ChIP Fragment Report

Overview

ChIP Fragment Reports contain details about DNA fragments shown to be bound by transcription factors in vivo by Chromatin ImmunoPrecipitation (ChIP) or similar studies.

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

In addition, ChIP Fragment Reports provide information about genes in close vicinity to either end of the DNA fragment.

Please note: Genes have been associated with the DNA fragments based solely on their proximity. To provide information about the closely located genes, we mapped DNA fragments on the sequence build HSA_May2004 and then looked for annotated transcription start sites (TSS) and exons within a window of 150 kb on both sides of the fragment. The TSS or exon closest to each end of the DNA fragment was selected, and the respective gene was assigned to the fragment as "nearest gene". This procedure resulted in the association of one, two, or zero gene(s) with each fragment.

Each Chip ChIP Fragment 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 Chip Report are hyperlinked to the corresponding Reports. For example, transcription factors shown to bind the DNA fragment described in the Chip Report are listed, with links to their corresponding Locus Reports.

Chip ChIP Fragment Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a ChIP Fragment Report

The general structure of a ChIP Fragment Report is described below.

Access help by clicking the help menu and clicking the ChIP fragment 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: .

Fragment Information

Describes the characteristics of the DNA fragment.

Species

Identifies the species of the DNA fragment.

Genes nearest to the fragment

Identifies genes located within 150 kb of the DNA fragment, hyperlinked to the corresponding Locus Report. One "nearest gene" on each side of the fragment is displayed.

Binding Factor Information

Experimental evidence

Factor which binds the fragment

Identifies transcription factors shown to bind the DNA fragment, including species, with hyperlinks to the corresponding Locus Reports. Click here for details about the TRANSFAC Quality scale.

Details of the experiment

Describes the materials and methods used in the experiment that identified the binding of the DNA fragment by a transcription factor.

Best supported binding site predicted by Match

Positional weight matrix

Matrix used to scan the sequence for a binding site for the above binding factor, with link to the Matrix Report. [Color code with which the highest scoring match for the used matrix is highlighted in the sequence below.]

Predicted binding site start position

Start position of the highest scoring match in the sequence.

Predicted binding site end position

End position of the highest scoring match in the sequence.

Core similarity score

Core similarity score (calculated by Match algorithm) of the highest scoring match in the sequence.

Matrix similarity score

Matrix similarity score (calculated by Match algorithm) of the highest scoring match in the sequence.

Fragment Sequence

Reference genome build & genomic positions

Identifies the source of the DNA sequence. Indicates the sequence build, chromosome number, absolute positions on the chromosome, and forward or reverse strand.

Sequence

Lists the sequence of the DNA fragment. Capital letters indicate the probes, and lower case letters indicate flanking regions added by TRANSFAC curators. Sequence within the DNA fragment that matches the binding site consensus sequence is highlighted.

Identifiers

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

BKL Accessions

Lists the identifier for the ChIP Fragment of the page.

External Identifiers

Accession number of corresponding entry in external database. For EMBL links, the position of the fragment in the EMBL nucleotide sequence are provided (first fragment position:last fragment position).

References

Displays list of references cited in the ChIP Fragment 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.