Pathway Name Avg Num Perturbations Total Perturbations Num Entities Min Mean Truth Max Mean Truth Min Mean Within Max Mean Within Min Mean Any Max Mean Within TCGA08_retinoblastoma 15.0 120.0 8.0 -0.125 0.054 1000.0 -1000.0 -0.003 -1000.0 PLK2 and PLK4 events 12.0 36.0 3.0 -0.101 0.01 1000.0 -1000.0 -0.0 -1000.0 HIF-1-alpha transcription factor network 12.0 928.0 76.0 -0.402 0.026 1000.0 -1000.0 -0.051 -1000.0 Syndecan-1-mediated signaling events 10.0 340.0 34.0 -0.155 0.018 1000.0 -1000.0 -0.014 -1000.0 Signaling events mediated by the Hedgehog family 9.0 512.0 52.0 -0.239 0.074 1000.0 -1000.0 -0.026 -1000.0 Signaling events mediated by Stem cell factor receptor (c-Kit) 9.0 705.0 78.0 -0.274 0.111 1000.0 -1000.0 -0.032 -1000.0 Ephrin B reverse signaling 8.0 404.0 48.0 -0.221 0.037 1000.0 -1000.0 -0.024 -1000.0 Glypican 1 network 7.0 344.0 48.0 -0.109 0.022 1000.0 -1000.0 -0.015 -1000.0 IGF1 pathway 7.0 417.0 57.0 -0.115 0.048 1000.0 -1000.0 -0.053 -1000.0 IL23-mediated signaling events 7.0 448.0 60.0 -0.481 0.017 1000.0 -1000.0 -0.041 -1000.0 IL12-mediated signaling events 6.0 576.0 87.0 -0.328 0.029 1000.0 -1000.0 -0.094 -1000.0 Osteopontin-mediated events 6.0 239.0 38.0 -0.138 0.017 1000.0 -1000.0 -0.021 -1000.0 Noncanonical Wnt signaling pathway 6.0 163.0 26.0 -0.091 0.019 1000.0 -1000.0 -0.027 -1000.0 IL4-mediated signaling events 6.0 552.0 91.0 -0.617 0.401 1000.0 -1000.0 -0.134 -1000.0 Nectin adhesion pathway 6.0 391.0 63.0 -0.146 0.032 1000.0 -1000.0 -0.042 -1000.0 TCR signaling in naïve CD8+ T cells 6.0 628.0 93.0 -0.112 0.026 1000.0 -1000.0 -0.043 -1000.0 Wnt signaling 6.0 46.0 7.0 -0.091 0.004 1000.0 -1000.0 -0.01 -1000.0 Calcineurin-regulated NFAT-dependent transcription in lymphocytes 6.0 444.0 68.0 -0.302 0.159 1000.0 -1000.0 -0.053 -1000.0 Plasma membrane estrogen receptor signaling 6.0 568.0 86.0 -0.19 0.175 1000.0 -1000.0 -0.057 -1000.0 FOXM1 transcription factor network 6.0 356.0 51.0 -0.437 0.018 1000.0 -1000.0 -0.134 -1000.0 FOXA2 and FOXA3 transcription factor networks 5.0 234.0 46.0 -0.197 0.053 1000.0 -1000.0 -0.051 -1000.0 BMP receptor signaling 5.0 412.0 81.0 -0.19 0.037 1000.0 -1000.0 -0.06 -1000.0 Endothelins 5.0 497.0 96.0 -0.209 0.018 1000.0 -1000.0 -0.04 -1000.0 TCGA08_p53 5.0 39.0 7.0 -0.091 0.062 1000.0 -1000.0 -0.005 -1000.0 Caspase cascade in apoptosis 4.0 309.0 74.0 -0.059 0.047 1000.0 -1000.0 -0.026 -1000.0 FAS signaling pathway (CD95) 4.0 220.0 47.0 -0.125 0.046 1000.0 -1000.0 -0.033 -1000.0 Signaling mediated by p38-alpha and p38-beta 4.0 198.0 44.0 -0.102 0.017 1000.0 -1000.0 -0.016 -1000.0 EPHB forward signaling 4.0 394.0 85.0 -0.099 0.063 1000.0 -1000.0 -0.052 -1000.0 Glypican 2 network 4.0 18.0 4.0 -0.028 -0.0 1000.0 -1000.0 -0.0 -1000.0 Nongenotropic Androgen signaling 4.0 252.0 52.0 -0.105 0.051 1000.0 -1000.0 -0.032 -1000.0 IL27-mediated signaling events 4.0 227.0 51.0 -0.19 0.082 1000.0 -1000.0 -0.042 -1000.0 LPA receptor mediated events 4.0 498.0 102.0 -0.147 0.018 1000.0 -1000.0 -0.049 -1000.0 IL6-mediated signaling events 4.0 313.0 75.0 -0.099 0.04 1000.0 -1000.0 -0.034 -1000.0 Syndecan-4-mediated signaling events 4.0 327.0 67.0 -0.123 0.026 1000.0 -1000.0 -0.024 -1000.0 Visual signal transduction: Rods 4.0 223.0 52.0 -0.117 0.036 1000.0 -1000.0 -0.043 -1000.0 LPA4-mediated signaling events 3.0 40.0 12.0 -0.02 0.01 1000.0 -1000.0 -0.008 -1000.0 Regulation of nuclear SMAD2/3 signaling 3.0 408.0 136.0 -0.427 0.091 1000.0 -1000.0 -0.022 -1000.0 Coregulation of Androgen receptor activity 3.0 229.0 76.0 -0.158 0.036 1000.0 -1000.0 -0.025 -1000.0 Thromboxane A2 receptor signaling 3.0 353.0 105.0 -0.095 0.045 1000.0 -1000.0 -0.044 -1000.0 Syndecan-2-mediated signaling events 3.0 222.0 69.0 -0.097 0.033 1000.0 -1000.0 -0.013 -1000.0 Cellular roles of Anthrax toxin 3.0 117.0 39.0 -0.075 0.017 1000.0 -1000.0 -0.013 -1000.0 Signaling events mediated by PTP1B 3.0 238.0 76.0 -0.195 0.036 1000.0 -1000.0 -0.033 -1000.0 Presenilin action in Notch and Wnt signaling 3.0 204.0 61.0 -0.168 0.052 1000.0 -1000.0 -0.02 -1000.0 p75(NTR)-mediated signaling 3.0 447.0 125.0 -0.162 0.05 1000.0 -1000.0 -0.048 -1000.0 PDGFR-alpha signaling pathway 3.0 154.0 44.0 -0.142 0.03 1000.0 -1000.0 -0.009 -1000.0 amb2 Integrin signaling 3.0 262.0 82.0 -0.087 0.025 1000.0 -1000.0 -0.038 -1000.0 Ceramide signaling pathway 3.0 279.0 76.0 -0.103 0.038 1000.0 -1000.0 -0.02 -1000.0 TRAIL signaling pathway 3.0 180.0 48.0 -0.044 0.017 1000.0 -1000.0 -0.015 -1000.0 IL1-mediated signaling events 3.0 241.0 62.0 -0.08 0.044 1000.0 -1000.0 -0.048 -1000.0 HIF-2-alpha transcription factor network 3.0 132.0 43.0 -0.073 0.036 1000.0 -1000.0 -0.043 -1000.0 S1P1 pathway 3.0 136.0 36.0 -0.122 0.017 1000.0 -1000.0 -0.042 -1000.0 Signaling mediated by p38-gamma and p38-delta 3.0 48.0 15.0 -0.032 0.018 1000.0 -1000.0 -0.009 -1000.0 Syndecan-3-mediated signaling events 3.0 113.0 35.0 -0.123 0.041 1000.0 -1000.0 -0.019 -1000.0 Integrins in angiogenesis 3.0 288.0 84.0 -0.114 0.033 1000.0 -1000.0 -0.051 -1000.0 HIV-1 Nef: Negative effector of Fas and TNF-alpha 3.0 163.0 45.0 -0.088 0.017 1000.0 -1000.0 -0.055 -1000.0 Canonical Wnt signaling pathway 3.0 203.0 51.0 -0.168 0.1 1000.0 -1000.0 -0.031 -1000.0 IL2 signaling events mediated by STAT5 3.0 69.0 22.0 -0.093 0.023 1000.0 -1000.0 -0.025 -1000.0 Class I PI3K signaling events 3.0 228.0 73.0 -0.052 0.032 1000.0 -1000.0 -0.028 -1000.0 VEGFR1 specific signals 3.0 187.0 56.0 -0.038 0.017 1000.0 -1000.0 -0.021 -1000.0 Regulation of Androgen receptor activity 3.0 257.0 70.0 -0.208 0.024 1000.0 -1000.0 -0.032 -1000.0 Ras signaling in the CD4+ TCR pathway 3.0 59.0 17.0 -0.045 0.025 1000.0 -1000.0 -0.014 -1000.0 Visual signal transduction: Cones 2.0 113.0 38.0 -0.044 0.023 1000.0 -1000.0 -0.008 -1000.0 JNK signaling in the CD4+ TCR pathway 2.0 48.0 17.0 -0.044 0.017 1000.0 -1000.0 -0.013 -1000.0 a4b1 and a4b7 Integrin signaling 2.0 14.0 5.0 -0.01 0.01 1000.0 -1000.0 -0.002 -1000.0 Arf6 signaling events 2.0 140.0 62.0 -0.028 0.018 1000.0 -1000.0 -0.012 -1000.0 Hedgehog signaling events mediated by Gli proteins 2.0 193.0 65.0 -0.402 0.047 1000.0 -1000.0 -0.049 -1000.0 Fc-epsilon receptor I signaling in mast cells 2.0 285.0 97.0 -0.103 0.029 1000.0 -1000.0 -0.043 -1000.0 PLK1 signaling events 2.0 176.0 85.0 -0.042 0.025 1000.0 -1000.0 -0.024 -1000.0 mTOR signaling pathway 2.0 115.0 53.0 -0.038 0.03 1000.0 -1000.0 -0.037 -1000.0 IFN-gamma pathway 2.0 195.0 68.0 -0.063 0.026 1000.0 -1000.0 -0.051 -1000.0 Glucocorticoid receptor regulatory network 2.0 330.0 114.0 -0.251 0.139 1000.0 -1000.0 -0.044 -1000.0 Paxillin-independent events mediated by a4b1 and a4b7 2.0 85.0 37.0 -0.038 0.026 1000.0 -1000.0 -0.015 -1000.0 Signaling events mediated by HDAC Class III 2.0 93.0 40.0 -0.059 0.043 1000.0 -1000.0 -0.01 -1000.0 Reelin signaling pathway 2.0 153.0 56.0 -0.047 0.041 1000.0 -1000.0 -0.045 -1000.0 Signaling events regulated by Ret tyrosine kinase 2.0 170.0 82.0 -0.051 0.024 1000.0 -1000.0 -0.049 -1000.0 ceramide signaling pathway 2.0 140.0 49.0 -0.06 0.02 1000.0 -1000.0 -0.017 -1000.0 RXR and RAR heterodimerization with other nuclear receptor 2.0 107.0 52.0 -0.126 0.043 1000.0 -1000.0 -0.023 -1000.0 Retinoic acid receptors-mediated signaling 2.0 152.0 58.0 -0.108 0.045 1000.0 -1000.0 -0.045 -1000.0 Paxillin-dependent events mediated by a4b1 2.0 72.0 36.0 -0.038 0.035 1000.0 -1000.0 -0.02 -1000.0 IL2 signaling events mediated by PI3K 2.0 163.0 58.0 -0.127 0.019 1000.0 -1000.0 -0.055 -1000.0 Calcium signaling in the CD4+ TCR pathway 2.0 78.0 31.0 -0.095 0.02 1000.0 -1000.0 -0.042 -1000.0 Signaling events mediated by VEGFR1 and VEGFR2 2.0 317.0 125.0 -0.04 0.03 1000.0 -1000.0 -0.059 -1000.0 Stabilization and expansion of the E-cadherin adherens junction 2.0 189.0 74.0 -0.103 0.039 1000.0 -1000.0 -0.053 -1000.0 BCR signaling pathway 2.0 243.0 99.0 -0.065 0.04 1000.0 -1000.0 -0.049 -1000.0 EGFR-dependent Endothelin signaling events 2.0 50.0 21.0 -0.042 0.026 1000.0 -1000.0 -0.04 -1000.0 PDGFR-beta signaling pathway 2.0 204.0 97.0 -0.055 0.044 1000.0 -1000.0 -0.045 -1000.0 Signaling events mediated by PRL 2.0 83.0 34.0 -0.073 0.026 1000.0 -1000.0 -0.016 -1000.0 E-cadherin signaling in keratinocytes 2.0 93.0 43.0 -0.037 0.021 1000.0 -1000.0 -0.015 -1000.0 Aurora B signaling 2.0 153.0 67.0 -0.061 0.021 1000.0 -1000.0 -0.04 -1000.0 Canonical NF-kappaB pathway 1.0 59.0 39.0 -0.036 0.043 1000.0 -1000.0 -0.053 -1000.0 Signaling events mediated by HDAC Class II 1.0 106.0 75.0 -0.099 0.04 1000.0 -1000.0 -0.029 -1000.0 BARD1 signaling events 1.0 95.0 57.0 -0.055 0.041 1000.0 -1000.0 -0.026 -1000.0 Sphingosine 1-phosphate (S1P) pathway 1.0 41.0 28.0 -0.05 0.026 1000.0 -1000.0 -0.011 -1000.0 Lissencephaly gene (LIS1) in neuronal migration and development 1.0 95.0 54.0 -0.085 0.048 1000.0 -1000.0 -0.057 -1000.0 Ephrin A reverse signaling 1.0 8.0 7.0 -0.0 0.019 1000.0 -1000.0 -0.004 -1000.0 Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 1.0 141.0 85.0 -0.144 0.049 1000.0 -1000.0 -0.041 -1000.0 Aurora A signaling 1.0 111.0 60.0 -0.04 0.039 1000.0 -1000.0 -0.007 -1000.0 Arf6 downstream pathway 1.0 56.0 43.0 -0.022 0.026 1000.0 -1000.0 -0.016 -1000.0 EPO signaling pathway 1.0 96.0 55.0 -0.082 0.035 1000.0 -1000.0 -0.043 -1000.0 S1P5 pathway 1.0 24.0 17.0 -0.05 0.017 1000.0 -1000.0 -0.01 -1000.0 Role of Calcineurin-dependent NFAT signaling in lymphocytes 1.0 154.0 83.0 -0.079 0.052 1000.0 -1000.0 -0.023 -1000.0 FoxO family signaling 1.0 79.0 64.0 -0.057 0.061 1000.0 -1000.0 -0.024 -1000.0 Atypical NF-kappaB pathway 1.0 50.0 31.0 -0.038 0.03 1000.0 -1000.0 -0.013 -1000.0 Regulation of p38-alpha and p38-beta 1.0 83.0 54.0 -0.058 0.041 1000.0 -1000.0 -0.035 -1000.0 TCGA08_rtk_signaling 1.0 38.0 26.0 -0.038 0.052 1000.0 -1000.0 -0.005 -1000.0 E-cadherin signaling in the nascent adherens junction 1.0 135.0 76.0 -0.038 0.035 1000.0 -1000.0 -0.048 -1000.0 Regulation of Telomerase 1.0 190.0 102.0 -0.099 0.047 1000.0 -1000.0 -0.066 -1000.0 Insulin Pathway 1.0 136.0 74.0 -0.099 0.054 1000.0 -1000.0 -0.05 -1000.0 S1P3 pathway 1.0 70.0 42.0 -0.048 0.026 1000.0 -1000.0 -0.022 -1000.0 Angiopoietin receptor Tie2-mediated signaling 1.0 127.0 88.0 -0.099 0.045 1000.0 -1000.0 -0.057 -1000.0 Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1.0 54.0 33.0 -0.132 0.049 1000.0 -1000.0 -0.02 -1000.0 Rapid glucocorticoid signaling 1.0 20.0 20.0 -0.006 0.017 1000.0 -1000.0 -0.003 -1000.0 Neurotrophic factor-mediated Trk receptor signaling 1.0 218.0 120.0 -0.065 0.052 1000.0 -1000.0 -0.046 -1000.0 S1P4 pathway 1.0 29.0 25.0 -0.05 0.026 1000.0 -1000.0 -0.013 -1000.0 E-cadherin signaling events 1.0 9.0 5.0 0.002 0.021 1000.0 -1000.0 -0.0 -1000.0 p38 MAPK signaling pathway 1.0 87.0 44.0 -0.04 0.034 1000.0 -1000.0 -0.048 -1000.0 ErbB2/ErbB3 signaling events 0.0 58.0 65.0 -0.042 0.04 1000.0 -1000.0 -0.039 -1000.0 Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0 20.0 23.0 -0.014 0.037 1000.0 -1000.0 -0.016 -1000.0 Nephrin/Neph1 signaling in the kidney podocyte 0.0 32.0 34.0 -0.014 0.04 1000.0 -1000.0 -0.011 -1000.0 ErbB4 signaling events 0.0 64.0 69.0 -0.058 0.05 1000.0 -1000.0 -0.057 -1000.0 Circadian rhythm pathway 0.0 16.0 22.0 -0.024 0.044 1000.0 -1000.0 -0.023 -1000.0 Aurora C signaling 0.0 5.0 7.0 -0.0 0.021 1000.0 -1000.0 -0.006 -1000.0 Insulin-mediated glucose transport 0.0 24.0 32.0 -0.057 0.036 1000.0 -1000.0 -0.012 -1000.0 Class I PI3K signaling events mediated by Akt 0.0 44.0 68.0 -0.057 0.05 1000.0 -1000.0 -0.016 -1000.0 Signaling events mediated by HDAC Class I 0.0 94.0 104.0 -0.052 0.045 1000.0 -1000.0 -0.026 -1000.0 Effects of Botulinum toxin 0.0 15.0 26.0 -0.02 0.036 1000.0 -1000.0 -0.015 -1000.0 Sumoylation by RanBP2 regulates transcriptional repression 0.0 7.0 27.0 -0.006 0.042 1000.0 -1000.0 -0.034 -1000.0 Arf6 trafficking events 0.0 26.0 71.0 -0.032 0.042 1000.0 -1000.0 -0.039 -1000.0 Class IB PI3K non-lipid kinase events 0.0 0.0 3.0 -0.017 0.017 1000.0 -1000.0 -0.003 -1000.0 Arf1 pathway 0.0 2.0 54.0 -0.002 0.037 1000.0 -1000.0 -0.011 -1000.0 Alternative NF-kappaB pathway 0.0 6.0 13.0 -0.0 0.044 1000.0 -1000.0 -0.004 -1000.0 Total 381 24513 7203 -13.8165449518 5.3405760665 131000 -131000 -4.11291721422 -131000