메뉴 건너뛰기




Volumn 15, Issue 2, 2012, Pages 177-184

Towards understanding how molecular networks evolve in plants

Author keywords

[No Author keywords available]

Indexed keywords

GENE REGULATORY NETWORK; GENETICS; PLANT; REVIEW;

EID: 84859896621     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2012.01.006     Document Type: Review
Times cited : (50)

References (73)
  • 2
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 2002, 9:67-103.
    • (2002) J Comput Biol , vol.9 , pp. 67-103
    • de Jong, H.1
  • 3
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • Feist A.M., Palsson B.O. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-667.
    • (2008) Nat Biotechnol , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 4
    • 70350482286 scopus 로고    scopus 로고
    • Evolution of biomolecular networks: lessons from metabolic and protein interactions
    • Yamada T., Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 2009, 10:791-803.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 791-803
    • Yamada, T.1    Bork, P.2
  • 5
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: a network-based approach to human disease
    • Barabasi A.L., Gulbahce N., Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2010, 12:56-68.
    • (2010) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabasi, A.L.1    Gulbahce, N.2    Loscalzo, J.3
  • 6
    • 34249041230 scopus 로고    scopus 로고
    • Exploring genetic interactions and networks with yeast
    • Boone C., Bussey H., Andrews B.J. Exploring genetic interactions and networks with yeast. Nat Rev Genet 2007, 8:437-449.
    • (2007) Nat Rev Genet , vol.8 , pp. 437-449
    • Boone, C.1    Bussey, H.2    Andrews, B.J.3
  • 7
    • 33748980210 scopus 로고    scopus 로고
    • Evolutionary systems biology: links between gene evolution and function
    • Koonin E.V., Wolf Y.I. Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol 2006, 17:481-487.
    • (2006) Curr Opin Biotechnol , vol.17 , pp. 481-487
    • Koonin, E.V.1    Wolf, Y.I.2
  • 8
    • 64049093033 scopus 로고    scopus 로고
    • A framework for evolutionary systems biology
    • Loewe L. A framework for evolutionary systems biology. BMC Syst Biol 2009, 3:27.
    • (2009) BMC Syst Biol , vol.3 , pp. 27
    • Loewe, L.1
  • 9
    • 67651039811 scopus 로고    scopus 로고
    • Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition
    • Freeling M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol 2009, 60:433-453.
    • (2009) Annu Rev Plant Biol , vol.60 , pp. 433-453
    • Freeling, M.1
  • 10
    • 0036303685 scopus 로고    scopus 로고
    • Evolution of enzymes in metabolism: a network perspective
    • Alves R., Chaleil R.A., Sternberg M.J. Evolution of enzymes in metabolism: a network perspective. J Mol Biol 2002, 320:751-770.
    • (2002) J Mol Biol , vol.320 , pp. 751-770
    • Alves, R.1    Chaleil, R.A.2    Sternberg, M.J.3
  • 12
    • 34447502516 scopus 로고    scopus 로고
    • A network perspective on the evolution of metabolism by gene duplication
    • Diaz-Mejia J.J., Perez-Rueda E., Segovia L. A network perspective on the evolution of metabolism by gene duplication. Genome Biol 2007, 8:R26.
    • (2007) Genome Biol , vol.8
    • Diaz-Mejia, J.J.1    Perez-Rueda, E.2    Segovia, L.3
  • 13
    • 33847634233 scopus 로고    scopus 로고
    • Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins
    • Veron A.S., Kaufmann K., Bornberg-Bauer E. Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Mol Biol Evol 2007, 24:670-678.
    • (2007) Mol Biol Evol , vol.24 , pp. 670-678
    • Veron, A.S.1    Kaufmann, K.2    Bornberg-Bauer, E.3
  • 14
    • 2942624207 scopus 로고    scopus 로고
    • Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
    • Papp B., Pal C., Hurst L.D. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 2004, 429:661-664.
    • (2004) Nature , vol.429 , pp. 661-664
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 15
    • 77950949952 scopus 로고    scopus 로고
    • The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution
    • Birchler J.A., Veitia R.A. The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 2010, 186:54-62.
    • (2010) New Phytol , vol.186 , pp. 54-62
    • Birchler, J.A.1    Veitia, R.A.2
  • 16
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • Kuepfer L., Sauer U., Blank L.M. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15:1421-1430.
    • (2005) Genome Res , vol.15 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 17
    • 84857780876 scopus 로고    scopus 로고
    • Evidence for network evolution in an Arabidopsis interactome map
    • Arabidopsis-Interactome-Mapping-Consortium
    • Arabidopsis-Interactome-Mapping-Consortium Evidence for network evolution in an Arabidopsis interactome map. Science 2011, 333:601-607.
    • (2011) Science , vol.333 , pp. 601-607
  • 18
    • 33646859550 scopus 로고    scopus 로고
    • Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
    • Casneuf T., De Bodt S., Raes J., Maere S., Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 2006, 7:R13.
    • (2006) Genome Biol , vol.7
    • Casneuf, T.1    De Bodt, S.2    Raes, J.3    Maere, S.4    Van de Peer, Y.5
  • 19
    • 33847249901 scopus 로고    scopus 로고
    • Specificity and evolvability in eukaryotic protein interaction networks
    • Beltrao P., Serrano L. Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 2007, 3:e25.
    • (2007) PLoS Comput Biol , vol.3
    • Beltrao, P.1    Serrano, L.2
  • 20
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 2001, 18:1283-1292.
    • (2001) Mol Biol Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 22
    • 48249124644 scopus 로고    scopus 로고
    • Protein complex evolution does not involve extensive network rewiring
    • van Dam T.J., Snel B. Protein complex evolution does not involve extensive network rewiring. PLoS Comput Biol 2008, 4:e1000132.
    • (2008) PLoS Comput Biol , vol.4
    • van Dam, T.J.1    Snel, B.2
  • 23
    • 84859890901 scopus 로고    scopus 로고
    • Redundancy and rewiring of genetic networks following genome-wide duplication events
    • this issue. doi:10.1016/j.pbi.2012.01.003
    • De Smet R, Van de Peer Y: Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr Opin Plant Biol 2012, , this issue. doi:10.1016/j.pbi.2012.01.003.
    • (2012) Curr Opin Plant Biol
    • De Smet, R.1    Van de Peer, Y.2
  • 24
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 25
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • Réka Albert: Scale-free networks in cell biology. J Cell Sci 2005, 118:4947-4957.
    • (2005) J Cell Sci , vol.118 , pp. 4947-4957
    • Réka, A.1
  • 26
    • 76349125292 scopus 로고    scopus 로고
    • Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
    • Lee I., Ambaru B., Thakkar P., Marcotte E.M., Rhee S.Y. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 2010, 28:149-156.
    • (2010) Nat Biotechnol , vol.28 , pp. 149-156
    • Lee, I.1    Ambaru, B.2    Thakkar, P.3    Marcotte, E.M.4    Rhee, S.Y.5
  • 28
    • 33745107471 scopus 로고    scopus 로고
    • Influence of metabolic network structure and function on enzyme evolution
    • Vitkup D., Kharchenko P., Wagner A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol 2006, 7:R39.
    • (2006) Genome Biol , vol.7
    • Vitkup, D.1    Kharchenko, P.2    Wagner, A.3
  • 29
    • 0842290925 scopus 로고    scopus 로고
    • Molecular evolution in large genetic networks: does connectivity equal constraint?
    • Hahn M.W., Conant G.C., Wagner A. Molecular evolution in large genetic networks: does connectivity equal constraint?. J Mol Evol 2004, 58:203-211.
    • (2004) J Mol Evol , vol.58 , pp. 203-211
    • Hahn, M.W.1    Conant, G.C.2    Wagner, A.3
  • 30
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond D.A., Raval A., Wilke C.O. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 2006, 23:327-337.
    • (2006) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 31
  • 32
    • 50949092459 scopus 로고    scopus 로고
    • Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
    • Zotenko E., Mestre J., O'Leary D.P., Przytycka T.M. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4:e1000140.
    • (2008) PLoS Comput Biol , vol.4
    • Zotenko, E.1    Mestre, J.2    O'Leary, D.P.3    Przytycka, T.M.4
  • 33
    • 70449647110 scopus 로고    scopus 로고
    • How to identify essential genes from molecular networks?
    • del Rio G., Koschutzki D., Coello G. How to identify essential genes from molecular networks?. BMC Syst Biol 2009, 3:102.
    • (2009) BMC Syst Biol , vol.3 , pp. 102
    • del Rio, G.1    Koschutzki, D.2    Coello, G.3
  • 34
    • 65449187535 scopus 로고    scopus 로고
    • Evolutionary rates and centrality in the yeast gene regulatory network
    • Jovelin R., Phillips P.C. Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol 2009, 10:R35.
    • (2009) Genome Biol , vol.10
    • Jovelin, R.1    Phillips, P.C.2
  • 35
    • 57149118625 scopus 로고    scopus 로고
    • Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
    • Kim W.K., Marcotte E.M. Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PLoS Comput Biol 2008, 4:e1000232.
    • (2008) PLoS Comput Biol , vol.4
    • Kim, W.K.1    Marcotte, E.M.2
  • 36
    • 34447624151 scopus 로고    scopus 로고
    • Gene essentiality, gene duplicability and protein connectivity in human and mouse
    • Liang H., Li W.H. Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet 2007, 23:375-378.
    • (2007) Trends Genet , vol.23 , pp. 375-378
    • Liang, H.1    Li, W.H.2
  • 37
    • 77952253818 scopus 로고    scopus 로고
    • Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication
    • Wu X., Qi X. Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. BMC Evol Biol 2010, 10:145.
    • (2010) BMC Evol Biol , vol.10 , pp. 145
    • Wu, X.1    Qi, X.2
  • 38
    • 79961064486 scopus 로고    scopus 로고
    • Factors that contribute to variation in evolutionary rate among Arabidopsis genes
    • Yang L., Gaut B.S. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol 2011, 28:2359-2369.
    • (2011) Mol Biol Evol , vol.28 , pp. 2359-2369
    • Yang, L.1    Gaut, B.S.2
  • 39
    • 33745020639 scopus 로고    scopus 로고
    • A metabolic network in the evolutionary context: multiscale structure and modularity
    • Spirin V., Gelfand M.S., Mironov A.A., Mirny L.A. A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci USA 2006, 103:8774-8779.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 8774-8779
    • Spirin, V.1    Gelfand, M.S.2    Mironov, A.A.3    Mirny, L.A.4
  • 41
    • 1542286745 scopus 로고    scopus 로고
    • Quantifying modularity in the evolution of biomolecular systems
    • Snel B., Huynen M.A. Quantifying modularity in the evolution of biomolecular systems. Genome Res 2004, 14:391-397.
    • (2004) Genome Res , vol.14 , pp. 391-397
    • Snel, B.1    Huynen, M.A.2
  • 42
    • 33644644466 scopus 로고    scopus 로고
    • Identification and analysis of evolutionarily cohesive functional modules in protein networks
    • Campillos M., von Mering C., Jensen L.J., Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 2006, 16:374-382.
    • (2006) Genome Res , vol.16 , pp. 374-382
    • Campillos, M.1    von Mering, C.2    Jensen, L.J.3    Bork, P.4
  • 43
    • 59149100474 scopus 로고    scopus 로고
    • Cohesive versus flexible evolution of functional modules in eukaryotes
    • Fokkens L., Snel B. Cohesive versus flexible evolution of functional modules in eukaryotes. PLoS Comput Biol 2009, 5:e1000276.
    • (2009) PLoS Comput Biol , vol.5
    • Fokkens, L.1    Snel, B.2
  • 45
    • 73349113515 scopus 로고    scopus 로고
    • Metabolic adaptation after whole genome duplication
    • van Hoek M.J., Hogeweg P. Metabolic adaptation after whole genome duplication. Mol Biol Evol 2009, 26:2441-2453.
    • (2009) Mol Biol Evol , vol.26 , pp. 2441-2453
    • van Hoek, M.J.1    Hogeweg, P.2
  • 46
    • 74549117172 scopus 로고    scopus 로고
    • Evolutionary plasticity and innovations in complex metabolic reaction networks
    • Matias Rodrigues J.F., Wagner A. Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput Biol 2009, 5:e1000613.
    • (2009) PLoS Comput Biol , vol.5
    • Matias Rodrigues, J.F.1    Wagner, A.2
  • 54
    • 78650647272 scopus 로고    scopus 로고
    • Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
    • Pop A., Huttenhower C., Iyer-Pascuzzi A., Benfey P.N., Troyanskaya O.G. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol 2010, 4:180.
    • (2010) BMC Syst Biol , vol.4 , pp. 180
    • Pop, A.1    Huttenhower, C.2    Iyer-Pascuzzi, A.3    Benfey, P.N.4    Troyanskaya, O.G.5
  • 55
    • 78049415019 scopus 로고    scopus 로고
    • Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis
    • Jimenez-Gomez J.M., Wallace A.D., Maloof J.N. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 2010, 6.
    • (2010) PLoS Genet , vol.6
    • Jimenez-Gomez, J.M.1    Wallace, A.D.2    Maloof, J.N.3
  • 56
    • 80052338881 scopus 로고    scopus 로고
    • Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana
    • Chan E.K., Rowe H.C., Corwin J.A., Joseph B., Kliebenstein D.J. Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biol 2011, 9:e1001125.
    • (2011) PLoS Biol , vol.9
    • Chan, E.K.1    Rowe, H.C.2    Corwin, J.A.3    Joseph, B.4    Kliebenstein, D.J.5
  • 57
    • 84859807430 scopus 로고    scopus 로고
    • Integrating rare-variant testing, function prediction, and gene network in composite resequencing-based genome-wide association studies (CR-GWAS)
    • Zhu C., Li X., Yu J. Integrating rare-variant testing, function prediction, and gene network in composite resequencing-based genome-wide association studies (CR-GWAS). Genes Genomes Genet 2011, 1:233-243.
    • (2011) Genes Genomes Genet , vol.1 , pp. 233-243
    • Zhu, C.1    Li, X.2    Yu, J.3
  • 60
    • 33746887057 scopus 로고    scopus 로고
    • Escalating model sizes and complexities call for standardized forms of representation
    • 2005.0011
    • Hucka M., Finney A. Escalating model sizes and complexities call for standardized forms of representation. Mol Syst Biol 2005, 1. 2005.0011.
    • (2005) Mol Syst Biol , vol.1
    • Hucka, M.1    Finney, A.2
  • 61
    • 33846551980 scopus 로고    scopus 로고
    • Empirical fitness landscapes reveal accessible evolutionary paths
    • Poelwijk F.J., Kiviet D.J., Weinreich D.M., Tans S.J. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 2007, 445:383-386.
    • (2007) Nature , vol.445 , pp. 383-386
    • Poelwijk, F.J.1    Kiviet, D.J.2    Weinreich, D.M.3    Tans, S.J.4
  • 62
    • 38149142837 scopus 로고    scopus 로고
    • Getting to grips with the plant metabolic network
    • Sweetlove L.J., Fell D., Fernie A.R. Getting to grips with the plant metabolic network. Biochem J 2008, 409:27-41.
    • (2008) Biochem J , vol.409 , pp. 27-41
    • Sweetlove, L.J.1    Fell, D.2    Fernie, A.R.3
  • 63
    • 38949195338 scopus 로고    scopus 로고
    • Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations
    • Lalonde S., Ehrhardt D.W., Loque D., Chen J., Rhee S.Y., Frommer W.B. Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations. Plant J 2008, 53:610-635.
    • (2008) Plant J , vol.53 , pp. 610-635
    • Lalonde, S.1    Ehrhardt, D.W.2    Loque, D.3    Chen, J.4    Rhee, S.Y.5    Frommer, W.B.6
  • 65
    • 35948931439 scopus 로고    scopus 로고
    • An Arabidopsis gene network based on the graphical Gaussian model
    • Ma S., Gong Q., Bohnert H.J. An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 2007, 17:1614-1625.
    • (2007) Genome Res , vol.17 , pp. 1614-1625
    • Ma, S.1    Gong, Q.2    Bohnert, H.J.3
  • 67
    • 79956139639 scopus 로고    scopus 로고
    • Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops
    • Mochida K., Uehara-Yamaguchi Y., Yoshida T., Sakurai T., Shinozaki K. Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol 2011, 52:785-803.
    • (2011) Plant Cell Physiol , vol.52 , pp. 785-803
    • Mochida, K.1    Uehara-Yamaguchi, Y.2    Yoshida, T.3    Sakurai, T.4    Shinozaki, K.5
  • 68
    • 77956674928 scopus 로고    scopus 로고
    • The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks
    • Ficklin S.P., Luo F., Feltus F.A. The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. Plant Physiol 2010, 154:13-24.
    • (2010) Plant Physiol , vol.154 , pp. 13-24
    • Ficklin, S.P.1    Luo, F.2    Feltus, F.A.3
  • 69
    • 79960657553 scopus 로고    scopus 로고
    • Gene coexpression network analysis as a source of functional annotation for rice genes
    • Childs K.L., Davidson R.M., Buell C.R. Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE 2011, 6:e22196.
    • (2011) PLoS ONE , vol.6
    • Childs, K.L.1    Davidson, R.M.2    Buell, C.R.3
  • 73
    • 77955695587 scopus 로고    scopus 로고
    • Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants
    • Zhang P., Dreher K., Karthikeyan A., Chi A., Pujar A., Caspi R., Karp P., Kirkup V., Latendresse M., Lee C., et al. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 2010, 153:1479-1491.
    • (2010) Plant Physiol , vol.153 , pp. 1479-1491
    • Zhang, P.1    Dreher, K.2    Karthikeyan, A.3    Chi, A.4    Pujar, A.5    Caspi, R.6    Karp, P.7    Kirkup, V.8    Latendresse, M.9    Lee, C.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.