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A database of mammalian mitochondrial localisation evidence, phenotypes and diseases

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Mitochondrial Gene Lists

External links:
Mitochondrial reference sets - IMPI and MitoCarta 2.0

Current data
MitoMiner contains two different reference sets of mitochondrial genes that have been determined in different ways:

  • The Integrated Mitochondrial Protein Index (IMPI). This reference set of mitochondrial genes was was developed by using machine learning techniques to objectively appraise the mass-spectrometry and GFP tagging data in MitoMiner combined with mitochondrial targeting sequence predictions and antibody localisation staining from the Human Protein Atlas. Support vector machine and random forest classification was used to objectively combine all of this evidence and select those proteins that have similar properties/evidence to characterised mitochondrial proteins. This approach solves the problem of deciding an arbitrary threshold for what level of evidence can be considered "mitochondrial". The IMPI dataset is recalculated every 6-12 months so to include the latest annotation and localisation data. More information can be found on the IMPI page.

  • The MitoCarta Inventory. This is a list of mouse and human mitochondrial proteins as defined by the MitoCarta Inventory of Mammalian Mitochondrial Genes (PubMed:18614015). This was generated from mass spectrometry performed on fourteen tissues alongside GFP tagging and then integrating this with the results of six other large-scale mitochondrial datasets. More information can be found on the MitoCarta page.

Many other genes will not be in these lists but may encode a protein that has some experimental evidence for mitochondrial localisation. These can be searched for on the 'Localisation Evidence' data category page. These are not necessarily non-mitochodrial that have been identified due to contamination. If a protein is low abundance, tissue specific or expression specific this may result in it being missed by a majority of studies. In addition many mitochondrial proteins are membrane bound and these are notoriously difficult to identify by mass spectrometry as most purification procedures are biased towards extracting soluble proteins.

View Reference set genes in MitoMiner
Related template queries

Search annotation (e.g. kinase activity) --> MitoCarta 2 mitochondrial genes

KEGG pathway --> MitoCarta mitochondrial genes

Search annotation (e.g. kinase activity) --> IMPI mitochondrial genes

KEGG pathway --> IMPI mitochondrial genes

Gene --> IMPI mitochondrial score

Choose IMPI score --> Gene list

Query starting points

These links will take you to the Query Builder pages which allow you to make new queries and create template queries of your own