Table 3.
Top canonical pathways and genes.
| Pathway | Gene | Day 2 | Day 7 | Day 14 | |||
|---|---|---|---|---|---|---|---|
| Interferon Signaling | Fold Change | p-value* | Fold Change | p-value* | Fold Change | p-value* | |
| IFI35 | 3.86 | 2.94E−14 | 2.84 | 9.43E−09 | 1.33 | 1.01E−01 | |
| IFIT1 | 13.11 | 1.02E−06 | 10.95 | 2.53E−05 | 2.95 | 3.88E−02 | |
| IFIT3 | 7.03 | 3.47E−08 | 7.34 | 2.57E−10 | 1.88 | 7.64E−02 | |
| IFITM1 | 2.38 | 1.66E−07 | 2.35 | 1.30E−06 | 1.61 | 6.35E−03 | |
| MX1 | 9.93 | 3.69E−09 | 6.89 | 4.17E−06 | 1.71 | 1.73E−01 | |
| OAS1 | 7.18 | 2.32E−08 | 7.42 | 6.46E−08 | 2.71 | 7.01E−03 | |
| SOCS1 | 2.43 | 5.90E−09 | 1.58 | 4.65E−02 | −1.20 | 1.19E−01 | |
| Activation of IRF by Cytosolic Factors | DDX58 | 5.00 | 2.85E−09 | 2.79 | 1.86E−03 | 1.85 | 2.69E−02 |
| DHX58 | 2.00 | 9.01E−10 | 1.50 | 4.94E−03 | 1.03 | 8.26E−01 | |
| IFIH1 | 4.50 | 7.41E−08 | 3.03 | 8.02E−04 | 2.36 | 4.12E−03 | |
| IFIT2 | 5.54 | 1.67E−12 | 4.36 | 1.81E−04 | 1.89 | 6.96E−02 | |
| IRF7 | 3.70 | 2.35E−09 | 3.68 | 1.85E−08 | 1.40 | 1.27E−01 | |
| ISG15 | 11.39 | 3.77E−11 | 11.20 | 2.76E−10 | 2.66 | 1.07E−02 | |
| ZBP1 | 3.94 | 1.32E−12 | 2.85 | 3.73E−09 | 1.72 | 3.11E−03 | |
| Role of Pattern Recognition Receptors | DDX58 | 5.00 | 2.85E−09 | 2.79 | 1.86E−03 | 1.85 | 2.69E−02 |
| in Recognition of Bacteria and | EIF2AK2 | 3.27 | 8.67E−10 | 2.96 | 1.42E−07 | 1.35 | 1.25E−01 |
| Viruses | IFIH1 | 4.50 | 7.41E−08 | 3.03 | 8.02E−04 | 2.36 | 4.12E−03 |
| IRF7 | 3.70 | 2.35E−09 | 3.68 | 1.85E−08 | 1.40 | 1.27E−01 | |
| OAS2 | 5.35 | 4.31E−12 | 4.97 | 2.57E−10 | 2.24 | 1.42E−03 | |
| OAS3 | 9.07 | 3.35E−12 | 8.20 | 1.58E−10 | 2.27 | 1.22E−02 | |
| Role of RIG1-like Receptors in Antiviral | DDX58 | 5.00 | 2.85E-09 | 2.79 | 1.86E-03 | 1.85 | 2.69E-02 |
| Innate Immunity | DDX60 | 3.53 | 1.44E-04 | 4.43 | 1.18E-05 | 3.49 | 3.78E-04 |
| DHX58 | 2.00 | 9.01E-10 | 1.50 | 4.94E-03 | 1.03 | 8.26E-01 | |
| TLR7 | 1.58 | 1.39E-06 | 1.12 | 7.93E-01 | −1.10 | 3.08E-01 | |
| Interleukin-6 Signaling | IL8 | −3.11 | 2.25E−02 | 1.36 | 8.85E−01 | 1.74 | 1.62E−01 |
| IL1RN | 3.46 | 4.00E−09 | 2.28 | 1.20E−03 | −1.19 | 5.68E−02 | |
| TNFAIP6 | 3.87 | 2.39E−06 | 2.84 | 2.31E−03 | 1.53 | 2.19E−01 | |
| Communication between Innate and | CXCL10 | 3.79 | 1.31E−12 | 2.10 | 5.95E−04 | 1.21 | 3.10E−01 |
| Adaptive Immune Cells | IL1RN | 3.46 | 4.00E−09 | 2.28 | 1.20E−03 | −1.19 | 5.68E−02 |
| TNFSF13B | 2.48 | 1.70E−05 | 1.96 | 1.27E−02 | 1.35 | 2.47E−01 | |
| JAK/STAT Signaling | SOCS1 | 2.43 | 5.90E−09 | 1.58 | 4.65E−02 | −1.20 | 1.19E−01 |
| STAT1 | 2.67 | 1.59E−05 | 1.99 | 2.68E−02 | 1.57 | 1.89E−02 | |
| STAT2 | 2.83 | 5.50E−09 | 2.19 | 1.10E−04 | 1.46 | 3.75E−02 | |
| Pathogenesis of Multiple Sclerosis | CXCL10 | 3.79 | 1.31E-12 | 2.10 | 5.95E-04 | 1.21 | 3.10E-01 |
| CCR1 | 1.80 | 1.80E+00 | 2.19 | 2.76E-02 | 1.23 | 4.23E-01 | |
| Oxidative Phosphorylation | ATP5J | −1.30 | 4.94E-01 | 1.34 | 8.34E-01 | 2.20 | 9.53E-03 |
| COX7B | −1.40 | 5.53E-01 | 1.60 | 8.10E-01 | 2.20 | 6.43E-02 | |
| COX7A2 | −1.27 | 5.13E-01 | 1.43 | 7.64E-01 | 2.04 | 1.35E-02 | |
| COX6C | −1.16 | 7.86E-01 | 1.80 | 6.65E-01 | 2.50 | 1.59E-02 | |
| UQCRB | −1.24 | 7.46E-01 | 1.67 | 8.08E-01 | 2.32 | 7.13E-02 | |
| UQCRH | −1.13 | 7.88E-01 | 1.46 | 7.79E-01 | 2.35 | 7.71E-03 | |
| PPA1 | −1.06 | 8.71E-01 | 1.44 | 6.94E-01 | 2.23 | 2.18E-03 | |
| NDUFA6 | −1.25 | 5.26E-01 | 1.48 | 7.12E-01 | 2.11 | 7.78E-03 | |
| UQCRQ | −1.18 | 7.41E-01 | 1.56 | 7.68E-01 | 2.22 | 2.44E-02 | |
| Protein Ubiquitination Pathway | PSMA3 | 1.17 | 7.02E−01 | 1.43 | 7.86E−01 | 2.42 | 5.05E−03 |
| UBR1 | −1.27 | 5.23E−01 | 1.16 | 9.30E−01 | 2.48 | 3.00E−03 | |
| USP1 | −1.74 | 7.37E−02 | 1.06 | 9.70E−01 | 2.32 | 8.32E−03 | |
| UBE3A | −1.54 | 1.91E−01 | 1.18 | 8.48E−01 | 2.07 | 7.17E−03 | |
| USP53 | −1.08 | 6.88E−01 | 1.21 | 9.10E−01 | 2.28 | 9.92E−03 | |
| PSMC6 | −1.72 | 3.37E−01 | 1.20 | 9.48E−01 | 2.71 | 2.57E−02 | |
| USP47 | −1.56 | 1.99E−01 | 1.21 | 8.97E−01 | 2.11 | 8.24E−03 | |
| USP16 | −1.64 | 1.67E−01 | 1.22 | 8.66E−01 | 2.22 | 6.24E−03 | |
| PSMA4 | 1.10 | 8.61E−01 | 1.69 | 7.09E−01 | 2.54 | 1.08E−02 | |
| HSP90AA1 | −1.02 | 9.78E−01 | 1.51 | 7.94E−01 | 2.91 | 4.74E−03 | |
| BIRC3 | −1.50 | 2.52E−01 | 1.09 | 9.63E−01 | 2.12 | 1.62E−02 | |
| BIRC2 | −1.38 | 4.13E−01 | 1.08 | 9.70E−01 | 2.22 | 5.80E−03 | |
| Regulation of eIF4 and p70S6K | ITGB1 | −1.23 | 5.79E-01 | 1.13 | 9.43E-01 | 2.38 | 4.12E-03 |
| Signaling | RPS6KB1 | −1.43 | 5.41E-02 | 1.09 | 9.15E-01 | 1.49 | 8.51E-03 |
| NRAS | −1.24 | 4.26E-01 | 1.18 | 8.84E-01 | 2.08 | 1.65E-03 | |
| RRAS2 | −1.39 | 2.32E-01 | 1.17 | 8.92E-01 | 2.31 | 4.53E-04 | |
| PIK3C2A | −1.57 | 1.79E-01 | −1.03 | 9.88E-01 | 2.03 | 9.01E-03 | |
| EIF1AX | −1.34 | 3.85E-01 | 1.20 | 8.99E-01 | 2.13 | 5.97E-03 | |
| EIF4A2 | −1.41 | 2.65E-01 | 1.17 | 9.07E-01 | 2.07 | 4.48E-03 | |
| EIF3E | −1.63 | 2.45E-01 | 1.10 | 9.65E-01 | 2.10 | 2.54E-02 | |
| EIF4E | −1.28 | 5.05E-01 | 1.13 | 9.43E-01 | 2.10 | 1.05E-02 | |
| ITGA4 | −1.28 | 4.94E-01 | −1.00 | 1.00E+00 | 2.09 | 1.08E-02 | |
| Ran Signaling | CSE1L | −1.28 | 3.47E-01 | 1.26 | 8.05E-01 | 2.00 | 2.11E-03 |
| RANBP2 | −1.48 | 2.48E-01 | −1.04 | 9.81E-01 | 2.09 | 7.33E-03 | |
| RAN | −1.45 | 3.05E-01 | 1.30 | 8.51E-01 | 2.60 | 2.11E-03 | |
| ERK5 signaling | YWHAQ | −1.25 | 4.08E−01 | 1.20 | 8.27E−01 | 2.27 | 4.00E−04 |
| IL6ST | −1.43 | 2.98E−01 | 1.24 | 8.51E−01 | 2.07 | 8.76E−03 | |
| RPS6KB1 | −1.58 | 1.82E−01 | 1.09 | 9.15E−01 | 2.11 | 7.34E−03 | |
| NRAS | −1.24 | 4.26E−01 | 1.21 | 7.60E−01 | 2.08 | 1.65E−03 | |
| RRAS2 | −1.39 | 2.32E−01 | 1.17 | 8.92E−01 | 2.31 | 4.53E−04 | |
| ATF2 | −1.48 | 2.86E−01 | 1.04 | 9.27E−01 | 2.32 | 5.48E−03 | |
| Natural Killer Cell Signaling | FYN | −1.45 | 1.65E−01 | 1.22 | 7.18E−01 | 2.09 | 1.44E−03 |
| PRKCI | −1.31 | 3.57E−01 | 1.26 | 7.35E−01 | 2.04 | 3.45E−03 | |
| NRAS | −1.24 | 4.26E−01 | 1.21 | 7.60E−01 | 2.08 | 1.65E−03 | |
| RRAS2 | −1.39 | 2.32E−01 | 1.17 | 8.92E−01 | 2.31 | 4.53E−04 | |
| PIK3C2A | −1.57 | 1.79E−01 | 1.23 | 6.55E−01 | 2.03 | 9.01E−03 | |
| KLRK1 | −1.11 | 7.89E−01 | 1.21 | 8.78E−01 | 2.01 | 8.80E−03 | |
| B Cell Development | IL7R | nd | nd | nd | nd | 2.13 | 4.13E−03 |
| IGKC | −1.02 | 9.57E−01 | 1.04 | 9.79E−01 | 2.44 | 6.13E−04 | |
| IGL@ | 1.30 | 8.19E−02 | 1.29 | 8.52E−01 | 6.01 | 2.87E−12 | |
| IGHM | −1.48 | 2.48E−01 | −1.28 | 8.48E−01 | 4.99 | 7.60E−04 | |
| T Cell Receptor Signaling | FYN | −1.45 | 1.65E-01 | 1.13 | 9.13E-01 | 2.09 | 1.44E-03 |
| CD28 | −1.57 | 1.72E-01 | 1.05 | 9.79E-01 | 2.57 | 9.73E-04 | |
| CAMK4 | −1.86 | 5.56E-02 | 1.04 | 9.83E-01 | 2.10 | 4.89E-03 | |
| RRAS2 | −1.39 | 2.32E-01 | 1.17 | 8.92E-01 | 2.31 | 4.53E-04 | |
| PI3KC2A | −1.57 | 1.79E-01 | −1.03 | 9.88E-01 | 2.03 | 9.01E-03 | |
| RASGRIP1 | −1.48 | 1.70E-01 | 1.23 | 8.50E-01 | 2.44 | 3.48E-04 | |
| CD3D | −1.14 | 7.40E-01 | 1.50 | 7.02E-01 | 2.24 | 4.84E-03 | |
| ITK | −1.44 | 1.83E-01 | 1.15 | 9.04E-01 | 2.12 | 1.44E-03 | |
*
p-values shown are FDR-corrected Step-up p-values.
nd = not detected
Transcripts which are both statistically significant and meet a 2-fold change of expression are indicated in bold text.