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Volumn 672, Issue , 2011, Pages 341-358

Informatics Approach to the Rational Design of siRNA Libraries

Author keywords

Bioinformatics; Cheminformatics; Gene silencing; QSAR; RNAi; siRNA

Indexed keywords

SMALL INTERFERING RNA;

EID: 79952116683     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-839-3_14     Document Type: Chapter
Times cited : (5)

References (41)
  • 1
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • 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.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 2
    • 4644336023 scopus 로고    scopus 로고
    • Revealing the world of RNA interference
    • Mello, C. C., and Conte, D., Jr. (2004) Revealing the world of RNA interference. Nature 431, 338–342.
    • (2004) Nature , vol.431 , pp. 338-342
    • Mello, C.C.1    Conte, D.2
  • 3
    • 67249096677 scopus 로고    scopus 로고
    • Nonviral methods for siRNA delivery
    • Gao, K., and Huang, L. (2009) Nonviral methods for siRNA delivery. Molecular Phar-maceutics 6, 651–658.
    • (2009) Molecular Phar-Maceutics , vol.6 , pp. 651-658
    • Gao, K.1    Huang, L.2
  • 5
    • 33846614547 scopus 로고    scopus 로고
    • In silico selection of active siRNA
    • Patzel, V. (2007) In silico selection of active siRNA. Drug Discovery Today 12, 139–148.
    • (2007) Drug Discovery Today , vol.12 , pp. 139-148
    • Patzel, V.1
  • 6
    • 3543036224 scopus 로고    scopus 로고
    • Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
    • Saetrom, P. (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20, 3055–3063.
    • (2004) Bioinformatics , vol.20 , pp. 3055-3063
    • Saetrom, P.1
  • 11
    • 39149106448 scopus 로고    scopus 로고
    • Efficient siRNA selection using hybridization thermodynamics
    • Lu, Z. J., and Mathews, D. H. (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research 36, 640–647.
    • (2008) Nucleic Acids Research , vol.36 , pp. 640-647
    • Lu, Z.J.1    Mathews, D.H.2
  • 12
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • Shabalina, S. A., Spiridonov, A. N., and Ogurtsov, A. Y. (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 7, 65.
    • (2006) BMC Bioinformatics , vol.7
    • Shabalina, S.A.1    Spiridonov, A.N.2    Ogurtsov, A.Y.3
  • 13
    • 67649236703 scopus 로고    scopus 로고
    • Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency
    • Klingelhoefer, J. W., Moutsianas, L., and Holmes, C. (2009) Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. Bioinformatics 25, 1594–1601.
    • (2009) Bioinformatics , vol.25 , pp. 1594-1601
    • Klingelhoefer, J.W.1    Moutsianas, L.2    Holmes, C.3
  • 14
    • 0035803583 scopus 로고    scopus 로고
    • Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
    • Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W., and Tuschl, T. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. The EMBO Journal 20, 6877–6888.
    • (2001) The EMBO Journal , vol.20 , pp. 6877-6888
    • Elbashir, S.M.1    Martinez, J.2    Patkaniowska, A.3    Lendeckel, W.4    Tuschl, T.5
  • 15
    • 0036351317 scopus 로고    scopus 로고
    • Analysis of gene function in somatic mammalian cells using small interfering RNAs
    • Elbashir, S. M., Harborth, J., Weber, K., and Tuschl, T. (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26, 199–213.
    • (2002) Methods , vol.26 , pp. 199-213
    • Elbashir, S.M.1    Harborth, J.2    Weber, K.3    Tuschl, T.4
  • 18
    • 33748209616 scopus 로고    scopus 로고
    • Efficient prediction of siR-NAs with siRNArules 1.0: An open-source JAVA approach to siRNA algorithms
    • Holen, T. (2006) Efficient prediction of siR-NAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms. RNA 12, 1620–1625.
    • (2006) RNA , vol.12 , pp. 1620-1625
    • Holen, T.1
  • 21
    • 53749093267 scopus 로고    scopus 로고
    • siDRM: An effective and generally applicable online siRNA design tool
    • 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.
    • (2008) Bioinformatics , vol.24 , pp. 2405-2406
    • Gong, W.1    Ren, Y.2    Zhou, H.3    Wang, Y.4    Kang, S.5    Li, T.6
  • 23
    • 2342564353 scopus 로고    scopus 로고
    • A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: Determinants of gene silencing for use in cell-based screens
    • 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 Research 32, 893–901.
    • (2004) Nucleic Acids Research , vol.32 , pp. 893-901
    • Hsieh, A.C.1    Bo, R.2    Manola, J.3    Vazquez, F.4    Bare, O.5    Khvorova, A.6    Scaringe, S.7    Sellers, W.R.8
  • 24
    • 3542992506 scopus 로고    scopus 로고
    • An effective method for selecting siRNA target sequences in mammalian cells
    • Takasaki, S., Kotani, S., and Konagaya, A. (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle 3, 790–795.
    • (2004) Cell Cycle , vol.3 , pp. 790-795
    • Takasaki, S.1    Kotani, S.2    Konagaya, A.3
  • 25
    • 10744225153 scopus 로고    scopus 로고
    • Asymmetry in the assembly of the RNAi enzyme complex
    • Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208.
    • (2003) Cell , vol.115 , pp. 199-208
    • Schwarz, D.S.1    Hutvagner, G.2    Du, T.3    Xu, Z.4    Aronin, N.5    Zamore, P.D.6
  • 26
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 27
    • 1942488998 scopus 로고    scopus 로고
    • The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region
    • Luo, K. Q., and Chang, D. C. (2004) The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochemical and Biophysical Research Communications 318, 303–310.
    • (2004) Biochemical and Biophysical Research Communications , vol.318 , pp. 303-310
    • Luo, K.Q.1    Chang, D.C.2
  • 30
    • 33845631509 scopus 로고    scopus 로고
    • Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
    • 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 Bioinformatics 7, 516.
    • (2006) BMC Bioinformatics , vol.7
    • Gong, W.1    Ren, Y.2    Xu, Q.3    Wang, Y.4    Lin, D.5    Zhou, H.6    Li, T.7
  • 31
    • 33645822531 scopus 로고    scopus 로고
    • siRecords: An extensive database of mammalian siRNAs with efficacy ratings
    • Ren, Y., Gong, W., Xu, Q., Zheng, X., Lin, D., Wang, Y., and Li, T. (2006) siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics 22, 1027–1028.
    • (2006) Bioinformatics , vol.22 , pp. 1027-1028
    • Ren, Y.1    Gong, W.2    Xu, Q.3    Zheng, X.4    Lin, D.5    Wang, Y.6    Li, T.7
  • 32
    • 58149185133 scopus 로고    scopus 로고
    • siRecords: A database of mammalian RNAi experiments and efficacies
    • Ren, Y., Gong, W., Zhou, H., Wang, Y., Xiao, F., and Li, T. (2009) siRecords: a database of mammalian RNAi experiments and efficacies. Nucleic Acids Research 37, D146–D149.
    • (2009) Nucleic Acids Research , vol.37 , pp. D146-D149
    • Ren, Y.1    Gong, W.2    Zhou, H.3    Wang, Y.4    Xiao, F.5    Li, T.6
  • 33
    • 34447274081 scopus 로고    scopus 로고
    • Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features
    • 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.
    • (2007) BMC Bioinformatics , vol.8
    • Peek, A.S.1
  • 34
    • 33746772726 scopus 로고    scopus 로고
    • Demonstration of two novel methods for predicting functional siRNA efficiency
    • Jia, P., Shi, T., Cai, Y., and Li, Y. (2006) Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics 7, 271.
    • (2006) BMC Bioinformatics , vol.7
    • Jia, P.1    Shi, T.2    Cai, Y.3    Li, Y.4
  • 35
    • 34547650779 scopus 로고    scopus 로고
    • RFRCDB-siRNA: Improved design of siRNAs by random forest regression model coupled with database searching
    • Jiang, P., Wu, H., Da, Y., Sang, F., Wei, J., Sun, X., and Lu, Z. (2007) RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searching. Computer Methods and Programs in Biomedicine 87, 230–238.
    • (2007) Computer Methods and Programs in Biomedicine , vol.87 , pp. 230-238
    • Jiang, P.1    Wu, H.2    Da, Y.3    Sang, F.4    Wei, J.5    Sun, X.6    Lu, Z.7
  • 36
    • 3242890471 scopus 로고    scopus 로고
    • siRNA selection server: An automated siRNA oligonucleotide prediction server
    • Yuan, B., Latek, R., Hossbach, M., Tuschl, T., and Lewitter, F. (2004) siRNA selection server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Research 32, W130–W134.
    • (2004) Nucleic Acids Research , vol.32 , pp. W130-W134
    • Yuan, B.1    Latek, R.2    Hossbach, M.3    Tuschl, T.4    Lewitter, F.5
  • 37
    • 33747869038 scopus 로고    scopus 로고
    • siVirus: Web-based antiviral siRNA design software for highly diver- gent viral sequences
    • Naito, Y., Ui-Tei, K., Nishikawa, T., Takebe, Y., and Saigo, K. (2006) siVirus: web-based antiviral siRNA design software for highly diver- gent viral sequences. Nucleic Acids Research 34, W448–W450.
    • (2006) Nucleic Acids Research , vol.34 , pp. W448-W450
    • Naito, Y.1    Ui-Tei, K.2    Nishikawa, T.3    Takebe, Y.4    Saigo, K.5
  • 38
    • 48449098277 scopus 로고    scopus 로고
    • Oligo-Walk: An online siRNA design tool utilizing hybridization thermodynamics
    • Lu, Z. J., and Mathews, D. H. (2008) Oligo-Walk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research 36, W104–W108.
    • (2008) Nucleic Acids Research , vol.36 , pp. W104-W108
    • Lu, Z.J.1    Mathews, D.H.2
  • 39
    • 48449097534 scopus 로고    scopus 로고
    • AsiDesigner: Exon-based siRNA design server considering alternative splicing
    • Park, Y. K., Park, S. M., Choi, Y. C., Lee, D., Won, M., and Kim, Y. J. (2008) AsiDesigner: exon-based siRNA design server considering alternative splicing. Nucleic Acids Research 36, W97–W103.
    • (2008) Nucleic Acids Research , vol.36 , pp. W97-W103
    • Park, Y.K.1    Park, S.M.2    Choi, Y.C.3    Lee, D.4    Won, M.5    Kim, Y.J.6
  • 40
    • 0032474777 scopus 로고    scopus 로고
    • New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids
    • Sandberg, M., Eriksson, L., Jonsson, J., Sjostrom, M., and Wold, S. (1998) New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. Journal of Medicinal Chemistry 41, 2481–2491.
    • (1998) Journal of Medicinal Chemistry , vol.41 , pp. 2481-2491
    • Sandberg, M.1    Eriksson, L.2    Jonsson, J.3    Sjostrom, M.4    Wold, S.5


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