A resampling-based meta-analysis for detection of differential gene expression in breast cancer

BMC Cancer

Volumn 8, Issue , 2008, Pages

  Gur Dedeoglu, Bala ^a   Konu, Ozlen ^a   Kir, Serkan ^a   Ozturk, Ahmet Rasit ^a   Bozkurt, Betul ^b   Ergul, Gulusan ^b   Yulug, Isik G ^a  

^a BILKENT UNIVERSITY   (Turkey)

^b ANKARA TRAINING AND RESEARCH HOSPITAL   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR 3; BINDING PROTEIN; PROTEIN ADAMTS1; PROTEIN COX6C; PROTEIN FN1; PROTEIN GSN; PROTEIN GSPT1; PROTEIN ID4; PROTEIN IGFBP6; PROTEIN NME1; PROTEIN PRNP; PROTEIN RAD21; PROTEIN SPTBN1; SECRETED FRIZZLED RELATED PROTEIN 1; SECURIN; TRANSCRIPTION FACTOR MAF; UNCLASSIFIED DRUG; VASCULOTROPIN RECEPTOR 1;

ARTICLE; BREAST CANCER; CANCER GENETICS; CLINICAL ARTICLE; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTRADUCTAL CARCINOMA; LUNG CARCINOMA; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SAMPLE SIZE; VALIDATION PROCESS; BREAST; BREAST TUMOR; DNA MICROARRAY; FEMALE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; META ANALYSIS; METABOLISM; NONPARAMETRIC TEST; PAGET NIPPLE DISEASE; REPRODUCIBILITY;

BREAST; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; CARCINOMA, LOBULAR; DATABASES, GENETIC; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; STATISTICS, NONPARAMETRIC;

EID: 60649092138     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-8-396     Document Type: Article

References (55)

1. Sorlie T Tibshirani R Parker J Hastie T Marron JS Nobel A Deng S Johnsen H Pesich R Geisler S Demeter J Perou CM Lonning PE Brown PO Borresen-Dale AL Bodstein D Repeated observation of breast tumor subtypes in independent gene expression data sets Proc Natl Acad Sci USA 2003, 100:8418-8423 166244 12829800 10.1073/pnas.0932692100
2. Zhao H Langerod A Ji Y Nowels KW Nesland JM Tibshirani R Bukholm IK Karesen R Botstein D Borresen-Dale AL Jeffrey SS Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast Mol Biol Cell 2004, 15:2523-2536 420079 15034139 10.1091/ mbc.E03-11-0786
3. van't Veer LJ Dai H Vijver van de MJ He YD Hart AA Mao M Peterse HL Kooy van der 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
4. Farmer P Bonnefoi H Becette V Tubiana-Hulin M Fumoleau P Larsimont D Macgrogan G Bergh J Cameron D Goldstein D Duss S Nicoulaz AL Brisken C Fiche M Delorenzi M Iggo R Identification of molecular apocrine breast tumours by microarray analysis Oncogene 2005, 24:4660-4671 10.1038/ sj.onc.1208561 15897907
5. Turashvili G Bouchal J Baumforth K Wei W Dziechciarkova M Ehrmann J Klein J Fridman E Skarda J Srovnal J Hajduch M Murray P Kolar Z Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis BMC Cancer 2007, 7:55 1852112 17389037 10.1186/1471-2407-7-55
6. Grigoriadis A Mackay A Reis-Filho JS Steele D Iseli C Stevenson BJ Jongeneel CV Valgeirsson H Fenwick K Iravani M Leao M Simpson AJ Strausberg RL Jat PS Ashworth A Neville AM O'Hare MJ Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data Breast Cancer Res 2006, 8:R56 1779497 17014703 10.1186/bcr1604
7. Richardson AL Wang ZC De Nicolo A Lu X Brown M Miron A Liao X Iglehart JD Livingston DM Ganesan S X chromosomal abnormalities in basal-like human breast cancer Cancer Cell 2006, 9:121-132 10.1016/ j.ccr.2006.01.013 16473279
8. Karnoub AE Dash AB Vo AP Sullivan A Brooks MW Bell GW Richardson AL Polyak K Tubo R Weinberg RA Mesenchymal stem cells within tumor stroma promote breast cancer metastasis Nature 2007, 449:557-563 10.1038/ nature06188 17914389
9. Tripathi A King C de la Morenas A Perry VK Burke B Antoine GA Hirsch EF Kavanah M Mendez J Stone M Gerry NP Lenburg ME Rosenberg CL Gene expression abnormalities in histologically normal breast epithelium of breast cancer patients Int J Cancer 2008, 122:1557-1566 10.1002/ ijc.23267 18058819
10. Smith DD Saetrom P Snøve O Jr Lundberg C Rivas GE Glackin C Larson GP Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation BMC Bioinformatics 2008, 9:63 2275244 18226260 10.1186/ 1471-2105-9-63
11. Thomassen M Tan Q Kruse TA Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis Breast Cancer Res Treat 2009, 113(2):239-249 10.1007/ s10549-008-9927-2 18293085
12. Hu Z Fan C Oh DS Marron JS He X Qaqish BF Livasy C Carey LA Reynolds E Dressler L Nobel A Parker J Ewend MG Sawyer LR Wu J Liu Y Nanda R Tretiakova M Ruiz Orrico A Dreher D Palazzo JP Perreard L Nelson E Mone M Hansen H Mullins M Quackenbush JF Ellis MJ Olopade OI Bernard PS Perou CM The molecular portraits of breast tumors are conserved across microarray platforms BMC Genomics 2006, 7:96 1468408 16643655 10.1186/ 1471-2164-7-96
13. Moreau Y Aerts S De Moor B De Strooper B Dabrowski M Comparison and meta-analysis of microarray data: From the bench to the computer desk Trends Genet 2003, 19:570-577 10.1016/j.tig.2003.08.006 14550631
14. Rhodes DR Barrette TR Rubin MA Ghosh D Chinnaiyan AM Meta-analysis of microarrays: Interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer Cancer Res 2002, 62:4427-4433 12154050
15. Choi JK Yu U Kim S Yoo OJ Combining multiple microarray studies and modeling interstudy variation Bioinformatics 2003, 19(Suppl 1):i84-90 10.1093/bioinformatics/btg1010 12855442
16. Toedling J Spang R Assessment of Five Microarray Experiments on Gene Expression Profiling of Breast Cancer Poster Presentation RECOMB 2003 http://citeseer.ist.psu.edu/611350.html
17. 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
18. Qiu X Xiao Y Gordon A Yakovlev A Assessing stability of gene selection in microarray data analysis BMC Bioinformatics 2006, 7:50 1403808 16451725 10.1186/1471-2105-7-50
19. Pavlidis P Qin J Arango V Mann JJ Sibille E Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex Neurochem Res 2004, 29:1213-1222 10.1023/B:NERE.0000023608.29741.45 15176478
20. 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, 565:93-100 10.1016/ j.febslet.2004.05.087 15135059
21. 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, 24:5079-5088 10.1038/sj.onc.1208696 15897887
22. Arpino G Bardou VJ Clark GM Elledge RM Infiltrating lobular carcinoma of the breast: Tumor characteristics and clinical outcome Breast Cancer Res 2004, 6:R149-156 400666 15084238 10.1186/bcr767
23. Korkola JE DeVries S Fridlyand J Hwang ES Estep AL Chen YY Chew KL Dairkee SH Jensen RM Waldman FM Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis Cancer Res 2003, 63:7167-7175 14612510
24. Weigelt B Horlings H Kreike B Hayes M Hauptmann M Wessels L de Jong D Vijver Van de M Veer LjV Peterse J Refinement of breast cancer classification by molecular characterization of histological special types J Pathol 2008, 216:141-150 10.1002/path.2407 18720457
25. Li CI Malone KE Porter PL Weiss NS Tang MT Daling JR Reproductive and anthropometric factors in relation to the risk of lobular and ductal breast carcinoma among women 65-79 years of age Int J Cancer 2003, 107:647-651 10.1002/ijc.11465 14520705
26. Biometric Research Branch http://linus.nci.nih.gov/BRB-ArrayTools.html
27. Stanford Microarray Database http://genome-www5.stanford.edu/
28. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/
29. Pfaffl MW A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res 2001, 29:e45 55695 11328886 10.1093/ nar/29.9.e45
30. 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, 101:9309-9314 438973 15184677 10.1073/pnas.0401994101
31. Xu L Geman D Winslow RL Large-scale integration of cancer microarray data identifies a robust common cancer signature BMC Bioinformatics 2007, 8:275 1950528 17663766 10.1186/1471-2105-8-275
32. Bertucci F Orsetti B Nègre V Finetti P Rougé C Ahomadegbe JC Bibeau F Mathieu MC Treilleux I Jacquemier J Ursule L Martinec A Wang Q Bénard J Puisieux A Birnbaum D Theillet C Lobular and ductal carcinomas of the breast have distinct genomic and expression profiles Oncogene 2008, 27:5359-5372 10.1038/onc.2008.158 18490921
33. Ben-Shaul Y Bergman H Soreq H Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression Bioinformatics 2005, 21:1129-1137 10.1093/bioinformatics/bti149 15550480
34. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing J Roy Statis Soc Ser 1995, 57:289-300
35. Yoder BJ Wilkinson EJ Massoll NA Molecular and morphologic distinctions between infiltrating ductal and lobular carcinoma of the breast Breast J 2007, 13:172-179 10.1111/j.1524-4741.2007.00393.x 17319859
36. Simpson PT Reis-Filho JS Lambros MB Jones C Steele D Mackay A Iravani M Fenwick K Dexter T Jones A Reid L Da Silva L Shin SJ Hardisson D Ashworth A Schmitt FC Palacios J Lakhani SR Molecular profiling pleomorphic lobular carcinomas of the breast: Evidence for a common molecular genetic pathway with classic lobular carcinomas J Pathol 2008, 215:231-244 10.1002/path.2358 18473330
37. Sarrió D Moreno-Bueno G Hardisson D Sánchez-Estévez C Guo M Herman JG Gamallo C Esteller M Palacios J Epigenetic and genetic alterations of APC and CDH1 genes in lobular breast cancer: relationships with abnormal E-cadherin and catenin expression and microsatellite instability Int J Cancer 2003, 106:208-215 10.1002/ ijc.11197 12800196
38. Caldeira JR Prando EC Quevedo FC Neto FA Rainho CA Rogatto SR CDH1 promoter hypermethylation and E-cadherin protein expression in infiltrating breast cancer BMC Cancer 2006, 6:48 1523210 16512896 10.1186/1471-2407-6-48
39. Friedrichs N Jäger R Paggen E Rudlowski C Merkelbach-Bruse S Schorle H Buettner R Distinct spatial expression patterns of AP-2alpha and AP-2gamma in non-neoplastic human breast and breast cancer Mod Pathol 2005, 18:431-438 10.1038/modpathol.3800292 15467710
40. Pellikainen J Kataja V Ropponen K Kellokoski J Pietiläinen T Böhm J Eskelinen M Kosma VM Reduced nuclear expression of transcription factor AP-2 associates with aggressive breast cancer Clin Cancer Res 2002, 8:3487-3495 12429639
41. Sládek NE Aldehyde dehydrogenase-mediated cellular relative insensitivity to the oxazaphosphorines Curr Pharm Des 1999, 5:607-625 10469894
42. Fadare O Tavassoli FA The phenotypic spectrum of basal-like breast cancers: A critical appraisal Adv Anat Pathol 2007, 14:358-373 10.1097/ PAP.0b013e31814b26fe 17717437
43. Nielsen TO Hsu FD Jensen K Cheang M Karaca G Hu Z Hernandez-Boussard T Livasy C Cowan D Dressler L Akslen LA Ragaz J Gown AM Gilks CB Rijn van de M Perou CM Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma Clin Cancer Res 2004, 10:5367-5374 10.1158/1078-0432.CCR-04-0220 15328174
44. Abd El-Rehim DM Pinder SE Paish CE Bell J Blamey RW Robertson JF Nicholson RI Ellis IO Expression of luminal and basal cytokeratins in human breast carcinoma J Pathol 2004, 203:661-671 10.1002/path.1559 15141381
45. Moriya T Kasajima A Ishida K Kariya Y Akahira J Endoh M Watanabe M Sasano H New trends of immunohistochemistry for making differential diagnosis of breast lesions Med Mol Morphol 2006, 39:8-13 10.1007/ s00795-006-0309-8 16575508
46. Liu ZB Liu GY Yang WT Di GH Lu JS Shen KW Shen ZZ Shao ZM Wu J Triple-negative breast cancer types exhibit a distinct poor clinical characteristic in lymph node-negative Chinese patients Oncol Rep 2008, 20:987-994 18813844
47. Sotiriou C Neo SY McShane LM Korn EL Long PM Jazaeri A Martiat P Fox SB Harris AL Liu ET Breast cancer classification and prognosis based on gene expression profiles from a population-based study Proc Natl Acad Sci USA 2003, 100:10393-10398 193572 12917485 10.1073/pnas.1732912100
48. Noetzel E Veeck J Niederacher D Galm O Horn F Hartmann A Knüchel R Dahl E Promoter methylation-associated loss of ID4 expression is a marker of tumour recurrence in human breast cancer BMC Cancer 2008, 8:154 2435120 18513385 10.1186/1471-2407-8-154
49. Umetani N Mori T Koyanagi K Shinozaki M Kim J Giuliano AE Hoon DS Aberrant hypermethylation of ID4 gene promoter region increases risk of lymph node metastasis in T1 breast cancer Oncogene 2005, 24:4721-4727 10.1038/sj.onc.1208538 15897910
50. de Candia P Akram M Benezra R Brogi E Id4 messenger RNA and estrogen receptor expression: Inverse correlation in human normal breast epithelium and carcinoma Hum Pathol 2006, 37:1032-1041 10.1016/ j.humpath.2006.03.004 16867866
51. Klopocki E Kristiansen G Wild PJ Klaman I Castanos-Velez E Singer G Stohr R Simon R Sauter G Leibiger H Essers L Weber B Hermann K Rosenthal A Hartmann A Dahl E Loss of SFRP1 is associated with breast cancer progression and poor prognosis in early stage tumors Int J Oncol 2004, 25:641-649 15289865
52. Kawano Y Kypta R Secreted antagonists of the Wnt signalling pathway J Cell Sci 2003, 116:2627-2634 10.1242/jcs.00623 12775774
53. Cheang MC Voduc D Bajdik C Leung S McKinney S Chia SK Perou CM Nielsen TO Basal-like breast cancer defined by five biomarkers has superior prognostic value than triple-negative phenotype Clin Cancer Res 2008, 14:1368-1376 10.1158/1078-0432.CCR-07-1658 18316557
54. Arnes JB Bégin LR Stefansson IM Brunet JS Nielsen TO Foulkes WD Akslen LA Expression of EGFR in relation to BRCA1 status, basal-like markers and prognosis in breast cancer J Clin Pathol 2008 18682421
55. Yin X Dewille JW Hai T A potential dichotomous role of ATF3, an adaptive-response gene, in cancer development Oncogene 2008, 27:2118-2127 10.1038/sj.onc.1210861 17952119