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Fig. 6 | Genome Biology

Fig. 6

From: Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis

Fig. 6

Individual impact of rare and frequent gene CNAs with high impact on survival signatures. Characterization of TCGA cohorts GBM, OV, and LUAD. a–f Average impact of gene deletions (a–c) and amplifications (d–f) on the expression of cohort-specific survival signature genes. The average impact value of each specific gene CNA quantifies the average contribution of this gene CNA to the variation of the expression levels of all cohort-specific survival signature genes in percentage of explained variance. The vertical gray dashed line at 1 % of patients defines the cutoff used to separate rare from frequent CNAs. The x-axes are in logarithmic scale. g–i Corresponding joint functional annotation of deleted and amplified impact genes. Genes were classified as rarely (CNA frequency <1 %) or frequently (CNA frequency ≥1 %) mutated. The proportion of genes in selected functional classes are shown. Significant enrichment of an individual category is shown above bars as * (p<0.05) and ** (p<0.01, Fisher’s exact test). Note that the height of the bars doses not necessarily correlate with significance due to the different sizes of the functional classes. CC cell cycle, CI cell–cell interaction, CNA copy number alteration, DR DNA replication, GBM glioblastoma multiforme, GL glycolysis, KC known cancer genes, KP kinases and phosphatases, LUAD lung adenocarcinoma, MP metabolic pathways, OP oxidative phosphorylation, OV ovarian serous cystadenocarcinoma, SP signaling pathways, TCGA The Cancer Genome Atlas, TF transcription factors, TM telomere maintenance

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