Table 4. Regulated transcription factors and their predicted genes that regulated up or down.
| TF | P | FDR | I | TG | RC% | Tx | H | Predicted Genes Regulated |
|---|---|---|---|---|---|---|---|---|
| JUND | 0.00E+00 | 2.89E-03 | 9 | 28 | 0 | None | 3 | Up-JUN,F3,PLAUR,VGF,IL6,TIMP1,NR4A1,CDKN1A,FOSL1 |
| ATF1 | 0.00E+00 | 6.61E-03 | 9 | 59 | 1 | None | 3 | Up-SLC20A1,JUN,HK2,IL6,HSPA5,FOS,PLAUR,INHBA; Down-UGT8 |
| STAT1 | 2.00E-05 | 8.26E-03 | 8 | 61 | 1 | None | 3 | Up-ICAM1,CSF1,IRF1,FOS,CXCL10,SOCS3,TIMP1,CDKN1A |
| HIF1A | 2.00E-05 | 8.68E-03 | 7 | 45 | 0 | None | 3 | Up-PFKFB3,ADM,HMOX1,NR4A1,CTGF,SERPINE1,TIMP1 |
| JUNB | 0.00E+00 | 3.31E-03 | 7 | 20 | 1 | None | 3 | Up-TGM1,VGF,CDKN1A,IL6,PLAUR,TIMP1,JUN |
| PPARG | 1.00E-05 | 7.44E-03 | 7 | 41 | 1 | None | 3 | Up-SERPINE1,NR1D1,SAT1,GADD45A,GADD45B,CDNK1A,ANGPTL4 |
| PPARD | 1.30E-04 | 9.92E-03 | 4 | 14 | 1 | None | 3 | Up-SERPINE1,GADD45B,ANGPTL4,GADD45A |
| ETV4 | 1.40E-04 | 8.88E-03 | 7 | 31 | 1 | None | 24 | Up-TIMP1,VIM,MMP3,PLAUR,PCNA,RAD51; Down-SLC9A3 |
| SMAD3 | 0.00E+00 | 9.52E-04 | 9 | 63 | 1 | None | 120 | Up-TAGLN,COL6A3,TIMP1,VIM,COL6A1,COL6A2,FN1,COL1A1; Down-TNFSF11 |
| NOTCH1 | 1.00E-05 | 1.91E-03 | 6 | 40 | 0 | None | 120 | Up-MCM6,MYC,TAGLN,ADAM19; Down-TNFRSF11,REN |
| TCF7L2 | 7.00E-05 | 4.29E-03 | 6 | 61 | 1 | None | 120 | Up-CD44,TAGLN,VIM,MYC,MYBL2; Down-TNFRSF11 |
| ETV4 | 4.10E-04 | 6.67E-03 | 4 | 31 | 1 | None | 120 | Up-TIMP1,VIM; Down-SLC9A3,PTGS2 |
| SMAD7 | 6.10E-04 | 7.62E-03 | 3 | 15 | 0 | None | 120 | Up-COL6A2,COL6A3,COL1A1 |
| SMAD4 | 1.73E-03 | 8.10E-03 | 4 | 45 | 0 | None | 120 | Up-TIMP1,TAGLN,CLDN1; Down-TNFRSF11 |
| NFIC | 1.73E-03 | 8.57E-03 | 4 | 45 | 0 | None | 120 | Up-CLU,COL1A1; Down-SLC2A4,SLC9A3 |
| SMAD1 | 1.96E-03 | 9.05E-03 | 3 | 22 | 0 | None | 120 | Up-TAGLN,MYC; Down-TNFRSF11 |
| SMAD3 | 0.00E+00 | 3.72E-03 | 10 | 63 | 1 | Dex | 3 | Up-CTGF,VIM,SERPINE1,EDN1,ZFP36,BAMBI,JUN,TIMP1,PTHLH,CYR61 |
| JUNB | 0.00E+00 | 6.61E-03 | 7 | 20 | 1 | Dex | 3 | Up-IL6,TIMP1,CDKN1A,PLAUR,VGF,TGM1,JUN |
| ATF4 | 3.00E-05 | 8.68E-03 | 5 | 18 | 1 | Dex | 3 | Up-HSPA5,HMOX1,DDIT3,PPP1R15A,ASNS |
| HIF1A | 4.00E-05 | 9.09E-03 | 7 | 45 | 1 | Dex | 3 | Up-SERPINE1,CTGF,PFKB3,HMOX1,TIMP1,NR4A1,ADM |
| FOSL1 | 3.00E-05 | 4.88E-03 | 3 | 4 | 0 | Dex | 24 | Up-CCNA2,PLAUR,FOSL1 |
| NFE2L2 | 3.00E-05 | 5.29E-03 | 5 | 19 | 0 | Dex | 24 | Up-NQO1,GPX2,HMOX1; Down-NQO2,GCLC |
| E2F2 | 4.00E-05 | 6.10E-03 | 6 | 32 | 1 | Dex | 24 | Up-MCM6,MYC,CDC6,CDC45,E2F1,MCM5 |
| SMAD1 | 7.00E-05 | 6.50E-03 | 5 | 22 | 1 | Dex | 24 | Up-GADD45B,MYC,CDKN1A; Down-TNFRSF11,PDGFC |
| SMAD4 | 2.80E-04 | 9.76E-03 | 6 | 45 | 1 | Dex | 24 | Up-CLDN1,CDKN1A,TIMP1,COL7A1,COL6A2; Down-TNFRSF11,HNF4A |
| SMAD7 | 0.00E+00 | 4.31E-03 | 7 | 15 | 0 | Dex | 120 | Up-COL3A1,COL1A1,COL6A3,HMOX1,COL5A2,COL1A2,COL6A2 |
| SMAD2 | 3.30E-04 | 8.94E-03 | 5 | 21 | 1 | Dex | 120 | Up-COL7A1,TGFB1,TAGLN; Down-TNFRSF11,TIMP3 |
| JUN | 0.00E+00 | 5.05E-04 | 11 | 131 | 1 | VPA | 3 | Up-EDN1,SLC20A1,PTX3,PLAUR,DDIT3,TFPI2,JUN,FOSL1,HBEGF,CSF1,IL6 |
| ESR1 | 0.00E+00 | 1.01E-03 | 7 | 54 | 0 | VPA | 3 | Up-CDKN1A,MYC,JUN,GADD45B,JUNB,HSPB1,SERPINE1 |
| EGR1 | 0.00E+00 | 3.54E-03 | 9 | 91 | 0 | VPA | 3 | Up-IL6,ICAM1,HMOX1,CSF1,GDF15,TFPI2,JUN,CEBPB,SERPINE1 |
| JUND | 0.00E+00 | 4.04E-03 | 5 | 28 | 0 | VPA | 3 | Up-JUN,IL6,CDKN1A,FOSL1,PLAUR |
| ATF4 | 1.00E-05 | 5.56E-03 | 4 | 18 | 0 | VPA | 3 | Up-DDIT3,PPP1R15A,HMOX1,HSPA5 |
| RELA | 1.00E-05 | 6.57E-03 | 7 | 84 | 0 | VPA | 3 | Up-ICAM,GADD45B,CXCL10,MYC,IL6,PTX3,CXCL1 |
| JUNB | 2.00E-05 | 7.07E-03 | 4 | 20 | 0 | VPA | 3 | Up-CDKN1A,PLAUR,IL6,JUN |
| REL | 3.00E-05 | 8.08E-03 | 4 | 23 | 0 | VPA | 3 | Up-ICAM1,IL6,CXCL1; Down-TNFSF10 |
| SMAD1 | 3.00E-05 | 8.59E-03 | 4 | 22 | 0 | VPA | 3 | Up-CDKN1A,GADD45B,BAMBI,MYC |
| TCF7L2 | 1.40E-04 | 9.09E-03 | 5 | 61 | 1 | VPA | 3 | Up-EDN1,MYC,MAP3K6,BAMBI; Down-DKK1 |
| STAT1 | 1.40E-04 | 9.60E-03 | 5 | 61 | 0 | VPA | 3 | Up-CDKN1A,CXCL10,CSF1,ICAM1,SOCS3 |
| E2F3 | 1.00E-05 | 5.45E-03 | 9 | 36 | 1 | VPA | 24 | Up-MCM5,CDC45,CDKN1A,PLK4,MCM6,CDC6,PLK1,E2F1; Down-PCSK6 |
| E2F2 | 3.00E-05 | 7.37E-03 | 8 | 32 | 1 | VPA | 24 | Up-E2F1,CDC6,MCM6,MCM5,PLK1,PLK4,CDC45; Down-PCSK6 |
TF, Transcription factor; P, Probability; FDR, False Discovery Rate; I, Interaction; TG, Target Gene; RC, Random Control; Tx, Treatment; H, Hours Post-ischemia reperfusion; None, No treatment; Dex, Dexamethazone; VPA, Valproic Acid. All treatment groups (None, Dex, and VPA) were queried with TFactS at each time point (3, 24, and 120 hours) by using the up and down regulated gene lists presented in Supplementary information S5 Table. To reduce the complexity of the data, only TF that has a random control <2%, p<0.01, FDR<0.01 and more than two gene targets were presented (see the full queries in supplementary information S6 Table). The total number of target genes for a given transcription factor (i.e. JUNB has 20 target genes) is a property of the TFactS database. The intersection (I) of the target genes (TGs) in the microarray analysis with the transcription factors (TFs) in the database is presented.