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lncSLdb: a resource for long non-coding RNA subcellular localization.

Xiao Wen1, Lin Gao1, Xingli Guo1

  • 1School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China.

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|September 17, 2018
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Summary
This summary is machine-generated.

Researchers developed lncSLdb, a database for long non-coding RNA (lncRNA) subcellular localization. This resource aids in understanding lncRNA functions and molecular mechanisms through location data.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Long non-coding RNAs (lncRNAs) are crucial for cellular functions, but their roles remain largely unknown.
  • Subcellular localization of lncRNAs offers insights into their specific functions and biological processes.
  • Characterizing thousands of lncRNAs requires efficient tools for managing and analyzing localization data.

Purpose of the Study:

  • To develop a comprehensive, database-driven application for storing and managing lncRNA subcellular localization data.
  • To provide researchers with a platform for functional characterization of lncRNAs based on their location.
  • To facilitate the investigation of lncRNA functions and molecular mechanisms through subcellular localization.

Main Methods:

  • Literature mining to collect qualitative and quantitative subcellular localization information for lncRNAs.
  • Development of a database-driven application (lncSLdb) for data storage and management.
  • Classification of lncRNA transcripts into basic and subtype localization categories (nucleus, cytoplasm, nucleus/cytoplasm, chromosome, nucleoplasm, ribosome).

Main Results:

  • The lncSLdb currently contains over 11,000 transcripts from three species.
  • lncRNAs are classified into nucleus, cytoplasm, and nucleus/cytoplasm localization types, with subtypes for chromosome, nucleoplasm, and ribosome.
  • The system offers browsing, downloading, and advanced search functionalities (gene symbols, genome coordinates, sequence similarity).

Conclusions:

  • lncSLdb serves as a valuable and convenient platform for researchers studying lncRNA functions.
  • The database aids in understanding the molecular mechanisms of lncRNAs by leveraging subcellular localization data.
  • This resource supports the functional characterization of a large number of lncRNAs.