Matrix Report


Matrix Reports contain information about nucleotide distribution matrices of aligned transcription factor binding site sequences. The sequences may have been obtained by in vitro selection studies (SELEX) or from compiled sites of genes. Matrices can also be based on in vivo binding fragments from ChIP-chip or ChIP-Seq experiments. In either case, the source is indicated.

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

Each Matrix Report is similarly organized and comprises different blocks for properties curated. Other BKL Reports mentioned in the Matrix Report are hyperlinked to the corresponding Reports. For example, (where available) transcription factor binding sites used to derive the matrix are listed on the Matrix Report, with links to their corresponding Site Reports or composite element Evidence Reports.

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

Anatomy of a Matrix Report

The general structure of a Matrix Report is described below.

  • Access help by clicking the help menu  help  and clicking the Matrix 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  .

Positional Weight Matrix Describes the characteristics of the matrix. help
Matrix overview
Sequence logo
A matrix logo, which displays the consensus sequence graphically, is shown. The reverse complement consensus sequence is displayed to the right.

Nucleotide position frequency
Displays the nucleotide frequency matrix. Read down to identify the binding site and across to identify the nucleotide frequency at that particular binding site position. The derived IUPAC consensus is provided in the last column. Click here for more information about the Matrix block. The nucleotide frequency matrix for the reverse complement is displayed to the right.
Experimental Basis for Positional Weight Matrix Construction
Transcription factors
Lists the transcription factors from which binding sites were used for matrix construction, hyperlinked to corresponding Locus Reports. The count of binding sites contributed to the calculation of the positional weight matrix by each factor is displayed in the bar graph.
Aligned Binding Sites
Lists the transcription factor binding sites used to generate the matrix, with links to the corresponding Site Reports. Includes the part of the sequence within the matrix window, the start of the matrix window (and the displayed sequence) relative to the complete sequence as given in the Site Report. The aligned binding sites are not given for all matrices. (This depends on the availability of the sites, e.g. not for all SELEX matrices the sites have been published. Also, for ChIP-based matrices no site alignments are given.).

The following information is provided for each site, when available: the transcription factor hyperlinked to the corresponding Locus Report, the gene from which the binding site was derived hyperlinked to the corresponding Locus Report, a graphical summary of the experimental evidence supporting the TF-DNA binding interaction hyperlinked to the detailed Site Report, the experimental source, and the references supporting the TF-DNA binding interaction.

The experimental evidence categories are organized as:

CI - chromatin immunoprecipitation
DM - DNA modification (methylation, etc)
FA - functional analysis
FO - footprinting
GS - simple gel shift/gel retardation
IP - immunoprecipitation
SS - supershift/competitive gel shift
OT - other

All experimental methods that do not fall into one of the other categories will be assigned to the OT (other) category.
Matrix type
Specifies whether a matrix is specific for a factor, or more generally representative of a family of related factors. Best ranking factor-specific matrices in a performance assessment are labelled as "recommended".
Matrix classification
For matrices built from vertebrate transcription factors, specifies the class that the matrix has been assigned to based on a matrix clustering algorithm submitted for publication. As of the 2012.3 release there are 44 classes: AP2-EREBP, ARID, ATHOOK, BHLH, BHSH, BZIP, CHCH, CU-FIST, DM, E2, E2F, ETS, FORKHEAD, GCM, GENINI, GRAINY, HISTONE, HMG, HOX, HSF, IRF, MADS, MYB, NAM, P53, REL, RFX, RUNT, SAND, SMAD, STAT, SWI4, TBP, TBX, TCP, TEA, WRKY, ZFC2H2, ZFC4-NR, ZFC6, ZFDOF, ZFGATA, ZFPHD, ZFRING. Matrices that do not fall into one of these classes are classified as "unclassified".
Matrix category
Describes which method was used to create the matrix. Possible methods include matrix compiled from individual genomic sites, SELEX (CASTing, SAAB, Target Detection Assay), and more.
Application details
Provides additional information about the experimental source of the binding sites used for matrix construction, the experimental approach applied to obtain this set, etc.
Number of sequences used
Provides information about the number of binding sites used for matrix construction.
Additional transcription factors linked to the matrix
Lists those transcription factors which did not contribute binding sites to the construction of the matrix but which are linked to the matrix, usually through homology.
Profile Membership
Displays information about the profiles that the matrix is a part of
Profiles which include this matrix
When relevant, lists whether the matrix of the page is part of the vertebrate non-redundant (VNR) or other profile for use in Match analysis.
Other vertebrate non-redundant (VNR) matrices that this matrix represents
When relevant, lists the group of matrices that the matrix of the page represents in the vertebrate non-redundant profile (VNR) for use in Match analysis.
Related matrices
Displays related matrices
This matrix is an older version of
When relevant, lists any newer versions of this matrix, such as a version that was created after additional binding sites became available.
This matrix is a newer version of
When relevant, lists any older versions of this matrix, such as a version that was created before additional binding sites became available.
Related family matrices
Lists related matrices that are generally applicable to a family of transcription factors to which the factors used to construct this positional weight matrix belong.
Related factor-specific matrices
Lists other matrices that have been constructed using the factors used to construct this positional weight matrix or their orthologs.

Identifiers Displays the identifiers associated with the matrix.  
BKL Accessions
Lists the identifier for the matrix of the page.
Similar matrix in
Lists closely related matrices in public databases including JASPAR and UnIPROBE.

Lists references from which whole sets of sequences or complete matrix was derived, including for the individual binding site sequences. Matrices constructed by us, typically have a link to a "TRANSFAC Report", which describes the way we used for site alignment and matrix construction.

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 PubMed 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.
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