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InterMitoBase: An Annotated Database and Analysis Platform of Protein-Protein Interactions for Human Mitochondria

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InterMitoBase: An Annotated Database and Analysis Platform of Protein-Protein Interactions for Human Mitochondria

Zuguang Gu et al. BMC Genomics.

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.

Figures

Figure 1
Figure 1
Workflow of data collection. The PPIs in InterMitoBase are collected from PubMed, KEGG, and other PPI databases of HPRD, BioGRID, IntAct and DIP.
Figure 2
Figure 2
Venn diagram of PPIs among InterMitoBase, BioGRID, DIP, HPRD and IntAct.
Figure 3
Figure 3
System architecture of InterMitoBase.
Figure 4
Figure 4
Main contents of InterMitoBase. InterMitoBase is composed of three sections, i.e., the protein searching section, the interaction retrieving section and the network analysis section.
Figure 5
Figure 5
Web pages in InterMitoBase. A) Search page; B) Outcome page of the queried proteins; C) Record page of PPIs; D) Page for network visualization and functional analysis; E) Page for degree distribution.

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