Table S1.
Genes overexpressed in simultaneous siRNA knockdown of mutant-p53 and TNF versus control group
| Position | Gene symbol | Fold regulation | Comments | P-value | RT2 catalog |
|---|---|---|---|---|---|
| A03 | APAF1 | 1.5115 | Okay | 0.103217 | PPH00752A |
| A05 | BAG1 | 1.8226 | Okay | 0.024718 | PPH00076F |
| A06 | BAG3 | 1.2977 | Okay | 0.088557 | PPH01036C |
| A07 | BAG4 | 1.2681 | Okay | 0.229984 | PPH01039B |
| A10 | BCL10 | 1.2858 | Okay | 0.019143 | PPH00890F |
| B02 | BCL2L10 | 1.6502 | B | 0.41272 | PPH15924B |
| B03 | BCL2L11 | 1.4668 | Okay | 0.017838 | PPH00893F |
| B04 | BCL2L2 | 1.3098 | Okay | 0.073331 | PPH00081E |
| B05 | BCLAF1 | 1.3007 | Okay | 0.07925 | PPH10187F |
| B07 | BID | 1.4433 | Okay | 0.432661 | PPH00084C |
| B08 | BIK | 3.3081 | B | 0.281268 | PPH00363C |
| B09 | NAIP | 1.6125 | Okay | 0.011279 | PPH00909E |
| B10 | BIRC2 | 1.3159 | Okay | 0.025975 | PPH00340B |
| B11 | BIRC3 | 1.6238 | Okay | 0.003131 | PPH00326B |
| C02 | BIRC8 | 8.511 | B | 0.261706 | PPH17361A |
| C03 | BNIP1 | 1.2828 | Okay | 0.062077 | PPH00308C |
| C05 | BNIP3 | 1.8523 | Okay | 0.067107 | PPH00301C |
| C07 | BRAF | 1.4499 | A | 0.006529 | PPH00712A |
| C08 | NOD1 | 3.4806 | A | 0.013481 | PPH00891C |
| C09 | CARD6 | 1.522 | Okay | 0.005088 | PPH14265F |
| C10 | CARD8 | 1.9399 | A | 0.022517 | |
| C11 | CASP1 | 1.9579 | Okay | 0.000375 | PPH00105C |
| C12 | CASP10 | 1.4136 | A | 0.00387 | PPH00106F |
| D03 | CASP3 | 1.3717 | Okay | 0.130571 | PPH00107C |
| D04 | CASP4 | 1.4006 | Okay | 0.002718 | PPH00366F |
| D05 | CASP5 | 1.5397 | B | 0.20244 | PPH00108G |
| D07 | CASP7 | 6.1447 | Okay | 0.067402 | PPH00110C |
| D08 | CASP8 | 2.1926 | Okay | 0.015031 | PPH00359F |
| D10 | CD40 | 3.5292 | B | 0.211046 | PPH00296D |
| E01 | CIDEA | 7.3242 | A | 0.133091 | PPH00899C |
| E04 | DAPK1 | 1.5612 | Okay | 0.111299 | PPH00273F |
| E07 | FAS | 2.0037 | Okay | 0.001615 | PPH00141B |
| E10 | HRK | 1.8738 | B | 0.189269 | PPH00369B |
| F02 | MCL1 | 1.4466 | Okay | 0.010779 | PPH00397E |
| F04 | PYCARD | 4.1106 | A | 0.160589 | PPH00907A |
| F05 | RIPK2 | 1.3623 | Okay | 0.07601 | PPH00881C |
| F07 | TNFRSF10A | 1.8058 | B | 0.190581 | PPH00842A |
| F09 | TNFRSF11B | 1.5648 | Okay | 0.061664 | PPH01049B |
| F10 | TNFRSF1A | 1.3037 | Okay | 0.082667 | PPH00346C |
| F11 | TNFRSF21 | 1.3281 | Okay | 0.179478 | PPH00262A |
| G01 | CD27 | 1.46 | B | 0.409667 | PPH00269F |
| G03 | TNFSF10 | 6.7865 | A | 0.000892 | PPH00242F |
| G04 | CD70 | 1.3037 | B | 0.502198 | PPH00258F |
| G05 | TNFSF8 | 1.7769 | B | 0.398514 | PPH00268A |
| G07 | TP53BP2 | 1.8738 | Okay | 0.007362 | PPH00394F |
| G08 | TP73 | 8.6698 | A | 0.277694 | PPH00725A |
| H02 | HPRT1 | 1.583 | Okay | 0.020772 | PPH01018C |
| A08 | BAK1 | −1.754 | Okay | 0.025932 | PPH00077F |
| A11 | BCL2 | −1.4955 | B | 0.16068 | PPH00079B |
| C04 | BNIP2 | −1.6029 | Okay | 0.014515 | PPH14371F |
| D11 | CD40LG | −1.4247 | C | 0.30247 | PPH00259C |
| E02 | CIDEB | −1.4247 | Okay | 0.419176 | PPH00913C |
| E06 | FADD | −2.1644 | Okay | 0.086067 | PPH00367A |
| E09 | GADD45A | −3.2883 | Okay | 0.127505 | PPH00148B |
| E12 | LTA | −1.2751 | B | 0.728907 | PPH00337F |
| F01 | LTBR | −1.7703 | Okay | 0.114093 | PPH00816C |
| F03 | NOL3 | −1.3857 | Okay | 0.324792 | PPH00902F |
| F06 | TNF | −1.7909 | Okay | 0.012084 | PPH00341F |
| G06 | TP53 | −3.0823 | Okay | 0.003315 | PPH00213F |
| G09 | TRADD | −1.305 | Okay | 0.080608 | PPH00392F |
| G10 | TRAF2 | −1.4479 | Okay | 0.166957 | PPH00352B |
| G12 | TRAF4 | −8.8193 | Okay | 0.161911 | PPH00753B |
| H04 | GAPDH | −1.351 | Okay | 0.133959 | PPH00150F |
Notes: Test group: Simultaneous siRNA knockdown of mutant-p53 and TNF reported to control group: untreated cells; fold difference, 1.25; P-value 0.05. Arrays included in test group: p53 + TNF 1, p53 + TNF 2, p53 + TNF 3; arrays included in control group: C1, C2, C3. A: This gene’s average threshold cycle is relatively high (>30) in either the control or the test sample and is reasonably low in the other sample (<30). These data mean that the gene’s expression is relatively low in one sample and reasonably detected in the other sample, suggesting that the actual fold-change value is at least as large as the calculated and reported fold-change result. This fold-change result may also have greater variations if P-value >0.05; therefore, it is important to have a sufficient number of biological replicates to validate the result for this gene. B: This gene’s average threshold cycle is relatively high (>30), meaning that its relative expression level is low in both control and test samples, and the P-value for the fold change is either unavailable or relatively high (P>0.05). This fold-change result may also have greater variations; therefore, it is important to have a sufficient number of biological replicates to validate the result for this gene. C: This gene’s average threshold cycle is either not determined or greater than the defined cut-off value (default 35) in both samples, meaning that its expression was undetected, making this fold-change result erroneous and uninterpretable. Fold change and fold regulation: Fold change (2−ΔΔCt) is the normalized gene expression (2−ΔCt) in the test sample divided by the normalized gene expression (2−ΔCt) in the control sample. Fold regulation represents the fold-change results in a biologically meaningful way. Fold-change values greater than 1 indicate a positive- or an upregulation, and the fold regulation is equal to the fold change. The P-values are calculated based on a Student’s t-test of the replicate 2−ΔCt values for each gene in the control group and treatment groups, and the P-values <0.05 are indicated in bold font.
Abbreviation: TNF, tumor necrosis factor.