Additional file 2: of Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis

Figure S1: Consensus cluster plus output from unsupervised clustering of 750 highly variant lncRNAs in the NAC cohort. Figure S2: Molecular subtyping of the NAC cohort using the TCGA 2017 classifier. Figure S3: Survival analysis for lncRNA clusters stratified by the basal/squamous mRNA subtype in the NAC cohort. Figure S4. Survival analysis for lncRNA clusters in TCGA cohort. Figure S5: Expression of select MIBC marker genes associated with the luminal subtype in the LPL-C3 and LPL-Other tumors. Figure S6: Expression of select MIBC marker genes associated with the basal subtype in the LPL-C3 and LPL-Other tumors. Figure S7: Expression of select MIBC marker genes associated with the immune oncology in the LPL-C3 and LPL-Other tumors. Figure S8: Expression of select genes associated with EMT in the LPL-C3 and LPL-Other tumors. Figure S9: Sample purity estimates. Figure S10: Scatterplots for the observed correlation between EMT hallmark scores and purity estimates. Figure S11: Contribution of immune-associated lncRNAs to consensus clustering solution in the NAC cohort. Figure S12: Expression of select genes associated with SHH and urothelial differentiation in the LPL-C3 and LPL-Other tumors. Figure S13: Correlation of gene expression and pathway activity with respect to mutation status in the TCGA cohort. Figure S14: RB1 expression. Figure S15: Survival analysis of LPL-C3 patients stratified by node positivity. Figure S16: Biological pathways differentially activated between tumors classed as FGFR3+ by the GC and other tumors. Figure S17: Biological pathways differentially active between tumors classed as FGFR3+ by the GC and other tumors. (PDF 4062 kb)