Limits...
MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.

Smith AC, Robinson AJ - Mol. Cell Proteomics (2009)

Bottom Line: Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze.To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information.Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane.

View Article: PubMed Central - PubMed

Affiliation: MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB20XY, United Kingdom.

ABSTRACT
Mitochondria are a vital component of eukaryotic cells with functions that extend beyond energy production to include metabolism, signaling, cell growth, and apoptosis. Their dysfunction is implicated in a large number of metabolic, degenerative, and age-related human diseases. Therefore, it is important to characterize and understand the mitochondrion. Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze. To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information. The proteomics data of 33 publications from both mass spectrometry and green fluorescent protein tagging experiments were imported and integrated with protein annotation from UniProt and genome projects, metabolic pathway data from Kyoto Encyclopedia of Genes and Genomes, homology relationships from HomoloGene, and disease information from Online Mendelian Inheritance in Man. We demonstrate the strengths of MitoMiner by investigating these data sets and show that the number of different mitochondrial proteins that have been reported is about 3700, although the number of proteins common to both animals and yeast is about 1400, and membrane proteins appear to be underrepresented. Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane. The data and advanced capabilities of MitoMiner provide a framework for further mitochondrial analysis and future systems level modeling of mitochondrial physiology.

Show MeSH
The Web page of the Query Builder 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 “show all proteins that are present in KEGG pathway 00071 (fatty acid metabolism) in H. sapiens and have evidence of mitochondrial localization by either mass spectrometry or GFP experiments.”
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2690483&req=5

f4: The Web page of the Query Builder 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 “show all proteins that are present in KEGG pathway 00071 (fatty acid metabolism) in H. sapiens and have evidence of mitochondrial localization by either mass spectrometry or GFP experiments.”

Mentions: Advanced querying of data in MitoMiner is provided by the InterMine Query Builder. Exceptionally flexible queries can be created by using Boolean logic to combine constraints on the attributes of any data type defined in the model. In addition, the Query Builder specifies the data fields that are shown in the results table and in what order. Any identifiers in the results table, such as a UniProt accession number, are linked to the report page for that entry, and the results can be exported in a variety of formats, including Microsoft Excel. For example, the query “show all proteins that are present in fatty acid metabolism (KEGG pathway 00071) in human and that have either mass spectrometry or GFP experimental evidence for mitochondrial localization” was built in the Query Builder starting from the data category of KEGG metabolic pathways and incorporating the constraint for mitochondrial localization of proteins via the EC cross-reference (Fig. 4). To execute the query, the InterMine system coordinated the required integration of data from UniProt, experimental proteomics, and metabolic pathways. The results confirmed that many human proteins of fatty acid metabolism, as defined in KEGG, have experimental evidence of mitochondrial localization (Fig. 5).


MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.

Smith AC, Robinson AJ - Mol. Cell Proteomics (2009)

The Web page of the Query Builder 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 “show all proteins that are present in KEGG pathway 00071 (fatty acid metabolism) in H. sapiens and have evidence of mitochondrial localization by either mass spectrometry or GFP experiments.”
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2690483&req=5

f4: The Web page of the Query Builder 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 “show all proteins that are present in KEGG pathway 00071 (fatty acid metabolism) in H. sapiens and have evidence of mitochondrial localization by either mass spectrometry or GFP experiments.”
Mentions: Advanced querying of data in MitoMiner is provided by the InterMine Query Builder. Exceptionally flexible queries can be created by using Boolean logic to combine constraints on the attributes of any data type defined in the model. In addition, the Query Builder specifies the data fields that are shown in the results table and in what order. Any identifiers in the results table, such as a UniProt accession number, are linked to the report page for that entry, and the results can be exported in a variety of formats, including Microsoft Excel. For example, the query “show all proteins that are present in fatty acid metabolism (KEGG pathway 00071) in human and that have either mass spectrometry or GFP experimental evidence for mitochondrial localization” was built in the Query Builder starting from the data category of KEGG metabolic pathways and incorporating the constraint for mitochondrial localization of proteins via the EC cross-reference (Fig. 4). To execute the query, the InterMine system coordinated the required integration of data from UniProt, experimental proteomics, and metabolic pathways. The results confirmed that many human proteins of fatty acid metabolism, as defined in KEGG, have experimental evidence of mitochondrial localization (Fig. 5).

Bottom Line: Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze.To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information.Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane.

View Article: PubMed Central - PubMed

Affiliation: MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB20XY, United Kingdom.

ABSTRACT
Mitochondria are a vital component of eukaryotic cells with functions that extend beyond energy production to include metabolism, signaling, cell growth, and apoptosis. Their dysfunction is implicated in a large number of metabolic, degenerative, and age-related human diseases. Therefore, it is important to characterize and understand the mitochondrion. Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze. To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information. The proteomics data of 33 publications from both mass spectrometry and green fluorescent protein tagging experiments were imported and integrated with protein annotation from UniProt and genome projects, metabolic pathway data from Kyoto Encyclopedia of Genes and Genomes, homology relationships from HomoloGene, and disease information from Online Mendelian Inheritance in Man. We demonstrate the strengths of MitoMiner by investigating these data sets and show that the number of different mitochondrial proteins that have been reported is about 3700, although the number of proteins common to both animals and yeast is about 1400, and membrane proteins appear to be underrepresented. Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane. The data and advanced capabilities of MitoMiner provide a framework for further mitochondrial analysis and future systems level modeling of mitochondrial physiology.

Show MeSH