TY - CHAP AU - Taiz, L. AU - Zeiger, E. PY - 2006 DA - 2006// TI - Cytokinins: regulators of cell divition BT - Plant Physiol PB - Sinauer Associates Inc. Publishers CY - Sunderland, MA, USA ID - Taiz2006 ER - TY - JOUR AU - Lovegrove, A. AU - Hooley, R. PY - 2000 DA - 2000// TI - Gibberellin and abscisic acid signalling in aleurone JO - Trends Plant Sci VL - 5 UR - https://doi.org/10.1016/S1360-1385(00)01571-5 DO - 10.1016/S1360-1385(00)01571-5 ID - Lovegrove2000 ER - TY - JOUR AU - Ruzicka, K. AU - Ljung, K. AU - Vanneste, S. AU - Podhorska, R. AU - Beeckman, T. AU - Friml, J. AU - Benkova, E. PY - 2007 DA - 2007// TI - Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.052126 DO - 10.1105/tpc.107.052126 ID - Ruzicka2007 ER - TY - JOUR AU - Bari, R. AU - Jones, J. D. PY - 2009 DA - 2009// TI - Role of plant hormones in plant defense responses JO - Plant Mol Biol VL - 69 UR - https://doi.org/10.1007/s11103-008-9435-0 DO - 10.1007/s11103-008-9435-0 ID - Bari2009 ER - TY - JOUR AU - Truman, W. M. AU - Bennett, M. H. AU - Turnbull, C. G. AU - Grant, M. R. PY - 2010 DA - 2010// TI - Arabidopsis auxin mutants are compromised in systemic acquired resistance and exhibit aberrant accumulation of various indolic compounds JO - Plant Physiol VL - 152 UR - https://doi.org/10.1104/pp.109.152173 DO - 10.1104/pp.109.152173 ID - Truman2010 ER - TY - JOUR AU - Yamamoto, Y. Y. AU - Ichida, H. AU - Matsui, M. AU - Obokata, J. AU - Sakurai, T. AU - Satou, M. AU - Seki, M. AU - Shinozaki, K. AU - Abe, T. PY - 2007 DA - 2007// TI - Identification of plant promoter constituents by analysis of local distribution of short sequences JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-67 DO - 10.1186/1471-2164-8-67 ID - Yamamoto2007 ER - TY - CHAP AU - Yamamoto, Y. Y. AU - Obokata, J. ED - Russe, A. S. PY - 2009 DA - 2009// TI - Extraction of position-sensitive promoter constituents BT - Computational biology: new research PB - Nova Science Publishers CY - Hauppauge, NY ID - Yamamoto2009 ER - TY - JOUR AU - Yamamoto, Y. Y. AU - Yoshitsugu, T. AU - Sakurai, T. AU - Seki, M. AU - Shinozaki, K. AU - Obokata, J. PY - 2009 DA - 2009// TI - Heterogeneity of Arabidopsis core promoters revealed by high density TSS analysis JO - Plant J VL - 60 UR - https://doi.org/10.1111/j.1365-313X.2009.03958.x DO - 10.1111/j.1365-313X.2009.03958.x ID - Yamamoto2009 ER - TY - JOUR AU - FitzGerald, P. C. AU - Shlyakhtenko, A. AU - Mir, A. A. AU - Vinson, C. PY - 2004 DA - 2004// TI - Clustering of DNA sequences in human promoters JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1953904 DO - 10.1101/gr.1953904 ID - FitzGerald2004 ER - TY - JOUR AU - Thijs, G. AU - Marchal, K. AU - Lescot, M. AU - Rombauts, S. AU - De Moor, B. AU - Rouze, P. AU - Moreau, Y. PY - 2002 DA - 2002// TI - A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes JO - J Comput Biol VL - 9 UR - https://doi.org/10.1089/10665270252935566 DO - 10.1089/10665270252935566 ID - Thijs2002 ER - TY - JOUR AU - Lawrence, C. E. AU - Altschul, S. F. AU - Boguski, M. S. AU - Liu, J. S. AU - Neuwald, A. F. AU - Wootton, J. C. PY - 1993 DA - 1993// TI - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment JO - Science VL - 262 UR - https://doi.org/10.1126/science.8211139 DO - 10.1126/science.8211139 ID - Lawrence1993 ER - TY - JOUR AU - Bailey, T. L. AU - Elkan, C. PY - 1994 DA - 1994// TI - Fitting a mixture model by expectation maximization to discover motifs in biopolymers JO - Proc Int Conf Intell Syst Mol Biol VL - 2 ID - Bailey1994 ER - TY - CHAP AU - Okumura, T. AU - Makiguchi, H. AU - Makita, Y. AU - Yamashita, R. AU - Nakai, K. PY - 2007 DA - 2007// TI - Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. BT - Nucleic Acids Res. UR - https://doi.org/10.1093/nar/gkm362 DO - 10.1093/nar/gkm362 ID - Okumura2007 ER - TY - JOUR AU - Yamaguchi-Shinozaki, K. AU - Shinozaki, K. PY - 1994 DA - 1994// TI - A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress JO - Plant Cell VL - 6 UR - https://doi.org/10.1105/tpc.6.2.251 DO - 10.1105/tpc.6.2.251 ID - Yamaguchi-Shinozaki1994 ER - TY - JOUR AU - Narusaka, Y. AU - Nakashima, K. AU - Shinwari, Z. K. AU - Sakuma, Y. AU - Furihata, T. AU - Abe, H. AU - Narusaka, M. AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. PY - 2003 DA - 2003// TI - Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses JO - Plant J VL - 34 UR - https://doi.org/10.1046/j.1365-313X.2003.01708.x DO - 10.1046/j.1365-313X.2003.01708.x ID - Narusaka2003 ER - TY - JOUR AU - Kilian, J. AU - Whitehead, D. AU - Horak, J. AU - Wanke, D. AU - Weinl, S. AU - Batistic, O. AU - D'Angelo, C. AU - Bornberg-Bauer, E. AU - Kudla, J. AU - Harter, K. PY - 2007 DA - 2007// TI - The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses JO - Plant J VL - 50 UR - https://doi.org/10.1111/j.1365-313X.2007.03052.x DO - 10.1111/j.1365-313X.2007.03052.x ID - Kilian2007 ER - TY - JOUR AU - Goda, H. AU - Sasaki, E. AU - Akiyama, K. AU - Maruyama-Nakashita, A. AU - Nakabayashi, K. AU - Li, W. AU - Ogawa, M. AU - Yamauchi, Y. AU - Preston, J. AU - Aoki, K. PY - 2008 DA - 2008// TI - The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access JO - Plant J VL - 55 UR - https://doi.org/10.1111/j.1365-313X.2008.03510.x DO - 10.1111/j.1365-313X.2008.03510.x ID - Goda2008 ER - TY - JOUR AU - Maruyama, K. AU - Sakuma, Y. AU - Kasuga, M. AU - Ito, Y. AU - Seki, M. AU - Goda, H. AU - Shimada, Y. AU - Yoshida, S. AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. PY - 2004 DA - 2004// TI - Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems JO - Plant J VL - 38 UR - https://doi.org/10.1111/j.1365-313X.2004.02100.x DO - 10.1111/j.1365-313X.2004.02100.x ID - Maruyama2004 ER - TY - JOUR AU - Yamamoto, Y. Y. AU - Obokata, J. PY - 2008 DA - 2008// TI - ppdb, a plant promoter database JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm785 DO - 10.1093/nar/gkm785 ID - Yamamoto2008 ER - TY - JOUR AU - Liu, Q. AU - Kasuga, M. AU - Sakuma, Y. AU - Abe, H. AU - Miura, S. AU - Yamaguchi-Shinozaki, K. AU - Shinozaki, K. PY - 1998 DA - 1998// TI - Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis JO - Plant Cell VL - 10 UR - https://doi.org/10.1105/tpc.10.8.1391 DO - 10.1105/tpc.10.8.1391 ID - Liu1998 ER - TY - JOUR AU - Sakuma, Y. AU - Liu, Q. AU - Dubouzet, J. G. AU - Abe, H. AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. PY - 2002 DA - 2002// TI - DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression JO - Biochem Biophys Res Commun VL - 290 UR - https://doi.org/10.1006/bbrc.2001.6299 DO - 10.1006/bbrc.2001.6299 ID - Sakuma2002 ER - TY - JOUR AU - Haake, V. AU - Cook, D. AU - Riechmann, J. L. AU - Pineda, O. AU - Thomashow, M. F. AU - Zhang, J. Z. PY - 2002 DA - 2002// TI - Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis JO - Plant Physiol VL - 130 UR - https://doi.org/10.1104/pp.006478 DO - 10.1104/pp.006478 ID - Haake2002 ER - TY - JOUR AU - Shen, Q. AU - Zhang, P. AU - Ho, T. H. PY - 1996 DA - 1996// TI - Modular nature of abscisic acid (ABA) response complexes: composite promoter units that are necessary and sufficient for ABA induction of gene expression in barley JO - Plant Cell VL - 8 UR - https://doi.org/10.1105/tpc.8.7.1107 DO - 10.1105/tpc.8.7.1107 ID - Shen1996 ER - TY - JOUR AU - Gomez-Porras, J. L. AU - Riano-Pachon, D. M. AU - Dreyer, I. AU - Mayer, J. E. AU - Mueller-Roeber, B. PY - 2007 DA - 2007// TI - Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-260 DO - 10.1186/1471-2164-8-260 ID - Gomez-Porras2007 ER - TY - JOUR AU - Yamaguchi-Shinozaki, K. AU - Shinozaki, K. PY - 2005 DA - 2005// TI - Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters JO - Trends Plant Sci VL - 10 UR - https://doi.org/10.1016/j.tplants.2004.12.012 DO - 10.1016/j.tplants.2004.12.012 ID - Yamaguchi-Shinozaki2005 ER - TY - JOUR AU - Lebel, E. AU - Heifetz, P. AU - Thorne, L. AU - Uknes, S. AU - Ryals, J. AU - Ward, E. PY - 1998 DA - 1998// TI - Functional analysis of regulatory sequences controlling PR-1 gene expression in Arabidopsis JO - Plant J VL - 16 UR - https://doi.org/10.1046/j.1365-313x.1998.00288.x DO - 10.1046/j.1365-313x.1998.00288.x ID - Lebel1998 ER - TY - CHAP AU - Pape, S. AU - Thurow, C. AU - Gatz, C. PY - 2010 DA - 2010// TI - The Arabidopsis thaliana PR-1 Promoter Contains Multiple Integration Sites for the Co-activator NPR1 and the Repressor SNI1 BT - Plant Physiol ID - Pape2010 ER - TY - JOUR AU - Yoo, S. D. AU - Cho, Y. AU - Sheen, J. PY - 2009 DA - 2009// TI - Emerging connections in the ethylene signaling network JO - Trends Plant Sci VL - 14 UR - https://doi.org/10.1016/j.tplants.2009.02.007 DO - 10.1016/j.tplants.2009.02.007 ID - Yoo2009 ER - TY - JOUR AU - Negi, S. AU - Ivanchenko, M. G. AU - Muday, G. K. PY - 2008 DA - 2008// TI - Ethylene regulates lateral root formation and auxin transport in Arabidopsis thaliana JO - Plant J VL - 55 UR - https://doi.org/10.1111/j.1365-313X.2008.03495.x DO - 10.1111/j.1365-313X.2008.03495.x ID - Negi2008 ER - TY - JOUR AU - Rao, M. V. AU - Paliyath, G. AU - Ormrod, D. P. AU - Murr, D. P. AU - Watkins, C. B. PY - 1997 DA - 1997// TI - Influence of salicylic acid on H2O2 production, oxidative stress, and H2O2-metabolizing enzymes. Salicylic acid-mediated oxidative damage requires H2O2 JO - Plant Physiol VL - 115 UR - https://doi.org/10.1104/pp.115.1.137 DO - 10.1104/pp.115.1.137 ID - Rao1997 ER - TY - JOUR AU - Seki, M. AU - Narusaka, M. AU - Kamiya, A. AU - Ishida, J. AU - Satou, M. AU - Sakurai, T. AU - Nakajima, M. AU - Enju, A. AU - Akiyama, K. AU - Oono, Y. PY - 2002 DA - 2002// TI - Functional annotation of a full-length Arabidopsis cDNA collection JO - Science VL - 296 UR - https://doi.org/10.1126/science.1071006 DO - 10.1126/science.1071006 ID - Seki2002 ER - TY - STD TI - TAIR. [http://www.arabidopsis.org/] UR - http://www.arabidopsis.org/ ID - ref32 ER - TY - STD TI - Melina II. [http://melina2.hgc.jp/] UR - http://melina2.hgc.jp/ ID - ref33 ER - TY - STD TI - ClustalW. [http://www.ebi.ac.uk/Tools/msa/clustalw2/] UR - http://www.ebi.ac.uk/Tools/msa/clustalw2/ ID - ref34 ER - TY - STD TI - WebLogo. [http://weblogo.berkeley.edu/] UR - http://weblogo.berkeley.edu/ ID - ref35 ER - TY - STD TI - ppdb. [http://ppdb.agr.gifu-u.ac.jp] UR - http://ppdb.agr.gifu-u.ac.jp ID - ref36 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Crooks, G. E. AU - Hon, G. AU - Chandonia, J. M. AU - Brenner, S. E. PY - 2004 DA - 2004// TI - WebLogo: a sequence logo generator JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.849004 DO - 10.1101/gr.849004 ID - Crooks2004 ER - TY - JOUR AU - Yamamoto, Y. Y. AU - Shimada, Y. AU - Kimura, M. AU - Manabe, K. AU - Sekine, Y. AU - Matsui, M. AU - Ryuto, H. AU - Fukunishi, N. AU - Abe, T. AU - Yoshida, S. PY - 2004 DA - 2004// TI - Global classification of transcriptional responses to light stress in Arabidopsis thaliana JO - Endocytobio Cell Res VL - 15 ID - Yamamoto2004 ER - TY - JOUR AU - Foster, R. AU - Izawa, T. AU - Chua, N. H. PY - 1994 DA - 1994// TI - Plant bZIP proteins gather at ACGT elements JO - Faseb J VL - 8 ID - Foster1994 ER - TY - JOUR AU - Yang, T. AU - Poovaiah, B. W. PY - 2002 DA - 2002// TI - A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M207941200 DO - 10.1074/jbc.M207941200 ID - Yang2002 ER - TY - JOUR AU - Urano, K. AU - Kurihara, Y. AU - Seki, M. AU - Shinozaki, K. PY - 2010 DA - 2010// TI - 'Omics' analyses of regulatory networks in plant abiotic stress responses JO - Curr Opin Plant Biol VL - 13 UR - https://doi.org/10.1016/j.pbi.2009.12.006 DO - 10.1016/j.pbi.2009.12.006 ID - Urano2010 ER - TY - JOUR AU - Yanagisawa, S. PY - 2004 DA - 2004// TI - Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants JO - Plant Cell Physiol VL - 45 UR - https://doi.org/10.1093/pcp/pch055 DO - 10.1093/pcp/pch055 ID - Yanagisawa2004 ER - TY - JOUR AU - Gurr, S. J. AU - Rushton, P. J. PY - 2005 DA - 2005// TI - Engineering plants with increased disease resistance: how are we going to express it? JO - Trends Biotechnol VL - 23 UR - https://doi.org/10.1016/j.tibtech.2005.04.009 DO - 10.1016/j.tibtech.2005.04.009 ID - Gurr2005 ER - TY - JOUR AU - Rushton, P. J. AU - Somssich, I. E. AU - Ringler, P. AU - Shen, Q. J. PY - 2010 DA - 2010// TI - WRKY transcription factors JO - Trends Plant Sci VL - 15 UR - https://doi.org/10.1016/j.tplants.2010.02.006 DO - 10.1016/j.tplants.2010.02.006 ID - Rushton2010 ER - TY - JOUR AU - Ulmasov, T. AU - Hagen, G. AU - Guilfoyle, T. J. PY - 1999 DA - 1999// TI - Dimerization and DNA binding of auxin response factors JO - Plant J VL - 19 UR - https://doi.org/10.1046/j.1365-313X.1999.00538.x DO - 10.1046/j.1365-313X.1999.00538.x ID - Ulmasov1999 ER -