A Random Walk-Based Method to Identify Candidate Genes Associated With Lymphoma

Minjie Sheng; Haiying Cai; Qin Yang; Jing Li; Jian Zhang; Jian Zhang; Jian Zhang; Jian Zhang; Jian Zhang; Lihua Liu

doi:10.3389/fgene.2021.792754

Frontiers in Genetics (Nov 2021)

A Random Walk-Based Method to Identify Candidate Genes Associated With Lymphoma

Minjie Sheng,
Haiying Cai,
Qin Yang,
Jing Li,
Jian Zhang,
Jian Zhang,
Jian Zhang,
Jian Zhang,
Jian Zhang,
Lihua Liu

Affiliations

Minjie Sheng: Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
Haiying Cai: Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
Qin Yang: Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
Jing Li: Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
Jian Zhang: Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
Jian Zhang: Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
Jian Zhang: Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
Jian Zhang: National Clinical Research Center for Eye Diseases, Shanghai, China
Jian Zhang: Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
Lihua Liu: Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China

DOI: https://doi.org/10.3389/fgene.2021.792754
Journal volume & issue: Vol. 12

Abstract

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Lymphoma is a serious type of cancer, especially for adolescents and elder adults, although this malignancy is quite rare compared with other types of cancer. The cause of this malignancy remains ambiguous. Genetic factor is deemed to be highly associated with the initiation and progression of lymphoma, and several genes have been related to this disease. Determining the pathogeny of lymphoma by identifying the related genes is important. In this study, we presented a random walk-based method to infer the novel lymphoma-associated genes. From the reported 1,458 lymphoma-associated genes and protein–protein interaction network, raw candidate genes were mined by using the random walk with restart algorithm. The determined raw genes were further filtered by using three screening tests (i.e., permutation, linkage, and enrichment tests). These tests could control false-positive genes and screen out essential candidate genes with strong linkages to validate the lymphoma-associated genes. A total of 108 inferred genes were obtained. Analytical results indicated that some inferred genes, such as RAC3, TEC, IRAK2/3/4, PRKCE, SMAD3, BLK, TXK, PRKCQ, were associated with the initiation and progression of lymphoma.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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