Table 2.
Subsets of differentially expressed genes in NTUH and NCI datasets.
| Gene symbol | Gene name | p-value‡ | q-value‡ | source§ | ER+/ER− |
|---|---|---|---|---|---|
| Intersection subset | |||||
| BTF3 | Basic transcription factor 3 | 1.10E-06 | 0.000189 | T | ↑ |
| 1.35E-06 | 3.43E-05 | U | ↑ | ||
| TFF3 | Trefoil factor 3 Cyclin-dependent | 5.48E-07 | 0.000135 | T | ↑ |
| 1.35E-06 | 3.43E-05 | U | ↑ | ||
| ESR1* | Estrogen receptor 1 | 5.48E-07 | 0.000135 | T | ↑ |
| 1.35E-06 | 3.43E-05 | U | ↑ | ||
| 1.35E-06 | 3.43E-05 | ||||
| GATA3* | GATA binding protein 3 | 5.48E-07 | 0.000135 | T | ↑ |
| 1.35E-06 | 3.43E-05 | U | ↑ | ||
| 1.35E-06 | 3.43E-05 | ||||
| CDKN2A* | kinase inhibitor 2A | 5.48E-07 | 0.000135 | T | ↓ |
| 1.35E-06 | 3.43E-05 | U | ↓ | ||
| 1.35E-06 | 3.43E-05 | ||||
| Mutually exclusive subset | |||||
| DDB2 | Damage-specific DNA binding protein 2 | 5.48E-07 | 0.000135 | T | ↑ |
| KIAA0020 | KIAA0020 | 5.48E-07 | 0.000135 | T | ↓ |
| NPY1R | Neuropeptide Y receptor Y1 | 5.48E-07 | 0.000135 | T | ↑ |
| TCEAL1 | Transcription elongation factor A (SII)-like 1 | 1.64E-06 | 0.000247 | T | ↑ |
| ABCD3 | ATP-binding cassette, sub-family D (ALD), member 3 | 1.35E-06 | 3.43E-05 | U | ↑ |
| AOC3 | Amine oxidase, copper containing 3 (vascular adhesion protein 1) | 1.35E-06 | 3.43E-05 | U | ↑ |
| APS | Adaptor protein with pleckstrin homology and src homology 2 domains | 1.35E-06 | 3.43E-05 | U | ↓ |
| ATP1B3 | ATPase, Na+/K+ transporting, beta 3 polypeptide | 1.35E-06 | 3.43E-05 | U | ↓ |
| BLR1 | Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5) | 2.70E-06 | 5.46E-05 | U | ↓ |
| BTG2 | BTG family, member 2 | 1.35E-06 | 3.43E-05 | U | ↑ |
| BUB1 | BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) | 1.35E-06 | 3.43E-05 | U | ↓ |
| CCNE1 | Cyclin E1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| CCNG2* | Cyclin G2 | 1.35E-06 | 3.43E-05 | U | ↑ |
| CD79A* | CD79a molecule | 1.35E-06 | 3.43E-05 | U | ↓ |
| 2.70E-06 | 5.46E-05 | ||||
| CDK2AP1* | CDK2-associated protein 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| 1.35E-06 | 3.43E-05 | ||||
| CFLAR* | CASP8 and FADD-like apoptosis regulator | 1.35E-06 | 3.43E-05 | U | ↓ |
| 1.35E-06 | 3.43E-05 | ||||
| DMWD | dystrophia myotonica-containing WD repeat motif | 2.70E-06 | 5.46E-05 | U | ↓ |
| DPP6 | Dipeptidyl-peptidase 6 | 1.35E-06 | 3.43E-05 | U | ↑ |
| DRG1 | Developmentally regulated GTP binding protein 1 | 2.70E-06 | 5.46E-05 | U | ↓ |
| DSC2 | Desmocollin 2 | 2.70E-06 | 5.46E-05 | U | ↓ |
| E2F3* | E2F transcription factor 3 | 1.35E-06 | 3.43E-05 | U | ↓ |
| 1.35E-06 | 3.43E-05 | ||||
| FABP7 | Fatty acid binding protein 7, brain | 1.35E-06 | 3.43E-05 | U | ↓ |
| FCGRT | Fc fragment of IgG, receptor, transporter, alpha | 1.35E-06 | 3.43E-05 | U | ↑ |
| FUT8 | Fucosyltransferase 8 (alpha (1,6) fucosyltransferase) | 1.35E-06 | 3.43E-05 | U | ↑ |
| GATA6 | GATA binding protein 6 | 1.35E-06 | 3.43E-05 | U | ↓ |
| GBP1 | Guanylate binding protein 1, interferon-inducible, 67 kDa | 1.35E-06 | 3.43E-05 | U | ↓ |
| HSD17B4 | Hydroxysteroid (17-beta) dehydrogenase 4 | 1.35E-06 | 3.43E-05 | U | ↑ |
| HSPC121 | protein tyrosine phosphatase-like A domain containing 1 | 1.35E-06 | 3.43E-05 | U | ↑ |
| IL2RG | Interleukin 2 receptor, gamma (severe combined immunodeficiency) | 2.70E-06 | 5.46E-05 | U | ↓ |
| IL6ST | Interleukin 6 signal transducer (gp130, oncostatin M receptor) | 1.35E-06 | 3.43E-05 | U | ↑ |
| ILK | Integrin-linked kinase | 1.35E-06 | 3.43E-05 | U | ↓ |
| IMPDH1 | IMP (inosine monophosphate) dehydrogenase 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| IRAK1 | Interleukin-1 receptor-associated kinase 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| ISL1 | ISL1 transcription factor, LIM/homeodomain, (islet-1) | 1.35E-06 | 3.43E-05 | U | ↑ |
| KLK5 | Kallikrein 5 | 1.35E-06 | 3.43E-05 | U | ↓ |
| KRT6B* | keratin 6B | 1.35E-06 | 3.43E-05 | U | ↓ |
| 1.35E-06 | 3.43E-05 | ||||
| KRT7 | keratin 7 | 1.35E-06 | 3.43E-05 | U | ↓ |
| LPIN1 | Lipin 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| LRBA | LPS-responsive vesicle trafficking, beach and anchor containing | 1.35E-06 | 3.43E-05 | U | ↑ |
| LYN* | V-yes-1 Yamaguchi sarcoma viral related oncogene homolog | 1.35E-06 | 3.43E-05 | U | ↓ |
| 1.35E-06 | 3.43E-05 | ||||
| MAP2K3 | Mitogen-activated protein kinase kinase 3 | 1.35E-06 | 3.43E-05 | U | ↓ |
| MCM6 | MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae) | 1.35E-06 | 3.43E-05 | U | ↓ |
| MCP(CD46) | membrane cofactor protein | 1.35E-06 | 3.43E-05 | U | ↑ |
| MMP7 | Matrix metallopeptidase 7 (matrilysin, uterine) | 1.35E-06 | 3.43E-05 | U | ↓ |
| MSN | Moesin | 1.35E-06 | 3.43E-05 | U | ↓ |
| MYB* | V-myb myeloblastosis viral oncogene homolog (avian) | 1.35E-06 | 3.43E-05 | U | ↑ |
| 1.35E-06 | 3.43E-05 | ||||
| MYBL1 | v-myb myeloblastosis viral oncogene homolog (avian)-like 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| MYC | V-myc myelocytomatosis viral oncogene homolog (avian) | 8.09E-06 | 0.000104 | U | ↑ |
| MYO6 | myosin VI | 1.35E-06 | 3.43E-05 | U | ↑ |
| NFATC3 | Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3 | 1.35E-06 | 3.43E-05 | U | ↓ |
| NFIB | Nuclear factor I/B | 1.35E-06 | 3.43E-05 | U | ↓ |
| NME3* | Non-metastatic cells 3, protein expressed in | 1.35E-06 | 3.43E-05 | U | ↑ |
| 1.35E-06 | 3.43E-05 | ||||
| NP | Nucleoside phosphorylase | 1.35E-06 | 3.43E-05 | U | ↓ |
| NSEP1 | Y box binding protein 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| NUMA1 | Nuclear mitotic apparatus protein 1 | 1.35E-06 | 3.43E-05 | U | ↑ |
| OAS1 | 2′,5′-oligoadenylate synthetase 1, 40/46 kDa | 1.35E-06 | 3.43E-05 | U | ↑ |
| PFKP | Phosphofructokinase, platelet | 1.35E-06 | 3.43E-05 | U | ↓ |
| PTP4A2* | Protein tyrosine phosphatase type IVA, member 2 | 1.35E-06 | 3.43E-05 | U | ↑ |
| 1.35E-06 | 3.43E-05 | ||||
| PTPNS1 | protein tyrosine phosphatase, non-receptor type substrate 1 | 1.35E-06 | 3.43E-05 | U | ↓ |
| RAB7 | RAB7, member RAS oncogene family | 1.35E-06 | 3.43E-05 | U | ↑ |
| SDC4 | Syndecan 4 (amphiglycan, ryudocan) | 1.35E-06 | 3.43E-05 | U | ↑ |
| SIAH2* | Seven in absentia homolog 2 (Drosophila) | 1.35E-06 | 3.43E-05 | U | ↑ |
| 1.35E-06 | 3.43E-05 | ||||
| 1.35E-06 | 3.43E-05 | ||||
| SKIP | SPHK1 (sphingosine kinase type 1) interacting protein | 1.35E-06 | 3.43E-05 | U | ↑ |
| UCP2 | Uncoupling protein 2 (mitochondrial, proton carrier) | 2.70E-06 | 5.46E-05 | U | ↓ |
| VAMP2 | Vesicle-associated membrane protein 2 (synaptobrevin 2) | 1.35E-06 | 3.43E-05 | U | ↓ |
| WWP1 | WW domain containing E3 ubiquitin protein ligase 1 | 1.35E-06 | 3.43E-05 | U | ↑ |
| XBP1 | X-box binding protein 1 | 1.35E-06 | 3.43E-05 | U | ↑ |
*
The expression values of these genes were detected by two or more probes in the microarrays from either NTUH or NCI dataset. Hence two or more p-values and q-values were calculated and shown together.
‡
p-value and q-value were calculated using the software, EDGE. Numbers have been rounded off.
§
T for NTUH dataset and U for NCI dataset.
↑, higher expression in ER+ samples; ↓lower expression in ER- samples.