Classification between normal and tumor tissues based on the pair-wise gene expression ratio

BMC Cancer

Volumn 4, Issue , 2004, Pages

  Yap, Yee Leng ^a   Zhang, Xue Wu ^a   Ling, M T ^b   Wang, Xiang Hong ^b   Wong, Y C ^b,c   Danchin, Antoine ^d  

^a HKU PASTEUR RESEARCH CENTRE   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

^d INSTITUT PASTEUR   (France)

Author keywords

Adipsin; Colon cancer; Hepsin; Monocyte derived neutrophil activating protein; Prostate cancer

Indexed keywords

ADENINE NUCLEOTIDE TRANSLOCASE; ADIPSIN; ALDEHYDE REDUCTASE; AMINO ACID TRANSFER RNA LIGASE; BINDING PROTEIN; CARRIER PROTEIN; COLLAGEN; COMPLEMENT FACTOR D; COMPLEMENTARY DNA; CORE PROTEIN; DESMIN; EPITHELIAL CELL ADHESION MOLECULE; FIBRILLARIN; GLUTATHIONE TRANSFERASE; GROWTH FACTOR; GUANINE NUCLEOTIDE BINDING PROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; INTERLEUKIN 8; MATRIX PROTEIN; MESSENGER RNA; MYOSIN HEAVY CHAIN; MYOSIN LIGHT CHAIN; PHOSPHOTRANSFERASE; PROTEIN PRECURSOR; REGULATOR PROTEIN; RETINOL BINDING PROTEIN; SERINE PROTEINASE; TRANSCRIPTION FACTOR IIIA; TUMOR MARKER; UROGUANYLIN; DIAGNOSTIC AGENT;

ARTICLE; CANCER CLASSIFICATION; CLINICAL FEATURE; COLON CANCER; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DIAGNOSTIC ACCURACY; DIAGNOSTIC PROCEDURE; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MODEL; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROSTATE CANCER; RELIABILITY; SIGNAL NOISE RATIO; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STATISTICAL PARAMETERS; TISSUE TYPES; VARIANCE; COLON; COLON TUMOR; CYTOLOGY; DNA MICROARRAY; DNA PROBE; FEMALE; GENE EXPRESSION; GENETICS; MALE; METHODOLOGY; PATHOLOGY; PROSTATE; PROSTATE TUMOR;

COLON; COLONIC NEOPLASMS; DNA PROBES; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PROSTATE; PROSTATIC NEOPLASMS;

EID: 13144300125     PISSN: 14712407     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2407-4-72     Document Type: Article

References (54)

1. Hanahan D, Weinberg RA: The hallmarks of cancer. Cell 2000, 100:57-70.
2. Simon R, Radmacher MD, Dobbin K, McShane LM: Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003, 95:14-18.
3. Krajewski P, Bocianowski J: Statistical methods for microarray assays. J Appl Genet 2002, 43:269-278.
4. Zhang H, Yu CY, Singer B, Xiong M: Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci U S A 2001, 98:6730-6735.
5. Ambroise C, McLachlan GJ: Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci U S A 2002, 99:6562-6566.
6. Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301:102-105.
7. Bo T, Jonassen I: New feature subset selection procedures for classification of expression profiles. Genome Biol 2002, 3:RESEARCH0017.
8. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A 1999, 96:6745-6750.
9. Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR: Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002, 1:203-209.
10. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4: 06-425.
11. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM: Delineation of prognostic biomarkers in prostate cancer. Nature 2001, 412: 22-826.
12. Li L, Darden TA, Weinberg CR, Levine AJ, Pedersen LG: Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Comb Chem High Throughput Screen 2001, 4:727-739.
13. Kishino H, Waddell PJ: Correspondence analysis of genes and tissue types and finding genetic links from microarray data. Genome Inform Ser Workshop Genome Inform 2000, 11:83-95.
14. Kriajevska MV, Cardenas MN, Grigorian MS, Ambartsumian NS, Georgiev GP, Lukanidin EM: Non-muscle myosin heavy chain as a possible target for protein encoded by metastasis-related mts-1 gene. J Biol Chem 1994, 269:19679-19682.
15. Lamant L, Gascoyne RD, Duplantier MM, Armstrong F, Raghab A, Chhanabhai M, Rajcan-Separovic E, Raghab J, Delsol G, Espinos E: Non-muscle myosin heavy chain (MYH9): a new partner fused to ALK in anaplastic large cell lymphoma. Genes Chromosomes Cancer 2003, 37:427-432.
16. Xu L, Xie K, Mukaida N, Matsushima K, Fidler IJ: Hypoxia-induced elevation in interleukin-8 expression by human ovarian carcinoma cells. Cancer Res 1999, 59:5822-5829.
17. Gutgemann A, Golob M, Muller S, Buettner R, Bosserhoff AK: Isolation of invasion-associated cDNAs in melanoma. Arch Dermatol Res 2001, 293:283-290.
18. Stephan C, Yousef GM, Scorilas A, Jung K, Jung M, Kristiansen G, Hauptmann S, Kishi T, Nakamura T, Loening SA, Diamandis EP: Hepsin is highly over expressed in and a new candidate for a prognostic indicator in prostate cancer. J Urol 2004, 171:187-191.
19. Ernst T, Hergenhahn M, Kenzelmann M, Cohen CD, Ikinger U, Kretzler M, Hollstein M, Grone HJ: [Gene expression profiling in prostatic cancer]. Verh Dtsch Ges Pathol 2002, 86:165-175.
20. Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Harvey SC, Ehrenberg M, Frank J: Corrigendum: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy Nat Struct Biol 2003, 10:1074.
21. Kikuno R, Nagase T, Waki M, Ohara O: HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. Nucleic Acids Res 2002, 30:166-168.
22. Nakayama M, Kikuno R, Ohara O: Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs. Genome Res 2002, 12:1773-1784.
23. Bektic J, Wrulich OA, Dobler G, Kofler K, Ueberall F, Culig Z, Bartsch G, Klocker H: Identification of genes involved in estrogenic action in the human prostate using microarray analysis. Genomics 2004, 83:34-44.
24. Quackenbush J: Microarray data normalization and transformation. Nat Genet 2002, 32 Suppl:496-501.
25. Hoffmann R, Seidl T, Dugas M: Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol 2002, 3:RESEARCH0033.
26. Cherian MG, Jayasurya A, Bay BH: Metallothioneins in human tumors and potential roles in carcinogenesis. Mutat Res 2003, 533:201-209.
27. Saad RS, Liu YL, Nathan G, Celebrezze J, Medich D, Silverman JF: Endoglin (CD105) and vascular endothelial growth factor as prognostic markers in colorectal cancer. Mod Pathol 2004, 17: 97-203.
28. Haga K: [The mechanism for reduced expression of gelsolin, tumor suppressor protein, in bladder cancer]. Hokkaido Igaku Zasshi 2003, 78:29-37.
29. Campa MJ, Wang MZ, Howard B, Fitzgerald MC, Patz E. F., Jr.: Protein expression profiling identifies macrophage migration inhibitory factor and cyclophilin a as potential molecular targets in non-small cell lung cancer. Cancer Res 2003, 63:1652-1656.
30. Chow ML, Moler EJ, Mian IS: Identifying marker genes in transcription profiling data using a mixture of feature relevance experts Physiol Genomics 2001, 5:99-111.
31. Nagase T, Ishikawa K, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O: Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res 1998, 5: 1-39.
32. Ghigna C, Moroni M, Porta C, Riva S, Biamonti G: Altered expression of heterogenous nuclear ribonucleoproteins and SR factors in human colon adenocarcinomas. Cancer Res 1998, 58: 818-5824.
33. Chaurand P, DaGue BB, Pearsall RS, Threadgill DW, Caprioli RM: Profiling proteins from azoxymethane-induced colon tumors at the molecular level by matrix-assisted laser desorption/ionization mass spectrometry. Proteomics 2001, 1:1320-1326.
34. Nicholson KM, Anderson NG: The protein kinase B/Akt signalling pathway in human malignancy. Cell Signal 2002, 14: 81-395.
35. Cheong HK, Park JY, Kim EH, Lee C, Kim S, Kim Y, Choi BS, Cheong C: Structure of the N-terminal extension of human aspartyl-tRNA synthetase: implications for its biological function. Int J Biochem Cell Biol 2003, 35:1548-1557.
36. DeFatta RJ, Chervenak RP, De Benedetti A: A cancer gene therapy approach through translational control of a suicide gene. Cancer Gene Ther 2002, 9:505-512.
37. Derenzini M, Trere D, Pession A, Montanaro L, Sirri V, Ochs RL: Nucleolar function and size in cancer cells. Am J Pathol 1998, 152:1291-1297.
38. Eray M, Tuomikoski T, Wu H, Nordstrom T, Andersson LC, Knuutila S, Kaartinen M: Cross-linking of surface IgG induces apoptosis in a bcl-2 expressing human follicular lymphoma line of mature B cell phenotype. Int Immunol 1994, 6:1817-1827.
39. Sreedharan SP, Huang JX, Cheung MC, Goetzl EJ: Structure, expression, and chromosomal localization of the type I human vasoactive intestinal peptide receptor gene. Proc Natl Acad Sci U S A 1995, 92:2939-2943.
40. Currie, Shailubhai K, Yu HH, Karunanandaa K, Wang JY, Eber S. L, Wang Y, Joo NS, Kim HD, Miedema BW, Abbas SZ, Boddupalli SS, Currie MG, Forte LR: Uroguanylin treatment suppresses polyp formation in the Apc(Min/+) mouse and induces apoptosis in human colon adenocarcinoma cells via cyclic GMP. Cancer Res 2000, 60:5151-5157.
41. Gali H, Sieckman GL, Hoffman TJ, Kiefer GE, Chin DT, Forte LR, Volkert WA: Synthesis and in vitro evaluation of an 111Inlabeled ST-peptide enterotoxin (ST) analogue for specific targeting of guanylin receptors on human colonic cancers. Anticancer Res 2001, 21: 785-2792.
42. Adhami VM, Ahmad N, Mukhtar H: Molecular targets for green tea in prostate cancer prevention. J Nutr 2003, 133: 417S-2424S.
43. Melendez JA, Davies KJ: Manganese superoxide dismutase modulates interleukin-1alpha levels in HT-1080 fibrosarcoma cells. J Biol Chem 1996, 271:18898-18903.
44. Costantino L, Ferrari AM, Gamberini MC, Rastelli G: Nitrophenyl derivatives as aldose reductase inhibitors. Bioorg Med Chem 2002, 10:3923-3931.
45. Nithipatikom K, Isbell MA, Lindholm PF, Kajdacsy-Balla A, Kaul S, Campell WB: Requirement of cyclooxygenase-2 expression and prostaglandins for human prostate cancer cell invasion. Clin Exp Metastasis 2002, 19:593-601.
46. Zhang JP, Ying K, Xiao ZY, Zhou B, Huang QS, Wu HM, Yin M, Xie Y, Mao YM, Rui YC: Analysis of gene expression profiles in human HL-60 cell exposed to cantharidin using cDNA microarray. Int J Cancer 2004, 108:212-218.
47. Ricci G, Caccuri AM, Lo Bello M, Parker MW, Nuccetelli M, Turella P, Stella L, Di Iorio EE, Federici G: Glutathione transferase P1-1: self-preservation of an anti-cancer enzyme. Biochem J 2003, 376:71-76.
48. Eder IE, Haag P, Basik M, Mousses S, Bektic J, Bartsch G, Klocker H: Gene expression changes following androgen receptor elimination in LNCaP prostate cancer cells. Mol Carcinog 2003, 37:181-191.
49. Stahl JA, Leone A, Rosengard AM, Porter L, King CR, Steeg PS: Identification of a second human nm23 gene, nm23-H2. Cancer Res 1991, 51:445-449.
50. Carollo M, Parente L, D'Alessandro N: Dexamethasone-induced cytotoxic activity and drug resistance effects in androgenindependent prostate tumor PC-3 cells are mediated by lipocortin 1. Oncol Res 1998, 10:245-254.
51. Matsui H, Kubochi K, Okazaki I, Yoshino K, Ishibiki K, Kitajima M: Collagen biosynthesis in gastric cancer: immunohistochemical analysis of prolyl 4-hydroxylase. J Surg Oncol 1999, 70:239-246.
52. Chesi M, Bergsagel PL, Shonukan OO, Martelli ML, Brents LA, Chen T, Schrock E, Ried T, Kuehl WM: Frequent dysregulation of the c-maf proto-oncogene at 16q23 by translocation to an Ig locus in multiple myeloma. Blood 1998, 91:4457-4463.
53. Postel EH, Berberich SJ, Flint SJ, Ferrone CA: Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis. Science 1993, 261:478-480.
54. Huang KS, Wallner BP, Mattaliano RJ, Tizard R, Burne C, Frey A, Hession C, McGray P, Sinclair LK, Chow EP: Two human 35 kd inhibitors of phospholipase A2 are related to substrates of pp60vsrc and of the epidermal growth factor receptor/kinase. Cell 1986, 46:191-199.