Biomedical application of fuzzy association rules for identifying breast cancer biomarkers

Medical and Biological Engineering and Computing

Volumn 50, Issue 9, 2012, Pages 981-990

  Lopez, F J ^a   Cuadros, M ^a   Cano, C ^a   Concha, A ^b   Blanco, A ^a  

^a UNIVERSITY OF GRANADA   (Spain)

^b HOSPITAL UNIVERSITARIO VIRGEN DE LAS NIEVES   (Spain)

Author keywords

Breast cancer; Fuzzy association rules

Indexed keywords

BIOMEDICAL APPLICATIONS; BIOMEDICAL DATA; BREAST CANCER; COMPUTATIONAL TECHNIQUE; DATA SETS; EXPRESSION DATA; EXPRESSION LEVELS; FLUORESCENCE IN SITU HYBRIDIZATION; FUZZY ASSOCIATION RULE; HIGH-THROUGHPUT; INTERESTING RULES; LYMPH NODE; MICROARRAY DATA; MICROARRAY TECHNOLOGIES; PROGESTERONE RECEPTOR; PROGNOSTIC FACTORS; TESTING METHODOLOGY; TUMOR GRADES; TUMOR SIZE;

ASSOCIATION RULES; DATA MINING; DIAGNOSIS; FLUORESCENCE MICROSCOPY; FUZZY RULES; MEDICAL APPLICATIONS; TUMORS;

DISEASES;

TUMOR MARKER; TUMOR PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BREAST TUMOR; COMPUTER ASSISTED DIAGNOSIS; FEMALE; FUZZY LOGIC; HUMAN; METABOLISM; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; BREAST NEOPLASMS; DIAGNOSIS, COMPUTER-ASSISTED; FEMALE; FUZZY LOGIC; HUMANS; NEOPLASM PROTEINS; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TUMOR MARKERS, BIOLOGICAL;

EID: 84866731395     PISSN: 01400118     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11517-012-0914-8     Document Type: Article

References (56)

1. Agrawal R, Imielinski T, Swami A (1993) Mining association rules between sets of items in large databases. In: Proceedings of the ACM SIGMOD INTL conference on management of data (ACM SIGMOD 93), Washington, USA, pp 207-216
2. Barrett T, Troup D, Wilhite S, Ledoux P et al (2011) NCBI GEO: archive for functional genomics data sets 10 years on. Nucleic Acids Res 39(suppl 1):D1005
3. Bebek G, Yankg J (2007) Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinform 8:335-347
4. Bempt IV, Van Loo P, Drijkoningen M, Neven P et al (2008) Polysomy 17 in breast cancer: clinicopathologic significance and impact on HER-2 testing. J Clin Oncol 26(30):4869-4874
5. Berzal F, Blanco I, Sanchez D, Vila MA (2004) Measuring the accuracy and interest of association rules: a new framework. Intell Data Anal 6:221-235
6. Bownds S, Tong-On P, Rosenberg SA, Parkhurst M (2001) Induction of tumor-reactive cytotoxic T lymphocytes using a peptide from NY-ESO-1 modified at the carboxy-terminus to enhance HLA-A2. 1 binding affinity and stability in solution. J Immunother 24(1):1-9
7. Brennan D, Ek S, Doyle E, Drew T et al (2009) The transcription factor Sox11 is a prognostic factor for improved recurrence-free survival in epithelial ovarian cancer. Eur J Cancer 45(8):1510-1517
8. Brennan DJ, Ek S, Doyle E, Drew T et al (2009) The transcription factor Sox11 is a prognostic factor for improved recurrence-free survival in epithelial ovarian cancer. Eur J Cancer 45(8):1510-1517
9. Burcombe R., Wilson GD, Dowsett M, Khan I et al (2006) Evaluation of Ki-67 proliferation and apoptotic index before, during and after neoadjuvant chemotherapy for primary breast cancer. Breast Cancer Res 8(3):31-33
10. Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O et al (2006) Integrated analysis of gene expression by association rules discovery. BMC Bioinform 7:54-69
11. Cheng CJ, Lin YC, Tsai MT, Chen CS et al (2009) SCUBE2 suppresses breast tumor cell proliferation and confers a favorable prognosis in invasive breast cancer. Cancer Res 69(8):3634-3641
12. Chibon F, de Mascarel I, Sierankowski G, Brouste V et al (2009) Prediction of HER2 gene status in Her2 2? invasive breast cancer: a study of 108 cases comparing ASCO/CAP and FDA recommendations. Modern pathology: an official journal of the United States and Canadian Academy of Pathology, Inc 22(3):403-409
13. Cuadros M, Cano C, Lopez F, Talavera P, Garcia-Perez I, Blanco A, Concha A (2011) Her2 status in breast cancer: experience of a spanish national reference centre. Clin Transl Oncol 13:335-340. doi:10.1007/s12094-011-0663-4
14. Cuadros M, Villegas R (2009) Systematic review of HER2 breast cancer testing. Appl Immunohistochem Mol Morphol 17(1):1-7
15. Delgado M, Marin N, Sanchez D, Vila MA (2003) Fuzzy association rules: general model and applications. IEEE Trans Fuzzy Syst 11:214-225
16. Dy P, Penzo-Mendez A, Wang H, Pedraza C, Macklin W, Lefebvre V (2008) The three SoxC proteins-Sox4, Sox11 and Sox12-exhibit overlapping expression patterns and molecular properties. Nucl Acids Res 36:3101-3117
17. Ek S, Dictor M, Jerkeman M, Jirstrom K, Borrebaeck C (2008) Nuclear expression of the non B cell lineage Sox11 transcription factor identifies mantle cell lymphoma. Blood 111(2):800
18. En-lin S, Sheng-guo C, Huaqiao W (2010) The expression of EFEMP1 in cervical carcinoma and its relationship with prognosis. Gynecologic Oncology 117:417-422
19. Esseghir S, Todd SK, Hunt T, Poulsom R et al (2007) A role for glial cell derived neurotrophic factor induced expression by inflammatory cytokines and RET/GFR {alpha} 1 receptor up-regulation in breast cancer. Cancer Res 67(4):11732-11741
20. Esteva FJ, Sahin AA, Cristofanilli M, Arun B et al (2002) Molecular prognostic factors for breast cancer metastasis and survival. Semin Radiat Oncol 12(14):319-328
21. Galea M, Blamey R, Elston C, Ellis I (1992) The Nottingham Prognostic Index in primary breast cancer. Breast Cancer Res Treat 22(3):207-219
22. Garcia F, Lopez F, Cano C, Blanco A (2009) Fisim: a new similarity measure between transcription factor binding sites based on the fuzzy integral. BMC Bioinform 10(1):224
23. Geng L, Hamilton HJ (2006) Interestingness measures for data mining: a survey. ACM Comput Surv 38(3) Article 9, 1-32
24. HZhang BP (2004) Using randomization to determine a false discovery rate for rule discovery. In: Proceedings of the fourteenth workshop on information technologies and systems, pp 140-145
25. Helms MW, Kemming D, Pospisil H, Vogt U et al (2008) Squalene epoxidase, located on chromosome 8q24. 1, is upreg-ulated in 8q+ breast cancer and indicates poor clinical outcome in stage I and II disease. Br J Cancer 99(5):774-780
26. Hu B, Thirtamara-Rajamani K, Sim H, Viapiano M (2009) Fibulin-3 is uniquely upregulated in malignant gliomas and promotes tumor cell motility and invasion. Mol Cancer Res 7(11):1756
27. Huang Y, Li Y (2004) Prediction of protein subcellular locations using fuzzy k-nn method. Bioinformatics 20(1):21-28
28. Irizarry RA, Bolstad BM, Collin F, Cope LM et al (2003) Summaries of affymetrix genechip probe level data. Nucliec Acids Res 31(4):e15
29. Iruela-Arispe ML, Porter P, Bornstein P, Sage EH (1996) Thrombospondin-1, an inhibitor of angiogenesis, is regulated by progesterone in the human endometrium. J Clin Invest 97(2):403-412
30. Ito LS, Iwata H, Hamajima N, Saito T et al (1997) Expression of interleukin-1B in human breast carcinoma. Cancer 80:421-433
31. Klosgen W (1996) Explora: a multipattern and multistrategy discovery assistant advances in knowledge discovery and data mining. MIT Press, Menlo Park
32. Labhart P, Karmakar S, Salicru EM, Egan BS et al (2005) Identification of target genes in breast cancer cells directly regulated by the SRC-3/AIB1 coactivator. Proc Natl Acad Sci 102(5):1339-1344
33. Lee C, Appleby V, Orme A, Chan W, Scotting P (2002) Differential expression of SOX4 and SOX11 in medulloblastoma. J Neuro Oncol 57(3):201-214
34. Lee SR, Ramos SM, Ko A, Masiello D et al (2002) AR and ER interaction with a p21-activated kinase (PAK6). Mol Endocrinol 16(1):85-99
35. Leung K, Wong K, Chan T, Wong M, Lee K, Lau C, Tsui S (2010) Discovering protein-DNA binding sequence patterns using association rule mining. Nucl Acids Res 38:6424-6437
36. Lopez FJ, Blanco A, Garcia F, Cano C et al (2008) Fuzzy association rules for biological data analysis: a case study on yeast. BMC Bioinform 9:107-115
37. Morgan XC, Ni S, Miranker DP, Iyer VR (2007) Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinform 8:445-458
38. Pan Y (2006) Advances in the discovery of cis regulatory elements 1:326-336
39. Pritchard K, Shepherd L, O'Malley F, Andrulis I et al (2006) HER2 and responsiveness of breast cancer to adjuvant chemotherapy. New Engl J Med 354(20):2103
40. Rinott R, Carmeli B, Kent C, Landau D, Maman Y, Rubin Y, Slonim N (2011) Prognostic data-driven clinical decision support-formulation and implications. Stud Health Technol Inform 169:140
41. Sadr-Nabavi A, Ramser J, Volkmann J, Naehrig J et al (2009) Decreased expression of angiogenesis antagonist EFEMP1 in sporadic breast cancer is caused by aberrant promoter methylation and points to an impact of EFEMP1 as molecular biomarker. Int J Cancer 124(7):1727-1735
42. Sadr-Nabavi A, Ramser J, Volkmann J, Naehrig J et al (2009) Decreased expression of angiogenesis antagonist EFEMP1 in sporadic breast cancer is caused by aberrant promoter methylation and points to an impact of EFEMP1 as molecular biomarker. Int J Cancer 124(7):1727-1735
43. Sassen A, Rochon J, Wild P, Hartmann A, Hofstaedter F, Schwarz S, Brockhoff G (2008) Cytogenetic analysis of HER1/EGFR, HER2, HER3 and HER4 in 278 breast cancer patients. Breast Cancer Res 10(1):R2
44. Sauter G, Lee J, Bartlett J, Slamon D, Press M (2009) Guidelines for human epidermal growth factor receptor 2 testing: biologic and methodologic considerations. J Clin Oncol 27(8):1323
45. Seeliger H, Camaj P, Ischenko I, Kleespies A, De Toni E, Thieme S, Blum H, Assmann G, Jauch K, Bruns C (2009) EFEMP1 expression promotes in vivo tumor growth in human pancreatic adenocarcinoma. Mol Cancer Res 7(2):189
46. Sims AH (2009) Bioinformatics and breast cancer: what can high-thoroughput genomic approaches actually tell us? J Clin Pathol 62:879-885
47. Slamon D, Clark G, Wong S, Levin W, Ullrich A, McGuire W (1987) Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235(4785):177
48. Slamon D, Godolphin W, Jones L, Holt J et al (1989) Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 244(4905):707
49. Stockert E, Jager E, Chen YT, Scanlan MJ et al (1998) A survey of the humoral immune response of cancer patients to a panel of human tumor antigens. J Exp Med 187(8):1349-1354
50. Thogersen VB, Sorensen BS, Poulsen SS, Orntoft TF et al (2001) A subclass of HER1 ligands are prognostic markers for survival in bladder cancer patients. Cancer Res 61:6227-6233
51. Thomassen M, Tan Q, Kruse TA (2009) Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis. Breast Cancer Res Treat 113(2):239-249
52. Toyoda H, Komurasaki T, Uchida D, Morimoto S (1997) Distribution of mRNA for human epiregulin, a differentially expressed member of the epidermal growth factor family. Bio-chem J 326(Pt 1):69-75
53. Vanden Bempt I, Vanhentenrijk V, Drijkoningen M, Wlodarska I, Vandenberghe P, De Wolf-Peeters C (2005) Real-time reverse transcription-PCR and fluorescence in-situ hybridization are complementary to understand the mechanisms involved in HER-2/neu overexpression in human breast carcinomas. Histopathology 46(4):431-441
54. Weigle B, Ebner R, Temme A, Schwind S et al (2005) Highly specific overexpression of the transcription factor SOX11 in human malignant gliomas. Oncol Reports 13(1):139-144
55. Zadeh LA (1965) Fuzzy sets. Inform Control 8(3):338-353
56. Zimmerman HJ (2001) Fuzzy sets theory and its applications. Kluwer Academic Publishers, Boston