Fig. 3: Graphical summary of the properties of NED genes (N = 49) compared to non-NED (N = 925) and essential genes (N = 157) in S. cerevisiae, considering aerobic conditions.

The NED genes have more protein-protein and genetic interactions than the non-NED ones. The protein-protein interactions (ppi) for these genes are even higher than for the essential genes, while the essentials have more genetic interactions than all the other genes on average (Mann–Whitney two-sided test used for statistical significance). Moreover, a significantly higher fraction (69%) of NED genes are singletons (do not have a paralog) compared to non-NED genes (32%; Chi-square test p-value < 7.2e-8). Thus the NED genes rarely have back-up copies, making them very difficult to remove during the construction of the MMNs. Genetic interactions were based on Costanzo et al. ¹⁹, protein-protein interactions were based on the highly confident interactions set of Batada et al. ²³. Singletons were calculated with BLASTp and homology cut-off of E-value < 1e-5. For the boxplots, each box spans from the first quartile (Q1) to the third quartile (Q3). The horizontal line inside the box represents the center/median value (Q2), while the dotted horizontal line represents the mean. The box whiskers span from the box’s edges +/− 1.5 times the interquartile range (IQR: Q3-Q1). The dots outside the box whiskers represent the outliers. Source data are provided as a Source Data file: Fig. 3 Source Data Source File.xlsx.