TABLE 3.
Kinetic analysis of genes altered in C57BL/10 mouse brain infected with scrapie strain 22L assayed with the JAK/STAT and IL-6/STAT3 arraysa
| New or previously observed gene | At 70 days p.i. |
At 94 days p.i. |
At 131 days p.i. |
Description | |||
|---|---|---|---|---|---|---|---|
| FCb | P valuec | FC | P value | FC | P value | ||
| Newly identified genes | |||||||
| Tlr4 | —d | — | 7.2 | 2 × 10−2 | 11.4 | 3 × 10−3 | Toll-like receptor 4 |
| Gbp1e | — | — | 4.2 | 1 × 10−6 | 11.5 | <1 × 10−6 | Guanylate-binding protein 1 |
| Tnfrsf10b | — | — | — | — | 2.7 | 2 × 10−3 | TNFR superfamily, member 10b |
| Il4ra | — | — | — | — | 2.1 | 2 × 10−4 | IL-4Rα |
| Cd80e | — | — | — | — | 2.0 | 5 × 10−2 | CD80 antigen |
| Previously observed genes | |||||||
| Oas1a | 3.1 | 9 × 10−4 | 8.8 | 6 × 10−6 | 24.6 | <1 × 10−6 | 2′-5′ oligoadenylate synthetase 1A |
| Isg15 | 3.0 | 3 × 10−5 | 6.6 | 4 × 10−6 | 22.9 | <1 × 10−6 | ISG15 ubiquitin-like modifier |
| Osmr | 2.8 | 9 × 10−4 | 7.0 | 1 × 10−4 | 18.2 | 1 × 10−3 | Oncostatin M receptor |
| A2 m | 2.1 | 1 × 10−3 | 5.7 | 5 × 10−3 | 19.5 | <1 × 10−6 | α2-Macroglobulin |
| Socs3 | 2.0 | 1 × 10−3 | 2.6 | 6 × 10−6 | 6.6 | 3 × 10−4 | Suppressor of cytokine signaling 3 |
| Tnfrsf1a | 2.0 | 7 × 10−3 | 3.1 | 1 × 10−4 | 6.1 | 1 × 10−6 | TNFR superfamily, member 1a |
| Fcgr1e | — | — | 3.6 | 1 × 10−6 | 7.9 | <1 × 10−6 | Fc receptor, IgG, high affinity I |
| Irf9 | — | — | 3.5 | <1 × 10−6 | 6.7 | <1 × 10−6 | Interferon regulatory factor 9 |
| Cebpde | — | — | 3.2 | 4 × 10−5 | 8.1 | 6 × 10−6 | CCAAT/enhancer-binding protein, delta |
| Ptprc | — | — | 2.9 | 2 × 10−6 | 6.1 | 6 × 10−5 | Protein tyrosine phosphatase, receptor type C |
| Stat1e | — | — | 2.7 | <1 × 10−6 | 5.0 | <1 × 10−6 | Signal transducer and activator of transcription 1 |
| Lif | — | — | 2.4 | 3 × 10−3 | 4.4 | 1 × 10−2 | Leukemia inhibitory factor |
| Cxcr4 | — | — | 2.3 | 2 × 10−2 | 2.3 | 3 × 10−3 | Chemokine (C-X-C motif) receptor 4 |
| Fas | — | — | 2.2 | 1 × 10−5 | 5.2 | 1 × 10−6 | Fas (TNFR superfamily member 6) |
| Sfpi1 | — | — | 2.2 | 3 × 10−6 | 4.5 | <1 × 10−6 | SFFV proviral integration 1 |
| Csf3r | — | — | 2.0 | 1 × 10−3 | 5.8 | <1 × 10−6 | Colony-stimulating factor 3 receptor (granulocyte) |
| Tnfrsf1be | — | — | 2.0 | 5 × 10−4 | 3.3 | 8 × 10−5 | TNFR superfamily, member 1b |
| Nos2e | — | — | — | — | 2.9 | 2 × 10−3 | Nitric oxide synthase 2, inducible |
| Stat3e | — | — | — | — | 2.9 | 1 × 10−6 | Signal transducer and activator of transcription 3 |
| Irf1e | — | — | — | — | 2.8 | 4 × 10−5 | Interferon regulatory factor 1 |
| Csf1r | — | — | — | — | 2.8 | <1 × 10−6 | Colony-stimulating factor 1 receptor |
| Myce | — | — | — | — | 2.6 | 7 × 10−6 | Myelocytomatosis oncogene |
| Il1r1 | — | — | — | — | 2.6 | 5 × 10−4 | IL-1R, type I |
| Cd40e | — | — | — | — | 2.5 | 6 × 10−3 | CD40 antigen |
| Ccnd1 | — | — | — | — | 2.3 | 6 × 10−6 | Cyclin D1 |
| Jak3 | — | — | — | — | 3.0 | 5 × 10−4 | Janus kinase 3 |
| Socs1 | — | — | — | — | 2.3 | 3 × 10−3 | Suppressor of cytokine signaling 1 |
| Stat2 | — | — | — | — | 2.2 | 2 × 10−4 | Signal transducer and activator of transcription 2 |
| Hgfe | — | — | — | — | 2.0 | 4 × 10−3 | Hepatocyte growth factor |
| Ifngr1 | — | — | — | — | 2.0 | 2 × 10−5 | Interferon gamma receptor 1 |
| Nfkbiae | — | — | — | — | 2.0 | 1 × 10−3 | NF-κB light polypeptide gene enhancer in B cells inhibitor, alpha |
a
Values for Ccl3, Ccl4, Ccl5, Ccl12, Csf1, Cxcl9, Cxcl10, Il1a, Il1b, Il2rg, Il6ra, Il10ra, Il10rb, Osm, Tnf, Tnfsf10, and Tnfsf11, which were all increased in these arrays, have been omitted from this table; the values are presented in Table 1.
b
FC, fold change of 22L-infected mice (n = 3) relative to mock-infected controls (n = 4).
c
Calculated by using a two-tailed t test.
d
—, FC and/or P value did not meet our criteria (≥2-fold change, P value ≤ 5 × 10−2).
e
A gene that is a known target for NF-κB.