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

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

doi:10.6026/97320630018053

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

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

Authors

Tadaaki Katsuda¹, Noriko Sato¹, Kaoru Mogushi^{2

3}, Takeshi Hase^{2

3

4

5}, Masaaki Muramatsu¹

Affiliations

¹ 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.
² Institute of Education, Tokyo Medical and Dental University, 20F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
³ Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan.
⁴ The Systems Biology Institute, SaiseiIkedayama Bldg. 5-10-25 Higashi Gotanda Shinagawa, Tokyo, 141-0022, Japan.
⁵ SBX BioSciences, Inc, 1600 - 925 West Georgia Street, Vancouver, BC V6C 3L2, Canada.

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.

Keywords: Sub-GOFA; clonal mosaicism; function; logical; semantic; similarity; sub-gene ontology; tool.