Spectral analysis of microarray gene expression time series data of Plasmodium falciparum

International Journal of Bioinformatics Research and Applications

Volumn 4, Issue 3, 2008, Pages 337-349

  Du, Liping ^a,b   Wu, Shuanhu ^a,c   Liew, Alan Wee Chung ^d   Smith, David K ^e   Yan, Hong ^a,f  

^a CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY BEIJING   (China)

^c YANTAI UNIVERSITY   (China)

^d GRIFFITH UNIVERSITY   (Australia)

^e UNIVERSITY OF HONG KONG   (Hong Kong)

^f UNIVERSITY OF SYDNEY   (Australia)

Author keywords

AR; Autoregressive; Bioinformatics; Gene target; Microarray time series analysis; Model; Plasmodium falciparum; Singular spectrum analysis; SSA

Indexed keywords

MALARIA VACCINE;

ARTICLE; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; FOURIER ANALYSIS; GENE EXPRESSION; GENE IDENTIFICATION; GENE TARGETING; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; PLASMODIUM FALCIPARUM; QUANTITATIVE ANALYSIS; SPECTROSCOPY;

PLASMODIUM FALCIPARUM;

EID: 47749135602     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.019579     Document Type: Article

References (18)

1. Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J.C. and DeRisi, J.L. (2003) 'The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum', Plos Biolog., Vol. 1, pp.1-16.
2. Du, L., Wu, S., Liew, A.W.C., Smith, D. and Yan, H. (2006) 'Parametric spectral analysis of malaria gene expression time series data', in Berthold, M., Glen, R. and Fischer, I. (Eds.): Proc. Second International Symposium on Computational Life Sciences, Lecture Notes in Bioinformatics', Springer-Verlag, Vol. 4216, September 27-29, Cambridge, UK, pp.32-41.
3. Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E. and Bowman, S. (2002) 'Genome sequence of the human malaria parasite', Plasmodium falciparum', Nature, Vol. 419, pp.498-511.
4. Golyandina, N., Nekrutkin, V. and Zhigljavsky, A. (2001) Analysis of Time Series Structure: SSA and Related Techniques, Chapman and Hall/CRC, Boca Raton, Florida.
5. Keppenne, C.L. and Ghil, M. (1992) 'Adaptive filtering and prediction of the southern oscillation index', J. Geophys. Res., Vol. 97, pp.20449-20454.
6. Le Roch, K.G., Zhou, Y.Y., Blair, P.L., Grainger, M., Moch, J.K., Haynes, J.D., de la Vega, P., Holder, A.A., Batalov, S. and Carucci, D.J. (2003) 'Discovery of gene function by expression profiling of the malaria parasite life cycle', Science, Vol. 301, pp.1503-1508.
7. Liew, A.W.C., Xian, J., Wu, S., Smith, D. and Yan, H. (2007) 'Spectral estimation in unevenly sampled space of periodically expressed microarray time series data', BMC Bioinformatics, Vol. 8, No. 137, pp.1-19.
8. Liu, L., Hawkins, D.M., Ghosh, S. and Yong, S.S. (2003) 'Robust singular value decomposition analysis of microarray data', PNAS, Vol. 100, pp.13167-13172.
9. Marple, S.L. (1987) Digital Spectral Analysis: with Applications, Prentice-Hall, Englewood Cliffs, New Jersey.
10. Penland, C., Ghil, M. and Weickmann, K.M. (1991) 'Adaptive filtering and maximum entropy spectra with application to changes in atmospheric angular momentum', J. Geophys. Res., Vol. 96, pp.22659-22671.
11. Rajarajeswari, B., Eyke, H., Nils, W. and Jörg, K. (2005) 'Clustering of gene expression data using a local shape-based similarity measure', Bioinformatics, Vol. 21, pp.1069-1077.
12. Rustici, G., Mata, J., Kivinen, K., Lió, P., Penkett, C.J., Burns, G., Hayles, J., Brazma, A., Nurse, P. and Bähler, J. (2004) 'Periodic gene expression program of the fission yeast cell cycle', Nature Genetics, Vol. 36, pp.809-817.
13. 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 hybridisation', Mol. Biol. Cell., Bozdech, Vol. 9, pp.3273-3297.
14. Vautard, R. and Ghil, M. (1989) 'Singular spectrum analysis in nonlinear dynamics, with applications to paleoclimatic time series', Physica D., Vol. 35, pp.395-424.
15. Vautard, R., Yiou, P. and Ghil, M. (1992) 'Singular-spectrum analysis: a toolkit for short, noisy chaotic signals', Physica D, Vol. 58, pp.95-126.
16. Yan, H. (Ed.) (2002) Signal Processing for Magnetic Resonance Imaging and Spectroscopy, Marcel Dekker, New York.
17. Yan, H. and Pham, T. (2007) 'Spectral estimation techniques for DNA sequence and microarray data analysis', Current Bioinformatics,Vol. 2, pp.145-156.
18. Yeung, L.K., Szeto, L.K., Liew, A.W.C. and Yan, H. (2004) 'Dominant spectral component analysis for transcriptional regulations using microarray time series data', Bioinformatics, Vol. 20, pp.742-749.