DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

ABSTRACT

SUMMARY: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported. AVAILABILITY AND IMPLEMENTATION DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http//www.bioconductor.org/packages/release/bioc/html/DOSE.html). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT gcyu@connect.hku.hk or tqyhe@jnu.edu.cn.