Extended Data Fig. 1: Development and Validation of the Y Chromosome Transcriptional Signature (YchrS).
From: Concurrent loss of the Y chromosome in cancer and T cells impacts outcome
a. Differential gene expression analysis for Y Chromosome genes comparing LOYDNA and WTYDNA male TCGA samples. Dot color represents -log10 adjusted P-values for each gene. Vertical lines indicate log2FC of -1 and 1 and the horizontal line indicates -log10 adjusted P-values of 200. The 9 genes used for the RNA-based YchrS are annotated. b. YchrS scores in LOYDNA and WTYDNA TCGA tumor samples, where samples are separated by cancer types. Boxes denote the median (center line) and the first and third quartiles (lower and upper edges of the box). Whiskers extend to either the minimum or maximum values within 1.5 × the interquartile range (IQR). Any data points outside these whiskers are considered outliers. c. Distribution of chromosome segments and corresponding Copy Number Alteration (CNA). Each dot represents one chromosome segment in a particular cell line, with midpoint location shown in X axis and log2 mean CNA shown in Y axis. The color of the dots represents the YchrS level of the samples. d. Average CNA at the chromosome level for the 625 CCLE male cell lines with available Y chromosome CNA, with the lines separated into WTYBR (n = 442) and LOYBR (n = 183) groups. Data presentation as in (a). Two‐sided Wilcoxon rank‐sum test. e. YchrS and corresponding average CNA of each chromosome for samples in (d). Each dot represents a cell line, with YchrS level shown by color.
