ArticlePLoS computational biology2011
Network clustering revealed the systemic alterations of mitochondrial protein expression.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Advances in research on propofol-induced postoperative cognitive dysfunction via Piezo channels.Frontiers in molecular neuroscience · 2025Review
- Unraveling the role and mechanism of mitochondria in postoperative cognitive dysfunction: a narrative review.Journal of neuroinflammation · 2024Review
- Transcriptome profiling for developmental stages Protaetia brevitarsis seulensis with focus on wing development and metamorphosis.PloS one · 2023Article
- Network-based machine learning approach to predict immunotherapy response in cancer patients.Nature communications · 2022Article
- Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients.Nature communications · 2020Article
- Cell-penetrating artificial mitochondria-targeting peptide-conjugated metallothionein 1A alleviates mitochondrial damage in Parkinson's disease models.Experimental & molecular medicine · 2018Article
- Transcriptome profiling of whisker follicles in methamphetamine self-administered rats.Scientific reports · 2018Article
- miR-24-mediated knockdown of H2AX damages mitochondria and the insulin signaling pathway.Experimental & molecular medicine · 2017Article
- Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks.Nucleic acids research · 2016Article
- Spatiotemporal positioning of multipotent modules in diverse biological networks.Cellular and molecular life sciences : CMLS · 2014Review
- Mitochondrial proteome remodeling in ischemic heart failure.Life sciences · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mitochondrial protein repertoire varies depending on the cellular state. Protein component modifications caused by mitochondrial DNA (mtDNA) depletion are related to a wide range of human diseases; however, little is known about how nuclear-encoded mitochondrial proteins (mt proteome) changes under such dysfunctional states. In this study, we investigated the systemic alterations of mtDNA-depleted (ρ(0)) mitochondria by using network analysis of gene expression data. By modularizing the quantified proteomics data into protein functional networks, systemic properties of mitochondrial dysfunction were analyzed. We discovered that up-regulated and down-regulated proteins were organized into two predominant subnetworks that exhibited distinct biological processes. The down-regulated network modules are involved in typical mitochondrial functions, while up-regulated proteins are responsible for mtDNA repair and regulation of mt protein expression and transport. Furthermore, comparisons of proteome and transcriptome data revealed that ρ(0) cells attempted to compensate for mtDNA depletion by modulating the coordinated expression/transport of mt proteins. Our results demonstrate that mt protein composition changed to remodel the functional organization of mitochondrial protein networks in response to dysfunctional cellular states. Human mt protein functional networks provide a framework for understanding how cells respond to mitochondrial dysfunctions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.