Mitochondrial protein compositions change to remodel the organization of mt protein functional networks in response to changes in cellular states. Analysis of mt protein functional networks elucidated the biological implications of mt regulatory mechanisms under dysfunctional mt states. Our efforts of systematic data-integrative analysis to evaluate the reliability of proteomics data and to identify important functional modules of mitochondrial proteins can be valuable to computational biology community working on gene expression and proteomics analysis. First, we applied a data-integrative approach to select protein list by using various databases, proteomics datasets, and protein functional network. Mitochondrial proteins were organized into functional modules to identify significantly altered biological processes under different cellular states. The framework of our systematic data-integrative analysis may be useful to reliable proteome analyses for other cellular systems. Second, organizing the thousand mitochondrial proteins into groups of up-or downregulated ones and identifying functional modules are necessary steps in getting an in-depth understanding of the complex molecular mechanism of mitochondria. Third, mapping both mitochondrial proteins and mRNA expression information together is critical to understand the cooperative expression regulation of mitochondrial functional modules. Such multidimensional data analysis can be a valuable asset to develop novel system level models and methods. Also, experimental biologists can utilize our dataset as a resource for target selection to elucidate regulatory mechanisms of mt proteins under dysfunctional mt states.