TABLE 1.
Differentially expressed genes in mice mono-colonized with L. acidophilus NCFM compared to germfree micea
| Gene | Product | GO biological process(es) | DE log2 fold change | FDR-adjusted P value |
|---|---|---|---|---|
| Upregulation | ||||
| Pla2g4c | Phospholipase A2, group IVC (cytosolic, calcium-dependent) |
Glycerophospholipid catabolic process | Δ 7.20 | 6.59E−06 |
| Duox2 | Dual oxidase 2 | Superoxide anion generation | Δ 3.04 | 4.3E−03 |
| Duoxa2 | Dual oxidase maturation factor 2 | Regulation of inflammatory response | Δ 4.39 | 1.38E−05 |
| Rnase2a | Ribonuclease, RNase A family, 2A (liver, eosinophil-derived neurotoxin) |
RNA phosphodiester bond hydrolysis | Δ 3.88 | 1.39E−02 |
| Insl3 | Insulin-like 3 | Negative regulation of cell proliferation/ apoptotic process |
Δ 3.59 | 8.80E−03 |
| Xlr3b | X-linked lymphocyte-regulated 3B | Spermatid development/meiotic cell cycle | Δ 3.53 | 4.07E−09 |
| AA467197 | Response to bacterium | Δ 3.44 | 4.32E−02 | |
| St3gal4 | ST3 β-galactoside α-2,3-sialyltransferase 4 | Glycoprotein biosynthesis process, sialylation |
Δ 3.27 | 1.39E−02 |
| Gsdmc2 | Gasdermin C2 | Programmed cell death, pyroptosis | Δ 3.19 | 6.56E−03 |
| Gsdmc3 | Gasdermin C3 | Programmed cell death, pyroptosis | Δ 3.26 | 6.67E−03 |
| Gsdmc4 | Gasdermin C4 | Programmed cell death, pyroptosis | Δ 3.10 | 6.67E−03 |
| Mcpt2 | Mast cell protease 2 | Proteolysis | Δ 3.05 | 3.69E−02 |
| Capn13 | Calpain 13 | Proteolysis | Δ 2.44 | 1.01E−02 |
| Gm2000 | Δ 2.00 | 1.24E−03 | ||
| Ciart | Circadian-associated repressor of transcription |
Rhythmic process, circadian regulation of gene expression |
Δ 2.03 | 6.56E−03 |
| Dbp | D site albumin promoter-binding protein | Rhythmic process | Δ 1.35 | 4.17E−03 |
| Per3 | Period circadian clock 3 | Rhythmic process | Δ 1.08 | 3.64E−02 |
| Downregulation | ||||
| Asdurf | ∇ −5.33 | 2.40E−02 | ||
| Gm28539 | ∇ −5.21 | 1.38E−05 | ||
| Sprr1a | Small proline-rich protein 1A | Peptide cross-linking, keratinocyte differentiation |
∇ −2.33 | 8.80E−03 |
| Lancl3 | LanC lantibiotic synthetase component C-like 3 |
∇ −2.18 | 3.35E−02 | |
| Tnfsf15 | Tumor necrosis factor (ligand) superfamily, member 15 |
Activation of cysteine-type endopeptidase activity involved in apoptotic process |
∇ −1.92 | 3.56E−02 |
| P2ry4 | Pyrimidinergic receptor P2Y, G protein coupled, 4 |
Regulation of presynaptic cytosolic calcium ion concn, G-protein-coupled receptor signaling pathway |
∇ −1.89 | 6.56E−03 |
| Tmppe | Transmembrane protein with metallophosphoesterase domain |
∇ −1.88 | 4.82E−02 | |
a
GO, gene ontology; DE, differentially expressed.