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Figure 2 | Genome Medicine

Figure 2

From: A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis

Figure 2

A genome-wide screen for Yor1-ΔF gene interaction. (A) Time-lapse imaging was used to measure the growth phenotypes of haploid double mutants. Shown are example spot cultures (time indicated below each image) for strains with deletion suppressor and deletion enhancer effects on oligomycin sensitivity, along with a yor1-ΔF single mutant control, grown on media containing 0.2 μg/mL oligomycin. (B) To quantify phenotypes, spot culture image series were analyzed for pixel density and fit to a logistic growth equation [14]. See Materials and Methods and Additional File 1 - Discussion B for further details. (C) Multiple concentrations of oligomycin were used to assess the interaction strength for each gene deletion, using the growth parameter, L, corresponding to the time at which a culture reaches its half maximal density, K (r denotes the maximum specific rate). Gene deletion suppressor effects (interactions reducing L) are highlighted in green, whereas gene deletion enhancer effects (interactions increasing L) are indicated by blue. The three panels contain growth curves for the deletion strains shown in panel A at different oligomycin concentrations (0, 0.15, and 0.25 μg/mL). G(t) is the logistic fit for the data obtained for each culture time series; raw values for culture growth are indicated by black circles (WT/Ref), green squares (hlj1-Δ0 strain), and blue triangles (sop4-Δ0 strain). (D) Gene interaction is shown for hlj1-Δ0 (green squares) and sop4-Δ0 (blue triangles). Divergence of L for the double mutants is displayed as a function of oligomycin concentration, compared to the phenotypic distribution of replicates of the yor1-ΔF670/R1116T single mutant (gray diamonds represent the distribution of central 95% of L values for 768 single mutant replicates). The data for the double mutants were shifted by their difference with the single mutant (median response) at the zero oligomycin concentration (filled symbols), correcting for growth differences not attributable to oligomycin response. To quantify interactions, the data for each deletion mutant were first fit to a quadratic equation, and then the difference between the deletion mutant and the reference median was taken at an indicated concentration of oligomycin. To highlight the interactions, the raw data (left panel) were transformed to remove the oligomycin dose effect (right panel). (E) A scatter plot of interaction scores for pairs of gene deletion strains with overlapping open reading frames (obtained at oligomycin = 0.25 µg/mL). The open reading frames with a greater degree functional annotation in SGD were designated as the 'ORFs', and those with less functional annotation designated 'overlapping genomic regions' [78]. (F) The affect of oligomycin dose on the growth curve parameters (left to right), L (time to half carrying capacity, K (carrying capacity), and r (maximum specific rate), and the area under the curve ('A'), for 384 replicates of the yor1-ΔF single mutant strain. Each diamond represents the central 95% of the standardized data for that oligomycin dose. The data for each parameter at each dose was standardized (arbitrary units) by subtracting the mean and dividing by the standard deviation of the group not treated with oligomycin. The oligomycin = 0 group is centered at 0. Using standard units for the data allows the dose trend between the panels to be directly compared. The oligomycin dose effect is greatest for L, followed by AUC, and with minor effects on K and r.

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