gtex-expressionlisted

# Integrating GTEx Tissue Expression with ENCODE Regulatory Data Use GTEx gene expression across 54 human tissues to validate ENCODE regulatory element activity, establish enhancer-gene links, and provide tissue-specific expression context for functional genomics findings. ## Scientific Rationale **The question**: "Is the gene near my ENCODE regulatory element actually expressed in the tissue where the element is active?" ENCODE catalogs where regulatory elements exist (enhancers, promoters, insulators) but does not directly measure gene expression across a broad tissue panel. GTEx (Genotype-Tissue Expression) fills this gap by providing RNA-seq-based gene expression measurements across 54 human tissues from ~1,000 post-mortem donors. Integrating the two answers a fundamental question: does the regulatory landscape match the transcriptional output? An active enhancer (H3K27ac+, ATAC-seq+) near a gene in pancreas tissue is much more meaningful if GTEx confirms the gene is highly expressed in pancreas. Conversely, an ENCODE enhancer near a gene with zero expression in the relevant tissue suggests the enhancer regulates a different gene, or acts in a cell-type subpopulation not captured by bulk GTEx. ### What GTEx Provides - **Median gene expression (TPM)** across 54 human tissues from ~1,000 donors - **Transcript-level expression** for isoform analysis - **eQTLs** — variants associated with gene expression in specific tissues (cis and trans) - **sQTLs** — variants associ