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. 2015 Feb 9;10(2):e0115692.
doi: 10.1371/journal.pone.0115692. eCollection 2015.

HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology

Yue Deng  1 , Lin Gao  2 , Bingbo Wang  2 , Xingli Guo  2
Affiliations

HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology

Yue Deng et al. PLoS One. .

Abstract

Background: Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO.

Results: HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA).

Conclusions: HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Framework of HPOSim.
Users can use HPOSim to calculate semantic similarity for HPO terms, genes and diseases. HPOSim can also be used to identify enriched HPO terms for gene set and disease set.
Figure 2
Figure 2. Example of the structure of HPO.
HPO term Abnormality of the joints of the lower limbs (HP:0100491) and all its ancestor terms are shown. Each term in the HPO describes a phenotypic abnormality. Terms are related to parent terms by “is a” relationships in the form of a directed acyclic graph. If a disease or a gene is annotated to a term, it will also be annotated to all of its ancestors.
See this image and copyright information in PMC

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