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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.

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