Table 4.
List of all loci with significantly changed chromatin interactions after TNF stimulation and expression of associated genes after TNF stimulation
| Locus | Interacting gene | Base mean expression | log2Fold Change | lfcSE | stat | p value | padj |
|---|---|---|---|---|---|---|---|
| 12 | SPRED2 | 772.22 | − 0.34 | 0.08 | − 4.36 | 1.29E−05 | 7.23E−05 |
| 19 | SLC4A7 | 3702.62 | − 0.23 | 0.13 | − 1.80 | 0.072 | 0.145 |
| 20 | PXK | 1012.38 | − 0.33 | 0.11 | − 3.05 | 0.002 | 0.008 |
| 23 | RBPJ | 5319.00 | − 0.56 | 0.22 | − 2.51 | 0.012 | 0.032 |
| 24 | IL6ST | 18,850.31 | 0.72 | 0.08 | 8.91 | 4.91E−19 | 2.30E−17 |
| 30 | TNFAIP3 | 7841.42 | 4.57 | 0.19 | 23.43 | 2.14E−121 | 3.51E−118 |
| 34 | CDK6 | 4906.40 | 0.92 | 0.12 | 7.89 | 3.05E−15 | 9.21E−14 |
| 35 | TNPO3 | 1671.71 | 0.05 | 0.07 | 0.76 | 0.449 | 0.597 |
| 41 | PHF19 | 1065.75 | 0.71 | 0.14 | 5.09 | 3.56E−07 | 2.74E−06 |
| 42 | TRAF1 | 1041.51 | 2.80 | 0.22 | 12.65 | 1.14E−36 | 1.98E−34 |
| 48 | VPS37C | 552.68 | 0.71 | 0.07 | 10.56 | 4.76E−26 | 3.90E−24 |
| 52 | CDK2 | 648.74 | 0.85 | 0.13 | 6.69 | 2.23E−11 | 3.72E−10 |
| 52 | RAB5B | 1805.92 | − 0.24 | 0.06 | − 4.06 | 4.88E−05 | 2.42E−04 |
| 52 | RNF41 | 1878.98 | − 0.63 | 0.11 | − 5.62 | 1.93E−08 | 1.88E−07 |
| 52 | ANKRD52 | 1954.38 | 0.23 | 0.07 | 3.09 | 0.002 | 0.007 |
| 52 | CNPY2 | 1033.14 | 0.37 | 0.07 | 5.30 | 1.16E−07 | 9.89E−07 |
| 52 | PAN2 | 312.46 | − 0.23 | 0.08 | − 2.80 | 0.005 | 0.015 |
| 52 | STAT2 | 4951.27 | 0.74 | 0.20 | 3.77 | 1.64E−04 | 7.21E−04 |
| 52 | TIMELESS | 728.81 | 1.11 | 0.14 | 8.10 | 5.66E−16 | 1.87E−14 |
| 52 | GLS2 | 18.80 | 0.34 | 0.26 | 1.31 | 0.191 | 0.317 |
| 53 | SLC26A10 | 10.97 | − 0.29 | 0.39 | − 0.75 | 0.455 | 0.603 |
| 53 | OS9 | 5461.71 | − 0.12 | 0.07 | − 1.83 | 0.068 | 0.138 |
| 53 | AGAP2 | 5.83 | 0.43 | 0.31 | 1.36 | 0.173 | 0.294 |
| 53 | TSPAN31 | 370.51 | − 0.29 | 0.11 | − 2.56 | 0.010 | 0.028 |
| 53 | CDK4 | 1630.73 | 0.06 | 0.07 | 0.88 | 0.378 | 0.529 |
| 53 | AVIL | 64.47 | − 0.44 | 0.15 | − 2.93 | 0.003 | 0.011 |
| 53 | CTDSP2 | 3707.75 | − 0.47 | 0.06 | − 7.79 | 6.45E−15 | 1.85E−13 |
| 54 | SH2B3 | 1493.15 | 0.52 | 0.10 | 5.29 | 1.25E−07 | 1.06E−06 |
| 54 | ATXN2 | 781.23 | − 0.05 | 0.08 | − 0.71 | 0.478 | 0.625 |
| 64 | ORMDL3 | 800.27 | 0.40 | 0.08 | 4.75 | 1.99E−06 | 1.32E−05 |
| 64 | PSMD3 | 1842.20 | 0.18 | 0.05 | 3.66 | 2.53E−04 | 0.001 |
| 65;68 | IFNAR2 | 644.38 | 2.81 | 0.11 | 26.14 | 1.14E−150 | 2.92E−147 |
| 68 | IFNAR1 | 2355.18 | 0.95 | 0.08 | 12.55 | 3.95E−36 | 6.53E−34 |
| 68 | IFNGR2 | 1248.98 | 1.10 | 0.08 | 12.90 | 4.71E−38 | 9.03E−36 |
| 68 | ITSN1 | 1138.10 | − 0.24 | 0.11 | − 2.10 | 0.036 | 0.080 |
Genes with a log2fold change > ± 0.5 and padj < 0.05 are marked in bold. lfcSE standard error for log2 fold change, stat statistic value for the null hypothesis, padj p value adjusted for multiple testing using Benjamini-Hochberg