Table 5 Significantly expressed Hallmark pathways in Matrigel and Myogel compared to plastic and Myogel compared to Matrigel. Results of the gene set enrichment analysis. (GSEA) show the significantly expressed Hallmark pathways in different culturing conditions compared to fresh tissue sample. The pathways that passed the filter criteria had FDR q-val < 0.05. ES, enrichment score; NES, normalized enrichment score
MATRIGEL VS PLASTIC | |||||||||
|---|---|---|---|---|---|---|---|---|---|
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
KRAS SIGNALING UP | 0.44 | 1.95 | 0.000 | 0.00 | G2M CHECKPOINT | -0.55 | -2.69 | 0.000 | 0.00 |
INFLAMMATORY RESPONSE | 0.41 | 1.84 | 0.000 | 0.00 | INTERFERON ALPHA RESPONSE | -0.59 | -2.59 | 0.000 | 0.00 |
ALLOGRAFT REJECTION | 0.37 | 1.69 | 0.000 | 0.01 | E2F TARGETS | -0.52 | -2.58 | 0.000 | 0.00 |
UNFOLDED PROTEIN RESPONSE | -0.53 | -2.41 | 0.000 | 0.00 | |||||
MITOTIC SPINDLE | -0.49 | -2.38 | 0.000 | 0.00 | |||||
MYC TARGETS V1 | -0.49 | -2.37 | 0.000 | 0.00 | |||||
EPITHELIAL MESENCHYMAL TRANSITION | -0.44 | -2.17 | 0.000 | 0.00 | |||||
MYC TARGETS V2 | -0.53 | -2.10 | 0.000 | 0.00 | |||||
MTORC1 SIGNALING | -0.40 | -1.96 | 0.000 | 0.00 | |||||
UV RESPONSE DN | -0.42 | -1.95 | 0.000 | 0.00 | |||||
APICAL JUNCTION | -0.38 | -1.85 | 0.000 | 0.00 | |||||
INTERFERON GAMMA RESPONSE | -0.37 | -1.77 | 0.000 | 0.01 | |||||
MYOGENESIS | -0.34 | -1.62 | 0.000 | 0.02 | |||||
OXIDATIVE PHOSPHORYLATION | -0.31 | -1.48 | 0.000 | 0.02 | |||||
ADIPOGENESIS | -0.31 | -1.48 | 0.000 | 0.02 | |||||
ANDROGEN RESPONSE | -0.33 | -1.47 | 0.011 | 0.02 | |||||
PROTEIN SECRETION | -0.33 | -1.45 | 0.014 | 0.00 | |||||
MYOGEL VS PLASTIC | |||||||||
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
KRAS SIGNALING UP | 0.41 | 1.83 | 0.000 | 0.01 | INTERFERON ALPHA RESPONSE | -0.61 | -2.49 | 0.000 | 0.00 |
COAGULATION | 0.44 | 1.79 | 0.000 | 0.01 | INTERFERON GAMMA RESPONSE | -0.47 | -2.15 | 0.000 | 0.00 |
EPITHELIAL MESENCHYMAL TRANSITION | -0.39 | -1.80 | 0.000 | 0.00 | |||||
MYOGENESIS | -0.36 | -1.59 | 0.000 | 0.02 | |||||
ESTROGEN RESPONSE EARLY | -0.32 | -1.47 | 0.002 | 0.04 | |||||
MYOGEL VS MATRIGEL | |||||||||
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
G2M CHECKPOINT | 0.54 | 2.68 | 0.000 | 0.00 | INFLAMMATORY RESPONSE | -0.36 | -1.72 | 0.000 | 0.01 |
E2F TARGETS | 0.52 | 2.58 | 0.000 | 0.00 | ALLOGRAFT REJECTION | -0.35 | -1.65 | 0.000 | 0.01 |
MYC TARGETS V1 | 0.50 | 2.48 | 0.000 | 0.00 | |||||
MITOTIC SPINDLE | 0.46 | 2.30 | 0.000 | 0.00 | |||||
OXIDATIVE PHOSPHORYLATION | 0.44 | 2.18 | 0.000 | 0.00 | |||||
MYC TARGETS V2 | 0.52 | 2.09 | 0.000 | 0.00 | |||||
UNFOLDED PROTEIN RESPONSE | 0.44 | 2.03 | 0.000 | 0.00 | |||||
UV RESPONSE DN | 0.41 | 1.97 | 0.000 | 0.00 | |||||
MTORC1 SIGNALING | 0.38 | 1.89 | 0.000 | 0.00 | |||||
PROTEIN SECRETION | 0.40 | 1.77 | 0.000 | 0.00 | |||||
TGF BETA SIGNALING | 0.42 | 1.65 | 0.007 | 0.01 | |||||
ANDROGEN RESPONSE | 0.36 | 1.60 | 0.005 | 0.01 | |||||
ADIPOGENESIS | 0.32 | 1.59 | 0.000 | 0.01 | |||||
EPITHELIAL MESENCHYMAL TRANSITION | 0.30 | 1.53 | 0.002 | 0.02 | |||||
APICAL JUNCTION | 0.31 | 1.52 | 0.002 | 0.02 | |||||
DNA REPAIR | 0.31 | 1.47 | 0.009 | 0.03 | |||||
FATTY ACID METABOLISM | 0.30 | 1.45 | 0.011 | 0.03 | |||||
SPERMATOGENESIS | 0.32 | 1.45 | 0.010 | 0.03 | |||||