SEARCH

SEARCH BY CITATION

REFERENCES

  • Akiyama K., Chikayama E., Yuasa H., Shimada Y., Tohge T., Shinozaki K., Yokota Hirai M., Sakurai T., Kikuchi J. & Saito K. (2008) Prime: a web site that assembles tools for metabolomics and transcriptomics. In Silico Biology 8, 339345.
  • Aoki K., Ogata Y. & Shibata D. (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant and Cell Physiology 48, 381390.
  • Bader G.D., Donaldson I., Wolting C., Ouellette B.F., Pawson T. & Hogue C.W. (2001) BIND – the biomolecular interaction network database. Nucleic Acids Research 29, 242245.
  • Birnbaum K., Shasha D.E., Wang J.Y., Jung J.W., Lambert G.M., Galbraith D.W. & Benfey P.N. (2003) A gene expression map of the Arabidopsis root. Science 302, 19561960.
  • Brown D.M., Zeef L.A.H., Ellis J., Goodacre R. & Turner S.R. (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. The Plant Cell 17, 22812295.
  • Bülow L., Schindler M., Choi C. & Hehl R. (2004) PathoPlant: a database on plant-pathogen interactions. In Silico Biology 4, 529536.
  • Cocuron J.-C., Lerouxel O., Drakakaki G., Alonso A.P., Liepman A.H., Keegstra K., Raikhel N. & Wilkerson C.G. (2007) A gene from the cellulose synthase-like C family encodes a beta-1,4 glucan synthase. Proceedings of the National Academy of Sciences of the United States of America 104, 85508555.
  • Craigon D.J., James N., Okyrere J., Higgins J., Jotham J. & May S. (2004) NASCArrays: a reposiotory for microarray data generated by NASC's transciptomics service. Nucleic Acids Research 32, D575D577.
  • Daub C.O., Steuer R., Selbig J. & Kloska S. (2004) Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data. BMC Bioinformatics 5, 118.
  • Dong J., MacAlister C.A. & Bergmann D.C. (2009) Control of asymmetric cell divisions in Arabidopsis by dynamic localization of BASL protein. Cell 137, 13201330.
  • Edgar R., Domrachev M. & Lash A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research 30, 207210.
  • Ehlting J., Provart N.J. & Werck-Reichhart D. (2006) Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis. Biochemical Society Transactions 34, 11921198.
  • D'Erfurth I., Jolivet S., Froger N., Catrice O., Novatchkova M., Simon M., Jenczewski E. & Mercier R. (2008) Mutations in AtPS1 (Arabidopsis thaliana parallel spindle 1) lead to the production of diploid pollen grains. PLoS Genetics 4, e1000274.
  • Fisher R.A. (1915) Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population. Biometrika 10, 507521.
  • De La Fuente A., Bing N., Hoeschele I. & Mendes P. (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20, 35653574.
  • Gachon C., 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, 229245.
  • Geisler-Lee J., O'Toole N., Ammar R., Provart N.J., Millar A.H. & Geisler M. (2007) A predicted interactome for Arabidopsis. Plant Physiology 145, 317329.
  • Goda H., Sasaki E., Akiyama K., et al. (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. The Plant Journal 55, 526542.
  • Gutierrez R.A., Shasha D.E. & Coruzzi G.M. (2005) Systems biology for the virtual plant. Plant Physiology 138, 550554.
  • Hara K., Kajita R., Torii K.U., Bergmann D.C. & Kakimoto T. (2007) The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule. Genes & Development 21, 17201725.
  • Harr B. & Schlotterer C. (2006) Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Research 34, e8.
  • Hirai M.Y., Yano M., Goodenowe D.B., Kanaya S., Kimura T., Awazuhara M., Arita M., Fujiwara T. & Saito K. (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 101, 1020510210.
  • Hirai M.Y., Sugiyama K., Sawada Y., et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proceedings of the National Academy of Sciences of the United States of America 104, 64786483.
  • Horan K., Jang C., Bailey-Serres J., Mittler R., Shelton C., Harper J.F., Zhu J.-K., Cushman J.C., Gollery M. & Girke T. (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiology 147, 4157.
  • Hubbell E., Liu W.-M. & Mei R. (2002) Robust estimators for expression analysis. Bioinformatics 18, 15851592.
  • Ihmels J., Levy R. & Barkai N. (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nature Biotechnology 22, 8692.
  • Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B. & Speed T.P. (2003a) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 31, e15.
  • Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U. & Speed T.P. (2003b) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249264.
  • Jiang N., Leach L.J., Hu X., Potokina E., Jia T., Druka A., Waugh R., Kearsey M.J. & Luo Z.W. (2008) Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics 9, 284.
  • Kilian J., Whitehead D., Horak J., Wanke D., Weinl S., Batistic O., D'Angelo C., Bornberg-Bauer E., Kudla J. & Harter K. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. The Plant Journal 50, 347363.
  • Koo A.J.K., Chung H.S., Kobayashi Y. & Howe G.A. (2006) Identification of a peroxisomal acyl-activating enzyme involved in the biosynthesis of jasmonic acid in Arabidopsis. Journal of Biological Chemistry 281, 3351133520.
  • Laubinger S., Zeller G., Henz S.R., Sachsenberg T., Widmer C.K., Naouar N., Vuylsteke M., Schölkopf B., Rätsch G. & Weigel D. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biology 9, R112.
  • Lee H.K., Hsu A.K., Sajdak J., Qin J. & Pavlidis P. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Research 14, 10851094.
  • Li C. & Hung Wong W. (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biology 2, RESEARCH0032.
  • Lim W.K., Wang K., Lefebvre C. & Califano A. (2007) Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 23, i282i288.
  • Lisso J., Steinhauser D., Altmann T., Kopka J. & Mussig C. (2005) Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Research 33, 26852696.
  • Long T.A., Brady S.M. & Benfey P.N. (2008) Systems approaches to identifying gene regulatory networks in plants. Annual Review of Cell and Developmental Biology 24, 81103.
  • Ma S., Gong Q. & Bohnert H.J. (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Research 17, 16141625.
  • Manfield I.W., Jen C.-H., Pinney J.W., Michalopoulos I., Bradford J.R., Gilmartin P.M. & Westhead D.R. (2006) Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Research 34, W504W509.
  • Margolin A.A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Dalla Favera R. & Califano A. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 (Suppl. 1), S7.
  • Mentzen W. & Wurtele E. (2008) Regulon organization of Arabidopsis. BMC Plant Biology 8, 99.
  • Morant M., Jorgensen K., Schaller H., Pinot F., Moller B.L., Werck-Reichhart D. & Bak S. (2007) CYP703 is an ancient cytochrome p450 in land plants catalyzing in-chain hydroxylation of lauric acid to provide building blocks for sporopollenin synthesis in pollen. The Plant Cell 19, 14731487.
  • Mostafavi S., Ray D., Warde-Farley D., Grouios C. & Morris Q. (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biology 9, S4.
  • Mutwil M., Obro J., Willats W.G.T. & Persson S. (2008) GeneCAT – novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Research 36, W320W326.
  • Nikiforova V.J., Daub C.O., Hesse H., Willmitzer L. & Hoefgen R. (2005) Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. Journal of Experimental Botany 56, 18871896.
  • Van Noort V., Snel B. & Huynen M.A. (2003) Predicting gene function by conserved co-expression. Trends in Genetics 19, 238242.
  • Obayashi T., Hayashi S., Saeki M., Ohta H. & Kinoshita K. (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Research 37, D987D991.
  • Persson S., Wei H., Milne J., Page G.P. & Somerville C.R. (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences of the United States of America 102, 86338638.
  • Prieto C., Risueño A., Fontanillo C. & De Las Rivas J. (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One 3, e3911.
  • Rawat A., Seifert G. & Deng Y. (2008) Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data. BMC Bioinformatics 9, S7.
  • Rocca-Serra P., Brazma A., Parkinson H., et al. (2003) Arrayexpress: a public database of gene expression data at EBI. Current Research in Biology 326, 10751078.
  • Saito K., Hirai M.Y. & Yonekura-Sakakibara K. (2008) Decoding genes with coexpression networks and metabolomics –‘majority report by precogs. Trends in Plant Science 13, 3643.
  • Sakurai N. & Shibata D. (2006) KaPPA-view for integrating quantitative transcriptomic and metabolomic data on plant metabolic pathway maps. Journal of Pesticide Science 31, 293295.
  • Schäfer J. & Strimmer K. (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21, 754764.
  • Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Scholkopf B., Weigel D. & Lohmann J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37, 501506.
  • Spirtes P., Glymour C.N. & Scheines R. (1993) Causation, Prediction, and Search 2nd edn, MIT Press, Cambridge, MA, USA.
  • Srinivasasainagendra V., Page G.P., Mehta T., Coulibaly I. & Loraine A.E. (2008) CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiology 147, 10041016.
  • Steinhauser D., Usadel B., Luedemann A., Thimm O. & Kopka J. (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20, 36473651.
  • Steuer R., Kurths J., Daub C.O., Weise J. & Selbig J. (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18 (Suppl. 2), S231S240.
  • Stuart J.M., Segal E., Koller D. & Kim S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249255.
  • Sweetlove L.J. & Fernie A.R. (2005) Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytologist 168, 924.
  • Takabayashi A., Ishikawa N., Obayashi T., Ishida S., Obokata J., Endo T. & Sato F. (2009) Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches. The Plant Journal 57, 207219.
  • Toufighi K., Brady M., Austin R., Ly E. & Provart N. (2005) The botany array resource: e-northerns, expression angling, and promoter analyses. The Plant Journal 43, 153163.
  • Trivedi P., Edwards J., Wang J., et al. (2005) HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data. BMC Bioinformatics 6, 86.
  • Vicinanza M., D'Angelo G., Di Campli A. & De Matteis M.A. (2008) Function and dysfunction of the PI system in membrane trafficking. The EMBO Journal 27, 24572470.
  • Wei H., Persson S., Mehta T., Srinivasasainagendra V., Chen L., Page G.P., Somerville C. & Loraine A. (2006) Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiology 142, 762774.
  • Wille A., Zimmermann P., Vranova E., et al. (2004) Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biology 5, R92.
  • Wolfe C., Kohane I. & Butte A. (2005) Systematic survey reveals general applicability of ‘guilt-by-association’ within gene coexpression networks. BMC Bioinformatics 6, 227.
  • Wu L.F., Hughes T.R., Davierwala A.P., Robinson M.D., Stoughton R. & Altschuler S.J. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics 31, 255265.
  • Wu Z., Irizarry R.A., Gentleman R., Martinez-Murillo F. & Spencer F. (2004) A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 99, 909917.
  • Yu H., Luscombe N.M., Qian J. & Gerstein M. (2003) Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends in Genetics 19, 422427.
  • Yu H., Ito T., Zhao Y., Peng J., Kumar P. & Meyerowitz E.M. (2004) Floral homeotic genes are targets of gibberellin signaling in flower development. Proceedings of the National Academy of Sciences of the United States of America 101, 78277832.
  • Yule G.U. (1907) On the theory of correlation for any number of variables, treated by a new system of notation. Proceedings of the Royal Society of London, Series A 79, 182193.
  • Zimmermann P., Hirsch-Hoffman M., Hennig L. & Gruissem W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiology 136, 26212632.