Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages 2823-2832

  Fernández, Miguel A ^a   Rueda, Cristina ^a   Peddada, Shyamal D ^b  

^a UNIVERSITY OF VALLADOLID   (Spain)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACE2 GENE; ARTICLE; CDC18 GENE; CELL CYCLE; EVOLUTION; GENE; GENE EXPRESSION; GENE IDENTIFICATION; HHF1 GENE; HTA2 GENE; HUMAN; MIK1 GENE; NONHUMAN; PLO1 GENE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; STATISTICAL ANALYSIS;

DATA INTERPRETATION, STATISTICAL; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENES, CDC; GENES, FUNGAL; HUMANS; PERIODICITY; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

EID: 84860200052     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1077     Document Type: Article

References (31)

1. Hartwell, L. and Kastan, M. (1994) Cell cycle control and cancer. Science, 266, 1821-1828.
2. Elledge, S. (1996) Cell cycle check points: preventing an identity crisis. Science, 274, 1664-1671.
3. Jensen, L.J., Jensen, T.S., de Lichtenberg, U., Brunak, S. and Bork, P. (2006) Co-evolution of transcriptional and posttranslational cell-cycle regulation. Nature, 443, 594-597. (Pubitemid 44527297)
4. Rustici, G., Mata, J., Kivinen, K., Lió , P., Penkett, C.J., Burns, G., Hayles, J., Brazma, A., Nurse, P. and Bähler, J. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat. Genet., 36, 809-817. (Pubitemid 39014097)
5. Bahler, J. (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet., 39, 69-94. (Pubitemid 43011108)
6. Cho, R., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockart, D.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73. (Pubitemid 128378967)
7. Spellman, P., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297. (Pubitemid 28551928)
8. de Lichtenberg, U., Wernersson, R., Jensen, T.S., Nielsen, H.B., Fausbøll, A., Schmidt, P., Hansen, F.B., Knudsen, S. and Brunak, S. (2005) New weakly expressed cell cycle-regulated genes in yeast. Yeast, 22, 1191-1201. (Pubitemid 41762882)
9. Pramila, T., Wu, W., Miles, S., Noble, W.S. and Breeden, L.L. (2006) The forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev., 20, 2266-2278.
10. Rustici, G. (2004) Periodic gene expression program of the fission yeast cell cycle. PhD Dissertation. Darwin College, Cambridge University, Cambridge, UK.
11. Oliva, A., Rosebrock, A., Ferrezuelo, F., Pyne, S., Chen, H., Skiena, S., Futcher, B. and Leatherwood, J. (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol., 3, 1239-1260. (Pubitemid 41032191)
12. Peng, X., Karuturi, R.K.M., Miller, L.D., Lin, K., Jia, Y., Kondu, P., Wang, L., Wong, L.S., Liu, E.T., Balasubramanian, M.K. et al. (2005) Identification of cell cycle-regulated genes in fission yeast. Mol. Biol. Cell, 16, 1026-1042. (Pubitemid 40349543)
13. Whitfield, M., Sherlock, G., Saldanha, A.J., Murray, J.I., Ball, C.A., Alexander, K.E., Matese, J.C., Perou, C.M., Hurt, M.M., Brown, P.O. et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell, 13, 1977-2000. (Pubitemid 34651487)
14. Menges, M., Hennig, L., Gruissem, W. and Murray, J.A. (2002) Cell cycle-regulated gene expression in Arabidopsis. J. Biol. Chem., 277, 41987-42002. (Pubitemid 35257513)
15. Menges, M., Hennig, L., Gruissem, W. and Murray, J.A. (2003) Genome-wide gene expression in an Arabidopsis cell suspension. Plant Mol. Biol., 53, 423-442. (Pubitemid 38345338)
16. Gauthier, N., Larsen, M.E., Wernersson, R., de Lichtenberg, U., Jensen, L.J., Brunak, S. and Jensen, T.S. (2008) Cyclebase.org-a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res., 36, D854-D859. (Pubitemid 351149835)
17. Caretta-Cartozo, C., de los Rios, P., Piazza, F. and Lió , P. (2007) Bottleneck genes and community structure in the cell cycle network of S. pombe. PLoS Comput. Biol., 3, 968-976.
18. Moura, D., Castilhos, B., Immich, B., Cañedo, A.D., Henriques, J.A.P., Lenz, G. and Saffi, J. (2010) Kin3 protein, a NIMA-related kinase of Saccharomyces cerevisiae, is involved in DNA adduct damage response. Cell cycle, 9, 2220-2229.
19. Liu, D., Umbach, D.M., Peddada, S.D., Li, L., Crockett, P.W. and Weinberg, C.R. (2004) A random-periods model for expression of cell-cycle genes. Proc. Natl Acad. Sci. USA, 101, 7240-7245. (Pubitemid 38638017)
20. Rueda, C., Fernández, M. and Peddada, S.D. (2009) Estimation of parameters subject to order restriction on a circle with application to estimation of phase angles of cell-cycle genes. J. Am. Stat. Assoc., 104, 338-347.
21. Jothi, R., Przytycka, T. and Aravind, L. (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics, 8, 173.
22. Bushel, P., Heard, N., Gutman, R., Liu, L., Peddada, S. and Pyne, S. (2009) Dissecting the fission yeast regulatory network reveals phasespecific control elements of its cell cycle. BMC Syst. Biol., 3, 93.
23. Liu, J., Smith, C., DeRyckere, D., DeAngelis, K., Martin, G. and Berger, J. (2000) Structure and function of Cdc6/Cdc18: implications for origin recognition and check point control. Mol. Cell, 6, 637-648.
24. Rhind, N. and Russell, P. (2001) Roles of the mitotic inhibitors Wee1 and Mik1 in the G2 DNA damage and replication check points. Mol. Cell Biol., 21, 1499-1508. (Pubitemid 32156370)
25. Wang, B., Feng, L., Hu, Y., Huang, S.H., Reynolds, C.P., Wu, L. and Jong, A.Y. (1999) The essential role of Saccharomyces cerevisiae CDC6 nucleotide-binding site in cell growth, DNA synthesis, and Orc1 association. J. Biol. Chem., 274, 8291-8298.
26. Bartholomew, D.J. (1961) A test of homogeneity for means under restricted alternatives. J. R. Stat. Soc. Ser. B, 23, 239-281.
27. Robertson, T. and Wegman, E.J. (1978) Likelihood ratio tests for order restrictions for exponential families. Ann. Stat., 6, 485-505.
28. Iverson, G.J. and Harp, S.A. (1987) A conditional likelihood ratio test for order restrictions in exponential families. Math. Soc. Sci., 14, 141-159.
29. Menéndez, J.A., Rueda, C. and Salvador, B. (1991) Conditional test for testing a face of the tree order cone. Commun. Stat. Simul. Comput., 20, 751-762.
30. Mardia, K. and Jupp, P. (2000) Directional Statistics. John-Wiley & Sons, Chichester.
31. Robertson, T., Wright, F.T. and Dykstra, R.L. (1988) Order Restricted Statistical Inference. Wiley, New York.