siRecords: A database of mammalian RNAi experiments and efficacies

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Ren, Yongliang ^a   Gong, Wuming ^a   Zhou, Haiyan ^a   Wang, Yejun ^a   Xiao, Feifei ^a   Li, Tongbin ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; EXPERIMENTAL STUDY; GENE SILENCING; GENE TARGETING; HUMAN; NONHUMAN; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; RNA INTERFERENCE;

ANIMALS; DATABASES, NUCLEIC ACID; MAMMALS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

MAMMALIA;

EID: 58149185133     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn817     Document Type: Article

References (39)

1. Fire,A., Xu,S., Montgomery,M.K., Kostas,S.A., Driver,S.E. and Mello,C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
2. Gunsalus,K.C. and Piano,F. (2005) RNAi as a tool to study cell biology: building the genome-phenome bridge. Curr. Opin. Cell Biol., 17, 3-8.
3. Xia,X.G., Zhou,H. and Xu,Z. (2005) Promises and challenges in developing RNAi as a research tool and therapy for neurodegenerative diseases. Neurodegener. Dis., 2, 220-231.
4. Kim,D.H. and Rossi,J.J. (2007) Strategies for silencing human disease using RNA interference. Nat. Rev. Genet.,8, 173-184.
5. Hadj-Slimane,R., Lepelletier,Y., Lopez,N., Garbay,C. and Raynaud,F. (2007) Short interfering RNA (siRNA), a novel therapeutic tool acting on angiogenesis. Biochimie, 89, 1234-1244.
6. de Fougerolles,A., Vornlocher,H.P., Maraganore,J. and Lieberman,J. (2007) Interfering with disease: A progress report on siRNA-based therapeutics. Nat. Rev. Drug Discov., 6, 443-453.
7. Kuhn,R., Streif,S. and Wurst,W. (2007) RNA interference in mice. Handbook Exp. Pharmacol., 149-176.
8. Gaither,A. and Iourgenko,V. (2007) RNA interference technologies and their use in cancer research. Curr. Opin. Oncol., 19, 50-54.
9. Inoue,A., Sawata,S.Y. and Taira,K. (2006) Molecular design and delivery of siRNA. J. Drug Target, 14, 448-455.
10. Devi,G.R. (2006) siRNA-based approaches in cancer therapy. Cancer Gene Ther., 13, 819-829.
11. Kurreck,J. (2006) siRNA E.ciency: Structure or Sequence-That Is the Question. J. Biomed. Biotechnol., 2006, 83757.
12. Mittal,V. (2004) Improving the e.ciency of RNA interference in mammals. Nat. Rev. Genet., 5, 355-365.
13. Peek,A.S. and Behlke,M.A. (2007) Design of active small interfering RNAs. Curr. Opin. Mol. Ther., 9, 110-118.
14. Gong,W., Ren,Y., Xu,Q., Wang,Y., Lin,D., Zhou,H. and Li,T. (2006) Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. BMC Bioinform., 7, 516.
15. Patzel,V. (2007) In silico selection of active siRNA. Drug Discov. Today, 12, 139-148.
16. Matveeva,O., Nechipurenko,Y., Rossi,L., Moore,B., Saetrom,P., Ogurtsov,A.Y., Atkins,J.F. and Shabalina,S.A. (2007) Comparison of approaches for rational siRNA design leading to a new effecient and transparent method. Nucleic Acids Res., 35, e63.
17. Holen,T., Amarzguioui,M., Wiiger,M.T., Babaie,E. and Prydz,H. (2002) Positional e.ects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res., 30, 1757-1766.
18. Amarzguioui,M. and Prydz,H. (2004) An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun., 316 1050-1058.
19. Takasaki,S., Kotani,S. and Konagaya,A. (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle, 3, 790-795.
20. Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nat. Biotechnol., 22, 326-330.
21. Wang,L. and Mu,F.Y. (2004) A Web-based design center for vector-based siRNA and siRNA cassette. Bioinformatics, 20, 1818-1820.
22. Cui,W., Ning,J., Naik,U.P. and Duncan,M.K. (2004) OptiRNAi, an RNAi design tool. Comput. Methods Programs Biomed., 75, 67-73.
23. Poliseno,L., Evangelista,M., Mercatanti,A., Mariani,L., Citti,L. and Rainaldi,G. (2004) The energy pro.ling of short interfering RNAs is highly predictive of their activity. Oligonucleotides, 14, 227-232.
24. Khvorova,A., Reynolds,A. and Jayasena,S.D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
25. Hsieh,A.C., Bo,R., Manola,J., Vazquez,F., Bare,O., Khvorova,A., Scaringe,S. and Sellers,W.R. (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: Determinants of gene silencing for use in cell-based screens. Nucleic Acids Res., 32 893-901.
26. Tafer,H., Ameres,S.L., Obernosterer,G., Gebeshuber,C.A., Schroeder,R., Martinez,J. and Hofacker,I.L. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol., 26, 578-583.
27. Shao,Y., Chan,C.Y., Maliyekkel,A., Lawrence,C.E., Roninson,I.B. and Ding,Y. (2007) Effect of target secondary structure on RNAi effeciency. RNA, 13, 1631-1640.
28. Schubert,S., Grunweller,A., Erdmann,V.A. and Kurreck,J. (2005) Local RNA target structure infuences siRNA efficacy: Systematic analysis of intentionally designed binding regions. J. Mol. Biol., 348, 883-893.
29. McManus,M.T., Haines,B.B., Dillon,C.P., Whitehurst,C.E., van Parijs,L., Chen,J. and Sharp,P.A. (2002) Small interfering RNA-mediated gene silencing in T lymphocytes. J. Immunol., 169, 5754-5760.
30. McManus,M.T. and Sharp,P.A. (2002) Gene silencing in mammals by small interfering RNAs. Nat. Rev. Genet., 3, 737-747.
31. Elmaagacli,A.H., Koldeho.,M., Peceny,R., Klein-Hitpass,L., Ottinger,H., Beelen,D.W. and Opalka,B. (2005) WT1 and BCRABL specific small interfering RNA have additive effects in the induction of apoptosis in leukemic cells. Haematologica, 90, 326-334.
32. Nicholson,L.J., Philippe,M., Paine,A.J., Mann,D.A. and Dolphin,C.T. (2005) RNA interference mediated in human primary cells via recombinant baculoviral vectors. Mol. Ther., 11, 638-644.
33. Guan,R., Tapang,P., Leverson,J.D., Albert,D., Giranda,V.L. and Luo,Y. (2005) Small interfering RNA-mediated Polo-like kinase 1 depletion preferentially reduces the survival of p53-defective, oncogenic transformed cells and inhibits tumor growth in animals. Cancer Res. 65, 2698-2704.
34. Spankuch-Schmitt,B., Bereiter-Hahn,J., Kaufmann,M. and Strebhardt,K. (2002) E.ect of RNA silencing of polo-like kinase-1 (PLK1) on apoptosis and spindle formation in human cancer cells. J. Natl Cancer Inst., 94, 1863-1877.
35. Atkinson,P.J., Young,K.W., Ennion,S.J., Kew,J.N., Nahorski,S.R. and Challiss,R.A. (2006) Altered expression of G(q/11alpha) protein shapes mGlu1 and mGlu5 receptor-mediated single cell inositol 1,4,5-trisphosphate and Ca(2+) signaling. Mol. Pharmacol., 69 174-184.
36. Birmingham,A., Anderson,E., Sullivan,K., Reynolds,A., Boese,Q., Leake,D., Karpilow,J. and Khvorova,A. (2007) A protocol for designing siRNAs with high functionality and specificity. Nat. Protoc., 2 2068-2078.
37. Chalk,A.M., Wahlestedt,C. and Sonnhammer,E.L. (2004) Improved and automated prediction of effective siRNA. Biochem. Biophys. Res. Commun., 319, 264-274.
38. Saetrom,P. and Snove,O. (2004) A comparison of siRNA efficacy predictors. Biochem. Biophys. Res. Commun., 321, 247-253.
39. Gong,W., Ren,Y., Zhou,H., Wang,Y., Kang,S. and Li,T. (2008) siDRM: An effective and generally applicable online siRNA design tool. Bioinformatics, 24, 2405-2406.