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Related Experiment Video

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Experimentally Validated Plant lncRNAs in EVLncRNAs Database.

Bailing Zhou1,2, Huiying Zhao3, Jiafeng Yu1,2

  • 1Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China.

Methods in Molecular Biology (Clifton, N.J.)
|April 5, 2019
PubMed
Summary

EVLncRNAs curates experimentally validated plant long noncoding RNAs (lncRNAs) from diverse species. This database offers enhanced functional and disease information, expanding upon existing resources for plant lncRNA research.

Keywords:
DatabaseExperimentally validatedLncRNALow-throughputManually curatedPlant

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Plant long noncoding RNAs (lncRNAs) are crucial for biological processes.
  • Existing databases often lack comprehensive, experimentally validated lncRNA data, especially for plants.
  • Current resources are limited in scale and scope, focusing narrowly on specific aspects like disease or interactions.

Purpose of the Study:

  • To establish EVLncRNAs, a comprehensive database of experimentally validated plant lncRNAs.
  • To integrate data from multiple sources and include novel functional and disease-specific information.
  • To provide a user-friendly platform for accessing, searching, and submitting plant lncRNA data.

Main Methods:

  • Curating lncRNAs validated by low-throughput experiments up to May 2016.
  • Integrating data from specialized databases: lncRNAdb, LncRANDisease, Lnc2Cancer, and PLNIncRBase.
  • Supplementing data with additional functional and disease-specific information from NCBI and Ensembl.

Main Results:

  • EVLncRNAs version 1.0 contains 1543 lncRNAs from 77 species, including 428 plant lncRNAs from 44 plant species.
  • The dataset excludes lncRNAs derived from microarray and deep sequencing, focusing on low-throughput experimental validation.
  • Approximately 40% of entries in EVLncRNAs include novel interaction and additional information not previously available.

Conclusions:

  • EVLncRNAs serves as a valuable, curated resource for experimentally validated plant lncRNAs.
  • The database enhances understanding of lncRNA functions and their roles in plant biology and disease.
  • EVLncRNAs facilitates further research by providing accessible, integrated, and updated lncRNA information.