亚基因本体功能分析工具（Sub-GOFA）：一种利用语义（逻辑）相似性对克隆镶嵌现象进行亚基因本体功能分析的工具。

Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity.

作者信息

Katsuda Tadaaki, Sato Noriko, Mogushi Kaoru, Hase Takeshi, Muramatsu Masaaki

机构信息

Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 24F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.

Institute of Education, Tokyo Medical and Dental University, 20F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.

出版信息

Bioinformation. 2022 Jan 31;18(1):53-60. doi: 10.6026/97320630018053. eCollection 2022.

DOI:10.6026/97320630018053

PMID:35815201

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9200605/

Abstract

Clonal mosaicism (a detectable post-zygotic mutational event in cellular subpopulations) is common in cancer patients. Detected segments of clonal mosaicism are usually bundled into large-locus regions for statistical analysis. However, low-frequency genes are overlooked and are not sufficient to elucidate qualitative differences between cancer patients and non-patients. Therefore, it is of interest to develop and describe a tool named Sub-GOFA for Sub-Gene Ontology function analysis in clonal mosaicism using semantic similarity. Sub-GOFA measures the semantic (logical) similarity among patients using the sub-GO network structures of various sizes segmented from the gene ontology (GO) for clustering analysis. The sub-GO's root-terms with significant differences are extracted as disease-associated genetic functions. Sub-GOFA selected a high ratio of cancer-associated genes under validation with acceptable threshold.

摘要

克隆镶嵌现象（细胞亚群中可检测到的合子后突变事件）在癌症患者中很常见。检测到的克隆镶嵌片段通常被捆绑到大型基因座区域进行统计分析。然而，低频基因被忽视了，并且不足以阐明癌症患者与非患者之间的质性差异。因此，开发并描述一种名为Sub-GOFA的工具用于使用语义相似性对克隆镶嵌现象进行亚基因本体功能分析很有意义。Sub-GOFA使用从基因本体（GO）中分割出的各种大小的亚GO网络结构来测量患者之间的语义（逻辑）相似性，以进行聚类分析。具有显著差异的亚GO根术语被提取为疾病相关的遗传功能。在可接受的阈值验证下，Sub-GOFA选择了高比例的癌症相关基因。