메뉴 건너뛰기




Volumn 23, Issue 2, 2013, Pages 365-376

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

Author keywords

[No Author keywords available]

Indexed keywords

RAPAMYCIN;

EID: 84873392956     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.138628.112     Document Type: Article
Times cited : (63)

References (55)
  • 1
    • 84857780876 scopus 로고    scopus 로고
    • Evidence for network evolution in an arabidopsis interactome map
    • Arabidopsis Interactome Mapping Consortium
    • Arabidopsis Interactome Mapping Consortium. 2011. Evidence for network evolution in an Arabidopsis interactome map. Science 333: 601-607.
    • (2011) Science , vol.333 , pp. 601-607
  • 4
    • 16344369007 scopus 로고    scopus 로고
    • Clustering of gene expression data using a local shape-based similarity measure
    • Balasubramaniyan R, Hullermeier E, Weskamp N, Kamper J. 2005. Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics 21: 1069-1077.
    • (2005) Bioinformatics , vol.21 , pp. 1069-1077
    • Balasubramaniyan, R.1    Hullermeier, E.2    Weskamp, N.3    Kamper, J.4
  • 8
    • 75649108602 scopus 로고    scopus 로고
    • Multilayered control of gene expression by stressactivated protein kinases
    • de Nadal E, Posas F. 2010. Multilayered control of gene expression by stressactivated protein kinases. EMBO J 29: 4-13.
    • (2010) EMBO J , vol.29 , pp. 4-13
    • De Nadal, E.1    Posas, F.2
  • 10
    • 41849115550 scopus 로고    scopus 로고
    • A semisupervised method for predicting transcription factor-gene interactions in escherichia coli
    • doi: 10.1371/journal. pcbi.1000044
    • Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. 2008. A semisupervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 4: e1000044. doi: 10.1371/journal. pcbi.1000044.
    • (2008) PLoS Comput Biol , vol.4
    • Ernst, J.1    Beg, Q.K.2    Kay, K.A.3    Balázsi, G.4    Oltvai, Z.N.5    Bar-Joseph, Z.6
  • 11
    • 33751195256 scopus 로고    scopus 로고
    • Topological basis of signal integration in the transcriptional-regulatory network of the yeast, saccharomyces cerevisiae
    • doi: 10.1186/1471-2105-7-478
    • Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN. 2006. Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics 7: 478. doi: 10.1186/1471-2105-7-478.
    • (2006) BMC Bioinformatics , vol.7 , pp. 478
    • Farkas, I.J.1    Wu, C.2    Chennubhotla, C.3    Bahar, I.4    Oltvai, Z.N.5
  • 15
    • 67650663220 scopus 로고    scopus 로고
    • Backup in gene regulatory networks explains differences between binding and knockout results
    • doi: 10.1038/msb. 2009 33
    • Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. 2009. Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol 5: 276. doi: 10.1038/msb.2009.33.
    • (2009) Mol Syst Biol , vol.5 , Issue.276
    • Gitter, A.1    Siegfried, Z.2    Klutstein, M.3    Fornes, O.4    Oliva, B.5    Simon, I.6    Bar-Joseph, Z.7
  • 16
    • 79952112240 scopus 로고    scopus 로고
    • Computational methods for analyzing dynamic regulatory networks
    • Gitter A, Lu Y, Bar-Joseph Z. 2010. Computational methods for analyzing dynamic regulatory networks. Methods Mol Biol 674: 419-441.
    • (2010) Methods Mol Biol , vol.674 , pp. 419-441
    • Gitter, A.1    Lu, Y.2    Bar-Joseph, Z.3
  • 17
    • 79952321999 scopus 로고    scopus 로고
    • Discovering pathways by orienting edges in protein interaction networks
    • doi: 10.1093/nar/gkq1207
    • Gitter A, Klein-Seetharaman J, Gupta A, Bar-Joseph Z. 2011. Discovering pathways by orienting edges in protein interaction networks. Nucleic Acids Res 39: e22. doi: 10.1093/nar/gkq1207.
    • (2011) Nucleic Acids Res , vol.39
    • Gitter, A.1    Klein-Seetharaman, J.2    Gupta, A.3    Bar-Joseph, Z.4
  • 18
    • 78650116700 scopus 로고    scopus 로고
    • Inference of hierarchical regulatory network of estrogen-dependent breast cancer through chip-based data
    • doi: 10.1186/1752-0509-4-170
    • Gu F, Hsu H-K, Hsu P-Y, Wu J, Ma Y, Parvin J, Huang Tim, Jin V. 2010. Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. BMC Syst Biol 4: 170. doi: 10.1186/1752-0509-4-170.
    • (2010) BMC Syst Biol , vol.4 , pp. 170
    • Gu, F.1    Hsu, H.-.K.2    Hsu, P.-.Y.3    Wu, J.4    Ma, Y.5    Parvin, J.6    Huang, T.7    Jin, V.8
  • 21
    • 71149097450 scopus 로고    scopus 로고
    • Control of high osmolarity signalling in the yeast saccharomyces cerevisiae
    • Hohmann S. 2009. Control of high osmolarity signalling in the yeast Saccharomyces cerevisiae. FEBS Lett 583: 4025-4029.
    • (2009) FEBS Lett , vol.583 , pp. 4025-4029
    • Hohmann, S.1
  • 23
    • 70350452746 scopus 로고    scopus 로고
    • Integration of proteomic, transcriptional, and interactome data reveals hidden signaling components
    • doi: 10.1126/scisignal.2000350
    • Huang SC, Fraenkel E. 2009. Integration of proteomic, transcriptional, and interactome data reveals hidden signaling components. Sci Signal 2: ra40. doi: 10.1126/scisignal.2000350.
    • (2009) Sci Signal , vol.2
    • Huang, S.C.1    Fraenkel, E.2
  • 24
    • 77954147517 scopus 로고    scopus 로고
    • Using genereg to construct time delay gene regulatory networks
    • doi: 10.1186/1756-0500-3-142
    • Huang Tao, Liu L, Qian Z, Tu K, Li Y, Xie L. 2010. Using GeneReg to construct time delay gene regulatory networks. BMC Res Notes 3: 142. doi: 10.1186/1756-0500-3-142.
    • (2010) BMC Res Notes , vol.3 , pp. 142
    • Tao, H.1    Liu, L.2    Qian, Z.3    Tu, K.4    Li, Y.5    Xie, L.6
  • 25
    • 15044353444 scopus 로고    scopus 로고
    • Transcription control reprogramming in genetic backup circuits
    • Kafri R, Bar-Even A, Pilpel Y. 2005. Transcription control reprogramming in genetic backup circuits. Nat Genet 37: 295-299.
    • (2005) Nat Genet , vol.37 , pp. 295-299
    • Kafri, R.1    Bar-Even, A.2    Pilpel, Y.3
  • 26
    • 39549122441 scopus 로고    scopus 로고
    • Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy
    • Kafri R, Dahan O, Levy J, Pilpel Y. 2008. Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy. Proc Natl Acad Sci 105: 1243-1248.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 1243-1248
    • Kafri, R.1    Dahan, O.2    Levy, J.3    Pilpel, Y.4
  • 27
    • 0033982936 scopus 로고    scopus 로고
    • Kegg: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 31
    • 32544433476 scopus 로고    scopus 로고
    • Edge: Extraction and analysis of differential gene expression
    • Leek JT, Monsen E, Dabney AR, Storey JD. 2006. EDGE: extraction and analysis of differential gene expression. Bioinformatics 22: 507-508.
    • (2006) Bioinformatics , vol.22 , pp. 507-508
    • Leek, J.T.1    Monsen, E.2    Dabney, A.R.3    Storey, J.D.4
  • 32
    • 39849087243 scopus 로고    scopus 로고
    • A systematic approach to detecting transcription factors in response to environmental stresses
    • doi: 10.1186/1471-2105-8-473
    • Lin L-H, Lee H-C, Li W-H, Chen B-S. 2007. A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics 8: 473. doi: 10.1186/1471-2105-8-473.
    • (2007) BMC Bioinformatics , vol.8 , pp. 473
    • Lin, L.-.H.1    Lee, H.-.C.2    Li, W.-.H.3    Chen, B-.S.4
  • 33
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for saccharomyces cerevisiae
    • doi: 10.1186/1471-2105-7-113
    • MacIsaac K, Wang T, Gordon DB, Gifford D, Stormo GD, Fraenkel E. 2006. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113. doi: 10.1186/1471-2105-7-113.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.1    Wang, T.2    Gordon, D.B.3    Gifford, D.4    Stormo, G.D.5    Fraenkel, E.6
  • 36
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. 2006. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6    Mann, M.7
  • 37
    • 34547830859 scopus 로고    scopus 로고
    • Spine: A framework for signaling-regulatory pathway inference from cause-effect experiments
    • Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. 2007. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics 23: i359-i366.
    • (2007) Bioinformatics , vol.23
    • Ourfali, O.1    Shlomi, T.2    Ideker, T.3    Ruppin, E.4    Sharan, R.5
  • 38
    • 76749100265 scopus 로고    scopus 로고
    • Network-free inference of knockout effects in yeast
    • doi: 10.1371/journal.pcbi.1000635
    • Peleg T, Yosef N, Ruppin E, Sharan R. 2010. Network-free inference of knockout effects in yeast. PLoS Comput Biol 6: e1000635. doi: 10.1371/journal.pcbi.1000635.
    • (2010) PLoS Comput Biol , vol.6
    • Peleg, T.1    Yosef, N.2    Ruppin, E.3    Sharan, R.4
  • 39
    • 77956855921 scopus 로고    scopus 로고
    • The highosmolarity glycerol (hog) and cell wall integrity (cwi) signalling pathways interplay: A yeast dialogue between mapk routes
    • Rodríguez-Pena JM, García R, Nombela C, Arroyo J. 2010. The highosmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast 27: 495-502.
    • (2010) Yeast , vol.27 , pp. 495-502
    • Rodríguez-Pena, J.M.1    García, R.2    Nombela, C.3    Arroyo, J.4
  • 40
    • 66449128185 scopus 로고    scopus 로고
    • Specific and global regulation of mrna stability during osmotic stress in saccharomyces cerevisiae
    • Romero-Santacreu L, Moreno J, Pérez-Ortín JE, Alepuz P. 2009. Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA 15: 1110-1120.
    • (2009) RNA , vol.15 , pp. 1110-1120
    • Romero-Santacreu, L.1    Moreno, J.2    Pérez-Ortín, J.E.3    Alepuz, P.4
  • 41
    • 4444352289 scopus 로고    scopus 로고
    • Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data
    • Schmitt WA, Raab RM, Stephanopoulos G. 2004. Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res 14: 1654-1663.
    • (2004) Genome Res , vol.14 , pp. 1654-1663
    • Schmitt, W.A.1    Raab, R.M.2    Stephanopoulos, G.3
  • 44
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 98: 5116-5121.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 48
    • 42649117688 scopus 로고    scopus 로고
    • A hidden spatial-temporal markov random field model for network-based analysis of time course gene expression data
    • Wei Z, Li Hongzhe. 2008. A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data. Ann Appl Stat 2: 408-429.
    • (2008) Ann Appl Stat , vol.2 , pp. 408-429
    • Wei, Z.1    Li, H.2
  • 49
    • 50449107120 scopus 로고    scopus 로고
    • Stress resistance and signal fidelity independent of nuclear mapk function
    • Westfall PJ, Patterson JC, Chen RE, Thorner J. 2008. Stress resistance and signal fidelity independent of nuclear MAPK function. Proc Natl Acad Sci 105: 12212-12217.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 12212-12217
    • Westfall, P.J.1    Patterson, J.C.2    Chen, R.E.3    Thorner, J.4
  • 55
    • 77952663448 scopus 로고    scopus 로고
    • Timedelay-aracne: Reverse engineering of gene networks from time-course data by an information theoretic approach
    • doi: 10.1186/1471-2105-11-154
    • Zoppoli P, Morganella S, Ceccarelli M. 2010. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 11: 154. doi: 10.1186/1471-2105-11-154.
    • (2010) BMC Bioinformatics , vol.11 , Issue.154
    • Zoppoli, P.1    Morganella, S.2    Ceccarelli, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.