메뉴 건너뛰기




Volumn 55, Issue 1, 2014, Pages

RARGE II: An integrated phenotype database of arabidopsis mutant traits using a controlled vocabulary

Author keywords

Arabidopsis; Database; Gene function; Mutant line; Ontology; Phenotype

Indexed keywords

ARABIDOPSIS; ARTICLE; COMPUTER INTERFACE; CONTROLLED VOCABULARY; DATA BASE; GENE FUNCTION; GENE ONTOLOGY; GENETIC DATABASE; GENETICS; HISTOLOGY; INTERNET; MOLECULAR GENETICS; MUTANT LINE; MUTATION; ONTOLOGY; PHENOTYPE; PLANT GENE; QUANTITATIVE TRAIT;

EID: 84892770133     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pct165     Document Type: Article
Times cited : (25)

References (40)
  • 1
    • 84857226999 scopus 로고    scopus 로고
    • KNApSAcK family databases: Integrated metabolite-plant species databases for multifaceted plant research
    • Afendi, F.M., Okada, T., Yamazaki, M., Hirai-Morita, A., Nakamura, Y., Nakamura, K. et al. (2012) KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol. 53: e1.
    • (2012) Plant Cell Physiol. , vol.53
    • Afendi, F.M.1    Okada, T.2    Yamazaki, M.3    Hirai-Morita, A.4    Nakamura, Y.5    Nakamura, K.6
  • 2
    • 53249144283 scopus 로고    scopus 로고
    • PRIMe: A web site that assembles tools for metabolomics and transcriptomics
    • Akiyama, K., Chikayama, E., Yuasa, H., Shimada, Y., Tohge, T., Shinozaki, K. et al. (2008) PRIMe: a web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 8: 339-345.
    • (2008) Silico Biol. , vol.8 , pp. 339-345
    • Akiyama, K.1    Chikayama, E.2    Yuasa, H.3    Shimada, Y.4    Tohge, T.5    Shinozaki, K.6
  • 4
    • 0035112091 scopus 로고    scopus 로고
    • Arabidopsis gene knockout: Phenotypes wanted
    • Bouché, N. and Bouchez, D. (2001) Arabidopsis gene knockout: phenotypes wanted. Curr. Opin. Plant Biol. 4: 111-117.
    • (2001) Curr. Opin. Plant Biol. , vol.4 , pp. 111-117
    • Bouché, N.1    Bouchez, D.2
  • 6
    • 0027549278 scopus 로고
    • A versatile system for detecting transposition in Arabidopsis
    • Fedoroff, N.V. and Smith, D.L. (1993) A versatile system for detecting transposition in Arabidopsis. Plant J. 3: 273-289.
    • (1993) Plant J. , vol.3 , pp. 273-289
    • Fedoroff, N.V.1    Smith, D.L.2
  • 8
    • 33845523291 scopus 로고    scopus 로고
    • The FOX hunting system: An alternative gain-of-function gene hunting technique
    • Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y. et al. (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J. 48: 974-985.
    • (2006) Plant J. , vol.48 , pp. 974-985
    • Ichikawa, T.1    Nakazawa, M.2    Kawashima, M.3    Iizumi, H.4    Kuroda, H.5    Kondou, Y.6
  • 9
    • 10744222323 scopus 로고    scopus 로고
    • Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed pheno-types in T1 generation
    • Ichikawa, T., Nakazawa, M., Kawashima, M., Muto, S., Gohda, K., Suzuki, K. et al. (2003) Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed pheno-types in T1 generation. Plant J. 36: 421-429.
    • (2003) Plant J. , vol.36 , pp. 421-429
    • Ichikawa, T.1    Nakazawa, M.2    Kawashima, M.3    Muto, S.4    Gohda, K.5    Suzuki, K.6
  • 10
    • 44349195100 scopus 로고    scopus 로고
    • COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine
    • Katsir, L., Schilmiller, A.L., Staswick, P.E., He, S.Y. and Howe, G.A. (2008) COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine. Proc. Natl Acad. Sci. USA 105: 7100-7105.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7100-7105
    • Katsir, L.1    Schilmiller, A.L.2    Staswick, P.E.3    He, S.Y.4    Howe, G.A.5
  • 11
    • 0037624063 scopus 로고    scopus 로고
    • Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice
    • Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N. et al. (2003) Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice. Science 301: 376-379.
    • (2003) Science , vol.301 , pp. 376-379
    • Kikuchi, S.1    Satoh, K.2    Nagata, T.3    Kawagashira, N.4    Doi, K.5    Kishimoto, N.6
  • 12
    • 77952508420 scopus 로고    scopus 로고
    • High-throughput characterization of plant gene functions by using gain-of-function technology
    • Kondou, Y., Higuchi, M. and Matsui, M. (2010) High-throughput characterization of plant gene functions by using gain-of-function technology. Annu. Rev. Plant Biol. 61: 373-393.
    • (2010) Annu. Rev. Plant Biol. , vol.61 , pp. 373-393
    • Kondou, Y.1    Higuchi, M.2    Matsui, M.3
  • 13
    • 61349141170 scopus 로고    scopus 로고
    • Systematic approaches to using the FOX hunting system to identify useful rice genes
    • Kondou, Y., Higuchi, M., Takahashi, S., Sakurai, T., Ichikawa, T., Kuroda, H. et al. (2009) Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J. 57: 883-894.
    • (2009) Plant J. , vol.57 , pp. 883-894
    • Kondou, Y.1    Higuchi, M.2    Takahashi, S.3    Sakurai, T.4    Ichikawa, T.5    Kuroda, H.6
  • 15
    • 12144289987 scopus 로고    scopus 로고
    • A collection of 11 800 single-copy Ds trans-poson insertion lines in Arabidopsis
    • Kuromori, T., Hirayama, T., Kiyosue, Y., Takabe, H., Mizukado, S., Sakurai, T. et al. (2004) A collection of 11 800 single-copy Ds trans-poson insertion lines in Arabidopsis. Plant J. 37: 897-905.
    • (2004) Plant J. , vol.37 , pp. 897-905
    • Kuromori, T.1    Hirayama, T.2    Kiyosue, Y.3    Takabe, H.4    Mizukado, S.5    Sakurai, T.6
  • 16
    • 67651097787 scopus 로고    scopus 로고
    • Phenome analysis in plant species using loss-of-function and gain-of-function mutants
    • Kuromori, T., Takahashi, S., Kondou, Y., Shinozaki, K. and Matsui, M. (2009) Phenome analysis in plant species using loss-of-function and gain-of-function mutants. Plant Cell Physiol. 50: 1215-1231.
    • (2009) Plant Cell Physiol. , vol.50 , pp. 1215-1231
    • Kuromori, T.1    Takahashi, S.2    Kondou, Y.3    Shinozaki, K.4    Matsui, M.5
  • 17
    • 33746567801 scopus 로고    scopus 로고
    • A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis
    • Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., Imura, Y. et al. (2006) A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J. 47: 640-651.
    • (2006) Plant J. , vol.47 , pp. 640-651
    • Kuromori, T.1    Wada, T.2    Kamiya, A.3    Yuguchi, M.4    Yokouchi, T.5    Imura, Y.6
  • 19
    • 84876480423 scopus 로고    scopus 로고
    • Building an efficient curation workflow for the Arabidopsis literature corpus
    • Li, D., Berardini, T.Z., Muller, R.J. and Huala, E. (2012) Building an efficient curation workflow for the Arabidopsis literature corpus. Database 2012: bas047.
    • (2012) Database , vol.2012
    • Li, D.1    Berardini, T.Z.2    Muller, R.J.3    Huala, E.4
  • 20
    • 84892741439 scopus 로고    scopus 로고
    • The Plant Organelles Database 3 (PODB3) update 2014: Integrating electron micrographs and new options for plant organelle research
    • press
    • Mano, S., Nakamura, T., Kondo, M., Miwa, T., Nishikawa, S.I., Mimura, T. et al. (2014) The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research. Plant Cell Physiol. 55 (in press).
    • (2014) Plant Cell Physiol. , pp. 55
    • Mano, S.1    Nakamura, T.2    Kondo, M.3    Miwa, T.4    Nishikawa, S.I.5    Mimura, T.6
  • 21
    • 0032478095 scopus 로고    scopus 로고
    • Functional genomics: Probing plant gene function and expression with transposons
    • Martienssen, R.A. (1998) Functional genomics: probing plant gene function and expression with transposons. Proc. Natl Acad. Sci. USA 95: 2021-2026.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2021-2026
    • Martienssen, R.A.1
  • 23
    • 75749136937 scopus 로고    scopus 로고
    • The Chloroplast Function Database: A large-scale collection of Arabidopsis Ds/Spm-or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis
    • Myouga, F., Akiyama, K., Motohashi, R., Kuromori, T., Ito, T., Iizumi, H. et al. (2010) The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm-or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis. Plant J. 61: 529-542.
    • (2010) Plant J. , vol.61 , pp. 529-542
    • Myouga, F.1    Akiyama, K.2    Motohashi, R.3    Kuromori, T.4    Ito, T.5    Iizumi, H.6
  • 24
    • 84874240821 scopus 로고    scopus 로고
    • The Chloroplast Function Database II: A comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins
    • Myouga, F., Akiyama, K., Tomonaga, Y., Kato, A., Sato, Y., Kobayashi, M. et al. (2013) The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins. Plant Cell Physiol. 54: e2.
    • (2013) Plant Cell Physiol. , vol.54
    • Myouga, F.1    Akiyama, K.2    Tomonaga, Y.3    Kato, A.4    Sato, Y.5    Kobayashi, M.6
  • 27
    • 0034030591 scopus 로고    scopus 로고
    • Functional genomics in Arabidopsis: Large-scale insertional mutagenesis complements the genome sequencing project
    • Parinov, S. and Sundaresan, V. (2000) Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project. Curr. Opin. Biotechnol. 11: 157-161.
    • (2000) Curr. Opin. Biotechnol. , vol.11 , pp. 157-161
    • Parinov, S.1    Sundaresan, V.2
  • 28
    • 33645739638 scopus 로고    scopus 로고
    • PTAC2,-6, and-12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression
    • Pfalz, J., Liere, K., Kandlbinder, A., Dietz, K.-J. and Oelmüller, R. (2006) pTAC2,-6, and-12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell 18: 176-197.
    • (2006) Plant Cell , vol.18 , pp. 176-197
    • Pfalz, J.1    Liere, K.2    Kandlbinder, A.3    Dietz, K.-J.4    Oelmüller, R.5
  • 29
    • 79951562921 scopus 로고    scopus 로고
    • RiceFOX: A database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function
    • Sakurai, T., Kondou, Y., Akiyama, K., Kurotani, A., Higuchi, M., Ichikawa, T. et al. (2011) RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol. 52: 265-273.
    • (2011) Plant Cell Physiol. , vol.52 , pp. 265-273
    • Sakurai, T.1    Kondou, Y.2    Akiyama, K.3    Kurotani, A.4    Higuchi, M.5    Ichikawa, T.6
  • 30
    • 13444312017 scopus 로고    scopus 로고
    • RARGE: A large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
    • Sakurai, T., Satou, M., Akiyama, K., Iida, K., Seki, M., Kuromori, T. et al. (2005) RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res. 33: D647-D650.
    • (2005) Nucleic Acids Res. , vol.33
    • Sakurai, T.1    Satou, M.2    Akiyama, K.3    Iida, K.4    Seki, M.5    Kuromori, T.6
  • 31
    • 84874251578 scopus 로고    scopus 로고
    • PRIMe update: Innovative content for plant metabolomics and integration of gene expression and metabolite accumulation
    • Sakurai, T., Yamada, Y., Sawada, Y., Matsuda, F., Akiyama, K., Shinozaki, K. et al. (2013) PRIMe update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant Cell Physiol. 54: e5.
    • (2013) Plant Cell Physiol. , vol.54
    • Sakurai, T.1    Yamada, Y.2    Sawada, Y.3    Matsuda, F.4    Akiyama, K.5    Shinozaki, K.6
  • 32
    • 20244377471 scopus 로고    scopus 로고
    • Functional annotation of a full-length Arabidopsis cDNA collection
    • Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145.
    • (2002) Science , vol.296 , pp. 141-145
    • Seki, M.1    Narusaka, M.2    Kamiya, A.3    Ishida, J.4    Satou, M.5    Sakurai, T.6
  • 33
    • 0029055907 scopus 로고
    • Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis
    • Springer, P.S., McCombie, W.R., Sundaresan, V. and Martienssen, R.A. (1995) Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science 268: 877-880.
    • (1995) Science , vol.268 , pp. 877-880
    • Springer, P.S.1    McCombie, W.R.2    Sundaresan, V.3    Martienssen, R.A.4
  • 34
    • 0029085425 scopus 로고
    • Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements
    • Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J.D., Dean, C. et al. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9: 1797-1810.
    • (1995) Genes Dev. , vol.9 , pp. 1797-1810
    • Sundaresan, V.1    Springer, P.2    Volpe, T.3    Haward, S.4    Jones, J.D.5    Dean, C.6
  • 35
    • 33846501703 scopus 로고    scopus 로고
    • Arabidopsis systemic immunity uses conserved defense signaling pathways and is mediated by jasmonates
    • Truman, W., Bennett, M.H., Kubigsteltig, I., Turnbull, C. and Grant, M. (2007) Arabidopsis systemic immunity uses conserved defense signaling pathways and is mediated by jasmonates. Proc. Natl Acad. Sci. USA 104: 1075-1080.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 1075-1080
    • Truman, W.1    Bennett, M.H.2    Kubigsteltig, I.3    Turnbull, C.4    Grant, M.5
  • 38
    • 0032524404 scopus 로고    scopus 로고
    • COI1: An Arabidopsis gene required for jasmonate-regulated defense and fertility
    • Xie, D.X., Feys, B.F., James, S., Nieto-Rostro, M. and Turner, J.G. (1998) COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 280: 1091-1094.
    • (1998) Science , vol.280 , pp. 1091-1094
    • Xie, D.X.1    Feys, B.F.2    James, S.3    Nieto-Rostro, M.4    Turner, J.G.5
  • 39
    • 70349667440 scopus 로고    scopus 로고
    • The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor
    • Yan, J., Zhang, C., Gu, M., Bai, Z., Zhang, W., Qi, T. et al. (2009) The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor. Plant Cell 21: 2220-2236.
    • (2009) Plant Cell , vol.21 , pp. 2220-2236
    • Yan, J.1    Zhang, C.2    Gu, M.3    Bai, Z.4    Zhang, W.5    Qi, T.6
  • 40
    • 84860796697 scopus 로고    scopus 로고
    • Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade
    • Yang, D.-L., Yao, J., Mei, C.-S., Tong, X.-H., Zeng, L.-J., Li, Q. et al. (2012) Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc. Natl Acad. Sci. USA 109: E1192-E1200.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109
    • Yang, D.-L.1    Yao, J.2    Mei, C.-S.3    Tong, X.-H.4    Zeng, L.-J.5    Li, Q.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.