A comparative analysis of gene-expression data of multiple cancer types

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Xu, Kun ^a,b   Cui, Juan ^a   Olman, Victor ^a   Yang, Qing ^c   Puett, David ^a   Xu, Ying ^a,c  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ACCURACY; ARTICLE; BREAST CANCER; CANCER DIAGNOSIS; CANCER THERAPY; CANCER TISSUE; COLON CANCER; COMPARATIVE STUDY; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION; KIDNEY CANCER; LUNG CANCER; MALIGNANT NEOPLASTIC DISEASE; MARKER GENE; MICROARRAY ANALYSIS; PANCREAS CANCER; PREDICTION; PROSTATE CANCER; PROTEIN BLOOD LEVEL; PROTEIN EXPRESSION; PROTEIN SECRETION; SIGNAL TRANSDUCTION; STOMACH CANCER; SURVIVAL RATE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; NEOPLASM;

GENE EXPRESSION PROFILING; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SURVIVAL RATE;

EID: 78149447865     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013696     Document Type: Article

References (63)

1. WHO (2006) Data and statistics. World Health Organization.
2. Ries LAG MD, Krapcho M (2008) SEER Cancer Statistics Review, 1975-2005 National Cancer Institute.
3. Catalona WJ, Smith DS, Wolfert RL, Wang TJ, Rittenhouse HG, et al. (1995) Evaluation of percentage of free serum prostate-specific antigen to improve specificity of prostate cancer screening. JAMA 274: 1214-1220.
4. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, et al. (2001) Delineation of prognostic biomarkers in prostate cancer. Nature 412: 822-826.
5. Matei D, Graeber TG, Baldwin RL, Karlan BY, Rao J, et al. (2002) Gene expression in epithelial ovarian carcinoma. Oncogene 21: 6289-6298.
6. Cui J, Liu Q, Puett D, Xu Y (2008) Computational prediction of human proteins that can be secreted into the bloodstream. Bioinformatics 24: 2370-2375.
7. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, et al. (2004) Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 101: 9309-9314.
8. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
9. Lin C-CCaC-J (2001) LIBSVM: a library for support vector machines.Software
10. available at http://www.csie.ntu.edu.tw/,cjlin/libsvm.
11. Dennis G, Jr., Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
12. Pau Ni IB, Zakaria Z, Muhammad R, Abdullah N, Ibrahim N, et al. (2010) Gene expression patterns distinguish breast carcinomas from normal breast tissues: The Malaysian context. Pathol Res Pract.
13. Pedraza V, Gomez-Capilla JA, Escaramis G, Gomez C, Torne P, et al. (2010) Gene expression signatures in breast cancer distinguish phenotype characteristics, histologic subtypes, and tumor invasiveness. Cancer 116: 486-496.
14. Miyoshi Y, Funahashi T, Kihara S, Taguchi T, Tamaki Y, et al. (2003) Association of serum adiponectin levels with breast cancer risk. Clin Cancer Res 9: 5699-5704.
15. Parr C, Watkins G, Mansel RE, Jiang WG (2004) The hepatocyte growth factor regulatory factors in human breast cancer. Clin Cancer Res 10: 202-211.
16. Sloan EK, Stanley KL, Anderson RL (2004) Caveolin-1 inhibits breast cancer growth and metastasis. Oncogene 23: 7893-7897.
17. Jiang WG, Douglas-Jones A, Mansel RE (2003) Expression of peroxisome-proliferator activated receptor-gamma (PPARgamma) and the PPARgamma co-activator, PGC-1, in human breast cancer correlates with clinical outcomes. Int J Cancer 106: 752-757.
18. Le Jan S, Amy C, Cazes A, Monnot C, Lamande N, et al. (2003) Angiopoietin-like 4 is a proangiogenic factor produced during ischemia and in conventional renal cell carcinoma. Am J Pathol 162: 1521-1528.
19. Ki DH, Jeung HC, Park CH, Kang SH, Lee GY, et al. (2007) Whole genome analysis for liver metastasis gene signatures in colorectal cancer. Int J Cancer 121: 2005-2012.
20. Jiang X, Tan J, Li J, Kivimae S, Yang X, et al. (2008) DACT3 is an epigenetic regulator of Wnt/beta-catenin signaling in colorectal cancer and is a therapeutic target of histone modifications. Cancer Cell 13: 529-541.
21. Behrens P, Mathiak M, Mangold E, Kirdorf S, Wellmann A, et al. (2003) Stromal expression of invasion-promoting, matrix-degrading proteases MMP-1 and -9 and the Ets 1 transcription factor in HNPCC carcinomas and sporadic colorectal cancers. Int J Cancer 107: 183-188.
22. Wang WS, Chen PM, Wang HS, Liang WY, Su Y (2006) Matrix metalloproteinase-7 increases resistance to Fas-mediated apoptosis and is a poor prognostic factor of patients with colorectal carcinoma. Carcinogenesis 27: 1113-1120.
23. Jones J, Otu H, Spentzos D, Kolia S, Inan M, et al. (2005) Gene signatures of progression and metastasis in renal cell cancer. Clin Cancer Res 11: 5730-5739.
24. Someya S, Yamasoba T, Kujoth GC, Pugh TD, Weindruch R, et al. (2008) The role of mtDNA mutations in the pathogenesis of age-related hearing loss in mice carrying a mutator DNA polymerase gamma. Neurobiol Aging 29: 1080-1092.
25. Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, et al. (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 463: 360-363.
26. Hart TC, Gorry MC, Hart PS, Woodard AS, Shihabi Z, et al. (2002) Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy. J Med Genet 39: 882-892.
27. Landi MT, Dracheva T, Rotunno M, Figueroa JD, Liu H, et al. (2008) Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS One 3: e1651.
28. Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, et al. (2007) Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics 8: 140.
29. Park SS, Kim JE, Kim YA, Kim YC, Kim SW (2005) Caveolin-1 is down-regulated and inversely correlated with HER2 and EGFR expression status in invasive ductal carcinoma of the breast. Histopathology 47: 625-630.
30. Ho CC, Huang PH, Huang HY, Chen YH, Yang PC, et al. (2002) Up-regulated caveolin-1 accentuates the metastasis capability of lung adenocarcinoma by inducing filopodia formation. Am J Pathol 161: 1647-1656.
31. Bridges JP, Wert SE, Nogee LM, Weaver TE (2003) Expression of a human surfactant protein C mutation associated with interstitial lung disease disrupts lung development in transgenic mice. J Biol Chem 278: 52739-52746.
32. Kholodnyuk ID, Kozireva S, Kost-Alimova M, Kashuba V, Klein G, et al. (2006) Down regulation of 3p genes, LTF, SLC38A3 and DRR1, upon growth of human chromosome 3-mouse fibrosarcoma hybrids in severe combined immunodeficiency mice. Int J Cancer 119: 99-107.
33. Badea L, Herlea V, Dima SO, Dumitrascu T, Popescu I (2008) Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia. Hepatogastroenterology 55: 2016-2027.
34. Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, et al. (2009) FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer Cell 16: 259-266.
35. Tang L, Dai DL, Su M, Martinka M, Li G, et al. (2006) Aberrant expression of collagen triple helix repeat containing 1 in human solid cancers. Clin Cancer Res 12: 3716-3722.
36. Groundwater P, Beck SA, Barton C, Adamson C, Ferrier IN, et al. (1990) Alteration of serum and urinary lipolytic activity with weight loss in cachectic cancer patients. Br J Cancer 62: 816-821.
37. Mechtcheriakova D, Wlachos A, Sobanov J, Kopp T, Reuschel R, et al. (2007) Sphingosine 1-phosphate phosphatase 2 is induced during inflammatory responses. Cell Signal 19: 748-760.
38. Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, et al. (2005) Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer 5: 45.
39. Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, et al. (2004) Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 101: 811-816.
40. Varadhachary A, Wolf JS, Petrak K, O'Malley BW, Jr., Spadaro M, et al. (2004) Oral lactoferrin inhibits growth of established tumors and potentiates conventional chemotherapy. Int J Cancer 111: 398-403.
41. Soulitzis N, Karyotis I, Delakas D, Spandidos DA (2006) Expression analysis of peptide growth factors VEGF, FGF2, TGFB1, EGF and IGF1 in prostate cancer and benign prostatic hyperplasia. Int J Oncol 29: 305-314.
42. Chan JM, Stampfer MJ, Ma J, Gann P, Gaziano JM, et al. (2002) Insulin-like growth factor-I (IGF-I) and IGF binding protein-3 as predictors of advanced-stage prostate cancer. J Natl Cancer Inst 94: 1099-1106.
43. Kane R, Godson C, O'Brien C (2008) Chordin-like 1, a bone morphogenetic protein-4 antagonist, is upregulated by hypoxia in human retinal pericytes and plays a role in regulating angiogenesis. Mol Vis 14: 1138-1148.
44. Chen X, Leung SY, Yuen ST, Chu KM, Ji J, et al. (2003) Variation in gene expression patterns in human gastric cancers. Mol Biol Cell 14: 3208-3215.
45. D'Errico M, de Rinaldis E, Blasi MF, Viti V, Falchetti M, et al. (2009) Genome-wide expression profile of sporadic gastric cancers with microsatellite instability. Eur J Cancer 45: 461-469.
46. Peng Z (2010) Expression data from gastric cancer (GSE19826). In: Hospital SJTUAFPs, editor. Shanghai.
47. Chen WB, Lenschow W, Tiede K, Fischer JW, Kalthoff H, et al. (2002) Smad4/ DPC4-dependent regulation of biglycan gene expression by transforming growth factor-beta in pancreatic tumor cells. J Biol Chem 277: 36118-36128.
48. Ning PF, Sun LP, Liu HJ, Yuan Y (2004) Expression of pepsinogen C in gastric cancer and its precursor. Zhonghua Yi Xue Za Zhi 84: 818-821.
49. Broutet N, Plebani M, Sakarovitch C, Sipponen P, Megraud F (2003) Pepsinogen A, pepsinogen C, and gastrin as markers of atrophic chronic gastritis in European dyspeptics. Br J Cancer 88: 1239-1247.www.cancer.org (2006) Cancer Facts & Figures. In: Society AC, ed.
50. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70.
51. Varis A, Zaika A, Puolakkainen P, Nagy B, Madrigal I, et al. (2004) Coamplified and overexpressed genes at ERBB2 locus in gastric cancer. Int J Cancer 109: 548-553.
52. Koren R, Rath-Wolfson L, Ram E, Itzhac OB, Schachter B, et al. (2004) Prognostic value of Topoisomerase II in female breast cancer. Oncol Rep 12: 915-919.
53. Chekerov R, Klaman I, Zafrakas M, Konsgen D, Mustea A, et al. (2006) Altered expression pattern of topoisomerase IIalpha in ovarian tumor epithelial and stromal cells after platinum-based chemotherapy. Neoplasia 8: 38-45.
54. Aota Y, Sumi M, Iguchi T, Okabe S, Gotoh A, et al. (2004) Type I CD36 deficiency in hematologic disorder. Haematologica 89: EIM17.
55. Herb F, Thye T, Niemann S, Browne EN, Chinbuah MA, et al. (2008) ALOX5 variants associated with susceptibility to human pulmonary tuberculosis. Hum Mol Genet 17: 1052-1060.
56. Piovan E, Tosello V, Indraccolo S, Cabrelle A, Baesso I, et al. (2005) Chemokine receptor expression in EBV-associated lymphoproliferation in hu/SCID mice: implications for CXCL12/CXCR4 axis in lymphoma generation. Blood 105: 931-939.
57. Lee HY, Kim MK, Park KS, Bae YH, Yun J, et al. (2005) Serum amyloid A stimulates matrix-metalloproteinase-9 upregulation via formyl peptide receptor like-1-mediated signaling in human monocytic cells. Biochem Biophys Res Commun 330: 989-998.
58. Mulla CM, Geras-Raaka E, Raaka BM, Gershengorn MC (2009) High levels of thyrotropin-releasing hormone receptors activate programmed cell death in human pancreatic precursors. Pancreas 38: 197-202.
59. Ababneh M, Gotz C, Montenarh M (2001) Downregulation of the cdc2/cyclin B protein kinase activity by binding of p53 to p34(cdc2). Biochem Biophys Res Commun 283: 507-512.
60. Eguchi T, Takaki T, Itadani H, Kotani H (2007) RB silencing compromises the DNA damage-induced G2/M checkpoint and causes deregulated expression of the ECT2 oncogene. Oncogene 26: 509-520.
61. Li H, Lu Q, Dong LH, Xue H, Zhou HY, et al. (2007) [Expression of fatty acid binding protein in human breast cancer tissues]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 23: 312-316.
62. Ohlsson G, Moreira JM, Gromov P, Sauter G, Celis JE (2005) Loss of expression of the adipocyte-type fatty acid-binding protein (A-FABP) is associated with progression of human urothelial carcinomas. Mol Cell Proteomics 4: 570-581.
63. Zhang J, Jin X, Fang S, Wang R, Li Y, et al. (2005) The functional polymorphism in the matrix metalloproteinase-7 promoter increases susceptibility to esophageal squamous cell carcinoma, gastric cardiac adenocarcinoma and non-small cell lung carcinoma. Carcinogenesis 26: 1748-1753.