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Table 4 An example demonstrating the construction of the response variable for AUC computation

From: New methods for separating causes from effects in genomics data

a) b)
Variable 1 Causal Edge Variable 2 Variable 1 Causal Edge Variable 2 Response
NOTCH1 ABCF2 NOTCH1 ABCF2 +
NOTCH1 EIF4E EIF4E NOTCH1 -
NOTCH1 SFRS3 NOTCH1 SFRS3 +
NOTCH1 NUP98 NUP98 NOTCH1 -
NOTCH1 CYCS NOTCH1 CYCS +
NOTCH1 ZNHIT ZNHIT NOTCH1 -
NOTCH1 ATM NOTCH1 ATM +
NOTCH1 TIMM9 TIMM9 NOTCH1 -
  1. A fragment of the gold standard is shown in a). The edges always point from a transcription factor (NOTCH1) to its target gene. 50% of the edges are represented as "transcription factor → gene" and the other 50% as "gene ← transcription factor" in b). This constructs a response variable with positives corresponding to "→" edges (shown in black) and negatives corresponding to "←" edges (shown in red).