title: Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma.
abstract: Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT. We found significant candidate circRNAs expression alterations between normal and tumor samples. Additionally, the PCGs associated with these candidate circRNAs were also found have discriminative expression patterns between normal and tumor samples. The enrichment analysis illustrated that these PCGs were predominantly enriched for liver/cardiovascular-related diseases such as atherosclerosis, myocardial ischemia and coronary heart disease, and participated in various metabolic processes. Together, a further network analysis indicated that these PCGs play important roles in the regulatory and the PPI network. Finally, we built a classification model to distinguish normal and tumor samples by using candidate circRNAs and their associated genes, respectively. Both of them obtained satisfactory results (~ 0.99 of AUC for circRNA and PCG). Our findings suggested that the circRNA could be a critical factor in HCC, providing a useful resource to explore the pathogenesis of HCC.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Life Science, Sichuan University, Chengdu, China.
authors.forename: Yongcheng
authors.initials: Y
authors.lastname: Dong
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Ziyan
authors.initials: Z
authors.lastname: Huang
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Qifan
authors.initials: Q
authors.lastname: Kuang
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Yiming
authors.initials: Y
authors.lastname: Wu
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Yizhou
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, China.
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
mesh_terms: D000465:Algorithms; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D012313:RNA; D000079962:RNA, Circular
chemical_list: D000079962:RNA, Circular; D012313:RNA