Please use this identifier to cite or link to this item: http://buratest.brunel.ac.uk/handle/2438/8093
Title: Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
Authors: Anvar, SY
Tucker, A
Vinciotti, V
Venema, A
van Ommen, G-JB
van der Maarel, SM
Raz, V
't Hoen, PAC
Keywords: Science & Technology;Life Sciences & Biomedicine;Biochemical Research Methods;Mathematical & Computational Biology;Biochemistry & Molecular Biology;Biochemical Research Methods;Mathematical & Computational Biology;Oculopharyngeal Muscular-Dystrophy Muscular-Dystrophy;Gene regulatory networks;Expression Data;Bayesian Networks;Model;Consequences;Modularity;Toxicity;Noise
Issue Date: 2011
Publisher: Public Library of Science
Citation: PLoS Computational Biology, 7(11), Article e1002258, 2011
Abstract: Gene regulatory networks give important insights into the mechanisms underlying physiology and pathophysiology. The derivation of gene regulatory networks from high-throughput expression data via machine learning strategies is problematic as the reliability of these models is often compromised by limited and highly variable samples, heterogeneity in transcript isoforms, noise, and other artifacts. Here, we develop a novel algorithm, dubbed Dandelion, in which we construct and train intraspecies Bayesian networks that are translated and assessed on independent test sets from other species in a reiterative procedure. The interspecies disease networks are subjected to multi-layers of analysis and evaluation, leading to the identification of the most consistent relationships within the network structure. In this study, we demonstrate the performance of our algorithms on datasets from animal models of oculopharyngeal muscular dystrophy (OPMD) and patient materials. We show that the interspecies network of genes coding for the proteasome provide highly accurate predictions on gene expression levels and disease phenotype. Moreover, the cross-species translation increases the stability and robustness of these networks. Unlike existing modeling approaches, our algorithms do not require assumptions on notoriously difficult one-to-one mapping of protein orthologues or alternative transcripts and can deal with missing data. We show that the identified key components of the OPMD disease network can be confirmed in an unseen and independent disease model. This study presents a state-of-the-art strategy in constructing interspecies disease networks that provide crucial information on regulatory relationships among genes, leading to better understanding of the disease molecular mechanisms.
Description: © 2011 Anvar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
URI: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002258
http://bura.brunel.ac.uk/handle/2438/8093
DOI: http://dx.doi.org/10.1371/journal.pcbi.1002258
ISSN: 1553-734X
Appears in Collections:Publications
Dept of Computer Science Research Papers

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