Metabolic and co-expression network-based analyses associated with nitrate response in rice
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Caitlin M. A. Simopoulos | P. McNicholas | T. Zhu | S. Rothstein | Lining Guo | J. Casaretto | Y. Bi | Viktoriya Coneva | A. El-kereamy | D. Guevara | Jonathan Cohn | D. Alexander
[1] S. Horvath,et al. A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.
[2] G. Ragsdell. Systems , 2002, Economics of Visual Art.
[3] Jianming Li,et al. The Arabidopsis Transthyretin-Like Protein Is a Potential Substrate of BRASSINOSTEROID-INSENSITIVE 1 , 2004, The Plant Cell Online.
[4] R. C. Muchow. NITROGEN UTILIZATION EFFICIENCY IN MAIZE AND GRAIN SORGHUM , 1998 .
[5] F. Daniel-Vedele,et al. Arabidopsis Roots and Shoots Show Distinct Temporal Adaptation Patterns toward Nitrogen Starvation1[W] , 2011, Plant Physiology.
[6] Benjamin M. Bolstad,et al. affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..
[7] T. Zhu,et al. Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA , 2007, Plant Molecular Biology.
[8] Jun Dong,et al. Geometric Interpretation of Gene Coexpression Network Analysis , 2008, PLoS Comput. Biol..
[9] S. Mccouch,et al. Identification of QTLs associated with physiological nitrogen use efficiency in rice. , 2007, Molecules and cells.
[10] M. Stitt,et al. Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis. , 2009, Plant, cell & environment.
[11] Bin Zhang,et al. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R , 2008, Bioinform..
[12] Mark Stitt,et al. Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] , 2004, Plant Physiology.
[13] Y. Tsay,et al. AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. , 2009, The Plant journal : for cell and molecular biology.
[14] Florent Murat,et al. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. , 2011, The Plant journal : for cell and molecular biology.
[15] S. Rhee,et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.
[16] L. Sodek,et al. Growth and stress conditions cause similar changes in xylem amino acids for different legume species , 2006 .
[17] C. Witte,et al. The biochemistry of nitrogen mobilization: purine ring catabolism. , 2011, Trends in plant science.
[18] S. Thomine,et al. ATP Binding to the C Terminus of the Arabidopsis thaliana Nitrate/Proton Antiporter, AtCLCa, Regulates Nitrate Transport into Plant Vacuoles* , 2009, The Journal of Biological Chemistry.
[19] Q. Shen,et al. Comparing nitrate storage and remobilization in two rice cultivars that differ in their nitrogen use efficiency. , 2007, Journal of experimental botany.
[20] J. Dubcovsky,et al. A NAC Gene Regulating Senescence Improves Grain Protein, Zinc, and Iron Content in Wheat , 2006, Science.
[21] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[22] M. Hirai,et al. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis , 2007, Proceedings of the National Academy of Sciences.
[23] D. Beghin,et al. Genetic differences for nitrogen uptake and nitrogen utilisation efficiencies in winter wheat. , 2000 .
[24] T. Zhu,et al. Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase. , 2009, Plant biotechnology journal.
[25] X. Yang,et al. Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize[W][OA] , 2011, Plant Physiology.
[26] Yutaka Sato,et al. Global transcriptome profile of rice root in response to essential macronutrient deficiency , 2013, Plant signaling & behavior.
[27] A. Dobermann,et al. Agroecosystems, Nitrogen-use Efficiency, and Nitrogen Management , 2002, Ambio.
[28] M. S. Fernandes,et al. Isoforms of plasma membrane H(+)-ATPase in rice root and shoot are differentially induced by starvation and resupply of NO₃⁻ or NH₄+. , 2011, Plant science : an international journal of experimental plant biology.
[29] A. Danchin,et al. Bmc Genomics , 2004 .
[30] Zhuo Shen,et al. Large-scale analysis of phosphorylated proteins in maize leaf , 2011, Planta.
[31] Yann LeCun,et al. Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate , 2010, Genome Biology.
[32] Tomás C. Moyano,et al. Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots , 2013, Proceedings of the National Academy of Sciences.
[33] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[34] Y. Tsay,et al. CHL1 Functions as a Nitrate Sensor in Plants , 2009, Cell.
[35] Tong Zhu,et al. Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis , 2007, BMC Genomics.
[36] Xianghua Li,et al. Expression Profiles of 10,422 Genes at Early Stage of Low Nitrogen Stress in Rice Assayed using a cDNA Microarray , 2006, Plant Molecular Biology.
[37] J. Hancock,et al. NO way back: nitric oxide and programmed cell death in Arabidopsis thaliana suspension cultures. , 2000, The Plant journal : for cell and molecular biology.
[38] H. Thomas,et al. The stay-green trait. , 2014, Journal of experimental botany.
[39] M. Sorrells,et al. Systems Genetics of Environmental Response in the Mature Wheat Embryo , 2013, Genetics.
[40] K. Schubert. Products of Biological Nitrogen Fixation in Higher Plants: Synthesis, Transport, and Metabolism , 1986 .
[41] A. Good,et al. Physiological analysis of nitrogen-efficient rice overexpressing alanine aminotransferase under different N regimes , 2013 .
[42] K. Krupinska,et al. Leaf senescence and nutrient remobilisation in barley and wheat. , 2008, Plant biology.
[43] B. Ney,et al. The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches. , 2007, Journal of experimental botany.
[44] S. Rothstein,et al. Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency. , 2011, Journal of experimental botany.
[45] Xiang Li,et al. Nitrogen deprivation promotes Populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks. , 2013, The New phytologist.
[46] T. Zhu,et al. Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. , 2009, Plant, cell & environment.
[47] S. Rothstein,et al. Functional Characterization of the Rice UDP-glucose 4-epimerase 1, OsUGE1: A Potential Role in Cell Wall Carbohydrate Partitioning during Limiting Nitrogen Conditions , 2014, PloS one.
[48] S. Rothstein. Returning to Our Roots: Making Plant Biology Research Relevant to Future Challenges in Agriculture , 2007, The Plant Cell Online.
[49] Zhou Du,et al. agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..
[50] M. Sagi,et al. A critical role for ureides in dark and senescence-induced purine remobilization is unmasked in the Atxdh1 Arabidopsis mutant. , 2008, The Plant journal : for cell and molecular biology.
[51] Andy M. Yip,et al. Gene network interconnectedness and the generalized topological overlap measure , 2007, BMC Bioinformatics.
[52] M. Pineda,et al. Molecular analysis of ureide accumulation under drought stress in Phaseolus vulgaris L. , 2010, Plant, cell & environment.
[53] Wei-Po Lee,et al. Computational methods for discovering gene networks from expression data , 2009, Briefings Bioinform..
[54] W. Schulze,et al. Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings , 2012, The Plant journal : for cell and molecular biology.
[55] K. Wimmers,et al. Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties , 2013, BMC Genomics.
[56] P. Juskiw,et al. Genetic Variability in Nitrogen Use Efficiency of Spring Barley , 2009 .
[57] D. Lawlor. Carbon and nitrogen assimilation in relation to yield: mechanisms are the key to understanding production systems. , 2002, Journal of experimental botany.
[58] Mathieu Sebilo,et al. Long-term fate of nitrate fertilizer in agricultural soils , 2013, Proceedings of the National Academy of Sciences.
[59] G. Robertson,et al. Nitrogen in Agriculture: Balancing the Cost of an Essential Resource , 2009 .
[60] Y. Fukuta,et al. Genetic variations in dry matter production and physiological nitrogen use efficiency in rice (Oryza sativa L.) varieties , 2009 .
[61] Rongchen Wang,et al. Genomic Analysis of a Nutrient Response in Arabidopsis Reveals Diverse Expression Patterns and Novel Metabolic and Potential Regulatory Genes Induced by Nitrate , 2000, Plant Cell.
[62] Peter Langfelder,et al. Eigengene networks for studying the relationships between co-expression modules , 2007, BMC Systems Biology.
[63] A. Basra,et al. Enhancing the Efficiency of Nitrogen Utilization in Plants , 2006 .
[64] Guohua Xu,et al. Plant nitrogen assimilation and use efficiency. , 2012, Annual review of plant biology.
[65] Shunsuke Watanabe,et al. RNA interference‐mediated suppression of xanthine dehydrogenase reveals the role of purine metabolism in drought tolerance in Arabidopsis , 2010, FEBS letters.
[66] K. Vinod,et al. QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice. , 2008, Journal of integrative plant biology.
[67] M. Wopereis,et al. Crops that feed the world 7: Rice , 2012, Food Security.
[68] F. Maathuis,et al. The cyclic nucleotide cGMP is involved in plant hormone signalling and alters phosphorylation of Arabidopsis thaliana root proteins , 2012, Journal of experimental botany.
[69] Rodrigo A. Gutiérrez,et al. Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments , 2014, Front. Plant Sci..
[70] A. Good,et al. Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression of alanine aminotransferase. , 2008, Plant biotechnology journal.
[71] Chris Gehring,et al. Adenyl cyclases and cAMP in plant signaling - past and present , 2010, Cell communication and signaling : CCS.
[72] T. Zhu,et al. Transcriptome response to nitrogen starvation in rice , 2012, Journal of Biosciences.
[73] Qian Liu,et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice , 2014, Nature Genetics.
[74] Rafael A. Cañas,et al. Can genetic variability for nitrogen metabolism in the developing ear of maize be exploited to improve yield? , 2012, The New phytologist.
[75] Yoshiaki Nagamura,et al. RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions , 2010, Nucleic Acids Res..