Brennan DJ, Kelly C, Rexhepaj E, Dervan PA, Duffy MJ, Gallagher WM: Contribution of DNA and tissue microarray technology to the identification and validation of biomarkers and personalized medicine in breast cancer. Cancer Genomics Proteomics. 2007, 4: 121-134.
CAS
PubMed
Google Scholar
Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer patients. New Engl J Med. 2004, 351: 2817-2826. 10.1056/NEJMoa041588.
Article
CAS
PubMed
Google Scholar
Almeida A, Paul Thiery J, Magdelénat H, Radvanyi F: Gene expression analysis by real-time reverse transcription polymerase chain reaction: influence of tissue handling. Anala Biochem. 2004, 328: 101-108. 10.1016/j.ab.2004.02.004.
Article
CAS
Google Scholar
Spruessel A, Steimann G, Jung M, Lee SA, Carr T, Fentz AK, Spangenberg J, Zornig C, Juhl HH, David KA: Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques. 2004, 36: 1030-1037.
CAS
PubMed
Google Scholar
Mager SR, Oomen MH, Morente MM, Ratcliffe C, Knox K, Kerr DJ, Pezzella F, Riegman PH: Standard operating procedure for the collection of fresh frozen tissue samples. Eur J Cancer. 2007, 43: 828-834. 10.1016/j.ejca.2007.01.002.
Article
CAS
PubMed
Google Scholar
Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T: Effects of ischemia on gene expression. J Surg Res. 2001, 99: 222-227. 10.1006/jsre.2001.6195.
Article
CAS
PubMed
Google Scholar
Blackhall FH, Pintilie M, Wigle DA, Jurisica I, Liu N, Radulovich N, Johnston MR, Keshavjee S, Tsao MS: Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection. Neoplasia. 2004, 6: 761-767. 10.1593/neo.04301.
Article
PubMed
PubMed Central
Google Scholar
Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, Rubin MA: Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. Am J Pathol. 2002, 161: 1743-1748.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miyatake Y, Ikeda H, Michimata R, Koizumi S, Ishizu A, Nishimura N, Yoshiki T: Differential modulation of gene expression among rat tissues with warm ischemia. Exp Mol Pathol. 2004, 77: 222-230. 10.1016/j.yexmp.2004.07.004.
Article
CAS
PubMed
Google Scholar
Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, Van't Veer L, Piccart M, Bontempi G, Sotiriou C: Comparison of Prognostic Gene Expression signatures for Breast Cancer. BMC Genomics. 2008, 9: 394-10.1186/1471-2164-9-394.
Article
PubMed
PubMed Central
Google Scholar
Cappelletti V, Gariboldi M, De Cecco L, Toffanin S, Reid JF, Lusa L, Bajetta E, Celio L, Greco M, Fabbri A, Pierotti MA, Daidone MG: Patterns and changes in gene expression following neo-adjuvant anti-estrogen treatment in estrogen receptor-positive breast cancer. Endocr Relat Cancer. 2008, 15: 439-449. 10.1677/ERC-07-0274.
Article
CAS
PubMed
Google Scholar
Gorla L, Cantu M, Miccichè F, Patelli C, Mondellini P, Pierotti MA, Bongarzone I: RET oncoproteins induce tyrosine phosphorylation changes of proteins involved in RNA metabolism. Cell Signal. 2006, 18: 2272-2282. 10.1016/j.cellsig.2006.05.016.
Article
CAS
PubMed
Google Scholar
Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C: BioArray Software Environment (BASE): A Platform for Comprehensive Management and Analysis of Microarray Data. Genome Biology. 2002, 3: software0003.1-0003.6. 10.1186/gb-2002-3-8-software0003.
Article
Google Scholar
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 3: e15-10.1093/nar/30.4.e15.
Article
Google Scholar
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y: Analysis of Gene Expression Data Using BRB-Array Tools. Cancer Informatics. 2007, 3: 11-17.
PubMed
PubMed Central
Google Scholar
Diehn M, Sherlock G, Binkley G, Jin H, Metese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003, 31: 219-223. 10.1093/nar/gkg014.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN: MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biology. 2003, 4: R27-10.1186/gb-2003-4-4-r27.
Article
PubMed
PubMed Central
Google Scholar
Beekman JM, Reischl J, Henderson D, Bauer D, Ternes R, Peña C, Lathia C, Heubach JF: Recovery of microarray-quality RNA from frozen EDTA blood samples. J Pharmacol Toxicol Methods. 2009, 59: 44-49. 10.1016/j.vascn.2008.10.003.
Article
CAS
PubMed
Google Scholar
Fleige S, Walf V, Huch S, Prgomet C, Sehm J, Pfaffl MW: Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol Lett. 2006, 28: 1601-1613. 10.1007/s10529-006-9127-2.
Article
CAS
PubMed
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Stat Soc, Ser B. 1995, 57: 289-300.
Google Scholar
Rommel C, Camps M, Ji H: PI3K delta and PI3K gamma: partners in crime in inflammation in rheumatoid arthritis and beyond?. Nat Rev Immunol. 2007, 3: 191-201. 10.1038/nri2036.
Article
Google Scholar
Lee KS, Park SJ, Kim SR, Min KH, Jin SM, Puri KD, Lee YC: Phosphoinositide 3-kinase-delta inhibitor reduces vascular permeability in a murine model of asthma. J Allergy Clin Immunol. 2006, 118: 403-9. 10.1016/j.jaci.2006.04.041.
Article
CAS
PubMed
Google Scholar
Ivanov SV, Salnikow K, Ivanova AV, Bai L, Lerman MI: Hypoxic repression of STAT1 and its downstream genes by a pVHL/HIF-1 target DEC1/STRA13. Oncogene. 2007, 26: 802-12. 10.1038/sj.onc.1209842.
Article
CAS
PubMed
Google Scholar
Huang Q, Gumireddy K, Schrier M, le Sage C, Nagel R, Nair S, Egan DA, Li A, Huang G, Klein-Szanto AJ, Gimotty PA, Katsaros D, Coukos G, Zhang L, Puré E, Agami R: The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat Cell Biol. 2008, 10: 202-210. 10.1038/ncb1681.
Article
CAS
PubMed
Google Scholar
Diaz LK, Zhou X, Wright ET, Cristofanilli M, Smith T, Yang Y, Sneige N, Sahin A, Gilcrease MZ: CD44 expression is associated with increased survival in node-negative invasive breast carcinoma. Clin Cancer Res. 2005, 11: 3309-3314. 10.1158/1078-0432.CCR-04-2184.
Article
CAS
PubMed
Google Scholar
Lopez JI, Camenisch TD, Stevens MV, Sands BJ, McDonald J, Schroeder JA: CD44 attenuates metastatic invasion during breast cancer progression. Cancer Res. 2005, 65: 6755-6763. 10.1158/0008-5472.CAN-05-0863.
Article
CAS
PubMed
Google Scholar
Meijer D, Sieuwerts AM, Look MP, van Agthoven T, Foekens JA, Dorssers LC: Fibroblast growth factor receptor 4 predicts failure on tamoxifen therapy in patients with recurrent breast cancer. Endocr Relat Cancer. 2008, 15: 101-111. 10.1677/ERC-07-0080.
Article
CAS
PubMed
Google Scholar
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, Rijn van de M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lønning P, Børresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumour subclasses with clinical implications. Proc Natl Acad Sci. 2001, 98: 10869-10874. 10.1073/pnas.191367098.
Article
CAS
PubMed
PubMed Central
Google Scholar
Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C: Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol. 2007, 25: 1239-1246. 10.1200/JCO.2006.07.1522.
Article
CAS
PubMed
Google Scholar
Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, Rijn van de 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
Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JE, Liu ET, Bergh J, Kuznetsov VA, Miller LD: 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
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: 530-536. 10.1038/415530a.
Article
Google Scholar
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: 96-10.1186/1471-2164-7-96.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA: Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005, 365: 671-679.
Article
CAS
PubMed
Google Scholar
Paik S, Tang G, Shak S, Kim C, Baker J, Kim W: 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
Stoner M, Saville B, Wormke M, Dean D, Burghardt R, Safe S: Hypoxia induces proteasome-dependent degradation of estrogen receptor alpha in ZR-75 breast cancer cells. Mol Endocrinol. 2002, 16: 2231-2242. 10.1210/me.2001-0347.
Article
CAS
PubMed
Google Scholar
Cooper C, Liu GY, Niu YL, Santos S, Murphy LC, Watson PH: Intermittent hypoxia induces proteasome-dependent down-regulation of estrogen receptor alpha in human breast carcinoma. Clin Cancer Res. 2004, 10: 8720-8727. 10.1158/1078-0432.CCR-04-1235.
Article
CAS
PubMed
Google Scholar
Helczynska K, Kronblad A, Jogi A, Nilsson E, Beckman S, Landberg G, Palman S: Hypoxia promotes a dedifferentiated phenotype in ductal breast carcinoma in situ. Cancer Res. 2003, 63: 1441-1444.
CAS
PubMed
Google Scholar
Bos R, Zhong H, Hanrahan CF, Mommers EC, Semenza GL, Pinedo HM, Abeloff MD, Simons JW, van Diest PJ, Wall van der E: Levels of hypoxia-inducible factor-1 alpha during breast carcinogenesis. J Natl Cancer Inst. 2001, 93: 309-314. 10.1093/jnci/93.4.309.
Article
CAS
PubMed
Google Scholar