deepBase v3.0 adds ncRNAs expression profiles of exosomes

in Databases, Publications November 13, 2020

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. Researchers at Sun Yat-sen University have updated deepBase to version 3.0 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. The researchers 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, they constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. They 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.

Introduction and usage of deepBase v3.0

(A) Browse page for ncRNAs with its detailed information, expression, and evolutionary conservation pages. (B) Expression page for ncRNAs with a detailed expression profile. (C) Evolutionary conservation of lncRNAs across 14 species. (D) Prognoses associated with cancer-related lncRNAs and detailed pages containing KM-plots of corresponding ncRNAs. (E) Multiple analysis interfaces for gene, expression, and function predictions. (F) Exosome expression page and detailed information for exosome expression profiles.

Availability – deepBase v3.0 is available at: http://rna.sysu.edu.cn/deepbase3/index.html

Xie F, Liu S, Wang J, Xuan J, Zhang X, Qu L, Zheng L, Yang J. (2020) deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]