Cross-cohort per-gene evidence matrix for a shared nasal polyp-inflammatory bowel disease transcriptional program

Per-gene evidence matrix for a shared epithelial-immune transcriptional program in nasal polyps (NP) and inflammatory bowel disease (IBD). The matrix covers 590 genes (NP x ulcerative colitis 551 union NP x Crohn's disease 226, direction-consistent shared differentially expressed genes; core 187 = intersection) and, for each gene, the per-layer measurements behind the manuscript: bulk discovery (GSE338426, 14 NP vs 8 controls) and IBD discovery (GSE75214), independent nasal validation (GSE198950), dupilumab and placebo paired contrasts (GSE267331), donor-level single-cell pseudobulk (nasal GSE235711 epithelial and immune; gut GSE116222 epithelial and inflamed subgroup), GeoMx spatial contrasts (GSE235714, CD45 and PanCK compartments and compartment comparison), and gut mucosal proteomics (PXD050335), plus four evidence-layer badges (bulk, single-cell, spatial, protein) and the dupilumab significance flag. Column definitions, source files, QC checks (direction consistency 590/590; core = intersection) and limitations (GeoMx per-gene FDR 0/169 at 40 ROIs; gut single-cell thin at n=6 vs 3; GSE198950 underpowered at 23/590 DEGs) are documented in evidence_matrix_README.md; input file md5s are in evidence_matrix_qc.txt. Built 2026-10-28 by build_evidence_matrix.R. Companion to the NP x IBD multi-omics manuscript revision (queryable evidence resource).