Fig. 3.

Higher-order epistasis among knockouts and multiple loci is an important contributor to background effects. In a, for each mutation-responsive two-locus effect, we partitioned the individual and joint contributions of the two loci. L1 and L2 refer to the involved loci, while KO denotes the relevant knockout. We determined the relative phenotypic variance explained (PVE) by interactions between a knockout and each individual locus (i.e., KO × L1 and KO × L2) and higher-order epistasis involving a knockout and the two loci (i.e., KO × L1 × L2). Similarly, in b, for each mutation-responsive three-locus effect, we determined the relative PVE for all possible mutation-responsive one-, two-, and three-locus effects involving the participating loci. In both a and b, relative PVE values were calculated using sum of squares obtained from ANOVA tables, as described in Methods. Mutation-responsive effects that interact with multiple knockouts are shown multiple times, once for each relevant knockout