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




PI3K_only Data Details

GSE14934c
Cell Line:HEK-HT (kidney)
Modification:Ras (G12V,Y40C) activation mutants said to be mostly activating PI3K
Time:not specified
Control Samples: GSM373089, GSM373094, GSM373099, GSM373104, GSM373109
Experimental Samples: GSM373093, GSM373098, GSM373103, GSM373108, GSM373113

GSE3737
Cell Line:PC3 (prostate cancer cell)
Modification:treatment with arachidonic acid (AA) should activate PI3K
Time:2 h
Control Samples: GSM86082
Experimental Samples: GSM86085, GSM86086

GSE6521b
Cell Line:MCF-7 breast cancer cells
Modification:Treatment with U0126 (MEK inhibitor) + HRG (heregulin ErbB3 Ligand)
Time:45 min
Control Samples: GSM149913
Experimental Samples: GSM149933

GSE6521c
Cell Line:MCF-7 breast cancer cells
Modification:Treatment with U0126 (MEK inhibitor) + HRG (heregulin ErbB3 Ligand)
Time:90 min
Control Samples: GSM149913
Experimental Samples: GSM149935

GSE7403b
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior U0126 treatment
Time:30 min
Control Samples: GSM178575, GSM178576
Experimental Samples: GSM178571, GSM178572

GSE7403d
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior U0126 treatment
Time:60 min
Control Samples: GSM178583
Experimental Samples: GSM178579, GSM178580

GSE7403f
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior U0126 treatment
Time:2 h
Control Samples: GSM178590, GSM178591
Experimental Samples: GSM178586, GSM178587

GSE7403h
Cell Line:SH-SY5Y (Neuroblastoma cells)
Modification:PDGF treatment with 60 min prior U0126 treatment
Time:4 h
Control Samples: GSM178606, GSM178607
Experimental Samples: GSM178602, GSM178603

GSE7562a
Cell Line:A431
Modification:PTEN hcRNA knockdown
Time:not specified (until log Phase)
Control Samples: GSM183432, GSM183433
Experimental Samples: GSM183434, GSM183435

GSE7562b
Cell Line:HCC827
Modification:PTEN hcRNA knockdown
Time:not specified (until log Phase)
Control Samples: GSM183436, GSM183437
Experimental Samples: GSM183438, GSM183439

GSE7562c
Cell Line:SKBR3
Modification:PTEN hcRNA knockdown
Time:not specified (until log Phase)
Control Samples: GSM183440, GSM183441
Experimental Samples: GSM183442, GSM183443