Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Gupta, Shobhit ^a   Zink, Dorothea ^b   Korn, Bernhard ^b   Vingron, Martin ^a   Haas, Stefan A ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b Geriat Resrc Ctr for Genome Res   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PROTEOME; ISOPROTEIN;

ACCURACY; ALTERNATIVE RNA SPLICING; ARTICLE; CALCULATION; CONTROLLED STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE MAPPING; GENETIC TRANSCRIPTION; PREDICTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TISSUE SPECIFICITY; VALIDATION PROCESS; ANTIBODY SPECIFICITY; BIOLOGY; BRAIN LEVEL; CHEMISTRY; FEMALE; GENETICS; HUMAN; MALE; METABOLISM; METHODOLOGY; PLACENTA; PREDICTIVE VALUE; TESTIS;

ALTERNATIVE SPLICING; BRAIN CHEMISTRY; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; FEMALE; HUMANS; MALE; ORGAN SPECIFICITY; PLACENTA; PREDICTIVE VALUE OF TESTS; PROTEIN ISOFORMS; TESTIS;

EID: 9144258614     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-72     Document Type: Article

References (36)

1. Yan C, Zhao AZ, Bently JK, Beavo JA: The calmodulin-dependent phosphodiesterase gene PDElc encodes several functionally different splice variants in a tissue specific manner. J Biol Chem 1996, 271(41):25699-25706.
2. Karpova AY, Howley PM, Ronco LV: Dual utilization of an acceptor/donor splice site governs the alter native splicing of the IRF-3 gene. Genes Dev 2000, 14(22):2813-2818.
3. Jin X, Turcott E, Englehardt S, Mize GJ, Morris DR: The two upstream open reading frames of oncogene mdm2 have different translational regulatory properties. J Biol Chem 2003, 278(28):25716-25721.
4. Caceras JF, Kornblihtt AR: Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet 2002, 18(4):186-193.
5. Cooper TA, Mattox W: The regulation of splice-site selection and its role in human disease. Am J Hum Genet 1997, 61:259-266.
6. Yamamoto M, Wakatsuki T, Hada A, Ryo A: Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods 2001, 250:45-46.
7. 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(13):2850-2859.
8. Kan Z, States D, Gish W: Selecting for functional alternative splices in ESTs. Genome Res 2002, 12 1837-1845.
9. Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, Muilu J: ASD: the Alternative Splicing Database. Nucleic Acids Res 2004, 32:D64-D69.
10. Coward E, Haas SA, Vingron M: SpliceNest: visualization of gene structure and alternative splicing based on EST clusters. Trends Genet 2002, 18(1):53-55.
11. Gupta S, Zink D, Korn B, Vingron M, Haas SA: Genome-wide identification and classification of alternative splicing based on EST data. Bioinformatics 2004 in press.
12. Xu Q, Modrek B, Lee C: Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res 2002, 30(17):3754-3766.
13. Megy K, Audic S, Claverie J: Heart-specific genes revealed by expressed sequence tag (EST) sampling. Genome Biol 2002, 3(12):RESEARCH0074.
14. Xu Q, Lee C: Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res 2003, 31(19) 5635-5643.
15. Bonaldo MF, Lennon G, Soares MB: Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 1996, 6(9):791-806.
16. Sagerstrom CG, Sun BI, Sive HL: Subtractive cloning: past, present, and future. Annu Rev Biochem 1997, 66:751-783.
17. Schmitt AO, Specht T, Beckmann G, Dahl E, Pilarsky CP, Hinzmann B, Rosenthal A: Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues. Nucleic Acids Res 1999, 27(21):4251-4260.
18. Putilina T, Jaworski C, Gentleman S, McDonald B, Kadiri M, Wong P: Analysis of a human cDNA containing a tissue-specific alternatively spliced LIM domain. Biochem Biophys Res Commun 1998, 252(2):433-439.
19. Wang Z, S LH, Yang H, Gere S, Hu Y, Buetow KH, Lee MP: Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res 2003, 63(3):655-657.
20. Corn PG, El-Deiry WS: Derangement of growth and differentiation control in oncogenesis. Bioassays 2002, 24(1) 83-90.
21. Malumbres M, Carnero A: Cell cycle deregulation: a common motif in cancer. Prog Cell Cycle Res 2003, 5:5-18.
22. Matsushita M, Yamazaki R, Ikeda H, Kawakami Y: Preferentially expressed antigen of melanoma (PRAME) in the development of diagnostic and therapeutic methods for hematological malignancies. Leuk Lymphoma 2003, 44(3):439-444.
23. Hillman RT, Green RE, Brenner SE: An unappreciated role for RNA surveillance. Genome Biol 2004, 5(2):R8.
24. 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 USA 2003, 100(1) 189-192.
25. Hao H, Tyshenko MG, Walker VK: Dihydrofolate reductase of Drosophila. Cloning and expression of a gene with a rare transcript. J Biol Chem 1994, 269(21):15179-15185.
26. Wieder R, Wang H, Shirke S, Wang Q, Menzel T, Feirt N, Jakubowski AA, Gabrilove JL: Low level expression of basic FGF upregulates Bcl-2 and delays apoptosis, but high intracellular levels are required to induce transformation in NIH 3T3 cells. Growth Factors 1997, 15(1):41-60.
27. Geerlings TH, Faber AW, Bister MD, Vos JC, Raue HA: Rio2p, an evolutionarily conserved, low abundant protein kinase essential for processing of 20 S Pre-rRNA in Saccharomyces cerevisiae. J Biol Chem 2003, 278(25):22537-22545.
28. Delaloy C, Lu J, Houot A, Disse-Nicodeme S, Gasc J, Corvol P, Jeunemaitre X: Multiple promoters in the WNKI gene: one controls expression of a kidney-specific kinase-defective isoform. Mol Cell Biol 2003, 24:9208-9221.
29. Phiel CJ, Gabbeta V, Parsons LM, Rothblat D, Harvey RP, McHugh KM: Differential binding of an SRF/NK-2/MEF2 transcription factor complex in normal versus neoplastic smooth muscle tissues. J Biol Chem 2001, 276(37):34637-34650.
30. Naiki T, Nagaki M, Shidoji Y, Kojima H, Imose M, Kato T, Ohishi N, Yagi K, Moriwaki H: Analysis of gene expression profile induced by hepatocybe nuclear factor 4alpha in hepatoma cells using an oligonucleotide microarray. J Biol Chem 2002, 277(16) 14011-14019.
31. Ariel M, McCarrey J, Cedar H: Methylation patterns of testis-specific genes. Proc Natl Acad Sci 1991, 88 2317-2321.
32. Bergman Y, Mostoslavsky R: DNA Methylation: regulation of gene expression and role in immune system. Biochim Biophys Acta 1997, 1333(1):F29-F50.
33. 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(5653):2141-2144.
34. Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M: GeneNest: automated generation and visualization of gene indices. Trends Genet 2000, 16(11):299-300.
35. Haas SA, Hild M, Wright APH, Hain T, Talibi D, Vingron M: Genome-scale design of PCR primers and long oligomers for DNA microarrays Nucleic Acids Res 2003, 31(19):5576-5581.
36. Tureci O, Sahin U, Koslowski M, Buss B, Bell C, Ball-weber P, Zwick C, Eberle T, Zuber M, Villena-Heinsen C, Seitz G, Pfreundschuh M: A novel tumour associated leucine zipper protein targeting to sites of gene transcription and splicing. Oncogene 2002, 21(24) 3879-3888.