| Model
Name: |
Short name for the model. In case of modules the name is composed of
the names for the two transcription factors involved. |
| Model: |
The table contains the parameters that were used to define the model
using FastM.
For each individual element
- the type of the element (e.g. Matrix or IUPAC),
- the name of the element (e.g. matrix family used),
- the DNA strand on which the element has to be found,
- the parameters of the element (e.g. core and matrix similarity),
and
- the allowed distance range (in basepairs) to the following
element
are listed. |
| Origin: |
This section shows information on the origin of the model, i.e.
- a reference for further information on the model (e.g. experimental
verification of the function of the model)
- the gene description
- the accession number of the sequence that was used for definition
of the model
- the organisms in which the module was defined and/or is evolutionarily
conserved.
If no organism is given, the module was defined in an organism that
is not yet available in ElDorado. Please see the gene description in
this case.
|
| Sequence: |
The sequence of the promoter module is shown together with the
accession number from which it has been extracted (±5 bp of the module match). |
| Function: |
A short description of the function of the model (e.g. how the model
is involved in the regulation of the described promoter). |
| Quality
Assessment: |
The quality assessment shows the results of quality checks applied
to the models.
Examples are:
- Number of false positive matches in a negative test set (false positive
rate) with default ModelInspector threshold.
- Number of matches per 10,000 basepairs in the human genome with default
ModelInspector threshold.
|
| Promoter
Matches: |
The value given is the percentage of promoters in which a match to the
module is found. The absolute number of promoter sequences with module
match is given in parentheses. The following promoter sequences were scanned:
- Vertebrate Modules: 314,000 human, mouse, and rat promoter
sequences with an average length of 650 bp
- Plant Modules: 71,000 promoter sequences of Arabidopsis thaliana
and rice with an average length of 626 bp
|
