In silico perturbation results and analysis record for a shared nasal polyp-inflammatory bowel disease transcriptional program

In silico perturbation results and complete analysis record accompanying the manuscript on a shared epithelial-immune transcriptional program in nasal polyps and inflammatory bowel disease. Five candidate regulators (epithelial JUNB and CEBPD; immune IKZF1, SPI1 and REL) were tested in four single-cell compartments (nasal epithelium and nasal immune cells from GSE235711; Crohn's disease colon immune and epithelial cells from Kong et al. 2023, Single Cell Portal SCP1884). The manuscript's perturbation method is Geneformer (deletion perturbation; per-target impact components): the four *_geneformer_del_stats.csv files, the 10-row verdict table impacts_table.csv (rule: impact component 1 with >=40% of total shift = Strong; component 1 with <40% = Supportive; component 0 = Not impacted) and the run script gf_run_npibd.py (Kaggle GPU, forward batch size 8) are included. Two further methods, scTenifoldKnk and CellOracle, were run earlier under a pre-specified protocol (thresholds fixed 2026-10-28); their complete results are archived here as an analysis record only and are not used for any manuscript conclusion: ko_celloracle_*.csv (nasal: CEBPD and SPI1 Supportive, other targets Reversed; gut: 0/5 Supportive), ko_sctenifold_*_summary.csv and *_dRegulation.csv (nasal 5/5 Neutral; gut completed for IKZF1 only (Neutral), the remaining gut targets not run by decision), ko_adjudication.csv (nasal adjudication under the pre-specified two-method rule: no two-method agreement). File-level details are in ko_analysis_record_README.md.