Gershon D: DNA microarrays: more than gene expression. Nature. 2005, 437: 1195-1198. 10.1038/4371195a.
Article
CAS
PubMed
Google Scholar
Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al: Molecular portraits of human breast tumours. Nature. 2000, 406: 747-752. 10.1038/35021093.
Article
CAS
PubMed
Google Scholar
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 2001, 98: 10869-10874. 10.1073/pnas.191367098.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA. 2003, 100: 8418-8423. 10.1073/pnas.0932692100.
Article
CAS
PubMed
PubMed Central
Google Scholar
van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, et al: Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002, 415: 530-536. 10.1038/415530a.
Article
PubMed
Google Scholar
Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, et al: Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005, 365: 671-679.
Article
CAS
PubMed
Google Scholar
van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002, 347: 1999-2009. 10.1056/NEJMoa021967.
Article
CAS
PubMed
Google Scholar
Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, et al: Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst. 2006, 98: 1183-1192.
Article
CAS
PubMed
Google Scholar
Foekens JA, Atkins D, Zhang Y, Sweep FC, Harbeck N, Paradiso A, Cufer T, Sieuwerts AM, Talantov D, Span PN, et al: Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol. 2006, 24: 1665-1671. 10.1200/JCO.2005.03.9115.
Article
CAS
PubMed
Google Scholar
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000, 403: 503-511. 10.1038/35000501.
Article
CAS
PubMed
Google Scholar
Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI, Gascoyne RD, Muller-Hermelink HK, Smeland EB, Giltnane JM, et al: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med. 2002, 346: 1937-1947. 10.1056/NEJMoa012914.
Article
PubMed
Google Scholar
Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM: A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci USA. 2003, 100: 9991-9996. 10.1073/pnas.1732008100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis RE, Brown KD, Siebenlist U, Staudt LM: Constitutive nuclear factor κB activity is required for survival of activated B cell-like diffuse large B cell lymphoma cells. J Exp Med. 2001, 194: 1861-1874. 10.1084/jem.194.12.1861.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck SG, Gutierrez MC, Elledge R, Mohsin S, Osborne CK, Chamness GC, Allred DC, et al: Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet. 2003, 362: 362-369. 10.1016/S0140-6736(03)14023-8.
Article
CAS
PubMed
Google Scholar
Iwao-Koizumi K, Matoba R, Ueno N, Kim SJ, Ando A, Miyoshi Y, Maeda E, Noguchi S, Kato K: Prediction of docetaxel response in human breast cancer by gene expression profiling. J Clin Oncol. 2005, 23: 422-431. 10.1200/JCO.2005.09.078.
Article
CAS
PubMed
Google Scholar
Ayers M, Symmans WF, Stec J, Damokosh AI, Clark E, Hess K, Lecocke M, Metivier J, Booser D, Ibrahim N, et al: Gene expression profiles predict complete pathologic response to neoadjuvant paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide chemotherapy in breast cancer. J Clin Oncol. 2004, 22: 2284-2293. 10.1200/JCO.2004.05.166.
Article
CAS
PubMed
Google Scholar
Hess KR, Anderson K, Symmans WF, Valero V, Ibrahim N, Mejia JA, Booser D, Theriault RL, Buzdar AU, Dempsey PJ, et al: Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol. 2006, 24: 4236-4244. 10.1200/JCO.2006.05.6861.
Article
CAS
PubMed
Google Scholar
Folgueira MA, Carraro DM, Brentani H, Patrao DF, Barbosa EM, Netto MM, Caldeira JR, Katayama ML, Soares FA, Oliveira CT, et al: Gene expression profile associated with response to doxorubicin-based therapy in breast cancer. Clin Cancer Res. 2005, 11: 7434-7443. 10.1158/1078-0432.CCR-04-0548.
Article
CAS
PubMed
Google Scholar
Dressman HK, Hans C, Bild A, Olson JA, Rosen E, Marcom PK, Liotcheva VB, Jones EL, Vujaskovic Z, Marks J, et al: Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy. Clin Cancer Res. 2006, 12: 819-826. 10.1158/1078-0432.CCR-05-1447.
Article
CAS
PubMed
Google Scholar
Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, et al: A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell. 2004, 5: 607-616. 10.1016/j.ccr.2004.05.015.
Article
CAS
PubMed
Google Scholar
Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, et al: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004, 351: 2817-2826. 10.1056/NEJMoa041588.
Article
CAS
PubMed
Google Scholar
Paik S, Tang G, Shak S, Kim C, Baker J, Kim W, Cronin M, Baehner FL, Watson D, Bryant J, et al: Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol. 2006, 24: 3726-3734. 10.1200/JCO.2005.04.7985.
Article
CAS
PubMed
Google Scholar
Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS: Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res. 2001, 61: 5979-5984.
CAS
PubMed
Google Scholar
Gruvberger-Saal SK, Eden P, Ringner M, Baldetorp B, Chebil G, Borg A, Ferno M, Peterson C, Meltzer PS: Predicting continuous values of prognostic markers in breast cancer from microarray gene expression profiles. Mol Cancer Ther. 2004, 3: 161-168.
CAS
PubMed
Google Scholar
Symmans WF, Sotiriou C, Anderson SK, Hatzis C, Valero V, Booser DJ, Larsimont D, Desmedt C, Gold DL, Sneige N, et al: Measurements of estrogen receptor and reporter genes from microarrays determine receptor status and time to recurrence following adjuvant tamoxifen therapy. Breast Cancer Res Treat. 2005, 94 (Suppl 1): 308a-
Google Scholar
Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, et al: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA. 2005, 102: 13550-13555. 10.1073/pnas.0506230102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kho PS, Wang Z, Zhuang L, Li Y, Chew JL, Ng HH, Liu ET, Yu Q: p53-regulated transcriptional program associated with genotoxic stress-induced apoptosis. J Biol Chem. 2004, 279: 21183-21192. 10.1074/jbc.M311912200.
Article
CAS
PubMed
Google Scholar
Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, et al: Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res. 2006, 66: 10292-10301. 10.1158/0008-5472.CAN-05-4414.
Article
CAS
PubMed
Google Scholar
Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al: Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006, 98: 262-272.
Article
CAS
PubMed
Google Scholar
Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sorlie T, Dai H, He YD, van't Veer LJ, Bartelink H, et al: Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci USA. 2005, 102: 3738-3743. 10.1073/pnas.0409462102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Desai KV, Xiao N, Wang W, Gangi L, Greene J, Powell JI, Dickson R, Furth P, Hunter K, Kucherlapati R, et al: Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc Natl Acad Sci USA. 2002, 99: 6967-6972. 10.1073/pnas.102172399.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang E, Ishida S, Pittman J, Dressman H, Bild A, Kloos M, D'Amico M, Pestell RG, West M, Nevins JR: Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet. 2003, 34: 226-230. 10.1038/ng1167.
Article
CAS
PubMed
Google Scholar
Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, et al: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006, 439: 353-357. 10.1038/nature04296.
Article
CAS
PubMed
Google Scholar
Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, Cragun J, Cottrill H, Kelley MJ, Petersen R, et al: Genomic signatures to guide the use of chemotherapeutics. Nat Med. 2006, 12: 1294-1300. 10.1038/nm1491.
Article
CAS
PubMed
Google Scholar
Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, et al: Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000, 24: 227-235. 10.1038/73432.
Article
CAS
PubMed
Google Scholar
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. 10.1073/pnas.0401994101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, et al: Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA. 2003, 100: 5974-5979. 10.1073/pnas.0931261100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenwald A, Wright G, Wiestner A, Chan WC, Connors JM, Campo E, Gascoyne RD, Grogan TM, Muller-Hermelink HK, Smeland EB, et al: The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. Cancer Cell. 2003, 3: 185-197. 10.1016/S1535-6108(03)00028-X.
Article
CAS
PubMed
Google Scholar
Dai H, van't Veer L, Lamb J, He YD, Mao M, Fine BM, Bernards R, van de Vijver M, Deutsch P, Sachs A, et al: A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res. 2005, 65: 4059-4066. 10.1158/0008-5472.CAN-04-3953.
Article
CAS
PubMed
Google Scholar
Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, et al: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002, 13: 1977-2000. 10.1091/mbc.02-02-0030..
Article
CAS
PubMed
PubMed Central
Google Scholar
Gasch AP, Eisen MB: Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 2002, 3: RESEARCH0059-10.1186/gb-2002-3-11-research0059.
Article
PubMed
PubMed Central
Google Scholar
Peng X, Karuturi RK, Miller LD, Lin K, Jia Y, Kondu P, Wang L, Wong LS, Liu ET, Balasubramanian MK, et al: Identification of cell cycle-regulated genes in fission yeast. Mol Biol Cell. 2005, 16: 1026-1042. 10.1091/mbc.E04-04-0299.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kristensen VN, Edvardsen H, Tsalenko A, Nordgard SH, Sorlie T, Sharan R, Vailaya A, Ben-Dor A, Lonning PE, Lien S, et al: Genetic variation in putative regulatory loci controlling gene expression in breast cancer. Proc Natl Acad Sci USA. 2006, 103: 7735-7740. 10.1073/pnas.0601893103.
Article
CAS
PubMed
PubMed Central
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kauraniemi P, Barlund M, Monni O, Kallioniemi A: New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res. 2001, 61: 8235-8240.
CAS
PubMed
Google Scholar
Ray ME, Yang ZQ, Albertson D, Kleer CG, Washburn JG, Macoska JA, Ethier SP: Genomic and expression analysis of the 8p11-12 amplicon in human breast cancer cell lines. Cancer Res. 2004, 64: 40-47. 10.1158/0008-5472.CAN-03-1022.
Article
CAS
PubMed
Google Scholar
Yang ZQ, Streicher KL, Ray ME, Abrams J, Ethier SP: Multiple interacting oncogenes on the 8p11-p12 amplicon in human breast cancer. Cancer Res. 2006, 66: 11632-11643. 10.1158/0008-5472.CAN-06-2946.
Article
CAS
PubMed
Google Scholar
Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO: Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2004, 2: E7-10.1371/journal.pbio.0020007.
Article
PubMed
PubMed Central
Google Scholar
Adler AS, Lin M, Horlings H, Nuyten DS, van de Vijver MJ, Chang HY: Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet. 2006, 38: 421-430. 10.1038/ng1752.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van't Veer LJ, Perou CM: Concordance among gene-expression-based predictors for breast cancer. N Engl J Med. 2006, 355: 560-569. 10.1056/NEJMoa052933.
Article
CAS
PubMed
Google Scholar