Fig. 4
From: Integrated exome and RNA sequencing of dedifferentiated liposarcoma
Comparative analysis of well-differentiated (WD) and dedifferentiated (DD) components from DDLPS. a–c Representative somatic mutations (nonsynonymous SNVs and INDELs) (a), SCNAs (b), and SVs (c) in WD and DD components from the same patients. In a, the circle size and numbers indicate the number of somatic mutations in WD or DD. A boxed gene, OTP1, indicates a common somatic mutation in the sample. In b, copy numbers were plotted according to the order of the chromosomal regions, from chromosome 1 (top) to 22 (bottom) and chromosome X. Red lines indicate segmented exome circular binary segmentation calls. The segmentation size is based on the exome capture kit bed file. Solid arrows indicate 12q15; empty arrows indicate 1p32.1. In c, two representative cases are presented, with others presented in Supplementary Fig. 9. d Multidimensional scaling analysis of expression profiles of paired WD and DD. Six pairs of WD and DD were analyzed. e, f GSEA analysis comparing the expression profiles of DD and WD. The gene sets most enriched in DD (e) and WD (f) are shown. g, h Volcano plots of the DD-specific gain (g) and loss (h) of genes. The red and blue dots denote large magnitude fold-changes (more than 2 or less than ½; horizontal axis) and high statistical significance (more than 1.301 of −log10 of P-value by one-sided paired T test; vertical axis), respectively.
