lncRNAKB

lncRNAKB provides an integrated knowledgebase of 77,199 human long non-coding RNAs (224,286 transcripts) to support investigation of tissue-specific expression, genetic regulation, functional inference, phylogenetic conservation, and trait associations.

Key Features:

• Integration of annotations: Systematic integration of annotations from six independent databases yielding a consolidated set of 77,199 lncRNAs and 224,286 transcripts.
• RNA-seq expression profiles: Expression patterns derived from RNA-seq across thousands of samples from 31 solid human normal tissues sourced from GTEx.
• Co-expression modules and pathway enrichment: Thousands of co-expression modules identified by network analysis accompanied by pathway enrichment analyses to aid functional inference.
• cis-eQTLs: Millions of cis-eQTLs computed using whole genome sequence genotype data from GTEx to characterize genetic regulation of lncRNA expression.
• Tissue-specificity, conservation, and coding potential scores: Scores assessing tissue-specificity, phylogenetic conservation, and coding potential for lncRNAs.
• Trait associations from GWAS: Tissue-specific lncRNA–trait associations derived from 323 Genome-Wide Association Studies conducted by the UK Biobank.

Scientific Applications:

• Functional annotation: Use co-expression modules and pathway enrichment results to infer biological functions of lncRNAs.
• Genetic studies: Leverage cis-eQTLs computed from GTEx whole genome sequence genotype data to study genetic regulation of lncRNA expression.
• Disease and trait association research: Employ tissue-specific lncRNA–trait associations from UK Biobank GWAS to identify candidate lncRNAs linked to traits and diseases.

Methodology:

Integration of annotations from six independent databases; processing of GTEx RNA-seq to derive tissue expression profiles across 31 solid human normal tissues; computation of cis-eQTLs using GTEx whole genome sequence genotype data; network analysis to identify co-expression modules; and pathway enrichment analyses.