AUTHOR=Yan Huan , Chai Hua , Zhao Huiying 

TITLE=Detecting lncRNA–Cancer Associations by Combining miRNAs, Genes, and Prognosis With Matrix Factorization

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.639872

DOI=10.3389/fgene.2021.639872

ISSN=1664-8021

ABSTRACT=Motivation: Long non-coding RNAs (lncRNAs) play important roles in cancer development. Predic-tion of lncRNA-cancer association is necessary for efficiently discovering biomarkers and designing treatment for cancers. Currently, several methods have been developed to predict lncRNA-cancer associations. However, most of them do not consider the relationships between lncRNA with other molecules and with cancer prognosis, which has limited the accuracy of the prediction. 

Method: Here, we constructed relationship matrices between 1679 lncRNAs, 2759 miRNAs, 16410 genes and cancer prognosis on three types of cancers (breast, lung and colorectal cancers) to predict lncRNA-cancer associations. The matrices were iteratively reconstructed by matrix factorization to optimize low-rank size. This method is called DRACA (Detecting lncRNA Cancer Association).
Results: Application of this method in prediction of lncRNAs-breast cancer, lncRNA-lung cancer, and lncRNA-colorectal cancer associations achieved AUC 0.810, 0.796, and 0.795, respectively by ten-fold cross validations. The performances of DRACA in predicting associations between lncRNAs with three kinds of cancers were at least 6.6%, 7.2%, and 6.9% better than other methods, respectively. To our knowledge, this is the first method employing cancer prognosis in prediction of lncRNA-cancer associations. When removing the relationships between cancer prognosis and genes, the AUCs were decreased 7.2%, 0.6%, and 5.0% for breast, lung, and colorectal cancers, respectively. Moreover, the predicted lncRNAs were found with greater numbers of somatic mutations than the lncRNAs not predicted as cancer associated for three types of cancers. DRACA predicted many novel lncRNAs, whose expressions were found related to survival rates of patients.