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Cited by 162Bioinformatics and Genomic NetworksMitochondrial Function and PathologyAdvanced Proteomics Techniques and Applications

MitoMiner v3.1, an update on the mitochondrial proteomics database

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Smith, Anthony C., Robinson, Alan J.·2016·Nucleic Acids Research
DOI 10.1093/nar/gkv1001PMC PMC4702766
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Abstract

Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately and comprehensively defined, despite many studies. To support mitochondrial research, we developed MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk), a freely accessible mitochondrial proteomics database. MitoMiner integrates different types of subcellular localisation evidence with protein information from public resources, and so provides a comprehensive central resource for data on mitochondrial protein localisation. Here we report important updates to the database including the addition of subcellular immunofluorescent staining results from the Human Protein Atlas, computational predictions of mitochondrial targeting sequences, and additional large-scale mass-spectrometry and GFP tagging data sets. This evidence is shared across the 12 species in MitoMiner (now including Schizosaccharomyces pombe) by homology mapping. MitoMiner provides multiple ways of querying the data including simple text searches, predefined queries and custom queries created using the interactive QueryBuilder. For remote programmatic access, API's are available for several programming languages. This combination of data and flexible querying makes MitoMiner a unique platform to investigate mitochondrial proteins, with application in mitochondrial research and prioritising candidate mitochondrial disease genes.

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  • Using MitoMiner 4.0 and the Gene Ontology "Mitochondrion" category, 953 proteins associated with mitochondria were identified.

    “Using the MitoMiner 4.0 database [73] and the Gene Ontology “Mitochondrion” category [74, 75], we identified 953 proteins associated with mitochondria; the levels of 42% of those proteins were significantly changed by apoE4 expression, again with equal numbers increased and decreased (Fig. 5A).”

    From Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function (2019) · cites this paper as [73]

    The Introduction identifies MitoMiner as a database for investigating mitochondrial proteins and says it incorporates Gene Ontology annotations. But this paper describes MitoMiner v3.1, not the cited version 4.0. The 953-protein count is presented as the citing authors’ own result, not a finding attributed to this source. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 29

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Cited by

Sorted by citations

Authors
Smith, A. C., & Robinson, A. J.
Affiliations
MRC Mitochondrial Biology Unit (GB)
Corresponding author
Robinson, Alan J.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2015-10-01
Volume
44
Issue
D1
Pages
D1258-D1261
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkv1001
PMC
PMC4702766
OpenAlex
W2173943232
Cited by
162
References
0
Citations by year
2026: 5 · 2025: 5 · 2024: 4 · 2023: 4 · 2022: 22 · 2021: 22 · 2020: 25 · 2019: 27 · 2018: 21 · 2017: 15 · 2016: 12
FWCI
6.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
Medical Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Keywords
mitochondrial proteome, mitochondrial targeting sequence, GFP tagging, mass spectrometry, Schizosaccharomyces pombe
MeSH terms
Animals, Cattle, Humans, Mass Spectrometry, Protein Sorting Signals, Mitochondrial Proteins, Databases, Protein, Proteomics, Green Fluorescent Proteins, Mice, Rats

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