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Volumn 158, Issue 4, 2012, Pages 1487-1502

Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches

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LYCOPERSICON ESCULENTUM;

EID: 84859336922     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.111.188367     Document Type: Article
Times cited : (55)

References (71)
  • 1
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 3
    • 34249697574 scopus 로고    scopus 로고
    • Approaches for extracting practical information from gene co-expression networks in plant biology
    • Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390
    • (2007) Plant Cell Physiol , vol.48 , pp. 381-390
    • Aoki, K.1    Ogata, Y.2    Shibata, D.3
  • 4
    • 77956679288 scopus 로고    scopus 로고
    • Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
    • AtiasO, Chor B, ChamovitzDA(2009) Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC Syst Biol 3: 86
    • (2009) BMC Syst Biol , vol.3 , pp. 86
    • Atias, O.1    Chor, B.2    Chamovitz, D.A.3
  • 5
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 8
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300
    • (1995) J R Stat Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 77950537784 scopus 로고    scopus 로고
    • Source to sink: Regulation of carotenoid biosynthesis in plants
    • Cazzonelli CI, Pogson BJ (2010) Source to sink: regulation of carotenoid biosynthesis in plants. Trends Plant Sci 15: 266-274
    • (2010) Trends Plant Sci , vol.15 , pp. 266-274
    • Cazzonelli, C.I.1    Pogson, B.J.2
  • 12
    • 0031200962 scopus 로고    scopus 로고
    • A gene fusion at a homeobox locus: Alterations in leaf shape and implications for morphological evolution
    • Chen JJ, Janssen BJ, Williams A, Sinha N (1997) A gene fusion at a homeobox locus: alterations in leaf shape and implications for morphological evolution. Plant Cell 9: 1289-1304
    • (1997) Plant Cell , vol.9 , pp. 1289-1304
    • Chen, J.J.1    Janssen, B.J.2    Williams, A.3    Sinha, N.4
  • 13
    • 77954311470 scopus 로고    scopus 로고
    • Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms
    • Chia BK, Karuturi RK (2010) Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms. Algorithms Mol Biol 5: 23
    • (2010) Algorithms Mol Biol , vol.5 , pp. 23
    • Chia, B.K.1    Karuturi, R.K.2
  • 14
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • Choi JK, Yu U, Yoo OJ, Kim S (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355
    • (2005) Bioinformatics , vol.21 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 15
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Systems 1695. http://igraph. sf.net
    • (2006) InterJournal Complex Systems , vol.1695
    • Csardi, G.1    Nepusz, T.2
  • 16
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking': Identification of dysfunctional regulatory networks in diseases
    • de la Fuente A (2010) From 'differential expression' to 'differential networking': identification of dysfunctional regulatory networks in diseases. Trends Genet 26: 326-333
    • (2010) Trends Genet , vol.26 , pp. 326-333
    • de la Fuente, A.1
  • 17
    • 34548550573 scopus 로고    scopus 로고
    • Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
    • Elo LL, Järvenpää H, Oresic M, Lahesmaa R, Aittokallio T (2007) Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103
    • (2007) Bioinformatics , vol.23 , pp. 2096-2103
    • Elo, L.L.1    Järvenpää, H.2    Oresic, M.3    Lahesmaa, R.4    Aittokallio, T.5
  • 19
    • 76349097837 scopus 로고    scopus 로고
    • Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach
    • Fukushima A, Kanaya S, Arita M (2009a) Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach. Plant Biotechnol 26: 485-493
    • (2009) Plant Biotechnol , vol.26 , pp. 485-493
    • Fukushima, A.1    Kanaya, S.2    Arita, M.3
  • 21
    • 78650676139 scopus 로고    scopus 로고
    • Metabolomic correlation-network modules in Arabidopsis based on a graphclustering approach
    • Fukushima A, Kusano M, Redestig H, Arita M, Saito K (2011) Metabolomic correlation-network modules in Arabidopsis based on a graphclustering approach. BMC Syst Biol 5: 1
    • (2011) BMC Syst Biol , vol.5 , pp. 1
    • Fukushima, A.1    Kusano, M.2    Redestig, H.3    Arita, M.4    Saito, K.5
  • 22
    • 39249083203 scopus 로고    scopus 로고
    • Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content
    • Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J (2008) Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J 53: 717-730
    • (2008) Plant J , vol.53 , pp. 717-730
    • Galpaz, N.1    Wang, Q.2    Menda, N.3    Zamir, D.4    Hirschberg, J.5
  • 23
    • 1342288026 scopus 로고    scopus 로고
    • Affy: Analysis of Affymetrix GeneChip data at the probe level
    • Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy: analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 26
    • 70449358722 scopus 로고    scopus 로고
    • A methodology for the analysis of differential coexpression across the human lifespan
    • Gillis J, Pavlidis P (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics 10: 306
    • (2009) BMC Bioinformatics , vol.10 , pp. 306
    • Gillis, J.1    Pavlidis, P.2
  • 28
    • 34147133691 scopus 로고    scopus 로고
    • Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
    • Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM (2007) Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8: R7
    • (2007) Genome Biol , vol.8
    • Gutiérrez, R.A.1    Lejay, L.V.2    Dean, A.3    Chiaromonte, F.4    Shasha, D.E.5    Coruzzi, G.M.6
  • 33
    • 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 EM, Rhee SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 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
  • 34
    • 54349096842 scopus 로고    scopus 로고
    • Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    • Li M, Chen JE, Wang JX, Hu B, Chen G (2008) Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 9: 398
    • (2008) BMC Bioinformatics , vol.9 , pp. 398
    • Li, M.1    Chen, J.E.2    Wang, J.X.3    Hu, B.4    Chen, G.5
  • 35
    • 34248329496 scopus 로고    scopus 로고
    • Convergent evolution in the BAHD family of acyl transferases: Identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana
    • Luo J, Nishiyama Y, Fuell C, Taguchi G, Elliott K, Hill L, Tanaka Y, Kitayama M, Yamazaki M, Bailey P, et al (2007) Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Plant J 50: 678-695
    • (2007) Plant J , vol.50 , pp. 678-695
    • Luo, J.1    Nishiyama, Y.2    Fuell, C.3    Taguchi, G.4    Elliott, K.5    Hill, L.6    Tanaka, Y.7    Kitayama, M.8    Yamazaki, M.9    Bailey, P.10
  • 36
    • 35948931439 scopus 로고    scopus 로고
    • An Arabidopsis gene network based on the graphical Gaussian model
    • Ma S, Gong Q, Bohnert HJ (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17: 1614-1625
    • (2007) Genome Res , vol.17 , pp. 1614-1625
    • Ma, S.1    Gong, Q.2    Bohnert, H.J.3
  • 37
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks
    • Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21: 3448-3449
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 39
  • 40
    • 77953230084 scopus 로고    scopus 로고
    • ORTom: A multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato
    • Miozzi L, Provero P, Accotto GP (2010) ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Mol Biol 73: 519-532
    • (2010) Plant Mol Biol , vol.73 , pp. 519-532
    • Miozzi, L.1    Provero, P.2    Accotto, G.P.3
  • 42
    • 32044454046 scopus 로고    scopus 로고
    • Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation
    • Morgenthal K, Weckwerth W, Steuer R (2006) Metabolomic networks in plants: transitions from pattern recognition to biological interpretation. Biosystems 83: 108-117
    • (2006) Biosystems , vol.83 , pp. 108-117
    • Morgenthal, K.1    Weckwerth, W.2    Steuer, R.3
  • 45
    • 79951562208 scopus 로고    scopus 로고
    • ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    • Obayashi T, Nishida K, Kasahara K, Kinoshita K (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 52: 213-219
    • (2011) Plant Cell Physiol , vol.52 , pp. 213-219
    • Obayashi, T.1    Nishida, K.2    Kasahara, K.3    Kinoshita, K.4
  • 46
    • 77952799294 scopus 로고    scopus 로고
    • CoP: A database for characterizing co-expressed gene modules with biological information in plants
    • Ogata Y, Suzuki H, Sakurai N, Shibata D (2010) CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26: 1267-1268
    • (2010) Bioinformatics , vol.26 , pp. 1267-1268
    • Ogata, Y.1    Suzuki, H.2    Sakurai, N.3    Shibata, D.4
  • 47
    • 77951137933 scopus 로고    scopus 로고
    • Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
    • Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, et al (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17: 105-116
    • (2010) DNA Res , vol.17 , pp. 105-116
    • Ozaki, S.1    Ogata, Y.2    Suda, K.3    Kurabayashi, A.4    Suzuki, T.5    Yamamoto, N.6    Iijima, Y.7    Tsugane, T.8    Fujii, T.9    Konishi, C.10
  • 49
    • 20844445318 scopus 로고    scopus 로고
    • Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
    • Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 8633-8638
    • Persson, S.1    Wei, H.2    Milne, J.3    Page, G.P.4    Somerville, C.R.5
  • 50
    • 37849020436 scopus 로고    scopus 로고
    • Decoding genes with coexpression networks and metabolomics: 'majority report by precogs'
    • Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics: 'majority report by precogs.' Trends Plant Sci 13: 36-43
    • (2008) Trends Plant Sci , vol.13 , pp. 36-43
    • Saito, K.1    Hirai, M.Y.2    Yonekura-Sakakibara, K.3
  • 51
    • 78651340558 scopus 로고    scopus 로고
    • KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
    • Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, et al (2011) KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res 39: D677-D684
    • (2011) Nucleic Acids Res , vol.39
    • Sakurai, N.1    Ara, T.2    Ogata, Y.3    Sano, R.4    Ohno, T.5    Sugiyama, K.6    Hiruta, A.7    Yamazaki, K.8    Yano, K.9    Aoki, K.10
  • 53
    • 75949127736 scopus 로고    scopus 로고
    • Metabolic networks: How to identify key components in the regulation of metabolism and growth
    • Stitt M, Sulpice R, Keurentjes J (2010) Metabolic networks: how to identify key components in the regulation of metabolism and growth. Plant Physiol 152: 428-444
    • (2010) Plant Physiol , vol.152 , pp. 428-444
    • Stitt, M.1    Sulpice, R.2    Keurentjes, J.3
  • 54
    • 45449097447 scopus 로고    scopus 로고
    • Fdrtool: A versatile R package for estimating local and tail area-based false discovery rates
    • Strimmer K (2008) fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24: 1461-1462
    • (2008) Bioinformatics , vol.24 , pp. 1461-1462
    • Strimmer, K.1
  • 55
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 58
    • 77954396635 scopus 로고    scopus 로고
    • Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function
    • Tohge T, Fernie AR (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 5: 1210-1227
    • (2010) Nat Protoc , vol.5 , pp. 1210-1227
    • Tohge, T.1    Fernie, A.R.2
  • 61
    • 0035984046 scopus 로고    scopus 로고
    • Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing
    • Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456
    • (2002) Plant Cell , vol.14 , pp. 1441-1456
    • van der Hoeven, R.1    Ronning, C.2    Giovannoni, J.3    Martin, G.4    Tanksley, S.5
  • 63
    • 34247504045 scopus 로고    scopus 로고
    • Tomato linalool synthase is induced in trichomes by jasmonic acid
    • van Schie CC, Haring MA, Schuurink RC (2007) Tomato linalool synthase is induced in trichomes by jasmonic acid. Plant Mol Biol 64: 251-263
    • (2007) Plant Mol Biol , vol.64 , pp. 251-263
    • van Schie, C.C.1    Haring, M.A.2    Schuurink, R.C.3
  • 65
    • 78649679994 scopus 로고    scopus 로고
    • Recent advances in clustering methods for protein interaction networks
    • Wang J, LiM, Deng Y, Pan Y (2010) Recent advances in clustering methods for protein interaction networks. BMC Genomics (Suppl 3) 11: S10
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 3
    • Wang, J.1    Li, M.2    Deng, Y.3    Pan, Y.4
  • 66
    • 34547649056 scopus 로고    scopus 로고
    • CoXpress: Differential co-expression in gene expression data
    • Watson M (2006) CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 7: 509
    • (2006) BMC Bioinformatics , vol.7 , pp. 509
    • Watson, M.1
  • 67
    • 2442647715 scopus 로고    scopus 로고
    • Differential metabolic networks unravel the effects of silent plant phenotypes
    • Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci USA 101: 7809-7814
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7809-7814
    • Weckwerth, W.1    Loureiro, M.E.2    Wenzel, K.3    Fiehn, O.4
  • 70
    • 34447502537 scopus 로고    scopus 로고
    • Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics
    • Yonekura-Sakakibara K, Tohge T, Niida R, Saito K (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 282: 14932-14941
    • (2007) J Biol Chem , vol.282 , pp. 14932-14941
    • Yonekura-Sakakibara, K.1    Tohge, T.2    Niida, R.3    Saito, K.4
  • 71
    • 0000234892 scopus 로고
    • Flavonoids content of tomato plants for the study of the nutritional status
    • Zornoza P, Esteban RM (1984) Flavonoids content of tomato plants for the study of the nutritional status. Plant Soil 82: 269-271
    • (1984) Plant Soil , vol.82 , pp. 269-271
    • Zornoza, P.1    Esteban, R.M.2


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