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Figure 4 | BMC Genomics

Figure 4

From: Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells

Figure 4

Genes associated with the AML-ETO/N-CoR signature have the greatest recovery upon AML1-ETO knockdown. (A) The cumulative distribution of t scores, \( C(t)={\displaystyle {\int}_{-\infty}^tP(s)ds} \), comparing changes in gene expression for each of the clusters (Figure 3A) due to reduction in mRNA levels of the AML1-ETO fusion protein [30] is shown. For a given gene, the t score is the estimated log fold-change between conditions divided by its standard error: we observe that C(t) is shifted significantly (p < 4.6 × 10−10 using a t-test) to higher t for Cluster I compared to either Clusters II or III. The inset shows the probability distributions, P(t), for each cluster. (B) Volcano plot of expression differences due to RNAi mediated knockdown of AML1-ETO [30] showing genes from each of the clusters. The horizontal axis shows log2(fold-change), with vertical lines indicating cutoffs of 2-fold in either direction. The upper panel displays the distributions of log2(fold-change) for each of the clusters, again with a significant shift (p < 4 × 10−9 using a t-test) to higher fold-changes for Cluster I, relative to the other two clusters. (C) Distributions of t scores, as in (A) using expression profiling data collected over several time-points in Kasumi-1 cells under knockdown of the AML1-ETO mRNA [24]. We observe that C(t) is shifted significantly (p < 2.9 × 10−8 using a t-test) to higher t for Cluster I compared to either Clusters II or III. (D) Volcano plot of expression differences due to knockdown of AML1-ETO [24] showing genes from each of the clusters. The upper panel displays the distributions of log2(fold-change) for each of the clusters, again with a significant shift (p < 3.5 × 10−8 using a t-test) to higher fold-changes for Cluster I, relative to the other two clusters.

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