Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Yang, Xinan ^a   Sun, Xiao ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSTIC ACCURACY; GENE EXPRESSION PROFILES; INTEGRATIVE ANALYSIS; MICROARRAY ANALYSIS; MULTIPLE DATA SETS; PROGNOSTIC MARKERS; STATISTICAL TECHNIQUES; SUPPORT VECTOR MACHINE ALGORITHM;

ALGORITHMS; GENE EXPRESSION; MICROARRAYS; TUMORS;

DISEASES;

ALGORITHM; ANGIOGENESIS; ARTICLE; CANCER; CANCER GENE THERAPY; CANCER PATIENT; CANCER RECURRENCE; CANCER SURVIVAL; CLINICAL STUDY; DIAGNOSTIC ACCURACY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE TARGETING; GLIOMA; HAZARD RATIO; HUMAN; LEUKEMIA; LUNG CANCER; MESOTHELIOMA; MICROARRAY ANALYSIS; OUTCOME ASSESSMENT; PROGNOSIS; PROSTATE CANCER; PROTEIN DEGRADATION; SOLID TUMOR; STATISTICAL ANALYSIS; SUPPORT VECTOR MACHINE; AUTOMATED PATTERN RECOGNITION; COMPUTER ASSISTED DIAGNOSIS; EVALUATION; INFORMATION RETRIEVAL; META ANALYSIS; METABOLISM; METHODOLOGY; NEOPLASM; PROTEIN DATABASE;

TUMOR MARKER; TUMOR PROTEIN;

ALGORITHMS; DATABASES, PROTEIN; DIAGNOSIS, COMPUTER-ASSISTED; HUMANS; INFORMATION STORAGE AND RETRIEVAL; META-ANALYSIS; NEOPLASM PROTEINS; NEOPLASMS; PATTERN RECOGNITION, AUTOMATED; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 34247388455     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-118     Document Type: Article

References (67)

1. van 't Veer LJ Dai H van de Vijver MJ He YD Hart AAM Mao M Peterse HL van der Kooy K Marton MJ Witteveen AT Schreiber GJ Kerkhoven RM Roberts C Linsley PS Bernards R Friend SH Gene expression profiling predicts clinical outcome of breast cancer Nature 2002 415 6871 530-536 10.1038/ 415530a 11823860
2. van de Vijver MJ He YD van't Veer LJ Dai H Hart AAM Voskuil DW Schreiber GJ Peterse JL Roberts C Marton MJ Parrish M Atsma D Witteveen A Glas A Delahaye L van der Velde T Bartelink H Rodenhuis S Rutgers ET Friend SH Bernards R A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 2002 347 25 1999-2009 10.1056/NEJMoa021967 12490681
3. Huang E Cheng SH Dressman H Pittmane J Tsou MH Horng CF Bild A Iversen ES Liao M Chen CM West M Nevins JR Huang AT Gene expression predictors of breast cancer outcomes Lancet 2003 361 9369 1590-1596 10.1016/ S0140-6736(03)13308-9 12747878
4. Nevins JR Huang ES Dressman H Pittman J Huang AT West M Towards integrated clinico-genomic models for personalized medicine: Combining gene expression signatures and clinical factors in breast cancer outcomes prediction Hum Mol Genet 2003 12 Spec No 2 R153-157 10.1093/hmg/ ddg287 12928487
5. Gordon GJ Jensen RV Hsiao LL Gullans SR Blumenstock JE Richards WG Jaklitsch MT Sugarbaker DJ Bueno R Using Gene Expression Ratios to Predict Outcome Among Patients With Mesothelioma Journal of the National Cancer Institute 2003 95 8 598-605 12697852
6. Futschik ME Sullivan M Reeve A Kasabov N Prediction of clinical behaviour and treatment for cancers Appl Bioinformatics 2003 2 3 Suppl S53-58 15130817
7. Choi JK Choi JY Kim DG Choi DW Kim BY Lee KH Yeom YI Yoo HS Yoo OJ Kim S Integrative analysis of multiple gene expression profiles applied to liver cancer study FEBS Lett 2004 565 1-3 93-100 10.1016/ j.febslet.2004.05.087 15135059
8. Cario G Stanulla M Fine BM Teuffel O Neuhoff NV Schrauder A Flohr T SchACURfer BW Bartram CR Welte K Schlegelberger B Schrappe M Distinct gene expression profiles determine molecular treatment response in childhood acute lymphoblastic leukemia Blood 2005 105 2 821-826 10.1182/ blood-2004-04-1552 15388585
9. Bloom G Yang IV Boulware D Kwong KY Coppola D Eschrich S Quackenbush J Yeatman TJ Multi-platform, multi-site, microarray-based human tumor classification Am J Pathol 2004 164 9-16 1602228 14695313
10. Larkin JE Frank BC Gavras H Sultana R Quackenbush J Independence and reproducibility across microarray platforms Nature Methods 2005 2 5 337-344 10.1038/nmeth757 15846360
11. Warnat P Eils R Brors B Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes BMC Bioinformatics 2005 6 265 1312314 16271137 10.1186/1471-2105-6-265
12. Bammler T Beyer RP Bhattacharya S Boorman GA Boyles A Bradford BU Bumgarner RE Bushel PR Chaturvedi K Choi D Cunningham ML Deng S Dressman HK Fannin RD Farin FM Freedman JH Fry RC Harper A Humble MC Hurban P Kavanagh TJ Kaufmann WK Kerr KF Jing L Lapidus JA Lasarev MR Li J Li YJ Lobenhofer EK Lu X Malek RL Milton S Nagalla SR O'malley JP Palmer VS Pattee P Paules RS Perou CM Phillips K Qin LX Qiu Y Quigley SD Rodland M Rusyn I Samson LD Schwartz DA Shi Y Shin JL Sieber SO Slifer S Speer MC Spencer PS Sproles DI Swenberg JA Suk WA Sullivan RC Tian R Tennant RW Todd SA Tucker CJ Houten BV Weis BK Xuan S HZ Standardizing global gene expression analysis between laboratories and across platforms Nature Methods 2005 2 5 351-356 10.1038/nmeth754 15846362
13. Grutzmann R Boriss H Ammerpohl O Luttges J Kalthoff H Schackert HK Kloppel G Saeger HD Pilarsky C Meta-analysis of microarray data on pancreatic cancer defines a set of commonly dysregulated genes Oncogene 2005 24 32 5079-5088 10.1038/sj.onc.1208696 15897887
14. Rhodes DR Chinnaiyan AM Integrative analysis of the cancer transcriptome Nature Genet 2005 37 Suppl S31-37 10.1038/ng1570 15920528
15. Bernards R Weinberg RA Metastasis genes: A progression puzzle Nature 2002 418 6900 823 10.1038/418823a 12192390
16. Yang X Bentink S Spang R Detecting common gene expression patterns in multiple cancer outcome entities Biomed Microdevices 2005 7 3 247-251 10.1007/s10544-005-3032-7 16133813
17. Glinsky GV Berezovska O Glinskii AB Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer J Clin Invest 2005 115 6 1503-1521 1136989 15931389 10.1172/JCI23412
18. Rhodes DR Yu J Shanker K Deshpande N Varambally R Ghosh D Barrette T Pandey A Chinnaiyan AM Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression Proc Natl Acad Sci USA 2004 101 25 9309-9314 438973 15184677 10.1073/pnas.0401994101
19. Finocchiaro G Mancuso F Muller H Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control BMC Bioinformatics 2005 6 Suppl 4 S14 10.1186/1471-2105-6-S4-S14 16351740
20. Segal E Friedman N Koller D Regev A A module map showing conditional activity of expression modules in cancer Nature Genet 2004 36 10 1090-1098 15448693
21. Yang X Bentink S Scheid S Spang R Similarities of ordered gene lists J Bioinform Comput Biol 2006 4 3 693-708 10.1142/S0219720006002120 16960970
22. Ross ME Zhou X Song G Shurtleff SA Girtman K Williams WK Liu HC Mahfouz R Raimondi SC Lenny N Patel A Downing JR Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 2003 102 8 2951-2959 10.1182/blood-2003-01-0338 12730115
23. Yeoh EJ Ross ME Shurtleff SA Williams WK Patel D Mahfouz R Behm FG Raimondi SC Relling MV Patel A Cheng C Campana D Wilkins D Zhou X Li J Liu H Pui CH Evans WE Naeve C Wong L Downing JR Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling Cancer Cell 2002 1 2 133-143 10.1016/S1535-6108(02)00032-6 12086872
24. Scheid S Spang R Twilight; a Bioconductor package for estimating the local false discovery rate Bioinformatics 2005 21 12 2921-2922 10.1093/ bioinformatics/bti436 15817688
25. Storey JD Tibshirani R Statistical significance for genome-wide studies Proc Natl Acad Sci USA 2003 100 16 9440-9445 170937 12883005 10.1073/ pnas.1530509100
26. Pepe MS Longton G Anderson GL Schummer M Selecting Differentially Expressed Genes from Microarray Experiments Biometrics 2003 59 133-142 10.1111/1541-0420.00016 12762450
27. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M Loda M Weber G Mark EJ Lander ES Wong W Johnson BE Golub TR Sugarbaker DJ Meyerson M Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc Natl Acad Sci USA 2001 98 24 13790-13795 61120 11707567 10.1073/pnas.191502998
28. Kaufman L Rousseeuw PJ Finding Groups in Data: An Introduction to Cluster Analysis New York: John Wiley and Sons, Inc 1990
29. Xu JZ Guo Z Zhang M Li X Li YJ Rao SQ Peeling off the hidden genetic heterogeneities of cancers based on disease-relevant functional modules Mol Med 2006 12 1-3 25-33 1514552 16838067
30. Harms KL Chen X The C terminus of p53 family proteins is a cell fate determinant Mol Cell Biol 2005 25 5 2014-2030 549381 15713654 10.1128/ MCB.25.5.2014-2030.2005
31. Silha JV Sheppard PC Mishra S Gui Y Schwartz J Dodd JG Murphy LJ Insulin-like growth factor (IGF) binding protein-3 attenuates prostate tumor growth by IGF-dependent and IGF-independent mechanisms Endocrinology 2006 147 5 2112-2121 10.1210/en.2005-1270 16469805
32. Fischer H Stenling R Rubio C Lindblom A Colorectal carcinogenesis is associated with stromal expression of COL11A1 and COL5A2 Carcinogenesis 2001 22 6 875-878 10.1093/carcin/22.6.875 11375892
33. Genkai N Homma J Sano M Tanaka R Yamanaka R Increased expression of pituitary tumor-transforming gene (PTTG)-1 is correlated with poor prognosis in glioma patients Oncol Rep 2006 15 6 1569-1574 16685397
34. Rasmussen HH Orntoft TF Wolf H Celis JE Towards a comprehensive database of proteins from the urine of patients with bladder cancer J Urol 1996 155 6 2113-2119 10.1016/S0022-5347(01)66119-6 8618346
35. Banerjee AG Bhattacharyya I Vishwanatha JK Identification of genes and molecular pathways involved in the progression of premalignant oral epithelia Mol Cancer Ther 2005 4 6 865-875 10.1158/1535-7163.MCT-05-0033 15956244
36. Cho-Rok J Yoo J Jang YJ Kim S Chu IS Yeom YI Choi JY Im DS Adenovirus-mediated transfer of siRNA against PTTG1 inhibits liver cancer cell growth in vitro and in vivo Hepatology 2006 43 5 1042-1052 10.1002/hep.21137 16628636
37. Li X Rao S Wang Y Gong B Gene mining: A novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling Nucleic Acids Res 2004 32 9 2685-2694 419591 15148356 10.1093/nar/gkh563
38. Singh D Febbo PG Ross K Jackson DG Manola J Ladd C Tamayo P Renshaw AA D'Amico AV Richie JP Lander E Loda M Kantoff PW Golub TR Sellers WR Gene expression correlates of clinical prostate cancer behavior Cancer Cell 2002 1 203-209 10.1016/S1535-6108(02)00030-2 12086878
39. Lossos IS Czerwinski DK Alizadeh AA Wechser MA Tibshirani R Botstein D Levy R Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes N Engl J Med 2004 350 18 1828-1837 10.1056/ NEJMoa032520 15115829
40. Ifon ET Pang ALY Johnson W Cashman K Zimmerman S Muralidhar S Chan WY Casey J Rosenthal LJ U94 alters FN1 and ANGPTL4 gene expression and inhibits tumorigenesis of prostate cancer cell line PC3 Cancer Cell Int 2005 5 19 1200560 15972109 10.1186/1475-2867-5-19
41. Sasaki H Yu CY Dai M Tam C Loda M Auclair D Chen LB Elias A Elevated serum periostin levels in patients with bone metastases from breast but not lung cancer Breast Cancer Res Treat 2003 77 3 245-252 10.1023/ A:1021899904332 12602924
42. Sasaki H Lo KM Chen LB Auclair D Nakashima Y Moriyama S Fukai I Tam C Loda M Fujii Y Expression of Periostin, homologous with an insect cell adhesion molecule, as a prognostic marker in non-small cell lung cancers Jpn J Cancer Res 2001 92 8 869-873 11509119
43. Gillette JM Chan DC Nielsen-Preiss SM Annexin 2 expression is reduced in human osteosarcoma metastases J Cell Biochem 2004 92 4 820-832 10.1002/ jcb.20117 15211578
44. Banerjee AG Liu J Yuan Y Gopalakrishnan VK Johansson SL Dinda AK Gupta NP Trevino L Vishwanatha JK Expression of biomarkers modulating prostate cancer angiogenesis: Differential expression of annexin II in prostate carcinomas from India and USA Mol Cancer 2003 2 34 270077 14613585 10.1186/1476-4598-2-34
45. Sumi Y Muramatsu H Takei Y Hata KI Ueda M Muramatsu T Midkine, a heparin-binding growth factor, promotes growth and glycosaminoglycan synthesis of endothelial cells through its action on smooth muscle cells in an artificial blood vessel model J Cell Sci 2002 115 2659-2667 12077357
46. Muramatsu T Midkine and pleiotrophin: Two related proteins involved in development, survival, inflammation and tumorigenesis J Biochem (Tokyo) 2002 132 3 359-371 12204104
47. Kadomatsu K Muramatsu T Midkine and pleiotrophin in neural development and cancer Cancer Lett 2004 204 2 127-143 10.1016/S0304-3835(03)00450-6 15013213
48. Ikematsu S Nakagawara A Nakamura Y Sakuma S Wakai K Muramatsu T Kadomatsu K Correlation of elevated level of blood midkine with poor prognostic factors of human neuroblastomas Br J Cancer 2003 88 10 1522-1526 10.1038/sj.bjc.6600938 12771916
49. Shimada H Nabeya Y Tagawa M Okazumi S Matsubara H Kadomatsu K Muramatsu T Ikematsu S Sakuma S Ochiai T Preoperative serum midkine concentration is a prognostic marker for esophageal squamous cell carcinoma Cancer Sci 2003 94 7 628-632 10.1111/j.1349-7006.2003.tb01494.x 12841873
50. Roversi G Pfundt R Moroni RF Magnani I van Reijmersdal S Pollo B Straatman H Larizza L Schoenmakers EFPM Identification of novel genomic markers related to progression to glioblastoma through genomic profiling of 25 primary glioma cell lines Oncogene 2006 25 10 1571-1583 10.1038/ sj.onc.1209177 16247447
51. He P Varticovski L Bowman ED Fukuoka J Welsh JA Miura K Jen J Gabrielson E Brambilla E Travis WD Harris CC Identification of carboxypeptidase E and gamma-glutamyl hydrolase as biomarkers for pulmonary neuroendocrine tumors by cDNA microarray Hum Pathol 2004 35 10 1196-1209 10.1016/ j.humpath.2004.06.014 15492986
52. Sasson R Dantes A Tajima K Amsterdam A Novel genes modulated by FSH in normal and immortalized FSH-responsive cells: New insights into the mechanism of FSH action FASEB J 2003 17 10 1256-1266 10.1096/ fj.02-0740com 12832290
53. Zhang D Samani AA Brodt P The role of the IGF-I receptor in the regulation of matrix metalloproteinases, tumor invasion and metastasis Horm Metab Res 2003 35 11-12 802-808 14710361
54. Shao R Bao S Bai X Blanchette C Anderson RM Dang T Gishizky ML Marks JR Wang XF Acquired expression of periostin by human breast cancers promotes tumor angiogenesis through up-regulation of vascular endothelial growth factor receptor 2 expression Mol Cell Biol 2004 24 9 3992-4003 387763 15082792 10.1128/MCB.24.9.3992-4003.2004
55. Chen WB Lenschow W Tiede K Fischer JW Kalthoff H Ungefroren H Smad4/ DPC4-dependent regulation of biglycan gene expression by transforming growth factor-beta in pancreatic tumor cells J Biol Chem 2002 277 39 36118-36128 10.1074/jbc.M203709200 12140283
56. Grzesiak JJ Clopton P Chalberg C Smith K Burton DW Silletti S Moossa AR Deftos LJ Bouvet M The extracellular matrix differentially regulates the expression of PTHrP and the PTH/PTHrP receptor in FG pancreatic cancer cells Pancreas 2004 29 2 85-92 10.1097/00006676-200408000-00001 15257098
57. Sun XT Zhang MY Shu C Li Q Yan XG Cheng N Qiu YD Ding YT Differential gene expression during capillary morphogenesis in a microcarrier-based three-dimensional in vitro model of angiogenesis with focus on chemokines and chemokine receptors World J Gastroenterol 2005 11 15 2283-2290 15818740
58. Kakar SS Jennes L Molecular cloning and characterization of the tumor transforming gene (TUTR1): A novel gene in human tumorigenesis Cytogenet Cell Genet 1999 84 3-4 211-216 10.1159/000015261 10393434
59. Ramaswamy S Ross KN Lander ES Golub TR A molecular signature of metastasis in primary solid tumors Nature Genet 2003 33 49-54 10.1038/ ng1060 12469122
60. Hamid T Malik MT Kakar SS Ectopic expression of PTTG1/securin promotes tumorigenesis in human embryonic kidney cells Mol Cancer 2005 4 3 546418 15649325 10.1186/1476-4598-4-3
61. Huber W von Heydebreck A Sultmann H Poustka A Vingron M Variance stabilization applied to microarray data calibration and to the quantification of differential expression Bioinformatics 2002 18 Suppl 1 S96-104 12169536
62. Woo Y Affourtit J Daigle S Viale A Johnson K Naggert J Churchill G A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms J Biomol Tech 2004 15 4 276-284 15585824
63. affymetrix comparison_spreadsheets http://www.affymetrix.com/support/ technical/comparison_spreadsheets.affx
64. Chiaretti S Li X Gentleman R Vitale A Vignetti M Mandelli F Ritz J Foa R Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival Blood 2004 103 7 2771-2778 10.1182/ blood-2003-09-3243 14684422
65. Shai R Shi T Kremen TJ Horvath S Liau LM Cloughesy TF Mischel PS Nelson SF Gene expression profiling identifies molecular subtypes of gliomas Oncogene 2003 22 31 4918-4923 10.1038/sj.onc.1206753 12894235
66. Lottaz C Yang X Scheid S Spang R OrderedList - a bioconductor package for detecting similarity in ordered gene lists Bioinformatics 2006 22 18 2315-2316 10.1093/bioinformatics/btl385 16844712
67. Michiels S Koscielny S Hill C Prediction of cancer outcome with microarrays: A multiple random validation strategy Lancet 2005 365 9458 488-492 10.1016/S0140-6736(05)17866-0 15705458