CAMIRADA: Cancer microRNA association discovery algorithm, a case study on breast cancer

• Published in: Journal of biomedical informatics Vol. 94; p. 103180
• Main Authors: Shamsizadeh, Sepideh, Goliaei, Sama, Razaghi Moghadam, Zahra
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2019
• Subjects: Co-expression network; Differentially expressed gene; Diseases gene; microRNAs; Transcription factors; microRNAs; Transcription factors; Differentially expressed gene; Diseases gene; Co-expression network
• ISSN: 1532-0464; 1532-0480
• DOI: 10.1016/j.jbi.2019.103180

[Display omitted] •microRNA can be used as biomarkers for early diagnosis and treatment of cancer.•Determining which microRNA is associated with which cancer is a big challenge.•CAMIRADA is a new computational framework which find the relationship between microRNAs and cancer and it ranked microRNAs.•CAMIRADA showed TFs and DEGs influence to identify microRNAs related to breast cancer.•CAMIRADA predicted eight novel microRNAs associated to breast cancer. In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes and a gene may regulate several microRNAs, so determining which microRNA is associated with which cancer is a big challenge. Many computational methods have been performed to detect micoRNAs association with cancer, but more effort is needed with higher accuracy. Increasing research has shown that relationship between microRNAs and TFs play a significant role in the diagnosis of cancer. Therefore, we developed a new computational framework (CAMIRADA) to identify cancer-related microRNAs based on the relationship between microRNAs and disease genes (DG) in the protein network, the functional relationships between microRNAs and Transcription Factors (TF) on the co-expression network, and the relationship between microRNAs and the Differential Expression Gene (DEG) on co-expression network. The CAMIRADA was applied to assess breast cancer data from two HMDD and miR2Disease databases. In this study, the AUC for the 65 microRNAs of the top of the list was 0.95, which was more accurate than the similar methods used to detect microRNAs associated with the cancer artery.