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. 2020 Jun;38(6):675-678.
doi: 10.1038/s41587-020-0546-8.

Visualizing and interpreting cancer genomics data via the Xena platform

Mary J Goldman #  1 , Brian Craft #  2 , Mim Hastie  3 , Kristupas Repečka  4 , Fran McDade  3 , Akhil Kamath  5 , Ayan Banerjee  6 , Yunhai Luo  7 , Dave Rogers  3 , Angela N Brooks  2   8 , Jingchun Zhu  2 , David Haussler  2
Affiliations

Visualizing and interpreting cancer genomics data via the Xena platform

Mary J Goldman et al. Nat Biotechnol. 2020 Jun.
No abstract available

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Conflict of interest statement

Competing interests

The authors declare no competing interests.

Figures

Fig. 1 |
Fig. 1 |. Xena’s architecture to securely join public and private data.
Data always flow from the Xena Hubs to the Xena Browser for visualization and integration. a, The user’s web browser (for example, Google Chrome) requests the Xena Browser code and runs it. b, using the Xena Browser, the user requests a visualization, initiating a request for data from the Xena Browser’s list of public hubs. Simultaneously with this request, the Xena Browser requests data from the private local hub on the user’s computer. c, The Xena Browser code combines data from all Xena Hubs together into one coherent visualization. The user can then interact with the visualization to trigger a new data request.
Fig. 2 |
Fig. 2 |. An example Xena Browser Visual Spreadsheet examining published ERG–TMPRSS2 (ETS transcription factor–transmembrane serine protease 2) fusion calls in TCGA PRAD (prostate cancer) by combining data from local and public Xena hubs.
a, A user downloads ERG-TMPRSS2 fusion calls on TCGA PRAD samples from Gao et al. (n = 492) and loads the data into their own local Xena Hub. b, TCGA copy number, gene expression and mutation data from the same samples are available via the public TCGA hub. c, The user then compares the fusion calls to the public data using Xena Browser Visual Spreadsheet. Column B is the fusion call from Gao et al. Column C is copy number variation data, zoomed in to a region of chromosome 21 (37–44 Mb). Amplifications are in red and deletions are in blue. The diagram at the top shows genes along the chromosome; red genes are on the positive strand and blue are on the negative strand. Columns D is ERG gene expression and Column E is ERG exon expression. expression is colored red to green for high to low expression. The gene diagram at the top shows exons as boxes, with tall coding regions and shorter untranslated regions. Column F is SPOP (speckle type BTB/POZ protein) mutation status and also has a gene diagram at the top. The position of each mutation is marked in relation to the gene diagram and colored by its functional impact: mutations computationally predicted to truncate a transcript, such as frameshift or nonsense mutations, are in red and missense mutations are in blue. We can see that the fusion calls are highly consistent with the characteristic overexpression of ERG (columns D and E). However, only a subset of those samples in which a fusion was called can be seen to also have the fusion event observed in the copy number data via an intrachromosomal deletion of chromosome 21 that fuses TMPRSS2 to ERG, as shown in column C. This observation is consistent with the 63.3% validation rate described in Gao et al.. SPOP mutations (blue tick marks in column F) are mutually exclusive with the fusion event. Rows are sorted by the leftmost data column (column B) and sub-sorted on columns thereafter.
See this image and copyright information in PMC

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