Table 2.
Top 5 upstream regulators for each category described in this study, along with their respective p-values and target molecules (genes and complexes). Here, “p-value of overlap” indicates the significance of overlap between genes of this dataset and those influenced by the upstream regulator, using Fisher’s exact t-test [37]. Arrows indicate the direction of gene expression (increased or decreased) in infected versus uninfected mice, based on the averaged expression values for strains included in each response. Additional information for these regulators and molecules, including descriptions and chromosomal locations, is found in Supplementary Table S1.
| Top 5 Upstream Regulators | p-Value of Overlap | Target Molecules |
|---|---|---|
| Overall (Infected vs. Sham) | ||
| NFIA ↑ | 1.37 × 10−3 | GABRA6 ↓ |
| miR-122-5p (miRNAs w/seed GGAGUGU) | 4.42 × 10−3 | TBX19 ↓ |
| TAF7L ↓ | 5.16 × 10−3 | TBX19 ↓ |
| EP300 ↓ | 2.39 × 10−2 | TBX19 ↓ |
| GATA2 ↑ | 2.69 × 10−2 | TBX19 ↓ |
| Resistant | ||
| MSH2 ↑ | 1.30 × 10−5 | IGHG1 ↑, IGKC ↑ |
| IL21R ↑ | 7.54 × 10−5 | IGHG1 ↑, IGKC ↑ |
| CXCL10 ↑ | 1.77 × 10−4 | Ccl6 ↓, IGKC ↑ |
| HSP-990 | 6.24 × 10−4 | HLA-A ↑ |
| Raet1d ↑/Raet1e ↑ | 6.24 × 10−4 | HLA-A ↑ |
| Resilient | ||
| MSH2 ↑ | 4.33 × 10−5 | IGHG1 ↑, Ighg2b ↑, IGKC ↑ |
| PNPT1 ↑ | 5.38 × 10−5 | Apol9a ↑/Apol9b ↑, GBP6 ↑, IFI16 ↑, IFIH1 ↑, Oas1b ↑ |
| Irgm1 ↑ | 1.54 × 10−4 | Apol9a ↑/Apol9b ↑, GBP6 ↑, IFI16 ↑, IFIH1 ↑, Oas1b ↑, Oas1d↓ (includes others) |
| IFNB1 ↑ | 1.63 × 10−4 | GBP3 ↑, GBP6 ↑, GLP2R ↑, HLA-A ↑, IFI16 ↑, IFIH1 ↑, MCM10 ↑, Oas1b ↑, Oas1d ↓ (includes others), TRIM6-TRIM34 ↑ |
| ELAVL1 ↓ | 3.09 × 10−4 | CASP9 ↓, GBP6 ↑, HLA-A ↑, IFI16 ↑, IFIH1 ↑, Igha ↑, Igkv8-30 ↑, Oas1b ↑ |
| Susceptible | ||
| GNAS ↑ | 5.07 × 10−4 | GDF9 ↓, PRL ↓ |
| BIM 23A760 | 5.82 × 10−4 | PRL ↓ |
| IQUB ↑ | 5.82 × 10−4 | PRL ↓ |
| RHOQ ↓ | 5.82 × 10−4 | PRL ↓ |
| UBE2Q1 ↑ | 5.82 × 10−4 | PRL ↓ |