ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides.

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and primary microRNAs (pri-miRNAs), are recognized for their critical roles in biological functions and disease.
• Emerging evidence indicates that ncRNAs possess the capability to encode proteins or peptides, a phenomenon that expands our understanding of the "central dogma" of molecular biology.
• Information regarding ncRNA-encoded proteins and peptides is currently fragmented across numerous scientific publications, hindering comprehensive analysis and exploration by the research community.

Purpose of the Study:

• To establish a centralized, curated database named ncEP (noncoding RNA-encoded Proteins) for systematically collecting and organizing information on proteins and peptides encoded by ncRNAs.
• To provide researchers with a readily accessible and user-friendly platform for exploring experimentally validated data on ncRNA translation.
• To facilitate the study of ncRNA translation by consolidating scattered knowledge into a single, comprehensive resource.

Main Methods:

• Systematic literature review and data mining of over 2000 candidate articles to identify studies reporting experimentally validated ncRNA-encoded proteins or peptides.
• Development of the ncEP database, incorporating data on 74 proteins/peptides, 22 lncRNAs, 11 circRNAs, 9 pri-miRNAs, and 37 other ncRNAs from 18 species.
• Implementation of a user-friendly web interface for data searching, browsing, visualization, downloading, and submission.

Main Results:

• The ncEP database comprises 80 entries, detailing low-throughput experimentally validated (LTEV) proteins or peptides derived from various types of ncRNAs.
• The database covers findings from more than 50 published articles, spanning 18 different species, providing a broad scope of ncRNA translation.
• A significant portion of the entries (74 proteins/peptides) highlights the growing evidence for protein production from noncoding genetic elements.

Conclusions:

• The ncEP database serves as a valuable and relatively comprehensive repository for experimentally validated proteins and peptides encoded by ncRNAs.
• This resource significantly enhances the accessibility of crucial information on ncRNA translation, addressing the previous fragmentation of data.
• ncEP is expected to enrich the knowledge base concerning the translation of ncRNAs and support further investigations into this expanding field of molecular biology.