Fig 2: Identification of a CMTM7-related subtype in TCGA-BRCA (A) Average silhouette coefficient for k = 1 to k = 10. (B) Consensus clustering matrix of TCGA-BRCA samples using the expression matrix of CMTM7 and its co-expressed genes for k = 2. (C) Principal component analysis of TCGA-BRCA samples based on the expression matrix of all genes. (D) Volcano plot showing the differentially expressed genes (DEGs) for the CMTM7-high and CMTM7-low groups. (E) Functional enrichment analysis of DEGs for the CMTM7-high and CMTM7-low groups. (F–I) Boxplot showing the immune score, stromal score, ESTIMATE score, and tumor purity between the CMTM7-high and CMTM7-low groups. Horizontal lines in the boxplots represent the median, the lower and upper hinges correspond to the first and third quartiles, respectively, and the whiskers extend from the hinge up to 1.5 times the interquartile range from the hinge. The Wilcoxon rank-sum test was performed to measure the difference between two groups.

Fig 3: Identification of relevant modules associated with CMTM7 expression in TCGA-BRCA. (A) Analysis of the scale-free fitting indices for different soft-thresholding powers (β). (B) Mean connectivity analysis of different soft-thresholding powers. (C) Clustering dendrograms of genes were based on dissimilarity, topological overlap, and module colors. As a result, 13 co-expressed modules except the gray module were constructed and labeled with different colors. These modules were arranged from large to small according to the number of genes included. (D) Heatmap of the correlation between module eigengenes and CMTM7 expression of BRCA. The yellow gene module was revealed to exhibit the highest correlation with CMTM7 expression. (E) Scatter plots showing the relationship between MM and GS in the yellow module.

Fig 4: CMTM7 correlated with inflamed TME and predicted the immunotherapeutic response. (A) Correlation between CMTM7 expression and immune score in the GSE173839 cohort. (B) Heatmap showing the enrichment scores of immune subpopulations and immune-related signaling pathways in GSE173839. (C) Heatmap showing the gene expression matrix of immune checkpoint inhibitors in GSE173839. (D) Correlation between CMTM7 expression and immune score in the GSE194040 cohort. (E) Heatmap showing the enrichment scores of immune subpopulations and immune-related signaling pathways in GSE194040. (F) Heatmap showing the gene expression matrix of immune checkpoint inhibitors in GSE194040. (G) Barplot showing the percentage of complete remission (CR) and non-complete remission (NR) in the CMTM7-high and CMTM7-low groups in GSE173839. (H) ROC curves showing the predictive values of immunotherapeutic response for CMTM7, PD-L1, and PD-1 in the GSE173839 cohort. (I) Barplot showing the percentage of CR and NR patients in the CMTM7-high and CMTM7-low groups in the GSE194040 cohort. (J) ROC curves showing the predictive values of the immunotherapeutic response for CMTM7, PD-L1, and PD-1 in the GSE194040 cohort.

Fig 5: CMTM7 predicts the molecular subtype in BRCA. (A) Correlations between CMTM7 and clinicopathological features in BRCA. (B–I) Boxplot showing the expression level of CMTM7 among the subtypes of each clinicopathological feature. Horizontal lines in the boxplots represent the median, the lower and upper hinges correspond to the first and third quartiles, respectively, and the whiskers extend from the hinge up to 1.5 times the interquartile range from the hinge. The Wilcoxon rank-sum test was performed to measure the difference between two groups.