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Figure 3 | BMC Bioinformatics

Figure 3

From: Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

Figure 3

Validation of the method on a regular grid consisting of 40 × 30 reactions (pixel). Random gene expression data was generated and mapped onto the nodes of the grid. The 44 samples were divided into two classes differing only significantly in the reactions of three randomly chosen pathways (red arrows). Up-regulation of these reactions in one class was achieved by adding a constant value Δ to their expression levels. Our technique revealed significantly less false positives (FP) than the standard t-test for all chosen values of Δ. The last row shows the desired outcome after 100 runs (TP: true positives, FP: false positives, TN: true positives, FN: false negatives).

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BMC Bioinformatics

ISSN: 1471-2105

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