Extended Data Fig. 7: Enrichment of malignant cell and CAF programs in genes differentially expressed with treatment regimen.
Fold enrichment of overlap (x axis) between gene program signatures (top 200 genes; rows) and genes differentially expressed (q < 0.05) in CRT (n = 14) vs. untreated (n = 18) (left), CRTL (n = 5) vs. untreated (middle), or CRTL vs. CRT (right). * Bonferroni adjusted p < 0.05, two-sided hypergeometric test. Exact p-values for significant comparisons were untreated-CRT: CYS-untreated = 8.54 × 10−6, CYS-CRT = 7.36 × 10−4, CYG-untreated = 9.53 × 10−7, CYG-CRT = 5.96 × 10−4, MYC-CRT = 3.72 × 10−2, ADH-M-CRT = 2.95 × 10−2, RBS-untreated = 2.25 × 10−2, TNF-CRT = 5.61 × 10−3, ACN-untreated = 2.87 × 10−2, ACN-CRT = 1.51 × 10−6, CLS-untreated = 4.77 × 10−5, CLS-CRT = 3.72 × 10−2, BSL-untreated = 2.44 × 10−2, BSL-CRT = 2.65 × 10−5, SQM-CRT = 5.10 × 10−3, MES-untreated = 2.16 × 10−3, MES-CRT = 1.09 × 10−4, NEN-untreated = 4.83 × 10−3, NRP-untreated = 2.58×10−3, NRP-CRT = 6.06 × 10−10, ADH-F-untreated = 1.03 × 10−8, ADH-F-CRT = 3.68 × 10−43, IMM-untreated = 6.12 × 10−6, IMM-CRT = 5.24 × 10−8, MYO-untreated = 3.66 × 10−72, MYO-CRT = 5.60 × 10−4, NRT-untreated = 4.56 × 10−4, NRT-CRT = 5.60 × 10−7; untreated-CRTL: CYS-untreated = 9.45 × 10−19, CYS-CRT = 4.91 × 10−3, CYG-untreated = 1.04 × 10−13, ADH-M-CRT = 1.10 × 10−21, RBS-untreated = 7.60 × 10−3, RBS-CRT = 4.91 × 10−3, IFN-CRT = 4.49 × 10−2, ACN-untreated = 9.62 × 10−3, ACN-CRT = 4.14 × 10−6, SQM-untreated = 2.65 × 10−16, MES-CRT = 9.59 × 10−6, NEN-untreated = 1.43 × 10−2, NRP-untreated = 6.79 × 10−3, NRP-CRT = 2.74 × 10−20, ADH-F-untreated = 7.60 × 10−21, ADH-F-CRT = 1.54 × 10−151, IMM-untreated = 2.58 × 10−9, MYO-untreated = 4.80 × 10−6, MYO-CRT = 2.09 × 10−5, NRT-untreated = 2.57 × 10−10; CRT-CRTL: MYC-CRT = 3.07 × 10−2, ADH-M-CRTL = 4.17 × 10−8, IFN-CRTL = 1.99 × 10−2, ADH-F-CRT = 7.16 × 10−7, ADH-F-CRTL = 5.88 × 10−60, IMM-CRTL = 2.56 × 10−2.
