Figure 1.

State-Dependent Genetic Interactions of Wnt Signaling Enable the Estimation of Signed Functional Relations

(A) Schematic workflow for state-dependent genetic interaction analysis.

(B) Wnt pathway activity z-scores in S2R⁺ cells of 28,950 independent double-stranded RNAs (dsRNAs) covering 14,331 genes of the Drosophila genome. The scores of the two independent dsRNA designs against core Wnt pathway components known to affect the activity positively (green) or negatively (red) are labeled.

(C and D) Combinatorial RNAi to quantify genetic interactions within the Wnt pathway. Single knockdown phenotypes were estimated from phenotypes of two independent dsRNAs in 144 different genetic backgrounds each (error bars show SE of median determined by bootstrapping). The white dashed bar indicates the expected combinatorial knockdown effect for each gene pair using a multiplicative neutrality function. The measured combinatorial phenotype illustrates the median of the four possible combinations of two independent dsRNA designs against each gene. The difference between the expected and measured combinatorial phenotype is quantified as a π-score for each genetic interaction (yellow if positive, blue if negative at false discovery rate <1%). The data are presented at log₂ scale. Examples show measurements in the Wnt-active state, for all three states see Figures S3A, S3B, S3D, and S3E.

(E) Reproducibility of π-scores with rescreened (four replicates each) query genes evi/wls and Axn, which cover the secreting cell and the destruction complex. Further rescreened query genes are illustrated in Figure S2E. Correlations are highly significant (p < 2.2e−16).

(F) Genetic interaction (π) scores between 14 core pathway components in Drosophila S2R⁺ and 1182-4H cells (PCC, 0.78; p < 2.2e−16). Gene pairs from (C) and (D) and Figure S3C are highlighted.

(G–I) Genetic interaction scores in the three Wnt pathway states: baseline state, and after induction by Wg expression or Apc and Apc2 knockdown (low Wg levels). Candidate and query genes have the same order in each panel.