Liu Xinhua, Gao Ling, Peng Yonglin, Fang Zhonghai, Wang Ju
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China.
School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China.
Front Genet. 2023 Jul 11;14:1185790. doi: 10.3389/fgene.2023.1185790. eCollection 2023.
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. 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. We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.
表型相似性计算应有助于改进药物再利用。在本研究中，基于描述OMIM中所存表型的医学主题词（MeSH）术语，我们提出了一种方法，即PheSom（基于MeSH的表型相似性），来测量表型之间的相似性。PheSom计算两个表型之间重叠的MeSH术语数量，然后根据词频-逆文档频率（FIDC）考虑每个表型中每个MeSH术语的权重。与表型相关的基因用于评估我们的方法。最终获得了一个7739×7739的相似性得分矩阵，并且随着相似性得分的增加，表型对的数量显著减少。此外，随着表型之间相似性得分的增加，与表型相关基因的重叠率显著提高，这支持了我们方法的可靠性。我们预计我们的方法可应用于识别复杂疾病的新型治疗方法。
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