JEPSLD: a judgmental eukaryotic protein subcellular location database
Date
2013
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Publisher
University of Delaware
Abstract
Proteins play a key role in every biological process. Moreover, they localize to specific compartments or organelles within the cell. Knowledge of the subcellular location of proteins can help elucidate their function, interaction partners and role in disease. Several protein databases have been developed to store information relevant to the subcellular location of proteins in certain organisms. However, there is no current central database that stores all available information about the subcellular location of eukaryotic proteins.
In the work presented here, we surveyed protein databases that store the location of eukaryotic proteins, and selected those that are up-to-date and contain experimental evidence pertaining to the proteins' subcellular location. Five protein data sources were selected, and the relevant data were obtained from them and stored in a new database that we have developed, namely, the Judgmental Eukaryotic Protein Subcellular Location Database (JEPSLD). The JEPSLD database also stores information about proteins that localize to multiple compartments. In addition, for each protein entry, the database contains information about tissue, cell line, cell type, images and PubMed IDs, when available. A user interface allows users to query the database using gene name, protein name, protein accession numbers such as UniProtKB/SwissProt IDs and gene identifiers such as Entrez gene ID and Ensembl gene ID. Overall, the JEPSLD database is the largest eukaryotic protein subcellular location database to date, storing information about 113,525 eukaryotic proteins. The database will be publicly available and the entire dataset can be downloaded from the JEPSLD database in XML format.