Fig. 4: Gene set enrichment analyses according to minimal residual disease status and baseline versus relapse status. | Nature Communications

Fig. 4: Gene set enrichment analyses according to minimal residual disease status and baseline versus relapse status.

From: Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia

Fig. 4

a Summarized pre-treatment gene set enrichment analysis of hallmark gene sets according to treatment arm and according to EOT MRD6 and MRD + status. Positive normalized enrichment scores (NES) indicates gene sets enriched in MRD + and negative NES indicates gene sets enriched in MRD6. b Patient-level gene set enrichment analysis of relapse versus baseline samples in both arms. Significantly enriched hallmark gene sets (adjusted p-value <0.05) are highlighted, positive NES indicate enrichment in relapsed samples. P-values derived from non-parametric permutation test and adjusted for multiple testing using the Benjamini-Hochberg procedure. c Leading edge analysis of baseline (left) versus relapse (right) samples based on ‘TNFa signalling via NFkB’, ‘G2M checkpoint’ and ‘MYC targets V1’ gene sets, which were significantly enriched at relapse. d Gene set variation analysis of selected inflammatory pathways before Ven-Obi (D, n = 29) or Clb-Obi (e, n = 15) treatment (baseline) and at relapse (progression); two-sided Wilcoxon signed-rank test, not adjusted for multiple testing. box plots represent lower quartile, median and upper quartile, whiskers extend to a maximum of 1.5 × IQR beyond the box, points indicate outliers. NES, normalized enrichment score; MRD, minimal residual disease, EOT, end of treatment. Source data of differential gene expression analyses are provided as Source Data file.

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