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 24.0 192.0 8.0 -0.321 0.133 1000.0 -1000.0 -0.028 -1000.0 FOXA2 and FOXA3 transcription factor networks 18.0 833.0 46.0 -0.817 0.009 1000.0 -1000.0 -0.124 -1000.0 Signaling events mediated by the Hedgehog family 16.0 883.0 52.0 -0.481 0.24 1000.0 -1000.0 -0.088 -1000.0 IL23-mediated signaling events 10.0 653.0 60.0 -0.473 0.011 1000.0 -1000.0 -0.172 -1000.0 Ephrin A reverse signaling 9.0 68.0 7.0 -0.089 0.0 1000.0 -1000.0 -0.031 -1000.0 Glypican 1 network 9.0 457.0 48.0 -0.295 0.067 1000.0 -1000.0 -0.046 -1000.0 TCGA08_p53 9.0 67.0 7.0 -0.248 0.134 1000.0 -1000.0 -0.018 -1000.0 p75(NTR)-mediated signaling 8.0 1065.0 125.0 -0.265 0.011 1000.0 -1000.0 -0.101 -1000.0 IL4-mediated signaling events 8.0 787.0 91.0 -0.72 0.496 1000.0 -1000.0 -0.177 -1000.0 Signaling mediated by p38-alpha and p38-beta 8.0 352.0 44.0 -0.172 0.011 1000.0 -1000.0 -0.049 -1000.0 Class IB PI3K non-lipid kinase events 8.0 24.0 3.0 -0.073 -1000.0 1000.0 -1000.0 -0.02 -1000.0 Nephrin/Neph1 signaling in the kidney podocyte 7.0 253.0 34.0 -0.149 0.011 1000.0 -1000.0 -0.067 -1000.0 S1P5 pathway 7.0 121.0 17.0 -0.236 0.131 1000.0 -1000.0 -0.058 -1000.0 Ephrin B reverse signaling 7.0 374.0 48.0 -0.173 0.101 1000.0 -1000.0 -0.076 -1000.0 Syndecan-4-mediated signaling events 7.0 480.0 67.0 -0.211 0.035 1000.0 -1000.0 -0.087 -1000.0 TCR signaling in naïve CD8+ T cells 6.0 615.0 93.0 -0.138 0.072 1000.0 -1000.0 -0.085 -1000.0 Glypican 2 network 6.0 24.0 4.0 -0.054 -1000.0 1000.0 -1000.0 -0.039 -1000.0 Wnt signaling 6.0 45.0 7.0 -0.106 -0.015 1000.0 -1000.0 -0.03 -1000.0 Syndecan-1-mediated signaling events 5.0 182.0 34.0 -0.162 0.011 1000.0 -1000.0 -0.073 -1000.0 HIF-1-alpha transcription factor network 5.0 408.0 76.0 -0.324 0.027 1000.0 -1000.0 -0.187 -1000.0 BMP receptor signaling 5.0 478.0 81.0 -0.291 0.031 1000.0 -1000.0 -0.098 -1000.0 amb2 Integrin signaling 5.0 438.0 82.0 -0.176 0.011 1000.0 -1000.0 -0.085 -1000.0 Glucocorticoid receptor regulatory network 5.0 681.0 114.0 -0.626 0.289 1000.0 -1000.0 -0.084 -1000.0 Signaling events regulated by Ret tyrosine kinase 5.0 432.0 82.0 -0.144 0.011 1000.0 -1000.0 -0.09 -1000.0 Endothelins 5.0 516.0 96.0 -0.299 0.018 1000.0 -1000.0 -0.085 -1000.0 LPA receptor mediated events 5.0 555.0 102.0 -0.195 0.03 1000.0 -1000.0 -0.094 -1000.0 Calcineurin-regulated NFAT-dependent transcription in lymphocytes 5.0 378.0 68.0 -0.311 0.083 1000.0 -1000.0 -0.156 -1000.0 Visual signal transduction: Rods 5.0 295.0 52.0 -0.292 0.011 1000.0 -1000.0 -0.088 -1000.0 IL12-mediated signaling events 4.0 425.0 87.0 -0.215 0.039 1000.0 -1000.0 -0.139 -1000.0 Visual signal transduction: Cones 4.0 175.0 38.0 -0.185 0.011 1000.0 -1000.0 -0.064 -1000.0 Osteopontin-mediated events 4.0 173.0 38.0 -0.185 0.012 1000.0 -1000.0 -0.114 -1000.0 IL1-mediated signaling events 4.0 250.0 62.0 -0.187 0.053 1000.0 -1000.0 -0.092 -1000.0 EPHB forward signaling 4.0 412.0 85.0 -0.146 0.116 1000.0 -1000.0 -0.094 -1000.0 Calcium signaling in the CD4+ TCR pathway 4.0 127.0 31.0 -0.249 0.012 1000.0 -1000.0 -0.112 -1000.0 BCR signaling pathway 4.0 456.0 99.0 -0.164 0.011 1000.0 -1000.0 -0.1 -1000.0 EGFR-dependent Endothelin signaling events 4.0 103.0 21.0 -0.138 0.011 1000.0 -1000.0 -0.077 -1000.0 Neurotrophic factor-mediated Trk receptor signaling 4.0 538.0 120.0 -0.387 0.142 1000.0 -1000.0 -0.082 -1000.0 ErbB4 signaling events 3.0 241.0 69.0 -0.235 0.063 1000.0 -1000.0 -0.092 -1000.0 Sphingosine 1-phosphate (S1P) pathway 3.0 105.0 28.0 -0.236 0.011 1000.0 -1000.0 -0.063 -1000.0 Noncanonical Wnt signaling pathway 3.0 100.0 26.0 -0.106 0.011 1000.0 -1000.0 -0.085 -1000.0 Thromboxane A2 receptor signaling 3.0 368.0 105.0 -0.133 0.025 1000.0 -1000.0 -0.075 -1000.0 Syndecan-2-mediated signaling events 3.0 263.0 69.0 -0.162 0.036 1000.0 -1000.0 -0.06 -1000.0 Arf6 signaling events 3.0 237.0 62.0 -0.138 0.015 1000.0 -1000.0 -0.07 -1000.0 Hedgehog signaling events mediated by Gli proteins 3.0 202.0 65.0 -0.444 0.043 1000.0 -1000.0 -0.067 -1000.0 EPO signaling pathway 3.0 207.0 55.0 -0.189 0.011 1000.0 -1000.0 -0.102 -1000.0 RXR and RAR heterodimerization with other nuclear receptor 3.0 176.0 52.0 -0.158 0.022 1000.0 -1000.0 -0.066 -1000.0 S1P1 pathway 3.0 143.0 36.0 -0.11 0.011 1000.0 -1000.0 -0.059 -1000.0 Syndecan-3-mediated signaling events 3.0 111.0 35.0 -0.123 0.011 1000.0 -1000.0 -0.067 -1000.0 Canonical Wnt signaling pathway 3.0 153.0 51.0 -0.174 0.034 1000.0 -1000.0 -0.063 -1000.0 Effects of Botulinum toxin 3.0 97.0 26.0 -0.12 0.015 1000.0 -1000.0 -0.063 -1000.0 IL27-mediated signaling events 3.0 175.0 51.0 -0.198 0.038 1000.0 -1000.0 -0.091 -1000.0 Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 3.0 108.0 33.0 -0.328 0.031 1000.0 -1000.0 -0.073 -1000.0 S1P4 pathway 3.0 99.0 25.0 -0.236 0.016 1000.0 -1000.0 -0.059 -1000.0 LPA4-mediated signaling events 2.0 35.0 12.0 -0.045 0.018 1000.0 -1000.0 -0.021 -1000.0 Caspase cascade in apoptosis 2.0 189.0 74.0 -0.098 0.031 1000.0 -1000.0 -0.058 -1000.0 Coregulation of Androgen receptor activity 2.0 185.0 76.0 -0.387 0.021 1000.0 -1000.0 -0.062 -1000.0 Signaling events mediated by PTP1B 2.0 208.0 76.0 -0.139 0.015 1000.0 -1000.0 -0.085 -1000.0 Presenilin action in Notch and Wnt signaling 2.0 160.0 61.0 -0.173 0.031 1000.0 -1000.0 -0.081 -1000.0 Fc-epsilon receptor I signaling in mast cells 2.0 277.0 97.0 -0.193 0.024 1000.0 -1000.0 -0.101 -1000.0 Paxillin-independent events mediated by a4b1 and a4b7 2.0 106.0 37.0 -0.193 0.011 1000.0 -1000.0 -0.081 -1000.0 Reelin signaling pathway 2.0 147.0 56.0 -0.127 0.018 1000.0 -1000.0 -0.082 -1000.0 FAS signaling pathway (CD95) 2.0 117.0 47.0 -0.117 0.011 1000.0 -1000.0 -0.049 -1000.0 Signaling mediated by p38-gamma and p38-delta 2.0 30.0 15.0 -0.017 0.02 1000.0 -1000.0 -0.035 -1000.0 Retinoic acid receptors-mediated signaling 2.0 127.0 58.0 -0.136 0.015 1000.0 -1000.0 -0.083 -1000.0 IL2 signaling events mediated by PI3K 2.0 121.0 58.0 -0.149 0.024 1000.0 -1000.0 -0.089 -1000.0 Integrins in angiogenesis 2.0 210.0 84.0 -0.187 0.017 1000.0 -1000.0 -0.096 -1000.0 Stabilization and expansion of the E-cadherin adherens junction 2.0 167.0 74.0 -0.207 0.046 1000.0 -1000.0 -0.094 -1000.0 IGF1 pathway 2.0 125.0 57.0 -0.055 0.011 1000.0 -1000.0 -0.1 -1000.0 S1P3 pathway 2.0 101.0 42.0 -0.064 0.017 1000.0 -1000.0 -0.065 -1000.0 Angiopoietin receptor Tie2-mediated signaling 2.0 182.0 88.0 -0.11 0.062 1000.0 -1000.0 -0.117 -1000.0 Regulation of Androgen receptor activity 2.0 174.0 70.0 -0.39 0.024 1000.0 -1000.0 -0.083 -1000.0 ErbB2/ErbB3 signaling events 1.0 125.0 65.0 -0.11 0.039 1000.0 -1000.0 -0.076 -1000.0 Regulation of nuclear SMAD2/3 signaling 1.0 263.0 136.0 -0.265 0.093 1000.0 -1000.0 -0.083 -1000.0 Lissencephaly gene (LIS1) in neuronal migration and development 1.0 66.0 54.0 -0.084 0.02 1000.0 -1000.0 -0.101 -1000.0 JNK signaling in the CD4+ TCR pathway 1.0 29.0 17.0 -0.031 0.024 1000.0 -1000.0 -0.067 -1000.0 a4b1 and a4b7 Integrin signaling 1.0 5.0 5.0 -0.013 0.003 1000.0 -1000.0 -0.041 -1000.0 Cellular roles of Anthrax toxin 1.0 72.0 39.0 -0.071 0.016 1000.0 -1000.0 -0.031 -1000.0 Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 1.0 156.0 85.0 -0.058 0.029 1000.0 -1000.0 -0.084 -1000.0 Arf6 downstream pathway 1.0 75.0 43.0 -0.082 0.045 1000.0 -1000.0 -0.047 -1000.0 IFN-gamma pathway 1.0 89.0 68.0 -0.094 0.036 1000.0 -1000.0 -0.11 -1000.0 Nectin adhesion pathway 1.0 114.0 63.0 -0.067 0.021 1000.0 -1000.0 -0.075 -1000.0 Ceramide signaling pathway 1.0 108.0 76.0 -0.133 0.029 1000.0 -1000.0 -0.07 -1000.0 Signaling events mediated by HDAC Class III 1.0 69.0 40.0 -0.186 0.02 1000.0 -1000.0 -0.045 -1000.0 HIV-1 Nef: Negative effector of Fas and TNF-alpha 1.0 78.0 45.0 -0.092 0.02 1000.0 -1000.0 -0.093 -1000.0 Regulation of p38-alpha and p38-beta 1.0 86.0 54.0 -0.139 0.011 1000.0 -1000.0 -0.064 -1000.0 Nongenotropic Androgen signaling 1.0 83.0 52.0 -0.062 0.035 1000.0 -1000.0 -0.064 -1000.0 TCGA08_rtk_signaling 1.0 28.0 26.0 -0.04 0.035 1000.0 -1000.0 -0.027 -1000.0 IL6-mediated signaling events 1.0 107.0 75.0 -0.086 0.056 1000.0 -1000.0 -0.097 -1000.0 E-cadherin signaling in the nascent adherens junction 1.0 84.0 76.0 -0.083 0.05 1000.0 -1000.0 -0.082 -1000.0 IL2 signaling events mediated by STAT5 1.0 32.0 22.0 -0.065 0.02 1000.0 -1000.0 -0.063 -1000.0 Class I PI3K signaling events 1.0 127.0 73.0 -0.139 0.011 1000.0 -1000.0 -0.074 -1000.0 Regulation of Telomerase 1.0 148.0 102.0 -0.138 0.039 1000.0 -1000.0 -0.111 -1000.0 Plasma membrane estrogen receptor signaling 1.0 152.0 86.0 -0.063 0.016 1000.0 -1000.0 -0.089 -1000.0 PDGFR-beta signaling pathway 1.0 107.0 97.0 -0.1 0.053 1000.0 -1000.0 -0.099 -1000.0 Signaling events mediated by PRL 1.0 55.0 34.0 -0.166 0.028 1000.0 -1000.0 -0.063 -1000.0 E-cadherin signaling in keratinocytes 1.0 47.0 43.0 -0.04 0.03 1000.0 -1000.0 -0.076 -1000.0 FOXM1 transcription factor network 1.0 54.0 51.0 -0.335 0.164 1000.0 -1000.0 -0.195 -1000.0 E-cadherin signaling events 1.0 5.0 5.0 -0.017 0.011 1000.0 -1000.0 -0.044 -1000.0 Signaling events mediated by Stem cell factor receptor (c-Kit) 1.0 128.0 78.0 -0.191 0.031 1000.0 -1000.0 -0.073 -1000.0 Ras signaling in the CD4+ TCR pathway 1.0 17.0 17.0 -0.017 0.03 1000.0 -1000.0 -0.052 -1000.0 Aurora B signaling 1.0 70.0 67.0 -0.132 0.031 1000.0 -1000.0 -0.077 -1000.0 Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0 0.0 23.0 0.0 0.041 1000.0 -1000.0 -0.072 -1000.0 Canonical NF-kappaB pathway 0.0 30.0 39.0 -0.071 0.063 1000.0 -1000.0 -0.094 -1000.0 Signaling events mediated by HDAC Class II 0.0 36.0 75.0 -0.037 0.03 1000.0 -1000.0 -0.067 -1000.0 BARD1 signaling events 0.0 21.0 57.0 -0.01 0.054 1000.0 -1000.0 -0.067 -1000.0 PLK2 and PLK4 events 0.0 0.0 3.0 0.011 0.02 1000.0 -1000.0 -0.023 -1000.0 Circadian rhythm pathway 0.0 21.0 22.0 -0.057 0.034 1000.0 -1000.0 -0.072 -1000.0 Aurora A signaling 0.0 38.0 60.0 -0.085 0.029 1000.0 -1000.0 -0.061 -1000.0 Aurora C signaling 0.0 4.0 7.0 -0.015 0.011 1000.0 -1000.0 -0.046 -1000.0 PLK1 signaling events 0.0 16.0 85.0 -0.01 0.022 1000.0 -1000.0 -0.055 -1000.0 Insulin-mediated glucose transport 0.0 13.0 32.0 -0.091 0.028 1000.0 -1000.0 -0.077 -1000.0 PDGFR-alpha signaling pathway 0.0 13.0 44.0 -0.03 0.028 1000.0 -1000.0 -0.064 -1000.0 mTOR signaling pathway 0.0 3.0 53.0 -0.019 0.022 1000.0 -1000.0 -0.062 -1000.0 Class I PI3K signaling events mediated by Akt 0.0 43.0 68.0 -0.091 0.035 1000.0 -1000.0 -0.061 -1000.0 TRAIL signaling pathway 0.0 36.0 48.0 -0.035 0.043 1000.0 -1000.0 -0.075 -1000.0 ceramide signaling pathway 0.0 40.0 49.0 -0.082 0.021 1000.0 -1000.0 -0.059 -1000.0 HIF-2-alpha transcription factor network 0.0 34.0 43.0 -0.078 0.036 1000.0 -1000.0 -0.104 -1000.0 Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0 67.0 83.0 -0.139 0.054 1000.0 -1000.0 -0.098 -1000.0 Signaling events mediated by HDAC Class I 0.0 65.0 104.0 -0.096 0.042 1000.0 -1000.0 -0.07 -1000.0 FoxO family signaling 0.0 26.0 64.0 -0.108 0.123 1000.0 -1000.0 -0.091 -1000.0 Paxillin-dependent events mediated by a4b1 0.0 23.0 36.0 -0.025 0.02 1000.0 -1000.0 -0.075 -1000.0 Atypical NF-kappaB pathway 0.0 13.0 31.0 -0.025 0.026 1000.0 -1000.0 -0.072 -1000.0 Signaling events mediated by VEGFR1 and VEGFR2 0.0 108.0 125.0 -0.033 0.068 1000.0 -1000.0 -0.098 -1000.0 Sumoylation by RanBP2 regulates transcriptional repression 0.0 1.0 27.0 -0.004 0.025 1000.0 -1000.0 -0.06 -1000.0 Arf6 trafficking events 0.0 38.0 71.0 -0.055 0.038 1000.0 -1000.0 -0.068 -1000.0 Insulin Pathway 0.0 59.0 74.0 -0.11 0.031 1000.0 -1000.0 -0.085 -1000.0 VEGFR1 specific signals 0.0 11.0 56.0 -0.013 0.047 1000.0 -1000.0 -0.081 -1000.0 Rapid glucocorticoid signaling 0.0 16.0 20.0 -0.018 0.011 1000.0 -1000.0 -0.043 -1000.0 p38 MAPK signaling pathway 0.0 32.0 44.0 -0.094 0.025 1000.0 -1000.0 -0.074 -1000.0 Arf1 pathway 0.0 7.0 54.0 -0.018 0.024 1000.0 -1000.0 -0.045 -1000.0 Alternative NF-kappaB pathway 0.0 4.0 13.0 -0.008 0.011 1000.0 -1000.0 -0.075 -1000.0 Total 373 23158 7203 -20.1138103351 -1994.72165531 131000 -131000 -10.116106 -131000