Table 4.
Most enriched pathway clusters as determined by DAVID functional annotation clustering of up-regulated and down- regulated DE genes in CTR vs. LPS in mouse spleens.
| Annotation Cluster 1: Enrichment Score: 4.25 | |||||
|---|---|---|---|---|---|
| Category | Term | Genes | Count | p-Value | Benjamini |
| GOTERM_BP_DIRECT | Inflammatory response | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5, Il1a, Il6, Nos2, Pparg, Tlr4 | 10 | 5.80 × 10−11 | 4.20 × 10−8 |
| GOTERM_BP_DIRECT | Neutrophil chemotaxis | Fgr, Ccl11, Ccl17, Ccl25, Cscl11, Cxcl5 | 6 | 1.40 × 10−8 | 5.20 × 10−6 |
| GOTERM_BP_DIRECT | positive regulation of ERK1 and ERK2 cascade | Ccl11, Ccl17, Ccl25, Il1a, Il6, Notch1, Tlr4 | 7 | 9.50 × 10−8 | 2.30 × 10−5 |
| GOTERM_MF_DIRECT | Cytokine activity | Ccl11, Ccl17, Ccl25, Cxcl5, Grn, Il1a, Il6 | 7 | 1.30 × 10−7 | 9.30 × 10−6 |
| GOTERM_MF_DIRECT | Chemokine activity | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 1.30 × 10−7 | 9.30 × 10−6 |
| GOTERM_BP_DIRECT | Chemokine-mediated signaling pathway | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 2.20 × 10−7 | 4.10 × 10−5 |
| GOTERM_BP_DIRECT | Immune response | Ccl11, Ccl25, CxCl11, Cxcl5, Il1a, H2-k1, Tlr4 | 8 | 3.20 × 10−7 | 4.60 × 10−4 |
| KEGG_PATHWAY | Viral protein interaction with cytokine and cytokine receptor | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5, Il6 | 6 | 6.60 × 10−7 | 7.30 × 10−4 |
| REACTOME_PATHWAY | Chemokine receptors bind chemokines | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 2.40 × 10−6 | 3.30 × 10−4 |
| GOTERM_BP_DIRECT | Cellular response to interferon-gamma | Ccl11, Ccl17, Ccl25, Nos2, Tlr4 | 5 | 4.10 × 10−6 | 4.90 × 10−4 |
| GOTERM_BP_DIRECT | Chemotaxis | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 9.10 × 10−6 | 8.30 × 10−4 |
| KEGG_PATHWAY | Cytokine–cytokine receptor interaction | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5, Il1a, Il6 | 7 | 1.00 × 10−5 | 4.00 × 10−4 |
| GOTERM_BP_DIRECT | Antimicrobial humoral immune response mediated by antimicrobial peptide | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 1.10 × 10−5 | 8.50 × 10−4 |
| GOTERM_BP_DIRECT | Killing of cells of other organisms | Ccl11, Ccl17, Ccl25, Lyz2 | 4 | 1.90 × 10−5 | 1.40 × 10−3 |
| GOTERM_BP_DIRECT | Cellular response to interleukin-1 | Ccl11, Ccl17, Ccl25, Il6 | 4 | 7.20 × 10−5 | 4.80 × 10−3 |
| REACTOME_PATHWAY | Peptide ligand-binding receptors | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 3.20 × 10−5 | 2.10 × 10−2 |
| GOTERM_MF_DIRECT | CCR chemokine receptor binding | Ccl11, Ccl17, Ccl25 | 3 | 3.50 × 10−4 | 1.70 × 10−2 |
| KEGG_PATHWAY | Chemokine signaling pathway | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 3.80 × 10−4 | 6.10 × 10−2 |
| GOTERM_BP_DIRECT | Cellular response to tumor necrosis factor | Ccl11, Ccl17, Ccl25, Il6 | 4 | 4.00 × 10−4 | 1.60 × 10−2 |
| GOTERM_BP_DIRECT | Lymphocyte chemotaxis | Ccl11, Ccl17, Ccl25 | 3 | 4.10 × 10−4 | 1.60 × 10−2 |
| GOTERM_BP_DIRECT | Monocyte chemotaxis | Ccl11, Ccl17, Ccl25 | 3 | 6.20 × 10−4 | 2.20 × 10−2 |
| KEGG_PATHWAY | IL-17 signaling pathway | Ccl11, Ccl17, Ccl25, Il6 | 4 | 6.50 × 10−4 | 8.10 × 10−3 |
| REACTOME_PATHWAY | Class A/1 (Rhodopsin-like receptors) | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 2.10 × 10−3 | 9.30 × 10−2 |
| GOTERM_BP_DIRECT | Cell chemotaxis | Ccl17, Ccl25, Cxcl11 | 3 | 3.50 × 10−3 | 7.50 × 10−2 |
| REACTOME_PATHWAY | GPCR ligand binding | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 5.20 × 10−3 | 1.20 × 10−1 |
| REACTOME_PATHWAY | G alpha (i) signaling events | Ccl11, Ccl25, Cxcl11, Cxcl5 | 4 | 1.30 × 10−2 | 2.50 × 10−1 |
| GOTERM_BP_DIRECT | Positive regulation of GTPase activity | Ccl11, Ccl17, Ccl25 | 3 | 1.60 × 10−2 | 2.20 × 10−1 |
| REACTOME_PATHWAY | Signaling by GPCR | Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5 | 5 | 2.20 × 10−2 | 3.60 × 10−1 |
| REACTOME_PATHWAY | Signal transduction | Fyn, Ccl11, Ccl17, Ccl25, Cxcl11, Cxcl5, Il6, Notch1 | 8 | 8.20 × 10−2 | 8.90 × 10−1 |
| REACTOME_PATHWAY | GPCR downstream signaling | Ccl11, Ccl25, Cxcl11, Cxcl5 | 4 | 8.50 × 10−2 | 8.90 × 10−1 |
| GOTERM_BP_DIRECT | G-protein coupled receptor signaling pathway | Ccl11, Ccl17, Ccl25 | 3 | 5.20 × 10−1 | 1.00 × 10−1 |
| Annotation Cluster 2: Enrichment Score: 3.07 | |||||
| GOTERM_BP_DIRECT | Cellular response to lipopolysaccharide | Cxcl11, Cxcl5, Il1a, Il6, Nos2, Tlr4 | 6 | 8.90 × 10−6 | 8.30 × 10−4 |
| KEGG_PATHWAY | Pertussis | Cxcl5, Il1a, Il6, Nos2, Tlr4 | 5 | 1.10 × 10−5 | 4.00 × 10−4 |
| KEGG_PATHWAY | Tuberculosis | Fcgr3, Fcgr2b, Il1a, Nos2, Tlr4 | 6 | 1.50 × 10−5 | 4.30 × 10−4 |
| GOTERM_BP_DIRECT | Positive regulation of interleukin-6 production | Il1a, Il6, Nos2, Tlr4 | 4 | 1.80 × 10−4 | 1.00 × 10−2 |
| GOTERM_BP_DIRECT | Positive regulation of apoptotic process | Il6, Nos2, Notch1, Pparg, Tlr4 | 5 | 5.00 × 10−4 | 1.80 × 10−2 |
| GOTERM_BP_DIRECT | Positive regulation of interleukin-8 production | Il6, Nos2, Tlr4 | 3 | 1.60 × 10−3 | 3.90 × 10−2 |
| GOTERM_BP_DIRECT | Signal transduction | Ccl17, Cxcl11, Il6, Nos2, Pparg, Tlr4 | 6 | 1.00 × 10−2 | 1.60 × 10−1 |
| KEGG_PATHWAY | Toll-like receptor signaling pathway | Cxcl11, Il6, Tlr4 | 3 | 1.50 × 10−2 | 1.00 × 10−1 |
| KEGG_PATHWAY | Chagas disease | Il6, Nos2, Tlr4 | 3 | 1.60 × 10−2 | 1.00 × 10−1 |
| KEGG_PATHWAY | Amoebiasis | Il6, Nos2, Tlr4 | 3 | 1.70 × 10−2 | 1.10 × 10−1 |
| KEGG_PATHWAY | HIF-1 signaling pathway | Il6, Nos2, Tlr4 | 3 | 1.90 × 10−2 | 1.10 × 10−1 |
Category: original database/resource where the terms origin; Term: enriched terms associated with our gene list; Count: genes involved in the term; p-value: Benjamini adjusted p-value GOTERM: Gene Ontology Term; BP: biological process; MF: molecular function.