Table 1.
Top 20 IPA-predicted activated upstream regulators in memory CD4 and CD8 T cells from HC and PLWH stimulated in vitro with IL-27.
| Memory CD4 T cells |
Memory CD8 T cells |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| HC |
HIV+ |
HC |
HIV+ |
||||||||
| Upstream regulator | Activation Z score | p value of overlap | Upstream Regulator | Activation Z score | p value of overlap | Upstream regulator | Activation Z score | p value of overlap | Upstream regulator | Activation Z score | p value of overlap |
| STAT1 | 6.82 | 8.75 × 10−68 | Interferon alpha | 5.86 | 2.98 × 10−72 | STAT1 | 6.22 | 1.01 × 10−61 | STAT1 | 6.08 | 2.37 × 10−65 |
| Interferon alpha | 5.19 | 7.66 × 10−65 | STAT1 | 6.74 | 4.06 × 10−72 | Interferon alpha | 4.69 | 6.94 × 10−57 | Interferon alpha | 4.87 | 2.94 × 10−56 |
| IFNA2 | 6.35 | 4.93 × 10−61 | IFNL1 | 6.67 | 6.56 × 10−68 | IFNG | 7.49 | 2.16E-50 | IFNG | 7.05 | 2.00 × 10−53 |
| IFNL1 | 6.30 | 3.03E-60 | IFNA2 | 6.72 | 1.65 × 10−67 | IFNL1 | 5.47 | 5.79 × 10−47 | IFNL1 | 5.81 | 4.26E-50 |
| IFNG | 8.19 | 5.04 × 10−59 | IFNG | 8.58 | 2.29 × 10−66 | IFNA2 | 5.49 | 4.27 × 10−46 | IFNA2 | 5.66 | 1.18 × 10−44 |
| NONO | 6.24 | 4.59E-50 | NONO | 6.69 | 4.62 × 10−57 | PRL | 5.35 | 3.83 × 10−37 | NONO | 5.94 | 9.08 × 10−41 |
| PRL | 6.13 | 6.24 × 10−46 | PRL | 6.36 | 2.02 × 10−48 | NONO | 5.43 | 7.27 × 10−36 | RC3H1 | −4.70 | 6.20 × 10−33 |
| MAPK1 | −5.67 | 1.02 × 10−38 | MAPK1 | −6.24 | 2.60 × 10−44 | RC3H1 | −4.49 | 5.19 × 10−33 | PRL | 5.35 | 7.68 × 10−33 |
| IRGM | −4.77 | 8.30 × 10−38 | IRGM | −5.41 | 7.87 × 10−42 | MAPK1 | −4.98 | 1.04 × 10−32 | MAPK1 | −5.32 | 2.63 × 10−32 |
| IRF3 | 5.74 | 2.56 × 10−37 | IRF3 | 5.74 | 2.54 × 10−39 | Irgm1 | −4.57 | 3.90 × 10−31 | Irgm1 | −4.33 | 4.95 × 10−29 |
| STAT3 | 1.13 | 1.69 × 10−35 | Irgm1 | −5.13 | 3.67 × 10−38 | STAT3 | 1.03 | 8.52 × 10−31 | IRF3 | 4.95 | 8.03 × 10−29 |
| Irgm1 | −5.16 | 1.89 × 10−35 | STAT3 | 1.40 | 1.73 × 10−37 | IRF3 | 4.76 | 6.24E-30 | Ifnar | 4.32 | 7.41 × 10−28 |
| TCR | 2.00 | 4.22 × 10−35 | TRIM24 | −5.54 | 3.20 × 10−37 | Ifnar | 4.21 | 8.25E-30 | IRGM | −4.57 | 8.02 × 10−28 |
| TRIM24 | −5.51 | 3.10 × 10−33 | RC3H1 | −5.01 | 1.63 × 10−36 | TRIM24 | −4.94 | 2.11 × 10−29 | TLR9 | 4.32 | 6.84 × 10−27 |
| RC3H1 | −5.19 | 3.26 × 10−33 | TCR | 2.91 | 1.31 × 10−34 | IRGM | −4.46 | 5.98 × 10−29 | TLR4 | 3.66 | 1.58 × 10−26 |
| PNPT1 | −4.76 | 4.28 × 10−32 | IL1RN | −5.47 | 3.04 × 10−34 | TLR9 | 4.83 | 9.86 × 10−29 | STAT3 | 0.42 | 4.24 × 10−26 |
| IL1RN | −4.68 | 2.05 × 10−31 | Ifnar | 4.93 | 6.64 × 10−34 | TCR | 2.91 | 2.90 × 10−26 | TRIM24 | −4.94 | 9.18 × 10−26 |
| TLR3 | 4.22 | 6.24 × 10−31 | PNPT1 | −4.76 | 1.39E-30 | TLR3 | 4.27 | 1.19 × 10−25 | TCR | 2.19 | 3.05 × 10−25 |
| TLR9 | 4.26 | 4.08E-30 | CNOT7 | −2.62 | 6.69E-30 | IRF7 | 4.38 | 2.57 × 10−24 | IRF7 | 4.10 | 1.79 × 10−24 |
| Ifnar | 5.08 | 1.49 × 10−29 | RNY3 | 4.36 | 1.34 × 10−29 | IFNB1 | 4.22 | 1.39 × 10−23 | RNY3 | 3.87 | 4.52 × 10−23 |
Lists of differentially expressed gene transcripts (DEGs) selected by criteria: | log2(FC) | > 1 and adjusted p values (<0.05) were generated for each condition and used as input in IPA software. Activation Z-score are based on a model that assigns random regulation directions for predicted upstream regulators. The p value of overlap was used to rank the significance associated for each Upstream Regulator. The pvalue indicates the significance of the overlap between the genes targeted by the upstream regulator in the database and the experimental dataset.