Table 1.
Gene sets analysis of differentially expressed and methylated genes in activated vs. quiescent T cells
| RNA-seq | ||||
|---|---|---|---|---|
| Gene set | NGenes | Direction | P value | FDR |
| E2F_TARGETS | 213 | Up | 0.00 | 0.00 |
| MYC_TARGETS_V1 | 215 | Up | 0.00 | 0.00 |
| MTORC1_SIGNALING | 202 | Up | 0.00 | 0.00 |
| G2M_CHECKPOINT | 196 | Up | 0.00 | 0.00 |
| MYC_TARGETS_V2 | 54 | Up | 0.00 | 0.00 |
| OXIDATIVE_PHOSPHORYLATION | 219 | Up | 0.00 | 0.00 |
| FATTY_ACID_METABOLISM | 147 | Up | 0.00 | 0.00 |
| GLYCOLYSIS | 191 | Up | 0.00 | 0.00 |
| UNFOLDED_PROTEIN_RESPONSE | 109 | Up | 0.00 | 0.00 |
| DNA_REPAIR | 158 | Up | 0.00 | 0.00 |
| CHOLESTEROL_HOMEOSTASIS | 75 | Up | 0.00 | 0.00 |
| ADIPOGENESIS | 195 | Up | 0.00 | 0.00 |
| IL2_STAT5_SIGNALING | 205 | Up | 0.00 | 0.00 |
| TNFA_SIGNALING_VIA_NFKB | 201 | Up | 0.00 | 0.00 |
| HYPOXIA | 189 | Up | 0.00 | 0.00 |
| APOPTOSIS | 165 | Up | 0.00 | 0.00 |
| REACTIVE_OXIGEN_SPECIES_PATHWAY | 50 | Up | 0.00 | 0.00 |
| UV_RESPONSE_UP | 169 | Up | 0.00 | 0.00 |
| INTERFERON_GAMMA_RESPONSE | 245 | Up | 0.00 | 0.00 |
| PEROXISOME | 92 | Up | 0.00 | 0.00 |
| DNA methylation | ||||
| Gene sets | NGenes | DM | P value | FDR |
| APOPTOSIS | 161 | 6 | 0.01 | 0.06 |
| MITOTIC_SPINDLE | 200 | 7 | 0.01 | 0.05 |
| COMPLEMENT | 200 | 7 | 0.01 | 0.05 |
| HEME_METABOLISM | 200 | 7 | 0.01 | 0.05 |
| PI3K_AKT_MTOR_SIGNALING | 105 | 5 | 0.01 | 0.05 |
| TGF_BETA_SIGNALING | 54 | 4 | 0.00 | 0.03 |
| IL2_STAT5_SIGNALING | 200 | 8 | 0.00 | 0.03 |
| INFLAMMATORY_RESPONSE | 200 | 9 | 0.00 | 0.01 |
| TNFA_SIGNALING_VIA_NFKB | 200 | 10 | 0.00 | 0.00 |
| ALLOGRAFT_REJECTION | 200 | 10 | 0.00 | 0.00 |
| UV_RESPONSE_DN | 144 | 10 | 0.00 | 0.00 |
DM: differentially methylated; FDR: false discovery rate, P value