An evidence-based approach to identify aging-related genes in Caenorhabditis elegans

TitleAn evidence-based approach to identify aging-related genes in Caenorhabditis elegans
Publication TypeJournal Article
Year of Publication2015
AuthorsCallahan, A, Cifuentes, JJ, Dumontier, M
JournalBMC Bioinformatics
Volume16:40
Date Published02/2015
Type of ArticleResearch article
KeywordsAging, C. elegans, Data integration, Hypothesis evaluation, Lifespan, Linked data, Semantic Web, SPARQL, SPARQL inferencing notation
AbstractBackground: Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This research has generated large amounts of experimental data that is increasingly difficult to integrate and analyze with existing databases and domain knowledge. To address this challenge, we demonstrate a scalable and effective approach for automatic evidence gathering and evaluation that leverages existing experimental data and literature-curated facts to identify genes involved in aging and lifespan regulation in C. elegans. Results: We developed a semantic knowledge base for aging by integrating data about C. elegans genes from WormBase with data about 2005 human and model organism genes from GenAge and 149 genes from GenDR, and with the Bio2RDF network of linked data for the life sciences. Using HyQue (a Semantic Web tool for hypothesis-based querying and evaluation) to interrogate this knowledge base, we examined 48,231 C. elegans genes for their role in modulating lifespan and aging. HyQue identified 24 novel but well-supported candidate aging-related genes for further experimental validation. Conclusions: We use semantic technologies to discover candidate aging genes whose effects on lifespan are not yet well understood. Our customized HyQue system, the aging research knowledge base it operates over, and HyQue evaluations of all C. elegans genes are freely available at http://hyque.semanticscience.org.
URLhttp://www.biomedcentral.com/1471-2105/16/40
DOI10.1186/s12859-015-0469-4
Refereed DesignationRefereed