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

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


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.

Abraham et al. BMC Bioinformatics 2010 11:277   doi:10.1186/1471-2105-11-277

Open Data