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




TGFB Data Details

GSE10847
Cell Line:H522 (lung cancer cells)
Modification:treated with TGF-beta and transduced with BRG1, TR-II
Time:2 h
Control Samples: GSM275309
Experimental Samples: GSM275311

GSE13837a
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347194

GSE13837b
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347197

GSE13837c
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347330

GSE13837d
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347733

GSE13837e
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347734

GSE13837f
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347735

GSE13837g
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347741

GSE13837h
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347742

GSE13837i
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347743

GSE13837j
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347765

GSE13837k
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347766

GSE13837l
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347767

GSE13837m
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM347841

GSE13837n
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM347842

GSE13837o
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM347843

GSE13837p
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:1 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348024

GSE13837q
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:2 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348027

GSE13837r
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TGFb 10 ng/ml
Time:4 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348028

GSE14491
Cell Line:MDA-MB-231 (human metastatic breast cell line)
Modification:treated with TGF-beta (5g/ml) and transfection of GFP-shRNA
Time:3 h
Control Samples: GSM361954, GSM361955, GSM361956, GSM361957
Experimental Samples: GSM361958, GSM361959, GSM361960, GSM361961

GSE1724a
Cell Line:lung fibroblast (tissue sample: normal tissue)
Modification:TGF-1 (4 ng/ml) treatment
Time:4 h
Control Samples: GSM29911, GSM29915, GSM29918
Experimental Samples: GSM29913, GSM29916, GSM29919

GSE1724b
Cell Line:lung fibroblasts from patient with fibrosing alveolitis associated with systemic sclerosis (FASSc1)
Modification:TGF-1 (4 ng/ml) treatment
Time:4 h
Control Samples: GSM29923, GSM29928, GSM29933
Experimental Samples: GSM29925, GSM29931, GSM29935

GSE1724c
Cell Line:lung fibroblasts from a patient with idiopathic pulmonary fibrosis (IPF1)
Modification:TGF-1 (4 ng/ml) treatment
Time:4 h
Control Samples: GSM29938, GSM29944, GSM29950
Experimental Samples: GSM29941, GSM29947, GSM29952

GSE1802a
Cell Line:umbilical cord blood CD34+ cells C
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31092
Experimental Samples: GSM31096

GSE1802b
Cell Line:umbilical cord blood CD34+ cells E
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31094
Experimental Samples: GSM31097

GSE1802c
Cell Line:umbilical cord blood CD34+ cells F
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31095
Experimental Samples: GSM31098

GSE1802d
Cell Line:umbilical cord blood CD34+ cells C
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31092
Experimental Samples: GSM31099

GSE1802e
Cell Line:umbilical cord blood CD34+ cells D
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31093
Experimental Samples: GSM31100

GSE1802f
Cell Line:umbilical cord blood CD34+ cells E
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31094
Experimental Samples: GSM31101

GSE1802g
Cell Line:umbilical cord blood CD34+ cells F
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31095
Experimental Samples: GSM31102

GSE1805a
Cell Line:M091 acute myelogenous leukemia cells A
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31119
Experimental Samples: GSM31123

GSE1805b
Cell Line:M091 acute myelogenous leukemia cells B
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31117
Experimental Samples: GSM31122

GSE1805c
Cell Line:M091 acute myelogenous leukemia cells C
Modification:TGF-beta treatment
Time:2 h
Control Samples: GSM31120
Experimental Samples: GSM31124

GSE1805d
Cell Line:M091 acute myelogenous leukemia cells B
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31117
Experimental Samples: GSM31126

GSE1805e
Cell Line:M091 acute myelogenous leukemia cells C
Modification:TGF-beta treatment
Time:4 h
Control Samples: GSM31120
Experimental Samples: GSM31127

GSE5457
Cell Line:A549 (carcinomic human alveolar basal epithelial cell)
Modification:TGF-1
Time:4 h
Control Samples: GSM124905, GSM124906
Experimental Samples: GSM124909, GSM124910

GSE8730a
Cell Line:odontoblasts (tissue sample from the molar teeth)
Modification:TGF-1 treatment
Time:1 h (5 h existent but not taken)
Control Samples: GSM216537
Experimental Samples: GSM216538

GSE8730b
Cell Line:pulp tissue (tissue sample from the molar teeth)
Modification:TGF-1
Time:1 h (5 h existent but not taken)
Control Samples: GSM216541
Experimental Samples: GSM216546