Additional file 1 of Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes

Additional file 1: Readme. Index page for the constituent tables in this file. Table S1. Clinical phenotype for the 96 patients in the BCPP cohort. Table S2. Somatic mutations: Single Nucleotide variants (SNVs) and Insertion/ Deletions (InDels) identified from Whole-exome sequencing (WES). Table S3. All mutated genes ordered by their mutation recurrence count. Table S4. GISITIC identified focal Copy Number Amplification peaks. Table S5. GISITIC identified focal Copy Number Deletion peaks. Table S6. MSigDB (hallmark gene sets) for genes differentially expressed in Bad versus Good outcome in G3pT1 tumours. Table S7. Differentially expressed genes in ARNT altered versus samples wild-type for ARNT. Table S8. Differentially expressed in ERBB2 altered versus samples wild-type for ERBB2. Table S9. Genomic alteration recurrence frequencies as identified in NMIBC (this cohort) and TCGA MIBC (as seen in cBioPortal).