Table 1.
PGM impact analysis
| Name | Control sample | Random sample | p-value | AgNPs sample | Random sample | p-value |
|---|---|---|---|---|---|---|
| ADAM23 | 2.426 | 1.773 | 0.152 | 2.186 | 1.589 | 0.108 |
| APC | 0.85 | 1.794 | 0.014 | 1.514 | 1.609 | 0.724 |
| APEX1 | 1.138 | 1.699 | 0.131 | 1.175 | 1.737 | 0.347 |
| ATR | 1.184 | 1.839 | 0.096 | 1.351 | 1.636 | 0.357 |
| ATRX | 0.959 | 1.598 | 0.074 | 0.995 | 1.737 | 0.052 |
| AURKB | 1.179 | 1.808 | 0.048 | 1.64 | 1.728 | 0.969 |
| BAG1 | 1.205 | 1.719 | 0.337 | 1.228 | 1.647 | 0.141 |
| BBC3 | 1.214 | 1.754 | 0.337 | 1.461 | 1.719 | 0.583 |
| BCCIP | 1.184 | 1.7 | 0.17 | 1.277 | 1.778 | 0.232 |
| BCL2L10 | 2.422 | 1.689 | 0.202 | 2.267 | 1.707 | 0.232 |
| BCL2L11 | 1.142 | 1.651 | 0.147 | 1.456 | 1.658 | 0.543 |
| BIRC6 | 1.12 | 1.795 | 0.034 | 1.387 | 1.682 | 0.468 |
| BNIP2 | 0.751 | 1.761 | 0.013 | 1.759 | 1.837 | 0.86 |
| CASP4 | 2.301 | 1.667 | 0.084 | 1.753 | 1.709 | 0.953 |
| CASP5 | 2.248 | 1.648 | 0.057 | 1.737 | 1.677 | 0.875 |
| CCNA2 | 1.068 | 1.679 | 0.217 | 1.332 | 1.679 | 0.695 |
| CCNB2 | 0.237 | 1.775 | 3.70E-03 | 1.428 | 1.681 | 0.444 |
| CCNC | 1.144 | 1.67 | 0.121 | 0.86 | 1.688 | 0.068 |
| CDC16 | 1.196 | 1.786 | 0.062 | 1.197 | 1.602 | 0.239 |
| CDC25C | 1.173 | 1.756 | 0.347 | 1.062 | 1.601 | 0.152 |
| CDH1 | 2.537 | 1.693 | 0.117 | 2.977 | 1.773 | 7.65E-03 |
| CDH13 | 2.585 | 1.722 | 0.052 | 2.611 | 1.749 | 0.024 |
| CDH6 | 2.423 | 1.745 | 0.149 | 2.697 | 1.77 | 0.016 |
| CHD4 | 1.257 | 1.759 | 0.141 | 1.556 | 1.618 | 0.922 |
| CKS2 | 0.529 | 1.771 | 0.012 | 1.26 | 1.602 | 0.377 |
| CNTN1 | 2.253 | 1.698 | 0.039 | 1.82 | 1.819 | 0.937 |
| COL14A1 | 2.536 | 1.723 | 0.099 | 2.527 | 1.703 | 0.031 |
| COL15A1 | 2.305 | 1.749 | 0.121 | 2.429 | 1.645 | 0.02 |
| COL1A1 | 2.28 | 1.62 | 0.121 | 2.288 | 1.854 | 0.141 |
| COL4A2 | 2.445 | 1.592 | 0.039 | 7.09E-05 | 4.30E-05 | 0.05 |
| COL6A1 | 2.465 | 1.69 | 0.045 | 2.586 | 1.577 | 0.011 |
| COL8A1 | 2.46 | 1.643 | 0.021 | 2.543 | 1.716 | 0.029 |
| COX5A | 0.982 | 1.609 | 0.081 | 1.32 | 1.693 | 0.158 |
| CRY1 | 1.311 | 1.811 | 0.29 | 1.264 | 1.695 | 0.239 |
| CSNK2A2 | 1.263 | 1.75 | 0.17 | 0.998 | 1.675 | 0.088 |
| CTBP1 | 1.129 | 1.77 | 0.084 | 1.197 | 1.772 | 0.141 |
| CTGF | 2.2 | 1.623 | 0.065 | 2.673 | 1.593 | 0.013 |
| CUL1 | 0.904 | 1.732 | 0.045 | 1.271 | 1.648 | 0.421 |
| CXCL1 | 2.58 | 1.752 | 0.023 | 2.048 | 1.665 | 0.399 |
| CXCR4 | 2.646 | 1.636 | 0.136 | 2.513 | 1.588 | 0.052 |
| CYCS | 1.104 | 1.716 | 0.176 | 1.925 | 1.671 | 0.41 |
| DKC1 | 0.808 | 1.658 | 0.039 | 0.801 | 1.745 | 0.036 |
| EDN1 | 2.488 | 1.727 | 0.096 | 2.258 | 1.64 | 0.176 |
| ERCC1 | 1.209 | 1.742 | 0.121 | 1.065 | 1.704 | 0.057 |
| ESR1 | 1.12 | 1.63 | 0.176 | 1.781 | 1.79 | 0.596 |
| F3 | 2.692 | 1.687 | 0.043 | 1.955 | 1.648 | 0.505 |
| FANCA | 1.074 | 1.58 | 0.377 | 1.485 | 1.695 | 0.468 |
| FANCD2 | 0.96 | 1.747 | 0.033 | 1.246 | 1.739 | 0.141 |
| FLT4 | 1.121 | 1.911 | 0.024 | 2.163 | 1.771 | 0.317 |
| GADD45A | 1.131 | 1.62 | 0.317 | 1.579 | 1.771 | 0.48 |
| GSTP1 | 2.184 | 1.553 | 0.202 | 1.045 | 1.761 | 0.041 |
| GTSE1 | 1.103 | 1.739 | 0.136 | 1.851 | 1.718 | 0.799 |
| HPSE | 2.388 | 1.708 | 0.176 | 2.248 | 1.7 | 0.117 |
| HRAS | 0.901 | 1.576 | 0.065 | 1.837 | 1.682 | 0.754 |
| HRK | 2.3 | 1.686 | 0.176 | 2.763 | 1.67 | 0.016 |
| ICAM1 | 1.309 | 1.839 | 0.388 | 1.635 | 1.616 | 0.754 |
| IGFBP7 | 2.865 | 1.811 | 0.014 | 2.359 | 1.733 | 0.202 |
| IL18 | 2.618 | 1.764 | 0.048 | 1.717 | 1.564 | 0.922 |
| IL1B | 2.259 | 1.701 | 0.074 | 2.818 | 1.685 | 7.21E-03 |
| ITGA4 | 2.643 | 1.64 | 0.027 | 2.229 | 1.715 | 0.317 |
| ITGAM | 1.055 | 1.704 | 0.071 | 1.617 | 1.657 | 0.906 |
| ITGB3 | 1.171 | 1.668 | 0.299 | 2.388 | 1.706 | 0.05 |
| JAG1 | 2.177 | 1.631 | 0.108 | 2.385 | 1.761 | 0.099 |
| KISS1R | 2.497 | 1.811 | 0.17 | 1.897 | 1.715 | 0.739 |
| KRT14 | 2.695 | 1.703 | 0.045 | 2.514 | 1.63 | 0.024 |
| KRT5 | 2.723 | 1.737 | 0.034 | 2.276 | 1.62 | 0.121 |
| LAMA1 | 2.584 | 1.631 | 6.04E-03 | 2.49 | 1.688 | 0.024 |
| LAMA2 | 2.241 | 1.653 | 0.117 | 1.346 | 1.649 | 0.308 |
| LAMA3 | 2.454 | 1.615 | 0.074 | 1.709 | 1.651 | 0.953 |
| LAMB3 | 2.57 | 1.679 | 0.018 | 2.236 | 1.686 | 0.131 |
| LEP | 0.765 | 1.704 | 0.036 | 1.075 | 1.73 | 0.055 |
| LPL | 2.847 | 1.8 | 0.02 | 3.047 | 1.714 | 6.04E-03 |
| MAP2K3 | 1.126 | 1.766 | 0.078 | 1.241 | 1.724 | 0.164 |
| MCL1 | 1.115 | 1.651 | 0.152 | 1.357 | 1.669 | 0.347 |
| MCM2 | 1.128 | 1.789 | 0.264 | 1.311 | 1.751 | 0.232 |
| MLH1 | 0.968 | 1.783 | 0.065 | 0.593 | 1.759 | 8.59E-03 |
| MMP1 | 2.303 | 1.72 | 0.141 | 2.022 | 1.743 | 0.377 |
| MMP13 | 2.539 | 1.702 | 0.084 | 2.514 | 1.604 | 0.057 |
| MMP15 | 0.885 | 1.661 | 0.152 | 0.966 | 1.633 | 0.124 |
| MMP3 | 2.703 | 1.723 | 0.029 | 2.931 | 1.759 | 4.19E-03 |
| MMP7 | 3.075 | 1.579 | 6.41E-03 | 2.354 | 1.641 | 0.141 |
| MSH2 | 1.067 | 1.676 | 0.196 | 1.023 | 1.747 | 0.028 |
| MTA1 | 0.937 | 1.761 | 0.022 | 0.909 | 1.719 | 0.028 |
| MYC | 0.912 | 1.652 | 0.045 | 1.043 | 1.905 | 0.041 |
| NOTCH1 | 1.254 | 1.751 | 0.29 | 1.069 | 1.826 | 0.05 |
| OCLN | 2.433 | 1.587 | 0.117 | 2.984 | 1.649 | 5.69E-03 |
| PECAM1 | 2.311 | 1.687 | 0.182 | 2.36 | 1.772 | 0.126 |
| PFKL | 1.05 | 1.786 | 0.041 | 1.915 | 1.672 | 0.439 |
| PMS1 | 1.182 | 1.687 | 0.255 | 1.039 | 1.811 | 0.074 |
| PNKP | 1.027 | 1.794 | 0.029 | 1.879 | 1.736 | 0.61 |
| RAD17 | 0.904 | 1.712 | 0.06 | 1.65 | 1.71 | 0.891 |
| RAD50 | 0.845 | 1.681 | 0.022 | 1.625 | 1.607 | 0.906 |
| RAD51 | 1.196 | 1.72 | 0.224 | 1.156 | 1.691 | 0.224 |
| RBBP8 | 1.255 | 1.771 | 0.377 | 1.906 | 1.705 | 0.583 |
| REV1 | 1.007 | 1.72 | 0.084 | 1.36 | 1.711 | 0.264 |
| RIPK2 | 2.256 | 1.7 | 0.202 | 1.822 | 1.653 | 0.638 |
| S1PR1 | 2.463 | 1.718 | 0.068 | 2.055 | 1.689 | 0.213 |
| SELE | 2.276 | 1.734 | 0.126 | 1.454 | 1.783 | 0.255 |
| SERPINF1 | 2.298 | 1.712 | 0.131 | 2.613 | 1.685 | 7.21E-03 |
| SGCE | 2.191 | 1.599 | 0.088 | 2.213 | 1.584 | 0.232 |
| SNAI1 | 1.202 | 1.76 | 0.281 | 1.849 | 1.781 | 1 |
| SOD1 | 1.104 | 1.686 | 0.096 | 1.451 | 1.754 | 0.337 |
| SPARC | 3.026 | 1.711 | 7.21E-03 | 3.077 | 1.702 | 5.36E-03 |
| SPHK1 | 1.148 | 1.681 | 0.247 | 1.536 | 1.771 | 0.41 |
| SRC | 1.258 | 1.798 | 0.399 | 1.607 | 1.75 | 0.739 |
| SSTR2 | 2.149 | 1.633 | 0.119 | 2.104 | 1.67 | 0.57 |
| SUMO1 | 1.225 | 1.782 | 0.152 | 1.804 | 1.626 | 0.638 |
| TBX2 | 2.356 | 1.715 | 0.078 | 2.139 | 1.663 | 0.192 |
| TFF3 | 2.369 | 1.738 | 0.114 | 2.737 | 1.847 | 0.033 |
| TGFB2 | 2.593 | 1.722 | 0.062 | 2.084 | 1.717 | 0.299 |
| THBS2 | 2.771 | 1.772 | 0.06 | 3.078 | 1.601 | 5.36E-03 |
| TIMP1 | 2.199 | 1.521 | 0.272 | 1.805 | 1.671 | 0.754 |
| TIMP3 | 2.491 | 1.542 | 0.022 | 1.96 | 1.747 | 0.596 |
| TNFRSF11B | 2.362 | 1.786 | 0.182 | 2.062 | 1.61 | 0.224 |
| TNFRSF1A | 1.005 | 1.6 | 0.078 | 1.102 | 1.679 | 0.108 |
| TP73 | 2.275 | 1.731 | 0.074 | 2.165 | 1.729 | 0.17 |
| TRAF2 | 1.066 | 1.714 | 0.068 | 0.653 | 1.702 | 0.013 |
| VCAM1 | 2.525 | 1.654 | 0.034 | 2.139 | 1.724 | 0.543 |
| VCAN | 2.496 | 1.663 | 0.048 | 2.29 | 1.624 | 0.041 |
| VEGFC | 2.325 | 1.568 | 0.055 | 2.197 | 1.759 | 0.299 |
| XBP1 | 2.611 | 1.623 | 0.033 | 2.43 | 1.788 | 0.131 |
Note: p≤0.05, FDR≤0.05.
Abbreviations: PGM, probabilistic graphical models; AgNPs, silver nanoparticles; FDR, false discovery rate.