PARADIGM pathway analysis of mRNASeq expression and copy number data
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1X066BP
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 47 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 115
Signaling mediated by p38-alpha and p38-beta 89
Angiopoietin receptor Tie2-mediated signaling 88
Glypican 2 network 85
IL23-mediated signaling events 73
Ephrin A reverse signaling 72
Endothelins 67
Glucocorticoid receptor regulatory network 65
Aurora B signaling 65
IL4-mediated signaling events 62
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 497 . 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 ( 497 ).

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
FOXM1 transcription factor network 0.2314 115 5867 51 0.007 0.31 1000 -1000 -0.064 -1000
Signaling mediated by p38-alpha and p38-beta 0.1791 89 3946 44 -0.13 0.026 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1771 88 7787 88 -0.27 0.077 1000 -1000 -0.054 -1000
Glypican 2 network 0.1710 85 340 4 0.032 0.07 1000 -1000 0.027 -1000
IL23-mediated signaling events 0.1469 73 4425 60 -0.21 0.047 1000 -1000 -0.065 -1000
Ephrin A reverse signaling 0.1449 72 507 7 -0.039 0.022 1000 -1000 -0.005 -1000
Endothelins 0.1348 67 6477 96 -0.2 0.03 1000 -1000 -0.035 -1000
Glucocorticoid receptor regulatory network 0.1308 65 7423 114 -0.34 0.16 1000 -1000 -0.035 -1000
Aurora B signaling 0.1308 65 4393 67 -0.041 0.13 1000 -1000 -0.029 -1000
IL4-mediated signaling events 0.1247 62 5715 91 -0.17 0.16 1000 -1000 -0.065 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1127 56 1917 34 -0.032 0.034 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.0966 48 2733 56 -0.051 0.07 1000 -1000 -0.013 -1000
Thromboxane A2 receptor signaling 0.0946 47 4949 105 -0.11 0.045 1000 -1000 -0.032 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0946 47 3223 68 -0.12 0.081 1000 -1000 -0.049 -1000
HIF-1-alpha transcription factor network 0.0926 46 3498 76 -0.018 0.17 1000 -1000 -0.016 -1000
IL12-mediated signaling events 0.0885 44 3905 87 -0.13 0.077 1000 -1000 -0.045 -1000
PLK1 signaling events 0.0865 43 3691 85 -0.025 0.1 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.0845 42 3566 84 -0.088 0.11 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0845 42 3325 78 -0.11 0.031 1000 -1000 -0.033 -1000
Aurora C signaling 0.0805 40 286 7 0 0.088 1000 -1000 -0.008 -1000
EPHB forward signaling 0.0805 40 3452 85 -0.073 0.087 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.0805 40 4113 102 -0.055 0.14 1000 -1000 -0.066 -1000
Signaling events mediated by the Hedgehog family 0.0785 39 2056 52 -0.019 0.042 1000 -1000 -0.011 -1000
amb2 Integrin signaling 0.0785 39 3210 82 -0.077 0.14 1000 -1000 -0.015 -1000
Ras signaling in the CD4+ TCR pathway 0.0785 39 668 17 -0.077 0.037 1000 -1000 -0.013 -1000
IL6-mediated signaling events 0.0765 38 2864 75 -0.15 0.079 1000 -1000 -0.021 -1000
FOXA2 and FOXA3 transcription factor networks 0.0724 36 1677 46 -0.017 0.11 1000 -1000 -0.05 -1000
Signaling events regulated by Ret tyrosine kinase 0.0704 35 2908 82 -0.037 0.061 1000 -1000 -0.036 -1000
Syndecan-1-mediated signaling events 0.0684 34 1187 34 0 0.14 1000 -1000 -0.014 -1000
Ephrin B reverse signaling 0.0684 34 1635 48 -0.017 0.033 1000 -1000 -0.034 -1000
S1P1 pathway 0.0684 34 1248 36 -0.19 0.025 1000 -1000 -0.016 -1000
TCR signaling in naïve CD8+ T cells 0.0684 34 3194 93 -0.059 0.073 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 0.0684 34 1070 31 -0.041 0.036 1000 -1000 -0.03 -1000
Nongenotropic Androgen signaling 0.0684 34 1787 52 -0.12 0.065 1000 -1000 -0.018 -1000
p75(NTR)-mediated signaling 0.0624 31 3911 125 -0.053 0.069 1000 -1000 -0.037 -1000
EPO signaling pathway 0.0624 31 1725 55 -0.033 0.045 1000 -1000 -0.018 -1000
S1P5 pathway 0.0624 31 527 17 -0.04 0.038 1000 -1000 -0.009 -1000
EGFR-dependent Endothelin signaling events 0.0624 31 658 21 -0.028 0.049 1000 -1000 -0.025 -1000
Noncanonical Wnt signaling pathway 0.0584 29 759 26 -0.036 0.035 1000 -1000 -0.021 -1000
Glypican 1 network 0.0563 28 1373 48 -0.032 0.096 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 0.0563 28 731 26 -0.024 0.061 1000 -1000 -0.006 -1000
Fc-epsilon receptor I signaling in mast cells 0.0543 27 2624 97 -0.06 0.041 1000 -1000 -0.034 -1000
BCR signaling pathway 0.0543 27 2676 99 -0.099 0.069 1000 -1000 -0.039 -1000
BMP receptor signaling 0.0523 26 2134 81 -0.072 0.068 1000 -1000 -0.006 -1000
JNK signaling in the CD4+ TCR pathway 0.0503 25 439 17 -0.12 0.067 1000 -1000 -0.022 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0503 25 2200 85 -0.12 0.038 1000 -1000 -0.043 -1000
S1P4 pathway 0.0503 25 647 25 -0.04 0.047 1000 -1000 -0.007 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0483 24 1273 52 -0.044 0.067 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 0.0483 24 1060 43 -0.091 0.094 1000 -1000 -0.041 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0483 24 2975 120 -0.075 0.12 1000 -1000 -0.033 -1000
Visual signal transduction: Cones 0.0463 23 910 38 -0.016 0.044 1000 -1000 -0.01 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0443 22 1240 54 -0.036 0.078 1000 -1000 -0.022 -1000
Plasma membrane estrogen receptor signaling 0.0443 22 1943 86 -0.13 0.056 1000 -1000 -0.024 -1000
Arf6 signaling events 0.0423 21 1349 62 -0.008 0.059 1000 -1000 -0.023 -1000
FAS signaling pathway (CD95) 0.0423 21 1012 47 -0.19 0.032 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0402 20 1159 57 -0.031 0.049 1000 -1000 -0.042 -1000
Osteopontin-mediated events 0.0402 20 782 38 -0.046 0.055 1000 -1000 -0.017 -1000
PDGFR-alpha signaling pathway 0.0402 20 899 44 -0.13 0.05 1000 -1000 -0.021 -1000
Visual signal transduction: Rods 0.0402 20 1040 52 -0.022 0.063 1000 -1000 -0.016 -1000
Signaling events mediated by PRL 0.0402 20 698 34 -0.035 0.051 1000 -1000 -0.027 -1000
Aurora A signaling 0.0382 19 1196 60 -0.028 0.098 1000 -1000 -0.015 -1000
IL2 signaling events mediated by PI3K 0.0382 19 1122 58 -0.033 0.09 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.0382 19 157 8 -0.017 0.072 1000 -1000 -0.005 -1000
IGF1 pathway 0.0382 19 1117 57 -0.031 0.059 1000 -1000 -0.018 -1000
Insulin Pathway 0.0382 19 1425 74 -0.12 0.1 1000 -1000 -0.031 -1000
Syndecan-2-mediated signaling events 0.0362 18 1298 69 -0.013 0.045 1000 -1000 -0.025 -1000
TCGA08_p53 0.0362 18 130 7 -0.018 0.025 1000 -1000 -0.006 -1000
Rapid glucocorticoid signaling 0.0362 18 378 20 -0.014 0.032 1000 -1000 -0.006 -1000
ErbB2/ErbB3 signaling events 0.0342 17 1162 65 -0.05 0.036 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 0.0342 17 1321 76 -0.025 0.087 1000 -1000 -0.012 -1000
Ceramide signaling pathway 0.0342 17 1294 76 -0.02 0.068 1000 -1000 -0.012 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0342 17 642 37 -0.026 0.071 1000 -1000 -0.01 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0342 17 2203 125 -0.058 0.051 1000 -1000 -0.037 -1000
IL27-mediated signaling events 0.0342 17 868 51 -0.33 0.08 1000 -1000 -0.027 -1000
Wnt signaling 0.0342 17 120 7 -0.015 0.035 1000 -1000 -0.001 -1000
IL2 signaling events mediated by STAT5 0.0342 17 375 22 -0.037 0.058 1000 -1000 -0.017 -1000
Syndecan-4-mediated signaling events 0.0342 17 1157 67 -0.033 0.14 1000 -1000 -0.027 -1000
Caspase cascade in apoptosis 0.0322 16 1203 74 -0.034 0.061 1000 -1000 -0.022 -1000
Cellular roles of Anthrax toxin 0.0322 16 626 39 -0.016 0.029 1000 -1000 -0.014 -1000
Signaling events mediated by PTP1B 0.0322 16 1250 76 -0.13 0.13 1000 -1000 -0.017 -1000
Nectin adhesion pathway 0.0322 16 1014 63 -0.012 0.058 1000 -1000 -0.017 -1000
Regulation of p38-alpha and p38-beta 0.0322 16 881 54 -0.044 0.057 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0302 15 2098 136 -0.047 0.21 1000 -1000 -0.033 -1000
a4b1 and a4b7 Integrin signaling 0.0302 15 75 5 0.025 0.034 1000 -1000 0.026 -1000
Presenilin action in Notch and Wnt signaling 0.0302 15 963 61 -0.019 0.07 1000 -1000 -0.034 -1000
IL1-mediated signaling events 0.0302 15 954 62 -0.044 0.065 1000 -1000 -0.03 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0302 15 1148 74 -0.14 0.05 1000 -1000 -0.04 -1000
ceramide signaling pathway 0.0282 14 731 49 -0.009 0.036 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 0.0282 14 745 51 -0.01 0.13 1000 -1000 -0.027 -1000
S1P3 pathway 0.0282 14 627 42 -0.029 0.038 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 0.0262 13 891 65 -0.2 0.062 1000 -1000 -0.022 -1000
mTOR signaling pathway 0.0262 13 703 53 -0.14 0.044 1000 -1000 -0.022 -1000
Class I PI3K signaling events 0.0262 13 986 73 -0.042 0.049 1000 -1000 -0.019 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0262 13 459 33 -0.016 0.069 1000 -1000 -0.01 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0241 12 544 45 -0.023 0.061 1000 -1000 -0.02 -1000
Retinoic acid receptors-mediated signaling 0.0221 11 657 58 -0.036 0.047 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 0.0221 11 1146 97 -0.092 0.078 1000 -1000 -0.035 -1000
FoxO family signaling 0.0201 10 659 64 -0.001 0.1 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 0.0201 10 153 15 -0.023 0.029 1000 -1000 -0.017 -1000
Paxillin-dependent events mediated by a4b1 0.0201 10 388 36 -0.044 0.052 1000 -1000 -0.03 -1000
VEGFR1 specific signals 0.0201 10 571 56 -0.051 0.043 1000 -1000 -0.018 -1000
E-cadherin signaling in keratinocytes 0.0201 10 458 43 -0.023 0.044 1000 -1000 -0.013 -1000
IFN-gamma pathway 0.0181 9 665 68 -0.031 0.071 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 0.0181 9 245 26 -0.009 0.042 1000 -1000 -0.011 -1000
E-cadherin signaling in the nascent adherens junction 0.0181 9 737 76 -0.032 0.055 1000 -1000 -0.035 -1000
p38 MAPK signaling pathway 0.0181 9 438 44 -0.027 0.071 1000 -1000 -0.007 -1000
Regulation of Androgen receptor activity 0.0181 9 685 70 -0.088 0.036 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 0.0161 8 98 12 -0.014 0.018 1000 -1000 -0.009 -1000
Class I PI3K signaling events mediated by Akt 0.0161 8 544 68 -0.027 0.048 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class III 0.0141 7 315 40 -0.047 0.048 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0141 7 629 83 -0.031 0.047 1000 -1000 -0.011 -1000
Regulation of Telomerase 0.0141 7 746 102 -0.023 0.12 1000 -1000 -0.044 -1000
Canonical NF-kappaB pathway 0.0121 6 244 39 -0.015 0.052 1000 -1000 -0.012 -1000
ErbB4 signaling events 0.0101 5 388 69 -0.025 0.056 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 0.0101 5 162 31 -0.014 0.031 1000 -1000 -0.011 -1000
Class IB PI3K non-lipid kinase events 0.0101 5 15 3 -0.028 0.028 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 0.0080 4 323 75 -0.025 0.063 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0080 4 157 35 -0.005 0.069 1000 -1000 -0.013 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0060 3 99 28 -0.013 0.048 1000 -1000 -0.009 -1000
TRAIL signaling pathway 0.0060 3 160 48 -0.017 0.047 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class I 0.0060 3 352 104 -0.049 0.061 1000 -1000 -0.042 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 60 23 0.01 0.049 1000 -1000 -0.004 -1000
Circadian rhythm pathway 0.0040 2 51 22 -0.012 0.038 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0040 2 119 43 -0.051 0.052 1000 -1000 -0.032 -1000
Arf6 trafficking events 0.0040 2 187 71 -0.045 0.047 1000 -1000 -0.038 -1000
Arf1 pathway 0.0040 2 147 54 -0.01 0.046 1000 -1000 -0.009 -1000
PLK2 and PLK4 events 0.0020 1 5 3 -0.016 0.026 1000 -1000 -0.009 -1000
Insulin-mediated glucose transport 0.0020 1 52 32 -0.017 0.044 1000 -1000 -0.01 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 -0.019 0.057 1000 -1000 -0.026 -1000
E-cadherin signaling events 0.0000 0 0 5 0.023 0.044 1000 -1000 0.025 -1000
Alternative NF-kappaB pathway 0.0000 0 12 13 0 0.067 1000 -1000 0 -1000
Total NA 3158 189326 7203 -7.3 8.7 131000 -131000 -3 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.26 0.48 0.92 106 -1 17 123
PLK1 0.19 0.23 0.6 94 -10000 0 94
BIRC5 0.19 0.24 0.59 93 -0.91 2 95
HSPA1B 0.26 0.49 0.93 108 -0.99 18 126
MAP2K1 0.092 0.12 0.25 133 -10000 0 133
BRCA2 0.24 0.53 0.93 109 -1 28 137
FOXM1 0.28 0.58 1 123 -1.2 21 144
XRCC1 0.25 0.48 0.9 108 -1 18 126
FOXM1B/p19 0.014 0.34 0.7 17 -1 27 44
Cyclin D1/CDK4 0.21 0.43 0.8 103 -0.92 20 123
CDC2 0.28 0.52 0.95 126 -1 21 147
TGFA 0.2 0.45 0.79 110 -0.89 29 139
SKP2 0.25 0.52 0.94 111 -1 23 134
CCNE1 0.039 0.042 0.13 36 -10000 0 36
CKS1B 0.25 0.48 0.87 124 -0.96 21 145
RB1 0.1 0.31 0.59 79 -0.8 21 100
FOXM1C/SP1 0.22 0.47 0.86 97 -1.1 20 117
AURKB 0.13 0.32 0.59 80 -0.85 23 103
CENPF 0.3 0.53 1 124 -1 17 141
CDK4 0.045 0.049 0.13 65 -10000 0 65
MYC 0.16 0.4 0.8 83 -0.87 15 98
CHEK2 0.089 0.11 0.25 129 -10000 0 129
ONECUT1 0.22 0.46 0.82 114 -0.95 22 136
CDKN2A 0.007 0.12 0.22 75 -0.16 119 194
LAMA4 0.25 0.5 0.91 110 -1.1 22 132
FOXM1B/HNF6 0.22 0.49 0.85 104 -1.1 22 126
FOS 0.14 0.58 0.92 98 -1 50 148
SP1 0.03 0.018 0.12 13 -10000 0 13
CDC25B 0.25 0.48 0.91 108 -1 17 125
response to radiation 0.06 0.084 0.16 173 -10000 0 173
CENPB 0.25 0.48 0.92 105 -1 17 122
CENPA 0.3 0.52 0.97 134 -1 15 149
NEK2 0.31 0.53 0.98 136 -1 16 152
HIST1H2BA 0.25 0.48 0.91 108 -1 18 126
CCNA2 0.067 0.095 0.28 76 -10000 0 76
EP300 0.025 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.26 0.53 0.96 110 -1.1 21 131
CCNB2 0.27 0.5 0.97 109 -0.99 18 127
CCNB1 0.28 0.53 0.97 123 -1 19 142
ETV5 0.23 0.54 0.93 109 -1.1 28 137
ESR1 0.24 0.51 0.91 108 -1 27 135
CCND1 0.21 0.45 0.84 108 -0.92 21 129
GSK3A 0.075 0.091 0.21 123 -10000 0 123
Cyclin A-E1/CDK1-2 0.12 0.13 0.31 108 -10000 0 108
CDK2 0.035 0.033 0.12 14 -10000 0 14
G2/M transition of mitotic cell cycle 0.072 0.1 0.19 173 -10000 0 173
FOXM1B/Cbp/p300 0.16 0.41 0.73 74 -0.99 24 98
GAS1 0.2 0.56 0.92 107 -1.1 40 147
MMP2 0.24 0.5 0.91 110 -1.1 21 131
RB1/FOXM1C 0.13 0.41 0.78 78 -0.98 23 101
CREBBP 0.025 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.13 0.34 0.3 6 -0.76 104 110
MKNK1 0.026 0.003 -10000 0 -10000 0 0
MAPK14 -0.029 0.14 0.19 1 -0.29 106 107
ATF2/c-Jun -0.05 0.14 0.27 1 -0.29 99 100
MAPK11 -0.026 0.14 0.23 6 -0.29 101 107
MITF -0.048 0.16 0.2 1 -0.35 101 102
MAPKAPK5 -0.045 0.16 0.2 1 -0.34 101 102
KRT8 -0.043 0.15 0.22 2 -0.34 100 102
MAPKAPK3 0.025 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.038 0.2 0.25 4 -0.4 106 110
CEBPB -0.043 0.15 0.23 2 -0.34 99 101
SLC9A1 -0.047 0.16 0.2 1 -0.34 105 106
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.061 0.18 0.24 1 -0.35 118 119
p38alpha-beta/MNK1 -0.014 0.17 0.24 2 -0.33 103 105
JUN -0.051 0.13 0.27 1 -0.28 98 99
PPARGC1A -0.11 0.22 0.2 1 -0.38 159 160
USF1 -0.046 0.16 0.24 2 -0.34 101 103
RAB5/GDP/GDI1 -0.025 0.12 -10000 0 -0.25 97 97
NOS2 -0.066 0.24 0.29 28 -0.47 102 130
DDIT3 -0.046 0.16 0.2 1 -0.33 104 105
RAB5A 0.025 0.005 -10000 0 -10000 0 0
HSPB1 -0.038 0.14 0.28 21 -0.29 87 108
p38alpha-beta/HBP1 -0.013 0.16 0.23 1 -0.33 95 96
CREB1 -0.049 0.17 0.31 1 -0.36 99 100
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.067 0.13 0.2 2 -0.3 101 103
RPS6KA4 -0.044 0.16 0.37 1 -0.33 103 104
PLA2G4A -0.07 0.14 0.2 2 -0.31 104 106
GDI1 -0.046 0.16 0.24 2 -0.34 105 107
TP53 -0.073 0.18 0.22 3 -0.42 95 98
RPS6KA5 -0.051 0.16 0.2 1 -0.35 103 104
ESR1 -0.055 0.17 0.2 1 -0.35 111 112
HBP1 0.024 0.008 -10000 0 -10000 0 0
MEF2C -0.054 0.17 0.23 2 -0.36 107 109
MEF2A -0.049 0.16 0.2 1 -0.35 104 105
EIF4EBP1 -0.06 0.19 0.31 1 -0.41 98 99
KRT19 -0.063 0.18 0.2 1 -0.37 115 116
ELK4 -0.045 0.16 0.24 2 -0.34 101 103
ATF6 -0.046 0.16 0.24 2 -0.34 102 104
ATF1 -0.048 0.16 0.31 1 -0.36 98 99
p38alpha-beta/MAPKAPK2 -0.015 0.17 0.24 2 -0.33 103 105
p38alpha-beta/MAPKAPK3 -0.013 0.17 0.24 2 -0.33 101 103
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.21 0.37 0.47 1 -0.77 136 137
NCK1/PAK1/Dok-R -0.11 0.17 -10000 0 -0.38 131 131
NCK1/Dok-R -0.22 0.41 -10000 0 -0.85 141 141
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.066 0.11 0.23 143 -10000 0 143
RELA 0.025 0.006 -10000 0 -10000 0 0
SHC1 0.024 0.006 -10000 0 -10000 0 0
Rac/GDP 0.017 0.006 -10000 0 -10000 0 0
F2 0.077 0.13 0.27 147 -10000 0 147
TNIP2 0.025 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.21 0.4 -10000 0 -0.82 141 141
FN1 0.027 0.02 0.24 4 -10000 0 4
PLD2 -0.25 0.42 -10000 0 -0.89 143 143
PTPN11 0.025 0.006 -10000 0 -10000 0 0
GRB14 0.061 0.082 0.24 82 -10000 0 82
ELK1 -0.23 0.39 -10000 0 -0.82 142 142
GRB7 0.025 0.004 -10000 0 -10000 0 0
PAK1 0.025 0.006 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.43 -10000 0 -0.86 141 141
CDKN1A -0.15 0.27 0.4 2 -0.58 104 106
ITGA5 0.025 0.011 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.22 0.42 -10000 0 -0.86 141 141
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:NO -0.15 0.28 0.46 3 -0.58 134 137
PLG -0.25 0.43 -10000 0 -0.89 143 143
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.35 -10000 0 -0.73 136 136
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
ANGPT2 -0.14 0.25 0.4 1 -0.63 73 74
BMX -0.25 0.43 -10000 0 -0.89 142 142
ANGPT1 -0.27 0.45 -10000 0 -1 131 131
tube development -0.17 0.29 0.53 1 -0.62 129 130
ANGPT4 0.021 0.017 0.24 1 -10000 0 1
response to hypoxia -0.018 0.029 -10000 0 -0.063 127 127
Tie2/Ang1/GRB14 -0.23 0.45 -10000 0 -0.9 143 143
alpha5/beta1 Integrin 0.032 0.034 0.19 1 -0.16 13 14
FGF2 0.023 0.015 0.25 1 -10000 0 1
STAT5A (dimer) -0.18 0.34 -10000 0 -0.72 121 121
mol:L-citrulline -0.15 0.28 0.46 3 -0.58 134 137
AGTR1 0.06 0.082 0.24 80 -10000 0 80
MAPK14 -0.24 0.44 -10000 0 -0.9 141 141
Tie2/SHP2 -0.15 0.33 -10000 0 -0.9 70 70
TEK -0.17 0.36 -10000 0 -0.99 70 70
RPS6KB1 -0.2 0.36 -10000 0 -0.75 139 139
Angiotensin II/AT1 0.038 0.068 0.17 82 -0.15 20 102
Tie2/Ang1/GRB2 -0.25 0.44 -10000 0 -0.91 143 143
MAPK3 -0.24 0.39 -10000 0 -0.84 141 141
MAPK1 -0.24 0.39 -10000 0 -0.84 141 141
Tie2/Ang1/GRB7 -0.25 0.44 -10000 0 -0.91 143 143
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.25 0.43 -10000 0 -0.9 142 142
PI3K -0.24 0.42 -10000 0 -0.87 140 140
FES -0.25 0.44 -10000 0 -0.9 142 142
Crk/Dok-R -0.22 0.42 -10000 0 -0.85 143 143
Tie2/Ang1/ABIN2 -0.25 0.44 -10000 0 -0.91 143 143
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.33 0.44 2 -0.69 138 140
STAT5A 0.025 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.36 0.51 2 -0.73 131 133
Tie2/Ang2 -0.22 0.38 -10000 0 -0.83 122 122
Tie2/Ang1 -0.26 0.46 -10000 0 -0.94 143 143
FOXO1 -0.19 0.33 0.46 2 -0.7 134 136
ELF1 0.009 0.034 -10000 0 -0.13 11 11
ELF2 -0.24 0.42 -10000 0 -0.88 141 141
mol:Choline -0.24 0.41 -10000 0 -0.86 143 143
cell migration -0.062 0.099 -10000 0 -0.22 134 134
FYN -0.19 0.32 0.54 1 -0.7 127 128
DOK2 0.019 0.021 0.24 3 -10000 0 3
negative regulation of cell cycle -0.13 0.24 0.4 2 -0.53 105 107
ETS1 -0.047 0.12 0.24 1 -0.25 130 131
PXN -0.14 0.31 0.47 6 -0.62 126 132
ITGB1 0.025 0.004 -10000 0 -10000 0 0
NOS3 -0.17 0.32 0.46 3 -0.66 134 137
RAC1 0.024 0.008 -10000 0 -10000 0 0
TNF -0.051 0.14 0.25 11 -0.26 140 151
MAPKKK cascade -0.24 0.41 -10000 0 -0.86 143 143
RASA1 0.024 0.007 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.24 0.44 -10000 0 -0.9 141 141
NCK1 0.024 0.007 -10000 0 -10000 0 0
vasculogenesis -0.13 0.26 0.45 3 -0.52 134 137
mol:Phosphatidic acid -0.24 0.41 -10000 0 -0.86 143 143
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP -0.15 0.28 0.46 3 -0.58 134 137
Rac1/GTP -0.18 0.33 -10000 0 -0.7 135 135
MMP2 -0.25 0.43 -10000 0 -0.89 142 142
Glypican 2 network

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
MDK 0.032 0.039 0.24 16 -10000 0 16
GPC2 0.07 0.091 0.24 104 -10000 0 104
GPC2/Midkine 0.069 0.072 0.2 109 -0.16 1 110
neuron projection morphogenesis 0.069 0.072 0.2 109 -0.16 1 110
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.14 0.59 0.94 31 -1.2 79 110
IL23A -0.16 0.6 0.97 26 -1.3 73 99
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.54 0.8 12 -1.1 95 107
positive regulation of T cell mediated cytotoxicity -0.15 0.67 1 35 -1.2 96 131
ITGA3 -0.14 0.56 0.85 28 -1.2 75 103
IL17F -0.082 0.38 0.65 35 -0.68 93 128
IL12B 0.04 0.12 0.32 57 -10000 0 57
STAT1 (dimer) -0.16 0.6 0.81 28 -1.2 95 123
CD4 -0.12 0.56 0.92 29 -1.1 74 103
IL23 -0.15 0.57 0.88 26 -1.2 73 99
IL23R 0.025 0.23 0.75 20 -0.78 11 31
IL1B -0.17 0.63 0.97 27 -1.3 83 110
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.12 0.56 0.94 32 -1.1 77 109
TYK2 0.018 0.067 0.19 32 -10000 0 32
STAT4 0.031 0.035 0.24 13 -10000 0 13
STAT3 0.026 0.007 0.1 1 -10000 0 1
IL18RAP 0.032 0.042 0.25 16 -10000 0 16
IL12RB1 0.027 0.092 0.29 35 -10000 0 35
PIK3CA 0.025 0.008 0.1 1 -10000 0 1
IL12Rbeta1/TYK2 0.026 0.095 0.28 30 -0.21 6 36
IL23R/JAK2 0.03 0.23 0.63 24 -0.78 8 32
positive regulation of chronic inflammatory response -0.15 0.67 1 35 -1.2 96 131
natural killer cell activation -0.002 0.017 -10000 0 -0.06 22 22
JAK2 0.028 0.093 0.25 43 -10000 0 43
PIK3R1 0.024 0.009 0.1 1 -10000 0 1
NFKB1 0.018 0.024 0.1 1 -10000 0 1
RELA 0.017 0.024 0.1 1 -10000 0 1
positive regulation of dendritic cell antigen processing and presentation -0.13 0.55 0.88 26 -1.1 73 99
ALOX12B -0.14 0.56 0.87 30 -1.1 80 110
CXCL1 -0.21 0.67 0.96 31 -1.2 124 155
T cell proliferation -0.15 0.67 1 35 -1.2 96 131
NFKBIA 0.017 0.024 0.1 1 -10000 0 1
IL17A -0.033 0.34 0.6 48 -0.55 69 117
PI3K -0.16 0.56 0.76 19 -1.1 94 113
IFNG 0.013 0.059 0.19 30 -0.11 5 35
STAT3 (dimer) -0.15 0.54 0.77 20 -1 94 114
IL18R1 0.025 0.012 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.057 0.41 0.72 41 -0.73 73 114
IL18/IL18R 0.047 0.064 0.21 17 -0.14 27 44
macrophage activation -0.005 0.032 0.069 40 -0.045 60 100
TNF -0.16 0.61 0.98 27 -1.3 77 104
STAT3/STAT4 -0.15 0.57 0.8 24 -1.1 95 119
STAT4 (dimer) -0.16 0.61 0.85 29 -1.2 95 124
IL18 0.024 0.013 -10000 0 -10000 0 0
IL19 -0.13 0.55 0.89 28 -1.1 73 101
STAT5A (dimer) -0.16 0.6 0.8 28 -1.2 96 124
STAT1 0.029 0.028 0.24 8 -10000 0 8
SOCS3 0.024 0.026 0.24 6 -10000 0 6
CXCL9 -0.11 0.57 0.92 34 -1.1 73 107
MPO -0.16 0.6 0.88 29 -1.2 95 124
positive regulation of humoral immune response -0.15 0.67 1 35 -1.2 96 131
IL23/IL23R/JAK2/TYK2 -0.17 0.73 1 35 -1.3 96 131
IL6 -0.21 0.67 0.92 33 -1.2 125 158
STAT5A 0.025 0.005 -10000 0 -10000 0 0
IL2 0.011 0.035 0.27 2 -0.07 2 4
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.017 -10000 0 -0.06 22 22
CD3E -0.12 0.57 0.92 30 -1.1 74 104
keratinocyte proliferation -0.15 0.67 1 35 -1.2 96 131
NOS2 -0.15 0.59 0.89 34 -1.1 85 119
Ephrin A reverse signaling

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
MAPKKK cascade -0.014 0.078 0.17 1 -0.14 134 135
EFNA5 0.022 0.014 0.24 1 -10000 0 1
FYN -0.039 0.054 0.18 3 -0.14 96 99
neuron projection morphogenesis -0.014 0.078 0.17 1 -0.14 134 135
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.014 0.078 0.17 1 -0.14 134 135
EPHA5 0.02 0.018 0.24 2 -10000 0 2
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.12 0.25 25 -0.28 52 77
PTK2B 0.018 0.012 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.37 0.36 1 -0.87 97 98
EDN1 -0.002 0.098 0.21 36 -0.18 69 105
EDN3 0.017 0.019 0.24 2 -10000 0 2
EDN2 0.03 0.033 0.24 11 -10000 0 11
HRAS/GDP -0.082 0.18 0.28 6 -0.42 83 89
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.048 0.14 0.2 4 -0.34 70 74
ADCY4 -0.062 0.13 0.2 34 -0.28 78 112
ADCY5 -0.069 0.14 0.2 31 -0.31 89 120
ADCY6 -0.06 0.13 0.21 34 -0.28 77 111
ADCY7 -0.06 0.12 0.19 29 -0.27 76 105
ADCY1 -0.049 0.13 0.19 29 -0.28 70 99
ADCY2 -0.06 0.13 0.2 33 -0.29 76 109
ADCY3 -0.06 0.13 0.2 33 -0.27 77 110
ADCY8 -0.054 0.11 0.18 18 -0.28 62 80
ADCY9 -0.059 0.13 0.2 34 -0.28 77 111
arachidonic acid secretion -0.14 0.28 0.31 9 -0.54 123 132
ETB receptor/Endothelin-1/Gq/GTP -0.044 0.12 0.18 1 -0.28 80 81
GNAO1 0.019 0.011 -10000 0 -10000 0 0
HRAS 0.028 0.024 0.24 6 -10000 0 6
ETA receptor/Endothelin-1/G12/GTP -0.004 0.13 0.3 23 -0.27 47 70
ETA receptor/Endothelin-1/Gs/GTP -0.032 0.15 0.29 21 -0.28 84 105
mol:GTP -0.003 0.007 -10000 0 -10000 0 0
COL3A1 -0.048 0.12 0.26 30 -0.32 38 68
EDNRB 0.02 0.018 0.24 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.06 0.14 0.25 19 -0.38 68 87
CYSLTR1 -0.06 0.14 0.25 25 -0.39 46 71
SLC9A1 -0.021 0.083 0.17 24 -0.2 44 68
mol:GDP -0.093 0.2 0.28 9 -0.44 86 95
SLC9A3 -0.15 0.38 0.36 1 -0.81 102 103
RAF1 -0.099 0.21 0.28 11 -0.43 104 115
JUN -0.12 0.28 0.4 1 -0.7 70 71
JAK2 -0.052 0.12 0.25 25 -0.29 52 77
mol:IP3 -0.049 0.14 0.2 3 -0.35 59 62
ETA receptor/Endothelin-1 -0.02 0.16 0.35 25 -0.29 84 109
PLCB1 0.018 0.017 -10000 0 -10000 0 0
PLCB2 0.018 0.024 0.24 2 -0.049 2 4
ETA receptor/Endothelin-3 -0.06 0.12 0.2 3 -0.2 180 183
FOS -0.16 0.33 0.35 7 -0.84 86 93
Gai/GDP -0.17 0.35 -10000 0 -0.76 123 123
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.072 0.17 0.26 7 -0.41 71 78
BCAR1 0.021 0.01 -10000 0 -10000 0 0
PRKCB1 -0.053 0.14 0.19 4 -0.34 63 67
GNAQ 0.012 0.025 -10000 0 -0.057 5 5
GNAZ 0.023 0.008 -10000 0 -10000 0 0
GNAL 0.018 0.012 -10000 0 -10000 0 0
Gs family/GDP -0.1 0.2 0.26 6 -0.43 98 104
ETA receptor/Endothelin-1/Gq/GTP -0.051 0.15 0.21 4 -0.35 72 76
MAPK14 -0.05 0.12 0.18 2 -0.29 73 75
TRPC6 -0.18 0.4 0.36 1 -0.94 97 98
GNAI2 0.025 0.004 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.024 0.013 0.24 1 -10000 0 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.046 0.13 0.18 1 -0.29 79 80
ETB receptor/Endothelin-2 0.009 0.076 0.19 12 -0.16 70 82
ETB receptor/Endothelin-3 -0.042 0.11 0.19 2 -0.18 174 176
ETB receptor/Endothelin-1 -0.009 0.099 0.21 9 -0.21 66 75
MAPK3 -0.16 0.31 0.35 7 -0.75 91 98
MAPK1 -0.16 0.32 0.35 7 -0.75 94 101
Rac1/GDP -0.081 0.18 0.32 4 -0.41 80 84
cAMP biosynthetic process -0.043 0.16 0.29 21 -0.32 71 92
MAPK8 -0.14 0.35 0.34 1 -0.74 100 101
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.058 0.14 0.16 2 -0.33 86 88
p130Cas/CRK/Src/PYK2 -0.15 0.27 0.31 6 -0.6 104 110
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.081 0.18 0.32 4 -0.41 80 84
COL1A2 -0.05 0.15 0.27 17 -0.37 53 70
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.007 0.098 0.21 9 -0.19 76 85
mol:DAG -0.049 0.14 0.2 3 -0.35 58 61
MAP2K2 -0.13 0.25 0.31 9 -0.59 93 102
MAP2K1 -0.13 0.25 0.32 9 -0.57 96 105
EDNRA -0.009 0.1 0.2 25 -0.2 72 97
positive regulation of muscle contraction -0.038 0.11 0.22 40 -0.26 44 84
Gq family/GDP -0.072 0.19 0.27 1 -0.4 88 89
HRAS/GTP -0.082 0.18 0.27 7 -0.41 80 87
PRKCH -0.057 0.14 0.21 3 -0.35 62 65
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.058 0.14 0.2 4 -0.36 62 66
PRKCB -0.069 0.16 0.2 6 -0.38 75 81
PRKCE -0.052 0.13 0.25 3 -0.34 59 62
PRKCD -0.057 0.14 0.2 5 -0.35 62 67
PRKCG -0.055 0.14 0.22 5 -0.35 59 64
regulation of vascular smooth muscle contraction -0.2 0.4 0.4 4 -1 86 90
PRKCQ -0.058 0.14 0.21 3 -0.37 60 63
PLA2G4A -0.15 0.31 0.34 7 -0.6 123 130
GNA14 0.011 0.026 -10000 0 -0.05 15 15
GNA15 0.013 0.023 -10000 0 -0.054 2 2
GNA12 0.023 0.008 -10000 0 -10000 0 0
GNA11 0.013 0.023 -10000 0 -0.057 1 1
Rac1/GTP -0.004 0.13 0.3 23 -0.24 66 89
MMP1 0.012 0.19 0.29 63 -0.6 27 90
Glucocorticoid receptor regulatory network

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
PCK2 0.062 0.11 0.28 21 -0.43 1 22
SMARCC2 0.009 0.044 -10000 0 -0.098 68 68
SMARCC1 0.008 0.045 -10000 0 -0.1 69 69
TBX21 -0.05 0.16 0.35 8 -0.39 52 60
SUMO2 0.028 0.022 0.1 6 -10000 0 6
STAT1 (dimer) 0.035 0.038 0.21 18 -10000 0 18
FKBP4 0.024 0.007 -10000 0 -10000 0 0
FKBP5 0.025 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.088 0.12 0.28 81 -0.17 2 83
PRL -0.057 0.12 -10000 0 -0.44 5 5
cortisol/GR alpha (dimer)/TIF2 0.088 0.24 0.49 99 -0.36 16 115
RELA -0.019 0.11 0.19 26 -0.18 130 156
FGG 0.14 0.25 0.45 136 -0.34 21 157
GR beta/TIF2 0.043 0.14 0.28 74 -0.22 23 97
IFNG -0.16 0.29 0.48 10 -0.6 105 115
apoptosis 0.11 0.21 0.53 69 -0.44 1 70
CREB1 0.013 0.11 0.17 2 -0.28 51 53
histone acetylation -0.04 0.17 0.32 21 -0.38 66 87
BGLAP -0.071 0.15 0.34 4 -0.42 23 27
GR/PKAc 0.091 0.12 0.29 67 -0.16 2 69
NF kappa B1 p50/RelA -0.028 0.2 0.35 27 -0.32 120 147
SMARCD1 0.009 0.045 -10000 0 -0.1 69 69
MDM2 0.072 0.11 0.22 127 -0.12 2 129
GATA3 0.025 0.034 0.24 5 -10000 0 5
AKT1 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.058 0.13 0.43 1 -0.42 25 26
GSK3B 0.027 0.021 0.1 4 -10000 0 4
NR1I3 0.11 0.21 0.55 55 -0.63 3 58
CSN2 0.11 0.21 0.38 136 -0.31 22 158
BRG1/BAF155/BAF170/BAF60A 0.015 0.13 -10000 0 -0.3 67 67
NFATC1 0.023 0.008 -10000 0 -10000 0 0
POU2F1 0.026 0.011 -10000 0 -10000 0 0
CDKN1A -0.035 0.14 -10000 0 -1.4 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.006 0.015 0.087 4 -10000 0 4
SFN 0.023 0.008 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.077 0.12 0.28 60 -0.16 3 63
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.083 0.26 0.53 57 -0.6 32 89
JUN -0.085 0.18 0.32 9 -0.38 89 98
IL4 -0.071 0.14 -10000 0 -0.35 62 62
CDK5R1 0.037 0.049 0.25 23 -10000 0 23
PRKACA 0.026 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.042 0.08 0.17 24 -0.19 57 81
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.096 0.12 0.29 72 -0.16 2 74
cortisol/GR alpha (monomer) 0.16 0.31 0.57 138 -0.41 17 155
NCOA2 0.018 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.029 0.11 0.26 6 -0.19 112 118
AP-1/NFAT1-c-4 -0.15 0.27 0.38 13 -0.5 147 160
AFP -0.053 0.16 0.49 2 -0.48 4 6
SUV420H1 0.025 0.006 -10000 0 -10000 0 0
IRF1 0.11 0.16 0.38 81 -10000 0 81
TP53 0.029 0.017 -10000 0 -10000 0 0
PPP5C 0.026 0.003 -10000 0 -10000 0 0
KRT17 -0.26 0.41 0.41 6 -0.84 140 146
KRT14 -0.32 0.5 -10000 0 -1.1 146 146
TBP 0.031 0.022 -10000 0 -0.2 1 1
CREBBP 0.052 0.14 0.26 106 -0.25 39 145
HDAC1 0.024 0.016 -10000 0 -0.12 6 6
HDAC2 0.021 0.012 -10000 0 -0.051 2 2
AP-1 -0.15 0.28 0.38 13 -0.5 147 160
MAPK14 0.028 0.02 0.1 2 -10000 0 2
MAPK10 0.028 0.022 0.13 2 -10000 0 2
MAPK11 0.032 0.035 0.23 9 -10000 0 9
KRT5 -0.34 0.46 0.54 2 -0.91 184 186
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.035 0.038 0.21 18 -10000 0 18
CGA -0.1 0.3 0.38 11 -0.8 59 70
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.055 0.17 0.36 73 -0.35 15 88
MAPK3 0.028 0.022 0.13 2 -10000 0 2
MAPK1 0.028 0.02 0.11 1 -10000 0 1
ICAM1 -0.12 0.24 0.42 13 -0.5 102 115
NFKB1 -0.02 0.11 0.19 27 -0.19 128 155
MAPK8 -0.072 0.18 0.29 15 -0.33 112 127
MAPK9 0.027 0.02 0.11 1 -10000 0 1
cortisol/GR alpha (dimer) 0.11 0.21 0.53 68 -0.46 1 69
BAX -0.027 0.076 -10000 0 -10000 0 0
POMC -0.21 0.43 0.65 1 -1.3 56 57
EP300 0.053 0.14 0.26 111 -0.26 40 151
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.5 113 -0.38 10 123
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.089 0.18 89 -10000 0 89
SGK1 -0.062 0.42 0.51 5 -1 71 76
IL13 -0.22 0.36 0.44 15 -0.7 143 158
IL6 -0.18 0.38 0.43 35 -0.77 120 155
PRKACG 0.019 0.005 -10000 0 -10000 0 0
IL5 -0.2 0.3 0.46 5 -0.66 111 116
IL2 -0.18 0.28 0.45 2 -0.59 116 118
CDK5 0.025 0.014 -10000 0 -10000 0 0
PRKACB 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
IL8 -0.14 0.3 0.43 21 -0.6 110 131
CDK5R1/CDK5 0.046 0.041 0.2 23 -10000 0 23
NF kappa B1 p50/RelA/PKAc 0.005 0.16 0.32 27 -0.26 99 126
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.25 0.48 129 -0.35 10 139
SMARCA4 0.009 0.045 -10000 0 -0.099 67 67
chromatin remodeling 0.049 0.2 0.35 80 -0.35 28 108
NF kappa B1 p50/RelA/Cbp 0.006 0.22 0.36 63 -0.37 77 140
JUN (dimer) -0.085 0.18 0.31 9 -0.38 89 98
YWHAH 0.025 0.004 -10000 0 -10000 0 0
VIPR1 -0.051 0.14 0.32 2 -0.33 66 68
NR3C1 0.11 0.2 0.39 117 -0.26 9 126
NR4A1 -0.017 0.15 0.25 8 -0.44 51 59
TIF2/SUV420H1 0.008 0.061 -10000 0 -0.16 53 53
MAPKKK cascade 0.11 0.21 0.53 69 -0.44 1 70
cortisol/GR alpha (dimer)/Src-1 0.15 0.26 0.5 136 -0.38 12 148
PBX1 0.026 0.011 -10000 0 -10000 0 0
POU1F1 0.022 0.023 0.27 3 -10000 0 3
SELE -0.2 0.37 0.43 17 -0.77 127 144
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.048 0.2 0.36 80 -0.35 28 108
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.25 0.48 129 -0.35 10 139
mol:cortisol 0.1 0.19 0.34 139 -0.22 16 155
MMP1 -0.055 0.28 0.33 27 -0.91 39 66
Aurora B signaling

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
Condensin I complex 0.063 0.09 0.21 110 -0.17 3 113
STMN1 0.031 0.074 0.14 144 -10000 0 144
Aurora B/RasGAP/Survivin 0.11 0.12 0.28 148 -0.15 1 149
Chromosomal passenger complex/Cul3 protein complex 0.042 0.069 0.16 101 -0.16 6 107
BIRC5 0.1 0.11 0.25 165 -10000 0 165
DES -0.041 0.25 -10000 0 -0.57 72 72
Aurora C/Aurora B/INCENP 0.077 0.064 0.18 136 -0.12 1 137
Aurora B/TACC1 0.048 0.059 0.16 95 -0.13 1 96
Aurora B/PP2A 0.075 0.069 0.18 139 -10000 0 139
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.018 0.024 0.17 1 -10000 0 1
mitotic metaphase/anaphase transition -0.002 0.005 -10000 0 -10000 0 0
NDC80 0.031 0.079 0.15 141 -10000 0 141
Cul3 protein complex 0.041 0.043 -10000 0 -0.14 25 25
KIF2C 0.061 0.085 0.21 91 -0.24 2 93
PEBP1 0.026 0.007 -10000 0 -10000 0 0
KIF20A 0.1 0.1 0.24 171 -10000 0 171
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.071 0.069 0.18 132 -10000 0 132
SEPT1 0.031 0.034 0.24 12 -10000 0 12
SMC2 0.025 0.006 -10000 0 -10000 0 0
SMC4 0.025 0.012 0.24 1 -10000 0 1
NSUN2/NPM1/Nucleolin 0.021 0.16 0.33 17 -0.41 46 63
PSMA3 0.026 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.004 -10000 0 -10000 0 0
H3F3B 0.039 0.05 0.12 138 -10000 0 138
AURKB 0.085 0.1 0.24 145 -10000 0 145
AURKC 0.027 0.017 0.24 3 -10000 0 3
CDCA8 0.053 0.07 0.25 53 -10000 0 53
cytokinesis 0.067 0.099 0.24 104 -10000 0 104
Aurora B/Septin1 0.099 0.13 0.29 120 -0.21 1 121
AURKA 0.027 0.054 0.24 26 -10000 0 26
INCENP 0.029 0.007 -10000 0 -10000 0 0
KLHL13 0.025 0.006 -10000 0 -10000 0 0
BUB1 0.068 0.091 0.24 104 -10000 0 104
hSgo1/Aurora B/Survivin 0.12 0.14 0.31 156 -0.13 1 157
EVI5 0.027 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.098 0.098 0.27 78 -0.15 1 79
SGOL1 0.065 0.085 0.24 91 -10000 0 91
CENPA 0.086 0.12 0.25 136 -0.15 6 142
NCAPG 0.096 0.1 0.24 159 -10000 0 159
Aurora B/HC8 Proteasome 0.075 0.07 0.18 141 -10000 0 141
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.072 0.069 0.18 134 -10000 0 134
RHOA 0.025 0.005 -10000 0 -10000 0 0
NCAPH 0.082 0.096 0.24 126 -10000 0 126
NPM1 0.031 0.098 0.25 5 -0.26 28 33
RASA1 0.024 0.007 -10000 0 -10000 0 0
KLHL9 0.025 0.004 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.075 0.069 0.18 141 -10000 0 141
PPP1CC 0.025 0.006 -10000 0 -10000 0 0
Centraspindlin 0.1 0.11 0.28 102 -0.16 1 103
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 0.029 0.099 0.24 5 -0.26 30 35
MYLK 0.007 0.076 0.12 79 -0.21 40 119
KIF23 0.043 0.056 0.25 32 -10000 0 32
VIM 0.029 0.071 0.14 142 -10000 0 142
RACGAP1 0.031 0.024 0.26 5 -10000 0 5
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.03 0.1 0.23 2 -0.28 30 32
Chromosomal passenger complex 0.082 0.11 0.23 147 -10000 0 147
Chromosomal passenger complex/EVI5 0.13 0.13 0.34 119 -0.14 1 120
TACC1 0.019 0.011 -10000 0 -10000 0 0
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 0.12 0.47 0.81 41 -1.1 28 69
STAT6 (cleaved dimer) -0.009 0.42 0.57 4 -1.1 40 44
IGHG1 0.14 0.26 0.52 89 -0.43 4 93
IGHG3 0.095 0.44 0.67 47 -1.1 31 78
AKT1 0.076 0.32 0.55 52 -0.66 36 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.078 0.29 0.52 54 -0.66 24 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 0.096 0.33 0.58 58 -0.69 30 88
THY1 0.12 0.48 0.83 44 -1.1 28 72
MYB 0.036 0.046 0.24 23 -10000 0 23
HMGA1 0.026 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.11 0.42 0.67 77 -0.84 41 118
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.091 0.34 0.58 58 -0.8 26 84
SP1 0.028 0.013 0.14 3 -0.099 2 5
INPP5D 0.024 0.007 -10000 0 -10000 0 0
SOCS5 -0.015 0.055 -10000 0 -0.14 26 26
STAT6 (dimer)/ETS1 0.049 0.46 0.7 33 -1.1 40 73
SOCS1 0.07 0.34 0.59 45 -0.72 34 79
SOCS3 -0.001 0.5 0.61 46 -1.1 70 116
FCER2 0.13 0.48 0.86 56 -1 37 93
PARP14 0.03 0.022 0.11 5 -0.075 4 9
CCL17 0.14 0.5 0.88 55 -1.1 30 85
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.095 0.3 0.53 63 -0.63 27 90
T cell proliferation 0.079 0.46 0.72 38 -1.1 34 72
IL4R/JAK1 0.081 0.45 0.71 34 -1.1 30 64
EGR2 0.12 0.54 0.9 51 -1.3 34 85
JAK2 0.054 0.084 0.19 72 -10000 0 72
JAK3 0.018 0.052 0.26 13 -0.085 10 23
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
JAK1 0.033 0.053 0.15 31 -10000 0 31
COL1A2 0.12 0.24 0.53 39 -1.1 3 42
CCL26 0.14 0.49 0.89 46 -1.1 28 74
IL4R 0.14 0.53 0.91 57 -1.2 30 87
PTPN6 -0.012 0.041 -10000 0 -0.092 23 23
IL13RA2 0.033 0.6 0.82 42 -1.2 67 109
IL13RA1 0.056 0.084 0.18 73 -10000 0 73
IRF4 0.051 0.39 0.66 37 -1.1 32 69
ARG1 0.13 0.24 0.59 43 -0.57 2 45
CBL 0.085 0.38 0.61 62 -0.78 41 103
GTF3A 0.037 0.032 0.14 39 -0.097 1 40
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 0.087 0.12 0.26 87 -0.16 1 88
IRF4/BCL6 0.006 0.32 0.48 9 -1.1 31 40
CD40LG 0.04 0.071 0.27 33 -0.11 13 46
MAPK14 0.06 0.42 0.62 61 -0.85 54 115
mitosis 0.079 0.31 0.55 54 -0.62 36 90
STAT6 0.16 0.59 1 63 -1.3 30 93
SPI1 0.035 0.032 0.13 42 -10000 0 42
RPS6KB1 0.074 0.3 0.52 54 -0.61 35 89
STAT6 (dimer) 0.16 0.59 1 63 -1.3 30 93
STAT6 (dimer)/PARP14 0.088 0.47 0.73 36 -1.2 30 66
mast cell activation -0.014 0.028 -10000 0 -0.079 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.06 0.35 0.59 50 -0.7 39 89
FRAP1 0.076 0.32 0.55 52 -0.66 36 88
LTA 0.13 0.5 0.9 46 -1.2 29 75
FES 0.025 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.17 0.58 1.3 30 -1 68 98
CCL11 0.11 0.46 0.77 45 -1.1 29 74
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.095 0.33 0.57 59 -0.68 34 93
IL2RG 0.019 0.056 0.26 17 -0.082 11 28
IL10 0.097 0.52 0.81 47 -1.2 42 89
IRS1 0.025 0.005 -10000 0 -10000 0 0
IRS2 0.026 0.018 0.24 3 -10000 0 3
IL4 0.13 0.26 0.6 58 -0.7 7 65
IL5 0.12 0.48 0.83 41 -1.2 28 69
IL4/IL4R/JAK1/IL13RA1/JAK2 0.16 0.45 0.8 77 -0.87 28 105
COL1A1 0.15 0.28 0.65 49 -1.1 2 51
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 0.072 0.45 0.71 21 -1.2 29 50
IL2R gamma/JAK3 0.035 0.076 0.31 19 -0.16 12 31
TFF3 0.16 0.48 0.84 58 -1.1 29 87
ALOX15 0.14 0.55 0.85 64 -1.1 47 111
MYBL1 0.021 0.01 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.1 0.44 0.72 55 -0.98 32 87
SHC1 0.025 0.006 -10000 0 -10000 0 0
CEBPB 0.034 0.027 0.12 39 -10000 0 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.097 0.32 0.55 62 -0.69 24 86
mol:PI-3-4-5-P3 0.077 0.32 0.56 52 -0.66 36 88
PI3K 0.073 0.34 0.57 49 -0.72 36 85
DOK2 0.019 0.021 0.24 3 -10000 0 3
ETS1 -0.022 0.056 0.18 1 -0.13 44 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.096 0.27 0.5 66 -0.57 23 89
ITGB3 -0.019 0.63 0.78 46 -1.2 81 127
PIGR -0.002 0.66 0.84 55 -1.1 93 148
IGHE -0.053 0.097 0.19 12 -0.22 73 85
MAPKKK cascade 0.097 0.27 0.5 66 -0.56 23 89
BCL6 0.017 0.023 -10000 0 -0.053 41 41
OPRM1 0.11 0.47 0.8 39 -1.1 28 67
RETNLB 0.12 0.47 0.82 43 -1.1 28 71
SELP 0.11 0.49 0.8 43 -1.2 31 74
AICDA 0.097 0.44 0.72 34 -1.1 28 62
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.002 0.085 0.17 90 -0.18 10 100
KIRREL 0.022 0.014 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.002 0.085 0.19 10 -0.17 90 100
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.024 0.007 -10000 0 -10000 0 0
WASL 0.024 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.081 0.22 2 -0.13 88 90
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.014 0.07 -10000 0 -0.17 78 78
FYN -0.025 0.058 0.21 12 -0.13 70 82
mol:Ca2+ 0.025 0.079 0.21 2 -0.13 87 89
mol:DAG 0.026 0.08 0.21 2 -0.13 87 89
NPHS2 -0.011 0.032 0.23 3 -10000 0 3
mol:IP3 0.026 0.08 0.21 2 -0.13 87 89
regulation of endocytosis 0.011 0.068 0.16 9 -0.12 88 97
Nephrin/NEPH1/podocin/Cholesterol 0.017 0.073 0.17 12 -0.12 89 101
establishment of cell polarity 0.002 0.085 0.18 10 -0.17 90 100
Nephrin/NEPH1/podocin/NCK1-2 0.034 0.081 0.25 1 -0.12 84 85
Nephrin/NEPH1/beta Arrestin2 0.012 0.07 0.17 9 -0.12 88 97
NPHS1 0.002 0.047 0.24 11 -0.044 42 53
Nephrin/NEPH1/podocin 0.013 0.07 0.17 13 -0.12 92 105
TJP1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.007 -10000 0 -10000 0 0
NCK2 0.026 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.027 0.08 0.22 2 -0.13 87 89
CD2AP 0.025 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.028 0.081 0.19 12 -0.13 86 98
GRB2 0.025 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.032 0.073 0.22 12 -0.16 84 96
cytoskeleton organization -0.032 0.063 0.2 3 -0.17 74 77
Nephrin/NEPH1 0.007 0.06 0.15 10 -0.11 91 101
Nephrin/NEPH1/ZO-1 0.017 0.076 0.18 10 -0.14 88 98
Reelin 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
CDK5R1/CDK5 0.041 0.033 0.19 21 -10000 0 21
VLDLR 0.025 0.005 -10000 0 -10000 0 0
CRKL 0.025 0.004 -10000 0 -10000 0 0
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
FYN 0.022 0.009 -10000 0 -10000 0 0
ITGA3 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/Fyn 0.052 0.053 0.19 47 -0.13 6 53
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.041 0.2 1 -0.13 12 13
AKT1 -0.043 0.081 0.13 3 -0.16 127 130
MAP2K7 0.025 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.006 -10000 0 -10000 0 0
DAB1 0.016 0.019 0.24 2 -10000 0 2
RELN/LRP8/DAB1 0.001 0.087 0.19 31 -0.12 128 159
LRPAP1/LRP8 0.039 0.019 0.19 6 -10000 0 6
RELN/LRP8/DAB1/Fyn 0.006 0.088 0.19 30 -0.12 128 158
DAB1/alpha3/beta1 Integrin -0.002 0.086 0.22 1 -0.13 118 119
long-term memory -0.016 0.1 0.21 7 -0.14 168 175
DAB1/LIS1 0.008 0.092 0.29 1 -0.13 112 113
DAB1/CRLK/C3G -0.001 0.084 -10000 0 -0.13 116 116
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DAB1/NCK2 0.01 0.095 0.29 1 -0.13 119 120
ARHGEF2 0.025 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.02 0.015 0.24 1 -10000 0 1
CDK5R1 0.036 0.046 0.24 23 -10000 0 23
RELN 0.05 0.073 0.24 60 -10000 0 60
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.054 0.056 0.2 50 -0.13 5 55
GRIN2A/RELN/LRP8/DAB1/Fyn -0.012 0.11 0.2 24 -0.14 176 200
MAPK8 0.024 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.001 0.085 0.18 28 -0.12 131 159
ITGB1 0.025 0.004 -10000 0 -10000 0 0
MAP1B -0.04 0.072 0.16 14 -0.15 110 124
RELN/LRP8 0.061 0.056 0.2 58 -0.13 4 62
GRIN2B/RELN/LRP8/DAB1/Fyn 0.009 0.091 0.2 24 -0.12 119 143
PI3K 0.03 0.028 -10000 0 -0.18 6 6
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.028 -10000 0 -0.16 9 9
RAP1A -0.031 0.097 0.32 18 -0.19 1 19
PAFAH1B1 0.024 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.025 0.011 0.24 1 -10000 0 1
CRLK/C3G 0.036 0.011 -10000 0 -10000 0 0
GRIN2B 0.018 0.013 0.24 1 -10000 0 1
NCK2 0.026 0.003 -10000 0 -10000 0 0
neuron differentiation -0.036 0.09 0.17 1 -0.24 37 38
neuron adhesion -0.037 0.1 0.32 20 -0.21 1 21
LRP8 0.028 0.026 0.24 7 -10000 0 7
GSK3B -0.045 0.077 0.19 2 -0.16 122 124
RELN/VLDLR/DAB1/Fyn 0.004 0.086 0.18 27 -0.12 130 157
MAP3K11 0.025 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.035 0.089 0.17 1 -0.17 129 130
CDK5 0.024 0.007 -10000 0 -10000 0 0
MAPT 0 0.06 0.75 3 -10000 0 3
neuron migration -0.051 0.098 0.24 11 -0.2 96 107
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.036 0.091 0.17 1 -0.25 37 38
RELN/VLDLR 0.07 0.057 0.2 55 -0.12 5 60
Thromboxane A2 receptor 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
TGM2 0.028 0.027 0.24 7 -10000 0 7
GNB1/GNG2 -0.051 0.073 -10000 0 -0.18 109 109
AKT1 -0.019 0.12 0.34 12 -0.25 12 24
EGF 0.042 0.061 0.24 40 -10000 0 40
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.012 0.075 0.26 19 -0.2 5 24
mol:Ca2+ -0.041 0.16 0.4 12 -0.29 104 116
LYN -0.014 0.059 0.27 10 -0.2 4 14
RhoA/GTP -0.021 0.064 0.16 4 -0.13 96 100
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.05 0.18 0.38 18 -0.33 105 123
GNG2 0.025 0.004 -10000 0 -10000 0 0
ARRB2 0.024 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.019 0.12 0.22 2 -0.34 46 48
G beta5/gamma2 -0.065 0.097 -10000 0 -0.24 108 108
PRKCH -0.052 0.18 0.4 13 -0.34 107 120
DNM1 0.025 0.012 0.24 1 -10000 0 1
TXA2/TP beta/beta Arrestin3 0.012 0.017 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.024 0.013 0.24 1 -10000 0 1
G12 family/GTP -0.062 0.13 -10000 0 -0.3 101 101
ADRBK1 0.025 0.006 -10000 0 -10000 0 0
ADRBK2 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.032 0.012 -10000 0 -0.13 1 1
mol:GDP 0.022 0.12 0.33 24 -0.32 9 33
mol:NADP 0.026 0.025 0.24 6 -10000 0 6
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 0.018 0.012 -10000 0 -10000 0 0
mol:IP3 -0.056 0.19 0.42 12 -0.37 106 118
cell morphogenesis 0.032 0.012 -10000 0 -0.13 1 1
PLCB2 -0.083 0.24 0.49 9 -0.49 109 118
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.001 0.072 0.24 23 -0.2 7 30
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.015 0.07 0.26 14 -0.21 6 20
RHOA 0.025 0.005 -10000 0 -10000 0 0
PTGIR 0.045 0.063 0.24 44 -10000 0 44
PRKCB1 -0.057 0.19 0.4 12 -0.36 111 123
GNAQ 0.025 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.025 0.24 6 -10000 0 6
TXA2/TXA2-R family -0.089 0.25 0.48 10 -0.5 111 121
LCK -0.013 0.071 0.24 20 -0.2 4 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.016 0.055 0.22 1 -0.15 27 28
TXA2-R family/G12 family/GDP/G beta/gamma 0.015 0.054 -10000 0 -0.39 7 7
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.017 0.052 -10000 0 -0.16 24 24
MAPK14 -0.031 0.13 0.32 21 -0.23 101 122
TGM2/GTP -0.067 0.21 0.48 9 -0.41 105 114
MAPK11 -0.031 0.13 0.32 18 -0.23 101 119
ARHGEF1 -0.031 0.09 0.25 7 -0.18 98 105
GNAI2 0.025 0.004 -10000 0 -10000 0 0
JNK cascade -0.06 0.2 0.42 12 -0.37 111 123
RAB11/GDP 0.025 0.009 -10000 0 -10000 0 0
ICAM1 -0.039 0.15 0.38 12 -0.27 109 121
cAMP biosynthetic process -0.055 0.18 0.4 12 -0.34 104 116
Gq family/GTP/EBP50 0.003 0.058 0.24 11 -0.16 35 46
actin cytoskeleton reorganization 0.032 0.012 -10000 0 -0.13 1 1
SRC -0.014 0.066 0.27 12 -0.2 4 16
GNB5 0.025 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.1 0.28 26 -0.21 21 47
VCAM1 -0.042 0.16 0.34 16 -0.29 111 127
TP beta/Gq family/GDP/G beta5/gamma2 -0.019 0.12 0.22 2 -0.34 46 48
platelet activation -0.041 0.17 0.38 20 -0.29 102 122
PGI2/IP 0.031 0.046 0.17 44 -0.15 4 48
PRKACA 0.008 0.05 -10000 0 -0.15 35 35
Gq family/GDP/G beta5/gamma2 -0.012 0.1 0.23 2 -0.3 44 46
TXA2/TP beta/beta Arrestin2 0.003 0.042 -10000 0 -0.32 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.047 0.13 2 -0.16 31 33
mol:DAG -0.064 0.21 0.43 12 -0.4 110 122
EGFR 0.021 0.01 -10000 0 -10000 0 0
TXA2/TP alpha -0.079 0.23 0.47 11 -0.46 106 117
Gq family/GTP -0.009 0.048 0.14 1 -0.15 47 48
YES1 -0.013 0.069 0.27 14 -0.2 4 18
GNAI2/GTP 0.002 0.05 -10000 0 -0.15 26 26
PGD2/DP 0.008 0.043 0.17 1 -0.15 32 33
SLC9A3R1 0.025 0.005 -10000 0 -10000 0 0
FYN -0.012 0.066 0.25 14 -0.2 5 19
mol:NO 0.026 0.025 0.24 6 -10000 0 6
GNA15 0.024 0.007 -10000 0 -10000 0 0
PGK/cGMP -0.007 0.072 0.17 6 -0.13 117 123
RhoA/GDP 0.024 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.065 0.24 1 -0.18 18 19
NOS3 0.026 0.025 0.24 6 -10000 0 6
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.054 0.18 0.4 12 -0.34 108 120
PRKCB -0.063 0.19 0.39 12 -0.37 111 123
PRKCE -0.052 0.18 0.4 12 -0.34 108 120
PRKCD -0.059 0.19 0.41 11 -0.37 107 118
PRKCG -0.058 0.19 0.42 12 -0.37 108 120
muscle contraction -0.083 0.24 0.46 11 -0.47 111 122
PRKCZ -0.054 0.18 0.41 12 -0.33 110 122
ARR3 0.021 0.011 0.24 1 -10000 0 1
TXA2/TP beta 0.011 0.058 0.17 2 -0.16 25 27
PRKCQ -0.054 0.18 0.4 13 -0.35 110 123
MAPKKK cascade -0.077 0.22 0.45 10 -0.44 111 121
SELE -0.056 0.18 0.37 13 -0.35 112 125
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.062 0.24 1 -0.18 19 20
ROCK1 0.025 0.006 -10000 0 -10000 0 0
GNA14 0.025 0.005 -10000 0 -10000 0 0
chemotaxis -0.11 0.28 0.55 7 -0.58 111 118
GNA12 0.023 0.008 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.051 0.069 0.23 47 -0.072 5 52
NFATC2 0.055 0.18 0.44 23 -0.4 25 48
NFATC3 0.04 0.088 0.24 36 -0.22 11 47
CD40LG -0.023 0.29 0.56 30 -0.7 39 69
ITCH -0.021 0.072 0.26 1 -0.16 94 95
CBLB -0.021 0.073 0.26 1 -0.16 95 96
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.008 0.32 0.55 60 -0.71 34 94
JUNB 0.03 0.034 0.24 12 -10000 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.091 0.17 1 -0.19 100 101
T cell anergy -0.058 0.13 0.29 3 -0.3 94 97
TLE4 0.028 0.12 0.36 16 -0.36 13 29
Jun/NFAT1-c-4/p21SNFT 0.033 0.27 0.6 25 -0.68 29 54
AP-1/NFAT1-c-4 0.019 0.34 0.67 39 -0.76 38 77
IKZF1 0.034 0.13 0.38 23 -0.41 9 32
T-helper 2 cell differentiation -0.11 0.27 0.4 7 -0.59 62 69
AP-1/NFAT1 0.027 0.18 0.39 40 -0.32 39 79
CALM1 -0.004 0.065 -10000 0 -0.13 100 100
EGR2 0 0.31 0.61 34 -1 22 56
EGR3 -0.01 0.32 0.58 34 -1 30 64
NFAT1/FOXP3 0.062 0.18 0.43 47 -0.34 17 64
EGR1 0.033 0.052 0.24 25 -0.046 11 36
JUN 0.021 0.038 0.2 6 -0.069 2 8
EGR4 0.081 0.099 0.25 128 -0.047 6 134
mol:Ca2+ -0.02 0.049 0.077 4 -0.11 106 110
GBP3 -0.007 0.18 0.32 9 -0.48 50 59
FOSL1 0.036 0.057 0.24 33 -10000 0 33
NFAT1-c-4/MAF/IRF4 0.027 0.25 0.61 16 -0.7 25 41
DGKA 0.027 0.12 0.35 14 -0.34 10 24
CREM 0.025 0.006 -10000 0 -0.063 1 1
NFAT1-c-4/PPARG 0.016 0.25 0.55 15 -0.71 27 42
CTLA4 0.04 0.17 0.39 62 -0.33 14 76
NFAT1-c-4 (dimer)/EGR1 0.024 0.28 0.6 27 -0.74 28 55
NFAT1-c-4 (dimer)/EGR4 0.055 0.28 0.59 38 -0.68 28 66
FOS 0.022 0.045 0.22 9 -0.21 3 12
IFNG -0.011 0.22 0.5 20 -0.61 18 38
T cell activation 0.008 0.18 0.51 8 -0.56 12 20
MAF 0.021 0.01 -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 -0.026 0.22 0.64 20 -0.52 32 52
TNF 0.002 0.26 0.53 32 -0.71 29 61
FASLG -0.067 0.41 0.7 11 -1.2 43 54
TBX21 0.041 0.057 0.24 29 -10000 0 29
BATF3 0.035 0.046 0.24 22 -10000 0 22
PRKCQ 0.029 0.041 0.26 10 -0.12 8 18
PTPN1 0.024 0.11 0.29 13 -0.32 14 27
NFAT1-c-4/ICER1 0.021 0.25 0.53 16 -0.7 26 42
GATA3 0.018 0.012 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.01 0.22 0.5 20 -0.6 18 38
IL2RA 0.01 0.31 0.53 60 -0.68 36 96
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.025 0.11 0.3 10 -0.35 10 20
E2F1 0.035 0.042 0.25 18 -10000 0 18
PPARG 0.025 0.019 0.24 3 -10000 0 3
SLC3A2 0.027 0.12 0.35 13 -0.34 11 24
IRF4 0.035 0.048 0.24 24 -10000 0 24
PTGS2 -0.041 0.29 0.55 23 -0.71 42 65
CSF2 -0.027 0.27 0.55 22 -0.68 37 59
JunB/Fra1/NFAT1-c-4 0.021 0.27 0.58 25 -0.73 26 51
IL4 -0.12 0.28 0.41 6 -0.62 62 68
IL5 -0.031 0.27 0.55 20 -0.68 37 57
IL2 0.007 0.18 0.51 8 -0.57 12 20
IL3 -0.021 0.11 -10000 0 -0.58 12 12
RNF128 -0.056 0.15 0.31 4 -0.34 99 103
NFATC1 0.026 0.22 0.53 29 -0.64 20 49
CDK4 -0.005 0.2 0.57 13 -0.56 14 27
PTPRK 0.025 0.11 0.3 12 -0.32 14 26
IL8 -0.027 0.29 0.57 28 -0.69 40 68
POU2F1 0.025 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.071 0.23 0.44 44 -0.54 20 64
HDAC7 0.023 0.013 -10000 0 -0.046 8 8
HIF1A/ARNT/Cbp/p300/Src-1 0.11 0.3 0.57 38 -0.66 30 68
SMAD4 0.024 0.008 -10000 0 -10000 0 0
ID2 0.089 0.24 0.48 36 -0.55 22 58
AP1 0.006 0.082 0.26 4 -0.17 77 81
ABCG2 0.078 0.25 0.48 36 -0.58 22 58
HIF1A 0.04 0.071 0.23 10 -0.15 4 14
TFF3 0.15 0.27 0.5 87 -0.54 19 106
GATA2 0.022 0.022 0.24 1 -0.058 16 17
AKT1 0.035 0.086 0.22 13 -0.18 26 39
response to hypoxia 0.017 0.073 0.15 41 -0.16 35 76
MCL1 0.084 0.23 0.48 32 -0.55 19 51
NDRG1 0.068 0.21 0.48 27 -0.5 19 46
SERPINE1 0.091 0.25 0.52 45 -0.55 21 66
FECH 0.083 0.23 0.49 35 -0.54 20 55
FURIN 0.093 0.24 0.48 36 -0.54 20 56
NCOA2 0.014 0.023 -10000 0 -0.051 23 23
EP300 0.034 0.12 0.27 17 -0.32 28 45
HMOX1 0.096 0.24 0.5 39 -0.54 20 59
BHLHE40 0.088 0.24 0.48 36 -0.55 21 57
BHLHE41 0.09 0.24 0.48 37 -0.56 19 56
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.084 0.11 0.36 9 -10000 0 9
ENG 0.032 0.087 0.36 9 -10000 0 9
JUN 0.023 0.019 0.27 1 -0.053 6 7
RORA 0.092 0.24 0.48 37 -0.55 20 57
ABCB1 0.004 0.13 0.49 1 -0.78 9 10
TFRC 0.089 0.24 0.48 36 -0.54 21 57
CXCR4 0.09 0.24 0.51 35 -0.56 20 55
TF 0.071 0.25 0.49 35 -0.52 29 64
CITED2 0.093 0.24 0.48 35 -0.55 20 55
HIF1A/ARNT 0.17 0.33 0.74 38 -0.69 13 51
LDHA 0.034 0.084 0.43 2 -0.76 2 4
ETS1 0.085 0.24 0.48 35 -0.56 19 54
PGK1 0.093 0.24 0.49 36 -0.55 20 56
NOS2 0.094 0.25 0.5 46 -0.52 26 72
ITGB2 0.093 0.24 0.5 38 -0.55 20 58
ALDOA 0.09 0.23 0.48 36 -0.55 20 56
Cbp/p300/CITED2 0.076 0.29 0.51 34 -0.7 31 65
FOS 0.023 0.026 0.26 4 -0.049 2 6
HK2 0.091 0.24 0.49 36 -0.55 19 55
SP1 0.026 0.017 -10000 0 -0.11 7 7
GCK 0.017 0.3 0.53 5 -1.2 25 30
HK1 0.088 0.23 0.48 35 -0.56 19 54
NPM1 0.092 0.24 0.48 36 -0.55 20 56
EGLN1 0.084 0.23 0.48 33 -0.55 20 53
CREB1 0.029 0.009 0.14 3 -10000 0 3
PGM1 0.089 0.24 0.48 36 -0.55 20 56
SMAD3 0.026 0.002 -10000 0 -10000 0 0
EDN1 -0.018 0.29 0.57 4 -0.91 36 40
IGFBP1 0.083 0.23 0.49 38 -0.54 20 58
VEGFA 0.061 0.25 0.49 21 -0.57 35 56
HIF1A/JAB1 0.035 0.061 0.21 5 -0.18 1 6
CP 0.086 0.26 0.51 45 -0.54 26 71
CXCL12 0.087 0.24 0.49 34 -0.59 19 53
COPS5 0.017 0.022 -10000 0 -0.048 21 21
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 0.09 0.24 0.48 36 -0.55 19 55
EGLN3 0.089 0.24 0.48 34 -0.54 22 56
CA9 0.088 0.24 0.49 40 -0.54 20 60
TERT 0.13 0.26 0.51 75 -0.54 18 93
ENO1 0.09 0.24 0.48 36 -0.55 20 56
PFKL 0.091 0.24 0.48 36 -0.54 20 56
NCOA1 0.022 0.016 -10000 0 -0.054 2 2
ADM 0.099 0.25 0.52 44 -0.55 20 64
ARNT 0.038 0.071 0.21 14 -0.18 4 18
HNF4A 0.028 0.058 0.24 27 -0.1 23 50
ADFP 0.071 0.23 0.44 44 -0.54 20 64
SLC2A1 0.065 0.24 0.5 18 -0.56 33 51
LEP 0.081 0.23 0.48 39 -0.55 20 59
HIF1A/ARNT/Cbp/p300 0.1 0.3 0.59 34 -0.67 30 64
EPO -0.009 0.31 0.51 13 -0.76 50 63
CREBBP 0.035 0.12 0.26 19 -0.3 27 46
HIF1A/ARNT/Cbp/p300/HDAC7 0.1 0.3 0.58 34 -0.65 31 65
PFKFB3 0.09 0.24 0.48 35 -0.55 20 55
NT5E 0.071 0.24 0.49 31 -0.56 23 54
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.037 0.13 0.36 37 -0.27 13 50
TBX21 0.013 0.37 0.75 33 -0.93 33 66
B2M 0.026 0.016 -10000 0 -0.063 12 12
TYK2 0.026 0.049 0.15 26 -10000 0 26
IL12RB1 0.034 0.075 0.28 27 -10000 0 27
GADD45B 0.03 0.32 0.69 32 -0.83 27 59
IL12RB2 0.028 0.057 0.2 23 -10000 0 23
GADD45G 0.046 0.32 0.65 43 -0.79 28 71
natural killer cell activation 0.011 0.036 0.094 55 -0.043 9 64
RELB 0.026 0.003 -10000 0 -10000 0 0
RELA 0.025 0.006 -10000 0 -10000 0 0
IL18 0.028 0.026 0.11 12 -10000 0 12
IL2RA 0.059 0.08 0.24 76 -10000 0 76
IFNG 0.037 0.054 0.24 31 -10000 0 31
STAT3 (dimer) 0.026 0.3 0.55 47 -0.68 38 85
HLA-DRB5 -0.003 0.009 0.021 3 -0.023 65 68
FASLG 0.009 0.37 0.72 34 -0.92 38 72
NF kappa B2 p52/RelB -0.015 0.3 0.48 14 -0.78 40 54
CD4 0.018 0.033 0.25 5 -0.038 58 63
SOCS1 0.026 0.018 0.24 3 -10000 0 3
EntrezGene:6955 -0.002 0.014 0.026 36 -0.028 79 115
CD3D 0.027 0.057 0.26 23 -0.046 46 69
CD3E 0.021 0.041 0.26 9 -0.061 12 21
CD3G 0.024 0.051 0.26 17 -0.053 18 35
IL12Rbeta2/JAK2 0.038 0.083 0.26 26 -0.17 17 43
CCL3 0.013 0.38 0.7 41 -0.97 34 75
CCL4 0.014 0.35 0.7 37 -0.84 37 74
HLA-A 0.001 0.01 0.025 42 -0.042 13 55
IL18/IL18R 0.077 0.11 0.3 57 -0.16 23 80
NOS2 -0.003 0.4 0.7 36 -1 42 78
IL12/IL12R/TYK2/JAK2/SPHK2 0.038 0.13 0.35 37 -0.24 15 52
IL1R1 0.011 0.34 0.69 31 -0.86 34 65
IL4 -0.017 0.048 -10000 0 -0.13 38 38
JAK2 0.026 0.048 0.15 26 -10000 0 26
EntrezGene:6957 -0.002 0.013 0.025 37 -0.027 70 107
TCR/CD3/MHC I/CD8 -0.02 0.2 0.33 18 -0.6 35 53
RAB7A 0.058 0.29 0.66 34 -0.75 18 52
lysosomal transport 0.06 0.28 0.65 35 -0.7 18 53
FOS -0.13 0.49 0.59 20 -1.1 91 111
STAT4 (dimer) 0.051 0.32 0.61 49 -0.72 33 82
STAT5A (dimer) 0.006 0.32 0.6 27 -0.77 41 68
GZMA 0.008 0.35 0.72 29 -0.98 28 57
GZMB -0.006 0.38 0.69 32 -0.99 39 71
HLX 0.032 0.039 0.24 16 -10000 0 16
LCK 0.008 0.36 0.68 38 -0.83 41 79
TCR/CD3/MHC II/CD4 -0.03 0.14 0.26 16 -0.25 95 111
IL2/IL2R 0.073 0.089 0.23 74 -0.16 24 98
MAPK14 0.045 0.33 0.68 37 -0.84 26 63
CCR5 0.026 0.33 0.69 31 -0.87 27 58
IL1B 0.037 0.072 0.23 41 -10000 0 41
STAT6 0.043 0.15 0.44 35 -0.49 2 37
STAT4 0.031 0.035 0.24 13 -10000 0 13
STAT3 0.025 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.028 0.24 8 -10000 0 8
NFKB1 0.025 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.018 0.24 3 -10000 0 3
IL12B 0.04 0.082 0.25 46 -10000 0 46
CD8A 0.028 0.031 0.27 6 -0.06 11 17
CD8B 0.029 0.035 0.26 9 -0.063 12 21
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.037 0.13 0.26 13 -0.36 37 50
IL2RB 0.028 0.027 0.24 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.3 0.6 51 -0.66 33 84
IL2RG 0.032 0.038 0.24 15 -10000 0 15
IL12 0.049 0.097 0.27 47 -0.17 8 55
STAT5A 0.025 0.005 -10000 0 -10000 0 0
CD247 0.024 0.051 0.26 17 -0.044 48 65
IL2 0.022 0.015 0.24 2 -10000 0 2
SPHK2 0.025 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.027 0.057 0.18 30 -10000 0 30
IL12/IL12R/TYK2/JAK2 0.018 0.39 0.71 47 -0.89 41 88
MAP2K3 0.039 0.33 0.65 41 -0.82 29 70
RIPK2 0.02 0.011 -10000 0 -10000 0 0
MAP2K6 0.042 0.33 0.67 38 -0.84 28 66
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.004 0.01 0.023 4 -0.025 74 78
IL18RAP 0.035 0.051 0.22 25 -10000 0 25
IL12Rbeta1/TYK2 0.042 0.083 0.27 30 -0.21 6 36
EOMES -0.029 0.21 -10000 0 -1 18 18
STAT1 (dimer) 0.047 0.3 0.64 41 -0.67 36 77
T cell proliferation 0.048 0.26 0.54 49 -0.56 31 80
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.029 0.026 0.13 4 -10000 0 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.21 0.43 7 -0.57 34 41
ATF2 0.036 0.3 0.64 35 -0.78 26 61
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.025 0.046 0.1 4 -0.11 104 108
BUB1B 0.036 0.061 0.13 111 -0.1 3 114
PLK1 0.021 0.037 0.1 59 -0.083 4 63
PLK1S1 0.015 0.029 0.14 8 -0.15 5 13
KIF2A 0.012 0.039 0.14 22 -0.1 1 23
regulation of mitotic centrosome separation 0.021 0.037 0.1 59 -0.083 4 63
GOLGA2 0.024 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.076 0.078 0.2 122 -0.12 4 126
WEE1 0.023 0.042 0.22 5 -0.28 3 8
cytokinesis 0.049 0.097 0.18 107 -0.16 6 113
PP2A-alpha B56 0.066 0.097 -10000 0 -0.5 10 10
AURKA 0.022 0.036 0.13 37 -0.14 1 38
PICH/PLK1 0.017 0.069 0.2 44 -0.13 1 45
CENPE 0.024 0.057 0.15 62 -0.1 1 63
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.04 0.14 22 -0.1 1 23
PPP2CA 0.025 0.005 -10000 0 -10000 0 0
FZR1 0.025 0.005 -10000 0 -10000 0 0
TPX2 0.041 0.054 0.12 141 -0.18 1 142
PAK1 0.024 0.006 -10000 0 -10000 0 0
SPC24 0.086 0.098 0.24 136 -10000 0 136
FBXW11 0.025 0.004 -10000 0 -10000 0 0
CLSPN 0.025 0.055 0.14 56 -0.23 9 65
GORASP1 0.025 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.015 14 -10000 0 14
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.01 0.021 0.056 54 -0.045 4 58
G2 phase of mitotic cell cycle -0.001 0.002 0.01 5 -10000 0 5
STAG2 0.026 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.015 0.036 -10000 0 -0.43 3 3
spindle elongation 0.021 0.037 0.1 59 -0.083 4 63
ODF2 0.024 0.007 -10000 0 -10000 0 0
BUB1 0.043 0.1 -10000 0 -0.54 10 10
TPT1 -0.023 0.076 0.13 5 -0.17 97 102
CDC25C 0.064 0.074 0.14 160 -0.23 8 168
CDC25B 0.023 0.018 0.25 1 -10000 0 1
SGOL1 0.025 0.046 0.11 104 -0.1 4 108
RHOA 0.025 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.04 0.039 0.19 15 -0.16 2 17
CDC14B -0.009 0.003 -10000 0 -10000 0 0
CDC20 0.098 0.1 0.24 163 -10000 0 163
PLK1/PBIP1 0.018 0.041 0.11 58 -0.083 1 59
mitosis -0.002 0.003 0.024 1 -10000 0 1
FBXO5 0.012 0.035 0.14 19 -10000 0 19
CDC2 0.001 0.003 0.011 17 -0.009 12 29
NDC80 0.024 0.007 -10000 0 -10000 0 0
metaphase plate congression 0.019 0.028 0.14 3 -0.19 3 6
ERCC6L 0.026 0.059 0.21 31 -0.16 2 33
NLP/gamma Tubulin 0.01 0.025 0.084 22 -0.073 7 29
microtubule cytoskeleton organization -0.023 0.075 0.13 5 -0.17 97 102
G2/M transition DNA damage checkpoint -0.001 0.002 0.016 3 -10000 0 3
PPP1R12A 0.025 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.016 3 -10000 0 3
PLK1/PRC1-2 0.097 0.096 0.22 168 -0.1 1 169
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.028 0.18 2 -0.1 1 3
RAB1A 0.025 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.015 0.032 0.088 56 -0.074 1 57
mitotic prometaphase 0 0.002 0.019 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.04 0.18 14 -10000 0 14
microtubule-based process 0.083 0.089 0.2 173 -0.083 3 176
Golgi organization 0.021 0.037 0.1 59 -0.083 4 63
Cohesin/SA2 0.033 0.028 0.12 20 -0.095 1 21
PPP1CB/MYPT1 0.036 0.009 -10000 0 -10000 0 0
KIF20A 0.1 0.1 0.24 171 -10000 0 171
APC/C/CDC20 0.083 0.09 0.2 167 -0.1 1 168
PPP2R1A 0.026 0.003 -10000 0 -10000 0 0
chromosome segregation 0.017 0.041 0.11 58 -0.082 1 59
PRC1 0.036 0.047 0.24 24 -10000 0 24
ECT2 0.03 0.075 0.22 53 -0.1 1 54
C13orf34 0.016 0.031 0.087 54 -0.068 4 58
NUDC 0.019 0.028 0.14 3 -0.19 3 6
regulation of attachment of spindle microtubules to kinetochore 0.036 0.061 0.13 111 -0.099 3 114
spindle assembly 0.015 0.03 0.095 37 -0.072 4 41
spindle stabilization 0.015 0.029 0.14 8 -0.14 5 13
APC/C/HCDH1 0.018 0.015 -10000 0 -0.13 4 4
MKLP2/PLK1 0.083 0.09 0.2 173 -0.084 3 176
CCNB1 0.033 0.044 0.25 19 -10000 0 19
PPP1CB 0.026 0.004 -10000 0 -10000 0 0
BTRC 0.024 0.006 -10000 0 -10000 0 0
ROCK2 -0.004 0.1 0.18 8 -0.32 43 51
TUBG1 0.009 0.039 0.12 5 -0.16 18 23
G2/M transition of mitotic cell cycle 0.009 0.03 0.13 13 -0.16 2 15
MLF1IP 0.003 0.041 0.14 39 -10000 0 39
INCENP 0.025 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.02 0.063 0.19 5 -0.17 44 49
alphaV beta3 Integrin 0.007 0.088 0.19 1 -0.17 92 93
PTK2 -0.073 0.16 0.3 10 -0.34 100 110
IGF1R 0.026 0.01 0.24 1 -10000 0 1
PI4KB 0.025 0.006 -10000 0 -10000 0 0
MFGE8 0.025 0.004 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
CDKN1B -0.025 0.13 0.22 2 -0.36 54 56
VEGFA 0.026 0.023 0.24 5 -10000 0 5
ILK -0.021 0.13 0.22 1 -0.37 47 48
ROCK1 0.025 0.006 -10000 0 -10000 0 0
AKT1 -0.029 0.11 0.19 1 -0.34 48 49
PTK2B -0.036 0.054 0.17 4 -0.21 21 25
alphaV/beta3 Integrin/JAM-A 0.011 0.1 0.18 33 -0.15 110 143
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.058 0.099 0.19 137 -0.14 49 186
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.067 0.2 15 -0.15 37 52
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.04 0.1 0.16 2 -0.28 49 51
alphaV/beta3 Integrin/Syndecan-1 0.008 0.08 -10000 0 -0.14 102 102
PI4KA 0.025 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.004 0.1 0.22 1 -0.19 92 93
PI4 Kinase 0.036 0.01 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.029 0.089 0.19 52 -0.14 81 133
RPS6KB1 -0.051 0.093 0.4 5 -0.26 38 43
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.078 0.17 -10000 0 -0.37 107 107
GPR124 0.019 0.012 -10000 0 -10000 0 0
MAPK1 -0.081 0.17 -10000 0 -0.36 111 111
PXN 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.006 0.086 -10000 0 -0.16 101 101
cell adhesion 0.026 0.084 -10000 0 -0.17 47 47
ANGPTL3 0.11 0.11 0.24 193 -10000 0 193
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.06 0.19 5 -0.15 44 49
IGF-1R heterotetramer 0.026 0.01 0.24 1 -10000 0 1
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
TGFBR2 0.024 0.006 -10000 0 -10000 0 0
ITGB3 0.02 0.011 -10000 0 -10000 0 0
IGF1 0.031 0.041 0.24 17 -10000 0 17
RAC1 0.024 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.008 0.07 -10000 0 -0.13 86 86
apoptosis 0.025 0.005 -10000 0 -10000 0 0
CD47 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.014 0.072 -10000 0 -0.14 89 89
VCL 0.024 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.013 0.1 0.19 1 -0.18 124 125
CSF1 0.025 0.006 -10000 0 -10000 0 0
PIK3C2A -0.018 0.12 0.22 1 -0.37 44 45
PI4 Kinase/Pyk2 -0.059 0.069 0.096 21 -0.22 40 61
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.015 0.092 0.2 4 -0.15 107 111
FAK1/Vinculin -0.054 0.15 0.28 14 -0.3 94 108
alphaV beta3/Integrin/ppsTEM5 0.009 0.07 -10000 0 -0.13 86 86
RHOA 0.025 0.005 -10000 0 -10000 0 0
VTN 0.046 0.068 0.24 51 -10000 0 51
BCAR1 0.021 0.01 -10000 0 -10000 0 0
FGF2 0.024 0.013 0.24 1 -10000 0 1
F11R -0.016 0.01 0.14 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.014 0.074 -10000 0 -0.14 89 89
alphaV/beta3 Integrin/TGFBR2 0.012 0.077 -10000 0 -0.15 87 87
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.048 0.039 -10000 0 -0.13 11 11
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.015 0.066 -10000 0 -0.12 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.027 0.02 0.24 4 -10000 0 4
alphaV/beta3 Integrin/Pyk2 -0.006 0.073 0.17 2 -0.15 66 68
SDC1 0.024 0.006 -10000 0 -10000 0 0
VAV3 -0.023 0.04 0.19 7 -0.22 8 15
PTPN11 0.025 0.006 -10000 0 -10000 0 0
IRS1 0.025 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.054 0.14 0.29 11 -0.3 87 98
cell migration -0.063 0.13 0.25 11 -0.29 85 96
ITGAV 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.012 0.1 0.26 1 -0.16 93 94
SPP1 0.056 0.076 0.24 69 -10000 0 69
KDR 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.025 0.005 -10000 0 -10000 0 0
COL4A3 0.025 0.012 0.24 1 -10000 0 1
angiogenesis -0.088 0.18 0.24 3 -0.39 110 113
Rac1/GTP -0.029 0.048 0.19 8 -0.21 7 15
EDIL3 0.02 0.015 0.24 1 -10000 0 1
cell proliferation 0.012 0.077 -10000 0 -0.15 87 87
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.047 0.14 0.28 2 -0.42 56 58
CRKL -0.051 0.15 0.21 1 -0.43 57 58
HRAS -0.03 0.14 0.26 1 -0.4 54 55
mol:PIP3 -0.016 0.15 0.26 5 -0.39 51 56
SPRED1 0.025 0.005 -10000 0 -10000 0 0
SPRED2 0.025 0.004 -10000 0 -10000 0 0
GAB1 -0.048 0.16 -10000 0 -0.45 59 59
FOXO3 -0.02 0.15 0.29 6 -0.38 52 58
AKT1 -0.019 0.16 0.3 6 -0.41 53 59
BAD -0.016 0.15 0.32 13 -0.39 52 65
megakaryocyte differentiation -0.044 0.15 -10000 0 -0.43 58 58
GSK3B -0.014 0.15 0.34 9 -0.39 52 61
RAF1 -0.027 0.12 0.22 7 -0.33 53 60
SHC1 0.025 0.006 -10000 0 -10000 0 0
STAT3 -0.048 0.16 -10000 0 -0.44 59 59
STAT1 -0.11 0.34 -10000 0 -0.96 64 64
HRAS/SPRED1 -0.014 0.13 -10000 0 -0.34 52 52
cell proliferation -0.048 0.15 -10000 0 -0.44 59 59
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
TEC 0.025 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.03 0.17 0.26 2 -0.45 57 59
HRAS/SPRED2 -0.014 0.12 -10000 0 -0.34 53 53
LYN/TEC/p62DOK -0.009 0.15 -10000 0 -0.42 51 51
MAPK3 -0.013 0.099 0.26 17 -0.24 51 68
STAP1 -0.042 0.17 0.27 3 -0.46 59 62
GRAP2 0.026 0.015 0.24 2 -10000 0 2
JAK2 -0.095 0.29 -10000 0 -0.82 64 64
STAT1 (dimer) -0.11 0.34 -10000 0 -0.93 65 65
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.011 0.17 0.32 1 -0.45 56 57
actin filament polymerization -0.042 0.15 0.24 5 -0.43 52 57
LYN 0.022 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.066 0.23 0.33 2 -0.63 63 65
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.023 0.15 -10000 0 -0.4 55 55
PI3K -0.013 0.17 0.31 1 -0.44 55 56
PTEN 0.021 0.011 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.1 0.39 -10000 0 -1.1 57 57
MAPK8 -0.048 0.16 -10000 0 -0.45 58 58
STAT3 (dimer) -0.048 0.15 -10000 0 -0.44 59 59
positive regulation of transcription -0.009 0.086 0.23 18 -0.19 51 69
mol:GDP -0.027 0.15 0.26 2 -0.42 55 57
PIK3C2B -0.047 0.15 0.31 1 -0.44 60 61
CBL/CRKL -0.033 0.15 -10000 0 -0.41 56 56
FER -0.049 0.16 -10000 0 -0.44 61 61
SH2B3 -0.047 0.15 -10000 0 -0.44 60 60
PDPK1 -0.013 0.14 0.27 14 -0.36 49 63
SNAI2 -0.055 0.16 0.33 1 -0.47 59 60
positive regulation of cell proliferation -0.08 0.27 -10000 0 -0.74 64 64
KITLG 0.015 0.025 -10000 0 -10000 0 0
cell motility -0.08 0.27 -10000 0 -0.74 64 64
PTPN6 0.024 0.015 -10000 0 -10000 0 0
EPOR -0.007 0.13 -10000 0 -0.78 2 2
STAT5A (dimer) -0.066 0.23 -10000 0 -0.63 63 63
SOCS1 0.026 0.018 0.24 3 -10000 0 3
cell migration 0.019 0.15 0.41 58 -0.2 4 62
SOS1 0.025 0.005 -10000 0 -10000 0 0
EPO 0.027 0.054 0.24 25 -10000 0 25
VAV1 0.025 0.012 0.24 1 -10000 0 1
GRB10 -0.048 0.15 0.33 1 -0.42 59 60
PTPN11 0.024 0.013 -10000 0 -10000 0 0
SCF/KIT -0.044 0.16 -10000 0 -0.45 62 62
GO:0007205 0.003 0.008 -10000 0 -10000 0 0
MAP2K1 -0.022 0.1 0.26 16 -0.26 52 68
CBL 0.025 0.006 -10000 0 -10000 0 0
KIT -0.11 0.38 -10000 0 -1.1 58 58
MAP2K2 -0.022 0.1 0.26 16 -0.26 52 68
SHC/Grb2/SOS1 -0.008 0.16 -10000 0 -0.43 54 54
STAT5A -0.068 0.24 -10000 0 -0.65 63 63
GRB2 0.025 0.005 -10000 0 -10000 0 0
response to radiation -0.055 0.16 0.33 1 -0.46 59 60
SHC/GRAP2 0.031 0.037 0.19 2 -0.16 15 17
PTPRO -0.043 0.15 -10000 0 -0.44 56 56
SH2B2 -0.045 0.15 0.2 1 -0.43 54 55
DOK1 0.025 0.004 -10000 0 -10000 0 0
MATK -0.021 0.16 0.2 3 -0.41 58 61
CREBBP 0.015 0.056 0.16 10 -0.13 58 68
BCL2 -0.1 0.35 -10000 0 -1.2 35 35
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.065 0.18 136 -0.12 1 137
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.013 0.019 -10000 0 -0.3 1 1
AURKB 0.088 0.1 0.24 145 -10000 0 145
AURKC 0.027 0.017 0.24 3 -10000 0 3
EPHB forward signaling

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
Ephrin A5/EPHB2 0.018 0.052 0.17 3 -0.14 42 45
cell-cell adhesion 0.055 0.051 0.14 97 -10000 0 97
Ephrin B/EPHB2/RasGAP 0.039 0.073 0.2 10 -0.14 47 57
ITSN1 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.032 0.02 0.17 3 -0.13 4 7
Ephrin B1/EPHB1 -0.015 0.075 -10000 0 -0.13 137 137
HRAS/GDP -0.024 0.085 -10000 0 -0.19 57 57
Ephrin B/EPHB1/GRB7 -0.002 0.098 0.2 4 -0.14 150 154
Endophilin/SYNJ1 -0.025 0.051 0.19 9 -0.24 4 13
KRAS 0.024 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.002 0.097 0.2 4 -0.13 148 152
endothelial cell migration 0.043 0.035 0.17 11 -0.14 4 15
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.025 0.004 -10000 0 -10000 0 0
PAK1 -0.022 0.069 0.21 23 -0.27 4 27
HRAS 0.028 0.024 0.24 6 -10000 0 6
RRAS -0.027 0.05 0.17 8 -0.25 5 13
DNM1 0.025 0.012 0.24 1 -10000 0 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.042 0.078 0.2 21 -0.21 24 45
lamellipodium assembly -0.055 0.051 -10000 0 -0.14 97 97
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.053 0.11 -10000 0 -0.21 124 124
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
EPHB2 0.027 0.017 0.24 3 -10000 0 3
EPHB3 0.026 0.018 0.24 3 -10000 0 3
EPHB1 0.017 0.012 -10000 0 -10000 0 0
EPHB4 0.023 0.008 -10000 0 -10000 0 0
mol:GDP -0.036 0.072 0.17 14 -0.22 26 40
Ephrin B/EPHB2 0.031 0.066 0.18 11 -0.13 56 67
Ephrin B/EPHB3 0.032 0.062 0.18 12 -0.12 51 63
JNK cascade -0.042 0.084 0.31 18 -0.25 4 22
Ephrin B/EPHB1 -0.008 0.09 0.18 5 -0.13 152 157
RAP1/GDP -0.04 0.088 0.24 13 -0.22 31 44
EFNB2 0.031 0.04 0.24 16 -10000 0 16
EFNB3 0.019 0.012 -10000 0 -10000 0 0
EFNB1 0.026 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.001 0.079 0.18 10 -0.12 131 141
RAP1B 0.025 0.005 -10000 0 -10000 0 0
RAP1A 0.025 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.019 0.098 0.18 1 -0.19 74 75
Rap1/GTP -0.063 0.054 0.074 4 -0.21 23 27
axon guidance 0.017 0.051 0.17 3 -0.14 42 45
MAPK3 -0.06 0.094 0.18 3 -0.26 55 58
MAPK1 -0.061 0.094 0.18 2 -0.26 58 60
Rac1/GDP -0.045 0.078 0.27 5 -0.22 33 38
actin cytoskeleton reorganization -0.057 0.051 -10000 0 -0.17 47 47
CDC42/GDP -0.039 0.089 0.24 14 -0.22 33 47
PI3K 0.048 0.037 0.18 11 -0.14 4 15
EFNA5 0.022 0.014 0.24 1 -10000 0 1
Ephrin B2/EPHB4 0.034 0.026 0.17 13 -10000 0 13
Ephrin B/EPHB2/Intersectin/N-WASP -0.006 0.072 0.17 1 -0.19 57 58
CDC42 0.026 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.061 0.053 0.064 3 -0.21 22 25
PTK2 0.087 0.22 0.58 77 -10000 0 77
MAP4K4 -0.042 0.085 0.31 18 -0.25 4 22
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.025 0.016 0.24 2 -10000 0 2
Intersectin/N-WASP 0.034 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.046 0.099 0.3 21 -0.24 21 42
MAP2K1 -0.057 0.099 -10000 0 -0.26 61 61
WASL 0.024 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.006 0.09 0.2 2 -0.13 135 137
cell migration -0.073 0.13 0.29 11 -0.3 68 79
NRAS 0.025 0.004 -10000 0 -10000 0 0
SYNJ1 -0.026 0.051 0.19 9 -0.24 4 13
PXN 0.025 0.006 -10000 0 -10000 0 0
TF -0.033 0.055 0.16 3 -0.21 31 34
HRAS/GTP -0.013 0.084 0.15 3 -0.14 106 109
Ephrin B1/EPHB1-2 -0.003 0.08 0.18 2 -0.13 135 137
cell adhesion mediated by integrin 0.016 0.046 0.17 5 -0.21 5 10
RAC1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP -0.013 0.087 0.17 5 -0.14 110 115
RAC1-CDC42/GTP -0.061 0.053 -10000 0 -0.21 21 21
RASA1 0.024 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.048 0.075 0.29 3 -0.22 32 35
ruffle organization -0.028 0.12 0.33 33 -0.22 18 51
NCK1 0.024 0.007 -10000 0 -10000 0 0
receptor internalization -0.032 0.044 0.15 6 -0.23 5 11
Ephrin B/EPHB2/KALRN 0.042 0.071 0.2 13 -0.13 49 62
ROCK1 -0.008 0.044 0.18 24 -0.12 2 26
RAS family/GDP -0.056 0.05 -10000 0 -0.18 44 44
Rac1/GTP -0.057 0.054 -10000 0 -0.14 97 97
Ephrin B/EPHB1/Src/Paxillin -0.054 0.11 0.17 1 -0.21 154 155
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.032 0.059 0.17 1 -0.14 42 43
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.09 0.25 5 -0.23 29 34
AP1 -0.008 0.091 0.2 1 -0.15 119 120
mol:PIP3 -0.045 0.053 -10000 0 -0.16 70 70
AKT1 -0.004 0.089 0.32 17 -0.2 4 21
PTK2B -0.055 0.11 0.23 2 -0.23 121 123
RHOA 0.001 0.043 0.19 7 -0.26 4 11
PIK3CB 0.024 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.076 0.21 25 -0.23 14 39
MAGI3 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.006 -10000 0 -10000 0 0
apoptosis -0.02 0.073 -10000 0 -0.17 84 84
HRAS/GDP 0.021 0.017 0.17 6 -10000 0 6
positive regulation of microtubule depolymerization -0.049 0.11 0.25 12 -0.26 58 70
NF kappa B1 p50/RelA -0.008 0.084 -10000 0 -0.2 57 57
endothelial cell migration -0.021 0.055 0.27 1 -0.3 12 13
ADCY4 -0.032 0.12 0.22 3 -0.36 48 51
ADCY5 -0.044 0.15 0.22 2 -0.42 55 57
ADCY6 -0.031 0.12 0.22 4 -0.36 48 52
ADCY7 -0.027 0.12 0.22 4 -0.35 44 48
ADCY1 -0.03 0.12 0.22 2 -0.37 45 47
ADCY2 -0.035 0.13 0.22 4 -0.37 52 56
ADCY3 -0.031 0.12 0.22 4 -0.35 49 53
ADCY8 -0.029 0.11 -10000 0 -0.35 42 42
ADCY9 -0.032 0.12 0.22 3 -0.36 48 51
GSK3B -0.05 0.11 0.25 11 -0.22 110 121
arachidonic acid secretion -0.043 0.12 -10000 0 -0.36 53 53
GNG2 0.025 0.008 -10000 0 -0.057 1 1
TRIP6 0.011 0.029 -10000 0 -0.23 6 6
GNAO1 -0.02 0.056 0.12 1 -0.26 22 23
HRAS 0.028 0.024 0.24 6 -10000 0 6
NFKBIA -0.024 0.099 0.33 10 -0.22 47 57
GAB1 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0 0.19 -10000 0 -0.8 25 25
JUN 0.025 0.011 0.24 1 -10000 0 1
LPA/LPA2/NHERF2 0.034 0.022 0.17 5 -0.1 4 9
TIAM1 -0.016 0.21 -10000 0 -0.93 25 25
PIK3R1 0.023 0.01 -10000 0 -0.058 1 1
mol:IP3 -0.019 0.069 0.18 23 -0.23 13 36
PLCB3 -0.01 0.04 0.18 20 -10000 0 20
FOS 0.023 0.022 0.24 4 -10000 0 4
positive regulation of mitosis -0.043 0.12 -10000 0 -0.36 53 53
LPA/LPA1-2-3 0.015 0.078 0.18 5 -0.14 86 91
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.01 -10000 0 -10000 0 0
stress fiber formation -0.029 0.1 0.29 9 -0.28 38 47
GNAZ -0.024 0.054 0.12 1 -0.2 36 37
EGFR/PI3K-beta/Gab1 -0.044 0.057 -10000 0 -0.2 36 36
positive regulation of dendritic cell cytokine production 0.014 0.077 0.18 5 -0.14 86 91
LPA/LPA2/MAGI-3 0.033 0.018 -10000 0 -0.1 4 4
ARHGEF1 -0.008 0.074 0.19 47 -0.2 7 54
GNAI2 -0.022 0.041 0.12 1 -0.15 40 41
GNAI3 -0.023 0.042 0.12 1 -0.15 41 42
GNAI1 -0.02 0.04 0.12 1 -0.16 32 33
LPA/LPA3 -0.003 0.062 0.17 7 -0.15 70 77
LPA/LPA2 0.018 0.016 -10000 0 -0.12 4 4
LPA/LPA1 0.005 0.059 0.16 1 -0.18 43 44
HB-EGF/EGFR 0.054 0.07 0.12 207 -0.14 20 227
HBEGF 0.068 0.084 0.14 256 -10000 0 256
mol:DAG -0.019 0.069 0.18 23 -0.23 13 36
cAMP biosynthetic process -0.031 0.14 0.29 15 -0.36 54 69
NFKB1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
LYN -0.011 0.11 0.3 23 -0.23 41 64
GNAQ -0.01 0.055 0.093 1 -0.15 59 60
LPAR2 0.026 0.003 -10000 0 -10000 0 0
LPAR3 0.025 0.028 0.24 7 -10000 0 7
LPAR1 0.018 0.043 -10000 0 -0.28 9 9
IL8 -0.017 0.18 0.38 21 -0.39 71 92
PTK2 -0.028 0.047 0.17 6 -0.2 8 14
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
CASP3 -0.021 0.074 -10000 0 -0.17 84 84
EGFR 0.021 0.01 -10000 0 -10000 0 0
PLCG1 -0.019 0.062 0.15 1 -0.18 55 56
PLD2 -0.032 0.061 0.18 13 -0.21 16 29
G12/G13 0.033 0.052 0.18 1 -0.14 33 34
PI3K-beta 0.004 0.046 -10000 0 -0.2 12 12
cell migration -0.009 0.062 -10000 0 -0.25 22 22
SLC9A3R2 0.027 0.023 0.24 5 -10000 0 5
PXN -0.029 0.1 0.3 8 -0.28 39 47
HRAS/GTP -0.044 0.13 0.12 1 -0.37 52 53
RAC1 0.024 0.008 -10000 0 -10000 0 0
MMP9 0.14 0.11 0.24 258 -10000 0 258
PRKCE 0.024 0.008 -10000 0 -10000 0 0
PRKCD -0.02 0.082 0.22 26 -0.24 15 41
Gi(beta/gamma) -0.032 0.12 0.14 6 -0.34 50 56
mol:LPA -0.001 0.014 0.071 1 -0.086 10 11
TRIP6/p130 Cas/FAK1/Paxillin -0.012 0.08 -10000 0 -0.26 19 19
MAPKKK cascade -0.043 0.12 -10000 0 -0.36 53 53
contractile ring contraction involved in cytokinesis 0.002 0.044 0.2 8 -0.26 4 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.01 0.055 0.09 6 -0.15 60 66
GNA15 -0.011 0.059 0.093 1 -0.16 58 59
GNA12 0.023 0.008 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.05 0.11 0.25 12 -0.26 59 71
GNA11 -0.011 0.06 0.09 6 -0.16 58 64
Rac1/GTP -0.001 0.2 -10000 0 -0.86 24 24
MMP2 -0.021 0.055 0.27 1 -0.3 12 13
Signaling events mediated by the Hedgehog family

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
TGFB2 0.004 0.1 0.28 3 -0.44 20 23
IHH 0.042 0.059 0.23 32 -0.11 14 46
SHH Np/Cholesterol/GAS1 -0.006 0.069 0.11 37 -0.13 93 130
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.006 0.068 0.13 93 -0.11 37 130
SMO/beta Arrestin2 0.012 0.092 -10000 0 -0.31 22 22
SMO -0.003 0.081 -10000 0 -0.3 25 25
AKT1 -0.003 0.092 -10000 0 -0.36 16 16
ARRB2 0.024 0.007 -10000 0 -10000 0 0
BOC 0.024 0.006 -10000 0 -10000 0 0
ADRBK1 0.025 0.006 -10000 0 -10000 0 0
heart looping -0.003 0.081 -10000 0 -0.3 25 25
STIL -0.01 0.09 0.19 36 -0.25 19 55
DHH N/PTCH2 0.037 0.032 0.19 7 -0.16 8 15
DHH N/PTCH1 0.018 0.07 -10000 0 -0.21 34 34
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DHH 0.027 0.018 0.24 3 -10000 0 3
PTHLH -0.008 0.14 0.35 2 -0.57 20 22
determination of left/right symmetry -0.003 0.081 -10000 0 -0.3 25 25
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
skeletal system development -0.008 0.13 0.35 2 -0.57 20 22
IHH N/Hhip 0.022 0.09 0.17 32 -0.21 53 85
DHH N/Hhip 0.019 0.064 0.19 6 -0.16 51 57
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.003 0.081 -10000 0 -0.3 25 25
pancreas development 0.024 0.019 0.24 3 -10000 0 3
HHAT 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.03 0.028 -10000 0 -0.18 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.023 0.014 0.24 1 -10000 0 1
somite specification -0.003 0.081 -10000 0 -0.3 25 25
SHH Np/Cholesterol/PTCH1 -0.004 0.079 0.16 6 -0.23 29 35
SHH Np/Cholesterol/PTCH2 0.004 0.062 0.11 44 -0.12 70 114
SHH Np/Cholesterol/Megalin -0.004 0.069 0.12 44 -0.13 90 134
SHH 0 0.046 0.14 43 -10000 0 43
catabolic process 0.005 0.072 0.19 1 -0.24 34 35
SMO/Vitamin D3 -0.005 0.088 0.28 2 -0.28 24 26
SHH Np/Cholesterol/Hhip -0.005 0.074 0.11 43 -0.14 88 131
LRP2 0.026 0.031 0.24 9 -10000 0 9
receptor-mediated endocytosis -0.019 0.093 0.23 1 -0.29 27 28
SHH Np/Cholesterol/BOC 0.002 0.061 0.11 41 -0.12 75 116
SHH Np/Cholesterol/CDO 0.005 0.059 0.11 44 -0.12 69 113
mesenchymal cell differentiation 0.005 0.074 0.14 88 -0.11 43 131
mol:Vitamin D3 0.005 0.091 0.19 26 -0.26 21 47
IHH N/PTCH2 0.039 0.059 0.17 33 -0.16 22 55
CDON 0.026 0.018 0.24 3 -10000 0 3
IHH N/PTCH1 0.019 0.081 0.26 3 -0.24 34 37
Megalin/LRPAP1 0.023 0.058 0.19 9 -0.16 39 48
PTCH2 0.027 0.02 0.24 4 -10000 0 4
SHH Np/Cholesterol -0.019 0.047 0.072 43 -0.12 71 114
PTCH1 0.005 0.073 0.19 1 -0.24 34 35
HHIP 0.024 0.019 0.24 3 -10000 0 3
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.023 0.071 0.27 6 -0.15 21 27
alphaM/beta2 Integrin/GPIbA 0.024 0.071 0.3 6 -0.16 13 19
alphaM/beta2 Integrin/proMMP-9 0.1 0.11 0.2 207 -0.16 12 219
PLAUR 0.029 0.028 0.24 8 -10000 0 8
HMGB1 0.009 0.038 0.1 1 -0.059 106 107
alphaM/beta2 Integrin/Talin 0.027 0.065 0.27 5 -0.12 15 20
AGER 0.018 0.061 0.24 20 -0.06 107 127
RAP1A 0.025 0.004 -10000 0 -10000 0 0
SELPLG 0.027 0.025 0.24 6 -10000 0 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.024 0.13 0.32 16 -0.19 104 120
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.14 0.11 0.24 258 -10000 0 258
CYR61 0.028 0.027 0.24 7 -10000 0 7
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.098 0.22 1 -0.24 35 36
RHOA 0.025 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.024 0.006 -10000 0 -10000 0 0
MYH2 -0.018 0.11 0.19 9 -0.28 39 48
MST1R 0.026 0.021 0.24 4 -10000 0 4
leukocyte activation during inflammatory response -0.015 0.096 0.18 7 -0.15 128 135
APOB 0.02 0.018 0.24 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.023 0.013 0.24 1 -10000 0 1
JAM3 0.024 0.006 -10000 0 -10000 0 0
GP1BA 0.025 0.019 0.24 3 -10000 0 3
alphaM/beta2 Integrin/CTGF 0.021 0.075 0.24 7 -0.15 32 39
alphaM/beta2 Integrin -0.01 0.1 0.19 15 -0.26 37 52
JAM3 homodimer 0.024 0.006 -10000 0 -10000 0 0
ICAM2 0.026 0.011 0.24 1 -10000 0 1
ICAM1 0.03 0.033 0.24 11 -10000 0 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.01 0.1 0.19 15 -0.26 36 51
cell adhesion 0.024 0.07 0.3 6 -0.16 13 19
NFKB1 -0.046 0.18 0.37 22 -0.31 109 131
THY1 0.028 0.028 0.24 8 -10000 0 8
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.088 0.17 8 -0.15 145 153
alphaM/beta2 Integrin/LRP/tPA 0.032 0.072 0.24 10 -0.18 9 19
IL6 -0.077 0.25 0.33 54 -0.5 103 157
ITGB2 0.012 0.046 0.26 5 -0.068 34 39
elevation of cytosolic calcium ion concentration 0.032 0.08 0.28 11 -0.16 17 28
alphaM/beta2 Integrin/JAM2/JAM3 0.031 0.079 0.29 4 -0.17 22 26
JAM2 0.025 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.059 0.09 0.24 29 -0.15 11 40
alphaM/beta2 Integrin/uPA/Plg 0.036 0.08 0.22 20 -0.16 16 36
RhoA/GTP -0.017 0.11 0.2 14 -0.29 37 51
positive regulation of phagocytosis -0.005 0.095 0.29 4 -0.25 23 27
Ron/MSP 0.051 0.059 0.19 58 -0.16 10 68
alphaM/beta2 Integrin/uPAR/uPA 0.034 0.081 0.28 11 -0.16 17 28
alphaM/beta2 Integrin/uPAR 0.029 0.072 0.25 13 -0.12 16 29
PLAU 0.025 0.012 0.24 1 -10000 0 1
PLAT 0.025 0.036 0.24 12 -10000 0 12
actin filament polymerization -0.02 0.11 0.2 10 -0.27 40 50
MST1 0.05 0.07 0.24 56 -10000 0 56
alphaM/beta2 Integrin/lipoprotein(a) -0.012 0.099 0.2 7 -0.15 128 135
TNF -0.058 0.19 0.4 19 -0.35 103 122
RAP1B 0.025 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.023 0.073 0.29 5 -0.17 17 22
fibrinolysis 0.035 0.079 0.22 20 -0.16 16 36
HCK 0.025 0.011 0.24 1 -10000 0 1
dendritic cell antigen processing and presentation -0.01 0.1 0.19 15 -0.26 36 51
VTN 0.046 0.068 0.24 51 -10000 0 51
alphaM/beta2 Integrin/CYR61 0.026 0.074 0.24 12 -0.14 23 35
LPA 0.025 0.028 0.24 7 -10000 0 7
LRP1 0.026 0.011 0.24 1 -10000 0 1
cell migration 0.061 0.087 0.2 38 -0.17 13 51
FN1 0.027 0.02 0.24 4 -10000 0 4
alphaM/beta2 Integrin/Thy1 0.028 0.071 0.23 13 -0.13 16 29
MPO 0.023 0.008 -10000 0 -10000 0 0
KNG1 0.045 0.073 0.24 58 -10000 0 58
RAP1/GDP 0.033 0.009 -10000 0 -10000 0 0
ROCK1 -0.02 0.11 0.19 10 -0.28 35 45
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.047 0.24 23 -10000 0 23
CTGF 0.025 0.012 0.24 1 -10000 0 1
alphaM/beta2 Integrin/Hck 0.026 0.07 0.29 5 -0.14 19 24
ITGAM 0.01 0.043 0.22 3 -0.06 112 115
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.034 0.078 0.32 7 -0.18 12 19
HP 0.043 0.069 0.24 51 -10000 0 51
leukocyte adhesion 0.007 0.12 0.28 14 -0.23 36 50
SELP 0.024 0.006 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.045 0.17 0.33 1 -0.42 58 59
MAP3K8 0.02 0.018 0.24 1 -10000 0 1
FOS -0.037 0.14 0.24 2 -0.34 55 57
PRKCA 0.017 0.019 -10000 0 -0.039 1 1
PTPN7 0.026 0.052 0.24 22 -0.034 72 94
HRAS 0.028 0.025 0.24 6 -0.023 1 7
PRKCB 0.015 0.018 -10000 0 -0.032 2 2
NRAS 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.033 0.17 6 -10000 0 6
MAPK3 -0.009 0.091 -10000 0 -0.47 4 4
MAP2K1 -0.077 0.19 -10000 0 -0.39 107 107
ELK1 0.016 0.024 -10000 0 -0.04 40 40
BRAF -0.06 0.16 -10000 0 -0.37 89 89
mol:GTP -0.001 0.002 0.003 4 -0.004 84 88
MAPK1 -0.014 0.1 -10000 0 -0.45 12 12
RAF1 -0.067 0.16 -10000 0 -0.36 101 101
KRAS 0.024 0.008 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.043 0.2 0.6 18 -0.52 6 24
CRP 0.052 0.22 0.6 30 -0.52 6 36
cell cycle arrest 0.042 0.21 0.61 22 -0.56 8 30
TIMP1 0.042 0.21 0.56 19 -0.7 11 30
IL6ST 0.019 0.027 0.13 4 -0.066 6 10
Rac1/GDP -0.024 0.17 0.35 18 -0.35 66 84
AP1 0.031 0.13 0.38 4 -0.48 13 17
GAB2 0.024 0.008 -10000 0 -10000 0 0
TNFSF11 0.041 0.21 0.6 20 -0.65 9 29
HSP90B1 0.04 0.1 0.51 2 -0.59 5 7
GAB1 0.025 0.007 -10000 0 -10000 0 0
MAPK14 -0.09 0.23 0.33 7 -0.53 86 93
AKT1 0.02 0.064 0.32 1 -0.46 4 5
FOXO1 0.013 0.061 0.3 1 -0.44 4 5
MAP2K6 -0.061 0.19 0.27 17 -0.42 87 104
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.01 0.18 0.39 28 -0.36 54 82
MITF -0.035 0.16 0.27 26 -0.34 76 102
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.003 -10000 0 -10000 0 0
A2M -0.058 0.3 -10000 0 -1.1 35 35
CEBPB 0.029 0.009 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.007 0.1 0.32 3 -0.43 11 14
STAT3 0.033 0.21 0.61 22 -0.59 8 30
STAT1 0.022 0.082 0.35 1 -0.85 3 4
CEBPD 0.063 0.21 0.64 23 -0.6 2 25
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.031 0.028 -10000 0 -0.18 6 6
JUN 0.026 0.011 0.24 1 -10000 0 1
PIAS3/MITF -0.029 0.17 0.3 19 -0.33 77 96
MAPK11 -0.091 0.23 0.34 6 -0.53 85 91
STAT3 (dimer)/FOXO1 0.025 0.17 0.51 21 -0.51 2 23
GRB2/SOS1/GAB family -0.018 0.15 0.29 7 -0.29 82 89
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.035 0.15 0.23 19 -0.28 98 117
GRB2 0.025 0.008 -10000 0 -10000 0 0
JAK2 0.025 0.005 -10000 0 -10000 0 0
LBP 0.056 0.2 0.57 29 -0.55 4 33
PIK3R1 0.024 0.008 -10000 0 -10000 0 0
JAK1 0.021 0.025 0.11 1 -0.073 3 4
MYC 0.079 0.22 0.59 36 -0.6 2 38
FGG 0.043 0.21 0.59 24 -0.52 6 30
macrophage differentiation 0.042 0.21 0.61 22 -0.56 8 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.13 0.27 22 -0.21 72 94
JUNB 0.03 0.23 0.59 19 -0.88 11 30
FOS 0.023 0.023 0.24 4 -10000 0 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.026 0.17 0.31 26 -0.36 74 100
STAT1/PIAS1 0.004 0.16 0.35 27 -0.33 35 62
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.066 -10000 0 -0.44 5 5
STAT3 (dimer) 0.038 0.22 0.61 22 -0.58 8 30
PRKCD 0.014 0.2 0.45 34 -0.46 22 56
IL6R 0.019 0.023 0.1 2 -0.06 3 5
SOCS3 -0.15 0.36 0.34 6 -0.98 67 73
gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.085 0.22 6 -0.14 71 77
Rac1/GTP -0.018 0.18 0.35 24 -0.35 64 88
HCK 0.025 0.011 0.24 1 -10000 0 1
MAPKKK cascade 0.018 0.11 0.34 1 -0.52 11 12
bone resorption 0.042 0.2 0.59 20 -0.61 9 29
IRF1 0.044 0.21 0.64 19 -0.6 2 21
mol:GDP -0.034 0.17 0.29 26 -0.35 75 101
SOS1 0.025 0.008 -10000 0 -10000 0 0
VAV1 -0.035 0.17 0.3 26 -0.35 75 101
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.095 0.25 0.3 5 -0.55 93 98
PTPN11 0.014 0.089 -10000 0 -0.67 7 7
IL6/IL6RA 0.005 0.11 0.22 43 -0.17 110 153
gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.078 0.2 2 -0.14 77 79
gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.078 0.2 2 -0.14 77 79
IL6 0.045 0.075 0.27 46 -10000 0 46
PIAS3 0.025 0.005 -10000 0 -10000 0 0
PTPRE 0.007 0.038 0.1 1 -0.11 17 18
PIAS1 0.026 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.032 0.14 0.21 20 -0.25 113 133
LMO4 0.025 0.034 0.16 4 -0.12 5 9
STAT3 (dimer)/PIAS3 0.02 0.2 0.57 16 -0.56 9 25
MCL1 0.023 0.08 0.4 3 -0.73 1 4
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.039 0.21 0.55 27 -0.58 9 36
PCK1 0.065 0.2 0.56 30 -0.67 5 35
HNF4A 0.052 0.28 0.77 27 -0.74 18 45
KCNJ11 0.053 0.23 0.57 28 -0.61 8 36
AKT1 0.071 0.15 0.44 28 -0.32 2 30
response to starvation 0.006 0.036 0.12 18 -0.14 9 27
DLK1 0.033 0.28 0.6 26 -0.68 31 57
NKX2-1 0.018 0.14 0.36 28 -0.33 6 34
ACADM 0.036 0.21 0.54 26 -0.59 9 35
TAT 0.051 0.2 0.64 23 -0.56 7 30
CEBPB 0.035 0.032 0.14 12 -0.073 12 24
CEBPA 0.043 0.038 0.17 12 -0.067 10 22
TTR 0.11 0.32 0.59 54 -1 19 73
PKLR 0.058 0.24 0.61 37 -0.6 8 45
APOA1 0.033 0.36 0.87 26 -1.1 20 46
CPT1C 0.037 0.23 0.55 27 -0.68 12 39
ALAS1 0.035 0.16 0.51 11 -0.56 1 12
TFRC 0.069 0.23 0.63 27 -0.61 10 37
FOXF1 0.02 0.011 -10000 0 -10000 0 0
NF1 0.028 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.058 0.08 0.25 62 -0.17 2 64
CPT1A 0.048 0.22 0.56 30 -0.59 8 38
HMGCS1 0.044 0.22 0.56 26 -0.6 8 34
NR3C1 0.036 0.036 0.21 12 -10000 0 12
CPT1B 0.062 0.24 0.56 39 -0.59 9 48
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.023 0.14 1 -0.17 2 3
GCK 0.034 0.25 0.54 33 -0.66 20 53
CREB1 0.039 0.035 0.18 9 -0.2 1 10
IGFBP1 0.042 0.18 0.57 25 -0.56 2 27
PDX1 0.058 0.19 0.56 20 -1.2 2 22
UCP2 0.045 0.22 0.56 27 -0.62 9 36
ALDOB 0.071 0.26 0.74 31 -0.64 6 37
AFP 0.06 0.11 0.32 39 -0.26 1 40
BDH1 0.046 0.21 0.56 26 -0.59 9 35
HADH 0.051 0.22 0.57 22 -0.66 5 27
F2 0.05 0.31 0.85 26 -0.83 8 34
HNF1A 0.058 0.08 0.25 62 -0.17 2 64
G6PC 0.062 0.12 0.49 17 -10000 0 17
SLC2A2 0.07 0.2 0.68 24 -0.49 2 26
INS -0.017 0.047 0.24 11 -0.12 27 38
FOXA1 0.088 0.091 0.25 85 -0.23 2 87
FOXA3 0.097 0.11 0.32 67 -0.25 6 73
FOXA2 0.091 0.32 0.83 37 -0.67 10 47
ABCC8 0.011 0.3 0.58 26 -0.64 50 76
ALB 0.081 0.14 0.32 64 -0.73 2 66
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.013 0.032 -10000 0 -0.32 3 3
Crk/p130 Cas/Paxillin -0.037 0.072 -10000 0 -0.21 55 55
JUN -0.019 0.075 0.14 6 -0.27 22 28
HRAS 0.028 0.024 0.24 6 -10000 0 6
RET51/GFRalpha1/GDNF/GRB10 0.051 0.084 0.19 61 -0.15 46 107
RAP1A 0.025 0.004 -10000 0 -10000 0 0
FRS2 0.025 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.054 0.089 0.19 71 -0.15 53 124
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.023 0.066 0.18 3 -0.14 59 62
RHOA 0.025 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.043 0.079 -10000 0 -0.14 52 52
GRB7 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.054 0.088 0.19 71 -0.15 52 123
MAPKKK cascade 0.016 0.073 0.17 2 -0.18 43 45
BCAR1 0.021 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.022 0.065 0.18 1 -0.14 65 66
lamellipodium assembly -0.01 0.078 -10000 0 -0.21 47 47
RET51/GFRalpha1/GDNF/SHC 0.052 0.088 0.19 69 -0.14 51 120
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.024 0.058 0.18 1 -0.13 55 56
RET9/GFRalpha1/GDNF/Shank3 0.025 0.058 0.18 1 -0.13 57 58
MAPK3 -0.017 0.073 0.23 19 -0.21 10 29
DOK1 0.025 0.004 -10000 0 -10000 0 0
DOK6 0.028 0.038 0.24 14 -10000 0 14
PXN 0.025 0.006 -10000 0 -10000 0 0
neurite development -0.017 0.063 0.21 14 -0.2 9 23
DOK5 0.028 0.03 0.24 9 -10000 0 9
GFRA1 0.023 0.013 0.24 1 -10000 0 1
MAPK8 -0.01 0.075 0.16 6 -0.26 20 26
HRAS/GTP 0.042 0.093 0.27 2 -0.18 45 47
tube development 0.023 0.059 0.2 10 -0.13 55 65
MAPK1 -0.016 0.075 0.23 22 -0.21 11 33
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.005 0.059 -10000 0 -0.17 53 53
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
PDLIM7 0.026 0.015 0.24 2 -10000 0 2
RET51/GFRalpha1/GDNF/Dok6 0.053 0.092 -10000 0 -0.14 55 55
SHC1 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.05 0.09 0.19 67 -0.15 52 119
RET51/GFRalpha1/GDNF/Dok5 0.051 0.1 0.2 73 -0.16 58 131
PRKCA 0.024 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.017 0.17 6 -10000 0 6
CREB1 -0.006 0.08 -10000 0 -0.24 31 31
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.006 0.062 -10000 0 -0.18 53 53
RET51/GFRalpha1/GDNF/Grb7 0.054 0.088 0.19 70 -0.14 53 123
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.061 0.082 0.24 81 -10000 0 81
DOK4 0.023 0.008 -10000 0 -10000 0 0
JNK cascade -0.019 0.074 0.17 1 -0.26 22 23
RET9/GFRalpha1/GDNF/FRS2 0.025 0.057 0.18 1 -0.13 54 55
SHANK3 0.025 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.007 -10000 0 -10000 0 0
NCK1 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.062 -10000 0 -0.18 53 53
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.075 0.17 1 -0.18 53 54
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.005 0.081 0.17 6 -0.2 50 56
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.006 0.078 0.17 3 -0.19 52 55
PI3K -0.015 0.11 0.23 4 -0.29 52 56
SOS1 0.025 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.034 0.061 0.18 1 -0.13 55 56
GRB10 0.024 0.008 -10000 0 -10000 0 0
activation of MAPKK activity 0 0.074 0.17 1 -0.19 49 50
RET51/GFRalpha1/GDNF/FRS2 0.054 0.086 0.19 69 -0.14 50 119
GAB1 0.025 0.004 -10000 0 -10000 0 0
IRS1 0.025 0.005 -10000 0 -10000 0 0
IRS2 0.026 0.018 0.24 3 -10000 0 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.006 0.079 0.17 4 -0.19 53 57
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.095 0.19 67 -0.16 59 126
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GDNF 0.023 0.007 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.051 0.093 0.19 70 -0.15 59 129
Rac1/GTP -0.009 0.092 -10000 0 -0.25 47 47
RET9/GFRalpha1/GDNF 0.012 0.057 0.17 1 -0.14 57 58
GFRalpha1/GDNF 0.012 0.068 0.19 1 -0.17 57 58
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.004 -10000 0 -10000 0 0
CCL5 0.028 0.026 0.24 7 -10000 0 7
SDCBP 0.021 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.032 0.11 0.24 24 -0.29 18 42
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.035 0.11 0.23 24 -0.28 20 44
Syndecan-1/Syntenin 0.033 0.1 0.23 19 -0.28 16 35
MAPK3 0.026 0.1 0.21 28 -0.27 19 47
HGF/MET 0.014 0.076 0.19 9 -0.19 49 58
TGFB1/TGF beta receptor Type II 0.025 0.004 -10000 0 -10000 0 0
BSG 0.026 0.01 0.24 1 -10000 0 1
keratinocyte migration 0.035 0.11 0.22 24 -0.28 20 44
Syndecan-1/RANTES 0.039 0.12 0.24 31 -0.28 24 55
Syndecan-1/CD147 0.049 0.12 0.24 29 -0.28 20 49
Syndecan-1/Syntenin/PIP2 0.029 0.096 0.21 17 -0.26 16 33
LAMA5 0.025 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.028 0.094 0.21 17 -0.26 16 33
MMP7 0.045 0.068 0.24 50 -10000 0 50
HGF 0.026 0.031 0.24 9 -10000 0 9
Syndecan-1/CASK 0.018 0.099 0.19 16 -0.27 21 37
Syndecan-1/HGF/MET 0.029 0.12 0.22 17 -0.28 35 52
regulation of cell adhesion 0.013 0.1 0.2 28 -0.27 19 47
HPSE 0.028 0.029 0.24 8 -10000 0 8
positive regulation of cell migration 0.032 0.11 0.24 24 -0.29 18 42
SDC1 0.029 0.1 0.23 19 -0.3 17 36
Syndecan-1/Collagen 0.032 0.11 0.24 24 -0.29 18 42
PPIB 0.027 0.017 0.24 3 -10000 0 3
MET 0.021 0.01 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
MMP9 0.14 0.11 0.24 258 -10000 0 258
MAPK1 0.026 0.1 0.21 29 -0.27 20 49
homophilic cell adhesion 0.032 0.11 0.24 27 -0.29 19 46
MMP1 0.049 0.073 0.24 60 -10000 0 60
Ephrin B reverse signaling

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
EFNB2 0.031 0.04 0.24 16 -10000 0 16
EPHB2 0.027 0.018 0.24 3 -10000 0 3
EFNB1 -0.017 0.012 0.14 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.083 -10000 0 -0.13 109 109
Ephrin B2/EPHB1-2 0.001 0.078 0.18 10 -0.12 131 141
neuron projection morphogenesis -0.005 0.07 -10000 0 -0.12 111 111
Ephrin B1/EPHB1-2/Tiam1 0.001 0.082 0.18 2 -0.13 120 122
DNM1 0.025 0.012 0.24 1 -10000 0 1
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.051 0.2 1 -0.43 7 8
YES1 0.001 0.084 -10000 0 -0.64 8 8
Ephrin B1/EPHB1-2/NCK2 0.002 0.08 0.18 2 -0.13 119 121
PI3K 0.027 0.064 -10000 0 -0.46 7 7
mol:GDP -0.002 0.079 0.17 2 -0.13 121 123
ITGA2B 0.026 0.023 0.24 5 -10000 0 5
endothelial cell proliferation 0.033 0.025 0.17 13 -10000 0 13
FYN 0.001 0.082 -10000 0 -0.66 7 7
MAP3K7 -0.006 0.051 -10000 0 -0.46 6 6
FGR 0.004 0.084 -10000 0 -0.63 8 8
TIAM1 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
RGS3 0.024 0.006 -10000 0 -10000 0 0
cell adhesion -0.014 0.075 -10000 0 -0.44 8 8
LYN 0.002 0.083 -10000 0 -0.64 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.081 -10000 0 -0.63 8 8
Ephrin B1/EPHB1-2 -0.003 0.059 -10000 0 -0.49 7 7
SRC 0.005 0.083 -10000 0 -0.63 8 8
ITGB3 0.02 0.011 -10000 0 -10000 0 0
EPHB1 0.017 0.012 -10000 0 -10000 0 0
EPHB4 0.023 0.008 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.026 0.17 13 -10000 0 13
alphaIIb/beta3 Integrin -0.003 0.079 0.19 2 -0.16 98 100
BLK -0.014 0.1 -10000 0 -0.65 8 8
HCK 0.002 0.084 -10000 0 -0.64 8 8
regulation of stress fiber formation 0.001 0.077 0.13 119 -0.17 2 121
MAPK8 -0.012 0.058 0.2 4 -0.41 8 12
Ephrin B1/EPHB1-2/RGS3 0 0.079 0.18 2 -0.13 120 122
endothelial cell migration 0.001 0.065 0.2 25 -0.37 7 32
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.008 -10000 0 -10000 0 0
regulation of focal adhesion formation 0.001 0.077 0.13 119 -0.17 2 121
chemotaxis 0.001 0.078 0.13 120 -0.17 2 122
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.001 0.075 0.15 2 -0.13 110 112
angiogenesis -0.003 0.059 -10000 0 -0.49 7 7
LCK 0.006 0.084 -10000 0 -0.63 8 8
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 0.011 0.066 0.18 5 -0.17 44 49
PDGFRB 0.017 0.024 0.24 2 -10000 0 2
SPHK1 -0.006 0.085 -10000 0 -0.63 7 7
mol:S1P -0.012 0.082 0.34 1 -0.53 7 8
S1P1/S1P/Gi -0.099 0.19 0.19 3 -0.37 133 136
GNAO1 0.014 0.019 -10000 0 -0.038 1 1
PDGFB-D/PDGFRB/PLCgamma1 -0.078 0.18 0.24 3 -0.37 109 112
PLCG1 -0.096 0.17 0.18 4 -0.38 111 115
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.024 0.24 2 -10000 0 2
GNAI2 0.016 0.022 -10000 0 -0.042 1 1
GNAI3 0.016 0.022 -10000 0 -0.039 1 1
GNAI1 0.016 0.023 0.24 1 -0.039 1 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.027 0.04 0.084 5 -0.14 44 49
S1P1/S1P -0.033 0.085 0.23 2 -0.29 20 22
negative regulation of cAMP metabolic process -0.096 0.18 0.19 3 -0.36 133 136
MAPK3 -0.13 0.24 0.24 4 -0.53 112 116
calcium-dependent phospholipase C activity -0.002 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
KDR 0.017 0.019 -10000 0 -0.059 1 1
PLCB2 -0.027 0.084 0.26 6 -0.27 18 24
RAC1 0.024 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.073 -10000 0 -0.25 22 22
receptor internalization -0.032 0.078 0.15 4 -0.27 21 25
PTGS2 -0.19 0.36 0.36 1 -0.89 97 98
Rac1/GTP -0.025 0.071 -10000 0 -0.25 20 20
RHOA 0.025 0.005 -10000 0 -10000 0 0
VEGFA 0.02 0.029 0.24 5 -0.035 1 6
negative regulation of T cell proliferation -0.096 0.18 0.19 3 -0.36 133 136
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.02 -10000 0 -10000 0 0
MAPK1 -0.13 0.24 0.23 3 -0.54 113 116
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.098 0.25 5 -0.25 36 41
ABCC1 0.016 0.02 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.027 0.14 0.33 31 -0.36 27 58
FYN 0.009 0.17 0.34 39 -0.43 32 71
LAT/GRAP2/SLP76 0.021 0.14 0.34 27 -0.36 30 57
IKBKB 0.02 0.011 -10000 0 -10000 0 0
AKT1 0.017 0.14 0.34 42 -0.32 30 72
B2M 0.026 0.01 -10000 0 -10000 0 0
IKBKG -0.001 0.052 0.15 28 -0.12 16 44
MAP3K8 0.025 0.011 0.24 1 -10000 0 1
mol:Ca2+ -0.016 0.013 0.062 3 -0.049 12 15
integrin-mediated signaling pathway 0.026 0.034 -10000 0 -0.13 21 21
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.18 0.38 37 -0.45 31 68
TRPV6 0.073 0.3 1.1 37 -10000 0 37
CD28 0.042 0.059 0.25 37 -10000 0 37
SHC1 0.008 0.16 0.32 38 -0.41 33 71
receptor internalization -0.003 0.16 0.3 23 -0.35 52 75
PRF1 -0.011 0.22 0.55 5 -0.85 22 27
KRAS 0.024 0.007 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
COT/AKT1 0.024 0.13 0.34 37 -0.28 28 65
LAT 0.005 0.16 0.32 32 -0.4 33 65
EntrezGene:6955 0 0.003 0.03 1 -10000 0 1
CD3D 0.035 0.049 0.25 23 -10000 0 23
CD3E 0.029 0.033 0.26 9 -10000 0 9
CD3G 0.031 0.043 0.25 17 -10000 0 17
RASGRP2 0 0.039 0.1 11 -0.16 19 30
RASGRP1 0.013 0.15 0.39 35 -0.34 30 65
HLA-A 0.001 0.005 0.036 4 -10000 0 4
RASSF5 0.024 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.026 0.034 -10000 0 -0.13 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.089 0.24 47 -0.12 19 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.043 -10000 0 -0.17 26 26
PRKCA -0.009 0.085 0.22 26 -0.2 29 55
GRAP2 0.026 0.015 0.24 2 -10000 0 2
mol:IP3 -0.006 0.088 0.16 2 -0.28 33 35
EntrezGene:6957 0.001 0.005 0.036 4 -10000 0 4
TCR/CD3/MHC I/CD8 -0.004 0.13 0.28 15 -0.46 23 38
ORAI1 -0.059 0.25 0.35 16 -0.95 33 49
CSK 0.006 0.15 0.29 32 -0.41 31 63
B7 family/CD28 0.045 0.17 0.45 25 -0.41 26 51
CHUK 0.024 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0 0.16 0.32 24 -0.44 35 59
PTPN6 -0.002 0.14 0.28 26 -0.42 30 56
VAV1 0 0.16 0.32 26 -0.42 35 61
Monovalent TCR/CD3 0.005 0.095 0.28 17 -0.22 41 58
CBL 0.025 0.006 -10000 0 -10000 0 0
LCK 0.013 0.16 0.32 39 -0.44 27 66
PAG1 0.02 0.15 0.23 74 -0.47 22 96
RAP1A 0.025 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.16 0.31 23 -0.42 36 59
CD80 0.038 0.056 0.25 32 -10000 0 32
CD86 0.028 0.028 0.25 7 -10000 0 7
PDK1/CARD11/BCL10/MALT1 -0.003 0.058 -10000 0 -0.21 23 23
HRAS 0.028 0.024 0.24 6 -10000 0 6
GO:0035030 0.005 0.13 0.32 26 -0.34 28 54
CD8A 0.029 0.027 0.27 6 -10000 0 6
CD8B 0.03 0.032 0.25 9 -10000 0 9
PTPRC 0.028 0.028 0.25 7 -10000 0 7
PDK1/PKC theta 0.011 0.17 0.42 39 -0.4 28 67
CSK/PAG1 0.019 0.15 0.27 50 -0.44 23 73
SOS1 0.025 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.011 -10000 0 -10000 0 0
GRAP2/SLP76 0.021 0.15 0.36 19 -0.41 32 51
STIM1 -0.016 0.17 1.1 7 -0.94 5 12
RAS family/GTP 0.024 0.099 0.28 38 -0.16 34 72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.17 0.31 21 -0.37 51 72
mol:DAG -0.032 0.07 -10000 0 -0.25 34 34
RAP1A/GDP 0.015 0.041 0.12 38 -0.055 18 56
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.032 0.043 0.25 17 -0.037 1 18
cytotoxic T cell degranulation -0.009 0.21 0.55 5 -0.81 22 27
RAP1A/GTP -0.001 0.014 -10000 0 -0.06 21 21
mol:PI-3-4-5-P3 0.014 0.16 0.36 38 -0.38 30 68
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0 0.12 0.45 2 -0.36 31 33
NRAS 0.025 0.004 -10000 0 -10000 0 0
ZAP70 0.049 0.068 0.24 52 -10000 0 52
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0 0.13 0.37 10 -0.37 29 39
MALT1 0.023 0.013 0.24 1 -10000 0 1
TRAF6 0.025 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.037 0.056 0.24 12 -0.2 15 27
CARD11 0.026 0.026 0.24 6 -10000 0 6
PRKCB -0.014 0.088 0.24 21 -0.21 39 60
PRKCE -0.006 0.081 0.22 26 -0.21 22 48
PRKCQ 0.006 0.18 0.38 38 -0.45 30 68
LCP2 0.027 0.02 0.24 4 -10000 0 4
BCL10 0.025 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.019 0.13 0.32 45 -0.28 29 74
IKK complex 0.006 0.091 0.25 42 -0.11 29 71
RAS family/GDP -0.001 0.01 -10000 0 -0.036 15 15
MAP3K14 0.015 0.11 0.28 38 -0.21 28 66
PDPK1 0.017 0.14 0.36 42 -0.31 28 70
TCR/CD3/MHC I/CD8/Fyn -0.008 0.18 0.36 13 -0.52 34 47
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.003 0.037 0.11 27 -10000 0 27
NFATC2 -0.001 0.038 0.11 27 -0.17 2 29
NFATC3 -0.003 0.036 0.11 27 -10000 0 27
CD40LG -0.025 0.18 0.42 35 -0.32 45 80
PTGS2 -0.041 0.17 0.37 32 -0.33 73 105
JUNB 0.03 0.034 0.24 12 -10000 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.027 0.12 8 -10000 0 8
CaM/Ca2+ 0.016 0.027 0.12 8 -10000 0 8
CALM1 0.019 0.024 0.11 2 -10000 0 2
JUN 0.02 0.027 0.17 3 -10000 0 3
mol:Ca2+ 0.001 0.01 0.071 3 -10000 0 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.009 -10000 0 -10000 0 0
FOSL1 0.036 0.057 0.24 33 -10000 0 33
CREM 0.025 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.02 0.13 0.36 26 -0.21 26 52
FOS 0.021 0.031 0.21 6 -10000 0 6
IFNG -0.017 0.17 0.39 43 -0.3 33 76
AP-1/NFAT1-c-4 0.019 0.2 0.53 29 -0.32 49 78
FASLG -0.024 0.17 0.4 35 -0.3 49 84
NFAT1-c-4/ICER1 0.002 0.087 0.23 22 -0.17 21 43
IL2RA -0.005 0.19 0.37 68 -0.29 47 115
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSF2 -0.027 0.16 0.37 33 -0.29 45 78
JunB/Fra1/NFAT1-c-4 0.002 0.12 0.28 25 -0.19 45 70
IL4 -0.029 0.15 0.36 31 -0.29 45 76
IL2 -0.009 0.15 -10000 0 -0.9 13 13
IL3 -0.012 0.13 -10000 0 -0.63 20 20
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
BATF3 0.034 0.046 0.24 22 -10000 0 22
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.006 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 -0.008 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.052 -10000 0 -0.12 49 49
regulation of S phase of mitotic cell cycle -0.008 0.065 -10000 0 -0.19 46 46
GNAO1 0.019 0.011 -10000 0 -10000 0 0
HRAS 0.026 0.026 0.24 6 -0.028 7 13
SHBG/T-DHT 0.015 0.019 0.15 5 -0.12 3 8
PELP1 0.022 0.012 -10000 0 -0.044 1 1
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.046 0.058 0.2 7 -0.16 58 65
T-DHT/AR -0.001 0.049 -10000 0 -0.15 43 43
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.004 4 -0.008 84 88
GNAI2 0.025 0.004 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.024 0.013 0.24 1 -10000 0 1
mol:GDP -0.035 0.084 -10000 0 -0.3 43 43
cell proliferation -0.077 0.16 0.32 8 -0.4 80 88
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
FOS -0.12 0.27 0.3 4 -0.69 84 88
mol:Ca2+ -0.009 0.023 -10000 0 -0.072 52 52
MAPK3 -0.057 0.12 0.3 11 -0.28 75 86
MAPK1 -0.034 0.095 0.21 5 -0.23 69 74
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 0.005 4 -0.005 83 87
cAMP biosynthetic process 0.002 0.023 0.088 11 -0.12 3 14
GNG2 0.025 0.004 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 0.005 4 -0.005 83 87
HRAS/GTP 0.015 0.059 -10000 0 -0.094 96 96
actin cytoskeleton reorganization 0.03 0.023 -10000 0 -0.14 4 4
SRC 0.023 0.01 -10000 0 -0.036 1 1
voltage-gated calcium channel activity -0.001 0.002 0.005 4 -0.005 83 87
PI3K 0.028 0.024 -10000 0 -0.15 6 6
apoptosis 0.065 0.16 0.4 84 -0.27 8 92
T-DHT/AR/PELP1 0.011 0.049 -10000 0 -0.13 46 46
HRAS/GDP -0.016 0.087 -10000 0 -0.28 43 43
CREB1 -0.07 0.18 0.27 8 -0.43 84 92
RAC1-CDC42/GTP 0.038 0.027 -10000 0 -0.14 4 4
AR 0.021 0.013 -10000 0 -0.033 4 4
GNB1 0.026 0.003 -10000 0 -10000 0 0
RAF1 -0.036 0.053 0.21 8 -0.18 7 15
RAC1-CDC42/GDP -0.002 0.091 -10000 0 -0.28 43 43
T-DHT/AR/PELP1/Src 0.018 0.055 -10000 0 -0.12 44 44
MAP2K2 -0.045 0.059 0.2 7 -0.16 59 66
T-DHT/AR/PELP1/Src/PI3K -0.008 0.064 -10000 0 -0.19 45 45
GNAZ 0.023 0.008 -10000 0 -10000 0 0
SHBG 0.024 0.024 0.24 5 -10000 0 5
Gi family/GNB1/GNG2/GDP -0.051 0.13 -10000 0 -0.32 76 76
mol:T-DHT 0 0.002 -10000 0 -0.008 16 16
RAC1 0.024 0.008 -10000 0 -10000 0 0
GNRH1 -0.003 0.022 0.14 11 -10000 0 11
Gi family/GTP -0.032 0.081 -10000 0 -0.23 58 58
CDC42 0.026 0.003 -10000 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 0.037 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.04 0.029 0.19 15 -0.16 1 16
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.045 0.069 0.2 2 -0.13 59 61
NGF (dimer)/p75(NTR)/BEX1 -0.021 0.11 0.19 6 -0.16 169 175
NT-4/5 (dimer)/p75(NTR) -0.018 0.1 -10000 0 -0.2 115 115
IKBKB 0.02 0.011 -10000 0 -10000 0 0
AKT1 -0.027 0.06 0.17 27 -0.22 5 32
IKBKG 0.026 0.002 -10000 0 -10000 0 0
BDNF 0.02 0.011 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.047 0.067 0.19 44 -0.14 36 80
FURIN 0.026 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.002 0.09 -10000 0 -0.16 110 110
LINGO1 0.048 0.067 0.24 51 -10000 0 51
Sortilin/TRAF6/NRIF -0.038 0.013 -10000 0 -10000 0 0
proBDNF (dimer) 0.02 0.011 -10000 0 -10000 0 0
NTRK1 0.027 0.029 0.24 8 -10000 0 8
RTN4R 0.025 0.004 -10000 0 -10000 0 0
neuron apoptosis -0.041 0.11 0.31 8 -0.34 24 32
IRAK1 0.026 0.002 -10000 0 -10000 0 0
SHC1 -0.033 0.04 0.1 2 -0.14 54 56
ARHGDIA 0.025 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.069 0.2 7 -0.13 58 65
MAGEH1 0.029 0.026 0.24 7 -10000 0 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.038 0.068 0.2 2 -0.14 58 60
Mammalian IAPs/DIABLO 0.061 0.024 0.2 2 -0.13 2 4
proNGF (dimer) 0.025 0.015 0.24 2 -10000 0 2
MAGED1 0.026 0.01 0.24 1 -10000 0 1
APP 0.025 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.011 -10000 0 -10000 0 0
ZNF274 0.026 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.051 -10000 0 -0.12 59 59
NGF 0.025 0.015 0.24 2 -10000 0 2
cell cycle arrest -0.01 0.063 0.24 11 -0.18 2 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.001 0.058 -10000 0 -0.17 46 46
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.001 0.093 -10000 0 -0.16 110 110
NCSTN 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0.025 0.065 0.19 2 -0.14 60 62
PSENEN 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide -0.026 0.045 0.17 11 -0.13 41 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.002 0.051 0.16 1 -0.27 3 4
p75(NTR)/beta APP 0.02 0.055 -10000 0 -0.16 40 40
BEX1 0.02 0.026 0.24 5 -10000 0 5
mol:GDP -0.028 0.041 0.093 2 -0.13 60 62
NGF (dimer) 0.057 0.085 0.2 73 -0.13 51 124
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.059 0.068 0.2 44 -0.13 36 80
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
RAC1/GTP 0.022 0.053 0.16 2 -0.12 56 58
MYD88 0.025 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.026 0.065 0.19 2 -0.14 60 62
RHOB 0.025 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.041 0.029 0.19 16 -10000 0 16
NT3 (dimer) 0.022 0.01 -10000 0 -10000 0 0
TP53 -0.039 0.073 0.22 18 -0.2 20 38
PRDM4 -0.033 0.044 0.17 7 -0.13 56 63
BDNF (dimer) 0.022 0.12 0.2 78 -0.15 128 206
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SORT1 0.025 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.04 0.066 -10000 0 -0.13 59 59
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.066 0.2 2 -0.13 57 59
RHOC 0.025 0.004 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
MAPK10 -0.039 0.1 0.4 7 -0.26 44 51
DIABLO 0.025 0.005 -10000 0 -10000 0 0
SMPD2 -0.026 0.045 0.17 11 -0.13 41 52
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.025 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.027 0.065 0.19 2 -0.14 60 62
PSEN1 0.025 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.004 0.078 -10000 0 -0.18 69 69
MAPK8 -0.043 0.1 0.44 6 -0.26 49 55
MAPK9 -0.039 0.1 0.39 7 -0.26 44 51
APAF1 0.025 0.006 -10000 0 -10000 0 0
NTF3 0.022 0.01 -10000 0 -10000 0 0
NTF4 0.02 0.011 -10000 0 -10000 0 0
NDN 0.025 0.005 -10000 0 -10000 0 0
RAC1/GDP 0.017 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.036 0.068 -10000 0 -0.13 61 61
p75 CTF/Sortilin/TRAF6/NRIF 0.06 0.028 -10000 0 -0.13 6 6
RhoA-B-C/GTP 0.025 0.064 0.18 2 -0.14 60 62
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.022 0.092 -10000 0 -0.14 109 109
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.014 0.091 -10000 0 -0.15 110 110
PRKACB 0.025 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.002 0.08 -10000 0 -0.16 95 95
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.018 0.24 3 -10000 0 3
BIRC2 0.025 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.009 0.068 0.24 9 -0.16 28 37
BAD -0.039 0.12 0.32 19 -0.27 48 67
RIPK2 0.02 0.011 -10000 0 -10000 0 0
NGFR 0.023 0.008 -10000 0 -10000 0 0
CYCS -0.033 0.046 0.19 8 -0.22 2 10
ADAM17 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.032 0.062 0.2 2 -0.13 48 50
BCL2L11 -0.042 0.12 0.3 18 -0.27 48 66
BDNF (dimer)/p75(NTR) -0.014 0.096 -10000 0 -0.18 111 111
PI3K 0.032 0.067 0.2 1 -0.13 58 59
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.066 0.2 2 -0.13 58 60
NDNL2 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.012 0.24 1 -10000 0 1
NGF (dimer)/p75(NTR) 0.013 0.068 0.19 2 -0.16 60 62
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.039 0.067 0.2 2 -0.13 59 61
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.003 -10000 0 -10000 0 0
PLG 0.031 0.047 0.24 23 -10000 0 23
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.053 0.074 0.14 3 -0.17 117 120
SQSTM1 0.025 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.001 -10000 0 -10000 0 0
CASP3 -0.036 0.11 0.3 18 -0.26 47 65
E2F1 0.033 0.041 0.24 18 -10000 0 18
CASP9 0.026 0.003 -10000 0 -10000 0 0
IKK complex 0.025 0.081 -10000 0 -0.22 22 22
NGF (dimer)/TRKA 0.02 0.064 0.19 10 -0.16 45 55
MMP7 0.045 0.068 0.24 50 -10000 0 50
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.068 0.2 2 -0.13 56 58
MMP3 0.035 0.055 0.24 31 -10000 0 31
APAF-1/Caspase 9 -0.051 0.036 -10000 0 -0.19 4 4
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.11 0.37 7 -0.37 10 17
CRKL -0.006 0.077 0.17 51 -0.17 5 56
mol:DAG 0.002 0.074 0.23 3 -0.21 37 40
HRAS -0.009 0.094 0.3 23 -0.19 3 26
MAPK8 0.003 0.08 0.18 67 -0.15 3 70
RAP1A -0.007 0.078 0.17 51 -0.18 6 57
GAB1 -0.007 0.079 0.25 17 -0.17 7 24
MAPK14 0.004 0.084 0.18 70 -0.14 4 74
EPO 0.031 0.051 0.24 25 -10000 0 25
PLCG1 0.002 0.075 0.23 3 -0.21 37 40
EPOR/TRPC2/IP3 Receptors 0.027 0.038 0.23 11 -10000 0 11
RAPGEF1 0.024 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.02 0.084 0.19 30 -0.14 77 107
GAB1/SHC/GRB2/SOS1 0.028 0.07 0.27 4 -0.18 4 8
EPO/EPOR (dimer) 0.027 0.073 0.19 32 -0.17 41 73
IRS2 -0.01 0.072 0.17 40 -0.18 6 46
STAT1 0.004 0.084 0.25 6 -0.22 43 49
STAT5B 0.002 0.078 0.23 3 -0.21 43 46
cell proliferation 0.008 0.098 0.21 79 -0.14 4 83
GAB1/SHIP/PIK3R1/SHP2/SHC -0.033 0.063 0.15 1 -0.22 15 16
TEC -0.007 0.077 0.25 16 -0.18 6 22
SOCS3 0.024 0.026 0.24 6 -10000 0 6
STAT1 (dimer) 0.004 0.083 0.25 6 -0.22 43 49
JAK2 0.022 0.021 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.045 0.073 0.31 1 -0.13 45 46
EPO/EPOR 0.027 0.073 0.19 32 -0.17 41 73
LYN 0.02 0.014 -10000 0 -10000 0 0
TEC/VAV2 -0.014 0.066 0.21 9 -0.18 4 13
elevation of cytosolic calcium ion concentration 0.027 0.038 0.23 11 -10000 0 11
SHC1 0.025 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.032 0.065 0.19 25 -0.14 38 63
mol:IP3 0.002 0.074 0.23 3 -0.21 37 40
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.02 0.076 0.22 11 -0.22 12 23
SH2B3 0.021 0.021 -10000 0 -10000 0 0
NFKB1 0.004 0.084 0.18 71 -0.14 4 75
EPO/EPOR (dimer)/JAK2/SOCS3 -0.013 0.074 0.17 2 -0.17 73 75
PTPN6 -0.006 0.071 0.16 51 -0.18 6 57
TEC/VAV2/GRB2 -0.013 0.069 0.22 6 -0.19 3 9
EPOR 0.027 0.038 0.23 11 -10000 0 11
INPP5D 0.024 0.007 -10000 0 -10000 0 0
mol:GDP -0.012 0.074 0.22 7 -0.19 3 10
SOS1 0.025 0.005 -10000 0 -10000 0 0
PLCG2 0.022 0.018 0.24 2 -10000 0 2
CRKL/CBL/C3G -0.014 0.068 0.2 10 -0.2 3 13
VAV2 -0.01 0.07 0.23 13 -0.18 5 18
CBL -0.01 0.073 0.17 41 -0.18 6 47
SHC/Grb2/SOS1 0.02 0.057 -10000 0 -0.13 39 39
STAT5A 0.002 0.078 0.23 3 -0.21 43 46
GRB2 0.025 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.012 0.088 0.26 2 -0.29 17 19
LYN/PLCgamma2 0.026 0.025 0.19 2 -0.16 2 4
PTPN11 0.025 0.006 -10000 0 -10000 0 0
BTK -0.004 0.082 0.18 48 -0.18 8 56
BCL2 -0.007 0.17 0.38 7 -0.64 23 30
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.038 0.12 0.22 119 -10000 0 119
GNAI2 0.025 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.057 -10000 0 -0.13 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.011 -10000 0 -10000 0 0
RhoA/GTP -0.038 0.12 -10000 0 -0.22 118 118
negative regulation of cAMP metabolic process -0.04 0.12 -10000 0 -0.24 111 111
GNAZ 0.023 0.008 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNA12 0.023 0.008 -10000 0 -10000 0 0
S1PR5 0.021 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.04 0.12 -10000 0 -0.24 111 111
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.013 0.24 1 -10000 0 1
EGFR-dependent Endothelin 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
HRAS 0.028 0.024 0.24 6 -10000 0 6
EGFR 0.021 0.01 -10000 0 -10000 0 0
EGF/EGFR 0.016 0.088 0.16 34 -0.14 90 124
EGF/EGFR dimer/SHC/GRB2/SOS1 0.049 0.076 -10000 0 -0.13 48 48
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.008 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.042 0.061 0.24 40 -10000 0 40
EGF/EGFR dimer/SHC 0.033 0.075 0.19 33 -0.15 52 85
mol:GDP 0.043 0.072 -10000 0 -0.13 48 48
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.028 0.032 0.24 10 -10000 0 10
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.027 0.058 -10000 0 -0.13 45 45
SHC1 0.025 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.042 0.068 -10000 0 -0.13 45 45
FRAP1 -0.028 0.039 -10000 0 -0.13 48 48
EGF/EGFR dimer 0.021 0.081 0.19 34 -0.17 56 90
SOS1 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.012 0.08 0.19 9 -0.19 60 69
Noncanonical Wnt signaling pathway

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
NFATC2 0.021 0.01 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.11 0.23 1 -0.26 36 37
mol:DAG -0.031 0.094 0.17 20 -0.25 35 55
PLCG1 -0.032 0.096 0.18 20 -0.26 35 55
YES1 -0.026 0.083 0.15 6 -0.27 31 37
FZD3 0.019 0.012 -10000 0 -10000 0 0
FZD6 0.02 0.011 -10000 0 -10000 0 0
G protein -0.003 0.11 0.28 4 -0.26 35 39
MAP3K7 -0.036 0.091 0.18 18 -0.25 40 58
mol:Ca2+ -0.03 0.092 0.17 20 -0.25 35 55
mol:IP3 -0.031 0.094 0.17 20 -0.25 35 55
NLK 0.002 0.079 -10000 0 -0.76 5 5
GNB1 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.034 0.1 0.2 20 -0.24 50 70
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.015 0.091 0.17 7 -0.21 71 78
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
GNAS -0.028 0.085 0.15 6 -0.26 33 39
GO:0007205 -0.025 0.098 0.2 24 -0.24 37 61
WNT6 0.024 0.028 0.24 7 -10000 0 7
WNT4 0.025 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.025 0.11 0.21 1 -0.27 38 39
GNG2 0.025 0.004 -10000 0 -10000 0 0
WNT5A 0.029 0.035 0.24 12 -10000 0 12
WNT11 0.035 0.047 0.24 23 -10000 0 23
CDC42 -0.03 0.083 0.14 3 -0.26 31 34
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.03 0.045 0.19 1 -0.13 27 28
fibroblast growth factor receptor signaling pathway 0.03 0.045 0.19 1 -0.13 27 28
LAMA1 0.033 0.046 0.24 22 -10000 0 22
PRNP 0.025 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.013 0.065 -10000 0 -0.16 58 58
SMAD2 -0.017 0.041 0.17 18 -10000 0 18
GPC1/PrPc/Cu2+ 0.033 0.01 -10000 0 -0.13 1 1
GPC1/Laminin alpha1 0.036 0.05 0.19 22 -0.16 17 39
TDGF1 0.024 0.026 0.24 6 -10000 0 6
CRIPTO/GPC1 0.016 0.064 0.19 5 -0.16 53 58
APP/GPC1 0.036 0.016 -10000 0 -0.16 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.03 0.041 0.13 6 -0.14 50 56
FLT1 0.026 0.015 0.24 2 -10000 0 2
GPC1/TGFB/TGFBR1/TGFBR2 0.045 0.029 -10000 0 -0.14 9 9
SERPINC1 0.038 0.054 0.24 31 -10000 0 31
FYN -0.027 0.04 0.14 5 -0.14 45 50
FGR -0.031 0.042 0.13 7 -0.14 52 59
positive regulation of MAPKKK cascade -0.032 0.099 0.26 13 -0.25 50 63
SLIT2 0.022 0.009 -10000 0 -10000 0 0
GPC1/NRG 0.005 0.062 -10000 0 -0.16 57 57
NRG1 0.016 0.013 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.041 0.05 0.21 6 -0.14 28 34
LYN -0.027 0.036 0.1 4 -0.14 40 44
mol:Spermine -0.009 0.001 -10000 0 -10000 0 0
cell growth 0.03 0.045 0.19 1 -0.13 27 28
BMP signaling pathway -0.026 0.003 -10000 0 -10000 0 0
SRC -0.031 0.041 0.13 6 -0.14 52 58
TGFBR1 0.025 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.096 0.1 0.24 161 -10000 0 161
GPC1 0.026 0.003 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.025 0.006 -10000 0 -10000 0 0
VEGFA 0.026 0.023 0.24 5 -10000 0 5
BLK -0.014 0.06 0.14 33 -0.16 34 67
HCK -0.031 0.042 0.13 7 -0.14 51 58
FGF2 0.024 0.013 0.24 1 -10000 0 1
FGFR1 0.019 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer 0.026 0.015 0.24 2 -10000 0 2
TGFBR2 0.024 0.006 -10000 0 -10000 0 0
cell death 0.035 0.015 -10000 0 -0.16 2 2
ATIII/GPC1 0.045 0.039 0.19 30 -0.16 1 31
PLA2G2A/GPC1 0.079 0.085 0.19 158 -0.16 18 176
LCK -0.029 0.045 0.13 13 -0.14 49 62
neuron differentiation 0.005 0.062 -10000 0 -0.16 57 57
PrPc/Cu2+ 0.019 0.003 -10000 0 -10000 0 0
APP 0.025 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.006 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.008 0.007 0.14 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.03 0.19 8 -0.16 5 13
STXBP1 0.024 0.007 -10000 0 -10000 0 0
ACh/CHRNA1 0.035 0.079 0.19 85 -0.085 51 136
RAB3GAP2/RIMS1/UNC13B 0.046 0.031 0.19 8 -0.14 4 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.026 0.025 0.24 6 -10000 0 6
mol:ACh -0.01 0.046 0.089 36 -0.1 62 98
RAB3GAP2 0.025 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.013 0.064 0.15 1 -0.14 48 49
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.035 0.079 0.19 85 -0.085 51 136
UNC13B 0.026 0.015 0.24 2 -10000 0 2
CHRNA1 0.061 0.083 0.24 84 -10000 0 84
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.062 0.14 12 -0.14 53 65
SNAP25 -0.024 0.068 0.098 1 -0.19 68 69
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.025 0.032 0.24 9 -10000 0 9
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.011 0.12 1 -0.13 1 2
STX1A/SNAP25 fragment 1/VAMP2 0.013 0.064 0.15 1 -0.14 48 49
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.022 0.24 4 -10000 0 4
LAT2 -0.012 0.075 0.16 5 -0.25 30 35
AP1 0.001 0.14 0.29 4 -0.37 34 38
mol:PIP3 0.007 0.14 0.34 39 -0.32 24 63
IKBKB 0.007 0.12 0.28 50 -0.2 32 82
AKT1 -0.013 0.11 0.34 33 -0.2 12 45
IKBKG -0.006 0.1 0.26 35 -0.2 36 71
MS4A2 0.024 0.024 0.24 4 -10000 0 4
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 0.002 0.11 0.26 34 -0.29 23 57
mol:Ca2+ 0.01 0.12 0.29 45 -0.25 24 69
LYN 0.021 0.012 -10000 0 -10000 0 0
CBLB -0.011 0.075 0.15 6 -0.26 29 35
SHC1 0.025 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.039 0.034 -10000 0 -0.12 18 18
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.007 -10000 0 -10000 0 0
PLD2 -0.018 0.077 0.27 21 -0.2 12 33
PTPN13 -0.004 0.12 0.34 2 -0.5 14 16
PTPN11 0.021 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.005 0.13 0.39 31 -0.27 16 47
SYK 0.025 0.014 0.24 1 -10000 0 1
GRB2 0.025 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.003 0.093 -10000 0 -0.3 28 28
LAT -0.01 0.076 0.15 7 -0.26 28 35
PAK2 0.003 0.12 0.27 32 -0.3 28 60
NFATC2 -0.06 0.14 -10000 0 -0.39 77 77
HRAS -0.002 0.11 0.25 19 -0.32 30 49
GAB2 0.025 0.006 -10000 0 -10000 0 0
PLA2G1B 0.015 0.088 -10000 0 -0.8 5 5
Fc epsilon R1 0.025 0.074 0.18 7 -0.16 58 65
Antigen/IgE/Fc epsilon R1 0.025 0.066 0.17 7 -0.14 57 64
mol:GDP -0.006 0.1 0.25 6 -0.34 29 35
JUN 0.025 0.011 0.24 1 -10000 0 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
FOS 0.023 0.022 0.24 4 -10000 0 4
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.004 0.08 0.16 5 -0.26 32 37
CHUK -0.003 0.11 0.27 37 -0.2 34 71
KLRG1 -0.012 0.067 0.14 7 -0.21 35 42
VAV1 -0.015 0.08 0.16 8 -0.28 30 38
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.012 0.076 0.14 7 -0.26 30 37
negative regulation of mast cell degranulation 0 0.085 0.17 7 -0.26 29 36
BTK 0 0.1 0.25 5 -0.36 23 28
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.021 0.11 0.16 3 -0.28 58 61
GAB2/PI3K/SHP2 -0.043 0.042 -10000 0 -0.17 31 31
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.011 0.077 0.16 1 -0.23 41 42
RAF1 0.016 0.093 -10000 0 -0.88 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.041 0.096 0.22 14 -0.18 62 76
FCER1G 0.024 0.022 0.24 3 -10000 0 3
FCER1A 0.022 0.011 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/Fyn 0.029 0.066 0.18 6 -0.13 55 61
MAPK3 0.011 0.087 -10000 0 -0.8 5 5
MAPK1 0.01 0.09 -10000 0 -0.83 5 5
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.022 0.19 -10000 0 -0.53 49 49
DUSP1 0.024 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA -0.013 0.051 0.12 15 -0.13 29 44
actin cytoskeleton reorganization -0.003 0.12 -10000 0 -0.51 14 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.006 0.1 0.23 5 -0.29 36 41
FER -0.01 0.073 0.14 6 -0.26 26 32
RELA 0.025 0.006 -10000 0 -10000 0 0
ITK 0.002 0.06 0.12 25 -0.27 16 41
SOS1 0.025 0.005 -10000 0 -10000 0 0
PLCG1 0 0.12 0.27 21 -0.32 31 52
cytokine secretion -0.014 0.031 0.067 2 -0.096 32 34
SPHK1 -0.01 0.078 0.15 10 -0.26 30 40
PTK2 -0.004 0.13 -10000 0 -0.54 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.001 0.097 0.21 2 -0.3 30 32
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.13 0.34 29 -0.3 32 61
MAP2K2 0.007 0.088 -10000 0 -0.82 5 5
MAP2K1 0.008 0.088 -10000 0 -0.82 5 5
MAP2K7 0.025 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.002 0.069 0.18 5 -0.2 32 37
MAP2K4 -0.037 0.25 -10000 0 -0.85 41 41
Fc epsilon R1/FcgammaRIIB 0.038 0.084 0.22 15 -0.16 57 72
mol:Choline -0.017 0.076 0.27 21 -0.19 12 33
SHC/Grb2/SOS1 0.029 0.091 0.24 2 -0.25 27 29
FYN 0.022 0.009 -10000 0 -10000 0 0
DOK1 0.025 0.004 -10000 0 -10000 0 0
PXN 0 0.13 0.36 10 -0.5 14 24
HCLS1 -0.01 0.074 0.16 6 -0.26 28 34
PRKCB -0.009 0.13 0.3 35 -0.26 39 74
FCGR2B 0.029 0.035 0.24 12 -10000 0 12
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0 0.087 0.18 7 -0.27 29 36
LCP2 0.027 0.02 0.24 4 -10000 0 4
PLA2G4A -0.015 0.085 0.14 7 -0.27 35 42
RASA1 0.024 0.007 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.017 0.076 0.27 21 -0.19 12 33
IKK complex 0.007 0.11 0.26 50 -0.17 20 70
WIPF1 0.025 0.006 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.021 0.14 0.3 20 -0.34 36 56
IKBKB -0.004 0.12 0.31 17 -0.26 39 56
AKT1 0.03 0.11 0.27 59 -0.19 9 68
IKBKG 0.03 0.08 0.29 18 -0.24 6 24
CALM1 0.014 0.086 0.27 11 -0.3 10 21
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 -0.043 0.19 0.33 20 -0.44 59 79
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.085 0.27 7 -0.32 11 18
DOK1 0.025 0.004 -10000 0 -10000 0 0
AP-1 -0.005 0.088 0.3 14 -0.22 18 32
LYN 0.022 0.01 -10000 0 -10000 0 0
BLNK 0.024 0.007 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
BCR complex 0.046 0.084 0.24 52 -0.17 26 78
CD22 -0.004 0.1 0.26 19 -0.29 30 49
CAMK2G 0.011 0.081 0.26 10 -0.31 8 18
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
INPP5D 0.024 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.025 0.045 0.096 35 -0.21 3 38
GO:0007205 0.015 0.086 0.27 8 -0.32 11 19
SYK 0.025 0.012 0.24 1 -10000 0 1
ELK1 0.012 0.088 0.26 11 -0.3 12 23
NFATC1 0.012 0.11 0.25 35 -0.28 18 53
B-cell antigen/BCR complex 0.046 0.084 0.24 52 -0.17 26 78
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.016 0.048 0.16 17 -0.12 6 23
HRAS 0.023 0.083 0.24 24 -0.24 7 31
NFKBIA 0.016 0.048 0.16 17 -0.12 6 23
NF-kappa-B/RelA/I kappa B beta 0.02 0.044 0.15 20 -10000 0 20
RasGAP/Csk 0.069 0.086 0.26 46 -0.14 31 77
mol:GDP 0.018 0.088 0.26 8 -0.29 13 21
PTEN 0.021 0.011 -10000 0 -10000 0 0
CD79B 0.032 0.039 0.24 16 -10000 0 16
NF-kappa-B/RelA/I kappa B alpha 0.02 0.044 0.15 20 -10000 0 20
GRB2 0.025 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.008 0.15 0.34 23 -0.41 24 47
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
mol:IP3 0.017 0.08 0.26 8 -0.34 9 17
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.002 0.092 0.26 11 -0.31 13 24
CHUK 0.016 0.11 0.3 17 -0.28 30 47
IBTK 0.022 0.009 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.027 0.081 0.27 9 -0.3 6 15
PTPN6 -0.013 0.096 0.21 24 -0.28 29 53
RELA 0.025 0.006 -10000 0 -10000 0 0
BCL2A1 0.015 0.034 0.12 21 -10000 0 21
VAV2 -0.005 0.11 0.25 21 -0.41 15 36
ubiquitin-dependent protein catabolic process 0.017 0.048 0.16 17 -0.12 7 24
BTK 0.025 0.094 -10000 0 -0.92 4 4
CD19 0.002 0.1 0.22 38 -0.31 26 64
MAP4K1 0.037 0.049 0.24 26 -10000 0 26
CD72 0.034 0.044 0.24 20 -10000 0 20
PAG1 0.021 0.011 -10000 0 -10000 0 0
MAPK14 -0.037 0.17 0.33 20 -0.38 58 78
SH3BP5 0.025 0.005 -10000 0 -10000 0 0
PIK3AP1 0.012 0.083 0.26 4 -0.35 11 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.017 0.1 0.26 16 -0.31 27 43
RAF1 0.021 0.085 0.25 26 -0.24 6 32
RasGAP/p62DOK/SHIP 0.059 0.093 0.31 19 -0.15 44 63
CD79A 0.048 0.068 0.24 53 -10000 0 53
re-entry into mitotic cell cycle -0.004 0.087 0.29 14 -0.22 17 31
RASA1 0.024 0.007 -10000 0 -10000 0 0
MAPK3 0.015 0.085 0.27 23 -0.22 5 28
MAPK1 0.013 0.08 0.28 18 -0.22 5 23
CD72/SHP1 -0.001 0.12 0.31 26 -0.32 23 49
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.038 0.17 0.32 21 -0.38 59 80
actin cytoskeleton organization 0.002 0.11 0.26 28 -0.34 16 44
NF-kappa-B/RelA 0.04 0.083 0.29 17 -0.19 1 18
Calcineurin 0.023 0.072 0.25 5 -0.3 6 11
PI3K -0.036 0.07 -10000 0 -0.27 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.011 0.083 0.23 7 -0.35 15 22
SOS1 0.025 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.068 0.3 0.41 12 -0.71 77 89
DAPP1 -0.099 0.31 0.44 2 -0.8 76 78
cytokine secretion 0.013 0.11 0.25 35 -0.27 17 52
mol:DAG 0.017 0.08 0.26 8 -0.34 9 17
PLCG2 0.022 0.018 0.24 2 -10000 0 2
MAP2K1 0.017 0.081 0.25 22 -0.23 6 28
B-cell antigen/BCR complex/FcgammaRIIB 0.054 0.088 0.25 50 -0.15 32 82
mol:PI-3-4-5-P3 -0.014 0.07 0.19 19 -0.22 14 33
ETS1 0.01 0.085 0.28 16 -0.31 6 22
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.062 0.075 0.25 34 -0.14 20 54
B-cell antigen/BCR complex/LYN 0.006 0.097 0.25 16 -0.3 25 41
MALT1 0.023 0.013 0.24 1 -10000 0 1
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 -0.002 0.11 0.26 23 -0.36 15 38
B-cell antigen/BCR complex/LYN/SYK 0.03 0.11 0.32 16 -0.31 19 35
CARD11 0.026 0.1 0.29 31 -0.34 7 38
FCGR2B 0.029 0.035 0.24 12 -10000 0 12
PPP3CA 0.026 0.018 0.24 3 -10000 0 3
BCL10 0.025 0.004 -10000 0 -10000 0 0
IKK complex 0.014 0.062 0.2 33 -0.11 6 39
PTPRC 0.027 0.027 0.24 7 -10000 0 7
PDPK1 -0.006 0.069 0.21 24 -0.17 10 34
PPP3CB 0.025 0.005 -10000 0 -10000 0 0
PPP3CC 0.018 0.012 -10000 0 -10000 0 0
POU2F2 0.013 0.031 0.11 16 -0.082 2 18
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.024 0.089 0.2 6 -0.14 95 101
SMAD6-7/SMURF1 0.039 0.032 -10000 0 -0.14 9 9
NOG 0.023 0.014 0.24 1 -10000 0 1
SMAD9 -0.072 0.19 -10000 0 -0.42 102 102
SMAD4 0.023 0.008 -10000 0 -10000 0 0
SMAD5 -0.006 0.069 0.22 2 -0.26 16 18
BMP7/USAG1 -0.05 0.12 -10000 0 -0.2 174 174
SMAD5/SKI 0.007 0.078 0.23 4 -0.26 16 20
SMAD1 0.014 0.034 -10000 0 -0.24 1 1
BMP2 0.024 0.012 0.24 1 -10000 0 1
SMAD1/SMAD1/SMAD4 0.026 0.035 -10000 0 -0.22 1 1
BMPR1A 0.023 0.008 -10000 0 -10000 0 0
BMPR1B 0.026 0.018 0.24 3 -10000 0 3
BMPR1A-1B/BAMBI 0.05 0.036 0.19 19 -0.12 4 23
AHSG 0.035 0.058 0.24 35 -10000 0 35
CER1 0.023 0.031 0.24 9 -10000 0 9
BMP2-4/CER1 0.03 0.064 0.19 8 -0.16 40 48
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.007 0.095 0.23 1 -0.29 33 34
BMP2-4 (homodimer) 0.018 0.068 0.19 1 -0.2 41 42
RGMB 0.023 0.008 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.068 0.048 0.2 45 -0.13 2 47
RGMA 0.025 0.006 -10000 0 -10000 0 0
SMURF1 0.023 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.009 0.088 0.16 1 -0.27 37 38
BMP2-4/USAG1 -0.022 0.1 0.19 1 -0.17 154 155
SMAD6/SMURF1/SMAD5 0.005 0.071 0.25 1 -0.27 13 14
SOSTDC1 0.015 0.013 -10000 0 -10000 0 0
BMP7/BMPR2/BMPR1A-1B 0.024 0.075 0.2 3 -0.13 90 93
SKI 0.026 0.003 -10000 0 -10000 0 0
BMP6 (homodimer) 0.05 0.07 0.24 57 -10000 0 57
HFE2 0.044 0.068 0.24 50 -10000 0 50
ZFYVE16 0.024 0.007 -10000 0 -10000 0 0
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
BMP2-4/CHRD 0.042 0.074 0.19 38 -0.17 37 75
SMAD5/SMAD5/SMAD4 0.008 0.075 0.28 3 -0.26 15 18
MAPK1 0.025 0.004 -10000 0 -10000 0 0
TAK1/TAB family 0.002 0.082 -10000 0 -0.26 25 25
BMP7 (homodimer) 0.021 0.015 0.24 1 -10000 0 1
NUP214 0.025 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.056 0.061 0.19 78 -10000 0 78
SMAD1/SKI 0.031 0.045 0.29 3 -0.23 2 5
SMAD6 0.025 0.004 -10000 0 -10000 0 0
CTDSP2 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.037 0.071 0.19 32 -0.17 36 68
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.037 0.054 0.24 31 -10000 0 31
BMPR2 (homodimer) 0.026 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.047 0.021 0.19 3 -10000 0 3
BMPR1A-1B (homodimer) 0.033 0.023 0.19 2 -0.14 4 6
CHRDL1 0.019 0.011 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.029 0.046 0.33 4 -0.23 2 6
SMAD6-7/SMURF1/SMAD1 0.039 0.046 0.32 1 -0.23 2 3
SMAD6/SMURF1 0.023 0.008 -10000 0 -10000 0 0
BAMBI 0.034 0.043 0.24 20 -10000 0 20
SMURF2 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.008 0.11 0.19 1 -0.18 127 128
BMP2-4/GREM1 0.027 0.089 0.19 30 -0.17 67 97
SMAD7 0.024 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.066 0.19 -10000 0 -0.4 109 109
SMAD1/SMAD6 0.025 0.039 0.28 2 -0.23 2 4
TAK1/SMAD6 0.03 0.016 -10000 0 -10000 0 0
BMP7 0.021 0.015 0.24 1 -10000 0 1
BMP6 0.05 0.07 0.24 57 -10000 0 57
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.011 0.092 -10000 0 -0.29 34 34
PPM1A 0.025 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.03 0.047 0.36 3 -0.23 2 5
SMAD7/SMURF1 0.031 0.015 -10000 0 -10000 0 0
CTDSPL 0.025 0.004 -10000 0 -10000 0 0
PPP1CA 0.025 0.006 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.027 0.02 0.24 4 -10000 0 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.028 0.12 -10000 0 -0.33 50 50
CHRD 0.043 0.061 0.24 41 -10000 0 41
BMPR2 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.015 0.092 0.16 1 -0.32 30 31
BMP4 0.024 0.007 -10000 0 -10000 0 0
FST 0.023 0.02 0.24 3 -10000 0 3
BMP2-4/NOG 0.014 0.089 0.19 2 -0.18 76 78
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.033 0.073 0.2 2 -0.12 75 77
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.063 0.072 0.26 29 -0.15 21 50
MAP4K1 0.037 0.049 0.24 26 -10000 0 26
MAP3K8 0.025 0.011 0.24 1 -10000 0 1
PRKCB 0.019 0.011 -10000 0 -10000 0 0
DBNL 0.024 0.008 -10000 0 -10000 0 0
CRKL 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.056 0.22 4 -0.31 6 10
JUN -0.12 0.24 0.35 1 -0.53 122 123
MAP3K7 0.007 0.051 0.21 5 -0.29 4 9
GRAP2 0.026 0.015 0.24 2 -10000 0 2
CRK 0.024 0.007 -10000 0 -10000 0 0
MAP2K4 0 0.07 0.24 10 -0.29 10 20
LAT 0.031 0.036 0.24 13 -10000 0 13
LCP2 0.027 0.02 0.24 4 -10000 0 4
MAPK8 -0.12 0.26 -10000 0 -0.55 122 122
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.064 0.23 5 -0.3 7 12
LAT/GRAP2/SLP76/HPK1/HIP-55 0.067 0.072 0.26 28 -0.14 19 47
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.019 0.054 -10000 0 -0.16 39 39
CRKL -0.01 0.12 0.28 5 -0.42 20 25
mol:PIP3 -0.001 0.069 -10000 0 -0.73 4 4
AKT1 -0.003 0.078 0.36 3 -0.6 4 7
PTK2B 0.018 0.012 -10000 0 -10000 0 0
RAPGEF1 -0.004 0.12 0.31 17 -0.39 20 37
RANBP10 0.023 0.009 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.027 0.07 0.19 9 -0.16 48 57
MAP3K5 -0.001 0.12 0.31 13 -0.4 20 33
HGF/MET/CIN85/CBL/ENDOPHILINS 0.038 0.071 0.2 9 -0.16 47 56
AP1 -0.026 0.07 0.18 7 -0.16 60 67
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
apoptosis -0.12 0.31 -10000 0 -0.74 94 94
STAT3 (dimer) -0.025 0.095 -10000 0 -0.27 48 48
GAB1/CRKL/SHP2/PI3K 0.011 0.12 0.26 3 -0.4 20 23
INPP5D 0.024 0.007 -10000 0 -10000 0 0
CBL/CRK 0.004 0.12 0.32 7 -0.4 20 27
PTPN11 0.025 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.011 -10000 0 -10000 0 0
ELK1 0.005 0.1 0.33 37 -10000 0 37
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.01 0.061 -10000 0 -0.23 23 23
PAK1 -0.002 0.086 0.39 8 -0.59 3 11
HGF/MET/RANBP10 0.023 0.069 0.19 7 -0.16 49 56
HRAS -0.035 0.17 0.24 1 -0.5 51 52
DOCK1 -0.012 0.11 0.26 7 -0.4 21 28
GAB1 -0.009 0.12 0.25 5 -0.44 20 25
CRK -0.01 0.12 0.31 7 -0.42 20 27
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.032 0.16 -10000 0 -0.46 57 57
JUN 0.025 0.011 0.24 1 -10000 0 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.011 0.065 -10000 0 -0.19 50 50
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
cell morphogenesis -0.02 0.14 0.33 22 -0.36 38 60
GRB2/SHC 0.018 0.075 0.16 16 -0.18 46 62
FOS 0.023 0.022 0.24 4 -10000 0 4
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.004 0.1 0.33 37 -10000 0 37
HGF/MET/MUC20 0.014 0.064 0.17 9 -0.16 50 59
cell migration 0.017 0.074 0.16 16 -0.18 46 62
GRB2 0.025 0.005 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.015 0.054 -10000 0 -0.15 42 42
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.007 0.073 -10000 0 -0.23 41 41
MET/MUC20 0.003 0.048 -10000 0 -0.15 42 42
RAP1B 0 0.13 0.35 22 -0.4 17 39
RAP1A -0.004 0.12 0.32 19 -0.4 17 36
HGF/MET/RANBP9 0.027 0.071 0.19 9 -0.16 49 58
RAF1 -0.029 0.16 0.29 2 -0.48 50 52
STAT3 -0.023 0.093 -10000 0 -0.27 45 45
cell proliferation -0.022 0.14 0.32 16 -0.36 46 62
RPS6KB1 -0.002 0.043 -10000 0 -0.24 9 9
MAPK3 -0.005 0.097 0.48 6 -10000 0 6
MAPK1 0.001 0.12 0.41 28 -10000 0 28
RANBP9 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.009 0.14 0.32 10 -0.4 31 41
SRC -0.022 0.07 -10000 0 -0.22 40 40
PI3K 0.016 0.078 0.16 14 -0.19 46 60
MET/Glomulin 0.014 0.026 -10000 0 -0.12 13 13
SOS1 0.025 0.005 -10000 0 -10000 0 0
MAP2K1 -0.024 0.16 0.3 10 -0.45 50 60
MET 0.021 0.01 -10000 0 -10000 0 0
MAP4K1 0.002 0.12 0.3 9 -0.43 20 29
PTK2 0.021 0.01 -10000 0 -10000 0 0
MAP2K2 -0.024 0.16 0.31 12 -0.45 50 62
BAD -0.002 0.084 0.39 6 -0.65 3 9
MAP2K4 -0.004 0.11 0.3 12 -0.36 21 33
SHP2/GRB2/SOS1/GAB1 0.005 0.11 -10000 0 -0.33 34 34
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PXN 0.025 0.006 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.02 0.058 -10000 0 -0.19 47 47
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF 0.026 0.031 0.24 9 -10000 0 9
RASA1 0.024 0.007 -10000 0 -10000 0 0
NCK1 0.024 0.007 -10000 0 -10000 0 0
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.018 0.078 0.16 17 -0.19 47 64
PDPK1 0 0.076 0.24 4 -0.63 4 8
HGF/MET/SHIP 0.022 0.084 0.19 8 -0.19 55 63
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.011 -10000 0 -10000 0 0
CDC42/GTP -0.012 0.098 -10000 0 -0.26 43 43
PLCG1 -0.022 0.089 0.15 4 -0.22 71 75
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.004 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
G12/G13 0.034 0.013 -10000 0 -10000 0 0
cell migration -0.012 0.096 -10000 0 -0.26 43 43
S1PR5 0.021 0.01 -10000 0 -10000 0 0
S1PR4 0.034 0.044 0.24 20 -10000 0 20
MAPK3 -0.023 0.089 0.15 4 -0.22 72 76
MAPK1 -0.021 0.088 0.15 4 -0.22 70 74
S1P/S1P5/Gi -0.04 0.12 -10000 0 -0.24 111 111
GNAI1 0.024 0.013 0.24 1 -10000 0 1
CDC42/GDP 0.019 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.057 -10000 0 -0.13 67 67
RHOA 0 0.065 0.19 44 -10000 0 44
S1P/S1P4/Gi -0.016 0.096 0.17 3 -0.23 73 76
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.008 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.031 0.18 17 -10000 0 17
GNA12 0.023 0.008 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.026 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.009 0.056 0.31 6 -0.97 1 7
VDR 0.026 0.015 0.24 2 -10000 0 2
FAM120B 0.025 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.017 0.097 0.32 2 -0.28 25 27
RXRs/LXRs/DNA/Oxysterols -0.017 0.12 0.39 2 -0.4 23 25
MED1 0.025 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.012 0.071 2 -0.06 2 4
RARs/THRs/DNA/Src-1 0.012 0.042 0.17 1 -0.16 25 26
RXRs/NUR77 0.023 0.091 0.22 12 -0.14 88 100
RXRs/PPAR -0.023 0.088 -10000 0 -0.18 101 101
NCOR2 0.025 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.02 0.17 2 -0.15 5 7
RARs/VDR/DNA/Vit D3 0.051 0.038 0.18 2 -0.13 15 17
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.025 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.015 0.24 2 -10000 0 2
RARs/RARs/DNA/9cRA 0.036 0.033 -10000 0 -0.12 13 13
RARG 0.025 0.006 -10000 0 -10000 0 0
RPS6KB1 0.002 0.059 0.53 5 -0.4 1 6
RARs/THRs/DNA/SMRT 0.011 0.04 -10000 0 -0.16 23 23
THRA 0.025 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.02 0.17 2 -0.15 5 7
RXRs/PPAR/9cRA/PGJ2/DNA 0.014 0.085 0.3 2 -0.16 29 31
NR1H4 0.026 0.044 0.24 18 -10000 0 18
RXRs/LXRs/DNA 0.03 0.1 0.37 1 -0.22 22 23
NR1H2 0.025 0.02 0.1 1 -0.056 23 24
NR1H3 0.024 0.021 0.11 1 -0.064 18 19
RXRs/VDR/DNA/Vit D3 0.02 0.082 0.21 8 -0.12 91 99
NR4A1 0.028 0.03 0.24 9 -10000 0 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.04 0.096 0.19 3 -0.17 147 150
RXRG 0.021 0.032 0.22 7 -0.058 17 24
RXR alpha/CCPG 0.033 0.021 -10000 0 -10000 0 0
RXRA 0.023 0.02 0.1 1 -0.057 23 24
RXRB 0.024 0.021 0.11 1 -0.064 18 19
THRB 0.028 0.026 0.24 7 -10000 0 7
PPARG 0.025 0.019 0.24 3 -10000 0 3
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF -0.044 0.2 0.51 2 -0.87 24 26
mol:Oxysterols 0.001 0.011 0.065 2 -0.058 1 3
cholesterol transport -0.016 0.12 0.39 2 -0.4 23 25
PPARA 0.025 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.025 0.006 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.024 0.086 0.18 1 -0.19 93 94
SREBF1 -0.021 0.11 0.35 2 -0.5 6 8
RXRs/RXRs/DNA/9cRA 0.014 0.085 0.29 2 -0.13 104 106
ABCA1 -0.024 0.11 0.4 2 -0.4 22 24
RARs/THRs 0.067 0.04 0.2 5 -0.13 12 17
RXRs/FXR -0.004 0.1 0.22 13 -0.14 140 153
BCL2 0.022 0.009 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.014 0.14 0.35 1 -0.78 13 14
oxygen homeostasis 0.005 0.015 0.1 2 -0.081 1 3
TCEB2 0.028 0.027 0.24 7 -10000 0 7
TCEB1 0.021 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.038 0.083 0.26 4 -0.23 5 9
EPO 0.026 0.2 0.42 22 -0.42 40 62
FIH (dimer) 0.022 0.028 0.14 1 -0.097 1 2
APEX1 0.023 0.031 -10000 0 -10000 0 0
SERPINE1 0.053 0.19 0.48 29 -0.38 22 51
FLT1 -0.004 0.17 -10000 0 -0.69 25 25
ADORA2A 0.041 0.17 0.39 34 -0.38 15 49
germ cell development 0.055 0.19 0.46 31 -0.38 27 58
SLC11A2 0.048 0.17 0.4 27 -0.39 15 42
BHLHE40 0.051 0.18 0.43 29 -0.42 16 45
HIF1AN 0.022 0.028 0.14 1 -0.097 1 2
HIF2A/ARNT/SIRT1 0.053 0.14 0.36 26 -0.27 12 38
ETS1 0.025 0.031 0.18 3 -0.12 17 20
CITED2 0.024 0.076 0.38 1 -0.58 5 6
KDR -0.02 0.22 -10000 0 -0.84 31 31
PGK1 0.054 0.18 0.42 30 -0.39 15 45
SIRT1 0.022 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.094 0.22 0.54 29 -0.43 15 44
EPAS1 0.028 0.09 0.24 29 -0.22 7 36
SP1 0.026 0.017 0.14 1 -0.1 7 8
ABCG2 0.04 0.19 0.43 28 -0.4 35 63
EFNA1 0.048 0.17 0.42 25 -0.39 15 40
FXN 0.037 0.17 0.38 34 -0.38 15 49
POU5F1 0.055 0.19 0.46 31 -0.39 27 58
neuron apoptosis -0.091 0.21 0.42 15 -0.53 28 43
EP300 0.025 0.004 -10000 0 -10000 0 0
EGLN3 0.022 0.027 -10000 0 -10000 0 0
EGLN2 0.023 0.028 0.13 2 -0.098 1 3
EGLN1 0.022 0.028 0.14 1 -0.097 1 2
VHL/Elongin B/Elongin C 0.041 0.027 0.19 4 -10000 0 4
VHL 0.025 0.005 -10000 0 -10000 0 0
ARNT 0.023 0.033 0.16 2 -10000 0 2
SLC2A1 0.042 0.17 0.38 37 -0.38 15 52
TWIST1 0.062 0.19 0.44 44 -0.39 15 59
ELK1 0.028 0.008 0.14 2 -10000 0 2
HIF2A/ARNT/Cbp/p300 0.059 0.14 0.35 22 -0.28 8 30
VEGFA 0.047 0.19 0.42 31 -0.39 25 56
CREBBP 0.025 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.025 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.011 0.06 -10000 0 -0.18 35 35
NT3 (dimer)/TRKC -0.011 0.097 -10000 0 -0.2 97 97
NT3 (dimer)/TRKB 0 0.096 0.19 1 -0.17 104 105
SHC/Grb2/SOS1/GAB1/PI3K 0.014 0.027 -10000 0 -0.18 8 8
RAPGEF1 0.024 0.006 -10000 0 -10000 0 0
BDNF 0.02 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
NTRK1 0.027 0.029 0.24 8 -10000 0 8
NTRK2 0.022 0.014 0.24 1 -10000 0 1
NTRK3 0.021 0.01 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB -0.019 0.11 0.19 1 -0.18 142 143
neuron apoptosis 0.047 0.14 0.35 66 -10000 0 66
SHC 2-3/Grb2 -0.05 0.16 0.28 1 -0.38 66 67
SHC1 0.025 0.006 -10000 0 -10000 0 0
SHC2 -0.047 0.14 -10000 0 -0.37 55 55
SHC3 -0.067 0.17 -10000 0 -0.44 68 68
STAT3 (dimer) 0.029 0.008 0.15 1 -10000 0 1
NT3 (dimer)/TRKA 0.014 0.086 0.19 8 -0.16 80 88
RIN/GDP 0.004 0.09 0.26 18 -0.22 15 33
GIPC1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.024 0.007 -10000 0 -10000 0 0
DNAJA3 -0.036 0.083 0.15 1 -0.23 63 64
RIN/GTP 0.025 0.038 0.17 31 -10000 0 31
CCND1 -0.014 0.013 0.27 1 -10000 0 1
MAGED1 0.026 0.01 0.24 1 -10000 0 1
PTPN11 0.025 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.011 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.047 0.017 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.086 0.092 0.19 185 -0.14 25 210
TRKA/NEDD4-2 0.027 0.051 0.19 15 -0.16 22 37
ELMO1 0.023 0.008 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.028 0.02 -10000 0 -0.13 5 5
NGF 0.025 0.015 0.24 2 -10000 0 2
HRAS 0.028 0.024 0.24 6 -10000 0 6
DOCK1 0.025 0.006 -10000 0 -10000 0 0
GAB2 0.025 0.006 -10000 0 -10000 0 0
RIT2 0.035 0.055 0.24 31 -10000 0 31
RIT1 0.025 0.006 -10000 0 -10000 0 0
FRS2 0.025 0.005 -10000 0 -10000 0 0
DNM1 0.025 0.012 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.01 0.091 -10000 0 -0.22 64 64
mol:GDP -0.015 0.11 0.3 18 -0.32 19 37
NGF (dimer) 0.025 0.015 0.24 2 -10000 0 2
RhoG/GDP 0.016 0.012 -10000 0 -0.15 2 2
RIT1/GDP -0.006 0.083 0.26 12 -0.22 17 29
TIAM1 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.003 0.1 0.19 1 -0.18 111 112
KIDINS220/CRKL/C3G 0.036 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.034 0.015 -10000 0 -0.16 1 1
FRS2 family/SHP2 0.048 0.017 -10000 0 -0.14 1 1
SHC/GRB2/SOS1/GAB1 0.059 0.023 -10000 0 -0.13 1 1
RIT1/GTP 0.018 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.022 0.01 -10000 0 -10000 0 0
RAP1/GDP -0.009 0.063 0.14 4 -0.19 18 22
KIDINS220/CRKL 0.025 0.004 -10000 0 -10000 0 0
BDNF (dimer) 0.02 0.011 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.031 0.062 0.18 17 -0.14 42 59
Schwann cell development -0.022 0.022 -10000 0 -0.077 35 35
EHD4 0.025 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.059 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.014 0.036 -10000 0 -0.16 9 9
RAP1B 0.025 0.005 -10000 0 -10000 0 0
RAP1A 0.025 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.029 0.11 -10000 0 -0.19 137 137
ABL1 0.025 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.075 -10000 0 -0.3 19 19
STAT3 0.029 0.008 0.15 1 -10000 0 1
axon guidance -0.075 0.079 0.1 1 -0.25 67 68
MAPK3 0.016 0.069 0.23 12 -0.14 18 30
MAPK1 0.016 0.07 0.23 13 -0.14 19 32
CDC42/GDP -0.003 0.087 0.25 16 -0.22 17 33
NTF3 0.022 0.01 -10000 0 -10000 0 0
NTF4 0.02 0.011 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.031 0.06 0.19 9 -0.14 42 51
PI3K 0.03 0.028 -10000 0 -0.18 6 6
FRS3 0.026 0.003 -10000 0 -10000 0 0
FAIM 0.024 0.007 -10000 0 -10000 0 0
GAB1 0.025 0.004 -10000 0 -10000 0 0
RASGRF1 -0.039 0.099 0.15 4 -0.26 66 70
SOS1 0.025 0.005 -10000 0 -10000 0 0
MCF2L -0.045 0.06 -10000 0 -0.17 83 83
RGS19 0.025 0.011 0.24 1 -10000 0 1
CDC42 0.026 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.1 0.27 6 -0.4 15 21
Rac1/GDP -0.005 0.078 0.26 8 -0.22 16 24
NGF (dimer)/TRKA/GRIT 0.02 0.054 0.17 10 -0.14 45 55
neuron projection morphogenesis -0.034 0.17 -10000 0 -0.76 17 17
NGF (dimer)/TRKA/NEDD4-2 0.031 0.062 0.19 17 -0.14 42 59
MAP2K1 -0.011 0.071 0.22 36 -10000 0 36
NGFR 0.023 0.008 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.005 0.053 0.17 1 -0.17 39 40
RAS family/GTP/PI3K 0.013 0.022 -10000 0 -0.21 3 3
FRS2 family/SHP2/GRB2/SOS1 0.067 0.028 -10000 0 -0.13 1 1
NRAS 0.025 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
PRKCI 0.024 0.012 0.24 1 -10000 0 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.003 -10000 0 -10000 0 0
MAPKKK cascade -0.056 0.2 -10000 0 -0.52 69 69
RASA1 0.024 0.007 -10000 0 -10000 0 0
TRKA/c-Abl 0.028 0.048 0.19 8 -0.16 23 31
SQSTM1 0.025 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.009 0.099 0.2 1 -0.17 109 110
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.064 -10000 0 -0.13 41 41
MATK 0.12 0.11 0.24 213 -10000 0 213
NEDD4L 0.028 0.037 0.24 13 -10000 0 13
RAS family/GDP -0.022 0.048 -10000 0 -0.15 35 35
NGF (dimer)/TRKA -0.025 0.091 0.16 1 -0.23 68 69
Rac1/GTP -0.052 0.073 -10000 0 -0.21 67 67
FRS2 family/SHP2/CRK family 0.066 0.029 -10000 0 -0.13 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.045 0.16 5 -0.11 38 43
RGS9BP 0.026 0.01 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.021 0.021 0.24 4 -10000 0 4
mol:Na + 0.027 0.03 0.16 19 -10000 0 19
mol:ADP -0.016 0.015 0.14 4 -10000 0 4
GNAT2 0.026 0.02 0.24 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.013 0.078 0.19 4 -0.14 100 104
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.029 0.022 0.19 7 -10000 0 7
GRK7 0.021 0.007 -10000 0 -10000 0 0
CNGB3 0.02 0.033 0.24 10 -10000 0 10
Cone Metarhodopsin II/X-Arrestin 0.015 0.008 0.17 1 -10000 0 1
mol:Ca2+ 0.038 0.095 0.18 130 -10000 0 130
Cone PDE6 0.024 0.076 0.2 2 -0.12 92 94
Cone Metarhodopsin II 0.025 0.015 0.16 4 -10000 0 4
Na + (4 Units) 0.044 0.047 0.17 50 -10000 0 50
GNAT2/GDP 0.023 0.073 0.18 6 -0.12 97 103
GNB5 0.025 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.012 0.031 0.17 11 -10000 0 11
Cone Transducin 0.032 0.049 0.18 5 -0.12 38 43
SLC24A2 0.042 0.064 0.24 44 -10000 0 44
GNB3/GNGT2 0.02 0.054 0.19 1 -0.16 38 39
GNB3 0.022 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.019 0.014 0.17 4 -10000 0 4
CNGA3 0.028 0.039 0.24 15 -10000 0 15
ARR3 0.021 0.011 0.24 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.027 0.03 0.17 19 -10000 0 19
mol:Pi 0.012 0.078 0.19 4 -0.14 100 104
Cone CNG Channel 0.039 0.035 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.042 0.064 0.24 44 -10000 0 44
RGS9 0.021 0.021 0.24 3 -10000 0 3
PDE6C 0.018 0.006 -10000 0 -10000 0 0
GNGT2 0.026 0.011 0.24 1 -10000 0 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.021 0.24 4 -10000 0 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.025 0.005 -10000 0 -10000 0 0
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
NUDC 0.026 0.002 -10000 0 -10000 0 0
RELN/LRP8 0.061 0.056 0.2 58 -0.13 4 62
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.025 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.004 0.064 0.18 40 -10000 0 40
IQGAP1/CaM 0.037 0.008 -10000 0 -10000 0 0
DAB1 0.016 0.019 0.24 2 -10000 0 2
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
PLA2G7 0.078 0.094 0.24 119 -10000 0 119
CALM1 0.025 0.005 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.019 0.19 6 -10000 0 6
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.006 -10000 0 -10000 0 0
CDK5R1 0.036 0.046 0.24 23 -10000 0 23
LIS1/Poliovirus Protein 3A -0.013 0.004 -10000 0 -10000 0 0
CDK5R2 0.047 0.066 0.24 50 -10000 0 50
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.004 0.093 0.19 28 -0.14 131 159
YWHAE 0.024 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.018 0.092 0.26 46 -0.19 1 47
MAP1B -0.008 0.047 -10000 0 -0.19 30 30
RAC1 0.007 0.003 -10000 0 -10000 0 0
p35/CDK5 -0.002 0.07 0.2 38 -10000 0 38
RELN 0.05 0.073 0.24 60 -10000 0 60
PAFAH/LIS1 0.053 0.064 0.17 106 -0.14 1 107
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.016 0.049 0.15 6 -0.18 1 7
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.088 0.17 2 -0.25 20 22
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.02 0.088 0.26 46 -0.17 1 47
LIS1/IQGAP1 0.021 0.007 -10000 0 -10000 0 0
RHOA 0.007 0.003 -10000 0 -10000 0 0
PAFAH1B1 -0.017 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.032 0.04 0.24 17 -10000 0 17
PAFAH1B2 0.024 0.007 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.004 0.045 -10000 0 -0.14 27 27
NDEL1/Katanin 60/Dynein heavy chain 0.011 0.089 0.28 31 -10000 0 31
LRP8 0.028 0.026 0.24 7 -10000 0 7
NDEL1/Katanin 60 0.015 0.091 0.26 45 -0.19 1 46
P39/CDK5 0.008 0.083 0.19 63 -10000 0 63
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.007 -10000 0 -10000 0 0
CDK5 -0.011 0.045 0.18 16 -10000 0 16
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.007 -10000 0 -10000 0 0
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.001 0.086 0.18 27 -0.12 127 154
RELN/VLDLR 0.07 0.057 0.2 55 -0.12 5 60
CDC42 0.007 0.003 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.056 0.047 0.18 20 -0.13 19 39
ER alpha/Gai/GDP/Gbeta gamma -0.05 0.14 -10000 0 -0.37 59 59
AKT1 -0.026 0.17 -10000 0 -0.67 31 31
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.021 0.18 -10000 0 -0.67 31 31
mol:Ca2+ -0.014 0.048 0.16 1 -0.35 4 5
IGF1R 0.026 0.01 0.24 1 -10000 0 1
E2/ER alpha (dimer)/Striatin 0.017 0.053 0.17 1 -0.14 47 48
SHC1 0.025 0.006 -10000 0 -10000 0 0
apoptosis 0.024 0.16 0.64 31 -10000 0 31
RhoA/GTP -0.029 0.021 0.067 6 -0.12 13 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.12 0.23 1 -0.31 50 51
regulation of stress fiber formation 0.028 0.057 0.2 5 -0.16 27 32
E2/ERA-ERB (dimer) 0.034 0.041 0.17 20 -0.13 15 35
KRAS 0.024 0.007 -10000 0 -10000 0 0
G13/GTP 0.027 0.027 0.16 1 -0.12 15 16
pseudopodium formation -0.028 0.057 0.16 27 -0.2 5 32
E2/ER alpha (dimer)/PELP1 0.027 0.031 0.17 1 -0.13 16 17
GRB2 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.025 0.004 -10000 0 -10000 0 0
GNAO1 0.019 0.011 -10000 0 -10000 0 0
HRAS 0.028 0.024 0.24 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.025 0.13 0.28 3 -0.41 31 34
E2/ER beta (dimer) 0.025 0.029 0.17 19 -10000 0 19
mol:GDP 0.008 0.056 0.18 2 -0.22 22 24
mol:NADP -0.025 0.13 0.28 3 -0.41 31 34
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
mol:IP3 -0.014 0.048 -10000 0 -0.31 6 6
IGF-1R heterotetramer 0.026 0.01 0.24 1 -10000 0 1
PLCB1 -0.003 0.049 -10000 0 -0.3 5 5
PLCB2 -0.003 0.051 -10000 0 -0.3 6 6
IGF1 0.031 0.041 0.24 17 -10000 0 17
mol:L-citrulline -0.025 0.13 0.28 3 -0.41 31 34
RHOA 0.025 0.005 -10000 0 -10000 0 0
Gai/GDP -0.13 0.28 -10000 0 -0.61 122 122
JNK cascade 0.024 0.029 0.17 19 -10000 0 19
BCAR1 0.021 0.01 -10000 0 -10000 0 0
ESR2 0.034 0.042 0.24 19 -10000 0 19
GNAQ 0.025 0.005 -10000 0 -10000 0 0
ESR1 0.025 0.012 0.24 1 -10000 0 1
Gq family/GDP/Gbeta gamma -0.021 0.15 -10000 0 -0.41 49 49
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.011 0.07 -10000 0 -0.48 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.022 0.13 0.23 1 -0.32 53 54
GNAZ 0.023 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.014 0.031 0.17 1 -0.15 16 17
STRN 0.023 0.008 -10000 0 -10000 0 0
GNAL 0.018 0.012 -10000 0 -10000 0 0
PELP1 0.024 0.007 -10000 0 -10000 0 0
MAPK11 -0.007 0.029 0.11 27 -10000 0 27
GNAI2 0.025 0.004 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.024 0.013 0.24 1 -10000 0 1
HBEGF -0.024 0.15 0.38 6 -0.34 53 59
cAMP biosynthetic process -0.003 0.066 0.11 20 -0.11 119 139
SRC -0.052 0.14 0.19 2 -0.36 58 60
PI3K 0.03 0.028 -10000 0 -0.18 6 6
GNB1 0.026 0.003 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.036 0.062 -10000 0 -0.22 21 21
SOS1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.034 0.1 0.14 1 -0.27 60 61
Gs family/GTP 0.002 0.071 0.14 20 -0.11 119 139
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.021 0.18 6 -10000 0 6
vasodilation -0.023 0.13 0.26 4 -0.39 31 35
mol:DAG -0.014 0.048 -10000 0 -0.31 6 6
Gs family/GDP/Gbeta gamma -0.011 0.076 -10000 0 -0.23 29 29
MSN -0.03 0.059 0.17 27 -0.21 5 32
Gq family/GTP 0.007 0.056 -10000 0 -0.31 6 6
mol:PI-3-4-5-P3 -0.02 0.17 -10000 0 -0.65 31 31
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.023 0.13 0.39 31 -0.26 4 35
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.06 0.18 2 -0.21 24 26
NOS3 -0.027 0.14 0.33 2 -0.43 31 33
GNA11 0.024 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.15 0.35 2 -0.46 37 39
E2/ER alpha (dimer)/PELP1/Src -0.024 0.13 0.26 3 -0.32 54 57
ruffle organization -0.028 0.057 0.16 27 -0.2 5 32
ROCK2 -0.02 0.057 0.18 26 -0.2 4 30
GNA14 0.025 0.005 -10000 0 -10000 0 0
GNA15 0.024 0.007 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
MMP9 -0.016 0.14 0.34 5 -0.34 48 53
MMP2 -0.048 0.14 0.25 3 -0.35 57 60
Arf6 signaling events

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
CENTA1/KIF3B 0.023 0.018 -10000 0 -0.13 1 1
ARNO/beta Arrestin1-2 0.026 0.097 -10000 0 -0.75 7 7
EGFR 0.021 0.01 -10000 0 -10000 0 0
EPHA2 0.025 0.019 0.24 3 -10000 0 3
USP6 0.024 0.008 -10000 0 -10000 0 0
IQSEC1 0.025 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.021 0.081 0.19 34 -0.17 56 90
ARRB2 0.008 0.011 0.12 4 -10000 0 4
mol:GTP 0.005 0.041 0.13 12 -0.15 6 18
ARRB1 0.025 0.005 -10000 0 -10000 0 0
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR 0.027 0.025 0.24 6 -10000 0 6
EGF 0.042 0.061 0.24 40 -10000 0 40
somatostatin receptor activity 0 0 0.001 39 -0.001 16 55
ARAP2 0.025 0.004 -10000 0 -10000 0 0
mol:GDP 0.013 0.086 0.21 31 -0.22 20 51
mol:PI-3-4-5-P3 0 0 0.001 34 -0.001 4 38
ITGA2B 0.026 0.023 0.24 5 -10000 0 5
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.057 0.2 3 -0.13 39 42
ADAP1 0.024 0.013 0.24 1 -10000 0 1
KIF13B 0.019 0.012 -10000 0 -10000 0 0
HGF/MET 0.014 0.076 0.19 9 -0.2 49 58
PXN 0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.018 0.1 0.27 39 -0.2 19 58
EGFR/EGFR/EGF/EGF/ARFGEP100 0.033 0.075 0.19 33 -0.15 54 87
ADRB2 0.027 0.022 0.24 5 -10000 0 5
receptor agonist activity 0 0 0.001 20 0 12 32
actin filament binding 0 0 0.001 39 0 16 55
SRC 0.025 0.005 -10000 0 -10000 0 0
ITGB3 0.02 0.011 -10000 0 -10000 0 0
GNAQ 0.025 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 47 -0.001 5 52
ARF6/GDP -0.003 0.12 0.31 11 -0.3 30 41
ARF6/GDP/GULP/ACAP1 0.037 0.09 0.24 21 -0.22 15 36
alphaIIb/beta3 Integrin/paxillin/GIT1 0.02 0.077 0.2 2 -0.13 96 98
ACAP1 0.032 0.047 0.24 22 -10000 0 22
ACAP2 0.024 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.025 0.2 4 -10000 0 4
EFNA1 0.025 0.006 -10000 0 -10000 0 0
HGF 0.026 0.031 0.24 9 -10000 0 9
CYTH3 -0.008 0.012 0.14 3 -10000 0 3
CYTH2 0.004 0.12 -10000 0 -0.97 7 7
NCK1 0.024 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 42 0 13 55
endosomal lumen acidification 0 0 0.001 37 0 23 60
microtubule-based process 0 0 -10000 0 0 5 5
GULP1 0.026 0.015 0.24 2 -10000 0 2
GNAQ/ARNO 0.021 0.11 -10000 0 -0.86 7 7
mol:Phosphatidic acid 0 0 0 14 -10000 0 14
PIP3-E 0 0 0 25 0 3 28
MET 0.021 0.01 -10000 0 -10000 0 0
GNA14 0.025 0.005 -10000 0 -10000 0 0
GNA15 0.024 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 45 -0.001 10 55
GNA11 0.024 0.006 -10000 0 -10000 0 0
LHCGR 0.019 0.023 0.24 4 -10000 0 4
AGTR1 0.059 0.082 0.24 80 -10000 0 80
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.025 0.2 4 -10000 0 4
IPCEF1/ARNO 0.022 0.12 -10000 0 -0.81 7 7
alphaIIb/beta3 Integrin -0.003 0.079 0.19 2 -0.16 98 100
FAS signaling pathway (CD95)

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
SPTAN1 -0.002 0.049 0.18 24 -0.18 4 28
RFC1 -0.008 0.033 0.22 2 -0.18 5 7
PRKDC 0.013 0.069 0.22 44 -0.18 3 47
RIPK1 0.021 0.019 -10000 0 -10000 0 0
CASP7 -0.013 0.098 -10000 0 -0.54 13 13
FASLG/FAS/FADD/FAF1 -0.014 0.065 0.17 4 -0.2 25 29
MAP2K4 -0.057 0.17 0.3 8 -0.32 104 112
mol:ceramide -0.018 0.11 0.24 5 -0.26 34 39
GSN -0.004 0.044 0.22 12 -0.18 4 16
FASLG/FAS/FADD/FAF1/Caspase 8 -0.015 0.08 0.22 3 -0.21 33 36
FAS 0.014 0.025 -10000 0 -0.042 6 6
BID -0.029 0.019 -10000 0 -0.15 11 11
MAP3K1 -0.019 0.11 0.28 7 -0.31 18 25
MAP3K7 0.014 0.02 -10000 0 -10000 0 0
RB1 -0.006 0.024 -10000 0 -0.17 1 1
CFLAR 0.021 0.02 -10000 0 -10000 0 0
HGF/MET 0.028 0.071 0.19 9 -0.17 46 55
ARHGDIB -0.005 0.039 0.17 15 -0.18 5 20
FADD 0.014 0.026 -10000 0 -0.046 2 2
actin filament polymerization 0.003 0.044 0.18 4 -0.21 13 17
NFKB1 -0.008 0.11 -10000 0 -0.58 4 4
MAPK8 -0.089 0.22 0.35 9 -0.47 108 117
DFFA -0.008 0.031 0.22 1 -0.18 5 6
DNA fragmentation during apoptosis -0.007 0.036 0.21 4 -0.18 5 9
FAS/FADD/MET 0.016 0.061 -10000 0 -0.15 39 39
CFLAR/RIP1 0.032 0.028 -10000 0 -10000 0 0
FAIM3 0.03 0.033 0.24 11 -10000 0 11
FAF1 0.015 0.029 -10000 0 -0.043 54 54
PARP1 -0.009 0.029 0.13 10 -0.18 5 15
DFFB -0.007 0.036 0.21 4 -0.18 5 9
CHUK -0.014 0.1 -10000 0 -0.5 5 5
FASLG 0.023 0.05 0.24 17 -0.049 8 25
FAS/FADD 0.019 0.04 -10000 0 -0.17 6 6
HGF 0.026 0.031 0.24 9 -10000 0 9
LMNA -0.01 0.032 0.19 4 -0.16 3 7
CASP6 -0.008 0.029 0.13 11 -0.18 4 15
CASP10 0.015 0.028 0.24 1 -0.044 9 10
CASP3 -0.001 0.03 0.16 12 -0.21 1 13
PTPN13 0.025 0.005 -10000 0 -10000 0 0
CASP8 -0.028 0.023 -10000 0 -0.17 11 11
IL6 -0.19 0.48 -10000 0 -1.1 106 106
MET 0.021 0.01 -10000 0 -10000 0 0
ICAD/CAD -0.011 0.037 0.24 4 -0.17 5 9
FASLG/FAS/FADD/FAF1/Caspase 10 -0.019 0.11 0.24 5 -0.26 34 39
activation of caspase activity by cytochrome c -0.029 0.019 -10000 0 -0.15 11 11
PAK2 -0.001 0.047 0.21 15 -0.18 3 18
BCL2 0.022 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.016 0.061 -10000 0 -0.16 51 51
ATM 0.024 0.007 -10000 0 -10000 0 0
UBE2D3 0.025 0.004 -10000 0 -10000 0 0
PRKDC 0.022 0.014 0.24 1 -10000 0 1
ATR 0.024 0.007 -10000 0 -10000 0 0
UBE2L3 0.025 0.004 -10000 0 -10000 0 0
FANCD2 0.013 0.007 -10000 0 -10000 0 0
protein ubiquitination 0.041 0.06 -10000 0 -0.12 44 44
XRCC5 0.025 0.004 -10000 0 -10000 0 0
XRCC6 0.025 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.04 0.023 -10000 0 -10000 0 0
MRE11A 0.025 0.005 -10000 0 -10000 0 0
DNA-PK 0.043 0.022 0.19 1 -10000 0 1
FA complex/FANCD2/Ubiquitin 0.005 0.051 0.21 1 -0.32 1 2
FANCF 0.025 0.004 -10000 0 -10000 0 0
BRCA1 0.025 0.011 0.24 1 -10000 0 1
CCNE1 0.028 0.022 0.24 5 -10000 0 5
CDK2/Cyclin E1 0.038 0.017 0.19 5 -10000 0 5
FANCG 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.016 0.061 0.19 1 -0.16 51 52
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.006 -10000 0 -10000 0 0
NBN 0.02 0.011 -10000 0 -10000 0 0
FANCA 0.034 0.053 0.24 28 -10000 0 28
DNA repair -0.017 0.065 0.37 3 -0.27 1 4
BRCA1/BARD1/ubiquitin 0.016 0.061 0.19 1 -0.16 51 52
BARD1/DNA-PK 0.035 0.061 0.2 1 -0.13 50 51
FANCL 0.025 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.016 0.061 0.16 51 -10000 0 51
BRCA1/BARD1/CTIP/M/R/N Complex 0.001 0.059 -10000 0 -0.16 44 44
BRCA1/BACH1/BARD1/TopBP1 0.027 0.058 0.19 1 -0.14 49 50
BRCA1/BARD1/P53 0.033 0.06 0.2 1 -0.13 47 48
BARD1/CSTF1/BRCA1 0.03 0.058 0.19 1 -0.14 49 50
BRCA1/BACH1 0.025 0.011 0.24 1 -10000 0 1
BARD1 0.023 0.008 -10000 0 -10000 0 0
PCNA 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.059 0.19 1 -0.14 51 52
BRCA1/BARD1/UbcH7 0.029 0.059 0.19 1 -0.14 51 52
BRCA1/BARD1/RAD51/PCNA 0.049 0.068 0.2 25 -0.13 43 68
BARD1/DNA-PK/P53 0.037 0.064 0.2 1 -0.13 41 42
BRCA1/BARD1/Ubiquitin 0.016 0.061 0.19 1 -0.16 51 52
BRCA1/BARD1/CTIP 0.016 0.052 0.17 1 -0.13 50 51
FA complex 0.019 0.038 0.18 7 -0.16 7 14
BARD1/EWS 0.016 0.061 -10000 0 -0.16 53 53
RBBP8 -0.017 0.006 -10000 0 -10000 0 0
TP53 0.022 0.009 -10000 0 -10000 0 0
TOPBP1 0.024 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.031 0.059 0.13 47 -0.19 1 48
BRCA1/BARD1 0.046 0.063 -10000 0 -0.13 44 44
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0.053 -10000 0 -0.15 53 53
CDK2 0.025 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.042 0.058 0.24 37 -10000 0 37
RAD50 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.016 0.061 0.19 1 -0.16 51 52
EWSR1 0.025 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.025 0.066 0.19 9 -0.25 4 13
NF kappa B1 p50/RelA/I kappa B alpha -0.031 0.081 0.29 4 -0.29 13 17
alphaV/beta3 Integrin/Osteopontin/Src 0.054 0.058 0.19 64 -0.17 3 67
AP1 -0.009 0.11 0.36 2 -0.27 29 31
ILK -0.025 0.067 0.21 10 -0.25 3 13
bone resorption -0.039 0.072 0.21 4 -0.22 34 38
PTK2B 0.018 0.012 -10000 0 -10000 0 0
PYK2/p130Cas 0.027 0.084 0.28 3 -0.19 9 12
ITGAV 0.024 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.017 0.062 -10000 0 -0.17 45 45
alphaV/beta3 Integrin/Osteopontin 0.031 0.094 0.2 52 -0.14 78 130
MAP3K1 -0.024 0.061 0.2 7 -0.2 9 16
JUN 0.025 0.012 0.24 1 -10000 0 1
MAPK3 -0.027 0.071 0.22 12 -0.25 11 23
MAPK1 -0.028 0.071 0.23 11 -0.25 11 22
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.026 0.06 0.19 9 -0.21 13 22
ITGB3 0.02 0.014 -10000 0 -10000 0 0
NFKBIA -0.026 0.076 0.26 4 -0.28 16 20
FOS 0.023 0.023 0.24 4 -10000 0 4
CD44 0.025 0.006 -10000 0 -10000 0 0
CHUK 0.024 0.007 -10000 0 -10000 0 0
PLAU -0.043 0.17 0.43 2 -1 12 14
NF kappa B1 p50/RelA -0.036 0.083 0.26 4 -0.36 11 15
BCAR1 0.021 0.01 -10000 0 -10000 0 0
RELA 0.025 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0 0.078 -10000 0 -0.16 90 90
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.026 0.068 0.2 10 -0.22 9 19
VAV3 -0.03 0.075 0.23 10 -0.22 26 36
MAP3K14 -0.024 0.069 0.22 10 -0.26 4 14
ROCK2 0.023 0.008 -10000 0 -10000 0 0
SPP1 0.055 0.078 0.24 69 -10000 0 69
RAC1 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.071 0.2 7 -0.22 24 31
MMP2 -0.046 0.082 0.24 4 -0.32 16 20
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.014 0.029 0.22 1 -0.056 51 52
PDGF/PDGFRA/CRKL 0.019 0.048 0.17 1 -0.17 21 22
positive regulation of JUN kinase activity 0.048 0.041 -10000 0 -0.13 17 17
CRKL 0.025 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.012 0.094 0.19 17 -0.17 105 122
AP1 -0.13 0.25 0.28 4 -0.67 80 84
mol:IP3 -0.03 0.038 0.083 1 -0.21 13 14
PLCG1 -0.03 0.038 0.083 1 -0.22 13 14
PDGF/PDGFRA/alphaV Integrin 0.018 0.048 0.17 1 -0.16 22 23
RAPGEF1 0.024 0.006 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.038 0.083 1 -0.21 13 14
CAV3 0.027 0.042 0.24 17 -10000 0 17
CAV1 0.021 0.01 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.05 0.042 -10000 0 -0.13 17 17
PDGF/PDGFRA/Shf 0.019 0.049 0.18 2 -0.17 20 22
FOS -0.13 0.24 0.26 5 -0.66 80 85
JUN -0.033 0.029 0.18 1 -0.22 3 4
oligodendrocyte development 0.018 0.048 0.17 1 -0.16 22 23
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
mol:DAG -0.03 0.038 0.083 1 -0.21 13 14
PDGF/PDGFRA 0.014 0.029 0.22 1 -0.056 51 52
actin cytoskeleton reorganization 0.019 0.049 0.17 1 -0.18 20 21
SRF -0.011 0.018 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.027 0.051 -10000 0 -0.16 22 22
PDGF/PDGFRA/Crk/C3G 0.03 0.046 0.17 1 -0.14 18 19
JAK1 -0.024 0.028 0.12 1 -0.18 12 13
ELK1/SRF -0.033 0.042 0.15 11 -0.18 19 30
SHB 0.025 0.005 -10000 0 -10000 0 0
SHF 0.026 0.011 0.24 1 -10000 0 1
CSNK2A1 0.031 0.018 -10000 0 -10000 0 0
GO:0007205 -0.029 0.049 -10000 0 -0.23 21 21
SOS1 0.025 0.005 -10000 0 -10000 0 0
Ras protein signal transduction 0.048 0.041 -10000 0 -0.13 17 17
PDGF/PDGFRA/SHB 0.019 0.049 0.17 1 -0.18 20 21
PDGF/PDGFRA/Caveolin-1 0 0.081 0.17 1 -0.21 57 58
ITGAV 0.025 0.005 -10000 0 -10000 0 0
ELK1 -0.036 0.051 0.22 1 -0.22 21 22
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.017 0.048 0.17 1 -0.16 22 23
JAK-STAT cascade -0.024 0.028 0.12 1 -0.18 12 13
cell proliferation 0.019 0.049 0.18 2 -0.17 20 22
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.015 0.01 0.17 2 -10000 0 2
Metarhodopsin II/Arrestin 0.025 0.014 0.17 3 -10000 0 3
PDE6G/GNAT1/GTP 0.042 0.041 0.17 48 -10000 0 48
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.02 0.015 0.24 2 -10000 0 2
GRK1 0.021 0.021 0.24 4 -10000 0 4
CNG Channel 0.027 0.065 0.21 1 -0.13 50 51
mol:Na + 0.039 0.043 0.19 4 -0.12 8 12
mol:ADP 0.021 0.021 0.24 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.013 0.078 0.19 4 -0.14 100 104
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.049 0.05 0.23 4 -0.13 7 11
CNGB1 0.025 0.031 0.24 9 -10000 0 9
RDH5 0.026 0.018 0.24 3 -10000 0 3
SAG 0.019 0.011 0.24 1 -10000 0 1
mol:Ca2+ -0.011 0.076 0.33 14 -10000 0 14
Na + (4 Units) -0.018 0.046 0.14 4 -0.13 7 11
RGS9 0.021 0.021 0.24 3 -10000 0 3
GNB1/GNGT1 0.03 0.015 0.19 2 -10000 0 2
GNAT1/GDP 0.02 0.073 0.18 6 -0.12 97 103
GUCY2D 0.046 0.071 0.24 55 -10000 0 55
GNGT1 0.018 0.016 0.24 2 -10000 0 2
GUCY2F 0.019 0.01 0.24 1 -10000 0 1
GNB5 0.025 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.022 0.053 0.1 43 -0.13 49 92
mol:11-cis-retinal 0.026 0.018 0.24 3 -10000 0 3
mol:cGMP 0.045 0.045 0.2 11 -0.13 6 17
GNB1 0.026 0.003 -10000 0 -10000 0 0
Rhodopsin 0.027 0.037 0.18 5 -0.16 14 19
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 0.027 0.018 0.24 3 -10000 0 3
Metarhodopsin II 0.024 0.017 0.16 6 -10000 0 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.063 0.059 0.2 59 -0.13 6 65
RGS9BP 0.026 0.01 0.24 1 -10000 0 1
Metarhodopsin II/Transducin 0.009 0.01 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.044 0.025 0.17 14 -0.12 1 15
PDE6A/B 0.009 0.074 0.19 1 -0.18 63 64
mol:Pi 0.012 0.078 0.19 4 -0.14 100 104
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.019 0.17 4 -10000 0 4
PDE6B 0.023 0.013 0.24 1 -10000 0 1
PDE6A 0.026 0.018 0.24 3 -10000 0 3
PDE6G 0.046 0.065 0.24 48 -10000 0 48
RHO 0.02 0.016 0.24 2 -10000 0 2
PDE6 0.022 0.11 0.29 1 -0.15 117 118
GUCA1A 0.023 0.015 0.24 2 -10000 0 2
GC2/GCAP Family 0.055 0.027 0.19 11 -0.13 1 12
GUCA1C 0.018 0.011 0.24 1 -10000 0 1
GUCA1B 0.032 0.038 0.24 15 -10000 0 15
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.028 0.022 0.24 5 -10000 0 5
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.022 0.009 -10000 0 -10000 0 0
CDKN1A 0.011 0.04 -10000 0 -0.39 4 4
PRL-3/alpha Tubulin 0.051 0.056 0.19 66 -10000 0 66
mol:Ca2+ -0.025 0.069 0.13 39 -0.17 58 97
AGT 0.045 0.067 0.24 49 -10000 0 49
CCNA2 -0.009 0.04 0.25 3 -10000 0 3
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
EGR1 0.013 0.029 0.14 24 -10000 0 24
CDK2/Cyclin E1 0.04 0.057 0.3 3 -0.34 6 9
MAPK3 0.006 0.053 0.14 66 -10000 0 66
PRL-2 /Rab GGTase beta 0.037 0.008 -10000 0 -10000 0 0
MAPK1 0.006 0.053 0.14 66 -10000 0 66
PTP4A1 -0.009 0.018 -10000 0 -10000 0 0
PTP4A3 0.05 0.077 0.24 66 -10000 0 66
PTP4A2 0.026 0.003 -10000 0 -10000 0 0
ITGB1 0.006 0.052 0.14 64 -10000 0 64
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.058 0.23 1 -0.31 7 8
Rab GGTase beta/Rab GGTase alpha 0.037 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.013 0.049 -10000 0 -10000 0 0
RABGGTA 0.026 0.003 -10000 0 -10000 0 0
BCAR1 -0.035 0.051 -10000 0 -0.17 60 60
RHOC 0.026 0.061 0.23 1 -0.31 8 9
RHOA 0.027 0.054 0.23 1 -0.31 5 6
cell motility 0.034 0.081 0.37 6 -0.3 6 12
PRL-1/alpha Tubulin -0.015 0.046 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.038 0.066 0.19 54 -0.16 18 72
ROCK1 0.03 0.069 0.38 1 -0.3 6 7
RABGGTB 0.025 0.005 -10000 0 -10000 0 0
CDK2 0.025 0.005 -10000 0 -10000 0 0
mitosis -0.016 0.032 -10000 0 -10000 0 0
ATF5 0.028 0.022 0.24 5 -10000 0 5
Aurora A signaling

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
Aurora A/GADD45A 0.004 0.044 -10000 0 -0.15 6 6
BIRC5 0.098 0.1 0.24 165 -10000 0 165
NFKBIA -0.015 0.034 0.27 4 -10000 0 4
CPEB1 0.02 0.018 0.24 2 -10000 0 2
AKT1 -0.015 0.032 0.28 3 -10000 0 3
NDEL1 0.023 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.002 0.036 0.2 1 -10000 0 1
NDEL1/TACC3 0.022 0.059 0.23 17 -10000 0 17
GADD45A 0.025 0.005 -10000 0 -10000 0 0
GSK3B -0.002 0.03 -10000 0 -10000 0 0
PAK1/Aurora A 0.003 0.043 -10000 0 -0.14 8 8
MDM2 0.025 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.027 0.074 0.14 135 -10000 0 135
TP53 -0.015 0.069 -10000 0 -0.22 50 50
DLG7 -0.008 0.023 -10000 0 -10000 0 0
AURKAIP1 0.03 0.03 0.24 9 -10000 0 9
ARHGEF7 0.024 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.023 0.063 0.24 17 -10000 0 17
G2/M transition of mitotic cell cycle 0.002 0.036 0.2 1 -10000 0 1
AURKA -0.006 0.032 -10000 0 -10000 0 0
AURKB 0.053 0.059 0.14 138 -10000 0 138
CDC25B 0 0.026 0.16 1 -0.29 1 2
G2/M transition checkpoint -0.007 0.025 -10000 0 -0.11 6 6
mRNA polyadenylation -0.027 0.062 0.16 2 -0.14 51 53
Aurora A/CPEB -0.028 0.062 0.16 2 -0.14 51 53
Aurora A/TACC1/TRAP/chTOG 0.017 0.049 -10000 0 -0.14 2 2
BRCA1 0.025 0.011 0.24 1 -10000 0 1
centrosome duplication 0.003 0.043 -10000 0 -0.14 8 8
regulation of centrosome cycle 0.021 0.058 0.22 17 -10000 0 17
spindle assembly 0.016 0.048 -10000 0 -0.14 2 2
TDRD7 0.025 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.064 0.075 0.22 31 -10000 0 31
CENPA 0.059 0.064 0.16 122 -0.18 1 123
Aurora A/PP2A 0.003 0.043 -10000 0 -0.13 6 6
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.002 0.025 0.18 2 -0.16 1 3
negative regulation of DNA binding -0.016 0.07 -10000 0 -0.21 51 51
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.01 -10000 0 -10000 0 0
RASA1 0.024 0.007 -10000 0 -10000 0 0
Ajuba/Aurora A -0.007 0.025 -10000 0 -0.11 6 6
mitotic prometaphase -0.002 0.027 0.069 53 -10000 0 53
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.032 -10000 0 -10000 0 0
TACC1 0.019 0.011 -10000 0 -10000 0 0
TACC3 0.041 0.057 0.24 35 -10000 0 35
Aurora A/Antizyme1 0.017 0.052 0.18 5 -10000 0 5
Aurora A/RasGAP 0.004 0.042 -10000 0 -0.14 6 6
OAZ1 0.025 0.004 -10000 0 -10000 0 0
RAN 0.025 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.002 0.03 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.045 0.026 -10000 0 -0.14 6 6
Importin alpha/Importin beta/TPX2 0.027 0.074 0.14 135 -10000 0 135
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.013 0.06 0.16 36 -10000 0 36
PAK1 0.025 0.006 -10000 0 -10000 0 0
CKAP5 0.025 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.073 -10000 0 -0.38 5 5
UGCG -0.033 0.18 -10000 0 -0.6 44 44
AKT1/mTOR/p70S6K/Hsp90/TERT 0.064 0.12 0.29 45 -0.35 10 55
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.031 0.18 -10000 0 -0.6 44 44
mol:DAG -0.005 0.11 -10000 0 -0.81 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.13 0.3 18 -0.39 26 44
FRAP1 0.034 0.15 0.32 27 -0.44 26 53
FOXO3 0.035 0.12 0.32 27 -0.34 15 42
AKT1 0.038 0.12 0.33 24 -0.37 15 39
GAB2 0.024 0.011 -10000 0 -10000 0 0
SMPD1 0.022 0.037 -10000 0 -0.49 1 1
SGMS1 0.012 0.087 -10000 0 -0.58 9 9
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 -0.011 0.019 -10000 0 -0.15 6 6
CALM1 0.025 0.005 -10000 0 -10000 0 0
cell proliferation 0.025 0.15 0.32 25 -0.36 38 63
EIF3A 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.031 -10000 0 -0.18 6 6
RPS6KB1 0.021 0.09 -10000 0 -0.68 7 7
mol:sphingomyelin -0.005 0.11 -10000 0 -0.81 9 9
natural killer cell activation 0.001 0.003 0.016 1 -10000 0 1
JAK3 0.031 0.034 0.25 11 -10000 0 11
PIK3R1 0.023 0.012 -10000 0 -10000 0 0
JAK1 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MYC 0.078 0.15 0.44 35 -0.43 4 39
MYB 0.032 0.069 0.38 2 -10000 0 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.03 0.11 0.28 25 -0.31 15 40
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.089 -10000 0 -0.63 7 7
mol:PI-3-4-5-P3 0.031 0.1 0.27 25 -0.31 15 40
Rac1/GDP -0.008 0.022 -10000 0 -0.15 4 4
T cell proliferation 0.027 0.1 0.25 28 -0.29 15 43
SHC1 0.024 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.005 0.017 0.084 23 -10000 0 23
PRKCZ 0.025 0.1 0.26 25 -0.3 15 40
NF kappa B1 p50/RelA 0.04 0.13 0.31 16 -0.4 26 42
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.075 0.26 8 -0.31 13 21
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.006 -10000 0 -10000 0 0
IL2RA 0.059 0.08 0.24 76 -10000 0 76
IL2RB 0.029 0.028 0.25 7 -10000 0 7
TERT 0.09 0.1 0.24 149 -10000 0 149
E2F1 0.035 0.063 0.35 2 -0.38 3 5
SOS1 0.024 0.011 -10000 0 -10000 0 0
RPS6 0.026 0.014 0.24 2 -10000 0 2
mol:cAMP -0.003 0.009 -10000 0 -0.045 23 23
PTPN11 0.025 0.011 -10000 0 -10000 0 0
IL2RG 0.033 0.039 0.25 15 -10000 0 15
actin cytoskeleton organization 0.027 0.1 0.25 28 -0.29 15 43
GRB2 0.024 0.011 -10000 0 -10000 0 0
IL2 0.022 0.018 0.24 2 -10000 0 2
PIK3CA 0.024 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.041 0.038 0.17 7 -0.14 4 11
LCK 0.03 0.031 0.25 9 -10000 0 9
BCL2 0.015 0.19 0.37 8 -0.75 23 31
TCGA08_retinoblastoma

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
CDKN2B 0.02 0.024 -10000 0 -10000 0 0
CDKN2C 0.015 0.033 0.22 3 -0.066 7 10
CDKN2A 0.072 0.089 0.25 100 -0.063 1 101
CCND2 -0.016 0.032 -10000 0 -0.13 10 10
RB1 0.014 0.036 0.17 6 -10000 0 6
CDK4 -0.015 0.033 -10000 0 -0.2 3 3
CDK6 -0.017 0.039 -10000 0 -0.16 15 15
G1/S progression -0.013 0.041 0.17 5 -0.16 7 12
IGF1 pathway

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
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTK2 0.021 0.01 -10000 0 -10000 0 0
CRKL -0.021 0.04 0.13 3 -0.16 28 31
GRB2/SOS1/SHC 0.047 0.017 -10000 0 -10000 0 0
HRAS 0.028 0.024 0.24 6 -10000 0 6
IRS1/Crk 0.01 0.046 0.1 15 -0.15 31 46
IGF-1R heterotetramer/IGF1/PTP1B 0.039 0.054 0.18 15 -0.14 29 44
AKT1 -0.018 0.063 0.17 29 -0.21 8 37
BAD -0.022 0.058 0.17 24 -0.24 5 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.021 0.038 0.15 1 -0.16 26 27
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.053 0.26 1 -0.16 31 32
RAF1 -0.004 0.068 0.25 4 -0.37 6 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.061 0.27 1 -0.15 31 32
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.022 0.056 0.16 15 -0.16 32 47
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.018 0.064 0.17 28 -0.21 8 36
GNB2L1 0.027 0.02 0.24 4 -10000 0 4
positive regulation of MAPKKK cascade 0.004 0.079 0.28 14 -0.31 5 19
PXN 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.045 0.13 1 -0.15 27 28
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.059 0.057 0.24 3 -0.12 28 31
IGF-1R heterotetramer 0.023 0.026 0.25 1 -0.062 31 32
IGF-1R heterotetramer/IGF1/IRS/Nck 0.035 0.056 0.17 13 -0.15 31 44
Crk/p130 Cas/Paxillin 0.032 0.055 0.26 1 -0.14 30 31
IGF1R 0.023 0.026 0.25 1 -0.062 31 32
IGF1 0.032 0.041 0.24 17 -10000 0 17
IRS2/Crk -0.023 0.041 0.1 14 -0.16 26 40
PI3K 0.039 0.062 0.27 1 -0.15 32 33
apoptosis 0.023 0.045 0.18 3 -0.17 2 5
HRAS/GDP 0.021 0.017 0.17 6 -10000 0 6
PRKCD -0.008 0.072 0.18 3 -0.27 27 30
RAF1/14-3-3 E 0.002 0.073 0.26 8 -0.35 5 13
BAD/14-3-3 -0.024 0.047 0.18 2 -0.18 3 5
PRKCZ -0.019 0.063 0.17 26 -0.21 8 34
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.045 0.13 11 -0.24 3 14
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.005 0.077 0.17 2 -0.28 31 33
BCAR1 0.021 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.047 0.053 0.25 2 -0.13 26 28
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.025 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.02 0.052 0.16 4 -0.15 31 35
GRB10 0.024 0.008 -10000 0 -10000 0 0
PTPN11 -0.023 0.041 0.15 1 -0.16 30 31
IRS1 -0.015 0.05 0.12 20 -0.16 31 51
IRS2 -0.021 0.041 0.13 5 -0.16 27 32
IGF-1R heterotetramer/IGF1 0.027 0.065 0.19 17 -0.19 32 49
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDPK1 -0.015 0.065 0.18 25 -0.22 8 33
YWHAE 0.024 0.007 -10000 0 -10000 0 0
PRKD1 -0.008 0.073 0.18 3 -0.28 27 30
SHC1 0.025 0.006 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP 0.023 0.065 -10000 0 -0.13 56 56
TC10/GTP 0.02 0.055 -10000 0 -0.12 51 51
Insulin Receptor/Insulin/IRS1/Shp2 0.055 0.042 0.19 10 -0.14 12 22
HRAS 0.028 0.024 0.24 6 -10000 0 6
APS homodimer 0.029 0.038 0.24 14 -10000 0 14
GRB14 0.061 0.082 0.24 82 -10000 0 82
FOXO3 -0.12 0.25 -10000 0 -0.54 125 125
AKT1 -0.003 0.083 0.24 30 -0.22 5 35
INSR 0.027 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.008 -10000 0 -10000 0 0
SORBS1 0.02 0.011 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
PTPN1 -0.013 0.023 0.14 8 -10000 0 8
CAV1 -0.019 0.036 0.2 4 -0.2 9 13
CBL/APS/CAP/Crk-II/C3G 0.039 0.069 0.2 9 -0.13 51 60
Insulin Receptor/Insulin/IRS1/NCK2 0.058 0.039 0.19 11 -0.13 11 22
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.041 -10000 0 -0.16 12 12
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.05 -10000 0 -0.27 9 9
RPS6KB1 -0.01 0.076 0.22 27 -0.21 5 32
PARD6A 0.025 0.024 0.24 5 -10000 0 5
CBL 0.025 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.012 0.068 -10000 0 -0.59 6 6
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.01 0.068 0.15 37 -0.22 5 42
HRAS/GTP -0.038 0.032 -10000 0 -0.13 28 28
Insulin Receptor 0.027 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.064 0.044 -10000 0 -0.13 12 12
PRKCI 0.019 0.05 -10000 0 -0.3 8 8
Insulin Receptor/Insulin/GRB14/PDK1 -0.017 0.049 0.083 65 -0.16 13 78
SHC1 0.025 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.032 0.061 -10000 0 -0.45 6 6
PI3K 0.048 0.046 -10000 0 -0.16 12 12
NCK2 0.026 0.003 -10000 0 -10000 0 0
RHOQ 0.025 0.004 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.017 0.17 6 -10000 0 6
AKT2 -0.004 0.079 0.23 28 -0.22 5 33
PRKCZ 0.02 0.048 -10000 0 -0.3 10 10
SH2B2 0.03 0.038 0.24 14 -10000 0 14
SHC/SHIP -0.027 0.041 0.16 6 -0.21 5 11
F2RL2 0.1 0.11 0.24 173 -10000 0 173
TRIP10 0.025 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.046 0.025 0.17 12 -10000 0 12
TC10/GTP/CIP4/Exocyst 0.034 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.067 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.007 -10000 0 -10000 0 0
NCK1 0.024 0.007 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.032 0.067 0.2 9 -0.13 54 63
TC10/GDP 0.019 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.056 0.031 0.19 11 -10000 0 11
INPP5D -0.02 0.038 0.18 8 -0.16 11 19
SOS1 0.025 0.005 -10000 0 -10000 0 0
SGK1 -0.099 0.27 -10000 0 -0.72 76 76
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.006 -10000 0 -10000 0 0
IRS1 0.025 0.005 -10000 0 -10000 0 0
p62DOK/RasGAP 0.033 0.061 -10000 0 -0.46 6 6
INS -0.008 0.042 0.24 12 -10000 0 12
mol:PI-3-4-P2 -0.02 0.038 0.18 8 -0.16 11 19
GRB2 0.025 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.012 0.057 0.22 11 -0.21 3 14
PTPRA 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.034 0.007 -10000 0 -10000 0 0
PDPK1 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.012 0.036 -10000 0 -0.17 13 13
Insulin Receptor/Insulin/IRS1 0.043 0.035 0.17 11 -0.12 14 25
Insulin Receptor/Insulin/IRS3 0.037 0.025 0.18 12 -10000 0 12
Par3/Par6 0.087 0.069 0.18 151 -0.12 1 152
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.016 0.033 0.2 4 -0.15 11 15
EPHB2 0.027 0.017 0.24 3 -10000 0 3
Syndecan-2/TACI 0.032 0.061 0.21 42 -0.13 7 49
LAMA1 0.033 0.046 0.24 22 -10000 0 22
Syndecan-2/alpha2 ITGB1 0.019 0.058 -10000 0 -0.14 43 43
HRAS 0.028 0.024 0.24 6 -10000 0 6
Syndecan-2/CASK -0.005 0.012 0.09 1 -0.12 4 5
ITGA5 0.025 0.011 0.24 1 -10000 0 1
BAX -0.013 0.023 0.26 1 -10000 0 1
EPB41 0.026 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.015 -10000 0 -0.12 4 4
LAMA3 0.023 0.014 0.24 1 -10000 0 1
EZR 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.01 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.016 0.024 0.17 1 -0.14 7 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.057 -10000 0 -0.16 45 45
dendrite morphogenesis 0.018 0.024 0.17 3 -0.15 5 8
Syndecan-2/GM-CSF 0.017 0.028 0.22 6 -0.13 4 10
determination of left/right symmetry -0.005 0.007 0.12 1 -10000 0 1
Syndecan-2/PKC delta 0.017 0.017 -10000 0 -0.13 4 4
GNB2L1 0.027 0.02 0.24 4 -10000 0 4
MAPK3 0.018 0.077 0.18 84 -0.12 4 88
MAPK1 0.021 0.08 0.18 91 -0.12 4 95
Syndecan-2/RACK1 0.031 0.031 0.19 9 -0.11 4 13
NF1 0.026 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.005 0.007 0.12 1 -10000 0 1
ITGA2 0.022 0.01 -10000 0 -10000 0 0
MAPK8 -0.008 0.01 0.19 1 -10000 0 1
Syndecan-2/alpha2/beta1 Integrin 0.029 0.062 0.22 14 -0.13 35 49
Syndecan-2/Kininogen 0.036 0.067 0.2 58 -0.13 4 62
ITGB1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.021 0.084 0.18 96 -10000 0 96
Syndecan-2/CASK/Protein 4.1 0.016 0.015 -10000 0 -0.12 4 4
extracellular matrix organization 0.017 0.02 -10000 0 -0.16 4 4
actin cytoskeleton reorganization 0.016 0.033 0.2 4 -0.15 11 15
Syndecan-2/Caveolin-2/Ras 0.02 0.044 0.17 3 -0.14 27 30
Syndecan-2/Laminin alpha3 0.009 0.037 0.17 1 -0.13 28 29
Syndecan-2/RasGAP 0.038 0.033 0.2 8 -0.11 3 11
alpha5/beta1 Integrin 0.032 0.034 0.19 1 -0.16 13 14
PRKCD 0.025 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.018 0.024 0.17 3 -0.15 5 8
GO:0007205 0.001 0.004 0.068 1 -10000 0 1
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.021 0.024 0.17 5 -10000 0 5
RHOA 0.025 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.042 0.062 0.24 42 -10000 0 42
RASA1 0.024 0.007 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.057 -10000 0 -0.16 45 45
Syndecan-2/Synbindin 0.017 0.017 -10000 0 -0.13 4 4
TGFB1 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.018 0.078 0.18 87 -0.12 4 91
FN1 0.027 0.02 0.24 4 -10000 0 4
Syndecan-2/IL8 0.02 0.056 0.2 24 -0.13 25 49
SDC2 -0.005 0.007 0.12 1 -10000 0 1
KNG1 0.045 0.073 0.24 58 -10000 0 58
Syndecan-2/Neurofibromin 0.017 0.017 -10000 0 -0.13 4 4
TRAPPC4 0.025 0.006 -10000 0 -10000 0 0
CSF2 0.023 0.025 0.24 6 -10000 0 6
Syndecan-2/TGFB1 0.017 0.02 -10000 0 -0.16 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.015 -10000 0 -0.12 4 4
Syndecan-2/Ezrin 0.029 0.022 -10000 0 -0.12 4 4
PRKACA 0.023 0.082 0.18 99 -0.12 4 103
angiogenesis 0.02 0.056 0.2 24 -0.13 25 49
MMP2 0.023 0.013 0.24 1 -10000 0 1
IL8 0.034 0.048 0.24 24 -10000 0 24
calcineurin-NFAT signaling pathway 0.032 0.061 0.21 42 -0.13 7 49
TCGA08_p53

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
CDKN2A 0.021 0.059 0.14 100 -10000 0 100
TP53 0.014 0.017 -10000 0 -10000 0 0
Senescence 0.011 0.03 -10000 0 -0.18 8 8
Apoptosis 0.011 0.03 -10000 0 -0.18 8 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.018 0.063 0.29 14 -10000 0 14
MDM4 0.025 0.005 -10000 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.004 0.069 -10000 0 -0.12 114 114
MAPK9 0.005 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.01 0.14 2 -10000 0 2
GNB1/GNG2 0.032 0.019 -10000 0 -0.13 6 6
GNB1 0.026 0.003 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.014 0.054 -10000 0 -0.11 117 117
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.009 0.013 0.033 117 -10000 0 117
GNAL 0.018 0.012 -10000 0 -10000 0 0
GNG2 0.025 0.004 -10000 0 -10000 0 0
CRH 0.016 0.016 0.24 2 -10000 0 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.033 -10000 0 -0.21 12 12
MAPK11 0.007 0.014 0.12 8 -10000 0 8
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.008 0.053 2 -10000 0 2
RAS family/GTP 0.01 0.096 0.28 3 -0.21 20 23
NFATC4 -0.038 0.057 0.25 7 -0.19 5 12
ERBB2IP 0.023 0.011 -10000 0 -0.036 1 1
HSP90 (dimer) 0.025 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.058 0.18 4 -0.18 16 20
JUN -0.006 0.082 0.26 9 -0.28 1 10
HRAS 0.028 0.024 0.24 6 -0.03 1 7
DOCK7 -0.043 0.051 0.19 3 -0.17 16 19
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.011 0.058 0.17 2 -0.14 49 51
AKT1 -0.009 0.007 -10000 0 -10000 0 0
BAD -0.014 0.007 0.091 1 -10000 0 1
MAPK10 -0.02 0.062 0.19 22 -0.15 3 25
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.063 0.19 4 -0.18 16 20
RAF1 -0.014 0.1 0.26 19 -0.23 19 38
ErbB2/ErbB3/neuregulin 2 -0.023 0.072 -10000 0 -0.14 126 126
STAT3 -0.011 0.19 -10000 0 -0.88 22 22
cell migration -0.011 0.087 0.25 31 -0.16 4 35
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.011 0.2 0.45 7 -0.5 26 33
FOS -0.032 0.2 0.35 13 -0.42 84 97
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.031 0.058 0.18 4 -0.18 16 20
MAPK3 0.003 0.16 0.38 12 -0.45 12 24
MAPK1 0 0.17 0.43 7 -0.48 15 22
JAK2 -0.042 0.051 0.19 3 -0.17 15 18
NF2 0 0.053 -10000 0 -0.66 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.059 -10000 0 -0.18 47 47
NRG1 0.016 0.014 -10000 0 -10000 0 0
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
MAPK8 -0.05 0.09 0.23 3 -0.22 57 60
MAPK9 -0.021 0.057 0.17 21 -0.14 1 22
ERBB2 -0.023 0.01 -10000 0 -10000 0 0
ERBB3 0.024 0.007 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
apoptosis 0.012 0.01 -10000 0 -0.071 1 1
STAT3 (dimer) -0.012 0.19 -10000 0 -0.86 23 23
RNF41 -0.02 0.008 -10000 0 -10000 0 0
FRAP1 -0.008 0.004 0.03 1 -10000 0 1
RAC1-CDC42/GTP -0.041 0.036 0.072 1 -0.13 45 46
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.015 -10000 0 -0.15 2 2
CHRNA1 0.019 0.15 0.37 15 -0.35 13 28
myelination -0.021 0.097 0.32 24 -0.2 3 27
PPP3CB -0.041 0.048 0.18 3 -0.16 16 19
KRAS 0.024 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.005 0.078 -10000 0 -0.18 39 39
NRG2 0.017 0.012 -10000 0 -10000 0 0
mol:GDP -0.011 0.059 -10000 0 -0.18 47 47
SOS1 0.025 0.005 -10000 0 -10000 0 0
MAP2K2 -0.015 0.11 0.27 19 -0.26 18 37
SRC 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.043 0.05 0.19 3 -0.17 16 19
MAP2K1 -0.023 0.17 0.48 2 -0.46 22 24
heart morphogenesis -0.031 0.058 0.18 4 -0.18 16 20
RAS family/GDP 0.007 0.091 0.24 2 -0.18 40 42
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.007 0.055 -10000 0 -0.69 3 3
CHRNE 0.003 0.024 0.13 5 -0.13 1 6
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.007 -10000 0 -10000 0 0
nervous system development -0.031 0.058 0.18 4 -0.18 16 20
CDC42 0.026 0.003 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.024 0.016 0.17 1 -0.095 6 7
SVIL 0.023 0.014 -10000 0 -0.084 6 6
ZNF318 0.026 0.018 0.18 6 -10000 0 6
JMJD2C 0.002 0.01 0.12 1 -0.12 2 3
T-DHT/AR/Ubc9 0.016 0.052 -10000 0 -0.11 63 63
CARM1 0.025 0.008 -10000 0 -0.05 1 1
PRDX1 0.026 0.003 -10000 0 -10000 0 0
PELP1 0.024 0.008 -10000 0 -10000 0 0
CTNNB1 0.024 0.012 -10000 0 -0.072 6 6
AKT1 0.025 0.008 -10000 0 -10000 0 0
PTK2B 0.018 0.014 -10000 0 -0.071 4 4
MED1 0.026 0.007 -10000 0 -10000 0 0
MAK 0.087 0.1 0.24 141 -0.059 1 142
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.022 0.015 -10000 0 -0.084 6 6
GSN 0.024 0.013 -10000 0 -0.088 5 5
NCOA2 0.017 0.013 -10000 0 -0.044 1 1
NCOA6 0.024 0.013 -10000 0 -0.086 6 6
DNA-PK 0.043 0.028 0.22 5 -10000 0 5
NCOA4 0.024 0.008 -10000 0 -10000 0 0
PIAS3 0.024 0.013 -10000 0 -0.072 7 7
cell proliferation 0.059 0.1 0.21 117 -0.41 6 123
XRCC5 0.025 0.007 -10000 0 -10000 0 0
UBE3A 0.024 0.016 -10000 0 -0.11 6 6
T-DHT/AR/SNURF 0.012 0.06 -10000 0 -0.12 70 70
FHL2 -0.017 0.14 -10000 0 -0.68 21 21
RANBP9 0.025 0.013 -10000 0 -0.09 6 6
JMJD1A 0.002 0.009 -10000 0 -0.13 2 2
CDK6 0.023 0.009 -10000 0 -10000 0 0
TGFB1I1 0.022 0.019 -10000 0 -0.12 6 6
T-DHT/AR/CyclinD1 0.017 0.052 0.17 1 -0.11 60 61
XRCC6 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.017 0.063 -10000 0 -0.14 67 67
CTDSP1 0.025 0.009 -10000 0 -0.046 4 4
CTDSP2 0.026 0.013 0.12 7 -10000 0 7
BRCA1 0.024 0.017 0.24 1 -0.087 6 7
TCF4 0.023 0.013 0.12 2 -10000 0 2
CDKN2A 0.069 0.09 0.25 100 -10000 0 100
SRF 0.02 0.036 -10000 0 -0.14 22 22
NKX3-1 -0.01 0.029 -10000 0 -0.14 8 8
KLK3 -0.025 0.15 -10000 0 -1.2 7 7
TMF1 0.024 0.008 -10000 0 -0.043 1 1
HNRNPA1 0.026 0.009 0.12 1 -10000 0 1
AOF2 0 0.009 -10000 0 -0.073 7 7
APPL1 -0.017 0.014 0.1 6 -10000 0 6
T-DHT/AR/Caspase 8 0.017 0.053 -10000 0 -0.11 64 64
AR 0.019 0.023 -10000 0 -0.067 27 27
UBA3 0.024 0.009 -10000 0 -0.043 5 5
PATZ1 0.025 0.008 -10000 0 -10000 0 0
PAWR 0.024 0.008 -10000 0 -0.04 2 2
PRKDC 0.022 0.016 0.27 1 -10000 0 1
PA2G4 0.025 0.01 0.11 1 -10000 0 1
UBE2I 0.025 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.017 0.048 -10000 0 -0.1 64 64
RPS6KA3 0.024 0.015 -10000 0 -0.094 7 7
T-DHT/AR/ARA70 0.016 0.052 -10000 0 -0.11 66 66
LATS2 0.025 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.017 0.048 0.13 1 -0.12 44 45
Cyclin D3/CDK11 p58 0.019 0.003 -10000 0 -10000 0 0
VAV3 0.022 0.014 -10000 0 -0.074 6 6
KLK2 -0.001 0.048 -10000 0 -0.6 2 2
CASP8 0.026 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.011 0.078 -10000 0 -0.19 55 55
TMPRSS2 -0.012 0.078 -10000 0 -0.38 18 18
CCND1 0.024 0.015 0.24 1 -0.062 5 6
PIAS1 0.025 0.016 -10000 0 -0.11 6 6
mol:T-DHT -0.002 0.016 -10000 0 -0.059 30 30
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.024 0.024 -10000 0 -0.17 7 7
T-DHT/AR/CDK6 0.012 0.057 -10000 0 -0.12 68 68
CMTM2 0.023 0.017 0.24 2 -10000 0 2
SNURF 0.024 0.007 -10000 0 -10000 0 0
ZMIZ1 0.02 0.026 -10000 0 -0.074 29 29
CCND3 0.026 0.003 -10000 0 -10000 0 0
TGIF1 0.024 0.01 0.12 1 -10000 0 1
FKBP4 0.023 0.015 -10000 0 -0.09 7 7
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.017 0.006 -10000 0 -10000 0 0
MAP4K4 -0.007 0.05 -10000 0 -0.27 5 5
BAG4 0.018 0.012 -10000 0 -10000 0 0
PKC zeta/ceramide 0.006 0.07 -10000 0 -0.19 41 41
NFKBIA 0.025 0.004 -10000 0 -10000 0 0
BIRC3 0.026 0.018 0.24 3 -10000 0 3
BAX 0.001 0.059 -10000 0 -0.34 12 12
RIPK1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0 0.1 0.72 10 -10000 0 10
BAD -0.008 0.071 0.2 11 -0.2 37 48
SMPD1 0.012 0.06 0.19 24 -0.14 5 29
RB1 -0.014 0.062 -10000 0 -0.19 39 39
FADD/Caspase 8 -0.005 0.058 0.2 5 -0.27 5 10
MAP2K4 -0.016 0.061 0.17 2 -0.18 39 41
NSMAF 0.022 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.017 0.068 0.18 9 -0.2 38 47
EGF 0.042 0.061 0.24 40 -10000 0 40
mol:ceramide -0.009 0.069 -10000 0 -0.2 42 42
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.012 0.009 -10000 0 -10000 0 0
ASAH1 0.019 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.062 -10000 0 -0.19 39 39
cell proliferation 0.001 0.074 0.23 3 -0.19 34 37
BID 0.002 0.11 -10000 0 -0.63 11 11
MAP3K1 -0.013 0.063 0.19 1 -0.19 39 40
EIF2A -0.008 0.071 0.18 28 -0.19 30 58
TRADD 0.023 0.009 -10000 0 -10000 0 0
CRADD 0.025 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.068 0.19 10 -0.21 30 40
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.07 0.19 9 -0.2 33 42
Cathepsin D/ceramide 0.007 0.069 -10000 0 -0.2 38 38
FADD -0.005 0.054 0.19 5 -0.27 5 10
KSR1 -0.017 0.069 0.19 1 -0.2 43 44
MAPK8 -0.011 0.074 -10000 0 -0.22 31 31
PRKRA -0.013 0.062 0.21 2 -0.19 40 42
PDGFA 0.023 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.006 -10000 0 -10000 0 0
IGF1 0.031 0.041 0.24 17 -10000 0 17
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.068 -10000 0 -0.2 42 42
CTSD 0.025 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.036 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.002 0.079 0.25 3 -0.21 33 36
PRKCD 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.003 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.012 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.036 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.025 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.002 0.05 0.14 1 -0.22 8 9
TNFR1A/BAG4/TNF-alpha 0.025 0.057 0.19 9 -0.14 40 49
mol:Sphingosine-1-phosphate -0.017 0.006 -10000 0 -10000 0 0
MAP2K1 -0.02 0.066 0.17 11 -0.2 34 45
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.006 -10000 0 -10000 0 0
CYCS 0.017 0.055 0.14 18 -0.21 10 28
TNFRSF1A 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.021 0.039 -10000 0 -0.16 18 18
EIF2AK2 -0.016 0.059 0.19 3 -0.19 37 40
TNF-alpha/TNFR1A/FAN 0.034 0.049 0.19 10 -0.14 24 34
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.036 -10000 0 -0.23 1 1
MAP2K2 -0.02 0.068 0.2 10 -0.2 33 43
SMPD3 -0.002 0.082 0.18 10 -0.29 26 36
TNF 0.029 0.035 0.24 12 -10000 0 12
PKC zeta/PAR4 0.036 0.009 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.01 0.066 0.15 21 -0.17 37 58
NF kappa B1/RelA/I kappa B alpha 0.068 0.025 -10000 0 -10000 0 0
AIFM1 0.01 0.06 0.13 15 -0.2 12 27
BCL2 0.022 0.009 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.049 0.17 7 -0.2 20 27
CRKL 0.025 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
DOCK1 0.025 0.006 -10000 0 -10000 0 0
ITGA4 0.029 0.033 0.24 11 -10000 0 11
alpha4/beta7 Integrin/MAdCAM1 0.071 0.073 0.2 78 -0.14 20 98
EPO 0.032 0.05 0.24 25 -10000 0 25
alpha4/beta7 Integrin 0.029 0.059 0.24 10 -0.17 27 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.04 0.19 11 -0.16 13 24
EPO/EPOR (dimer) 0.028 0.07 0.19 32 -0.16 41 73
lamellipodium assembly 0.008 0.038 -10000 0 -0.34 1 1
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.03 0.028 -10000 0 -0.18 6 6
ARF6 0.025 0.004 -10000 0 -10000 0 0
JAK2 0.003 0.062 0.15 3 -0.16 50 53
PXN 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
MADCAM1 0.066 0.086 0.24 92 -10000 0 92
cell adhesion 0.069 0.071 0.19 78 -0.14 20 98
CRKL/CBL 0.036 0.013 -10000 0 -0.16 1 1
ITGB1 0.025 0.004 -10000 0 -10000 0 0
SRC -0.021 0.038 0.17 10 -0.23 1 11
ITGB7 0.025 0.018 0.24 3 -10000 0 3
RAC1 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.046 0.051 0.23 14 -0.14 17 31
p130Cas/Crk/Dock1 -0.026 0.041 0.18 2 -0.21 3 5
VCAM1 0.028 0.028 0.24 8 -10000 0 8
RHOA 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.042 0.2 10 -0.13 13 23
BCAR1 -0.022 0.031 0.17 3 -0.22 1 4
EPOR 0.03 0.031 0.24 10 -10000 0 10
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.008 0.039 -10000 0 -0.35 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0 0.076 -10000 0 -0.16 90 90
AKT1 -0.025 0.13 0.35 7 -0.39 41 48
PTK2B -0.045 0.09 -10000 0 -0.42 21 21
VEGFR2 homodimer/Frs2 0.006 0.092 -10000 0 -0.42 21 21
CAV1 0.021 0.01 -10000 0 -10000 0 0
CALM1 0.025 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.014 0.097 -10000 0 -0.4 21 21
endothelial cell proliferation -0.03 0.14 0.35 13 -0.44 28 41
mol:Ca2+ -0.041 0.084 0.17 6 -0.41 20 26
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.027 0.097 -10000 0 -0.39 20 20
RP11-342D11.1 -0.036 0.084 0.16 7 -0.4 21 28
CDH5 0.023 0.008 -10000 0 -10000 0 0
VEGFA homodimer 0.051 0.049 0.2 5 -0.12 27 32
SHC1 0.025 0.006 -10000 0 -10000 0 0
SHC2 0.031 0.032 0.24 11 -10000 0 11
HRAS/GDP 0.016 0.09 -10000 0 -0.37 20 20
SH2D2A 0.034 0.046 0.24 22 -10000 0 22
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.011 0.11 0.3 1 -0.38 23 24
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.018 0.1 -10000 0 -0.4 21 21
VEGFR1 homodimer 0.026 0.015 0.24 2 -10000 0 2
SHC/GRB2/SOS1 0.035 0.1 -10000 0 -0.4 20 20
GRB10 -0.039 0.081 -10000 0 -0.4 20 20
PTPN11 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.034 0.1 -10000 0 -0.38 21 21
HRAS 0.028 0.024 0.24 6 -10000 0 6
VEGF/Rho/ROCK1/Integrin Complex -0.038 0.11 -10000 0 -0.36 35 35
HIF1A 0.025 0.004 -10000 0 -10000 0 0
FRS2 0.025 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.024 0.095 -10000 0 -0.39 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.026 0.011 0.24 1 -10000 0 1
Nck/Pak 0.032 0.025 -10000 0 -0.16 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.098 -10000 0 -0.41 21 21
mol:GDP 0.024 0.096 -10000 0 -0.39 20 20
mol:NADP -0.004 0.1 0.34 12 -0.33 23 35
eNOS/Hsp90 0.002 0.092 0.29 6 -0.32 23 29
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
mol:IP3 -0.041 0.085 0.17 6 -0.42 20 26
HIF1A/ARNT 0.035 0.014 -10000 0 -0.16 1 1
SHB 0.025 0.005 -10000 0 -10000 0 0
VEGFA 0.027 0.023 0.24 5 -10000 0 5
VEGFC 0.026 0.011 0.24 1 -10000 0 1
FAK1/Vinculin -0.052 0.16 0.27 3 -0.47 43 46
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.001 0.12 -10000 0 -0.42 24 24
PTPN6 0.024 0.007 -10000 0 -10000 0 0
EPAS1 0.016 0.064 0.25 1 -0.28 21 22
mol:L-citrulline -0.004 0.1 0.34 12 -0.33 23 35
ITGAV 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.028 0.097 -10000 0 -0.38 21 21
VEGFR2 homodimer/VEGFA homodimer 0.015 0.1 -10000 0 -0.43 21 21
VEGFR2/3 heterodimer 0.006 0.095 -10000 0 -0.44 21 21
VEGFB 0.025 0.005 -10000 0 -10000 0 0
MAPK11 -0.034 0.094 0.23 3 -0.42 21 24
VEGFR2 homodimer -0.034 0.098 -10000 0 -0.5 21 21
FLT1 0.026 0.015 0.24 2 -10000 0 2
NEDD4 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.049 0.095 0.25 4 -0.43 21 25
MAPK1 -0.048 0.097 0.26 5 -0.43 21 26
VEGFA145/NRP2 0.016 0.067 0.19 4 -0.16 55 59
VEGFR1/2 heterodimer 0.005 0.097 -10000 0 -0.45 21 21
KDR -0.034 0.098 -10000 0 -0.5 21 21
VEGFA165/NRP1/VEGFR2 homodimer 0.008 0.11 -10000 0 -0.41 24 24
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.045 0.1 0.24 10 -0.44 21 31
PI3K -0.018 0.12 -10000 0 -0.5 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.013 0.097 -10000 0 -0.4 21 21
FES -0.042 0.089 0.17 7 -0.42 21 28
GAB1 -0.016 0.12 -10000 0 -0.38 39 39
VEGFR2 homodimer/VEGFA homodimer/Src 0.014 0.098 -10000 0 -0.41 21 21
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
SOS1 0.025 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.005 0.095 0.35 3 -0.37 22 25
VEGFR2 homodimer/VEGFA homodimer/Yes 0.014 0.098 -10000 0 -0.42 20 20
PI3K/GAB1 -0.023 0.14 -10000 0 -0.41 42 42
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.032 0.1 -10000 0 -0.4 19 19
PRKACA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.02 0.092 -10000 0 -0.41 21 21
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
CDC42 -0.042 0.087 0.17 7 -0.41 21 28
actin cytoskeleton reorganization 0.018 0.1 -10000 0 -0.4 21 21
PTK2 -0.058 0.15 -10000 0 -0.48 41 41
EDG1 -0.036 0.084 0.16 7 -0.4 21 28
mol:DAG -0.041 0.085 0.17 6 -0.42 20 26
CaM/Ca2+ -0.041 0.08 -10000 0 -0.39 20 20
MAP2K3 -0.045 0.084 -10000 0 -0.4 21 21
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.024 0.11 -10000 0 -0.41 20 20
PLCG1 -0.041 0.086 0.17 6 -0.42 20 26
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.098 -10000 0 -0.39 20 20
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
YES1 0.024 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.013 0.099 -10000 0 -0.41 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.013 0.098 -10000 0 -0.41 21 21
cell migration -0.053 0.15 0.25 1 -0.45 45 46
mol:PI-3-4-5-P3 -0.016 0.11 -10000 0 -0.47 22 22
FYN 0.022 0.009 -10000 0 -10000 0 0
VEGFB/NRP1 -0.038 0.08 0.16 6 -0.39 20 26
mol:NO -0.004 0.1 0.34 12 -0.33 23 35
PXN 0.025 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.072 -10000 0 -0.37 20 20
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.004 0.094 -10000 0 -0.41 20 20
VHL 0.025 0.005 -10000 0 -10000 0 0
ITGB3 0.02 0.011 -10000 0 -10000 0 0
NOS3 -0.006 0.11 0.35 12 -0.37 23 35
VEGFR2 homodimer/VEGFA homodimer/Sck 0.016 0.097 -10000 0 -0.4 21 21
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.043 0.087 0.28 3 -0.43 19 22
PRKCB -0.045 0.094 -10000 0 -0.42 24 24
VCL 0.024 0.008 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.086 0.17 7 -0.4 21 28
VEGFR1/2 heterodimer/VEGFA homodimer 0.014 0.1 0.32 1 -0.42 21 22
VEGFA165/NRP2 0.016 0.067 0.19 4 -0.16 55 59
MAPKKK cascade -0.039 0.088 0.4 2 -0.38 17 19
NRP2 0.024 0.007 -10000 0 -10000 0 0
VEGFC homodimer 0.026 0.011 0.24 1 -10000 0 1
NCK1 0.024 0.007 -10000 0 -10000 0 0
ROCK1 0.025 0.006 -10000 0 -10000 0 0
FAK1/Paxillin -0.05 0.15 0.3 3 -0.46 41 44
MAP3K13 -0.042 0.088 0.17 4 -0.41 22 26
PDPK1 -0.041 0.096 0.24 1 -0.41 22 23
IL27-mediated signaling events

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
TGFB1 0.031 0.021 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.005 0.14 0.68 11 -0.49 3 14
IL27/IL27R/JAK1 0.054 0.18 0.45 7 -0.82 9 16
TBX21 0.039 0.17 0.42 27 -0.48 10 37
IL12B 0.039 0.055 0.25 30 -10000 0 30
IL12A -0.005 0.018 0.14 6 -10000 0 6
IL6ST 0.022 0.02 0.19 1 -10000 0 1
IL27RA/JAK1 0.012 0.14 0.44 1 -0.97 9 10
IL27 0.029 0.044 0.25 15 -10000 0 15
TYK2 0.03 0.016 0.12 3 -10000 0 3
T-helper cell lineage commitment 0.004 0.12 0.41 7 -10000 0 7
T-helper 2 cell differentiation -0.005 0.14 0.68 11 -0.49 3 14
T cell proliferation during immune response -0.005 0.14 0.68 11 -0.49 3 14
MAPKKK cascade 0.005 0.14 0.49 3 -0.68 11 14
STAT3 0.025 0.005 -10000 0 -10000 0 0
STAT2 0.025 0.004 -10000 0 -10000 0 0
STAT1 0.033 0.029 0.24 9 -10000 0 9
IL12RB1 0.034 0.042 0.25 18 -10000 0 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.034 0.18 0.45 23 -0.44 13 36
IL27/IL27R/JAK2/TYK2 0.005 0.14 0.49 3 -0.7 11 14
positive regulation of T cell mediated cytotoxicity 0.005 0.14 0.49 3 -0.68 11 14
STAT1 (dimer) 0.08 0.22 0.49 79 -0.64 9 88
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.028 0.01 0.14 1 -10000 0 1
STAT2 (dimer) 0.007 0.14 0.43 3 -0.65 11 14
T cell proliferation 0.007 0.14 0.4 9 -0.66 11 20
IL12/IL12R/TYK2/JAK2 0.049 0.11 0.46 6 -0.54 7 13
IL17A 0.008 0.12 0.41 7 -10000 0 7
mast cell activation -0.005 0.14 0.68 11 -0.49 3 14
IFNG 0.013 0.041 0.13 31 -0.095 7 38
T cell differentiation 0 0.006 0.017 17 -0.021 10 27
STAT3 (dimer) 0.006 0.14 0.43 3 -0.66 11 14
STAT5A (dimer) 0.006 0.14 0.39 4 -0.66 11 15
STAT4 (dimer) 0.011 0.15 0.4 9 -0.66 11 20
STAT4 0.031 0.035 0.24 13 -10000 0 13
T cell activation -0.005 0.009 0.11 2 -0.091 1 3
IL27R/JAK2/TYK2 0.015 0.15 0.38 1 -0.88 9 10
GATA3 -0.33 0.5 0.65 3 -1.1 145 148
IL18 -0.008 0.005 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.006 0.14 0.39 4 -0.64 11 15
IL27/EBI3 0.048 0.047 0.21 24 -0.16 4 28
IL27RA -0.008 0.15 -10000 0 -1 9 9
IL6 0.043 0.072 0.26 46 -10000 0 46
STAT5A 0.025 0.005 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.005 0.07 0.43 10 -10000 0 10
IL1B -0.001 0.031 0.14 22 -10000 0 22
EBI3 0.033 0.035 0.26 9 -10000 0 9
TNF -0.004 0.023 0.14 12 -10000 0 12
Wnt 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
Noncanonical Wnts/FZD -0.015 0.091 0.17 7 -0.21 71 78
FZD6 0.02 0.011 -10000 0 -10000 0 0
WNT6 0.024 0.028 0.24 7 -10000 0 7
WNT4 0.025 0.004 -10000 0 -10000 0 0
FZD3 0.019 0.012 -10000 0 -10000 0 0
WNT5A 0.029 0.035 0.24 12 -10000 0 12
WNT11 0.035 0.047 0.24 23 -10000 0 23
IL2 signaling events mediated by STAT5

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
GAB2 0.025 0.006 -10000 0 -10000 0 0
ELF1 0.037 0.053 0.15 61 -0.27 4 65
CCNA2 0.058 0.079 0.24 74 -10000 0 74
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
JAK3 0.031 0.032 0.24 11 -10000 0 11
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
JAK1 0.025 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.018 0.089 0.29 9 -0.34 10 19
SHC1 0.025 0.006 -10000 0 -10000 0 0
SP1 0.015 0.064 0.15 1 -0.27 23 24
IL2RA 0.02 0.1 0.27 62 -0.51 4 66
IL2RB 0.028 0.027 0.24 7 -10000 0 7
SOS1 0.025 0.005 -10000 0 -10000 0 0
IL2RG 0.032 0.038 0.24 15 -10000 0 15
G1/S transition of mitotic cell cycle -0.006 0.2 0.35 17 -0.65 29 46
PTPN11 0.025 0.006 -10000 0 -10000 0 0
CCND2 -0.037 0.11 0.27 1 -0.51 23 24
LCK 0.03 0.029 0.24 9 -10000 0 9
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL2 0.022 0.015 0.24 2 -10000 0 2
CDK6 0.023 0.009 -10000 0 -10000 0 0
CCND3 0.019 0.092 0.34 9 -0.36 4 13
Syndecan-4-mediated signaling events

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
PTK2 0.032 0.078 0.24 4 -0.32 14 18
Syndecan-4/Syndesmos 0.071 0.13 0.3 12 -0.56 10 22
positive regulation of JNK cascade 0.07 0.13 0.3 11 -0.48 12 23
Syndecan-4/ADAM12 0.075 0.13 0.3 14 -0.56 10 24
CCL5 0.028 0.026 0.24 7 -10000 0 7
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
DNM2 0.026 0.003 -10000 0 -10000 0 0
ITGA5 0.025 0.011 0.24 1 -10000 0 1
SDCBP 0.021 0.01 -10000 0 -10000 0 0
PLG 0.017 0.056 0.24 23 -0.067 15 38
ADAM12 0.034 0.044 0.24 20 -10000 0 20
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.018 0.037 8 -10000 0 8
Syndecan-4/Laminin alpha1 0.069 0.14 0.33 11 -0.52 12 23
Syndecan-4/CXCL12/CXCR4 0.073 0.13 0.31 11 -0.52 12 23
Syndecan-4/Laminin alpha3 0.06 0.13 0.29 8 -0.56 11 19
MDK 0.032 0.039 0.24 16 -10000 0 16
Syndecan-4/FZD7 0.07 0.14 0.3 13 -0.5 14 27
Syndecan-4/Midkine 0.077 0.13 0.33 13 -0.57 9 22
FZD7 0.025 0.005 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.055 0.13 0.29 1 -0.48 13 14
THBS1 0.026 0.023 0.24 5 -10000 0 5
integrin-mediated signaling pathway 0.065 0.13 0.3 11 -0.51 11 22
positive regulation of MAPKKK cascade 0.07 0.13 0.3 11 -0.48 12 23
Syndecan-4/TACI 0.08 0.14 0.32 20 -0.55 11 31
CXCR4 0.026 0.025 0.24 6 -10000 0 6
cell adhesion 0.002 0.052 0.19 7 -0.24 14 21
Syndecan-4/Dynamin 0.073 0.13 0.3 13 -0.54 11 24
Syndecan-4/TSP1 0.07 0.13 0.31 10 -0.53 11 21
Syndecan-4/GIPC 0.072 0.13 0.3 12 -0.54 11 23
Syndecan-4/RANTES 0.073 0.14 0.3 12 -0.51 13 25
ITGB1 0.025 0.004 -10000 0 -10000 0 0
LAMA1 0.033 0.046 0.24 22 -10000 0 22
LAMA3 0.023 0.014 0.24 1 -10000 0 1
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.024 0.11 0.7 9 -0.25 1 10
Syndecan-4/alpha-Actinin 0.071 0.13 0.3 13 -0.57 10 23
TFPI 0.031 0.038 0.24 15 -10000 0 15
F2 0.04 0.054 0.25 27 -0.072 3 30
alpha5/beta1 Integrin 0.032 0.034 0.19 1 -0.16 13 14
positive regulation of cell adhesion 0.049 0.13 0.31 9 -0.5 14 23
ACTN1 0.025 0.005 -10000 0 -10000 0 0
TNC 0.023 0.008 -10000 0 -10000 0 0
Syndecan-4/CXCL12 0.068 0.13 0.3 10 -0.52 12 22
FGF6 0.018 0.015 0.24 2 -10000 0 2
RHOA 0.025 0.005 -10000 0 -10000 0 0
CXCL12 0.025 0.012 0.24 1 -10000 0 1
TNFRSF13B 0.042 0.062 0.24 42 -10000 0 42
FGF2 0.024 0.013 0.24 1 -10000 0 1
FGFR1 0.019 0.011 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.052 0.12 0.28 8 -0.54 11 19
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.029 0.25 4 -0.068 11 15
cell migration -0.022 0.011 -10000 0 -10000 0 0
PRKCD 0.018 0.021 -10000 0 -0.1 4 4
vasculogenesis 0.069 0.13 0.3 10 -0.51 11 21
SDC4 0.059 0.13 0.3 8 -0.59 10 18
Syndecan-4/Tenascin C 0.066 0.13 0.3 11 -0.54 11 22
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.063 0.12 0.3 8 -0.59 8 16
MMP9 0.14 0.11 0.25 258 -10000 0 258
Rac1/GTP 0.002 0.053 0.19 7 -0.24 14 21
cytoskeleton organization 0.07 0.12 0.3 12 -0.53 10 22
GIPC1 0.026 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.074 0.14 0.33 17 -0.51 12 29
Caspase cascade in apoptosis

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
TOP1 0.005 0.071 0.21 4 -0.3 15 19
ACTA1 -0.03 0.087 0.21 6 -0.32 21 27
NUMA1 0.007 0.068 0.21 4 -0.32 11 15
SPTAN1 -0.005 0.085 0.2 26 -0.3 17 43
LIMK1 0.001 0.093 0.21 39 -0.28 19 58
BIRC3 0.026 0.018 0.24 3 -10000 0 3
BIRC2 0.025 0.006 -10000 0 -10000 0 0
BAX 0.026 0.015 0.24 2 -10000 0 2
CASP10 -0.017 0.04 0.12 24 -0.14 15 39
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
PTK2 0.001 0.072 0.2 3 -0.29 17 20
DIABLO 0.025 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.084 0.2 26 -0.3 17 43
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.025 0.006 -10000 0 -10000 0 0
GSN -0.007 0.084 0.2 23 -0.3 17 40
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.004 0.16 -10000 0 -0.55 33 33
BID -0.002 0.024 0.13 4 -0.11 12 16
MAP3K1 -0.034 0.12 -10000 0 -0.36 54 54
TRADD 0.023 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.011 0.083 0.23 13 -0.32 17 30
CASP9 0.026 0.003 -10000 0 -10000 0 0
DNA repair 0.003 0.047 0.21 13 -10000 0 13
neuron apoptosis 0.001 0.12 -10000 0 -0.62 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.002 0.078 0.26 6 -0.37 11 17
APAF1 0.025 0.006 -10000 0 -10000 0 0
CASP6 0.01 0.095 -10000 0 -0.84 4 4
TRAF2 0.025 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.017 0.08 0.26 9 -0.3 17 26
CASP7 -0.004 0.058 0.22 1 -0.24 11 12
KRT18 0.019 0.035 -10000 0 -0.49 1 1
apoptosis -0.007 0.079 0.3 7 -0.35 11 18
DFFA -0.015 0.077 0.22 6 -0.3 19 25
DFFB -0.013 0.079 0.22 10 -0.3 18 28
PARP1 -0.003 0.047 -10000 0 -0.21 13 13
actin filament polymerization 0.001 0.096 0.28 17 -0.27 22 39
TNF 0.029 0.035 0.24 12 -10000 0 12
CYCS 0.003 0.038 0.18 7 -0.14 5 12
SATB1 0.007 0.099 0.37 4 -0.81 4 8
SLK -0.012 0.078 0.24 9 -0.29 19 28
p15 BID/BAX 0.011 0.043 0.15 2 -0.17 14 16
CASP2 0 0.057 0.2 14 -0.19 13 27
JNK cascade 0.034 0.12 0.36 54 -10000 0 54
CASP3 -0.011 0.079 0.2 8 -0.3 20 28
LMNB2 0.014 0.096 0.26 14 -0.34 13 27
RIPK1 0.025 0.005 -10000 0 -10000 0 0
CASP4 0.025 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.061 0.024 0.2 2 -0.13 2 4
negative regulation of DNA binding -0.003 0.16 -10000 0 -0.54 33 33
stress fiber formation -0.012 0.077 0.24 9 -0.28 19 28
GZMB -0.01 0.036 0.15 22 -10000 0 22
CASP1 0.003 0.041 -10000 0 -0.23 14 14
LMNB1 0.016 0.1 0.28 14 -0.34 15 29
APP 0.001 0.12 -10000 0 -0.63 16 16
TNFRSF1A 0.024 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.001 -10000 0 -10000 0 0
VIM -0.004 0.075 0.27 4 -0.35 11 15
LMNA 0.017 0.082 0.27 12 -0.32 8 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.048 0.14 1 -0.19 11 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.013 0.081 0.23 12 -0.3 19 31
APAF-1/Caspase 9 0.014 0.076 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis 0.007 0.068 0.21 4 -0.31 11 15
CFL2 -0.001 0.097 0.27 21 -0.28 18 39
GAS2 -0.011 0.074 0.2 9 -0.29 18 27
positive regulation of apoptosis 0.019 0.095 0.27 16 -0.39 6 22
PRF1 0.026 0.021 0.24 4 -10000 0 4
Cellular roles of Anthrax toxin

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
ANTXR1 0.025 0.011 0.24 1 -10000 0 1
ANTXR2 0.025 0.005 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.007 -10000 0 -0.036 21 21
monocyte activation -0.011 0.11 0.24 2 -0.33 45 47
MAP2K2 0.004 0.073 -10000 0 -0.56 8 8
MAP2K1 -0.01 0.007 -10000 0 -0.039 21 21
MAP2K7 -0.009 0.006 -10000 0 -0.039 20 20
MAP2K6 -0.007 0.015 0.077 11 -0.039 19 30
CYAA -0.016 0.021 0.06 1 -0.11 21 22
MAP2K4 -0.009 0.007 -10000 0 -0.039 18 18
IL1B -0.014 0.04 0.15 3 -0.11 48 51
Channel 0.026 0.033 0.16 1 -0.12 21 22
NLRP1 -0.009 0.013 -10000 0 -0.061 18 18
CALM1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.001 0.053 -10000 0 -0.4 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.007 0.036 21 -10000 0 21
MAPK3 -0.009 0.007 -10000 0 -0.039 20 20
MAPK1 -0.009 0.006 -10000 0 -0.039 18 18
PGR -0.011 0.021 -10000 0 -0.11 18 18
PA/Cellular Receptors 0.027 0.036 0.17 1 -0.14 21 22
apoptosis -0.004 0.007 -10000 0 -0.036 21 21
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.032 0.16 1 -0.12 21 22
macrophage activation -0.013 0.012 0.14 2 -10000 0 2
TNF 0.029 0.035 0.24 12 -10000 0 12
VCAM1 -0.01 0.11 0.24 2 -0.34 44 46
platelet activation 0.001 0.053 -10000 0 -0.4 8 8
MAPKKK cascade 0.005 0.019 0.086 1 -0.11 5 6
IL18 -0.012 0.029 0.11 2 -0.15 15 17
negative regulation of macrophage activation -0.004 0.007 -10000 0 -0.036 21 21
LEF -0.004 0.007 -10000 0 -0.036 21 21
CASP1 -0.004 0.01 -10000 0 -0.054 13 13
mol:cAMP 0.001 0.054 -10000 0 -0.41 8 8
necrosis -0.004 0.007 -10000 0 -0.036 21 21
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.031 0.16 1 -0.11 21 22
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.026 0.014 0.24 2 -10000 0 2
Jak2/Leptin Receptor 0.033 0.1 0.27 7 -0.34 13 20
PTP1B/AKT1 0.025 0.071 0.24 6 -0.21 7 13
FYN 0.022 0.009 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.018 0.073 0.21 12 -0.22 8 20
EGFR 0.021 0.015 -10000 0 -10000 0 0
EGF/EGFR 0.022 0.089 0.2 13 -0.21 28 41
CSF1 0.025 0.006 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
INSR 0.026 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.015 0.082 0.21 9 -0.22 27 36
Insulin Receptor/Insulin 0.037 0.071 0.22 6 -0.2 4 10
HCK 0.025 0.011 0.24 1 -10000 0 1
CRK 0.024 0.007 -10000 0 -10000 0 0
TYK2 0.012 0.073 0.23 10 -0.22 7 17
EGF 0.039 0.063 0.24 40 -10000 0 40
YES1 0.024 0.006 -10000 0 -10000 0 0
CAV1 0.008 0.1 0.26 19 -0.26 26 45
TXN 0.025 0.014 0.24 1 -10000 0 1
PTP1B/IRS1/GRB2 0.029 0.081 0.21 2 -0.24 11 13
cell migration -0.018 0.073 0.22 8 -0.21 12 20
STAT3 0.025 0.005 -10000 0 -10000 0 0
PRLR 0.035 0.047 0.25 22 -10000 0 22
ITGA2B 0.025 0.024 0.24 5 -10000 0 5
CSF1R 0.026 0.011 0.24 1 -10000 0 1
Prolactin Receptor/Prolactin 0.035 0.057 0.19 28 -0.16 20 48
FGR 0.026 0.01 0.24 1 -10000 0 1
PTP1B/p130 Cas 0.022 0.065 0.22 4 -0.21 6 10
Crk/p130 Cas 0.027 0.072 0.24 3 -0.22 5 8
DOK1 0.019 0.074 0.24 15 -0.21 5 20
JAK2 0.024 0.092 0.27 4 -0.34 13 17
Jak2/Leptin Receptor/Leptin 0.008 0.095 0.24 4 -0.26 17 21
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
PTPN1 0.018 0.074 0.21 12 -0.22 8 20
LYN 0.022 0.01 -10000 0 -10000 0 0
CDH2 0.022 0.033 0.24 9 -10000 0 9
SRC 0.021 0.071 -10000 0 -0.35 13 13
ITGB3 0.02 0.011 -10000 0 -10000 0 0
CAT1/PTP1B 0.008 0.11 0.27 28 -0.25 27 55
CAPN1 0.025 0.007 -10000 0 -10000 0 0
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.035 0.074 0.22 2 -0.27 4 6
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.098 0.24 6 -0.26 23 29
negative regulation of transcription 0.024 0.092 0.26 5 -0.34 13 18
FCGR2A 0.025 0.015 0.24 2 -10000 0 2
FER 0.024 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.003 0.08 0.19 2 -0.16 98 100
BLK 0.031 0.058 0.24 32 -10000 0 32
Insulin Receptor/Insulin/Shc 0.048 0.026 0.19 12 -10000 0 12
RHOA 0.026 0.007 -10000 0 -10000 0 0
LEPR 0.024 0.01 -10000 0 -10000 0 0
BCAR1 0.021 0.01 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.028 0.13 0.22 17 -0.29 52 69
PRL 0.016 0.027 0.24 4 -10000 0 4
SOCS3 -0.13 0.38 -10000 0 -1.1 68 68
SPRY2 0.021 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.044 0.039 0.19 11 -0.14 13 24
CSF1/CSF1R 0.03 0.082 0.23 4 -0.25 10 14
Ras protein signal transduction -0.005 0.084 0.47 13 -10000 0 13
IRS1 0.025 0.005 -10000 0 -10000 0 0
INS 0.017 0.039 0.24 12 -10000 0 12
LEP 0.018 0.036 0.24 10 -10000 0 10
STAT5B 0.023 0.077 0.23 10 -0.26 7 17
STAT5A 0.023 0.077 0.23 10 -0.26 7 17
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.075 0.22 9 -0.21 8 17
CSN2 -0.001 0.055 -10000 0 -0.42 1 1
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
LAT 0.019 0.09 -10000 0 -0.38 17 17
YBX1 0.031 0.005 -10000 0 -10000 0 0
LCK 0.03 0.029 0.24 9 -10000 0 9
SHC1 0.025 0.006 -10000 0 -10000 0 0
NOX4 0.13 0.11 0.24 230 -10000 0 230
Nectin adhesion 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
PDGFRB 0.026 0.014 0.24 2 -10000 0 2
alphaV beta3 Integrin 0 0.076 -10000 0 -0.16 90 90
PTK2 -0.008 0.088 -10000 0 -0.31 29 29
positive regulation of JNK cascade 0.004 0.084 -10000 0 -0.27 35 35
CDC42/GDP 0.025 0.12 0.34 4 -0.36 32 36
Rac1/GDP 0.02 0.12 0.33 3 -0.35 29 32
RAP1B 0.025 0.005 -10000 0 -10000 0 0
RAP1A 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.11 -10000 0 -0.32 34 34
nectin-3/I-afadin 0.036 0.047 0.19 21 -0.16 14 35
RAPGEF1 -0.004 0.12 0.32 6 -0.39 29 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.01 0.12 -10000 0 -0.43 30 30
PDGFB-D/PDGFRB 0.026 0.014 0.24 2 -10000 0 2
TLN1 -0.012 0.023 0.099 1 -10000 0 1
Rap1/GTP -0.002 0.083 -10000 0 -0.29 29 29
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.045 0.015 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.036 0.047 0.19 21 -0.16 14 35
PVR 0.026 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.003 -10000 0 -10000 0 0
mol:GDP 0.013 0.14 0.37 4 -0.42 32 36
MLLT4 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.058 0.056 0.2 17 -0.15 16 33
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.011 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 0.084 -10000 0 -0.28 28 28
PVRL1 0.025 0.006 -10000 0 -10000 0 0
PVRL3 0.034 0.047 0.24 23 -10000 0 23
PVRL2 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.008 -10000 0 -10000 0 0
CDH1 0.023 0.009 -10000 0 -10000 0 0
CLDN1 0.022 0.014 0.24 1 -10000 0 1
JAM-A/CLDN1 0.036 0.072 0.2 17 -0.13 60 77
SRC -0.006 0.13 -10000 0 -0.47 30 30
ITGB3 0.02 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.011 -10000 0 -10000 0 0
FARP2 0.008 0.14 0.36 1 -0.43 32 33
RAC1 0.024 0.008 -10000 0 -10000 0 0
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.048 0.045 0.19 21 -0.14 14 35
nectin-1/I-afadin 0.035 0.011 -10000 0 -10000 0 0
nectin-2/I-afadin 0.037 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.046 0.044 0.19 17 -0.14 14 31
CDC42/GTP/IQGAP1/filamentous actin 0.034 0.005 -10000 0 -10000 0 0
F11R 0.025 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.004 0.084 -10000 0 -0.27 35 35
alphaV/beta3 Integrin/Talin 0.001 0.072 0.2 11 -0.2 14 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.037 0.009 -10000 0 -10000 0 0
PIP5K1C -0.006 0.023 0.095 6 -0.11 13 19
VAV2 0.012 0.13 0.35 1 -0.42 32 33
RAP1/GDP 0.023 0.11 0.32 2 -0.34 30 32
ITGAV 0.025 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.048 0.045 0.19 21 -0.14 14 35
nectin-3(dimer)/I-afadin/I-afadin 0.036 0.047 0.19 21 -0.16 14 35
Rac1/GTP 0.013 0.1 -10000 0 -0.34 28 28
PTPRM 0.008 0.027 0.13 6 -0.11 14 20
E-cadherin/beta catenin/alpha catenin 0.057 0.036 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.03 0.031 0.24 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.024 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.043 0.075 -10000 0 -0.15 161 161
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.004 -10000 0 -10000 0 0
FYN 0.022 0.009 -10000 0 -10000 0 0
MAP3K12 0.025 0.005 -10000 0 -10000 0 0
FGR 0.026 0.01 0.24 1 -10000 0 1
p38 alpha/TAB1 -0.044 0.078 -10000 0 -0.24 49 49
PRKG1 0.018 0.012 -10000 0 -10000 0 0
DUSP8 0.028 0.022 0.24 5 -10000 0 5
PGK/cGMP/p38 alpha -0.041 0.11 0.18 3 -0.26 66 69
apoptosis -0.043 0.075 -10000 0 -0.23 49 49
RAL/GTP 0.03 0.012 -10000 0 -10000 0 0
LYN 0.022 0.01 -10000 0 -10000 0 0
DUSP1 0.024 0.006 -10000 0 -10000 0 0
PAK1 0.025 0.006 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.057 0.024 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.032 0.011 -10000 0 -10000 0 0
MAPK11 -0.026 0.12 0.26 20 -0.28 47 67
BLK 0.031 0.058 0.24 32 -10000 0 32
HCK 0.025 0.011 0.24 1 -10000 0 1
MAP2K3 0.025 0.005 -10000 0 -10000 0 0
DUSP16 0.023 0.009 -10000 0 -10000 0 0
DUSP10 0.025 0.005 -10000 0 -10000 0 0
TRAF6/MEKK3 0.032 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.018 0.11 0.24 20 -0.28 37 57
positive regulation of innate immune response -0.027 0.14 0.29 21 -0.32 46 67
LCK 0.03 0.029 0.24 9 -10000 0 9
p38alpha-beta/MKP7 -0.018 0.14 0.31 15 -0.31 44 59
p38alpha-beta/MKP5 -0.021 0.14 0.31 14 -0.32 42 56
PGK/cGMP -0.027 0.075 -10000 0 -0.15 129 129
PAK2 0.024 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.026 0.14 0.32 14 -0.31 46 60
CDC42 0.026 0.003 -10000 0 -10000 0 0
RALB 0.025 0.006 -10000 0 -10000 0 0
RALA 0.023 0.008 -10000 0 -10000 0 0
PAK3 0.016 0.012 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.011 0.029 -10000 0 -0.053 14 14
HSPA8 0.024 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.031 0.059 0.22 1 -0.15 16 17
AKT1 0.026 0.008 -10000 0 -0.078 1 1
GSC 0.097 0.17 0.44 13 -0.9 3 16
NKX2-5 0 0.003 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.064 0.25 6 -0.34 1 7
SMAD2-3/SMAD4/SP1 0.071 0.059 0.31 2 -0.24 3 5
SMAD4 0.02 0.038 0.14 1 -0.13 5 6
CBFB 0.023 0.008 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.001 0.081 0.18 11 -0.14 88 99
SMAD3/SMAD4/VDR 0.052 0.062 0.24 3 -0.16 3 6
MYC 0.03 0.049 0.24 24 -10000 0 24
CDKN2B -0.029 0.13 -10000 0 -0.68 9 9
AP1 0.003 0.071 0.41 1 -0.25 10 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.001 0.075 -10000 0 -0.25 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.003 0.051 0.18 1 -0.19 27 28
SP3 0.025 0.006 -10000 0 -10000 0 0
CREB1 0.026 0.003 -10000 0 -10000 0 0
FOXH1 0.054 0.077 0.26 58 -10000 0 58
SMAD3/SMAD4/GR 0.023 0.065 -10000 0 -0.16 13 13
GATA3 0.013 0.045 -10000 0 -0.19 17 17
SKI/SIN3/HDAC complex/NCoR1 0.004 0.048 -10000 0 -0.22 5 5
MEF2C/TIF2 0.021 0.054 0.25 8 -0.36 1 9
endothelial cell migration -0.004 0.22 0.95 20 -0.37 1 21
MAX 0.017 0.029 -10000 0 -0.062 54 54
RBBP7 0.025 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.004 -10000 0 -10000 0 0
RUNX2 0.026 0.011 0.24 1 -10000 0 1
RUNX3 0.029 0.028 0.24 8 -10000 0 8
RUNX1 0.025 0.012 0.24 1 -10000 0 1
CTBP1 0.025 0.004 -10000 0 -10000 0 0
NR3C1 0.015 0.03 -10000 0 -0.062 56 56
VDR 0.026 0.015 0.24 2 -10000 0 2
CDKN1A 0.001 0.11 0.38 2 -0.98 5 7
KAT2B 0.014 0.022 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.079 0.085 0.3 24 -0.17 1 25
DCP1A 0.025 0.005 -10000 0 -10000 0 0
SKI 0.026 0.004 -10000 0 -10000 0 0
SERPINE1 0.004 0.23 0.37 1 -0.96 20 21
SMAD3/SMAD4/ATF2 0.026 0.062 -10000 0 -0.14 26 26
SMAD3/SMAD4/ATF3 0.028 0.086 0.24 16 -0.17 43 59
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.027 0.052 0.19 2 -0.15 3 5
JUN -0.01 0.064 0.25 4 -0.26 9 13
SMAD3/SMAD4/IRF7 0.044 0.057 0.27 2 -0.13 1 3
TFE3 0.027 0.02 -10000 0 -0.076 14 14
COL1A2 0.016 0.053 0.28 3 -0.71 2 5
mesenchymal cell differentiation -0.038 0.049 0.17 1 -0.2 1 2
DLX1 0.21 0.078 0.24 423 -10000 0 423
TCF3 0.025 0.004 -10000 0 -10000 0 0
FOS 0.022 0.025 0.24 4 -10000 0 4
SMAD3/SMAD4/Max 0.027 0.06 -10000 0 -0.14 1 1
Cbp/p300/SNIP1 0.044 0.028 -10000 0 -0.14 3 3
ZBTB17 0.025 0.004 -10000 0 -10000 0 0
LAMC1 -0.01 0.036 0.19 3 -10000 0 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.038 0.048 0.2 1 -10000 0 1
IRF7 0.036 0.046 0.24 23 -10000 0 23
ESR1 0.024 0.014 0.24 1 -0.06 3 4
HNF4A 0.032 0.051 0.24 27 -10000 0 27
MEF2C 0.037 0.085 0.21 60 -0.25 2 62
SMAD2-3/SMAD4 0.052 0.055 0.22 2 -0.21 2 4
Cbp/p300/Src-1 0.027 0.045 -10000 0 -0.15 3 3
IGHV3OR16-13 0.006 0.018 -10000 0 -0.34 1 1
TGIF2/HDAC complex 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.011 0.025 -10000 0 -0.046 4 4
SKIL 0.025 0.019 0.24 3 -10000 0 3
HDAC1 0.026 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.01 -10000 0 -10000 0 0
SNIP1 0.026 0.006 -10000 0 -10000 0 0
GCN5L2 -0.002 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.048 0.058 0.24 4 -0.15 1 5
MSG1/HSC70 0.005 0.081 0.19 11 -0.16 89 100
SMAD2 0.032 0.024 -10000 0 -0.14 3 3
SMAD3 0.007 0.039 -10000 0 -0.11 9 9
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.048 0.18 2 -0.17 6 8
SMAD2/SMAD2/SMAD4 -0.004 0.056 0.2 3 -0.17 18 21
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 0.018 0.012 -10000 0 -10000 0 0
NCOA1 0.025 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.033 0.03 0.19 11 -0.16 4 15
SMAD2-3/SMAD4/SP1/MIZ-1 0.08 0.061 0.31 2 -0.25 2 4
IFNB1 -0.014 0.039 0.19 4 -10000 0 4
SMAD3/SMAD4/MEF2C 0.069 0.079 0.27 16 -0.27 2 18
CITED1 0.026 0.036 0.24 12 -10000 0 12
SMAD2-3/SMAD4/ARC105 0.064 0.056 0.24 1 -0.24 1 2
RBL1 0.024 0.008 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.055 0.21 1 -0.3 5 6
RUNX1-3/PEBPB2 0.044 0.029 0.19 6 -0.13 3 9
SMAD7 0.007 0.079 0.29 1 -0.37 5 6
MYC/MIZ-1 0.036 0.038 0.19 24 -10000 0 24
SMAD3/SMAD4 -0.037 0.13 0.25 8 -0.34 40 48
IL10 -0.047 0.086 0.25 8 -0.3 19 27
PIASy/HDAC complex 0.024 0.019 -10000 0 -0.062 2 2
PIAS3 0.013 0.022 -10000 0 -10000 0 0
CDK2 0.011 0.025 -10000 0 -10000 0 0
IL5 -0.046 0.071 0.24 6 -0.22 12 18
CDK4 0.011 0.026 -10000 0 -0.047 3 3
PIAS4 0.024 0.019 -10000 0 -0.062 2 2
ATF3 0.033 0.049 0.24 24 -10000 0 24
SMAD3/SMAD4/SP1 0.042 0.056 0.29 2 -0.21 5 7
FOXG1 0.009 0.065 0.24 32 -10000 0 32
FOXO3 -0.015 0.007 -10000 0 -10000 0 0
FOXO1 -0.014 0.008 -10000 0 -0.095 1 1
FOXO4 -0.017 0.005 -10000 0 -0.095 1 1
heart looping 0.036 0.085 0.21 60 -0.25 2 62
CEBPB 0.025 0.007 -10000 0 -0.056 1 1
SMAD3/SMAD4/DLX1 0.15 0.08 0.21 134 -10000 0 134
MYOD1 0.023 0.034 0.24 11 -10000 0 11
SMAD3/SMAD4/HNF4 0.041 0.059 0.23 6 -0.13 2 8
SMAD3/SMAD4/GATA3 -0.009 0.1 0.28 3 -0.19 53 56
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.019 0.24 3 -10000 0 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.059 0.054 0.27 2 -0.15 1 3
SMAD3/SMAD4/SP1-3 0.059 0.054 0.29 2 -0.24 2 4
MED15 0.025 0.004 -10000 0 -10000 0 0
SP1 0.026 0.017 -10000 0 -0.12 5 5
SIN3B 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.077 0.082 0.29 25 -0.17 2 27
ITGB5 -0.014 0.044 0.19 9 -0.22 2 11
TGIF/SIN3/HDAC complex/CtBP 0.005 0.044 -10000 0 -0.25 2 2
SMAD3/SMAD4/AR 0.022 0.068 0.2 1 -0.14 37 38
AR 0.023 0.008 -10000 0 -10000 0 0
negative regulation of cell growth -0.002 0.069 0.24 1 -0.24 11 12
SMAD3/SMAD4/MYOD 0.035 0.057 0.21 10 -0.14 6 16
E2F5 0.021 0.015 0.24 1 -10000 0 1
E2F4 0.023 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.091 0.081 0.29 22 -10000 0 22
SMAD2-3/SMAD4/FOXO1-3a-4 0.009 0.037 -10000 0 -0.31 4 4
TFDP1 0.024 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.026 0.081 0.42 1 -0.26 9 10
SMAD3/SMAD4/RUNX2 0.038 0.05 0.2 1 -0.17 1 2
TGIF2 0.025 0.005 -10000 0 -10000 0 0
TGIF1 0.024 0.007 -10000 0 -10000 0 0
ATF2 0.023 0.008 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.025 0.004 -10000 0 -10000 0 0
ITGB7 0.025 0.018 0.24 3 -10000 0 3
ITGA4 0.029 0.033 0.24 11 -10000 0