The Nuclear Envelope is a double membrane system surrounding the nucleus of eukaryotic cells. It consists of two membranes with distinct features, the outer and the inner nuclear membranes. A large number of proteins located at the Envelope have been identified, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus and the correct positioning of the nucleus in the cell to chromatin tethering, genome organization, regulation of signaling cascades and even transporting enormous cargo. In fact, it is already prominent that the complexity of the Nuclear Envelope rivals that of the plasma membrane.
NucEnvDB is a publicly available database of Nuclear Envelope proteins and their interactions. The database currently contains information on 2953 manually annotated proteins with known presence in the Nuclear Envelope, obtained from 397 species. Each database entry contains useful annotation including a detailed description of the protein's subcellular location, its position in the Nuclear Envelope, its interactions with other proteins and cross-references to major biological repositories.
Through the NucEnvDB web interface, users can perform simple or advanced text searches, as well as BLAST and HMMER queries against the database's protein sequences and domains. Furthermore, they can create, analyze and export protein-protein interaction networks from the database's components, using a specially designed network preparation pipeline that applies Cytoscape.js and the Markov Clustering algorithm (MCL). Finally, they can perform functional enrichment analysis on database components using WebGestaltR, an R implementation of the WEB-based Gene SeT AnaLysis Toolkit (WebGestalt). The entire database is available for download in text, FASTA and XML formats.
NucEnvDB is currently the only available repository focused on the Nuclear Envelope and its protein components. Given the rising interest in studying the Nuclear Envelope, a previously unattended subcellular component, we expect NucEnvDB to be a valuable resource for genome-wide and/or proteome-wide analyses and, potentially, the design of novel prediction algorithms aimed at Nuclear Envelope proteins.
Baltoumas, F.A.*, Sofras, D.T.*, Hamodrakas, S.J. & Iconomidou, V.A.
NucEnvDB: a database of Nuclear Envelope proteins and their interactions
* Equally contributing authors