SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets

 Home   Run SPEED   Download Annotations   Database Statistics   Suggest Pathways   Help 

The SPEED database stores z-score normalized microarray data from perturbation experiments for specific signaling pathways. All microarray data is downloaded from the Gene Expression Omnibus (GEO) at NCBI. The GEO series for the perturbation experiments are noted per pathway.


Number of Genes: 21485
Number of Measurements: 5896213
TLR Experiments: 39
GSE3720, GSE1541, GSE15219, GSE510316, GSE2706, GSE7850, GSE53982, GSE16650, GSE518047, GSE3491, GSE5504, GSE4748, GSE15038, GSE8608, GSE9988, GSE5883
TGFB Experiments: 38
GSE10847, GSE1724, GSE14491, GSE13837, GSE1805, GSE1802, GSE8730, GSE5457
H2O2 Experiments: 2
GSE5339
MAPK_only Experiments: 4
GSE6521, GSE3542, GSE14934
IL-1 Experiments: 6
GSE9120, GSE973, GSE8515
MAPK_PI3K Experiments: 39
GSE6521, GSE6783, GSE13009, GSE11729, GSE8471, GSE6784, GSE3542, GSE7403, GSE14934, GSE6462, GSE14256, GSE10778
VEGF Experiments: 25
GSE18913, GSE11228, GSE3891, GSE18195, GSE837, GSE17777, GSE15464, GSE10778
PI3K_only Experiments: 11
GSE3737, GSE6521, GSE7403, GSE14934, GSE7562
Wnt Experiments: 6
GSE11916, GSE1473, GSE14107, GSE16186, GSE17385
JAK-STAT Experiments: 14
GSE1925, GSE8059, GSE8687, GSE19082, GSE440, GSE10685, GSE1432, GSE3183
TNFa Experiments: 31
GSE1474, GSE9055, GSE11467, GSE13837, GSE516, GSE2624, GSE8166, GSE2489




MAPK_PI3K Data Details

GSE10778a
Cell Line:human umbilical vein endothelial cells (HUVEC)
Modification:Treatment with EGF
Time:30 min
Control Samples: GSM272113
Experimental Samples: GSM272118

GSE10778b
Cell Line:human umbilical vein endothelial cells (HUVEC)
Modification:Treatment with EGF
Time:1 h
Control Samples: GSM272113
Experimental Samples: GSM272119

GSE10778c
Cell Line:human umbilical vein endothelial cells (HUVEC)
Modification:Treatment with EGF
Time:2.5 h
Control Samples: GSM272113
Experimental Samples: GSM272120

GSE11729a
Cell Line:H1299 human non-small cell lung cancer cells
Modification:Treatment with EGF
Time:30 min
Control Samples: GSM297647
Experimental Samples: GSM297648

GSE11729b
Cell Line:H1299 human non-small cell lung cancer cells
Modification:Treatment with EGF
Time:1 h
Control Samples: GSM297647
Experimental Samples: GSM297649

GSE11729c
Cell Line:H1299 human non-small cell lung cancer cells
Modification:Treatment with EGF
Time:2 h
Control Samples: GSM297647
Experimental Samples: GSM297650

GSE11729d
Cell Line:H1299 human non-small cell lung cancer cells
Modification:Treatment with EGF
Time:4 h
Control Samples: GSM297647
Experimental Samples: GSM297651

GSE13009a
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with EGF
Time:30 min
Control Samples: GSM325937
Experimental Samples: GSM325944, GSM325945

GSE13009b
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with EGF
Time:1 h
Control Samples: GSM325937
Experimental Samples: GSM325948, GSM325949

GSE13009c
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with EGF
Time:2 h
Control Samples: GSM325937
Experimental Samples: GSM325952, GSM325953

GSE13009d
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with EGF
Time:4 h
Control Samples: GSM325937
Experimental Samples: GSM325956, GSM325957

GSE13009e
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with HRG
Time:30 min
Control Samples: GSM325937
Experimental Samples: GSM325978, GSM325979

GSE13009f
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with HRG
Time:1 h
Control Samples: GSM325937
Experimental Samples: GSM325982, GSM325983

GSE13009g
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with HRG
Time:2 h
Control Samples: GSM325937
Experimental Samples: GSM325986, GSM325987

GSE13009h
Cell Line:MCF7 human breast cancer cells
Modification:Treatment with HRG
Time:4 h
Control Samples: GSM325937
Experimental Samples: GSM325990, GSM325991

GSE14256a
Cell Line:Human foreskin fibroblasts (AG01518)
Modification:Treatment with platelet-derived growth factor-BB (PDGF-BB)
Time:1 h
Control Samples: GSM356969, GSM356970
Experimental Samples: GSM356966, GSM356973

GSE14256b
Cell Line:Human foreskin fibroblasts (AG01518)
Modification:Treatment with bFGF (basic fibroblast growth factor)
Time:1 h
Control Samples: GSM356969, GSM356970
Experimental Samples: GSM356968, GSM356971

GSE14934a
Cell Line:HEK-HT (kidney)
Modification:Ras (G12V) activation mutants
Time:not specified
Control Samples: GSM373089, GSM373094, GSM373099, GSM373104, GSM373109
Experimental Samples: GSM373090, GSM373095, GSM373100, GSM373105, GSM373110

GSE3542a
Cell Line:MCF-7 (breast cancer cells)
Modification:co-transfected with constituitively active erbB-2
Time:not specified
Control Samples: GSM81189, GSM81190, GSM81191
Experimental Samples: GSM81195, GSM81196, GSM81197

GSE3542d
Cell Line:MCF-7 (breast cancer cells)
Modification:co-transfected with ligand-inducible EGFR
Time:not specified
Control Samples: GSM81189, GSM81190, GSM81191
Experimental Samples: GSM81201, GSM81202, GSM81203

GSE6462a
Cell Line:MCF-7 (human breast cancer)
Modification:treatment with EGF (10nm)
Time:45 min
Control Samples: GSM148516
Experimental Samples: GSM148543

GSE6462b
Cell Line:MCF-7 (human breast cancer)
Modification:treatment with EGF (10nm)
Time:90 min
Control Samples: GSM148516
Experimental Samples: GSM148544

GSE6462c
Cell Line:MCF-7 (human breast cancer)
Modification:treatment with 10 nm HRG= heregulin Erb3/4 Ligand
Time:45 min
Control Samples: GSM148517
Experimental Samples: GSM148570

GSE6462d
Cell Line:MCF-7 (human breast cancer)
Modification:treatment with 10 nm HRG= heregulin Erb3/4 Ligand
Time:90 min
Control Samples: GSM148517
Experimental Samples: GSM148572

GSE6521d
Cell Line:MCF-7 breast cancer cells
Modification:Treatment with HRG (heregulin ErbB3 Ligand)
Time:45 min
Control Samples: GSM149913
Experimental Samples: GSM149919

GSE6521e
Cell Line:MCF-7 breast cancer cells
Modification:Treatment with HRG (heregulin ErbB3 Ligand)
Time:90 min
Control Samples: GSM149913
Experimental Samples: GSM149921

GSE6783a
Cell Line:HELA (Human cervical carcinoma cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:20 min
Control Samples: GSM156764
Experimental Samples: GSM156765

GSE6783b
Cell Line:HELA (Human cervical carcinoma cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:1 h
Control Samples: GSM156764
Experimental Samples: GSM156767

GSE6783c
Cell Line:HELA (Human cervical carcinoma cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:2 h
Control Samples: GSM156764
Experimental Samples: GSM156768

GSE6783d
Cell Line:HELA (Human cervical carcinoma cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:4 h
Control Samples: GSM156764
Experimental Samples: GSM156769

GSE6784a
Cell Line:MCF-10A (mammary epithelial cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:20 min
Control Samples: GSM156771
Experimental Samples: GSM156772

GSE6784b
Cell Line:MCF-10A (mammary epithelial cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:1 h
Control Samples: GSM156771
Experimental Samples: GSM156774

GSE6784c
Cell Line:MCF-10A (mammary epithelial cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:2 h
Control Samples: GSM156771
Experimental Samples: GSM156775

GSE6784d
Cell Line:MCF-10A (mammary epithelial cell line)
Modification:EGF treatment after 24 h serum starvation (Control 0 h)
Time:4 h
Control Samples: GSM156771
Experimental Samples: GSM156776

GSE7403a
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior DMSO treatment
Time:30 min
Control Samples: GSM178575, GSM178576
Experimental Samples: GSM178569, GSM178570

GSE7403c
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior DMSO treatment
Time:60 min
Control Samples: GSM178583
Experimental Samples: GSM178577, GSM178578

GSE7403e
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior DMSO treatment
Time:2 h
Control Samples: GSM178590, GSM178591
Experimental Samples: GSM178584, GSM178585

GSE7403g
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior DMSO treatment
Time:4 h
Control Samples: GSM178606, GSM178607
Experimental Samples: GSM178600, GSM178601

GSE8471
Cell Line:MCF7
Modification:HRG stimulated (ErbB Ligand)
Time:2 h after stimulation
Control Samples: GSM210180
Experimental Samples: GSM210181