The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family

Abstract

The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. The current version builds upon previous versions by the addition of new, complete sets of homeodomain sequences from fully sequenced genomes, the expansion of existing curated homeodomain information and the improvement of data accessibility through better search tools and more complete data integration. This release contains 1534 full-length homeodomain-containing sequences, 93 experimentally derived homeodomain structures, 101 homeodomain protein-protein interactions, 107 homeodomain DNA-binding sites and 206 homeodomain proteins implicated in human genetic disorders.Database URL: The Homeodomain Resource is freely available and can be accessed at http://research.nhgri.nih.gov/homeodomain/

Figure 1.

HDR relational framework. The relational design connecting the Homeodomain Resource's 14 primary tables are illustrated in the figure. Primary keys are indicated in red, foreign keys in green and keys characterized as both primary and foreign in blue. The new database design is centered around data found in the ‘Proteins’ table. All proteins are lineage-specific and linked to the ‘Organisms’ table. A single protein may contain one or more homeodomains related to the ‘Proteins_Homeodomains’ table. DNA-binding targets, protein–protein interactions, 3D structures and homeodomains implicated in human disorders are normalized and linked to the ‘Proteins’ table. External annotation from multiple databases are integrated via the ‘External_Ids’ table. Database entries are referenced with their primary citation via the ‘Publications’ table.

Figure 2.

The Homeodomain Resource provides a simple search query interface, allowing the user to either query part or all of the Resource (top). Selecting ‘Entire Database’ from the pull-down menu returns a summary screen, indicating how many entries of each type were identified (bottom). Clicking on any of the hyperlinked numbers in the table takes the user directly to that set of results. In addition, overall navigation within the site has been improved with the addition of sidebar tools and links to complete datasets in each homeodomain category.

Figure 3.

Search results from a query of protein–protein interactions data for the interaction of homeodomain proteins Lhx2 and Msx1 (SEARCH ‘Protein-Protein Interactions’ FOR ‘MSX1’) (top). Each protein–protein interaction entry within the Homeodomain Resource is hyperlinked to the corresponding entry in BIND, which provides additional details on the mechanism(s) of interaction (bottom). See text for additional details.