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Module


Module overview

Modules are a combination of two or more binding sites for transcription factors known to produce a regulatory effect by acting in a synergistic or antagonistic manner.

The module overview lists all modules contained in MatBase grouped by the same sections as the matrix families and matrices. There are modules for vertebrates, plants and a single one for fungi. As you can see from the screenshot below (which has been reduced to only a few entries), the overview will give you the module name, the function, a list of one or more organisms where the module has been found and the target gene(s) of the module. Clicking on the module name will take you to the 'module result', which has additional information. If you want more information about a target gene, you can either click on the ElDorado or the EntrezGene link provided. If you want to find modules for a target gene, simply enter that gene as a search term on the search page.

module overview

Module result

module result

Information on the result page:

Module Name Short name for the model. In case of modules the name is composed of the names for the two transcription factors involved.
Function A short description of the function of the module (e.g. how the module is involved in the regulation of the described promoter).
Module Definition Lists the detailed composition of the module, including the matrix families of the matrices the module consists of. Clicking on a matrix family name will take you to the 'matrix family result'. In addition the strand and search parameters for each matrix are given, as well as the distances between the separate elements.
Gene The description for the gene that is regulated by the module.
Gene ID(s) The GeneID(s) for the target gene(s) from the EntrezGene database. Click on the ElDorado or EntrezGene link to get more information on the gene.
Accession no. The accession number for that gene.
Sequence(s) 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).
References The references for the publications the module is based on. Clicking on the reference id will take you to the 'reference result' for that id.
Organisms

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.

Clicking on a taxon id will take you to NCBI's taxonomy browser.

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: 311,000 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

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