|Table of Contents|

[1] Wu Jiansheng, Hu Minjing, Zhou Tong, Weng Jianhong, et al. Support vector machine for prediction of siRNA silencing efficacy [J]. Journal of Southeast University (English Edition), 2006, 22 (4): 501-504. [doi:10.3969/j.issn.1003-7985.2006.04.012]
Copy

Support vector machine for prediction of siRNA silencing efficacy()
Share:

Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]

Volumn:
22
Issue:
2006 4
Page:
501-504
Research Field:
Biological Science and Medical Engineering
Publishing date:
2006-12-30

Info

Title:
Support vector machine for prediction of siRNA silencing efficacy
Author(s):
Wu Jiansheng Hu Minjing Zhou Tong Weng Jianhong Jiang Peng Sun Xiao
State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
Keywords:
short interfering ribonucleic acid(siRNA) support vector machine base-base correlation receive operating characteristic(ROC)curve
PACS:
Q52
DOI:
10.3969/j.issn.1003-7985.2006.04.012
Abstract:
In order to assist the design of short interfering ribonucleic acids(siRNA), 573 non-redundant siRNAs were collected from published literatures and the relationship between siRNAs sequences and RNA interference(RNAi)effect is analyzed by a support vector machine(SVM)based algorithm relied on a base-base correlation(BBC)feature. The results show that the proposed algorithm has the highest area under curve(AUC)value(0.73)of the receive operating characteristic(ROC)curve and the greatest r value(0.43)of the Pearson’s correlation coefficient. This indicates that the proposed algorithm is better than the published algorithms on the collected datasets and that more attention should be paid to the base-base correlation information in future siRNA design.

References:

[1] Fire A, Xu S, Montgomery M K, et al.Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans [J].Nature, 1998, 391(6669):806-811.
[2] Bernstein E, Caudy A A, Hammond S M, et al.Role for a bidentate ribonuclease in the initiation step of RNA interference [J].Nature, 2001, 409(6818):363-366.
[3] Nykanen A, Haley B, Zamore P.ATP requirements and small interfering RNA structure in the RNA interference pathway [J].Cell, 2001, 107(3):309-321.
[4] Saetrom P, Snove O Jr.A comparison of siRNA efficacy predictors [J].Biochem Biophys Res Commun, 2004, 321(1):247-253.
[5] Amarzguioui M, Prydz H.An algorithm for selection of functional siRNA sequences [J].Biochem Biophys Res Commun, 2004, 316(4):1050-1058.
[6] Reynolds A, Leake D, Boese Q, et al.Rational siRNA design for RNA interference [J].Nature Biotech, 2004, 22(3):326-330.
[7] Ui-Tei K, Naito Y, Takahashi F, et al.Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference [J].Nucleic Acids Res, 2004, 32(3):936-948.
[8] Takasaki S, Kotani S, Konagaya A.An effective method for selecting siRNA target sequences in mammalian cells [J].Cell Cycle, 2004, 3(6):790-795.
[9] Vapnik V N.The nature of statistical learning theory [M].Springer, 1995.
[10] Liu Z H, Jiao D, Sun X.Classifying genomics sequences by sequence feature analysis[J].Genomics Proteomics Bioinformatics, 2005, 3(4):201-205.
[11] Egan J P.Signal detection theory and ROC analysis [M].New York:Academic Press, 1975.
[12] Sætrom P, Snöve O J.A comparison of siRNA efficacy predictors [J].Biochem Biophys Res Commun, 2004, 321(1):247-253.

Memo

Memo:
Biographies: Wu Jiansheng(1979—), male, graduate;Sun Xiao(corresponding author), male, doctor, professor, xsun@seu.edu.cn.
Last Update: 2006-12-20