Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser
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1 Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser Melissa S. Cline 1*, Brian Craft 1, Teresa Swatloski 1, Mary Goldman 1, Singer Ma 1, David Haussler 1, Jingchun Zhu 1 1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz * Correspondence and requests for materials should be addressed to Melissa S. Cline (cline@soe.ucsc.edu)
2 Supplementary Material Supplementary Figure 1. Pan- Cancer subtypes defined by RNA (k=16) or protein expression (k=8) data show strong overall concordance with tumor's tissue of origin. Each panel is a stacked bar graph (UCSC Cancer Genomics Browser proportions view) of the Pan- Cancer RNA (1st column) and protein expression (2nd column) subtype designations in each of the 12 TCGA cohorts. A view of this figure is at cancer.ucsc.edu/proj/site/hgheatmap/#?bookmark=srs1. OV: ovarian serous cystadeno. GBM: glioblastoma multiforme. COAD: colon adeno. BLCA: bladder urothelial. KIRC: kidney clear cell. UCEC: uterine corpus endometrioid. READ: rectum adeno. HNSC: head and neck squamous cell. AML: acute myeloid leukemia. BRCA: breast invasive. LUAD: lung adeno. LUSC: lung squamous cell.
3 OV GBM non-basal BRCA BLCA KIRC UCEC basal BRCA HNSC AML COADREAD LUAD LUSC 1 2 mutation Supplementary Figure 2. Pan- Cancer subtypes defined by copy number (k=8) or somatic mutation (k=14) data show less overall concordance with tumor's tissue of origin. Each panel is a stacked bar graph (UCSC Cancer Genomics Browser proportions view) of the Pan- Cancer copy number (, 1st column) and somatic mutation (2nd column) subtype designations in individual TCGA cohort. The colon and rectum adeno cohorts are combined. The breast cohort is split into basal and non- basal subgroups. A view of the figure is under the bookmark: cancer.ucsc.edu/proj/site/hgheatmap/#?bookmark=srs2. OV: ovarian serous cystadeno. GBM: glioblastoma multiforme. BRCA: breast invasive. BLCA: bladder urothelial. KIRC: kidney clear cell. UCEC: uterine corpus endometrioid. HNSC: head and neck squamous cell. AML: acute myeloid leukemia. COADREAD: colon and rectum adeno. LUAD: lung adeno. LUSC: lung squamous cell. The Pan- Cancer subtype designations, as made by all five data types individually (RNAseq, protein expression, DNA methylation, copy number, or somatic mutations), can be viewed under the UCSC Cancer Genome Browser at cancer.ucsc.edu/proj/site/hgheatmap/#?bookmark=srs2b.
4 TCGA Dataset Group Gene Exon Seg Gistic2 Gene-level DNA Methyl Protein Somatic Mutation PARA- DIGM OS RFS Pan- Cancer Subtypes Acute myeloid leukemia Y Y Bladder urothelial Y Y Y Brain lower grade glioma Y Y Breast invasive Y Y Cervical squamous cell and Y Y Endocervical adeno Colon & rectum adeno Y Y Y Colon adeno Y Y Y Diffuse large B- cell lymphoma Esophageal Y Glioblastoma multiforme Y Y Head & neck squamous cell Y Y Y Kidney chromophobe Y Y Kidney clear cell Y Y Kidney papillary cell Y Liver hepatocellular Y Y Lung adeno Y Y Y Lung cancer Y Y Y Lung squamous cell Y Y Y Ovarian serous cystadeno Y Y Pancreatic adeno Y Y Prostate adeno Y Rectum adeno Y Y Y Sarcoma Y Skin cutaneous melanoma Y Y Stomach adeno Y Y Thyroid Y Y Uterine carcinosarcoma 1 Uterine corpus endometrioid Y Y Y
5 Supplementary Table 1. Summary of the TCGA data hosted at the UCSC Cancer Genomics Browser. Number of genomic datasets per data type and TCGA cohort are shown. The table also lists the availability of curated overall or recurrence free survival information, and Pan-Cancer subtype designations (Stuart et al, to be submitted to Nature). OS: overall survival. RFS: recurrence free survival. PARADIGM: PARADIGM pathway inference results 2.
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