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




TNFa Data Details

GSE11467
Cell Line:MCF-7 (human breast cancer cell)
Modification:treated with TNFa (10ng/ml)
Time:2 h
Control Samples: GSM288961, GSM288962, GSM288963
Experimental Samples: GSM288967, GSM288968, GSM288969

GSE13837aTNF
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347196

GSE13837bTNF
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347328

GSE13837cTNF
Cell Line:synovial fibroblasts, female, age 65, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM347191, GSM347193
Experimental Samples: GSM347332

GSE13837dTNF
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347737

GSE13837eTNF
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347738

GSE13837fTNF
Cell Line:synovial fibroblasts, male, age 56, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM347340, GSM347342
Experimental Samples: GSM347739

GSE13837gTNF
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347746

GSE13837hTNF
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347747

GSE13837iTNF
Cell Line:synovial fibroblasts, male, age 65, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM347764, GSM347745
Experimental Samples: GSM347748

GSE13837jTNF
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347819

GSE13837kTNF
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347837

GSE13837lTNF
Cell Line:synovial fibroblasts, female, age 57, osteoarthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM347799, GSM347840
Experimental Samples: GSM347838

GSE13837mTNF
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM348017

GSE13837nTNF
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM348018

GSE13837oTNF
Cell Line:synovial fibroblasts, female, age 57, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM347845, GSM348023
Experimental Samples: GSM348020

GSE13837pTNF
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:1 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348031

GSE13837qTNF
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:2 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348034

GSE13837rTNF
Cell Line:synovial fibroblasts, female, age 67, rheumatoid arthritis
Modification:treated with TNFa 10 ng/ml
Time:4 h
Control Samples: GSM348030, GSM348037
Experimental Samples: GSM348035

GSE1474a
Cell Line:CaCo-2 (Colon cell line)
Modification:treated with TNFa
Time:4 h
Control Samples: GSM24832, GSM24833, GSM24834
Experimental Samples: GSM24841, GSM24842, GSM24843

GSE1474b
Cell Line:T84
Modification:treated with TNFa
Time:4 h
Control Samples: GSM24844, GSM24845, GSM24846
Experimental Samples: GSM24853, GSM24854, GSM24855

GSE2489a
Cell Line:Epidermis Keratinocytes
Modification:treated with TNFa
Time:1 h
Control Samples: GSM47302, GSM47304
Experimental Samples: GSM47311

GSE2489b
Cell Line:Epidermis Keratinocytes
Modification:treated with TNFa
Time:4 h
Control Samples: GSM47305, GSM47306
Experimental Samples: GSM47312

GSE2624a
Cell Line:human cervical epithelioid carcinoma cell line HeLa expressing tTA pBI-EGFP- IkBa Mut
Modification:treated with TNFa 25ng/ml and Doxycyline (2 mg/ml) to take IKB-inhibition away
Time:1 h
Control Samples: GSM50301, GSM50310, GSM50319, GSM50327
Experimental Samples: GSM50302, GSM50312, GSM50320, GSM50328

GSE2624b
Cell Line:human cervical epithelioid carcinoma cell line HeLa expressing tTA pBI-EGFP- IkBa Mut
Modification:treated with TNFa 25ng/ml and Doxycyline (2 mg/ml) to take IKB-inhibition away
Time:3 h
Control Samples: GSM50301, GSM50310, GSM50319, GSM50327
Experimental Samples: GSM50304, GSM50313, GSM50321, GSM50329

GSE516
Cell Line:human arthritic synoviocytes
Modification:treated with TNFa
Time:4 h
Control Samples: GSM7735
Experimental Samples: GSM7736

GSE8166
Cell Line:human umbilical vein endothelial cells)
Modification:treated with TNFa 1ng/ml cultured in M199 medium
Time:3 h
Control Samples: GSM202176
Experimental Samples: GSM202183

GSE9055a
Cell Line:HUVEC (Human umbilical vein cells)
Modification:treated with TNFa 10 ng/ml after 18 h serum starvation
Time:0.5 h
Control Samples: GSM229941
Experimental Samples: GSM229910

GSE9055b
Cell Line:HUVEC (Human umbilical vein cells)
Modification:treated with TNFa 10 ng/ml after 18 h serum starvation
Time:1 h
Control Samples: GSM229941
Experimental Samples: GSM229912

GSE9055c
Cell Line:HUVEC (Human umbilical vein cells)
Modification:treated with TNFa 10 ng/ml after 18 h serum starvation
Time:2 h
Control Samples: GSM229941
Experimental Samples: GSM229916

GSE9055d
Cell Line:HUVEC (Human umbilical vein cells)
Modification:treated with TNFa 10 ng/ml after 18 h serum starvation
Time:4 h
Control Samples: GSM229941
Experimental Samples: GSM229924