AbuQamar S, Chen X, Dhawan R, Bluhm B, Salmeron J, Lam S, Dietrich RA, Mengiste T (2006) Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection. Plant J 48:28-44 Arkin A, Ross J (1994) Computational functions in biochemical reaction networks. Bio-phys J 67:560-578

Assmann SM (2004) Plant G proteins, phytohormones, and plasticity: three questions and a speculation. Sci STKE 2004: re20 Bader GD, Hogue CW (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20:991-997 Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286:509512

Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-113 Bulow L, Schindler M, Choi C, Hehl R (2004) PathoPlant: a database on plant-pathogen interactions. In Silico Biol 4:529-536 Bulow L, Schindler M, Hehl R (2007) PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. Nucleic Acids Res 35:D841-D845

Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 32:D575-D577

de Torres M, Sanchez P, Fernandez-Delmond I, Grant M (2003) Expression profiling of the host response to bacterial infection: the transition from basal to induced defence responses in RPM1-mediated resistance. Plant J 33:665-676 Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35:D766-D770 Devoto A, and Turner JG (2005) Jasmonate - regulated Arabidopsis stress signalling network. Physiologia Plantarum 123:161-172

Devoto A, Ellis C, Magusin A, Chang HS, Chilcott C, Zhu T, Turner JG (2005) Expression profiling reveals COI1 to be a key regulator of genes involved in wound- and methyl jasmonate-induced secondary metabolism, defence, and hormone interactions. Plant Mol Biol 58:497-513

Dreher K, Callis J (2007) Ubiquitin, hormones and biotic stress in plants. Ann Bot (Lond) Du P, Gong J, Syrkin Wurtele E, Dickerson JA (2005) Modeling gene expression networks using fuzzy logic. IEEE Trans Syst Man Cybern B Cybern 35:1351-1359 Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210 Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868 Enright AJ, Ouzounis CA (2000) GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics 16:451-457 Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575-1584 Erdos P, Renyi A (1960) On the evolution of Random Graphs. Publ Math Inst Hung Acad Sci 5:17-61

Everitt BS (1993) Cluster Analysis, 3rd edn. Edward Arnold, London Feys B, Benedetti CE, Penfold CN, Turner JG (1994) Arabidopsis mutants selected for resistance to the phytotoxin coronatine are male sterile, insensitive to methyl jasmonate, and resistant to a bacterial pathogen. Plant Cell 6:751-759 Finkelstein RR, Gampala SS, Rock CD (2002) Abscisic acid signalling in seeds and seedlings. Plant Cell 14 Suppl: S15-45 Friedman N (2003) Probabilistic models for identifying regulation networks. Bioinfor-matics 19(2):II57

Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shi-nozaki K (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signalling networks. Curr Opin Plant Biol 9:436-442

Galuschka C, Schindler M, Bulow L, Hehl R (2007) AthaMap web tools for the analysis and identification of co-regulated genes. Nucleic Acids Res 35:D857-D862 Genoud T, Buchala AJ, Chua NH, Metraux JP (2002) Phytochrome signalling modulates the SA-perceptive pathway in Arabidopsis. Plant J 31:87-95 Genoud T, Metraux JP (1999) Crosstalk in plant cell signalling: structure and function of the genetic network. Trends Plant Sci 4:503-507 Genoud T, Trevino Santa Cruz MB, Metraux JP (2001) Numeric simulation of plant signalling networks. Plant Physiol 126:1430-1437 Gfeller A, Liechti R, Farmer EE (2006) Arabidopsis jasmonate signalling pathway. Sci STKE 2006: cm1

Gollub J, Ball CA, Sherlock G (2006) The Stanford Microarray Database: a user's guide.

Methods Mol Biol 338:191-208 Grant M, Lamb C (2006) Systemic immunity. Curr Opin Plant Biol 9:414-420 Grant MR, Godiard L, Straube E, Ashfield T, Lewald J, Sattler A, Innes RW, Dangl JL (1995) Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269:843-846

Guo H, Ecker JR (2004) The ethylene signalling pathway: new insights. Curr Opin Plant Biol 7:40-49

Halim VA, Vess A, Scheel D, Rosahl S (2006) The role of salicylic acid and jasmonic acid in pathogen defence. Plant Biol (Stuttg) 8:307-313

Husmeier D (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 19:2271-2282

Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Green-blatt JF, Gerstein M (2003) A Bayesian networks approach for predicting proteinprotein interactions from genomic data. Science 302:449-453 Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WG, Gilmartin PM, West-head DR (2006) The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis. Plant J 46:336-348 Jensen FV (1997) Introduction to Bayesian Networks. Springer,

Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42 Jones AM, Thomas V, Bennett MH, Mansfield J, Grant M (2006) Modifications to the Arabidopsis defense proteome occur prior to significant transcriptional change in response to inoculation with Pseudomonas syringae. Plant Physiol 142:1603-1620 Kim JT (2001) transsys: A generic formalism for modelling regulatory networks in morphogenesis. In: Kelemen J, Sosik P (eds) Advances in Artificial Life (Proceedings of the 6th European Conference on Artificial Life), vol 2159 of Lecture Notes in Artificial Intelligence. Springer, Berlin Heidelberg New York, pp 242-251 Kim JT (2005) Effects of spatial growth on gene expression dynamics and on regulatory network reconstruction. ECAL 2005, LNAI 3630:825-834 Kinkema M, Fan W, DongX (2000) Nuclear localization of NPR1 is required for activation of PR gene expression. Plant Cell 12:2339-2350 Klipp E, Liebermeister W (2006) Mathematical modeling of intracellular signalling pathways. BMC Neurosci 7(1):S10 Kobayashi T, Chen L, Aihara K (2002) Design of genetic switches with only positive feedback loops. Proc IEEE Comput Soc Bioinform Conf 1:151-162 Krogan NJ, Cagney G , Yu H , Zhong G , Guo X , Ignatchenko A , Li J, Pu S , Datta N , Tikuisis AP, Punna T, Peregrin-Alvarez JM , Shales M , Zhang X , DaveyM , Robinson MD, Paccanaro A , Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Staros-tine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K , Thompson NJ , Musso G , St Onge P, Ghanny S , LamMH, Butland G , Altaf-Ul AM , Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637-643 Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comp Graph Statistics 5:299-314

Li S, Assmann SM, Albert R (2006) Predicting essential components of signal trans-duction networks: a dynamic model of guard cell abscisic acid signalling. PLoS Biol 4:e312

Liechti R, Gfeller A, Farmer EE (2006) Jasmonate signalling pathway. Sci STKE 2006: cm2 Lorenzo O, Solano R (2005) Molecular players regulating the jasmonate signalling network. Curr Opin Plant Biol 8:532-540 Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M (2005) Assessing the limits of genomic data integration for predicting protein networks. Genome Res 15:945-953 Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402:83-86 Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34:D169-D172

Nemhauser JL, Hong F, Chory J (2006) Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 126:467-475 Nurnberger T, Brunner F, Kemmerling B, Piater L (2004) Innate immunity in plants and animals: striking similarities and obvious differences. Immunol Rev 198:249-266 Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35:D863-D869 Paccanaro A, Casbon JA, Saqi MA (2006) Spectral clustering of protein sequences. Nucleic

Acids Res 34:1571-1580 Paccanaro A, Chennubhotla C (2003) Spectral clustering of protein sequences. In: International Joint Conference on Neural Networks - IJCNN. Portland, Oregon, USA Paccanaro A, Trifonov V, Yu H (2005) Inferring protein-protein interactions using interaction network topologies. In: International Joint Conference on Neural Networks -IJCNN 2005. Montreal, Canada Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A (2007) ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35:D747-D750 Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F (2004) Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics 20:1361-1372 Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31:224-228

Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J (2002) Building and analysing genome-

wide gene disruption networks. Bioinformatics 18(2):S202-S210 Sasaki-Sekimoto Y, Taki N, Obayashi T, Aono M, Matsumoto F, Sakurai N, Suzuki H, Hirai MY, Noji M, Saito K, Masuda T, Takamiya K, Shibata D, Ohta H (2005) Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis. Plant J 44:653-668 Schwartz MA, Baron V (1999) Interactions between mitogenic stimuli, or, a thousand and one connections. Curr Opin Cell Biol 11:197-202 Staswick PE, Tiryaki I (2004) The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell 16:2117-2127 Steffens NO, Galuschka C, Schindler M, Bulow L, Hehl R (2005) AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. Nucleic Acids Res 33:W397-W402 Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20:3647-3651 Stintzi A, Weber H, Reymond P, Browse J, Farmer EE (2001) Plant defense in the absence of jasmonic acid: the role of cyclopentenones. Proc Natl Acad Sci USA 98:12837-12842 Sun TP, Gubler F (2004) Molecular mechanism of gibberellin signalling in plants. Annu

Rev Plant Biol 55:197-223 Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914-939

Toufighi K, Brady SM, Austin R, Ly E, Provart NJ (2005) The Botany Array Resource: e-

Northerns, Expression Angling, and promoter analyses. Plant J 43:153-163 Trevino Santa Cruz MB, Genoud D, Metraux JP, Genoud T (2005) Update in bioinformat-ics. Toward a digital database of plant cell signalling networks: advantages, limitations and predictive aspects of the digital model. Phytochemistry 66:267-276 Truman W, Bennett MH, Kubigsteltig I, Turnbull C, Grant M (2007) Arabidopsis systemic immunity uses conserved defense signalling pathways and is mediated by jasmonates. Proc Natl Acad Sci USA 104:1075-1080 Truman W, de Zabala MT, Grant M (2006) Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance. Plant J 46:14-33 van Dongen S (2000) Graph clustering by flow simulation. PhD Thesis, University of Utrecht van Someren EP, Wessels LF, Backer E, Reinders MJ (2002) Genetic network modeling.

Pharmacogenomics 3:507-525 Vert G, Nemhauser JL, Geldner N, Hong F, Chory J (2005) Molecular mechanisms of steroid hormone signalling in plants. Annu Rev Cell Dev Biol 21:177-201 von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403

Walker MG, Volkmuth W, Sprinzak E, Hodgson D, Klingler T (1999) Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res 9:1198-1203 Wang Y et al. (2006) Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics 22:2413-2420 Wang D, Amornsiripanitch N, Dong X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2:e123

Wang D, Weaver ND, Kesarwani M, Dong X (2005) Induction of protein secretory pathway is required for systemic acquired resistance. Science 308:1036-1040 Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot (Lond) 95:707-735

Xie DX, Feys BF, James S, Nieto-Rostro M, Turner JG (1998) COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 280:1091-1094 Yu H, Paccanaro A, Trifonov V, Gerstein M (2006) Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22:823-829 Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621-2632

Plant Cell Monogr (10)

L. Bogre and G. Beemster: Plant Growth Signaling

DOI 10.1007/7089_2007_159/Published online: 26 January 2008

© Springer-Verlag Berlin Heidelberg 2008

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