| Description |
This tool enables identification of common transcription factor binding sites in a set of genes submitted
by the user. The genes (max. 100) 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). A restriction to highly conserved binding sites can be specified
as explained before (Search description). Genes potentially
regulated post-transcriptionally by small RNAs can be excluded from the analysis. The result of an analysis
is displayed as data table and can also be visualized graphically.
A data table shows all matching binding sites and lists the genes, binding
transcription factors, factor families, absolute and relative positions, and if applicable, additional
information on the scores of individual binding sites that can be compared to maximum and threshold score of
the matrix screening. This result list can by resorted by multiple criteria. An overview table can be selected
to display all factors giving the number of binding sites in the gene set as well as their relative orientation
up- and downstream from the translation start sites. Furthermore, a table can be displayed that lists the factors'
binding sites distributions among the set of genes. This table gives the number of genes harboring common
transcription factor binding sites, the total number of binding sites and a overrepresentation ratio (both rounded)
calculated from an expectation value for each factor. The tables always display the complete datasets irrespective
of the selection of factor families for the graphical display. Factor family names in the table display can be
selected to tag them for graphical display.
The graphical display can be selected showing all submitted gene regions being aligned relative to their gene
translation start sites. In the graphical display, only binding sites from factors belonging to the factor
families selected are displayed. A colour code for each factor family enables easy differentiation. Binding
sites matching the annotated DNA strand are displayed above the gene strand, appearance below indicates reverse
complement orientation of the binding site. Additional information on a specific binding site is given in a
mouse-over window, general information on the transcription factor can be displayed in a pop-up window by
selecting the respective binding 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 display can easily be
saved as PNG-image using the browser's "save image as..." functionality.
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