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InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria.

Gu Z, Li J, Gao S, Gong M, Wang J, Xu H, Zhang C, Wang J - BMC Genomics (2011)

Bottom Line: Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria.It also works as a platform by integrating several on-line tools for the PPI analysis.As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China.

ABSTRACT

Background: The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria. Investigations examining mitochondria are expanding to the system level because of the accumulation of mitochondrial proteomes and human interactome. Consequently, the development of a database that provides the entire protein interaction map of the human mitochondrion is urgently required.

Results: InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties.

Conclusions: InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.

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Venn diagram of PPIs among InterMitoBase, BioGRID, DIP, HPRD and IntAct.
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Figure 2: Venn diagram of PPIs among InterMitoBase, BioGRID, DIP, HPRD and IntAct.

Mentions: The current version of InterMitoBase contains 5,883 PPIs of 2,813 proteins (490/2323 mitochondrial/non-mitochondrial proteins) collected from PubMed, KEGG, HPRD, BioGRID, IntAct and DIP. A comparison between the PPI databases of HPRD, BioGRID, IntAct and DIP, InterMitoBase is specifically designed for human mitochondria, which aims at all the possible PPIs that are closely related to human mitochondrial functions. This new database covers: (i) PPIs involved in biological pathways mediated by mitochondrial proteins; (ii) the PPIs between mitochondrial and non-mitochondrial proteins; and (iii) PPIs between mitochondrial and mitochondrial proteins. 1,640 PPIs in InterMitoBase are new ones that have not been covered by any of the four PPI databases (see Figure 2). More than 80% of the new interactions (1420/1640) have been manually curated from literature abstracts isolated from PubMed.


InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria.

Gu Z, Li J, Gao S, Gong M, Wang J, Xu H, Zhang C, Wang J - BMC Genomics (2011)

Venn diagram of PPIs among InterMitoBase, BioGRID, DIP, HPRD and IntAct.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3142533&req=5

Figure 2: Venn diagram of PPIs among InterMitoBase, BioGRID, DIP, HPRD and IntAct.
Mentions: The current version of InterMitoBase contains 5,883 PPIs of 2,813 proteins (490/2323 mitochondrial/non-mitochondrial proteins) collected from PubMed, KEGG, HPRD, BioGRID, IntAct and DIP. A comparison between the PPI databases of HPRD, BioGRID, IntAct and DIP, InterMitoBase is specifically designed for human mitochondria, which aims at all the possible PPIs that are closely related to human mitochondrial functions. This new database covers: (i) PPIs involved in biological pathways mediated by mitochondrial proteins; (ii) the PPIs between mitochondrial and non-mitochondrial proteins; and (iii) PPIs between mitochondrial and mitochondrial proteins. 1,640 PPIs in InterMitoBase are new ones that have not been covered by any of the four PPI databases (see Figure 2). More than 80% of the new interactions (1420/1640) have been manually curated from literature abstracts isolated from PubMed.

Bottom Line: Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria.It also works as a platform by integrating several on-line tools for the PPI analysis.As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China.

ABSTRACT

Background: The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria. Investigations examining mitochondria are expanding to the system level because of the accumulation of mitochondrial proteomes and human interactome. Consequently, the development of a database that provides the entire protein interaction map of the human mitochondrion is urgently required.

Results: InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties.

Conclusions: InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.

Show MeSH