Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk

Abstract

Colon cancer is considered as a complex disease that consists of metastatic seeding in early stages. Such disease is not simply caused by the action of a single RNA, but is associated with disorders of many kinds of RNAs and their regulation relationships. Hence, it is of great significance to study the complex regulatory roles among mRNAs, miRNAs and lncRNAs for further understanding the pathogenic mechanism of colon cancer. In this study, we constructed a heterogeneous network consisting of differentially expressed mRNAs, miRNAs and lncRNAs. This contains three kinds of vertices and six types of edges. All RNAs were re-divided into three categories, which were “related”, “irrelevant” and “unlabeled”. They were processed by dynamic excitation restart random walk (RW-DIR) for identifying colon cancer-related RNAs. Ten RNAs were finally obtained related to colon cancer, which were hsa-miR-2682-5p, hsa-miR-1277-3p, ANGPTL1, SLC22A18AS, FENDRR, PHLPP2, hsa-miR-302a-5p, APCDD1, MEX3A and hsa-miR-509-3-5p. Numerical experiments have indicated that the proposed network construction framework and the following RW-DIR algorithm are effective for identifying colon cancer-related RNAs, and this kind of analysis framework can also be easily extended to other diseases, effectively narrowing the scope of biological experimental research.

LncRNA SLC7A11-AS1 promotes the progression of hepatocellular carcinoma by mediating KLF9 ubiquitination

“…PHLPP2 is a phosphatase, and massive studies have found that the expression of PHLPP2 was decreased in multi-tumors, such as oral squamous cell carcinoma, lung cancer [41,42]. A review suggested that PHLPP2 had a favorable prognosis for lung cancer, breast cancer, and colon cancer [43]. Moreover, a study published in 2018 proposed that berberine inhibited the AKT pathway to suppress HCC progression by enhancing PHLPP2 expression [23], suggesting PHLPP2 plays a suppressing role in HCC.…”