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




MAPK_only Data Details

GSE14934b
Cell Line:HEK-HT (kidney)
Modification:Ras (G12V,T35S) activation mutants said to be mostly activating Raf
Time:not specified
Control Samples: GSM373089, GSM373094, GSM373099, GSM373104, GSM373109
Experimental Samples: GSM373091, GSM373096, GSM373101, GSM373106, GSM373111

GSE3542b
Cell Line:MCF-7 (breast cancer cells)
Modification:co-transfected with constituitively active MEK
Time:not specified
Control Samples: GSM81189, GSM81190, GSM81191
Experimental Samples: GSM81198, GSM81199, GSM81200

GSE3542c
Cell Line:MCF-7 (breast cancer cells)
Modification:co-transfected with constituitively active Raf
Time:not specified
Control Samples: GSM81189, GSM81190, GSM81191
Experimental Samples: GSM81204, GSM81205, GSM81206

GSE6521a
Cell Line:MCF-7 breast cancer cells
Modification:Treatment with U0126 (MEK inhibitor)
Time:90 min
Control Samples: GSM149913
Experimental Samples: GSM149928