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Pattern Analysis and Prediction of O-Linked Glycosylation Sites in Protein by Principal Component Subspace Analysis

  • Yen-Wei Chen
  • Xuemei Yang
  • Masahiro Ito
  • Ikuko Nishikawa
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4693)

Abstract

Glycosylation is one of the most important post-translation modifications steps in the synthesis of membrane and secreted proteins and more than half of all proteins are glycosylated. In this paper, we propose a principal component analysis (PCA) based subspace approach for pattern analysis and prediction of O-glycosylation sites in protein. PCA is used to find principal components and subspaces of glycosylated residues and nonglycoslylated residues, respectively. From the calculated principal compoents, we found that the glycosylted proteins all have a high serine, threonine and proline content. The prediction can be viewed as a 4-classes classification problem or 2-classes classification problems. We project the protein sequence (test vector) into each subspace and calculate the distance between the test vector and its projection on the subspace. The protein sequence can be classified into the “nearest” class. The prediction accuracy for nonglycosylated sites (negative sites) is about 70%-90%, and the accuracy for O-glycosylated sites (positive sites) is about 70%-100%.

Keywords

Protein O-linked glycosylation principal component analysis  pattern analysis prediction 

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References

  1. 1.
    Hart, G.W.: Glycosylation. Curr. Opin. Cell Biol. 4, 1017–1023 (1992)CrossRefGoogle Scholar
  2. 2.
    Bause, A.: J. Biochem. 209, 331–336 (1983)Google Scholar
  3. 3.
    Gavel, Y., von Heijne, G.: 3, 433–442 (1990)Google Scholar
  4. 4.
    Wilson, I.B.H., Gavel, Y., Heijne, G.: Amino acid distributions around O-linked glycosylation sites. Biochem. J. 275, 529–534 (1991)CrossRefGoogle Scholar
  5. 5.
    Elhammer, A.P., Poorman, R.A., Brown, E., Maggiora, L.L., Hoogerheide, J.G., Kezdy, F.J.: The specificity of UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferase as inferred from a database of in vivo substrates and from the in vitro glycosylation of proteins and peptides. J. Biol. Chem. 268, 10029–10038 (1993)Google Scholar
  6. 6.
    Hansen, J.E., Lund, O., Engelbrecht, J., Bohr, H., Nielsen, J.O., Hansen, J.S., Brubak, S.: Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GaINAc: polypeptide N-acetylgalactosaminyltransferase. Biochem. J. 308, 801–813 (1995)CrossRefGoogle Scholar
  7. 7.
    Eisenhaber, B.B., Eisenhaber, F.: Prediction of potential GPI-modification sites in proprotein sequences. J. Mol. Biol. 292, 741–758 (1999)CrossRefGoogle Scholar
  8. 8.
    Julenius, K., Molgaard, A., Gupta, R., Brunak, S.: Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15, 153–164 (2004)CrossRefGoogle Scholar
  9. 9.
    Nishikawa, I., Sakamoto, H., Nouno, I., Iritani, T., Sakakibara, K., Ito, M.: Prediction of the O-glycosylation sites in protein by layered neural networks and support vector machines. In: Gabrys, B., Howlett, R.J., Jain, L.C. (eds.) KES 2006. LNCS (LNAI), vol. 4252, pp. 953–960. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  10. 10.
    Li, S., Liu, B., Zeng, R., Cai, Y., Li, Y.: Predicting O-glycosylation sites in mammalian proteins by using SVMs. Computational Biology and Chemistry 30, 203–208 (2006)CrossRefzbMATHGoogle Scholar
  11. 11.
    Bishop, C.M.: Neural Network for Pattern Recognition. Oxford University Press, Oxford (1995)Google Scholar
  12. 12.

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Yen-Wei Chen
    • 1
    • 2
  • Xuemei Yang
    • 2
    • 3
  • Masahiro Ito
    • 2
  • Ikuko Nishikawa
    • 2
  1. 1.Elect & Information Eng. School, Central South Univ. of Forestry and Technology, Changsha 410004China
  2. 2.College of Information Science and Eng., Ritsumeikan Univ., Shiga, 525-8577Japan
  3. 3.Department of Mathematics, Xianyang Normal Univ., Xianyang 712000China

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