Maximizing biomarker discovery by minimizing gene signatures

BMC Genomics

Volumn 12, Issue SUPPL. 5, 2011, Pages

  Chang, Chang ^a   Wang, Junwei ^a   Zhao, Chen ^a   Fostel, Jennifer ^b   Tong, Weida ^c   Bushel, Pierre R ^b   Deng, Youping ^d   Pusztai, Lajos ^e   Symmans, W Fraser ^e   Shi, Tieliu ^a  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^d RUSH MEDICAL COLLEGE   (United States)

^e UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ACCURACY; ARTICLE; BREAST CANCER; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; ESTROGEN RECEPTOR 1 GENE; GENE; GENE SIGNATURE; GENOMICS; INTERMETHOD COMPARISON; MINIMZE FEATURE SIZE; PREDICTION; SENSITIVITY AND SPECIFICITY; STATISTICAL CONCEPTS; VALIDATION PROCESS; ALGORITHM; BREAST TUMOR; DNA MICROARRAY; FEMALE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; METHODOLOGY; PATHOLOGY;

ALGORITHMS; BIOLOGICAL MARKERS; BREAST NEOPLASMS; DATABASES, GENETIC; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84255163353     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S5-S6     Document Type: Article

References (41)

1. Gene signature. , http://en.wikipedia.org/wiki/Gene_signature
2. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28(8):827-838. 10.1038/nbt.1665, 20676074.
3. Ding C, Peng H. Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol 2005, 3:185-205. 10.1142/S0219720005001004, 15852500.
4. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and feature reduction. Trends Biotechnol 2001, 19:189-193. 10.1016/S0167-7799(01)01599-2, 11301132.
5. Huang T, Cui W, Hu L, Feng K, Li Y-X, Cai Y-D. Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS One 2009, 4:e8126. 10.1371/journal.pone.0008126, 2780314, 19956587.
6. Fishel I, Kaufman A, Ruppin E. Meta-analysis of gene expression data: a predictor-based approach. Bioinformatics 2007, 23:1599-1606. 10.1093/bioinformatics/btm149, 17463023.
7. Natsoulis G, Pearson CI, Gollub J, P Eynon B, Ferng J, Nair R, Idury R, Lee MD, Fielden MR, Brennan RJ, et al. The liver pharmacological and xenobiotic gene response repertoire. Mol Syst Biol 2008, 4:175. 2290941, 18364709.
8. Guyon I, Weston J, Barnhill S, Vapnik V. Gene selection for cancer classification using support vector machines. Machine Learning 2002, 46:389-422.
9. Liu Q, Sung AH, Chen Z, Liu J, Huang X, Deng Y. Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data. PLoS One 2009, 4:e8250. 10.1371/journal.pone.0008250, 2789385, 20011240.
10. Natsoulis G, Ghaoui LE, Lanckriet GRG, Tolley AM, Leroy F, Dunlea S, Eynon BP, Pearson CI, Tugendreich S, Jarnagin K. Classification of a large microarray data set: Algorithm comparison and analysis of drug signatures. Genome Res 2005, 15:724-736. 10.1101/gr.2807605, 1088301, 15867433.
11. Kim SY, Kim YS. A gene sets approach for identifying prognostic gene signatures for outcome prediction. BMC Genomics 2008, 9:177-187. 10.1186/1471-2164-9-177, 2364634, 18416850.
12. Brown M, Grundy W, Lin D, Cristianini N, Sugnet C, Furey T, Ares MJ, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000, 97:262-267. 10.1073/pnas.97.1.262, 26651, 10618406.
13. Foekens JA, Atkins D, Zhang Y, Sweep FCGJ, Harbeck N, Paradiso A, Cufer T, Sieuwerts AM, Talantov D, Span PN, et al. Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol 2006, 24:1665-1671. 10.1200/JCO.2005.03.9115, 16505412.
14. Hess K, Anderson K, Symmans W, Valero V, Ibrahim N, Mejia J, Booser D, Theriault RL, Buzdar AU, Dempsey PJ, et al. Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol 2006, 24:4236-4244. 10.1200/JCO.2006.05.6861, 16896004.
15. Moggs J, Murphy T, Lim F, Moore D, Stuckey R, Antrobus K, Kimber I, Orphanides G. Anti-proliferative effect of estrogen in breast cancer cells that re-express ERalpha is mediated by aberrant regulation of cell cycle genes. J Mol Endocrinol 2005, 34:535-551. 10.1677/jme.1.01677, 15821115.
16. Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, Larsimont D, Macgrogan G, Bergh J, Cameron D, Goldstein D, et al. Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 2005, 24:4660-4671. 10.1038/sj.onc.1208561, 15897907.
17. Lin C, Vega V, Thomsen J, Zhang T, Kong S, Xie M, Chiu K, Lipovich L, Barnett DH, Stossi F, et al. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 2007, 3:e87. 10.1371/journal.pgen.0030087, 1885282, 17542648.
18. Wang Y, Klijn JGM, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679.
19. Zeeberg B, Feng W, Wang G, Wang M, Fojo A, Sunshine M, Narasimhan S, Kane D, Reinhold W, Lababidi S, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biology 2003, 4:R28. 10.1186/gb-2003-4-4-r28, 154579, 12702209.
20. Chen S-C, Chang H-K, Lin Y-C, Hsueh S, Cheung Y-C, Leung W-M, Tsai C-S, Lo Y-F, Tsai H-P, Shen S-C, et al. High pathologic complete response in HER 2-positive locally advanced breast cancer after primary systemic chemotherapy with weekly docetaxel and epirubicin. Japan J Clin Oncol 2008, 38:99-105.
21. Siek J, Lee LQ, Lumsdaine A. The Boost Graph Library: User Guide and Reference Manual 2002, Addison-Wesley.
22. Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE, Futschik ME. UniHI: an entry gate to the human protein interactome. Nucleic Acids Res 2006, 35:D590-D594. 1781159, 17158159.
23. Li W, Yang Y. How many genes are needed for a discriminant microarray data analysis? 2002, 137-150. Kluwer Academic.
24. Barnett DH, Sheng S, Charn TH, Waheed A, Sly WS, Lin C-Y, Liu ET, Katzenellenbogen BS. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. Cancer Res 2008, 68:3505-3515. 10.1158/0008-5472.CAN-07-6151, 18451179.
25. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, 35:D26-D31. 10.1093/nar/gkl993, 1761442, 17148475.
26. Andre F, Hatzis C, Anderson K, Sotiriou C, Mazouni C, Mejia J, Wang B, Hortobagyi GN, Symmans WF, Pusztai L. Microtubule-associated protein-tau is a bifunctional predictor of endocrine sensitivity and chemotherapy resistance in estrogen receptor-positive breast cancer. Clin Cancer Res 2007, 13:2061-2067. 10.1158/1078-0432.CCR-06-2078, 17404087.
27. Lacroix M, Leclercq G. About GATA3, HNF3A, and XBP1, three genes co-expressed with the oestrogen receptor-α gene (ESR1) in breast cancer. Mol Cell Endocrinol 2004, 219:1-7. 10.1016/j.mce.2004.02.021, 15149721.
28. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
29. van't Veer LJ, Dai H, van der V, He YD, Hart AA, 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, 415:530-653. 10.1038/415530a, 11823860.
30. Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 2005, 7:R953-R964. 10.1186/bcr1325, 1410752, 16280042.
31. 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. New Engl J Med 2004, 351:2817-2826. 10.1056/NEJMoa041588, 15591335.
32. Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Bioinformatics 2008, 1:28.
33. Lindley DV. The philosophy of statistics. The Statistician 2000, 49:293-337.
34. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, (31):e15.
35. Witten IH, Frank E. Data Mining: Practical Machine Learning Tools and Techniques 2005, San Francisco: Morgan Kaufmann, 2.
36. Han J, Kamber M. Data Mining: Concepts and Techniques 2001, San Francisco: Morgan Kaufmann.
37. Kilpinen S, Autio R, Ojala K, Iljin K, Bucher E, Sara H, Pisto T, Saarela M, Skotheim R, Björkman M, et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol 2008, 9:R139. 10.1186/gb-2008-9-9-r139, 2592717, 18803840.
38. Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16:412-424. 10.1093/bioinformatics/16.5.412, 10871264.
39. Rody A, Holtrich U, Solbach C, Kourtis K, Minckwitz G, Engels K, Kissler S, Gätje R, Karn T, Kaufmann M. Methylation of estrogen receptor ß promoter correlates with loss of ER-ß expression in mammary carcinoma and is an early indication marker in premalignant lesions. Endocr Relat Cancer 2005, 12:903-916. 10.1677/erc.1.01088, 16322330.
40. Wilson CL, Sims AH, Howell A, Miller CJ, Clarke RB. Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue. Endocr Relat Cancer 2006, 13:617-628. 10.1677/erc.1.01165, 16728587.
41. Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T. Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003, 100:5974-5979. 10.1073/pnas.0931261100, 156311, 12714683.