Table 2 Significantly expressed hallmark pathways in all culturing conditions compared to fresh tissue sample. Results of the gene set enrichment analysis (GSEA) shows the significantly expressed hallmark pathways in three culturing conditions (plastic, Matrigel, and Myogel) compared to fresh tissue sample. The pathways that passed the filter criteria had a FDR q-val < 0.05. ES, enrichment score; NES, normalized enrichment score
MATRIGEL VS FRESH TISSUE | |||||||||
|---|---|---|---|---|---|---|---|---|---|
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
MYC TARGETS V1 | 0.69 | 3.75 | 0.000 | 0.00 | INTERFERON ALPHA RESPONSE | -0.54 | -2.41 | 0.000 | 0.00 |
OXIDATIVE PHOSPHORYLATION | 0.62 | 3.37 | 0.000 | 0.00 | INTERFERON GAMMA RESPONSE | -0.46 | -2.27 | 0.000 | 0.00 |
E2F TARGETS | 0.57 | 3.12 | 0.000 | 0.00 | KRAS SIGNALING DN | -0.44 | -2.09 | 0.000 | 0.00 |
UNFOLDED PROTEIN RESPONSE | 0.60 | 2.98 | 0.000 | 0.00 | HEDGEHOG SIGNALING | -0.47 | -1.66 | 0.007 | 0.01 |
MYC TARGETS V2 | 0.67 | 2.95 | 0.000 | 0.00 | APICAL SURFACE | -0.41 | -1.53 | 0.027 | 0.03 |
G2M CHECKPOINT | 0.53 | 2.86 | 0.000 | 0.00 | WNT BETA CATENIN SIGNALING | -0.39 | -1.44 | 0.047 | 0.05 |
DNA REPAIR | 0.52 | 2.70 | 0.000 | 0.00 | |||||
ADIPOGENESIS | 0.47 | 2.54 | 0.000 | 0.00 | |||||
MTORC1 SIGNALING | 0.47 | 2.53 | 0.000 | 0.00 | |||||
REACTIVE OXYGEN SPECIES PATHWAY | 0.59 | 2.51 | 0.000 | 0.00 | |||||
PROTEIN SECRETION | 0.49 | 2.34 | 0.000 | 0.00 | |||||
PEROXISOME | 0.40 | 1.91 | 0.000 | 0.00 | |||||
UV RESPONSE UP | 0.35 | 1.85 | 0.000 | 0.00 | |||||
GLYCOLYSIS | 0.34 | 1.85 | 0.000 | 0.00 | |||||
XENOBIOTIC METABOLISM | 0.33 | 1.76 | 0.000 | 0.00 | |||||
FATTY ACID METABOLISM | 0.33 | 1.72 | 0.000 | 0.00 | |||||
ANDROGEN RESPONSE | 0.36 | 1.70 | 0.003 | 0.00 | |||||
TGF BETA SIGNALING | 0.39 | 1.68 | 0.000 | 0.00 | |||||
EPITHELIAL MESENCHYMAL TRANSITION | 0.30 | 1.65 | 0.000 | 0.00 | |||||
PI3K AKT MTOR SIGNALING | 0.32 | 1.58 | 0.003 | 0.01 | |||||
MITOTIC SPINDLE | 0.29 | 1.58 | 0.000 | 0.01 | |||||
HEME METABOLISM | 0.27 | 1.45 | 0.003 | 0.02 | |||||
MATRIGEL VS FRESH TISSUE | |||||||||
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
MYC TARGETS V1 | 0.68 | 3.64 | 0.000 | 0.00 | INTERFERON ALPHA RESPONSE | -0.64 | -2.78 | 0.0000 | 0.00 |
OXIDATIVE PHOSPHORYLATION | 0.62 | 3.31 | 0.000 | 0.00 | INTERFERON GAMMA RESPONSE | -0.51 | -2.44 | 0.0000 | 0.00 |
UNFOLDED PROTEIN RESPONSE | 0.57 | 2.82 | 0.000 | 0.00 | KRAS SIGNALING DN | -0.46 | -2.17 | 0.0000 | 0.00 |
MYC TARGETS V2 | 0.65 | 2.82 | 0.000 | 0.00 | HEDGEHOG SIGNALING | -0.49 | -1.72 | 0.0034 | 0.00 |
DNA REPAIR | 0.53 | 2.75 | 0.000 | 0.00 | |||||
E2F TARGETS | 0.51 | 2.73 | 0.000 | 0.00 | |||||
REACTIVE OXYGEN SPECIES PATHWAY | 0.60 | 2.51 | 0.000 | 0.00 | |||||
G2M CHECKPOINT | 0.44 | 2.38 | 0.000 | 0.00 | |||||
MTORC1 SIGNALING | 0.44 | 2.33 | 0.000 | 0.00 | |||||
ADIPOGENESIS | 0.43 | 2.31 | 0.000 | 0.00 | |||||
PROTEIN SECRETION | 0.46 | 2.16 | 0.000 | 0.00 | |||||
PEROXISOME | 0.40 | 1.94 | 0.000 | 0.00 | |||||
GLYCOLYSIS | 0.34 | 1.82 | 0.000 | 0.00 | |||||
UV RESPONSE UP | 0.35 | 1.80 | 0.000 | 0.00 | |||||
XENOBIOTIC METABOLISM | 0.33 | 1.74 | 0.000 | 0.00 | |||||
TGF BETA SIGNALING | 0.40 | 1.70 | 0.003 | 0.00 | |||||
FATTY ACID METABOLISM | 0.32 | 1.67 | 0.000 | 0.00 | |||||
ANDROGEN RESPONSE | 0.34 | 1.64 | 0.000 | 0.00 | |||||
PI3K AKT MTOR SIGNALING | 0.31 | 1.51 | 0.010 | 0.01 | |||||
HEME METABOLISM | 0.27 | 1.44 | 0.004 | 0.02 | |||||
MYOGEL VS FRESH TISSUE | |||||||||
UPREGULATED | DOWNREGULATED | ||||||||
HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val | HALLMARK PATHWAY | ES | NES | NOM p-val | FDR q-val |
MYC TARGETS V1 | 0.68 | 3.65 | 0.000 | 0.00 | INTERFERON ALPHA RESPONSE | -0.59 | 0.00 | 0.000 | 0.00 |
OXIDATIVE PHOSPHORYLATION | 0.63 | 3.39 | 0.000 | 0.00 | INTERFERON GAMMA RESPONSE | -0.48 | 0.00 | 0.000 | 0.00 |
E2F TARGETS | 0.56 | 3.09 | 0.000 | 0.00 | KRAS SIGNALING DN | -0.45 | 0.00 | 0.000 | 0.00 |
MYC TARGETS V2 | 0.65 | 2.80 | 0.000 | 0.00 | HEDGEHOG SIGNALING | -0.44 | 0.02 | 0.022 | 0.02 |
UNFOLDED PROTEIN RESPONSE | 0.57 | 2.80 | 0.000 | 0.00 | |||||
G2M CHECKPOINT | 0.52 | 2.78 | 0.000 | 0.00 | |||||
DNA REPAIR | 0.53 | 2.76 | 0.000 | 0.00 | |||||
ADIPOGENESIS | 0.46 | 2.47 | 0.000 | 0.00 | |||||
MTORC1 SIGNALING | 0.45 | 2.45 | 0.000 | 0.00 | |||||
REACTIVE OXYGEN SPECIES PATHWAY | 0.59 | 2.41 | 0.000 | 0.00 | |||||
PROTEIN SECRETION | 0.49 | 2.32 | 0.000 | 0.00 | |||||
PEROXISOME | 0.40 | 1.94 | 0.000 | 0.00 | |||||
UV RESPONSE UP | 0.36 | 1.89 | 0.000 | 0.00 | |||||
ANDROGEN RESPONSE | 0.39 | 1.89 | 0.000 | 0.00 | |||||
GLYCOLYSIS | 0.35 | 1.88 | 0.000 | 0.00 | |||||
TGF BETA SIGNALING | 0.40 | 1.72 | 0.000 | 0.00 | |||||
PI3K AKT MTOR SIGNALING | 0.35 | 1.70 | 0.000 | 0.00 | |||||
FATTY ACID METABOLISM | 0.33 | 1.70 | 0.000 | 0.00 | |||||
XENOBIOTIC METABOLISM | 0.31 | 1.67 | 0.000 | 0.00 | |||||
HEME METABOLISM | 0.31 | 1.62 | 0.000 | 0.00 | |||||