메뉴 건너뛰기




Volumn 23, Issue 3, 2005, Pages 377-383

Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; DRUG DOSAGE; ENZYME INHIBITION; ENZYME KINETICS; RNA;

EID: 21444452397     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1075     Document Type: Article
Times cited : (308)

References (48)
  • 1
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
    • (2000) Cell , vol.102 , pp. 109-126
    • Hughes, T.R.1
  • 2
    • 0035023305 scopus 로고    scopus 로고
    • Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli
    • Courcelle, J., Khodursky, A., Peter, B., Brown, P.O. & Hanawalt, P.C. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158, 41-64 (2001).
    • (2001) Genetics , vol.158 , pp. 41-64
    • Courcelle, J.1    Khodursky, A.2    Peter, B.3    Brown, P.O.4    Hanawalt, P.C.5
  • 3
    • 1842532337 scopus 로고    scopus 로고
    • Chemogenomics: An emerging strategy for rapid target and drug discovery
    • Bredel, M. & Jacoby, E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet. 5, 262-275 (2004).
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 262-275
    • Bredel, M.1    Jacoby, E.2
  • 4
    • 2342624566 scopus 로고    scopus 로고
    • Microarray reality checks in the context of a complex disease
    • Miklos, G.L.G. & Maleszka, R. Microarray reality checks in the context of a complex disease. Nat. Biotechnol. 22, 615-621 (2004).
    • (2004) Nat. Biotechnol. , vol.22 , pp. 615-621
    • Miklos, G.L.G.1    Maleszka, R.2
  • 5
    • 0033048778 scopus 로고    scopus 로고
    • Genomic profiling of drug sensitivities via induced haploinsufficiency
    • Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet 21, 278-283 (1999).
    • (1999) Nat. Genet , vol.21 , pp. 278-283
    • Giaever, G.1
  • 6
    • 9144268287 scopus 로고    scopus 로고
    • Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast
    • Giaever, G. et al. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. USA 101, 793-798 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 793-798
    • Giaever, G.1
  • 7
    • 10744225364 scopus 로고    scopus 로고
    • Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes
    • Lum, P.Y. et al. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116, 121-137 (2004).
    • (2004) Cell , vol.116 , pp. 121-137
    • Lum, P.Y.1
  • 8
    • 0347473810 scopus 로고    scopus 로고
    • Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways
    • Parsons, A.B. et al. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22, 62-69 (2004).
    • (2004) Nat. Biotechnol. , vol.22 , pp. 62-69
    • Parsons, A.B.1
  • 9
    • 0031730097 scopus 로고    scopus 로고
    • Drug target validation and identification of secondary drug target effects using DNA microarrays
    • Marton, M.J. et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4, 1293-1301 (1998).
    • (1998) Nat. Med. , vol.4 , pp. 1293-1301
    • Marton, M.J.1
  • 10
    • 33544473220 scopus 로고    scopus 로고
    • Methods for identifying pathways of drug action. US Patent No. 5,965,352 (2003)
    • Stoughton, R. & Friend, S.H. Methods for identifying pathways of drug action. US Patent No. 5,965,352 (2003).
    • Stoughton, R.1    Friend, S.H.2
  • 11
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph, Z. et al. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21, 1337-1342 (2003).
    • (2003) Nat. Biotechnol. , vol.21 , pp. 1337-1342
    • Bar-Joseph, Z.1
  • 12
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer, M.A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185-198 (2004).
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 13
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J. & Palsson, B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92-96 (2004).
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 14
    • 0036683181 scopus 로고    scopus 로고
    • Linking the genes: Inferring quantitative gene networks from microarray data
    • de la Fuente, A., Brazhnik, P. & Mendes, P. Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet. 18, 395-398 (2002).
    • (2002) Trends Genet. , vol.18 , pp. 395-398
    • De La Fuente, A.1    Brazhnik, P.2    Mendes, P.3
  • 15
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105 (2003).
    • (2003) Science , vol.301 , pp. 102-105
    • Gardner, T.S.1    Di Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 16
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch, A.P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
    • (2000) Mol. Biol. Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1
  • 17
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • Herrgard, M.J., Covert, M.W. & Palsson, B.O. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15, 70-77 (2004).
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 70-77
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 18
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
    • (2001) Science , vol.292 , pp. 929-934
    • Ideker, T.1
  • 19
    • 0345824737 scopus 로고    scopus 로고
    • Network component analysis: Reconstruction of regulatory signals in biological systems
    • Liao, J.C. et al. Network component analysis: reconstruction of regulatory signals in biological systems. Proc. Natl. Acad. Sci. USA 100, 15522-15527 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15522-15527
    • Liao, J.C.1
  • 20
    • 12344318183 scopus 로고    scopus 로고
    • Making the most of it: Pathway reconstruction and integrative simulation using the data at hand
    • Rice, J. & Stolovitzky, G. Making the most of it: pathway reconstruction and integrative simulation using the data at hand. Drug Discov. Today: BioSilico 2, 70-77 (2004).
    • (2004) Drug Discov. Today: BioSilico , vol.2 , pp. 70-77
    • Rice, J.1    Stolovitzky, G.2
  • 21
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen, M., Rosenberg, R., Shraiman, B.I. & Alon, U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA 99, 10555-10560 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Alon, U.4
  • 22
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
    • Tegner, J., Yeung, M.K., Hasty, J. & Collins, J.J. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. USA 100, 5944-5949 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.2    Hasty, J.3    Collins, J.J.4
  • 23
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • Yeung, M.K.S., Tegner, J. & Collins, J.J. Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. USA 99, 6163-6168 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6163-6168
    • Yeung, M.K.S.1    Tegner, J.2    Collins, J.J.3
  • 24
    • 0036789922 scopus 로고    scopus 로고
    • Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
    • Kholodenko, B.N. et al. Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl. Acad. Sci. USA 99, 12841-12846 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12841-12846
    • Kholodenko, B.N.1
  • 25
    • 0036366689 scopus 로고    scopus 로고
    • Combining location and expression data for principled discovery of genetic regulatory network
    • Hartemink, A.J., Gifford, O.K., Jaakkola, T.S. & Young, R.A. Combining location and expression data for principled discovery of genetic regulatory network. Proc. Pacific. Symp. Biocomp. 7, 437-449 (2002).
    • (2002) Proc. Pacific. Symp. Biocomp. , vol.7 , pp. 437-449
    • Hartemink, A.J.1    Gifford, O.K.2    Jaakkola, T.S.3    Young, R.A.4
  • 26
    • 2942612846 scopus 로고    scopus 로고
    • Using a quantitative blueprint to reprogram the dynamics of the flagella gene network
    • Kalir, S. & Alon, U. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell 117, 713-720 (2004).
    • (2004) Cell , vol.117 , pp. 713-720
    • Kalir, S.1    Alon, U.2
  • 27
    • 4444352289 scopus 로고    scopus 로고
    • Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data
    • Schmitt, W.A.J., Raab, R.M. & Stephanopoulos, G. Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res. 14, 1654-1663 (2004).
    • (2004) Genome Res. , vol.14 , pp. 1654-1663
    • Schmitt, W.A.J.1    Raab, R.M.2    Stephanopoulos, G.3
  • 28
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • Dempster, A., Laird, N. & Rubin, D. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. [Ser. B] 139, 1-38 (1977).
    • (1977) J. R. Stat. Soc. [Ser. B] , vol.139 , pp. 1-38
    • Dempster, A.1    Laird, N.2    Rubin, D.3
  • 29
    • 3142536716 scopus 로고    scopus 로고
    • Exploration of essential gene functions via titratable promoter alleles
    • Mnaimneh, S. et al. Exploration of essential gene functions via titratable promoter alleles. Cell 118, 31-44 (2004).
    • (2004) Cell , vol.118 , pp. 31-44
    • Mnaimneh, S.1
  • 30
    • 0037436085 scopus 로고    scopus 로고
    • Effect of catalase-specific inhibitor 3-amino-1,2,4-triazole on yeast peroxisomal catalase in vivo
    • Ueda, M. et al. Effect of catalase-specific inhibitor 3-amino-1,2,4-triazole on yeast peroxisomal catalase in vivo. FEMS Microbiol. Lett. 219, 93-98 (2003).
    • (2003) FEMS Microbiol. Lett. , vol.219 , pp. 93-98
    • Ueda, M.1
  • 31
    • 0037423223 scopus 로고    scopus 로고
    • Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxes feedback inhibition of ribonucleotide reductase
    • Chabes, A. et al. Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxes feedback inhibition of ribonucleotide reductase. Cell 112, 391-401 (2003).
    • (2003) Cell , vol.112 , pp. 391-401
    • Chabes, A.1
  • 32
    • 0033982936 scopus 로고    scopus 로고
    • Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Kegg, G.S.2
  • 33
    • 0035733710 scopus 로고    scopus 로고
    • Genes required for ionizing radiation resistance in yeast
    • Bennett, C. et al. Genes required for ionizing radiation resistance in yeast. Nat. Genet. 29, 426-434 (2001).
    • (2001) Nat. Genet. , vol.29 , pp. 426-434
    • Bennett, C.1
  • 34
    • 0038397236 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae Dap1p, a novel DNA damage response protein related to the mammalian membrane-associated progesterone receptor
    • Hand, R.A., Jia, N., Bard, M. & Craven, R.J. Saccharomyces cerevisiae Dap1p, a novel DNA damage response protein related to the mammalian membrane-associated progesterone receptor. Eukaryot. Cell 2, 306-317 (2003).
    • (2003) Eukaryot. Cell , vol.2 , pp. 306-317
    • Hand, R.A.1    Jia, N.2    Bard, M.3    Craven, R.J.4
  • 35
    • 0014132523 scopus 로고
    • Thioredoxin 2: Cleavage with cyanogen bromide
    • Holmgren, A. & Reichard, P. Thioredoxin 2: cleavage with cyanogen bromide. Eur. J. Biochem. 2, 187-196 (1967).
    • (1967) Eur. J. Biochem. , vol.2 , pp. 187-196
    • Holmgren, A.1    Reichard, P.2
  • 39
    • 0033031437 scopus 로고    scopus 로고
    • DNA arrays for analysis of gene expression
    • Eisen, M.B. & Brown, P.O. DNA arrays for analysis of gene expression. Meth. Enzymol. 303, 179-205 (1999).
    • (1999) Meth. Enzymol. , vol.303 , pp. 179-205
    • Eisen, M.B.1    Brown, P.O.2
  • 41
    • 0041829399 scopus 로고    scopus 로고
    • Terbinafine resistance in a pleiotropic yeast mutant is caused by a single point mutation in the ERG1 gene
    • Klobucnikova, V. et al. Terbinafine resistance in a pleiotropic yeast mutant is caused by a single point mutation in the ERG1 gene. Biochem. Biophys. Res. Commun. 309, 666-671 (2003).
    • (2003) Biochem. Biophys. Res. Commun. , vol.309 , pp. 666-671
    • Klobucnikova, V.1
  • 42
    • 0003191839 scopus 로고
    • Targeted selection of recombinant clones through gene dosage effects
    • Rine, J., Hansen, W., Hardeman, E. & Davis, R.W. Targeted selection of recombinant clones through gene dosage effects. Proc. Natl. Acad. Sci. USA 80, 6750-6754 (1983).
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6750-6754
    • Rine, J.1    Hansen, W.2    Hardeman, E.3    Davis, R.W.4
  • 43
    • 0032412784 scopus 로고    scopus 로고
    • Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae
    • Daum, G., Lees, N.D., Bard, M. & Dickson, R. Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast 14, 1471-1510 (1998).
    • (1998) Yeast , vol.14 , pp. 1471-1510
    • Daum, G.1    Lees, N.D.2    Bard, M.3    Dickson, R.4
  • 44
    • 0024418861 scopus 로고
    • Relationships between sensitivity to hydroxyurea and 4-methyl-5-amino-1- formylisoquinoline thiosemicarbazone (MAIO) and ribonucleotide reductase RNR2 mRNA levels in strains of Saccharomyces cerevisiae
    • Rittberg, D.A. & Wright, J.A. Relationships between sensitivity to hydroxyurea and 4-methyl-5-amino-1-formylisoquinoline thiosemicarbazone (MAIO) and ribonucleotide reductase RNR2 mRNA levels in strains of Saccharomyces cerevisiae. Biochem. Cell Biol. 67, 352-357 (1989).
    • (1989) Biochem. Cell Biol. , vol.67 , pp. 352-357
    • Rittberg, D.A.1    Wright, J.A.2
  • 45
    • 0019131222 scopus 로고
    • Binding of cycloheximide to ribosomes from wild-type and mutant strains of Saccharomyces cerevisiae
    • Stocklein, W. & Piepersberg, W. Binding of cycloheximide to ribosomes from wild-type and mutant strains of Saccharomyces cerevisiae. Antimicrob. Agents Chemother. 18, 863-867 (1980).
    • (1980) Antimicrob. Agents Chemother. , vol.18 , pp. 863-867
    • Stocklein, W.1    Piepersberg, W.2
  • 46
    • 0021679168 scopus 로고
    • Asparagine-linked glycosylation in Saccharomyces cerevisiae: Genetic analysis of an early step
    • Barnes, G., Hansen, W.J., Holcomb, C.L. & Rine, J. Asparagine-linked glycosylation in Saccharomyces cerevisiae: genetic analysis of an early step. Mol. Cell Biol. 4, 2381-2388 (1984).
    • (1984) Mol. Cell Biol. , vol.4 , pp. 2381-2388
    • Barnes, G.1    Hansen, W.J.2    Holcomb, C.L.3    Rine, J.4
  • 47
    • 0028061202 scopus 로고
    • Nikkomycin Z is a specific inhibitor of Saccharomyces cerevisiae chitin synthase isozyme Chs3 in vitro and in vivo
    • Gaughran, J.P., Lai, M.H., Kirsch, D.R. & Silverman, S.J. Nikkomycin Z is a specific inhibitor of Saccharomyces cerevisiae chitin synthase isozyme Chs3 in vitro and in vivo. J. Bacteriol. 175, 5857-5860 (1994).
    • (1994) J. Bacteriol. , vol.175 , pp. 5857-5860
    • Gaughran, J.P.1    Lai, M.H.2    Kirsch, D.R.3    Silverman, S.J.4
  • 48
    • 0345731468 scopus 로고    scopus 로고
    • Yeast life-span extension by calorie restriction is independent of NAD fluctuation
    • Anderson, R.M. et al. Yeast life-span extension by calorie restriction is independent of NAD fluctuation. Science 302, 2124-2126(2003).
    • (2003) Science , vol.302 , pp. 2124-2126
    • Anderson, R.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.