Matrix Name:  The MatInspector matrices have an identifier
that indicates one of the following seven groups



Description:  Further information for a matrix or matrix family.  
Family:  Each matrix belongs to a socalled
matrix family, where functionally similar matrices are grouped together,
eliminating redundant matches by MatInspector (if the family option was
selected).
E. g. the matrix family V$NFKB includes 5 similar matrices for NFkappaB (V$NFKAPPAB.01, V$NFKAPPAB.02, V$NFKAPPAB.03, V$NFKAPPAB50.01, V$NFKAPPAB65.01) as well as 1 matrix for the NFkappaB related factor cRel (V$CREL.01). 

Transcription factors:  List of transcription factors that are
represented by this matrix family.
The following information is given for each transcription factor:


Tissues:  Tissues that are associated with
the transcription factors represented by the matrix family. The tissue
association has been determined by evaluation of all PubMed abstracts
(cocitations of transcription factors and tissues).
The transcription factors are grouped into three tissue classes:
List of available tissues:
Tissues are assigned to matrix families, not individual matrices. The tissue associations of matrix families are determined by automatic evaluation of all PubMed abstracts (cocitations of transcription factors and tissues) and subsequent manual curation. Note: Up to now, tissue association is only available for vertebrate matrices. 

Modules:  Experimentally verified promoter
modules that include this matrix family as one element.
Promoter modules are functional elements consisting of at least two transcription factor binding sites which are shown to act synergistically or antagonistically. 

References:  References for the original source of sequences/oligonucleotides for the matrix with author, title and citation.  
Statistical basis:  Shows more information about how many sequences/oligonucleotides were used to create the matrix description.  
Random expectation (revalue):  The revalue for each individual
matrix gives an expectation value for the number of matches per 1000
base pairs of random DNA sequence (that is, it indicates how well a matrix
is defined).
Since there are binding sites that are biologically quite "loosely" defined, a high revalue is not necessarily a sign of a "bad" matrix description. A very low revalue might even be a sign of a description that is too strict. 

Promoter matches:  The value given is the percentage
of promoters in which a match to the matrix / matrix family is
found with optimized matrix similarity. In order to determine
the promoter matches, promoter sequences are extracted from ElDorado.
The following promoter sequences are scanned for the different matrix
groups:


Optimized matrix threshold:  This matrix similarity is
the optimized value defined in a way that a minimum number of matches
is found in nonregulatory test sequences (i.e. with this matrix similarity
the number of false positive matches is minimized).
This matrix similarity is used when the user checks "Optimized" as the matrix similarity threshold for MatInspector. 

Length:  Length of the matrix / matrix family in base pairs. All matrices in a family are of the same (uneven) length.  
Anchor:  All matrices in a family are of the same (uneven) length and have an anchor position assigned which is the center position of the matrix. This assures that matrices of a family match exactly at the same position.  
Nucleotide Distribution Matrix:  The nucleotide distribution matrix shows the nucleotide frequencies observed in aligned binding sites of the corresponding transcription factor.  
Profile:  The profile of a matrix is a graphical
representation of the Civector, i.e. the degree of
conservation at each position of the matrix.
The IUPAC string consensus is
a representation of the matrix based on the following rules (adapted
from Cavener, Nucleic Acids Res. 15, 13531361, 1987):


Core:  The core sequence of a matrix is defined as the (usually 4) highest conserved, consecutive positions of the matrix.  
Civector:  The Civector (consensus index vector) for the matrix represents the degree of conservation of each position within the matrix. The maximum Civalue of 100 is reached by a position with total conservation of one nucleotide, whereas the minimum value of 0 only occurs at a position with equal distribution of all four nucleotides and gaps.  
Sequence logo  A graphical representation of the matrix consensus generated using the algorithm described in

For further reading please refer to the MatInspector publications.
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