TY - JOUR AU - Beer, D. G. AU - Kardia, S. L. AU - Huang, C. C. AU - Giordano, T. J. AU - Levin, A. M. AU - Misek, D. E. PY - 2002 DA - 2002// TI - Gene-expression profiles predict survival of patients with lung adenocarcinoma JO - Nat Med. VL - 8 ID - Beer2002 ER - TY - JOUR AU - Glas, A. M. AU - Kersten, M. J. AU - Delahaye, L. J. AU - Witteveen, A. T. AU - Kibbelaar, R. E. AU - Velds, A. PY - 2005 DA - 2005// TI - Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment JO - Blood. VL - 105 UR - https://doi.org/10.1182/blood-2004-06-2298 DO - 10.1182/blood-2004-06-2298 ID - Glas2005 ER - TY - JOUR AU - Glinsky, G. V. AU - Glinskii, A. B. AU - Stephenson, A. J. AU - Hoffman, R. M. AU - Gerald, W. L. PY - 2004 DA - 2004// TI - Gene expression profiling predicts clinical outcome of prostate cancer JO - J Clin Invest. VL - 113 UR - https://doi.org/10.1172/JCI20032 DO - 10.1172/JCI20032 ID - Glinsky2004 ER - TY - JOUR AU - Pomeroy, S. L. AU - Tamayo, P. AU - Gaasenbeek, M. AU - Sturla, L. M. AU - Angelo, M. AU - McLaughlin, M. E. PY - 2002 DA - 2002// TI - Prediction of central nervous system embryonal tumour outcome based on gene expression JO - Nature. VL - 415 UR - https://doi.org/10.1038/415436a DO - 10.1038/415436a ID - Pomeroy2002 ER - TY - JOUR AU - Veer, L. J. AU - Dai, H. AU - Vijver, M. J. AU - He, Y. D. AU - Hart, A. A. AU - Mao, M. PY - 2002 DA - 2002// TI - Gene expression profiling predicts clinical outcome of breast cancer JO - Nature. VL - 415 UR - https://doi.org/10.1038/415530a DO - 10.1038/415530a ID - Veer2002 ER - TY - JOUR AU - Reis-Filho, J. S. AU - Pusztai, L. PY - 2011 DA - 2011// TI - Gene expression profiling in breast cancer: classification, prognostication, and prediction JO - Lancet. VL - 378 UR - https://doi.org/10.1016/S0140-6736(11)61539-0 DO - 10.1016/S0140-6736(11)61539-0 ID - Reis-Filho2011 ER - TY - JOUR AU - Shi, L. AU - Campbell, G. AU - Jones, W. D. AU - Campagne, F. AU - Wen, Z. AU - Walker, S. J. PY - 2010 DA - 2010// TI - The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models JO - Nat Biotechnol. VL - 28 UR - https://doi.org/10.1038/nbt.1665 DO - 10.1038/nbt.1665 ID - Shi2010 ER - TY - JOUR AU - Su, Z. AU - Łabaj, P. P. AU - Li, S. AU - Thierry-Mieg, J. AU - Thierry-Mieg, D. AU - Shi, W. PY - 2014 DA - 2014// TI - A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium JO - Nat Biotech. VL - 32 UR - https://doi.org/10.1038/nbt.2957 DO - 10.1038/nbt.2957 ID - Su2014 ER - TY - JOUR AU - Djebali, S. AU - Davis, C. A. AU - Merkel, A. AU - Dobin, A. AU - Lassmann, T. AU - Mortazavi, A. PY - 2012 DA - 2012// TI - Landscape of transcription in human cells JO - Nature. VL - 489 UR - https://doi.org/10.1038/nature11233 DO - 10.1038/nature11233 ID - Djebali2012 ER - TY - JOUR AU - Ozsolak, F. AU - Milos, P. M. PY - 2011 DA - 2011// TI - RNA sequencing: advances, challenges and opportunities JO - Nat Rev Genet. VL - 12 UR - https://doi.org/10.1038/nrg2934 DO - 10.1038/nrg2934 ID - Ozsolak2011 ER - TY - JOUR AU - Sultan, M. AU - Schulz, M. H. AU - Richard, H. AU - Magen, A. AU - Klingenhoff, A. AU - Scherf, M. PY - 2008 DA - 2008// TI - A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome JO - Science. VL - 321 UR - https://doi.org/10.1126/science.1160342 DO - 10.1126/science.1160342 ID - Sultan2008 ER - TY - JOUR AU - Ferreira, P. G. AU - Jares, P. AU - Rico, D. AU - Gomez-Lopez, G. AU - Martinez-Trillos, A. AU - Villamor, N. PY - 2014 DA - 2014// TI - Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia JO - Genome Res. VL - 24 UR - https://doi.org/10.1101/gr.152132.112 DO - 10.1101/gr.152132.112 ID - Ferreira2014 ER - TY - JOUR PY - 2013 DA - 2013// TI - Comprehensive molecular characterization of clear cell renal cell carcinoma JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12222 DO - 10.1038/nature12222 ID - ref13 ER - TY - JOUR AU - Volinia, S. AU - Croce, C. M. PY - 2013 DA - 2013// TI - Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer JO - Proc Natl Acad Sci U S A. VL - 110 UR - https://doi.org/10.1073/pnas.1304977110 DO - 10.1073/pnas.1304977110 ID - Volinia2013 ER - TY - JOUR AU - Maris, J. M. AU - Hogarty, M. D. AU - Bagatell, R. AU - Cohn, S. L. PY - 2007 DA - 2007// TI - Neuroblastoma JO - Lancet. VL - 369 UR - https://doi.org/10.1016/S0140-6736(07)60983-0 DO - 10.1016/S0140-6736(07)60983-0 ID - Maris2007 ER - TY - JOUR AU - Oberthuer, A. AU - Berthold, F. AU - Warnat, P. AU - Hero, B. AU - Kahlert, Y. AU - Spitz, R. PY - 2006 DA - 2006// TI - Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification JO - J Clin Oncol. VL - 24 UR - https://doi.org/10.1200/JCO.2006.06.1879 DO - 10.1200/JCO.2006.06.1879 ID - Oberthuer2006 ER - TY - JOUR AU - Ohira, M. AU - Oba, S. AU - Nakamura, Y. AU - Isogai, E. AU - Kaneko, S. AU - Nakagawa, A. PY - 2005 DA - 2005// TI - Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas JO - Cancer Cell. VL - 7 UR - https://doi.org/10.1016/j.ccr.2005.03.019 DO - 10.1016/j.ccr.2005.03.019 ID - Ohira2005 ER - TY - JOUR AU - Oberthuer, A. AU - Hero, B. AU - Berthold, F. AU - Juraeva, D. AU - Faldum, A. AU - Kahlert, Y. PY - 2010 DA - 2010// TI - Prognostic impact of gene expression-based classification for neuroblastoma JO - J Clin Oncol. VL - 28 UR - https://doi.org/10.1200/JCO.2009.27.3367 DO - 10.1200/JCO.2009.27.3367 ID - Oberthuer2010 ER - TY - JOUR AU - Asgharzadeh, S. AU - Pique-Regi, R. AU - Sposto, R. AU - Wang, H. AU - Yang, Y. AU - Shimada, H. PY - 2006 DA - 2006// TI - Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification JO - J Natl Cancer Inst. VL - 98 UR - https://doi.org/10.1093/jnci/djj330 DO - 10.1093/jnci/djj330 ID - Asgharzadeh2006 ER - TY - JOUR AU - Vermeulen, J. AU - Preter, K. AU - Naranjo, A. AU - Vercruysse, L. AU - Roy, N. AU - Hellemans, J. PY - 2009 DA - 2009// TI - Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study JO - Lancet Oncol. VL - 10 UR - https://doi.org/10.1016/S1470-2045(09)70154-8 DO - 10.1016/S1470-2045(09)70154-8 ID - Vermeulen2009 ER - TY - JOUR AU - Pruitt, K. D. AU - Brown, G. R. AU - Hiatt, S. M. AU - Thibaud-Nissen, F. AU - Astashyn, A. AU - Ermolaeva, O. PY - 2014 DA - 2014// TI - RefSeq: an update on mammalian reference sequences JO - Nucleic Acids Res. VL - 42 UR - https://doi.org/10.1093/nar/gkt1114 DO - 10.1093/nar/gkt1114 ID - Pruitt2014 ER - TY - JOUR AU - Thierry-Mieg, D. AU - Thierry-Mieg, J. PY - 2006 DA - 2006// TI - AceView: a comprehensive cDNA-supported gene and transcripts annotation JO - Genome Biol. VL - 7 UR - https://doi.org/10.1186/gb-2006-7-s1-s12 DO - 10.1186/gb-2006-7-s1-s12 ID - Thierry-Mieg2006 ER - TY - JOUR AU - Harrow, J. AU - Frankish, A. AU - Gonzalez, J. M. AU - Tapanari, E. AU - Diekhans, M. AU - Kokocinski, F. PY - 2012 DA - 2012// TI - GENCODE: the reference human genome annotation for The ENCODE Project JO - Genome Res. VL - 22 UR - https://doi.org/10.1101/gr.135350.111 DO - 10.1101/gr.135350.111 ID - Harrow2012 ER - TY - JOUR AU - Guo, L. AU - Lobenhofer, E. K. AU - Wang, C. AU - Shippy, R. AU - Harris, S. C. AU - Zhang, L. PY - 2006 DA - 2006// TI - Rat toxicogenomic study reveals analytical consistency across microarray platforms JO - Nat Biotechnol. VL - 24 UR - https://doi.org/10.1038/nbt1238 DO - 10.1038/nbt1238 ID - Guo2006 ER - TY - JOUR AU - Shi, L. AU - Reid, L. H. AU - Jones, W. D. AU - Shippy, R. AU - Warrington, J. A. AU - Baker, S. C. PY - 2006 DA - 2006// TI - The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements JO - Nat Biotechnol. VL - 24 UR - https://doi.org/10.1038/nbt1239 DO - 10.1038/nbt1239 ID - Shi2006 ER - TY - JOUR AU - Lenos, K. AU - Grawenda, A. M. AU - Lodder, K. AU - Kuijjer, M. L. AU - Teunisse, A. F. AU - Repapi, E. PY - 2012 DA - 2012// TI - Alternate splicing of the p53 inhibitor HDMX offers a superior prognostic biomarker than p53 mutation in human cancer JO - Cancer Res. VL - 72 UR - https://doi.org/10.1158/0008-5472.CAN-12-0215 DO - 10.1158/0008-5472.CAN-12-0215 ID - Lenos2012 ER - TY - JOUR AU - Nishi, T. AU - Lee, P. S. AU - Oka, K. AU - Levin, V. A. AU - Tanase, S. AU - Morino, Y. PY - 1991 DA - 1991// TI - Differential expression of two types of the neurofibromatosis type 1 (NF1) gene transcripts related to neuronal differentiation JO - Oncogene. VL - 6 ID - Nishi1991 ER - TY - JOUR AU - Futreal, P. A. AU - Coin, L. AU - Marshall, M. AU - Down, T. AU - Hubbard, T. AU - Wooster, R. PY - 2004 DA - 2004// TI - A census of human cancer genes JO - Nat Rev Cancer. VL - 4 UR - https://doi.org/10.1038/nrc1299 DO - 10.1038/nrc1299 ID - Futreal2004 ER - TY - BOOK AU - Littell, R. C. AU - Milliken, G. A. AU - Stroup, W. W. AU - Wolfinger, R. D. AU - Schabenberger, O. PY - 2006 DA - 2006// TI - SAS system for mixed models PB - SAS Institute Inc. CY - Cary, NC ID - Littell2006 ER - TY - JOUR AU - Prensner, J. R. AU - Iyer, M. K. AU - Balbin, O. A. AU - Dhanasekaran, S. M. AU - Cao, Q. AU - Brenner, J. C. PY - 2011 DA - 2011// TI - Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression JO - Nat Biotechnol. VL - 29 UR - https://doi.org/10.1038/nbt.1914 DO - 10.1038/nbt.1914 ID - Prensner2011 ER - TY - JOUR AU - Simon, R. PY - 2005 DA - 2005// TI - Roadmap for developing and validating therapeutically relevant genomic classifiers JO - J Clin Oncol. VL - 23 UR - https://doi.org/10.1200/JCO.2005.02.8712 DO - 10.1200/JCO.2005.02.8712 ID - Simon2005 ER - TY - JOUR AU - Garcia, I. AU - Mayol, G. AU - Rios, J. AU - Domenech, G. AU - Cheung, N. K. AU - Oberthuer, A. PY - 2012 DA - 2012// TI - A three-gene expression signature model for risk stratification of patients with neuroblastoma JO - Clin Cancer Res. VL - 18 UR - https://doi.org/10.1158/1078-0432.CCR-11-2483 DO - 10.1158/1078-0432.CCR-11-2483 ID - Garcia2012 ER - TY - JOUR AU - Stricker, T. P. PY - 2014 DA - 2014// TI - Morales La Madrid A, Chlenski A, Guerrero L, Salwen HR, Gosiengfiao Y, et al. Validation of a prognostic multi-gene signature in high-risk neuroblastoma using the high throughput digital NanoString nCounter system JO - Mol Oncol VL - 8 UR - https://doi.org/10.1016/j.molonc.2014.01.010 DO - 10.1016/j.molonc.2014.01.010 ID - Stricker2014 ER - TY - JOUR AU - Brodeur, G. M. AU - Pritchard, J. AU - Berthold, F. AU - Carlsen, N. L. AU - Castel, V. AU - Castelberry, R. P. PY - 1993 DA - 1993// TI - Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment JO - J Clin Oncol. VL - 11 ID - Brodeur1993 ER - TY - JOUR AU - Oberthuer, A. AU - Juraeva, D. AU - Li, L. AU - Kahlert, Y. AU - Westermann, F. AU - Eils, R. PY - 2010 DA - 2010// TI - Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients JO - Pharmacogenomics J. VL - 10 UR - https://doi.org/10.1038/tpj.2010.53 DO - 10.1038/tpj.2010.53 ID - Oberthuer2010 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. M. AU - Kwan, G. AU - Baren, M. J. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotech. VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Pervouchine, D. D. AU - Knowles, D. G. AU - Guigo, R. PY - 2013 DA - 2013// TI - Intron-centric estimation of alternative splicing from RNA-seq data JO - Bioinformatics. VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts678 DO - 10.1093/bioinformatics/bts678 ID - Pervouchine2013 ER - TY - STD TI - Therneau T. A Package for Survival Analysis in S. R package version 2.36-12. 2012. Available at: http://CRAN.R-project.org/package=survival. UR - http://cran.r-project.org/package=survival ID - ref39 ER -