VPS45 and infection: The PPI analysis among all the 2,255 DEGs indicated a ratio of 7,063/2,632 (2.7 ×) of protein-protein networks for CK-SCN4/CK-SCN5, including 866/194 activation (4.5 ×), 2715/1381 (2 ×) binding, 781/280 (2.8 ×) catalysis, 401/104 (3.9 ×) expression, 462/96 (4.8 ×) inhibition, 874/166 (5.3 ×) ptmod (post translational modification), and 964/411 (2.3 ×) reaction, indicating soybean resistant response to the SCN4 infection activated more protein–protein interactions than a susceptible response to the SCN5 infection, especially in post translational modification, inhibition, and activation.