Composite Element (Compel) Report

Overview

Click here for a review of composite elements.

Each Compel 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 Compel Report are hyperlinked to the corresponding Reports. For example, genes with binding sites for the composite element described on the Compel Report are listed, with links to their corresponding Locus Reports.

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

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

Anatomy of a Compel Report

The general structure of a Compel Report is described below.

Access help by clicking the help menu and clicking the Composite element report help link.
Navigate to the desired section of the report by opening the table of contents

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

Composite Element Information

Describes the characteristics of the composite element.

Gene

Identifies the gene that the composite element is associated with. The gene name is hyperlinked to the corresponding Locus Report.

Sequence [FASTA export button]

Lists the sequence of the composite element. The sequences of transcription factor binding sites are displayed in upper case letters. The sequence of the spacer between the transcription factor sites is displayed in lower case. If the spacer is too long to be displayed on the Compel Report, it is replaced by "..." (TGACTCT...GGGTTTTCC, for example).

Position

Identifies the position of the composite element relative to the transcription start site or to a reference point stated above.

Number of components

Lists the number of transcription factor binding sites that comprise the composite element (2 or 3).

Binding factors and sites

Indicates the positions of the transcription factor binding sites and lists the transcription factors that bind these sites. Transcription factor names are hyperlinked to their corresponding Locus Reports.

Coordinated effect of the components

Identifies the effect of the relationship between transcription factors that comprise the composite element. Types of effects are specified as synergism or antagonism. Click here for additional information about synergistic and antagonistic composite elements.

Group assignment

Identifies the Compel Group that the composite element has been placed in. Synergistic composite elements consisting of two binding sites for transcription factors are classified into groups by structural and functional similarity. Composite elements within one group contain binding sites for the same factor families.

Functional class

Lists the functional classification of the composite element. For example, one transcription factor that comprises the composite element could be inducible, while another is tissue-restricted. Click here for details about how composite elements are functionally classified in TRANSCompel.

Mechanism of action

Provides insight into the molecular mechanisms involved in the function of the composite element.
For synergistic composite elements, possible mechanisms include:

cooperative binding of factors to DNA
interactions with common co-activator
interactions with basal transcription complex
possible role of nucleosome
DNA bending by one of the factors

For antagonistic composite elements, possible mechanisms include:

competition for DNA binding site
competition for common co-activator.

Comments

Includes general information, e.g. on the role of this composite element in regulation of the gene.

Matrices

Lists binding matrices for the transcription factors that comprises sites/components of the composite element. Matrix names are hyperlinked to the corresponding Matrix Report.

Identifiers

Displays BIOBASE accession numbers, DrugBank, and PubChem IDs

BIOBASE accession

Displays the BIOBASE accession number.

Evidence Information

Describes the evidence for the existence of the composite element. Note that multiple pieces of experimental evidence are presented in individual blocks on the Compel Report.

Experiment Type

Identifies the type of experiment done to confirm interactions between the transcription factors within a composite element. Click here to access details about the types of experiments described in TRANSCompel.

Conclusion of the Experiment

Provides the conclusions drawn from the experiment done to confirm interactions between transcription factors within a composite element. Click here to access details about the types of experiments and the conclusions drawn from these experiments.

Source of Experimental Materials

Provides information about source (cell type, tissue, species) used in the experiment done to confirm interactions between transcription factors within a composite element. Additional details about the source are accessible by clicking on [details], which opens a detailed Property Report.

View the Evidence Report

Identifier for the specific piece of evidence that confirms interactions between the transcription factors within composite elements. The evidence identifier is hyperlinked to an Evidence Report that provides details about the experiment.

References

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.