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An inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Using the same strategy we have now reconstructed this inventory separately for human and for mouse based on (i) improved gene transcript models, (ii) updated literature curation, including results from proteomic analyses of mitochondrial sub-compartments, (iii) improved homology mapping and (iv) updated versions of all seven original data sets. The updated human MitoCarta2.0 consists of 1158 human genes, including 918 genes in the original inventory as well as 240 additional genes. The updated mouse MitoCarta2.0 consists of 1158 genes, including 967 genes in the original inventory plus 191 additional genes. The improved MitoCarta 2.0 inventory provides a molecular framework for system-level analysis of mammalian mitochondria.
AMPDB / Arabidopsis Mitochondrial Protein Database
Provides information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. AMPDB contains more than 29 100 proteins obtained from 17 public resources and represent about 500 unique identifications. It can be queried with a series of mitochondrial-specific characteristics such as targeting pre-sequence predictions, and orthology to yeast, human mitochondrial proteins and the mitochondrial progenitor Rickettsia.
MPIC / Mitochondrial Protein Import Components
Provides searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest.
MPA / Mitochondrial Protein Atlas
Provides information about human mitochondrial proteins. The MPA database contains 911 unique protein entries associated with experimentally validated and referenced mitochondrial localization. This database includes other information as experimentally validated and referenced information defining structure, function, interactions with other mitochondrial protein atlas (MPA) proteins, and involvement in pathologies. It supplies a prototype for other information sources allowing a distinction between what has been confirmed and what remains to be verified.
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The central database contains manually evaluated yeast, mouse, and human reference proteins, which show convincing evidence of a mitochondrial location. In addition, entries from genome-wide approaches that suggest protein localization are integrated and serve to compile a combined score for each candidate, which provides a best estimate of mitochondrial localization. Furthermore, MitoP2 integrates information on the orthology between species, including Saccharomyces cerevisiae, mouse, human, Arabidopsis thaliana, and Neurospora crassa, thus mutually enhancing evidence across species.
A large-scale relational database that is automatically updated to keep pace with advances in mitochondrial proteomics and is curated to assure that the designation of proteins as mitochondrial reflects gene ontology (GO) annotations supported by high-quality evidence codes. A set of postulates is proposed to help define which proteins are authentic components of mitochondria. A web interface is provided to permit members of the mitochondrial research community to suggest modifications in protein annotations or mitochondrial status.
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