Figure 1

Cancer comparator. The cancer comparison macro view uses a parallel coordinates [31] to provide a cross disease comparison. In this case the visualizations are used to show the differences in gene disruptions, measured by examining structural aberration, between a carcinoma (Colon Cancer), a sarcoma (Ovarian Cancer) and GlioBlastoma (GBM). The values shown on each axis are the number of patients in which the specific gene has been disrupted. The visualization uses the Protoviz libraries, and provides blending and color coding to portray the trends of gene disruptions across the cancers. The visualization allows for range selection across the different axis, so that specific patterns across the cancers can be identified. The parallel coordinates allows for the queries to be performed directly on the data set. In the example (1a) the question being asked is which set of genes show a high level of structural aberration in GBM and a low level of structural aberration in ovarian cancer. The range selection tool has been used to select all genes that have shown aberrations in more than 27 (out of 43) patients in GBM, and also only show aberrations in less than 6 of the ovarian patients. The genes that show these characteristics are HYDIN, DNAH3 and OR2L13. HYDIN aberrations [34, 35] are known to cause Hydrocephalus (water on the brain), and so the disruption of this gene in the brain produces a aberration that induces a survival physiological change. DNAH3 produces a Dynein protein and has been shown to be over expressed in ovarian cancer, under expressed in GBM [36] and also to be important in APC mutation based carcinogenesis in colon adenocarcinoma [37]. The OR2L13 olfactory gene is one without obvious function, however it is one of the main 44 recurrently mutated genes in this disease [38]. Figure 1b shows a second query, where the selection tool is used to identify all genes that show a high level of structural aberration across all three cancers. All the genes have been identified by others as being important in cancer and generally appear on multiple gene lists as complied by the MSKCC TCGA gene ranker tool [39]. The three genes that score lowest on this tool are PKHD1 [40] which is known to be involved in colorectal adenocarcinoma, DYNA9 which is involved in cilia transduction signals related to tumorgenesis important in Hedgehog and Wnt pathways [41], and SYNE1 which has recently been implicated in GBM [42]. SYNE1 is followed through the linked tools in Figures 2 and 3 to show the types of information that can be discovered and visualized.