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Volumn 35, Issue SUPPL. 1, 2007, Pages

ATTED-II: A database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

EID: 33846061087     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl783     Document Type: Article
Times cited : (332)

References (44)
  • 3
    • 0347122079 scopus 로고    scopus 로고
    • CIBEX: Center for information biology gene expression database
    • Ikeo,K., Ishi-i,J., Tamura,T., Gojobori,T. and Tateno,Y. (2003) CIBEX: center for information biology gene expression database. C. R. Biol., 326, 1079-1082.
    • (2003) C. R. Biol. , vol.326 , pp. 1079-1082
    • Ikeo, K.1    Ishi-i, J.2    Tamura, T.3    Gojobori, T.4    Tateno, Y.5
  • 4
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • Rhee,S.Y., Beavis,W., Berardini,T.Z., Chen,G., Dixon,D., Doyle,A., Garcia-Hernandez,M., Huala,E., Lander,G., Montoya,M. et al. (2003) The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res., 31, 224-228.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 224-228
    • Rhee, S.Y.1    Beavis, W.2    Berardini, T.Z.3    Chen, G.4    Dixon, D.5    Doyle, A.6    Garcia-Hernandez, M.7    Huala, E.8    Lander, G.9    Montoya, M.10
  • 5
    • 0347968038 scopus 로고    scopus 로고
    • NASCArrays: A repository for microarray data generated by NASC's transcriptomics service
    • Craigon,D.J., James,N., Okyere,J., Higgins,J., Jotham,J. and May,S. (2004) NASCArrays: A repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res., 32, D575-D577.
    • (2004) Nucleic Acids Res. , vol.32
    • Craigon, D.J.1    James, N.2    Okyere, J.3    Higgins, J.4    Jotham, J.5    May, S.6
  • 7
    • 22044437388 scopus 로고    scopus 로고
    • The Botany Array Resource: E-Northerns, Expression Angling, and promoter analyses
    • Toufighi,K., Brady,S.M., Austin,R., Ly,E. and Provart,N.J. (2005) The Botany Array Resource: E-Northerns, Expression Angling, and promoter analyses. Plant J., 43, 153-163.
    • (2005) Plant J. , vol.43 , pp. 153-163
    • Toufighi, K.1    Brady, S.M.2    Austin, R.3    Ly, E.4    Provart, N.J.5
  • 9
    • 27244438560 scopus 로고    scopus 로고
    • Gene-expression analysis and network discovery using Genevestigator
    • Zimmermann,P., Hennig,L. and Gruissem,W. (2005) Gene-expression analysis and network discovery using Genevestigator. Trends Plant Sci., 10, 407-409.
    • (2005) Trends Plant Sci. , vol.10 , pp. 407-409
    • Zimmermann, P.1    Hennig, L.2    Gruissem, W.3
  • 10
    • 18744415447 scopus 로고    scopus 로고
    • Identification of brassinosteroid-related genes by means of transcript co-response analyses
    • Lisso,J., Steinhauser,D., Altmann,T., Kopka,J. and Mussig,C. (2005) Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Res., 33, 2685-2696.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2685-2696
    • Lisso, J.1    Steinhauser, D.2    Altmann, T.3    Kopka, J.4    Mussig, C.5
  • 11
    • 20844445318 scopus 로고    scopus 로고
    • Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
    • Persson,S., Wei,H., Milne,J., Page,G.P. and Somerville,C.R. (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl Acad. Sci. USA, 102, 8633-8638.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 8633-8638
    • Persson, S.1    Wei, H.2    Milne, J.3    Page, G.P.4    Somerville, C.R.5
  • 13
    • 23644461190 scopus 로고    scopus 로고
    • Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: Functional and evolutionary implications
    • Gachon,C.M., Langlois-Meurinne,M., Henry,Y. and Saindrenan,P. (2005) Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: Functional and evolutionary implications. Plant Mol. Biol., 58, 229-245.
    • (2005) Plant Mol. Biol. , vol.58 , pp. 229-245
    • Gachon, C.M.1    Langlois-Meurinne, M.2    Henry, Y.3    Saindrenan, P.4
  • 14
    • 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
  • 15
    • 0036085047 scopus 로고    scopus 로고
    • PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    • Lescot,M., Dehais,P., Thijs,G., Marchal,K., Moreau,Y., Van de Peer,Y., Rouze,P., and Rombauts,S. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30, 325-327.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 325-327
    • Lescot, M.1    Dehais, P.2    Thijs, G.3    Marchal, K.4    Moreau, Y.5    Van de Peer, Y.6    Rouze, P.7    Rombauts, S.8
  • 16
    • 0142045636 scopus 로고    scopus 로고
    • DNA microarray data and contextual analysis of correlation graphs
    • Rougemont,J. and Hingamp,P. (2003) DNA microarray data and contextual analysis of correlation graphs. BMC Bioinformatics, 4, 15.
    • (2003) BMC Bioinformatics , vol.4 , pp. 15
    • Rougemont, J.1    Hingamp, P.2
  • 18
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson,O., Nielsen,H., Brunak,S. and von Heijne,G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300, 1005-1016.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    von Heijne, G.4
  • 20
    • 33646907417 scopus 로고    scopus 로고
    • AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks
    • Palaniswamy,S.K., James,S., Sun,H., Lamb,R.S., Davuluri,R.V. and Grotewold,E. (2006) AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol., 140, 818-829.
    • (2006) Plant Physiol. , vol.140 , pp. 818-829
    • Palaniswamy, S.K.1    James, S.2    Sun, H.3    Lamb, R.S.4    Davuluri, R.V.5    Grotewold, E.6
  • 25
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 26
    • 3142656622 scopus 로고    scopus 로고
    • JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis
    • Lorenzo,O., Chico,J.M., Sanchez-Serrano,J.J. and Solano,R. (2004) JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell, 16, 1938-1950.
    • (2004) Plant Cell , vol.16 , pp. 1938-1950
    • Lorenzo, O.1    Chico, J.M.2    Sanchez-Serrano, J.J.3    Solano, R.4
  • 27
    • 0345099604 scopus 로고    scopus 로고
    • An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense
    • Chen,F., D'Auria,J.C., Tholl,D., Ross,J.R., Gershenzon,J., Noel,J.P. and Pichersky,E. (2003) An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant J., 36, 577-588.
    • (2003) Plant J. , vol.36 , pp. 577-588
    • Chen, F.1    D'Auria, J.C.2    Tholl, D.3    Ross, J.R.4    Gershenzon, J.5    Noel, J.P.6    Pichersky, E.7
  • 29
    • 0037709898 scopus 로고    scopus 로고
    • Functional identification of AtTPS03 as (E)-β-ocimene synthase: A monoterpene synthase catalyzing jasmonate- and wound-induced volatile formation in Arabidopsis thaliana
    • Faldt,J., Arimura,G., Gershenzon,J., Takabayashi,J. and Bohlmann,J. (2003) Functional identification of AtTPS03 as (E)-β-ocimene synthase: a monoterpene synthase catalyzing jasmonate- and wound-induced volatile formation in Arabidopsis thaliana. Planta, 216, 745-751.
    • (2003) Planta , vol.216 , pp. 745-751
    • Faldt, J.1    Arimura, G.2    Gershenzon, J.3    Takabayashi, J.4    Bohlmann, J.5
  • 30
    • 0038532263 scopus 로고    scopus 로고
    • A new member of plant CS-lyases. A cystine lyase from Arabidopsis thaliana
    • Jones,P.R., Manabe,T., Awazuhara,M. and Saito,K. (2003) A new member of plant CS-lyases. A cystine lyase from Arabidopsis thaliana. J. Biol. Chem., 278, 10291-10296.
    • (2003) J. Biol. Chem. , vol.278 , pp. 10291-10296
    • Jones, P.R.1    Manabe, T.2    Awazuhara, M.3    Saito, K.4
  • 31
    • 0029047317 scopus 로고
    • A chloroplast lipoxygenase is required for wound-induced jasmonic acid accumulation in Arabidopsis
    • Bell,E., Creelman,R.A. and Mullet,J.E. (1995) A chloroplast lipoxygenase is required for wound-induced jasmonic acid accumulation in Arabidopsis. Proc. Natl Acad. Sci. USA, 92, 8675-8679.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8675-8679
    • Bell, E.1    Creelman, R.A.2    Mullet, J.E.3
  • 32
    • 0034119379 scopus 로고    scopus 로고
    • Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis
    • Reymond,P., Weber,H., Damond,M. and Farmer,E.E. (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell, 12, 707-720.
    • (2000) Plant Cell , vol.12 , pp. 707-720
    • Reymond, P.1    Weber, H.2    Damond, M.3    Farmer, E.E.4
  • 33
    • 0035980068 scopus 로고    scopus 로고
    • Monitoring of methyl jasmonate-responsive genes in Arabidopsis by cDNA macroarray: Self-activation of jasmonic acid biosynthesis and crosstalk with other phytohormone signaling pathways
    • Sasaki,Y., Asamizu,E., Shibata,D., Nakamura,Y., Kaneko,T., Awai,K., Amagai,M., Kuwata,C., Tsugane,T., Masuda,T. et al. (2001) Monitoring of methyl jasmonate-responsive genes in Arabidopsis by cDNA macroarray: self-activation of jasmonic acid biosynthesis and crosstalk with other phytohormone signaling pathways. DNA Res., 8, 153-161.
    • (2001) DNA Res. , vol.8 , pp. 153-161
    • Sasaki, Y.1    Asamizu, E.2    Shibata, D.3    Nakamura, Y.4    Kaneko, T.5    Awai, K.6    Amagai, M.7    Kuwata, C.8    Tsugane, T.9    Masuda, T.10
  • 34
    • 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, 3074-3081.
    • (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
  • 35
    • 0034695679 scopus 로고    scopus 로고
    • ABFs, a family of ABA-responsive element binding factors
    • Choi,H., Hong,J., Ha,J., Kang,J. and Kim,S.Y. (2000) ABFs, a family of ABA-responsive element binding factors. J. Biol. Chem., 275, 1723-1730.
    • (2000) J. Biol. Chem. , vol.275 , pp. 1723-1730
    • Choi, H.1    Hong, J.2    Ha, J.3    Kang, J.4    Kim, S.Y.5
  • 37
    • 4544236638 scopus 로고    scopus 로고
    • Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter
    • Tran,L.S., Nakashima,K, Sakuma,Y., Simpson,S.D., Fujita,Y., Maruyama,K., Fujita,M., Seki,M., Shinozaki,K. and Yamaguchi-Shinozaki,K. (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell, 16, 2481-2498.
    • (2004) Plant Cell , vol.16 , pp. 2481-2498
    • Tran, L.S.1    Nakashima, K.2    Sakuma, Y.3    Simpson, S.D.4    Fujita, Y.5    Maruyama, K.6    Fujita, M.7    Seki, M.8    Shinozaki, K.9    Yamaguchi-Shinozaki, K.10
  • 38
    • 0030139810 scopus 로고    scopus 로고
    • Transcription factor veracity: Is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh?
    • Lu,G., Paul,A.L., McCarty,D.R. and Ferl,R.J. (1996) Transcription factor veracity: Is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh? Plant Cell, 8, 847-857.
    • (1996) Plant Cell , vol.8 , pp. 847-857
    • Lu, G.1    Paul, A.L.2    McCarty, D.R.3    Ferl, R.J.4
  • 41
    • 0345863918 scopus 로고    scopus 로고
    • AthaMap: An online resource for in silico, transcription factor binding sites in the Arabidopsis thaliana genome
    • Steffens,N.O., Galuschka,C., Schindler,M., Bulow,L. and Hehl,R. (2004) AthaMap: An online resource for in silico, transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res., 32, D368-D372.
    • (2004) Nucleic Acids Res. , vol.32
    • Steffens, N.O.1    Galuschka, C.2    Schindler, M.3    Bulow, L.4    Hehl, R.5
  • 42
    • 8444251706 scopus 로고    scopus 로고
    • Motif detection in Arabidopsis: Correlation with gene expression data
    • Janaki,C. and Joshi,R.R. (2004) Motif detection in Arabidopsis: correlation with gene expression data. In Silico Biol., 4, 149-161.
    • (2004) In Silico Biol. , vol.4 , pp. 149-161
    • Janaki, C.1    Joshi, R.R.2
  • 43
    • 25444522648 scopus 로고    scopus 로고
    • Genome wide analysis of Arabidopsis core promoters
    • Molina,C. and Grotewold,E. (2005) Genome wide analysis of Arabidopsis core promoters. BMC Genomics, 6, 25.
    • (2005) BMC Genomics , vol.6 , pp. 25
    • Molina, C.1    Grotewold, E.2
  • 44
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker,H.J., Li,H. and Siggia,E.D. (2001) Regulatory element detection using correlation with expression. Nature Genet., 27, 167-171.
    • (2001) Nature Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3


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