Skip to main content

Table 1 The degree of pathway perturbation as related to the exposure concentration of naphthenic acids (NAs).

From: Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment

KEGG pathway name (entry) low mid high Involved genes (total number)
Ribosome (eco03010) 0.32 0.40 0.45 rplN, rplY, rpmB, rpsB, rpsJ, rpsL, rpsM, rpsO, rpsP, rpsT, rpsU, rrnA, rrnB, rrnC, rrnD, rrnH (16)
Metabolic pathways (eco01100) 0.45 0.42 0.69 aceB, acnB, aspA, gatY, ilvC, lpxC, manX, ribB, rpiA, serC (10)
Microbial metabolism in diverse environments (eco01120) 0.59 0.45 0.78 aceB, acnB, manX, rpiA, serC (5)
Biosynthesis of amino acids (eco01230) 0.55 0.38 0.95 acnB, ilvC, rpiA, serC (4)
Biosynthesis of secondary metabolites (eco01110) 0.55 0.63 0.95 acnB, ilvC, rpiA, yfbE (4)
Amino sugar and nucleotide sugar metabolism (eco00520) 0.61 0.52 0.79 manX, ptsG, yfbE (3)
2-Oxocarboxylic acid metabolism (eco01210) 0.10 0.25 1.00 acnB, ilvC (2)
Aminoacyl-tRNA biosynthesis (eco00970) 0.71 0.67 1.00 ileX, tyrS (2)
Glycerophospholipid metabolism (eco00564) 0.39 0.37 0.76 glpA, glpD (2)
Glyoxylate and dicarboxylate metabolism (eco00630) 0.30 0.49 0.79 aceB, acnB (2)
Nitrogen metabolism (eco00910) 0.68 0.73 0.80 aspA, yadF (2)
Phosphotransferase system (PTS) (eco02060) 0.41 0.37 0.62 ptsG, treB (2)
ABC transporters (eco02010) 0.48 0.50 0.67 oppA (1)
Citrate cycle (TCA cycle) (eco00020) 0.20 0.50 1.00 acnB (1)
Fructose and mannose metabolism (eco00051) 0.33 0.24 0.52 manX (1)
Glycolysis/Gluconeogenesis (eco00010) 0.50 0.33 0.83 ptsG (1)
Lipopolysaccharide biosynthesis (eco00540) 0.17 0.38 0.73 lpxC (1)
Oxidative phosphorylation (eco00190) 0.00 0.00 1.00 ppa (1)
Pantothenate and CoA biosynthesis (eco00770) 0.00 0.00 1.00 ilvC (1)
Propanoate metabolism (eco00640) 0.20 0.50 1.00 acnB (1)
Pyruvate metabolism (eco00620) 0.41 0.49 0.59 aceB (1)
Valine, leucine and isoleucine biosynthesis (eco00290) 0.00 0.00 1.00 ilvC (1)
  1. Twenty-two KEGG pathways were identified as being altered in a concentration-dependent manner by exposure to NAs (low = 10 mg/l, mid = 100 mg/l, high = 1000 mg/l). The perturbation degree was determined as the average percentage edge change per gene for all genes involved in a particular pathway, and concentration-dependence was defined as high > mid and high > low in perturbation degree. Note that perturbation degrees are expressed in decimals instead of percentages.