Functional Region Report


Functional Region Reports contain information about regulatory regions of a gene, for which some functionality has been shown under certain conditions. The functional region can be part of a larger functional region (a whole promoter or enhancer, for example). The functional region can also contain smaller functional regions with transcription factor binding sites and composite elements that are required for their functionality. Thus, a hierarchy of regulatory regions can be built, from transcription factor binding sites to the whole promoter (or other regulatory region) of a gene. In many cases, however, the functional region has not been dissected completely.

Please note: Functional Region Reports are only available for BKL subscribers who have licensed the TRANSFAC module.

Each Functional Region Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. When additional details are provided, the property blocks contain links to detailed Property Reports. Other BKL Reports mentioned in the Functional Region Report are hyperlinked to the corresponding Reports. For example, genes that contain the functional region described in the Report are listed, with links to their corresponding Locus Reports.

Functiional Region Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a Functional Region Report

The general structure of a Functional Region Report is described below.

  • Access help by clicking the help menu  help  and clicking the Site report help link.

  • Navigate to the desired section of the report by opening the table of contents  toc

Points of navigation within the report are indicated by the following visual cues.

  • Links to additional reports within the BKL are presented as regular text links.

  • Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:  external link  .

  • Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:  expand content  .

Functional Region Information Describes the characteristics of a functional region. help
Identifies the name of the functional region.
Describes the function of the functional region.
Regulated Gene
Provides the name and species of the Gene the functional region is associated with, with a link to the corresponding Locus Report.
General location or type of the region
Describes the type of functional region (promoter or enhancer, for example).
Provides the location of the functional region (From:... To:...), using a reference point if not the transcription start site (TSS).
Displays free text comments that provide additional details about the functional region (structural composition, for example).

Region hierarchy Displays details about the functional region's position in a functional region hierarchy.
Part of region
Indicates the names and positions of parent functional regions, with links to the corresponding Functional Region Reports.
Contains region
Indicates the names and positions of child functional regions, with links to the corresponding Functional Region Reports.

Regulatory elements Displays details about regulatory elements found in the functional region.  
Transcription factor binding sites
Identifies transcription factor binding sites that are part of the functional region, as well as the locations of the binding sites. Also lists transcription factors that bind the sites. Hyperlinks to the corresponding Site Reports for the binding sites and to the corresponding Locus Reports for the transcription factors.
Composite elements
Identifies composite elements (compels) that are part of the functional regions. Hyperlinks to the corresponding Composite Element Reports.

References Displays list of references cited in the Functional Region Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [more ...] to view all references. View abstracts via webservice, by additionally clicking the [+] which appears.

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