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Volumn 50, Issue 2, 2007, Pages 347-363

The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses

Author keywords

Abiotic stress; AtGenExpress; Bioinformatics; Gene expression; Microarray

Indexed keywords

BIOINFORMATICS; GENE EXPRESSION; MICROARRAYS; RNA; ULTRAVIOLET RADIATION;

EID: 34247200577     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2007.03052.x     Document Type: Article
Times cited : (1148)

References (41)
  • 1
    • 0034730610 scopus 로고    scopus 로고
    • Alteration of stimulus-specific guard cell calcium oscillations and stomatal closing in the Arabidopsis det3 mutant
    • Allen, G.J., Chu, S.P., Schumacher, K. et al. (2000) Alteration of stimulus-specific guard cell calcium oscillations and stomatal closing in the Arabidopsis det3 mutant. Science, 289, 2338-2342.
    • (2000) Science , vol.289 , pp. 2338-2342
    • Allen, G.J.1    Chu, S.P.2    Schumacher, K.3
  • 2
    • 3242715114 scopus 로고    scopus 로고
    • Reactive oxygen species: Metabolism, oxidative stress, and signal transduction
    • Apel, K. and Hirt, H. (2004) Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annu. Rev. Plant Biol. 55, 373-399.
    • (2004) Annu. Rev. Plant Biol , vol.55 , pp. 373-399
    • Apel, K.1    Hirt, H.2
  • 3
    • 33845609562 scopus 로고    scopus 로고
    • Cismotifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves
    • Berendzen, K.W., Stüber, K., Harter, K. and Wanke, D. (2006) Cismotifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics, 7, 522-541.
    • (2006) BMC Bioinformatics , vol.7 , pp. 522-541
    • Berendzen, K.W.1    Stüber, K.2    Harter, K.3    Wanke, D.4
  • 4
    • 24644481999 scopus 로고    scopus 로고
    • Order preserving clustering over multiple time course experiments
    • Bleuler, S. and Zitzler, E. (2005) Order preserving clustering over multiple time course experiments. Lecture Notes in Computer Science, 3449, 33-43.
    • (2005) Lecture Notes in Computer Science , vol.3449 , pp. 33-43
    • Bleuler, S.1    Zitzler, E.2
  • 5
    • 33344454751 scopus 로고    scopus 로고
    • Unravelling abiotic stress tolerance mechanisms: Getting genomics going
    • Bohnert, H.J., Gong, Q. and Ma, S. (2006) Unravelling abiotic stress tolerance mechanisms: Getting genomics going. Curr. Opin. Plant Biol. 9, 180-188.
    • (2006) Curr. Opin. Plant Biol , vol.9 , pp. 180-188
    • Bohnert, H.J.1    Gong, Q.2    Ma, S.3
  • 6
    • 25444461919 scopus 로고    scopus 로고
    • Vector analysis as a fast and easy method to compare gene expression in responses between different experimental background
    • Breitling, R., Armengaud, P. and Amtmann, A. (2005) Vector analysis as a fast and easy method to compare gene expression in responses between different experimental background. BMC Bioinformatics, 6, 181-188.
    • (2005) BMC Bioinformatics , vol.6 , pp. 181-188
    • Breitling, R.1    Armengaud, P.2    Amtmann, A.3
  • 8
    • 4644360515 scopus 로고    scopus 로고
    • Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues
    • Casati, P. and Walbot, V. (2004) Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues. Genome Biol. 5, R16.
    • (2004) Genome Biol , vol.5
    • Casati, P.1    Walbot, V.2
  • 10
    • 0036010572 scopus 로고    scopus 로고
    • Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses
    • Chen, W., Provart, N.J., Glazebrook, J. et al. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell, 14, 559-574.
    • (2002) Plant Cell , vol.14 , pp. 559-574
    • Chen, W.1    Provart, N.J.2    Glazebrook, J.3
  • 12
    • 33344455077 scopus 로고    scopus 로고
    • The zinc-finger protein ZAT12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis
    • Davletova, S., Schlauch, K., Coutu, J. and Mittler, R. (2005) The zinc-finger protein ZAT12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol. 139, 847-856.
    • (2005) Plant Physiol , vol.139 , pp. 847-856
    • Davletova, S.1    Schlauch, K.2    Coutu, J.3    Mittler, R.4
  • 13
    • 0034813646 scopus 로고    scopus 로고
    • Regulation of the Arabidopsis transcriptome by oxidative stress
    • Desikan, R., A-H-Mackerness, S., Hancock, J.T. and Neill, S.J. (2001) Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiol. 127, 159-172.
    • (2001) Plant Physiol , vol.127 , pp. 159-172
    • Desikan, R.1    A-H-Mackerness, S.2    Hancock, J.T.3    Neill, S.J.4
  • 14
    • 0036671216 scopus 로고    scopus 로고
    • Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway
    • Fowler, S. and Thomashow, M.F. (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell, 14, 1675-1690.
    • (2002) Plant Cell , vol.14 , pp. 1675-1690
    • Fowler, S.1    Thomashow, M.F.2
  • 15
    • 3042750616 scopus 로고    scopus 로고
    • Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana
    • Hirai, M.Y., Yano, M., Goodenowe, D.B., Kanaya, S., Kimura, T., Awazuhara, M., Arita, M., Fujiwara, T. and Saito, K. (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 101, 10205-10210.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 10205-10210
    • Hirai, M.Y.1    Yano, M.2    Goodenowe, D.B.3    Kanaya, S.4    Kimura, T.5    Awazuhara, M.6    Arita, M.7    Fujiwara, T.8    Saito, K.9
  • 17
    • 0033990432 scopus 로고    scopus 로고
    • Calcium signaling during abiotic stress in plants
    • Knight, H. (2000) Calcium signaling during abiotic stress in plants. Int. Rev. Cytol. 195, 269-324.
    • (2000) Int. Rev. Cytol , vol.195 , pp. 269-324
    • Knight, H.1
  • 18
    • 0035206163 scopus 로고    scopus 로고
    • Abiotic stress signalling pathways: Specificity and cross-talk
    • Knight, H. and Knight, M.R. (2001) Abiotic stress signalling pathways: specificity and cross-talk. Trends Plant Sci. 6, 262-267.
    • (2001) Trends Plant Sci , vol.6 , pp. 262-267
    • Knight, H.1    Knight, M.R.2
  • 19
    • 0036909761 scopus 로고    scopus 로고
    • Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress
    • Kreps, J.A., Wu, Y., Chang, H.-S., Zhu, T., Wang, X. and Harper, J.F. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130, 2129-2141.
    • (2002) Plant Physiol , vol.130 , pp. 2129-2141
    • Kreps, J.A.1    Wu, Y.2    Chang, H.-S.3    Zhu, T.4    Wang, X.5    Harper, J.F.6
  • 20
    • 0036017859 scopus 로고    scopus 로고
    • Cross talk between signalling pathways in pathogen defense
    • Kunkel, B.N. and Brooks, D.M. (2002) Cross talk between signalling pathways in pathogen defense. Curr. Opin. Plant Biol. 5, 325-331.
    • (2002) Curr. Opin. Plant Biol , vol.5 , pp. 325-331
    • Kunkel, B.N.1    Brooks, D.M.2
  • 21
    • 0343953411 scopus 로고    scopus 로고
    • The involvement of hydrogen peroxide in plant responses to stresses
    • Kuzniak, E. and Urbanek, H. (2000) The involvement of hydrogen peroxide in plant responses to stresses. Acta Physiol. Plant. 22, 195-203.
    • (2000) Acta Physiol. Plant , vol.22 , pp. 195-203
    • Kuzniak, E.1    Urbanek, H.2
  • 22
    • 33645025500 scopus 로고    scopus 로고
    • Dissecting salt stress pathways
    • Ma, S., Gong, Q. and Bohnert, H.J. (2006) Dissecting salt stress pathways. J. Exp. Bot. 57, 1097-1107.
    • (2006) J. Exp. Bot , vol.57 , pp. 1097-1107
    • Ma, S.1    Gong, Q.2    Bohnert, H.J.3
  • 23
    • 0141857861 scopus 로고    scopus 로고
    • Stress response, cell death and signalling: The many faces of reactive oxygen species
    • Mahalingam, R. and Fedoroff, N. (2003) Stress response, cell death and signalling: the many faces of reactive oxygen species. Physiol. Plant. 119, 56-68.
    • (2003) Physiol. Plant , vol.119 , pp. 56-68
    • Mahalingam, R.1    Fedoroff, N.2
  • 25
    • 0034860366 scopus 로고    scopus 로고
    • Repression domains of class II ERF transcriptional repressors share an essential motif for active repression
    • Ohta, M., Matsui, K., Hiratsu, K., Shinshi, H. and Ohme-Takagi, M. (2001) Repression domains of class II ERF transcriptional repressors share an essential motif for active repression. Plant Cell, 13, 1959-1968.
    • (2001) Plant Cell , vol.13 , pp. 1959-1968
    • Ohta, M.1    Matsui, K.2    Hiratsu, K.3    Shinshi, H.4    Ohme-Takagi, M.5
  • 27
    • 2342501846 scopus 로고    scopus 로고
    • Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
    • Redman, J.C., Haas, B.J., Tanimoto, T. and Town, C.D. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 38, 545-561.
    • (2004) Plant J , vol.38 , pp. 545-561
    • Redman, J.C.1    Haas, B.J.2    Tanimoto, T.3    Town, C.D.4
  • 28
    • 14744281201 scopus 로고    scopus 로고
    • Balancing the generation and elimination of reactive oxygen species
    • Rodriguez, R. and Redman, R. (2005) Balancing the generation and elimination of reactive oxygen species. Proc. Natl Acad. Sci. USA, 102, 3175-3176.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 3175-3176
    • Rodriguez, R.1    Redman, R.2
  • 29
    • 0036851187 scopus 로고    scopus 로고
    • Global changes in gene expression in response to high light in Arabidopsis
    • Rossel, J.B., Wilson, I.W. and Pogson, B.J. (2002) Global changes in gene expression in response to high light in Arabidopsis. Plant Physiol. 130, 1109-1120.
    • (2002) Plant Physiol , vol.130 , pp. 1109-1120
    • Rossel, J.B.1    Wilson, I.W.2    Pogson, B.J.3
  • 30
    • 0035999364 scopus 로고    scopus 로고
    • Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound- induced signaling
    • Rushton, P.J., Reinstaedler, A., Lipka, V., Lippok, B. and Somssich, I.E. (2002) Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound- induced signaling. Plant Cell, 14, 749-762.
    • (2002) Plant Cell , vol.14 , pp. 749-762
    • Rushton, P.J.1    Reinstaedler, A.2    Lipka, V.3    Lippok, B.4    Somssich, I.E.5
  • 31
    • 13744249154 scopus 로고    scopus 로고
    • Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high salinity stress conditions
    • Sakamoto, H., Maruyama, K., Sakuma, Y., Meshi, T., Iwabuchi, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2004) Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high salinity stress conditions. Plant Physiol. 136, 2734-2746.
    • (2004) Plant Physiol , vol.136 , pp. 2734-2746
    • Sakamoto, H.1    Maruyama, K.2    Sakuma, Y.3    Meshi, T.4    Iwabuchi, M.5    Shinozaki, K.6    Yamaguchi-Shinozaki, K.7
  • 32
    • 0347243182 scopus 로고    scopus 로고
    • Nonlinear component analysis as a kernel eigenvalue problem
    • Schoelkopf, B., Smola, A. and Mueller, K.-R. (1998) Nonlinear component analysis as a kernel eigenvalue problem. J. Neural Comp. 10, 1299-1319.
    • (1998) J. Neural Comp , vol.10 , pp. 1299-1319
    • Schoelkopf, B.1    Smola, A.2    Mueller, K.-R.3
  • 33
    • 0035107803 scopus 로고    scopus 로고
    • Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray
    • Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K. (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell, 13, 61-72.
    • (2001) Plant Cell , vol.13 , pp. 61-72
    • Seki, M.1    Narusaka, M.2    Abe, H.3    Kasuga, M.4    Yamaguchi-Shinozaki, K.5    Carninci, P.6    Hayashizaki, Y.7    Shinozaki, K.8
  • 34
    • 0036679053 scopus 로고    scopus 로고
    • Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    • Seki, M., Narusaka, M., Ishida, J. et al. (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J. 31, 279-292.
    • (2002) Plant J , vol.31 , pp. 279-292
    • Seki, M.1    Narusaka, M.2    Ishida, J.3
  • 35
    • 0141725442 scopus 로고    scopus 로고
    • Regulatory network of gene expression in the drought and cold stress responses
    • Shinozaki, K., Yamaguchi-Shinozaki, K. and Seki, M. (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6, 410-417.
    • (2003) Curr. Opin. Plant Biol , vol.6 , pp. 410-417
    • Shinozaki, K.1    Yamaguchi-Shinozaki, K.2    Seki, M.3
  • 36
    • 33845789612 scopus 로고    scopus 로고
    • The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana
    • doi 10.1534/genetics.106.061374
    • Swindell, W.R. (2006) The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana. Genetics, doi 10.1534/genetics.106.061374.
    • (2006) Genetics
    • Swindell, W.R.1
  • 37
    • 23944460533 scopus 로고    scopus 로고
    • Signalling and gene regulation in response to ultraviolet light
    • Ulm, R. and Nagy, F. (2005) Signalling and gene regulation in response to ultraviolet light. Curr. Opin. Plant Biol. 8, 477-482.
    • (2005) Curr. Opin. Plant Biol , vol.8 , pp. 477-482
    • Ulm, R.1    Nagy, F.2
  • 38
    • 0842299514 scopus 로고    scopus 로고
    • Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis
    • Ulm, R., Baumann, A., Oravecz, A., Máté, Z., Ádám, É., Oakeley, E.J., Schäfer, E. and Nagy, F. (2004) Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis. Proc. Natl Acad. Sci. USA, 101, 1397-1402.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 1397-1402
    • Ulm, R.1    Baumann, A.2    Oravecz, A.3    Máté, Z.4    Ádám, E.5    Oakeley, E.J.6    Schäfer, E.7    Nagy, F.8
  • 39
    • 33847290320 scopus 로고    scopus 로고
    • The regulatory code for transcriptional response diversity and ist relation to genome structural properties in Arabidopsis thaliana
    • doi:10.1371/journal.pgen.0030011.eor
    • Walther, D., Brunnemann, R. and Selbig, J. (2007) The regulatory code for transcriptional response diversity and ist relation to genome structural properties in Arabidopsis thaliana. PLoS Genetics, doi:10.1371/journal.pgen.0030011.eor.
    • (2007) PLoS Genetics
    • Walther, D.1    Brunnemann, R.2    Selbig, J.3
  • 41
    • 0036273511 scopus 로고    scopus 로고
    • Cell signaling during cold, drought, and salt stress
    • Xiong, L., Schumaker, K.S. and Zhu, J-K. (2002) Cell signaling during cold, drought, and salt stress. Plant Cell, 14 (Supplement 2002), S165-S183.
    • (2002) Plant Cell , vol.14 , Issue.SUPPL.EMENT
    • Xiong, L.1    Schumaker, K.S.2    Zhu, J.-K.3


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