Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

Molecular Cancer

Volumn 9, Issue , 2010, Pages

  Colak, Dilek ^a   Chishti, Muhammad A ^b   Al Bakheet, Al Bandary ^a   Al Qahtani, Ahmed ^a,c   Shoukri, Mohamed M ^a   Goyns, Malcolm H ^d   Ozand, Pinar T ^e   Quackenbush, John ^f   Park, Ben H ^g   Kaya, Namik ^a  

^a KING FAISAL SPECIALIST HOSPITAL AND RESEARCH CENTER   (Saudi Arabia)

^b KING SAUD UNIVERSITY   (Saudi Arabia)

^c KING SAUD UNIVERSITY   (Saudi Arabia)

^d Immorgene Concepts Ltd   (United Kingdom)

^e Duzen Laboratories   (Turkey)

^f DANA FARBER CANCER INSTITUTE   (United States)

^g JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE P38; MYC PROTEIN; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN KINASE B; PROTEIN P53; SMAD3 PROTEIN; TRANSFORMING GROWTH FACTOR BETA; TUMOR MARKER;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CLINICAL ARTICLE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; EARLY CANCER; EARLY DIAGNOSIS; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; LIVER CELL CARCINOMA; LIVER REGENERATION; LIVER RESECTION; MALE; MALIGNANT TRANSFORMATION; MICROARRAY ANALYSIS; MOLECULAR MECHANICS; NONHUMAN; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; SPECIES CONSERVATION; TRANSCRIPTION REGULATION; TUMOR DIFFERENTIATION; AGING; ANIMAL; CELL DIFFERENTIATION; COMPARATIVE STUDY; DNA MICROARRAY; GENETICS; GENOMICS; LIVER TUMOR; PATHOLOGY;

RATTUS;

AGING; ANIMALS; CARCINOMA, HEPATOCELLULAR; CELL DIFFERENTIATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOMICS; LIVER NEOPLASMS, EXPERIMENTAL; LIVER REGENERATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 77953307122     PISSN: None     EISSN: 14764598     Source Type: Journal    
DOI: 10.1186/1476-4598-9-146     Document Type: Article

References (102)

1. El-Serag HB, Rudolph KL. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 2007, 132:2557-2576. 10.1053/j.gastro.2007.04.061, 17570226.
2. Altekruse SF, McGlynn KA, Reichman ME. Hepatocellular carcinoma incidence, mortality, and survival trends in the United States from 1975 to 2005. J Clin Oncol 2009, 27:1485-1491. 10.1200/JCO.2008.20.7753, 2668555, 19224838.
3. Nguyen MH, Whittemore AS, Garcia RT, Tawfeek SA, Ning J, Lam S, Wright TL, Keeffe EB. Role of ethnicity in risk for hepatocellular carcinoma in patients with chronic hepatitis C and cirrhosis. Clin Gastroenterol Hepatol 2004, 2:820-824. 10.1016/S1542-3565(04)00353-2, 15354283.
4. Farazi PA, DePinho RA. Hepatocellular carcinoma pathogenesis: from genes to environment. Nat Rev Cancer 2006, 6:674-687. 10.1038/nrc1934, 16929323.
5. El-Serag HB. Hepatocellular carcinoma: recent trends in the United States. Gastroenterology 2004, 127:S27-34. 10.1053/j.gastro.2004.09.013, 15508094.
6. El-Serag HB. Epidemiology of hepatocellular carcinoma in USA. Hepatol Res 2007, 37(Suppl 2):S88-94. 10.1111/j.1872-034X.2007.00168.x, 17877502.
7. Su WH, Chao CC, Yeh SH, Chen DS, Chen PJ, Jou YS. OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. Nucleic Acids Res 2007, 35:D727-731. 10.1093/nar/gkl845, 1669730, 17098932.
8. Wurmbach E, Chen YB, Khitrov G, Zhang W, Roayaie S, Schwartz M, Fiel I, Thung S, Mazzaferro V, Bruix J, et al. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 2007, 45:938-947. 10.1002/hep.21622, 17393520.
9. Luo JH, Ren B, Keryanov S, Tseng GC, Rao UN, Monga SP, Strom S, Demetris AJ, Nalesnik M, Yu YP, et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 2006, 44:1012-1024. 10.1002/hep.21328, 1769554, 17006932.
10. Woo HG, Park ES, Lee JS, Lee YH, Ishikawa T, Kim YJ, Thorgeirsson SS. Identification of potential driver genes in human liver carcinoma by genomewide screening. Cancer Res 2009, 69:4059-4066. 10.1158/0008-5472.CAN-09-0164, 2750086, 19366792.
11. Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC, Simon R, Li Y, Robles AI, Chen Y, et al. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 2003, 9:416-423. 10.1038/nm843, 12640447.
12. Shackel NA, Seth D, Haber PS, Gorrell MD, McCaughan GW. The hepatic transcriptome in human liver disease. Comp Hepatol 2006, 5:6. 10.1186/1476-5926-5-6, 1665460, 17090326.
13. Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, et al. Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Res 2003, 63:859-864.
14. Nam SW, Park JY, Ramasamy A, Shevade S, Islam A, Long PM, Park CK, Park SE, Kim SY, Lee SH, et al. Molecular changes from dysplastic nodule to hepatocellular carcinoma through gene expression profiling. Hepatology 2005, 42:809-818. 10.1002/hep.20878, 16175600.
15. Geigl JB, Langer S, Barwisch S, Pfleghaar K, Lederer G, Speicher MR. Analysis of gene expression patterns and chromosomal changes associated with aging. Cancer Res 2004, 64:8550-8557. 10.1158/0008-5472.CAN-04-2151, 15574761.
16. Yau C, Fedele V, Roydasgupta R, Fridlyand J, Hubbard A, Gray JW, Chew K, Dairkee SH, Moore DH, Schittulli F, et al. Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers. Breast Cancer Res 2007, 9:R59. 10.1186/bcr1765, 2216076, 17850661.
17. Thomas RP, Guigneaux M, Wood T, Evers BM. Age-associated changes in gene expression patterns in the liver. J Gastrointest Surg 2002, 6:445-453. discussion 454, 10.1016/S1091-255X(01)00010-5, 12022999.
18. Lee JS, Chu IS, Mikaelyan A, Calvisi DF, Heo J, Reddy JK, Thorgeirsson SS. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat Genet 2004, 36:1306-1311. 10.1038/ng1481, 15565109.
19. Perez-Carreon JI, Lopez-Garcia C, Fattel-Fazenda S, Arce-Popoca E, Aleman-Lazarini L, Hernandez-Garcia S, Le Berre V, Sokol S, Francois JM, Villa-Trevino S. Gene expression profile related to the progression of preneoplastic nodules toward hepatocellular carcinoma in rats. Neoplasia 2006, 8:373-383. 10.1593/neo.05841, 1592455, 16790086.
20. Paoloni M, Davis S, Lana S, Withrow S, Sangiorgi L, Picci P, Hewitt S, Triche T, Meltzer P, Khanna C. Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression. BMC Genomics 2009, 10:625. 10.1186/1471-2164-10-625, 2803201, 20028558.
21. Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 2005, 37:48-55.
22. Ellwood-Yen K, Graeber TG, Wongvipat J, Iruela-Arispe ML, Zhang J, Matusik R, Thomas GV, Sawyers CL. Myc-driven murine prostate cancer shares molecular features with human prostate tumors. Cancer Cell 2003, 4:223-238. 10.1016/S1535-6108(03)00197-1, 14522256.
23. Lee JS, Thorgeirsson SS. Comparative and integrative functional genomics of HCC. Oncogene 2006, 25:3801-3809. 10.1038/sj.onc.1209561, 16799621.
24. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005, 436:117-122. 10.1038/nature03664, 16001072.
25. Thorgeirsson SS, Lee JS, Grisham JW. Molecular prognostication of liver cancer: end of the beginning. J Hepatol 2006, 44:798-805. 10.1016/j.jhep.2006.01.008, 16488507.
26. Cifola I, Spinelli R, Beltrame L, Peano C, Fasoli E, Ferrero S, Bosari S, Signorini S, Rocco F, Perego R, et al. Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile. Mol Cancer 2008, 7:6. 10.1186/1476-4598-7-6, 2253555, 18194544.
27. Mas VR, Maluf DG, Archer KJ, Yanek K, Kong X, Kulik L, Freise CE, Olthoff KM, Ghobrial RM, McIver P, Fisher R. Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma. Mol Med 2009, 15:85-94. 10.2119/molmed.2008.00110, 2605622, 19098997.
28. Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2001, 2:RESEARCH0042. 10.1186/gb-2001-2-10-research0042, 57797, 11597334.
29. Tsafrir D, Bacolod M, Selvanayagam Z, Tsafrir I, Shia J, Zeng Z, Liu H, Krier C, Stengel RF, Barany F, et al. Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res 2006, 66:2129-2137. 10.1158/0008-5472.CAN-05-2569, 16489013.
30. Moinzadeh P, Breuhahn K, Stutzer H, Schirmacher P. Chromosome alterations in human hepatocellular carcinomas correlate with aetiology and histological grade--results of an explorative CGH meta-analysis. Br J Cancer 2005, 92:935-941. 10.1038/sj.bjc.6602448, 2361895, 15756261.
31. Albertson DG, Collins C, McCormick F, Gray JW. Chromosome aberrations in solid tumors. Nat Genet 2003, 34:369-376. 10.1038/ng1215, 12923544.
32. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002, 99:12963-12968. 10.1073/pnas.162471999, 130569, 12297621.
33. Chiang DY, Villanueva A, Hoshida Y, Peix J, Newell P, Minguez B, LeBlanc AC, Donovan DJ, Thung SN, Sole M, et al. Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Res 2008, 68:6779-6788. 10.1158/0008-5472.CAN-08-0742, 2587454, 18701503.
34. Boyault S, Rickman DS, de Reynies A, Balabaud C, Rebouissou S, Jeannot E, Herault A, Saric J, Belghiti J, Franco D, et al. Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology 2007, 45:42-52. 10.1002/hep.21467, 17187432.
35. Liao YL, Sun YM, Chau GY, Chau YP, Lai TC, Wang JL, Horng JT, Hsiao M, Tsou AP. Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma. Oncogene 2008,
36. Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR. A stem cell molecular signature. Science 2002, 298:601-604. 10.1126/science.1073823, 12228721.
37. Dudoit SSP, Boldrick JC. Multiple hypothesis testing in microarray Experiments. Statist Scie 2003, 18:71-103.
38. Liu YF, Zha BS, Zhang HL, Zhu XJ, Li YH, Zhu J, Guan XH, Feng ZQ, Zhang JP. Characteristic gene expression profiles in the progression from liver cirrhosis to carcinoma induced by diethylnitrosamine in a rat model. J Exp Clin Cancer Res 2009, 28:107. 10.1186/1756-9966-28-107, 2729293, 19638242.
39. Thorgeirsson SS, Grisham JW. Molecular pathogenesis of human hepatocellular carcinoma. Nat Genet 2002, 31:339-346. 10.1038/ng0802-339, 12149612.
40. Wanless IR. International consensus on histologic diagnosis of early hepatocellular neoplasia. Hepatol Res 2007, 37(Suppl 2):S139-141. 10.1111/j.1872-034X.2007.00177.x, 17877475.
41. Francois P, Garzoni C, Bento M, Schrenzel J. Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources. J Microbiol Methods 2007, 68:385-391. 10.1016/j.mimet.2006.09.022, 17112614.
42. Kleinbaum DG, Kupper LL, Morgenstern H. Confounding. Epidemiological Research- Principles and Quantitative Methods 243-267. New York.
43. Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, et al. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 2006, 24:1162-1169. 10.1038/nbt1238, 17061323.
44. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161. 10.1038/nbt1239, 16964229.
45. Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics 2003, 3:180-188. 10.1007/s10142-003-0087-5, 12884057.
46. Panteva M, Korkaya H, Jameel S. Hepatitis viruses and the MAPK pathway: is this a survival strategy?. Virus Res 2003, 92:131-140. 10.1016/S0168-1702(02)00356-8, 12686421.
47. Wu CH, Sahoo D, Arvanitis C, Bradon N, Dill DL, Felsher DW. Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet 2008, 4:e1000090. 10.1371/journal.pgen.1000090, 2390767, 18535662.
48. Chang Q, Chen J, Beezhold KJ, Castranova V, Shi X, Chen F. JNK1 activation predicts the prognostic outcome of the human hepatocellular carcinoma. Mol Cancer 2009, 8:64. 10.1186/1476-4598-8-64, 2732591, 19686584.
49. Liu J, Ahiekpor A, Li L, Li X, Arbuthnot P, Kew M, Feitelson MA. Increased expression of ErbB-2 in liver is associated with hepatitis B × antigen and shorter survival in patients with liver cancer. Int J Cancer 2009, 125:1894-1901. 10.1002/ijc.24580, 19610068.
50. Fusco O, Querzoli P, Nenci I, Natoli C, Brakebush C, Ullrich A, Iacobelli S. 90K (MAC-2 BP) gene expression in breast cancer and evidence for the production of 90 K by peripheral-blood mononuclear cells. Int J Cancer 1998, 79:23-26. 10.1002/(SICI)1097-0215(19980220)79:1<23::AID-IJC5>3.0.CO;2-Y, 9495353.
51. Kim SJ, Lee SJ, Sung HJ, Choi IK, Choi CW, Kim BS, Kim JS, Yu W, Hwang HS, Kim IS. Increased serum 90 K and Galectin-3 expression are associated with advanced stage and a worse prognosis in diffuse large B-cell lymphomas. Acta Haematol 2008, 120:211-216. 10.1159/000193223, 19153476.
52. Vasko V, Espinosa AV, Scouten W, He H, Auer H, Liyanarachchi S, Larin A, Savchenko V, Francis GL, de la Chapelle A, et al. Gene expression and functional evidence of epithelial-to-mesenchymal transition in papillary thyroid carcinoma invasion. Proc Natl Acad Sci USA 2007, 104:2803-2808. 10.1073/pnas.0610733104, 1815262, 17296934.
53. Yamada S, Ohira M, Horie H, Ando K, Takayasu H, Suzuki Y, Sugano S, Hirata T, Goto T, Matsunaga T, et al. Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas. Oncogene 2004, 23:5901-5911. 10.1038/sj.onc.1207782, 15221005.
54. Ma W, Cai S, Du J, Tan Y, Chen H, Guo Z, Hu H, Fang R, Cai S. SDF-1/54-DCN: a novel recombinant chimera with dual inhibitory effects on proliferation and chemotaxis of tumor cells. Biol Pharm Bull 2008, 31:1086-1091. 10.1248/bpb.31.1086, 18520035.
55. Bi X, Tong C, Dockendorff A, Bancroft L, Gallagher L, Guzman G, Iozzo RV, Augenlicht LH, Yang W. Genetic deficiency of decorin causes intestinal tumor formation through disruption of intestinal cell maturation. Carcinogenesis 2008, 29:1435-1440. 10.1093/carcin/bgn141, 2811538, 18550571.
56. Luo SM, Tan WM, Deng WX, Zhuang SM, Luo JW. Expression of albumin, IGF-1, IGFBP-3 in tumor tissues and adjacent non-tumor tissues of hepatocellular carcinoma patients with cirrhosis. World J Gastroenterol 2005, 11:4272-4276.
57. Sato T, Oshima T, Yoshihara K, Yamamoto N, Yamada R, Nagano Y, Fujii S, Kunisaki C, Shiozawa M, Akaike M, et al. Overexpression of the fibroblast growth factor receptor-1 gene correlates with liver metastasis in colorectal cancer. Oncol Rep 2009, 21:211-216.
58. Pollmann MA, Shao Q, Laird DW, Sandig M. Connexin 43 mediated gap junctional communication enhances breast tumor cell diapedesis in culture. Breast Cancer Res 2005, 7:R522-534. 10.1186/bcr1042, 1175070, 15987459.
59. Bea S, Salaverria I, Armengol L, Pinyol M, Fernandez V, Hartmann EM, Jares P, Amador V, Hernandez L, Navarro A, et al. Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling. Blood 2009, 113:3059-3069. 10.1182/blood-2008-07-170183, 2662646, 18984860.
60. Kajiyama H, Kikkawa F, Suzuki T, Shibata K, Ino K, Mizutani S. Prolonged survival and decreased invasive activity attributable to dipeptidyl peptidase IV overexpression in ovarian carcinoma. Cancer Res 2002, 62:2753-2757.
61. Zhu L, Gibson P, Currle DS, Tong Y, Richardson RJ, Bayazitov IT, Poppleton H, Zakharenko S, Ellison DW, Gilbertson RJ. Prominin 1 marks intestinal stem cells that are susceptible to neoplastic transformation. Nature 2009, 457:603-607. 10.1038/nature07589, 2633030, 19092805.
62. Ma O, Cai WW, Zender L, Dayaram T, Shen J, Herron AJ, Lowe SW, Man TK, Lau CC, Donehower LA. MMP13, Birc2 (cIAP1), and Birc3 (cIAP2), amplified on chromosome 9, collaborate with p53 deficiency in mouse osteosarcoma progression. Cancer Res 2009, 69:2559-2567. 10.1158/0008-5472.CAN-08-2929, 2663905, 19276372.
63. Huang W, Yu LF, Zhong J, Wu W, Zhu JY, Jiang FX, Wu YL. Stat3 is involved in angiotensin II-induced expression of MMP2 in gastric cancer cells. Dig Dis Sci 2009, 54:2056-2062. 10.1007/s10620-008-0617-z, 19082717.
64. Ibanez de Caceres I, Dulaimi E, Hoffman AM, Al-Saleem T, Uzzo RG, Cairns P. Identification of novel target genes by an epigenetic reactivation screen of renal cancer. Cancer Res 2006, 66:5021-5028. 10.1158/0008-5472.CAN-05-3365, 16707423.
65. Chen C, Mendez E, Houck J, Fan W, Lohavanichbutr P, Doody D, Yueh B, Futran ND, Upton M, Farwell DG, et al. Gene expression profiling identifies genes predictive of oral squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev 2008, 17:2152-2162. 10.1158/1055-9965.EPI-07-2893, 2575803, 18669583.
66. Rubinstein R, Simon I. MILANO--custom annotation of microarray results using automatic literature searches. BMC Bioinformatics 2005, 6:12. 10.1186/1471-2105-6-12, 547913, 15661078.
67. Patil MA, Chua MS, Pan KH, Lin R, Lih CJ, Cheung ST, Ho C, Li R, Fan ST, Cohen SN, et al. An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Oncogene 2005, 24:3737-3747. 10.1038/sj.onc.1208479, 15735714.
68. Zhao X, Weir BA, LaFramboise T, Lin M, Beroukhim R, Garraway L, Beheshti J, Lee JC, Naoki K, Richards WG, et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 2005, 65:5561-5570. 10.1158/0008-5472.CAN-04-4603, 15994928.
69. Marchetti A, Tinari N, Buttitta F, Chella A, Angeletti CA, Sacco R, Mucilli F, Ullrich A, Iacobelli S. Expression of 90 K (Mac-2 BP) correlates with distant metastasis and predicts survival in stage I non-small cell lung cancer patients. Cancer Res 2002, 62:2535-2539.
70. Kholova I, Ludvikova M, Ryska A, Topolcan O, Pikner R, Pecen L, Cap J, Holubec L. Diagnostic role of markers dipeptidyl peptidase IV and thyroid peroxidase in thyroid tumors. Anticancer Res 2003, 23:871-875.
71. Halbersztadt A, Halon A, Pajak J, Robaczynski J, Rabczynski J, St Gabrys M. [The role of matrix metalloproteinases in tumor invasion and metastasis]. Ginekol Pol 2006, 77:63-71.
72. Samantaray S, Sharma R, Chattopadhyaya TK, Gupta SD, Ralhan R. Increased expression of MMP-2 and MMP-9 in esophageal squamous cell carcinoma. J Cancer Res Clin Oncol 2004, 130:37-44. 10.1007/s00432-003-0500-4, 14569466.
73. McKenna GJ, Chen Y, Smith RM, Meneghetti A, Ong C, McMaster R, Scudamore CH, Chung SW. A role for matrix metalloproteinases and tumor host interaction in hepatocellular carcinomas. Am J Surg 2002, 183:588-594. 10.1016/S0002-9610(02)00833-4, 12034400.
74. Asamoto M, Hokaiwado N, Cho Y-M, Shirai T. Effects of genetic background on prostate and taste bud carcinogenesis due to SV40 T antigen expression under probasin gene promoter control. Carcinogenesis 2002, 23:463-467. 10.1093/carcin/23.3.463, 11895861.
75. Yamashita S, Wakazono K, Nomoto T, Tsujino Y, Kuramoto T, Ushijima T. Expression Quantitative Trait Loci Analysis of 13 Genes in the Rat Prostate. Genetics 2005, 171:1231-1238. 10.1534/genetics.104.038174, 1456825, 16079240.
76. Dillner K, Kindblom J, Flores-Morales A, Shao R, Tornell J, Norstedt G, Wennbo H. Gene Expression Analysis of Prostate Hyperplasia in Mice Overexpressing the Prolactin Gene Specifically in the Prostate. Endocrinology 2003, 144:4955-4966. 10.1210/en.2003-0415, 12960074.
77. Maffey AH, Ishibashi T, He C, Wang X, White AR, Hendy SC, Nelson CC, Rennie PS, Ausio J. Probasin promoter assembles into a strongly positioned nucleosome that permits androgen receptor binding. Mol Cell Endocrinol 2007, 268:10-19. 10.1016/j.mce.2007.01.009, 17316977.
78. Nikitovic D, Berdiaki A, Zafiropoulos A, Katonis P, Tsatsakis A, Karamanos NK, Tzanakakis GN. Lumican expression is positively correlated with the differentiation and negatively with the growth of human osteosarcoma cells. Febs J 2008, 275:350-361.
79. Eshchenko TY, Rykova VI, Chernakov AE, Sidorov SV, Grigorieva EV. Expression of different proteoglycans in human breast tumors. Biochemistry (Mosc) 2007, 72:1016-1020. 10.1134/S0006297907090143, 17922662.
80. Ishiwata T, Cho K, Kawahara K, Yamamoto T, Fujiwara Y, Uchida E, Tajiri T, Naito Z. Role of lumican in cancer cells and adjacent stromal tissues in human pancreatic cancer. Oncol Rep 2007, 18:537-543.
81. Seya T, Tanaka N, Shinji S, Yokoi K, Koizumi M, Teranishi N, Yamashita K, Tajiri T, Ishiwata T, Naito Z. Lumican expression in advanced colorectal cancer with nodal metastasis correlates with poor prognosis. Oncol Rep 2006, 16:1225-1230.
82. Kelemen LE, Couch FJ, Ahmed S, Dunning AM, Pharoah PD, Easton DF, Fredericksen ZS, Vierkant RA, Pankratz VS, Goode EL, et al. Genetic variation in stromal proteins decorin and lumican with breast cancer: investigations in two case-control studies. Breast Cancer Res 2008, 10:R98. 10.1186/bcr2201, 2656894, 19036156.
83. Yee J, Sadar MD, Sin DD, Kuzyk M, Xing L, Kondra J, McWilliams A, Man SF, Lam S. Connective tissue-activating peptide III: a novel blood biomarker for early lung cancer detection. J Clin Oncol 2009, 27:2787-2792. 10.1200/JCO.2008.19.4233, 2698017, 19414677.
84. Marshall KW, Mohr S, Khettabi FE, Nossova N, Chao S, Bao W, Ma J, Li XJ, Liew CC. A blood-based biomarker panel for stratifying current risk for colorectal cancer. Int J Cancer 2010, 126:1177-1186.
85. Lonneborg A. Biomarkers for Alzheimer disease in cerebrospinal fluid, urine, and blood. Mol Diagn Ther 2008, 12:307-320.
86. Aaroe J, Lindahl T, Dumeaux V, Saebo S, Tobin D, Hagen N, Skaane P, Lonneborg A, Sharma P, Borresen-Dale AL. Gene expression profiling of peripheral blood cells for early detection of breast cancer. Breast Cancer Res 2010, 12:R7. 10.1186/bcr2472, 2880427, 20078854.
87. Kurian SM, Le-Niculescu H, Patel SD, Bertram D, Davis J, Dike C, Yehyawi N, Lysaker P, Dustin J, Caligiuri M, et al. Identification of blood biomarkers for psychosis using convergent functional genomics. Mol Psychiatry 2009,
88. Lonneborg A, Aaroe J, Dumeaux V, Borresen-Dale AL. Found in transcription: gene expression and other novel blood biomarkers for the early detection of breast cancer. Expert Rev Anticancer Ther 2009, 9:1115-1123. 10.1586/era.09.31, 19671031.
89. Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, Hersch SM, Hogarth P, Bouzou B, Jensen RV, Krainc D. Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease. Proc Natl Acad Sci USA 2005, 102:11023-11028. 10.1073/pnas.0504921102, 1182457, 16043692.
90. Terminology of nodular hepatocellular lesions. International Working Party. Hepatology 1995, 22:983-993.
91. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
92. Li C, Hung Wong W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001, 2:RESEARCH0032. 55329, 11532216.
93. Wu Z, Irizarry RA. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12:882-893. 10.1089/cmb.2005.12.882, 16108723.
94. Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nat Biotechnol 2004, 22:656-658. author reply 658, 10.1038/nbt0604-656b, 15175677.
95. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
96. Sherman BT, Huang DW, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 2007, 8:426. 10.1186/1471-2105-8-426, 2186358, 17980028.
97. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70. 10.1186/gb-2003-4-10-r70, 328459, 14519205.
98. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 2003, 13:2129-2141. 10.1101/gr.772403, 403709, 12952881.
99. Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res 2006, 34:W645-650. 10.1093/nar/gkl229, 1538848, 16912992.
100. Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J. RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol 2001, 2:SOFTWARE0002. 10.1186/gb-2001-2-11-software0002, 138985, 16173164.
101. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19:368-375. 10.1093/bioinformatics/btf877, 12584122.
102. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.