PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1X065JZ
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1X065JZ
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 48 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
TCGA08_retinoblastoma 365
HIF-1-alpha transcription factor network 202
Nephrin/Neph1 signaling in the kidney podocyte 179
TCR signaling in naïve CD8+ T cells 141
TCGA08_p53 139
Syndecan-4-mediated signaling events 117
Aurora B signaling 115
FOXA2 and FOXA3 transcription factor networks 110
Glypican 1 network 108
FOXM1 transcription factor network 105
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 506 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 506 ).

Pathway.Name Significance.Ratio 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
TCGA08_retinoblastoma 0.7213 365 2924 8 -0.84 0.22 1000 -1000 -0.032 -1000
HIF-1-alpha transcription factor network 0.3992 202 15410 76 -1.3 0.026 1000 -1000 -0.16 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.3538 179 6089 34 -0.61 0.016 1000 -1000 -0.098 -1000
TCR signaling in naïve CD8+ T cells 0.2787 141 13205 93 -0.66 0.33 1000 -1000 -0.12 -1000
TCGA08_p53 0.2747 139 975 7 -0.65 0.31 1000 -1000 -0.024 -1000
Syndecan-4-mediated signaling events 0.2312 117 7840 67 -0.65 0.11 1000 -1000 -0.13 -1000
Aurora B signaling 0.2273 115 7712 67 -0.41 0.016 1000 -1000 -0.1 -1000
FOXA2 and FOXA3 transcription factor networks 0.2174 110 5096 46 -1.2 0.025 1000 -1000 -0.1 -1000
Glypican 1 network 0.2134 108 5193 48 -0.56 0.045 1000 -1000 -0.068 -1000
FOXM1 transcription factor network 0.2075 105 5388 51 -0.82 0.04 1000 -1000 -0.2 -1000
IL12-mediated signaling events 0.2016 102 8881 87 -0.7 0.16 1000 -1000 -0.16 -1000
PDGFR-alpha signaling pathway 0.1976 100 4419 44 -0.28 0.034 1000 -1000 -0.087 -1000
amb2 Integrin signaling 0.1621 82 6784 82 -0.56 0.016 1000 -1000 -0.12 -1000
JNK signaling in the CD4+ TCR pathway 0.1443 73 1254 17 -0.41 0.016 1000 -1000 -0.1 -1000
IL4-mediated signaling events 0.1383 70 6370 91 -0.84 0.54 1000 -1000 -0.19 -1000
EGFR-dependent Endothelin signaling events 0.1383 70 1489 21 -0.67 0.016 1000 -1000 -0.11 -1000
Aurora C signaling 0.1364 69 483 7 -0.4 0.012 1000 -1000 -0.061 -1000
Syndecan-1-mediated signaling events 0.1304 66 2274 34 -0.42 0.016 1000 -1000 -0.098 -1000
Glypican 2 network 0.1304 66 266 4 -0.12 -1000 1000 -1000 -0.058 -1000
HIF-2-alpha transcription factor network 0.1285 65 2804 43 -0.76 0.33 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 0.1245 63 4694 74 -0.32 0.16 1000 -1000 -0.078 -1000
VEGFR1 specific signals 0.1245 63 3578 56 -0.47 0.045 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.1146 58 3539 60 -0.4 0.021 1000 -1000 -0.19 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1126 57 1905 33 -0.83 0.016 1000 -1000 -0.09 -1000
BMP receptor signaling 0.1087 55 4526 81 -0.7 0.016 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.0968 49 2578 52 -0.44 0.12 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 0.0850 43 4205 97 -0.33 0.04 1000 -1000 -0.14 -1000
IL27-mediated signaling events 0.0830 42 2142 51 -0.61 0.076 1000 -1000 -0.13 -1000
Effects of Botulinum toxin 0.0791 40 1056 26 -0.37 0.016 1000 -1000 -0.088 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0791 40 2720 68 -0.55 0.063 1000 -1000 -0.17 -1000
S1P1 pathway 0.0771 39 1427 36 -0.37 0.018 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0751 38 267 7 -0.056 0 1000 -1000 -0.05 -1000
Arf6 signaling events 0.0731 37 2323 62 -0.67 0.016 1000 -1000 -0.084 -1000
Calcium signaling in the CD4+ TCR pathway 0.0731 37 1151 31 -0.46 0.016 1000 -1000 -0.16 -1000
p75(NTR)-mediated signaling 0.0672 34 4314 125 -0.42 0.016 1000 -1000 -0.15 -1000
IL2 signaling events mediated by STAT5 0.0672 34 750 22 -0.45 0.038 1000 -1000 -0.06 -1000
IL2 signaling events mediated by PI3K 0.0652 33 1934 58 -0.44 0.031 1000 -1000 -0.12 -1000
LPA4-mediated signaling events 0.0632 32 394 12 -0.16 0.026 1000 -1000 -0.038 -1000
PLK1 signaling events 0.0593 30 2582 85 -0.39 0.016 1000 -1000 -0.08 -1000
BCR signaling pathway 0.0593 30 3034 99 -0.33 0.034 1000 -1000 -0.13 -1000
Coregulation of Androgen receptor activity 0.0573 29 2219 76 -0.92 0.033 1000 -1000 -0.082 -1000
IL6-mediated signaling events 0.0553 28 2118 75 -0.28 0.076 1000 -1000 -0.12 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0534 27 1465 54 -0.65 0.031 1000 -1000 -0.13 -1000
EPO signaling pathway 0.0534 27 1485 55 -0.29 0.018 1000 -1000 -0.14 -1000
Regulation of Telomerase 0.0534 27 2829 102 -0.67 0.051 1000 -1000 -0.16 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0534 27 2149 78 -0.31 0.045 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 0.0514 26 3048 114 -0.41 0.16 1000 -1000 -0.093 -1000
Integrins in angiogenesis 0.0514 26 2206 84 -0.37 0.039 1000 -1000 -0.13 -1000
Aurora A signaling 0.0455 23 1434 60 -0.25 0.053 1000 -1000 -0.082 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0455 23 2052 88 -0.32 0.074 1000 -1000 -0.14 -1000
Visual signal transduction: Rods 0.0455 23 1199 52 -0.28 0.016 1000 -1000 -0.11 -1000
Signaling events mediated by PTP1B 0.0435 22 1713 76 -0.67 0.049 1000 -1000 -0.12 -1000
Reelin signaling pathway 0.0435 22 1246 56 -0.24 0.016 1000 -1000 -0.12 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0415 21 974 45 -0.57 0.061 1000 -1000 -0.12 -1000
Syndecan-2-mediated signaling events 0.0395 20 1389 69 -0.56 0.055 1000 -1000 -0.087 -1000
Endothelins 0.0375 19 1828 96 -0.35 0.088 1000 -1000 -0.11 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0375 19 2314 120 -0.17 0.14 1000 -1000 -0.13 -1000
Wnt signaling 0.0336 17 122 7 -0.071 0.016 1000 -1000 -0.079 -1000
Regulation of nuclear SMAD2/3 signaling 0.0316 16 2305 136 -0.45 0.095 1000 -1000 -0.11 -1000
Thromboxane A2 receptor signaling 0.0316 16 1783 105 -0.67 0.066 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0316 16 605 37 -0.29 0.025 1000 -1000 -0.11 -1000
S1P3 pathway 0.0316 16 672 42 -0.37 0.062 1000 -1000 -0.081 -1000
Presenilin action in Notch and Wnt signaling 0.0296 15 973 61 -0.18 0.091 1000 -1000 -0.1 -1000
LPA receptor mediated events 0.0296 15 1599 102 -0.41 0.061 1000 -1000 -0.14 -1000
PLK2 and PLK4 events 0.0277 14 42 3 -0.016 0.01 1000 -1000 -0.031 -1000
Ceramide signaling pathway 0.0277 14 1107 76 -0.67 0.23 1000 -1000 -0.095 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0257 13 384 28 -0.13 0.025 1000 -1000 -0.081 -1000
FoxO family signaling 0.0257 13 867 64 -0.57 0.12 1000 -1000 -0.11 -1000
FAS signaling pathway (CD95) 0.0257 13 625 47 -0.43 0.029 1000 -1000 -0.071 -1000
Class I PI3K signaling events 0.0257 13 977 73 -0.45 0.036 1000 -1000 -0.1 -1000
E-cadherin signaling events 0.0257 13 68 5 -0.023 0.016 1000 -1000 -0.061 -1000
ErbB4 signaling events 0.0237 12 833 69 -0.18 0.1 1000 -1000 -0.12 -1000
IFN-gamma pathway 0.0237 12 840 68 -0.38 0.017 1000 -1000 -0.14 -1000
Canonical Wnt signaling pathway 0.0237 12 662 51 -0.18 0.094 1000 -1000 -0.097 -1000
Nongenotropic Androgen signaling 0.0237 12 633 52 -0.17 0.071 1000 -1000 -0.091 -1000
Regulation of Androgen receptor activity 0.0237 12 860 70 -0.96 0.04 1000 -1000 -0.099 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0217 11 1405 125 -0.39 0.043 1000 -1000 -0.15 -1000
S1P5 pathway 0.0198 10 177 17 -0.13 0.043 1000 -1000 -0.081 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0198 10 771 74 -0.67 0.099 1000 -1000 -0.13 -1000
Visual signal transduction: Cones 0.0178 9 342 38 -0.041 0.016 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 0.0178 9 250 26 -0.11 0.016 1000 -1000 -0.14 -1000
a4b1 and a4b7 Integrin signaling 0.0178 9 45 5 -0.02 0.016 1000 -1000 -0.054 -1000
S1P4 pathway 0.0178 9 249 25 -0.13 0.035 1000 -1000 -0.081 -1000
TCGA08_rtk_signaling 0.0158 8 229 26 -0.28 0.041 1000 -1000 -0.032 -1000
Signaling events regulated by Ret tyrosine kinase 0.0138 7 649 82 -0.064 0.027 1000 -1000 -0.12 -1000
Canonical NF-kappaB pathway 0.0119 6 260 39 -0.19 0.075 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 0.0119 6 213 34 -0.058 0.046 1000 -1000 -0.084 -1000
Class IB PI3K non-lipid kinase events 0.0119 6 18 3 -0.006 0.006 1000 -1000 -0.015 -1000
p38 MAPK signaling pathway 0.0119 6 264 44 -0.1 0.049 1000 -1000 -0.091 -1000
ErbB2/ErbB3 signaling events 0.0099 5 379 65 -0.14 0.059 1000 -1000 -0.11 -1000
Insulin-mediated glucose transport 0.0099 5 177 32 -0.086 0.066 1000 -1000 -0.088 -1000
Signaling events mediated by HDAC Class III 0.0099 5 224 40 -0.06 0.031 1000 -1000 -0.082 -1000
IL1-mediated signaling events 0.0099 5 370 62 -0.093 0.061 1000 -1000 -0.15 -1000
Ephrin B reverse signaling 0.0099 5 279 48 -0.027 0.032 1000 -1000 -0.11 -1000
Signaling mediated by p38-gamma and p38-delta 0.0099 5 81 15 0 0.037 1000 -1000 -0.056 -1000
Syndecan-3-mediated signaling events 0.0099 5 177 35 -0.04 0.016 1000 -1000 -0.11 -1000
E-cadherin signaling in the nascent adherens junction 0.0099 5 389 76 -0.026 0.067 1000 -1000 -0.11 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0079 4 365 85 -0.035 0.079 1000 -1000 -0.11 -1000
Arf6 downstream pathway 0.0079 4 214 43 -0.033 0.033 1000 -1000 -0.065 -1000
Paxillin-dependent events mediated by a4b1 0.0079 4 155 36 -0.027 0.031 1000 -1000 -0.096 -1000
EPHB forward signaling 0.0079 4 345 85 -0.073 0.07 1000 -1000 -0.14 -1000
Ras signaling in the CD4+ TCR pathway 0.0079 4 80 17 -0.037 0.055 1000 -1000 -0.076 -1000
BARD1 signaling events 0.0059 3 223 57 -0.17 0.043 1000 -1000 -0.11 -1000
Cellular roles of Anthrax toxin 0.0059 3 119 39 -0.022 0.027 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0059 3 324 86 -0.17 0.072 1000 -1000 -0.12 -1000
E-cadherin signaling in keratinocytes 0.0059 3 134 43 -0.29 0.053 1000 -1000 -0.12 -1000
Osteopontin-mediated events 0.0040 2 107 38 -0.03 0.099 1000 -1000 -0.14 -1000
Hedgehog signaling events mediated by Gli proteins 0.0040 2 131 65 -0.063 0.093 1000 -1000 -0.089 -1000
ceramide signaling pathway 0.0040 2 138 49 -0.12 0.054 1000 -1000 -0.063 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0040 2 128 52 -0.031 0.092 1000 -1000 -0.093 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0040 2 174 83 -0.086 0.081 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class I 0.0040 2 210 104 -0.03 0.064 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0040 2 156 54 -0.04 0.073 1000 -1000 -0.078 -1000
Arf6 trafficking events 0.0040 2 175 71 -0.13 0.058 1000 -1000 -0.11 -1000
IGF1 pathway 0.0040 2 119 57 -0.066 0.071 1000 -1000 -0.14 -1000
Insulin Pathway 0.0040 2 192 74 -0.035 0.055 1000 -1000 -0.14 -1000
PDGFR-beta signaling pathway 0.0040 2 232 97 -0.055 0.087 1000 -1000 -0.14 -1000
Signaling events mediated by HDAC Class II 0.0020 1 121 75 -0.027 0.051 1000 -1000 -0.094 -1000
Circadian rhythm pathway 0.0020 1 29 22 -0.019 0.065 1000 -1000 -0.091 -1000
mTOR signaling pathway 0.0020 1 62 53 -0.007 0.044 1000 -1000 -0.085 -1000
Class I PI3K signaling events mediated by Akt 0.0020 1 89 68 -0.086 0.06 1000 -1000 -0.11 -1000
Nectin adhesion pathway 0.0020 1 63 63 -0.016 0.08 1000 -1000 -0.1 -1000
Retinoic acid receptors-mediated signaling 0.0020 1 114 58 -0.025 0.063 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 0.0020 1 52 31 -0.022 0.036 1000 -1000 -0.1 -1000
Signaling mediated by p38-alpha and p38-beta 0.0020 1 52 44 -0.042 0.051 1000 -1000 -0.089 -1000
Alternative NF-kappaB pathway 0.0020 1 14 13 -0.005 0.016 1000 -1000 -0.09 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.062 1000 -1000 -0.11 -1000
TRAIL signaling pathway 0.0000 0 25 48 -0.002 0.071 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.082 -1000
Rapid glucocorticoid signaling 0.0000 0 11 20 -0.005 0.016 1000 -1000 -0.059 -1000
Arf1 pathway 0.0000 0 29 54 -0.009 0.044 1000 -1000 -0.064 -1000
Total NA 4080 212932 7203 -40 -990 131000 -131000 -14 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.01 0.094 -10000 0 -0.87 6 6
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.84 0.17 -10000 0 -0.87 487 487
CCND2 0.18 0.048 0.19 486 -10000 0 486
RB1 -0.2 0.05 -10000 0 -0.21 486 486
CDK4 0.22 0.051 0.22 486 -10000 0 486
CDK6 0.2 0.054 0.21 486 -0.18 1 487
G1/S progression 0.2 0.054 0.21 486 -10000 0 486
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 -0.97 0.53 -9999 0 -1.3 316 316
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.91 299 299
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.97 0.53 -9999 0 -1.3 315 315
AP1 -0.015 0.09 -9999 0 -0.57 13 13
ABCG2 -0.97 0.53 -9999 0 -1.3 307 307
HIF1A -0.1 0.069 -9999 0 -0.9 2 2
TFF3 -0.98 0.54 -9999 0 -1.3 309 309
GATA2 -0.001 0.12 -9999 0 -0.74 12 12
AKT1 -0.093 0.053 -9999 0 -10000 0 0
response to hypoxia -0.12 0.058 -9999 0 -10000 0 0
MCL1 -0.97 0.53 -9999 0 -1.3 315 315
NDRG1 -0.97 0.53 -9999 0 -1.3 307 307
SERPINE1 -1 0.57 -9999 0 -1.4 316 316
FECH -0.97 0.53 -9999 0 -1.3 307 307
FURIN -0.97 0.53 -9999 0 -1.3 308 308
NCOA2 -0.001 0.095 -9999 0 -0.75 8 8
EP300 -0.099 0.075 -9999 0 -0.39 3 3
HMOX1 -0.99 0.55 -9999 0 -1.4 309 309
BHLHE40 -0.97 0.53 -9999 0 -1.3 316 316
BHLHE41 -1.1 0.58 -9999 0 -1.4 318 318
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.079 0.057 -9999 0 -0.6 2 2
ENG -0.058 0.063 -9999 0 -10000 0 0
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.97 0.53 -9999 0 -1.3 319 319
ABCB1 -0.3 0.42 -9999 0 -1.3 67 67
TFRC -0.97 0.53 -9999 0 -1.3 315 315
CXCR4 -1.1 0.6 -9999 0 -1.5 316 316
TF -1 0.58 -9999 0 -1.4 302 302
CITED2 -0.97 0.53 -9999 0 -1.3 308 308
HIF1A/ARNT -1.3 0.86 -9999 0 -1.7 328 328
LDHA -0.085 0.063 -9999 0 -0.85 2 2
ETS1 -0.97 0.53 -9999 0 -1.3 307 307
PGK1 -0.97 0.53 -9999 0 -1.3 308 308
NOS2 -0.98 0.53 -9999 0 -1.3 309 309
ITGB2 -1 0.57 -9999 0 -1.4 324 324
ALDOA -0.97 0.53 -9999 0 -1.3 308 308
Cbp/p300/CITED2 -0.97 0.54 -9999 0 -1.4 290 290
FOS -0.003 0.12 -9999 0 -0.75 13 13
HK2 -1.2 0.59 -9999 0 -1.5 378 378
SP1 0.021 0.03 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.1 10 10
HK1 -0.97 0.53 -9999 0 -1.3 318 318
NPM1 -0.97 0.53 -9999 0 -1.3 308 308
EGLN1 -0.97 0.53 -9999 0 -1.3 307 307
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.97 0.53 -9999 0 -1.3 319 319
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.091 0.17 -9999 0 -0.8 18 18
IGFBP1 -1 0.58 -9999 0 -1.4 314 314
VEGFA -0.77 0.41 -9999 0 -1.1 231 231
HIF1A/JAB1 -0.054 0.048 -9999 0 -0.7 2 2
CP -1.2 0.59 -9999 0 -1.5 370 370
CXCL12 -0.98 0.53 -9999 0 -1.3 320 320
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.97 0.53 -9999 0 -1.3 307 307
EGLN3 -1.3 0.51 -9999 0 -1.5 394 394
CA9 -1.3 0.48 -9999 0 -1.5 404 404
TERT -1 0.55 -9999 0 -1.4 307 307
ENO1 -0.97 0.53 -9999 0 -1.3 307 307
PFKL -0.97 0.53 -9999 0 -1.3 308 308
NCOA1 0.015 0.003 -9999 0 -10000 0 0
ADM -1 0.57 -9999 0 -1.4 321 321
ARNT -0.099 0.047 -9999 0 -10000 0 0
HNF4A -0.045 0.22 -9999 0 -0.75 43 43
ADFP -0.98 0.53 -9999 0 -1.3 321 321
SLC2A1 -0.62 0.34 -9999 0 -0.97 168 168
LEP -1 0.55 -9999 0 -1.4 324 324
HIF1A/ARNT/Cbp/p300 -0.7 0.34 -9999 0 -0.93 301 301
EPO -0.61 0.39 -9999 0 -1.1 176 176
CREBBP -0.098 0.073 -9999 0 -0.35 5 5
HIF1A/ARNT/Cbp/p300/HDAC7 -0.74 0.39 -9999 0 -1 305 305
PFKFB3 -0.97 0.53 -9999 0 -1.3 319 319
NT5E -0.97 0.53 -9999 0 -1.3 307 307
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.48 0.26 0.62 392 -10000 0 392
KIRREL -0.054 0.1 -10000 0 -0.82 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.49 0.26 -10000 0 -0.62 392 392
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.53 0.31 -10000 0 -0.84 219 219
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.41 0.26 -10000 0 -0.67 219 219
FYN -0.5 0.3 -10000 0 -0.8 219 219
mol:Ca2+ -0.52 0.31 -10000 0 -0.83 219 219
mol:DAG -0.53 0.31 -10000 0 -0.84 219 219
NPHS2 -0.41 0.38 -10000 0 -0.81 244 244
mol:IP3 -0.53 0.31 -10000 0 -0.84 219 219
regulation of endocytosis -0.47 0.28 -10000 0 -0.75 219 219
Nephrin/NEPH1/podocin/Cholesterol -0.54 0.31 -10000 0 -0.65 419 419
establishment of cell polarity -0.48 0.26 -10000 0 -0.62 392 392
Nephrin/NEPH1/podocin/NCK1-2 -0.49 0.29 -10000 0 -0.79 219 219
Nephrin/NEPH1/beta Arrestin2 -0.48 0.29 -10000 0 -0.77 219 219
NPHS1 -0.61 0.33 -10000 0 -0.79 390 390
Nephrin/NEPH1/podocin -0.51 0.3 -10000 0 -0.81 219 219
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.034 -10000 0 -0.75 1 1
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.53 0.31 -10000 0 -0.84 219 219
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.53 0.31 -10000 0 -0.84 219 219
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.49 0.3 -10000 0 -0.79 219 219
cytoskeleton organization -0.53 0.32 -10000 0 -0.85 219 219
Nephrin/NEPH1 -0.36 0.2 -10000 0 -0.47 392 392
Nephrin/NEPH1/ZO-1 -0.39 0.22 -10000 0 -0.51 392 392
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.68 231 231
FYN -0.41 0.5 -10000 0 -0.92 235 235
LAT/GRAP2/SLP76 -0.36 0.39 -10000 0 -0.75 234 234
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.25 0.29 -10000 0 -0.54 235 235
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.08 0.072 -10000 0 -0.19 81 81
MAP3K8 0.012 0.055 -10000 0 -0.86 2 2
mol:Ca2+ -0.11 0.045 -10000 0 -0.14 286 286
integrin-mediated signaling pathway -0.018 0.1 -10000 0 -0.58 16 16
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.41 0.45 -10000 0 -0.85 245 245
TRPV6 -0.66 0.26 -10000 0 -0.76 438 438
CD28 -0.057 0.23 -10000 0 -0.87 38 38
SHC1 -0.44 0.49 -10000 0 -0.93 238 238
receptor internalization -0.51 0.56 -10000 0 -1.1 240 240
PRF1 -0.48 0.6 -10000 0 -1.1 234 234
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.18 0.22 -10000 0 -0.41 216 216
LAT -0.5 0.53 -10000 0 -1 251 251
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 228 228
CD3E -0.34 0.44 -10000 0 -0.87 204 204
CD3G -0.33 0.43 -10000 0 -0.87 199 199
RASGRP2 -0.022 0.029 -10000 0 -0.14 2 2
RASGRP1 -0.23 0.28 -10000 0 -0.51 226 226
HLA-A 0.007 0.04 -10000 0 -0.87 1 1
RASSF5 -0.012 0.15 -10000 0 -0.86 16 16
RAP1A/GTP/RAPL -0.018 0.1 -10000 0 -0.58 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.082 -10000 0 -0.14 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 101 101
PRKCA -0.14 0.17 -10000 0 -0.31 177 177
GRAP2 -0.043 0.22 -10000 0 -0.86 34 34
mol:IP3 -0.16 0.34 0.26 167 -0.5 219 386
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.52 0.63 -10000 0 -1.1 241 241
ORAI1 0.33 0.13 0.38 437 -10000 0 437
CSK -0.45 0.51 -10000 0 -0.97 237 237
B7 family/CD28 -0.52 0.52 -10000 0 -1 237 237
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.56 0.62 -10000 0 -1.2 241 241
PTPN6 -0.44 0.53 -10000 0 -0.99 229 229
VAV1 -0.48 0.53 -10000 0 -1 247 247
Monovalent TCR/CD3 -0.46 0.53 -10000 0 -1 229 229
CBL 0.014 0.034 -10000 0 -0.75 1 1
LCK -0.44 0.53 -10000 0 -0.97 235 235
PAG1 -0.45 0.51 -10000 0 -0.97 238 238
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.63 -10000 0 -1.2 236 236
CD80 -0.19 0.37 -10000 0 -0.87 113 113
CD86 -0.13 0.32 -10000 0 -0.87 80 80
PDK1/CARD11/BCL10/MALT1 -0.18 0.17 -10000 0 -0.38 147 147
HRAS 0.014 0.039 -10000 0 -0.86 1 1
GO:0035030 -0.36 0.42 -10000 0 -0.77 237 237
CD8A -0.39 0.44 -10000 0 -0.87 230 230
CD8B -0.3 0.42 -10000 0 -0.87 181 181
PTPRC -0.087 0.27 -10000 0 -0.87 55 55
PDK1/PKC theta -0.32 0.36 -10000 0 -0.69 234 234
CSK/PAG1 -0.44 0.5 -10000 0 -0.94 235 235
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.03 -10000 0 -0.68 1 1
GRAP2/SLP76 -0.43 0.44 -10000 0 -0.88 236 236
STIM1 0.17 0.064 -10000 0 -10000 0 0
RAS family/GTP -0.063 0.12 -10000 0 -0.25 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.59 0.66 -10000 0 -1.2 240 240
mol:DAG -0.2 0.26 -10000 0 -0.46 231 231
RAP1A/GDP -0.013 0.036 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.41 -10000 0 -0.87 165 165
cytotoxic T cell degranulation -0.45 0.55 -10000 0 -1 234 234
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.31 0.35 -10000 0 -0.66 243 243
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.26 0.44 0.3 107 -0.7 230 337
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.45 0.44 -10000 0 -0.86 270 270
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.38 0.35 -10000 0 -0.73 237 237
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.5 0.56 -10000 0 -1.1 236 236
CARD11 -0.17 0.36 -10000 0 -0.86 108 108
PRKCB -0.14 0.17 -10000 0 -0.32 186 186
PRKCE -0.14 0.17 -10000 0 -0.31 203 203
PRKCQ -0.39 0.42 -10000 0 -0.8 244 244
LCP2 -0.04 0.21 -10000 0 -0.86 32 32
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.2 0.24 -10000 0 -0.44 234 234
IKK complex -0.027 0.085 -10000 0 -10000 0 0
RAS family/GDP -0.012 0.012 -10000 0 -0.11 1 1
MAP3K14 -0.13 0.18 -10000 0 -0.32 172 172
PDPK1 -0.23 0.27 -10000 0 -0.51 227 227
TCR/CD3/MHC I/CD8/Fyn -0.56 0.65 -10000 0 -1.2 233 233
TCGA08_p53

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
CDKN2A -0.65 0.13 -10000 0 -0.68 487 487
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.037 -10000 0 -10000 0 0
Apoptosis -0.17 0.037 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.062 0.32 487 -10000 0 487
MDM4 0.014 0.039 -10000 0 -0.86 1 1
Syndecan-4-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
PTK2 -0.055 0.14 -9999 0 -0.54 38 38
Syndecan-4/Syndesmos -0.47 0.39 -9999 0 -0.84 231 231
positive regulation of JNK cascade -0.54 0.37 -9999 0 -0.84 276 276
Syndecan-4/ADAM12 -0.57 0.5 -9999 0 -1 255 255
CCL5 -0.36 0.43 -9999 0 -0.86 215 215
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.048 0.23 -9999 0 -0.86 37 37
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.37 0.37 -9999 0 -0.72 265 265
ADAM12 -0.23 0.39 -9999 0 -0.86 140 140
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.48 0.4 -9999 0 -0.86 233 233
Syndecan-4/CXCL12/CXCR4 -0.59 0.43 -9999 0 -0.94 276 276
Syndecan-4/Laminin alpha3 -0.47 0.4 -9999 0 -0.85 236 236
MDK -0.048 0.23 -9999 0 -0.86 37 37
Syndecan-4/FZD7 -0.47 0.39 -9999 0 -0.84 232 232
Syndecan-4/Midkine -0.5 0.42 -9999 0 -0.88 242 242
FZD7 0.014 0.034 -9999 0 -0.75 1 1
Syndecan-4/FGFR1/FGF -0.44 0.34 -9999 0 -0.77 234 234
THBS1 0.011 0.059 -9999 0 -0.75 3 3
integrin-mediated signaling pathway -0.45 0.36 -9999 0 -0.79 236 236
positive regulation of MAPKKK cascade -0.54 0.37 -9999 0 -0.84 276 276
Syndecan-4/TACI -0.51 0.42 -9999 0 -0.89 244 244
CXCR4 -0.28 0.41 -9999 0 -0.86 170 170
cell adhesion -0.007 0.12 -9999 0 -0.51 14 14
Syndecan-4/Dynamin -0.47 0.39 -9999 0 -0.84 231 231
Syndecan-4/TSP1 -0.47 0.39 -9999 0 -0.84 233 233
Syndecan-4/GIPC -0.47 0.39 -9999 0 -0.84 232 232
Syndecan-4/RANTES -0.65 0.46 -9999 0 -1 285 285
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.007 0.13 -9999 0 -0.76 15 15
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.067 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.47 0.39 -9999 0 -0.85 232 232
TFPI 0.003 0.1 -9999 0 -0.8 8 8
F2 -0.32 0.42 -9999 0 -0.86 191 191
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.66 37 37
positive regulation of cell adhesion -0.46 0.38 -9999 0 -0.82 238 238
ACTN1 0.012 0.052 -9999 0 -0.8 2 2
TNC -0.002 0.12 -9999 0 -0.75 12 12
Syndecan-4/CXCL12 -0.48 0.4 -9999 0 -0.85 236 236
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.001 0.11 -9999 0 -0.75 11 11
TNFRSF13B -0.071 0.26 -9999 0 -0.86 49 49
FGF2 0.008 0.078 -9999 0 -0.77 5 5
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.48 0.39 -9999 0 -0.85 231 231
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.04 0.23 -9999 0 -0.83 38 38
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.046 -9999 0 -0.84 1 1
vasculogenesis -0.44 0.37 -9999 0 -0.79 233 233
SDC4 -0.52 0.43 -9999 0 -0.93 231 231
Syndecan-4/Tenascin C -0.48 0.39 -9999 0 -0.84 236 236
Syndecan-4/PI-4-5-P2/PKC alpha -0.08 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.47 0.39 -9999 0 -0.84 231 231
MMP9 -0.4 0.44 -9999 0 -0.86 243 243
Rac1/GTP -0.008 0.12 -9999 0 -0.53 14 14
cytoskeleton organization -0.44 0.36 -9999 0 -0.79 231 231
GIPC1 0.014 0.034 -9999 0 -0.75 1 1
Syndecan-4/TFPI -0.47 0.39 -9999 0 -0.85 235 235
Aurora B signaling

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
Condensin I complex -0.24 0.32 -9999 0 -0.68 161 161
STMN1 -0.29 0.34 -9999 0 -0.66 240 240
Aurora B/RasGAP/Survivin -0.41 0.48 -9999 0 -0.87 246 246
Chromosomal passenger complex/Cul3 protein complex -0.17 0.23 -9999 0 -0.49 147 147
BIRC5 -0.26 0.41 -9999 0 -0.89 151 151
DES -0.38 0.34 -9999 0 -0.63 249 249
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 241 241
Aurora B/TACC1 -0.26 0.3 -9999 0 -0.57 240 240
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 240 240
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.073 0.09 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.41 0.5 -9999 0 -0.89 244 244
Cul3 protein complex -0.015 0.083 -9999 0 -0.48 16 16
KIF2C -0.16 0.18 -9999 0 -0.34 197 197
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.39 0.44 -9999 0 -0.86 232 232
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 241 241
SEPT1 -0.095 0.29 -9999 0 -0.86 64 64
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.18 0.24 -9999 0 -0.47 146 146
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.005 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 240 240
AURKB -0.4 0.44 -9999 0 -0.87 240 240
AURKC 0.012 0.055 -9999 0 -0.86 2 2
CDCA8 -0.026 0.17 -9999 0 -0.89 19 19
cytokinesis -0.35 0.37 -9999 0 -0.74 212 212
Aurora B/Septin1 -0.37 0.42 -9999 0 -0.83 204 204
AURKA 0.002 0.096 -9999 0 -0.87 6 6
INCENP 0.008 0.009 -9999 0 -10000 0 0
KLHL13 -0.008 0.13 -9999 0 -0.75 16 16
BUB1 -0.38 0.44 -9999 0 -0.86 225 225
hSgo1/Aurora B/Survivin -0.4 0.49 -9999 0 -0.85 247 247
EVI5 0.009 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.34 -9999 0 -0.71 195 195
SGOL1 -0.016 0.16 -9999 0 -0.86 18 18
CENPA -0.3 0.35 -9999 0 -0.63 247 247
NCAPG -0.29 0.42 -9999 0 -0.86 174 174
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 240 240
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 240 240
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.14 0.33 -9999 0 -0.86 87 87
NPM1 -0.22 0.24 -9999 0 -0.47 240 240
RASA1 0.014 0.034 -9999 0 -0.75 1 1
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 240 240
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.35 0.38 -9999 0 -0.77 201 201
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.22 0.24 -9999 0 -0.47 240 240
MYLK -0.17 0.21 -9999 0 -0.39 240 240
KIF23 -0.007 0.11 -9999 0 -0.88 8 8
VIM -0.35 0.4 -9999 0 -0.73 254 254
RACGAP1 0.003 0.056 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.22 0.24 -9999 0 -0.47 240 240
Chromosomal passenger complex -0.35 0.41 -9999 0 -0.76 234 234
Chromosomal passenger complex/EVI5 -0.37 0.48 -9999 0 -1 145 145
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.48 -10000 0 -1.2 101 101
PCK1 -0.94 0.71 -10000 0 -1.4 306 306
HNF4A -0.58 0.58 -10000 0 -1.4 133 133
KCNJ11 -0.45 0.51 -10000 0 -1.3 92 92
AKT1 -0.17 0.18 -10000 0 -10000 0 0
response to starvation -0.02 0.038 -10000 0 -10000 0 0
DLK1 -0.56 0.58 -10000 0 -1.3 144 144
NKX2-1 -0.056 0.21 0.58 1 -0.84 4 5
ACADM -0.45 0.48 -10000 0 -1.2 95 95
TAT -0.52 0.35 -10000 0 -0.93 157 157
CEBPB -0.024 0.14 -10000 0 -0.92 12 12
CEBPA -0.019 0.13 -10000 0 -0.9 10 10
TTR -0.89 0.48 -10000 0 -1.2 328 328
PKLR -0.51 0.56 -10000 0 -1.4 117 117
APOA1 -0.56 0.56 -10000 0 -1.3 132 132
CPT1C -0.45 0.48 -10000 0 -1.2 107 107
ALAS1 -0.17 0.19 -10000 0 -10000 0 0
TFRC -0.63 0.42 -10000 0 -1 211 211
FOXF1 -0.002 0.12 -10000 0 -0.84 10 10
NF1 0.025 0.001 -10000 0 -10000 0 0
HNF1A (dimer) -0.003 0.087 -10000 0 -0.79 5 5
CPT1A -0.45 0.48 -10000 0 -1.2 109 109
HMGCS1 -0.45 0.48 -10000 0 -1.2 110 110
NR3C1 0.003 0.065 -10000 0 -0.96 1 1
CPT1B -0.47 0.5 -10000 0 -1.2 106 106
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.017 0.005 -10000 0 -10000 0 0
GCK -0.46 0.49 -10000 0 -1.2 117 117
CREB1 -0.028 0.065 -10000 0 -10000 0 0
IGFBP1 -0.32 0.42 -10000 0 -1 115 115
PDX1 -0.19 0.22 -10000 0 -1 6 6
UCP2 -0.45 0.48 -10000 0 -1.2 101 101
ALDOB -0.94 0.62 -10000 0 -1.3 348 348
AFP -0.71 0.5 -10000 0 -1 296 296
BDH1 -0.6 0.57 -10000 0 -1.3 174 174
HADH -0.44 0.49 -10000 0 -1.2 99 99
F2 -0.66 0.62 -10000 0 -1.4 177 177
HNF1A -0.003 0.087 -10000 0 -0.79 5 5
G6PC -0.81 0.66 -10000 0 -1.5 241 241
SLC2A2 -0.32 0.48 -10000 0 -1.7 45 45
INS 0.01 0.055 -10000 0 -10000 0 0
FOXA1 -0.37 0.39 -10000 0 -1 118 118
FOXA3 -0.61 0.37 -10000 0 -0.86 313 313
FOXA2 -0.52 0.57 -10000 0 -1.4 111 111
ABCC8 -0.45 0.49 -10000 0 -1.2 101 101
ALB -1.2 0.49 -10000 0 -1.4 438 438
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.054 -10000 0 -0.49 6 6
fibroblast growth factor receptor signaling pathway -0.006 0.053 -10000 0 -0.49 6 6
LAMA1 -0.007 0.13 -10000 0 -0.76 15 15
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.56 108 108
SMAD2 0.045 0.021 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.022 -10000 0 -0.49 1 1
GPC1/Laminin alpha1 -0.018 0.099 -10000 0 -0.57 16 16
TDGF1 -0.56 0.32 -10000 0 -0.75 382 382
CRIPTO/GPC1 -0.42 0.24 -10000 0 -0.56 382 382
APP/GPC1 -0.002 0.035 -10000 0 -0.56 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.35 0.22 -10000 0 -0.48 382 382
FLT1 0.007 0.087 -10000 0 -0.86 5 5
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.021 -10000 0 -0.48 1 1
SERPINC1 -0.055 0.22 -10000 0 -0.76 45 45
FYN -0.35 0.22 -10000 0 -0.48 382 382
FGR -0.36 0.22 -10000 0 -0.48 382 382
positive regulation of MAPKKK cascade -0.36 0.24 -10000 0 -0.49 382 382
SLIT2 -0.15 0.31 -10000 0 -0.75 107 107
GPC1/NRG -0.019 0.1 -10000 0 -0.56 17 17
NRG1 -0.008 0.13 -10000 0 -0.75 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.26 0.3 -10000 0 -0.58 226 226
LYN -0.35 0.22 -10000 0 -0.48 382 382
mol:Spermine 0.014 0.026 -10000 0 -0.57 1 1
cell growth -0.006 0.053 -10000 0 -0.49 6 6
BMP signaling pathway -0.014 0.034 0.75 1 -10000 0 1
SRC -0.35 0.22 -10000 0 -0.48 382 382
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.064 0.24 -10000 0 -0.86 43 43
GPC1 0.014 0.034 -10000 0 -0.75 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.37 0.44 -10000 0 -0.86 225 225
BLK -0.39 0.26 -10000 0 -0.52 387 387
HCK -0.38 0.24 -10000 0 -0.5 392 392
FGF2 0.008 0.078 -10000 0 -0.77 5 5
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.087 -10000 0 -0.86 5 5
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.035 -10000 0 -0.56 2 2
ATIII/GPC1 -0.052 0.17 -10000 0 -0.58 46 46
PLA2G2A/GPC1 -0.058 0.19 -10000 0 -0.66 44 44
LCK -0.38 0.24 -10000 0 -0.5 390 390
neuron differentiation -0.019 0.1 -10000 0 -0.56 17 17
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.034 -10000 0 -0.75 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.2 0.68 -10000 0 -1.2 122 122
PLK1 -0.11 0.41 -10000 0 -0.79 128 128
BIRC5 -0.14 0.43 -10000 0 -0.78 151 151
HSPA1B -0.2 0.68 -10000 0 -1.2 122 122
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.2 0.69 -10000 0 -1.2 123 123
FOXM1 -0.38 1 -10000 0 -1.8 133 133
XRCC1 -0.2 0.68 -10000 0 -1.2 119 119
FOXM1B/p19 -0.5 0.49 0.51 1 -1.2 133 134
Cyclin D1/CDK4 -0.19 0.61 -10000 0 -1.1 109 109
CDC2 -0.22 0.72 -10000 0 -1.3 133 133
TGFA -0.17 0.6 -10000 0 -1.1 112 112
SKP2 -0.2 0.68 -10000 0 -1.2 122 122
CCNE1 0.003 0.1 -10000 0 -0.87 7 7
CKS1B -0.2 0.68 -10000 0 -1.2 121 121
RB1 -0.19 0.26 -10000 0 -0.69 90 90
FOXM1C/SP1 -0.29 0.78 -10000 0 -1.5 130 130
AURKB -0.26 0.46 -10000 0 -0.76 211 211
CENPF -0.22 0.72 -10000 0 -1.3 120 120
CDK4 0.02 0.022 -10000 0 -10000 0 0
MYC -0.16 0.6 -10000 0 -1 120 120
CHEK2 0.038 0.063 -10000 0 -0.91 1 1
ONECUT1 -0.2 0.65 -10000 0 -1.2 119 119
CDKN2A -0.82 0.17 -10000 0 -0.85 487 487
LAMA4 -0.29 0.7 -10000 0 -1.2 135 135
FOXM1B/HNF6 -0.29 0.79 -10000 0 -1.5 122 122
FOS -0.21 0.69 -10000 0 -1.2 125 125
SP1 0.017 0.005 -10000 0 -10000 0 0
CDC25B -0.2 0.68 -10000 0 -1.2 119 119
response to radiation 0.013 0.05 -10000 0 -10000 0 0
CENPB -0.2 0.68 -10000 0 -1.2 122 122
CENPA -0.3 0.78 -10000 0 -1.4 144 144
NEK2 -0.25 0.75 -10000 0 -1.4 132 132
HIST1H2BA -0.21 0.68 -10000 0 -1.2 122 122
CCNA2 -0.16 0.36 -10000 0 -0.88 100 100
EP300 0.014 0.034 -10000 0 -0.75 1 1
CCNB1/CDK1 -0.28 0.81 -10000 0 -1.5 127 127
CCNB2 -0.25 0.76 -10000 0 -1.4 133 133
CCNB1 -0.22 0.72 -10000 0 -1.3 123 123
ETV5 -0.2 0.68 -10000 0 -1.2 118 118
ESR1 -0.2 0.68 -10000 0 -1.2 120 120
CCND1 -0.19 0.63 -10000 0 -1.1 116 116
GSK3A 0.036 0.041 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.083 0.28 -10000 0 -0.64 101 101
CDK2 0.015 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.43 0.59 -10000 0 -1.3 137 137
GAS1 -0.24 0.71 -10000 0 -1.2 135 135
MMP2 -0.2 0.68 -10000 0 -1.2 122 122
RB1/FOXM1C -0.22 0.67 -10000 0 -1.2 120 120
CREBBP 0.016 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.17 0.26 -10000 0 -0.65 69 69
TBX21 -0.54 0.68 -10000 0 -1.3 198 198
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.022 -10000 0 -10000 0 0
IL12RB1 -0.27 0.43 -10000 0 -0.9 156 156
GADD45B -0.29 0.43 -10000 0 -0.83 135 135
IL12RB2 -0.11 0.31 -10000 0 -0.87 73 73
GADD45G -0.31 0.43 -10000 0 -0.84 143 143
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.002 0.1 -10000 0 -0.87 7 7
IL2RA -0.16 0.35 -10000 0 -0.86 102 102
IFNG -0.38 0.44 -10000 0 -0.86 230 230
STAT3 (dimer) -0.37 0.47 -10000 0 -0.88 195 195
HLA-DRB5 -0.039 0.21 -10000 0 -0.86 32 32
FASLG -0.6 0.7 -10000 0 -1.3 221 221
NF kappa B2 p52/RelB -0.52 0.54 -10000 0 -1.1 202 202
CD4 0.002 0.11 -10000 0 -0.86 8 8
SOCS1 0.005 0.095 -10000 0 -0.86 6 6
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 228 228
CD3E -0.34 0.43 -10000 0 -0.87 204 204
CD3G -0.33 0.43 -10000 0 -0.87 199 199
IL12Rbeta2/JAK2 -0.085 0.25 -10000 0 -0.68 73 73
CCL3 -0.48 0.63 -10000 0 -1.2 185 185
CCL4 -0.5 0.66 -10000 0 -1.3 181 181
HLA-A 0.009 0.04 -10000 0 -0.86 1 1
IL18/IL18R -0.12 0.3 -10000 0 -0.6 141 141
NOS2 -0.36 0.5 -10000 0 -0.96 159 159
IL12/IL12R/TYK2/JAK2/SPHK2 -0.16 0.26 -10000 0 -0.65 66 66
IL1R1 -0.44 0.59 -10000 0 -1.2 164 164
IL4 0.013 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.022 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.7 0.82 -10000 0 -1.5 248 248
RAB7A -0.23 0.37 -10000 0 -0.79 49 49
lysosomal transport -0.22 0.36 -10000 0 -0.74 50 50
FOS -0.38 0.5 -10000 0 -0.95 195 195
STAT4 (dimer) -0.4 0.53 -10000 0 -0.99 191 191
STAT5A (dimer) -0.65 0.61 -10000 0 -1.3 230 230
GZMA -0.56 0.7 -10000 0 -1.3 209 209
GZMB -0.53 0.67 -10000 0 -1.3 193 193
HLX -0.085 0.28 -10000 0 -0.86 58 58
LCK -0.52 0.69 -10000 0 -1.3 202 202
TCR/CD3/MHC II/CD4 -0.37 0.47 -10000 0 -0.86 222 222
IL2/IL2R -0.42 0.42 -10000 0 -0.71 300 300
MAPK14 -0.3 0.44 -10000 0 -0.83 153 153
CCR5 -0.45 0.59 -10000 0 -1.1 188 188
IL1B 0.002 0.097 -10000 0 -0.86 6 6
STAT6 -0.082 0.15 -10000 0 -10000 0 0
STAT4 -0.036 0.21 -10000 0 -0.86 30 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.039 -10000 0 -0.86 1 1
NFKB1 0.014 0.034 -10000 0 -0.75 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.094 0.29 -10000 0 -0.89 60 60
CD8A -0.39 0.44 -10000 0 -0.87 230 230
CD8B -0.3 0.42 -10000 0 -0.87 181 181
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.16 0.26 0.64 69 -10000 0 69
IL2RB -0.45 0.44 -10000 0 -0.86 267 267
proteasomal ubiquitin-dependent protein catabolic process -0.36 0.47 -10000 0 -0.88 186 186
IL2RG -0.043 0.22 -10000 0 -0.86 34 34
IL12 -0.071 0.24 -10000 0 -0.71 61 61
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.27 0.41 -10000 0 -0.87 165 165
IL2 -0.008 0.12 -10000 0 -0.86 10 10
SPHK2 0.013 0.048 -10000 0 -0.75 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.047 -10000 0 -0.91 1 1
IL12/IL12R/TYK2/JAK2 -0.58 0.78 -10000 0 -1.4 211 211
MAP2K3 -0.3 0.44 -10000 0 -0.83 157 157
RIPK2 0.014 0.039 -10000 0 -0.86 1 1
MAP2K6 -0.3 0.44 -10000 0 -0.83 157 157
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.078 -10000 0 -0.86 4 4
IL18RAP -0.21 0.39 -10000 0 -0.87 129 129
IL12Rbeta1/TYK2 -0.21 0.34 -10000 0 -0.72 156 156
EOMES -0.3 0.37 -10000 0 -0.74 209 209
STAT1 (dimer) -0.44 0.51 -10000 0 -0.97 219 219
T cell proliferation -0.26 0.37 -10000 0 -0.68 162 162
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.81 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.37 0.33 -10000 0 -0.76 173 173
ATF2 -0.27 0.41 -10000 0 -0.79 125 125
PDGFR-alpha signaling 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
PDGFRA -0.28 0.37 -9999 0 -0.75 196 196
PDGF/PDGFRA/CRKL -0.21 0.26 -9999 0 -0.55 196 196
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.52 1 1
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.56 199 199
AP1 -0.16 0.25 -9999 0 -1.2 13 13
mol:IP3 -0.19 0.29 -9999 0 -0.56 196 196
PLCG1 -0.2 0.29 -9999 0 -0.56 196 196
PDGF/PDGFRA/alphaV Integrin -0.21 0.26 -9999 0 -0.55 196 196
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.56 196 196
CAV3 -0.001 0.067 -9999 0 -0.86 3 3
CAV1 -0.047 0.23 -9999 0 -0.86 36 36
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/Shf -0.21 0.27 -9999 0 -0.55 197 197
FOS -0.12 0.27 -9999 0 -1.2 13 13
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.26 -9999 0 -0.54 196 196
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
mol:DAG -0.19 0.29 -9999 0 -0.56 196 196
PDGF/PDGFRA -0.28 0.37 -9999 0 -0.74 196 196
actin cytoskeleton reorganization -0.21 0.26 -9999 0 -0.54 196 196
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
PI3K -0.18 0.22 -9999 0 -0.46 197 197
PDGF/PDGFRA/Crk/C3G -0.18 0.22 -9999 0 -0.46 196 196
JAK1 -0.19 0.28 -9999 0 -0.54 196 196
ELK1/SRF -0.15 0.19 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.034 -9999 0 -0.75 1 1
CSNK2A1 0.018 0.022 -9999 0 -10000 0 0
GO:0007205 -0.2 0.3 -9999 0 -0.57 196 196
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/SHB -0.21 0.26 -9999 0 -0.55 196 196
PDGF/PDGFRA/Caveolin-1 -0.26 0.3 -9999 0 -0.58 225 225
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.26 -9999 0 -0.49 196 196
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
PDGF/PDGFRA/Crk -0.21 0.26 -9999 0 -0.55 196 196
JAK-STAT cascade -0.19 0.28 -9999 0 -0.54 196 196
cell proliferation -0.21 0.26 -9999 0 -0.54 197 197
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 -0.14 0.28 -9999 0 -0.67 102 102
alphaM/beta2 Integrin/GPIbA -0.13 0.28 -9999 0 -0.67 98 98
alphaM/beta2 Integrin/proMMP-9 -0.4 0.42 -9999 0 -0.74 270 270
PLAUR -0.029 0.19 -9999 0 -0.86 26 26
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.28 -9999 0 -0.67 97 97
AGER -0.14 0.33 -9999 0 -0.86 88 88
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.042 0.22 -9999 0 -0.86 33 33
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.22 0.33 -9999 0 -0.66 163 163
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.41 0.44 -9999 0 -0.86 243 243
CYR61 0.007 0.083 -9999 0 -0.75 6 6
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.56 113 113
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.019 0.16 -9999 0 -0.75 23 23
MYH2 -0.35 0.26 -9999 0 -0.64 182 182
MST1R 0.005 0.093 -9999 0 -0.78 7 7
leukocyte activation during inflammatory response -0.28 0.35 -9999 0 -0.63 216 216
APOB -0.27 0.41 -9999 0 -0.85 167 167
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.006 0.093 -9999 0 -0.84 6 6
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.034 -9999 0 -0.75 1 1
alphaM/beta2 Integrin/CTGF -0.14 0.29 -9999 0 -0.67 102 102
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.54 218 218
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.003 0.13 -9999 0 -0.86 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.24 -9999 0 -0.53 218 218
cell adhesion -0.13 0.28 -9999 0 -0.67 98 98
NFKB1 -0.17 0.37 -9999 0 -0.95 60 60
THY1 0.014 0.034 -9999 0 -0.75 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.28 -9999 0 -0.59 168 168
alphaM/beta2 Integrin/LRP/tPA -0.13 0.27 -9999 0 -0.62 99 99
IL6 -0.2 0.41 -9999 0 -0.92 95 95
ITGB2 -0.15 0.34 -9999 0 -0.86 95 95
elevation of cytosolic calcium ion concentration -0.15 0.29 -9999 0 -0.63 117 117
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.26 -9999 0 -0.62 97 97
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.13 0.28 -9999 0 -0.71 62 62
alphaM/beta2 Integrin/uPA/Plg -0.35 0.34 -9999 0 -0.78 133 133
RhoA/GTP -0.37 0.27 -9999 0 -0.68 182 182
positive regulation of phagocytosis -0.25 0.27 -9999 0 -0.7 107 107
Ron/MSP -0.018 0.11 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.15 0.3 -9999 0 -0.64 117 117
alphaM/beta2 Integrin/uPAR -0.16 0.32 -9999 0 -0.7 113 113
PLAU 0.002 0.1 -9999 0 -0.75 9 9
PLAT -0.004 0.12 -9999 0 -0.75 13 13
actin filament polymerization -0.33 0.24 -9999 0 -0.61 182 182
MST1 0.002 0.11 -9999 0 -0.85 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.28 0.36 -9999 0 -0.64 216 216
TNF -0.15 0.34 -9999 0 -0.84 64 64
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.14 0.28 -9999 0 -0.66 106 106
fibrinolysis -0.35 0.33 -9999 0 -0.76 133 133
HCK -0.033 0.2 -9999 0 -0.86 28 28
dendritic cell antigen processing and presentation -0.3 0.24 -9999 0 -0.53 218 218
VTN -0.1 0.28 -9999 0 -0.76 78 78
alphaM/beta2 Integrin/CYR61 -0.14 0.28 -9999 0 -0.66 103 103
LPA 0.002 0.067 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.4 -9999 0 -0.69 272 272
FN1 -0.05 0.23 -9999 0 -0.86 38 38
alphaM/beta2 Integrin/Thy1 -0.13 0.28 -9999 0 -0.67 98 98
MPO -0.013 0.15 -9999 0 -0.86 16 16
KNG1 -0.56 0.32 -9999 0 -0.75 379 379
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.33 0.26 -9999 0 -0.64 171 171
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.39 0.38 -9999 0 -0.75 265 265
CTGF 0.005 0.089 -9999 0 -0.75 7 7
alphaM/beta2 Integrin/Hck -0.16 0.35 -9999 0 -0.79 101 101
ITGAM -0.02 0.17 -9999 0 -0.86 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.34 -9999 0 -0.74 106 106
HP -0.2 0.38 -9999 0 -0.86 127 127
leukocyte adhesion -0.18 0.27 -9999 0 -0.81 51 51
SELP -0.019 0.16 -9999 0 -0.75 23 23
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.41 0.54 -9999 0 -0.91 228 228
MAP4K1 -0.33 0.43 -9999 0 -0.86 201 201
MAP3K8 0.012 0.055 -9999 0 -0.86 2 2
PRKCB 0.007 0.082 -9999 0 -0.82 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.15 0.3 -9999 0 -0.62 120 120
JUN 0.003 0.075 -9999 0 -0.53 4 4
MAP3K7 -0.15 0.3 -9999 0 -0.62 120 120
GRAP2 -0.043 0.22 -9999 0 -0.86 34 34
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.13 0.29 -9999 0 -0.59 120 120
LAT -0.23 0.4 -9999 0 -0.86 144 144
LCP2 -0.04 0.21 -9999 0 -0.86 32 32
MAPK8 -0.009 0.079 -9999 0 -0.57 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.2 0.29 -9999 0 -0.66 120 120
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.39 0.51 -9999 0 -1.2 120 120
IL4-mediated signaling 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
BCL2L1 -0.48 0.48 -10000 0 -1.2 105 105
STAT6 (cleaved dimer) -0.58 0.5 -10000 0 -1.2 156 156
IGHG1 -0.17 0.19 -10000 0 -0.68 11 11
IGHG3 -0.47 0.46 -10000 0 -1.1 117 117
AKT1 -0.28 0.34 -10000 0 -0.84 81 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.25 0.32 -10000 0 -0.81 85 85
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.81 61 61
THY1 -0.48 0.48 -10000 0 -1.2 89 89
MYB -0.22 0.39 -10000 0 -0.86 139 139
HMGA1 0.014 0.039 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.42 -10000 0 -1 114 114
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.8 63 63
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.009 0.078 -10000 0 -0.86 4 4
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.48 -10000 0 -1.2 141 141
SOCS1 -0.33 0.34 -10000 0 -0.83 61 61
SOCS3 -0.3 0.34 -10000 0 -0.95 57 57
FCER2 -0.41 0.44 -10000 0 -1.2 72 72
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.5 0.5 -10000 0 -1.3 96 96
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.28 -10000 0 -0.79 52 52
T cell proliferation -0.5 0.52 -10000 0 -1.2 118 118
IL4R/JAK1 -0.48 0.48 -10000 0 -1.2 105 105
EGR2 -0.49 0.5 -10000 0 -1.3 88 88
JAK2 0.007 0.024 -10000 0 -10000 0 0
JAK3 -0.16 0.36 -10000 0 -0.86 104 104
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
JAK1 0.007 0.016 -10000 0 -10000 0 0
COL1A2 -0.21 0.3 -10000 0 -0.89 66 66
CCL26 -0.49 0.49 -10000 0 -1.2 92 92
IL4R -0.51 0.51 -10000 0 -1.3 105 105
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.55 0.56 -10000 0 -1.3 125 125
IL13RA1 0.007 0.024 -10000 0 -10000 0 0
IRF4 -0.27 0.42 -10000 0 -0.96 123 123
ARG1 -0.17 0.26 -10000 0 -0.78 42 42
CBL -0.36 0.4 -10000 0 -0.96 106 106
GTF3A 0.011 0.029 -10000 0 -10000 0 0
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
IL13RA1/JAK2 -0.006 0.044 -10000 0 -10000 0 0
IRF4/BCL6 -0.27 0.38 -10000 0 -0.9 119 119
CD40LG -0.076 0.29 -10000 0 -0.91 53 53
MAPK14 -0.35 0.4 -10000 0 -0.98 96 96
mitosis -0.26 0.32 -10000 0 -0.79 81 81
STAT6 -0.55 0.56 -10000 0 -1.4 112 112
SPI1 -0.098 0.3 -10000 0 -0.86 68 68
RPS6KB1 -0.24 0.31 -10000 0 -0.8 61 61
STAT6 (dimer) -0.55 0.56 -10000 0 -1.4 112 112
STAT6 (dimer)/PARP14 -0.51 0.52 -10000 0 -1.3 114 114
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.36 -10000 0 -0.91 93 93
FRAP1 -0.28 0.34 -10000 0 -0.84 81 81
LTA -0.6 0.56 -10000 0 -1.3 144 144
FES 0.013 0.048 -10000 0 -0.75 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 112 -10000 0 112
CCL11 -0.69 0.61 -10000 0 -1.3 209 209
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.29 0.34 -10000 0 -0.88 85 85
IL2RG -0.038 0.22 -10000 0 -0.85 34 34
IL10 -0.5 0.51 -10000 0 -1.3 99 99
IRS1 0.011 0.059 -10000 0 -0.75 3 3
IRS2 0.002 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.13 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 91 91
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.38 -10000 0 -0.91 84 84
COL1A1 -0.41 0.43 -10000 0 -0.92 192 192
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.49 -10000 0 -1.3 82 82
IL2R gamma/JAK3 -0.16 0.37 -10000 0 -0.83 108 108
TFF3 -0.5 0.51 -10000 0 -1.2 107 107
ALOX15 -0.48 0.48 -10000 0 -1.2 88 88
MYBL1 -0.047 0.23 -10000 0 -0.86 36 36
T-helper 2 cell differentiation -0.43 0.42 -10000 0 -0.99 115 115
SHC1 0.014 0.039 -10000 0 -0.86 1 1
CEBPB -0.001 0.14 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.3 -10000 0 -0.78 67 67
mol:PI-3-4-5-P3 -0.28 0.34 -10000 0 -0.84 81 81
PI3K -0.3 0.36 -10000 0 -0.92 81 81
DOK2 -0.038 0.21 -10000 0 -0.86 31 31
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.27 -10000 0 -0.77 53 53
ITGB3 -0.48 0.49 -10000 0 -1.2 92 92
PIGR -0.84 0.71 -10000 0 -1.5 260 260
IGHE 0.027 0.091 0.29 7 -0.37 4 11
MAPKKK cascade -0.21 0.27 -10000 0 -0.75 53 53
BCL6 0.013 0.005 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 96 96
RETNLB -0.49 0.48 -10000 0 -1.2 91 91
SELP -0.51 0.53 -10000 0 -1.3 97 97
AICDA -0.62 0.55 -10000 0 -1.2 174 174
EGFR-dependent Endothelin signaling events

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
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0 0.11 -9999 0 -0.85 9 9
EGF/EGFR -0.38 0.16 -9999 0 -0.86 26 26
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.36 0.14 -9999 0 -0.9 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.055 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 455 455
EGF/EGFR dimer/SHC -0.44 0.16 -9999 0 -0.49 456 456
mol:GDP -0.36 0.14 -9999 0 -0.88 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.014 0.16 -9999 0 -0.86 17 17
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.33 0.13 -9999 0 -0.82 10 10
SHC1 0.014 0.039 -9999 0 -0.86 1 1
HRAS/GDP -0.34 0.13 -9999 0 -0.82 10 10
FRAP1 -0.35 0.13 -9999 0 -0.85 9 9
EGF/EGFR dimer -0.51 0.18 -9999 0 -0.57 456 456
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.025 0.12 -9999 0 -0.66 19 19
Aurora C signaling

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
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.25 0.27 -9999 0 -0.53 241 241
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.065 0.068 -9999 0 -10000 0 0
AURKB -0.4 0.44 -9999 0 -0.86 240 240
AURKC 0.012 0.055 -9999 0 -0.86 2 2
Syndecan-1-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
TGFB1 0.007 0.087 -9999 0 -0.86 5 5
CCL5 -0.36 0.43 -9999 0 -0.86 215 215
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.59 89 89
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 -0.2 0.22 -9999 0 -0.56 89 89
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.56 89 89
MAPK3 -0.16 0.2 -9999 0 -0.54 51 51
HGF/MET -0.034 0.15 -9999 0 -0.66 26 26
TGFB1/TGF beta receptor Type II 0.007 0.087 -9999 0 -0.86 5 5
BSG 0.014 0.039 -9999 0 -0.86 1 1
keratinocyte migration -0.2 0.21 -9999 0 -0.55 89 89
Syndecan-1/RANTES -0.42 0.33 -9999 0 -0.68 268 268
Syndecan-1/CD147 -0.2 0.19 -9999 0 -0.53 90 90
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 89 89
LAMA5 0.014 0.034 -9999 0 -0.75 1 1
positive regulation of cell-cell adhesion -0.21 0.18 -9999 0 -0.52 89 89
MMP7 -0.12 0.3 -9999 0 -0.76 90 90
HGF -0.021 0.17 -9999 0 -0.8 23 23
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.57 89 89
Syndecan-1/HGF/MET -0.23 0.22 -9999 0 -0.58 105 105
regulation of cell adhesion -0.15 0.2 -9999 0 -0.67 15 15
HPSE 0.013 0.048 -9999 0 -0.75 2 2
positive regulation of cell migration -0.22 0.23 -9999 0 -0.59 89 89
SDC1 -0.22 0.23 -9999 0 -0.6 89 89
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.59 89 89
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.087 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.41 0.44 -9999 0 -0.86 243 243
MAPK1 -0.16 0.2 -9999 0 -0.54 51 51
homophilic cell adhesion -0.22 0.22 -9999 0 -0.58 89 89
MMP1 -0.15 0.34 -9999 0 -0.83 99 99
Glypican 2 network

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
MDK -0.048 0.23 -9999 0 -0.86 37 37
GPC2 -0.087 0.28 -9999 0 -0.86 59 59
GPC2/Midkine -0.12 0.28 -9999 0 -0.73 85 85
neuron projection morphogenesis -0.12 0.28 -9999 0 -0.73 85 85
HIF-2-alpha transcription factor network

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
MMP14 -0.027 0.081 -10000 0 -0.73 6 6
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.011 0.065 -10000 0 -0.82 3 3
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.64 3 3
EPO -0.4 0.41 -10000 0 -0.9 140 140
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.014 -10000 0 -10000 0 0
SERPINE1 -0.34 0.41 -10000 0 -0.92 112 112
FLT1 -0.018 0.078 -10000 0 -0.76 5 5
ADORA2A -0.3 0.34 -10000 0 -0.82 75 75
germ cell development -0.39 0.44 -10000 0 -0.88 193 193
SLC11A2 -0.28 0.34 -10000 0 -0.81 75 75
BHLHE40 -0.28 0.34 -10000 0 -0.81 75 75
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.52 205 205
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.023 0.058 -10000 0 -1.2 1 1
KDR -0.015 0.067 -10000 0 -1.4 1 1
PGK1 -0.28 0.34 -10000 0 -0.81 75 75
SIRT1 0.014 0.005 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.34 0.42 -10000 0 -0.86 147 147
EPAS1 -0.27 0.19 -10000 0 -0.44 208 208
SP1 0.026 0.005 -10000 0 -10000 0 0
ABCG2 -0.28 0.34 -10000 0 -0.82 76 76
EFNA1 -0.28 0.34 -10000 0 -0.81 76 76
FXN -0.3 0.34 -10000 0 -0.82 75 75
POU5F1 -0.42 0.47 -10000 0 -0.94 193 193
neuron apoptosis 0.33 0.4 0.82 147 -10000 0 147
EP300 0.014 0.034 -10000 0 -0.75 1 1
EGLN3 -0.76 0.3 -10000 0 -0.87 444 444
EGLN2 0.012 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.042 -10000 0 -0.54 3 3
VHL 0.016 0 -10000 0 -10000 0 0
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.31 0.37 -10000 0 -0.9 80 80
TWIST1 -0.3 0.34 -10000 0 -0.83 78 78
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.56 76 76
VEGFA -0.46 0.49 -10000 0 -0.94 231 231
CREBBP 0.016 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.13 0.26 -10000 0 -0.58 101 101
ACTA1 -0.19 0.35 -10000 0 -0.67 162 162
NUMA1 -0.13 0.26 -10000 0 -0.58 101 101
SPTAN1 -0.18 0.35 -10000 0 -0.66 161 161
LIMK1 -0.18 0.35 -10000 0 -0.66 162 162
BIRC3 -0.12 0.32 -10000 0 -0.86 78 78
BIRC2 0.012 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.46 -10000 0 -0.86 178 178
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.015 0.003 -10000 0 -10000 0 0
PTK2 -0.13 0.26 -10000 0 -0.49 161 161
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.34 -10000 0 -0.65 161 161
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.18 0.35 -10000 0 -0.66 161 161
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.29 0.28 -10000 0 -0.54 274 274
BID -0.088 0.17 -10000 0 -0.37 99 99
MAP3K1 -0.043 0.11 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.18 0.35 -10000 0 -0.66 161 161
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.012 0.094 -10000 0 -0.21 35 35
neuron apoptosis 0.011 0.045 -10000 0 -0.62 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.34 -10000 0 -0.77 99 99
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.048 0.15 -10000 0 -0.52 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.34 -10000 0 -0.77 99 99
CASP7 0.05 0.13 0.34 78 -10000 0 78
KRT18 -0.001 0.046 -10000 0 -0.3 2 2
apoptosis -0.17 0.32 -10000 0 -0.69 106 106
DFFA -0.18 0.35 -10000 0 -0.8 99 99
DFFB -0.18 0.35 -10000 0 -0.66 161 161
PARP1 -0.012 0.095 0.21 35 -10000 0 35
actin filament polymerization 0.16 0.32 0.72 100 -10000 0 100
TNF 0.003 0.1 -10000 0 -0.8 8 8
CYCS -0.067 0.13 -10000 0 -0.28 99 99
SATB1 -0.035 0.15 -10000 0 -0.48 3 3
SLK -0.18 0.35 -10000 0 -0.66 161 161
p15 BID/BAX -0.072 0.15 -10000 0 -10000 0 0
CASP2 0.031 0.089 -10000 0 -10000 0 0
JNK cascade 0.042 0.11 -10000 0 -10000 0 0
CASP3 -0.2 0.37 -10000 0 -0.71 161 161
LMNB2 0.012 0.085 -10000 0 -0.39 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.08 0.19 -10000 0 -0.52 78 78
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.54 274 274
stress fiber formation -0.18 0.34 -10000 0 -0.65 161 161
GZMB -0.32 0.5 -10000 0 -0.97 178 178
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.009 0.089 -10000 0 -0.36 7 7
APP 0.011 0.045 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.66 107 107
LMNA 0.011 0.085 -10000 0 -0.41 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.03 0.073 -10000 0 -0.41 7 7
LRDD 0.004 0.1 -10000 0 -0.84 7 7
SREBF1 -0.18 0.35 -10000 0 -0.66 162 162
APAF-1/Caspase 9 -0.009 0.063 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.12 0.26 -10000 0 -0.57 101 101
CFL2 -0.16 0.33 -10000 0 -0.75 100 100
GAS2 -0.2 0.36 -10000 0 -0.66 165 165
positive regulation of apoptosis 0.016 0.085 -10000 0 -0.4 3 3
PRF1 -0.2 0.38 -10000 0 -0.86 126 126
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.073 -9999 0 -0.68 5 5
VEGFR1 homodimer/NRP1 -0.009 0.074 -9999 0 -0.62 7 7
mol:DAG -0.26 0.29 -9999 0 -0.52 281 281
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 226 226
CaM/Ca2+ -0.27 0.25 -9999 0 -0.92 7 7
HIF1A 0.019 0.058 -9999 0 -0.73 2 2
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.23 0.21 -9999 0 -0.94 6 6
PLCG1 -0.27 0.29 -9999 0 -0.52 281 281
NOS3 -0.18 0.24 -9999 0 -0.85 6 6
CBL 0.014 0.034 -9999 0 -0.75 1 1
mol:NO -0.17 0.24 -9999 0 -0.8 6 6
FLT1 0.031 0.088 -9999 0 -0.71 7 7
PGF -0.47 0.44 -9999 0 -0.86 280 280
VEGFR1 homodimer/NRP2/VEGFR121 -0.24 0.27 -9999 0 -0.53 231 231
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.76 6 6
endothelial cell proliferation -0.2 0.26 -9999 0 -0.86 8 8
mol:Ca2+ -0.26 0.29 -9999 0 -0.52 281 281
MAPK3 -0.21 0.26 -9999 0 -0.88 6 6
MAPK1 -0.21 0.26 -9999 0 -0.88 6 6
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
PLGF homodimer -0.47 0.44 -9999 0 -0.86 280 280
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.047 0.23 -9999 0 -0.86 36 36
VEGFA homodimer -0.37 0.44 -9999 0 -0.86 225 225
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 226 226
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.85 6 6
PI3K -0.27 0.25 -9999 0 -0.99 7 7
PRKCA -0.24 0.27 -9999 0 -0.89 7 7
PRKCB -0.24 0.28 -9999 0 -0.9 9 9
VEGFR1 homodimer/PLGF homodimer -0.32 0.29 -9999 0 -0.58 281 281
VEGFA -0.37 0.44 -9999 0 -0.86 225 225
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.52 281 281
RASA1 0.045 0.08 -9999 0 -0.65 6 6
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.031 0.088 -9999 0 -0.7 7 7
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.034 -9999 0 -0.75 1 1
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.8 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.25 -9999 0 -0.96 7 7
mol:L-citrulline -0.17 0.24 -9999 0 -0.8 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.94 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -0.53 227 227
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.93 7 7
PDPK1 -0.22 0.27 -9999 0 -1 6 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -1 5 5
mol:NADP -0.17 0.24 -9999 0 -0.8 6 6
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.25 -9999 0 -0.92 6 6
VEGFR1 homodimer/NRP2 -0.016 0.098 -9999 0 -0.61 12 12
IL23-mediated 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
CCL2 -0.26 0.48 -10000 0 -1.1 63 63
IL23A -0.24 0.47 -10000 0 -1.1 46 46
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.39 -10000 0 -1 76 76
positive regulation of T cell mediated cytotoxicity -0.29 0.52 -10000 0 -1.1 88 88
ITGA3 -0.24 0.47 -10000 0 -1 66 66
IL17F -0.15 0.34 -10000 0 -0.75 29 29
IL12B -0.088 0.29 -10000 0 -0.88 60 60
STAT1 (dimer) -0.28 0.5 -10000 0 -1.1 79 79
CD4 -0.25 0.47 -10000 0 -1.1 59 59
IL23 -0.28 0.48 -10000 0 -1.1 63 63
IL23R -0.014 0.15 -10000 0 -0.8 10 10
IL1B -0.26 0.48 -10000 0 -1.1 60 60
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.25 0.47 -10000 0 -1.1 67 67
TYK2 0.015 0.024 -10000 0 -10000 0 0
STAT4 -0.036 0.21 -10000 0 -0.86 30 30
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.22 0.39 -10000 0 -0.88 129 129
IL12RB1 -0.26 0.42 -10000 0 -0.89 156 156
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
IL12Rbeta1/TYK2 -0.2 0.34 -10000 0 -0.7 156 156
IL23R/JAK2 -0.012 0.16 -10000 0 -0.75 10 10
positive regulation of chronic inflammatory response -0.29 0.52 -10000 0 -1.1 88 88
natural killer cell activation 0.002 0.012 0.063 10 -10000 0 10
JAK2 0.021 0.034 -10000 0 -10000 0 0
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
NFKB1 0.01 0.034 -10000 0 -0.74 1 1
RELA 0.011 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.46 -10000 0 -1.1 63 63
ALOX12B -0.31 0.5 -10000 0 -1.1 77 77
CXCL1 -0.29 0.52 -10000 0 -1.1 82 82
T cell proliferation -0.29 0.52 -10000 0 -1.1 88 88
NFKBIA 0.011 0.009 -10000 0 -10000 0 0
IL17A -0.1 0.29 -10000 0 -0.6 5 5
PI3K -0.34 0.4 -10000 0 -1 87 87
IFNG -0.052 0.069 0.13 4 -0.12 229 233
STAT3 (dimer) -0.32 0.38 -10000 0 -1 76 76
IL18R1 -0.004 0.1 -10000 0 -0.81 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.19 0.38 -10000 0 -0.8 81 81
IL18/IL18R -0.17 0.28 -10000 0 -0.61 141 141
macrophage activation -0.017 0.018 -10000 0 -0.044 20 20
TNF -0.26 0.49 -10000 0 -1.1 67 67
STAT3/STAT4 -0.36 0.43 -10000 0 -1.1 96 96
STAT4 (dimer) -0.3 0.53 -10000 0 -1.2 89 89
IL18 -0.003 0.1 -10000 0 -0.86 7 7
IL19 -0.26 0.46 -10000 0 -1 67 67
STAT5A (dimer) -0.28 0.5 -10000 0 -1.1 82 82
STAT1 0.014 0.039 -10000 0 -0.86 1 1
SOCS3 0.012 0.055 -10000 0 -0.86 2 2
CXCL9 -0.4 0.59 -10000 0 -1.1 154 154
MPO -0.26 0.48 -10000 0 -1.1 67 67
positive regulation of humoral immune response -0.29 0.52 -10000 0 -1.1 88 88
IL23/IL23R/JAK2/TYK2 -0.31 0.54 -10000 0 -1.2 87 87
IL6 -0.3 0.53 -10000 0 -1.1 89 89
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.017 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 10 -10000 0 10
CD3E -0.39 0.6 -10000 0 -1.1 159 159
keratinocyte proliferation -0.29 0.52 -10000 0 -1.1 88 88
NOS2 -0.25 0.47 -10000 0 -1.1 67 67
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.006 0.13 -9999 0 -0.78 14 14
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.065 -9999 0 -0.82 3 3
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.048 -9999 0 -0.39 1 1
HIF1A -0.098 0.04 -9999 0 -0.42 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.035 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 487 487
ARNT/IPAS -0.016 0.097 -9999 0 -0.59 14 14
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.048 -9999 0 -0.39 1 1
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.049 -9999 0 -0.55 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.048 -9999 0 -0.39 1 1
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 443 443
HIF1A/RACK1/Elongin B/Elongin C -0.067 0.05 -9999 0 -0.59 3 3
VHL 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.048 -9999 0 -0.39 1 1
EGLN3 -0.75 0.29 -9999 0 -0.86 444 444
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.002 0.022 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.55 0.11 -9999 0 -0.57 487 487
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.6 0.31 -9999 0 -0.86 268 268
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.32 -9999 0 -0.84 81 81
SMAD9 -0.063 0.082 -9999 0 -0.58 9 9
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.52 18 18
BMP7/USAG1 -0.7 0.34 -9999 0 -0.8 441 441
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 14 14
SMAD1 0.002 0.042 -9999 0 -10000 0 0
BMP2 0.009 0.07 -9999 0 -0.78 4 4
SMAD1/SMAD1/SMAD4 0 0.001 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.35 -9999 0 -0.75 346 346
BMPR1A-1B/BAMBI -0.33 0.23 -9999 0 -0.48 349 349
AHSG -0.011 0.13 -9999 0 -0.86 11 11
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.007 0.059 -9999 0 -0.5 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.49 18 18
BMP2-4 (homodimer) -0.008 0.067 -9999 0 -0.58 7 7
RGMB 0.012 0.055 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.79 5 5
RGMA 0.008 0.075 -9999 0 -0.75 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.17 0.13 -9999 0 -0.56 18 18
BMP2-4/USAG1 -0.32 0.24 -9999 0 -0.88 7 7
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 14 14
SOSTDC1 -0.48 0.36 -9999 0 -0.75 327 327
BMP7/BMPR2/BMPR1A-1B -0.58 0.3 -9999 0 -0.86 249 249
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.095 -9999 0 -0.75 8 8
HFE2 -0.019 0.16 -9999 0 -0.86 18 18
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.018 0.1 -9999 0 -0.56 16 16
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.5 14 14
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.5 14 14
BMP7 (homodimer) -0.5 0.35 -9999 0 -0.75 340 340
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.023 0.12 -9999 0 -0.62 19 19
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.019 0.1 -9999 0 -0.54 18 18
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.33 -9999 0 -0.76 122 122
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.26 -9999 0 -0.56 346 346
CHRDL1 -0.38 0.38 -9999 0 -0.75 263 263
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.005 0.089 -9999 0 -0.75 7 7
SMURF2 0.014 0.034 -9999 0 -0.75 1 1
BMP2-4/CHRDL1 -0.25 0.25 -9999 0 -0.48 265 265
BMP2-4/GREM1 -0.12 0.22 -9999 0 -0.64 12 12
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.087 -9999 0 -0.54 9 9
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.5 0.36 -9999 0 -0.75 340 340
BMP6 0.004 0.095 -9999 0 -0.75 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.13 -9999 0 -0.46 18 18
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.18 -9999 0 -0.6 62 62
CHRD -0.002 0.12 -9999 0 -0.78 11 11
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 18 18
BMP4 0.011 0.059 -9999 0 -0.75 3 3
FST -0.074 0.25 -9999 0 -0.77 58 58
BMP2-4/NOG -0.096 0.21 -9999 0 -0.56 87 87
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.55 0.29 -9999 0 -0.81 249 249
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.25 0.26 -10000 0 -0.74 32 32
IHH -0.099 0.23 -10000 0 -0.82 46 46
SHH Np/Cholesterol/GAS1 -0.038 0.13 -10000 0 -0.45 42 42
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.037 0.13 0.45 42 -10000 0 42
SMO/beta Arrestin2 -0.15 0.15 -10000 0 -0.6 33 33
SMO -0.13 0.19 -10000 0 -0.64 33 33
AKT1 -0.042 0.093 -10000 0 -0.46 1 1
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.13 0.19 -10000 0 -0.63 33 33
STIL -0.096 0.17 -10000 0 -0.67 10 10
DHH N/PTCH2 -0.045 0.16 -10000 0 -0.63 36 36
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.62 36 36
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
DHH -0.001 0.11 -10000 0 -0.75 11 11
PTHLH -0.44 0.41 -10000 0 -0.74 315 315
determination of left/right symmetry -0.13 0.19 -10000 0 -0.63 33 33
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
skeletal system development -0.44 0.4 -10000 0 -0.73 315 315
IHH N/Hhip -0.2 0.31 -10000 0 -0.66 156 156
DHH N/Hhip -0.15 0.26 -10000 0 -0.58 135 135
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.19 -10000 0 -0.63 33 33
pancreas development -0.18 0.33 -10000 0 -0.76 126 126
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.033 0.19 -10000 0 -0.75 32 32
somite specification -0.13 0.19 -10000 0 -0.63 33 33
SHH Np/Cholesterol/PTCH1 -0.14 0.14 -10000 0 -0.55 36 36
SHH Np/Cholesterol/PTCH2 -0.036 0.13 -10000 0 -0.5 36 36
SHH Np/Cholesterol/Megalin -0.048 0.15 -10000 0 -0.49 50 50
SHH 0.017 0.088 -10000 0 -0.57 11 11
catabolic process -0.16 0.19 -10000 0 -0.65 32 32
SMO/Vitamin D3 -0.11 0.18 -10000 0 -0.58 36 36
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.46 132 132
LRP2 -0.051 0.22 -10000 0 -0.75 44 44
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.77 19 19
SHH Np/Cholesterol/BOC -0.01 0.065 -10000 0 -0.45 11 11
SHH Np/Cholesterol/CDO -0.071 0.18 -10000 0 -0.52 68 68
mesenchymal cell differentiation 0.12 0.21 0.46 132 -10000 0 132
mol:Vitamin D3 -0.11 0.17 -10000 0 -0.56 36 36
IHH N/PTCH2 -0.085 0.22 -10000 0 -0.62 69 69
CDON -0.085 0.28 -10000 0 -0.86 58 58
IHH N/PTCH1 -0.16 0.2 -10000 0 -0.66 32 32
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.56 44 44
PTCH2 -0.028 0.19 -10000 0 -0.86 25 25
SHH Np/Cholesterol -0.01 0.067 -10000 0 -0.46 11 11
PTCH1 -0.16 0.2 -10000 0 -0.66 32 32
HHIP -0.18 0.33 -10000 0 -0.76 126 126
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.16 0.23 -9999 0 -0.69 60 60
AP1 -0.16 0.21 -9999 0 -0.56 82 82
mol:PIP3 -0.24 0.34 -9999 0 -0.7 139 139
IKBKB -0.089 0.16 -9999 0 -0.34 71 71
AKT1 -0.17 0.21 -9999 0 -0.73 22 22
IKBKG -0.089 0.16 -9999 0 -0.34 83 83
MS4A2 -0.19 0.36 -9999 0 -0.86 113 113
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.035 -9999 0 -0.75 1 1
MAP3K1 -0.12 0.26 -9999 0 -0.6 77 77
mol:Ca2+ -0.16 0.24 -9999 0 -0.48 139 139
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.12 0.15 -9999 0 -0.54 21 21
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.002 0.031 -9999 0 -0.48 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.078 -9999 0 -0.86 4 4
PLD2 -0.18 0.28 -9999 0 -0.92 20 20
PTPN13 -0.07 0.16 -9999 0 -0.48 23 23
PTPN11 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.045 0.17 -9999 0 -0.41 4 4
SYK 0.008 0.049 -9999 0 -0.76 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.3 0.32 -9999 0 -0.76 135 135
LAT -0.26 0.3 -9999 0 -0.65 154 154
PAK2 -0.15 0.29 -9999 0 -0.64 110 110
NFATC2 -0.068 0.087 -9999 0 -0.63 2 2
HRAS -0.18 0.32 -9999 0 -0.7 117 117
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.04 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.32 -9999 0 -0.62 210 210
Antigen/IgE/Fc epsilon R1 -0.24 0.3 -9999 0 -0.58 210 210
mol:GDP -0.21 0.35 -9999 0 -0.77 123 123
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.035 -9999 0 -0.75 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.13 0.16 -9999 0 -0.57 21 21
CHUK -0.089 0.16 -9999 0 -0.34 75 75
KLRG1 -0.12 0.15 -9999 0 -0.55 21 21
VAV1 -0.2 0.32 -9999 0 -0.69 130 130
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.15 -9999 0 -0.54 22 22
negative regulation of mast cell degranulation -0.11 0.15 -9999 0 -0.56 23 23
BTK -0.18 0.24 -9999 0 -0.63 92 92
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.22 -9999 0 -0.58 83 83
GAB2/PI3K/SHP2 -0.19 0.24 -9999 0 -0.82 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.15 -9999 0 -0.55 21 21
RAF1 0.026 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.31 0.39 -9999 0 -1 82 82
FCER1G -0.16 0.34 -9999 0 -0.87 95 95
FCER1A -0.023 0.16 -9999 0 -0.77 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.28 -9999 0 -0.55 196 196
MAPK3 0.04 0.026 -9999 0 -10000 0 0
MAPK1 0.04 0.026 -9999 0 -10000 0 0
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
MAPK8 -0.011 0.07 -9999 0 -10000 0 0
DUSP1 0.014 0.039 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.071 0.074 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.075 0.16 -9999 0 -0.48 21 21
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.22 0.29 -9999 0 -0.73 111 111
FER -0.12 0.16 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.15 0.19 -9999 0 -0.42 158 158
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.2 0.36 -9999 0 -0.76 125 125
cytokine secretion -0.051 0.053 -9999 0 -10000 0 0
SPHK1 -0.16 0.22 -9999 0 -0.65 56 56
PTK2 -0.078 0.16 -9999 0 -0.5 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.25 0.31 -9999 0 -0.77 106 106
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.31 -9999 0 -0.68 106 106
MAP2K2 0.035 0.032 -9999 0 -0.42 1 1
MAP2K1 0.036 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.12 0.15 -9999 0 -0.53 21 21
MAP2K4 0.017 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.33 0.4 -9999 0 -0.73 221 221
mol:Choline -0.18 0.28 -9999 0 -0.89 20 20
SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.51 16 16
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.063 0.15 -9999 0 -0.47 16 16
HCLS1 -0.13 0.18 -9999 0 -0.67 29 29
PRKCB -0.14 0.23 -9999 0 -0.48 113 113
FCGR2B -0.14 0.34 -9999 0 -0.86 93 93
IGHE -0.005 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.16 -9999 0 -0.57 23 23
LCP2 -0.04 0.21 -9999 0 -0.86 32 32
PLA2G4A -0.12 0.16 -9999 0 -0.55 24 24
RASA1 0.014 0.034 -9999 0 -0.75 1 1
mol:Phosphatidic acid -0.18 0.28 -9999 0 -0.89 20 20
IKK complex -0.048 0.13 -9999 0 -0.28 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.008 0.087 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.076 0.2 0.61 31 -0.44 3 34
IL27/IL27R/JAK1 -0.08 0.35 0.57 1 -0.86 55 56
TBX21 -0.2 0.41 0.5 1 -0.76 148 149
IL12B -0.095 0.28 -10000 0 -0.87 60 60
IL12A 0.008 0.032 -10000 0 -0.68 1 1
IL6ST -0.013 0.14 -10000 0 -0.76 16 16
IL27RA/JAK1 0.011 0.063 -10000 0 -0.7 1 1
IL27 -0.046 0.22 -10000 0 -0.88 32 32
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.076 0.2 0.61 31 -0.44 3 34
T cell proliferation during immune response 0.076 0.2 0.61 31 -0.44 3 34
MAPKKK cascade -0.076 0.2 0.44 3 -0.61 31 34
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.86 1 1
IL12RB1 -0.26 0.41 -10000 0 -0.87 156 156
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.72 92 93
IL27/IL27R/JAK2/TYK2 -0.078 0.2 0.44 3 -0.62 31 34
positive regulation of T cell mediated cytotoxicity -0.076 0.2 0.44 3 -0.61 31 34
STAT1 (dimer) -0.065 0.51 0.54 117 -1 66 183
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.081 0.18 0.39 3 -0.62 23 26
T cell proliferation -0.12 0.25 0.4 1 -0.7 49 50
IL12/IL12R/TYK2/JAK2 -0.18 0.27 -10000 0 -0.75 45 45
IL17A -0.025 0.13 -10000 0 -0.74 2 2
mast cell activation 0.076 0.2 0.61 31 -0.44 3 34
IFNG -0.041 0.066 0.12 3 -0.11 230 233
T cell differentiation -0.011 0.011 0.03 3 -0.026 135 138
STAT3 (dimer) -0.081 0.18 0.39 3 -0.62 24 27
STAT5A (dimer) -0.081 0.18 0.39 3 -0.62 23 26
STAT4 (dimer) -0.11 0.24 0.39 2 -0.75 44 46
STAT4 -0.036 0.21 -10000 0 -0.86 30 30
T cell activation -0.012 0.008 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.042 0.1 -10000 0 -0.64 2 2
GATA3 -0.61 0.68 -10000 0 -1.3 244 244
IL18 0.005 0.081 -10000 0 -0.68 7 7
positive regulation of mast cell cytokine production -0.08 0.18 0.38 3 -0.6 24 27
IL27/EBI3 -0.12 0.33 -10000 0 -0.83 83 83
IL27RA -0.003 0.063 -10000 0 -0.75 1 1
IL6 -0.087 0.28 -10000 0 -0.81 63 63
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0 0.088 0.41 1 -0.59 10 11
IL1B 0.006 0.073 -10000 0 -0.66 6 6
EBI3 -0.12 0.31 -10000 0 -0.88 73 73
TNF 0.004 0.08 -10000 0 -0.63 8 8
Effects of Botulinum toxin

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
STX1A 0.007 0.073 -9999 0 -0.66 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.021 0.12 -9999 0 -0.66 16 16
STXBP1 0.014 0.034 -9999 0 -0.75 1 1
ACh/CHRNA1 -0.28 0.31 -9999 0 -0.63 224 224
RAB3GAP2/RIMS1/UNC13B -0.018 0.1 -9999 0 -0.57 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.016 0.15 -9999 0 -0.86 16 16
mol:ACh -0.009 0.053 -9999 0 -0.13 77 77
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.28 0.31 -9999 0 -0.62 224 224
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.37 0.44 -9999 0 -0.86 224 224
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.083 0.2 -9999 0 -0.54 82 82
SNAP25 -0.038 0.12 -9999 0 -0.33 73 73
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.75 82 82
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.065 -9999 0 -0.56 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.35 -10000 0 -1.1 67 67
NFATC2 -0.08 0.24 -10000 0 -0.77 13 13
NFATC3 -0.021 0.064 -10000 0 -10000 0 0
CD40LG -0.24 0.44 -10000 0 -1.1 57 57
ITCH 0.054 0.059 -10000 0 -10000 0 0
CBLB 0.054 0.059 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.55 0.56 -10000 0 -1.2 188 188
JUNB 0.013 0.048 -10000 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.012 0.059 -10000 0 -10000 0 0
T cell anergy 0.022 0.095 -10000 0 -0.6 1 1
TLE4 -0.03 0.17 -10000 0 -0.75 5 5
Jun/NFAT1-c-4/p21SNFT -0.24 0.27 -10000 0 -1 24 24
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -1.2 38 38
IKZF1 -0.13 0.36 -10000 0 -0.89 90 90
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.74 95 95
AP-1/NFAT1 -0.094 0.16 -10000 0 -0.68 12 12
CALM1 0.028 0.037 -10000 0 -10000 0 0
EGR2 -0.1 0.28 -10000 0 -1.3 8 8
EGR3 -0.11 0.29 -10000 0 -1.5 7 7
NFAT1/FOXP3 -0.29 0.4 -10000 0 -0.99 99 99
EGR1 0.001 0.11 -10000 0 -0.74 11 11
JUN 0.006 0.022 -10000 0 -10000 0 0
EGR4 0.006 0.078 -10000 0 -0.86 4 4
mol:Ca2+ 0.009 0.041 -10000 0 -10000 0 0
GBP3 -0.034 0.18 -10000 0 -0.86 7 7
FOSL1 -0.026 0.19 -10000 0 -0.86 24 24
NFAT1-c-4/MAF/IRF4 -0.27 0.36 -10000 0 -0.91 94 94
DGKA -0.034 0.19 -10000 0 -1.1 6 6
CREM 0.015 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.21 -10000 0 -1.1 6 6
CTLA4 -0.44 0.58 -10000 0 -1 234 234
NFAT1-c-4 (dimer)/EGR1 -0.17 0.24 -10000 0 -1.1 11 11
NFAT1-c-4 (dimer)/EGR4 -0.17 0.22 -10000 0 -1.1 7 7
FOS -0.014 0.12 -10000 0 -0.76 13 13
IFNG -0.49 0.51 -10000 0 -1 224 224
T cell activation -0.049 0.22 -10000 0 -0.82 16 16
MAF 0.016 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.063 0.2 0.91 3 -10000 0 3
TNF -0.095 0.28 -10000 0 -1.1 12 12
FASLG -0.33 0.47 -10000 0 -0.97 61 61
TBX21 -0.3 0.43 -10000 0 -0.93 160 160
BATF3 -0.062 0.25 -10000 0 -0.86 45 45
PRKCQ -0.034 0.13 -10000 0 -0.75 15 15
PTPN1 -0.03 0.17 -10000 0 -0.84 3 3
NFAT1-c-4/ICER1 -0.17 0.21 -10000 0 -1.2 5 5
GATA3 -0.35 0.38 -10000 0 -0.75 244 244
T-helper 1 cell differentiation -0.48 0.5 -10000 0 -0.99 224 224
IL2RA -0.39 0.46 -10000 0 -1.1 126 126
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.03 0.17 -10000 0 -0.75 5 5
E2F1 -0.081 0.28 -10000 0 -0.85 61 61
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.03 0.17 -10000 0 -0.75 5 5
IRF4 -0.18 0.37 -10000 0 -0.86 116 116
PTGS2 -0.21 0.4 -10000 0 -1.1 33 33
CSF2 -0.21 0.4 -10000 0 -1.1 32 32
JunB/Fra1/NFAT1-c-4 -0.17 0.22 -10000 0 -0.96 10 10
IL4 -0.36 0.29 -10000 0 -0.78 88 88
IL5 -0.2 0.38 -10000 0 -1 26 26
IL2 -0.05 0.22 -10000 0 -0.84 16 16
IL3 -0.05 0.049 -10000 0 -10000 0 0
RNF128 0.032 0.16 -10000 0 -0.79 19 19
NFATC1 -0.063 0.2 -10000 0 -0.91 3 3
CDK4 0.034 0.18 -10000 0 -10000 0 0
PTPRK -0.03 0.17 -10000 0 -0.75 5 5
IL8 -0.22 0.42 -10000 0 -1.1 40 40
POU2F1 0.016 0.003 -10000 0 -10000 0 0
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.66 225 225
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.029 0.1 -9999 0 -0.36 41 41
mol:S1P -0.023 0.093 -9999 0 -0.36 14 14
S1P1/S1P/Gi -0.044 0.14 -9999 0 -0.5 12 12
GNAO1 0.009 0.085 -9999 0 -0.84 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.053 0.084 -9999 0 -0.66 1 1
PLCG1 -0.026 0.13 -9999 0 -0.49 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.01 0.059 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.24 0.3 -9999 0 -0.58 225 225
S1P1/S1P -0.2 0.21 -9999 0 -0.42 226 226
negative regulation of cAMP metabolic process -0.043 0.14 -9999 0 -0.48 12 12
MAPK3 -0.035 0.16 -9999 0 -0.56 23 23
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.014 0.034 -9999 0 -0.75 1 1
PLCB2 -0.19 0.26 -9999 0 -0.67 56 56
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.17 0.17 -9999 0 -0.5 21 21
receptor internalization -0.19 0.19 -9999 0 -0.39 226 226
PTGS2 -0.044 0.23 -9999 0 -0.98 24 24
Rac1/GTP -0.17 0.17 -9999 0 -0.5 21 21
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.37 0.44 -9999 0 -0.86 225 225
negative regulation of T cell proliferation -0.043 0.14 -9999 0 -0.48 12 12
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.059 -9999 0 -0.75 3 3
MAPK1 -0.035 0.16 -9999 0 -0.56 23 23
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.62 21 21
ABCC1 0.016 0.002 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.055 0.16 -9999 0 -0.53 53 53
EFNA5 -0.056 0.22 -9999 0 -0.76 47 47
FYN -0.026 0.16 -9999 0 -0.48 53 53
neuron projection morphogenesis -0.055 0.16 -9999 0 -0.53 53 53
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.056 0.17 -9999 0 -0.53 53 53
EPHA5 -0.008 0.11 -9999 0 -0.86 8 8
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.043 -9999 0 -0.49 4 4
ARNO/beta Arrestin1-2 -0.017 0.062 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.034 -9999 0 -0.75 1 1
USP6 0.014 0.039 -9999 0 -0.86 1 1
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.51 0.18 -9999 0 -0.57 456 456
ARRB2 -0.013 0.1 -9999 0 -0.39 36 36
mol:GTP -0.01 0.048 -9999 0 -0.23 2 2
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.085 0.28 -9999 0 -0.86 58 58
EGF -0.67 0.23 -9999 0 -0.75 455 455
somatostatin receptor activity 0 0 -9999 0 -0.001 18 18
ARAP2 0.013 0.048 -9999 0 -0.75 2 2
mol:GDP -0.056 0.093 -9999 0 -0.33 23 23
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 7 7
ITGA2B -0.015 0.16 -9999 0 -0.86 18 18
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
ADAP1 0.01 0.068 -9999 0 -0.75 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.034 0.15 -9999 0 -0.66 26 26
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.086 0.089 -9999 0 -0.33 21 21
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.44 0.16 -9999 0 -0.49 456 456
ADRB2 0.013 0.048 -9999 0 -0.75 2 2
receptor agonist activity 0 0 -9999 0 0 14 14
actin filament binding 0 0 -9999 0 -0.001 18 18
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.011 0.059 -9999 0 -0.75 3 3
GNAQ 0.015 0.002 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 10 10
ARF6/GDP -0.066 0.14 -9999 0 -0.4 5 5
ARF6/GDP/GULP/ACAP1 -0.22 0.26 -9999 0 -0.53 190 190
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.021 0.1 -9999 0 -0.52 17 17
ACAP1 -0.31 0.42 -9999 0 -0.86 188 188
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.042 0.15 -9999 0 -0.59 36 36
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
HGF -0.022 0.17 -9999 0 -0.8 23 23
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.014 0.034 -9999 0 -0.75 1 1
fibronectin binding 0 0 -9999 0 -0.001 11 11
endosomal lumen acidification 0 0 -9999 0 -0.001 20 20
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.011 0.14 -9999 0 -0.75 18 18
GNAQ/ARNO 0.009 0.01 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 2 2
MET 0.007 0.087 -9999 0 -0.86 5 5
GNA14 0.005 0.089 -9999 0 -0.75 7 7
GNA15 -0.009 0.14 -9999 0 -0.86 14 14
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 10 10
GNA11 0.012 0.048 -9999 0 -0.75 2 2
LHCGR -0.054 0.22 -9999 0 -0.86 35 35
AGTR1 -0.027 0.18 -9999 0 -0.75 28 28
desensitization of G-protein coupled receptor protein signaling pathway -0.042 0.15 -9999 0 -0.59 36 36
IPCEF1/ARNO -0.34 0.13 -9999 0 -0.82 8 8
alphaIIb/beta3 Integrin -0.027 0.13 -9999 0 -0.64 21 21
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.013 0.047 -9999 0 -10000 0 0
NFATC2 -0.016 0.06 -9999 0 -0.6 2 2
NFATC3 -0.013 0.047 -9999 0 -10000 0 0
CD40LG -0.3 0.42 -9999 0 -0.94 98 98
PTGS2 -0.29 0.39 -9999 0 -0.86 92 92
JUNB 0.013 0.048 -9999 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.02 0.018 -9999 0 -10000 0 0
CALM1 0.006 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.026 0.19 -9999 0 -0.86 24 24
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.73 35 35
FOS -0.014 0.12 -9999 0 -0.76 13 13
IFNG -0.44 0.52 -9999 0 -0.98 218 218
AP-1/NFAT1-c-4 -0.41 0.41 -9999 0 -1.1 92 92
FASLG -0.46 0.52 -9999 0 -0.98 221 221
NFAT1-c-4/ICER1 -0.079 0.078 -9999 0 -0.56 2 2
IL2RA -0.34 0.45 -9999 0 -1 103 103
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.28 0.38 -9999 0 -0.87 90 90
JunB/Fra1/NFAT1-c-4 -0.093 0.12 -9999 0 -0.57 17 17
IL4 -0.28 0.37 -9999 0 -0.83 87 87
IL2 -0.012 0.11 -9999 0 -0.76 10 10
IL3 -0.028 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.062 0.25 -9999 0 -0.86 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.025 -9999 0 -0.56 1 1
Necdin/E2F1 -0.083 0.22 -9999 0 -0.68 62 62
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.077 0.2 -9999 0 -0.98 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.3 -9999 0 -0.56 241 241
NT-4/5 (dimer)/p75(NTR) -0.05 0.18 -9999 0 -0.67 38 38
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.031 0.22 -9999 0 -0.95 9 9
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.1 0.3 -9999 0 -0.86 68 68
MGDIs/NGR/p75(NTR)/LINGO1 -0.07 0.2 -9999 0 -0.61 58 58
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.24 -9999 0 -0.61 95 95
LINGO1 -0.022 0.18 -9999 0 -0.86 22 22
Sortilin/TRAF6/NRIF -0.001 0.015 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.3 -9999 0 -0.86 68 68
NTRK1 -0.045 0.21 -9999 0 -0.76 39 39
RTN4R 0.004 0.1 -9999 0 -0.84 7 7
neuron apoptosis -0.065 0.23 -9999 0 -0.67 29 29
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.058 0.24 -9999 0 -0.63 73 73
ARHGDIA 0.014 0.034 -9999 0 -0.75 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.083 0.21 -9999 0 -0.58 71 71
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.085 0.21 -9999 0 -0.58 72 72
Mammalian IAPs/DIABLO -0.08 0.19 -9999 0 -0.52 78 78
proNGF (dimer) -0.065 0.25 -9999 0 -0.86 47 47
MAGED1 0.014 0.039 -9999 0 -0.86 1 1
APP 0.014 0.034 -9999 0 -0.75 1 1
NT-4/5 (dimer) -0.003 0.086 -9999 0 -0.86 5 5
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.078 0.2 -9999 0 -0.54 71 71
NGF -0.066 0.25 -9999 0 -0.86 47 47
cell cycle arrest -0.011 0.25 -9999 0 -0.56 71 71
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.044 0.11 -9999 0 -0.57 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.044 0.15 -9999 0 -0.58 38 38
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.089 0.23 -9999 0 -0.63 72 72
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.043 0.22 -9999 0 -0.57 71 71
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.034 0.086 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.044 0.17 -9999 0 -0.66 34 34
BEX1 -0.27 0.37 -9999 0 -0.75 187 187
mol:GDP -0.07 0.24 -9999 0 -0.64 72 72
NGF (dimer) -0.35 0.3 -9999 0 -0.84 86 86
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.064 0.18 -9999 0 -0.56 58 58
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
RAC1/GTP -0.079 0.2 -9999 0 -0.56 72 72
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.09 0.23 -9999 0 -0.63 72 72
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.08 0.22 -9999 0 -0.66 61 61
NT3 (dimer) 0.005 0.093 -9999 0 -0.78 7 7
TP53 -0.04 0.22 -9999 0 -0.91 7 7
PRDM4 -0.043 0.22 -9999 0 -0.57 71 71
BDNF (dimer) -0.42 0.36 -9999 0 -0.88 138 138
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
SORT1 0.014 0.034 -9999 0 -0.75 1 1
activation of caspase activity -0.076 0.19 -9999 0 -0.96 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.083 0.21 -9999 0 -0.58 71 71
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.022 0.21 -9999 0 -0.63 22 22
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.043 0.22 -9999 0 -0.57 71 71
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.091 0.23 -9999 0 -0.63 73 73
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.051 0.18 -9999 0 -0.66 39 39
MAPK8 -0.02 0.2 -9999 0 -0.63 21 21
MAPK9 -0.02 0.2 -9999 0 -0.63 21 21
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.093 -9999 0 -0.78 7 7
NTF4 -0.003 0.086 -9999 0 -0.86 5 5
NDN 0.011 0.059 -9999 0 -0.75 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.07 0.18 -9999 0 -0.91 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.019 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.089 0.23 -9999 0 -0.62 72 72
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.097 0.21 -9999 0 -0.97 7 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.22 -9999 0 -0.56 93 93
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.089 0.23 -9999 0 -0.66 68 68
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 78 78
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.009 0.24 -9999 0 -0.54 56 56
BAD -0.009 0.2 -9999 0 -0.59 21 21
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
NGFR -0.042 0.22 -9999 0 -0.86 33 33
CYCS -0.033 0.22 -9999 0 -0.96 9 9
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.083 0.21 -9999 0 -0.58 72 72
BCL2L11 -0.008 0.2 -9999 0 -0.59 21 21
BDNF (dimer)/p75(NTR) -0.13 0.28 -9999 0 -0.7 95 95
PI3K -0.083 0.21 -9999 0 -0.58 71 71
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.083 0.21 -9999 0 -0.58 71 71
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.1 0.26 -9999 0 -0.72 72 72
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.084 0.21 -9999 0 -0.58 72 72
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.059 -9999 0 -0.75 3 3
PLG -0.39 0.38 -9999 0 -0.75 265 265
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.12 0.23 -9999 0 -0.68 41 41
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.003 0.18 -9999 0 -0.53 21 21
E2F1 -0.09 0.29 -9999 0 -0.86 61 61
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.07 0.15 -9999 0 -0.59 13 13
NGF (dimer)/TRKA -0.1 0.24 -9999 0 -0.63 84 84
MMP7 -0.12 0.3 -9999 0 -0.76 90 90
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.077 0.2 -9999 0 -0.54 71 71
MMP3 -0.071 0.25 -9999 0 -0.86 46 46
APAF-1/Caspase 9 -0.11 0.17 -9999 0 -0.69 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.046 0.14 -9999 0 -0.73 1 1
CCNA2 -0.16 0.35 -9999 0 -0.86 100 100
PIK3CA 0.015 0.034 -9999 0 -0.75 1 1
JAK3 -0.16 0.36 -9999 0 -0.86 104 104
PIK3R1 0.015 0.034 -9999 0 -0.75 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.25 -9999 0 -0.66 58 58
SHC1 0.015 0.039 -9999 0 -0.86 1 1
SP1 0.024 0.022 -9999 0 -10000 0 0
IL2RA -0.12 0.33 -9999 0 -0.77 103 103
IL2RB -0.45 0.44 -9999 0 -0.86 267 267
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.042 0.22 -9999 0 -0.86 34 34
G1/S transition of mitotic cell cycle -0.047 0.2 -9999 0 -0.53 17 17
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.051 -9999 0 -0.77 2 2
LCK -0.021 0.18 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.007 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.034 -9999 0 -0.75 1 1
CCND3 -0.079 0.21 -9999 0 -0.66 28 28
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.12 0.24 -10000 0 -0.76 36 36
UGCG -0.023 0.047 -10000 0 -0.84 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.082 0.19 -10000 0 -0.49 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.057 -10000 0 -0.83 1 1
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.16 -10000 0 -0.56 35 35
FRAP1 -0.086 0.23 -10000 0 -0.62 48 48
FOXO3 -0.077 0.22 -10000 0 -0.66 32 32
AKT1 -0.094 0.24 -10000 0 -0.64 51 51
GAB2 0.016 0.003 -10000 0 -10000 0 0
SMPD1 -0.021 0.03 -10000 0 -10000 0 0
SGMS1 -0.021 0.03 -10000 0 -10000 0 0
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 0.026 0.033 -10000 0 -0.48 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.023 0.098 -10000 0 -0.43 2 2
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
RPS6KB1 -0.029 0.088 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.16 0.36 -10000 0 -0.86 104 104
PIK3R1 0.017 0.034 -10000 0 -0.74 1 1
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.034 -10000 0 -0.75 1 1
MYC -0.077 0.22 -10000 0 -0.66 34 34
MYB -0.19 0.34 -10000 0 -0.73 139 139
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.12 0.26 -10000 0 -0.68 61 61
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.037 0.068 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 -0.12 0.25 -10000 0 -0.66 61 61
Rac1/GDP 0.01 0.033 -10000 0 -0.43 2 2
T cell proliferation -0.098 0.24 -10000 0 -0.64 51 51
SHC1 0.014 0.039 -10000 0 -0.86 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.009 0.026 -10000 0 -0.05 139 139
PRKCZ -0.1 0.25 -10000 0 -0.67 51 51
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.58 29 29
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.15 0.26 -10000 0 -0.58 100 100
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 102 102
IL2RB -0.44 0.44 -10000 0 -0.86 267 267
TERT -0.11 0.3 -10000 0 -0.86 70 70
E2F1 -0.1 0.2 -10000 0 -0.37 175 175
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.012 0.055 -10000 0 -0.86 2 2
mol:cAMP 0.004 0.013 0.025 139 -10000 0 139
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.04 0.22 -10000 0 -0.86 34 34
actin cytoskeleton organization -0.098 0.24 -10000 0 -0.64 51 51
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 -0.005 0.12 -10000 0 -0.86 10 10
PIK3CA 0.017 0.034 -10000 0 -0.74 1 1
Rac1/GTP 0.031 0.035 -10000 0 -0.41 2 2
LCK -0.019 0.18 -10000 0 -0.85 22 22
BCL2 -0.053 0.18 -10000 0 -0.53 24 24
LPA4-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
ADCY4 0.026 0.023 -9999 0 -0.49 1 1
ADCY5 0.005 0.1 -9999 0 -0.49 22 22
ADCY6 0.025 0.043 -9999 0 -0.93 1 1
ADCY7 0.008 0.11 -9999 0 -0.58 16 16
ADCY1 0.014 0.084 -9999 0 -0.5 13 13
ADCY2 -0.13 0.26 -9999 0 -0.58 131 131
ADCY3 0.026 0.023 -9999 0 -0.49 1 1
ADCY8 -0.16 0.28 -9999 0 -0.58 157 157
PRKCE 0.014 0.026 -9999 0 -0.57 1 1
ADCY9 0.026 0.023 -9999 0 -0.49 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.091 0.17 -9999 0 -0.5 50 50
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.058 0.29 18 -10000 0 18
BUB1B -0.024 0.12 -10000 0 -0.5 26 26
PLK1 -0.012 0.059 -10000 0 -0.2 10 10
PLK1S1 0.001 0.031 -10000 0 -10000 0 0
KIF2A -0.004 0.073 -10000 0 -0.56 4 4
regulation of mitotic centrosome separation -0.013 0.059 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.33 -10000 0 -0.71 124 124
WEE1 -0.002 0.056 -10000 0 -0.32 2 2
cytokinesis -0.2 0.27 -10000 0 -0.5 232 232
PP2A-alpha B56 -0.14 0.16 -10000 0 -10000 0 0
AURKA -0.003 0.045 -10000 0 -0.29 6 6
PICH/PLK1 -0.045 0.16 -10000 0 -0.84 18 18
CENPE -0.065 0.21 -10000 0 -0.62 60 60
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.072 -10000 0 -0.55 4 4
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.034 -10000 0 -0.75 1 1
TPX2 -0.051 0.12 -10000 0 -0.25 125 125
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.073 0.26 -10000 0 -0.86 51 51
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.026 0.096 -10000 0 -0.28 58 58
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.009 -10000 0 -0.02 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0.001 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.013 0.059 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.17 0.19 -10000 0 -0.46 9 9
TPT1 0.001 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 235 235
CDC25B 0.007 0.088 -10000 0 -0.88 5 5
SGOL1 0 0.058 -10000 0 -0.29 18 18
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.024 0.1 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.057 0.24 -10000 0 -0.86 42 42
PLK1/PBIP1 -0.042 0.12 -10000 0 -0.59 18 18
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.002 0.045 -10000 0 -0.21 2 2
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.17 0.36 -10000 0 -0.86 108 108
metaphase plate congression -0.005 0.041 -10000 0 -10000 0 0
ERCC6L -0.037 0.16 -10000 0 -0.82 18 18
NLP/gamma Tubulin -0.003 0.035 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0.001 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.26 0.29 -10000 0 -0.56 232 232
GRASP65/GM130/RAB1/GTP/PLK1 -0.014 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.038 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 119 119
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.043 -10000 0 -10000 0 0
microtubule-based process -0.25 0.31 -10000 0 -0.58 232 232
Golgi organization -0.013 0.059 -10000 0 -0.2 10 10
Cohesin/SA2 -0.025 0.045 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.39 0.44 -10000 0 -0.86 232 232
APC/C/CDC20 -0.047 0.18 -10000 0 -0.64 42 42
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.041 0.11 -10000 0 -0.57 18 18
PRC1 0.005 0.095 -10000 0 -0.86 6 6
ECT2 0 0.053 -10000 0 -10000 0 0
C13orf34 0.003 0.043 -10000 0 -10000 0 0
NUDC -0.005 0.041 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.024 0.12 -10000 0 -0.5 26 26
spindle assembly -0.007 0.048 -10000 0 -0.16 8 8
spindle stabilization 0.001 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.022 -10000 0 -0.49 1 1
MKLP2/PLK1 -0.25 0.31 -10000 0 -0.59 232 232
CCNB1 0.001 0.11 -10000 0 -0.87 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.005 0.049 -10000 0 -0.46 2 2
TUBG1 0.001 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.099 -10000 0 -0.71 9 9
MLF1IP -0.012 0.13 -10000 0 -0.69 18 18
INCENP 0.009 0.008 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.054 0.17 -10000 0 -0.42 37 37
IKBKB -0.024 0.1 -10000 0 -10000 0 0
AKT1 -0.024 0.13 -10000 0 -0.32 4 4
IKBKG -0.024 0.11 -10000 0 -0.3 3 3
CALM1 -0.042 0.1 -10000 0 -0.5 3 3
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
MAP3K1 -0.11 0.25 -10000 0 -0.63 69 69
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 -10000 0 -0.5 4 4
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.012 0.09 -10000 0 -0.26 2 2
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.034 -10000 0 -0.75 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
BCR complex -0.17 0.3 -10000 0 -0.68 126 126
CD22 -0.15 0.23 -10000 0 -0.67 51 51
CAMK2G -0.03 0.098 -10000 0 -0.49 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.078 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.11 0.19 -10000 0 -0.84 4 4
GO:0007205 -0.056 0.11 -10000 0 -0.5 4 4
SYK 0.013 0.048 -10000 0 -0.75 2 2
ELK1 -0.043 0.1 -10000 0 -0.5 3 3
NFATC1 -0.072 0.2 -10000 0 -0.5 64 64
B-cell antigen/BCR complex -0.17 0.3 -10000 0 -0.68 126 126
PAG1/CSK -0.003 0.042 -10000 0 -0.66 2 2
NFKBIB 0.004 0.039 -10000 0 -0.13 1 1
HRAS -0.038 0.12 -10000 0 -0.49 4 4
NFKBIA 0.005 0.038 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.013 0.032 -10000 0 -0.18 1 1
RasGAP/Csk -0.21 0.32 -10000 0 -0.99 45 45
mol:GDP -0.051 0.1 0.29 1 -0.47 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.011 0.067 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.013 0.032 -10000 0 -0.19 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.08 0.22 -10000 0 -0.57 62 62
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
mol:IP3 -0.066 0.1 0.27 1 -0.51 4 5
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.041 0.11 -10000 0 -0.48 6 6
CHUK -0.024 0.11 -10000 0 -0.3 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.13 0.2 -10000 0 -0.54 81 81
PTPN6 -0.14 0.21 -10000 0 -0.68 38 38
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.011 0.068 -10000 0 -0.14 104 104
VAV2 -0.17 0.28 -10000 0 -0.8 71 71
ubiquitin-dependent protein catabolic process 0.01 0.037 -10000 0 -0.12 1 1
BTK -0.087 0.17 0.46 1 -0.41 103 104
CD19 -0.19 0.33 -10000 0 -0.89 76 76
MAP4K1 -0.33 0.43 -10000 0 -0.86 201 201
CD72 -0.19 0.37 -10000 0 -0.86 118 118
PAG1 0.012 0.055 -10000 0 -0.86 2 2
MAPK14 -0.084 0.22 -10000 0 -0.53 60 60
SH3BP5 0.014 0.034 -10000 0 -0.75 1 1
PIK3AP1 -0.038 0.11 -10000 0 -0.54 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.23 -10000 0 -0.6 65 65
RAF1 -0.026 0.11 -10000 0 -0.53 2 2
RasGAP/p62DOK/SHIP -0.2 0.31 -10000 0 -0.97 46 46
CD79A -0.2 0.38 -10000 0 -0.86 126 126
re-entry into mitotic cell cycle -0.012 0.09 -10000 0 -0.26 2 2
RASA1 0.014 0.034 -10000 0 -0.75 1 1
MAPK3 -0.002 0.1 -10000 0 -10000 0 0
MAPK1 -0.002 0.1 -10000 0 -0.42 2 2
CD72/SHP1 -0.23 0.33 -10000 0 -0.82 97 97
NFKB1 0.014 0.034 -10000 0 -0.75 1 1
MAPK8 -0.084 0.22 -10000 0 -0.53 60 60
actin cytoskeleton organization -0.098 0.26 -10000 0 -0.67 65 65
NF-kappa-B/RelA 0.034 0.059 -10000 0 -10000 0 0
Calcineurin -0.043 0.07 -10000 0 -10000 0 0
PI3K -0.14 0.22 -10000 0 -0.6 67 67
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.062 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.27 0.32 -10000 0 -0.74 131 131
DAPP1 -0.11 0.18 -10000 0 -0.61 35 35
cytokine secretion -0.066 0.19 -10000 0 -0.46 64 64
mol:DAG -0.066 0.1 0.27 1 -0.51 4 5
PLCG2 0.003 0.1 -10000 0 -0.82 8 8
MAP2K1 -0.014 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.25 0.37 -10000 0 -0.72 174 174
mol:PI-3-4-5-P3 -0.098 0.15 -10000 0 -0.42 41 41
ETS1 -0.018 0.092 -10000 0 -0.44 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.22 -10000 0 -0.98 3 3
B-cell antigen/BCR complex/LYN -0.14 0.22 -10000 0 -0.57 69 69
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.11 0.28 -10000 0 -0.73 65 65
B-cell antigen/BCR complex/LYN/SYK -0.16 0.25 -10000 0 -0.67 62 62
CARD11 -0.15 0.26 -10000 0 -0.62 108 108
FCGR2B -0.14 0.34 -10000 0 -0.86 93 93
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.005 0.047 -10000 0 -10000 0 0
PTPRC -0.08 0.27 -10000 0 -0.86 55 55
PDPK1 -0.061 0.1 -10000 0 -0.37 2 2
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0 0.058 -10000 0 -0.14 64 64
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.036 -9999 0 -0.79 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.023 -9999 0 -10000 0 0
JMJD2C 0 0.021 -9999 0 -0.11 17 17
T-DHT/AR/Ubc9 -0.077 0.11 -9999 0 -0.55 24 24
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.014 0.009 -9999 0 -10000 0 0
MAK 0.014 0.045 -9999 0 -0.86 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.01 0.062 -9999 0 -0.78 3 3
GSN 0.015 0.008 -9999 0 -10000 0 0
NCOA2 0.003 0.095 -9999 0 -0.75 8 8
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.026 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.028 0.037 -9999 0 -0.61 1 1
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.093 0.14 -9999 0 -0.58 37 37
FHL2 -0.04 0.11 -9999 0 -1.1 5 5
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.056 -9999 0 -0.14 437 437
CDK6 0.014 0.034 -9999 0 -0.75 1 1
TGFB1I1 0.013 0.039 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.15 -9999 0 -0.6 43 43
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.59 24 24
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.017 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 487 487
SRF 0.026 0.012 -9999 0 -10000 0 0
NKX3-1 -0.19 0.07 -9999 0 -10000 0 0
KLK3 0.024 0.15 -9999 0 -0.7 20 20
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.013 -9999 0 -10000 0 0
AOF2 -0.001 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.11 -9999 0 -0.54 24 24
AR -0.069 0.16 -9999 0 -0.79 24 24
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.013 -9999 0 -10000 0 0
PAWR 0.014 0.034 -9999 0 -0.75 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.1 -9999 0 -0.5 24 24
RPS6KA3 0.013 0.036 -9999 0 -0.79 1 1
T-DHT/AR/ARA70 -0.078 0.11 -9999 0 -0.55 24 24
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.068 0.1 -9999 0 -0.5 24 24
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.006 0.13 -9999 0 -0.75 14 14
KLK2 -0.083 0.14 -9999 0 -0.8 17 17
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.067 0.12 -9999 0 -0.59 21 21
TMPRSS2 -0.92 0.36 -9999 0 -1.1 437 437
CCND1 -0.018 0.17 -9999 0 -0.86 19 19
PIAS1 0.014 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.027 -9999 0 -0.072 427 427
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.56 24 24
CMTM2 -0.005 0.13 -9999 0 -0.86 12 12
SNURF -0.009 0.13 -9999 0 -0.75 16 16
ZMIZ1 -0.031 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.013 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.14 0.3 -9999 0 -0.71 55 55
CRP -0.2 0.39 -9999 0 -0.91 88 88
cell cycle arrest -0.17 0.35 -9999 0 -0.78 80 80
TIMP1 -0.15 0.33 -9999 0 -0.77 67 67
IL6ST -0.012 0.13 -9999 0 -0.74 16 16
Rac1/GDP -0.14 0.26 -9999 0 -0.59 85 85
AP1 0.021 0.11 -9999 0 -0.55 3 3
GAB2 0.011 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.37 -9999 0 -0.84 80 80
HSP90B1 0.005 0.088 -9999 0 -10000 0 0
GAB1 0.014 0.006 -9999 0 -10000 0 0
MAPK14 0.018 0.13 -9999 0 -0.69 3 3
AKT1 0.06 0.035 -9999 0 -10000 0 0
FOXO1 0.076 0.024 -9999 0 -10000 0 0
MAP2K6 -0.016 0.14 -9999 0 -0.68 4 4
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.27 -9999 0 -0.64 68 68
MITF -0.023 0.14 -9999 0 -0.8 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.002 0.13 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0.001 0.069 -9999 0 -10000 0 0
STAT3 -0.18 0.36 -9999 0 -0.82 80 80
STAT1 -0.005 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.31 -9999 0 -0.75 42 42
PIK3CA 0.016 0.034 -9999 0 -0.75 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.017 0.13 -9999 0 -0.75 2 2
MAPK11 0.017 0.13 -9999 0 -0.7 4 4
STAT3 (dimer)/FOXO1 -0.07 0.27 -9999 0 -0.64 21 21
GRB2/SOS1/GAB family -0.046 0.11 -9999 0 -0.67 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.038 0.15 -9999 0 -0.63 12 12
GRB2 0.014 0.006 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.28 0.45 -9999 0 -0.88 158 158
PIK3R1 0.016 0.034 -9999 0 -0.75 1 1
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.32 -9999 0 -0.79 48 48
FGG -0.27 0.43 -9999 0 -0.85 136 136
macrophage differentiation -0.17 0.35 -9999 0 -0.78 80 80
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.068 0.17 -9999 0 -0.54 33 33
JUNB -0.13 0.3 -9999 0 -0.74 41 41
FOS -0.01 0.12 -9999 0 -0.76 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.034 0.15 -9999 0 -0.45 20 20
STAT1/PIAS1 -0.046 0.16 -9999 0 -0.49 19 19
GRB2/SOS1/GAB family/SHP2/PI3K 0.021 0.038 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.82 80 80
PRKCD -0.14 0.3 -9999 0 -0.69 63 63
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.033 0.12 -9999 0 -0.66 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.089 -9999 0 -0.47 16 16
Rac1/GTP -0.18 0.23 -9999 0 -0.6 91 91
HCK -0.033 0.2 -9999 0 -0.86 28 28
MAPKKK cascade 0.026 0.061 -9999 0 -10000 0 0
bone resorption -0.18 0.35 -9999 0 -0.78 80 80
IRF1 -0.14 0.31 -9999 0 -0.75 42 42
mol:GDP -0.15 0.26 -9999 0 -0.59 97 97
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.6 97 97
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.003 0.12 -9999 0 -0.74 2 2
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.078 0.21 -9999 0 -0.63 63 63
gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.084 -9999 0 -0.47 16 16
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.084 -9999 0 -0.47 16 16
IL6 -0.091 0.28 -9999 0 -0.82 63 63
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.017 0.017 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.034 0.13 -9999 0 -0.83 2 2
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.29 -9999 0 -0.75 80 80
MCL1 0.075 0.023 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 168 168
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.11 0.22 -9999 0 -0.52 6 6
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.65 0.37 -9999 0 -0.86 386 386
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.86 66 66
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.24 -9999 0 -0.49 178 178
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.16 -9999 0 -0.59 16 16
MAP1B -0.001 0.02 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.17 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 167 167
PAFAH/LIS1 -0.44 0.24 -9999 0 -0.57 386 386
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.099 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.7 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.13 0.19 -9999 0 -0.64 16 16
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.034 -9999 0 -0.75 1 1
PAFAH1B2 0.014 0.034 -9999 0 -0.75 1 1
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.16 -9999 0 -0.56 16 16
LRP8 0.014 0.039 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.13 0.16 -9999 0 -0.59 16 16
P39/CDK5 -0.18 0.23 -9999 0 -0.86 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.093 0.21 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.2 -9999 0 -0.63 3 3
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
CDC42 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 -0.02 0.18 -9999 0 -10000 0 0
CRKL -0.094 0.22 -9999 0 -10000 0 0
mol:DAG -0.12 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -0.7 1 1
MAPK8 -0.13 0.25 -9999 0 -0.48 178 178
RAP1A -0.094 0.22 -9999 0 -10000 0 0
GAB1 -0.094 0.22 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.48 178 178
EPO -0.29 0.42 -9999 0 -0.85 178 178
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.19 0.26 -9999 0 -0.55 179 179
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.31 -9999 0 -0.65 178 178
IRS2 -0.1 0.23 -9999 0 -0.88 2 2
STAT1 -0.065 0.21 -9999 0 -10000 0 0
STAT5B -0.07 0.21 -9999 0 -10000 0 0
cell proliferation -0.11 0.24 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.11 0.15 -9999 0 -0.71 1 1
TEC -0.094 0.22 -9999 0 -10000 0 0
SOCS3 0.012 0.055 -9999 0 -0.86 2 2
STAT1 (dimer) -0.063 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -10000 0 0
EPO/EPOR -0.23 0.31 -9999 0 -0.65 178 178
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.081 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 178 178
mol:IP3 -0.12 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.14 0.26 -9999 0 -0.48 178 178
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 1 1
PTPN6 -0.11 0.23 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.12 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.009 0.078 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.12 0.17 -9999 0 -0.73 1 1
VAV2 -0.094 0.22 -9999 0 -10000 0 0
CBL -0.095 0.22 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.12 0.17 -9999 0 -10000 0 0
STAT5A -0.07 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.045 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.01 0.078 -9999 0 -0.62 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.28 -9999 0 -0.88 26 26
BCL2 -0.02 0.18 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.28 -9999 0 -0.85 72 72
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.015 0.09 -9999 0 -0.57 13 13
IFNAR2 0.015 0.007 -9999 0 -10000 0 0
AKT1 0.014 0.07 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.005 0.053 -9999 0 -0.6 4 4
NFX1/SIN3/HDAC complex 0.045 0.054 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 455 455
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.8 70 70
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.38 -9999 0 -0.75 238 238
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.23 -9999 0 -0.75 47 47
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.24 0.29 -9999 0 -0.89 70 70
CCND1 -0.22 0.27 -9999 0 -0.8 75 75
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.034 -9999 0 -0.75 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0.003 0.027 -9999 0 -10000 0 0
CDKN1B -0.22 0.3 -9999 0 -0.55 230 230
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.018 0.16 -9999 0 -0.86 18 18
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.006 0.12 -9999 0 -0.76 13 13
IFN-gamma/IRF1 -0.29 0.32 -9999 0 -0.65 230 230
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.003 0.13 -9999 0 -0.86 11 11
Telomerase -0.02 0.16 -9999 0 -0.47 8 8
IRF1 0.016 0.04 -9999 0 -0.86 1 1
ESR1 0.007 0.07 -9999 0 -0.78 4 4
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.022 -9999 0 -0.49 1 1
ubiquitin-dependent protein catabolic process 0.051 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.007 0.033 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM -0.001 0.023 -9999 0 -0.52 1 1
SMAD3 0.025 0.068 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.25 -9999 0 -0.76 62 62
NR2F2 0.009 0.012 -9999 0 -10000 0 0
MAPK3 0.009 0.097 -9999 0 -0.67 10 10
MAPK1 0.009 0.097 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.007 0.086 -9999 0 -0.86 5 5
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.023 -9999 0 -0.52 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.52 0.18 -9999 0 -0.57 456 456
MYC -0.017 0.16 -9999 0 -0.86 18 18
IL2 -0.008 0.12 -9999 0 -0.86 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.007 0.087 -9999 0 -0.86 5 5
TRF2/BLM -0.013 0.091 -9999 0 -0.62 11 11
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.21 0.26 -9999 0 -0.81 63 63
SP1/HDAC2 0.007 0.014 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.18 0.23 -9999 0 -0.75 47 47
Smad3/Myc -0.019 0.13 -9999 0 -0.6 22 22
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.85 230 230
Telomerase/PinX1 -0.18 0.23 -9999 0 -0.75 47 47
Telomerase/AKT1/mTOR/p70S6K -0.012 0.079 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.18 0.23 -9999 0 -0.75 47 47
response to DNA damage stimulus 0.004 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.23 -9999 0 -0.75 47 47
E2F1 -0.091 0.29 -9999 0 -0.86 61 61
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.14 0.33 -9999 0 -0.86 88 88
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.17 0.26 -10000 0 -0.53 87 87
CRKL 0.018 0.11 -10000 0 -0.45 20 20
HRAS -0.042 0.18 -10000 0 -0.51 38 38
mol:PIP3 -0.003 0.11 -10000 0 -0.44 20 20
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.014 0.034 -10000 0 -0.75 1 1
GAB1 0.007 0.12 -10000 0 -0.49 20 20
FOXO3 0.025 0.1 -10000 0 -0.59 4 4
AKT1 0.014 0.11 -10000 0 -0.45 20 20
BAD 0.023 0.11 -10000 0 -0.59 5 5
megakaryocyte differentiation -0.069 0.21 -10000 0 -0.45 107 107
GSK3B 0.025 0.1 -10000 0 -0.59 4 4
RAF1 -0.01 0.15 -10000 0 -0.45 9 9
SHC1 0.014 0.039 -10000 0 -0.86 1 1
STAT3 0.007 0.12 -10000 0 -0.49 20 20
STAT1 -0.015 0.24 -10000 0 -1 20 20
HRAS/SPRED1 -0.067 0.12 -10000 0 -0.43 17 17
cell proliferation 0.008 0.12 -10000 0 -0.48 20 20
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.12 -10000 0 -0.47 22 22
HRAS/SPRED2 -0.067 0.12 -10000 0 -0.43 18 18
LYN/TEC/p62DOK -0.017 0.099 -10000 0 -0.66 4 4
MAPK3 0.012 0.11 -10000 0 -0.37 2 2
STAP1 -0.31 0.22 -10000 0 -0.42 382 382
GRAP2 -0.043 0.22 -10000 0 -0.86 34 34
JAK2 -0.066 0.18 -10000 0 -0.79 27 27
STAT1 (dimer) -0.013 0.23 -10000 0 -1 20 20
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.12 0.21 -10000 0 -0.46 125 125
actin filament polymerization 0.003 0.12 -10000 0 -0.47 25 25
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.29 0.23 -10000 0 -0.86 29 29
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
CBL/CRKL/GRB2 -0.014 0.091 -10000 0 -0.59 4 4
PI3K -0.019 0.1 -10000 0 -0.45 21 21
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.34 -10000 0 -1.3 22 22
MAPK8 0.007 0.12 -10000 0 -0.49 20 20
STAT3 (dimer) 0.008 0.12 -10000 0 -0.48 20 20
positive regulation of transcription 0.015 0.098 -10000 0 -0.31 1 1
mol:GDP -0.11 0.19 -10000 0 -0.62 41 41
PIK3C2B 0.007 0.12 -10000 0 -0.49 20 20
CBL/CRKL 0.026 0.11 -10000 0 -0.62 4 4
FER 0.006 0.12 -10000 0 -0.5 22 22
SH2B3 0.007 0.12 -10000 0 -0.49 20 20
PDPK1 0.007 0.1 -10000 0 -0.56 5 5
SNAI2 0.007 0.12 -10000 0 -0.51 20 20
positive regulation of cell proliferation 0.001 0.18 -10000 0 -0.69 27 27
KITLG 0.001 0.1 -10000 0 -0.77 9 9
cell motility 0.001 0.18 -10000 0 -0.69 27 27
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.04 0.071 -10000 0 -10000 0 0
STAT5A (dimer) 0.004 0.16 -10000 0 -0.58 28 28
SOCS1 0.005 0.095 -10000 0 -0.86 6 6
cell migration 0.04 0.19 0.5 64 -10000 0 64
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.29 0.42 -10000 0 -0.85 178 178
VAV1 -0.19 0.37 -10000 0 -0.86 119 119
GRB10 0.007 0.12 -10000 0 -0.49 20 20
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.034 0.11 -10000 0 -0.45 32 32
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.006 0.12 -10000 0 -0.42 2 2
CBL 0.014 0.034 -10000 0 -0.75 1 1
KIT -0.009 0.28 -10000 0 -1.1 27 27
MAP2K2 0.005 0.12 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.018 0.1 -10000 0 -0.61 5 5
STAT5A 0.003 0.16 -10000 0 -0.6 28 28
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.007 0.12 -10000 0 -0.49 20 20
SHC/GRAP2 -0.046 0.17 -10000 0 -0.66 35 35
PTPRO -0.071 0.22 -10000 0 -0.46 107 107
SH2B2 0.002 0.13 -10000 0 -0.48 25 25
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.042 0.19 -10000 0 -0.51 64 64
CREBBP 0.045 0.012 -10000 0 -10000 0 0
BCL2 0.043 0.068 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.24 0.41 -10000 0 -0.82 161 161
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.054 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.004 0.1 -10000 0 -0.84 7 7
GR alpha/HSP90/FKBP51/HSP90 0.053 0.13 0.39 4 -0.58 7 11
PRL -0.014 0.11 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.57 75 -0.62 2 77
RELA 0.004 0.076 -10000 0 -10000 0 0
FGG -0.14 0.43 0.59 11 -0.72 150 161
GR beta/TIF2 0.052 0.14 0.42 5 -0.54 8 13
IFNG -0.41 0.43 -10000 0 -0.86 207 207
apoptosis -0.094 0.21 -10000 0 -0.8 2 2
CREB1 -0.015 0.1 -10000 0 -0.42 1 1
histone acetylation 0.016 0.13 0.38 7 -0.5 4 11
BGLAP -0.008 0.13 -10000 0 -0.74 3 3
GR/PKAc 0.064 0.1 0.4 2 -0.6 1 3
NF kappa B1 p50/RelA 0.011 0.15 -10000 0 -0.58 7 7
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.046 0.093 0.33 7 -10000 0 7
GATA3 -0.35 0.38 -10000 0 -0.74 244 244
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.029 0.15 -10000 0 -0.74 12 12
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.058 0.23 -10000 0 -0.83 12 12
CSN2 0.044 0.19 0.5 4 -0.66 1 5
BRG1/BAF155/BAF170/BAF60A 0.003 0.013 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.02 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.053 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 61 61
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.007 0.21 0.39 1 -0.6 20 21
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.22 -10000 0 -0.84 12 12
JUN -0.21 0.24 -10000 0 -0.61 81 81
IL4 -0.022 0.12 -10000 0 -0.63 1 1
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 0.3 4 -0.64 101 105
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.059 0.12 0.41 2 -0.6 4 6
cortisol/GR alpha (monomer) 0.15 0.34 0.67 85 -0.8 1 86
NCOA2 0.004 0.095 -10000 0 -0.75 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.055 0.14 -10000 0 -0.83 13 13
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.81 103 103
AFP -0.35 0.56 -10000 0 -1.4 106 106
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.083 0.15 0.54 5 -0.62 1 6
TP53 0.044 0.021 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.25 0.41 -10000 0 -1.2 66 66
KRT14 -0.14 0.29 -10000 0 -0.83 69 69
TBP 0.028 0.01 -10000 0 -10000 0 0
CREBBP 0.045 0.078 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.32 0.34 -10000 0 -0.82 105 105
MAPK14 0.011 0.007 -10000 0 -10000 0 0
MAPK10 0.004 0.076 -10000 0 -0.76 5 5
MAPK11 0.009 0.04 -10000 0 -0.88 1 1
KRT5 -0.26 0.38 -10000 0 -0.93 100 100
interleukin-1 receptor activity 0.001 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.055 -10000 0 -1.2 1 1
CGA -0.13 0.37 -10000 0 -1.2 50 50
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.087 0.15 0.49 25 -10000 0 25
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.011 0.007 -10000 0 -10000 0 0
ICAM1 -0.048 0.23 -10000 0 -0.75 28 28
NFKB1 0.003 0.086 -10000 0 -0.9 1 1
MAPK8 -0.14 0.19 -10000 0 -0.52 36 36
MAPK9 0.011 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.1 0.22 -10000 0 -0.86 2 2
BAX 0.052 0.029 -10000 0 -10000 0 0
POMC -0.036 0.17 -10000 0 -0.86 6 6
EP300 0.043 0.083 -10000 0 -0.6 1 1
cortisol/GR alpha (dimer)/p53 0.16 0.28 0.59 82 -0.7 1 83
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.071 0.29 1 -10000 0 1
SGK1 0.1 0.095 -10000 0 -10000 0 0
IL13 -0.35 0.28 -10000 0 -0.77 103 103
IL6 -0.12 0.38 -10000 0 -0.98 69 69
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.29 0.21 -10000 0 -0.73 32 32
IL2 -0.17 0.25 -10000 0 -0.76 37 37
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.077 0.3 -10000 0 -0.92 42 42
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.11 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.26 0.58 58 -0.65 1 59
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.15 0.42 27 -10000 0 27
NF kappa B1 p50/RelA/Cbp 0.06 0.14 -10000 0 -0.94 1 1
JUN (dimer) -0.21 0.24 -10000 0 -0.61 81 81
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.058 0.22 -10000 0 -0.92 19 19
NR3C1 0.079 0.19 0.5 31 -0.94 1 32
NR4A1 0.001 0.13 -10000 0 -0.73 16 16
TIF2/SUV420H1 -0.009 0.07 -10000 0 -0.56 8 8
MAPKKK cascade -0.094 0.21 -10000 0 -0.8 2 2
cortisol/GR alpha (dimer)/Src-1 0.15 0.28 0.58 81 -0.8 1 82
PBX1 -0.003 0.13 -10000 0 -0.74 15 15
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.096 0.37 -10000 0 -1.3 38 38
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.42 27 -10000 0 27
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.26 0.58 58 -0.65 1 59
mol:cortisol 0.062 0.19 0.41 61 -10000 0 61
MMP1 -0.23 0.4 -10000 0 -0.98 99 99
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 225 225
alphaV beta3 Integrin -0.008 0.067 -9999 0 -0.55 7 7
PTK2 -0.14 0.23 -9999 0 -0.55 46 46
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.039 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.084 0.19 -9999 0 -0.53 78 78
VEGFA -0.37 0.44 -9999 0 -0.86 225 225
ILK -0.084 0.19 -9999 0 -0.53 78 78
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.077 0.18 -9999 0 -0.5 70 70
PTK2B -0.19 0.27 -9999 0 -0.88 1 1
alphaV/beta3 Integrin/JAM-A -0.069 0.15 -9999 0 -0.52 10 10
CBL 0.014 0.034 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.48 235 235
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.065 -9999 0 -0.52 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.14 -9999 0 -0.47 43 43
alphaV/beta3 Integrin/Syndecan-1 -0.008 0.063 -9999 0 -0.48 9 9
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.14 -9999 0 -0.82 3 3
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Osteopontin -0.007 0.056 -9999 0 -0.48 7 7
RPS6KB1 -0.042 0.13 -9999 0 -0.75 3 3
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.041 0.093 -9999 0 -0.69 4 4
GPR124 0.012 0.055 -9999 0 -0.86 2 2
MAPK1 -0.041 0.093 -9999 0 -0.69 4 4
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Tumstatin -0.057 0.16 -9999 0 -0.48 60 60
cell adhesion -0.17 0.18 -9999 0 -0.83 1 1
ANGPTL3 -0.33 0.38 -9999 0 -0.75 232 232
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 225 225
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.011 0.059 -9999 0 -0.75 3 3
IGF1 0.005 0.095 -9999 0 -0.86 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.005 0.051 -9999 0 -0.51 5 5
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.003 0.037 -9999 0 -0.48 3 3
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.016 0.093 -9999 0 -0.54 15 15
CSF1 0.014 0.034 -9999 0 -0.75 1 1
PIK3C2A -0.086 0.2 -9999 0 -0.54 79 79
PI4 Kinase/Pyk2 -0.23 0.24 -9999 0 -0.76 44 44
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 225 225
FAK1/Vinculin -0.11 0.18 -9999 0 -0.56 3 3
alphaV beta3/Integrin/ppsTEM5 -0.005 0.051 -9999 0 -0.52 5 5
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.1 0.28 -9999 0 -0.76 78 78
BCAR1 0.014 0.034 -9999 0 -0.75 1 1
FGF2 0.008 0.078 -9999 0 -0.77 5 5
F11R 0.025 0.061 -9999 0 -0.58 5 5
alphaV/beta3 Integrin/Lactadherin -0.004 0.045 -9999 0 -0.5 4 4
alphaV/beta3 Integrin/TGFBR2 -0.003 0.037 -9999 0 -0.48 3 3
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.042 -9999 0 -0.86 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.003 0.034 -9999 0 -0.44 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.05 0.23 -9999 0 -0.86 38 38
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.88 1 1
SDC1 0.007 0.083 -9999 0 -0.75 6 6
VAV3 0.039 0.085 -9999 0 -0.8 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.011 0.059 -9999 0 -0.75 3 3
FAK1/Paxillin -0.11 0.18 -9999 0 -0.56 3 3
cell migration -0.088 0.17 -9999 0 -0.52 2 2
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.062 0.14 -9999 0 -1.1 1 1
SPP1 0.01 0.068 -9999 0 -0.75 4 4
KDR 0.014 0.034 -9999 0 -0.75 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.072 0.24 -9999 0 -0.75 58 58
angiogenesis 0.004 0.15 -9999 0 -0.67 4 4
Rac1/GTP -0.012 0.068 -9999 0 -0.73 1 1
EDIL3 -0.005 0.13 -9999 0 -0.79 13 13
cell proliferation -0.003 0.036 -9999 0 -0.48 3 3
Aurora A 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
Aurora A/GADD45A 0.02 0.045 -9999 0 -10000 0 0
BIRC5 -0.25 0.4 -9999 0 -0.86 151 151
NFKBIA 0.047 0.04 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.76 99 99
AKT1 0.047 0.04 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.018 0.041 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.076 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.014 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.02 0.045 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.011 0.059 -9999 0 -0.75 3 3
TPX2 -0.14 0.3 -9999 0 -0.67 125 125
TP53 0.025 0.037 -9999 0 -10000 0 0
DLG7 0.02 0.044 -9999 0 -0.29 6 6
AURKAIP1 0.011 0.062 -9999 0 -0.79 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.08 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.017 0.041 -9999 0 -10000 0 0
AURKA 0.027 0.055 -9999 0 -0.34 6 6
AURKB -0.14 0.15 -9999 0 -0.29 240 240
CDC25B 0.018 0.063 -9999 0 -0.58 2 2
G2/M transition checkpoint 0.015 0.054 -9999 0 -0.44 3 3
mRNA polyadenylation -0.072 0.19 -9999 0 -0.44 99 99
Aurora A/CPEB -0.072 0.19 -9999 0 -0.45 99 99
Aurora A/TACC1/TRAP/chTOG 0.022 0.044 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.02 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.007 0.066 -9999 0 -0.73 4 4
spindle assembly -0.003 0.023 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.22 -9999 0 -0.47 151 151
CENPA -0.12 0.14 -9999 0 -0.3 167 167
Aurora A/PP2A 0.02 0.045 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.053 0.036 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.037 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.034 -9999 0 -0.75 1 1
Ajuba/Aurora A 0.015 0.054 -9999 0 -0.44 3 3
mitotic prometaphase 0.037 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.05 -9999 0 -0.34 6 6
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.009 0.078 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.018 0.062 -9999 0 -0.52 2 2
Aurora A/RasGAP 0.019 0.051 -9999 0 -0.48 1 1
OAZ1 0.014 0.039 -9999 0 -0.86 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.66 125 125
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.09 0.25 -9999 0 -0.52 125 125
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-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
AKT1 -0.087 0.31 -10000 0 -0.91 29 29
NCK1/PAK1/Dok-R -0.084 0.11 -10000 0 -0.41 33 33
NCK1/Dok-R -0.086 0.27 -10000 0 -1.1 31 31
PIK3CA 0.004 0.034 -10000 0 -0.75 1 1
mol:beta2-estradiol -0.006 0.039 0.32 5 -10000 0 5
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.006 0.04 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.32 0.42 -10000 0 -0.85 191 191
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.059 0.24 -10000 0 -0.97 30 30
FN1 -0.05 0.23 -10000 0 -0.86 38 38
PLD2 0.031 0.3 -10000 0 -1.1 30 30
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.027 0.17 -10000 0 -0.75 28 28
ELK1 0.06 0.27 -10000 0 -0.97 30 30
GRB7 0.005 0.089 -10000 0 -0.75 7 7
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.3 -10000 0 -1 44 44
CDKN1A -0.11 0.31 -10000 0 -0.66 24 24
ITGA5 -0.048 0.23 -10000 0 -0.86 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.086 0.27 -10000 0 -1.1 31 31
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.051 0.26 -10000 0 -0.65 29 29
PLG -0.19 0.35 -10000 0 -1.3 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.21 -10000 0 -0.85 29 29
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.035 -10000 0 -0.75 1 1
ANGPT2 -0.21 0.38 -10000 0 -0.64 165 165
BMX -0.038 0.34 -10000 0 -1.1 30 30
ANGPT1 0.074 0.2 -10000 0 -1.2 8 8
tube development -0.13 0.34 -10000 0 -0.73 25 25
ANGPT4 -0.018 0.15 -10000 0 -0.87 15 15
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.046 0.32 -10000 0 -1.2 30 30
alpha5/beta1 Integrin -0.049 0.17 -10000 0 -0.66 37 37
FGF2 0.009 0.08 -10000 0 -0.77 5 5
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 25 25
mol:L-citrulline -0.051 0.26 -10000 0 -0.65 29 29
AGTR1 -0.037 0.17 -10000 0 -0.75 28 28
MAPK14 -0.006 0.31 -10000 0 -1.2 29 29
Tie2/SHP2 -0.063 0.26 -10000 0 -1.1 28 28
TEK -0.049 0.29 -10000 0 -1.2 28 28
RPS6KB1 -0.049 0.28 -10000 0 -0.87 29 29
Angiotensin II/AT1 -0.044 0.13 -10000 0 -0.58 28 28
Tie2/Ang1/GRB2 -0.025 0.3 -10000 0 -1.1 30 30
MAPK3 0.043 0.28 -10000 0 -1 30 30
MAPK1 0.043 0.28 -10000 0 -1 30 30
Tie2/Ang1/GRB7 -0.03 0.31 -10000 0 -1.2 30 30
NFKB1 0.014 0.034 -10000 0 -0.75 1 1
MAPK8 0.03 0.3 -10000 0 -1.1 30 30
PI3K -0.073 0.32 -10000 0 -1.1 29 29
FES -0.011 0.32 -10000 0 -1.1 30 30
Crk/Dok-R -0.085 0.27 -10000 0 -1.1 30 30
Tie2/Ang1/ABIN2 -0.025 0.3 -10000 0 -1.1 30 30
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.076 0.29 -10000 0 -0.8 29 29
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.049 0.28 -10000 0 -0.87 29 29
Tie2/Ang2 -0.19 0.41 -10000 0 -0.99 31 31
Tie2/Ang1 0.022 0.33 -10000 0 -1.2 30 30
FOXO1 -0.11 0.31 -10000 0 -0.81 29 29
ELF1 0.023 0.036 -10000 0 -0.73 1 1
ELF2 0.026 0.31 -10000 0 -1.1 30 30
mol:Choline 0.034 0.29 -10000 0 -1 30 30
cell migration -0.056 0.071 -10000 0 -10000 0 0
FYN -0.16 0.36 -10000 0 -0.85 25 25
DOK2 -0.038 0.21 -10000 0 -0.86 31 31
negative regulation of cell cycle -0.098 0.3 -10000 0 -0.6 24 24
ETS1 0.028 0.038 -10000 0 -10000 0 0
PXN -0.027 0.25 -10000 0 -0.7 29 29
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.062 0.28 -10000 0 -0.75 29 29
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.008 0.11 -10000 0 -0.79 8 8
MAPKKK cascade 0.034 0.29 -10000 0 -1 30 30
RASA1 0.014 0.034 -10000 0 -0.75 1 1
Tie2/Ang1/Shc -0.005 0.31 -10000 0 -1.1 30 30
NCK1 0.014 0.034 -10000 0 -0.75 1 1
vasculogenesis -0.042 0.24 -10000 0 -0.58 29 29
mol:Phosphatidic acid 0.034 0.29 -10000 0 -1 30 30
mol:Angiotensin II -0.017 0.022 -10000 0 -10000 0 0
mol:NADP -0.051 0.26 -10000 0 -0.65 29 29
Rac1/GTP -0.13 0.19 -10000 0 -0.8 29 29
MMP2 0.025 0.31 -10000 0 -1.1 30 30
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.009 0.079 -9999 0 -0.68 7 7
Metarhodopsin II/Arrestin -0.019 0.1 -9999 0 -0.59 16 16
PDE6G/GNAT1/GTP -0.013 0.085 -9999 0 -0.56 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.006 0.1 -9999 0 -0.86 7 7
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.95 12 12
mol:Na + -0.11 0.21 -9999 0 -0.81 19 19
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.11 0.22 -9999 0 -0.85 19 19
CNGB1 -0.009 0.13 -9999 0 -0.86 11 11
RDH5 -0.003 0.12 -9999 0 -0.83 11 11
SAG 0.001 0.039 -9999 0 -0.86 1 1
mol:Ca2+ -0.067 0.22 -9999 0 -0.78 19 19
Na + (4 Units) -0.1 0.19 -9999 0 -0.74 19 19
RGS9 -0.007 0.14 -9999 0 -0.81 14 14
GNB1/GNGT1 -0.23 0.32 -9999 0 -0.66 172 172
GNAT1/GDP -0.037 0.13 -9999 0 -0.53 14 14
GUCY2D -0.028 0.18 -9999 0 -0.86 23 23
GNGT1 -0.28 0.41 -9999 0 -0.86 172 172
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.15 -9999 0 -0.6 27 27
mol:11-cis-retinal -0.003 0.12 -9999 0 -0.83 11 11
mol:cGMP -0.039 0.14 -9999 0 -0.52 36 36
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.034 0.14 -9999 0 -0.65 26 26
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.12 0.3 -9999 0 -0.75 93 93
Metarhodopsin II -0.016 0.093 -9999 0 -0.55 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.041 0.14 -9999 0 -0.54 38 38
RGS9BP -0.016 0.15 -9999 0 -0.75 21 21
Metarhodopsin II/Transducin -0.11 0.16 -9999 0 -0.62 11 11
GCAP Family/Ca ++ -0.017 0.098 -9999 0 -0.56 15 15
PDE6A/B -0.035 0.15 -9999 0 -0.66 27 27
mol:Pi -0.034 0.13 -9999 0 -0.5 35 35
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.27 -9999 0 -0.55 174 174
PDE6B 0.007 0.083 -9999 0 -0.75 6 6
PDE6A -0.024 0.18 -9999 0 -0.86 22 22
PDE6G 0.008 0.078 -9999 0 -0.77 5 5
RHO -0.016 0.15 -9999 0 -0.86 15 15
PDE6 -0.056 0.16 -9999 0 -0.83 8 8
GUCA1A -0.009 0.12 -9999 0 -0.86 9 9
GC2/GCAP Family -0.017 0.098 -9999 0 -0.56 15 15
GUCA1C 0.001 0.048 -9999 0 -0.75 2 2
GUCA1B 0.007 0.087 -9999 0 -0.86 5 5
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.047 0.1 -10000 0 -0.47 9 9
PTP1B/AKT1 -0.032 0.047 -10000 0 -0.41 2 2
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.049 0.053 -10000 0 -0.39 5 5
EGFR -0.014 0.12 -10000 0 -0.87 9 9
EGF/EGFR -0.37 0.14 -10000 0 -0.41 454 454
CSF1 0.014 0.034 -10000 0 -0.75 1 1
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.086 -10000 0 -0.44 17 17
Insulin Receptor/Insulin -0.008 0.034 -10000 0 -10000 0 0
HCK -0.033 0.2 -10000 0 -0.86 28 28
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.035 0.05 -10000 0 -0.44 2 2
EGF -0.67 0.23 -10000 0 -0.75 455 455
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 39 39
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.032 0.051 -10000 0 -0.43 5 5
cell migration 0.049 0.053 0.39 5 -10000 0 5
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.093 0.25 -10000 0 -0.75 64 64
ITGA2B -0.029 0.16 -10000 0 -0.86 18 18
CSF1R 0.004 0.1 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.072 0.19 -10000 0 -0.57 64 64
FGR 0.011 0.067 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.052 -10000 0 -0.41 4 4
Crk/p130 Cas -0.031 0.042 -10000 0 -0.42 2 2
DOK1 -0.019 0.046 -10000 0 -0.38 2 2
JAK2 -0.053 0.11 -10000 0 -0.38 23 23
Jak2/Leptin Receptor/Leptin -0.053 0.13 -10000 0 -0.52 9 9
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
PTPN1 -0.049 0.053 -10000 0 -0.39 5 5
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.007 0.13 -10000 0 -0.75 15 15
SRC 0 0.021 -10000 0 -10000 0 0
ITGB3 -0.003 0.058 -10000 0 -0.75 3 3
CAT1/PTP1B -0.24 0.14 -10000 0 -0.56 40 40
CAPN1 0.002 0.005 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.009 0.043 -10000 0 -0.63 1 1
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.035 0.12 -10000 0 -0.6 3 3
negative regulation of transcription -0.052 0.11 -10000 0 -0.38 23 23
FCGR2A -0.024 0.18 -10000 0 -0.86 23 23
FER -0.001 0.048 -10000 0 -0.76 2 2
alphaIIb/beta3 Integrin -0.027 0.13 -10000 0 -0.65 21 21
BLK -0.04 0.21 -10000 0 -0.86 32 32
Insulin Receptor/Insulin/Shc -0.001 0.026 -10000 0 -0.59 1 1
RHOA 0.002 0.005 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.034 -10000 0 -0.75 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.22 0.15 -10000 0 -0.55 59 59
PRL 0.001 0.004 -10000 0 -10000 0 0
SOCS3 0.028 0.049 -10000 0 -0.72 2 2
SPRY2 0.001 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.038 -10000 0 -0.49 3 3
CSF1/CSF1R -0.038 0.076 -10000 0 -0.53 10 10
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.011 0.059 -10000 0 -0.75 3 3
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.075 0.26 -10000 0 -0.86 50 50
STAT5B -0.045 0.068 -10000 0 -0.46 5 5
STAT5A -0.045 0.068 -10000 0 -0.46 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.05 -10000 0 -0.42 3 3
CSN2 -0.007 0.068 -10000 0 -10000 0 0
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
LAT -0.1 0.17 -10000 0 -0.35 146 146
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.022 0.18 -10000 0 -0.85 22 22
SHC1 0.014 0.039 -10000 0 -0.86 1 1
NOX4 -0.006 0.075 -10000 0 -0.76 5 5
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.012 0.055 -9999 0 -0.86 2 2
RELN/VLDLR/Fyn -0.16 0.23 -9999 0 -0.48 167 167
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.002 0.04 -9999 0 -0.81 1 1
AKT1 -0.067 0.16 -9999 0 -0.57 2 2
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.46 179 179
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 18 18
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.82 1 1
long-term memory -0.21 0.25 -9999 0 -0.88 24 24
DAB1/LIS1 -0.14 0.18 -9999 0 -0.86 1 1
DAB1/CRLK/C3G -0.13 0.18 -9999 0 -0.82 1 1
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
DAB1/NCK2 -0.14 0.19 -9999 0 -0.86 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.3 -9999 0 -0.83 75 75
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 167 167
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
RELN/LRP8/Fyn -0.16 0.23 -9999 0 -0.48 168 168
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.26 -9999 0 -0.9 24 24
MAPK8 0.016 0.001 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.45 178 178
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.88 2 2
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 168 168
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.9 2 2
PI3K -0.002 0.035 -9999 0 -0.56 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.042 -9999 0 -0.66 2 2
RAP1A -0.11 0.17 -9999 0 -0.75 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.048 -9999 0 -0.75 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.055 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.028 0.12 -9999 0 -0.54 2 2
neuron adhesion -0.05 0.19 -9999 0 -0.71 1 1
LRP8 0.014 0.039 -9999 0 -0.86 1 1
GSK3B -0.053 0.15 -9999 0 -0.54 2 2
RELN/VLDLR/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 17 17
MAP3K11 0.014 0.034 -9999 0 -0.75 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.61 2 2
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.015 0.084 -9999 0 -0.69 6 6
neuron migration -0.059 0.21 -9999 0 -0.61 1 1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.057 0.1 -9999 0 -0.54 2 2
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 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 0.014 0.034 -9999 0 -0.75 1 1
Caspase 8 (4 units) -0.097 0.092 -9999 0 -10000 0 0
NEF -0.058 0.084 -9999 0 -10000 0 0
NFKBIA 0.001 0.045 -9999 0 -10000 0 0
BIRC3 -0.071 0.31 -9999 0 -0.79 78 78
CYCS -0.078 0.14 -9999 0 -0.43 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.37 0.48 -9999 0 -1 165 165
MAP2K7 -0.041 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.06 0.071 -9999 0 -0.42 3 3
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.091 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.051 0.12 -9999 0 -0.46 1 1
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.051 0.12 -9999 0 -0.46 1 1
MAPK8 -0.028 0.1 -9999 0 -10000 0 0
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.039 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.13 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.047 0.067 -9999 0 -10000 0 0
CHUK 0.061 0.075 -9999 0 -0.46 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.4 0.44 -9999 0 -0.74 271 271
TNF 0.003 0.1 -9999 0 -0.8 8 8
FASLG -0.57 0.61 -9999 0 -1.1 271 271
NFKB1 0 0.055 -9999 0 -0.74 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.069 -9999 0 -0.52 9 9
CASP6 -0.048 0.052 -9999 0 -10000 0 0
CASP7 -0.061 0.21 -9999 0 -0.55 52 52
RELA 0.001 0.045 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.061 0.21 -9999 0 -0.55 52 52
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.025 -9999 0 -0.56 1 1
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.08 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.56 52 52
BCL2 -0.016 0.096 -9999 0 -10000 0 0
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 -0.043 0.15 -9999 0 -0.58 38 38
EPHB2 0 0.11 -9999 0 -0.77 10 10
Syndecan-2/TACI -0.056 0.17 -9999 0 -0.58 49 49
LAMA1 -0.007 0.13 -9999 0 -0.76 15 15
Syndecan-2/alpha2 ITGB1 -0.01 0.067 -9999 0 -0.49 7 7
HRAS 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.048 0.23 -9999 0 -0.86 37 37
BAX 0.055 0.001 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.002 0.11 -9999 0 -0.86 8 8
Syndecan-2/MMP2 -0.007 0.061 -9999 0 -0.56 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.004 0.05 -9999 0 -0.56 4 4
dendrite morphogenesis -0.01 0.069 -9999 0 -0.5 10 10
Syndecan-2/GM-CSF -0.017 0.098 -9999 0 -0.58 15 15
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.026 -9999 0 -0.58 1 1
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
MAPK3 0.021 0.095 -9999 0 -0.52 15 15
MAPK1 0.021 0.095 -9999 0 -0.52 15 15
Syndecan-2/RACK1 -0.002 0.031 -9999 0 -0.5 2 2
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.01 0.068 -9999 0 -0.75 4 4
MAPK8 0.047 0.001 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.015 0.081 -9999 0 -0.65 2 2
Syndecan-2/Kininogen -0.36 0.21 -9999 0 -0.48 379 379
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.048 0.032 -9999 0 -0.46 2 2
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.006 0.057 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.043 0.15 -9999 0 -0.57 38 38
Syndecan-2/Caveolin-2/Ras -0.009 0.069 -9999 0 -0.52 9 9
Syndecan-2/Laminin alpha3 -0.008 0.067 -9999 0 -0.58 7 7
Syndecan-2/RasGAP -0.003 0.044 -9999 0 -0.67 2 2
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.66 37 37
PRKCD 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.07 -9999 0 -0.5 10 10
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.003 0.042 -9999 0 -0.83 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.071 0.26 -9999 0 -0.86 49 49
RASA1 0.014 0.034 -9999 0 -0.75 1 1
alpha2/beta1 Integrin -0.004 0.05 -9999 0 -0.56 4 4
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.087 -9999 0 -0.86 5 5
CASP3 0.043 0.025 -9999 0 -0.52 1 1
FN1 -0.05 0.23 -9999 0 -0.86 38 38
Syndecan-2/IL8 -0.036 0.14 -9999 0 -0.56 33 33
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.56 0.32 -9999 0 -0.75 379 379
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.019 0.15 -9999 0 -0.86 15 15
Syndecan-2/TGFB1 -0.006 0.057 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.044 0 -9999 0 -10000 0 0
angiogenesis -0.036 0.14 -9999 0 -0.56 33 33
MMP2 0.006 0.093 -9999 0 -0.84 6 6
IL8 -0.04 0.21 -9999 0 -0.84 33 33
calcineurin-NFAT signaling pathway -0.056 0.17 -9999 0 -0.57 49 49
Endothelins

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
AKT1 0.006 0.22 -10000 0 -0.88 3 3
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.086 0.12 -10000 0 -0.76 2 2
EDN1 -0.017 0.2 -10000 0 -0.76 18 18
EDN3 -0.02 0.16 -10000 0 -0.86 17 17
EDN2 -0.088 0.28 -10000 0 -0.82 63 63
HRAS/GDP 0.051 0.17 -10000 0 -0.7 9 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.021 0.15 -10000 0 -0.5 16 16
ADCY4 0.008 0.17 -10000 0 -0.74 3 3
ADCY5 -0.01 0.2 -10000 0 -0.69 14 14
ADCY6 0.007 0.17 -10000 0 -0.74 3 3
ADCY7 -0.007 0.19 -10000 0 -0.72 7 7
ADCY1 -0.002 0.18 -10000 0 -0.74 4 4
ADCY2 -0.12 0.27 -10000 0 -0.71 28 28
ADCY3 0.008 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.27 -10000 0 -0.74 33 33
ADCY9 0.008 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.077 0.15 -10000 0 -0.53 10 10
ETB receptor/Endothelin-1/Gq/GTP 0.035 0.11 -10000 0 -0.46 11 11
GNAO1 0.007 0.085 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
ETA receptor/Endothelin-1/G12/GTP -0.016 0.22 0.38 69 -0.82 3 72
ETA receptor/Endothelin-1/Gs/GTP -0.015 0.21 0.36 69 -0.79 3 72
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.046 0.34 -10000 0 -0.95 52 52
EDNRB 0.006 0.069 -10000 0 -0.78 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.045 0.3 -10000 0 -0.75 48 48
CYSLTR1 0.005 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.015 0.11 -10000 0 -0.39 2 2
mol:GDP 0.045 0.18 -10000 0 -0.7 11 11
SLC9A3 -0.35 0.3 -10000 0 -0.53 318 318
RAF1 0.047 0.17 -10000 0 -0.68 10 10
JUN 0.088 0.12 -10000 0 -0.57 1 1
JAK2 0.006 0.22 -10000 0 -0.88 3 3
mol:IP3 0.018 0.17 -10000 0 -0.58 16 16
ETA receptor/Endothelin-1 -0.029 0.28 0.45 69 -0.65 19 88
PLCB1 0.003 0.1 -10000 0 -0.75 9 9
PLCB2 -0.08 0.28 -10000 0 -0.86 56 56
ETA receptor/Endothelin-3 -0.024 0.15 -10000 0 -0.68 19 19
FOS 0.059 0.2 -10000 0 -0.86 15 15
Gai/GDP 0.038 0.07 -10000 0 -0.63 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.002 0.24 -10000 0 -0.77 16 16
BCAR1 0.014 0.034 -10000 0 -0.75 1 1
PRKCB1 0.019 0.16 -10000 0 -0.55 16 16
GNAQ 0.02 0.004 -10000 0 -10000 0 0
GNAZ 0.011 0.059 -10000 0 -0.75 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.044 0.11 -10000 0 -0.61 11 11
ETA receptor/Endothelin-1/Gq/GTP 0.044 0.14 -10000 0 -0.5 9 9
MAPK14 0.024 0.13 -10000 0 -0.56 10 10
TRPC6 0.086 0.13 -10000 0 -0.81 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.059 -10000 0 -0.75 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.14 -10000 0 -0.55 13 13
ETB receptor/Endothelin-2 -0.084 0.21 -10000 0 -0.62 66 66
ETB receptor/Endothelin-3 -0.03 0.13 -10000 0 -0.66 20 20
ETB receptor/Endothelin-1 -0.034 0.16 -10000 0 -0.62 19 19
MAPK3 0.06 0.19 -10000 0 -0.72 17 17
MAPK1 0.06 0.19 -10000 0 -0.72 17 17
Rac1/GDP 0.052 0.17 -10000 0 -0.71 8 8
cAMP biosynthetic process -0.062 0.19 -10000 0 -0.65 10 10
MAPK8 0.08 0.13 -10000 0 -0.58 2 2
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.029 0.092 -10000 0 -0.57 3 3
p130Cas/CRK/Src/PYK2 0.073 0.17 -10000 0 -0.7 8 8
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.052 0.17 -10000 0 -0.68 9 9
COL1A2 -0.1 0.34 -10000 0 -0.88 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.079 0.22 -10000 0 -0.63 65 65
mol:DAG 0.018 0.17 -10000 0 -0.58 16 16
MAP2K2 0.057 0.18 -10000 0 -0.7 10 10
MAP2K1 0.057 0.17 -10000 0 -0.68 10 10
EDNRA -0.009 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.017 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.033 0.14 -10000 0 -0.7 14 14
HRAS/GTP 0.036 0.17 -10000 0 -0.69 11 11
PRKCH 0.029 0.16 -10000 0 -0.6 12 12
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.029 0.16 -10000 0 -0.66 9 9
PRKCB 0.024 0.18 -10000 0 -0.71 13 13
PRKCE 0.028 0.16 -10000 0 -0.59 13 13
PRKCD 0.028 0.16 -10000 0 -0.64 10 10
PRKCG 0.003 0.2 -10000 0 -0.69 21 21
regulation of vascular smooth muscle contraction 0.058 0.23 -10000 0 -1 15 15
PRKCQ 0.016 0.18 -10000 0 -0.64 17 17
PLA2G4A 0.077 0.16 -10000 0 -0.57 10 10
GNA14 0.009 0.09 -10000 0 -0.75 7 7
GNA15 -0.006 0.14 -10000 0 -0.86 14 14
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.016 0.048 -10000 0 -0.75 2 2
Rac1/GTP -0.015 0.22 0.38 69 -0.82 3 72
MMP1 -0.13 0.37 -10000 0 -0.85 99 99
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.059 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.041 0.16 -10000 0 -0.61 34 34
NT3 (dimer)/TRKB -0.13 0.25 -10000 0 -0.54 125 125
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.022 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.1 0.3 -10000 0 -0.86 68 68
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.045 0.21 -10000 0 -0.76 39 39
NTRK2 -0.13 0.3 -10000 0 -0.75 96 96
NTRK3 -0.03 0.18 -10000 0 -0.75 30 30
NT-4/5 (dimer)/TRKB -0.13 0.25 -10000 0 -0.55 123 123
neuron apoptosis 0.14 0.18 0.57 48 -10000 0 48
SHC 2-3/Grb2 -0.16 0.2 -10000 0 -0.64 48 48
SHC1 0.014 0.039 -10000 0 -0.86 1 1
SHC2 -0.097 0.14 -10000 0 -0.52 33 33
SHC3 -0.16 0.24 -10000 0 -0.64 87 87
STAT3 (dimer) 0.013 0.067 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.081 0.2 -10000 0 -0.56 74 74
RIN/GDP 0.049 0.064 -10000 0 -0.32 1 1
GIPC1 0.014 0.034 -10000 0 -0.75 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.068 0.14 -10000 0 -0.63 13 13
RIN/GTP -0.001 0.03 -10000 0 -0.68 1 1
CCND1 0.01 0.16 -10000 0 -0.78 19 19
MAGED1 0.014 0.039 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.086 -10000 0 -0.86 5 5
SHC/GRB2/SOS1 -0.001 0.025 -10000 0 -0.57 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.14 0.27 -10000 0 -0.59 123 123
TRKA/NEDD4-2 -0.045 0.16 -10000 0 -0.58 39 39
ELMO1 0.012 0.055 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.043 -10000 0 -0.55 3 3
NGF -0.066 0.25 -10000 0 -0.86 47 47
HRAS 0.014 0.039 -10000 0 -0.86 1 1
DOCK1 0.014 0.034 -10000 0 -0.75 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.039 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.002 0.12 -10000 0 -0.86 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.068 0.14 -10000 0 -0.59 15 15
mol:GDP 0.063 0.087 -10000 0 -0.48 2 2
NGF (dimer) -0.065 0.25 -10000 0 -0.86 47 47
RhoG/GDP -0.003 0.042 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.063 -10000 0 -0.31 1 1
TIAM1 0.014 0.034 -10000 0 -0.75 1 1
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
BDNF (dimer)/TRKB -0.17 0.26 -10000 0 -0.55 152 152
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.039 -10000 0 -0.61 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.023 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.093 -10000 0 -0.78 7 7
RAP1/GDP -0.008 0.031 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.1 0.3 -10000 0 -0.86 68 68
ubiquitin-dependent protein catabolic process -0.091 0.21 -10000 0 -0.55 84 84
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.24 -10000 0 -0.82 30 30
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.05 0.078 -10000 0 -10000 0 0
STAT3 0.013 0.067 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.76 30 30
MAPK3 -0.096 0.26 -10000 0 -0.57 90 90
MAPK1 -0.096 0.26 -10000 0 -0.57 90 90
CDC42/GDP 0.055 0.063 -10000 0 -0.31 1 1
NTF3 0.005 0.093 -10000 0 -0.78 7 7
NTF4 -0.003 0.086 -10000 0 -0.86 5 5
NGF (dimer)/TRKA/FAIM -0.09 0.2 -10000 0 -0.54 84 84
PI3K -0.002 0.035 -10000 0 -0.56 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.078 0.16 -10000 0 -0.6 22 22
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0 0.14 -10000 0 -0.52 34 34
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.05 0.065 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.063 -10000 0 -0.31 1 1
NGF (dimer)/TRKA/GRIT -0.092 0.21 -10000 0 -0.56 84 84
neuron projection morphogenesis -0.02 0.14 -10000 0 -0.57 6 6
NGF (dimer)/TRKA/NEDD4-2 -0.091 0.21 -10000 0 -0.55 84 84
MAP2K1 0.053 0.024 -10000 0 -10000 0 0
NGFR -0.042 0.22 -10000 0 -0.86 33 33
NGF (dimer)/TRKA/GIPC/GAIP -0.054 0.12 -10000 0 -0.59 3 3
RAS family/GTP/PI3K -0.002 0.03 -10000 0 -0.6 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.059 -10000 0 -0.75 3 3
MAPKKK cascade -0.096 0.18 -10000 0 -0.61 44 44
RASA1 0.014 0.034 -10000 0 -0.75 1 1
TRKA/c-Abl -0.044 0.15 -10000 0 -0.57 39 39
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.15 0.24 -10000 0 -0.6 67 67
NGF (dimer)/TRKA/p62/Atypical PKCs -0.078 0.18 -10000 0 -0.87 3 3
MATK -0.068 0.26 -10000 0 -0.86 48 48
NEDD4L 0.014 0.034 -10000 0 -0.75 1 1
RAS family/GDP -0.008 0.032 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.074 0.15 -10000 0 -0.48 35 35
Rac1/GTP -0.044 0.084 -10000 0 -0.42 6 6
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.065 0.13 -9999 0 -0.6 8 8
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.014 0.16 -9999 0 -0.86 17 17
WNT4 -0.071 0.24 -9999 0 -0.75 57 57
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.059 -9999 0 -0.75 3 3
WNT11 -0.041 0.2 -9999 0 -0.76 37 37
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.014 0.035 -10000 0 -0.73 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.022 0.088 -10000 0 -0.52 4 4
AKT1 0.02 0.006 -10000 0 -10000 0 0
GSC -0.028 0.23 -10000 0 -0.76 43 43
NKX2-5 -0.049 0.22 -10000 0 -0.86 34 34
muscle cell differentiation 0.034 0.11 0.57 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.037 0.079 -10000 0 -10000 0 0
SMAD4 0.032 0.03 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.003 0.047 -10000 0 -0.56 2 2
SMAD3/SMAD4/VDR 0.011 0.051 -10000 0 -10000 0 0
MYC -0.03 0.16 -10000 0 -0.86 18 18
CDKN2B 0.055 0.091 -10000 0 -0.67 6 6
AP1 0.059 0.076 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.013 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.043 0.07 -10000 0 -0.53 1 1
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.06 0.25 -10000 0 -0.88 43 43
SMAD3/SMAD4/GR 0.009 0.045 -10000 0 -0.6 1 1
GATA3 -0.35 0.38 -10000 0 -0.74 244 244
SKI/SIN3/HDAC complex/NCoR1 0.054 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 -0.076 0.2 -10000 0 -0.81 20 20
endothelial cell migration 0.095 0.26 0.73 72 -10000 0 72
MAX 0.018 0.017 -10000 0 -10000 0 0
RBBP7 0.015 0.005 -10000 0 -10000 0 0
RBBP4 0.013 0.034 -10000 0 -0.75 1 1
RUNX2 -0.009 0.14 -10000 0 -0.86 14 14
RUNX3 -0.35 0.43 -10000 0 -0.86 213 213
RUNX1 -0.048 0.23 -10000 0 -0.86 37 37
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.016 0.043 -10000 0 -0.87 1 1
VDR 0.011 0.059 -10000 0 -0.75 3 3
CDKN1A 0.083 0.075 -10000 0 -0.64 2 2
KAT2B 0.013 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.054 0.18 -10000 0 -0.61 43 43
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.005 -10000 0 -10000 0 0
SERPINE1 -0.098 0.26 -10000 0 -0.74 72 72
SMAD3/SMAD4/ATF2 0.008 0.038 -10000 0 -0.48 1 1
SMAD3/SMAD4/ATF3 0.005 0.054 -10000 0 -0.49 4 4
SAP30 -0.016 0.16 -10000 0 -0.86 18 18
Cbp/p300/PIAS3 0.007 0.036 -10000 0 -0.45 1 1
JUN 0.074 0.073 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.01 0.11 -10000 0 -0.56 16 16
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.095 0.25 -10000 0 -0.75 66 66
mesenchymal cell differentiation 0.007 0.1 0.59 14 -10000 0 14
DLX1 -0.45 0.44 -10000 0 -0.86 269 269
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.005 0.12 -10000 0 -0.74 13 13
SMAD3/SMAD4/Max 0.011 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.02 -10000 0 -10000 0 0
ZBTB17 -0.002 0.046 -10000 0 -0.72 2 2
LAMC1 0.071 0.042 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.031 -10000 0 -10000 0 0
IRF7 -0.011 0.16 -10000 0 -0.85 17 17
ESR1 0.002 0.072 -10000 0 -0.76 4 4
HNF4A -0.049 0.21 -10000 0 -0.75 43 43
MEF2C -0.008 0.22 -10000 0 -0.8 20 20
SMAD2-3/SMAD4 0.005 0.032 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.029 -10000 0 -0.46 1 1
IGHV3OR16-13 -0.049 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.005 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.01 0.036 -10000 0 -10000 0 0
MSG1/HSC70 0.002 0.044 -10000 0 -0.67 2 2
SMAD2 0.022 0.02 -10000 0 -10000 0 0
SMAD3 0.032 0.027 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.062 0.034 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.032 -10000 0 -0.53 1 1
NCOR1 0.015 0.005 -10000 0 -10000 0 0
NCOA2 0.004 0.095 -10000 0 -0.75 8 8
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.035 0.15 -10000 0 -0.66 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.076 0.085 -10000 0 -10000 0 0
IFNB1 0.047 0.1 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.013 0.21 -10000 0 -0.78 18 18
CITED1 0.011 0.055 -10000 0 -0.86 2 2
SMAD2-3/SMAD4/ARC105 0.007 0.031 -10000 0 -10000 0 0
RBL1 0.016 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.076 0.065 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.28 0.32 -10000 0 -0.61 235 235
SMAD7 0.078 0.085 -10000 0 -10000 0 0
MYC/MIZ-1 -0.025 0.13 -10000 0 -0.65 20 20
SMAD3/SMAD4 -0.02 0.12 -10000 0 -10000 0 0
IL10 -0.19 0.31 -10000 0 -0.99 31 31
PIASy/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.25 -10000 0 -0.75 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.01 -10000 0 -10000 0 0
ATF3 0.01 0.068 -10000 0 -0.75 4 4
SMAD3/SMAD4/SP1 -0.012 0.053 -10000 0 -10000 0 0
FOXG1 -0.026 0.17 -10000 0 -0.86 20 20
FOXO3 0.037 0.009 -10000 0 -10000 0 0
FOXO1 0.036 0.009 -10000 0 -10000 0 0
FOXO4 0.036 0.009 -10000 0 -10000 0 0
heart looping -0.008 0.22 -10000 0 -0.79 20 20
CEBPB -0.003 0.13 -10000 0 -0.86 12 12
SMAD3/SMAD4/DLX1 -0.31 0.29 -10000 0 -0.58 269 269
MYOD1 -0.04 0.2 -10000 0 -0.86 27 27
SMAD3/SMAD4/HNF4 -0.034 0.14 -10000 0 -0.51 29 29
SMAD3/SMAD4/GATA3 -0.23 0.25 -10000 0 -0.67 31 31
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.23 0.28 -10000 0 -0.72 39 39
SMAD3/SMAD4/SP1-3 -0.005 0.043 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.012 0.05 -10000 0 -10000 0 0
SIN3B 0.015 0.005 -10000 0 -10000 0 0
SIN3A 0.015 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.079 0.22 -10000 0 -0.79 28 28
ITGB5 0.084 0.065 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.014 0.11 -10000 0 -0.54 10 10
AR -0.021 0.16 -10000 0 -0.75 24 24
negative regulation of cell growth 0.065 0.067 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.023 0.14 -10000 0 -0.6 27 27
E2F5 0.014 0.034 -10000 0 -0.75 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.042 0.15 -10000 0 -0.65 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 0.077 0.044 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.007 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 14 14
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.014 0.034 -10000 0 -0.75 1 1
Thromboxane A2 receptor signaling

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
TGM2 -0.004 0.12 -10000 0 -0.86 10 10
GNB1/GNG2 -0.034 0.063 -10000 0 -0.22 14 14
AKT1 0.054 0.1 -10000 0 -0.25 1 1
EGF -0.67 0.23 -10000 0 -0.75 455 455
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.032 0.081 -10000 0 -0.61 2 2
mol:Ca2+ 0.041 0.14 -10000 0 -0.33 26 26
LYN -0.03 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.037 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.049 0.15 -10000 0 -0.37 24 24
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.076 -10000 0 -0.42 6 6
G beta5/gamma2 -0.045 0.083 -10000 0 -0.3 15 15
PRKCH 0.042 0.16 -10000 0 -0.39 21 21
DNM1 -0.002 0.12 -10000 0 -0.86 10 10
TXA2/TP beta/beta Arrestin3 -0.013 0.042 -10000 0 -0.27 10 10
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.11 0.31 -10000 0 -0.86 75 75
G12 family/GTP -0.043 0.092 -10000 0 -0.32 26 26
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.11 0.31 12 -10000 0 12
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.002 0.12 -10000 0 -0.75 12 12
mol:IP3 0.037 0.17 -10000 0 -0.42 26 26
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.027 0.22 -10000 0 -0.53 44 44
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.055 0.13 -10000 0 -0.6 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.052 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.013 0.052 -10000 0 -0.8 2 2
PRKCB1 0.037 0.16 -10000 0 -0.38 43 43
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.035 0.21 -10000 0 -0.53 43 43
LCK -0.047 0.12 -10000 0 -0.6 12 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.041 0.096 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.041 0.096 -10000 0 -10000 0 0
MAPK14 0.054 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.036 0.19 -10000 0 -0.48 28 28
MAPK11 0.053 0.11 -10000 0 -0.38 2 2
ARHGEF1 0.041 0.088 -10000 0 -0.32 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.044 0.17 -10000 0 -0.39 43 43
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.044 0.13 -10000 0 -0.32 29 29
cAMP biosynthetic process 0.034 0.16 -10000 0 -0.39 30 30
Gq family/GTP/EBP50 0.026 0.058 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.03 0.071 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.087 0.1 -10000 0 -0.41 15 15
VCAM1 0.043 0.14 -10000 0 -0.33 33 33
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.076 -10000 0 -0.42 6 6
platelet activation 0.066 0.15 -10000 0 -0.34 15 15
PGI2/IP -0.002 0.039 -10000 0 -0.62 2 2
PRKACA -0.052 0.12 -10000 0 -0.34 77 77
Gq family/GDP/G beta5/gamma2 0.025 0.076 -10000 0 -0.42 6 6
TXA2/TP beta/beta Arrestin2 -0.013 0.059 -10000 0 -0.41 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.13 -10000 0 -10000 0 0
mol:DAG 0.036 0.18 -10000 0 -0.43 43 43
EGFR 0 0.11 -10000 0 -0.85 9 9
TXA2/TP alpha 0.033 0.21 -10000 0 -0.54 30 30
Gq family/GTP -0.005 0.052 -10000 0 -0.27 6 6
YES1 -0.03 0.071 -10000 0 -10000 0 0
GNAI2/GTP -0.035 0.083 -10000 0 -10000 0 0
PGD2/DP -0.1 0.24 -10000 0 -0.68 75 75
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.03 0.071 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.009 0.14 -10000 0 -0.86 14 14
PGK/cGMP -0.012 0.075 -10000 0 -0.49 12 12
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.047 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.042 0.16 -10000 0 -0.39 20 20
PRKCB 0.04 0.16 -10000 0 -0.43 22 22
PRKCE 0.043 0.16 -10000 0 -0.4 21 21
PRKCD 0.041 0.16 -10000 0 -0.38 40 40
PRKCG 0.029 0.19 -10000 0 -0.44 48 48
muscle contraction 0.042 0.2 -10000 0 -0.49 43 43
PRKCZ 0.049 0.16 -10000 0 -0.37 26 26
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.04 0.094 -10000 0 -10000 0 0
PRKCQ 0.034 0.17 -10000 0 -0.41 27 27
MAPKKK cascade 0.035 0.19 -10000 0 -0.46 42 42
SELE 0.037 0.16 -10000 0 -0.41 40 40
TP beta/GNAI2/GDP/G beta/gamma -0.038 0.09 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.005 0.089 -10000 0 -0.75 7 7
chemotaxis 0.035 0.23 -10000 0 -0.61 42 42
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.013 0.048 -10000 0 -0.75 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.015 0.088 -9999 0 -0.52 15 15
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.034 -9999 0 -0.75 1 1
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin/MAdCAM1 -0.028 0.12 -9999 0 -0.52 27 27
EPO -0.29 0.42 -9999 0 -0.86 178 178
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 15 15
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.66 178 178
lamellipodium assembly 0 0.036 -9999 0 -0.53 2 2
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.12 0.16 -9999 0 -0.66 5 5
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
MADCAM1 -0.008 0.13 -9999 0 -0.86 12 12
cell adhesion -0.028 0.12 -9999 0 -0.52 27 27
CRKL/CBL -0.001 0.025 -9999 0 -0.56 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.014 0.13 -9999 0 -0.52 24 24
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.032 0.13 -9999 0 -0.56 29 29
p130Cas/Crk/Dock1 -0.025 0.1 -9999 0 -0.8 1 1
VCAM1 -0.007 0.14 -9999 0 -0.82 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.015 0.088 -9999 0 -0.52 15 15
BCAR1 0.025 0.13 -9999 0 -0.5 24 24
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.034 -9999 0 -0.75 1 1
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.038 -9999 0 -0.55 2 2
S1P3 pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.045 -9999 0 -10000 0 0
GNAO1 0.01 0.085 -9999 0 -0.84 5 5
S1P/S1P3/G12/G13 -0.001 0.019 -9999 0 -0.44 1 1
AKT1 -0.002 0.013 -9999 0 -10000 0 0
AKT3 -0.024 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.059 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.034 -9999 0 -0.75 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.053 0.05 -9999 0 -0.54 1 1
MAPK3 0.062 0.047 -9999 0 -0.5 1 1
MAPK1 0.062 0.047 -9999 0 -0.5 1 1
JAK2 -0.021 0.13 -9999 0 -0.48 2 2
CXCR4 -0.12 0.25 -9999 0 -0.47 171 171
FLT1 0.01 0.087 -9999 0 -0.86 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.047 -9999 0 -0.5 1 1
S1P/S1P3/Gi 0.053 0.05 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.036 -9999 0 -0.49 1 1
VEGFA -0.37 0.44 -9999 0 -0.86 225 225
S1P/S1P2/Gi 0.049 0.044 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 226 226
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.028 0.07 -9999 0 -10000 0 0
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.059 -9999 0 -0.75 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.005 0.089 -9999 0 -0.75 7 7
GNA15 -0.009 0.14 -9999 0 -0.86 14 14
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.013 0.048 -9999 0 -0.75 2 2
Rac1/GTP -0.005 0.036 -9999 0 -0.49 1 1
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.029 -10000 0 -0.66 1 1
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.005 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.057 0.22 -10000 0 -0.75 48 48
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.096 0.16 -10000 0 -0.34 141 141
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.014 0.034 -10000 0 -0.75 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH -0.001 0.028 -10000 0 -0.64 1 1
WIF1 0.001 0.078 -10000 0 -0.77 5 5
NOTCH1 -0.001 0.03 -10000 0 -0.68 1 1
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.089 0.28 -10000 0 -0.86 60 60
DKK1 -0.018 0.16 -10000 0 -0.83 20 20
beta catenin/beta TrCP1 0.083 0.084 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.007 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.004 0.12 -10000 0 -0.76 13 13
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.007 -10000 0 -10000 0 0
CTNNB1 0.079 0.091 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.094 0.21 -10000 0 -0.57 83 83
HNF1A -0.003 0.075 -10000 0 -0.75 5 5
CTBP1 0.005 0.008 -10000 0 -10000 0 0
MYC 0.005 0.14 -10000 0 -0.73 18 18
NKD1 -0.18 0.34 -10000 0 -0.75 132 132
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.038 0.12 -10000 0 -0.64 1 1
apoptosis -0.095 0.16 -10000 0 -0.34 141 141
Delta 1/NOTCHprecursor -0.001 0.028 -10000 0 -0.64 1 1
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.029 0.022 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.005 0.033 -10000 0 -0.47 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.089 0.22 -10000 0 -0.62 73 73
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.015 0.013 -10000 0 -10000 0 0
CCND1 0.004 0.15 -10000 0 -0.73 19 19
WNT1 -0.027 0.19 -10000 0 -0.86 24 24
Axin1/APC/beta catenin 0.081 0.052 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 24 24
NOTCH1 precursor/DVL1 -0.003 0.034 -10000 0 -0.58 1 1
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.012 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.038 0.12 -10000 0 -0.66 1 1
PPP2R5D 0.091 0.16 0.36 131 -10000 0 131
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.029 0.12 -10000 0 -0.52 25 25
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
LPA receptor mediated events

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 -0.021 0.089 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
AP1 -0.031 0.1 -9999 0 -0.6 1 1
mol:PIP3 -0.027 0.092 -9999 0 -0.55 1 1
AKT1 -0.014 0.058 -9999 0 -10000 0 0
PTK2B 0.033 0.06 -9999 0 -10000 0 0
RHOA 0.036 0.035 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.051 0.052 -9999 0 -0.48 1 1
MAGI3 0.013 0.048 -9999 0 -0.75 2 2
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.022 0.086 -9999 0 -0.38 26 26
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
positive regulation of microtubule depolymerization 0.046 0.07 -9999 0 -0.38 3 3
NF kappa B1 p50/RelA -0.019 0.074 -9999 0 -10000 0 0
endothelial cell migration 0.006 0.14 -9999 0 -0.54 28 28
ADCY4 0.031 0.12 -9999 0 -0.47 24 24
ADCY5 0.022 0.13 -9999 0 -0.49 27 27
ADCY6 0.031 0.12 -9999 0 -0.47 24 24
ADCY7 0.026 0.13 -9999 0 -0.48 24 24
ADCY1 0.026 0.13 -9999 0 -0.48 25 25
ADCY2 -0.018 0.14 -9999 0 -0.52 24 24
ADCY3 0.031 0.12 -9999 0 -0.47 24 24
ADCY8 -0.028 0.14 -9999 0 -0.49 24 24
ADCY9 0.031 0.12 -9999 0 -0.47 24 24
GSK3B 0.042 0.057 -9999 0 -10000 0 0
arachidonic acid secretion 0.038 0.11 -9999 0 -0.44 22 22
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0.001 0.008 -9999 0 -10000 0 0
GNAO1 0.006 0.12 -9999 0 -0.48 27 27
HRAS 0.014 0.039 -9999 0 -0.86 1 1
NFKBIA 0.061 0.062 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.054 -9999 0 -0.86 2 2
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.48 1 1
TIAM1 -0.003 0.064 -9999 0 -1 2 2
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
mol:IP3 0.051 0.053 -9999 0 -0.49 1 1
PLCB3 0.037 0.024 -9999 0 -0.43 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
positive regulation of mitosis 0.038 0.11 -9999 0 -0.44 22 22
LPA/LPA1-2-3 -0.026 0.1 -9999 0 -0.44 26 26
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.034 -9999 0 -0.75 1 1
stress fiber formation 0.039 0.077 -9999 0 -10000 0 0
GNAZ 0.009 0.12 -9999 0 -0.48 25 25
EGFR/PI3K-beta/Gab1 -0.028 0.096 -9999 0 -0.57 1 1
positive regulation of dendritic cell cytokine production -0.026 0.1 -9999 0 -0.44 26 26
LPA/LPA2/MAGI-3 -0.003 0.032 -9999 0 -0.48 2 2
ARHGEF1 0.03 0.096 -9999 0 -0.49 1 1
GNAI2 0.012 0.11 -9999 0 -0.47 22 22
GNAI3 0.012 0.11 -9999 0 -0.47 22 22
GNAI1 0.009 0.12 -9999 0 -0.48 25 25
LPA/LPA3 -0.007 0.061 -9999 0 -0.67 4 4
LPA/LPA2 -0.001 0.013 -9999 0 -10000 0 0
LPA/LPA1 -0.028 0.12 -9999 0 -0.51 28 28
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 249 249
HBEGF -0.3 0.35 -9999 0 -0.66 243 243
mol:DAG 0.051 0.053 -9999 0 -0.49 1 1
cAMP biosynthetic process 0.019 0.12 -9999 0 -0.46 23 23
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.061 0.062 -9999 0 -10000 0 0
GNAQ -0.004 0.036 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.003 0.078 -9999 0 -0.86 4 4
LPAR1 -0.013 0.16 -9999 0 -0.73 22 22
IL8 -0.081 0.2 -9999 0 -0.48 43 43
PTK2 0.024 0.1 -9999 0 -0.48 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.086 -9999 0 -0.38 26 26
EGFR 0 0.11 -9999 0 -0.85 9 9
PLCG1 0.019 0.054 -9999 0 -0.41 4 4
PLD2 0.024 0.1 -9999 0 -0.48 4 4
G12/G13 -0.021 0.089 -9999 0 -0.42 22 22
PI3K-beta -0.016 0.068 -9999 0 -0.52 1 1
cell migration -0.009 0.035 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.75 1 1
PXN 0.039 0.078 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.099 -9999 0 -0.45 22 22
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.41 0.44 -9999 0 -0.86 243 243
PRKCE 0.013 0.034 -9999 0 -0.75 1 1
PRKCD 0.059 0.055 -9999 0 -10000 0 0
Gi(beta/gamma) -0.026 0.098 -9999 0 -0.44 24 24
mol:LPA 0.003 0.024 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.018 0.081 -9999 0 -10000 0 0
MAPKKK cascade 0.038 0.11 -9999 0 -0.44 22 22
contractile ring contraction involved in cytokinesis 0.036 0.035 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.009 0.06 -9999 0 -0.4 11 11
GNA15 -0.015 0.078 -9999 0 -0.42 17 17
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.046 0.071 -9999 0 -0.39 3 3
GNA11 -0.006 0.043 -9999 0 -0.39 6 6
Rac1/GTP -0.002 0.058 -9999 0 -0.91 2 2
MMP2 0.006 0.14 -9999 0 -0.54 28 28
PLK2 and PLK4 events

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
PLK2 -0.016 0.16 -9999 0 -0.86 18 18
PLK4 0.01 0.067 -9999 0 -0.86 3 3
regulation of centriole replication 0.002 0.14 -9999 0 -0.66 21 21
Ceramide signaling pathway

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
SPHK2 0.027 0.045 -10000 0 -0.56 3 3
MAP4K4 0.025 0.094 -10000 0 -0.48 1 1
BAG4 0.014 0.034 -10000 0 -0.75 1 1
PKC zeta/ceramide -0.099 0.047 -10000 0 -0.48 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.32 -10000 0 -0.86 78 78
BAX -0.042 0.019 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.046 0.008 -10000 0 -10000 0 0
BAD -0.098 0.043 -10000 0 -0.45 2 2
SMPD1 0.026 0.042 -10000 0 -0.28 1 1
RB1 -0.096 0.038 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.088 -10000 0 -10000 0 0
MAP2K4 -0.081 0.036 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.085 0.058 -10000 0 -0.59 4 4
EGF -0.67 0.23 -10000 0 -0.75 455 455
mol:ceramide -0.12 0.04 0.2 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.026 -10000 0 -0.56 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.095 0.038 -10000 0 -10000 0 0
cell proliferation -0.053 0.061 -10000 0 -0.46 10 10
BID -0.012 0.066 -10000 0 -10000 0 0
MAP3K1 -0.096 0.038 -10000 0 -10000 0 0
EIF2A -0.067 0.034 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.065 0.053 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.065 0.053 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.097 0.036 -10000 0 -0.27 1 1
FADD 0.025 0.094 -10000 0 -0.48 1 1
KSR1 -0.1 0.061 -10000 0 -0.63 4 4
MAPK8 -0.075 0.038 -10000 0 -0.34 2 2
PRKRA -0.096 0.038 -10000 0 -10000 0 0
PDGFA 0.014 0.034 -10000 0 -0.75 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.005 0.095 -10000 0 -0.86 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.04 0.2 2 -10000 0 2
CTSD 0.014 0.034 -10000 0 -0.75 1 1
regulation of nitric oxide biosynthetic process -0.001 0.025 -10000 0 -0.56 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.055 0.067 -10000 0 -0.5 10 10
PRKCD 0.014 0.039 -10000 0 -0.86 1 1
PRKCZ 0.011 0.059 -10000 0 -0.75 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.026 -10000 0 -0.56 1 1
RelA/NF kappa B1 -0.001 0.025 -10000 0 -0.56 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.034 -10000 0 -0.75 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.034 0.078 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.069 -10000 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0.027 0.045 -10000 0 -0.56 3 3
MAP2K1 -0.071 0.055 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.063 0.024 -10000 0 -0.23 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.034 -10000 0 -0.75 1 1
TNFR1A/BAG4 -0.001 0.025 -10000 0 -0.56 1 1
EIF2AK2 -0.081 0.036 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.008 0.066 -10000 0 -0.52 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.037 -10000 0 -10000 0 0
MAP2K2 -0.072 0.054 -10000 0 -0.55 4 4
SMPD3 0.026 0.052 -10000 0 -0.33 2 2
TNF 0.003 0.1 -10000 0 -0.8 8 8
PKC zeta/PAR4 -0.004 0.05 -10000 0 -0.56 4 4
mol:PHOSPHOCHOLINE 0.23 0.083 0.26 455 -10000 0 455
NF kappa B1/RelA/I kappa B alpha -0.004 0.039 -10000 0 -10000 0 0
AIFM1 -0.063 0.025 -10000 0 -0.23 1 1
BCL2 0.016 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0.048 -9999 0 -0.75 2 2
SPHK1 -0.055 0.24 -9999 0 -0.86 41 41
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.094 -9999 0 -0.3 43 43
GNAO1 0.007 0.085 -9999 0 -0.84 5 5
mol:Sphinganine-1-P -0.028 0.19 -9999 0 -0.66 43 43
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.055 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.034 -9999 0 -0.75 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.022 0.073 -9999 0 -0.29 2 2
S1PR5 -0.13 0.32 -9999 0 -0.86 83 83
S1PR4 -0.026 0.19 -9999 0 -0.86 24 24
GNAI1 0.011 0.059 -9999 0 -0.75 3 3
S1P/S1P5/G12 -0.1 0.2 -9999 0 -0.54 83 83
S1P/S1P3/Gq 0.025 0.096 -9999 0 -0.42 16 16
S1P/S1P4/Gi 0.025 0.095 -9999 0 -0.38 12 12
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.059 -9999 0 -0.75 3 3
GNA14 0.005 0.089 -9999 0 -0.75 7 7
GNA15 -0.009 0.14 -9999 0 -0.86 14 14
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.013 0.048 -9999 0 -0.75 2 2
ABCC1 0.016 0 -9999 0 -10000 0 0
FoxO family 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
G6PC -0.57 0.68 -9999 0 -1.3 236 236
PLK1 -0.13 0.37 -9999 0 -0.79 93 93
CDKN1B 0.061 0.16 -9999 0 -10000 0 0
FOXO3 -0.039 0.23 -9999 0 -0.66 14 14
KAT2B 0.012 0.041 -9999 0 -0.79 1 1
FOXO1/SIRT1 -0.14 0.21 -9999 0 -10000 0 0
CAT -0.028 0.23 -9999 0 -0.89 7 7
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.007 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 153 153
MAPK10 0.032 0.05 -9999 0 -0.43 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.045 -9999 0 -10000 0 0
response to oxidative stress -0.029 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.025 0.2 -9999 0 -0.62 7 7
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 -0.006 0.042 -9999 0 -0.75 1 1
BCL2L11 0.012 0.044 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -10000 0 0
mol:GDP -0.029 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.099 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.086 -9999 0 -10000 0 0
MST1 0 0.11 -9999 0 -0.86 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.097 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.038 0.019 -9999 0 -10000 0 0
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.035 0.028 -9999 0 -10000 0 0
SOD2 0.013 0.21 -9999 0 -0.7 6 6
RBL2 0.022 0.17 -9999 0 -1.3 1 1
RAL/GDP 0.009 0.024 -9999 0 -10000 0 0
CHUK 0.013 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.004 -9999 0 -10000 0 0
CSNK1G2 0.014 0.034 -9999 0 -0.75 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.34 0.39 -9999 0 -0.72 254 254
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.002 -9999 0 -10000 0 0
IKBKB 0.013 0.02 -9999 0 -10000 0 0
CCNB1 -0.031 0.24 -9999 0 -0.92 10 10
FOXO1-3a-4/beta catenin -0.07 0.1 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.013 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.042 -9999 0 -10000 0 0
SFN -0.086 0.28 -9999 0 -0.83 61 61
CDK2 -0.018 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.012 0.1 -9999 0 -10000 0 0
CREBBP -0.018 0.041 -9999 0 -10000 0 0
FBXO32 -0.027 0.22 -9999 0 -0.79 8 8
BCL6 0.024 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.043 -10000 0 -10000 0 0
RFC1 0.012 0.043 -10000 0 -10000 0 0
PRKDC 0.012 0.043 -10000 0 -10000 0 0
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.023 0.066 0.25 6 -10000 0 6
FASLG/FAS/FADD/FAF1 -0.13 0.16 -10000 0 -0.35 22 22
MAP2K4 -0.084 0.16 -10000 0 -0.43 23 23
mol:ceramide -0.15 0.2 -10000 0 -0.48 31 31
GSN 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.17 0.18 -10000 0 -0.44 22 22
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.019 0.067 -10000 0 -10000 0 0
MAP3K1 -0.035 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.012 0.043 -10000 0 -10000 0 0
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.038 0.15 -10000 0 -0.58 33 33
ARHGDIB 0.012 0.043 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.043 -10000 0 -10000 0 0
NFKB1 -0.065 0.077 -10000 0 -0.71 1 1
MAPK8 -0.082 0.18 -10000 0 -0.52 23 23
DFFA 0.012 0.043 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.043 -10000 0 -10000 0 0
FAS/FADD/MET -0.006 0.057 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.046 0.22 -10000 0 -0.86 36 36
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.012 0.043 -10000 0 -10000 0 0
DFFB 0.012 0.043 -10000 0 -10000 0 0
CHUK -0.053 0.067 -10000 0 -0.66 1 1
FASLG -0.43 0.44 -10000 0 -0.86 254 254
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.021 0.17 -10000 0 -0.8 23 23
LMNA 0.01 0.047 -10000 0 -0.52 1 1
CASP6 0.012 0.043 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.014 0.05 -10000 0 -10000 0 0
PTPN13 0.002 0.1 -10000 0 -0.75 9 9
CASP8 0.029 0.1 0.4 36 -10000 0 36
IL6 -0.13 0.33 -10000 0 -0.96 63 63
MET 0.007 0.087 -10000 0 -0.86 5 5
ICAD/CAD 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.15 0.2 -10000 0 -0.49 31 31
activation of caspase activity by cytochrome c 0.019 0.067 -10000 0 -10000 0 0
PAK2 0.012 0.043 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
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 -0.001 0.017 -9999 0 -10000 0 0
DAPP1 0.029 0.11 -9999 0 -0.54 9 9
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.26 -9999 0 -0.74 53 53
mol:DAG -0.069 0.15 -9999 0 -0.31 60 60
HRAS 0.015 0.039 -9999 0 -0.86 1 1
RAP1A 0.017 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.019 0.073 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.019 -9999 0 -10000 0 0
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
ADAP1 -0.004 0.037 -9999 0 -10000 0 0
ARAP3 -0.001 0.019 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.011 0.067 -9999 0 -0.86 3 3
mol:Ca2+ -0.022 0.078 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.034 -9999 0 -0.75 1 1
ZAP70 -0.45 0.44 -9999 0 -0.86 270 270
mol:IP3 -0.035 0.11 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.019 0.073 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.017 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.021 -9999 0 -10000 0 0
BLNK 0.014 0.034 -9999 0 -0.75 1 1
actin cytoskeleton reorganization 0.045 0.081 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.054 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.017 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.018 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.2 0.24 -9999 0 -0.56 128 128
BLK -0.04 0.21 -9999 0 -0.86 32 32
PDPK1 0.014 0.034 -9999 0 -0.75 1 1
CYTH1 -0.001 0.018 -9999 0 -10000 0 0
HCK -0.033 0.2 -9999 0 -0.86 28 28
CYTH3 -0.001 0.018 -9999 0 -10000 0 0
CYTH2 -0.001 0.018 -9999 0 -10000 0 0
KRAS 0.017 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.024 -9999 0 -0.54 1 1
SGK1 -0.001 0.027 -9999 0 -0.6 1 1
INPP5D 0.009 0.078 -9999 0 -0.86 4 4
mol:GDP 0.01 0.077 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.048 -9999 0 -0.75 2 2
ARF6/GDP -0.004 0.017 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.019 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
VAV1 -0.19 0.37 -9999 0 -0.86 119 119
mol:PI-3-4-P2 0.025 0.062 -9999 0 -0.66 4 4
RAS family/GTP/PI3K Class I -0.001 0.02 -9999 0 -10000 0 0
PLEKHA1 0.036 0.054 -9999 0 -0.57 4 4
Rac1/GDP 0.019 0.073 -9999 0 -10000 0 0
LAT -0.23 0.4 -9999 0 -0.86 144 144
Rac1/GTP 0 0.1 -9999 0 -10000 0 0
ITK -0.14 0.21 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.11 0.21 -9999 0 -0.46 77 77
LCK -0.022 0.18 -9999 0 -0.85 22 22
BTK -0.096 0.18 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.023 0.1 -9999 0 -0.5 23 23
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.56 21 21
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.059 -9999 0 -0.75 3 3
CDH1 -0.016 0.15 -9999 0 -0.75 21 21
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.071 -10000 0 -0.4 1 1
epithelial cell differentiation -0.05 0.11 -10000 0 -0.57 1 1
ITCH 0.055 0.018 -10000 0 -10000 0 0
WWP1 -0.097 0.067 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR 0 0.11 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.019 0.081 -10000 0 -0.57 1 1
PTPRZ1 -0.079 0.25 -10000 0 -0.76 59 59
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.054 0.074 -10000 0 -0.6 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.084 0.094 -10000 0 -0.58 9 9
ADAM17 0.055 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.086 -10000 0 -0.47 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.61 11 11
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.076 0.078 -10000 0 -0.54 9 9
GRIN2B -0.057 0.092 -10000 0 -0.61 3 3
ErbB4/ErbB2/betacellulin -0.13 0.16 -10000 0 -0.52 68 68
STAT1 0.014 0.039 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.081 0.25 -10000 0 -0.75 64 64
E4ICDs/ETO2 -0.11 0.08 -10000 0 -0.7 2 2
axon guidance -0.018 0.071 -10000 0 -10000 0 0
NEDD4 0.052 0.052 -10000 0 -0.73 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.072 0.19 -10000 0 -0.57 64 64
CBFA2T3 0.012 0.055 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.065 0.039 -10000 0 -0.52 1 1
MAPK3 -0.03 0.083 -10000 0 -0.6 1 1
STAT1 (dimer) -0.11 0.073 -10000 0 -0.54 1 1
MAPK1 -0.03 0.083 -10000 0 -0.6 1 1
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.078 0.082 -10000 0 -0.54 10 10
NRG1 0.035 0.11 -10000 0 -0.56 16 16
NRG3 -0.002 0.12 -10000 0 -0.86 10 10
NRG2 -0.002 0.12 -10000 0 -0.85 10 10
NRG4 -0.056 0.22 -10000 0 -0.77 45 45
heart development -0.018 0.071 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.081 -10000 0 -0.53 10 10
ERBB2 0.052 0.04 -10000 0 -0.56 2 2
WWOX/E4ICDs -0.11 0.076 -10000 0 -0.55 2 2
SHC1 0.014 0.039 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.15 0.15 -10000 0 -0.57 49 49
apoptosis 0.1 0.062 0.38 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.089 -10000 0 -0.52 11 11
ErbB4/ErbB2/epiregulin -0.099 0.13 -10000 0 -0.57 34 34
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.18 -10000 0 -0.59 75 75
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.14 -10000 0 -0.51 49 49
MDM2 -0.1 0.074 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.078 -10000 0 -0.52 9 9
STAT5A -0.006 0.066 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.085 0.1 -10000 0 -0.56 17 17
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.029 -10000 0 -0.66 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.048 -10000 0 -10000 0 0
STAT5A (dimer) -0.053 0.12 -10000 0 -0.62 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.008 0.063 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.042 0.22 -10000 0 -0.86 33 33
BTC -0.098 0.27 -10000 0 -0.75 75 75
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.018 0.071 -10000 0 -10000 0 0
ERBB4 -0.14 0.086 -10000 0 -0.47 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.1 0.13 -10000 0 -0.51 42 42
glial cell differentiation 0.1 0.048 -10000 0 -10000 0 0
WWOX 0.014 0.039 -10000 0 -0.86 1 1
cell proliferation -0.075 0.16 -10000 0 -0.63 10 10
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.2 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.15 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.028 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.1 0.09 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.13 0.22 -9999 0 -10000 0 0
MAP3K11 -0.15 0.23 -9999 0 -0.8 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.27 0.29 -9999 0 -0.74 107 107
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.069 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.2 0.21 -9999 0 -1 2 2
STAT1 -0.15 0.23 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.38 0.43 -9999 0 -0.85 230 230
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.075 0.084 -9999 0 -0.47 1 1
mol:Ca2+ -0.19 0.21 -9999 0 -10000 0 0
MAPK3 -0.089 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.089 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.026 0.15 -9999 0 -0.63 3 3
SMAD7 -0.021 0.081 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.17 0.19 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.85 230 230
apoptosis -0.037 0.12 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.36 -9999 0 -0.75 166 166
CAMK2B -0.1 0.28 -9999 0 -0.76 76 76
FRAP1 -0.11 0.2 -9999 0 -10000 0 0
PRKCD -0.12 0.21 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.1 0.09 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.034 -9999 0 -0.74 1 1
IRF1 -0.059 0.19 -9999 0 -0.93 1 1
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.01 0.084 -9999 0 -0.73 6 6
mol:GDP -0.16 0.17 -9999 0 -10000 0 0
CASP1 -0.021 0.081 -9999 0 -10000 0 0
PTGES2 0.013 0.048 -9999 0 -0.75 2 2
IRF9 0.017 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.15 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.1 0.09 -9999 0 -0.37 1 1
PTPN11 -0.16 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.005 0.018 -10000 0 -10000 0 0
AES 0.004 0.016 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 24 24
TLE1 0.004 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.049 0.099 -10000 0 -0.44 1 1
WIF1 -0.001 0.077 -10000 0 -0.77 5 5
beta catenin/RanBP3 0.003 0.1 0.36 18 -10000 0 18
KREMEN2 -0.089 0.28 -10000 0 -0.86 60 60
DKK1 -0.018 0.16 -10000 0 -0.83 20 20
beta catenin/beta TrCP1 0.056 0.093 -10000 0 -10000 0 0
FZD1 0.016 0.004 -10000 0 -10000 0 0
AXIN2 0.01 0.1 -10000 0 -1.4 2 2
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.017 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.072 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.039 0.082 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.003 0.076 -10000 0 -0.74 5 5
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.007 0.15 -10000 0 -0.75 18 18
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.094 0.21 -10000 0 -0.57 83 83
NKD1 -0.18 0.34 -10000 0 -0.75 132 132
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.025 0.11 -10000 0 -0.52 24 24
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.1 0.52 3 -10000 0 3
LEF1 -0.021 0.15 -10000 0 -0.87 15 15
DVL1 0.003 0.034 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.082 0.07 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.089 0.22 -10000 0 -0.62 73 73
LRP6 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.005 0.018 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.008 0.15 -10000 0 -0.75 19 19
WNT1 -0.027 0.19 -10000 0 -0.86 24 24
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.002 -10000 0 -10000 0 0
FRAT1 0.014 0.005 -10000 0 -10000 0 0
PPP2R5D 0.094 0.15 0.35 131 -10000 0 131
APC -0.017 0.1 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.012 0.063 0.27 5 -10000 0 5
CREBBP 0.005 0.017 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.021 0.093 -10000 0 -0.44 24 24
regulation of S phase of mitotic cell cycle -0.015 0.069 -10000 0 -0.62 1 1
GNAO1 0.007 0.085 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
SHBG/T-DHT -0.051 0.15 -10000 0 -0.5 52 52
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.047 0.092 -10000 0 -10000 0 0
T-DHT/AR -0.027 0.12 -10000 0 -0.57 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 13 13
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.059 -10000 0 -0.75 3 3
mol:GDP -0.027 0.12 -10000 0 -0.56 24 24
cell proliferation 0.071 0.11 -10000 0 -0.64 4 4
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
FOS 0.056 0.15 -10000 0 -0.81 13 13
mol:Ca2+ -0.003 0.015 -10000 0 -0.11 4 4
MAPK3 0.063 0.1 -10000 0 -0.57 4 4
MAPK1 0.044 0.055 -10000 0 -0.29 4 4
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process -0.046 0.15 -10000 0 -0.48 52 52
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.02 0.086 -10000 0 -0.45 5 5
actin cytoskeleton reorganization -0.002 0.024 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K -0.002 0.031 -10000 0 -0.49 2 2
apoptosis -0.06 0.096 0.43 12 -10000 0 12
T-DHT/AR/PELP1 -0.023 0.1 -10000 0 -0.49 24 24
HRAS/GDP -0.026 0.12 -10000 0 -0.53 25 25
CREB1 0.061 0.1 -10000 0 -0.47 12 12
RAC1-CDC42/GTP -0.002 0.024 -10000 0 -10000 0 0
AR -0.02 0.16 -10000 0 -0.75 24 24
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.035 0.094 -10000 0 -0.45 4 4
RAC1-CDC42/GDP -0.024 0.11 -10000 0 -0.49 24 24
T-DHT/AR/PELP1/Src -0.021 0.094 -10000 0 -0.44 24 24
MAP2K2 0.046 0.094 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.015 0.069 -10000 0 -0.63 1 1
GNAZ 0.011 0.059 -10000 0 -0.75 3 3
SHBG -0.063 0.23 -10000 0 -0.75 52 52
Gi family/GNB1/GNG2/GDP -0.008 0.045 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.17 0.31 -10000 0 -0.68 137 137
Gi family/GTP -0.014 0.059 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
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 0.031 0.002 -9999 0 -10000 0 0
SMARCC1 0.026 0.01 -9999 0 -10000 0 0
REL 0.009 0.059 -9999 0 -0.74 3 3
HDAC7 -0.096 0.085 -9999 0 -0.67 3 3
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.014 0.034 -9999 0 -0.75 1 1
KAT2B 0.014 0.034 -9999 0 -0.75 1 1
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0.001 0.047 -9999 0 -0.59 3 3
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.087 -9999 0 -0.72 3 3
MAP2K6 -0.003 0.06 -9999 0 -0.77 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -1.3 4 4
NCOA2 0.003 0.095 -9999 0 -0.75 8 8
CEBPA -0.002 0.12 -9999 0 -0.86 10 10
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.091 0.094 -9999 0 -0.55 2 2
NR0B1 -0.05 0.21 -9999 0 -0.86 32 32
EGR1 -0.001 0.11 -9999 0 -0.75 11 11
RXRs/9cRA -0.004 0.048 -9999 0 -0.54 4 4
AR/RACK1/Src -0.014 0.058 -9999 0 -0.58 2 2
AR/GR 0.002 0.084 -9999 0 -0.72 3 3
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.004 0.012 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.082 -9999 0 -0.79 2 2
SRC 0.004 0.042 -9999 0 -10000 0 0
NR3C1 0.014 0.039 -9999 0 -0.86 1 1
KLK3 -0.054 0.19 -9999 0 -0.74 23 23
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.025 0.051 -9999 0 -0.59 3 3
TMPRSS2 -0.96 0.38 -9999 0 -1.1 437 437
RXRG 0.006 0.078 -9999 0 -0.86 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.014 0.034 -9999 0 -0.75 1 1
KLK2 -0.021 0.13 -9999 0 -0.63 18 18
AR -0.009 0.085 -9999 0 -0.55 4 4
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 -0.002 0.12 -9999 0 -0.75 12 12
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.17 0.35 -9999 0 -0.86 103 103
T-DHT/AR/RACK1/Src -0.014 0.057 -9999 0 -0.6 2 2
positive regulation of transcription -0.002 0.12 -9999 0 -0.75 12 12
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.18 0.36 -9999 0 -0.86 112 112
T-DHT/AR/TIF2 0.021 0.067 -9999 0 -0.75 2 2
T-DHT/AR/Hsp90 -0.026 0.049 -9999 0 -0.62 2 2
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.009 0.046 -9999 0 -0.5 3 3
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.014 0.008 -9999 0 -10000 0 0
POU2F1 0.005 0.015 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.064 0.14 -9999 0 -0.61 25 25
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.003 0.043 -9999 0 -0.56 3 3
AKT1 -0.053 0.2 -9999 0 -0.71 3 3
PTK2B -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.003 0.042 -9999 0 -0.83 1 1
CAV1 -0.047 0.23 -9999 0 -0.86 36 36
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.22 0.25 -9999 0 -1.2 1 1
endothelial cell proliferation -0.039 0.19 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.039 -9999 0 -0.86 1 1
VEGFA homodimer -0.23 0.26 -9999 0 -0.52 225 225
SHC1 0.014 0.039 -9999 0 -0.86 1 1
SHC2 0.007 0.082 -9999 0 -0.82 5 5
HRAS/GDP -0.17 0.19 -9999 0 -0.83 2 2
SH2D2A -0.26 0.41 -9999 0 -0.86 162 162
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.39 0.34 -9999 0 -1 64 64
VEGFR1 homodimer 0.007 0.087 -9999 0 -0.86 5 5
SHC/GRB2/SOS1 -0.18 0.2 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.014 0.039 -9999 0 -0.86 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.084 0.094 -9999 0 -0.58 1 1
HIF1A 0.013 0.048 -9999 0 -0.75 2 2
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.001 0.025 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.22 0.25 -9999 0 -1.2 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.061 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.051 0.18 -9999 0 -0.57 1 1
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
mol:IP3 -0.16 0.26 -9999 0 -1.1 1 1
HIF1A/ARNT -0.002 0.035 -9999 0 -0.56 2 2
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.37 0.43 -9999 0 -0.86 225 225
VEGFC 0.014 0.039 -9999 0 -0.86 1 1
FAK1/Vinculin -0.1 0.22 -9999 0 -1 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.21 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.037 -9999 0 -0.72 1 1
mol:L-citrulline -0.061 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.22 0.25 -9999 0 -1.2 1 1
VEGFR2/3 heterodimer -0.003 0.042 -9999 0 -0.83 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -0.84 2 2
VEGFR2 homodimer 0.043 0.05 -9999 0 -0.73 2 2
FLT1 0.007 0.087 -9999 0 -0.86 5 5
NEDD4 0.015 0.048 -9999 0 -0.74 2 2
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.3 0.33 -9999 0 -0.66 230 230
VEGFR1/2 heterodimer -0.008 0.07 -9999 0 -0.61 6 6
KDR 0.043 0.051 -9999 0 -0.73 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -1 1 1
PI3K -0.16 0.18 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.2 1 1
FES -0.16 0.27 -9999 0 -1 2 2
GAB1 -0.16 0.19 -9999 0 -0.8 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.22 0.25 -9999 0 -1.2 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.08 0.2 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.22 0.25 -9999 0 -1.2 1 1
PI3K/GAB1 -0.053 0.19 -9999 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.1 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.045 -9999 0 -0.77 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.16 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.38 0.33 -9999 0 -1 64 64
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.26 -9999 0 -1.1 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -1 1 1
MAP2K3 -0.14 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.16 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.22 0.25 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.22 0.25 -9999 0 -1.2 1 1
cell migration -0.05 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.7 6 6
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.061 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.19 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.016 0 -9999 0 -10000 0 0
ITGB3 0.011 0.059 -9999 0 -0.75 3 3
NOS3 -0.071 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -1.1 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.14 0.25 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 5 5
VEGFA165/NRP2 -0.3 0.33 -9999 0 -0.66 230 230
MAPKKK cascade -0.16 0.18 -9999 0 -0.8 2 2
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.039 -9999 0 -0.86 1 1
NCK1 0.014 0.034 -9999 0 -0.75 1 1
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.1 0.22 -9999 0 -1 1 1
MAP3K13 -0.16 0.27 -9999 0 -1.2 1 1
PDPK1 -0.071 0.2 -9999 0 -0.76 3 3
S1P5 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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.043 0.091 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.096 0.22 -9999 0 -0.58 83 83
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.085 -9999 0 -0.84 5 5
RhoA/GTP -0.044 0.092 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.012 0.12 -9999 0 -10000 0 0
GNAZ 0.011 0.059 -9999 0 -0.75 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.13 0.32 -9999 0 -0.86 83 83
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.051 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.059 -9999 0 -0.75 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.059 -9999 0 -10000 0 0
epithelial cell differentiation -0.017 0.08 -9999 0 -10000 0 0
CYFIP2 0.004 0.095 -9999 0 -0.75 8 8
ENAH 0.078 0.066 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.034 -9999 0 -0.75 1 1
MYO6 0.032 0.098 -9999 0 -0.78 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.059 -9999 0 -0.48 8 8
AQP5 -0.17 0.24 -9999 0 -0.53 155 155
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.084 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.017 0.12 -9999 0 -0.84 1 1
EGF -0.67 0.23 -9999 0 -0.75 455 455
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.051 0.16 -9999 0 -0.84 7 7
cortical microtubule organization -0.017 0.08 -9999 0 -10000 0 0
GO:0000145 0.034 0.08 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.081 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.014 0.063 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.05 0.085 -9999 0 -0.58 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.034 0.085 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.032 -9999 0 -10000 0 0
CDH1 -0.016 0.15 -9999 0 -0.75 21 21
EGFR/EGFR/EGF/EGF -0.35 0.15 -9999 0 -0.78 27 27
RhoA/GDP -0.015 0.074 -9999 0 -10000 0 0
actin cytoskeleton organization 0.041 0.093 -9999 0 -0.72 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.005 0.095 -9999 0 -0.86 6 6
DIAPH1 -0.011 0.087 -9999 0 -0.7 8 8
Wnt receptor signaling pathway 0.017 0.08 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.064 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.041 0.096 -9999 0 -0.75 2 2
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
LPP 0.043 0.09 -9999 0 -0.8 1 1
Ephrin A1/EPHA2 -0.016 0.075 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.063 -9999 0 -10000 0 0
MGAT3 0.017 0.13 -9999 0 -0.87 1 1
HGF/MET -0.037 0.13 -9999 0 -0.95 4 4
HGF -0.021 0.17 -9999 0 -0.8 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.099 0.071 -9999 0 -10000 0 0
KIAA1543 0.036 0.13 -9999 0 -0.86 6 6
KIFC3 0.033 0.087 -9999 0 -10000 0 0
NCK1 0.014 0.034 -9999 0 -0.75 1 1
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.033 0.094 -9999 0 -0.87 1 1
NCK1/GIT1 -0.001 0.025 -9999 0 -0.56 1 1
mol:GDP -0.017 0.08 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.034 0.085 -9999 0 -10000 0 0
PIP5K1C 0.034 0.085 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.055 -9999 0 -10000 0 0
adherens junction assembly 0.058 0.12 -9999 0 -0.79 7 7
IGF-1R heterotetramer/IGF1 -0.02 0.085 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.087 -9999 0 -0.86 5 5
PLEKHA7 0.031 0.1 -9999 0 -0.78 3 3
mol:GTP -0.003 0.035 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.07 0.077 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.059 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.041 0.093 -9999 0 -0.72 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.031 0.12 -9999 0 -0.51 31 31
RGS9BP -0.016 0.15 -9999 0 -0.75 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.013 0.086 -9999 0 -0.59 11 11
mol:ADP 0.011 0.044 -9999 0 -0.68 2 2
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.026 -9999 0 -0.58 1 1
GRK7 0.008 0.055 -9999 0 -0.86 2 2
CNGB3 -0.008 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.12 -9999 0 -0.64 15 15
Cone PDE6 -0.032 0.12 -9999 0 -0.53 11 11
Cone Metarhodopsin II -0.002 0.035 -9999 0 -0.55 2 2
Na + (4 Units) -0.019 0.11 -9999 0 -0.64 15 15
GNAT2/GDP -0.029 0.11 -9999 0 -0.47 11 11
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.044 -9999 0 -0.54 3 3
Cone Transducin -0.033 0.13 -9999 0 -0.53 31 31
SLC24A2 -0.009 0.1 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.041 0.16 -9999 0 -0.66 31 31
GNB3 -0.037 0.21 -9999 0 -0.86 30 30
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.067 -9999 0 -0.86 3 3
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.013 0.087 -9999 0 -0.59 11 11
mol:Pi -0.034 0.13 -9999 0 -0.5 35 35
Cone CNG Channel -0.013 0.085 -9999 0 -0.96 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.1 -9999 0 -0.86 7 7
RGS9 -0.007 0.14 -9999 0 -0.81 14 14
PDE6C 0.003 0.055 -9999 0 -0.86 2 2
GNGT2 0.014 0.039 -9999 0 -0.86 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.039 -9999 0 -0.86 1 1
Noncanonical Wnt signaling pathway

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
NFATC2 0.012 0.052 -9999 0 -0.8 2 2
GNB1/GNG2 -0.055 0.11 -9999 0 -0.54 8 8
mol:DAG 0.009 0.13 -9999 0 -10000 0 0
PLCG1 0.008 0.13 -9999 0 -10000 0 0
YES1 -0.012 0.14 -9999 0 -0.56 8 8
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.051 0.1 -9999 0 -0.5 7 7
MAP3K7 -0.094 0.22 -9999 0 -0.56 40 40
mol:Ca2+ 0.009 0.13 -9999 0 -10000 0 0
mol:IP3 0.009 0.13 -9999 0 -10000 0 0
NLK -0.007 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.24 -9999 0 -0.61 47 47
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.065 0.13 -9999 0 -0.6 8 8
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.012 0.14 -9999 0 -0.56 8 8
GO:0007205 0.01 0.13 -9999 0 -10000 0 0
WNT6 -0.014 0.16 -9999 0 -0.86 17 17
WNT4 -0.071 0.24 -9999 0 -0.75 57 57
NFAT1/CK1 alpha -0.049 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.059 -9999 0 -0.75 3 3
WNT11 -0.041 0.2 -9999 0 -0.76 37 37
CDC42 -0.001 0.14 -9999 0 -0.53 8 8
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 15 15
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 15 15
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.085 -9999 0 -0.84 5 5
CDC42/GTP -0.016 0.06 -9999 0 -10000 0 0
PLCG1 0.035 0.076 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.016 0.059 -9999 0 -10000 0 0
S1PR5 -0.13 0.32 -9999 0 -0.86 83 83
S1PR4 -0.026 0.19 -9999 0 -0.86 24 24
MAPK3 0.035 0.076 -9999 0 -10000 0 0
MAPK1 0.035 0.076 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.051 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.059 -9999 0 -0.75 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.096 0.22 -9999 0 -0.58 83 83
RHOA 0.018 0.11 -9999 0 -0.49 24 24
S1P/S1P4/Gi -0.019 0.068 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.059 -9999 0 -0.75 3 3
S1P/S1P4/G12/G13 -0.025 0.11 -9999 0 -0.53 24 24
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.28 0.37 -9999 0 -0.75 196 196
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0 0.11 -9999 0 -0.85 9 9
AKT 0.035 0.03 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.087 -9999 0 -0.86 5 5
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.011 0.067 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.042 0.098 -9999 0 -0.38 5 5
ERBB2 0.013 0.048 -9999 0 -0.75 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.023 0.092 -9999 0 -0.29 6 6
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.036 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.035 0.095 -9999 0 -0.48 6 6
JUN 0.027 0.11 -9999 0 -0.53 6 6
HRAS 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.052 0.16 -9999 0 -0.7 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.052 0.16 -9999 0 -0.7 11 11
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.13 -9999 0 -0.47 43 43
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.046 0.14 -9999 0 -0.67 9 9
GRB7 0.005 0.089 -9999 0 -0.75 7 7
RET51/GFRalpha1/GDNF -0.052 0.16 -9999 0 -0.7 11 11
MAPKKK cascade -0.041 0.12 -9999 0 -0.71 6 6
BCAR1 0.014 0.034 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.038 0.13 -9999 0 -0.46 42 42
lamellipodium assembly -0.033 0.09 -9999 0 -0.44 6 6
RET51/GFRalpha1/GDNF/SHC -0.053 0.16 -9999 0 -0.69 12 12
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC -0.037 0.12 -9999 0 -0.46 40 40
RET9/GFRalpha1/GDNF/Shank3 -0.036 0.12 -9999 0 -0.46 39 39
MAPK3 0.006 0.15 -9999 0 -0.77 5 5
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.002 0.12 -9999 0 -0.75 12 12
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.042 0.13 -9999 0 -0.73 5 5
DOK5 -0.006 0.13 -9999 0 -0.76 14 14
GFRA1 -0.039 0.2 -9999 0 -0.76 36 36
MAPK8 0.017 0.11 -9999 0 -0.57 6 6
HRAS/GTP -0.048 0.14 -9999 0 -0.84 6 6
tube development -0.033 0.11 -9999 0 -0.5 6 6
MAPK1 0.006 0.15 -9999 0 -0.77 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.08 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.078 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.058 0.17 -9999 0 -0.87 12 12
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.052 0.16 -9999 0 -0.7 11 11
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.19 -9999 0 -0.8 18 18
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
CREB1 -0.031 0.097 -9999 0 -0.54 5 5
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.081 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.057 0.18 -9999 0 -0.8 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.014 0.15 -9999 0 -0.76 19 19
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.027 0.11 -9999 0 -0.52 6 6
RET9/GFRalpha1/GDNF/FRS2 -0.036 0.12 -9999 0 -0.46 39 39
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.034 -9999 0 -0.75 1 1
NCK1 0.014 0.034 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.082 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.1 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.035 0.11 -9999 0 -0.61 6 6
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.11 -9999 0 -0.77 5 5
PI3K -0.05 0.14 -9999 0 -0.74 6 6
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.033 0.11 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.03 0.092 -9999 0 -0.53 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.052 0.16 -9999 0 -0.7 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.011 0.059 -9999 0 -0.75 3 3
IRS2 0.002 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.11 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF/PKC alpha -0.052 0.16 -9999 0 -0.7 11 11
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.067 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.054 0.16 -9999 0 -0.7 11 11
Rac1/GTP -0.039 0.11 -9999 0 -0.54 6 6
RET9/GFRalpha1/GDNF -0.039 0.14 -9999 0 -0.51 39 39
GFRalpha1/GDNF -0.045 0.16 -9999 0 -0.59 39 39
Canonical NF-kappaB pathway

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
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.074 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.16 0.28 -9999 0 -0.67 119 119
NFKBIA 0.063 0.021 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
IKBKG -0.047 0.084 -9999 0 -10000 0 0
IKK complex/A20 -0.041 0.08 -9999 0 -0.59 2 2
NEMO/A20/RIP2 0.014 0.039 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.043 0.077 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.034 0.062 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.19 0.37 -9999 0 -0.86 119 119
NFKB1 0.019 0.034 -9999 0 -0.74 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.034 -9999 0 -0.75 1 1
TNF/TNFR1A -0.01 0.077 -9999 0 -0.61 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
NF kappa B1 p50/RelA -0.001 0.02 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.021 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.038 0.07 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.035 0.064 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.004 0.1 -10000 0 -0.86 7 7
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0 -10000 0 -10000 0 0
CDKN1A 0.04 0.035 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.021 0.12 -10000 0 -0.66 16 16
mol:Ca2+ -0.017 0.16 0.4 16 -0.65 23 39
AGT -0.022 0.18 -10000 0 -0.82 23 23
CCNA2 -0.058 0.23 -10000 0 -0.88 6 6
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 0.02 0.085 -10000 0 -0.55 11 11
CDK2/Cyclin E1 -0.01 0.058 -10000 0 -0.47 7 7
MAPK3 0.009 0.12 -10000 0 -0.66 16 16
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.12 -10000 0 -0.66 16 16
PTP4A1 0.041 0.068 -10000 0 -10000 0 0
PTP4A3 -0.012 0.15 -10000 0 -0.86 16 16
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.009 0.12 -10000 0 -0.66 16 16
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.031 0.059 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.002 0.035 -10000 0 -0.56 2 2
PRL-1/ATF-5 0.042 0.075 -10000 0 -10000 0 0
RABGGTA 0.013 0.048 -10000 0 -0.75 2 2
BCAR1 0.012 0.076 0.4 16 -0.58 1 17
RHOC 0.031 0.059 -10000 0 -10000 0 0
RHOA 0.031 0.059 -10000 0 -10000 0 0
cell motility 0.037 0.061 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.046 0.063 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.021 0.12 -10000 0 -0.66 16 16
ROCK1 0.037 0.062 -10000 0 -10000 0 0
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.041 0.068 -10000 0 -10000 0 0
ATF5 0.011 0.067 -10000 0 -0.86 3 3
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.006 0.087 0.78 6 -10000 0 6
PI3K Class IB/PDE3B 0.006 0.087 -10000 0 -0.78 6 6
PDE3B 0.006 0.087 -10000 0 -0.79 6 6
p38 MAPK signaling pathway

Figure S89.  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 S89.  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
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.014 0.034 -10000 0 -0.75 1 1
MAP2K3 0.038 0.044 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.049 0.045 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.003 0.13 -10000 0 -0.85 11 11
TXN 0.011 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
GADD45A 0.016 0 -10000 0 -10000 0 0
GADD45B 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
MAP3K6 0.014 0.034 -10000 0 -0.75 1 1
MAP3K7 0.016 0 -10000 0 -10000 0 0
MAP3K4 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.001 0.025 -10000 0 -0.56 1 1
TAK1/TAB family 0 0.009 0.2 1 -10000 0 1
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.014 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.1 0.28 -10000 0 -0.76 76 76
CCM2 0.016 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.075 0.18 -10000 0 -0.5 76 76
MAPK11 0.014 0.039 -10000 0 -0.86 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.067 0.16 -10000 0 -0.45 76 76
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 0.017 0.051 -10000 0 -0.41 7 7
TAOK2 0.022 0.019 -10000 0 -0.41 1 1
TAOK3 0.022 0.019 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.016 0 -10000 0 -10000 0 0
MAP3K10 0.014 0.034 -10000 0 -0.75 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TRX/ASK1 0 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.011 0.071 -10000 0 -0.5 10 10
ErbB2/ErbB3 signaling events

Figure S90.  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 S90.  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 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.075 -10000 0 -0.72 3 3
NFATC4 0.047 0.078 -10000 0 -0.54 2 2
ERBB2IP 0.008 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.018 0.078 -10000 0 -0.64 1 1
JUN 0.036 0.079 -10000 0 -0.41 2 2
HRAS 0.013 0.039 -10000 0 -0.86 1 1
DOCK7 0.019 0.092 -10000 0 -0.62 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.023 0.1 -10000 0 -0.87 2 2
AKT1 0.016 0.002 -10000 0 -10000 0 0
BAD 0.026 0.036 -10000 0 -0.54 2 2
MAPK10 -0.011 0.045 -10000 0 -0.39 1 1
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.085 -10000 0 -0.72 1 1
RAF1 0.038 0.096 -10000 0 -0.68 3 3
ErbB2/ErbB3/neuregulin 2 -0.02 0.098 -10000 0 -0.49 21 21
STAT3 0 0.002 -10000 0 -10000 0 0
cell migration 0.059 0.056 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.093 0.26 -10000 0 -0.6 9 9
FOS -0.04 0.19 -10000 0 -0.48 15 15
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.078 -10000 0 -0.64 1 1
MAPK3 -0.061 0.21 -10000 0 -0.56 8 8
MAPK1 -0.061 0.21 -10000 0 -0.56 8 8
JAK2 0.019 0.089 -10000 0 -0.6 1 1
NF2 -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.005 0.091 -10000 0 -0.82 2 2
NRG1 -0.015 0.13 -10000 0 -0.75 16 16
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.024 0.083 -10000 0 -0.44 2 2
MAPK9 -0.008 0.037 -10000 0 -10000 0 0
ERBB2 -0.002 0.036 -10000 0 -0.58 2 2
ERBB3 -0.005 0.1 -10000 0 -0.75 9 9
SHC1 0.007 0.039 -10000 0 -0.86 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.002 0.023 0.37 1 -10000 0 1
STAT3 (dimer) 0 0.002 -10000 0 -10000 0 0
RNF41 0.038 0.005 -10000 0 -10000 0 0
FRAP1 0.014 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.012 0.053 -10000 0 -0.41 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.031 -10000 0 -0.49 2 2
CHRNA1 -0.14 0.28 -10000 0 -0.45 224 224
myelination 0.05 0.075 -10000 0 -0.49 2 2
PPP3CB 0.019 0.083 -10000 0 -0.55 1 1
KRAS 0.015 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.015 0.07 -10000 0 -0.72 2 2
NRG2 -0.002 0.12 -10000 0 -0.85 10 10
mol:GDP 0.006 0.09 -10000 0 -0.82 2 2
SOS1 0.009 0.008 -10000 0 -10000 0 0
MAP2K2 0.044 0.098 -10000 0 -0.7 2 2
SRC 0.016 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.019 0.088 -10000 0 -0.6 1 1
MAP2K1 -0.044 0.18 -10000 0 -0.57 8 8
heart morphogenesis -0.018 0.078 -10000 0 -0.64 1 1
RAS family/GDP -0.015 0.074 -10000 0 -0.72 3 3
GRB2 0.009 0.008 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.02 0.027 -10000 0 -0.24 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.016 0.002 -10000 0 -10000 0 0
nervous system development -0.018 0.078 -10000 0 -0.64 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

Figure S91.  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 S91.  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
Insulin responsive Vesicles -0.006 0.035 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.064 0.089 0.32 32 -0.36 1 33
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.031 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.067 0.25 -10000 0 -0.86 46 46
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.043 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.059 -10000 0 -0.75 3 3
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.032 0.084 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.066 0.093 0.33 32 -0.4 1 33
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.034 0 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 61 61
LNPEP 0.014 0.034 -10000 0 -0.75 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

Figure S92.  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 S92.  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
EP300 0.014 0.034 -10000 0 -0.75 1 1
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.044 0.66 2 -10000 0 2
CDKN1A -0.003 0.041 -10000 0 -0.65 2 2
KAT2B 0.014 0.034 -10000 0 -0.75 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0.001 0.023 0.53 1 -10000 0 1
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.03 0.016 -10000 0 -0.34 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.003 0.12 -10000 0 -0.86 9 9
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.16 -10000 0 -0.66 28 28
PPARGC1A -0.06 0.23 -10000 0 -0.75 50 50
FHL2 0.008 0.078 -10000 0 -0.77 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.008 -10000 0 -10000 0 0
HIST2H4A 0.025 0.044 -10000 0 -0.67 2 2
SIRT1/FOXO3a 0.001 0.016 0.32 1 -10000 0 1
SIRT1 0.001 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.001 0.019 -10000 0 -10000 0 0
apoptosis -0.001 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.048 0.15 -10000 0 -0.49 50 50
p53/SIRT1 0.001 0.024 0.38 2 -10000 0 2
SIRT1/FOXO4 0 0.015 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.004 0.046 -10000 0 -0.53 1 1
HIST1H1E 0.029 0.022 -10000 0 -0.32 2 2
SIRT1/p300 -0.001 0.026 -10000 0 -0.56 1 1
muscle cell differentiation 0.031 0.13 0.57 28 -10000 0 28
TP53 0.001 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.011 0.088 -10000 0 -0.67 9 9
ACSS2 0.028 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.031 0.13 -10000 0 -0.57 28 28
IL1-mediated signaling events

Figure S93.  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 S93.  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 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.059 -9999 0 -0.75 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.03 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.087 0.22 -9999 0 -0.62 71 71
IL1A -0.007 0.13 -9999 0 -0.86 12 12
IL1B 0.023 0.074 -9999 0 -0.65 6 6
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -10000 0 0
IL1R2 -0.08 0.26 -9999 0 -0.79 60 60
IL1R1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.025 -9999 0 -10000 0 0
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.016 0.001 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.041 0.046 -9999 0 -10000 0 0
JUN 0.061 0.03 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.07 -9999 0 -0.78 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.09 -9999 0 -0.53 1 1
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.015 0.084 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.01 0.07 -9999 0 -0.52 8 8
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
MAPK8 0.052 0.031 -9999 0 -10000 0 0
IRAK1 0.031 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -9999 0 -0.66 17 17
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.035 -9999 0 -0.56 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.032 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.01 0.07 -9999 0 -0.52 8 8
IL1 beta/IL1R2 -0.067 0.18 -9999 0 -0.52 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.071 -9999 0 -1 1 1
IRAK3 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.009 0.061 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.048 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.018 0.1 -9999 0 -0.57 15 15
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.009 0.075 -9999 0 -0.83 4 4
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.007 0.049 -9999 0 -10000 0 0
CASP1 0.016 0 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.093 0.23 -9999 0 -0.63 75 75
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.009 0.065 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.007 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.032 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
IL1RN -0.014 0.16 -9999 0 -0.86 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.043 0.033 -9999 0 -10000 0 0
Ephrin B reverse signaling

Figure S94.  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 S94.  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 0.016 0 -10000 0 -10000 0 0
EPHB2 0 0.11 -10000 0 -0.77 10 10
EFNB1 0.017 0.097 -10000 0 -0.66 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.096 -10000 0 -0.75 3 3
Ephrin B2/EPHB1-2 -0.012 0.082 -10000 0 -0.54 11 11
neuron projection morphogenesis -0.018 0.092 -10000 0 -0.71 3 3
Ephrin B1/EPHB1-2/Tiam1 -0.021 0.1 -10000 0 -0.81 3 3
DNM1 -0.002 0.12 -10000 0 -0.86 10 10
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.022 0.094 -10000 0 -0.67 9 9
YES1 -0.015 0.12 -10000 0 -0.9 9 9
Ephrin B1/EPHB1-2/NCK2 -0.02 0.1 -10000 0 -0.81 2 2
PI3K -0.012 0.099 -10000 0 -0.7 10 10
mol:GDP -0.021 0.1 -10000 0 -0.8 3 3
ITGA2B -0.015 0.16 -10000 0 -0.86 18 18
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.015 0.12 -10000 0 -0.9 9 9
MAP3K7 -0.013 0.095 -10000 0 -0.72 9 9
FGR -0.016 0.12 -10000 0 -0.89 9 9
TIAM1 0.014 0.034 -10000 0 -0.75 1 1
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion 0.018 0.14 -10000 0 -0.69 11 11
LYN -0.015 0.12 -10000 0 -0.9 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.016 0.11 -10000 0 -0.84 9 9
Ephrin B1/EPHB1-2 -0.016 0.1 -10000 0 -0.78 9 9
SRC -0.015 0.12 -10000 0 -0.89 9 9
ITGB3 0.011 0.059 -10000 0 -0.75 3 3
EPHB1 0.011 0.062 -10000 0 -0.79 3 3
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.027 0.13 -10000 0 -0.64 21 21
BLK -0.023 0.12 -10000 0 -0.89 9 9
HCK -0.022 0.13 -10000 0 -0.94 9 9
regulation of stress fiber formation 0.02 0.098 0.8 2 -10000 0 2
MAPK8 0.032 0.09 -10000 0 -0.63 9 9
Ephrin B1/EPHB1-2/RGS3 -0.02 0.1 -10000 0 -0.81 2 2
endothelial cell migration -0.009 0.082 -10000 0 -0.61 9 9
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.011 0.11 -10000 0 -0.85 9 9
regulation of focal adhesion formation 0.02 0.098 0.8 2 -10000 0 2
chemotaxis 0.02 0.098 0.8 2 -10000 0 2
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
Rac1/GTP -0.019 0.095 -10000 0 -0.74 3 3
angiogenesis -0.016 0.1 -10000 0 -0.78 9 9
LCK -0.021 0.12 -10000 0 -0.91 9 9
Signaling mediated by p38-gamma and p38-delta

Figure S95.  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 S95.  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 0.036 0.053 -9999 0 -0.5 5 5
SNTA1 0.012 0.052 -9999 0 -0.8 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.037 0.046 -9999 0 -0.48 4 4
MAPK12 0.028 0.086 -9999 0 -0.49 13 13
CCND1 0.014 0.07 -9999 0 -0.3 19 19
p38 gamma/SNTA1 0.032 0.09 -9999 0 -0.51 11 11
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.028 0.085 -9999 0 -0.49 13 13
MAP2K6 0.03 0.042 -9999 0 -0.47 3 3
MAPT 0.032 0.069 -9999 0 -0.5 6 6
MAPK13 0.026 0.052 -9999 0 -0.56 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.018 -9999 0 -0.39 1 1
Syndecan-3-mediated signaling events

Figure S96.  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 S96.  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 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 0.069 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.011 0.073 -9999 0 -0.49 11 11
POMC 0.012 0.052 -9999 0 -0.8 2 2
EGFR 0 0.11 -9999 0 -0.85 9 9
Syndecan-3/EGFR -0.009 0.066 -9999 0 -0.49 8 8
AGRP 0.007 0.048 -9999 0 -0.75 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.008 0.13 -9999 0 -0.86 11 11
long-term memory -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.032 0.12 -9999 0 -0.49 27 27
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.019 -9999 0 -0.42 1 1
MC4R -0.009 0.11 -9999 0 -0.86 8 8
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.012 0.14 -9999 0 -0.75 18 18
FGFR/FGF/Syndecan-3 -0.001 0.019 -9999 0 -0.43 1 1
neuron projection morphogenesis -0.022 0.088 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.002 0.031 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.01 0.065 -9999 0 -0.47 1 1
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.019 -9999 0 -0.43 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.031 0.12 -9999 0 -0.47 33 33
IL8 -0.04 0.21 -9999 0 -0.84 33 33
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.018 -9999 0 -0.41 1 1
alpha-MSH/MC4R -0.013 0.091 -9999 0 -0.66 10 10
Gamma Secretase 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S97.  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 S97.  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 -0.021 0.1 -9999 0 -0.51 21 21
KLHL20 -0.013 0.046 -9999 0 -0.35 2 2
CYFIP2 0.004 0.095 -9999 0 -0.75 8 8
Rac1/GDP 0.067 0.077 -9999 0 -10000 0 0
ENAH -0.021 0.1 -9999 0 -0.51 21 21
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.047 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -9999 0 -0.22 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.085 -9999 0 -10000 0 0
RAPGEF1 0.053 0.1 -9999 0 -10000 0 0
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.11 -9999 0 -0.54 21 21
CRK 0.042 0.11 -9999 0 -0.47 21 21
E-cadherin/gamma catenin/alpha catenin -0.023 0.1 -9999 0 -0.5 23 23
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.021 0.1 -9999 0 -0.51 21 21
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.035 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.019 -9999 0 -0.44 1 1
PI3K -0.01 0.045 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.026 0.12 -9999 0 -0.58 23 23
TIAM1 0.014 0.034 -9999 0 -0.75 1 1
E-cadherin(dimer)/Ca2+ -0.017 0.081 -9999 0 -10000 0 0
AKT1 -0.005 0.025 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
CDH1 -0.016 0.15 -9999 0 -0.75 21 21
RhoA/GDP 0.067 0.076 -9999 0 -10000 0 0
actin cytoskeleton organization -0.01 0.034 -9999 0 -0.24 2 2
CDC42/GDP 0.067 0.076 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.015 0.069 -9999 0 -0.47 2 2
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.018 0.085 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.017 0.083 -9999 0 -0.42 21 21
mol:GDP 0.063 0.087 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.059 -9999 0 -0.75 3 3
p120 catenin/RhoA/GDP -0.013 0.06 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.036 0.063 -9999 0 -0.26 19 19
NME1 0.016 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.021 0.1 -9999 0 -0.51 21 21
regulation of cell-cell adhesion -0.009 0.042 -9999 0 -10000 0 0
WASF2 -0.005 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.055 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.088 -9999 0 -0.81 1 1
CCND1 -0.016 0.065 -9999 0 -0.33 19 19
VAV2 0.049 0.1 -9999 0 -0.5 1 1
RAP1/GDP -0.011 0.057 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.11 -9999 0 -0.5 21 21
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.018 0.083 -9999 0 -0.78 1 1
E-cadherin/beta catenin -0.019 0.091 -9999 0 -0.46 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.021 0.1 -9999 0 -0.51 21 21
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
Rac1/GTP -0.02 0.071 -9999 0 -0.6 1 1
E-cadherin/beta catenin/alpha catenin -0.02 0.095 -9999 0 -0.48 21 21
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.11 -9999 0 -0.55 21 21
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S98.  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 S98.  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 -0.007 0.066 -9999 0 -0.66 5 5
CRKL 0.04 0.066 -9999 0 -0.46 2 2
mol:PIP3 -0.03 0.003 -9999 0 -10000 0 0
AKT1 0 0.02 -9999 0 -0.45 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.049 0.063 -9999 0 -0.43 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
HGF/MET/SHIP2 -0.029 0.13 -9999 0 -0.57 26 26
MAP3K5 -0.022 0.12 -9999 0 -0.41 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.027 0.12 -9999 0 -0.61 15 15
AP1 -0.015 0.083 -9999 0 -0.52 13 13
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
apoptosis 0.003 0.11 -9999 0 -0.7 12 12
STAT3 (dimer) 0.041 0.079 -9999 0 -0.53 3 3
GAB1/CRKL/SHP2/PI3K -0.011 0.055 -9999 0 -0.59 2 2
INPP5D 0.009 0.078 -9999 0 -0.86 4 4
CBL/CRK 0.046 0.069 -9999 0 -0.51 3 3
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 0 0.03 -9999 0 -0.29 5 5
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.009 0.039 -9999 0 -0.34 2 2
PAK1 0.01 0.019 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.029 0.13 -9999 0 -0.57 26 26
HRAS 0.031 0.099 -9999 0 -0.71 3 3
DOCK1 0.048 0.069 -9999 0 -0.51 3 3
GAB1 0.03 0.069 -9999 0 -0.44 3 3
CRK 0.04 0.066 -9999 0 -0.46 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.023 0.1 -9999 0 -0.54 14 14
JUN 0.016 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.013 0.061 -9999 0 -0.4 5 5
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
cell morphogenesis 0.079 0.085 -9999 0 -0.66 2 2
GRB2/SHC -0.012 0.058 -9999 0 -0.53 3 3
FOS -0.004 0.12 -9999 0 -0.76 13 13
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0 0.03 -9999 0 -0.29 5 5
HGF/MET/MUC20 -0.03 0.13 -9999 0 -0.58 26 26
cell migration -0.012 0.057 -9999 0 -0.52 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.014 0.034 -9999 0 -0.75 1 1
MET/RANBP10 -0.007 0.066 -9999 0 -0.66 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.073 -9999 0 -0.58 3 3
MET/MUC20 -0.007 0.067 -9999 0 -0.68 5 5
RAP1B 0.057 0.06 -9999 0 -10000 0 0
RAP1A 0.057 0.06 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.029 0.13 -9999 0 -0.57 26 26
RAF1 0.04 0.094 -9999 0 -0.66 3 3
STAT3 -0.015 0.067 -9999 0 -0.54 3 3
cell proliferation 0.054 0.1 -9999 0 -0.62 4 4
RPS6KB1 -0.004 0.02 -9999 0 -10000 0 0
MAPK3 -0.006 0.027 -9999 0 -0.27 5 5
MAPK1 -0.006 0.027 -9999 0 -0.27 5 5
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.014 0.094 -9999 0 -10000 0 0
SRC 0.042 0.079 -9999 0 -0.54 3 3
PI3K -0.013 0.062 -9999 0 -0.54 4 4
MET/Glomulin 0.009 0.062 -9999 0 -0.61 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.05 0.088 -9999 0 -0.59 3 3
MET 0.007 0.087 -9999 0 -0.86 5 5
MAP4K1 -0.035 0.12 -9999 0 -0.4 12 12
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.049 0.09 -9999 0 -0.59 3 3
BAD 0.008 0.045 -9999 0 -0.91 1 1
MAP2K4 -0.01 0.11 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.012 0.057 -9999 0 -0.56 2 2
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.012 0.054 -9999 0 -0.49 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.021 0.17 -9999 0 -0.8 23 23
RASA1 0.014 0.034 -9999 0 -0.75 1 1
NCK1 0.014 0.034 -9999 0 -0.75 1 1
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.013 0.06 -9999 0 -0.53 3 3
PDPK1 -0.014 0.021 -9999 0 -0.49 1 1
HGF/MET/SHIP -0.034 0.14 -9999 0 -0.59 29 29
Arf6 downstream pathway

Figure S99.  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 S99.  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 0.019 0.17 -10000 0 -0.71 26 26
regulation of axonogenesis -0.033 0.035 -10000 0 -10000 0 0
myoblast fusion 0.016 0.07 0.32 26 -10000 0 26
mol:GTP -0.01 0.043 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.041 0.45 1 -10000 0 1
ARF1/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.035 -10000 0 -10000 0 0
mol:Choline 0.033 0.031 -10000 0 -10000 0 0
lamellipodium assembly -0.017 0.073 -10000 0 -0.33 26 26
MAPK3 0.024 0.069 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.041 -10000 0 -0.45 1 1
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.071 -10000 0 -0.32 26 26
ARF1/GDP 0.02 0.07 -10000 0 -10000 0 0
ARF6 0.009 0.024 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.016 0.034 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.069 -10000 0 -10000 0 0
actin filament bundle formation 0.014 0.062 -10000 0 -10000 0 0
KALRN -0.013 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.025 -10000 0 -0.56 1 1
RhoA/GDP -0.015 0.063 -10000 0 -10000 0 0
NME1 0.017 0.004 -10000 0 -10000 0 0
Rac1/GDP -0.015 0.063 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.01 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.017 0.074 -10000 0 -0.33 26 26
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.01 0.043 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.043 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GDP -0.016 0.071 -10000 0 -0.32 26 26
ARF6/GTP/RAB11FIP3/RAB11A -0.006 0.03 -10000 0 -0.46 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.021 0.035 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.034 -10000 0 -0.75 1 1
tube morphogenesis -0.017 0.073 -10000 0 -0.33 26 26
ruffle organization 0.033 0.035 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.043 -10000 0 -10000 0 0
PLD2 0.021 0.035 -10000 0 -10000 0 0
PIP5K1A 0.033 0.035 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.033 0.031 -10000 0 -10000 0 0
Rac1/GTP -0.017 0.074 -10000 0 -0.33 26 26
Paxillin-dependent events mediated by a4b1

Figure S100.  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 S100.  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 0.016 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.012 -10000 0 -10000 0 0
DOCK1 0.014 0.034 -10000 0 -0.75 1 1
ITGA4 -0.01 0.15 -10000 0 -0.86 15 15
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.02 0.11 -10000 0 -0.66 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.017 0.097 -10000 0 -0.57 15 15
alpha4/beta7 Integrin/Paxillin -0.015 0.088 -10000 0 -0.52 15 15
lamellipodium assembly -0.001 0.044 -10000 0 -0.77 1 1
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
PI3K -0.002 0.035 -10000 0 -0.56 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.016 0 -10000 0 -10000 0 0
PXN 0.031 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
ARF6/GTP -0.013 0.074 -10000 0 -10000 0 0
cell adhesion -0.014 0.081 -10000 0 -10000 0 0
CRKL/CBL -0.001 0.025 -10000 0 -0.56 1 1
alpha4/beta1 Integrin/Paxillin -0.015 0.088 -10000 0 -0.52 15 15
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.002 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.027 0.11 -10000 0 -0.48 24 24
p130Cas/Crk/Dock1 -0.002 0.03 -10000 0 -0.48 2 2
VCAM1 -0.007 0.14 -10000 0 -0.82 14 14
alpha4/beta1 Integrin/Paxillin/Talin -0.014 0.082 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.014 0.082 -10000 0 -0.48 15 15
BCAR1 0.014 0.034 -10000 0 -0.75 1 1
mol:GDP 0.014 0.081 0.48 15 -10000 0 15
CBL 0.014 0.034 -10000 0 -0.75 1 1
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.014 0.082 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.051 -10000 0 -0.93 1 1
EPHB forward signaling

Figure S101.  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 S101.  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 -0.056 0.16 -10000 0 -0.5 57 57
cell-cell adhesion 0.013 0.072 0.63 3 -10000 0 3
Ephrin B/EPHB2/RasGAP -0.014 0.08 -10000 0 -0.81 1 1
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
Ephrin B1/EPHB3 -0.014 0.081 -10000 0 -0.5 14 14
Ephrin B1/EPHB1 -0.003 0.04 -10000 0 -0.52 3 3
HRAS/GDP -0.008 0.052 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.013 0.072 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.036 0.085 -10000 0 -0.75 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.008 0.056 -10000 0 -10000 0 0
endothelial cell migration -0.002 0.025 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 0.005 0.089 -10000 0 -0.75 7 7
PAK1 0.048 0.083 -10000 0 -0.76 1 1
HRAS 0.014 0.039 -10000 0 -0.86 1 1
RRAS 0.036 0.086 -10000 0 -0.77 1 1
DNM1 -0.002 0.12 -10000 0 -0.86 10 10
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.043 0.061 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.072 -10000 0 -0.63 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.005 0.036 -10000 0 -10000 0 0
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
EPHB2 0 0.11 -10000 0 -0.77 10 10
EPHB3 -0.006 0.13 -10000 0 -0.76 14 14
EPHB1 0.011 0.062 -10000 0 -0.79 3 3
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.058 -10000 0 -10000 0 0
Ephrin B/EPHB2 -0.014 0.08 -10000 0 -0.6 3 3
Ephrin B/EPHB3 -0.017 0.09 -10000 0 -0.71 3 3
JNK cascade 0.041 0.084 -10000 0 -0.79 2 2
Ephrin B/EPHB1 -0.008 0.058 -10000 0 -0.5 1 1
RAP1/GDP -0.002 0.051 -10000 0 -10000 0 0
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 0.005 0.089 -10000 0 -0.75 7 7
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.012 0.082 -10000 0 -0.54 11 11
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.015 0.08 -10000 0 -0.71 3 3
Rap1/GTP -0.013 0.073 -10000 0 -0.64 3 3
axon guidance -0.056 0.16 -10000 0 -0.49 57 57
MAPK3 0.065 0.04 -10000 0 -10000 0 0
MAPK1 0.065 0.04 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.054 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.011 0.058 -10000 0 -0.5 2 2
CDC42/GDP -0.002 0.054 -10000 0 -10000 0 0
PI3K -0.002 0.025 -10000 0 -10000 0 0
EFNA5 -0.056 0.22 -10000 0 -0.76 47 47
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.056 -10000 0 -0.61 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.014 0.076 -10000 0 -0.64 4 4
PTK2 0.002 0.017 -10000 0 -10000 0 0
MAP4K4 0.041 0.085 -10000 0 -0.8 2 2
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.011 0.058 -10000 0 -0.5 3 3
MAP2K1 0.057 0.042 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.012 0.083 -10000 0 -0.66 5 5
cell migration 0.067 0.047 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.036 0.087 -10000 0 -0.77 1 1
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.073 0.23 -10000 0 -0.79 3 3
HRAS/GTP -0.015 0.085 -10000 0 -0.72 4 4
Ephrin B1/EPHB1-2 -0.012 0.082 -10000 0 -0.54 11 11
cell adhesion mediated by integrin 0.01 0.064 0.47 7 -10000 0 7
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.016 0.086 -10000 0 -0.75 3 3
RAC1-CDC42/GTP -0.022 0.099 -10000 0 -0.78 5 5
RASA1 0.014 0.034 -10000 0 -0.75 1 1
RAC1-CDC42/GDP -0.002 0.051 -10000 0 -10000 0 0
ruffle organization 0.07 0.088 -10000 0 -0.65 3 3
NCK1 0.014 0.034 -10000 0 -0.75 1 1
receptor internalization 0.036 0.11 -10000 0 -0.72 1 1
Ephrin B/EPHB2/KALRN -0.014 0.078 -10000 0 -0.81 1 1
ROCK1 0.021 0.078 -10000 0 -0.44 14 14
RAS family/GDP -0.011 0.058 -10000 0 -0.53 1 1
Rac1/GTP -0.014 0.077 -10000 0 -0.69 3 3
Ephrin B/EPHB1/Src/Paxillin -0.006 0.04 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

Figure S102.  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 S102.  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 0.049 0.12 -9999 0 -0.68 5 5
MAP3K8 0.013 0.055 -9999 0 -0.86 2 2
FOS 0.041 0.11 -9999 0 -0.57 5 5
PRKCA 0.017 0.003 -9999 0 -10000 0 0
PTPN7 -0.037 0.21 -9999 0 -0.86 32 32
HRAS 0.014 0.039 -9999 0 -0.86 1 1
PRKCB 0.009 0.084 -9999 0 -0.82 5 5
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.024 -9999 0 -0.53 1 1
MAPK3 0.029 0.085 -9999 0 -0.52 3 3
MAP2K1 0.055 0.056 -9999 0 -0.5 4 4
ELK1 0.017 0.003 -9999 0 -10000 0 0
BRAF -0.004 0.044 -9999 0 -0.48 3 3
mol:GTP 0 0.001 -9999 0 -0.006 12 12
MAPK1 0.029 0.085 -9999 0 -0.52 3 3
RAF1 -0.004 0.044 -9999 0 -0.46 4 4
KRAS 0.016 0.001 -9999 0 -10000 0 0
BARD1 signaling events

Figure S103.  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 S103.  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 -0.004 0.05 -10000 0 -0.56 4 4
ATM 0.014 0.034 -10000 0 -0.75 1 1
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.034 0.019 -10000 0 -0.4 1 1
protein ubiquitination -0.01 0.073 -10000 0 -0.88 1 1
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.034 0.068 -10000 0 -0.51 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.016 0 -10000 0 -10000 0 0
CCNE1 0.004 0.1 -10000 0 -0.86 7 7
CDK2/Cyclin E1 -0.009 0.078 -10000 0 -0.66 7 7
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.05 -10000 0 -0.56 4 4
FANCE 0.014 0.039 -10000 0 -0.86 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.17 0.36 -10000 0 -0.86 107 107
DNA repair 0.043 0.14 -10000 0 -0.59 12 12
BRCA1/BARD1/ubiquitin -0.004 0.05 -10000 0 -0.56 4 4
BARD1/DNA-PK -0.003 0.038 -10000 0 -10000 0 0
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.004 0.05 0.56 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex -0.004 0.043 -10000 0 -0.78 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/P53 -0.003 0.038 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BACH1 0.016 0 -10000 0 -10000 0 0
BARD1 0.01 0.068 -10000 0 -0.75 4 4
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/UbcH7 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/RAD51/PCNA -0.018 0.093 -10000 0 -0.52 14 14
BARD1/DNA-PK/P53 -0.003 0.035 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.05 -10000 0 -0.56 4 4
BRCA1/BARD1/CTIP -0.005 0.054 -10000 0 -0.86 1 1
FA complex -0.057 0.11 -10000 0 -0.57 1 1
BARD1/EWS -0.004 0.05 -10000 0 -0.56 4 4
RBBP8 0.029 0.047 -10000 0 -1 1 1
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.038 -10000 0 -10000 0 0
BRCA1/BARD1 -0.011 0.074 -10000 0 -0.9 1 1
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.005 0.051 -10000 0 -0.57 4 4
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.009 0.14 -10000 0 -0.86 14 14
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.05 -10000 0 -0.56 4 4
EWSR1 0.016 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S104.  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 S104.  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 0.014 0.034 -10000 0 -0.75 1 1
ANTXR2 0.014 0.034 -10000 0 -0.75 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.006 -10000 0 -0.094 2 2
monocyte activation 0.006 0.086 -10000 0 -0.37 21 21
MAP2K2 -0.002 0.036 -10000 0 -0.8 1 1
MAP2K1 0 0.005 -10000 0 -10000 0 0
MAP2K7 0 0.005 -10000 0 -10000 0 0
MAP2K6 -0.003 0.034 -10000 0 -0.43 3 3
CYAA 0.02 0.028 -10000 0 -0.42 2 2
MAP2K4 0 0.005 -10000 0 -10000 0 0
IL1B 0.016 0.06 -10000 0 -0.49 6 6
Channel -0.002 0.028 -10000 0 -0.45 2 2
NLRP1 -0.005 0.052 -10000 0 -0.52 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.006 0.094 2 -10000 0 2
MAPK3 0 0.005 -10000 0 -10000 0 0
MAPK1 0 0.005 -10000 0 -10000 0 0
PGR -0.016 0.082 -10000 0 -0.44 18 18
PA/Cellular Receptors -0.002 0.031 -10000 0 -0.49 2 2
apoptosis 0 0.006 -10000 0 -0.094 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.026 -10000 0 -0.42 2 2
macrophage activation 0.027 0.006 -10000 0 -10000 0 0
TNF 0.003 0.1 -10000 0 -0.8 8 8
VCAM1 -0.015 0.082 -10000 0 -0.37 21 21
platelet activation 0 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.01 -10000 0 -10000 0 0
IL18 0.015 0.067 -10000 0 -0.51 7 7
negative regulation of macrophage activation 0 0.006 -10000 0 -0.094 2 2
LEF 0 0.006 -10000 0 -0.094 2 2
CASP1 -0.003 0.024 -10000 0 -0.23 5 5
mol:cAMP 0 0.007 -10000 0 -10000 0 0
necrosis 0 0.006 -10000 0 -0.094 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.027 -10000 0 -0.43 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S105.  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 S105.  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 -0.01 0.067 -10000 0 -0.5 6 6
ER alpha/Gai/GDP/Gbeta gamma 0.054 0.055 -10000 0 -10000 0 0
AKT1 0.046 0.074 -10000 0 -0.82 3 3
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.041 0.074 -10000 0 -0.84 3 3
mol:Ca2+ -0.014 0.18 -10000 0 -0.68 11 11
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.007 0.066 -10000 0 -0.58 6 6
SHC1 0.014 0.039 -10000 0 -0.86 1 1
apoptosis -0.046 0.071 0.78 3 -10000 0 3
RhoA/GTP -0.004 0.038 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.007 0.046 -10000 0 -10000 0 0
regulation of stress fiber formation -0.068 0.045 0.54 1 -10000 0 1
E2/ERA-ERB (dimer) -0.012 0.079 -10000 0 -0.54 11 11
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.004 0.042 -10000 0 -0.47 4 4
pseudopodium formation 0.068 0.045 -10000 0 -0.54 1 1
E2/ER alpha (dimer)/PELP1 -0.004 0.046 -10000 0 -0.51 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
GNAO1 0.007 0.085 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.063 0.062 -10000 0 -0.49 3 3
E2/ER beta (dimer) -0.009 0.076 -10000 0 -0.65 7 7
mol:GDP -0.009 0.061 -10000 0 -0.47 4 4
mol:NADP 0.063 0.062 -10000 0 -0.49 3 3
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
mol:IP3 -0.016 0.19 -10000 0 -0.73 11 11
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 -0.023 0.098 -10000 0 -0.58 9 9
PLCB2 -0.067 0.16 -10000 0 -0.48 62 62
IGF1 0.005 0.095 -10000 0 -0.86 6 6
mol:L-citrulline 0.063 0.062 -10000 0 -0.49 3 3
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.048 -10000 0 -0.63 1 1
JNK cascade -0.009 0.075 -10000 0 -0.64 7 7
BCAR1 0.014 0.034 -10000 0 -0.75 1 1
ESR2 0.004 0.099 -10000 0 -0.83 7 7
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 0.009 0.07 -10000 0 -0.78 4 4
Gq family/GDP/Gbeta gamma -0.015 0.07 -10000 0 -0.51 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.052 0.033 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.046 -10000 0 -10000 0 0
GNAZ 0.011 0.059 -10000 0 -0.75 3 3
E2/ER alpha (dimer) -0.005 0.053 -10000 0 -0.6 4 4
STRN 0.011 0.059 -10000 0 -0.75 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.016 0.073 -10000 0 -0.56 8 8
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.059 -10000 0 -0.75 3 3
HBEGF -0.043 0.14 -10000 0 -0.51 6 6
cAMP biosynthetic process -0.01 0.064 -10000 0 -0.44 11 11
SRC 0.063 0.053 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.008 0.053 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.01 0.05 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.065 -10000 0 -0.45 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.024 -10000 0 -0.53 1 1
vasodilation 0.062 0.06 -10000 0 -0.47 3 3
mol:DAG -0.016 0.19 -10000 0 -0.73 11 11
Gs family/GDP/Gbeta gamma -0.007 0.048 -10000 0 -10000 0 0
MSN 0.07 0.049 -10000 0 -0.6 1 1
Gq family/GTP -0.018 0.077 -10000 0 -0.46 10 10
mol:PI-3-4-5-P3 0.041 0.071 -10000 0 -0.8 3 3
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.062 0.06 0.47 3 -10000 0 3
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.056 -10000 0 -0.45 3 3
NOS3 0.063 0.064 -10000 0 -0.52 3 3
GNA11 0.013 0.048 -10000 0 -0.75 2 2
MAPKKK cascade 0.072 0.069 -10000 0 -0.59 4 4
E2/ER alpha (dimer)/PELP1/Src -0.007 0.046 -10000 0 -0.48 3 3
ruffle organization 0.068 0.045 -10000 0 -0.54 1 1
ROCK2 -0.005 0.046 -10000 0 -0.68 1 1
GNA14 0.005 0.089 -10000 0 -0.75 7 7
GNA15 -0.009 0.14 -10000 0 -0.86 14 14
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.17 0.25 -10000 0 -0.66 8 8
MMP2 0.065 0.081 -10000 0 -0.66 3 3
E-cadherin signaling in keratinocytes

Figure S106.  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 S106.  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 0.057 0.053 -10000 0 -0.46 1 1
adherens junction organization 0.04 0.08 -10000 0 -0.53 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.061 -10000 0 -10000 0 0
FMN1 0.022 0.12 -10000 0 -0.67 2 2
mol:IP3 -0.008 0.041 -10000 0 -0.48 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.066 -10000 0 -0.71 1 1
CTNNB1 0.001 0.006 -10000 0 -10000 0 0
AKT1 0.053 0.058 -10000 0 -0.51 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.11 -10000 0 -0.53 21 21
CTNND1 0.016 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.075 -10000 0 -0.56 2 2
VASP 0.044 0.073 -10000 0 -0.67 1 1
ZYX 0.044 0.073 -10000 0 -0.67 1 1
JUB 0.042 0.081 -10000 0 -0.58 2 2
EGFR(dimer) -0.021 0.083 -10000 0 -0.48 9 9
E-cadherin/beta catenin-gamma catenin -0.022 0.1 -10000 0 -0.48 23 23
mol:PI-3-4-5-P3 -0.01 0.048 -10000 0 -0.54 1 1
PIK3CA 0.015 0.034 -10000 0 -0.75 1 1
PI3K -0.01 0.049 -10000 0 -0.56 1 1
FYN -0.24 0.13 -10000 0 -0.62 2 2
mol:Ca2+ -0.008 0.04 -10000 0 -0.47 1 1
JUP -0.003 0.058 -10000 0 -0.74 3 3
PIK3R1 0.015 0.034 -10000 0 -0.75 1 1
mol:DAG -0.008 0.041 -10000 0 -0.48 1 1
CDH1 -0.031 0.15 -10000 0 -0.75 21 21
RhoA/GDP -0.014 0.061 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.044 0.072 -10000 0 -0.65 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR 0 0.11 -10000 0 -0.85 9 9
CASR -0.29 0.15 -10000 0 -0.54 17 17
RhoA/GTP -0.007 0.035 -10000 0 -10000 0 0
AKT2 0.053 0.058 -10000 0 -0.51 1 1
actin cable formation 0.032 0.12 -10000 0 -0.64 2 2
apoptosis 0.009 0.044 0.49 1 -10000 0 1
CTNNA1 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.015 0.067 -10000 0 -10000 0 0
PIP5K1A 0.044 0.077 -10000 0 -0.58 2 2
PLCG1 -0.008 0.042 -10000 0 -0.49 1 1
Rac1/GTP -0.019 0.075 -10000 0 -0.6 1 1
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure S107.  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 S107.  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 -0.009 0.059 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.057 -9999 0 -0.68 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.049 -9999 0 -0.55 4 4
AP1 -0.017 0.084 -9999 0 -0.71 4 4
ILK 0.062 0.057 -9999 0 -10000 0 0
bone resorption -0.024 0.098 -9999 0 -0.76 2 2
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.007 0.049 -9999 0 -10000 0 0
ITGAV 0.022 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.14 -9999 0 -0.66 23 23
alphaV/beta3 Integrin/Osteopontin -0.007 0.054 -9999 0 -0.48 3 3
MAP3K1 0.063 0.058 -9999 0 -10000 0 0
JUN 0.016 0.002 -9999 0 -10000 0 0
MAPK3 0.074 0.076 -9999 0 -10000 0 0
MAPK1 0.074 0.076 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
MAPK8 0.076 0.057 -9999 0 -10000 0 0
ITGB3 0.018 0.059 -9999 0 -0.74 3 3
NFKBIA 0.087 0.077 -9999 0 -10000 0 0
FOS -0.003 0.12 -9999 0 -0.76 13 13
CD44 -0.021 0.18 -9999 0 -0.86 21 21
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU 0.086 0.17 -9999 0 -1.1 9 9
NF kappa B1 p50/RelA -0.011 0.058 -9999 0 -0.64 1 1
BCAR1 0.014 0.034 -9999 0 -0.75 1 1
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.003 0.042 -9999 0 -0.55 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.059 0.064 -9999 0 -10000 0 0
VAV3 0.057 0.098 -9999 0 -0.78 1 1
MAP3K14 0.061 0.077 -9999 0 -0.5 4 4
ROCK2 0.013 0.048 -9999 0 -0.75 2 2
SPP1 0.016 0.067 -9999 0 -0.74 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.015 0.074 -9999 0 -0.71 1 1
MMP2 0.099 0.12 -9999 0 -0.76 6 6
Hedgehog signaling events mediated by Gli proteins

Figure S108.  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 S108.  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 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.021 -9999 0 -0.48 1 1
forebrain development 0.054 0.094 -9999 0 -0.5 2 2
GNAO1 0.007 0.085 -9999 0 -0.84 5 5
SMO/beta Arrestin2 -0.002 0.039 -9999 0 -0.61 2 2
SMO 0.015 0.034 -9999 0 -0.75 1 1
ARRB2 0.014 0.039 -9999 0 -0.86 1 1
GLI3/SPOP 0.061 0.025 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex -0.019 0.097 -9999 0 -0.52 18 18
GNAI1 0.011 0.059 -9999 0 -0.75 3 3
XPO1 0.019 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.014 0.061 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 18 18
mol:GDP 0.015 0.034 -9999 0 -0.74 1 1
MIM/GLI2A 0.023 0.008 -9999 0 -10000 0 0
IFT88 0.014 0.034 -9999 0 -0.75 1 1
GNAI3 0.016 0.005 -9999 0 -10000 0 0
GLI2 0.058 0.03 -9999 0 -10000 0 0
GLI3 0.055 0.026 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0.034 -9999 0 -0.75 1 1
GNG2 0.016 0 -9999 0 -10000 0 0
Gi family/GTP 0.044 0.053 -9999 0 -0.55 1 1
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.057 0.044 -9999 0 -10000 0 0
GLI2/Su(fu) 0.075 0.037 -9999 0 -10000 0 0
FOXA2 -0.063 0.23 -9999 0 -0.83 38 38
neural tube patterning 0.054 0.094 -9999 0 -0.5 2 2
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.014 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.034 -9999 0 -0.75 1 1
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.023 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.054 0.094 -9999 0 -0.5 2 2
SUFU 0.037 0.022 -9999 0 -10000 0 0
LGALS3 -0.005 0.13 -9999 0 -0.86 12 12
catabolic process 0.093 0.03 -9999 0 -10000 0 0
GLI3A/CBP 0.017 0.055 -9999 0 -10000 0 0
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 0.055 0.095 -9999 0 -0.51 2 2
RAB23 0.016 0 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.013 0.083 -9999 0 -0.54 12 12
GNAZ 0.011 0.059 -9999 0 -0.75 3 3
RBBP4 0.014 0.034 -9999 0 -0.75 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.062 0.028 -9999 0 -10000 0 0
STK36 0.019 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.051 0.048 -9999 0 -0.49 1 1
PTCH1 0.061 0.1 -9999 0 -1.1 1 1
MIM/GLI1 0.05 0.15 -9999 0 -0.71 1 1
CREBBP 0.017 0.055 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.057 0.048 -9999 0 -10000 0 0
ceramide signaling pathway

Figure S109.  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 S109.  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 0.027 0.1 -9999 0 -0.41 1 1
BAG4 0.014 0.034 -9999 0 -0.75 1 1
BAD 0.03 0.046 -9999 0 -0.42 2 2
NFKBIA 0.016 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 78 78
BAX 0.031 0.036 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.027 -9999 0 -0.099 1 1
IKBKB 0.037 0.096 -9999 0 -10000 0 0
MAP2K2 0.046 0.053 -9999 0 -0.38 4 4
MAP2K1 0.047 0.051 -9999 0 -0.38 4 4
SMPD1 0.019 0.027 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.037 0.098 -9999 0 -10000 0 0
MAP2K4 0.041 0.035 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.097 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.054 0.052 -9999 0 -0.38 4 4
response to UV 0.001 0 -9999 0 -0.003 4 4
RAF1 0.039 0.053 -9999 0 -0.41 4 4
CRADD 0.016 0.001 -9999 0 -10000 0 0
mol:ceramide 0.022 0.038 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.016 0.001 -9999 0 -10000 0 0
MAP3K1 0.032 0.036 -9999 0 -10000 0 0
TRADD 0.016 0.001 -9999 0 -10000 0 0
RELA/p50 0.016 0 -9999 0 -10000 0 0
MAPK3 0.05 0.051 -9999 0 -0.37 4 4
MAPK1 0.05 0.051 -9999 0 -0.37 4 4
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.027 0.1 -9999 0 -10000 0 0
KSR1 0.029 0.056 -9999 0 -0.45 4 4
MAPK8 0.049 0.033 -9999 0 -10000 0 0
TRAF2 0.016 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.037 0.096 -9999 0 -10000 0 0
TNF R/SODD -0.001 0.025 -9999 0 -0.56 1 1
TNF 0.003 0.1 -9999 0 -0.8 8 8
CYCS 0.032 0.038 -9999 0 -10000 0 0
IKBKG 0.037 0.096 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.1 -9999 0 -0.44 1 1
RELA 0.016 0 -9999 0 -10000 0 0
RIPK1 0.016 0.001 -9999 0 -10000 0 0
AIFM1 0.033 0.038 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.009 0.069 -9999 0 -0.52 9 9
TNFRSF1A 0.016 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.028 0.03 -9999 0 -10000 0 0
NSMAF 0.028 0.099 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -0.003 4 4
BCL2 0.016 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

Figure S110.  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 S110.  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 -0.005 0.073 -9999 0 -0.73 5 5
VDR 0.011 0.059 -9999 0 -0.75 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.076 0.051 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.086 0.063 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.009 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.073 -9999 0 -10000 0 0
RXRs/NUR77 -0.008 0.089 -9999 0 -0.5 6 6
RXRs/PPAR 0.058 0.03 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.044 -9999 0 -0.57 3 3
RARs/VDR/DNA/Vit D3 -0.004 0.04 -9999 0 -10000 0 0
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.058 -9999 0 -0.75 3 3
RARs/RARs/DNA/9cRA -0.001 0.026 -9999 0 -0.41 2 2
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.035 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.019 0.073 -9999 0 -10000 0 0
THRA 0.014 0.034 -9999 0 -0.75 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.003 0.044 -9999 0 -0.57 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.005 0.057 -9999 0 -0.5 4 4
NR1H4 -0.01 0.14 -9999 0 -0.75 17 17
RXRs/LXRs/DNA 0.008 0.057 -9999 0 -10000 0 0
NR1H2 0.023 0.034 -9999 0 -0.74 1 1
NR1H3 0.025 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.005 0.053 -9999 0 -0.48 4 4
NR4A1 -0.007 0.13 -9999 0 -0.76 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.04 0.069 -9999 0 -0.41 2 2
RXRG 0.015 0.078 -9999 0 -0.85 4 4
RXR alpha/CCPG 0 0.004 -9999 0 -10000 0 0
RXRA 0.024 0.005 -9999 0 -10000 0 0
RXRB 0.025 0.006 -9999 0 -10000 0 0
THRB -0.031 0.18 -9999 0 -0.75 31 31
PPARG 0.016 0 -9999 0 -10000 0 0
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.084 0.13 -9999 0 -0.87 8 8
mol:Oxysterols 0.009 0.007 -9999 0 -10000 0 0
cholesterol transport 0.086 0.063 -9999 0 -10000 0 0
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0.048 -9999 0 -0.75 2 2
RXRs/NUR77/BCL2 -0.01 0.056 -9999 0 -10000 0 0
SREBF1 0.092 0.066 -9999 0 -0.66 1 1
RXRs/RXRs/DNA/9cRA 0.005 0.057 -9999 0 -0.5 4 4
ABCA1 0.091 0.072 -9999 0 -0.65 2 2
RARs/THRs -0.027 0.099 -9999 0 -10000 0 0
RXRs/FXR -0.009 0.094 -9999 0 -0.5 7 7
BCL2 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S111.  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 S111.  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 0.016 0 -10000 0 -10000 0 0
NFATC1 0.075 0.027 -10000 0 -10000 0 0
NFATC2 0.054 0.029 -10000 0 -10000 0 0
NFATC3 0.028 0.04 -10000 0 -0.49 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.032 0.072 -10000 0 -0.46 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.013 0.054 -10000 0 -0.52 2 2
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.001 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0.003 -10000 0 -10000 0 0
BAD 0.012 0.052 -10000 0 -0.8 2 2
CABIN1/MEF2D 0.037 0.068 -10000 0 -0.43 4 4
Calcineurin A alpha-beta B1/BCL2 0.016 0 -10000 0 -10000 0 0
FKBP8 0.014 0.034 -10000 0 -0.75 1 1
activation-induced cell death of T cells -0.037 0.067 0.43 4 -10000 0 4
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 61 61
MAP3K8 0.013 0.055 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.002 0.024 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.01 0.056 -10000 0 -10000 0 0
CABIN1 0.032 0.073 -10000 0 -0.47 4 4
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0.013 0.048 -10000 0 -0.75 2 2
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.035 -10000 0 -0.56 2 2
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.016 0.003 -10000 0 -10000 0 0
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.028 -10000 0 -10000 0 0
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.025 -10000 0 -0.56 1 1
CASP3 0.016 0.003 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.02 -10000 0 -0.39 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.077 -10000 0 -0.47 2 2
PRKCB 0.007 0.082 -10000 0 -0.82 5 5
PRKCE 0.014 0.034 -10000 0 -0.75 1 1
JNK2/NFAT4 -0.003 0.034 -10000 0 -0.44 3 3
BAD/BCL-XL -0.002 0.039 -10000 0 -0.61 2 2
PRKCD 0.014 0.039 -10000 0 -0.86 1 1
NUP214 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.059 -10000 0 -0.75 3 3
PRKCA 0.016 0 -10000 0 -10000 0 0
PRKCG -0.03 0.18 -10000 0 -0.86 22 22
PRKCQ -0.007 0.13 -10000 0 -0.75 15 15
FKBP38/BCL2 -0.001 0.025 -10000 0 -0.56 1 1
EP300 0.015 0.034 -10000 0 -0.74 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.08 0.029 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.022 -10000 0 -0.5 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.031 -10000 0 -0.49 2 2
NFATc/ERK1 0.081 0.026 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.013 0.055 -10000 0 -0.53 2 2
NR4A1 0.073 0.13 -10000 0 -0.67 15 15
GSK3B 0.016 0.003 -10000 0 -10000 0 0
positive T cell selection 0.028 0.04 -10000 0 -0.49 3 3
NFAT1/CK1 alpha -0.002 0.015 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0.003 -10000 0 -10000 0 0
AKAP5 0.013 0.048 -10000 0 -0.75 2 2
MEF2D 0.016 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.08 0.029 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S112.  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 S112.  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
NF kappa B/RelA -0.008 0.059 -9999 0 -0.55 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.049 -9999 0 -0.54 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.059 -9999 0 -0.75 3 3
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.032 -9999 0 -0.73 1 1
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.041 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.003 0.027 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.046 0.043 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.003 0.027 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.063 0.025 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA 0.048 0.048 -9999 0 -0.65 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.002 0.12 -9999 0 -0.75 12 12
GATA1 -0.021 0.17 -9999 0 -0.86 20 20
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.009 0.046 -9999 0 -0.53 2 2
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.014 0.034 -9999 0 -0.75 1 1
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.032 -9999 0 -10000 0 0
KAT2B 0.014 0.034 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.008 0.038 -9999 0 -10000 0 0
SIN3 complex -0.019 0.096 -9999 0 -0.52 18 18
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 18 18
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.004 0.037 -9999 0 -0.64 1 1
YY1/HDAC2 -0.001 0.032 -9999 0 -0.73 1 1
YY1/HDAC1 -0.001 0.032 -9999 0 -0.73 1 1
NuRD/MBD2 Complex (MeCP1) 0.064 0.011 -9999 0 -10000 0 0
PPARG -0.006 0.048 -9999 0 -0.4 4 4
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.003 0.027 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.025 -9999 0 -0.52 1 1
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.032 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.039 0.038 -9999 0 -0.81 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.034 0.019 -9999 0 -0.4 1 1
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.03 -9999 0 -0.67 1 1
YY1/SAP30/HDAC1 -0.019 0.098 -9999 0 -0.52 19 19
EP300 0.014 0.034 -9999 0 -0.75 1 1
STAT3 (dimer non-phopshorylated) 0.034 0.019 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.032 -9999 0 -10000 0 0
histone deacetylation 0.063 0.011 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.004 0.027 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.014 0.07 -9999 0 -0.42 12 12
GATA1/HDAC1 -0.026 0.13 -9999 0 -0.66 20 20
GATA1/HDAC3 -0.024 0.1 -9999 0 -0.52 20 20
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.01 0.077 -9999 0 -0.61 8 8
SIN3/HDAC complex/Mad/Max 0.056 0.041 -9999 0 -10000 0 0
NuRD Complex -0.001 0.02 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.022 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.019 -9999 0 -10000 0 0
GATA1/Fog1 -0.03 0.14 -9999 0 -0.65 23 23
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
negative regulation of cell growth 0.056 0.04 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.064 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.046 -9999 0 -0.38 4 4
SIN3/HDAC complex/NCoR1 -0.006 0.029 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.012 0.052 -9999 0 -0.8 2 2
MBD2 0.016 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure S113.  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 S113.  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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.011 0.059 -9999 0 -0.75 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.006 0.038 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
MAP3K12 0.014 0.034 -9999 0 -0.75 1 1
FGR 0.011 0.067 -9999 0 -0.86 3 3
p38 alpha/TAB1 -0.012 0.038 -9999 0 -0.31 2 2
PRKG1 -0.002 0.12 -9999 0 -0.75 12 12
DUSP8 0.014 0.034 -9999 0 -0.75 1 1
PGK/cGMP/p38 alpha -0.018 0.062 -9999 0 -0.34 12 12
apoptosis -0.012 0.037 -9999 0 -0.3 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 0.014 0.039 -9999 0 -0.86 1 1
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.056 0.085 -9999 0 -0.42 2 2
BLK -0.04 0.21 -9999 0 -0.86 32 32
HCK -0.033 0.2 -9999 0 -0.86 28 28
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.011 0.067 -9999 0 -0.86 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.056 0.066 -9999 0 -0.34 2 2
positive regulation of innate immune response 0.067 0.092 -9999 0 -0.44 2 2
LCK -0.022 0.18 -9999 0 -0.85 22 22
p38alpha-beta/MKP7 0.073 0.088 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.07 0.094 -9999 0 -10000 0 0
PGK/cGMP -0.014 0.087 -9999 0 -0.57 12 12
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.072 0.09 -9999 0 -0.42 2 2
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.008 0.14 -9999 0 -0.83 14 14
Arf6 trafficking events

Figure S114.  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 S114.  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
SLC2A4 -0.004 0.13 -9999 0 -0.81 12 12
CLTC 0.043 0 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.036 0 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
CD59 0.039 0 -9999 0 -10000 0 0
CPE -0.001 0.12 -9999 0 -0.58 22 22
CTNNB1 0.016 0 -9999 0 -10000 0 0
membrane fusion 0 0 -9999 0 -10000 0 0
CTNND1 0.044 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.044 0 -9999 0 -10000 0 0
TSHR -0.045 0.2 -9999 0 -0.59 58 58
INS 0.017 0.001 -9999 0 -10000 0 0
BIN1 0.016 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.025 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.038 0.022 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 0.028 0.056 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 -0.048 0.23 -9999 0 -0.86 37 37
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.016 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.058 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.031 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.025 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 -0.043 0.15 -9999 0 -0.58 37 37
ACAP1 -0.019 0.024 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.032 0.012 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.043 0.011 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.016 0 -9999 0 -10000 0 0
exocyst 0 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.044 0 -9999 0 -10000 0 0
NME1 0.025 0 -9999 0 -10000 0 0
clathrin coat assembly 0.043 0 -9999 0 -10000 0 0
IL2RA -0.016 0.11 -9999 0 -10000 0 0
VAMP3 0.025 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.061 -9999 0 -0.43 7 7
EXOC6 0.016 0 -9999 0 -10000 0 0
PLD1 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.045 0 -9999 0 -10000 0 0
SDC1 0.036 0.03 -9999 0 -10000 0 0
ARF6/GDP 0 0 -9999 0 -10000 0 0
EXOC7 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.007 0.031 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.016 0 -9999 0 -10000 0 0
ADRB2 0.05 0.027 -9999 0 -0.37 2 2
EXOC3 0.016 0 -9999 0 -10000 0 0
ASAP2 0.016 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0 0 -9999 0 -10000 0 0
KLC1 0.016 0 -9999 0 -10000 0 0
AVPR2 -0.13 0.21 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.026 -9999 0 -10000 0 0
IGF1 pathway

Figure S115.  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 S115.  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 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL 0.029 0.055 -10000 0 -0.41 6 6
GRB2/SOS1/SHC -0.001 0.025 -10000 0 -0.57 1 1
HRAS 0.014 0.039 -10000 0 -0.86 1 1
IRS1/Crk -0.007 0.05 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.056 -10000 0 -0.52 6 6
AKT1 0.055 0.061 -10000 0 -0.72 1 1
BAD 0.062 0.072 -10000 0 -1.1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.055 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.05 -10000 0 -0.41 6 6
RAF1 0.068 0.057 -10000 0 -0.7 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.047 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.007 0.055 -10000 0 -0.45 6 6
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
RPS6KB1 0.055 0.061 -10000 0 -0.72 1 1
GNB2L1 0.014 0.039 -10000 0 -0.86 1 1
positive regulation of MAPKKK cascade 0.059 0.05 -10000 0 -0.57 1 1
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.049 -10000 0 -0.5 1 1
IGF-1R heterotetramer 0.015 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.05 -10000 0 -0.41 6 6
Crk/p130 Cas/Paxillin -0.007 0.046 -10000 0 -10000 0 0
IGF1R 0.015 0.012 -10000 0 -10000 0 0
IGF1 0.006 0.094 -10000 0 -0.85 6 6
IRS2/Crk 0.029 0.083 -10000 0 -0.48 8 8
PI3K -0.008 0.052 -10000 0 -10000 0 0
apoptosis -0.066 0.06 0.79 1 -10000 0 1
HRAS/GDP -0.001 0.03 -10000 0 -0.68 1 1
PRKCD 0.05 0.057 -10000 0 -0.82 1 1
RAF1/14-3-3 E 0.071 0.05 -10000 0 -0.57 1 1
BAD/14-3-3 0.068 0.065 -10000 0 -0.89 1 1
PRKCZ 0.052 0.069 -10000 0 -0.72 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.006 0.043 -10000 0 -0.57 1 1
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.042 0.048 -10000 0 -10000 0 0
BCAR1 0.014 0.034 -10000 0 -0.75 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.007 0.054 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.007 0.05 -10000 0 -0.41 6 6
GRB10 0.016 0 -10000 0 -10000 0 0
PTPN11 0.029 0.055 -10000 0 -0.41 6 6
IRS1 0.019 0.059 -10000 0 -0.42 9 9
IRS2 0.02 0.087 -10000 0 -0.47 14 14
IGF-1R heterotetramer/IGF1 -0.008 0.071 -10000 0 -0.65 6 6
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 0.045 0.064 -10000 0 -0.77 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 0.05 0.049 -10000 0 -10000 0 0
SHC1 0.014 0.039 -10000 0 -0.86 1 1
Insulin Pathway

Figure S116.  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 S116.  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
CBL/APS/CAP -0.008 0.058 -9999 0 -10000 0 0
TC10/GTP -0.006 0.049 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.034 -9999 0 -10000 0 0
HRAS 0.014 0.039 -9999 0 -0.86 1 1
APS homodimer 0.007 0.087 -9999 0 -0.86 5 5
GRB14 -0.027 0.17 -9999 0 -0.75 28 28
FOXO3 -0.003 0.013 -9999 0 -10000 0 0
AKT1 -0.022 0.086 -9999 0 -0.66 2 2
INSR 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
SORBS1 0.014 0.034 -9999 0 -0.75 1 1
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.049 0.001 -9999 0 -10000 0 0
CAV1 -0.005 0.14 -9999 0 -0.51 36 36
CBL/APS/CAP/Crk-II/C3G -0.006 0.054 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.034 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.038 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.002 0.022 -9999 0 -10000 0 0
RPS6KB1 0.055 0.096 -9999 0 -0.59 2 2
PARD6A 0.011 0.059 -9999 0 -0.75 3 3
CBL 0.014 0.034 -9999 0 -0.75 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.019 0.075 -9999 0 -0.59 2 2
HRAS/GTP -0.007 0.054 -9999 0 -0.73 1 1
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.003 0.038 -9999 0 -10000 0 0
PRKCI -0.005 0.02 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.024 0.094 -9999 0 -0.73 2 2
SHC1 0.014 0.039 -9999 0 -0.86 1 1
negative regulation of MAPKKK cascade -0.002 0.037 -9999 0 -0.82 1 1
PI3K -0.004 0.039 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
AKT2 -0.022 0.086 -9999 0 -0.66 2 2
PRKCZ -0.009 0.057 -9999 0 -0.7 3 3
SH2B2 0.007 0.087 -9999 0 -0.86 5 5
SHC/SHIP -0.007 0.062 -9999 0 -0.57 4 4
F2RL2 -0.035 0.2 -9999 0 -0.86 29 29
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.024 -9999 0 -0.55 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.022 -9999 0 -0.5 1 1
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.034 -9999 0 -0.75 1 1
NCK1 0.014 0.034 -9999 0 -0.75 1 1
CBL/APS/CAP/Crk-II -0.007 0.058 -9999 0 -0.52 5 5
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.024 -9999 0 -0.54 1 1
INPP5D 0.03 0.066 -9999 0 -0.61 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.001 0.006 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.011 0.059 -9999 0 -0.75 3 3
p62DOK/RasGAP -0.002 0.037 -9999 0 -0.84 1 1
INS 0.005 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.03 0.065 -9999 0 -0.6 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.033 0.14 -9999 0 -0.74 5 5
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.014 0.034 -9999 0 -0.75 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.002 0.026 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.035 -9999 0 -0.46 3 3
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.031 0.12 -9999 0 -0.5 29 29
PDGFR-beta signaling pathway

Figure S117.  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 S117.  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 -0.035 0.12 -9999 0 -0.48 9 9
PDGFB-D/PDGFRB/SLAP -0.032 0.14 -9999 0 -0.67 24 24
PDGFB-D/PDGFRB/APS/CBL -0.007 0.061 -9999 0 -0.56 6 6
AKT1 -0.002 0.022 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.014 0.14 -9999 0 -0.49 9 9
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
FGR -0.003 0.029 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.041 -9999 0 -10000 0 0
MYC 0.043 0.13 -9999 0 -0.57 18 18
SHC1 0.014 0.039 -9999 0 -0.86 1 1
HRAS/GDP -0.002 0.039 -9999 0 -0.88 1 1
LRP1/PDGFRB/PDGFB 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.038 0.041 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.005 0.089 -9999 0 -0.75 7 7
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.032 0.14 -9999 0 -0.67 24 24
HRAS 0.014 0.039 -9999 0 -0.86 1 1
HIF1A 0.087 0.041 -9999 0 -0.6 1 1
GAB1 0.033 0.075 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.036 0.081 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.037 0.12 -9999 0 -0.53 6 6
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
mol:IP3 0.038 0.041 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.066 -9999 0 -0.57 7 7
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.023 0.086 -9999 0 -10000 0 0
PTPN2 0.016 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.034 -9999 0 -0.75 1 1
VAV2 0.036 0.087 -9999 0 -10000 0 0
CBL 0.014 0.034 -9999 0 -0.75 1 1
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.018 0.082 -9999 0 -0.64 2 2
PDGFRB 0.016 0.006 -9999 0 -10000 0 0
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.02 0.082 -9999 0 -10000 0 0
ABL1 0.034 0.06 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.033 0.07 -9999 0 -10000 0 0
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.014 0.039 -9999 0 -0.86 1 1
cell proliferation 0.044 0.12 -9999 0 -0.51 18 18
SLA -0.026 0.19 -9999 0 -0.86 24 24
actin cytoskeleton reorganization 0.001 0.025 -9999 0 -10000 0 0
SRC -0.001 0.013 -9999 0 -10000 0 0
PI3K -0.002 0.025 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.008 0.062 -9999 0 -0.49 8 8
SH2B2 0.007 0.087 -9999 0 -0.86 5 5
PLCgamma1/SPHK1 0.013 0.14 -9999 0 -0.51 9 9
LYN -0.001 0.013 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.024 -9999 0 -10000 0 0
SPHK1 -0.055 0.24 -9999 0 -0.86 41 41
EDG1 0.001 0.003 -9999 0 -10000 0 0
mol:DAG 0.038 0.041 -9999 0 -10000 0 0
PLCG1 0.039 0.041 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.021 -9999 0 -0.48 1 1
YES1 -0.001 0.013 -9999 0 -10000 0 0
cell migration -0.001 0.021 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 -0.001 0.021 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.75 1 1
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.019 -9999 0 -10000 0 0
FYN -0.001 0.013 -9999 0 -10000 0 0
DOK1 0.044 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.03 -9999 0 -0.68 1 1
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 0.046 0.1 -9999 0 -10000 0 0
PRKCD 0.042 0.029 -9999 0 -0.53 1 1
FER 0.041 0.033 -9999 0 -10000 0 0
MAPKKK cascade -0.001 0.022 -9999 0 -10000 0 0
RASA1 0.042 0.025 -9999 0 -10000 0 0
NCK1 0.014 0.034 -9999 0 -0.75 1 1
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.018 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.033 0.059 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.001 0.02 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

Figure S118.  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 S118.  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
G beta1gamma2/HDAC5 -0.001 0.019 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 -0.026 0.13 -10000 0 -0.66 20 20
GATA1/HDAC5 -0.027 0.13 -10000 0 -0.66 21 21
GATA2/HDAC5 -0.014 0.089 -10000 0 -0.56 13 13
HDAC5/BCL6/BCoR -0.001 0.021 -10000 0 -0.48 1 1
HDAC9 0.016 0 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.025 -10000 0 -0.57 1 1
HDAC4/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC5/YWHAB -0.001 0.025 -10000 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.002 0.12 -10000 0 -0.75 12 12
HDAC4/RFXANK -0.001 0.029 -10000 0 -0.66 1 1
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.034 -10000 0 -0.75 1 1
HDAC5 0.014 0.034 -10000 0 -0.75 1 1
GNB1/GNG2 0 0 -10000 0 -10000 0 0
Histones -0.003 0.041 -10000 0 -0.84 1 1
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.025 -10000 0 -0.56 1 1
HDAC4/Ubc9 0 0 -10000 0 -10000 0 0
HDAC7 0.016 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.025 -10000 0 -0.56 1 1
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.002 0.039 -10000 0 -0.61 2 2
CAMK4 0.013 0.048 -10000 0 -0.75 2 2
Tubulin/HDAC6 -0.001 0.021 -10000 0 -0.48 1 1
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 -0.021 0.17 -10000 0 -0.86 20 20
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0 -10000 0 -10000 0 0
NR3C1 0.014 0.039 -10000 0 -0.86 1 1
SUMO1/HDAC4 0 0 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0 0 -10000 0 -10000 0 0
Tubulin -0.001 0.025 -10000 0 -0.56 1 1
HDAC4/14-3-3 E 0 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.016 0 -10000 0 -10000 0 0
BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -10000 0 -10000 0 0
HDAC4/SRF -0.002 0.03 -10000 0 -0.48 2 2
HDAC4/ER alpha -0.005 0.052 -10000 0 -0.59 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.051 0.044 -10000 0 -0.83 1 1
cell motility -0.001 0.021 -10000 0 -0.48 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 0.016 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 0.009 0.07 -10000 0 -0.78 4 4
HDAC6/HDAC11 -0.002 0.035 -10000 0 -0.56 2 2
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0.016 0 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.014 0.034 -10000 0 -0.75 1 1
HDAC11 0.013 0.048 -10000 0 -0.75 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.014 0.039 -10000 0 -0.86 1 1
nuclear import 0.001 0.018 0.39 1 -10000 0 1
Circadian rhythm pathway

Figure S119.  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 S119.  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 -0.001 0.013 -10000 0 -10000 0 0
CLOCK 0.019 0.034 -10000 0 -0.74 1 1
TIMELESS/CRY2 0.056 0.022 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.029 -10000 0 -0.66 1 1
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.054 0.063 -10000 0 -1.3 1 1
ARNTL 0.02 0.002 -10000 0 -10000 0 0
TIMELESS 0.056 0.025 -10000 0 -10000 0 0
NPAS2 0.005 0.11 -10000 0 -0.74 10 10
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.019 0.007 0.14 1 -10000 0 1
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.019 0.007 -10000 0 -0.14 1 1
PER1 0.016 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.076 -10000 0 -0.46 11 11
BMAL1/CLOCK 0.065 0.051 -10000 0 -0.82 1 1
S phase of mitotic cell cycle -0.001 0.013 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.013 -10000 0 -10000 0 0
mol:NADPH 0.019 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.056 0.022 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.039 -10000 0 -0.86 1 1
mTOR signaling pathway

Figure S120.  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 S120.  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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.003 0.035 -10000 0 -0.4 2 2
FRAP1 0.02 0.012 -10000 0 -10000 0 0
AKT1 -0.003 0.036 -10000 0 -0.58 1 1
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.028 -10000 0 -0.46 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.009 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.025 -10000 0 -0.42 1 1
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.031 -10000 0 -0.39 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.036 0.024 -10000 0 -0.34 1 1
MAP3K5 0.014 0.001 -10000 0 -10000 0 0
PIK3R1 0.014 0.034 -10000 0 -0.75 1 1
apoptosis 0.014 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 3 3
EIF4B 0.044 0.021 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.032 -10000 0 -0.45 2 2
eIF4E/eIF4G1/eIF4A1 0 0.005 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.037 -10000 0 -0.37 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.042 0.018 -10000 0 -0.24 1 1
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.024 -10000 0 -0.41 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 3 3
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.043 -10000 0 -0.75 1 1
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.008 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.023 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.03 -10000 0 -0.5 1 1
tumor necrosis factor receptor activity 0 0 0.002 3 -10000 0 3
RPS6 0.012 0.055 -10000 0 -0.86 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.009 0.033 -10000 0 -0.42 3 3
INS 0 0.001 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.003 0.032 -10000 0 -0.39 1 1
EIF4EBP1 -0.007 0.1 -10000 0 -0.46 24 24
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
PPP2R5D 0.029 0.012 -10000 0 -10000 0 0
peptide biosynthetic process 0.023 0.001 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.004 1 1
EEF2 0.023 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.003 0.089 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S121.  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 S121.  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 0.031 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.002 0.03 -9999 0 -0.52 1 1
CDKN1B 0.051 0.007 -9999 0 -10000 0 0
CDKN1A 0.048 0.033 -9999 0 -0.47 2 2
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.051 0.007 -9999 0 -10000 0 0
AKT1 0 0.006 -9999 0 -10000 0 0
BAD 0.012 0.052 -9999 0 -0.8 2 2
AKT3 0.022 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.051 0.007 -9999 0 -10000 0 0
AKT1/ASK1 0 0.005 -9999 0 -10000 0 0
BAD/YWHAZ -0.002 0.033 -9999 0 -0.52 2 2
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.016 0 -9999 0 -10000 0 0
JNK cascade 0 0.005 -9999 0 -10000 0 0
TSC1 0.051 0.007 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0.005 -9999 0 -10000 0 0
EP300 0.014 0.034 -9999 0 -0.75 1 1
mol:GDP 0 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.051 0.007 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.033 0.017 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.04 0.053 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.051 0.007 -9999 0 -10000 0 0
CASP9 0.051 0.007 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.057 0.007 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.021 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.002 0.031 -9999 0 -0.44 2 2
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.003 -9999 0 -10000 0 0
CHUK 0.051 0.007 -9999 0 -10000 0 0
BAD/BCL-XL -0.002 0.029 -9999 0 -0.56 1 1
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.022 0.019 -9999 0 -0.41 1 1
FOXO1-3a-4/14-3-3 family 0.059 0.06 -9999 0 -10000 0 0
PDPK1 0.014 0.034 -9999 0 -0.75 1 1
MDM2 0.051 0.007 -9999 0 -10000 0 0
MAPKKK cascade 0 0.005 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.001 0.021 -9999 0 -10000 0 0
TSC1/TSC2 0.059 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.02 -9999 0 -10000 0 0
glucose import 0.029 0.081 -9999 0 -0.52 7 7
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.043 0.005 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.029 0.082 -9999 0 -0.52 7 7
GSK3A 0.051 0.007 -9999 0 -10000 0 0
FOXO1 0.051 0.007 -9999 0 -10000 0 0
GSK3B 0.051 0.007 -9999 0 -10000 0 0
SFN -0.086 0.28 -9999 0 -0.83 61 61
G1/S transition of mitotic cell cycle 0.06 0.007 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.035 0.079 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S122.  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 S122.  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 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.003 0.043 -9999 0 -0.56 3 3
PTK2 -0.003 0.03 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.002 0.023 -9999 0 -10000 0 0
CDC42/GDP 0.077 0.032 -9999 0 -10000 0 0
Rac1/GDP 0.08 0.032 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.002 0.028 -9999 0 -10000 0 0
nectin-3/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
RAPGEF1 0.075 0.034 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.068 0.037 -9999 0 -0.51 2 2
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 0.046 0.016 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.019 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.079 0.038 -9999 0 -0.48 2 2
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
PI3K -0.003 0.035 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.001 0.019 -9999 0 -10000 0 0
PVRL1 0.016 0 -9999 0 -10000 0 0
PVRL3 0.013 0.048 -9999 0 -0.75 2 2
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
CDH1 -0.016 0.15 -9999 0 -0.75 21 21
CLDN1 0.008 0.08 -9999 0 -0.79 5 5
JAM-A/CLDN1 -0.006 0.053 -9999 0 -0.52 2 2
SRC -0.003 0.036 -9999 0 -0.57 2 2
ITGB3 0.011 0.059 -9999 0 -0.75 3 3
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.069 0.045 -9999 0 -0.5 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.002 0.03 -9999 0 -0.48 2 2
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.002 0.03 -9999 0 -0.48 2 2
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.002 0.023 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.003 0.029 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.001 0.014 -9999 0 -10000 0 0
VAV2 0.069 0.036 -9999 0 -0.48 2 2
RAP1/GDP -0.002 0.023 -9999 0 -10000 0 0
ITGAV 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.002 0.03 -9999 0 -0.48 2 2
nectin-3(dimer)/I-afadin/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
Rac1/GTP -0.002 0.024 -9999 0 -0.37 2 2
PTPRM -0.001 0.017 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.015 0.074 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

Figure S123.  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 S123.  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 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.011 0.059 -10000 0 -0.75 3 3
Cbp/p300/PCAF -0.002 0.041 -10000 0 -0.92 1 1
EP300 0.014 0.034 -10000 0 -0.75 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.056 0.034 -10000 0 -0.44 1 1
KAT2B 0.014 0.034 -10000 0 -0.75 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.031 0.038 0.24 1 -0.3 2 3
RAR alpha/9cRA/Cyclin H -0.008 0.036 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.053 0.037 -10000 0 -0.48 1 1
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.002 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.009 0.039 -10000 0 -10000 0 0
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.044 -10000 0 -0.57 3 3
RXRs/RARs/NRIP1/9cRA 0.063 0.081 -10000 0 -0.52 1 1
NCOA2 0.004 0.095 -10000 0 -0.75 8 8
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.058 -10000 0 -0.75 3 3
RARG 0.017 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.001 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.017 0.001 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.018 0.073 -10000 0 -10000 0 0
RARA 0.026 0.057 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.048 0.061 -10000 0 -0.89 1 1
PRKCA 0.021 0.001 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.055 0.083 -10000 0 -0.57 1 1
RXRG 0.012 0.091 -10000 0 -0.38 26 26
RXRA 0.037 0.054 -10000 0 -10000 0 0
RXRB 0.017 0.084 -10000 0 -0.37 22 22
VDR/Vit D3/DNA -0.003 0.044 -10000 0 -0.57 3 3
RBP1 0.009 0.075 -10000 0 -0.83 4 4
CRBP1/9-cic-RA -0.005 0.058 -10000 0 -0.65 4 4
RARB 0.016 0.048 -10000 0 -0.75 2 2
PRKCG -0.025 0.18 -10000 0 -0.86 22 22
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.054 0.083 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.061 0.074 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.046 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.055 0.083 -10000 0 -0.57 1 1
positive regulation of DNA binding -0.008 0.035 -10000 0 -10000 0 0
NRIP1 0.053 0.092 -10000 0 -1.2 1 1
RXRs/RARs 0.046 0.081 -10000 0 -0.41 1 1
RXRs/RXRs/DNA/9cRA -0.017 0.073 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.025 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S124.  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 S124.  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 -0.003 0.042 -9999 0 -0.66 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.004 0.042 -9999 0 -0.48 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.039 -9999 0 -10000 0 0
NFKBIA 0.028 0.056 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.021 -9999 0 -0.48 1 1
ARRB2 0.022 0.018 -9999 0 -0.39 1 1
REL 0.011 0.059 -9999 0 -0.75 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.003 0.042 -9999 0 -0.54 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.021 -9999 0 -0.48 1 1
PIK3CA 0.014 0.034 -9999 0 -0.75 1 1
NF kappa B1 p50 dimer 0.025 0.026 -9999 0 -0.56 1 1
PIK3R1 0.014 0.034 -9999 0 -0.75 1 1
NFKB1 0.03 0.026 -9999 0 -0.56 1 1
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.036 0.055 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.008 0.037 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.035 -9999 0 -0.56 2 2
NF kappa B1 p50/RelA 0.036 0.056 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.048 -9999 0 -0.75 2 2
I kappa B alpha/PIK3R1 0.034 0.056 -9999 0 -0.39 1 1
cell death -0.008 0.036 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.004 0.042 -9999 0 -0.48 4 4
LCK -0.022 0.18 -9999 0 -0.85 22 22
BCL3 0.012 0.055 -9999 0 -0.86 2 2
Signaling mediated by p38-alpha and p38-beta

Figure S125.  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 S125.  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
PTGS2 0.011 0.25 -9999 0 -1.1 24 24
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.024 0.071 -9999 0 -10000 0 0
ATF2/c-Jun 0.045 0.062 -9999 0 -0.61 1 1
MAPK11 0.022 0.081 -9999 0 -0.84 1 1
MITF 0.045 0.088 -9999 0 -10000 0 0
MAPKAPK5 0.045 0.088 -9999 0 -10000 0 0
KRT8 0.044 0.09 -9999 0 -10000 0 0
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.033 0.11 -9999 0 -0.62 1 1
CEBPB 0.035 0.11 -9999 0 -10000 0 0
SLC9A1 0.045 0.088 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.051 0.093 -9999 0 -0.82 1 1
p38alpha-beta/MNK1 -0.018 0.072 -9999 0 -10000 0 0
JUN 0.046 0.062 -9999 0 -0.6 1 1
PPARGC1A 0.002 0.15 -9999 0 -0.75 2 2
USF1 0.045 0.088 -9999 0 -10000 0 0
RAB5/GDP/GDI1 -0.013 0.049 -9999 0 -10000 0 0
NOS2 0.039 0.13 -9999 0 -0.84 7 7
DDIT3 0.042 0.093 -9999 0 -10000 0 0
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 0.048 0.084 -9999 0 -0.67 2 2
p38alpha-beta/HBP1 -0.018 0.072 -9999 0 -10000 0 0
CREB1 0.05 0.091 -9999 0 -10000 0 0
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.049 0.076 -9999 0 -10000 0 0
RPS6KA4 0.045 0.088 -9999 0 -10000 0 0
PLA2G4A 0.044 0.094 -9999 0 -0.88 1 1
GDI1 0.045 0.088 -9999 0 -10000 0 0
TP53 0.047 0.11 -9999 0 -10000 0 0
RPS6KA5 0.045 0.088 -9999 0 -10000 0 0
ESR1 0.041 0.095 -9999 0 -10000 0 0
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C 0.045 0.088 -9999 0 -10000 0 0
MEF2A 0.045 0.088 -9999 0 -10000 0 0
EIF4EBP1 0.044 0.094 -9999 0 -0.43 1 1
KRT19 -0.042 0.21 -9999 0 -0.88 9 9
ELK4 0.045 0.088 -9999 0 -10000 0 0
ATF6 0.045 0.088 -9999 0 -10000 0 0
ATF1 0.05 0.091 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK2 -0.018 0.072 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 -0.018 0.072 -9999 0 -0.5 1 1
Alternative NF-kappaB pathway

Figure S126.  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 S126.  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 -0.005 0.059 -9999 0 -0.66 4 4
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.043 -9999 0 -0.48 4 4
NFKB1 0.014 0.034 -9999 0 -0.75 1 1
MAP3K14 0.009 0.078 -9999 0 -0.86 4 4
NF kappa B1 p50/RelB -0.001 0.025 -9999 0 -0.56 1 1
RELB 0.016 0 -9999 0 -10000 0 0
NFKB2 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S127.  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 S127.  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
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.019 0 -9999 0 -10000 0 0
SMAD3 0.057 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.062 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.027 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.025 -9999 0 -0.56 1 1
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.014 0.034 -9999 0 -0.75 1 1
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
TRAIL signaling pathway

Figure S128.  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 S128.  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 0.014 0.034 -9999 0 -0.75 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.025 -9999 0 -0.56 1 1
MAP2K4 0.063 0.018 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
TNFRSF10B 0.014 0.039 -9999 0 -0.86 1 1
TNFRSF10A 0.014 0.034 -9999 0 -0.75 1 1
SMPD1 -0.001 0.017 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.002 0.039 -9999 0 -0.61 2 2
TRAIL/TRAILR3 -0.002 0.039 -9999 0 -0.61 2 2
TRAIL/TRAILR1 -0.002 0.035 -9999 0 -0.56 2 2
TRAIL/TRAILR4 -0.001 0.025 -9999 0 -0.56 1 1
TRAIL/TRAILR1/DAP3/GTP -0.002 0.028 -9999 0 -0.44 2 2
IKK complex -0.001 0.009 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.03 0.026 -9999 0 -0.56 1 1
MAP3K1 -0.001 0.015 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.034 -9999 0 -0.75 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.018 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
MAPK1 0.03 0.026 -9999 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.025 -9999 0 -10000 0 0
mol:ceramide -0.001 0.017 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
MAPK8 0.071 0.017 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.039 -9999 0 -0.86 1 1
CHUK 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.03 -9999 0 -0.48 2 2
DAP3 0.016 0 -9999 0 -10000 0 0
CASP10 -0.002 0.025 -9999 0 -10000 0 0
JNK cascade -0.001 0.025 -9999 0 -0.56 1 1
TRAIL (trimer) 0.014 0.034 -9999 0 -0.75 1 1
TNFRSF10C 0.014 0.039 -9999 0 -0.86 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.025 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD -0.002 0.033 -9999 0 -0.52 2 2
cell death -0.001 0.017 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.018 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.014 0.039 -9999 0 -0.86 1 1
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.028 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  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 S129.  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 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.039 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

Figure S130.  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 S130.  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
Gs family/GDP/Gbeta gamma 0 0 -9999 0 -10000 0 0
MAPK9 0.011 0 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.003 0.068 -9999 0 -0.68 5 5
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.011 0 -9999 0 -10000 0 0
Gs family/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.016 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
CRH -0.005 0.086 -9999 0 -0.86 5 5
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0.001 -9999 0 -10000 0 0
MAPK11 0.011 0.018 -9999 0 -0.4 1 1
Arf1 pathway

Figure S131.  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 S131.  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
coatomer protein complex -0.001 0.023 -9999 0 -0.52 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.009 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.002 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 0.002 0.11 -9999 0 -0.86 8 8
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.014 0.026 -9999 0 -0.57 1 1
mol:PI-4-5-P2 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.021 -9999 0 -0.47 1 1
mol:Choline -0.001 0.017 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.017 -9999 0 -0.39 1 1
ARF1/GDP -0.001 0.021 -9999 0 -0.47 1 1
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.019 -9999 0 -0.42 1 1
ARFIP2 0 0.003 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.035 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.006 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.011 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.006 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.044 0.033 -9999 0 -10000 0 0
PLD2 -0.001 0.017 -9999 0 -0.38 1 1
ARF-GAP1/v-SNARE 0.014 0.026 -9999 0 -0.57 1 1
PIP5K1A -0.001 0.017 -9999 0 -0.39 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.009 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.017 -9999 0 -0.38 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.026 -9999 0 -0.57 1 1
GOSR2 0 0.007 -9999 0 -10000 0 0
USO1 0 0.007 -9999 0 -10000 0 0
GBF1 0 0.007 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.009 0.072 -9999 0 -0.57 8 8
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 506 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MW.A4EC TCGA.MM.A564 TCGA.EU.5907 TCGA.EU.5906
109_MAP3K5 0.074 0.074 0.074 0.074
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0 -0.75 -0.75 -0.75
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR -0.43 -0.43 -0.43 0
30_TGFB1/TGF beta receptor Type II 0.015 0.021 0.015 0.015
84_STAT5B -0.031 -0.14 -0.031 -0.031
84_STAT5A -0.031 -0.14 -0.031 -0.031
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/6044644/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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