Identification of significant periodic genes in microarray gene expression data

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Chen, Jie ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL CELL CYCLE; GENE EXPRESSION DATA; HUMAN CANCER CELLS; MICROARRAY EXPERIMENTS; MICROARRAY GENE EXPRESSION DATA; STATISTICAL HYPOTHESIS TESTING; STATISTICAL INFERENCE; TIME-SERIES GENE EXPRESSION DATA;

CELL CULTURE; CELL PROLIFERATION; CELLS; EXPERIMENTS; GENE EXPRESSION; TESTING; TIME SERIES;

MICROARRAYS;

ARTICLE; BACTERIAL CELL; CANCER CELL CULTURE; CELL CYCLE; DATA ANALYSIS; DNA MICROARRAY; FIBROBLAST; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENOMICS; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; METHODOLOGY; NONHUMAN; STATISTICAL SIGNIFICANCE; STATISTICS; TIME SERIES ANALYSIS; YEAST CELL; ALGORITHM; BACTERIAL GENE; BIOLOGICAL MODEL; BIOLOGY; FUNGAL GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LABORATORY DIAGNOSIS; METABOLISM; PROCEDURES; STATISTICAL ANALYSIS; STATISTICAL MODEL; TIME; TUMOR CELL LINE;

BACTERIA (MICROORGANISMS);

ALGORITHMS; CELL CYCLE; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; FALSE POSITIVE REACTIONS; FIBROBLASTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, BACTERIAL; GENES, FUNGAL; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TIME FACTORS;

EID: 29144484744     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-286     Document Type: Article

References (22)

1. Wichert S, Folianos K, Strimmer K: Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 2004, 20: 5-20.
2. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Bostein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 1998, 9: 3273-3297.
3. Cho RJ, Huang M, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhardt DJ, Campbell MJ: Transcriptional regulation and function during the human cell cycle. Nature Genetics 2001, 27:48-54.
4. Shedden K, Cooper S: Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proceedings of the National Academy of Science USA 2002a, 99: 4379-4384.
5. Shedden K, Cooper S: Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucleic Acids Research 2002b, 30: 2920-2929.
6. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Marese JC, Perou CM, Hurt MM, Brown PO, Botstein D: Identification of Genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell 2002, 13: 1977-2000.
7. Fisher RA: Tests of significance in Harmonic Analysis. Proceedings of the Royal Society of London, Series A 1929, 125: 54-59.
8. Bartlett MS: An introduction to Stochastic Processes with Special Reference to Methods and Applications 2nd ed., Cambridge University Press, Cambridge 1966.
9. Durbin J: Tests of serial independence based on the cumulated periodogram. Bulletin of the International Statistical Institute 1967, 42: 1039-1049.
10. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 1995, B57: 289-300.
11. Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L: Global analysis of the genetic network controlling a bacterial cell cycle. Science 2000, 290: 2144-2148.
12. Bacterial cell cycle data [http://caulobacter.stanford.edu/CellCycle/DownloadData.htm]
13. NCBI [www.ncbi.nlm.nih.gov]
14. Yeast cell cycle data [http://genome-www.stanford.edu/cellcycle]
15. Yeast genome website [http://db.yeastgenome.org]
16. Human fibroblasts data [http://www.salk.edu/docs/labs/chipdata]
17. Human cancer cell line data [http://genome-www.stanford.edu/Human-CellCycle/Hela]
18. Davis HT: The Analysis of Economic Time Series, Principia Press, Bloomington, Indiana; 1941.
19. Wilks SS: Mathematical Statistics, Wiley, New York; 1962.
20. Priestley MB Spectral Analysis and Time Series, Academic Press: San Diego; 1981.
21. Fuller WA: Introduction to Statistical Time Series, 2nd ed., Wiley-Interscience: New York; 1996.
22. Durbin J: Tests for serial correlation in regression analysis based on the periodogram of least-squares residuals. Biometrika 1969, 56: 1-15.