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Volumn 3, Issue , 2009, Pages

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; GUANINE NUCLEOTIDE EXCHANGE FACTOR; MANNOSYLTRANSFERASE; PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 74549207963     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-115     Document Type: Article
Times cited : (16)

References (37)
  • 2
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • 10.1038/nature04670, 16554755
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440(7084):637-643. 10.1038/nature04670, 16554755.
    • (2006) Nature , vol.440 , Issue.7084 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5    Ignatchenko, A.6    Li, J.7    Pu, S.8    Datta, N.9    Tikuisis, A.P.10
  • 3
    • 36748999400 scopus 로고    scopus 로고
    • New modes of translational control in development, behavior, and disease
    • 10.1016/j.molcel.2007.11.018, 18082597
    • Sonenberg N, Hinnebusch AG. New modes of translational control in development, behavior, and disease. Mol Cell 2007, 28(5):721-729. 10.1016/j.molcel.2007.11.018, 18082597.
    • (2007) Mol Cell , vol.28 , Issue.5 , pp. 721-729
    • Sonenberg, N.1    Hinnebusch, A.G.2
  • 4
    • 32044465506 scopus 로고    scopus 로고
    • TOR signaling in growth and metabolism
    • 10.1016/j.cell.2006.01.016, 16469695
    • Wullschleger S, Loewith R, Hall MN. TOR signaling in growth and metabolism. Cell 2006, 124(3):471-484. 10.1016/j.cell.2006.01.016, 16469695.
    • (2006) Cell , vol.124 , Issue.3 , pp. 471-484
    • Wullschleger, S.1    Loewith, R.2    Hall, M.N.3
  • 5
    • 0036463736 scopus 로고    scopus 로고
    • Autophagy in the eukaryotic cell
    • 10.1128/EC.01.1.11-21.2002, 118053, 12455967
    • Reggiori F, Klionsky DJ. Autophagy in the eukaryotic cell. Eukaryot Cell 2002, 1(1):11-21. 10.1128/EC.01.1.11-21.2002, 118053, 12455967.
    • (2002) Eukaryot Cell , vol.1 , Issue.1 , pp. 11-21
    • Reggiori, F.1    Klionsky, D.J.2
  • 6
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • 10.1126/science.1094068, 14764868
    • Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303(5659):799-805. 10.1126/science.1094068, 14764868.
    • (2004) Science , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 7
    • 11144319853 scopus 로고    scopus 로고
    • Use of logic relationships to decipher protein network organization
    • 10.1126/science.1103330, 15618515
    • Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. Use of logic relationships to decipher protein network organization. Science 2004, 306(5705):2246-2249. 10.1126/science.1103330, 15618515.
    • (2004) Science , vol.306 , Issue.5705 , pp. 2246-2249
    • Bowers, P.M.1    Cokus, S.J.2    Eisenberg, D.3    Yeates, T.O.4
  • 8
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
    • 10.1073/pnas.96.8.4285, 16324, 10200254
    • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96(8):4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.8 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3    Eisenberg, D.4    Yeates, T.O.5
  • 9
    • 27144556456 scopus 로고    scopus 로고
    • Utilizing logical relationships in genomic data to decipher cellular processes
    • 10.1111/j.1742-4658.2005.04946.x, 16218945
    • Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D. Utilizing logical relationships in genomic data to decipher cellular processes. Febs J 2005, 272(20):5110-5118. 10.1111/j.1742-4658.2005.04946.x, 16218945.
    • (2005) Febs J , vol.272 , Issue.20 , pp. 5110-5118
    • Bowers, P.M.1    O'Connor, B.D.2    Cokus, S.J.3    Sprinzak, E.4    Yeates, T.O.5    Eisenberg, D.6
  • 11
    • 23844534426 scopus 로고    scopus 로고
    • Importance of cell wall mannoproteins for septum formation in Saccharomyces cerevisiae
    • 10.1002/yea.1242, 16034811
    • Schmidt M, Strenk ME, Boyer MP, Fritsch BJ. Importance of cell wall mannoproteins for septum formation in Saccharomyces cerevisiae. Yeast 2005, 22(9):715-723. 10.1002/yea.1242, 16034811.
    • (2005) Yeast , vol.22 , Issue.9 , pp. 715-723
    • Schmidt, M.1    Strenk, M.E.2    Boyer, M.P.3    Fritsch, B.J.4
  • 12
    • 0037160121 scopus 로고    scopus 로고
    • The components of the Saccharomyces cerevisiae mannosyltransferase complex M-Pol I have distinct functions in mannan synthesis
    • 10.1074/jbc.M208023200, 12235155
    • Stolz J, Munro S. The components of the Saccharomyces cerevisiae mannosyltransferase complex M-Pol I have distinct functions in mannan synthesis. J Biol Chem 2002, 277(47):44801-44808. 10.1074/jbc.M208023200, 12235155.
    • (2002) J Biol Chem , vol.277 , Issue.47 , pp. 44801-44808
    • Stolz, J.1    Munro, S.2
  • 13
    • 0033525512 scopus 로고    scopus 로고
    • The Saccharomyces cerevisiae protein Mnn10p/Bed1p is a subunit of a Golgi mannosyltransferase complex
    • 10.1074/jbc.274.10.6579, 10037752
    • Jungmann J, Rayner JC, Munro S. The Saccharomyces cerevisiae protein Mnn10p/Bed1p is a subunit of a Golgi mannosyltransferase complex. J Biol Chem 1999, 274(10):6579-6585. 10.1074/jbc.274.10.6579, 10037752.
    • (1999) J Biol Chem , vol.274 , Issue.10 , pp. 6579-6585
    • Jungmann, J.1    Rayner, J.C.2    Munro, S.3
  • 14
    • 3943059566 scopus 로고    scopus 로고
    • Roles of N-linked glycans in the endoplasmic reticulum
    • 10.1146/annurev.biochem.73.011303.073752, 15189166
    • Helenius A, Aebi M. Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 2004, 73:1019-1049. 10.1146/annurev.biochem.73.011303.073752, 15189166.
    • (2004) Annu Rev Biochem , vol.73 , pp. 1019-1049
    • Helenius, A.1    Aebi, M.2
  • 15
    • 19344370199 scopus 로고    scopus 로고
    • Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing
    • 10.1016/j.ceb.2005.04.001, 15901498
    • Granneman S, Baserga SJ. Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing. Curr Opin Cell Biol 2005, 17(3):281-286. 10.1016/j.ceb.2005.04.001, 15901498.
    • (2005) Curr Opin Cell Biol , vol.17 , Issue.3 , pp. 281-286
    • Granneman, S.1    Baserga, S.J.2
  • 17
    • 0036787003 scopus 로고    scopus 로고
    • Components of an interdependent unit within the SSU processome regulate and mediate its activity
    • 10.1128/MCB.22.20.7258-7267.2002, 139808, 12242301
    • Wehner KA, Gallagher JE, Baserga SJ. Components of an interdependent unit within the SSU processome regulate and mediate its activity. Mol Cell Biol 2002, 22(20):7258-7267. 10.1128/MCB.22.20.7258-7267.2002, 139808, 12242301.
    • (2002) Mol Cell Biol , vol.22 , Issue.20 , pp. 7258-7267
    • Wehner, K.A.1    Gallagher, J.E.2    Baserga, S.J.3
  • 18
    • 33749379882 scopus 로고    scopus 로고
    • Global translational responses to oxidative stress impact upon multiple levels of protein synthesis
    • 10.1074/jbc.M601545200, 16849329
    • Shenton D, Smirnova JB, Selley JN, Carroll K, Hubbard SJ, Pavitt GD, Ashe MP, Grant CM. Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J Biol Chem 2006, 281(39):29011-29021. 10.1074/jbc.M601545200, 16849329.
    • (2006) J Biol Chem , vol.281 , Issue.39 , pp. 29011-29021
    • Shenton, D.1    Smirnova, J.B.2    Selley, J.N.3    Carroll, K.4    Hubbard, S.J.5    Pavitt, G.D.6    Ashe, M.P.7    Grant, C.M.8
  • 20
  • 21
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • 10.1038/ng1165, 12740579
    • Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34(2):166-176. 10.1038/ng1165, 12740579.
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 22
    • 65249176527 scopus 로고    scopus 로고
    • Stress-Dependent Coordination of Transcriptome and Translatome in Yeast
    • 10.1371/journal.pbio.1000105, 2675909, 19419242
    • Halbeisen RE, Gerber A, eacute P. Stress-Dependent Coordination of Transcriptome and Translatome in Yeast. PLoS Biology 2009, 7(5):e105. 10.1371/journal.pbio.1000105, 2675909, 19419242.
    • (2009) PLoS Biology , vol.7 , Issue.5
    • Halbeisen, R.E.1    Gerber, A.2    eacute, P.3
  • 23
    • 39749140606 scopus 로고    scopus 로고
    • Strategy of transcription regulation in the budding yeast
    • 10.1371/journal.pone.0000250, 1803021, 17327914
    • Levy S, Ihmels J, Carmi M, Weinberger A, Friedlander G, Barkai N. Strategy of transcription regulation in the budding yeast. PLoS ONE 2007, 2(2):e250. 10.1371/journal.pone.0000250, 1803021, 17327914.
    • (2007) PLoS ONE , vol.2 , Issue.2
    • Levy, S.1    Ihmels, J.2    Carmi, M.3    Weinberger, A.4    Friedlander, G.5    Barkai, N.6
  • 24
    • 0024546509 scopus 로고
    • The scanning model for translation: an update
    • 10.1083/jcb.108.2.229, 2115416, 2645293
    • Kozak M. The scanning model for translation: an update. J Cell Biol 1989, 108(2):229-241. 10.1083/jcb.108.2.229, 2115416, 2645293.
    • (1989) J Cell Biol , vol.108 , Issue.2 , pp. 229-241
    • Kozak, M.1
  • 25
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • 10.1126/science.1105103, 15692050
    • de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science 2005, 307(5710):724-727. 10.1126/science.1105103, 15692050.
    • (2005) Science , vol.307 , Issue.5710 , pp. 724-727
    • de Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 26
    • 33749148764 scopus 로고    scopus 로고
    • Modularity of the transcriptional response of protein complexes in yeast
    • 10.1016/j.jmb.2006.06.024, 16973176
    • Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ. Modularity of the transcriptional response of protein complexes in yeast. J Mol Biol 2006, 363(2):589-610. 10.1016/j.jmb.2006.06.024, 16973176.
    • (2006) J Mol Biol , vol.363 , Issue.2 , pp. 589-610
    • Simonis, N.1    Gonze, D.2    Orsi, C.3    van Helden, J.4    Wodak, S.J.5
  • 27
    • 0036772367 scopus 로고    scopus 로고
    • Conservation of gene co-regulation in prokaryotes and eukaryotes
    • discussion 410., 10.1016/S0167-7799(02)02032-2, 12220896
    • Teichmann SA, Babu MM. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol 2002, 20(10):407-410. discussion 410., 10.1016/S0167-7799(02)02032-2, 12220896.
    • (2002) Trends Biotechnol , vol.20 , Issue.10 , pp. 407-410
    • Teichmann, S.A.1    Babu, M.M.2
  • 28
    • 24344498648 scopus 로고    scopus 로고
    • A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae
    • 10.1101/gr.3847105, 1199545, 16109970
    • Petti AA, Church GM. A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res 2005, 15(9):1298-1306. 10.1101/gr.3847105, 1199545, 16109970.
    • (2005) Genome Res , vol.15 , Issue.9 , pp. 1298-1306
    • Petti, A.A.1    Church, G.M.2
  • 30
    • 1542357674 scopus 로고    scopus 로고
    • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
    • 10.1073/pnas.0308661100, 365731, 14973197
    • Tanay A, Sharan R, Kupiec M, Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci USA 2004, 101(9):2981-2986. 10.1073/pnas.0308661100, 365731, 14973197.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.9 , pp. 2981-2986
    • Tanay, A.1    Sharan, R.2    Kupiec, M.3    Shamir, R.4
  • 31
    • 39049127598 scopus 로고    scopus 로고
    • Revealing targeted therapy for human cancer by gene module maps
    • 10.1158/0008-5472.CAN-07-0382, 18199530
    • Wong DJ, Nuyten DS, Regev A, Lin M, Adler AS, Segal E, Vijver MJ, Chang HY. Revealing targeted therapy for human cancer by gene module maps. Cancer Res 2008, 68(2):369-378. 10.1158/0008-5472.CAN-07-0382, 18199530.
    • (2008) Cancer Res , vol.68 , Issue.2 , pp. 369-378
    • Wong, D.J.1    Nuyten, D.S.2    Regev, A.3    Lin, M.4    Adler, A.S.5    Segal, E.6    Vijver, M.J.7    Chang, H.Y.8
  • 34
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • 10.1186/1471-2105-7-113, 1435934, 16522208
    • MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:113. 10.1186/1471-2105-7-113, 1435934, 16522208.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.D.1    Wang, T.2    Gordon, D.B.3    Gifford, D.K.4    Stormo, G.D.5    Fraenkel, E.6
  • 35
    • 2142754126 scopus 로고    scopus 로고
    • Ribosome biogenesis: of knobs and RNA processing
    • 10.1016/j.yexcr.2004.03.016, 15120992
    • Granneman S, Baserga SJ. Ribosome biogenesis: of knobs and RNA processing. Exp Cell Res 2004, 296(1):43-50. 10.1016/j.yexcr.2004.03.016, 15120992.
    • (2004) Exp Cell Res , vol.296 , Issue.1 , pp. 43-50
    • Granneman, S.1    Baserga, S.J.2
  • 36
    • 28844478867 scopus 로고    scopus 로고
    • EIF2B, a mediator of general and gene-specific translational control
    • Pavitt GD. eIF2B, a mediator of general and gene-specific translational control. Biochem Soc Trans 2005, 33(Pt 6):1487-1492.
    • (2005) Biochem Soc Trans , vol.33 , Issue.PART. 6 , pp. 1487-1492
    • Pavitt, G.D.1
  • 37
    • 0038309329 scopus 로고    scopus 로고
    • The molecular mechanism of autophagy
    • 1430730, 12865942
    • Wang CW, Klionsky DJ. The molecular mechanism of autophagy. Mol Med 2003, 9(3-4):65-76. 1430730, 12865942.
    • (2003) Mol Med , vol.9 , Issue.3-4 , pp. 65-76
    • Wang, C.W.1    Klionsky, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.