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Volumn 27, Issue 13, 2011, Pages

Physical Module Networks: An integrative approach for reconstructing transcription regulation

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 79959454002     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr222     Document Type: Article
Times cited : (37)

References (48)
  • 1
    • 70349882120 scopus 로고    scopus 로고
    • Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
    • Amit, I. et al. (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science, 326, 257-263.
    • (2009) Science , vol.326 , pp. 257-263
    • Amit, I.1
  • 2
    • 67649982744 scopus 로고    scopus 로고
    • Diversity and complexity in DNA recognition by transcription factors
    • Badis, G. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
    • (2009) Science , vol.324 , pp. 1720-1723
    • Badis, G.1
  • 3
    • 33750238153 scopus 로고    scopus 로고
    • Stratus not altocumulus: a new view of the yeast protein interaction network
    • Batada, N. et al (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol., 4, e317.
    • (2006) PLoS Biol , vol.4
    • Batada, N.1
  • 4
    • 0002460150 scopus 로고
    • The ALARM monitoring system: a case study with two probabilistic inference techniques for belief networks
    • Beinlich, I. et al. (1989) The ALARM monitoring system: a case study with two probabilistic inference techniques for belief networks. In Proceedings of the 2nd European Conference on AI in Medicine, 38, 247-256.
    • (1989) Proceedings of the 2nd European Conference on AI in Medicine , vol.38 , pp. 247-256
    • Beinlich, I.1
  • 5
    • 0002610737 scopus 로고
    • On a routing problem
    • Bellman, R. (1958) On a routing problem. Q. Appl. Math., 16, 87-90.
    • (1958) Q. Appl. Math. , vol.16 , pp. 87-90
    • Bellman, R.1
  • 6
    • 45449115390 scopus 로고    scopus 로고
    • Variation in homeodomain DNA binding revealed by highresolution analysis of sequence preferences
    • Berger, M. et al. (2008) Variation in homeodomain DNA binding revealed by highresolution analysis of sequence preferences. Cell, 133, 1266-1276.
    • (2008) Cell , vol.133 , pp. 1266-1276
    • Berger, M.1
  • 7
    • 77953077420 scopus 로고    scopus 로고
    • Aglobal protein kinase and phosphatase interaction network in yeast
    • Breitkreutz, A. et al (2010)Aglobal protein kinase and phosphatase interaction network in yeast. Science, 328, 1043-1046.
    • (2010) Science , vol.328 , pp. 1043-1046
    • Breitkreutz, A.1
  • 8
    • 84984933073 scopus 로고    scopus 로고
    • Structure and function of a transcriptional network activated by the MAPK Hog1
    • Capaldi, A. et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet., 40, 1300-1306.
    • (2008) Nat. Genet. , vol.40 , pp. 1300-1306
    • Capaldi, A.1
  • 9
    • 46749127803 scopus 로고    scopus 로고
    • Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia
    • Chang, L. et al. (2008) Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol., 9, R38.
    • (2008) Genome Biol , vol.9
    • Chang, L.1
  • 10
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 11
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • Gao, F. et al. (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics, 5, 31.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, F.1
  • 12
    • 1542284074 scopus 로고    scopus 로고
    • Clb6/Cdc28 and Cdc14 regulate phosphorylation status and cellular localization of Swi6
    • Geymonat, M. et al. (2004) Clb6/Cdc28 and Cdc14 regulate phosphorylation status and cellular localization of Swi6. Mol. Cell Biol., 24, 2277-2285.
    • (2004) Mol. Cell Biol. , vol.24 , pp. 2277-2285
    • Geymonat, M.1
  • 13
    • 0034721670 scopus 로고    scopus 로고
    • The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p
    • Goldmark, J. et al. (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell, 103, 423-433.
    • (2000) Cell , vol.103 , pp. 423-433
    • Goldmark, J.1
  • 14
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison, C. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.1
  • 15
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart, G. et al. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol., 7, 120.
    • (2006) Genome Biol , vol.7 , pp. 120
    • Hart, G.1
  • 16
    • 0036366689 scopus 로고    scopus 로고
    • Combining location and expression data for principled discovery of genetic regulatory network models
    • Hartemink, A.J. et al. (2002) Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput., 437-449.
    • (2002) Pac. Symp. Biocomput. , pp. 437-449
    • Hartemink, A.J.1
  • 17
    • 33745178476 scopus 로고    scopus 로고
    • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in saccharomyces cerevisiae
    • Herrgard, M. et al. (2006) Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in saccharomyces cerevisiae. Genome Res., 16, 627-635.
    • (2006) Genome Res , vol.16 , pp. 627-635
    • Herrgard, M.1
  • 18
    • 0036894656 scopus 로고    scopus 로고
    • Complex transcriptional circuitry at the G1/S transition in saccharomyces cerevisiae
    • Horak, C. et al. (2002) Complex transcriptional circuitry at the G1/S transition in saccharomyces cerevisiae. Genes Dev., 16, 3017-3033.
    • (2002) Genes Dev , vol.16 , pp. 3017-3033
    • Horak, C.1
  • 19
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • Hu, Z. et al. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet., 39, 683-687.
    • (2007) Nat. Genet. , vol.39 , pp. 683-687
    • Hu, Z.1
  • 20
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes, T. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
    • (2000) Cell , vol.102 , pp. 109-126
    • Hughes, T.1
  • 21
    • 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 (Suppl. 1), S233-S240.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1
  • 22
    • 0030716393 scopus 로고    scopus 로고
    • Identification of the Saccharomyces cerevisiae genes STB1-STB5 encoding Sin3p binding proteins
    • Kasten, M. and Stillman, D. (1997). Identification of the Saccharomyces cerevisiae genes STB1-STB5 encoding Sin3p binding proteins. Mol. Gen. Genet., 256, 376-386.
    • (1997) Mol. Gen. Genet. , vol.256 , pp. 376-386
    • Kasten, M.1    Stillman, D.2
  • 23
    • 67749113808 scopus 로고    scopus 로고
    • Transcriptional regulatory circuits: predicting numbers from alphabets
    • Kim, H. et al. (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science, 325, 429-432.
    • (2009) Science , vol.325 , pp. 429-432
    • Kim, H.1
  • 25
    • 0034612501 scopus 로고    scopus 로고
    • Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters
    • Koranda, M. et al. (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature, 406, 94-98.
    • (2000) Nature , vol.406 , pp. 94-98
    • Koranda, M.1
  • 26
    • 57149100949 scopus 로고    scopus 로고
    • Apredictive model of the oxygen and heme regulatory network in yeast
    • Kundaje, A. et al. (2008)Apredictive model of the oxygen and heme regulatory network in yeast. PLoS Comput. Biol., 4, e1000224.
    • (2008) PLoS Comput. Biol. , vol.4
    • Kundaje, A.1
  • 27
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee, T. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.1
  • 28
    • 33749037129 scopus 로고    scopus 로고
    • Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
    • Lee, S-I. et al. (2006) Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc. Natl Acad. Sci. USA, 103, 14062-14067.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 14062-14067
    • Lee, S.-I.1
  • 29
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • MacIsaac, K. et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.1
  • 30
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • Maslov, S. and Sneppen, K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913.
    • (2002) Science , vol.296 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 31
    • 4444231731 scopus 로고    scopus 로고
    • Role of the N-terminal region of Rap1p in the transcriptional activation of glycolytic genes in Saccharomyces cerevisiae
    • Mizuno, T. et al. (2004) Role of the N-terminal region of Rap1p in the transcriptional activation of glycolytic genes in Saccharomyces cerevisiae. Yeast, 21, 851-866.
    • (2004) Yeast , vol.21 , pp. 851-866
    • Mizuno, T.1
  • 32
    • 3142536716 scopus 로고    scopus 로고
    • Exploration of essential gene functions via titratable promoter alleles
    • Mnaimneh, S. et al. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell, 118, 31-44.
    • (2004) Cell , vol.118 , pp. 31-44
    • Mnaimneh, S.1
  • 33
    • 2442718023 scopus 로고    scopus 로고
    • Using protein-protein interactions for refining gene networks estimated from microarray data by bayesian networks
    • Nariai, N. et al. (2004) Using protein-protein interactions for refining gene networks estimated from microarray data by bayesian networks. Pac. Symp. Biocomput., 336-347.
    • (2004) Pac. Symp. Biocomput. , pp. 336-347
    • Nariai, N.1
  • 34
    • 0034076869 scopus 로고    scopus 로고
    • Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms
    • Olson, K. et al. (2000) Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms. Mol. Cell Biol., 20, 4199-4209.
    • (2000) Mol. Cell Biol. , vol.20 , pp. 4199-4209
    • Olson, K.1
  • 35
    • 34547830859 scopus 로고    scopus 로고
    • SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    • Ourfali, O. et al. (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics, 23, i359-i366.
    • (2007) Bioinformatics , vol.23
    • Ourfali, O.1
  • 36
    • 76749100265 scopus 로고    scopus 로고
    • Network-free inference of knockout effects in yeast
    • Peleg, T. et al. (2010) Network-free inference of knockout effects in yeast. PLoS Comput. Biol., 6, e1000635.
    • (2010) PLoS Comput. Biol. , vol.6
    • Peleg, T.1
  • 37
    • 33747379083 scopus 로고    scopus 로고
    • The forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle
    • Pramila, T. et al. (2006) The forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev., 20, 2266-2278.
    • (2006) Genes Dev , vol.20 , pp. 2266-2278
    • Pramila, T.1
  • 38
    • 41849123062 scopus 로고    scopus 로고
    • Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics
    • Ramsey, S.A. et al. (2008) Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput. Biol., 4, e1000021.
    • (2008) PLoS Comput. Biol. , vol.4
    • Ramsey, S.A.1
  • 39
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal, E. et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176.
    • (2003) Nat. Genet. , vol.34 , pp. 166-176
    • Segal, E.1
  • 40
    • 21844455527 scopus 로고    scopus 로고
    • Learning module networks
    • Segal, E. et al. (2005) Learning module networks. J. Mach. Learn. Res., 6, 557-588.
    • (2005) J. Mach. Learn. Res. , vol.6 , pp. 557-588
    • Segal, E.1
  • 41
    • 72249103485 scopus 로고    scopus 로고
    • A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection
    • Shapira, S. et al (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell, 139, 1255-1267.
    • (2009) Cell , vol.139 , pp. 1255-1267
    • Shapira, S.1
  • 42
    • 0029557246 scopus 로고
    • UME6 is a central component of a developmental regulatory switch controlling meiosis-specific gene expression
    • Steber, C. and Esposito, R. (1995) UME6 is a central component of a developmental regulatory switch controlling meiosis-specific gene expression. Proc. Natl Acad. Sci. USA, 92, 12490-12494.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 12490-12494
    • Steber, C.1    Esposito, R.2
  • 43
    • 65149083962 scopus 로고    scopus 로고
    • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    • Suzuki, H. et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet., 41, 553-562.
    • (2009) Nat. Genet. , vol.41 , pp. 553-562
    • Suzuki, H.1
  • 44
    • 0036138322 scopus 로고    scopus 로고
    • How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps
    • Wagner, A. (2001). How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. Bioinformatics, 17, 1183-1197.
    • (2001) Bioinformatics , vol.17 , pp. 1183-1197
    • Wagner, A.1
  • 45
    • 3142550630 scopus 로고    scopus 로고
    • Physical network models
    • Yeang, C. et al. (2004) Physical network models. J. Comput. Biol., 11, 243-262.
    • (2004) J. Comput. Biol. , vol.11 , pp. 243-262
    • Yeang, C.1
  • 46
    • 61349114190 scopus 로고    scopus 로고
    • Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
    • Yeger-Lotem, E. et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet., 41, 316-323.
    • (2009) Nat. Genet. , vol.41 , pp. 316-323
    • Yeger-Lotem, E.1
  • 47
    • 62549145762 scopus 로고    scopus 로고
    • Toward accurate reconstruction of functional protein networks
    • Yosef, N. et al. (2009) Toward accurate reconstruction of functional protein networks. Mol. Syst. Biol., 5, 248.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 248
    • Yosef, N.1
  • 48
    • 12744261506 scopus 로고    scopus 로고
    • A new dynamic bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
    • Zou, M. and Conzen, S.D. (2005). A new dynamic bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics, 21, 71-79.
    • (2005) Bioinformatics , vol.21 , pp. 71-79
    • Zou, M.1    Conzen, S.D.2


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