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Inverse Potts model improves accuracy of phylogenetic profiling
MOTIVATION: Phylogenetic profiling is a powerful computational method for revealing the functions of function-unknown genes. Although conventional similarity metrics in phylogenetic profiling achieved high prediction accuracy, they have two estimation biases: an evolutionary bias and a spurious corr...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8963296/ https://www.ncbi.nlm.nih.gov/pubmed/35060594 http://dx.doi.org/10.1093/bioinformatics/btac034 |
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author | Fukunaga, Tsukasa Iwasaki, Wataru |
author_facet | Fukunaga, Tsukasa Iwasaki, Wataru |
author_sort | Fukunaga, Tsukasa |
collection | PubMed |
description | MOTIVATION: Phylogenetic profiling is a powerful computational method for revealing the functions of function-unknown genes. Although conventional similarity metrics in phylogenetic profiling achieved high prediction accuracy, they have two estimation biases: an evolutionary bias and a spurious correlation bias. While previous studies reduced the evolutionary bias by considering a phylogenetic tree, few studies have analyzed the spurious correlation bias. RESULTS: To reduce the spurious correlation bias, we developed metrics based on the inverse Potts model (IPM) for phylogenetic profiling. We also developed a metric based on both the IPM and a phylogenetic tree. In an empirical dataset analysis, we demonstrated that these IPM-based metrics improved the prediction performance of phylogenetic profiling. In addition, we found that the integration of several metrics, including the IPM-based metrics, had superior performance to a single metric. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/fukunagatsu/Ipm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8963296 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-89632962022-03-29 Inverse Potts model improves accuracy of phylogenetic profiling Fukunaga, Tsukasa Iwasaki, Wataru Bioinformatics Original Papers MOTIVATION: Phylogenetic profiling is a powerful computational method for revealing the functions of function-unknown genes. Although conventional similarity metrics in phylogenetic profiling achieved high prediction accuracy, they have two estimation biases: an evolutionary bias and a spurious correlation bias. While previous studies reduced the evolutionary bias by considering a phylogenetic tree, few studies have analyzed the spurious correlation bias. RESULTS: To reduce the spurious correlation bias, we developed metrics based on the inverse Potts model (IPM) for phylogenetic profiling. We also developed a metric based on both the IPM and a phylogenetic tree. In an empirical dataset analysis, we demonstrated that these IPM-based metrics improved the prediction performance of phylogenetic profiling. In addition, we found that the integration of several metrics, including the IPM-based metrics, had superior performance to a single metric. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/fukunagatsu/Ipm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-01-21 /pmc/articles/PMC8963296/ /pubmed/35060594 http://dx.doi.org/10.1093/bioinformatics/btac034 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Fukunaga, Tsukasa Iwasaki, Wataru Inverse Potts model improves accuracy of phylogenetic profiling |
title | Inverse Potts model improves accuracy of phylogenetic profiling |
title_full | Inverse Potts model improves accuracy of phylogenetic profiling |
title_fullStr | Inverse Potts model improves accuracy of phylogenetic profiling |
title_full_unstemmed | Inverse Potts model improves accuracy of phylogenetic profiling |
title_short | Inverse Potts model improves accuracy of phylogenetic profiling |
title_sort | inverse potts model improves accuracy of phylogenetic profiling |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8963296/ https://www.ncbi.nlm.nih.gov/pubmed/35060594 http://dx.doi.org/10.1093/bioinformatics/btac034 |
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