1. deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
- Author
-
Jian-Hua Yang, Jun-Hao Wang, Fangzhou Xie, Xiao-Qin Zhang, Jiajia Xuan, Ling-Ling Zheng, Liang-Hu Qu, and Shu-Rong Liu
- Subjects
RNA, Untranslated ,AcademicSubjects/SCI00010 ,Gene regulatory network ,RNA-Seq ,Computational biology ,Biology ,Exosomes ,Genome ,Deep sequencing ,User-Computer Interface ,03 medical and health sciences ,0302 clinical medicine ,RNA, Transfer ,Circular RNA ,microRNA ,Genetics ,Database Issue ,Animals ,Humans ,Gene Regulatory Networks ,Small nucleolar RNA ,030304 developmental biology ,0303 health sciences ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Prognosis ,Gene expression profiling ,Gene Expression Regulation ,Databases, Nucleic Acid ,030217 neurology & neurosurgery - Abstract
Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.
- Published
- 2020