메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

A novel method to identify cooperative functional modules: Study of module coordination in the Saccharomyces cerevisiae cell cycle

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CELLULAR FUNCTION; COOPERATIVE INTERACTIONS; COOPERATIVE MECHANISMS; DYNAMIC COORDINATION; FUNCTIONAL COMPONENTS; FUNCTIONAL MODULES; SACCHAROMYCES CEREVISIAE CELLS;

EID: 79960152265     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-281     Document Type: Article
Times cited : (17)

References (51)
  • 1
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: preparing the next generation of molecular biologists
    • 10.1016/S0092-8674(00)80922-8, 9476889
    • Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 1998, 92:291-294. 10.1016/S0092-8674(00)80922-8, 9476889.
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 3
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • 10.1073/pnas.0237338100, 298738, 12538875
    • Rivees A, Galitski T. Modular organization of cellular networks. Proc Natl Acad Sci USA 2003, 100(3):1128-1133. 10.1073/pnas.0237338100, 298738, 12538875.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.3 , pp. 1128-1133
    • Rivees, A.1    Galitski, T.2
  • 4
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • 10.1038/35011540, 10591225
    • Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-C52. 10.1038/35011540, 10591225.
    • (1999) Nature , vol.402
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3    Murray, A.W.4
  • 5
    • 24344498648 scopus 로고    scopus 로고
    • A network of trancriptionally coordinated functional modules in Saccharomyces cerevisiae
    • 10.1101/gr.3847105, 1199545, 16109970
    • Petti AA, Church GM. A network of trancriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Research 2005, 15:1298-1306. 10.1101/gr.3847105, 1199545, 16109970.
    • (2005) Genome Research , vol.15 , pp. 1298-1306
    • Petti, A.A.1    Church, G.M.2
  • 6
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • 10.1038/nature04532, 16429126
    • Gavin A. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636. 10.1038/nature04532, 16429126.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.1
  • 7
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • 10.1038/nature02782, 15372033
    • Luscombe N, Babu M, Yu H, Snyder M, Teichmann S, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312. 10.1038/nature02782, 15372033.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.1    Babu, M.2    Yu, H.3    Snyder, M.4    Teichmann, S.5    Gerstein, M.6
  • 8
    • 13544254744 scopus 로고    scopus 로고
    • Identifying combinatorial regulation of transcription factors and binding motifs
    • 10.1186/gb-2004-5-8-r56, 507881, 15287978
    • Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 2004, 5:R56. 10.1186/gb-2004-5-8-r56, 507881, 15287978.
    • (2004) Genome Biology , vol.5
    • Kato, M.1    Hata, N.2    Banerjee, N.3    Futcher, B.4    Zhang, M.Q.5
  • 9
    • 0038427234 scopus 로고    scopus 로고
    • Crosstalk between Ras2p-controlled mitogen-activated protein kinase and cAMP pathways during invasive growth of Saccharomyces cerevisiae
    • 25273, 10233147
    • Mösch HU, Kübler E, Krappmann S, Fink GR, Braus GH. Crosstalk between Ras2p-controlled mitogen-activated protein kinase and cAMP pathways during invasive growth of Saccharomyces cerevisiae. Mol Biol Cell 1999, 10(5):1325-1335. 25273, 10233147.
    • (1999) Mol Biol Cell , vol.10 , Issue.5 , pp. 1325-1335
    • Mösch, H.U.1    Kübler, E.2    Krappmann, S.3    Fink, G.R.4    Braus, G.H.5
  • 10
    • 33750703602 scopus 로고    scopus 로고
    • Crosstalk between cAMP-PKA and MAP kinase pathways is a key regulatory design necessary to regulate FLO11 expression
    • 10.1016/j.bpc.2006.06.012, 16863676
    • Sengupta N, Vinod PK, Venkatesh KV. Crosstalk between cAMP-PKA and MAP kinase pathways is a key regulatory design necessary to regulate FLO11 expression. Biophysical Chemistry 2007, 125(1):59-71. 10.1016/j.bpc.2006.06.012, 16863676.
    • (2007) Biophysical Chemistry , vol.125 , Issue.1 , pp. 59-71
    • Sengupta, N.1    Vinod, P.K.2    Venkatesh, K.V.3
  • 14
    • 0033982936 scopus 로고    scopus 로고
    • KEGG:Kyoto Encyclopedia of Genes and Genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG:Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 15
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 10.1073/pnas.95.25.14863, 24541, 9843981
    • Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 16
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical Organization of Modularity in Metabolic Networks
    • 10.1126/science.1073374, 12202830
    • Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297(5586):1551-1555. 10.1126/science.1073374, 12202830.
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabási, A.L.5
  • 17
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 2007, 1(8).
    • (2007) BMC Syst Biol , vol.1 , Issue.8
    • Ulitsky, I.1    Shamir, R.2
  • 18
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(2).
    • (2003) BMC Bioinformatics , vol.4 , Issue.2
    • Bader, G.D.1    Hogue, C.W.2
  • 19
    • 84888282387 scopus 로고    scopus 로고
    • The differential clustering approach for comparative gene expression analysis: application to the Candida albicans transcription program
    • Ihmels SBJ, Berman J, Barkai N. The differential clustering approach for comparative gene expression analysis: application to the Candida albicans transcription program. PLoS Genetics 2005, 1(3).
    • (2005) PLoS Genetics , vol.1 , Issue.3
    • Ihmels, S.B.J.1    Berman, J.2    Barkai, N.3
  • 20
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • 10.1038/ng776, 11694880
    • Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29(4):482-486. 10.1038/ng776, 11694880.
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 21
    • 13844271592 scopus 로고    scopus 로고
    • Detection of parallel functional modules by comparative analysis of genome sequences
    • 10.1038/nbt1065, 15696156
    • Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences. Nature Biotechnology 2005, 23:253-260. 10.1038/nbt1065, 15696156.
    • (2005) Nature Biotechnology , vol.23 , pp. 253-260
    • Li, H.1    Pellegrini, M.2    Eisenberg, D.3
  • 22
    • 24644464205 scopus 로고    scopus 로고
    • Study of coordinative gene expression at the biological process level
    • 10.1093/bioinformatics/bti599, 16076891
    • Yu T, Sun W, Yuan S, Li KC. Study of coordinative gene expression at the biological process level. Bioinformatics 2005, 21(18):3651-3657. 10.1093/bioinformatics/bti599, 16076891.
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3651-3657
    • Yu, T.1    Sun, W.2    Yuan, S.3    Li, K.C.4
  • 23
    • 45449101889 scopus 로고    scopus 로고
    • A global pathway crosstalk network
    • 10.1093/bioinformatics/btn200, 18434343
    • Li Y, Agarwal P, Rajagopalan D. A global pathway crosstalk network. Bioinformatics 2008, 24(12):1442-1447. 10.1093/bioinformatics/btn200, 18434343.
    • (2008) Bioinformatics , vol.24 , Issue.12 , pp. 1442-1447
    • Li, Y.1    Agarwal, P.2    Rajagopalan, D.3
  • 24
    • 0032814464 scopus 로고    scopus 로고
    • Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein
    • 84370, 10409718
    • Ho Y, Costanzo M, Moore L, Kobayashi R, Andrews BJ. Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol cell Biol 1999, 19(8):5267-5278. 84370, 10409718.
    • (1999) Mol cell Biol , vol.19 , Issue.8 , pp. 5267-5278
    • Ho, Y.1    Costanzo, M.2    Moore, L.3    Kobayashi, R.4    Andrews, B.J.5
  • 25
    • 0030062491 scopus 로고    scopus 로고
    • Switching transcription on and off during the yeast cell cycle: Cln/Cdc28 kinases activate bound transcription factor SBF (Swi4/Swi6) at start, whereas Clb/Cdc28 kinases displace it from the promoter in G2
    • 10.1101/gad.10.2.129, 8566747
    • Koch C, Schleiffer A, Ammerer G, Nasmyth K. Switching transcription on and off during the yeast cell cycle: Cln/Cdc28 kinases activate bound transcription factor SBF (Swi4/Swi6) at start, whereas Clb/Cdc28 kinases displace it from the promoter in G2. Genes Dev 1996, 10(2):129-141. 10.1101/gad.10.2.129, 8566747.
    • (1996) Genes Dev , vol.10 , Issue.2 , pp. 129-141
    • Koch, C.1    Schleiffer, A.2    Ammerer, G.3    Nasmyth, K.4
  • 26
    • 0024094565 scopus 로고
    • Functions of microtubules in the Saccharomyces cerevisiae cell cycle
    • 10.1083/jcb.107.4.1409, 2115239, 3049620
    • Jacobs CW, Adams AE, Szaniszlo PJ, Pringle JR. Functions of microtubules in the Saccharomyces cerevisiae cell cycle. J Cell Biol 1988, 107(4):1409-1426. 10.1083/jcb.107.4.1409, 2115239, 3049620.
    • (1988) J Cell Biol , vol.107 , Issue.4 , pp. 1409-1426
    • Jacobs, C.W.1    Adams, A.E.2    Szaniszlo, P.J.3    Pringle, J.R.4
  • 27
    • 0027582189 scopus 로고
    • Control of the yeast cell cycle by the Cdc28 protein kinase
    • 10.1016/0955-0674(93)90099-C, 8507488
    • Nasmyth K. Control of the yeast cell cycle by the Cdc28 protein kinase. Curr Opin Cell Biol 1993, 5(2):166-179. 10.1016/0955-0674(93)90099-C, 8507488.
    • (1993) Curr Opin Cell Biol , vol.5 , Issue.2 , pp. 166-179
    • Nasmyth, K.1
  • 28
    • 0032055349 scopus 로고    scopus 로고
    • DNA damage checkpoints update: getting molecular
    • 10.1016/S0959-437X(98)80140-8, 9610409
    • Weinert T. DNA damage checkpoints update: getting molecular. Curr Opin Genet Dev 1998, 8(2):185-193. 10.1016/S0959-437X(98)80140-8, 9610409.
    • (1998) Curr Opin Genet Dev , vol.8 , Issue.2 , pp. 185-193
    • Weinert, T.1
  • 29
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • 10.1126/science.1099511, 15567862
    • Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004, 306(5701):1555-1558. 10.1126/science.1099511, 15567862.
    • (2004) Science , vol.306 , Issue.5701 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 30
    • 84934437322 scopus 로고    scopus 로고
    • Integrating functional genomics data
    • 10.1007/978-1-60327-429-6_14, 18712309
    • Lee I, Marcotte EM. Integrating functional genomics data. Methods Mol Biol 2008, 453:267-278. 10.1007/978-1-60327-429-6_14, 18712309.
    • (2008) Methods Mol Biol , vol.453 , pp. 267-278
    • Lee, I.1    Marcotte, E.M.2
  • 31
    • 47549098627 scopus 로고    scopus 로고
    • Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
    • 10.1186/gb-2008-9-s1-s5, 2559989, 18834496
    • Kim WK, Krumpelman C, Marcotte EM. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol 2008, 9(Suppl 1):S5. 10.1186/gb-2008-9-s1-s5, 2559989, 18834496.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 1
    • Kim, W.K.1    Krumpelman, C.2    Marcotte, E.M.3
  • 32
    • 4444352289 scopus 로고    scopus 로고
    • Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data
    • 10.1101/gr.2439804, 509275, 15289483
    • Schmitt WA, Raab RM, Stephanopoulos G. Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Research 2004, 14(8):1654-1663. 10.1101/gr.2439804, 509275, 15289483.
    • (2004) Genome Research , vol.14 , Issue.8 , pp. 1654-1663
    • Schmitt, W.A.1    Raab, R.M.2    Stephanopoulos, G.3
  • 33
    • 13444283846 scopus 로고    scopus 로고
    • Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae
    • 10.1093/nar/gkh978, 535686, 15585665
    • Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res 2004, 32:6414-6424. 10.1093/nar/gkh978, 535686, 15585665.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6414-6424
    • Chen, Y.1    Xu, D.2
  • 34
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • 10.1093/bioinformatics/bti722, 16234317
    • Choi JK, Yu U, Yoo OJ, Kim S. Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 2005, 21(24):4348-4355. 10.1093/bioinformatics/bti722, 16234317.
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 35
    • 50949084896 scopus 로고    scopus 로고
    • Geometric Interpretation of Gene Coexpression Network Analysis
    • 10.1371/journal.pcbi.1000117, 2446438, 18704157
    • Horvath S, Dong J. Geometric Interpretation of Gene Coexpression Network Analysis. PLoS Comput Biol 2008, 4(8):e1000117. 10.1371/journal.pcbi.1000117, 2446438, 18704157.
    • (2008) PLoS Comput Biol , vol.4 , Issue.8
    • Horvath, S.1    Dong, J.2
  • 37
    • 71749094192 scopus 로고    scopus 로고
    • Arabidopsis gene co-expression network and its functional modules
    • 10.1186/1471-2105-10-346, 2772859, 19845953
    • Mao L, Van Hemert JL, Dash S, Dickerson JA. Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 2009, 10:346. 10.1186/1471-2105-10-346, 2772859, 19845953.
    • (2009) BMC Bioinformatics , vol.10 , pp. 346
    • Mao, L.1    Van Hemert, J.L.2    Dash, S.3    Dickerson, J.A.4
  • 38
    • 5044245707 scopus 로고    scopus 로고
    • Gene co-expression network topology provides a framework for molecular characterization of cellular state
    • 10.1093/bioinformatics/bth234, 15130938
    • Carter SL, Brechbühler CM, Griffin M, Bond AT. Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 2004, 20(14):2242-2250. 10.1093/bioinformatics/bth234, 15130938.
    • (2004) Bioinformatics , vol.20 , Issue.14 , pp. 2242-2250
    • Carter, S.L.1    Brechbühler, C.M.2    Griffin, M.3    Bond, A.T.4
  • 40
    • 14844285655 scopus 로고    scopus 로고
    • Comparison of computational methods for the identification of cell cycle-regulated genes
    • 10.1093/bioinformatics/bti093, 15513999
    • de Lichtenberg U, Jensen LJ, Fausbøl A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 2005, 21:1164-1171. 10.1093/bioinformatics/bti093, 15513999.
    • (2005) Bioinformatics , vol.21 , pp. 1164-1171
    • de Lichtenberg, U.1    Jensen, L.J.2    Fausbøl, A.3    Jensen, T.S.4    Bork, P.5    Brunak, S.6
  • 42
    • 77952088459 scopus 로고    scopus 로고
    • An overview of Cdk1-controlled targets and processes
    • 10.1186/1747-1028-5-11, 2876151, 20465793
    • Enserink JM, Kolodner RD. An overview of Cdk1-controlled targets and processes. Cell Div 2010, 5:11. 10.1186/1747-1028-5-11, 2876151, 20465793.
    • (2010) Cell Div , vol.5 , pp. 11
    • Enserink, J.M.1    Kolodner, R.D.2
  • 43
    • 70350573969 scopus 로고    scopus 로고
    • The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression
    • 10.1038/emboj.2009.229, 2760106, 19680226
    • Wade SL, Poorey K, Bekiranov S, Auble DT. The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression. EMBO J 2009, 28(19):2919-2931. 10.1038/emboj.2009.229, 2760106, 19680226.
    • (2009) EMBO J , vol.28 , Issue.19 , pp. 2919-2931
    • Wade, S.L.1    Poorey, K.2    Bekiranov, S.3    Auble, D.T.4
  • 44
    • 33746719425 scopus 로고    scopus 로고
    • The fork'ed path to mitosis
    • 138864, 11277966
    • Jorgensen P, Tyers M. The fork'ed path to mitosis. Genome Biol 2000, 1(3):REVIEWS1022. 138864, 11277966.
    • (2000) Genome Biol , vol.1 , Issue.3
    • Jorgensen, P.1    Tyers, M.2
  • 47
    • 0034098727 scopus 로고    scopus 로고
    • Systematic management and analysis of yeast gene expression data
    • 10.1101/gr.10.4.431, 10779484
    • Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Research 2000, 10(4):431-445. 10.1101/gr.10.4.431, 10779484.
    • (2000) Genome Research , vol.10 , Issue.4 , pp. 431-445
    • Aach, J.1    Rindone, W.2    Church, G.M.3
  • 49
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • 10.1089/cmb.2005.12.835, 16108720
    • Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 2005, 12(6):835-846. 10.1089/cmb.2005.12.835, 16108720.
    • (2005) J Comput Biol , vol.12 , Issue.6 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.M.5
  • 50
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest-path analysis of gene expression data
    • 10.1073/pnas.192159399, 130537, 12196633
    • Zhou X, Kao MC, Wong WH. Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci USA 2002, 99(20):12783-12788. 10.1073/pnas.192159399, 130537, 12196633.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.20 , pp. 12783-12788
    • Zhou, X.1    Kao, M.C.2    Wong, W.H.3
  • 51
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
    • Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000, 418-429.
    • (2000) Pac Symp Biocomput , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.