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Volumn 195, Issue 3, 2012, Pages 707-720

CORNET 2.0: Integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

Author keywords

Arabidopsis; Bioinformatics; CORNET; Data integration; Maize; Networks

Indexed keywords

ARABIDOPSIS PROTEIN; TRANSCRIPTION FACTOR;

EID: 84863780541     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2012.04184.x     Document Type: Article
Times cited : (84)

References (67)
  • 3
    • 84857780876 scopus 로고    scopus 로고
    • Evidence for network evolution in an Arabidopsis interactome map
    • Arabidopsis Interactome Mapping Consortium
    • Arabidopsis Interactome Mapping Consortium. 2011. Evidence for network evolution in an Arabidopsis interactome map. Science 333: 601-607.
    • (2011) Science , vol.333 , pp. 601-607
  • 7
    • 33344459577 scopus 로고    scopus 로고
    • Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication
    • Bomblies K, Doebley JF. 2006. Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication. Genetics 172: 519-531.
    • (2006) Genetics , vol.172 , pp. 519-531
    • Bomblies, K.1    Doebley, J.F.2
  • 8
    • 0038686862 scopus 로고    scopus 로고
    • Duplicate floricaula/leafy homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize
    • Bomblies K, Wang RL, Ambrose BA, Schmidt RJ, Meeley RB, Doebley J. 2003. Duplicate floricaula/leafy homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize. Development 130: 2385-2395.
    • (2003) Development , vol.130 , pp. 2385-2395
    • Bomblies, K.1    Wang, R.L.2    Ambrose, B.A.3    Schmidt, R.J.4    Meeley, R.B.5    Doebley, J.6
  • 9
    • 66149174897 scopus 로고    scopus 로고
    • Web-queryable large-scale data sets for hypothesis generation in plant biology
    • Brady SM, Provart NJ. 2009. Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21: 1034-1051.
    • (2009) Plant Cell , vol.21 , pp. 1034-1051
    • Brady, S.M.1    Provart, N.J.2
  • 10
    • 27644451872 scopus 로고    scopus 로고
    • Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics
    • Brown DM, Zeef LAH, Ellis J, Goodacre R, Turner SR. 2005. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 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
  • 11
    • 38649120826 scopus 로고    scopus 로고
    • In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
    • Casneuf T, Van de Peer Y, Huber W. 2007. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics 8: 461.
    • (2007) BMC Bioinformatics , vol.8 , pp. 461
    • Casneuf, T.1    Van de Peer, Y.2    Huber, W.3
  • 13
    • 38549123986 scopus 로고    scopus 로고
    • Atpid: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology
    • Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y et al. 2008. Atpid: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. Nucleic Acids Research 36: D999-D1008.
    • (2008) Nucleic Acids Research , vol.36
    • Cui, J.1    Li, P.2    Li, G.3    Xu, F.4    Zhao, C.5    Li, Y.6    Yang, Z.7    Wang, G.8    Yu, Q.9    Li, Y.10
  • 15
    • 68849117733 scopus 로고    scopus 로고
    • Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
    • De Bodt S, Proost S, Vandepoele K, Rouze P, Van de Peer Y. 2009. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10: 288.
    • (2009) BMC Genomics , vol.10 , pp. 288
    • De Bodt, S.1    Proost, S.2    Vandepoele, K.3    Rouze, P.4    Van de Peer, Y.5
  • 17
    • 23644461190 scopus 로고    scopus 로고
    • Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications
    • Gachon CMM, Langlois-Meurinne M, Henry Y, Saindrenan P. 2005. Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. Plant Molecular Biology 58: 229-245.
    • (2005) Plant Molecular Biology , vol.58 , pp. 229-245
    • Gachon, C.M.M.1    Langlois-Meurinne, M.2    Henry, Y.3    Saindrenan, P.4
  • 18
    • 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
  • 21
    • 58149141548 scopus 로고    scopus 로고
    • TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation
    • Gonzalez A, Mendenhall J, Huo Y, Lloyd A. 2009. TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. Developmental Biology 325: 412-421.
    • (2009) Developmental Biology , vol.325 , pp. 412-421
    • Gonzalez, A.1    Mendenhall, J.2    Huo, Y.3    Lloyd, A.4
  • 31
    • 67849092455 scopus 로고    scopus 로고
    • Plan2l: a web tool for integrated text mining and literature-based bioentity relation extraction
    • Krallinger M, Rodriguez-Penagos C, Tendulkar A, Valencia A. 2009. Plan2l: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Research 37: W160-W165.
    • (2009) Nucleic Acids Research , vol.37
    • Krallinger, M.1    Rodriguez-Penagos, C.2    Tendulkar, A.3    Valencia, A.4
  • 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. Nature Biotechnology 28: 149-156.
    • (2010) Nature Biotechnology , vol.28 , pp. 149-156
    • Lee, I.1    Ambaru, B.2    Thakkar, P.3    Marcotte, E.M.4    Rhee, S.Y.5
  • 34
    • 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 TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M 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 Physiology 151: 16-33.
    • (2009) Plant Physiology , vol.151 , pp. 16-33
    • Lee, T.H.1    Kim, Y.K.2    Pham, T.T.3    Song, S.I.4    Kim, J.K.5    Kang, K.Y.6    An, G.7    Jung, K.H.8    Galbraith, D.W.9    Kim, M.10
  • 35
    • 0141519279 scopus 로고    scopus 로고
    • Orthomcl: identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ Jr, Roos DS. 2003. Orthomcl: identification of ortholog groups for eukaryotic genomes. Genome Research 13: 2178-2189.
    • (2003) Genome Research , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 36
    • 62549129855 scopus 로고    scopus 로고
    • The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis
    • Li SF, Milliken ON, Pham H, Seyit R, Napoli R, Preston J, Koltunow AM, Parish RW. 2009. The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis. Plant Cell 21: 72-89.
    • (2009) Plant Cell , vol.21 , pp. 72-89
    • Li, S.F.1    Milliken, O.N.2    Pham, H.3    Seyit, R.4    Napoli, R.5    Preston, J.6    Koltunow, A.M.7    Parish, R.W.8
  • 37
    • 18744415447 scopus 로고    scopus 로고
    • Identification of brassinosteroid-related genes by means of transcript co-response analyses
    • Lisso J, Steinhauser D, Altmann T, Kopka J, Müssig C. 2005. Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Research 33: 2685-2696.
    • (2005) Nucleic Acids Research , vol.33 , pp. 2685-2696
    • Lisso, J.1    Steinhauser, D.2    Altmann, T.3    Kopka, J.4    Müssig, C.5
  • 38
    • 77952903335 scopus 로고    scopus 로고
    • Genomics and bioinformatics resources for crop improvement
    • Mochida K, Shinozaki K. 2010. Genomics and bioinformatics resources for crop improvement. Plant and Cell Physiology 51: 497-523.
    • (2010) Plant and Cell Physiology , vol.51 , pp. 497-523
    • Mochida, K.1    Shinozaki, K.2
  • 39
    • 83255189512 scopus 로고    scopus 로고
    • Advances in omics and bioinformatics tools for systems analyses of plant functions
    • Mochida K, Shinozaki K. 2011. Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant and Cell Physiology 52: 2017-2038.
    • (2011) Plant and Cell Physiology , vol.52 , pp. 2017-2038
    • Mochida, K.1    Shinozaki, K.2
  • 40
    • 77951168442 scopus 로고    scopus 로고
    • Omics meet networks - using systems approaches to infer regulatory networks in plants
    • Moreno-Risueno MA, Busch W, Benfey PN. 2010. Omics meet networks - using systems approaches to infer regulatory networks in plants. Current Opinion in Plant Biology 13: 126-131.
    • (2010) Current Opinion in Plant Biology , vol.13 , pp. 126-131
    • Moreno-Risueno, M.A.1    Busch, W.2    Benfey, P.N.3
  • 41
    • 14044254746 scopus 로고    scopus 로고
    • Textpresso: an ontology-based information retrieval and extraction system for biological literature
    • Muller HM, Kenny EE, Sternberg PW. 2004. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biology 2: e309.
    • (2004) PLoS Biology , vol.2
    • Muller, H.M.1    Kenny, E.E.2    Sternberg, P.W.3
  • 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
  • 49
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis information resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M et al. 2003. The Arabidopsis information resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 31: 224-228.
    • (2003) Nucleic Acids Research , vol.31 , pp. 224-228
    • Rhee, S.Y.1    Beavis, W.2    Berardini, T.Z.3    Chen, G.4    Dixon, D.5    Doyle, A.6    Garcia-Hernandez, M.7    Huala, E.8    Lander, G.9    Montoya, M.10
  • 53
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater GS, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 54
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 55
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3: Article3.
    • (2004) Statistical Applications in Genetics and Molecular Biology , vol.3
    • Smyth, G.K.1
  • 59
    • 80053186137 scopus 로고    scopus 로고
    • Evolution and applications of plant pathway resources and databases
    • Sucaet Y, Deva T. 2011. Evolution and applications of plant pathway resources and databases. Briefings in Bioinformatics 12: 530-544.
    • (2011) Briefings in Bioinformatics , vol.12 , pp. 530-544
    • Sucaet, Y.1    Deva, T.2
  • 60
    • 22044437388 scopus 로고    scopus 로고
    • The botany array resource: e-northerns, expression angling, and promoter analyses
    • Toufighi K, Brady SM, Austin R, Ly E, Provart NJ. 2005. The botany array resource: e-northerns, expression angling, and promoter analyses. Plant Journal 43: 153-163.
    • (2005) Plant Journal , vol.43 , pp. 153-163
    • Toufighi, K.1    Brady, S.M.2    Austin, R.3    Ly, E.4    Provart, N.J.5
  • 64
    • 66649122827 scopus 로고    scopus 로고
    • Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    • Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y. 2009. Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiology 150: 535-546.
    • (2009) Plant Physiology , vol.150 , pp. 535-546
    • Vandepoele, K.1    Quimbaya, M.2    Casneuf, T.3    De Veylder, L.4    Van de Peer, Y.5


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