List of proteins that were discovered to be under-represented in CD, using the without a priori 2D-DIGE approach
| Lineage | Protein name | Cellular function/pathway | 2D-DIGE | SRM (fold change) |
|---|---|---|---|---|
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | flagellins FliC | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | UgpB | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | S-layer proteins | Nutrient acquisition and sensing of the environment | ||
| Bacteria; Firmicutes; NA; NA; NA; NA | S-layer proteins | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | UshA | Nucleotide transport and metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | ARO8 | Transcription, amino acid transport and metabolism | – | |
| Bacteria, Firmicutes, Clostridia, Clostridiales, Ruminococcaceae, Faecalibacterium, Faecalibacterium prausnitzii | Tig | Folding of newly synthesised proteins | – | |
| Bacteria; Firmicutes; NA; NA; NA; NA | IlvC | Amino acid transport and metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | MetH | Amino acid transport and metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | PrdF | Amino acid transport and metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | IscU | General metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | FixB | General metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | AtoB | General metabolism | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | GapA | Glycolysis | – | |
| Bacteria; Firmicutes; Clostridia; Clostridiales; NA; NA | Unknown function | Unknown | – | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; NA; NA | Surface proteins | Nutrient acquisition and sensing of the environment | – | −(3.2) |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; NA; NA | Lipoprotein | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella | TktA-TktB | Energy saving and maintenance of a high flux of carbon within both glycolysis and pentose phosphate pathways | – | |
| Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella | GapA | Glycolysis | – | −(14) |
| Escherichia | Outer membrane proteins | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; NA; NA; NA; NA; NA | ABC transporters | Nutrient acquisition and sensing of the environment | – | |
| Bacteria; NA; NA; NA; NA; NA | PckA | Energy saving and maintenance of a high flux of carbon within both glycolysis and pentose phosphate pathways | – | |
| Bacteria; NA; NA; NA; NA; NA | Unknown function | Unknown | – | |
| HUMAN | Fragments of GP2 | Coating bacterial cells | – | −(2.4) |
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.