PARADIGM pathway analysis of mRNASeq expression data
Glioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C19C6WMR
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 data. Broad Institute of MIT and Harvard. doi:10.7908/C19C6WMR
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 64 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
TCGA08_retinoblastoma 173
IL23-mediated signaling events 151
FOXM1 transcription factor network 143
Ephrin A reverse signaling 132
Syndecan-1-mediated signaling events 131
Aurora B signaling 127
IL12-mediated signaling events 107
IL4-mediated signaling events 106
Syndecan-4-mediated signaling events 94
Effects of Botulinum toxin 93
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 669 . 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 ( 669 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.2586 173 1385 8 -0.15 0.11 1000 -1000 -0.016 -1000
IL23-mediated signaling events 0.2257 151 9118 60 -0.7 0.015 1000 -1000 -0.16 -1000
FOXM1 transcription factor network 0.2138 143 7342 51 -0.46 0.032 1000 -1000 -0.16 -1000
Ephrin A reverse signaling 0.1973 132 928 7 -0.12 0 1000 -1000 -0.03 -1000
Syndecan-1-mediated signaling events 0.1958 131 4475 34 -0.32 0.015 1000 -1000 -0.063 -1000
Aurora B signaling 0.1898 127 8562 67 -0.39 0.015 1000 -1000 -0.069 -1000
IL12-mediated signaling events 0.1599 107 9385 87 -0.51 0.1 1000 -1000 -0.12 -1000
IL4-mediated signaling events 0.1584 106 9713 91 -0.72 0.5 1000 -1000 -0.13 -1000
Syndecan-4-mediated signaling events 0.1405 94 6322 67 -0.27 0.048 1000 -1000 -0.093 -1000
Effects of Botulinum toxin 0.1390 93 2418 26 -0.2 0.015 1000 -1000 -0.065 -1000
Glypican 2 network 0.1390 93 375 4 -0.085 -0.021 1000 -1000 -0.034 -1000
TCR signaling in naïve CD8+ T cells 0.1345 90 8405 93 -0.25 0.064 1000 -1000 -0.08 -1000
Signaling events mediated by the Hedgehog family 0.1330 89 4676 52 -0.2 0.15 1000 -1000 -0.076 -1000
Signaling events regulated by Ret tyrosine kinase 0.1300 87 7188 82 -0.26 0.015 1000 -1000 -0.089 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1300 87 5962 68 -0.43 0.16 1000 -1000 -0.12 -1000
E-cadherin signaling events 0.1241 83 419 5 -0.11 0.015 1000 -1000 -0.047 -1000
Osteopontin-mediated events 0.1091 73 2807 38 -0.22 0.016 1000 -1000 -0.1 -1000
a4b1 and a4b7 Integrin signaling 0.1076 72 363 5 -0.089 -0.027 1000 -1000 -0.042 -1000
HIF-1-alpha transcription factor network 0.1061 71 5459 76 -0.28 0.082 1000 -1000 -0.11 -1000
Glypican 1 network 0.1046 70 3370 48 -0.22 0.034 1000 -1000 -0.048 -1000
amb2 Integrin signaling 0.1046 70 5751 82 -0.25 0.015 1000 -1000 -0.087 -1000
Reelin signaling pathway 0.1031 69 3873 56 -0.31 0.015 1000 -1000 -0.087 -1000
Endothelins 0.1031 69 6709 96 -0.25 0.015 1000 -1000 -0.076 -1000
Aurora C signaling 0.1016 68 479 7 -0.18 0 1000 -1000 -0.043 -1000
Thromboxane A2 receptor signaling 0.1001 67 7051 105 -0.2 0.052 1000 -1000 -0.074 -1000
Caspase cascade in apoptosis 0.0957 64 4740 74 -0.17 0.05 1000 -1000 -0.047 -1000
PLK1 signaling events 0.0957 64 5440 85 -0.23 0.054 1000 -1000 -0.049 -1000
TCGA08_p53 0.0927 62 440 7 -0.12 0.062 1000 -1000 -0.014 -1000
Signaling mediated by p38-alpha and p38-beta 0.0927 62 2730 44 -0.15 0.015 1000 -1000 -0.055 -1000
p75(NTR)-mediated signaling 0.0897 60 7536 125 -0.22 0.015 1000 -1000 -0.095 -1000
PDGFR-alpha signaling pathway 0.0897 60 2669 44 -0.15 0.029 1000 -1000 -0.055 -1000
Visual signal transduction: Cones 0.0852 57 2190 38 -0.18 0.018 1000 -1000 -0.068 -1000
Arf6 signaling events 0.0837 56 3501 62 -0.24 0.015 1000 -1000 -0.068 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0837 56 4811 85 -0.17 0.015 1000 -1000 -0.079 -1000
FOXA2 and FOXA3 transcription factor networks 0.0837 56 2576 46 -0.3 0.019 1000 -1000 -0.065 -1000
IL1-mediated signaling events 0.0807 54 3359 62 -0.24 0.067 1000 -1000 -0.095 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0777 52 4580 88 -0.22 0.021 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0747 50 5812 114 -0.41 0.24 1000 -1000 -0.068 -1000
IL6-mediated signaling events 0.0747 50 3823 75 -0.24 0.066 1000 -1000 -0.085 -1000
Rapid glucocorticoid signaling 0.0732 49 981 20 -0.15 0.02 1000 -1000 -0.04 -1000
Visual signal transduction: Rods 0.0732 49 2559 52 -0.19 0.015 1000 -1000 -0.089 -1000
Ras signaling in the CD4+ TCR pathway 0.0732 49 844 17 -0.11 0.015 1000 -1000 -0.046 -1000
Calcium signaling in the CD4+ TCR pathway 0.0717 48 1515 31 -0.22 0.014 1000 -1000 -0.089 -1000
LPA receptor mediated events 0.0717 48 4930 102 -0.25 0.027 1000 -1000 -0.09 -1000
Integrins in angiogenesis 0.0703 47 4005 84 -0.15 0.019 1000 -1000 -0.093 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0688 46 1714 37 -0.13 0.015 1000 -1000 -0.061 -1000
Retinoic acid receptors-mediated signaling 0.0688 46 2678 58 -0.19 0.033 1000 -1000 -0.071 -1000
Syndecan-3-mediated signaling events 0.0673 45 1591 35 -0.22 0.015 1000 -1000 -0.061 -1000
IL2 signaling events mediated by STAT5 0.0673 45 991 22 -0.16 0.024 1000 -1000 -0.047 -1000
EGFR-dependent Endothelin signaling events 0.0658 44 944 21 -0.13 0.015 1000 -1000 -0.077 -1000
BMP receptor signaling 0.0628 42 3471 81 -0.19 0.052 1000 -1000 -0.089 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0613 41 2143 52 -0.14 0.026 1000 -1000 -0.072 -1000
BCR signaling pathway 0.0613 41 4142 99 -0.21 0.037 1000 -1000 -0.098 -1000
ErbB2/ErbB3 signaling events 0.0583 39 2574 65 -0.16 0.026 1000 -1000 -0.066 -1000
Syndecan-2-mediated signaling events 0.0583 39 2738 69 -0.22 0.038 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.0583 39 3834 97 -0.26 0.048 1000 -1000 -0.094 -1000
S1P1 pathway 0.0583 39 1425 36 -0.13 0.015 1000 -1000 -0.06 -1000
Wnt signaling 0.0568 38 268 7 -0.042 -0.006 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0568 38 4669 120 -0.2 0.12 1000 -1000 -0.073 -1000
LPA4-mediated signaling events 0.0553 37 449 12 -0.048 0.015 1000 -1000 -0.027 -1000
Nongenotropic Androgen signaling 0.0553 37 1971 52 -0.082 0.015 1000 -1000 -0.064 -1000
Coregulation of Androgen receptor activity 0.0538 36 2758 76 -0.2 0.029 1000 -1000 -0.046 -1000
Regulation of nuclear SMAD2/3 signaling 0.0523 35 4865 136 -0.29 0.28 1000 -1000 -0.073 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0508 34 1841 54 -0.19 0.032 1000 -1000 -0.11 -1000
S1P5 pathway 0.0478 32 547 17 -0.1 0.056 1000 -1000 -0.052 -1000
Signaling events mediated by PTP1B 0.0463 31 2399 76 -0.24 0.028 1000 -1000 -0.092 -1000
Presenilin action in Notch and Wnt signaling 0.0463 31 1944 61 -0.28 0.039 1000 -1000 -0.076 -1000
IL2 signaling events mediated by PI3K 0.0463 31 1812 58 -0.17 0.034 1000 -1000 -0.083 -1000
Canonical Wnt signaling pathway 0.0463 31 1615 51 -0.28 0.1 1000 -1000 -0.064 -1000
E-cadherin signaling in the nascent adherens junction 0.0463 31 2364 76 -0.11 0.02 1000 -1000 -0.087 -1000
PLK2 and PLK4 events 0.0448 30 91 3 -0.007 -0.004 1000 -1000 -0.02 -1000
FAS signaling pathway (CD95) 0.0448 30 1455 47 -0.2 0.017 1000 -1000 -0.051 -1000
Signaling events mediated by HDAC Class III 0.0433 29 1188 40 -0.1 0.091 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0419 28 1459 51 -0.17 0.02 1000 -1000 -0.078 -1000
JNK signaling in the CD4+ TCR pathway 0.0404 27 468 17 -0.072 0.019 1000 -1000 -0.068 -1000
Noncanonical Wnt signaling pathway 0.0404 27 717 26 -0.11 0.015 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0404 27 2040 74 -0.19 0.062 1000 -1000 -0.094 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0404 27 2112 78 -0.067 0.045 1000 -1000 -0.069 -1000
ErbB4 signaling events 0.0389 26 1836 69 -0.14 0.082 1000 -1000 -0.089 -1000
TCGA08_rtk_signaling 0.0389 26 697 26 -0.16 0.029 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.0374 25 981 39 -0.13 0.022 1000 -1000 -0.037 -1000
Ceramide signaling pathway 0.0374 25 1917 76 -0.13 0.026 1000 -1000 -0.059 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0344 23 789 34 -0.056 0.015 1000 -1000 -0.07 -1000
Aurora A signaling 0.0344 23 1412 60 -0.19 0.033 1000 -1000 -0.064 -1000
Plasma membrane estrogen receptor signaling 0.0344 23 1997 86 -0.13 0.04 1000 -1000 -0.081 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0329 22 617 28 -0.1 0.015 1000 -1000 -0.048 -1000
Ephrin B reverse signaling 0.0329 22 1095 48 -0.11 0.087 1000 -1000 -0.068 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0314 21 1808 83 -0.2 0.057 1000 -1000 -0.076 -1000
Signaling mediated by p38-gamma and p38-delta 0.0314 21 326 15 -0.017 0.034 1000 -1000 -0.03 -1000
S1P4 pathway 0.0314 21 546 25 -0.1 0.029 1000 -1000 -0.054 -1000
Nectin adhesion pathway 0.0299 20 1266 63 -0.11 0.04 1000 -1000 -0.075 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0299 20 940 45 -0.13 0.031 1000 -1000 -0.087 -1000
EPHB forward signaling 0.0299 20 1769 85 -0.083 0.047 1000 -1000 -0.093 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0299 20 677 33 -0.16 0.044 1000 -1000 -0.068 -1000
HIF-2-alpha transcription factor network 0.0284 19 829 43 -0.077 0.049 1000 -1000 -0.082 -1000
Regulation of Androgen receptor activity 0.0284 19 1335 70 -0.15 0.049 1000 -1000 -0.065 -1000
Insulin-mediated glucose transport 0.0269 18 604 32 -0.12 0.038 1000 -1000 -0.064 -1000
Regulation of Telomerase 0.0269 18 1927 102 -0.13 0.052 1000 -1000 -0.11 -1000
E-cadherin signaling in keratinocytes 0.0269 18 776 43 -0.11 0.029 1000 -1000 -0.073 -1000
TRAIL signaling pathway 0.0254 17 846 48 -0.046 0.041 1000 -1000 -0.071 -1000
S1P3 pathway 0.0254 17 745 42 -0.088 0.019 1000 -1000 -0.059 -1000
EPO signaling pathway 0.0239 16 924 55 -0.18 0.067 1000 -1000 -0.094 -1000
Regulation of p38-alpha and p38-beta 0.0239 16 871 54 -0.13 0.026 1000 -1000 -0.062 -1000
Paxillin-dependent events mediated by a4b1 0.0224 15 565 36 -0.11 0.042 1000 -1000 -0.075 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0224 15 1923 125 -0.11 0.055 1000 -1000 -0.099 -1000
Hedgehog signaling events mediated by Gli proteins 0.0209 14 960 65 -0.091 0.073 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0209 14 729 49 -0.12 0.026 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 0.0209 14 445 31 -0.098 0.032 1000 -1000 -0.043 -1000
p38 MAPK signaling pathway 0.0209 14 641 44 -0.068 0.024 1000 -1000 -0.065 -1000
IFN-gamma pathway 0.0194 13 885 68 -0.22 0.076 1000 -1000 -0.093 -1000
BARD1 signaling events 0.0179 12 721 57 -0.063 0.034 1000 -1000 -0.073 -1000
Insulin Pathway 0.0179 12 940 74 -0.22 0.039 1000 -1000 -0.095 -1000
VEGFR1 specific signals 0.0164 11 624 56 -0.091 0.046 1000 -1000 -0.084 -1000
Canonical NF-kappaB pathway 0.0149 10 415 39 -0.13 0.095 1000 -1000 -0.084 -1000
Class I PI3K signaling events 0.0149 10 784 73 -0.098 0.035 1000 -1000 -0.069 -1000
Signaling events mediated by PRL 0.0149 10 370 34 -0.052 0.025 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0135 9 198 22 -0.018 0.04 1000 -1000 -0.072 -1000
Arf6 downstream pathway 0.0135 9 392 43 -0.038 0.033 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class I 0.0135 9 939 104 -0.13 0.063 1000 -1000 -0.07 -1000
IGF1 pathway 0.0135 9 561 57 -0.049 0.053 1000 -1000 -0.097 -1000
Class IB PI3K non-lipid kinase events 0.0135 9 27 3 -0.007 0.007 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 0.0105 7 570 75 -0.15 0.042 1000 -1000 -0.061 -1000
Arf6 trafficking events 0.0105 7 524 71 -0.14 0.051 1000 -1000 -0.071 -1000
PDGFR-beta signaling pathway 0.0105 7 762 97 -0.057 0.072 1000 -1000 -0.089 -1000
Class I PI3K signaling events mediated by Akt 0.0075 5 370 68 -0.12 0.058 1000 -1000 -0.058 -1000
FoxO family signaling 0.0075 5 359 64 -0.12 0.1 1000 -1000 -0.063 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0030 2 59 23 -0.012 0.054 1000 -1000 -0.077 -1000
mTOR signaling pathway 0.0030 2 156 53 -0.004 0.038 1000 -1000 -0.063 -1000
Alternative NF-kappaB pathway 0.0030 2 27 13 -0.004 0.015 1000 -1000 -0.07 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0015 1 53 27 -0.007 0.035 1000 -1000 -0.06 -1000
Arf1 pathway 0.0000 0 29 54 -0.004 0.041 1000 -1000 -0.049 -1000
Total NA 5444 299411 7203 -22 5.9 131000 -131000 -9.2 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.1 0.24 -10000 0 -0.58 134 134
CDKN2C -0.042 0.18 -10000 0 -0.54 79 79
CDKN2A -0.15 0.27 -10000 0 -0.58 186 186
CCND2 0.1 0.17 0.33 193 -0.15 3 196
RB1 -0.11 0.18 -10000 0 -0.35 196 196
CDK4 0.11 0.18 0.37 192 -10000 0 192
CDK6 0.11 0.19 0.37 191 -0.17 15 206
G1/S progression 0.093 0.18 0.34 196 -10000 0 196
IL23-mediated signaling events

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
CCL2 -0.62 0.58 -10000 0 -1.2 249 249
IL23A -0.6 0.56 -10000 0 -1.2 259 259
NF kappa B1 p50/RelA/I kappa B alpha -0.59 0.51 -10000 0 -1.1 259 259
positive regulation of T cell mediated cytotoxicity -0.64 0.63 -10000 0 -1.3 256 256
ITGA3 -0.57 0.53 -10000 0 -1.2 217 217
IL17F -0.36 0.34 -10000 0 -0.75 181 181
IL12B -0.021 0.058 -10000 0 -0.65 4 4
STAT1 (dimer) -0.62 0.6 -10000 0 -1.2 260 260
CD4 -0.54 0.51 -10000 0 -1.1 222 222
IL23 -0.59 0.53 -10000 0 -1.2 256 256
IL23R -0.083 0.087 -10000 0 -0.6 1 1
IL1B -0.65 0.61 -10000 0 -1.3 263 263
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.55 0.51 -10000 0 -1.2 207 207
TYK2 0.002 0.017 -10000 0 -10000 0 0
STAT4 -0.14 0.27 -10000 0 -0.6 165 165
STAT3 0.015 0 -10000 0 -10000 0 0
IL18RAP -0.079 0.22 -10000 0 -0.6 102 102
IL12RB1 -0.033 0.15 -10000 0 -0.65 36 36
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.029 0.11 -10000 0 -0.49 36 36
IL23R/JAK2 -0.094 0.11 -10000 0 -0.59 1 1
positive regulation of chronic inflammatory response -0.64 0.63 -10000 0 -1.3 256 256
natural killer cell activation 0.008 0.008 0.052 1 -10000 0 1
JAK2 0.008 0.02 -10000 0 -10000 0 0
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
NFKB1 0.012 0.003 -10000 0 -10000 0 0
RELA 0.012 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.56 0.5 -10000 0 -1.1 257 257
ALOX12B -0.62 0.57 -10000 0 -1.2 252 252
CXCL1 -0.61 0.56 -10000 0 -1.2 251 251
T cell proliferation -0.64 0.63 -10000 0 -1.3 256 256
NFKBIA 0.011 0.023 -10000 0 -0.59 1 1
IL17A -0.27 0.27 -10000 0 -0.59 132 132
PI3K -0.6 0.53 -10000 0 -1.2 257 257
IFNG -0.022 0.033 -10000 0 -0.11 13 13
STAT3 (dimer) -0.57 0.49 -10000 0 -1.1 253 253
IL18R1 -0.048 0.19 -10000 0 -0.6 70 70
IL23/IL23R/JAK2/TYK2/SOCS3 -0.35 0.32 -10000 0 -0.73 170 170
IL18/IL18R -0.1 0.22 -10000 0 -0.45 173 173
macrophage activation -0.028 0.018 -10000 0 -0.045 204 204
TNF -0.63 0.6 -10000 0 -1.3 255 255
STAT3/STAT4 -0.66 0.54 -10000 0 -1.2 284 284
STAT4 (dimer) -0.67 0.6 -10000 0 -1.3 279 279
IL18 -0.026 0.16 -10000 0 -0.61 45 45
IL19 -0.55 0.51 -10000 0 -1.2 208 208
STAT5A (dimer) -0.61 0.6 -10000 0 -1.3 252 252
STAT1 0.001 0.092 -10000 0 -0.59 16 16
SOCS3 -0.18 0.29 -10000 0 -0.6 214 214
CXCL9 -0.66 0.58 -10000 0 -1.2 274 274
MPO -0.62 0.56 -10000 0 -1.2 249 249
positive regulation of humoral immune response -0.64 0.63 -10000 0 -1.3 256 256
IL23/IL23R/JAK2/TYK2 -0.7 0.74 -10000 0 -1.5 255 255
IL6 -0.64 0.58 -10000 0 -1.2 262 262
STAT5A 0.005 0.081 -10000 0 -0.62 11 11
IL2 0.006 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.008 0.052 1 -10000 0 1
CD3E -0.63 0.58 -10000 0 -1.3 251 251
keratinocyte proliferation -0.64 0.63 -10000 0 -1.3 256 256
NOS2 -0.58 0.53 -10000 0 -1.2 227 227
FOXM1 transcription factor network

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
NFATC3 -0.24 0.68 -10000 0 -1.2 179 179
PLK1 -0.014 0.23 -10000 0 -0.63 62 62
BIRC5 -0.27 0.57 -10000 0 -1 210 210
HSPA1B -0.26 0.68 -10000 0 -1.2 185 185
MAP2K1 0.028 0.049 -10000 0 -10000 0 0
BRCA2 -0.26 0.7 -10000 0 -1.2 188 188
FOXM1 -0.42 0.97 -10000 0 -1.8 197 197
XRCC1 -0.24 0.68 -10000 0 -1.2 181 181
FOXM1B/p19 -0.45 0.57 0.47 4 -1.2 205 209
Cyclin D1/CDK4 -0.23 0.63 -10000 0 -1.1 180 180
CDC2 -0.27 0.72 -10000 0 -1.3 197 197
TGFA -0.21 0.61 -10000 0 -1 181 181
SKP2 -0.25 0.68 -10000 0 -1.2 187 187
CCNE1 0.011 0.055 -10000 0 -0.6 5 5
CKS1B -0.25 0.68 -10000 0 -1.2 175 175
RB1 -0.19 0.28 -10000 0 -0.71 99 99
FOXM1C/SP1 -0.33 0.79 -10000 0 -1.4 196 196
AURKB -0.28 0.59 -10000 0 -1.1 207 207
CENPF -0.28 0.73 -10000 0 -1.3 186 186
CDK4 -0.015 0.14 -10000 0 -0.6 38 38
MYC -0.2 0.6 -10000 0 -1 179 179
CHEK2 0.01 0.12 -10000 0 -0.64 20 20
ONECUT1 -0.25 0.66 -10000 0 -1.2 189 189
CDKN2A -0.16 0.28 -10000 0 -0.61 186 186
LAMA4 -0.25 0.68 -10000 0 -1.2 188 188
FOXM1B/HNF6 -0.34 0.81 -10000 0 -1.5 191 191
FOS -0.32 0.71 -10000 0 -1.2 227 227
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.24 0.68 -10000 0 -1.2 182 182
response to radiation 0.009 0.046 -10000 0 -10000 0 0
CENPB -0.24 0.68 -10000 0 -1.2 174 174
CENPA -0.32 0.76 -10000 0 -1.3 208 208
NEK2 -0.32 0.77 -10000 0 -1.3 215 215
HIST1H2BA -0.25 0.68 -10000 0 -1.2 183 183
CCNA2 -0.074 0.22 -10000 0 -0.61 97 97
EP300 0.012 0.043 -10000 0 -0.62 3 3
CCNB1/CDK1 -0.34 0.82 -10000 0 -1.5 190 190
CCNB2 -0.34 0.78 -10000 0 -1.4 219 219
CCNB1 -0.28 0.74 -10000 0 -1.3 189 189
ETV5 -0.26 0.69 -10000 0 -1.2 193 193
ESR1 -0.26 0.69 -10000 0 -1.2 196 196
CCND1 -0.23 0.64 -10000 0 -1.1 179 179
GSK3A 0.032 0.037 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.027 0.19 -10000 0 -0.43 104 104
CDK2 0.002 0.094 -10000 0 -0.61 15 15
G2/M transition of mitotic cell cycle 0.009 0.055 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.46 0.6 -10000 0 -1.3 206 206
GAS1 -0.26 0.69 -10000 0 -1.2 180 180
MMP2 -0.26 0.69 -10000 0 -1.2 186 186
RB1/FOXM1C -0.25 0.67 -10000 0 -1.2 180 180
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
Ephrin A reverse signaling

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
MAPKKK cascade -0.12 0.22 -9999 0 -0.46 177 177
EFNA5 -0.068 0.21 -9999 0 -0.61 89 89
FYN -0.088 0.21 -9999 0 -0.42 177 177
neuron projection morphogenesis -0.12 0.22 -9999 0 -0.46 177 177
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.12 0.22 -9999 0 -0.46 177 177
EPHA5 -0.11 0.25 -9999 0 -0.61 131 131
Syndecan-1-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
TGFB1 0.006 0.077 -9999 0 -0.62 10 10
CCL5 -0.093 0.24 -9999 0 -0.6 117 117
SDCBP 0.015 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.5 205 205
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.2 0.23 -9999 0 -0.54 155 155
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.53 154 154
MAPK3 -0.16 0.21 -9999 0 -0.49 140 140
HGF/MET -0.19 0.26 -9999 0 -0.51 255 255
TGFB1/TGF beta receptor Type II 0.006 0.077 -9999 0 -0.62 10 10
BSG 0.015 0 -9999 0 -10000 0 0
keratinocyte migration -0.2 0.22 -9999 0 -0.53 155 155
Syndecan-1/RANTES -0.25 0.27 -9999 0 -0.59 201 201
Syndecan-1/CD147 -0.18 0.22 -9999 0 -0.51 154 154
Syndecan-1/Syntenin/PIP2 -0.2 0.2 -9999 0 -0.52 154 154
LAMA5 0.012 0.042 -9999 0 -0.61 3 3
positive regulation of cell-cell adhesion -0.2 0.2 -9999 0 -0.5 154 154
MMP7 -0.22 0.3 -9999 0 -0.6 247 247
HGF -0.088 0.23 -9999 0 -0.6 113 113
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.48 205 205
Syndecan-1/HGF/MET -0.32 0.31 -9999 0 -0.63 273 273
regulation of cell adhesion -0.15 0.2 -9999 0 -0.46 140 140
HPSE -0.048 0.19 -9999 0 -0.62 67 67
positive regulation of cell migration -0.22 0.23 -9999 0 -0.5 205 205
SDC1 -0.22 0.24 -9999 0 -0.51 205 205
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.5 205 205
PPIB 0.015 0 -9999 0 -10000 0 0
MET -0.16 0.28 -9999 0 -0.6 194 194
PRKACA 0.015 0 -9999 0 -10000 0 0
MMP9 -0.25 0.3 -9999 0 -0.6 285 285
MAPK1 -0.16 0.21 -9999 0 -0.49 140 140
homophilic cell adhesion -0.21 0.23 -9999 0 -0.5 205 205
MMP1 -0.1 0.24 -9999 0 -0.6 124 124
Aurora B 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
Condensin I complex -0.15 0.3 -9999 0 -0.61 177 177
STMN1 -0.12 0.22 -9999 0 -0.45 210 210
Aurora B/RasGAP/Survivin -0.22 0.33 -9999 0 -0.61 257 257
Chromosomal passenger complex/Cul3 protein complex -0.14 0.24 -9999 0 -0.45 212 212
BIRC5 -0.2 0.3 -9999 0 -0.63 225 225
DES -0.39 0.48 -9999 0 -0.84 285 285
Aurora C/Aurora B/INCENP -0.11 0.19 -9999 0 -0.36 234 234
Aurora B/TACC1 -0.11 0.18 -9999 0 -0.38 209 209
Aurora B/PP2A -0.13 0.22 -9999 0 -0.44 209 209
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.032 0.079 -9999 0 -0.18 115 115
mitotic metaphase/anaphase transition -0.001 0.006 -9999 0 -10000 0 0
NDC80 -0.24 0.36 -9999 0 -0.68 251 251
Cul3 protein complex -0.02 0.085 -9999 0 -0.38 35 35
KIF2C -0.19 0.34 -9999 0 -0.51 261 261
PEBP1 0.008 0.037 -9999 0 -0.65 2 2
KIF20A -0.23 0.31 -9999 0 -0.61 263 263
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.13 0.22 -9999 0 -0.44 209 209
SEPT1 0.013 0.033 -9999 0 -0.59 2 2
SMC2 0.015 0 -9999 0 -10000 0 0
SMC4 -0.015 0.13 -9999 0 -0.59 34 34
NSUN2/NPM1/Nucleolin -0.18 0.34 -9999 0 -0.86 119 119
PSMA3 0.015 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.004 -9999 0 -10000 0 0
H3F3B -0.085 0.16 -9999 0 -0.32 210 210
AURKB -0.18 0.3 -9999 0 -0.62 209 209
AURKC -0.015 0.13 -9999 0 -0.6 33 33
CDCA8 -0.12 0.25 -9999 0 -0.62 136 136
cytokinesis -0.35 0.45 -9999 0 -0.87 251 251
Aurora B/Septin1 -0.3 0.43 -9999 0 -0.82 245 245
AURKA -0.039 0.17 -9999 0 -0.59 59 59
INCENP 0.008 0.037 -9999 0 -0.64 2 2
KLHL13 0.012 0.043 -9999 0 -0.62 3 3
BUB1 -0.14 0.27 -9999 0 -0.61 170 170
hSgo1/Aurora B/Survivin -0.3 0.42 -9999 0 -0.75 278 278
EVI5 0.013 0.003 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.41 -9999 0 -0.8 252 252
SGOL1 -0.16 0.28 -9999 0 -0.6 191 191
CENPA -0.23 0.36 -9999 0 -0.64 247 247
NCAPG -0.15 0.28 -9999 0 -0.61 180 180
Aurora B/HC8 Proteasome -0.13 0.22 -9999 0 -0.44 209 209
NCAPD2 0.012 0.046 -9999 0 -0.59 4 4
Aurora B/PP1-gamma -0.13 0.22 -9999 0 -0.44 209 209
RHOA 0.015 0 -9999 0 -10000 0 0
NCAPH -0.091 0.23 -9999 0 -0.61 114 114
NPM1 -0.14 0.25 -9999 0 -0.49 203 203
RASA1 0.015 0 -9999 0 -10000 0 0
KLHL9 -0.015 0.14 -9999 0 -0.62 32 32
mitotic prometaphase -0.008 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.21 -9999 0 -0.44 209 209
PPP1CC 0.015 0 -9999 0 -10000 0 0
Centraspindlin -0.35 0.47 -9999 0 -0.89 256 256
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.14 0.25 -9999 0 -0.49 203 203
MYLK -0.093 0.17 -9999 0 -0.32 222 222
KIF23 -0.17 0.28 -9999 0 -0.62 193 193
VIM -0.19 0.27 -9999 0 -0.5 279 279
RACGAP1 0.006 0.048 -9999 0 -0.61 4 4
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.14 0.25 -9999 0 -0.53 169 169
Chromosomal passenger complex -0.28 0.43 -9999 0 -0.76 255 255
Chromosomal passenger complex/EVI5 -0.25 0.38 -9999 0 -0.75 226 226
TACC1 0.015 0 -9999 0 -10000 0 0
PPP2R5D 0.015 0 -9999 0 -10000 0 0
CUL3 0.015 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.11 0.17 -10000 0 -0.38 115 115
TBX21 -0.42 0.48 -10000 0 -1 216 216
B2M 0.004 0.084 -10000 0 -0.59 13 13
TYK2 0.004 0.02 -10000 0 -10000 0 0
IL12RB1 -0.03 0.15 -10000 0 -0.65 36 36
GADD45B -0.31 0.38 -10000 0 -0.86 143 143
IL12RB2 -0.11 0.24 -10000 0 -0.62 121 121
GADD45G -0.35 0.43 -10000 0 -0.92 167 167
natural killer cell activation -0.015 0.025 -10000 0 -10000 0 0
RELB 0.01 0.057 -10000 0 -0.59 6 6
RELA 0.015 0 -10000 0 -10000 0 0
IL18 -0.03 0.16 -10000 0 -0.62 45 45
IL2RA -0.17 0.28 -10000 0 -0.6 193 193
IFNG -0.002 0.061 -10000 0 -0.59 7 7
STAT3 (dimer) -0.34 0.36 -10000 0 -0.72 252 252
HLA-DRB5 -0.13 0.26 -10000 0 -0.6 159 159
FASLG -0.4 0.46 -10000 0 -0.93 221 221
NF kappa B2 p52/RelB -0.42 0.41 -10000 0 -0.85 265 265
CD4 0.008 0.062 -10000 0 -0.59 7 7
SOCS1 -0.059 0.2 -10000 0 -0.59 82 82
EntrezGene:6955 -0.001 0.009 -10000 0 -10000 0 0
CD3D -0.15 0.27 -10000 0 -0.61 173 173
CD3E -0.15 0.27 -10000 0 -0.61 174 174
CD3G -0.042 0.17 -10000 0 -0.6 58 58
IL12Rbeta2/JAK2 -0.079 0.18 -10000 0 -0.46 121 121
CCL3 -0.51 0.58 -10000 0 -1.2 247 247
CCL4 -0.49 0.57 -10000 0 -1.1 258 258
HLA-A 0.005 0.08 -10000 0 -0.59 12 12
IL18/IL18R -0.088 0.24 -10000 0 -0.47 173 173
NOS2 -0.38 0.46 -10000 0 -0.95 193 193
IL12/IL12R/TYK2/JAK2/SPHK2 -0.077 0.14 -10000 0 -0.37 70 70
IL1R1 -0.41 0.47 -10000 0 -0.96 226 226
IL4 0.015 0.045 -10000 0 -0.54 3 3
JAK2 0.004 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.28 -10000 0 -0.68 104 104
RAB7A -0.26 0.32 -10000 0 -0.74 116 116
lysosomal transport -0.24 0.31 -10000 0 -0.7 117 117
FOS -0.32 0.44 -10000 0 -0.95 166 166
STAT4 (dimer) -0.37 0.41 -10000 0 -0.82 238 238
STAT5A (dimer) -0.43 0.42 -10000 0 -0.87 260 260
GZMA -0.5 0.55 -10000 0 -1.1 264 264
GZMB -0.46 0.52 -10000 0 -1.1 233 233
HLX 0.004 0.082 -10000 0 -0.6 12 12
LCK -0.47 0.52 -10000 0 -0.98 277 277
TCR/CD3/MHC II/CD4 -0.18 0.28 -10000 0 -0.54 201 201
IL2/IL2R -0.19 0.26 -10000 0 -0.5 207 207
MAPK14 -0.32 0.4 -10000 0 -0.82 187 187
CCR5 -0.38 0.47 -10000 0 -1.1 157 157
IL1B -0.18 0.29 -10000 0 -0.63 191 191
STAT6 -0.095 0.12 0.25 1 -0.25 81 82
STAT4 -0.14 0.27 -10000 0 -0.6 165 165
STAT3 0.015 0 -10000 0 -10000 0 0
STAT1 0.001 0.092 -10000 0 -0.59 16 16
NFKB1 0.015 0 -10000 0 -10000 0 0
NFKB2 0.014 0.025 -10000 0 -0.62 1 1
IL12B -0.011 0.054 -10000 0 -0.63 4 4
CD8A -0.066 0.21 -10000 0 -0.61 88 88
CD8B -0.032 0.17 -10000 0 -0.61 51 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.1 0.17 0.38 114 -10000 0 114
IL2RB -0.11 0.25 -10000 0 -0.6 140 140
proteasomal ubiquitin-dependent protein catabolic process -0.34 0.37 -10000 0 -0.75 237 237
IL2RG -0.038 0.17 -10000 0 -0.6 58 58
IL12 -0.019 0.095 -10000 0 -0.48 24 24
STAT5A 0.005 0.081 -10000 0 -0.62 11 11
CD247 -0.02 0.14 -10000 0 -0.61 37 37
IL2 0.001 0.003 -10000 0 -10000 0 0
SPHK2 0.015 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.015 0.11 -10000 0 -0.63 20 20
IL12/IL12R/TYK2/JAK2 -0.46 0.55 -10000 0 -1 269 269
MAP2K3 -0.33 0.4 -10000 0 -0.81 196 196
RIPK2 0.015 0 -10000 0 -10000 0 0
MAP2K6 -0.33 0.4 -10000 0 -0.81 198 198
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.1 0.24 -10000 0 -0.61 124 124
IL18RAP -0.083 0.22 -10000 0 -0.61 102 102
IL12Rbeta1/TYK2 -0.022 0.12 -10000 0 -0.49 36 36
EOMES -0.019 0.19 -10000 0 -0.87 16 16
STAT1 (dimer) -0.33 0.36 -10000 0 -0.73 231 231
T cell proliferation -0.27 0.3 -10000 0 -0.61 220 220
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.052 0.19 -10000 0 -0.61 70 70
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.34 0.29 -10000 0 -0.68 220 220
ATF2 -0.3 0.37 -10000 0 -0.78 169 169
IL4-mediated signaling events

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
BCL2L1 -0.44 0.47 -10000 0 -1.1 153 153
STAT6 (cleaved dimer) -0.53 0.47 -10000 0 -1 249 249
IGHG1 -0.17 0.2 -10000 0 -0.47 91 91
IGHG3 -0.44 0.45 -10000 0 -1 197 197
AKT1 -0.26 0.3 -10000 0 -0.71 131 131
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.24 0.3 -10000 0 -0.74 110 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.25 0.27 -10000 0 -0.65 123 123
THY1 -0.46 0.49 -10000 0 -1.2 154 154
MYB -0.081 0.22 -10000 0 -0.6 104 104
HMGA1 0.007 0.07 -10000 0 -0.6 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.36 -10000 0 -0.79 203 203
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.28 -10000 0 -0.66 123 123
SP1 0.02 0.014 -10000 0 -10000 0 0
INPP5D 0.007 0.071 -10000 0 -0.6 9 9
SOCS5 0.03 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.52 0.49 -10000 0 -1.1 239 239
SOCS1 -0.35 0.35 -10000 0 -0.81 166 166
SOCS3 -0.44 0.48 -10000 0 -1 222 222
FCER2 -0.43 0.42 -10000 0 -1 140 140
PARP14 0.003 0.078 -10000 0 -0.6 11 11
CCL17 -0.46 0.48 -10000 0 -1.1 165 165
GRB2 0.014 0.023 -10000 0 -0.59 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.24 -10000 0 -0.64 88 88
T cell proliferation -0.46 0.49 -10000 0 -1.1 179 179
IL4R/JAK1 -0.45 0.46 -10000 0 -1.1 171 171
EGR2 -0.54 0.55 -10000 0 -1.3 188 188
JAK2 -0.002 0.026 -10000 0 -10000 0 0
JAK3 -0.058 0.2 -10000 0 -0.6 78 78
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
JAK1 0.005 0.013 -10000 0 -10000 0 0
COL1A2 -0.21 0.31 -10000 0 -0.85 90 90
CCL26 -0.46 0.49 -10000 0 -1.2 155 155
IL4R -0.48 0.5 -10000 0 -1.2 170 170
PTPN6 0.016 0.081 -10000 0 -0.61 11 11
IL13RA2 -0.72 0.61 -10000 0 -1.3 321 321
IL13RA1 -0.01 0.076 -10000 0 -0.66 8 8
IRF4 -0.17 0.31 -10000 0 -1.1 47 47
ARG1 -0.15 0.24 -10000 0 -0.78 55 55
CBL -0.33 0.34 -10000 0 -0.77 181 181
GTF3A 0.007 0.048 -10000 0 -0.62 2 2
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.014 0.065 -10000 0 -0.48 8 8
IRF4/BCL6 -0.14 0.29 -10000 0 -1.1 46 46
CD40LG -0.028 0.16 -10000 0 -0.6 47 47
MAPK14 -0.37 0.38 -10000 0 -0.84 203 203
mitosis -0.25 0.28 -10000 0 -0.67 127 127
STAT6 -0.51 0.55 -10000 0 -1.2 184 184
SPI1 -0.002 0.11 -10000 0 -0.61 19 19
RPS6KB1 -0.24 0.27 -10000 0 -0.66 117 117
STAT6 (dimer) -0.52 0.55 -10000 0 -1.2 184 184
STAT6 (dimer)/PARP14 -0.49 0.5 -10000 0 -1.1 186 186
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.33 -10000 0 -0.75 161 161
FRAP1 -0.26 0.3 -10000 0 -0.71 131 131
LTA -0.47 0.5 -10000 0 -1.2 170 170
FES 0.011 0.048 -10000 0 -0.61 4 4
T-helper 1 cell differentiation 0.5 0.53 1.2 189 -10000 0 189
CCL11 -0.44 0.45 -10000 0 -1.1 160 160
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.32 -10000 0 -0.73 141 141
IL2RG -0.04 0.17 -10000 0 -0.6 58 58
IL10 -0.55 0.59 -10000 0 -1.3 209 209
IRS1 0.009 0.065 -10000 0 -0.62 7 7
IRS2 0.014 0.023 -10000 0 -0.59 1 1
IL4 -0.11 0.12 -10000 0 -0.69 3 3
IL5 -0.45 0.47 -10000 0 -1.1 159 159
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.37 -10000 0 -0.84 169 169
COL1A1 -0.42 0.53 -10000 0 -1 227 227
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.48 -10000 0 -1.2 150 150
IL2R gamma/JAK3 -0.074 0.2 -10000 0 -0.49 120 120
TFF3 -0.47 0.49 -10000 0 -1.2 160 160
ALOX15 -0.46 0.48 -10000 0 -1.1 156 156
MYBL1 0.011 0.052 -10000 0 -0.59 5 5
T-helper 2 cell differentiation -0.4 0.39 -10000 0 -0.89 191 191
SHC1 0.001 0.092 -10000 0 -0.59 16 16
CEBPB -0.002 0.11 -10000 0 -0.61 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.26 -10000 0 -0.64 115 115
mol:PI-3-4-5-P3 -0.26 0.3 -10000 0 -0.71 131 131
PI3K -0.28 0.32 -10000 0 -0.76 131 131
DOK2 -0.085 0.23 -10000 0 -0.6 109 109
ETS1 0.022 0.063 -10000 0 -0.58 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.23 -10000 0 -0.62 81 81
ITGB3 -0.51 0.54 -10000 0 -1.2 185 185
PIGR -0.52 0.55 -10000 0 -1.3 174 174
IGHE 0.023 0.063 -10000 0 -0.28 7 7
MAPKKK cascade -0.19 0.23 -10000 0 -0.61 80 80
BCL6 0.017 0.006 -10000 0 -10000 0 0
OPRM1 -0.46 0.47 -10000 0 -1.1 164 164
RETNLB -0.46 0.47 -10000 0 -1.1 144 144
SELP -0.46 0.48 -10000 0 -1.2 144 144
AICDA -0.44 0.45 -10000 0 -1.1 167 167
Syndecan-4-mediated signaling events

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
PTK2 -0.017 0.084 -9999 0 -0.33 1 1
Syndecan-4/Syndesmos -0.18 0.26 -9999 0 -0.57 149 149
positive regulation of JNK cascade -0.2 0.23 -9999 0 -0.54 157 157
Syndecan-4/ADAM12 -0.27 0.3 -9999 0 -0.58 285 285
CCL5 -0.093 0.24 -9999 0 -0.6 117 117
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.015 0 -9999 0 -10000 0 0
ITGA5 -0.026 0.15 -9999 0 -0.59 46 46
SDCBP 0.015 0 -9999 0 -10000 0 0
PLG 0.002 0.046 -9999 0 -0.58 4 4
ADAM12 -0.17 0.28 -9999 0 -0.59 204 204
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.044 0.051 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.22 0.28 -9999 0 -0.6 186 186
Syndecan-4/CXCL12/CXCR4 -0.19 0.27 -9999 0 -0.58 157 157
Syndecan-4/Laminin alpha3 -0.21 0.28 -9999 0 -0.59 179 179
MDK -0.071 0.21 -9999 0 -0.6 93 93
Syndecan-4/FZD7 -0.21 0.29 -9999 0 -0.62 165 165
Syndecan-4/Midkine -0.22 0.28 -9999 0 -0.59 198 198
FZD7 -0.046 0.19 -9999 0 -0.62 65 65
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.54 139 139
THBS1 -0.15 0.27 -9999 0 -0.6 176 176
integrin-mediated signaling pathway -0.2 0.28 -9999 0 -0.59 176 176
positive regulation of MAPKKK cascade -0.2 0.23 -9999 0 -0.54 157 157
Syndecan-4/TACI -0.19 0.26 -9999 0 -0.58 151 151
CXCR4 -0.016 0.14 -9999 0 -0.61 33 33
cell adhesion 0.01 0.087 -9999 0 -0.33 27 27
Syndecan-4/Dynamin -0.18 0.26 -9999 0 -0.57 148 148
Syndecan-4/TSP1 -0.26 0.3 -9999 0 -0.61 238 238
Syndecan-4/GIPC -0.18 0.26 -9999 0 -0.57 148 148
Syndecan-4/RANTES -0.23 0.29 -9999 0 -0.62 188 188
ITGB1 0.012 0.04 -9999 0 -0.59 3 3
LAMA1 -0.071 0.22 -9999 0 -0.62 91 91
LAMA3 -0.054 0.2 -9999 0 -0.61 74 74
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.048 0.058 -9999 0 -0.51 2 2
Syndecan-4/alpha-Actinin -0.2 0.28 -9999 0 -0.59 179 179
TFPI -0.13 0.26 -9999 0 -0.61 154 154
F2 -0.008 0.061 -9999 0 -0.59 7 7
alpha5/beta1 Integrin -0.031 0.12 -9999 0 -0.45 46 46
positive regulation of cell adhesion -0.24 0.3 -9999 0 -0.6 210 210
ACTN1 -0.026 0.15 -9999 0 -0.59 46 46
TNC -0.053 0.19 -9999 0 -0.61 73 73
Syndecan-4/CXCL12 -0.19 0.26 -9999 0 -0.57 156 156
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CXCL12 0 0.095 -9999 0 -0.61 16 16
TNFRSF13B -0.003 0.069 -9999 0 -0.59 9 9
FGF2 0.013 0.034 -9999 0 -0.61 2 2
FGFR1 0.012 0.041 -9999 0 -0.6 3 3
Syndecan-4/PI-4-5-P2 -0.19 0.26 -9999 0 -0.54 191 191
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.023 0.16 -9999 0 -0.58 48 48
cell migration -0.011 0.022 -9999 0 -10000 0 0
PRKCD -0.002 0.12 -9999 0 -0.6 24 24
vasculogenesis -0.25 0.29 -9999 0 -0.58 238 238
SDC4 -0.2 0.27 -9999 0 -0.57 186 186
Syndecan-4/Tenascin C -0.21 0.29 -9999 0 -0.62 176 176
Syndecan-4/PI-4-5-P2/PKC alpha -0.035 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.18 0.26 -9999 0 -0.57 148 148
MMP9 -0.25 0.3 -9999 0 -0.6 285 285
Rac1/GTP -0.006 0.086 -9999 0 -0.34 26 26
cytoskeleton organization -0.17 0.24 -9999 0 -0.54 149 149
GIPC1 0.014 0.023 -9999 0 -0.59 1 1
Syndecan-4/TFPI -0.25 0.28 -9999 0 -0.61 192 192
Effects of Botulinum toxin

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
STX1A -0.042 0.15 -9999 0 -0.44 83 83
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.098 0.18 -9999 0 -0.44 147 147
STXBP1 -0.014 0.13 -9999 0 -0.59 32 32
ACh/CHRNA1 -0.16 0.2 -9999 0 -0.42 231 231
RAB3GAP2/RIMS1/UNC13B -0.082 0.15 -9999 0 -0.37 147 147
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.12 0.26 -9999 0 -0.61 147 147
mol:ACh -0.032 0.071 -9999 0 -0.14 186 186
RAB3GAP2 0.015 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.13 0.23 -9999 0 -0.55 127 127
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.16 0.2 -9999 0 -0.42 231 231
UNC13B 0.014 0.025 -9999 0 -0.62 1 1
CHRNA1 -0.2 0.29 -9999 0 -0.6 230 230
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.15 0.23 -9999 0 -0.46 229 229
SNAP25 -0.067 0.13 -9999 0 -0.27 184 184
VAMP2 0.008 0.007 -9999 0 -0.17 1 1
SYT1 -0.2 0.29 -9999 0 -0.6 229 229
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.043 0.18 -9999 0 -0.48 86 86
STX1A/SNAP25 fragment 1/VAMP2 -0.13 0.23 -9999 0 -0.55 127 127
Glypican 2 network

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
MDK -0.071 0.21 -9999 0 -0.6 93 93
GPC2 -0.021 0.15 -9999 0 -0.61 38 38
GPC2/Midkine -0.085 0.18 -9999 0 -0.47 122 122
neuron projection morphogenesis -0.085 0.18 -9999 0 -0.46 122 122
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.15 0.21 -10000 0 -0.48 160 160
FYN -0.16 0.29 -10000 0 -0.59 171 171
LAT/GRAP2/SLP76 -0.17 0.23 -10000 0 -0.53 156 156
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.11 0.2 -10000 0 -0.4 166 166
B2M 0 0.085 -10000 0 -0.6 13 13
IKBKG -0.034 0.047 -10000 0 -0.16 14 14
MAP3K8 -0.005 0.11 -10000 0 -0.59 22 22
mol:Ca2+ -0.025 0.044 -10000 0 -0.12 91 91
integrin-mediated signaling pathway -0.008 0.054 -10000 0 -0.38 14 14
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.17 0.28 -10000 0 -0.57 181 181
TRPV6 -0.11 0.24 -10000 0 -0.62 120 120
CD28 -0.089 0.23 -10000 0 -0.61 110 110
SHC1 -0.17 0.29 -10000 0 -0.59 176 176
receptor internalization -0.14 0.26 -10000 0 -0.56 155 155
PRF1 -0.2 0.39 -10000 0 -0.93 118 118
KRAS 0.014 0.023 -10000 0 -0.59 1 1
GRB2 0.014 0.023 -10000 0 -0.59 1 1
COT/AKT1 -0.084 0.17 -10000 0 -0.35 140 140
LAT -0.17 0.29 -10000 0 -0.59 180 180
EntrezGene:6955 -0.003 0.006 -10000 0 -10000 0 0
CD3D -0.15 0.27 -10000 0 -0.61 173 173
CD3E -0.15 0.28 -10000 0 -0.61 174 174
CD3G -0.044 0.17 -10000 0 -0.6 58 58
RASGRP2 -0.005 0.026 -10000 0 -0.18 3 3
RASGRP1 -0.11 0.21 -10000 0 -0.42 152 152
HLA-A 0.001 0.08 -10000 0 -0.59 12 12
RASSF5 0.002 0.09 -10000 0 -0.61 14 14
RAP1A/GTP/RAPL -0.008 0.055 -10000 0 -0.38 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.066 -10000 0 -0.12 64 64
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.064 0.082 -10000 0 -0.24 62 62
PRKCA -0.079 0.11 -10000 0 -0.27 98 98
GRAP2 -0.034 0.17 -10000 0 -0.61 53 53
mol:IP3 -0.1 0.2 0.23 61 -0.42 128 189
EntrezGene:6957 -0.003 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.24 -10000 0 -0.53 150 150
ORAI1 0.064 0.13 0.33 118 -0.43 2 120
CSK -0.17 0.29 -10000 0 -0.59 176 176
B7 family/CD28 -0.25 0.31 -10000 0 -0.66 207 207
CHUK 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.19 0.33 -10000 0 -0.66 183 183
PTPN6 -0.18 0.3 -10000 0 -0.61 179 179
VAV1 -0.17 0.3 -10000 0 -0.6 182 182
Monovalent TCR/CD3 -0.14 0.23 -10000 0 -0.42 233 233
CBL 0.014 0.025 -10000 0 -0.62 1 1
LCK -0.18 0.32 -10000 0 -0.63 189 189
PAG1 -0.17 0.29 -10000 0 -0.6 173 173
RAP1A 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.19 0.33 -10000 0 -0.66 181 181
CD80 -0.095 0.24 -10000 0 -0.61 116 116
CD86 -0.017 0.14 -10000 0 -0.62 33 33
PDK1/CARD11/BCL10/MALT1 -0.078 0.099 -10000 0 -0.27 82 82
HRAS 0.015 0 -10000 0 -10000 0 0
GO:0035030 -0.18 0.28 -10000 0 -0.55 203 203
CD8A -0.07 0.21 -10000 0 -0.61 88 88
CD8B -0.036 0.17 -10000 0 -0.62 51 51
PTPRC -0.028 0.15 -10000 0 -0.61 43 43
PDK1/PKC theta -0.13 0.24 -10000 0 -0.51 152 152
CSK/PAG1 -0.16 0.28 -10000 0 -0.58 169 169
SOS1 0.015 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.092 -10000 0 -0.48 22 22
GRAP2/SLP76 -0.19 0.27 -10000 0 -0.59 176 176
STIM1 0.037 0.064 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.088 -10000 0 -0.18 39 39
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.15 0.28 -10000 0 -0.59 155 155
mol:DAG -0.11 0.16 0.14 1 -0.37 141 142
RAP1A/GDP -0.004 0.029 -10000 0 -10000 0 0
PLCG1 0.015 0 -10000 0 -10000 0 0
CD247 -0.021 0.14 -10000 0 -0.61 37 37
cytotoxic T cell degranulation -0.19 0.36 -10000 0 -0.86 122 122
RAP1A/GTP -0.003 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.24 -10000 0 -0.47 180 180
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.25 0.26 50 -0.54 130 180
NRAS 0.015 0 -10000 0 -10000 0 0
ZAP70 -0.038 0.17 -10000 0 -0.6 57 57
GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
LAT/GRAP2/SLP76/VAV1 -0.17 0.22 -10000 0 -0.52 155 155
MALT1 0.015 0 -10000 0 -10000 0 0
TRAF6 0.013 0.035 -10000 0 -0.62 2 2
CD8 heterodimer -0.078 0.21 -10000 0 -0.52 116 116
CARD11 -0.001 0.1 -10000 0 -0.62 17 17
PRKCB -0.11 0.12 -10000 0 -0.29 139 139
PRKCE -0.083 0.11 -10000 0 -0.27 111 111
PRKCQ -0.16 0.27 -10000 0 -0.55 175 175
LCP2 0.007 0.072 -10000 0 -0.61 9 9
BCL10 0.015 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.09 0.17 -10000 0 -0.34 165 165
IKK complex -0.008 0.065 -10000 0 -0.12 11 11
RAS family/GDP -0.007 0.009 -10000 0 -10000 0 0
MAP3K14 -0.056 0.13 -10000 0 -0.29 84 84
PDPK1 -0.1 0.19 -10000 0 -0.39 151 151
TCR/CD3/MHC I/CD8/Fyn -0.2 0.34 -10000 0 -0.66 193 193
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.32 -10000 0 -0.64 160 160
IHH -0.018 0.1 -10000 0 -0.58 14 14
SHH Np/Cholesterol/GAS1 -0.099 0.17 -10000 0 -0.37 181 181
LRPAP1 0.015 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.099 0.17 0.36 181 -10000 0 181
SMO/beta Arrestin2 -0.042 0.19 -10000 0 -0.61 36 36
SMO -0.052 0.2 -10000 0 -0.65 37 37
AKT1 0.001 0.094 -10000 0 -0.48 2 2
ARRB2 0.015 0 -10000 0 -10000 0 0
BOC 0.009 0.064 -10000 0 -0.61 7 7
ADRBK1 0.015 0 -10000 0 -10000 0 0
heart looping -0.051 0.2 -10000 0 -0.64 37 37
STIL -0.1 0.23 -10000 0 -0.57 90 90
DHH N/PTCH2 -0.062 0.16 -10000 0 -0.45 93 93
DHH N/PTCH1 -0.084 0.22 -10000 0 -0.58 65 65
PIK3CA 0.015 0 -10000 0 -10000 0 0
DHH -0.058 0.2 -10000 0 -0.6 79 79
PTHLH -0.12 0.36 -10000 0 -0.87 95 95
determination of left/right symmetry -0.051 0.2 -10000 0 -0.64 37 37
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
skeletal system development -0.12 0.35 -10000 0 -0.86 95 95
IHH N/Hhip -0.11 0.22 -10000 0 -0.5 159 159
DHH N/Hhip -0.15 0.23 -10000 0 -0.48 208 208
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.051 0.2 -10000 0 -0.64 37 37
pancreas development -0.12 0.26 -10000 0 -0.61 150 150
HHAT -0.002 0.1 -10000 0 -0.62 18 18
PI3K -0.002 0.03 -10000 0 -0.46 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.029 0.16 -10000 0 -0.59 49 49
somite specification -0.051 0.2 -10000 0 -0.64 37 37
SHH Np/Cholesterol/PTCH1 -0.1 0.23 -10000 0 -0.57 81 81
SHH Np/Cholesterol/PTCH2 -0.084 0.15 -10000 0 -0.35 161 161
SHH Np/Cholesterol/Megalin -0.19 0.22 -10000 0 -0.4 314 314
SHH -0.079 0.2 -10000 0 -0.45 148 148
catabolic process -0.055 0.21 -10000 0 -0.58 53 53
SMO/Vitamin D3 -0.092 0.23 -10000 0 -0.59 73 73
SHH Np/Cholesterol/Hhip -0.15 0.21 -10000 0 -0.39 259 259
LRP2 -0.2 0.3 -10000 0 -0.61 225 225
receptor-mediated endocytosis -0.19 0.23 -10000 0 -0.6 120 120
SHH Np/Cholesterol/BOC -0.079 0.15 -10000 0 -0.35 152 152
SHH Np/Cholesterol/CDO -0.092 0.16 -10000 0 -0.36 170 170
mesenchymal cell differentiation 0.15 0.2 0.39 259 -10000 0 259
mol:Vitamin D3 -0.099 0.23 -10000 0 -0.57 81 81
IHH N/PTCH2 -0.006 0.1 -10000 0 -0.44 30 30
CDON -0.015 0.13 -10000 0 -0.61 32 32
IHH N/PTCH1 -0.056 0.21 -10000 0 -0.58 53 53
Megalin/LRPAP1 -0.15 0.21 -10000 0 -0.44 225 225
PTCH2 0 0.096 -10000 0 -0.62 16 16
SHH Np/Cholesterol -0.077 0.15 -10000 0 -0.35 148 148
PTCH1 -0.055 0.21 -10000 0 -0.58 53 53
HHIP -0.12 0.26 -10000 0 -0.61 150 150
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.049 0.055 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.12 0.16 -9999 0 -0.46 82 82
JUN -0.1 0.2 -9999 0 -0.53 80 80
HRAS 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.21 0.25 -9999 0 -0.49 222 222
RAP1A 0.015 0 -9999 0 -10000 0 0
FRS2 0.012 0.047 -9999 0 -0.6 4 4
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.21 0.25 -9999 0 -0.48 220 220
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.14 0.21 -9999 0 -0.4 234 234
RHOA 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.19 0.22 -9999 0 -0.66 81 81
GRB7 -0.038 0.16 -9999 0 -0.59 54 54
RET51/GFRalpha1/GDNF -0.21 0.25 -9999 0 -0.48 220 220
MAPKKK cascade -0.16 0.2 -9999 0 -0.61 80 80
BCAR1 0.014 0.025 -9999 0 -0.62 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.21 -9999 0 -0.4 231 231
lamellipodium assembly -0.12 0.14 -9999 0 -0.42 83 83
RET51/GFRalpha1/GDNF/SHC -0.21 0.26 -9999 0 -0.5 221 221
PIK3CA 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.14 0.21 -9999 0 -0.41 234 234
RET9/GFRalpha1/GDNF/Shank3 -0.14 0.21 -9999 0 -0.4 238 238
MAPK3 -0.15 0.23 -9999 0 -0.62 81 81
DOK1 0.014 0.025 -9999 0 -0.62 1 1
DOK6 -0.11 0.25 -9999 0 -0.62 134 134
PXN 0.015 0 -9999 0 -10000 0 0
neurite development -0.15 0.24 -9999 0 -0.57 114 114
DOK5 0.004 0.085 -9999 0 -0.62 12 12
GFRA1 -0.16 0.28 -9999 0 -0.61 186 186
MAPK8 -0.11 0.21 -9999 0 -0.54 86 86
HRAS/GTP -0.18 0.23 -9999 0 -0.69 78 78
tube development -0.13 0.19 -9999 0 -0.4 172 172
MAPK1 -0.15 0.23 -9999 0 -0.62 81 81
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.075 0.17 -9999 0 -0.33 171 171
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.035 -9999 0 -0.62 2 2
PDLIM7 0.003 0.083 -9999 0 -0.59 13 13
RET51/GFRalpha1/GDNF/Dok6 -0.26 0.31 -9999 0 -0.79 134 134
SHC1 0.001 0.092 -9999 0 -0.59 16 16
RET51/GFRalpha1/GDNF/Dok4 -0.21 0.25 -9999 0 -0.48 223 223
RET51/GFRalpha1/GDNF/Dok5 -0.21 0.25 -9999 0 -0.48 228 228
PRKCA 0.013 0.035 -9999 0 -0.62 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.21 -9999 0 -0.45 146 146
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.078 0.18 -9999 0 -0.39 97 97
RET51/GFRalpha1/GDNF/Grb7 -0.23 0.27 -9999 0 -0.49 267 267
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.13 0.26 -9999 0 -0.61 151 151
DOK4 0.009 0.065 -9999 0 -0.62 7 7
JNK cascade -0.1 0.2 -9999 0 -0.52 80 80
RET9/GFRalpha1/GDNF/FRS2 -0.14 0.2 -9999 0 -0.39 233 233
SHANK3 0.002 0.089 -9999 0 -0.6 14 14
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.078 0.17 -9999 0 -0.34 172 172
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.13 0.22 -9999 0 -0.6 80 80
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.13 0.22 -9999 0 -0.59 78 78
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.14 0.25 -9999 0 -0.68 83 83
PI3K -0.14 0.27 -9999 0 -0.7 84 84
SOS1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.13 0.19 -9999 0 -0.4 172 172
GRB10 0.006 0.075 -9999 0 -0.6 10 10
activation of MAPKK activity -0.12 0.22 -9999 0 -0.51 110 110
RET51/GFRalpha1/GDNF/FRS2 -0.21 0.25 -9999 0 -0.48 220 220
GAB1 0.014 0.025 -9999 0 -0.62 1 1
IRS1 0.009 0.065 -9999 0 -0.62 7 7
IRS2 0.014 0.023 -9999 0 -0.59 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.25 -9999 0 -0.68 83 83
RET51/GFRalpha1/GDNF/PKC alpha -0.21 0.25 -9999 0 -0.48 220 220
GRB2 0.014 0.023 -9999 0 -0.59 1 1
PRKACA 0.015 0 -9999 0 -10000 0 0
GDNF -0.062 0.2 -9999 0 -0.62 79 79
RAC1 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.21 0.25 -9999 0 -0.48 223 223
Rac1/GTP -0.14 0.18 -9999 0 -0.52 83 83
RET9/GFRalpha1/GDNF -0.15 0.22 -9999 0 -0.44 231 231
GFRalpha1/GDNF -0.17 0.25 -9999 0 -0.5 231 231
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.014 0.1 -10000 0 -0.6 14 14
NFATC2 -0.096 0.28 -10000 0 -0.71 79 79
NFATC3 -0.029 0.11 -10000 0 -0.31 9 9
CD40LG -0.34 0.47 -10000 0 -1 164 164
ITCH -0.02 0.12 -10000 0 -10000 0 0
CBLB -0.021 0.12 -10000 0 -0.51 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.39 0.44 -10000 0 -0.95 201 201
JUNB -0.029 0.16 -10000 0 -0.6 48 48
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.078 0.12 -10000 0 -10000 0 0
T cell anergy -0.076 0.19 -10000 0 -0.42 112 112
TLE4 -0.048 0.23 -10000 0 -0.7 43 43
Jun/NFAT1-c-4/p21SNFT -0.3 0.41 -10000 0 -0.97 146 146
AP-1/NFAT1-c-4 -0.42 0.55 -10000 0 -1.2 165 165
IKZF1 -0.058 0.25 -10000 0 -0.75 54 54
T-helper 2 cell differentiation -0.16 0.28 -10000 0 -0.71 87 87
AP-1/NFAT1 -0.15 0.23 -10000 0 -0.56 124 124
CALM1 -0.018 0.079 -10000 0 -10000 0 0
EGR2 -0.22 0.52 -10000 0 -1.2 110 110
EGR3 -0.22 0.52 -10000 0 -1.2 126 126
NFAT1/FOXP3 -0.097 0.23 -10000 0 -0.63 75 75
EGR1 -0.086 0.23 -10000 0 -0.61 105 105
JUN -0.007 0.071 -10000 0 -0.61 8 8
EGR4 -0.17 0.28 -10000 0 -0.61 192 192
mol:Ca2+ -0.037 0.086 -10000 0 -10000 0 0
GBP3 -0.14 0.35 -10000 0 -0.74 146 146
FOSL1 -0.14 0.27 -10000 0 -0.6 163 163
NFAT1-c-4/MAF/IRF4 -0.25 0.4 -10000 0 -0.94 137 137
DGKA -0.042 0.21 -10000 0 -0.59 54 54
CREM 0.013 0.033 -10000 0 -0.59 2 2
NFAT1-c-4/PPARG -0.26 0.42 -10000 0 -0.96 141 141
CTLA4 -0.099 0.28 -10000 0 -0.7 98 98
NFAT1-c-4 (dimer)/EGR1 -0.3 0.48 -10000 0 -1.1 154 154
NFAT1-c-4 (dimer)/EGR4 -0.34 0.44 -10000 0 -1 167 167
FOS -0.09 0.22 -10000 0 -0.62 95 95
IFNG -0.14 0.22 -10000 0 -0.73 47 47
T cell activation -0.13 0.26 -10000 0 -0.76 50 50
MAF 0.012 0.043 -10000 0 -0.62 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.38 0.82 120 -10000 0 120
TNF -0.38 0.49 -10000 0 -1 204 204
FASLG -0.26 0.51 -10000 0 -1.1 131 131
TBX21 -0.044 0.18 -10000 0 -0.6 66 66
BATF3 -0.054 0.19 -10000 0 -0.6 76 76
PRKCQ -0.021 0.15 -10000 0 -0.62 39 39
PTPN1 -0.042 0.21 -10000 0 -0.65 40 40
NFAT1-c-4/ICER1 -0.25 0.4 -10000 0 -0.94 136 136
GATA3 -0.11 0.25 -10000 0 -0.6 138 138
T-helper 1 cell differentiation -0.13 0.23 -10000 0 -0.71 48 48
IL2RA -0.37 0.4 -10000 0 -0.87 207 207
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.043 0.21 -10000 0 -0.6 53 53
E2F1 -0.01 0.13 -10000 0 -0.62 29 29
PPARG -0.015 0.13 -10000 0 -0.61 32 32
SLC3A2 -0.042 0.21 -10000 0 -0.62 45 45
IRF4 -0.037 0.17 -10000 0 -0.6 56 56
PTGS2 -0.37 0.51 -10000 0 -1.1 184 184
CSF2 -0.33 0.45 -10000 0 -1 154 154
JunB/Fra1/NFAT1-c-4 -0.32 0.44 -10000 0 -0.98 157 157
IL4 -0.16 0.29 -10000 0 -0.75 86 86
IL5 -0.33 0.45 -10000 0 -1 151 151
IL2 -0.14 0.27 -10000 0 -0.79 46 46
IL3 -0.07 0.11 -10000 0 -0.88 9 9
RNF128 -0.14 0.3 -10000 0 -0.6 197 197
NFATC1 -0.16 0.39 -10000 0 -0.82 120 120
CDK4 0.077 0.26 0.64 28 -0.62 12 40
PTPRK -0.042 0.21 -10000 0 -0.59 55 55
IL8 -0.43 0.51 -10000 0 -1 214 214
POU2F1 0.007 0.074 -10000 0 -0.62 9 9
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.079 0.16 -9999 0 -0.38 139 139
E-cadherin/beta catenin -0.09 0.18 -9999 0 -0.44 136 136
CTNNB1 0.015 0 -9999 0 -10000 0 0
JUP 0.008 0.069 -9999 0 -0.62 8 8
CDH1 -0.11 0.25 -9999 0 -0.61 136 136
Osteopontin-mediated 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
IKK alpha homodimer -0.094 0.22 -9999 0 -0.6 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.18 -9999 0 -0.58 57 57
alphaV/beta3 Integrin/Osteopontin/Src -0.1 0.18 -9999 0 -0.44 156 156
AP1 -0.12 0.26 -9999 0 -0.62 100 100
ILK -0.1 0.23 -9999 0 -0.65 51 51
bone resorption -0.11 0.26 -9999 0 -0.61 107 107
PTK2B -0.006 0.11 -9999 0 -0.59 23 23
PYK2/p130Cas -0.14 0.2 -9999 0 -0.62 67 67
ITGAV 0.016 0.025 -9999 0 -0.61 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.061 0.16 -9999 0 -0.46 90 90
alphaV/beta3 Integrin/Osteopontin -0.15 0.23 -9999 0 -0.47 189 189
MAP3K1 -0.11 0.23 -9999 0 -0.5 113 113
JUN 0.008 0.067 -9999 0 -0.6 8 8
MAPK3 -0.1 0.24 -9999 0 -0.53 112 112
MAPK1 -0.1 0.24 -9999 0 -0.53 112 112
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 -0.095 0.23 -9999 0 -0.58 74 74
ITGB3 -0.098 0.24 -9999 0 -0.6 125 125
NFKBIA -0.093 0.24 -9999 0 -0.53 112 112
FOS -0.074 0.22 -9999 0 -0.61 95 95
CD44 -0.055 0.2 -9999 0 -0.61 75 75
CHUK 0.015 0 -9999 0 -10000 0 0
PLAU -0.17 0.37 -9999 0 -0.85 128 128
NF kappa B1 p50/RelA -0.13 0.19 -9999 0 -0.61 57 57
BCAR1 0.014 0.025 -9999 0 -0.62 1 1
RELA 0.015 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.083 0.17 -9999 0 -0.44 126 126
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.11 0.25 -9999 0 -0.52 124 124
VAV3 -0.21 0.3 -9999 0 -0.69 139 139
MAP3K14 -0.11 0.24 -9999 0 -0.53 112 112
ROCK2 -0.001 0.1 -9999 0 -0.62 17 17
SPP1 -0.13 0.26 -9999 0 -0.6 155 155
RAC1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.22 0.25 -9999 0 -0.64 133 133
MMP2 -0.11 0.25 -9999 0 -0.59 85 85
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0.04 -9999 0 -0.59 3 3
ITGB7 -0.027 0.16 -9999 0 -0.61 45 45
ITGA4 -0.07 0.21 -9999 0 -0.6 92 92
alpha4/beta7 Integrin -0.089 0.18 -9999 0 -0.46 131 131
alpha4/beta1 Integrin -0.062 0.16 -9999 0 -0.45 92 92
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.11 0.55 -9999 0 -1.1 95 95
HDAC7 0.017 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.21 0.38 -9999 0 -0.94 105 105
SMAD4 0.017 0.002 -9999 0 -10000 0 0
ID2 -0.11 0.55 -9999 0 -1.1 97 97
AP1 -0.056 0.17 -9999 0 -0.46 97 97
ABCG2 -0.11 0.56 -9999 0 -1.1 98 98
HIF1A 0.01 0.1 -9999 0 -0.63 2 2
TFF3 -0.16 0.57 -9999 0 -1.1 112 112
GATA2 -0.002 0.11 -9999 0 -0.61 20 20
AKT1 0.007 0.11 -9999 0 -0.39 1 1
response to hypoxia -0.01 0.12 -9999 0 -0.25 15 15
MCL1 -0.11 0.55 -9999 0 -1.1 97 97
NDRG1 -0.11 0.56 -9999 0 -1.2 99 99
SERPINE1 -0.21 0.62 -9999 0 -1.2 133 133
FECH -0.11 0.55 -9999 0 -1.2 88 88
FURIN -0.11 0.55 -9999 0 -1.1 97 97
NCOA2 -0.018 0.14 -9999 0 -0.63 36 36
EP300 0.023 0.18 -9999 0 -0.34 43 43
HMOX1 -0.13 0.58 -9999 0 -1.2 96 96
BHLHE40 -0.11 0.56 -9999 0 -1.1 97 97
BHLHE41 -0.11 0.56 -9999 0 -1.2 92 92
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.019 0.057 -9999 0 -0.41 5 5
ENG 0.082 0.14 -9999 0 -0.66 5 5
JUN 0.008 0.067 -9999 0 -0.6 8 8
RORA -0.11 0.55 -9999 0 -1.1 95 95
ABCB1 -0.066 0.18 -9999 0 -1.4 10 10
TFRC -0.11 0.56 -9999 0 -1.1 98 98
CXCR4 -0.12 0.57 -9999 0 -1.2 95 95
TF -0.15 0.59 -9999 0 -1.2 115 115
CITED2 -0.11 0.55 -9999 0 -1.2 90 90
HIF1A/ARNT -0.28 0.54 -9999 0 -1.3 110 110
LDHA -0.06 0.15 -9999 0 -0.6 41 41
ETS1 -0.11 0.55 -9999 0 -1.2 88 88
PGK1 -0.11 0.56 -9999 0 -1.2 89 89
NOS2 -0.14 0.58 -9999 0 -1.2 106 106
ITGB2 -0.12 0.57 -9999 0 -1.2 99 99
ALDOA -0.11 0.55 -9999 0 -1.1 99 99
Cbp/p300/CITED2 -0.19 0.55 -9999 0 -1.2 97 97
FOS -0.073 0.22 -9999 0 -0.61 95 95
HK2 -0.12 0.56 -9999 0 -1.1 101 101
SP1 0.026 0.007 -9999 0 -10000 0 0
GCK -0.084 0.47 -9999 0 -1.1 86 86
HK1 -0.11 0.55 -9999 0 -1.1 97 97
NPM1 -0.11 0.55 -9999 0 -1.2 90 90
EGLN1 -0.11 0.55 -9999 0 -1.2 88 88
CREB1 0.023 0.006 -9999 0 -10000 0 0
PGM1 -0.11 0.55 -9999 0 -1.2 88 88
SMAD3 0.017 0.002 -9999 0 -10000 0 0
EDN1 -0.032 0.3 -9999 0 -0.91 35 35
IGFBP1 -0.16 0.58 -9999 0 -1.1 113 113
VEGFA -0.099 0.51 -9999 0 -0.98 113 113
HIF1A/JAB1 -0.014 0.036 -9999 0 -0.46 2 2
CP -0.2 0.6 -9999 0 -1.2 121 121
CXCL12 -0.11 0.56 -9999 0 -1.2 96 96
COPS5 0.016 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.11 0.55 -9999 0 -1.1 97 97
EGLN3 -0.11 0.56 -9999 0 -1.1 100 100
CA9 -0.19 0.62 -9999 0 -1.2 135 135
TERT -0.18 0.56 -9999 0 -1.2 105 105
ENO1 -0.11 0.55 -9999 0 -1.2 90 90
PFKL -0.11 0.55 -9999 0 -1.2 86 86
NCOA1 0.016 0.002 -9999 0 -10000 0 0
ADM -0.18 0.62 -9999 0 -1.2 128 128
ARNT 0 0.088 -9999 0 -10000 0 0
HNF4A -0.04 0.15 -9999 0 -0.59 42 42
ADFP -0.16 0.52 -9999 0 -1.1 103 103
SLC2A1 -0.057 0.45 -9999 0 -0.87 87 87
LEP -0.15 0.55 -9999 0 -1.2 98 98
HIF1A/ARNT/Cbp/p300 -0.23 0.39 -9999 0 -0.97 108 108
EPO -0.031 0.41 -9999 0 -0.95 45 45
CREBBP 0.024 0.18 -9999 0 -0.34 41 41
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.41 -9999 0 -1 109 109
PFKFB3 -0.11 0.55 -9999 0 -1.1 98 98
NT5E -0.11 0.56 -9999 0 -1.2 92 92
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.007 0.059 -10000 0 -0.46 10 10
fibroblast growth factor receptor signaling pathway -0.007 0.059 -10000 0 -0.46 10 10
LAMA1 -0.071 0.22 -10000 0 -0.62 91 91
PRNP 0.014 0.025 -10000 0 -0.62 1 1
GPC1/SLIT2 -0.11 0.19 -10000 0 -0.44 163 163
SMAD2 0.034 0.047 -10000 0 -0.31 12 12
GPC1/PrPc/Cu2+ -0.005 0.047 -10000 0 -0.41 8 8
GPC1/Laminin alpha1 -0.066 0.16 -10000 0 -0.46 95 95
TDGF1 -0.087 0.23 -10000 0 -0.61 108 108
CRIPTO/GPC1 -0.076 0.18 -10000 0 -0.46 110 110
APP/GPC1 -0.005 0.046 -10000 0 -0.43 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.038 0.16 -10000 0 -0.39 112 112
FLT1 0.014 0.025 -10000 0 -0.62 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.047 -10000 0 -0.36 12 12
SERPINC1 -0.004 0.1 -10000 0 -0.59 19 19
FYN -0.037 0.16 -10000 0 -0.39 110 110
FGR -0.04 0.16 -10000 0 -0.39 116 116
positive regulation of MAPKKK cascade -0.065 0.19 -10000 0 -0.46 94 94
SLIT2 -0.13 0.26 -10000 0 -0.6 157 157
GPC1/NRG -0.12 0.2 -10000 0 -0.44 188 188
NRG1 -0.15 0.28 -10000 0 -0.61 181 181
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.067 0.14 -10000 0 -0.36 122 122
LYN -0.039 0.16 -10000 0 -0.39 114 114
mol:Spermine 0.008 0.049 -10000 0 -0.44 8 8
cell growth -0.007 0.059 -10000 0 -0.46 10 10
BMP signaling pathway -0.008 0.066 0.59 8 -10000 0 8
SRC -0.038 0.16 -10000 0 -0.39 112 112
TGFBR1 0.014 0.025 -10000 0 -0.62 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.22 0.3 -10000 0 -0.61 250 250
GPC1 0.008 0.066 -10000 0 -0.59 8 8
TGFBR1 (dimer) 0.014 0.025 -10000 0 -0.62 1 1
VEGFA -0.091 0.23 -10000 0 -0.59 118 118
BLK -0.09 0.2 -10000 0 -0.4 188 188
HCK -0.046 0.17 -10000 0 -0.4 121 121
FGF2 0.013 0.034 -10000 0 -0.61 2 2
FGFR1 0.012 0.041 -10000 0 -0.6 3 3
VEGFR1 homodimer 0.014 0.025 -10000 0 -0.62 1 1
TGFBR2 0.012 0.04 -10000 0 -0.59 3 3
cell death -0.005 0.046 -10000 0 -0.42 8 8
ATIII/GPC1 -0.017 0.083 -10000 0 -0.42 27 27
PLA2G2A/GPC1 -0.17 0.22 -10000 0 -0.44 254 254
LCK -0.11 0.22 -10000 0 -0.41 213 213
neuron differentiation -0.12 0.2 -10000 0 -0.44 188 188
PrPc/Cu2+ -0.001 0.018 -10000 0 -0.46 1 1
APP 0.015 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.012 0.04 -10000 0 -0.59 3 3
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.077 0.18 -9999 0 -0.48 93 93
alphaM/beta2 Integrin/GPIbA -0.062 0.16 -9999 0 -0.52 67 67
alphaM/beta2 Integrin/proMMP-9 -0.21 0.23 -9999 0 -0.43 318 318
PLAUR -0.073 0.21 -9999 0 -0.59 97 97
HMGB1 0 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.053 0.15 -9999 0 -0.54 53 53
AGER -0.018 0.11 -9999 0 -0.64 19 19
RAP1A 0.015 0 -9999 0 -10000 0 0
SELPLG -0.012 0.13 -9999 0 -0.62 29 29
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.18 -9999 0 -0.67 45 45
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.25 0.3 -9999 0 -0.6 285 285
CYR61 -0.096 0.24 -9999 0 -0.61 119 119
TLN1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP -0.1 0.14 -9999 0 -0.42 81 81
RHOA 0.015 0 -9999 0 -10000 0 0
P-selectin oligomer -0.036 0.16 -9999 0 -0.59 52 52
MYH2 -0.1 0.18 -9999 0 -0.47 76 76
MST1R -0.003 0.11 -9999 0 -0.62 19 19
leukocyte activation during inflammatory response -0.1 0.18 -9999 0 -0.46 93 93
APOB -0.078 0.22 -9999 0 -0.6 99 99
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.025 0.15 -9999 0 -0.6 44 44
JAM3 0.014 0.023 -9999 0 -0.59 1 1
GP1BA 0.001 0.094 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/CTGF -0.072 0.18 -9999 0 -0.51 82 82
alphaM/beta2 Integrin -0.1 0.18 -9999 0 -0.47 87 87
JAM3 homodimer 0.014 0.023 -9999 0 -0.59 1 1
ICAM2 0.014 0.023 -9999 0 -0.59 1 1
ICAM1 -0.05 0.19 -9999 0 -0.6 72 72
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.18 -9999 0 -0.47 87 87
cell adhesion -0.061 0.16 -9999 0 -0.52 67 67
NFKB1 -0.14 0.27 -9999 0 -0.71 76 76
THY1 0.003 0.088 -9999 0 -0.62 13 13
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.072 0.15 -9999 0 -0.38 127 127
alphaM/beta2 Integrin/LRP/tPA -0.11 0.19 -9999 0 -0.45 101 101
IL6 -0.22 0.36 -9999 0 -0.86 115 115
ITGB2 -0.035 0.14 -9999 0 -0.64 36 36
elevation of cytosolic calcium ion concentration -0.17 0.26 -9999 0 -0.57 156 156
alphaM/beta2 Integrin/JAM2/JAM3 -0.042 0.14 -9999 0 -0.49 53 53
JAM2 0.014 0.025 -9999 0 -0.62 1 1
alphaM/beta2 Integrin/ICAM1 -0.1 0.2 -9999 0 -0.55 72 72
alphaM/beta2 Integrin/uPA/Plg -0.13 0.2 -9999 0 -0.45 149 149
RhoA/GTP -0.1 0.18 -9999 0 -0.5 74 74
positive regulation of phagocytosis -0.1 0.18 -9999 0 -0.56 65 65
Ron/MSP -0.041 0.13 -9999 0 -0.46 60 60
alphaM/beta2 Integrin/uPAR/uPA -0.17 0.26 -9999 0 -0.57 156 156
alphaM/beta2 Integrin/uPAR -0.11 0.2 -9999 0 -0.47 140 140
PLAU -0.13 0.26 -9999 0 -0.6 156 156
PLAT -0.11 0.24 -9999 0 -0.59 136 136
actin filament polymerization -0.096 0.17 -9999 0 -0.45 76 76
MST1 -0.025 0.15 -9999 0 -0.61 43 43
alphaM/beta2 Integrin/lipoprotein(a) -0.1 0.19 -9999 0 -0.47 93 93
TNF -0.2 0.35 -9999 0 -0.69 179 179
RAP1B 0.009 0.061 -9999 0 -0.59 7 7
alphaM/beta2 Integrin/uPA -0.14 0.22 -9999 0 -0.45 195 195
fibrinolysis -0.13 0.2 -9999 0 -0.44 150 150
HCK 0 0.096 -9999 0 -0.61 16 16
dendritic cell antigen processing and presentation -0.1 0.18 -9999 0 -0.47 87 87
VTN -0.017 0.14 -9999 0 -0.62 34 34
alphaM/beta2 Integrin/CYR61 -0.12 0.22 -9999 0 -0.49 153 153
LPA -0.016 0.12 -9999 0 -0.59 29 29
LRP1 0.013 0.035 -9999 0 -0.62 2 2
cell migration -0.2 0.24 -9999 0 -0.48 195 195
FN1 -0.028 0.16 -9999 0 -0.59 48 48
alphaM/beta2 Integrin/Thy1 -0.06 0.16 -9999 0 -0.52 66 66
MPO -0.11 0.25 -9999 0 -0.61 136 136
KNG1 -0.018 0.11 -9999 0 -0.59 25 25
RAP1/GDP -0.004 0.037 -9999 0 -0.36 7 7
ROCK1 -0.089 0.18 -9999 0 -0.47 69 69
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.046 -9999 0 -0.59 4 4
CTGF -0.016 0.14 -9999 0 -0.61 34 34
alphaM/beta2 Integrin/Hck -0.061 0.19 -9999 0 -0.62 55 55
ITGAM -0.034 0.15 -9999 0 -0.65 35 35
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.083 0.21 -9999 0 -0.6 68 68
HP -0.13 0.26 -9999 0 -0.6 153 153
leukocyte adhesion -0.095 0.16 -9999 0 -0.57 52 52
SELP -0.036 0.16 -9999 0 -0.59 52 52
Reelin signaling pathway

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
CDK5R1/CDK5 -0.037 0.12 -9999 0 -0.45 54 54
VLDLR -0.004 0.11 -9999 0 -0.62 20 20
CRKL 0.014 0.023 -9999 0 -0.59 1 1
LRPAP1 0.015 0 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
ITGA3 -0.028 0.16 -9999 0 -0.59 48 48
RELN/VLDLR/Fyn -0.13 0.19 -9999 0 -0.38 221 221
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.049 -9999 0 -10000 0 0
AKT1 -0.086 0.17 -9999 0 -0.48 57 57
MAP2K7 0.014 0.025 -9999 0 -0.62 1 1
RAPGEF1 0.013 0.035 -9999 0 -0.62 2 2
DAB1 -0.093 0.24 -9999 0 -0.62 114 114
RELN/LRP8/DAB1 -0.16 0.21 -9999 0 -0.39 281 281
LRPAP1/LRP8 -0.001 0.025 -9999 0 -0.46 2 2
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.64 46 46
DAB1/alpha3/beta1 Integrin -0.16 0.22 -9999 0 -0.63 83 83
long-term memory -0.31 0.31 -9999 0 -0.72 208 208
DAB1/LIS1 -0.15 0.19 -9999 0 -0.61 58 58
DAB1/CRLK/C3G -0.14 0.19 -9999 0 -0.59 59 59
PIK3CA 0.015 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.15 0.19 -9999 0 -0.61 58 58
ARHGEF2 0.014 0.025 -9999 0 -0.62 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.17 0.28 -9999 0 -0.6 195 195
CDK5R1 -0.035 0.17 -9999 0 -0.62 53 53
RELN -0.18 0.29 -9999 0 -0.61 211 211
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
RELN/LRP8/Fyn -0.12 0.17 -9999 0 -0.37 211 211
GRIN2A/RELN/LRP8/DAB1/Fyn -0.24 0.27 -9999 0 -0.68 140 140
MAPK8 0.007 0.074 -9999 0 -0.62 9 9
RELN/VLDLR/DAB1 -0.17 0.22 -9999 0 -0.4 287 287
ITGB1 0.012 0.04 -9999 0 -0.59 3 3
MAP1B -0.13 0.22 -9999 0 -0.63 58 58
RELN/LRP8 -0.12 0.17 -9999 0 -0.37 211 211
GRIN2B/RELN/LRP8/DAB1/Fyn -0.24 0.25 -9999 0 -0.66 131 131
PI3K -0.002 0.03 -9999 0 -0.46 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.032 0.12 -9999 0 -0.44 49 49
RAP1A -0.092 0.2 -9999 0 -0.55 59 59
PAFAH1B1 0.015 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.06 -9999 0 -0.62 6 6
CRLK/C3G -0.002 0.03 -9999 0 -0.44 3 3
GRIN2B -0.17 0.28 -9999 0 -0.6 200 200
NCK2 0.015 0 -9999 0 -10000 0 0
neuron differentiation -0.048 0.14 -9999 0 -0.42 44 44
neuron adhesion -0.092 0.22 -9999 0 -0.55 84 84
LRP8 0.013 0.035 -9999 0 -0.62 2 2
GSK3B -0.073 0.17 -9999 0 -0.49 44 44
RELN/VLDLR/DAB1/Fyn -0.16 0.21 -9999 0 -0.62 62 62
MAP3K11 0.015 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.1 0.18 -9999 0 -0.34 201 201
CDK5 0.014 0.023 -9999 0 -0.59 1 1
MAPT -0.009 0.14 -9999 0 -0.56 37 37
neuron migration -0.089 0.22 -9999 0 -0.54 75 75
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.049 0.14 -9999 0 -0.42 44 44
RELN/VLDLR -0.11 0.17 -9999 0 -0.37 133 133
Endothelins

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
AKT1 -0.1 0.23 -10000 0 -0.59 64 64
PTK2B -0.005 0.11 -10000 0 -0.59 23 23
mol:Ca2+ -0.042 0.24 -10000 0 -0.75 43 43
EDN1 -0.083 0.19 -10000 0 -0.65 41 41
EDN3 -0.056 0.2 -10000 0 -0.62 75 75
EDN2 -0.029 0.14 -10000 0 -0.59 40 40
HRAS/GDP -0.08 0.2 -10000 0 -0.5 65 65
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.045 0.16 -10000 0 -0.41 53 53
ADCY4 -0.15 0.26 -10000 0 -0.53 169 169
ADCY5 -0.18 0.3 -10000 0 -0.63 167 167
ADCY6 -0.15 0.26 -10000 0 -0.54 153 153
ADCY7 -0.15 0.26 -10000 0 -0.54 156 156
ADCY1 -0.2 0.28 -10000 0 -0.57 191 191
ADCY2 -0.17 0.29 -10000 0 -0.6 166 166
ADCY3 -0.15 0.26 -10000 0 -0.54 153 153
ADCY8 -0.18 0.28 -10000 0 -0.57 176 176
ADCY9 -0.15 0.26 -10000 0 -0.54 154 154
arachidonic acid secretion -0.069 0.21 -10000 0 -0.5 80 80
ETB receptor/Endothelin-1/Gq/GTP -0.031 0.15 -10000 0 -0.47 34 34
GNAO1 -0.012 0.13 -10000 0 -0.62 28 28
HRAS 0.014 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.094 0.22 0.34 36 -0.56 62 98
ETA receptor/Endothelin-1/Gs/GTP -0.17 0.27 0.32 31 -0.56 164 195
mol:GTP 0.001 0.005 -10000 0 -10000 0 0
COL3A1 -0.25 0.37 -10000 0 -0.67 258 258
EDNRB -0.035 0.16 -10000 0 -0.63 45 45
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.12 0.27 -10000 0 -0.74 62 62
CYSLTR1 -0.11 0.26 -10000 0 -0.66 70 70
SLC9A1 -0.067 0.11 0.21 20 -0.32 39 59
mol:GDP -0.095 0.21 -10000 0 -0.51 82 82
SLC9A3 -0.085 0.26 -10000 0 -0.73 62 62
RAF1 -0.089 0.21 -10000 0 -0.51 85 85
JUN -0.025 0.19 -10000 0 -0.65 22 22
JAK2 -0.1 0.23 -10000 0 -0.59 63 63
mol:IP3 -0.048 0.17 -10000 0 -0.48 46 46
ETA receptor/Endothelin-1 -0.14 0.27 0.4 37 -0.67 66 103
PLCB1 -0.03 0.16 -10000 0 -0.62 46 46
PLCB2 0.001 0.091 -10000 0 -0.62 14 14
ETA receptor/Endothelin-3 -0.099 0.2 -10000 0 -0.53 99 99
FOS -0.11 0.31 -10000 0 -0.8 91 91
Gai/GDP -0.022 0.2 -10000 0 -0.9 28 28
CRK 0.015 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.26 -10000 0 -0.57 99 99
BCAR1 0.015 0.025 -10000 0 -0.62 1 1
PRKCB1 -0.046 0.16 -10000 0 -0.45 49 49
GNAQ 0.015 0.007 -10000 0 -10000 0 0
GNAZ 0.012 0.043 -10000 0 -0.62 3 3
GNAL -0.13 0.27 -10000 0 -0.62 149 149
Gs family/GDP -0.18 0.22 -10000 0 -0.51 168 168
ETA receptor/Endothelin-1/Gq/GTP -0.042 0.16 -10000 0 -0.4 51 51
MAPK14 -0.026 0.15 -10000 0 -0.49 33 33
TRPC6 -0.047 0.25 -10000 0 -0.83 40 40
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 -0.02 0.15 -10000 0 -0.62 37 37
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.036 0.16 -10000 0 -0.49 39 39
ETB receptor/Endothelin-2 -0.053 0.16 -10000 0 -0.47 82 82
ETB receptor/Endothelin-3 -0.082 0.19 -10000 0 -0.49 111 111
ETB receptor/Endothelin-1 -0.09 0.19 -10000 0 -0.51 81 81
MAPK3 -0.11 0.29 -10000 0 -0.72 91 91
MAPK1 -0.11 0.29 -10000 0 -0.72 91 91
Rac1/GDP -0.08 0.2 -10000 0 -0.5 62 62
cAMP biosynthetic process -0.17 0.28 -10000 0 -0.58 170 170
MAPK8 -0.038 0.2 -10000 0 -0.6 44 44
SRC 0.013 0.035 -10000 0 -0.63 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.03 0.14 -10000 0 -0.44 43 43
p130Cas/CRK/Src/PYK2 -0.084 0.23 -10000 0 -0.57 66 66
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.08 0.2 -10000 0 -0.5 65 65
COL1A2 -0.16 0.33 -10000 0 -0.74 119 119
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.077 0.16 -10000 0 -0.5 67 67
mol:DAG -0.048 0.17 -10000 0 -0.48 46 46
MAP2K2 -0.092 0.24 -10000 0 -0.58 93 93
MAP2K1 -0.092 0.24 -10000 0 -0.58 93 93
EDNRA -0.069 0.18 0.24 15 -0.52 47 62
positive regulation of muscle contraction -0.078 0.2 -10000 0 -0.55 52 52
Gq family/GDP -0.11 0.18 -10000 0 -0.56 57 57
HRAS/GTP -0.09 0.2 -10000 0 -0.49 78 78
PRKCH -0.038 0.16 -10000 0 -0.5 35 35
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.039 0.16 -10000 0 -0.53 32 32
PRKCB -0.083 0.2 -10000 0 -0.48 73 73
PRKCE -0.044 0.17 -10000 0 -0.53 34 34
PRKCD -0.05 0.19 -10000 0 -0.54 50 50
PRKCG -0.15 0.23 -10000 0 -0.46 176 176
regulation of vascular smooth muscle contraction -0.13 0.36 -10000 0 -0.96 84 84
PRKCQ -0.057 0.19 -10000 0 -0.5 62 62
PLA2G4A -0.077 0.23 -10000 0 -0.55 80 80
GNA14 -0.009 0.12 -10000 0 -0.61 26 26
GNA15 -0.009 0.12 -10000 0 -0.61 26 26
GNA12 0.014 0.025 -10000 0 -0.62 1 1
GNA11 0.005 0.078 -10000 0 -0.63 10 10
Rac1/GTP -0.094 0.22 0.34 36 -0.55 62 98
MMP1 -0.051 0.28 -10000 0 -0.59 119 119
Aurora C 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
INCENP 0.013 0.035 -9999 0 -0.62 2 2
Aurora C/Aurora B/INCENP -0.12 0.17 -9999 0 -0.35 234 234
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.035 0.048 -9999 0 -0.24 1 1
AURKB -0.18 0.29 -9999 0 -0.61 209 209
AURKC -0.015 0.13 -9999 0 -0.6 33 33
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.061 -10000 0 -0.59 7 7
GNB1/GNG2 -0.077 0.08 -10000 0 -0.19 134 134
AKT1 -0.054 0.12 -10000 0 -0.23 53 53
EGF -0.038 0.18 -10000 0 -0.61 57 57
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.084 -10000 0 -0.4 6 6
mol:Ca2+ -0.089 0.16 -10000 0 -0.29 195 195
LYN 0.016 0.085 -10000 0 -0.39 8 8
RhoA/GTP -0.049 0.052 -10000 0 -0.14 12 12
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.1 0.19 -10000 0 -0.35 187 187
GNG2 0.009 0.06 -10000 0 -0.62 6 6
ARRB2 0.015 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.013 0.098 -10000 0 -0.39 30 30
G beta5/gamma2 -0.096 0.1 -10000 0 -0.25 122 122
PRKCH -0.1 0.18 -10000 0 -0.34 175 175
DNM1 -0.083 0.22 -10000 0 -0.6 107 107
TXA2/TP beta/beta Arrestin3 -0.037 0.073 -10000 0 -0.25 26 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.034 0.16 -10000 0 -0.59 52 52
G12 family/GTP -0.12 0.13 -10000 0 -0.3 189 189
ADRBK1 0.015 0 -10000 0 -10000 0 0
ADRBK2 0.011 0.049 -10000 0 -0.62 4 4
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.052 0.11 0.3 44 -10000 0 44
mol:NADP 0.009 0.06 -10000 0 -0.62 6 6
RAB11A 0.015 0 -10000 0 -10000 0 0
PRKG1 -0.032 0.17 -10000 0 -0.62 50 50
mol:IP3 -0.12 0.2 -10000 0 -0.37 195 195
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.16 0.26 -10000 0 -0.5 190 190
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.028 0.12 -10000 0 -0.42 13 13
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.012 0.094 -10000 0 -0.41 11 11
RHOA 0.015 0 -10000 0 -10000 0 0
PTGIR -0.043 0.18 -10000 0 -0.6 63 63
PRKCB1 -0.11 0.19 -10000 0 -0.36 198 198
GNAQ 0.015 0 -10000 0 -10000 0 0
mol:L-citrulline 0.009 0.06 -10000 0 -0.62 6 6
TXA2/TXA2-R family -0.17 0.27 -10000 0 -0.52 203 203
LCK -0.033 0.14 -10000 0 -0.41 38 38
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.032 0.077 -10000 0 -0.49 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.046 -10000 0 -0.79 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.03 0.074 -10000 0 -0.51 2 2
MAPK14 -0.06 0.13 -10000 0 -0.24 116 116
TGM2/GTP -0.13 0.22 -10000 0 -0.42 186 186
MAPK11 -0.061 0.13 -10000 0 -0.24 121 121
ARHGEF1 -0.045 0.1 -10000 0 -0.19 37 37
GNAI2 0.015 0 -10000 0 -10000 0 0
JNK cascade -0.12 0.2 -10000 0 -0.38 203 203
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.092 0.17 -10000 0 -0.3 204 204
cAMP biosynthetic process -0.11 0.19 -10000 0 -0.35 191 191
Gq family/GTP/EBP50 0.014 0.072 -10000 0 -0.26 29 29
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.018 0.08 -10000 0 -0.38 3 3
GNB5 0.015 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
EGF/EGFR -0.017 0.11 -10000 0 -0.34 21 21
VCAM1 -0.11 0.19 -10000 0 -0.37 194 194
TP beta/Gq family/GDP/G beta5/gamma2 0.013 0.098 -10000 0 -0.39 30 30
platelet activation -0.08 0.17 -10000 0 -0.3 185 185
PGI2/IP -0.041 0.13 -10000 0 -0.44 63 63
PRKACA -0.018 0.099 -10000 0 -0.33 26 26
Gq family/GDP/G beta5/gamma2 0.011 0.093 -10000 0 -0.36 30 30
TXA2/TP beta/beta Arrestin2 -0.053 0.13 -10000 0 -0.54 33 33
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.1 -10000 0 -0.39 13 13
mol:DAG -0.13 0.21 -10000 0 -0.41 198 198
EGFR -0.11 0.25 -10000 0 -0.6 138 138
TXA2/TP alpha -0.16 0.25 -10000 0 -0.48 190 190
Gq family/GTP -0.013 0.063 -10000 0 -0.23 40 40
YES1 0.018 0.08 -10000 0 -0.38 3 3
GNAI2/GTP -0.029 0.07 -10000 0 -0.45 3 3
PGD2/DP -0.034 0.12 -10000 0 -0.44 52 52
SLC9A3R1 0.014 0.025 -10000 0 -0.62 1 1
FYN 0.018 0.078 -10000 0 -0.38 3 3
mol:NO 0.009 0.06 -10000 0 -0.62 6 6
GNA15 -0.009 0.12 -10000 0 -0.61 26 26
PGK/cGMP -0.032 0.11 -10000 0 -0.39 55 55
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.034 0.084 -10000 0 -0.47 8 8
NOS3 0.009 0.06 -10000 0 -0.62 6 6
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.1 0.18 -10000 0 -0.34 176 176
PRKCB -0.13 0.2 -10000 0 -0.38 203 203
PRKCE -0.1 0.19 -10000 0 -0.35 176 176
PRKCD -0.12 0.2 -10000 0 -0.38 192 192
PRKCG -0.16 0.23 -10000 0 -0.43 234 234
muscle contraction -0.16 0.25 -10000 0 -0.48 206 206
PRKCZ -0.12 0.2 -10000 0 -0.36 205 205
ARR3 0.003 0.024 -10000 0 -0.59 1 1
TXA2/TP beta -0.033 0.079 -10000 0 -0.38 10 10
PRKCQ -0.11 0.19 -10000 0 -0.35 199 199
MAPKKK cascade -0.14 0.23 -10000 0 -0.45 191 191
SELE -0.11 0.18 -10000 0 -0.34 210 210
TP beta/GNAI2/GDP/G beta/gamma -0.031 0.076 -10000 0 -0.48 4 4
ROCK1 0.015 0 -10000 0 -10000 0 0
GNA14 -0.009 0.12 -10000 0 -0.61 26 26
chemotaxis -0.2 0.3 -10000 0 -0.6 200 200
GNA12 0.014 0.025 -10000 0 -0.62 1 1
GNA13 0.015 0 -10000 0 -10000 0 0
GNA11 0.006 0.078 -10000 0 -0.62 10 10
Rac1/GTP 0.004 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.049 0.16 0.21 2 -0.35 120 122
ACTA1 -0.072 0.2 0.26 3 -0.44 126 129
NUMA1 -0.052 0.17 0.21 2 -0.36 125 127
SPTAN1 -0.064 0.2 0.26 4 -0.43 120 124
LIMK1 -0.064 0.2 0.26 2 -0.43 119 121
BIRC3 -0.059 0.2 -10000 0 -0.6 81 81
BIRC2 0.015 0 -10000 0 -10000 0 0
BAX 0.015 0 -10000 0 -10000 0 0
CASP10 -0.1 0.23 -10000 0 -0.44 192 192
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.015 0 -10000 0 -10000 0 0
PTK2 -0.049 0.16 -10000 0 -0.35 120 120
DIABLO 0.015 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.062 0.2 0.26 5 -0.42 120 125
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
GSN -0.068 0.2 0.26 2 -0.43 121 123
MADD 0.012 0.043 -10000 0 -0.62 3 3
TFAP2A -0.17 0.29 -10000 0 -0.64 162 162
BID -0.044 0.12 -10000 0 -0.25 125 125
MAP3K1 -0.015 0.076 -10000 0 -0.23 8 8
TRADD 0.014 0.025 -10000 0 -0.62 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.002 0.018 -10000 0 -0.42 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.065 0.2 0.26 1 -0.44 119 120
CASP9 0.015 0.023 -10000 0 -0.59 1 1
DNA repair 0 0.069 0.21 1 -0.18 41 42
neuron apoptosis 0.01 0.044 -10000 0 -0.3 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.057 0.2 -10000 0 -0.41 121 121
APAF1 0.015 0 -10000 0 -10000 0 0
CASP6 -0.027 0.12 -10000 0 -0.54 10 10
TRAF2 0.015 0 -10000 0 -10000 0 0
ICAD/CAD -0.052 0.19 -10000 0 -0.42 110 110
CASP7 0.028 0.093 0.27 80 -0.23 3 83
KRT18 -0.081 0.21 -10000 0 -0.58 90 90
apoptosis -0.078 0.19 -10000 0 -0.41 111 111
DFFA -0.063 0.2 -10000 0 -0.43 118 118
DFFB -0.063 0.2 0.26 1 -0.43 118 119
PARP1 0 0.069 0.19 29 -0.22 1 30
actin filament polymerization 0.05 0.19 0.4 116 -10000 0 116
TNF -0.13 0.26 -10000 0 -0.6 152 152
CYCS -0.029 0.089 -10000 0 -0.24 46 46
SATB1 -0.029 0.13 -10000 0 -0.49 20 20
SLK -0.064 0.2 0.26 3 -0.43 119 122
p15 BID/BAX -0.032 0.11 -10000 0 -0.29 48 48
CASP2 -0.009 0.11 -10000 0 -0.42 13 13
JNK cascade 0.014 0.075 0.23 8 -10000 0 8
CASP3 -0.076 0.21 0.27 5 -0.46 119 124
LMNB2 -0.006 0.094 -10000 0 -0.42 10 10
RIPK1 0.015 0 -10000 0 -10000 0 0
CASP4 -0.053 0.19 -10000 0 -0.59 75 75
Mammalian IAPs/DIABLO -0.039 0.1 -10000 0 -0.32 81 81
negative regulation of DNA binding -0.17 0.29 -10000 0 -0.63 162 162
stress fiber formation -0.063 0.2 0.26 4 -0.42 119 123
GZMB -0.13 0.26 -10000 0 -0.52 192 192
CASP1 -0.027 0.13 -10000 0 -0.33 92 92
LMNB1 -0.014 0.1 -10000 0 -0.42 15 15
APP 0.01 0.045 -10000 0 -0.31 5 5
TNFRSF1A 0.002 0.09 -10000 0 -0.61 14 14
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.06 -10000 0 -0.44 12 12
VIM -0.084 0.19 0.25 1 -0.4 115 116
LMNA -0.007 0.095 -10000 0 -0.42 10 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.019 0.12 -10000 0 -0.41 19 19
LRDD 0.011 0.049 -10000 0 -0.62 4 4
SREBF1 -0.069 0.2 -10000 0 -0.43 124 124
APAF-1/Caspase 9 -0.004 0.047 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.051 0.17 0.21 2 -0.35 125 127
CFL2 -0.052 0.19 -10000 0 -0.41 116 116
GAS2 -0.082 0.21 0.26 3 -0.44 138 141
positive regulation of apoptosis -0.006 0.097 -10000 0 -0.43 10 10
PRF1 -0.093 0.24 -10000 0 -0.6 118 118
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.054 0.11 0.22 191 -10000 0 191
BUB1B -0.072 0.16 -10000 0 -0.33 174 174
PLK1 -0.006 0.054 -10000 0 -0.16 50 50
PLK1S1 0.004 0.027 -10000 0 -0.13 2 2
KIF2A 0.005 0.05 -10000 0 -0.29 2 2
regulation of mitotic centrosome separation -0.005 0.054 -10000 0 -0.16 50 50
GOLGA2 0.014 0.025 -10000 0 -0.62 1 1
Hec1/SPC24 -0.18 0.28 -10000 0 -0.48 280 280
WEE1 -0.018 0.1 -10000 0 -0.37 34 34
cytokinesis -0.14 0.23 -10000 0 -0.42 242 242
PP2A-alpha B56 -0.08 0.24 -10000 0 -0.67 86 86
AURKA -0.005 0.055 -10000 0 -0.17 55 55
PICH/PLK1 -0.068 0.21 -10000 0 -0.48 118 118
CENPE -0.053 0.16 -10000 0 -0.39 112 112
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.005 0.05 -10000 0 -0.28 2 2
PPP2CA 0.015 0 -10000 0 -10000 0 0
FZR1 0.015 0 -10000 0 -10000 0 0
TPX2 -0.025 0.091 -10000 0 -0.23 98 98
PAK1 -0.019 0.14 -10000 0 -0.59 37 37
SPC24 -0.17 0.28 -10000 0 -0.6 202 202
FBXW11 0.015 0 -10000 0 -10000 0 0
CLSPN -0.046 0.11 -10000 0 -0.24 149 149
GORASP1 0.015 0 -10000 0 -10000 0 0
metaphase 0 0.005 -10000 0 -0.016 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.002 0.027 -10000 0 -0.076 50 50
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.011 22 22
STAG2 0.015 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.017 -10000 0 -10000 0 0
spindle elongation -0.005 0.054 -10000 0 -0.16 50 50
ODF2 0.014 0.004 -10000 0 -10000 0 0
BUB1 -0.12 0.25 -10000 0 -0.74 86 86
TPT1 0.004 0.029 -10000 0 -0.14 4 4
CDC25C -0.072 0.15 -10000 0 -0.28 201 201
CDC25B 0.012 0.024 -10000 0 -0.58 1 1
SGOL1 -0.054 0.11 -10000 0 -0.22 191 191
RHOA 0.015 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.057 0.13 -10000 0 -0.36 86 86
CDC14B 0.013 0.004 -10000 0 -10000 0 0
CDC20 -0.17 0.28 -10000 0 -0.6 203 203
PLK1/PBIP1 -0.069 0.14 -10000 0 -0.38 114 114
mitosis 0.001 0.007 0.027 18 -0.034 1 19
FBXO5 0 0.052 -10000 0 -0.2 14 14
CDC2 -0.002 0.006 -10000 0 -0.015 98 98
NDC80 -0.17 0.28 -10000 0 -0.61 199 199
metaphase plate congression 0.003 0.033 -10000 0 -10000 0 0
ERCC6L -0.093 0.19 -10000 0 -0.48 106 106
NLP/gamma Tubulin 0.001 0.03 -10000 0 -0.13 3 3
microtubule cytoskeleton organization 0.004 0.029 -10000 0 -0.14 4 4
G2/M transition DNA damage checkpoint 0 0.002 0.01 6 -0.011 1 7
PPP1R12A 0.015 0.001 -10000 0 -10000 0 0
interphase 0 0.002 0.01 6 -0.011 1 7
PLK1/PRC1-2 -0.13 0.22 -10000 0 -0.39 263 263
GRASP65/GM130/RAB1/GTP/PLK1 -0.008 0.032 -10000 0 -0.33 1 1
RAB1A 0.015 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.048 -10000 0 -0.44 1 1
mitotic prometaphase -0.001 0.003 -10000 0 -0.012 14 14
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.071 -10000 0 -10000 0 0
microtubule-based process -0.13 0.2 -10000 0 -0.38 263 263
Golgi organization -0.005 0.054 -10000 0 -0.16 50 50
Cohesin/SA2 -0.016 0.038 -10000 0 -0.2 3 3
PPP1CB/MYPT1 0 0.024 -10000 0 -0.42 2 2
KIF20A -0.23 0.3 -10000 0 -0.61 263 263
APC/C/CDC20 -0.1 0.19 -10000 0 -0.38 203 203
PPP2R1A 0.015 0 -10000 0 -10000 0 0
chromosome segregation -0.068 0.14 -10000 0 -0.37 114 114
PRC1 -0.012 0.12 -10000 0 -0.59 30 30
ECT2 -0.007 0.094 -10000 0 -0.43 25 25
C13orf34 0.003 0.048 -10000 0 -0.44 1 1
NUDC 0.003 0.033 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.071 0.16 -10000 0 -0.32 174 174
spindle assembly -0.001 0.043 -10000 0 -0.12 44 44
spindle stabilization 0.004 0.027 -10000 0 -0.13 2 2
APC/C/HCDH1 0.021 0.002 -10000 0 -10000 0 0
MKLP2/PLK1 -0.13 0.2 -10000 0 -0.38 263 263
CCNB1 -0.068 0.21 -10000 0 -0.59 92 92
PPP1CB 0.013 0.033 -10000 0 -0.59 2 2
BTRC 0.015 0 -10000 0 -10000 0 0
ROCK2 -0.001 0.08 -10000 0 -0.44 17 17
TUBG1 0.004 0.027 -10000 0 -0.14 1 1
G2/M transition of mitotic cell cycle -0.058 0.12 -10000 0 -0.35 86 86
MLF1IP -0.066 0.18 -10000 0 -0.46 114 114
INCENP 0.011 0.036 -10000 0 -0.63 2 2
TCGA08_p53

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
CDKN2A -0.12 0.21 -10000 0 -0.45 186 186
TP53 -0.037 0.093 0.23 4 -0.44 13 17
Senescence -0.037 0.092 0.23 4 -0.44 13 17
Apoptosis -0.037 0.092 0.23 4 -0.44 13 17
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.062 0.13 0.26 173 -0.32 13 186
MDM4 0 0.095 -10000 0 -0.59 17 17
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.38 -9999 0 -1.1 84 84
MKNK1 0.011 0.049 -9999 0 -0.62 4 4
MAPK14 -0.044 0.13 -9999 0 -0.35 24 24
ATF2/c-Jun -0.021 0.13 -9999 0 -0.64 13 13
MAPK11 -0.046 0.13 -9999 0 -0.38 26 26
MITF -0.041 0.16 -9999 0 -0.42 26 26
MAPKAPK5 -0.039 0.15 -9999 0 -0.34 108 108
KRT8 -0.11 0.22 -9999 0 -0.43 165 165
MAPKAPK3 0.013 0.035 -9999 0 -0.62 2 2
MAPKAPK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.065 0.19 -9999 0 -0.43 109 109
CEBPB -0.051 0.18 -9999 0 -0.38 118 118
SLC9A1 -0.04 0.16 -9999 0 -0.35 108 108
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.041 0.17 -9999 0 -0.43 36 36
p38alpha-beta/MNK1 -0.039 0.16 -9999 0 -0.45 27 27
JUN -0.021 0.13 -9999 0 -0.64 13 13
PPARGC1A -0.051 0.18 -9999 0 -0.38 116 116
USF1 -0.039 0.15 -9999 0 -0.34 108 108
RAB5/GDP/GDI1 -0.053 0.09 -9999 0 -0.36 8 8
NOS2 -0.095 0.28 -9999 0 -0.98 40 40
DDIT3 -0.048 0.16 -9999 0 -0.35 110 110
RAB5A 0.015 0 -9999 0 -10000 0 0
HSPB1 -0.034 0.15 -9999 0 -0.44 32 32
p38alpha-beta/HBP1 -0.037 0.15 -9999 0 -0.42 23 23
CREB1 -0.043 0.17 -9999 0 -0.36 118 118
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.026 0.14 -9999 0 -0.5 11 11
RPS6KA4 -0.039 0.15 -9999 0 -0.34 108 108
PLA2G4A -0.042 0.16 -9999 0 -0.57 23 23
GDI1 -0.039 0.15 -9999 0 -0.4 26 26
TP53 -0.059 0.19 -9999 0 -0.43 113 113
RPS6KA5 -0.053 0.18 -9999 0 -0.37 125 125
ESR1 -0.052 0.17 -9999 0 -0.36 119 119
HBP1 0.015 0 -9999 0 -10000 0 0
MEF2C -0.048 0.16 -9999 0 -0.36 113 113
MEF2A -0.039 0.15 -9999 0 -0.34 108 108
EIF4EBP1 -0.045 0.17 -9999 0 -0.36 120 120
KRT19 -0.1 0.22 -9999 0 -0.57 64 64
ELK4 -0.039 0.15 -9999 0 -0.34 108 108
ATF6 -0.039 0.15 -9999 0 -0.34 108 108
ATF1 -0.043 0.17 -9999 0 -0.36 118 118
p38alpha-beta/MAPKAPK2 -0.037 0.15 -9999 0 -0.42 23 23
p38alpha-beta/MAPKAPK3 -0.038 0.16 -9999 0 -0.43 25 25
p75(NTR)-mediated 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
Sortilin/TRAF6 -0.003 0.035 -10000 0 -0.46 4 4
Necdin/E2F1 -0.077 0.18 -10000 0 -0.48 108 108
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.08 0.15 -10000 0 -0.63 19 19
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.2 -10000 0 -0.43 176 176
NT-4/5 (dimer)/p75(NTR) -0.078 0.17 -10000 0 -0.45 115 115
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.044 0.17 -10000 0 -0.63 18 18
IKBKG 0.015 0 -10000 0 -10000 0 0
BDNF -0.079 0.22 -10000 0 -0.59 104 104
MGDIs/NGR/p75(NTR)/LINGO1 -0.1 0.19 -10000 0 -0.42 166 166
FURIN 0.015 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.19 -10000 0 -0.41 174 174
LINGO1 -0.024 0.15 -10000 0 -0.62 41 41
Sortilin/TRAF6/NRIF -0.002 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.079 0.22 -10000 0 -0.59 104 104
NTRK1 -0.021 0.14 -10000 0 -0.59 40 40
RTN4R -0.035 0.17 -10000 0 -0.61 54 54
neuron apoptosis -0.058 0.19 -10000 0 -0.52 50 50
IRAK1 0.015 0 -10000 0 -10000 0 0
SHC1 -0.079 0.2 -10000 0 -0.41 169 169
ARHGDIA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.095 0.17 -10000 0 -0.37 172 172
MAGEH1 -0.001 0.1 -10000 0 -0.62 17 17
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.13 0.21 -10000 0 -0.43 164 164
Mammalian IAPs/DIABLO -0.039 0.1 -10000 0 -0.32 81 81
proNGF (dimer) -0.062 0.2 -10000 0 -0.61 82 82
MAGED1 0.015 0 -10000 0 -10000 0 0
APP 0.015 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.015 0.11 -10000 0 -0.59 25 25
ZNF274 0.015 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.052 0.17 -10000 0 -0.34 159 159
NGF -0.062 0.2 -10000 0 -0.61 82 82
cell cycle arrest -0.076 0.16 -10000 0 -0.35 149 149
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.027 0.14 -10000 0 -0.5 21 21
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.066 0.15 -10000 0 -0.38 116 116
NCSTN 0.015 0 -10000 0 -10000 0 0
mol:GTP -0.096 0.18 -10000 0 -0.4 159 159
PSENEN 0.015 0 -10000 0 -10000 0 0
mol:ceramide -0.055 0.18 -10000 0 -0.36 159 159
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.023 0.13 -10000 0 -0.41 29 29
p75(NTR)/beta APP -0.061 0.15 -10000 0 -0.44 94 94
BEX1 -0.013 0.13 -10000 0 -0.62 30 30
mol:GDP -0.082 0.19 -10000 0 -0.41 159 159
NGF (dimer) -0.16 0.2 -10000 0 -0.37 300 300
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.093 0.17 -10000 0 -0.41 103 103
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
RAC1/GTP -0.083 0.16 -10000 0 -0.35 159 159
MYD88 0.008 0.07 -10000 0 -0.62 8 8
CHUK 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.096 0.18 -10000 0 -0.4 159 159
RHOB 0.014 0.023 -10000 0 -0.59 1 1
RHOA 0.015 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.019 0.088 -10000 0 -0.43 29 29
NT3 (dimer) -0.012 0.11 -10000 0 -0.59 24 24
TP53 -0.049 0.18 -10000 0 -0.59 33 33
PRDM4 -0.056 0.18 -10000 0 -0.36 159 159
BDNF (dimer) -0.21 0.24 -10000 0 -0.43 317 317
PIK3CA 0.015 0 -10000 0 -10000 0 0
SORT1 0.013 0.035 -10000 0 -0.62 2 2
activation of caspase activity -0.079 0.15 -10000 0 -0.62 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.088 0.17 -10000 0 -0.37 160 160
RHOC 0.012 0.041 -10000 0 -0.6 3 3
XIAP 0.015 0 -10000 0 -10000 0 0
MAPK10 -0.036 0.18 -10000 0 -0.5 40 40
DIABLO 0.015 0 -10000 0 -10000 0 0
SMPD2 -0.056 0.18 -10000 0 -0.36 159 159
APH1B 0.015 0 -10000 0 -10000 0 0
APH1A 0.015 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.097 0.18 -10000 0 -0.41 159 159
PSEN1 0.015 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.016 -10000 0 -0.42 1 1
NT3 (dimer)/p75(NTR) -0.077 0.18 -10000 0 -0.46 111 111
MAPK8 -0.038 0.18 -10000 0 -0.46 51 51
MAPK9 -0.035 0.17 -10000 0 -0.5 35 35
APAF1 0.015 0 -10000 0 -10000 0 0
NTF3 -0.012 0.11 -10000 0 -0.59 24 24
NTF4 -0.016 0.11 -10000 0 -0.59 25 25
NDN -0.068 0.22 -10000 0 -0.62 87 87
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.073 0.14 -10000 0 -0.58 17 17
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.039 -10000 0 -0.34 9 9
RhoA-B-C/GTP -0.095 0.18 -10000 0 -0.4 159 159
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.089 0.16 -10000 0 -0.62 27 27
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.097 0.18 -10000 0 -0.46 70 70
PRKACB 0.015 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.07 0.16 -10000 0 -0.44 107 107
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.059 0.2 -10000 0 -0.6 81 81
BIRC2 0.015 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.18 0.21 6 -0.44 106 112
BAD -0.027 0.17 -10000 0 -0.49 33 33
RIPK2 0.015 0 -10000 0 -10000 0 0
NGFR -0.072 0.22 -10000 0 -0.6 94 94
CYCS -0.043 0.17 -10000 0 -0.62 19 19
ADAM17 0.01 0.055 -10000 0 -0.62 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.087 0.16 -10000 0 -0.4 93 93
BCL2L11 -0.027 0.17 -10000 0 -0.49 33 33
BDNF (dimer)/p75(NTR) -0.12 0.22 -10000 0 -0.48 174 174
PI3K -0.087 0.16 -10000 0 -0.4 91 91
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.087 0.16 -10000 0 -0.36 159 159
NDNL2 0.015 0 -10000 0 -10000 0 0
YWHAE 0.015 0 -10000 0 -10000 0 0
PRKCI 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.21 -10000 0 -0.48 159 159
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.087 0.16 -10000 0 -0.36 159 159
TRAF6 0.013 0.035 -10000 0 -0.62 2 2
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
PLG -0.002 0.046 -10000 0 -0.59 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.092 0.21 -10000 0 -0.52 76 76
SQSTM1 0.015 0 -10000 0 -10000 0 0
NGFRAP1 0.015 0 -10000 0 -10000 0 0
CASP3 -0.022 0.16 -10000 0 -0.45 32 32
E2F1 -0.011 0.12 -10000 0 -0.6 29 29
CASP9 0.014 0.023 -10000 0 -0.59 1 1
IKK complex -0.075 0.14 -10000 0 -0.5 32 32
NGF (dimer)/TRKA -0.079 0.18 -10000 0 -0.46 116 116
MMP7 -0.22 0.3 -10000 0 -0.6 247 247
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.081 0.16 -10000 0 -0.64 19 19
MMP3 -0.054 0.18 -10000 0 -0.59 71 71
APAF-1/Caspase 9 -0.08 0.13 -10000 0 -0.48 40 40
PDGFR-alpha signaling 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
PDGFRA -0.07 0.21 -9999 0 -0.62 88 88
PDGF/PDGFRA/CRKL -0.058 0.15 -9999 0 -0.44 89 89
positive regulation of JUN kinase activity -0.049 0.12 -9999 0 -0.34 74 74
CRKL 0.014 0.023 -9999 0 -0.59 1 1
PDGF/PDGFRA/Caveolin-3 -0.074 0.17 -9999 0 -0.46 106 106
AP1 -0.15 0.3 -9999 0 -0.81 96 96
mol:IP3 -0.039 0.16 -9999 0 -0.45 88 88
PLCG1 -0.039 0.16 -9999 0 -0.45 88 88
PDGF/PDGFRA/alphaV Integrin -0.058 0.15 -9999 0 -0.44 88 88
RAPGEF1 0.013 0.035 -9999 0 -0.62 2 2
CRK 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ -0.039 0.16 -9999 0 -0.45 88 88
CAV3 -0.014 0.11 -9999 0 -0.59 25 25
CAV1 -0.064 0.2 -9999 0 -0.59 88 88
SHC/Grb2/SOS1 -0.05 0.12 -9999 0 -0.35 74 74
PDGF/PDGFRA/Shf -0.06 0.15 -9999 0 -0.44 91 91
FOS -0.11 0.32 -9999 0 -0.79 96 96
JUN -0.016 0.056 -9999 0 -0.49 8 8
oligodendrocyte development -0.058 0.15 -9999 0 -0.44 88 88
GRB2 0.014 0.023 -9999 0 -0.59 1 1
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
mol:DAG -0.039 0.16 -9999 0 -0.45 88 88
PDGF/PDGFRA -0.07 0.21 -9999 0 -0.62 88 88
actin cytoskeleton reorganization -0.06 0.15 -9999 0 -0.44 91 91
SRF 0.029 0.009 -9999 0 -10000 0 0
SHC1 0.001 0.092 -9999 0 -0.59 16 16
PI3K -0.049 0.13 -9999 0 -0.37 89 89
PDGF/PDGFRA/Crk/C3G -0.048 0.12 -9999 0 -0.36 89 89
JAK1 -0.034 0.16 -9999 0 -0.43 88 88
ELK1/SRF -0.001 0.12 -9999 0 -0.32 69 69
SHB 0.011 0.049 -9999 0 -0.62 4 4
SHF 0.011 0.049 -9999 0 -0.62 4 4
CSNK2A1 0.013 0.022 -9999 0 -10000 0 0
GO:0007205 -0.039 0.16 -9999 0 -0.46 88 88
SOS1 0.015 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.049 0.12 -9999 0 -0.34 74 74
PDGF/PDGFRA/SHB -0.06 0.15 -9999 0 -0.44 91 91
PDGF/PDGFRA/Caveolin-1 -0.11 0.22 -9999 0 -0.49 152 152
ITGAV 0.014 0.025 -9999 0 -0.62 1 1
ELK1 -0.028 0.15 -9999 0 -0.39 88 88
PIK3CA 0.015 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.057 0.15 -9999 0 -0.44 88 88
JAK-STAT cascade -0.034 0.16 -9999 0 -0.43 88 88
cell proliferation -0.06 0.15 -9999 0 -0.44 91 91
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.035 0.1 -9999 0 -0.34 70 70
RGS9BP 0.003 0.088 -9999 0 -0.62 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.009 0.047 -9999 0 -0.59 4 4
mol:Na + -0.11 0.17 -9999 0 -0.38 203 203
mol:ADP 0.018 0.05 -9999 0 -0.48 6 6
GNAT2 0.009 0.047 -9999 0 -0.59 4 4
RGS9-1/Gbeta5/R9AP -0.056 0.14 -9999 0 -0.4 93 93
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.012 0.067 -9999 0 -0.38 21 21
GRK7 0.01 0.04 -9999 0 -0.59 3 3
CNGB3 -0.008 0.099 -9999 0 -0.59 19 19
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -0.43 1 1
mol:Ca2+ -0.16 0.23 -9999 0 -0.4 294 294
Cone PDE6 -0.056 0.13 -9999 0 -0.69 7 7
Cone Metarhodopsin II -0.003 0.038 -9999 0 -0.38 6 6
Na + (4 Units) -0.18 0.22 -9999 0 -0.4 294 294
GNAT2/GDP -0.049 0.13 -9999 0 -0.52 15 15
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.006 0.068 -9999 0 -0.34 24 24
Cone Transducin -0.037 0.11 -9999 0 -0.36 70 70
SLC24A2 -0.13 0.26 -9999 0 -0.61 151 151
GNB3/GNGT2 -0.046 0.14 -9999 0 -0.46 67 67
GNB3 -0.025 0.16 -9999 0 -0.62 43 43
GNAT2/GTP -0.003 0.033 -9999 0 -0.43 4 4
CNGA3 -0.16 0.28 -9999 0 -0.6 185 185
ARR3 0.003 0.024 -9999 0 -0.59 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.12 0.18 -9999 0 -0.38 203 203
mol:Pi -0.056 0.14 -9999 0 -0.4 93 93
Cone CNG Channel -0.1 0.15 -9999 0 -0.63 11 11
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.13 0.26 -9999 0 -0.61 151 151
RGS9 -0.067 0.21 -9999 0 -0.62 87 87
PDE6C 0.004 0.04 -9999 0 -0.59 3 3
GNGT2 -0.009 0.12 -9999 0 -0.61 26 26
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.006 0.097 -9999 0 -0.59 18 18
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.032 0.11 -9999 0 -0.39 56 56
ARNO/beta Arrestin1-2 -0.02 0.079 -9999 0 -0.55 7 7
EGFR -0.11 0.25 -9999 0 -0.6 138 138
EPHA2 -0.017 0.14 -9999 0 -0.59 35 35
USP6 0.002 0.087 -9999 0 -0.6 14 14
IQSEC1 0.012 0.04 -9999 0 -0.59 3 3
EGFR/EGFR/EGF/EGF -0.13 0.21 -9999 0 -0.46 183 183
ARRB2 0.01 0.039 -9999 0 -0.25 15 15
mol:GTP 0.003 0.046 -9999 0 -0.18 10 10
ARRB1 0.003 0.088 -9999 0 -0.62 13 13
FBXO8 0.014 0.025 -9999 0 -0.62 1 1
TSHR -0.24 0.31 -9999 0 -0.61 268 268
EGF -0.038 0.18 -9999 0 -0.61 57 57
somatostatin receptor activity 0 0 -9999 0 -0.001 100 100
ARAP2 0.002 0.092 -9999 0 -0.62 14 14
mol:GDP -0.083 0.12 -9999 0 -0.28 127 127
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 56 56
ITGA2B -0.028 0.16 -9999 0 -0.62 46 46
ARF6 0.015 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.074 -9999 0 -0.34 6 6
ADAP1 -0.035 0.17 -9999 0 -0.61 54 54
KIF13B 0.012 0.043 -9999 0 -0.62 3 3
HGF/MET -0.19 0.26 -9999 0 -0.51 255 255
PXN 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.075 0.12 -9999 0 -0.28 97 97
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.11 0.18 -9999 0 -0.39 184 184
ADRB2 -0.011 0.13 -9999 0 -0.62 27 27
receptor agonist activity 0 0 -9999 0 0 109 109
actin filament binding 0 0 -9999 0 -0.001 103 103
SRC 0.013 0.035 -9999 0 -0.62 2 2
ITGB3 -0.099 0.24 -9999 0 -0.6 125 125
GNAQ 0.015 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 67 67
ARF6/GDP -0.011 0.11 -9999 0 -0.4 18 18
ARF6/GDP/GULP/ACAP1 -0.13 0.18 -9999 0 -0.45 111 111
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.083 0.15 -9999 0 -0.39 63 63
ACAP1 -0.046 0.18 -9999 0 -0.59 67 67
ACAP2 0.015 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.002 0.055 -9999 0 -0.36 15 15
EFNA1 0.012 0.041 -9999 0 -0.6 3 3
HGF -0.088 0.23 -9999 0 -0.6 113 113
CYTH3 0.013 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 87 87
endosomal lumen acidification 0 0 -9999 0 0 101 101
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.06 0.2 -9999 0 -0.62 80 80
GNAQ/ARNO 0.014 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 29 29
MET -0.16 0.28 -9999 0 -0.6 194 194
GNA14 -0.009 0.12 -9999 0 -0.61 26 26
GNA15 -0.009 0.12 -9999 0 -0.61 26 26
GIT1 0.014 0.025 -9999 0 -0.62 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 79 79
GNA11 0.006 0.078 -9999 0 -0.62 10 10
LHCGR -0.005 0.089 -9999 0 -0.59 15 15
AGTR1 -0.078 0.22 -9999 0 -0.6 101 101
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.055 -9999 0 -0.36 15 15
IPCEF1/ARNO -0.074 0.15 -9999 0 -0.57 12 12
alphaIIb/beta3 Integrin -0.11 0.2 -9999 0 -0.46 160 160
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.13 0.2 -9999 0 -0.44 194 194
CRKL -0.051 0.14 -9999 0 -0.46 14 14
mol:PIP3 -0.022 0.007 -9999 0 -10000 0 0
AKT1 0.002 0.02 -9999 0 -0.34 2 2
PTK2B -0.006 0.11 -9999 0 -0.59 23 23
RAPGEF1 -0.041 0.13 -9999 0 -0.45 14 14
RANBP10 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.16 0.23 -9999 0 -0.43 255 255
MAP3K5 -0.041 0.14 -9999 0 -0.46 24 24
HGF/MET/CIN85/CBL/ENDOPHILINS -0.15 0.2 -9999 0 -0.45 145 145
AP1 -0.079 0.16 -9999 0 -0.44 97 97
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.001 0.092 -9999 0 -0.59 16 16
apoptosis -0.084 0.22 -9999 0 -0.78 57 57
STAT3 (dimer) -0.056 0.15 -9999 0 -0.47 14 14
GAB1/CRKL/SHP2/PI3K -0.067 0.1 -9999 0 -0.46 11 11
INPP5D 0.007 0.071 -9999 0 -0.6 9 9
CBL/CRK -0.04 0.13 -9999 0 -0.45 13 13
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.015 0 -9999 0 -10000 0 0
PTEN 0.015 0 -9999 0 -10000 0 0
ELK1 -0.065 0.1 -9999 0 -0.22 194 194
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.055 0.08 -9999 0 -0.24 55 55
PAK1 -0.007 0.075 -9999 0 -0.31 39 39
HGF/MET/RANBP10 -0.16 0.23 -9999 0 -0.43 255 255
HRAS -0.11 0.24 -9999 0 -0.57 123 123
DOCK1 -0.041 0.13 -9999 0 -0.46 13 13
GAB1 -0.063 0.14 -9999 0 -0.31 124 124
CRK -0.051 0.14 -9999 0 -0.46 14 14
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.14 0.22 -9999 0 -0.59 105 105
JUN 0.008 0.067 -9999 0 -0.6 8 8
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.095 0.13 -9999 0 -0.31 145 145
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
cell morphogenesis -0.025 0.15 -9999 0 -0.49 10 10
GRB2/SHC -0.064 0.14 -9999 0 -0.5 27 27
FOS -0.073 0.22 -9999 0 -0.61 95 95
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.064 0.1 -9999 0 -0.22 194 194
HGF/MET/MUC20 -0.17 0.23 -9999 0 -0.44 255 255
cell migration -0.063 0.14 -9999 0 -0.49 27 27
GRB2 0.014 0.023 -9999 0 -0.59 1 1
CBL 0.014 0.025 -9999 0 -0.62 1 1
MET/RANBP10 -0.13 0.2 -9999 0 -0.44 194 194
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.069 0.16 -9999 0 -0.38 70 70
MET/MUC20 -0.13 0.2 -9999 0 -0.45 194 194
RAP1B -0.033 0.13 -9999 0 -0.46 16 16
RAP1A -0.03 0.13 -9999 0 -0.42 13 13
HGF/MET/RANBP9 -0.16 0.23 -9999 0 -0.43 255 255
RAF1 -0.098 0.23 -9999 0 -0.61 81 81
STAT3 -0.057 0.15 -9999 0 -0.48 14 14
cell proliferation -0.075 0.2 -9999 0 -0.59 29 29
RPS6KB1 -0.022 0.053 -9999 0 -10000 0 0
MAPK3 -0.065 0.092 -9999 0 -10000 0 0
MAPK1 -0.065 0.092 -9999 0 -10000 0 0
RANBP9 0.015 0 -9999 0 -10000 0 0
MAPK8 -0.018 0.13 -9999 0 -0.44 22 22
SRC -0.057 0.15 -9999 0 -0.46 14 14
PI3K -0.058 0.13 -9999 0 -0.32 55 55
MET/Glomulin -0.1 0.18 -9999 0 -0.39 194 194
SOS1 0.015 0 -9999 0 -10000 0 0
MAP2K1 -0.082 0.21 -9999 0 -0.56 81 81
MET -0.16 0.28 -9999 0 -0.6 194 194
MAP4K1 -0.048 0.14 -9999 0 -0.44 26 26
PTK2 0.015 0 -9999 0 -10000 0 0
MAP2K2 -0.082 0.21 -9999 0 -0.56 81 81
BAD 0.011 0.019 -9999 0 -0.32 2 2
MAP2K4 -0.029 0.13 -9999 0 -0.42 22 22
SHP2/GRB2/SOS1/GAB1 -0.1 0.15 -9999 0 -0.37 124 124
INPPL1 0.015 0 -9999 0 -10000 0 0
PXN 0.015 0 -9999 0 -10000 0 0
SH3KBP1 0.015 0 -9999 0 -10000 0 0
HGS -0.068 0.13 -9999 0 -0.3 123 123
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.088 0.23 -9999 0 -0.6 113 113
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
PTPRJ 0.013 0.034 -9999 0 -0.61 2 2
NCK/PLCgamma1 -0.056 0.13 -9999 0 -0.32 53 53
PDPK1 -0.008 0.016 -9999 0 -0.39 1 1
HGF/MET/SHIP -0.17 0.23 -9999 0 -0.44 260 260
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.38 -9999 0 -0.97 71 71
PCK1 -0.22 0.4 -9999 0 -1.1 87 87
HNF4A -0.21 0.41 -9999 0 -1.1 69 69
KCNJ11 -0.27 0.52 -9999 0 -1.1 127 127
AKT1 -0.08 0.17 -9999 0 -0.44 13 13
response to starvation -0.002 0.022 -9999 0 -10000 0 0
DLK1 -0.28 0.47 -9999 0 -1 130 130
NKX2-1 -0.084 0.24 -9999 0 -0.77 24 24
ACADM -0.18 0.38 -9999 0 -0.96 73 73
TAT -0.23 0.41 -9999 0 -1.1 80 80
CEBPB -0.002 0.1 -9999 0 -0.61 19 19
CEBPA -0.008 0.12 -9999 0 -0.62 26 26
TTR -0.16 0.29 -9999 0 -0.84 59 59
PKLR -0.19 0.39 -9999 0 -0.96 81 81
APOA1 -0.23 0.46 -9999 0 -1.2 79 79
CPT1C -0.18 0.38 -9999 0 -0.97 74 74
ALAS1 -0.062 0.2 -9999 0 -0.77 3 3
TFRC -0.17 0.3 -9999 0 -0.78 59 59
FOXF1 -0.007 0.12 -9999 0 -0.6 24 24
NF1 0.019 0.055 -9999 0 -0.62 5 5
HNF1A (dimer) 0.012 0.042 -9999 0 -0.68 1 1
CPT1A -0.18 0.38 -9999 0 -0.97 72 72
HMGCS1 -0.18 0.38 -9999 0 -0.98 71 71
NR3C1 -0.017 0.079 -9999 0 -10000 0 0
CPT1B -0.2 0.4 -9999 0 -1 85 85
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.008 0.031 -9999 0 -10000 0 0
GCK -0.26 0.47 -9999 0 -1 133 133
CREB1 0.003 0.051 -9999 0 -10000 0 0
IGFBP1 -0.23 0.49 -9999 0 -1.3 102 102
PDX1 -0.096 0.23 -9999 0 -0.73 20 20
UCP2 -0.2 0.41 -9999 0 -1 87 87
ALDOB -0.21 0.44 -9999 0 -1.1 90 90
AFP -0.11 0.2 -9999 0 -0.62 48 48
BDH1 -0.22 0.44 -9999 0 -1.1 95 95
HADH -0.19 0.4 -9999 0 -1 72 72
F2 -0.21 0.42 -9999 0 -1.1 68 68
HNF1A 0.012 0.042 -9999 0 -0.68 1 1
G6PC -0.047 0.17 -9999 0 -0.74 13 13
SLC2A2 -0.098 0.23 -9999 0 -0.69 9 9
INS 0.008 0.088 -9999 0 -0.6 5 5
FOXA1 -0.067 0.19 -9999 0 -0.59 62 62
FOXA3 -0.12 0.25 -9999 0 -0.61 113 113
FOXA2 -0.22 0.46 -9999 0 -1 104 104
ABCC8 -0.3 0.55 -9999 0 -1.2 152 152
ALB -0.15 0.34 -9999 0 -1 70 70
IL1-mediated signaling events

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
UBC13/UEV1A -0.001 0.016 -10000 0 -0.42 1 1
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.012 0.042 -10000 0 -0.61 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.087 0.13 -10000 0 -0.4 54 54
IRAK/TOLLIP 0.034 0.014 -10000 0 -0.31 1 1
IKBKB 0.015 0 -10000 0 -10000 0 0
IKBKG 0.015 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.2 0.25 -10000 0 -0.48 275 275
IL1A -0.091 0.23 -10000 0 -0.61 114 114
IL1B -0.13 0.24 -10000 0 -0.47 210 210
IRAK/TRAF6/p62/Atypical PKCs -0.023 0.076 -10000 0 -10000 0 0
IL1R2 -0.16 0.28 -10000 0 -0.6 193 193
IL1R1 -0.037 0.17 -10000 0 -0.6 57 57
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.05 0.14 0.23 1 -0.44 34 35
TOLLIP 0.015 0 -10000 0 -10000 0 0
TICAM2 0.001 0.093 -10000 0 -0.61 15 15
MAP3K3 0.015 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.067 0.047 -10000 0 -0.53 1 1
JUN 0.045 0.056 -10000 0 -0.53 1 1
MAP3K7 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.16 0.2 -10000 0 -0.63 66 66
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.13 0.2 -10000 0 -0.46 109 109
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.12 0.19 -10000 0 -0.65 37 37
IL1 beta fragment/IL1R1/IL1RAP -0.18 0.23 -10000 0 -0.49 150 150
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.042 0.045 -10000 0 -10000 0 0
IRAK1 0.028 0.016 -10000 0 -0.35 1 1
IL1RN/IL1R1 -0.16 0.24 -10000 0 -0.48 223 223
IRAK4 0.015 0 -10000 0 -10000 0 0
PRKCI 0.015 0 -10000 0 -10000 0 0
TRAF6 0.013 0.035 -10000 0 -0.62 2 2
PI3K -0.002 0.03 -10000 0 -0.46 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.07 0.16 -10000 0 -0.46 53 53
CHUK 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.18 0.23 -10000 0 -0.49 150 150
IL1 beta/IL1R2 -0.23 0.25 -10000 0 -0.44 344 344
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.18 -10000 0 -0.56 66 66
IRAK3 0.009 0.064 -10000 0 -0.61 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.16 0.21 -10000 0 -0.65 70 70
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.051 0.15 -10000 0 -0.45 37 37
IL1 alpha/IL1R1/IL1RAP -0.14 0.22 -10000 0 -0.42 222 222
RELA 0.015 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.015 0 -10000 0 -10000 0 0
MYD88 0.008 0.07 -10000 0 -0.62 8 8
IRAK/TRAF6/MEKK3 0.041 0.023 -10000 0 -0.31 2 2
IL1RAP -0.067 0.21 -10000 0 -0.59 90 90
UBE2N 0.015 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.13 0.17 -10000 0 -0.53 71 71
CASP1 -0.017 0.14 -10000 0 -0.6 35 35
IL1RN/IL1R2 -0.24 0.29 -10000 0 -0.53 306 306
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.17 0.22 -10000 0 -0.68 65 65
TMEM189-UBE2V1 0.007 0.024 -10000 0 -0.59 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.027 0.13 -10000 0 -0.43 28 28
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL1RN -0.16 0.28 -10000 0 -0.6 193 193
TRAF6/TAK1/TAB1/TAB2 -0.001 0.02 -10000 0 -0.31 2 2
MAP2K6 0.038 0.025 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.12 0.31 -10000 0 -0.84 68 68
NCK1/PAK1/Dok-R -0.11 0.14 -10000 0 -0.4 89 89
NCK1/Dok-R -0.17 0.31 -10000 0 -1 60 60
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.019 0.07 0.22 44 -10000 0 44
RELA 0.015 0 -10000 0 -10000 0 0
SHC1 0 0.092 -10000 0 -0.59 16 16
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.02 0.089 0.26 15 -0.54 6 21
TNIP2 0.015 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.28 -10000 0 -0.99 54 54
FN1 -0.028 0.16 -10000 0 -0.59 48 48
PLD2 -0.094 0.33 -10000 0 -1.1 54 54
PTPN11 0.013 0.035 -10000 0 -0.62 2 2
GRB14 -0.22 0.3 -10000 0 -0.6 252 252
ELK1 -0.065 0.3 -10000 0 -0.98 54 54
GRB7 -0.038 0.16 -10000 0 -0.59 54 54
PAK1 -0.018 0.14 -10000 0 -0.59 37 37
Tie2/Ang1/alpha5/beta1 Integrin -0.16 0.31 -10000 0 -1 68 68
CDKN1A -0.13 0.3 -10000 0 -0.68 105 105
ITGA5 -0.026 0.15 -10000 0 -0.59 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.17 0.31 -10000 0 -1 59 59
CRK 0.015 0 -10000 0 -10000 0 0
mol:NO -0.081 0.24 -10000 0 -0.62 70 70
PLG -0.1 0.33 -10000 0 -1.1 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.1 0.28 -10000 0 -0.83 63 63
GRB2 0.014 0.023 -10000 0 -0.59 1 1
PIK3R1 0.011 0.043 -10000 0 -0.63 3 3
ANGPT2 -0.18 0.33 -10000 0 -0.62 185 185
BMX -0.12 0.33 -10000 0 -1.1 57 57
ANGPT1 -0.14 0.36 -10000 0 -1.2 57 57
tube development -0.12 0.28 -10000 0 -0.65 108 108
ANGPT4 -0.048 0.18 -10000 0 -0.61 64 64
response to hypoxia -0.009 0.023 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.37 -10000 0 -1.2 66 66
alpha5/beta1 Integrin -0.031 0.12 -10000 0 -0.45 46 46
FGF2 0.015 0.034 -10000 0 -0.61 2 2
STAT5A (dimer) -0.15 0.33 -10000 0 -0.76 112 112
mol:L-citrulline -0.081 0.24 -10000 0 -0.62 70 70
AGTR1 -0.08 0.22 -10000 0 -0.6 101 101
MAPK14 -0.1 0.32 -10000 0 -1.1 56 56
Tie2/SHP2 -0.047 0.16 -10000 0 -0.95 16 16
TEK -0.025 0.19 -10000 0 -0.89 21 21
RPS6KB1 -0.099 0.28 -10000 0 -0.82 62 62
Angiotensin II/AT1 -0.061 0.16 -10000 0 -0.45 101 101
Tie2/Ang1/GRB2 -0.099 0.34 -10000 0 -1.1 54 54
MAPK3 -0.074 0.3 -10000 0 -1 54 54
MAPK1 -0.074 0.3 -10000 0 -1 54 54
Tie2/Ang1/GRB7 -0.13 0.34 -10000 0 -1.1 57 57
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 -0.098 0.33 -10000 0 -1.1 54 54
PI3K -0.13 0.33 -10000 0 -0.98 62 62
FES -0.11 0.32 -10000 0 -1.1 56 56
Crk/Dok-R -0.17 0.31 -10000 0 -1 59 59
Tie2/Ang1/ABIN2 -0.098 0.34 -10000 0 -1.1 54 54
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.28 -10000 0 -0.74 70 70
STAT5A 0.004 0.081 -10000 0 -0.62 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.099 0.28 -10000 0 -0.82 62 62
Tie2/Ang2 -0.18 0.37 -10000 0 -0.87 114 114
Tie2/Ang1 -0.11 0.35 -10000 0 -1.2 54 54
FOXO1 -0.12 0.3 -10000 0 -0.72 91 91
ELF1 0.021 0.015 -10000 0 -10000 0 0
ELF2 -0.097 0.32 -10000 0 -1.1 54 54
mol:Choline -0.085 0.32 -10000 0 -1.1 54 54
cell migration -0.066 0.081 -10000 0 -0.23 81 81
FYN -0.14 0.32 -10000 0 -0.75 104 104
DOK2 -0.085 0.23 -10000 0 -0.6 109 109
negative regulation of cell cycle -0.12 0.27 -10000 0 -0.61 105 105
ETS1 -0.007 0.09 -10000 0 -0.62 7 7
PXN -0.074 0.24 -10000 0 -0.68 60 60
ITGB1 0.012 0.04 -10000 0 -0.59 3 3
NOS3 -0.094 0.27 -10000 0 -0.71 69 69
RAC1 0.015 0 -10000 0 -10000 0 0
TNF -0.14 0.27 -10000 0 -0.62 153 153
MAPKKK cascade -0.085 0.32 -10000 0 -1.1 54 54
RASA1 0.015 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.11 0.34 -10000 0 -1.1 60 60
NCK1 0.015 0 -10000 0 -10000 0 0
vasculogenesis -0.071 0.22 -10000 0 -0.55 70 70
mol:Phosphatidic acid -0.085 0.32 -10000 0 -1.1 54 54
mol:Angiotensin II -0.003 0.009 -10000 0 -10000 0 0
mol:NADP -0.081 0.24 -10000 0 -0.62 70 70
Rac1/GTP -0.14 0.23 -10000 0 -0.76 62 62
MMP2 -0.11 0.34 -10000 0 -1.1 58 58
Glucocorticoid receptor regulatory network

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
PCK2 0.024 0.1 -10000 0 -0.75 5 5
SMARCC2 0.016 0.026 -10000 0 -0.62 1 1
SMARCC1 0.017 0.007 -10000 0 -10000 0 0
TBX21 -0.11 0.25 -10000 0 -0.73 78 78
SUMO2 0.013 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.003 0.11 -10000 0 -0.69 16 16
FKBP4 0.015 0 -10000 0 -10000 0 0
FKBP5 -0.068 0.21 -10000 0 -0.62 88 88
GR alpha/HSP90/FKBP51/HSP90 0.036 0.17 0.32 30 -0.38 23 53
PRL -0.05 0.11 -10000 0 -0.57 6 6
cortisol/GR alpha (dimer)/TIF2 0.19 0.25 0.54 144 -0.44 8 152
RELA -0.076 0.1 -10000 0 -0.28 14 14
FGG 0.17 0.18 0.48 75 -0.47 6 81
GR beta/TIF2 0.072 0.16 0.34 43 -0.42 35 78
IFNG -0.23 0.23 -10000 0 -0.66 79 79
apoptosis -0.014 0.19 0.56 25 -0.62 4 29
CREB1 0.012 0.032 -10000 0 -10000 0 0
histone acetylation -0.04 0.12 -10000 0 -0.37 44 44
BGLAP -0.049 0.13 -10000 0 -0.66 8 8
GR/PKAc 0.089 0.099 0.32 29 -10000 0 29
NF kappa B1 p50/RelA -0.14 0.2 -10000 0 -0.45 106 106
SMARCD1 0.017 0.007 -10000 0 -10000 0 0
MDM2 0.08 0.091 0.28 44 -0.24 6 50
GATA3 -0.1 0.25 -10000 0 -0.6 138 138
AKT1 0 0.027 -10000 0 -0.6 1 1
CSF2 -0.065 0.11 -10000 0 -0.54 9 9
GSK3B 0.013 0.011 -10000 0 -10000 0 0
NR1I3 0.032 0.18 0.55 21 -0.8 2 23
CSN2 0.14 0.14 0.42 40 -10000 0 40
BRG1/BAF155/BAF170/BAF60A 0.037 0.047 -10000 0 -0.68 1 1
NFATC1 -0.006 0.12 -10000 0 -0.62 23 23
POU2F1 0.007 0.075 -10000 0 -0.62 9 9
CDKN1A -0.044 0.31 -10000 0 -1.5 26 26
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.01 -10000 0 -10000 0 0
SFN -0.12 0.25 -10000 0 -0.6 141 141
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.033 0.21 0.31 18 -0.59 24 42
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.039 0.31 0.52 23 -0.79 72 95
JUN -0.17 0.2 -10000 0 -0.5 104 104
IL4 -0.079 0.15 -10000 0 -0.56 32 32
CDK5R1 -0.037 0.17 -10000 0 -0.62 53 53
PRKACA 0.015 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.21 0.23 18 -0.5 126 144
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.043 0.16 0.32 26 -0.37 1 27
cortisol/GR alpha (monomer) 0.24 0.27 0.64 154 -10000 0 154
NCOA2 -0.019 0.14 -10000 0 -0.62 36 36
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.12 0.22 -10000 0 -0.65 95 95
AP-1/NFAT1-c-4 -0.3 0.32 -10000 0 -0.72 176 176
AFP -0.14 0.2 -10000 0 -0.69 39 39
SUV420H1 0.015 0 -10000 0 -10000 0 0
IRF1 0.12 0.17 0.47 28 -0.55 9 37
TP53 0.001 0.14 -10000 0 -0.52 38 38
PPP5C 0.015 0 -10000 0 -10000 0 0
KRT17 -0.41 0.48 -10000 0 -1.1 198 198
KRT14 -0.13 0.19 -10000 0 -0.62 59 59
TBP 0.025 0.026 -10000 0 -0.57 1 1
CREBBP 0.034 0.059 -10000 0 -0.63 1 1
HDAC1 0.005 0.05 -10000 0 -0.63 4 4
HDAC2 0.015 0.004 -10000 0 -10000 0 0
AP-1 -0.31 0.32 -10000 0 -0.72 178 178
MAPK14 0.012 0.025 -10000 0 -0.59 1 1
MAPK10 0.009 0.056 -10000 0 -0.63 5 5
MAPK11 0.011 0.044 -10000 0 -0.62 3 3
KRT5 -0.41 0.46 -10000 0 -0.98 216 216
interleukin-1 receptor activity 0 0.004 -10000 0 -10000 0 0
NCOA1 0.018 0.007 -10000 0 -10000 0 0
STAT1 0.003 0.11 -10000 0 -0.69 16 16
CGA -0.073 0.14 -10000 0 -0.52 26 26
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.083 0.12 0.37 31 -10000 0 31
MAPK3 0.013 0.011 -10000 0 -10000 0 0
MAPK1 0.013 0.01 -10000 0 -10000 0 0
ICAM1 -0.24 0.33 -10000 0 -0.79 127 127
NFKB1 -0.076 0.1 -10000 0 -0.28 13 13
MAPK8 -0.14 0.18 -10000 0 -0.42 120 120
MAPK9 0.013 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.019 0.19 0.56 25 -0.66 4 29
BAX 0.012 0.1 -10000 0 -10000 0 0
POMC -0.13 0.25 -10000 0 -1.2 22 22
EP300 0.033 0.069 -10000 0 -0.62 3 3
cortisol/GR alpha (dimer)/p53 0.2 0.24 0.55 136 -10000 0 136
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.078 0.28 19 -0.25 1 20
SGK1 0.08 0.17 -10000 0 -1.4 7 7
IL13 -0.24 0.25 -10000 0 -0.74 72 72
IL6 -0.35 0.44 -10000 0 -0.92 214 214
PRKACG 0.005 0.047 -10000 0 -0.59 4 4
IL5 -0.2 0.2 -10000 0 -0.63 55 55
IL2 -0.23 0.23 -10000 0 -0.66 71 71
CDK5 0.013 0.024 -10000 0 -0.59 1 1
PRKACB 0.015 0 -10000 0 -10000 0 0
HSP90AA1 0.015 0 -10000 0 -10000 0 0
IL8 -0.4 0.46 -10000 0 -0.89 261 261
CDK5R1/CDK5 -0.033 0.13 -10000 0 -0.46 54 54
NF kappa B1 p50/RelA/PKAc -0.073 0.15 -10000 0 -0.42 14 14
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.21 0.52 146 -10000 0 146
SMARCA4 0.013 0.05 -10000 0 -0.62 4 4
chromatin remodeling 0.16 0.14 0.39 82 -0.56 1 83
NF kappa B1 p50/RelA/Cbp -0.067 0.17 -10000 0 -0.46 22 22
JUN (dimer) -0.17 0.2 -10000 0 -0.5 104 104
YWHAH 0.003 0.083 -10000 0 -0.59 13 13
VIPR1 -0.11 0.27 -10000 0 -0.76 83 83
NR3C1 0.14 0.16 0.46 78 -10000 0 78
NR4A1 -0.01 0.14 -10000 0 -0.54 38 38
TIF2/SUV420H1 -0.024 0.1 -10000 0 -0.46 36 36
MAPKKK cascade -0.014 0.19 0.56 25 -0.62 4 29
cortisol/GR alpha (dimer)/Src-1 0.22 0.23 0.54 159 -10000 0 159
PBX1 0.015 0.027 -10000 0 -0.62 1 1
POU1F1 0.005 0.015 -10000 0 -10000 0 0
SELE -0.3 0.39 -10000 0 -0.9 158 158
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.14 0.39 81 -0.57 1 82
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.21 0.52 146 -10000 0 146
mol:cortisol 0.13 0.16 0.35 167 -10000 0 167
MMP1 -0.19 0.31 -10000 0 -0.81 101 101
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.061 0.25 -10000 0 -0.73 33 33
CRP -0.07 0.25 -10000 0 -0.73 33 33
cell cycle arrest -0.086 0.28 -10000 0 -0.74 60 60
TIMP1 -0.17 0.32 -10000 0 -0.72 103 103
IL6ST -0.032 0.16 -10000 0 -0.62 46 46
Rac1/GDP -0.096 0.21 -10000 0 -0.5 89 89
AP1 -0.023 0.15 -10000 0 -0.49 22 22
GAB2 0.013 0.043 -10000 0 -0.62 3 3
TNFSF11 -0.076 0.26 -10000 0 -0.71 49 49
HSP90B1 0.006 0.15 -10000 0 -0.97 13 13
GAB1 0.015 0.025 -10000 0 -0.62 1 1
MAPK14 -0.16 0.27 -10000 0 -0.54 182 182
AKT1 0.059 0.051 -10000 0 -0.67 2 2
FOXO1 0.066 0.051 -10000 0 -0.62 2 2
MAP2K6 -0.13 0.24 -10000 0 -0.5 141 141
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.083 0.22 -10000 0 -0.55 72 72
MITF -0.1 0.21 -10000 0 -0.48 98 98
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.015 0 -10000 0 -10000 0 0
A2M 0.022 0.049 -10000 0 -10000 0 0
CEBPB 0.007 0.11 -10000 0 -0.61 19 19
GRB2/SOS1/GAB family/SHP2 -0.01 0.091 -10000 0 -0.65 4 4
STAT3 -0.09 0.29 -10000 0 -0.78 61 61
STAT1 -0.009 0.04 -10000 0 -0.27 1 1
CEBPD -0.11 0.35 -10000 0 -0.93 77 77
PIK3CA 0.017 0 -10000 0 -10000 0 0
PI3K 0.024 0.032 -10000 0 -0.45 3 3
JUN 0.007 0.066 -10000 0 -0.6 8 8
PIAS3/MITF -0.087 0.2 -10000 0 -0.48 72 72
MAPK11 -0.16 0.27 -10000 0 -0.54 184 184
STAT3 (dimer)/FOXO1 -0.008 0.23 -10000 0 -0.6 27 27
GRB2/SOS1/GAB family -0.088 0.14 -10000 0 -0.51 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.09 0.19 -10000 0 -0.44 89 89
GRB2 0.015 0.023 -10000 0 -0.59 1 1
JAK2 0.015 0 -10000 0 -10000 0 0
LBP -0.068 0.26 -10000 0 -0.68 55 55
PIK3R1 0.014 0.043 -10000 0 -0.62 3 3
JAK1 0.011 0.01 -10000 0 -10000 0 0
MYC -0.079 0.29 -10000 0 -0.88 44 44
FGG -0.072 0.25 -10000 0 -0.73 42 42
macrophage differentiation -0.086 0.28 -10000 0 -0.74 60 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.14 0.19 -10000 0 -0.48 94 94
JUNB -0.081 0.29 -10000 0 -0.88 42 42
FOS -0.074 0.22 -10000 0 -0.61 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.21 0.31 1 -0.47 125 126
STAT1/PIAS1 -0.082 0.19 -10000 0 -0.46 81 81
GRB2/SOS1/GAB family/SHP2/PI3K 0.042 0.054 -10000 0 -0.5 4 4
STAT3 (dimer) -0.088 0.29 -10000 0 -0.77 61 61
PRKCD -0.084 0.26 -10000 0 -0.65 69 69
IL6R -0.006 0.1 -10000 0 -0.62 19 19
SOCS3 -0.24 0.42 -10000 0 -0.85 172 172
gp130 (dimer)/JAK1/JAK1/LMO4 -0.007 0.11 -10000 0 -0.38 46 46
Rac1/GTP -0.1 0.22 -10000 0 -0.51 94 94
HCK 0 0.096 -10000 0 -0.61 16 16
MAPKKK cascade 0.015 0.088 -10000 0 -0.79 4 4
bone resorption -0.071 0.25 -10000 0 -0.66 52 52
IRF1 -0.071 0.26 -10000 0 -0.74 38 38
mol:GDP -0.11 0.22 0.29 1 -0.48 116 117
SOS1 0.015 0.002 -10000 0 -10000 0 0
VAV1 -0.11 0.22 -10000 0 -0.49 116 116
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.26 -10000 0 -0.5 184 184
PTPN11 -0.005 0.053 -10000 0 -0.91 2 2
IL6/IL6RA -0.14 0.24 -10000 0 -0.47 214 214
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.1 -10000 0 -0.38 46 46
gp130 (dimer)/JAK2/JAK2/LMO4 -0.008 0.1 -10000 0 -0.38 46 46
IL6 -0.18 0.29 -10000 0 -0.62 205 205
PIAS3 0.015 0 -10000 0 -10000 0 0
PTPRE 0.014 0.053 -10000 0 -0.62 4 4
PIAS1 0.013 0.035 -10000 0 -0.62 2 2
RAC1 0.015 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.092 0.17 0.28 1 -0.43 77 78
LMO4 0.012 0.013 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.14 0.23 0.37 1 -0.73 58 59
MCL1 0.066 0.046 -10000 0 -0.75 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.076 0.14 -10000 0 -0.34 151 151
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.11 0.2 -10000 0 -0.45 179 179
GNB1/GNG2 -0.004 0.037 -10000 0 -0.39 6 6
GNB1 0.015 0 -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 0.01 0.01 -10000 0 -0.26 1 1
Gs family/GTP -0.081 0.15 -10000 0 -0.36 149 149
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 0.02 0.038 0.092 149 -10000 0 149
GNAL -0.13 0.27 -10000 0 -0.62 149 149
GNG2 0.009 0.06 -10000 0 -0.62 6 6
CRH -0.15 0.27 -10000 0 -0.6 179 179
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.045 -10000 0 -0.38 9 9
MAPK11 0.009 0.026 -10000 0 -0.38 3 3
Visual signal transduction: Rods

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
mol:K + 0.015 0 -9999 0 -10000 0 0
GNAT1/GTP -0.019 0.09 -9999 0 -0.43 30 30
Metarhodopsin II/Arrestin -0.02 0.084 -9999 0 -0.37 37 37
PDE6G/GNAT1/GTP -0.046 0.12 -9999 0 -0.38 81 81
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.015 0.12 -9999 0 -0.59 30 30
GRK1 0.009 0.047 -9999 0 -0.59 4 4
CNG Channel -0.18 0.22 -9999 0 -0.63 85 85
mol:Na + -0.18 0.21 -9999 0 -0.6 94 94
mol:ADP 0.009 0.047 -9999 0 -0.59 4 4
RGS9-1/Gbeta5/R9AP -0.056 0.14 -9999 0 -0.4 93 93
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.19 0.22 -9999 0 -0.62 94 94
CNGB1 -0.14 0.26 -9999 0 -0.6 171 171
RDH5 -0.028 0.16 -9999 0 -0.59 48 48
SAG 0.002 0.024 -9999 0 -0.59 1 1
mol:Ca2+ -0.15 0.22 -9999 0 -0.57 94 94
Na + (4 Units) -0.17 0.2 -9999 0 -0.55 94 94
RGS9 -0.067 0.21 -9999 0 -0.62 87 87
GNB1/GNGT1 -0.004 0.04 -9999 0 -0.42 6 6
GNAT1/GDP -0.061 0.13 -9999 0 -0.35 80 80
GUCY2D -0.005 0.094 -9999 0 -0.59 17 17
GNGT1 -0.005 0.055 -9999 0 -0.59 6 6
GUCY2F 0.005 0.052 -9999 0 -0.59 5 5
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.073 0.18 -9999 0 -0.62 23 23
mol:11-cis-retinal -0.028 0.16 -9999 0 -0.59 48 48
mol:cGMP -0.099 0.17 -9999 0 -0.62 25 25
GNB1 0.015 0 -9999 0 -10000 0 0
Rhodopsin -0.053 0.14 -9999 0 -0.42 84 84
SLC24A1 0.015 0 -9999 0 -10000 0 0
CNGA1 -0.039 0.18 -9999 0 -0.61 57 57
Metarhodopsin II -0.02 0.078 -9999 0 -0.33 40 40
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.11 0.18 -9999 0 -0.43 98 98
RGS9BP 0.003 0.088 -9999 0 -0.62 13 13
Metarhodopsin II/Transducin -0.002 0.064 -9999 0 -0.35 2 2
GCAP Family/Ca ++ -0.1 0.18 -9999 0 -0.37 182 182
PDE6A/B -0.087 0.18 -9999 0 -0.44 131 131
mol:Pi -0.056 0.14 -9999 0 -0.4 93 93
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.018 0.076 -9999 0 -0.34 35 35
PDE6B -0.029 0.16 -9999 0 -0.61 47 47
PDE6A -0.064 0.2 -9999 0 -0.6 86 86
PDE6G -0.034 0.17 -9999 0 -0.61 52 52
RHO -0.02 0.14 -9999 0 -0.59 36 36
PDE6 -0.12 0.19 -9999 0 -0.62 49 49
GUCA1A -0.14 0.27 -9999 0 -0.6 168 168
GC2/GCAP Family -0.1 0.17 -9999 0 -0.41 95 95
GUCA1C -0.01 0.091 -9999 0 -0.59 16 16
GUCA1B -0.002 0.1 -9999 0 -0.62 18 18
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.08 0.23 -9999 0 -0.54 98 98
MAP3K8 -0.006 0.11 -9999 0 -0.59 22 22
FOS -0.075 0.21 -9999 0 -0.53 96 96
PRKCA 0.012 0.035 -9999 0 -0.62 2 2
PTPN7 -0.11 0.25 -9999 0 -0.61 135 135
HRAS 0.015 0.001 -9999 0 -10000 0 0
PRKCB -0.072 0.22 -9999 0 -0.6 94 94
NRAS 0.015 0.001 -9999 0 -10000 0 0
RAS family/GTP 0 0.012 -9999 0 -0.32 1 1
MAPK3 -0.063 0.18 -9999 0 -0.5 88 88
MAP2K1 -0.011 0.13 -9999 0 -0.44 39 39
ELK1 0.014 0.006 -9999 0 -10000 0 0
BRAF -0.048 0.12 -9999 0 -0.43 47 47
mol:GTP 0 0.002 -9999 0 -0.005 94 94
MAPK1 -0.063 0.18 -9999 0 -0.5 88 88
RAF1 -0.043 0.11 -9999 0 -0.43 39 39
KRAS 0.014 0.023 -9999 0 -0.59 1 1
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.005 0.08 -9999 0 -0.4 23 23
NFATC2 -0.036 0.13 -9999 0 -0.4 73 73
NFATC3 0.009 0.03 -9999 0 -10000 0 0
CD40LG -0.16 0.3 -9999 0 -0.76 82 82
PTGS2 -0.2 0.34 -9999 0 -0.74 139 139
JUNB -0.029 0.16 -9999 0 -0.6 48 48
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.011 -9999 0 -10000 0 0
CALM1 0.012 0.008 -9999 0 -10000 0 0
JUN 0.004 0.067 -9999 0 -0.6 8 8
mol:Ca2+ -0.007 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.015 -9999 0 -0.38 1 1
FOSL1 -0.14 0.27 -9999 0 -0.6 163 163
CREM 0.013 0.033 -9999 0 -0.59 2 2
Jun/NFAT1-c-4/p21SNFT -0.13 0.18 -9999 0 -0.56 72 72
FOS -0.078 0.22 -9999 0 -0.62 95 95
IFNG -0.15 0.27 -9999 0 -0.71 68 68
AP-1/NFAT1-c-4 -0.22 0.29 -9999 0 -0.74 116 116
FASLG -0.16 0.29 -9999 0 -0.74 77 77
NFAT1-c-4/ICER1 -0.069 0.13 -9999 0 -0.45 36 36
IL2RA -0.22 0.35 -9999 0 -0.72 163 163
FKBP12/FK506 -0.001 0.017 -9999 0 -0.43 1 1
CSF2 -0.15 0.28 -9999 0 -0.7 75 75
JunB/Fra1/NFAT1-c-4 -0.16 0.21 -9999 0 -0.54 103 103
IL4 -0.15 0.27 -9999 0 -0.68 75 75
IL2 -0.009 0.015 -9999 0 -10000 0 0
IL3 -0.029 0.1 -9999 0 -0.89 9 9
FKBP1A 0.014 0.023 -9999 0 -0.59 1 1
BATF3 -0.054 0.19 -9999 0 -0.6 76 76
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.007 0.074 -9999 0 -0.62 9 9
LPA receptor mediated events

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
GNB1/GNG2 -0.05 0.12 -9999 0 -0.36 72 72
NF kappa B1 p50/RelA/I kappa B alpha -0.035 0.082 -9999 0 -0.45 7 7
AP1 -0.11 0.18 -9999 0 -0.6 43 43
mol:PIP3 -0.11 0.16 -9999 0 -0.52 51 51
AKT1 0.027 0.1 -9999 0 -0.46 6 6
PTK2B -0.009 0.11 -9999 0 -0.34 34 34
RHOA 0.016 0.059 -9999 0 -0.34 6 6
PIK3CB 0.014 0.025 -9999 0 -0.62 1 1
mol:Ca2+ 0.014 0.084 -9999 0 -0.39 6 6
MAGI3 0.009 0.06 -9999 0 -0.62 6 6
RELA 0.015 0 -9999 0 -10000 0 0
apoptosis -0.037 0.14 -9999 0 -0.36 68 68
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.12 -9999 0 -0.36 36 36
NF kappa B1 p50/RelA -0.061 0.13 -9999 0 -0.51 31 31
endothelial cell migration -0.047 0.2 -9999 0 -0.48 106 106
ADCY4 -0.027 0.17 -9999 0 -0.44 73 73
ADCY5 -0.047 0.2 -9999 0 -0.47 102 102
ADCY6 -0.025 0.17 -9999 0 -0.44 73 73
ADCY7 -0.025 0.17 -9999 0 -0.45 73 73
ADCY1 -0.052 0.18 -9999 0 -0.46 91 91
ADCY2 -0.04 0.19 -9999 0 -0.46 91 91
ADCY3 -0.025 0.17 -9999 0 -0.44 73 73
ADCY8 -0.046 0.2 -9999 0 -0.51 85 85
ADCY9 -0.026 0.17 -9999 0 -0.44 73 73
GSK3B 0 0.1 -9999 0 -0.36 23 23
arachidonic acid secretion -0.018 0.16 -9999 0 -0.41 73 73
GNG2 0.009 0.06 -9999 0 -0.62 6 6
TRIP6 0.015 0.063 -9999 0 -0.39 10 10
GNAO1 -0.042 0.16 -9999 0 -0.41 93 93
HRAS 0.015 0 -9999 0 -10000 0 0
NFKBIA 0.003 0.12 -9999 0 -0.44 17 17
GAB1 0.014 0.025 -9999 0 -0.62 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.075 -9999 0 -1 3 3
JUN 0.008 0.067 -9999 0 -0.6 8 8
LPA/LPA2/NHERF2 -0.009 0.044 -9999 0 -0.38 8 8
TIAM1 -0.006 0.097 -9999 0 -1.4 3 3
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
mol:IP3 0.014 0.085 -9999 0 -0.4 6 6
PLCB3 0.024 0.047 -9999 0 -0.34 9 9
FOS -0.074 0.22 -9999 0 -0.61 95 95
positive regulation of mitosis -0.018 0.16 -9999 0 -0.41 73 73
LPA/LPA1-2-3 -0.075 0.16 -9999 0 -0.38 119 119
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.014 0.025 -9999 0 -0.62 1 1
stress fiber formation -0.011 0.12 -9999 0 -0.38 32 32
GNAZ -0.027 0.15 -9999 0 -0.4 70 70
EGFR/PI3K-beta/Gab1 -0.11 0.17 -9999 0 -0.55 51 51
positive regulation of dendritic cell cytokine production -0.075 0.15 -9999 0 -0.37 119 119
LPA/LPA2/MAGI-3 -0.012 0.056 -9999 0 -0.38 14 14
ARHGEF1 -0.004 0.12 -9999 0 -0.58 7 7
GNAI2 -0.025 0.14 -9999 0 -0.38 77 77
GNAI3 -0.025 0.14 -9999 0 -0.4 68 68
GNAI1 -0.047 0.17 -9999 0 -0.41 102 102
LPA/LPA3 -0.038 0.12 -9999 0 -0.45 50 50
LPA/LPA2 -0.011 0.054 -9999 0 -0.45 8 8
LPA/LPA1 -0.064 0.16 -9999 0 -0.4 106 106
HB-EGF/EGFR -0.22 0.27 -9999 0 -0.46 340 340
HBEGF -0.18 0.24 -9999 0 -0.44 288 288
mol:DAG 0.014 0.085 -9999 0 -0.4 6 6
cAMP biosynthetic process -0.033 0.18 -9999 0 -0.45 85 85
NFKB1 0.015 0 -9999 0 -10000 0 0
SRC 0.013 0.035 -9999 0 -0.62 2 2
GNB1 0.015 0.001 -9999 0 -10000 0 0
LYN 0.001 0.13 -9999 0 -0.47 19 19
GNAQ -0.004 0.085 -9999 0 -0.34 16 16
LPAR2 0.007 0.069 -9999 0 -0.62 8 8
LPAR3 -0.037 0.16 -9999 0 -0.59 50 50
LPAR1 -0.054 0.2 -9999 0 -0.62 68 68
IL8 -0.23 0.24 -9999 0 -0.48 277 277
PTK2 -0.036 0.16 -9999 0 -0.48 31 31
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.038 0.14 -9999 0 -0.37 68 68
EGFR -0.11 0.25 -9999 0 -0.6 138 138
PLCG1 -0.003 0.089 -9999 0 -0.32 19 19
PLD2 -0.037 0.16 -9999 0 -0.39 72 72
G12/G13 -0.048 0.12 -9999 0 -0.36 68 68
PI3K-beta -0.037 0.094 -9999 0 -0.46 13 13
cell migration -0.023 0.056 -9999 0 -0.27 6 6
SLC9A3R2 0.015 0 -9999 0 -10000 0 0
PXN -0.012 0.13 -9999 0 -0.39 32 32
HRAS/GTP -0.019 0.16 -9999 0 -0.42 73 73
RAC1 0.015 0 -9999 0 -10000 0 0
MMP9 -0.25 0.3 -9999 0 -0.6 285 285
PRKCE 0.002 0.09 -9999 0 -0.59 15 15
PRKCD 0.01 0.1 -9999 0 -0.41 14 14
Gi(beta/gamma) -0.021 0.16 -9999 0 -0.42 75 75
mol:LPA -0.006 0.043 -9999 0 -0.2 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.059 0.13 -9999 0 -0.53 21 21
MAPKKK cascade -0.018 0.16 -9999 0 -0.41 73 73
contractile ring contraction involved in cytokinesis 0.016 0.058 -9999 0 -0.34 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.016 0.1 -9999 0 -0.28 79 79
GNA15 -0.016 0.1 -9999 0 -0.34 35 35
GNA12 0.014 0.025 -9999 0 -0.62 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
MAPT -0.009 0.12 -9999 0 -0.37 36 36
GNA11 -0.009 0.094 -9999 0 -0.32 31 31
Rac1/GTP -0.003 0.082 -9999 0 -1.2 3 3
MMP2 -0.048 0.2 -9999 0 -0.48 106 106
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.077 0.16 -9999 0 -0.43 121 121
alphaV beta3 Integrin -0.068 0.14 -9999 0 -0.36 127 127
PTK2 -0.068 0.2 -9999 0 -0.52 54 54
IGF1R 0.005 0.081 -9999 0 -0.62 11 11
PI4KB 0.015 0 -9999 0 -10000 0 0
MFGE8 0.011 0.049 -9999 0 -0.62 4 4
SRC 0.013 0.035 -9999 0 -0.62 2 2
CDKN1B -0.047 0.13 -9999 0 -0.58 28 28
VEGFA -0.091 0.23 -9999 0 -0.59 118 118
ILK -0.047 0.13 -9999 0 -0.58 28 28
ROCK1 0.015 0 -9999 0 -10000 0 0
AKT1 -0.008 0.13 -9999 0 -0.54 28 28
PTK2B -0.085 0.22 -9999 0 -0.59 67 67
alphaV/beta3 Integrin/JAM-A -0.076 0.14 -9999 0 -0.64 12 12
CBL 0.014 0.025 -9999 0 -0.62 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.069 0.14 -9999 0 -0.36 127 127
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.021 0.1 -9999 0 -0.44 27 27
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.025 0.13 -9999 0 -0.45 12 12
alphaV/beta3 Integrin/Syndecan-1 -0.11 0.2 -9999 0 -0.44 165 165
PI4KA 0.009 0.061 -9999 0 -0.59 7 7
IGF-1R heterotetramer/IGF1/IRS1 -0.085 0.17 -9999 0 -0.58 48 48
PI4 Kinase -0.004 0.043 -9999 0 -0.42 7 7
PIK3CA 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.15 0.22 -9999 0 -0.44 231 231
RPS6KB1 -0.027 0.18 -9999 0 -0.54 48 48
TLN1 0.015 0 -9999 0 -10000 0 0
MAPK3 -0.068 0.13 -9999 0 -0.46 37 37
GPR124 0.01 0.057 -9999 0 -0.59 6 6
MAPK1 -0.068 0.13 -9999 0 -0.46 37 37
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
alphaV/beta3 Integrin/Tumstatin -0.13 0.2 -9999 0 -0.41 216 216
cell adhesion -0.058 0.12 -9999 0 -0.36 31 31
ANGPTL3 0.005 0.024 -9999 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.065 0.14 -9999 0 -0.36 122 122
IGF-1R heterotetramer 0.005 0.081 -9999 0 -0.62 11 11
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.04 -9999 0 -0.59 3 3
ITGB3 -0.099 0.24 -9999 0 -0.6 125 125
IGF1 -0.005 0.11 -9999 0 -0.61 22 22
RAC1 0.015 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.07 0.14 -9999 0 -0.36 129 129
apoptosis 0.014 0.025 -9999 0 -0.62 1 1
CD47 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.067 0.14 -9999 0 -0.36 126 126
VCL 0.011 0.053 -9999 0 -0.6 5 5
alphaV/beta3 Integrin/Del1 -0.12 0.2 -9999 0 -0.42 201 201
CSF1 0.004 0.085 -9999 0 -0.62 12 12
PIK3C2A -0.048 0.13 -9999 0 -0.58 28 28
PI4 Kinase/Pyk2 -0.11 0.18 -9999 0 -0.53 80 80
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.12 0.21 -9999 0 -0.53 97 97
FAK1/Vinculin -0.047 0.17 -9999 0 -0.43 35 35
alphaV beta3/Integrin/ppsTEM5 -0.071 0.15 -9999 0 -0.37 129 129
RHOA 0.015 0 -9999 0 -10000 0 0
VTN -0.017 0.14 -9999 0 -0.62 34 34
BCAR1 0.014 0.025 -9999 0 -0.62 1 1
FGF2 0.013 0.034 -9999 0 -0.61 2 2
F11R 0.019 0.061 -9999 0 -0.43 12 12
alphaV/beta3 Integrin/Lactadherin -0.07 0.14 -9999 0 -0.36 129 129
alphaV/beta3 Integrin/TGFBR2 -0.069 0.14 -9999 0 -0.36 127 127
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.053 -9999 0 -0.36 14 14
HSP90AA1 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.061 0.13 -9999 0 -0.33 126 126
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.028 0.16 -9999 0 -0.59 48 48
alphaV/beta3 Integrin/Pyk2 -0.085 0.22 -9999 0 -0.6 67 67
SDC1 -0.055 0.2 -9999 0 -0.6 77 77
VAV3 -0.08 0.17 -9999 0 -0.7 4 4
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
IRS1 0.009 0.065 -9999 0 -0.62 7 7
FAK1/Paxillin -0.045 0.17 -9999 0 -0.43 34 34
cell migration -0.032 0.16 -9999 0 -0.44 17 17
ITGAV 0.014 0.025 -9999 0 -0.62 1 1
PI3K -0.067 0.13 -9999 0 -0.58 14 14
SPP1 -0.13 0.26 -9999 0 -0.6 155 155
KDR 0.011 0.048 -9999 0 -0.61 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.025 -9999 0 -0.62 1 1
COL4A3 -0.097 0.24 -9999 0 -0.6 121 121
angiogenesis -0.019 0.16 -9999 0 -0.48 42 42
Rac1/GTP -0.098 0.13 -9999 0 -0.64 4 4
EDIL3 -0.084 0.23 -9999 0 -0.62 105 105
cell proliferation -0.069 0.14 -9999 0 -0.36 127 127
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.038 0.16 -9999 0 -0.45 47 47
CRKL 0.014 0.023 -9999 0 -0.59 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.025 -9999 0 -0.62 1 1
ITGA4 -0.07 0.21 -9999 0 -0.6 92 92
alpha4/beta7 Integrin/MAdCAM1 -0.13 0.19 -9999 0 -0.36 239 239
EPO -0.026 0.15 -9999 0 -0.59 43 43
alpha4/beta7 Integrin -0.089 0.18 -9999 0 -0.46 131 131
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.062 0.16 -9999 0 -0.45 92 92
EPO/EPOR (dimer) -0.028 0.11 -9999 0 -0.43 44 44
lamellipodium assembly 0.009 0.031 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K -0.002 0.03 -9999 0 -0.46 3 3
ARF6 0.015 0 -9999 0 -10000 0 0
JAK2 -0.013 0.11 -9999 0 -0.39 11 11
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
MADCAM1 -0.11 0.24 -9999 0 -0.6 133 133
cell adhesion -0.13 0.19 -9999 0 -0.36 239 239
CRKL/CBL -0.001 0.024 -9999 0 -0.44 2 2
ITGB1 0.012 0.04 -9999 0 -0.59 3 3
SRC -0.087 0.19 -9999 0 -0.37 152 152
ITGB7 -0.027 0.16 -9999 0 -0.61 45 45
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.13 0.19 -9999 0 -0.4 216 216
p130Cas/Crk/Dock1 -0.05 0.17 -9999 0 -0.57 17 17
VCAM1 -0.11 0.26 -9999 0 -0.62 137 137
RHOA 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.046 0.12 -9999 0 -0.36 44 44
BCAR1 -0.072 0.18 -9999 0 -0.63 16 16
EPOR 0.014 0.023 -9999 0 -0.59 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.025 -9999 0 -0.62 1 1
GIT1 0.014 0.025 -9999 0 -0.62 1 1
Rac1/GTP 0.009 0.031 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.011 0.049 -10000 0 -0.62 4 4
HDAC3 0.015 0 -10000 0 -10000 0 0
VDR -0.11 0.24 -10000 0 -0.6 132 132
Cbp/p300/PCAF -0.004 0.038 -10000 0 -0.38 7 7
EP300 0.012 0.043 -10000 0 -0.62 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.02 0.064 -10000 0 -0.41 6 6
KAT2B 0.012 0.042 -10000 0 -0.61 3 3
MAPK14 0.014 0.023 -10000 0 -0.59 1 1
AKT1 0.033 0.086 0.23 17 -0.37 3 20
RAR alpha/9cRA/Cyclin H -0.052 0.08 -10000 0 -0.49 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.017 0.069 -10000 0 -0.45 6 6
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.06 0.094 -10000 0 -0.5 10 10
NCOR2 0.013 0.035 -10000 0 -0.62 2 2
VDR/VDR/Vit D3 -0.088 0.18 -10000 0 -0.44 132 132
RXRs/RARs/NRIP1/9cRA -0.056 0.21 -10000 0 -0.46 108 108
NCOA2 -0.019 0.14 -10000 0 -0.62 36 36
NCOA3 0.015 0 -10000 0 -10000 0 0
NCOA1 0.015 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.11 0.24 -10000 0 -0.6 132 132
RARG 0.013 0.047 -10000 0 -0.59 4 4
RAR gamma1/9cRA -0.002 0.028 -10000 0 -0.36 4 4
MAPK3 0.016 0 -10000 0 -10000 0 0
MAPK1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.008 0.074 -10000 0 -0.62 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.18 0.24 -10000 0 -0.59 134 134
RARA -0.047 0.12 -10000 0 -0.26 119 119
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.093 -10000 0 -0.38 19 19
PRKCA 0.017 0.035 -10000 0 -0.62 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.076 0.21 -10000 0 -0.49 110 110
RXRG -0.15 0.24 -10000 0 -0.46 175 175
RXRA -0.032 0.11 -10000 0 -0.42 3 3
RXRB -0.077 0.16 -10000 0 -0.36 110 110
VDR/Vit D3/DNA -0.088 0.18 -10000 0 -0.44 132 132
RBP1 -0.18 0.28 -10000 0 -0.59 211 211
CRBP1/9-cic-RA -0.14 0.2 -10000 0 -0.44 211 211
RARB 0.013 0.053 -10000 0 -0.59 5 5
PRKCG -0.19 0.3 -10000 0 -0.6 230 230
MNAT1 0.014 0.023 -10000 0 -0.59 1 1
RAR alpha/RXRs -0.048 0.22 -10000 0 -0.48 108 108
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.041 0.18 -10000 0 -0.39 108 108
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.096 -10000 0 -0.4 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.076 0.21 -10000 0 -0.49 110 110
positive regulation of DNA binding -0.05 0.076 -10000 0 -0.46 2 2
NRIP1 -0.066 0.19 -10000 0 -0.6 36 36
RXRs/RARs -0.083 0.21 -10000 0 -0.49 110 110
RXRs/RXRs/DNA/9cRA -0.13 0.21 -10000 0 -0.55 110 110
PRKACA 0.015 0 -10000 0 -10000 0 0
CDK7 0.015 0 -10000 0 -10000 0 0
TFIIH -0.001 0.014 -10000 0 -0.35 1 1
RAR alpha/9cRA -0.036 0.055 -10000 0 -0.42 1 1
CCNH 0.015 0 -10000 0 -10000 0 0
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
RAR gamma2/9cRA -0.002 0.024 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.015 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.007 0.06 -9999 0 -0.52 6 6
Syndecan-3/Neurocan -0.024 0.098 -9999 0 -0.36 45 45
POMC -0.004 0.11 -9999 0 -0.61 21 21
EGFR -0.11 0.25 -9999 0 -0.6 138 138
Syndecan-3/EGFR -0.065 0.13 -9999 0 -0.31 141 141
AGRP -0.001 0.083 -9999 0 -0.59 13 13
NCSTN 0.015 0 -9999 0 -10000 0 0
PSENEN 0.015 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0 -9999 0 -10000 0 0
APH1A 0.015 0 -9999 0 -10000 0 0
NCAN -0.028 0.16 -9999 0 -0.62 45 45
long-term memory -0.003 0.039 -9999 0 -0.57 3 3
Syndecan-3/IL8 -0.12 0.15 -9999 0 -0.3 258 258
PSEN1 0.015 0 -9999 0 -10000 0 0
Src/Cortactin -0.001 0.025 -9999 0 -0.46 2 2
FYN 0.015 0 -9999 0 -10000 0 0
limb bud formation -0.004 0.044 -9999 0 -0.47 5 5
MC4R -0.1 0.24 -9999 0 -0.61 126 126
SRC 0.013 0.035 -9999 0 -0.62 2 2
PTN 0.007 0.071 -9999 0 -0.6 9 9
FGFR/FGF/Syndecan-3 -0.004 0.045 -9999 0 -0.48 5 5
neuron projection morphogenesis -0.025 0.1 -9999 0 -0.7 8 8
Syndecan-3/AgRP -0.009 0.058 -9999 0 -0.35 16 16
Syndecan-3/AgRP/MC4R -0.063 0.13 -9999 0 -0.33 80 80
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.004 0.045 -9999 0 -0.48 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.15 -9999 0 -0.3 258 258
IL8 -0.22 0.3 -9999 0 -0.6 256 256
Syndecan-3/Fyn/Cortactin -0.003 0.04 -9999 0 -0.59 3 3
Syndecan-3/CASK -0.003 0.043 -9999 0 -0.46 5 5
alpha-MSH/MC4R -0.096 0.19 -9999 0 -0.46 141 141
Gamma Secretase 0 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0.043 -9999 0 -0.62 3 3
ELF1 -0.067 0.14 -9999 0 -0.35 75 75
CCNA2 -0.074 0.22 -9999 0 -0.6 97 97
PIK3CA 0.016 0.001 -9999 0 -10000 0 0
JAK3 -0.056 0.2 -9999 0 -0.6 78 78
PIK3R1 0.013 0.043 -9999 0 -0.62 3 3
JAK1 0.016 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.063 0.19 -9999 0 -0.52 48 48
SHC1 0.002 0.092 -9999 0 -0.59 16 16
SP1 0.019 0.043 -9999 0 -0.35 6 6
IL2RA -0.16 0.32 -9999 0 -0.64 193 193
IL2RB -0.11 0.25 -9999 0 -0.6 140 140
SOS1 0.016 0.001 -9999 0 -10000 0 0
IL2RG -0.038 0.17 -9999 0 -0.6 58 58
G1/S transition of mitotic cell cycle -0.044 0.19 -9999 0 -0.52 63 63
PTPN11 0.014 0.035 -9999 0 -0.62 2 2
CCND2 0.024 0.098 -9999 0 -0.68 12 12
LCK -0.097 0.24 -9999 0 -0.6 123 123
GRB2 0.015 0.023 -9999 0 -0.59 1 1
IL2 0.001 0.003 -9999 0 -10000 0 0
CDK6 -0.037 0.17 -9999 0 -0.6 57 57
CCND3 -0.044 0.17 -9999 0 -0.53 16 16
EGFR-dependent Endothelin signaling events

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
HRAS 0.015 0 -9999 0 -10000 0 0
EGFR -0.11 0.25 -9999 0 -0.6 138 138
EGF/EGFR -0.12 0.17 -9999 0 -0.37 131 131
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.094 0.16 -9999 0 -0.64 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.011 0.12 -9999 0 -0.61 28 28
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.038 0.18 -9999 0 -0.61 57 57
EGF/EGFR dimer/SHC -0.11 0.19 -9999 0 -0.4 192 192
mol:GDP -0.093 0.16 -9999 0 -0.64 18 18
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.023 0.15 -9999 0 -0.6 41 41
GRB2/SOS1 -0.001 0.016 -9999 0 -0.42 1 1
HRAS/GTP -0.085 0.14 -9999 0 -0.59 18 18
SHC1 0.001 0.092 -9999 0 -0.59 16 16
HRAS/GDP -0.086 0.15 -9999 0 -0.6 18 18
FRAP1 -0.058 0.17 -9999 0 -0.61 18 18
EGF/EGFR dimer -0.13 0.21 -9999 0 -0.46 183 183
SOS1 0.015 0 -9999 0 -10000 0 0
GRB2 0.014 0.023 -9999 0 -0.59 1 1
ETA receptor/Endothelin-1 -0.045 0.14 -9999 0 -0.45 66 66
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.069 0.14 -9999 0 -0.66 11 11
SMAD6-7/SMURF1 -0.004 0.041 -9999 0 -0.37 8 8
NOG -0.094 0.24 -9999 0 -0.62 116 116
SMAD9 -0.053 0.16 -9999 0 -0.58 51 51
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD5 0.004 0.11 -9999 0 -0.46 17 17
BMP7/USAG1 -0.093 0.18 -9999 0 -0.44 140 140
SMAD5/SKI 0.012 0.11 -9999 0 -0.43 17 17
SMAD1 0.045 0.043 -9999 0 -0.33 1 1
BMP2 -0.098 0.24 -9999 0 -0.62 119 119
SMAD1/SMAD1/SMAD4 -0.006 0.033 -9999 0 -0.37 1 1
BMPR1A 0.014 0.025 -9999 0 -0.62 1 1
BMPR1B -0.016 0.14 -9999 0 -0.62 33 33
BMPR1A-1B/BAMBI -0.024 0.097 -9999 0 -0.4 39 39
AHSG -0.066 0.21 -9999 0 -0.61 86 86
CER1 -0.034 0.15 -9999 0 -0.59 47 47
BMP2-4/CER1 -0.1 0.21 -9999 0 -0.45 157 157
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.14 -9999 0 -0.45 38 38
BMP2-4 (homodimer) -0.096 0.21 -9999 0 -0.51 126 126
RGMB 0.009 0.063 -9999 0 -0.6 7 7
BMP6/BMPR2/BMPR1A-1B -0.029 0.1 -9999 0 -0.37 42 42
RGMA 0.002 0.091 -9999 0 -0.62 14 14
SMURF1 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.14 -9999 0 -0.44 37 37
BMP2-4/USAG1 -0.15 0.23 -9999 0 -0.45 224 224
SMAD6/SMURF1/SMAD5 0.012 0.11 -9999 0 -0.43 17 17
SOSTDC1 -0.11 0.24 -9999 0 -0.6 132 132
BMP7/BMPR2/BMPR1A-1B -0.023 0.089 -9999 0 -0.35 43 43
SKI 0.015 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.007 0.12 -9999 0 -0.6 24 24
HFE2 0.002 0.073 -9999 0 -0.59 10 10
ZFYVE16 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.088 0.18 -9999 0 -0.43 138 138
SMAD5/SMAD5/SMAD4 0.012 0.11 -9999 0 -0.43 17 17
MAPK1 0.015 0 -9999 0 -10000 0 0
TAK1/TAB family -0.044 0.095 -9999 0 -0.37 34 34
BMP7 (homodimer) 0.005 0.081 -9999 0 -0.62 11 11
NUP214 0.015 0 -9999 0 -10000 0 0
BMP6/FETUA -0.073 0.16 -9999 0 -0.44 109 109
SMAD1/SKI 0.052 0.041 -9999 0 -10000 0 0
SMAD6 0.01 0.059 -9999 0 -0.61 6 6
CTDSP2 0.001 0.092 -9999 0 -0.59 16 16
BMP2-4/FETUA -0.13 0.22 -9999 0 -0.44 195 195
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.28 -9999 0 -0.61 195 195
BMPR2 (homodimer) 0.015 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.005 0.04 -9999 0 -0.35 9 9
BMPR1A-1B (homodimer) -0.023 0.1 -9999 0 -0.46 34 34
CHRDL1 -0.073 0.22 -9999 0 -0.62 93 93
ENDOFIN/SMAD1 0.052 0.041 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.039 -9999 0 -0.42 1 1
SMAD6/SMURF1 0.015 0 -9999 0 -10000 0 0
BAMBI 0.008 0.067 -9999 0 -0.6 8 8
SMURF2 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.23 -9999 0 -0.46 193 193
BMP2-4/GREM1 -0.19 0.24 -9999 0 -0.44 281 281
SMAD7 0.013 0.035 -9999 0 -0.62 2 2
SMAD8A/SMAD8A/SMAD4 -0.021 0.16 -9999 0 -0.54 51 51
SMAD1/SMAD6 0.052 0.041 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.005 0.081 -9999 0 -0.62 11 11
BMP6 -0.007 0.12 -9999 0 -0.6 24 24
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.011 0.13 -9999 0 -0.4 39 39
PPM1A 0.015 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.052 0.041 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.025 -9999 0 -0.46 2 2
CTDSPL 0.014 0.025 -9999 0 -0.62 1 1
PPP1CA 0.014 0.023 -9999 0 -0.59 1 1
XIAP 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.015 0 -9999 0 -10000 0 0
PPP1R15A 0.008 0.065 -9999 0 -0.59 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.18 -9999 0 -0.47 64 64
CHRD 0.003 0.088 -9999 0 -0.62 13 13
BMPR2 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.026 0.15 -9999 0 -0.48 37 37
BMP4 -0.009 0.12 -9999 0 -0.62 25 25
FST -0.084 0.23 -9999 0 -0.61 107 107
BMP2-4/NOG -0.14 0.26 -9999 0 -0.52 186 186
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.021 0.082 -9999 0 -0.64 2 2
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.003 0.15 -10000 0 -1.3 9 9
VDR -0.11 0.24 -10000 0 -0.6 132 132
FAM120B 0.014 0.023 -10000 0 -0.59 1 1
RXRs/LXRs/DNA/9cRA -0.035 0.16 -10000 0 -0.45 34 34
RXRs/LXRs/DNA/Oxysterols -0.049 0.2 -10000 0 -0.61 32 32
MED1 0.015 0 -10000 0 -10000 0 0
mol:9cRA -0.004 0.022 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.026 0.075 -10000 0 -0.61 3 3
RXRs/NUR77 -0.039 0.16 -10000 0 -0.36 115 115
RXRs/PPAR -0.021 0.13 -10000 0 -0.37 33 33
NCOR2 0.013 0.035 -10000 0 -0.62 2 2
VDR/VDR/Vit D3 -0.088 0.18 -10000 0 -0.44 132 132
RARs/VDR/DNA/Vit D3 -0.064 0.13 -10000 0 -0.35 53 53
RARA 0.015 0 -10000 0 -10000 0 0
NCOA1 0.015 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.11 0.24 -10000 0 -0.6 132 132
RARs/RARs/DNA/9cRA -0.004 0.043 -10000 0 -0.4 7 7
RARG 0.012 0.046 -10000 0 -0.59 4 4
RPS6KB1 0.024 0.066 -10000 0 -0.41 9 9
RARs/THRs/DNA/SMRT 0.025 0.077 -10000 0 -0.61 3 3
THRA 0.001 0.095 -10000 0 -0.62 15 15
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.088 0.18 -10000 0 -0.44 132 132
RXRs/PPAR/9cRA/PGJ2/DNA -0.04 0.16 0.31 4 -0.36 111 115
NR1H4 -0.12 0.25 -10000 0 -0.6 142 142
RXRs/LXRs/DNA -0.022 0.16 -10000 0 -0.45 29 29
NR1H2 0.015 0.015 -10000 0 -10000 0 0
NR1H3 0.014 0.018 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.091 0.2 -10000 0 -0.4 156 156
NR4A1 -0.009 0.12 -10000 0 -0.59 27 27
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.065 0.15 -10000 0 -0.35 90 90
RXRG -0.091 0.24 -10000 0 -0.62 111 111
RXR alpha/CCPG 0.02 0.028 -10000 0 -0.43 2 2
RXRA 0.014 0.029 -10000 0 -0.62 1 1
RXRB 0.014 0.018 -10000 0 -10000 0 0
THRB -0.008 0.12 -10000 0 -0.6 25 25
PPARG -0.015 0.13 -10000 0 -0.61 32 32
PPARD 0.015 0 -10000 0 -10000 0 0
TNF -0.14 0.39 -10000 0 -1 88 88
mol:Oxysterols -0.003 0.02 -10000 0 -10000 0 0
cholesterol transport -0.048 0.2 -10000 0 -0.61 32 32
PPARA 0.015 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.011 0.053 -10000 0 -0.6 5 5
RXRs/NUR77/BCL2 -0.024 0.12 -10000 0 -0.29 105 105
SREBF1 -0.045 0.23 -10000 0 -0.86 24 24
RXRs/RXRs/DNA/9cRA -0.04 0.16 0.3 4 -0.36 111 115
ABCA1 -0.049 0.24 -10000 0 -0.88 30 30
RARs/THRs -0.022 0.089 -10000 0 -0.82 3 3
RXRs/FXR -0.1 0.21 -10000 0 -0.42 160 160
BCL2 0.012 0.043 -10000 0 -0.62 3 3
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.028 0.14 -10000 0 -0.38 55 55
IKBKB -0.005 0.075 -10000 0 -0.28 12 12
AKT1 -0.046 0.1 -10000 0 -0.26 41 41
IKBKG -0.003 0.079 -10000 0 -0.29 14 14
CALM1 -0.043 0.14 -10000 0 -0.41 60 60
PIK3CA 0.015 0 -10000 0 -10000 0 0
MAP3K1 -0.056 0.18 -10000 0 -0.51 65 65
MAP3K7 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.15 -10000 0 -0.42 71 71
DOK1 0.014 0.025 -10000 0 -0.62 1 1
AP-1 -0.02 0.097 -10000 0 -0.27 29 29
LYN 0.011 0.053 -10000 0 -0.6 5 5
BLNK -0.036 0.17 -10000 0 -0.62 54 54
SHC1 0.001 0.092 -10000 0 -0.59 16 16
BCR complex -0.084 0.19 -10000 0 -0.48 118 118
CD22 -0.18 0.22 -10000 0 -0.53 129 129
CAMK2G -0.033 0.14 -10000 0 -0.53 24 24
CSNK2A1 0.015 0 -10000 0 -10000 0 0
INPP5D 0.007 0.071 -10000 0 -0.6 9 9
SHC/GRB2/SOS1 -0.085 0.16 -10000 0 -0.61 38 38
GO:0007205 -0.056 0.16 -10000 0 -0.42 71 71
SYK -0.004 0.11 -10000 0 -0.62 20 20
ELK1 -0.044 0.15 -10000 0 -0.42 60 60
NFATC1 -0.054 0.17 -10000 0 -0.5 63 63
B-cell antigen/BCR complex -0.084 0.19 -10000 0 -0.48 118 118
PAG1/CSK -0.001 0.018 -10000 0 -0.46 1 1
NFKBIB 0.01 0.028 -10000 0 -10000 0 0
HRAS -0.035 0.15 -10000 0 -0.49 36 36
NFKBIA 0.01 0.028 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.016 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.17 0.21 -10000 0 -0.64 62 62
mol:GDP -0.049 0.15 0.23 2 -0.42 61 63
PTEN 0.015 0 -10000 0 -10000 0 0
CD79B -0.06 0.2 -10000 0 -0.6 81 81
NF-kappa-B/RelA/I kappa B alpha 0.016 0.023 -10000 0 -10000 0 0
GRB2 0.014 0.023 -10000 0 -0.59 1 1
PI3K/BCAP/CD19 -0.079 0.19 -10000 0 -0.52 75 75
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
mol:IP3 -0.061 0.16 -10000 0 -0.43 71 71
CSK 0.015 0 -10000 0 -10000 0 0
FOS -0.075 0.18 -10000 0 -0.52 51 51
CHUK -0.003 0.079 -10000 0 -0.29 15 15
IBTK 0.015 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.054 0.13 -10000 0 -0.54 28 28
PTPN6 -0.17 0.21 -10000 0 -0.52 124 124
RELA 0.015 0 -10000 0 -10000 0 0
BCL2A1 -0.008 0.051 -10000 0 -0.1 88 88
VAV2 -0.11 0.19 -10000 0 -0.62 56 56
ubiquitin-dependent protein catabolic process 0.015 0.027 -10000 0 -10000 0 0
BTK -0.039 0.2 0.37 4 -1.1 21 25
CD19 -0.11 0.19 -10000 0 -0.58 65 65
MAP4K1 -0.011 0.13 -10000 0 -0.62 28 28
CD72 -0.019 0.14 -10000 0 -0.59 38 38
PAG1 0.014 0.025 -10000 0 -0.62 1 1
MAPK14 -0.039 0.16 -10000 0 -0.44 60 60
SH3BP5 0.011 0.049 -10000 0 -0.62 4 4
PIK3AP1 -0.054 0.18 0.25 2 -0.51 59 61
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.049 0.2 -10000 0 -0.57 59 59
RAF1 -0.024 0.14 -10000 0 -0.51 27 27
RasGAP/p62DOK/SHIP -0.16 0.2 -10000 0 -0.62 64 64
CD79A -0.031 0.16 -10000 0 -0.6 50 50
re-entry into mitotic cell cycle -0.021 0.097 -10000 0 -0.27 29 29
RASA1 0.015 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.12 -10000 0 -0.45 20 20
MAPK1 -0.002 0.12 -10000 0 -0.45 20 20
CD72/SHP1 -0.15 0.23 -10000 0 -0.53 121 121
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 -0.042 0.16 -10000 0 -0.44 66 66
actin cytoskeleton organization -0.062 0.18 -10000 0 -0.52 54 54
NF-kappa-B/RelA 0.037 0.044 -10000 0 -10000 0 0
Calcineurin -0.049 0.11 -10000 0 -0.49 23 23
PI3K -0.13 0.17 -10000 0 -0.53 66 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.071 0.16 0.25 2 -0.46 71 73
SOS1 0.015 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.1 0.26 -10000 0 -0.78 71 71
DAPP1 -0.13 0.28 -10000 0 -0.89 65 65
cytokine secretion -0.049 0.16 -10000 0 -0.46 63 63
mol:DAG -0.061 0.16 -10000 0 -0.43 71 71
PLCG2 0.004 0.083 -10000 0 -0.61 12 12
MAP2K1 -0.013 0.13 -10000 0 -0.5 22 22
B-cell antigen/BCR complex/FcgammaRIIB -0.2 0.24 -10000 0 -0.44 305 305
mol:PI-3-4-5-P3 -0.098 0.12 -10000 0 -0.37 61 61
ETS1 -0.024 0.13 -10000 0 -0.48 24 24
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.095 0.19 -10000 0 -0.7 36 36
B-cell antigen/BCR complex/LYN -0.11 0.18 -10000 0 -0.52 79 79
MALT1 0.015 0 -10000 0 -10000 0 0
TRAF6 0.013 0.035 -10000 0 -0.62 2 2
RAC1 -0.067 0.19 -10000 0 -0.57 52 52
B-cell antigen/BCR complex/LYN/SYK -0.17 0.23 -10000 0 -0.64 86 86
CARD11 -0.052 0.17 -10000 0 -0.47 65 65
FCGR2B -0.21 0.3 -10000 0 -0.6 244 244
PPP3CA 0.013 0.033 -10000 0 -0.59 2 2
BCL10 0.015 0 -10000 0 -10000 0 0
IKK complex 0.006 0.036 -10000 0 -0.12 2 2
PTPRC -0.025 0.15 -10000 0 -0.61 43 43
PDPK1 -0.047 0.098 -10000 0 -0.26 42 42
PPP3CB 0.013 0.033 -10000 0 -0.59 2 2
PPP3CC 0.015 0 -10000 0 -10000 0 0
POU2F2 0.016 0.024 -10000 0 -0.11 11 11
ErbB2/ErbB3 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
USP8 0.02 0.016 -10000 0 -0.36 1 1
RAS family/GTP -0.071 0.17 -10000 0 -0.55 41 41
NFATC4 -0.059 0.14 -10000 0 -0.4 46 46
ERBB2IP 0.016 0.025 -10000 0 -0.62 1 1
HSP90 (dimer) 0.015 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.09 0.16 -10000 0 -0.52 33 33
JUN -0.009 0.099 -10000 0 -0.37 20 20
HRAS 0.015 0.001 -10000 0 -10000 0 0
DOCK7 -0.082 0.16 -10000 0 -0.51 36 36
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.14 0.2 -10000 0 -0.42 164 164
AKT1 0.011 0.018 -10000 0 -0.43 1 1
BAD 0.022 0.015 -10000 0 -0.36 1 1
MAPK10 -0.052 0.074 -10000 0 -0.25 37 37
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.095 0.18 -10000 0 -0.57 33 33
RAF1 -0.062 0.17 -10000 0 -0.52 41 41
ErbB2/ErbB3/neuregulin 2 -0.057 0.14 -10000 0 -0.38 101 101
STAT3 0.001 0.059 -10000 0 -1.1 2 2
cell migration -0.013 0.099 -10000 0 -0.25 20 20
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.15 0.28 -10000 0 -0.61 131 131
FOS -0.1 0.22 -10000 0 -0.41 170 170
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.09 0.16 -10000 0 -0.52 33 33
MAPK3 -0.12 0.24 -10000 0 -0.48 154 154
MAPK1 -0.12 0.24 -10000 0 -0.5 131 131
JAK2 -0.078 0.16 -10000 0 -0.49 33 33
NF2 -0.003 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.094 0.19 -10000 0 -0.38 162 162
NRG1 -0.16 0.28 -10000 0 -0.61 181 181
GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
MAPK8 -0.067 0.15 -10000 0 -0.41 39 39
MAPK9 -0.051 0.071 -10000 0 -0.24 26 26
ERBB2 -0.007 0.059 0.4 1 -0.45 11 12
ERBB3 -0.074 0.22 -10000 0 -0.62 92 92
SHC1 0 0.092 -10000 0 -0.59 16 16
RAC1 0.015 0 -10000 0 -10000 0 0
apoptosis 0 0.017 0.33 1 -10000 0 1
STAT3 (dimer) 0.002 0.057 -10000 0 -1 2 2
RNF41 0.026 0.016 -10000 0 -0.32 1 1
FRAP1 0.01 0.015 -10000 0 -0.37 1 1
RAC1-CDC42/GTP -0.073 0.1 -10000 0 -0.34 36 36
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.049 0.27 1 -0.37 11 12
CHRNA1 -0.15 0.28 -10000 0 -0.58 163 163
myelination -0.05 0.14 -10000 0 -0.38 47 47
PPP3CB -0.074 0.15 -10000 0 -0.45 35 35
KRAS 0.014 0.023 -10000 0 -0.59 1 1
RAC1-CDC42/GDP -0.065 0.17 -10000 0 -0.55 42 42
NRG2 0.009 0.065 -10000 0 -0.62 7 7
mol:GDP -0.093 0.19 -10000 0 -0.37 162 162
SOS1 0.015 0.001 -10000 0 -10000 0 0
MAP2K2 -0.059 0.17 -10000 0 -0.48 41 41
SRC 0.013 0.035 -10000 0 -0.62 2 2
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.08 0.16 -10000 0 -0.49 34 34
MAP2K1 -0.12 0.23 -10000 0 -0.52 100 100
heart morphogenesis -0.09 0.16 -10000 0 -0.52 33 33
RAS family/GDP -0.069 0.17 -10000 0 -0.55 40 40
GRB2 0.014 0.023 -10000 0 -0.59 1 1
PRKACA -0.007 0.009 -10000 0 -10000 0 0
CHRNE 0.007 0.042 -10000 0 -0.2 20 20
HSP90AA1 0.015 0 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.018 0.43 1 -10000 0 1
nervous system development -0.09 0.16 -10000 0 -0.52 33 33
CDC42 0.015 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.013 0.12 -9999 0 -0.37 72 72
EPHB2 0.007 0.071 -9999 0 -0.6 9 9
Syndecan-2/TACI -0.01 0.088 -9999 0 -0.38 34 34
LAMA1 -0.071 0.22 -9999 0 -0.62 91 91
Syndecan-2/alpha2 ITGB1 -0.071 0.15 -9999 0 -0.65 20 20
HRAS 0.015 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.015 0.073 -9999 0 -0.38 26 26
ITGA5 -0.026 0.15 -9999 0 -0.59 46 46
BAX 0.029 0.081 -9999 0 -10000 0 0
EPB41 0.01 0.054 -9999 0 -0.62 5 5
positive regulation of cell-cell adhesion -0.013 0.065 -9999 0 -0.33 26 26
LAMA3 -0.054 0.2 -9999 0 -0.61 74 74
EZR 0.009 0.06 -9999 0 -0.62 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.04 0.17 -9999 0 -0.59 61 61
Syndecan-2/MMP2 -0.012 0.13 -9999 0 -0.39 65 65
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.038 0.12 -9999 0 -0.45 57 57
dendrite morphogenesis 0.009 0.09 -9999 0 -0.38 34 34
Syndecan-2/GM-CSF -0.016 0.085 -9999 0 -0.38 33 33
determination of left/right symmetry 0.006 0.09 -9999 0 -0.44 26 26
Syndecan-2/PKC delta -0.001 0.12 -9999 0 -0.42 44 44
GNB2L1 0.015 0 -9999 0 -10000 0 0
MAPK3 0.011 0.08 -9999 0 -0.34 33 33
MAPK1 0.011 0.08 -9999 0 -0.34 33 33
Syndecan-2/RACK1 -0.012 0.06 -9999 0 -0.31 26 26
NF1 0.01 0.055 -9999 0 -0.62 5 5
FGFR/FGF/Syndecan-2 0.006 0.09 -9999 0 -0.44 26 26
ITGA2 -0.036 0.17 -9999 0 -0.61 55 55
MAPK8 0.02 0.09 -9999 0 -0.36 35 35
Syndecan-2/alpha2/beta1 Integrin -0.08 0.17 -9999 0 -0.61 30 30
Syndecan-2/Kininogen -0.02 0.1 -9999 0 -0.36 51 51
ITGB1 0.012 0.04 -9999 0 -0.59 3 3
SRC 0.03 0.07 -9999 0 -0.32 19 19
Syndecan-2/CASK/Protein 4.1 -0.016 0.073 -9999 0 -0.35 30 30
extracellular matrix organization 0.008 0.096 -9999 0 -0.4 33 33
actin cytoskeleton reorganization -0.013 0.12 -9999 0 -0.37 72 72
Syndecan-2/Caveolin-2/Ras -0.041 0.12 -9999 0 -0.34 81 81
Syndecan-2/Laminin alpha3 -0.03 0.15 -9999 0 -0.4 92 92
Syndecan-2/RasGAP -0.011 0.055 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.031 0.12 -9999 0 -0.45 46 46
PRKCD -0.008 0.12 -9999 0 -0.62 24 24
Syndecan-2 dimer 0.009 0.091 -9999 0 -0.38 34 34
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.069 -9999 0 -0.57 2 2
RHOA 0.015 0 -9999 0 -10000 0 0
SDCBP 0.015 0 -9999 0 -10000 0 0
TNFRSF13B -0.003 0.069 -9999 0 -0.59 9 9
RASA1 0.015 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.038 0.12 -9999 0 -0.45 57 57
Syndecan-2/Synbindin 0.014 0.077 -9999 0 -0.37 26 26
TGFB1 0.006 0.077 -9999 0 -0.62 10 10
CASP3 0.011 0.11 -9999 0 -0.37 46 46
FN1 -0.028 0.16 -9999 0 -0.59 48 48
Syndecan-2/IL8 -0.14 0.21 -9999 0 -0.38 270 270
SDC2 0.006 0.09 -9999 0 -0.44 26 26
KNG1 -0.018 0.11 -9999 0 -0.59 25 25
Syndecan-2/Neurofibromin 0.011 0.084 -9999 0 -0.37 31 31
TRAPPC4 0.015 0 -9999 0 -10000 0 0
CSF2 -0.006 0.064 -9999 0 -0.59 8 8
Syndecan-2/TGFB1 0.008 0.096 -9999 0 -0.4 33 33
Syndecan-2/Syntenin/PI-4-5-P2 -0.013 0.065 -9999 0 -0.34 26 26
Syndecan-2/Ezrin -0.015 0.078 -9999 0 -0.36 29 29
PRKACA 0.022 0.077 -9999 0 -0.33 31 31
angiogenesis -0.14 0.2 -9999 0 -0.38 270 270
MMP2 -0.025 0.15 -9999 0 -0.6 44 44
IL8 -0.22 0.3 -9999 0 -0.6 256 256
calcineurin-NFAT signaling pathway -0.01 0.088 -9999 0 -0.38 34 34
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.014 0.023 -9999 0 -0.59 1 1
LAT2 -0.056 0.18 -9999 0 -0.66 34 34
AP1 -0.1 0.17 -9999 0 -0.55 60 60
mol:PIP3 -0.065 0.2 -9999 0 -0.63 41 41
IKBKB -0.031 0.12 -9999 0 -0.3 40 40
AKT1 -0.053 0.17 -9999 0 -0.48 40 40
IKBKG -0.031 0.12 -9999 0 -0.3 39 39
MS4A2 -0.026 0.13 -9999 0 -0.59 32 32
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.001 -9999 0 -10000 0 0
MAP3K1 -0.016 0.15 -9999 0 -0.57 30 30
mol:Ca2+ -0.044 0.15 -9999 0 -0.44 41 41
LYN 0.009 0.055 -9999 0 -0.62 5 5
CBLB -0.044 0.14 -9999 0 -0.53 26 26
SHC1 0.001 0.092 -9999 0 -0.59 16 16
RasGAP/p62DOK -0.019 0.077 -9999 0 -0.33 39 39
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0.071 -9999 0 -0.6 9 9
PLD2 -0.094 0.19 -9999 0 -0.57 40 40
PTPN13 -0.033 0.14 -9999 0 -0.57 22 22
PTPN11 0.009 0.037 -9999 0 -0.64 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.13 -9999 0 -0.38 15 15
SYK -0.005 0.11 -9999 0 -0.64 20 20
GRB2 0.014 0.023 -9999 0 -0.59 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.18 -9999 0 -0.62 45 45
LAT -0.058 0.15 -9999 0 -0.45 49 49
PAK2 -0.028 0.17 -9999 0 -0.63 33 33
NFATC2 -0.1 0.19 -9999 0 -0.6 70 70
HRAS -0.041 0.19 -9999 0 -0.67 37 37
GAB2 0.012 0.043 -9999 0 -0.62 3 3
PLA2G1B 0.048 0.024 -9999 0 -10000 0 0
Fc epsilon R1 -0.16 0.22 -9999 0 -0.42 247 247
Antigen/IgE/Fc epsilon R1 -0.14 0.2 -9999 0 -0.38 247 247
mol:GDP -0.05 0.2 -9999 0 -0.74 37 37
JUN 0.008 0.067 -9999 0 -0.6 8 8
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.63 3 3
FOS -0.073 0.22 -9999 0 -0.61 95 95
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.08 0.14 -9999 0 -0.4 62 62
CHUK -0.031 0.12 -9999 0 -0.3 40 40
KLRG1 -0.049 0.14 -9999 0 -0.41 50 50
VAV1 -0.056 0.18 -9999 0 -0.6 41 41
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.044 0.14 -9999 0 -0.54 26 26
negative regulation of mast cell degranulation -0.041 0.14 -9999 0 -0.51 31 31
BTK -0.078 0.2 -9999 0 -0.73 38 38
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.15 0.22 -9999 0 -0.48 136 136
GAB2/PI3K/SHP2 -0.11 0.15 -9999 0 -0.53 40 40
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.063 0.16 -9999 0 -0.47 53 53
RAF1 0.036 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.24 0.26 -9999 0 -0.68 138 138
FCER1G -0.037 0.17 -9999 0 -0.61 55 55
FCER1A -0.17 0.28 -9999 0 -0.6 200 200
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.18 -9999 0 -0.42 118 118
MAPK3 0.047 0.024 -9999 0 -10000 0 0
MAPK1 0.047 0.024 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 0.005 0.086 -9999 0 -0.57 10 10
DUSP1 -0.02 0.14 -9999 0 -0.6 38 38
NF-kappa-B/RelA -0.036 0.051 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.039 0.14 -9999 0 -0.52 25 25
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.072 0.16 -9999 0 -0.68 31 31
FER -0.05 0.15 -9999 0 -0.48 40 40
RELA 0.015 0 -9999 0 -10000 0 0
ITK -0.092 0.15 -9999 0 -0.37 121 121
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG1 -0.048 0.2 -9999 0 -0.73 37 37
cytokine secretion -0.026 0.037 -9999 0 -10000 0 0
SPHK1 -0.064 0.17 -9999 0 -0.5 52 52
PTK2 -0.041 0.14 -9999 0 -0.55 25 25
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.19 -9999 0 -0.58 59 59
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.054 0.19 -9999 0 -0.61 37 37
MAP2K2 0.042 0.025 -9999 0 -10000 0 0
MAP2K1 0.042 0.025 -9999 0 -10000 0 0
MAP2K7 0.014 0.025 -9999 0 -0.62 1 1
KLRG1/SHP2 -0.072 0.12 -9999 0 -0.46 33 33
MAP2K4 0.02 0.038 -9999 0 -0.94 1 1
Fc epsilon R1/FcgammaRIIB -0.26 0.28 -9999 0 -0.52 283 283
mol:Choline -0.092 0.19 -9999 0 -0.56 40 40
SHC/Grb2/SOS1 -0.07 0.12 -9999 0 -0.49 35 35
FYN 0.015 0 -9999 0 -10000 0 0
DOK1 0.014 0.025 -9999 0 -0.62 1 1
PXN -0.03 0.13 -9999 0 -0.52 22 22
HCLS1 -0.056 0.17 -9999 0 -0.59 38 38
PRKCB -0.056 0.15 -9999 0 -0.4 60 60
FCGR2B -0.21 0.3 -9999 0 -0.6 244 244
IGHE -0.002 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.042 0.15 -9999 0 -0.52 31 31
LCP2 0.007 0.072 -9999 0 -0.61 9 9
PLA2G4A -0.058 0.16 -9999 0 -0.5 46 46
RASA1 0.015 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.092 0.19 -9999 0 -0.56 40 40
IKK complex -0.007 0.092 -9999 0 -0.24 19 19
WIPF1 0.014 0.023 -9999 0 -0.59 1 1
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.077 0.16 -9999 0 -0.43 121 121
PDGFRB 0.009 0.053 -9999 0 -0.6 5 5
SPHK1 -0.039 0.13 -9999 0 -0.74 19 19
mol:S1P -0.039 0.12 -9999 0 -0.61 22 22
S1P1/S1P/Gi -0.052 0.2 -9999 0 -0.52 54 54
GNAO1 -0.013 0.13 -9999 0 -0.63 28 28
PDGFB-D/PDGFRB/PLCgamma1 -0.034 0.18 -9999 0 -0.54 36 36
PLCG1 -0.041 0.18 -9999 0 -0.54 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.053 -9999 0 -0.59 5 5
GNAI2 0.014 0.007 -9999 0 -10000 0 0
GNAI3 0.013 0.007 -9999 0 -10000 0 0
GNAI1 -0.022 0.15 -9999 0 -0.63 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.05 0.15 -9999 0 -0.36 121 121
S1P1/S1P -0.083 0.14 -9999 0 -0.39 78 78
negative regulation of cAMP metabolic process -0.05 0.19 -9999 0 -0.5 54 54
MAPK3 -0.067 0.24 -9999 0 -0.55 100 100
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.01 0.048 -9999 0 -0.6 4 4
PLCB2 -0.042 0.15 -9999 0 -0.38 66 66
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.07 0.12 -9999 0 -0.35 61 61
receptor internalization -0.078 0.13 -9999 0 -0.37 78 78
PTGS2 -0.13 0.37 -9999 0 -0.91 106 106
Rac1/GTP -0.07 0.12 -9999 0 -0.36 49 49
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFA -0.092 0.23 -9999 0 -0.59 118 118
negative regulation of T cell proliferation -0.05 0.19 -9999 0 -0.5 54 54
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.044 -9999 0 -0.63 3 3
MAPK1 -0.067 0.24 -9999 0 -0.55 100 100
S1P1/S1P/PDGFB-D/PDGFRB -0.046 0.17 -9999 0 -0.42 64 64
ABCC1 0.012 0.041 -9999 0 -0.59 3 3
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.036 0.14 -9999 0 -0.42 39 39
FZD6 -0.033 0.16 -9999 0 -0.59 53 53
WNT6 -0.027 0.16 -9999 0 -0.6 46 46
WNT4 -0.042 0.18 -9999 0 -0.6 62 62
FZD3 0.012 0.043 -9999 0 -0.62 3 3
WNT5A -0.006 0.11 -9999 0 -0.61 23 23
WNT11 -0.024 0.15 -9999 0 -0.61 42 42
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.014 0.023 -10000 0 -0.59 1 1
RAS family/GTP/Tiam1 0.005 0.045 -10000 0 -0.34 4 4
NT3 (dimer)/TRKC -0.021 0.1 -10000 0 -0.48 29 29
NT3 (dimer)/TRKB -0.1 0.19 -10000 0 -0.42 159 159
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.044 -10000 0 -0.48 2 2
RAPGEF1 0.013 0.035 -10000 0 -0.62 2 2
BDNF -0.079 0.22 -10000 0 -0.59 104 104
PIK3CA 0.015 0 -10000 0 -10000 0 0
DYNLT1 0.01 0.058 -10000 0 -0.6 6 6
NTRK1 -0.021 0.14 -10000 0 -0.59 40 40
NTRK2 -0.046 0.19 -10000 0 -0.62 64 64
NTRK3 0.007 0.074 -10000 0 -0.62 9 9
NT-4/5 (dimer)/TRKB -0.1 0.19 -10000 0 -0.42 162 162
neuron apoptosis 0.12 0.16 0.42 98 -10000 0 98
SHC 2-3/Grb2 -0.13 0.17 -10000 0 -0.46 98 98
SHC1 0.001 0.092 -10000 0 -0.59 16 16
SHC2 -0.08 0.13 -10000 0 -0.44 47 47
SHC3 -0.14 0.21 -10000 0 -0.53 112 112
STAT3 (dimer) 0.014 0.057 -10000 0 -0.35 8 8
NT3 (dimer)/TRKA -0.085 0.17 -10000 0 -0.4 141 141
RIN/GDP -0.04 0.12 -10000 0 -0.3 29 29
GIPC1 0.014 0.023 -10000 0 -0.59 1 1
KRAS 0.014 0.023 -10000 0 -0.59 1 1
DNAJA3 -0.073 0.13 -10000 0 -0.38 63 63
RIN/GTP -0.16 0.22 -10000 0 -0.45 231 231
CCND1 0.013 0.13 -10000 0 -0.62 24 24
MAGED1 0.015 0 -10000 0 -10000 0 0
PTPN11 0.013 0.035 -10000 0 -0.62 2 2
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.015 0.11 -10000 0 -0.59 25 25
SHC/GRB2/SOS1 -0.009 0.055 -10000 0 -0.35 17 17
GRB2 0.014 0.023 -10000 0 -0.59 1 1
NGF (dimer)/TRKA/MATK -0.13 0.2 -10000 0 -0.41 208 208
TRKA/NEDD4-2 -0.033 0.12 -10000 0 -0.44 50 50
ELMO1 -0.001 0.1 -10000 0 -0.62 17 17
RhoG/GTP/ELMO1/DOCK1 -0.011 0.063 -10000 0 -0.39 18 18
NGF -0.062 0.2 -10000 0 -0.61 82 82
HRAS 0.015 0 -10000 0 -10000 0 0
DOCK1 0.014 0.025 -10000 0 -0.62 1 1
GAB2 0.012 0.043 -10000 0 -0.62 3 3
RIT2 -0.2 0.3 -10000 0 -0.61 231 231
RIT1 0.015 0 -10000 0 -10000 0 0
FRS2 0.012 0.047 -10000 0 -0.6 4 4
DNM1 -0.083 0.22 -10000 0 -0.6 107 107
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.078 0.14 -10000 0 -0.39 76 76
mol:GDP 0.038 0.095 -10000 0 -0.46 11 11
NGF (dimer) -0.062 0.2 -10000 0 -0.61 82 82
RhoG/GDP -0.012 0.073 -10000 0 -0.46 17 17
RIT1/GDP 0.037 0.066 -10000 0 -0.29 10 10
TIAM1 0.013 0.035 -10000 0 -0.62 2 2
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
BDNF (dimer)/TRKB -0.093 0.18 -10000 0 -0.4 155 155
KIDINS220/CRKL/C3G -0.002 0.03 -10000 0 -0.44 3 3
SHC/RasGAP -0.01 0.065 -10000 0 -0.42 16 16
FRS2 family/SHP2 -0.003 0.035 -10000 0 -0.37 6 6
SHC/GRB2/SOS1/GAB1 -0.008 0.054 -10000 0 -0.66 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.012 0.11 -10000 0 -0.59 24 24
RAP1/GDP -0.011 0.042 -10000 0 -0.3 7 7
KIDINS220/CRKL 0.014 0.023 -10000 0 -0.59 1 1
BDNF (dimer) -0.079 0.22 -10000 0 -0.59 104 104
ubiquitin-dependent protein catabolic process -0.072 0.16 -10000 0 -0.39 124 124
Schwann cell development -0.026 0.031 -10000 0 -10000 0 0
EHD4 0.012 0.04 -10000 0 -0.59 3 3
FRS2 family/GRB2/SOS1 -0.002 0.027 -10000 0 -0.32 5 5
FRS2 family/SHP2/CRK family/C3G/GAB2 0.044 0.048 -10000 0 -0.72 2 2
RAP1B 0.009 0.061 -10000 0 -0.59 7 7
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.083 0.16 -10000 0 -0.65 29 29
ABL1 0.014 0.025 -10000 0 -0.62 1 1
SH2B family/GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
Rap1/GTP -0.032 0.077 -10000 0 -0.64 4 4
STAT3 0.014 0.057 -10000 0 -0.35 8 8
axon guidance -0.079 0.16 -10000 0 -0.61 29 29
MAPK3 -0.086 0.2 -10000 0 -0.37 208 208
MAPK1 -0.086 0.2 -10000 0 -0.37 208 208
CDC42/GDP 0.037 0.066 -10000 0 -0.29 10 10
NTF3 -0.012 0.11 -10000 0 -0.59 24 24
NTF4 -0.016 0.11 -10000 0 -0.59 25 25
NGF (dimer)/TRKA/FAIM -0.069 0.15 -10000 0 -0.39 119 119
PI3K -0.002 0.03 -10000 0 -0.46 3 3
FRS3 0.015 0 -10000 0 -10000 0 0
FAIM 0.011 0.049 -10000 0 -0.62 4 4
GAB1 0.014 0.025 -10000 0 -0.62 1 1
RASGRF1 -0.15 0.2 -10000 0 -0.42 181 181
SOS1 0.015 0 -10000 0 -10000 0 0
MCF2L 0.004 0.11 -10000 0 -0.43 36 36
RGS19 0.015 0 -10000 0 -10000 0 0
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.088 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.066 -10000 0 -0.3 9 9
NGF (dimer)/TRKA/GRIT -0.068 0.15 -10000 0 -0.39 116 116
neuron projection morphogenesis -0.034 0.14 -10000 0 -0.51 14 14
NGF (dimer)/TRKA/NEDD4-2 -0.072 0.16 -10000 0 -0.39 124 124
MAP2K1 0.038 0.056 -10000 0 -0.61 1 1
NGFR -0.072 0.22 -10000 0 -0.6 94 94
NGF (dimer)/TRKA/GIPC/GAIP -0.04 0.14 -10000 0 -0.46 27 27
RAS family/GTP/PI3K 0.036 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.003 0.03 -10000 0 -10000 0 0
NRAS 0.015 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
PRKCI 0.015 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
MAPKKK cascade -0.075 0.18 -10000 0 -0.56 69 69
RASA1 0.015 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.026 0.1 -10000 0 -0.43 41 41
SQSTM1 0.015 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.085 0.16 -10000 0 -0.42 77 77
NGF (dimer)/TRKA/p62/Atypical PKCs -0.08 0.16 -10000 0 -0.67 18 18
MATK -0.09 0.23 -10000 0 -0.61 113 113
NEDD4L 0.005 0.079 -10000 0 -0.6 11 11
RAS family/GDP -0.009 0.037 -10000 0 -0.26 6 6
NGF (dimer)/TRKA -0.079 0.14 -10000 0 -0.41 64 64
Rac1/GTP -0.082 0.11 -10000 0 -0.33 62 62
FRS2 family/SHP2/CRK family -0.003 0.03 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.01 0.071 -9999 0 -0.37 23 23
ADCY5 -0.021 0.13 -9999 0 -0.4 71 71
ADCY6 0.015 0.058 -9999 0 -0.36 15 15
ADCY7 0.014 0.06 -9999 0 -0.37 16 16
ADCY1 -0.048 0.17 -9999 0 -0.42 108 108
ADCY2 -0.013 0.12 -9999 0 -0.39 59 59
ADCY3 0.015 0.058 -9999 0 -0.36 15 15
ADCY8 -0.025 0.13 -9999 0 -0.39 79 79
PRKCE 0.003 0.067 -9999 0 -0.44 15 15
ADCY9 0.014 0.064 -9999 0 -0.39 16 16
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.011 0.11 -9999 0 -0.38 32 32
Nongenotropic Androgen 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
PTK2 0.014 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.054 0.13 -10000 0 -0.34 108 108
regulation of S phase of mitotic cell cycle -0.009 0.11 -10000 0 -0.32 24 24
GNAO1 -0.012 0.13 -10000 0 -0.62 28 28
HRAS 0.015 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.012 0.069 -10000 0 -0.4 21 21
PELP1 0.013 0.035 -10000 0 -0.62 2 2
AKT1 0.013 0.017 -10000 0 -0.43 1 1
MAP2K1 -0.005 0.13 -10000 0 -0.4 24 24
T-DHT/AR -0.07 0.17 -10000 0 -0.46 102 102
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 95 95
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 -0.02 0.15 -10000 0 -0.62 37 37
mol:GDP -0.067 0.16 -10000 0 -0.47 86 86
cell proliferation -0.011 0.17 -10000 0 -0.56 25 25
PIK3CA 0.015 0 -10000 0 -10000 0 0
FOS -0.049 0.26 -10000 0 -0.64 95 95
mol:Ca2+ -0.012 0.024 -10000 0 -0.076 44 44
MAPK3 -0.006 0.15 -10000 0 -0.49 25 25
MAPK1 0.002 0.087 -10000 0 -0.28 18 18
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
mol:IP3 0 0.002 -10000 0 -0.004 95 95
cAMP biosynthetic process 0 0.07 -10000 0 -0.37 21 21
GNG2 0.009 0.06 -10000 0 -0.62 6 6
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 95 95
HRAS/GTP -0.05 0.12 -10000 0 -0.33 86 86
actin cytoskeleton reorganization -0.001 0.02 -10000 0 -10000 0 0
SRC 0.013 0.035 -10000 0 -0.62 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 95 95
PI3K -0.002 0.026 -10000 0 -0.39 3 3
apoptosis 0.011 0.16 0.42 63 -10000 0 63
T-DHT/AR/PELP1 -0.059 0.14 -10000 0 -0.39 103 103
HRAS/GDP -0.062 0.15 -10000 0 -0.45 82 82
CREB1 -0.014 0.17 -10000 0 -0.45 62 62
RAC1-CDC42/GTP -0.001 0.02 -10000 0 -10000 0 0
AR -0.082 0.23 -10000 0 -0.62 102 102
GNB1 0.015 0 -10000 0 -10000 0 0
RAF1 -0.012 0.13 -10000 0 -0.39 25 25
RAC1-CDC42/GDP -0.059 0.14 -10000 0 -0.42 82 82
T-DHT/AR/PELP1/Src -0.053 0.13 -10000 0 -0.36 103 103
MAP2K2 -0.005 0.13 -10000 0 -0.39 25 25
T-DHT/AR/PELP1/Src/PI3K -0.01 0.11 -10000 0 -0.33 23 23
GNAZ 0.012 0.043 -10000 0 -0.62 3 3
SHBG -0.005 0.11 -10000 0 -0.62 21 21
Gi family/GNB1/GNG2/GDP 0.008 0.12 -10000 0 -0.46 30 30
mol:T-DHT 0 0.001 -10000 0 -0.003 71 71
RAC1 0.015 0 -10000 0 -10000 0 0
GNRH1 0.003 0.07 -10000 0 -0.46 15 15
Gi family/GTP -0.044 0.097 -10000 0 -0.44 20 20
CDC42 0.015 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.014 0.004 -9999 0 -10000 0 0
SVIL -0.008 0.12 -9999 0 -0.59 25 25
ZNF318 0.019 0.019 -9999 0 -10000 0 0
JMJD2C -0.002 0.021 -9999 0 -0.088 37 37
T-DHT/AR/Ubc9 -0.052 0.16 -9999 0 -0.41 102 102
CARM1 0.015 0.001 -9999 0 -10000 0 0
PRDX1 -0.01 0.13 -9999 0 -0.62 27 27
PELP1 0.014 0.035 -9999 0 -0.62 2 2
CTNNB1 0.014 0.004 -9999 0 -10000 0 0
AKT1 0.015 0.024 -9999 0 -0.59 1 1
PTK2B -0.006 0.11 -9999 0 -0.59 23 23
MED1 0.016 0.005 -9999 0 -10000 0 0
MAK -0.057 0.2 -9999 0 -0.59 84 84
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.005 0.078 -9999 0 -0.63 10 10
GSN 0.006 0.074 -9999 0 -0.62 9 9
NCOA2 -0.019 0.14 -9999 0 -0.62 36 36
NCOA6 0.013 0.035 -9999 0 -0.62 2 2
DNA-PK 0.007 0.026 -9999 0 -10000 0 0
NCOA4 0.015 0.001 -9999 0 -10000 0 0
PIAS3 0.014 0.004 -9999 0 -10000 0 0
cell proliferation -0.055 0.13 -9999 0 -0.36 81 81
XRCC5 0.016 0.004 -9999 0 -10000 0 0
UBE3A 0.013 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.062 0.17 -9999 0 -0.42 114 114
FHL2 -0.056 0.21 -9999 0 -0.62 63 63
RANBP9 0.015 0.004 -9999 0 -10000 0 0
JMJD1A -0.007 0.055 -9999 0 -0.12 119 119
CDK6 -0.037 0.17 -9999 0 -0.6 57 57
TGFB1I1 0.004 0.079 -9999 0 -0.6 11 11
T-DHT/AR/CyclinD1 -0.066 0.18 -9999 0 -0.44 115 115
XRCC6 0.016 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.061 0.19 -9999 0 -0.42 115 115
CTDSP1 0.014 0.004 -9999 0 -10000 0 0
CTDSP2 0.004 0.093 -9999 0 -0.59 16 16
BRCA1 0.012 0.04 -9999 0 -0.59 3 3
TCF4 0.016 0.026 -9999 0 -0.62 1 1
CDKN2A -0.16 0.28 -9999 0 -0.61 186 186
SRF 0.017 0.031 -9999 0 -10000 0 0
NKX3-1 -0.075 0.18 -9999 0 -0.96 19 19
KLK3 -0.012 0.12 -9999 0 -0.51 1 1
TMF1 0.014 0.004 -9999 0 -10000 0 0
HNRNPA1 0.017 0.007 -9999 0 -10000 0 0
AOF2 -0.002 0.008 -9999 0 -10000 0 0
APPL1 0.029 0.021 -9999 0 -0.42 1 1
T-DHT/AR/Caspase 8 -0.06 0.16 -9999 0 -0.41 113 113
AR -0.09 0.23 -9999 0 -0.63 102 102
UBA3 0.014 0.004 -9999 0 -10000 0 0
PATZ1 0.017 0.007 -9999 0 -10000 0 0
PAWR -0.037 0.17 -9999 0 -0.6 56 56
PRKDC 0.016 0.004 -9999 0 -10000 0 0
PA2G4 0.017 0.008 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.046 0.14 -9999 0 -0.37 103 103
RPS6KA3 0.014 0.025 -9999 0 -0.62 1 1
T-DHT/AR/ARA70 -0.053 0.16 -9999 0 -0.41 102 102
LATS2 0.006 0.079 -9999 0 -0.6 11 11
T-DHT/AR/PRX1 -0.061 0.17 -9999 0 -0.4 117 117
Cyclin D3/CDK11 p58 -0.001 0.017 -9999 0 -0.43 1 1
VAV3 -0.2 0.29 -9999 0 -0.6 236 236
KLK2 -0.061 0.12 -9999 0 -0.51 37 37
CASP8 0.005 0.081 -9999 0 -0.59 12 12
T-DHT/AR/TIF2/CARM1 -0.057 0.18 -9999 0 -0.4 125 125
TMPRSS2 -0.15 0.31 -9999 0 -0.75 116 116
CCND1 -0.007 0.11 -9999 0 -0.6 24 24
PIAS1 0.011 0.036 -9999 0 -0.62 2 2
mol:T-DHT -0.011 0.033 -9999 0 -0.069 129 129
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.011 0.03 -9999 0 -0.62 1 1
T-DHT/AR/CDK6 -0.087 0.19 -9999 0 -0.42 147 147
CMTM2 -0.001 0.1 -9999 0 -0.62 18 18
SNURF -0.002 0.1 -9999 0 -0.62 18 18
ZMIZ1 0.003 0.061 -9999 0 -0.63 5 5
CCND3 0.014 0.023 -9999 0 -0.59 1 1
TGIF1 -0.003 0.11 -9999 0 -0.61 21 21
FKBP4 0.015 0.004 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.046 -10000 0 -0.62 3 3
HSPA8 0.014 0.025 -10000 0 -0.62 1 1
SMAD3/SMAD4/ER alpha -0.014 0.11 0.23 4 -0.4 24 28
AKT1 0.004 0.039 -10000 0 -0.68 1 1
GSC -0.17 0.5 -10000 0 -1.3 103 103
NKX2-5 -0.24 0.3 -10000 0 -0.6 270 270
muscle cell differentiation 0.16 0.18 0.54 88 -10000 0 88
SMAD2-3/SMAD4/SP1 -0.018 0.12 -10000 0 -0.44 10 10
SMAD4 -0.016 0.067 -10000 0 -0.4 1 1
CBFB 0.015 0 -10000 0 -10000 0 0
SAP18 0.015 0.003 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.032 0.13 -10000 0 -0.37 81 81
SMAD3/SMAD4/VDR -0.058 0.15 -10000 0 -0.41 47 47
MYC 0.007 0.11 -10000 0 -0.6 21 21
CDKN2B -0.22 0.56 -10000 0 -1.4 124 124
AP1 -0.016 0.15 -10000 0 -0.61 16 16
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.048 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.032 0.16 -10000 0 -0.46 35 35
SP3 0.018 0.008 -10000 0 -10000 0 0
CREB1 0.015 0 -10000 0 -10000 0 0
FOXH1 -0.011 0.099 -10000 0 -0.61 15 15
SMAD3/SMAD4/GR -0.005 0.065 -10000 0 -0.41 1 1
GATA3 -0.13 0.26 -10000 0 -0.63 138 138
SKI/SIN3/HDAC complex/NCoR1 0.05 0.035 -10000 0 -10000 0 0
MEF2C/TIF2 -0.14 0.21 -10000 0 -0.54 75 75
endothelial cell migration 0.28 0.51 1.4 105 -10000 0 105
MAX 0.027 0.021 -10000 0 -10000 0 0
RBBP7 0.015 0.003 -10000 0 -10000 0 0
RBBP4 0.015 0.003 -10000 0 -10000 0 0
RUNX2 0 0.097 -10000 0 -0.6 17 17
RUNX3 -0.027 0.16 -10000 0 -0.61 45 45
RUNX1 -0.057 0.2 -10000 0 -0.6 78 78
CTBP1 0.015 0 -10000 0 -10000 0 0
NR3C1 0.027 0.021 -10000 0 -10000 0 0
VDR -0.11 0.24 -10000 0 -0.6 132 132
CDKN1A -0.041 0.29 -10000 0 -1.1 34 34
KAT2B 0.012 0.042 -10000 0 -0.6 3 3
SMAD2/SMAD2/SMAD4/FOXH1 -0.033 0.11 -10000 0 -0.39 20 20
DCP1A 0.015 0 -10000 0 -10000 0 0
SKI 0.015 0.003 -10000 0 -10000 0 0
SERPINE1 -0.29 0.52 -10000 0 -1.4 103 103
SMAD3/SMAD4/ATF2 -0.024 0.078 -10000 0 -0.39 14 14
SMAD3/SMAD4/ATF3 -0.055 0.14 -10000 0 -0.44 63 63
SAP30 0.014 0.025 -10000 0 -0.63 1 1
Cbp/p300/PIAS3 0.017 0.056 -10000 0 -0.37 4 4
JUN -0.008 0.15 -10000 0 -0.62 15 15
SMAD3/SMAD4/IRF7 -0.034 0.1 -10000 0 -0.44 23 23
TFE3 0.005 0.035 -10000 0 -10000 0 0
COL1A2 -0.091 0.23 -10000 0 -0.56 113 113
mesenchymal cell differentiation 0.027 0.091 0.45 19 -10000 0 19
DLX1 -0.15 0.28 -10000 0 -0.61 177 177
TCF3 0.014 0.025 -10000 0 -0.62 1 1
FOS -0.07 0.22 -10000 0 -0.61 95 95
SMAD3/SMAD4/Max -0.005 0.065 -10000 0 -0.41 1 1
Cbp/p300/SNIP1 0.006 0.036 -10000 0 -0.37 4 4
ZBTB17 0.023 0.032 -10000 0 -0.53 1 1
LAMC1 -0.01 0.14 -10000 0 -0.59 32 32
TGIF2/HDAC complex/SMAD3/SMAD4 -0.02 0.071 -10000 0 -0.43 7 7
IRF7 -0.011 0.12 -10000 0 -0.6 29 29
ESR1 -0.003 0.11 -10000 0 -0.59 23 23
HNF4A -0.031 0.14 -10000 0 -0.59 42 42
MEF2C -0.13 0.21 -10000 0 -0.54 67 67
SMAD2-3/SMAD4 -0.036 0.075 -10000 0 -0.4 4 4
Cbp/p300/Src-1 0.013 0.044 -10000 0 -0.37 4 4
IGHV3OR16-13 -0.015 0.033 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0.054 -10000 0 -0.62 5 5
CREBBP 0.013 0.027 -10000 0 -0.61 1 1
SKIL 0.012 0.043 -10000 0 -0.62 3 3
HDAC1 0.011 0.049 -10000 0 -0.62 4 4
HDAC2 0.015 0.003 -10000 0 -10000 0 0
SNIP1 0.015 0.006 -10000 0 -10000 0 0
GCN5L2 -0.001 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.025 0.09 -10000 0 -0.41 9 9
MSG1/HSC70 -0.043 0.14 -10000 0 -0.43 80 80
SMAD2 -0.006 0.048 -10000 0 -10000 0 0
SMAD3 -0.005 0.06 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.068 -10000 0 -0.35 2 2
SMAD2/SMAD2/SMAD4 -0.004 0.042 -10000 0 -0.42 2 2
NCOR1 0.013 0.035 -10000 0 -0.62 2 2
NCOA2 -0.019 0.14 -10000 0 -0.62 36 36
NCOA1 0.015 0 -10000 0 -10000 0 0
MYOD/E2A -0.12 0.2 -10000 0 -0.44 179 179
SMAD2-3/SMAD4/SP1/MIZ-1 -0.009 0.12 -10000 0 -0.56 4 4
IFNB1 -0.006 0.11 -10000 0 -0.51 12 12
SMAD3/SMAD4/MEF2C -0.14 0.21 -10000 0 -0.52 76 76
CITED1 -0.058 0.2 -10000 0 -0.6 79 79
SMAD2-3/SMAD4/ARC105 -0.024 0.064 -10000 0 -0.4 2 2
RBL1 0.001 0.095 -10000 0 -0.62 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.056 0.22 -10000 0 -0.51 116 116
RUNX1-3/PEBPB2 -0.067 0.15 -10000 0 -0.38 117 117
SMAD7 -0.012 0.15 -10000 0 -0.56 14 14
MYC/MIZ-1 0.015 0.1 -10000 0 -0.46 18 18
SMAD3/SMAD4 -0.056 0.2 0.31 48 -0.42 98 146
IL10 -0.16 0.32 -10000 0 -0.68 147 147
PIASy/HDAC complex 0.017 0.028 -10000 0 -0.62 1 1
PIAS3 0.013 0.009 -10000 0 -10000 0 0
CDK2 0 0.092 -10000 0 -0.6 15 15
IL5 -0.088 0.21 -10000 0 -0.58 54 54
CDK4 -0.019 0.14 -10000 0 -0.59 38 38
PIAS4 0.017 0.028 -10000 0 -0.62 1 1
ATF3 -0.045 0.18 -10000 0 -0.6 65 65
SMAD3/SMAD4/SP1 -0.033 0.1 -10000 0 -0.43 9 9
FOXG1 -0.026 0.16 -10000 0 -0.62 43 43
FOXO3 0.012 0.048 -10000 0 -0.5 2 2
FOXO1 0.012 0.048 -10000 0 -0.5 2 2
FOXO4 0.01 0.057 -10000 0 -0.52 4 4
heart looping -0.13 0.21 -10000 0 -0.53 67 67
CEBPB -0.007 0.11 -10000 0 -0.62 19 19
SMAD3/SMAD4/DLX1 -0.12 0.18 -10000 0 -0.41 164 164
MYOD1 -0.16 0.27 -10000 0 -0.61 178 178
SMAD3/SMAD4/HNF4 -0.044 0.11 -10000 0 -0.4 36 36
SMAD3/SMAD4/GATA3 -0.13 0.21 -10000 0 -0.57 81 81
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.043 -10000 0 -0.62 3 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.064 0.15 -10000 0 -0.47 44 44
SMAD3/SMAD4/SP1-3 -0.01 0.1 -10000 0 -0.53 3 3
MED15 0.015 0 -10000 0 -10000 0 0
SP1 -0.001 0.05 -10000 0 -10000 0 0
SIN3B 0.014 0.025 -10000 0 -0.62 1 1
SIN3A 0.015 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.16 0.21 -10000 0 -0.46 107 107
ITGB5 0.019 0.12 -10000 0 -0.63 7 7
TGIF/SIN3/HDAC complex/CtBP 0.047 0.046 -10000 0 -0.46 1 1
SMAD3/SMAD4/AR -0.078 0.16 -10000 0 -0.42 102 102
AR -0.081 0.23 -10000 0 -0.62 102 102
negative regulation of cell growth -0.006 0.12 -10000 0 -0.46 19 19
SMAD3/SMAD4/MYOD -0.12 0.18 -10000 0 -0.4 165 165
E2F5 0.013 0.035 -10000 0 -0.62 2 2
E2F4 0.015 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.018 0.085 -10000 0 -0.38 7 7
SMAD2-3/SMAD4/FOXO1-3a-4 -0.029 0.15 -10000 0 -0.4 45 45
TFDP1 0.011 0.049 -10000 0 -0.62 4 4
SMAD3/SMAD4/AP1 -0.018 0.15 -10000 0 -0.65 14 14
SMAD3/SMAD4/RUNX2 -0.027 0.092 -10000 0 -0.45 19 19
TGIF2 0.01 0.054 -10000 0 -0.62 5 5
TGIF1 -0.005 0.11 -10000 0 -0.62 21 21
ATF2 0.004 0.085 -10000 0 -0.62 12 12
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0.049 -9999 0 -0.62 4 4
VLDLR -0.004 0.11 -9999 0 -0.62 20 20
LRPAP1 0.015 0 -9999 0 -10000 0 0
NUDC 0.015 0 -9999 0 -10000 0 0
RELN/LRP8 -0.12 0.17 -9999 0 -0.37 211 211
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.015 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.076 0.17 -9999 0 -0.67 3 3
IQGAP1/CaM -0.005 0.045 -9999 0 -0.44 7 7
DAB1 -0.093 0.24 -9999 0 -0.62 114 114
IQGAP1 0.009 0.064 -9999 0 -0.61 7 7
PLA2G7 -0.039 0.18 -9999 0 -0.61 58 58
CALM1 0.015 0 -9999 0 -10000 0 0
DYNLT1 0.01 0.058 -9999 0 -0.6 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.025 -9999 0 -0.46 2 2
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.014 0.025 -9999 0 -0.62 1 1
CDK5R1 -0.035 0.17 -9999 0 -0.62 53 53
LIS1/Poliovirus Protein 3A 0.02 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.24 -9999 0 -0.61 124 124
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.24 -9999 0 -0.44 287 287
YWHAE 0.015 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.092 0.22 -9999 0 -0.63 59 59
MAP1B -0.001 0.015 -9999 0 -0.27 2 2
RAC1 -0.002 0.017 -9999 0 -10000 0 0
p35/CDK5 -0.076 0.2 -9999 0 -0.63 34 34
RELN -0.18 0.29 -9999 0 -0.61 211 211
PAFAH/LIS1 -0.003 0.11 -9999 0 -0.37 58 58
LIS1/CLIP170 0.031 0.016 -9999 0 -0.38 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.1 0.15 -9999 0 -0.56 37 37
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.098 0.21 -9999 0 -0.6 61 61
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.11 0.24 -9999 0 -0.62 82 82
LIS1/IQGAP1 0.027 0.041 -9999 0 -0.37 7 7
RHOA -0.002 0.017 -9999 0 -10000 0 0
PAFAH1B1 0.027 0 -9999 0 -10000 0 0
PAFAH1B3 0.015 0 -9999 0 -10000 0 0
PAFAH1B2 0.003 0.088 -9999 0 -0.62 13 13
MAP1B/LIS1/Dynein heavy chain 0.027 0.03 -9999 0 -0.33 4 4
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.19 -9999 0 -0.61 60 60
LRP8 0.013 0.035 -9999 0 -0.62 2 2
NDEL1/Katanin 60 -0.092 0.22 -9999 0 -0.63 59 59
P39/CDK5 -0.11 0.22 -9999 0 -0.6 60 60
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.032 0 -9999 0 -10000 0 0
CDK5 -0.062 0.16 -9999 0 -0.63 3 3
PPP2R5D 0.015 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0.013 -9999 0 -0.33 1 1
CSNK2A1 0.015 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.2 -9999 0 -0.63 57 57
RELN/VLDLR -0.11 0.17 -9999 0 -0.37 133 133
CDC42 -0.002 0.017 -9999 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.056 0.11 0.48 17 -10000 0 17
GNAI2 0.015 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.073 0.15 -10000 0 -0.38 128 128
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.012 0.13 -10000 0 -0.62 28 28
RhoA/GTP -0.057 0.11 -10000 0 -0.49 17 17
negative regulation of cAMP metabolic process -0.035 0.14 -10000 0 -0.3 94 94
GNAZ 0.012 0.043 -10000 0 -0.62 3 3
GNAI3 0.015 0 -10000 0 -10000 0 0
GNA12 0.014 0.025 -10000 0 -0.62 1 1
S1PR5 -0.1 0.24 -10000 0 -0.61 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.035 0.14 -10000 0 -0.31 94 94
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
GNAI1 -0.02 0.15 -10000 0 -0.62 37 37
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.052 -10000 0 -0.59 5 5
Jak2/Leptin Receptor 0 0.1 0.21 47 -0.39 14 61
PTP1B/AKT1 -0.017 0.095 -10000 0 -0.35 10 10
FYN 0.015 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.028 0.1 -10000 0 -0.33 18 18
EGFR -0.11 0.25 -10000 0 -0.61 138 138
EGF/EGFR -0.12 0.17 -10000 0 -0.4 144 144
CSF1 0.004 0.085 -10000 0 -0.62 12 12
AKT1 0.014 0.023 -10000 0 -0.59 1 1
INSR 0.014 0.025 -10000 0 -0.63 1 1
PTP1B/N-cadherin -0.019 0.099 -10000 0 -0.34 14 14
Insulin Receptor/Insulin -0.032 0.064 -10000 0 -0.37 4 4
HCK 0 0.096 -10000 0 -0.61 16 16
CRK 0.015 0 -10000 0 -10000 0 0
TYK2 -0.017 0.099 -10000 0 -0.34 11 11
EGF -0.041 0.18 -10000 0 -0.62 57 57
YES1 0.013 0.035 -10000 0 -0.62 2 2
CAV1 -0.045 0.14 -10000 0 -0.38 45 45
TXN 0.013 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.022 0.097 -10000 0 -0.36 15 15
cell migration 0.028 0.1 0.33 18 -10000 0 18
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.021 0.15 -10000 0 -0.6 42 42
ITGA2B -0.029 0.16 -10000 0 -0.62 46 46
CSF1R -0.013 0.13 -10000 0 -0.62 30 30
Prolactin Receptor/Prolactin -0.018 0.12 -10000 0 -0.45 47 47
FGR 0.01 0.057 -10000 0 -0.59 6 6
PTP1B/p130 Cas -0.019 0.099 -10000 0 -0.34 14 14
Crk/p130 Cas -0.018 0.089 -10000 0 -0.35 7 7
DOK1 -0.007 0.094 -10000 0 -0.33 10 10
JAK2 0.001 0.089 -10000 0 -0.36 11 11
Jak2/Leptin Receptor/Leptin -0.17 0.23 -10000 0 -0.5 198 198
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
PTPN1 -0.028 0.1 -10000 0 -0.34 18 18
LYN 0.011 0.053 -10000 0 -0.6 5 5
CDH2 0.014 0.025 -10000 0 -0.62 1 1
SRC 0.007 0.051 -10000 0 -0.52 2 2
ITGB3 -0.099 0.24 -10000 0 -0.6 125 125
CAT1/PTP1B -0.057 0.14 -10000 0 -0.41 42 42
CAPN1 0.015 0.025 -10000 0 -0.63 1 1
CSK 0.015 0 -10000 0 -10000 0 0
PI3K -0.024 0.06 -10000 0 -0.43 1 1
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.17 0.23 -10000 0 -0.5 204 204
negative regulation of transcription 0.001 0.089 -10000 0 -0.36 11 11
FCGR2A -0.05 0.19 -10000 0 -0.6 70 70
FER 0 0.089 -10000 0 -0.63 13 13
alphaIIb/beta3 Integrin -0.11 0.2 -10000 0 -0.46 160 160
BLK -0.07 0.21 -10000 0 -0.59 91 91
Insulin Receptor/Insulin/Shc -0.012 0.066 -10000 0 -0.37 21 21
RHOA 0.016 0.003 -10000 0 -10000 0 0
LEPR 0.008 0.075 -10000 0 -0.6 10 10
BCAR1 0.014 0.025 -10000 0 -0.62 1 1
p210 bcr-abl/Grb2 0.014 0.023 -10000 0 -0.59 1 1
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.05 0.14 -10000 0 -0.45 36 36
PRL 0 0.056 -10000 0 -0.58 6 6
SOCS3 -0.24 0.44 -10000 0 -1.4 72 72
SPRY2 0.008 0.07 -10000 0 -0.59 9 9
Insulin Receptor/Insulin/IRS1 -0.007 0.053 -10000 0 -0.38 13 13
CSF1/CSF1R -0.038 0.13 -10000 0 -0.46 33 33
Ras protein signal transduction 0.025 0.039 -10000 0 -0.5 1 1
IRS1 0.009 0.065 -10000 0 -0.62 7 7
INS -0.004 0.053 -10000 0 -0.62 5 5
LEP -0.015 0.11 -10000 0 -0.59 23 23
STAT5B -0.011 0.093 -10000 0 -0.31 10 10
STAT5A -0.013 0.095 -10000 0 -0.35 10 10
GRB2 0.014 0.023 -10000 0 -0.59 1 1
PDGFB-D/PDGFRB -0.02 0.1 -10000 0 -0.37 18 18
CSN2 0.002 0.045 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
LAT -0.046 0.16 -10000 0 -0.48 63 63
YBX1 0.022 0.035 -10000 0 -0.61 2 2
LCK -0.098 0.24 -10000 0 -0.6 123 123
SHC1 0.001 0.092 -10000 0 -0.59 16 16
NOX4 -0.16 0.27 -10000 0 -0.6 188 188
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.051 0.15 -10000 0 -0.74 18 18
HDAC1 0.008 0.049 -10000 0 -0.62 4 4
AES 0.014 0.003 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
DTX1 0.006 0.077 -10000 0 -0.62 10 10
LRP6/FZD1 -0.006 0.051 -10000 0 -0.42 10 10
TLE1 0.013 0.035 -10000 0 -0.63 2 2
AP1 -0.027 0.13 -10000 0 -0.32 87 87
NCSTN 0.015 0 -10000 0 -10000 0 0
ADAM10 0.005 0.081 -10000 0 -0.62 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.065 -10000 0 -0.55 1 1
NICD/RBPSUH -0.017 0.098 -10000 0 -0.6 18 18
WIF1 -0.28 0.31 -10000 0 -0.6 322 322
NOTCH1 -0.017 0.1 -10000 0 -0.64 18 18
PSENEN 0.015 0 -10000 0 -10000 0 0
KREMEN2 -0.042 0.18 -10000 0 -0.6 63 63
DKK1 -0.13 0.26 -10000 0 -0.6 160 160
beta catenin/beta TrCP1 0.028 0.055 0.26 5 -10000 0 5
APH1B 0.015 0 -10000 0 -10000 0 0
APH1A 0.015 0 -10000 0 -10000 0 0
AXIN1 0 0.062 0.27 7 -0.46 4 11
CtBP/CBP/TCF1/TLE1/AES 0.029 0.045 0.29 2 -10000 0 2
PSEN1 0.015 0 -10000 0 -10000 0 0
FOS -0.073 0.22 -10000 0 -0.61 95 95
JUN 0.008 0.067 -10000 0 -0.6 8 8
MAP3K7 0.014 0.004 -10000 0 -10000 0 0
CTNNB1 0.02 0.058 0.26 7 -10000 0 7
MAPK3 0.015 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.098 0.18 -10000 0 -0.39 168 168
HNF1A 0.013 0.025 -10000 0 -0.63 1 1
CTBP1 0.014 0.003 -10000 0 -10000 0 0
MYC -0.012 0.23 -10000 0 -1.4 17 17
NKD1 -0.023 0.15 -10000 0 -0.62 40 40
FZD1 0.007 0.069 -10000 0 -0.59 9 9
NOTCH1 precursor/Deltex homolog 1 -0.021 0.11 -10000 0 -0.66 18 18
apoptosis -0.027 0.13 -10000 0 -0.32 87 87
Delta 1/NOTCHprecursor -0.051 0.15 -10000 0 -0.73 18 18
DLL1 -0.057 0.2 -10000 0 -0.62 76 76
PPARD 0.025 0.022 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.001 0.048 0.26 8 -0.27 4 12
DVL1 -0.022 0.033 -10000 0 -0.58 1 1
CSNK2A1 0.015 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.18 -10000 0 -0.38 212 212
LRP6 0.014 0.023 -10000 0 -0.59 1 1
CSNK1A1 0.015 0.003 -10000 0 -10000 0 0
NLK 0.017 0.01 -10000 0 -10000 0 0
CCND1 -0.001 0.18 -10000 0 -0.79 24 24
WNT1 -0.022 0.14 -10000 0 -0.59 38 38
Axin1/APC/beta catenin 0.03 0.064 0.3 8 -0.72 1 9
DKK2 -0.093 0.24 -10000 0 -0.6 117 117
NOTCH1 precursor/DVL1 -0.017 0.098 -10000 0 -0.6 18 18
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.006 0.072 -10000 0 -0.61 9 9
NOTCH/Deltex homolog 1 -0.021 0.11 -10000 0 -0.67 18 18
PPP2R5D 0.006 0.073 0.29 39 -10000 0 39
MAPK1 0.015 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.19 -10000 0 -0.4 158 158
RBPJ 0.014 0.023 -10000 0 -0.59 1 1
CREBBP 0.018 0.025 -10000 0 -0.63 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.043 0.18 -10000 0 -0.53 32 32
UGCG -0.023 0.12 -10000 0 -0.62 23 23
AKT1/mTOR/p70S6K/Hsp90/TERT -0.049 0.16 -10000 0 -0.44 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.02 0.12 -10000 0 -0.61 23 23
mol:DAG -0.003 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.076 0.12 -10000 0 -0.43 35 35
FRAP1 -0.042 0.18 -10000 0 -0.5 37 37
FOXO3 -0.036 0.18 -10000 0 -0.5 35 35
AKT1 -0.048 0.19 -10000 0 -0.54 36 36
GAB2 0.013 0.043 -10000 0 -0.63 3 3
SMPD1 -0.001 0.038 -10000 0 -10000 0 0
SGMS1 -0.001 0.038 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.028 -10000 0 -0.38 3 3
CALM1 0.015 0 -10000 0 -10000 0 0
cell proliferation -0.018 0.1 -10000 0 -0.39 15 15
EIF3A 0.014 0.025 -10000 0 -0.62 1 1
PI3K 0.025 0.033 -10000 0 -0.45 3 3
RPS6KB1 -0.006 0.065 -10000 0 -0.24 3 3
mol:sphingomyelin -0.003 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.013 1 1
JAK3 -0.054 0.2 -10000 0 -0.6 78 78
PIK3R1 0.015 0.043 -10000 0 -0.62 3 3
JAK1 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.015 0 -10000 0 -10000 0 0
MYC -0.045 0.22 -10000 0 -0.97 19 19
MYB -0.094 0.34 -10000 0 -1.1 52 52
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.065 0.19 -10000 0 -0.5 59 59
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.011 0.063 -10000 0 -0.38 1 1
mol:PI-3-4-5-P3 -0.062 0.19 -10000 0 -0.48 59 59
Rac1/GDP 0.031 0.026 -10000 0 -0.34 3 3
T cell proliferation -0.073 0.2 -10000 0 -0.52 71 71
SHC1 0.001 0.092 -10000 0 -0.59 16 16
RAC1 0.015 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.021 -10000 0 -0.05 104 104
PRKCZ -0.076 0.21 -10000 0 -0.54 71 71
NF kappa B1 p50/RelA -0.07 0.12 -10000 0 -0.44 30 30
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.058 0.19 -10000 0 -0.49 75 75
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
IL2RA -0.17 0.28 -10000 0 -0.6 193 193
IL2RB -0.11 0.25 -10000 0 -0.6 140 140
TERT -0.079 0.22 -10000 0 -0.61 94 94
E2F1 -0.034 0.15 -10000 0 -0.41 76 76
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.013 0.033 -10000 0 -0.59 2 2
mol:cAMP 0.001 0.01 0.024 104 -10000 0 104
PTPN11 0.014 0.035 -10000 0 -0.62 2 2
IL2RG -0.036 0.17 -10000 0 -0.6 58 58
actin cytoskeleton organization -0.073 0.2 -10000 0 -0.52 71 71
GRB2 0.015 0.023 -10000 0 -0.59 1 1
IL2 0.004 0.004 -10000 0 -10000 0 0
PIK3CA 0.018 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.029 -10000 0 -0.32 3 3
LCK -0.095 0.24 -10000 0 -0.6 123 123
BCL2 -0.022 0.16 -10000 0 -0.64 8 8
Canonical Wnt signaling pathway

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
HDAC1 0.001 0.052 -10000 0 -0.61 4 4
AES 0.004 0.018 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.006 0.051 -10000 0 -0.42 10 10
SMAD4 0.015 0 -10000 0 -10000 0 0
DKK2 -0.094 0.24 -10000 0 -0.6 117 117
TLE1 0.003 0.039 -10000 0 -0.63 2 2
MACF1 0.013 0.043 -10000 0 -0.62 3 3
CTNNB1 0.071 0.092 0.31 7 -0.35 1 8
WIF1 -0.28 0.31 -10000 0 -0.6 322 322
beta catenin/RanBP3 0.01 0.097 0.42 25 -10000 0 25
KREMEN2 -0.042 0.18 -10000 0 -0.6 63 63
DKK1 -0.13 0.26 -10000 0 -0.6 160 160
beta catenin/beta TrCP1 0.076 0.087 0.32 5 -10000 0 5
FZD1 0.008 0.069 -10000 0 -0.58 9 9
AXIN2 0.008 0.1 -10000 0 -1.2 3 3
AXIN1 0.015 0.025 -10000 0 -0.63 1 1
RAN 0.015 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.009 0.035 -10000 0 -0.49 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.096 0.054 0.35 1 -10000 0 1
Axin1/APC/GSK3 0.012 0.052 0.27 10 -10000 0 10
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.082 -10000 0 -0.48 4 4
HNF1A 0.004 0.031 -10000 0 -0.63 1 1
CTBP1 0.005 0.02 -10000 0 -10000 0 0
MYC -0.023 0.24 -10000 0 -1.4 18 18
RANBP3 0.015 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.098 0.18 -10000 0 -0.39 168 168
NKD1 -0.023 0.15 -10000 0 -0.62 40 40
TCF4 0.004 0.029 -10000 0 -0.58 1 1
TCF3 0.004 0.026 -10000 0 -0.49 1 1
WNT1/LRP6/FZD1/Axin1 -0.023 0.084 -10000 0 -0.54 3 3
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.021 0.11 0.49 24 -10000 0 24
LEF1 -0.003 0.068 -10000 0 -0.59 8 8
DVL1 0.056 0.055 0.23 1 -10000 0 1
CSNK2A1 0.015 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.069 -10000 0 -0.48 1 1
DKK1/LRP6/Kremen 2 -0.12 0.18 -10000 0 -0.38 212 212
LRP6 0.015 0.023 -10000 0 -0.59 1 1
CSNK1A1 0.005 0.021 -10000 0 -10000 0 0
NLK 0.016 0.004 -10000 0 -10000 0 0
CCND1 -0.012 0.19 -10000 0 -0.83 24 24
WNT1 -0.021 0.14 -10000 0 -0.59 38 38
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.007 0.072 -10000 0 -0.61 9 9
PPP2R5D 0.053 0.07 0.31 40 -10000 0 40
APC 0.024 0.088 -10000 0 -0.58 2 2
WNT1/LRP6/FZD1 0.098 0.11 0.22 274 -10000 0 274
CREBBP 0.004 0.031 -10000 0 -0.63 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.032 0.17 -9999 0 -0.48 78 78
KLHL20 -0.026 0.057 -9999 0 -0.29 11 11
CYFIP2 0.008 0.068 -9999 0 -0.61 8 8
Rac1/GDP 0.014 0.12 -9999 0 -0.58 3 3
ENAH -0.032 0.18 -9999 0 -0.48 78 78
AP1M1 0.015 0 -9999 0 -10000 0 0
RAP1B 0.009 0.061 -9999 0 -0.59 7 7
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.038 0.079 -9999 0 -0.5 4 4
ABI1/Sra1/Nap1 -0.017 0.04 -9999 0 -0.2 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.09 0.16 -9999 0 -0.4 94 94
RAPGEF1 -0.009 0.16 -9999 0 -0.41 79 79
CTNND1 0.015 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.075 0.16 -9999 0 -0.5 78 78
CRK -0.02 0.17 -9999 0 -0.44 78 78
E-cadherin/gamma catenin/alpha catenin -0.079 0.16 -9999 0 -0.38 139 139
alphaE/beta7 Integrin -0.032 0.11 -9999 0 -0.44 48 48
IQGAP1 0.009 0.064 -9999 0 -0.61 7 7
NCKAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.004 0.035 -9999 0 -0.32 8 8
DLG1 -0.032 0.17 -9999 0 -0.48 78 78
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.027 0.056 -9999 0 -0.33 4 4
MLLT4 0.014 0.025 -9999 0 -0.62 1 1
ARF6/GTP/NME1/Tiam1 -0.003 0.031 -9999 0 -0.33 6 6
PI3K -0.035 0.072 -9999 0 -0.45 4 4
ARF6 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.094 0.19 -9999 0 -0.46 139 139
TIAM1 0.013 0.035 -9999 0 -0.62 2 2
E-cadherin(dimer)/Ca2+ -0.062 0.12 -9999 0 -0.32 78 78
AKT1 -0.02 0.04 -9999 0 -0.26 2 2
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
CDH1 -0.11 0.25 -9999 0 -0.61 136 136
RhoA/GDP 0.013 0.12 -9999 0 -0.58 3 3
actin cytoskeleton organization -0.019 0.042 -9999 0 -0.21 11 11
CDC42/GDP 0.013 0.12 -9999 0 -0.58 3 3
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.026 0.11 -9999 0 -0.28 82 82
ITGB7 -0.027 0.16 -9999 0 -0.61 45 45
RAC1 0.015 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.066 0.13 -9999 0 -0.34 78 78
E-cadherin/Ca2+/beta catenin/alpha catenin -0.064 0.13 -9999 0 -0.32 136 136
mol:GDP 0.003 0.14 -9999 0 -0.75 3 3
CDC42/GTP/IQGAP1 -0.004 0.038 -9999 0 -0.38 7 7
JUP 0.008 0.069 -9999 0 -0.62 8 8
p120 catenin/RhoA/GDP -0.045 0.097 -9999 0 -0.59 3 3
RAC1/GTP/IQGAP1 -0.004 0.038 -9999 0 -0.38 7 7
PIP5K1C/AP1M1 -0.001 0.018 -9999 0 -0.46 1 1
RHOA 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.018 0.06 -9999 0 -0.23 24 24
NME1 0.012 0.046 -9999 0 -0.59 4 4
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.032 0.17 -9999 0 -0.48 78 78
regulation of cell-cell adhesion -0.034 0.07 -9999 0 -0.42 4 4
WASF2 -0.008 0.021 -9999 0 -10000 0 0
Rap1/GTP -0.044 0.093 -9999 0 -0.6 4 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.086 0.16 -9999 0 -0.65 22 22
CCND1 0.02 0.073 -9999 0 -0.29 24 24
VAV2 -0.016 0.17 -9999 0 -0.45 80 80
RAP1/GDP -0.043 0.095 -9999 0 -0.58 4 4
adherens junction assembly -0.029 0.17 -9999 0 -0.46 78 78
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.015 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0.025 -9999 0 -0.62 1 1
regulation of heterotypic cell-cell adhesion -0.081 0.15 -9999 0 -0.62 22 22
E-cadherin/beta catenin -0.067 0.14 -9999 0 -0.33 136 136
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.032 0.18 -9999 0 -0.48 79 79
PIK3CA 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.041 0.095 -9999 0 -0.49 13 13
E-cadherin/beta catenin/alpha catenin -0.075 0.15 -9999 0 -0.37 136 136
ITGAE 0.012 0.04 -9999 0 -0.59 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.077 0.17 -9999 0 -0.51 78 78
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.005 0.11 -9999 0 -0.59 22 22
PLK4 -0.007 0.11 -9999 0 -0.6 24 24
regulation of centriole replication -0.004 0.12 -9999 0 -0.44 45 45
FAS signaling pathway (CD95)

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
SPTAN1 0.005 0.05 0.26 3 -0.38 1 4
RFC1 0.005 0.048 0.26 3 -10000 0 3
PRKDC 0.005 0.048 0.26 3 -10000 0 3
RIPK1 0.017 0.004 -10000 0 -10000 0 0
CASP7 -0.011 0.068 0.26 15 -0.33 8 23
FASLG/FAS/FADD/FAF1 -0.02 0.091 0.23 17 -0.33 18 35
MAP2K4 -0.015 0.13 -10000 0 -0.4 13 13
mol:ceramide -0.011 0.11 -10000 0 -0.41 12 12
GSN 0 0.063 0.26 3 -0.38 8 11
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.095 -10000 0 -0.37 14 14
FAS -0.023 0.14 -10000 0 -0.61 37 37
BID 0.005 0.076 0.31 19 -0.35 13 32
MAP3K1 0.002 0.093 0.22 14 -0.32 7 21
MAP3K7 0.011 0.007 -10000 0 -10000 0 0
RB1 0.005 0.05 0.26 3 -0.38 1 4
CFLAR 0.017 0.004 -10000 0 -10000 0 0
HGF/MET -0.17 0.23 -10000 0 -0.44 257 257
ARHGDIB 0.003 0.053 0.26 3 -0.32 3 6
FADD 0.011 0.008 -10000 0 -10000 0 0
actin filament polymerization 0 0.063 0.37 8 -0.26 3 11
NFKB1 -0.05 0.075 -10000 0 -10000 0 0
MAPK8 -0.043 0.19 -10000 0 -0.43 75 75
DFFA 0.005 0.048 0.26 3 -10000 0 3
DNA fragmentation during apoptosis 0.005 0.048 0.26 3 -10000 0 3
FAS/FADD/MET -0.13 0.2 -10000 0 -0.41 208 208
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.016 0.14 -10000 0 -0.61 35 35
FAF1 0.01 0.036 -10000 0 -0.62 2 2
PARP1 0.005 0.05 0.26 3 -0.35 1 4
DFFB 0.005 0.048 0.26 3 -10000 0 3
CHUK -0.042 0.064 -10000 0 -10000 0 0
FASLG -0.023 0.13 -10000 0 -0.6 33 33
FAS/FADD -0.025 0.1 -10000 0 -0.44 37 37
HGF -0.088 0.23 -10000 0 -0.6 113 113
LMNA 0.001 0.061 0.24 3 -0.36 9 12
CASP6 0.001 0.062 0.26 3 -0.38 7 10
CASP10 0.011 0.008 -10000 0 -10000 0 0
CASP3 0.006 0.056 0.24 22 -0.24 8 30
PTPN13 0.009 0.065 -10000 0 -0.62 7 7
CASP8 0.009 0.095 0.36 31 -0.4 12 43
IL6 -0.2 0.43 -10000 0 -1.1 104 104
MET -0.16 0.28 -10000 0 -0.6 194 194
ICAD/CAD 0.005 0.045 0.24 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.012 0.11 -10000 0 -0.41 12 12
activation of caspase activity by cytochrome c 0.005 0.076 0.31 19 -0.35 13 32
PAK2 0.005 0.048 0.26 3 -10000 0 3
BCL2 0.013 0.043 -10000 0 -0.62 3 3
Signaling events mediated by HDAC Class III

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
EP300 0.012 0.043 -10000 0 -0.62 3 3
HDAC4 0.014 0.025 -10000 0 -0.62 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.055 0.42 8 -10000 0 8
CDKN1A -0.045 0.17 -10000 0 -0.6 53 53
KAT2B 0.012 0.042 -10000 0 -0.61 3 3
BAX 0.015 0 -10000 0 -10000 0 0
FOXO3 0.002 0.033 0.47 3 -0.28 1 4
FOXO1 0.014 0.025 -10000 0 -0.62 1 1
FOXO4 0.024 0.041 -10000 0 -0.38 6 6
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
TAT -0.088 0.23 -10000 0 -0.6 111 111
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.1 0.21 -10000 0 -0.45 178 178
PPARGC1A -0.002 0.1 -10000 0 -0.62 18 18
FHL2 -0.042 0.18 -10000 0 -0.59 63 63
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.01 0.034 -10000 0 -10000 0 0
HIST2H4A 0.025 0.055 -10000 0 -0.42 8 8
SIRT1/FOXO3a 0.01 0.037 0.3 3 -0.2 1 4
SIRT1 0.013 0.044 0.2 25 -10000 0 25
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.008 0.04 -10000 0 -0.38 2 2
SIRT1/Histone H1b -0.005 0.07 0.17 23 -0.28 20 43
apoptosis -0.009 0.033 -10000 0 -10000 0 0
SIRT1/PGC1A -0.002 0.07 -10000 0 -0.38 18 18
p53/SIRT1 0.018 0.12 0.35 52 -0.46 12 64
SIRT1/FOXO4 0.008 0.051 -10000 0 -0.32 6 6
FOXO1/FHL2/SIRT1 -0.023 0.1 -10000 0 -0.32 64 64
HIST1H1E 0.006 0.076 -10000 0 -0.33 20 20
SIRT1/p300 0.008 0.046 -10000 0 -0.46 3 3
muscle cell differentiation 0.091 0.17 0.37 178 -10000 0 178
TP53 0 0.098 -10000 0 -0.62 13 13
KU70/SIRT1/BAX 0.01 0.034 -10000 0 -10000 0 0
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
MEF2D 0.014 0.025 -10000 0 -0.62 1 1
HIV-1 Tat/SIRT1 -0.064 0.17 -10000 0 -0.43 111 111
ACSS2 0.031 0.024 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.091 0.17 -10000 0 -0.37 178 178
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 0.006 0.077 -10000 0 -0.62 10 10
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.004 0.11 0.51 7 -10000 0 7
IL27/IL27R/JAK1 -0.029 0.16 -10000 0 -0.65 9 9
TBX21 -0.038 0.22 -10000 0 -0.6 50 50
IL12B 0.001 0.047 -10000 0 -0.6 4 4
IL12A 0 0.08 -10000 0 -0.46 20 20
IL6ST -0.029 0.16 -10000 0 -0.63 46 46
IL27RA/JAK1 0.02 0.067 -10000 0 -1.3 1 1
IL27 -0.012 0.12 -10000 0 -0.59 28 28
TYK2 0.016 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.075 0.14 -10000 0 -0.75 5 5
T-helper 2 cell differentiation -0.004 0.11 0.51 7 -10000 0 7
T cell proliferation during immune response -0.004 0.11 0.51 7 -10000 0 7
MAPKKK cascade 0.004 0.11 -10000 0 -0.51 7 7
STAT3 0.015 0 -10000 0 -10000 0 0
STAT2 0.012 0.04 -10000 0 -0.59 3 3
STAT1 0.001 0.093 -10000 0 -0.59 16 16
IL12RB1 -0.019 0.14 -10000 0 -0.62 36 36
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.24 -10000 0 -0.56 59 59
IL27/IL27R/JAK2/TYK2 0.004 0.11 -10000 0 -0.51 7 7
positive regulation of T cell mediated cytotoxicity 0.004 0.11 -10000 0 -0.51 7 7
STAT1 (dimer) -0.046 0.25 0.53 35 -0.66 29 64
JAK2 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.015 0.004 -10000 0 -10000 0 0
STAT2 (dimer) 0.011 0.1 -10000 0 -0.48 8 8
T cell proliferation -0.087 0.18 -10000 0 -0.51 39 39
IL12/IL12R/TYK2/JAK2 0.008 0.083 -10000 0 -0.56 4 4
IL17A -0.075 0.14 -10000 0 -0.75 5 5
mast cell activation -0.004 0.11 0.51 7 -10000 0 7
IFNG 0.004 0.021 -10000 0 -0.095 5 5
T cell differentiation -0.004 0.005 -10000 0 -0.023 4 4
STAT3 (dimer) 0.012 0.1 -10000 0 -0.48 7 7
STAT5A (dimer) 0.007 0.11 -10000 0 -0.5 12 12
STAT4 (dimer) -0.069 0.18 -10000 0 -0.52 23 23
STAT4 -0.14 0.27 -10000 0 -0.6 165 165
T cell activation -0.009 0.01 0.079 7 -10000 0 7
IL27R/JAK2/TYK2 -0.013 0.1 -10000 0 -1.2 1 1
GATA3 -0.15 0.39 -10000 0 -0.91 105 105
IL18 -0.018 0.12 -10000 0 -0.45 45 45
positive regulation of mast cell cytokine production 0.012 0.1 -10000 0 -0.47 7 7
IL27/EBI3 -0.011 0.12 -10000 0 -0.44 44 44
IL27RA 0.014 0.07 -10000 0 -1.3 1 1
IL6 -0.17 0.28 -10000 0 -0.6 205 205
STAT5A 0.005 0.081 -10000 0 -0.62 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 0.002 0.032 0.47 1 -10000 0 1
IL1B -0.12 0.21 -10000 0 -0.45 191 191
EBI3 -0.002 0.1 -10000 0 -0.62 17 17
TNF -0.091 0.19 -10000 0 -0.45 152 152
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.058 0.14 -9999 0 -0.4 80 80
MAP4K1 -0.011 0.13 -9999 0 -0.62 28 28
MAP3K8 -0.005 0.11 -9999 0 -0.59 22 22
PRKCB -0.072 0.22 -9999 0 -0.6 94 94
DBNL 0.015 0 -9999 0 -10000 0 0
CRKL 0.014 0.023 -9999 0 -0.59 1 1
MAP3K1 0.012 0.11 -9999 0 -0.47 10 10
JUN -0.021 0.16 -9999 0 -0.53 47 47
MAP3K7 0.014 0.1 -9999 0 -0.47 10 10
GRAP2 -0.034 0.17 -9999 0 -0.61 53 53
CRK 0.015 0 -9999 0 -10000 0 0
MAP2K4 0.019 0.11 -9999 0 -0.44 13 13
LAT -0.011 0.13 -9999 0 -0.62 28 28
LCP2 0.007 0.072 -9999 0 -0.61 9 9
MAPK8 -0.028 0.16 -9999 0 -0.56 46 46
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.11 -9999 0 -0.46 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.054 0.14 -9999 0 -0.65 14 14
Noncanonical Wnt signaling pathway

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
NFATC2 -0.053 0.2 -9999 0 -0.61 73 73
GNB1/GNG2 -0.059 0.12 -9999 0 -0.5 20 20
mol:DAG -0.007 0.13 -9999 0 -0.45 20 20
PLCG1 -0.008 0.13 -9999 0 -0.46 20 20
YES1 -0.025 0.14 -9999 0 -0.46 25 25
FZD3 0.012 0.043 -9999 0 -0.62 3 3
FZD6 -0.033 0.16 -9999 0 -0.59 53 53
G protein -0.008 0.13 -9999 0 -0.47 20 20
MAP3K7 -0.096 0.17 -9999 0 -0.43 61 61
mol:Ca2+ -0.006 0.12 -9999 0 -0.43 20 20
mol:IP3 -0.007 0.13 -9999 0 -0.45 20 20
NLK -0.006 0.007 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.18 -9999 0 -0.47 64 64
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.036 0.14 -9999 0 -0.42 39 39
CSNK1A1 0.015 0 -9999 0 -10000 0 0
GNAS -0.024 0.14 -9999 0 -0.46 23 23
GO:0007205 -0.006 0.13 -9999 0 -0.5 12 12
WNT6 -0.027 0.16 -9999 0 -0.6 46 46
WNT4 -0.042 0.18 -9999 0 -0.6 62 62
NFAT1/CK1 alpha -0.079 0.13 -9999 0 -0.46 43 43
GNG2 0.009 0.06 -9999 0 -0.62 6 6
WNT5A -0.006 0.11 -9999 0 -0.61 23 23
WNT11 -0.024 0.15 -9999 0 -0.61 42 42
CDC42 -0.015 0.13 -9999 0 -0.45 22 22
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.019 0.11 -10000 0 -0.27 85 85
epithelial cell differentiation -0.062 0.12 -10000 0 -0.32 78 78
CYFIP2 0.008 0.068 -10000 0 -0.61 8 8
ENAH 0.018 0.11 -10000 0 -0.39 2 2
EGFR -0.11 0.25 -10000 0 -0.6 138 138
EPHA2 -0.017 0.14 -10000 0 -0.59 35 35
MYO6 -0.021 0.13 -10000 0 -10000 0 0
CTNNB1 0.015 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.004 0.04 -10000 0 -0.37 8 8
AQP5 -0.19 0.2 -10000 0 -0.51 163 163
CTNND1 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.13 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.15 -10000 0 -0.6 7 7
EGF -0.038 0.18 -10000 0 -0.61 57 57
NCKAP1 0.015 0 -10000 0 -10000 0 0
AQP3 -0.077 0.14 -10000 0 -0.54 34 34
cortical microtubule organization -0.062 0.12 -10000 0 -0.32 78 78
GO:0000145 -0.02 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.062 0.12 -10000 0 -0.32 78 78
MLLT4 0.014 0.025 -10000 0 -0.62 1 1
ARF6/GDP -0.058 0.11 -10000 0 -0.49 11 11
ARF6 0.015 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.074 -10000 0 -0.34 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.022 0.14 -10000 0 -0.42 12 12
PVRL2 0.014 0.025 -10000 0 -0.62 1 1
ZYX -0.029 0.14 -10000 0 -0.6 1 1
ARF6/GTP -0.017 0.066 -10000 0 -10000 0 0
CDH1 -0.11 0.25 -10000 0 -0.61 136 136
EGFR/EGFR/EGF/EGF -0.14 0.18 -10000 0 -0.59 53 53
RhoA/GDP -0.057 0.11 -10000 0 -10000 0 0
actin cytoskeleton organization -0.014 0.13 -10000 0 -0.58 1 1
IGF-1R heterotetramer 0.005 0.081 -10000 0 -0.62 11 11
GIT1 0.014 0.025 -10000 0 -0.62 1 1
IGF1R 0.005 0.081 -10000 0 -0.62 11 11
IGF1 -0.005 0.11 -10000 0 -0.61 22 22
DIAPH1 -0.003 0.065 -10000 0 -0.72 5 5
Wnt receptor signaling pathway 0.062 0.12 0.32 78 -10000 0 78
RHOA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.11 -10000 0 -0.49 11 11
CTNNA1 0.015 0 -10000 0 -10000 0 0
VCL -0.015 0.13 -10000 0 -0.6 1 1
EFNA1 0.012 0.041 -10000 0 -0.6 3 3
LPP -0.035 0.15 -10000 0 -0.56 11 11
Ephrin A1/EPHA2 -0.069 0.13 -10000 0 -0.56 10 10
SEC6/SEC8 -0.049 0.098 -10000 0 -0.54 2 2
MGAT3 -0.035 0.15 -10000 0 -0.62 7 7
HGF/MET -0.18 0.21 -10000 0 -0.61 91 91
HGF -0.088 0.23 -10000 0 -0.6 113 113
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.019 0.11 -10000 0 -0.27 85 85
actin cable formation 0.03 0.11 -10000 0 -0.37 5 5
KIAA1543 -0.077 0.2 -10000 0 -0.6 39 39
KIFC3 -0.022 0.13 -10000 0 -0.62 1 1
NCK1 0.015 0 -10000 0 -10000 0 0
EXOC3 0.015 0 -10000 0 -10000 0 0
ACTN1 -0.043 0.16 -10000 0 -0.59 10 10
NCK1/GIT1 -0.001 0.018 -10000 0 -0.46 1 1
mol:GDP -0.062 0.12 -10000 0 -0.32 78 78
EXOC4 0.015 0 -10000 0 -10000 0 0
STX4 -0.021 0.13 -10000 0 -10000 0 0
PIP5K1C -0.022 0.13 -10000 0 -10000 0 0
LIMA1 0.008 0.07 -10000 0 -0.62 8 8
ABI1 0.015 0 -10000 0 -10000 0 0
ROCK1 -0.05 0.093 -10000 0 -0.42 11 11
adherens junction assembly -0.056 0.19 -10000 0 -0.58 40 40
IGF-1R heterotetramer/IGF1 -0.068 0.13 -10000 0 -0.61 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.025 -10000 0 -0.46 2 2
MET -0.16 0.28 -10000 0 -0.6 194 194
PLEKHA7 -0.026 0.14 -10000 0 -0.62 5 5
mol:GTP -0.018 0.073 -10000 0 -0.34 6 6
establishment of epithelial cell apical/basal polarity 0.014 0.12 -10000 0 -0.51 2 2
cortical actin cytoskeleton stabilization -0.019 0.11 -10000 0 -0.27 85 85
regulation of cell-cell adhesion -0.014 0.13 -10000 0 -0.58 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.019 0.11 -10000 0 -0.27 85 85
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.021 0.12 -10000 0 -0.39 28 28
CRKL 0.027 0.11 -10000 0 -0.42 27 27
HRAS 0.005 0.14 -10000 0 -0.5 17 17
mol:PIP3 0.003 0.11 -10000 0 -0.4 32 32
SPRED1 0.015 0 -10000 0 -10000 0 0
SPRED2 0.011 0.054 -10000 0 -0.61 5 5
GAB1 0.019 0.12 -10000 0 -0.44 29 29
FOXO3 0.028 0.11 -10000 0 -0.38 28 28
AKT1 0.02 0.11 -10000 0 -0.42 28 28
BAD 0.028 0.11 -10000 0 -0.38 28 28
megakaryocyte differentiation 0.012 0.12 -10000 0 -0.4 42 42
GSK3B 0.028 0.11 -10000 0 -0.38 28 28
RAF1 0.017 0.12 -10000 0 -0.39 17 17
SHC1 0.001 0.092 -10000 0 -0.59 16 16
STAT3 0.019 0.11 -10000 0 -0.43 29 29
STAT1 0.013 0.24 -10000 0 -1 30 30
HRAS/SPRED1 -0.043 0.089 -10000 0 -0.39 17 17
cell proliferation 0.015 0.12 0.25 1 -0.39 43 44
PIK3CA 0.015 0 -10000 0 -10000 0 0
TEC -0.012 0.13 -10000 0 -0.6 30 30
RPS6KB1 0.018 0.12 0.24 1 -0.4 37 38
HRAS/SPRED2 -0.045 0.093 -10000 0 -0.39 21 21
LYN/TEC/p62DOK -0.037 0.11 -10000 0 -0.44 32 32
MAPK3 0.03 0.094 -10000 0 -0.32 6 6
STAP1 -0.007 0.15 -10000 0 -0.45 42 42
GRAP2 -0.034 0.17 -10000 0 -0.61 53 53
JAK2 -0.049 0.18 -10000 0 -0.82 30 30
STAT1 (dimer) 0.014 0.24 -10000 0 -0.98 30 30
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.065 0.13 -10000 0 -0.45 42 42
actin filament polymerization 0.012 0.12 -10000 0 -0.4 40 40
LYN 0.011 0.053 -10000 0 -0.6 5 5
STAP1/STAT5A (dimer) 0 0.18 -10000 0 -0.59 38 38
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
CBL/CRKL/GRB2 0.037 0.1 -10000 0 -0.37 27 27
PI3K 0.026 0.11 -10000 0 -0.41 27 27
PTEN 0.015 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.002 0.29 -10000 0 -1.2 29 29
MAPK8 0.015 0.12 0.25 1 -0.39 43 44
STAT3 (dimer) 0.02 0.11 -10000 0 -0.42 29 29
positive regulation of transcription 0.03 0.081 -10000 0 -0.26 5 5
mol:GDP -0.067 0.13 0.23 2 -0.5 29 31
PIK3C2B 0.012 0.13 0.25 1 -0.39 50 51
CBL/CRKL 0.034 0.11 -10000 0 -0.39 27 27
FER 0.013 0.12 -10000 0 -0.4 41 41
SH2B3 0.018 0.12 -10000 0 -0.42 33 33
PDPK1 0.012 0.1 -10000 0 -0.37 30 30
SNAI2 -0.015 0.15 -10000 0 -0.43 48 48
positive regulation of cell proliferation 0.02 0.18 -10000 0 -0.72 30 30
KITLG 0.011 0.076 -10000 0 -0.64 9 9
cell motility 0.02 0.18 -10000 0 -0.72 30 30
PTPN6 -0.006 0.08 -10000 0 -0.62 11 11
EPOR 0.045 0.082 -10000 0 -0.62 2 2
STAT5A (dimer) 0.02 0.15 -10000 0 -0.59 31 31
SOCS1 -0.059 0.2 -10000 0 -0.59 82 82
cell migration 0.035 0.16 0.35 89 -10000 0 89
SOS1 0.015 0 -10000 0 -10000 0 0
EPO -0.023 0.15 -10000 0 -0.59 43 43
VAV1 -0.01 0.12 -10000 0 -0.62 27 27
GRB10 0.015 0.12 -10000 0 -0.43 34 34
PTPN11 0.011 0.035 -10000 0 -0.62 2 2
SCF/KIT 0.01 0.12 0.24 10 -0.42 38 48
GO:0007205 -0.002 0.006 -10000 0 -10000 0 0
MAP2K1 0.026 0.1 -10000 0 -0.36 6 6
CBL 0.014 0.025 -10000 0 -0.62 1 1
KIT -0.007 0.29 -10000 0 -1.3 29 29
MAP2K2 0.026 0.1 -10000 0 -0.32 11 11
SHC/Grb2/SOS1 -0.03 0.1 -10000 0 -0.45 27 27
STAT5A 0.019 0.16 -10000 0 -0.61 30 30
GRB2 0.014 0.023 -10000 0 -0.59 1 1
response to radiation -0.014 0.15 -10000 0 -0.42 48 48
SHC/GRAP2 -0.045 0.14 -10000 0 -0.45 67 67
PTPRO 0.012 0.13 -10000 0 -0.41 42 42
SH2B2 0.012 0.13 -10000 0 -0.41 40 40
DOK1 0.014 0.025 -10000 0 -0.62 1 1
MATK -0.036 0.16 -10000 0 -0.36 89 89
CREBBP 0.042 0.028 -10000 0 -0.62 1 1
BCL2 0.041 0.12 -10000 0 -1.2 4 4
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 -10000 0 -0.45 6 6
epithelial cell differentiation -0.042 0.09 -10000 0 -0.47 8 8
ITCH 0.021 0.015 -10000 0 -10000 0 0
WWP1 0.025 0.056 -10000 0 -10000 0 0
FYN 0.015 0 -10000 0 -10000 0 0
EGFR -0.11 0.25 -10000 0 -0.6 138 138
PRL -0.003 0.056 -10000 0 -0.59 6 6
neuron projection morphogenesis -0.027 0.16 -10000 0 -0.52 13 13
PTPRZ1 0.007 0.074 -10000 0 -0.62 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.091 0.14 -10000 0 -0.58 13 13
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.071 0.17 -10000 0 -0.47 28 28
ADAM17 0.016 0.057 -10000 0 -0.62 5 5
ErbB4/ErbB4 0.02 0.071 -10000 0 -0.42 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.041 0.17 -10000 0 -0.41 110 110
NCOR1 0.013 0.035 -10000 0 -0.62 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.059 0.16 -10000 0 -0.44 26 26
GRIN2B -0.14 0.22 -10000 0 -0.59 65 65
ErbB4/ErbB2/betacellulin -0.035 0.15 -10000 0 -0.45 26 26
STAT1 0.001 0.092 -10000 0 -0.59 16 16
HBEGF 0.003 0.084 -10000 0 -0.59 13 13
PRLR -0.024 0.15 -10000 0 -0.61 42 42
E4ICDs/ETO2 0.004 0.1 -10000 0 -0.4 29 29
axon guidance -0.009 0.075 -10000 0 -0.38 2 2
NEDD4 0.014 0.065 -10000 0 -0.6 7 7
Prolactin receptor/Prolactin receptor/Prolactin -0.032 0.12 -10000 0 -0.45 47 47
CBFA2T3 -0.014 0.13 -10000 0 -0.62 31 31
ErbB4/ErbB2/HBEGF 0.022 0.085 -10000 0 -0.38 13 13
MAPK3 -0.037 0.16 -10000 0 -0.54 13 13
STAT1 (dimer) 0.014 0.082 -10000 0 -0.45 4 4
MAPK1 -0.037 0.16 -10000 0 -0.54 13 13
JAK2 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.064 0.17 -10000 0 -0.45 31 31
NRG1 -0.1 0.22 -10000 0 -0.45 183 183
NRG3 -0.09 0.24 -10000 0 -0.62 110 110
NRG2 0.009 0.065 -10000 0 -0.62 7 7
NRG4 -0.031 0.16 -10000 0 -0.59 50 50
heart development -0.009 0.075 -10000 0 -0.38 2 2
neural crest cell migration -0.064 0.17 -10000 0 -0.44 31 31
ERBB2 0.02 0.072 -10000 0 -0.43 16 16
WWOX/E4ICDs 0.022 0.059 -10000 0 -0.37 1 1
SHC1 0.001 0.092 -10000 0 -0.59 16 16
ErbB4/EGFR/neuregulin 4 -0.1 0.16 -10000 0 -0.49 47 47
apoptosis 0.082 0.17 0.44 110 -10000 0 110
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.018 0.076 -10000 0 -0.45 8 8
ErbB4/ErbB2/epiregulin -0.008 0.12 -10000 0 -0.4 26 26
ErbB4/ErbB4/betacellulin/betacellulin -0.046 0.15 -10000 0 -0.38 76 76
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.037 0.097 -10000 0 -0.5 14 14
MDM2 0.02 0.083 -10000 0 -0.39 13 13
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.092 0.14 -10000 0 -0.42 26 26
STAT5A -0.005 0.087 -10000 0 -0.43 8 8
ErbB4/EGFR/neuregulin 1 beta -0.13 0.22 -10000 0 -0.55 72 72
DLG4 0.005 0.077 -10000 0 -0.59 11 11
GRB2/SHC -0.011 0.066 -10000 0 -0.42 17 17
E4ICDs/TAB2/NCoR1 -0.016 0.047 -10000 0 -0.43 3 3
STAT5A (dimer) -0.045 0.096 -10000 0 -0.52 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0 0.07 -10000 0 -10000 0 0
LRIG1 0.003 0.088 -10000 0 -0.62 13 13
EREG -0.038 0.16 -10000 0 -0.59 55 55
BTC -0.089 0.23 -10000 0 -0.61 109 109
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.009 0.076 -10000 0 -0.38 2 2
ERBB4 0.02 0.071 -10000 0 -0.43 1 1
STAT5B 0.015 0 -10000 0 -10000 0 0
YAP1 -0.031 0.12 -10000 0 -0.6 29 29
GRB2 0.014 0.023 -10000 0 -0.59 1 1
ErbB4/ErbB2/neuregulin 4 0.001 0.11 -10000 0 -0.44 15 15
glial cell differentiation 0.016 0.047 0.42 3 -10000 0 3
WWOX 0.015 0 -10000 0 -10000 0 0
cell proliferation -0.093 0.19 -10000 0 -0.57 37 37
TCGA08_rtk_signaling

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
PDGFRA -0.068 0.21 -10000 0 -0.62 88 88
HRAS 0.015 0 -10000 0 -10000 0 0
EGFR -0.11 0.25 -10000 0 -0.6 138 138
AKT 0.021 0.05 -10000 0 -0.38 7 7
FOXO3 0.014 0.025 -10000 0 -0.62 1 1
AKT1 0.014 0.023 -10000 0 -0.59 1 1
FOXO1 0.014 0.025 -10000 0 -0.62 1 1
AKT3 0.01 0.06 -10000 0 -0.62 6 6
FOXO4 0.012 0.043 -10000 0 -0.62 3 3
MET -0.16 0.28 -10000 0 -0.6 194 194
PIK3CA 0.015 0 -10000 0 -10000 0 0
PIK3CB 0.014 0.025 -10000 0 -0.62 1 1
NRAS 0.015 0 -10000 0 -10000 0 0
PIK3CG -0.037 0.17 -10000 0 -0.61 56 56
PIK3R3 0.012 0.041 -10000 0 -0.6 3 3
PIK3R2 0.015 0 -10000 0 -10000 0 0
NF1 0.01 0.055 -10000 0 -0.62 5 5
RAS -0.062 0.12 0.24 1 -0.32 71 72
ERBB2 0.005 0.078 -10000 0 -0.59 11 11
proliferation/survival/translation -0.012 0.05 0.22 5 -10000 0 5
PI3K -0.038 0.12 -10000 0 -0.27 101 101
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
KRAS 0.014 0.023 -10000 0 -0.59 1 1
FOXO 0.029 0.033 -10000 0 -10000 0 0
AKT2 0.015 0 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.035 -10000 0 -0.62 2 2
ANTXR2 0.004 0.081 -10000 0 -0.59 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.011 -10000 0 -0.074 14 14
monocyte activation -0.13 0.24 -10000 0 -0.52 155 155
MAP2K2 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 -0.001 0.008 -10000 0 -10000 0 0
MAP2K7 -0.002 0.016 -10000 0 -0.34 1 1
MAP2K6 -0.002 0.016 -10000 0 -0.34 1 1
CYAA 0.011 0.048 -10000 0 -0.32 14 14
MAP2K4 -0.001 0.008 -10000 0 -10000 0 0
IL1B -0.079 0.15 -10000 0 -0.32 192 192
Channel -0.007 0.048 -10000 0 -0.34 14 14
NLRP1 -0.003 0.028 -10000 0 -0.34 4 4
CALM1 0.015 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.011 0.074 14 -10000 0 14
MAPK3 -0.001 0.008 -10000 0 -10000 0 0
MAPK1 -0.001 0.008 -10000 0 -10000 0 0
PGR -0.054 0.12 -10000 0 -0.35 103 103
PA/Cellular Receptors -0.008 0.053 -10000 0 -0.37 14 14
apoptosis -0.002 0.011 -10000 0 -0.074 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.012 0.046 -10000 0 -0.3 14 14
macrophage activation 0.022 0.01 -10000 0 -10000 0 0
TNF -0.13 0.26 -10000 0 -0.6 152 152
VCAM1 -0.13 0.24 -10000 0 -0.52 155 155
platelet activation -0.002 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.012 -10000 0 -10000 0 0
IL18 -0.006 0.09 -10000 0 -0.33 46 46
negative regulation of macrophage activation -0.002 0.011 -10000 0 -0.074 14 14
LEF -0.002 0.011 -10000 0 -0.074 14 14
CASP1 -0.004 0.02 -10000 0 -0.19 4 4
mol:cAMP -0.002 0.012 -10000 0 -10000 0 0
necrosis -0.002 0.011 -10000 0 -0.074 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.012 0.048 -10000 0 -0.32 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.01 0.12 -10000 0 -0.42 55 55
MAP4K4 -0.015 0.12 -10000 0 -0.46 18 18
BAG4 0.003 0.088 -10000 0 -0.62 13 13
PKC zeta/ceramide -0.022 0.097 0.18 11 -0.32 47 58
NFKBIA 0.014 0.023 -10000 0 -0.59 1 1
BIRC3 -0.059 0.2 -10000 0 -0.6 81 81
BAX 0.008 0.029 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
AKT1 0.025 0.029 -10000 0 -0.55 1 1
BAD 0.007 0.053 0.19 18 -10000 0 18
SMPD1 -0.018 0.088 -10000 0 -0.27 13 13
RB1 0.007 0.055 0.19 18 -0.43 1 19
FADD/Caspase 8 -0.003 0.12 -10000 0 -0.43 21 21
MAP2K4 0.014 0.056 -10000 0 -0.32 4 4
NSMAF 0.015 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.013 0.057 0.19 9 -0.3 5 14
EGF -0.038 0.18 -10000 0 -0.61 57 57
mol:ceramide -0.003 0.057 0.18 50 -10000 0 50
MADD 0.012 0.043 -10000 0 -0.62 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.12 -10000 0 -0.42 55 55
ASAH1 0.015 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.006 0.055 0.19 18 -0.42 1 19
cell proliferation -0.021 0.078 -10000 0 -0.41 15 15
BID -0.004 0.093 -10000 0 -0.38 15 15
MAP3K1 0.005 0.059 0.18 22 -0.35 4 26
EIF2A 0.022 0.053 -10000 0 -0.33 3 3
TRADD 0.014 0.025 -10000 0 -0.62 1 1
CRADD 0.015 0 -10000 0 -10000 0 0
MAPK3 0.026 0.054 -10000 0 -0.29 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.026 0.054 -10000 0 -0.29 4 4
Cathepsin D/ceramide 0.005 0.052 0.18 18 -0.32 1 19
FADD -0.015 0.12 -10000 0 -0.46 18 18
KSR1 0.005 0.06 0.18 22 -0.33 5 27
MAPK8 -0.002 0.079 0.19 11 -0.25 38 49
PRKRA 0.007 0.053 0.18 22 -10000 0 22
PDGFA -0.034 0.17 -10000 0 -0.59 55 55
TRAF2 0.015 0 -10000 0 -10000 0 0
IGF1 -0.005 0.11 -10000 0 -0.61 22 22
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.003 0.057 0.17 50 -10000 0 50
CTSD 0.014 0.023 -10000 0 -0.59 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.005 0.092 -10000 0 -0.45 15 15
PRKCD -0.008 0.12 -10000 0 -0.62 24 24
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.12 -10000 0 -0.42 55 55
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.036 0.17 -10000 0 -0.6 56 56
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.026 0.13 -10000 0 -0.5 18 18
TNFR1A/BAG4/TNF-alpha -0.098 0.17 -10000 0 -0.38 171 171
mol:Sphingosine-1-phosphate -0.01 0.12 -10000 0 -0.42 55 55
MAP2K1 0.021 0.055 -10000 0 -0.3 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
CYCS 0.009 0.04 0.16 11 -10000 0 11
TNFRSF1A 0.002 0.09 -10000 0 -0.61 14 14
NFKB1 0.015 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.018 0.091 -10000 0 -0.46 26 26
EIF2AK2 0.014 0.056 -10000 0 -0.36 3 3
TNF-alpha/TNFR1A/FAN -0.091 0.16 -10000 0 -0.37 164 164
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.08 -10000 0 -0.33 10 10
MAP2K2 0.021 0.055 -10000 0 -0.3 4 4
SMPD3 -0.054 0.15 -10000 0 -0.37 81 81
TNF -0.13 0.26 -10000 0 -0.6 152 152
PKC zeta/PAR4 -0.072 0.18 -10000 0 -0.47 102 102
mol:PHOSPHOCHOLINE 0.001 0.077 0.22 51 -10000 0 51
NF kappa B1/RelA/I kappa B alpha -0.05 0.12 -10000 0 -0.62 10 10
AIFM1 0.009 0.04 0.23 2 -10000 0 2
BCL2 0.012 0.043 -10000 0 -0.62 3 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.055 0.15 0.46 81 -10000 0 81
KIRREL -0.032 0.16 -10000 0 -0.63 47 47
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.056 0.15 -10000 0 -0.46 81 81
PLCG1 0.015 0 -10000 0 -10000 0 0
ARRB2 0.015 0 -10000 0 -10000 0 0
WASL 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.041 0.11 -10000 0 -0.64 4 4
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.003 0.092 -10000 0 -0.47 4 4
FYN -0.018 0.11 -10000 0 -0.35 43 43
mol:Ca2+ -0.041 0.11 -10000 0 -0.44 12 12
mol:DAG -0.041 0.11 -10000 0 -0.44 12 12
NPHS2 -0.005 0.044 -10000 0 -0.59 3 3
mol:IP3 -0.041 0.11 -10000 0 -0.44 12 12
regulation of endocytosis -0.035 0.096 -10000 0 -0.57 4 4
Nephrin/NEPH1/podocin/Cholesterol -0.043 0.12 -10000 0 -0.34 84 84
establishment of cell polarity -0.055 0.15 -10000 0 -0.46 81 81
Nephrin/NEPH1/podocin/NCK1-2 -0.037 0.1 -10000 0 -0.59 4 4
Nephrin/NEPH1/beta Arrestin2 -0.009 0.11 -10000 0 -0.58 4 4
NPHS1 -0.026 0.14 -10000 0 -0.59 38 38
Nephrin/NEPH1/podocin -0.036 0.11 -10000 0 -0.35 43 43
TJP1 0.015 0 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
NCK2 0.015 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.041 0.11 -10000 0 -0.64 4 4
CD2AP 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.042 0.11 -10000 0 -0.44 13 13
GRB2 0.014 0.023 -10000 0 -0.59 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.038 0.14 -10000 0 -0.4 48 48
cytoskeleton organization 0.005 0.11 -10000 0 -0.57 4 4
Nephrin/NEPH1 -0.04 0.11 -10000 0 -0.33 81 81
Nephrin/NEPH1/ZO-1 -0.044 0.12 -10000 0 -0.36 81 81
Aurora A 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
Aurora A/GADD45A 0 0.11 -9999 0 -0.38 38 38
BIRC5 -0.19 0.29 -9999 0 -0.6 225 225
NFKBIA 0.028 0.068 -9999 0 -0.32 2 2
CPEB1 0 0.098 -9999 0 -0.62 16 16
AKT1 0.028 0.068 -9999 0 -0.33 1 1
NDEL1 0.015 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.002 0.06 -9999 0 -0.31 3 3
NDEL1/TACC3 -0.01 0.1 -9999 0 -0.45 20 20
GADD45A -0.022 0.14 -9999 0 -0.59 41 41
GSK3B 0.021 0.016 -9999 0 -10000 0 0
PAK1/Aurora A 0.002 0.1 -9999 0 -0.34 34 34
MDM2 0.003 0.083 -9999 0 -0.59 13 13
JUB -0.007 0.12 -9999 0 -0.62 23 23
TPX2 -0.041 0.17 -9999 0 -0.44 98 98
TP53 0.021 0.069 -9999 0 -0.28 15 15
DLG7 0.016 0.066 -9999 0 -0.3 1 1
AURKAIP1 0.014 0.023 -9999 0 -0.59 1 1
ARHGEF7 0.015 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.011 0.11 -9999 0 -0.48 20 20
G2/M transition of mitotic cell cycle 0.002 0.06 -9999 0 -0.31 3 3
AURKA 0.022 0.082 -9999 0 -0.36 1 1
AURKB -0.099 0.14 -9999 0 -0.3 205 205
CDC25B 0.023 0.063 -9999 0 -0.28 1 1
G2/M transition checkpoint -0.009 0.082 -9999 0 -0.32 24 24
mRNA polyadenylation -0.006 0.083 -9999 0 -0.39 17 17
Aurora A/CPEB -0.006 0.084 -9999 0 -0.4 17 17
Aurora A/TACC1/TRAP/chTOG 0.009 0.059 -9999 0 -0.47 1 1
BRCA1 0.012 0.04 -9999 0 -0.59 3 3
centrosome duplication 0.002 0.1 -9999 0 -0.34 34 34
regulation of centrosome cycle -0.02 0.093 -9999 0 -0.45 20 20
spindle assembly -0.003 0.048 -9999 0 -0.46 1 1
TDRD7 0.013 0.035 -9999 0 -0.62 2 2
Aurora A/RasGAP/Survivin -0.1 0.15 -9999 0 -0.43 55 55
CENPA -0.093 0.14 -9999 0 -0.3 175 175
Aurora A/PP2A 0.023 0.064 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.033 0.059 -9999 0 -0.27 1 1
negative regulation of DNA binding 0.021 0.069 -9999 0 -0.28 15 15
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.018 -9999 0 -0.46 1 1
RASA1 0.015 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.009 0.082 -9999 0 -0.33 24 24
mitotic prometaphase 0.022 0.037 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.082 -9999 0 -0.36 1 1
TACC1 0.015 0 -9999 0 -10000 0 0
TACC3 -0.016 0.13 -9999 0 -0.59 34 34
Aurora A/Antizyme1 0.006 0.059 -9999 0 -10000 0 0
Aurora A/RasGAP 0.023 0.064 -9999 0 -10000 0 0
OAZ1 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.016 -9999 0 -10000 0 0
GIT1 0.014 0.025 -9999 0 -0.62 1 1
GIT1/beta-PIX/PAK1 -0.02 0.083 -9999 0 -0.36 38 38
Importin alpha/Importin beta/TPX2 -0.041 0.16 -9999 0 -0.44 98 98
PPP2R5D 0.015 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.019 0.15 -9999 0 -0.44 52 52
PAK1 -0.018 0.14 -9999 0 -0.59 37 37
CKAP5 0.015 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.03 0.094 -10000 0 -0.34 29 29
ER alpha/Gai/GDP/Gbeta gamma 0.015 0.12 -10000 0 -0.41 32 32
AKT1 0.022 0.11 -10000 0 -0.73 13 13
PIK3CA 0.015 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.019 0.11 -10000 0 -0.7 14 14
mol:Ca2+ -0.008 0.14 -10000 0 -0.49 29 29
IGF1R 0.005 0.081 -10000 0 -0.62 11 11
E2/ER alpha (dimer)/Striatin -0.027 0.1 -10000 0 -0.39 46 46
SHC1 0.001 0.092 -10000 0 -0.59 16 16
apoptosis -0.022 0.11 0.69 13 -10000 0 13
RhoA/GTP -0.009 0.048 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.03 0.096 -10000 0 -0.43 26 26
regulation of stress fiber formation -0.03 0.098 0.46 9 -10000 0 9
E2/ERA-ERB (dimer) -0.033 0.11 -10000 0 -0.38 59 59
KRAS 0.014 0.023 -10000 0 -0.59 1 1
G13/GTP -0.012 0.062 -10000 0 -0.34 23 23
pseudopodium formation 0.03 0.098 -10000 0 -0.46 9 9
E2/ER alpha (dimer)/PELP1 -0.014 0.072 -10000 0 -0.38 25 25
GRB2 0.014 0.023 -10000 0 -0.59 1 1
GNG2 0.009 0.06 -10000 0 -0.62 6 6
GNAO1 -0.012 0.13 -10000 0 -0.62 28 28
HRAS 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.023 0.11 -10000 0 -0.4 27 27
E2/ER beta (dimer) -0.024 0.1 -10000 0 -0.44 37 37
mol:GDP -0.025 0.083 -10000 0 -0.38 23 23
mol:NADP 0.023 0.11 -10000 0 -0.4 27 27
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
mol:IP3 -0.009 0.15 -10000 0 -0.51 29 29
IGF-1R heterotetramer 0.005 0.081 -10000 0 -0.62 11 11
PLCB1 -0.012 0.14 -10000 0 -0.49 26 26
PLCB2 0.004 0.12 -10000 0 -0.56 18 18
IGF1 -0.005 0.11 -10000 0 -0.61 22 22
mol:L-citrulline 0.023 0.11 -10000 0 -0.4 27 27
RHOA 0.015 0 -10000 0 -10000 0 0
Gai/GDP -0.042 0.16 -10000 0 -0.77 28 28
JNK cascade -0.024 0.1 -10000 0 -0.44 37 37
BCAR1 0.014 0.025 -10000 0 -0.62 1 1
ESR2 -0.019 0.14 -10000 0 -0.6 37 37
GNAQ 0.015 0 -10000 0 -10000 0 0
ESR1 -0.006 0.11 -10000 0 -0.61 23 23
Gq family/GDP/Gbeta gamma 0.016 0.11 -10000 0 -0.44 30 30
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.031 0.061 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.11 -10000 0 -0.47 32 32
GNAZ 0.012 0.043 -10000 0 -0.62 3 3
E2/ER alpha (dimer) -0.015 0.082 -10000 0 -0.45 23 23
STRN -0.008 0.12 -10000 0 -0.62 24 24
GNAL -0.13 0.27 -10000 0 -0.62 149 149
PELP1 0.013 0.035 -10000 0 -0.62 2 2
MAPK11 -0.001 0.093 -10000 0 -0.37 40 40
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 -0.02 0.15 -10000 0 -0.62 37 37
HBEGF -0.047 0.16 -10000 0 -0.52 37 37
cAMP biosynthetic process -0.095 0.16 -10000 0 -0.34 185 185
SRC 0.023 0.12 -10000 0 -0.42 26 26
PI3K -0.002 0.03 -10000 0 -0.46 3 3
GNB1 0.015 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.023 0.076 -10000 0 -0.37 14 14
SOS1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.038 0.1 -10000 0 -0.45 24 24
Gs family/GTP -0.097 0.17 -10000 0 -0.35 185 185
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0.012 -10000 0 -0.32 1 1
vasodilation 0.023 0.11 -10000 0 -0.38 27 27
mol:DAG -0.009 0.15 -10000 0 -0.51 29 29
Gs family/GDP/Gbeta gamma -0.075 0.13 -10000 0 -0.42 38 38
MSN 0.03 0.1 -10000 0 -0.51 9 9
Gq family/GTP -0.034 0.098 -10000 0 -0.45 21 21
mol:PI-3-4-5-P3 0.02 0.11 -10000 0 -0.68 14 14
NRAS 0.015 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.023 0.11 0.38 27 -10000 0 27
GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
RhoA/GDP -0.023 0.077 -10000 0 -0.35 23 23
NOS3 0.022 0.12 -10000 0 -0.41 27 27
GNA11 0.006 0.078 -10000 0 -0.62 10 10
MAPKKK cascade 0.027 0.12 -10000 0 -0.52 17 17
E2/ER alpha (dimer)/PELP1/Src -0.032 0.099 -10000 0 -0.45 26 26
ruffle organization 0.03 0.098 -10000 0 -0.46 9 9
ROCK2 0.04 0.076 -10000 0 -0.55 2 2
GNA14 -0.009 0.12 -10000 0 -0.61 26 26
GNA15 -0.009 0.12 -10000 0 -0.61 26 26
GNA13 0.015 0 -10000 0 -10000 0 0
MMP9 -0.099 0.2 -10000 0 -0.53 62 62
MMP2 0.011 0.14 -10000 0 -0.51 22 22
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.015 0 -9999 0 -10000 0 0
SPHK1 -0.025 0.15 -9999 0 -0.6 44 44
GNAI2 0.015 0 -9999 0 -10000 0 0
mol:S1P 0.009 0.069 -9999 0 -0.31 19 19
GNAO1 -0.012 0.13 -9999 0 -0.62 28 28
mol:Sphinganine-1-P -0.003 0.12 -9999 0 -0.44 44 44
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.013 0.053 -9999 0 -0.43 4 4
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.018 -9999 0 -0.46 1 1
S1PR3 -0.023 0.15 -9999 0 -0.6 41 41
S1PR2 0.011 0.053 -9999 0 -0.6 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.054 -9999 0 -0.27 19 19
S1PR5 -0.1 0.24 -9999 0 -0.61 128 128
S1PR4 0 0.096 -9999 0 -0.6 17 17
GNAI1 -0.02 0.15 -9999 0 -0.62 37 37
S1P/S1P5/G12 -0.045 0.15 -9999 0 -0.34 129 129
S1P/S1P3/Gq 0.001 0.11 -9999 0 -0.46 13 13
S1P/S1P4/Gi 0.012 0.11 -9999 0 -0.47 19 19
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.012 0.043 -9999 0 -0.62 3 3
GNA14 -0.009 0.12 -9999 0 -0.61 26 26
GNA15 -0.009 0.12 -9999 0 -0.61 26 26
GNA12 0.014 0.025 -9999 0 -0.62 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.006 0.078 -9999 0 -0.62 10 10
ABCC1 0.012 0.04 -9999 0 -0.59 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.003 0.085 -10000 0 -0.6 13 13
EPHB2 0.007 0.072 -10000 0 -0.6 9 9
EFNB1 -0.049 0.17 -10000 0 -0.44 110 110
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.084 0.15 -10000 0 -0.64 15 15
Ephrin B2/EPHB1-2 -0.054 0.14 -10000 0 -0.37 97 97
neuron projection morphogenesis -0.08 0.14 -10000 0 -0.61 15 15
Ephrin B1/EPHB1-2/Tiam1 -0.086 0.16 -10000 0 -0.7 15 15
DNM1 -0.083 0.22 -10000 0 -0.6 107 107
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.017 0.073 -10000 0 -0.73 6 6
YES1 -0.006 0.095 -10000 0 -0.99 6 6
Ephrin B1/EPHB1-2/NCK2 -0.085 0.16 -10000 0 -0.68 14 14
PI3K 0.016 0.077 -10000 0 -0.6 9 9
mol:GDP -0.087 0.16 -10000 0 -0.68 15 15
ITGA2B -0.028 0.16 -10000 0 -0.62 46 46
endothelial cell proliferation -0.01 0.062 -10000 0 -0.39 17 17
FYN -0.005 0.092 -10000 0 -0.97 6 6
MAP3K7 -0.004 0.075 -10000 0 -0.78 6 6
FGR -0.006 0.092 -10000 0 -0.96 6 6
TIAM1 0.013 0.035 -10000 0 -0.62 2 2
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
RGS3 0.012 0.046 -10000 0 -0.59 4 4
cell adhesion -0.048 0.16 -10000 0 -0.63 19 19
LYN -0.006 0.093 -10000 0 -0.97 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.008 0.088 -10000 0 -0.92 6 6
Ephrin B1/EPHB1-2 -0.011 0.081 -10000 0 -0.85 6 6
SRC -0.005 0.092 -10000 0 -0.96 6 6
ITGB3 -0.099 0.24 -10000 0 -0.6 125 125
EPHB1 -0.066 0.21 -10000 0 -0.62 84 84
EPHB4 0.011 0.052 -10000 0 -0.59 5 5
RAC1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.01 0.063 -10000 0 -0.39 17 17
alphaIIb/beta3 Integrin -0.11 0.2 -10000 0 -0.46 160 160
BLK -0.016 0.099 -10000 0 -1 6 6
HCK -0.008 0.1 -10000 0 -1 6 6
regulation of stress fiber formation 0.086 0.16 0.67 14 -10000 0 14
MAPK8 0.021 0.083 -10000 0 -0.57 10 10
Ephrin B1/EPHB1-2/RGS3 -0.087 0.16 -10000 0 -0.67 17 17
endothelial cell migration -0.009 0.084 -10000 0 -0.42 22 22
NCK2 0.015 0 -10000 0 -10000 0 0
PTPN13 0.004 0.076 -10000 0 -0.72 7 7
regulation of focal adhesion formation 0.086 0.16 0.67 14 -10000 0 14
chemotaxis 0.087 0.16 0.66 17 -10000 0 17
PIK3CA 0.015 0 -10000 0 -10000 0 0
Rac1/GTP -0.082 0.14 -10000 0 -0.63 15 15
angiogenesis -0.011 0.08 -10000 0 -0.84 6 6
LCK -0.025 0.1 -10000 0 -0.98 6 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.014 0.023 -10000 0 -0.59 1 1
NFATC1 0.032 0.099 -10000 0 -0.45 1 1
NFATC2 0.015 0.075 -10000 0 -0.27 16 16
NFATC3 -0.005 0.11 -10000 0 -0.42 43 43
YWHAE 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.069 0.18 -10000 0 -0.54 57 57
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.15 0.2 -10000 0 -0.49 124 124
BCL2/BAX -0.002 0.03 -10000 0 -0.46 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.003 -10000 0 -10000 0 0
BAX 0.015 0 -10000 0 -10000 0 0
MAPK14 0.014 0.023 -10000 0 -0.59 1 1
BAD 0.015 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.058 0.18 -10000 0 -0.52 57 57
Calcineurin A alpha-beta B1/BCL2 0.012 0.043 -10000 0 -0.62 3 3
FKBP8 0.015 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.057 0.18 0.5 57 -10000 0 57
KPNB1 0.015 0 -10000 0 -10000 0 0
KPNA2 0.014 0.023 -10000 0 -0.59 1 1
XPO1 0.015 0 -10000 0 -10000 0 0
SFN -0.12 0.25 -10000 0 -0.6 141 141
MAP3K8 -0.005 0.11 -10000 0 -0.59 22 22
NFAT4/CK1 alpha -0.021 0.069 -10000 0 -0.55 1 1
MEF2D/NFAT1/Cbp/p300 -0.024 0.073 -10000 0 -0.41 10 10
CABIN1 -0.07 0.19 -10000 0 -0.55 57 57
CALM1 0.015 0.003 -10000 0 -10000 0 0
RAN 0.015 0 -10000 0 -10000 0 0
MAP3K1 0.012 0.046 -10000 0 -0.59 4 4
CAMK4 -0.15 0.28 -10000 0 -0.61 176 176
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.015 0 -10000 0 -10000 0 0
YWHAH 0.003 0.083 -10000 0 -0.59 13 13
Calcineurin A alpha-beta B1/AKAP79/PKA -0.03 0.11 -10000 0 -0.42 48 48
YWHAB 0.015 0 -10000 0 -10000 0 0
MAPK8 0.007 0.074 -10000 0 -0.62 9 9
MAPK9 0.015 0 -10000 0 -10000 0 0
YWHAG 0.012 0.04 -10000 0 -0.59 3 3
FKBP1A 0.014 0.023 -10000 0 -0.59 1 1
NFAT1-c-4/YWHAQ -0.026 0.087 -10000 0 -0.49 2 2
PRKCH 0.015 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.035 -10000 0 -0.45 4 4
CASP3 0.013 0.033 -10000 0 -0.59 2 2
PIM1 0.009 0.061 -10000 0 -0.59 7 7
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.014 -10000 0 -0.37 1 1
apoptosis -0.001 0.017 -10000 0 -0.4 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.073 -10000 0 -0.33 1 1
PRKCB -0.072 0.22 -10000 0 -0.6 94 94
PRKCE 0.002 0.09 -10000 0 -0.59 15 15
JNK2/NFAT4 0.004 0.1 -10000 0 -0.38 42 42
BAD/BCL-XL -0.001 0.016 -10000 0 -0.42 1 1
PRKCD -0.008 0.12 -10000 0 -0.62 24 24
NUP214 0.015 0 -10000 0 -10000 0 0
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
PRKCA 0.013 0.035 -10000 0 -0.62 2 2
PRKCG -0.2 0.3 -10000 0 -0.6 230 230
PRKCQ -0.022 0.15 -10000 0 -0.62 39 39
FKBP38/BCL2 -0.002 0.03 -10000 0 -0.46 3 3
EP300 0.013 0.043 -10000 0 -0.62 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
NFATc/JNK1 0.034 0.1 -10000 0 -0.42 1 1
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 -0.001 0.017 -10000 0 -0.43 1 1
CSNK1A1 0.024 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.099 0.17 -10000 0 -0.38 176 176
NFATc/ERK1 0.039 0.094 -10000 0 -0.42 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.14 0.19 -10000 0 -0.48 125 125
NR4A1 0.034 0.13 -10000 0 -0.52 28 28
GSK3B 0.015 0.003 -10000 0 -10000 0 0
positive T cell selection -0.005 0.11 -10000 0 -0.42 43 43
NFAT1/CK1 alpha -0.018 0.041 -10000 0 -0.3 2 2
RCH1/ KPNB1 -0.001 0.016 -10000 0 -0.42 1 1
YWHAQ 0.015 0 -10000 0 -10000 0 0
PRKACA 0.015 0.003 -10000 0 -10000 0 0
AKAP5 -0.028 0.16 -10000 0 -0.59 48 48
MEF2D 0.015 0.025 -10000 0 -0.62 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.015 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.096 -10000 0 -0.4 2 2
CREBBP 0.015 0.025 -10000 0 -0.62 1 1
BCL2 0.012 0.043 -10000 0 -0.62 3 3
Signaling mediated by p38-gamma and p38-delta

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.003 0.12 -9999 0 -0.36 64 64
SNTA1 -0.015 0.13 -9999 0 -0.61 32 32
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 -0.004 0.12 -9999 0 -0.37 66 66
MAPK12 0.034 0.029 -9999 0 -0.34 3 3
CCND1 0.017 0.056 -9999 0 -0.42 8 8
p38 gamma/SNTA1 0.023 0.079 -9999 0 -0.32 23 23
MAP2K3 0.013 0.033 -9999 0 -0.59 2 2
PKN1 0.015 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.034 0.029 -9999 0 -0.34 3 3
MAP2K6 0.028 0.022 -9999 0 -0.34 2 2
MAPT -0.005 0.13 -9999 0 -0.38 57 57
MAPK13 -0.017 0.14 -9999 0 -0.44 64 64
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.02 0.018 -9999 0 -0.31 2 2
S1P4 pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.012 0.13 -9999 0 -0.62 28 28
CDC42/GTP -0.026 0.086 -9999 0 -0.5 12 12
PLCG1 0.018 0.1 -9999 0 -0.51 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.018 -9999 0 -0.46 1 1
cell migration -0.025 0.084 -9999 0 -0.48 12 12
S1PR5 -0.1 0.24 -9999 0 -0.61 128 128
S1PR4 0 0.096 -9999 0 -0.6 17 17
MAPK3 0.018 0.1 -9999 0 -0.51 12 12
MAPK1 0.018 0.1 -9999 0 -0.51 12 12
S1P/S1P5/Gi -0.035 0.14 -9999 0 -0.31 94 94
GNAI1 -0.02 0.15 -9999 0 -0.62 37 37
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.073 0.15 -9999 0 -0.38 128 128
RHOA 0.029 0.054 -9999 0 -0.3 18 18
S1P/S1P4/Gi 0.008 0.11 -9999 0 -0.53 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.043 -9999 0 -0.62 3 3
S1P/S1P4/G12/G13 -0.009 0.053 -9999 0 -0.33 18 18
GNA12 0.014 0.025 -9999 0 -0.62 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.052 -9999 0 -0.59 5 5
alphaV beta3 Integrin -0.081 0.17 -9999 0 -0.43 126 126
PTK2 -0.05 0.13 -9999 0 -0.54 32 32
positive regulation of JNK cascade -0.014 0.061 -9999 0 -0.33 22 22
CDC42/GDP 0.038 0.1 -9999 0 -0.45 22 22
Rac1/GDP 0.04 0.1 -9999 0 -0.45 22 22
RAP1B 0.009 0.061 -9999 0 -0.59 7 7
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.018 0.075 -9999 0 -0.41 22 22
nectin-3/I-afadin -0.015 0.081 -9999 0 -0.45 22 22
RAPGEF1 0.029 0.11 -9999 0 -0.52 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.021 0.12 -9999 0 -0.58 22 22
PDGFB-D/PDGFRB 0.011 0.052 -9999 0 -0.59 5 5
TLN1 0.029 0.057 -9999 0 -0.4 6 6
Rap1/GTP -0.017 0.072 -9999 0 -0.37 24 24
IQGAP1 0.009 0.064 -9999 0 -0.61 7 7
Rap1/GTP/I-afadin -0.004 0.035 -9999 0 -0.32 8 8
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.081 -9999 0 -0.45 22 22
PVR 0.015 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.015 0 -9999 0 -10000 0 0
mol:GDP 0.033 0.12 -9999 0 -0.57 22 22
MLLT4 0.014 0.025 -9999 0 -0.62 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K -0.014 0.072 -9999 0 -0.76 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.018 0.089 -9999 0 -0.46 27 27
positive regulation of lamellipodium assembly -0.016 0.067 -9999 0 -0.35 23 23
PVRL1 -0.01 0.12 -9999 0 -0.62 26 26
PVRL3 -0.005 0.11 -9999 0 -0.62 21 21
PVRL2 0.014 0.025 -9999 0 -0.62 1 1
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
CDH1 -0.11 0.25 -9999 0 -0.61 136 136
CLDN1 -0.022 0.15 -9999 0 -0.6 40 40
JAM-A/CLDN1 -0.035 0.1 -9999 0 -0.34 69 69
SRC -0.033 0.12 -9999 0 -0.66 22 22
ITGB3 -0.099 0.24 -9999 0 -0.6 125 125
nectin-1(dimer)/I-afadin/I-afadin -0.018 0.089 -9999 0 -0.46 27 27
FARP2 0.026 0.12 -9999 0 -0.55 22 22
RAC1 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.012 0.067 -9999 0 -0.38 22 22
nectin-1/I-afadin -0.018 0.089 -9999 0 -0.46 27 27
nectin-2/I-afadin -0.001 0.025 -9999 0 -0.46 2 2
RAC1/GTP/IQGAP1/filamentous actin -0.004 0.038 -9999 0 -0.38 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.027 0.1 -9999 0 -0.39 47 47
CDC42/GTP/IQGAP1/filamentous actin -0.004 0.038 -9999 0 -0.38 7 7
F11R 0.006 0.074 -9999 0 -0.59 10 10
positive regulation of filopodium formation -0.014 0.061 -9999 0 -0.33 22 22
alphaV/beta3 Integrin/Talin -0.014 0.14 -9999 0 -0.48 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.025 -9999 0 -0.46 2 2
nectin-2(dimer)/I-afadin/I-afadin -0.001 0.025 -9999 0 -0.46 2 2
PIP5K1C 0.021 0.061 -9999 0 -0.44 6 6
VAV2 0.024 0.13 -9999 0 -0.58 23 23
RAP1/GDP -0.02 0.083 -9999 0 -0.43 22 22
ITGAV 0.014 0.025 -9999 0 -0.62 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.013 0.069 -9999 0 -0.38 23 23
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.081 -9999 0 -0.45 22 22
Rac1/GTP -0.019 0.082 -9999 0 -0.43 23 23
PTPRM 0.012 0.064 -9999 0 -0.46 6 6
E-cadherin/beta catenin/alpha catenin -0.069 0.14 -9999 0 -0.61 12 12
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.003 0.088 -9999 0 -0.62 13 13
Caspase 8 (4 units) -0.026 0.076 -9999 0 -0.4 14 14
NEF -0.002 0.031 -9999 0 -10000 0 0
NFKBIA 0.005 0.042 -9999 0 -0.58 1 1
BIRC3 -0.022 0.2 -9999 0 -0.57 81 81
CYCS 0.026 0.089 -9999 0 -0.39 9 9
RIPK1 0.015 0 -9999 0 -10000 0 0
CD247 -0.023 0.16 -9999 0 -0.66 37 37
MAP2K7 0.02 0.081 -9999 0 -0.38 6 6
protein ubiquitination 0.027 0.091 -9999 0 -0.41 5 5
CRADD 0.015 0 -9999 0 -10000 0 0
DAXX 0.015 0 -9999 0 -10000 0 0
FAS -0.019 0.14 -9999 0 -0.6 37 37
BID 0.018 0.093 -9999 0 -0.41 10 10
NF-kappa-B/RelA/I kappa B alpha -0.032 0.087 -9999 0 -0.33 1 1
TRADD 0.014 0.025 -9999 0 -0.62 1 1
MAP3K5 0.005 0.081 -9999 0 -0.62 11 11
CFLAR 0.015 0 -9999 0 -10000 0 0
FADD 0.015 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.033 0.088 -9999 0 -0.33 1 1
MAPK8 0.024 0.084 -9999 0 -0.34 7 7
APAF1 0.015 0 -9999 0 -10000 0 0
TRAF1 0.003 0.086 -9999 0 -0.61 13 13
TRAF2 0.015 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.096 -9999 0 -0.4 13 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.009 0.11 -9999 0 -0.49 8 8
CHUK 0.027 0.096 -9999 0 -0.46 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.027 0.091 -9999 0 -0.59 4 4
TCRz/NEF -0.038 0.13 -9999 0 -0.45 56 56
TNF -0.13 0.26 -9999 0 -0.6 152 152
FASLG -0.022 0.17 -9999 0 -0.56 56 56
NFKB1 0.006 0.035 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.098 0.17 -9999 0 -0.38 171 171
CASP6 -0.02 0.069 -9999 0 -0.52 5 5
CASP7 0.023 0.18 -9999 0 -0.49 54 54
RELA 0.006 0.035 -9999 0 -10000 0 0
CASP2 0.015 0 -9999 0 -10000 0 0
CASP3 0.024 0.18 -9999 0 -0.49 54 54
TNFRSF1A 0.002 0.09 -9999 0 -0.61 14 14
TNFR1A/BAG4 -0.018 0.091 -9999 0 -0.46 26 26
CASP8 0.004 0.08 -9999 0 -0.59 12 12
CASP9 0.014 0.023 -9999 0 -0.59 1 1
MAP3K14 0.018 0.1 -9999 0 -0.52 5 5
APAF-1/Caspase 9 -0.053 0.13 -9999 0 -0.42 55 55
BCL2 0.031 0.082 -9999 0 -0.4 2 2
EPHB forward signaling

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.055 0.14 -10000 0 -0.39 95 95
cell-cell adhesion 0.047 0.12 0.57 16 -10000 0 16
Ephrin B/EPHB2/RasGAP -0.02 0.08 -10000 0 -0.64 3 3
ITSN1 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
SHC1 0.001 0.092 -10000 0 -0.59 16 16
Ephrin B1/EPHB3 -0.004 0.04 -10000 0 -0.37 8 8
Ephrin B1/EPHB1 -0.051 0.13 -10000 0 -0.4 86 86
HRAS/GDP -0.045 0.11 -10000 0 -0.54 16 16
Ephrin B/EPHB1/GRB7 -0.078 0.16 -10000 0 -0.65 24 24
Endophilin/SYNJ1 0.023 0.086 -10000 0 -0.59 3 3
KRAS 0.014 0.023 -10000 0 -0.59 1 1
Ephrin B/EPHB1/Src -0.056 0.14 -10000 0 -0.63 15 15
endothelial cell migration -0.009 0.057 -10000 0 -0.46 4 4
GRB2 0.014 0.023 -10000 0 -0.59 1 1
GRB7 -0.038 0.16 -10000 0 -0.59 54 54
PAK1 0.007 0.14 -10000 0 -0.57 21 21
HRAS 0.015 0 -10000 0 -10000 0 0
RRAS 0.02 0.096 -10000 0 -0.6 5 5
DNM1 -0.083 0.22 -10000 0 -0.6 107 107
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.014 0.14 -10000 0 -0.6 14 14
lamellipodium assembly -0.047 0.12 -10000 0 -0.57 16 16
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.007 0.14 -10000 0 -0.53 23 23
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
EPHB2 0.007 0.071 -10000 0 -0.6 9 9
EPHB3 0.011 0.048 -10000 0 -0.61 4 4
EPHB1 -0.065 0.21 -10000 0 -0.62 84 84
EPHB4 0.011 0.052 -10000 0 -0.59 5 5
mol:GDP -0.042 0.11 -10000 0 -0.48 20 20
Ephrin B/EPHB2 -0.02 0.082 -10000 0 -0.33 41 41
Ephrin B/EPHB3 -0.018 0.08 -10000 0 -0.34 35 35
JNK cascade -0.004 0.13 -10000 0 -0.68 5 5
Ephrin B/EPHB1 -0.056 0.14 -10000 0 -0.36 95 95
RAP1/GDP -0.038 0.095 -10000 0 -0.45 17 17
EFNB2 0.003 0.085 -10000 0 -0.6 13 13
EFNB3 -0.002 0.1 -10000 0 -0.61 18 18
EFNB1 0.012 0.046 -10000 0 -0.59 4 4
Ephrin B2/EPHB1-2 -0.054 0.14 -10000 0 -0.38 97 97
RAP1B 0.009 0.061 -10000 0 -0.59 7 7
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.047 0.12 -10000 0 -0.57 15 15
Rap1/GTP -0.047 0.11 -10000 0 -0.53 18 18
axon guidance -0.055 0.14 -10000 0 -0.39 95 95
MAPK3 0.012 0.12 -10000 0 -0.48 21 21
MAPK1 0.012 0.12 -10000 0 -0.48 21 21
Rac1/GDP 0.013 0.12 -10000 0 -0.48 15 15
actin cytoskeleton reorganization -0.035 0.087 -10000 0 -0.43 16 16
CDC42/GDP 0.013 0.12 -10000 0 -0.48 15 15
PI3K -0.009 0.058 -10000 0 -0.46 4 4
EFNA5 -0.068 0.21 -10000 0 -0.61 89 89
Ephrin B2/EPHB4 -0.01 0.062 -10000 0 -0.39 17 17
Ephrin B/EPHB2/Intersectin/N-WASP 0.028 0.069 -10000 0 -0.53 3 3
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP -0.044 0.11 -10000 0 -0.52 15 15
PTK2 0.013 0.032 -10000 0 -10000 0 0
MAP4K4 -0.004 0.13 -10000 0 -0.69 5 5
SRC 0.013 0.035 -10000 0 -0.62 2 2
KALRN -0.001 0.097 -10000 0 -0.59 18 18
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.02 0.14 -10000 0 -0.44 15 15
MAP2K1 0.003 0.13 -10000 0 -0.51 21 21
WASL 0.015 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.049 0.12 -10000 0 -0.36 84 84
cell migration 0.005 0.14 -10000 0 -0.53 21 21
NRAS 0.015 0 -10000 0 -10000 0 0
SYNJ1 0.023 0.088 -10000 0 -0.6 3 3
PXN 0.015 0 -10000 0 -10000 0 0
TF -0.015 0.15 -10000 0 -0.62 12 12
HRAS/GTP -0.049 0.12 -10000 0 -0.57 15 15
Ephrin B1/EPHB1-2 -0.05 0.13 -10000 0 -0.36 92 92
cell adhesion mediated by integrin 0.008 0.078 0.32 32 -10000 0 32
RAC1 0.015 0 -10000 0 -10000 0 0
mol:GTP -0.053 0.13 -10000 0 -0.62 15 15
RAC1-CDC42/GTP -0.046 0.12 -10000 0 -0.55 17 17
RASA1 0.015 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.035 0.091 -10000 0 -0.46 14 14
ruffle organization 0.016 0.14 -10000 0 -0.58 16 16
NCK1 0.015 0 -10000 0 -10000 0 0
receptor internalization -0.018 0.14 -10000 0 -0.7 7 7
Ephrin B/EPHB2/KALRN -0.027 0.092 -10000 0 -0.62 4 4
ROCK1 0.026 0.039 -10000 0 -0.32 8 8
RAS family/GDP -0.032 0.081 -10000 0 -0.48 8 8
Rac1/GTP -0.05 0.12 -10000 0 -0.61 16 16
Ephrin B/EPHB1/Src/Paxillin -0.007 0.13 -10000 0 -0.52 15 15
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.09 0.23 -9999 0 -0.61 112 112
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.015 0 -9999 0 -10000 0 0
TCEB1 0.015 0 -9999 0 -10000 0 0
HIF1A/p53 0.026 0.052 -9999 0 -0.29 13 13
HIF1A 0.024 0.028 -9999 0 -0.25 2 2
COPS5 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.015 -9999 0 -10000 0 0
FIH (dimer) 0.015 0 -9999 0 -10000 0 0
CDKN2A -0.16 0.28 -9999 0 -0.61 186 186
ARNT/IPAS -0.074 0.16 -9999 0 -0.44 112 112
HIF1AN 0.015 0 -9999 0 -10000 0 0
GNB2L1 0.015 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.032 0.027 -9999 0 -10000 0 0
CUL2 0.015 0 -9999 0 -10000 0 0
OS9 -0.007 0.11 -9999 0 -0.59 25 25
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.032 0.027 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.074 -9999 0 -0.34 13 13
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.015 -9999 0 -10000 0 0
VHL 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.032 0.027 -9999 0 -10000 0 0
EGLN3 0.003 0.088 -9999 0 -0.62 13 13
EGLN2 0.015 0 -9999 0 -10000 0 0
EGLN1 0.015 0 -9999 0 -10000 0 0
TP53 0.003 0.088 -9999 0 -0.62 13 13
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.012 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0.033 -9999 0 -0.59 2 2
HIF1A/p19ARF -0.056 0.15 -9999 0 -0.3 186 186
HIF-2-alpha transcription factor network

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.07 0.25 -10000 0 -0.77 64 64
oxygen homeostasis 0.004 0.022 -10000 0 -10000 0 0
TCEB2 0.015 0 -10000 0 -10000 0 0
TCEB1 0.015 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.013 0.055 -10000 0 -0.41 1 1
EPO 0.035 0.3 -10000 0 -0.75 41 41
FIH (dimer) 0.02 0.019 -10000 0 -10000 0 0
APEX1 0.017 0.021 -10000 0 -10000 0 0
SERPINE1 -0.077 0.4 -10000 0 -0.82 74 74
FLT1 0 0.073 -10000 0 -0.72 5 5
ADORA2A 0.034 0.3 -10000 0 -0.73 35 35
germ cell development 0.024 0.3 -10000 0 -0.71 42 42
SLC11A2 0.036 0.3 -10000 0 -0.73 36 36
BHLHE40 0.029 0.31 -10000 0 -0.76 41 41
HIF1AN 0.02 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.046 0.1 -10000 0 -0.38 17 17
ETS1 0.027 0.066 -10000 0 -0.61 7 7
CITED2 0.002 0.023 -10000 0 -10000 0 0
KDR -0.002 0.089 -10000 0 -0.87 5 5
PGK1 0.033 0.31 -10000 0 -0.78 36 36
SIRT1 0.015 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.032 0.34 -10000 0 -0.9 36 36
EPAS1 0.049 0.13 -10000 0 -0.37 5 5
SP1 0.02 0.018 -10000 0 -10000 0 0
ABCG2 0.032 0.31 -10000 0 -0.79 36 36
EFNA1 0.034 0.3 -10000 0 -0.74 37 37
FXN 0.035 0.3 -10000 0 -0.73 36 36
POU5F1 0.022 0.32 -10000 0 -0.74 42 42
neuron apoptosis -0.032 0.33 0.86 36 -10000 0 36
EP300 0.012 0.043 -10000 0 -0.62 3 3
EGLN3 0.007 0.091 -10000 0 -0.62 13 13
EGLN2 0.02 0.02 -10000 0 -10000 0 0
EGLN1 0.02 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.015 0 -10000 0 -10000 0 0
ARNT 0.017 0.021 -10000 0 -10000 0 0
SLC2A1 0.034 0.3 -10000 0 -0.74 36 36
TWIST1 -0.012 0.36 -10000 0 -0.82 65 65
ELK1 0.025 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.043 0.1 -10000 0 -0.44 8 8
VEGFA -0.009 0.37 -10000 0 -0.82 71 71
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
Regulation of Androgen receptor activity

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.037 -9999 0 -0.46 4 4
SMARCC1 0.009 0.014 -9999 0 -10000 0 0
REL -0.009 0.12 -9999 0 -0.61 27 27
HDAC7 0.039 0.094 -9999 0 -10000 0 0
JUN 0.007 0.067 -9999 0 -0.6 8 8
EP300 0.012 0.043 -9999 0 -0.62 3 3
KAT2B 0.012 0.042 -9999 0 -0.61 3 3
KAT5 0.015 0 -9999 0 -10000 0 0
MAPK14 0.025 0.028 -9999 0 -0.43 2 2
FOXO1 0.014 0.025 -9999 0 -0.62 1 1
T-DHT/AR 0.035 0.1 -9999 0 -0.4 2 2
MAP2K6 0.014 0.025 -9999 0 -0.62 1 1
BRM/BAF57 -0.003 0.035 -9999 0 -0.46 4 4
MAP2K4 0.015 0.006 -9999 0 -10000 0 0
SMARCA2 0.011 0.049 -9999 0 -0.62 4 4
PDE9A -0.032 0.13 -9999 0 -0.8 13 13
NCOA2 -0.02 0.14 -9999 0 -0.62 36 36
CEBPA -0.009 0.12 -9999 0 -0.62 26 26
EHMT2 0.012 0.035 -9999 0 -0.62 2 2
cell proliferation 0.049 0.12 -9999 0 -0.48 8 8
NR0B1 -0.15 0.27 -9999 0 -0.61 173 173
EGR1 -0.084 0.23 -9999 0 -0.61 105 105
RXRs/9cRA -0.058 0.13 -9999 0 -0.34 112 112
AR/RACK1/Src -0.003 0.069 -9999 0 -0.38 8 8
AR/GR 0.002 0.11 -9999 0 -0.38 16 16
GNB2L1 0.015 0.001 -9999 0 -10000 0 0
PKN1 0.015 0 -9999 0 -10000 0 0
RCHY1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.02 0.057 -9999 0 -0.45 9 9
T-DHT/AR/TIF2/CARM1 -0.016 0.11 -9999 0 -0.62 12 12
SRC 0.039 0.056 -9999 0 -10000 0 0
NR3C1 0.015 0 -9999 0 -10000 0 0
KLK3 -0.053 0.15 -9999 0 -0.55 18 18
APPBP2 0.015 0.007 -9999 0 -10000 0 0
TRIM24 0.014 0.024 -9999 0 -0.59 1 1
T-DHT/AR/TIP60 0.028 0.073 -9999 0 -0.43 6 6
TMPRSS2 -0.13 0.32 -9999 0 -1 61 61
RXRG -0.091 0.24 -9999 0 -0.62 111 111
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.025 -9999 0 -0.62 1 1
RXRB 0.015 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.008 0.065 -9999 0 -0.62 7 7
KLK2 0.009 0.14 -9999 0 -0.45 44 44
AR -0.005 0.12 -9999 0 -0.29 82 82
SENP1 0.015 0.001 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
MDM2 0.004 0.084 -9999 0 -0.59 13 13
SRY -0.052 0.18 -9999 0 -0.59 64 64
GATA2 -0.003 0.11 -9999 0 -0.61 20 20
MYST2 0.015 0.001 -9999 0 -10000 0 0
HOXB13 -0.12 0.25 -9999 0 -0.6 145 145
T-DHT/AR/RACK1/Src 0.034 0.076 -9999 0 -0.4 7 7
positive regulation of transcription -0.003 0.11 -9999 0 -0.61 20 20
DNAJA1 0.015 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.036 -9999 0 -0.25 4 4
NCOA1 0.018 0.005 -9999 0 -10000 0 0
SPDEF -0.039 0.17 -9999 0 -0.61 57 57
T-DHT/AR/TIF2 0.032 0.097 -9999 0 -0.51 12 12
T-DHT/AR/Hsp90 0.028 0.073 -9999 0 -0.43 6 6
GSK3B 0.015 0.004 -9999 0 -10000 0 0
NR2C1 0.015 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.034 0.055 -9999 0 -0.34 10 10
SIRT1 0.015 0 -9999 0 -10000 0 0
ZMIZ2 0.016 0.005 -9999 0 -10000 0 0
POU2F1 0.019 0.076 -9999 0 -0.62 9 9
T-DHT/AR/DAX-1 -0.062 0.17 -9999 0 -0.41 57 57
CREBBP 0.014 0.025 -9999 0 -0.62 1 1
SMARCE1 0.014 0.004 -9999 0 -10000 0 0
Insulin-mediated glucose transport

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.039 0.1 -10000 0 -0.37 41 41
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0.023 -10000 0 -0.59 1 1
AKT2 0.015 0 -10000 0 -10000 0 0
STXBP4 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.017 0.15 0.27 69 -0.41 38 107
YWHAZ 0.015 0 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.027 0.017 -10000 0 -0.42 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.003 0.083 -10000 0 -0.59 13 13
YWHAB 0.015 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.014 -10000 0 -0.35 1 1
YWHAG 0.012 0.04 -10000 0 -0.59 3 3
ASIP -0.083 0.23 -10000 0 -0.62 104 104
PRKCI 0.015 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.015 0 -10000 0 -10000 0 0
GYS1 0.038 0.009 -10000 0 -10000 0 0
PRKCZ -0.037 0.17 -10000 0 -0.62 55 55
TRIP10 0.009 0.065 -10000 0 -0.62 7 7
TC10/GTP/CIP4/Exocyst -0.004 0.039 -10000 0 -0.39 7 7
AS160/14-3-3 0.012 0.084 -10000 0 -0.34 1 1
VAMP2 0.014 0.023 -10000 0 -0.59 1 1
SLC2A4 0.014 0.16 0.28 69 -0.46 38 107
STX4 0.015 0 -10000 0 -10000 0 0
GSK3B 0.031 0.01 -10000 0 -10000 0 0
SFN -0.12 0.25 -10000 0 -0.6 141 141
LNPEP 0.002 0.092 -10000 0 -0.62 14 14
YWHAE 0.015 0 -10000 0 -10000 0 0
Regulation of Telomerase

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.11 0.38 -9999 0 -1.1 76 76
RAD9A 0.015 0 -9999 0 -10000 0 0
AP1 -0.056 0.17 -9999 0 -0.46 97 97
IFNAR2 0.014 0.007 -9999 0 -10000 0 0
AKT1 0.006 0.047 -9999 0 -0.27 3 3
ER alpha/Oestrogen -0.009 0.084 -9999 0 -0.45 23 23
NFX1/SIN3/HDAC complex 0.047 0.031 -9999 0 -10000 0 0
EGF -0.039 0.18 -9999 0 -0.61 57 57
SMG5 0.015 0 -9999 0 -10000 0 0
SMG6 0.014 0.025 -9999 0 -0.62 1 1
SP3/HDAC2 0.019 0.013 -9999 0 -10000 0 0
TERT/c-Abl -0.13 0.34 -9999 0 -1 73 73
SAP18 0.014 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.067 0.2 -9999 0 -0.59 83 83
WRN 0.013 0.035 -9999 0 -0.62 2 2
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.015 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.29 -9999 0 -0.92 71 71
Mad/Max 0.013 0.013 -9999 0 -10000 0 0
TERT -0.12 0.4 -9999 0 -1.2 75 75
CCND1 -0.096 0.34 -9999 0 -0.98 77 77
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.014 0.005 -9999 0 -10000 0 0
RBBP4 0.014 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.015 0 -9999 0 -10000 0 0
SIN3A 0.014 0.005 -9999 0 -10000 0 0
Telomerase/911 0.039 0.039 -9999 0 -10000 0 0
CDKN1B 0.013 0.09 -9999 0 -0.66 2 2
RAD1 0.015 0 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
XRCC6 0.015 0 -9999 0 -10000 0 0
SAP30 0.013 0.025 -9999 0 -0.62 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.007 0.067 -9999 0 -0.6 8 8
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.011 0.007 -9999 0 -10000 0 0
FOS -0.075 0.22 -9999 0 -0.61 95 95
IFN-gamma/IRF1 -0.023 0.099 -9999 0 -0.43 36 36
PARP2 0.015 0 -9999 0 -10000 0 0
BLM -0.026 0.16 -9999 0 -0.62 44 44
Telomerase -0.037 0.12 -9999 0 -0.42 41 41
IRF1 -0.009 0.12 -9999 0 -0.57 31 31
ESR1 -0.007 0.11 -9999 0 -0.61 23 23
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.052 0.033 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.052 0.033 -9999 0 -10000 0 0
HDAC1 0.01 0.049 -9999 0 -0.62 4 4
HDAC2 0.014 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.058 -9999 0 -0.45 10 10
ABL1 0.014 0.025 -9999 0 -0.62 1 1
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.015 0 -9999 0 -10000 0 0
HUS1 0.014 0.023 -9999 0 -0.59 1 1
RPS6KB1 0.015 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.32 -9999 0 -1 71 71
NR2F2 -0.001 0.1 -9999 0 -0.6 20 20
MAPK3 0.014 0.007 -9999 0 -10000 0 0
MAPK1 0.014 0.007 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.006 0.077 -9999 0 -0.62 10 10
NFKB1 0.015 0 -9999 0 -10000 0 0
HNRNPC 0.015 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.015 0 -9999 0 -10000 0 0
EGFR -0.11 0.25 -9999 0 -0.6 138 138
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.13 0.21 -9999 0 -0.46 183 183
MYC -0.006 0.11 -9999 0 -0.62 21 21
IL2 -0.002 0.014 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
TGFB1 0.006 0.077 -9999 0 -0.62 10 10
TRF2/BLM -0.027 0.1 -9999 0 -0.42 44 44
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.34 -9999 0 -1.1 71 71
SP1/HDAC2 0.022 0.017 -9999 0 -10000 0 0
PINX1 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.29 -9999 0 -0.92 71 71
Smad3/Myc 0.014 0.088 -9999 0 -0.39 30 30
911 complex -0.001 0.014 -9999 0 -0.35 1 1
IFNG 0.003 0.061 -9999 0 -0.58 7 7
Telomerase/PinX1 -0.12 0.29 -9999 0 -0.92 71 71
Telomerase/AKT1/mTOR/p70S6K 0.017 0.073 -9999 0 -10000 0 0
SIN3B 0.013 0.025 -9999 0 -0.63 1 1
YWHAE 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.12 0.29 -9999 0 -0.92 71 71
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.001 0.023 -9999 0 -0.42 2 2
Telomerase/hnRNP C1/C2 -0.12 0.29 -9999 0 -0.92 71 71
E2F1 -0.012 0.12 -9999 0 -0.6 29 29
ZNFX1 0.014 0.005 -9999 0 -10000 0 0
PIF1 -0.05 0.19 -9999 0 -0.61 70 70
NCL 0.015 0 -9999 0 -10000 0 0
DKC1 0.015 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.026 0.074 -10000 0 -0.48 3 3
adherens junction organization -0.017 0.12 -10000 0 -0.41 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.028 0.14 -10000 0 -0.44 14 14
FMN1 -0.045 0.16 -10000 0 -0.55 19 19
mol:IP3 -0.024 0.056 -10000 0 -0.48 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.009 0.11 -10000 0 -0.57 5 5
CTNNB1 0.017 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.083 -10000 0 -0.5 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.026 0.16 -10000 0 -0.43 80 80
CTNND1 0.016 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.001 0.11 -10000 0 -0.52 5 5
VASP 0.001 0.11 -10000 0 -0.53 5 5
ZYX -0.007 0.12 -10000 0 -0.53 6 6
JUB -0.01 0.13 -10000 0 -0.62 8 8
EGFR(dimer) -0.066 0.17 -10000 0 -0.5 35 35
E-cadherin/beta catenin-gamma catenin -0.077 0.15 -10000 0 -0.37 139 139
mol:PI-3-4-5-P3 -0.03 0.068 -10000 0 -0.46 5 5
PIK3CA 0.016 0.002 -10000 0 -10000 0 0
PI3K -0.03 0.069 -10000 0 -0.47 5 5
FYN 0.029 0.072 -10000 0 -0.5 1 1
mol:Ca2+ 0.016 0.073 -10000 0 -0.47 3 3
JUP 0.009 0.069 -10000 0 -0.61 8 8
PIK3R1 0.013 0.043 -10000 0 -0.63 3 3
mol:DAG -0.024 0.056 -10000 0 -0.48 3 3
CDH1 -0.11 0.25 -10000 0 -0.61 136 136
RhoA/GDP -0.028 0.14 -10000 0 -0.42 20 20
establishment of polarity of embryonic epithelium 0.001 0.11 -10000 0 -0.52 5 5
SRC 0.013 0.035 -10000 0 -0.62 2 2
RAC1 0.015 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
EGFR -0.11 0.25 -10000 0 -0.6 138 138
CASR 0.017 0.08 -10000 0 -0.4 6 6
RhoA/GTP -0.02 0.048 -10000 0 -0.42 3 3
AKT2 0.02 0.083 -10000 0 -0.5 3 3
actin cable formation -0.035 0.15 -10000 0 -0.53 19 19
apoptosis 0.026 0.06 0.42 5 -10000 0 5
CTNNA1 0.016 0.002 -10000 0 -10000 0 0
mol:GDP -0.039 0.15 -10000 0 -0.44 23 23
PIP5K1A 0.001 0.11 -10000 0 -0.53 5 5
PLCG1 -0.024 0.057 -10000 0 -0.49 3 3
Rac1/GTP -0.089 0.13 -10000 0 -0.46 35 35
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
TRAIL signaling pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.011 0.12 -10000 0 -0.6 28 28
positive regulation of NF-kappaB transcription factor activity -0.027 0.11 -10000 0 -0.44 41 41
MAP2K4 0.038 0.06 -10000 0 -0.38 1 1
IKBKB 0.015 0 -10000 0 -10000 0 0
TNFRSF10B 0.012 0.043 -10000 0 -0.62 3 3
TNFRSF10A -0.024 0.15 -10000 0 -0.61 42 42
SMPD1 0.014 0.048 -10000 0 -0.35 1 1
IKBKG 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.002 0.087 -10000 0 -0.59 14 14
TRAIL/TRAILR2 -0.02 0.094 -10000 0 -0.45 30 30
TRAIL/TRAILR3 -0.045 0.15 -10000 0 -0.48 63 63
TRAIL/TRAILR1 -0.046 0.14 -10000 0 -0.46 66 66
TRAIL/TRAILR4 -0.027 0.11 -10000 0 -0.44 41 41
TRAIL/TRAILR1/DAP3/GTP -0.035 0.11 -10000 0 -0.36 66 66
IKK complex -0.01 0.031 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.008 0.093 -10000 0 -0.44 28 28
MAP3K1 0.03 0.063 -10000 0 -0.34 2 2
TRAILR4 (trimer) 0.002 0.087 -10000 0 -0.59 14 14
TRADD 0.014 0.025 -10000 0 -0.62 1 1
TRAILR1 (trimer) -0.024 0.15 -10000 0 -0.61 42 42
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.018 0.083 -10000 0 -0.35 4 4
CFLAR 0.015 0 -10000 0 -10000 0 0
MAPK1 0.008 0.093 -10000 0 -0.44 28 28
TRAIL/TRAILR1/FADD/TRADD/RIP -0.032 0.098 -10000 0 -0.59 4 4
mol:ceramide 0.014 0.047 -10000 0 -0.35 1 1
FADD 0.015 0 -10000 0 -10000 0 0
MAPK8 0.041 0.072 -10000 0 -0.4 5 5
TRAF2 0.015 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.024 0.15 -10000 0 -0.6 43 43
CHUK 0.015 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.038 0.12 -10000 0 -0.39 66 66
DAP3 0.015 0 -10000 0 -10000 0 0
CASP10 -0.021 0.085 0.24 7 -0.4 15 22
JNK cascade -0.027 0.11 -10000 0 -0.44 41 41
TRAIL (trimer) -0.011 0.12 -10000 0 -0.6 28 28
TNFRSF10C -0.024 0.15 -10000 0 -0.6 43 43
TRAIL/TRAILR1/DAP3/GTP/FADD -0.032 0.1 -10000 0 -0.35 41 41
TRAIL/TRAILR2/FADD -0.017 0.079 -10000 0 -0.38 30 30
cell death 0.014 0.047 -10000 0 -0.35 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.033 0.057 -10000 0 -0.54 1 1
TRAILR2 (trimer) 0.012 0.043 -10000 0 -0.62 3 3
CASP8 -0.001 0.048 -10000 0 -0.82 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.014 0.066 -10000 0 -0.64 1 1
S1P3 pathway

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.052 -9999 0 -0.59 5 5
mol:S1P 0.002 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.012 0.099 -9999 0 -0.32 40 40
GNAO1 -0.01 0.13 -9999 0 -0.62 28 28
S1P/S1P3/G12/G13 0.008 0.09 -9999 0 -0.34 41 41
AKT1 -0.013 0.038 -9999 0 -0.35 3 3
AKT3 0.008 0.14 -9999 0 -1.2 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.052 -9999 0 -0.59 5 5
GNAI2 0.017 0.002 -9999 0 -10000 0 0
GNAI3 0.017 0.002 -9999 0 -10000 0 0
GNAI1 -0.019 0.15 -9999 0 -0.62 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.021 0.15 -9999 0 -0.6 41 41
S1PR2 0.011 0.053 -9999 0 -0.6 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.12 -9999 0 -0.52 14 14
MAPK3 0.019 0.11 -9999 0 -0.49 14 14
MAPK1 0.019 0.11 -9999 0 -0.49 14 14
JAK2 0.014 0.13 -9999 0 -0.48 24 24
CXCR4 0.002 0.14 -9999 0 -0.55 23 23
FLT1 0.018 0.025 -9999 0 -0.62 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.12 -9999 0 -0.52 15 15
S1P/S1P3/Gi 0.01 0.12 -9999 0 -0.53 14 14
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.033 0.09 -9999 0 -0.48 14 14
VEGFA -0.088 0.23 -9999 0 -0.58 118 118
S1P/S1P2/Gi 0.019 0.1 -9999 0 -0.37 27 27
VEGFR1 homodimer/VEGFA homodimer -0.048 0.17 -9999 0 -0.42 119 119
RHOA 0.015 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.001 0.1 -9999 0 -0.3 56 56
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.014 0.043 -9999 0 -0.63 3 3
G12/G13 -0.001 0.018 -9999 0 -0.46 1 1
GNA14 -0.009 0.12 -9999 0 -0.61 26 26
GNA15 -0.009 0.12 -9999 0 -0.61 26 26
GNA12 0.014 0.025 -9999 0 -0.62 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.006 0.078 -9999 0 -0.62 10 10
Rac1/GTP -0.033 0.09 -9999 0 -0.48 14 14
EPO signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.069 0.091 -9999 0 -0.67 2 2
CRKL 0.035 0.084 -9999 0 -0.46 2 2
mol:DAG 0.043 0.081 -9999 0 -0.43 4 4
HRAS 0.056 0.091 -9999 0 -0.47 6 6
MAPK8 0.016 0.1 -9999 0 -0.36 20 20
RAP1A 0.035 0.084 -9999 0 -0.46 2 2
GAB1 0.035 0.087 -9999 0 -0.62 2 2
MAPK14 0.021 0.089 -9999 0 -0.33 12 12
EPO -0.021 0.15 -9999 0 -0.58 43 43
PLCG1 0.043 0.083 -9999 0 -0.44 4 4
EPOR/TRPC2/IP3 Receptors 0.016 0.024 -9999 0 -0.58 1 1
RAPGEF1 0.013 0.035 -9999 0 -0.62 2 2
EPO/EPOR (dimer)/SOCS3 -0.14 0.2 -9999 0 -0.4 234 234
GAB1/SHC/GRB2/SOS1 -0.022 0.073 -9999 0 -0.52 6 6
EPO/EPOR (dimer) -0.001 0.11 -9999 0 -0.42 44 44
IRS2 0.035 0.084 -9999 0 -0.46 2 2
STAT1 0.048 0.097 -9999 0 -0.46 7 7
STAT5B 0.049 0.084 -9999 0 -0.46 4 4
cell proliferation 0.025 0.095 -9999 0 -0.35 15 15
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.082 -9999 0 -0.49 11 11
TEC 0.021 0.11 -9999 0 -0.51 7 7
SOCS3 -0.18 0.29 -9999 0 -0.6 214 214
STAT1 (dimer) 0.048 0.095 -9999 0 -0.45 7 7
JAK2 0.016 0.008 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
EPO/EPOR (dimer)/JAK2 0.041 0.092 -9999 0 -0.5 2 2
EPO/EPOR -0.001 0.11 -9999 0 -0.42 44 44
LYN 0.013 0.053 -9999 0 -0.6 5 5
TEC/VAV2 0.029 0.11 -9999 0 -0.52 6 6
elevation of cytosolic calcium ion concentration 0.016 0.024 -9999 0 -0.58 1 1
SHC1 0.001 0.092 -9999 0 -0.59 16 16
EPO/EPOR (dimer)/LYN 0.017 0.1 -9999 0 -0.34 49 49
mol:IP3 0.043 0.081 -9999 0 -0.43 4 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.022 0.073 -9999 0 -0.5 6 6
SH2B3 0.013 0.046 -9999 0 -0.58 4 4
NFKB1 0.021 0.088 -9999 0 -0.33 11 11
EPO/EPOR (dimer)/JAK2/SOCS3 -0.067 0.1 -9999 0 -0.34 26 26
PTPN6 0.027 0.087 -9999 0 -0.49 2 2
TEC/VAV2/GRB2 0.035 0.11 -9999 0 -0.49 6 6
EPOR 0.016 0.024 -9999 0 -0.58 1 1
INPP5D 0.007 0.071 -9999 0 -0.6 9 9
mol:GDP -0.023 0.074 -9999 0 -0.52 6 6
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG2 0.004 0.083 -9999 0 -0.61 12 12
CRKL/CBL/C3G 0.048 0.084 -9999 0 -0.53 2 2
VAV2 0.034 0.086 -9999 0 -0.46 2 2
CBL 0.035 0.084 -9999 0 -0.46 2 2
SHC/Grb2/SOS1 -0.024 0.075 -9999 0 -0.5 6 6
STAT5A 0.042 0.11 -9999 0 -0.54 10 10
GRB2 0.014 0.023 -9999 0 -0.59 1 1
STAT5 (dimer) 0.064 0.1 -9999 0 -0.52 9 9
LYN/PLCgamma2 -0.011 0.08 -9999 0 -0.55 13 13
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
BTK 0.024 0.11 -9999 0 -0.57 9 9
BCL2 0.067 0.11 -9999 0 -0.88 4 4
Regulation of p38-alpha and p38-beta

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.014 0.025 -9999 0 -0.62 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.015 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.031 0.11 -9999 0 -0.24 131 131
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0.035 -9999 0 -0.62 2 2
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.015 0 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
MAP3K12 0.015 0 -9999 0 -10000 0 0
FGR 0.01 0.057 -9999 0 -0.59 6 6
p38 alpha/TAB1 -0.021 0.052 -9999 0 -0.33 8 8
PRKG1 -0.032 0.17 -9999 0 -0.62 50 50
DUSP8 -0.006 0.11 -9999 0 -0.61 23 23
PGK/cGMP/p38 alpha -0.037 0.086 -9999 0 -0.32 34 34
apoptosis -0.02 0.05 -9999 0 -0.32 7 7
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.011 0.053 -9999 0 -0.6 5 5
DUSP1 -0.02 0.14 -9999 0 -0.6 38 38
PAK1 -0.018 0.14 -9999 0 -0.59 37 37
SRC 0.013 0.035 -9999 0 -0.62 2 2
RAC1/OSM/MEKK3/MKK3 -0.001 0.021 -9999 0 -10000 0 0
TRAF6 0.013 0.035 -9999 0 -0.62 2 2
RAC1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.014 0.023 -9999 0 -0.59 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.012 0.092 -9999 0 -0.39 9 9
BLK -0.07 0.21 -9999 0 -0.59 91 91
HCK 0 0.096 -9999 0 -0.61 16 16
MAP2K3 0.013 0.033 -9999 0 -0.59 2 2
DUSP16 0.015 0 -9999 0 -10000 0 0
DUSP10 -0.006 0.12 -9999 0 -0.62 23 23
TRAF6/MEKK3 -0.001 0.019 -9999 0 -0.36 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.02 0.078 -9999 0 -0.34 9 9
positive regulation of innate immune response 0.018 0.1 -9999 0 -0.43 9 9
LCK -0.098 0.24 -9999 0 -0.6 123 123
p38alpha-beta/MKP7 0.026 0.098 -9999 0 -0.43 7 7
p38alpha-beta/MKP5 0.016 0.11 -9999 0 -0.43 11 11
PGK/cGMP -0.034 0.12 -9999 0 -0.46 50 50
PAK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.009 0.12 -9999 0 -0.43 14 14
CDC42 0.015 0 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
PAK3 -0.13 0.27 -9999 0 -0.61 158 158
Paxillin-dependent events mediated by a4b1

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.014 0.023 -10000 0 -0.59 1 1
Rac1/GDP 0.008 0.02 -10000 0 -10000 0 0
DOCK1 0.014 0.025 -10000 0 -0.62 1 1
ITGA4 -0.07 0.21 -10000 0 -0.6 92 92
RAC1 0.015 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.089 0.18 -10000 0 -0.46 131 131
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.052 0.13 -10000 0 -0.38 92 92
alpha4/beta7 Integrin/Paxillin -0.066 0.14 -10000 0 -0.64 6 6
lamellipodium assembly 0.006 0.041 -10000 0 -0.41 4 4
PIK3CA 0.015 0 -10000 0 -10000 0 0
PI3K -0.002 0.03 -10000 0 -0.46 3 3
ARF6 0.015 0 -10000 0 -10000 0 0
TLN1 0.015 0 -10000 0 -10000 0 0
PXN 0.027 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
ARF6/GTP -0.038 0.096 -10000 0 -0.54 3 3
cell adhesion -0.042 0.11 -10000 0 -0.58 3 3
CRKL/CBL -0.001 0.024 -10000 0 -0.44 2 2
alpha4/beta1 Integrin/Paxillin -0.046 0.12 -10000 0 -0.63 3 3
ITGB1 0.012 0.04 -10000 0 -0.59 3 3
ITGB7 -0.027 0.16 -10000 0 -0.61 45 45
ARF6/GDP 0.008 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.1 0.16 -10000 0 -0.64 15 15
p130Cas/Crk/Dock1 -0.001 0.021 -10000 0 -0.38 2 2
VCAM1 -0.11 0.26 -10000 0 -0.62 137 137
alpha4/beta1 Integrin/Paxillin/Talin -0.042 0.11 -10000 0 -0.59 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.042 0.11 -10000 0 -0.59 3 3
BCAR1 0.014 0.025 -10000 0 -0.62 1 1
mol:GDP 0.042 0.11 0.58 3 -10000 0 3
CBL 0.014 0.025 -10000 0 -0.62 1 1
PRKACA 0.015 0 -10000 0 -10000 0 0
GIT1 0.014 0.025 -10000 0 -0.62 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.042 0.11 -10000 0 -0.59 3 3
Rac1/GTP 0.006 0.045 -10000 0 -0.45 4 4
Signaling events mediated by VEGFR1 and VEGFR2

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.081 0.17 -9999 0 -0.43 126 126
AKT1 0.055 0.11 -9999 0 -0.57 3 3
PTK2B -0.061 0.21 -9999 0 -0.56 69 69
VEGFR2 homodimer/Frs2 0.036 0.06 -9999 0 -0.58 4 4
CAV1 -0.064 0.2 -9999 0 -0.59 88 88
CALM1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.059 0.13 -9999 0 -0.55 11 11
endothelial cell proliferation 0.041 0.13 -9999 0 -0.47 6 6
mol:Ca2+ 0 0.14 -9999 0 -0.56 10 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.056 0.12 -9999 0 -0.59 6 6
RP11-342D11.1 -0.01 0.14 -9999 0 -0.57 10 10
CDH5 0.01 0.057 -9999 0 -0.59 6 6
VEGFA homodimer -0.055 0.12 -9999 0 -0.36 6 6
SHC1 0.001 0.092 -9999 0 -0.59 16 16
SHC2 0.012 0.043 -9999 0 -0.62 3 3
HRAS/GDP -0.05 0.11 -9999 0 -0.48 20 20
SH2D2A -0.092 0.23 -9999 0 -0.6 116 116
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.039 0.086 -9999 0 -0.52 7 7
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.11 0.18 -9999 0 -0.64 40 40
VEGFR1 homodimer 0.014 0.025 -9999 0 -0.62 1 1
SHC/GRB2/SOS1 -0.056 0.12 -9999 0 -0.54 20 20
GRB10 -0.004 0.16 -9999 0 -0.7 14 14
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
GRB2 0.014 0.023 -9999 0 -0.59 1 1
PAK1 -0.018 0.14 -9999 0 -0.59 37 37
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.054 0.12 -9999 0 -0.6 10 10
HRAS 0.015 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.12 -9999 0 -0.34 6 6
HIF1A 0.013 0.034 -9999 0 -0.61 2 2
FRS2 0.012 0.047 -9999 0 -0.6 4 4
oxygen and reactive oxygen species metabolic process -0.055 0.12 -9999 0 -0.58 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.078 -9999 0 -0.6 11 11
Nck/Pak -0.024 0.098 -9999 0 -0.43 37 37
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.058 0.12 -9999 0 -0.54 9 9
mol:GDP -0.054 0.12 -9999 0 -0.52 20 20
mol:NADP 0.042 0.11 -9999 0 -0.52 5 5
eNOS/Hsp90 0.047 0.11 -9999 0 -0.48 5 5
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
mol:IP3 0 0.14 -9999 0 -0.57 10 10
HIF1A/ARNT -0.001 0.024 -9999 0 -0.44 2 2
SHB 0.011 0.049 -9999 0 -0.62 4 4
VEGFA -0.089 0.23 -9999 0 -0.59 118 118
VEGFC -0.005 0.11 -9999 0 -0.6 22 22
FAK1/Vinculin -0.007 0.16 -9999 0 -0.54 9 9
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.19 -9999 0 -0.59 69 69
PTPN6 0.005 0.081 -9999 0 -0.62 11 11
EPAS1 0.024 0.035 -9999 0 -0.43 3 3
mol:L-citrulline 0.042 0.11 -9999 0 -0.52 5 5
ITGAV 0.014 0.025 -9999 0 -0.62 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.055 0.12 -9999 0 -0.52 11 11
VEGFR2 homodimer/VEGFA homodimer -0.062 0.13 -9999 0 -0.62 10 10
VEGFR2/3 heterodimer 0.032 0.077 -9999 0 -0.74 4 4
VEGFB 0.015 0 -9999 0 -10000 0 0
MAPK11 0.004 0.14 -9999 0 -0.56 10 10
VEGFR2 homodimer 0.037 0.06 -9999 0 -0.62 5 5
FLT1 0.014 0.025 -9999 0 -0.62 1 1
NEDD4 0.011 0.063 -9999 0 -0.6 7 7
MAPK3 -0.006 0.14 -9999 0 -0.53 10 10
MAPK1 -0.006 0.14 -9999 0 -0.53 10 10
VEGFA145/NRP2 -0.081 0.17 -9999 0 -0.43 125 125
VEGFR1/2 heterodimer 0.037 0.058 -9999 0 -0.61 5 5
KDR 0.037 0.06 -9999 0 -0.62 5 5
VEGFA165/NRP1/VEGFR2 homodimer -0.058 0.12 -9999 0 -0.59 12 12
SRC 0.013 0.035 -9999 0 -0.62 2 2
platelet activating factor biosynthetic process -0.003 0.14 -9999 0 -0.54 10 10
PI3K -0.041 0.091 -9999 0 -0.56 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.058 0.12 -9999 0 -0.54 9 9
FES -0.002 0.15 -9999 0 -0.58 11 11
GAB1 -0.042 0.095 -9999 0 -0.58 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.059 0.13 -9999 0 -0.55 10 10
CTNNB1 0.015 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.49 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes -0.058 0.12 -9999 0 -0.54 9 9
PI3K/GAB1 0.054 0.11 -9999 0 -0.51 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.064 0.12 -9999 0 -0.59 5 5
PRKACA 0.015 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.019 0.086 -9999 0 -0.68 5 5
HSP90AA1 0.015 0 -9999 0 -10000 0 0
CDC42 0 0.15 -9999 0 -0.58 10 10
actin cytoskeleton reorganization -0.11 0.18 -9999 0 -0.63 40 40
PTK2 -0.014 0.16 -9999 0 -0.57 7 7
EDG1 -0.01 0.14 -9999 0 -0.57 10 10
mol:DAG 0 0.14 -9999 0 -0.57 10 10
CaM/Ca2+ -0.049 0.1 -9999 0 -0.52 10 10
MAP2K3 0.001 0.15 -9999 0 -0.55 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.006 0.16 -9999 0 -0.72 14 14
PLCG1 0 0.15 -9999 0 -0.58 10 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.055 0.12 -9999 0 -0.55 10 10
IQGAP1 0.009 0.064 -9999 0 -0.61 7 7
YES1 0.013 0.035 -9999 0 -0.62 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.059 0.13 -9999 0 -0.56 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.063 0.13 -9999 0 -0.54 9 9
cell migration 0.025 0.15 -9999 0 -0.52 5 5
mol:PI-3-4-5-P3 0.035 0.12 -9999 0 -0.52 5 5
FYN 0.015 0 -9999 0 -10000 0 0
VEGFB/NRP1 0 0.14 -9999 0 -0.54 10 10
mol:NO 0.042 0.11 -9999 0 -0.52 5 5
PXN 0.015 0 -9999 0 -10000 0 0
HRAS/GTP -0.05 0.11 -9999 0 -0.48 20 20
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.006 0.16 -9999 0 -0.72 14 14
VHL 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.099 0.24 -9999 0 -0.6 125 125
NOS3 0.041 0.12 -9999 0 -0.59 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.059 0.13 -9999 0 -0.55 10 10
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.01 0.14 -9999 0 -0.53 11 11
PRKCB -0.035 0.18 -9999 0 -0.56 30 30
VCL 0.011 0.053 -9999 0 -0.6 5 5
VEGFA165/NRP1 -0.011 0.14 -9999 0 -0.58 10 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.058 0.13 -9999 0 -0.55 10 10
VEGFA165/NRP2 -0.081 0.17 -9999 0 -0.43 125 125
MAPKKK cascade 0.022 0.15 -9999 0 -0.62 12 12
NRP2 0.006 0.075 -9999 0 -0.61 10 10
VEGFC homodimer -0.005 0.11 -9999 0 -0.6 22 22
NCK1 0.015 0 -9999 0 -10000 0 0
ROCK1 0.015 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.005 0.16 -9999 0 -0.53 7 7
MAP3K13 -0.009 0.16 -9999 0 -0.58 14 14
PDPK1 0.043 0.11 -9999 0 -0.53 4 4
Hedgehog signaling events mediated by Gli proteins

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0.049 -9999 0 -0.62 4 4
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.009 0.057 -9999 0 -0.38 16 16
forebrain development -0.023 0.18 -9999 0 -0.44 83 83
GNAO1 -0.012 0.13 -9999 0 -0.63 28 28
SMO/beta Arrestin2 0.017 0.058 -9999 0 -0.44 10 10
SMO 0.006 0.077 -9999 0 -0.61 10 10
ARRB2 0.015 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.045 0.068 -9999 0 -0.61 1 1
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.015 0 -9999 0 -10000 0 0
GNAI2 0.015 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0.004 0.023 -9999 0 -0.34 2 2
GNAI1 -0.021 0.15 -9999 0 -0.63 37 37
XPO1 0.016 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.057 0.12 -9999 0 -0.52 26 26
SAP30 0.014 0.025 -9999 0 -0.62 1 1
mol:GDP 0.006 0.076 -9999 0 -0.61 10 10
MIM/GLI2A 0.015 0.042 -9999 0 -0.61 3 3
IFT88 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0.004 -9999 0 -10000 0 0
GLI2 0.05 0.032 -9999 0 -10000 0 0
GLI3 0.038 0.071 -9999 0 -0.41 4 4
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
SAP18 0.015 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.015 0 -9999 0 -10000 0 0
GNG2 0.009 0.06 -9999 0 -0.62 6 6
Gi family/GTP 0.01 0.11 -9999 0 -0.44 20 20
SIN3B 0.014 0.025 -9999 0 -0.62 1 1
SIN3A 0.015 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.055 0.062 -9999 0 -0.43 2 2
GLI2/Su(fu) 0.06 0.05 -9999 0 -10000 0 0
FOXA2 -0.042 0.13 -9999 0 -0.58 14 14
neural tube patterning -0.023 0.18 -9999 0 -0.44 83 83
SPOP 0.015 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.031 0.042 -9999 0 -0.37 4 4
GNB1 0.015 0 -9999 0 -10000 0 0
CSNK1G2 0.015 0 -9999 0 -10000 0 0
CSNK1G3 0.015 0 -9999 0 -10000 0 0
MTSS1 0.015 0.043 -9999 0 -0.61 3 3
embryonic limb morphogenesis -0.023 0.18 -9999 0 -0.44 83 83
SUFU 0.028 0.04 -9999 0 -0.45 2 2
LGALS3 -0.091 0.23 -9999 0 -0.59 118 118
catabolic process 0.073 0.065 -9999 0 -0.5 1 1
GLI3A/CBP -0.027 0.12 -9999 0 -0.35 46 46
KIF3A 0.011 0.049 -9999 0 -0.62 4 4
GLI1 -0.024 0.18 -9999 0 -0.45 81 81
RAB23 0.014 0.025 -9999 0 -0.62 1 1
CSNK1A1 0.015 0 -9999 0 -10000 0 0
IFT172 0.012 0.043 -9999 0 -0.62 3 3
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.028 0.14 -9999 0 -0.32 118 118
GNAZ 0.012 0.043 -9999 0 -0.63 3 3
RBBP4 0.015 0.001 -9999 0 -10000 0 0
CSNK1G1 0.014 0.023 -9999 0 -0.59 1 1
PIAS1 0.013 0.035 -9999 0 -0.62 2 2
PRKACA 0.015 0 -9999 0 -10000 0 0
GLI2/SPOP 0.054 0.03 -9999 0 -10000 0 0
STK36 0.016 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.018 0.1 -9999 0 -0.5 13 13
PTCH1 -0.033 0.25 -9999 0 -0.97 29 29
MIM/GLI1 -0.024 0.2 -9999 0 -0.59 39 39
CREBBP -0.027 0.12 -9999 0 -0.35 46 46
Su(fu)/SIN3/HDAC complex 0.057 0.029 -9999 0 -0.29 2 2
ceramide signaling pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.01 0.13 -10000 0 -0.51 18 18
BAG4 0.003 0.088 -10000 0 -0.62 13 13
BAD 0.013 0.045 -10000 0 -10000 0 0
NFKBIA 0.014 0.023 -10000 0 -0.59 1 1
BIRC3 -0.059 0.2 -10000 0 -0.6 81 81
BAX 0.013 0.045 -10000 0 -0.2 1 1
EnzymeConsortium:3.1.4.12 -0.001 0.034 -10000 0 -0.11 18 18
IKBKB -0.001 0.12 -10000 0 -0.48 17 17
MAP2K2 0.023 0.058 -10000 0 -0.37 4 4
MAP2K1 0.023 0.058 -10000 0 -0.37 4 4
SMPD1 0.006 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.002 0.12 -10000 0 -0.49 18 18
MAP2K4 0.018 0.052 -10000 0 -0.29 4 4
protein ubiquitination 0.001 0.12 -10000 0 -0.48 18 18
EnzymeConsortium:2.7.1.37 0.026 0.063 -10000 0 -0.39 4 4
response to UV 0 0.001 -10000 0 -0.003 5 5
RAF1 0.017 0.058 -10000 0 -0.37 5 5
CRADD 0.015 0 -10000 0 -10000 0 0
mol:ceramide 0.004 0.047 -10000 0 -0.16 14 14
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.014 -10000 0 -0.36 1 1
MADD 0.013 0.043 -10000 0 -0.63 3 3
MAP3K1 0.011 0.053 -10000 0 -0.29 5 5
TRADD 0.015 0.025 -10000 0 -0.63 1 1
RELA/p50 0.015 0 -10000 0 -10000 0 0
MAPK3 0.026 0.057 -10000 0 -0.36 4 4
MAPK1 0.026 0.057 -10000 0 -0.36 4 4
p50/RELA/I-kappa-B-alpha -0.001 0.016 -10000 0 -0.42 1 1
FADD -0.01 0.13 -10000 0 -0.51 18 18
KSR1 0.01 0.058 -10000 0 -0.36 6 6
MAPK8 0.022 0.061 -10000 0 -0.29 11 11
TRAF2 0.015 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK -0.001 0.12 -10000 0 -0.48 17 17
TNF R/SODD -0.018 0.091 -10000 0 -0.46 26 26
TNF -0.12 0.26 -10000 0 -0.6 152 152
CYCS 0.015 0.045 0.15 2 -0.19 1 3
IKBKG -0.001 0.12 -10000 0 -0.48 17 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.02 0.13 -10000 0 -0.55 18 18
RELA 0.015 0 -10000 0 -10000 0 0
RIPK1 0.015 0.001 -10000 0 -10000 0 0
AIFM1 0.015 0.045 0.15 2 -0.19 1 3
TNF/TNF R/SODD -0.097 0.17 -10000 0 -0.38 171 171
TNFRSF1A 0.002 0.09 -10000 0 -0.61 14 14
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.013 0.05 -10000 0 -0.73 1 1
NSMAF -0.01 0.12 -10000 0 -0.5 18 18
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 5 5
BCL2 0.012 0.043 -10000 0 -0.62 3 3
Atypical NF-kappaB pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.024 0.098 -9999 0 -0.42 38 38
FBXW11 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.015 0.079 -9999 0 -0.37 27 27
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.084 -9999 0 -0.43 4 4
NFKBIA -0.01 0.095 -9999 0 -0.24 65 65
MAPK14 0.014 0.023 -9999 0 -0.59 1 1
NF kappa B1 p105/p50 0.032 0 -9999 0 -10000 0 0
ARRB2 0.02 0.01 -9999 0 -0.25 1 1
REL -0.01 0.12 -9999 0 -0.61 27 27
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.01 0.089 -9999 0 -0.35 38 38
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
NFKB1 0.027 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.001 0.091 -9999 0 -0.36 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.082 -9999 0 -0.5 2 2
SRC 0.013 0.035 -9999 0 -0.62 2 2
PI3K -0.002 0.03 -9999 0 -0.46 3 3
NF kappa B1 p50/RelA -0.001 0.092 -9999 0 -0.36 7 7
IKBKB 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
SYK -0.004 0.11 -9999 0 -0.62 20 20
I kappa B alpha/PIK3R1 -0.003 0.093 -9999 0 -0.39 10 10
cell death 0.021 0.079 -9999 0 -0.48 2 2
NF kappa B1 p105/c-Rel 0.015 0.079 -9999 0 -0.37 27 27
LCK -0.098 0.24 -9999 0 -0.6 123 123
BCL3 -0.019 0.14 -9999 0 -0.59 38 38
p38 MAPK signaling pathway

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.006 0.045 -10000 0 -0.33 13 13
TRAF2/ASK1 -0.006 0.05 -10000 0 -0.39 11 11
ATM 0.015 0 -10000 0 -10000 0 0
MAP2K3 0.024 0.057 -10000 0 -0.31 4 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.075 -10000 0 -0.39 12 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.043 0.18 -10000 0 -0.61 63 63
TXN 0.01 0 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
GADD45A -0.022 0.14 -10000 0 -0.59 41 41
GADD45B -0.018 0.14 -10000 0 -0.6 36 36
MAP3K1 0.012 0.046 -10000 0 -0.59 4 4
MAP3K6 0.01 0.057 -10000 0 -0.59 6 6
MAP3K7 0.015 0 -10000 0 -10000 0 0
MAP3K4 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.011 0.07 -10000 0 -0.44 17 17
TAK1/TAB family 0.001 0.017 0.19 3 -0.18 2 5
RAC1/OSM/MEKK3 0 0.012 -10000 0 -0.32 1 1
TRAF2 0.015 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.029 -10000 0 -10000 0 0
TRAF6 0.009 0.021 -10000 0 -0.38 2 2
RAC1 0.015 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.068 0.21 -10000 0 -0.61 89 89
CCM2 0.014 0.023 -10000 0 -0.59 1 1
CaM/Ca2+/CAMKIIB -0.05 0.13 -10000 0 -0.38 89 89
MAPK11 0.012 0.043 -10000 0 -0.62 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.05 0.13 -10000 0 -0.35 95 95
OSM/MEKK3 -0.001 0.016 -10000 0 -0.42 1 1
TAOK1 -0.012 0.11 -10000 0 -0.36 56 56
TAOK2 0.019 0.021 -10000 0 -0.37 2 2
TAOK3 0.021 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0.023 -10000 0 -0.59 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.005 0.081 -10000 0 -0.62 11 11
MAP3K10 0.008 0.066 -10000 0 -0.59 8 8
MAP3K3 0.015 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.051 -10000 0 -0.38 11 11
GADD45/MTK1/MTK1 -0.063 0.14 -10000 0 -0.41 59 59
IFN-gamma pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.037 0.04 -9999 0 -0.32 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.014 0.023 -9999 0 -0.59 1 1
STAT1 (dimer)/Cbp/p300 0.029 0.1 -9999 0 -0.5 12 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.004 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.083 -9999 0 -0.35 27 27
CaM/Ca2+ -0.003 0.028 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.039 0.068 -9999 0 -0.36 5 5
AKT1 0.057 0.041 -9999 0 -10000 0 0
MAP2K1 0.055 0.045 -9999 0 -10000 0 0
MAP3K11 0.046 0.037 -9999 0 -10000 0 0
IFNGR1 0.017 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.13 0.19 -9999 0 -0.44 151 151
Rap1/GTP -0.006 0.045 -9999 0 -0.65 2 2
CRKL/C3G -0.002 0.03 -9999 0 -0.44 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.003 0.028 -9999 0 -10000 0 0
CEBPB 0.076 0.094 -9999 0 -0.61 5 5
STAT3 0.015 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.061 0.19 -9999 0 -1.1 14 14
STAT1 0.04 0.068 -9999 0 -0.37 5 5
CALM1 0.015 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0.001 0.06 -9999 0 -0.58 7 7
PIK3CA 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.046 0.067 -9999 0 -0.36 3 3
CEBPB/PTGES2/Cbp/p300 -0.011 0.048 -9999 0 -0.35 5 5
mol:Ca2+ -0.004 0.031 -9999 0 -0.32 1 1
MAPK3 0.065 0.049 -9999 0 -10000 0 0
STAT1 (dimer) -0.071 0.12 -9999 0 -0.52 27 27
MAPK1 0.065 0.049 -9999 0 -10000 0 0
JAK2 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
JAK1 0.017 0.003 -9999 0 -10000 0 0
CAMK2D 0.014 0.025 -9999 0 -0.62 1 1
DAPK1 0.067 0.12 -9999 0 -0.63 16 16
SMAD7 0.016 0.074 -9999 0 -0.26 6 6
CBL/CRKL/C3G -0.003 0.042 -9999 0 -0.8 1 1
PI3K -0.004 0.032 -9999 0 -10000 0 0
IFNG 0.001 0.06 -9999 0 -0.58 7 7
apoptosis 0.044 0.085 -9999 0 -0.45 16 16
CAMK2G 0.012 0.043 -9999 0 -0.62 3 3
STAT3 (dimer) 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.22 0.3 -9999 0 -0.6 251 251
CAMK2B -0.068 0.21 -9999 0 -0.61 89 89
FRAP1 0.056 0.039 -9999 0 -10000 0 0
PRKCD 0.048 0.072 -9999 0 -10000 0 0
RAP1B 0.009 0.061 -9999 0 -0.59 7 7
negative regulation of cell growth -0.053 0.083 -9999 0 -0.35 27 27
PTPN2 0.015 0 -9999 0 -10000 0 0
EP300 0.013 0.043 -9999 0 -0.63 3 3
IRF1 0.031 0.17 -9999 0 -0.67 25 25
STAT1 (dimer)/PIASy 0.005 0.071 -9999 0 -0.36 3 3
SOCS1 -0.074 0.24 -9999 0 -0.61 82 82
mol:GDP -0.004 0.04 -9999 0 -0.74 1 1
CASP1 0.007 0.098 -9999 0 -0.32 35 35
PTGES2 0.015 0 -9999 0 -10000 0 0
IRF9 0.06 0.042 -9999 0 -0.27 3 3
mol:PI-3-4-5-P3 -0.004 0.031 -9999 0 -10000 0 0
RAP1/GDP -0.006 0.047 -9999 0 -0.68 2 2
CBL 0.045 0.042 -9999 0 -0.57 1 1
MAP3K1 0.045 0.046 -9999 0 -10000 0 0
PIAS1 0.013 0.035 -9999 0 -0.62 2 2
PIAS4 0.015 0.025 -9999 0 -0.62 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.083 -9999 0 -0.35 27 27
PTPN11 0.038 0.038 -9999 0 -0.32 1 1
CREBBP 0.014 0.025 -9999 0 -0.62 1 1
RAPGEF1 0.013 0.035 -9999 0 -0.62 2 2
BARD1 signaling events

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.021 0.095 -10000 0 -0.45 31 31
ATM 0.015 0 -10000 0 -10000 0 0
UBE2D3 0.015 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
ATR 0.015 0 -10000 0 -10000 0 0
UBE2L3 0.015 0 -10000 0 -10000 0 0
FANCD2 0.018 0.063 -10000 0 -0.36 10 10
protein ubiquitination -0.024 0.091 -10000 0 -0.67 4 4
XRCC5 0.015 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.015 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.012 0.053 -10000 0 -0.4 8 8
FANCF 0.015 0 -10000 0 -10000 0 0
BRCA1 0.012 0.04 -10000 0 -0.59 3 3
CCNE1 0.011 0.052 -10000 0 -0.59 5 5
CDK2/Cyclin E1 -0.013 0.079 -10000 0 -0.47 18 18
FANCG 0.014 0.023 -10000 0 -0.59 1 1
BRCA1/BACH1/BARD1 -0.023 0.1 -10000 0 -0.46 33 33
FANCE 0.015 0 -10000 0 -10000 0 0
FANCC 0.014 0.025 -10000 0 -0.62 1 1
NBN 0.015 0 -10000 0 -10000 0 0
FANCA -0.023 0.15 -10000 0 -0.6 42 42
DNA repair 0.019 0.15 -10000 0 -0.49 23 23
BRCA1/BARD1/ubiquitin -0.023 0.1 -10000 0 -0.46 33 33
BARD1/DNA-PK -0.016 0.071 -10000 0 -10000 0 0
FANCL 0.015 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.021 0.095 0.45 31 -10000 0 31
BRCA1/BARD1/CTIP/M/R/N Complex 0.034 0.066 -10000 0 -0.43 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.019 0.085 -10000 0 -0.39 33 33
BRCA1/BARD1/P53 -0.024 0.092 -10000 0 -0.67 3 3
BARD1/CSTF1/BRCA1 -0.019 0.085 -10000 0 -0.39 33 33
BRCA1/BACH1 0.012 0.04 -10000 0 -0.59 3 3
BARD1 -0.014 0.13 -10000 0 -0.62 31 31
PCNA 0.009 0.061 -10000 0 -0.59 7 7
BRCA1/BARD1/UbcH5C -0.019 0.085 -10000 0 -0.39 33 33
BRCA1/BARD1/UbcH7 -0.019 0.085 -10000 0 -0.39 33 33
BRCA1/BARD1/RAD51/PCNA -0.061 0.14 -10000 0 -0.65 12 12
BARD1/DNA-PK/P53 -0.02 0.081 -10000 0 -0.64 2 2
BRCA1/BARD1/Ubiquitin -0.023 0.1 -10000 0 -0.46 33 33
BRCA1/BARD1/CTIP -0.018 0.084 -10000 0 -0.36 34 34
FA complex 0.034 0.058 -10000 0 -0.32 1 1
BARD1/EWS -0.021 0.095 -10000 0 -0.45 31 31
RBBP8 0.025 0.03 -10000 0 -0.42 3 3
TP53 0.003 0.088 -10000 0 -0.62 13 13
TOPBP1 0.015 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.023 0.091 0.66 3 -10000 0 3
BRCA1/BARD1 -0.024 0.092 -10000 0 -0.68 4 4
CSTF1 0.015 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.022 0.098 -10000 0 -0.46 31 31
CDK2 0.001 0.091 -10000 0 -0.6 15 15
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.063 0.2 -10000 0 -0.6 85 85
RAD50 0.015 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.023 0.1 -10000 0 -0.46 33 33
EWSR1 0.015 0 -10000 0 -10000 0 0
Insulin Pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.013 0.067 -9999 0 -0.76 2 2
TC10/GTP -0.008 0.056 -9999 0 -0.73 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.008 0.056 -9999 0 -0.44 8 8
HRAS 0.015 0 -9999 0 -10000 0 0
APS homodimer 0.001 0.094 -9999 0 -0.62 15 15
GRB14 -0.22 0.3 -9999 0 -0.6 252 252
FOXO3 -0.022 0.074 -9999 0 -0.66 8 8
AKT1 -0.059 0.15 -9999 0 -0.5 8 8
INSR 0.016 0.025 -9999 0 -0.62 1 1
Insulin Receptor/Insulin 0.039 0.03 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.006 0.075 -9999 0 -0.6 10 10
SORBS1 0.014 0.025 -9999 0 -0.62 1 1
CRK 0.015 0 -9999 0 -10000 0 0
PTPN1 0.039 0.03 -9999 0 -10000 0 0
CAV1 -0.018 0.12 -9999 0 -0.41 11 11
CBL/APS/CAP/Crk-II/C3G -0.009 0.062 -9999 0 -0.8 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.006 0.046 -9999 0 -0.35 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.044 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.036 0.051 -9999 0 -0.52 1 1
RPS6KB1 -0.045 0.14 -9999 0 -0.45 8 8
PARD6A 0.013 0.035 -9999 0 -0.62 2 2
CBL 0.014 0.025 -9999 0 -0.62 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.035 -9999 0 -0.84 1 1
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.083 0.11 -9999 0 -0.46 9 9
HRAS/GTP -0.014 0.058 -9999 0 -0.5 2 2
Insulin Receptor 0.016 0.025 -9999 0 -0.62 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.013 0.062 -9999 0 -10000 0 0
PRKCI -0.027 0.06 -9999 0 -0.58 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.1 0.13 -9999 0 -0.54 7 7
SHC1 0.001 0.092 -9999 0 -0.59 16 16
negative regulation of MAPKKK cascade 0.002 0.031 -9999 0 -0.71 1 1
PI3K -0.007 0.045 -9999 0 -10000 0 0
NCK2 0.015 0 -9999 0 -10000 0 0
RHOQ 0.015 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.058 0.15 -9999 0 -0.5 7 7
PRKCZ -0.067 0.16 -9999 0 -0.6 48 48
SH2B2 0.001 0.094 -9999 0 -0.62 15 15
SHC/SHIP 0.022 0.079 -9999 0 -0.59 2 2
F2RL2 -0.14 0.26 -9999 0 -0.6 168 168
TRIP10 0.009 0.065 -9999 0 -0.62 7 7
Insulin Receptor/Insulin/Shc -0.011 0.059 -9999 0 -0.33 21 21
TC10/GTP/CIP4/Exocyst -0.004 0.039 -9999 0 -0.39 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.01 0.053 -9999 0 -10000 0 0
RAPGEF1 0.013 0.035 -9999 0 -0.62 2 2
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.009 0.059 -9999 0 -0.39 13 13
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.016 0.072 -9999 0 -0.65 1 1
INPP5D 0.021 0.064 -9999 0 -0.35 12 12
SOS1 0.015 0 -9999 0 -10000 0 0
SGK1 -0.016 0.093 -9999 0 -0.92 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
IRS1 0.009 0.065 -9999 0 -0.62 7 7
p62DOK/RasGAP 0.002 0.031 -9999 0 -0.72 1 1
INS -0.001 0.053 -9999 0 -0.61 5 5
mol:PI-3-4-P2 0.021 0.063 -9999 0 -0.35 12 12
GRB2 0.014 0.023 -9999 0 -0.59 1 1
EIF4EBP1 -0.049 0.15 -9999 0 -0.49 14 14
PTPRA 0.017 0.003 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.004 0.039 -9999 0 -0.39 7 7
PDPK1 0.014 0.025 -9999 0 -0.62 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.03 0.051 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.007 0.047 -9999 0 -0.34 13 13
Insulin Receptor/Insulin/IRS3 -0.004 0.042 -9999 0 -0.44 6 6
Par3/Par6 -0.079 0.13 -9999 0 -0.3 176 176
VEGFR1 specific signals

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.036 0.037 -9999 0 -0.75 1 1
VEGFR1 homodimer/NRP1 0.025 0.037 -9999 0 -0.49 3 3
mol:DAG -0.002 0.13 -9999 0 -0.68 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.057 0.12 -9999 0 -0.7 1 1
CaM/Ca2+ 0.006 0.12 -9999 0 -0.64 1 1
HIF1A 0.022 0.036 -9999 0 -0.51 3 3
GAB1 0.014 0.025 -9999 0 -0.62 1 1
AKT1 0.023 0.12 -9999 0 -0.58 2 2
PLCG1 -0.002 0.13 -9999 0 -0.69 1 1
NOS3 0.028 0.12 -9999 0 -0.56 3 3
CBL 0.014 0.025 -9999 0 -0.62 1 1
mol:NO 0.028 0.12 -9999 0 -0.54 3 3
FLT1 0.034 0.042 -9999 0 -0.56 3 3
PGF -0.067 0.21 -9999 0 -0.61 88 88
VEGFR1 homodimer/NRP2/VEGFR121 -0.06 0.13 -9999 0 -0.64 4 4
CALM1 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.036 0.12 -9999 0 -0.52 3 3
endothelial cell proliferation -0.019 0.16 -9999 0 -0.57 17 17
mol:Ca2+ -0.002 0.13 -9999 0 -0.68 1 1
MAPK3 0.016 0.11 -9999 0 -0.59 1 1
MAPK1 0.016 0.11 -9999 0 -0.59 1 1
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
PLGF homodimer -0.067 0.21 -9999 0 -0.61 88 88
PRKACA 0.015 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.064 0.2 -9999 0 -0.59 88 88
VEGFA homodimer -0.091 0.23 -9999 0 -0.59 118 118
VEGFR1 homodimer/VEGFA homodimer -0.031 0.15 -9999 0 -0.75 1 1
platelet activating factor biosynthetic process 0.024 0.11 -9999 0 -0.57 1 1
PI3K -0.042 0.1 -9999 0 -0.65 1 1
PRKCA 0.007 0.12 -9999 0 -0.63 1 1
PRKCB -0.04 0.17 -9999 0 -0.62 17 17
VEGFR1 homodimer/PLGF homodimer -0.016 0.14 -9999 0 -0.75 1 1
VEGFA -0.091 0.23 -9999 0 -0.59 118 118
VEGFB 0.015 0 -9999 0 -10000 0 0
mol:IP3 -0.002 0.13 -9999 0 -0.68 1 1
RASA1 0.046 0.034 -9999 0 -0.69 1 1
NRP2 0.006 0.075 -9999 0 -0.61 10 10
VEGFR1 homodimer 0.034 0.042 -9999 0 -0.56 3 3
VEGFB homodimer 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.003 0.15 -9999 0 -0.51 13 13
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
mol:PI-3-4-5-P3 -0.041 0.1 -9999 0 -0.64 1 1
mol:L-citrulline 0.028 0.12 -9999 0 -0.54 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.051 0.11 -9999 0 -0.63 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.056 0.12 -9999 0 -0.69 1 1
CD2AP 0.015 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.039 0.096 -9999 0 -0.61 1 1
PDPK1 0.014 0.12 -9999 0 -0.6 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.057 0.12 -9999 0 -0.84 2 2
mol:NADP 0.028 0.12 -9999 0 -0.54 3 3
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.051 0.11 -9999 0 -0.62 2 2
VEGFR1 homodimer/NRP2 0.03 0.061 -9999 0 -0.75 1 1
Canonical NF-kappaB pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.095 0.037 -9999 0 -0.38 1 1
ERC1 0.012 0.042 -9999 0 -0.61 3 3
RIP2/NOD2 -0.019 0.089 -9999 0 -0.44 29 29
NFKBIA 0.055 0.023 -9999 0 -0.53 1 1
BIRC2 0.015 0 -9999 0 -10000 0 0
IKBKB 0.015 0 -9999 0 -10000 0 0
RIPK2 0.015 0 -9999 0 -10000 0 0
IKBKG -0.007 0.041 -9999 0 -0.72 1 1
IKK complex/A20 -0.064 0.11 -9999 0 -0.46 9 9
NEMO/A20/RIP2 0.015 0 -9999 0 -10000 0 0
XPO1 0.015 0 -9999 0 -10000 0 0
NEMO/ATM 0.052 0.049 -9999 0 -0.68 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.006 0.035 -9999 0 -0.6 1 1
BCL10/MALT1/TRAF6 -0.001 0.021 -9999 0 -0.38 2 2
NOD2 -0.012 0.13 -9999 0 -0.6 29 29
NFKB1 0.019 0.004 -9999 0 -10000 0 0
RELA 0.019 0.004 -9999 0 -10000 0 0
MALT1 0.015 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.015 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.11 0.19 -9999 0 -0.44 164 164
TRAF6 0.013 0.035 -9999 0 -0.62 2 2
PRKCA 0.013 0.035 -9999 0 -0.62 2 2
CHUK 0.015 0 -9999 0 -10000 0 0
UBE2D3 0.015 0 -9999 0 -10000 0 0
TNF -0.13 0.26 -9999 0 -0.6 152 152
NF kappa B1 p50/RelA 0 0.01 -9999 0 -10000 0 0
BCL10 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.023 -9999 0 -0.53 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.002 0.09 -9999 0 -0.61 14 14
IKK complex -0.006 0.035 -9999 0 -0.65 1 1
CYLD 0.014 0.025 -9999 0 -0.62 1 1
IKK complex/PKC alpha -0.006 0.042 -9999 0 -0.89 1 1
Class I PI3K signaling events

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.022 0.067 -9999 0 -10000 0 0
DAPP1 -0.016 0.13 -9999 0 -0.43 33 33
Src family/SYK family/BLNK-LAT/BTK-ITK -0.058 0.2 -9999 0 -0.63 45 45
mol:DAG -0.017 0.1 -9999 0 -0.29 28 28
HRAS 0.015 0.004 -9999 0 -10000 0 0
RAP1A 0.015 0.004 -9999 0 -10000 0 0
ARF5/GDP 0.035 0.054 -9999 0 -0.28 6 6
PLCG2 0.004 0.083 -9999 0 -0.61 12 12
PLCG1 0.015 0 -9999 0 -10000 0 0
ARF5 0.015 0 -9999 0 -10000 0 0
mol:GTP -0.025 0.076 -9999 0 -10000 0 0
ARF1/GTP -0.021 0.065 -9999 0 -0.41 1 1
RHOA 0.015 0 -9999 0 -10000 0 0
YES1 0.013 0.035 -9999 0 -0.62 2 2
RAP1A/GTP -0.024 0.075 -9999 0 -10000 0 0
ADAP1 -0.046 0.12 -9999 0 -0.56 16 16
ARAP3 -0.025 0.076 -9999 0 -10000 0 0
INPPL1 0.015 0 -9999 0 -10000 0 0
PREX1 0.007 0.074 -9999 0 -0.62 9 9
ARHGEF6 0.013 0.035 -9999 0 -0.62 2 2
ARHGEF7 0.015 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
NRAS 0.015 0.004 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
FGR 0.01 0.057 -9999 0 -0.59 6 6
mol:Ca2+ 0.001 0.057 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.013 0.035 -9999 0 -0.62 2 2
ZAP70 -0.038 0.17 -9999 0 -0.6 57 57
mol:IP3 -0.002 0.076 -9999 0 -0.22 4 4
LYN 0.011 0.053 -9999 0 -0.6 5 5
ARF1/GDP 0.035 0.054 -9999 0 -0.28 6 6
RhoA/GDP -0.022 0.062 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.025 -9999 0 -0.38 3 3
BLNK -0.036 0.17 -9999 0 -0.62 54 54
actin cytoskeleton reorganization 0.045 0.085 -9999 0 -0.36 5 5
SRC 0.013 0.035 -9999 0 -0.62 2 2
PLEKHA2 0.03 0.046 -9999 0 -0.36 9 9
RAC1 0.015 0 -9999 0 -10000 0 0
PTEN 0.004 0.011 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.022 0.067 -9999 0 -10000 0 0
RhoA/GTP -0.023 0.07 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.046 0.18 -9999 0 -0.55 47 47
BLK -0.07 0.21 -9999 0 -0.59 91 91
PDPK1 0.014 0.025 -9999 0 -0.62 1 1
CYTH1 -0.024 0.075 -9999 0 -0.56 1 1
HCK 0 0.096 -9999 0 -0.61 16 16
CYTH3 -0.023 0.07 -9999 0 -10000 0 0
CYTH2 -0.023 0.07 -9999 0 -10000 0 0
KRAS 0.014 0.024 -9999 0 -0.58 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.016 0.058 -9999 0 -0.46 7 7
SGK1 -0.018 0.063 -9999 0 -0.5 7 7
INPP5D 0.007 0.071 -9999 0 -0.6 9 9
mol:GDP 0.027 0.056 -9999 0 -0.3 6 6
SOS1 0.015 0 -9999 0 -10000 0 0
SYK -0.004 0.11 -9999 0 -0.62 20 20
ARF6/GDP -0.022 0.062 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.076 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.025 0.076 -9999 0 -10000 0 0
VAV1 -0.01 0.12 -9999 0 -0.62 27 27
mol:PI-3-4-P2 0.021 0.053 -9999 0 -0.44 9 9
RAS family/GTP/PI3K Class I 0.009 0.087 -9999 0 -10000 0 0
PLEKHA1 0.028 0.055 -9999 0 -0.36 13 13
Rac1/GDP 0.035 0.054 -9999 0 -0.28 6 6
LAT -0.011 0.13 -9999 0 -0.62 28 28
Rac1/GTP 0.033 0.073 -9999 0 -0.45 9 9
ITK -0.092 0.15 -9999 0 -0.53 25 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.031 0.14 -9999 0 -0.41 31 31
LCK -0.098 0.24 -9999 0 -0.6 123 123
BTK -0.032 0.085 -9999 0 -10000 0 0
Signaling events mediated by PRL

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.011 0.052 -10000 0 -0.59 5 5
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.02 0.14 -10000 0 -0.6 38 38
CDKN1A -0.011 0.12 -10000 0 -0.47 31 31
PRL-3/alpha Tubulin -0.003 0.036 -10000 0 -0.42 5 5
mol:Ca2+ -0.017 0.093 0.28 3 -0.47 26 29
AGT -0.01 0.12 -10000 0 -0.62 26 26
CCNA2 -0.052 0.17 -10000 0 -0.61 11 11
TUBA1B 0.013 0.033 -10000 0 -0.59 2 2
EGR1 -0.044 0.17 -10000 0 -0.44 105 105
CDK2/Cyclin E1 -0.003 0.13 -10000 0 -0.47 30 30
MAPK3 0.025 0.03 -10000 0 -0.42 3 3
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.03 -10000 0 -0.42 3 3
PTP4A1 -0.013 0.13 -10000 0 -10000 0 0
PTP4A3 0.012 0.04 -10000 0 -0.59 3 3
PTP4A2 0.015 0 -10000 0 -10000 0 0
ITGB1 0.023 0.042 -10000 0 -0.42 6 6
SRC 0.013 0.035 -10000 0 -0.62 2 2
RAC1 0.014 0.06 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.01 0.13 -10000 0 -10000 0 0
RABGGTA 0.015 0 -10000 0 -10000 0 0
BCAR1 0.001 0.026 0.28 3 -0.47 1 4
RHOC 0.013 0.063 -10000 0 -0.35 2 2
RHOA 0.014 0.06 -10000 0 -10000 0 0
cell motility 0.017 0.065 -10000 0 -10000 0 0
PRL-1/alpha Tubulin -0.006 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.026 0.1 -10000 0 -0.44 40 40
ROCK1 0.017 0.065 -10000 0 -10000 0 0
RABGGTB 0.015 0 -10000 0 -10000 0 0
CDK2 0.001 0.091 -10000 0 -0.6 15 15
mitosis -0.013 0.13 -10000 0 -10000 0 0
ATF5 0.006 0.073 -10000 0 -0.59 10 10
Circadian rhythm pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.009 0.068 -10000 0 -0.98 2 2
CLOCK -0.006 0.12 -10000 0 -0.62 26 26
TIMELESS/CRY2 0.037 0.087 -10000 0 -1.1 2 2
DEC1/BMAL1 -0.018 0.085 -10000 0 -0.42 29 29
ATR 0.015 0 -10000 0 -10000 0 0
NR1D1 0.04 0.077 -10000 0 -1 2 2
ARNTL 0.019 0.004 -10000 0 -10000 0 0
TIMELESS 0.038 0.086 -10000 0 -0.94 3 3
NPAS2 0.008 0.08 -10000 0 -0.61 11 11
CRY2 0.009 0.065 -10000 0 -0.62 7 7
mol:CO -0.015 0.014 0.096 10 -10000 0 10
CHEK1 0.013 0.033 -10000 0 -0.59 2 2
mol:HEME 0.015 0.014 -10000 0 -0.096 10 10
PER1 0.007 0.074 -10000 0 -0.62 9 9
BMAL/CLOCK/NPAS2 0.027 0.098 -10000 0 -0.37 37 37
BMAL1/CLOCK 0.032 0.12 -10000 0 -1.1 3 3
S phase of mitotic cell cycle -0.009 0.068 -10000 0 -0.98 2 2
TIMELESS/CHEK1/ATR -0.009 0.07 -10000 0 -1 2 2
mol:NADPH 0.015 0.014 -10000 0 -0.096 10 10
PER1/TIMELESS 0.036 0.09 -10000 0 -1.1 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.016 0.12 -10000 0 -0.59 29 29
Arf6 downstream pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.031 0.22 -10000 0 -1 12 12
regulation of axonogenesis -0.003 0.074 0.37 4 -10000 0 4
myoblast fusion 0.018 0.098 0.41 11 -10000 0 11
mol:GTP -0.023 0.056 -10000 0 -0.23 11 11
regulation of calcium-dependent cell-cell adhesion -0.013 0.071 0.39 6 -10000 0 6
ARF1/GTP -0.015 0.037 -10000 0 -10000 0 0
mol:GM1 -0.006 0.046 -10000 0 -10000 0 0
mol:Choline -0.006 0.1 -10000 0 -0.37 42 42
lamellipodium assembly -0.038 0.092 -10000 0 -0.44 11 11
MAPK3 -0.001 0.089 -10000 0 -0.34 10 10
ARF6/GTP/NME1/Tiam1 0.014 0.071 -10000 0 -0.39 6 6
ARF1 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.018 0.098 -10000 0 -0.41 11 11
ARF1/GDP -0.005 0.09 -10000 0 -0.37 11 11
ARF6 0.001 0.032 -10000 0 -10000 0 0
RAB11A 0.015 0 -10000 0 -10000 0 0
TIAM1 0.013 0.035 -10000 0 -0.62 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.089 -10000 0 -0.34 10 10
actin filament bundle formation 0.033 0.079 0.37 11 -10000 0 11
KALRN -0.035 0.082 -10000 0 -0.3 28 28
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.033 0.079 -10000 0 -0.38 11 11
NME1 0.011 0.048 -10000 0 -0.6 4 4
Rac1/GDP -0.033 0.079 -10000 0 -0.38 11 11
substrate adhesion-dependent cell spreading -0.023 0.056 -10000 0 -0.23 11 11
cortical actin cytoskeleton organization -0.038 0.093 -10000 0 -0.44 11 11
RAC1 0.015 0 -10000 0 -10000 0 0
liver development -0.023 0.056 -10000 0 -0.23 11 11
ARF6/GTP -0.023 0.056 -10000 0 -0.23 11 11
RhoA/GTP -0.015 0.037 -10000 0 -10000 0 0
mol:GDP -0.037 0.09 -10000 0 -0.42 11 11
ARF6/GTP/RAB11FIP3/RAB11A -0.011 0.028 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
PLD1 -0.02 0.11 -10000 0 -0.43 41 41
RAB11FIP3 0.015 0 -10000 0 -10000 0 0
tube morphogenesis -0.038 0.092 -10000 0 -0.44 11 11
ruffle organization 0.003 0.074 -10000 0 -0.37 4 4
regulation of epithelial cell migration -0.023 0.056 -10000 0 -0.23 11 11
PLD2 0.006 0.049 -10000 0 -0.42 1 1
PIP5K1A 0.002 0.074 -10000 0 -0.37 4 4
mol:Phosphatidic acid -0.006 0.1 -10000 0 -0.37 42 42
Rac1/GTP -0.038 0.093 -10000 0 -0.45 11 11
Signaling events mediated by HDAC Class I

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.074 0.13 -10000 0 -0.36 78 78
Ran/GTP/Exportin 1/HDAC1 -0.002 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.14 -10000 0 -0.32 78 78
SUMO1 0.015 0 -10000 0 -10000 0 0
ZFPM1 0.014 0.025 -10000 0 -0.62 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.026 0 -10000 0 -10000 0 0
FKBP3 0.015 0 -10000 0 -10000 0 0
Histones -0.033 0.065 -10000 0 -0.47 4 4
YY1/LSF 0.033 0.041 -10000 0 -0.44 3 3
SMG5 0.015 0 -10000 0 -10000 0 0
RAN 0.015 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.027 0.12 -10000 0 -0.46 2 2
I kappa B alpha/HDAC1 -0.013 0.094 -10000 0 -0.43 6 6
SAP18 0.015 0 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.26 78 78
HDAC1/Smad7 -0.003 0.036 -10000 0 -0.38 6 6
RANGAP1 0.015 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.01 0.087 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.053 0.029 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.008 0.1 -10000 0 -0.37 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.003 0.11 -10000 0 -0.61 20 20
GATA1 0.004 0.061 -10000 0 -0.59 7 7
Mad/Max 0 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.062 0.035 -10000 0 -10000 0 0
RBBP7 0.015 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0.015 0 -10000 0 -10000 0 0
MAX 0.015 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
NFKBIA -0.021 0.098 -10000 0 -0.34 2 2
KAT2B 0.012 0.042 -10000 0 -0.61 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.05 0.024 -10000 0 -10000 0 0
SIN3 complex -0.001 0.018 -10000 0 -0.34 2 2
SMURF1 0.015 0 -10000 0 -10000 0 0
CHD3 0.008 0.07 -10000 0 -0.62 8 8
SAP30 0.014 0.025 -10000 0 -0.62 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.013 0.035 -10000 0 -0.62 2 2
YY1/HDAC3 0.005 0.084 -10000 0 -0.33 2 2
YY1/HDAC2 0.034 0.027 -10000 0 -10000 0 0
YY1/HDAC1 0.032 0.041 -10000 0 -0.36 4 4
NuRD/MBD2 Complex (MeCP1) 0.053 0.029 -10000 0 -10000 0 0
PPARG -0.08 0.14 -10000 0 -0.37 95 95
HDAC8/hEST1B -0.001 0.015 -10000 0 -0.38 1 1
UBE2I 0.015 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -10000 0 -10000 0 0
TNFRSF1A 0.002 0.09 -10000 0 -0.61 14 14
HDAC3/SMRT (N-CoR2) -0.011 0.089 -10000 0 -0.32 4 4
MBD3L2 0 0.001 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.003 0.036 -10000 0 -0.38 6 6
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
NuRD/MBD3/MBD3L2 Complex 0.057 0.031 -10000 0 -10000 0 0
HDAC1 0.011 0.049 -10000 0 -0.62 4 4
HDAC3 -0.021 0.098 -10000 0 -0.34 2 2
HDAC2 0.015 0 -10000 0 -10000 0 0
YY1 0.033 0.032 -10000 0 -0.29 6 6
HDAC8 0.014 0.025 -10000 0 -0.62 1 1
SMAD7 0.013 0.035 -10000 0 -0.62 2 2
NCOR2 0.013 0.035 -10000 0 -0.62 2 2
MXD1 0.015 0 -10000 0 -10000 0 0
STAT3 0.029 0.03 -10000 0 -0.36 4 4
NFKB1 0.015 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.015 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 -0.006 0.042 -10000 0 -0.36 7 7
YY1/SAP30/HDAC1 -0.005 0.035 -10000 0 -0.33 5 5
EP300 0.012 0.043 -10000 0 -0.62 3 3
STAT3 (dimer non-phopshorylated) 0.029 0.03 -10000 0 -0.35 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.098 -10000 0 -0.34 2 2
histone deacetylation 0.053 0.029 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.084 -10000 0 -0.39 1 1
nuclear export 0.001 0.015 0.38 1 -10000 0 1
PRKACA 0.015 0 -10000 0 -10000 0 0
GATAD2B 0.015 0 -10000 0 -10000 0 0
GATAD2A 0.015 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.021 0.1 -10000 0 -0.35 22 22
GATA1/HDAC1 -0.007 0.055 -10000 0 -0.44 11 11
GATA1/HDAC3 -0.024 0.091 -10000 0 -0.35 9 9
CHD4 0.015 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.11 0.19 -10000 0 -0.44 164 164
SIN3/HDAC complex/Mad/Max 0.055 0.021 -10000 0 -10000 0 0
NuRD Complex 0.063 0.031 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.033 0.064 -10000 0 -0.46 4 4
SIN3B 0.014 0.025 -10000 0 -0.62 1 1
MTA2 0.015 0 -10000 0 -10000 0 0
SIN3A 0.015 0 -10000 0 -10000 0 0
XPO1 0.015 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.034 0.026 -10000 0 -0.31 4 4
HDAC complex -0.002 0.026 -10000 0 -0.34 4 4
GATA1/Fog1 -0.005 0.047 -10000 0 -0.43 8 8
FKBP25/HDAC1/HDAC2 -0.002 0.029 -10000 0 -0.38 4 4
TNF -0.13 0.26 -10000 0 -0.6 152 152
negative regulation of cell growth 0.055 0.02 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.053 0.029 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.065 0.12 -10000 0 -0.34 78 78
SIN3/HDAC complex/NCoR1 0.052 0.024 -10000 0 -10000 0 0
TFCP2 0.012 0.043 -10000 0 -0.62 3 3
NR2C1 0.015 0 -10000 0 -10000 0 0
MBD3 0.015 0 -10000 0 -10000 0 0
MBD2 0.015 0 -10000 0 -10000 0 0
IGF1 pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.015 0 -10000 0 -10000 0 0
PTK2 0.015 0 -10000 0 -10000 0 0
CRKL 0.013 0.09 -10000 0 -0.38 25 25
GRB2/SOS1/SHC -0.009 0.055 -10000 0 -0.35 17 17
HRAS 0.015 0 -10000 0 -10000 0 0
IRS1/Crk 0.013 0.089 -10000 0 -0.38 24 24
IGF-1R heterotetramer/IGF1/PTP1B -0.018 0.083 -10000 0 -0.4 24 24
AKT1 0.036 0.081 -10000 0 -0.63 4 4
BAD 0.044 0.077 -10000 0 -0.57 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.089 -10000 0 -0.38 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.012 0.097 -10000 0 -0.41 24 24
RAF1 0.048 0.074 -10000 0 -0.53 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.016 0.078 -10000 0 -0.72 4 4
YWHAZ 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.003 0.095 -10000 0 -0.37 34 34
PIK3CA 0.015 0 -10000 0 -10000 0 0
RPS6KB1 0.037 0.081 -10000 0 -0.63 4 4
GNB2L1 0.015 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.041 0.065 -10000 0 -0.45 4 4
PXN 0.015 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.016 -10000 0 -0.42 1 1
HRAS/GTP -0.02 0.079 -10000 0 -0.59 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.021 0.082 -10000 0 -0.61 4 4
IGF-1R heterotetramer 0.002 0.087 -10000 0 -0.66 11 11
IGF-1R heterotetramer/IGF1/IRS/Nck 0.013 0.089 -10000 0 -0.38 24 24
Crk/p130 Cas/Paxillin -0.015 0.078 -10000 0 -0.76 4 4
IGF1R 0.002 0.088 -10000 0 -0.66 11 11
IGF1 -0.007 0.12 -10000 0 -0.63 22 22
IRS2/Crk 0.022 0.086 -10000 0 -0.72 4 4
PI3K -0.017 0.08 -10000 0 -0.72 4 4
apoptosis -0.049 0.068 0.48 4 -10000 0 4
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD 0.016 0.12 -10000 0 -0.52 18 18
RAF1/14-3-3 E 0.053 0.066 -10000 0 -0.45 4 4
BAD/14-3-3 0.051 0.072 -10000 0 -0.52 4 4
PRKCZ 0.01 0.13 -10000 0 -0.59 11 11
Crk/p130 Cas/Paxillin/FAK1 -0.012 0.059 -10000 0 -0.56 4 4
PTPN1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.02 0.095 -10000 0 -0.42 25 25
BCAR1 0.014 0.025 -10000 0 -0.62 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.028 0.1 -10000 0 -0.52 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.015 0 -10000 0 -10000 0 0
IRS1/NCK2 0.013 0.088 -10000 0 -0.38 24 24
GRB10 0.006 0.075 -10000 0 -0.6 10 10
PTPN11 0.013 0.097 -10000 0 -0.41 24 24
IRS1 0.004 0.095 -10000 0 -0.37 34 34
IRS2 0.013 0.09 -10000 0 -0.38 25 25
IGF-1R heterotetramer/IGF1 -0.023 0.11 -10000 0 -0.49 31 31
GRB2 0.014 0.023 -10000 0 -0.59 1 1
PDPK1 0.028 0.085 -10000 0 -0.67 4 4
YWHAE 0.015 0 -10000 0 -10000 0 0
PRKD1 0.029 0.091 -10000 0 -0.43 18 18
SHC1 0.001 0.092 -10000 0 -0.59 16 16
Class IB PI3K non-lipid kinase events

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.007 0.073 0.61 9 -10000 0 9
PI3K Class IB/PDE3B 0.007 0.073 -10000 0 -0.62 9 9
PDE3B 0.007 0.073 -10000 0 -0.62 9 9
Signaling events mediated by HDAC Class II

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.004 0.034 -10000 0 -0.34 7 7
HDAC3 0.015 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.011 -10000 0 -10000 0 0
GATA1/HDAC4 -0.005 0.047 -10000 0 -0.43 8 8
GATA1/HDAC5 -0.005 0.047 -10000 0 -0.43 8 8
GATA2/HDAC5 -0.014 0.08 -10000 0 -0.46 20 20
HDAC5/BCL6/BCoR -0.002 0.035 -10000 0 -0.49 3 3
HDAC9 0.005 0.081 -10000 0 -0.62 11 11
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
HDAC4/ANKRA2 -0.001 0.018 -10000 0 -0.46 1 1
HDAC5/YWHAB -0.001 0.018 -10000 0 -0.46 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.026 0 -10000 0 -10000 0 0
GATA2 -0.003 0.11 -10000 0 -0.61 20 20
HDAC4/RFXANK -0.001 0.024 -10000 0 -0.44 2 2
BCOR 0.012 0.042 -10000 0 -0.61 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.025 -10000 0 -0.62 1 1
HDAC5 0.014 0.025 -10000 0 -0.62 1 1
GNB1/GNG2 -0.004 0.043 -10000 0 -0.46 6 6
Histones 0.042 0.046 -10000 0 -0.73 1 1
ADRBK1 0.015 0 -10000 0 -10000 0 0
HDAC4 0.014 0.025 -10000 0 -0.62 1 1
XPO1 0.015 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.018 -10000 0 -0.46 1 1
HDAC4/Ubc9 -0.001 0.018 -10000 0 -0.46 1 1
HDAC7 0.015 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.018 -10000 0 -0.46 1 1
TUBA1B 0.013 0.033 -10000 0 -0.59 2 2
HDAC6 0.015 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.024 -10000 0 -0.44 2 2
CAMK4 -0.15 0.28 -10000 0 -0.61 176 176
Tubulin/HDAC6 -0.003 0.032 -10000 0 -0.37 5 5
SUMO1 0.015 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
GATA1 0.004 0.061 -10000 0 -0.59 7 7
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.015 0 -10000 0 -10000 0 0
NR3C1 0.015 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.013 -10000 0 -0.31 1 1
SRF 0.015 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.018 -10000 0 -0.46 1 1
Tubulin -0.003 0.038 -10000 0 -0.44 5 5
HDAC4/14-3-3 E -0.001 0.018 -10000 0 -0.46 1 1
GNB1 0.015 0 -10000 0 -10000 0 0
RANGAP1 0.015 0 -10000 0 -10000 0 0
BCL6/BCoR -0.002 0.03 -10000 0 -0.44 3 3
HDAC4/HDAC3/SMRT (N-CoR2) -0.002 0.025 -10000 0 -0.38 3 3
HDAC4/SRF -0.097 0.16 -10000 0 -0.37 176 176
HDAC4/ER alpha -0.016 0.082 -10000 0 -0.44 24 24
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.042 0.046 -10000 0 -0.72 1 1
cell motility -0.003 0.032 -10000 0 -0.37 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.015 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 0.015 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0.025 -10000 0 -0.62 1 1
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 -0.006 0.11 -10000 0 -0.61 23 23
HDAC6/HDAC11 -0.001 0.025 -10000 0 -0.46 2 2
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.002 0.1 -10000 0 -0.59 19 19
RAN 0.015 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.01 0.052 -10000 0 -10000 0 0
GNG2 0.009 0.06 -10000 0 -0.62 6 6
NCOR2 0.013 0.035 -10000 0 -0.62 2 2
TUBB2A 0.012 0.043 -10000 0 -0.62 3 3
HDAC11 0.013 0.035 -10000 0 -0.62 2 2
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RANBP2 0.015 0 -10000 0 -10000 0 0
ANKRA2 0.015 0 -10000 0 -10000 0 0
RFXANK 0.014 0.023 -10000 0 -0.59 1 1
nuclear import -0.034 0.02 0.34 2 -10000 0 2
Arf6 trafficking events

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.062 0.2 -10000 0 -0.6 83 83
CLTC 0.034 0.024 -10000 0 -0.35 1 1
calcium ion-dependent exocytosis 0.022 0.041 -10000 0 -10000 0 0
Dynamin 2/GTP -0.002 0.025 -10000 0 -0.32 4 4
EXOC4 0.015 0 -10000 0 -10000 0 0
CD59 0.029 0.021 -10000 0 -10000 0 0
CPE 0.013 0.063 -10000 0 -0.39 16 16
CTNNB1 0.015 0 -10000 0 -10000 0 0
membrane fusion 0.02 0.044 -10000 0 -10000 0 0
CTNND1 0.036 0.025 -10000 0 -0.29 4 4
DNM2 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.029 -10000 0 -0.41 1 1
TSHR -0.14 0.2 -10000 0 -0.38 268 268
INS 0.009 0.043 -10000 0 -0.53 4 4
BIN1 0.014 0.025 -10000 0 -0.62 1 1
mol:Choline 0.02 0.044 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.03 -10000 0 -0.36 4 4
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.024 -10000 0 -0.32 4 4
JUP 0.026 0.035 -10000 0 -0.3 3 3
ASAP2/amphiphysin II -0.001 0.013 -10000 0 -0.35 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 -0.015 0.095 -10000 0 -0.32 15 15
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.007 0.074 -10000 0 -0.62 9 9
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.015 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.051 0.01 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.015 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.026 0.058 0.41 2 -10000 0 2
positive regulation of phagocytosis 0.022 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.005 0.045 -10000 0 -0.39 9 9
ACAP1 0.016 0.041 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.009 0.083 -10000 0 -0.3 4 4
clathrin heavy chain/ACAP1 0.036 0.033 -10000 0 -0.34 1 1
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0.033 -10000 0 -0.59 2 2
exocyst 0.051 0.01 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.036 0.025 -10000 0 -0.29 4 4
NME1 0.02 0.03 -10000 0 -0.36 4 4
clathrin coat assembly 0.034 0.024 -10000 0 -0.35 1 1
IL2RA -0.031 0.094 -10000 0 -0.29 5 5
VAMP3 0.022 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.037 0.088 -10000 0 -0.31 13 13
EXOC6 0.015 0 -10000 0 -10000 0 0
PLD1 -0.016 0.063 -10000 0 -0.29 31 31
PLD2 0 0.011 -10000 0 -0.29 1 1
EXOC5 0.015 0 -10000 0 -10000 0 0
PIP5K1C 0.032 0.03 -10000 0 -0.41 1 1
SDC1 0.007 0.064 -10000 0 -0.29 1 1
ARF6/GDP 0.019 0.029 -10000 0 -0.36 4 4
EXOC7 0.014 0.023 -10000 0 -0.59 1 1
E-cadherin/beta catenin -0.026 0.059 -10000 0 -0.42 2 2
mol:Phosphatidic acid 0.02 0.044 -10000 0 -10000 0 0
endocytosis 0.001 0.013 0.34 1 -10000 0 1
SCAMP2 0.015 0 -10000 0 -10000 0 0
ADRB2 0.028 0.071 -10000 0 -0.34 6 6
EXOC3 0.015 0 -10000 0 -10000 0 0
ASAP2 0.015 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.027 -10000 0 -0.32 4 4
KLC1 0.015 0 -10000 0 -10000 0 0
AVPR2 0.03 0.06 -10000 0 -0.32 5 5
RALA 0.015 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.021 0.05 -10000 0 -0.38 2 2
PDGFR-beta signaling pathway

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.019 0.078 -9999 0 -0.39 12 12
PDGFB-D/PDGFRB/SLAP -0.02 0.097 -9999 0 -0.44 34 34
PDGFB-D/PDGFRB/APS/CBL -0.012 0.071 -9999 0 -0.41 19 19
AKT1 0.067 0.038 -9999 0 -0.47 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.017 0.091 -9999 0 -0.43 9 9
PIK3CA 0.015 0 -9999 0 -10000 0 0
FGR 0 0.035 -9999 0 -10000 0 0
mol:Ca2+ 0.027 0.043 -9999 0 -10000 0 0
MYC 0.026 0.15 -9999 0 -0.81 18 18
SHC1 0.001 0.092 -9999 0 -0.59 16 16
HRAS/GDP 0.011 0.032 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.004 0.043 -9999 0 -0.41 7 7
GRB10 0.006 0.075 -9999 0 -0.6 10 10
PTPN11 0.013 0.035 -9999 0 -0.62 2 2
GO:0007205 0.027 0.043 -9999 0 -10000 0 0
PTEN 0.015 0 -9999 0 -10000 0 0
GRB2 0.014 0.023 -9999 0 -0.59 1 1
GRB7 -0.038 0.16 -9999 0 -0.59 54 54
PDGFB-D/PDGFRB/SHP2 -0.002 0.045 -9999 0 -0.43 7 7
PDGFB-D/PDGFRB/GRB10 -0.007 0.068 -9999 0 -0.46 14 14
cell cycle arrest -0.02 0.097 -9999 0 -0.44 34 34
HRAS 0.015 0 -9999 0 -10000 0 0
HIF1A 0.072 0.038 -9999 0 -0.41 1 1
GAB1 0.018 0.071 -9999 0 -0.39 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.022 0.074 -9999 0 -0.39 5 5
PDGFB-D/PDGFRB 0.008 0.037 -9999 0 -0.36 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.037 -9999 0 -0.42 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.022 0.085 -9999 0 -0.44 13 13
positive regulation of MAPKKK cascade -0.002 0.045 -9999 0 -0.43 7 7
PIK3R1 0.012 0.043 -9999 0 -0.62 3 3
mol:IP3 0.027 0.044 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.035 0.12 -9999 0 -0.44 57 57
SHB 0.011 0.049 -9999 0 -0.62 4 4
BLK -0.026 0.074 -9999 0 -0.52 5 5
PTPN2 0.015 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.037 -9999 0 -0.42 5 5
BCAR1 0.014 0.025 -9999 0 -0.62 1 1
VAV2 0.022 0.081 -9999 0 -0.41 6 6
CBL 0.014 0.025 -9999 0 -0.62 1 1
PDGFB-D/PDGFRB/DEP1 -0.002 0.044 -9999 0 -0.43 7 7
LCK -0.057 0.15 -9999 0 -0.54 48 48
PDGFRB 0.011 0.053 -9999 0 -0.59 5 5
ACP1 0.015 0 -9999 0 -10000 0 0
HCK -0.008 0.084 -9999 0 -0.6 11 11
ABL1 0.018 0.062 -9999 0 -0.36 5 5
PDGFB-D/PDGFRB/CBL 0.018 0.068 -9999 0 -0.37 4 4
PTPN1 0.015 0.003 -9999 0 -10000 0 0
SNX15 0.015 0 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
STAT1 0.001 0.092 -9999 0 -0.59 16 16
cell proliferation 0.028 0.14 -9999 0 -0.7 18 18
SLA -0.012 0.13 -9999 0 -0.61 29 29
actin cytoskeleton reorganization 0.052 0.046 -9999 0 -0.6 1 1
SRC 0 0.046 -9999 0 -0.52 3 3
PI3K -0.003 0.032 -9999 0 -0.53 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.039 0.12 -9999 0 -0.39 67 67
SH2B2 0.001 0.094 -9999 0 -0.62 15 15
PLCgamma1/SPHK1 0.017 0.094 -9999 0 -0.44 9 9
LYN 0 0.049 -9999 0 -0.64 2 2
LRP1 0.013 0.035 -9999 0 -0.62 2 2
SOS1 0.015 0 -9999 0 -10000 0 0
STAT5B 0.015 0 -9999 0 -10000 0 0
STAT5A 0.005 0.081 -9999 0 -0.62 11 11
NCK1-2/p130 Cas 0.002 0.03 -9999 0 -10000 0 0
SPHK1 -0.025 0.15 -9999 0 -0.6 44 44
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.027 0.044 -9999 0 -10000 0 0
PLCG1 0.027 0.044 -9999 0 -10000 0 0
NHERF/PDGFRB -0.003 0.033 -9999 0 -0.35 6 6
YES1 0 0.045 -9999 0 -0.58 2 2
cell migration -0.003 0.033 -9999 0 -0.35 6 6
SHC/Grb2/SOS1 -0.004 0.058 -9999 0 -0.57 3 3
SLC9A3R2 0.015 0 -9999 0 -10000 0 0
SLC9A3R1 0.014 0.025 -9999 0 -0.62 1 1
NHERF1-2/PDGFRB/PTEN -0.003 0.03 -9999 0 -0.34 1 1
FYN 0.003 0.031 -9999 0 -10000 0 0
DOK1 0.036 0.035 -9999 0 -0.33 2 2
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.014 0.023 -9999 0 -0.59 1 1
RAC1 0.03 0.1 -9999 0 -0.42 19 19
PRKCD 0.023 0.078 -9999 0 -0.35 24 24
FER 0.029 0.061 -9999 0 -0.34 14 14
MAPKKK cascade -0.009 0.055 -9999 0 -0.56 3 3
RASA1 0.037 0.032 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
NCK2 0.015 0 -9999 0 -10000 0 0
p62DOK/Csk 0.014 0.036 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.004 0.051 -9999 0 -0.44 9 9
chemotaxis 0.018 0.061 -9999 0 -0.35 5 5
STAT1-3-5/STAT1-3-5 -0.012 0.056 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.002 0.038 -9999 0 -0.44 5 5
PTPRJ 0.013 0.034 -9999 0 -0.61 2 2
Class I PI3K signaling events mediated by Akt

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.017 -10000 0 -0.42 1 1
BAD/BCL-XL/YWHAZ 0 0.012 -10000 0 -10000 0 0
CDKN1B 0.044 0.013 -10000 0 -10000 0 0
CDKN1A 0.018 0.089 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
FOXO3 0.043 0.019 -10000 0 -0.3 1 1
AKT1 -0.001 0.01 -10000 0 -10000 0 0
BAD 0.015 0 -10000 0 -10000 0 0
AKT3 0.017 0.047 -10000 0 -0.44 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.042 0.031 -10000 0 -0.39 3 3
AKT1/ASK1 -0.005 0.037 -10000 0 -10000 0 0
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.013 0.035 -10000 0 -0.62 2 2
RAF1 0.015 0 -10000 0 -10000 0 0
JNK cascade 0.005 0.036 -10000 0 -10000 0 0
TSC1 0.043 0.023 -10000 0 -0.3 2 2
YWHAZ 0.015 0 -10000 0 -10000 0 0
AKT1/RAF1 0.043 0.013 -10000 0 -10000 0 0
EP300 0.012 0.043 -10000 0 -0.62 3 3
mol:GDP 0.036 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.043 0.022 -10000 0 -0.43 1 1
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.029 0.013 -10000 0 -0.31 1 1
MAP3K5 0.005 0.081 -10000 0 -0.62 11 11
MAPKAP1 0.015 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.021 0.057 0.24 1 -10000 0 1
YWHAH 0.003 0.083 -10000 0 -0.59 13 13
AKT1S1 0.044 0.013 -10000 0 -10000 0 0
CASP9 0.043 0.018 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.051 0.013 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.025 -10000 0 -0.38 3 3
YWHAE 0.015 0 -10000 0 -10000 0 0
SRC 0.013 0.035 -10000 0 -0.62 2 2
AKT2/p21CIP1 -0.022 0.073 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.005 -10000 0 -10000 0 0
CHUK 0.044 0.013 -10000 0 -10000 0 0
BAD/BCL-XL 0.058 0.017 -10000 0 -10000 0 0
mTORC2 -0.001 0.019 -10000 0 -0.36 2 2
AKT2 0.02 0.015 -10000 0 -0.37 1 1
FOXO1-3a-4/14-3-3 family 0.039 0.063 -10000 0 -10000 0 0
PDPK1 0.014 0.025 -10000 0 -0.62 1 1
MDM2 0.038 0.046 -10000 0 -0.35 1 1
MAPKKK cascade -0.042 0.013 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.05 0.05 -10000 0 -0.39 1 1
TSC1/TSC2 0.05 0.028 -10000 0 -0.41 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.039 -10000 0 -0.37 1 1
glucose import -0.008 0.12 -10000 0 -0.32 83 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.12 -10000 0 -0.32 83 83
GSK3A 0.044 0.013 -10000 0 -10000 0 0
FOXO1 0.043 0.019 -10000 0 -10000 0 0
GSK3B 0.044 0.013 -10000 0 -10000 0 0
SFN -0.12 0.25 -10000 0 -0.6 141 141
G1/S transition of mitotic cell cycle 0.051 0.013 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.016 0.08 -10000 0 -0.37 1 1
PRKACA 0.015 0 -10000 0 -10000 0 0
KPNA1 0.015 0 -10000 0 -10000 0 0
HSP90AA1 0.015 0 -10000 0 -10000 0 0
YWHAG 0.012 0.04 -10000 0 -0.59 3 3
RHEB 0.015 0 -10000 0 -10000 0 0
CREBBP 0.014 0.025 -10000 0 -0.62 1 1
FoxO family signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.031 0.094 -9999 0 -10000 0 0
PLK1 0.035 0.25 -9999 0 -0.96 16 16
CDKN1B 0.095 0.13 -9999 0 -10000 0 0
FOXO3 0.057 0.18 -9999 0 -0.6 9 9
KAT2B 0.02 0.045 -9999 0 -0.6 3 3
FOXO1/SIRT1 0.003 0.056 -9999 0 -10000 0 0
CAT 0.062 0.18 -9999 0 -1.2 1 1
CTNNB1 0.015 0 -9999 0 -10000 0 0
AKT1 0.025 0.03 -9999 0 -0.6 1 1
FOXO1 0.036 0.067 -9999 0 -0.29 5 5
MAPK10 0.04 0.035 -9999 0 -0.32 5 5
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.1 0.067 -9999 0 -0.51 1 1
response to oxidative stress 0.01 0.022 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.007 0.15 -9999 0 -0.56 10 10
XPO1 0.016 0.001 -9999 0 -10000 0 0
EP300 0.014 0.043 -9999 0 -0.62 3 3
BCL2L11 0.034 0.086 -9999 0 -1.4 2 2
FOXO1/SKP2 0.035 0.07 -9999 0 -0.34 6 6
mol:GDP 0.01 0.022 -9999 0 -10000 0 0
RAN 0.017 0.002 -9999 0 -10000 0 0
GADD45A 0.077 0.16 -9999 0 -0.55 15 15
YWHAQ 0.015 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.055 0.069 -9999 0 -10000 0 0
MST1 -0.018 0.16 -9999 0 -0.61 43 43
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.02 0.1 -9999 0 -0.42 1 1
YWHAB 0.015 0 -9999 0 -10000 0 0
MAPK8 0.038 0.045 -9999 0 -0.32 9 9
MAPK9 0.043 0.016 -9999 0 -10000 0 0
YWHAG 0.012 0.04 -9999 0 -0.59 3 3
YWHAE 0.015 0 -9999 0 -10000 0 0
YWHAZ 0.015 0 -9999 0 -10000 0 0
SIRT1 0.007 0.012 -9999 0 -10000 0 0
SOD2 0.083 0.2 -9999 0 -0.62 10 10
RBL2 0.083 0.14 -9999 0 -1.2 1 1
RAL/GDP 0.03 0.021 -9999 0 -10000 0 0
CHUK 0.023 0.017 -9999 0 -10000 0 0
Ran/GTP 0.015 0.006 -9999 0 -10000 0 0
CSNK1G2 0.015 0 -9999 0 -10000 0 0
RAL/GTP 0.038 0.022 -9999 0 -10000 0 0
CSNK1G1 0.014 0.023 -9999 0 -0.59 1 1
FASLG 0.01 0.11 -9999 0 -0.48 10 10
SKP2 0.009 0.064 -9999 0 -0.61 7 7
USP7 0.017 0.002 -9999 0 -10000 0 0
IKBKB 0.023 0.017 -9999 0 -10000 0 0
CCNB1 0.032 0.24 -9999 0 -0.73 8 8
FOXO1-3a-4/beta catenin 0.019 0.11 -9999 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.07 -9999 0 -0.33 6 6
CSNK1A1 0.015 0 -9999 0 -10000 0 0
SGK1 0.016 0.067 -9999 0 -0.61 7 7
CSNK1G3 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.01 -9999 0 -10000 0 0
ZFAND5 0.1 0.06 -9999 0 -10000 0 0
SFN -0.12 0.25 -9999 0 -0.6 141 141
CDK2 0.002 0.092 -9999 0 -0.6 15 15
FOXO3A/14-3-3 0.031 0.089 -9999 0 -10000 0 0
CREBBP 0.015 0.027 -9999 0 -0.62 1 1
FBXO32 0.053 0.2 -9999 0 -1 5 5
BCL6 0.085 0.13 -9999 0 -10000 0 0
RALB 0.017 0.001 -9999 0 -10000 0 0
RALA 0.017 0.001 -9999 0 -10000 0 0
YWHAH 0.003 0.083 -9999 0 -0.59 13 13
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD2 0.019 0.018 -9999 0 -0.26 1 1
SMAD3 0.045 0.033 -9999 0 -10000 0 0
SMAD3/SMAD4 0.054 0.013 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.015 -9999 0 -0.38 1 1
SMAD2/SMAD2/SMAD4 -0.001 0.012 -9999 0 -10000 0 0
PPM1A 0.015 0 -9999 0 -10000 0 0
CALM1 0.015 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.026 0.015 -9999 0 -10000 0 0
MAP3K1 0.012 0.046 -9999 0 -0.59 4 4
TRAP-1/SMAD4 -0.012 0.072 -9999 0 -0.46 17 17
MAPK3 0.015 0 -9999 0 -10000 0 0
MAPK1 0.015 0 -9999 0 -10000 0 0
NUP214 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.015 0 -9999 0 -10000 0 0
CTDSP2 0.001 0.092 -9999 0 -0.59 16 16
CTDSPL 0.014 0.025 -9999 0 -0.62 1 1
KPNB1 0.015 0 -9999 0 -10000 0 0
TGFBRAP1 -0.001 0.1 -9999 0 -0.62 17 17
UBE2I 0.015 0 -9999 0 -10000 0 0
NUP153 0.015 0 -9999 0 -10000 0 0
KPNA2 0.014 0.023 -9999 0 -0.59 1 1
PIAS4 0.014 0.025 -9999 0 -0.62 1 1
mTOR signaling pathway

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0.049 -10000 0 -0.62 4 4
mol:PIP3 -0.004 0.036 -10000 0 -0.3 10 10
FRAP1 0.017 0.015 -10000 0 -10000 0 0
AKT1 0.03 0.036 -10000 0 -0.29 3 3
INSR 0.014 0.025 -10000 0 -0.62 1 1
Insulin Receptor/Insulin -0.003 0.037 -10000 0 -0.39 6 6
mol:GTP -0.004 0.031 -10000 0 -0.4 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.009 -10000 0 -10000 0 0
TSC2 0.014 0.025 -10000 0 -0.62 1 1
RHEB/GDP -0.004 0.027 -10000 0 -0.35 1 1
TSC1 0.013 0.035 -10000 0 -0.62 2 2
Insulin Receptor/IRS1 0.015 0.041 -10000 0 -0.36 8 8
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0.025 -10000 0 -0.62 1 1
RPS6KB1 0.031 0.021 -10000 0 -10000 0 0
MAP3K5 0.006 0.052 -10000 0 -0.4 11 11
PIK3R1 0.012 0.043 -10000 0 -0.62 3 3
apoptosis 0.006 0.052 -10000 0 -0.4 11 11
mol:LY294002 0 0 -10000 0 -0.002 7 7
EIF4B 0.038 0.019 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.019 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.015 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.042 -10000 0 -0.32 10 10
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.02 -10000 0 -10000 0 0
FKBP1A 0.015 0.023 -10000 0 -0.59 1 1
RHEB/GTP -0.004 0.026 -10000 0 -0.34 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 7 7
FKBP12/Rapamycin -0.001 0.017 -10000 0 -0.43 1 1
PDPK1 -0.004 0.035 -10000 0 -0.29 4 4
EIF4E 0.015 0 -10000 0 -10000 0 0
ASK1/PP5C 0.015 0.081 -10000 0 -0.61 11 11
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.004 0.033 -10000 0 -0.44 1 1
tumor necrosis factor receptor activity 0 0 0.002 7 -10000 0 7
RPS6 0.013 0.033 -10000 0 -0.59 2 2
PPP5C 0.015 0 -10000 0 -10000 0 0
EIF4G1 0.015 0 -10000 0 -10000 0 0
IRS1 0.006 0.041 -10000 0 -0.39 7 7
INS -0.004 0.053 -10000 0 -0.62 5 5
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.004 0.033 -10000 0 -0.29 3 3
EIF4EBP1 0.001 0.12 -10000 0 -1.1 7 7
PIK3CA 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.025 0.014 -10000 0 -10000 0 0
peptide biosynthetic process 0.017 0.034 -10000 0 -0.34 6 6
RHEB 0.015 0 -10000 0 -10000 0 0
EIF4A1 0.015 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.018 0.034 -10000 0 -0.34 6 6
eIF4E/4E-BP1 0.01 0.11 -10000 0 -1.1 7 7
Alternative NF-kappaB pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.003 0.03 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAP3K14 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.004 0.04 -9999 0 -0.43 6 6
RELB 0.01 0.057 -9999 0 -0.59 6 6
NFKB2 0.014 0.025 -9999 0 -0.62 1 1
NF kappa B2 p52/RelB -0.004 0.038 -9999 0 -0.37 7 7
regulation of B cell activation -0.004 0.037 -9999 0 -0.37 7 7
Sumoylation by RanBP2 regulates transcriptional repression

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0.049 -9999 0 -0.62 4 4
Ran/GTP/Exportin 1/HDAC4 0 0.01 -9999 0 -10000 0 0
MDM2/SUMO1 0.03 0.044 -9999 0 -0.28 13 13
HDAC4 0.014 0.025 -9999 0 -0.62 1 1
Ran/GTP/Exportin 1/HDAC1 -0.002 0.02 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.034 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.035 0.013 -9999 0 -0.31 1 1
SUMO1/HDAC1 0.034 0.026 -9999 0 -0.31 4 4
RANGAP1 0.015 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.007 0.046 -9999 0 -0.31 15 15
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.026 0 -9999 0 -10000 0 0
Ran/GTP 0.032 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.003 0.083 -9999 0 -0.59 13 13
UBE2I 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.015 0 -9999 0 -10000 0 0
PIAS1 0.013 0.035 -9999 0 -0.62 2 2
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.01 -9999 0 -0.26 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.008 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.001 -9999 0 -10000 0 0
CLTB 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.031 0 -9999 0 -10000 0 0
CD4 0.009 0.062 -9999 0 -0.59 7 7
CLTA 0.015 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.013 0.017 -9999 0 -0.43 1 1
mol:PI-4-5-P2 0 0.008 -9999 0 -0.2 1 1
ARF1/GTP 0 0.004 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.032 0.012 -9999 0 -0.28 1 1
mol:Choline 0 0.008 -9999 0 -0.21 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
DDEF1 0 0.008 -9999 0 -0.21 1 1
ARF1/GDP -0.001 0.012 -9999 0 -0.3 1 1
AP2M1 0.015 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.02 0 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.012 -9999 0 -0.3 1 1
ARFIP2 0 0.001 -9999 0 -10000 0 0
COPA 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.031 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.002 -9999 0 -10000 0 0
AP2A1 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.033 0.007 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.002 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.001 -9999 0 -10000 0 0
CYTH2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.001 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.041 0.019 -9999 0 -10000 0 0
PLD2 0 0.008 -9999 0 -0.21 1 1
ARF-GAP1/v-SNARE 0.013 0.017 -9999 0 -0.43 1 1
PIP5K1A 0 0.008 -9999 0 -0.2 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.006 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.008 -9999 0 -0.21 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.013 0.017 -9999 0 -0.43 1 1
GOSR2 0 0.003 -9999 0 -10000 0 0
USO1 0 0.003 -9999 0 -10000 0 0
GBF1 -0.001 0.024 -9999 0 -0.43 2 2
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.004 0.036 -9999 0 -0.36 7 7
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 669 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.065 -0.22 0.065 -0.22
47_PPARGC1A 0.015 0.015 0.015 0.015
105_BMP4 0.015 0.015 0.015 0.015
105_BMP6 0.015 0.015 0.015 0.015
105_BMP7 0.015 0.015 0.015 0.015
105_BMP2 0.015 0.015 0.015 0.015
131_RELN/VLDLR 0 0 -0.34 0
30_TGFB1/TGF beta receptor Type II 0.015 0.015 0.015 0.015
84_STAT5B 0.014 0.054 -0.12 0.13
84_STAT5A 0.014 0.054 -0.12 0.13
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBMLGG-TP/19438605/GBMLGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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