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Updated: May 6, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Published on: April 30, 2011
NPInter v2.0: an updated database of ncRNA interactions
Jiao Yuan1, Wei Wu, Chaoyong Xie
1Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Sciences, Beijing 100049, China and Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
NPInter v2.0 enhances understanding of noncoding RNA (ncRNA) interactions with proteins, RNAs, and DNA. This updated database provides a comprehensive resource for exploring functional ncRNA roles in biological processes.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Noncoding RNAs (ncRNAs) play crucial roles in cellular functions, acting as regulatory elements, structural components, and parts of enzymatic complexes.
- The number of experimentally verified ncRNA interactions, particularly with proteins, has rapidly increased due to advancements in high-throughput technologies like CLIP-seq.
- Understanding these interactions is vital for deciphering gene regulation and cellular mechanisms.
Purpose of the Study:
- To update and expand the NPInter database (version 2.0) with recent experimentally verified functional interactions involving noncoding RNAs.
- To provide a comprehensive and integrated resource for researchers studying ncRNA interactions across multiple species.
- To incorporate new functionalities for data retrieval and analysis within the NPInter database.
Main Methods:
- Systematic collection and curation of ncRNA interaction data from scientific literature and related databases.
- Integration of new interaction data, expanding the database to cover 18 species and over 201,107 entries.
- Development and incorporation of a BLAST alignment search service and interaction visualization tools.
Main Results:
- NPInter v2.0 significantly increases the number of documented ncRNA interactions, offering a more extensive resource than previous versions.
- The database now includes interactions for 18 species, broadening its applicability in comparative and evolutionary studies.
- New features, including BLAST search and visualization, enhance user accessibility and data exploration capabilities.
Conclusions:
- NPInter v2.0 serves as a valuable, up-to-date resource for studying the complex world of noncoding RNA interactions.
- The enhanced database facilitates research into the functional significance of ncRNAs in various biological contexts.
- The integrated tools empower researchers to efficiently query, analyze, and visualize ncRNA interaction networks.
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