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Table 4 Top gene sets for each ER/HER2 subtype

From: Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

Class # MSigDB Set Cat. Description Sign
ER-/HER2- 1 chr7q12 Cl Genes in cytogenetic band chr7q12 1
  2 COLLER_MYC_DN C2 Genes down-regulated by MYC in 293T (transformed fetal renal cell). -1
  3 IFNGPATHWAY C2 IFN gamma signaling pathway 1
  4 GRANDVAUX_IFN_NOT_IRF3_UP C2 Genes up-regulated by interferon-alpha, beta but not by IRF3 in Jurkat (T cell) 1
  5 GNF2_ST13 C4 Neighborhood of ST13 -1
  6 GNF2_CD48 C4 Neighborhood of CD48 1
  7 GNF2_GLTSCR2 C4 Neighborhood of GLTSCR2 -1
  8 MENSE_HYPOXIA_DN C2 List of Hypoxia-suppressed genes found in both Astrocytes and HeLa Cells -1
  9 HSA03010_RIBOSOME C2 Genes involved in ribosome -1
  10 GCM_TPT1 C4 Neighborhood of TPT1 -1
ER+/HER2- 1 GNF2_MKI67 C4 Neighborhood of MKI67 -1
  2 GNF2_TTK C4 Neighborhood of TTK -1
  3 GNF2_HMMR C4 Neighborhood of HMMR -1
  4 GNF2_CCNA2 C4 Neighborhood of CCNA2 -1
  5 GNF2_SMC2L1 C4 Neighborhood of SMC2L1 -1
  6 GNF2_ESPL1 C4 Neighborhood of ESPL1 -1
  7 GNF2_CDC20 C4 Neighborhood of CDC20 -1
  8 GNF2_H2AFX C4 Neighborhood of H2AFX -1
  9 GNF2_RRM2 C4 Neighborhood of RRM2 -1
  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
  2 chrlqll Cl Genes in cytogenetic band chrlqll 1
  3 DAC_FIBRO_DN C2 Downregulated by DAC treatment in LD419 fibroblast cells -1
  4 GNF2_MKI67 C4 Neighborhood of MKI67 -1
  5 GNF2_CCNA2 C4 Neighborhood of CCNA2 -1
  6 GNF2_TTK C4 Neighborhood of TTK -1
  7 GNF2_H2AFX C4 Neighborhood of H2AFX -1
  8 GNF2_HMMR C4 Neighborhood of HMMR -1
  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
  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
  1. Top 10 MSigDB sets for ER/HER2 molecular subtypes, chosen by the centroid classifier using the set centroid statistic. Sign = -1 if expression is negatively associated with long-term survival, and vice versa.