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. 2011 Jan;39(Database issue):D230-4.
doi: 10.1093/nar/gkq927. Epub 2010 Nov 11.

LocDB: Experimental Annotations of Localization for Homo Sapiens and Arabidopsis Thaliana

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Free PMC article

LocDB: Experimental Annotations of Localization for Homo Sapiens and Arabidopsis Thaliana

Shruti Rastogi et al. Nucleic Acids Res. .
Free PMC article

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).

Figures

Figure 1.
Figure 1.
Clustering of LocDB. We clustered the LocDB entries by BLASTclust (26) to explore whether or not some families are highly over-represented in LocDB, and found that they are not. For instance, 46% of HS and 43% of AT proteins in LocDB have levels of PIDE <25%, i.e. differ substantially in sequence. On the other end of the spectrum, only 8% of HS and 1% of AT proteins are very similar to each other (PIDE >98%). Note that levels of PIDE>70% usually suffice to infer similarity in localization at levels of about 75% (31), i.e. for over 80% of the LocDB entries no other entry could be used to predict localization by homology.
Figure 2.
Figure 2.
Example for screen dump from LocDB. The example shows a search with the protein CIPKN_ARATH. Arrows highlight input, output and the distinction between different aspects of the output.
Figure 3.
Figure 3.
Comparison between LocDB, UniProt, LOCATE and SUBA for experimental annotations of protein subcellular localizations. (a) The Venn diagram shows that LocDB has added annotations for 9469 HS proteins, not annotated in UniProt (2010_07) release (16) and LOCATE (1). (b) The Venn diagram shows that LocDB has added annotations for 827 AT proteins, not annotated in UniProt (2010_07) release (16) and SUBA (4).

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