Fig. 3: Gene expression profiling of tCLL, oCLL, and B cells from RNA-seq. | Leukemia

Fig. 3: Gene expression profiling of tCLL, oCLL, and B cells from RNA-seq.

From: Clinical and transcriptomic characterization of patients with chronic lymphocytic leukemia harboring t(14;19): an ERIC study

Fig. 3

A Dimensionality reduction by principal component analysis (PCA) performed on gene expression estimates. t(14;19) CLL patients (red crosses), control CLL (yellow triangles), and healthy donor B cell (blue circles) samples are displayed according to the first two principal components (PC1, horizontal axis; PC2, vertical axis) explaining the expression variability of the data (31.6% and 15.3%, respectively). B Volcano plot of the gene expression differences computed between t(14;19) CLL (tCLL) and other CLL without t(14;19) (oCLL). Dots and labels are colored according to the gene expression rank in tCLL (100% for the most expressed, 0% for the least expressed). C Western blotting analysis of Bcl-3 protein in tCLL and oCLL. The histogram in the bottom panel shows the densitometric analysis of Bcl-3/Actin, normalized to normal B cells, expressed as arbitrary units (A.I.). Expression levels, quantified by RNA-seq and RT-qPCR (DDCt method; GAPDH used as reference gene; Mean ± SD shown; A.U., Arbitrary Units) of BTK (D, E) and BCL2L11 (F, G) in patients with tCLL and oCLL. H Significant gene sets resulted from gene set enrichment analysis on the MSigDb hallmarks. Upward and downward arrows represent positive and negative normalized enrichment scores (NES), respectively, colored according to the magnitude of the NES (red indicates high positive, and blue indicates low negative). The arrow size indicates the statistical significance of the enrichment. I Heatmap of differentially expressed genes (rows) between t(14;19) CLL (tCLL), other CLL without t(14;19) (oCLL) samples, and B cells (columns). Pink and green cells represent gene-scaled expression, higher and lower than the gene mean of B cells, respectively. Columns are clustered according to the relative expression; rows are grouped according to differential expression significance, considering the three comparisons oCLL vs. B cells, tCLL vs. B cells, and tCLL vs. oCLL (dots in the panel mid sections indicate the significant comparisons). For each gene set, the enriched pathways are shown on the left side of the panel.

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