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Figure 3 | BMC Bioinformatics

Figure 3

From: PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment

Figure 3

The Feature Browser tool helps visualize correlations between gene expression levels and clinical parameters. Example of clinical data shown with the expression of CRABP2 (cellular retinoic acid binding proteins – a carrier protein for members of the vitamin A family). Three heatmaps show the expression for this gene grouped based on the clinical information. In the first heatmap, hormone receptor status is used to group the samples under positive (white bars in the first row) and negative (black bars in the first row). In the second heatmap, HER2 status is used to group the HER2 positive samples (white bars), and HER2 negative (black bars). The third heatmap groups the samples based on grade: grade I (white bars), grade II (orange bars), and grade III (black bars). This gene's expression level correlates with the hormone status (under expressed in hormone positive and over expressed in hormone positive) and tumor grade (over expressed in grade I and II, and under expressed in grade III). This tool thus enables the user to gain insights into clinical associations that were not used in the signature discovery process. The tool also can also generate heatmaps for any number of genes, allowing joint assessment of the expression for multiple expression profiles.

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