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Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

Figure 2

PCST constructed from the U87 datasets.

This is a composite network representing the union of the optimal solution to the original PCST problem and 10 suboptimal solutions where 15 percent of the nodes must be different from the optimal solution. TF: transcription factor. Node weight: the log2 fold changes in phosphorylation from the phosphoproteomic data comparing U87H to U87DK cells, or values from the expression regression procedure using the mRNA microarray, DNase-Seq and transcription factor motif data. The absolute value of node weights was used as penalty values for the PCST algorithm.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1002887.g002