Breast cancer prognosis by combinatorial analysis of gene expression data

Breast Cancer Research

Volumn 8, Issue 4, 2006, Pages

  Alexe, Gabriela ^a,b,c   Alexe, Sorin ^a   Axelrod, David E ^d,e   Bonates, Tibérius O ^a   Lozina, Irina I ^a   Reiss, Michael ^e,f   Hammer, Peter L ^a  

^a the State University of New Jersey   (United States)

^b IBM RESEARCH   (United States)

^c INSTITUTE FOR ADVANCED STUDY   (United States)

^d RUTGERS UNIVERSITY   (United States)

^e RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^f ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; GENETIC MARKER;

ARTICLE; BREAST CANCER; CANCER GENETICS; CLINICAL FEATURE; COMBINATORIAL CHEMISTRY; DIAGNOSTIC ACCURACY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENOMICS; HUMAN; NUCLEOTIDE SEQUENCE; PROGNOSIS; BIOLOGICAL MODEL; BREAST NEOPLASMS; FEMALE; GENETIC MARKER; GENETICS; STATISTICS; STATISTICS AND NUMERICAL DATA;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION PROFILING; GENETIC MARKERS; HUMANS; MODELS, GENETIC; PROGNOSIS; STATISTICS AS TOPIC;

EID: 33748139952     PISSN: 1465542X     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr1512     Document Type: Article

References (64)

1. Crama Y, Hammer PL, Ibaraki T: Cause-effect relationships and partially defined boolean functions. Ann Oper Res 1988, 16:299-326.
2. Boros E, Hammer PL, Ibaraki T, Kogan A, Mayoraz E, Muchnik I: An implementation of logical analysis of data. IEEE Trans Knowledge and Data Eng 2000, 12:292-306.
3. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, Mao M, Peterse HL, van der kooy K, Marton MJ, Witteveen AT, et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-535.
4. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
5. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
6. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, et al.: Molecular classification of cutaneous malignant melanoma by expression profiling. Nature 2000, 406:536-540.
7. Brown MPS, Grundy WN, Lin D, Cristanini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000, 97:252-267
8. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR: Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96:2907-2912.
9. Toronen P, Kolehmainen M, Wong G, Castren E: Analysis of gene expression data using self-organizing maps. FEBS Lett 1999, 451:142-146.
10. Chen JJ, Peck K, Hong TM, Yang SC, Sher YP, Shih JY, Wu R, Cheng JL, Roffler SR, Wu CW, et al.: Global analysis of gene expression in invasion by a lung cancer model. Cancer Res 2001, 61:5223-5240.
11. Getz G, Levine E, Domany E: Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad USA 2000, 97:12079-12084.
12. Huang X, Pan W: Linear regression and two-class classification with gene expression data. Bioinformatics 2003, 19:2072-2078.
13. Yang H, Haddad H, Thomas C, Alsaker K, Papoutsakis E: A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis. Proc Natl Acad Sci USA 2003, 100:1122-1227.
14. Zhang H, Yu C-Y, Singer B, Xiong M: Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci USA 2001, 98:6730-6735.
15. Sutter TR, He XR, Dimitrov P, Xu L, Narasimhan G, George EO, Sutter CH, Grubbs C, Savory R, Stephan-Gueldner M, et al.: Multiple comparisons model-based clustering and ternary pattern tree numerical display of gene response to treatment: procedure and application to the preclinical evaluation of chemopreventive agents. Mol Cancer Ther 2002, 1:1283-1292.
16. Zhang H, Yu C-Y, Singer B: Cell and tumor classification using gene expression data: construction of forests. Proc Natl Acad Sci USA 2003, 100:4168-4172.
17. Boulesteix AL, Tutz G, Strimmer KA: CART-based approach to discover emerging patterns in microarray data, Bioinformatics 2003, 19:2465-2472.
18. Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS: Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 2001, 61:5979-5984.
19. Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, et al.: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Med 2001, 7:673-679.
20. Brown PS, Grundy WN, Lin D, Cristianni N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000, 97:262-267.
21. Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D: Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 2000, 16:906-914.
22. Su AI, Welsh JB, Sapinoso LM, Kern SG, Dimitrov P, Lapp H, Schultz PG, Powell SM, Moskaluk CA, Frierson HF Jr, et al.: Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res 2001, 61:7388-7393.
23. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, et al: Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 2001, 98:15149-15154.
24. Hilsenbeck SG, Freidrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, Fuqua SA: Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J Natl Cancer Inst 1999, 91:453-459.
25. Tan Y, Shi L, Tong W, Wang C: Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data. Nucleic Acids Res 2005, 33:56-65.
26. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
27. Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P: 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol 2000, 1:0003.
28. Raychaudhuri S, Stuart JM, Altman RB: Principle components analysis to summarize microarray experiments: application to sporulation time series. Pacific Symp Biocomputing 2000, 5:452-463.
29. Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000, 97:10101-10106.
30. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV: Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci USA 2000, 97:8409-8414.
31. Alter O, Brown PO, Botstein D: Generalized singular value composition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci USA 2003, 100:3351-3356.
32. Liu L, Hawkins DM, Ghosh S, Young SS: Robust singular value decomposition analysis of microarray data. Proc Natl Acad Sci USA 2003, 100:13167-13172.
33. Khan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013,
34. Zhang H, Yu C-Y, Singer B, Xiong M: Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci USA 2001, 98:6730-6735.
35. Kuznetsov VA, Ivshina AV, Sen'ko OV, Kuznetsova AV: Syndrome approach for computer recognition of fuzzy systems and its application to immunological diagnostics and prognosis of human cancer. Math Comp Modelling 1996, 23:95-120.
36. Jackson AM, Ivshina AV, Senko O, Kuznetsova A, Sundan A, O'Donnell MA, Clinton S, Alexandroff AB, Selby PJ, James K, et al.: Prognosis of intravesical bacillus Calmette-Guerin therapy for superficial bladder cancer by immunological urinary measurements: statistically weighted syndromes analysis. J Urol 1998, 159:1054-1063.
37. Hammer A, Hammer PL, Muchnik I: Logical analysis of Chinese productivity patterns. Ann Oper Res 1999, 87:165-176.
38. Hammer PL, Kogan A, Lejeune MA: Country risk rating: statistical and combinatorial non-recursive models. RUTCOR Research Report, RRR 8-2004.
39. Lauer MS, Alexe S, Snader CEP, Blackstone E, Ishwaran H, Hammer PL: Use of the logical analysis of data method for assessing long-term mortality risk after exercise electrocardiography. Circulation 2002, 106:685-690.
40. Alexe S, Blackstone E, Hammer PL, Ishwaran H, Lauer MS, Pothier Snader CE: Coronary risk prediction by logical analysis of data. Ann Oper Res 2003, 119:15-42.
41. Abramson S, Alexe G, Hammer PL, Knight D, Kohn J: Using logical analysis of data (LAD) based modeling to understand patterns of physio-mechanical data which lead to specific cellular outcomes. J Biomed Materials Res A 2005, 73:116-24.
42. Brauner MW, Brauner N, Hammer PL, Lozina I, Valeyre D: Logical analysis of computed tomography data to differentiate entities of idiopathic interstitial pneumonias. In Biocomputing Data Mini ng in Medicine Edited by: Pardalos P. Springer Heidelberg, New York in press.
43. Alexe G, Alexe S, Axelrod DE, Weissmann D, Hammer PL: Logical analysis of diffuse large B-cell lymphomas. Artif Intell Med 2005, 34:235-267.
44. Alexe G, Alexe S, Hammer PL, Liotta L, Petricoin E, Reiss M: Logical analysis of the proteomic ovarian cancer dataset. Proteomics 2004, 3:766-783.
45. Boros E, Hammer PL, Ibaraki T, Kogan A: Logical analysis of numerical data. Math Progr 1997, 79:163-190.
46. Alexe G, Alexe S, Hammer PL, Vizvari B: Pattern-based feature selection in genomics and proteomics. Ann Oper Res 2006 in press.
47. Alexe G, Hammer PL: Spanned patterns in logical analysis of data. Discr Appl Math 2006, 154:1039-1049.
48. Alexe S, Hammer PL: Accelerated algorithm for pattern detection in logical analysis of data. Discr Appl Math 2006, 154:1050-1063.
49. Eckstein J, Hammer PL, Liu Y, Nediak M, Simeone B: The maximum box problem and its application to data analysis. Comp Opt Appl 2006 in press.
50. Hammer PL, Bonates TO: Logical analysis of data: from combinatorial optimization to medical applications. Ann Oper Res 2006 in press.
51. Alexe G, Alexe S, Hammer PL, Kogan A: Comprehensive vs. comprehensible classifiers in logical analysis of data. Discr Appl Math 2006 in press.
52. DAVID (Database for Annotation, Visualization and Integrated Discovery) [http://apps1.niaid.nih.gov/david]
53. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al.: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009.
54. Witten IH, Frank E: "Data Mining: Practical machine learning tools and techniques" 2nd edition. Morgan Kaufmann, San Francisco; 2005.
55. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer, class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
56. Ramaswamy S, Ross KN, Lander ES, Golub TR: A molecular signature of metastasis in primary solid tumors. Nat Genet 2003, 33:49-54.
57. Weigelt B, Glas AM, Wessels LF, Witteveen AT, Peterse JL, van't Veer LJ: Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci USA 2003, 100:15901-15905.
58. Dai H, van't Veer L, Lamb J, He YD, Mao M, Fine BM, Bernards R, van de Vijver M, Deutsch P, Sachs A, et al.: A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res 2005, 65:4059-4066.
59. Bertucci F, Houlgatte R, Granjeaud S, Nasser V, Loriod B, Beaudoing E, Hingamp P, Jacquemier J, Viens P, Bimbaum D, et al.: Prognosis of breast cancer and gene expression profiling using DNA arrays. Ann NY Acad Sci 2002, 975:217-231.
60. Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET: Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci USA 2003, 100:10393-10398.
61. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al.: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003, 100:8418-8423.
62. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874.
63. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR: Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci USA 2001, 98:11462-11467.
64. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, et al.: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826.