TABLE 3

Gene expression changes categorized by biological-process GO termsa

GO termExpression change in comparison of:
LB versus swimLB versus swarmSwim versus swarm
NegativePositiveNegativePositiveNegativePositive
CountFDRCountFDRCountFDRCountFDRCountFDRCountFDR
Carbohydrate catabolic process154.15E-02559.27E-27692.88E-38
Nitrogen compound biosynthetic process742.20E-25722.65E-20
Amine biosynthetic process152.79E-02486.76E-19412.76E-11
Anaerobic respiration82.63E-03272.24E-18256.47E-15181.15E-06
Iron ion transport102.63E-04261.27E-17262.62E-16
Di- and trivalent inorganic cation transport101.08E-03268.61E-16261.69E-14
Carboxylic acid biosynthetic process479.50E-16482.70E-14
Organic acid biosynthetic process471.13E-15483.20E-14
Aerobic respiration165.86E-12241.71E-15197.55E-09
Cellular amino acid biosynthetic process411.57E-14408.12E-12
Transition metal ion transport107.47E-03272.38E-14284.93E-14
Energy derivation by oxidation of organic compounds102.96E-02191.28E-07346.18E-14262.16E-06341.58E-12281.33E-06
Peptidyl-aspartic acid modification103.22E-13
Peptidyl-cysteine modification103.22E-13
Peptidyl-l-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid103.22E-13
Generation of precursor metabolites and energy213.86E-05422.82E-12371.77E-07384.25E-08401.12E-07
Cellular respiration181.72E-07308.45E-12261.78E-07298.17E-10262.42E-06
Sulfur metabolic process261.06E-10283.20E-11
Metal ion transport321.25E-09311.58E-07
Tricarboxylic acid cycle97.52E-05152.14E-08
  • a Negative, higher transcript amount under the first growth condition; positive, higher transcript amount under the second growth condition. Count data represent the number of genes from each GO term. All categories showed significant enrichment (FDR P, ≤0.001).