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Experimental Basis for Positional Weight Matrix Construction |
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Transcription factors |
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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. |
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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
SE - SELEX
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. |
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Matrix type |
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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". |
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Matrix classification |
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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". |
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Matrix category |
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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. |
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Application details |
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Provides additional information about the experimental source of
the binding sites used for matrix construction, the experimental
approach applied to obtain this set, etc. |
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Number of sequences used |
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Provides information about the number of binding sites used for
matrix construction. |
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Additional transcription factors linked to the matrix |
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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. |
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and clicking the Matrix report help link.
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