LncVar

LncVar catalogs genetic variations in long noncoding RNAs (lncRNAs) and annotates their regulatory, translational, and disease-associated impacts across six species.

Key Features:

• Data aggregation: Collects lncRNA annotations from databases such as NONCODE and integrates transcription factor binding sites and m6A modification sites mapped to lncRNAs.
• Variation integration: Systematically incorporates single nucleotide polymorphisms (SNPs) and structural variations located within lncRNA regions.
• Regulatory and modification impact assessment: Evaluates effects of genetic variations on transcriptional regulation and post-transcriptional m6A methylation.
• ORF and coding-impact analysis: Identifies putatively translated open reading frames (ORFs) in lncRNAs and distinguishes synonymous versus non-synonymous SNPs within these ORFs.
• eQTL integration: Includes expression quantitative trait loci (eQTL) data linking genetic variants to lncRNA expression changes.
• CNV and prognostic biomarker identification: Identifies lncRNAs located in copy number variation (CNV) regions as candidate prognostic biomarkers for cancers.
• Gene-fusion prediction from RNA-seq: Predicts lncRNA gene fusion events using RNA-seq data from cell lines.
• Cross-species coverage: Covers genetic variation data across six species to support comparative analyses.

Scientific Applications:

• Functional annotation of lncRNAs: Supports identification of regulatory and translational consequences of variants to elucidate lncRNA functions.
• Disease and cancer genomics: Enables linking of lncRNA-associated variants, CNVs, and gene fusions to disease mechanisms, particularly in cancers.
• Biomarker and therapeutic target discovery: Facilitates identification of candidate prognostic biomarkers and potential therapeutic targets within lncRNA regions.
• Comparative and evolutionary analyses: Provides cross-species variation data to support comparative genomics and evolutionary studies of lncRNAs.

Methodology:

Aggregates lncRNA annotations from sources including NONCODE, maps transcription factor binding sites and m6A modification sites to lncRNAs, integrates SNPs and structural variants, identifies putatively translated ORFs and classifies synonymous/non-synonymous SNPs, incorporates eQTLs, detects lncRNAs in CNV regions, and predicts lncRNA gene fusions using RNA-seq data from cell lines.