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. Author manuscript; available in PMC: 2013 Mar 27.
Published in final edited form as: Nature. 2012 Sep 9;489(7417):519–525. doi: 10.1038/nature11404

Figure 3. Gene expression subtypes integrated with genomic alterations.

Figure 3

Tumors are displayed as columns, grouped by gene expression subtype. Subtypes were compared by Kruskal-Wallis tests for continuous features and by Fisher’s exact tests for categorical features. Displayed features displayed showed significant association with gene expression subtype (P<0.05), except for CDKN2A alterations. deltaN expression percentage represents transcript isoform usage between the TP63 isoforms, deltaN and tap63, as determined by RNA-sequencing. Chromosomal instability (CIN) is defined by the mean of the absolute values of chromosome arm copy numbers from the GISTIC23,24 output. Absolute values are used so that amplification and deletion alterations are counted equally. Hypermethylation scores and iCluster assignments are described in Supplementary Figure S6.1 and S7.A1, respectively. CIN, methylation, gene expression, and deltaN values were standardized for display using z-score transformation.