한빛사 논문
Mengyuan Yang1,2,3,*,†, Huifen Lu1,2,†, Jiajia Liu3,4, Sijia Wu5, Pora Kim3,* and Xiaobo Zhou3,6,7,*
1West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China, 2Med-X Center for Informatics, Sichuan University, Chengdu 610041, China, 3Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, 4College of Electronic and Information Engineering, Tongji University, Shanghai, Shanghai 201804, China, 5School of Life Sciences and Technology, Xidian University, Xi’an 710126, China, 6McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA and 7School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
*To whom correspondence should be addressed. Correspondence may also be addressed to Pora Kim. Correspondence may also be addressed to Mengyuan Yang.
†The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
Abstract
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3′-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
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