Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm

International Journal of Molecular Sciences

Lei Yu¹  Siyao Liu¹  Shuyuan Wang¹  Jie Li¹  Jie Wu¹  Hui Liu¹  Li Zhang¹  Yun Xiao¹  Qian Song¹  Chaohan Xu¹  Qianqian Meng¹  Lei Yang¹  Weida Wang¹  Peng Xia¹ 

[1] College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China;

关键词: Circular RNA (circRNA);    breast cancer;    non-negative matrix factorization (NMF) algorithm;   

DOI  :  10.3390/ijms20040919

来源: DOAJ

【 摘 要 】

Circular RNA (circRNA), a kind of special endogenous RNA, has been shown to be implicated in crucial biological processes of multiple cancers as a gene regulator. However, the functional roles of circRNAs in breast cancer (BC) remain to be poorly explored, and relatively incomplete knowledge of circRNAs handles the identification and prediction of BC-related circRNAs. Towards this end, we developed a systematic approach to identify circRNA modules in the BC context through integrating circRNA, mRNA, miRNA, and pathway data based on a non-negative matrix factorization (NMF) algorithm. Thirteen circRNA modules were uncovered by our approach, containing 4164 nodes (80 circRNAs, 2703 genes, 63 miRNAs and 1318 pathways) and 67,959 edges in total. GO (Gene Ontology) function screening identified nine circRNA functional modules with 44 circRNAs. Within them, 31 circRNAs in eight modules having direct relationships with known BC-related genes, miRNAs or disease-related pathways were selected as BC candidate circRNAs. Functional enrichment results showed that they were closely related with BC-associated pathways, such as ‘KEGG (Kyoto Encyclopedia of Genes and Genomes) PATHWAYS IN CANCER’, ‘REACTOME IMMUNE SYSTEM’ and ‘KEGG MAPK SIGNALING PATHWAY’, ‘KEGG P53 SIGNALING PATHWAY’ or ‘KEGG WNT SIGNALING PATHWAY’, and could sever as potential circRNA biomarkers in BC. Comparison results showed that our approach could identify more BC-related functional circRNA modules in performance. In summary, we proposed a novel systematic approach dependent on the known disease information of mRNA, miRNA and pathway to identify BC-related circRNA modules, which could help identify BC-related circRNAs and benefits treatment and prognosis for BC patients.

【 授权许可】

Unknown