Structured polychotomous machine diagnosis of multiple cancer types using gene expression

Bioinformatics

Volumn 22, Issue 8, 2006, Pages 950-958

  Koo, Ja Yong ^a   Sohn, Insuk ^a   Kim, Sujong ^b,c   Lee, Jae Won ^a  

^a Korea University   (South Korea)

^b Hanyang University College of Medicine   (South Korea)

^c AmorePacific Corporation   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; BIOINFORMATICS; COMPUTER SIMULATION; DIAGNOSTIC ACCURACY; DISEASE CLASSIFICATION; DNA MICROARRAY; EXPRESSION VECTOR; GENE EXPRESSION; GENE NUMBER; GENE SEQUENCE; GENETIC DATABASE; HUMAN; INTERMETHOD COMPARISON; MARKER GENE; METHODOLOGY; MULTIPLE CANCER; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STATISTICS;

EID: 33645818761     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl029     Document Type: Article

References (53)

1. Aisenberg,A.C. et al. (1985) Rearrangement of the gene for the beta chain of the T-cell receptor in T-cell chronic lymphocytic leukemia and related disorders. N. Eng. J. Med., 313, 529-533.
2. Alizadeh,A. et al. (2000) Distinct types of diffuse large B-cell-lymphoma identified by gene expression profiling. Nature, 403, 503-511.
3. Alonso,M.A. and Weissman,S.M. (1987) cDNA cloning and sequence of MAL, a hydrophobic protein associated with human T-cell differentiation. Proc. Natl Acad. Sci. USA, 84, 1997-2001.
4. Antonov,A.V. et al. (2004) Optimization models for cancer classification: Extracting gene interaction information from microarray expression data. Bioinformatics, 20, 644-652.
5. Bertness,V. et al. (1985) T-cell receptor gene rearrangements as clinical markers of human T-cell lymphomas. N. Eng. J. Med., 313, 534-538.
6. Broberg,P. (2002) Ranking genes with respect to differential expression. Genome Biol., 3, preprintOO07.
7. Brown,P.O. and Botstein,D. (1999) Exploring the new world of the genome with DNA microarrays. Nat. Genet., 21 (Suppl. 1), 33-37.
8. Chang,C. and Lin,C. (2001) LIBSVM: A library for support vector machines.
9. Chilosi,M. et al. (1998) Differential expression of cyclin-dependent kinase 6 in cortical thymocytes and T-cell lymphoblastic lymphoma/ leukemia. Am. J. Pathol., 152, 209-217.
10. Dauphinot,L. et al. (2001) Analysis of the expression of cell cycle regulators in Ewing cell lines: EWS-FLI-1 modulates p57KIP2and c-Myc expression. Oncogene, 20, 3258-3265.
11. Dettling,M. (2004) BagBoosting for tumor classification with gene expression data. Bioinformatics, 20, 3583-3593.
12. Dudoit,S. et al. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc., 97, 77-87.
13. Eisen,M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
14. El-Badry,O.M. et al. (1990) Insulin-like growth factor II acts as an autocrine growth and motility factor in human rhabdomyosarcoma tumors. Cell Growth Differ., 1, 325-331.
15. Elenitoba-Johnson,K.S., Bohling,S.D., Jenson,S.D., Lin,Z., Monnin,K.A. and Lim,M.S. (2002) Fluorescence PCR quantification of cyclin D1 expression. J. Mol. Diagn., 4(2), 90-96.
16. Fears,S. et al. (2002) Differential expression of TCL1 during pre-B-cell acute lymphoblastic leukemia progression. Cancer Genet. Cytogenet., 135, 110-119.
17. Fink,J.R. and LeBien,T.W. (2001) Novel expression of cyclin-dependent kinase inhibitors in human B-cell precursors. Exp. Hematol., 29, 490-498.
18. Furey,T.S. et al. (2000) Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics, 16, 906-914.
19. Golub,T.R. et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
20. Guyon,I. et al. (2002) Gene selection for cancer classification using support vector machines. Mach. Learn., 46, 389-422.
21. Hastie,T., Tibshirani,R. and Friedman,J. (2002) The Elements of Statistical Learning: Data Mining, Inference and Prediction. Springer Verlag.
22. Khan,J. et al. (1999) cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene. Proc. Natl Acad. Sci. USA, 96, 13264-13269.
23. Khan,J. et al. (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med., 7, 673-679.
24. Kim,T. et al. (1995) Cloning and characterization of MVP17: A developmentally regulated myelin protein in oligodendrocytes. J. Neurosci. Res., 42, 413-422.
25. Kohno,T. et al. (2000) Identification of genes associated with the progression of adult T cell leukemia (ATL). Jpn. J. Cancer Res., 91, 1103-1110.
26. Kooperberg,C. et al. Polychotomous regression. J. Am. Stat. Assoc., 92, 117-127.
27. Lee,J.W. et al. (2005) An extensive comparison of recent classification tools applied to microarray data. Comput. Stat. Data Anal., 48, 869-885.
28. Lee,Y. and Lee,C.-K. (2003) Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics, 19, 1132-1139.
29. Lee,Y. et al. (2004) Structured multicategory support vector machines with ANOVA decompositon. Technical Report 743, Department of Statistics, University of Ohio State, OH.
30. Lekanne Deprez,R. H. et al. (1995) Cloning and characterization of NM1, a gene from chromosome 22q11, which is disrupted by a balanced translocation in a meningioma. Oncogene, 10, 1521-1528.
31. Lucas,J.J. et al. (2004) Cyclin-dependent kinase 6 inhibits proliferation of human mammary epithelial cells. Mol. Cancer Res., 2, 105-114.
32. Martin-Belmonte,F. et al. (1998) Expression ofthe MAL gene in the thyroid: The MAL proteolipid, component of glycolipidenriched membranes, is apically distributed in thyroid follicles. Endocrinology; 139, 2077-2084.
33. Millan,J. and Alonso,M.A. (1998) MAL, a novel integral membrane protein of human T lymphocytes, associates with glycosylphosphatidylinositol-anchored proteins and Src-like tyrosine kinases. Eur. J. Immunol., 28, 3675-3684.
34. Molenaar,J.J. et al. (2003) Rearrangements and increased expression of cyclin D1 (CCND1) in neuroblastoma. Genes Chromosomes Cancer, 36, 242-249.
35. Myer,D., Leisch,F and Hornik,K. (2003) The support vector machines under test. Neurocomputing, 55, 169-442.
36. Nakayama,I. et al. (2000) Activation of the TCL1 protein in B cell lymphomas. Pathol. Int., 50, 191-199.
37. Narducci,M.G. et al. (2000) Regulation of TCL1 expression in B- and T-cell lymphomas and reactive lymphoid tissues. Cancer Res., 60, 2095-2100.
38. O'Connor, N.T.J. et al. (1985) Rearrangement of the T-cell-receptor beta-chain gene in the diagnosis of lymphoproliferative disorders. Lancet, 8, 1295-1297.
39. Omura-Minamisawa,M. et al. (2000) Universal inactivation of both p16 and p15 but not downstream components is an essential event in the pathogenesis of T-cell acute lymphoblastic leukemia. Clin. Cancer Res., 6, 1219-1228.
40. Ramaswamy,S. et al. (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl Acad. Sci. USA, 98, 15149-15154.
41. Rao,C.R. (1973) Linear Statistical Inference and Its Applications. 2nd edn. Wiley, New York.
42. Schölkopf,B. and Smola,J. (2002) Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond. The MIT Press, Massachusetts.
43. Schwarz,G. (1978) Estimating the dimension of a model. Ann. Stat., 6, 461-464.
44. Shenoy-Scaria,A.M. et al. (1992) Signal transduction through decay-accelerating factor. Interaction of glycosyl-phosphatidylinositol anchor and protein tyrosine kinases p561ck and p59fyn 1. J. Immunol., 149, 3535-3541.
45. Takizawa,J. et al. (1998) Expression of the TCL1 gene at 14q32 in B-cell malignancies but not in adult T-cell leukemia. Jpn. J. Cancer Res., 89, 712-718.
46. Teitell,M. et al. (1999) TCL1 oncogene expression in AIDS-related lymphomas and lymphoid tissues. Proc. Natl Acad. Sci. USA, 96, 9809-9814.
47. Tibshirani,R. et al. (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA, 99, 6567-6572.
48. Vapnik,V. (1998) Statistical Learning Theory. Wiley, New York.
49. Virgilio,L. et al. (1993) Chromosome walking on the TCL1 locus involved in T-cell neoplasia. Proc. Natl Acad. Sci. USA, 90, 9275-9279.
50. Virgilio,L. et al. (1994) Identification of the TCL1 gene involved in T-cell malignancies. Proc. Natl Acad. Sci. USA, 91, 12530-12534.
51. Zacchetti,D. et al. (1995) VIP/MAL, a proteolipid in apical transport vesicles. FEBS Lett., 377, 465-469.
52. Zhang,J. et al. (2004) Selective usage of D-Type cyclins by Ewing's tumors and rhabdomyosarcomas. Cancer Res., 64, 6026-6034.
53. Zhu,J. and Hastie,T. (2001) Kernel logistic regression and the import vector machines. Adv. Neural Inf. Process. Syst., 14.