-Cuadrado AB, et al. 2005. Ace2p controls the expression of genes required for cell separation in Schizosaccharomyces pombe. Mol Biol Cell 16: 2003-2017.
3. 1 interval during the fission yeast mitotic cell cycle. EMBO J 21: 5745-5755.
4. Bähler J. 2005a. Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39: 69-94.
5. Bähler J. 2005b. A transcriptional pathway for cell separation in fission yeast. Cell Cycle 4: 39-41.
6. Buck V, Ng SS, Ruiz-Garcia AB, et al. 2004. Fkh2p and Sep1p regulate mitotic gene transcription in fission yeast. J Cell Sci 117: 5623-5632.
7. Bulmer R, Pic-Taylor A, Whitehall SK, et al. 2004. The forkhead transcription factor Fkh2 regulates the cell division cycle of Schizosaccharomyces pombe. Eukaryot Cell 3: 944-954.
8. Chen D, Toone WM, Mata J, et al. 2003. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214-229.
9. Cho RJ, Campbell MJ, Winzeler EA, et al. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2: 65-73.
10. Cooper S, Shedden K. 2003. Microarray analysis of gene expression during the cell cycle. Cell Chromosome 2: 1.
11. de Lichtenberg U, Jensen LJ, Fausboll A, et al. 2005. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21: 1164-1171.
12. de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S. 2003. Protein feature based identification of cell cycle regulated proteins in yeast. J Mol Biol 329: 663-674.
13. Dekker N, Speijer D, Grun CH, et al. 2004. Role of the alpha-glucanase Agn1p in fission-yeast cell separation. Mol Biol Cell 15: 3903-3914.
14. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14 863-14 868.
15. + gene encodes a member of the MCM family of replication proteins. J Cell Sci 107: 2779-2788.
16. Gilks WR, Tom BD, Brazma A. 2005. Fusing microarray experiments with multivariate regression. Bioinformatics 21(suppl 2): ii137-ii143.
17. Ihmels J, Bergmann S, Berman J, Barkai N. 2005. Comparative gene expression analysis by a differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1: e39.
18. Ishida S, Huang E, Zuzan H, et al. 2001. Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol 21: 4684-4699.
19. 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: 467-473.
20. +, a UV-inducible gene from Schizosaccharomyces pombe. Environ Mol Mutagen 30: 72-81.
21. Kruglyak S, Tang H. 2001. A new estimator of significance of correlation in time series data. J Comput Biol 8: 463-470.
22. Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L. 2000. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290: 2144-2148.
23. Lee KM, Miklos I, Du H, et al. 2005. Impairment of the TFIIH-associated CDK-activating kinase selectively affects cell cycle-regulated gene expression in fission yeast. Mol Biol Cell 16: 2734-2745.
24. Lopez-Aviles S, Grande M, Gonzalez M, et al. 2005. Inactivation of the Cdc25 phosphatase by the stress-activated Srk1 kinase in fission yeast. Mol Cell 17: 49-59.
25. Luan Y, Li H. 2004. Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. Bioinformatics 20: 332-339.
26. Lyne R, Burns G, Mata J, et al. 2003. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genom 4: 27.
27. Martín-Cuadrado AB, Dueñas E, Sipiczki M, Vázquez de Aldana CR, Del Rey F. 2003. The endo-β-1,3-glucanase eng1p is required for dissolution of the primary septum during cell separation in Schizosaccharomyces pombe. J Cell Sci 116: 1689-1698.
28. Mata J, Lyne R, Burns G, Bähler J. 2002. The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet 32: 143-147.
29. Menges M, Hennig L, Gruissem W, Murray JA. 2002. Cell cycle-regulated gene expression in Arabidopsis. J Biol Chem 277: 41 987-42 002.
30. Mitchison JM, Nurse P. 1985. Growth in cell length in the fission yeast Schizosaccharomyces pombe. J Cell Sci 75: 357-376.
31. Oliva A, Rosebrock A, Ferrezuelo F, et al. 2005. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol 3: e225.
32. Peng X, Karuturi RK, Miller LD, et al. 2005. Identification of cell cycle-regulated genes in fission yeast. Mol Biol Cell 16: 1026-1042.
33. Petersen J, Hagan IM. 2005. Polo kinase links the stress pathway to cell cycle control and tip growth in fission yeast. Nature 435: 507-512.
34. + expression. J Cell Sci 118: 5731-5742.
35. Plochocka-Zulinska D, Rasmussen G, Rasmussen C. 1995. Regulation of calcineurin gene expression in Schizosaccharomyces pombe. Dependence on the ste11 transcription factor. J Biol Chem 270: 24 794-24 799.
36. Rustici G, Mata J, Kivinen K, et al. 2004. Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36: 809-817.
37. Spellman PT, Sherlock G, Zhang MQ, et al. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
38. Szilagyi Z, Batta G, Enczi K, Sipiczki M. 2005. Characterisation of two novel fork-head gene homologues of Schizosaccharomyces pombe: their involvement in cell cycle and sexual differentiation. Gene 348: 101-109.
39. Tyers M. 2004. Cell cycle goes global. Curr Opin Cell Biol 16: 602-613.
40. 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.
41. Willbrand K, Radvanyi F, Nadal JP, Thiery JP, Fink TM. 2005. Identifying genes from up-down properties of microarray expression series. Bioinformatics 21: 3859-3864.
42. Wittenberg C, Reed SI. 2005. Cell cycle-dependent transcription in yeast: promoters, transcription factors, and transcriptomes. Oncogene 24: 2746-2755.
43. Zhao LP, Prentice R, Breeden L. 2001. Statistical modeling of large microarray datasets to identify stimulus-response profiles. Proc Natl Acad Sci USA 98: 5631-5636.