TABLE 5.
Full list of genes identified as potential upstream regulators of HIF‐2α from RNA sequencing data. Target molecules are among the 97 significantly (P < .005) DEGs between 5′‐mispair and EPAS1 morpholino samples identified by RNA sequencing
| Upstream of EPAS1 | |||||
|---|---|---|---|---|---|
| Upstream regulator | Expr log ratio | Molecule type | Activation z‐score | P‐value of overlap | Target molecules in dataset |
| GATA4 | Transcription regulator | −0.365 | 9.39E‐06 | CDX2,CLDN1,DLX3,FAP,FSTL4,POSTN,TNNC1 | |
| TAF4 | Transcription regulator | 3.14E‐05 | CDH1,CLDN1,DCN,PDGFC,VEGFD | ||
| CDX2 | −2.439 | Transcription regulator | 2.26E‐04 | APC,CDH1,CDX2,CLDN1,HNF1B | |
| FOXA2 | Transcription regulator | 1.04E‐03 | ALB,CDH1,CDX2,HADH,HNF1B | ||
| BMP4 | Growth factor | 1.17E‐03 | CDH1,CDX2,DLX3,POSTN,SCARB1 | ||
| TBX5 | Transcription regulator | 2.32E‐03 | FAP,POSTN,TNNC1 | ||
| FOXA1 | Transcription regulator | 3.33E‐03 | CDH1,CDX2,HADH,HNF1B | ||
| KLF4 | Transcription regulator | −1.324 | 3.56E‐03 | ALB,CDH1,CDX2,DLX3,LIN28A | |
| SKI | Transcription regulator | 3.74E‐03 | CDH1,FAP | ||
| SNAI3 | Transcription regulator | 3.97E‐03 | CDH1 | ||
| TGFB1 | Growth factor | 1.679 | 4.28E‐03 | ALB,CDH1,CHST8,CRHR2,DCN,EPHB2,F2,FAP,GLCE,GRHL2,HADH,PDGFC,POSTN,SCARB1,TLE4 | |
| KMT2D | Transcription regulator | 0.254 | 5.14E‐03 | ASL,SCARB1,TNNC1,WDR17 | |
| STAT5A | Transcription regulator | 5.44E‐03 | CDH1,SNTB1,TLE4,TNNC1,TSPAN8 | ||
| TFE3 | Transcription regulator | 5.91E‐03 | ALB,CDH1 | ||
| HOXA7 | Transcription regulator | 5.91E‐03 | CDH1,LY86 | ||
| CITED2 | Transcription regulator | 6.74E‐03 | CDX2,VEGFD | ||
| MYOD1 | Transcription regulator | −1.192 | 6.99E‐03 | CDX2,HADH,POSTN,TNNC1 | |
| GATA6 | Transcription regulator | −0.068 | 7.38E‐03 | CDX2,DLX3,HNF1B,TNNC1 | |
| CERS3 | Transcription regulator | 7.93E‐03 | ASAH1 | ||
| ALX1 | Transcription regulator | 7.93E‐03 | CDH1 | ||
| LMCD1 | Transcription regulator | 7.93E‐03 | TNNC1 | ||
| VAX2 | Transcription regulator | 7.93E‐03 | EPHB2 | ||
| TEAD4 | Transcription regulator | 8.53E‐03 | CDX2,TNNC1 | ||
| TWIST2 | Transcription regulator | 9.01E‐03 | CDH1,POSTN | ||
| BMP2 | Growth factor | 9.08E‐03 | CDH1,DLX3,PLXNA2,POSTN | ||
| CEBPA | Transcription regulator | −1.452 | 9.09E‐03 | ALB,ASL,CDH1,DLX3,HNF1B,LIN28A | |
| SOX2 | Transcription regulator | −0.529 | 1.02E‐02 | ALB,APC,CDX2,DLX3,LIN28A | |
| TFAP4 | Transcription regulator | 1.05E‐02 | CDH1,CLDN1 | ||
| POU5F1 | Transcription regulator | 1.332 | 1.08E‐02 | ALB,CDH1,CDX2,DLX3,LIN28A | |
| CBX5 | Transcription regulator | 1.14E‐02 | SNTB1,TLE4,TSPAN8 | ||
| HNF1B | −2.282 | Transcription regulator | 1.17E‐02 | ALB,CDH1,CLDN1 | |
| ISX | Transcription regulator | 1.19E‐02 | SCARB1 | ||
| CERS4 | Transcription regulator | 1.19E‐02 | ASAH1 | ||
| Tardbp | Transcription regulator | 1.19E‐02 | ERBB4 | ||
| EEF1D | Transcription regulator | 1.19E‐02 | CDH1 | ||
| SOX21 | Transcription regulator | 1.19E‐02 | CDX2 | ||
| JMY | Transcription regulator | 1.19E‐02 | CDH1 | ||
| POU2F1 | Transcription regulator | 1.25E‐02 | CDX2,HNF1B,TNNC1 | ||
| MEF2C | Transcription regulator | 1.25E‐02 | FAP,POSTN,TNNC1 | ||
| FGF1 | Growth factor | 1.36E‐02 | ALB,CDH1,POSTN | ||
| FGF16 | Growth factor | 1.58E‐02 | CDH1 | ||
| PDLIM1 | Transcription regulator | 1.58E‐02 | CDH1 | ||
| HAND2 | Transcription regulator | 1.63E‐02 | FAP,TNNC1 | ||
| VHL | Transcription regulator | 1.64E‐02 | CDH1,GLCE,SEC61G | ||
| FGF2 | Growth factor | 0.932 | 1.64E‐02 | ALB,CDH1,CDX2,DCN,PDGFC | |
| ZEB1 | Transcription regulator | 1.76E‐02 | CDH1,GRHL2 | ||
| ETV5 | Transcription regulator | 1.82E‐02 | CDH1,CLDN1 | ||
| WISP2 | Growth factor | 1.82E‐02 | CDH1,CLDN1 | ||
| TP63 | Transcription regulator | −1.807 | 1.89E‐02 | APC,CDH1,GRHL2,LIN28A,POSTN | |
| FOXI1 | Transcription regulator | 1.97E‐02 | SLC12A3 | ||
| RFXANK | Transcription regulator | 1.97E‐02 | EPHA3 | ||
| NFYB | Transcription regulator | 2.24E‐02 | APC,CDH1,DPP10,SCARB1 | ||
| CERS5 | Transcription regulator | 2.36E‐02 | ASAH1 | ||
| KLF8 | Transcription regulator | 2.36E‐02 | CDH1 | ||
| HMG20A | Transcription regulator | 2.36E‐02 | CDH1 | ||
| WISP3 | Growth factor | 2.36E‐02 | CDH1 | ||
| MEIS2 | Transcription regulator | 2.36E‐02 | CDH1 | ||
| ERF | Transcription regulator | 2.36E‐02 | CDH1 | ||
| DKK1 | Growth factor | 2.38E‐02 | EPHB2,TNNC1 | ||
| SNAI2 | Transcription regulator | 2.46E‐02 | CDH1,CLDN1 | ||
| YY1 | Transcription regulator | 2.52E‐02 | CDH1,DLX3,SCARB1,TNNC1 | ||
| MEF2D | Transcription regulator | 2.53E‐02 | CDH1,TNNC1 | ||
| CEBPB | Transcription regulator | 1.103 | 2.56E‐02 | ALB,DCN,DLX3,KRT15,SCARB1 | |
| ZNF100 | Transcription regulator | 2.75E‐02 | POSTN | ||
| ZNF85 | Transcription regulator | 2.75E‐02 | POSTN | ||
| ZNF254 | Transcription regulator | 2.75E‐02 | POSTN | ||
| ZNF431 | Transcription regulator | 2.75E‐02 | POSTN | ||
| ZNF43 | Transcription regulator | 2.75E‐02 | POSTN | ||
| ZNF429 | Transcription regulator | 2.75E‐02 | POSTN | ||
| NKX3‐2 | Transcription regulator | 2.75E‐02 | POSTN | ||
| EHMT1 | Transcription regulator | 2.75E‐02 | CDH1 | ||
| FOXN3 | Transcription regulator | 2.75E‐02 | CFAP36 | ||
| SOX9 | Transcription regulator | 2.84E‐02 | CDX2,KRT15 | ||
| SPDEF | Transcription regulator | 3.00E‐02 | APC,PTPRF | ||
| MYC | Transcription regulator | −0.039 | 3.12E‐02 | ALB,CDH1,CDX2,DLX3,F2,FAP,SCARB1,SLC25A21,TLE4 | |
| CERS6 | Transcription regulator | 3.14E‐02 | ASAH1 | ||
| TEAD3 | Transcription regulator | 3.14E‐02 | TNNC1 | ||
| GRIP1 | Transcription regulator | 3.14E‐02 | FRAS1 | ||
| ZNF91 | Transcription regulator | 3.14E‐02 | POSTN | ||
| LEP | Growth factor | −0.169 | 3.23E‐02 | ASAH1,ASL,CDH1,CRHR2,SCARB1 | |
| NFKBID | Transcription regulator | 3.52E‐02 | CDH1 | ||
| FGF3 | Growth factor | 3.52E‐02 | CDH1 | ||
| GLIS1 | Transcription regulator | 3.52E‐02 | LIN28A | ||
| TFAP2C | Transcription regulator | 3.59E‐02 | CDH1,CDX2 | ||
| PDX1 | Transcription regulator | 3.86E‐02 | ALB,PTPRF,TSPAN8 | ||
| WWC1 | Transcription regulator | 3.91E‐02 | CDH1 | ||
| PRDM16 | Transcription regulator | 3.91E‐02 | DCN | ||
| RYBP | Transcription regulator | 3.91E‐02 | CDX2 | ||
| LCOR | Transcription regulator | 3.91E‐02 | CDH1 | ||
| INHBA | Growth factor | 4.12E‐02 | CDH1,CPNE8,ERBB4 | ||
| CERS2 | Transcription regulator | 4.29E‐02 | ASAH1 | ||
| RFX2 | Transcription regulator | 4.29E‐02 | DCDC2 | ||
| GMNN | Transcription regulator | 4.32E‐02 | CDH1,CDX2 | ||
| CCND1 | Transcription regulator | 4.42E‐02 | CDH1,JKAMP,MYO7A,RMI2 | ||
| SMAD2 | Transcription regulator | 4.60E‐02 | CDH1,CDX2 | ||
| GATA5 | Transcription regulator | 4.67E‐02 | TNNC1 | ||
| AJUBA | Transcription regulator | 4.67E‐02 | CDH1 | ||
| MYOCD | Transcription regulator | 4.89E‐02 | FAP,TNNC1 | ||
Abbreviation: DEGs, differentially expressed genes; HIF, hypoxia inducible factor.