Table 2

Selectivity score based selection of GO terms and gene variations
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

Selected variables from the background information matrix Zthat 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.

Mehmood et al.

Mehmood et al. BMC Bioinformatics 2012 13:327   doi:10.1186/1471-2105-13-327

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