lncipedia

is a Data Source.

LncIPedia is a comprehensive public database for human long non-coding RNA (lncRNA) sequences and annotations, containing manually curated literature and detailed transcript information.

Domains

genomics, literature

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Homepage

lncipedia

Repository

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Infores ID

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FAIRsharing ID

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Product Summary

Publications

Preferred

Products

From this Resource
ID Name URL Category Format Description
lncipedia.search LncIPedia Search search GraphicalInterface http Web interface for searching and brows...
lncipedia.downloads LncIPedia Downloads download Product fasta Downloadable database files in FASTA,...
lncipedia.trackhub LncIPedia UCSC Trackhub hub.txt GraphicalInterface ❔ UCSC Genome Browser trackhub for dire...
lncipedia.igv LncIPedia IGV Integration download#anchor-igv Product http Integration files for Integrative Gen...
lncipedia.metadata LncIPedia Metadata download#anchor-metadata Product tsv Metadata files including locus conser...
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Details

LncIPedia

Overview

LncIPedia is a comprehensive public database for human long non-coding RNA (lncRNA) sequences and annotations. The database integrates lncRNA transcript data from multiple sources and provides manually curated literature associations, making it a valuable reference resource for lncRNA research.

Data Content

Current release (version 5.2, August 2018) contains:

  • 127,802 transcripts (107,039 in high-confidence set)
  • 56,946 genes (49,372 in high-confidence set)
  • 2,482 manually curated lncRNA articles with gene-specific annotations

The database provides:

  • Complete sequence information in FASTA format
  • Genomic annotations in GFF and BED formats
  • Both full database and high-confidence subset (excluding putative protein-coding genes)
  • Coverage for GRCh37/hg19 and GRCh38/hg38 genome assemblies

Key Features

  • Comprehensive Coverage: Aggregates lncRNA data from multiple sources into a unified resource
  • Literature Curation: Manual curation of publications describing lncRNA function and biology
  • Cross-species Conservation: Locus conservation data for chimpanzee, mouse, Drosophila, and zebrafish
  • Database Cross-references: Conversion tables to Ensembl and RefSeq identifiers
  • Version Tracking: Conversion tables between LncIPedia versions for maintaining consistent identifiers

Access Methods

  • Web Search Interface: Interactive search and browse functionality
  • Bulk Downloads: Complete database exports in multiple formats (FASTA, GFF, BED)
  • Custom Exports: User-defined data subsets via the search interface
  • Genome Browser Integration: UCSC Genome Browser trackhub and IGV visualization support
  • FTP Archive: Historical versions available for reproducible research

Visualization Tools

  • UCSC Genome Browser Trackhub: Direct integration for viewing lncRNA annotations in genome context
  • IGV Integration: Pre-configured files for the Integrative Genomics Viewer
  • BED Format Files: Compatible with standard genome visualization tools

Use Cases

  • Identifying and characterizing novel lncRNAs
  • Literature mining for lncRNA functional information
  • Comparative genomics of lncRNA loci across species
  • Integrating lncRNA annotations into genomic analyses
  • Training datasets for lncRNA prediction and classification methods
  • Reference annotations for transcriptome studies

Data Organization

  • Full Database: Complete set of all lncRNA transcripts
  • High Confidence Set: Curated subset excluding putative protein-coding genes
  • Metadata Files: Conservation data and identifier mappings
  • Multiple Genome Builds: Parallel annotations for hg19 and hg38

Management

LncIPedia is developed and maintained by researchers at:

  • Ghent University
  • VIB (Vlaams Instituut voor Biotechnologie / Flanders Institute for Biotechnology)

Licensing

LncIPedia download files are for non-commercial use only. Commercial use requires written approval from Ghent University.

Citation

If using LncIPedia, cite: Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. “LncIPedia 5: towards a reference set of human long non-coding RNAs.” Nucleic Acids Research. 2019. PMID:30371849

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Created: October 30, 2025 | Last modified: October 30, 2025