E-MAP approach. In an E-MAP, the genetic interactions of a given mutant with all other mutants generates a characteristic interaction profile and any two mutants get a correlation score describing the similarity of their interaction profiles, whereby a very positive correlation of interaction profiles suggests collaboration of the two genes for a single function [28]. As in the ESP-E-MAP report [28], in our MSP-E and MSP/C-MAPs the average of S PX-478 biological activity scores as a function of the correlation score gets increasingly negative, up to a correlation value of about +0.4, and abruptly becomes more positive at higher correlation values (Fig 2A and 2B). Similarly, the ratio of the number of interactions with significantly positive S scores over the number of interactions with significantly Quisinostat custom synthesis negative S scores drops up to a correlation of about 0.4 and then goes up again at higher correlation values (S1G and S1H Fig (Processing of raw E-MAP data)). As typical for E-MAPs, our data showed clustering of functionally related genes upon hierarchical clustering and confirmed some genes as “hyper-interactors” since their deletion generated many more interactions than the average deletion. Data also showed preferential interactions between genes of certain functional classes. This and a general statistical analysis of our data are to be found in S1 Text and S8 Fig (Heat maps and main clusters of the MSP-EMAP), S9 Fig (Enlargement of regions in heat maps of S8A and S8B Fig showing frequent interactions or correlations between genes belonging to two different clusters), S10 Fig (Frequency of significant interactions and correlations within and amongst different functional classes of genes) and S11 Fig (Interdependence of the number of interactions and correlations generated by the MSP-E-MAP).Flc proteins are implicated in an essential processThere were significant changes between the MSP- and the MSP/C-E-MAP in the sense that some genetic interactions were aggravated, others alleviated on Cerulenin as described inPLOS Genetics | DOI:10.1371/journal.pgen.July 27,5 /Yeast E-MAP for Identification of Membrane Transporters Operating Lipid Flip FlopS2 Text and S12 Fig (Comparison of E-MAPs with or without Cerulenin). We had hoped that potential lipid transporters could surface as pairs of less well characterized genes, which would interact more negatively on Cerulenin than without. However, we could not find many such pairs in our data. Most candidate genes were unattractive because of their known localization in the mitochondria, the vacuole or at the plasma membrane, because their interactions were with well-characterized genes not involved in lipid biosynthesis, or because they failed to generate strongly negative S scores. Therefore, we turned our attention to gene pairs giving strong negative interactions in both the MSP- and the MSP/C-E-MAP, which were not strongly aggravated on Cerulenin and in which the function is not fully understood. These criteria are met by the Flc proteins: The S score of the flc1 flc2 double mutant on Cerulenin drops from -11.8 to -12.7, but the double mutant contains two further paralogs, FLC3 and YOR365c, which still are in their wild type (WT) state. Flc proteins are widely conserved in fungi, and have three domains: 1) an Nterminal hydrophilic domain of 150?00 amino acids forming a lipid binding pocket (also present in the human Niemann-Pick type C2 protein required for the egress of cholesterol from late endosomes), 2) a 450 amino aci.E-MAP approach. In an E-MAP, the genetic interactions of a given mutant with all other mutants generates a characteristic interaction profile and any two mutants get a correlation score describing the similarity of their interaction profiles, whereby a very positive correlation of interaction profiles suggests collaboration of the two genes for a single function [28]. As in the ESP-E-MAP report [28], in our MSP-E and MSP/C-MAPs the average of S scores as a function of the correlation score gets increasingly negative, up to a correlation value of about +0.4, and abruptly becomes more positive at higher correlation values (Fig 2A and 2B). Similarly, the ratio of the number of interactions with significantly positive S scores over the number of interactions with significantly negative S scores drops up to a correlation of about 0.4 and then goes up again at higher correlation values (S1G and S1H Fig (Processing of raw E-MAP data)). As typical for E-MAPs, our data showed clustering of functionally related genes upon hierarchical clustering and confirmed some genes as “hyper-interactors” since their deletion generated many more interactions than the average deletion. Data also showed preferential interactions between genes of certain functional classes. This and a general statistical analysis of our data are to be found in S1 Text and S8 Fig (Heat maps and main clusters of the MSP-EMAP), S9 Fig (Enlargement of regions in heat maps of S8A and S8B Fig showing frequent interactions or correlations between genes belonging to two different clusters), S10 Fig (Frequency of significant interactions and correlations within and amongst different functional classes of genes) and S11 Fig (Interdependence of the number of interactions and correlations generated by the MSP-E-MAP).Flc proteins are implicated in an essential processThere were significant changes between the MSP- and the MSP/C-E-MAP in the sense that some genetic interactions were aggravated, others alleviated on Cerulenin as described inPLOS Genetics | DOI:10.1371/journal.pgen.July 27,5 /Yeast E-MAP for Identification of Membrane Transporters Operating Lipid Flip FlopS2 Text and S12 Fig (Comparison of E-MAPs with or without Cerulenin). We had hoped that potential lipid transporters could surface as pairs of less well characterized genes, which would interact more negatively on Cerulenin than without. However, we could not find many such pairs in our data. Most candidate genes were unattractive because of their known localization in the mitochondria, the vacuole or at the plasma membrane, because their interactions were with well-characterized genes not involved in lipid biosynthesis, or because they failed to generate strongly negative S scores. Therefore, we turned our attention to gene pairs giving strong negative interactions in both the MSP- and the MSP/C-E-MAP, which were not strongly aggravated on Cerulenin and in which the function is not fully understood. These criteria are met by the Flc proteins: The S score of the flc1 flc2 double mutant on Cerulenin drops from -11.8 to -12.7, but the double mutant contains two further paralogs, FLC3 and YOR365c, which still are in their wild type (WT) state. Flc proteins are widely conserved in fungi, and have three domains: 1) an Nterminal hydrophilic domain of 150?00 amino acids forming a lipid binding pocket (also present in the human Niemann-Pick type C2 protein required for the egress of cholesterol from late endosomes), 2) a 450 amino aci.
