Table 2.
Top 10 upregulated genes in 3D culture from differential expression analysis between monolayer and three spheroid conditions.
| polyHEMA (pHEMA) | Ultra-low attachment (ULA) | Methylcellulose (mCELL) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rank | Fold Change (linear) |
ANOVA p-value |
FDR p-value |
Gene Symbol |
Description | Fold Change (linear) |
ANOVA p-value |
FDR p-value |
Gene Symbol |
Description | Fold Change (linear) |
ANOVA p-value |
FDR p-value |
Gene Symbol |
Description |
| 1 | 47.93 | 1.79E-07 | 0.001206 | UGT2B15 | UDP glucuronosyltransferase 2 family, polypeptide B15 | 46.69 | 2.92E-07 | 5.08E-04 | UGT2B15 | UDP glucuronosyltransferase 2 family, polypeptide B15 | 41.34 | 4.39E-08 | 0.000355 | UGT2B15 | UDP glucuronosyltransferase 2 family, polypeptide B15 |
| 2 | 40.23 | 1.12E-07 | 0.000949 | UGT2B17 | UDP glucuronosyltransferase 2 family, polypeptide B17 | 38.24 | 1.71E-07 | 4.81E-04 | UGT2B17 | UDP glucuronosyltransferase 2 family, polypeptide B17 | 31.38 | 2.14E-07 | 0.000534 | UGT2B17 | UDP glucuronosyltransferase 2 family, polypeptide B17 |
| 3 | 24.63 | 0.000015 | 0.003028 | MIR21 | microRNA 21 | 27.78 | 0.000004 | 1.10E-03 | MIR21 | microRNA 21 | 24.11 | 0.000018 | 0.002121 | TNFSF10 | tumor necrosis factor (ligand) superfamily, member 10 |
| 4 | 19.67 | 0.00003 | 0.003846 | TNFSF10 | tumor necrosis factor (ligand) superfamily, member 10 | 25.41 | 0.000018 | 1.77E-03 | TNFSF10 | tumor necrosis factor (ligand) superfamily, member 10 | 21.9 | 0.000079 | 0.004237 | GDF15 | growth differentiation factor 15 |
| 5 | 16.55 | 0.000161 | 0.008027 | GDF15 | growth differentiation factor 15 | 16.07 | 0.000002 | 3.41E-03 | GDF15 | growth differentiation factor 15 | 16.46 | 0.000001 | 0.000775 | MIR21 | microRNA 21 |
| 6 | 15.18 | 0.00007 | 0.001521 | MSMB | microseminoprotein, beta- | 15.63 | 0.000046 | 4.23E-04 | CMAHP (non-coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene | 16.24 | 8.50E-07 | 0.000534 | MSMB | microseminoprotein, beta- |
| 7 | 15.12 | 0.00009 | 0.000525 | CMAHP (non-coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene | 15.48 | 0.000078 | 5.88E-04 | MSMB | microseminoprotein, beta- | 15.86 | 2.97E-07 | 0.000601 | CMAHP (non-coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene |
| 8 | 13.48 | 6.64E-07 | 0.000496 | CMAHP (coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene | 14.39 | 5.02E-08 | 3.02E-04 | CMAHP (coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene | 15.25 | 0.000023 | 0.000534 | CMAHP (coding) | cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene |
| 9 | 11.78 | 3.21E-08 | 0.003542 | LINC01087 | long intergenic non-protein coding RNA 1087 | 13.88 | 5.14E-07 | 1.10E-03 | TNFAIP3 | tumor necrosis factor, alpha-induced protein 3 | 12.69 | 3.92E-07 | 0.002055 | TNFAIP3 | tumor necrosis factor, alpha-induced protein 3 |
| 10 | 11.38 | 0.00001 | 0.005684 | TNFAIP3 | tumor necrosis factor, alpha-induced protein 3 | 13.75 | 0.000023 | 0.003158 | LINC01087 | long intergenic non-protein coding RNA 1087 | 10.96 | 2.32E-07 | 0.001067 | CAPN9 | calpain 9 |
Compilation of top 10 up-regulated genes in 3D from results of microarray differential expression (DE) analysis. Significant DE up-regulated genes from triplicate samples of MCF-7 2D versus 3D condition (polyHEMA, ultra-low attachment or methylcellulose) were determined based on cutoff of ANOVA p value of <0.05 and a fold change greater than 2 fold. (pHEMA: 1809 DE, 942 up-regulated in 3D; ULA: 2117 DE, 904 up-regulated in 3D; mCELL: 1822 DE, 809 up-regulated in 3D)
Transcript cluster IDs that were not annotated with a gene symbol or containing _hap (haplotype chromosomes) were excluded from top-10 and were as follows: TC05000962.hg.1, TC02000102.hg.1, TC10002067.hg.1, TC4_ctg9_hap1000004.hg.1