DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes

Abstract

The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.

Figure 1

The DG-CST database: examples of query interfaces. (A) The DG-CST home page. The quick search boxes are highlighted in color: the CST ID box in green; the gene box in black; and the BLAST box in red. (B) The list of all analyzed genes obtained following the link on the home page. (C) The DNA-based feature search page. (D) The advanced CST search page, where all annotated features may be used in combination or alone to query the database. (E) The gene-based CST search page, which allows a more detailed gene search.

Figure 2

The DG-CST database: data display. (A) Example of a gene entry (A2M) and the related CST list. (B) Graphical representation of the selected gene, accessible via the map link in (A). On mouse over, details of CST #250083 are displayed as an example. In this representation, CSTs are color-coded based on the number of matches with human ESTs. (C) Example of a CST entry with all annotations and the list of the corresponding CSTs conserved in other species. CST details are accessible either from the CST list of the gene page (A) or by clicking on the interactive graphical browser in (B). (D) Graphical representation of the sequence alignment of the orthologous CSTs shown in (C).