Time ordering of gene coexpression

Biostatistics

Volumn 7, Issue 4, 2006, Pages 569-584

  Leng, Xiaoyan ^a   Müller, Hans Georg ^b  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Curve alignment; Functional data analysis; Gene expression profiles; Microarray; Time dynamics; Warping

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOMETRY; CELL CYCLE; CYTOLOGY; DNA MICROARRAY; DROSOPHILA; FEMALE; FUNGAL GENE; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; MALE; METHODOLOGY; PRENATAL DEVELOPMENT; REGRESSION ANALYSIS; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL; STATISTICS; TIME;

ANIMALS; BIOMETRY; CELL CYCLE; DROSOPHILA; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENES, INSECT; LEAST-SQUARES ANALYSIS; MALE; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; TIME FACTORS;

EID: 33749651702     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxj026     Document Type: Article

References (28)

1. AACH, J. AND CHURCH, G. M. (2001). Aligning gene expression time series with time warping algorithms. Bioinformatics 17, 495-508.
2. ARBEITMAN, M. N., FURLONG, E. E. M., IMAM, F., JOHNSON, E., NULL, B. H., BAKER, B. S., KRASNOW, M. A., SCOTT, M. P., DAVIS, R. W. AND WHITE, K. P. (2002). Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270-2275.
3. ARKIN, A. AND ROSS, J. (1995). Statistical construction of chemical-reaction mechanisms from measured time-series. Journal of Physical Chemistry 99, 970-979.
4. ARKIN, A., SHEN, P. AND ROSS, J. (1997). A test case of correlation metric construction of a reaction pathway from measurements. Science 277, 1275-1279.
5. BÄHLER J. (2005). Cell cycle control of gene expression in budding and fission yeast. Annual Review of Genetics 39, 69-94.
6. BAR-JOSEPH, Z., GERBER, G., GIFFORD, D. K., JAAKKOLA, T. S. AND SIMON, I. (2003a). Continuous representation of time-series gene expression data. Journal of Computational Biology 10, 2-4.
7. BAR-JOSEPH, Z., GERBER, G., SIMON, I., GIFFORD, D. K. AND JAAKKOLA, T. S. (2003b). Comparing the continuous representation of time-series expression profiles to identify differently expressed genes. Proceedings of the National Academy of Sciences of the United States of America 100, 10146-10151.
8. BOZDECH, Z., LLINAS, M., PULLIAM, B. L., WONG, E. D., ZHU, J. AND DERISI, J. L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biology 1, 85-100.
9. BRODY, T. B. (1999). The Interactive Fly: gene networks, development and the Internet. Trends in Genetics 15, 333-334.
10. BUTTE, A. J., BAO, L., REIS, B. Y., WATKINS, T. W. AND KOHANE, I. S. (2001). Comparing the similarity of time-series gene expression using signal processing metrics. Journal of Biomedical Informatics 34, 396-405.
11. COOPER, S. AND SHEDDEN, K. (2003). Microarray analysis of gene expression during the cell cycle. Cell & Chromosome 2, 1-12.
12. FAN, J. AND GIJBELS, I. (1996). Local Polynomial Modelling and its Applications. London: Chapman and Hall.
13. FOE, V. E., ODELL, G. M. AND EDGAR, B. A. (1993). Mitosis and morphogenesis in the Drosophila embryo. In Bate, M. and Martinez-Arias, A. (eds.), The Development of Drosophila melanogaster. Long Island, NY: Cold Spring Harbor Laboratory Press.
14. FUKUNAGA, K. AND HOSTETLER, L. D. (1975). Estimation of the gradient of a density-function, with applications in pattern recognition. IEEE Transactions on Information Theory 21, 32-40.
15. GASSER, T. AND MÜLLER, H. G. (1984). Estimating regression functions and their derivatives by the kernel method. Scandinavian Journal of Statistics 11, 171-185.
16. GERVINI, D. AND GASSER, T. (2004). Self-modelling warping functions. Journal of the Royal Statistical Society, Series B 66, 959-971.
17. HECKMAN, N. E. AND ZAMAR, R. H. (2000). Comparing the shapes of regression functions. Biometrika 87, 135-144.
18. LIU, X. L. AND MÜLLER, H. G. (2003). Modes and clustering for time-warped gene expression profile data. Bioinformatics 19, 1937-1944.
19. LIU, X. L. AND MÜLLER, H. G. (2004). Functional convex averaging and synchronization for time-warped random curves. Journal of the American Statistical Association 99, 687-699.
20. LODISH, H., BERK, A., ZIPURSKY, L. S., MATSUDAIRA, P., BALTIMORE, D. AND DARNELL, J. (2000). Molecular Cell Biology, 4th edition. New York: W. H. Freeman and Company.
21. POLLARD, T. D. AND EARNSHAW, W. C. (2004). Cell Biology, 1st edition. Philadelphia, PA: W.B. Saunders.
22. QIAN, J., DOLLED-FILHART, M., LIN, J., YU, H. AND GERSTEIN, M. (2001). Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identified new, biologically relevant interactions. Journal of Molecular Biology 314, 1053-1066.
23. SILVERMAN, B. W. (1995). Incorporating parametric effects into functional principal components analysis. Journal of the Royal Statistical Society, Series B 57, 673-689.
24. SPELLMAN, P. T., 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 gene of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9, 3273-3297.
25. WANG, F. M. AND GASSER, T. (1997). Alignment of curves by dynamic time warping. Annals of Statistics 25, 1251-1276.
26. WEIGMANN, K., KLAPPER, R., STRASSER, T., RICKERT, C., TECHNAU, G. M., JÄCKLE, H., JANNING, W. AND KLÄMBT, C. (2003). FlyMove-a new way to look at development of Drosophila. Trends in Genetics 19, 310-311.
27. WONG, M. A. AND LANE, T. (1983). A k-th nearest neighbor clustering procedure. Journal of the Royal Statistical Society, Series B 45, 362-368.
28. YAO, F., MÜLLER, H. G. AND WANG, J. L. (2005). Functional data analysis for sparse longitudinal data. Journal of the American Statistical Association 100, 577-590.