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Hub Characterization of Tumor Protein P53 Using Artificial Neural Networks

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Advances in Computing and Communications (ACC 2011)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 190))

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Abstract

This paper presents a supervised Back Propagation Neural network (BPN) for the hub characterization of the tumor protein P53. This paper proposes a method to predict the P53 protein as Hub or Non-Hub from the sequence information of protein alone. The hubness characterization of this protein has been carried out using Hydrophobicity, one of the important physio-chemical properties of the amino acid. The proposed method has been tested on the P53 and its interacting proteins successfully. The same method on the whole set of Human proteins from the database HPRD and APID has shown around 90% of accuracy, sensitivity and specificity with the help of Artificial Neural Network (ANN).

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References

  1. Vazquez, A., Bond, E.E., Levine, A.J., Bond, G.L.: The genetics of the p53 pathway, apoptosis and cancer therapy. Nature Reviews Drug Discovery 7(12), 979–987 (2008)

    Article  Google Scholar 

  2. Prives, C., Hall, P.A.: The p53 pathway. The Journal of Pathology. Special Issue: Molecular and Cellular Themes in Cancer Research 187(1), 112–126 (1999)

    Google Scholar 

  3. Hsing, M., Byler, K.G., Cherkasov, A.: The use of Gene Ontology terms for predicting highly-connected ’hub’ nodes in protein-protein interaction networks. BMC Systems Biology 2, 80 (2008)

    Article  Google Scholar 

  4. Barabasi, A.L., Oltvai, Z.N.: Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5(2), 101–113 (2004)

    Article  Google Scholar 

  5. Srihari, S., et al.: Detecting Hubs and Quasi Cliques in Scale-free Networks. IEEE, Los Alamitos (2008)

    Google Scholar 

  6. Albert, R.: Scale-free networks in cell biology. J. Cell Sci. 118(Pt 21), 4947–4957 (2005)

    Article  Google Scholar 

  7. Bataba, N.N., Hurst, L.D., Tyers, M.: Evolutionary and Physiological Importance of Hub Proteins. PLOS Computational Biology 2(7), 748–756 (2006)

    Google Scholar 

  8. Agarwal, S., et al.: Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks. PLOS Computational Biology 6(6) (June 2010)

    Google Scholar 

  9. Aragues, R., et al.: Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. PLOS Computational Biology 3(9) (September 2007)

    Google Scholar 

  10. Vinod Chandra, S.S., Reshmi, G., Nair, A.S., S., S., Radhakrishna Pillai, M.: MTar: a computational microRNA target prediction architecture for human transcriptome. BMC Bioinformatics 11, S2, ISSN 1471-2105

    Google Scholar 

  11. Ying, X., Mural, R.J., Einstein, J.R., Shah, M.B., Uberbacher, E.: GRAIL: a multi-agent neural network system for gene identification. Proceedings of the IEEE 84(10) (1996)

    Google Scholar 

  12. Chae, M.H., Krull, F., Lorenzen, S., Knapp, E.: Predicting protein complex geometries with a neural network. Proteins 78(4), 1026–1039 (2010)

    Article  Google Scholar 

  13. Agrawal, R.K., et al.: A novel approach to predict protein-protein interaction using protein sequence data. Bioinformatics Trends 1(1) (2006)

    Google Scholar 

  14. http://www.hprd.org/ (release 9 dated May 24, 2010)

  15. Prieto, C., De Las Rivas, J.: APID: Agile Protein Interaction Data Analyzer. Nucl. Acids Res. 34, W228–W302 (2006)

    Article  Google Scholar 

  16. http://en.wikipedia.org/wiki/P53 (dated 18/9/2011 at 9.00 a.m.)

  17. http://www.ncbi.nlm.nih.gov/ (dated 18/9/2011 at 11.00 a.m.)

  18. Wutchy, S.: Scale-free behavior in protein domain networks. Mol. Bio. Evolution 18 (2001)

    Google Scholar 

  19. Ashok, V.: Determination of blood glucose concentration by back propogation neural network

    Google Scholar 

  20. Latha, A., Vijayakumar Reddy, K.: Performance Analysis on modeling of loop heat pipes using artificial neural network. Indian Journal of Science and Technology 3(4) (2010)

    Google Scholar 

  21. http://www.sigmaaldrich.com/life-science/metabolomics/learning-centre/amino-acid-reference-chart.html (dated July 15, 2010)

  22. Kim, P.M., Lu, L.J., Xia, Y.: Gerstein MB Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314, 1938–1941 (2006)

    Article  Google Scholar 

  23. Najafabadi, H.S., Salavati, R.: Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biology 9, R87 (2008)

    Article  Google Scholar 

  24. Bock, J.R., Gough, D.A.: Predicting protein-protein interaction from primary structure. Bioinformatics 17, 455–460 (2001)

    Article  Google Scholar 

  25. Shen, J., Zhang, J., Luo, X., Zhu, W., Yu, K., Chen, K., Li, Y., Jiang, H.: Predicting protein-protein interactions based only on sequence information. Proceedings of the National Academy of Sciences of the USA 104, 4337–4341 (2007)

    Article  Google Scholar 

  26. Qi, Y., Bar-Joseph, Z., Klein-Seetharaman, J.: Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 63(3), 490–500 (2006)

    Article  Google Scholar 

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Sajeev, J., Mahalakshmi, T. (2011). Hub Characterization of Tumor Protein P53 Using Artificial Neural Networks. In: Abraham, A., Lloret Mauri, J., Buford, J.F., Suzuki, J., Thampi, S.M. (eds) Advances in Computing and Communications. ACC 2011. Communications in Computer and Information Science, vol 190. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22709-7_32

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  • DOI: https://doi.org/10.1007/978-3-642-22709-7_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-22708-0

  • Online ISBN: 978-3-642-22709-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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