Publication:

• Current version;
  • This is the official reference for citing the current ATTED-II.
  • Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K. (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res., 37, D987-91. [PubMed] [PDF]
    
    
• Older version;
  • Please only cite this old reference when you refer to the old version of ATTED-II.
  • Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res., 35, D863-9. [PubMed] [PDF]
    
• Technical papers to construct ATTED-II;
  • For MR
    • Obayashi T, Kinoshita K. (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res., 16, 249-60. [PubMed] [PDF]
      
  • For stability of coexpression provided in CoexViewer
    • Kinoshita K, Obayashi T. (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics., 25. 2677-84. [PubMed] [PDF]
      
      
• Other related papers;
  • Coexpression database for mammals
    • Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K. (2008) COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res., 36. D77-82. [PubMed] [PDF]
      
  • Review of coexpression databases in plant
    • Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ. (2009) Coexpression Tools for Plant Biology: Opportunities for Hypothesis Generation and Caveats. Plant Cell and Environment, 32. 1633-51. [PubMed] [PDF]
      
      
• Acknowledgements;
  • Computation time is provided by the Super Computer System, Human Genome Center, Institute of Medical Science, The University of Tokyo.

Examples to use coexpression data in ATTED-II to estimate biological functions of target genes with disruptant analyses

• Identification of new members in a complex protein
• Identification of new members in a metabolic pathway
• Identification of new regulatory relationships

• Sugano SS et al. (2010) Stomagen positively regulates stomatal density in Arabidopsis. Nature, 463, 241-4 [PubMed]
• Sawada Y et al. (2009) Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. Plant Cell Physiology, 50, 1579-86 [PubMed]
• Okazaki Y et al. (2009) A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis. Plant Cell, 21, 892-909 [PubMed]
• Bednarek K et al. (2009) A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science, 323, 101-106 [PubMed]
• Ishihara S et al. (2008) NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis. Plant Cell Physiology, 49, 1066-1073. [PubMed]
• Yamada K et al. (2008) NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana. Plant Cell, 20, 2529-2540 [PubMed]
• Takabayashi A et al. (2008) Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches. Plant J, 57, 207-219. [PubMed]
• Yonekura-Sakakibara K et al. (2008) Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis. Plant Cell, 20, 2160-2176. [PubMed]
• Takahashi N et al. (2008) The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1. EMBO J, 27, 1840-1851. [PubMed]
• Ishihara S et al. (2007) Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis. Plant Physiology, 145, 668-679. [PubMed]
• Yonekura-Sakakibara K et al. (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem, 282, 14932-14941. [PubMed]
• Hirai MY et al. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA, 104, 6478-6483. [PubMed]