RegulonDB RegulonDB 10.7: Phrases Frame Help

Regulatory phrase form help


This table lists all regulated genes of the operon, their Multi-fun classes, the first genes of the regulated operons, all operons, simple regulons that keep the original definition of a regulon as the set of genes regulated by one and only one TF (Maas, 1964); and complex regulons is defined as a set of genes regulated by the same set of two or more TFs (Gutiérrez-Ríos et al., 2003). A simple regulatory phrase groups all transcription factor binding sites (TFBSs) for the same TF that work together regulating a promoter; complex phrases may include sites for different TFs working together.


Regulatory phrases
Regulatory phrase: A regulatory phrase is a group of transcription factor binding sites that work jointly in a regulatory mechanism. Phrases usually group multiple sites for the same TF, but they may also group sites for different TFs that are known to interact in their regulation of promoter activity.

Remote upstream site(s): TFBSs with a central position* of -93 or more relative to the regulated promoter are considered remote upstream. The information is displayed in following order: [TF, function, center position]; where TF is the regulatory protein that binds to the TFBS; function is the activation, repression or both (dual) effect of the TF on the regulated promoter; and center position is the distance from the TSS (+1) to the center of the TFBS. Negative numbers indicate that the site is upstream from the promoter; positive numbers mark downstream sites. When you hover the mouse over one of the values, a tooltip appears that shows the evidence classification as 'strong' or 'weak,' and their details. Moreover, the other phrases that regulate this promoter(s) contain a link to their corresponding regulatory phrase page.

Proximal site(s): Proximal TFBSs are those with a central position within the interval from -93 to +30 relative to the TSS (+1); from where the TF can in principle directly interact with RNA polymerase (REFS). The information is displayed in following order: [TF, function, center position]; where TF is the regulatory protein that binds to the TFBS; function is the activation, repression or both (dual) effect of the TF on the regulated promoter; and center position is the distance from the TSS (+1) to the center of the TFBS. Negative numbers indicate that the site is upstream from the promoter; positive numbers mark downstream sites. When you hover the mouse over one of the values, a tooltip appears that shows the evidence classification as 'strong' or 'weak,' and their details. Moreover, the other phrases that regulate this promoter(s) contain a link to their corresponding regulatory phrase page.

Remote downstream site(s): TFBSs downstream of position +30 relative to the regulated promoter are considered remote downstream. The information is displayed in following order: [TF, function, center position]; where TF is the regulatory protein that binds to the TFBS; function is the activation, repression or both (dual) effect of the TF on the regulated promoter; and center position is the distance from the TSS (+1) to the center of the TFBS. Negative numbers indicate that the site is upstream from the promoter; positive numbers mark downstream sites. When you hover the mouse over one of the values, a tooltip appears that shows the evidence classification as 'strong' or 'weak,' and their details. Moreover, the other phrases that regulate this promoter(s) contain a link to their corresponding regulatory phrase page.

Promoter name: Name of the regulated promoter

Regulatory phrases: A simple regulatory phrase groups TFBSs for the same TF that work together regulating a promoter usually contributing to the same effect on the promoter; complex phrases may include sites for different TFs working together.
The TFBSs are classified based on their position relative to the TSS (+1), as proximal, remote upstream or remote downstream. Proximal sites are those within the interval from -93 to +20; from where the TF can in principle directly interact with RNA polymerase. All other sites are considered remote, either upstream or downstream.

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