Figure 3
Genomic profiles of LundTax molecular subtypes in the TCGA cohort. (A) Differentially mutated genes. Black, mutation; white, wild type; gray, no data. (B) Selected differentially mutated biological processes among molecular subtypes. Three major biological processes were identified, FGFR3 signaling, apoptotic signaling pathway by TP53, and processes involved in genomic instability including RB1. Percentages in parentheses indicate the fraction of the mutated samples in the whole cohort for the given GO term. GO terms; GO:0072148, epithelial cell fate commitment; GO:1902178, fibroblast growth factor receptor apoptotic signaling pathway; GO0045839, negative regulation of mitosis; GO:0030330, DNA damage response signal transduction by p53 mediator; GO:0072332, intrinsic apoptotic signaling pathway by p53 class mediator; GO:0042149, cellular response to glucose starvation; GO:0007050, cell cycle arrest; GO:0030512, negative regulation of transforming growth factor beta receptor pathway; GO:0071922, regulation of cohesion localization to chromatin; GO:0071459, protein localization to chromosomes, centromeric region; GO:0031134, sister chromatid bi-orientation; GO0090230, regulation of centromere complex assembly; GO:0034088, maintenance of mitotic sister chromatid cohesion. (C) Selected genomic imbalances significantly (p < 0.05, Bonferroni corrected) associated with molecular subtypes. Light brown, gain; dark brown, amplification; light blue, loss; dark blue, homozygous loss. (D) Distribution of 6p22 (E2F3, CDKAL1, SOX4) and 11q13 (CCND1) amplifications across the molecular subtypes. Color codes as in panel C. Subtype abbreviations as in Fig. 1. Vertical lines, separate major molecular subtypes; dotted lines, separate subgroups of subtypes.
