a Five NMF metagene signatures are identified (NMF1–NMF5) with functional annotations. A heatmap shows that three NMF metagene signatures (NMF1–NMF3) are upregulated to varying degrees in CMT tumors (black), whereas NMF4 and NMF5 signatures are upregulated in normal tissue transcriptomes (gray). NMF clusters for individual CMTs are assigned according to the level of five NMF metagene signatures. The expression of selected EMT markers and claudin genes is also shown in a heatmap. The degrees of correlation between the expression signatures of tumor-initiating cells and CMT transcriptomes are depicted in signature correlation. b CMT tumors are classified into three subtypes (NMF1, NMF2, and NMF3), and their respective Kaplan–Meier survival curves are shown. The significance of survival differences across NMF clusters was estimated by log-rank test (two-sided). c Three NMF CMT subtypes were compared with histology types. d ESTIMATE-derived stromal and immune scores are plotted against the three NMF CMT clusters (92 NMF1, 35 NMF2, and 18 NMF3 CMTs, respectively). e Relative abundance of 12 immune cell subtypes estimated by CIBERSORT algorithms are shown for 92 NMF1, 35 NMF2, and 18 NMF3 CMTs.