MitoMiner: a data warehouse for mitochondrial proteomics data

Abstract

MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/) is a data warehouse for the storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed. The latest release of MitoMiner stores proteomics data sets from 46 studies covering 11 different species from eumetazoa, viridiplantae, fungi and protista. MitoMiner is implemented by using the open source InterMine data warehouse system, which provides a user interface allowing users to upload data for analysis, personal accounts to store queries and results and enables queries of any data in the data model. MitoMiner also provides lists of proteins for use in analyses, including the new MitoMiner mitochondrial proteome reference sets that specify proteins with substantial experimental evidence for mitochondrial localization. As further mitochondrial proteomics data sets from normal and diseased tissue are published, MitoMiner can be used to characterize the variability of the mitochondrial proteome between tissues and investigate how changes in the proteome may contribute to mitochondrial dysfunction and mitochondrial-associated diseases such as cancer, neurodegenerative diseases, obesity, diabetes, heart failure and the ageing process.

Figure 1.

The protein report page for the Cat eye syndrome critical region protein 5 (UniProt accession number Q9BXW7). This page reports that there is evidence for its mitochondrial localization in four tissues from five mass spectrometry studies including the human MitoCarta set and that the protein is included in the human MitoMiner mitochondrial reference set. However, a mitochondrial localization is not annotated in the UniProt keywords.

Figure 2.

The web page of the QueryBuilder for building bespoke queries. The Web page has three components: the model browser (top left) from which data classes and attributes of the object model are selected for inclusion in the query; the data classes included in the query, the constraints on their attributes and the Boolean logic used to combine them (top right) and the data columns to display and sort the output of the results (bottom). The query displayed is to ‘find all human proteins that are in the MitoMiner reference set and reported in five or more mass spectroscopy studies, but do not have a mitochondrial localization annotated in UniProt.’ The query returns 21 proteins and also specifies if the protein is in the MitoCarta reference set.

Figure 3.

Table widgets in MitoMiner summarizing properties of a list of human complex I proteins. The three widgets calculate: the number of proteins associated with diseases reported in OMIM (left), the number of homologs in other species as defined by HomoloGene (middle) and the metabolic pathways as defined by KEGG (right).