Gilbert W: Why genes in pieces?. Nature. 1978, 271: 501-. 10.1038/271501a0.
CAS
PubMed
Google Scholar
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008, 40: 1413-1415. 10.1038/ng.259.
CAS
PubMed
Google Scholar
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature. 2008, 456: 470-476. 10.1038/nature07509.
CAS
PubMed
PubMed Central
Google Scholar
Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R: GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006, 7: 1-9.
PubMed
Google Scholar
Zavolan M, Van Nimwegen E: The types and prevalence of alternative splice forms. Curr. Opin. Struct. Biol. 2006, 16: 362-367. 10.1016/j.sbi.2006.05.002.
CAS
PubMed
Google Scholar
Black DL: Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003, 72: 291-336. 10.1146/annurev.biochem.72.121801.161720.
CAS
PubMed
Google Scholar
Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, Mitiko : Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene. 2006, 380: 63-71. 10.1016/j.gene.2006.05.015.
CAS
PubMed
Google Scholar
Xing Y, Lee C: Relating alternative splicing to proteome complexity and genome evolution. Adv Exp Med Biol. 2007, 623: 36-49. 10.1007/978-0-387-77374-2_3.
PubMed
Google Scholar
Tazi J, Bakkour N, Stamm S: Alternative splicing and disease. Biochim Biophys Acta. 2009, 1792: 14-26. 10.1016/j.bbadis.2008.09.017.
CAS
PubMed
Google Scholar
Bartel F, Taubert H, Harris LC: Alternative and aberrant splicing of MDM2 mRNA in human cancer. Cancer Cell. 2002, 2: 9-15.
CAS
PubMed
Google Scholar
Hui L, Zhang X, Wu X, Lin Z, Wang Q, Li Y, Hu G: Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment. Oncogene. 2004, 23: 3013-3023. 10.1038/sj.onc.1207362.
CAS
PubMed
Google Scholar
Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, Durand M, Couture S, Froehlich U, Lapointe E, Lucier JF, Thibault P, Rancourt C, Tremblay K, Prinos P, Chabot B, Elela SA: Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol. 2009, 16: 670-676. 10.1038/nsmb.1608.
CAS
PubMed
Google Scholar
Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, Gervais-Bird J, Lapointe E, Froehlich U, Durand M, Gendron D, Brosseau JP, Thibault P, Lucier JF, Tremblay K, Prinos P, Wellinger RJ, Chabot B, Rancourt C, Elela SA: Identification of alternative splicing markers for breast cancer. Cancer Res. 2008, 68: 9525-9531. 10.1158/0008-5472.CAN-08-1769.
CAS
PubMed
Google Scholar
Brinkman BMN: Splice variants as cancer biomarkers. Clinical Biochemistry. 2004, 37: 584-594. 10.1016/j.clinbiochem.2004.05.015.
CAS
PubMed
Google Scholar
Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, Cheng CY, Shih MY, Liu CH, Chen CF: AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs. Bioinformation. 2005, 1: 16-8. 10.6026/97320630001016.
PubMed
PubMed Central
Google Scholar
Modrek B, Resch A, Grasso C, Lee C: Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 2001, 29: 2850-2859. 10.1093/nar/29.13.2850.
CAS
PubMed
PubMed Central
Google Scholar
Kirschbaum-Slager N, Parmigiani RB, Camargo AA, de Souza SJ: Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data. Physiol. Genomics. 2005, 21: 423-432. 10.1152/physiolgenomics.00237.2004.
CAS
PubMed
Google Scholar
Kan Z, Rouchka EC, Gish WR: Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 2001, 5: 889-900.
Google Scholar
Chen FC, Chen CJ, Ho JY, Huang TJ: Identificatyion and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics. 2006, 7: 136-10.1186/1471-2105-7-136.
PubMed
PubMed Central
Google Scholar
Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003, 302: 2141-2144. 10.1126/science.1090100.
CAS
PubMed
Google Scholar
Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y: Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006, 7: 325-10.1186/1471-2164-7-325.
PubMed
PubMed Central
Google Scholar
Cuperlovic-Culf M, Belacel N, Culf AS, Ouellette RJ: Microarray analysis of alternative splicing. OMICS. 2006, 10: 344-357. 10.1089/omi.2006.10.344.
CAS
PubMed
Google Scholar
Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM: Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet. 2008, 40: 1416-1425. 10.1038/ng.264.
CAS
PubMed
PubMed Central
Google Scholar
Ferreira EN, Rangel MC, Pineda PB, Vidal DO, Camargo AA, Souza SJ, Carraro DM: Heteroduplex formation and S1 digestion for mapping alternative splicing sites. Genet Mol Res. 2008, 7: 958-969. 10.4238/vol7-3X-Meeting012.
CAS
PubMed
Google Scholar
Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P: Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nat Methods. 2004, 3: 233-239.
Google Scholar
Thill G, Casteli V, Pallud S, Salanoubat M, Wincker P, de la Grange P, Auboet D, Schachter V, Weissenbach J: ASEtrap: a biological method for speeding up the exploration of spliceomes. Genome Res. 2006, 16: 776-786. 10.1101/gr.5063306.
CAS
PubMed
PubMed Central
Google Scholar
Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A: Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 1999, 27: 1558-1560. 10.1093/nar/27.6.1558.
CAS
PubMed
PubMed Central
Google Scholar
Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res. 1999, 9: 868-877. 10.1101/gr.9.9.868.
CAS
PubMed
PubMed Central
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12: 996-1006.
CAS
PubMed
PubMed Central
Google Scholar
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998, 9: 967-974.
Google Scholar
Maere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics. 2005, 21: 3448-3449. 10.1093/bioinformatics/bti551.
CAS
PubMed
Google Scholar
Lewis BP, Green RE, Brenner SE: Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A. 2003, 7: 189-192.
Google Scholar
Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE: Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics. 2003, 19: i118-21. 10.1093/bioinformatics/btg1015.
PubMed
Google Scholar
Venables JP, Koh CS, Froehlich U, Lapointe E, Couture S, Inkel L, Bramard A, Paquet ER, Watier V, Durand M, Lucier JF, Gervais-Bird J, Tremblay K, Prinos P, Klinck R, Elela SA, Chabot B: Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol. 2008, 28: 6033-6043. 10.1128/MCB.00726-08.
CAS
PubMed
PubMed Central
Google Scholar
Nardi A, Pomari E, Zambon D, Belvedere P, Colombo L, Dalla Valle L: Transcriptional control of human steroid sulfatase. J Steroid Biochem Mol Biol. 2009
Google Scholar
Jiang Z, Cote J, Kwon JM, Goate AM, Wu JY: Aberrant splicing of tau pre-mRNA caused by intronic mutations associated with the inherited dementia frontotemporal dementia with Parkinson linked cromossome 17. Molecular and Cellular Biology. 2000, 20: 4036-4048. 10.1128/MCB.20.11.4036-4048.2000.
CAS
PubMed
PubMed Central
Google Scholar
Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD: Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A. 1996, 93: 6025-6030. 10.1073/pnas.93.12.6025.
CAS
PubMed
PubMed Central
Google Scholar
Albanell J, Baselga J: Unraveling resistance to trastuzumab (Herceptin): insulin-like growth factor-I receptor, a new suspect. J Natl Cancer Inst. 2001, 93: 1830-183. 10.1093/jnci/93.24.1830.
CAS
PubMed
Google Scholar
Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, Baselga J, Norton L: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med. 2001, 344: 783-92. 10.1056/NEJM200103153441101.
CAS
PubMed
Google Scholar
Kumar CC, Madison V: Drugs targeted against protein kinases. Expert Opin Emerg Drugs. 2001, 6: 303-315. 10.1517/14728214.6.2.303.
CAS
PubMed
Google Scholar
Slamon D, Pegram M: Rationale for trastuzumab (Herceptin) in adjuvant breast cancer trials. Semin Oncol. 2001, 28: 13-19.
CAS
PubMed
Google Scholar
Harris RA, Eichholtz TJ, Hiles ID, Page MJ, O'Hare MJ: New model of ErbB-2 over-expression in human mammary luminal epithelial cells. Int J Cancer. 1999, 80: 477-484. 10.1002/(SICI)1097-0215(19990129)80:3<477::AID-IJC23>3.0.CO;2-W.
CAS
PubMed
Google Scholar
Press MF, Hung G, Godolphin W, Slamon DJ: Sensitivity of HER-2/neu antibodies in archival tissue samples: potential source of error in immunohistochemical studies of oncogene expression. Cancer Res. 1994, 54: 2771-2777.
CAS
PubMed
Google Scholar
Stamps AC, Davies SC, Burman J, O'Hare MJ: Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct. Int. J. Cancer. 1994, 57: 865-874. 10.1002/ijc.2910570616.
CAS
PubMed
Google Scholar
Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O’Hare MJ, Neville AM, Simpson AJG, Strausberg RL: Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. PNAS. 2003, 100: 4701-4705.
Google Scholar
dos Santos ML, Palanch CG, Salaorni S, Da Silva WA, Nagai MA: Transcriptome characterization of human mammary cell lines expressing different levels of ERBB2 by serial analysis of gene expression. Int J Oncol. 2006, 28: 1441-1461.
PubMed
Google Scholar
Fiori JL, Zhu TN, O'Connell MP, Hoek KS, Indig FE, Frank BP, Morris C, Kole S, Hasskamp J, Elias G, Weeraratna AT, Bernier M: Filamin A modulates kinase activation and intracellular trafficking of epidermal growth factor receptors in human melanoma cells. Endocrinology. 2009, 150: 2551-2560. 10.1210/en.2008-1344.
CAS
PubMed
PubMed Central
Google Scholar
Mukherji M, Brill LM, Ficarro SB, Hampton GM, Schultz PG: A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways. Biochemistry. 2006, 45: 15529-15540. 10.1021/bi060971c.
CAS
PubMed
Google Scholar
Yi J, Beckerle MC: The human TRIP6 gene encodes a LIM domain protein and maps to chromosome 7q22, a region associated with tumorigenesis. Genomics. 1998, 49: 314-316. 10.1006/geno.1998.5248.
CAS
PubMed
Google Scholar
Wang Y, Dooher JE, Koedood Zhao M, Gilmore TD: Characterization of mouse Trip6: a putative intracellular signaling protein. Gene. 1999, 234: 403-409. 10.1016/S0378-1119(99)00168-7.
CAS
PubMed
Google Scholar
Xu J, Lai YJ, Lin WC, Lin FT: TRIP6 enhances lysophosphatidic acid-induced cell migration by interacting with the lysophosphatidic acid 2 receptor. J Biol Chem. 2004, 279: 10459-10468.
CAS
PubMed
Google Scholar
Chastre E, Abdessamad M, Kruglov A, Bruyneel E, Bracke M, Di Gioia Y, Beckerle MC, van Roy F, Kotelevets L: TRIP6, a novel molecular partner of the MAGI-1 scaffolding molecule, promotes invasiveness. FASEB J. 2009, 23: 916-928. 10.1096/fj.08-106344.
CAS
PubMed
Google Scholar
Holt RA, Jones SJ: The new paradigm of flow cell sequencing. Genome Res. 2008, 18: 839-846. 10.1101/gr.073262.107.
CAS
PubMed
Google Scholar
Glisin V, Crkvenjakov R, Byus C: Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry. 1974, 13: 2633-2637. 10.1021/bi00709a025.
CAS
PubMed
Google Scholar
Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ: Sense-antisense pairs in mammals: Functional and evolutionary considerations. Genome Biol. 2007, 8: R40-10.1186/gb-2007-8-3-r40.
PubMed
PubMed Central
Google Scholar