Secondary interaction map showing published interactions. A list of potential secondary interactions (prey-prey), including interactions with bait proteins (bait-prey, primary interactions), was generated as described under “Experimental Procedures.” Each interaction was analyzed using BePro3, and the Bayes' odds were assigned for each interaction. Each interaction was then cross-referenced with the GS data set for published interactions, and those interactions seen in the literature were visualized using Cytoscape. Interactions shown in red involve bait proteins (square nodes, primary interactions), and secondary interactions are shown in blue. The width of each interaction line is proportional to the Bayes' odds, and the direction of the arrow indicates the interaction with the highest Bayes' odd. Where the Bayes' odds were equal to 0 in both directions, no arrow is shown. Interactions with proteins only detected using one of the search engines (Scaffold and Phenyx) are shown as a dotted line. Each interaction number (shown in red) indicates the corresponding reference (10, 19, 25, 26, 31, 32, 49, 50, 65–107). Green nodes indicate heparin binding molecules, and diamond nodes indicate heparan sulfate proteoglycans.