LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

Abstract

LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Currently, it contains entries for 19 604 UniProt proteins (HS: 13 342; AT: 6262). Each database entry contains the experimentally derived localization in Gene Ontology (GO) terminology, the experimental annotation of localization, localization predictions by state-of-the-art methods and, where available, the type of experimental information. LocDB is searchable by keyword, protein name and subcellular compartment, as well as by identifiers from UniProt, Ensembl and TAIR resources. In comparison to other public databases, LocDB as a resource adds about 10 000 experimental localization annotations for HS proteins and ∼900 for AS proteins. Over 40% of the proteins in LocDB have multiple localization annotations providing a better platform for development of new multiple localization prediction methods with higher coverage and accuracy. Links to all referenced databases are provided. LocDB will be updated regularly by our group (available at: http://www.rostlab.org/services/locDB).

The Nuclear Proteome of a Vertebrate

“…There are several subcellular localization databases, including Protein Atlas [17], Uniprot [18], LocDB [19], and GO [20] (Fig. 1E, Fig.…”

Prediction of Protein–Protein Interactions by Evidence Combining Methods

“…There are some reported methods for extracting negative datasets, such as: (1) Negative datasets are constructed by using random pairs which exclude the experimentally detected interactions [1], and as there are discordant numbers between high-confidence interactions and random pairs, the scale and structure of networks should be balanced between negative and positive datasets. This method may include undetected PPIs; (2) Negative examples are chosen based on the categories of their distinct functions, such as sub-cellular localization (can be accessed by tools such as LOCATE [38], PSORTdb 3.0 [39], LocDB [40]) and annotations (such as KEGG pathways, gene ontology (GO), and Enzyme Commission (EC)) [22,41]. However, these methods can also lead to biases due to varying definitions of categories [42]; (3) Another alternative approach is based on topological policy: choose pairs of separated proteins in existing PPI networks to represent non-interactions: defining negative samples as the protein pairs with the shortest path lengths exceed the median shortest paths in a GSP network [43], or further construct a GSN network based on the principle of keeping the composition and degree of a node identical to the GSP network [20].…”

Novel Therapeutic Proteins and Peptides

“…6 The intracellular compartment is beyond the reach of conventional proteins and peptides and the intracellular protein-protein interactions are, by and large, not tractable by small molecules. 6 The intracellular compartment is beyond the reach of conventional proteins and peptides and the intracellular protein-protein interactions are, by and large, not tractable by small molecules.…”

“…respectively. 6 Intracellular delivery, although possible in the laboratory, has not been demonstrated in the clinic. The first recombinant expressed medicines were the hormones somatostatin in 1977 and human insulin in 1979; 1,2 oxytocin represents the first chemical synthesis of a full peptide, which occurred in 1953.…”