Faculty, Staff and Student Publications
Publication Date
1-7-2022
Journal
Nucleic Acids Research
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.
Keywords
Alternative Splicing, Databases, Genetic, Humans, Knowledge Bases, Neoplasms, RNA, Long Noncoding, RNA, Messenger
DOI
10.1093/nar/gkab1035
PMID
34791419
PMCID
PMC8728133
PubMedCentral® Posted Date
11-17-2021
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Included in
Bioinformatics Commons, Biomedical Informatics Commons, Data Science Commons, Oncology Commons
