Fig. 2

WES and transcriptome sequencing of a primary tumor. a Circos plot summarizing WES and transcriptome analysis of primary tumor. Inner circle represents structural variants and gene fusions; second tier, copy number variations (blue, loss; red, gain); third tier, mRNA expression outlier analysis of cancer related genes within the top and bottom 10th percentile (green, under-expressed; orange, over-expressed); fourth tier (outer circle), somatic mutations localized to respective chromosomes. b Scatter-plot showing the t-SNE 2D projection for 3167 samples, including at least 100 samples (indicated in the figure) for each of the 34 tissue types represented in our pan-cancer database. Tissue ID is indicated by different colors and the carcinoid sample is indicated by a bold black dot and arrow. c Relative gene expression rank of outlier genes after z-normalization across a compendium of expression profiles from the GTEx database. A z-distribution is superimposed as reference. ACC adrenocortical carcinoma, BLCA bladder urothelial carcinoma, BRCA breast carcinoma, CESC cervical carcinoma, CHOL cholangiocarcinoma, COAD colon adenocarcinoma, DLBC diffuse large B-cell lymphoma, ESCA esophageal carcinoma, GBM glioblastoma multiforme, HNSC head and neck carcinoma, KICH kidney chromophobe, KIRC clear cell carcinoma of the kidney, KIRP renal papillary cell carcinoma, LAML acute myeloid leukemia, LGG low grade glioma, LIHC hepatocellular carcinoma, LUAD lung adenocarcinoma, LUSC lung squamous cell carcinoma, MESO mesothelioma, NET gastrointestinal neuroendocrine tumor, OV ovarian carcinoma, PAAD pancreatic adenocarcinoma, PCPG pheochromocytoma and paraganglioma, PRAD prostate adenocarcinoma, READ rectal adenocarcinoma, SARC sarcoma, SKCM cutaneous melanoma, STAD gastric adenocarcinoma, TGCT testicular germ cell tumor, THCA thyroid carcinoma, THYM thymoma, UCEC uterine corpus endometrial carcinoma, UCS uterine carcinosarcoma, UVM uveal melanoma