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DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.
Dimitra Karagkouni1,2,3, Maria D Paraskevopoulou1,2, Spyros Tastsoglou1,2
1DIANA-Lab, Department of Electrical and Computer Engineering, Univ. of Thessaly, 38221 Volos, Greece.
Nucleic Acids Research
|November 17, 2019
Summary
DIANA-LncBase v3.0 is a comprehensive database of microRNA (miRNA) targets on long non-coding RNAs (lncRNAs), featuring over half a million experimentally validated interactions. This updated resource offers new visualization tools and data on lncRNA expression, advancing non-coding RNA research.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- MicroRNAs (miRNAs) regulate gene expression by targeting messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs).
- Understanding miRNA-lncRNA interactions is crucial for deciphering complex regulatory networks and cellular functions.
- Existing databases often lack comprehensive, experimentally validated data on miRNA-lncRNA interactions across diverse cell types and tissues.
Purpose of the Study:
- To present DIANA-LncBase v3.0, an updated and expanded reference repository of experimentally supported miRNA targets on lncRNAs.
- To incorporate novel functionalities, including advanced data analysis tools and visualization of miRNA-lncRNA interactions and lncRNA expression profiles.
- To provide a valuable resource for researchers investigating the roles of non-coding RNAs in biological processes.
Main Methods:
- Manual curation of scientific literature and analysis of over 300 high-throughput datasets.
- Application of a microCLIP framework, a CLIP-Seq-guided algorithm, to analyze 236 AGO-CLIP-Seq libraries.
- Integration of 14 experimental methodologies across 243 distinct human and mouse cell types and tissues.
Main Results:
- DIANA-LncBase v3.0 contains approximately half a million entries, representing ~240,000 unique tissue and cell type-specific miRNA-lncRNA pairs.
- Catalogued ~370,000 miRNA binding events, with a significant portion derived from AGO-CLIP data, indicating high confidence.
- Introduced new features, including short variant information for over 67,000 target sites and lncRNA expression profiles in various cellular compartments.
Conclusions:
- DIANA-LncBase v3.0 is a significantly enhanced resource for studying miRNA-lncRNA interactions, offering a vast collection of validated data.
- The database's new functionalities, particularly interactive visualizations, provide novel insights into lncRNA functions and regulatory mechanisms.
- This updated repository serves as a critical asset for advancing non-coding RNA research and understanding their roles in health and disease.
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