LncBook

LncBook is a comprehensive resource for human long non-coding RNAs (lncRNAs) that provides high-quality annotations at multiple omics levels. It is maintained by the National Genomics Data Center (NGDC) at the China National Center for Bioinformation.

Database Contents

LncBook accommodates a comprehensive, high-quality collection of 95,243 human lncRNA genes and 323,950 lncRNA transcripts. These lncRNAs are integrated from five major resources: RefLnc, GENCODE v33, CHESS v2.2, FANTOM-CAT, and BIGTranscriptome. The database applies strict quality control measures, removing transcripts with redundancy, background noise, mapping errors, as well as pseudogenes, small RNAs, and miRNA precursors. Coding potential is estimated using four algorithms (CPC2, LGC, CPAT, and PLEK), with transcripts identified as lncRNAs by at least three algorithms retained.

Multi-omics Annotations

LncBook provides comprehensive annotations at different omics levels:

Evolutionary Conservation

• Conservation features characterized across 40 vertebrates
• 139,306 homologous genes identified for 22,347 human lncRNA genes
• Gene age classification from human-specific to Euteleostomi

Genome Variation

• 959,138 disease/trait-associated variants
• Variants from COSMIC (confirmed somatic mutations), ClinVar (pathogenic/benign variants), and GWAS Catalog
• Associations with 50,165 lncRNA genes

DNA Methylation

• Profiles across 16 diseases: 14 cancers and 2 neurodevelopmental disorders
• Data from TCGA and GEO
• 19,543 featured lncRNA genes with differential methylation in promoter or body regions

Expression Profiles

• Expression data across 337 biological conditions
• Organized into 9 biological contexts: normal tissue/cell line, organ development, preimplantation embryo, cell differentiation, subcellular localization, exosome, cancer cell line, virus infection, and circadian rhythm
• 24,157 featured lncRNA genes (specifically/consistently/differentially/dynamically/periodically expressed)
• Data from LncExpDB covering gene expression capacity and tissue/cell specificity

Small Proteins

• 34,012 small proteins encoded by lncRNAs
• Identified from 5,743 lncRNA genes
• Supported by Ribo-seq or mass spectrometry evidence from SmProt

Molecular Interactions

• 772,745 lncRNA-protein interactions identified for 2,005 lncRNA genes
• Based on 848,077 RNA Binding Protein (RBP) binding sites from ENCODE (150 RBPs in HepG2 and K562 cell lines)
• 146,092,274 predicted lncRNA-miRNA interactions
• Predictions from three tools: miRanda, TargetScan, and RNAhybrid

Tools and Features

LncBook provides several useful tools for lncRNA analysis:

1. ID Conversion Tool: Convert identifiers across 14 different resources
2. BLAST Search: Sequence similarity search using NCBI BLAST+
3. Classification Tool: Annotate genomic locations of lncRNAs
4. LGC Tool: Predict coding potential using the LGC algorithm based on feature relationships

Data Organization

The database is gene-centric with user-friendly web interfaces. Each lncRNA gene has a dedicated web page with nine sections: gene summary, transcript information, coding potential, conservation, variation, methylation, expression, small protein, and interaction. The database allows interactive visualization and customized comparisons across different omics features. All data and figures are freely downloadable.

Integration with Related Resources

LncBook works in close partnership with:

• LncExpDB: Expression database of human long non-coding RNAs
• LncRNAWiki: Knowledgebase with literature curation results
• RNAcentral: International database of non-coding RNA sequences (LncBook data is integrated into RNAcentral)

Latest Updates

Version 2.1 (September 2024):

• Integrated newly identified lncRNAs from 10 expert databases
• Identified full-length lncRNA transcripts using 94 PacBio long-read RNA sequencing datasets
• Expanded from 323,950 to 526,318 lncRNA transcripts
• Note: v2.1 is ongoing and unstable; v2.0 is recommended for analysis

Version 2.0 (June 2022):

• Incorporated 119,722 new transcripts and 9,632 new genes
• Updated gene structure for 21,305 lncRNAs
• Added conservation features across 40 vertebrates
• Integrated small protein annotations
• Expanded expression profiles to 9 biological contexts
• Increased disease types for methylation profiles from 9 to 16
• Enhanced interaction predictions and annotations