| Description |
On this page, a tool is provided that permits detection of colocalizing TFBS of pairs of TFs included
in AthaMap. The colocalization tool may be helpful to identify combinatorial elements. From the
drop-down list, two different or two identical transcription factors can be selected for a
colocalization analysis. For TFs with binding sites determined by
matrix-based screenings, an optional restriction score can be applied in order to restrict to highly
conserved bindings sites only. As the TFBS for TBP (TATA box) and CBF (CAAT box) are also positionally
defined, the score restrictions are not applicable to TFBS from TBP and CBF. Furthermore, a score
restriction cannot be applied to sites determined by pattern search or to combinatorial elements.
The transcription start sites (TSS) annotated to AthaMap can also be selected for colocalization
analysis. Values between 0bp and 100bp are allowed as maximum spacer lengths.
The result of the colocalization analysis is displayed on the same page and provides information on
the absolute chromosomal positions of colocalizing TFBS and the orientation of the sites. Additionally,
the nearest genes and the positions relative to the translation start are provided. Via an implemented
link, this list of genes can directly be submitted to the PathoPlant expression analysis form to
identify conditions that co-regulate this set of genes. In the colocalization result list, the absolute
positions are directly linked to the AthaMap sequence display of the corresponding region in the
Arabidopsis genome with the respective colocalizing binding sites being highlighted. The
"show overview" function displayed on the result page gives a summary on the total number of
colocalizations obtained for each spacer length up to the maximum spacer selected. 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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