A maximum entropy algorithm for rhythmic analysis of genome-wide expression patterns

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002

Volumn , Issue , 2002, Pages 237-245

  Langmead, C J ^a   McClung, C R ^b   Donald, B R ^a,b,c  

^a Dartmouth Department of Computer Science_Dartmouth College   (United States)

^b Dartmouth College   (United States)

^c DARTMOUTH COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; DNA; FREQUENCY DOMAIN ANALYSIS; GENE EXPRESSION; GENES; OPTIMIZATION; SPECTRUM ANALYSIS;

BI-CRITERION OPTIMIZATIONS; BIOLOGICAL PROCESS; EXPRESSION PATTERNS; EXPRESSION PROFILE; GENE EXPRESSION DATA; MAXIMUM ENTROPY ALGORITHMS; RHYTHMIC ANALYSIS; SPECTRAL RECONSTRUCTION;

MAXIMUM ENTROPY METHODS;

DROSOPHILA PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CELL CYCLE; CHROMOSOME MAP; CIRCADIAN RHYTHM; DNA MICROARRAY; ENTROPY; EVALUATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PERIODICITY; PHYSIOLOGY;

ALGORITHMS; CELL CYCLE; CHROMOSOME MAPPING; CIRCADIAN RHYTHM; DROSOPHILA PROTEINS; ENTROPY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; PERIODICITY; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 0242653535     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2002.1039346     Document Type: Conference Paper

References (35)

1. Stanford Microarray Database. http://genome-www4.stanford.edu/MicroArray/SMD/.
2. H. Araki, R. K. Hamatake, A. Morrison, A. L. Johnson, L. H. Johnston, and S. A. Cloning DPB3, the gene encoding the third subunit of DNA polymerase II of Saccharomyces cerevisiae. Nucleic Acids Res, 19:4867-4872, 1991.
3. I. Barrodale and R. Ericson. An algorithm for least-squares linear prediction and maximum entropy spectral analysis. Part 1 : theory and Part 2 : fortran program. Geophys, 45:420-446, 1980.
4. K. Birnbaum, P. N. Benfey, and D. E. Shasha. cis Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor/cis Element Relationships. Genome Res, 11:1567-1573, 2001.
5. J. Burg. Maximum entropy spectral analysis. PhD thesis, Dep. Geophysics Stanford Univ, 1975.
6. L. H. Caro, G. J. Smits, P. van Egmond, J. W. Chapman, and F. M. Klis. Transcription of multiple cell wall protein-encoding genes in Saccharomyces cerevisiae is deferentially regulated during the cell cycle. FEMS Microbiol. Lett, 161:345-349, 1998.
7. J. W. Chapman and J. L. H. The yeast gene, dbf4, essential for entry into s phase is cell cycle regulated. Exp. Cell Res., 180:419-428, 1989.
8. R. Cho, M. Campbell, E. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. Wolfsberg, A. Gabrielian, D. Landsman, D. Lockhart, and R. Davis. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2:65-73, 1998.
9. A. Claridge-Chang, H. Wijnen, F. Naef, C. Boothroyd, N. Rajewsky, and M. W. Young. Circadian Regulation of Gene Expression Systems in the Drosophila Head. Neuron, 32:657-671, 2001.
10. B. R. Donald, D. Kapur, and J. Mundy. Symbolic and Numerical Computation for Artificial Intelligence, chapter 8, "Distance metrics for comparing shapes in the plane," by D. Huttenlocher and K. Kedem, pages 201-219. Academic Press, Harcourt Jovanovich, London, 1992.
11. H. B. Dowse, J. C. Hall, and J. M. Ringo. Circadian and ultradian rhythms in period mutants of Drosophila melanogaster. Behavior Genetics, 17:19-35, 1987.
12. H. B. Dowse and J. M. Ringo. The Search for Hidden Periodicities in Biological Time Series Revisited. J. theor. Biol., 139:487-515, 1989.
13. M. Eisen, P. T. Spellman, D. Botstein, and P. O. Brown. Cluster Analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci., 95(25):14863-14868, 1998.
14. V. Filkov, S. Skiena, and J. Zhi. Analysis Techniques for Microarray Time-Series Data. Proc. of the 5th Ann.Intl. Conf. on Comput. Biol., pages 124-131, 2001.
15. I. Fitch, C. Dahmann, U. Surana, A. Amon, K. Nasmyth, L. Goetsch, B. Byers, and F. B. Characterization of four B-type cyclin genes of the budding yeast Saccharomyces cerevisiae. Mol. Biol. Cell, 3:805-818, 1992.
16. C. Grundschober, F. Delaunay, A. Phlhofer, G. Triqueneaux, V. Laudet, T. Bartfai, and P. Nef. Circadian Regulation of Diverse Gene Products Revealed by mRNA Expression Profiling of Synchronized Fibroblasts. J. Biol. Chem., 276:46751-46758, 2001.
17. S. Harmer, J. B. Hogenesch, M. Straume, H. S. Chang, B. Han, T. Zhu, X. Wang, J. A. Kreps, and S. A. Kay. Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock. Science, 290:2110-2113, 2000.
18. D. P. Huttenlocher and K. Kedem. Computing the minimum Hausdorff distance for point sets under translation. Proc. 6th ACM Symp. Computational Geom., pages 340-349, 1990.
19. J. C. Igual, A. L. Johnson, and L. H. Johnston. Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J., 15:5001-5013, 1996.
20. V. R. Iyer, M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, J. C. F. Lee, J. M. Trent, L. M. Staudt, J. J. Hudson, M. S. Boguski, D. Lashkari, D. Shalon, D. Botstein, and P. O. Brown. The transcriptional program in the response of human fibroblasts to serum. Science, 283:83-87, 1999.
21. L. H. Johnston, J. H. White, A. L. Johnson, G. Lucchini, and P. Plevani. Expression of the yeast DNA primase gene, PRI1, is regulated within the mitotic cell cycle and in meiosis. Mol. Gen. Genet., 221:44-48, 1990.
22. C. J. Langmead, A. K. Yan, C. R. McClung, and B. R. Donald. Phase-independent rhythmic analysis of genome-wide expression patterns. Proc. of the 6th Ann. Intl. Conf. on Research in Comput. Biol. (RECOMB) Washington, D.C., April 18-22), pages 205-215, 2002.
23. J. Levine, P. Funes, H. Dowse, and J. Hall. Signal analysis of behavioral and molecular cycles. BMC Neurosci, 3, 2002.
24. S. Marple. A new autoregressive spectrum analysis algorithm. IEEE Trans. Acoust. Speech Signal Processing, ASSP-28:441-454, 1980.
25. M. J. McDonald and M. Rosbash. Microarray analysis and organization of circadian gene expression in Drosophila. Cell, 107:567-578, 2001.
26. W. Press, B. Flannery, S. Teukolski, and W. Vettering. Numerical recipes : the art of scientific computing, chapter 13, Fourier and Spectral Applications, pages 572-575. Cambridge University Press, Cambridge, 1988.
27. R. Schaffer, J. Landgraf, M. Accerbi, V. Simon, M. Larson, and E. Wisman. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell, 13:113-123, 2001.
28. W. Siede, G. W. Robinson, D. Kalainov, T. Malley, and E. C. Friedberg. Regulation of the RAD2 gene of Saccharomyces cerevisiae. Mol. Microbiol, 3:1697-1707, 1989.
29. J. Skilling and S. F. Gull. Maximum Entropy and Bayesian Methods in Inverse Problems, chapter "Algorithms and applications" by Skilling, J. and Gull, S. F., pages 83-132. Reidel Publishing Co, Dordrecht, Holland, 1985.
30. P. Spellman, G. Sherlock, M. Q. Zhang, R. I. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell, 9:3273-3297, 1998.
31. K. Storch, O. Lipan, I. Leykin, N. Viswanathan, F. Davis, W. Wong, and C. Weitz. Extensive and divergent circadian gene expression in liver and heart. Nature, 417:78-82, 2002.
32. T. Ulrich and T. Bishop. Maximum entropy spectral analysis and autoregressive decomposition. Rev. Geophys. Space Phys., 13:183-200, 1975.
33. J. Wan, H. Xu, and M. Grunstein. Cdc14 of Saccharomyces cerevisiae. Cloning, sequence analysis, and transcription during the cell cycle. J. Biol. Chem., 267:11274-11280, 1992.
34. J. H. White, S. R. Green, D. G. Barker, L. B. Dumas, and L. H. Johnston. The cdc8 transcript is cell cycle regulated in yeast and is expressed coordinately with cdc9 and cdc21 at a point preceding histone transcription. Exp. Cell Res., 171:223-231, 1987.
35. K. Yagita, F. Tamanini, G. T. J. van der Horst, and H. Okamura. Molecular Mechanisms of the Biological Clock in Cultured Fibroblasts. Science, 292:278-281, 2001.