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MitoMiner integrates protein data from UniProt with annotation from the Gene Ontology project, homology data from HomoloGene, metabolic pathway data from KEGG, tissue expression data from the Human Protein Atlas and disease data from OMIM. This is combined with experimental mitochondrial localisation data from a large number of mass-spectrometry and GFP tagging proteomic studies and data from the Human Protein Atlas. These data sources have been integrated to allow sophisticated data mining queries spanning these many different sources.
MitoMiner currently contains data for mammals (H. sapiens, M. musculus, R. norvegicus, B. taurus), fruit flies (D. melanogaster), plants (A. thaliana), yeasts (S. pombe, S. cerevisiae) as well as a host of other organisms (N. crassa, P. falciparum, T. thermophila and G. lamblia).
Attempting to describe which proteins in an organism are localised within the mitochondria is important for the investigation of mitochondrial diseases as well as general mitochondrial biology. MitoMiner includes several reference sets of the mitochondrial proteome including the Broad's MitoCarta Inventory and the new MRC-MBU Integrated Mitochondrial Protein Index (IMPI). The IMPI reference set is a collection of proteins with strong evidence for mitochondrial localisation gathered from the MitoMiner database and objectively appraised by two machine learning techniques. Many clues to mitochondrial localisation exist such as targeting sequences and mitochondrial specific protein domains, as well as direct evidence for mitochondrial localisation such as mass spectrometry and antibody staining. As no one indicator is as accurate as all indicators combined, IMPI uses machine learning to objectively combine all evidence available for a protein and select those that have similar properties to characterised mitochondrial proteins. This approach solves the problem of deciding an arbitrary threshold for what level of evidence can be considered mitochondrial.
Smith, A. C., Blackshaw, J. A. and Robinson, A. J. (2011).
MitoMiner: a data warehouse for mitochondrial proteomics data
Nucleic Acids Res., 40, 1160-1167.
Smith, A. C. & Robinson, A. J. (2009).
MitoMiner: an integrated database for the storage and analysis of mitochondrial proteomics data
Mol. Cell. Proteomics 9, 1324-1337.