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GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System

Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases....

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Autores principales: Chen, Chi-Wei, Huang, Lan-Ying, Liao, Chia-Feng, Chang, Kai-Po, Chu, Yen-Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660635/
https://www.ncbi.nlm.nih.gov/pubmed/33114312
http://dx.doi.org/10.3390/ijms21217891
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author Chen, Chi-Wei
Huang, Lan-Ying
Liao, Chia-Feng
Chang, Kai-Po
Chu, Yen-Wei
author_facet Chen, Chi-Wei
Huang, Lan-Ying
Liao, Chia-Feng
Chang, Kai-Po
Chu, Yen-Wei
author_sort Chen, Chi-Wei
collection PubMed
description Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases. If we can accurately predict human phosphorylation sites, this could help to solve human diseases. Therefore, we developed a kinase-specific phosphorylation prediction system, GasPhos, and proposed a new feature selection approach, called Gas, based on the ant colony system and a genetic algorithm and used performance evaluation strategies focused on different kinases to choose the best learning model. Gas uses the mean decrease Gini index (MDGI) as a heuristic value for path selection and adopts binary transformation strategies and new state transition rules. GasPhos can predict phosphorylation sites for six kinases and showed better performance than other phosphorylation prediction tools. The disease-related phosphorylated proteins that were predicted with GasPhos are also discussed. Finally, Gas can be applied to other issues that require feature selection, which could help to improve prediction performance.
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spelling pubmed-76606352020-11-13 GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System Chen, Chi-Wei Huang, Lan-Ying Liao, Chia-Feng Chang, Kai-Po Chu, Yen-Wei Int J Mol Sci Article Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases. If we can accurately predict human phosphorylation sites, this could help to solve human diseases. Therefore, we developed a kinase-specific phosphorylation prediction system, GasPhos, and proposed a new feature selection approach, called Gas, based on the ant colony system and a genetic algorithm and used performance evaluation strategies focused on different kinases to choose the best learning model. Gas uses the mean decrease Gini index (MDGI) as a heuristic value for path selection and adopts binary transformation strategies and new state transition rules. GasPhos can predict phosphorylation sites for six kinases and showed better performance than other phosphorylation prediction tools. The disease-related phosphorylated proteins that were predicted with GasPhos are also discussed. Finally, Gas can be applied to other issues that require feature selection, which could help to improve prediction performance. MDPI 2020-10-24 /pmc/articles/PMC7660635/ /pubmed/33114312 http://dx.doi.org/10.3390/ijms21217891 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chen, Chi-Wei
Huang, Lan-Ying
Liao, Chia-Feng
Chang, Kai-Po
Chu, Yen-Wei
GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title_full GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title_fullStr GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title_full_unstemmed GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title_short GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System
title_sort gasphos: protein phosphorylation site prediction using a new feature selection approach with a ga-aided ant colony system
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660635/
https://www.ncbi.nlm.nih.gov/pubmed/33114312
http://dx.doi.org/10.3390/ijms21217891
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