Table 1 Top 50 upregulated and 50 downregulated differentially expressed genes (DEGs) in 3D-MH compared to 2D-MH (log₂FC ≥ 1.0 or ≤ − 1.0, FDR < 0.05)
Upregulated | Downregulated | ||||
|---|---|---|---|---|---|
Gene ID | Log₂FC | FDR | Gene ID | Log₂FC | FDR |
GC | 5.81 | 5.30E-22 | NPPB | -7.012 | 1.70E-24 |
ADH1A | 5.73 | 5.60E-32 | SLC2A3 | -5.464 | 7.75E-146 |
CFHR2 | 5.48 | 1.31E-09 | LCN15 | -4.499 | 1.32E-40 |
PAX4 | 5.17 | 3.95E-12 | MS4A18 | -3.879 | 2.28E-09 |
SLCO1B1 | 5.00 | 3.54E-13 | PNCK | -3.554 | 3.43E-29 |
AKR1C1 | 4.85 | 1.53E-18 | ERVH48-1 | -3.460 | 9.53E-10 |
CPB2 | 4.74 | 2.79E-21 | CP | -3.451 | 3.21E-10 |
ADH6 | 4.64 | 3.86E-09 | SLC2A5 | -3.229 | 1.23E-18 |
HAMP | 4.37 | 4.79E-10 | EGLN3 | -2.642 | 1.22E-11 |
ARG1 | 4.29 | 5.22E-09 | DUOX2 | -2.641 | 2.39E-19 |
UGT2B17 | 4.26 | 8.92E-21 | PRTG | -2.430 | 8.61E-10 |
BHMT | 4.08 | 1.97E-11 | SPAG4 | -2.394 | 2.65E-09 |
GUCA2B | 4.07 | 1.11E-11 | GABRA2 | -2.254 | 1.52E-20 |
ENPP3 | 3.95 | 2.67E-14 | FGF23 | -2.125 | 1.01E-13 |
MT1E | 3.92 | 3.07E-09 | HAPLN3 | -2.110 | 1.34E-14 |
GCG | 3.58 | 2.17E-25 | HLA-DRB5 | -2.108 | 4.73E-10 |
UGT2B4 | 3.58 | 4.73E-09 | VLDLR | -2.051 | 7.62E-13 |
CYP4A11 | 3.54 | 9.63E-10 | ARHGAP29 | -1.948 | 5.95E-10 |
CD4 | 3.53 | 4.59E-16 | HLA-DRB1 | -1.936 | 2.79E-21 |
HAL | 3.30 | 2.13E-15 | PDK1 | -1.925 | 1.12E-22 |
REP15 | 3.27 | 2.18E-16 | PFKP | -1.786 | 5.17E-11 |
UGT2B15 | 3.08 | 2.60E-11 | PTN | -1.768 | 4.42E-10 |
PON1 | 3.04 | 2.12E-20 | FRMD4A | -1.716 | 1.43E-12 |
AGMO | 3.00 | 5.72E-13 | COL4A2 | -1.713 | 3.99E-11 |
LPA | 2.95 | 1.49E-20 | SLFN13 | -1.705 | 1.01E-13 |
NECAB1 | 2.69 | 2.09E-09 | HILPDA | -1.668 | 1.17E-12 |
AADAC | 2.46 | 1.30E-10 | ZNF550 | -1.629 | 3.01E-10 |
ASS1 | 2.43 | 1.57E-11 | SLC6A8 | -1.581 | 8.61E-10 |
OTC | 2.40 | 1.66E-10 | ABCA2 | -1.551 | 3.13E-17 |
ALDH1L1 | 2.30 | 9.53E-10 | TRIM6 | -1.547 | 2.62E-09 |
DPYD | 2.16 | 6.73E-12 | PRSS12 | -1.537 | 1.30E-13 |
TFF3 | 2.03 | 8.21E-13 | PROM1 | -1.536 | 3.99E-09 |
LRRC31 | 2.00 | 9.41E-16 | COL4A6 | -1.505 | 4.37E-11 |
CPS1 | 1.99 | 1.93E-30 | SLC7A1 | -1.505 | 1.70E-14 |
PLG | 1.85 | 2.39E-10 | ANKS1A | -1.453 | 9.48E-20 |
ACADSB | 1.69 | 2.16E-13 | FZD7 | -1.417 | 8.37E-10 |
SERPINA5 | 1.68 | 1.16E-09 | SLC4A4 | -1.395 | 1.82E-09 |
ABAT | 1.67 | 1.63E-16 | BARD1 | -1.385 | 2.26E-10 |
MSRB1 | 1.54 | 4.93E-09 | DBF4B | -1.384 | 2.50E-10 |
HYAL1 | 1.53 | 1.72E-12 | SLC25A29 | -1.352 | 8.37E-10 |
DHRS7 | 1.51 | 6.02E-09 | PTPN14 | -1.250 | 1.90E-11 |
PBLD | 1.45 | 2.49E-10 | ZNF714 | -1.185 | 8.48E-10 |
HADH | 1.40 | 2.67E-14 | MDC1 | -1.163 | 1.74E-10 |
ADI1 | 1.35 | 2.13E-10 | RBM3 | -1.147 | 4.81E-09 |
FAHD1 | 1.35 | 3.29E-09 | OTUD3 | -1.143 | 2.60E-09 |
HSD17B11 | 1.25 | 2.38E-14 | SEZ6L2 | -1.108 | 2.00E-14 |
MT-ND3 | 1.23 | 2.28E-11 | UNC13C | -1.074 | 3.21E-10 |
NDRG2 | 1.22 | 5.83E-15 | GTPBP3 | -1.033 | 3.50E-10 |
TMEM251 | 1.18 | 2.93E-12 | COL4A5 | -1.025 | 1.86E-11 |
SDHB | 1.05 | 8.99E-09 | CPE | -1.000 | 5.51E-11 |