Identification of single- and multiple-class specific signature genes from gene expression profiles by group marker index

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Tsai, Yu Shuen ^a   Aguan, Kripamoy ^b   Pal, Nikhil R ^c   Chung, I Fang ^a  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b NORTH EASTERN HILL UNIVERSITY   (India)

^c INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROBLAST GROWTH FACTOR RECEPTOR 4; TUMOR MARKER;

ANALYTIC METHOD; ARTICLE; BURKITT LYMPHOMA; CAV1 GENE; CD99 GENE; CDK6 GENE; CENTRAL NERVOUS SYSTEM; CLINICAL EFFECTIVENESS; CODON; CONTROLLED STUDY; CSDA GENE; CTNNA1 GENE; DBNDD1 GENE; DOWN REGULATION; ELF1 GENE; EST GENE; EWING SARCOMA; FCGRT GENE; FGFR4 GENE; FVT1 GENE; GAS1 GENE; GENE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC DATABASE; GROUP MARKER INDEX; GSTA4 GENE; HLA DMA GENE; HUMAN; IL4R GENE; INTERMETHOD COMPARISON; LEUKEMIA; LUNG CANCER; MATHEMATICAL ANALYSIS; MLLT11 GENE; NEUROBLASTOMA; ONCOGENE MYC; PBX1 GENE; PCNA GENE; PLD3 GENE; PLTP GENE; PTPN12 GENE; PTPRF GENE; RHABDOMYOSARCOMA; RND3 GENE; SGCA GENE; SIGNAL TRANSDUCTION; TP5313 GENE; UPREGULATION; WAS GENE; XPO6 GENE; YAP1 GENE; GENE EXPRESSION REGULATION; GENETICS; LUNG TUMOR; SAMPLE SIZE; TUMOR GENE;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; LEUKEMIA; LUNG NEOPLASMS; SAMPLE SIZE; SIGNAL TRANSDUCTION; TUMOR MARKERS, BIOLOGICAL;

EID: 80052344469     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024259     Document Type: Article

References (87)

1. Tsai YS, Lin CT, Tseng GC, Chung IF, Pal NR, (2008) Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems. BMC Bioinformatics 9: 425 doi:10.1186/1471-2105-9-425.
2. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537 doi:10.1126/science.286.5439.531.
3. Dudoit S, Fridlyand J, Speed TP, (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 97: 77-87 doi:10.1198/016214502753479248.
4. Guyon I, Weston J, Barnhill S, Vapnik V, (2002) Gene selection for cancer classification using support vector machines. Mach Learn 46: 389-422.
5. Pal NR, Aguan K, Sharma A, Amari SI, (2007) Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering. BMC Bioinformatics 8: 5 doi:10.1186/1471-2105-8-5.
6. Saeys Y, Inza I, Larrañaga P, (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23: 2507-2517 doi:10.1093/bioinformatics/btm344.
7. Tusher VG, Tibshirani R, Chu G, (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121 doi:10.1073/pnas.091062498.
8. Opgen-Rhein R, Strimmer K, (2007) Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Stat Appl Genet Mol Biol 6: 9 doi:10.2202/1544-6115.1252.
9. Zuber V, Strimmer K, (2009) Gene ranking and biomarker discovery under correlation. Bioinformatics 25: 2700-2707 doi:10.1093/bioinformatics/btp460.
10. Liu XX, Krishnan A, Mondry A, (2005) An Entropy-based gene selection method for cancer classification using microarray data. BMC Bioinformatics 6: 76 doi:10.1186/1471-2105-6-76.
11. Huerta EB, Duval B, Hao JK, (2008) Fuzzy logic for elimination of redundant information of microarray data. Genomics Proteomics Bioinformatics 6 (2): 61-73 doi:10.1016/S1672-0229(08)60021-2.
12. Li L, Weinberg CR, Darden TA, Pedersen LG, (2001) Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 17: 1131-1142 doi:10.1093/bioinformatics/17.12.1131.
13. Ooi CH, Tan P, (2003) Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. Bioinformatics 19: 37-44 doi:10.1093/bioinformatics/19.1.37.
14. Jirapech-Umpai T, Aitken S, (2005) Feature selection and classification for microarray data analysis: evolutionary methods for identifying predictive genes. BMC Bioinformatics 6: 148 doi:10.1186/1471-2105-6-148.
15. Niijima S, Kuhara S, (2006) Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE. BMC Bioinformatics 7: 543 doi:10.1186/1471-2105-7-543.
16. Zhou X, Tuck DP, (2007) MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data. Bioinformatics 23: 1106-1114 doi:10.1093/bioinformatics/btm036.
17. Yousef M, Jung S, Showe LC, Showe MK, (2007) Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data. BMC Bioinformatics 8: 144 doi:10.1186/1471-2105-8-144.
18. Yousef M, Ketany M, Manevitz L, Showe LC, Showe MK, (2009) Classification and biomarker identification using gene network modules and support vector machines. BMC Bioinformatics 10: 337 doi:10.1186/1471-2105-10-337.
19. Pavlidis P, Noble WS, (2001) Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2: 42 doi:10.1186/gb-2001-2-10-research0042.
20. Hulshizer R, Blalock EM, (2007) Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data. BMC Bioinformatics 8: 240 doi:10.1186/1471-2105-8-240.
21. Khan J, Wei JS, Ringnér M, Saal LH, Ladanyi M, et al. (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7: 673-679 doi:10.1038/89044.
22. Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, et al. (2002) MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 30: 41-47 doi:10.1038/ng765.
23. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, et al. (2002) Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415: 436-442 doi:10.1038/415436a.
24. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 98: 13790-13795 doi:10.1073/pnas.191502998.
25. Khan J, Wei JS, Ringnér M, Saal LH, Ladanyi M, et al. (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7: 673-679 doi:10.1038/89044.
26. Baird K, Davis S, Antonescu CR, Harper UL, Walker RL, et al. (2005) Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res 65: 9226-9235 doi:10.1158/0008-5472.CAN-05-1699.
27. Yu Y, Khan J, Khanna C, Helman L, Meltzer PS, et al. (2004) Expression profiling identifies the cytoskeletal organizer ezrin and the developmental homeoprotein Six-1 as key metastatic regulators. Nat Med 10: 175-181 doi:10.1038/nm966.
28. Davicioni E, Finckenstein FG, Shahbazian V, Buckley JD, Triche TJ, et al. (2006) Identification of a PAX-FKHR gene expression signature that defines molecular classes and determines the prognosis of alveolar rhabdomyosarcomas. Cancer Res 66: 6936-6946 doi:10.1158/0008-5472.CAN-05-457.
29. Taylor JG VI, Cheuk AT, Tsang PS, Chung JY, Song YK, et al. (2009) Identification of FGFR4-activating mutations in human rhabdomyosarcomas that promote metastasis in xenotransplanted models. J Clin Invest 119: 3395-3407 doi:10.1172/JCI39703.
30. Cerisano V, Aalto Y, Perdichizzi S, Bernard G, Manara MC, et al. (2004) Molecular mechanisms of CD99-induced caspase-independent cell death and cell-cell adhesion in Ewing's sarcoma cells: actin and zyxin as key intracellular mediators. Oncogene 23: 5664-5674 doi:10.1038/sj.onc.1207741.
31. Rocchi A, Manara MC, Sciandra M, Zambelli D, Nardi F, et al. (2010) CD99 inhibits neural differentiation of human Ewing sarcoma cells and thereby contributes to oncogenesis. J Clin Invest 120: 668-680 doi:10.1172/JCI36667.
32. Scotlandi K, Baldini N, Cerisano V, Manara MC, Benini S, et al. (2000) CD99 engagement: an effective therapeutic strategy for Ewing tumors. Cancer Res 60: 5134-5142.
33. Salagierski M, Verhaegh GW, Jannink SA, Smit FP, Hessels D, et al. (2009) Differential expression of PCA3 and its overlapping PRUNE2 transcript in prostate cancer. Prostrate 70: 70-78 doi:10.1002/pros.21040.
34. Maekawa M, Ishizaki T, Boku S, Watanabe N, Fujita A, et al. (1999) Signaling from Rho to the actin cytoskeleton through protein kinases ROCK and LIM-kinase. Science 285: 895-958 doi:10.1126/science.285.5429.895.
35. Wang M, Liu YE, Greene J, Sheng S, Fuchs A, et al. (1997) Inhibition of tumor growth and metastasis of human breast cancer cells transfected with tissue inhibitor of metalloproteinase 4. Oncogene 14: 2767-2774.
36. Kostyukova AS, Rapp BA, Choy A, Greenfield NJ, Hitchcock-DeGregori SE, (2005) Structural requirements of tropomodulin for tropomyosin binding and actin filament capping. Biochemistry 44: 4905-4910 doi:10.1021/bi047468.
37. Dilley WG, Kalyanaraman S, Verma S, Cobb JP, Laramie JM, et al. (2005) Global gene expression in neuroendocrine tumors from patients with the MEN1 syndrome. Mol Cancer 4: 9 doi:10.1186/1476-4598-4-9.
38. Bishopric NH, Jayasena V, Webster KA, (1992) Positive regulation of the skeletal alpha-actin gene by Fos and Jun in cardiac myocytes. J Biol Chem 267: 25535-25540.
39. Seo S, Lim JW, Yellajoshyula D, Chang LW, Kroll KL, (2007) Neurogenin and NeuroD direct transcriptional targets and their regulatory enhancers. EMBO J 26: 5093-5108 doi:10.1038/sj.emboj.7601923.
40. Martoglio AM, Tom BD, Starkey M, Corps AN, Charnock-Jones DS, et al. (2000) Changes in tumorigenesis- and angiogenesis-related gene transcript abundance profiles in ovarian cancer detected by tailored high density cDNA arrays. Mol Med 6: 750-765.
41. Yap CT, Simpson TI, Pratt T, Price DJ, Maciver SK, (2005) The motility of glioblastoma tumour cells is modulated by intracellular cofilin expression in a concentration-dependent manner. Cell Motil Cytoskeleton 60: 153-165 doi:10.1002/cm.20053.
42. Campbell DH, deFazio A, Sutherland RL, Daly RJ, (1996) Expression and tyrosine phosphorylation of EMS1 in human breast cancer cell lines. Int J Cancer 68: 485-92.
43. Patel AM, Incognito LS, Schechter GL, Wasilenko WJ, Somers KD, (1996) Amplification and expression of EMS-1 (cortactin) in head and neck squamous cell carcinoma cell lines. Oncogene 12: 31-35.
44. Ishii H, Baffa R, Numata SI, Murakumo Y, Rattan S, et al. (1999) The FEZ1 gene at chromosome 8p22 encodes a leucine-zipper protein, and its expression is altered in multiple human tumors. Proc Natl Acad Sci USA 96: 3928-3933.
45. Liu Q, Jones TI, Tang VW, Brieher WM, Jones PL, (2010) Facioscapulohumeral muscular dystrophy region gene-1 (FRG-1) is an actin-bundling protein associated with muscle-attachment sites. J Cell Sci 123: 1116-1123 doi:10.1242/jcs.058958.
46. Gerlitz G, Bustin M, (2010) Efficient cell migration requires global chromatin condensation. J Cell Sci 123: 2207-2217 doi:10.1242/jcs.058271.
47. Bustin M, (1999) Regulation of DNA-Dependent Activities by the Functional Motifs of the High Mobility-Group Chromosomal Proteins. Mol Cell Biol 19 (8): 5237-5246.
48. Linial M, Miller K, Scheller RH, (1989) VAT-1: an abundant membrane protein from Torpedo cholinergic synaptic vesicles. Neuron 2: 1265-1273.
49. Han C, Chen T, Yang M, Li N, Liu H, et al. (2009) Human SCAMP5, a Novel Secretory Carrier Membrane Protein, Facilitates Calcium-Triggered Cytokine Secretion by Interaction with SNARE Machinery. J Immunol 182: 2986-2996 doi:10.4049/jimmunol.0802002.
50. Depaz IM, de Las Heras R, Kroon PA, Wilce PA, (2005) Changes in neuronal protein 22 expression and cytoskeletal association in the alcohol-dependent and withdrawn rat brain. J Neurosci Res 81: 253-60 doi:10.1002/jnr.20563.
51. Gu Y, Ihara Y, (2000) Evidence that collapsin response mediator protein-2 is involved in the dynamics of microtubules. J Biol Chem 275: 17917-20 doi:10.1074/jbc.C000179200.
52. Lan MS, Breslin MB, (2009) Structure, expression, and biological function of INSM1 transcription factor in neuroendocrine differentiation. FASEB J 23 (7): 2024-2033 doi:10.1096/fj.08-125971.
53. Liu WD, Wang HW, Muguira M, Breslin MB, Lan MS, (2006) INSM1 functions as a transcriptional repressor of the neuroD/β2 gene through the recruitment of cyclin D1 and histone deacetylases. Biochem J. 397 (Pt 1): 169-177 doi:10.1042/BJ20051669.
54. Ren WZ, Ng GY, Wang RX, Wu PH, O'Dowd BF, et al. (1994) The identification of NP25: a novel protein that is differentially expressed by neuronal subpopulations. Brain Res Mol Brain Res 22: 173-185.
55. Yamashita N, Uchida Y, Ohshima T, Hirai S, Nakamura F, et al. (2006) Collapsin response mediator protein 1 mediates reelin signaling in cortical neuronal migration. J Neuroscience 26 (51): 13357-13362 doi:10.1523/JNEUROSCI.4276-06.2006.
56. Atz ME, Rollins B, Vawter MP, (2007) NCAM1 association study of bipolar disorder and schizophrenia: polymorphisms and alternatively spliced isoforms lead to similarities and differences. Psychiatr Genet 17 (2): 55-67 doi:10.1097/YPG.0b013e328012d850.
57. Fernández-Chacón R, Südhof TC, (2000) Novel SCAMPs Lacking NPF Repeats: Ubiquitous and Synaptic Vesicle-Specific Forms Implicate SCAMPs in Multiple Membrane-Trafficking Functions. J Neurosci 20 (21): 7941-7950.
58. Watanabe H, Mizutani T, Haraguch T, Yamamichi N, Minoguchi S, et al. (2006) SWI/SNF complex is essential for NRSF-mediated suppression of neuronal genes in human nonsmall cell lung carcinoma cell lines. Oncogene 25: 470-479 doi:10.1038/sj.onc.1209068.
59. Tian T, Hao J, Xu A, Hao J, Luo C, et al. (2007) Determination of metastasis-associated proteins in non-small-cell lung cancer by comparative proteomic analysis. Cancer Sci 98: 1265-74 doi:10.1111/j.1349-7006.2007.00514.x.
60. Zhang L, Fogg DK, Waisman DM, (2004) RNA interference-mediated silencing of the S100A10 gene attenuates plasmin generation and invasiveness of Colo 222 colorectal cancer cells. J Biol Chem 279: 2053-2062 doi:10.1074/jbc.M310357200.
61. Martins L, Matsuo SE, Ebina KN, Kulcsar MA, Friguglietti CU, et al. (2002) Galectin-3 messenger ribonucleic acid and protein are expressed in benign thyroid tumors. J Clin Endocrinol Metab 87: 4806-10 doi:10.1210/jc.2002-020094.
62. Yoshimura A, Gemma A, Hosoya Y, Komaki E, Hosomi Y, et al. (2003) Increased expression of the LGALS3 (galactin 3) gene is human non-small cell lung cancer. Genes Chromosomes Cancer 37: 159-64 doi:10.1002/gcc.10205.
63. McHugh BJ, Buttery R, Lad Y, Banks S, Haslett C, et al. (2010) Integrin activation by Fam38A uses a novel mechanism of R-Ras targeting to the endoplasmic reticulum. J Cell Sci 123: 51-61 doi:10.1242/jcs.056424.
64. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-D360 doi:10.1093/nar/gkp896.
65. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354-357 doi:10.1093/nar/gkj102.
66. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30 doi:10.1093/nar/28.1.27.
67. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 4 (1): 44-57 doi:10.1038/nprot.2008.211.
68. Huang DW, Sherman BT, Lempicki RA, (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37 (1): 1-13 doi:10.1093/nar/gkn923.
69. van Alphen RJ, Wiemer EAC, Burger H, Eskens ALM, (2009) The spliceosome as target for anticancer treatment. Br J Cancer 100 (2): 228-232 doi:10.1038/sj.bjc.6604801.
70. Nahar R, Müschen M, (2009) Pre-B cell receptor signaling in acute lymphoblastic leukemia. Cell Cycle 8 (23): 3874-3877 doi:10.4161/cc.8.23.10035.
71. Downing JR, (1999) The AML1-ETO chimaeric transcription factor in acute myeloid leukaemia: biology and clinical significance. Br J Haematol 106 (2): 296-308 doi:10.1046/j.1365-2141.1999.01377.x.
72. Sun L, Heerema N, Crotty L, Wu X, Navara C et al, (1999) Expression of dominant-negative and mutant isoforms of the antileukemic transcription factor Ikaros in infant acute lymphoblastic leukemia. Proc Natl Acad Sci USA 96 (2): 680-685.
73. Mengubas K, Jabbar S, Nye K, Wilkes S, Hoffbrand AV, et al. (1994) Inactivation of calcium ion-regulating inositol polyphosphate 2nd-messengers is impaired in subpopulations of human leukemia-cells. Leukemia 8 (10): 1718-1725.
74. Fiancette R, Vincent c, Donnard M, Bordessoule d, Turlure P, et al. (2009) Genes encoding multiple forms of phospholipase A2 are expressed in immature forms of human leukemic blasts. Leukemia 23: 1196-1199 doi:10.1038/leu.2009.36.
75. Agatha G, Häfer R, Zintl F, (2001) Fatty acid composition of lymphocyte membrane phospholipids in children with acute leukemia. Cancer Lett 173 (2): 139-144.
76. Chiarini F, Falà F, Tazzari PL, Ricci F, Astolfi A, et al. (2009) Dual inhibition of class IA phosphatidylinositol 3-kinase and mammalian target of Rapamycin as a new therapeutic option for T-cell acute lymphoblastic leukemia. Cancer Res 69: 3520-3528 doi:10.1158/0008-5472.CAN-08-4884.
77. Aifantis I, Raetz E, Buonamici S, (2008) Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol 8: 380-390 doi:10.1038/nri2304.
78. Zweidler-McKay PA, He Y, Xu L, Rodriguez CG, Karnell FG, et al. (2005) Notch signaling is a potent inducer of growth arrest and apoptosis in a wide range of B-cell malignancies. Blood 106 (12): 3898-3906 doi:10.1182/blood-2005-01-0355.
79. Tavor S, Eisenbach M, Jacob-Hirsch J, Golan T, Petit I, et al. (2008) The CXCR4 antagonist AMD3100 impairs survival of human AML cells and induces their differentiation. Leukemia 22: 2151-2158 doi:10.1038/leu.2008.238.
80. Bruserud Ø, Gjertsen BT, Ulvestad E, (2002) Expression of Fcε-receptors by human acute myelogenous leukemia (AML) blasts: studies of high- and low- (CD23) affinity receptor expression and the effects of IgE-mediated receptor ligation on functional AML blast characteristics. Leuk Res 26 (5): 515-521 doi:10.1016/S0145-2126(01)00165-5.
81. Cancelas JA, Lee AW, Prabhakar R, Stringer KF, Zheng Y, et al. (2005) Rac GTPases differentially integrate signals regulating hematopoietic stem cell localization. Nat Med 11: 886-891 doi:10.1038/nm1274.
82. Gu Y, Filippi MD, Cancelas JA, Siefring JE, Williams EP, et al. (2003) Hematopoietic cell regulation by Rac1 and Rac2 guanosine triphosphatases. Science 302: 445-449 doi:10.1126/science.1088485.
83. Kuroda K, Takenoyama M, Baba T, Shigematsu Y, Shiota H, et al. (2009) Identification of ribosomal protein L19 as a novel tumor antigen recognized by autologous cytotoxic T lymphocytes in lung adenocarcinoma. Cancer Sci 101 (1): 46-55 doi:10.1111/j.1349-7006.2009.01351.x.
84. Nadano D, Notsu T, Matsuda T, Sato TA, (2002) A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells. Biochim Biophys Acta 1577 (3): 430-436 doi:10.1016/S0167-4781(02)00445-1.
85. Ocak S, Yamashita H, Udyavar AR, Miller AN, Gonzalez AL, et al. (2010) DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway. Oncogene 29: 6331-6342 doi:10.1038/onc.2010.362.
86. Mukhopadhyay NK, Gordon GJ, Chen CJ, Bueno R, David J, Sugarbaker DJ, et al. (2007) Activation of focal adhesion kinase in human lung cancer cells involves multiple and potentially parallel signaling events. J Cell Mol Med 9 (2): 387-397 doi:10.1111/j.1582-4934.2005.tb00364.x.
87. R Development Core Team (2010) R: A language and environment for statistical computing. Vienna, Austria R Foundation for Statistical Computing ISBN 3-900051-07-0, URL http://www.R-project.org/.