Identifying periodically expressed trascripts in microarry time series data

Bioinformatics

Volumn 20, Issue 1, 2004, Pages 5-20

  Wichert, Sofia ^a   Fonkianos, Konstantinos ^b   Strimmer, Korbinian ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF CYPRUS   (Cyprus)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CELL; CELL CYCLE; CELL SYNCHRONIZATION; CONTROLLED STUDY; DNA MICROARRAY; FIBROBLAST; FISHER EXACT TEST; GENE ACTIVATION; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC VARIABILITY; HELA CELL; HUMAN; NONHUMAN; PERIODICITY; PRIORITY JOURNAL; PROCESS MODEL; SIGNAL DETECTION; STATISTICAL ANALYSIS; STATISTICAL CONCEPTS; STATISTICAL SIGNIFICANCE; TIME SERIES ANALYSIS; YEAST CELL;

ALGORITHMS; CAULOBACTER CRESCENTUS; CELL CYCLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PERIODICITY; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TIME FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); MARTES PENNANTI;

EID: 0347093600     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg364     Document Type: Article

References (14)

1. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. JR Statist. Soc. B, 57, 289-300.
2. Cho,R.J., Huang,M., Dong,H., Steinmetz,L., Sapinoso,L., Hampton,G., Elledge,S.J., Davis,R.W., Lockhardt,D.J. and Campbell,M.J. (2001) Transcriptional regulation and function during the human cell cycle. Nat. Genet., 27, 48-54.
3. Cooper,S. (2003) Reappraisal of serum starvation, the restriction point, G0, and G1-phase arrest points. FASEB J., 17, 333-340.
4. Fellenberg,K., Hauser,N.C., Brors,B., Neutzner,A., Hoheisel,J.D. and Vingron,M. (2001) Correspondence analysis applied to microarray data. Proc. Natl Acad. Sci. USA, 98, 10781-10786.
5. Fisher,R.A. (1929) Tests of significance in harmonic analysis. Proc. R. Soc. A, 125, 54-59.
6. Laub,M.T., McAdams,H.H., Feldblyum,T., Fraser,C.M. and Shapiro,L. (2000) Global analysis of the genetic network controlling a bacterial cell cycle. Science, 290, 2144-2148.
7. Priestley,M.B. (1981) Spectral Analysis and Time Series. Academic Press, London,
8. Rifkin,S.A. and Kim,J. (2002) Geometry of gene expression dynamics. Bioinformatics, 18, 1176-1183.
9. Shedden,K. and Cooper,S. (2002a) Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proc. Natl Acad. Sci. USA, 99, 4379-4384.
10. Shedden,K. and Cooper,S. (2002b) Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucleic Acids Res., 30, 2920-2929.
11. 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 genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
12. Strimmer,K. (2003) Modeling gene expression measurement error: a quasi-likelihood approach. BMC Bioinformatics, 4, 10.
13. Welch,P.D. (1967) The use of fast fourier transform for the estimation of power spectra: a method based on time averaging over short, modified periodograms. IEEE Trans. Audio Electroacoust., AU-15, 70-73.
14. Whitfield,M.L., Sherlock,G., Saldanha,A.J., Murrary,J.I., Ball,C.A., Alexander,K.E., Matese,J.C., Perou,C.M., Hurt,M.M., Brown,P.O. and Botstein,D. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell, 13, 1977-2000.