Searching for Alternative Splicing With a Joint Model on Probe Measurability and Expression Intensities

References

• Benjamini , Y. and Hochberg , Y. 1995 . “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing,” . Journal of the Royal Statistical Society, Series B , 57 : 289 – 300 .
   Web of Science ®Google Scholar
• Brinkman , B. 2004 . “Splice Variants as Cancer Biomarkers,” . Clinical Biochemistry , 37 : 584 – 594 .
   PubMed Web of Science ®Google Scholar
• Castellani , P. , Siri , A. , Rosellini , C. , Infusini , E. , Borsi , L. and Zardi , L. 1986 . “Transformed Human Cells Release Different Fibronectin Variants Than Do Normal Cells,” . Journal of Cell Biology , 103 : 1671 – 1677 .
   PubMed Web of Science ®Google Scholar
• Cheung , H. C. , Baggerly , K. A. , Tsavachidis , S. , Bachinski , L. L. , Neubauer , V. L. , Nixon , T. J. , Aldape , K. D. , Cote , G. J. and Krahe , R. 2008 . “Global Analysis of Aberrant Pre-mRNA Splicing in Glioblastoma Using Exon Expression Arrays,” . BMC Genomics , 9 : 216
   PubMed Web of Science ®Google Scholar
• Cline , M. , Blume , J. , Cawley , S. , Clark , T. , Hu , J. S. , Lu , G. , Salomonis , N. , Wang , H. and Williams , A. 2005 . “ANOSVA: A Statistical Method for Detecting Splice Variation From Expression Data,” . Bioinformatics , 21 : i107 – i115 .
   PubMed Web of Science ®Google Scholar
• David , H. A. and Nagaraja , H. N. 2003 . Order Statistics (3rd ed.) , Hoboken , NJ : Wiley .
   Google Scholar
• French , P. J. , Peeters , J. , Horsman , S. , Duijm , E. , Siccama , I. , Bent , M. J. , Luider , T. M. , Kros , J. M. , Spek , P. and Smitt , P. A. S. 2007 . “Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays,” . Cancer Research , 67 : 5635 – 5642 .
   PubMed Web of Science ®Google Scholar
• Gaidatzis , D. , Jacobeit , K. , Oakeley , E. J. and Stadler , M. B. 2009 . “Overestimation of Alternative Splicing Caused by Variable Probe Characteristics in Exon Arrays,” . Nucleic Acids Research , 37 ( 16 ) : e107
   PubMed Web of Science ®Google Scholar
• Ghosh , A. , Stewart , D. and Matlashewski , G. 2004 . “Regulation of Human p53 Activity and Cell Localization by Alternative Splicing,” . Molecular Cell Biology , 24 : 7987 – 7997 .
   PubMed Web of Science ®Google Scholar
• Grabowski , P. J. and Black , D. L. 2001 . “Alternative RNA Splicing in the Nervous System,” . Progress in Neurobiology , 65 : 289 – 308 .
   PubMed Web of Science ®Google Scholar
• Hubbell , E. 2005 . PLIER: An M-Estimator for Expression Array , Affymetrix White Paper. Santa Clara, CA : Affymetrix Inc .
   Google Scholar
• Ip , J. Y. , Tong , A. , Pan , Q. , Topp , J. D. , Blencowe , B. J. and Lynch , K. W. 2007 . “Global Analysis of Alternative Splicing During T-Cell Activation,” . RNA , 13 : 563 – 572 .
   PubMed Web of Science ®Google Scholar
• Koenker , R. 2005 . Quantile Regression , Cambridge : Cambridge University Press .
   Google Scholar
• Krawczak , M. , Reiss , J. and Cooper , D. N. 1992 . “The Mutational Spectrum of Single Base-Pair Substitutions in mRNA Splice Junctions of Human Genes: Causes and Consequences,” . Human Genetics , 90 : 41 – 54 .
   PubMed Web of Science ®Google Scholar
• Lee , S. B. and Haber , D. A. 2001 . “Wilms Tumor and the WT1 Gene,” . Experimental Cell Research , 264 : 74 – 99 .
   PubMed Web of Science ®Google Scholar
• Maniatis , T. and Tasic , B. 2002 . “Alternative PremRNA Splicing and Proteome Expansion in Metazoans,” . Nature , 418 : 236 – 243 .
   PubMed Web of Science ®Google Scholar
• Matlin , A. J. , Clark , F. and Smith , C. W. J. 2005 . “Understanding Alternative Splicing: Toward a Cellular Code,” . Nature Reviews Molecular Cell Biology , 6 : 386 – 398 .
   PubMed Web of Science ®Google Scholar
• Pan , Q. , Shai , O. , Lee , L. J. , Frey , B. J. and Blencowe , B. J. 2008 . “Deep Surveying of Alternative Splicing Complexity in the Human Transcriptome by High-Throughput Sequencing,” . Nature Genetics , 40 : 1413 – 1415 .
   PubMed Web of Science ®Google Scholar
• Pepe , M. S. 2003 . The Statistical Evaluation of Medical Tests for Classification and Prediction , Oxford : Oxford University Press .
   Google Scholar
• Purdom , E. , Simpson , K. M. , Robinson , M. D. , Conboy , J. G. , Lapuk , A. V. and Speed , T. P. 2008 . “FIRMA: A Method for Detection of Alternative Splicing From Exon Array Data,” . Bioinformatics , 24 : 1707 – 1714 .
   PubMed Web of Science ®Google Scholar
• Scheffer , H. , Van Der Vlies , P. , Burton , M. , Verlind , E. , Moll , A. C. , Imhof , S. M. and Buys , C. H. 2000 . “Two Novel Germline Mutations of the Retinoblastoma Gene (RB1) That Show Incomplete Penetrance, One Splice Site and One Missense,” . Journal of Medical Genetics , 37 : E6
   PubMedGoogle Scholar
• Schwerk , C. and Schulze-Osthoff , K. 2005 . “Regulation of Apoptosis by Alternative Pre-mRNA Splicing,” . Molecular Cell , 19 : 1 – 13 .
   PubMed Web of Science ®Google Scholar
• Steenbergh , P. H. , Hoppener , J. W. , Zandberg , J. , Van de Ven , W. J. , Jansz , H. S. and Lips , C. J. 1984 . “Calcitonin Gene Related Peptide Coding Sequence is Conserved in the Human Genome and is Expressed in Medullary Thyroid Carcinoma,” . Journal of Clinical Endocrinology and Metabolism , 59 : 358 – 360 .
   PubMed Web of Science ®Google Scholar
• Venables , J. P. 2004 . “Aberrant and Alternative Splicing in Cancer,” . Cancer Research , 64 : 7647 – 7654 .
   PubMed Web of Science ®Google Scholar
• Venables , J. P. , Klinck , R. , Bramard , A. , Inkel , L. , Dufresne-Martin , G. , Koh , C. , Gervais-Bird , J. , Lapointe , E. , Froehlich , U. , Durand , M. , Gendron , D. , Rosseau , J. , Thibault , P. , Lucier , J. , Tremblay , K. , Prinos , P. , Wellinger , R. J. , Chabot , B. , Rancourt , C. and Elela , S. A. 2008 . “Identification of Alternative Splicing Markers for Breast Cancer,” . Cancer Research , 68 : 9525
   PubMed Web of Science ®Google Scholar
• Wang , E. T. , Sandberg , R. , Luo , S. , Khrebtukova , I. , Zhang , L. , Mayr , C. , Kingsmore , S. F. , Schroth , G. P. and Burge , C. B. 2008 . “Alternative Isoform Regulation in Human Tissue Transcriptomes,” . Nature , 456 : 470 – 476 .
   PubMed Web of Science ®Google Scholar
• Wang , G. S. and Cooper , T. A. 2007 . “Splicing in Disease: Disruption of the Splicing Code and the Decoding Machinery,” . Nature Reviews Genetics , 8 : 749 – 761 .
   PubMed Web of Science ®Google Scholar
• Wang , H. 2009 . “Inference on Quantile Regression for Heteroscedastic Mixed Models,” . Statistica Sinica , 19 : 1247 – 1261 .
   Web of Science ®Google Scholar
• Xing , Y. , Stoilov , P. , Kapur , K. , Han , A. , Jiang , H. , Shen , S. , Black , D. L. and Wong , W. H. 2008 . “MADS: A New and Improved Method for Analysis of Differential Alternative Splicing by Exon-Tiling Microarrays,” . RNA , 14 : 1470 – 1479 .
   PubMed Web of Science ®Google Scholar
• Xu , Q. , Modrek , B. and Lee , C. 2002 . “Genome-Wide Detection of Tissue-Specific Alternative Splicing in the Human Transcriptome,” . Nucleic Acids Research , 30 : 3754 – 3766 .
   PubMed Web of Science ®Google Scholar
• Yang , Y. 2003 . “Regression With Multiple Candidate Models: Selecting or Mixing?” . Statistica Sinica , 13 : 783 – 809 .
   Web of Science ®Google Scholar
• Yu , K. and Moyeed , R. A. 2001 . “Bayesian Quantile Regression,” . Statistics & Probability Letters , 54 ( 4 ) : 437 – 447 .
   Web of Science ®Google Scholar
• Zweig , M. H. and Campbell , G. 1993 . “Receiver-Operating Characteristic (ROC) Plots: A Fundamental Evaluation Tool in Clinical Medicine,” . Clinical Chemistry , 39 : 561 – 577 .
   PubMed Web of Science ®Google Scholar