Discovering New Gene Functionalities from Random Perturbations of Known Gene Ontological Annotations

Giacomo Domeniconi, Marco Masseroli, Gianluca Moro, Pietro Pinoli

2014

Abstract

Genomic annotations describing functional features of genes and proteins through controlled terminologies and ontologies are extremely valuable, especially for computational analyses aimed at inferring new biomedical knowledge. Thanks to the biology revolution led by the introduction of the novel DNA sequencing technologies, several repositories of such annotations have becoming available in the last decade; among them, the ones including Gene Ontology annotations are the most relevant. Nevertheless, the available set of genomic annotations is incomplete, and only some of the available annotations represent highly reliable human curated information. In this paper we propose a novel representation of the annotation discovery problem, so as to enable applying supervised algorithms to predict Gene Ontology annotations of different organism genes. In order to use supervised algorithms despite labeled data to train the prediction model are not available, we propose a random perturbation method of the training set, which creates a new annotation matrix to be used to train the model to recognize new annotations. We tested the effectiveness of our approach on nine Gene Ontology annotation datasets. Obtained results demonstrated that our technique is able to improve novel annotation predictions with respect to state of the art unsupervised methods.

Paper Citation

in Harvard Style

Domeniconi G., Masseroli M., Moro G. and Pinoli P. (2014). Discovering New Gene Functionalities from Random Perturbations of Known Gene Ontological Annotations . In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2014) ISBN 978-989-758-048-2, pages 107-116. DOI: 10.5220/0005087801070116

in Bibtex Style

@conference{kdir14,
author={Giacomo Domeniconi and Marco Masseroli and Gianluca Moro and Pietro Pinoli},
title={Discovering New Gene Functionalities from Random Perturbations of Known Gene Ontological Annotations},
booktitle={Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2014)},
year={2014},
pages={107-116},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005087801070116},
isbn={978-989-758-048-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2014)
TI - Discovering New Gene Functionalities from Random Perturbations of Known Gene Ontological Annotations
SN - 978-989-758-048-2
AU - Domeniconi G.
AU - Masseroli M.
AU - Moro G.
AU - Pinoli P.
PY - 2014
SP - 107
EP - 116
DO - 10.5220/0005087801070116