Commenced in January 2007
Paper Count: 31097
Analysis of Physicochemical Properties on Prediction of R5, X4 and R5X4 HIV-1 Coreceptor Usage
Abstract:Bioinformatics methods for predicting the T cell coreceptor usage from the array of membrane protein of HIV-1 are investigated. In this study, we aim to propose an effective prediction method for dealing with the three-class classification problem of CXCR4 (X4), CCR5 (R5) and CCR5/CXCR4 (R5X4). We made efforts in investigating the coreceptor prediction problem as follows: 1) proposing a feature set of informative physicochemical properties which is cooperated with SVM to achieve high prediction test accuracy of 81.48%, compared with the existing method with accuracy of 70.00%; 2) establishing a large up-to-date data set by increasing the size from 159 to 1225 sequences to verify the proposed prediction method where the mean test accuracy is 88.59%, and 3) analyzing the set of 14 informative physicochemical properties to further understand the characteristics of HIV-1coreceptors.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1084816Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2096
[ 1] D. Unutmaz, "T cell signaling mechanisms that regulate HIV-1 infection," Immunologic Research, vol. 23, no. 2-3, pp. 167-177, June 2001.
[ 2] D. C. Chan,. D. Fass, J. M. Berger, "Core Structure of gp41 from the HIV Envelope Glycoprotein," Cell, vol. 89, pp. 263-273, April 18, 1997.
[ 3] M. L. Greenberg, S. F. Lacey, C.-Ho Chen, Dani P. Bolognesi and Kent J. Weinhold, "T cell signaling mechanisms that regulate HIV-1 infection," Springer Seminars in Immunopatholog , vol. 18, no. 3, pp. 355-369, Sep. 1997.
[ 4] M. S. Hirsch, T.-C. Chou, V. A. Johnson, M. A. Barlow, D. P. Merrill, "Three-drug synergistic inhibition of HIV-1 replication in vitro by zidovudine, recombinant soluble CD4, and recombinant interferon-alpha A," Journal of Infectious Diseases, Health, 1990.
[ 5] T. L. Hoffman, C. C. Labranche, W. Zhang, G. Canziani, J. Robinson, I. Chaiken, J. A. Hoxie, and R. W. Doms, "Stable exposure of the coreceptor-binding site in a CD4-independent HIV-1 envelope protein," Proc. Natl. Acad. Sci. USA, Medical Science, Vol. 96, May 1999, pp. 6359-6364.
[ 6] C. Garrido, V. Roulet, N. Chueca, E. Poveda, A. Aguilera, K. Skrabal, N. Zahonero, S. Carlos, F. Garc├¡a, J. L. Faudon, V. Soriano, and C. d. Mendoza, "Evaluation of Eight Different Bioinformatics Tools To Predict Viral Tropism in Different Human Immunodeficiency Virus Type 1 Subtypes," Journal of Clinical Microbiology, vol. 46, no. 3, pp. 887-891, Mar. 2008.
[ 7] T. Sing, A. J Low, N. Beerenwinkel, O. Sander, P. Cheung, F. S Domingues, J. B├╝ch, M. D├ñmer, R. Kaiser, T. Lengauer and P R. Harrigan "Predicting HIV coreceptor usage on the basis of genetic and clinical covariates," Antiviral therapy, vol. 12, pp. 1097-1106, 2007
[ 8] S. Boisvert, M. Marchand, F. Laviolette and J. Corbei, "HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels," Retrovirology, vol.5, no.110, doi:10.1186/1742-4690-5-110, 2008.
[ 9] Cormier, E., and T. Dragic, "The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor," J. Virol., vol.76, pp.8953-8957, 2002.
 O. Sander, T. Sing, I. Sommer, A. Low, P. Cheung, P. Harrigan, T. Lengauer,and F. Domingues, "Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage," PLoS Comput. Biol. 3:e58, 2007.
 W. Resch, N. Hoffman, and R. Swanstrom, "Improved success of phenotype prediction of the HIV type 1 from envelope variable loop 3 sequence using neural networks," Virology, vol. 288, pp.51-62, 2001.
 C. Pastore, R. Nedellec, A. Ramos, S. Pontow, L. Ratner, and D. Mosier, "HIV type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations," J. Virol., vol. 80, pp. 750-758, 2006.
 J. Weber, "The pathogenesis of HIV-1 infection," British Medical Bulletin, vol. 58, pp.61-72, 2001.
 S. L. Lamers, M. Salemi, M. S. McGrath, and G. B. Fogel, "Prediction of R5, X4, and R5X4 HIV-1 Coreceptor Usage with Evolved Neural Networks," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, No. 2, pp. 291-300, April-June 2008.
W.-L. Huang, C.-W. Tung, H.-L. Huang, S.-F. Hwang, S.-Y. Ho, "ProLoc: Prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features," BioSystems, vol. 90, pp. 573-581, 2007.
 Chun-Wei Tung and Shinn-Ying Ho, "POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties," Bioinformatics, vol. 23, no. 8, pp. 942-949, 2007.
 Chun-Wei Tung and Shinn-Ying Ho, "Computational identification of ubiquitylation sites from protein sequences," BMC Bioinformatics, vol. 9:310, July 2008.
 Los Alamos National Laboratory HIV Sequence Database, http://www.hiv.lanl.gov/.
 S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama, M. Kanehisa, "AAindex: amino acid index database," progress report 2008. Nucleic Acids Res 2008, 36(Database issue):D202-205.
 JR Quinlan. C4.5: programs for machine learning. In. San Mateo, CA: Morgan Kaufmann. 1993.
 C. C. Chang, and, C. J. Lin (2001) LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm.
 S. Y. Ho, J. H. Chen, and M. H. Huang.,"Inheritable genetic algorithm for bi-objective 0/1 combinatorial optimization problems and its applications," IEEE Trans. Syst. Man Cybern. Part B-Cybern., vol. 34, pp. 609-620, 2004a.
 S. Y. Ho, L. S. Shu, and J. H. Chen," Intelligent evolutionary algorithms for large parameter optimization problems," IEEE Trans. Evol. Comput., vol. 8, pp. 522-541, 2004b.
 M. A. Jensen and A. B. van ÔÇÿt Wout, "Predicting HIV-1 coreceptor usage with sequence analysis," IDS Rev, vol. 5, 2003, pp. 104-112.
 D. R. Briggs, D. L. Tuttle, J. W. Sleasman, M. M. Goodenow, "Envelope V3 amino acid sequence predicts HIV-1 phenotype (coreceptor usage and tropism for macrophages," AIDS, vol. 14, 2000, pp. 2937-2939.
 W. Resch, N. Hoffman, R. Swanstrom, "Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks," Virology, vol. 288, pp. 51-62, 2001
 S. Pillai, B Good, D. Richman, J. Corbeil, "A new perspective on V3 phenotype prediction," AIDS Res Hum Retroviruses, vol. 19, pp. 145-149, 2003.
 M. A. Jensen, et al., "Improved coreceptor usage prediction and genotypic monitoring of R5-toX4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences," J Virol, vol. 77, pp. 13376-13388, 2003.
 T. Sing, N. Beerenwinkel, T. Lengauer, "Learning mixtures of localized rules by maximizing the area under the ROC curve," Proceedings of 1st International Workshop on ROC Analysis in Artificial Intelligence, 22 August 2004, pp. 89-96