Improved fourier transform method for unsupervised cell-cycle regulated gene prediction

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 194-203

  Krishna Murthy, Karuturi R ^a   Hua, Liu Jian ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

Cell cycle; Fourier transform; Gene prediction; Microarray

Indexed keywords

ALGORITHMS; CELL CULTURE; FOURIER TRANSFORMS; GENES; GROWTH KINETICS; LEAST SQUARES APPROXIMATIONS; MATHEMATICAL MODELS; RANDOM PROCESSES; RNA; SAMPLING; SYNCHRONIZATION; YEAST;

CELL CYCLES; GENE PREDICTION; IMPROVED FOURIER TRANSFORMS (IFT); MICROARRAYS;

CYTOLOGY;

CELL CYCLE PROTEIN; TUMOR PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CELL CYCLE; CLUSTER ANALYSIS; DNA MICROARRAY; FOURIER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HELA CELL; HUMAN; METABOLISM; METHODOLOGY;

ALGORITHMS; CELL CYCLE; CELL CYCLE PROTEINS; CLUSTER ANALYSIS; FOURIER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; NEOPLASM PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED;

EID: 14044275098     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (26)

1. Alter, O., Brown,P.O. and Botstein,D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA, 97, 10101-10106.
2. Burnham,A.J., MacGregor,J.F. and Viveros,R. (1999) Latent variable multivariate regression modeling. Chemometrics and Intelligent Laboratory Systems, 48, 16780.
3. Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfeberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. and Davis,R.W. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell., 2, 65-73.
4. Doolin,M.T., Johnson,A.L., Johnston,L.H. and Butler,G. (2001) Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p. Mol. Microbiol., 40, 422-432.
5. 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.
6. Fodor,S.P. Rava,R.P., Huang,X.C., Pease,A.C., Holmes,C.P. and Adams,C.L. (1993) Multiplexed biochemical assays with biological chips. Nature, 364,555-556.
7. Heyer,L.J., Kruglyak,S. and Yooseph,S. (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res., 9, 1106-1115.
8. Ho,Y., Costanzo,M., Moore,L., Kobayashi,R. and Andrews,B.J. (1999) Regulation of transcription at the Saccharomyces cerevisiae start transition by Stbl, a Swi6-binding protein. Mol. Cell. Biol., 19, 5267-5278.
9. Holter,N.S., Mitra,M., Maritan,A., Cieplak,M., Banavar,J.R. and Fedoroff,N.V. (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl Acad. Sci. USA, 97, 8409-8414.
10. Johansson, D., Lindgren, P. and Berglund, A. A Multivariate Approach Applied to Microarray data for Identification of Genes with Cell-Cycle Coupled Transcription. Bioinformatics, 19(4):467-473, 2003.
11. Klevecz,R.R. (2000) Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data. Funct. Integr Genomics, 1, 186-192.
12. Krishna Murthy, K.R., Vega, V.B., Friendly Neighbors Method for Unsupervised Determination of Gene Significance in Time-course Microarray Data. in the Proc. of IEEE Symposium on BIBE'2004, Taichung, Taiwan, May 19-21,2004.
13. Lander,E.S. (1999) Array of hope. Nature Genet., 21, 3-4. Martens,H. and Naes,T. (1989) Multivariate Calibration. Wiley, Chichester.
14. Lander,E.S. (1999) Array of hope. Nature Genet., 21, 3-4. Martens,H. and Naes,T. (1989) Multivariate Calibration. Wiley, Chichester.
15. Lathi, B.P., Signals, Systems and Communication, John Wiley & Sons, 1965.
16. Menges,M., Hennings, L., Gruissem, W., and Murray, J.A.H. Cell Cycle-regulated Gene Expression in Arabidopsis, Journal of Biological Chemistry, 277(44):41987-42002, November 2002.
17. Rifkin, S.A. and Kim, J. Geometry of Gene Expression Dynamics. Bioinformatics, 18:1176-1183, 2002.
18. Rodriguez-Pena,J.M., Cid,V.J., Arroyo,J. and Nombela,C. (2000) A novel family of cell wall-related proteins regulated differently during the yeast life cycle. Mol. Cell. Biol., 20, 3245-3255.
19. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
20. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Bostein, D., and Futcher, B. (1998) Comprehensive Identification of Cell Cycle-regulated Genes of the S. cerevisiae Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell, 9, 3273-3297.
21. Tamayo,P., Slonim,D., Mesirov,J., Zhu,Q., Kitareewan,S., Dmitrovsky,E., Lander,E.S. and Golub,T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
22. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
23. Whitefield, M.L., Sherlock, G., Saldanha, A.L., Murray, J.L., Ball, C.A., Alexander, K.E., Matese, J.C., Perou, C.M., Hurt, M.M., Brown, P.O. and Botstein, D. Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors, Molecular Biology of the Cell, 13:1977-2000, June 2002.
24. Wold,H. (1966) Estimation of principal components and related models by iterative least squares. In Krishnaiah,P.A.R. (ed.), In Multivariate Analysis. Academic press, New York.
25. Wold,S., Ruhe,A., Wold,H. and Dunn,III,W.J. (1984) The collinearity problem in linear regression, the partial least squares approach to generalized inverses. SIAM J. Sci. Stat. Comput., 5, 735-743.
26. Zhao,L.P., Prentice,R. and Breeden,L. (2001) Statistical modeling of large microarray data sets to identify stimulusresponse profiles. Proc. Natl Acad. Sci. USA, 98, 5631-5636.