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

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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




JAK-STAT Data Details

GSE10685
Cell Line:skeletal muscle biopsies
Modification:patients treated with IL-6 infusion
Time:3 h
Control Samples: GSM269808, GSM269811, GSM269932
Experimental Samples: GSM269809, GSM269834, GSM269933

GSE1432a
Cell Line:primary human microglial cells Y20
Modification:treated with IFN-gamma (respective time control)
Time:1 h
Control Samples: GSM26928
Experimental Samples: GSM23899

GSE1432b
Cell Line:primary human microglial cells B18
Modification:treated with IFN-gamma (respective time control)
Time:1 h
Control Samples: GSM26926
Experimental Samples: GSM23887

GSE1432c
Cell Line:primary human microglial cells W
Modification:treated with IFN-gamma (respective time control)
Time:1 h
Control Samples: GSM26927
Experimental Samples: GSM23895

GSE1432d
Cell Line:primary human microglial cells O
Modification:treated with IFN-gamma (respective time control)
Time:1 h
Control Samples: GSM26925
Experimental Samples: GSM23893

GSE19082a
Cell Line:HMEC (human microvascular endothelial cells)
Modification:treated with IFN-gamma 1 ng/ml (respective time control)
Time:3 h
Control Samples: GSM472434, GSM472438, GSM472442, GSM472446
Experimental Samples: GSM472436, GSM472440, GSM472444, GSM472448

GSE19082b
Cell Line:HMEC (human microvascular endothelial cells)
Modification:treated with IL-6 50 U/ml (respective time control)
Time:1 h
Control Samples: GSM472434, GSM472438, GSM472442, GSM472446
Experimental Samples: GSM472435, GSM472439, GSM472443, GSM472447

GSE1925a
Cell Line:primary human CD14+ macrophages Pool1
Modification:treated with IFN-gamma
Time:3 h
Control Samples: GSM34595
Experimental Samples: GSM34596

GSE1925b
Cell Line:primary human CD14+ macrophages Pool2
Modification:treated with IFN-gamma
Time:3 h
Control Samples: GSM34601
Experimental Samples: GSM34602

GSE1925c
Cell Line:primary human CD14+ macrophages Pool3
Modification:treated with IFN-gamma
Time:3 h
Control Samples: GSM34607
Experimental Samples: GSM34608

GSE3183
Cell Line:A549 (Human bronchial cell line)
Modification:treated with IL-13
Time:4 h
Control Samples: GSM47468, GSM47462, GSM47472
Experimental Samples: GSM47461, GSM47464, GSM47473

GSE440
Cell Line:Foreskin keratinocytes
Modification:treated with IFN-gamma (respective time control)
Time:1 h
Control Samples: GSM6709
Experimental Samples: GSM7765

GSE8059
Cell Line:NK (Primary Natural Killer cells)
Modification:treated with IL-2
Time:2 h
Control Samples: GSM198942
Experimental Samples: GSM198943

GSE8687
Cell Line:Sez-4
Modification:starved of IL-2 and activated with IL-2
Time:4 h after stimulation (16 h IL-2 pre-starvation)
Control Samples: GSM215362, GSM215363, GSM215361
Experimental Samples: GSM215365, GSM215366, GSM215364