Semantic similarity based feature extraction from microarray expression data

International Journal of Data Mining and Bioinformatics

Volumn 3, Issue 3, 2009, Pages 333-345

  Cho, Young Rae ^a   Zhang, Aidong ^a   Xu, Xian ^b  

^a State University of New York   (United States)

^b MICROSOFT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; DNA MICROARRAY; GENE EXPRESSION PROFILING; METHODOLOGY; SEMANTICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEMANTICS;

EID: 68049118577     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2009.026705     Document Type: Article

References (25)

1. Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D. and Levine, A.J. (1999) 'Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissue probed by oligonucleotide arrays', Proc. Natl. Acad. Sci. USA, Vol. 96, No. 12, pp.6745-6750.
2. Alter, O., Brown, P.O. and Botstein, D. (2000) 'Singular value decomposition for genome-wide expression data processing and modeling', Proc. Natl. Acad. Sci. USA, Vol. 97, No. 18, pp.10101-10106.
3. Ben-Dor, A., Bruhn, L., Friedman, N., Nachman, I., Schummer, M. and Yakhini, Z. (2000) 'Tissue classification with gene expression profiles', Journal of Computational Biology, Vol. 7, pp.559-583.
4. Bo, T.H. and Jonassen, I. (2002) 'New feature subset selection procedures for classification of expression profiles', Genome Biology Vol. 3, No. 4, pp.17.1-17.11.
5. Chen, D., Liu, Z., Ma, X. and Hua, D. (2005) 'Selecting genes by test statistics', Journal of Biomedicine and Biotechnology, Vol. 2, pp.132-138.
6. Ding, C. and Peng, H. (2005) 'Minimum redundancy feature selection from microarray gene expression data', Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, pp.185-205.
7. Doherty, J.M., Carmichael, L.K. and Mills, J.C. (2006) 'GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions', BMC Bioinformatics, Vol. 7, p.151.
8. Fang, Z., Yang, J., Li, Y., Luo, Q. and Liu, L. (2006) 'Knowledge guided analysis of microarray data', Journal of Biomedical Informatics, Vol. 39, pp.401-411.
9. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A., Bloomfield, C.D. and Lander, E.S. (1999) 'Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring', Science, Vol. 286, pp.531-537.
10. Jaeger, J., Sengupta, R. and Ruzzo, W.L. (2003) 'Improved gene selection for classification of microarrays', Proceedings of Pacific Symposium of Biocomputing (PSB), Lihue, HI, pp.53-64.
11. Jiang, J.J. and Conrath, D.W. (1997) 'Semantic similarity based on corpus statistics and lexical taxonomy', Proceedings of 10th International Conference on Research in Computational Linguistics, Taiwan, arXiv:cMp-lg/9709008v1.
12. Leacock, C. and Condorow, M. (1998) 'Combining local context and WordNet similarity for word sense identification', in Fellbaum, C. (Ed.): WordNet: An Electronic Lexical Database, The MIT Press, pp.265-283.
13. Lewin, A. and Grieve, I.C. (2006) 'Grouping gene ontology terms to improve the assessment of gene set enrichment in microarray data', BMC Bioinformatics, Vol. 7, p.426.
14. Li, W. and Grosse, I. (2003) 'Gene selection criterion for discriminant microarray data analysis based on extreme value distributions', Proceedings of 7th International Conference on Research in Computational Molecular Biology (RECOMB), Berlin, Germany, pp.217-223.
15. Lin, D. (1998) 'An information-theoretic definition of similarity', Proceedings of 15th International Conference on Machine Learning (ICML) Madison, WI, pp.296-304.
16. Mewes, H.W., Frishman, D., Mayer, K.F.X., Munsterkotter, M., Noubibou, O., Pagel, P., Rattei, T., Oesterheld, M., Ruepp, A. and Stumpflen, V. (2006) 'MIPS: Analysis and annotation of proteins from whole genomes in 2005', Nucleic Acids Research, Vol. 34, pp.D169-D172.
17. Resnik, P. (1995) 'Using information content to evaluate semantic similarity in a taxonomy', Proceedings of 14th International Joint Conference on Artificial Intelligence, Montreal, Quebec, pp.448-453.
18. The Gene Ontology Consortium (2006) 'The Gene Ontology (GO) project in 2006', Nucleic Acids Research, Vol. 34, pp.D322-D326.
19. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) 'Significance analysis of microarray applied to the ionizing radiation response', Proc. Natl. Acad. Sci. USA, Vol. 98, No. 9, pp.5116-5121.
20. Wang, Y., Makedon, F.S., Ford, J.C. and Pearlman, J. (2005) 'Hykgene: A hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data', Bioinformatics, Vol. 21, No. 8, pp.1530-1537.
21. Webb, A. (2002) Statistical Pattern Recognition, Johns Wiley and Sons Ltd.
22. Wu, Z. and Palmer, M. (1994) 'Verb semantics and lexical selection', Proceedings of 32th Annual Meeting of the Association for Computational Linguistics, Las Cruces, NM, pp.133-138.
23. Xing, E.P., Jordan, M.I. and Karp, R.M. (2001) 'Feature selection for high-dimensional genomic microarray data', Proceedings of 18th International Conference on Machine Learning (ICML), Williamstown, MA, pp.601-608.
24. Xu, X. and Zhang, A. (2005) 'Virtual gene: Using correlations between genes to select informative genes on microarray datasets', LNCS Transactions on Computational Systems Biology II, Vol. LNBI 3680, pp.138-152.
25. Yu, L. and Liu, H. (2004) 'Redundancy based feature selection for microarray data', Proceedings of 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), Seattle, WA, pp.737-742.