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The NPInter v5.0 database now contains over 2.5 million noncoding RNA interactions, doubling its previous size. This update significantly expands RNA-DNA interactions and includes new data on viral RNA interactions and RNA-binding proteins.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Noncoding RNAs (ncRNAs) are crucial regulators of biological processes through biomolecular interactions.
  • Advancements in high-throughput sequencing have generated extensive data on ncRNA interactions.

Purpose of the Study:

  • To update and expand the NPInter database (version 5.0) with comprehensive ncRNA interaction data.
  • To provide a centralized resource for researchers studying ncRNA interactions.

Main Methods:

  • Manual literature mining and high-throughput data processing to curate ncRNA interactions.
  • Integration of global RNA-DNA interactions from iMARGI, ChAR-seq, and GRID-seq datasets.
  • Inclusion of SARS-CoV-2 host-virus RNA interactions and lncRNA expression specificity from scRNA-seq data.

Main Results:

  • The NPInter database now houses 2,596,695 ncRNA interaction entries, a significant increase from the previous version.
  • RNA-DNA interactions expanded from 888,915 to 8,329,382.
  • A new RBP module was introduced to detail RNA-binding protein interactions.

Conclusions:

  • NPInter v5.0 offers a vastly expanded and informative resource for ncRNA interactions.
  • The updated database facilitates research into ncRNA functions, including viral interactions and cell-type specific expression.
  • The inclusion of RNA-binding protein data enhances the utility for studying gene regulation.