Death domain resource: an integrated protein domain database

Summary form only given. Traditional domain database only provides the sequence related information, such as the consensus sequence or a position-specific scoring matrix. The so-called integrated domain databases, such as InterPro or CDD (conserved domain database), only integrates the information from different types of domain databases. The functional information, such as alternative splicing, tissue, protein interactions, etc., are usually missing. Therefore, it is important to have an integrated protein domain database, which will create a user-centric environment for biologists. The advantage of creating an integrated database for domains, instead of genes, is to discover the relations within a gene family. We have used death domain as an example to explain how to integrate the genome, transcriptome, and proteome information together. In this user-centric bioinformatics environment, the users may use information to make observations and even to create hypothesis for biomedical research. In other words, information integration is essential for information-driven biomedical research. For example, by integrating the alternative splicing and the protein domain information, a protein variant that may show inhibitory effect on signal transduction can be observed. By integrating tissue information with alternative splicing, protein variant that will be expressed in a given type of tissue might be revealed. Besides, by integrating tissue and histology information with pathway, the difference of a pathway in normal versus tumor cells would be clear. This system can be readily be applied to other protein domains. Thus, we name the whole program package "integrated domain resource (IDR)". The ultimate goal for this database is to integrate medical information into the system, so the relation of genotype and phenotype can be established in the future.