Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 71 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 152
HIF-1-alpha transcription factor network 116
LPA receptor mediated events 104
TCGA08_retinoblastoma 97
Osteopontin-mediated events 92
Syndecan-1-mediated signaling events 91
Endothelins 91
PDGFR-alpha signaling pathway 84
Cellular roles of Anthrax toxin 76
Ephrin B reverse signaling 75
Results

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

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.1
FOXM1 transcription factor network 152 7768 51 -0.66 0.022 1000 -1000 -0.014 -1000
HIF-1-alpha transcription factor network 116 8866 76 -0.16 0.034 1000 -1000 -0.01 -1000
LPA receptor mediated events 104 10638 102 -0.086 0.023 1000 -1000 -0.03 -1000
TCGA08_retinoblastoma 97 783 8 -0.023 0.022 1000 -1000 -0.003 -1000
Osteopontin-mediated events 92 3508 38 -0.22 0.023 1000 -1000 0 -1000
Syndecan-1-mediated signaling events 91 3097 34 -0.087 0.023 1000 -1000 0 -1000
Endothelins 91 8784 96 -0.21 0.023 1000 -1000 0 -1000
PDGFR-alpha signaling pathway 84 3736 44 -0.15 0.031 1000 -1000 0.002 -1000
Cellular roles of Anthrax toxin 76 2970 39 -0.1 0.022 1000 -1000 -0.011 -1000
Ephrin B reverse signaling 75 3622 48 -0.2 0.051 1000 -1000 -0.032 -1000
TCGA08_p53 74 524 7 -0.069 0.019 1000 -1000 -0.001 -1000
Nectin adhesion pathway 73 4644 63 -0.081 0.033 1000 -1000 -0.025 -1000
amb2 Integrin signaling 71 5896 82 -0.13 0.034 1000 -1000 0 -1000
Thromboxane A2 receptor signaling 69 7290 105 -0.21 0.052 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 68 204 3 -0.002 0.016 1000 -1000 0.018 -1000
Fc-epsilon receptor I signaling in mast cells 68 6652 97 -0.088 0.026 1000 -1000 -0.017 -1000
Syndecan-4-mediated signaling events 65 4380 67 -0.11 0.027 1000 -1000 -0.007 -1000
IL4-mediated signaling events 64 5911 91 -0.33 0.17 1000 -1000 -0.1 -1000
IL23-mediated signaling events 64 3862 60 -0.27 0.025 1000 -1000 -0.002 -1000
Nongenotropic Androgen signaling 62 3248 52 -0.13 0.066 1000 -1000 -0.014 -1000
TRAIL signaling pathway 60 2893 48 -0.038 0.023 1000 -1000 -0.003 -1000
IL6-mediated signaling events 58 4354 75 -0.12 0.025 1000 -1000 -0.014 -1000
BARD1 signaling events 57 3277 57 -0.035 0.027 1000 -1000 -0.035 -1000
IL1-mediated signaling events 57 3541 62 -0.074 0.045 1000 -1000 0 -1000
EPHB forward signaling 57 4913 85 -0.028 0.036 1000 -1000 -0.018 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 56 4827 85 -0.17 0.023 1000 -1000 -0.013 -1000
IGF1 pathway 56 3206 57 -0.021 0.035 1000 -1000 -0.015 -1000
Integrins in angiogenesis 55 4661 84 -0.056 0.033 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 50 252 5 0.004 0.019 1000 -1000 0.018 -1000
PLK1 signaling events 50 4277 85 -0.063 0.025 1000 -1000 -0.012 -1000
IFN-gamma pathway 50 3433 68 -0.053 0.034 1000 -1000 -0.015 -1000
Caspase cascade in apoptosis 47 3537 74 -0.064 0.044 1000 -1000 -0.013 -1000
Signaling events mediated by PTP1B 47 3637 76 -0.094 0.075 1000 -1000 -0.019 -1000
Canonical Wnt signaling pathway 46 2352 51 -0.19 0.084 1000 -1000 -0.014 -1000
Ras signaling in the CD4+ TCR pathway 46 790 17 -0.026 0.024 1000 -1000 0 -1000
Noncanonical Wnt signaling pathway 45 1183 26 -0.033 0.026 1000 -1000 -0.005 -1000
Paxillin-independent events mediated by a4b1 and a4b7 45 1685 37 -0.041 0.033 1000 -1000 0 -1000
IL12-mediated signaling events 44 3861 87 -0.26 0.026 1000 -1000 -0.052 -1000
Signaling events mediated by the Hedgehog family 44 2330 52 -0.083 0.034 1000 -1000 -0.016 -1000
TCR signaling in naïve CD8+ T cells 44 4131 93 -0.05 0.033 1000 -1000 -0.021 -1000
Circadian rhythm pathway 43 966 22 -0.08 0.024 1000 -1000 -0.007 -1000
BMP receptor signaling 43 3553 81 -0.074 0.049 1000 -1000 -0.019 -1000
FoxO family signaling 43 2775 64 -0.27 0.041 1000 -1000 -0.004 -1000
Stabilization and expansion of the E-cadherin adherens junction 42 3112 74 -0.059 0.035 1000 -1000 -0.027 -1000
Aurora A signaling 41 2494 60 -0.064 0.037 1000 -1000 0 -1000
Reelin signaling pathway 41 2337 56 -0.018 0.055 1000 -1000 0 -1000
Paxillin-dependent events mediated by a4b1 41 1503 36 -0.032 0.035 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 41 1773 43 -0.012 0.026 1000 -1000 -0.008 -1000
Ephrin A reverse signaling 39 276 7 0 0.023 1000 -1000 0 -1000
Retinoic acid receptors-mediated signaling 39 2278 58 -0.098 0.029 1000 -1000 -0.009 -1000
IL2 signaling events mediated by PI3K 39 2301 58 -0.11 0.023 1000 -1000 -0.024 -1000
Arf6 downstream pathway 38 1668 43 -0.027 0.031 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 38 1648 43 -0.098 0.041 1000 -1000 -0.087 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 38 1719 45 -0.06 0.038 1000 -1000 0.001 -1000
Syndecan-2-mediated signaling events 37 2618 69 -0.018 0.027 1000 -1000 -0.001 -1000
BCR signaling pathway 37 3748 99 -0.057 0.032 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 36 1683 46 -0.17 0.042 1000 -1000 -0.007 -1000
ceramide signaling pathway 36 1779 49 -0.014 0.038 1000 -1000 0 -1000
E-cadherin signaling in the nascent adherens junction 36 2803 76 -0.059 0.041 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 36 1226 34 -0.014 0.023 1000 -1000 0 -1000
FAS signaling pathway (CD95) 34 1617 47 -0.054 0.042 1000 -1000 -0.01 -1000
EGFR-dependent Endothelin signaling events 34 727 21 0 0.041 1000 -1000 0 -1000
Aurora B signaling 34 2282 67 -0.065 0.033 1000 -1000 -0.01 -1000
Plasma membrane estrogen receptor signaling 33 2922 86 -0.055 0.051 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 32 4032 125 -0.039 0.055 1000 -1000 -0.017 -1000
TCGA08_rtk_signaling 32 848 26 -0.014 0.028 1000 -1000 -0.018 -1000
ErbB2/ErbB3 signaling events 31 2036 65 -0.072 0.023 1000 -1000 -0.016 -1000
Wnt signaling 31 218 7 -0.033 0.022 1000 -1000 0.008 -1000
ErbB4 signaling events 30 2136 69 -0.068 0.046 1000 -1000 -0.012 -1000
Class I PI3K signaling events 29 2164 73 -0.008 0.041 1000 -1000 -0.004 -1000
S1P4 pathway 29 747 25 -0.003 0.03 1000 -1000 0 -1000
RXR and RAR heterodimerization with other nuclear receptor 27 1407 52 -0.029 0.06 1000 -1000 -0.002 -1000
Atypical NF-kappaB pathway 27 848 31 0 0.023 1000 -1000 0 -1000
Signaling mediated by p38-gamma and p38-delta 26 401 15 -0.05 0.023 1000 -1000 0 -1000
S1P3 pathway 26 1121 42 -0.054 0.03 1000 -1000 -0.002 -1000
Regulation of Androgen receptor activity 26 1839 70 -0.095 0.033 1000 -1000 -0.004 -1000
Nephrin/Neph1 signaling in the kidney podocyte 25 852 34 -0.023 0.049 1000 -1000 -0.02 -1000
Canonical NF-kappaB pathway 25 976 39 0 0.037 1000 -1000 0 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 25 1393 54 -0.015 0.029 1000 -1000 0 -1000
PDGFR-beta signaling pathway 25 2425 97 -0.059 0.046 1000 -1000 -0.016 -1000
E-cadherin signaling events 25 129 5 0.018 0.025 1000 -1000 0.019 -1000
Regulation of Telomerase 24 2473 102 -0.13 0.046 1000 -1000 0 -1000
Arf6 signaling events 23 1459 62 -0.017 0.036 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 23 1447 61 -0.18 0.042 1000 -1000 -0.016 -1000
EPO signaling pathway 23 1287 55 -0.006 0.058 1000 -1000 0 -1000
Glucocorticoid receptor regulatory network 23 2637 114 -0.13 0.046 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 22 266 12 0 0.014 1000 -1000 0 -1000
Coregulation of Androgen receptor activity 22 1690 76 -0.01 0.033 1000 -1000 -0.008 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 22 1556 68 -0.08 0.092 1000 -1000 -0.038 -1000
IL2 signaling events mediated by STAT5 22 492 22 -0.077 0.032 1000 -1000 0.001 -1000
Neurotrophic factor-mediated Trk receptor signaling 22 2740 120 -0.058 0.056 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 20 2820 136 -0.13 0.071 1000 -1000 -0.035 -1000
Signaling events mediated by VEGFR1 and VEGFR2 19 2408 125 -0.019 0.055 1000 -1000 -0.022 -1000
p38 MAPK signaling pathway 19 848 44 -0.012 0.043 1000 -1000 0 -1000
Glypican 1 network 18 901 48 -0.021 0.039 1000 -1000 -0.02 -1000
Ceramide signaling pathway 18 1401 76 -0.012 0.044 1000 -1000 -0.002 -1000
S1P5 pathway 18 319 17 -0.007 0.023 1000 -1000 -0.012 -1000
Syndecan-3-mediated signaling events 18 634 35 -0.009 0.034 1000 -1000 0 -1000
Signaling events mediated by HDAC Class III 17 696 40 -0.036 0.042 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 17 1813 104 -0.036 0.052 1000 -1000 -0.03 -1000
Regulation of p38-alpha and p38-beta 17 929 54 -0.007 0.057 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 585 33 -0.002 0.053 1000 -1000 0 -1000
Class IB PI3K non-lipid kinase events 17 51 3 -0.019 0.019 1000 -1000 -0.019 -1000
mTOR signaling pathway 16 876 53 -0.015 0.032 1000 -1000 -0.019 -1000
Arf6 trafficking events 16 1201 71 -0.025 0.033 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 15 1300 82 -0.008 0.056 1000 -1000 -0.021 -1000
Signaling mediated by p38-alpha and p38-beta 15 669 44 -0.008 0.033 1000 -1000 0 -1000
Hedgehog signaling events mediated by Gli proteins 14 911 65 -0.005 0.053 1000 -1000 -0.015 -1000
Insulin-mediated glucose transport 14 453 32 0 0.033 1000 -1000 0 -1000
Class I PI3K signaling events mediated by Akt 14 1013 68 -0.026 0.047 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 14 1268 88 -0.029 0.057 1000 -1000 -0.035 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 13 1082 83 -0.006 0.048 1000 -1000 -0.013 -1000
Insulin Pathway 13 1031 74 -0.012 0.063 1000 -1000 -0.013 -1000
Sphingosine 1-phosphate (S1P) pathway 12 343 28 0 0.037 1000 -1000 0 -1000
JNK signaling in the CD4+ TCR pathway 12 205 17 -0.002 0.044 1000 -1000 0 -1000
S1P1 pathway 12 467 36 -0.001 0.028 1000 -1000 -0.013 -1000
Glypican 2 network 12 49 4 0.021 0.029 1000 -1000 0.019 -1000
Calcium signaling in the CD4+ TCR pathway 12 385 31 -0.002 0.089 1000 -1000 -0.011 -1000
VEGFR1 specific signals 12 680 56 0 0.039 1000 -1000 -0.002 -1000
Signaling events mediated by HDAC Class II 11 876 75 -0.034 0.059 1000 -1000 -0.013 -1000
Effects of Botulinum toxin 11 306 26 0 0.041 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 11 313 27 -0.013 0.047 1000 -1000 -0.013 -1000
Aurora C signaling 10 70 7 0 0.033 1000 -1000 -0.003 -1000
IL27-mediated signaling events 10 560 51 -0.006 0.034 1000 -1000 -0.021 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 9 226 23 -0.013 0.043 1000 -1000 0 -1000
Arf1 pathway 8 446 54 -0.01 0.032 1000 -1000 -0.004 -1000
Alternative NF-kappaB pathway 8 110 13 0 0.055 1000 -1000 0 -1000
Visual signal transduction: Rods 7 368 52 0 0.065 1000 -1000 0 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 7 567 78 -0.013 0.037 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 6 136 20 0 0.025 1000 -1000 0 -1000
Visual signal transduction: Cones 2 83 38 0 0.064 1000 -1000 0 -1000
Total 4817 278349 7203 -8.1 5.2 131000 -131000 -1.4 -131000
FOXM1 transcription factor network

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.43 0.59 -10000 0 -1.1 201 201
PLK1 -0.062 0.29 -10000 0 -1.3 30 30
BIRC5 -0.061 0.29 -10000 0 -1.3 29 29
HSPA1B -0.44 0.59 -10000 0 -1.1 216 216
MAP2K1 0.001 0.044 -10000 0 -0.16 3 3
BRCA2 -0.44 0.6 -10000 0 -1.1 201 201
FOXM1 -0.66 0.96 -10000 0 -1.7 216 216
XRCC1 -0.43 0.59 -10000 0 -1.1 200 200
FOXM1B/p19 -0.54 0.66 -10000 0 -1.2 228 228
Cyclin D1/CDK4 -0.44 0.55 -10000 0 -1 234 234
CDC2 -0.5 0.67 -10000 0 -1.3 212 212
TGFA -0.39 0.52 -10000 0 -0.95 219 219
SKP2 -0.44 0.6 -10000 0 -1.1 202 202
CCNE1 -0.001 0.049 -10000 0 -0.13 70 70
CKS1B -0.44 0.6 -10000 0 -1.1 204 204
RB1 -0.36 0.45 -10000 0 -0.85 212 212
FOXM1C/SP1 -0.53 0.71 -10000 0 -1.3 222 222
AURKB -0.069 0.3 -10000 0 -1.3 32 32
CENPF -0.48 0.62 -10000 0 -1.2 225 225
CDK4 0.008 0.027 -10000 0 -0.14 9 9
MYC -0.39 0.52 -10000 0 -0.96 223 223
CHEK2 -0.003 0.051 -10000 0 -0.14 26 26
ONECUT1 -0.44 0.57 -10000 0 -1.1 220 220
CDKN2A 0.013 0.023 0.093 1 -0.13 12 13
LAMA4 -0.48 0.62 -10000 0 -1.2 219 219
FOXM1B/HNF6 -0.55 0.72 -10000 0 -1.3 220 220
FOS -0.52 0.64 -10000 0 -1.2 238 238
SP1 0.021 0.011 -10000 0 -0.052 5 5
CDC25B -0.44 0.59 -10000 0 -1.1 202 202
response to radiation -0.012 0.032 -10000 0 -10000 0 0
CENPB -0.43 0.59 -10000 0 -1.1 195 195
CENPA -0.43 0.59 -10000 0 -1.1 197 197
NEK2 -0.44 0.61 -10000 0 -1.1 208 208
HIST1H2BA -0.43 0.59 -10000 0 -1.1 201 201
CCNA2 0.01 0.034 -10000 0 -0.13 29 29
EP300 0.022 0.01 -10000 0 -0.12 2 2
CCNB1/CDK1 -0.58 0.78 -10000 0 -1.5 204 204
CCNB2 -0.46 0.62 -10000 0 -1.2 217 217
CCNB1 -0.48 0.65 -10000 0 -1.2 209 209
ETV5 -0.49 0.63 -10000 0 -1.2 224 224
ESR1 -0.47 0.61 -10000 0 -1.1 224 224
CCND1 -0.44 0.56 -10000 0 -1 237 237
GSK3A 0.003 0.042 -10000 0 -0.16 10 10
Cyclin A-E1/CDK1-2 -0.037 0.1 -10000 0 -0.17 147 147
CDK2 0.015 0.025 -10000 0 -0.13 14 14
G2/M transition of mitotic cell cycle -0.015 0.038 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.49 0.66 -10000 0 -1.2 216 216
GAS1 -0.44 0.6 -10000 0 -1.1 212 212
MMP2 -0.53 0.64 -10000 0 -1.2 246 246
RB1/FOXM1C -0.49 0.58 -10000 0 -1.1 239 239
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
HIF-1-alpha transcription factor network

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.13 0.34 -9999 0 -0.56 161 161
HDAC7 -0.001 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.067 0.34 -9999 0 -0.6 100 100
SMAD4 0.023 0.007 -9999 0 -0.12 1 1
ID2 -0.13 0.34 -9999 0 -0.56 160 160
AP1 -0.03 0.087 -9999 0 -0.15 161 161
ABCG2 -0.13 0.34 -9999 0 -0.56 161 161
HIF1A -0.017 0.091 -9999 0 -0.13 136 136
TFF3 -0.13 0.34 -9999 0 -0.56 168 168
GATA2 0.019 0.023 -9999 0 -0.099 18 18
AKT1 -0.005 0.073 -9999 0 -0.11 104 104
response to hypoxia -0.021 0.064 -9999 0 -0.11 124 124
MCL1 -0.13 0.34 -9999 0 -0.56 159 159
NDRG1 -0.14 0.35 -9999 0 -0.58 166 166
SERPINE1 -0.14 0.33 -9999 0 -0.56 164 164
FECH -0.13 0.34 -9999 0 -0.56 159 159
FURIN -0.13 0.34 -9999 0 -0.56 159 159
NCOA2 0.023 0.013 -9999 0 -0.1 5 5
EP300 0 0.089 -9999 0 -0.22 26 26
HMOX1 -0.13 0.35 -9999 0 -0.57 163 163
BHLHE40 -0.14 0.33 -9999 0 -0.56 164 164
BHLHE41 -0.14 0.33 -9999 0 -0.56 164 164
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.034 0.12 -9999 0 -0.18 59 59
ENG 0.005 0.089 -9999 0 -0.18 53 53
JUN 0.014 0.033 -9999 0 -0.12 30 30
RORA -0.13 0.34 -9999 0 -0.56 160 160
ABCB1 -0.026 0.11 -9999 0 -0.68 5 5
TFRC -0.14 0.35 -9999 0 -0.58 169 169
CXCR4 -0.14 0.35 -9999 0 -0.57 173 173
TF -0.13 0.34 -9999 0 -0.56 160 160
CITED2 -0.13 0.34 -9999 0 -0.56 162 162
HIF1A/ARNT -0.084 0.44 -9999 0 -0.73 113 113
LDHA -0.09 0.3 -9999 0 -0.99 54 54
ETS1 -0.13 0.35 -9999 0 -0.58 160 160
PGK1 -0.13 0.35 -9999 0 -0.57 165 165
NOS2 -0.14 0.33 -9999 0 -0.56 164 164
ITGB2 -0.14 0.35 -9999 0 -0.58 167 167
ALDOA -0.13 0.34 -9999 0 -0.56 160 160
Cbp/p300/CITED2 -0.12 0.36 -9999 0 -0.65 125 125
FOS -0.006 0.054 -9999 0 -0.12 95 95
HK2 -0.13 0.34 -9999 0 -0.56 164 164
SP1 0.031 0.009 -9999 0 -0.11 1 1
GCK 0.002 0.12 -9999 0 -0.42 1 1
HK1 -0.13 0.34 -9999 0 -0.56 159 159
NPM1 -0.13 0.34 -9999 0 -0.56 159 159
EGLN1 -0.12 0.34 -9999 0 -0.56 161 161
CREB1 0.023 0.028 -9999 0 -0.075 42 42
PGM1 -0.13 0.34 -9999 0 -0.57 165 165
SMAD3 0.022 0.016 -9999 0 -0.12 7 7
EDN1 -0.037 0.19 -9999 0 -1 14 14
IGFBP1 -0.12 0.34 -9999 0 -0.56 159 159
VEGFA -0.093 0.29 -9999 0 -0.52 132 132
HIF1A/JAB1 -0.005 0.085 -9999 0 -0.17 77 77
CP -0.15 0.36 -9999 0 -0.58 175 175
CXCL12 -0.15 0.35 -9999 0 -0.57 176 176
COPS5 0.02 0.022 -9999 0 -0.11 13 13
SMAD3/SMAD4 0.029 0.032 -9999 0 -0.12 24 24
BNIP3 -0.14 0.34 -9999 0 -0.56 169 169
EGLN3 -0.15 0.35 -9999 0 -0.59 167 167
CA9 -0.15 0.34 -9999 0 -0.55 181 181
TERT -0.12 0.34 -9999 0 -0.56 159 159
ENO1 -0.13 0.34 -9999 0 -0.57 159 159
PFKL -0.13 0.34 -9999 0 -0.56 159 159
NCOA1 0.023 0.009 -9999 0 -0.12 2 2
ADM -0.14 0.34 -9999 0 -0.57 163 163
ARNT -0.009 0.07 -9999 0 -0.097 153 153
HNF4A 0.027 0.009 -9999 0 -0.12 2 2
ADFP -0.14 0.35 -9999 0 -0.58 170 170
SLC2A1 -0.097 0.29 -9999 0 -0.52 133 133
LEP -0.12 0.34 -9999 0 -0.56 159 159
HIF1A/ARNT/Cbp/p300 -0.077 0.34 -9999 0 -0.61 105 105
EPO -0.076 0.28 -9999 0 -0.59 82 82
CREBBP -0.002 0.09 -9999 0 -0.22 29 29
HIF1A/ARNT/Cbp/p300/HDAC7 -0.08 0.35 -9999 0 -0.62 109 109
PFKFB3 -0.13 0.34 -9999 0 -0.57 162 162
NT5E -0.16 0.36 -9999 0 -0.59 177 177
LPA receptor mediated events

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.021 0.074 -10000 0 -0.13 138 138
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.092 -10000 0 -0.19 89 89
AP1 -0.058 0.074 -10000 0 -0.13 250 250
mol:PIP3 -0.051 0.063 -10000 0 -0.14 157 157
AKT1 -0.015 0.07 -10000 0 -0.16 54 54
PTK2B -0.028 0.066 -10000 0 -0.14 123 123
RHOA -0.009 0.054 -10000 0 -0.35 6 6
PIK3CB 0.015 0.03 -10000 0 -0.12 24 24
mol:Ca2+ -0.004 0.039 -10000 0 -0.11 37 37
MAGI3 0.018 0.026 -10000 0 -0.12 18 18
RELA 0.023 0.009 -10000 0 -0.12 2 2
apoptosis -0.035 0.07 -10000 0 -0.16 121 121
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
positive regulation of microtubule depolymerization -0.019 0.06 -10000 0 -0.12 125 125
NF kappa B1 p50/RelA -0.04 0.062 -10000 0 -0.13 141 141
endothelial cell migration -0.086 0.14 -10000 0 -0.23 247 247
ADCY4 -0.043 0.097 -10000 0 -0.2 135 135
ADCY5 -0.045 0.098 -10000 0 -0.2 141 141
ADCY6 -0.043 0.098 -10000 0 -0.2 134 134
ADCY7 -0.042 0.097 -10000 0 -0.2 134 134
ADCY1 -0.042 0.097 -10000 0 -0.2 134 134
ADCY2 -0.043 0.097 -10000 0 -0.2 135 135
ADCY3 -0.043 0.098 -10000 0 -0.2 135 135
ADCY8 -0.048 0.098 -10000 0 -0.2 138 138
ADCY9 -0.045 0.1 -10000 0 -0.2 141 141
GSK3B -0.024 0.064 -10000 0 -0.13 126 126
arachidonic acid secretion -0.041 0.091 -10000 0 -0.19 129 129
GNG2 0.02 0.018 -10000 0 -0.12 9 9
TRIP6 0.002 0.05 -10000 0 -0.25 19 19
GNAO1 -0.04 0.073 -10000 0 -0.11 246 246
HRAS 0.023 0.006 -10000 0 -0.12 1 1
NFKBIA -0.03 0.085 -10000 0 -0.2 78 78
GAB1 0.02 0.021 -10000 0 -0.12 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.023 0.22 -10000 0 -0.87 37 37
JUN 0.014 0.033 -10000 0 -0.12 30 30
LPA/LPA2/NHERF2 -0.01 0.035 -10000 0 -0.062 140 140
TIAM1 -0.041 0.26 -10000 0 -1 37 37
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.004 0.039 -10000 0 -0.11 37 37
PLCB3 -0.003 0.032 -10000 0 -0.05 140 140
FOS -0.005 0.053 -10000 0 -0.12 95 95
positive regulation of mitosis -0.041 0.091 -10000 0 -0.19 129 129
LPA/LPA1-2-3 -0.037 0.061 -10000 0 -0.098 247 247
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
stress fiber formation -0.026 0.075 -10000 0 -0.14 138 138
GNAZ -0.035 0.071 -10000 0 -0.11 249 249
EGFR/PI3K-beta/Gab1 -0.053 0.065 -10000 0 -0.14 157 157
positive regulation of dendritic cell cytokine production -0.037 0.06 -10000 0 -0.098 247 247
LPA/LPA2/MAGI-3 -0.009 0.036 -10000 0 -0.063 136 136
ARHGEF1 -0.02 0.062 -10000 0 -0.12 128 128
GNAI2 -0.035 0.071 -10000 0 -0.11 247 247
GNAI3 -0.039 0.077 -10000 0 -0.11 247 247
GNAI1 -0.045 0.081 -10000 0 -0.12 247 247
LPA/LPA3 -0.021 0.031 -10000 0 -0.053 247 247
LPA/LPA2 -0.021 0.031 -10000 0 -0.052 247 247
LPA/LPA1 -0.052 0.082 -10000 0 -0.14 247 247
HB-EGF/EGFR -0.003 0.06 -10000 0 -0.13 77 77
HBEGF 0.004 0.039 -10000 0 -0.078 95 95
mol:DAG -0.004 0.039 -10000 0 -0.11 37 37
cAMP biosynthetic process -0.045 0.096 -10000 0 -0.2 135 135
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
SRC 0.023 0.009 -10000 0 -0.12 2 2
GNB1 0.023 0.007 -10000 0 -0.12 1 1
LYN -0.03 0.089 -10000 0 -0.22 74 74
GNAQ -0.012 0.038 -10000 0 -0.069 125 125
LPAR2 0 0 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.034 0.049 -10000 0 -0.084 247 247
IL8 -0.083 0.15 -10000 0 -0.34 110 110
PTK2 -0.029 0.063 -10000 0 -0.091 245 245
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
CASP3 -0.035 0.07 -10000 0 -0.16 121 121
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PLCG1 -0.007 0.041 -10000 0 -0.066 134 134
PLD2 -0.026 0.06 -10000 0 -0.087 247 247
G12/G13 -0.019 0.073 -10000 0 -0.14 128 128
PI3K-beta -0.04 0.06 0.084 1 -0.19 49 50
cell migration -0.012 0.078 -10000 0 -0.23 47 47
SLC9A3R2 0.017 0.028 -10000 0 -0.12 22 22
PXN -0.027 0.076 -10000 0 -0.14 138 138
HRAS/GTP -0.042 0.093 -10000 0 -0.19 129 129
RAC1 0.023 0.002 -10000 0 -10000 0 0
MMP9 0 0.05 -10000 0 -0.12 81 81
PRKCE 0.021 0.017 -10000 0 -0.12 8 8
PRKCD -0.005 0.045 -10000 0 -0.12 45 45
Gi(beta/gamma) -0.043 0.096 -10000 0 -0.19 140 140
mol:LPA -0.034 0.049 -10000 0 -0.084 247 247
TRIP6/p130 Cas/FAK1/Paxillin -0.022 0.093 -10000 0 -0.16 135 135
MAPKKK cascade -0.041 0.091 -10000 0 -0.19 129 129
contractile ring contraction involved in cytokinesis -0.008 0.054 -10000 0 -0.35 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.009 0.029 -10000 0 -0.057 128 128
GNA15 -0.011 0.035 -10000 0 -0.058 145 145
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MAPT -0.019 0.061 -10000 0 -0.12 126 126
GNA11 -0.009 0.028 -10000 0 -0.056 124 124
Rac1/GTP -0.026 0.24 -10000 0 -0.92 37 37
MMP2 -0.086 0.14 -10000 0 -0.23 247 247
TCGA08_retinoblastoma

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.017 0.017 -10000 0 -0.085 8 8
CDKN2C 0.008 0.044 -10000 0 -0.12 56 56
CDKN2A 0.014 0.023 -10000 0 -0.12 12 12
CCND2 0.015 0.052 0.12 107 -10000 0 107
RB1 -0.023 0.061 0.091 1 -0.12 136 137
CDK4 0.022 0.068 0.13 137 -0.12 17 154
CDK6 0.014 0.073 0.13 131 -0.13 39 170
G1/S progression 0.02 0.065 0.12 138 -0.09 1 139
Osteopontin-mediated events

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.047 0.11 -9999 0 -0.22 124 124
NF kappa B1 p50/RelA/I kappa B alpha -0.067 0.17 -9999 0 -0.31 141 141
alphaV/beta3 Integrin/Osteopontin/Src -0.038 0.11 -9999 0 -0.19 164 164
AP1 -0.12 0.16 -9999 0 -0.3 186 186
ILK -0.047 0.099 -9999 0 -0.22 106 106
bone resorption -0.041 0.11 -9999 0 -0.2 146 146
PTK2B 0.023 0.009 -9999 0 -0.12 2 2
PYK2/p130Cas -0.022 0.11 -9999 0 -0.2 117 117
ITGAV 0.008 0.035 -9999 0 -0.12 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.07 -9999 0 -0.12 125 125
alphaV/beta3 Integrin/Osteopontin -0.042 0.12 -9999 0 -0.19 171 171
MAP3K1 -0.05 0.1 -9999 0 -0.2 134 134
JUN 0.012 0.033 -9999 0 -0.12 30 30
MAPK3 -0.064 0.12 -9999 0 -0.25 139 139
MAPK1 -0.064 0.13 -9999 0 -0.25 140 140
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.053 0.1 -9999 0 -0.2 143 143
ITGB3 -0.001 0.048 -9999 0 -0.12 71 71
NFKBIA -0.081 0.16 -9999 0 -0.32 144 144
FOS -0.007 0.054 -9999 0 -0.12 95 95
CD44 0.011 0.038 -9999 0 -0.12 41 41
CHUK 0.021 0.013 -9999 0 -0.12 4 4
PLAU -0.22 0.4 -9999 0 -1 106 106
NF kappa B1 p50/RelA -0.068 0.17 -9999 0 -0.36 122 122
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
RELA 0.023 0.009 -9999 0 -0.12 2 2
alphaV beta3 Integrin -0.027 0.088 -9999 0 -0.16 139 139
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.047 0.1 -9999 0 -0.2 134 134
VAV3 -0.055 0.11 -9999 0 -0.2 153 153
MAP3K14 -0.054 0.11 -9999 0 -0.2 152 152
ROCK2 0.019 0.021 -9999 0 -0.12 11 11
SPP1 0.008 0.034 -9999 0 -0.12 31 31
RAC1 0.023 0.002 -9999 0 -10000 0 0
Rac1/GTP -0.05 0.11 -9999 0 -0.19 149 149
MMP2 -0.13 0.16 -9999 0 -0.28 244 244
Syndecan-1-mediated signaling events

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CCL5 0.005 0.044 -9999 0 -0.12 60 60
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
FGFR/FGF2/Syndecan-1 -0.083 0.12 -9999 0 -0.25 132 132
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.073 0.12 -9999 0 -0.24 139 139
Syndecan-1/Syntenin -0.076 0.13 -9999 0 -0.24 151 151
MAPK3 -0.06 0.12 -9999 0 -0.21 138 138
HGF/MET -0.017 0.074 -9999 0 -0.14 118 118
TGFB1/TGF beta receptor Type II 0.019 0.023 -9999 0 -0.12 14 14
BSG 0.022 0.013 -9999 0 -0.12 4 4
keratinocyte migration -0.072 0.12 -9999 0 -0.23 139 139
Syndecan-1/RANTES -0.087 0.14 -9999 0 -0.25 168 168
Syndecan-1/CD147 -0.062 0.12 -9999 0 -0.22 138 138
Syndecan-1/Syntenin/PIP2 -0.074 0.12 -9999 0 -0.23 153 153
LAMA5 0.019 0.025 -9999 0 -0.12 17 17
positive regulation of cell-cell adhesion -0.073 0.12 -9999 0 -0.22 153 153
MMP7 -0.022 0.06 -9999 0 -0.12 144 144
HGF 0.02 0.023 -9999 0 -0.12 14 14
Syndecan-1/CASK -0.079 0.12 -9999 0 -0.24 132 132
Syndecan-1/HGF/MET -0.087 0.13 -9999 0 -0.22 197 197
regulation of cell adhesion -0.058 0.11 -9999 0 -0.24 97 97
HPSE 0.014 0.034 -9999 0 -0.12 33 33
positive regulation of cell migration -0.083 0.12 -9999 0 -0.25 132 132
SDC1 -0.084 0.12 -9999 0 -0.25 132 132
Syndecan-1/Collagen -0.083 0.12 -9999 0 -0.25 132 132
PPIB 0.023 0.003 -9999 0 -10000 0 0
MET 0 0.047 -9999 0 -0.12 70 70
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
MMP9 0 0.05 -9999 0 -0.12 81 81
MAPK1 -0.061 0.12 -9999 0 -0.21 138 138
homophilic cell adhesion -0.082 0.12 -9999 0 -0.25 132 132
MMP1 -0.007 0.058 -9999 0 -0.12 115 115
Endothelins

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.075 0.13 0.27 6 -0.24 170 176
PTK2B 0.022 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.041 0.16 -10000 0 -0.47 46 46
EDN1 -0.057 0.11 0.2 6 -0.18 208 214
EDN3 0.02 0.023 -10000 0 -0.12 14 14
EDN2 0.018 0.027 -10000 0 -0.12 20 20
HRAS/GDP -0.068 0.14 -10000 0 -0.31 104 104
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.05 0.11 0.2 3 -0.23 106 109
ADCY4 -0.059 0.11 0.2 6 -0.2 164 170
ADCY5 -0.062 0.11 0.2 5 -0.2 169 174
ADCY6 -0.058 0.11 0.2 6 -0.2 162 168
ADCY7 -0.058 0.11 0.2 6 -0.2 162 168
ADCY1 -0.058 0.11 0.2 6 -0.2 161 167
ADCY2 -0.059 0.11 0.2 6 -0.2 163 169
ADCY3 -0.059 0.11 0.2 6 -0.2 162 168
ADCY8 -0.067 0.11 0.2 4 -0.2 175 179
ADCY9 -0.06 0.11 0.2 6 -0.2 163 169
arachidonic acid secretion -0.13 0.23 -10000 0 -0.44 154 154
ETB receptor/Endothelin-1/Gq/GTP -0.022 0.082 -10000 0 -0.2 59 59
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.022 0.006 -10000 0 -0.12 1 1
ETA receptor/Endothelin-1/G12/GTP -0.053 0.14 0.32 6 -0.22 163 169
ETA receptor/Endothelin-1/Gs/GTP -0.051 0.13 0.3 6 -0.21 160 166
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.13 0.19 0.28 6 -0.35 206 212
EDNRB -0.012 0.054 -10000 0 -0.088 152 152
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.14 0.28 6 -0.26 141 147
CYSLTR1 -0.084 0.15 0.28 5 -0.28 158 163
SLC9A1 -0.043 0.088 0.19 6 -0.17 134 140
mol:GDP -0.08 0.15 0.21 2 -0.32 109 111
SLC9A3 -0.059 0.16 -10000 0 -0.44 48 48
RAF1 -0.092 0.18 -10000 0 -0.38 125 125
JUN -0.081 0.27 -10000 0 -0.83 55 55
JAK2 -0.082 0.14 0.27 6 -0.25 183 189
mol:IP3 -0.053 0.12 -10000 0 -0.26 86 86
ETA receptor/Endothelin-1 -0.086 0.17 0.36 6 -0.29 178 184
PLCB1 0.011 0.034 -10000 0 -0.12 32 32
PLCB2 0.019 0.018 -10000 0 -0.12 8 8
ETA receptor/Endothelin-3 -0.02 0.077 0.16 6 -0.13 140 146
FOS -0.17 0.34 -10000 0 -0.84 108 108
Gai/GDP 0.013 0.062 -10000 0 -0.47 3 3
CRK 0.021 0.016 -10000 0 -0.12 7 7
mol:Ca ++ -0.1 0.16 0.27 3 -0.32 157 160
BCAR1 0.023 0.011 -10000 0 -0.12 3 3
PRKCB1 -0.053 0.12 -10000 0 -0.25 90 90
GNAQ 0.019 0.017 -10000 0 -0.12 6 6
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
GNAL 0.021 0.018 -10000 0 -0.12 9 9
Gs family/GDP -0.067 0.14 -10000 0 -0.3 104 104
ETA receptor/Endothelin-1/Gq/GTP -0.043 0.12 0.2 5 -0.23 104 109
MAPK14 -0.028 0.086 -10000 0 -0.2 76 76
TRPC6 -0.043 0.17 -10000 0 -0.51 40 40
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.032 0.09 -10000 0 -0.21 74 74
ETB receptor/Endothelin-2 0.004 0.048 -10000 0 -0.12 38 38
ETB receptor/Endothelin-3 0.007 0.043 -10000 0 -0.1 34 34
ETB receptor/Endothelin-1 -0.05 0.1 0.17 5 -0.18 164 169
MAPK3 -0.16 0.3 -10000 0 -0.73 112 112
MAPK1 -0.16 0.31 -10000 0 -0.74 113 113
Rac1/GDP -0.068 0.14 -10000 0 -0.31 103 103
cAMP biosynthetic process -0.04 0.1 0.2 6 -0.2 109 115
MAPK8 -0.058 0.19 -10000 0 -0.51 69 69
SRC 0.023 0.009 -10000 0 -0.12 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.034 0.095 -10000 0 -0.24 67 67
p130Cas/CRK/Src/PYK2 -0.055 0.15 -10000 0 -0.38 66 66
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.068 0.14 -10000 0 -0.31 103 103
COL1A2 -0.14 0.23 0.28 5 -0.46 167 172
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.023 0.08 0.16 6 -0.13 142 148
mol:DAG -0.053 0.12 -10000 0 -0.26 87 87
MAP2K2 -0.12 0.23 -10000 0 -0.54 117 117
MAP2K1 -0.12 0.23 -10000 0 -0.53 116 116
EDNRA -0.05 0.1 0.2 6 -0.17 190 196
positive regulation of muscle contraction -0.06 0.12 0.24 6 -0.21 163 169
Gq family/GDP -0.046 0.14 -10000 0 -0.3 93 93
HRAS/GTP -0.07 0.14 -10000 0 -0.3 101 101
PRKCH -0.053 0.12 -10000 0 -0.25 94 94
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.058 0.12 -10000 0 -0.26 98 98
PRKCB -0.054 0.11 -10000 0 -0.25 92 92
PRKCE -0.052 0.12 -10000 0 -0.26 89 89
PRKCD -0.056 0.12 -10000 0 -0.26 96 96
PRKCG -0.051 0.12 -10000 0 -0.26 89 89
regulation of vascular smooth muscle contraction -0.21 0.4 -10000 0 -1 108 108
PRKCQ -0.059 0.12 -10000 0 -0.26 94 94
PLA2G4A -0.14 0.25 -10000 0 -0.48 154 154
GNA14 0.018 0.022 -10000 0 -0.12 11 11
GNA15 0.019 0.019 -10000 0 -0.12 8 8
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA11 0.021 0.015 -10000 0 -0.12 5 5
Rac1/GTP -0.054 0.14 0.32 6 -0.23 162 168
MMP1 0.019 0.14 0.2 30 -0.6 12 42
PDGFR-alpha signaling pathway

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.004 0.046 -10000 0 -0.13 59 59
PDGF/PDGFRA/CRKL -0.009 0.068 -10000 0 -0.13 124 124
positive regulation of JUN kinase activity 0.01 0.068 -10000 0 -0.1 117 117
CRKL 0.023 0.009 -10000 0 -0.12 2 2
PDGF/PDGFRA/Caveolin-3 -0.01 0.068 -10000 0 -0.13 122 122
AP1 -0.15 0.26 -10000 0 -0.64 114 114
mol:IP3 -0.007 0.046 -10000 0 -0.072 148 148
PLCG1 -0.007 0.046 -10000 0 -0.072 148 148
PDGF/PDGFRA/alphaV Integrin -0.037 0.094 -10000 0 -0.15 193 193
RAPGEF1 0.023 0 -10000 0 -10000 0 0
CRK 0.021 0.016 -10000 0 -0.12 7 7
mol:Ca2+ -0.011 0.053 -10000 0 -0.08 159 159
CAV3 0.022 0.011 -10000 0 -0.12 3 3
CAV1 0.012 0.039 -10000 0 -0.12 43 43
SHC/Grb2/SOS1 0.011 0.069 -10000 0 -0.1 117 117
PDGF/PDGFRA/Shf -0.009 0.068 -10000 0 -0.11 155 155
FOS -0.14 0.26 -10000 0 -0.63 114 114
JUN -0.019 0.045 0.26 4 -0.13 35 39
oligodendrocyte development -0.037 0.094 -10000 0 -0.15 193 193
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:DAG -0.007 0.046 -10000 0 -0.072 148 148
PDGF/PDGFRA -0.004 0.046 -10000 0 -0.13 59 59
actin cytoskeleton reorganization -0.009 0.068 -10000 0 -0.13 122 122
SRF 0.024 0.022 -10000 0 -0.069 23 23
SHC1 0.023 0.001 -10000 0 -10000 0 0
PI3K -0.014 0.084 -10000 0 -0.13 152 152
PDGF/PDGFRA/Crk/C3G 0.007 0.061 -10000 0 -0.11 100 100
JAK1 0.003 0.032 -10000 0 -0.076 61 61
ELK1/SRF -0.011 0.066 -10000 0 -0.13 115 115
SHB 0.023 0.009 -10000 0 -0.12 2 2
SHF 0.023 0.009 -10000 0 -0.12 2 2
CSNK2A1 0.031 0.021 0.066 1 -0.1 6 7
GO:0007205 -0.023 0.072 -10000 0 -0.14 110 110
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Ras protein signal transduction 0.01 0.068 -10000 0 -0.1 117 117
PDGF/PDGFRA/SHB -0.009 0.068 -10000 0 -0.13 122 122
PDGF/PDGFRA/Caveolin-1 -0.02 0.08 -10000 0 -0.15 135 135
ITGAV 0.013 0.032 -10000 0 -0.12 28 28
ELK1 -0.024 0.07 -10000 0 -0.12 146 146
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PDGF/PDGFRA/Crk -0.01 0.068 -10000 0 -0.11 159 159
JAK-STAT cascade 0.004 0.032 -10000 0 -0.076 61 61
cell proliferation -0.009 0.067 -10000 0 -0.11 155 155
Cellular roles of Anthrax toxin

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.007 0.043 -10000 0 -0.12 54 54
ANTXR2 0.013 0.036 -10000 0 -0.12 36 36
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.013 -10000 0 -0.034 102 102
monocyte activation -0.1 0.16 -10000 0 -0.35 156 156
MAP2K2 0.006 0.052 -10000 0 -0.66 3 3
MAP2K1 0 0.015 -10000 0 -0.031 80 80
MAP2K7 0 0.014 -10000 0 -0.028 105 105
MAP2K6 -0.005 0.024 -10000 0 -0.041 132 132
CYAA -0.016 0.048 -10000 0 -0.11 102 102
MAP2K4 -0.001 0.016 -10000 0 -0.029 105 105
IL1B -0.009 0.035 -10000 0 -0.073 94 94
Channel -0.003 0.06 -10000 0 -0.098 144 144
NLRP1 -0.001 0.015 -10000 0 -0.032 81 81
CALM1 0.022 0.014 -10000 0 -0.12 5 5
negative regulation of phagocytosis 0.001 0.054 -10000 0 -0.46 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.013 0.034 102 -10000 0 102
MAPK3 -0.001 0.015 -10000 0 -0.031 83 83
MAPK1 -0.001 0.019 -10000 0 -0.033 108 108
PGR -0.011 0.027 -10000 0 -0.044 195 195
PA/Cellular Receptors -0.004 0.066 -10000 0 -0.11 144 144
apoptosis -0.007 0.013 -10000 0 -0.034 102 102
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.058 -10000 0 -0.12 102 102
macrophage activation 0.003 0.018 -10000 0 -0.053 29 29
TNF 0.02 0.02 -10000 0 -0.12 11 11
VCAM1 -0.1 0.16 -10000 0 -0.36 156 156
platelet activation 0.001 0.054 -10000 0 -0.46 7 7
MAPKKK cascade 0.003 0.02 0.048 52 -10000 0 52
IL18 -0.011 0.039 -10000 0 -0.076 110 110
negative regulation of macrophage activation -0.007 0.013 -10000 0 -0.034 102 102
LEF -0.007 0.013 -10000 0 -0.034 102 102
CASP1 -0.005 0.024 -10000 0 -0.043 106 106
mol:cAMP 0.001 0.055 -10000 0 -0.46 7 7
necrosis -0.007 0.013 -10000 0 -0.034 102 102
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.001 0.056 -10000 0 -0.091 144 144
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.007 0.041 -10000 0 -0.12 50 50
EPHB2 0.022 0.021 -10000 0 -0.12 11 11
EFNB1 0.023 0.018 -10000 0 -0.068 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.055 -10000 0 -0.15 11 11
Ephrin B2/EPHB1-2 0.011 0.062 -10000 0 -0.1 101 101
neuron projection morphogenesis 0.029 0.046 -10000 0 -0.15 11 11
Ephrin B1/EPHB1-2/Tiam1 0.04 0.056 -10000 0 -0.1 48 48
DNM1 0.022 0.019 -10000 0 -0.12 10 10
cell-cell signaling 0.002 0.004 -10000 0 -10000 0 0
MAP2K4 -0.12 0.21 -10000 0 -0.47 149 149
YES1 -0.19 0.31 -10000 0 -0.71 149 149
Ephrin B1/EPHB1-2/NCK2 0.051 0.043 -10000 0 -0.094 24 24
PI3K -0.13 0.22 -10000 0 -0.47 154 154
mol:GDP 0.038 0.055 -10000 0 -0.1 48 48
ITGA2B 0.023 0.006 -10000 0 -0.12 1 1
endothelial cell proliferation 0.001 0.058 -10000 0 -0.1 124 124
FYN -0.2 0.31 -10000 0 -0.71 149 149
MAP3K7 -0.13 0.22 -10000 0 -0.5 149 149
FGR -0.18 0.31 -10000 0 -0.69 149 149
TIAM1 0.015 0.032 -10000 0 -0.12 28 28
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
RGS3 0.023 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.2 -10000 0 -0.43 159 159
LYN -0.2 0.31 -10000 0 -0.71 149 149
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.28 -10000 0 -0.64 149 149
Ephrin B1/EPHB1-2 -0.15 0.24 -10000 0 -0.54 149 149
SRC -0.18 0.31 -10000 0 -0.69 149 149
ITGB3 0.004 0.047 -10000 0 -0.12 68 68
EPHB1 0.018 0.032 -10000 0 -0.12 28 28
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.058 -10000 0 -0.1 124 124
alphaIIb/beta3 Integrin 0.01 0.053 -10000 0 -0.096 107 107
BLK -0.18 0.31 -10000 0 -0.7 149 149
HCK -0.19 0.31 -10000 0 -0.7 149 149
regulation of stress fiber formation -0.049 0.042 0.093 24 -10000 0 24
MAPK8 -0.12 0.2 -10000 0 -0.44 151 151
Ephrin B1/EPHB1-2/RGS3 0.051 0.043 -10000 0 -0.094 24 24
endothelial cell migration -0.12 0.18 -10000 0 -0.41 152 152
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTPN13 -0.013 0.058 -10000 0 -0.13 112 112
regulation of focal adhesion formation -0.049 0.042 0.093 24 -10000 0 24
chemotaxis -0.049 0.042 0.093 24 -10000 0 24
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
Rac1/GTP 0.038 0.051 -10000 0 -0.15 11 11
angiogenesis -0.15 0.23 -10000 0 -0.53 149 149
LCK -0.18 0.31 -10000 0 -0.69 149 149
TCGA08_p53

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.007 0.013 -10000 0 -0.077 12 12
TP53 -0.051 0.11 0.18 14 -0.24 127 141
Senescence -0.069 0.12 0.18 14 -0.26 157 171
Apoptosis -0.069 0.12 0.18 14 -0.26 157 171
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.002 0.011 0.057 11 -0.084 4 15
MDM4 0.019 0.023 -10000 0 -0.12 14 14
Nectin adhesion pathway

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
alphaV beta3 Integrin -0.018 0.081 -9999 0 -0.16 107 107
PTK2 -0.073 0.15 -9999 0 -0.31 140 140
positive regulation of JNK cascade -0.052 0.11 -9999 0 -0.26 116 116
CDC42/GDP -0.044 0.17 -9999 0 -0.35 116 116
Rac1/GDP -0.043 0.17 -9999 0 -0.35 117 117
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
CDC42/GTP -0.044 0.15 -9999 0 -0.32 116 116
nectin-3/I-afadin -0.02 0.08 -9999 0 -0.15 119 119
RAPGEF1 -0.06 0.17 -9999 0 -0.38 115 115
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.073 0.19 -9999 0 -0.43 115 115
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
TLN1 -0.037 0.097 -9999 0 -0.23 88 88
Rap1/GTP -0.063 0.12 -9999 0 -0.28 117 117
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
Rap1/GTP/I-afadin 0.016 0.059 -9999 0 -0.11 85 85
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.02 0.08 -9999 0 -0.15 119 119
PVR 0.022 0.011 -9999 0 -0.12 3 3
Necl-5(dimer) 0.022 0.011 -9999 0 -0.12 3 3
mol:GDP -0.066 0.2 -9999 0 -0.43 116 116
MLLT4 0.014 0.032 -9999 0 -0.12 29 29
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K -0.009 0.085 -9999 0 -0.11 179 179
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
positive regulation of lamellipodium assembly -0.059 0.12 -9999 0 -0.28 124 124
PVRL1 0.022 0.011 -9999 0 -0.12 3 3
PVRL3 0.003 0.046 -9999 0 -0.12 66 66
PVRL2 0.019 0.023 -9999 0 -0.12 15 15
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
CDH1 0.021 0.016 -9999 0 -0.12 6 6
CLDN1 -0.003 0.051 -9999 0 -0.12 87 87
JAM-A/CLDN1 -0.029 0.087 -9999 0 -0.12 216 216
SRC -0.081 0.21 -9999 0 -0.48 115 115
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
nectin-1(dimer)/I-afadin/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
FARP2 -0.063 0.19 -9999 0 -0.42 116 116
RAC1 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.003 0.072 -9999 0 -0.12 120 120
nectin-1/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
nectin-2/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
RAC1/GTP/IQGAP1/filamentous actin 0.017 0.044 -9999 0 -0.12 48 48
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.003 0.072 -9999 0 -0.12 119 119
CDC42/GTP/IQGAP1/filamentous actin 0.018 0.043 -9999 0 -0.11 54 54
F11R 0.023 0.007 -9999 0 -0.12 1 1
positive regulation of filopodium formation -0.052 0.11 -9999 0 -0.26 116 116
alphaV/beta3 Integrin/Talin -0.053 0.11 -9999 0 -0.22 142 142
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
nectin-2(dimer)/I-afadin/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
PIP5K1C -0.046 0.1 -9999 0 -0.25 93 93
VAV2 -0.076 0.21 -9999 0 -0.44 126 126
RAP1/GDP -0.044 0.16 -9999 0 -0.33 117 117
ITGAV 0.013 0.032 -9999 0 -0.12 28 28
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.007 0.074 -9999 0 -0.12 128 128
nectin-3(dimer)/I-afadin/I-afadin -0.02 0.08 -9999 0 -0.15 119 119
Rac1/GTP -0.051 0.16 -9999 0 -0.34 124 124
PTPRM -0.056 0.11 -9999 0 -0.2 174 174
E-cadherin/beta catenin/alpha catenin 0.033 0.07 -9999 0 -0.18 25 25
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.023 0.002 -9999 0 -10000 0 0
amb2 Integrin signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.03 0.083 -9999 0 -0.13 181 181
alphaM/beta2 Integrin/GPIbA 0.022 0.059 -9999 0 -0.11 77 77
alphaM/beta2 Integrin/proMMP-9 -0.005 0.081 -9999 0 -0.13 129 129
PLAUR 0.018 0.024 -9999 0 -0.12 15 15
HMGB1 0.023 0.008 -9999 0 -0.041 1 1
alphaM/beta2 Integrin/Talin 0.015 0.069 -9999 0 -0.12 95 95
AGER 0.022 0.017 -9999 0 -0.11 7 7
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
SELPLG 0.02 0.021 -9999 0 -0.12 12 12
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.034 0.07 -9999 0 -0.15 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 0 0.05 -9999 0 -0.12 81 81
CYR61 0.002 0.047 -9999 0 -0.12 70 70
TLN1 0.021 0.012 -9999 0 -0.12 3 3
Rap1/GTP -0.099 0.15 -9999 0 -0.28 174 174
RHOA 0.023 0.006 -9999 0 -0.12 1 1
P-selectin oligomer 0.018 0.027 -9999 0 -0.12 21 21
MYH2 -0.12 0.15 -9999 0 -0.28 208 208
MST1R 0.017 0.029 -9999 0 -0.12 23 23
leukocyte activation during inflammatory response 0.027 0.052 -9999 0 -0.091 76 76
APOB 0.022 0.011 -9999 0 -0.12 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.015 0.059 -9999 0 -0.12 128 128
JAM3 0.02 0.02 -9999 0 -0.12 11 11
GP1BA 0.022 0.012 -9999 0 -0.12 4 4
alphaM/beta2 Integrin/CTGF 0.003 0.073 -9999 0 -0.12 118 118
alphaM/beta2 Integrin -0.12 0.16 -9999 0 -0.33 157 157
JAM3 homodimer 0.02 0.02 -9999 0 -0.12 11 11
ICAM2 0.017 0.029 -9999 0 -0.12 23 23
ICAM1 0 0.048 -9999 0 -0.12 74 74
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.16 -9999 0 -0.33 157 157
cell adhesion 0.021 0.059 -9999 0 -0.11 77 77
NFKB1 0.021 0.072 -9999 0 -0.21 27 27
THY1 -0.003 0.049 -9999 0 -0.12 79 79
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Lipoprotein(a) 0.03 0.014 -9999 0 -0.062 12 12
alphaM/beta2 Integrin/LRP/tPA -0.016 0.087 -9999 0 -0.12 203 203
IL6 0.007 0.094 -9999 0 -0.34 17 17
ITGB2 0.013 0.032 -9999 0 -0.098 37 37
elevation of cytosolic calcium ion concentration -0.016 0.1 -9999 0 -0.15 153 153
alphaM/beta2 Integrin/JAM2/JAM3 0.027 0.063 -9999 0 -0.1 83 83
JAM2 0.014 0.035 -9999 0 -0.12 35 35
alphaM/beta2 Integrin/ICAM1 0.004 0.088 -9999 0 -0.15 89 89
alphaM/beta2 Integrin/uPA/Plg -0.006 0.088 -9999 0 -0.13 142 142
RhoA/GTP -0.13 0.16 -9999 0 -0.3 216 216
positive regulation of phagocytosis -0.078 0.14 -9999 0 -0.28 139 139
Ron/MSP 0.027 0.031 -9999 0 -0.14 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.015 0.1 -9999 0 -0.15 153 153
alphaM/beta2 Integrin/uPAR 0.012 0.077 -9999 0 -0.15 88 88
PLAU -0.007 0.055 -9999 0 -0.12 102 102
PLAT -0.001 0.049 -9999 0 -0.12 76 76
actin filament polymerization -0.12 0.14 -9999 0 -0.27 208 208
MST1 0.022 0.012 -9999 0 -0.12 4 4
alphaM/beta2 Integrin/lipoprotein(a) 0.031 0.054 -9999 0 -0.092 76 76
TNF 0.015 0.076 -9999 0 -0.28 12 12
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
alphaM/beta2 Integrin/uPA -0.02 0.091 -9999 0 -0.15 143 143
fibrinolysis -0.007 0.086 -9999 0 -0.13 142 142
HCK 0.019 0.024 -9999 0 -0.12 15 15
dendritic cell antigen processing and presentation -0.12 0.16 -9999 0 -0.33 157 157
VTN 0.023 0.009 -9999 0 -0.12 2 2
alphaM/beta2 Integrin/CYR61 -0.01 0.08 -9999 0 -0.13 144 144
LPA 0.021 0.019 -9999 0 -0.12 10 10
LRP1 0.014 0.032 -9999 0 -0.12 29 29
cell migration -0.044 0.086 -9999 0 -0.13 235 235
FN1 -0.013 0.056 -9999 0 -0.12 114 114
alphaM/beta2 Integrin/Thy1 -0.026 0.085 -9999 0 -0.13 197 197
MPO 0.023 0.009 -9999 0 -0.12 2 2
KNG1 0.022 0.011 -9999 0 -0.12 3 3
RAP1/GDP 0.015 0.05 -9999 0 -0.12 61 61
ROCK1 -0.12 0.15 -9999 0 -0.28 208 208
ELA2 0.022 0.011 -9999 0 -0.12 3 3
PLG 0.023 0.009 -9999 0 -0.12 2 2
CTGF 0.012 0.036 -9999 0 -0.12 37 37
alphaM/beta2 Integrin/Hck 0.017 0.07 -9999 0 -0.13 84 84
ITGAM 0.021 0.019 -9999 0 -0.11 9 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.03 0.066 -9999 0 -0.11 81 81
HP -0.035 0.063 -9999 0 -0.12 193 193
leukocyte adhesion -0.009 0.088 -9999 0 -0.17 66 66
SELP 0.018 0.028 -9999 0 -0.12 21 21
Thromboxane A2 receptor signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.046 -10000 0 -0.12 65 65
GNB1/GNG2 -0.069 0.081 -10000 0 -0.18 194 194
AKT1 -0.055 0.11 -10000 0 -0.19 195 195
EGF 0.02 0.021 -10000 0 -0.12 12 12
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.026 0.029 -10000 0 -0.11 7 7
mol:Ca2+ -0.096 0.15 -10000 0 -0.29 196 196
LYN 0.024 0.031 -10000 0 -0.13 8 8
RhoA/GTP -0.036 0.069 -10000 0 -0.12 197 197
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.17 -10000 0 -0.34 195 195
GNG2 0.02 0.018 -10000 0 -0.12 9 9
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.047 -10000 0 -0.24 12 12
G beta5/gamma2 -0.091 0.11 -10000 0 -0.23 194 194
PRKCH -0.12 0.18 -10000 0 -0.35 196 196
DNM1 0.021 0.019 -10000 0 -0.12 10 10
TXA2/TP beta/beta Arrestin3 0.017 0.014 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.023 0.006 -10000 0 -0.12 1 1
G12 family/GTP -0.12 0.13 -10000 0 -0.29 197 197
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
ADRBK2 0.015 0.032 -10000 0 -0.12 28 28
RhoA/GTP/ROCK1 0.027 0.021 -10000 0 -0.1 14 14
mol:GDP 0.05 0.12 0.3 49 -10000 0 49
mol:NADP 0.023 0 -10000 0 -10000 0 0
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
PRKG1 0.018 0.026 -10000 0 -0.12 19 19
mol:IP3 -0.12 0.19 -10000 0 -0.36 196 196
cell morphogenesis 0.027 0.021 -10000 0 -0.1 14 14
PLCB2 -0.17 0.25 -10000 0 -0.49 196 196
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.026 0.029 -10000 0 -0.12 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.032 -10000 0 -0.14 7 7
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PTGIR 0.023 0.002 -10000 0 -10000 0 0
PRKCB1 -0.13 0.19 -10000 0 -0.37 196 196
GNAQ 0.021 0.016 -10000 0 -0.12 6 6
mol:L-citrulline 0.023 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.18 0.26 -10000 0 -0.51 195 195
LCK 0.026 0.029 -10000 0 -0.11 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.042 0.026 -10000 0 -0.12 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.061 -10000 0 -0.43 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.041 0.028 -10000 0 -0.12 6 6
MAPK14 -0.073 0.12 -10000 0 -0.22 196 196
TGM2/GTP -0.14 0.21 -10000 0 -0.4 203 203
MAPK11 -0.072 0.12 -10000 0 -0.22 195 195
ARHGEF1 -0.053 0.094 -10000 0 -0.17 197 197
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
JNK cascade -0.13 0.19 -10000 0 -0.38 195 195
RAB11/GDP 0.023 0.007 -10000 0 -0.12 1 1
ICAM1 -0.11 0.16 -10000 0 -0.32 195 195
cAMP biosynthetic process -0.11 0.17 -10000 0 -0.33 200 200
Gq family/GTP/EBP50 0.017 0.042 -10000 0 -0.13 31 31
actin cytoskeleton reorganization 0.027 0.021 -10000 0 -0.1 14 14
SRC 0.026 0.029 -10000 0 -0.11 6 6
GNB5 0.023 0.009 -10000 0 -0.12 2 2
GNB1 0.023 0.007 -10000 0 -0.12 1 1
EGF/EGFR 0.018 0.057 -10000 0 -0.13 38 38
VCAM1 -0.12 0.17 -10000 0 -0.34 195 195
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.047 -10000 0 -0.24 12 12
platelet activation -0.094 0.16 -10000 0 -0.29 196 196
PGI2/IP 0.015 0.017 -10000 0 -0.15 6 6
PRKACA 0.021 0.023 -10000 0 -0.15 8 8
Gq family/GDP/G beta5/gamma2 0.027 0.046 -10000 0 -0.22 12 12
TXA2/TP beta/beta Arrestin2 0.016 0.033 -10000 0 -0.26 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.021 0.021 -10000 0 -0.14 8 8
mol:DAG -0.14 0.21 -10000 0 -0.41 196 196
EGFR 0.015 0.03 -10000 0 -0.12 25 25
TXA2/TP alpha -0.15 0.23 -10000 0 -0.45 198 198
Gq family/GTP 0.014 0.037 -10000 0 -0.14 25 25
YES1 0.024 0.032 -10000 0 -0.14 8 8
GNAI2/GTP 0.02 0.029 -10000 0 -0.12 6 6
PGD2/DP 0.017 0.004 -10000 0 -0.078 1 1
SLC9A3R1 0.016 0.031 -10000 0 -0.12 26 26
FYN 0.02 0.035 -10000 0 -0.13 13 13
mol:NO 0.023 0 -10000 0 -10000 0 0
GNA15 0.021 0.017 -10000 0 -0.12 8 8
PGK/cGMP 0.028 0.016 -10000 0 -0.057 19 19
RhoA/GDP 0.023 0.006 -10000 0 -0.12 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.045 -10000 0 -0.15 7 7
NOS3 0.023 0 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.35 197 197
PRKCB -0.12 0.18 -10000 0 -0.34 196 196
PRKCE -0.12 0.18 -10000 0 -0.35 196 196
PRKCD -0.13 0.19 -10000 0 -0.37 196 196
PRKCG -0.13 0.19 -10000 0 -0.37 196 196
muscle contraction -0.16 0.24 -10000 0 -0.47 195 195
PRKCZ -0.11 0.17 -10000 0 -0.33 195 195
ARR3 0.023 0.006 -10000 0 -0.12 1 1
TXA2/TP beta 0.033 0.035 -10000 0 -0.13 7 7
PRKCQ -0.12 0.18 -10000 0 -0.35 197 197
MAPKKK cascade -0.15 0.22 -10000 0 -0.43 196 196
SELE -0.094 0.15 -10000 0 -0.28 195 195
TP beta/GNAI2/GDP/G beta/gamma 0.052 0.035 -10000 0 -0.2 2 2
ROCK1 0.022 0.009 -10000 0 -0.12 2 2
GNA14 0.02 0.02 -10000 0 -0.12 11 11
chemotaxis -0.21 0.3 -10000 0 -0.6 194 194
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
GNA11 0.022 0.014 -10000 0 -0.12 5 5
Rac1/GTP 0.015 0.015 -10000 0 -0.15 5 5
PLK2 and PLK4 events

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.002 0.05 -9999 0 -0.12 81 81
PLK4 0.016 0.028 -9999 0 -0.12 22 22
regulation of centriole replication -0.002 0.047 -9999 0 -0.091 101 101
Fc-epsilon receptor I signaling in mast cells

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.02 0.019 -9999 0 -0.12 10 10
LAT2 -0.033 0.11 -9999 0 -0.2 134 134
AP1 -0.068 0.18 -9999 0 -0.37 108 108
mol:PIP3 -0.037 0.14 -9999 0 -0.26 128 128
IKBKB -0.014 0.082 -9999 0 -0.15 126 126
AKT1 -0.025 0.071 -9999 0 -0.14 112 112
IKBKG -0.013 0.082 -9999 0 -0.16 101 101
MS4A2 0.026 0.014 -9999 0 -0.13 3 3
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
MAP3K1 -0.038 0.13 -9999 0 -0.28 98 98
mol:Ca2+ -0.026 0.11 -9999 0 -0.2 128 128
LYN 0.02 0.014 -9999 0 -0.12 4 4
CBLB -0.032 0.1 -9999 0 -0.2 129 129
SHC1 0.023 0.001 -9999 0 -10000 0 0
RasGAP/p62DOK -0.005 0.065 -9999 0 -0.1 132 132
positive regulation of cell migration 0.011 0.01 -9999 0 -0.077 7 7
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.008 0.051 -9999 0 -0.092 96 96
PTPN13 -0.088 0.2 -9999 0 -0.5 70 70
PTPN11 0.021 0.013 -9999 0 -0.12 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.035 0.11 -9999 0 -0.26 66 66
SYK 0.016 0.028 -9999 0 -0.12 20 20
GRB2 0.023 0.006 -9999 0 -0.12 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.12 -9999 0 -0.26 130 130
LAT -0.032 0.1 -9999 0 -0.2 134 134
PAK2 -0.043 0.14 -9999 0 -0.31 95 95
NFATC2 -0.003 0.061 -9999 0 -0.42 10 10
HRAS -0.047 0.15 -9999 0 -0.28 132 132
GAB2 0.007 0.041 -9999 0 -0.12 50 50
PLA2G1B 0.017 0.11 -9999 0 -0.92 8 8
Fc epsilon R1 0.003 0.062 -9999 0 -0.094 129 129
Antigen/IgE/Fc epsilon R1 0.006 0.055 -9999 0 -0.078 133 133
mol:GDP -0.057 0.17 -9999 0 -0.32 131 131
JUN 0.014 0.033 -9999 0 -0.12 30 30
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
FOS -0.005 0.053 -9999 0 -0.12 95 95
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.037 0.11 -9999 0 -0.21 138 138
CHUK -0.017 0.085 -9999 0 -0.16 128 128
KLRG1 -0.015 0.088 -9999 0 -0.21 77 77
VAV1 -0.034 0.11 -9999 0 -0.21 129 129
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.032 0.1 -9999 0 -0.2 135 135
negative regulation of mast cell degranulation -0.026 0.086 -9999 0 -0.2 71 71
BTK -0.064 0.19 -9999 0 -0.42 90 90
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.1 -9999 0 -0.21 122 122
GAB2/PI3K/SHP2 -0.046 0.06 -9999 0 -0.14 115 115
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.002 0.073 -9999 0 -0.23 40 40
RAF1 0.011 0.12 -9999 0 -0.99 8 8
Fc epsilon R1/FcgammaRIIB/SHIP -0.008 0.083 -9999 0 -0.12 182 182
FCER1G 0.002 0.044 -9999 0 -0.12 62 62
FCER1A 0.018 0.028 -9999 0 -0.12 20 20
Antigen/IgE/Fc epsilon R1/Fyn 0.002 0.066 -9999 0 -0.092 127 127
MAPK3 0.015 0.12 -9999 0 -0.93 8 8
MAPK1 0.014 0.12 -9999 0 -0.93 8 8
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.007 0.13 -9999 0 -0.53 26 26
DUSP1 -0.004 0.052 -9999 0 -0.12 90 90
NF-kappa-B/RelA -0.005 0.061 -9999 0 -0.12 102 102
actin cytoskeleton reorganization -0.066 0.2 -9999 0 -0.51 65 65
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.037 0.14 -9999 0 -0.29 98 98
FER -0.032 0.1 -9999 0 -0.2 131 131
RELA 0.023 0.009 -9999 0 -0.12 2 2
ITK -0.004 0.05 -9999 0 -0.24 13 13
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG1 -0.054 0.16 -9999 0 -0.3 133 133
cytokine secretion -0.005 0.044 -9999 0 -0.086 103 103
SPHK1 -0.033 0.1 -9999 0 -0.19 137 137
PTK2 -0.07 0.21 -9999 0 -0.57 57 57
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.26 132 132
EDG1 0.011 0.01 -9999 0 -0.077 7 7
mol:DAG -0.035 0.14 -9999 0 -0.26 126 126
MAP2K2 0.01 0.12 -9999 0 -0.94 8 8
MAP2K1 0.013 0.11 -9999 0 -0.93 8 8
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
KLRG1/SHP2 -0.014 0.084 -9999 0 -0.2 68 68
MAP2K4 0.012 0.12 -9999 0 -0.84 11 11
Fc epsilon R1/FcgammaRIIB -0.009 0.09 -9999 0 -0.13 182 182
mol:Choline -0.008 0.05 -9999 0 -0.091 96 96
SHC/Grb2/SOS1 -0.011 0.12 -9999 0 -0.19 133 133
FYN 0.011 0.037 -9999 0 -0.12 40 40
DOK1 0.021 0.016 -9999 0 -0.12 7 7
PXN -0.06 0.19 -9999 0 -0.49 65 65
HCLS1 -0.035 0.12 -9999 0 -0.23 115 115
PRKCB -0.026 0.11 -9999 0 -0.2 128 128
FCGR2B 0.004 0.044 -9999 0 -0.12 60 60
IGHE -0.001 0.003 -9999 0 -10000 0 0
KLRG1/SHIP -0.027 0.087 -9999 0 -0.21 71 71
LCP2 0.013 0.033 -9999 0 -0.12 31 31
PLA2G4A -0.045 0.11 -9999 0 -0.22 132 132
RASA1 0.021 0.012 -9999 0 -0.12 3 3
mol:Phosphatidic acid -0.008 0.05 -9999 0 -0.091 96 96
IKK complex -0.006 0.068 -9999 0 -0.14 90 90
WIPF1 0.02 0.02 -9999 0 -0.12 11 11
Syndecan-4-mediated signaling events

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.11 0.2 -10000 0 -0.37 177 177
Syndecan-4/Syndesmos -0.08 0.18 -10000 0 -0.4 102 102
positive regulation of JNK cascade -0.1 0.18 -10000 0 -0.4 112 112
Syndecan-4/ADAM12 -0.094 0.18 -10000 0 -0.41 102 102
CCL5 0.005 0.044 -10000 0 -0.12 60 60
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
DNM2 0.02 0.022 -10000 0 -0.12 13 13
ITGA5 0.013 0.036 -10000 0 -0.12 38 38
SDCBP 0.021 0.01 -10000 0 -0.12 2 2
PLG 0.027 0.011 -10000 0 -0.1 2 2
ADAM12 -0.01 0.06 -10000 0 -0.12 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.019 -10000 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.008 0.009 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.088 0.18 -10000 0 -0.41 102 102
Syndecan-4/CXCL12/CXCR4 -0.11 0.19 -10000 0 -0.42 112 112
Syndecan-4/Laminin alpha3 -0.094 0.18 -10000 0 -0.42 103 103
MDK 0.021 0.014 -10000 0 -0.12 5 5
Syndecan-4/FZD7 -0.086 0.18 -10000 0 -0.41 102 102
Syndecan-4/Midkine -0.081 0.18 -10000 0 -0.4 102 102
FZD7 0.015 0.031 -10000 0 -0.12 27 27
Syndecan-4/FGFR1/FGF -0.068 0.17 -10000 0 -0.38 101 101
THBS1 -0.004 0.053 -10000 0 -0.12 92 92
integrin-mediated signaling pathway -0.098 0.18 -10000 0 -0.41 105 105
positive regulation of MAPKKK cascade -0.1 0.18 -10000 0 -0.4 112 112
Syndecan-4/TACI -0.079 0.18 -10000 0 -0.4 102 102
CXCR4 0.012 0.032 -10000 0 -0.12 29 29
cell adhesion -0.054 0.096 -10000 0 -0.19 166 166
Syndecan-4/Dynamin -0.081 0.18 -10000 0 -0.41 102 102
Syndecan-4/TSP1 -0.1 0.18 -10000 0 -0.41 109 109
Syndecan-4/GIPC -0.081 0.18 -10000 0 -0.4 102 102
Syndecan-4/RANTES -0.096 0.19 -10000 0 -0.43 102 102
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
LAMA1 0 0.053 -10000 0 -0.12 89 89
LAMA3 0.006 0.043 -10000 0 -0.12 55 55
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA 0.001 0.052 0.079 4 -0.16 40 44
Syndecan-4/alpha-Actinin -0.082 0.18 -10000 0 -0.41 103 103
TFPI 0.018 0.026 -10000 0 -0.12 19 19
F2 0.02 0.016 -10000 0 -0.12 4 4
alpha5/beta1 Integrin 0.016 0.048 -10000 0 -0.1 76 76
positive regulation of cell adhesion -0.097 0.18 -10000 0 -0.41 106 106
ACTN1 0.022 0.011 -10000 0 -0.12 3 3
TNC -0.004 0.053 -10000 0 -0.12 93 93
Syndecan-4/CXCL12 -0.1 0.19 -10000 0 -0.43 102 102
FGF6 0.022 0.012 -10000 0 -0.12 4 4
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CXCL12 -0.003 0.051 -10000 0 -0.12 86 86
TNFRSF13B 0.023 0 -10000 0 -10000 0 0
FGF2 0.023 0.009 -10000 0 -0.12 2 2
FGFR1 0.008 0.043 -10000 0 -0.12 54 54
Syndecan-4/PI-4-5-P2 -0.089 0.17 -10000 0 -0.4 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.056 -10000 0 -0.12 114 114
cell migration -0.005 0.005 -10000 0 -10000 0 0
PRKCD 0.023 0.019 -10000 0 -0.12 8 8
vasculogenesis -0.099 0.18 -10000 0 -0.4 109 109
SDC4 -0.09 0.18 -10000 0 -0.43 102 102
Syndecan-4/Tenascin C -0.1 0.18 -10000 0 -0.42 105 105
Syndecan-4/PI-4-5-P2/PKC alpha -0.006 0.007 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.085 0.18 -10000 0 -0.41 102 102
MMP9 0.001 0.051 -10000 0 -0.12 81 81
Rac1/GTP -0.054 0.098 -10000 0 -0.19 166 166
cytoskeleton organization -0.077 0.17 -10000 0 -0.39 102 102
GIPC1 0.019 0.023 -10000 0 -0.12 15 15
Syndecan-4/TFPI -0.081 0.18 -10000 0 -0.4 102 102
IL4-mediated signaling events

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.16 0.46 -10000 0 -1 88 88
STAT6 (cleaved dimer) -0.25 0.38 -10000 0 -0.94 106 106
IGHG1 -0.031 0.2 -10000 0 -0.39 48 48
IGHG3 -0.16 0.42 -10000 0 -0.93 94 94
AKT1 -0.12 0.34 -10000 0 -0.76 87 87
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.34 -10000 0 -0.81 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.37 -10000 0 -0.83 88 88
THY1 -0.33 0.62 -10000 0 -1.2 170 170
MYB 0.011 0.038 -10000 0 -0.12 41 41
HMGA1 0.012 0.037 -10000 0 -0.12 40 40
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.33 -10000 0 -0.68 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.13 0.37 -10000 0 -0.83 88 88
SP1 -0.002 0.049 -10000 0 -0.09 109 109
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.017 0.023 -10000 0 -0.088 3 3
STAT6 (dimer)/ETS1 -0.17 0.45 -10000 0 -0.96 101 101
SOCS1 -0.096 0.32 -10000 0 -0.65 95 95
SOCS3 -0.11 0.34 -10000 0 -0.81 71 71
FCER2 -0.099 0.33 -10000 0 -0.69 82 82
PARP14 0.014 0.032 -10000 0 -0.12 28 28
CCL17 -0.15 0.45 -10000 0 -1 81 81
GRB2 0.023 0.006 -10000 0 -0.12 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.078 0.27 -10000 0 -0.58 82 82
T cell proliferation -0.18 0.47 -10000 0 -1 99 99
IL4R/JAK1 -0.17 0.46 -10000 0 -1 96 96
EGR2 -0.15 0.45 -10000 0 -1 85 85
JAK2 0.014 0.05 -10000 0 -0.14 16 16
JAK3 0.023 0.016 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
JAK1 0.024 0.021 -10000 0 -0.13 2 2
COL1A2 -0.24 0.54 -10000 0 -1.3 112 112
CCL26 -0.16 0.46 -10000 0 -1 89 89
IL4R -0.17 0.49 -10000 0 -1.1 90 90
PTPN6 0.023 0.018 -10000 0 -0.12 2 2
IL13RA2 -0.16 0.45 -10000 0 -1 85 85
IL13RA1 0.015 0.049 -10000 0 -0.13 13 13
IRF4 0.001 0.13 -10000 0 -0.85 2 2
ARG1 -0.001 0.16 -10000 0 -0.79 4 4
CBL -0.1 0.31 -10000 0 -0.64 98 98
GTF3A -0.013 0.055 -10000 0 -0.096 144 144
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL13RA1/JAK2 0.004 0.092 -10000 0 -0.16 75 75
IRF4/BCL6 -0.004 0.12 -10000 0 -0.84 2 2
CD40LG 0.031 0.012 -10000 0 -0.12 2 2
MAPK14 -0.11 0.33 -10000 0 -0.68 94 94
mitosis -0.11 0.32 -10000 0 -0.71 87 87
STAT6 -0.18 0.52 -10000 0 -1.1 93 93
SPI1 0.027 0.021 -10000 0 -0.12 12 12
RPS6KB1 -0.1 0.31 -10000 0 -0.68 90 90
STAT6 (dimer) -0.18 0.51 -10000 0 -1.1 93 93
STAT6 (dimer)/PARP14 -0.19 0.47 -10000 0 -1 96 96
mast cell activation 0.001 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.12 0.36 -10000 0 -0.79 88 88
FRAP1 -0.12 0.34 -10000 0 -0.76 87 87
LTA -0.15 0.45 -10000 0 -1 81 81
FES 0.022 0.011 -10000 0 -0.12 3 3
T-helper 1 cell differentiation 0.17 0.5 1.1 93 -10000 0 93
CCL11 -0.18 0.47 -10000 0 -1 98 98
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.12 0.35 -10000 0 -0.78 88 88
IL2RG 0 0.051 -10000 0 -0.12 82 82
IL10 -0.15 0.44 -10000 0 -0.99 86 86
IRS1 0.019 0.023 -10000 0 -0.12 14 14
IRS2 0.021 0.016 -10000 0 -0.12 7 7
IL4 0.003 0.14 -10000 0 -10000 0 0
IL5 -0.15 0.45 -10000 0 -1 84 84
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.14 0.43 -10000 0 -0.89 94 94
COL1A1 -0.3 0.6 -10000 0 -1.3 139 139
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.47 -10000 0 -1 89 89
IL2R gamma/JAK3 -0.008 0.072 -10000 0 -0.13 116 116
TFF3 -0.17 0.47 -10000 0 -1 91 91
ALOX15 -0.15 0.45 -10000 0 -1 83 83
MYBL1 0.017 0.028 -10000 0 -0.12 22 22
T-helper 2 cell differentiation -0.15 0.42 -10000 0 -0.88 99 99
SHC1 0.023 0.001 -10000 0 -10000 0 0
CEBPB 0.023 0.032 -10000 0 -0.12 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.37 -10000 0 -0.81 89 89
mol:PI-3-4-5-P3 -0.12 0.34 -10000 0 -0.76 87 87
PI3K -0.13 0.37 -10000 0 -0.82 87 87
DOK2 0.02 0.021 -10000 0 -0.12 12 12
ETS1 0.012 0.036 -10000 0 -0.12 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.074 0.26 -10000 0 -0.56 85 85
ITGB3 -0.2 0.51 -10000 0 -1.1 100 100
PIGR -0.18 0.46 -10000 0 -1 93 93
IGHE 0.001 0.06 0.17 16 -0.18 8 24
MAPKKK cascade -0.072 0.26 -10000 0 -0.55 85 85
BCL6 0.018 0.02 -10000 0 -0.12 10 10
OPRM1 -0.15 0.45 -10000 0 -1 83 83
RETNLB -0.15 0.45 -10000 0 -0.98 87 87
SELP -0.16 0.45 -10000 0 -0.99 85 85
AICDA -0.15 0.43 -10000 0 -0.96 85 85
IL23-mediated signaling events

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.27 0.57 -9999 0 -1.2 130 130
IL23A -0.2 0.5 -9999 0 -1.2 92 92
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.49 -9999 0 -1.1 92 92
positive regulation of T cell mediated cytotoxicity -0.22 0.56 -9999 0 -1.2 116 116
ITGA3 -0.24 0.54 -9999 0 -1.2 122 122
IL17F -0.11 0.32 -9999 0 -0.68 100 100
IL12B 0.016 0.04 -9999 0 -10000 0 0
STAT1 (dimer) -0.22 0.53 -9999 0 -1.1 116 116
CD4 -0.21 0.52 -9999 0 -1.2 103 103
IL23 -0.18 0.48 -9999 0 -1.1 90 90
IL23R 0.002 0.089 -9999 0 -10000 0 0
IL1B -0.22 0.54 -9999 0 -1.2 101 101
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.46 -9999 0 -1.1 87 87
TYK2 0.013 0.034 -9999 0 -0.14 7 7
STAT4 0.02 0.02 -9999 0 -0.12 11 11
STAT3 0.022 0.011 -9999 0 -0.12 3 3
IL18RAP 0.022 0.018 -9999 0 -0.13 8 8
IL12RB1 0.015 0.03 -9999 0 -0.15 1 1
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
IL12Rbeta1/TYK2 0.021 0.04 -9999 0 -0.11 8 8
IL23R/JAK2 -0.001 0.12 -9999 0 -0.34 1 1
positive regulation of chronic inflammatory response -0.22 0.56 -9999 0 -1.2 116 116
natural killer cell activation 0 0.008 -9999 0 -10000 0 0
JAK2 0.012 0.046 -9999 0 -0.13 16 16
PIK3R1 0.016 0.031 -9999 0 -0.12 27 27
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
RELA 0.022 0.01 -9999 0 -0.12 2 2
positive regulation of dendritic cell antigen processing and presentation -0.17 0.45 -9999 0 -1.1 90 90
ALOX12B -0.18 0.46 -9999 0 -1.1 91 91
CXCL1 -0.23 0.52 -9999 0 -1.1 117 117
T cell proliferation -0.22 0.56 -9999 0 -1.2 116 116
NFKBIA 0.016 0.028 -9999 0 -0.12 21 21
IL17A -0.073 0.26 -9999 0 -0.52 100 100
PI3K -0.2 0.5 -9999 0 -1.2 97 97
IFNG -0.005 0.026 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.48 -9999 0 -1.1 99 99
IL18R1 0.021 0.022 -9999 0 -0.12 13 13
IL23/IL23R/JAK2/TYK2/SOCS3 -0.086 0.28 -9999 0 -0.6 90 90
IL18/IL18R 0.015 0.061 -9999 0 -0.1 84 84
macrophage activation -0.009 0.021 -9999 0 -0.044 87 87
TNF -0.19 0.5 -9999 0 -1.2 87 87
STAT3/STAT4 -0.19 0.51 -9999 0 -1.2 97 97
STAT4 (dimer) -0.21 0.53 -9999 0 -1.1 116 116
IL18 0.004 0.046 -9999 0 -0.12 66 66
IL19 -0.18 0.47 -9999 0 -1.1 92 92
STAT5A (dimer) -0.21 0.53 -9999 0 -1.1 112 112
STAT1 0.014 0.031 -9999 0 -0.12 26 26
SOCS3 0.015 0.032 -9999 0 -0.12 28 28
CXCL9 -0.26 0.55 -9999 0 -1.2 129 129
MPO -0.18 0.46 -9999 0 -1.1 91 91
positive regulation of humoral immune response -0.22 0.56 -9999 0 -1.2 116 116
IL23/IL23R/JAK2/TYK2 -0.24 0.61 -9999 0 -1.3 110 110
IL6 -0.2 0.48 -9999 0 -1.1 91 91
STAT5A 0.022 0.013 -9999 0 -0.12 4 4
IL2 0.025 0.014 -9999 0 -0.13 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.008 -9999 0 -10000 0 0
CD3E -0.2 0.5 -9999 0 -1.1 96 96
keratinocyte proliferation -0.22 0.56 -9999 0 -1.2 116 116
NOS2 -0.18 0.46 -9999 0 -0.97 117 117
Nongenotropic Androgen signaling

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.009 -10000 0 -0.078 6 6
GNB1/GNG2 0.012 0.058 -10000 0 -0.1 94 94
regulation of S phase of mitotic cell cycle -0.018 0.085 -10000 0 -0.16 130 130
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.022 0.006 -10000 0 -0.12 1 1
SHBG/T-DHT 0.015 0.005 -10000 0 -0.062 2 2
PELP1 0.022 0.009 -10000 0 -0.12 2 2
AKT1 0.01 0.012 -10000 0 -0.077 10 10
MAP2K1 -0.013 0.061 -10000 0 -0.11 113 113
T-DHT/AR -0.013 0.059 -10000 0 -0.12 120 120
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 103 103
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
mol:GDP -0.047 0.096 -10000 0 -0.25 92 92
cell proliferation -0.063 0.16 -10000 0 -0.37 107 107
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
FOS -0.13 0.29 -10000 0 -0.7 107 107
mol:Ca2+ -0.008 0.022 -10000 0 -0.045 112 112
MAPK3 -0.042 0.11 -10000 0 -0.25 110 110
MAPK1 -0.032 0.1 -10000 0 -0.21 106 106
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.001 0.002 -10000 0 -0.004 103 103
cAMP biosynthetic process 0.01 0.015 0.058 17 -10000 0 17
GNG2 0.02 0.018 -10000 0 -0.12 9 9
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 103 103
HRAS/GTP 0.006 0.054 -10000 0 -0.092 86 86
actin cytoskeleton reorganization 0.016 0.047 -10000 0 -0.099 66 66
SRC 0.022 0.009 -10000 0 -0.13 2 2
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 103 103
PI3K 0.008 0.055 -10000 0 -0.1 96 96
apoptosis 0.066 0.17 0.38 113 -10000 0 113
T-DHT/AR/PELP1 0.002 0.053 -10000 0 -0.095 122 122
HRAS/GDP -0.027 0.1 -10000 0 -0.23 94 94
CREB1 -0.072 0.18 -10000 0 -0.41 112 112
RAC1-CDC42/GTP 0.023 0.051 -10000 0 -0.1 66 66
AR 0.008 0.039 -10000 0 -0.12 43 43
GNB1 0.023 0.007 -10000 0 -0.12 1 1
RAF1 -0.008 0.053 -10000 0 -0.085 128 128
RAC1-CDC42/GDP -0.014 0.1 -10000 0 -0.22 94 94
T-DHT/AR/PELP1/Src 0.014 0.053 -10000 0 -0.098 85 85
MAP2K2 -0.015 0.062 -10000 0 -0.12 115 115
T-DHT/AR/PELP1/Src/PI3K -0.018 0.086 -10000 0 -0.16 130 130
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
SHBG 0.023 0.009 -10000 0 -0.12 2 2
Gi family/GNB1/GNG2/GDP 0.002 0.076 -10000 0 -0.24 32 32
mol:T-DHT -0.001 0.001 -10000 0 -0.003 83 83
RAC1 0.023 0.002 -10000 0 -10000 0 0
GNRH1 0.011 0.009 -10000 0 -0.077 6 6
Gi family/GTP -0.018 0.07 -10000 0 -0.15 95 95
CDC42 0.023 0.002 -10000 0 -10000 0 0
TRAIL signaling pathway

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.001 0.046 -9999 0 -0.12 67 67
positive regulation of NF-kappaB transcription factor activity -0.021 0.079 -9999 0 -0.15 129 129
MAP2K4 -0.008 0.086 -9999 0 -0.23 34 34
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
TNFRSF10B 0.022 0.014 -9999 0 -0.12 5 5
TNFRSF10A 0.019 0.021 -9999 0 -0.12 12 12
SMPD1 -0.013 0.053 -9999 0 -0.16 9 9
IKBKG 0.023 0.009 -9999 0 -0.12 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.023 -9999 0 -0.12 15 15
TRAIL/TRAILR2 -0.02 0.078 -9999 0 -0.12 197 197
TRAIL/TRAILR3 -0.02 0.075 -9999 0 -0.12 204 204
TRAIL/TRAILR1 -0.025 0.082 -9999 0 -0.12 213 213
TRAIL/TRAILR4 -0.021 0.08 -9999 0 -0.15 129 129
TRAIL/TRAILR1/DAP3/GTP -0.006 0.069 -9999 0 -0.11 142 142
IKK complex 0.006 0.079 -9999 0 -0.28 32 32
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.014 0.021 -9999 0 -0.14 10 10
MAPK3 0.006 0.032 -9999 0 -0.074 71 71
MAP3K1 -0.008 0.087 -9999 0 -0.16 121 121
TRAILR4 (trimer) 0.019 0.023 -9999 0 -0.12 15 15
TRADD 0.023 0.006 -9999 0 -0.12 1 1
TRAILR1 (trimer) 0.019 0.021 -9999 0 -0.12 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.011 0.083 -9999 0 -0.14 138 138
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 0.005 0.034 -9999 0 -0.076 73 73
TRAIL/TRAILR1/FADD/TRADD/RIP 0.015 0.073 -9999 0 -0.094 140 140
mol:ceramide -0.013 0.053 -9999 0 -0.16 9 9
FADD 0.023 0.009 -9999 0 -0.12 2 2
MAPK8 -0.007 0.084 -9999 0 -0.22 40 40
TRAF2 0.023 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.025 -9999 0 -0.12 18 18
CHUK 0.021 0.013 -9999 0 -0.12 4 4
TRAIL/TRAILR1/FADD -0.007 0.074 -9999 0 -0.12 137 137
DAP3 0.023 0.007 -9999 0 -0.12 1 1
CASP10 -0.038 0.098 -9999 0 -0.2 122 122
JNK cascade -0.021 0.079 -9999 0 -0.15 129 129
TRAIL (trimer) 0.001 0.046 -9999 0 -0.12 67 67
TNFRSF10C 0.019 0.026 -9999 0 -0.12 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD 0.004 0.069 -9999 0 -0.098 142 142
TRAIL/TRAILR2/FADD -0.002 0.071 -9999 0 -0.12 129 129
cell death -0.013 0.052 -9999 0 -0.16 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.079 -9999 0 -0.14 131 131
TRAILR2 (trimer) 0.022 0.014 -9999 0 -0.12 5 5
CASP8 -0.002 0.11 -9999 0 -0.66 15 15
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.019 0.071 -9999 0 -0.091 132 132
IL6-mediated signaling events

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.072 0.32 -10000 0 -0.77 71 71
CRP -0.063 0.3 -10000 0 -0.74 65 65
cell cycle arrest -0.09 0.36 -10000 0 -0.82 79 79
TIMP1 -0.11 0.35 -10000 0 -0.75 105 105
IL6ST 0.016 0.03 -10000 0 -0.079 36 36
Rac1/GDP -0.019 0.17 -10000 0 -0.36 76 76
AP1 -0.06 0.21 -10000 0 -0.46 98 98
GAB2 0.01 0.042 -10000 0 -0.12 50 50
TNFSF11 -0.063 0.3 -10000 0 -0.74 65 65
HSP90B1 0.007 0.18 -10000 0 -1.2 11 11
GAB1 0.022 0.022 -10000 0 -0.12 12 12
MAPK14 -0.031 0.17 -10000 0 -0.46 57 57
AKT1 -0.018 0.15 -10000 0 -0.38 54 54
FOXO1 -0.015 0.15 -10000 0 -0.37 51 51
MAP2K6 -0.03 0.16 -10000 0 -0.36 77 77
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.028 0.2 -10000 0 -0.41 90 90
MITF -0.02 0.15 -10000 0 -0.34 74 74
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.016 -10000 0 -0.12 7 7
A2M -0.12 0.39 -10000 0 -1.2 63 63
CEBPB 0.023 0.036 -10000 0 -0.11 36 36
GRB2/SOS1/GAB family/SHP2 -0.03 0.18 0.24 6 -0.37 94 100
STAT3 -0.1 0.38 -10000 0 -0.89 79 79
STAT1 -0.088 0.28 -10000 0 -0.84 68 68
CEBPD -0.071 0.31 -10000 0 -0.77 66 66
PIK3CA 0.021 0.017 -10000 0 -0.12 7 7
PI3K 0.009 0.066 -10000 0 -0.15 65 65
JUN 0.014 0.033 -10000 0 -0.12 30 30
PIAS3/MITF -0.014 0.15 -10000 0 -0.32 74 74
MAPK11 -0.03 0.17 -10000 0 -0.46 57 57
STAT3 (dimer)/FOXO1 -0.086 0.34 -10000 0 -0.7 98 98
GRB2/SOS1/GAB family 0.003 0.12 0.22 6 -0.23 79 85
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.12 -10000 0 -0.25 84 84
GRB2 0.025 0.008 -10000 0 -0.12 1 1
JAK2 0.017 0.025 -10000 0 -0.12 16 16
LBP -0.038 0.25 -10000 0 -0.56 72 72
PIK3R1 0.016 0.031 -10000 0 -0.12 27 27
JAK1 0.022 0.015 -10000 0 -0.056 10 10
MYC -0.12 0.4 -10000 0 -0.88 106 106
FGG -0.063 0.3 -10000 0 -0.73 67 67
macrophage differentiation -0.09 0.36 -10000 0 -0.82 79 79
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.094 -10000 0 -0.15 102 102
JUNB -0.11 0.37 -10000 0 -0.86 88 88
FOS -0.005 0.053 -10000 0 -0.12 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.023 0.16 -10000 0 -0.36 74 74
STAT1/PIAS1 -0.031 0.18 -10000 0 -0.35 92 92
GRB2/SOS1/GAB family/SHP2/PI3K -0.024 0.16 -10000 0 -0.32 87 87
STAT3 (dimer) -0.099 0.38 -10000 0 -0.88 79 79
PRKCD -0.044 0.26 -10000 0 -0.53 89 89
IL6R 0.018 0.025 -10000 0 -0.082 24 24
SOCS3 -0.047 0.22 -10000 0 -0.86 31 31
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.08 -10000 0 -0.14 82 82
Rac1/GTP -0.024 0.18 -10000 0 -0.39 79 79
HCK 0.019 0.024 -10000 0 -0.12 15 15
MAPKKK cascade -0.049 0.22 -10000 0 -0.5 95 95
bone resorption -0.057 0.29 -10000 0 -0.69 65 65
IRF1 -0.12 0.41 -10000 0 -0.95 95 95
mol:GDP -0.025 0.16 -10000 0 -0.35 79 79
SOS1 0.019 0.028 -10000 0 -0.12 20 20
VAV1 -0.025 0.16 -10000 0 -0.36 79 79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.03 0.18 -10000 0 -0.45 69 69
PTPN11 -0.007 0.16 -10000 0 -0.83 19 19
IL6/IL6RA 0.007 0.063 -10000 0 -0.13 66 66
gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.061 -10000 0 -0.12 65 65
gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.076 -10000 0 -0.14 93 93
IL6 0.005 0.049 -10000 0 -0.1 86 86
PIAS3 0.02 0.022 -10000 0 -0.12 13 13
PTPRE 0.022 0.018 0.079 19 -10000 0 19
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.003 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.097 -10000 0 -0.22 73 73
LMO4 0.021 0.023 -10000 0 -0.081 15 15
STAT3 (dimer)/PIAS3 -0.087 0.35 -10000 0 -0.81 79 79
MCL1 -0.014 0.16 -10000 0 -0.65 17 17
BARD1 signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.016 0.052 -10000 0 -0.12 70 70
ATM 0.018 0.022 -10000 0 -0.12 13 13
UBE2D3 0.023 0.001 -10000 0 -10000 0 0
PRKDC 0.021 0.015 -10000 0 -0.12 6 6
ATR 0.02 0.015 -10000 0 -0.12 5 5
UBE2L3 0.022 0.012 -10000 0 -0.12 4 4
FANCD2 -0.008 0.096 -10000 0 -0.24 69 69
protein ubiquitination -0.016 0.086 -10000 0 -0.16 77 77
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.023 0.065 -10000 0 -0.14 64 64
MRE11A 0.02 0.017 -10000 0 -0.12 7 7
DNA-PK 0.026 0.06 -10000 0 -0.14 60 60
FA complex/FANCD2/Ubiquitin 0.01 0.093 -10000 0 -0.32 27 27
FANCF 0.022 0.011 -10000 0 -0.12 3 3
BRCA1 0.015 0.03 -10000 0 -0.12 24 24
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
CDK2/Cyclin E1 -0.016 0.075 -10000 0 -0.15 110 110
FANCG 0.021 0.016 -10000 0 -0.12 7 7
BRCA1/BACH1/BARD1 -0.001 0.071 -10000 0 -0.13 125 125
FANCE 0.023 0 -10000 0 -10000 0 0
FANCC 0.022 0.014 -10000 0 -0.12 5 5
NBN 0.02 0.015 -10000 0 -0.12 5 5
FANCA 0.021 0.019 -10000 0 -0.12 10 10
DNA repair -0.014 0.11 -10000 0 -0.3 45 45
BRCA1/BARD1/ubiquitin -0.001 0.071 -10000 0 -0.13 125 125
BARD1/DNA-PK 0.027 0.076 -10000 0 -0.14 80 80
FANCL 0.018 0.023 -10000 0 -0.12 14 14
mRNA polyadenylation -0.015 0.052 0.12 70 -10000 0 70
BRCA1/BARD1/CTIP/M/R/N Complex -0.035 0.14 -10000 0 -0.33 73 73
BRCA1/BACH1/BARD1/TopBP1 0.008 0.072 -10000 0 -0.13 104 104
BRCA1/BARD1/P53 -0.026 0.092 -10000 0 -0.12 252 252
BARD1/CSTF1/BRCA1 0.013 0.065 -10000 0 -0.12 94 94
BRCA1/BACH1 0.015 0.03 -10000 0 -0.12 24 24
BARD1 0.016 0.029 -10000 0 -0.12 23 23
PCNA 0.019 0.018 -10000 0 -0.12 8 8
BRCA1/BARD1/UbcH5C 0.015 0.063 -10000 0 -0.12 88 88
BRCA1/BARD1/UbcH7 0.013 0.065 -10000 0 -0.12 93 93
BRCA1/BARD1/RAD51/PCNA 0 0.085 -10000 0 -0.12 155 155
BARD1/DNA-PK/P53 -0.008 0.096 -10000 0 -0.11 224 224
BRCA1/BARD1/Ubiquitin -0.001 0.071 -10000 0 -0.13 125 125
BRCA1/BARD1/CTIP -0.011 0.083 -10000 0 -0.13 157 157
FA complex 0.018 0.074 -10000 0 -0.17 61 61
BARD1/EWS 0.018 0.049 -10000 0 -0.12 63 63
RBBP8 0.011 0.029 -10000 0 -0.077 47 47
TP53 0.011 0.029 -10000 0 -0.12 22 22
TOPBP1 0.021 0.016 -10000 0 -0.12 6 6
G1/S transition of mitotic cell cycle 0.027 0.091 0.12 252 -10000 0 252
BRCA1/BARD1 -0.013 0.09 -10000 0 -0.16 77 77
CSTF1 0.023 0.007 -10000 0 -0.12 1 1
BARD1/EWS-Fli1 0.002 0.045 -10000 0 -0.12 62 62
CDK2 0.018 0.023 -10000 0 -0.12 14 14
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.015 0.03 -10000 0 -0.12 25 25
RAD50 0.021 0.014 -10000 0 -0.12 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.071 -10000 0 -0.13 125 125
EWSR1 0.023 0.001 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.014 0.022 -10000 0 -0.14 11 11
PRKCZ 0.023 0 -10000 0 -10000 0 0
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 6 6
ERC1 0.016 0.029 -10000 0 -0.12 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.063 0.15 -10000 0 -0.29 127 127
IRAK/TOLLIP 0.028 0.026 -10000 0 -0.1 15 15
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
IKBKG 0.023 0.009 -10000 0 -0.12 2 2
IL1 alpha/IL1R2 0.014 0.048 -10000 0 -0.15 23 23
IL1A 0.017 0.029 -10000 0 -0.12 24 24
IL1B 0.002 0.039 -10000 0 -0.085 82 82
IRAK/TRAF6/p62/Atypical PKCs 0.036 0.059 -10000 0 -0.16 16 16
IL1R2 0.007 0.045 -10000 0 -0.12 62 62
IL1R1 0.003 0.046 -10000 0 -0.12 66 66
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.063 0.15 0.16 1 -0.28 137 138
TOLLIP 0.022 0.011 -10000 0 -0.12 3 3
TICAM2 0.021 0.014 -10000 0 -0.12 5 5
MAP3K3 0.023 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.033 0.051 -10000 0 -0.14 37 37
IKK complex/ELKS 0.024 0.092 -10000 0 -0.24 50 50
JUN 0.011 0.048 -10000 0 -0.16 29 29
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.051 0.12 -10000 0 -0.21 142 142
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.001 0.077 -10000 0 -0.11 134 134
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.087 -10000 0 -0.17 67 67
IL1 beta fragment/IL1R1/IL1RAP -0.056 0.1 -10000 0 -0.15 243 243
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 0.013 0.051 -10000 0 -0.17 28 28
IRAK1 0.016 0.023 -10000 0 -0.087 23 23
IL1RN/IL1R1 -0.007 0.07 -10000 0 -0.11 159 159
IRAK4 0.019 0.02 -10000 0 -0.12 10 10
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
PI3K 0.007 0.065 -10000 0 -0.13 96 96
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.074 0.15 -10000 0 -0.3 137 137
CHUK 0.021 0.013 -10000 0 -0.12 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.056 0.1 -10000 0 -0.15 243 243
IL1 beta/IL1R2 -0.036 0.089 -10000 0 -0.15 181 181
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.057 -10000 0 -0.19 18 18
NF kappa B1 p50/RelA -0.05 0.11 -10000 0 -0.2 149 149
IRAK3 0.009 0.042 -10000 0 -0.12 52 52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.05 0.12 -10000 0 -0.2 154 154
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.03 0.11 -10000 0 -0.27 61 61
IL1 alpha/IL1R1/IL1RAP -0.014 0.078 -10000 0 -0.13 131 131
RELA 0.023 0.009 -10000 0 -0.12 2 2
MAP3K7IP1 0.023 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.014 -10000 0 -0.12 5 5
MYD88 0.023 0.006 -10000 0 -0.12 1 1
IRAK/TRAF6/MEKK3 0.039 0.031 -10000 0 -0.095 23 23
IL1RAP 0.009 0.039 -10000 0 -0.12 44 44
UBE2N 0.023 0.007 -10000 0 -0.12 1 1
IRAK/TRAF6 -0.046 0.098 -10000 0 -0.19 140 140
CASP1 0.006 0.04 -10000 0 -0.12 48 48
IL1RN/IL1R2 0.011 0.053 -10000 0 -0.094 105 105
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.045 0.1 -10000 0 -0.15 196 196
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.037 0.13 -10000 0 -0.29 93 93
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL1RN 0.019 0.024 -10000 0 -0.12 16 16
TRAF6/TAK1/TAB1/TAB2 0.041 0.054 -10000 0 -0.2 17 17
MAP2K6 0.014 0.051 -10000 0 -0.18 25 25
EPHB forward signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.011 0.049 -10000 0 -0.097 88 88
cell-cell adhesion 0.023 0.039 0.14 38 -10000 0 38
Ephrin B/EPHB2/RasGAP 0.016 0.076 -10000 0 -0.099 143 143
ITSN1 0.022 0.011 -10000 0 -0.12 3 3
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SHC1 0.023 0.001 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.022 0.034 -10000 0 -0.087 46 46
Ephrin B1/EPHB1 0.024 0.027 -10000 0 -0.068 43 43
HRAS/GDP -0.002 0.07 -10000 0 -0.14 98 98
Ephrin B/EPHB1/GRB7 0.018 0.071 -10000 0 -0.096 119 119
Endophilin/SYNJ1 -0.001 0.052 -10000 0 -0.087 124 124
KRAS 0.014 0.034 -10000 0 -0.12 33 33
Ephrin B/EPHB1/Src 0.024 0.067 -10000 0 -0.091 108 108
endothelial cell migration 0.001 0.071 -10000 0 -0.11 145 145
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GRB7 0.018 0.026 -10000 0 -0.12 18 18
PAK1 -0.003 0.057 -10000 0 -0.091 136 136
HRAS 0.023 0.006 -10000 0 -0.12 1 1
RRAS -0.006 0.056 -10000 0 -0.095 127 127
DNM1 0.021 0.019 -10000 0 -0.12 10 10
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0 0.049 -10000 0 -0.087 109 109
lamellipodium assembly -0.023 0.039 -10000 0 -0.14 38 38
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.051 -10000 0 -0.16 30 30
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
EPHB2 0.02 0.02 -10000 0 -0.12 11 11
EPHB3 0.019 0.024 -10000 0 -0.12 15 15
EPHB1 0.016 0.032 -10000 0 -0.12 28 28
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
mol:GDP -0.01 0.079 -10000 0 -0.17 99 99
Ephrin B/EPHB2 0.012 0.066 -10000 0 -0.097 123 123
Ephrin B/EPHB3 0.011 0.065 -10000 0 -0.095 123 123
JNK cascade 0.015 0.045 -10000 0 -0.1 56 56
Ephrin B/EPHB1 0.013 0.063 -10000 0 -0.095 108 108
RAP1/GDP 0.001 0.084 -10000 0 -0.15 117 117
EFNB2 0.007 0.041 -10000 0 -0.12 50 50
EFNB3 0.018 0.026 -10000 0 -0.12 19 19
EFNB1 0.021 0.018 -10000 0 -0.12 9 9
Ephrin B2/EPHB1-2 0.006 0.061 -10000 0 -0.1 101 101
RAP1B 0.019 0.02 -10000 0 -0.12 10 10
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
CDC42/GTP 0.008 0.077 -10000 0 -0.12 122 122
Rap1/GTP -0.028 0.045 -10000 0 -0.14 59 59
axon guidance 0.011 0.049 -10000 0 -0.097 88 88
MAPK3 0.008 0.063 -10000 0 -0.19 17 17
MAPK1 0.008 0.063 -10000 0 -0.19 18 18
Rac1/GDP 0.001 0.079 -10000 0 -0.15 98 98
actin cytoskeleton reorganization -0.025 0.045 -10000 0 -0.14 51 51
CDC42/GDP 0.001 0.079 -10000 0 -0.15 97 97
PI3K 0.004 0.074 -10000 0 -0.11 145 145
EFNA5 0.014 0.033 -10000 0 -0.12 30 30
Ephrin B2/EPHB4 0 0.058 -10000 0 -0.096 141 141
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.08 -10000 0 -0.15 116 116
CDC42 0.023 0.002 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.042 -10000 0 -0.13 53 53
PTK2 -0.001 0.051 -10000 0 -0.2 33 33
MAP4K4 0.015 0.045 -10000 0 -0.1 56 56
SRC 0.023 0.009 -10000 0 -0.12 2 2
KALRN 0.015 0.033 -10000 0 -0.12 30 30
Intersectin/N-WASP 0.031 0.022 -10000 0 -0.11 12 12
neuron projection morphogenesis 0.005 0.07 -10000 0 -0.16 44 44
MAP2K1 0.005 0.066 -10000 0 -0.12 89 89
WASL 0.023 0.009 -10000 0 -0.12 2 2
Ephrin B1/EPHB1-2/NCK1 0.036 0.056 -10000 0 -0.11 55 55
cell migration 0.002 0.077 -10000 0 -0.15 97 97
NRAS 0.022 0.011 -10000 0 -0.12 3 3
SYNJ1 -0.001 0.052 -10000 0 -0.088 124 124
PXN 0.022 0.014 -10000 0 -0.12 5 5
TF -0.001 0.049 -10000 0 -0.082 127 127
HRAS/GTP 0.01 0.063 -10000 0 -0.15 29 29
Ephrin B1/EPHB1-2 0.032 0.039 -10000 0 -0.11 26 26
cell adhesion mediated by integrin 0.014 0.047 0.1 102 -10000 0 102
RAC1 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0.011 0.069 -10000 0 -0.16 29 29
RAC1-CDC42/GTP -0.024 0.039 -10000 0 -0.13 39 39
RASA1 0.021 0.012 -10000 0 -0.12 3 3
RAC1-CDC42/GDP 0.009 0.08 -10000 0 -0.15 91 91
ruffle organization 0.004 0.057 -10000 0 -0.14 40 40
NCK1 0.02 0.019 -10000 0 -0.12 9 9
receptor internalization 0 0.049 -10000 0 -0.082 125 125
Ephrin B/EPHB2/KALRN 0.019 0.073 -10000 0 -0.097 131 131
ROCK1 0.017 0.028 -10000 0 -0.097 24 24
RAS family/GDP -0.028 0.049 -10000 0 -0.15 47 47
Rac1/GTP -0.024 0.041 -10000 0 -0.14 38 38
Ephrin B/EPHB1/Src/Paxillin 0 0.071 -10000 0 -0.14 100 100
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.018 0.078 -10000 0 -0.12 192 192
CRKL -0.026 0.11 -10000 0 -0.34 32 32
mol:PIP3 -0.002 0.049 0.22 24 -10000 0 24
AKT1 0.004 0.039 0.17 23 -0.1 10 33
PTK2B 0.023 0.009 -10000 0 -0.12 2 2
RAPGEF1 -0.021 0.1 -10000 0 -0.32 31 31
RANBP10 0.023 0.009 -10000 0 -0.12 2 2
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
HGF/MET/SHIP2 -0.002 0.069 -10000 0 -0.11 122 122
MAP3K5 -0.014 0.1 -10000 0 -0.3 37 37
HGF/MET/CIN85/CBL/ENDOPHILINS 0.011 0.067 -10000 0 -0.097 126 126
AP1 -0.04 0.075 -10000 0 -0.14 167 167
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis -0.17 0.32 -10000 0 -0.75 124 124
STAT3 (dimer) -0.022 0.099 -10000 0 -0.28 38 38
GAB1/CRKL/SHP2/PI3K -0.015 0.12 -10000 0 -0.3 52 52
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.014 0.11 -10000 0 -0.32 32 32
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
PTEN 0.022 0.008 -10000 0 -0.12 1 1
ELK1 -0.021 0.058 0.25 12 -10000 0 12
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.016 0.082 -10000 0 -0.19 63 63
PAK1 0.002 0.042 0.16 22 -0.099 26 48
HGF/MET/RANBP10 0 0.067 -10000 0 -0.11 118 118
HRAS -0.084 0.21 -10000 0 -0.48 122 122
DOCK1 -0.026 0.11 -10000 0 -0.31 41 41
GAB1 -0.031 0.11 -10000 0 -0.35 33 33
CRK -0.026 0.11 -10000 0 -0.33 32 32
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.073 0.19 -10000 0 -0.42 122 122
JUN 0.014 0.033 -10000 0 -0.12 30 30
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.028 0.077 -10000 0 -0.17 119 119
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
cell morphogenesis -0.028 0.12 -10000 0 -0.27 67 67
GRB2/SHC -0.006 0.078 -10000 0 -0.14 128 128
FOS -0.005 0.053 -10000 0 -0.12 95 95
GLMN 0.004 0.013 0.076 7 -0.049 17 24
cell motility -0.021 0.058 0.25 12 -10000 0 12
HGF/MET/MUC20 -0.011 0.062 -10000 0 -0.092 196 196
cell migration -0.006 0.077 -10000 0 -0.14 128 128
GRB2 0.023 0.006 -10000 0 -0.12 1 1
CBL 0.023 0.006 -10000 0 -0.12 1 1
MET/RANBP10 -0.015 0.074 -10000 0 -0.12 187 187
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.092 -10000 0 -0.27 30 30
MET/MUC20 -0.028 0.068 -10000 0 -0.12 186 186
RAP1B -0.019 0.1 -10000 0 -0.3 35 35
RAP1A -0.019 0.1 -10000 0 -0.3 37 37
HGF/MET/RANBP9 -0.003 0.071 -10000 0 -0.12 126 126
RAF1 -0.077 0.2 -10000 0 -0.46 123 123
STAT3 -0.02 0.098 -10000 0 -0.3 31 31
cell proliferation -0.036 0.13 -10000 0 -0.26 124 124
RPS6KB1 -0.018 0.077 -10000 0 -0.26 37 37
MAPK3 -0.025 0.075 0.69 5 -10000 0 5
MAPK1 -0.021 0.092 0.7 8 -10000 0 8
RANBP9 0.021 0.014 -10000 0 -0.12 5 5
MAPK8 -0.015 0.12 -10000 0 -0.35 46 46
SRC -0.016 0.086 -10000 0 -0.25 30 30
PI3K -0.022 0.092 -10000 0 -0.16 128 128
MET/Glomulin -0.003 0.05 -10000 0 -0.097 95 95
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K1 -0.068 0.19 -10000 0 -0.42 123 123
MET 0 0.047 -10000 0 -0.12 70 70
MAP4K1 -0.014 0.1 -10000 0 -0.33 28 28
PTK2 0.021 0.016 -10000 0 -0.12 6 6
MAP2K2 -0.07 0.19 -10000 0 -0.43 123 123
BAD 0.008 0.037 0.16 23 -0.096 10 33
MAP2K4 -0.011 0.097 -10000 0 -0.27 38 38
SHP2/GRB2/SOS1/GAB1 -0.029 0.12 -10000 0 -0.22 130 130
INPPL1 0.021 0.017 -10000 0 -0.12 8 8
PXN 0.022 0.014 -10000 0 -0.12 5 5
SH3KBP1 0.02 0.019 -10000 0 -0.12 10 10
HGS -0.022 0.071 -10000 0 -0.15 119 119
PLCgamma1/PKC 0.012 0.026 -10000 0 -0.1 26 26
HGF 0.02 0.023 -10000 0 -0.12 14 14
RASA1 0.021 0.012 -10000 0 -0.12 3 3
NCK1 0.02 0.019 -10000 0 -0.12 9 9
PTPRJ 0.02 0.019 -10000 0 -0.12 9 9
NCK/PLCgamma1 -0.014 0.085 -10000 0 -0.15 131 131
PDPK1 0.001 0.043 0.19 24 -0.11 9 33
HGF/MET/SHIP -0.011 0.062 -10000 0 -0.092 196 196
IGF1 pathway

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTK2 0.021 0.016 -10000 0 -0.12 6 6
CRKL -0.005 0.054 -10000 0 -0.12 91 91
GRB2/SOS1/SHC 0.035 0.041 -10000 0 -0.12 30 30
HRAS 0.023 0.006 -10000 0 -0.12 1 1
IRS1/Crk -0.001 0.057 -10000 0 -0.12 91 91
IGF-1R heterotetramer/IGF1/PTP1B 0.008 0.062 -10000 0 -0.12 89 89
AKT1 -0.01 0.06 -10000 0 -0.11 108 108
BAD -0.007 0.057 -10000 0 -0.1 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.054 -10000 0 -0.12 91 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.062 -10000 0 -0.12 105 105
RAF1 -0.004 0.092 -10000 0 -0.48 12 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.01 0.07 -10000 0 -0.11 110 110
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.004 0.063 -10000 0 -0.13 91 91
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
RPS6KB1 -0.011 0.063 -10000 0 -0.12 110 110
GNB2L1 0.023 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.079 0.2 7 -0.38 12 19
PXN 0.022 0.014 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.021 0.045 -10000 0 -0.12 50 50
HRAS/GTP -0.002 0.052 -10000 0 -0.1 89 89
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.022 0.068 -10000 0 -0.12 46 46
IGF-1R heterotetramer 0.012 0.033 -10000 0 -0.093 41 41
IGF-1R heterotetramer/IGF1/IRS/Nck 0.008 0.062 -10000 0 -0.12 91 91
Crk/p130 Cas/Paxillin 0.021 0.06 -10000 0 -0.099 86 86
IGF1R 0.012 0.033 -10000 0 -0.093 41 41
IGF1 0.001 0.047 -10000 0 -0.076 124 124
IRS2/Crk 0.004 0.054 -10000 0 -0.11 87 87
PI3K 0 0.076 -10000 0 -0.11 147 147
apoptosis -0.003 0.057 0.12 59 -10000 0 59
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
PRKCD -0.015 0.093 -10000 0 -0.2 93 93
RAF1/14-3-3 E 0.007 0.084 -10000 0 -0.4 12 12
BAD/14-3-3 0.003 0.06 -10000 0 -0.12 59 59
PRKCZ -0.009 0.059 -10000 0 -0.11 107 107
Crk/p130 Cas/Paxillin/FAK1 0.004 0.069 -10000 0 -0.15 55 55
PTPN1 0.023 0.006 -10000 0 -0.12 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.016 0.095 -10000 0 -0.21 89 89
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.019 0.061 -10000 0 -0.095 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IRS1/NCK2 0.002 0.058 -10000 0 -0.12 91 91
GRB10 0.022 0.014 -10000 0 -0.12 5 5
PTPN11 -0.006 0.057 -10000 0 -0.12 92 92
IRS1 -0.011 0.058 -10000 0 -0.13 91 91
IRS2 -0.005 0.054 -10000 0 -0.12 92 92
IGF-1R heterotetramer/IGF1 -0.012 0.076 -10000 0 -0.16 91 91
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDPK1 -0.011 0.064 -10000 0 -0.11 141 141
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKD1 -0.021 0.097 -10000 0 -0.21 98 98
SHC1 0.023 0.001 -10000 0 -10000 0 0
Integrins in angiogenesis

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.049 -9999 0 -0.12 58 58
alphaV beta3 Integrin -0.001 0.073 -9999 0 -0.13 107 107
PTK2 -0.029 0.13 -9999 0 -0.27 92 92
IGF1R 0.013 0.032 -9999 0 -0.12 28 28
PI4KB 0.022 0.014 -9999 0 -0.12 5 5
MFGE8 0.006 0.043 -9999 0 -0.12 56 56
SRC 0.023 0.009 -9999 0 -0.12 2 2
CDKN1B -0.006 0.085 -9999 0 -0.34 28 28
VEGFA 0.019 0.021 -9999 0 -0.12 11 11
ILK 0.013 0.04 -9999 0 -0.31 3 3
ROCK1 0.022 0.009 -9999 0 -0.12 2 2
AKT1 0.014 0.038 -9999 0 -0.28 3 3
PTK2B -0.011 0.063 -9999 0 -0.11 139 139
alphaV/beta3 Integrin/JAM-A 0.014 0.068 -9999 0 -0.1 114 114
CBL 0.023 0.006 -9999 0 -0.12 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.001 0.073 -9999 0 -0.13 107 107
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.07 -9999 0 -0.11 107 107
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.095 -9999 0 -0.25 51 51
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.074 -9999 0 -0.13 113 113
PI4KA 0.021 0.016 -9999 0 -0.12 7 7
IGF-1R heterotetramer/IGF1/IRS1 -0.055 0.086 -9999 0 -0.16 152 152
PI4 Kinase 0.028 0.032 -9999 0 -0.12 24 24
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
alphaV/beta3 Integrin/Osteopontin -0.03 0.098 -9999 0 -0.16 164 164
RPS6KB1 -0.056 0.082 -9999 0 -0.16 163 163
TLN1 0.021 0.012 -9999 0 -0.12 3 3
MAPK3 -0.054 0.14 -9999 0 -0.34 102 102
GPR124 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 -0.055 0.14 -9999 0 -0.34 102 102
PXN 0.022 0.014 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
alphaV/beta3 Integrin/Tumstatin -0.001 0.073 -9999 0 -0.13 107 107
cell adhesion -0.03 0.097 -9999 0 -0.18 117 117
ANGPTL3 0.022 0.011 -9999 0 -0.12 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.044 -9999 0 -0.11 38 38
IGF-1R heterotetramer 0.013 0.032 -9999 0 -0.12 28 28
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
TGFBR2 0.02 0.02 -9999 0 -0.12 11 11
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
IGF1 0.007 0.045 -9999 0 -0.12 60 60
RAC1 0.023 0.002 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.001 0.073 -9999 0 -0.13 107 107
apoptosis 0.013 0.032 -9999 0 -0.12 28 28
CD47 0.021 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/CD47 -0.009 0.084 -9999 0 -0.14 124 124
VCL 0.021 0.013 -9999 0 -0.12 4 4
alphaV/beta3 Integrin/Del1 -0.03 0.083 -9999 0 -0.14 161 161
CSF1 0.013 0.033 -9999 0 -0.12 31 31
PIK3C2A -0.012 0.1 -9999 0 -0.36 41 41
PI4 Kinase/Pyk2 0.001 0.059 -9999 0 -0.14 49 49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.001 0.079 -9999 0 -0.12 139 139
FAK1/Vinculin -0.016 0.12 -9999 0 -0.23 95 95
alphaV beta3/Integrin/ppsTEM5 -0.001 0.073 -9999 0 -0.13 107 107
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VTN 0.023 0.009 -9999 0 -0.12 2 2
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
FGF2 0.023 0.009 -9999 0 -0.12 2 2
F11R 0.022 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/Lactadherin -0.028 0.088 -9999 0 -0.14 170 170
alphaV/beta3 Integrin/TGFBR2 -0.006 0.079 -9999 0 -0.14 112 112
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.015 0.075 -9999 0 -0.12 112 112
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.005 0.074 -9999 0 -0.12 124 124
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.013 0.056 -9999 0 -0.12 114 114
alphaV/beta3 Integrin/Pyk2 0 0.072 -9999 0 -0.16 49 49
SDC1 0.021 0.018 -9999 0 -0.12 9 9
VAV3 -0.012 0.074 -9999 0 -0.14 118 118
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
IRS1 0.019 0.023 -9999 0 -0.12 14 14
FAK1/Paxillin -0.014 0.11 -9999 0 -0.23 87 87
cell migration -0.011 0.11 -9999 0 -0.21 92 92
ITGAV 0.013 0.032 -9999 0 -0.12 28 28
PI3K 0.006 0.083 -9999 0 -0.17 61 61
SPP1 0.012 0.032 -9999 0 -0.12 28 28
KDR 0.021 0.019 -9999 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.032 -9999 0 -0.12 28 28
COL4A3 0.023 0.009 -9999 0 -0.12 2 2
angiogenesis -0.056 0.16 -9999 0 -0.37 102 102
Rac1/GTP -0.007 0.075 -9999 0 -0.18 54 54
EDIL3 -0.007 0.057 -9999 0 -0.12 109 109
cell proliferation -0.006 0.079 -9999 0 -0.14 112 112
a4b1 and a4b7 Integrin signaling

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
ITGA4 0.015 0.03 -9999 0 -0.12 24 24
alpha4/beta7 Integrin 0.004 0.065 -9999 0 -0.13 106 106
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 101 101
PLK1 signaling events

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.012 0.057 0.18 53 -10000 0 53
BUB1B -0.028 0.1 -10000 0 -0.22 93 93
PLK1 -0.009 0.049 -10000 0 -0.1 94 94
PLK1S1 -0.003 0.022 0.027 4 -0.047 87 91
KIF2A -0.006 0.047 -10000 0 -0.11 77 77
regulation of mitotic centrosome separation -0.009 0.048 -10000 0 -0.1 94 94
GOLGA2 0.023 0.006 -10000 0 -0.12 1 1
Hec1/SPC24 -0.015 0.088 -10000 0 -0.15 136 136
WEE1 -0.014 0.076 -10000 0 -0.18 71 71
cytokinesis -0.053 0.14 -10000 0 -0.31 112 112
PP2A-alpha B56 -0.036 0.24 -10000 0 -0.7 61 61
AURKA -0.025 0.09 -10000 0 -0.26 70 70
PICH/PLK1 -0.024 0.1 -10000 0 -0.17 147 147
CENPE -0.005 0.046 -10000 0 -0.11 73 73
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
positive regulation of microtubule depolymerization -0.006 0.047 -10000 0 -0.11 77 77
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.023 0 -10000 0 -10000 0 0
TPX2 -0.034 0.099 -10000 0 -0.26 90 90
PAK1 0.016 0.029 -10000 0 -0.12 23 23
SPC24 0.016 0.029 -10000 0 -0.12 24 24
FBXW11 0.023 0.003 -10000 0 -10000 0 0
CLSPN 0 0.035 -10000 0 -0.18 7 7
GORASP1 0.023 0.006 -10000 0 -0.12 1 1
metaphase -0.001 0.004 -10000 0 -0.014 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.022 0.027 4 -0.047 87 91
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.009 56 56
STAG2 0.02 0.02 -10000 0 -0.12 10 10
GRASP65/GM130/RAB1/GTP 0.017 0.031 -10000 0 -10000 0 0
spindle elongation -0.009 0.048 -10000 0 -0.1 94 94
ODF2 0.021 0.014 -10000 0 -0.12 5 5
BUB1 -0.063 0.25 -10000 0 -0.77 61 61
TPT1 0.001 0.035 -10000 0 -0.16 16 16
CDC25C -0.016 0.096 -10000 0 -0.37 34 34
CDC25B 0.015 0.025 -10000 0 -0.13 14 14
SGOL1 -0.012 0.057 -10000 0 -0.18 53 53
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CCNB1/CDK1 -0.028 0.13 -10000 0 -0.24 138 138
CDC14B 0.011 0.004 -10000 0 -0.085 1 1
CDC20 0.016 0.027 -10000 0 -0.12 19 19
PLK1/PBIP1 -0.003 0.042 -10000 0 -0.096 72 72
mitosis 0.003 0.009 0.026 63 -0.011 1 64
FBXO5 -0.019 0.07 -10000 0 -0.15 93 93
CDC2 0.007 0.04 -10000 0 -0.12 46 46
NDC80 0.008 0.038 -10000 0 -0.12 43 43
metaphase plate congression 0 0.042 -10000 0 -0.16 21 21
ERCC6L -0.033 0.12 -10000 0 -0.23 135 135
NLP/gamma Tubulin -0.002 0.029 -10000 0 -0.08 49 49
microtubule cytoskeleton organization 0.001 0.035 -10000 0 -0.16 16 16
G2/M transition DNA damage checkpoint 0 0.002 0.01 16 -10000 0 16
PPP1R12A 0.022 0.008 -10000 0 -0.12 1 1
interphase 0 0.002 0.01 16 -10000 0 16
PLK1/PRC1-2 -0.015 0.095 -10000 0 -0.17 121 121
GRASP65/GM130/RAB1/GTP/PLK1 0.024 0.053 -10000 0 -0.12 49 49
RAB1A 0.023 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.011 0.051 -10000 0 -0.11 88 88
mitotic prometaphase -0.001 0.003 0.02 6 -0.01 24 30
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.058 -10000 0 -0.23 18 18
microtubule-based process -0.01 0.072 -10000 0 -0.14 102 102
Golgi organization -0.009 0.048 -10000 0 -0.1 94 94
Cohesin/SA2 -0.003 0.054 -10000 0 -0.12 84 84
PPP1CB/MYPT1 0.024 0.039 -10000 0 -0.14 28 28
KIF20A 0.009 0.038 -10000 0 -0.12 43 43
APC/C/CDC20 -0.005 0.069 -10000 0 -0.13 101 101
PPP2R1A 0.022 0.009 -10000 0 -0.12 2 2
chromosome segregation -0.003 0.042 -10000 0 -0.095 72 72
PRC1 0.015 0.03 -10000 0 -0.12 25 25
ECT2 -0.021 0.072 -10000 0 -0.14 112 112
C13orf34 -0.01 0.05 -10000 0 -0.11 86 86
NUDC 0 0.042 -10000 0 -0.16 21 21
regulation of attachment of spindle microtubules to kinetochore -0.028 0.099 -10000 0 -0.22 93 93
spindle assembly -0.005 0.037 -10000 0 -0.08 86 86
spindle stabilization -0.003 0.022 0.027 4 -0.047 87 91
APC/C/HCDH1 0.025 0.007 -10000 0 -0.089 2 2
MKLP2/PLK1 -0.01 0.073 -10000 0 -0.14 102 102
CCNB1 0.014 0.028 -10000 0 -0.12 21 21
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.023 0.002 -10000 0 -10000 0 0
ROCK2 -0.016 0.095 -10000 0 -0.33 42 42
TUBG1 0 0.039 -10000 0 -0.17 18 18
G2/M transition of mitotic cell cycle -0.043 0.12 -10000 0 -0.23 138 138
MLF1IP 0.01 0.011 -10000 0 -0.079 8 8
INCENP 0.022 0.009 -10000 0 -0.12 2 2
IFN-gamma pathway

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.08 -10000 0 -0.14 101 101
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.023 0.009 -10000 0 -0.12 2 2
STAT1 (dimer)/Cbp/p300 -0.019 0.13 -10000 0 -0.22 123 123
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.081 -10000 0 -0.16 94 94
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.093 -10000 0 -0.2 134 134
CaM/Ca2+ 0.01 0.077 -10000 0 -0.15 69 69
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
STAT1 (dimer)/SHP2 -0.018 0.093 -10000 0 -0.19 95 95
AKT1 -0.014 0.081 -10000 0 -0.18 84 84
MAP2K1 -0.007 0.068 -10000 0 -0.15 76 76
MAP3K11 -0.007 0.067 -10000 0 -0.14 75 75
IFNGR1 0.016 0.026 -10000 0 -0.12 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.014 0.082 -10000 0 -0.29 27 27
Rap1/GTP -0.023 0.056 -10000 0 -0.16 59 59
CRKL/C3G 0.034 0.01 -10000 0 -0.094 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.023 0.079 -10000 0 -0.14 74 74
CEBPB -0.014 0.15 -10000 0 -0.41 52 52
STAT3 0.022 0.011 -10000 0 -0.12 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.11 -10000 0 -0.99 3 3
STAT1 -0.019 0.087 -10000 0 -0.2 81 81
CALM1 0.022 0.014 -10000 0 -0.12 5 5
IFN-gamma (dimer) 0.01 0.039 -10000 0 -0.12 43 43
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
STAT1 (dimer)/PIAS1 -0.015 0.091 -10000 0 -0.18 93 93
CEBPB/PTGES2/Cbp/p300 -0.036 0.11 -10000 0 -0.3 64 64
mol:Ca2+ 0.005 0.078 -10000 0 -0.13 101 101
MAPK3 -0.009 0.11 -10000 0 -0.55 12 12
STAT1 (dimer) -0.041 0.15 -10000 0 -0.27 134 134
MAPK1 -0.013 0.13 -10000 0 -0.61 15 15
JAK2 0.016 0.026 -10000 0 -0.13 16 16
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
JAK1 0.02 0.012 -10000 0 -0.12 2 2
CAMK2D 0.018 0.024 -10000 0 -0.12 16 16
DAPK1 -0.015 0.16 -10000 0 -0.48 48 48
SMAD7 -0.009 0.064 -10000 0 -0.11 116 116
CBL/CRKL/C3G 0.017 0.068 -10000 0 -0.15 53 53
PI3K -0.004 0.092 -10000 0 -0.18 89 89
IFNG 0.01 0.039 -10000 0 -0.12 43 43
apoptosis -0.018 0.13 0.22 1 -0.39 47 48
CAMK2G 0.023 0.006 -10000 0 -0.12 1 1
STAT3 (dimer) 0.022 0.011 -10000 0 -0.12 3 3
CAMK2A 0.023 0.006 -10000 0 -0.12 1 1
CAMK2B 0.023 0.009 -10000 0 -0.12 2 2
FRAP1 -0.012 0.077 -10000 0 -0.17 79 79
PRKCD -0.016 0.086 -10000 0 -0.19 84 84
RAP1B 0.019 0.02 -10000 0 -0.12 10 10
negative regulation of cell growth -0.053 0.093 -10000 0 -0.2 134 134
PTPN2 0.023 0.007 -10000 0 -0.12 1 1
EP300 0.022 0.01 -10000 0 -0.12 2 2
IRF1 -0.038 0.13 -10000 0 -0.27 105 105
STAT1 (dimer)/PIASy -0.015 0.089 0.19 3 -0.19 80 83
SOCS1 0.007 0.096 -10000 0 -1.2 3 3
mol:GDP 0.015 0.065 -10000 0 -0.14 54 54
CASP1 -0.031 0.095 -10000 0 -0.17 156 156
PTGES2 0.023 0.009 -10000 0 -0.12 2 2
IRF9 0.004 0.071 -10000 0 -0.15 72 72
mol:PI-3-4-5-P3 -0.013 0.085 -10000 0 -0.18 89 89
RAP1/GDP 0.006 0.073 -10000 0 -0.17 56 56
CBL -0.006 0.066 -10000 0 -0.15 69 69
MAP3K1 -0.008 0.071 -10000 0 -0.16 76 76
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
PIAS4 0.023 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.093 -10000 0 -0.2 134 134
PTPN11 -0.01 0.067 -10000 0 -0.13 102 102
CREBBP 0.02 0.016 -10000 0 -0.12 6 6
RAPGEF1 0.023 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.004 0.11 -10000 0 -0.26 49 49
ACTA1 0.023 0.073 0.15 59 -0.2 18 77
NUMA1 0.001 0.11 0.17 9 -0.25 62 71
SPTAN1 0.019 0.077 0.15 60 -0.2 21 81
LIMK1 0.025 0.072 0.15 61 -0.22 13 74
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
BAX 0.023 0 -10000 0 -10000 0 0
CASP10 0.005 0.036 -10000 0 -0.072 89 89
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.008 0.14 0.16 12 -0.31 67 79
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
apoptotic nuclear changes 0.019 0.076 0.15 60 -0.2 21 81
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.009 -10000 0 -0.12 2 2
GSN 0.021 0.074 0.15 57 -0.21 18 75
MADD 0.023 0.006 -10000 0 -0.12 1 1
TFAP2A -0.03 0.15 -10000 0 -0.48 48 48
BID 0.01 0.037 -10000 0 -0.085 34 34
MAP3K1 0.009 0.08 -10000 0 -0.36 20 20
TRADD 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.025 0.041 -10000 0 -0.16 23 23
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.006 0.076 0.14 36 -0.21 25 61
CASP9 0.021 0.014 -10000 0 -0.12 5 5
DNA repair -0.023 0.074 0.26 22 -0.13 75 97
neuron apoptosis -0.026 0.16 -10000 0 -0.56 42 42
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.01 0.1 0.17 34 -0.27 30 64
APAF1 0.021 0.014 -10000 0 -0.12 5 5
CASP6 -0.055 0.25 -10000 0 -0.78 58 58
TRAF2 0.023 0 -10000 0 -10000 0 0
ICAD/CAD 0.028 0.069 0.15 60 -0.21 13 73
CASP7 0.044 0.077 0.19 104 -0.19 6 110
KRT18 -0.014 0.12 -10000 0 -0.56 22 22
apoptosis -0.006 0.13 0.18 29 -0.31 59 88
DFFA 0.025 0.072 0.15 60 -0.22 13 73
DFFB 0.025 0.072 0.15 62 -0.22 13 75
PARP1 0.024 0.074 0.13 74 -0.26 22 96
actin filament polymerization -0.025 0.069 0.2 14 -0.15 59 73
TNF 0.02 0.02 -10000 0 -0.12 11 11
CYCS -0.005 0.049 -10000 0 -0.18 28 28
SATB1 -0.064 0.24 -10000 0 -0.75 59 59
SLK 0.018 0.077 0.15 60 -0.21 18 78
p15 BID/BAX 0.016 0.044 -10000 0 -0.1 34 34
CASP2 0.008 0.066 -10000 0 -0.23 18 18
JNK cascade -0.009 0.079 0.36 20 -10000 0 20
CASP3 0.023 0.077 0.16 62 -0.2 19 81
LMNB2 -0.002 0.099 -10000 0 -0.26 62 62
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP4 0.015 0.029 -10000 0 -0.12 23 23
Mammalian IAPs/DIABLO -0.019 0.084 -10000 0 -0.13 157 157
negative regulation of DNA binding -0.03 0.15 -10000 0 -0.47 48 48
stress fiber formation 0.018 0.076 0.15 60 -0.2 18 78
GZMB 0.005 0.045 -10000 0 -0.1 79 79
CASP1 -0.064 0.14 -10000 0 -0.28 148 148
LMNB1 -0.028 0.14 -10000 0 -0.28 103 103
APP -0.026 0.16 -10000 0 -0.57 41 41
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.002 -10000 0 -10000 0 0
VIM -0.003 0.13 0.18 30 -0.32 57 87
LMNA -0.008 0.11 -10000 0 -0.27 72 72
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.07 -10000 0 -0.23 21 21
LRDD 0.022 0.015 -10000 0 -0.12 6 6
SREBF1 0.024 0.074 0.15 62 -0.22 14 76
APAF-1/Caspase 9 0.027 0.11 0.26 16 -0.75 8 24
nuclear fragmentation during apoptosis 0.001 0.11 0.17 9 -0.25 62 71
CFL2 0.025 0.07 0.15 59 -0.2 14 73
GAS2 0.023 0.072 0.15 60 -0.21 15 75
positive regulation of apoptosis -0.014 0.12 -10000 0 -0.3 66 66
PRF1 0.013 0.036 -10000 0 -0.12 37 37
Signaling events mediated by PTP1B

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.042 -10000 0 -0.12 52 52
Jak2/Leptin Receptor -0.043 0.13 0.21 1 -0.36 60 61
PTP1B/AKT1 -0.06 0.1 -10000 0 -0.23 97 97
FYN 0.011 0.037 -10000 0 -0.12 40 40
p210 bcr-abl/PTP1B -0.075 0.1 -10000 0 -0.26 98 98
EGFR 0.014 0.031 -10000 0 -0.13 25 25
EGF/EGFR -0.058 0.1 -10000 0 -0.23 109 109
CSF1 0.013 0.033 -10000 0 -0.12 31 31
AKT1 0.02 0.019 -10000 0 -0.12 10 10
INSR 0.021 0.017 -10000 0 -0.12 8 8
PTP1B/N-cadherin -0.094 0.12 -10000 0 -0.24 187 187
Insulin Receptor/Insulin -0.031 0.091 -10000 0 -0.2 77 77
HCK 0.019 0.024 -10000 0 -0.12 15 15
CRK 0.021 0.016 -10000 0 -0.12 7 7
TYK2 -0.068 0.1 -10000 0 -0.25 96 96
EGF 0.018 0.022 -10000 0 -0.13 12 12
YES1 0.02 0.018 -10000 0 -0.12 8 8
CAV1 -0.056 0.096 -10000 0 -0.24 89 89
TXN 0.019 0.015 -10000 0 -0.12 5 5
PTP1B/IRS1/GRB2 -0.055 0.11 -10000 0 -0.23 104 104
cell migration 0.075 0.1 0.26 98 -10000 0 98
STAT3 0.021 0.011 -10000 0 -0.12 3 3
PRLR 0.014 0.042 -10000 0 -0.12 53 53
ITGA2B 0.022 0.006 -10000 0 -0.13 1 1
CSF1R 0.014 0.031 -10000 0 -0.12 27 27
Prolactin Receptor/Prolactin 0.035 0.035 -10000 0 -0.18 2 2
FGR 0.023 0.006 -10000 0 -0.12 1 1
PTP1B/p130 Cas -0.063 0.1 -10000 0 -0.24 96 96
Crk/p130 Cas -0.052 0.1 -10000 0 -0.23 96 96
DOK1 -0.056 0.094 -10000 0 -0.23 88 88
JAK2 -0.052 0.13 -10000 0 -0.39 57 57
Jak2/Leptin Receptor/Leptin -0.056 0.12 -10000 0 -0.24 130 130
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
PTPN1 -0.075 0.1 -10000 0 -0.26 99 99
LYN 0.021 0.013 -10000 0 -0.12 4 4
CDH2 -0.015 0.057 -10000 0 -0.12 120 120
SRC -0.008 0.054 -10000 0 -0.61 2 2
ITGB3 0.003 0.047 -10000 0 -0.12 68 68
CAT1/PTP1B -0.058 0.12 -10000 0 -0.26 103 103
CAPN1 0.02 0.013 -10000 0 -0.12 4 4
CSK 0.023 0.009 -10000 0 -0.12 2 2
PI3K -0.033 0.1 -10000 0 -0.2 98 98
mol:H2O2 0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.05 0.12 -10000 0 -0.23 131 131
negative regulation of transcription -0.05 0.13 -10000 0 -0.38 57 57
FCGR2A 0.013 0.031 -10000 0 -0.12 26 26
FER 0.019 0.018 -10000 0 -0.12 8 8
alphaIIb/beta3 Integrin 0.008 0.053 -10000 0 -0.1 100 100
BLK 0.022 0.015 -10000 0 -0.12 6 6
Insulin Receptor/Insulin/Shc 0.043 0.022 -10000 0 -0.11 8 8
RHOA 0.021 0.007 -10000 0 -0.13 1 1
LEPR 0.018 0.028 -10000 0 -0.12 21 21
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
p210 bcr-abl/Grb2 0.023 0.006 -10000 0 -0.12 1 1
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 0 0.087 -10000 0 -0.22 47 47
PRL 0.027 0.013 -10000 0 -0.13 3 3
SOCS3 -0.031 0.23 -10000 0 -1.2 22 22
SPRY2 -0.009 0.055 -10000 0 -0.12 103 103
Insulin Receptor/Insulin/IRS1 0.039 0.03 -10000 0 -0.11 12 12
CSF1/CSF1R -0.077 0.13 -10000 0 -0.26 138 138
Ras protein signal transduction 0.029 0.034 0.093 48 -0.16 5 53
IRS1 0.019 0.023 -10000 0 -0.12 14 14
INS 0.022 0.011 -10000 0 -0.13 3 3
LEP 0.022 0.006 -10000 0 -0.12 1 1
STAT5B -0.06 0.1 -10000 0 -0.24 98 98
STAT5A -0.062 0.1 -10000 0 -0.24 106 106
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDGFB-D/PDGFRB -0.069 0.1 -10000 0 -0.24 110 110
CSN2 0.04 0.027 -10000 0 -10000 0 0
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
LAT -0.083 0.19 -10000 0 -0.5 87 87
YBX1 0.033 0.015 -10000 0 -0.18 2 2
LCK 0.022 0.015 -10000 0 -0.12 6 6
SHC1 0.023 0.001 -10000 0 -10000 0 0
NOX4 -0.021 0.062 -10000 0 -0.12 152 152
Canonical Wnt signaling pathway

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.037 0.047 0.11 128 -0.089 10 138
AES 0.036 0.042 0.099 124 -0.11 10 134
FBXW11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 66 66
SMAD4 0.022 0.007 -10000 0 -0.12 1 1
DKK2 0.023 0.011 -10000 0 -0.12 3 3
TLE1 0.033 0.038 0.1 85 -0.11 8 93
MACF1 0.016 0.026 -10000 0 -0.12 18 18
CTNNB1 0.021 0.098 0.18 8 -0.31 27 35
WIF1 0.02 0.022 -10000 0 -0.12 13 13
beta catenin/RanBP3 0.084 0.19 0.38 135 -0.35 13 148
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 33 33
beta catenin/beta TrCP1 0.033 0.096 0.19 8 -0.29 28 36
FZD1 0.023 0.006 -10000 0 -0.12 1 1
AXIN2 -0.037 0.16 -10000 0 -0.64 20 20
AXIN1 0.023 0.011 -10000 0 -0.12 3 3
RAN 0.024 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.036 0.083 -10000 0 -0.48 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.11 0.24 8 -0.29 39 47
Axin1/APC/GSK3 0.027 0.06 -10000 0 -0.25 16 16
Axin1/APC/GSK3/beta catenin/Macf1 0.03 0.068 -10000 0 -0.24 20 20
HNF1A 0.037 0.038 0.1 111 -0.12 3 114
CTBP1 0.037 0.04 0.1 110 -0.11 7 117
MYC -0.17 0.44 -10000 0 -1.3 74 74
RANBP3 0.023 0.009 -10000 0 -0.12 2 2
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 32 32
NKD1 0.022 0.012 -10000 0 -0.12 4 4
TCF4 0.036 0.042 0.1 120 -0.093 8 128
TCF3 0.037 0.039 0.1 93 -0.12 5 98
WNT1/LRP6/FZD1/Axin1 0.044 0.044 -10000 0 -0.097 36 36
Ran/GTP 0.018 0.012 -10000 0 -0.14 3 3
CtBP/CBP/TCF/TLE1/AES 0.08 0.23 0.45 130 -0.34 15 145
LEF1 0.011 0.057 0.095 86 -0.11 75 161
DVL1 0.027 0.076 -10000 0 -0.32 19 19
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.025 0.14 -10000 0 -0.29 79 79
DKK1/LRP6/Kremen 2 0.027 0.047 -10000 0 -0.11 34 34
LRP6 0.014 0.034 -10000 0 -0.12 32 32
CSNK1A1 0.04 0.044 0.11 125 -0.13 1 126
NLK 0.017 0.022 -10000 0 -0.13 11 11
CCND1 -0.19 0.45 -10000 0 -1.3 84 84
WNT1 0.023 0.009 -10000 0 -0.12 2 2
GSK3A 0.021 0.019 -10000 0 -0.12 10 10
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
FRAT1 0.023 0.006 -10000 0 -0.12 1 1
PPP2R5D 0.018 0.044 -10000 0 -0.19 17 17
APC 0.022 0.033 -10000 0 -0.085 38 38
WNT1/LRP6/FZD1 0.018 0.056 -10000 0 -0.15 36 36
CREBBP 0.035 0.037 0.1 96 -0.1 5 101
Ras signaling in the CD4+ TCR pathway

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.026 0.13 -9999 0 -0.25 110 110
MAP3K8 0.021 0.009 -9999 0 -0.12 2 2
FOS -0.014 0.093 -9999 0 -0.29 26 26
PRKCA 0.008 0.037 -9999 0 -0.12 40 40
PTPN7 0.017 0.013 -9999 0 -10000 0 0
HRAS 0.022 0.006 -9999 0 -0.12 1 1
PRKCB -0.003 0.006 -9999 0 -0.01 194 194
NRAS 0.021 0.012 -9999 0 -0.12 3 3
RAS family/GTP 0.024 0.043 -9999 0 -0.11 38 38
MAPK3 0.002 0.068 -9999 0 -0.44 6 6
MAP2K1 -0.017 0.091 -9999 0 -0.29 46 46
ELK1 0.015 0.02 -9999 0 -0.13 6 6
BRAF -0.016 0.086 -9999 0 -0.3 42 42
mol:GTP -0.001 0.002 -9999 0 -0.003 187 187
MAPK1 0 0.076 -9999 0 -0.44 9 9
RAF1 -0.017 0.085 -9999 0 -0.29 47 47
KRAS 0.013 0.034 -9999 0 -0.12 33 33
Noncanonical Wnt signaling pathway

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.02 0.019 -9999 0 -0.12 10 10
GNB1/GNG2 -0.012 0.11 -9999 0 -0.23 68 68
mol:DAG -0.018 0.095 -9999 0 -0.21 76 76
PLCG1 -0.019 0.097 -9999 0 -0.21 76 76
YES1 -0.029 0.1 -9999 0 -0.26 63 63
FZD3 0.013 0.032 -9999 0 -0.12 29 29
FZD6 0.017 0.023 -9999 0 -0.12 13 13
G protein -0.009 0.1 -9999 0 -0.22 68 68
MAP3K7 -0.014 0.084 -9999 0 -0.18 82 82
mol:Ca2+ -0.017 0.093 -9999 0 -0.2 76 76
mol:IP3 -0.018 0.095 -9999 0 -0.21 76 76
NLK 0.026 0.045 -9999 0 -0.98 1 1
GNB1 0.023 0.007 -9999 0 -0.12 1 1
CAMK2A -0.015 0.087 -9999 0 -0.19 76 76
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.033 0.1 -9999 0 -0.26 61 61
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
GNAS -0.028 0.098 -9999 0 -0.25 61 61
GO:0007205 -0.021 0.093 -9999 0 -0.21 76 76
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.022 0.011 -9999 0 -0.12 3 3
NFAT1/CK1 alpha -0.01 0.11 -9999 0 -0.22 82 82
GNG2 0.02 0.018 -9999 0 -0.12 9 9
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 82 82
CDC42 -0.025 0.096 -9999 0 -0.24 63 63
Paxillin-independent events mediated by a4b1 and a4b7

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.076 -9999 0 -0.17 89 89
CRKL 0.023 0.009 -9999 0 -0.12 2 2
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
DOCK1 0.019 0.02 -9999 0 -0.12 10 10
ITGA4 0.015 0.03 -9999 0 -0.12 24 24
alpha4/beta7 Integrin/MAdCAM1 0.032 0.059 -9999 0 -0.1 78 78
EPO 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta7 Integrin 0.004 0.065 -9999 0 -0.13 106 106
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.021 0.016 -9999 0 -0.12 7 7
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 101 101
EPO/EPOR (dimer) 0.032 0.019 -9999 0 -0.08 15 15
lamellipodium assembly 0.004 0.087 -9999 0 -0.26 34 34
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K 0.007 0.065 -9999 0 -0.13 96 96
ARF6 0.023 0.003 -9999 0 -10000 0 0
JAK2 0.003 0.081 -9999 0 -0.18 73 73
PXN 0.022 0.014 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
MADCAM1 0.023 0.006 -9999 0 -0.12 1 1
cell adhesion 0.03 0.058 -9999 0 -0.1 78 78
CRKL/CBL 0.033 0.013 -9999 0 -0.099 5 5
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC -0.038 0.074 -9999 0 -0.13 186 186
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.041 0.09 -9999 0 -0.15 186 186
p130Cas/Crk/Dock1 -0.021 0.075 -9999 0 -0.16 77 77
VCAM1 -0.019 0.06 -9999 0 -0.12 139 139
RHOA 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.033 0.057 -9999 0 -0.098 74 74
BCAR1 -0.033 0.068 -9999 0 -0.11 186 186
EPOR 0.02 0.021 -9999 0 -0.12 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.023 0.006 -9999 0 -0.12 1 1
GIT1 0.022 0.012 -9999 0 -0.12 4 4
Rac1/GTP 0.004 0.09 -9999 0 -0.26 34 34
IL12-mediated signaling events

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.001 0.094 -10000 0 -0.22 49 49
TBX21 -0.081 0.27 -10000 0 -0.72 57 57
B2M 0.024 0.006 -10000 0 -10000 0 0
TYK2 0.015 0.029 -10000 0 -0.13 7 7
IL12RB1 0.017 0.024 -10000 0 -0.12 1 1
GADD45B -0.09 0.32 -10000 0 -0.85 60 60
IL12RB2 0.014 0.033 -10000 0 -0.13 15 15
GADD45G -0.079 0.28 -10000 0 -0.76 53 53
natural killer cell activation -0.003 0.018 -10000 0 -0.041 36 36
RELB 0.022 0.011 -10000 0 -0.12 3 3
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL18 0.004 0.047 -10000 0 -0.12 66 66
IL2RA 0.021 0.017 -10000 0 -0.12 8 8
IFNG 0.013 0.038 -10000 0 -0.12 41 41
STAT3 (dimer) -0.073 0.27 -10000 0 -0.59 87 87
HLA-DRB5 -0.014 0.058 -10000 0 -0.12 119 119
FASLG -0.083 0.28 -10000 0 -0.71 61 61
NF kappa B2 p52/RelB -0.077 0.27 -10000 0 -0.61 88 88
CD4 0.012 0.029 -10000 0 -0.13 21 21
SOCS1 0.016 0.031 -10000 0 -0.12 27 27
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.004 0.045 -10000 0 -0.13 56 56
CD3E 0.012 0.034 -10000 0 -0.12 29 29
CD3G -0.001 0.051 -10000 0 -0.13 78 78
IL12Rbeta2/JAK2 0.009 0.063 -10000 0 -0.14 59 59
CCL3 -0.1 0.32 -10000 0 -0.85 63 63
CCL4 -0.09 0.27 -10000 0 -0.61 88 88
HLA-A 0.021 0.018 -10000 0 -0.12 8 8
IL18/IL18R 0.025 0.076 -10000 0 -0.12 83 83
NOS2 -0.082 0.26 -10000 0 -0.56 93 93
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.091 -10000 0 -0.23 41 41
IL1R1 -0.17 0.42 -10000 0 -1 101 101
IL4 0.026 0.021 0.073 3 -0.11 3 6
JAK2 0.012 0.033 -10000 0 -0.13 16 16
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.38 38 38
RAB7A -0.063 0.26 -10000 0 -0.64 69 69
lysosomal transport -0.058 0.25 -10000 0 -0.6 69 69
FOS -0.26 0.48 -10000 0 -1.1 130 130
STAT4 (dimer) -0.073 0.28 -10000 0 -0.62 85 85
STAT5A (dimer) -0.082 0.28 -10000 0 -0.6 91 91
GZMA -0.11 0.34 -10000 0 -0.88 68 68
GZMB -0.1 0.31 -10000 0 -0.8 64 64
HLX 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.092 0.29 -10000 0 -0.65 87 87
TCR/CD3/MHC II/CD4 -0.11 0.21 -10000 0 -0.35 188 188
IL2/IL2R 0.013 0.068 -10000 0 -0.1 114 114
MAPK14 -0.084 0.3 -10000 0 -0.69 81 81
CCR5 -0.063 0.25 -10000 0 -0.69 44 44
IL1B 0.005 0.044 -10000 0 -0.12 49 49
STAT6 -0.025 0.14 -10000 0 -0.39 34 34
STAT4 0.02 0.02 -10000 0 -0.12 11 11
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT1 0.014 0.031 -10000 0 -0.12 26 26
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
NFKB2 0.023 0.009 -10000 0 -0.12 2 2
IL12B 0.018 0.023 -10000 0 -10000 0 0
CD8A 0.024 0.011 -10000 0 -0.12 3 3
CD8B 0.024 0.015 -10000 0 -0.12 6 6
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.001 0.093 0.22 49 -10000 0 49
IL2RB 0.019 0.024 -10000 0 -0.12 16 16
proteasomal ubiquitin-dependent protein catabolic process -0.065 0.26 -10000 0 -0.57 85 85
IL2RG -0.002 0.05 -10000 0 -0.12 82 82
IL12 0.004 0.063 -10000 0 -0.13 58 58
STAT5A 0.022 0.013 -10000 0 -0.12 4 4
CD247 0.021 0.01 -10000 0 -10000 0 0
IL2 0.022 0.011 -10000 0 -0.12 3 3
SPHK2 0.022 0.011 -10000 0 -0.12 3 3
FRAP1 0.022 0.013 -10000 0 -0.12 4 4
IL12A -0.001 0.051 -10000 0 -0.12 70 70
IL12/IL12R/TYK2/JAK2 -0.099 0.3 -10000 0 -0.68 88 88
MAP2K3 -0.078 0.29 -10000 0 -0.67 82 82
RIPK2 0.013 0.034 -10000 0 -0.12 32 32
MAP2K6 -0.096 0.3 -10000 0 -0.66 89 89
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.032 -10000 0 -0.13 24 24
IL18RAP 0.022 0.02 -10000 0 -0.12 8 8
IL12Rbeta1/TYK2 0.024 0.037 -10000 0 -0.15 3 3
EOMES 0.018 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.097 0.28 -10000 0 -0.59 101 101
T cell proliferation -0.06 0.22 -10000 0 -0.48 87 87
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.024 -10000 0 -0.12 13 13
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.2 -10000 0 -0.52 87 87
ATF2 -0.076 0.28 -10000 0 -0.63 84 84
Signaling events mediated by the Hedgehog family

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.083 0.19 -10000 0 -0.4 135 135
IHH -0.002 0.048 -10000 0 -0.076 141 141
SHH Np/Cholesterol/GAS1 0.023 0.028 -10000 0 -0.098 16 16
LRPAP1 0.018 0.024 -10000 0 -0.12 15 15
dorsoventral neural tube patterning -0.022 0.028 0.097 16 -10000 0 16
SMO/beta Arrestin2 -0.01 0.11 -10000 0 -0.29 9 9
SMO -0.018 0.11 -10000 0 -0.3 9 9
AKT1 -0.017 0.11 -10000 0 -0.33 39 39
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
BOC 0.011 0.039 -10000 0 -0.12 44 44
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
heart looping -0.018 0.11 -10000 0 -0.3 9 9
STIL -0.016 0.082 -10000 0 -0.22 16 16
DHH N/PTCH2 0.034 0.011 -10000 0 -0.09 4 4
DHH N/PTCH1 -0.019 0.099 -10000 0 -0.18 135 135
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
DHH 0.022 0.011 -10000 0 -0.12 3 3
PTHLH -0.072 0.18 -10000 0 -0.38 135 135
determination of left/right symmetry -0.018 0.11 -10000 0 -0.3 9 9
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
skeletal system development -0.072 0.18 -10000 0 -0.37 135 135
IHH N/Hhip 0.016 0.039 -10000 0 -0.11 17 17
DHH N/Hhip 0.029 0.024 -10000 0 -0.073 28 28
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.018 0.11 -10000 0 -0.3 9 9
pancreas development 0.017 0.029 -10000 0 -0.12 24 24
HHAT 0.022 0.011 -10000 0 -0.12 3 3
PI3K 0.007 0.065 -10000 0 -0.13 96 96
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.035 -10000 0 -0.12 35 35
somite specification -0.018 0.11 -10000 0 -0.3 9 9
SHH Np/Cholesterol/PTCH1 -0.013 0.087 -10000 0 -0.15 135 135
SHH Np/Cholesterol/PTCH2 0.03 0.012 -10000 0 -0.1 3 3
SHH Np/Cholesterol/Megalin 0.007 0.039 -10000 0 -0.098 20 20
SHH 0.022 0.011 -10000 0 -0.086 5 5
catabolic process -0.033 0.11 -10000 0 -0.21 135 135
SMO/Vitamin D3 -0.01 0.097 -10000 0 -0.24 9 9
SHH Np/Cholesterol/Hhip 0.027 0.019 -10000 0 -0.099 3 3
LRP2 -0.016 0.064 -10000 0 -0.12 148 148
receptor-mediated endocytosis -0.02 0.098 -10000 0 -0.28 8 8
SHH Np/Cholesterol/BOC 0.02 0.033 -10000 0 -0.1 23 23
SHH Np/Cholesterol/CDO 0.018 0.036 -10000 0 -0.098 36 36
mesenchymal cell differentiation -0.027 0.019 0.099 3 -10000 0 3
mol:Vitamin D3 -0.011 0.088 -10000 0 -0.15 135 135
IHH N/PTCH2 0.021 0.032 -10000 0 -0.13 4 4
CDON 0.013 0.035 -10000 0 -0.12 35 35
IHH N/PTCH1 -0.028 0.11 -10000 0 -0.21 135 135
Megalin/LRPAP1 -0.011 0.065 -10000 0 -0.093 200 200
PTCH2 0.023 0.009 -10000 0 -0.12 2 2
SHH Np/Cholesterol 0.018 0.009 -10000 0 -0.1 2 2
PTCH1 -0.033 0.11 -10000 0 -0.21 135 135
HHIP 0.017 0.029 -10000 0 -0.12 24 24
TCR signaling in naïve CD8+ T cells

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.004 0.14 -10000 0 -0.32 65 65
FYN -0.047 0.18 -10000 0 -0.4 86 86
LAT/GRAP2/SLP76 -0.009 0.15 -10000 0 -0.32 79 79
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 -0.009 0.13 -10000 0 -0.3 76 76
B2M 0.022 0.007 -10000 0 -10000 0 0
IKBKG 0.008 0.044 -10000 0 -0.091 65 65
MAP3K8 0.023 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.004 0.011 -10000 0 -0.035 41 41
integrin-mediated signaling pathway 0.021 0.035 -10000 0 -0.096 44 44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.023 0.18 -10000 0 -0.42 75 75
TRPV6 0.003 0.017 -10000 0 -0.13 6 6
CD28 0.022 0.011 -10000 0 -0.12 3 3
SHC1 -0.019 0.16 -10000 0 -0.4 63 63
receptor internalization -0.014 0.14 -10000 0 -0.35 63 63
PRF1 -0.019 0.18 -10000 0 -0.74 23 23
KRAS 0.014 0.034 -10000 0 -0.12 33 33
GRB2 0.023 0.006 -10000 0 -0.12 1 1
COT/AKT1 0.004 0.11 -10000 0 -0.24 75 75
LAT -0.019 0.16 -10000 0 -0.4 63 63
EntrezGene:6955 0 0.003 -10000 0 -0.023 1 1
CD3D 0.008 0.044 -10000 0 -0.12 56 56
CD3E 0.015 0.033 -10000 0 -0.13 29 29
CD3G 0.002 0.051 -10000 0 -0.12 78 78
RASGRP2 0.007 0.015 -10000 0 -10000 0 0
RASGRP1 -0.017 0.14 -10000 0 -0.29 87 87
HLA-A 0.02 0.019 -10000 0 -0.13 8 8
RASSF5 0.02 0.022 -10000 0 -0.12 13 13
RAP1A/GTP/RAPL 0.022 0.035 -10000 0 -0.096 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.05 -10000 0 -0.09 77 77
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.054 -10000 0 -0.14 81 81
PRKCA -0.005 0.08 -10000 0 -0.18 75 75
GRAP2 0.022 0.012 -10000 0 -0.12 4 4
mol:IP3 -0.044 0.098 0.098 3 -0.26 75 78
EntrezGene:6957 0 0.004 -10000 0 -0.023 2 2
TCR/CD3/MHC I/CD8 -0.014 0.13 -10000 0 -0.35 53 53
ORAI1 0 0.023 0.091 6 -0.15 7 13
CSK -0.019 0.16 -10000 0 -0.4 63 63
B7 family/CD28 -0.007 0.16 -10000 0 -0.35 73 73
CHUK 0.021 0.013 -10000 0 -0.12 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.026 0.17 -10000 0 -0.43 66 66
PTPN6 -0.023 0.16 -10000 0 -0.39 66 66
VAV1 -0.023 0.16 -10000 0 -0.4 68 68
Monovalent TCR/CD3 -0.015 0.095 -10000 0 -0.2 96 96
CBL 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.036 0.17 -10000 0 -0.39 81 81
PAG1 -0.019 0.16 -10000 0 -0.4 62 62
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
TCR/CD3/MHC I/CD8/LCK -0.028 0.17 -10000 0 -0.42 68 68
CD80 0.019 0.024 -10000 0 -0.12 15 15
CD86 0.013 0.034 -10000 0 -0.12 32 32
PDK1/CARD11/BCL10/MALT1 -0.027 0.066 -10000 0 -0.18 76 76
HRAS 0.023 0.006 -10000 0 -0.12 1 1
GO:0035030 -0.016 0.13 -10000 0 -0.3 73 73
CD8A 0.022 0.012 -10000 0 -0.13 3 3
CD8B 0.021 0.016 -10000 0 -0.13 6 6
PTPRC -0.004 0.051 -10000 0 -0.12 86 86
PDK1/PKC theta -0.016 0.15 -10000 0 -0.35 76 76
CSK/PAG1 -0.014 0.15 -10000 0 -0.39 62 62
SOS1 0.017 0.027 -10000 0 -0.12 20 20
peptide-MHC class I 0.012 0.073 -10000 0 -0.19 57 57
GRAP2/SLP76 -0.015 0.17 -10000 0 -0.37 79 79
STIM1 -0.002 0.032 -10000 0 -0.17 18 18
RAS family/GTP 0.007 0.07 -10000 0 -0.14 72 72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.014 0.15 -10000 0 -0.37 63 63
mol:DAG -0.041 0.088 -10000 0 -0.23 81 81
RAP1A/GDP 0.005 0.026 -10000 0 -0.05 63 63
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
CD247 0.023 0.004 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.017 0.18 -10000 0 -0.67 25 25
RAP1A/GTP -0.002 0.009 -10000 0 -0.037 25 25
mol:PI-3-4-5-P3 -0.015 0.15 -10000 0 -0.35 75 75
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.12 0.12 3 -0.33 74 77
NRAS 0.022 0.011 -10000 0 -0.12 3 3
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
GRB2/SOS1 0.021 0.045 -10000 0 -0.12 50 50
LAT/GRAP2/SLP76/VAV1 -0.013 0.14 -10000 0 -0.33 76 76
MALT1 0.017 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
CD8 heterodimer 0.033 0.016 -10000 0 -0.099 1 1
CARD11 0.017 0.028 -10000 0 -0.12 22 22
PRKCB -0.03 0.063 -10000 0 -0.17 81 81
PRKCE 0 0.079 -10000 0 -0.18 71 71
PRKCQ -0.023 0.17 -10000 0 -0.39 76 76
LCP2 0.013 0.033 -10000 0 -0.12 31 31
BCL10 0.023 0.001 -10000 0 -10000 0 0
regulation of survival gene product expression -0.005 0.11 -10000 0 -0.26 76 76
IKK complex 0.007 0.044 -10000 0 -0.083 53 53
RAS family/GDP -0.006 0.01 -10000 0 -0.036 33 33
MAP3K14 0.008 0.087 -10000 0 -0.18 75 75
PDPK1 -0.007 0.12 -10000 0 -0.28 75 75
TCR/CD3/MHC I/CD8/Fyn -0.03 0.19 -10000 0 -0.48 66 66
Circadian rhythm pathway

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.068 0.31 -10000 0 -1 51 51
CLOCK 0.017 0.024 -10000 0 -0.052 49 49
TIMELESS/CRY2 -0.064 0.31 -10000 0 -1 50 50
DEC1/BMAL1 0.024 0.039 -10000 0 -0.14 25 25
ATR 0.02 0.015 -10000 0 -0.12 5 5
NR1D1 -0.01 0.11 -10000 0 -0.36 50 50
ARNTL 0.018 0.023 -10000 0 -0.051 37 37
TIMELESS -0.08 0.33 -10000 0 -1.1 50 50
NPAS2 0.002 0.049 -10000 0 -0.097 94 94
CRY2 0.023 0 -10000 0 -10000 0 0
mol:CO 0.001 0.042 0.13 50 -10000 0 50
CHEK1 0.012 0.035 -10000 0 -0.12 34 34
mol:HEME -0.001 0.042 -10000 0 -0.13 50 50
PER1 0.022 0.014 -10000 0 -0.12 5 5
BMAL/CLOCK/NPAS2 0 0.087 -10000 0 -0.12 155 155
BMAL1/CLOCK -0.033 0.19 -10000 0 -0.55 56 56
S phase of mitotic cell cycle -0.068 0.31 -10000 0 -1 51 51
TIMELESS/CHEK1/ATR -0.071 0.32 -10000 0 -1.1 51 51
mol:NADPH -0.001 0.042 -10000 0 -0.13 50 50
PER1/TIMELESS -0.064 0.31 -10000 0 -1.1 50 50
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.022 0.011 -10000 0 -0.12 3 3
BMP receptor signaling

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.035 0.091 -9999 0 -0.12 243 243
SMAD6-7/SMURF1 0.042 0.029 -9999 0 -0.13 11 11
NOG 0.017 0.029 -9999 0 -0.12 23 23
SMAD9 0.02 0.05 -9999 0 -0.54 2 2
SMAD4 0.022 0.007 -9999 0 -0.12 1 1
SMAD5 0 0.094 -9999 0 -0.29 33 33
BMP7/USAG1 -0.074 0.094 -9999 0 -0.13 369 369
SMAD5/SKI 0.011 0.094 -9999 0 -0.27 33 33
SMAD1 0.021 0.073 -9999 0 -0.28 26 26
BMP2 0.022 0.014 -9999 0 -0.12 5 5
SMAD1/SMAD1/SMAD4 -0.003 0.065 -9999 0 -0.25 26 26
BMPR1A 0.02 0.014 -9999 0 -0.12 4 4
BMPR1B 0.008 0.04 -9999 0 -0.12 48 48
BMPR1A-1B/BAMBI -0.026 0.087 -9999 0 -0.14 161 161
AHSG 0.023 0.009 -9999 0 -0.12 2 2
CER1 0.022 0.012 -9999 0 -0.12 4 4
BMP2-4/CER1 0.033 0.039 -9999 0 -0.12 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.003 0.1 -9999 0 -0.26 49 49
BMP2-4 (homodimer) 0.02 0.041 -9999 0 -0.087 69 69
RGMB 0.023 0.009 -9999 0 -0.12 2 2
BMP6/BMPR2/BMPR1A-1B 0.013 0.076 -9999 0 -0.12 114 114
RGMA 0.021 0.017 -9999 0 -0.12 8 8
SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.004 0.077 -9999 0 -0.17 74 74
BMP2-4/USAG1 -0.014 0.07 -9999 0 -0.12 118 118
SMAD6/SMURF1/SMAD5 0.011 0.094 -9999 0 -0.27 33 33
SOSTDC1 -0.018 0.062 -9999 0 -0.12 146 146
BMP7/BMPR2/BMPR1A-1B -0.033 0.093 -9999 0 -0.13 219 219
SKI 0.022 0.011 -9999 0 -0.12 3 3
BMP6 (homodimer) 0.02 0.023 -9999 0 -0.12 14 14
HFE2 0.023 0.009 -9999 0 -0.12 2 2
ZFYVE16 0.02 0.018 -9999 0 -0.12 8 8
MAP3K7 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/CHRD 0.033 0.038 -9999 0 -0.11 16 16
SMAD5/SMAD5/SMAD4 0.009 0.096 -9999 0 -0.28 36 36
MAPK1 0.021 0.016 -9999 0 -0.12 7 7
TAK1/TAB family 0.022 0.096 -9999 0 -0.22 50 50
BMP7 (homodimer) -0.009 0.055 -9999 0 -0.12 106 106
NUP214 0.023 0.007 -9999 0 -0.12 1 1
BMP6/FETUA 0.032 0.017 -9999 0 -0.071 16 16
SMAD1/SKI 0.033 0.072 -9999 0 -0.26 26 26
SMAD6 0.02 0.02 -9999 0 -0.12 11 11
CTDSP2 0.022 0.01 -9999 0 -0.12 2 2
BMP2-4/FETUA 0.033 0.039 -9999 0 -0.12 15 15
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
GREM1 0.008 0.044 -9999 0 -0.12 58 58
BMPR2 (homodimer) 0.021 0.014 -9999 0 -0.12 5 5
GADD34/PP1CA 0.03 0.047 -9999 0 -0.12 46 46
BMPR1A-1B (homodimer) -0.011 0.081 -9999 0 -0.16 105 105
CHRDL1 -0.008 0.055 -9999 0 -0.12 103 103
ENDOFIN/SMAD1 0.03 0.076 -9999 0 -0.27 27 27
SMAD6-7/SMURF1/SMAD1 0.049 0.076 -9999 0 -0.25 27 27
SMAD6/SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BAMBI -0.004 0.054 -9999 0 -0.12 95 95
SMURF2 0.022 0.013 -9999 0 -0.12 4 4
BMP2-4/CHRDL1 -0.014 0.072 -9999 0 -0.12 135 135
BMP2-4/GREM1 0.023 0.049 -9999 0 -0.12 30 30
SMAD7 0.023 0.003 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.028 0.052 -9999 0 -0.36 4 4
SMAD1/SMAD6 0.033 0.073 -9999 0 -0.26 26 26
TAK1/SMAD6 0.027 0.035 -9999 0 -0.14 21 21
BMP7 -0.009 0.055 -9999 0 -0.12 106 106
BMP6 0.02 0.023 -9999 0 -0.12 14 14
MAP3K7IP2 0.02 0.016 -9999 0 -0.12 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.003 0.083 -9999 0 -0.22 44 44
PPM1A 0.023 0.001 -9999 0 -10000 0 0
SMAD1/SMURF2 0.031 0.075 -9999 0 -0.27 26 26
SMAD7/SMURF1 0.031 0.023 -9999 0 -0.13 11 11
CTDSPL 0.023 0.006 -9999 0 -0.12 1 1
PPP1CA 0.023 0.002 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.022 0.011 -9999 0 -0.12 3 3
PPP1R15A 0.019 0.025 -9999 0 -0.12 17 17
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.002 0.08 -9999 0 -0.21 51 51
CHRD 0.023 0.006 -9999 0 -0.12 1 1
BMPR2 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.005 0.088 -9999 0 -0.24 43 43
BMP4 0.009 0.042 -9999 0 -0.12 52 52
FST 0.004 0.049 -9999 0 -0.12 73 73
BMP2-4/NOG 0.027 0.047 -9999 0 -0.12 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.023 0.091 -9999 0 -0.12 220 220
FoxO family signaling

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.023 0.06 -9999 0 -0.41 1 1
PLK1 -0.15 0.36 -9999 0 -0.79 98 98
CDKN1B -0.05 0.19 -9999 0 -0.35 111 111
FOXO3 -0.13 0.32 -9999 0 -0.5 206 206
KAT2B -0.011 0.027 -9999 0 -0.045 194 194
FOXO1/SIRT1 0.025 0.065 -9999 0 -0.24 15 15
CAT -0.16 0.38 -9999 0 -0.87 93 93
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
AKT1 0.009 0.038 -9999 0 -0.063 56 56
FOXO1 0.016 0.066 -9999 0 -0.27 11 11
MAPK10 0.013 0.042 -9999 0 -0.1 39 39
mol:GTP 0 0.003 -9999 0 -10000 0 0
FOXO4 0.011 0.13 -9999 0 -0.36 36 36
response to oxidative stress -0.008 0.029 -9999 0 -0.05 122 122
FOXO3A/SIRT1 -0.14 0.3 -9999 0 -0.48 204 204
XPO1 0.022 0.01 -9999 0 -0.12 2 2
EP300 0.024 0.01 -9999 0 -0.12 2 2
BCL2L11 0.005 0.086 -9999 0 -1.3 2 2
FOXO1/SKP2 0.022 0.069 -9999 0 -0.25 17 17
mol:GDP -0.008 0.029 -9999 0 -0.05 122 122
RAN 0.024 0.003 -9999 0 -10000 0 0
GADD45A -0.081 0.27 -9999 0 -0.75 57 57
YWHAQ 0.023 0.003 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.086 -9999 0 -0.27 21 21
MST1 0.007 0.034 -9999 0 -0.053 56 56
CSNK1D 0.023 0.001 -9999 0 -10000 0 0
CSNK1E 0.022 0.015 -9999 0 -0.12 6 6
FOXO4/14-3-3 family 0.013 0.12 -9999 0 -0.28 50 50
YWHAB 0.023 0.007 -9999 0 -0.12 1 1
MAPK8 0.016 0.042 -9999 0 -0.12 29 29
MAPK9 0.015 0.042 -9999 0 -0.13 27 27
YWHAG 0.02 0.022 -9999 0 -0.12 13 13
YWHAE 0.022 0.014 -9999 0 -0.12 5 5
YWHAZ 0.023 0.003 -9999 0 -10000 0 0
SIRT1 0.02 0.008 -9999 0 -10000 0 0
SOD2 -0.092 0.3 -9999 0 -0.64 98 98
RBL2 -0.083 0.27 -9999 0 -0.62 73 73
RAL/GDP 0.019 0.043 -9999 0 -0.13 26 26
CHUK 0.007 0.034 -9999 0 -0.054 56 56
Ran/GTP 0.017 0.014 -9999 0 -0.14 3 3
CSNK1G2 0.022 0.011 -9999 0 -0.12 3 3
RAL/GTP 0.022 0.044 -9999 0 -0.12 26 26
CSNK1G1 0.023 0.009 -9999 0 -0.12 2 2
FASLG 0.007 0.068 -9999 0 -1.2 1 1
SKP2 0.018 0.024 -9999 0 -0.12 16 16
USP7 0.02 0.02 -9999 0 -0.12 10 10
IKBKB 0.007 0.036 -9999 0 -0.054 68 68
CCNB1 -0.18 0.42 -9999 0 -0.94 106 106
FOXO1-3a-4/beta catenin -0.036 0.21 -9999 0 -0.38 102 102
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.068 -9999 0 -0.25 18 18
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
SGK1 -0.011 0.027 -9999 0 -0.045 194 194
CSNK1G3 0.022 0.007 -9999 0 -0.12 1 1
Ran/GTP/Exportin 1 0.027 0.032 -9999 0 -0.12 25 25
ZFAND5 0.019 0.12 -9999 0 -0.65 6 6
SFN 0.014 0.032 -9999 0 -0.12 29 29
CDK2 0.022 0.023 -9999 0 -0.12 14 14
FOXO3A/14-3-3 -0.005 0.13 -9999 0 -0.31 53 53
CREBBP 0.025 0.016 -9999 0 -0.12 6 6
FBXO32 -0.27 0.5 -9999 0 -1 156 156
BCL6 -0.12 0.34 -9999 0 -0.81 77 77
RALB 0.023 0.008 -9999 0 -0.12 1 1
RALA 0.023 0.009 -9999 0 -0.12 2 2
YWHAH 0.021 0.014 -9999 0 -0.12 5 5
Stabilization and expansion of the E-cadherin adherens junction

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0 0.088 -10000 0 -0.18 86 86
epithelial cell differentiation 0.029 0.059 -10000 0 -0.12 67 67
CYFIP2 0.02 0.018 -10000 0 -0.12 8 8
ENAH 0.009 0.056 -10000 0 -0.13 51 51
EGFR 0.015 0.03 -10000 0 -0.12 25 25
EPHA2 0.02 0.022 -10000 0 -0.12 13 13
MYO6 0.01 0.057 -10000 0 -0.12 67 67
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
ABI1/Sra1/Nap1 0.03 0.05 -10000 0 -0.12 53 53
AQP5 -0.059 0.15 -10000 0 -0.32 122 122
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.049 -10000 0 -0.11 67 67
regulation of calcium-dependent cell-cell adhesion 0.014 0.05 -10000 0 -0.11 67 67
EGF 0.02 0.021 -10000 0 -0.12 12 12
NCKAP1 0.023 0.004 -10000 0 -10000 0 0
AQP3 0.012 0.076 -10000 0 -0.28 24 24
cortical microtubule organization 0.029 0.059 -10000 0 -0.12 67 67
GO:0000145 0.008 0.045 -10000 0 -0.1 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.061 -10000 0 -0.12 67 67
MLLT4 0.014 0.032 -10000 0 -0.12 29 29
ARF6/GDP -0.022 0.05 -10000 0 -0.17 43 43
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.062 -10000 0 -0.11 75 75
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.015 0.058 -10000 0 -0.18 30 30
PVRL2 0.019 0.023 -10000 0 -0.12 15 15
ZYX 0.011 0.054 -10000 0 -0.12 67 67
ARF6/GTP 0.035 0.063 -10000 0 -0.1 80 80
CDH1 0.021 0.016 -10000 0 -0.12 6 6
EGFR/EGFR/EGF/EGF 0.015 0.062 -10000 0 -0.19 24 24
RhoA/GDP 0.03 0.058 -10000 0 -0.21 16 16
actin cytoskeleton organization 0.009 0.059 -10000 0 -0.13 66 66
IGF-1R heterotetramer 0.013 0.032 -10000 0 -0.12 28 28
GIT1 0.022 0.012 -10000 0 -0.12 4 4
IGF1R 0.013 0.032 -10000 0 -0.12 28 28
IGF1 0.007 0.045 -10000 0 -0.12 60 60
DIAPH1 -0.022 0.2 -10000 0 -0.56 70 70
Wnt receptor signaling pathway -0.029 0.059 0.12 67 -10000 0 67
RHOA 0.023 0.006 -10000 0 -0.12 1 1
RhoA/GTP -0.022 0.049 -10000 0 -0.17 42 42
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
VCL 0.009 0.061 -10000 0 -0.13 66 66
EFNA1 0.014 0.031 -10000 0 -0.12 26 26
LPP 0.012 0.054 -10000 0 -0.19 23 23
Ephrin A1/EPHA2 0.012 0.064 -10000 0 -0.19 28 28
SEC6/SEC8 -0.02 0.049 -10000 0 -0.19 32 32
MGAT3 0.014 0.051 -10000 0 -0.11 67 67
HGF/MET -0.006 0.071 -10000 0 -0.18 45 45
HGF 0.02 0.023 -10000 0 -0.12 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0.089 -10000 0 -0.18 86 86
actin cable formation 0.012 0.08 -10000 0 -0.19 49 49
KIAA1543 0.013 0.05 -10000 0 -0.18 23 23
KIFC3 0.015 0.05 -10000 0 -0.11 67 67
NCK1 0.02 0.019 -10000 0 -0.12 9 9
EXOC3 0.023 0.009 -10000 0 -0.12 2 2
ACTN1 0.013 0.057 -10000 0 -0.12 67 67
NCK1/GIT1 0.022 0.043 -10000 0 -0.12 45 45
mol:GDP 0.029 0.059 -10000 0 -0.12 67 67
EXOC4 0.022 0.007 -10000 0 -0.12 1 1
STX4 0.014 0.052 -10000 0 -0.11 67 67
PIP5K1C 0.015 0.05 -10000 0 -0.11 67 67
LIMA1 0.019 0.023 -10000 0 -0.12 14 14
ABI1 0.022 0.009 -10000 0 -0.12 2 2
ROCK1 0.011 0.06 -10000 0 -0.16 39 39
adherens junction assembly 0.022 0.059 -10000 0 -0.23 15 15
IGF-1R heterotetramer/IGF1 0 0.071 -10000 0 -0.17 47 47
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.013 0.054 -10000 0 -0.15 43 43
MET 0 0.047 -10000 0 -0.12 70 70
PLEKHA7 0.013 0.052 -10000 0 -0.11 67 67
mol:GTP 0.028 0.061 -10000 0 -0.11 75 75
establishment of epithelial cell apical/basal polarity 0.013 0.062 -10000 0 -0.18 34 34
cortical actin cytoskeleton stabilization 0 0.088 -10000 0 -0.18 86 86
regulation of cell-cell adhesion 0.009 0.059 -10000 0 -0.13 66 66
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0.089 -10000 0 -0.18 86 86
Aurora A signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.001 0.074 -10000 0 -0.18 70 70
BIRC5 0.018 0.023 -10000 0 -0.12 14 14
NFKBIA 0.013 0.039 0.11 8 -0.13 24 32
CPEB1 0.02 0.023 -10000 0 -0.12 14 14
AKT1 0.018 0.027 0.11 8 -0.1 12 20
NDEL1 0.023 0.006 -10000 0 -0.12 1 1
Aurora A/BRCA1 -0.006 0.069 -10000 0 -0.16 69 69
NDEL1/TACC3 0.006 0.075 -10000 0 -0.16 74 74
GADD45A 0.014 0.032 -10000 0 -0.12 29 29
GSK3B 0.021 0.013 0.071 9 -0.12 3 12
PAK1/Aurora A 0.003 0.071 -10000 0 -0.17 69 69
MDM2 0.02 0.02 -10000 0 -0.12 11 11
JUB 0.018 0.024 -10000 0 -0.12 15 15
TPX2 0.017 0.017 -10000 0 -0.071 16 16
TP53 -0.064 0.13 -10000 0 -0.25 179 179
DLG7 0.012 0.026 0.11 2 -0.059 40 42
AURKAIP1 0.02 0.021 -10000 0 -0.12 12 12
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.006 0.08 -10000 0 -0.17 74 74
G2/M transition of mitotic cell cycle -0.006 0.069 -10000 0 -0.15 69 69
AURKA -0.004 0.078 0.14 8 -0.2 67 75
AURKB 0.003 0.064 -10000 0 -0.27 23 23
CDC25B 0.006 0.067 -10000 0 -0.25 29 29
G2/M transition checkpoint -0.001 0.067 -10000 0 -0.15 75 75
mRNA polyadenylation 0.006 0.061 -10000 0 -0.15 67 67
Aurora A/CPEB 0.006 0.061 -10000 0 -0.15 67 67
Aurora A/TACC1/TRAP/chTOG 0.006 0.091 -10000 0 -0.18 75 75
BRCA1 0.015 0.03 -10000 0 -0.12 24 24
centrosome duplication 0.003 0.071 -10000 0 -0.17 69 69
regulation of centrosome cycle 0.005 0.074 -10000 0 -0.16 74 74
spindle assembly 0.005 0.09 -10000 0 -0.18 75 75
TDRD7 0.014 0.031 -10000 0 -0.12 27 27
Aurora A/RasGAP/Survivin 0.005 0.082 -10000 0 -0.16 81 81
CENPA 0.012 0.044 -10000 0 -0.31 9 9
Aurora A/PP2A 0.007 0.068 -10000 0 -0.16 67 67
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.025 0.096 -10000 0 -0.23 78 78
negative regulation of DNA binding -0.063 0.13 -10000 0 -0.25 179 179
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.034 0.01 -10000 0 -0.071 5 5
RASA1 0.021 0.012 -10000 0 -0.12 3 3
Ajuba/Aurora A -0.001 0.068 -10000 0 -0.15 75 75
mitotic prometaphase 0.002 0.018 0.073 32 -10000 0 32
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.077 0.14 8 -0.2 67 75
TACC1 0.014 0.035 -10000 0 -0.12 34 34
TACC3 0.014 0.032 -10000 0 -0.12 29 29
Aurora A/Antizyme1 0.005 0.077 -10000 0 -0.16 76 76
Aurora A/RasGAP 0.005 0.073 -10000 0 -0.18 67 67
OAZ1 0.017 0.025 -10000 0 -0.12 17 17
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.02 0.019 0.071 9 -0.12 8 17
GIT1 0.022 0.012 -10000 0 -0.12 4 4
GIT1/beta-PIX/PAK1 0.037 0.036 -10000 0 -0.11 21 21
Importin alpha/Importin beta/TPX2 0.017 0.017 -10000 0 -0.071 16 16
PPP2R5D 0.022 0.014 -10000 0 -0.12 5 5
Aurora A/TPX2 -0.003 0.082 -10000 0 -0.2 74 74
PAK1 0.016 0.029 -10000 0 -0.12 23 23
CKAP5 0.021 0.013 -10000 0 -0.12 4 4
Reelin signaling pathway

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.022 0.042 -9999 0 -0.1 52 52
VLDLR 0.01 0.038 -9999 0 -0.12 41 41
CRKL 0.023 0.009 -9999 0 -0.12 2 2
LRPAP1 0.018 0.024 -9999 0 -0.12 15 15
FYN 0.011 0.037 -9999 0 -0.12 40 40
ITGA3 0.012 0.034 -9999 0 -0.12 33 33
RELN/VLDLR/Fyn -0.006 0.073 -9999 0 -0.13 102 102
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.042 -9999 0 -0.093 31 31
AKT1 -0.015 0.078 -9999 0 -0.15 112 112
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
RAPGEF1 0.023 0 -9999 0 -10000 0 0
DAB1 0.022 0.011 -9999 0 -0.12 3 3
RELN/LRP8/DAB1 0.025 0.042 -9999 0 -0.11 21 21
LRPAP1/LRP8 0.015 0.054 -9999 0 -0.12 72 72
RELN/LRP8/DAB1/Fyn 0.02 0.056 -9999 0 -0.096 63 63
DAB1/alpha3/beta1 Integrin -0.006 0.069 -9999 0 -0.14 60 60
long-term memory 0.016 0.062 -9999 0 -0.13 20 20
DAB1/LIS1 0.016 0.067 -9999 0 -0.14 25 25
DAB1/CRLK/C3G 0.012 0.057 -9999 0 -0.13 21 21
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
DAB1/NCK2 0.019 0.067 -9999 0 -0.14 22 22
ARHGEF2 0.022 0.009 -9999 0 -0.12 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.001 0.052 -9999 0 -0.12 86 86
CDK5R1 0.023 0.006 -9999 0 -0.12 1 1
RELN 0.001 0.053 -9999 0 -0.12 88 88
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
RELN/LRP8/Fyn 0.009 0.061 -9999 0 -0.12 62 62
GRIN2A/RELN/LRP8/DAB1/Fyn 0.015 0.066 -9999 0 -0.096 89 89
MAPK8 0.021 0.015 -9999 0 -0.12 6 6
RELN/VLDLR/DAB1 0.011 0.055 -9999 0 -0.1 69 69
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
MAP1B -0.006 0.056 -9999 0 -0.11 96 96
RELN/LRP8 0.015 0.058 -9999 0 -0.12 53 53
GRIN2B/RELN/LRP8/DAB1/Fyn 0.029 0.061 -9999 0 -0.093 65 65
PI3K 0.007 0.065 -9999 0 -0.13 96 96
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.004 0.063 -9999 0 -0.12 111 111
RAP1A 0.005 0.05 -9999 0 -0.13 26 26
PAFAH1B1 0.021 0.018 -9999 0 -0.12 9 9
MAPK8IP1 0.017 0.029 -9999 0 -0.12 24 24
CRLK/C3G 0.034 0.01 -9999 0 -0.094 3 3
GRIN2B 0.021 0.019 -9999 0 -0.12 10 10
NCK2 0.023 0.006 -9999 0 -0.12 1 1
neuron differentiation 0.017 0.057 -9999 0 -0.18 23 23
neuron adhesion -0.004 0.061 -9999 0 -0.13 67 67
LRP8 0.02 0.021 -9999 0 -0.12 12 12
GSK3B -0.011 0.074 -9999 0 -0.14 113 113
RELN/VLDLR/DAB1/Fyn 0.006 0.066 -9999 0 -0.1 103 103
MAP3K11 0.022 0.014 -9999 0 -0.12 5 5
RELN/VLDLR/DAB1/P13K -0.018 0.083 -9999 0 -0.16 111 111
CDK5 0.015 0.032 -9999 0 -0.12 28 28
MAPT 0.01 0.016 -9999 0 -0.094 5 5
neuron migration -0.014 0.079 -9999 0 -0.19 52 52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.057 -9999 0 -0.18 23 23
RELN/VLDLR 0.007 0.071 -9999 0 -0.11 119 119
Paxillin-dependent events mediated by a4b1

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.009 -10000 0 -0.12 2 2
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
DOCK1 0.019 0.02 -10000 0 -0.12 10 10
ITGA4 0.015 0.03 -10000 0 -0.12 24 24
RAC1 0.023 0.002 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.004 0.065 -10000 0 -0.13 106 106
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.016 -10000 0 -0.12 7 7
alpha4/beta1 Integrin 0.02 0.059 -10000 0 -0.12 75 75
alpha4/beta7 Integrin/Paxillin 0.021 0.055 -10000 0 -0.1 79 79
lamellipodium assembly 0.001 0.12 -10000 0 -0.3 63 63
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.007 0.065 -10000 0 -0.13 96 96
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.021 0.012 -10000 0 -0.12 3 3
PXN 0.021 0.014 -10000 0 -0.071 13 13
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
ARF6/GTP 0.031 0.051 -10000 0 -0.14 10 10
cell adhesion 0.026 0.062 -10000 0 -0.098 96 96
CRKL/CBL 0.033 0.013 -10000 0 -0.099 5 5
alpha4/beta1 Integrin/Paxillin 0.022 0.053 -10000 0 -0.1 76 76
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
ITGB7 0.019 0.024 -10000 0 -0.12 15 15
ARF6/GDP 0.02 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.022 0.082 -10000 0 -0.12 187 187
p130Cas/Crk/Dock1 0.035 0.04 -10000 0 -0.11 34 34
VCAM1 -0.019 0.06 -10000 0 -0.12 139 139
alpha4/beta1 Integrin/Paxillin/Talin 0.027 0.063 -10000 0 -0.098 96 96
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.055 -10000 0 -0.09 76 76
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
mol:GDP -0.032 0.054 0.09 76 -10000 0 76
CBL 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GIT1 0.022 0.012 -10000 0 -0.12 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.027 0.063 -10000 0 -0.098 96 96
Rac1/GTP -0.001 0.13 -10000 0 -0.33 63 63
E-cadherin signaling in keratinocytes

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation -0.005 0.1 -10000 0 -0.27 51 51
adherens junction organization -0.007 0.12 -10000 0 -0.27 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.098 -10000 0 -0.25 49 49
FMN1 -0.002 0.11 -10000 0 -0.25 68 68
mol:IP3 -0.002 0.092 -10000 0 -0.24 50 50
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.004 0.11 -10000 0 -0.26 66 66
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
AKT1 0.001 0.097 -10000 0 -0.26 47 47
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.13 -10000 0 -0.36 47 47
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.1 -10000 0 -0.24 67 67
VASP -0.001 0.11 -10000 0 -0.25 67 67
ZYX -0.004 0.11 -10000 0 -0.26 67 67
JUB -0.005 0.11 -10000 0 -0.25 68 68
EGFR(dimer) -0.001 0.11 -10000 0 -0.26 69 69
E-cadherin/beta catenin-gamma catenin 0.026 0.052 -10000 0 -0.11 63 63
mol:PI-3-4-5-P3 0.003 0.1 -10000 0 -0.27 46 46
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.004 0.11 -10000 0 -0.28 46 46
FYN -0.012 0.11 -10000 0 -0.27 69 69
mol:Ca2+ -0.002 0.09 -10000 0 -0.23 50 50
JUP 0.019 0.021 -10000 0 -0.12 12 12
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:DAG -0.002 0.092 -10000 0 -0.24 50 50
CDH1 0.02 0.016 -10000 0 -0.12 6 6
RhoA/GDP 0.002 0.097 -10000 0 -0.25 47 47
establishment of polarity of embryonic epithelium -0.001 0.1 -10000 0 -0.24 67 67
SRC 0.023 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
RHOA 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
CASR 0.001 0.086 -10000 0 -0.24 42 42
RhoA/GTP 0.006 0.089 -10000 0 -0.25 40 40
AKT2 0 0.097 -10000 0 -0.24 51 51
actin cable formation 0.001 0.1 -10000 0 -0.24 67 67
apoptosis 0.004 0.099 0.25 53 -10000 0 53
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
mol:GDP -0.006 0.097 -10000 0 -0.25 52 52
PIP5K1A -0.001 0.11 -10000 0 -0.25 67 67
PLCG1 -0.003 0.094 -10000 0 -0.24 50 50
Rac1/GTP 0.004 0.11 -10000 0 -0.28 48 48
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.017 0.04 -9999 0 -0.089 68 68
EFNA5 0.014 0.033 -9999 0 -0.12 30 30
FYN 0.007 0.043 -9999 0 -0.12 40 40
neuron projection morphogenesis 0.017 0.04 -9999 0 -0.089 68 68
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.017 0.041 -9999 0 -0.089 68 68
EPHA5 0.023 0.009 -9999 0 -0.12 2 2
Retinoic acid receptors-mediated signaling

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.02 -10000 0 -0.12 10 10
HDAC3 0.023 0.002 -10000 0 -10000 0 0
VDR 0.019 0.022 -10000 0 -0.12 13 13
Cbp/p300/PCAF 0.02 0.043 -10000 0 -0.14 35 35
EP300 0.022 0.01 -10000 0 -0.12 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.095 -10000 0 -0.22 63 63
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -0.12 1 1
AKT1 0.019 0.089 0.17 78 -0.2 29 107
RAR alpha/9cRA/Cyclin H -0.016 0.12 -10000 0 -0.22 106 106
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.081 -10000 0 -0.2 55 55
CDC2 0.006 0.04 -10000 0 -0.12 46 46
response to UV -0.001 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.006 0.062 -10000 0 -0.15 52 52
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.008 0.035 -10000 0 -0.12 36 36
RXRs/RARs/NRIP1/9cRA -0.044 0.19 -10000 0 -0.48 72 72
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
NCOA3 0.021 0.012 -10000 0 -0.12 3 3
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARG 0.02 0.016 -10000 0 -0.12 6 6
RAR gamma1/9cRA 0.024 0.028 -10000 0 -0.11 18 18
MAPK3 0.02 0.015 -10000 0 -0.12 5 5
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
MAPK8 0.019 0.018 -10000 0 -0.12 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.036 0.14 -10000 0 -0.32 90 90
RARA 0.01 0.056 -10000 0 -0.13 49 49
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.086 -10000 0 -0.22 54 54
PRKCA 0.008 0.043 -10000 0 -0.088 78 78
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.063 0.21 -10000 0 -0.54 74 74
RXRG -0.006 0.07 -10000 0 -0.19 56 56
RXRA -0.034 0.11 -10000 0 -0.21 94 94
RXRB 0.003 0.064 -10000 0 -0.18 46 46
VDR/Vit D3/DNA 0.008 0.035 -10000 0 -0.12 36 36
RBP1 0.01 0.035 -10000 0 -0.12 35 35
CRBP1/9-cic-RA -0.019 0.065 -10000 0 -0.13 138 138
RARB 0.012 0.036 -10000 0 -0.12 33 33
PRKCG 0.018 0.025 -10000 0 -0.052 52 52
MNAT1 0.023 0.007 -10000 0 -0.12 1 1
RAR alpha/RXRs -0.021 0.16 -10000 0 -0.36 81 81
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.016 0.13 -10000 0 -0.28 79 79
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.099 -10000 0 -0.25 51 51
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.06 0.21 -10000 0 -0.54 73 73
positive regulation of DNA binding -0.02 0.11 -10000 0 -0.2 106 106
NRIP1 -0.098 0.32 -10000 0 -0.98 58 58
RXRs/RARs -0.048 0.17 -10000 0 -0.4 93 93
RXRs/RXRs/DNA/9cRA -0.042 0.14 -10000 0 -0.32 95 95
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
CDK7 0.018 0.023 -10000 0 -0.12 14 14
TFIIH 0.029 0.053 -10000 0 -0.13 46 46
RAR alpha/9cRA 0.023 0.071 -10000 0 -0.2 26 26
CCNH 0.02 0.022 -10000 0 -0.12 13 13
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
RAR gamma2/9cRA 0.025 0.05 -10000 0 -0.18 16 16
IL2 signaling events mediated by PI3K

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.16 -10000 0 -0.69 21 21
UGCG -0.001 0.079 -10000 0 -0.73 5 5
AKT1/mTOR/p70S6K/Hsp90/TERT -0.031 0.16 -10000 0 -0.32 101 101
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.078 -10000 0 -0.71 5 5
mol:DAG -0.043 0.2 -10000 0 -0.89 29 29
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.04 0.18 -10000 0 -0.38 96 96
FRAP1 -0.053 0.2 -10000 0 -0.43 97 97
FOXO3 -0.053 0.2 -10000 0 -0.41 105 105
AKT1 -0.058 0.21 -10000 0 -0.44 103 103
GAB2 0.007 0.041 -10000 0 -0.12 50 50
SMPD1 0.006 0.042 -10000 0 -0.52 1 1
SGMS1 -0.029 0.16 -10000 0 -0.68 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.05 -10000 0 -0.13 67 67
CALM1 0.022 0.014 -10000 0 -0.12 5 5
cell proliferation -0.039 0.16 -10000 0 -0.31 103 103
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.008 0.067 -10000 0 -0.15 67 67
RPS6KB1 -0.031 0.18 -10000 0 -0.82 23 23
mol:sphingomyelin -0.043 0.2 -10000 0 -0.89 29 29
natural killer cell activation -0.001 0.003 -10000 0 -0.013 2 2
JAK3 0.022 0.016 -10000 0 -0.066 13 13
PIK3R1 0.015 0.033 -10000 0 -0.1 35 35
JAK1 0.022 0.013 -10000 0 -0.12 2 2
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MYC -0.11 0.32 -10000 0 -0.85 80 80
MYB -0.064 0.29 -10000 0 -1.1 41 41
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.039 0.16 -10000 0 -0.32 104 104
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.008 0.17 -10000 0 -0.78 22 22
mol:PI-3-4-5-P3 -0.037 0.15 -10000 0 -0.31 104 104
Rac1/GDP 0.008 0.051 -10000 0 -0.12 66 66
T cell proliferation -0.032 0.14 -10000 0 -0.29 104 104
SHC1 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.019 -10000 0 -0.064 41 41
PRKCZ -0.033 0.15 -10000 0 -0.3 104 104
NF kappa B1 p50/RelA -0.035 0.19 -10000 0 -0.38 102 102
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.12 -10000 0 -0.33 50 50
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL2RA 0.02 0.018 -10000 0 -0.12 8 8
IL2RB 0.019 0.025 -10000 0 -0.089 25 25
TERT 0.023 0 -10000 0 -10000 0 0
E2F1 -0.016 0.13 -10000 0 -0.42 44 44
SOS1 0.016 0.027 -10000 0 -0.12 20 20
RPS6 0.023 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0.009 0.031 39 -10000 0 39
PTPN11 0.021 0.012 -10000 0 -0.12 3 3
IL2RG -0.002 0.051 -10000 0 -0.12 85 85
actin cytoskeleton organization -0.032 0.14 -10000 0 -0.29 104 104
GRB2 0.022 0.007 -10000 0 -0.12 1 1
IL2 0.023 0.014 -10000 0 -0.054 13 13
PIK3CA 0.02 0.019 -10000 0 -0.1 9 9
Rac1/GTP 0.02 0.057 -10000 0 -0.11 66 66
LCK 0.022 0.017 -10000 0 -0.064 16 16
BCL2 -0.033 0.17 -10000 0 -0.42 56 56
Arf6 downstream pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.027 0.22 -10000 0 -0.83 37 37
regulation of axonogenesis -0.005 0.059 0.18 43 -10000 0 43
myoblast fusion 0 0.1 0.38 37 -10000 0 37
mol:GTP 0 0.065 -10000 0 -0.22 44 44
regulation of calcium-dependent cell-cell adhesion -0.007 0.087 0.16 100 -10000 0 100
ARF1/GTP 0.013 0.055 -10000 0 -0.16 45 45
mol:GM1 -0.002 0.048 -10000 0 -0.16 44 44
mol:Choline 0.004 0.051 -10000 0 -0.15 45 45
lamellipodium assembly -0.006 0.12 -10000 0 -0.41 44 44
MAPK3 0.005 0.085 -10000 0 -0.28 44 44
ARF6/GTP/NME1/Tiam1 0.008 0.088 -10000 0 -0.16 100 100
ARF1 0.018 0.028 -10000 0 -0.12 21 21
ARF6/GDP 0 0.1 -10000 0 -0.38 37 37
ARF1/GDP 0.005 0.1 -10000 0 -0.33 44 44
ARF6 0.016 0.035 -10000 0 -0.12 35 35
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
TIAM1 0.014 0.034 -10000 0 -0.13 28 28
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.004 0.087 -10000 0 -0.28 45 45
actin filament bundle formation -0.007 0.1 0.34 44 -10000 0 44
KALRN 0.002 0.08 -10000 0 -0.29 37 37
RAB11FIP3/RAB11A 0.031 0.023 -10000 0 -0.13 11 11
RhoA/GDP 0.007 0.1 -10000 0 -0.34 44 44
NME1 0.014 0.031 -10000 0 -0.12 24 24
Rac1/GDP 0.007 0.1 -10000 0 -0.34 44 44
substrate adhesion-dependent cell spreading 0 0.065 -10000 0 -0.22 44 44
cortical actin cytoskeleton organization -0.007 0.12 -10000 0 -0.41 44 44
RAC1 0.023 0.002 -10000 0 -10000 0 0
liver development 0 0.065 -10000 0 -0.22 44 44
ARF6/GTP 0 0.065 -10000 0 -0.22 44 44
RhoA/GTP 0.016 0.056 -10000 0 -0.17 44 44
mol:GDP -0.005 0.11 -10000 0 -0.36 44 44
ARF6/GTP/RAB11FIP3/RAB11A 0.029 0.052 -10000 0 -0.13 50 50
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PLD1 0 0.059 -10000 0 -0.18 44 44
RAB11FIP3 0.022 0.011 -10000 0 -0.12 3 3
tube morphogenesis -0.006 0.12 -10000 0 -0.41 44 44
ruffle organization 0.005 0.059 -10000 0 -0.18 43 43
regulation of epithelial cell migration 0 0.065 -10000 0 -0.22 44 44
PLD2 0.01 0.05 -10000 0 -0.16 45 45
PIP5K1A 0.005 0.059 -10000 0 -0.18 43 43
mol:Phosphatidic acid 0.004 0.051 -10000 0 -0.15 45 45
Rac1/GTP -0.007 0.12 -10000 0 -0.41 44 44
HIF-2-alpha transcription factor network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.098 0.3 -10000 0 -0.93 63 63
oxygen homeostasis 0.001 0.01 -10000 0 -10000 0 0
TCEB2 0.023 0.006 -10000 0 -0.12 1 1
TCEB1 0.022 0.011 -10000 0 -0.12 3 3
VHL/Elongin B/Elongin C/HIF2A 0.008 0.11 -10000 0 -0.21 61 61
EPO 0.004 0.19 -10000 0 -0.38 46 46
FIH (dimer) 0.023 0.013 -10000 0 -0.12 1 1
APEX1 0.02 0.026 -10000 0 -0.12 11 11
SERPINE1 -0.015 0.19 -10000 0 -0.39 56 56
FLT1 -0.027 0.23 -10000 0 -0.76 46 46
ADORA2A -0.01 0.17 -10000 0 -0.38 52 52
germ cell development -0.018 0.2 -10000 0 -0.37 78 78
SLC11A2 -0.011 0.19 -10000 0 -0.39 63 63
BHLHE40 -0.013 0.18 -10000 0 -0.36 68 68
HIF1AN 0.023 0.013 -10000 0 -0.12 1 1
HIF2A/ARNT/SIRT1 0.012 0.14 -10000 0 -0.27 54 54
ETS1 0.027 0.037 -10000 0 -0.11 33 33
CITED2 0.025 0.079 -10000 0 -0.86 3 3
KDR -0.027 0.22 -10000 0 -0.74 46 46
PGK1 -0.013 0.2 -10000 0 -0.4 71 71
SIRT1 0.023 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.022 0.23 -10000 0 -0.44 52 52
EPAS1 -0.009 0.11 -10000 0 -0.21 90 90
SP1 0.016 0.034 -10000 0 -0.077 59 59
ABCG2 -0.007 0.19 -10000 0 -0.39 57 57
EFNA1 -0.019 0.2 -10000 0 -0.4 77 77
FXN -0.011 0.17 -10000 0 -0.38 52 52
POU5F1 -0.02 0.2 -10000 0 -0.38 78 78
neuron apoptosis -0.021 0.23 0.43 52 -10000 0 52
EP300 0.022 0.01 -10000 0 -0.12 2 2
EGLN3 -0.001 0.051 -10000 0 -0.12 84 84
EGLN2 0.023 0.014 -10000 0 -0.12 2 2
EGLN1 0.023 0.014 -10000 0 -0.12 2 2
VHL/Elongin B/Elongin C 0.041 0.029 -10000 0 -0.12 15 15
VHL 0.021 0.016 -10000 0 -0.12 7 7
ARNT 0.023 0.021 -10000 0 -0.12 4 4
SLC2A1 -0.024 0.19 -10000 0 -0.4 70 70
TWIST1 -0.011 0.17 -10000 0 -0.38 53 53
ELK1 0.028 0.019 -10000 0 -0.1 9 9
HIF2A/ARNT/Cbp/p300 0.008 0.15 -10000 0 -0.28 57 57
VEGFA -0.013 0.2 -10000 0 -0.41 63 63
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.022 0.012 -9999 0 -0.12 4 4
Caspase 8 (4 units) 0.023 0.084 -9999 0 -0.25 34 34
NEF 0.005 0.007 -9999 0 -0.066 5 5
NFKBIA -0.001 0.039 -9999 0 -0.066 109 109
BIRC3 -0.058 0.13 -9999 0 -0.21 206 206
CYCS 0.013 0.071 -9999 0 -0.22 30 30
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
CD247 0.028 0.008 -9999 0 -0.11 1 1
MAP2K7 0.018 0.091 -9999 0 -0.36 19 19
protein ubiquitination 0.021 0.067 -9999 0 -0.22 17 17
CRADD 0.023 0.009 -9999 0 -0.12 2 2
DAXX 0.022 0.012 -9999 0 -0.12 4 4
FAS 0.016 0.025 -9999 0 -0.12 17 17
BID 0.021 0.065 -9999 0 -0.24 28 28
NF-kappa-B/RelA/I kappa B alpha -0.021 0.11 -9999 0 -0.18 146 146
TRADD 0.023 0.006 -9999 0 -0.12 1 1
MAP3K5 0.018 0.025 -9999 0 -0.12 17 17
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
FADD 0.023 0.009 -9999 0 -0.12 2 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.11 -9999 0 -0.18 146 146
MAPK8 0.02 0.09 -9999 0 -0.35 19 19
APAF1 0.021 0.014 -9999 0 -0.12 5 5
TRAF1 0.023 0.001 -9999 0 -10000 0 0
TRAF2 0.023 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.068 -9999 0 -0.26 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.019 0.075 -9999 0 -0.22 27 27
CHUK 0.021 0.071 -9999 0 -0.24 17 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.068 -9999 0 -0.11 81 81
TCRz/NEF 0.028 0.014 -9999 0 -0.16 2 2
TNF 0.02 0.02 -9999 0 -0.12 11 11
FASLG 0.029 0.021 -9999 0 -0.16 5 5
NFKB1 0.004 0.031 -9999 0 -0.055 86 86
TNFR1A/BAG4/TNF-alpha 0.038 0.034 -9999 0 -0.11 20 20
CASP6 -0.041 0.21 -9999 0 -0.53 79 79
CASP7 -0.058 0.19 -9999 0 -0.41 117 117
RELA 0.003 0.032 -9999 0 -0.05 102 102
CASP2 0.022 0.009 -9999 0 -0.12 2 2
CASP3 -0.06 0.2 -9999 0 -0.41 118 118
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
TNFR1A/BAG4 0.027 0.034 -9999 0 -0.14 18 18
CASP8 0.023 0.004 -9999 0 -10000 0 0
CASP9 0.022 0.014 -9999 0 -0.12 5 5
MAP3K14 0.022 0.071 -9999 0 -0.21 27 27
APAF-1/Caspase 9 -0.028 0.12 -9999 0 -0.22 128 128
BCL2 0.02 0.087 -9999 0 -0.31 22 22
Syndecan-2-mediated signaling events

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.018 0.069 -9999 0 -0.16 81 81
EPHB2 0.02 0.02 -9999 0 -0.12 11 11
Syndecan-2/TACI 0.014 0.043 -9999 0 -0.11 47 47
LAMA1 0 0.053 -9999 0 -0.12 89 89
Syndecan-2/alpha2 ITGB1 -0.007 0.08 -9999 0 -0.17 58 58
HRAS 0.023 0.006 -9999 0 -0.12 1 1
Syndecan-2/CASK -0.001 0.039 -9999 0 -0.11 47 47
ITGA5 0.013 0.036 -9999 0 -0.12 38 38
BAX 0.025 0.021 -9999 0 -10000 0 0
EPB41 0.02 0.019 -9999 0 -0.12 9 9
positive regulation of cell-cell adhesion 0.004 0.05 -9999 0 -0.1 84 84
LAMA3 0.006 0.043 -9999 0 -0.12 55 55
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.039 -9999 0 -0.12 45 45
Syndecan-2/MMP2 -0.016 0.066 -9999 0 -0.16 68 68
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.007 0.061 -9999 0 -0.15 60 60
dendrite morphogenesis 0.01 0.049 -9999 0 -0.12 49 49
Syndecan-2/GM-CSF 0.014 0.043 -9999 0 -0.11 48 48
determination of left/right symmetry 0.011 0.025 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.01 0.049 -9999 0 -0.12 54 54
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
MAPK3 0.014 0.039 -9999 0 -0.094 48 48
MAPK1 0.013 0.039 -9999 0 -0.096 48 48
Syndecan-2/RACK1 0.024 0.043 -9999 0 -0.087 54 54
NF1 0.018 0.02 -9999 0 -0.12 10 10
FGFR/FGF/Syndecan-2 0.011 0.025 -9999 0 -10000 0 0
ITGA2 0.011 0.038 -9999 0 -0.12 41 41
MAPK8 0.02 0.023 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.005 0.07 -9999 0 -0.17 35 35
Syndecan-2/Kininogen 0.014 0.043 -9999 0 -0.11 47 47
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC 0.017 0.036 -9999 0 -0.15 2 2
Syndecan-2/CASK/Protein 4.1 0.009 0.045 -9999 0 -0.1 61 61
extracellular matrix organization 0.01 0.049 -9999 0 -0.12 53 53
actin cytoskeleton reorganization -0.018 0.069 -9999 0 -0.16 81 81
Syndecan-2/Caveolin-2/Ras 0.009 0.062 -9999 0 -0.11 95 95
Syndecan-2/Laminin alpha3 -0.001 0.06 -9999 0 -0.14 62 62
Syndecan-2/RasGAP 0.027 0.051 -9999 0 -0.15 7 7
alpha5/beta1 Integrin 0.016 0.048 -9999 0 -0.1 76 76
PRKCD 0.02 0.018 -9999 0 -0.12 8 8
Syndecan-2 dimer 0.011 0.049 -9999 0 -0.12 49 49
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.026 0.047 -9999 0 -0.14 7 7
RHOA 0.023 0.006 -9999 0 -0.12 1 1
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
TNFRSF13B 0.023 0 -9999 0 -10000 0 0
RASA1 0.021 0.012 -9999 0 -0.12 3 3
alpha2/beta1 Integrin 0.007 0.061 -9999 0 -0.15 60 60
Syndecan-2/Synbindin 0.006 0.05 -9999 0 -0.12 56 56
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CASP3 0.01 0.043 -9999 0 -0.1 54 54
FN1 -0.013 0.056 -9999 0 -0.12 114 114
Syndecan-2/IL8 0.001 0.055 -9999 0 -0.13 61 61
SDC2 0.011 0.025 -9999 0 -10000 0 0
KNG1 0.022 0.011 -9999 0 -0.12 3 3
Syndecan-2/Neurofibromin 0.007 0.051 -9999 0 -0.13 52 52
TRAPPC4 0.016 0.025 -9999 0 -0.12 16 16
CSF2 0.023 0.009 -9999 0 -0.12 2 2
Syndecan-2/TGFB1 0.01 0.049 -9999 0 -0.12 53 53
Syndecan-2/Syntenin/PI-4-5-P2 0.004 0.05 -9999 0 -0.1 84 84
Syndecan-2/Ezrin 0.012 0.04 -9999 0 -0.097 51 51
PRKACA 0.008 0.045 -9999 0 -0.11 53 53
angiogenesis 0.001 0.055 -9999 0 -0.13 61 61
MMP2 -0.015 0.059 -9999 0 -0.12 128 128
IL8 0.004 0.047 -9999 0 -0.12 69 69
calcineurin-NFAT signaling pathway 0.014 0.043 -9999 0 -0.11 47 47
BCR signaling pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.024 0.11 -10000 0 -0.25 76 76
IKBKB 0.013 0.077 0.2 7 -0.25 23 30
AKT1 -0.008 0.06 0.14 11 -0.15 45 56
IKBKG 0.012 0.068 -10000 0 -0.24 19 19
CALM1 -0.008 0.1 0.16 4 -0.31 44 48
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
MAP3K1 -0.029 0.13 -10000 0 -0.33 62 62
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
mol:Ca2+ -0.012 0.11 0.16 4 -0.3 50 54
DOK1 0.021 0.016 -10000 0 -0.12 7 7
AP-1 -0.014 0.077 0.14 1 -0.18 72 73
LYN 0.02 0.013 -10000 0 -0.12 4 4
BLNK 0.014 0.033 -10000 0 -0.12 31 31
SHC1 0.023 0.001 -10000 0 -10000 0 0
BCR complex 0.028 0.026 -10000 0 -0.077 32 32
CD22 -0.04 0.1 -10000 0 -0.25 70 70
CAMK2G -0.003 0.099 0.15 4 -0.28 44 48
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.001 0.052 -10000 0 -0.14 37 37
GO:0007205 -0.012 0.11 0.16 4 -0.3 50 54
SYK 0.016 0.027 -10000 0 -0.12 20 20
ELK1 -0.008 0.1 0.16 4 -0.31 43 47
NFATC1 -0.014 0.084 -10000 0 -0.23 54 54
B-cell antigen/BCR complex 0.028 0.026 -10000 0 -0.077 32 32
PAG1/CSK 0.032 0.02 -10000 0 -0.1 12 12
NFKBIB 0.008 0.045 -10000 0 -0.13 46 46
HRAS -0.001 0.087 0.13 2 -0.25 43 45
NFKBIA 0.011 0.041 -10000 0 -0.12 36 36
NF-kappa-B/RelA/I kappa B beta 0.014 0.043 -10000 0 -0.12 41 41
RasGAP/Csk 0.023 0.067 -10000 0 -0.11 22 22
mol:GDP -0.011 0.11 0.15 4 -0.3 51 55
PTEN 0.022 0.008 -10000 0 -0.12 1 1
CD79B 0.023 0.006 -10000 0 -0.12 1 1
NF-kappa-B/RelA/I kappa B alpha 0.014 0.04 -10000 0 -0.11 41 41
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PI3K/BCAP/CD19 -0.029 0.13 -10000 0 -0.37 54 54
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.012 0.11 0.16 4 -0.31 50 54
CSK 0.023 0.009 -10000 0 -0.12 2 2
FOS -0.023 0.11 0.15 2 -0.29 56 58
CHUK -0.004 0.096 -10000 0 -0.28 45 45
IBTK 0.02 0.016 -10000 0 -0.12 6 6
CARD11/BCL10/MALT1/TAK1 0.006 0.1 0.19 1 -0.25 51 52
PTPN6 -0.036 0.095 -10000 0 -0.24 71 71
RELA 0.023 0.009 -10000 0 -0.12 2 2
BCL2A1 0.009 0.034 -10000 0 -0.08 52 52
VAV2 -0.031 0.11 -10000 0 -0.31 55 55
ubiquitin-dependent protein catabolic process 0.012 0.045 -10000 0 -0.12 46 46
BTK -0.05 0.25 -10000 0 -1.1 32 32
CD19 -0.032 0.095 -10000 0 -0.29 41 41
MAP4K1 0.02 0.023 -10000 0 -0.12 14 14
CD72 0.023 0.006 -10000 0 -0.12 1 1
PAG1 0.022 0.014 -10000 0 -0.12 5 5
MAPK14 -0.021 0.11 -10000 0 -0.29 61 61
SH3BP5 0.021 0.015 -10000 0 -0.12 6 6
PIK3AP1 -0.009 0.11 0.17 4 -0.34 44 48
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.012 0.13 -10000 0 -0.3 81 81
RAF1 0.002 0.083 0.13 3 -0.24 42 45
RasGAP/p62DOK/SHIP 0.015 0.062 -10000 0 -0.084 131 131
CD79A 0.016 0.032 -10000 0 -0.12 28 28
re-entry into mitotic cell cycle -0.014 0.076 0.14 1 -0.18 71 72
RASA1 0.021 0.012 -10000 0 -0.12 3 3
MAPK3 0.009 0.074 0.13 3 -0.21 36 39
MAPK1 0.008 0.074 0.13 3 -0.22 36 39
CD72/SHP1 -0.026 0.095 -10000 0 -0.24 58 58
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 -0.022 0.11 -10000 0 -0.29 62 62
actin cytoskeleton organization -0.024 0.098 -10000 0 -0.28 55 55
NF-kappa-B/RelA 0.022 0.096 -10000 0 -0.23 52 52
Calcineurin 0.014 0.098 -10000 0 -0.26 44 44
PI3K -0.038 0.075 -10000 0 -0.23 51 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.11 0.17 4 -0.34 42 46
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Bam32/HPK1 -0.042 0.18 -10000 0 -0.55 46 46
DAPP1 -0.057 0.19 -10000 0 -0.61 46 46
cytokine secretion -0.012 0.08 0.16 1 -0.22 54 55
mol:DAG -0.012 0.11 0.16 4 -0.31 50 54
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
MAP2K1 0.006 0.079 0.13 3 -0.22 39 42
B-cell antigen/BCR complex/FcgammaRIIB 0.009 0.063 -10000 0 -0.11 99 99
mol:PI-3-4-5-P3 -0.034 0.057 0.095 1 -0.18 49 50
ETS1 -0.006 0.098 0.15 2 -0.27 50 52
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.029 0.069 -10000 0 -0.15 29 29
B-cell antigen/BCR complex/LYN -0.037 0.1 -10000 0 -0.31 41 41
MALT1 0.017 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 -0.026 0.1 -10000 0 -0.29 55 55
B-cell antigen/BCR complex/LYN/SYK -0.004 0.091 -10000 0 -0.22 52 52
CARD11 -0.009 0.11 0.16 4 -0.3 46 50
FCGR2B 0.004 0.044 -10000 0 -0.12 60 60
PPP3CA 0.021 0.014 -10000 0 -0.12 5 5
BCL10 0.023 0.001 -10000 0 -10000 0 0
IKK complex 0.012 0.039 0.1 16 -0.098 24 40
PTPRC -0.004 0.051 -10000 0 -0.12 86 86
PDPK1 -0.01 0.054 0.13 13 -0.13 50 63
PPP3CB 0.023 0.003 -10000 0 -10000 0 0
PPP3CC 0.022 0.011 -10000 0 -0.12 3 3
POU2F2 0.012 0.033 -10000 0 -0.075 53 53
FOXA2 and FOXA3 transcription factor networks

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.056 0.28 -10000 0 -0.63 63 63
PCK1 -0.16 0.41 -10000 0 -1.1 83 83
HNF4A -0.11 0.36 -10000 0 -0.75 104 104
KCNJ11 -0.012 0.27 -10000 0 -0.64 37 37
AKT1 -0.004 0.16 -10000 0 -0.32 42 42
response to starvation -0.019 0.045 -10000 0 -0.13 71 71
DLK1 -0.028 0.28 -10000 0 -0.64 49 49
NKX2-1 -0.01 0.15 -10000 0 -0.49 2 2
ACADM -0.069 0.3 -10000 0 -0.66 72 72
TAT -0.025 0.2 -10000 0 -0.58 16 16
CEBPB 0.021 0.032 -10000 0 -0.12 29 29
CEBPA 0.029 0.015 -10000 0 -0.12 5 5
TTR 0.011 0.16 -10000 0 -0.83 4 4
PKLR -0.045 0.27 -10000 0 -0.62 51 51
APOA1 -0.17 0.49 -10000 0 -1.1 109 109
CPT1C -0.052 0.27 -10000 0 -0.64 50 50
ALAS1 -0.012 0.19 -10000 0 -0.86 6 6
TFRC -0.1 0.4 -10000 0 -0.99 77 77
FOXF1 0.015 0.012 -10000 0 -0.11 5 5
NF1 0.024 0.026 -10000 0 -0.13 12 12
HNF1A (dimer) 0.042 0.019 -10000 0 -0.13 5 5
CPT1A -0.064 0.29 -10000 0 -0.65 69 69
HMGCS1 -0.059 0.29 -10000 0 -0.67 56 56
NR3C1 0.035 0.017 -10000 0 -0.11 5 5
CPT1B -0.047 0.27 -10000 0 -0.64 47 47
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.013 -10000 0 -0.14 2 2
GCK -0.045 0.27 -10000 0 -0.62 49 49
CREB1 -0.009 0.07 -10000 0 -0.17 76 76
IGFBP1 -0.014 0.16 -10000 0 -0.54 6 6
PDX1 0.028 0.17 -10000 0 -0.76 4 4
UCP2 -0.093 0.33 -10000 0 -0.7 91 91
ALDOB -0.012 0.27 -10000 0 -0.63 39 39
AFP 0.017 0.051 -10000 0 -0.3 3 3
BDH1 -0.07 0.3 -10000 0 -0.64 74 74
HADH -0.021 0.28 -10000 0 -0.62 52 52
F2 -0.066 0.34 -10000 0 -0.83 41 41
HNF1A 0.042 0.019 -10000 0 -0.13 5 5
G6PC 0.025 0.076 -10000 0 -0.42 1 1
SLC2A2 0.021 0.18 -10000 0 -0.66 2 2
INS 0.009 0.012 0.16 1 -0.14 2 3
FOXA1 0.035 0.03 -10000 0 -0.17 4 4
FOXA3 0.002 0.097 -10000 0 -0.19 76 76
FOXA2 -0.008 0.32 -10000 0 -0.7 47 47
ABCC8 -0.012 0.27 -10000 0 -0.64 37 37
ALB 0.017 0.051 -10000 0 -0.32 2 2
ceramide signaling pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.012 0.11 -10000 0 -0.21 118 118
BAG4 0.022 0.012 -10000 0 -0.12 4 4
BAD 0.007 0.036 -10000 0 -0.11 20 20
NFKBIA 0.016 0.028 -10000 0 -0.12 21 21
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BAX 0.007 0.036 -10000 0 -0.11 19 19
EnzymeConsortium:3.1.4.12 0 0.027 -10000 0 -0.063 41 41
IKBKB -0.009 0.11 -10000 0 -0.2 119 119
MAP2K2 0.013 0.036 -10000 0 -0.1 25 25
MAP2K1 0.015 0.033 -10000 0 -0.099 20 20
SMPD1 0.005 0.028 -10000 0 -0.094 16 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.2 119 119
MAP2K4 0.008 0.039 -10000 0 -0.1 33 33
protein ubiquitination -0.012 0.11 -10000 0 -0.25 59 59
EnzymeConsortium:2.7.1.37 0.017 0.034 -10000 0 -0.11 12 12
response to UV 0 0 -10000 0 -0.001 8 8
RAF1 0.011 0.035 -10000 0 -0.1 24 24
CRADD 0.023 0.009 -10000 0 -0.12 2 2
mol:ceramide 0.003 0.038 -10000 0 -0.11 23 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0.041 -10000 0 -0.097 61 61
MADD 0.023 0.006 -10000 0 -0.12 1 1
MAP3K1 0.004 0.04 -10000 0 -0.12 30 30
TRADD 0.023 0.006 -10000 0 -0.12 1 1
RELA/p50 0.023 0.009 -10000 0 -0.12 2 2
MAPK3 0.017 0.035 -10000 0 -0.12 11 11
MAPK1 0.016 0.037 -10000 0 -0.12 16 16
p50/RELA/I-kappa-B-alpha 0.018 0.049 -10000 0 -0.12 61 61
FADD -0.01 0.11 -10000 0 -0.2 118 118
KSR1 0.008 0.036 -10000 0 -0.11 20 20
MAPK8 0.008 0.042 -10000 0 -0.11 37 37
TRAF2 0.024 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.013 0.11 -10000 0 -0.2 119 119
TNF R/SODD 0.027 0.034 -10000 0 -0.14 18 18
TNF 0.02 0.02 -10000 0 -0.12 11 11
CYCS 0.006 0.038 0.097 1 -0.11 22 23
IKBKG -0.009 0.11 -10000 0 -0.19 119 119
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.22 118 118
RELA 0.023 0.009 -10000 0 -0.12 2 2
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
AIFM1 0.001 0.044 0.097 1 -0.12 33 34
TNF/TNF R/SODD 0.038 0.034 -10000 0 -0.11 20 20
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.13 -10000 0 -0.67 17 17
NSMAF -0.011 0.11 -10000 0 -0.21 118 118
response to hydrogen peroxide 0 0 -10000 0 -0.001 8 8
BCL2 0.016 0.031 -10000 0 -0.12 27 27
E-cadherin signaling in the nascent adherens junction

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.009 0.13 -9999 0 -0.41 49 49
KLHL20 -0.012 0.085 -9999 0 -0.19 67 67
CYFIP2 0.02 0.018 -9999 0 -0.12 8 8
Rac1/GDP 0.012 0.091 -9999 0 -0.22 55 55
ENAH -0.01 0.13 -9999 0 -0.4 50 50
AP1M1 0.021 0.017 -9999 0 -0.12 8 8
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
CDC42/GTP 0.011 0.07 -9999 0 -0.2 34 34
ABI1/Sra1/Nap1 -0.028 0.049 -9999 0 -0.14 73 73
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.055 -9999 0 -0.1 63 63
RAPGEF1 0 0.11 -9999 0 -0.34 49 49
CTNND1 0.023 0.004 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.01 0.13 -9999 0 -0.41 49 49
CRK -0.005 0.12 -9999 0 -0.37 49 49
E-cadherin/gamma catenin/alpha catenin 0.025 0.06 -9999 0 -0.13 61 61
alphaE/beta7 Integrin 0.026 0.035 -9999 0 -0.11 33 33
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
NCKAP1 0.023 0.004 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.015 0.059 -9999 0 -0.11 85 85
DLG1 -0.01 0.13 -9999 0 -0.41 49 49
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.05 -9999 0 -0.16 53 53
MLLT4 0.014 0.032 -9999 0 -0.12 29 29
ARF6/GTP/NME1/Tiam1 0.018 0.056 -9999 0 -0.11 71 71
PI3K -0.028 0.065 -9999 0 -0.2 53 53
ARF6 0.023 0.003 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.017 0.054 -9999 0 -0.13 61 61
TIAM1 0.015 0.032 -9999 0 -0.12 28 28
E-cadherin(dimer)/Ca2+ 0.033 0.061 -9999 0 -0.12 67 67
AKT1 0.005 0.049 -9999 0 -0.12 50 50
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
CDH1 0.02 0.016 -9999 0 -0.12 6 6
RhoA/GDP 0.013 0.091 -9999 0 -0.22 54 54
actin cytoskeleton organization -0.007 0.064 -9999 0 -0.14 67 67
CDC42/GDP 0.013 0.091 -9999 0 -0.23 53 53
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.08 -9999 0 -0.19 66 66
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.036 0.065 -9999 0 -0.13 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0.049 -9999 0 -0.11 64 64
mol:GDP 0.001 0.1 -9999 0 -0.26 54 54
CDC42/GTP/IQGAP1 0.018 0.043 -9999 0 -0.11 54 54
JUP 0.019 0.021 -9999 0 -0.12 12 12
p120 catenin/RhoA/GDP 0.017 0.094 -9999 0 -0.24 52 52
RAC1/GTP/IQGAP1 0.017 0.044 -9999 0 -0.12 48 48
PIP5K1C/AP1M1 0.033 0.014 -9999 0 -0.14 1 1
RHOA 0.023 0.006 -9999 0 -0.12 1 1
CDC42 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
positive regulation of S phase of mitotic cell cycle -0.014 0.063 -9999 0 -0.12 119 119
NME1 0.015 0.03 -9999 0 -0.12 24 24
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.011 0.14 -9999 0 -0.42 51 51
regulation of cell-cell adhesion -0.018 0.05 -9999 0 -0.18 35 35
WASF2 -0.002 0.036 -9999 0 -0.079 66 66
Rap1/GTP 0.013 0.08 -9999 0 -0.23 34 34
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.041 0.064 -9999 0 -0.1 76 76
CCND1 -0.018 0.076 -9999 0 -0.15 119 119
VAV2 -0.019 0.17 -9999 0 -0.54 45 45
RAP1/GDP 0.016 0.087 -9999 0 -0.24 37 37
adherens junction assembly -0.01 0.13 -9999 0 -0.4 51 51
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.022 0.009 -9999 0 -0.12 2 2
PIP5K1C 0.023 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.033 0.064 -9999 0 -0.17 23 23
E-cadherin/beta catenin 0.008 0.056 -9999 0 -0.23 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.008 0.13 -9999 0 -0.4 49 49
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
Rac1/GTP -0.059 0.11 -9999 0 -0.32 66 66
E-cadherin/beta catenin/alpha catenin 0.026 0.058 -9999 0 -0.13 64 64
ITGAE 0.023 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.14 -9999 0 -0.42 49 49
Signaling events mediated by PRL

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
mol:Halofuginone 0.003 0.025 -10000 0 -0.18 10 10
ITGA1 0.014 0.03 -10000 0 -0.12 24 24
CDKN1A 0.014 0.059 -10000 0 -0.29 18 18
PRL-3/alpha Tubulin 0.014 0.051 -10000 0 -0.1 83 83
mol:Ca2+ 0.018 0.076 0.28 41 -10000 0 41
AGT 0.02 0.02 -10000 0 -0.12 11 11
CCNA2 -0.001 0.094 -10000 0 -0.59 12 12
TUBA1B 0.023 0 -10000 0 -10000 0 0
EGR1 -0.002 0.06 -10000 0 -0.34 12 12
CDK2/Cyclin E1 0.006 0.074 -10000 0 -0.27 22 22
MAPK3 0.014 0.027 -10000 0 -0.072 46 46
PRL-2 /Rab GGTase beta 0.009 0.063 -10000 0 -0.13 87 87
MAPK1 0.013 0.031 -10000 0 -0.083 47 47
PTP4A1 0.001 0.092 -10000 0 -0.57 12 12
PTP4A3 0.011 0.038 -10000 0 -0.12 42 42
PTP4A2 0.022 0.009 -10000 0 -0.12 2 2
ITGB1 0.013 0.028 -10000 0 -0.074 48 48
SRC 0.023 0.009 -10000 0 -0.12 2 2
RAC1 -0.014 0.11 -10000 0 -0.34 54 54
Rab GGTase beta/Rab GGTase alpha 0.012 0.058 -10000 0 -0.13 79 79
PRL-1/ATF-5 -0.003 0.095 -10000 0 -0.54 12 12
RABGGTA 0.023 0.006 -10000 0 -0.12 1 1
BCAR1 0.02 0.076 0.28 41 -10000 0 41
RHOC -0.013 0.11 -10000 0 -0.35 51 51
RHOA -0.014 0.11 -10000 0 -0.34 54 54
cell motility -0.011 0.11 -10000 0 -0.32 57 57
PRL-1/alpha Tubulin 0 0.094 -10000 0 -0.54 12 12
PRL-3/alpha1 Integrin -0.012 0.08 -10000 0 -0.13 161 161
ROCK1 -0.012 0.11 -10000 0 -0.32 57 57
RABGGTB 0.017 0.022 -10000 0 -0.12 12 12
CDK2 0.018 0.023 -10000 0 -0.12 14 14
mitosis 0.001 0.091 -10000 0 -0.57 12 12
ATF5 0.018 0.027 -10000 0 -0.12 20 20
FAS signaling pathway (CD95)

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.003 0.039 0.15 3 -0.26 10 13
RFC1 0.003 0.04 0.16 4 -0.26 10 14
PRKDC 0.003 0.039 0.16 4 -0.25 10 14
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP7 0.002 0.091 0.2 2 -0.45 16 18
FASLG/FAS/FADD/FAF1 0.036 0.085 0.16 118 -0.17 42 160
MAP2K4 -0.001 0.11 -10000 0 -0.3 41 41
mol:ceramide 0.005 0.094 -10000 0 -0.26 36 36
GSN 0.002 0.038 0.16 1 -0.26 10 11
FASLG/FAS/FADD/FAF1/Caspase 8 0.042 0.09 0.16 111 -0.25 19 130
FAS 0.016 0.026 -10000 0 -0.12 17 17
BID 0.005 0.017 0.25 2 -0.069 1 3
MAP3K1 0.001 0.093 0.17 2 -0.29 35 37
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
RB1 0.001 0.041 0.16 4 -0.25 11 15
CFLAR 0.022 0.011 -10000 0 -0.12 3 3
HGF/MET -0.054 0.089 -10000 0 -0.14 247 247
ARHGDIB -0.002 0.043 0.16 3 -0.28 10 13
FADD 0.022 0.01 -10000 0 -0.12 2 2
actin filament polymerization -0.002 0.038 0.25 10 -0.16 1 11
NFKB1 -0.037 0.2 -10000 0 -0.74 38 38
MAPK8 -0.001 0.12 -10000 0 -0.34 38 38
DFFA 0.003 0.04 0.16 4 -0.25 11 15
DNA fragmentation during apoptosis 0.003 0.04 0.16 4 -0.25 11 15
FAS/FADD/MET -0.014 0.082 -10000 0 -0.13 164 164
CFLAR/RIP1 0.03 0.027 -10000 0 -0.12 16 16
FAIM3 0.022 0.012 -10000 0 -0.12 4 4
FAF1 0.021 0.015 -10000 0 -0.12 5 5
PARP1 0.004 0.037 0.16 4 -0.24 10 14
DFFB 0.003 0.04 0.16 4 -0.25 11 15
CHUK -0.034 0.19 -10000 0 -0.71 38 38
FASLG 0.022 0.014 -10000 0 -0.13 4 4
FAS/FADD 0.012 0.056 -10000 0 -0.13 67 67
HGF 0.02 0.023 -10000 0 -0.12 14 14
LMNA 0 0.047 0.14 4 -0.25 14 18
CASP6 -0.003 0.05 0.16 4 -0.29 12 16
CASP10 0.018 0.02 -10000 0 -0.12 10 10
CASP3 -0.002 0.046 0.18 4 -0.28 11 15
PTPN13 -0.012 0.056 -10000 0 -0.12 112 112
CASP8 -0.005 0.018 0.15 6 -10000 0 6
IL6 -0.038 0.21 -10000 0 -0.75 35 35
MET 0 0.047 -10000 0 -0.12 70 70
ICAD/CAD 0.007 0.038 0.15 2 -0.22 12 14
FASLG/FAS/FADD/FAF1/Caspase 10 0.005 0.095 -10000 0 -0.27 36 36
activation of caspase activity by cytochrome c 0.005 0.017 0.25 2 -0.069 1 3
PAK2 0.003 0.04 0.16 4 -0.25 11 15
BCL2 0.016 0.031 -10000 0 -0.12 27 27
EGFR-dependent Endothelin signaling events

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.023 0.006 -9999 0 -0.12 1 1
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EGF/EGFR 0.013 0.053 -9999 0 -0.092 80 80
EGF/EGFR dimer/SHC/GRB2/SOS1 0.041 0.058 -9999 0 -0.094 67 67
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.014 0.035 -9999 0 -0.12 34 34
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.02 0.021 -9999 0 -0.12 12 12
EGF/EGFR dimer/SHC 0.03 0.046 -9999 0 -0.11 40 40
mol:GDP 0.036 0.056 -9999 0 -0.094 67 67
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.009 0.043 -9999 0 -0.12 54 54
GRB2/SOS1 0.021 0.045 -9999 0 -0.12 50 50
HRAS/GTP 0.023 0.045 -9999 0 -0.14 12 12
SHC1 0.023 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.036 0.052 -9999 0 -0.16 9 9
FRAP1 0.016 0.044 -9999 0 -0.087 67 67
EGF/EGFR dimer 0.016 0.05 -9999 0 -0.11 73 73
SOS1 0.017 0.027 -9999 0 -0.12 20 20
GRB2 0.023 0.006 -9999 0 -0.12 1 1
ETA receptor/Endothelin-1 0.008 0.056 -9999 0 -0.096 115 115
Aurora B signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.05 0.17 -9999 0 -0.34 102 102
STMN1 0.019 0.019 -9999 0 -0.069 23 23
Aurora B/RasGAP/Survivin 0.018 0.072 -9999 0 -0.16 70 70
Chromosomal passenger complex/Cul3 protein complex -0.001 0.087 -9999 0 -0.27 41 41
BIRC5 0.018 0.023 -9999 0 -0.12 14 14
DES -0.029 0.23 -9999 0 -0.95 32 32
Aurora C/Aurora B/INCENP 0.033 0.039 -9999 0 -0.11 32 32
Aurora B/TACC1 0.014 0.048 -9999 0 -0.13 42 42
Aurora B/PP2A 0.02 0.048 -9999 0 -0.12 58 58
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.005 0.061 -9999 0 -0.2 47 47
mitotic metaphase/anaphase transition 0.002 0.005 -9999 0 -10000 0 0
NDC80 0.009 0.032 -9999 0 -0.081 55 55
Cul3 protein complex 0.016 0.056 -9999 0 -0.11 58 58
KIF2C -0.065 0.21 -9999 0 -0.48 93 93
PEBP1 0.022 0.008 -9999 0 -0.12 1 1
KIF20A 0.009 0.038 -9999 0 -0.12 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.012 0.058 -9999 0 -0.15 59 59
SEPT1 0.022 0.014 -9999 0 -0.12 5 5
SMC2 0.015 0.03 -9999 0 -0.12 25 25
SMC4 0.018 0.025 -9999 0 -0.12 17 17
NSUN2/NPM1/Nucleolin -0.024 0.17 -9999 0 -0.66 33 33
PSMA3 0.019 0.021 -9999 0 -0.12 11 11
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B -0.001 0.065 -9999 0 -0.21 47 47
AURKB 0.018 0.027 -9999 0 -0.12 19 19
AURKC 0.023 0.006 -9999 0 -0.12 1 1
CDCA8 0.019 0.021 -9999 0 -0.12 11 11
cytokinesis -0.04 0.2 -9999 0 -0.47 73 73
Aurora B/Septin1 -0.022 0.19 -9999 0 -0.45 68 68
AURKA 0.015 0.028 -9999 0 -0.12 21 21
INCENP 0.021 0.011 -9999 0 -0.12 2 2
KLHL13 -0.001 0.053 -9999 0 -0.12 89 89
BUB1 0.017 0.026 -9999 0 -0.12 17 17
hSgo1/Aurora B/Survivin 0.011 0.078 -9999 0 -0.16 77 77
EVI5 0.021 0.016 -9999 0 -0.12 6 6
RhoA/GTP -0.022 0.18 -9999 0 -0.38 80 80
SGOL1 0.016 0.028 -9999 0 -0.12 22 22
CENPA -0.036 0.17 -9999 0 -0.36 87 87
NCAPG 0.01 0.037 -9999 0 -0.12 39 39
Aurora B/HC8 Proteasome 0.009 0.063 -9999 0 -0.14 75 75
NCAPD2 0.015 0.03 -9999 0 -0.12 25 25
Aurora B/PP1-gamma 0.012 0.059 -9999 0 -0.15 61 61
RHOA 0.023 0.006 -9999 0 -0.12 1 1
NCAPH 0.019 0.02 -9999 0 -0.12 10 10
NPM1 -0.01 0.12 -9999 0 -0.41 39 39
RASA1 0.021 0.012 -9999 0 -0.12 3 3
KLHL9 0.023 0.007 -9999 0 -0.12 1 1
mitotic prometaphase -0.001 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.063 -9999 0 -0.14 75 75
PPP1CC 0.022 0.005 -9999 0 -10000 0 0
Centraspindlin -0.032 0.19 -9999 0 -0.42 80 80
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
NSUN2 -0.01 0.11 -9999 0 -0.39 40 40
MYLK -0.005 0.066 -9999 0 -0.21 50 50
KIF23 0.013 0.034 -9999 0 -0.12 32 32
VIM 0.016 0.028 -9999 0 -0.09 28 28
RACGAP1 0.017 0.025 -9999 0 -0.12 16 16
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.02 0.12 -9999 0 -0.37 57 57
Chromosomal passenger complex -0.035 0.17 -9999 0 -0.35 88 88
Chromosomal passenger complex/EVI5 0.032 0.084 -9999 0 -0.22 36 36
TACC1 0.014 0.035 -9999 0 -0.12 34 34
PPP2R5D 0.022 0.014 -9999 0 -0.12 5 5
CUL3 0.023 0.004 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.036 0.049 -10000 0 -0.094 62 62
ER alpha/Gai/GDP/Gbeta gamma 0.006 0.094 -10000 0 -0.26 53 53
AKT1 -0.054 0.23 -10000 0 -0.6 78 78
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.055 0.23 -10000 0 -0.61 78 78
mol:Ca2+ 0.011 0.069 -10000 0 -0.25 30 30
IGF1R 0.013 0.032 -10000 0 -0.12 28 28
E2/ER alpha (dimer)/Striatin 0.014 0.047 -10000 0 -0.1 72 72
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis 0.051 0.22 0.57 78 -10000 0 78
RhoA/GTP -0.016 0.034 -10000 0 -0.15 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.008 0.1 -10000 0 -0.25 59 59
regulation of stress fiber formation -0.007 0.049 0.14 38 -10000 0 38
E2/ERA-ERB (dimer) 0.018 0.041 -10000 0 -0.12 43 43
KRAS 0.014 0.034 -10000 0 -0.12 33 33
G13/GTP 0.014 0.041 -10000 0 -0.091 72 72
pseudopodium formation 0.007 0.049 -10000 0 -0.14 38 38
E2/ER alpha (dimer)/PELP1 0.018 0.041 -10000 0 -0.098 60 60
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GNG2 0.02 0.018 -10000 0 -0.12 9 9
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.023 0.006 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.13 -10000 0 -0.32 69 69
E2/ER beta (dimer) 0.017 0.004 -10000 0 -0.077 1 1
mol:GDP 0.002 0.075 -10000 0 -0.24 44 44
mol:NADP -0.012 0.13 -10000 0 -0.32 69 69
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 0.01 0.071 -10000 0 -0.26 30 30
IGF-1R heterotetramer 0.013 0.032 -10000 0 -0.12 28 28
PLCB1 0.009 0.072 -10000 0 -0.26 30 30
PLCB2 0.016 0.069 -10000 0 -0.26 28 28
IGF1 0.007 0.045 -10000 0 -0.12 60 60
mol:L-citrulline -0.012 0.13 -10000 0 -0.32 69 69
RHOA 0.023 0.006 -10000 0 -0.12 1 1
Gai/GDP 0.023 0.057 -10000 0 -0.53 2 2
JNK cascade 0.017 0.004 -10000 0 -0.077 1 1
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
ESR2 0.023 0.006 -10000 0 -0.12 1 1
GNAQ 0.021 0.016 -10000 0 -0.12 6 6
ESR1 0.018 0.024 -10000 0 -0.12 15 15
Gq family/GDP/Gbeta gamma 0.031 0.062 -10000 0 -0.3 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.086 -10000 0 -0.51 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.008 0.1 -10000 0 -0.25 59 59
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
E2/ER alpha (dimer) 0.002 0.045 -10000 0 -0.13 58 58
STRN 0.022 0.013 -10000 0 -0.12 4 4
GNAL 0.021 0.018 -10000 0 -0.12 9 9
PELP1 0.023 0.009 -10000 0 -0.12 2 2
MAPK11 0.021 0.003 -10000 0 -0.057 1 1
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
HBEGF -0.025 0.1 -10000 0 -0.25 65 65
cAMP biosynthetic process 0.016 0.032 -10000 0 -0.086 44 44
SRC 0.004 0.096 -10000 0 -0.25 62 62
PI3K 0.007 0.065 -10000 0 -0.13 96 96
GNB1 0.023 0.007 -10000 0 -0.12 1 1
G13/GDP/Gbeta gamma 0.023 0.076 -10000 0 -0.2 46 46
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IGF-1R heterotetramer/IGF1 -0.038 0.072 -10000 0 -0.22 63 63
Gs family/GTP 0.022 0.035 -10000 0 -0.087 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.043 -10000 0 -0.11 38 38
vasodilation -0.011 0.12 -10000 0 -0.31 69 69
mol:DAG 0.01 0.071 -10000 0 -0.26 30 30
Gs family/GDP/Gbeta gamma 0.005 0.068 -10000 0 -0.2 45 45
MSN 0.007 0.051 -10000 0 -0.15 38 38
Gq family/GTP 0.015 0.073 -10000 0 -0.27 28 28
mol:PI-3-4-5-P3 -0.053 0.22 -10000 0 -0.59 78 78
NRAS 0.022 0.011 -10000 0 -0.12 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.011 0.12 0.31 69 -10000 0 69
GRB2/SOS1 0.021 0.045 -10000 0 -0.12 50 50
RhoA/GDP 0.014 0.076 -10000 0 -0.22 46 46
NOS3 -0.013 0.13 -10000 0 -0.34 69 69
GNA11 0.022 0.014 -10000 0 -0.12 5 5
MAPKKK cascade -0.005 0.15 -10000 0 -0.43 55 55
E2/ER alpha (dimer)/PELP1/Src 0.003 0.1 -10000 0 -0.26 59 59
ruffle organization 0.007 0.049 -10000 0 -0.14 38 38
ROCK2 0.01 0.049 -10000 0 -0.15 23 23
GNA14 0.02 0.02 -10000 0 -0.12 11 11
GNA15 0.021 0.017 -10000 0 -0.12 8 8
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MMP9 -0.012 0.099 -10000 0 -0.25 61 61
MMP2 -0.018 0.1 -10000 0 -0.26 65 65
p75(NTR)-mediated signaling

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.02 0.048 -10000 0 -0.15 39 39
Necdin/E2F1 0.016 0.046 -10000 0 -0.089 84 84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.039 0.048 -10000 0 -0.098 51 51
NGF (dimer)/p75(NTR)/BEX1 -0.008 0.054 -10000 0 -0.075 210 210
NT-4/5 (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.085 9 9
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 0.009 0.045 -10000 0 -0.1 63 63
IKBKG 0.023 0.009 -10000 0 -0.12 2 2
BDNF 0.022 0.011 -10000 0 -0.12 3 3
MGDIs/NGR/p75(NTR)/LINGO1 0.04 0.031 -10000 0 -0.12 13 13
FURIN 0.02 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75(NTR)/Sortilin 0.035 0.042 -10000 0 -0.12 33 33
LINGO1 0.018 0.026 -10000 0 -0.12 19 19
Sortilin/TRAF6/NRIF 0.003 0.054 -10000 0 -0.17 24 24
proBDNF (dimer) 0.022 0.011 -10000 0 -0.12 3 3
NTRK1 0.023 0.006 -10000 0 -0.12 1 1
RTN4R 0.021 0.018 -10000 0 -0.12 9 9
neuron apoptosis -0.039 0.12 -10000 0 -0.34 38 38
IRAK1 0.019 0.023 -10000 0 -0.12 14 14
SHC1 0.019 0.011 -10000 0 -0.063 9 9
ARHGDIA 0.016 0.032 -10000 0 -0.12 29 29
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
Gamma Secretase 0.034 0.067 -10000 0 -0.097 89 89
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.025 0.05 -10000 0 -0.11 59 59
MAGEH1 0.018 0.024 -10000 0 -0.12 16 16
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.021 0.051 -10000 0 -0.11 53 53
Mammalian IAPs/DIABLO -0.019 0.083 -10000 0 -0.13 157 157
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.02 0.019 -10000 0 -0.12 10 10
APP 0.022 0.008 -10000 0 -0.12 1 1
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.023 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.029 0.028 -10000 0 -0.1 12 12
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.042 0.098 60 -0.099 33 93
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.063 -10000 0 -0.16 60 60
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.027 0.023 -10000 0 -0.12 10 10
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
mol:GTP 0.022 0.034 -10000 0 -0.094 42 42
PSENEN 0.016 0.03 -10000 0 -0.12 24 24
mol:ceramide 0.016 0.034 -10000 0 -0.11 33 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.004 0.091 -10000 0 -0.3 31 31
p75(NTR)/beta APP 0.023 0.043 -10000 0 -0.13 41 41
BEX1 -0.017 0.062 -10000 0 -0.12 145 145
mol:GDP 0.006 0.01 -10000 0 -0.068 9 9
NGF (dimer) -0.028 0.064 -10000 0 -0.1 197 197
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.041 -10000 0 -0.11 21 21
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
RAC1/GTP 0.025 0.016 -10000 0 -0.073 13 13
MYD88 0.023 0.006 -10000 0 -0.12 1 1
CHUK 0.021 0.013 -10000 0 -0.12 4 4
NGF (dimer)/p75(NTR)/PKA 0.022 0.034 -10000 0 -0.094 42 42
RHOB 0.022 0.014 -10000 0 -0.12 5 5
RHOA 0.023 0.006 -10000 0 -0.12 1 1
MAGE-G1/E2F1 0.032 0.018 -10000 0 -0.088 12 12
NT3 (dimer) -0.003 0.056 -10000 0 -0.12 101 101
TP53 0.011 0.047 -10000 0 -0.18 23 23
PRDM4 0.017 0.032 -10000 0 -0.1 33 33
BDNF (dimer) -0.021 0.069 -10000 0 -0.096 203 203
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SORT1 0.02 0.018 -10000 0 -0.12 8 8
activation of caspase activity 0.034 0.046 -10000 0 -0.098 51 51
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.032 0.042 -10000 0 -0.11 40 40
RHOC 0.023 0.002 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.022 0.054 -10000 0 -0.18 20 20
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
SMPD2 0.016 0.034 -10000 0 -0.11 33 33
APH1B 0.014 0.032 -10000 0 -0.12 29 29
APH1A 0.023 0.009 -10000 0 -0.12 2 2
proNGF (dimer)/p75(NTR)/Sortilin 0.021 0.038 -10000 0 -0.1 45 45
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
APAF-1/Pro-Caspase 9 0.025 0.041 -10000 0 -0.16 23 23
NT3 (dimer)/p75(NTR) 0.011 0.048 -10000 0 -0.078 118 118
MAPK8 0.022 0.058 -10000 0 -0.2 20 20
MAPK9 0.022 0.054 -10000 0 -0.19 19 19
APAF1 0.021 0.014 -10000 0 -0.12 5 5
NTF3 -0.003 0.056 -10000 0 -0.12 101 101
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.007 0.044 -10000 0 -0.12 59 59
RAC1/GDP 0.016 0.015 -10000 0 -0.15 5 5
RhoA-B-C/GDP 0.04 0.035 -10000 0 -0.084 34 34
p75 CTF/Sortilin/TRAF6/NRIF 0.037 0.059 -10000 0 -0.12 62 62
RhoA-B-C/GTP 0.022 0.034 -10000 0 -0.094 42 42
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.045 -10000 0 -0.18 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.045 0.046 -10000 0 -0.1 40 40
PRKACB 0.019 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75 ECD 0.022 0.045 -10000 0 -0.15 33 33
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
neuron projection morphogenesis 0.003 0.055 0.1 46 -0.14 34 80
BAD 0.021 0.06 -10000 0 -0.2 19 19
RIPK2 0.013 0.034 -10000 0 -0.12 32 32
NGFR 0.021 0.017 -10000 0 -0.12 8 8
CYCS 0.015 0.042 -10000 0 -0.11 47 47
ADAM17 0.019 0.021 -10000 0 -0.12 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.05 -10000 0 -0.11 54 54
BCL2L11 0.021 0.06 -10000 0 -0.2 20 20
BDNF (dimer)/p75(NTR) 0.032 0.017 -10000 0 -0.084 11 11
PI3K 0.021 0.054 -10000 0 -0.11 63 63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.033 0.038 -10000 0 -0.1 35 35
NDNL2 0.023 0.009 -10000 0 -0.12 2 2
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
NGF (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.085 9 9
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.029 0.046 -10000 0 -0.11 47 47
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0 -10000 0 -10000 0 0
PLG 0.023 0.009 -10000 0 -0.12 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.05 -10000 0 -0.16 33 33
SQSTM1 0.021 0.014 -10000 0 -0.12 5 5
NGFRAP1 0.022 0.009 -10000 0 -0.12 2 2
CASP3 0.021 0.059 -10000 0 -0.19 19 19
E2F1 0.021 0.016 -10000 0 -0.12 7 7
CASP9 0.022 0.014 -10000 0 -0.12 5 5
IKK complex 0.021 0.08 -10000 0 -0.22 33 33
NGF (dimer)/TRKA 0.017 0.004 -10000 0 -0.077 1 1
MMP7 -0.022 0.06 -10000 0 -0.12 144 144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.042 0.042 -10000 0 -0.097 40 40
MMP3 0.017 0.029 -10000 0 -0.12 23 23
APAF-1/Caspase 9 -0.037 0.061 -10000 0 -0.16 86 86
TCGA08_rtk_signaling

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.004 0.044 -10000 0 -0.12 59 59
HRAS 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
AKT 0 0.065 0.14 5 -0.12 83 88
FOXO3 0.021 0.017 -10000 0 -0.12 8 8
AKT1 0.021 0.019 -10000 0 -0.12 10 10
FOXO1 0.023 0.009 -10000 0 -0.12 2 2
AKT3 -0.004 0.056 -10000 0 -0.12 102 102
FOXO4 0.023 0 -10000 0 -10000 0 0
MET 0 0.047 -10000 0 -0.12 70 70
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PIK3CB 0.015 0.03 -10000 0 -0.12 24 24
NRAS 0.022 0.011 -10000 0 -0.12 3 3
PIK3CG 0.011 0.037 -10000 0 -0.12 39 39
PIK3R3 0.012 0.036 -10000 0 -0.12 37 37
PIK3R2 0.017 0.03 -10000 0 -0.12 25 25
NF1 0.018 0.02 -10000 0 -0.12 10 10
RAS 0.005 0.061 0.15 33 -0.15 43 76
ERBB2 0.02 0.021 -10000 0 -0.12 12 12
proliferation/survival/translation 0.002 0.074 0.23 36 -10000 0 36
PI3K -0.014 0.075 0.13 9 -0.14 105 114
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
KRAS 0.014 0.034 -10000 0 -0.12 33 33
FOXO 0.028 0.037 0.14 9 -0.033 13 22
AKT2 0.019 0.025 -10000 0 -0.12 17 17
PTEN 0.022 0.008 -10000 0 -0.12 1 1
ErbB2/ErbB3 signaling events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.012 0.012 -10000 0 -0.057 15 15
RAS family/GTP 0.004 0.084 -10000 0 -0.18 54 54
NFATC4 0.001 0.053 0.18 6 -0.14 21 27
ERBB2IP 0.021 0.019 -10000 0 -0.12 9 9
HSP90 (dimer) 0.023 0.003 -10000 0 -10000 0 0
mammary gland morphogenesis 0 0.066 0.19 7 -0.14 42 49
JUN 0.004 0.07 -10000 0 -10000 0 0
HRAS 0.023 0.006 -10000 0 -0.12 1 1
DOCK7 -0.005 0.066 0.19 6 -0.16 42 48
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.017 0.061 0.21 7 -0.1 88 95
AKT1 0.01 0.012 -10000 0 -0.078 10 10
BAD 0.013 0.011 -10000 0 -0.057 13 13
MAPK10 0.002 0.045 0.14 6 -0.1 41 47
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.071 0.2 7 -0.15 39 46
RAF1 -0.005 0.085 -10000 0 -0.18 59 59
ErbB2/ErbB3/neuregulin 2 0.004 0.054 -10000 0 -0.11 88 88
STAT3 -0.003 0.17 -10000 0 -0.93 19 19
cell migration 0.001 0.053 0.16 5 -0.13 37 42
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.063 0.21 -10000 0 -0.52 67 67
FOS -0.072 0.2 -10000 0 -0.41 127 127
NRAS 0.021 0.011 -10000 0 -0.12 3 3
mol:Ca2+ 0 0.066 0.19 7 -0.14 42 49
MAPK3 -0.04 0.17 -10000 0 -0.47 48 48
MAPK1 -0.042 0.17 -10000 0 -0.47 51 51
JAK2 -0.005 0.065 0.19 6 -0.16 41 47
NF2 0.013 0.046 -10000 0 -0.73 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.012 0.051 0.13 8 -0.16 28 36
NRG1 0.02 0.017 -10000 0 -0.12 8 8
GRB2/SOS1 0.021 0.045 -10000 0 -0.12 50 50
MAPK8 -0.012 0.092 0.18 6 -0.19 97 103
MAPK9 0.003 0.044 0.14 5 -0.11 35 40
ERBB2 0 0.048 0.27 15 -10000 0 15
ERBB3 0.013 0.031 -10000 0 -0.12 26 26
SHC1 0.023 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
apoptosis -0.009 0.017 0.13 4 -10000 0 4
STAT3 (dimer) -0.002 0.17 -10000 0 -0.91 19 19
RNF41 0.013 0.012 -10000 0 -0.047 17 17
FRAP1 0.013 0.011 -10000 0 -0.057 14 14
RAC1-CDC42/GTP -0.006 0.05 -10000 0 -0.13 41 41
ErbB2/ErbB2/HSP90 (dimer) 0.012 0.028 -10000 0 -0.12 20 20
CHRNA1 -0.025 0.14 -10000 0 -0.34 50 50
myelination 0 0.053 0.18 6 -0.15 20 26
PPP3CB -0.001 0.058 0.18 6 -0.14 33 39
KRAS 0.014 0.034 -10000 0 -0.12 33 33
RAC1-CDC42/GDP 0.017 0.074 -10000 0 -0.13 84 84
NRG2 0.023 0.006 -10000 0 -0.12 1 1
mol:GDP 0.012 0.051 0.13 8 -0.16 28 36
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K2 -0.01 0.09 -10000 0 -0.18 78 78
SRC 0.023 0.009 -10000 0 -0.12 2 2
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.002 0.063 0.19 5 -0.16 35 40
MAP2K1 -0.043 0.16 -10000 0 -0.4 57 57
heart morphogenesis 0 0.066 0.19 7 -0.14 42 49
RAS family/GDP 0.012 0.085 -10000 0 -0.18 50 50
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.01 0.048 -10000 0 -0.77 2 2
CHRNE 0.01 0.019 -10000 0 -10000 0 0
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.012 0.078 10 -10000 0 10
nervous system development 0 0.066 0.19 7 -0.14 42 49
CDC42 0.023 0.002 -10000 0 -10000 0 0
Wnt signaling

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.033 0.1 -9999 0 -0.26 61 61
FZD6 0.017 0.023 -9999 0 -0.12 13 13
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.022 0.011 -9999 0 -0.12 3 3
FZD3 0.013 0.032 -9999 0 -0.12 29 29
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 82 82
ErbB4 signaling events

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.046 0.2 -10000 0 -0.79 33 33
epithelial cell differentiation -0.037 0.19 -10000 0 -0.65 40 40
ITCH 0.027 0.027 0.085 4 -0.072 28 32
WWP1 -0.051 0.28 -10000 0 -1.2 33 33
FYN 0.011 0.037 -10000 0 -0.12 40 40
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PRL 0.022 0.011 -10000 0 -0.12 3 3
neuron projection morphogenesis -0.015 0.16 -10000 0 -0.53 39 39
PTPRZ1 0.021 0.018 -10000 0 -0.12 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.007 0.18 -10000 0 -0.59 39 39
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.035 0.18 -10000 0 -0.66 39 39
ADAM17 0.023 0.031 0.085 1 -0.087 33 34
ErbB4/ErbB4 -0.035 0.21 -10000 0 -0.8 37 37
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.053 0.2 -10000 0 -0.8 33 33
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.18 -10000 0 -0.62 42 42
GRIN2B -0.035 0.17 -10000 0 -0.59 42 42
ErbB4/ErbB2/betacellulin -0.04 0.18 -10000 0 -0.64 40 40
STAT1 0.014 0.031 -10000 0 -0.12 26 26
HBEGF 0.018 0.026 -10000 0 -0.12 19 19
PRLR 0.01 0.042 -10000 0 -0.12 53 53
E4ICDs/ETO2 -0.044 0.2 -10000 0 -0.79 33 33
axon guidance -0.06 0.23 -10000 0 -0.81 40 40
NEDD4 0.024 0.034 0.085 6 -0.082 41 47
Prolactin receptor/Prolactin receptor/Prolactin 0.024 0.032 -10000 0 -0.15 2 2
CBFA2T3 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/HBEGF -0.031 0.18 -10000 0 -0.64 38 38
MAPK3 -0.016 0.16 -10000 0 -0.55 39 39
STAT1 (dimer) -0.056 0.21 -10000 0 -0.75 38 38
MAPK1 -0.016 0.16 -10000 0 -0.55 39 39
JAK2 0.017 0.025 -10000 0 -0.12 16 16
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.18 -10000 0 -0.64 39 39
NRG1 0.021 0.027 -10000 0 -0.075 26 26
NRG3 0.005 0.048 -10000 0 -0.12 72 72
NRG2 0.023 0.006 -10000 0 -0.12 1 1
NRG4 0.001 0.047 -10000 0 -0.12 70 70
heart development -0.06 0.23 -10000 0 -0.81 40 40
neural crest cell migration -0.03 0.18 -10000 0 -0.62 39 39
ERBB2 0.021 0.027 -10000 0 -0.067 32 32
WWOX/E4ICDs -0.044 0.2 -10000 0 -0.79 33 33
SHC1 0.023 0.001 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.068 0.2 -10000 0 -0.63 46 46
apoptosis 0.046 0.19 0.7 38 -10000 0 38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.044 0.2 -10000 0 -0.79 33 33
ErbB4/ErbB2/epiregulin -0.03 0.18 -10000 0 -0.65 38 38
ErbB4/ErbB4/betacellulin/betacellulin -0.054 0.2 -10000 0 -0.79 34 34
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.027 0.19 -10000 0 -0.64 39 39
MDM2 -0.032 0.2 -10000 0 -0.74 37 37
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.024 0.17 -10000 0 -0.59 39 39
STAT5A -0.055 0.22 -10000 0 -0.78 40 40
ErbB4/EGFR/neuregulin 1 beta -0.035 0.18 -10000 0 -0.65 38 38
DLG4 0.023 0.009 -10000 0 -0.12 2 2
GRB2/SHC 0.033 0.019 -10000 0 -0.13 7 7
E4ICDs/TAB2/NCoR1 -0.04 0.2 -10000 0 -0.72 37 37
STAT5A (dimer) -0.037 0.21 -10000 0 -0.73 40 40
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 6 6
STAT5B (dimer) -0.05 0.22 -10000 0 -0.78 40 40
LRIG1 0.01 0.037 -10000 0 -0.12 40 40
EREG 0.021 0.017 -10000 0 -0.12 8 8
BTC 0.01 0.039 -10000 0 -0.12 43 43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.06 0.23 -10000 0 -0.82 40 40
ERBB4 -0.033 0.21 -10000 0 -0.8 37 37
STAT5B 0.023 0.006 -10000 0 -0.12 1 1
YAP1 0.002 0.077 -10000 0 -0.5 11 11
GRB2 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/neuregulin 4 -0.049 0.18 -10000 0 -0.6 45 45
glial cell differentiation 0.039 0.2 0.71 37 -10000 0 37
WWOX 0.023 0.006 -10000 0 -0.12 1 1
cell proliferation -0.068 0.21 -10000 0 -0.63 53 53
Class I PI3K signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.005 0.042 -10000 0 -0.11 48 48
DAPP1 0.005 0.08 -10000 0 -0.25 27 27
Src family/SYK family/BLNK-LAT/BTK-ITK 0 0.12 -10000 0 -0.34 39 39
mol:DAG 0.015 0.066 0.16 14 -0.15 38 52
HRAS 0.023 0.008 -10000 0 -0.13 1 1
RAP1A 0.022 0.012 -10000 0 -0.12 3 3
ARF5/GDP 0.003 0.086 -10000 0 -0.2 62 62
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
ARF5 0.02 0.018 -10000 0 -0.12 9 9
mol:GTP -0.006 0.038 -10000 0 -0.11 54 54
ARF1/GTP 0.003 0.05 0.16 21 -0.12 41 62
RHOA 0.023 0.006 -10000 0 -0.12 1 1
YES1 0.02 0.018 -10000 0 -0.12 8 8
RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
ADAP1 -0.005 0.036 -10000 0 -0.1 54 54
ARAP3 -0.006 0.038 -10000 0 -0.11 54 54
INPPL1 0.021 0.017 -10000 0 -0.12 8 8
PREX1 0.021 0.017 -10000 0 -0.12 8 8
ARHGEF6 0.014 0.032 -10000 0 -0.12 28 28
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
ARF1 0.018 0.028 -10000 0 -0.12 21 21
NRAS 0.022 0.012 -10000 0 -0.12 3 3
FYN 0.011 0.037 -10000 0 -0.12 40 40
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0.012 0.038 0.092 14 -0.077 38 52
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.032 -10000 0 -0.12 28 28
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
mol:IP3 0.013 0.05 0.12 11 -0.11 38 49
LYN 0.021 0.013 -10000 0 -0.12 4 4
ARF1/GDP 0.002 0.088 -10000 0 -0.21 59 59
RhoA/GDP 0.014 0.067 0.18 17 -0.15 44 61
PDK1/Src/Hsp90 0.041 0.032 -10000 0 -0.12 19 19
BLNK 0.014 0.033 -10000 0 -0.12 31 31
actin cytoskeleton reorganization 0.005 0.087 0.19 17 -0.23 42 59
SRC 0.023 0.009 -10000 0 -0.12 2 2
PLEKHA2 0.013 0.011 -10000 0 -0.057 12 12
RAC1 0.023 0.002 -10000 0 -10000 0 0
PTEN 0.022 0.009 -10000 0 -0.12 1 1
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.006 0.042 -10000 0 -0.11 47 47
RhoA/GTP 0.013 0.052 0.17 22 -0.11 40 62
Src family/SYK family/BLNK-LAT 0.006 0.097 -10000 0 -0.29 31 31
BLK 0.022 0.015 -10000 0 -0.12 6 6
PDPK1 0.023 0.007 -10000 0 -0.12 1 1
CYTH1 -0.005 0.036 -10000 0 -0.1 54 54
HCK 0.019 0.024 -10000 0 -0.12 15 15
CYTH3 -0.005 0.036 -10000 0 -0.1 54 54
CYTH2 -0.005 0.036 -10000 0 -0.1 54 54
KRAS 0.014 0.035 -10000 0 -0.12 33 33
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.054 0.13 22 -0.21 20 42
SGK1 0.008 0.05 -10000 0 -0.21 20 20
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.086 -10000 0 -0.21 61 61
SOS1 0.017 0.027 -10000 0 -0.12 20 20
SYK 0.016 0.027 -10000 0 -0.12 20 20
ARF6/GDP 0.008 0.064 0.17 19 -0.15 45 64
mol:PI-3-4-5-P3 -0.004 0.039 0.085 1 -0.11 54 55
ARAP3/RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
VAV1 0.02 0.02 -10000 0 -0.12 10 10
mol:PI-3-4-P2 0.01 0.011 -10000 0 -0.077 8 8
RAS family/GTP/PI3K Class I 0.026 0.058 0.19 22 -0.11 54 76
PLEKHA1 0.013 0.012 -10000 0 -0.057 15 15
Rac1/GDP 0.004 0.087 -10000 0 -0.2 60 60
LAT 0.022 0.011 -10000 0 -0.12 3 3
Rac1/GTP -0.001 0.1 -10000 0 -0.24 71 71
ITK -0.002 0.04 -10000 0 -0.1 58 58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.083 0.19 14 -0.2 39 53
LCK 0.022 0.015 -10000 0 -0.12 6 6
BTK -0.003 0.043 -10000 0 -0.11 56 56
S1P4 pathway

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.01 0.042 -9999 0 -0.12 51 51
CDC42/GTP 0.008 0.067 -9999 0 -0.13 86 86
PLCG1 -0.001 0.065 -9999 0 -0.14 86 86
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.022 0.011 -9999 0 -0.12 3 3
GNAI3 0.021 0.008 -9999 0 -0.12 1 1
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
cell migration 0.007 0.065 -9999 0 -0.13 86 86
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0 0.066 -9999 0 -0.14 86 86
MAPK1 0 0.066 -9999 0 -0.14 86 86
S1P/S1P5/Gi -0.003 0.069 -9999 0 -0.15 86 86
GNAI1 0.012 0.035 -9999 0 -0.12 35 35
CDC42/GDP 0.016 0.012 -9999 0 -0.15 3 3
S1P/S1P5/G12 0.016 0.006 -9999 0 -0.12 1 1
RHOA 0.021 0.02 -9999 0 -0.1 14 14
S1P/S1P4/Gi -0.003 0.069 -9999 0 -0.15 86 86
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.011 -9999 0 -0.12 3 3
S1P/S1P4/G12/G13 0.026 0.021 -9999 0 -0.096 16 16
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
CDC42 0.023 0.002 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.021 0.2 -10000 0 -0.97 24 24
VDR 0.019 0.022 -10000 0 -0.12 13 13
FAM120B 0.022 0.011 -10000 0 -0.12 3 3
RXRs/LXRs/DNA/9cRA 0.025 0.095 -10000 0 -0.24 54 54
RXRs/LXRs/DNA/Oxysterols 0.019 0.13 -10000 0 -0.35 59 59
MED1 0.021 0.014 -10000 0 -0.12 5 5
mol:9cRA 0.002 0.016 -10000 0 -0.047 49 49
RARs/THRs/DNA/Src-1 -0.003 0.087 -10000 0 -0.29 24 24
RXRs/NUR77 0.033 0.067 0.18 8 -0.13 27 35
RXRs/PPAR 0.032 0.039 -10000 0 -0.16 5 5
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.008 0.035 -10000 0 -0.12 36 36
RARs/VDR/DNA/Vit D3 0.029 0.056 -10000 0 -0.1 66 66
RARA 0.023 0 -10000 0 -10000 0 0
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARs/RARs/DNA/9cRA 0.025 0.045 -10000 0 -0.094 57 57
RARG 0.021 0.015 -10000 0 -0.12 6 6
RPS6KB1 -0.004 0.091 -10000 0 -0.32 39 39
RARs/THRs/DNA/SMRT -0.002 0.083 -10000 0 -0.27 24 24
THRA 0.022 0.015 -10000 0 -0.12 6 6
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.035 -10000 0 -0.12 36 36
RXRs/PPAR/9cRA/PGJ2/DNA 0.041 0.074 0.27 14 -0.16 16 30
NR1H4 0.021 0.017 -10000 0 -0.12 8 8
RXRs/LXRs/DNA 0.06 0.085 -10000 0 -0.16 54 54
NR1H2 0.021 0.027 -10000 0 -0.13 10 10
NR1H3 0.02 0.029 -10000 0 -0.12 13 13
RXRs/VDR/DNA/Vit D3 0.039 0.059 0.17 6 -0.13 23 29
NR4A1 0.003 0.049 -10000 0 -0.12 74 74
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.022 0.049 -10000 0 -0.21 9 9
RXRG 0.006 0.05 -10000 0 -0.12 68 68
RXR alpha/CCPG 0.031 0.026 -10000 0 -0.12 9 9
RXRA 0.021 0.025 -10000 0 -0.11 10 10
RXRB 0.024 0.02 -10000 0 -0.037 33 33
THRB 0.011 0.036 -10000 0 -0.12 36 36
PPARG 0.018 0.028 -10000 0 -0.12 22 22
PPARD 0.023 0.009 -10000 0 -0.12 2 2
TNF 0.022 0.13 -10000 0 -0.51 8 8
mol:Oxysterols 0.001 0.015 -10000 0 -0.041 53 53
cholesterol transport 0.02 0.13 -10000 0 -0.34 59 59
PPARA 0.022 0.012 -10000 0 -0.12 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.034 -10000 0 -0.12 33 33
RXRs/NUR77/BCL2 0.013 0.045 -10000 0 -0.15 23 23
SREBF1 0.022 0.13 -10000 0 -0.51 8 8
RXRs/RXRs/DNA/9cRA 0.041 0.073 0.26 14 -0.16 16 30
ABCA1 -0.029 0.27 -10000 0 -0.82 57 57
RARs/THRs 0.027 0.072 -10000 0 -0.1 104 104
RXRs/FXR 0.049 0.057 0.18 8 -0.12 15 23
BCL2 0.016 0.031 -10000 0 -0.12 27 27
Atypical NF-kappaB pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.03 0.026 -9999 0 -0.094 21 21
FBXW11 0.023 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.022 0.04 -9999 0 -0.11 41 41
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.073 -9999 0 -0.19 35 35
NFKBIA 0.001 0.066 -9999 0 -0.15 78 78
MAPK14 0.023 0.007 -9999 0 -0.12 1 1
NF kappa B1 p105/p50 0.022 0.042 -9999 0 -0.12 40 40
ARRB2 0.014 0.035 -9999 0 -0.2 14 14
REL 0.022 0.014 -9999 0 -0.12 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.042 -9999 0 -0.12 40 40
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.04 -9999 0 -0.11 40 40
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
NF kappa B1 p50 dimer 0.012 0.044 -9999 0 -0.13 48 48
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
NFKB1 0.02 0.014 -9999 0 -0.071 10 10
RELA 0.023 0.009 -9999 0 -0.12 2 2
positive regulation of anti-apoptosis 0.013 0.051 -9999 0 -0.13 53 53
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.02 0.075 -9999 0 -0.2 35 35
SRC 0.023 0.009 -9999 0 -0.12 2 2
PI3K 0.007 0.065 -9999 0 -0.13 96 96
NF kappa B1 p50/RelA 0.013 0.052 -9999 0 -0.13 53 53
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -9999 0 -10000 0 0
SYK 0.016 0.027 -9999 0 -0.12 20 20
I kappa B alpha/PIK3R1 0.008 0.069 -9999 0 -0.14 78 78
cell death 0.02 0.072 -9999 0 -0.19 35 35
NF kappa B1 p105/c-Rel 0.022 0.04 -9999 0 -0.11 41 41
LCK 0.022 0.015 -9999 0 -0.12 6 6
BCL3 0.02 0.023 -9999 0 -0.12 14 14
Signaling mediated by p38-gamma and p38-delta

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.019 0.016 -9999 0 -0.058 18 18
SNTA1 0.023 0.009 -9999 0 -0.12 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.021 -9999 0 -0.074 21 21
MAPK12 0.01 0.027 -9999 0 -0.15 7 7
CCND1 -0.05 0.14 -9999 0 -0.36 89 89
p38 gamma/SNTA1 0.005 0.057 -9999 0 -0.16 40 40
MAP2K3 0.023 0.006 -9999 0 -0.12 1 1
PKN1 0.016 0.031 -9999 0 -0.12 26 26
G2/M transition checkpoint 0.003 0.044 -9999 0 -0.15 36 36
MAP2K6 0.008 0.028 -9999 0 -0.05 79 79
MAPT 0.007 0.039 -9999 0 -0.13 28 28
MAPK13 0.019 0.019 -9999 0 -0.079 17 17
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.001 0.058 -9999 0 -0.21 37 37
S1P3 pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
mol:S1P -0.002 0.007 -9999 0 -0.029 24 24
S1P1/S1P/Gi 0.008 0.065 -9999 0 -0.22 31 31
GNAO1 0.008 0.043 -9999 0 -0.12 51 51
S1P/S1P3/G12/G13 0.024 0.024 -9999 0 -0.097 16 16
AKT1 0.006 0.059 -9999 0 -0.36 7 7
AKT3 -0.054 0.23 -9999 0 -1 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
GNAI2 0.02 0.014 -9999 0 -0.044 15 15
GNAI3 0.02 0.012 -9999 0 -0.12 1 1
GNAI1 0.01 0.036 -9999 0 -0.12 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.002 0.008 -9999 0 -0.031 24 24
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.021 0.016 -9999 0 -0.12 7 7
mol:Ca2+ -0.016 0.088 -9999 0 -0.22 55 55
MAPK3 -0.012 0.084 -9999 0 -0.22 52 52
MAPK1 -0.013 0.085 -9999 0 -0.22 51 51
JAK2 -0.023 0.1 -9999 0 -0.25 69 69
CXCR4 -0.021 0.092 -9999 0 -0.24 62 62
FLT1 0.019 0.019 -9999 0 -0.06 18 18
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
SRC -0.012 0.083 -9999 0 -0.22 49 49
S1P/S1P3/Gi -0.016 0.089 -9999 0 -0.22 55 55
RAC1 0.023 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.085 -9999 0 -0.22 46 46
VEGFA 0.017 0.024 -9999 0 -0.12 11 11
S1P/S1P2/Gi -0.011 0.076 -9999 0 -0.15 106 106
VEGFR1 homodimer/VEGFA homodimer 0.016 0.055 -9999 0 -0.15 44 44
RHOA 0.023 0.006 -9999 0 -0.12 1 1
S1P/S1P3/Gq 0.014 0.045 -9999 0 -0.15 34 34
GNAQ 0.021 0.016 -9999 0 -0.12 6 6
GNAZ 0.02 0.014 -9999 0 -0.031 24 24
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
GNA11 0.022 0.014 -9999 0 -0.12 5 5
Rac1/GTP -0.005 0.085 -9999 0 -0.22 46 46
Regulation of Androgen receptor activity

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.015 -9999 0 -0.07 13 13
SMARCC1 0 0.17 -9999 0 -1.1 13 13
REL 0.021 0.014 -9999 0 -0.12 5 5
HDAC7 -0.018 0.096 -9999 0 -0.19 88 88
JUN 0.014 0.033 -9999 0 -0.12 30 30
EP300 0.022 0.01 -9999 0 -0.12 2 2
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.025 -9999 0 -0.071 34 34
FOXO1 0.023 0.009 -9999 0 -0.12 2 2
T-DHT/AR -0.001 0.11 -9999 0 -0.21 79 79
MAP2K6 0.012 0.035 -9999 0 -0.12 33 33
BRM/BAF57 0.007 0.062 -9999 0 -0.12 110 110
MAP2K4 0.022 0.012 -9999 0 -0.12 3 3
SMARCA2 0.012 0.036 -9999 0 -0.12 36 36
PDE9A -0.095 0.31 -9999 0 -0.86 79 79
NCOA2 0.022 0.013 -9999 0 -0.12 4 4
CEBPA 0.022 0.014 -9999 0 -0.12 5 5
EHMT2 0.023 0.009 -9999 0 -0.12 2 2
cell proliferation -0.011 0.11 -9999 0 -0.26 53 53
NR0B1 0.013 0.038 -9999 0 -0.12 41 41
EGR1 -0.005 0.054 -9999 0 -0.12 99 99
RXRs/9cRA 0.033 0.033 -9999 0 -0.096 4 4
AR/RACK1/Src 0.011 0.073 -9999 0 -0.18 42 42
AR/GR -0.013 0.085 -9999 0 -0.16 109 109
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
PKN1 0.016 0.031 -9999 0 -0.12 26 26
RCHY1 0.018 0.022 -9999 0 -0.12 13 13
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
MAPK8 0.018 0.018 -9999 0 -0.074 9 9
T-DHT/AR/TIF2/CARM1 0.01 0.084 -9999 0 -0.16 65 65
SRC 0.015 0.027 -9999 0 -0.071 14 14
NR3C1 0.021 0.015 -9999 0 -0.12 5 5
KLK3 0.004 0.047 -9999 0 -10000 0 0
APPBP2 0.019 0.017 -9999 0 -0.12 6 6
TRIM24 0.023 0.014 -9999 0 -0.12 5 5
T-DHT/AR/TIP60 -0.014 0.071 -9999 0 -0.15 80 80
TMPRSS2 0.002 0.092 -9999 0 -0.68 4 4
RXRG 0.006 0.047 -9999 0 -0.12 68 68
mol:9cRA 0 0 -9999 0 -0.003 1 1
RXRA 0.021 0.017 -9999 0 -0.12 8 8
RXRB 0.023 0 -9999 0 -10000 0 0
CARM1 0.019 0.026 -9999 0 -0.12 19 19
NR2C2 0.023 0.006 -9999 0 -0.12 1 1
KLK2 0.019 0.072 -9999 0 -0.25 13 13
AR -0.01 0.074 -9999 0 -0.16 96 96
SENP1 0.022 0.011 -9999 0 -0.12 3 3
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
MDM2 0.018 0.02 -9999 0 -0.12 11 11
SRY 0.021 0.008 -9999 0 -0.11 2 2
GATA2 0.02 0.022 -9999 0 -0.12 13 13
MYST2 0.022 0.011 -9999 0 -0.12 3 3
HOXB13 0.02 0.026 -9999 0 -0.12 19 19
T-DHT/AR/RACK1/Src 0.006 0.074 -9999 0 -0.17 48 48
positive regulation of transcription 0.02 0.022 -9999 0 -0.12 13 13
DNAJA1 0.02 0.012 -9999 0 -0.13 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.09 -9999 0 -0.28 48 48
NCOA1 0.025 0.032 -9999 0 -0.16 15 15
SPDEF 0.012 0.042 -9999 0 -0.12 50 50
T-DHT/AR/TIF2 -0.006 0.088 -9999 0 -0.23 55 55
T-DHT/AR/Hsp90 -0.003 0.078 -9999 0 -0.18 60 60
GSK3B 0.022 0.011 -9999 0 -0.12 3 3
NR2C1 0.021 0.01 -9999 0 -0.12 2 2
mol:T-DHT 0.013 0.028 -9999 0 -0.07 16 16
SIRT1 0.023 0.003 -9999 0 -10000 0 0
ZMIZ2 0.02 0.014 -9999 0 -0.12 5 5
POU2F1 0.017 0.041 -9999 0 -0.077 78 78
T-DHT/AR/DAX-1 -0.007 0.077 -9999 0 -0.17 65 65
CREBBP 0.021 0.015 -9999 0 -0.12 6 6
SMARCE1 0.023 0.011 -9999 0 -0.12 3 3
Nephrin/Neph1 signaling in the kidney podocyte

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.023 0.042 0.11 47 -10000 0 47
KIRREL 0.018 0.028 -10000 0 -0.12 20 20
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.023 0.043 -10000 0 -0.11 47 47
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
WASL 0.023 0.009 -10000 0 -0.12 2 2
Nephrin/NEPH1/podocin/CD2AP 0.036 0.056 -10000 0 -0.11 64 64
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.053 -10000 0 -0.14 34 34
FYN 0.014 0.034 -10000 0 -0.11 26 26
mol:Ca2+ 0.041 0.047 -10000 0 -0.11 38 38
mol:DAG 0.042 0.048 -10000 0 -0.11 38 38
NPHS2 0.022 0.014 -10000 0 -0.082 7 7
mol:IP3 0.042 0.048 -10000 0 -0.11 38 38
regulation of endocytosis 0.031 0.045 -10000 0 -0.1 29 29
Nephrin/NEPH1/podocin/Cholesterol 0.034 0.035 -10000 0 -0.1 27 27
establishment of cell polarity 0.023 0.042 -10000 0 -0.11 47 47
Nephrin/NEPH1/podocin/NCK1-2 0.049 0.054 -10000 0 -0.095 56 56
Nephrin/NEPH1/beta Arrestin2 0.033 0.046 -10000 0 -0.1 29 29
NPHS1 0.021 0.02 -10000 0 -0.13 9 9
Nephrin/NEPH1/podocin 0.025 0.045 -10000 0 -0.11 28 28
TJP1 0.021 0.01 -10000 0 -0.12 2 2
NCK1 0.02 0.019 -10000 0 -0.12 9 9
NCK2 0.023 0.006 -10000 0 -0.12 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.043 0.048 -10000 0 -0.11 38 38
CD2AP 0.02 0.017 -10000 0 -0.12 7 7
Nephrin/NEPH1/podocin/GRB2 0.047 0.042 -10000 0 -0.11 28 28
GRB2 0.023 0.006 -10000 0 -0.12 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.019 0.029 -10000 0 -0.087 27 27
cytoskeleton organization 0.022 0.047 -10000 0 -0.13 30 30
Nephrin/NEPH1 0.022 0.029 -10000 0 -0.072 47 47
Nephrin/NEPH1/ZO-1 0.027 0.055 -10000 0 -0.13 55 55
Canonical NF-kappaB pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0.02 -9999 0 -0.055 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.11 -9999 0 -0.26 54 54
ERC1 0.016 0.029 -9999 0 -0.12 24 24
RIP2/NOD2 0.013 0.053 -9999 0 -0.11 81 81
NFKBIA 0.001 0.087 -9999 0 -0.22 60 60
BIRC2 0.021 0.013 -9999 0 -0.12 4 4
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
RIPK2 0.013 0.034 -9999 0 -0.12 32 32
IKBKG 0.012 0.091 -9999 0 -0.32 29 29
IKK complex/A20 0.037 0.096 -9999 0 -0.27 35 35
NEMO/A20/RIP2 0.013 0.034 -9999 0 -0.12 32 32
XPO1 0.022 0.01 -9999 0 -0.12 2 2
NEMO/ATM 0.017 0.1 -9999 0 -0.3 39 39
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.023 0.002 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.025 0.03 -9999 0 -0.11 26 26
IKK complex/ELKS 0.021 0.094 -9999 0 -0.28 35 35
BCL10/MALT1/TRAF6 0.034 0.043 -9999 0 -0.12 31 31
NOD2 0.023 0.006 -9999 0 -0.12 1 1
NFKB1 0.017 0.023 -9999 0 -0.062 33 33
RELA 0.019 0.022 -9999 0 -0.061 29 29
MALT1 0.017 0.026 -9999 0 -0.12 19 19
cIAP1/UbcH5C 0.021 0.047 -9999 0 -0.14 45 45
ATM 0.018 0.022 -9999 0 -0.12 13 13
TNF/TNFR1A 0.025 0.036 -9999 0 -0.14 19 19
TRAF6 0.022 0.009 -9999 0 -0.12 2 2
PRKCA 0.011 0.037 -9999 0 -0.12 40 40
CHUK 0.021 0.013 -9999 0 -0.12 4 4
UBE2D3 0.023 0.001 -9999 0 -10000 0 0
TNF 0.02 0.02 -9999 0 -0.12 11 11
NF kappa B1 p50/RelA 0.029 0.075 -9999 0 -0.15 75 75
BCL10 0.023 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.086 -9999 0 -0.22 60 60
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.02 -9999 0 -0.056 27 27
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
IKK complex 0.029 0.098 -9999 0 -0.29 35 35
CYLD 0.023 0.007 -9999 0 -0.12 1 1
IKK complex/PKC alpha 0.024 0.1 -9999 0 -0.28 38 38
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.021 0.014 -10000 0 -0.12 5 5
VLDLR 0.01 0.038 -10000 0 -0.12 41 41
LRPAP1 0.018 0.024 -10000 0 -0.12 15 15
NUDC 0.022 0.011 -10000 0 -0.12 3 3
RELN/LRP8 0.015 0.058 -10000 0 -0.12 53 53
CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
KATNA1 0.02 0.02 -10000 0 -0.12 10 10
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.006 0.047 -10000 0 -0.11 53 53
IQGAP1/CaM 0.016 0.054 -10000 0 -0.15 51 51
DAB1 0.022 0.011 -10000 0 -0.12 3 3
IQGAP1 0.02 0.017 -10000 0 -0.12 7 7
PLA2G7 0.004 0.045 -10000 0 -0.12 61 61
CALM1 0.022 0.014 -10000 0 -0.12 5 5
DYNLT1 0.018 0.023 -10000 0 -0.12 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.015 0.054 -10000 0 -0.12 72 72
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.009 -10000 0 -0.12 2 2
CDK5R1 0.023 0.006 -10000 0 -0.12 1 1
LIS1/Poliovirus Protein 3A 0.012 0.023 -10000 0 -0.086 26 26
CDK5R2 0.022 0.011 -10000 0 -0.12 3 3
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.06 -10000 0 -0.12 69 69
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
NDEL1/14-3-3 E 0.023 0.055 -10000 0 -0.15 24 24
MAP1B -0.015 0.059 0.2 3 -0.19 47 50
RAC1 0.014 0.048 -10000 0 -0.36 7 7
p35/CDK5 0.008 0.054 -10000 0 -0.15 22 22
RELN 0.001 0.053 -10000 0 -0.12 88 88
PAFAH/LIS1 0.015 0.038 -10000 0 -0.13 14 14
LIS1/CLIP170 0.029 0.028 -10000 0 -0.13 11 11
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.016 0.063 -10000 0 -0.15 39 39
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.014 0.098 -10000 0 -0.21 93 93
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.011 0.052 -10000 0 -0.15 22 22
LIS1/IQGAP1 0.025 0.034 -10000 0 -0.16 13 13
RHOA 0.014 0.048 -10000 0 -0.3 9 9
PAFAH1B1 0.02 0.015 -10000 0 -0.071 15 15
PAFAH1B3 0.014 0.032 -10000 0 -0.12 29 29
PAFAH1B2 0.022 0.013 -10000 0 -0.12 4 4
MAP1B/LIS1/Dynein heavy chain 0.009 0.054 0.13 3 -0.13 54 57
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.065 -10000 0 -0.17 25 25
LRP8 0.02 0.021 -10000 0 -0.12 12 12
NDEL1/Katanin 60 0.021 0.056 -10000 0 -0.14 30 30
P39/CDK5 0.008 0.053 -10000 0 -0.14 22 22
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.029 -10000 0 -0.13 11 11
CDK5 0.004 0.043 -10000 0 -0.099 56 56
PPP2R5D 0.022 0.014 -10000 0 -0.12 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.023 -10000 0 -0.11 11 11
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
RELN/VLDLR/DAB1/LIS1 0.021 0.059 -10000 0 -0.092 81 81
RELN/VLDLR 0.007 0.071 -10000 0 -0.11 119 119
CDC42 0.015 0.04 -10000 0 -0.27 7 7
PDGFR-beta signaling pathway

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.025 0.07 -10000 0 -0.21 19 19
PDGFB-D/PDGFRB/SLAP 0.02 0.039 -10000 0 -0.093 36 36
PDGFB-D/PDGFRB/APS/CBL 0.022 0.028 -10000 0 -0.06 57 57
AKT1 0.008 0.053 -10000 0 -0.12 45 45
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.068 -10000 0 -0.23 19 19
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
FGR 0.014 0.04 -10000 0 -0.19 4 4
mol:Ca2+ 0.011 0.065 -10000 0 -0.26 15 15
MYC -0.059 0.26 -10000 0 -0.7 76 76
SHC1 0.023 0.001 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.038 -10000 0 -0.086 38 38
LRP1/PDGFRB/PDGFB 0.024 0.053 -10000 0 -0.11 57 57
GRB10 0.022 0.014 -10000 0 -0.12 5 5
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
GO:0007205 0.011 0.066 -10000 0 -0.27 15 15
PTEN 0.022 0.008 -10000 0 -0.12 1 1
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GRB7 0.018 0.026 -10000 0 -0.12 18 18
PDGFB-D/PDGFRB/SHP2 0.017 0.045 -10000 0 -0.091 77 77
PDGFB-D/PDGFRB/GRB10 0.021 0.039 -10000 0 -0.082 66 66
cell cycle arrest 0.02 0.039 -10000 0 -0.093 36 36
HRAS 0.023 0.006 -10000 0 -0.12 1 1
HIF1A 0.007 0.054 -10000 0 -0.13 52 52
GAB1 0.006 0.08 -10000 0 -0.22 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.078 -10000 0 -0.2 44 44
PDGFB-D/PDGFRB 0.032 0.039 -10000 0 -0.096 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.047 -10000 0 -0.097 77 77
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.018 0.086 -10000 0 -0.19 52 52
positive regulation of MAPKKK cascade 0.017 0.045 -10000 0 -0.091 77 77
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 0.011 0.066 -10000 0 -0.27 15 15
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.009 -10000 0 -0.12 2 2
PDGFB-D/PDGFRB/GRB7 0.017 0.046 -10000 0 -0.1 48 48
SHB 0.023 0.009 -10000 0 -0.12 2 2
BLK 0.014 0.039 -10000 0 -0.18 7 7
PTPN2 0.022 0.008 -10000 0 -0.13 1 1
PDGFB-D/PDGFRB/SNX15 0.024 0.033 -10000 0 -0.074 55 55
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
VAV2 -0.004 0.11 -10000 0 -0.24 82 82
CBL 0.023 0.006 -10000 0 -0.12 1 1
PDGFB-D/PDGFRB/DEP1 0.017 0.046 -10000 0 -0.09 81 81
LCK 0.014 0.039 -10000 0 -0.18 6 6
PDGFRB 0.01 0.043 -10000 0 -0.12 52 52
ACP1 0.021 0.014 -10000 0 -0.12 5 5
HCK -0.001 0.091 -10000 0 -0.4 21 21
ABL1 0.007 0.068 -10000 0 -0.19 31 31
PDGFB-D/PDGFRB/CBL 0.007 0.082 -10000 0 -0.24 27 27
PTPN1 0.022 0.007 -10000 0 -0.13 1 1
SNX15 0.023 0 -10000 0 -10000 0 0
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT1 0.014 0.031 -10000 0 -0.12 26 26
cell proliferation -0.049 0.23 -10000 0 -0.62 76 76
SLA 0.02 0.019 -10000 0 -0.12 10 10
actin cytoskeleton reorganization 0.031 0.041 -10000 0 -0.12 13 13
SRC 0.015 0.038 -10000 0 -0.2 2 2
PI3K -0.021 0.04 -10000 0 -0.13 44 44
PDGFB-D/PDGFRB/GRB7/SHC 0.03 0.042 -10000 0 -0.13 17 17
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.019 0.07 -10000 0 -0.23 19 19
LYN -0.021 0.13 -10000 0 -0.44 45 45
LRP1 0.014 0.032 -10000 0 -0.12 29 29
SOS1 0.017 0.027 -10000 0 -0.12 20 20
STAT5B 0.023 0.006 -10000 0 -0.12 1 1
STAT5A 0.022 0.013 -10000 0 -0.12 4 4
NCK1-2/p130 Cas 0.046 0.052 -10000 0 -0.11 22 22
SPHK1 0.022 0.015 -10000 0 -0.12 6 6
EDG1 0.022 0.016 -10000 0 -0.12 7 7
mol:DAG 0.011 0.066 -10000 0 -0.27 15 15
PLCG1 0.011 0.068 -10000 0 -0.27 15 15
NHERF/PDGFRB 0.024 0.049 -10000 0 -0.12 28 28
YES1 -0.011 0.12 -10000 0 -0.44 33 33
cell migration 0.024 0.049 -10000 0 -0.12 28 28
SHC/Grb2/SOS1 0.044 0.051 -10000 0 -0.11 20 20
SLC9A3R2 0.017 0.028 -10000 0 -0.12 22 22
SLC9A3R1 0.016 0.031 -10000 0 -0.12 26 26
NHERF1-2/PDGFRB/PTEN 0.031 0.056 -10000 0 -0.1 50 50
FYN -0.021 0.12 -10000 0 -0.38 46 46
DOK1 0.021 0.029 -10000 0 -0.11 10 10
HRAS/GTP 0.017 0.008 -10000 0 -0.11 2 2
PDGFB 0.022 0.011 -10000 0 -0.12 3 3
RAC1 -0.022 0.16 -10000 0 -0.4 82 82
PRKCD 0.019 0.031 -10000 0 -0.11 15 15
FER 0.02 0.03 -10000 0 -0.1 13 13
MAPKKK cascade -0.007 0.028 0.058 15 -0.11 17 32
RASA1 0.02 0.03 -10000 0 -0.12 10 10
NCK1 0.02 0.019 -10000 0 -0.12 9 9
NCK2 0.023 0.006 -10000 0 -0.12 1 1
p62DOK/Csk 0.032 0.033 -10000 0 -0.091 18 18
PDGFB-D/PDGFRB/SHB 0.023 0.033 -10000 0 -0.074 57 57
chemotaxis 0.007 0.067 -10000 0 -0.18 31 31
STAT1-3-5/STAT1-3-5 0.021 0.058 -10000 0 -0.13 28 28
Bovine Papilomavirus E5/PDGFRB 0.007 0.03 -10000 0 -0.081 55 55
PTPRJ 0.02 0.019 -10000 0 -0.12 9 9
E-cadherin signaling events

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.025 0.057 -9999 0 -0.12 63 63
E-cadherin/beta catenin 0.018 0.053 -9999 0 -0.15 47 47
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
JUP 0.019 0.021 -9999 0 -0.12 12 12
CDH1 0.021 0.016 -9999 0 -0.12 6 6
Regulation of Telomerase

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.047 0.18 -10000 0 -0.47 45 45
RAD9A 0.023 0 -10000 0 -10000 0 0
AP1 -0.031 0.087 -10000 0 -0.15 159 159
IFNAR2 0.018 0.02 -10000 0 -0.13 8 8
AKT1 0.012 0.041 -10000 0 -0.17 7 7
ER alpha/Oestrogen 0.002 0.046 -10000 0 -0.13 58 58
NFX1/SIN3/HDAC complex 0.009 0.089 -10000 0 -0.26 36 36
EGF 0.02 0.022 -10000 0 -0.13 12 12
SMG5 0.022 0.011 -10000 0 -0.12 3 3
SMG6 0.022 0.011 -10000 0 -0.12 3 3
SP3/HDAC2 0.026 0.031 -10000 0 -0.13 13 13
TERT/c-Abl -0.042 0.17 -10000 0 -0.44 46 46
SAP18 0.023 0.003 -10000 0 -10000 0 0
MRN complex 0.023 0.065 -10000 0 -0.14 64 64
WT1 0.019 0.016 -10000 0 -0.12 5 5
WRN 0.019 0.02 -10000 0 -0.12 10 10
SP1 0.02 0.015 -10000 0 -0.14 1 1
SP3 0.023 0.003 -10000 0 -10000 0 0
TERF2IP 0.023 0.009 -10000 0 -0.12 2 2
Telomerase/Nucleolin -0.033 0.17 -10000 0 -0.4 58 58
Mad/Max 0.032 0.015 -10000 0 -0.084 2 2
TERT -0.048 0.18 -10000 0 -0.48 42 42
CCND1 -0.13 0.37 -10000 0 -0.98 83 83
MAX 0.023 0.004 -10000 0 -10000 0 0
RBBP7 0.021 0.012 -10000 0 -0.12 3 3
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
TERF2 0.025 0.017 0.082 38 -0.12 1 39
PTGES3 0.014 0.036 -10000 0 -0.12 36 36
SIN3A 0.021 0.014 -10000 0 -0.12 5 5
Telomerase/911 0.017 0.096 -10000 0 -0.35 26 26
CDKN1B -0.015 0.095 -10000 0 -0.32 34 34
RAD1 0.02 0.021 -10000 0 -0.12 12 12
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.023 0.001 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.032 -10000 0 -0.12 14 14
UBE3A 0.023 0.004 -10000 0 -10000 0 0
JUN 0.014 0.033 -10000 0 -0.12 30 30
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.021 -10000 0 -0.15 8 8
FOS -0.006 0.053 -10000 0 -0.12 95 95
IFN-gamma/IRF1 -0.007 0.086 -10000 0 -0.16 112 112
PARP2 0.018 0.026 -10000 0 -0.12 18 18
BLM 0.015 0.032 -10000 0 -0.12 28 28
Telomerase 0.013 0.1 -10000 0 -0.4 24 24
IRF1 0.004 0.058 -10000 0 -0.13 69 69
ESR1 0.017 0.024 -10000 0 -0.12 15 15
KU/TER 0.018 0.058 -10000 0 -0.17 44 44
ATM/TRF2 0.02 0.049 -10000 0 -0.13 51 51
ubiquitin-dependent protein catabolic process 0.013 0.088 -10000 0 -0.26 33 33
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.013 0.09 -10000 0 -0.26 33 33
HDAC1 0.019 0.02 -10000 0 -0.12 10 10
HDAC2 0.017 0.024 -10000 0 -0.12 12 12
ATM -0.012 0.067 0.14 1 -0.26 38 39
SMAD3 0.019 0.019 -10000 0 -0.072 21 21
ABL1 0.022 0.007 -10000 0 -0.12 1 1
MXD1 0.021 0.018 -10000 0 -0.12 8 8
MRE11A 0.02 0.017 -10000 0 -0.12 7 7
HUS1 0.023 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.014 -10000 0 -0.12 5 5
TERT/NF kappa B1/14-3-3 -0.024 0.17 -10000 0 -0.43 36 36
NR2F2 0.023 0.014 -10000 0 -0.12 4 4
MAPK3 0.021 0.016 -10000 0 -0.091 8 8
MAPK1 0.02 0.017 -10000 0 -0.087 10 10
TGFB1/TGF beta receptor Type II 0.019 0.023 -10000 0 -0.12 14 14
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
HNRNPC 0.022 0.012 -10000 0 -0.12 4 4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.012 0.067 0.14 1 -0.26 38 39
NBN 0.02 0.015 -10000 0 -0.12 5 5
EGFR 0.015 0.03 -10000 0 -0.12 25 25
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.015 0.051 -10000 0 -0.12 64 64
MYC 0.015 0.028 -10000 0 -0.12 20 20
IL2 0.02 0.017 -10000 0 -0.12 3 3
KU 0.018 0.058 -10000 0 -0.17 44 44
RAD50 0.021 0.014 -10000 0 -0.12 5 5
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
TGFB1 0.019 0.023 -10000 0 -0.12 14 14
TRF2/BLM 0.024 0.043 -10000 0 -0.095 57 57
FRAP1 0.022 0.013 -10000 0 -0.12 4 4
KU/TERT -0.035 0.18 -10000 0 -0.44 50 50
SP1/HDAC2 0.025 0.038 -10000 0 -0.14 19 19
PINX1 0.021 0.017 -10000 0 -0.12 8 8
Telomerase/EST1A -0.029 0.17 -10000 0 -0.39 57 57
Smad3/Myc 0.016 0.046 -10000 0 -0.15 29 29
911 complex 0.043 0.024 -10000 0 -0.11 9 9
IFNG 0.009 0.047 -10000 0 -0.11 71 71
Telomerase/PinX1 -0.032 0.17 -10000 0 -0.4 56 56
Telomerase/AKT1/mTOR/p70S6K 0.004 0.11 -10000 0 -0.35 29 29
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Telomerase/EST1B -0.03 0.17 -10000 0 -0.39 57 57
response to DNA damage stimulus -0.004 0.03 0.052 1 -0.12 38 39
MRN complex/TRF2/Rap1 0.046 0.06 -10000 0 -0.11 54 54
TRF2/WRN 0.024 0.042 -10000 0 -0.1 49 49
Telomerase/hnRNP C1/C2 -0.029 0.17 -10000 0 -0.4 55 55
E2F1 0.02 0.018 -10000 0 -0.12 7 7
ZNFX1 0.018 0.022 -10000 0 -0.12 12 12
PIF1 0.023 0.006 -10000 0 -0.12 1 1
NCL 0.022 0.008 -10000 0 -0.12 1 1
DKC1 0.022 0.011 -10000 0 -0.12 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Arf6 signaling events

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.017 -9999 0 -0.078 18 18
ARNO/beta Arrestin1-2 0.029 0.019 -9999 0 -0.077 11 11
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EPHA2 0.02 0.022 -9999 0 -0.12 13 13
USP6 0.023 0.006 -9999 0 -0.12 1 1
IQSEC1 0.023 0.006 -9999 0 -0.12 1 1
EGFR/EGFR/EGF/EGF 0.016 0.05 -9999 0 -0.11 73 73
ARRB2 0.017 0.018 -9999 0 -0.2 3 3
mol:GTP 0.003 0.006 -9999 0 -0.04 1 1
ARRB1 0.02 0.022 -9999 0 -0.12 13 13
FBXO8 0.022 0.011 -9999 0 -0.12 3 3
TSHR 0.013 0.038 -9999 0 -0.12 41 41
EGF 0.02 0.021 -9999 0 -0.12 12 12
somatostatin receptor activity 0 0 -9999 0 0 27 27
ARAP2 0 0 -9999 0 0 26 26
mol:GDP 0.015 0.046 -9999 0 -0.16 26 26
mol:PI-3-4-5-P3 0 0 -9999 0 0 27 27
ITGA2B 0.023 0.006 -9999 0 -0.12 1 1
ARF6 0.023 0.003 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.062 -9999 0 -0.11 75 75
ADAP1 0 0 -9999 0 0 26 26
KIF13B 0.02 0.022 -9999 0 -0.12 13 13
HGF/MET -0.017 0.074 -9999 0 -0.14 121 121
PXN 0.022 0.014 -9999 0 -0.12 5 5
ARF6/GTP 0.022 0.059 -9999 0 -0.2 27 27
EGFR/EGFR/EGF/EGF/ARFGEP100 0.03 0.046 -9999 0 -0.11 40 40
ADRB2 0.023 0.006 -9999 0 -0.12 1 1
receptor agonist activity 0 0 -9999 0 0 27 27
actin filament binding 0 0 -9999 0 0 27 27
SRC 0.023 0.009 -9999 0 -0.12 2 2
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
GNAQ 0.021 0.016 -9999 0 -0.12 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 27 27
ARF6/GDP 0.021 0.05 -9999 0 -0.25 11 11
ARF6/GDP/GULP/ACAP1 0.017 0.061 -9999 0 -0.16 29 29
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.05 -9999 0 -0.096 39 39
ACAP1 0 0 -9999 0 0 13 13
ACAP2 0 0 -9999 0 0 26 26
LHCGR/beta Arrestin2 0.023 0.016 -9999 0 -0.14 3 3
EFNA1 0.014 0.031 -9999 0 -0.12 26 26
HGF 0.02 0.023 -9999 0 -0.12 14 14
CYTH3 0 0 -9999 0 -0.001 27 27
CYTH2 0 0.001 -9999 0 -0.004 27 27
NCK1 0.02 0.019 -9999 0 -0.12 9 9
fibronectin binding 0 0 -9999 0 0 28 28
endosomal lumen acidification 0 0 -9999 0 0 18 18
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.005 0.045 -9999 0 -0.12 63 63
GNAQ/ARNO 0.015 0.007 -9999 0 -0.047 6 6
mol:Phosphatidic acid 0 0 -9999 0 0 26 26
PIP3-E 0.018 0.028 -9999 0 -0.12 22 22
MET 0 0.047 -9999 0 -0.12 70 70
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GIT1 0.022 0.012 -9999 0 -0.12 4 4
mol:PI-4-5-P2 0 0 -9999 0 -0.001 27 27
GNA11 0.022 0.014 -9999 0 -0.12 5 5
LHCGR 0.022 0.014 -9999 0 -0.12 5 5
AGTR1 0.022 0.012 -9999 0 -0.12 4 4
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.016 -9999 0 -0.14 3 3
IPCEF1/ARNO 0.026 0.038 -9999 0 -0.084 41 41
alphaIIb/beta3 Integrin 0.01 0.053 -9999 0 -0.096 107 107
Presenilin action in Notch and Wnt signaling

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.015 0.12 -10000 0 -0.48 29 29
HDAC1 0.027 0.027 0.092 18 -0.1 10 28
AES 0.023 0.021 -10000 0 -0.12 10 10
FBXW11 0.023 0.003 -10000 0 -10000 0 0
DTX1 0.023 0.009 -10000 0 -0.12 2 2
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 66 66
TLE1 0.022 0.02 0.075 1 -0.11 10 11
AP1 -0.004 0.071 -10000 0 -0.2 46 46
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
ADAM10 0.022 0.013 -10000 0 -0.12 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.056 0.18 -10000 0 -0.49 49 49
NICD/RBPSUH 0.013 0.12 -10000 0 -0.48 29 29
WIF1 0.02 0.022 -10000 0 -0.12 13 13
NOTCH1 0.001 0.12 -10000 0 -0.51 29 29
PSENEN 0.016 0.03 -10000 0 -0.12 24 24
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 33 33
beta catenin/beta TrCP1 -0.005 0.081 -10000 0 -0.28 30 30
APH1B 0.014 0.032 -10000 0 -0.12 29 29
APH1A 0.023 0.009 -10000 0 -0.12 2 2
AXIN1 -0.001 0.046 0.19 4 -0.3 2 6
CtBP/CBP/TCF1/TLE1/AES 0.038 0.094 0.18 108 -0.2 22 130
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
FOS -0.005 0.053 -10000 0 -0.12 95 95
JUN 0.014 0.033 -10000 0 -0.12 30 30
MAP3K7 0.024 0.017 -10000 0 -0.12 5 5
CTNNB1 -0.016 0.078 -10000 0 -0.28 29 29
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 32 32
HNF1A 0.024 0.014 -10000 0 -0.12 4 4
CTBP1 0.024 0.018 -10000 0 -0.12 7 7
MYC -0.15 0.42 -10000 0 -1.2 73 73
NKD1 0.023 0.012 -10000 0 -0.12 4 4
FZD1 0.023 0.006 -10000 0 -0.12 1 1
NOTCH1 precursor/Deltex homolog 1 0.014 0.12 -10000 0 -0.48 29 29
apoptosis -0.004 0.071 -10000 0 -0.2 46 46
Delta 1/NOTCHprecursor 0.013 0.12 -10000 0 -0.48 29 29
DLL1 0.022 0.012 -10000 0 -0.12 4 4
PPARD 0.001 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.033 0.067 -10000 0 -0.098 89 89
APC -0.004 0.057 0.19 4 -0.23 21 25
DVL1 0.017 0.066 -10000 0 -0.3 20 20
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
MAP3K7IP1 0.026 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.027 0.047 -10000 0 -0.11 34 34
LRP6 0.014 0.034 -10000 0 -0.12 32 32
CSNK1A1 0.022 0.007 -10000 0 -0.12 1 1
NLK 0.029 0.042 -10000 0 -0.22 11 11
CCND1 -0.18 0.43 -10000 0 -1.2 82 82
WNT1 0.023 0.009 -10000 0 -0.12 2 2
Axin1/APC/beta catenin -0.001 0.086 0.2 3 -0.28 27 30
DKK2 0.022 0.011 -10000 0 -0.12 3 3
NOTCH1 precursor/DVL1 0.014 0.13 -10000 0 -0.44 34 34
GSK3B 0.023 0.011 -10000 0 -0.12 3 3
FRAT1 0.024 0.007 -10000 0 -0.12 1 1
NOTCH/Deltex homolog 1 0.016 0.12 -10000 0 -0.48 29 29
PPP2R5D 0.009 0.041 -10000 0 -0.16 22 22
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
WNT1/LRP6/FZD1 0.042 0.045 -10000 0 -0.096 37 37
RBPJ 0.023 0.006 -10000 0 -0.12 1 1
CREBBP 0.017 0.018 -10000 0 -0.12 6 6
EPO signaling pathway

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.015 0.15 -9999 0 -0.45 36 36
CRKL 0.029 0.037 -9999 0 -0.1 10 10
mol:DAG 0.026 0.075 -9999 0 -0.19 46 46
HRAS 0.032 0.045 -9999 0 -0.11 20 20
MAPK8 0.021 0.041 -9999 0 -0.11 43 43
RAP1A 0.026 0.045 -9999 0 -0.16 16 16
GAB1 0.027 0.038 -9999 0 -0.1 12 12
MAPK14 0.022 0.041 -9999 0 -0.11 44 44
EPO 0.025 0.008 -9999 0 -0.12 1 1
PLCG1 0.026 0.076 -9999 0 -0.2 46 46
EPOR/TRPC2/IP3 Receptors 0.022 0.022 -9999 0 -0.12 12 12
RAPGEF1 0.023 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.035 0.043 -9999 0 -0.11 32 32
GAB1/SHC/GRB2/SOS1 0.042 0.052 -9999 0 -0.12 20 20
EPO/EPOR (dimer) 0.034 0.022 -9999 0 -0.082 15 15
IRS2 0.028 0.038 -9999 0 -0.1 11 11
STAT1 0.02 0.1 -9999 0 -0.26 53 53
STAT5B 0.032 0.076 -9999 0 -0.22 31 31
cell proliferation 0.02 0.038 -9999 0 -0.1 44 44
GAB1/SHIP/PIK3R1/SHP2/SHC 0.022 0.046 -9999 0 -0.11 25 25
TEC 0.02 0.045 -9999 0 -0.12 24 24
SOCS3 0.015 0.032 -9999 0 -0.12 28 28
STAT1 (dimer) 0.021 0.098 -9999 0 -0.25 53 53
JAK2 0.019 0.025 -9999 0 -0.12 16 16
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
EPO/EPOR (dimer)/JAK2 0.058 0.054 -9999 0 -0.11 10 10
EPO/EPOR 0.034 0.022 -9999 0 -0.082 15 15
LYN 0.022 0.014 -9999 0 -0.12 4 4
TEC/VAV2 0.021 0.059 -9999 0 -0.12 31 31
elevation of cytosolic calcium ion concentration 0.022 0.022 -9999 0 -0.12 12 12
SHC1 0.023 0.001 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.039 0.052 -9999 0 -0.13 43 43
mol:IP3 0.026 0.075 -9999 0 -0.19 46 46
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.029 0.047 -9999 0 -0.13 18 18
SH2B3 0.024 0.004 -9999 0 -10000 0 0
NFKB1 0.018 0.053 -9999 0 -0.15 43 43
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.06 -9999 0 -0.17 64 64
PTPN6 0.025 0.038 -9999 0 -0.089 29 29
TEC/VAV2/GRB2 0.029 0.062 -9999 0 -0.12 32 32
EPOR 0.022 0.022 -9999 0 -0.12 12 12
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP 0.042 0.053 -9999 0 -0.12 20 20
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG2 0.02 0.02 -9999 0 -0.12 11 11
CRKL/CBL/C3G 0.053 0.042 -9999 0 -0.13 4 4
VAV2 0.027 0.037 -9999 0 -0.1 8 8
CBL 0.029 0.038 -9999 0 -0.11 10 10
SHC/Grb2/SOS1 0.03 0.045 -9999 0 -0.13 16 16
STAT5A 0.03 0.079 -9999 0 -0.21 42 42
GRB2 0.023 0.006 -9999 0 -0.12 1 1
STAT5 (dimer) 0.049 0.088 -9999 0 -0.24 31 31
LYN/PLCgamma2 0.02 0.05 -9999 0 -0.13 54 54
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
BTK 0.022 0.047 -9999 0 -0.15 21 21
BCL2 0.019 0.12 -9999 0 -0.41 22 22
Glucocorticoid receptor regulatory network

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.011 0.059 -10000 0 -0.7 2 2
SMARCC2 0.022 0.012 -10000 0 -0.12 4 4
SMARCC1 0.023 0.003 -10000 0 -10000 0 0
TBX21 0.042 0.047 -10000 0 -0.31 1 1
SUMO2 0.021 0.005 -10000 0 -10000 0 0
STAT1 (dimer) -0.007 0.08 -10000 0 -0.17 93 93
FKBP4 0.02 0.02 -10000 0 -0.12 10 10
FKBP5 0.006 0.043 -10000 0 -0.12 56 56
GR alpha/HSP90/FKBP51/HSP90 -0.013 0.082 0.24 1 -0.2 43 44
PRL 0.045 0.057 -10000 0 -0.5 1 1
cortisol/GR alpha (dimer)/TIF2 -0.02 0.11 0.43 3 -0.34 3 6
RELA -0.02 0.075 -10000 0 -0.14 121 121
FGG -0.016 0.1 0.45 1 -0.32 3 4
GR beta/TIF2 -0.006 0.07 0.23 2 -0.21 21 23
IFNG -0.003 0.12 -10000 0 -0.45 4 4
apoptosis -0.052 0.16 -10000 0 -0.45 32 32
CREB1 0.033 0.008 -10000 0 -10000 0 0
histone acetylation 0.028 0.081 0.28 7 -0.28 19 26
BGLAP 0.042 0.075 -10000 0 -0.87 2 2
GR/PKAc 0.028 0.063 0.23 2 -0.15 21 23
NF kappa B1 p50/RelA -0.044 0.14 -10000 0 -0.26 142 142
SMARCD1 0.021 0.018 -10000 0 -0.12 9 9
MDM2 -0.003 0.047 0.14 1 -0.22 9 10
GATA3 0.037 0.022 -10000 0 -0.12 11 11
AKT1 0.015 0.022 0.15 2 -0.13 10 12
CSF2 0.03 0.055 -10000 0 -10000 0 0
GSK3B 0.02 0.012 -10000 0 -0.13 3 3
NR1I3 -0.038 0.15 -10000 0 -0.49 8 8
CSN2 -0.015 0.093 0.32 2 -0.29 3 5
BRG1/BAF155/BAF170/BAF60A 0.041 0.052 -10000 0 -0.11 45 45
NFATC1 0.033 0.013 -10000 0 -0.11 3 3
POU2F1 0.031 0.008 -10000 0 -0.11 1 1
CDKN1A -0.041 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.004 -10000 0 -10000 0 0
SFN 0.014 0.032 -10000 0 -0.12 29 29
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.007 0.086 0.24 1 -0.18 64 65
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.28 -10000 0 -0.72 92 92
JUN 0.021 0.089 -10000 0 -0.28 10 10
IL4 0.046 0.048 -10000 0 -0.3 1 1
CDK5R1 0.022 0.007 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
cortisol/GR alpha (monomer)/AP-1 -0.043 0.079 0.19 12 -0.19 72 84
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.006 0.079 0.24 1 -0.17 44 45
cortisol/GR alpha (monomer) -0.039 0.12 0.48 3 -0.38 3 6
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.014 0.079 -10000 0 -0.14 134 134
AP-1/NFAT1-c-4 -0.012 0.15 -10000 0 -0.36 45 45
AFP 0.017 0.083 -10000 0 -0.56 1 1
SUV420H1 0.021 0.015 -10000 0 -0.12 6 6
IRF1 -0.095 0.24 -10000 0 -0.6 86 86
TP53 0.026 0.033 -10000 0 -10000 0 0
PPP5C 0.022 0.014 -10000 0 -0.12 5 5
KRT17 -0.011 0.15 -10000 0 -0.71 12 12
KRT14 -0.006 0.2 0.49 7 -1.1 15 22
TBP 0.031 0.026 -10000 0 -0.32 2 2
CREBBP 0.023 0.052 0.3 15 -0.13 5 20
HDAC1 0.013 0.02 -10000 0 -0.13 10 10
HDAC2 0.018 0.021 -10000 0 -0.12 12 12
AP-1 -0.012 0.15 -10000 0 -0.36 45 45
MAPK14 0.02 0.008 -10000 0 -0.13 1 1
MAPK10 0.011 0.037 -10000 0 -0.13 38 38
MAPK11 0.021 0.004 -10000 0 -10000 0 0
KRT5 -0.07 0.26 -10000 0 -0.89 46 46
interleukin-1 receptor activity -0.002 0.001 -10000 0 -10000 0 0
NCOA1 0.024 0.01 -10000 0 -0.08 4 4
STAT1 -0.007 0.08 -10000 0 -0.17 93 93
CGA 0.043 0.059 -10000 0 -0.41 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.046 0.11 0.29 6 -0.34 34 40
MAPK3 0.019 0.015 -10000 0 -0.13 5 5
MAPK1 0.019 0.017 -10000 0 -0.12 7 7
ICAM1 -0.13 0.32 -10000 0 -0.79 102 102
NFKB1 -0.031 0.097 -10000 0 -0.18 139 139
MAPK8 0.033 0.076 -10000 0 -0.23 9 9
MAPK9 0.019 0.012 -10000 0 -0.12 3 3
cortisol/GR alpha (dimer) -0.055 0.17 -10000 0 -0.47 33 33
BAX -0.039 0.12 -10000 0 -10000 0 0
POMC 0.029 0.082 -10000 0 -10000 0 0
EP300 0.023 0.047 0.29 14 -0.13 1 15
cortisol/GR alpha (dimer)/p53 -0.045 0.12 0.5 1 -0.36 4 5
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.058 0.26 15 -0.21 7 22
SGK1 0.001 0.1 0.34 14 -0.32 31 45
IL13 0.021 0.089 -10000 0 -0.52 1 1
IL6 -0.028 0.15 -10000 0 -0.58 18 18
PRKACG 0.023 0.009 -10000 0 -0.12 2 2
IL5 0.025 0.089 -10000 0 -10000 0 0
IL2 0.004 0.11 -10000 0 -0.42 3 3
CDK5 0.014 0.032 -10000 0 -0.12 28 28
PRKACB 0.019 0.02 -10000 0 -0.12 11 11
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
IL8 -0.055 0.22 -10000 0 -0.75 41 41
CDK5R1/CDK5 0.019 0.042 -10000 0 -0.11 52 52
NF kappa B1 p50/RelA/PKAc -0.002 0.12 -10000 0 -0.18 130 130
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.4 2 -0.33 2 4
SMARCA4 0.015 0.031 -10000 0 -0.12 27 27
chromatin remodeling -0.009 0.092 0.27 2 -0.31 15 17
NF kappa B1 p50/RelA/Cbp -0.02 0.13 0.34 8 -0.25 80 88
JUN (dimer) 0.021 0.089 -10000 0 -0.28 10 10
YWHAH 0.021 0.014 -10000 0 -0.12 5 5
VIPR1 0.043 0.045 -10000 0 -0.22 2 2
NR3C1 -0.015 0.081 0.32 2 -0.33 10 12
NR4A1 0.01 0.048 -10000 0 -10000 0 0
TIF2/SUV420H1 0.02 0.048 -10000 0 -0.14 40 40
MAPKKK cascade -0.052 0.16 -10000 0 -0.45 32 32
cortisol/GR alpha (dimer)/Src-1 -0.013 0.11 0.44 3 -0.32 2 5
PBX1 0.029 0.014 -10000 0 -0.11 4 4
POU1F1 0.03 0.014 -10000 0 -0.13 4 4
SELE -0.006 0.11 -10000 0 -0.34 10 10
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.009 0.092 0.27 2 -0.31 15 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.4 2 -0.33 2 4
mol:cortisol -0.027 0.065 0.26 3 -10000 0 3
MMP1 -0.038 0.16 -10000 0 -0.95 12 12
LPA4-mediated signaling events

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.012 0.014 -9999 0 -0.057 22 22
ADCY5 0.009 0.02 -9999 0 -0.06 42 42
ADCY6 0.013 0.01 -9999 0 -0.057 11 11
ADCY7 0.014 0.009 -9999 0 -0.057 8 8
ADCY1 0.013 0.013 -9999 0 -0.067 12 12
ADCY2 0.012 0.013 -9999 0 -0.057 18 18
ADCY3 0.012 0.013 -9999 0 -0.057 18 18
ADCY8 0.002 0.03 -9999 0 -0.061 99 99
PRKCE 0.01 0.011 -9999 0 -0.077 8 8
ADCY9 0.012 0.015 -9999 0 -0.064 17 17
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.012 0.032 -9999 0 -0.18 11 11
Coregulation of Androgen receptor activity

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.014 0.035 -9999 0 -0.12 35 35
SVIL 0.016 0.031 <