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Table 2 Selectivity score based selection of GO terms and gene variations

From: Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression

Phenotypes

Influential gene variations and GO terms

Melibiose 2% Rate

Paralog, frame shift variations, transport, stop codon variations, cellular protein catabolic process, transposition, copy number variations, response to stress, DNA metabolic process, mitochondrion organization, Essential.gene, RNA metabolic process, cellular amino acid and derivative metabolic process, response to chemical stimulus, response to chemical stimulus and metabolism

Melibiose 2% Efficiency

Copy number variations, transposition, Paralog, frame shift variations, stop codon variations, transport, cellular amino acid and derivative metabolic process, response to chemical stimulus, cell cycle, signal transduction, conjugation, RNA metabolic process, translation, mitochondrion organization, cellular carbohydrate metabolic process

Cupper chloride 0.375 mM Rate

Stop codon variations, Paralog, transposition, frame shift variations, copy number variations, RNA metabolic process, transport, protein modification process, response to stress, generation of precursor metabolites and energy, cellular respiration, DNA metabolic process, transcription, response to chemical stimulus, chromosome organization

Cupper chloride 0.375 mM Efficiency

Paralog, frame shift variations, transport, transposition, stop codon variations, Essential.gene, copy number variations, cellular amino acid and derivative metabolic process, RNA metabolic process, response to stress, protein modification process, chromosome organization, ribosome biogenesis, cell cycle, response to chemical stimulus

NaCl 0.85 M Rate

Generation of precursor metabolites and energy, cellular respiration, frame shift variations, stop codon variations, Paralog, copy number variations, transport, heterocycle metabolic process, sporulation resulting in formation of a cellular spore, transposition, transcription, cellular carbohydrate metabolic process, Essential.gene, RNA metabolic process, protein modification process

NaCl 1.25 M Rate

Cellular respiration, stop codon variations, frame shift variations, Paralog, generation of precursor metabolites and energy, Essential.gene, cellular lipid metabolic process, RNA metabolic process, transport, mitochondrion organization, cofactor metabolic process, transposition, response to chemical stimulus, transcription, DNA metabolic process

NaCl 0.85 M Efficiency

Paralog, transposition, transport, conjugation, frame shift variations, stop codon variations, signal transduction, RNA metabolic process, response to stress, chromosome organization, response to chemical stimulus, translation, ribosome biogenesis, mitochondrion organization, cellular amino acid and derivative metabolic process

NaCl 1.25 M Efficiency

Transposition, Paralog, copy number variations, frame shift variations, stop codon variations, response to stress, protein modification process, chromosome organization, transport, cellular amino acid and derivative metabolic process, translation, conjugation, RNA metabolic process, Essential.gene, mitochondrion organization

Maltose 2% Rate

Paralog, transposition, frame shift variations, stop codon variations, RNA metabolic process, response to chemical stimulus, transport, transcription, DNA metabolic process, copy number variations, response to stress, protein modification process, cellular amino acid and derivative metabolic process, heterocycle metabolic process, cellular aromatic compound metabolic process

Maltose 2% Efficiency

stop codon variations, generation of precursor metabolites and energy, Paralog, cellular amino acid and derivative metabolic process, transposition, cellular respiration, Essential.gene, protein modification process, heterocycle metabolic process, cellular aromatic compound metabolic process, transport, frame shift variations, RNA metabolic process, ribosome biogenesis, response to chemical stimulus

Galactose 2% Rate

DNA metabolic process, stop codon variations, translation, generation of precursor metabolites and energy, cellular respiration, Paralog, mitochondrion organization, copy number variations, cellular amino acid and derivative metabolic process, frame shift variations, transport, Essential.gene, response to stress, chromosome organization, meiosis

Galactose 2% Efficiency

Paralog, DNA metabolic process, frame shift variations, RNA metabolic process, stop codon variations, transport, generation of precursor metabolites and energy, cellular respiration, copy number variations, mitochondrion organization, cellular amino acid and derivative metabolic process, heterocycle metabolic process, transposition, protein folding, chromosome organization

Heat 37° Rate

Frame shift variations, transport, Paralog, generation of precursor metabolites and energy, heterocycle metabolic process, Essential.gene, cellular protein catabolic process, DNA metabolic process, mitochondrion organization, cellular respiration, transposition, stop codon variations, copy number variations, RNA metabolic process, transcription

Heat 40° Rate

Paralog, transport, frame shift variations, generation of precursor metabolites and energy, cellular protein catabolic process, heterocycle metabolic process, copy number variations, transposition, stop codon variations, DNA metabolic process, translation, response to stress, protein modification process, conjugation, Essential.gene

Heat 37° Efficiency

Generation of precursor metabolites and energy, DNA metabolic process, cellular amino acid and derivative metabolic process, cellular respiration, heterocycle metabolic process, stop codon variations, Essential.gene, RNA metabolic process, cofactor metabolic process, vitamin metabolic process, transposition, translation, Paralog, frame shift variations, transport

Heat 40° Efficiency

Paralog, frame shift variations, copy number variations, transport, transposition, protein modification process, cellular carbohydrate metabolic process, cellular amino acid and derivative metabolic process, heterocycle metabolic process, RNA metabolic process, response to stress, generation of precursor metabolites and energy, cell cycle, signal transduction, conjugation

Sodium arsenite oxide 3.5 mM Rate

Stop codon variations, Paralog, frame shift variations, copy number variations, cellular amino acid and derivative metabolic process, transposition, transport, response to stress, RNA metabolic process, conjugation, translation, transcription, protein modification process, Essential.gene, chromosome organization

Sodium arsenite oxide 5 mM Rate

Stop codon variations, copy number variations, transposition, frame shift variations, transport, generation of precursor metabolites and energy, cellular respiration, Paralog, protein modification process, Essential.gene, transcription, cell cycle, DNA metabolic process, response to chemical stimulus, ribosome biogenesis

Sodium arsenite oxide 3.5 mM Efficiency

Paralog, stop codon variations, frame shift variations, transposition, copy number variations, RNA metabolic process, cellular amino acid and derivative metabolic process, transport, DNA metabolic process, translation, cellular carbohydrate metabolic process, peroxisome organization, response to stress, protein modification process, transcription

Sodium arsenite oxide 5 mM Efficiency

Paralog, frame shift variations, stop codon variations, transposition, copy number variations, transport, protein modification process, cellular carbohydrate metabolic process, generation of precursor metabolites and energy, cellular respiration, Essential.gene, RNA metabolic process, response to stress, response to chemical stimulus, translation

  1. Selected variables from the background information matrix Z that have a selectivity score above 0.2 for each phenotype obtained through the proposed model. Variables correspond to the presence or absence of specific gene amplifications, and the presence or absence of premature stop codons and frameshifts.