Fig. 1.

A hypothetical example of epistasis analysis with three genes, u, v and w. Nodes in the central graph represent mutant phenotypes. The phenotypic difference between a double knockout [e.g. $R(u\Delta v\Delta )$] and a single knockout mutant [e.g. $R(v\Delta )$] is represented with the length of the corresponding dotted edge. Expected double mutant phenotypes, which assume no interaction between genes (see also Section 2.1), are denoted with E [e.g. $E(u\Delta v\Delta )$]. A double mutant $u\Delta v\Delta$ (a) has a phenotype similar to that of a single mutant $v\Delta$, which indicates that v is epistatic to u. From the activity of genes v and w (b) we conjecture that gene v partially depends on gene w, i.e. v also acts through a separate pathway because their double mutant $v\Delta w\Delta$ has a phenotype that is equally similar to the single knockout $R(w\Delta )$ and the expected phenotype $E(v\Delta w\Delta )$. The phenotype of double knockout $u\Delta w\Delta$ (c) is close to the expected phenotype of $u\Delta w\Delta ,E(u\Delta w\Delta ),$ which may be explained by u and w acting independently in parallel pathways. Gene ordering from these three relations is preserved in the joint network (d), which is a candidate pathway of genes u, v and w