Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency

Bioinformatics

Volumn 25, Issue 13, 2009, Pages 1594-1601

  Klingelhoefer, Jochen W ^a   Moutsianas, Loukas ^b   Holmes, Chris ^b,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c MRC MAMMALIAN GENETICS UNIT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA INDUCED SILENCING COMPLEX; SMALL INTERFERING RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BAYES THEOREM; COMPUTER SIMULATION; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC DATABASE; HUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; RNA INTERFERENCE; STOCHASTIC MODEL; THERMODYNAMICS; UNCERTAINTY;

ALGORITHMS; BAYES THEOREM; MODELS, GENETIC; RNA INTERFERENCE; RNA, SMALL INTERFERING; RNA-INDUCED SILENCING COMPLEX; SEQUENCE ANALYSIS, RNA;

MAMMALIA;

EID: 67649236703     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp284     Document Type: Article

References (51)

1. Aza-Blanc,P. et al. (2003) Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell, 12, 627-637.
2. Alexandrescu,A. (2001) Modern C++ Design: Generic Programming and Design Patterens Applied. Addision Wesley Professional, Boston.
3. Bernardo,J.M. and Smith,A.F.M. (2000) Bayesian Theory (Wiley Series in Probability and Statistics), Wiley.
4. Ding,Y. et al. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32, W135-W141.
5. Elbashir,S.M. et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
6. Fedorov,Y. et al. (2006) Off-target effects by siRNA can induce toxic phenotype, RNA 12, 1188-1196.
7. Gelman,A. et al. (2003) Bayesian Data Analysis, 2nd edn. ( Texts in Statistical Science), Chapman & Hall/CRC.
8. Giddings,M.C. et al. (2000) ODNBase - a web database for antisense oligonucleotide effectiveness studies. Bioinformatics, 16, 843-844.
9. Gong,W. et al. (2006) Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. BMC Bioinformatics, 7, 516.
10. Gong,W. et al (2008) siDRM: An effective and generally applicable online siRNA design tool, Bioinformatics, 24, 2405-2406.
11. Harboth,J. et al (2003) Sequence, chemical and structural variation of small interfering RNA sans short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev. 13, 83-105.
12. Holen,T. et al. (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res., 30, 1757-1766.
13. Holen,T. (2006) Efficient prediction of siRNAs with siRNArules 1.0: An open-source, JAVA approach to siRNA algorithms. RNA, 12, 1620-1625.
14. Hsieh,A.C. et al. (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.
15. Hu,X. et al. (2004) Relative gene-silencing efficacies of small interefering RNAs targeting sense and antisense transcripts from the same genetic locus. Nucleic Acids Res., 32, 4609-4617.
16. Huesken,D. et al. (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotech., 23, 995-1001.
17. Jackson,A.L. et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotech., 21, 635-637.
18. Jackson,A.L. and Linsey,P.S. (2004) Noise amidst the silence: Off-target effects of siRNAs? Trends Genet., 20, 521-524.
19. Jagla,B. et al. (2005) Sequence characteristics of functional siRNAs. RNA, 6, 864-72.
20. Kass,R.E. and Wasserman,L. (1995) A reference Bayesian test for nested hypotheses and its relationship to the Schwarz criterion, J. Am. Stat. Assoc., 90, 928-934.
21. Kass,R.E. and Raftery,A.E. (1995). Bayes factors. J. Am. Stat. Assoc. 90, 773-795.
22. Katoh,T. and Suzuki,T. (2007) Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Res., 35, e27.
23. Kawasaki,H. et al. (2003) siRNAs generated by recombinant human dicer induce specific and significant but target site-independent gene silencing in human cells. Nucleic Acids Res., 31, 981-987.
24. Khvorova,A. et al. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216
25. Kumar,R. et al. (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Res., 13, 2333-2340.
26. Ladunga,I. (2007) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res., 35, 433-440.
27. Leuschner,P.J.F. et al. (2006) Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep., 7, 314-320.
28. Lodish,H. et al. (2004) Molecular Cell Biology, 5th edn. WH Freeman: New York.
29. Lu,Z.J. and Mathews,D.H. (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res., 36, 640-647.
30. Matveeva,O. et al. (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res., 35, e63.
31. Miyagishi,M. and Taira,K. (2005) siRNA becomes smart and intelligent. Nature Biotech., 23, 946-947.
32. Pancoska,P. et al. (2004) Efficient RNA interference depends on global context of the target sequence: Quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA. Nucleic Acids Res., 32, 1469-1479.
33. Patzel,V. et al. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nature Biotech., 23, 1440-1444.
34. Peek,A.S. (2007) Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features. BMC Bioinformatics, 8, 182-201.
35. Pei,Y. and Tuschl,T. (2006) On the art of identifying effective and specific siRNAs. Nature Meth., 3, 670-676.
36. Persengiev,S. et al. (2004) Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA, 10, 12-18.
37. Phipps,K.A. et al. (2004) Small interfering RNA molecules as potential anti-human rhinovirus agents: In vitro potency, specificity, and mechanism. Antiviral Res., 61, 49-55.
38. Pruit,K.D. et al. (2007) Nucleic Acids Res., 35 Database Issue), D61-D65.
39. Raftery,A.E. (1995) Bayesian model selection in social research. Sociological Meth., 25, 111-163.
40. Ren,Y. et al. (2009) siRecords: A database of mammalian RNAi experiments and efficacies, Nucleic Acids Res., 37, D146-D149.
41. Reynolds,A. et al. (2004) Rational siRNA design for RNA interference. Nat. Biotech., 22, 326-330.
42. Saetrom,P. (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics, 20, 3055-3063.
43. Semizarov,D. et al. (2003) Specificity of short interfering RNA determined through gene expression signatures. PNAS, 100, 6347-6352.
44. Shabalina,S.A. et al. (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics, 7, 65.
45. Shao,Y. et al. (2006) Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res., 34, 5660-5669.
46. Shao,Y. et al. (2007) Effect of target secondary structure on RNAi efficiency. RNA, 13, 1631-1640.
47. Teramoto,R. et al. (2005) Prediction of siRNA functionality using generalized string kernel and support vector machine. FEBS Lett., 579, 2878-2882.
48. Ui-Tei,K. et al. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA intereference. Nucleic Acids Res., 32, 936-948.
49. Vert,J.P. et al. (2007)An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics, 7, 520.
50. Vickers,T.A. et al. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. J. Biol. Chem., 278, 7108-7118.
51. Wang,Y. et al. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex, Nature, 456, 921-926.