NPInter v5.0: ncRNA interaction database in a new era.

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.