Figure 2. Differentially regulated transcription factor, kinase, and phosphatase activities cancer vs. healthy tissue.

1. Bar plot displaying the normalized enrichment score (NES, proxy of activity change) of the 25 up‐ or down‐regulated TF and top 25 up‐ or down‐regulated kinase and phosphatases activities between kidney tumor and adjacent healthy tissue.
2. Right panel shows the 10 most changing RNA abundances of the STAT2 regulated transcripts . Left panel shows the change of abundances of all STAT2 regulated transcripts that were used to estimate its activity change. X‐axis represents log fold change of regulated transcripts multiplied by the sign of regulation (−1 for inhibition and 1 for activation of transcription). Y‐axis represents the significance of the log fold change (−log₁₀ of P‐value, LIMMA moderated unpaired t‐test P‐values). The black line is defined by the following function when fold change is negative : y = abs(hAss − 1 + x/(x + vAss)); and y = abs(hAss − 1 + x/(x − vAss)) when fold change is positive. abs() is the absolute value, hAss is the horizontal asymptote (hAss = 1.3) and vAss is the vertical asymptote (vAss = 0.3).
3. Right panel shows the 10 most changing phosphopeptide abundances of the CDK7 regulated phosphopeptides. Left panel shows the change of abundances of all CDK7 regulated phosphopeptides that were used to estimate its activity change. X‐axis represents log fold change of regulated transcripts multiplied by the sign of regulation (−1 for inhibition and 1 for activation of transcription). Y‐axis represents the significance of the log fold change (−log₁₀ of P‐value, LIMMA moderated unpaired t‐test P‐values). The black line is defined by the following function when fold change is negative : y = abs(hAss − 1 + x/(x + vAss)); and y = abs(hAss − 1 + x/(x − vAss)) when fold change is positive. Where abs() is the absolute value, hAss is the horizontal asymptote (hAss = 1.3) and vAss is the vertical asymptote (vAss = 0.3).