PATRI, a Genomics Data Integration Tool for Biomarker Discovery

Figure 4

Translational” analysis of vemurafenib sensitivity in melanoma cell lines and clinical samples. Results of PATRI “Translational” analysis workflow performed on a panel of melanoma cell lines sensitive or resistant to vemurafenib treatment and on a panel of 478 TCGA melanoma clinical samples. (a) List of melanoma cell lines with respective vemurafenib IC50 values. A threshold of 1μM was chosen to define “Sensitive” and “Resistant” cell lines. (b) Heatmap dendrogram for the results of PATRI odds ratio mutational analysis in “Sensitive” versus “Resistant” melanoma cell lines. Red, mutated genes; green, wild type genes. (c) Heatmap representing hierarchical cluster mutation analysis via random forest categorization of the predicted “Sensitive” or “Resistant” 478 melanoma TCGA samples, based on 3 selected mutated genes: BRAF, MSH3, ALPK2 (sample IDs could not be represented on the lower part of the graph). (d) Box plot representing the reported age distribution in predicted “Sensitive” (avg. 54.3) and “Resistant” (avg. 60.3) clinical melanoma sample groups. The displayed data correspond to the column “Age” in the TCGA Skin Cutaneous Melanoma (TCGA, Provisional) Clinical Data annotation file.

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