Table 2:
Representative
cancer pathways enriched by top SNEA regulators found in patient tumors. Two
metastatic tumors in lung from form the patient with metastatic colon cancer
were analyzed. Receptor signaling
pathways were considered activated only if at least one of its hormones or
receptors was among SNEA regulators in patient. Such key regulators are shown
in bold font in the last column. First
column shows the tumor type for which the pathway was built based on SNEA
regulators profile. All pathways were
enriched with major expression regulators identified by SNEA with p-value
smaller than 0.05 according to Fisher exact test.
|
Patient tumor |
Pathway |
# SNEA regulators in pathway |
# entities in pathway |
Names of SNEA regulators in pathway |
|
Liver cancer liver biopsy |
EGFR activation by apoptotic clearance |
7 |
69 |
HBEGF,EREG,LPAR2,S1PR1,S1PR3,LPA receptor,S1PR |
|
Liver cancer liver biopsy |
N1->N2 neutrophil polarization |
8 |
44 |
ELN,CCL4,CCR5,CD7,SECTM1,DEFB4A,SERPINA1,SERPINB1 |
|
Liver cancer liver biopsy |
PDGF ->EMT |
8 |
50 |
ZEB1,SNAI2,SNAI1,PDGFD |
|
Liver cancer liver biopsy |
"Eat me" signals in apoptotic
clearance |
6 |
60 |
OLR1,ANXA1,THBS1,alpha5beta5 integrin |
|
Liver cancer liver biopsy |
EGF->FOXM1/FOXOA |
6 |
111 |
FOXF1,SNAI2,SNAI1,HBEGF,EREG |
|
Liver cancer liver biopsy |
M1->M2 macrophage polarization |
4 |
43 |
ASGR1,MRC1,CHIA,CHIT1 |
|
Liver cancer liver biopsy |
Coagulation cascade in cancer |
5 |
63 |
THBD,F10,F13A1,F2,F13B |
|
Liver cancer liver biopsy |
Hypoxia->EMT |
5 |
43 |
KLF5,SNAI2,EGLN1 |
|
Liver cancer liver biopsy |
Lymphotoxin B
signaling |
2 |
38 |
LTBR,LTA |
|
Breast cancer metastasis in lung |
ECM->EMT |
11 |
126 |
AGER,SPARC,HSPG2,S100A7,CTGF,IGF2,TNC,PAK1,PTK2B,IGFBP,LPA
receptor |
|
Breast cancer metastasis in lung |
F2 modulation of vascular permeability |
4 |
62 |
F2,PLG,RHOA,ROCK1 |
|
Breast cancer metastasis in lung |
EGF->FOXM1/FOXOA |
7 |
111 |
CAT,KLF8,ERBB2,PAK1,PTK2B,CCND1,CCNB1 |
|
Breast cancer metastasis in lung |
OSM signaling |
9 |
168 |
TNFRSF11B,OSM,THBS1,PLAU,CCND1,S100A8,S100A9,CRP,DEFB4A |
|
Breast cancer metastasis in lung |
Coagulation cascade in cancer |
4 |
63 |
F2,PLG,PLAU,TFPI |
|
Breast cancer metastasis in lung |
PDGF-D->EMT |
4 |
85 |
PDGFD,IGF2,PAK1,PTK2B |
|
Colon cancer metastasis in liver |
Coagulation cascade in cancer |
8 |
63 |
F3,TFPI2,F7,F10,F12,PLG,PLAU,plasmin |
|
Colon cancer metastasis in liver |
OSM signaling |
13 |
168 |
CEBPA,CEBPB,MYC,PPARD,F3,IL6,OSM,CYR61,PLAU,MMP3,SERPINA1,S100A4,acute-phase
protein |
|
Colon cancer metastasis in liver |
TGFB loop |
7 |
116 |
FOXM1,KLF5,TCF7L2,KRT8,CTGF,TGFB2,MMP3 |
|
Colon cancer metastasis in liver |
ECM->EMT |
7 |
126 |
FOXM1,MYC,EIF4E,EIF4EBP1,CTGF,S100A4,RPS6K |
|
Colon cancer metastasis in liver |
Cell cycle |
5 |
144 |
TFDP1,MYC,ZBTB17,TGFB2,E2F |
|
colon cancer metastasis in lung cancer |
VEGFR->endothelial proliferation |
7 |
74 |
ELK1,SRF,KDR,VEGFA,GRB2,MAPK14,endostatin |
|
colon cancer metastasis in lung cancer |
EDN->EMT |
7 |
81 |
ELK1,SRF,EDN3,EDN1,PRKCD,MAPK14,GNA13 |
|
colon cancer metastasis in lung cancer |
ECM->EMT |
9 |
126 |
GATA6,SRF,HBEGF,VEGFA,GRB2,MAPK14,BCAR1,ADAM17,LPA receptor |
|
colon cancer metastasis in lung cancer |
EGFR activation by apoptotic clearance |
6 |
69 |
HBEGF,LPAR3,LPAR1,ADAM17,LPA receptor,Ga12/13 |
|
colon cancer metastasis in lung cancer |
EGF->EMT |
7 |
104 |
GATA6,KLF5,SRF,HBEGF,GRB2,MAPK14,BCAR1 |
|
colon cancer metastasis in lung cancer |
Hypoxia->ROS->HIF-> Angiogenesis |
4 |
49 |
HIF3A,TEK,KDR,VEGFA |
|
colon cancer metastasis in lung cancer |
PDGF-D->EMT |
5 |
85 |
TCF7,VEGFA,PDGFD,GRB2,MAPK14 |
|
colon cancer metastasis in lung cancer-2 |
Hypoxia->ROS->HIF->Angiogenesis |
7 |
49 |
YBX1,HIF3A,EPAS1,TEK,KDR,VEGFA,RHOC |
|
colon cancer metastasis in lung cancer-2 |
ECM->EMT |
12 |
126 |
YBX1,FOXM1,EGFR,ACTG2,SPARC,HBEGF,VEGFA,IGF2,MAPK14,SRC,ADAM17,LPA |
|
colon cancer metastasis in lung cancer-2 |
Hypoxia->EMT |
6 |
43 |
CDH1,YBX1,KLF5,HIF3A,EPAS1,VEGFA |
|
colon cancer metastasis in lung cancer-2 |
TGFB loop |
10 |
116 |
CDH1,FOXM1,KLF5,CD44,ACTG2,VEGFA,TGFB2,SMAD7,MMP3,MMP9 |
|
colon cancer metastasis in lung cancer-2 |
F2 modulation of vascular permeability |
3 |
62 |
F2,PLG,SRC |
|
colon cancer metastasis in lung cancer-2 |
Bombesin
trans-activation of EGFR |
5 |
51 |
EGFR,HBEGF,SRC,GRPR,ADAM17 |
|
colon cancer metastasis in lung cancer-2 |
EGFR activation by apoptotic clearance |
6 |
69 |
PPAP2B,EGFR,HBEGF,ADAM17,LPA,Ga12/13 |
|
colon cancer metastasis in lung cancer-2 |
EGF->EMT |
8 |
104 |
YBX1,FOXM1,KLF5,EGFR,ACTG2,HBEGF,MAPK14,SRC |
|
colon cancer metastasis in lung cancer-2 |
IGF1R ->EMT |
4 |
51 |
YBX1,ACTG2,IGF2,SRC |
|
colon cancer metastasis in lung cancer-2 |
oxLDL->apoptosis |
2 |
20 |
OLR1,NAD(P)H oxidase |
|
colon cancer metastasis in lung cancer-2 |
"Find me" signals in apoptotic
clearance |
6 |
90 |
IL6R,PRKCD,MMP9,ADAM17,phospholipase D,sphinganine kinase |