Fig 1.
Blue-framed rectangles represent processes, orange-shaped parallelograms represent input data.
Fig 2.
The main component of the breast cancer interaction network.
Blue nodes represent TFs, red nodes represent genes, green nodes represent miRNAs. The higher node degree is, the bigger is the node size. Edges are colored according to node types they connect.
Fig 3.
The first major strongly connected component.
Nodes corresponding to apoptosis, hypoxia and DNA damage responses are colored in blue, nodes corresponding to apoptosis and hypoxia response are colored in red, while nodes associated only to apoptosis, hypoxia response and DNA damage response are colored in orange, purple and green, respectively. The arrows and T-shaped lines signify activation and repression, respectively.
Fig 4.
The second major strongly connected component.
TFs are colored in blue, miRNAs are colored in green. The arrows and T-shaped lines signify activation and repression, respectively.
Fig 5.
Performance of the eight-gene signature on the validation set (GSE1456).
(A) ROC curve (AUC = 0.78). (B) Kaplan-Meier plot (logrank test p = 0.0015).
Fig 6.
Neighborhood of genes overrepresented in prognostic signatures.
Diamond-shaped nodes correspond to fourteen overrepresented genes. Blue nodes correspond to TFs, red nodes correspond to genes, green nodes correspond to miRNAs. The arrows and T-shaped lines signify activation and repression, respectively.
Fig 7.
Classifier construction pipeline.
Green-framed ellipses denote lists of input genes (pipeline can be evaluated in two ways), blue-framed rectangles represent processes, orange-shaped parallelograms represent input data.