Table 1

Functional network generated by Ingenuity knowledge database analysis
Hub gene
 Score
 GATMs
 Top functions
TNF↑
 34
 35
 Lipid metabolism, small molecule biochemistry, cell death
IFNG↑
 34
 35
 Lipid metabolism, molecular transport, small molecule biochemistry
IL1B↑
 34
 35
 Immune response, cellular movement, haematological system development and function
MYC↑
 34
 35
 Cell cycle, cellular movement, cancer
CCL2↑, KDR↓, VEGF↓
 34
 35
 Cellular movement, cancer, tumour morphology
SRC↑
 34
 35
 Haematological system development and function, immune and lymphatic system development and function, tissue morphology
BCL2↑
 34
 35
 Cancer, cell death, cell morphology
AGT↓
 34
 35
 Cell-to-cell signalling and interaction, haematological system development and function, immune and lymphatic system development and function
TIMP1↑, EDN1↓
 34
 35
 Cancer, cellular movement, cellular development
LEP↓
 34
 35
 Lipid metabolism, molecular transport, small molecule biochemistry
AR↓
 34
 35
 Cellular growth and proliferation, gene expression, cellular development
IGF2↓, ERBB3↑
 34
 35
 DNA replication, recombination, and repair, cancer, cell cycle
HOXA9↓, CDH1↑
 34
 35
 Cellular growth and proliferation, cell death, cancer
ARNT2↑, ZAP70↑
 34
 35
 Cellular growth and proliferation, haematological system development and function, immune response
PPARA↓, IL6, SERBF1
 15
 24
 Lipid metabolism, small molecule biochemistry, molecular transport
CDC42, RAC1
 13
 22
 Cell signalling, free radical scavenging, nucleic acid metabolism
ERBB2↑
 12
 17
 Cancer, tumour morphology, cell cycle
FN1
 12
 21
 Cell-to-cell signalling and interaction, cellular movement, reproductive system development and function
FOS
 12
 21
 Gene expression, cell cycle, haematological system development and function
IGF1, CCND1, BMP2
 12
 21
 Cellular growth and proliferation, connective tissue development and function, skeletal and muscular system development and function
IL4
 12
 21
 Cellular assembly and organization, cell cycle, DNA replication, recombination, and repair
NFYB
 11
 16
 Cancer, cell cycle, cellular assembly and organization
IL13, MAPK8, NFKB1
 11
 20
 Haematological system development and function, immune and lymphatic system development and function, tissue morphology
STAT3, INSR, PTPN
 11
 20
 Cellular growth and proliferation, haematological system development and function, immune response
NFKBIA, CD40LG, HGF
 11
 20
 Cell death, cellular movement, haematological system development and function
KRAS, CDKN1A
 10
 19
 Cellular growth and proliferation, cell signalling, cancer
TNF↑
 10
 19
 Carbohydrate metabolism, molecular transport, small molecule biochemistry

Out of the 55 available networks, only those containing at least 10 genes associated with mammary tumour microenvironment (GATMs) are shown. ↑ and ↓ indicate gene expression increasing and decreasing on passing from the pre-neoplastic condition to neoplasia, respectively.

Calogero et al. Breast Cancer Research 2007 9:211   doi:10.1186/bcr1745