ncRNA-eQTL

ncRNA-eQTL provides genome-wide mapping of expression quantitative trait loci (eQTLs) that link genetic variants to non-coding RNA (ncRNA) expression using genotype and expression profiles from over 8,700 TCGA samples across 33 cancer types to enable study of variant–ncRNA associations and clinical relevance.

Key Features:

• Genome-wide eQTL analysis: Performs eQTL mapping using genotype and expression data from over 8,700 samples sourced from The Cancer Genome Atlas (TCGA) covering 33 cancer types.
• Identification of ncRNA-eQTLs: Detects eQTL–ncRNA pairs in both cis-eQTL and trans-eQTL contexts, reporting 6,133,278 cis-eQTL–ncRNA pairs and 721,122 trans-eQTL–ncRNA pairs.
• Survival analysis: Associates eQTLs with patient survival and identifies 8,312 eQTLs linked to patient survival times.
• Integration with GWAS data: Links identified eQTLs to genome-wide association study (GWAS) loci, reporting 262,332 ncRNA-eQTLs that overlap known disease- and trait-associated variants.

Scientific Applications:

• Understanding tumorigenesis: Elucidates how risk alleles modulate ncRNA expression in cancer to inform molecular mechanisms of tumorigenesis and cancer development.
• Phenotypic variation studies: Supports investigation of human complex phenotypic variation by relating genetic variants to ncRNA expression across cancer types.
• Prognostic marker identification: Enables identification of eQTLs associated with patient survival as potential prognostic markers for various cancers.

Methodology:

A computational pipeline integrates genotype data with ncRNA expression profiles to systematically identify cis- and trans-eQTL–ncRNA pairs, perform survival association analyses, and integrate identified eQTLs with GWAS loci.