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




TLR Data Details

GSE15038
Cell Line:U937 cells (Activated macropahges)
Modification:treated with LPS
Time:2 h
Control Samples: GSM375671
Experimental Samples: GSM375673

GSE15219
Cell Line:Human monocyte
Modification:treated with LPS 10 ng/ml
Time:3 h
Control Samples: GSM380032, GSM380033
Experimental Samples: GSM380034, GSM380035

GSE1541a
Cell Line:A549 (Alveolar Epithelial Cells line)
Modification:treated with LPS
Time:1 h
Control Samples: GSM26477, GSM26478
Experimental Samples: GSM26481, GSM26482

GSE1541b
Cell Line:A549 (Alveolar Epithelial Cells line)
Modification:treated with LPS
Time:4 h
Control Samples: GSM26479, GSM26480
Experimental Samples: GSM26483, GSM26484

GSE16650
Cell Line:Beas-B2 (Human Bronchial Epithelial Cells)
Modification:treated with LPS 1 g/ml
Time:4 h
Control Samples: GSM417770, GSM417776
Experimental Samples: GSM417772, GSM417778

GSE2706
Cell Line:Monocyte derived dendritic cells
Modification:treated with LPS
Time:2 h
Control Samples: GSM52346, GSM52353, GSM52360
Experimental Samples: GSM52340, GSM52347, GSM52354

GSE3491a
Cell Line:GENDER: MALE TISSUE: WHOLE BLOOD LPS RESPONSE: HIGH
Modification:treated with LPS 10 NG/ML
Time:4 h
Control Samples: GSM78606
Experimental Samples: GSM78607

GSE3491b
Cell Line:GENDER: MALE TISSUE: WHOLE BLOOD LPS RESPONSE: HIGH
Modification:treated with LPS 10 NG/ML
Time:4 h
Control Samples: GSM79057
Experimental Samples: GSM79058

GSE3491c
Cell Line:GENDER: FEMALE TISSUE: WHOLE BLOOD LPS RESPONSE: HIGH
Modification:treated with LPS 10 NG/ML
Time:4 h
Control Samples: GSM79064
Experimental Samples: GSM79067

GSE3720a
Cell Line:expanded peripheral blood Vd1 gd T lymphocytes
Modification:treated with LPS 10 mg/mL
Time:4 h
Control Samples: GSM85804, GSM85805
Experimental Samples: GSM85806, GSM85807

GSE3720b
Cell Line:expanded peripheral blood Vd2 gd T lymphocytes
Modification:treated with LPS 10 mg/mL
Time:4 h
Control Samples: GSM85810, GSM85811
Experimental Samples: GSM85812, GSM85813

GSE4748
Cell Line:Monocyte derived dendritic cells
Modification:treated with LPS 0.5 g/ml
Time:3 h
Control Samples: GSM107453, GSM107458
Experimental Samples: GSM107455, GSM107460

GSE510316
Cell Line:monocyte-derived dendritic cells
Modification:treated with LPS 1 g/ml
Time:4 h
Control Samples: GSM260689
Experimental Samples: GSM260690

GSE518047a
Cell Line:H929 (Multiple Myeloma Cell Line)
Modification:transfected with NIK
Time:undefined
Control Samples: GSM451261, GSM451264, GSM451267
Experimental Samples: GSM451262, GSM451265, GSM451268

GSE518047b
Cell Line:H929 (Multiple Myeloma Cell Line)
Modification:transfected with IKKB
Time:undefined
Control Samples: GSM451261, GSM451264, GSM451267
Experimental Samples: GSM451263, GSM451266, GSM451269

GSE518047c
Cell Line:SACHI (Multiple Myeloma Cell Line)
Modification:transfected with NIK
Time:undefined
Control Samples: GSM451270, GSM451273, GSM451276
Experimental Samples: GSM451271, GSM451274, GSM451277

GSE518047d
Cell Line:SACHI (Multiple Myeloma Cell Line)
Modification:transfected with IKKB
Time:undefined
Control Samples: GSM451270, GSM451273, GSM451276
Experimental Samples: GSM451272, GSM451275, GSM451278

GSE53982a
Cell Line:Human CD16+, CCR3- peripheral blood neutrophils
Modification:treated with LPS 100 ng/ml
Time:1 h
Control Samples: GSM90843, GSM90844
Experimental Samples: GSM90847

GSE53982b
Cell Line:Macrophages differentiated from isolated CD14+ monocytes in the presence of GM-CSF
Modification:treated with LPS 100 ng/ml
Time:4 h
Control Samples: GSM90838, GSM90839
Experimental Samples: GSM90840, GSM90841

GSE5504a
Cell Line:human peripheral blood derived monocytes
Modification:treated with LPS
Time:2 h
Control Samples: GSM126988, GSM126993
Experimental Samples: GSM126994, GSM126995

GSE5504b
Cell Line:human peripheral blood derived monocytes
Modification:treated with LPS
Time:4 h
Control Samples: GSM126988, GSM126993
Experimental Samples: GSM126996, GSM126997

GSE5883
Cell Line:HMVEC-L (Microvascular endothelial cells, lung)
Modification:treated with LPS 10 ng
Time:4 h
Control Samples: GSM114564, GSM114565, GSM114566, GSM114567
Experimental Samples: GSM114552, GSM114553, GSM114554, GSM114555

GSE7850a
Cell Line:Retinal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190517, GSM190518
Experimental Samples: GSM190519, GSM190520

GSE7850b
Cell Line:Choroidal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190521, GSM190522
Experimental Samples: GSM190523, GSM190524

GSE7850c
Cell Line:Retinal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190525, GSM190526
Experimental Samples: GSM190527, GSM190528

GSE7850d
Cell Line:Choroidal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190529, GSM190530
Experimental Samples: GSM190531, GSM190532

GSE7850e
Cell Line:Retinal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190533, GSM190534
Experimental Samples: GSM190535, GSM190536

GSE7850f
Cell Line:Choroidal endothelial cell
Modification:treated with LPS 10 100 ng/mL
Time:4 h
Control Samples: GSM190537, GSM190538
Experimental Samples: GSM190539, GSM190540

GSE8608
Cell Line:monocyte-derived macrophages of 13 male healthy subjects
Modification:treated with LPS 10ng/ml
Time:4 h
Control Samples: GSM213500
Experimental Samples: GSM213511

GSE9988a
Cell Line:Human monocytes (donor 1)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252485
Experimental Samples: GSM252451

GSE9988b
Cell Line:Human monocytes (donor 2)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252481
Experimental Samples: GSM252448

GSE9988c
Cell Line:Human monocytes (donor 3)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252480
Experimental Samples: GSM252447

GSE9988d
Cell Line:Human monocytes (donor 4)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252479
Experimental Samples: GSM252444

GSE9988e
Cell Line:Human monocytes (donor 5)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252482
Experimental Samples: GSM252450

GSE9988f
Cell Line:Human monocytes (donor 6)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252478
Experimental Samples: GSM252452

GSE9988g
Cell Line:Human monocytes (donor 7)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252483
Experimental Samples: GSM252443

GSE9988h
Cell Line:Human monocytes (donor 8)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252477
Experimental Samples: GSM252454

GSE9988i
Cell Line:Human monocytes (donor 9)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252484
Experimental Samples: GSM252449

GSE9988j
Cell Line:Human monocytes (donor 11)
Modification:treated with LPS
Time:2 h
Control Samples: GSM252476
Experimental Samples: GSM252453