Table 2 Statistically significant reactome46 pathways identified (\(\hbox {FDR}< 3\times 10^{-3}\) results shown).
From: Longitudinal saliva omics responses to immune perturbation: a case study
Reactome pathway | Matched IDs | p value | FDR |
|---|---|---|---|
A. Total saliva mRNA: \(\mathbf{TF} \Delta\) | |||
(i) Class: Lag 1, G1S1 | |||
 Endosomal/vacuolar pathway | 15 | \(1.6\times 10^{-9}\) | \(1.6\times 10^{-6}\) |
 Antigen presentation: folding, assembly and peptide loading of class I MHC | 16 | \(4.0\times 10^{-9}\) | \(2.0\times 10^{-6}\) |
 Interferon gamma signaling | 22 | \(1.8\times 10^{-7}\) | \(5.9\times 10^{-5}\) |
 ER-Phagosome pathway | 17 | \(5.0\times 10^{-7}\) | \(1.1\times 10^{-4}\) |
 Interferon alpha/beta signaling | 18 | \(5.7\times 10^{-7}\) | \(1.1\times 10^{-4}\) |
 Antigen processing-cross presentation | 17 | \(2.7\times 10^{-6}\) | \(4.4\times 10^{-4}\) |
 Insulin-like growth factor-2 mRNA binding proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 5 | \(1.6\times 10^{-5}\) | \(2.2\times 10^{-3}\) |
 Attenuation phase | 8 | \(1.8\times 10^{-5}\) | \(2.2\times 10^{-3}\) |
 Interferon signaling | 24 | \(2.5\times 10^{-5}\) | \(2.8\times 10^{-3}\) |
 Neutrophil degranulation | 27 | \(2.8\times 10^{-5}\) | \(2.8\times 10^{-3}\) |
(ii) Class: Lag 1, G1S2 | |||
 Translocation of ZAP-70 to Immunological synapse | 14 | \(1.1\times 10^{-16}\) | \(2.2\times 10^{-14}\) |
 Phosphorylation of CD3 and TCR zeta chains | 14 | \(1.1\times 10^{-16}\) | \(2.2\times 10^{-14}\) |
 Generation of second messenger molecules | 15 | \(1.1\times 10^{-16}\) | \(2.2\times 10^{-14}\) |
 PD-1 signaling | 14 | \(1.1\times 10^{-16}\) | \(2.2\times 10^{-14}\) |
 Interferon gamma signaling | 22 | \(1.8\times 10^{-15}\) | \(2.8\times 10^{-13}\) |
 Costimulation by the CD28 family | 15 | \(2.4\times 10^{-14}\) | \(3.1\times 10^{-12}\) |
 TCR signaling | 17 | \(4.2\times 10^{-14}\) | \(4.7\times 10^{-12}\) |
 Downstream TCR signaling | 16 | \(4.8\times 10^{-14}\) | \(4.7\times 10^{-12}\) |
 Interferon signaling | 23 | \(1.7\times 10^{-12}\) | \(1.5\times 10^{-10}\) |
 MHC class II antigen presentation | 14 | \(1.1\times 10^{-10}\) | \(8.8\times 10^{-9}\) |
 Cytokine signaling in immune system | 33 | \(5.5\times 10^{-8}\) | \(3.9\times 10^{-6}\) |
 Insulin-like growth factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 5 | \(1.6\times 10^{-7}\) | \(1.0\times 10^{-5}\) |
 Immune system | 50 | \(1.1\times 10^{-6}\) | \(6.4\times 10^{-5}\) |
 Neutrophil degranulation | 16 | \(8.2\times 10^{-6}\) | \(4.6\times 10^{-4}\) |
 Adaptive immune system | 23 | \(3.3\times 10^{-5}\) | \(1.7\times 10^{-3}\) |
B. Total saliva mRNA: TFD | |||
(i) Class: Lag 1, G1S1 | |||
 Endosomal/vacuolar pathway | 16 | \(4.1\times 10^{-11}\) | \(3.6\times 10^{-8}\) |
 Interferon alpha/beta signaling | 22 | \(1.3\times 10^{-10}\) | \(5.7\times 10^{-8}\) |
 Interferon signaling | 29 | \(8.9\times 10^{-9}\) | \(2.6\times 10^{-6}\) |
 Cytokine signaling in immune system | 59 | \(2.8\times 10^{-9}\) | \(4.6\times 10^{-6}\) |
 Interferon gamma signaling | 22 | \(3.1\times 10^{-8}\) | \(5.3\times 10^{-6}\) |
 Antigen presentation: folding, assembly and peptide loading of class I MHC | 14 | \(5.4\times 10^{-8}\) | \(7.8\times 10^{-6}\) |
 Insulin-like growth factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 6 | \(4.3\times 10^{-7}\) | \(4.8\times 10^{-5}\) |
 Immune system | 97 | \(4.4\times 10^{-7}\) | \(4.8\times 10^{-5}\) |
 Antigen processing-cross presentation | 17 | \(6.7\times 10^{-7}\) | \(6.5\times 10^{-5}\) |
 Interleukin-4 and interleukin-13 signaling | 18 | \(7.8\times 10^{-7}\) | \(6.7\times 10^{-5}\) |
 ER-phagosome pathway | 14 | \(1.4\times 10^{-5}\) | \(1.1\times 10^{-3}\) |
(ii) Class: Lag 1, G1S2 | |||
 Response of EIF2AK4 (GCN2) to amino acid deficiency | 13 | \(3.6\times 10^{-7}\) | \(1.5\times 10^{-4}\) |
 Cytokine signaling in immune system | 51 | \(4.1\times 10^{-7}\) | \(1.5\times 10^{-4}\) |
 Immune system | 88 | \(4.9\times 10^{-7}\) | \(1.5\times 10^{-4}\) |
 ATF4 activates genes in response to endoplasmic reticulum stress | 7 | \(4.4\times 10^{-6}\) | \(9.8\times 10^{-4}\) |
 Innate immune system | 48 | \(7.1\times 10^{-6}\) | \(1.3\times 10^{-3}\) |
 PERK regulates gene expression | 7 | \(1.7\times 10^{-5}\) | \(2.0\times 10^{-3}\) |
 CLEC7A/inflammasome pathway | 4 | \(1.8\times 10^{-5}\) | \(2.0\times 10^{-3}\) |
 Interleukin-1 processing | 4 | \(1.8\times 10^{-5}\) | \(2.0\times 10^{-3}\) |
