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Artículo

A Factor Graph Approach to Automated GO Annotation

Spetale, Flavio EzequielIcon ; Krsticevic, Flavia JorgelinaIcon ; Roda, FernandoIcon ; Bulacio, Pilar Estela
Fecha de publicación: 01/2016
Editorial: Public Library of Science
Revista: Plos One
e-ISSN: 1932-6203
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Ciencias de la Computación

Resumen

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.
Palabras clave: Graph , Gene Ontology , Svm , Algorithm
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/43947
DOI: http://dx.doi.org/10.1371/journal.pone.0146986
URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146986
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Articulos de CENTRO INT.FRANCO ARG.D/CS D/L/INF.Y SISTEM.
Citación
Spetale, Flavio Ezequiel; Krsticevic, Flavia Jorgelina; Roda, Fernando; Bulacio, Pilar Estela; A Factor Graph Approach to Automated GO Annotation; Public Library of Science; Plos One; 11; 1; 1-2016; 1-16; e0146986
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