메뉴 건너뛰기




Volumn 27, Issue 19, 2011, Pages 2707-2713

Contextual analysis of RNAI-based functional screens using interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS C VIRUS;

EID: 80053452300     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr469     Document Type: Article
Times cited : (11)

References (50)
  • 1
    • 69549110058 scopus 로고    scopus 로고
    • Knowledge based identification of essential signaling from genome-scale siRNA experiments
    • Bankhead,A. et al. (2009) Knowledge based identification of essential signaling from genome-scale siRNA experiments. BMC Syst. Biol., 3, 80.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 80
    • Bankhead, A.1
  • 2
    • 78149489180 scopus 로고    scopus 로고
    • RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells
    • Bauer,J.A. et al. (2010) RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells. Breast Cancer Res., 12, R41.
    • (2010) Breast Cancer Res. , vol.12
    • Bauer, J.A.1
  • 3
    • 12144289681 scopus 로고    scopus 로고
    • A large-scale RNAi screen in human cells identifies new components of the p53 pathway
    • Berns,K. et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature, 428, 431-437.
    • (2004) Nature , vol.428 , pp. 431-437
    • Berns, K.1
  • 4
    • 68349112682 scopus 로고    scopus 로고
    • Statistical methods for analysis of high-throughput RNA interference screens
    • Birmingham,A. et al. (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat. Methods, 6, 569-575.
    • (2009) Nat. Methods , vol.6 , pp. 569-575
    • Birmingham, A.1
  • 5
    • 39349097864 scopus 로고    scopus 로고
    • Identification of host proteins required for HIV infection through a functional genomic screen
    • Brass,A. et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science, 15, 921-926.
    • (2008) Science , vol.15 , pp. 921-926
    • Brass, A.1
  • 6
    • 72549116887 scopus 로고    scopus 로고
    • The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus
    • Brass,A.L. et al. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell, 139, 1243-1254.
    • (2009) Cell , vol.139 , pp. 1243-1254
    • Brass, A.L.1
  • 7
    • 20844450402 scopus 로고    scopus 로고
    • Differential network expression during drug and stress response
    • Cabusora,L. et al. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
    • (2005) Bioinformatics , vol.21 , pp. 2898-2905
    • Cabusora, L.1
  • 8
    • 78149465975 scopus 로고    scopus 로고
    • A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity
    • Chia,N.Y. et al. (2010) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature, 468, 316-320.
    • (2010) Nature , vol.468 , pp. 316-320
    • Chia, N.Y.1
  • 9
    • 39049097168 scopus 로고    scopus 로고
    • Median absolute deviation to improve hit selection for genomescale RNAi screens
    • Chung,N. et al. (2008) Median absolute deviation to improve hit selection for genomescale RNAi screens. J. Biomol. Screen., 13, 149-158.
    • (2008) J. Biomol. Screen. , vol.13 , pp. 149-158
    • Chung, N.1
  • 10
    • 76249128583 scopus 로고    scopus 로고
    • Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles
    • Corless,L. et al. (2010) Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles. J. Gen. Virol., 91, 362-372.
    • (2010) J. Gen. Virol. , vol.91 , pp. 362-372
    • Corless, L.1
  • 11
    • 34447265020 scopus 로고    scopus 로고
    • Herpes simplex virus type 1 cytoplasmic envelopment requires functional Vps4
    • Crump,C.M. et al. (2007) Herpes simplex virus type 1 cytoplasmic envelopment requires functional Vps4. J. Virol., 81, 7380-7387.
    • (2007) J. Virol. , vol.81 , pp. 7380-7387
    • Crump, C.M.1
  • 12
    • 18244400410 scopus 로고    scopus 로고
    • Functional genomic analysis of the Wnt-wingless signaling pathway
    • DasGupta,R. et al. (2005) Functional genomic analysis of the Wnt-wingless signaling pathway. Science, 308, 826-833.
    • (2005) Science , vol.308 , pp. 826-833
    • DasGupta, R.1
  • 13
    • 60749090295 scopus 로고    scopus 로고
    • Gene-set analysis and reduction
    • Dinu,I. et al. (2009) Gene-set analysis and reduction. Brief. Bioinformatics, 10, 24-34.
    • (2009) Brief. Bioinformatics , vol.10 , pp. 24-34
    • Dinu, I.1
  • 14
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: an integrated exact approach
    • Dittrich,M.T. et al. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231.
    • (2008) Bioinformatics , vol.24
    • Dittrich, M.T.1
  • 15
    • 33646187810 scopus 로고    scopus 로고
    • High-throughput RNAi screening in cultured cells: a user's guide
    • Echeverri,C.J. and Perrimon,N. (2006) High-throughput RNAi screening in cultured cells: a user's guide. Nat. Rev. Genet., 7, 373-384.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 373-384
    • Echeverri, C.J.1    Perrimon, N.2
  • 16
    • 17944363138 scopus 로고    scopus 로고
    • Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding
    • Garrus,J.E. et al. (2001) Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell, 107, 55-65.
    • (2001) Cell , vol.107 , pp. 55-65
    • Garrus, J.E.1
  • 17
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: methodological issues
    • Goeman,J.J. and Buhlmann,P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987.
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Buhlmann, P.2
  • 18
    • 80053442100 scopus 로고    scopus 로고
    • Edge-based scoring and searching method for identifying conditionresponsive protein-protein interaction sub-network
    • Guo,Z. et al. (2007) Edge-based scoring and searching method for identifying conditionresponsive protein-protein interaction sub-network. Bioinformatics, 63, 3912-3918.
    • (2007) Bioinformatics , vol.63 , pp. 3912-3918
    • Guo, Z.1
  • 19
    • 0038014879 scopus 로고    scopus 로고
    • Co-clustering of biological networks and gene expression data
    • Hanisch,D. et al. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics, 18 (Suppl. 1), S145-S154.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Hanisch, D.1
  • 20
    • 0033518234 scopus 로고    scopus 로고
    • From molceular to modular cell biology
    • Hartwell,L.H. et al. (1999) From molceular to modular cell biology. Nature, 402, C47-C52.
    • (1999) Nature , vol.402
    • Hartwell, L.H.1
  • 21
    • 64349096829 scopus 로고    scopus 로고
    • Agenome-wide RNAi screen identifies a new transcriptional module required for self-renewal
    • Hu,G. et al. (2009)Agenome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev., 23, 837-848.
    • (2009) Genes Dev. , vol.23 , pp. 837-848
    • Hu, G.1
  • 22
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker,T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18, S233-S240.
    • (2002) Bioinformatics , vol.18
    • Ideker, T.1
  • 23
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8-a global view on proteins and their functional interactions in 630 organisms
    • Jensen,L.J. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
    • (2009) Nucleic Acids Res. , vol.37
    • Jensen, L.J.1
  • 24
    • 78049437880 scopus 로고    scopus 로고
    • Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data
    • Komurov,K. et al. (2010) Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PLoS Comput. Biol., 6, e1000889.
    • (2010) PLoS Comput. Biol. , vol.6
    • Komurov, K.1
  • 25
    • 35848929692 scopus 로고    scopus 로고
    • Aprobability-based approach for the analysis of large-scale RNAi screens
    • König,R. et al. (2007)Aprobability-based approach for the analysis of large-scale RNAi screens. Nat. Methods, 4, 847-849.
    • (2007) Nat. Methods , vol.4 , pp. 847-849
    • König, R.1
  • 26
    • 34548157926 scopus 로고    scopus 로고
    • Hepatitis B virus maturation is sensitive to functional inhibition of ESCRT-III, Vps4, and gamma 2-adaptin
    • Lambert,C. et al. (2007) Hepatitis B virus maturation is sensitive to functional inhibition of ESCRT-III, Vps4, and gamma 2-adaptin. J. Virol., 81, 9050-9060.
    • (2007) J. Virol. , vol.81 , pp. 9050-9060
    • Lambert, C.1
  • 27
    • 70349513508 scopus 로고    scopus 로고
    • A genome-wide genetic screen for host factors required for hepatitis C virus propagation
    • Li,Q. et al. (2009) A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc. Natl Acad. Sci. USA, 106, 16410-16415.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 16410-16415
    • Li, Q.1
  • 28
    • 38949165049 scopus 로고    scopus 로고
    • Comparative evaluation of gene-set analysis methods
    • Liu,Q. et al. (2007) Comparative evaluation of gene-set analysis methods. BMC Bioinformatics, 8, 431.
    • (2007) BMC Bioinformatics , vol.8 , pp. 431
    • Liu, Q.1
  • 29
    • 32344448950 scopus 로고    scopus 로고
    • Statistical practice in high-throughput screening data analysis
    • Malo,N. et al. (2006) Statistical practice in high-throughput screening data analysis. Nat. Biotechnol., 24, 167-175.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 167-175
    • Malo, N.1
  • 30
    • 0035658023 scopus 로고    scopus 로고
    • HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress
    • Martin-Serrano,J. et al. (2001) HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress. Nat. Med., 7, 1313-1319.
    • (2001) Nat. Med. , vol.7 , pp. 1313-1319
    • Martin-Serrano, J.1
  • 31
    • 77956482678 scopus 로고    scopus 로고
    • Gene set analysis exploiting the topology of a pathway
    • Massa,M.S. et al. (2010) Gene set analysis exploiting the topology of a pathway. BMC Syst. Biol., 4, 121.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 121
    • Massa, M.S.1
  • 32
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • Nacu,S. et al. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858.
    • (2007) Bioinformatics , vol.23 , pp. 850-858
    • Nacu, S.1
  • 33
    • 15944402798 scopus 로고    scopus 로고
    • Inferring pathways from gene lists using a literature-derived network of biological relationships
    • Rajagopalan,D. and Agarwal,P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
    • (2005) Bioinformatics , vol.21 , pp. 788-793
    • Rajagopalan, D.1    Agarwal, P.2
  • 34
    • 38449105972 scopus 로고    scopus 로고
    • Hepatitis C virus infection: a current review
    • Senecal,D.L. and Morelli,J. (2007) Hepatitis C virus infection: a current review. JAAPA, 20, 21-25.
    • (2007) JAAPA , vol.20 , pp. 21-25
    • Senecal, D.L.1    Morelli, J.2
  • 35
    • 34047202181 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    • Shoemaker,B.A. and Panchenko,A.R. (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol., 3, e42.
    • (2007) PLoS Comput. Biol. , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 36
    • 3142706495 scopus 로고    scopus 로고
    • New methods for joint analysis of biological networks and expression data
    • Sohler,F. et al. (2004) New methods for joint analysis of biological networks and expression data. Bioinformatics, 20, 1517-1521.
    • (2004) Bioinformatics , vol.20 , pp. 1517-1521
    • Sohler, F.1
  • 37
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey,J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc., 64, 479--498.
    • (2002) J. R. Stat. Soc. , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 38
    • 61849160363 scopus 로고    scopus 로고
    • Afunctional genomic screen identifies cellular cofactors of hepatitis C virus replication
    • Tai,A. et al. (2009)Afunctional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe, 5, 298-307.
    • (2009) Cell Host Microbe , vol.5 , pp. 298-307
    • Tai, A.1
  • 39
    • 58049215467 scopus 로고    scopus 로고
    • Anovel signaling pathway impact analysis
    • Tarca,A.L. et al. (2009)Anovel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
    • (2009) Bioinformatics , vol.25 , pp. 75-82
    • Tarca, A.L.1
  • 40
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • Ulitsky,I. and Shamir,R. (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol., 1, 8.
    • (2007) BMC Syst. Biol. , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 41
    • 0035830505 scopus 로고    scopus 로고
    • A biological atlas of functional maps
    • Vidal,M. (2001) A biological atlas of functional maps. Cell, 104, 333-339.
    • (2001) Cell , vol.104 , pp. 333-339
    • Vidal, M.1
  • 42
    • 67649124461 scopus 로고    scopus 로고
    • A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila
    • Wang,L. et al. (2009) A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics, 10, 220.
    • (2009) BMC Genomics , vol.10 , pp. 220
    • Wang, L.1
  • 43
    • 51249111048 scopus 로고    scopus 로고
    • An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme
    • Wiles,A.M. et al. (2008) An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme. J. Biomol. Screen., 13, 777-784.
    • (2008) J. Biomol. Screen. , vol.13 , pp. 777-784
    • Wiles, A.M.1
  • 44
    • 73049104551 scopus 로고    scopus 로고
    • An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation
    • Wurdak,H. et al. (2010) An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation. Cell Stem Cell, 6, 37-47.
    • (2010) Cell Stem Cell , vol.6 , pp. 37-47
    • Wurdak, H.1
  • 45
    • 56349121125 scopus 로고    scopus 로고
    • An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer
    • Zender,L. et al. (2008) An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell, 135, 852-864.
    • (2008) Cell , vol.135 , pp. 852-864
    • Zender, L.1
  • 46
    • 0033003760 scopus 로고    scopus 로고
    • A simple statistical parameter for use in evaluation and validation of high throughput screening assays
    • Zhang,J.H. et al. (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen., 4, 67-73.
    • (1999) J. Biomol. Screen. , vol.4 , pp. 67-73
    • Zhang, J.H.1
  • 47
    • 34547809341 scopus 로고    scopus 로고
    • A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays
    • Zhang,J.H. (2007a) A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays. J. Biomol. Screen., 12, 645-655.
    • (2007) J. Biomol. Screen. , vol.12 , pp. 645-655
    • Zhang, J.H.1
  • 48
    • 33947167826 scopus 로고    scopus 로고
    • A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays
    • Zhang,J.H. (2007b) A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics, 89, 552-561.
    • (2007) Genomics , vol.89 , pp. 552-561
    • Zhang, J.H.1
  • 49
    • 34547485288 scopus 로고    scopus 로고
    • A high-throughput siRNA library screen identifies osteogenic suppressors in human mesenchymal stem cells
    • Zhao,Y. and Ding,S. (2007) A high-throughput siRNA library screen identifies osteogenic suppressors in human mesenchymal stem cells. Proc. Natl Acad. Sci. USA, 104, 9673-9678.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9673-9678
    • Zhao, Y.1    Ding, S.2
  • 50
    • 55249088255 scopus 로고    scopus 로고
    • Genome-scale RNAi screen for host factors required for HIV replication
    • Zhou,H. et al. (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe, 4, 495-504.
    • (2008) Cell Host Microbe , vol.4 , pp. 495-504
    • Zhou, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.