Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data

• Published in: Nucleic acids research 2021-01, Vol.49 (D1), p.D1251-D1258
• Main Authors: Gao, Yue, Shang, Shipeng, Guo, Shuang, Li, Xin, Zhou, Hanxiao, Liu, Hongjia, Sun, Yue, Wang, Junwei, Wang, Peng, Zhi, Hui, Li, Xia, Ning, Shangwei, Zhang, Yunpeng
• Format: Article
• Language: English
• Subjects: Apoptosis - genetics; Autophagy - genetics; Database Issue; Databases, Genetic; DNA Methylation; Drug Resistance, Neoplasm - genetics; Enhancer Elements, Genetic; Epithelial-Mesenchymal Transition - genetics; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Internet; MicroRNAs - classification; MicroRNAs - genetics; MicroRNAs - metabolism; Mutation; Neoplasms - classification; Neoplasms - drug therapy; Neoplasms - genetics; Recurrence; RNA, Circular - classification; RNA, Circular - genetics; RNA, Circular - metabolism; RNA, Long Noncoding - classification; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Neoplasm - classification; RNA, Neoplasm - genetics; RNA, Neoplasm - metabolism; Single-Cell Analysis; Software; Transcription Factors - classification; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa1006

Abstract An updated Lnc2Cancer 3.0 (http://www.bio-bigdata.net/lnc2cancer or http://bio-bigdata.hrbmu.edu.cn/lnc2cancer) database, which includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing (RNA-seq) and single-cell RNA-seq (scRNA-seq) are described. Lnc2Cancer 3.0 was updated with several new features, including (i) Increased cancer-associated lncRNA entries over the previous version. The current release includes 9254 lncRNA-cancer associations, with 2659 lncRNAs and 216 cancer subtypes. (ii) Newly adding 1049 experimentally supported circRNA-cancer associations, with 743 circRNAs and 70 cancer subtypes. (iii) Experimentally supported regulatory mechanisms of cancer-related lncRNAs and circRNAs, involving microRNAs, transcription factors (TF), genetic variants, methylation and enhancers were included. (iv) Appending experimentally supported biological functions of cancer-related lncRNAs and circRNAs including cell growth, apoptosis, autophagy, epithelial mesenchymal transformation (EMT), immunity and coding ability. (v) Experimentally supported clinical relevance of cancer-related lncRNAs and circRNAs in metastasis, recurrence, circulation, drug resistance, and prognosis was included. Additionally, two flexible online tools, including RNA-seq and scRNA-seq web tools, were developed to enable fast and customizable analysis and visualization of lncRNAs in cancers. Lnc2Cancer 3.0 is a valuable resource for elucidating the associations between lncRNA, circRNA and cancer.