title: DOSim: an R package for similarity between diseases based on Disease Ontology.
abstract: BACKGROUND
  The construction of the Disease Ontology (DO) has helped promote the investigation of diseases and disease risk factors. DO enables researchers to analyse disease similarity by adopting semantic similarity measures, and has expanded our understanding of the relationships between different diseases and to classify them. Simultaneously, similarities between genes can also be analysed by their associations with similar diseases. As a result, disease heterogeneity is better understood and insights into the molecular pathogenesis of similar diseases have been gained. However, bioinformatics tools that provide easy and straight forward ways to use DO to study disease and gene similarity simultaneously are required.
  
  
  RESULTS
  We have developed an R-based software package (DOSim) to compute the similarity between diseases and to measure the similarity between human genes in terms of diseases. DOSim incorporates a DO-based enrichment analysis function that can be used to explore the disease feature of an independent gene set. A multilayered enrichment analysis (GO and KEGG annotation) annotation function that helps users explore the biological meaning implied in a newly detected gene module is also part of the DOSim package. We used the disease similarity application to demonstrate the relationship between 128 different DO cancer terms. The hierarchical clustering of these 128 different cancers showed modular characteristics. In another case study, we used the gene similarity application on 361 obesity-related genes. The results revealed the complex pathogenesis of obesity. In addition, the gene module detection and gene module multilayered annotation functions in DOSim when applied on these 361 obesity-related genes helped extend our understanding of the complex pathogenesis of obesity risk phenotypes and the heterogeneity of obesity-related diseases.
  
  
  CONCLUSIONS
  DOSim can be used to detect disease-driven gene modules, and to annotate the modules for functions and pathways. The DOSim package can also be used to visualise DO structure. DOSim can reflect the modular characteristic of disease related genes and promote our understanding of the complex pathogenesis of diseases. DOSim is available on the Comprehensive R Archive Network (CRAN) or http://bioinfo.hrbmu.edu.cn/dosim.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Li
authors.forename: Binsheng
authors.initials: B
authors.lastname: Gong
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Chao
authors.initials: C
authors.lastname: Wu
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
authors.forename: Shaoqi
authors.initials: S
authors.lastname: Rao
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D009765:Obesity / Q000235:genetics; D012660:Semantics; D012984:Software; D018875:Vocabulary, Controlled