Table 2 A gene set differentially co-expressed by ER-status (p-value = 1.34 × 10−252 and coefficient = −1.117) only and insignificant for the other cofactors: coefficients/p-values for p53 and Grade are 0.294/1.05E-51 and 0.095/9.33E-09 respectively. Co-expression of the set occurs in ER-negative tumors only ER dependent differential expression, ER binding sites and p53 binding sites are also given for the gene set
From: MultiDCoX: Multi-factor analysis of differential co-expression
No. | Gene | ER (DE) | ER Binding Site | Gene Description |
|---|---|---|---|---|
1. | BRCA2 | Yes (up) | dist >100Â kb | breast cancer 2, early onset |
2. | ABCC3 | Yes (down) | Yes(dist = 20.96 kb) | ATP-binding cassette, sub-family C (CFTR/MRP), member 3 |
3. | ITGB6 | Yes (down) | dist >100Â kb | integrin, beta 6 |
4. | ABCC11 | No | Yes(dist = 68.96 kb) | ATP-binding cassette, sub-family C (CFTR/MRP), member 11 |
5. | SNED1 | No | Yes(dist = 94.62 kb) | Insulin-responsive sequence DNA- binding protein 1 |
6. | NQO1 | Yes (down) | Yes(dist = 32.63 kb) | NAD(P)H dehydrogenase, quinone 1 |
7. | LOC254057 | No | NA | uncharacterized LOC254057 |
8. | SPDEF | No | Yes(dist = 1.159 kb) | SAM pointed domain containing ets transcription factor |
9. | FABP4 | No | Yes(dist = 1.159 kb) | fatty acid binding protein 4, adipocyte |
10. | CEACAM6 | Yes (down) | Yes(dist = 19.05 kb) | carcinoembryonic antigen-related cell adhesion molecule 6 |
11. | DUSP4 | No | Yes(dist = 19.138 kb) | dual specificity phosphatase 4 |
12. | SERHL2 | No | Yes(dist = 32.63 kb) | serine hydrolase-like 2 |
13. | RBP4 | No | Yes(dist = 20.489 kb) | retinol binding protein 4, plasma |
14. | PTK6 | Yes (down) | dist >100Â kb | PTK6 protein tyrosine kinase 6 |
15. | TMC5 | No | dist >100Â kb | transmembrane channel-like 5 |
16. | EEF1A2 | No | dist >100Â kb | eukaryotic translation elongation factor 1 alpha 2 |
17. | CLIC3 | Yes (down) | Yes(dist = 0.317 kb) | chloride intracellular channel 3 |
18. | LBP | No | dist >100Â kb | lipopolysaccharide binding protein |
19. | MMP1 | No | dist >100Â kb | matrix metallopeptidase 1 (interstitial collagenase) |
20. | FAM5C | No | dist >100Â kb | family with sequence similarity 5, member C |
21. | AGR2 | Yes (up) | Yes(dist = 2.154 kb) | anterior gradient 2 homolog (Xenopus laevis) |