Table 3.
List of differentially expressed genes that best distinguish TNF-resistant cells (HPV18) from TNF-sensitive cells (PHK and HPV16), in normal culture conditions or upon treatment with TNF for 3 hours
| (PHK and HPV16) vs HPV18 | (PHK_TNF and HPV16_TNF) vs HPV18_TNF | ||||
| GENE | GENE NAME | FOLD | p VALUE | FOLD | p VALUE |
| ABCE1 | ATP-binding cassette, sub-family E (OABP), member 1 | 0.592 | 0.001384 | ---- | ---- |
| ACBD5 | acyl-Coenzyme A binding domain containing 5 | ---- | ---- | 0.378 | 0.00086 |
| ALDH3A2 | encoding aldehyde dehydrogenase 3 family, member A2 | 1.623 | 0.00122 | ---- | ---- |
| APG12L | APG12 autophagy 12-like (S. cerevisiae) | 1.739 | 0.000924 | ---- | ---- |
| APPBP1 | amyloid beta precursor protein binding protein 1 | 0.540 | 0.000283 | ---- | ---- |
| ARF4L | ADP-ribosylation factor 4-like | ---- | ---- | 0.578 | 5.70E-05 |
| BCLAF1 | BCL2-associated transcription factor 1 | 0.611 | 0.000876 | ---- | ---- |
| BOC | brother of CDO | ---- | ---- | 2.337 | 6.00E-06 |
| CCNA2 | cyclin A2 | 0.577 | 0.000604 | ---- | ---- |
| CDCA2 | cell division cycle associated 2 | ---- | ---- | 0.539 | 7.20E-05 |
| CDK2AP1 | CDK2-associated protein 1 | ---- | ---- | 1.523 | 0.000148 |
| CPSF3 | cleavage and polyadenylation specific factor 3 | 0.586 | 0.000466 | ---- | ---- |
| CYP1B1 | cytochrome P450, family 1, subfamily B, polypeptide 1 | 0.499 | 0.001386 | ---- | ---- |
| DEK | DEK oncogene | 0.480 | 0.000278 | ---- | ---- |
| FAM31C | family with sequence similarity 31, member C | ---- | ---- | 2.548 | 0.000663 |
| FLJ20105 | hypothetical protein LOC54821 | 0.026 | 5.00E-06 | 0.029 | 2.00E-06 |
| GALNAC4S-6ST | B cell RAG associated protein | 1.827 | 0.000145 | 1.673 | 0.000215 |
| H105E3 | encoding NAD(P) dependent steroid dehydrogenase-like | ---- | ---- | 0.569 | 6.80E-05 |
| HLCS | holocarboxylase synthetase | ---- | ---- | 1.551 | 0.00011 |
| JPH3 | junctophilin 3 | 0.154 | 0.000192 | ---- | ---- |
| KIAA0795 | kelch-like 18 (Drosophila) | 0.857 | 0.001325 | ---- | ---- |
| KIAA1023 | IQ motif containing E | 1.575 | 0.000723 | ---- | ---- |
| KIF1B | kinesin family member 1B | ---- | ---- | 0.570 | 0.000632 |
| KLK7 | encoding kallikrein 7 (chymotryptic, stratum corneum) | 0.421 | 0.000416 | 0.374 | 2.30E-05 |
| LCN2 | lipocalin 2 (oncogene 24p3) | ---- | ---- | 0.216 | 0.000686 |
| LOC151242 | protein phosphatase 1, regulatory (inhibitor) | 1.928 | 0.000268 | ---- | ---- |
| Lrp2bp | low density lipoprotein receptor-related protein binding protein | 0.629 | 0.000574 | ---- | ---- |
| MAPRE1 | encoding microtubule-associated protein, RP/EB family, member 1 | 0.410 | 0.001068 | 0.503 | 4.20E-05 |
| MBD2 | methyl-CpG binding domain protein 2 | 0.680 | 0.001247 | ---- | ---- |
| MGC35048 | hypothetical protein MGC35048 | ---- | ---- | 0.499 | 0.000211 |
| MRPS6 | mitochondrial ribosomal protein S6 | ---- | ---- | 1.460 | 0.000161 |
| MYO5B | acetyl-Coenzyme A acyltransferase 2 | 0.353 | 0.000104 | 0.292 | 4.10E-05 |
| NMES1 | normal mucosa of esophagus specific 1 | 0.324 | 0.000294 | 0.244 | 7.00E-06 |
| NPR2 | encoding natriuretic peptide receptor B/guanylate cyclase B | ---- | ---- | 0.435 | 0.000234 |
| ODC1 | ornithine decarboxylase 1 | 1.660 | 0.000886 | ---- | ---- |
| PI3 | protease inhibitor 3, skin-derived (SKALP) | 0.213 | 0.000274 | 0.207 | 1.80E-05 |
| PROS1 | protein S (alpha) | 1.807 | 0.000633 | ---- | ---- |
| PTP4A1 | protein tyrosine phosphatase type IVA, member 1 | 0.478 | 0.000385 | 0.497 | 1.80E-05 |
| RRAGA | Ras-related GTP binding A | ---- | ---- | 1.510 | 0.000301 |
| RUTBC3 | RUN and TBC1 domain 3 | 0.518 | 0.000704 | 0.450 | 0.000131 |
| S100P | S100 calcium binding protein P | 0.101 | 0 | 0.102 | 0 |
| SDCBP | syndecan binding protein (syntenin) | 0.456 | 0.000395 | ---- | ---- |
| SFRP1 | secreted frizzled-related protein 1 | ---- | ---- | 0.502 | 5.10E-05 |
| SLC35B3 | solute carrier family 35, member B3 | ---- | ---- | 1.990 | 0.000304 |
| STAF65 (gamma) | SPTF-associated factor 65 gamma | 0.021 | 1.00E-06 | 0.028 | 0 |
| THBS1 | thrombospondin 1 | ---- | ---- | 2.712 | 0.000225 |
| VMP1 | likely ortholog of rat vacuole membrane protein 1 | ---- | ---- | 1.547 | 0.000899 |
| YME1L1 | YME1-like 1 (S. cerevisiae) | 0.373 | 2.60E-05 | 0.333 | 5.00E-06 |
*Genes are listed in alphabetical order. Underlined genes were identified as differentially expressed between TNF sensitive and TNF resistant cells in both culture conditions.