Fig. 8
Mutations of key oncogenic pathways in NPC tumor lines. a Genetic landscape in NPC PDXs and cell lines. Somatic mutations in the newly established PDXs/cell lines and C666-1 are illustrated in mutation plot. Gray box with character inside indicates heterozygous mutation, while orange box with character(s) inside indicates homozygous mutation. S, missense single-nucleotide variant (SNV); D, deletion; V, inversion; T, tandem duplication; I, indel; *, nonsense SNV. b Activation of NF-κB and PI3K pathways in EBV+ve NPC xenografts and cell lines by transcriptome study. Gene expression levels were quantified by RNA sequencing and subjected to GSEA for pathway enrichment analysis. Enrichment score (ES) indicates the degree to which the specified gene sets are overrepresented at the top/bottom of a ranked list of total protein-coding genes in individual PDX/cell line. Normalized enrichment score (NES) computes density of modified genes in the dataset with random expectancies, normalized by gene numbers found in each gene cluster. False discovery rate (FDR) is calculated by comparing actual data with 1000 Monte-Carlo simulations. For each enrichment plot, top portion: running ES for the specified gene set; middle portion: where the member of gene set appears in the ranked list of all protein-coding genes; bottom portion: value of the ranking metric as a measurement of gene’s correlation with phenotype (EBV+ve or EBV–ve)
