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. 2023 Jul 11:14:1185790.
doi: 10.3389/fgene.2023.1185790. eCollection 2023.

PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary

Xinhua Liu  1   2 , Ling Gao  1 , Yonglin Peng  3 , Zhonghai Fang  2 , Ju Wang  2
Affiliations

PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary

Xinhua Liu et al. Front Genet. .

Abstract

Background: Phenotype similarity calculation should be used to help improve drug repurposing. In this study, based on the MeSH terms describing the phenotypes deposited in OMIM, we proposed a method, namely, PheSom (Phenotype Similarity On MeSH), to measure the similarity between phenotypes. PheSom counted the number of overlapping MeSH terms between two phenotypes and then took the weight of every MeSH term within each phenotype into account according to the term frequency-inverse document frequency (FIDC). Phenotype-related genes were used for the evaluation of our method. Results: A 7,739 × 7,739 similarity score matrix was finally obtained and the number of phenotype pairs was dramatically decreased with the increase of similarity score. Besides, the overlapping rates of phenotype-related genes were remarkably increased with the increase of similarity score between phenotypes, which supports the reliability of our method. Conclusion: We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.

Keywords: FIDC; OMIM; mesh; phenotype; similarity score.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Flow chart of this study.
FIGURE 2
FIGURE 2
Number of phenotype pairs within different similarity score bins in VOR (A) and VW (B) methods.
FIGURE 3
FIGURE 3
The overlapping rates of phenotypes-related genes within different similarity score bins in VOR (A) and VM (B) methods. Blue histograms and red lines represented VOR/VW methods and random gene assignment processes, respectively.
FIGURE 4
FIGURE 4
Phenotype comparison results of breast cancer. (A) Distribution of similarity scores calculated by VW, VOR, Phenosim, Renisk, et al., and Jiang and Conrath (1997), between breast cancer and the 658 phenotypes that had similarity scores greater than 0 obtained through the VW method. (B) Venn diagram depicting overlaps of phenotypes that had similarity scores with breast cancer greater than 0 in all the five methods. (C) Venn diagram depicting overlaps of phenotypes that had similarity scores with breast cancer greater than 0.2 in all the five methods.
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