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 43.0 350.0 8.0 -0.279 0.148 1000.0 -1000.0 -0.018 -1000.0 Syndecan-1-mediated signaling events 21.0 721.0 34.0 -0.239 0.012 1000.0 -1000.0 -0.051 -1000.0 IL23-mediated signaling events 21.0 1318.0 60.0 -0.618 0.012 1000.0 -1000.0 -0.147 -1000.0 IL4-mediated signaling events 19.0 1742.0 91.0 -0.662 0.586 1000.0 -1000.0 -0.142 -1000.0 Wnt signaling 19.0 137.0 7.0 -0.145 0.007 1000.0 -1000.0 -0.031 -1000.0 TCGA08_p53 16.0 114.0 7.0 -0.213 0.108 1000.0 -1000.0 -0.008 -1000.0 IL12-mediated signaling events 15.0 1324.0 87.0 -0.344 0.077 1000.0 -1000.0 -0.109 -1000.0 Signaling events mediated by the Hedgehog family 15.0 822.0 52.0 -0.162 0.156 1000.0 -1000.0 -0.05 -1000.0 TCR signaling in naïve CD8+ T cells 15.0 1425.0 93.0 -0.195 0.096 1000.0 -1000.0 -0.08 -1000.0 Glypican 2 network 15.0 63.0 4.0 -0.06 -0.056 1000.0 -1000.0 -0.013 -1000.0 Noncanonical Wnt signaling pathway 13.0 341.0 26.0 -0.145 0.012 1000.0 -1000.0 -0.057 -1000.0 amb2 Integrin signaling 13.0 1069.0 82.0 -0.178 0.015 1000.0 -1000.0 -0.076 -1000.0 Signaling mediated by p38-alpha and p38-beta 13.0 602.0 44.0 -0.141 0.012 1000.0 -1000.0 -0.047 -1000.0 Syndecan-4-mediated signaling events 13.0 931.0 67.0 -0.251 0.03 1000.0 -1000.0 -0.089 -1000.0 HIF-1-alpha transcription factor network 12.0 935.0 76.0 -0.413 0.02 1000.0 -1000.0 -0.135 -1000.0 BMP receptor signaling 12.0 1028.0 81.0 -0.276 0.031 1000.0 -1000.0 -0.09 -1000.0 Glucocorticoid receptor regulatory network 12.0 1467.0 114.0 -0.641 0.353 1000.0 -1000.0 -0.069 -1000.0 Calcineurin-regulated NFAT-dependent transcription in lymphocytes 12.0 816.0 68.0 -0.319 0.114 1000.0 -1000.0 -0.121 -1000.0 Glypican 1 network 11.0 539.0 48.0 -0.218 0.016 1000.0 -1000.0 -0.03 -1000.0 BCR signaling pathway 11.0 1120.0 99.0 -0.222 0.014 1000.0 -1000.0 -0.08 -1000.0 p75(NTR)-mediated signaling 10.0 1350.0 125.0 -0.188 0.037 1000.0 -1000.0 -0.089 -1000.0 Reelin signaling pathway 10.0 615.0 56.0 -0.162 0.03 1000.0 -1000.0 -0.071 -1000.0 Caspase cascade in apoptosis 9.0 694.0 74.0 -0.124 0.063 1000.0 -1000.0 -0.039 -1000.0 Ephrin A reverse signaling 9.0 63.0 7.0 -0.027 -0.0 1000.0 -1000.0 -0.015 -1000.0 Thromboxane A2 receptor signaling 9.0 968.0 105.0 -0.1 0.029 1000.0 -1000.0 -0.061 -1000.0 Signaling events regulated by Ret tyrosine kinase 9.0 790.0 82.0 -0.114 0.012 1000.0 -1000.0 -0.077 -1000.0 Class IB PI3K non-lipid kinase events 9.0 27.0 3.0 -0.039 -1000.0 1000.0 -1000.0 -0.012 -1000.0 IL1-mediated signaling events 8.0 537.0 62.0 -0.181 0.058 1000.0 -1000.0 -0.086 -1000.0 Endothelins 8.0 851.0 96.0 -0.147 0.015 1000.0 -1000.0 -0.083 -1000.0 Calcium signaling in the CD4+ TCR pathway 8.0 263.0 31.0 -0.215 0.012 1000.0 -1000.0 -0.088 -1000.0 IL27-mediated signaling events 8.0 419.0 51.0 -0.322 0.055 1000.0 -1000.0 -0.069 -1000.0 LPA receptor mediated events 8.0 822.0 102.0 -0.148 0.023 1000.0 -1000.0 -0.082 -1000.0 IGF1 pathway 8.0 501.0 57.0 -0.117 0.021 1000.0 -1000.0 -0.079 -1000.0 Visual signal transduction: Rods 8.0 467.0 52.0 -0.196 0.012 1000.0 -1000.0 -0.071 -1000.0 Signaling events mediated by Stem cell factor receptor (c-Kit) 8.0 672.0 78.0 -0.11 0.056 1000.0 -1000.0 -0.074 -1000.0 Coregulation of Androgen receptor activity 7.0 558.0 76.0 -0.329 0.022 1000.0 -1000.0 -0.047 -1000.0 Nephrin/Neph1 signaling in the kidney podocyte 7.0 261.0 34.0 -0.054 0.012 1000.0 -1000.0 -0.044 -1000.0 ErbB4 signaling events 7.0 494.0 69.0 -0.201 0.049 1000.0 -1000.0 -0.081 -1000.0 Osteopontin-mediated events 7.0 292.0 38.0 -0.086 0.012 1000.0 -1000.0 -0.093 -1000.0 JNK signaling in the CD4+ TCR pathway 7.0 122.0 17.0 -0.064 0.012 1000.0 -1000.0 -0.035 -1000.0 Integrins in angiogenesis 7.0 666.0 84.0 -0.173 0.019 1000.0 -1000.0 -0.074 -1000.0 EPHB forward signaling 7.0 679.0 85.0 -0.09 0.078 1000.0 -1000.0 -0.076 -1000.0 Nongenotropic Androgen signaling 7.0 414.0 52.0 -0.169 0.021 1000.0 -1000.0 -0.048 -1000.0 EGFR-dependent Endothelin signaling events 7.0 162.0 21.0 -0.083 0.018 1000.0 -1000.0 -0.054 -1000.0 Rapid glucocorticoid signaling 7.0 151.0 20.0 -0.179 0.012 1000.0 -1000.0 -0.017 -1000.0 Neurotrophic factor-mediated Trk receptor signaling 7.0 847.0 120.0 -0.179 0.134 1000.0 -1000.0 -0.073 -1000.0 Syndecan-2-mediated signaling events 6.0 423.0 69.0 -0.142 0.034 1000.0 -1000.0 -0.034 -1000.0 Arf6 signaling events 6.0 410.0 62.0 -0.094 0.012 1000.0 -1000.0 -0.052 -1000.0 Fc-epsilon receptor I signaling in mast cells 6.0 670.0 97.0 -0.118 0.027 1000.0 -1000.0 -0.085 -1000.0 S1P5 pathway 6.0 102.0 17.0 -0.087 0.071 1000.0 -1000.0 -0.032 -1000.0 Ephrin B reverse signaling 6.0 303.0 48.0 -0.073 0.043 1000.0 -1000.0 -0.064 -1000.0 IL6-mediated signaling events 6.0 474.0 75.0 -0.124 0.057 1000.0 -1000.0 -0.082 -1000.0 LPA4-mediated signaling events 5.0 63.0 12.0 -0.071 0.018 1000.0 -1000.0 -0.022 -1000.0 ErbB2/ErbB3 signaling events 5.0 328.0 65.0 -0.128 0.026 1000.0 -1000.0 -0.065 -1000.0 Sphingosine 1-phosphate (S1P) pathway 5.0 151.0 28.0 -0.087 0.016 1000.0 -1000.0 -0.03 -1000.0 Signaling events mediated by PTP1B 5.0 393.0 76.0 -0.106 0.016 1000.0 -1000.0 -0.073 -1000.0 PDGFR-alpha signaling pathway 5.0 245.0 44.0 -0.052 0.02 1000.0 -1000.0 -0.053 -1000.0 Nectin adhesion pathway 5.0 374.0 63.0 -0.069 0.022 1000.0 -1000.0 -0.063 -1000.0 Syndecan-3-mediated signaling events 5.0 189.0 35.0 -0.199 0.037 1000.0 -1000.0 -0.045 -1000.0 Stabilization and expansion of the E-cadherin adherens junction 5.0 391.0 74.0 -0.111 0.043 1000.0 -1000.0 -0.082 -1000.0 Angiopoietin receptor Tie2-mediated signaling 5.0 501.0 88.0 -0.112 0.035 1000.0 -1000.0 -0.117 -1000.0 Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 5.0 166.0 33.0 -0.287 0.037 1000.0 -1000.0 -0.046 -1000.0 FOXM1 transcription factor network 5.0 258.0 51.0 -0.291 0.112 1000.0 -1000.0 -0.17 -1000.0 Ras signaling in the CD4+ TCR pathway 5.0 100.0 17.0 -0.063 0.023 1000.0 -1000.0 -0.03 -1000.0 Regulation of nuclear SMAD2/3 signaling 4.0 604.0 136.0 -0.233 0.063 1000.0 -1000.0 -0.071 -1000.0 Visual signal transduction: Cones 4.0 184.0 38.0 -0.053 0.012 1000.0 -1000.0 -0.051 -1000.0 Lissencephaly gene (LIS1) in neuronal migration and development 4.0 267.0 54.0 -0.162 0.025 1000.0 -1000.0 -0.087 -1000.0 a4b1 and a4b7 Integrin signaling 4.0 22.0 5.0 -0.014 0.005 1000.0 -1000.0 -0.015 -1000.0 Cellular roles of Anthrax toxin 4.0 191.0 39.0 -0.068 0.013 1000.0 -1000.0 -0.022 -1000.0 FOXA2 and FOXA3 transcription factor networks 4.0 213.0 46.0 -0.302 0.018 1000.0 -1000.0 -0.098 -1000.0 RXR and RAR heterodimerization with other nuclear receptor 4.0 249.0 52.0 -0.16 0.039 1000.0 -1000.0 -0.036 -1000.0 S1P1 pathway 4.0 169.0 36.0 -0.088 0.012 1000.0 -1000.0 -0.05 -1000.0 FAS signaling pathway (CD95) 4.0 216.0 47.0 -0.191 0.014 1000.0 -1000.0 -0.04 -1000.0 IL2 signaling events mediated by PI3K 4.0 239.0 58.0 -0.089 0.03 1000.0 -1000.0 -0.077 -1000.0 Effects of Botulinum toxin 4.0 127.0 26.0 -0.071 0.012 1000.0 -1000.0 -0.061 -1000.0 IL2 signaling events mediated by STAT5 4.0 100.0 22.0 -0.102 0.013 1000.0 -1000.0 -0.039 -1000.0 Plasma membrane estrogen receptor signaling 4.0 421.0 86.0 -0.111 0.024 1000.0 -1000.0 -0.075 -1000.0 E-cadherin signaling in keratinocytes 4.0 177.0 43.0 -0.05 0.025 1000.0 -1000.0 -0.061 -1000.0 S1P4 pathway 4.0 115.0 25.0 -0.087 0.016 1000.0 -1000.0 -0.045 -1000.0 E-cadherin signaling events 4.0 24.0 5.0 -0.027 0.012 1000.0 -1000.0 -0.029 -1000.0 Regulation of Androgen receptor activity 4.0 338.0 70.0 -0.368 0.021 1000.0 -1000.0 -0.065 -1000.0 Hedgehog signaling events mediated by Gli proteins 3.0 211.0 65.0 -0.098 0.048 1000.0 -1000.0 -0.052 -1000.0 Presenilin action in Notch and Wnt signaling 3.0 201.0 61.0 -0.116 0.035 1000.0 -1000.0 -0.069 -1000.0 IFN-gamma pathway 3.0 247.0 68.0 -0.077 0.022 1000.0 -1000.0 -0.088 -1000.0 HIF-2-alpha transcription factor network 3.0 132.0 43.0 -0.056 0.063 1000.0 -1000.0 -0.084 -1000.0 Signaling mediated by p38-gamma and p38-delta 3.0 53.0 15.0 -0.024 0.019 1000.0 -1000.0 -0.033 -1000.0 HIV-1 Nef: Negative effector of Fas and TNF-alpha 3.0 178.0 45.0 -0.078 0.029 1000.0 -1000.0 -0.08 -1000.0 Canonical Wnt signaling pathway 3.0 201.0 51.0 -0.116 0.048 1000.0 -1000.0 -0.054 -1000.0 Regulation of p38-alpha and p38-beta 3.0 164.0 54.0 -0.096 0.03 1000.0 -1000.0 -0.052 -1000.0 E-cadherin signaling in the nascent adherens junction 3.0 254.0 76.0 -0.053 0.03 1000.0 -1000.0 -0.074 -1000.0 Regulation of Telomerase 3.0 318.0 102.0 -0.146 0.04 1000.0 -1000.0 -0.095 -1000.0 S1P3 pathway 3.0 137.0 42.0 -0.086 0.02 1000.0 -1000.0 -0.035 -1000.0 Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 2.0 222.0 85.0 -0.092 0.02 1000.0 -1000.0 -0.065 -1000.0 Ceramide signaling pathway 2.0 180.0 76.0 -0.111 0.022 1000.0 -1000.0 -0.044 -1000.0 Paxillin-independent events mediated by a4b1 and a4b7 2.0 110.0 37.0 -0.032 0.021 1000.0 -1000.0 -0.048 -1000.0 TRAIL signaling pathway 2.0 142.0 48.0 -0.019 0.035 1000.0 -1000.0 -0.059 -1000.0 Role of Calcineurin-dependent NFAT signaling in lymphocytes 2.0 169.0 83.0 -0.094 0.044 1000.0 -1000.0 -0.062 -1000.0 TCGA08_rtk_signaling 2.0 66.0 26.0 -0.057 0.033 1000.0 -1000.0 -0.02 -1000.0 Class I PI3K signaling events 2.0 206.0 73.0 -0.096 0.028 1000.0 -1000.0 -0.054 -1000.0 Insulin Pathway 2.0 171.0 74.0 -0.065 0.034 1000.0 -1000.0 -0.076 -1000.0 PDGFR-beta signaling pathway 2.0 208.0 97.0 -0.055 0.052 1000.0 -1000.0 -0.067 -1000.0 Aurora B signaling 2.0 190.0 67.0 -0.163 0.023 1000.0 -1000.0 -0.065 -1000.0 Canonical NF-kappaB pathway 1.0 45.0 39.0 -0.048 0.068 1000.0 -1000.0 -0.077 -1000.0 Signaling events mediated by HDAC Class II 1.0 117.0 75.0 -0.056 0.032 1000.0 -1000.0 -0.04 -1000.0 BARD1 signaling events 1.0 104.0 57.0 -0.013 0.057 1000.0 -1000.0 -0.054 -1000.0 Arf6 downstream pathway 1.0 44.0 43.0 -0.02 0.023 1000.0 -1000.0 -0.036 -1000.0 Aurora C signaling 1.0 13.0 7.0 -0.01 -0.0 1000.0 -1000.0 -0.028 -1000.0 EPO signaling pathway 1.0 99.0 55.0 -0.025 0.047 1000.0 -1000.0 -0.082 -1000.0 Signaling events mediated by HDAC Class III 1.0 72.0 40.0 -0.102 0.019 1000.0 -1000.0 -0.039 -1000.0 ceramide signaling pathway 1.0 63.0 49.0 -0.048 0.027 1000.0 -1000.0 -0.045 -1000.0 Signaling events mediated by HDAC Class I 1.0 124.0 104.0 -0.072 0.051 1000.0 -1000.0 -0.067 -1000.0 Retinoic acid receptors-mediated signaling 1.0 100.0 58.0 -0.043 0.037 1000.0 -1000.0 -0.066 -1000.0 Paxillin-dependent events mediated by a4b1 1.0 57.0 36.0 -0.032 0.028 1000.0 -1000.0 -0.061 -1000.0 Atypical NF-kappaB pathway 1.0 50.0 31.0 -0.023 0.028 1000.0 -1000.0 -0.039 -1000.0 Signaling events mediated by VEGFR1 and VEGFR2 1.0 187.0 125.0 -0.024 0.067 1000.0 -1000.0 -0.078 -1000.0 VEGFR1 specific signals 1.0 87.0 56.0 -0.024 0.046 1000.0 -1000.0 -0.046 -1000.0 Signaling events mediated by PRL 1.0 66.0 34.0 -0.086 0.033 1000.0 -1000.0 -0.031 -1000.0 p38 MAPK signaling pathway 1.0 62.0 44.0 -0.067 0.024 1000.0 -1000.0 -0.062 -1000.0 Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0 0.0 23.0 0.012 0.043 1000.0 -1000.0 -0.055 -1000.0 PLK2 and PLK4 events 0.0 0.0 3.0 0.012 0.021 1000.0 -1000.0 -0.02 -1000.0 Circadian rhythm pathway 0.0 14.0 22.0 -0.019 0.04 1000.0 -1000.0 -0.044 -1000.0 Aurora A signaling 0.0 54.0 60.0 -0.03 0.032 1000.0 -1000.0 -0.042 -1000.0 PLK1 signaling events 0.0 39.0 85.0 -0.006 0.034 1000.0 -1000.0 -0.039 -1000.0 Insulin-mediated glucose transport 0.0 31.0 32.0 -0.031 0.029 1000.0 -1000.0 -0.054 -1000.0 mTOR signaling pathway 0.0 36.0 53.0 -0.008 0.031 1000.0 -1000.0 -0.047 -1000.0 Class I PI3K signaling events mediated by Akt 0.0 36.0 68.0 -0.032 0.045 1000.0 -1000.0 -0.052 -1000.0 FoxO family signaling 0.0 35.0 64.0 -0.068 0.13 1000.0 -1000.0 -0.07 -1000.0 Sumoylation by RanBP2 regulates transcriptional repression 0.0 9.0 27.0 -0.007 0.031 1000.0 -1000.0 -0.048 -1000.0 Arf6 trafficking events 0.0 70.0 71.0 -0.064 0.04 1000.0 -1000.0 -0.075 -1000.0 Arf1 pathway 0.0 8.0 54.0 -0.006 0.027 1000.0 -1000.0 -0.029 -1000.0 Alternative NF-kappaB pathway 0.0 0.0 13.0 0.0 0.037 1000.0 -1000.0 -0.036 -1000.0 Total 760 45128 7203 -16.5745442627 -994.599700042 131000 -131000 -7.88705947982 -131000