The genes then ordered proceeding from Chr. I to XVI and on each chromosome from the end of the left arm towards the end of the right arm. This rearranged S score matrix (S3C Table) was transformed into the heat map shown here. Arrows point to some short green lines corresponding to a strong negative interaction of a single gene with all MSP set genes in a certain chromosomal region as follows: Arrow 2: CHO1 interacting with Chr. VII bp 63’048 to 202’273, encompassing EMC4 (= YGL231C), OST5, VRG4, YIP4, TPN1, YIP5 and AIM14 (= YGL160W). Arrow 3, PCP1 interacting with Chr. XII bp 41’280 to 211’933 encompassing YBT1 (= YLL048C), GPI13, RRT7, POM33, THI73, IZH3 and SMF3 (= YLR034C). Arrow 4, TDA5 interacting with Chr. XV bp 114’138 to 242’747 encompassing WSC3 (= YOL105C), IZH4, YPQ1, PHM7, YOL079W, DSC2, RRT8 and LDS2 (= YOL047C). Arrow 5, CTR1 (YPR124W) interacting with Chr. XII bp 323’544 to 444’688 encompassing SUL2 (= YLR092W), ZRT2, NHA1 and YLR152C. Arrow 6, COT1 (YOR316C) at the extreme end of Chr. XV interacting with the centromeric region of the same chromosome (bp 240’204 to 423’732) encompassing RRT8 (= YOL048C), LDS2, ALG6, DFG16, AKR2, IRC23 and RSB1 (= YOR049C). Arrow 7, pointing the vertical green line shows QDR2 interacting with Chr. VIII bp 256’360 to 467’914 encompassing YHR078W, HXT5, YHR140W, CHS7, PEX28, LAM1 and SVP26 (= YHR181W). Finally arrow 8, shows COS6 interacting with Chr. XIV bp 8’330 to 34’696 encompassing COS1 (= YNL336W), PFA3, LEM3, KRE1 and VNX1 (= YNL321W). This however is a false hit as we found out that cos6::kanMX in our library is in fact cos1::KanMX; the confusion arises because the two genes have very similar coding and flanking sequences. 16 well-delimitated grey zones along the diagonal correspond to the negative genetic interactions within each of the 16 chromosomes that were disregarded because of the close linkage of the interacting genes; the size of each zone is proportional to the number of MSPs on that chromosome, not the chromosome. doi:10.1371/journal.pgen.1006160.gsingle deletions on another chromosome or a distant region of the same chromosome appear as short green or red stripes; they are pointed out by numbered arrows, whereby arrow 1 points to the interactions of chs1 with genes on the right arm of Chr. II discussed above (Fig 11A). Importantly, these chromosomally SCH 530348 web clustered interactions do not involve the “hyper-PLOS Genetics | DOI:10.1371/journal.pgen.July 27,19 /Yeast E-MAP for Identification of Membrane Transporters Operating Lipid Flip Flopinteractors” that show interactions throughout the heat map (S8A Fig (Heat maps and main clusters of the MSP-E-MAP)). We believe that these regionally concentrated negative interactions with a deletion at a distant locus (e.g. chs1) are caused by non-declared intergenic suppressor mutations that rescue the growth defect caused by the distant deletions. For example, a gain of function suppressor SP600125 custom synthesis mutation in CHS2 present in the chs1::ura3MX query strain may be present in all crosses of that query except the ones with genes in the vicinity of CHS2, where the kanMX-marked array gene will be selected for and the suppressor in CHS2 is likely to be lost. Such a suppressor mutation in CHS2 would not exist in elo2 and elo3 queries and, if it existed, would not have any genetic interaction with elo2 and elo3 strains, explaining the absence of a regional effect around CST26 in the elo2 cst26 and elo3 cst26 mutants (Fig 11A). (The strong negative S sco.The genes then ordered proceeding from Chr. I to XVI and on each chromosome from the end of the left arm towards the end of the right arm. This rearranged S score matrix (S3C Table) was transformed into the heat map shown here. Arrows point to some short green lines corresponding to a strong negative interaction of a single gene with all MSP set genes in a certain chromosomal region as follows: Arrow 2: CHO1 interacting with Chr. VII bp 63’048 to 202’273, encompassing EMC4 (= YGL231C), OST5, VRG4, YIP4, TPN1, YIP5 and AIM14 (= YGL160W). Arrow 3, PCP1 interacting with Chr. XII bp 41’280 to 211’933 encompassing YBT1 (= YLL048C), GPI13, RRT7, POM33, THI73, IZH3 and SMF3 (= YLR034C). Arrow 4, TDA5 interacting with Chr. XV bp 114’138 to 242’747 encompassing WSC3 (= YOL105C), IZH4, YPQ1, PHM7, YOL079W, DSC2, RRT8 and LDS2 (= YOL047C). Arrow 5, CTR1 (YPR124W) interacting with Chr. XII bp 323’544 to 444’688 encompassing SUL2 (= YLR092W), ZRT2, NHA1 and YLR152C. Arrow 6, COT1 (YOR316C) at the extreme end of Chr. XV interacting with the centromeric region of the same chromosome (bp 240’204 to 423’732) encompassing RRT8 (= YOL048C), LDS2, ALG6, DFG16, AKR2, IRC23 and RSB1 (= YOR049C). Arrow 7, pointing the vertical green line shows QDR2 interacting with Chr. VIII bp 256’360 to 467’914 encompassing YHR078W, HXT5, YHR140W, CHS7, PEX28, LAM1 and SVP26 (= YHR181W). Finally arrow 8, shows COS6 interacting with Chr. XIV bp 8’330 to 34’696 encompassing COS1 (= YNL336W), PFA3, LEM3, KRE1 and VNX1 (= YNL321W). This however is a false hit as we found out that cos6::kanMX in our library is in fact cos1::KanMX; the confusion arises because the two genes have very similar coding and flanking sequences. 16 well-delimitated grey zones along the diagonal correspond to the negative genetic interactions within each of the 16 chromosomes that were disregarded because of the close linkage of the interacting genes; the size of each zone is proportional to the number of MSPs on that chromosome, not the chromosome. doi:10.1371/journal.pgen.1006160.gsingle deletions on another chromosome or a distant region of the same chromosome appear as short green or red stripes; they are pointed out by numbered arrows, whereby arrow 1 points to the interactions of chs1 with genes on the right arm of Chr. II discussed above (Fig 11A). Importantly, these chromosomally clustered interactions do not involve the “hyper-PLOS Genetics | DOI:10.1371/journal.pgen.July 27,19 /Yeast E-MAP for Identification of Membrane Transporters Operating Lipid Flip Flopinteractors” that show interactions throughout the heat map (S8A Fig (Heat maps and main clusters of the MSP-E-MAP)). We believe that these regionally concentrated negative interactions with a deletion at a distant locus (e.g. chs1) are caused by non-declared intergenic suppressor mutations that rescue the growth defect caused by the distant deletions. For example, a gain of function suppressor mutation in CHS2 present in the chs1::ura3MX query strain may be present in all crosses of that query except the ones with genes in the vicinity of CHS2, where the kanMX-marked array gene will be selected for and the suppressor in CHS2 is likely to be lost. Such a suppressor mutation in CHS2 would not exist in elo2 and elo3 queries and, if it existed, would not have any genetic interaction with elo2 and elo3 strains, explaining the absence of a regional effect around CST26 in the elo2 cst26 and elo3 cst26 mutants (Fig 11A). (The strong negative S sco.