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Fig. 4 | Genome Medicine

Fig. 4

From: Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

Fig. 4

Validation of targets in an independent ccRCC patient cohort from The Cancer Genome Atlas (TCGA). a Heatmap of enrichment scores in TCGA patient cohort (KIRC). Shown are 50 signatures that were identified as ccRCC-enriched in analysis of cohort 1 and proximal tubule cells. Signatures that were not enriched by an enrichment score of ≥ 0.5 in at least 80% of TCGA cohort samples are marked by blue asterisks. Genes exclusively included in those signatures were removed in further analyses. b Kernel density estimate of mean log2 gene expression levels in TCGA ccRCC tumor samples. Mean log2 expression levels of the 173 candidate genes are marked in red. The minimal expression threshold was set at the local minimum of the estimated frequency distribution at a log2 expression of 6.5 (gray vertical intersected line). All candidates passed the threshold. c Volcano plot of gene expression fold changes in tumors compared to non-tumor tissues. Shown are the values of the unpaired analysis. Expression values that passed the set thresholds at FC > 0 and p < 0.05 in both unpaired and paired analyses are marked in red. d Plotted are the coefficients of variation (CV) in percent. The intersected line marks the set threshold of CV ≤ 10% for candidate selection. Candidates that did not pass the threshold are printed in black

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