Table 4.
Differentially expressed genes in TNC cDNA vs. shRNA cell lines
| Gene Name | logFC | PValue | adj.p |
|---|---|---|---|
| MIR30A | −7.866092897 | 2.51674E-50 | 3.9996E-46 |
| AC119673.1 | −5.51977944 | 3.22561E-14 | 7.32306E-11 |
| RPS3AP5 | −3.022216042 | 4.38211E-10 | 4.0965E-07 |
| AC007743.1 | −2.374800701 | 1.81455E-08 | 1.35278E-05 |
| AL163952.1 | −2.225772302 | 9.52366E-06 | 0.001872888 |
| CTD-2269F5.1 | −2.180041946 | 0.000403098 | 0.025023561 |
| RP11-777B9.5 | −2.123763807 | 2.03315E-07 | 0.000100971 |
| FSIP2 | −2.121252851 | 1.13045E-06 | 0.000403974 |
| RPL4P5 | 2.070466961 | 0.0002471 | 0.018610989 |
| SAMD12 | 2.077983472 | 0.000150356 | 0.014061765 |
| TNFSF15 | 2.09066531 | 0.000821066 | 0.038724462 |
| SNORA84 | 2.212964724 | 4.60974E-07 | 0.000203494 |
| RN7SL825P | 2.21448533 | 2.17857E-05 | 0.003532848 |
| AC092299.8 | 2.347033959 | 1.55329E-05 | 0.002773582 |
| GCNT3 | 2.370843556 | 0.000972904 | 0.043553199 |
| RP6-42F4.1 | 2.453535316 | 2.25622E-08 | 1.494E-05 |
| RP11-553A10.1 | 2.484443136 | 0.001201734 | 0.048910983 |
| RP11-290D2.6 | 2.494377813 | 1.86588E-05 | 0.003188456 |
| SNORA76 | 2.503062118 | 3.45134E-05 | 0.005126049 |
| SNORD3C | 2.578909604 | 5.76928E-06 | 0.00130979 |
| SNORA54 | 2.680209334 | 1.90238E-11 | 2.51939E-08 |
| CA9 | 2.683101502 | 0.000191849 | 0.016161347 |
| CTA-85E5.6 | 2.749870719 | 4.52651E-09 | 3.99641E-06 |
| FRK | 2.751839555 | 1.18463E-08 | 9.90845E-06 |
| RP11-504P24.8 | 2.777831969 | 2.00742E-10 | 2.2787E-07 |
| RP11-676 J15.1 | 2.80969822 | 0.000726166 | 0.035617995 |
| SPINK1 | 2.838338406 | 0.000284132 | 0.020068546 |
| WASH5P | 2.896364617 | 2.37249E-27 | 1.88518E-23 |
| RN7SKP185 | 2.897676479 | 9.16004E-13 | 1.81964E-09 |
| RP11-230G5.2 | 2.921550791 | 5.15934E-05 | 0.00717505 |
| CTD-2256P15.1 | 3.208660084 | 0.000516546 | 0.029320523 |
| SNORA80B | 3.276449172 | 1.68241E-12 | 2.97077E-09 |
| SFTA1P | 3.678556083 | 2.99678E-06 | 0.000780734 |
| RP11-457 M11.2 | 3.793167305 | 2.15375E-11 | 2.63288E-08 |
| TNC | 5.130171422 | 3.0407E-21 | 1.20807E-17 |
| RP11-182 L21.5 | 5.497636404 | 5.54817E-12 | 8.01559E-09 |
| PTMAP5 | 5.663770365 | 4.27628E-15 | 1.13264E-11 |
| LL22NC03-N14H11.1 | 7.391276313 | 7.34761E-27 | 3.89227E-23 |
TNC expression was modified in pediatric supratentorial high-grade glioma (HGG n = 1) and brainstem glioma (DIPG n = 3) cell lines via lentiviral transfection of TNC shRNA and cDNA, with resulting gene expressions determined via RNA-Seq. Results were filtered for statistical significance (Log2Fold Change > 2 or < −2, adjusted p-value < 0.05), with 173 differentially expressed genes identified between TNC cDNA and shRNA cell lines. Of these, 38 genes, listed here, demonstrated the same expression pattern across all lines by experimental condition, including TNC and miRNA30, with differential expression values (cDNA vs shRNA, Log2Fold Change), pvalue and adjusted p-value indicated