Galardini M~Beltrao P, 2019

Pubmed ID 31885205
Title The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.
Authors Marco Galardini, Bede P Busby, Cristina Vieitez, Alistair S Dunham, Athanasios Typas, Pedro Beltrao
Abstract Loss-of-function (LoF) mutations associated with disease do not manifest equally in different individuals. The impact of the genetic background on the consequences of LoF mutations remains poorly characterized. Here, we systematically assessed the changes in gene deletion phenotypes for 3,786 gene knockouts in four Saccharomyces cerevisiae strains and 38 conditions. We observed 18.5% of deletion phenotypes changing between pairs of strains on average with a small fraction conserved in all four strains. Conditions causing higher wild-type growth differences and the deletion of pleiotropic genes showed above-average changes in phenotypes. In addition, we performed a genome-wide association study (GWAS) for growth under the same conditions for a panel of 925 yeast isolates. Gene-condition associations derived from GWAS were not enriched for genes with deletion phenotypes under the same conditions. However, cases where the results were congruent indicate the most likely mechanism underlying the GWAS signal. Overall, these results show a high degree of genetic background dependencies for LoF phenotypes.
Citation Mol. Syst. Biol. 2019; 15:e8831

Datasets

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Paper Phenotype Condition Medium Collection Tested mutants Data Details
Galardini M~Beltrao P, 2019 growth (colony size) 2,4-D [3 mM] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) temperature [39ºC], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) 5-fluorouracil [500 uM] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) 6-azauracil [8 mM] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) 6-azauracil [8 mM], temperature [39ºC], time [48 h] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) acetic acid [0.63%] SC hap a 3,433 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) amphotericin B [100 uM] SC + DMSO hap a 4,860 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) amphotericin B [100 uM], oxygen [0%] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) oxygen [0%] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) cadmium dichloride [250 uM] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) caffeine [15 mM] SC hap a 3,433 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) caffeine [20 mM] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) caspofungin [6.5 nM], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) clozapine [350 uM] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) cycloheximide [625 nM] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) doxorubicin [75 uM] SC hap a 3,405 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) glucose [20%] SC (-C) hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) glycerol [2%], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) maltose [2%] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.4 M] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.4 M], temperature [39ºC], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.6 M], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.6 M], temperature [39ºC], time [48 h] SC hap a 4,860 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) nickel sulfate [2 mM] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) paraquat [1.2 mM], time [48 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) glucitol [1 M] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) standard SC + DMSO [1%] hap a 4,859 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) standard SD + His + Leu + Lys + Ura, -N hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) standard SD + His + Leu + Lys + Ura (2) hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) standard SC, 25mM HEPES hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) temperature [39ºC], time [72 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) 6-azauracil [8 mM], temperature [39ºC], time [72 h] SC + DMSO hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) caspofungin [6.5 nM], time [72 h] SC hap a 4,837 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) glycerol [2%], time [72 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.4 M], temperature [39ºC], time [72 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.6 M], time [72 h] SC hap a 4,861 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) sodium chloride [0.6 M], temperature [39ºC], time [72 h] SC hap a 4,860 Quantitative
Galardini M~Beltrao P, 2019 growth (colony size) paraquat [1.2 mM], time [72 h] SC hap a 4,861 Quantitative

Curation history

Tested strains

Dec. 10, 2019 Ready to load.
Dec. 12, 2019 Loaded.

Data

Dec. 10, 2019 Ready to load.
Dec. 12, 2019 Loaded.