Fig. 4: Integrated methylation and expression analysis of differentially methylated CpG sites between T-ALL and T-LBL. | Blood Cancer Journal

Fig. 4: Integrated methylation and expression analysis of differentially methylated CpG sites between T-ALL and T-LBL.

From: DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma

Fig. 4

a PCA scoring plot showing separate clustering of Basso´s cohort of pediatric T-ALL (n = 10) and T-LBL (n = 20) samples based on log transformed average signal of 100 (219 probes) out of 110 unique genes corresponding to the 128 DM-CpGs. The gene expression data of T-ALL and T-LBL samples, analyzed by HG-U133Plus2.0 GeneChip arrays, was retrieved from the public data repository (GSE29986) (Basso, Mussolin et al. 2011). b Mean methylation levels at single CpG site resolution in PEG10 (+sense strand) and SGCE (-antisense strand) promoter regions are compared between T-ALL (gray), T-LBL (yellow) and non-malignant lymph node (cyan) and bone marrow (blue) reference samples. The significant differentially methylated CpG sites are marked and the 95% confidence interval, based on the T distribution, is represented by dashed lines while the mean avg. β is represented as a solid line. c Boxplots comparing the gene expression of neighboring SGCE and PEG10 genes in T-ALL (n = 10) and T-LBL (n = 20) patient cohort (Basso, Mussolin et al. 2011). The p-value is determined by Welch´s two sample T-test.

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