Table 1 The numbers of loci showing significant (q-value < 0.05) differential expression in RNA-Seq are shown as the total of each functional category and for each comparison of conditions (combination of YRR1 allele and growth medium)
Functional CategoryaTotal Per CategoryExpression ChangeS96, 4NQO/YPDYJM789, 4NQO/YPDS96-I775E, 4NQO/YPDYJM789/S96, 4NQOS96-I775E/S96, 4NQOS96-I775E/YJM789, 4NQOYJM789/S96, YPDS96-I775E/S96, YPDS96-I775E/YJM789, YPDS96-I775E YPD/YJM789 4NQO
All loci tested6717Up750510609611610855390385671
DNA damage328Up31242402309716
Oxidative stress106Up443532022424187
Protein folding116Up202824182122026
Purine biosynthesis and RNR genes64Up148703101113
Pyrimidine biosynthesis19Up2120100125
Nucleotide salvage18Up1110000124
  • The condition before “/” is the numerator and the one after is the denominator for differential expression. 4NQO, 4-nitroquinoline-1-oxide; YPD, Yeast Peptone Dextrose; RNR, ribonucleotide-diphosphate reductase.

  • a The genes in specific functional categories were found through Gene Ontology (GO) term search within S. cerevisiae on AmiGO2 ( DNA damage: GO:0006974 representing “cellular response to DNA damage stimulus”; Oxidative stress: GO:0006979 representing “response to oxidative stress”; Protein folding: GO:0006457 representing “protein folding”; Purine biosynthesis and RNR genes: GO:0006164 representing “purine nucleotide biosynthetic process,” as well as RNR1, RNR2, RNR3, and RNR4 genes; Pyrimidine biosynthesis: GO:0006221 representing “pyrimidine nucleotide biosynthetic process”; and Nucleotide salvage: union of GO:0043173 representing “nucleotide salvage,” GO:0043101 representing “purine-containing compound salvage,” and GO:0008655 representing “pyrimidine-containing compound salvage.”