메뉴 건너뛰기




Volumn 20, Issue 2, 2013, Pages 151-162

TreeTFDB: An integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics

Author keywords

Cis Motif; Database; Expression; Transcription factor; Tree crops

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTION FACTOR;

EID: 84879170851     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dss040     Document Type: Article
Times cited : (21)

References (43)
  • 1
    • 0034671865 scopus 로고    scopus 로고
    • Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes
    • Riechmann, J.L., Heard, J., Martin, G., et al. 2000, Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes, Science, 290, 2105-10.
    • (2000) Science , vol.290 , pp. 2105-2110
    • Riechmann, J.L.1    Heard, J.2    Martin, G.3
  • 2
    • 77956447296 scopus 로고    scopus 로고
    • Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach
    • Tran, L.S., Nishiyama, R., Yamaguchi-Shinozaki, K. and Shinozaki, K. 2010, Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach, GM Crops, 1, 32-9.
    • (2010) GM Crops , vol.1 , pp. 32-39
    • Tran, L.S.1    Nishiyama, R.2    Yamaguchi-Shinozaki, K.3    Shinozaki, K.4
  • 3
    • 79751533964 scopus 로고    scopus 로고
    • Progress studies of drought-responsive genes in rice
    • Hadiarto, T. and Tran, L.S. 2011, Progress studies of drought-responsive genes in rice, Plant Cell Rep., 30, 297-310.
    • (2011) Plant Cell Rep. , vol.30 , pp. 297-310
    • Hadiarto, T.1    Tran, L.S.2
  • 4
    • 84868345850 scopus 로고    scopus 로고
    • Potentials toward genetic engineering of drought-tolerant soybean
    • Thao, N.P. and Tran, L.S. 2011, Potentials toward genetic engineering of drought-tolerant soybean, Crit. Rev. Biotechnol., 32, 349-62.
    • (2011) Crit. Rev. Biotechnol. , vol.32 , pp. 349-362
    • Thao, N.P.1    Tran, L.S.2
  • 5
    • 84873117349 scopus 로고    scopus 로고
    • System biology-based approaches towards understanding drought tolerance in food crops
    • doi:10.3109/07388551.2012.659174
    • Jogaiah, S., Ramsandra Govind, S. and Tran, L.S. 2012, System biology-based approaches towards understanding drought tolerance in food crops, Crit. Rev. Biotechnol., doi:10.3109/07388551.2012.659174.
    • (2012) Crit. Rev. Biotechnol.
    • Jogaiah, S.1    Ramsandra Govind, S.2    Tran, L.S.3
  • 6
    • 84856416305 scopus 로고    scopus 로고
    • Transcriptional switches direct plant organ formation and patterning
    • Moreno-Risueno, M.A., Van Norman, J.M. and Benfey, P.N. 2012, Transcriptional switches direct plant organ formation and patterning, Curr. Top. Dev. Biol., 98, 229-57.
    • (2012) Curr. Top. Dev. Biol. , vol.98 , pp. 229-257
    • Moreno-Risueno, M.A.1    Van Norman, J.M.2    Benfey, P.N.3
  • 7
    • 35748944541 scopus 로고    scopus 로고
    • Plant gene networks in osmotic stress response: From genes to regulatory networks
    • Tran, L.S., Nakashima, K., Shinozaki, K. and Yamaguchi-Shinozaki, K. 2007, Plant gene networks in osmotic stress response: From genes to regulatory networks, Methods Enzymol., 428, 109-28.
    • (2007) Methods Enzymol. , vol.428 , pp. 109-128
    • Tran, L.S.1    Nakashima, K.2    Shinozaki, K.3    Yamaguchi-Shinozaki, K.4
  • 8
    • 57749089790 scopus 로고    scopus 로고
    • Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stressresponsive gene expression
    • Qin, F., Sakuma, Y., Tran, L.S., et al. 2008, Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stressresponsive gene expression, Plant Cell, 20, 1693-707.
    • (2008) Plant Cell , vol.20 , pp. 1693-1707
    • Qin, F.1    Sakuma, Y.2    Tran, L.S.3
  • 9
    • 84861716982 scopus 로고    scopus 로고
    • Multiple histone methyl and acetyltransferase complex components bind the HLA-DRA gene
    • Choi, N.M. and Boss, J.M. 2012, Multiple histone methyl and acetyltransferase complex components bind the HLA-DRA gene, PLoS One, 7, e37554.
    • (2012) PLoS One , vol.7
    • Choi, N.M.1    Boss, J.M.2
  • 10
    • 13744261322 scopus 로고    scopus 로고
    • Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters
    • Yamaguchi-Shinozaki, K. and Shinozaki, K. 2005, Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters, Trends Plant Sci., 10, 88-94.
    • (2005) Trends Plant Sci. , vol.10 , pp. 88-94
    • Yamaguchi-Shinozaki, K.1    Shinozaki, K.2
  • 11
    • 77954962725 scopus 로고    scopus 로고
    • Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean
    • Tran, L.S. and Mochida, K. 2010, Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean, Plant Signal Behav., 5, 255-7.
    • (2010) Plant Signal Behav. , vol.5 , pp. 255-257
    • Tran, L.S.1    Mochida, K.2
  • 12
    • 77954987186 scopus 로고    scopus 로고
    • A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond
    • Tran, L.S. and Mochida, K. 2010, A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond, Plant Signal Behav., 5, 550-2.
    • (2010) Plant Signal Behav. , vol.5 , pp. 550-552
    • Tran, L.S.1    Mochida, K.2
  • 13
    • 78650517886 scopus 로고    scopus 로고
    • Functional genomics of soybean for improvement of productivity in adverse conditions
    • Tran, L.S. and Mochida, K. 2010, Functional genomics of soybean for improvement of productivity in adverse conditions, Funct. Integr. Genomics, 10, 447-62.
    • (2010) Funct. Integr. Genomics , vol.10 , pp. 447-462
    • Tran, L.S.1    Mochida, K.2
  • 14
    • 77952903335 scopus 로고    scopus 로고
    • Genomics and bioinformatics resources for crop improvement
    • Mochida, K. and Shinozaki, K. 2010, Genomics and bioinformatics resources for crop improvement, Plant Cell Physiol., 51, 497-523.
    • (2010) Plant Cell Physiol. , vol.51 , pp. 497-523
    • Mochida, K.1    Shinozaki, K.2
  • 15
    • 33646596265 scopus 로고    scopus 로고
    • RARTF: Database and tools for complete sets of Arabidopsis transcription factors
    • Iida, K., Seki, M., Sakurai, T., et al. 2005, RARTF: Database and tools for complete sets of Arabidopsis transcription factors, DNA Res., 12, 247-56.
    • (2005) DNA Res. , vol.12 , pp. 247-256
    • Iida, K.1    Seki, M.2    Sakurai, T.3
  • 16
    • 33646884846 scopus 로고    scopus 로고
    • DRTF: A database of rice transcription factors
    • Gao, G., Zhong, Y., Guo, A., et al. 2006, DRTF: A database of rice transcription factors, Bioinformatics, 22, 1286-7.
    • (2006) Bioinformatics , vol.22 , pp. 1286-1287
    • Gao, G.1    Zhong, Y.2    Guo, A.3
  • 17
    • 75249102751 scopus 로고    scopus 로고
    • In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean
    • Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. 2009, In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean, DNA Res., 16, 353-69.
    • (2009) DNA Res. , vol.16 , pp. 353-369
    • Mochida, K.1    Yoshida, T.2    Sakurai, T.3    Yamaguchi-Shinozaki, K.4    Shinozaki, K.5    Tran, L.S.6
  • 18
    • 77649328902 scopus 로고    scopus 로고
    • SoyDB: A knowledge database of soybean transcription factors
    • Wang, Z., Libault, M., Joshi, T., et al. 2010, SoyDB: A knowledge database of soybean transcription factors, BMC Plant Biol., 10, 14.
    • (2010) BMC Plant Biol. , vol.10 , pp. 14
    • Wang, Z.1    Libault, M.2    Joshi, T.3
  • 20
    • 42249096792 scopus 로고    scopus 로고
    • DATFAP: A database of primers and homology alignments for transcription factors from 13 plant species
    • Fredslund, J. 2008, DATFAP: A database of primers and homology alignments for transcription factors from 13 plant species, BMC Genomics, 9, 140.
    • (2008) BMC Genomics , vol.9 , pp. 140
    • Fredslund, J.1
  • 21
    • 58449094652 scopus 로고    scopus 로고
    • GRASSIUS: A platform for comparative regulatory genomics across the grasses
    • Yilmaz, A., Nishiyama, M.Y. Jr, Fuentes, B.G., et al. 2009, GRASSIUS: A platform for comparative regulatory genomics across the grasses, Plant Physiol., 149, 171-80.
    • (2009) Plant Physiol. , vol.149 , pp. 171-180
    • Yilmaz, A.1    Nishiyama Jr., M.Y.2    Fuentes, B.G.3
  • 23
    • 77950465255 scopus 로고    scopus 로고
    • LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors
    • Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. 2010, LegumeTFDB: An integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors, Bioinformatics, 26, 290-1.
    • (2010) Bioinformatics , vol.26 , pp. 290-291
    • Mochida, K.1    Yoshida, T.2    Sakurai, T.3    Yamaguchi-Shinozaki, K.4    Shinozaki, K.5    Tran, L.S.6
  • 24
    • 80054694145 scopus 로고    scopus 로고
    • In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants
    • Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. 2011, In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants, DNA Res., 18, 321-32.
    • (2011) DNA Res. , vol.18 , pp. 321-332
    • Mochida, K.1    Yoshida, T.2    Sakurai, T.3    Yamaguchi-Shinozaki, K.4    Shinozaki, K.5    Tran, L.S.6
  • 25
    • 78651337578 scopus 로고    scopus 로고
    • PlantTFDB 2.0: Update and improvement of the comprehensive plant transcription factor database
    • Zhang, H., Jin, J., Tang, L., et al. 2011, PlantTFDB 2.0: Update and improvement of the comprehensive plant transcription factor database, Nucleic Acids Res., 39, D1114-7.
    • (2011) Nucleic Acids Res. , vol.39
    • Zhang, H.1    Jin, J.2    Tang, L.3
  • 26
    • 83255189512 scopus 로고    scopus 로고
    • Advances in omics and bioinformatics tools for systems analyses of plant functions
    • Mochida, K. and Shinozaki, K. 2011, Advances in omics and bioinformatics tools for systems analyses of plant functions, Plant Cell Physiol., 52, 2017-38.
    • (2011) Plant Cell Physiol. , vol.52 , pp. 2017-2038
    • Mochida, K.1    Shinozaki, K.2
  • 27
    • 79951842938 scopus 로고    scopus 로고
    • Sequence analysis of the genome of an oil-bearing tree
    • Sato, S., Hirakawa, H., Isobe, S., et al. 2011, Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L, DNA Res., 18, 65-76.
    • (2011) Jatropha curcas L, DNA Res. , vol.18 , pp. 65-76
    • Sato, S.1    Hirakawa, H.2    Isobe, S.3
  • 28
    • 67650100882 scopus 로고    scopus 로고
    • TriFLDB: A database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics
    • Mochida, K., Yoshida, T., Sakurai, T., Ogihara, Y. and Shinozaki, K. 2009, TriFLDB: A database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics, Plant Physiol., 150, 1135-46.
    • (2009) Plant Physiol. , vol.150 , pp. 1135-1146
    • Mochida, K.1    Yoshida, T.2    Sakurai, T.3    Ogihara, Y.4    Shinozaki, K.5
  • 29
    • 43149094164 scopus 로고    scopus 로고
    • Pfam 10 years on: 10,000 families and still growing
    • Sammut, S.J., Finn, R.D. and Bateman, A. 2008, Pfam 10 years on: 10,000 families and still growing, Brief Bioinform., 9, 210-9.
    • (2008) Brief Bioinform. , vol.9 , pp. 210-219
    • Sammut, S.J.1    Finn, R.D.2    Bateman, A.3
  • 30
    • 34447312197 scopus 로고    scopus 로고
    • DPTF: A database of poplar transcription factors
    • Zhu, Q.H., Guo, A.Y., Gao, G., et al. 2007, DPTF: A database of poplar transcription factors, Bioinformatics, 23, 1307-8.
    • (2007) Bioinformatics , vol.23 , pp. 1307-1308
    • Zhu, Q.H.1    Guo, A.Y.2    Gao, G.3
  • 31
    • 38549144806 scopus 로고    scopus 로고
    • The Arabidopsis information resource (TAIR): Gene structure and function annotation
    • Swarbreck, D., Wilks, C., Lamesch, P., et al. 2008, The Arabidopsis information resource (TAIR): Gene structure and function annotation, Nucleic Acids Res., 36, D1009-14.
    • (2008) Nucleic Acids Res. , vol.36
    • Swarbreck, D.1    Wilks, C.2    Lamesch, P.3
  • 32
    • 0032918558 scopus 로고    scopus 로고
    • Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    • Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. 1999, Plant cis-acting regulatory DNA elements (PLACE) database: 1999, Nucleic Acids Res., 27, 297-300.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 297-300
    • Higo, K.1    Ugawa, Y.2    Iwamoto, M.3    Korenaga, T.4
  • 33
    • 84870217274 scopus 로고    scopus 로고
    • Brassinosteroid signaling network and regulation of photomorphogenesis
    • Wang, Z.Y., Bai, M.Y., Oh, E. and Zhu, J.Y. 2012, Brassinosteroid signaling network and regulation of photomorphogenesis, Ann. Rev. Genet., 46, 701-24.
    • (2012) Ann. Rev. Genet. , vol.46 , pp. 701-724
    • Wang, Z.Y.1    Bai, M.Y.2    Oh, E.3    Zhu, J.Y.4
  • 34
    • 75949096070 scopus 로고    scopus 로고
    • Using the Generic Genome Browser (GBrowse)
    • Donlin, M.J. 2009, Using the Generic Genome Browser (GBrowse), Curr. Protoc. Bioinform., 28, 9.9.1-25.
    • (2009) Curr. Protoc. Bioinform. , vol.28 , pp. 991-995
    • Donlin, M.J.1
  • 35
    • 84856514988 scopus 로고    scopus 로고
    • Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways
    • Brown, A.P., Kroon, J.T., Swarbreck, D., et al. 2012, Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways, PLoS One, 7, e30100.
    • (2012) PLoS One , vol.7
    • Brown, A.P.1    Kroon, J.T.2    Swarbreck, D.3
  • 36
    • 77958506746 scopus 로고    scopus 로고
    • Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: A timeline of loss, gain, expansion, and correlation with complexity
    • Lang, D., Weiche, B., Timmerhaus, G., et al. 2010, Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: A timeline of loss, gain, expansion, and correlation with complexity, Genome Biol. Evol., 2, 488-503.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 488-503
    • Lang, D.1    Weiche, B.2    Timmerhaus, G.3
  • 37
    • 33847290320 scopus 로고    scopus 로고
    • The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana
    • Walther, D., Brunnemann, R. and Selbig, J. 2007, The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana, PLoS Genet., 3, e11.
    • (2007) PLoS Genet. , vol.3
    • Walther, D.1    Brunnemann, R.2    Selbig, J.3
  • 38
    • 25144457599 scopus 로고    scopus 로고
    • Cis-regulatory element based targeted gene finding: Genome-wide identification of abscisic acid-and abiotic stress-responsive genes in Arabidopsis thaliana
    • Zhang, W., Ruan, J., Ho, T.H., You, Y., Yu, T. and Quatrano, R.S. 2005, Cis-regulatory element based targeted gene finding: Genome-wide identification of abscisic acid-and abiotic stress-responsive genes in Arabidopsis thaliana, Bioinformatics, 21, 3074-81.
    • (2005) Bioinformatics , vol.21 , pp. 3074-3081
    • Zhang, W.1    Ruan, J.2    Ho, T.H.3    You, Y.4    Yu, T.5    Quatrano, R.S.6
  • 39
    • 33845723596 scopus 로고    scopus 로고
    • Functional conservation of a root hair cell-specific cis-element in angiosperms with different root hair distribution patterns
    • Kim, D.W., Lee, S.H., Choi, S.B., et al. 2006, Functional conservation of a root hair cell-specific cis-element in angiosperms with different root hair distribution patterns, Plant Cell, 18, 2958-70.
    • (2006) Plant Cell , vol.18 , pp. 2958-2970
    • Kim, D.W.1    Lee, S.H.2    Choi, S.B.3
  • 40
    • 67650175435 scopus 로고    scopus 로고
    • Cis-element-and transcriptomebased screening of root hair-specific genes and their functional characterization in Arabidopsis
    • Won, S.K., Lee, Y.J., Lee, H.Y., Heo, Y.K., Cho, M. and Cho, H.T. 2009, Cis-element-and transcriptomebased screening of root hair-specific genes and their functional characterization in Arabidopsis, Plant Physiol., 150, 1459-73.
    • (2009) Plant Physiol. , vol.150 , pp. 1459-1473
    • Won, S.K.1    Lee, Y.J.2    Lee, H.Y.3    Heo, Y.K.4    Cho, M.5    Cho, H.T.6
  • 41
    • 80052576152 scopus 로고    scopus 로고
    • Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana
    • Zou, C., Sun, K., Mackaluso, J.D., et al. 2011, Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA, 108, 14992-7.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 14992-14997
    • Zou, C.1    Sun, K.2    Mackaluso, J.D.3
  • 42
    • 66649122827 scopus 로고    scopus 로고
    • Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    • Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L. and Van de Peer, Y. 2009, Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks, Plant Physiol., 150, 535-46.
    • (2009) Plant Physiol. , vol.150 , pp. 535-546
    • Vandepoele, K.1    Quimbaya, M.2    Casneuf, T.3    De Veylder, L.4    Van De Peer, Y.5
  • 43
    • 84867022595 scopus 로고    scopus 로고
    • Contribution of genomics to gene discovery in plant abiotic stress responses
    • Ma, Y., Qin, F. and Tran, L.S. 2012, Contribution of genomics to gene discovery in plant abiotic stress responses, Mol. Plant, 5, 1176-8.
    • (2012) Mol. Plant , vol.5 , pp. 1176-1178
    • Ma, Y.1    Qin, F.2    Tran, L.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.