MAASE: An alternative splicing database designed for supporting splicing microarray applications

RNA

Volumn 11, Issue 12, 2005, Pages 1767-1776

  Zheng, Christina L ^a,c   Kwon, Young Soo ^b   Hai Ri, L I ^b   Zhang, Kui ^b   Coutinho Mansfield, Gabriela ^b   Yang, Canzhu ^b   Murlidharan Nair, T ^c   Gribskov, Michael ^d   Xiang Dong, F U ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d PURDUE UNIVERSITY   (United States)

Author keywords

Alternative splicing; Database; Manual annotation; Splicing array

Indexed keywords

MESSENGER RNA;

ARTICLE; DATA ANALYSIS; DATA BASE; GENE SEQUENCE; GENOMICS; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN PROCESSING;

ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENOME; MICROARRAY ANALYSIS; RNA SPLICING; RNA, MESSENGER; USER-COMPUTER INTERFACE;

EUKARYOTA;

EID: 28344432224     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2650905     Document Type: Article

References (29)

1. Baelde, H.J., Eikmans, M., van Vliet, A.I., Bergijk, E.C., de Heer, E., and Bruijn, J.A. 2004. Alternatively spliced isoforms of fibronectin in immune-mediated glomerulosclerosis: The role of TGFβ and IL-4. J. Pathol. 204: 248-257.
2. Beck, S., Penque, D., Garcia, S., Gomes, A., Farinha, C., Mata, L., Gulbenkian, S., Gil Ferreira, K., Duarte, A., Pacheco, P., et al. 1999. Cystic fibrosis patients with the 3272-26A→G mutation have mild disease, leaky alternative mRNA splicing, and CFTR protein at the cell membrane. Hum. Mutat. 14: 133-144.
3. Caceres, J.F. and Kornblihtt, A.R. 2002. Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet. 18: 186-193.
4. Clark, T.A., Sugnet, C.W., and Ares Jr., M., 2002. Genome-wide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-910.
5. Cooper, T.A. and Mattox, W. 1997 The regulation of splice site selection, and its role in human disease. Am. J. Hum. Genet. 61: 259-266.
6. Croft, L., Schandorff, S., Clark, F., Burrage, K., Arctander, P., and Mattick, J.S. 2000. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat. Genet. 24: 340-341.
7. Dralyuk, I., Brudno, M., Gelfand, M.S., Zorn, M., and Dubchak, I. 2000. ASDB: Database of alternatively spliced genes. Nucleic Acids Res. 28: 296-297.
8. Dredge, B.K., Polydorides, A.D., and Darnell, R.B. 2001. The splice of life: Alternative splicing and neurological disease. Nat. Rev. Neurosci. 2: 43-50.
9. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
10. Garcia-Blanco, M.A., Baraniak, A.P., and Lasda, E.L. 2004. Alternative splicing in disease and therapy. Nat. Biotechnol. 22: 535-546.
11. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D., and Bairoch, A. 2003. ExPASy: The proteomics server for indepth protein knowledge and analysis. Nucleic Acids Res. 31: 3784-3788.
12. Huang, Y.H., Chen, Y.T., Lai, J.J., Yang, S.T., and Yang, U.C. 2002. PALS db: Putative alternative splicing database. Nucleic Acids Res. 30: 186-190.
13. Ji, H., Zhou, Q., Wen, F., Xia, H., Lu, X., and Li, Y. 2001. AsMamDB: An alternative splice database of mammals. Nucleic Acids Res. 29: 260-263.
14. Jiang, H., Mankodi, A., Swanson, M.S., Moxley, R.T., and Thornton, C.A. 2004. Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons. Hum. Mol. Genet. 13: 3079-3088.
15. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R., and Shoemaker, D.D. 2003. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
16. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. 2003. The UCSC Genome Browser Database. Nucleic Acids Res. 31: 51-54.
17. Kent, W.J. 2002. BLAT - The BLAST-like alignment tool. Genome Res. 12: 656-664.
18. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
19. Lee, C., Atanelov, L., Modrek, B., and Xing, Y. 2003. ASAP: The Alternative Splicing Annotation Project. Nucleic Acids Res. 31: 101-105.
20. Mankodi, A., Takahashi, M.P., Jiang, H., Beck, C.L., Bowers, W.J., Moxley, R.T., Cannon, S.C., and Thornton, C.A. 2002. Expanded CUG repeats trigger aberrant splicing of ClC-1 chloride channel pre-mRNA and hyperexcitability of skeletal muscle in myotonic dystrophy. Mol. Cell 10: 35-44.
21. Modrek, B., Resch, A., Grasso, C., and Lee, C. 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29: 2850-2859.
22. Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D., et al. 2004. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell 16: 929-941.
23. Pospisil, H., Herrmann, A., Bortfeldt, R.H., and Reich, J.G. 2004. EASED: Extended Alternatively Spliced EST Database. Nucleic Acids Res. 32 Database issue: D70-D74.
24. Thabard, W., Barille, S., Collette, M., Harousseau, J.L., Rapp, M.J., Bataille, R., and Amiot, M. 1999. Myeloma cells release soluble interleukin-6Rα in relation to disease progression by two distinct mechanisms: Alternative splicing and proteolytic cleavage. Clin. Cancer Res. 5: 2693-2697.
25. Thanaraj, T.A., Stamm, S., Clark, F., Riethoven, J.J., Le Texier, V., and Muilu, J. 2004. ASD: The Alternative Splicing Database. Nucleic Acids Res. 32 Database issue: D64-D69.
26. Tomonaga, K., Kobayashi, T., Lee, B.J., Watanabe, M., Kamitani, W., and Ikuta, K. 2000. Identification of alternative splicing and negative splicing activity of a nonsegmented negative-strand RNA virus, Borna disease virus. Proc. Natl. Acad. Sci. 97: 12788-12793.
27. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
28. Yeakley, J.M., Fan, J.B., Doucet, D., Luo, L., Wickham, E., Ye, Z., Chee, M.S., and Fu, X.D. 2002. Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol. 20: 353-358.
29. Zheng, C.L., Nair, T.M., Gribskov, M., Kwon, Y.S., Li, H.R., and Fu, X.D. 2004. A database designed to computationally aid an experimental approach to alternative splicing. Pac. Symp. Biocomput. 78-88.