High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE.
24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA. Only a tiny subset was functionally evaluated with certainty so far, while the pathogenicity of the vast majority was only assessed in-silico by software predictors. Since these tools pro...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-06-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005628&type=printable |
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| author | Stefano Castellana Caterina Fusilli Gianluigi Mazzoccoli Tommaso Biagini Daniele Capocefalo Massimo Carella Angelo Luigi Vescovi Tommaso Mazza |
| author_facet | Stefano Castellana Caterina Fusilli Gianluigi Mazzoccoli Tommaso Biagini Daniele Capocefalo Massimo Carella Angelo Luigi Vescovi Tommaso Mazza |
| author_sort | Stefano Castellana |
| collection | DOAJ |
| description | 24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA. Only a tiny subset was functionally evaluated with certainty so far, while the pathogenicity of the vast majority was only assessed in-silico by software predictors. Since these tools proved to be rather incongruent, we have designed and implemented APOGEE, a machine-learning algorithm that outperforms all existing prediction methods in estimating the harmfulness of mitochondrial non-synonymous genome variations. We provide a detailed description of the underlying algorithm, of the selected and manually curated training and test sets of variants, as well as of its classification ability. |
| format | Article |
| id | doaj-art-1e27cf97c79e44cc84c7c1abe13134fd |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2017-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-1e27cf97c79e44cc84c7c1abe13134fd2025-08-20T02:03:47ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582017-06-01136e100562810.1371/journal.pcbi.1005628High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE.Stefano CastellanaCaterina FusilliGianluigi MazzoccoliTommaso BiaginiDaniele CapocefaloMassimo CarellaAngelo Luigi VescoviTommaso Mazza24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA. Only a tiny subset was functionally evaluated with certainty so far, while the pathogenicity of the vast majority was only assessed in-silico by software predictors. Since these tools proved to be rather incongruent, we have designed and implemented APOGEE, a machine-learning algorithm that outperforms all existing prediction methods in estimating the harmfulness of mitochondrial non-synonymous genome variations. We provide a detailed description of the underlying algorithm, of the selected and manually curated training and test sets of variants, as well as of its classification ability.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005628&type=printable |
| spellingShingle | Stefano Castellana Caterina Fusilli Gianluigi Mazzoccoli Tommaso Biagini Daniele Capocefalo Massimo Carella Angelo Luigi Vescovi Tommaso Mazza High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. PLoS Computational Biology |
| title | High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. |
| title_full | High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. |
| title_fullStr | High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. |
| title_full_unstemmed | High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. |
| title_short | High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. |
| title_sort | high confidence assessment of functional impact of human mitochondrial non synonymous genome variations by apogee |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005628&type=printable |
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