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 |
