SySAP: A system-level predictor of deleterious single amino acid polymorphisms

Protein and Cell

Volumn 3, Issue 1, 2012, Pages 38-43

  Huang, Tao ^a,b   Wang, Chuan ^a   Zhang, Guoqing ^a   Xie, Lu ^b   Li, Yixue ^a,b  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

deleterious single amino acid polymorphisms; predictor; web server

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; GENETICS; HUMAN; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; REPRODUCIBILITY;

AMINO ACID;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, PROTEIN; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84862245195     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-011-1130-2     Document Type: Article

References (50)

1. Ahmad, S., and Sarai, A. (2005). PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 6, 33.
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
3. Atchley, W. R., Zhao, J., Fernandes, A. D., and Drüke, T. (2005). Solving the protein sequence metric problem. Proc Natl Acad Sci U S A 102, 6395-6400.
4. Baldi, P., Brunak, S., Chauvin, Y., Andersen, C. A., and Nielsen, H. (2000). Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16, 412-424.
5. Burke, D. F., Worth, C. L., Priego, E. M., Cheng, T., Smink, L. J., Todd, J. A., and Blundell, T. L. (2007). Genome bioinformatic analysis of nonsynonymous SNPs. BMC Bioinformatics 8, 301.
6. Cai, Y., Huang, T., Hu, L., Shi, X., Xie, L., and Li, Y. Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids. 2011 Jan 26. [Epub ahead of print].
7. Cai, Y. D., Huang, T., Feng, K. Y., Hu, L., and Xie, L. (2010). A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas. PLoS One 5, e12726.
8. Care, M. A., Needham, C. J., Bulpitt, A. J., and Westhead, D. R. (2007). Deleterious SNP prediction: be mindful of your training data! Bioinformatics 23, 664-672.
9. Chou, K. C. (2001). Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 43, 246-255.
10. Chou, K. C. (2011). Some remarks on protein attribute prediction and pseudo amino acid composition. J Theor Biol 273, 236-247.
11. Chou, K. C., and Shen, H. B. (2007). Recent progress in protein subcellular location prediction. Anal Biochem 370, 1-16.
12. Chou, K. C., and Shen, H. B. (2008). Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc 3, 153-162.
13. Chou, K. C., Wu, Z. C., and Xiao, X. (2011). iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One 6, e18258.
14. Chou, K. C., and Zhang, C. T. (1995). Prediction of protein structural classes. Crit Rev Biochem Mol Biol 30, 275-349.
15. Esmaeili, M., Mohabatkar, H., and Mohsenzadeh, S. (2010). Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses. J Theor Biol 263, 203-209.
16. Fan, R.-E., Chang, K.-W., Hsieh, C.-J., Wang, X.-R., and Lin, C.-J. (2008). LIBLINEAR: A library for large linear classification. J Mach Learn Res 9, 1871-1874.
17. Freeman, L. C. (1979). Centrality in social networks: Conceptual clarification. Soc Networks 1, 215-239.
18. Georgiou, D. N., Karakasidis, T. E., Nieto, J. J., and Torres, A. (2009). Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition. J Theor Biol 257, 17-26.
19. Grantham, R. (1974). Amino acid difference formula to help explain protein evolution. Science 185, 862-864.
20. Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., and McKusick, V. A. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33, D514-D517.
21. Hsieh, C.-J., Chang, K.-W., Lin, C.-J., Keerthi, S. S., and Sundararajan, S. (2008). A dual coordinate descent method for large-scale linear SVM. In: Proceedings of the 25th international conference on Machine learning. Helsinki, Finland: ACM, 408-415.
22. Hu, L., Huang, T., Shi, X., Lu, W. C., Cai, Y. D., and Chou, K. C. (2011a). Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PLoS One 6, e14556.
23. Hu, L. L., Huang, T., Cai, Y. D., and Chou, K. C. (2011b). Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS One 6, e22989.
24. Huang, T., Chen, L., Cai, Y. D., and Chou, K. C. (2011a). Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS One 6, e25297.
25. Huang, T., Cui, W., Hu, L., Feng, K., Li, Y. X., and Cai, Y. D. (2009). Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS One 4, e8126.
26. Huang, T., Niu, S., Xu, Z., Huang, Y., Kong, X., Cai, Y. D., and Chou, K. C. (2011b). Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties. PLoS One 6, e22940.
27. Huang, T., Shi, X. H., Wang, P., He, Z., Feng, K. Y., Hu, L., Kong, X., Li, Y. X., Cai, Y. D., and Chou, K. C. (2010a). Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 5, e10972.
28. Huang, T., Tu, K., Shyr, Y., Wei, C. C., Xie, L., and Li, Y. X. (2008). The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med 6, 44.
29. Huang, T., Wang, P., Ye, Z. Q., Xu, H., He, Z., Feng, K. Y., Hu, L., Cui, W., Wang, K., Dong, X., et al. (2010b). Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PLoS One 5, e11900.
30. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., et al. (2009). STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37, D412-D416.
31. Kawashima, S., Ogata, H., and Kanehisa, M. (1999). AAindex: amino acid index database. Nucleic Acids Res 27, 368-369.
32. Keerthi, S. S., Sundararajan, S., Chang, K.-W., Hsieh, C.-J., and Lin, C.-J. (2008). A sequential dual method for large scale multi-class linear svms. In: Proceeding of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining. Las Vegas, Nevada, USA: ACM, 408-416.
33. Li, S., Xi, L., Li, J., Wang, C., Lei, B., Shen, Y., Liu, H., Yao, X., and Li, B. (2011). In silico prediction of deleterious single amino acid polymorphisms from amino acid sequence. J Comput Chem 32, 1211-1216.
34. Lin, C.-J., Weng, R. C., and Keerthi, S. S. (2008). Trust region newton method for logistic regression. J Mach Learn Res 9, 627-650.
35. Lin, W. Z., Fang, J. A., Xiao, X., and Chou, K. C. (2011). iDNA-Prot: identification of DNA binding proteins using random forest with grey model. PLoS One 6, e24756.
36. Mohabatkar, H. (2010). Prediction of cyclin proteins using Chou's pseudo amino acid composition. Protein Pept Lett 17, 1207-1214.
37. Ng, P. C., and Henikoff, S. (2002). Accounting for human polymorphisms predicted to affect protein function. Genome Res 12, 436-446.
38. Ng, P. C., and Henikoff, S. (2003). SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31, 3812-3814.
39. Niu, S., Huang, T., Feng, K., Cai, Y., and Li, Y. (2010). Prediction of tyrosine sulfation with mRMR feature selection and analysis. J Proteome Res 9, 6490-6497.
40. Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., and Obradovic, Z. (2006). Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7, 208.
41. Qiu, J. D., Huang, J. H., Shi, S. P., and Liang, R. P. (2010). Using the concept of Chou's pseudo amino acid composition to predict enzyme family classes: an approach with support vector machine based on discrete wavelet transform. Protein Pept Lett 17, 715-722.
42. Ramensky, V., Bork, P., and Sunyaev, S. (2002). Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30, 3894-3900.
43. Sharan, R., Ulitsky, I., and Shamir, R. (2007). Network-based prediction of protein function. Mol Syst Biol 3, 88.
44. Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., and Sirotkin, K. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29, 308-311.
45. Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S., Abeysinghe, S., Krawczak, M., and Cooper, D. N. (2003). Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21, 577-581.
46. Wang, P., Xiao, X., and Chou, K. C. (2011). NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features. PLoS One 6, e23505.
47. Wu, Z. C., Xiao, X., and Chou, K. C. (2011). iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. Mol Biosyst 7, 3287-3297.
48. Xiao, X., Wu, Z. C., and Chou, K. C. (2011). A multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites. PLoS One 6, e20592.
49. Ye, Z. Q., Zhao, S. Q., Gao, G., Liu, X. Q., Langlois, R. E., Lu, H., and Wei, L. (2007). Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). Bioinformatics 23, 1444-1450.
50. Zeng, Y. H., Guo, Y. Z., Xiao, R. Q., Yang, L., Yu, L. Z., and Li, M. L. (2009). Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J Theor Biol 259, 366-372.