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Table 1 Enriched gene sets after 10, 20 and 40 minutes of treatment with fosfomycin.

From: Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation

  Downregulation Upregulation
Gene set 10 min 20 min 40 min 10 min 20 min 40 min
AMINO ACID BIOSYNTHESIS_ASPARTATE FAMILY 0.000 0.003 0.005    
AMINO ACID BIOSYNTHESIS_OTHER   0.171     
TRANSPORT AND BINDING PROTEINS_AMINO ACIDS, PEPTIDES AND AMINES   0.000 0.010    
TRANSPORT AND BINDING PROTEINS_CARBOHYDRATES, ORGANIC ALCOHOLS, AND ACIDS   0.090 0.008    
TRANSPORT AND BINDING PROTEINS_CATIONS AND IRON CARRYING COMPOUNDS   0.078 0.228    
TRANSPORT AND BINDING PROTEINS_UNKNOWN SUBSTRATE   0.092 0.022    
ENERGY METABOLISM_AMINO ACIDS AND AMINES   0.135 0.008    
ENERGY METABOLISM_ATP-PROTON MOTIVE FORCE INTERCONVERSION, BIOSYNTHESIS AND DEGRADATION OF POLYSACCHARIDES, PYRUVATE DEHYDROGENASE    0.005    
ENERGY METABOLISM_GLYCOLYSIS_GLUCONEOGENESIS   0.088 0.238    
ENERGY METABOLISM_SUGARS AND TCA CYCLE   0.077 0.089    
SIGNAL TRANSDUCTION_PTS   0.033 0.008    
CELL ENVELOPE_BIOSYNTHESIS AND DEGRADATION OF MUREIN SACCULUS AND PEPTIDOGLYCAN      0.068 0.015
CELL ENVELOPE_BIOSYNTHESIS AND DEGRADATION OF SURFACE POLYSACCHARIDES AND LIPOPOLYSACCHARIDES   0.000 0.009 0.228   
CELL ENVELOPE_OTHER   0.087     
CELLULAR PROCESSES_CELL DIVISION      0.238 0.051
CELLULAR PROCESSES_PATHOGENESIS   0.237     
CELLULAR PROCESSES_TOXIN PRODUCTION AND RESISTANCE    0.068    
CENTRAL INTERMEDIARY METABOLISM_NITROGEN METABOLISM AND AMINO SUGARS      0.046  
CENTRAL INTERMEDIARY METABOLISM_OTHER   0.140     
PURINES, PYRIMIDINES, NUCLEOSIDES, AND NUCLEOTIDES   0.000   0.036   
REGULATORY FUNCTIONS_OTHER       0.169
PROTEIN SYNTHESIS_TRNA AMINOACYLATION   0.083     
PROTEIN FATE_DEGRADATION OF PROTEINS, PEPTIDES, AND GLYCOPEPTIDES      0.238 0.220
PROTEIN FATE_PROTEIN AND PEPTIDE SECRETION AND TRAFFICKING      0.071 0.020
PROTEIN FATE_PROTEIN MODIFICATION AND REPAIR_PROTEIN FOLDING AND STABILIZATION      0.132 0.000
PROTEIN SYNTHESIS_RIBOSOMAL PROTEINS: SYNTHESIS AND MODIFICATION_TRANSLATION FACTORS     0.001   0.005
PROTEIN SYNTHESIS_TRNA AND RRNA BASE MODIFICATION       0.241
TRANSCRIPTION       0.030
DNA METABOLISM       0.249
  1. Downregulation corresponds to negative correlation and upregulation corresponds to positive correlation with the fosfomycin concentration. Numbers show false discovery rates (FDR). Only gene sets with FDR < 0.25 in at least one time point are shown; bold is used when FDR < 0.05.
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