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Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691668/ https://www.ncbi.nlm.nih.gov/pubmed/23531338 http://dx.doi.org/10.1186/1748-7188-8-10 |
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author | Kourmpetis, Yiannis AI van Dijk, Aalt DJ ter Braak, Cajo JF |
author_facet | Kourmpetis, Yiannis AI van Dijk, Aalt DJ ter Braak, Cajo JF |
author_sort | Kourmpetis, Yiannis AI |
collection | PubMed |
description | Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one. We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project. |
format | Online Article Text |
id | pubmed-3691668 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36916682013-06-28 Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes Kourmpetis, Yiannis AI van Dijk, Aalt DJ ter Braak, Cajo JF Algorithms Mol Biol Research Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one. We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project. BioMed Central 2013-03-27 /pmc/articles/PMC3691668/ /pubmed/23531338 http://dx.doi.org/10.1186/1748-7188-8-10 Text en Copyright © 2013 Kourmpetis 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. |
spellingShingle | Research Kourmpetis, Yiannis AI van Dijk, Aalt DJ ter Braak, Cajo JF Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title | Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title_full | Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title_fullStr | Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title_full_unstemmed | Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title_short | Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes |
title_sort | gene ontology consistent protein function prediction: the falcon algorithm applied to six eukaryotic genomes |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691668/ https://www.ncbi.nlm.nih.gov/pubmed/23531338 http://dx.doi.org/10.1186/1748-7188-8-10 |
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