Prediction of DNA 8mers, 9mers and 10mers as cis-elements responsive to a
given stimulus is performed with the tool cis-elements. One stimulus can be selected
to retrieve putatively functional cis-elements with different types of specificity.
Each stimulus was assigned into a category depending on its type, i.e. abiotic,
biotic (excluding fungi), fungi and other (hormone, developmental, etc) stimuli.
Such categories can be seen within the brackets on the right side of each stimulus
in the selection list. Two kinds of settings (default and advanced) can be selected
for cis-element searching. A search using default settings will retrieve cis-elements
with a length of 8 to 10 nucleotides and putatively responsive exclusively to stimuli
belonging to the selected stimulus and its group.
A search using the advanced settings permits a more detailed parameter selection.
By clicking "advanced settings" the available options are displayed. It is possible
to select further sequence specificity by checking the different available stimulus
group. Each selected group will result in cis-elements being responsive to stimuli
belonging to that group. It is also possible to search cis-elements that are
exclusively responsive to the stimulus selected by clicking the advanced option
"only for selected stimulus". If a search is carried out where no further sequence
specificity is selected all cis-elements responsive to the selected stimulus
are retrieved. Finally the cis-elements length (in nucleotides) can also be
selected as a search parameter.
Predicted cis-elements are shown in a result table containing several columns.
The first column displays the sequence and its reverse complement.
Each sequence can be clicked in order to perform an in silico expression analysis.
The second column shows the number of genes containing the sequence within their
promoters and the third column represents the mean induction factor of those genes.
A p-value which indicates the significance of the mean induction factor is displayed
in the fourth column. Further columns show the number of stimuli from the different
groups (abiotic, biotic, fungi and other) to which the cis-element is predicted to
be responsive to.