Table 1.
Pathway analysis with DAVID using phosphosites that were significantly increased in the 3D culture samples compared to 2D culture samples or identified only in the 3D culture samples (adjusted p value < 0.05).
| Term | Number of genes | p value | adjusted p value by Benjamini |
|---|---|---|---|
| HCT116 spheroid vs HCT116 cell (D method) | |||
| RNA transport | 48 | 3.38E-11 | 8.63E-09 |
| Regulation of actin cytoskeleton | 49 | 1.69E-08 | 2.15E-06 |
| Insulin signaling pathway | 36 | 9.21E-08 | 7.83E-06 |
| ErbB signaling pathway | 27 | 1.30E-07 | 8.30E-06 |
| Proteoglycans in cancer | 45 | 1.90E-07 | 9.71E-06 |
| Tight junction | 35 | 2.47E-07 | 1.05E-05 |
| Endocytosis | 53 | 2.91E-07 | 1.06E-05 |
| MAPK signaling pathway | 48 | 1.43E-05 | 4.55E-04 |
| Focal adhesion | 41 | 1.80E-05 | 5.09E-04 |
| Bacterial invasion of epithelial cells | 21 | 4.53E-05 | 0.0012 |
| Pathogenic Escherichia coli infection | 16 | 7.45E-05 | 0.0017 |
| Neurotrophin signaling pathway | 27 | 8.20E-05 | 0.0017 |
| Insulin resistance | 25 | 1.00E-04 | 0.0020 |
| mTOR signaling pathway | 17 | 1.01E-04 | 0.0018 |
| Salmonella infection | 21 | 1.16E-04 | 0.0020 |
| Adherens junction | 19 | 1.26E-04 | 0.0020 |
| Fc gamma R-mediated phagocytosis | 21 | 1.39E-04 | 0.0021 |
| Thyroid hormone signaling pathway | 25 | 2.43E-04 | 0.0034 |
| AMPK signaling pathway | 26 | 2.83E-04 | 0.0038 |
| Epstein-Barr virus infection | 35 | 3.91E-04 | 0.0050 |
| Non-small cell lung cancer | 15 | 8.15E-04 | 0.0098 |
| HCT116 spheroid vs HCT116 cell (CR method) | |||
| Ribosome | 48 | 1.97E-18 | 4.78E-16 |
| Epstein-Barr virus infection | 42 | 7.68E-09 | 9.29E-07 |
| Pathogenic Escherichia coli infection | 19 | 5.79E-08 | 4.67E-06 |
| Regulation of actin cytoskeleton | 41 | 4.88E-07 | 2.95E-05 |
| Salmonella infection | 23 | 6.43E-07 | 3.11E-05 |
| Endocytosis | 46 | 1.10E-06 | 4.42E-05 |
| AMPK signaling pathway | 28 | 1.75E-06 | 6.06E-05 |
| Focal adhesion | 38 | 5.03E-06 | 1.52E-04 |
| Neurotrophin signaling pathway | 26 | 1.32E-05 | 3.54E-04 |
| Proteoglycans in cancer | 36 | 1.64E-05 | 3.96E-04 |
| Insulin signaling pathway | 28 | 2.01E-05 | 4.42E-04 |
| Carbon metabolism | 24 | 4.29E-05 | 8.66E-04 |
| mTOR signaling pathway | 16 | 5.39E-05 | 0.0010 |
| Spliceosome | 26 | 8.10E-05 | 0.0014 |
| Protein processing in endoplasmic reticulum | 30 | 1.25E-04 | 0.0020 |
| RNA transport | 30 | 1.71E-04 | 0.0026 |
| Proteasome | 13 | 1.73E-04 | 0.0025 |
| Bacterial invasion of epithelial cells | 18 | 1.78E-04 | 0.0024 |
| ErbB signaling pathway | 19 | 2.32E-04 | 0.0030 |
| Endometrial cancer | 14 | 2.44E-04 | 0.0029 |
| Biosynthesis of antibiotics | 34 | 2.97E-04 | 0.0034 |
| Biosynthesis of amino acids | 17 | 3.02E-04 | 0.0033 |
| Glycolysis/Gluconeogenesis | 16 | 3.10E-04 | 0.0033 |
| Shigellosis | 15 | 6.27E-04 | 0.0063 |
| Renal cell carcinoma | 15 | 7.40E-04 | 0.0071 |
Terms regarding phosphosignaling pathways that are commonly significant in the both 3D culture samples are indicated in bold font.