Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Tsai, Yu Shuen ^a   Lin, Chin Teng ^b   Tseng, George C ^c   Chung, I Fang ^a   Pal, Nikhil Ranjan ^d  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^c UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^d INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SIGNIFICANCE; CENTRAL NERVOUS SYSTEMS; COMPUTATIONAL PROTOCOLS; DISCRIMINATING POWER; MULTI-CLASS PROBLEMS; NEAREST MEAN CLASSIFIERS; NEAREST NEIGHBOR CLASSIFIERS; PREDICTION ACCURACY;

DESIGN; DIAGNOSIS; DISEASES; FORECASTING; POLYMERASE CHAIN REACTION; SIGNAL TO NOISE RATIO; SUPPORT VECTOR MACHINES; TUMORS;

GENE EXPRESSION;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; COMPUTER ASSISTED DIAGNOSIS; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETICS; HUMAN; METHODOLOGY; NEOPLASM; TUMOR GENE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DIAGNOSIS, COMPUTER-ASSISTED; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENETIC MARKERS; HUMANS; NEOPLASMS;

EID: 58149510473     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-425     Document Type: Article

References (67)

1. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci 1998, 95:14863-14868. 9843981 9843981 24541
2. 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. 10521349 10521349
3. 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 1999, 96:2907-2912. 10077610 10077610 15868
4. Dudoit S Fridlyand J Speed TP Comparison of discrimination methods for the classification of tumors using gene expression data J Am Stats Assoc 2002, 97:77-87.
5. Statnikov A Aliferis CF Tsamardinos I Hardin D Levy S A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis Bioinformatics 2005, 21:631-643. 15374862 15374862
6. Wang Y Makedon FS Ford JC Pearlman J HykGene: A hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data Bioinformatics 2005, 21:1530-1537. 15585531 15585531
7. Kim KJ Cho SB Ensemble classifiers based on correlation analysis for DNA microarray classification Neurocomputing 2006, 70:187-199.
8. Niijima S Kuhara S Recursive gene selection based on maximum margin criterion: A comparison with SVM-RFE BMC Bioinformatics 2006, 7:543. 17187691 17187691 1790716
9. Guyon I Weston J Barnhill S Vapnil V Gene selection for cancer classification using support vector machines Machine Learning 2002, 46:389-422.
10. Pal NR Aguan K Sharma A Amari SI Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering BMC Bioinformatics 2007, 8:5. 1770936 17207284
11. Pavlidis P Noble WS Analysis of strain and regional variation in gene expression in mouse brain Genome Biol 2001, 2(Research0042). 11597334 11597334 57797
12. 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 2001, 98:15149-15154. 11742071 11742071 64998
13. 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 Nat Med 2001, 7:673-679. 11385503 11385503 1282521
14. Armstrong SA Staunton JE Silverman LB Pieters R den Boer ML Minden MD Sallan SE Lander ES Golub TR Korsmeyer SJ Translocations specify a distinct gene expression profile that distinguishes a unique leukemia Nat Genet 2002, 30:41-47. 11731795
15. Pomeroy SL Tamayo P Gaasenbeek M Sturla LM Angelo M McLaughlin ME Kim JY Goumnerova LC Black PM Lau C et al Prediction of central nervous system embryonal tumour outcome based on gene expression Nature 2002, 415:436-442. 11807556 11807556
16. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M et al Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc Natl Acad Sci 2001, 98:13790-13795. 11707567 11707567 61120
17. Morris JS Yin G Baggerly K Wu C Zhang L Pooling information across different studies and oligonucleotide chip types to identify prognostic genes for lung cancer Methods of Microarray Data Analysis IV New York: Springer Shoemaker JS, Lin SM 2005, 51-66.
18. Futreal PA Coin L Marshall M Down T Hubbard T Wooster R Rahman N Stratton MR A census of human cancer genes Nat Rev Cancer 2004, 4:177-183. 14993899
19. Hong H Tong W Perkins R Fang H Xie Q Shi L Multiclass decision forest - a novel pattern recognition method for multiclass classification in microarray data analysis DNA Cell Biol 2004, 23:685-694. 15585126
20. Pasic S Vujic D Djuricic S Jevtic D Grujic B Burkitt lymphoma-induced ileocolic intussusception in Wiskott-Aldrich syndrome J Pediatr Hematol Oncol 2006, 28:48-49. 16394894 16394894
21. Filipovich AH Mathur A Kamat D Shapiro RS Primary immunodeficiencies: genetic risk factors for lymphoma Cancer Res 1992, (Suppl 52):5465s-5467s. 1327508
22. Sullivan KE Mullen CA Blaese RM Winkelstein JA A multiinstitutional survey of the Wiskott Aldrich syndrome J Pediatr 1994, 125:876-885. 7996359 7996359
23. Ochs HD The Wiskott-Aldrich syndrome Clin Rev Allergy Immunol 2001, 20:61-86. 11269229
24. Palenzuela G Bernard F Gardiner Q Mondain M Malignant B cell non-Hodgkin's lymphoma of the larynx in children with Wiskott Aldrich syndrome Int J Pediatr Otorhinolaryngol 2003, 67:989-993. 12907055 12907055
25. Tse W Meshinchi S Alonzo TA Stirewalt DL Gerbing RB Woods WG Appelbaum FR Radich JP Elevated expression of the AF1q gene, an MLL fusion partner, is an independent adverse prognostic factor in pediatric acute myeloid leukemia Blood 2004, 104:3058-3063. 15217837 15217837
26. Li DQ Hou YF Wu J Chen Y Lu JS Di GH Ou ZL Shen ZZ Ding J Shao ZM Gene expression profile analysis of an isogenic tumor metastasis model reveals a functional role for oncogene AF1Q in breast cancer metastasis Eur J Cancer 2006, 42:3274-3286. 16979889 16979889
27. Eswarakumar VP Lax I Schlessinger J Cellular signaling by fibroblast growth factor receptors Cytokine Growth Factor Rev 2005, 16:139-149. 15863030 15863030
28. Qian ZR Sano T Asa SL Yamada S Horiguchi H Tashiro T Li CC Hirokawa M Kovacs K Ezzat S Cytoplasmic expression of fibroblast growth factor receptor-4 in human pituitary adenomas: Relation to tumor type, size, proliferation, and invasiveness J Clin Endocrinol Metab 2004, 89:1904-1911. 15070963 15070963
29. Wang J Stockton DW Ittmann M The fibroblast growth factor receptor-4 arg388 allele is associated with prostate cancer initiation and progression Clin Cancer Res 2004, 10:6169-6178. 15448004 15448004
30. Ezzat S Huang P Dackiw A Asa SL Dual inhibition of RET and FGFR4 restrains medullary thyroid cancer cell growth Clin Cancer Res 2005, 11:1336-1341. 15709206 15709206
31. Nakamura N Iijima T Mase K Furuya S Kano J Morishita Y Noguchi M Phenotypic differences of proliferating fibroblasts in the stroma of lung adenocarcinoma and normal bronchus tissue Cancer Sci 2004, 95:226-232. 15016321 15016321
32. Rimokh R Gadoux M Bertheas MF Berger F Garoscio M Deléage G Germain D Magaud JP FVT-1, a novel human transcription unit affected by variant translocation t(2;18)(p11;q21) of follicular lymphoma Blood 1993, 81:136-142. 8417785 8417785
33. Fiucci G Ravid D Reich R Liscovitch M Caveolin-1 inhibits anchorage-independent growth, anoikis and invasiveness in MCF-7 human breast cancer cells Oncogene 2002, 21:2365-2375. 11948420 11948420
34. Engelman JA Wykoff CC Yasuhara S Song KS Okamoto T Lisanti MP Recombinant expression of caveolin-1 in oncogenically transformed cells abrogates anchorage-independent growth J Biol Chem 1997, 272:16374-16381. 9195944 9195944
35. Lee SW Reimer CL Oh P Campbell DB Schnitzer JE Tumor cell growth inhibition by caveolin re-expression in human breast cancer cells Oncogene 1998, 16:1391-1397. 9525738 9525738
36. Hurlstone AF Reid G Reeves JR Fraser J Strathdee G Rahilly M Parkinson EK Black DM Analysis of the caveolin-1 gene at human chromosome 7q31.1 in primary tumours and tumour-derived cell lines Oncogene 1999, 18:1881-1990. 10086342 10086342
37. Hayashi K Matsuda S Machida K Yamamoto T Fukuda Y Nimura Y Hayakawa T Hamaguchi M Invasion activating caveolin-1 mutation in human scirrhous breast cancers Cancer Res 2001, 61:2361-2364. 11289096 11289096
38. Wiechen K Diatchenko L Agoulnik A Scharff KM Schober H Arlt K Zhumabayeva B Siebert PD Dietel M R S et al Caveolin-1 is down-regulated in human ovarian carcinoma and acts as a candidate tumor suppressor gene Am J Pathol 2001, 159:1635-1643. 1867061 11696424
39. Bélanger MM Roussel E Couet J Caveolin-1 is down-regulated in human lung carcinoma and acts as a candidate tumor suppressor gene Chest 2004, 125-106S.
40. Han SY Druck T Huebner K Candidate tumor suppressor genes at FRA7G are coamplified with MET and do not suppress malignancy in a gastric cancer Genomics 2003, 81:105-107. 12620387
41. Nishiu M Yanagawa R Nakatsuka S Yao M Tsunoda T Nakamura Y Aozasa K Microarray analysis of gene-expression profiles in diffuse large B-cell lymphoma: Identification of genes related to disease progression Jpn J Cancer Res 2002, 93:894-901. 12716467 12716467
42. Knyazev YP Cheburkin YV Spikermann K Peter S Jenster G Bangma KH Karelin MI Shkolnik MI Urbanskii AI Evtushenko VI et al The cDNA microarray profiling of protein kinases and phosphatases: Molecular portrait of human prostate carcinomas Molecular Biology 2003, 37:89-101.
43. Dall'Era MA True LD Siegel AF Porter MP Sherertz TM Liu AY Differential expression of CD10 in prostate cancer and its clinical implication BMC Urol 2007, 7:3. 17335564 17335564 1829163
44. Dragovic T Sekosan M Becker RP Erdös EG Detection of neutral endopeptidase 24.11 (neprilysin) in human hepatocellular carcinomas by immunocytochemistry Anticancer Res 1997, 17:3233-3238. 9413153 9413153
45. Tomoda C Cushman R Takeout E Monkish K Hattori T Kitano H CD10 expression is useful in the diagnosis of follicular carcinoma and follicular variant of papillary thyroid carcinoma Thyroid 2003, 13:291-295. 12729479
46. Sato Y Itoh F Hinoda Y Ohe Y Nakagawa N Ueda R Yachi A Imai K Expression of CD10/neutral endopeptidase in normal and malignant tissues of the human stomach and colon J Gastroenterol 1996, 31:12-17. 8808423 8808423
47. Tsutsumi S Taketani T Nishimura K Ge X Taki T Sugita K Ishii E Hanada R Ohki M Aburatani H et al Two distinct gene expression signatures in pediatric acute lymphoblastic leukemia with MLL rearrangements Cancer Res 2003, 63:4882-4887. 12941810 12941810
48. Ross ME Mahfouz R Onciu M Liu HC Zhou X Song G Shurtleff SA Pounds S Cheng C Ma J et al Gene expression profiling of pediatric acute myelogenous leukemia Blood 2004, 104:3679-3687. 15226186 15226186
49. Saussez S Decaestecker C Lorfevre F Cucu DR Mortuaire G Chevalier D Wacreniez A Kaltner H André S Toubeau G et al High level of galectin-1 expression is a negative prognostic predictor of recurrence in laryngeal squamous cell carcinomas Int J Oncol 2007, 30:1109-1117. 17390012 17390012
50. Shen D Nooraie F Elshimali Y Lonsberry V He J Bose S Chia D Seligson D Chang HR Goodglick L Decreased expression of annexin A1 is correlated with breast cancer development and progression as determined by a tissue microarray analysis Hum Pathol 2006, 37:1583-1591. 16949910 16949910
51. Silistino-Souza R Rodrigues-Lisoni FC Cury PM Maniglia JV Raposo LS Tajara EH Christian HC Oliani SM Annexin 1: Differential expression in tumor and mast cells in human larynx cancer Int J Cancer 2007, 120:2582-2589. 17340616 17340616
52. Masaki T Tokuda M Ohnishi M Watanabe S Fujimura T Miyamoto K Itano T Matsui H Arima K Shirai M et al Enhanced expression of the protein kinase substrate annexin in human hepatocellular carcinoma Hepatology 1996, 24:72-81. 8707286 8707286
53. Ahn SH Sawada H Ro JY Nicolson GL Differential expression of annexin I in human mammary ductal epithelial cells in normal and benign and malignant breast tissues Clin Exp Metastasis 1997, 15:151-156. 9062391
54. Loging WT Lal A Siu IM Loney TL Wikstrand CJ Marra MA Prange C Bigner DD Strausberg RL Riggins GJ Identifying potential tumor markers and antigens by database mining and rapid expression screening Genome Res 2000, 10:1393-1402. 310902 10984457
55. Bai XF Ni XG Zhao P Liu SM Wang HX Guo B Zhou LP Liu F Zhang JS Wang K et al Overexpression of annexin 1 in pancreatic cancer and its clinical significance World J Gastroenterol 2004, 10:1466-1470. 15133855
56. Paweletz CP Ornstein DK Roth MJ Bichsel VE Gillespie JW Calvert VS Vocke CD Hewitt SM Duray PH Herring J et al Loss of annexin 1 correlates with early onset of tumorigenesis in esophageal and prostate carcinoma Cancer Res 2000, 60:6293-6297. 11103786
57. Garcia Pedrero JM Fernandez MP Morgan RO Herrero Zapatero A Gonzalez MV Suarez Nieto C Rodrigo JP Annexin A1 down-regulation in head and neck cancer is associated with epithelial differentiation status Am J Pathol 2004, 164:73-79. 1602219 14695321
58. Vishwanatha JK Salazar E Gopalakrishnan VK Absence of annexin I expression in B-cell non-Hodgkin's lymphomas and cell lines BMC Cancer 2004, 4:8. 385236 15070421
59. Lowe AW Olsen M Hao Y Lee SP Lee KT Chen X Rijn van de M Brown PO Gene expression patterns in pancreatic tumors, cells and tissues PLoS ONE 2007, 2:e323. 1824711 17389914
60. Goto Y De Silva MG Toscani A Prabhakar BS Notkins AL Lan MS A novel human insulinoma-associated cDNA, IA-1, encodes a protein with zinc-finger DNA-binding motifs J Biol Chem 1992, 267:15252-15257. 1634555
61. Pedersen N Pedersen MW Lan MS Breslin MB Poulsen HS The insulinoma-associated 1: A novel promoter for targeted cancer gene therapy for small-cell lung cancer Cancer Gene Ther 2006, 13:375-384. 16052225
62. O'Brien C Cavet G Pandita A Hu X Haydu L Mohan S Toy K Rivers CS Modrusan Z Amler LC Lackner MR Functional genomics identifies ABCC3 as a mediator of taxane resistance in HER2-amplified breast cancer Cancer Res 2008, 68:5380-5389. 18593940
63. König J Hartel M Nies AT Martignoni ME Guo J Buchler MW Friess H Keppler D Expression and localization of human multidrug resistance protein (ABCC) family members in pancreatic carcinoma Int J Cancer 2005, 115:359-367. 15688370
64. Benderra Z Faussat AM Sayada L Perrot JY Tang R Chaoui D Morjani H Marzac C Marie JP Legrand O MRP3, BCRP, and P-glycoprotein activities are prognostic factors in adult acute myeloid leukemia Clin Cancer Res 2005, 11:7764-7772. 16278398
65. Borczuk AC Gorenstein L Walter KL Assaad AA Wang L Powell CA Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways Am J Pathol 2003, 163:1949-1960. 1892411 14578194
66. Ordonez NG The diagnostic utility of immunohistochemistry in distinguishing between epithelioid mesotheliomas and squamous carcinomas of the lung: A comparative study Mod Pathol 2006, 19:417-428. 16415794
67. Sammon JW A non-linear mapping for data structure analysis IEEE Trans Comput 1969, C-18:401-409.