Table 3.
TRF genes whose expression levels were changed >1.5-fold by ATRA at one or more time points
| Symbol | RefSeq ID | 6 h | 12 h | 24 h | 36 h | 48 h | Detection |
|---|---|---|---|---|---|---|---|
| BHLHB2 | NM_003670 | 2.06 | 2.02 | 2.21 | 2.28 | 2.46 | Illumina |
| CEBPA | NM_004364 | 1.49 | 1.49 | 1.69 | 1.89 | 2.04 | Illumina |
| CEBPD | NM_005195 | 0.89 | 0.74 | 0.72 | 0.63 | 0.56 | Illumina |
| CEBPG | NM_001806 | 1.12 | 1.29 | 1.49 | 1.56 | 1.81 | Illumina |
| CUTL1 | NM_181500 | 1.36 | 1.07 | 1.01 | 2.20 | 2.09 | Illumina |
| DDIT3 | NM_004083 | 2.22 | 2.01 | 2.38 | 4.09 | 3.98 | Illumina |
| DEAF1 | NM_021008 | 0.75 (0.06) | 0.67 (0.13) | 0.75 (0.13) | 0.85 (0.20) | 0.91 (0.29) | qPCR |
| EGR1 | NM_001964 | 0.94 | 0.69 | 0.94 | 3.15 | 5.15 | Illumina |
| ELF4 | NM_001421 | 1.36 | 1.90 | 1.16 | 0.92 | 1.46 | Illumina |
| ETV6 | NM_001987 | 1.00 | 1.03 | 1.12 | 1.56 | 1.20 | Illumina |
| FOS | NM_005252 | 0.51 (0.22) | 0.27 (0.06) | 0.55 (0.18) | 0.46 (0.08) | 0.76 (0.21) | qPCR |
| FOSL2 | NM_005253 | 0.80 | 0.64 | 0.98 | 0.88 | 1.10 | Illumina |
| FOXF1 | NM_001451 | 0.91 (0.03) | 1 (0.05) | 0.88 (0.13) | 1.11 (0.14) | 2.19 (0.41) | qPCR |
| FOXF2 | NM_001452 | 1.14 (0.06) | 1.12 (0.03) | 1 (0.31) | 2.19 (0.62) | 4.32 (1.13) | qPCR |
| FOXJ2 | NM_018416 | 0.68 (0.05) | 0.79 (0.11) | 1.11 (0.12) | 1.56 (0.01) | 4.63 (0.33) | qPCR |
| GABPB2 | NM_016655 | 1.21 | 1.14 | 1.09 | 1.36 | 1.79 | Illumina |
| GFI1 | NM_005263 | 0.83 | 0.84 | 0.89 | 0.57 | 0.93 | Illumina |
| GFI1B | NM_004188 | 0.42 (0.08) | 0.39 (0.08) | 0.35 (0.06) | 0.4 (0.05) | 0.34 (0.02) | qPCR |
| GLI1 | NM_005269 | 1.86 (0.46) | 1.5 (0.43) | 0.72 (0.26) | 0.91 (0.06) | 1.02 (0.50) | qPCR |
| HIF1A | NM_181054 | 0.97 (0.21) | 0.82 (0.12) | 0.6 (0.11) | 1.03 (0.17) | 0.77 (0.2) | qPCR |
| HNF4A | NM_178850 | 0.62 (0.08) | 0.9 (0.1) | 0.95 (0.15) | 0.99 (0.06) | 1.02 (0.17) | qPCR |
| HNF4G | NM_004133 | 0.67 (0.1) | 0.72 (0.14) | 0.94 (0.21) | 1.24 (0.24) | 1.23 (0.32) | qPCR |
| HOXA5 | NM_019102 | 4.50 | 3.59 | 3.70 | 4.34 | 4.27 | Illumina |
| IRF1 | NM_002198 | 1.01 | 0.86 | 1.19 | 1.35 | 1.73 | Illumina |
| JUN | NM_002228 | 0.87 (0.23) | 0.82 (0.25) | 0.79 (0.20) | 1.41 (0.35) | 1.68 (0.37) | qPCR |
| JUNB | NM_002229 | 0.75 (0.13) | 0.63 (0.05) | 0.86 (0.23) | 1.09 (0.13) | 1.53 (0.35) | qPCR |
| MAD | NM_002357 | 1.5 (0.09) | 1.17 (0.13) | 1.25 (0.21) | 1.79 (0.08) | 1.87 (0.43) | qPCR |
| MAFF | NM_152878 | 1.1 (0.08) | 1.03 (0.49) | 1.11 (0.25) | 1.49 (0.16) | 2.6 (0.46) | qPCR |
| MAFK | NM_002360 | 1.31 (0.09) | 1.21 (0.18) | 1.06 (0.14) | 1.22 (0.20) | 2.2 (0.49) | qPCR |
| NFATC2 | NM_012340 | 0.36 (0.07) | 0.54 (0.03) | 0.81 (0.05) | 1.02 (0.09) | 1.12 (0.21) | qPCR |
| NR1H3 | NM_005693 | 0.98 (0.38) | 0.93 (0.18) | 1.07 (0.11) | 0.94 (0.38) | 1.98 (0.44) | qPCR |
| NR1H4 | NM_005123 | 0.90 | 1.20 | 1.49 | 1.58 | 1.47 | Illumina |
| NR1I2 | NM_022002 | 0.85 | 0.58 | 0.63 | 0.60 | 0.58 | Illumina |
| NR2F1 | NM_005654 | 0.86 | 0.53 | 0.67 | 0.71 | 0.63 | Illumina |
| NRF1 | NM_005011 | 0.63 (0.06) | 0.84 (0.17) | 1.4 (0.33) | 1.28 (0.33) | 1.51 (0.34) | qPCR |
| PAX6 | NM_000280 | 2.14 (0.23) | 1.58 (0.28) | 1.5 (0.05) | 1.47 (0.23) | 2.97 (0.40) | qPCR |
| PAX8 | NM_013992 | 1.04 | 0.77 | 1.08 | 0.76 | 0.67 | Illumina |
| PBX3 | NM_006195 | 0.55 | 1.08 | 1.06 | 0.90 | 1.13 | Illumina |
| PGR | NM_000926 | 1 (0.23) | 0.93 (0.26) | 0.98 (0.28) | 1.03 (0.27) | 1.99 (0.25) | qPCR |
| POU6F1 | XM_352901 | 1.6 (0.34) | 1.53 (0.24) | 1.12 (0.21) | 1.11 (0.05) | 0.67 (0.15) | qPCR |
| RARA | NM_000964 | 1.48 | 1.56 | 1.52 | 2.21 | 2.65 | Illumina |
| RARB | NM_016152 | 7.37 (2.74) | 7.11 (2.12) | 9.64 (3.05) | 10.62 (3.62) | 12.44 (3.96) | qPCR |
| RARG | NM_000966 | 0.57 (0.24) | 0.78 (0.16) | 0.56 (0.19) | 0.74 (0.09) | 0.75 (0.07) | qPCR |
| RFX5 | NM_000449 | 0.84 | 0.84 | 0.94 | 0.74 | 0.58 | Illumina |
| RFXANK | NM_134440 | 0.82 | 0.64 | 1.05 | 1.39 | 1.10 | Illumina |
| RXRA | NM_002957 | 0.66 | 0.73 | 0.88 | 0.81 | 0.67 | Illumina |
| SP2 | NM_003110 | 0.98 | 0.95 | 0.63 | 0.90 | 0.77 | Illumina |
| SREBF1 | NM_004176 | 2.26 | 2.31 | 2.31 | 2.21 | 2.20 | Illumina |
| SREBF2 | NM_004599 | 0.66 | 0.77 | 1.35 | 1.44 | 1.14 | Illumina |
| SRY | NM_003140 | 0.5 (0.08) | 0.69 (0.04) | 0.82 (0.05) | 0.59 (0.05) | 0.51 (0.04) | qPCR |
| STAT2 | NM_005419 | 0.99 | 1.08 | 0.97 | 0.72 | 0.64 | Illumina |
| STAT6 | NM_003153 | 1.19 | 0.91 | 1.04 | 0.65 | 0.81 | Illumina |
| TCF2 | NM_000458 | 0.80 | 1.07 | 0.86 | 0.86 | 0.68 | Illumina |
| TCF7 | NM_003202 | 1.40 | 1.17 | 1.33 | 1.45 | 1.95 | Illumina |
| TP53 | NM_000546 | 1.20 | 1.27 | 0.69 | 0.94 | 1.59 | Illumina |
| USF2 | NM_003367 | 1.34 | 1.09 | 1.25 | 1.50 | 1.51 | Illumina |
| VDR | NM_000376 | 1.53 (0.16) | 1.45 (0.13) | 0.92 (0.08) | 0.84 (0.03) | 0.77 (0.16) | qPCR |
| ZBTB33 | NM_006777 | 0.7 (0.01) | 0.56 (0.01) | 0.69 (0.00) | 0.66 (0.04) | 0.56 (0.09) | qPCR |
| ZIC2 | NM_007129 | 1.15 | 1.14 | 1.23 | 1.24 | 1.93 | Illumina |
| ZNF219 | NM_016423 | 0.84 | 0.73 | 0.65 | 0.91 | 0.77 | Illumina |
| ZNF238 | NM_006352 | 0.68 (0.38) | 0.72 (0.18) | 0.74 (0.13) | 1.08 (0.08) | 0.63 (0.15) | qPCR |
Expression levels of the genes not detected by microarray were analyzed using qRT–PCR. The expression ratio represents the ratio of expression levels in the cells treated with ATRA to that in those incubated with only DMSO for the periods of time indicated. Results are the average of two or three groups of data analyzed with Illumina microarrays and the average of four data sets (a combination of two sets of biological replicates) obtained by qRT–PCR analysis with SD values in parenthesis.