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Volumn 3, Issue NOV, 2012, Pages

Co-expression and co-responses: Within and beyond transcription

Author keywords

Correlation analysis; Gene annotation; Gene expression; Network analysis; Plant metabolism

Indexed keywords


EID: 84881317781     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00248     Document Type: Review
Times cited : (26)

References (76)
  • 1
    • 84863727506 scopus 로고    scopus 로고
    • AtABCG29 is a monolignol transporter involved in lignin biosynthesis
    • Alejandro, S., Lee, Y., Tohge, T., Sudre, D., Osorio, S., Park, J., et al. (2012). AtABCG29 is a monolignol transporter involved in lignin biosynthesis. Curr. Biol. 10, 1207-1212.
    • (2012) Curr. Biol. , vol.10 , pp. 1207-1212
    • Alejandro, S.1    Lee, Y.2    Tohge, T.3    Sudre, D.4    Osorio, S.5    Park, J.6
  • 2
    • 77954071738 scopus 로고    scopus 로고
    • Correlation network analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
    • doi: 10.1186/1752-0509-4-62
    • Allen, E., Moing, A., Ebbels, T. M., Maucourt, M., Tomos, A. D., Rolin, D., et al. (2010). Correlation network analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. BMC Syst. Biol. 4, 62. doi: 10.1186/1752-0509-4-62
    • (2010) BMC Syst. Biol. , vol.4 , pp. 62
    • Allen, E.1    Moing, A.2    Ebbels, T.M.3    Maucourt, M.4    Tomos, A.D.5    Rolin, D.6
  • 3
    • 77954395693 scopus 로고    scopus 로고
    • Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria
    • Araújo, W. L., Ishizaki, K., Nunes-Nesi, A., Larson, T. R., Tohge, T., Krahnert, I., et al. (2010). Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria. Plant Cell 22, 1549-1563.
    • (2010) Plant Cell , vol.22 , pp. 1549-1563
    • Araújo, W.L.1    Ishizaki, K.2    Nunes-Nesi, A.3    Larson, T.R.4    Tohge, T.5    Krahnert, I.6
  • 4
    • 80052415236 scopus 로고    scopus 로고
    • Analysis of a range of catabolic mutants provides evidence that phytanoyl-coenzyme A does not act as a substrate of the electron-transfer flavoprotein/electron-transfer flavoprotein: Ubiquinone oxidoreductase complex in Arabidopsis during dark-induced senescence
    • Araujo, W. L., Ishizaki, K., Nunes-Nesi, A., Tohge, T., Larson, T. R., Krahnert, I., et al. (2011). Analysis of a range of catabolic mutants provides evidence that phytanoyl-coenzyme A does not act as a substrate of the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex in Arabidopsis during dark-induced senescence. Plant Physiol. 157, 55-69.
    • (2011) Plant Physiol. , vol.157 , pp. 55-69
    • Araujo, W.L.1    Ishizaki, K.2    Nunes-Nesi, A.3    Tohge, T.4    Larson, T.R.5    Krahnert, I.6
  • 5
    • 80052334837 scopus 로고    scopus 로고
    • Protein degradation-an alternative respiratory substrate for stressed plants
    • Araújo, W. L., Tohge, T., Ishizaki, K., Leaver, C. J., and Fernie, A. R. (2011). Protein degradation-an alternative respiratory substrate for stressed plants. Trends Plant Sci. 16, 489-498.
    • (2011) Trends Plant Sci. , vol.16 , pp. 489-498
    • Araújo, W.L.1    Tohge, T.2    Ishizaki, K.3    Leaver, C.J.4    Fernie, A.R.5
  • 6
    • 80052722558 scopus 로고    scopus 로고
    • SEED: Efficient clustering of next-generation sequences
    • Bao, E., Jiang, T., Kaloshian, I., and Girke, T. (2011). SEED: efficient clustering of next-generation sequences. Bioinformatics 27, 2502-2509.
    • (2011) Bioinformatics , vol.27 , pp. 2502-2509
    • Bao, E.1    Jiang, T.2    Kaloshian, I.3    Girke, T.4
  • 7
    • 79959350055 scopus 로고    scopus 로고
    • Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions
    • Bassel, G. W., Lan, H., Glaab, E., Gibbs, D. J., Gerjets, T., Krasnogor, N., et al. (2011). Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc. Natl. Acad. Sci. U.S.A. 108, 9709-9714.
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 9709-9714
    • Bassel, G.W.1    Lan, H.2    Glaab, E.3    Gibbs, D.J.4    Gerjets, T.5    Krasnogor, N.6
  • 8
    • 27644451872 scopus 로고    scopus 로고
    • Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics
    • Brown, D. M., Zeef, L. A. H., Ellis, J., Goodacre, R., and Turner, S. R. (2005). Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell17, 2281-2295.
    • (2005) Plant Cell , vol.17 , pp. 2281-2295
    • Brown, D.M.1    Zeef, L.A.H.2    Ellis, J.3    Goodacre, R.4    Turner, S.R.5
  • 9
    • 84870725271 scopus 로고    scopus 로고
    • Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models
    • doi: 10.3389/fpls.2012.00124
    • Chen, J., Lalonde, S., Obrdlik, P., Noorani Vatani, A., Parsa, S., Vilarino, C., et al. (2012). Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Front. Plant Sci. 3:124. doi: 10.3389/fpls.2012.00124
    • (2012) Front. Plant Sci. , vol.3 , pp. 124
    • Chen, J.1    Lalonde, S.2    Obrdlik, P.3    Noorani Vatani, A.4    Parsa, S.5    Vilarino, C.6
  • 10
    • 79960657553 scopus 로고    scopus 로고
    • Gene coexpression network analysis as a source of functional annotation for rice genes
    • doi: 10.1371/journal.pone.0022196
    • Childs, K. L., Davidson, R. M., and Buell, C. R. (2011). Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE 6, e22196. doi: 10.1371/journal.pone.0022196
    • (2011) PLoS ONE , vol.6
    • Childs, K.L.1    Davidson, R.M.2    Buell, C.R.3
  • 13
    • 84863780541 scopus 로고    scopus 로고
    • CORNET 2.0: Integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
    • De Bodt, S., Hollunder, J., Nelissen, H., Meulemeester, N., and Inzé, D. (2012). CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol. 195, 707-720.
    • (2012) New Phytol. , vol.195 , pp. 707-720
    • De Bodt, S.1    Hollunder, J.2    Nelissen, H.3    Meulemeester, N.4    Inzé, D.5
  • 14
    • 77949368165 scopus 로고    scopus 로고
    • TobEA: An atlas of tobacco gene expression from seed to senescence
    • doi: 10.1186/1471-2164-11-142
    • Edwards, K. D., Bombarely, A., Story, G. W., Allen, F., Mueller, L. A., Coates, S. A., et al. (2010). TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics 11, 142. doi: 10.1186/1471-2164-11-142
    • (2010) BMC Genomics , vol.11 , pp. 142
    • Edwards, K.D.1    Bombarely, A.2    Story, G.W.3    Allen, F.4    Mueller, L.A.5    Coates, S.A.6
  • 15
    • 33745459298 scopus 로고    scopus 로고
    • Identification of a vacuolar sucrose transporter in barley and Arabidopsis mesophyll cells by a tonoplast proteomic approach
    • Endler, A., Meyer, S., Schelbert, S., Schneider, T., Weschke, W., Peters, S. W., et al. (2006). Identification of a vacuolar sucrose transporter in barley and Arabidopsis mesophyll cells by a tonoplast proteomic approach. Plant Physiol. 141, 196-207.
    • (2006) Plant Physiol. , vol.141 , pp. 196-207
    • Endler, A.1    Meyer, S.2    Schelbert, S.3    Schneider, T.4    Weschke, W.5    Peters, S.W.6
  • 16
    • 24744468755 scopus 로고    scopus 로고
    • From single genes to co-expression networks: Extracting knowledge from barley functional genomics
    • Faccioli, P., Provero, P., Herrmann, C., Stanca, A. M., Morcia, C., and Terzi, V. (2005). From single genes to co-expression networks: extracting knowledge from barley functional genomics. Plant Mol. Biol. 58, 739-750.
    • (2005) Plant Mol. Biol. , vol.58 , pp. 739-750
    • Faccioli, P.1    Provero, P.2    Herrmann, C.3    Stanca, A.M.4    Morcia, C.5    Terzi, V.6
  • 17
    • 79959995342 scopus 로고    scopus 로고
    • Gene coexpression network alignment and conservation of gene modules between two grass species: Maize and rice
    • Ficklin, S. P., and Feltus, F. A. (2011). Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiol. 156, 1244-1256.
    • (2011) Plant Physiol. , vol.156 , pp. 1244-1256
    • Ficklin, S.P.1    Feltus, F.A.2
  • 18
    • 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., and Feltus, F. A. (2010). The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. Plant Physiol. 154, 13-24.
    • (2010) Plant Physiol. , vol.154 , pp. 13-24
    • Ficklin, S.P.1    Luo, F.2    Feltus, F.A.3
  • 19
    • 76349097837 scopus 로고    scopus 로고
    • Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach
    • Fukushima, A., Kanaya, S., and Arita, M. (2009). 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
  • 20
    • 84859336922 scopus 로고    scopus 로고
    • Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
    • Fukushima, A., Nishizawa, T., Hayakumo, M., Hikosaka, S., Saito, K., Goto, E., et al. (2012). Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol. 158, 1487-1502.
    • (2012) Plant Physiol. , vol.158 , pp. 1487-1502
    • Fukushima, A.1    Nishizawa, T.2    Hayakumo, M.3    Hikosaka, S.4    Saito, K.5    Goto, E.6
  • 21
    • 79951574076 scopus 로고    scopus 로고
    • OryzaExpress: An integrated database of gene expression networks and omics annotations in rice
    • Hamada, K., Hongo, K., Suwabe, K., Shimizu, A., Nagayama, T., Abe, R., et al. (2011). OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol. 52, 220-229.
    • (2011) Plant Cell Physiol. , vol.52 , pp. 220-229
    • Hamada, K.1    Hongo, K.2    Suwabe, K.3    Shimizu, A.4    Nagayama, T.5    Abe, R.6
  • 22
    • 84859117267 scopus 로고    scopus 로고
    • Advances in plant genome sequencing
    • Hamilton, J. P., and Buell, C. R. (2012). Advances in plant genome sequencing. Plant J. 70, 177-190.
    • (2012) Plant J. , vol.70 , pp. 177-190
    • Hamilton, J.P.1    Buell, C.R.2
  • 23
    • 38149040817 scopus 로고    scopus 로고
    • A global survey of gene regulation during cold acclimation in Arabidopsis thaliana
    • doi: 10.1371/journal.pgen.0010026
    • Hannah, M. A., Heyer, A. G., and Hincha, D. K. (2005). A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet. 1, 179-196. doi: 10.1371/journal.pgen.0010026
    • (2005) PLoS Genet. , vol.1 , pp. 179-196
    • Hannah, M.A.1    Heyer, A.G.2    Hincha, D.K.3
  • 24
    • 34547526914 scopus 로고    scopus 로고
    • Omics-based identifica-tion of Arabidopsis Myb transcrip-tion factors regulating aliphatic glucosinolate biosynthesis
    • Hirai, M. Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., et al. (2007). Omics-based identifica-tion of Arabidopsis Myb transcrip-tion factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 104, 6478-6483.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 6478-6483
    • Hirai, M.Y.1    Sugiyama, K.2    Sawada, Y.3    Tohge, T.4    Obayashi, T.5    Suzuki, A.6
  • 25
    • 50649114261 scopus 로고    scopus 로고
    • Annotating genes of known and unknown function by large-scale coexpression analysis
    • Horan, K., Jang, C., Bailey-Serres, J., Mittler, R., Shelton, C., Harper, J. F., et al. (2008). Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol. 147, 41-57.
    • (2008) Plant Physiol. , vol.147 , pp. 41-57
    • Horan, K.1    Jang, C.2    Bailey-Serres, J.3    Mittler, R.4    Shelton, C.5    Harper, J.F.6
  • 26
    • 80052394788 scopus 로고    scopus 로고
    • Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network
    • Hwang, S., Rhee, S. Y., Marcotte, E. M., and Lee, I. (2011). Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat. Protoc. 6, 1429-1442.
    • (2011) Nat. Protoc. , vol.6 , pp. 1429-1442
    • Hwang, S.1    Rhee, S.Y.2    Marcotte, E.M.3    Lee, I.4
  • 28
    • 84859516508 scopus 로고    scopus 로고
    • Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation
    • Lee, J. M., Joung, J.-G., McQuinn, R., Chung, M.-Y., Fei, Z., Tieman, D., et al. (2012). Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. Plant J. 70, 191-204.
    • (2012) Plant J. , vol.70 , pp. 191-204
    • Lee, J.M.1    Joung, J.-G.2    McQuinn, R.3    Chung, M.-Y.4    Fei, Z.5    Tieman, D.6
  • 29
    • 70349215646 scopus 로고    scopus 로고
    • RiceArrayNet: A database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice
    • Lee, T.-H., Kim, Y.-K., Pham, T. T. M., Song, S. I., Kim, J.-K., Kang, K. Y., et al. (2009). RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol. 151, 16-33.
    • (2009) Plant Physiol. , vol.151 , pp. 16-33
    • Lee, T.-H.1    Kim, Y.-K.2    Pham, T.T.M.3    Song, S.I.4    Kim, J.-K.5    Kang, K.Y.6
  • 30
    • 84864483625 scopus 로고    scopus 로고
    • RobiNA: A user-friendly, integrated software solution for RNA-seq-based transcriptomics
    • Lohse, M., Bolger, A., Nagel, A., Fernie, A., Lunn, J., Stitt, M., et al. (2012). RobiNA: a user-friendly, integrated software solution for RNA-seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627.
    • (2012) Nucleic Acids Res. , vol.40
    • Lohse, M.1    Bolger, A.2    Nagel, A.3    Fernie, A.4    Lunn, J.5    Stitt, M.6
  • 31
    • 84859708494 scopus 로고    scopus 로고
    • Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum)
    • Manickavelu, A., Kawaura, K., Oishi, K., Shin-I, T., Kohara, Y., Yahiaoui, N., et al. (2012). Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res. 19, 165-177.
    • (2012) DNA Res. , vol.19 , pp. 165-177
    • Manickavelu, A.1    Kawaura, K.2    Oishi, K.3    Shin, I.T.4    Kohara, Y.5    Yahiaoui, N.6
  • 32
    • 71749094192 scopus 로고    scopus 로고
    • Arabidopsis gene co-expression network and its functional modules
    • doi: 10.1186/1471-2105-10-346
    • Mao, L., Van Hemert, J. L., Dash, S., and Dickerson, J. A. (2009). Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 10, 346. doi: 10.1186/1471-2105-10-346
    • (2009) BMC Bioinformatics , vol.10 , pp. 346
    • Mao, L.1    Van Hemert, J.L.2    Dash, S.3    Dickerson, J.A.4
  • 33
    • 84855184956 scopus 로고    scopus 로고
    • Tissue-and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation
    • Matas, A. J., Yeats, T. H., Buda, G. J., Zheng, Y., Chatterjee, S., Tohge, T., et al. (2011). Tissue-and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23, 3893-3910.
    • (2011) Plant Cell , vol.23 , pp. 3893-3910
    • Matas, A.J.1    Yeats, T.H.2    Buda, G.J.3    Zheng, Y.4    Chatterjee, S.5    Tohge, T.6
  • 34
    • 33644655130 scopus 로고    scopus 로고
    • Repressor-and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression
    • McGrath, K. C., Dombrecht, B., Manners, J. M., Schenk, P. M., Edgar, C. I., Maclean, D. J., et al. (2005). Repressor-and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol. 139, 949-959.
    • (2005) Plant Physiol. , vol.139 , pp. 949-959
    • McGrath, K.C.1    Dombrecht, B.2    Manners, J.M.3    Schenk, P.M.4    Edgar, C.I.5    McLean, D.J.6
  • 35
    • 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., and Shinozaki, K. (2011). Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol. 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
  • 36
    • 63549110574 scopus 로고    scopus 로고
    • Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development
    • Mounet, F., Moing, A., Garcia, V., Petit, J., Maucourt, M., Deborde, C., et al. (2009). Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol. 149, 1505-1528.
    • (2009) Plant Physiol. , vol.149 , pp. 1505-1528
    • Mounet, F.1    Moing, A.2    Garcia, V.3    Petit, J.4    Maucourt, M.5    Deborde, C.6
  • 37
    • 79959970191 scopus 로고    scopus 로고
    • Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice
    • Movahedi, S., Van de Peer, Y., and Vandepoele, K. (2011). Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol. 156, 1316-1330.
    • (2011) Plant Physiol. , vol.156 , pp. 1316-1330
    • Movahedi, S.1    Van de Peer, Y.2    Vandepoele, K.3
  • 38
    • 79955581503 scopus 로고    scopus 로고
    • PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species
    • Mutwil, M., Klie, S., Tohge, T., Giorgi, F. M., Wilkins, O., Campbell, M. M., et al. (2011). PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23, 895-910.
    • (2011) Plant Cell , vol.23 , pp. 895-910
    • Mutwil, M.1    Klie, S.2    Tohge, T.3    Giorgi, F.M.4    Wilkins, O.5    Campbell, M.M.6
  • 39
    • 48449091196 scopus 로고    scopus 로고
    • GeneCAT-novel webtools that combine BLAST and co-expression analyses
    • Mutwil, M., Obro, J., Willats, W. G. T., and Persson, S. (2008). GeneCAT-novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res. 36, W320-W326.
    • (2008) Nucleic Acids Res. , vol.36
    • Mutwil, M.1    Obro, J.2    Willats, W.G.T.3    Persson, S.4
  • 41
    • 33645236494 scopus 로고    scopus 로고
    • In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: Expression analysis of multiple isoforms of serine acetyltransferase
    • Noji, M., Kawashima, C. G., Obayashi, T., and Saito, K. (2006). In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: expression analysis of multiple isoforms of serine acetyltransferase. Amino Acids 30, 163-171.
    • (2006) Amino Acids , vol.30 , pp. 163-171
    • Noji, M.1    Kawashima, C.G.2    Obayashi, T.3    Saito, K.4
  • 43
    • 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., and 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
  • 44
    • 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., and 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
  • 45
    • 80052398971 scopus 로고    scopus 로고
    • Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions
    • Osorio, S., Alba, R., Damasceno, C. M. B., Lopez-Casado, G., Lohse, M., Zanor, M. I., et al. (2011). Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol. 157, 405-425.
    • (2011) Plant Physiol. , vol.157 , pp. 405-425
    • Osorio, S.1    Alba, R.2    Damasceno, C.M.B.3    Lopez-Casado, G.4    Lohse, M.5    Zanor, M.I.6
  • 46
    • 84864718892 scopus 로고    scopus 로고
    • Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behaviour
    • Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A. R., and Giovannoni, J. J. (2012). Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behaviour. Plant Physiol. 159, 1713-1729.
    • (2012) Plant Physiol. , vol.159 , pp. 1713-1729
    • Osorio, S.1    Alba, R.2    Nikoloski, Z.3    Kochevenko, A.4    Fernie, A.R.5    Giovannoni, J.J.6
  • 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., 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
  • 48
    • 84866080959 scopus 로고    scopus 로고
    • BAR expressolog identification: Expression profile similarity ranking of homologous genes in plant species
    • Patel, R. V., Nahal, H. K., Breit, R., and Provart, N. J. (2012). BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J. 71, 1038-1050.
    • (2012) Plant J. , vol.71 , pp. 1038-1050
    • Patel, R.V.1    Nahal, H.K.2    Breit, R.3    Provart, N.J.4
  • 49
    • 84900844908 scopus 로고    scopus 로고
    • Large-scale coexpression analysis reveals novel genes involved in cellulose biosynthesis
    • Persson, S., Wei, H., Milne, J., Page, G., and Somerville, C. (2005a). Large-scale coexpression analysis reveals novel genes involved in cellulose biosynthesis. Plant Biol. (Rockville) 2005, 176.
    • (2005) Plant Biol. (Rockville) , pp. 176
    • Persson, S.1    Wei, H.2    Milne, J.3    Page, G.4    Somerville, C.5
  • 50
    • 20844445318 scopus 로고    scopus 로고
    • Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
    • Persson, S., Wei, H. R., Milne, J., Page, G. P., and Somerville, C. R. (2005b). Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl. Acad. Sci. U.S.A. 102, 8633-8638.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 8633-8638
    • Persson, S.1    Wei, H.R.2    Milne, J.3    Page, G.P.4    Somerville, C.R.5
  • 52
    • 83555173359 scopus 로고    scopus 로고
    • Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development
    • Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., et al. (2011). Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J. 68, 999-1013.
    • (2011) Plant J. , vol.68 , pp. 999-1013
    • Rohrmann, J.1    Tohge, T.2    Alba, R.3    Osorio, S.4    Caldana, C.5    McQuinn, R.6
  • 53
    • 84865548194 scopus 로고    scopus 로고
    • Large-scale co-expression approach to dissect secondary cell wall formation across plant species
    • doi: 10.3389/fpls.2011.00023
    • Ruprecht, C., Mutwil, M., Saxe, F., Eder, M., Nikoloski, Z., and Persson, S. (2011). Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Front. Plant Sci. 2:23. doi: 10.3389/fpls.2011.00023
    • (2011) Front. Plant Sci. , vol.2 , pp. 23
    • Ruprecht, C.1    Mutwil, M.2    Saxe, F.3    Eder, M.4    Nikoloski, Z.5    Persson, S.6
  • 54
    • 37849020436 scopus 로고    scopus 로고
    • Decoding genes with coexpression networks and metabolomics-"majority report by precogs. "
    • Saito, K., Hirai, M. Y., and 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
  • 55
    • 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., 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
  • 56
  • 57
    • 79955726394 scopus 로고    scopus 로고
    • Fast-forward genetics enabled by new sequencing technologies
    • Schneeberger, K., and Weigel, D. (2011). Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci. 16, 282-288.
    • (2011) Trends Plant Sci. , vol.16 , pp. 282-288
    • Schneeberger, K.1    Weigel, D.2
  • 59
    • 51549093662 scopus 로고    scopus 로고
    • CressExpress: A tool for large-scale mining of expression data from Arabidopsis
    • Srinivasasainagendra, V., Page, G. P., Mehta, T., Coulibaly, I., and Loraine, A. E. (2008). CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol. 147, 1004-1016.
    • (2008) Plant Physiol. , vol.147 , pp. 1004-1016
    • Srinivasasainagendra, V.1    Page, G.P.2    Mehta, T.3    Coulibaly, I.4    Loraine, A.E.5
  • 62
    • 77954396635 scopus 로고    scopus 로고
    • Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function
    • Tohge, T., and Fernie, A. R. (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
  • 63
    • 84856635485 scopus 로고    scopus 로고
    • Transcriptional and metabolic programs following exposure of plants to UV-B irradiation
    • Tohge, T., Kusano, M., Fukushima, A., Saito, K., and Fernie, A. (2011a). Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. Plant Signal Behav. 6, 1987-1992.
    • (2011) Plant Signal Behav. , vol.6 , pp. 1987-1992
    • Tohge, T.1    Kusano, M.2    Fukushima, A.3    Saito, K.4    Fernie, A.5
  • 64
    • 17044369876 scopus 로고    scopus 로고
    • Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor
    • Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., et al. (2005). Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J. 42, 218-235.
    • (2005) Plant J. , vol.42 , pp. 218-235
    • Tohge, T.1    Nishiyama, Y.2    Hirai, M.Y.3    Yano, M.4    Nakajima, J.5    Awazuhara, M.6
  • 66
    • 34247598751 scopus 로고    scopus 로고
    • Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes
    • Tohge, T., Yonekura-Sakakibara, K., Niida, R., Watanabe-Takahashi, A., and Saito, K. (2007). Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis genes. Pure Appl. Chem. 79, 811-823.
    • (2007) Pure Appl. Chem. , vol.79 , pp. 811-823
    • Tohge, T.1    Yonekura-Sakakibara, K.2    Niida, R.3    Watanabe-Takahashi, A.4    Saito, K.5
  • 67
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Tomato Genome Consortium
    • Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641.
    • (2012) Nature , vol.485 , pp. 635-641
  • 68
    • 22044437388 scopus 로고    scopus 로고
    • The Botany Array Resource: E-Northerns, expression angling, and promoter analyses
    • Toufighi, K., Brady, S. M., Austin, R., Ly, E., and Provart, N. J. (2005). The Botany Array Resource: e-Northerns, expression angling, and promoter analyses. Plant J. 43, 153-163.
    • (2005) Plant J. , vol.43 , pp. 153-163
    • Toufighi, K.1    Brady, S.M.2    Austin, R.3    Ly, E.4    Provart, N.J.5
  • 71
    • 70449115789 scopus 로고    scopus 로고
    • Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
    • Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F. M., Bassel, G. W., Tanimoto, M., et al. (2009). Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32, 1633-1651.
    • (2009) Plant Cell Environ. , vol.32 , pp. 1633-1651
    • Usadel, B.1    Obayashi, T.2    Mutwil, M.3    Giorgi, F.M.4    Bassel, G.W.5    Tanimoto, M.6
  • 72
    • 84861770973 scopus 로고    scopus 로고
    • Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes
    • Wada, M., Takahashi, H., Altaf-Ul-Amin, M., Nakamura, K., Hirai, M. Y., Ohta, D., et al. (2012). Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes. Gene503, 56-64.
    • (2012) Gene , vol.503 , pp. 56-64
    • Wada, M.1    Takahashi, H.2    Altaf-Ul-Amin, M.3    Nakamura, K.4    Hirai, M.Y.5    Ohta, D.6
  • 73
    • 57749089675 scopus 로고    scopus 로고
    • Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis
    • Yonekura-Sakakibara, K., Tohge, T., Matsuda, F., Nakabayashi, R., Takayama, H., Niida, R., et al. (2008). Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20, 2160-2176.
    • (2008) Plant Cell , vol.20 , pp. 2160-2176
    • Yonekura-Sakakibara, K.1    Tohge, T.2    Matsuda, F.3    Nakabayashi, R.4    Takayama, H.5    Niida, R.6
  • 74
    • 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., and 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
  • 75
    • 33847051248 scopus 로고    scopus 로고
    • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
    • Zhang, L., King, O., Wong, S., Goldberg, D., Tong, A., Lesage, G., et al. (2005). Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J. Biol. 4, 6.
    • (2005) J. Biol. , vol.4 , pp. 6
    • Zhang, L.1    King, O.2    Wong, S.3    Goldberg, D.4    Tong, A.5    Lesage, G.6
  • 76
    • 13444264729 scopus 로고    scopus 로고
    • GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox
    • Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L., and Gruissem, W. (2004). GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136, 2621-2632.
    • (2004) Plant Physiol. , vol.136 , pp. 2621-2632
    • Zimmermann, P.1    Hirsch-Hoffmann, M.2    Hennig, L.3    Gruissem, W.4


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