Fig. 5: Gene expression subtypes.

a Tumors were separated into four clusters by unsupervised analyses based on differentially expressed mRNA patterns (showing 540 representative genes). Top to bottom: AA signature, tumor stage information; normalized abundance heatmap for 98 mRNAs; profile of silhouette width calculated from the consensus membership heatmap, Wcm; covariates for recurrent copy number alteration regions, and mutations in BAP1, CSMD3, SETD2, MTOR, PTEN, TP53, ARID1A, PIK3CA, and PBRM1. Some important genes related to the cell cycle, angiogenesis, and the EMT are listed on the left. b Overall, the scores of gene sets associated with EMT, angiogenesis, and cell cycle process in patients with thrombus were increased compared with patients with no thrombus. The phenomenon of immune cell infiltration was complex; CAF infiltration was more obvious in patients with thrombus, but T-cell and B-cell infiltration was more common in non-thrombus patients. Each dot presents one sample. The box plot displays the first and third quartiles (top and bottom of the boxes), the median (band inside the boxes), and the lowest and highest point within 1.5 times the interquartile range of the lower and higher quartile (whiskers). Wilcoxon rank-sum test, *p < 0.05, **p < 0.01, ***p < 0.001. The source data underlying Fig.  5a are provided as a Source Data file.