Table 1.
Pathways up- and down-regulated from acute (H2&H6) to biofilm infection (D5&D9).
| Pathwaysa with up-regulated genes overrepresented | p value** |
|---|---|
| Alginate biosynthesis (PseudoCyc, PseudoCAP, UniPathway) | 8.74E−11, 1.37E−09, 1.83E−03 |
| Starch and sucrose metabolism (KEGG, KEGG-InterPro, PseudoCAP) | 2.13E−07, 7.46E−05, 1.01E−03 |
| Apr type I secretion system (PseudoCAP) | 2.73E−05 |
| Pyrroloquinoline quinone biosynthesis (PseudoCAP, UniPathway) | 1.47E−04, 4.63E−04 |
| Ethanol oxidation pathway (PseudoCAP) | 2.01E−04 |
| l-2-Amino-4-methoxy-trans-3-butenoic acid (AMB) biosynthesis (PseudoCAP) | 1.01E−03 |
| Fructose and mannose metabolism (KEGG) | 5.37E−03 |
| Pyruvate decarboxylation to acetyl CoA (PseudoCyc) | 6.67E−03 |
| Anaerobic respiration (PseudoCyc) | 4.40E−02 |
| Pathways with down-regulated genes overrepresented | p value |
|---|---|
| Ribosome (KEGG) | 9.36E−45 |
| Adenosine ribonucleotides de novo biosynthesis (PseudoCyc) | 1.11E−12 |
| Sulfur metabolism (KEGG) | 7.86E−09 |
| Oxidative phosphorylation (KEGG, PseudoCAP) | 2.55E−05, 4.704E−04 |
| Type III secretion (PseudoCAP) | 3.36E−05 |
| Metabolic pathways (KEGG) | 9.24E−05 |
| Lipopolysaccharide biosynthesis (UniPathway) | 1.89E−04 |
| Citrate cycle (TCA cycle) (KEGG, PseudoCAP, KEGG-InterPro, UniPathway) | 2.25E−04, 3.31E−03, 7.44E−03, 7.44E−03 |
| Protein export (KEGG) | 2.40E−04 |
| Selenocompound metabolism (KEGG-InterPro) | 5.37E−04 |
| Superpathway of thiamin diphosphate biosynthesis I (PseudoCyc) | 6.11E−04 |
| Glutathione metabolism (KEGG-InterPro) | 8.52E−04 |
| Anaerobic respiration (PseudoCyc) | 1.46E−03 |
| Cationic antimicrobial peptide (CAMP) resistance (KEGG) | 1.48E−03 |
| l-Histidine biosynthesis (UniPathway) | 2.81E−03 |
| Acetyl-CoA assimilation (PseudoCyc) | 4.09E−03 |
| Beta-Alanine metabolism (KEGG) | 4.21E−03 |
| Purine metabolism (PseudoCAP, KEGG) | 5.44E−03, 5.50E−03 |
| Pantothenate and CoA biosynthesis (PseudoCAP) | 6.54E−03 |
| 4-Amino-4-deoxy-alpha-l-arabinose undecaprenyl phosphate biosynthesis (UniPathway) | 6.86E−03 |
| S-Adenosylmethioninamine biosynthesis (UniPathway) | 6.86E−03 |
| Spermidine biosynthesis (UniPathway) | 6.86E−03 |
| Two-component regulatory systems (PseudoCAP) | 6.86E−03 |
| UDP-4-deoxy-4-formamido-beta-l-arabinose biosynthesis (UniPathway) | 6.86E−03 |
| Biosynthesis of secondary metabolites (KEGG) | 7.62E−03 |
**p values for pathways overrepresented with up- and down-regulated genes (Fisher’s exact test implemented in the R package GeneOverlap).
aPathways were downloaded from http://www.pseudomonas.com/pathways/list on 2/27/2019 and included KEGG (120), KEGG-InterPro (135), PseudoCAP (126), PseudoCyc (238), and UniPathway (165) pathways—the parentheses in this sentence are numbers of pathways per database.