Identifying Differentially Expressed Genes for Time-course Microarray Data through Functional Data Analysis

Statistics in Biosciences

Volumn 2, Issue 2, 2010, Pages 95-119

  Chen, Kun ^a,b   Wang, Jane Ling ^b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Differentially expressed genes; False discovery rate; Functional data analysis; Functional principal component; Hybrid EM; Time course gene expression

Indexed keywords

MESSENGER RNA;

ANALYSIS OF VARIANCE; ARTICLE; B SPLINE BASIS FUNCTION; CAENORHABDITIS ELEGANS; FUNCTIONAL PRINCIPAL COMPONENT ANALYSIS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC SELECTION; GENETIC VARIABILITY; MICROARRAY ANALYSIS; NONHUMAN; NONPARAMETRIC TEST; PRIORITY JOURNAL; SIMULATION; STATISTICAL ANALYSIS;

CAENORHABDITIS ELEGANS;

EID: 78650070612     PISSN: 18671764     EISSN: 18671772     Source Type: Journal    
DOI: 10.1007/s12561-010-9024-z     Document Type: Article

References (25)

1. Ash RB, Gardner MF (1975) Topics in stochastic processes. Academic Press, New York.
2. Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS (2003) Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci USA 100(18): 10146-10151.
3. Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I (2003) Continuous representations of time-series gene expression data. J Comput Biol 10(3-4): 341-356.
4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate-A practical and powerful approach to multiple testing. J R Stat Soc B 57(1): 289-300.
5. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32: 490-495.
6. Efron B, Tibshirani R, Storey JD, Tusher V (2001) Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc 96(456): 1151-1160.
7. Hong F, Li H (2006) Functional hierarchical models for identifying genes with different time-course expression profiles. Biometrics 62(2): 534-544.
8. Joyce E, Popper S, Falkow S (2009) Streptococcus pneumoniae nasopharyngeal colonization induces type i interferons and interferon-induced gene expression. BMC Genomics 10: 404.
9. Leek JT, Monsen E, Dabney AR, Storey JD (2006) Edge: Extraction and analysis of differential gene expression. Bioinformatics 22: 507-508.
10. Leng X, Müller HG (2006) Classification using functional data analysis for temporal gene expression data. Bioinformatics 22: 68-76.
11. Liu X, Müller HG (2003) Modes and clustering for time-warped gene expression profile data. Bioinformatics 19: 1937-1944.
12. Liu X, Yang M (2009) Identifying temporally differentially expressed genes through functional principal component analysis. Biostatistics 10: 667-679.
13. Newton MA, Noueiry A, Sarkar D, Ahlquist P (2004) Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5(2): 155-176.
14. Park T, Yi SG, Lee S, Lee SY, Yoo DH, Ahn JI, Lee YS (2003) Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics 19(6): 694-703.
15. Ramsay J, Silverman B (1997) Functional data analysis. Springer, New York.
16. Rice J, Wu C (2001) Nonparametric mixed effects models for unequally sampled noisy curves. Biometrics 57: 253-259.
17. Saaf A, Halbleib J, Chen X, Yuen S, Leung S, Nelson W, Brown P (2007) Parallels between global transcriptional programs of polarizing caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer. Mol Biol Cell 18: 4245-4260.
18. Storey JD, Tibshirani R (2003) Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 100(16): 9440-9445.
19. Storey JD, Xiao WZ, Leek JT, Tompkins RG, Davis RW (2005) Significance analysis of time course microarray experiments. Proc Natl Acad Sci USA 102(36): 12837-12842.
20. Tai Y, Speed T (2006) A multivariate empirical Bayes statistic for replicated microarray time course data. Ann Stat 34(5): 2387-2412.
21. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98(9): 5116-5121.
22. Wang J, Kim SK (2003) Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130(8): 1621-1634.
23. Xu XL, Olson JM, Zhao LP (2002) A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Hum Mol Genet 11(17): 1977-1985.
24. Yao F, Müller HG, Wang JL (2005) Functional data analysis for sparse longitudinal data. J Am Stat Assoc 100(470): 577-590.
25. Yuan M, Kendziorski C (2006) Hidden Markov models for microarray time course data in multiple biological conditions. J Am Stat Assoc 101: 1323-1332.