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Exon Structure Analysis via PCA and ICA of Short-Time Fourier Transform

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Advances in Natural Computation (ICNC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3611))

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Abstract

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.

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References

  1. Anastassiou, D.: Frequency-domain analysis of biomolecular sequences. Bioinformatics 16, 1073–1081 (2000)

    Article  MathSciNet  Google Scholar 

  2. Beyerbach, D., Nawab, H.: Principal components analysis of the short-time Fourier transform. In: Proc. IEEE ICASSP, pp. 1725–1728 (1991)

    Google Scholar 

  3. Bingham, E., Hyvarinen, A.: A fast fixed-point algorithm for independent component analysis of complex-valued signals. Int. J. of Neural Systems 10(1), 1–8 (2000)

    Google Scholar 

  4. Fickett, J.W.: Recognition of protein coding regions in DNA sequences. Nucleic Acids Research 10, 5303–5318 (1982)

    Article  Google Scholar 

  5. Fodor, I.K., Kamath, C.: Dimension reduction in the atmospheric sciences, Computing in Science and Engineering special issue on High Dimensional Data, submitted, UCRL-JC-146972 (2002)

    Google Scholar 

  6. Guigo, R.: DNA composition, codon usage and exon prediction. In: Bishop, M.J. (ed.) Genetic Databases. Academic Press, London (1999)

    Google Scholar 

  7. Jollife, I.T.: Principal component analysis. Springer, New York (2002)

    Google Scholar 

  8. Li, W., Marr, T.G., Kaneko, K.: Understanding long-range correlations in DNA sequences. Physica D 75, 392–416 (1994)

    Article  MATH  Google Scholar 

  9. Mitra, S.K.: Digital Signal Processing: A Computer-Based Approach, 2nd edn. McGraw-Hill, New York (2000)

    Google Scholar 

  10. Salzberg, S.L.: Locating protein coding regions in human DNA using a decision tree algorithm. Journal of Computational Biology 2(3), 473–485 (1995)

    Article  Google Scholar 

  11. Silverman, B.D., Linsker, R.: A measure of DNA periodicity. J. Theor. Biol. 118, 295–300 (1986)

    Article  Google Scholar 

  12. Snyder, E.E., Stormo, G.D.: Identification of protein coding regions in genomic DNA. Journal of Molecular Biology 248, 1–18 (1995)

    Article  Google Scholar 

  13. Tiwari, S., Ramachandran, S., Bhattacharya, A., Bhattacharya, S., Ramaswamy, R.: Prediction of probable genes by Fourier analysis of genomic sequences. CABIOS 113, 263–270 (1997)

    Google Scholar 

  14. Vaidyanathan, P.P., Yoon, B.: Gene and exon prediction using allpass-based filters. In: Workshop on Genomic Signal Processing and Statistics (GENSIPS), Raleigh, NC (2002)

    Google Scholar 

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Hwang, C., Chiu, D., Sohn, I. (2005). Exon Structure Analysis via PCA and ICA of Short-Time Fourier Transform. In: Wang, L., Chen, K., Ong, Y.S. (eds) Advances in Natural Computation. ICNC 2005. Lecture Notes in Computer Science, vol 3611. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11539117_45

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  • DOI: https://doi.org/10.1007/11539117_45

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28325-6

  • Online ISBN: 978-3-540-31858-3

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