Figure 4. Annotating physical interactions with signs of activation or suppression.

The filamentous growth pathway in yeast is displayed in frame A; The high osmolarity glycerol (HOG) pathway is displayed in frame B. Literature curated interaction signs are denoted by the arrow type: regular (activating), cut (suppressing), or none (unassigned). Node colors correspond to a specific partition of the respective genes into two groups made by the sign-annotation algorithm. Gray nodes represent proteins that could not be assigned to a group due to a lack of data. Physical edges connecting proteins of different groups are predicted as suppressing, and edges connecting proteins of the same group are predicted as activating. SPINE, in contrast, assigns signs to proteins, meaning that all the out-going edges of a protein are assigned the same sign. Proteins that were predicted by SPINE to be activators are displayed as hexagons. Proteins that were predicted by SPINE as suppressors are displayed as squares.