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Gene Analysis
This tool enables identification of common transcription factor (TF) binding sites and small RNA target sites in a set of genes submitted by the user. The genes (max. 200) to be queried must be submitted with their Arabidopsis gene identifiers (AGI format: AtxGnnnnn) separated by carriage returns. The default region to be queried is -500bp to +50bp relative to the transcription start site (TSS) if known, otherwise relative to the translation start site (ATG). The maximum search window is 5,000bp ranging from -2000bp to +3000bp. Individual factor families, small RNAs and micro RNAs (MIR) can be selected for analysis. A restriction to highly conserved TF binding sites can be specified for matrix-based binding sites as explained before (Search description). The maximum psRNATarget score of 5.0 is used to display putative miRNA target sites. The psRNATarget score of the miRNA target sites and the score of the matrix based TF binding sites are displayed in the result table. The result can also be visualized graphically.
The data table shows all matching binding and target sites and lists the genes, predicted binding transcription factors or small RNAs, factor and miRNA families, absolute and relative positions, and if applicable, additional information on the scores of individual binding and miRNA target sites. This result list can by resorted by multiple criteria. An overview table can be selected to display all factors and small RNAs giving the number of binding and target sites in the gene set as well as their relative orientation. Furthermore, a table can be displayed that lists the distributions of binding and target sites among the set of genes. This table gives the number of genes harboring common transcription factor binding sites and small RNA target sites, the total number of binding and target sites and a overrepresentation ratio (both rounded) calculated from an expectation value for each factor and small RNA.
The graphical display can be selected showing all submitted gene regions being aligned relative to their gene translation start sites. A colour code enables easy differentiation of factor families and small RNAs. Binding and target sites matching the annotated DNA strand are displayed above the gene strand, appearance below indicates reverse complement orientation of the binding and target site. Additional information on a specific binding or target site is given in a mouse-over window, general information on the transcription factor or small RNA can be displayed in a pop-up window by selecting the respective binding or target site. A detailed view on the respective gene region can be achieved by selecting the gene strand which results in a new sequence display window. The graphical displays can easily be saved as PNG-images using the browser's "save image as..." functionality. On the result page, genes potentially regulated by small RNA and miRNA are identified in italics and bold, respectively. By selecting "exclude genes putatively regulated by smallRNA" or "exclude genes putatively regulated by miRNA" these genes are excluded from the analysis.

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