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
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

Wnt Data Details

Cell Line:Huh7 (hepatocellular carcinoma derived)
Modification:High TCF activity Huh7 cell line was compared to control Huh7 cell line (TCF the crucial transcription factor for Wnt)
Time:not specified
Control Samples: GSM301104, GSM301105, GSM301106
Experimental Samples: GSM301119, GSM301132, GSM301133

Cell Line:parental PC9 (Lung adenocarcinoma cell line)
Modification:Wnt3a stimulation after serum starvation (0.2 %)
Time:3 h
Control Samples: GSM354009, GSM354010
Experimental Samples: GSM354011, GSM354012

Cell Line:parental H2030 (Lung adenocarcinoma cell line)
Modification:Wnt3a stimulation after serum starvation (0.2 %)
Time:3 h
Control Samples: GSM354017, GSM354018
Experimental Samples: GSM354019, GSM354020

Cell Line:HEK293 (kidney cell)
Modification:infected with RCAS-beta-cateninS37A or RCAS-GFP
Time:not specified
Control Samples: GSM24858, GSM24859, GSM24860, GSM24861
Experimental Samples: GSM24862, GSM24863, GSM24864, GSM24865

Cell Line:T253 (mesenchymal stem cell)
Modification:hMSC overexpressing activated LRP5 (Wnt Co-Receptor) and Wnt3a stimulation
Time:1 h
Control Samples: GSM406373, GSM406374, GSM406375
Experimental Samples: GSM406376, GSM406377, GSM406378

Cell Line:Multiple myeloma line MM1.S
Modification:cells lentivirally infected with control shRNA or beta-catenin shRNA vectors
Time:not specified
Control Samples: GSM434408, GSM434409, GSM434410
Experimental Samples: GSM434411, GSM434412, GSM434413