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Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
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deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from
Ling-Ling Zheng1, Jun-Hao Li1, Jie Wu1
1RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
Nucleic Acids Research
|November 22, 2015
Summary
The deepBase v2.0 platform offers a comprehensive resource for studying non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). It decodes their evolution, expression, and function across 19 species.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are critical regulators of cellular functions.
- A significant portion of these ncRNAs remain functionally uncharacterized, highlighting a gap in current biological understanding.
Purpose of the Study:
- To present deepBase v2.0, an updated bioinformatics platform for comprehensive analysis of ncRNA evolution, expression, and function.
- To provide extensive resources for researchers investigating diverse ncRNAs across multiple species.
Main Methods:
- Updated deepBase v2.0 database incorporating 588 small RNA sequencing (sRNA-Seq) datasets for ncRNA-derived small RNAs.
- Development of the lncSeeker pipeline for identifying high-confidence long non-coding RNAs (lncRNAs).
- Integration of expression profiling, functional genomic data, and protein-lncRNA co-expression networks via the lncFunction web-server.
Main Results:
- deepBase v2.0 now includes the most extensive collection of ncRNA-derived small RNAs.
- Identification of 176,680 high-confidence lncRNAs across 14 species, including species-specific and conserved lncRNAs.
- Annotation of 14,867 human circRNAs, with 1,260 orthologous to mouse circRNAs.
- Development of the lncFunction web-server for predicting lncRNA functions.
Conclusions:
- deepBase v2.0 serves as a valuable, updated resource for ncRNA research.
- The study provides significant insights into the evolution, expression, and functional potential of diverse ncRNAs.
- The findings are expected to accelerate experimental research and the discovery of novel ncRNA functions.
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