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CodLncScape Provides a Self-Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs
Tianyuan Liu1, Huiyuan Qiao2, Zixu Wang3
1Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba, 3058577, Japan.
Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|April 11, 2024
Summary
This study introduces codLncScape, a comprehensive framework for exploring coding long non-coding RNAs (lncRNAs). It provides a database, analysis tools, and a web platform to advance research on these functionally diverse molecules.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Recent research indicates that long non-coding RNAs (lncRNAs) can encode proteins, termed coding lncRNAs, with diverse biological functions.
- The landscape of coding lncRNAs is not well-defined due to the nascent and fragmented nature of current research.
Purpose of the Study:
- To develop a comprehensive framework, codLncScape, for exploring coding lncRNAs.
- To establish a manually curated knowledge base of experimentally validated coding lncRNAs.
- To investigate the expression, diagnostic potential, and biological associations of coding lncRNAs.
Main Methods:
- Creation of codLncDB, a manually compiled knowledge base of 353 experimentally validated coding lncRNA entries.
- Development of codLncFlow for analyzing expression characteristics and diagnostic potential in pan-cancer and spermatogenesis contexts.
- Implementation of codLncWeb as a platform for accessing coding lncRNA knowledge.
- Utilization of codLncNLP for knowledge mining and database updates.
Main Results:
- codLncDB successfully compiles 353 experimentally validated coding lncRNA entries.
- codLncFlow reveals expression patterns and diagnostic potential of coding lncRNAs in pan-cancer and spermatogenesis.
- codLncWeb provides a user-friendly platform for accessing coding lncRNA information.
- codLncNLP facilitates efficient knowledge mining and database enrichment.
Conclusions:
- codLncScape offers a robust ecosystem for coding lncRNA research.
- The framework aims to accelerate systematic investigation and understanding of coding lncRNAs.
- This integrated approach supports the advancement of knowledge in the field of coding lncRNAs.
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