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Volumn 9, Issue 5, 2012, Pages 624-632

Z' factor including siRNA design quality parameter in RNAi screening experiments

Author keywords

Bioinformatics; High content screening; Off targets; Quality control; RNAi; RNAi libraries

Indexed keywords

OLIGONUCLEOTIDE; SMALL INTERFERING RNA;

EID: 84862222160     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.19759     Document Type: Article
Times cited : (11)

References (31)
  • 1
    • 0033003760 scopus 로고    scopus 로고
    • A simple statistical parameter for use in evaluation and validation of high throughput screening assays
    • PMID:10838414
    • Zhang JH, Chung TDY, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 1999; 4:67-73; PMID:10838414; http://dx.doi.org/10.1177/ 108705719900400206.
    • (1999) J Biomol Screen , vol.4 , pp. 67-73
    • Zhang, J.H.1    Chung, T.D.Y.2    Oldenburg, K.R.3
  • 2
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • PMID:9486653
    • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-11; PMID:9486653; http://dx.doi.org/10.1038/35888.
    • (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
  • 4
    • 33645724270 scopus 로고    scopus 로고
    • RNA interference: Perspectives and caveats
    • PMID:19771205
    • Kurreck J. RNA interference: Perspectives and caveats. J RNAi Gene Silencing 2005; 1:50-1; PMID:19771205.
    • (2005) J RNAi Gene Silencing , vol.1 , pp. 50-51
    • Kurreck, J.1
  • 5
    • 28444499697 scopus 로고    scopus 로고
    • Translating RNA interference into therapies for human disease
    • PMID:16296951
    • Mahanthappa N. Translating RNA interference into therapies for human disease. Pharmacogenomics 2005; 6:879-83; PMID:16296951; http://dx.doi.org/10. 2217/14622416.6.8.879.
    • (2005) Pharmacogenomics , vol.6 , pp. 879-883
    • Mahanthappa, N.1
  • 6
    • 23044449556 scopus 로고    scopus 로고
    • First clinical data on RNAi
    • PMID:16055013
    • Whelan J. First clinical data on RNAi. Drug Discov Today 2005; 10:1014-5; PMID:16055013; http://dx.doi.org/10.1016/S1359-6446(05)03547-6.
    • (2005) Drug Discov Today , vol.10 , pp. 1014-1015
    • Whelan, J.1
  • 7
    • 33747036112 scopus 로고    scopus 로고
    • Silent running: The race to the clinic
    • PMID:16900171
    • Silent running: the race to the clinic. Nature 2006; 442:614-5; PMID:16900171; http://dx.doi.org/10.1038/442614a.
    • (2006) Nature , vol.442 , pp. 614-615
  • 8
    • 5644246304 scopus 로고    scopus 로고
    • A cell-based β-lactamase reporter gene assay for the identification of inhibitors of hepatitis C virus replication
    • PMID:15494142
    • Zuck P, Murray EM, Stec E, Grobler JA, Simon AJ, Strulovici B, et al. A cell-based β-lactamase reporter gene assay for the identification of inhibitors of hepatitis C virus replication. Anal Biochem 2004; 334:344-55; PMID:15494142; http://dx.doi.org/10.1016/j.ab.2004.07.031.
    • (2004) Anal Biochem , vol.334 , pp. 344-355
    • Zuck, P.1    Murray, E.M.2    Stec, E.3    Grobler, J.A.4    Simon, A.J.5    Strulovici, B.6
  • 9
    • 20444419344 scopus 로고    scopus 로고
    • Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance
    • PMID:15864305
    • MacKeigan JP, Murphy LO, Blenis J. Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat Cell Biol 2005; 7:591-600; PMID:15864305; http://dx.doi.org/10.1038/ncb1258.
    • (2005) Nat Cell Biol , vol.7 , pp. 591-600
    • MacKeigan, J.P.1    Murphy, L.O.2    Blenis, J.3
  • 10
    • 28444451148 scopus 로고    scopus 로고
    • A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway
    • PMID:16311596
    • Nybakken K, Vokes SA, Lin TY, McMahon AP, Perrimon NA. A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat Genet 2005; 37:1323-32; PMID:16311596; http://dx.doi.org/10.1038/ng1682.
    • (2005) Nat Genet , vol.37 , pp. 1323-1332
    • Nybakken, K.1    Vokes, S.A.2    Lin, T.Y.3    McMahon, A.P.4    Perrimon, N.A.5
  • 11
    • 21844440569 scopus 로고    scopus 로고
    • Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis
    • PMID:15889048
    • Pelkmans L, Fava E, Grabner H, Hannus M, Habermann B, Krausz E, et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 2005; 436:78-86; PMID:15889048; http://dx.doi.org/10.1038/ nature03571.
    • (2005) Nature , vol.436 , pp. 78-86
    • Pelkmans, L.1    Fava, E.2    Grabner, H.3    Hannus, M.4    Habermann, B.5    Krausz, E.6
  • 12
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences
    • PMID:15044091
    • Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 2004; 316:1050-8; PMID:15044091; http://dx.doi.org/10.1016/j.bbrc.2004.02.157.
    • (2004) Biochem Biophys Res Commun , vol.316 , pp. 1050-1058
    • Amarzguioui, M.1    Prydz, H.2
  • 13
    • 0036752785 scopus 로고    scopus 로고
    • RNAi in human cells: Basic structural and functional features of small interfering RNA
    • PMID:12408823
    • Chiu YL, Rana TM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell 2002; 10:549-61; PMID:12408823; http://dx.doi.org/10.1016/S1097-2765(02)00652-4.
    • (2002) Mol Cell , vol.10 , pp. 549-561
    • Chiu, Y.L.1    Rana, T.M.2
  • 14
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • PMID:14567918
    • Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003; 115:209-16; PMID:14567918; http://dx.doi.org/10.1016/ S0092-8674(03)00801-8.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 16
    • 10744225153 scopus 로고    scopus 로고
    • Asymmetry in the assembly of the RNAi enzyme complex
    • PMID:14567917
    • Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003; 115:199-208; PMID:14567917; http://dx.doi.org/10.1016/S0092-8674(03)00759-1.
    • (2003) Cell , vol.115 , pp. 199-208
    • Schwarz, D.S.1    Hutvágner, G.2    Du, T.3    Xu, Z.4    Aronin, N.5    Zamore, P.D.6
  • 17
    • 1642346273 scopus 로고    scopus 로고
    • Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
    • PMID:14769950
    • Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 2004; 32:936-48; PMID:14769950; http://dx.doi.org/10.1093/nar/gkh247.
    • (2004) Nucleic Acids Res , vol.32 , pp. 936-948
    • Ui-Tei, K.1    Naito, Y.2    Takahashi, F.3    Haraguchi, T.4    Ohki-Hamazaki, H.5    Juni, A.6
  • 18
    • 34347229441 scopus 로고    scopus 로고
    • sIR: SiRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database
    • PMID:17540034
    • Shah JK, Garner HR, White MA, Shames DS, Minna JD. sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. BMC Bioinformatics 2007; 8:178; PMID:17540034; http://dx.doi.org/10.1186/1471-2105-8-178.
    • (2007) BMC Bioinformatics , vol.8 , pp. 178
    • Shah, J.K.1    Garner, H.R.2    White, M.A.3    Shames, D.S.4    Minna, J.D.5
  • 19
    • 75649110049 scopus 로고    scopus 로고
    • Selection of hyperfunctional siRNAs with improved potency and specificity
    • PMID:19846596
    • Wang X, Wang X, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ. Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res 2009; 37:152; PMID:19846596; http://dx.doi.org/10.1093/nar/gkp864.
    • (2009) Nucleic Acids Res , vol.37 , pp. 152
    • Wang, X.1    Wang, X.2    Varma, R.K.3    Beauchamp, L.4    Magdaleno, S.5    Sendera, T.J.6
  • 20
    • 0038121109 scopus 로고    scopus 로고
    • Specificity of short interfering RNA determined through gene expression signatures
    • PMID:12746500
    • Semizarov D, Frost L, Sarthy A, Kroeger PA, Halbert DN, Fesik SW. Specificity of short interfering RNA determined through gene expression signatures. Proc Natl Acad Sci USA 2003; 100:6347-52; PMID:12746500; http://dx.doi.org/10.1073/pnas.1131959100.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 6347-6352
    • Semizarov, D.1    Frost, L.2    Sarthy, A.3    Kroeger, P.A.4    Halbert, D.N.5    Fesik, S.W.6
  • 21
    • 3042602447 scopus 로고    scopus 로고
    • Kinetic analysis of the RNAi enzyme complex
    • PMID:15170178
    • Haley B, Zamore PD. Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 2004; 11:599-606; PMID:15170178; http://dx.doi.org/10.1038/ nsmb780.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 599-606
    • Haley, B.1    Zamore, P.D.2
  • 22
    • 0035803583 scopus 로고    scopus 로고
    • Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
    • PMID:11726523
    • Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 2001; 20:6877-88; PMID:11726523; http://dx.doi.org/10.1093/emboj/20.23.6877.
    • (2001) EMBO J , vol.20 , pp. 6877-6888
    • Elbashir, S.M.1    Martinez, J.2    Patkaniowska, A.3    Lendeckel, W.4    Tuschl, T.5
  • 23
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • PMID:17130148
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007; 35:61-5; PMID:17130148; http://dx.doi.org/10.1093/nar/ gkl842.
    • (2007) Nucleic Acids Res , vol.35 , pp. 61-65
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 24
    • 78149391411 scopus 로고    scopus 로고
    • A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export
    • PMID:21048991
    • Wild T, Horvath P, Wyler E, Widmann B, Badertscher L, Zemp I, et al. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLoS Biol 2010; 8:1000522; PMID:21048991; http://dx.doi.org/10.1371/journal.pbio.1000522.
    • (2010) PLoS Biol , vol.8 , pp. 1000522
    • Wild, T.1    Horvath, P.2    Wyler, E.3    Widmann, B.4    Badertscher, L.5    Zemp, I.6
  • 25
    • 0037685280 scopus 로고    scopus 로고
    • Expression profiling reveals off-target gene regulation by RNAi
    • PMID:12754523
    • Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, et al. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 2003; 21:635-7; PMID:12754523; http://dx.doi.org/10.1038/nbt831.
    • (2003) Nat Biotechnol , vol.21 , pp. 635-637
    • Jackson, A.L.1    Bartz, S.R.2    Schelter, J.3    Kobayashi, S.V.4    Burchard, J.5    Mao, M.6
  • 26
    • 33646188259 scopus 로고    scopus 로고
    • 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
    • PMID:16489337
    • Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, et al. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 2006; 3:199-204; PMID:16489337; http://dx.doi.org/10.1038/nmeth854.
    • (2006) Nat Methods , vol.3 , pp. 199-204
    • Birmingham, A.1    Anderson, E.M.2    Reynolds, A.3    Ilsley-Tyree, D.4    Leake, D.5    Fedorov, Y.6
  • 27
    • 33745612464 scopus 로고    scopus 로고
    • Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity
    • PMID:16682560
    • Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, et al. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 2006; 12:1179-87; PMID:16682560; http://dx.doi.org/10.1261/rna.25706.
    • (2006) RNA , vol.12 , pp. 1179-1187
    • Jackson, A.L.1    Burchard, J.2    Schelter, J.3    Chau, B.N.4    Cleary, M.5    Lim, L.6
  • 28
    • 0037440005 scopus 로고    scopus 로고
    • Tolerance for mutations and chemical modifications in a siRNA
    • PMID:12527766
    • Amarzguioui M, Holen T, Babaie E, Prydz H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 2003; 31:589-95; PMID:12527766; http://dx.doi.org/10.1093/nar/gkg147.
    • (2003) Nucleic Acids Res , vol.31 , pp. 589-595
    • Amarzguioui, M.1    Holen, T.2    Babaie, E.3    Prydz, H.4
  • 29
    • 84862209837 scopus 로고    scopus 로고
    • web page
    • HCDC web page, bioinformatics module: [http://hcdc.ethz.ch/index.php? view=article&id=25].
    • Bioinformatics Module
  • 31
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • PMID:7265238
    • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981; 147:195-7; PMID:7265238; http://dx.doi.org/10.1016/0022-2836(81) 90087-5.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.