Phase coupled meta-analysis: Sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast

BMC Genomics

Volumn 10, Issue , 2009, Pages 440-

  Pyne, Saumyadipta ^a,b   Gutman, Roee ^c   Kim, Chang S ^d   Futcher, Bruce ^e  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD UNIVERSITY   (United States)

^d Sookmyung Women's University   (South Korea)

^e STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CYCLE PROGRESSION; CONTROLLED STUDY; FUNGAL GENETICS; FUNGAL METABOLISM; GENE EXPRESSION REGULATION; GENE VECTOR; GENOME ANALYSIS; NONHUMAN; OSCILLATION; PREDICTION; SCHIZOSACCHAROMYCES POMBE; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS;

CELL CYCLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, CDC; GENES, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCHIZOSACCHAROMYCES; SENSITIVITY AND SPECIFICITY;

SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 70349741133     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-440     Document Type: Article

References (37)

1. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ. A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular cell 1998, 2(1):65-73. 10.1016/S1097-2765(00)80114-8, 9702192.
2. Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science (New York, NY) 2000, 290(5499):2144-2148.
3. Menges M, Hennig L, Gruissem W, Murray JA. Cell cycle-regulated gene expression in Arabidopsis. The Journal of biological chemistry 2002, 277(44):41987-42002. 10.1074/jbc.M207570200, 12169696.
4. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular biology of the cell 1998, 9(12):3273-3297. 25624, 9843569.
5. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular biology of the cell 2002, 13(6):1977-2000. 10.1091/mbc.02-02-0030., 117619, 12058064.
6. de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (Oxford, England) 2005, 21(7):1164-1171. 10.1093/bioinformatics/bti093, 15513999.
7. Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bahler J. Periodic gene expression program of the fission yeast cell cycle. Nature genetics 2004, 36(8):809-817. 10.1038/ng1377, 15195092.
8. Peng X, Karuturi RK, Miller LD, Lin K, Jia Y, Kondu P, Wang L, Wong LS, Liu ET, Balasubramanian MK. Identification of cell cycle-regulated genes in fission yeast. Molecular biology of the cell 2005, 16(3):1026-1042. 10.1091/mbc.E04-04-0299, 551471, 15616197.
9. Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, Skiena S, Futcher B, Leatherwood J. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS biology 2005, 3(7):e225. 10.1371/journal.pbio.0030225, 1157095,1157095, 15966770.
10. Pyne S, Futcher B, Skiena S. Meta-Analysis of Microarray Data. Bioinformatics Algorithms: Techniques and Applications 2008, Mandoiu IaAZ: Wiley-Interscience; Hoboken, NJ.
11. Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bahler J. The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast (Chichester, England) 2006, 23(4):261-277. 10.1002/yea.1351, 1828074, 16544289.
12. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57(1):289-300.
13. Fisher NI. Statistical Analysis of Circular Data. 1996, Cambridge University Press; New York.
14. Kaufman L, Rousseeuw PJ. Finding Groups in Data: An Introduction to Cluster Analysis. 2006, Wiley, John & Sons, Incorporated; Hoboken, NJ.
15. Rousseeuw PJ. Silhouettes - a Graphical Aid to the Interpretation and Validation of Cluster-Analysis. Journal of Computational and Applied Mathematics 1987, 20:53-65.
16. Kim CS, Bae CS, Tcha HJ. A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data. BMC bioinformatics 2008, 9:56. 10.1186/1471-2105-9-56, 2335309, 18221564.
17. Allefeld C, Kurths J. An approach to multivariate phase synchronization analysis and its application to event-related potentials. International Journal of Bifurcation and Chaos 2004, 14(2):417-426.
18. Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Proceedings of the Pacific Symposium on Biocomputing 2001, 127-138.
19. Fu Y, Frith MC, Haverty PM, Weng Z. MotifViz: an analysis and visualization tool for motif discovery. Nucleic acids research 2004, (32 Web Server):W420-423. 10.1093/nar/gkh426, 441564, 15215422.
20. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R. The TRANSFAC system on gene expression regulation. Nucleic acids research 2001, 29(1):281-283. 10.1093/nar/29.1.281, 29801, 11125113.
21. O'Brien KP, Remm M, Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic acids research 2005, (33 Database):D476-480. 540061, 15608241.
22. Penkett CJ, Morris JA, Wood V, Bahler J. YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic acids research 2006, (34 Web Server):W330-334. 10.1093/nar/gkl311, 1538793, 16845020.
23. Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic acids research 2008, (36 Database):D854-859. 2238932, 17940094.
24. Lu X, Zhang W, Qin ZS, Kwast KE, Liu JS. Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic acids research 2004, 32(2):447-455. 10.1093/nar/gkh205, 373332, 14739237.
25. Liu D, Umbach DM, Peddada SD, Li L, Crockett PW, Weinberg CR. A random-periods model for expression of cell-cycle genes. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(19):7240-7245. 10.1073/pnas.0402285101, 409903, 15123814.
26. Caretta-Cartozo C, De Los Rios P, Piazza F, Lio P. Bottleneck genes and community structure in the cell cycle network of S. pombe. PLoS computational biology 2007, 3(6):e103. 10.1371/journal.pcbi.0030103, 1885277,1885277, 17542643.
27. Langmead CJ, Yan AK, McClung CR, Donald BR. Phase-independent rhythmic analysis of genome-wide expression patterns. J Comput Biol 2003, 10(3-4):521-536. 10.1089/10665270360688165, 12935342.
28. Tsiporkova E, Boeva V. Fusing time series expression data through hybrid aggregation and hierarchical merge. Bioinformatics (Oxford, England) 2008, 24(16):i63-69. 10.1093/bioinformatics/btn264, 18689841.
29. Rao JS, Sengupta A. Topics in Circular Statistics. 2001, World Scientific Publishing Company; Singapore.
30. Zhang N, Gong ZZ, Minden M, Lu M. The HOX-11 (TCL-3) homeobox proto-oncogene encodes a nuclear protein that undergoes cell cycle-dependent regulation. Oncogene 1993, 8(12):3265-3270.
31. Kawabe T, Muslin AJ, Korsmeyer SJ. HOX11 interacts with protein phosphatases PP2A and PP1 and disrupts a G2/M cell-cycle checkpoint. Nature 1997, 385(6615):454-458. 10.1038/385454a0, 9009195.
32. Futschik ME, Herzel H. Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics (Oxford, England) 2008, 24(8):1063-1069. 10.1093/bioinformatics/btn072, 18310054.
33. Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome biology 2008, 9(6):403. 10.1186/gb-2008-9-6-403, 2481420, 18598377.
34. Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z. Combined analysis reveals a core set of cycling genes. Genome biology 2007, 8(7):R146. 10.1186/gb-2007-8-7-r146, 2323241, 17650318.
35. Ptitsyn AA, Zvonic S, Conrad SA, Scott LK, Mynatt RL, Gimble JM. Circadian clocks are resounding in peripheral tissues. PLoS computational biology 2006, 2(3):e16. 10.1371/journal.pcbi.0020016, 1391918,1391918, 16532060.
36. Ptitsyn AA, Zvonic S, Gimble JM. Permutation test for periodicity in short time series data. BMC bioinformatics 2006, 7(Suppl 2):S10. 10.1186/1471-2105-7-S2-S10, 1683571, 17118131.
37. Ptitsyn AA, Zvonic S, Gimble JM. Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes. PLoS computational biology 2007, 3(6):e120. 10.1371/journal.pcbi.0030120, 1892608,1892608, 17571920.