Promoter Report

Overview

For detailed background information about the promoter sequences and their features, click here.

Each Promoter Report, presented as a web page, has different blocks of information for Promoter features and the Promoter sequence. When the curation in these blocks refers to information that exists on another BKL Report, a hyperlink is provided that connects to the corresponding BKL Report. For example, the Promoter Report includes information about the gene the promoter is associated with and provides a link to the corresponding Locus Report for that gene.

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

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

Anatomy of a Promoter Report

The general structure of a Promoter Report is described below.

Access help by clicking the help menu and clicking the Promoter 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: .
Links providing an option to download content are indicated by a green bubble, such as the FASTA link shown here: .

Promoter Information

Provides general information such as the corresponding gene or synonyms for a promoter and the location of the virtual TSS that defines the promoter.

<<img src="../../img/help.gif" alt="help" border="0" >

Identifier

For species other than human, mouse and rat, this field provides the unique identifier that comprises the species acronym, the gene number, and the gene symbol in the following format: @{species}_@{gene_number}_@{gene_symbol}. If multiple promoters exist for a particular gene, an index number, separated by an underscore, is added after the gene number.

Gene

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

Synonyms of the gene

Lists other acronyms or names for the promoter's gene.

Genomic coordinates

Gives the chromosomal location of the promoter.

Reference genome build, genomic positions & score points

For non-human, mouse and rat promoters two comment lines are defined for each entry: One of the lines contains a definition of the sequence fragment on the genome assembly, with build info, chromosome, absolute positions, and strand; the other line notes the evidence score points, in absolute numbers as well as the percentage of points accumulated for the promoter entry.

Virtual TSS score

For human, mouse and rat promoters this field provides the evidence score points, in absolute numbers as well as the percentage of points accumulated for the promoter entry.

Promoter Sequence

Displays the promoter sequence.

This block provides a dynamic view of the promoter sequence (from -10,000 to +1,000 relative to the virtual TSS). Selected features are displayed above the sequence - to add or remove features select or deselect the check box in front of the desired feature. Intervals of species conservation, as defined by the 46-way phast cons (for human) and 60-way phastcons (for mouse) placental tracks at UCSC, are shown below the sequence.

Features

Describes the characteristics of a promoter.

ChIP-on-chip/-Seq fragments

Identifies DNA fragments shown in vivo to be bound by a transcription factor, based on ChIP-on-chip or related experiments. Cell line/ tissue (and treatment) from which the bound fragments were derived are added in parentheses. ChIP-on-chip fragment names are hyperlinked to the corresponding Chip Report.

Histone modifications

Identifies DNA fragments shown in vivo to be bound by histones with a particular modification, based on ChIP-on-chip or related experiments. Cell line/ tissue (and treatment) from which the bound fragments were derived are included in parentheses.

DNA modifications

Identifies DNA fragments carrying a particular modification in vivo, based on ChIP-on-chip or related experiments. Type of modification is given in square brackets. Cell line/ tissue (and treatment) from which the fragments were derived are included in parentheses.

TRANSFAC binding sites

Displays transcription factor binding sites within the promoter sequence. The factor name is hyperlinked to the corresponding Locus Report.

TSSs

Identifies transcription start sites from Ensembl, with hyperlinks to the corresponding information.

SNPs

Identifies single nucleotide polymorphisms (SNPs), with hyperlinks to corresponding dbSNP reports.

Repeats

Lists repeats, including positions.

CpG islands

Identifies CpG Islands, including positions and GC content.

DNase hypersensitivity sites

Lists intervals identified by DNase hypersensitivity experiments, which suggests that the DNA within the interval would be accessible for binding. The tissue or cell type examined by the experiment is listed. All data in this table is derived from ENCODE.

Match predicted transcription factor binding sites

For each ChIP-ChIP or ChIP-Seq experiment for which a matrix exists, Match was used to predict the most likely region within the fragment interval that was bound by the factor under investigation. For each DNase hypersensitivity experiment, a subset of TRANSFAC's vertebrate non-redundant profile was used in a Match analysis to identify those factors that are most likely to bind within the accessible intervals of DNA.

Identifiers

Displays internal and external identifiers associated with the gene that the promoter is associated with.

BKL Accessions

Lists the identifier for the promoter of the page.

External Identifiers

Displays hyperlinks to corresponding entries of the promoter's gene in external databases. The links comprise entries in the respective nomenclature database (HGNC for human, MGI for mouse, and RGNC for rat), Entrez Gene, Ensembl, RefSeq, UniGene, UniProt and Affymetrix probe set IDs.

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.