Table 4 Top gene sets for each ER/HER2 subtype
Class | # | MSigDB Set | Cat. | Description | Sign |
|---|---|---|---|---|---|
ER-/HER2- | 1 | chr7q12 | Cl | Genes in cytogenetic band chr7q12 | 1 |
| Â | 2 | COLLER_MYC_DN | C2 | Genes down-regulated by MYC in 293T (transformed fetal renal cell). | -1 |
| Â | 3 | IFNGPATHWAY | C2 | IFN gamma signaling pathway | 1 |
| Â | 4 | GRANDVAUX_IFN_NOT_IRF3_UP | C2 | Genes up-regulated by interferon-alpha, beta but not by IRF3 in Jurkat (T cell) | 1 |
| Â | 5 | GNF2_ST13 | C4 | Neighborhood of ST13 | -1 |
| Â | 6 | GNF2_CD48 | C4 | Neighborhood of CD48 | 1 |
| Â | 7 | GNF2_GLTSCR2 | C4 | Neighborhood of GLTSCR2 | -1 |
| Â | 8 | MENSE_HYPOXIA_DN | C2 | List of Hypoxia-suppressed genes found in both Astrocytes and HeLa Cells | -1 |
| Â | 9 | HSA03010_RIBOSOME | C2 | Genes involved in ribosome | -1 |
| Â | 10 | GCM_TPT1 | C4 | Neighborhood of TPT1 | -1 |
ER+/HER2- | 1 | GNF2_MKI67 | C4 | Neighborhood of MKI67 | -1 |
| Â | 2 | GNF2_TTK | C4 | Neighborhood of TTK | -1 |
| Â | 3 | GNF2_HMMR | C4 | Neighborhood of HMMR | -1 |
| Â | 4 | GNF2_CCNA2 | C4 | Neighborhood of CCNA2 | -1 |
| Â | 5 | GNF2_SMC2L1 | C4 | Neighborhood of SMC2L1 | -1 |
| Â | 6 | GNF2_ESPL1 | C4 | Neighborhood of ESPL1 | -1 |
| Â | 7 | GNF2_CDC20 | C4 | Neighborhood of CDC20 | -1 |
| Â | 8 | GNF2_H2AFX | C4 | Neighborhood of H2AFX | -1 |
| Â | 9 | GNF2_RRM2 | C4 | Neighborhood of RRM2 | -1 |
| Â | 10 | ZHAN_MM_CD138_PR_VS_ REST | C2 | 50 top ranked SAM-defined over-expressed genes in each subgroup_PR | -1 |
HER2+ | 1 | chr4p | Cl | Genes in cytogenetic band chr4p | -1 |
| Â | 2 | chrlqll | Cl | Genes in cytogenetic band chrlqll | 1 |
| Â | 3 | DAC_FIBRO_DN | C2 | Downregulated by DAC treatment in LD419 fibroblast cells | -1 |
| Â | 4 | GNF2_MKI67 | C4 | Neighborhood of MKI67 | -1 |
| Â | 5 | GNF2_CCNA2 | C4 | Neighborhood of CCNA2 | -1 |
| Â | 6 | GNF2_TTK | C4 | Neighborhood of TTK | -1 |
| Â | 7 | GNF2_H2AFX | C4 | Neighborhood of H2AFX | -1 |
| Â | 8 | GNF2_HMMR | C4 | Neighborhood of HMMR | -1 |
| Â | 9 | CROONQUIST_L6_RAS_DN | C2 | Genes dowmregulated in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus those with N-ras-activating mutations. | -1 |
| Â | 10 | CROONQUIST_L6_STARVE_UP | C2 | Genes upregulated in multiple myeloma cells exposed to the pro-proliferative cytokine IL-6 versus those that were IL-6-starved. | -1 |