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References

  • 1
    Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001; 29: 36571.
  • 2
    Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucleic Acids Res 2007; 35: D7605.
  • 3
    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: 5707.
  • 4
    Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2007; 131: 1129.
  • 5
    Vasudevan S, Tong Y, Steitz JA. Switching from repression to activation: microRNAs can up-regulate translation. Science 2007; 318: 19314.
  • 6
    Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev: Cancer 2006; 6: 85766.
  • 7
    He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, Volinia S, Calin GA, Liu CG, Franssila K, Suster S, Kloos RT, Croce CM, et al. The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci USA 2005; 102: 1907580.
  • 8
    Calin GA, Croce CM. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res 2006; 66: 73904.
  • 9
    Bando T, Kato Y, Ihara Y, Yamagishi F, Tsukada K, Isobe M. Loss of heterozygosity of 14q32 in colorectal carcinoma. Cancer Genet Cytogenet 1999; 111: 1615.
  • 10
    Cazals-Hatem D, Rebouissou S, Bioulac-Sage P, Bluteau O, Blanche H, Franco D, Monges G, Belghiti J, Sa Cunha A, Laurent-Puig P, Degott C, Zucman-Rossi J. Clinical and molecular analysis of combined hepatocellular-cholangiocarcinomas. J Hepatol 2004; 41: 2928.
  • 11
    Yoshimoto T, Matsuura K, Karnan S, Tagawa H, Nakada C, Tanigawa M, Tsukamoto Y, Uchida T, Kashima K, Akizuki S, Takeuchi I, Sato F, et al. High-resolution analysis of DNA copy number alterations and gene expression in renal clear cell carcinoma. J Pathol 2007; 213: 392401.
  • 12
    Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3: Article 3.
  • 13
    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): S96104.
  • 14
    Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006; 34: D1404.
  • 15
    Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005; 21: 206775.
  • 16
    Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008; 5: e184.
  • 17
    Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8: 11827.
  • 18
    Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.
  • 19
    Ambs S, Prueitt RL, Yi M, Hudson RS, Howe TM, Petrocca F, Wallace TA, Liu CG, Volinia S, Calin GA, Yfantis HG, Stephens RM, et al. Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res 2008; 68: 616270.
  • 20
    Arndt GM, Dossey L, Cullen LM, Lai A, Druker R, Eisbacher M, Zhang C, Tran N, Fan H, Retzlaff K, Bittner A, Raponi M. Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer. BMC Cancer 2009; 9: 374.
  • 21
    Avissar M, Christensen BC, Kelsey KT, Marsit CJ. MicroRNA expression ratio is predictive of head and neck squamous cell carcinoma. Clin Cancer Res 2009; 15: 28505.
  • 22
    Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, Tavare S, Caldas C, et al. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 2007; 8: R214.
  • 23
    Ferretti E, De Smaele E, Po A, Di Marcotullio L, Tosi E, Espinola MS, Di Rocco C, Riccardi R, Giangaspero F, Farcomeni A, Nofroni I, Laneve P, et al. MicroRNA profiling in human medulloblastoma. Int J Cancer 2009; 124: 56877.
  • 24
    Godlewski J, Nowicki MO, Bronisz A, Williams S, Otsuki A, Nuovo G, Raychaudhury A, Newton HB, Chiocca EA, Lawler S. Targeting of the Bmi-1 oncogene/stem cell renewal factor by microRNA-128 inhibits glioma proliferation and self-renewal. Cancer Res 2008; 68: 912530.
  • 25
    Gramantieri L, Ferracin M, Fornari F, Veronese A, Sabbioni S, Liu CG, Calin GA, Giovannini C, Ferrazzi E, Grazi GL, Croce CM, Bolondi L, et al. Cyclin G1 is a target of miR-122a, a microRNA frequently down-regulated in human hepatocellular carcinoma. Cancer Res 2007; 67: 60929.
  • 26
    Guo Y, Chen Z, Zhang L, Zhou F, Shi S, Feng X, Li B, Meng X, Ma X, Luo M, Shao K, Li N, et al. Distinctive microRNA profiles relating to patient survival in esophageal squamous cell carcinoma. Cancer Res 2008; 68: 2633.
  • 27
    Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Menard S, et al. MicroRNA signatures in human ovarian cancer. Cancer Res 2007; 67: 8699707.
  • 28
    Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V, Ginzinger D, Getts R, Haqq C. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 2006; 5: 24.
  • 29
    Navon R, Wang H, Steinfeld I, Tsalenko A, Ben-Dor A, Yakhini Z. Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PLoS One 2009; 4: e8003.
  • 30
    Pineau P, Volinia S, McJunkin K, Marchio A, Battiston C, Terris B, Mazzaferro V, Lowe SW, Croce CM, Dejean A. miR-221 overexpression contributes to liver tumorigenesis. Proc Natl Acad Sci USA 2010; 107: 2649.
  • 31
    Raponi M, Dossey L, Jatkoe T, Wu X, Chen G, Fan H, Beer DG. MicroRNA classifiers for predicting prognosis of squamous cell lung cancer. Cancer Res 2009; 69: 577683.
  • 32
    Schaefer A, Jung M, Mollenkopf HJ, Wagner I, Stephan C, Jentzmik F, Miller K, Lein M, Kristiansen G, Jung K. Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer 2010; 126: 116676.
  • 33
    Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TL, Kwong DL, Au GK, Liu CG, Calin GA, et al. MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 2008; 299: 42536.
  • 34
    Su H, Yang JR, Xu T, Huang J, Xu L, Yuan Y, Zhuang SM. MicroRNA-101, down-regulated in hepatocellular carcinoma, promotes apoptosis and suppresses tumorigenicity. Cancer Res 2009; 69: 113542.
  • 35
    Tanaka M, Oikawa K, Takanashi M, Kudo M, Ohyashiki J, Ohyashiki K, Kuroda M. Down-regulation of miR-92 in human plasma is a novel marker for acute leukemia patients. PLoS One 2009; 4: e5532.
  • 36
    Ueda T, Volinia S, Okumura H, Shimizu M, Taccioli C, Rossi S, Alder H, Liu CG, Oue N, Yasui W, Yoshida K, Sasaki H, et al. Relation between microRNA expression and progression and prognosis of gastric cancer: a microRNA expression analysis. Lancet Oncol 2010; 11: 13646.
  • 37
    Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 2006; 103: 225761.
  • 38
    Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, Calin GA, Liu CG, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006; 9: 18998.
  • 39
    Agueli C, Cammarata G, Salemi D, Dagnino L, Nicoletti R, La Rosa M, Messana F, Marfia A, Bica MG, Coniglio ML, Pagano M, Fabbiano F, et al. 14q32/miRNA clusters loss of heterozygosity in acute lymphoblastic leukemia is associated with up-regulation of BCL11a. Am J Hematol 2010; 85: 5758.
  • 40
    Choi HJ, Lee H, Kim H, Kwon JE, Kang HJ, You KT, Rhee H, Noh SH, Paik YK, Hyung WJ, Kim H. MicroRNA expression profile of gastrointestinal stromal tumors is distinguished by 14q loss and anatomic site. Int J Cancer 126: 164050.
  • 41
    Bargaje R, Hariharan M, Scaria V, Pillai B. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA 2009; 16: 1625.
  • 42
    Elo LL, Lahti L, Skottman H, Kylaniemi M, Lahesmaa R, Aittokallio T. Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res 2005; 33: e193.
  • 43
    Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, et al. MicroRNA expression profiles classify human cancers. Nature 2005; 435: 8348.
  • 44
    Wong TS, Liu XB, Wong BY, Ng RW, Yuen AP, Wei WI. Mature miR-184 as potential oncogenic microRNA of squamous cell carcinoma of tongue. Clin Cancer Res 2008; 14: 258892.
  • 45
    Bartkova J, Thullberg M, Slezak P, Jaramillo E, Rubio C, Thomassen LH, Bartek J. Aberrant expression of G1-phase cell cycle regulators in flat and exophytic adenomas of the human colon. Gastroenterology 2001; 120: 16808.
  • 46
    Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004; 14: 70815.
  • 47
    Beitz E. TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon. Bioinformatics 2000; 16: 1359.