Table 1.
Comparison of the top five functional effects caused by Aggregatibacter actinomycetemcomitans (Aa) and Aggregatibacter actinomycetemcomitans plus Lactobacillus fermentum (Aa+Lf) stimulation of bone marrow‐derived macrophages from wild‐type (WT) and NOD1 knockout (NOD1 –/–) mice
| Gene cluster | Aa stim/WT | Aa stim/NOD1−/− | ||
|---|---|---|---|---|
| Functional annotation | Score | Functional annotation | Score | |
| 1 | Defence response, inflammatory response, positive regulation of multicellular organism process, response to wounding | 10·78 | Immune response, defence response, inflammatory response, response to wounding | 17·54 |
| 2 | Immune response, cytokine, cytokine activity, macrophage, lymphokine | 8·52 | Cytokine, cytokine activity, macrophage, lymphokine, JAK‐STAT signalling pathway | 8·53 |
| 3 | Haematopoietic cell lineage, JAK‐STAT signalling activity, growth factor activity | 6·40 | Response to bacterium, regulation of interleukin‐6 production, response to molecule of bacterial origin, positive regulation of NF‐κB transcription factor activity | 6·16 |
| 4 | Response to bacterium, regulation of interleukin‐6 production, response to molecule of bacterial origin, positive regulation of cytokine production | 5·92 | Positive regulation of protein kinase cascade, positive regulation of cytokine production, positive regulation of signal transduction | 5·98 |
| 5 | Immunoregulation, acute‐phase response, acute inflammatory response, homeostatic process | 5·23 | Macrophage, immunoregulation, negative regulation of transport, acute inflammatory response | 5·18 |
| Gene cluster | Aa+Lf stim/WT | Aa+Lf stim/NOD1−/− | ||
|---|---|---|---|---|
| Functional annotation (top 5) | Score | Functional annotation (top 5) | Score | |
| 1 | Immune response, cytokine, cytokine activity, JAK‐STAT signalling pathway, cytokine network | 11·66 | Regulation of IκB/NF‐κB cascade, response to bacterium, regulation of interleukin‐6 production, regulation of cellular response to stress | 8·97 |
| 2 | Defence response, inflammatory response, response to wounding | 10·09 | Regulation of transcription factor activity, innate immune response‐activating signal transduction, defence response to Gram‐positive bacterium | 6·93 |
| 3 | Macrophage, immune system development, leucocyte differentiation | 4·57 | Regulation of tumour necrosis factor production, response to lipoteichoic acid | 6·34 |
| 4 | Lymphokine, regulation of cytokine production, response to bacterium, immunoregulation | 4·49 | Cytokine, cytokine activity, macrophage, lymphokine, interleukin‐10 anti‐inflammatory signalling pathway | 6·32 |
| 5 | Signal, disulphide bond, glycoprotein | 4·24 | Immune system development, leucocyte differentiation | 5·47 |
The functional‐describing terms and enrichment scores (Fisher Exact Statistics in DAVID system, referring to one‐tail Fisher Exact Probability Value used for gene‐enrichment analysis) were obtained from the lists of up‐regulated genes expressed by Aa‐ and Aa+Lf‐stimulated macrophages using the Database for Annotation, Visualization and Integrated Discovery (DAVID) algorithm.