Table 3 Predicted PPI upstream/downstream relations that are validate by recent literature.

From: A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks

Signaling pathway

PPI upstream/downstream relations validated by recent literature

TGF-β

SKI--->SMAD332; TP53--->SMAD333; ATF3--->SMAD334; SMAD3--->SP135; SMAD3--->SKIL36; SMAD3--->AR37

TNF-α

TNFRSF1A--->TRAF38; TRAF2--->RIPK139; TRAF2--->FLNA40; PIAS3--->RELA41; RELA--->NFKB242

EGFR

EGFR--->GAB143; EGFR--->GRB244; SRC--->EGFR45; GRB2--->SOS146

WNT

BTRC--->CTNNB147; GSK3B--->CTNNB148; AKT1--->GSK3B49

  1. We take only four signaling pathways from NetPath database as examples. For each signaling pathway, only several examples are provided. The square bracketed number that follows the predictions denotes the reference number of literature.