The data in DMDM can be visualized at three levels: gene, protein and protein domain. A search within DMDM can be performed at any of these three levels, or by disease name, using multiple search options. For instance, users may search by description, which is useful when only a keyword about the molecular entity is known, or by any gene or protein identifier. The results of the search in any of the layers consist of a summary of the information at the top of the page that includes a description, identifiers and external links to the gene, protein or domain. The summary is followed by either a graphical display of the information and/or tables of domain and mutational information, with key identifiers and relevant links. Proteins, both in the gene and protein layers, are depicted as a scaled bar that indicates the amino acid positions; the corresponding domains are shown below the bar. By selecting a region of the protein, information and links about the subset of mutations found around that region are displayed on a separate page along with a graphical display of each mutation.
The domain layer, an example of which is illustrated in , displays three levels of information: sequence logos, mutational data and conserved functional features/sites for each domain position. Multiple sequence alignment information, obtained from CDD for each conserved domain model, is displayed using sequence logos [WebLogo software (Crooks et al.
)]. Mutational data for each human protein with one or more domains is represented by histograms under each position on the sequence logo. The third level, which was extracted from the CDD manual annotation and which is displayed below the histogram bars, provides the functional information for each domain position. The height of the histogram's bars represents the number of mutations found at individual domain positions for all human proteins that match that domain. Polymorphisms are represented in blue and disease mutations in red.
Screen shots of two DMDM queries using: (a) the NP_001073594 protein (GI:122056476) and (b) the CASc (cd00032) domain. The above display only shows a subset of the actual results available to users on the DMDM site.
Redundant mutations that share location, amino acid types and gene, but that are in different proteins are counted only once. When selecting a position on the histogram bar, a list of all mutations in that position, including redundancies, are displayed on a separate page. The upper left boxes in domain pages can be used to locate a particular protein position in the display. The check boxes provide control over the display of functional features shown for each domain position. The histogram bars provide a unique display of all the available information regarding human mutations, polymorphisms and disease mutations that were mapped to a particular domain position.