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PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection

BACKGROUND: Assessment of potential allergenicity of protein is necessary whenever transgenic proteins are introduced into the food chain. Bioinformatics approaches in allergen prediction have evolved appreciably in recent years to increase sophistication and performance. However, what are the criti...

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Detalles Bibliográficos
Autores principales: Wang, Jing, Zhang, Dabing, Li, Jing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029432/
https://www.ncbi.nlm.nih.gov/pubmed/24565053
http://dx.doi.org/10.1186/1752-0509-7-S5-S9
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author Wang, Jing
Zhang, Dabing
Li, Jing
author_facet Wang, Jing
Zhang, Dabing
Li, Jing
author_sort Wang, Jing
collection PubMed
description BACKGROUND: Assessment of potential allergenicity of protein is necessary whenever transgenic proteins are introduced into the food chain. Bioinformatics approaches in allergen prediction have evolved appreciably in recent years to increase sophistication and performance. However, what are the critical features for protein's allergenicity have been not fully investigated yet. RESULTS: We presented a more comprehensive model in 128 features space for allergenic proteins prediction by integrating various properties of proteins, such as biochemical and physicochemical properties, sequential features and subcellular locations. The overall accuracy in the cross-validation reached 93.42% to 100% with our new method. Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection (IFS) procedure were applied to obtain which features are essential for allergenicity. Results of the performance comparisons showed the superior of our method to the existing methods used widely. More importantly, it was observed that the features of subcellular locations and amino acid composition played major roles in determining the allergenicity of proteins, particularly extracellular/cell surface and vacuole of the subcellular locations for wheat and soybean. To facilitate the allergen prediction, we implemented our computational method in a web application, which can be available at http://gmobl.sjtu.edu.cn/PREAL/index.php. CONCLUSIONS: Our new approach could improve the accuracy of allergen prediction. And the findings may provide novel insights for the mechanism of allergies.
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spelling pubmed-40294322014-06-17 PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection Wang, Jing Zhang, Dabing Li, Jing BMC Syst Biol Research BACKGROUND: Assessment of potential allergenicity of protein is necessary whenever transgenic proteins are introduced into the food chain. Bioinformatics approaches in allergen prediction have evolved appreciably in recent years to increase sophistication and performance. However, what are the critical features for protein's allergenicity have been not fully investigated yet. RESULTS: We presented a more comprehensive model in 128 features space for allergenic proteins prediction by integrating various properties of proteins, such as biochemical and physicochemical properties, sequential features and subcellular locations. The overall accuracy in the cross-validation reached 93.42% to 100% with our new method. Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection (IFS) procedure were applied to obtain which features are essential for allergenicity. Results of the performance comparisons showed the superior of our method to the existing methods used widely. More importantly, it was observed that the features of subcellular locations and amino acid composition played major roles in determining the allergenicity of proteins, particularly extracellular/cell surface and vacuole of the subcellular locations for wheat and soybean. To facilitate the allergen prediction, we implemented our computational method in a web application, which can be available at http://gmobl.sjtu.edu.cn/PREAL/index.php. CONCLUSIONS: Our new approach could improve the accuracy of allergen prediction. And the findings may provide novel insights for the mechanism of allergies. BioMed Central 2013-12-09 /pmc/articles/PMC4029432/ /pubmed/24565053 http://dx.doi.org/10.1186/1752-0509-7-S5-S9 Text en Copyright © 2013 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Wang, Jing
Zhang, Dabing
Li, Jing
PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title_full PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title_fullStr PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title_full_unstemmed PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title_short PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
title_sort preal: prediction of allergenic protein by maximum relevance minimum redundancy (mrmr) feature selection
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029432/
https://www.ncbi.nlm.nih.gov/pubmed/24565053
http://dx.doi.org/10.1186/1752-0509-7-S5-S9
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