TABLE 1.
Reactome pathway enrichment analysis. Statistically significant pathways (FDR 0.05) are summarized for saliva DN communities C0 and C1. In the full analysis, we omitted small communities with fewer than 8 genes Reimand et al. (2019); Gene Set Enrichment Analysis (2022), and 12 communities (C0 to C11) qualified for the pathway analysis.
| Pathway Name | Entities FDR | Submitted entities found |
|---|---|---|
| Saliva DN: C0 | ||
| Antigen Presentation: Folding, assembly and peptide loading of class I MHC | 1.2E-14 | HLA-B, NAA15 |
| Endosomal/Vacuolar pathway | 1.2E-14 | HLA-B |
| Interferon gamma signaling | 1.2E-14 | STAT1, IRF1, HLA-B, PTPN6 |
| Class I MHC mediated antigen processing and presentation | 1.2E-14 | PSMD8, TLR1, CDH1, RPN1, GBF1, HLA-B, UBR4, CYBA, NAA15, ELOC, FBXO32, FBXO11 |
| ER-Phagosome pathway | 1.2E-14 | PSMD8, TLR1, RPN1, HLA-B |
| Interferon alpha/beta signaling | 1.2E-14 | STAT1, IRF1, HLA-B, PTPN6 |
| Interferon Signaling | 1.2E-14 | EIF4A1, STAT1, IRF1, HLA-B, PTPN6, ARIH1 |
| Antigen processing-Cross presentation | 1.2E-14 | PSMD8, TLR1, RPN1, HLA-B, CYBA |
| Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | 1.2E-14 | CDH1, CD81, HLA-B, FCGR2B |
| Cytokine Signaling in Immune system | 1.1E-11 | EIF4A1, STAT1, IRF1, HLA-B, PTPN6, ARIH1 |
| Adaptive Immune System | 4.1E-09 | CD81, TCF25, RPN1, GBF1, HLA-B, UBR4, CYBA, PPP2R5D, FBXO32, FBXO11, ANKRD9, TLR1, PSMD8, CDH1, AKT2, PTPN6, ELOC, NAA15, FCGR2B, SIPA1, ARF5 |
| Immune System | 1.3E-05 | CCDC71L, DDX3Y, EIF4A1, ASAH1, IL1RN, SERPINA1, TCF25, CD81, RPN1, RPLP0, UBR4, TNFAIP3, CSF2RA, PLD2, PSMD8, ANKRD9, CDH1, AKT2, OLR1, ELOC, ARIH1, SERPINB2, TNFSF14, GSTO1, STAT1, GBF1, HLA-B, CYBA, PPP2R5D, FBXO32, FBXO11, FGR, CEACAM3, CLEC4A, TLR1, IRF1, TCP1, TXNIP, PTPN6, CYSTM1, NAA15, FCGR2B, SIPA1, BIRC2, ARF5, TRIM56 |
| Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | 3.2E-03 | SERPINB2, GSTO1, TCP1, RPLP0, ARF5 |
| Interleukin-12 family signaling | 4.6E-03 | SERPINB2, GSTO1, STAT1, TCP1, RPLP0, ARF5 |
| Interleukin-12 signaling | 8.0E-03 | SERPINB2, GSTO1, TCP1, RPLP0, ARF5 |
| Saliva DN: C1 | ||
| Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA | 2.7E-03 | CD44 |
| Nuclear Events (kinase and transcription factor activation) | 1.8E-02 | PPP2CB, TF, ID2, CHD4, FOS, DUSP6, DNM2 |
| FOXO-mediated transcription of cell death genes | 1.8E-02 | BCL2L11, BCL6, NFYC |
| Signaling by NTRKs | 2.4E-02 | PPP2CB, RALA, TF, ID2, CLTA, FURIN, CHD4, FOS, DUSP6, DNM2 |
| Signaling by NTRK1 (TRKA) | 2.6E-02 | PPP2CB, RALA, TF, ID2, CLTA, CHD4, FOS, DUSP6, DNM2 |
| Immune System | 2.9E-02 | NAPA, RALA, CIITA, AHCYL1, RPN2, UNC93B1, JADE1, CLTA, BCL10, CFP, TANK, GNS, FCAR, STK10, PPP2CB, BCL2L11, TRIM29, ALOX5, NLRP3, FLNA, SIRPA, SLC12A6, IL6R, GBP4, RAP1GAP2, DDX17, CR1, WSB1, CISH, SH2D3C, KLHL21, FNDC3A, FOS, LILRB3, MTOR, DUSP6, VEGFA, DNM2, TF, ZNFX1, NASP, BCL6, MAN2B1, TACC2, CD300C, CALM1, CD44, LGMN |
| Cytokine Signaling in Immune system | 3.6E-02 | RALA, CIITA, CISH, RPN2, SH2D3C, FNDC3A, FOS, MTOR, DUSP6, VEGFA, PPP2CB, ZNFX1, BCL2L11, NASP, BCL6, TRIM29, ALOX5, FLNA, IL6R, GBP4, CD44 |
| trans-Golgi Network Vesicle Budding | 3.9E-02 | NAPA, CPD, CLTA, GNS, CLINT1, DNM2 |
| NGF-stimulated transcription | 3.9E-02 | TF, ID2, CHD4, FOS, DNM2 |