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 53.0 429.0 8.0 -0.278 0.158 1000.0 -1000.0 -0.013 -1000.0 HIF-1-alpha transcription factor network 34.0 2615.0 76.0 -0.557 0.02 1000.0 -1000.0 -0.071 -1000.0 Wnt signaling 26.0 188.0 7.0 -0.204 -0.006 1000.0 -1000.0 -0.022 -1000.0 IL23-mediated signaling events 26.0 1594.0 60.0 -0.603 0.016 1000.0 -1000.0 -0.146 -1000.0 TCGA08_p53 23.0 167.0 7.0 -0.216 0.123 1000.0 -1000.0 -0.014 -1000.0 IL4-mediated signaling events 22.0 2023.0 91.0 -0.63 0.568 1000.0 -1000.0 -0.124 -1000.0 Osteopontin-mediated events 21.0 823.0 38.0 -0.237 0.018 1000.0 -1000.0 -0.095 -1000.0 Noncanonical Wnt signaling pathway 21.0 562.0 26.0 -0.204 0.018 1000.0 -1000.0 -0.041 -1000.0 Signaling mediated by p38-alpha and p38-beta 21.0 924.0 44.0 -0.257 0.018 1000.0 -1000.0 -0.018 -1000.0 Calcineurin-regulated NFAT-dependent transcription in lymphocytes 21.0 1465.0 68.0 -0.578 0.216 1000.0 -1000.0 -0.095 -1000.0 Syndecan-1-mediated signaling events 19.0 650.0 34.0 -0.236 0.018 1000.0 -1000.0 -0.04 -1000.0 Nectin adhesion pathway 19.0 1200.0 63.0 -0.208 0.028 1000.0 -1000.0 -0.074 -1000.0 IL1-mediated signaling events 19.0 1183.0 62.0 -0.288 0.061 1000.0 -1000.0 -0.084 -1000.0 Endothelins 19.0 1863.0 96.0 -0.313 0.018 1000.0 -1000.0 -0.067 -1000.0 Glucocorticoid receptor regulatory network 18.0 2143.0 114.0 -0.59 0.341 1000.0 -1000.0 -0.072 -1000.0 Signaling events mediated by the Hedgehog family 17.0 913.0 52.0 -0.302 0.1 1000.0 -1000.0 -0.039 -1000.0 Glypican 1 network 17.0 855.0 48.0 -0.122 0.078 1000.0 -1000.0 -0.034 -1000.0 Fc-epsilon receptor I signaling in mast cells 17.0 1690.0 97.0 -0.198 0.044 1000.0 -1000.0 -0.09 -1000.0 BCR signaling pathway 17.0 1742.0 99.0 -0.258 0.028 1000.0 -1000.0 -0.09 -1000.0 Signaling events mediated by Stem cell factor receptor (c-Kit) 17.0 1387.0 78.0 -0.231 0.101 1000.0 -1000.0 -0.055 -1000.0 IL12-mediated signaling events 16.0 1410.0 87.0 -0.297 0.049 1000.0 -1000.0 -0.1 -1000.0 Ephrin B reverse signaling 16.0 795.0 48.0 -0.134 0.119 1000.0 -1000.0 -0.073 -1000.0 Calcium signaling in the CD4+ TCR pathway 16.0 526.0 31.0 -0.336 0.029 1000.0 -1000.0 -0.064 -1000.0 EGFR-dependent Endothelin signaling events 16.0 336.0 21.0 -0.209 0.027 1000.0 -1000.0 -0.082 -1000.0 Syndecan-2-mediated signaling events 15.0 1088.0 69.0 -0.24 0.018 1000.0 -1000.0 -0.032 -1000.0 IGF1 pathway 15.0 864.0 57.0 -0.133 0.063 1000.0 -1000.0 -0.092 -1000.0 Thromboxane A2 receptor signaling 14.0 1512.0 105.0 -0.179 0.046 1000.0 -1000.0 -0.064 -1000.0 TCR signaling in naïve CD8+ T cells 14.0 1325.0 93.0 -0.137 0.027 1000.0 -1000.0 -0.075 -1000.0 EPHB forward signaling 14.0 1244.0 85.0 -0.155 0.144 1000.0 -1000.0 -0.095 -1000.0 Arf6 signaling events 13.0 829.0 62.0 -0.158 0.027 1000.0 -1000.0 -0.03 -1000.0 BMP receptor signaling 13.0 1101.0 81.0 -0.312 0.041 1000.0 -1000.0 -0.097 -1000.0 amb2 Integrin signaling 13.0 1143.0 82.0 -0.189 0.018 1000.0 -1000.0 -0.085 -1000.0 Syndecan-4-mediated signaling events 13.0 889.0 67.0 -0.123 0.018 1000.0 -1000.0 -0.1 -1000.0 PLK2 and PLK4 events 12.0 36.0 3.0 -0.051 0.015 1000.0 -1000.0 -0.016 -1000.0 S1P1 pathway 12.0 434.0 36.0 -0.24 0.018 1000.0 -1000.0 -0.071 -1000.0 FAS signaling pathway (CD95) 12.0 572.0 47.0 -0.212 0.036 1000.0 -1000.0 -0.04 -1000.0 IL27-mediated signaling events 12.0 635.0 51.0 -0.307 0.151 1000.0 -1000.0 -0.093 -1000.0 FOXM1 transcription factor network 12.0 638.0 51.0 -0.324 0.073 1000.0 -1000.0 -0.146 -1000.0 FOXA2 and FOXA3 transcription factor networks 11.0 518.0 46.0 -0.15 0.032 1000.0 -1000.0 -0.03 -1000.0 PDGFR-alpha signaling pathway 11.0 499.0 44.0 -0.195 0.033 1000.0 -1000.0 -0.067 -1000.0 IFN-gamma pathway 11.0 748.0 68.0 -0.214 0.021 1000.0 -1000.0 -0.087 -1000.0 Syndecan-3-mediated signaling events 11.0 405.0 35.0 -0.26 0.031 1000.0 -1000.0 -0.042 -1000.0 LPA receptor mediated events 11.0 1187.0 102.0 -0.246 0.036 1000.0 -1000.0 -0.074 -1000.0 TRAIL signaling pathway 10.0 484.0 48.0 -0.087 0.018 1000.0 -1000.0 -0.074 -1000.0 HIF-2-alpha transcription factor network 10.0 442.0 43.0 -0.157 0.029 1000.0 -1000.0 -0.065 -1000.0 Glypican 2 network 10.0 42.0 4.0 -0.037 -0.0 1000.0 -1000.0 -0.007 -1000.0 IL6-mediated signaling events 10.0 798.0 75.0 -0.148 0.04 1000.0 -1000.0 -0.074 -1000.0 E-cadherin signaling events 10.0 54.0 5.0 -0.034 0.008 1000.0 -1000.0 -0.012 -1000.0 Signaling events mediated by PTP1B 9.0 698.0 76.0 -0.163 0.074 1000.0 -1000.0 -0.08 -1000.0 p75(NTR)-mediated signaling 9.0 1230.0 125.0 -0.271 0.031 1000.0 -1000.0 -0.096 -1000.0 Integrins in angiogenesis 9.0 810.0 84.0 -0.216 0.027 1000.0 -1000.0 -0.096 -1000.0 Canonical Wnt signaling pathway 9.0 476.0 51.0 -0.277 0.08 1000.0 -1000.0 -0.051 -1000.0 Nongenotropic Androgen signaling 9.0 472.0 52.0 -0.078 0.024 1000.0 -1000.0 -0.062 -1000.0 Stabilization and expansion of the E-cadherin adherens junction 9.0 685.0 74.0 -0.172 0.035 1000.0 -1000.0 -0.087 -1000.0 E-cadherin signaling in keratinocytes 9.0 403.0 43.0 -0.093 0.018 1000.0 -1000.0 -0.066 -1000.0 Caspase cascade in apoptosis 8.0 605.0 74.0 -0.095 0.048 1000.0 -1000.0 -0.031 -1000.0 Coregulation of Androgen receptor activity 8.0 632.0 76.0 -0.291 0.043 1000.0 -1000.0 -0.04 -1000.0 Visual signal transduction: Cones 8.0 309.0 38.0 -0.103 0.021 1000.0 -1000.0 -0.068 -1000.0 Presenilin action in Notch and Wnt signaling 8.0 546.0 61.0 -0.277 0.035 1000.0 -1000.0 -0.076 -1000.0 Reelin signaling pathway 8.0 474.0 56.0 -0.153 0.041 1000.0 -1000.0 -0.081 -1000.0 HIV-1 Nef: Negative effector of Fas and TNF-alpha 8.0 392.0 45.0 -0.14 0.028 1000.0 -1000.0 -0.093 -1000.0 Plasma membrane estrogen receptor signaling 8.0 707.0 86.0 -0.12 0.035 1000.0 -1000.0 -0.083 -1000.0 Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8.0 280.0 33.0 -0.29 0.037 1000.0 -1000.0 -0.036 -1000.0 Regulation of nuclear SMAD2/3 signaling 7.0 983.0 136.0 -0.321 0.118 1000.0 -1000.0 -0.061 -1000.0 ErbB4 signaling events 7.0 548.0 69.0 -0.147 0.036 1000.0 -1000.0 -0.083 -1000.0 Sphingosine 1-phosphate (S1P) pathway 7.0 218.0 28.0 -0.097 0.022 1000.0 -1000.0 -0.021 -1000.0 Ephrin A reverse signaling 7.0 51.0 7.0 -0.017 0.015 1000.0 -1000.0 -0.013 -1000.0 Cellular roles of Anthrax toxin 7.0 294.0 39.0 -0.081 0.018 1000.0 -1000.0 -0.024 -1000.0 Arf6 downstream pathway 7.0 333.0 43.0 -0.049 0.023 1000.0 -1000.0 -0.039 -1000.0 Signaling events mediated by VEGFR1 and VEGFR2 7.0 876.0 125.0 -0.092 0.04 1000.0 -1000.0 -0.106 -1000.0 IL2 signaling events mediated by STAT5 7.0 170.0 22.0 -0.112 0.032 1000.0 -1000.0 -0.037 -1000.0 VEGFR1 specific signals 7.0 437.0 56.0 -0.086 0.018 1000.0 -1000.0 -0.041 -1000.0 Neurotrophic factor-mediated Trk receptor signaling 7.0 898.0 120.0 -0.239 0.107 1000.0 -1000.0 -0.081 -1000.0 Visual signal transduction: Rods 7.0 405.0 52.0 -0.153 0.023 1000.0 -1000.0 -0.089 -1000.0 Ras signaling in the CD4+ TCR pathway 7.0 132.0 17.0 -0.059 0.016 1000.0 -1000.0 -0.042 -1000.0 Hedgehog signaling events mediated by Gli proteins 6.0 416.0 65.0 -0.253 0.048 1000.0 -1000.0 -0.067 -1000.0 Ceramide signaling pathway 6.0 517.0 76.0 -0.126 0.052 1000.0 -1000.0 -0.042 -1000.0 Signaling mediated by p38-gamma and p38-delta 6.0 97.0 15.0 -0.048 0.018 1000.0 -1000.0 -0.021 -1000.0 IL2 signaling events mediated by PI3K 6.0 395.0 58.0 -0.13 0.021 1000.0 -1000.0 -0.078 -1000.0 TCGA08_rtk_signaling 6.0 163.0 26.0 -0.093 0.032 1000.0 -1000.0 -0.021 -1000.0 Regulation of Telomerase 6.0 613.0 102.0 -0.206 0.057 1000.0 -1000.0 -0.097 -1000.0 Regulation of Androgen receptor activity 6.0 444.0 70.0 -0.403 0.047 1000.0 -1000.0 -0.076 -1000.0 Lissencephaly gene (LIS1) in neuronal migration and development 5.0 274.0 54.0 -0.107 0.038 1000.0 -1000.0 -0.089 -1000.0 a4b1 and a4b7 Integrin signaling 5.0 29.0 5.0 -0.013 0.018 1000.0 -1000.0 -0.019 -1000.0 Signaling events mediated by HDAC Class III 5.0 220.0 40.0 -0.129 0.034 1000.0 -1000.0 -0.033 -1000.0 RXR and RAR heterodimerization with other nuclear receptor 5.0 299.0 52.0 -0.079 0.048 1000.0 -1000.0 -0.034 -1000.0 Retinoic acid receptors-mediated signaling 5.0 295.0 58.0 -0.106 0.036 1000.0 -1000.0 -0.08 -1000.0 E-cadherin signaling in the nascent adherens junction 5.0 400.0 76.0 -0.089 0.031 1000.0 -1000.0 -0.085 -1000.0 Class I PI3K signaling events 5.0 422.0 73.0 -0.052 0.033 1000.0 -1000.0 -0.059 -1000.0 Insulin Pathway 5.0 417.0 74.0 -0.109 0.057 1000.0 -1000.0 -0.087 -1000.0 Angiopoietin receptor Tie2-mediated signaling 5.0 441.0 88.0 -0.109 0.056 1000.0 -1000.0 -0.105 -1000.0 JNK signaling in the CD4+ TCR pathway 4.0 76.0 17.0 -0.058 0.021 1000.0 -1000.0 -0.037 -1000.0 Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 4.0 350.0 85.0 -0.107 0.046 1000.0 -1000.0 -0.081 -1000.0 Paxillin-independent events mediated by a4b1 and a4b7 4.0 183.0 37.0 -0.053 0.027 1000.0 -1000.0 -0.053 -1000.0 ceramide signaling pathway 4.0 221.0 49.0 -0.095 0.033 1000.0 -1000.0 -0.043 -1000.0 FoxO family signaling 4.0 279.0 64.0 -0.145 0.11 1000.0 -1000.0 -0.069 -1000.0 Paxillin-dependent events mediated by a4b1 4.0 157.0 36.0 -0.053 0.037 1000.0 -1000.0 -0.074 -1000.0 Atypical NF-kappaB pathway 4.0 146.0 31.0 -0.039 0.034 1000.0 -1000.0 -0.025 -1000.0 S1P3 pathway 4.0 200.0 42.0 -0.05 0.022 1000.0 -1000.0 -0.029 -1000.0 PDGFR-beta signaling pathway 4.0 398.0 97.0 -0.087 0.048 1000.0 -1000.0 -0.083 -1000.0 Signaling events mediated by PRL 4.0 158.0 34.0 -0.054 0.027 1000.0 -1000.0 -0.027 -1000.0 Class IB PI3K non-lipid kinase events 4.0 12.0 3.0 -0.005 0.005 1000.0 -1000.0 -0.014 -1000.0 Aurora B signaling 4.0 306.0 67.0 -0.184 0.033 1000.0 -1000.0 -0.073 -1000.0 ErbB2/ErbB3 signaling events 3.0 238.0 65.0 -0.064 0.039 1000.0 -1000.0 -0.076 -1000.0 Aurora A signaling 3.0 224.0 60.0 -0.046 0.04 1000.0 -1000.0 -0.027 -1000.0 mTOR signaling pathway 3.0 211.0 53.0 -0.043 0.035 1000.0 -1000.0 -0.064 -1000.0 Signaling events regulated by Ret tyrosine kinase 3.0 318.0 82.0 -0.118 0.036 1000.0 -1000.0 -0.086 -1000.0 Role of Calcineurin-dependent NFAT signaling in lymphocytes 3.0 269.0 83.0 -0.076 0.056 1000.0 -1000.0 -0.082 -1000.0 Regulation of p38-alpha and p38-beta 3.0 186.0 54.0 -0.039 0.039 1000.0 -1000.0 -0.06 -1000.0 Effects of Botulinum toxin 3.0 101.0 26.0 -0.067 0.02 1000.0 -1000.0 -0.064 -1000.0 Arf6 trafficking events 3.0 263.0 71.0 -0.045 0.042 1000.0 -1000.0 -0.07 -1000.0 p38 MAPK signaling pathway 3.0 152.0 44.0 -0.023 0.031 1000.0 -1000.0 -0.07 -1000.0 Canonical NF-kappaB pathway 2.0 111.0 39.0 -0.063 0.074 1000.0 -1000.0 -0.079 -1000.0 Circadian rhythm pathway 2.0 53.0 22.0 -0.016 0.04 1000.0 -1000.0 -0.038 -1000.0 EPO signaling pathway 2.0 144.0 55.0 -0.044 0.045 1000.0 -1000.0 -0.086 -1000.0 PLK1 signaling events 2.0 177.0 85.0 -0.032 0.042 1000.0 -1000.0 -0.051 -1000.0 Insulin-mediated glucose transport 2.0 80.0 32.0 -0.057 0.03 1000.0 -1000.0 -0.033 -1000.0 Class I PI3K signaling events mediated by Akt 2.0 171.0 68.0 -0.057 0.059 1000.0 -1000.0 -0.058 -1000.0 S1P5 pathway 2.0 38.0 17.0 -0.032 0.018 1000.0 -1000.0 -0.019 -1000.0 Rapid glucocorticoid signaling 2.0 55.0 20.0 -0.035 0.025 1000.0 -1000.0 -0.02 -1000.0 S1P4 pathway 2.0 54.0 25.0 -0.032 0.027 1000.0 -1000.0 -0.024 -1000.0 Alternative NF-kappaB pathway 2.0 30.0 13.0 -0.004 0.036 1000.0 -1000.0 -0.023 -1000.0 LPA4-mediated signaling events 1.0 16.0 12.0 -0.038 0.025 1000.0 -1000.0 -0.029 -1000.0 Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1.0 35.0 23.0 -0.003 0.037 1000.0 -1000.0 -0.041 -1000.0 Signaling events mediated by HDAC Class II 1.0 140.0 75.0 -0.05 0.043 1000.0 -1000.0 -0.05 -1000.0 BARD1 signaling events 1.0 105.0 57.0 -0.027 0.051 1000.0 -1000.0 -0.051 -1000.0 Signaling events mediated by HDAC Class I 1.0 183.0 104.0 -0.037 0.065 1000.0 -1000.0 -0.066 -1000.0 Nephrin/Neph1 signaling in the kidney podocyte 0.0 26.0 34.0 -0.018 0.04 1000.0 -1000.0 -0.04 -1000.0 Aurora C signaling 0.0 5.0 7.0 -0.002 0.028 1000.0 -1000.0 -0.031 -1000.0 Sumoylation by RanBP2 regulates transcriptional repression 0.0 20.0 27.0 -0.006 0.042 1000.0 -1000.0 -0.057 -1000.0 Arf1 pathway 0.0 39.0 54.0 -0.007 0.034 1000.0 -1000.0 -0.039 -1000.0 Total 1198 70406 7203 -20.0286431398 6.34891823677 131000 -131000 -7.88994948205 -131000