ATTED-II   version 5.5

ATTED-II; Arabidopsis thaliana trans-factor and cis-element prediction database



(last update) 2010.01.19

Home:

  • Recent update

    [2009.10.22] Contents on ATTED-II are licensed under CC-BY. [license]
    [2009.10.08] An incorrect link to the download page of Rice coexpression data was fixed. (Download)
    [2009.09.20] A paper to show the effectiveness of MR was made available. (PDF)
    [more]

  • Aim of ATTED-II

    ATTED-II provides co-regulated gene relationships in Arabidopsis thaliana to estimate gene functions.

  • Basic contents of ATTED-II

    • Coexpressed genes
      • Data source; publicly available microarray data (58 experiments, 1388 slides) collected by AtGenExpress.
      • Coexpression measure; Mutual rank (MR) based on weighted Pearson's correlation coefficients. [more]
      • Examples;
        As gene lists As gene networks
      • Search; [Gene search for coexpressed genes]

    • Predicted cis elements
      • Method; CEG
        Absolute CEG value corresponds significance of cis element. Higher CEG value means more significant. [more]
      • Region; 200-bp upstream region from transcription start site (TSS).
        For cis element prediction, we use position preferences in promoter to reduce false positives. Position preference of all reported cis elements if it has some position preference in promoter are in the region up to 200-bp upstream from TSS.
      • Example;


        cis elements in 200-bp upstream region of a gene position preference of a cis elements sample specificity of a cis elements
      • Browsing; [list of 304 heptamer cis elements]

    • Visualized gene expression
      • These are few databases that show the gene expressions as graphs, although gene expression data are fundamental information for molecular biology. ATTED-II simply presents graphs of the gene expression pattern for each gene.
      • Example;

  • License

    • Contents on ATTED-II are licensed under a Creative Commons Attribution 2.1 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
      Downloadable data, results of tools, figures and web snapshots can be used for publication, presentation and any other purposes. In such cases, to avoid misunderstanding, we ask you to add version number of ATTED-II or each coexpression data.