Figure 3.
Surrogate PD and ID gene expression signatures. (A) A schematic representation of the methodology used to define the surrogate gene expression signatures. (B-C) A heat map (left) depicting the gene expression of PD (B) and ID (C) signatures. Gene expression levels are presented as row z scores. The SPD and SID signature enrichment scores for each sample are indicated below. Genes listed from top to bottom and left to right correspond to the rows from the heat map from top to bottom. A box plot (right) compares the SPD or SID values between U-CLL and M-CLL. Statistical significance was assessed using 2-tailed Student t tests. (D) HRs and P values for the multivariate Cox regression model, including SPD and SID as predictors of TTFT. Independent cases from the H3K27ac series were used for this analysis. Both scores were standardized as z scores for easier comparison and interpretation. P values were calculated using the Wald test. (E) Box plots depicting the PD and ID scores in mature healthy B cells and CLL in 2 independent cohorts. Statistical significance was determined using 2-tailed Student t tests. (F) A scatterplot showing the correlation between the balance scores obtained from H3K27ac ChIP-seq and RNA-seq. Pearson correlation coefficient was calculated, and the P value was determined using a 2-tailed test, assuming the coefficient to follow a t distribution with 64 degrees of freedom. (G) HR and P value for the univariate Cox regression model, including SB as a predictor of TTFT. Independent cases from the H3K27ac series were used for this analysis. The balance score was standardized as a z score for easier comparison and interpretation. The P value was calculated using the Wald test. (H) Cox regression model assessing Binet A stage CLL cases, using balance score and IGHV mutational status as predictors and TTFT as the end point variable. Independent cases from the H3K27ac series were analyzed, with P values calculated via the Wald test. (I) Box plots comparing the balance score between CLL groups in the external UK cohort.28 Statistical significance was determined using the Tukey's Honest Significant Difference post hoc test. ∗∗∗∗P < .0001; ∗∗∗P < .001; ∗∗P < .01; ∗P < .05; ns, not significant.

Surrogate PD and ID gene expression signatures. (A) A schematic representation of the methodology used to define the surrogate gene expression signatures. (B-C) A heat map (left) depicting the gene expression of PD (B) and ID (C) signatures. Gene expression levels are presented as row z scores. The SPD and SID signature enrichment scores for each sample are indicated below. Genes listed from top to bottom and left to right correspond to the rows from the heat map from top to bottom. A box plot (right) compares the SPD or SID values between U-CLL and M-CLL. Statistical significance was assessed using 2-tailed Student t tests. (D) HRs and P values for the multivariate Cox regression model, including SPD and SID as predictors of TTFT. Independent cases from the H3K27ac series were used for this analysis. Both scores were standardized as z scores for easier comparison and interpretation. P values were calculated using the Wald test. (E) Box plots depicting the PD and ID scores in mature healthy B cells and CLL in 2 independent cohorts. Statistical significance was determined using 2-tailed Student t tests. (F) A scatterplot showing the correlation between the balance scores obtained from H3K27ac ChIP-seq and RNA-seq. Pearson correlation coefficient was calculated, and the P value was determined using a 2-tailed test, assuming the coefficient to follow a t distribution with 64 degrees of freedom. (G) HR and P value for the univariate Cox regression model, including SB as a predictor of TTFT. Independent cases from the H3K27ac series were used for this analysis. The balance score was standardized as a z score for easier comparison and interpretation. The P value was calculated using the Wald test. (H) Cox regression model assessing Binet A stage CLL cases, using balance score and IGHV mutational status as predictors and TTFT as the end point variable. Independent cases from the H3K27ac series were analyzed, with P values calculated via the Wald test. (I) Box plots comparing the balance score between CLL groups in the external UK cohort.28 Statistical significance was determined using the Tukey's Honest Significant Difference post hoc test. ∗∗∗∗P < .0001; ∗∗∗P < .001; ∗∗P < .01; ∗P < .05; ns, not significant.

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