Prioritizing single-nucleotide variations that potentially regulate alternative splicing

BMC Proceedings

Volumn 5, Issue SUPPL. 9, 2011, Pages

  Teng, Mingxiang ^a   Wang, Yadong ^a   Wang, Guohua ^a   Jung, Jeesun ^b   Edenberg, Howard J ^b   Sanford, Jeremy R ^c   Liu, Yunlong ^b  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN;

CONFERENCE PAPER; GENE FREQUENCY; GENETIC IDENTIFICATION; GENETIC TRAIT; GENETIC VARIABILITY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN BINDING; RNA SEQUENCE; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 82455214951     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/1753-6561-5-S9-S40     Document Type: Conference Paper

References (19)

1. Mechanisms of alternative pre-messenger RNA splicing. DL Black, Annu Rev Biochem 2003 72 291 336 10.1146/annurev.biochem.72.121801.161720 12626338 (Pubitemid 36930448)
2. Alternative isoform regulation in human tissue transcriptomes. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB, Nature 2008 456 470 476 10.1038/nature07509 18978772 (Pubitemid 352759009)
3. Alternative splicing in cancer: noise, functional, or systematic? Skotheim RI, Nees M, Int J Biochem Cell Biol 2007 39 1432 1449 10.1016/j.biocel.2007.02.016 17416541 (Pubitemid 47031033)
4. Aberrant RNA splicing and its functional consequences in cancer cells. Fackenthal JD, Godley LA, Dis Model Mech 2008 1 37 425 10.1242/dmm.000331 19048051
5. RNA-binding proteins: modular design for efficient function. Lunde BM, Moore C, Varani G, Nat Rev Mol Cell Biol 2007 8 479 490 10.1038/nrm2178 17473849 (Pubitemid 46809150)
6. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO, PLoS Biol 2008 6 255 10.1371/journal.pbio.0060255 18959479
7. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y, Genome Res 2009 19 381 394 19116412
8. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Ray D, Kazan H, Chan ET, Castillo LP, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR, Nat Biotechnol 2009 27 667 670 10.1038/nbt.1550 19561594
9. SIFT: predicting amino acid changes that affect protein function. Ng PC, Henikoff S, Nucleic Acids Res 2003 31 3812 3814 10.1093/nar/gkg509 12824425 (Pubitemid 37442253)
10. Human non-synonymous SNPs: server and survey. Ramensky V, Bork P, Sunyaev S, Nucleic Acids Res 2002 30 3894 3900 10.1093/nar/gkf493 12202775 (Pubitemid 35012462)
11. SNPs3D: candidate gene and SNP selection for association studies. Yue P, Melamud E, Moult J, BMC Bioinformatics 2006 7 166 10.1186/1471-2105-7-166 16551372
12. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Stone EA, Sidow A, Genome Res 2005 15 978 986 10.1101/gr.3804205 15965030 (Pubitemid 40994218)
13. Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand WH, Samani NJ, et al. Nat Genet 2007 39 1329 1337 10.1038/ng.2007.17 17952073 (Pubitemid 350041542)
14. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Cartegni L, Chew SL, Krainer AR, Nat Rev Genet 2002 3 285 298 10.1038/nrg775 11967553 (Pubitemid 34279797)
15. Genetic Analysis Workshop 17 mini-exome simulation. Almasy LA, Dyer TD, Peralta JM, Kent JW Jr, Charlesworth JC, Curran JE, Blangero J, BMC Proc 2011 5 suppl 9 2 21810212
16. The human genome browser at UCSC. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D, Genome Res 2002 12 996 1006 12045153 (Pubitemid 34662293)
17. What is principal component analysis? Ringner M, Nat Biotechnol 2008 26 303 304 10.1038/nbt0308-303 18327243 (Pubitemid 351355122)
18. CLIP: a method for identifying protein-RNA interaction sites in living cells. Ule J, Jensen K, Mele A, Darnell RB, Methods 2005 37 376 386 10.1016/j.ymeth.2005.07.018 16314267 (Pubitemid 41682508)
19. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH, Nat Struct Mol Biol 2009 16 130 137 10.1038/nsmb.1545 19136955