LncRBase

LncRBase catalogs and annotates 549,648 long non-coding RNAs across Human, Mouse, Rat, Fruitfly, Zebrafish, Chicken, Cow, and C.elegans to support analyses of lncRNA function, regulation, and cancer-associated variation.

Key Features:

• Species coverage: Annotates 549,648 lncRNAs from Human, Mouse, Rat, Fruitfly, Zebrafish, Chicken, Cow, and C.elegans.
• Transcription Factor Binding Sites (TFBS): Provides TFBS annotations within lncRNA promoter regions.
• Sub-cellular Localization: Reports sub-cellular localization patterns of lncRNAs.
• lnc-pri-miRNAs and sORFs: Identifies lncRNA-derived primary microRNAs (lnc-pri-miRNAs) and potential small open reading frames (sORFs) within lncRNAs.
• Manually Curated Interactions and Disease Associations: Contains manually curated interacting target molecules and disease associations for lncRNA genes.
• Tissue Distribution Data: Provides distribution of lncRNAs across multiple tissues in all covered species.
• ClinicLSNP Module: Catalogs lncRNA variants associated with breast, ovarian, and cervical cancers using data from 561 RNA-Seq datasets and analyzes overlaps of variants with repeat elements, CpG islands (CGIs), TFBS within lncRNA loci, SNPs in trait-associated linkage disequilibrium regions, predicts potentially pathogenic variants, and assesses SNP impacts on lncRNA secondary structure.

Scientific Applications:

• Gene regulation studies: Enables investigation of lncRNA regulatory mechanisms via TFBS annotations and promoter analyses.
• Cancer genomics and variant discovery: Supports identification and characterization of cancer-associated lncRNA variants, including breast, ovarian, and cervical cancers, via the ClinicLSNP module.
• Structural impact assessment: Facilitates assessment of SNP effects on lncRNA secondary structure and prediction of potentially pathogenic variants.
• Comparative and tissue-specific studies: Enables cross-species comparison and tissue distribution analyses of lncRNAs across the eight covered species.
• Functional annotation: Supports identification of lnc-pri-miRNAs and sORFs to expand functional annotation of lncRNAs.

Methodology:

Annotation and cataloging of lncRNAs across species; TFBS annotation in promoter regions; reporting of sub-cellular localization and tissue distribution; identification of lnc-pri-miRNAs and sORFs; manual curation of interactions and disease associations; aggregation of variants from 561 RNA-Seq datasets; overlap analyses with repeat elements, CpG islands (CGIs), TFBS, and SNPs in trait-associated linkage disequilibrium regions; prediction of potentially pathogenic variants; assessment of SNP impacts on lncRNA secondary structure.