Table 1.
Comparison of HPOSim and other HPO-based tools.
Figure 1.
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.
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.
Table 2.
Gene modules of the aging network.
Table 3.
Top 10 enriched HPO terms by the NOA method and hypergeometric enrichment.
Table 4.
Disease modules of the cancer entries in OMIM.