List of proteins that were discovered to be over-represented in CD, using the without a priori 2D-DIGE approach
| Lineage | Protein name | Cellular function/pathway | 2D-DIGE | SRM (fold change) |
|---|---|---|---|---|
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | AhpC | Protection against oxidative stress | + | + (4.4) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | Pnp | Protection against oxidative stress | + | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; NA; NA | ProS | Protein synthesis, folding, and repair | + | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | FusA | Protein synthesis, folding, and repair | + | + (5.2) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | DnaK | Protein synthesis, folding, and repair | + | + (4.1) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | ClpB | Protein synthesis, folding, and repair | + | + (4.8) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | PPi-dependent PfK | Energy saving and maintenance of a high flux of carbon within both glycolysis and pentose phosphate pathways | + | + (3.9) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | TktA-TktB | Energy saving and maintenance of a high flux of carbon within both glycolysis and pentose phosphate pathways | + | + (5.2) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | FumA-FumB | Biosynthesis of precursors through the reductive branch of the tricarboxylic acid cycle | + | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | KorA | Biosynthesis of precursors through the reductive branch of the tricarboxylic acid cycle | + | + (4.3) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | TonB-dependent receptors | Nutrient acquisition and sensing of the environment | + | + (11.3) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | Other cell envelope proteins | Nutrient acquisition and sensing of the environment | + | |
| Bacteria; Bacteroidetes; NA; NA; NA; NA | TonB-dependent receptors | Nutrient acquisition and sensing of the environment | + | |
| Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | PepD | Adhesion and colonisation | + | + (3.9) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides | ACH1 | Pyruvate metabolism | + | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides/Porphyromonadaceae; Parabacteroides | PckA | Energy saving and maintenance of a high flux of carbon within both glycolysis and pentose phosphate pathways | + | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Ruminococcus | type 1 dockerins | Cellulosome assembly | + | + (27.8) |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | AtpA | ATP production | + | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Blautia | AckA | ATP production | + | |
| Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; NA | Dnak | Protein synthesis, folding, and repair | + | |
| Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Bilophila | DsrA | Energy conservation by reducing sulfite | + | |
| Human | IgA immunoglobulins | Coating bacterial cells | + | |
| Human | Carboxypeptidase A1 | Coating bacterial cells | + |
Those that were confirmed by SRM are indicated in the last column on the right, with their fold change.
CD, Crohn's disease; SRM, selected reaction monitoring; 2D-DIGE, two-dimensional difference gel electrophoresis; NA, not assigned.