PARADIGM pathway analysis of mRNASeq expression and copy number data
Brain Lower Grade Glioma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1WM1C1Q
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1WM1C1Q
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 53 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
Ephrin A reverse signaling 78
IL23-mediated signaling events 74
FOXM1 transcription factor network 57
Signaling mediated by p38-alpha and p38-beta 54
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 54
Aurora B signaling 54
IL12-mediated signaling events 52
Thromboxane A2 receptor signaling 48
Signaling events regulated by Ret tyrosine kinase 48
TCR signaling in naïve CD8+ T cells 47
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 463 . 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 ( 463 ).

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
Ephrin A reverse signaling 0.1685 78 547 7 -0.056 0 1000 -1000 -0.009 -1000
IL23-mediated signaling events 0.1598 74 4489 60 -0.51 0.026 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 0.1231 57 2926 51 -0.28 0.026 1000 -1000 -0.096 -1000
Signaling mediated by p38-alpha and p38-beta 0.1166 54 2394 44 -0.093 0.026 1000 -1000 -0.021 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1166 54 3684 68 -0.29 0.16 1000 -1000 -0.084 -1000
Aurora B signaling 0.1166 54 3663 67 -0.27 0.045 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.1123 52 4588 87 -0.4 0.071 1000 -1000 -0.061 -1000
Thromboxane A2 receptor signaling 0.1037 48 5108 105 -0.14 0.033 1000 -1000 -0.032 -1000
Signaling events regulated by Ret tyrosine kinase 0.1037 48 3965 82 -0.076 0.026 1000 -1000 -0.044 -1000
TCR signaling in naïve CD8+ T cells 0.1015 47 4425 93 -0.18 0.21 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 0.1015 47 1231 26 -0.087 0.026 1000 -1000 -0.003 -1000
Syndecan-1-mediated signaling events 0.0972 45 1557 34 -0.073 0.026 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.0950 44 2323 52 -0.089 0.047 1000 -1000 -0.022 -1000
Endothelins 0.0950 44 4318 96 -0.13 0.026 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 0.0907 42 2819 67 -0.095 0.028 1000 -1000 -0.033 -1000
Reelin signaling pathway 0.0886 41 2318 56 -0.1 0.06 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 0.0864 40 2651 65 -0.1 0.037 1000 -1000 -0.063 -1000
TCGA08_retinoblastoma 0.0842 39 314 8 -0.023 0.042 1000 -1000 -0.001 -1000
Syndecan-3-mediated signaling events 0.0799 37 1327 35 -0.062 0.062 1000 -1000 -0.013 -1000
FOXA2 and FOXA3 transcription factor networks 0.0778 36 1685 46 -0.22 0.029 1000 -1000 -0.08 -1000
Caspase cascade in apoptosis 0.0756 35 2591 74 -0.14 0.049 1000 -1000 -0.039 -1000
IL4-mediated signaling events 0.0756 35 3246 91 -0.42 0.27 1000 -1000 -0.1 -1000
amb2 Integrin signaling 0.0756 35 2882 82 -0.15 0.028 1000 -1000 -0.025 -1000
Arf6 signaling events 0.0734 34 2167 62 -0.14 0.053 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.0734 34 4261 125 -0.07 0.062 1000 -1000 -0.049 -1000
BCR signaling pathway 0.0734 34 3403 99 -0.1 0.042 1000 -1000 -0.049 -1000
HIF-1-alpha transcription factor network 0.0713 33 2559 76 -0.1 0.061 1000 -1000 -0.046 -1000
E-cadherin signaling events 0.0713 33 166 5 -0.044 0.025 1000 -1000 0.005 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0691 32 2752 85 -0.16 0.04 1000 -1000 -0.03 -1000
Nongenotropic Androgen signaling 0.0670 31 1637 52 -0.072 0.036 1000 -1000 -0.021 -1000
LPA receptor mediated events 0.0670 31 3241 102 -0.11 0.028 1000 -1000 -0.067 -1000
Visual signal transduction: Rods 0.0670 31 1656 52 -0.1 0.026 1000 -1000 -0.017 -1000
Osteopontin-mediated events 0.0648 30 1154 38 -0.05 0.026 1000 -1000 -0.023 -1000
Ras signaling in the CD4+ TCR pathway 0.0648 30 515 17 -0.052 0.034 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 0.0626 29 1276 44 -0.098 0.033 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0626 29 1813 62 -0.075 0.047 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0605 28 2122 74 -0.064 0.058 1000 -1000 -0.057 -1000
EGFR-dependent Endothelin signaling events 0.0605 28 589 21 -0.032 0.037 1000 -1000 -0.031 -1000
Aurora C signaling 0.0583 27 193 7 -0.078 0.012 1000 -1000 -0.012 -1000
Glucocorticoid receptor regulatory network 0.0583 27 3141 114 -0.28 0.15 1000 -1000 -0.038 -1000
Ceramide signaling pathway 0.0583 27 2056 76 -0.07 0.045 1000 -1000 -0.026 -1000
Glypican 2 network 0.0583 27 110 4 -0.004 0.002 1000 -1000 0.006 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0562 26 1424 54 -0.067 0.034 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 0.0562 26 2527 97 -0.058 0.041 1000 -1000 -0.057 -1000
PLK1 signaling events 0.0562 26 2285 85 -0.082 0.039 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 0.0540 25 979 38 -0.054 0.033 1000 -1000 -0.01 -1000
a4b1 and a4b7 Integrin signaling 0.0540 25 126 5 -0.01 0.011 1000 -1000 0.005 -1000
Glypican 1 network 0.0540 25 1239 48 -0.079 0.049 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0540 25 1334 52 -0.16 0.066 1000 -1000 -0.042 -1000
Noncanonical Wnt signaling pathway 0.0518 24 635 26 -0.049 0.026 1000 -1000 -0.031 -1000
S1P5 pathway 0.0518 24 409 17 -0.054 0.025 1000 -1000 -0.009 -1000
Ephrin B reverse signaling 0.0518 24 1172 48 -0.032 0.026 1000 -1000 -0.023 -1000
Calcium signaling in the CD4+ TCR pathway 0.0518 24 764 31 -0.09 0.026 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0497 23 398 17 -0.024 0.026 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 0.0497 23 1368 58 -0.083 0.05 1000 -1000 -0.034 -1000
IL6-mediated signaling events 0.0497 23 1750 75 -0.1 0.04 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0497 23 2071 88 -0.085 0.028 1000 -1000 -0.05 -1000
BMP receptor signaling 0.0475 22 1855 81 -0.076 0.044 1000 -1000 -0.034 -1000
TCGA08_rtk_signaling 0.0475 22 574 26 -0.047 0.061 1000 -1000 -0.004 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0454 21 795 37 -0.04 0.045 1000 -1000 -0.022 -1000
FAS signaling pathway (CD95) 0.0454 21 1005 47 -0.12 0.039 1000 -1000 -0.053 -1000
Rapid glucocorticoid signaling 0.0454 21 439 20 -0.076 0.027 1000 -1000 -0.002 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0454 21 2563 120 -0.12 0.074 1000 -1000 -0.037 -1000
Regulation of nuclear SMAD2/3 signaling 0.0432 20 2782 136 -0.19 0.16 1000 -1000 -0.04 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0432 20 706 34 -0.016 0.042 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.0432 20 1061 51 -0.13 0.065 1000 -1000 -0.038 -1000
E-cadherin signaling in the nascent adherens junction 0.0432 20 1593 76 -0.044 0.048 1000 -1000 -0.049 -1000
IL2 signaling events mediated by PI3K 0.0410 19 1123 58 -0.067 0.041 1000 -1000 -0.03 -1000
EPHB forward signaling 0.0410 19 1634 85 -0.031 0.055 1000 -1000 -0.051 -1000
E-cadherin signaling in keratinocytes 0.0410 19 828 43 -0.043 0.027 1000 -1000 -0.028 -1000
Presenilin action in Notch and Wnt signaling 0.0389 18 1121 61 -0.13 0.062 1000 -1000 -0.035 -1000
EPO signaling pathway 0.0389 18 999 55 -0.032 0.07 1000 -1000 -0.024 -1000
TCGA08_p53 0.0389 18 128 7 -0.019 0.025 1000 -1000 -0.008 -1000
IL2 signaling events mediated by STAT5 0.0389 18 415 22 -0.029 0.027 1000 -1000 -0.028 -1000
Coregulation of Androgen receptor activity 0.0367 17 1316 76 -0.084 0.05 1000 -1000 -0.022 -1000
Cellular roles of Anthrax toxin 0.0367 17 680 39 -0.14 0.029 1000 -1000 -0.026 -1000
Signaling events mediated by PTP1B 0.0367 17 1337 76 -0.081 0.039 1000 -1000 -0.044 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0367 17 1372 78 -0.017 0.036 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 0.0346 16 1104 69 -0.062 0.04 1000 -1000 -0.031 -1000
IL27-mediated signaling events 0.0346 16 822 51 -0.082 0.027 1000 -1000 -0.044 -1000
Plasma membrane estrogen receptor signaling 0.0346 16 1389 86 -0.042 0.038 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class III 0.0324 15 636 40 -0.063 0.05 1000 -1000 -0.022 -1000
S1P1 pathway 0.0324 15 551 36 -0.089 0.025 1000 -1000 -0.036 -1000
LPA4-mediated signaling events 0.0302 14 168 12 -0.031 0.004 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0302 14 707 49 -0.061 0.037 1000 -1000 -0.033 -1000
Integrins in angiogenesis 0.0302 14 1181 84 -0.023 0.056 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 0.0302 14 786 54 -0.052 0.055 1000 -1000 -0.046 -1000
Wnt signaling 0.0302 14 104 7 -0.01 0.009 1000 -1000 -0.013 -1000
S1P4 pathway 0.0302 14 369 25 -0.054 0.044 1000 -1000 -0.021 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0281 13 376 28 -0.054 0.032 1000 -1000 -0.014 -1000
Class I PI3K signaling events 0.0281 13 1004 73 -0.075 0.048 1000 -1000 -0.036 -1000
Signaling events mediated by PRL 0.0281 13 442 34 -0.057 0.033 1000 -1000 -0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0259 12 1035 83 -0.09 0.051 1000 -1000 -0.028 -1000
Paxillin-dependent events mediated by a4b1 0.0259 12 450 36 -0.037 0.047 1000 -1000 -0.026 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0259 12 551 45 -0.061 0.06 1000 -1000 -0.038 -1000
ErbB4 signaling events 0.0238 11 802 69 -0.069 0.044 1000 -1000 -0.029 -1000
BARD1 signaling events 0.0238 11 643 57 -0.043 0.052 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 0.0238 11 360 32 -0.038 0.051 1000 -1000 -0.028 -1000
Regulation of Telomerase 0.0238 11 1168 102 -0.12 0.064 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 0.0238 11 835 70 -0.067 0.036 1000 -1000 -0.037 -1000
TRAIL signaling pathway 0.0216 10 492 48 -0.001 0.061 1000 -1000 -0.027 -1000
Signaling mediated by p38-gamma and p38-delta 0.0216 10 157 15 -0.017 0.026 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 0.0216 10 327 31 -0.022 0.038 1000 -1000 -0.015 -1000
Nectin adhesion pathway 0.0194 9 627 63 -0.044 0.066 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0194 9 968 97 -0.073 0.071 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 0.0173 8 365 43 -0.06 0.062 1000 -1000 -0.045 -1000
Insulin Pathway 0.0173 8 654 74 -0.07 0.063 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0173 8 268 33 -0.032 0.066 1000 -1000 -0.027 -1000
Aurora A signaling 0.0151 7 433 60 -0.059 0.059 1000 -1000 -0.016 -1000
IFN-gamma pathway 0.0151 7 498 68 -0.097 0.055 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class I 0.0151 7 813 104 -0.061 0.058 1000 -1000 -0.028 -1000
S1P3 pathway 0.0151 7 299 42 0 0.039 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0130 6 393 65 -0.004 0.058 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 0.0130 6 444 68 -0.033 0.048 1000 -1000 -0.03 -1000
IGF1 pathway 0.0130 6 387 57 -0.015 0.064 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 0.0130 6 297 44 -0.018 0.042 1000 -1000 -0.02 -1000
Canonical NF-kappaB pathway 0.0108 5 224 39 -0.061 0.059 1000 -1000 -0.028 -1000
Arf6 downstream pathway 0.0108 5 215 43 -0.043 0.05 1000 -1000 -0.02 -1000
FoxO family signaling 0.0108 5 380 64 -0.03 0.082 1000 -1000 -0.047 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0108 5 641 125 -0.018 0.068 1000 -1000 -0.032 -1000
VEGFR1 specific signals 0.0108 5 292 56 -0.037 0.055 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 0.0108 5 15 3 -0.019 0.019 1000 -1000 -0.007 -1000
PLK2 and PLK4 events 0.0086 4 13 3 0.001 0.016 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0086 4 98 22 -0.007 0.039 1000 -1000 -0.033 -1000
mTOR signaling pathway 0.0086 4 250 53 -0.017 0.04 1000 -1000 -0.035 -1000
Arf6 trafficking events 0.0086 4 337 71 -0.051 0.049 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0065 3 295 75 -0.09 0.071 1000 -1000 -0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0022 1 34 23 -0.001 0.049 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0.0022 1 17 13 0 0.059 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 14 27 0 0.061 1000 -1000 -0.026 -1000
Arf1 pathway 0.0000 0 48 54 -0.001 0.039 1000 -1000 -0.015 -1000
Total NA 2899 168447 7203 -11 6.3 131000 -131000 -4.2 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.047 0.14 -10000 0 -0.28 106 106
EFNA5 -0.026 0.13 -10000 0 -0.29 75 75
FYN -0.051 0.12 0.18 5 -0.29 84 89
neuron projection morphogenesis -0.047 0.14 -10000 0 -0.28 106 106
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.047 0.14 -10000 0 -0.28 106 106
EPHA5 -0.056 0.16 -10000 0 -0.43 65 65
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 -0.44 0.55 -9999 0 -1.2 117 117
IL23A -0.45 0.55 -9999 0 -1.3 105 105
NF kappa B1 p50/RelA/I kappa B alpha -0.4 0.55 -9999 0 -1.2 112 112
positive regulation of T cell mediated cytotoxicity -0.47 0.61 -9999 0 -1.4 116 116
ITGA3 -0.41 0.51 -9999 0 -1.2 106 106
IL17F -0.27 0.32 -9999 0 -0.73 112 112
IL12B -0.02 0.044 -9999 0 -0.17 2 2
STAT1 (dimer) -0.44 0.58 -9999 0 -1.3 116 116
CD4 -0.39 0.5 -9999 0 -1.2 108 108
IL23 -0.43 0.53 -9999 0 -1.3 107 107
IL23R -0.2 0.38 -9999 0 -0.98 76 76
IL1B -0.48 0.6 -9999 0 -1.4 116 116
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.4 0.5 -9999 0 -1.2 104 104
TYK2 -0.008 0.035 -9999 0 -10000 0 0
STAT4 -0.063 0.16 -9999 0 -0.26 145 145
STAT3 0.026 0.003 -9999 0 -10000 0 0
IL18RAP -0.026 0.13 -9999 0 -0.28 77 77
IL12RB1 -0.031 0.099 -9999 0 -0.38 27 27
PIK3CA 0.026 0.004 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.023 0.08 -9999 0 -0.33 20 20
IL23R/JAK2 -0.19 0.36 -9999 0 -1.1 57 57
positive regulation of chronic inflammatory response -0.47 0.61 -9999 0 -1.4 116 116
natural killer cell activation 0.005 0.007 -9999 0 -10000 0 0
JAK2 -0.009 0.042 -9999 0 -10000 0 0
PIK3R1 0.026 0.003 -9999 0 -10000 0 0
NFKB1 0.023 0.006 -9999 0 -10000 0 0
RELA 0.023 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.41 0.5 -9999 0 -1.2 108 108
ALOX12B -0.46 0.56 -9999 0 -1.2 140 140
CXCL1 -0.44 0.55 -9999 0 -1.2 125 125
T cell proliferation -0.47 0.61 -9999 0 -1.4 116 116
NFKBIA 0.023 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.25 -9999 0 -0.56 103 103
PI3K -0.42 0.56 -9999 0 -1.3 112 112
IFNG -0.019 0.031 -9999 0 -0.11 18 18
STAT3 (dimer) -0.39 0.52 -9999 0 -1.2 112 112
IL18R1 -0.009 0.11 -9999 0 -0.27 55 55
IL23/IL23R/JAK2/TYK2/SOCS3 -0.27 0.37 -9999 0 -0.84 88 88
IL18/IL18R -0.005 0.13 -9999 0 -0.3 69 69
macrophage activation -0.02 0.02 -9999 0 -0.045 95 95
TNF -0.47 0.6 -9999 0 -1.4 112 112
STAT3/STAT4 -0.44 0.56 -9999 0 -1.2 126 126
STAT4 (dimer) -0.47 0.59 -9999 0 -1.3 126 126
IL18 0.002 0.092 -9999 0 -0.43 18 18
IL19 -0.4 0.5 -9999 0 -1.2 103 103
STAT5A (dimer) -0.44 0.58 -9999 0 -1.3 117 117
STAT1 0.021 0.027 -9999 0 -10000 0 0
SOCS3 -0.032 0.12 -9999 0 -0.43 31 31
CXCL9 -0.48 0.57 -9999 0 -1.2 137 137
MPO -0.47 0.57 -9999 0 -1.3 136 136
positive regulation of humoral immune response -0.47 0.61 -9999 0 -1.4 116 116
IL23/IL23R/JAK2/TYK2 -0.51 0.71 -9999 0 -1.5 115 115
IL6 -0.42 0.56 -9999 0 -1.3 109 109
STAT5A 0.016 0.067 -9999 0 -0.4 11 11
IL2 0.01 0.019 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.007 -9999 0 -10000 0 0
CD3E -0.44 0.56 -9999 0 -1.3 123 123
keratinocyte proliferation -0.47 0.61 -9999 0 -1.4 116 116
NOS2 -0.42 0.52 -9999 0 -1.2 113 113
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 -0.18 0.5 -9999 0 -1.2 73 73
PLK1 0.01 0.14 -9999 0 -1.4 4 4
BIRC5 -0.19 0.52 -9999 0 -1.4 69 69
HSPA1B -0.2 0.51 -9999 0 -1.2 78 78
MAP2K1 0.011 0.046 -9999 0 -0.17 1 1
BRCA2 -0.2 0.52 -9999 0 -1.2 80 80
FOXM1 -0.28 0.73 -9999 0 -1.7 79 79
XRCC1 -0.18 0.5 -9999 0 -1.2 73 73
FOXM1B/p19 -0.2 0.51 -9999 0 -1.2 75 75
Cyclin D1/CDK4 -0.18 0.46 -9999 0 -1.1 76 76
CDC2 -0.2 0.53 -9999 0 -1.2 80 80
TGFA -0.17 0.45 -9999 0 -1 82 82
SKP2 -0.19 0.51 -9999 0 -1.2 77 77
CCNE1 0.016 0.022 -9999 0 -0.13 2 2
CKS1B -0.18 0.5 -9999 0 -1.2 73 73
RB1 -0.11 0.33 -9999 0 -0.9 50 50
FOXM1C/SP1 -0.23 0.6 -9999 0 -1.4 81 81
AURKB -0.25 0.57 -9999 0 -1.4 87 87
CENPF -0.2 0.54 -9999 0 -1.3 73 73
CDK4 0.014 0.026 -9999 0 -10000 0 0
MYC -0.17 0.44 -9999 0 -1 81 81
CHEK2 0.005 0.063 -9999 0 -0.26 9 9
ONECUT1 -0.18 0.49 -9999 0 -1.1 77 77
CDKN2A -0.014 0.11 -9999 0 -0.43 30 30
LAMA4 -0.19 0.5 -9999 0 -1.2 75 75
FOXM1B/HNF6 -0.24 0.61 -9999 0 -1.4 77 77
FOS -0.26 0.57 -9999 0 -1.2 114 114
SP1 0.025 0.009 -9999 0 -10000 0 0
CDC25B -0.18 0.5 -9999 0 -1.2 73 73
response to radiation 0 0.026 -9999 0 -10000 0 0
CENPB -0.18 0.5 -9999 0 -1.2 74 74
CENPA -0.21 0.55 -9999 0 -1.3 77 77
NEK2 -0.23 0.57 -9999 0 -1.3 85 85
HIST1H2BA -0.19 0.5 -9999 0 -1.2 73 73
CCNA2 -0.013 0.11 -9999 0 -0.25 58 58
EP300 0.022 0.043 -9999 0 -0.43 4 4
CCNB1/CDK1 -0.23 0.61 -9999 0 -1.5 73 73
CCNB2 -0.23 0.58 -9999 0 -1.4 80 80
CCNB1 -0.2 0.53 -9999 0 -1.3 74 74
ETV5 -0.2 0.51 -9999 0 -1.2 78 78
ESR1 -0.2 0.52 -9999 0 -1.2 83 83
CCND1 -0.18 0.47 -9999 0 -1.1 78 78
GSK3A 0.013 0.038 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.013 0.094 -9999 0 -0.29 27 27
CDK2 0.013 0.051 -9999 0 -0.34 6 6
G2/M transition of mitotic cell cycle -0.002 0.031 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.2 0.56 -9999 0 -1.3 79 79
GAS1 -0.18 0.5 -9999 0 -1.2 73 73
MMP2 -0.19 0.51 -9999 0 -1.2 74 74
RB1/FOXM1C -0.2 0.5 -9999 0 -1.1 81 81
CREBBP 0.026 0.002 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.093 0.32 -10000 0 -0.99 50 50
MKNK1 0.022 0.01 -10000 0 -10000 0 0
MAPK14 -0.013 0.12 -10000 0 -0.29 64 64
ATF2/c-Jun -0.016 0.095 -10000 0 -0.41 9 9
MAPK11 -0.017 0.12 -10000 0 -0.3 67 67
MITF -0.02 0.13 -10000 0 -0.33 66 66
MAPKAPK5 -0.021 0.13 -10000 0 -0.34 67 67
KRT8 -0.056 0.18 -10000 0 -0.37 97 97
MAPKAPK3 0.024 0.022 -10000 0 -0.43 1 1
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.024 0.17 -10000 0 -0.42 67 67
CEBPB -0.029 0.15 -10000 0 -0.38 64 64
SLC9A1 -0.034 0.15 -10000 0 -0.39 65 65
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.016 0.14 -10000 0 -0.33 66 66
p38alpha-beta/MNK1 -0.006 0.14 -10000 0 -0.34 65 65
JUN -0.014 0.092 -10000 0 -0.41 9 9
PPARGC1A -0.035 0.17 -10000 0 -0.39 74 74
USF1 -0.019 0.13 -10000 0 -0.34 65 65
RAB5/GDP/GDI1 -0.008 0.1 -10000 0 -0.25 66 66
NOS2 -0.049 0.23 -10000 0 -0.92 22 22
DDIT3 -0.021 0.13 -10000 0 -0.34 67 67
RAB5A 0.025 0.004 -10000 0 -10000 0 0
HSPB1 0.015 0.15 0.28 65 -0.28 60 125
p38alpha-beta/HBP1 -0.002 0.13 -10000 0 -0.34 56 56
CREB1 -0.023 0.14 -10000 0 -0.36 64 64
RAB5/GDP 0.019 0.003 -10000 0 -10000 0 0
EIF4E -0.028 0.12 0.24 4 -0.3 63 67
RPS6KA4 -0.019 0.13 -10000 0 -0.34 64 64
PLA2G4A -0.036 0.13 0.2 1 -0.33 64 65
GDI1 -0.02 0.13 -10000 0 -0.34 67 67
TP53 -0.046 0.16 -10000 0 -0.43 66 66
RPS6KA5 -0.026 0.14 -10000 0 -0.34 72 72
ESR1 -0.03 0.15 -10000 0 -0.35 73 73
HBP1 0.02 0.011 -10000 0 -10000 0 0
MEF2C -0.023 0.14 -10000 0 -0.35 66 66
MEF2A -0.022 0.14 -10000 0 -0.36 66 66
EIF4EBP1 -0.028 0.14 -10000 0 -0.36 65 65
KRT19 -0.054 0.17 -10000 0 -0.35 100 100
ELK4 -0.02 0.13 -10000 0 -0.34 65 65
ATF6 -0.019 0.13 -10000 0 -0.34 65 65
ATF1 -0.026 0.15 -10000 0 -0.37 66 66
p38alpha-beta/MAPKAPK2 0.005 0.14 -10000 0 -0.34 65 65
p38alpha-beta/MAPKAPK3 0.003 0.15 -10000 0 -0.34 66 66
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.003 0.076 -10000 0 -0.24 31 31
NFATC2 -0.082 0.23 -10000 0 -0.57 53 53
NFATC3 -0.033 0.11 -10000 0 -0.27 55 55
CD40LG -0.23 0.38 -10000 0 -0.92 90 90
ITCH -0.024 0.091 -10000 0 -0.22 79 79
CBLB -0.023 0.094 -10000 0 -0.41 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.35 -10000 0 -0.82 79 79
JUNB 0.005 0.075 -10000 0 -0.2 40 40
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.027 0.11 -10000 0 -0.26 80 80
T cell anergy -0.066 0.16 0.26 1 -0.39 80 81
TLE4 -0.059 0.17 -10000 0 -0.52 36 36
Jun/NFAT1-c-4/p21SNFT -0.18 0.42 -10000 0 -0.96 88 88
AP-1/NFAT1-c-4 -0.23 0.47 -10000 0 -1.1 90 90
IKZF1 -0.063 0.18 -10000 0 -0.56 38 38
T-helper 2 cell differentiation -0.14 0.28 -10000 0 -0.84 38 38
AP-1/NFAT1 -0.063 0.18 -10000 0 -0.42 64 64
CALM1 -0.01 0.072 -10000 0 -0.19 1 1
EGR2 -0.21 0.48 -10000 0 -1.3 61 61
EGR3 -0.25 0.53 -10000 0 -1.3 79 79
NFAT1/FOXP3 -0.053 0.19 -10000 0 -0.46 51 51
EGR1 -0.039 0.13 -10000 0 -0.32 65 65
JUN 0.009 0.03 -10000 0 -0.14 4 4
EGR4 -0.092 0.17 -10000 0 -0.4 95 95
mol:Ca2+ -0.025 0.061 -10000 0 -0.15 80 80
GBP3 -0.085 0.23 0.27 1 -0.6 66 67
FOSL1 -0.028 0.13 -10000 0 -0.43 36 36
NFAT1-c-4/MAF/IRF4 -0.18 0.41 -10000 0 -0.94 89 89
DGKA -0.056 0.16 -10000 0 -0.46 38 38
CREM 0.023 0.023 -10000 0 -0.43 1 1
NFAT1-c-4/PPARG -0.18 0.41 -10000 0 -0.96 89 89
CTLA4 -0.078 0.19 -10000 0 -0.5 58 58
NFAT1-c-4 (dimer)/EGR1 -0.21 0.45 -10000 0 -1 90 90
NFAT1-c-4 (dimer)/EGR4 -0.23 0.44 -10000 0 -1 91 91
FOS -0.041 0.14 -10000 0 -0.3 79 79
IFNG -0.1 0.2 -10000 0 -0.65 31 31
T cell activation -0.11 0.22 -10000 0 -0.65 37 37
MAF 0.023 0.037 -10000 0 -0.43 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.36 0.81 89 -10000 0 89
TNF -0.29 0.42 -10000 0 -0.97 108 108
FASLG -0.24 0.52 -10000 0 -1.2 84 84
TBX21 -0.005 0.1 -10000 0 -0.3 39 39
BATF3 0 0.093 -10000 0 -0.26 42 42
PRKCQ 0.013 0.067 -10000 0 -0.38 12 12
PTPN1 -0.056 0.16 -10000 0 -0.46 38 38
NFAT1-c-4/ICER1 -0.18 0.41 -10000 0 -0.95 88 88
GATA3 -0.035 0.13 -10000 0 -0.27 88 88
T-helper 1 cell differentiation -0.099 0.2 -10000 0 -0.63 32 32
IL2RA -0.17 0.31 -10000 0 -0.77 67 67
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 0.16 -10000 0 -0.45 38 38
E2F1 0.017 0.056 -10000 0 -0.35 7 7
PPARG 0.009 0.08 -10000 0 -0.34 20 20
SLC3A2 -0.054 0.16 -10000 0 -0.49 30 30
IRF4 -0.009 0.11 -10000 0 -0.28 51 51
PTGS2 -0.24 0.41 -10000 0 -0.98 93 93
CSF2 -0.23 0.38 -10000 0 -0.93 90 90
JunB/Fra1/NFAT1-c-4 -0.19 0.41 -10000 0 -0.94 88 88
IL4 -0.14 0.29 -10000 0 -0.89 37 37
IL5 -0.22 0.38 -10000 0 -0.92 90 90
IL2 -0.11 0.22 -10000 0 -0.66 36 36
IL3 -0.023 0.078 -10000 0 -0.64 3 3
RNF128 -0.085 0.21 -10000 0 -0.52 80 80
NFATC1 -0.16 0.36 -10000 0 -0.82 89 89
CDK4 0.1 0.2 0.61 29 -10000 0 29
PTPRK -0.055 0.16 -10000 0 -0.5 30 30
IL8 -0.25 0.41 -10000 0 -0.96 97 97
POU2F1 0.026 0.004 -10000 0 -10000 0 0
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 -0.075 0.2 0.16 1 -0.42 95 96
STMN1 -0.052 0.12 0.19 2 -0.32 75 77
Aurora B/RasGAP/Survivin -0.06 0.19 -10000 0 -0.41 96 96
Chromosomal passenger complex/Cul3 protein complex -0.072 0.15 -10000 0 -0.35 85 85
BIRC5 -0.065 0.17 -10000 0 -0.46 68 68
DES -0.27 0.47 -10000 0 -0.89 151 151
Aurora C/Aurora B/INCENP -0.015 0.11 -10000 0 -0.24 86 86
Aurora B/TACC1 -0.03 0.11 -10000 0 -0.26 84 84
Aurora B/PP2A -0.039 0.14 -10000 0 -0.31 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.021 0.061 -10000 0 -0.15 87 87
mitotic metaphase/anaphase transition 0.001 0.006 -10000 0 -10000 0 0
NDC80 -0.1 0.2 0.2 5 -0.36 134 139
Cul3 protein complex 0.045 0.029 -10000 0 -0.26 2 2
KIF2C -0.1 0.26 -10000 0 -0.51 95 95
PEBP1 0.015 0.036 -10000 0 -0.45 2 2
KIF20A -0.083 0.18 -10000 0 -0.31 146 146
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.04 0.14 -10000 0 -0.31 85 85
SEPT1 0.024 0.026 -10000 0 -0.19 5 5
SMC2 0.025 0.004 -10000 0 -10000 0 0
SMC4 0.017 0.035 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.13 0.31 -10000 0 -0.76 87 87
PSMA3 0.025 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.047 0.12 -10000 0 -0.3 85 85
AURKB -0.08 0.18 -10000 0 -0.45 85 85
AURKC 0.012 0.047 -10000 0 -0.17 22 22
CDCA8 -0.008 0.073 -10000 0 -0.46 7 7
cytokinesis -0.17 0.34 0.25 1 -0.77 99 100
Aurora B/Septin1 -0.14 0.33 0.26 2 -0.73 98 100
AURKA 0.018 0.037 -10000 0 -0.44 1 1
INCENP 0.015 0.022 -10000 0 -10000 0 0
KLHL13 0.024 0.03 -10000 0 -0.43 2 2
BUB1 -0.045 0.15 -10000 0 -0.42 57 57
hSgo1/Aurora B/Survivin -0.086 0.23 -10000 0 -0.37 149 149
EVI5 0.021 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.12 0.3 -10000 0 -0.66 94 94
SGOL1 -0.049 0.15 -10000 0 -0.28 111 111
CENPA -0.11 0.26 0.22 1 -0.56 99 100
NCAPG -0.062 0.16 -10000 0 -0.43 70 70
Aurora B/HC8 Proteasome -0.039 0.14 -10000 0 -0.31 85 85
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.04 0.14 -10000 0 -0.31 85 85
RHOA 0.025 0.004 -10000 0 -10000 0 0
NCAPH -0.015 0.12 -10000 0 -0.27 65 65
NPM1 -0.089 0.21 -10000 0 -0.52 87 87
RASA1 0.026 0.003 -10000 0 -10000 0 0
KLHL9 0.023 0.008 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.14 -10000 0 -0.31 85 85
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin -0.14 0.32 0.2 1 -0.7 99 100
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.089 0.21 -10000 0 -0.52 87 87
MYLK -0.051 0.12 -10000 0 -0.3 91 91
KIF23 -0.044 0.14 -10000 0 -0.27 100 100
VIM -0.083 0.14 0.18 3 -0.31 122 125
RACGAP1 0.017 0.023 -10000 0 -0.13 5 5
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.092 0.22 -10000 0 -0.53 87 87
Chromosomal passenger complex -0.14 0.3 0.19 1 -0.67 98 99
Chromosomal passenger complex/EVI5 -0.047 0.2 -10000 0 -0.37 104 104
TACC1 0.025 0.005 -10000 0 -10000 0 0
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
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 -0.072 0.13 -10000 0 -0.36 53 53
TBX21 -0.34 0.46 -10000 0 -1 117 117
B2M 0.024 0.017 -10000 0 -10000 0 0
TYK2 -0.003 0.034 -10000 0 -10000 0 0
IL12RB1 -0.026 0.1 -10000 0 -0.44 21 21
GADD45B -0.24 0.35 -10000 0 -0.84 77 77
IL12RB2 -0.049 0.12 -10000 0 -0.24 95 95
GADD45G -0.26 0.38 -10000 0 -0.83 105 105
natural killer cell activation -0.012 0.02 -10000 0 -10000 0 0
RELB 0.02 0.026 -10000 0 -0.2 4 4
RELA 0.025 0.005 -10000 0 -10000 0 0
IL18 -0.005 0.094 -10000 0 -0.44 18 18
IL2RA -0.015 0.077 -10000 0 -0.18 60 60
IFNG -0.007 0.021 -10000 0 -0.13 4 4
STAT3 (dimer) -0.24 0.33 -10000 0 -0.72 121 121
HLA-DRB5 -0.051 0.15 -10000 0 -0.43 55 55
FASLG -0.3 0.42 -10000 0 -0.98 100 100
NF kappa B2 p52/RelB -0.3 0.43 -10000 0 -0.88 127 127
CD4 0.017 0.036 -10000 0 -0.23 6 6
SOCS1 0.007 0.07 -10000 0 -0.43 8 8
EntrezGene:6955 -0.001 0.008 -10000 0 -10000 0 0
CD3D -0.036 0.12 -10000 0 -0.43 33 33
CD3E -0.054 0.15 -10000 0 -0.41 57 57
CD3G 0.006 0.041 -10000 0 -0.13 22 22
IL12Rbeta2/JAK2 -0.028 0.097 -10000 0 -0.27 43 43
CCL3 -0.39 0.55 -10000 0 -1.2 116 116
CCL4 -0.4 0.56 -10000 0 -1.3 112 112
HLA-A 0.023 0.021 -10000 0 -10000 0 0
IL18/IL18R -0.023 0.14 -10000 0 -0.31 70 70
NOS2 -0.29 0.41 -10000 0 -0.94 100 100
IL12/IL12R/TYK2/JAK2/SPHK2 -0.064 0.13 -10000 0 -0.36 49 49
IL1R1 -0.32 0.45 0.48 1 -0.99 115 116
IL4 0.017 0.034 -10000 0 -10000 0 0
JAK2 -0.003 0.035 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.052 0.14 -10000 0 -0.49 28 28
RAB7A -0.2 0.3 0.52 1 -0.74 58 59
lysosomal transport -0.19 0.28 0.51 1 -0.69 61 62
FOS -0.25 0.45 -10000 0 -1.1 84 84
STAT4 (dimer) -0.29 0.38 0.5 1 -0.78 133 134
STAT5A (dimer) -0.3 0.43 -10000 0 -0.88 134 134
GZMA -0.37 0.5 -10000 0 -1.1 131 131
GZMB -0.36 0.5 -10000 0 -1.1 131 131
HLX 0.018 0.048 -10000 0 -0.43 4 4
LCK -0.34 0.47 -10000 0 -0.94 140 140
TCR/CD3/MHC II/CD4 -0.074 0.17 -10000 0 -0.44 64 64
IL2/IL2R -0.002 0.11 -10000 0 -0.24 70 70
MAPK14 -0.24 0.36 -10000 0 -0.78 102 102
CCR5 -0.28 0.42 -10000 0 -0.97 92 92
IL1B -0.095 0.16 -10000 0 -0.43 77 77
STAT6 -0.072 0.11 -10000 0 -0.44 4 4
STAT4 -0.063 0.16 -10000 0 -0.26 145 145
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.027 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.031 -10000 0 -0.43 2 2
IL12B -0.011 0.037 -10000 0 -0.16 1 1
CD8A -0.025 0.13 -10000 0 -0.43 39 39
CD8B -0.004 0.11 -10000 0 -0.33 39 39
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.071 0.13 0.35 53 -10000 0 53
IL2RB -0.029 0.13 -10000 0 -0.43 37 37
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.34 0.49 1 -0.71 132 133
IL2RG 0 0.088 -10000 0 -0.22 48 48
IL12 -0.018 0.083 -10000 0 -0.34 19 19
STAT5A 0.016 0.067 -10000 0 -0.4 11 11
CD247 0.008 0.065 -10000 0 -0.43 7 7
IL2 -0.014 0.009 -10000 0 -10000 0 0
SPHK2 0.021 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.022 0.097 -10000 0 -0.43 21 21
IL12/IL12R/TYK2/JAK2 -0.36 0.51 -10000 0 -1 133 133
MAP2K3 -0.24 0.36 -10000 0 -0.75 115 115
RIPK2 0.024 0.007 -10000 0 -10000 0 0
MAP2K6 -0.24 0.36 -10000 0 -0.78 106 106
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.034 0.13 -10000 0 -0.43 40 40
IL18RAP -0.034 0.13 -10000 0 -0.29 77 77
IL12Rbeta1/TYK2 -0.016 0.084 -10000 0 -0.34 20 20
EOMES 0.015 0.13 -10000 0 -0.98 6 6
STAT1 (dimer) -0.24 0.33 -10000 0 -0.72 114 114
T cell proliferation -0.2 0.27 0.49 1 -0.56 130 131
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.016 0.11 -10000 0 -0.28 55 55
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.23 0.3 -10000 0 -0.63 129 129
ATF2 -0.22 0.33 0.51 1 -0.73 101 102
Thromboxane A2 receptor signaling

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
TGM2 0.023 0.015 -10000 0 -0.13 4 4
GNB1/GNG2 -0.056 0.079 -10000 0 -0.18 116 116
AKT1 -0.032 0.12 0.28 9 -0.23 53 62
EGF -0.007 0.11 -10000 0 -0.43 26 26
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.076 0.33 17 -0.22 2 19
mol:Ca2+ -0.052 0.16 0.33 7 -0.29 117 124
LYN 0.009 0.083 0.32 18 -0.25 4 22
RhoA/GTP -0.026 0.063 -10000 0 -0.13 104 104
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.069 0.18 0.31 10 -0.35 119 129
GNG2 0.022 0.042 -10000 0 -0.43 4 4
ARRB2 0.026 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.004 0.1 -10000 0 -0.41 20 20
G beta5/gamma2 -0.069 0.1 -10000 0 -0.24 115 115
PRKCH -0.066 0.18 0.33 7 -0.34 115 122
DNM1 -0.031 0.12 -10000 0 -0.23 103 103
TXA2/TP beta/beta Arrestin3 -0.008 0.047 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.003 0.064 -10000 0 -0.16 50 50
G12 family/GTP -0.069 0.14 -10000 0 -0.3 109 109
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
ADRBK2 0.023 0.031 -10000 0 -0.33 3 3
RhoA/GTP/ROCK1 0.033 0.008 -10000 0 -10000 0 0
mol:GDP 0.024 0.11 0.29 20 -0.31 9 29
mol:NADP 0.016 0.036 -10000 0 -0.43 2 2
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.01 0.12 -10000 0 -0.43 33 33
mol:IP3 -0.07 0.19 0.35 7 -0.37 117 124
cell morphogenesis 0.033 0.008 -10000 0 -10000 0 0
PLCB2 -0.1 0.25 0.39 6 -0.5 117 123
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.01 0.086 0.31 14 -0.2 15 29
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.071 0.3 8 -0.25 9 17
RHOA 0.025 0.004 -10000 0 -10000 0 0
PTGIR 0.012 0.05 -10000 0 -0.19 19 19
PRKCB1 -0.072 0.19 0.33 6 -0.36 120 126
GNAQ 0.025 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0.036 -10000 0 -0.43 2 2
TXA2/TXA2-R family -0.11 0.26 0.4 5 -0.52 119 124
LCK -0.002 0.088 0.34 16 -0.2 11 27
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.047 -10000 0 -0.2 9 9
TXA2-R family/G12 family/GDP/G beta/gamma -0.047 0.17 -10000 0 -0.44 70 70
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.009 0.049 -10000 0 -0.2 9 9
MAPK14 -0.042 0.13 0.25 11 -0.23 116 127
TGM2/GTP -0.083 0.21 0.38 3 -0.41 119 122
MAPK11 -0.043 0.12 0.25 11 -0.23 117 128
ARHGEF1 -0.037 0.085 0.14 1 -0.18 107 108
GNAI2 0.025 0.005 -10000 0 -10000 0 0
JNK cascade -0.078 0.2 0.35 7 -0.38 119 126
RAB11/GDP 0.025 0.006 -10000 0 -10000 0 0
ICAM1 -0.056 0.15 0.3 6 -0.28 121 127
cAMP biosynthetic process -0.068 0.18 0.35 7 -0.34 119 126
Gq family/GTP/EBP50 0.004 0.071 0.24 6 -0.22 33 39
actin cytoskeleton reorganization 0.033 0.008 -10000 0 -10000 0 0
SRC 0.003 0.063 0.3 8 -0.23 2 10
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.01 0.13 0.31 29 -0.26 29 58
VCAM1 -0.078 0.18 0.3 6 -0.36 120 126
TP beta/Gq family/GDP/G beta5/gamma2 -0.004 0.1 -10000 0 -0.41 20 20
platelet activation -0.053 0.16 0.31 12 -0.3 119 131
PGI2/IP 0.01 0.035 -10000 0 -0.3 4 4
PRKACA 0.004 0.039 -10000 0 -0.24 8 8
Gq family/GDP/G beta5/gamma2 -0.003 0.097 -10000 0 -0.38 20 20
TXA2/TP beta/beta Arrestin2 -0.026 0.13 -10000 0 -0.48 34 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.003 0.038 -10000 0 -0.22 9 9
mol:DAG -0.081 0.21 0.37 6 -0.41 117 123
EGFR -0.013 0.12 -10000 0 -0.43 34 34
TXA2/TP alpha -0.096 0.24 0.41 6 -0.46 119 125
Gq family/GTP -0.004 0.065 0.21 3 -0.21 35 38
YES1 0.009 0.081 0.34 16 -0.24 3 19
GNAI2/GTP 0.003 0.046 -10000 0 -0.2 9 9
PGD2/DP 0.005 0.044 -10000 0 -0.1 50 50
SLC9A3R1 0.022 0.037 -10000 0 -0.43 3 3
FYN 0.01 0.079 0.32 17 -0.22 2 19
mol:NO 0.016 0.036 -10000 0 -0.43 2 2
GNA15 0.011 0.077 -10000 0 -0.36 17 17
PGK/cGMP 0.006 0.07 -10000 0 -0.25 28 28
RhoA/GDP 0.025 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.025 0.055 -10000 0 -0.22 9 9
NOS3 0.016 0.036 -10000 0 -0.43 2 2
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.064 0.18 0.31 9 -0.34 117 126
PRKCB -0.077 0.18 0.35 5 -0.36 121 126
PRKCE -0.069 0.18 0.32 8 -0.35 115 123
PRKCD -0.079 0.2 0.32 7 -0.39 119 126
PRKCG -0.088 0.2 0.36 7 -0.38 121 128
muscle contraction -0.1 0.24 0.39 5 -0.48 120 125
PRKCZ -0.072 0.18 0.33 7 -0.34 122 129
ARR3 -0.008 0.018 -10000 0 -0.13 1 1
TXA2/TP beta 0.011 0.052 -10000 0 -0.21 11 11
PRKCQ -0.067 0.18 0.3 9 -0.35 114 123
MAPKKK cascade -0.091 0.22 0.37 6 -0.44 119 125
SELE -0.068 0.17 0.3 6 -0.32 119 125
TP beta/GNAI2/GDP/G beta/gamma 0.026 0.054 -10000 0 -0.21 9 9
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.007 0.087 -10000 0 -0.35 23 23
chemotaxis -0.14 0.29 0.39 5 -0.61 120 125
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
GNA11 0.018 0.056 -10000 0 -0.43 7 7
Rac1/GTP 0.016 0.007 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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 -0.009 0.075 -10000 0 -0.4 11 11
Crk/p130 Cas/Paxillin -0.05 0.12 -10000 0 -0.28 68 68
JUN -0.061 0.14 -10000 0 -0.41 40 40
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.016 0.14 -10000 0 -0.28 95 95
RAP1A 0.021 0.01 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.024 0.16 -10000 0 -0.29 117 117
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.004 0.12 -10000 0 -0.26 76 76
RHOA 0.025 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.038 0.15 -10000 0 -0.26 122 122
GRB7 0.003 0.042 -10000 0 -0.13 36 36
RET51/GFRalpha1/GDNF -0.018 0.16 -10000 0 -0.28 105 105
MAPKKK cascade -0.048 0.15 -10000 0 -0.28 110 110
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.003 0.12 -10000 0 -0.26 76 76
lamellipodium assembly -0.035 0.1 -10000 0 -0.26 57 57
RET51/GFRalpha1/GDNF/SHC -0.023 0.16 -10000 0 -0.29 113 113
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.002 0.12 -10000 0 -0.26 74 74
RET9/GFRalpha1/GDNF/Shank3 -0.005 0.12 -10000 0 -0.26 77 77
MAPK3 -0.076 0.12 0.17 3 -0.35 44 47
DOK1 0.025 0.021 -10000 0 -0.43 1 1
DOK6 -0.016 0.13 -10000 0 -0.38 47 47
PXN 0.026 0.003 -10000 0 -10000 0 0
neurite development -0.068 0.13 -10000 0 -0.39 38 38
DOK5 0.015 0.067 -10000 0 -0.43 10 10
GFRA1 -0.015 0.12 -10000 0 -0.43 32 32
MAPK8 -0.063 0.15 -10000 0 -0.28 119 119
HRAS/GTP -0.034 0.17 -10000 0 -0.31 115 115
tube development -0.001 0.12 0.2 9 -0.25 73 82
MAPK1 -0.076 0.12 0.17 3 -0.35 44 47
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.11 -10000 0 -0.26 74 74
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
PDLIM7 0.023 0.02 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.025 0.18 -10000 0 -0.31 118 118
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RET51/GFRalpha1/GDNF/Dok4 -0.033 0.17 -10000 0 -0.3 124 124
RET51/GFRalpha1/GDNF/Dok5 -0.025 0.16 -10000 0 -0.28 116 116
PRKCA 0.024 0.022 -10000 0 -0.43 1 1
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
CREB1 -0.041 0.14 -10000 0 -0.32 76 76
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.11 -10000 0 -0.26 72 72
RET51/GFRalpha1/GDNF/Grb7 -0.027 0.16 -10000 0 -0.29 115 115
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.045 0.15 -10000 0 -0.43 57 57
DOK4 0.009 0.086 -10000 0 -0.43 17 17
JNK cascade -0.062 0.13 0.19 1 -0.41 39 40
RET9/GFRalpha1/GDNF/FRS2 -0.003 0.12 -10000 0 -0.26 76 76
SHANK3 0.021 0.035 -10000 0 -0.43 2 2
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.022 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.1 -10000 0 -0.25 72 72
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.15 -10000 0 -0.29 113 113
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.16 -10000 0 -0.29 118 118
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.15 -10000 0 -0.29 109 109
PI3K -0.06 0.17 0.23 1 -0.39 72 73
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.007 0.12 -10000 0 -0.25 73 73
GRB10 0.021 0.023 -10000 0 -0.43 1 1
activation of MAPKK activity -0.053 0.15 -10000 0 -0.37 62 62
RET51/GFRalpha1/GDNF/FRS2 -0.025 0.16 -10000 0 -0.28 118 118
GAB1 0.024 0.022 -10000 0 -0.43 1 1
IRS1 0.025 0.021 -10000 0 -0.43 1 1
IRS2 0.024 0.022 -10000 0 -0.43 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.054 0.15 -10000 0 -0.3 109 109
RET51/GFRalpha1/GDNF/PKC alpha -0.025 0.16 -10000 0 -0.29 115 115
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GDNF -0.034 0.15 -10000 0 -0.38 64 64
RAC1 0.023 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.024 0.16 -10000 0 -0.29 115 115
Rac1/GTP -0.037 0.13 -10000 0 -0.31 57 57
RET9/GFRalpha1/GDNF -0.027 0.12 -10000 0 -0.28 77 77
GFRalpha1/GDNF -0.034 0.14 -10000 0 -0.34 77 77
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.046 0.17 0.25 10 -0.38 67 77
FYN -0.072 0.21 0.28 10 -0.47 71 81
LAT/GRAP2/SLP76 -0.076 0.18 0.24 3 -0.41 73 76
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.16 0.25 12 -0.34 71 83
B2M 0.02 0.021 -10000 0 -10000 0 0
IKBKG -0.014 0.051 0.09 15 -0.12 29 44
MAP3K8 0.017 0.04 -10000 0 -0.16 16 16
mol:Ca2+ -0.016 0.027 0.089 12 -0.072 36 48
integrin-mediated signaling pathway 0.022 0.039 -10000 0 -0.24 8 8
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.082 0.21 0.29 8 -0.47 72 80
TRPV6 0.21 0.53 1.1 107 -0.45 40 147
CD28 -0.024 0.12 -10000 0 -0.32 57 57
SHC1 -0.073 0.2 0.24 20 -0.45 73 93
receptor internalization -0.061 0.16 0.24 2 -0.4 58 60
PRF1 -0.12 0.34 -10000 0 -0.96 55 55
KRAS 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.042 0.13 0.22 15 -0.29 64 79
LAT -0.084 0.2 0.26 6 -0.46 73 79
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.039 0.12 -10000 0 -0.44 33 33
CD3E -0.054 0.15 -10000 0 -0.4 61 61
CD3G 0.003 0.041 -10000 0 -0.13 32 32
RASGRP2 -0.003 0.019 -10000 0 -0.16 2 2
RASGRP1 -0.067 0.17 0.27 13 -0.35 81 94
HLA-A 0.019 0.024 -10000 0 -10000 0 0
RASSF5 0.015 0.062 -10000 0 -0.29 15 15
RAP1A/GTP/RAPL 0.022 0.039 -10000 0 -0.24 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.067 0.16 33 -0.12 16 49
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.039 0.068 -10000 0 -0.18 61 61
PRKCA -0.046 0.091 0.15 3 -0.22 61 64
GRAP2 -0.008 0.1 -10000 0 -0.26 54 54
mol:IP3 -0.064 0.14 0.2 17 -0.33 74 91
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.058 0.14 -10000 0 -0.41 51 51
ORAI1 -0.18 0.43 0.59 5 -0.96 105 110
CSK -0.076 0.2 0.23 13 -0.45 74 87
B7 family/CD28 -0.067 0.22 0.28 5 -0.46 76 81
CHUK 0.025 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.091 0.21 0.24 2 -0.48 82 84
PTPN6 -0.081 0.2 0.22 7 -0.46 73 80
VAV1 -0.078 0.21 0.23 13 -0.47 75 88
Monovalent TCR/CD3 -0.046 0.12 -10000 0 -0.27 83 83
CBL 0.024 0.007 -10000 0 -10000 0 0
LCK -0.089 0.23 0.26 15 -0.49 82 97
PAG1 -0.072 0.2 0.23 14 -0.46 71 85
RAP1A 0.021 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.09 0.21 0.27 1 -0.48 76 77
CD80 -0.002 0.075 -10000 0 -0.18 50 50
CD86 0.001 0.096 -10000 0 -0.44 20 20
PDK1/CARD11/BCL10/MALT1 -0.041 0.085 -10000 0 -0.22 61 61
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.079 0.17 0.21 15 -0.4 77 92
CD8A -0.028 0.13 -10000 0 -0.42 41 41
CD8B -0.008 0.11 -10000 0 -0.34 39 39
PTPRC -0.003 0.098 -10000 0 -0.26 45 45
PDK1/PKC theta -0.066 0.19 0.31 12 -0.41 71 83
CSK/PAG1 -0.071 0.19 0.26 8 -0.45 68 76
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.029 0.029 -10000 0 -0.16 3 3
GRAP2/SLP76 -0.073 0.2 0.25 5 -0.45 74 79
STIM1 -0.002 0.2 1.2 10 -0.82 1 11
RAS family/GTP -0.01 0.082 0.18 23 -0.17 33 56
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.064 0.16 0.27 1 -0.42 58 59
mol:DAG -0.073 0.12 0.12 3 -0.29 80 83
RAP1A/GDP 0.003 0.028 0.084 15 -0.063 4 19
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.008 0.065 -10000 0 -0.44 7 7
cytotoxic T cell degranulation -0.11 0.32 -10000 0 -0.9 56 56
RAP1A/GTP -0.001 0.007 -10000 0 -0.062 2 2
mol:PI-3-4-5-P3 -0.067 0.18 0.28 9 -0.4 71 80
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.079 0.18 0.24 9 -0.41 74 83
NRAS 0.021 0.01 -10000 0 -10000 0 0
ZAP70 -0.007 0.1 -10000 0 -0.25 55 55
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.089 0.17 -10000 0 -0.41 75 75
MALT1 0.025 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
CD8 heterodimer -0.025 0.13 -10000 0 -0.31 72 72
CARD11 0.011 0.068 -10000 0 -0.36 13 13
PRKCB -0.054 0.096 0.15 5 -0.23 71 76
PRKCE -0.048 0.093 0.15 4 -0.22 64 68
PRKCQ -0.076 0.21 0.31 10 -0.45 75 85
LCP2 0.02 0.034 -10000 0 -0.43 1 1
BCL10 0.021 0.01 -10000 0 -10000 0 0
regulation of survival gene product expression -0.047 0.14 0.22 17 -0.3 71 88
IKK complex -0.003 0.059 0.15 27 -0.11 9 36
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.034 0.1 0.18 17 -0.22 62 79
PDPK1 -0.054 0.15 0.27 11 -0.33 70 81
TCR/CD3/MHC I/CD8/Fyn -0.093 0.23 0.24 1 -0.54 79 80
Effects of Botulinum toxin

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
STX1A -0.012 0.051 -10000 0 -0.3 9 9
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.016 0.12 -10000 0 -0.31 57 57
STXBP1 0.016 0.044 -10000 0 -0.15 24 24
ACh/CHRNA1 -0.04 0.11 0.13 8 -0.24 82 90
RAB3GAP2/RIMS1/UNC13B 0.013 0.1 -10000 0 -0.26 55 55
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.044 0.15 -10000 0 -0.31 96 96
mol:ACh -0.007 0.057 0.1 54 -0.12 61 115
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.029 0.12 -10000 0 -0.23 95 95
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.04 0.11 0.13 8 -0.24 82 90
UNC13B 0.024 0.022 -10000 0 -0.43 1 1
CHRNA1 -0.062 0.15 -10000 0 -0.43 60 60
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.054 0.13 0.11 9 -0.21 152 161
SNAP25 -0.041 0.097 -10000 0 -0.26 74 74
VAMP2 0.005 0 -10000 0 -10000 0 0
SYT1 -0.087 0.17 -10000 0 -0.27 177 177
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.001 0.055 -10000 0 -0.17 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.029 0.12 -10000 0 -0.23 95 95
Syndecan-1-mediated signaling events

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
TGFB1 0.021 0.023 -10000 0 -0.43 1 1
CCL5 -0.029 0.13 -10000 0 -0.43 39 39
SDCBP 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.064 0.14 0.25 5 -0.32 64 69
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.055 0.14 0.2 11 -0.37 44 55
Syndecan-1/Syntenin -0.047 0.14 0.24 16 -0.37 43 59
MAPK3 -0.05 0.13 0.2 12 -0.37 36 48
HGF/MET -0.039 0.12 -10000 0 -0.29 73 73
TGFB1/TGF beta receptor Type II 0.021 0.023 -10000 0 -0.43 1 1
BSG 0.024 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.054 0.14 0.2 11 -0.36 45 56
Syndecan-1/RANTES -0.069 0.16 0.24 14 -0.39 56 70
Syndecan-1/CD147 -0.041 0.14 0.24 4 -0.37 39 43
Syndecan-1/Syntenin/PIP2 -0.046 0.14 0.23 14 -0.36 43 57
LAMA5 0.024 0.023 -10000 0 -0.43 1 1
positive regulation of cell-cell adhesion -0.046 0.14 0.22 13 -0.35 43 56
MMP7 -0.07 0.16 -10000 0 -0.43 67 67
HGF -0.007 0.087 -10000 0 -0.2 59 59
Syndecan-1/CASK -0.068 0.12 -10000 0 -0.31 65 65
Syndecan-1/HGF/MET -0.073 0.16 0.24 4 -0.36 73 77
regulation of cell adhesion -0.043 0.14 0.26 24 -0.36 35 59
HPSE -0.017 0.13 -10000 0 -0.43 37 37
positive regulation of cell migration -0.064 0.14 0.25 5 -0.32 64 69
SDC1 -0.062 0.13 0.2 1 -0.32 71 72
Syndecan-1/Collagen -0.064 0.14 0.25 5 -0.32 64 69
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.047 0.14 -10000 0 -0.26 106 106
PRKACA 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.045 0.13 -10000 0 -0.23 125 125
MAPK1 -0.05 0.13 0.2 11 -0.36 36 47
homophilic cell adhesion -0.061 0.14 0.22 12 -0.32 64 76
MMP1 -0.007 0.047 -10000 0 -0.43 1 1
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 -0.042 0.19 -10000 0 -0.58 47 47
IHH 0.012 0.055 -10000 0 -0.19 7 7
SHH Np/Cholesterol/GAS1 -0.01 0.085 0.15 13 -0.24 47 60
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.01 0.084 0.24 47 -0.15 13 60
SMO/beta Arrestin2 -0.005 0.11 -10000 0 -0.36 29 29
SMO -0.017 0.11 -10000 0 -0.37 31 31
AKT1 0.001 0.098 -10000 0 -0.46 13 13
ARRB2 0.026 0.002 -10000 0 -10000 0 0
BOC 0.022 0.038 -10000 0 -0.31 5 5
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
heart looping -0.017 0.11 -10000 0 -0.36 31 31
STIL -0.009 0.13 0.19 54 -0.27 57 111
DHH N/PTCH2 0.003 0.088 -10000 0 -0.31 31 31
DHH N/PTCH1 -0.019 0.12 -10000 0 -0.28 72 72
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DHH -0.01 0.11 -10000 0 -0.3 49 49
PTHLH -0.059 0.25 -10000 0 -0.77 47 47
determination of left/right symmetry -0.017 0.11 -10000 0 -0.36 31 31
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
skeletal system development -0.058 0.25 -10000 0 -0.76 47 47
IHH N/Hhip -0.039 0.14 -10000 0 -0.34 69 69
DHH N/Hhip -0.05 0.14 -10000 0 -0.32 91 91
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.017 0.11 -10000 0 -0.36 31 31
pancreas development -0.058 0.16 -10000 0 -0.43 66 66
HHAT 0.012 0.076 -10000 0 -0.43 13 13
PI3K 0.038 0.007 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.015 0.045 -10000 0 -0.43 2 2
somite specification -0.017 0.11 -10000 0 -0.36 31 31
SHH Np/Cholesterol/PTCH1 -0.034 0.11 -10000 0 -0.26 83 83
SHH Np/Cholesterol/PTCH2 -0.017 0.083 0.15 1 -0.24 51 52
SHH Np/Cholesterol/Megalin -0.056 0.12 0.15 8 -0.28 97 105
SHH -0.03 0.097 -10000 0 -0.31 47 47
catabolic process -0.017 0.12 -10000 0 -0.34 46 46
SMO/Vitamin D3 -0.031 0.12 0.23 2 -0.31 43 45
SHH Np/Cholesterol/Hhip -0.048 0.12 0.15 6 -0.27 87 93
LRP2 -0.089 0.18 -10000 0 -0.3 162 162
receptor-mediated endocytosis -0.063 0.14 -10000 0 -0.38 53 53
SHH Np/Cholesterol/BOC -0.014 0.081 -10000 0 -0.24 49 49
SHH Np/Cholesterol/CDO -0.019 0.088 -10000 0 -0.25 52 52
mesenchymal cell differentiation 0.047 0.12 0.27 87 -0.15 6 93
mol:Vitamin D3 0 0.14 0.2 58 -0.26 83 141
IHH N/PTCH2 0.023 0.053 -10000 0 -0.37 5 5
CDON 0.003 0.092 -10000 0 -0.43 19 19
IHH N/PTCH1 -0.01 0.12 -10000 0 -0.35 46 46
Megalin/LRPAP1 -0.05 0.14 -10000 0 -0.31 93 93
PTCH2 0.015 0.05 -10000 0 -0.43 5 5
SHH Np/Cholesterol -0.019 0.076 0.2 1 -0.24 47 48
PTCH1 -0.017 0.12 -10000 0 -0.34 46 46
HHIP -0.058 0.16 -10000 0 -0.43 66 66
Endothelins

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
AKT1 -0.055 0.13 0.24 1 -0.27 99 100
PTK2B 0.018 0.032 -10000 0 -0.13 21 21
mol:Ca2+ -0.044 0.22 -10000 0 -0.76 27 27
EDN1 -0.034 0.11 0.21 1 -0.32 36 37
EDN3 0.006 0.089 -10000 0 -0.43 18 18
EDN2 -0.005 0.029 -10000 0 -0.13 15 15
HRAS/GDP -0.053 0.17 0.27 8 -0.44 42 50
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.035 0.12 -10000 0 -0.33 44 44
ADCY4 -0.066 0.13 -10000 0 -0.28 94 94
ADCY5 -0.07 0.14 -10000 0 -0.3 95 95
ADCY6 -0.064 0.13 -10000 0 -0.28 93 93
ADCY7 -0.064 0.13 -10000 0 -0.27 94 94
ADCY1 -0.069 0.14 -10000 0 -0.29 100 100
ADCY2 -0.068 0.14 -10000 0 -0.3 84 84
ADCY3 -0.064 0.13 -10000 0 -0.27 95 95
ADCY8 -0.079 0.14 -10000 0 -0.3 110 110
ADCY9 -0.064 0.13 -10000 0 -0.28 91 91
arachidonic acid secretion -0.065 0.2 0.29 11 -0.46 69 80
ETB receptor/Endothelin-1/Gq/GTP -0.028 0.12 -10000 0 -0.28 60 60
GNAO1 0.02 0.052 -10000 0 -0.43 6 6
HRAS 0.024 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.013 0.13 -10000 0 -0.25 81 81
ETA receptor/Endothelin-1/Gs/GTP -0.039 0.15 -10000 0 -0.26 136 136
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.1 0.21 0.23 1 -0.5 79 80
EDNRB -0.013 0.12 -10000 0 -0.4 37 37
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.064 0.15 0.24 1 -0.42 48 49
CYSLTR1 -0.062 0.15 0.24 1 -0.47 32 33
SLC9A1 -0.033 0.097 0.17 1 -0.25 54 55
mol:GDP -0.064 0.18 0.28 9 -0.46 47 56
SLC9A3 -0.073 0.25 -10000 0 -0.66 50 50
RAF1 -0.07 0.19 0.27 9 -0.43 67 76
JUN -0.036 0.18 -10000 0 -0.63 23 23
JAK2 -0.054 0.13 0.24 1 -0.29 77 78
mol:IP3 -0.043 0.14 -10000 0 -0.37 43 43
ETA receptor/Endothelin-1 -0.04 0.17 0.41 1 -0.32 102 103
PLCB1 0.008 0.084 -10000 0 -0.43 16 16
PLCB2 0.01 0.075 -10000 0 -0.43 12 12
ETA receptor/Endothelin-3 -0.017 0.11 -10000 0 -0.32 39 39
FOS -0.11 0.31 0.33 8 -0.89 55 63
Gai/GDP -0.003 0.15 -10000 0 -0.73 16 16
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca ++ -0.072 0.16 0.22 1 -0.42 57 58
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
PRKCB1 -0.043 0.13 -10000 0 -0.38 38 38
GNAQ 0.024 0.011 -10000 0 -10000 0 0
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
GNAL -0.023 0.14 -10000 0 -0.42 49 49
Gs family/GDP -0.073 0.17 0.27 4 -0.41 61 65
ETA receptor/Endothelin-1/Gq/GTP -0.03 0.12 0.19 1 -0.3 46 47
MAPK14 -0.034 0.12 -10000 0 -0.4 28 28
TRPC6 -0.048 0.23 -10000 0 -0.82 27 27
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.034 0.13 -10000 0 -0.35 41 41
ETB receptor/Endothelin-2 -0.003 0.088 -10000 0 -0.31 32 32
ETB receptor/Endothelin-3 -0.002 0.11 -10000 0 -0.34 42 42
ETB receptor/Endothelin-1 -0.025 0.13 -10000 0 -0.31 60 60
MAPK3 -0.098 0.27 0.32 10 -0.76 57 67
MAPK1 -0.099 0.27 0.33 9 -0.76 57 66
Rac1/GDP -0.054 0.16 0.29 2 -0.46 38 40
cAMP biosynthetic process -0.07 0.15 0.22 1 -0.36 69 70
MAPK8 -0.048 0.21 -10000 0 -0.65 34 34
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.023 0.1 0.16 1 -0.32 34 35
p130Cas/CRK/Src/PYK2 -0.049 0.18 0.33 10 -0.54 32 42
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.054 0.16 0.34 1 -0.46 38 39
COL1A2 -0.058 0.16 -10000 0 -0.44 42 42
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.016 0.09 -10000 0 -0.26 32 32
mol:DAG -0.043 0.14 -10000 0 -0.37 43 43
MAP2K2 -0.079 0.22 0.34 14 -0.56 61 75
MAP2K1 -0.087 0.22 0.27 7 -0.59 59 66
EDNRA -0.034 0.12 0.21 1 -0.35 33 34
positive regulation of muscle contraction -0.023 0.13 0.21 36 -0.28 50 86
Gq family/GDP -0.047 0.17 -10000 0 -0.44 45 45
HRAS/GTP -0.061 0.17 0.25 10 -0.43 49 59
PRKCH -0.043 0.13 -10000 0 -0.39 36 36
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.041 0.14 0.24 6 -0.4 36 42
PRKCB -0.054 0.14 -10000 0 -0.39 43 43
PRKCE -0.044 0.14 0.22 1 -0.41 32 33
PRKCD -0.052 0.15 -10000 0 -0.43 40 40
PRKCG -0.075 0.15 -10000 0 -0.39 56 56
regulation of vascular smooth muscle contraction -0.13 0.36 0.38 7 -1.1 55 62
PRKCQ -0.038 0.15 0.22 17 -0.43 34 51
PLA2G4A -0.072 0.22 0.3 9 -0.5 69 78
GNA14 0.005 0.088 -10000 0 -0.36 22 22
GNA15 0.01 0.077 -10000 0 -0.36 17 17
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA11 0.017 0.056 -10000 0 -0.43 7 7
Rac1/GTP -0.013 0.13 -10000 0 -0.25 92 92
MMP1 0.017 0.1 0.41 11 -0.84 1 12
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.069 0.24 1 -0.42 5 6
Syndecan-4/Syndesmos -0.061 0.2 0.31 1 -0.46 84 85
positive regulation of JNK cascade -0.055 0.2 0.3 1 -0.43 85 86
Syndecan-4/ADAM12 -0.07 0.21 0.33 1 -0.46 86 87
CCL5 -0.029 0.13 -10000 0 -0.43 39 39
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.025 0.006 -10000 0 -10000 0 0
ITGA5 0.016 0.048 -10000 0 -0.43 3 3
SDCBP 0.025 0.006 -10000 0 -10000 0 0
PLG 0.001 0.025 -10000 0 -0.14 3 3
ADAM12 -0.006 0.089 -10000 0 -0.43 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.22 0.31 1 -0.48 87 88
Syndecan-4/CXCL12/CXCR4 -0.057 0.21 0.31 1 -0.46 85 86
Syndecan-4/Laminin alpha3 -0.072 0.21 0.31 1 -0.48 87 88
MDK -0.004 0.1 -10000 0 -0.43 21 21
Syndecan-4/FZD7 -0.079 0.22 -10000 0 -0.5 87 87
Syndecan-4/Midkine -0.068 0.21 0.31 1 -0.47 83 84
FZD7 -0.017 0.13 -10000 0 -0.43 41 41
Syndecan-4/FGFR1/FGF -0.046 0.2 0.3 1 -0.44 77 78
THBS1 -0.021 0.11 -10000 0 -0.22 89 89
integrin-mediated signaling pathway -0.068 0.21 0.31 1 -0.46 85 86
positive regulation of MAPKKK cascade -0.055 0.2 0.3 1 -0.43 85 86
Syndecan-4/TACI -0.064 0.2 0.31 1 -0.46 85 86
CXCR4 0.012 0.071 -10000 0 -0.26 23 23
cell adhesion 0.015 0.033 0.2 9 -0.16 3 12
Syndecan-4/Dynamin -0.065 0.2 -10000 0 -0.46 84 84
Syndecan-4/TSP1 -0.073 0.21 0.31 1 -0.47 85 86
Syndecan-4/GIPC -0.064 0.2 -10000 0 -0.46 84 84
Syndecan-4/RANTES -0.078 0.21 0.31 1 -0.48 86 87
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
LAMA1 -0.019 0.13 -10000 0 -0.36 53 53
LAMA3 -0.005 0.1 -10000 0 -0.43 24 24
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.027 0.14 0.84 12 -0.4 1 13
Syndecan-4/alpha-Actinin -0.062 0.2 0.31 1 -0.46 85 86
TFPI -0.024 0.12 -10000 0 -0.24 86 86
F2 0.006 0.031 -10000 0 -0.14 1 1
alpha5/beta1 Integrin 0.028 0.038 -10000 0 -0.27 4 4
positive regulation of cell adhesion -0.095 0.22 0.3 1 -0.48 94 95
ACTN1 0.014 0.043 -10000 0 -0.43 1 1
TNC -0.008 0.11 -10000 0 -0.43 24 24
Syndecan-4/CXCL12 -0.064 0.2 0.31 1 -0.46 85 86
FGF6 -0.013 0.01 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
CXCL12 0.02 0.04 -10000 0 -0.24 8 8
TNFRSF13B -0.002 0.027 -10000 0 -10000 0 0
FGF2 0.023 0.031 -10000 0 -0.43 2 2
FGFR1 0.024 0.022 -10000 0 -0.43 1 1
Syndecan-4/PI-4-5-P2 -0.08 0.19 -10000 0 -0.46 85 85
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.034 -10000 0 -0.13 17 17
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.003 0.092 -10000 0 -0.41 21 21
vasculogenesis -0.07 0.2 0.31 1 -0.46 85 86
SDC4 -0.079 0.2 -10000 0 -0.48 85 85
Syndecan-4/Tenascin C -0.071 0.22 0.31 1 -0.48 85 86
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.06 0.2 0.31 1 -0.46 82 83
MMP9 -0.048 0.13 -10000 0 -0.32 67 67
Rac1/GTP 0.015 0.033 0.2 9 -0.16 3 12
cytoskeleton organization -0.058 0.2 0.31 1 -0.44 84 85
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
Syndecan-4/TFPI -0.076 0.21 0.33 1 -0.48 85 86
Reelin signaling pathway

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
CDK5R1/CDK5 0.018 0.064 -10000 0 -0.31 16 16
VLDLR 0.016 0.061 -10000 0 -0.43 8 8
CRKL 0.026 0.003 -10000 0 -10000 0 0
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ITGA3 0.016 0.047 -10000 0 -0.17 22 22
RELN/VLDLR/Fyn 0.002 0.1 -10000 0 -0.26 55 55
MAPK8IP1/MKK7/MAP3K11/JNK1 0.06 0.053 -10000 0 -0.22 12 12
AKT1 -0.045 0.1 -10000 0 -0.25 85 85
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
DAB1 -0.036 0.14 -10000 0 -0.36 68 68
RELN/LRP8/DAB1 -0.019 0.11 -10000 0 -0.24 85 85
LRPAP1/LRP8 0.031 0.022 -10000 0 -0.31 1 1
RELN/LRP8/DAB1/Fyn -0.013 0.11 -10000 0 -0.23 80 80
DAB1/alpha3/beta1 Integrin -0.016 0.11 -10000 0 -0.23 75 75
long-term memory -0.1 0.17 -10000 0 -0.32 136 136
DAB1/LIS1 -0.009 0.11 -10000 0 -0.23 81 81
DAB1/CRLK/C3G -0.016 0.11 -10000 0 -0.23 68 68
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.006 0.12 -10000 0 -0.23 81 81
ARHGEF2 0.024 0.022 -10000 0 -0.43 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.074 0.17 -10000 0 -0.29 145 145
CDK5R1 0.003 0.1 -10000 0 -0.42 24 24
RELN -0.043 0.14 -10000 0 -0.29 94 94
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.003 0.093 -10000 0 -0.25 49 49
GRIN2A/RELN/LRP8/DAB1/Fyn -0.039 0.16 -10000 0 -0.28 118 118
MAPK8 0.015 0.067 -10000 0 -0.43 10 10
RELN/VLDLR/DAB1 -0.026 0.11 -10000 0 -0.24 91 91
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
MAP1B -0.028 0.12 0.16 3 -0.24 86 89
RELN/LRP8 0.005 0.093 -10000 0 -0.25 48 48
GRIN2B/RELN/LRP8/DAB1/Fyn -0.041 0.15 -10000 0 -0.27 122 122
PI3K 0.038 0.007 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.038 -10000 0 -0.27 4 4
RAP1A -0.019 0.12 0.3 8 -0.34 10 18
PAFAH1B1 0.026 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.043 -10000 0 -0.43 4 4
CRLK/C3G 0.037 0.008 -10000 0 -10000 0 0
GRIN2B -0.079 0.17 -10000 0 -0.43 76 76
NCK2 0.026 0.002 -10000 0 -10000 0 0
neuron differentiation -0.025 0.12 -10000 0 -0.35 39 39
neuron adhesion -0.014 0.12 0.33 10 -0.38 9 19
LRP8 0.021 0.023 -10000 0 -0.43 1 1
GSK3B -0.048 0.1 -10000 0 -0.24 83 83
RELN/VLDLR/DAB1/Fyn -0.019 0.11 -10000 0 -0.24 85 85
MAP3K11 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.045 0.11 -10000 0 -0.26 88 88
CDK5 0.02 0.011 -10000 0 -10000 0 0
MAPT 0.005 0.096 0.78 5 -0.4 7 12
neuron migration -0.034 0.16 0.23 50 -0.3 80 130
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.026 0.12 -10000 0 -0.36 39 39
RELN/VLDLR 0.008 0.095 -10000 0 -0.23 54 54
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.037 0.13 -10000 0 -0.25 90 90
NFATC4 -0.058 0.089 0.22 2 -0.21 97 99
ERBB2IP 0.026 0.021 -10000 0 -0.43 1 1
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.05 0.12 -10000 0 -0.24 106 106
JUN -0.022 0.085 0.19 4 -0.36 10 14
HRAS 0.024 0.006 -10000 0 -10000 0 0
DOCK7 -0.066 0.1 -10000 0 -0.24 105 105
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.036 0.13 -10000 0 -0.26 109 109
AKT1 0.003 0.007 -10000 0 -10000 0 0
BAD -0.005 0.004 -10000 0 -10000 0 0
MAPK10 -0.031 0.065 0.17 2 -0.22 7 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.12 -10000 0 -0.26 106 106
RAF1 -0.045 0.13 0.25 8 -0.34 36 44
ErbB2/ErbB3/neuregulin 2 -0.004 0.082 0.16 2 -0.25 40 42
STAT3 0.027 0.046 -10000 0 -0.91 1 1
cell migration -0.022 0.078 0.21 13 -0.2 11 24
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.1 0.25 0.35 2 -0.61 72 74
FOS -0.082 0.2 0.28 3 -0.41 105 108
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.12 -10000 0 -0.24 106 106
MAPK3 -0.079 0.21 0.36 2 -0.52 59 61
MAPK1 -0.082 0.21 0.36 2 -0.51 62 64
JAK2 -0.068 0.098 -10000 0 -0.24 104 104
NF2 0.004 0.036 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.055 0.13 0.17 2 -0.27 108 110
NRG1 -0.08 0.18 -10000 0 -0.43 89 89
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
MAPK8 -0.056 0.12 -10000 0 -0.26 102 102
MAPK9 -0.03 0.063 0.17 3 -0.19 7 10
ERBB2 -0.022 0.011 -10000 0 -10000 0 0
ERBB3 -0.02 0.13 -10000 0 -0.36 54 54
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
apoptosis 0.003 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.045 -10000 0 -0.89 1 1
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.004 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.042 0.076 -10000 0 -0.18 91 91
ErbB2/ErbB2/HSP90 (dimer) 0.001 0.022 -10000 0 -10000 0 0
CHRNA1 -0.089 0.24 0.32 2 -0.63 63 65
myelination -0.056 0.089 0.23 3 -0.24 29 32
PPP3CB -0.066 0.092 -10000 0 -0.22 106 106
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.027 0.12 -10000 0 -0.23 98 98
NRG2 0.025 0.022 -10000 0 -0.43 1 1
mol:GDP -0.056 0.13 0.17 2 -0.27 109 111
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.048 0.13 0.24 10 -0.35 34 44
SRC 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.069 0.098 -10000 0 -0.24 106 106
MAP2K1 -0.088 0.2 -10000 0 -0.54 43 43
heart morphogenesis -0.05 0.12 -10000 0 -0.24 106 106
RAS family/GDP -0.029 0.13 0.22 2 -0.25 91 93
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.007 0.037 -10000 0 -0.74 1 1
CHRNE -0.003 0.032 0.1 1 -0.19 9 10
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.007 -10000 0 -10000 0 0
nervous system development -0.05 0.12 -10000 0 -0.24 106 106
CDC42 0.022 0.009 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.002 0.08 -10000 0 -0.31 24 24
CDKN2C 0.011 0.04 -10000 0 -0.18 2 2
CDKN2A -0.016 0.11 -10000 0 -0.38 33 33
CCND2 0.017 0.07 0.22 41 -0.13 3 44
RB1 -0.023 0.08 0.12 1 -0.24 45 46
CDK4 0.022 0.079 0.25 44 -0.17 1 45
CDK6 0.019 0.082 0.25 41 -0.14 7 48
G1/S progression 0.042 0.1 0.26 69 -0.25 3 72
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.025 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.01 0.14 -9999 0 -0.35 55 55
Syndecan-3/Neurocan -0.04 0.14 -9999 0 -0.37 67 67
POMC 0.015 0.063 -9999 0 -0.27 17 17
EGFR -0.013 0.12 -9999 0 -0.43 34 34
Syndecan-3/EGFR -0.048 0.15 -9999 0 -0.32 94 94
AGRP 0.012 0.023 -9999 0 -0.13 4 4
NCSTN 0.025 0.004 -9999 0 -10000 0 0
PSENEN 0.022 0.009 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.003 -9999 0 -10000 0 0
APH1A 0.026 0.004 -9999 0 -10000 0 0
NCAN 0.001 0.1 -9999 0 -0.42 25 25
long-term memory -0.012 0.14 -9999 0 -0.35 63 63
Syndecan-3/IL8 -0.053 0.16 -9999 0 -0.32 113 113
PSEN1 0.025 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.036 0.011 -9999 0 -10000 0 0
FYN 0.025 0.005 -9999 0 -10000 0 0
limb bud formation -0.044 0.14 -9999 0 -0.38 67 67
MC4R -0.05 0.16 -9999 0 -0.33 93 93
SRC 0.025 0.005 -9999 0 -10000 0 0
PTN 0.019 0.024 -9999 0 -0.43 1 1
FGFR/FGF/Syndecan-3 -0.044 0.14 -9999 0 -0.38 67 67
neuron projection morphogenesis -0.012 0.14 -9999 0 -0.35 55 55
Syndecan-3/AgRP -0.028 0.14 -9999 0 -0.37 67 67
Syndecan-3/AgRP/MC4R -0.043 0.16 -9999 0 -0.38 68 68
Fyn/Cortactin 0.036 0.01 -9999 0 -10000 0 0
SDC3 -0.045 0.14 -9999 0 -0.39 67 67
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.052 0.16 -9999 0 -0.32 113 113
IL8 -0.062 0.15 -9999 0 -0.43 59 59
Syndecan-3/Fyn/Cortactin -0.012 0.14 -9999 0 -0.36 63 63
Syndecan-3/CASK -0.043 0.13 -9999 0 -0.37 67 67
alpha-MSH/MC4R -0.025 0.13 -9999 0 -0.32 68 68
Gamma Secretase 0.062 0.031 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.3 -10000 0 -0.81 46 46
PCK1 -0.18 0.4 -10000 0 -1.1 58 58
HNF4A -0.14 0.32 -10000 0 -0.92 45 45
KCNJ11 -0.17 0.4 -10000 0 -1 65 65
AKT1 -0.067 0.18 -10000 0 -0.42 51 51
response to starvation -0.003 0.027 -10000 0 -0.31 2 2
DLK1 -0.15 0.35 -10000 0 -0.88 60 60
NKX2-1 -0.057 0.18 -10000 0 -0.98 4 4
ACADM -0.13 0.29 -10000 0 -0.79 48 48
TAT -0.18 0.39 -10000 0 -1.2 45 45
CEBPB 0.012 0.075 -10000 0 -0.43 12 12
CEBPA 0.016 0.048 -10000 0 -0.33 6 6
TTR -0.12 0.27 0.57 2 -0.82 35 37
PKLR -0.13 0.3 -10000 0 -0.82 45 45
APOA1 -0.18 0.4 -10000 0 -1.1 52 52
CPT1C -0.12 0.3 -10000 0 -0.82 44 44
ALAS1 -0.061 0.18 0.46 1 -0.62 7 8
TFRC -0.14 0.3 -10000 0 -0.84 45 45
FOXF1 0.018 0.045 0.19 2 -0.26 7 9
NF1 0.029 0.022 -10000 0 -0.43 1 1
HNF1A (dimer) 0.025 0.027 -10000 0 -0.44 1 1
CPT1A -0.13 0.3 -10000 0 -0.81 47 47
HMGCS1 -0.13 0.3 -10000 0 -0.83 43 43
NR3C1 -0.014 0.087 -10000 0 -0.19 77 77
CPT1B -0.15 0.32 -10000 0 -0.82 59 59
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.024 0.013 -10000 0 -10000 0 0
GCK -0.16 0.37 0.5 1 -0.9 69 70
CREB1 0.006 0.06 -10000 0 -0.18 36 36
IGFBP1 -0.22 0.48 -10000 0 -1.3 77 77
PDX1 -0.056 0.16 -10000 0 -0.66 4 4
UCP2 -0.14 0.32 -10000 0 -0.84 51 51
ALDOB -0.14 0.34 -10000 0 -0.89 52 52
AFP -0.037 0.1 -10000 0 -0.39 14 14
BDH1 -0.15 0.35 -10000 0 -0.91 57 57
HADH -0.13 0.32 -10000 0 -0.85 46 46
F2 -0.15 0.34 -10000 0 -0.98 38 38
HNF1A 0.025 0.027 -10000 0 -0.44 1 1
G6PC -0.038 0.16 -10000 0 -0.81 12 12
SLC2A2 -0.061 0.19 -10000 0 -0.55 13 13
INS 0.009 0.084 0.2 52 -0.39 3 55
FOXA1 -0.007 0.084 0.19 1 -0.27 29 30
FOXA3 -0.044 0.14 -10000 0 -0.37 57 57
FOXA2 -0.14 0.37 -10000 0 -0.89 58 58
ABCC8 -0.19 0.41 -10000 0 -0.98 76 76
ALB -0.07 0.23 -10000 0 -0.92 28 28
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.031 0.12 -10000 0 -0.41 21 21
ACTA1 -0.059 0.14 -10000 0 -0.34 71 71
NUMA1 -0.031 0.12 -10000 0 -0.38 27 27
SPTAN1 -0.055 0.14 0.18 5 -0.34 66 71
LIMK1 -0.031 0.15 0.19 38 -0.34 62 100
BIRC3 -0.003 0.1 -10000 0 -0.43 23 23
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
CASP10 -0.059 0.1 0.16 1 -0.29 68 69
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0 -10000 0 -10000 0 0
PTK2 -0.035 0.12 -10000 0 -0.36 32 32
DIABLO 0.026 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.053 0.14 0.18 5 -0.34 66 71
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.002 -10000 0 -10000 0 0
GSN -0.058 0.14 0.19 3 -0.34 71 74
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.14 0.29 -10000 0 -0.59 124 124
BID -0.027 0.07 0.11 1 -0.18 67 68
MAP3K1 -0.013 0.069 -10000 0 -0.44 5 5
TRADD 0.025 0.021 -10000 0 -0.43 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.032 0.016 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.052 0.14 0.19 5 -0.34 66 71
CASP9 0.022 0.012 -10000 0 -0.13 1 1
DNA repair 0.012 0.06 0.27 8 -0.16 7 15
neuron apoptosis 0.015 0.067 -10000 0 -0.62 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.042 0.14 0.22 1 -0.32 68 69
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.015 0.17 -10000 0 -0.94 11 11
TRAF2 0.025 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.05 0.14 0.31 8 -0.32 68 76
CASP7 -0.009 0.099 0.24 20 -0.31 16 36
KRT18 -0.061 0.21 -10000 0 -0.58 60 60
apoptosis -0.056 0.15 0.31 1 -0.46 32 33
DFFA -0.054 0.14 0.19 7 -0.34 69 76
DFFB -0.054 0.14 0.19 5 -0.34 69 74
PARP1 -0.013 0.061 0.16 7 -0.27 8 15
actin filament polymerization 0.029 0.14 0.32 61 -0.22 14 75
TNF -0.061 0.16 -10000 0 -0.43 62 62
CYCS -0.013 0.059 0.19 4 -0.18 18 22
SATB1 -0.016 0.16 -10000 0 -0.87 11 11
SLK -0.057 0.14 -10000 0 -0.34 69 69
p15 BID/BAX -0.014 0.067 -10000 0 -0.17 62 62
CASP2 0.001 0.091 0.2 26 -0.31 12 38
JNK cascade 0.013 0.068 0.43 5 -10000 0 5
CASP3 -0.06 0.14 0.18 2 -0.35 70 72
LMNB2 0.024 0.11 0.23 10 -0.42 11 21
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CASP4 0.015 0.045 -10000 0 -0.15 26 26
Mammalian IAPs/DIABLO 0.049 0.068 -10000 0 -0.24 23 23
negative regulation of DNA binding -0.13 0.29 -10000 0 -0.58 124 124
stress fiber formation -0.056 0.13 -10000 0 -0.33 69 69
GZMB -0.057 0.13 -10000 0 -0.29 93 93
CASP1 0.003 0.05 -10000 0 -0.29 12 12
LMNB1 0.02 0.13 0.24 9 -0.49 11 20
APP 0.015 0.068 -10000 0 -0.63 4 4
TNFRSF1A 0.019 0.049 -10000 0 -0.34 7 7
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.021 -10000 0 -0.31 1 1
VIM -0.054 0.15 0.33 1 -0.45 33 34
LMNA 0.026 0.11 0.23 10 -0.39 10 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.094 -10000 0 -0.34 16 16
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.064 0.14 -10000 0 -0.33 77 77
APAF-1/Caspase 9 -0.07 0.22 -10000 0 -0.62 62 62
nuclear fragmentation during apoptosis -0.03 0.12 -10000 0 -0.37 27 27
CFL2 -0.03 0.14 0.22 14 -0.33 61 75
GAS2 -0.06 0.14 0.19 1 -0.33 74 75
positive regulation of apoptosis 0.027 0.12 0.23 13 -0.4 13 26
PRF1 -0.018 0.12 -10000 0 -0.28 65 65
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.37 -10000 0 -1.1 36 36
STAT6 (cleaved dimer) -0.28 0.39 -10000 0 -1 72 72
IGHG1 -0.1 0.2 -10000 0 -0.95 13 13
IGHG3 -0.24 0.35 -10000 0 -0.94 53 53
AKT1 -0.18 0.32 -10000 0 -0.89 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.31 -10000 0 -0.9 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.92 58 58
THY1 -0.25 0.39 -10000 0 -1.2 38 38
MYB -0.013 0.11 -10000 0 -0.43 28 28
HMGA1 0.025 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.32 -10000 0 -0.8 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.34 -10000 0 -0.92 60 60
SP1 0.025 0.019 -10000 0 -10000 0 0
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
SOCS5 0.033 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.39 -10000 0 -1 62 62
SOCS1 -0.21 0.28 -10000 0 -0.73 56 56
SOCS3 -0.23 0.38 -10000 0 -1 63 63
FCER2 -0.26 0.4 -10000 0 -1.1 53 53
PARP14 0.017 0.048 -10000 0 -0.23 12 12
CCL17 -0.25 0.36 -10000 0 -1.1 35 35
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.25 -10000 0 -0.68 49 49
T cell proliferation -0.27 0.39 -10000 0 -1.1 57 57
IL4R/JAK1 -0.25 0.36 -10000 0 -1 42 42
EGR2 -0.32 0.48 -10000 0 -1.3 60 60
JAK2 -0.007 0.041 -10000 0 -10000 0 0
JAK3 -0.012 0.1 -10000 0 -0.25 54 54
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.022 -10000 0 -10000 0 0
COL1A2 -0.088 0.2 -10000 0 -1.2 8 8
CCL26 -0.22 0.38 -10000 0 -1.1 36 36
IL4R -0.26 0.38 -10000 0 -1.1 41 41
PTPN6 0.019 0.062 -10000 0 -0.42 8 8
IL13RA2 -0.42 0.56 -10000 0 -1.3 112 112
IL13RA1 -0.011 0.067 -10000 0 -0.46 6 6
IRF4 -0.12 0.33 -10000 0 -1.3 30 30
ARG1 -0.088 0.21 -10000 0 -0.92 17 17
CBL -0.19 0.3 -10000 0 -0.76 69 69
GTF3A 0.001 0.053 -10000 0 -0.15 27 27
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.008 0.069 -10000 0 -0.33 6 6
IRF4/BCL6 -0.11 0.31 -10000 0 -1.2 30 30
CD40LG 0.002 0.054 -10000 0 -10000 0 0
MAPK14 -0.22 0.33 -10000 0 -0.81 75 75
mitosis -0.17 0.3 -10000 0 -0.82 54 54
STAT6 -0.28 0.4 -10000 0 -1.1 50 50
SPI1 0.016 0.061 -10000 0 -0.25 17 17
RPS6KB1 -0.16 0.29 -10000 0 -0.79 54 54
STAT6 (dimer) -0.28 0.41 -10000 0 -1.1 50 50
STAT6 (dimer)/PARP14 -0.26 0.39 -10000 0 -1.1 55 55
mast cell activation 0.007 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.19 0.31 -10000 0 -0.86 56 56
FRAP1 -0.18 0.32 -10000 0 -0.89 54 54
LTA -0.28 0.42 -10000 0 -1.2 48 48
FES 0.024 0.025 -10000 0 -0.2 4 4
T-helper 1 cell differentiation 0.27 0.4 1.1 51 -10000 0 51
CCL11 -0.24 0.35 -10000 0 -1.1 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.3 -10000 0 -0.85 51 51
IL2RG -0.003 0.088 -10000 0 -0.22 47 47
IL10 -0.33 0.51 -10000 0 -1.4 71 71
IRS1 0.025 0.021 -10000 0 -0.43 1 1
IRS2 0.024 0.022 -10000 0 -0.43 1 1
IL4 -0.063 0.13 -10000 0 -1 3 3
IL5 -0.25 0.36 -10000 0 -1.1 34 34
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.33 -10000 0 -0.91 44 44
COL1A1 -0.27 0.5 -10000 0 -1.4 74 74
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.24 0.36 -10000 0 -1.1 33 33
IL2R gamma/JAK3 -0.011 0.1 -10000 0 -0.27 50 50
TFF3 -0.25 0.36 -10000 0 -1.1 34 34
ALOX15 -0.25 0.36 -10000 0 -1.1 37 37
MYBL1 0.024 0.011 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.92 63 63
SHC1 0.024 0.015 -10000 0 -0.13 4 4
CEBPB 0.012 0.075 -10000 0 -0.41 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.33 -10000 0 -0.91 60 60
mol:PI-3-4-5-P3 -0.18 0.32 -10000 0 -0.89 54 54
PI3K -0.19 0.35 -10000 0 -0.98 54 54
DOK2 -0.017 0.11 -10000 0 -0.24 72 72
ETS1 0.024 0.046 -10000 0 -0.42 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.65 47 47
ITGB3 -0.27 0.41 -10000 0 -1.2 45 45
PIGR -0.34 0.52 -10000 0 -1.4 72 72
IGHE 0.011 0.058 0.16 8 -0.2 12 20
MAPKKK cascade -0.13 0.23 -10000 0 -0.64 47 47
BCL6 0.026 0.005 -10000 0 -10000 0 0
OPRM1 -0.25 0.36 -10000 0 -1.1 35 35
RETNLB -0.25 0.36 -10000 0 -1.1 35 35
SELP -0.25 0.36 -10000 0 -1.1 39 39
AICDA -0.23 0.35 -10000 0 -1.1 33 33
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.013 0.13 -10000 0 -0.33 51 51
alphaM/beta2 Integrin/GPIbA -0.016 0.13 -10000 0 -0.32 56 56
alphaM/beta2 Integrin/proMMP-9 -0.041 0.15 -10000 0 -0.31 85 85
PLAUR 0.011 0.043 -10000 0 -0.14 30 30
HMGB1 0.008 0.032 -10000 0 -0.11 2 2
alphaM/beta2 Integrin/Talin -0.006 0.12 -10000 0 -0.32 43 43
AGER -0.006 0.084 -10000 0 -0.4 16 16
RAP1A 0.021 0.01 -10000 0 -10000 0 0
SELPLG 0.002 0.1 -10000 0 -0.43 23 23
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.036 0.16 -10000 0 -0.28 123 123
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.045 0.13 -10000 0 -0.23 125 125
CYR61 -0.017 0.11 -10000 0 -0.25 65 65
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.12 -10000 0 -0.37 28 28
RHOA 0.025 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.003 0.042 -10000 0 -0.13 36 36
MYH2 -0.041 0.11 -10000 0 -0.38 24 24
MST1R 0.019 0.052 -10000 0 -0.39 7 7
leukocyte activation during inflammatory response -0.022 0.14 -10000 0 -0.3 66 66
APOB -0.026 0.13 -10000 0 -0.43 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.013 0.068 -10000 0 -0.43 9 9
JAM3 0.024 0.007 -10000 0 -10000 0 0
GP1BA 0.012 0.076 -10000 0 -0.39 15 15
alphaM/beta2 Integrin/CTGF -0.018 0.13 -10000 0 -0.33 53 53
alphaM/beta2 Integrin -0.045 0.13 -10000 0 -0.37 38 38
JAM3 homodimer 0.024 0.007 -10000 0 -10000 0 0
ICAM2 0.025 0.004 -10000 0 -10000 0 0
ICAM1 0.011 0.062 -10000 0 -0.19 31 31
phagocytosis triggered by activation of immune response cell surface activating receptor -0.045 0.13 -10000 0 -0.37 36 36
cell adhesion -0.016 0.13 -10000 0 -0.31 56 56
NFKB1 -0.11 0.2 -10000 0 -0.43 102 102
THY1 0.015 0.062 -10000 0 -0.43 8 8
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.006 0.083 -10000 0 -0.25 40 40
alphaM/beta2 Integrin/LRP/tPA 0.004 0.12 -10000 0 -0.33 38 38
IL6 -0.13 0.24 -10000 0 -0.67 62 62
ITGB2 -0.016 0.1 -10000 0 -0.33 32 32
elevation of cytosolic calcium ion concentration -0.011 0.13 -10000 0 -0.3 55 55
alphaM/beta2 Integrin/JAM2/JAM3 0.009 0.11 -10000 0 -0.32 36 36
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.002 0.13 -10000 0 -0.28 68 68
alphaM/beta2 Integrin/uPA/Plg -0.015 0.13 -10000 0 -0.32 51 51
RhoA/GTP -0.037 0.12 -10000 0 -0.34 33 33
positive regulation of phagocytosis -0.042 0.15 -10000 0 -0.4 47 47
Ron/MSP 0.013 0.086 -10000 0 -0.31 30 30
alphaM/beta2 Integrin/uPAR/uPA -0.01 0.13 -10000 0 -0.31 54 54
alphaM/beta2 Integrin/uPAR -0.015 0.12 -10000 0 -0.32 46 46
PLAU -0.002 0.084 -10000 0 -0.19 58 58
PLAT 0.006 0.053 -10000 0 -0.13 55 55
actin filament polymerization -0.037 0.11 0.19 1 -0.37 23 24
MST1 -0.001 0.1 -10000 0 -0.43 24 24
alphaM/beta2 Integrin/lipoprotein(a) -0.019 0.14 -10000 0 -0.31 66 66
TNF -0.15 0.27 -10000 0 -0.63 96 96
RAP1B 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.023 0.13 -10000 0 -0.32 59 59
fibrinolysis -0.017 0.13 -10000 0 -0.32 51 51
HCK 0.013 0.067 -10000 0 -0.43 9 9
dendritic cell antigen processing and presentation -0.045 0.13 -10000 0 -0.37 36 36
VTN 0.011 0.078 -10000 0 -0.43 13 13
alphaM/beta2 Integrin/CYR61 -0.036 0.14 -10000 0 -0.32 67 67
LPA 0.004 0.04 -10000 0 -10000 0 0
LRP1 0.026 0.004 -10000 0 -10000 0 0
cell migration -0.054 0.14 -10000 0 -0.3 85 85
FN1 0.02 0.029 -10000 0 -0.13 17 17
alphaM/beta2 Integrin/Thy1 -0.011 0.12 -10000 0 -0.33 46 46
MPO -0.052 0.15 -10000 0 -0.29 111 111
KNG1 -0.008 0.032 -10000 0 -0.13 20 20
RAP1/GDP 0.028 0.014 -10000 0 -10000 0 0
ROCK1 -0.035 0.11 -10000 0 -0.38 23 23
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.01 0.017 -10000 0 -10000 0 0
CTGF 0.006 0.083 -10000 0 -0.43 14 14
alphaM/beta2 Integrin/Hck -0.013 0.14 -10000 0 -0.36 46 46
ITGAM -0.022 0.12 -10000 0 -0.42 33 33
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.006 0.15 -10000 0 -0.4 45 45
HP -0.031 0.13 -10000 0 -0.43 37 37
leukocyte adhesion -0.033 0.15 -10000 0 -0.35 53 53
SELP 0.003 0.042 -10000 0 -0.13 36 36
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.025 0.033 -10000 0 -0.26 4 4
ARNO/beta Arrestin1-2 -0.093 0.31 -10000 0 -0.8 70 70
EGFR -0.013 0.12 -10000 0 -0.43 34 34
EPHA2 0.011 0.046 -10000 0 -0.43 2 2
USP6 0.023 0.02 -10000 0 -10000 0 0
IQSEC1 0.023 0.028 -10000 0 -0.43 1 1
EGFR/EGFR/EGF/EGF -0.015 0.12 -10000 0 -0.33 54 54
ARRB2 0.011 0.007 -10000 0 -10000 0 0
mol:GTP 0.009 0.041 0.18 5 -0.18 7 12
ARRB1 0.013 0.073 -10000 0 -0.43 12 12
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR -0.087 0.17 -10000 0 -0.27 174 174
EGF -0.007 0.11 -10000 0 -0.43 26 26
somatostatin receptor activity 0 0 0.001 51 -0.001 22 73
ARAP2 0.015 0.07 -10000 0 -0.43 11 11
mol:GDP -0.016 0.13 0.19 39 -0.29 42 81
mol:PI-3-4-5-P3 0 0 0.001 66 -0.001 12 78
ITGA2B -0.014 0.12 -10000 0 -0.43 36 36
ARF6 0.026 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.037 -10000 0 -0.25 3 3
ADAP1 0.015 0.048 -10000 0 -0.43 4 4
KIF13B 0.025 0.005 -10000 0 -10000 0 0
HGF/MET -0.039 0.12 -10000 0 -0.29 73 73
PXN 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.003 0.12 0.26 45 -0.26 28 73
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.11 -10000 0 -0.28 55 55
ADRB2 0.003 0.1 -10000 0 -0.42 24 24
receptor agonist activity 0 0 0 21 0 21 42
actin filament binding 0 0 0.001 52 0 27 79
SRC 0.025 0.005 -10000 0 -10000 0 0
ITGB3 -0.003 0.088 -10000 0 -0.2 59 59
GNAQ 0.025 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 61 -0.001 13 74
ARF6/GDP -0.023 0.14 0.23 4 -0.41 30 34
ARF6/GDP/GULP/ACAP1 -0.012 0.16 0.22 26 -0.36 42 68
alphaIIb/beta3 Integrin/paxillin/GIT1 0.033 0.099 -10000 0 -0.25 49 49
ACAP1 0.009 0.062 -10000 0 -0.43 5 5
ACAP2 0.025 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.022 0.007 -10000 0 -10000 0 0
EFNA1 0.024 0.013 -10000 0 -10000 0 0
HGF -0.007 0.087 -10000 0 -0.2 59 59
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.14 0.37 -10000 0 -1 69 69
NCK1 0.025 0.022 -10000 0 -0.43 1 1
fibronectin binding 0 0 0.001 58 0 21 79
endosomal lumen acidification 0 0 0.001 53 0 31 84
microtubule-based process 0 0 -10000 0 0 11 11
GULP1 -0.018 0.13 -10000 0 -0.43 41 41
GNAQ/ARNO -0.11 0.34 -10000 0 -0.93 69 69
mol:Phosphatidic acid 0 0 0 15 -10000 0 15
PIP3-E 0 0 0 33 0 12 45
MET -0.047 0.14 -10000 0 -0.26 106 106
GNA14 0.007 0.088 -10000 0 -0.35 23 23
GNA15 0.011 0.077 -10000 0 -0.36 17 17
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 58 -0.001 15 73
GNA11 0.018 0.056 -10000 0 -0.43 7 7
LHCGR 0.009 0.029 -10000 0 -10000 0 0
AGTR1 -0.002 0.1 -10000 0 -0.3 39 39
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.007 -10000 0 -10000 0 0
IPCEF1/ARNO -0.12 0.32 -10000 0 -0.87 69 69
alphaIIb/beta3 Integrin -0.013 0.11 -10000 0 -0.32 50 50
p75(NTR)-mediated 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
Sortilin/TRAF6 0.029 0.026 -10000 0 -0.28 2 2
Necdin/E2F1 0.014 0.08 -10000 0 -0.31 24 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.012 0.12 -10000 0 -0.24 73 73
NGF (dimer)/p75(NTR)/BEX1 -0.024 0.13 -10000 0 -0.28 90 90
NT-4/5 (dimer)/p75(NTR) -0.007 0.092 -10000 0 -0.29 38 38
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.032 0.094 0.18 8 -0.23 72 80
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF -0.011 0.092 -10000 0 -0.18 80 80
MGDIs/NGR/p75(NTR)/LINGO1 -0.005 0.14 -10000 0 -0.3 73 73
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.008 0.1 -10000 0 -0.26 50 50
LINGO1 0.001 0.1 -10000 0 -0.43 25 25
Sortilin/TRAF6/NRIF 0.025 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.011 0.091 -10000 0 -0.18 80 80
NTRK1 0.015 0.057 -10000 0 -0.43 6 6
RTN4R -0.006 0.11 -10000 0 -0.43 28 28
neuron apoptosis -0.066 0.16 0.28 9 -0.46 32 41
IRAK1 0.026 0.003 -10000 0 -10000 0 0
SHC1 -0.04 0.11 0.19 1 -0.27 73 74
ARHGDIA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.062 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.002 0.12 -10000 0 -0.25 77 77
MAGEH1 0.018 0.056 -10000 0 -0.43 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.017 0.14 -10000 0 -0.27 96 96
Mammalian IAPs/DIABLO 0.049 0.067 -10000 0 -0.24 23 23
proNGF (dimer) -0.028 0.14 -10000 0 -0.36 58 58
MAGED1 0.026 0.002 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.15 11 11
ZNF274 0.021 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.02 0.095 -10000 0 -0.23 70 70
NGF -0.029 0.14 -10000 0 -0.36 58 58
cell cycle arrest -0.038 0.09 0.25 10 -0.21 71 81
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.023 0.098 -10000 0 -0.24 69 69
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.01 0.083 -10000 0 -0.25 38 38
NCSTN 0.025 0.004 -10000 0 -10000 0 0
mol:GTP -0.011 0.12 -10000 0 -0.27 75 75
PSENEN 0.022 0.009 -10000 0 -10000 0 0
mol:ceramide -0.034 0.099 0.18 6 -0.24 73 79
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.024 0.096 -10000 0 -0.32 21 21
p75(NTR)/beta APP 0.003 0.093 -10000 0 -0.31 34 34
BEX1 0.008 0.089 -10000 0 -0.43 18 18
mol:GDP -0.047 0.1 -10000 0 -0.27 75 75
NGF (dimer) -0.028 0.13 -10000 0 -0.25 108 108
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.011 0.13 -10000 0 -0.28 72 72
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.009 0.096 -10000 0 -0.23 65 65
MYD88 0.021 0.043 -10000 0 -0.37 5 5
CHUK 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.011 0.12 -10000 0 -0.27 75 75
RHOB 0.025 0.013 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.028 0.043 -10000 0 -0.31 5 5
NT3 (dimer) 0.006 0.031 -10000 0 -0.13 15 15
TP53 -0.022 0.11 0.22 29 -0.25 46 75
PRDM4 -0.035 0.1 0.18 6 -0.25 74 80
BDNF (dimer) -0.016 0.12 -10000 0 -0.26 82 82
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
SORT1 0.02 0.023 -10000 0 -0.43 1 1
activation of caspase activity 0.007 0.11 -10000 0 -0.23 73 73
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.001 0.12 -10000 0 -0.25 74 74
RHOC 0.02 0.023 -10000 0 -0.43 1 1
XIAP 0.026 0 -10000 0 -10000 0 0
MAPK10 -0.019 0.14 0.3 24 -0.33 34 58
DIABLO 0.026 0.003 -10000 0 -10000 0 0
SMPD2 -0.035 0.099 0.18 6 -0.25 73 79
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.012 0.12 -10000 0 -0.27 76 76
PSEN1 0.025 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.032 0.015 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.002 0.092 -10000 0 -0.3 35 35
MAPK8 -0.028 0.13 0.31 13 -0.33 35 48
MAPK9 -0.017 0.14 0.3 25 -0.32 35 60
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.031 -10000 0 -0.13 15 15
NTF4 -0.003 0.033 -10000 0 -0.16 11 11
NDN -0.003 0.11 -10000 0 -0.43 29 29
RAC1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.007 0.1 -10000 0 -0.22 71 71
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.044 -10000 0 -0.24 5 5
RhoA-B-C/GTP -0.011 0.12 -10000 0 -0.27 75 75
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.098 -10000 0 -0.25 43 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.019 0.1 -10000 0 -0.26 44 44
PRKACB 0.021 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.006 0.078 -10000 0 -0.32 17 17
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.003 0.1 -10000 0 -0.43 23 23
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.052 0.1 0.16 3 -0.26 76 79
BAD -0.02 0.14 0.29 27 -0.34 33 60
RIPK2 0.024 0.007 -10000 0 -10000 0 0
NGFR -0.019 0.12 -10000 0 -0.43 34 34
CYCS -0.028 0.092 0.23 7 -0.24 60 67
ADAM17 0.022 0.043 -10000 0 -0.43 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.002 0.11 -10000 0 -0.25 66 66
BCL2L11 -0.022 0.14 0.28 24 -0.34 34 58
BDNF (dimer)/p75(NTR) -0.021 0.11 -10000 0 -0.31 50 50
PI3K 0.002 0.11 -10000 0 -0.25 72 72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.002 0.12 -10000 0 -0.25 74 74
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.038 0.13 -10000 0 -0.32 76 76
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.002 0.12 -10000 0 -0.25 73 73
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
PLG -0.01 0.017 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.046 0.12 0.26 3 -0.28 79 82
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.002 -10000 0 -10000 0 0
CASP3 -0.019 0.13 0.28 25 -0.32 34 59
E2F1 0.014 0.055 -10000 0 -0.2 22 22
CASP9 0.022 0.012 -10000 0 -0.13 1 1
IKK complex -0.025 0.13 -10000 0 -0.31 43 43
NGF (dimer)/TRKA -0.013 0.11 -10000 0 -0.3 52 52
MMP7 -0.07 0.16 -10000 0 -0.43 67 67
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.009 0.11 -10000 0 -0.23 71 71
MMP3 -0.004 0.046 -10000 0 -0.14 39 39
APAF-1/Caspase 9 -0.032 0.088 -10000 0 -0.32 15 15
BCR signaling pathway

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
JUN -0.06 0.18 0.26 7 -0.41 78 85
IKBKB 0.013 0.09 0.24 14 -0.31 3 17
AKT1 -0.024 0.098 0.25 22 -0.22 36 58
IKBKG 0.002 0.093 0.23 13 -0.26 15 28
CALM1 -0.041 0.14 0.23 1 -0.38 48 49
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 -0.038 0.19 0.3 14 -0.49 48 62
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.15 0.21 4 -0.39 52 56
DOK1 0.025 0.021 -10000 0 -0.43 1 1
AP-1 -0.045 0.11 0.2 3 -0.27 66 69
LYN 0.02 0.036 -10000 0 -0.43 2 2
BLNK -0.02 0.13 -10000 0 -0.38 51 51
SHC1 0.024 0.015 -10000 0 -0.13 4 4
BCR complex -0.009 0.1 -10000 0 -0.27 51 51
CD22 -0.073 0.16 -10000 0 -0.46 48 48
CAMK2G -0.037 0.13 0.21 3 -0.44 29 32
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
SHC/GRB2/SOS1 -0.029 0.11 -10000 0 -0.26 61 61
GO:0007205 -0.042 0.16 0.21 4 -0.4 52 56
SYK 0.009 0.08 -10000 0 -0.43 14 14
ELK1 -0.04 0.15 0.22 2 -0.44 37 39
NFATC1 -0.046 0.15 0.25 5 -0.43 44 49
B-cell antigen/BCR complex -0.009 0.1 -10000 0 -0.27 51 51
PAG1/CSK 0.036 0.01 -10000 0 -10000 0 0
NFKBIB 0.016 0.046 0.12 20 -0.13 12 32
HRAS -0.031 0.14 0.24 5 -0.42 30 35
NFKBIA 0.015 0.046 0.12 22 -0.13 12 34
NF-kappa-B/RelA/I kappa B beta 0.021 0.04 0.12 20 -10000 0 20
RasGAP/Csk -0.001 0.13 -10000 0 -0.24 96 96
mol:GDP -0.037 0.15 0.22 2 -0.44 39 41
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.009 0.11 -10000 0 -0.27 54 54
NF-kappa-B/RelA/I kappa B alpha 0.021 0.04 0.12 20 -10000 0 20
GRB2 0.025 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.061 0.18 0.28 3 -0.53 45 48
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.044 0.16 0.22 2 -0.4 52 54
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.059 0.15 0.22 2 -0.43 42 44
CHUK -0.009 0.099 0.23 9 -0.29 22 31
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.003 0.15 0.24 9 -0.46 26 35
PTPN6 -0.073 0.16 0.22 2 -0.47 50 52
RELA 0.025 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.038 0.11 4 -0.12 2 6
VAV2 -0.058 0.16 -10000 0 -0.52 40 40
ubiquitin-dependent protein catabolic process 0.018 0.046 0.12 20 -0.13 12 32
BTK -0.013 0.2 -10000 0 -1.1 14 14
CD19 -0.061 0.15 -10000 0 -0.42 54 54
MAP4K1 0.013 0.061 -10000 0 -0.33 12 12
CD72 0.016 0.047 -10000 0 -0.43 3 3
PAG1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.03 0.16 0.28 16 -0.42 46 62
SH3BP5 0.022 0.038 -10000 0 -0.43 3 3
PIK3AP1 -0.042 0.16 -10000 0 -0.42 51 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.057 0.23 -10000 0 -0.57 51 51
RAF1 -0.028 0.13 0.24 5 -0.43 25 30
RasGAP/p62DOK/SHIP -0.009 0.13 -10000 0 -0.24 88 88
CD79A -0.001 0.084 -10000 0 -0.23 40 40
re-entry into mitotic cell cycle -0.045 0.11 0.2 3 -0.26 66 69
RASA1 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.11 0.24 4 -0.42 17 21
MAPK1 -0.024 0.11 0.25 3 -0.42 17 20
CD72/SHP1 -0.063 0.17 0.27 8 -0.45 49 57
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.034 0.16 0.28 14 -0.41 50 64
actin cytoskeleton organization -0.03 0.16 0.3 16 -0.45 37 53
NF-kappa-B/RelA 0.042 0.079 0.23 19 -0.2 8 27
Calcineurin -0.012 0.13 -10000 0 -0.43 26 26
PI3K -0.07 0.13 -10000 0 -0.39 47 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.044 0.17 -10000 0 -0.43 53 53
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.073 0.28 -10000 0 -0.79 54 54
DAPP1 -0.1 0.31 -10000 0 -0.9 54 54
cytokine secretion -0.042 0.14 0.24 6 -0.4 44 50
mol:DAG -0.044 0.16 0.22 2 -0.4 52 54
PLCG2 0.019 0.05 -10000 0 -0.43 5 5
MAP2K1 -0.026 0.12 0.24 4 -0.4 24 28
B-cell antigen/BCR complex/FcgammaRIIB -0.031 0.14 -10000 0 -0.25 114 114
mol:PI-3-4-5-P3 -0.059 0.095 -10000 0 -0.3 40 40
ETS1 -0.026 0.13 0.27 4 -0.41 28 32
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.13 -10000 0 -0.26 81 81
B-cell antigen/BCR complex/LYN -0.053 0.16 -10000 0 -0.45 51 51
MALT1 0.025 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
RAC1 -0.038 0.16 0.29 10 -0.48 36 46
B-cell antigen/BCR complex/LYN/SYK -0.054 0.18 0.27 1 -0.47 49 50
CARD11 -0.022 0.17 0.25 20 -0.41 49 69
FCGR2B -0.058 0.16 -10000 0 -0.27 131 131
PPP3CA 0.025 0.011 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
IKK complex 0.008 0.048 0.14 20 -0.12 6 26
PTPRC -0.003 0.098 -10000 0 -0.26 45 45
PDPK1 -0.036 0.08 0.2 13 -0.21 35 48
PPP3CB 0.024 0.013 -10000 0 -0.13 3 3
PPP3CC 0.025 0.005 -10000 0 -10000 0 0
POU2F2 0.02 0.032 0.14 17 -10000 0 17
HIF-1-alpha transcription factor network

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
PKM2 -0.055 0.31 -10000 0 -0.79 40 40
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.032 0.34 -10000 0 -0.75 48 48
SMAD4 0.026 0.004 -10000 0 -10000 0 0
ID2 -0.056 0.31 -10000 0 -0.78 41 41
AP1 -0.01 0.1 -10000 0 -0.28 50 50
ABCG2 -0.057 0.32 -10000 0 -0.8 40 40
HIF1A 0.008 0.068 -10000 0 -0.19 1 1
TFF3 -0.06 0.32 -10000 0 -0.78 42 42
GATA2 0.013 0.069 -10000 0 -0.34 14 14
AKT1 -0.004 0.087 -10000 0 -0.22 20 20
response to hypoxia -0.019 0.075 -10000 0 -0.18 39 39
MCL1 -0.055 0.31 -10000 0 -0.79 40 40
NDRG1 -0.068 0.31 -10000 0 -0.8 41 41
SERPINE1 -0.083 0.32 -10000 0 -0.78 49 49
FECH -0.055 0.31 -10000 0 -0.78 40 40
FURIN -0.055 0.31 -10000 0 -0.78 41 41
NCOA2 -0.003 0.11 -10000 0 -0.43 29 29
EP300 -0.014 0.13 -10000 0 -0.31 52 52
HMOX1 -0.06 0.32 -10000 0 -0.8 42 42
BHLHE40 -0.061 0.32 -10000 0 -0.81 41 41
BHLHE41 -0.06 0.32 -10000 0 -0.84 40 40
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.061 0.1 -10000 0 -10000 0 0
ENG 0.017 0.078 0.27 2 -10000 0 2
JUN 0.018 0.023 -10000 0 -0.13 8 8
RORA -0.056 0.31 -10000 0 -0.78 41 41
ABCB1 -0.021 0.12 -10000 0 -0.73 8 8
TFRC -0.055 0.31 -10000 0 -0.78 41 41
CXCR4 -0.06 0.32 -10000 0 -0.79 45 45
TF -0.072 0.34 -10000 0 -0.8 48 48
CITED2 -0.055 0.31 -10000 0 -0.78 41 41
HIF1A/ARNT -0.022 0.4 -10000 0 -0.92 38 38
LDHA -0.01 0.14 -10000 0 -0.96 7 7
ETS1 -0.059 0.31 -10000 0 -0.79 39 39
PGK1 -0.056 0.31 -10000 0 -0.78 41 41
NOS2 -0.064 0.33 -10000 0 -0.8 43 43
ITGB2 -0.064 0.33 -10000 0 -0.83 41 41
ALDOA -0.055 0.31 -10000 0 -0.79 40 40
Cbp/p300/CITED2 -0.079 0.37 -10000 0 -0.84 55 55
FOS -0.031 0.14 -10000 0 -0.29 82 82
HK2 -0.063 0.33 -10000 0 -0.8 45 45
SP1 0.031 0.008 -10000 0 -10000 0 0
GCK -0.1 0.43 -10000 0 -1.3 46 46
HK1 -0.055 0.31 -10000 0 -0.79 40 40
NPM1 -0.055 0.31 -10000 0 -0.79 39 39
EGLN1 -0.055 0.31 -10000 0 -0.79 40 40
CREB1 0.03 0.008 -10000 0 -10000 0 0
PGM1 -0.057 0.31 -10000 0 -0.78 40 40
SMAD3 0.027 0.003 -10000 0 -10000 0 0
EDN1 -0.075 0.28 -10000 0 -0.82 39 39
IGFBP1 -0.092 0.33 -10000 0 -0.79 51 51
VEGFA -0.046 0.28 -10000 0 -0.65 46 46
HIF1A/JAB1 0.023 0.054 -10000 0 -10000 0 0
CP -0.097 0.35 -10000 0 -0.83 52 52
CXCL12 -0.058 0.32 -10000 0 -0.78 42 42
COPS5 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.008 -10000 0 -10000 0 0
BNIP3 -0.056 0.31 -10000 0 -0.78 41 41
EGLN3 -0.058 0.32 -10000 0 -0.8 42 42
CA9 -0.068 0.32 -10000 0 -0.79 44 44
TERT -0.082 0.33 -10000 0 -0.79 49 49
ENO1 -0.055 0.31 -10000 0 -0.77 41 41
PFKL -0.055 0.31 -10000 0 -0.78 40 40
NCOA1 0.026 0.002 -10000 0 -10000 0 0
ADM -0.066 0.32 -10000 0 -0.78 45 45
ARNT 0.008 0.069 -10000 0 -0.27 1 1
HNF4A -0.004 0.054 -10000 0 -0.13 39 39
ADFP -0.069 0.31 -10000 0 -0.76 43 43
SLC2A1 -0.049 0.28 -10000 0 -0.65 44 44
LEP -0.059 0.29 -10000 0 -0.77 38 38
HIF1A/ARNT/Cbp/p300 -0.043 0.35 -10000 0 -0.77 48 48
EPO -0.039 0.24 -10000 0 -0.73 20 20
CREBBP -0.01 0.12 -10000 0 -0.3 48 48
HIF1A/ARNT/Cbp/p300/HDAC7 -0.03 0.34 -10000 0 -0.76 45 45
PFKFB3 -0.061 0.31 -10000 0 -0.81 38 38
NT5E -0.058 0.32 -10000 0 -0.78 43 43
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.11 -9999 0 -0.27 55 55
E-cadherin/beta catenin -0.015 0.11 -9999 0 -0.31 52 52
CTNNB1 0.025 0.004 -9999 0 -10000 0 0
JUP 0.02 0.052 -9999 0 -0.39 7 7
CDH1 -0.044 0.15 -9999 0 -0.43 52 52
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.022 0.1 -10000 0 -0.31 48 48
CRKL 0.01 0.15 0.25 20 -0.46 19 39
mol:PIP3 0.001 0.041 -10000 0 -0.84 1 1
AKT1 -0.003 0.044 0.28 1 -0.73 1 2
PTK2B 0.018 0.032 -10000 0 -0.13 21 21
RAPGEF1 0.012 0.14 0.28 11 -0.44 18 29
RANBP10 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.005 0.11 -10000 0 -0.24 72 72
MAP3K5 -0.008 0.16 0.26 14 -0.45 31 45
HGF/MET/CIN85/CBL/ENDOPHILINS 0.006 0.11 -10000 0 -0.26 51 51
AP1 -0.009 0.11 0.15 2 -0.24 50 52
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
apoptosis -0.16 0.38 -10000 0 -0.8 114 114
STAT3 (dimer) -0.006 0.091 0.21 5 -0.23 49 54
GAB1/CRKL/SHP2/PI3K 0.037 0.14 0.28 5 -0.44 17 22
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
CBL/CRK 0.02 0.14 0.3 7 -0.44 19 26
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
ELK1 0.04 0.16 0.32 107 -10000 0 107
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.009 0.067 -10000 0 -0.28 11 11
PAK1 -0.005 0.059 0.26 1 -0.7 1 2
HGF/MET/RANBP10 -0.004 0.11 -10000 0 -0.24 73 73
HRAS -0.05 0.2 -10000 0 -0.6 50 50
DOCK1 0.008 0.14 0.26 17 -0.45 18 35
GAB1 -0.001 0.14 0.24 5 -0.47 20 25
CRK 0.01 0.15 0.27 15 -0.46 19 34
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.19 -10000 0 -0.53 59 59
JUN 0.019 0.022 -10000 0 -0.13 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.082 -10000 0 -0.24 56 56
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.018 0.14 0.3 27 -0.44 11 38
GRB2/SHC 0.004 0.089 0.19 7 -0.21 54 61
FOS -0.03 0.14 -10000 0 -0.29 82 82
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.04 0.16 0.32 107 -10000 0 107
HGF/MET/MUC20 -0.031 0.1 -10000 0 -0.24 73 73
cell migration 0.004 0.087 0.19 7 -0.21 54 61
GRB2 0.025 0.005 -10000 0 -10000 0 0
CBL 0.024 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.021 0.1 -10000 0 -0.31 48 48
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.085 -10000 0 -0.24 50 50
MET/MUC20 -0.031 0.098 -10000 0 -0.3 48 48
RAP1B 0.013 0.14 0.29 13 -0.43 17 30
RAP1A 0.012 0.14 0.29 12 -0.42 17 29
HGF/MET/RANBP9 -0.005 0.11 -10000 0 -0.24 73 73
RAF1 -0.026 0.2 0.35 2 -0.56 50 52
STAT3 -0.008 0.089 -10000 0 -0.24 49 49
cell proliferation 0 0.15 0.3 12 -0.36 51 63
RPS6KB1 -0.005 0.044 -10000 0 -0.23 5 5
MAPK3 0.026 0.15 0.48 6 -10000 0 6
MAPK1 0.035 0.17 0.61 11 -10000 0 11
RANBP9 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.007 0.15 0.3 5 -0.44 25 30
SRC -0.019 0.079 0.16 1 -0.23 50 51
PI3K 0.005 0.09 0.19 8 -0.22 54 62
MET/Glomulin -0.037 0.094 -10000 0 -0.29 48 48
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 -0.022 0.19 0.33 3 -0.52 50 53
MET -0.047 0.14 -10000 0 -0.26 106 106
MAP4K1 -0.006 0.17 0.26 21 -0.48 30 51
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.016 0.2 0.32 15 -0.52 50 65
BAD 0 0.051 0.26 1 -0.7 1 2
MAP2K4 -0.006 0.16 0.3 10 -0.41 32 42
SHP2/GRB2/SOS1/GAB1 -0.009 0.14 -10000 0 -0.34 54 54
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PXN 0.026 0.003 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.025 0.075 0.18 2 -0.22 54 56
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.007 0.087 -10000 0 -0.2 59 59
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.022 -10000 0 -0.43 1 1
PTPRJ 0.024 0.022 -10000 0 -0.43 1 1
NCK/PLCgamma1 0.004 0.094 0.19 8 -0.22 58 66
PDPK1 -0.001 0.046 0.32 1 -0.78 1 2
HGF/MET/SHIP -0.007 0.11 -10000 0 -0.25 75 75
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.098 -10000 0 -0.23 69 69
regulation of S phase of mitotic cell cycle -0.011 0.083 -10000 0 -0.22 63 63
GNAO1 0.02 0.052 -10000 0 -0.43 6 6
HRAS 0.024 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.014 0.031 -10000 0 -0.26 6 6
PELP1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.028 0.099 0.18 24 -0.22 63 87
T-DHT/AR -0.033 0.11 -10000 0 -0.25 89 89
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 48 48
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.018 0.038 -10000 0 -0.43 3 3
mol:GDP -0.05 0.13 -10000 0 -0.38 65 65
cell proliferation -0.041 0.16 0.28 8 -0.43 47 55
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
FOS -0.072 0.25 0.27 1 -0.79 49 50
mol:Ca2+ -0.008 0.02 -10000 0 -0.058 42 42
MAPK3 -0.034 0.13 0.27 8 -0.32 45 53
MAPK1 -0.014 0.09 0.22 1 -0.3 16 17
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 48 48
cAMP biosynthetic process 0 0.033 0.23 1 -0.24 6 7
GNG2 0.022 0.043 -10000 0 -0.43 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 48 48
HRAS/GTP -0.001 0.096 -10000 0 -0.22 64 64
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 48 48
PI3K 0.034 0.006 -10000 0 -10000 0 0
apoptosis 0.031 0.15 0.43 48 -0.24 6 54
T-DHT/AR/PELP1 -0.013 0.1 -10000 0 -0.26 65 65
HRAS/GDP -0.037 0.13 -10000 0 -0.36 65 65
CREB1 -0.035 0.16 0.25 6 -0.46 48 54
RAC1-CDC42/GTP 0.036 0.023 -10000 0 -10000 0 0
AR -0.047 0.16 -10000 0 -0.35 89 89
GNB1 0.022 0.01 -10000 0 -10000 0 0
RAF1 -0.019 0.099 0.18 25 -0.22 64 89
RAC1-CDC42/GDP -0.02 0.13 -10000 0 -0.32 65 65
T-DHT/AR/PELP1/Src 0.005 0.1 -10000 0 -0.24 65 65
MAP2K2 -0.029 0.095 0.18 20 -0.29 15 35
T-DHT/AR/PELP1/Src/PI3K -0.011 0.083 -10000 0 -0.22 63 63
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
SHBG 0.02 0.052 -10000 0 -0.43 6 6
Gi family/GNB1/GNG2/GDP -0.033 0.12 -10000 0 -0.35 37 37
mol:T-DHT 0 0.001 -10000 0 -0.002 35 35
RAC1 0.023 0.009 -10000 0 -10000 0 0
GNRH1 0.002 0.034 -10000 0 -0.3 5 5
Gi family/GTP -0.023 0.071 -10000 0 -0.21 37 37
CDC42 0.022 0.009 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.014 0.088 -10000 0 -0.22 53 53
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.11 0.24 15 -0.31 27 42
AP1 -0.028 0.1 -10000 0 -0.22 86 86
mol:PIP3 -0.035 0.086 -10000 0 -0.22 72 72
AKT1 0 0.1 0.27 14 -0.25 22 36
PTK2B -0.006 0.093 0.18 9 -0.26 34 43
RHOA 0.003 0.076 0.22 14 -0.33 6 20
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.073 0.22 18 -0.29 10 28
MAGI3 0.02 0.023 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.02 0.085 -10000 0 -0.27 45 45
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.09 0.23 5 -0.28 18 23
NF kappa B1 p50/RelA -0.022 0.11 -10000 0 -0.28 52 52
endothelial cell migration -0.021 0.11 -10000 0 -0.3 49 49
ADCY4 -0.014 0.12 -10000 0 -0.34 46 46
ADCY5 -0.015 0.12 -10000 0 -0.34 47 47
ADCY6 -0.013 0.12 -10000 0 -0.34 46 46
ADCY7 -0.013 0.12 -10000 0 -0.34 46 46
ADCY1 -0.032 0.12 -10000 0 -0.36 45 45
ADCY2 -0.017 0.12 -10000 0 -0.35 48 48
ADCY3 -0.013 0.12 -10000 0 -0.34 46 46
ADCY8 -0.034 0.14 -10000 0 -0.4 52 52
ADCY9 -0.013 0.12 -10000 0 -0.34 46 46
GSK3B -0.006 0.09 0.19 4 -0.28 20 24
arachidonic acid secretion -0.019 0.12 -10000 0 -0.32 53 53
GNG2 0.022 0.042 -10000 0 -0.43 4 4
TRIP6 0.013 0.028 -10000 0 -0.34 1 1
GNAO1 -0.018 0.089 -10000 0 -0.26 54 54
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA -0.017 0.12 0.24 16 -0.34 29 45
GAB1 0.024 0.022 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.11 -10000 0 -0.84 7 7
JUN 0.019 0.022 -10000 0 -0.13 8 8
LPA/LPA2/NHERF2 0.027 0.042 -10000 0 -0.26 7 7
TIAM1 0.015 0.14 -10000 0 -1 7 7
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 -0.01 0.067 0.2 11 -0.29 10 21
PLCB3 0.017 0.05 0.18 22 -0.23 7 29
FOS -0.031 0.14 -10000 0 -0.29 82 82
positive regulation of mitosis -0.019 0.12 -10000 0 -0.32 53 53
LPA/LPA1-2-3 0.008 0.094 -10000 0 -0.24 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
stress fiber formation 0.003 0.097 0.21 7 -0.28 19 26
GNAZ -0.015 0.085 -10000 0 -0.25 49 49
EGFR/PI3K-beta/Gab1 -0.029 0.093 -10000 0 -0.23 70 70
positive regulation of dendritic cell cytokine production 0.007 0.093 -10000 0 -0.23 54 54
LPA/LPA2/MAGI-3 0.019 0.045 -10000 0 -0.26 8 8
ARHGEF1 0.015 0.096 0.2 53 -0.2 42 95
GNAI2 -0.014 0.083 -10000 0 -0.25 47 47
GNAI3 -0.002 0.06 -10000 0 -0.25 22 22
GNAI1 -0.014 0.081 -10000 0 -0.25 45 45
LPA/LPA3 0.002 0.035 -10000 0 -0.16 8 8
LPA/LPA2 0.011 0.044 -10000 0 -0.2 15 15
LPA/LPA1 -0.015 0.1 -10000 0 -0.3 49 49
HB-EGF/EGFR -0.036 0.11 -10000 0 -0.27 71 71
HBEGF -0.036 0.094 -10000 0 -0.29 47 47
mol:DAG -0.01 0.067 0.2 11 -0.29 10 21
cAMP biosynthetic process -0.016 0.14 0.32 8 -0.34 52 60
NFKB1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
LYN -0.014 0.12 0.24 17 -0.37 28 45
GNAQ 0.001 0.038 -10000 0 -0.25 7 7
LPAR2 0.016 0.058 -10000 0 -0.43 7 7
LPAR3 -0.009 0.043 -10000 0 -0.13 45 45
LPAR1 -0.023 0.13 -10000 0 -0.39 49 49
IL8 -0.11 0.2 0.34 8 -0.45 98 106
PTK2 -0.013 0.089 0.19 21 -0.22 51 72
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.02 0.086 -10000 0 -0.27 45 45
EGFR -0.013 0.12 -10000 0 -0.43 34 34
PLCG1 -0.013 0.062 0.15 6 -0.22 23 29
PLD2 -0.012 0.093 0.19 25 -0.22 54 79
G12/G13 0.018 0.083 -10000 0 -0.23 42 42
PI3K-beta -0.021 0.084 -10000 0 -0.27 26 26
cell migration 0.01 0.053 0.24 1 -0.24 5 6
SLC9A3R2 0.025 0.01 -10000 0 -0.13 2 2
PXN 0.002 0.099 0.21 5 -0.28 19 24
HRAS/GTP -0.02 0.12 -10000 0 -0.32 53 53
RAC1 0.023 0.009 -10000 0 -10000 0 0
MMP9 -0.045 0.13 -10000 0 -0.23 125 125
PRKCE 0.022 0.035 -10000 0 -0.44 2 2
PRKCD -0.009 0.097 0.22 27 -0.31 23 50
Gi(beta/gamma) -0.019 0.13 -10000 0 -0.35 52 52
mol:LPA -0.001 0.022 -10000 0 -0.16 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.005 0.094 0.33 1 -0.38 8 9
MAPKKK cascade -0.019 0.12 -10000 0 -0.32 53 53
contractile ring contraction involved in cytokinesis 0.002 0.085 0.22 18 -0.35 7 25
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.009 0.063 0.12 1 -0.26 24 25
GNA15 -0.007 0.061 -10000 0 -0.27 20 20
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
MAPT -0.008 0.092 0.24 4 -0.28 18 22
GNA11 -0.002 0.049 -10000 0 -0.26 13 13
Rac1/GTP 0.028 0.12 -10000 0 -0.9 7 7
MMP2 -0.021 0.11 -10000 0 -0.3 49 49
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.01 0.032 -10000 0 -0.3 2 2
Metarhodopsin II/Arrestin 0.011 0.056 -10000 0 -0.26 15 15
PDE6G/GNAT1/GTP 0.008 0.071 -10000 0 -0.26 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.007 0.048 -10000 0 -0.43 2 2
GRK1 0.02 0.026 -10000 0 -0.43 1 1
CNG Channel -0.049 0.14 -10000 0 -0.25 132 132
mol:Na + -0.068 0.13 -10000 0 -0.24 143 143
mol:ADP 0.02 0.026 -10000 0 -0.43 1 1
RGS9-1/Gbeta5/R9AP 0.018 0.09 -10000 0 -0.27 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.057 0.14 -10000 0 -0.25 143 143
CNGB1 -0.073 0.15 -10000 0 -0.43 56 56
RDH5 0.016 0.037 -10000 0 -10000 0 0
SAG -0.008 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.11 0.32 3 -0.32 38 41
Na + (4 Units) -0.079 0.12 -10000 0 -0.23 137 137
RGS9 -0.012 0.12 -10000 0 -0.39 41 41
GNB1/GNGT1 0.02 0.016 -10000 0 -10000 0 0
GNAT1/GDP 0.026 0.083 -10000 0 -0.23 37 37
GUCY2D 0.007 0.031 -10000 0 -0.13 15 15
GNGT1 -0.012 0.01 -10000 0 -10000 0 0
GUCY2F 0.012 0.023 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.021 0.089 0.15 2 -0.24 57 59
mol:11-cis-retinal 0.016 0.037 -10000 0 -10000 0 0
mol:cGMP -0.005 0.11 -10000 0 -0.24 70 70
GNB1 0.022 0.01 -10000 0 -10000 0 0
Rhodopsin 0.011 0.069 -10000 0 -0.3 15 15
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.017 0.12 -10000 0 -0.43 36 36
Metarhodopsin II 0.015 0.052 -10000 0 -0.23 16 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.005 0.12 -10000 0 -0.25 71 71
RGS9BP 0.017 0.048 -10000 0 -0.43 5 5
Metarhodopsin II/Transducin -0.003 0.046 -10000 0 -0.25 12 12
GCAP Family/Ca ++ -0.006 0.11 -10000 0 -0.25 72 72
PDE6A/B -0.002 0.098 -10000 0 -0.31 36 36
mol:Pi 0.018 0.09 -10000 0 -0.27 38 38
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.022 0.03 -10000 0 -0.24 1 1
PDE6B 0 0.095 -10000 0 -0.43 19 19
PDE6A -0.002 0.092 -10000 0 -0.24 45 45
PDE6G -0.002 0.1 -10000 0 -0.43 23 23
RHO -0.007 0.087 -10000 0 -0.43 15 15
PDE6 0.007 0.13 -10000 0 -0.24 84 84
GUCA1A -0.059 0.15 -10000 0 -0.27 124 124
GC2/GCAP Family 0.007 0.12 -10000 0 -0.25 72 72
GUCA1C -0.007 0.029 -10000 0 -10000 0 0
GUCA1B 0.012 0.079 -10000 0 -0.41 15 15
Osteopontin-mediated 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
IKK alpha homodimer -0.007 0.089 -10000 0 -0.22 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.095 0.3 4 -0.42 3 7
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.095 -10000 0 -0.3 35 35
AP1 -0.019 0.13 -10000 0 -0.37 24 24
ILK -0.015 0.084 -10000 0 -0.23 44 44
bone resorption -0.031 0.13 0.32 2 -0.35 39 41
PTK2B 0.018 0.032 -10000 0 -0.13 21 21
PYK2/p130Cas 0.018 0.12 -10000 0 -0.26 51 51
ITGAV 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.1 -10000 0 -0.31 44 44
alphaV/beta3 Integrin/Osteopontin 0.015 0.11 -10000 0 -0.26 48 48
MAP3K1 -0.019 0.087 0.19 6 -0.23 48 54
JUN 0.019 0.022 -10000 0 -0.13 8 8
MAPK3 -0.027 0.086 0.19 4 -0.22 58 62
MAPK1 -0.027 0.082 0.2 3 -0.22 58 61
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.028 0.087 0.19 4 -0.24 48 52
ITGB3 -0.002 0.089 -10000 0 -0.2 59 59
NFKBIA -0.026 0.085 0.19 2 -0.29 15 17
FOS -0.03 0.14 -10000 0 -0.29 82 82
CD44 -0.015 0.12 -10000 0 -0.31 56 56
CHUK 0.025 0.006 -10000 0 -10000 0 0
PLAU -0.047 0.19 -10000 0 -1.1 12 12
NF kappa B1 p50/RelA 0.003 0.1 -10000 0 -0.34 13 13
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.018 0.07 -10000 0 -0.31 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.026 0.1 0.19 6 -0.28 51 57
VAV3 -0.05 0.099 0.19 3 -0.26 59 62
MAP3K14 -0.02 0.088 0.19 4 -0.24 48 52
ROCK2 0.012 0.078 -10000 0 -0.43 14 14
SPP1 -0.022 0.12 -10000 0 -0.43 35 35
RAC1 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.094 0.18 2 -0.24 54 56
MMP2 -0.045 0.11 -10000 0 -0.39 24 24
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.039 0.2 -9999 0 -0.42 80 80
MAP3K8 0.016 0.04 -9999 0 -0.17 16 16
FOS -0.038 0.18 -9999 0 -0.44 62 62
PRKCA 0.02 0.025 -9999 0 -0.43 1 1
PTPN7 -0.052 0.15 -9999 0 -0.39 65 65
HRAS 0.024 0.006 -9999 0 -10000 0 0
PRKCB -0.012 0.1 -9999 0 -0.22 64 64
NRAS 0.021 0.01 -9999 0 -10000 0 0
RAS family/GTP 0.034 0.025 -9999 0 -10000 0 0
MAPK3 -0.029 0.16 -9999 0 -0.42 57 57
MAP2K1 0.002 0.11 -9999 0 -0.47 19 19
ELK1 0.021 0.017 -9999 0 -10000 0 0
BRAF -0.007 0.092 -9999 0 -0.4 20 20
mol:GTP 0 0.001 -9999 0 -0.004 53 53
MAPK1 -0.033 0.16 -9999 0 -0.43 60 60
RAF1 -0.003 0.094 -9999 0 -0.44 18 18
KRAS 0.025 0.005 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.028 0.14 -10000 0 -0.4 50 50
PDGF/PDGFRA/CRKL -0.003 0.1 -10000 0 -0.3 45 45
positive regulation of JUN kinase activity 0.031 0.083 -10000 0 -0.23 40 40
CRKL 0.026 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.009 0.1 -10000 0 -0.3 45 45
AP1 -0.093 0.25 -10000 0 -0.74 52 52
mol:IP3 -0.023 0.09 -10000 0 -0.31 37 37
PLCG1 -0.023 0.09 -10000 0 -0.32 37 37
PDGF/PDGFRA/alphaV Integrin -0.003 0.1 -10000 0 -0.3 45 45
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.09 -10000 0 -0.31 37 37
CAV3 0.003 0.029 -10000 0 -0.13 12 12
CAV1 0.007 0.049 -10000 0 -0.14 35 35
SHC/Grb2/SOS1 0.033 0.084 -10000 0 -0.23 40 40
PDGF/PDGFRA/Shf -0.005 0.11 -10000 0 -0.32 46 46
FOS -0.098 0.24 0.31 2 -0.74 52 54
JUN -0.02 0.025 0.16 1 -10000 0 1
oligodendrocyte development -0.003 0.1 -10000 0 -0.3 45 45
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:DAG -0.023 0.09 -10000 0 -0.31 37 37
PDGF/PDGFRA -0.028 0.14 -10000 0 -0.4 50 50
actin cytoskeleton reorganization -0.004 0.099 -10000 0 -0.3 45 45
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
PI3K 0.019 0.088 -10000 0 -0.25 43 43
PDGF/PDGFRA/Crk/C3G 0.018 0.089 -10000 0 -0.25 45 45
JAK1 -0.021 0.088 -10000 0 -0.3 41 41
ELK1/SRF -0.011 0.078 0.16 22 -0.25 35 57
SHB 0.025 0.004 -10000 0 -10000 0 0
SHF 0.022 0.042 -10000 0 -0.43 4 4
CSNK2A1 0.029 0.018 -10000 0 -10000 0 0
GO:0007205 -0.027 0.098 0.24 5 -0.34 37 42
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.031 0.083 -10000 0 -0.23 40 40
PDGF/PDGFRA/SHB -0.004 0.1 -10000 0 -0.3 45 45
PDGF/PDGFRA/Caveolin-1 -0.005 0.085 -10000 0 -0.31 28 28
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.033 0.086 0.2 5 -0.3 37 42
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.003 0.1 -10000 0 -0.3 45 45
JAK-STAT cascade -0.021 0.088 -10000 0 -0.3 41 41
cell proliferation -0.006 0.11 -10000 0 -0.31 46 46
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 0.033 0.012 -10000 0 -10000 0 0
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.024 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.021 0.1 -10000 0 -0.32 31 31
IRAK/TOLLIP 0.027 0.011 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
IKBKG 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.057 0.14 -10000 0 -0.31 93 93
IL1A -0.033 0.14 -10000 0 -0.27 90 90
IL1B -0.058 0.12 -10000 0 -0.32 71 71
IRAK/TRAF6/p62/Atypical PKCs 0.047 0.056 -10000 0 -0.21 12 12
IL1R2 -0.046 0.14 -10000 0 -0.25 115 115
IL1R1 0.002 0.089 -10000 0 -0.25 40 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.027 0.1 -10000 0 -0.33 28 28
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.016 0.064 -10000 0 -0.4 10 10
MAP3K3 0.025 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.032 0.054 0.24 2 -10000 0 2
JUN -0.006 0.042 0.16 17 -0.24 6 23
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.022 0.13 -10000 0 -0.25 83 83
IL1 alpha/IL1R1/IL1RAP/MYD88 0.016 0.12 -10000 0 -0.26 65 65
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.031 0.12 -10000 0 -0.24 65 65
IL1 beta fragment/IL1R1/IL1RAP -0.042 0.13 0.17 1 -0.27 89 90
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.05 0.17 22 -0.23 9 31
IRAK1 0.003 0.015 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.024 0.12 -10000 0 -0.29 61 61
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.028 0.11 -10000 0 -0.33 36 36
CHUK 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.042 0.13 0.17 1 -0.27 89 90
IL1 beta/IL1R2 -0.075 0.14 -10000 0 -0.29 106 106
IRAK/TRAF6/TAK1/TAB1/TAB2 0.033 0.018 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA -0.028 0.11 -10000 0 -0.24 77 77
IRAK3 0.021 0.043 -10000 0 -0.43 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.027 0.13 -10000 0 -0.26 89 89
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.099 -10000 0 -0.24 65 65
IL1 alpha/IL1R1/IL1RAP 0.004 0.12 -10000 0 -0.25 77 77
RELA 0.025 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.021 0.043 -10000 0 -0.37 5 5
IRAK/TRAF6/MEKK3 0.047 0.033 -10000 0 -0.23 1 1
IL1RAP 0.005 0.074 -10000 0 -0.43 9 9
UBE2N 0.026 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.043 0.11 -10000 0 -0.34 21 21
CASP1 0.01 0.071 -10000 0 -0.43 10 10
IL1RN/IL1R2 -0.055 0.14 -10000 0 -0.29 106 106
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.031 0.13 -10000 0 -0.26 84 84
TMEM189-UBE2V1 0.005 0.022 -10000 0 -0.13 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.11 -10000 0 -0.35 27 27
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
IL1RN -0.034 0.13 -10000 0 -0.43 38 38
TRAF6/TAK1/TAB1/TAB2 0.043 0.02 -10000 0 -0.22 1 1
MAP2K6 0.011 0.046 0.18 29 -0.21 2 31
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.009 0.081 -10000 0 -0.22 55 55
epithelial cell differentiation 0.025 0.085 -10000 0 -0.22 48 48
CYFIP2 0.023 0.033 -10000 0 -0.25 5 5
ENAH -0.024 0.06 0.27 3 -10000 0 3
EGFR -0.013 0.12 -10000 0 -0.43 34 34
EPHA2 0.011 0.046 -10000 0 -0.43 2 2
MYO6 -0.013 0.078 -10000 0 -0.21 44 44
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.046 0.025 -10000 0 -0.24 2 2
AQP5 -0.064 0.17 -10000 0 -0.44 63 63
CTNND1 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.076 -10000 0 -0.21 44 44
regulation of calcium-dependent cell-cell adhesion -0.016 0.081 0.18 16 -0.21 52 68
EGF -0.007 0.11 -10000 0 -0.43 26 26
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.019 0.1 -10000 0 -0.45 17 17
cortical microtubule organization 0.025 0.085 -10000 0 -0.22 48 48
GO:0000145 -0.026 0.068 0.16 17 -0.2 44 61
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.088 -10000 0 -0.22 48 48
MLLT4 0.024 0.022 -10000 0 -0.43 1 1
ARF6/GDP -0.036 0.055 -10000 0 -0.23 5 5
ARF6 0.026 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.037 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.083 -10000 0 -0.33 17 17
PVRL2 0.02 0.024 -10000 0 -0.28 2 2
ZYX -0.012 0.067 -10000 0 -0.21 37 37
ARF6/GTP 0.058 0.039 -10000 0 -0.24 3 3
CDH1 -0.044 0.15 -10000 0 -0.43 52 52
EGFR/EGFR/EGF/EGF -0.016 0.12 -10000 0 -0.24 88 88
RhoA/GDP 0.027 0.082 -10000 0 -0.21 48 48
actin cytoskeleton organization -0.028 0.074 0.17 16 -0.21 42 58
IGF-1R heterotetramer 0.025 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
IGF1R 0.025 0.004 -10000 0 -10000 0 0
IGF1 0.012 0.075 -10000 0 -0.43 12 12
DIAPH1 0.022 0.12 -10000 0 -0.6 6 6
Wnt receptor signaling pathway -0.025 0.085 0.22 48 -10000 0 48
RHOA 0.025 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.037 0.055 -10000 0 -0.23 5 5
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.029 0.075 0.17 16 -0.22 42 58
EFNA1 0.024 0.013 -10000 0 -10000 0 0
LPP -0.035 0.074 0.17 14 -0.21 9 23
Ephrin A1/EPHA2 0.015 0.078 -10000 0 -0.2 46 46
SEC6/SEC8 -0.014 0.058 -10000 0 -0.21 19 19
MGAT3 -0.016 0.082 0.18 16 -0.22 52 68
HGF/MET -0.025 0.12 -10000 0 -0.24 87 87
HGF -0.007 0.087 -10000 0 -0.2 59 59
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.009 0.082 -10000 0 -0.22 55 55
actin cable formation -0.003 0.096 0.4 8 -0.26 6 14
KIAA1543 -0.031 0.073 0.16 11 -0.22 48 59
KIFC3 -0.015 0.078 -10000 0 -0.22 47 47
NCK1 0.025 0.022 -10000 0 -0.43 1 1
EXOC3 0.025 0.004 -10000 0 -10000 0 0
ACTN1 -0.018 0.079 -10000 0 -0.21 46 46
NCK1/GIT1 0.037 0.017 -10000 0 -0.31 1 1
mol:GDP 0.025 0.085 -10000 0 -0.22 48 48
EXOC4 0.02 0.011 -10000 0 -10000 0 0
STX4 -0.013 0.078 0.18 16 -0.21 46 62
PIP5K1C -0.013 0.077 -10000 0 -0.21 44 44
LIMA1 0.019 0.056 -10000 0 -0.43 7 7
ABI1 0.024 0.008 -10000 0 -10000 0 0
ROCK1 -0.02 0.082 0.4 6 -10000 0 6
adherens junction assembly -0.009 0.088 0.28 9 -0.41 4 13
IGF-1R heterotetramer/IGF1 0.015 0.089 -10000 0 -0.22 55 55
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.029 0.028 -10000 0 -0.31 2 2
MET -0.047 0.14 -10000 0 -0.26 106 106
PLEKHA7 -0.018 0.082 0.19 1 -0.23 48 49
mol:GTP 0.052 0.036 -10000 0 -0.25 3 3
establishment of epithelial cell apical/basal polarity 0.02 0.12 0.33 22 -0.37 1 23
cortical actin cytoskeleton stabilization -0.009 0.081 -10000 0 -0.22 55 55
regulation of cell-cell adhesion -0.028 0.074 0.17 16 -0.21 42 58
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.009 0.082 -10000 0 -0.22 55 55
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.013 0.12 -10000 0 -0.43 34 34
EGF/EGFR -0.005 0.11 -10000 0 -0.24 73 73
EGF/EGFR dimer/SHC/GRB2/SOS1 0.024 0.1 -10000 0 -0.24 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.006 0.084 -10000 0 -0.43 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.007 0.11 -10000 0 -0.43 26 26
EGF/EGFR dimer/SHC 0.004 0.11 -10000 0 -0.28 52 52
mol:GDP 0.02 0.098 -10000 0 -0.24 51 51
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.003 0.085 -10000 0 -0.23 41 41
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.007 0.085 -10000 0 -0.22 50 50
SHC1 0.024 0.015 -10000 0 -0.13 4 4
HRAS/GDP 0.018 0.093 -10000 0 -0.23 50 50
FRAP1 -0.032 0.073 0.11 6 -0.23 51 57
EGF/EGFR dimer -0.015 0.12 -10000 0 -0.33 54 54
SOS1 0.026 0.002 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.005 0.088 -10000 0 -0.3 31 31
Aurora C signaling

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
INCENP 0.025 0.005 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.014 0.11 -9999 0 -0.23 86 86
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.008 0.031 -9999 0 -10000 0 0
AURKB -0.078 0.18 -9999 0 -0.43 85 85
AURKC 0.012 0.047 -9999 0 -0.17 22 22
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.05 0.095 -10000 0 -0.84 3 3
SMARCC2 0.025 0.016 -10000 0 -0.13 1 1
SMARCC1 0.024 0.016 -10000 0 -0.11 1 1
TBX21 -0.073 0.18 -10000 0 -0.62 35 35
SUMO2 0.023 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.032 -10000 0 -0.16 1 1
FKBP4 0.024 0.007 -10000 0 -10000 0 0
FKBP5 -0.039 0.15 -10000 0 -0.32 85 85
GR alpha/HSP90/FKBP51/HSP90 0.053 0.12 0.25 26 -0.23 39 65
PRL -0.036 0.068 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.12 0.19 0.45 67 -0.32 3 70
RELA -0.035 0.094 -10000 0 -0.26 26 26
FGG 0.096 0.14 0.38 50 -10000 0 50
GR beta/TIF2 0.059 0.12 0.25 43 -0.29 28 71
IFNG -0.14 0.19 -10000 0 -0.52 44 44
apoptosis 0.025 0.17 0.57 19 -0.54 5 24
CREB1 0.026 0.009 -10000 0 -10000 0 0
histone acetylation -0.052 0.11 -10000 0 -0.33 33 33
BGLAP -0.043 0.1 -10000 0 -0.78 2 2
GR/PKAc 0.078 0.07 0.25 20 -10000 0 20
NF kappa B1 p50/RelA -0.056 0.16 -10000 0 -0.31 104 104
SMARCD1 0.025 0.016 -10000 0 -0.11 1 1
MDM2 0.05 0.065 0.19 50 -10000 0 50
GATA3 -0.029 0.13 -10000 0 -0.41 43 43
AKT1 0.022 0.013 0.18 3 -10000 0 3
CSF2 -0.06 0.086 -10000 0 -0.43 1 1
GSK3B 0.024 0.016 -10000 0 -10000 0 0
NR1I3 0.032 0.17 0.57 17 -0.62 3 20
CSN2 0.079 0.12 0.32 45 -10000 0 45
BRG1/BAF155/BAF170/BAF60A 0.061 0.043 -10000 0 -0.22 8 8
NFATC1 0.008 0.087 -10000 0 -0.43 17 17
POU2F1 0.026 0.005 -10000 0 -10000 0 0
CDKN1A -0.051 0.3 -10000 0 -1.4 20 20
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.011 -10000 0 -10000 0 0
SFN -0.022 0.11 -10000 0 -0.43 24 24
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.037 0.12 0.26 13 -0.24 45 58
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.024 0.27 0.53 17 -0.77 42 59
JUN -0.08 0.14 0.27 2 -0.37 51 53
IL4 -0.063 0.11 -10000 0 -0.54 9 9
CDK5R1 0.003 0.1 -10000 0 -0.42 24 24
PRKACA 0.025 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.091 0.1 -10000 0 -0.3 59 59
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.053 0.11 0.26 11 -0.22 28 39
cortisol/GR alpha (monomer) 0.15 0.2 0.51 71 -10000 0 71
NCOA2 -0.004 0.11 -10000 0 -0.43 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.14 -10000 0 -0.35 69 69
AP-1/NFAT1-c-4 -0.17 0.24 -10000 0 -0.5 128 128
AFP -0.077 0.12 -10000 0 -0.54 1 1
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.089 0.098 0.38 13 -10000 0 13
TP53 0.001 0.13 -10000 0 -0.47 31 31
PPP5C 0.022 0.01 -10000 0 -10000 0 0
KRT17 -0.28 0.43 -10000 0 -1 101 101
KRT14 -0.061 0.087 -10000 0 -10000 0 0
TBP 0.03 0.017 -10000 0 -0.29 1 1
CREBBP 0.026 0.043 -10000 0 -0.24 11 11
HDAC1 0.02 0.009 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
AP-1 -0.17 0.24 -10000 0 -0.51 128 128
MAPK14 0.024 0.015 -10000 0 -10000 0 0
MAPK10 0.021 0.04 -10000 0 -0.44 3 3
MAPK11 0.021 0.039 -10000 0 -0.42 3 3
KRT5 -0.25 0.4 -10000 0 -0.96 94 94
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.027 0.009 -10000 0 -10000 0 0
STAT1 0.024 0.032 -10000 0 -0.16 1 1
CGA -0.052 0.087 -10000 0 -0.35 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.048 0.084 0.29 7 -0.31 2 9
MAPK3 0.024 0.016 -10000 0 -10000 0 0
MAPK1 0.024 0.015 -10000 0 -10000 0 0
ICAM1 -0.11 0.2 -10000 0 -0.54 48 48
NFKB1 -0.034 0.091 -10000 0 -0.2 70 70
MAPK8 -0.081 0.12 0.31 1 -0.33 58 59
MAPK9 0.024 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.023 0.18 0.57 19 -0.57 5 24
BAX -0.025 0.12 -10000 0 -10000 0 0
POMC -0.091 0.22 -10000 0 -1.4 9 9
EP300 0.021 0.06 -10000 0 -0.29 15 15
cortisol/GR alpha (dimer)/p53 0.13 0.19 0.47 59 -0.45 1 60
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.055 0.19 17 -10000 0 17
SGK1 0.006 0.22 -10000 0 -1.4 11 11
IL13 -0.13 0.19 -10000 0 -0.56 41 41
IL6 -0.16 0.31 -10000 0 -0.94 53 53
PRKACG 0.01 0.024 -10000 0 -0.13 4 4
IL5 -0.1 0.16 -10000 0 -0.6 12 12
IL2 -0.14 0.18 -10000 0 -0.48 60 60
CDK5 0.02 0.012 -10000 0 -10000 0 0
PRKACB 0.021 0.01 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.35 -10000 0 -0.89 82 82
CDK5R1/CDK5 0.017 0.065 -10000 0 -0.31 16 16
NF kappa B1 p50/RelA/PKAc -0.011 0.12 -10000 0 -0.31 24 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.43 67 -10000 0 67
SMARCA4 0.024 0.015 -10000 0 -10000 0 0
chromatin remodeling 0.084 0.11 0.32 41 -0.33 5 46
NF kappa B1 p50/RelA/Cbp -0.018 0.15 -10000 0 -0.37 33 33
JUN (dimer) -0.08 0.13 0.27 2 -0.36 51 53
YWHAH 0.019 0.032 -10000 0 -10000 0 0
VIPR1 -0.079 0.19 -10000 0 -0.68 36 36
NR3C1 0.088 0.12 0.34 53 -10000 0 53
NR4A1 0.006 0.092 -10000 0 -0.45 15 15
TIF2/SUV420H1 0.015 0.081 -10000 0 -0.31 27 27
MAPKKK cascade 0.025 0.17 0.57 19 -0.54 5 24
cortisol/GR alpha (dimer)/Src-1 0.15 0.18 0.45 73 -10000 0 73
PBX1 0.025 0.022 -10000 0 -0.43 1 1
POU1F1 0.001 0.021 -10000 0 -10000 0 0
SELE -0.16 0.29 -10000 0 -0.82 60 60
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.085 0.11 0.32 41 -0.34 5 46
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.43 67 -10000 0 67
mol:cortisol 0.072 0.11 0.29 63 -10000 0 63
MMP1 -0.041 0.093 -10000 0 -0.94 2 2
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.006 0.022 -10000 0 -0.31 1 1
MAP4K4 -0.016 0.09 -10000 0 -0.37 14 14
BAG4 0.015 0.067 -10000 0 -0.43 10 10
PKC zeta/ceramide -0.035 0.14 0.14 1 -0.3 69 70
NFKBIA 0.026 0.003 -10000 0 -10000 0 0
BIRC3 -0.003 0.1 -10000 0 -0.43 23 23
BAX -0.061 0.14 -10000 0 -0.35 81 81
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.002 0.036 0.66 1 -10000 0 1
BAD -0.038 0.13 0.2 10 -0.28 65 75
SMPD1 -0.009 0.077 0.17 6 -0.17 60 66
RB1 -0.042 0.12 0.15 2 -0.27 66 68
FADD/Caspase 8 -0.005 0.092 -10000 0 -0.39 12 12
MAP2K4 -0.042 0.11 -10000 0 -0.28 57 57
NSMAF 0.025 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.039 0.12 0.18 6 -0.27 60 66
EGF -0.007 0.11 -10000 0 -0.43 26 26
mol:ceramide -0.044 0.13 0.14 1 -0.28 68 69
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.008 0.022 -10000 0 -0.31 1 1
ASAH1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.042 0.12 0.15 2 -0.27 66 68
cell proliferation -0.02 0.11 -10000 0 -0.38 26 26
BID -0.005 0.1 -10000 0 -0.61 6 6
MAP3K1 -0.043 0.12 -10000 0 -0.27 66 66
EIF2A -0.043 0.11 0.34 1 -0.3 44 45
TRADD 0.025 0.021 -10000 0 -0.43 1 1
CRADD 0.026 0.002 -10000 0 -10000 0 0
MAPK3 -0.03 0.097 0.17 6 -0.43 16 22
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.031 0.097 0.17 6 -0.38 20 26
Cathepsin D/ceramide -0.03 0.13 0.14 1 -0.27 66 67
FADD -0.016 0.089 -10000 0 -0.36 14 14
KSR1 -0.043 0.12 0.13 1 -0.28 65 66
MAPK8 -0.07 0.16 -10000 0 -0.42 47 47
PRKRA -0.043 0.12 0.13 2 -0.27 66 68
PDGFA 0.016 0.034 -10000 0 -0.43 1 1
TRAF2 0.025 0.004 -10000 0 -10000 0 0
IGF1 0.012 0.075 -10000 0 -0.43 12 12
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.044 0.13 0.14 1 -0.28 68 69
CTSD 0.025 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.036 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.021 0.12 -10000 0 -0.41 26 26
PRKCD 0.005 0.095 -10000 0 -0.43 21 21
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.008 0.022 -10000 0 -0.31 1 1
RelA/NF kappa B1 0.037 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.006 0.079 -10000 0 -0.23 35 35
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.096 -10000 0 -0.34 19 19
TNFR1A/BAG4/TNF-alpha 0.001 0.12 -10000 0 -0.27 68 68
mol:Sphingosine-1-phosphate 0.006 0.022 -10000 0 -0.31 1 1
MAP2K1 -0.039 0.11 0.17 7 -0.29 48 55
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
CYCS -0.032 0.083 -10000 0 -0.21 70 70
TNFRSF1A 0.019 0.049 -10000 0 -0.34 7 7
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.024 0.058 -10000 0 -0.31 13 13
EIF2AK2 -0.044 0.12 0.16 2 -0.27 63 65
TNF-alpha/TNFR1A/FAN 0.008 0.11 -10000 0 -0.27 59 59
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.08 -10000 0 -0.55 5 5
MAP2K2 -0.033 0.091 0.17 8 -0.27 36 44
SMPD3 -0.021 0.1 0.16 2 -0.28 38 40
TNF -0.061 0.16 -10000 0 -0.43 62 62
PKC zeta/PAR4 0.006 0.083 -10000 0 -0.31 26 26
mol:PHOSPHOCHOLINE -0.012 0.088 0.19 26 -0.2 48 74
NF kappa B1/RelA/I kappa B alpha 0.045 0.073 -10000 0 -0.23 25 25
AIFM1 -0.043 0.094 -10000 0 -0.23 70 70
BCL2 0.021 0.043 -10000 0 -0.43 4 4
Glypican 2 network

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
MDK -0.004 0.1 -9999 0 -0.43 21 21
GPC2 0.002 0.087 -9999 0 -0.37 21 21
GPC2/Midkine 0 0.093 -9999 0 -0.32 34 34
neuron projection morphogenesis 0 0.093 -9999 0 -0.32 34 34
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.016 0.061 -10000 0 -0.43 8 8
LRPAP1 0.025 0.004 -10000 0 -10000 0 0
NUDC 0.022 0.01 -10000 0 -10000 0 0
RELN/LRP8 0.005 0.093 -10000 0 -0.25 48 48
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
KATNA1 0.025 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.008 0.11 0.18 74 -0.23 46 120
IQGAP1/CaM 0.034 0.027 -10000 0 -0.29 2 2
DAB1 -0.036 0.14 -10000 0 -0.36 68 68
IQGAP1 0.022 0.033 -10000 0 -0.23 6 6
PLA2G7 -0.007 0.11 -10000 0 -0.32 44 44
CALM1 0.025 0.009 -10000 0 -10000 0 0
DYNLT1 0.023 0.03 -10000 0 -0.43 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.031 0.022 -10000 0 -0.31 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.022 -10000 0 -0.43 1 1
CDK5R1 0.003 0.1 -10000 0 -0.42 24 24
LIS1/Poliovirus Protein 3A 0.01 0.002 -10000 0 -10000 0 0
CDK5R2 -0.052 0.16 -10000 0 -0.43 71 71
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.03 0.12 -10000 0 -0.27 91 91
YWHAE 0.026 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.017 0.18 0.32 70 -0.43 25 95
MAP1B 0.005 0.013 -10000 0 -0.26 1 1
RAC1 0.011 0.012 -10000 0 -0.15 2 2
p35/CDK5 -0.019 0.09 0.18 8 -0.23 54 62
RELN -0.043 0.14 -10000 0 -0.29 94 94
PAFAH/LIS1 0.01 0.067 0.17 1 -0.26 25 26
LIS1/CLIP170 0.027 0.015 -10000 0 -0.26 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.026 0.11 -10000 0 -0.37 23 23
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.067 0.15 -10000 0 -0.3 116 116
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.041 0.13 0.23 11 -0.46 25 36
LIS1/IQGAP1 0.025 0.022 -10000 0 -0.26 2 2
RHOA 0.013 0.012 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.01 -10000 0 -10000 0 0
PAFAH1B2 0.013 0.073 -10000 0 -0.43 12 12
MAP1B/LIS1/Dynein heavy chain 0.025 0.019 -10000 0 -0.17 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.022 0.18 0.32 69 -0.44 23 92
LRP8 0.021 0.023 -10000 0 -0.43 1 1
NDEL1/Katanin 60 0.016 0.18 0.32 71 -0.43 25 96
P39/CDK5 -0.035 0.11 0.21 10 -0.25 77 87
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.029 0.069 0.18 6 -0.22 44 50
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.013 -10000 0 -0.22 1 1
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.019 0.11 -10000 0 -0.24 84 84
RELN/VLDLR 0.008 0.095 -10000 0 -0.23 54 54
CDC42 0.009 0.032 -10000 0 -0.46 2 2
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.008 -10000 0 -10000 0 0
LAT2 -0.02 0.11 0.17 4 -0.39 24 28
AP1 -0.01 0.16 0.25 1 -0.58 20 21
mol:PIP3 -0.006 0.16 0.3 30 -0.46 25 55
IKBKB 0.006 0.11 0.24 34 -0.27 18 52
AKT1 -0.027 0.1 0.31 20 -0.34 5 25
IKBKG 0.002 0.1 0.23 24 -0.26 20 44
MS4A2 -0.006 0.037 -10000 0 -0.13 23 23
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 -0.004 0.13 0.32 9 -0.47 19 28
mol:Ca2+ 0.001 0.13 0.27 34 -0.34 25 59
LYN 0.021 0.037 -10000 0 -0.45 2 2
CBLB -0.016 0.1 -10000 0 -0.37 19 19
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RasGAP/p62DOK 0.041 0.048 -10000 0 -0.24 13 13
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
PLD2 -0.036 0.1 0.27 17 -0.23 54 71
PTPN13 -0.006 0.13 -10000 0 -0.53 15 15
PTPN11 0.021 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.1 0.27 18 -0.3 12 30
SYK 0.01 0.082 -10000 0 -0.44 14 14
GRB2 0.025 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.027 0.14 0.21 5 -0.46 25 30
LAT -0.026 0.11 -10000 0 -0.32 33 33
PAK2 -0.005 0.14 0.3 9 -0.53 19 28
NFATC2 -0.047 0.14 -10000 0 -0.52 36 36
HRAS -0.01 0.15 0.24 10 -0.59 19 29
GAB2 0.025 0.005 -10000 0 -10000 0 0
PLA2G1B 0.026 0.088 -10000 0 -0.8 4 4
Fc epsilon R1 -0.012 0.12 -10000 0 -0.26 72 72
Antigen/IgE/Fc epsilon R1 -0.004 0.11 -10000 0 -0.24 72 72
mol:GDP -0.012 0.16 0.25 3 -0.6 21 24
JUN 0.019 0.022 -10000 0 -0.13 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
FOS -0.03 0.14 -10000 0 -0.29 82 82
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.1 -10000 0 -0.36 22 22
CHUK 0.001 0.099 0.22 25 -0.26 20 45
KLRG1 -0.02 0.093 0.16 3 -0.33 21 24
VAV1 -0.023 0.12 0.17 2 -0.45 23 25
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.013 0.1 0.18 5 -0.38 18 23
negative regulation of mast cell degranulation 0.001 0.1 0.23 4 -0.41 13 17
BTK -0.017 0.16 -10000 0 -0.67 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.14 -10000 0 -0.28 99 99
GAB2/PI3K/SHP2 -0.043 0.075 -10000 0 -0.23 45 45
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.02 0.11 0.19 1 -0.25 62 63
RAF1 0.021 0.093 -10000 0 -0.92 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.016 0.16 -10000 0 -0.27 111 111
FCER1G 0.005 0.089 -10000 0 -0.34 25 25
FCER1A -0.052 0.15 -10000 0 -0.44 50 50
Antigen/IgE/Fc epsilon R1/Fyn 0.014 0.11 -10000 0 -0.24 63 63
MAPK3 0.025 0.087 -10000 0 -0.8 4 4
MAPK1 0.024 0.091 -10000 0 -0.83 4 4
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.006 0.14 -10000 0 -0.54 20 20
DUSP1 0.008 0.077 -10000 0 -0.25 29 29
NF-kappa-B/RelA 0.005 0.057 0.13 9 -0.17 14 23
actin cytoskeleton reorganization -0.003 0.12 -10000 0 -0.51 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.009 0.14 0.26 3 -0.53 18 21
FER -0.023 0.11 -10000 0 -0.32 30 30
RELA 0.025 0.005 -10000 0 -10000 0 0
ITK -0.025 0.097 -10000 0 -0.35 34 34
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.003 0.16 0.29 16 -0.62 19 35
cytokine secretion -0.002 0.037 -10000 0 -0.15 4 4
SPHK1 -0.025 0.11 0.2 1 -0.38 25 26
PTK2 -0.004 0.13 -10000 0 -0.55 15 15
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.013 0.15 0.24 10 -0.5 23 33
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.16 0.3 26 -0.46 21 47
MAP2K2 0.024 0.093 -10000 0 -0.8 4 4
MAP2K1 0.016 0.087 -10000 0 -0.86 4 4
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.1 0.19 18 -0.36 14 32
MAP2K4 0.032 0.066 -10000 0 -1.4 1 1
Fc epsilon R1/FcgammaRIIB -0.033 0.16 -10000 0 -0.29 110 110
mol:Choline -0.036 0.099 0.27 17 -0.23 54 71
SHC/Grb2/SOS1 0.022 0.11 -10000 0 -0.36 19 19
FYN 0.025 0.005 -10000 0 -10000 0 0
DOK1 0.025 0.021 -10000 0 -0.43 1 1
PXN -0.002 0.12 -10000 0 -0.5 16 16
HCLS1 -0.022 0.11 -10000 0 -0.4 25 25
PRKCB -0.003 0.13 0.26 25 -0.34 23 48
FCGR2B -0.058 0.16 -10000 0 -0.27 131 131
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.001 0.11 0.23 4 -0.42 13 17
LCP2 0.02 0.034 -10000 0 -0.43 1 1
PLA2G4A -0.023 0.11 -10000 0 -0.37 29 29
RASA1 0.026 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.036 0.099 0.27 17 -0.23 54 71
IKK complex 0.009 0.092 0.24 32 -0.21 15 47
WIPF1 0.026 0.002 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.024 0.078 0.22 62 -0.091 6 68
BUB1B -0.031 0.1 0.12 2 -0.27 68 70
PLK1 0.003 0.032 0.079 21 -0.12 9 30
PLK1S1 0.007 0.029 0.11 3 -0.18 4 7
KIF2A 0 0.04 0.23 4 -0.2 5 9
regulation of mitotic centrosome separation 0.003 0.032 0.079 21 -0.12 9 30
GOLGA2 0.025 0.004 -10000 0 -10000 0 0
Hec1/SPC24 -0.037 0.14 -10000 0 -0.29 94 94
WEE1 -0.001 0.082 -10000 0 -0.35 21 21
cytokinesis -0.068 0.16 0.19 2 -0.38 93 95
PP2A-alpha B56 -0.036 0.23 -10000 0 -0.63 59 59
AURKA 0.008 0.026 0.1 2 -0.34 1 3
PICH/PLK1 -0.007 0.063 0.16 6 -0.22 23 29
CENPE -0.016 0.059 0.11 1 -0.25 22 23
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.04 0.23 4 -0.2 5 9
PPP2CA 0.026 0.003 -10000 0 -10000 0 0
FZR1 0.025 0.005 -10000 0 -10000 0 0
TPX2 -0.007 0.074 0.12 6 -0.27 30 36
PAK1 0.008 0.063 -10000 0 -0.44 5 5
SPC24 -0.048 0.15 -10000 0 -0.43 53 53
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.047 0.12 0.13 2 -0.26 102 104
GORASP1 0.025 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 2 -0.018 4 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.018 0.046 22 -0.06 10 32
G2 phase of mitotic cell cycle 0 0.002 0.013 3 -0.01 1 4
STAG2 0.026 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.013 0.07 -10000 0 -0.5 8 8
spindle elongation 0.003 0.032 0.079 21 -0.12 9 30
ODF2 0.026 0.005 -10000 0 -10000 0 0
BUB1 -0.057 0.24 -10000 0 -0.68 58 58
TPT1 -0.001 0.044 -10000 0 -0.18 21 21
CDC25C -0.032 0.12 0.14 1 -0.37 54 55
CDC25B 0.025 0.006 -10000 0 -10000 0 0
SGOL1 -0.024 0.078 0.091 6 -0.22 62 68
RHOA 0.025 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.041 -10000 0 -0.22 6 6
CDC14B 0.007 0.002 -10000 0 -10000 0 0
CDC20 -0.027 0.12 -10000 0 -0.25 81 81
PLK1/PBIP1 -0.015 0.064 0.087 1 -0.22 34 35
mitosis -0.002 0.003 0.023 2 -10000 0 2
FBXO5 0 0.031 0.11 2 -0.14 6 8
CDC2 0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.057 0.16 -10000 0 -0.43 66 66
metaphase plate congression -0.023 0.087 -10000 0 -0.23 66 66
ERCC6L -0.002 0.063 0.26 1 -0.22 22 23
NLP/gamma Tubulin 0.003 0.021 0.067 9 -0.087 6 15
microtubule cytoskeleton organization -0.001 0.044 -10000 0 -0.18 21 21
G2/M transition DNA damage checkpoint 0 0.002 0.013 2 -10000 0 2
PPP1R12A 0.026 0.003 -10000 0 -10000 0 0
interphase 0 0.002 0.013 2 -10000 0 2
PLK1/PRC1-2 -0.017 0.11 0.13 1 -0.23 92 93
GRASP65/GM130/RAB1/GTP/PLK1 0.037 0.036 -10000 0 -0.17 1 1
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.027 0.075 27 -0.089 8 35
mitotic prometaphase 0.002 0.007 0.018 66 -0.012 3 69
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.062 0.21 1 -0.26 9 10
microtubule-based process -0.035 0.11 0.11 3 -0.24 91 94
Golgi organization 0.003 0.032 0.079 21 -0.12 9 30
Cohesin/SA2 0.017 0.029 0.096 2 -0.12 5 7
PPP1CB/MYPT1 0.039 0.005 -10000 0 -10000 0 0
KIF20A -0.082 0.18 -10000 0 -0.3 150 150
APC/C/CDC20 -0.004 0.075 0.12 2 -0.23 36 38
PPP2R1A 0.021 0.01 -10000 0 -10000 0 0
chromosome segregation -0.014 0.063 0.086 1 -0.22 34 35
PRC1 0.019 0.031 -10000 0 -10000 0 0
ECT2 0.001 0.038 0.2 6 -0.17 3 9
C13orf34 0.003 0.027 0.071 24 -0.097 9 33
NUDC -0.023 0.088 -10000 0 -0.23 66 66
regulation of attachment of spindle microtubules to kinetochore -0.031 0.1 0.12 2 -0.27 68 70
spindle assembly 0.002 0.027 0.083 11 -0.1 8 19
spindle stabilization 0.007 0.029 0.11 3 -0.18 4 7
APC/C/HCDH1 0.023 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 -0.035 0.11 0.11 3 -0.24 91 94
CCNB1 0.017 0.036 -10000 0 -0.13 18 18
PPP1CB 0.026 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.006 -10000 0 -10000 0 0
ROCK2 -0.001 0.077 -10000 0 -0.38 16 16
TUBG1 0.007 0.021 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle -0.003 0.034 -10000 0 -0.23 5 5
MLF1IP -0.02 0.081 -10000 0 -0.31 31 31
INCENP 0.024 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.011 0.073 -10000 0 -0.22 40 40
RGS9BP 0.017 0.048 -10000 0 -0.43 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.02 0.026 -10000 0 -0.43 1 1
mol:Na + -0.019 0.088 -10000 0 -0.26 45 45
mol:ADP 0.005 0.021 -10000 0 -0.31 1 1
GNAT2 0.015 0.018 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.018 0.09 -10000 0 -0.27 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.02 0.023 -10000 0 -0.13 1 1
GRK7 0.018 0.021 -10000 0 -10000 0 0
CNGB3 0.005 0.031 -10000 0 -0.13 15 15
Cone Metarhodopsin II/X-Arrestin 0.013 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.054 0.11 0.18 17 -0.26 82 99
Cone PDE6 0.033 0.087 -10000 0 -0.24 37 37
Cone Metarhodopsin II 0.029 0.017 -10000 0 -0.23 1 1
Na + (4 Units) -0.023 0.12 -10000 0 -0.24 95 95
GNAT2/GDP 0.024 0.08 -10000 0 -0.22 37 37
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.004 0.029 0.18 7 -10000 0 7
Cone Transducin 0.012 0.079 -10000 0 -0.23 40 40
SLC24A2 -0.042 0.15 -10000 0 -0.3 93 93
GNB3/GNGT2 0.003 0.099 -10000 0 -0.31 41 41
GNB3 -0.003 0.11 -10000 0 -0.4 30 30
GNAT2/GTP 0.014 0.01 -10000 0 -10000 0 0
CNGA3 -0.048 0.14 -10000 0 -0.43 48 48
ARR3 -0.008 0.018 -10000 0 -0.13 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.088 -10000 0 -0.26 45 45
mol:Pi 0.018 0.09 -10000 0 -0.27 38 38
Cone CNG Channel 0.01 0.081 -10000 0 -0.21 41 41
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.042 0.15 -10000 0 -0.3 93 93
RGS9 -0.012 0.12 -10000 0 -0.39 41 41
PDE6C 0.003 0.025 -10000 0 -0.13 5 5
GNGT2 0.009 0.081 -10000 0 -0.31 23 23
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.006 0.033 -10000 0 -0.13 18 18
a4b1 and a4b7 Integrin 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
ITGB1 0.023 0.012 -9999 0 -0.13 2 2
ITGB7 0 0.095 -9999 0 -0.43 19 19
ITGA4 -0.01 0.11 -9999 0 -0.43 25 25
alpha4/beta7 Integrin -0.008 0.11 -9999 0 -0.28 55 55
alpha4/beta1 Integrin 0.011 0.079 -9999 0 -0.29 25 25
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.046 0.029 -10000 0 -0.24 3 3
fibroblast growth factor receptor signaling pathway 0.046 0.029 -10000 0 -0.24 3 3
LAMA1 -0.019 0.13 -10000 0 -0.36 53 53
PRNP 0.024 0.022 -10000 0 -0.43 1 1
GPC1/SLIT2 -0.017 0.11 -10000 0 -0.3 52 52
SMAD2 0.017 0.032 0.18 12 -0.24 1 13
GPC1/PrPc/Cu2+ 0.031 0.019 -10000 0 -0.26 1 1
GPC1/Laminin alpha1 0.002 0.099 -10000 0 -0.3 41 41
TDGF1 -0.032 0.14 -10000 0 -0.36 69 69
CRIPTO/GPC1 -0.007 0.11 -10000 0 -0.31 52 52
APP/GPC1 0.036 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.089 -10000 0 -0.27 49 49
FLT1 0.024 0.022 -10000 0 -0.43 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.022 -10000 0 -0.19 2 2
SERPINC1 0.016 0.027 -10000 0 -10000 0 0
FYN -0.017 0.086 -10000 0 -0.26 49 49
FGR -0.015 0.079 -10000 0 -0.26 41 41
positive regulation of MAPKKK cascade -0.054 0.16 0.23 17 -0.39 55 72
SLIT2 -0.045 0.15 -10000 0 -0.43 52 52
GPC1/NRG -0.043 0.13 -10000 0 -0.3 89 89
NRG1 -0.079 0.18 -10000 0 -0.43 88 88
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.018 -10000 0 -10000 0 0
LYN -0.021 0.09 -10000 0 -0.26 52 52
mol:Spermine 0.006 0.008 -10000 0 -10000 0 0
cell growth 0.046 0.029 -10000 0 -0.24 3 3
BMP signaling pathway -0.024 0.015 0.13 4 -10000 0 4
SRC -0.016 0.083 -10000 0 -0.26 46 46
TGFBR1 0.024 0.023 -10000 0 -0.43 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.029 0.081 -10000 0 -0.18 76 76
GPC1 0.024 0.015 -10000 0 -0.13 4 4
TGFBR1 (dimer) 0.024 0.023 -10000 0 -0.43 1 1
VEGFA 0.019 0.032 -10000 0 -0.13 21 21
BLK -0.049 0.11 -10000 0 -0.28 70 70
HCK -0.023 0.095 -10000 0 -0.28 51 51
FGF2 0.023 0.031 -10000 0 -0.43 2 2
FGFR1 0.024 0.022 -10000 0 -0.43 1 1
VEGFR1 homodimer 0.024 0.022 -10000 0 -0.43 1 1
TGFBR2 0.024 0.016 -10000 0 -10000 0 0
cell death 0.036 0.014 -10000 0 -10000 0 0
ATIII/GPC1 0.031 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 0.002 0.066 -10000 0 -0.28 15 15
LCK -0.039 0.11 -10000 0 -0.28 70 70
neuron differentiation -0.043 0.13 -10000 0 -0.3 89 89
PrPc/Cu2+ 0.018 0.016 -10000 0 -0.3 1 1
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.016 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.17 0.37 1 -1.1 8 9
VDR -0.015 0.11 -10000 0 -0.43 28 28
FAM120B 0.025 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.34 80 80
RXRs/LXRs/DNA/Oxysterols -0.075 0.22 -10000 0 -0.51 79 79
MED1 0.026 0.003 -10000 0 -10000 0 0
mol:9cRA -0.006 0.02 -10000 0 -0.098 1 1
RARs/THRs/DNA/Src-1 0.022 0.044 -10000 0 -0.22 14 14
RXRs/NUR77 0.01 0.11 -10000 0 -0.26 49 49
RXRs/PPAR -0.014 0.1 -10000 0 -0.32 28 28
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.3 28 28
RARs/VDR/DNA/Vit D3 0.041 0.072 -10000 0 -0.22 30 30
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA -0.015 0.11 -10000 0 -0.43 28 28
RARs/RARs/DNA/9cRA 0.034 0.035 -10000 0 -0.22 4 4
RARG 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.025 0.11 0.58 13 -0.43 8 21
RARs/THRs/DNA/SMRT 0.022 0.044 -10000 0 -0.22 14 14
THRA 0.023 0.037 -10000 0 -0.43 3 3
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.3 28 28
RXRs/PPAR/9cRA/PGJ2/DNA -0.005 0.11 -10000 0 -0.25 53 53
NR1H4 -0.042 0.13 -10000 0 -0.23 118 118
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.33 22 22
NR1H2 0.015 0.026 -10000 0 -10000 0 0
NR1H3 0.015 0.031 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.004 0.12 -10000 0 -0.25 67 67
NR4A1 0.01 0.065 -10000 0 -0.19 32 32
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.037 0.11 -10000 0 -0.27 61 61
RXRG -0.035 0.14 -10000 0 -0.43 51 51
RXR alpha/CCPG 0.026 0.028 -10000 0 -10000 0 0
RXRA 0.015 0.03 -10000 0 -10000 0 0
RXRB 0.015 0.031 -10000 0 -10000 0 0
THRB 0.015 0.058 -10000 0 -0.22 20 20
PPARG 0.009 0.08 -10000 0 -0.34 20 20
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF -0.16 0.37 -10000 0 -1 70 70
mol:Oxysterols -0.006 0.019 -10000 0 -10000 0 0
cholesterol transport -0.074 0.22 -10000 0 -0.5 79 79
PPARA 0.026 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.022 0.043 -10000 0 -0.43 4 4
RXRs/NUR77/BCL2 -0.015 0.094 -10000 0 -0.26 51 51
SREBF1 -0.086 0.25 -10000 0 -0.72 43 43
RXRs/RXRs/DNA/9cRA -0.005 0.11 -10000 0 -0.25 53 53
ABCA1 -0.088 0.25 -10000 0 -0.68 51 51
RARs/THRs 0.066 0.052 -10000 0 -0.22 13 13
RXRs/FXR -0.01 0.14 -10000 0 -0.28 78 78
BCL2 0.021 0.043 -10000 0 -0.43 4 4
Noncanonical Wnt signaling pathway

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
NFATC2 -0.02 0.13 -10000 0 -0.43 38 38
GNB1/GNG2 0.017 0.1 -10000 0 -0.27 33 33
mol:DAG 0.001 0.092 0.21 12 -0.26 27 39
PLCG1 0.001 0.094 0.21 12 -0.27 27 39
YES1 -0.015 0.085 -10000 0 -0.27 39 39
FZD3 0.022 0.037 -10000 0 -0.43 3 3
FZD6 0.015 0.039 -10000 0 -0.43 1 1
G protein 0.023 0.1 0.26 1 -0.28 26 27
MAP3K7 -0.048 0.11 0.21 13 -0.28 34 47
mol:Ca2+ 0.001 0.09 0.2 12 -0.26 27 39
mol:IP3 0.001 0.092 0.21 12 -0.26 27 39
NLK 0.01 0.046 -10000 0 -0.95 1 1
GNB1 0.022 0.01 -10000 0 -10000 0 0
CAMK2A -0.049 0.11 0.2 12 -0.28 48 60
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.01 0.091 -10000 0 -0.28 43 43
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
GNAS -0.015 0.083 0.16 1 -0.27 40 41
GO:0007205 -0.007 0.091 0.2 12 -0.27 25 37
WNT6 0.001 0.091 -10000 0 -0.43 17 17
WNT4 0.009 0.055 -10000 0 -0.43 4 4
NFAT1/CK1 alpha -0.004 0.12 0.35 2 -0.31 31 33
GNG2 0.022 0.043 -10000 0 -0.43 4 4
WNT5A 0.008 0.083 -10000 0 -0.33 22 22
WNT11 0.008 0.081 -10000 0 -0.43 14 14
CDC42 0 0.07 -10000 0 -0.29 15 15
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.011 0.097 0.23 55 -10000 0 55
GNAI2 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.093 -10000 0 -0.26 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.052 -10000 0 -0.43 6 6
RhoA/GTP -0.011 0.099 -10000 0 -0.23 55 55
negative regulation of cAMP metabolic process -0.02 0.1 -10000 0 -0.24 61 61
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNA12 0.022 0.009 -10000 0 -10000 0 0
S1PR5 -0.054 0.16 -10000 0 -0.29 114 114
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.02 0.1 -10000 0 -0.25 61 61
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
Ephrin B reverse signaling

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
EFNB2 0.021 0.03 -10000 0 -0.43 1 1
EPHB2 0.016 0.042 -10000 0 -0.44 3 3
EFNB1 -0.027 0.088 -10000 0 -0.31 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.097 -10000 0 -0.25 45 45
Ephrin B2/EPHB1-2 0.015 0.084 -10000 0 -0.25 38 38
neuron projection morphogenesis -0.011 0.087 -10000 0 -0.24 45 45
Ephrin B1/EPHB1-2/Tiam1 -0.011 0.11 -10000 0 -0.26 61 61
DNM1 -0.032 0.12 -10000 0 -0.23 102 102
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.011 0.091 -10000 0 -0.52 13 13
YES1 -0.007 0.14 -10000 0 -0.77 13 13
Ephrin B1/EPHB1-2/NCK2 -0.011 0.11 -10000 0 -0.26 62 62
PI3K 0.025 0.097 -10000 0 -0.52 13 13
mol:GDP -0.012 0.11 -10000 0 -0.26 61 61
ITGA2B -0.014 0.12 -10000 0 -0.43 36 36
endothelial cell proliferation 0.025 0.022 -10000 0 -0.26 1 1
FYN -0.006 0.13 -10000 0 -0.75 13 13
MAP3K7 -0.012 0.095 0.22 1 -0.55 13 14
FGR -0.01 0.13 -10000 0 -0.76 13 13
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RGS3 0.025 0.013 -10000 0 -10000 0 0
cell adhesion -0.015 0.12 -10000 0 -0.42 21 21
LYN -0.005 0.13 -10000 0 -0.75 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.12 -10000 0 -0.69 13 13
Ephrin B1/EPHB1-2 -0.012 0.1 -10000 0 -0.59 13 13
SRC -0.006 0.13 -10000 0 -0.74 13 13
ITGB3 -0.003 0.088 -10000 0 -0.2 59 59
EPHB1 -0.01 0.12 -10000 0 -0.43 36 36
EPHB4 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.023 -10000 0 -0.26 1 1
alphaIIb/beta3 Integrin -0.013 0.11 -10000 0 -0.32 50 50
BLK -0.012 0.13 -10000 0 -0.74 13 13
HCK -0.006 0.13 -10000 0 -0.76 13 13
regulation of stress fiber formation 0.012 0.11 0.26 62 -10000 0 62
MAPK8 -0.015 0.094 -10000 0 -0.51 13 13
Ephrin B1/EPHB1-2/RGS3 -0.011 0.11 -10000 0 -0.26 62 62
endothelial cell migration 0.024 0.11 0.27 10 -0.43 12 22
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTPN13 0.021 0.062 -10000 0 -0.56 5 5
regulation of focal adhesion formation 0.012 0.11 0.26 62 -10000 0 62
chemotaxis 0.012 0.11 0.26 62 -10000 0 62
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.092 -10000 0 -0.24 45 45
angiogenesis -0.011 0.1 -10000 0 -0.58 13 13
LCK -0.022 0.14 -10000 0 -0.77 13 13
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.008 0.053 -10000 0 -0.25 17 17
NFATC2 -0.021 0.073 -10000 0 -0.26 34 34
NFATC3 0.002 0.023 -10000 0 -0.13 1 1
CD40LG -0.07 0.14 0.32 3 -0.37 41 44
PTGS2 -0.09 0.18 0.36 1 -0.45 62 63
JUNB 0.005 0.075 -10000 0 -0.2 40 40
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.018 -10000 0 -10000 0 0
CALM1 0.02 0.016 -10000 0 -10000 0 0
JUN 0.015 0.024 -10000 0 -0.13 6 6
mol:Ca2+ -0.003 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.005 -10000 0 -10000 0 0
FOSL1 -0.028 0.13 -10000 0 -0.43 36 36
CREM 0.023 0.023 -10000 0 -0.43 1 1
Jun/NFAT1-c-4/p21SNFT -0.026 0.12 -10000 0 -0.35 26 26
FOS -0.035 0.14 -10000 0 -0.29 82 82
IFNG -0.069 0.14 0.29 2 -0.37 39 41
AP-1/NFAT1-c-4 -0.056 0.16 -10000 0 -0.41 41 41
FASLG -0.071 0.14 0.36 1 -0.37 41 42
NFAT1-c-4/ICER1 -0.023 0.093 -10000 0 -0.24 45 45
IL2RA -0.073 0.14 0.32 3 -0.38 51 54
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.07 0.14 0.33 2 -0.37 37 39
JunB/Fra1/NFAT1-c-4 -0.035 0.13 0.19 4 -0.27 77 81
IL4 -0.069 0.14 0.33 2 -0.37 37 39
IL2 -0.012 0.14 -10000 0 -0.92 11 11
IL3 0.011 0.059 -10000 0 -0.68 3 3
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
BATF3 0 0.093 -10000 0 -0.43 18 18
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.004 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.016 0.1 -10000 0 -0.26 49 49
MAP4K1 0.013 0.061 -10000 0 -0.33 12 12
MAP3K8 0.017 0.04 -10000 0 -0.16 16 16
PRKCB -0.008 0.1 -10000 0 -0.22 64 64
DBNL 0.022 0.009 -10000 0 -10000 0 0
CRKL 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 -0.008 0.086 0.17 1 -0.36 11 12
JUN -0.024 0.17 -10000 0 -0.6 34 34
MAP3K7 -0.008 0.085 -10000 0 -0.36 11 11
GRAP2 -0.008 0.1 -10000 0 -0.26 54 54
CRK 0.026 0.002 -10000 0 -10000 0 0
MAP2K4 -0.004 0.094 0.27 3 -0.36 12 15
LAT 0 0.11 -10000 0 -0.43 26 26
LCP2 0.02 0.034 -10000 0 -0.43 1 1
MAPK8 -0.022 0.18 -10000 0 -0.61 37 37
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.003 0.092 -10000 0 -0.29 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55 0.024 0.099 -10000 0 -0.25 44 44
Retinoic acid receptors-mediated signaling

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
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC3 0.026 0.003 -10000 0 -10000 0 0
VDR -0.015 0.11 -10000 0 -0.43 28 28
Cbp/p300/PCAF 0.048 0.031 -10000 0 -0.26 4 4
EP300 0.022 0.043 -10000 0 -0.43 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.075 -10000 0 -0.4 9 9
KAT2B 0.025 0.008 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.011 0.075 0.19 7 -0.35 8 15
RAR alpha/9cRA/Cyclin H -0.006 0.11 -10000 0 -0.4 8 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.064 0.18 1 -0.32 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.023 0.099 -10000 0 -0.4 15 15
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.3 28 28
RXRs/RARs/NRIP1/9cRA -0.072 0.18 -10000 0 -0.44 71 71
NCOA2 -0.004 0.11 -10000 0 -0.43 29 29
NCOA3 0.025 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA -0.015 0.11 -10000 0 -0.43 28 28
RARG 0.026 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.002 -10000 0 -10000 0 0
MAPK1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.016 0.067 -10000 0 -0.43 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.083 0.2 -10000 0 -0.43 92 92
RARA -0.022 0.095 -10000 0 -0.24 63 63
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.011 0.091 0.18 1 -0.36 17 18
PRKCA 0.026 0.022 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.077 0.19 -10000 0 -0.45 71 71
RXRG -0.058 0.16 -10000 0 -0.38 79 79
RXRA -0.023 0.083 -10000 0 -0.21 61 61
RXRB -0.025 0.097 -10000 0 -0.28 55 55
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.3 28 28
RBP1 -0.006 0.081 -10000 0 -0.16 77 77
CRBP1/9-cic-RA -0.002 0.055 -10000 0 -0.11 77 77
RARB 0.023 0.043 -10000 0 -0.43 4 4
PRKCG -0.062 0.15 -10000 0 -0.43 57 57
MNAT1 0.025 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.076 0.19 -10000 0 -0.44 76 76
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.057 0.16 -10000 0 -0.38 62 62
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.096 0.21 2 -0.34 17 19
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.072 0.19 -10000 0 -0.44 72 72
positive regulation of DNA binding -0.012 0.099 -10000 0 -0.37 8 8
NRIP1 -0.063 0.18 -10000 0 -0.58 22 22
RXRs/RARs -0.072 0.19 -10000 0 -0.44 73 73
RXRs/RXRs/DNA/9cRA -0.083 0.18 -10000 0 -0.42 86 86
PRKACA 0.025 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.003 -10000 0 -10000 0 0
TFIIH 0.05 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.009 0.09 -10000 0 -0.32 7 7
CCNH 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.002 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.017 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.01 0.2 0.48 6 -0.68 12 18
CRP -0.017 0.2 0.59 5 -0.68 12 17
cell cycle arrest -0.023 0.22 0.48 3 -0.71 19 22
TIMP1 -0.019 0.21 0.44 2 -0.71 21 23
IL6ST -0.005 0.1 -10000 0 -0.43 25 25
Rac1/GDP -0.053 0.17 -10000 0 -0.43 52 52
AP1 0.032 0.1 -10000 0 -0.81 1 1
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.019 0.2 0.48 2 -0.7 11 13
HSP90B1 0.011 0.17 -10000 0 -0.92 13 13
GAB1 0.025 0.022 -10000 0 -0.43 1 1
MAPK14 -0.078 0.2 -10000 0 -0.57 52 52
AKT1 0.035 0.047 -10000 0 -0.7 1 1
FOXO1 0.034 0.051 -10000 0 -0.66 1 1
MAP2K6 -0.064 0.17 0.2 1 -0.46 55 56
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.052 0.17 0.29 3 -0.45 48 51
MITF -0.053 0.16 -10000 0 -0.42 52 52
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.005 -10000 0 -10000 0 0
A2M 0.016 0.086 -10000 0 -1.2 2 2
CEBPB 0.017 0.075 -10000 0 -0.43 12 12
GRB2/SOS1/GAB family/SHP2 0.006 0.083 -10000 0 -0.56 3 3
STAT3 -0.03 0.23 0.53 2 -0.75 20 22
STAT1 0.015 0.047 -10000 0 -0.9 1 1
CEBPD -0.046 0.3 0.52 2 -1 30 32
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.007 -10000 0 -10000 0 0
JUN 0.019 0.022 -10000 0 -0.13 8 8
PIAS3/MITF -0.034 0.16 -10000 0 -0.43 42 42
MAPK11 -0.079 0.2 -10000 0 -0.57 52 52
STAT3 (dimer)/FOXO1 -0.011 0.17 -10000 0 -0.58 13 13
GRB2/SOS1/GAB family -0.016 0.16 -10000 0 -0.43 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.049 0.16 -10000 0 -0.44 46 46
GRB2 0.025 0.005 -10000 0 -10000 0 0
JAK2 0.025 0.006 -10000 0 -10000 0 0
LBP 0 0.19 0.46 5 -0.65 14 19
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.017 -10000 0 -10000 0 0
MYC -0.024 0.28 0.5 3 -0.89 31 34
FGG -0.021 0.2 0.49 2 -0.68 12 14
macrophage differentiation -0.023 0.22 0.48 3 -0.71 19 22
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.001 0.12 -10000 0 -0.27 57 57
JUNB -0.022 0.24 0.46 8 -0.8 20 28
FOS -0.03 0.14 -10000 0 -0.29 82 82
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.055 0.16 0.23 1 -0.42 57 58
STAT1/PIAS1 -0.025 0.16 0.24 1 -0.45 35 36
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.049 -10000 0 -0.74 1 1
STAT3 (dimer) -0.026 0.23 0.52 2 -0.75 19 21
PRKCD -0.028 0.23 0.36 38 -0.55 45 83
IL6R 0.006 0.077 -10000 0 -0.32 19 19
SOCS3 -0.1 0.32 0.39 2 -1.1 38 40
gp130 (dimer)/JAK1/JAK1/LMO4 0.021 0.074 -10000 0 -0.24 25 25
Rac1/GTP -0.053 0.17 -10000 0 -0.44 52 52
HCK 0.013 0.067 -10000 0 -0.43 9 9
MAPKKK cascade 0.031 0.082 -10000 0 -0.96 1 1
bone resorption -0.017 0.19 0.48 2 -0.64 12 14
IRF1 -0.017 0.2 0.5 3 -0.67 13 16
mol:GDP -0.061 0.17 0.2 1 -0.43 58 59
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.061 0.17 0.21 1 -0.44 58 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.26 -10000 0 -0.5 100 100
PTPN11 0.009 0.076 -10000 0 -0.69 5 5
IL6/IL6RA -0.029 0.12 -10000 0 -0.32 52 52
gp130 (dimer)/TYK2/TYK2/LMO4 0.023 0.07 -10000 0 -0.25 23 23
gp130 (dimer)/JAK2/JAK2/LMO4 0.022 0.071 -10000 0 -0.25 24 24
IL6 -0.045 0.13 -10000 0 -0.43 42 42
PIAS3 0.023 0.008 -10000 0 -10000 0 0
PTPRE 0.023 0.025 -10000 0 -0.44 1 1
PIAS1 0.022 0.042 -10000 0 -0.43 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.038 0.12 0.21 1 -0.31 63 64
LMO4 0.018 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.029 0.21 -10000 0 -0.69 21 21
MCL1 0.04 0.057 -10000 0 -0.62 1 1
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.053 0.24 -10000 0 -0.8 33 33
NCK1/PAK1/Dok-R -0.053 0.11 -10000 0 -0.39 34 34
NCK1/Dok-R -0.043 0.27 -10000 0 -1.1 26 26
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol 0.008 0.051 0.23 23 -10000 0 23
RELA 0.025 0.005 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
F2 0.01 0.06 0.25 21 -10000 0 21
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.017 0.25 -10000 0 -0.97 26 26
FN1 0.02 0.029 -10000 0 -0.13 17 17
PLD2 -0.051 0.26 -10000 0 -1.1 26 26
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 -0.07 0.16 -10000 0 -0.43 63 63
ELK1 -0.044 0.24 -10000 0 -0.97 26 26
GRB7 0.003 0.042 -10000 0 -0.13 36 36
PAK1 0.007 0.063 -10000 0 -0.43 5 5
Tie2/Ang1/alpha5/beta1 Integrin -0.024 0.26 -10000 0 -1 26 26
CDKN1A -0.069 0.25 -10000 0 -0.66 60 60
ITGA5 0.016 0.048 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.044 0.27 -10000 0 -1.1 26 26
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:NO -0.005 0.2 0.35 2 -0.56 36 38
PLG -0.055 0.26 -10000 0 -1.1 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.044 0.22 -10000 0 -0.82 27 27
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.003 -10000 0 -10000 0 0
ANGPT2 -0.071 0.26 -10000 0 -0.78 40 40
BMX -0.06 0.26 -10000 0 -1.1 26 26
ANGPT1 -0.07 0.29 -10000 0 -1.2 24 24
tube development -0.061 0.22 -10000 0 -0.68 44 44
ANGPT4 -0.01 0.1 -10000 0 -0.27 51 51
response to hypoxia -0.005 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.072 0.29 -10000 0 -1.2 26 26
alpha5/beta1 Integrin 0.028 0.038 -10000 0 -0.27 4 4
FGF2 0.023 0.031 -10000 0 -0.43 2 2
STAT5A (dimer) -0.072 0.28 -10000 0 -0.74 59 59
mol:L-citrulline -0.005 0.2 0.35 2 -0.56 36 38
AGTR1 -0.004 0.1 -10000 0 -0.3 39 39
MAPK14 -0.047 0.27 -10000 0 -1.1 27 27
Tie2/SHP2 -0.014 0.19 -10000 0 -1.1 10 10
TEK -0.015 0.2 -10000 0 -1.2 10 10
RPS6KB1 -0.041 0.23 -10000 0 -0.81 28 28
Angiotensin II/AT1 -0.003 0.072 -10000 0 -0.25 30 30
Tie2/Ang1/GRB2 -0.042 0.28 -10000 0 -1.1 26 26
MAPK3 -0.048 0.24 -10000 0 -1 26 26
MAPK1 -0.049 0.24 -10000 0 -1 26 26
Tie2/Ang1/GRB7 -0.046 0.28 -10000 0 -1.1 26 26
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.054 0.27 -10000 0 -1.1 26 26
PI3K -0.053 0.26 -10000 0 -0.98 27 27
FES -0.051 0.27 -10000 0 -1.1 27 27
Crk/Dok-R -0.043 0.27 -10000 0 -1.1 26 26
Tie2/Ang1/ABIN2 -0.042 0.28 -10000 0 -1.1 26 26
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.046 0.22 -10000 0 -0.68 39 39
STAT5A 0.015 0.067 -10000 0 -0.4 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.03 0.24 0.44 1 -0.81 28 29
Tie2/Ang2 -0.085 0.3 -10000 0 -0.94 44 44
Tie2/Ang1 -0.052 0.28 -10000 0 -1.2 26 26
FOXO1 -0.053 0.23 -10000 0 -0.71 44 44
ELF1 0.027 0.019 -10000 0 -10000 0 0
ELF2 -0.047 0.26 -10000 0 -1.1 26 26
mol:Choline -0.048 0.25 -10000 0 -1 26 26
cell migration -0.028 0.063 -10000 0 -0.22 32 32
FYN -0.072 0.25 -10000 0 -0.78 44 44
DOK2 -0.017 0.11 -10000 0 -0.24 72 72
negative regulation of cell cycle -0.06 0.22 -10000 0 -0.6 60 60
ETS1 0.009 0.071 -10000 0 -0.26 25 25
PXN -0.017 0.21 0.42 3 -0.68 28 31
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
NOS3 -0.013 0.22 -10000 0 -0.64 35 35
RAC1 0.023 0.009 -10000 0 -10000 0 0
TNF -0.071 0.17 -10000 0 -0.43 76 76
MAPKKK cascade -0.048 0.25 -10000 0 -1 26 26
RASA1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.045 0.28 -10000 0 -1.1 26 26
NCK1 0.025 0.022 -10000 0 -0.43 1 1
vasculogenesis 0.001 0.18 0.34 2 -0.51 36 38
mol:Phosphatidic acid -0.048 0.25 -10000 0 -1 26 26
mol:Angiotensin II -0.001 0.006 -10000 0 -10000 0 0
mol:NADP -0.005 0.2 0.35 2 -0.56 36 38
Rac1/GTP -0.037 0.21 -10000 0 -0.75 28 28
MMP2 -0.056 0.26 -10000 0 -1.1 26 26
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.033 0.1 -10000 0 -0.23 54 54
SMAD6-7/SMURF1 0.039 0.031 -10000 0 -0.26 2 2
NOG -0.029 0.14 -10000 0 -0.43 52 52
SMAD9 -0.046 0.18 -10000 0 -0.5 51 51
SMAD4 0.025 0.004 -10000 0 -10000 0 0
SMAD5 -0.022 0.11 -10000 0 -0.38 20 20
BMP7/USAG1 -0.007 0.092 -10000 0 -0.31 32 32
SMAD5/SKI -0.013 0.11 -10000 0 -0.37 21 21
SMAD1 0.018 0.052 -10000 0 -0.42 2 2
BMP2 -0.035 0.15 -10000 0 -0.43 60 60
SMAD1/SMAD1/SMAD4 0.023 0.052 -10000 0 -0.31 3 3
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B 0.002 0.1 -10000 0 -0.43 24 24
BMPR1A-1B/BAMBI 0.03 0.071 -10000 0 -0.26 23 23
AHSG -0.025 0.13 -10000 0 -0.3 69 69
CER1 -0.001 0.032 -10000 0 -0.13 18 18
BMP2-4/CER1 -0.006 0.13 -10000 0 -0.32 62 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.035 0.13 -10000 0 -0.43 31 31
BMP2-4 (homodimer) -0.018 0.14 -10000 0 -0.36 62 62
RGMB 0.019 0.049 -10000 0 -0.3 9 9
BMP6/BMPR2/BMPR1A-1B 0.044 0.074 -10000 0 -0.24 26 26
RGMA 0.015 0.067 -10000 0 -0.43 10 10
SMURF1 0.021 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.028 0.13 -10000 0 -0.39 36 36
BMP2-4/USAG1 -0.011 0.13 -10000 0 -0.3 73 73
SMAD6/SMURF1/SMAD5 -0.011 0.099 -10000 0 -0.38 17 17
SOSTDC1 -0.026 0.12 -10000 0 -0.43 28 28
BMP7/BMPR2/BMPR1A-1B 0.042 0.074 -10000 0 -0.24 28 28
SKI 0.022 0.01 -10000 0 -10000 0 0
BMP6 (homodimer) 0.018 0.048 -10000 0 -0.43 4 4
HFE2 0.012 0.024 -10000 0 -10000 0 0
ZFYVE16 0.026 0.003 -10000 0 -10000 0 0
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD -0.001 0.13 -10000 0 -0.31 63 63
SMAD5/SMAD5/SMAD4 -0.015 0.11 -10000 0 -0.36 23 23
MAPK1 0.026 0.003 -10000 0 -10000 0 0
TAK1/TAB family -0.013 0.1 -10000 0 -0.36 22 22
BMP7 (homodimer) 0.02 0.047 -10000 0 -0.43 5 5
NUP214 0.025 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.005 0.11 -10000 0 -0.32 42 42
SMAD1/SKI 0.025 0.057 -10000 0 -0.37 3 3
SMAD6 0.021 0.044 -10000 0 -0.33 6 6
CTDSP2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.022 0.16 -10000 0 -0.33 86 86
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.076 0.17 -10000 0 -0.43 80 80
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.022 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.018 0.077 -10000 0 -0.31 24 24
CHRDL1 -0.037 0.15 -10000 0 -0.43 59 59
ENDOFIN/SMAD1 0.03 0.06 0.3 1 -0.37 3 4
SMAD6-7/SMURF1/SMAD1 0.036 0.064 -10000 0 -0.35 4 4
SMAD6/SMURF1 0.02 0.011 -10000 0 -10000 0 0
BAMBI 0.022 0.017 -10000 0 -0.13 5 5
SMURF2 0.023 0.03 -10000 0 -0.43 2 2
BMP2-4/CHRDL1 -0.037 0.16 -10000 0 -0.3 113 113
BMP2-4/GREM1 -0.052 0.17 -10000 0 -0.3 133 133
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.18 -10000 0 -0.48 52 52
SMAD1/SMAD6 0.021 0.055 -10000 0 -0.36 3 3
TAK1/SMAD6 0.03 0.017 -10000 0 -10000 0 0
BMP7 0.02 0.048 -10000 0 -0.43 5 5
BMP6 0.018 0.048 -10000 0 -0.43 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.027 0.11 -10000 0 -0.38 29 29
PPM1A 0.025 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.029 0.06 0.3 1 -0.36 3 4
SMAD7/SMURF1 0.03 0.016 -10000 0 -10000 0 0
CTDSPL 0.024 0.022 -10000 0 -0.43 1 1
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.019 0.022 -10000 0 -0.13 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.051 0.15 -10000 0 -0.43 41 41
CHRD 0.024 0.03 -10000 0 -0.43 2 2
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.034 0.13 -10000 0 -0.42 35 35
BMP4 0.006 0.091 -10000 0 -0.43 19 19
FST -0.014 0.12 -10000 0 -0.27 63 63
BMP2-4/NOG -0.025 0.18 -10000 0 -0.4 75 75
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.042 0.07 -10000 0 -0.22 23 23
TCGA08_rtk_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
PDGFRA -0.022 0.14 -10000 0 -0.4 50 50
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.013 0.12 -10000 0 -0.43 34 34
AKT 0.039 0.1 0.26 41 -0.21 8 49
FOXO3 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.004 -10000 0 -10000 0 0
FOXO1 0.024 0.023 -10000 0 -0.43 1 1
AKT3 0.022 0.037 -10000 0 -0.43 3 3
FOXO4 0.025 0.021 -10000 0 -0.43 1 1
MET -0.047 0.14 -10000 0 -0.26 106 106
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
PIK3CG -0.01 0.099 -10000 0 -0.26 50 50
PIK3R3 0.021 0.014 -10000 0 -0.13 2 2
PIK3R2 0.025 0.006 -10000 0 -10000 0 0
NF1 0.025 0.021 -10000 0 -0.43 1 1
RAS -0.006 0.064 0.16 2 -0.15 61 63
ERBB2 0.024 0.019 -10000 0 -0.13 7 7
proliferation/survival/translation -0.026 0.075 0.28 14 -0.22 11 25
PI3K 0.02 0.11 0.24 56 -0.15 56 112
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
FOXO 0.061 0.085 0.22 70 -10000 0 70
AKT2 0.022 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.013 0.088 -10000 0 -0.28 40 40
CRKL 0.026 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.022 0.031 -10000 0 -0.43 2 2
ITGA4 -0.01 0.11 -10000 0 -0.43 25 25
alpha4/beta7 Integrin/MAdCAM1 0.003 0.13 -10000 0 -0.26 80 80
EPO 0.013 0.03 -10000 0 -0.18 6 6
alpha4/beta7 Integrin -0.008 0.11 -10000 0 -0.28 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.011 0.079 -10000 0 -0.29 25 25
EPO/EPOR (dimer) 0.027 0.026 -10000 0 -0.31 1 1
lamellipodium assembly 0.016 0.033 -10000 0 -0.26 4 4
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.003 -10000 0 -10000 0 0
JAK2 0.005 0.052 -10000 0 -0.22 21 21
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
MADCAM1 -0.04 0.14 -10000 0 -0.26 105 105
cell adhesion 0.001 0.13 -10000 0 -0.26 80 80
CRKL/CBL 0.036 0.011 -10000 0 -10000 0 0
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
SRC -0.028 0.1 0.18 23 -0.25 63 86
ITGB7 0 0.095 -10000 0 -0.43 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.11 -10000 0 -0.26 71 71
p130Cas/Crk/Dock1 -0.011 0.1 0.35 1 -0.27 11 12
VCAM1 -0.037 0.14 -10000 0 -0.43 47 47
RHOA 0.025 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.045 0.069 -10000 0 -0.24 23 23
BCAR1 -0.038 0.094 0.19 22 -0.23 64 86
EPOR 0.025 0.009 -10000 0 -0.13 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.024 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.034 -10000 0 -0.27 4 4
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.004 0.05 0.2 24 -0.2 2 26
RFC1 0 0.038 0.18 16 -0.2 2 18
PRKDC 0.007 0.054 0.2 31 -0.2 2 33
RIPK1 0.026 0.005 -10000 0 -10000 0 0
CASP7 -0.021 0.15 -10000 0 -0.57 28 28
FASLG/FAS/FADD/FAF1 0.001 0.058 0.19 13 -0.25 10 23
MAP2K4 -0.033 0.12 -10000 0 -0.37 25 25
mol:ceramide -0.002 0.075 -10000 0 -0.26 20 20
GSN -0.001 0.058 0.19 21 -0.3 7 28
FASLG/FAS/FADD/FAF1/Caspase 8 0.001 0.058 -10000 0 -0.26 6 6
FAS 0.008 0.071 -10000 0 -0.3 18 18
BID -0.009 0.057 0.28 16 -10000 0 16
MAP3K1 -0.028 0.11 0.22 1 -0.37 28 29
MAP3K7 0.024 0.006 -10000 0 -10000 0 0
RB1 0.001 0.039 0.18 17 -0.2 2 19
CFLAR 0.026 0.008 -10000 0 -0.12 1 1
HGF/MET -0.007 0.12 -10000 0 -0.25 74 74
ARHGDIB 0.007 0.053 0.2 30 -0.22 1 31
FADD 0.021 0.015 -10000 0 -10000 0 0
actin filament polymerization 0.005 0.063 0.23 16 -0.19 21 37
NFKB1 -0.015 0.12 -10000 0 -0.73 10 10
MAPK8 -0.053 0.16 -10000 0 -0.47 46 46
DFFA 0 0.036 0.17 16 -0.2 2 18
DNA fragmentation during apoptosis -0.002 0.047 0.18 17 -0.18 11 28
FAS/FADD/MET -0.008 0.1 -10000 0 -0.27 54 54
CFLAR/RIP1 0.039 0.01 -10000 0 -10000 0 0
FAIM3 0.002 0.091 -10000 0 -0.43 17 17
FAF1 0.018 0.017 -10000 0 -10000 0 0
PARP1 0 0.038 0.18 16 -0.2 2 18
DFFB 0 0.036 0.17 16 -0.2 2 18
CHUK -0.014 0.11 -10000 0 -0.7 9 9
FASLG 0.004 0.042 -10000 0 -10000 0 0
FAS/FADD 0.02 0.057 -10000 0 -0.32 10 10
HGF -0.007 0.087 -10000 0 -0.2 59 59
LMNA -0.001 0.045 0.2 9 -0.2 1 10
CASP6 0 0.039 0.18 17 -0.2 2 19
CASP10 0.021 0.016 -10000 0 -10000 0 0
CASP3 0.003 0.046 0.22 16 -0.22 2 18
PTPN13 0.02 0.048 -10000 0 -0.43 5 5
CASP8 -0.009 0.067 0.34 16 -10000 0 16
IL6 -0.12 0.39 -10000 0 -1.2 47 47
MET -0.047 0.14 -10000 0 -0.26 106 106
ICAD/CAD 0.001 0.045 0.35 4 -0.2 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.002 0.075 -10000 0 -0.27 19 19
activation of caspase activity by cytochrome c -0.009 0.057 0.28 16 -10000 0 16
PAK2 0.002 0.042 0.19 20 -0.22 1 21
BCL2 0.022 0.043 -10000 0 -0.43 4 4
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.01 0.083 -10000 0 -0.23 47 47
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.058 0.11 -10000 0 -0.3 72 72
GNB1/GNG2 0.027 0.03 -10000 0 -0.26 4 4
GNB1 0.022 0.01 -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 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.076 -10000 0 -0.23 49 49
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 0.007 0.019 0.063 49 -10000 0 49
GNAL -0.023 0.14 -10000 0 -0.42 49 49
GNG2 0.022 0.043 -10000 0 -0.43 4 4
CRH -0.076 0.16 -10000 0 -0.27 152 152
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.044 -10000 0 -0.3 10 10
MAPK11 0.005 0.024 -10000 0 -0.3 3 3
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.026 0.003 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.016 0.024 -10000 0 -0.26 2 2
NT3 (dimer)/TRKC 0.028 0.033 -10000 0 -0.34 2 2
NT3 (dimer)/TRKB 0.008 0.1 -10000 0 -0.26 52 52
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.026 -10000 0 -0.48 1 1
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
BDNF -0.011 0.092 -10000 0 -0.18 80 80
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.03 -10000 0 -0.43 2 2
NTRK1 0.015 0.057 -10000 0 -0.43 6 6
NTRK2 0.004 0.097 -10000 0 -0.43 22 22
NTRK3 0.022 0.043 -10000 0 -0.43 4 4
NT-4/5 (dimer)/TRKB 0.002 0.096 -10000 0 -0.26 48 48
neuron apoptosis 0.061 0.16 0.36 72 -10000 0 72
SHC 2-3/Grb2 -0.067 0.17 -10000 0 -0.39 72 72
SHC1 0.024 0.015 -10000 0 -0.13 4 4
SHC2 -0.034 0.11 -10000 0 -0.42 14 14
SHC3 -0.1 0.21 -10000 0 -0.52 79 79
STAT3 (dimer) 0.02 0.057 -10000 0 -0.33 11 11
NT3 (dimer)/TRKA 0.016 0.089 -10000 0 -0.25 43 43
RIN/GDP -0.003 0.082 0.22 7 -0.3 2 9
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
KRAS 0.025 0.005 -10000 0 -10000 0 0
DNAJA3 -0.05 0.1 -10000 0 -0.25 77 77
RIN/GTP -0.068 0.13 -10000 0 -0.3 100 100
CCND1 0.001 0.11 -10000 0 -0.7 11 11
MAGED1 0.026 0.002 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.15 11 11
SHC/GRB2/SOS1 0.05 0.013 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.015 0.13 -10000 0 -0.28 75 75
TRKA/NEDD4-2 0.025 0.054 -10000 0 -0.31 9 9
ELMO1 0.017 0.048 -10000 0 -0.43 5 5
RhoG/GTP/ELMO1/DOCK1 0.025 0.035 -10000 0 -0.25 6 6
NGF -0.029 0.14 -10000 0 -0.36 58 58
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK1 0.022 0.031 -10000 0 -0.43 2 2
GAB2 0.025 0.005 -10000 0 -10000 0 0
RIT2 -0.099 0.18 -10000 0 -0.3 174 174
RIT1 0.025 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
DNM1 -0.031 0.12 -10000 0 -0.23 103 103
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.035 0.1 -10000 0 -0.25 70 70
mol:GDP 0.028 0.073 0.27 7 -0.62 1 8
NGF (dimer) -0.028 0.14 -10000 0 -0.36 58 58
RhoG/GDP 0.013 0.034 -10000 0 -0.3 5 5
RIT1/GDP 0.025 0.053 0.19 4 -0.37 1 5
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.027 0.087 -10000 0 -0.26 36 36
KIDINS220/CRKL/C3G 0.037 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.051 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.024 -10000 0 -0.24 1 1
RIT1/GTP 0.019 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.031 -10000 0 -0.13 15 15
RAP1/GDP 0.021 0.04 -10000 0 -0.31 1 1
KIDINS220/CRKL 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer) -0.011 0.091 -10000 0 -0.18 80 80
ubiquitin-dependent protein catabolic process 0.004 0.1 -10000 0 -0.26 55 55
Schwann cell development -0.015 0.019 -10000 0 -10000 0 0
EHD4 0.024 0.016 -10000 0 -0.13 5 5
FRS2 family/GRB2/SOS1 0.063 0.017 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.032 0.03 -10000 0 -0.42 1 1
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.071 -10000 0 -0.22 28 28
ABL1 0.025 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.009 0.09 -10000 0 -0.32 9 9
STAT3 0.02 0.057 -10000 0 -0.33 11 11
axon guidance -0.003 0.066 -10000 0 -0.22 28 28
MAPK3 -0.037 0.11 0.18 11 -0.26 72 83
MAPK1 -0.037 0.11 0.18 11 -0.26 72 83
CDC42/GDP 0.031 0.052 0.2 6 -0.37 1 7
NTF3 0.006 0.031 -10000 0 -0.13 15 15
NTF4 -0.003 0.033 -10000 0 -0.16 11 11
NGF (dimer)/TRKA/FAIM 0.005 0.099 -10000 0 -0.26 53 53
PI3K 0.038 0.007 -10000 0 -10000 0 0
FRS3 0.026 0.002 -10000 0 -10000 0 0
FAIM 0.023 0.037 -10000 0 -0.43 3 3
GAB1 0.024 0.022 -10000 0 -0.43 1 1
RASGRF1 -0.074 0.12 -10000 0 -0.26 119 119
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L 0.002 0.029 -10000 0 -0.28 3 3
RGS19 0.025 0.006 -10000 0 -10000 0 0
CDC42 0.022 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.07 -10000 0 -0.61 2 2
Rac1/GDP 0.024 0.053 0.21 5 -0.36 1 6
NGF (dimer)/TRKA/GRIT -0.01 0.091 -10000 0 -0.25 52 52
neuron projection morphogenesis -0.033 0.12 -10000 0 -0.56 5 5
NGF (dimer)/TRKA/NEDD4-2 0.004 0.1 -10000 0 -0.26 55 55
MAP2K1 0.023 0.049 0.2 29 -0.23 1 30
NGFR -0.019 0.12 -10000 0 -0.43 34 34
NGF (dimer)/TRKA/GIPC/GAIP -0.026 0.1 -10000 0 -0.25 71 71
RAS family/GTP/PI3K 0.019 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.072 0.021 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
MAPKKK cascade -0.12 0.24 -10000 0 -0.51 101 101
RASA1 0.026 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.044 -10000 0 -0.31 6 6
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.04 0.079 -10000 0 -0.25 27 27
NGF (dimer)/TRKA/p62/Atypical PKCs 0.018 0.11 -10000 0 -0.24 58 58
MATK -0.026 0.13 -10000 0 -0.43 40 40
NEDD4L 0.02 0.042 -10000 0 -0.43 3 3
RAS family/GDP -0.006 0.021 -10000 0 -0.28 1 1
NGF (dimer)/TRKA -0.038 0.11 -10000 0 -0.26 77 77
Rac1/GTP -0.041 0.077 -10000 0 -0.24 24 24
FRS2 family/SHP2/CRK family 0.074 0.017 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.05 -10000 0 -0.43 4 4
HSPA8 0.023 0.024 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.016 0.092 0.21 3 -0.27 19 22
AKT1 0.015 0.035 -10000 0 -0.1 6 6
GSC -0.16 0.48 -10000 0 -1.4 59 59
NKX2-5 -0.015 0.088 -10000 0 -0.41 13 13
muscle cell differentiation 0.07 0.18 0.4 76 -10000 0 76
SMAD2-3/SMAD4/SP1 0.02 0.12 -10000 0 -0.29 25 25
SMAD4 -0.008 0.069 -10000 0 -0.23 11 11
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.032 0.075 -10000 0 -0.26 18 18
SMAD3/SMAD4/VDR 0.036 0.11 -10000 0 -0.25 31 31
MYC 0.007 0.09 -10000 0 -0.41 19 19
CDKN2B -0.19 0.49 -10000 0 -1.4 59 59
AP1 0 0.092 -10000 0 -0.28 21 21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.003 0.084 -10000 0 -0.29 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.037 0.14 -10000 0 -0.37 57 57
SP3 0.027 0.008 -10000 0 -10000 0 0
CREB1 0.026 0.002 -10000 0 -10000 0 0
FOXH1 -0.003 0.078 -10000 0 -0.36 13 13
SMAD3/SMAD4/GR 0.038 0.083 0.21 1 -0.24 6 7
GATA3 -0.051 0.14 -10000 0 -0.36 62 62
SKI/SIN3/HDAC complex/NCoR1 0.014 0.056 -10000 0 -0.3 11 11
MEF2C/TIF2 -0.035 0.13 0.27 2 -0.35 26 28
endothelial cell migration 0.16 0.46 1.3 65 -10000 0 65
MAX 0.032 0.019 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.022 0.01 -10000 0 -10000 0 0
RUNX2 0.017 0.053 -10000 0 -0.43 5 5
RUNX3 -0.003 0.096 -10000 0 -0.3 36 36
RUNX1 -0.006 0.099 -10000 0 -0.43 20 20
CTBP1 0.025 0.005 -10000 0 -10000 0 0
NR3C1 0.032 0.019 -10000 0 -10000 0 0
VDR -0.015 0.11 -10000 0 -0.43 28 28
CDKN1A -0.047 0.26 -10000 0 -1.3 20 20
KAT2B 0.021 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.009 0.13 -10000 0 -0.3 61 61
DCP1A 0.025 0.004 -10000 0 -10000 0 0
SKI 0.022 0.01 -10000 0 -10000 0 0
SERPINE1 -0.17 0.47 -10000 0 -1.3 65 65
SMAD3/SMAD4/ATF2 0.02 0.083 -10000 0 -0.24 15 15
SMAD3/SMAD4/ATF3 0.013 0.094 -10000 0 -0.28 18 18
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.061 0.2 6 -0.25 4 10
JUN -0.014 0.083 -10000 0 -0.28 20 20
SMAD3/SMAD4/IRF7 0.019 0.084 -10000 0 -0.29 9 9
TFE3 0.014 0.034 -10000 0 -10000 0 0
COL1A2 0.005 0.097 -10000 0 -0.88 5 5
mesenchymal cell differentiation -0.021 0.084 0.28 11 -10000 0 11
DLX1 -0.064 0.16 -10000 0 -0.43 67 67
TCF3 0.023 0.031 -10000 0 -0.43 2 2
FOS -0.03 0.14 -10000 0 -0.34 64 64
SMAD3/SMAD4/Max 0.037 0.083 0.21 2 -0.24 7 9
Cbp/p300/SNIP1 0.036 0.043 -10000 0 -0.25 4 4
ZBTB17 0.023 0.014 -10000 0 -10000 0 0
LAMC1 -0.01 0.061 0.21 1 -0.41 1 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.085 -10000 0 -0.31 11 11
IRF7 0.015 0.054 -10000 0 -0.39 6 6
ESR1 0.008 0.074 -10000 0 -0.28 23 23
HNF4A -0.006 0.04 -10000 0 -0.13 36 36
MEF2C -0.026 0.13 0.28 2 -0.35 23 25
SMAD2-3/SMAD4 0.008 0.1 -10000 0 -0.25 26 26
Cbp/p300/Src-1 0.043 0.049 -10000 0 -0.25 4 4
IGHV3OR16-13 0.001 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.019 0.052 -10000 0 -0.39 7 7
CREBBP 0.021 0.023 -10000 0 -10000 0 0
SKIL 0.02 0.052 -10000 0 -0.43 6 6
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
SNIP1 0.022 0.011 -10000 0 -10000 0 0
GCN5L2 0 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.083 -10000 0 -0.25 6 6
MSG1/HSC70 0.017 0.067 -10000 0 -0.3 15 15
SMAD2 0 0.058 -10000 0 -0.16 24 24
SMAD3 0.007 0.056 -10000 0 -0.21 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.061 -10000 0 -0.26 12 12
SMAD2/SMAD2/SMAD4 -0.006 0.043 -10000 0 -0.25 1 1
NCOR1 0.025 0.022 -10000 0 -0.43 1 1
NCOA2 -0.004 0.11 -10000 0 -0.43 29 29
NCOA1 0.026 0.002 -10000 0 -10000 0 0
MYOD/E2A -0.043 0.13 -10000 0 -0.31 79 79
SMAD2-3/SMAD4/SP1/MIZ-1 0.019 0.12 -10000 0 -0.29 25 25
IFNB1 -0.01 0.06 -10000 0 -0.32 4 4
SMAD3/SMAD4/MEF2C -0.011 0.14 -10000 0 -0.35 25 25
CITED1 0.002 0.085 -10000 0 -0.23 43 43
SMAD2-3/SMAD4/ARC105 0.022 0.1 -10000 0 -0.24 20 20
RBL1 0.012 0.076 -10000 0 -0.41 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.051 0.19 -10000 0 -0.55 54 54
RUNX1-3/PEBPB2 0.018 0.089 -10000 0 -0.24 46 46
SMAD7 -0.016 0.12 -10000 0 -0.41 14 14
MYC/MIZ-1 0.019 0.069 0.18 8 -0.29 17 25
SMAD3/SMAD4 -0.025 0.19 0.27 37 -0.45 59 96
IL10 -0.064 0.19 -10000 0 -0.52 55 55
PIASy/HDAC complex 0.022 0.023 -10000 0 -10000 0 0
PIAS3 0.02 0.017 -10000 0 -10000 0 0
CDK2 0.015 0.051 -10000 0 -0.44 4 4
IL5 -0.039 0.13 0.22 1 -0.36 33 34
CDK4 0.021 0.023 -10000 0 -10000 0 0
PIAS4 0.022 0.023 -10000 0 -10000 0 0
ATF3 0.003 0.081 -10000 0 -0.21 43 43
SMAD3/SMAD4/SP1 0.024 0.099 -10000 0 -0.31 11 11
FOXG1 0.001 0.1 -10000 0 -0.43 25 25
FOXO3 0.002 0.037 -10000 0 -0.14 2 2
FOXO1 0.001 0.039 -10000 0 -0.22 2 2
FOXO4 0.001 0.041 -10000 0 -0.26 2 2
heart looping -0.026 0.13 0.28 2 -0.35 23 25
CEBPB 0.007 0.077 -10000 0 -0.44 12 12
SMAD3/SMAD4/DLX1 -0.025 0.13 -10000 0 -0.28 75 75
MYOD1 -0.087 0.17 -10000 0 -0.43 83 83
SMAD3/SMAD4/HNF4 0.021 0.078 -10000 0 -0.25 8 8
SMAD3/SMAD4/GATA3 -0.024 0.15 -10000 0 -0.32 73 73
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.052 -10000 0 -0.43 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.11 -10000 0 -0.26 36 36
SMAD3/SMAD4/SP1-3 0.042 0.095 -10000 0 -0.32 6 6
MED15 0.026 0.003 -10000 0 -10000 0 0
SP1 0.014 0.038 -10000 0 -0.23 1 1
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.006 0.13 -10000 0 -0.27 73 73
ITGB5 -0.006 0.076 -10000 0 -0.49 4 4
TGIF/SIN3/HDAC complex/CtBP 0.014 0.068 -10000 0 -0.45 8 8
SMAD3/SMAD4/AR -0.02 0.13 -10000 0 -0.29 69 69
AR -0.047 0.16 -10000 0 -0.35 89 89
negative regulation of cell growth -0.005 0.094 -10000 0 -0.38 16 16
SMAD3/SMAD4/MYOD -0.036 0.14 -10000 0 -0.3 86 86
E2F5 0.023 0.031 -10000 0 -0.43 2 2
E2F4 0.026 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.013 0.11 -10000 0 -0.25 40 40
SMAD2-3/SMAD4/FOXO1-3a-4 -0.03 0.14 -10000 0 -0.4 50 50
TFDP1 0.024 0.022 -10000 0 -0.43 1 1
SMAD3/SMAD4/AP1 0.021 0.1 -10000 0 -0.28 21 21
SMAD3/SMAD4/RUNX2 0.021 0.084 -10000 0 -0.28 11 11
TGIF2 0.019 0.052 -10000 0 -0.39 7 7
TGIF1 0.017 0.055 -10000 0 -0.26 14 14
ATF2 0.018 0.06 -10000 0 -0.43 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.001 0.091 0.32 30 -10000 0 30
KIRREL -0.006 0.12 -10000 0 -0.44 30 30
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.001 0.091 -10000 0 -0.32 30 30
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.002 -10000 0 -10000 0 0
WASL 0.02 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.032 0.077 -10000 0 -0.24 30 30
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.001 0.065 -10000 0 -0.25 25 25
FYN -0.008 0.073 0.27 7 -0.23 31 38
mol:Ca2+ 0.029 0.077 -10000 0 -0.24 31 31
mol:DAG 0.03 0.077 -10000 0 -0.24 31 31
NPHS2 0.001 0.033 -10000 0 -0.44 1 1
mol:IP3 0.03 0.077 -10000 0 -0.24 31 31
regulation of endocytosis 0.026 0.069 -10000 0 -0.22 31 31
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.072 -10000 0 -0.24 31 31
establishment of cell polarity -0.001 0.091 -10000 0 -0.32 30 30
Nephrin/NEPH1/podocin/NCK1-2 0.042 0.079 -10000 0 -0.22 30 30
Nephrin/NEPH1/beta Arrestin2 0.027 0.071 -10000 0 -0.22 31 31
NPHS1 -0.001 0.054 -10000 0 -0.15 38 38
Nephrin/NEPH1/podocin 0.02 0.07 -10000 0 -0.23 31 31
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.022 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.031 0.078 -10000 0 -0.24 31 31
CD2AP 0.026 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.03 0.077 -10000 0 -0.24 30 30
GRB2 0.025 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.083 0.24 12 -0.23 38 50
cytoskeleton organization -0.016 0.079 0.2 10 -0.27 25 35
Nephrin/NEPH1 0.012 0.064 -10000 0 -0.22 30 30
Nephrin/NEPH1/ZO-1 0.024 0.078 -10000 0 -0.25 30 30
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.025 0.2 3 -10000 0 3
AES 0.026 0.019 0.17 4 -10000 0 4
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.016 -10000 0 -10000 0 0
SMAD4 0.025 0.004 -10000 0 -10000 0 0
DKK2 -0.037 0.14 -10000 0 -0.26 98 98
TLE1 0.026 0.03 0.18 4 -0.43 1 5
MACF1 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.048 0.098 0.28 26 -0.31 3 29
WIF1 -0.13 0.18 -10000 0 -0.27 236 236
beta catenin/RanBP3 0.018 0.11 0.41 25 -0.3 1 26
KREMEN2 -0.007 0.1 -10000 0 -0.43 22 22
DKK1 -0.033 0.13 -10000 0 -0.43 38 38
beta catenin/beta TrCP1 0.056 0.096 0.28 24 -0.29 3 27
FZD1 0.021 0.01 -10000 0 -10000 0 0
AXIN2 -0.001 0.13 0.57 12 -1.4 1 13
AXIN1 0.027 0.002 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.024 0.065 -10000 0 -0.6 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.065 0.093 0.28 19 -0.58 3 22
Axin1/APC/GSK3 0.032 0.073 0.25 12 -0.29 1 13
Axin1/APC/GSK3/beta catenin/Macf1 0.045 0.074 0.27 7 -0.41 2 9
HNF1A 0.027 0.03 0.19 4 -0.43 1 5
CTBP1 0.027 0.022 0.19 4 -10000 0 4
MYC 0.006 0.36 0.55 58 -1.5 20 78
RANBP3 0.025 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.28 59 59
NKD1 0.018 0.054 -10000 0 -0.39 7 7
TCF4 0.026 0.028 0.18 4 -0.39 1 5
TCF3 0.024 0.033 0.18 3 -0.37 2 5
WNT1/LRP6/FZD1/Axin1 0.051 0.03 -10000 0 -10000 0 0
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.021 0.13 0.5 27 -0.36 1 28
LEF1 0.025 0.027 0.18 4 -0.13 5 9
DVL1 0.028 0.035 -10000 0 -10000 0 0
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.062 0.11 0.3 15 -0.73 3 18
DKK1/LRP6/Kremen 2 0.009 0.11 -10000 0 -0.27 56 56
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.028 0.023 0.19 4 -10000 0 4
NLK 0.024 0.014 -10000 0 -0.15 1 1
CCND1 -0.022 0.26 0.56 17 -1.5 11 28
WNT1 0.01 0.039 -10000 0 -0.13 29 29
GSK3A 0.022 0.01 -10000 0 -10000 0 0
GSK3B 0.026 0.003 -10000 0 -10000 0 0
FRAT1 0.022 0.031 -10000 0 -0.43 2 2
PPP2R5D 0.027 0.055 0.29 6 -0.24 3 9
APC 0.039 0.08 0.19 93 -10000 0 93
WNT1/LRP6/FZD1 0.04 0.077 0.2 68 -10000 0 68
CREBBP 0.028 0.021 0.19 4 -10000 0 4
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.027 0.14 -10000 0 -0.43 47 47
KLHL20 0.011 0.071 0.16 5 -0.22 6 11
CYFIP2 0.023 0.033 -10000 0 -0.25 5 5
Rac1/GDP -0.003 0.094 0.26 4 -0.26 40 44
ENAH -0.031 0.14 -10000 0 -0.42 52 52
AP1M1 0.025 0.006 -10000 0 -10000 0 0
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.003 0.064 -10000 0 -0.24 1 1
ABI1/Sra1/Nap1 -0.014 0.036 -10000 0 -0.16 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.02 0.12 -10000 0 -0.26 63 63
RAPGEF1 -0.018 0.13 0.24 4 -0.38 48 52
CTNND1 0.025 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.15 -10000 0 -0.43 54 54
CRK -0.029 0.13 0.22 1 -0.4 48 49
E-cadherin/gamma catenin/alpha catenin 0.014 0.11 -10000 0 -0.27 55 55
alphaE/beta7 Integrin 0.018 0.072 -10000 0 -0.31 19 19
IQGAP1 0.022 0.033 -10000 0 -0.23 6 6
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.24 1 1
DLG1 -0.03 0.14 -10000 0 -0.42 52 52
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.013 0.044 -10000 0 -0.18 1 1
MLLT4 0.024 0.022 -10000 0 -0.43 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.012 -10000 0 -10000 0 0
PI3K -0.014 0.057 -10000 0 -0.23 1 1
ARF6 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.019 0.12 -10000 0 -0.32 55 55
TIAM1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.029 0.088 -10000 0 -0.22 48 48
AKT1 -0.003 0.042 0.14 1 -0.14 1 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.044 0.15 -10000 0 -0.43 52 52
RhoA/GDP 0.005 0.1 0.25 7 -0.26 42 49
actin cytoskeleton organization 0.015 0.061 0.16 18 -0.16 6 24
CDC42/GDP 0 0.098 0.25 4 -0.26 29 33
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.013 0.08 -10000 0 -0.23 53 53
ITGB7 0 0.095 -10000 0 -0.43 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.032 0.094 -10000 0 -0.24 48 48
E-cadherin/Ca2+/beta catenin/alpha catenin 0.016 0.085 -10000 0 -0.22 52 52
mol:GDP -0.011 0.11 0.26 8 -0.3 44 52
CDC42/GTP/IQGAP1 0.028 0.023 -10000 0 -0.23 2 2
JUP 0.02 0.052 -10000 0 -0.39 7 7
p120 catenin/RhoA/GDP 0.009 0.1 0.26 5 -0.27 41 46
RAC1/GTP/IQGAP1 0.028 0.024 -10000 0 -0.26 2 2
PIP5K1C/AP1M1 0.037 0.009 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.009 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.052 0.13 19 -0.17 14 33
NME1 0.026 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.031 0.14 -10000 0 -0.42 53 53
regulation of cell-cell adhesion -0.008 0.054 -10000 0 -0.21 1 1
WASF2 0.009 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.08 0.24 2 -0.26 1 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.028 0.12 -10000 0 -0.26 66 66
CCND1 0.012 0.061 0.16 15 -0.21 14 29
VAV2 -0.011 0.15 -10000 0 -0.62 6 6
RAP1/GDP 0.007 0.089 0.26 3 -0.26 4 7
adherens junction assembly -0.029 0.14 -10000 0 -0.41 53 53
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.008 -10000 0 -10000 0 0
PIP5K1C 0.025 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.015 0.12 -10000 0 -0.25 66 66
E-cadherin/beta catenin -0.028 0.1 -10000 0 -0.32 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.03 0.14 -10000 0 -0.42 50 50
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.085 -10000 0 -0.35 6 6
E-cadherin/beta catenin/alpha catenin 0.017 0.1 -10000 0 -0.26 52 52
ITGAE 0.026 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.028 0.15 -10000 0 -0.44 54 54
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 -0.034 0.14 -10000 0 -0.46 21 21
UGCG -0.017 0.14 -10000 0 -0.69 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT -0.038 0.15 0.23 2 -0.41 32 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.017 0.14 -10000 0 -0.66 19 19
mol:DAG -0.016 0.16 -10000 0 -0.82 16 16
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.15 0.25 1 -0.41 33 34
FRAP1 -0.031 0.17 0.27 2 -0.48 34 36
FOXO3 -0.029 0.16 0.27 2 -0.42 39 41
AKT1 -0.033 0.17 0.28 1 -0.45 39 40
GAB2 0.025 0.006 -10000 0 -10000 0 0
SMPD1 -0.012 0.12 -10000 0 -0.59 17 17
SGMS1 -0.009 0.11 -10000 0 -0.56 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
cell proliferation -0.011 0.14 0.24 3 -0.43 21 24
EIF3A 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.012 -10000 0 -10000 0 0
RPS6KB1 0.003 0.076 -10000 0 -1.1 1 1
mol:sphingomyelin -0.016 0.16 -10000 0 -0.82 16 16
natural killer cell activation 0 0.002 -10000 0 -0.012 12 12
JAK3 -0.009 0.1 -10000 0 -0.24 59 59
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.023 0.011 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.029 0.24 0.36 2 -0.89 24 26
MYB -0.067 0.31 -10000 0 -1.2 31 31
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.027 0.14 -10000 0 -0.35 48 48
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.077 -10000 0 -1 1 1
mol:PI-3-4-5-P3 -0.03 0.14 -10000 0 -0.34 48 48
Rac1/GDP 0.019 0.013 -10000 0 -10000 0 0
T cell proliferation -0.022 0.13 0.22 1 -0.35 34 35
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RAC1 0.022 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.017 -10000 0 -0.065 31 31
PRKCZ -0.02 0.13 0.22 1 -0.37 32 33
NF kappa B1 p50/RelA -0.011 0.16 0.27 2 -0.42 32 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.036 0.14 -10000 0 -0.42 44 44
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
IL2RA -0.008 0.078 -10000 0 -0.18 60 60
IL2RB -0.028 0.13 -10000 0 -0.43 37 37
TERT -0.044 0.13 -10000 0 -0.43 45 45
E2F1 -0.011 0.13 -10000 0 -0.44 35 35
SOS1 0.026 0.004 -10000 0 -10000 0 0
RPS6 0.024 0.01 -10000 0 -10000 0 0
mol:cAMP 0.001 0.008 0.032 31 -10000 0 31
PTPN11 0.025 0.008 -10000 0 -10000 0 0
IL2RG 0.001 0.089 -10000 0 -0.22 48 48
actin cytoskeleton organization -0.022 0.13 0.22 1 -0.35 34 35
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.041 0.025 -10000 0 -10000 0 0
LCK -0.021 0.12 -10000 0 -0.25 73 73
BCL2 -0.025 0.16 -10000 0 -0.56 20 20
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.089 -10000 0 -0.26 43 43
cell-cell adhesion 0.02 0.051 0.3 7 -10000 0 7
Ephrin B/EPHB2/RasGAP 0.055 0.058 -10000 0 -0.24 11 11
ITSN1 0.026 0.003 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
Ephrin B1/EPHB3 0.033 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.011 0.079 -10000 0 -0.26 36 36
HRAS/GDP 0.017 0.066 -10000 0 -0.31 8 8
Ephrin B/EPHB1/GRB7 0.041 0.1 -10000 0 -0.26 42 42
Endophilin/SYNJ1 0.011 0.055 -10000 0 -0.23 10 10
KRAS 0.025 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.044 0.09 -10000 0 -0.25 35 35
endothelial cell migration 0.041 0.028 -10000 0 -0.22 1 1
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.003 0.042 -10000 0 -0.13 36 36
PAK1 -0.012 0.065 0.35 2 -0.41 1 3
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS 0.009 0.053 -10000 0 -0.24 10 10
DNM1 -0.031 0.12 -10000 0 -0.23 103 103
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.006 0.082 0.19 15 -0.24 42 57
lamellipodium assembly -0.02 0.051 -10000 0 -0.3 7 7
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.076 -10000 0 -0.24 30 30
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPHB2 0.017 0.042 -10000 0 -0.43 3 3
EPHB3 0.025 0.011 -10000 0 -0.13 2 2
EPHB1 -0.01 0.12 -10000 0 -0.43 36 36
EPHB4 0.02 0.011 -10000 0 -10000 0 0
mol:GDP -0.003 0.059 0.23 3 -0.33 7 10
Ephrin B/EPHB2 0.043 0.054 -10000 0 -0.24 12 12
Ephrin B/EPHB3 0.052 0.045 -10000 0 -0.23 10 10
JNK cascade -0.005 0.08 0.22 12 -0.23 38 50
Ephrin B/EPHB1 0.03 0.091 -10000 0 -0.25 42 42
RAP1/GDP 0.043 0.095 0.23 56 -0.33 5 61
EFNB2 0.021 0.03 -10000 0 -0.43 1 1
EFNB3 0.016 0.064 -10000 0 -0.43 9 9
EFNB1 0.025 0.013 -10000 0 -0.13 3 3
Ephrin B2/EPHB1-2 0.016 0.084 -10000 0 -0.25 38 38
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.079 -10000 0 -0.33 10 10
Rap1/GTP -0.002 0.075 -10000 0 -0.3 11 11
axon guidance -0.006 0.088 -10000 0 -0.26 43 43
MAPK3 0 0.067 0.19 1 -0.28 9 10
MAPK1 0.001 0.067 0.19 1 -0.28 9 10
Rac1/GDP 0.024 0.085 0.23 37 -0.32 5 42
actin cytoskeleton reorganization -0.004 0.048 -10000 0 -0.29 6 6
CDC42/GDP 0.039 0.098 0.23 61 -0.32 6 67
PI3K 0.045 0.03 -10000 0 -0.22 1 1
EFNA5 -0.026 0.13 -10000 0 -0.29 75 75
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.047 -10000 0 -0.29 8 8
CDC42 0.022 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.072 -10000 0 -0.29 11 11
PTK2 0.054 0.16 0.53 47 -10000 0 47
MAP4K4 -0.005 0.081 0.22 12 -0.24 38 50
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.021 0.026 -10000 0 -0.13 13 13
Intersectin/N-WASP 0.03 0.017 -10000 0 -10000 0 0
neuron projection morphogenesis 0.031 0.12 0.3 62 -0.38 3 65
MAP2K1 0.004 0.07 -10000 0 -0.29 10 10
WASL 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.029 0.089 -10000 0 -0.25 38 38
cell migration 0.003 0.089 0.39 1 -0.36 8 9
NRAS 0.021 0.01 -10000 0 -10000 0 0
SYNJ1 0.011 0.056 -10000 0 -0.24 10 10
PXN 0.026 0.003 -10000 0 -10000 0 0
TF -0.022 0.075 0.17 16 -0.3 9 25
HRAS/GTP 0.016 0.084 -10000 0 -0.23 40 40
Ephrin B1/EPHB1-2 0.017 0.082 -10000 0 -0.24 38 38
cell adhesion mediated by integrin 0.003 0.047 0.22 9 -0.19 13 22
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0.019 0.089 -10000 0 -0.24 42 42
RAC1-CDC42/GTP -0.004 0.059 -10000 0 -0.31 7 7
RASA1 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.081 0.23 32 -0.32 4 36
ruffle organization 0.038 0.13 0.35 46 -0.43 3 49
NCK1 0.025 0.022 -10000 0 -0.43 1 1
receptor internalization -0.027 0.078 0.17 17 -0.25 26 43
Ephrin B/EPHB2/KALRN 0.055 0.059 -10000 0 -0.24 12 12
ROCK1 0.019 0.03 0.18 14 -10000 0 14
RAS family/GDP -0.007 0.045 -10000 0 -0.31 5 5
Rac1/GTP -0.001 0.059 -10000 0 -0.32 7 7
Ephrin B/EPHB1/Src/Paxillin 0.006 0.076 -10000 0 -0.24 36 36
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.056 0.19 1 -0.3 4 5
adherens junction organization -0.019 0.092 -10000 0 -0.26 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.001 0.081 -10000 0 -0.29 7 7
FMN1 -0.032 0.11 -10000 0 -0.27 53 53
mol:IP3 0.004 0.054 -10000 0 -0.25 5 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.092 -10000 0 -0.25 48 48
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.008 0.066 0.18 2 -0.29 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.37 45 45
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.085 -10000 0 -0.24 47 47
VASP -0.011 0.084 -10000 0 -0.25 34 34
ZYX -0.012 0.08 -10000 0 -0.25 40 40
JUB -0.009 0.087 -10000 0 -0.24 48 48
EGFR(dimer) -0.015 0.1 -10000 0 -0.26 47 47
E-cadherin/beta catenin-gamma catenin 0.001 0.1 -10000 0 -0.25 55 55
mol:PI-3-4-5-P3 0.024 0.075 0.21 2 -0.3 5 7
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.025 0.076 0.21 2 -0.31 5 7
FYN 0.002 0.051 -10000 0 -0.27 5 5
mol:Ca2+ 0.004 0.053 -10000 0 -0.25 5 5
JUP 0.021 0.052 -10000 0 -0.39 7 7
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG 0.004 0.054 -10000 0 -0.25 5 5
CDH1 -0.043 0.15 -10000 0 -0.41 55 55
RhoA/GDP 0.013 0.092 0.23 2 -0.29 7 9
establishment of polarity of embryonic epithelium -0.01 0.082 -10000 0 -0.24 34 34
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
EGFR -0.013 0.12 -10000 0 -0.43 34 34
CASR -0.004 0.05 -10000 0 -0.31 2 2
RhoA/GTP 0.016 0.054 -10000 0 -0.3 2 2
AKT2 0.01 0.057 0.18 2 -0.28 5 7
actin cable formation -0.029 0.098 0.18 1 -0.28 39 40
apoptosis -0.003 0.067 0.3 6 -0.19 4 10
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.017 0.073 -10000 0 -0.28 10 10
PIP5K1A -0.01 0.086 -10000 0 -0.24 47 47
PLCG1 0.004 0.055 -10000 0 -0.26 5 5
Rac1/GTP -0.006 0.1 -10000 0 -0.24 47 47
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.003 0.14 -10000 0 -0.54 21 21
HDAC1 0.022 0.015 -10000 0 -10000 0 0
AES 0.025 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.018 0.056 -10000 0 -0.39 8 8
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
TLE1 0.025 0.022 -10000 0 -0.43 1 1
AP1 -0.025 0.089 -10000 0 -0.25 52 52
NCSTN 0.025 0.004 -10000 0 -10000 0 0
ADAM10 0.017 0.063 -10000 0 -0.43 9 9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.067 -10000 0 -10000 0 0
NICD/RBPSUH 0.019 0.11 -10000 0 -0.49 21 21
WIF1 -0.13 0.18 -10000 0 -0.27 240 240
NOTCH1 0.003 0.12 -10000 0 -0.51 21 21
PSENEN 0.022 0.009 -10000 0 -10000 0 0
KREMEN2 -0.007 0.1 -10000 0 -0.43 22 22
DKK1 -0.033 0.13 -10000 0 -0.43 38 38
beta catenin/beta TrCP1 0.012 0.07 0.33 3 -0.38 1 4
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
AXIN1 0.007 0.045 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.021 0.047 0.29 4 -0.22 2 6
PSEN1 0.025 0.005 -10000 0 -10000 0 0
FOS -0.03 0.14 -10000 0 -0.29 82 82
JUN 0.019 0.022 -10000 0 -0.13 8 8
MAP3K7 0.025 0.007 -10000 0 -10000 0 0
CTNNB1 0.002 0.069 0.29 5 -0.39 1 6
MAPK3 0.026 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.008 0.11 -10000 0 -0.28 59 59
HNF1A 0.025 0.022 -10000 0 -0.43 1 1
CTBP1 0.025 0.007 -10000 0 -10000 0 0
MYC -0.037 0.29 -10000 0 -1.4 20 20
NKD1 0.018 0.054 -10000 0 -0.43 6 6
FZD1 0.021 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.015 0.12 -10000 0 -0.5 21 21
apoptosis -0.025 0.089 -10000 0 -0.25 52 52
Delta 1/NOTCHprecursor 0.001 0.14 -10000 0 -0.54 21 21
DLL1 -0.01 0.12 -10000 0 -0.43 35 35
PPARD 0.022 0.06 -10000 0 -1.1 1 1
Gamma Secretase 0.062 0.031 -10000 0 -10000 0 0
APC 0.003 0.068 -10000 0 -0.47 4 4
DVL1 -0.01 0.066 -10000 0 -0.26 23 23
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.008 0.11 -10000 0 -0.27 56 56
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
NLK 0.014 0.011 -10000 0 -10000 0 0
CCND1 -0.014 0.22 -10000 0 -1.3 13 13
WNT1 0.007 0.039 -10000 0 -0.13 30 30
Axin1/APC/beta catenin 0.005 0.088 0.28 5 -0.47 1 6
DKK2 -0.037 0.14 -10000 0 -0.26 98 98
NOTCH1 precursor/DVL1 -0.015 0.13 -10000 0 -0.52 20 20
GSK3B 0.026 0.003 -10000 0 -10000 0 0
FRAT1 0.023 0.031 -10000 0 -0.43 2 2
NOTCH/Deltex homolog 1 0.018 0.12 -10000 0 -0.5 21 21
PPP2R5D 0.01 0.048 0.24 6 -0.3 3 9
MAPK1 0.026 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.01 0.12 -10000 0 -0.24 84 84
RBPJ 0.025 0.004 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.059 0.079 0.36 1 -0.48 4 5
CRKL 0.054 0.08 0.23 37 -0.38 1 38
mol:DAG 0.028 0.049 -10000 0 -0.32 4 4
HRAS 0.05 0.084 0.27 30 -0.3 1 31
MAPK8 0.035 0.072 0.18 16 -0.25 10 26
RAP1A 0.047 0.079 0.23 37 -0.36 1 38
GAB1 0.052 0.082 0.23 39 -0.35 2 41
MAPK14 0.042 0.065 0.16 85 -0.26 2 87
EPO 0.019 0.031 -10000 0 -0.46 1 1
PLCG1 0.028 0.05 -10000 0 -0.32 4 4
EPOR/TRPC2/IP3 Receptors 0.029 0.014 -10000 0 -0.13 1 1
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.02 0.081 -10000 0 -0.27 26 26
GAB1/SHC/GRB2/SOS1 0.07 0.072 0.26 18 -0.33 2 20
EPO/EPOR (dimer) 0.03 0.031 -10000 0 -0.35 1 1
IRS2 0.05 0.081 0.22 35 -0.35 2 37
STAT1 0.035 0.059 -10000 0 -0.35 5 5
STAT5B 0.031 0.053 -10000 0 -0.34 4 4
cell proliferation 0.029 0.094 0.19 94 -0.23 9 103
GAB1/SHIP/PIK3R1/SHP2/SHC 0.047 0.055 -10000 0 -0.33 3 3
TEC 0.047 0.084 0.23 36 -0.25 5 41
SOCS3 -0.032 0.12 -10000 0 -0.43 31 31
STAT1 (dimer) 0.035 0.058 -10000 0 -0.34 5 5
JAK2 0.03 0.013 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.059 0.22 15 -0.22 5 20
EPO/EPOR 0.03 0.031 -10000 0 -0.35 1 1
LYN 0.021 0.037 -10000 0 -0.44 2 2
TEC/VAV2 0.048 0.071 0.2 24 -0.24 5 29
elevation of cytosolic calcium ion concentration 0.029 0.014 -10000 0 -0.13 1 1
SHC1 0.024 0.015 -10000 0 -0.13 4 4
EPO/EPOR (dimer)/LYN 0.044 0.038 -10000 0 -0.29 2 2
mol:IP3 0.028 0.049 -10000 0 -0.32 4 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.07 0.079 0.28 16 -0.33 3 19
SH2B3 0.03 0.016 -10000 0 -0.13 2 2
NFKB1 0.041 0.064 0.16 82 -0.26 2 84
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.054 -10000 0 -0.21 26 26
PTPN6 0.049 0.08 0.29 18 -0.22 5 23
TEC/VAV2/GRB2 0.056 0.071 0.21 22 -0.24 5 27
EPOR 0.029 0.014 -10000 0 -0.13 1 1
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
mol:GDP 0.07 0.073 0.26 18 -0.33 2 20
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 0.019 0.05 -10000 0 -0.43 5 5
CRKL/CBL/C3G 0.06 0.064 0.26 7 -0.2 1 8
VAV2 0.052 0.08 0.23 38 -0.38 1 39
CBL 0.051 0.078 0.23 36 -0.21 1 37
SHC/Grb2/SOS1 0.029 0.039 -10000 0 -0.36 1 1
STAT5A 0.025 0.073 -10000 0 -0.35 12 12
GRB2 0.025 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.078 -10000 0 -0.34 11 11
LYN/PLCgamma2 0.03 0.049 -10000 0 -0.27 9 9
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK 0.047 0.093 0.23 39 -0.28 10 49
BCL2 0.056 0.12 0.36 1 -0.73 8 9
TCGA08_p53

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
CDKN2A -0.019 0.078 -10000 0 -0.3 30 30
TP53 -0.015 0.069 -10000 0 -0.29 22 22
Senescence -0.015 0.069 -10000 0 -0.28 22 22
Apoptosis -0.015 0.069 -10000 0 -0.28 22 22
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.056 0.21 32 -10000 0 32
MDM4 0.025 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.01 0.063 -10000 0 -0.35 11 11
CCNA2 -0.008 0.1 -10000 0 -0.24 58 58
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
JAK3 -0.009 0.1 -10000 0 -0.24 59 59
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.01 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.02 0.13 0.23 1 -0.35 39 40
SHC1 0.024 0.015 -10000 0 -0.13 4 4
SP1 0.027 0.036 -10000 0 -0.33 4 4
IL2RA -0.018 0.11 -10000 0 -0.7 10 10
IL2RB -0.029 0.13 -10000 0 -0.43 37 37
SOS1 0.026 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.088 -10000 0 -0.22 48 48
G1/S transition of mitotic cell cycle 0.001 0.18 0.28 5 -0.48 38 43
PTPN11 0.026 0.003 -10000 0 -10000 0 0
CCND2 0.013 0.07 -10000 0 -0.7 4 4
LCK -0.021 0.12 -10000 0 -0.25 73 73
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL2 0.016 0.004 -10000 0 -10000 0 0
CDK6 0.003 0.082 -10000 0 -0.43 15 15
CCND3 -0.015 0.12 0.32 1 -0.44 8 9
Coregulation of Androgen receptor activity

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
NRIP1 0.025 0.004 -9999 0 -10000 0 0
SVIL 0.016 0.037 -9999 0 -0.28 2 2
ZNF318 0.026 0.003 -9999 0 -10000 0 0
JMJD2C 0 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.019 0.11 -9999 0 -0.26 72 72
CARM1 0.025 0.005 -9999 0 -10000 0 0
PRDX1 0.012 0.067 -9999 0 -0.43 10 10
PELP1 0.026 0.002 -9999 0 -10000 0 0
CTNNB1 0.025 0.004 -9999 0 -10000 0 0
AKT1 0.025 0.005 -9999 0 -10000 0 0
PTK2B 0.018 0.032 -9999 0 -0.13 21 21
MED1 0.026 0.003 -9999 0 -10000 0 0
MAK 0.007 0.061 -9999 0 -0.43 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.012 0.067 -9999 0 -0.43 10 10
GSN 0.019 0.053 -9999 0 -0.36 8 8
NCOA2 -0.004 0.11 -9999 0 -0.43 29 29
NCOA6 0.025 0.005 -9999 0 -10000 0 0
DNA-PK 0.05 0.014 -9999 0 -10000 0 0
NCOA4 0.025 0.005 -9999 0 -10000 0 0
PIAS3 0.023 0.008 -9999 0 -10000 0 0
cell proliferation -0.005 0.079 -9999 0 -0.52 9 9
XRCC5 0.026 0.002 -9999 0 -10000 0 0
UBE3A 0.026 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.027 0.12 -9999 0 -0.26 83 83
FHL2 -0.024 0.17 -9999 0 -0.99 13 13
RANBP9 0.026 0.004 -9999 0 -10000 0 0
JMJD1A -0.007 0.043 -9999 0 -0.13 47 47
CDK6 0.003 0.082 -9999 0 -0.43 15 15
TGFB1I1 0.022 0.039 -9999 0 -0.31 5 5
T-DHT/AR/CyclinD1 -0.027 0.12 -9999 0 -0.27 79 79
XRCC6 0.026 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.022 0.13 -9999 0 -0.25 98 98
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
BRCA1 0.025 0.013 -9999 0 -0.13 3 3
TCF4 0.024 0.022 -9999 0 -0.43 1 1
CDKN2A -0.015 0.12 -9999 0 -0.43 30 30
SRF 0.024 0.029 -9999 0 -0.13 11 11
NKX3-1 -0.037 0.15 -9999 0 -0.84 11 11
KLK3 0.005 0.045 -9999 0 -10000 0 0
TMF1 0.025 0.004 -9999 0 -10000 0 0
HNRNPA1 0.026 0.003 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.021 0.11 -9999 0 -0.26 74 74
AR -0.056 0.16 -9999 0 -0.4 76 76
UBA3 0.025 0.004 -9999 0 -10000 0 0
PATZ1 0.026 0.004 -9999 0 -10000 0 0
PAWR 0.006 0.079 -9999 0 -0.23 35 35
PRKDC 0.025 0.005 -9999 0 -10000 0 0
PA2G4 0.026 0.003 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.015 0.1 -9999 0 -0.23 72 72
RPS6KA3 0.025 0.021 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.019 0.11 -9999 0 -0.26 72 72
LATS2 0.018 0.043 -9999 0 -0.43 3 3
T-DHT/AR/PRX1 -0.023 0.11 -9999 0 -0.24 81 81
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -0.08 1 1
VAV3 -0.029 0.11 -9999 0 -0.43 25 25
KLK2 -0.043 0.12 -9999 0 -0.44 28 28
CASP8 0.02 0.034 -9999 0 -0.43 1 1
T-DHT/AR/TIF2/CARM1 -0.017 0.13 -9999 0 -0.27 77 77
TMPRSS2 -0.084 0.26 -9999 0 -0.92 38 38
CCND1 0.01 0.073 -9999 0 -0.43 11 11
PIAS1 0.022 0.042 -9999 0 -0.43 4 4
mol:T-DHT -0.006 0.021 -9999 0 -0.065 45 45
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.025 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.027 0.12 -9999 0 -0.28 71 71
CMTM2 0.013 0.072 -9999 0 -0.43 11 11
SNURF 0.013 0.073 -9999 0 -0.39 14 14
ZMIZ1 0.016 0.032 -9999 0 -10000 0 0
CCND3 0.026 0.008 -9999 0 -0.13 1 1
TGIF1 0.017 0.055 -9999 0 -0.26 14 14
FKBP4 0.024 0.007 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.042 -10000 0 -0.43 4 4
ANTXR2 0.02 0.037 -10000 0 -0.43 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.007 -10000 0 -0.058 6 6
monocyte activation -0.14 0.23 -10000 0 -0.43 159 159
MAP2K2 0.012 0.041 -10000 0 -0.61 2 2
MAP2K1 -0.003 0.008 -10000 0 -0.11 1 1
MAP2K7 -0.003 0.006 -10000 0 -10000 0 0
MAP2K6 -0.004 0.012 -10000 0 -0.22 1 1
CYAA -0.007 0.025 -10000 0 -0.21 6 6
MAP2K4 -0.003 0.008 -10000 0 -0.11 2 2
IL1B -0.043 0.08 0.17 2 -0.22 70 72
Channel 0.027 0.033 -10000 0 -0.23 6 6
NLRP1 -0.004 0.015 -10000 0 -0.22 2 2
CALM1 0.025 0.009 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.074 -10000 0 -0.39 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.007 0.058 6 -10000 0 6
MAPK3 -0.003 0.006 -10000 0 -10000 0 0
MAPK1 -0.003 0.006 -10000 0 -10000 0 0
PGR -0.021 0.059 -10000 0 -0.22 38 38
PA/Cellular Receptors 0.029 0.036 -10000 0 -0.25 6 6
apoptosis -0.001 0.007 -10000 0 -0.058 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.029 -10000 0 -0.22 6 6
macrophage activation -0.005 0.006 -10000 0 -10000 0 0
TNF -0.061 0.16 -10000 0 -0.43 62 62
VCAM1 -0.14 0.23 -10000 0 -0.44 157 157
platelet activation -0.003 0.074 -10000 0 -0.39 16 16
MAPKKK cascade -0.004 0.023 0.089 1 -0.077 33 34
IL18 -0.012 0.051 0.19 1 -0.24 18 19
negative regulation of macrophage activation -0.001 0.007 -10000 0 -0.058 6 6
LEF -0.001 0.007 -10000 0 -0.058 6 6
CASP1 -0.002 0.019 -10000 0 -0.1 11 11
mol:cAMP -0.003 0.075 -10000 0 -0.4 16 16
necrosis -0.001 0.007 -10000 0 -0.058 6 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.031 -10000 0 -0.22 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
Jak2/Leptin Receptor 0.004 0.13 0.26 1 -0.4 26 27
PTP1B/AKT1 0.013 0.095 0.19 5 -0.34 11 16
FYN 0.025 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.097 0.2 5 -0.35 12 17
EGFR -0.015 0.12 -10000 0 -0.44 34 34
EGF/EGFR -0.015 0.13 -10000 0 -0.3 54 54
CSF1 0.016 0.048 -10000 0 -0.43 5 5
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.025 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.012 0.099 0.2 4 -0.35 12 16
Insulin Receptor/Insulin 0.018 0.09 -10000 0 -0.37 8 8
HCK 0.013 0.067 -10000 0 -0.43 9 9
CRK 0.026 0.002 -10000 0 -10000 0 0
TYK2 0.008 0.1 0.29 18 -0.35 11 29
EGF -0.008 0.11 -10000 0 -0.43 27 27
YES1 0.022 0.037 -10000 0 -0.43 3 3
CAV1 0.019 0.12 0.25 34 -0.34 16 50
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.021 0.097 0.21 1 -0.34 11 12
cell migration -0.003 0.097 0.35 12 -0.2 5 17
STAT3 0.026 0.003 -10000 0 -10000 0 0
PRLR 0.006 0.091 -10000 0 -0.38 22 22
ITGA2B -0.013 0.12 -10000 0 -0.43 36 36
CSF1R 0.003 0.096 -10000 0 -0.43 21 21
Prolactin Receptor/Prolactin 0.019 0.068 -10000 0 -0.31 17 17
FGR 0.021 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.012 0.097 0.21 3 -0.34 12 15
Crk/p130 Cas 0.023 0.099 0.21 2 -0.34 11 13
DOK1 0.009 0.095 0.2 9 -0.39 9 18
JAK2 0 0.13 -10000 0 -0.42 27 27
Jak2/Leptin Receptor/Leptin -0.02 0.11 -10000 0 -0.33 23 23
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PTPN1 0.003 0.098 0.2 5 -0.36 12 17
LYN 0.02 0.036 -10000 0 -0.43 2 2
CDH2 0.024 0.022 -10000 0 -0.43 1 1
SRC 0.024 0.054 -10000 0 -0.37 4 4
ITGB3 -0.003 0.089 -10000 0 -0.2 59 59
CAT1/PTP1B -0.016 0.16 0.3 28 -0.38 35 63
CAPN1 0.025 0.022 -10000 0 -0.44 1 1
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.087 -10000 0 -0.37 7 7
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.022 0.1 -10000 0 -0.35 22 22
negative regulation of transcription 0.001 0.13 -10000 0 -0.41 27 27
FCGR2A 0.001 0.093 -10000 0 -0.27 38 38
FER 0.009 0.088 -10000 0 -0.44 17 17
alphaIIb/beta3 Integrin -0.012 0.12 -10000 0 -0.32 50 50
BLK -0.03 0.11 -10000 0 -0.2 99 99
Insulin Receptor/Insulin/Shc 0.038 0.03 -10000 0 -0.26 3 3
RHOA 0.026 0.005 -10000 0 -10000 0 0
LEPR 0.016 0.042 -10000 0 -0.21 11 11
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
p210 bcr-abl/Grb2 0.025 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.034 0.17 0.26 18 -0.42 44 62
PRL 0.004 0.02 -10000 0 -10000 0 0
SOCS3 -0.081 0.33 -10000 0 -1.3 33 33
SPRY2 0.023 0.029 -10000 0 -0.44 1 1
Insulin Receptor/Insulin/IRS1 0.039 0.032 -10000 0 -0.26 4 4
CSF1/CSF1R 0.005 0.11 0.21 2 -0.34 20 22
Ras protein signal transduction 0.014 0.11 0.52 18 -10000 0 18
IRS1 0.025 0.021 -10000 0 -0.43 1 1
INS 0.005 0.039 -10000 0 -0.43 3 3
LEP 0.007 0.019 -10000 0 -0.13 3 3
STAT5B 0.009 0.11 0.2 5 -0.38 13 18
STAT5A 0.005 0.11 0.2 4 -0.35 18 22
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.097 0.2 3 -0.35 11 14
CSN2 -0.011 0.061 -10000 0 -0.57 2 2
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
LAT -0.018 0.15 -10000 0 -0.45 44 44
YBX1 0.025 0.032 -10000 0 -0.43 2 2
LCK -0.022 0.12 -10000 0 -0.25 73 73
SHC1 0.024 0.015 -10000 0 -0.13 4 4
NOX4 -0.011 0.1 -10000 0 -0.22 70 70
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 -0.003 0.1 0.23 7 -0.4 19 26
CRKL -0.001 0.1 -10000 0 -0.42 20 20
HRAS 0.005 0.11 -10000 0 -0.36 21 21
mol:PIP3 0.012 0.1 0.31 6 -0.37 18 24
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.013 -10000 0 -10000 0 0
GAB1 0.002 0.1 -10000 0 -0.44 20 20
FOXO3 0.019 0.12 0.29 8 -0.38 23 31
AKT1 0.02 0.13 0.3 8 -0.41 25 33
BAD 0.023 0.13 0.31 10 -0.38 24 34
megakaryocyte differentiation -0.001 0.1 -10000 0 -0.4 21 21
GSK3B 0.019 0.13 0.3 9 -0.38 23 32
RAF1 0.004 0.094 0.26 1 -0.31 19 20
SHC1 0.024 0.015 -10000 0 -0.13 4 4
STAT3 0.003 0.1 -10000 0 -0.43 20 20
STAT1 -0.015 0.22 -10000 0 -0.9 25 25
HRAS/SPRED1 0.015 0.099 0.25 1 -0.31 19 20
cell proliferation -0.003 0.11 -10000 0 -0.44 21 21
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
TEC 0.014 0.066 -10000 0 -0.29 17 17
RPS6KB1 0.014 0.12 0.26 3 -0.43 21 24
HRAS/SPRED2 0.016 0.1 0.25 1 -0.3 20 21
LYN/TEC/p62DOK 0.028 0.12 -10000 0 -0.43 22 22
MAPK3 0.013 0.082 0.21 18 -0.26 8 26
STAP1 -0.002 0.1 -10000 0 -0.42 22 22
GRAP2 -0.008 0.1 -10000 0 -0.26 54 54
JAK2 -0.015 0.19 -10000 0 -0.77 25 25
STAT1 (dimer) -0.012 0.22 -10000 0 -0.88 25 25
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.022 0.12 -10000 0 -0.42 24 24
actin filament polymerization -0.004 0.099 0.34 4 -0.42 16 20
LYN 0.02 0.036 -10000 0 -0.43 2 2
STAP1/STAT5A (dimer) -0.012 0.16 -10000 0 -0.61 26 26
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.021 0.1 -10000 0 -0.39 19 19
PI3K 0.036 0.12 0.27 3 -0.41 18 21
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.01 0.25 -10000 0 -1.1 20 20
MAPK8 -0.003 0.11 -10000 0 -0.45 21 21
STAT3 (dimer) 0.003 0.1 -10000 0 -0.42 20 20
positive regulation of transcription 0.014 0.071 0.2 18 -0.21 8 26
mol:GDP 0.002 0.11 -10000 0 -0.38 22 22
PIK3C2B 0.001 0.1 -10000 0 -0.43 18 18
CBL/CRKL 0.01 0.1 -10000 0 -0.4 19 19
FER -0.005 0.12 -10000 0 -0.46 23 23
SH2B3 0.003 0.1 -10000 0 -0.43 20 20
PDPK1 0.011 0.1 0.32 7 -0.36 17 24
SNAI2 -0.002 0.11 0.38 1 -0.43 22 23
positive regulation of cell proliferation -0.009 0.19 -10000 0 -0.73 24 24
KITLG 0.016 0.07 -10000 0 -0.44 10 10
cell motility -0.009 0.19 -10000 0 -0.73 24 24
PTPN6 0.014 0.061 -10000 0 -0.43 8 8
EPOR 0.03 0.087 -10000 0 -1.2 1 1
STAT5A (dimer) -0.005 0.16 -10000 0 -0.61 26 26
SOCS1 0.007 0.07 -10000 0 -0.43 8 8
cell migration 0.017 0.11 0.43 23 -10000 0 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.016 0.03 -10000 0 -0.29 2 2
VAV1 0.004 0.09 -10000 0 -0.43 18 18
GRB10 -0.001 0.094 0.24 1 -0.41 17 18
PTPN11 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT 0.004 0.11 -10000 0 -0.45 20 20
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.007 0.082 0.22 6 -0.25 16 22
CBL 0.024 0.007 -10000 0 -10000 0 0
KIT -0.014 0.26 -10000 0 -1.2 19 19
MAP2K2 0.012 0.087 0.26 16 -0.25 15 31
SHC/Grb2/SOS1 0.036 0.11 -10000 0 -0.4 19 19
STAT5A -0.005 0.17 -10000 0 -0.63 26 26
GRB2 0.025 0.005 -10000 0 -10000 0 0
response to radiation -0.002 0.1 0.38 1 -0.42 22 23
SHC/GRAP2 0.011 0.08 -10000 0 -0.3 24 24
PTPRO -0.002 0.11 -10000 0 -0.41 21 21
SH2B2 -0.007 0.096 0.24 1 -0.43 16 17
DOK1 0.025 0.021 -10000 0 -0.43 1 1
MATK -0.017 0.12 -10000 0 -0.43 23 23
CREBBP 0.034 0.033 -10000 0 -10000 0 0
BCL2 0.009 0.2 -10000 0 -1.3 8 8
Syndecan-2-mediated 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
Syndecan-2/Fibronectin 0.016 0.044 0.16 1 -0.25 9 10
EPHB2 0.017 0.042 -10000 0 -0.43 3 3
Syndecan-2/TACI 0.014 0.042 -10000 0 -0.26 9 9
LAMA1 -0.019 0.13 -10000 0 -0.36 53 53
Syndecan-2/alpha2 ITGB1 0.021 0.093 -10000 0 -0.26 38 38
HRAS 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.002 0.037 -10000 0 -0.25 9 9
ITGA5 0.016 0.048 -10000 0 -0.43 3 3
BAX 0.001 0.033 -10000 0 -10000 0 0
EPB41 0.021 0.024 -10000 0 -0.28 2 2
positive regulation of cell-cell adhesion 0.017 0.036 -10000 0 -0.23 9 9
LAMA3 -0.005 0.1 -10000 0 -0.43 24 24
EZR 0.018 0.056 -10000 0 -0.43 7 7
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.014 0.04 -10000 0 -0.43 2 2
Syndecan-2/MMP2 0.011 0.057 -10000 0 -0.25 18 18
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.072 -10000 0 -0.31 19 19
dendrite morphogenesis 0.012 0.046 -10000 0 -0.24 12 12
Syndecan-2/GM-CSF 0.012 0.04 -10000 0 -0.26 9 9
determination of left/right symmetry 0.004 0.044 -10000 0 -0.3 9 9
Syndecan-2/PKC delta 0.007 0.076 -10000 0 -0.3 24 24
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.022 0.063 0.19 44 -0.23 9 53
MAPK1 0.02 0.062 0.19 41 -0.23 9 50
Syndecan-2/RACK1 0.029 0.039 -10000 0 -0.22 9 9
NF1 0.025 0.021 -10000 0 -0.43 1 1
FGFR/FGF/Syndecan-2 0.004 0.044 -10000 0 -0.3 9 9
ITGA2 0 0.097 -10000 0 -0.43 20 20
MAPK8 -0.001 0.052 -10000 0 -0.25 19 19
Syndecan-2/alpha2/beta1 Integrin 0.011 0.1 0.19 1 -0.26 53 54
Syndecan-2/Kininogen 0.011 0.043 -10000 0 -0.26 9 9
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
SRC 0.027 0.063 0.19 46 -0.21 9 55
Syndecan-2/CASK/Protein 4.1 0.013 0.038 -10000 0 -0.22 10 10
extracellular matrix organization 0.015 0.041 -10000 0 -0.24 10 10
actin cytoskeleton reorganization 0.016 0.043 0.16 1 -0.25 9 10
Syndecan-2/Caveolin-2/Ras 0.024 0.042 -10000 0 -0.23 9 9
Syndecan-2/Laminin alpha3 0.004 0.076 0.16 1 -0.29 25 26
Syndecan-2/RasGAP 0.04 0.041 -10000 0 -0.21 9 9
alpha5/beta1 Integrin 0.028 0.038 -10000 0 -0.27 4 4
PRKCD 0.005 0.095 -10000 0 -0.43 21 21
Syndecan-2 dimer 0.012 0.046 -10000 0 -0.24 12 12
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.029 0.042 0.18 9 -0.2 9 18
RHOA 0.025 0.004 -10000 0 -10000 0 0
SDCBP 0.025 0.006 -10000 0 -10000 0 0
TNFRSF13B -0.002 0.027 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.016 0.072 -10000 0 -0.31 19 19
Syndecan-2/Synbindin 0.018 0.04 -10000 0 -0.25 9 9
TGFB1 0.021 0.023 -10000 0 -0.43 1 1
CASP3 0.015 0.086 0.19 41 -0.28 23 64
FN1 0.02 0.029 -10000 0 -0.13 17 17
Syndecan-2/IL8 -0.028 0.099 0.17 4 -0.26 59 63
SDC2 0.004 0.044 -10000 0 -0.3 9 9
KNG1 -0.008 0.032 -10000 0 -0.13 20 20
Syndecan-2/Neurofibromin 0.019 0.04 -10000 0 -0.25 9 9
TRAPPC4 0.024 0.006 -10000 0 -10000 0 0
CSF2 -0.014 0.008 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.015 0.041 -10000 0 -0.24 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.036 -10000 0 -0.23 9 9
Syndecan-2/Ezrin 0.027 0.059 -10000 0 -0.3 12 12
PRKACA 0.026 0.063 0.19 43 -0.23 9 52
angiogenesis -0.028 0.099 0.17 4 -0.26 59 63
MMP2 0.013 0.068 -10000 0 -0.43 9 9
IL8 -0.062 0.15 -10000 0 -0.43 59 59
calcineurin-NFAT signaling pathway 0.014 0.042 -10000 0 -0.26 9 9
IL27-mediated signaling events

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
TGFB1 0.021 0.023 -10000 0 -0.43 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.001 0.088 0.36 5 -0.48 2 7
IL27/IL27R/JAK1 0.024 0.12 0.88 2 -0.32 1 3
TBX21 -0.018 0.16 0.43 17 -0.39 24 41
IL12B 0 0.023 -10000 0 -0.13 3 3
IL12A -0.007 0.062 -10000 0 -0.3 19 19
IL6ST 0.001 0.11 -10000 0 -0.43 26 26
IL27RA/JAK1 0.024 0.052 0.37 2 -10000 0 2
IL27 0.013 0.037 -10000 0 -0.13 22 22
TYK2 0.025 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.014 0.12 -10000 0 -0.5 3 3
T-helper 2 cell differentiation -0.001 0.088 0.36 5 -0.48 2 7
T cell proliferation during immune response -0.001 0.088 0.36 5 -0.48 2 7
MAPKKK cascade 0.001 0.088 0.48 2 -0.36 5 7
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT2 0.024 0.015 -10000 0 -10000 0 0
STAT1 0.021 0.029 -10000 0 -10000 0 0
IL12RB1 0 0.096 -10000 0 -0.43 20 20
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.033 0.16 0.43 15 -0.39 36 51
IL27/IL27R/JAK2/TYK2 0.001 0.088 0.48 2 -0.37 5 7
positive regulation of T cell mediated cytotoxicity 0.001 0.088 0.48 2 -0.36 5 7
STAT1 (dimer) 0.008 0.18 0.56 22 -0.45 7 29
JAK2 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.021 0.012 -10000 0 -10000 0 0
STAT2 (dimer) 0.02 0.096 0.39 3 -0.37 4 7
T cell proliferation -0.021 0.1 0.39 3 -0.36 10 13
IL12/IL12R/TYK2/JAK2 0.004 0.12 -10000 0 -0.77 8 8
IL17A -0.012 0.12 -10000 0 -0.48 2 2
mast cell activation -0.001 0.088 0.36 5 -0.48 2 7
IFNG 0.006 0.026 0.12 4 -0.11 5 9
T cell differentiation -0.002 0.004 -10000 0 -0.014 8 8
STAT3 (dimer) 0.02 0.097 0.32 6 -0.37 4 10
STAT5A (dimer) 0.015 0.11 0.39 3 -0.42 7 10
STAT4 (dimer) -0.009 0.13 0.39 3 -0.37 16 19
STAT4 -0.063 0.16 -10000 0 -0.26 145 145
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.027 0.071 -10000 0 -10000 0 0
GATA3 -0.082 0.42 0.62 32 -1.3 41 73
IL18 -0.009 0.062 -10000 0 -0.3 18 18
positive regulation of mast cell cytokine production 0.02 0.096 0.32 6 -0.37 4 10
IL27/EBI3 0.019 0.066 0.24 2 -0.28 16 18
IL27RA 0.009 0.032 -10000 0 -10000 0 0
IL6 -0.042 0.13 -10000 0 -0.43 41 41
STAT5A 0.016 0.067 -10000 0 -0.4 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.015 0.024 -10000 0 -10000 0 0
IL1B -0.056 0.11 -10000 0 -0.3 69 69
EBI3 0.011 0.077 0.14 2 -0.34 18 20
TNF -0.049 0.11 -10000 0 -0.3 62 62
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.034 0.066 -10000 0 -0.22 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.028 0.12 -10000 0 -0.41 16 16
AKT1 -0.012 0.18 -10000 0 -0.67 29 29
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.18 -10000 0 -0.69 29 29
mol:Ca2+ -0.021 0.095 -10000 0 -0.37 22 22
IGF1R 0.025 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.012 0.075 -10000 0 -0.27 29 29
SHC1 0.024 0.015 -10000 0 -0.13 4 4
apoptosis 0.01 0.17 0.64 29 -10000 0 29
RhoA/GTP 0.012 0.034 -10000 0 -0.2 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.002 0.12 -10000 0 -0.4 14 14
regulation of stress fiber formation 0.002 0.064 0.39 2 -0.18 14 16
E2/ERA-ERB (dimer) 0.017 0.062 -10000 0 -0.24 22 22
KRAS 0.025 0.005 -10000 0 -10000 0 0
G13/GTP 0.023 0.043 -10000 0 -0.23 11 11
pseudopodium formation -0.002 0.064 0.18 14 -0.39 2 16
E2/ER alpha (dimer)/PELP1 0.024 0.048 -10000 0 -0.26 11 11
GRB2 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.043 -10000 0 -0.43 4 4
GNAO1 0.02 0.052 -10000 0 -0.43 6 6
HRAS 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.002 0.13 0.28 2 -0.38 29 31
E2/ER beta (dimer) 0.011 0.046 -10000 0 -0.3 9 9
mol:GDP 0 0.07 0.14 1 -0.29 21 22
mol:NADP 0.002 0.13 0.28 2 -0.38 29 31
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.021 0.098 -10000 0 -0.39 22 22
IGF-1R heterotetramer 0.025 0.004 -10000 0 -10000 0 0
PLCB1 -0.012 0.092 -10000 0 -0.38 19 19
PLCB2 -0.013 0.099 -10000 0 -0.4 22 22
IGF1 0.012 0.075 -10000 0 -0.43 12 12
mol:L-citrulline 0.002 0.13 0.28 2 -0.38 29 31
RHOA 0.025 0.004 -10000 0 -10000 0 0
Gai/GDP 0.004 0.12 -10000 0 -0.62 16 16
JNK cascade 0.011 0.046 -10000 0 -0.3 9 9
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
ESR2 0.015 0.065 -10000 0 -0.32 14 14
GNAQ 0.025 0.004 -10000 0 -10000 0 0
ESR1 0.01 0.073 -10000 0 -0.27 23 23
Gq family/GDP/Gbeta gamma -0.026 0.18 -10000 0 -0.61 27 27
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.074 -10000 0 -1.2 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.001 0.12 -10000 0 -0.39 15 15
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
E2/ER alpha (dimer) 0.008 0.052 -10000 0 -0.3 11 11
STRN 0.007 0.091 -10000 0 -0.42 20 20
GNAL -0.023 0.14 -10000 0 -0.42 49 49
PELP1 0.026 0.002 -10000 0 -10000 0 0
MAPK11 0.006 0.044 -10000 0 -0.26 12 12
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
HBEGF -0.021 0.14 0.35 19 -0.35 22 41
cAMP biosynthetic process -0.009 0.087 -10000 0 -0.21 66 66
SRC -0.027 0.12 -10000 0 -0.38 18 18
PI3K 0.038 0.007 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.02 0.075 -10000 0 -0.26 22 22
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.025 0.092 -10000 0 -0.32 20 20
Gs family/GTP -0.003 0.091 -10000 0 -0.22 66 66
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.022 -10000 0 -10000 0 0
vasodilation 0.003 0.13 0.28 2 -0.36 29 31
mol:DAG -0.021 0.098 -10000 0 -0.39 22 22
Gs family/GDP/Gbeta gamma -0.013 0.089 -10000 0 -0.22 57 57
MSN -0.003 0.067 0.18 14 -0.42 2 16
Gq family/GTP -0.002 0.094 -10000 0 -0.37 22 22
mol:PI-3-4-5-P3 -0.007 0.18 -10000 0 -0.66 29 29
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.003 0.13 0.36 29 -0.28 2 31
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.074 -10000 0 -0.27 21 21
NOS3 0 0.14 0.28 2 -0.4 29 31
GNA11 0.018 0.056 -10000 0 -0.43 7 7
MAPKKK cascade -0.007 0.15 0.37 3 -0.44 38 41
E2/ER alpha (dimer)/PELP1/Src -0.001 0.12 0.26 8 -0.4 16 24
ruffle organization -0.002 0.064 0.18 14 -0.39 2 16
ROCK2 0.003 0.067 0.19 14 -0.28 2 16
GNA14 0.007 0.087 -10000 0 -0.35 23 23
GNA15 0.011 0.077 -10000 0 -0.36 17 17
GNA13 0.025 0.004 -10000 0 -10000 0 0
MMP9 -0.042 0.13 0.33 4 -0.36 27 31
MMP2 -0.017 0.13 0.28 10 -0.35 19 29
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.043 -10000 0 -0.43 4 4
HDAC4 0.025 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.026 -10000 0 -0.13 18 18
CDKN1A -0.037 0.13 -10000 0 -0.66 20 20
KAT2B 0.025 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
FOXO3 -0.003 0.035 0.37 4 -10000 0 4
FOXO1 0.024 0.023 -10000 0 -0.43 1 1
FOXO4 0.012 0.028 -10000 0 -0.25 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
TAT -0.023 0.12 -10000 0 -0.43 33 33
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.063 0.12 -10000 0 -0.31 82 82
PPARGC1A 0.009 0.084 -10000 0 -0.43 16 16
FHL2 0.005 0.082 -10000 0 -0.43 13 13
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.026 0.16 18 -10000 0 18
HIST2H4A 0.013 0.026 0.13 18 -10000 0 18
SIRT1/FOXO3a 0.021 0.037 0.26 4 -0.18 2 6
SIRT1 0.03 0.035 0.2 18 -10000 0 18
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.027 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.025 0.052 0.23 1 -0.22 13 14
apoptosis -0.045 0.031 -10000 0 -10000 0 0
SIRT1/PGC1A 0.025 0.059 0.14 17 -0.25 16 33
p53/SIRT1 0.038 0.089 0.39 18 -0.31 11 29
SIRT1/FOXO4 0.031 0.039 -10000 0 -0.22 5 5
FOXO1/FHL2/SIRT1 0.04 0.053 -10000 0 -0.23 14 14
HIST1H1E 0.007 0.043 -10000 0 -0.23 14 14
SIRT1/p300 0.037 0.041 -10000 0 -0.31 4 4
muscle cell differentiation 0.028 0.12 0.26 82 -0.22 10 92
TP53 0.019 0.08 0.2 19 -0.42 12 31
KU70/SIRT1/BAX 0.045 0.032 -10000 0 -10000 0 0
CREBBP 0.026 0.002 -10000 0 -10000 0 0
MEF2D 0.025 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.004 0.096 0.18 1 -0.3 33 34
ACSS2 0.014 0.025 0.13 18 -10000 0 18
SIRT1/PCAF/MYOD -0.028 0.12 0.22 10 -0.26 82 92
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.024 0.039 -10000 0 -0.23 4 4
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
SPHK1 -0.02 0.14 -10000 0 -0.72 17 17
mol:S1P -0.018 0.13 -10000 0 -0.63 17 17
S1P1/S1P/Gi -0.027 0.13 -10000 0 -0.38 43 43
GNAO1 0.015 0.054 -10000 0 -0.43 6 6
PDGFB-D/PDGFRB/PLCgamma1 -0.017 0.13 0.37 2 -0.35 43 45
PLCG1 -0.026 0.12 -10000 0 -0.36 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
GNAI2 0.021 0.015 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.04 -10000 0 -0.44 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.026 -10000 0 -0.19 4 4
S1P1/S1P -0.015 0.1 -10000 0 -0.47 16 16
negative regulation of cAMP metabolic process -0.026 0.12 -10000 0 -0.37 43 43
MAPK3 -0.048 0.18 -10000 0 -0.53 50 50
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
KDR 0.018 0.036 -10000 0 -0.43 2 2
PLCB2 -0.01 0.11 0.31 3 -0.44 17 20
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.087 -10000 0 -0.4 16 16
receptor internalization -0.015 0.096 -10000 0 -0.43 16 16
PTGS2 -0.089 0.32 -10000 0 -1 49 49
Rac1/GTP -0.014 0.082 -10000 0 -0.38 15 15
RHOA 0.025 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.033 -10000 0 -0.13 21 21
negative regulation of T cell proliferation -0.026 0.12 -10000 0 -0.37 43 43
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.026 -10000 0 -0.44 1 1
MAPK1 -0.048 0.18 -10000 0 -0.53 50 50
S1P1/S1P/PDGFB-D/PDGFRB -0.004 0.1 0.22 1 -0.4 16 17
ABCC1 0.025 0.015 -10000 0 -0.13 4 4
LPA4-mediated signaling events

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
ADCY4 -0.009 0.028 -10000 0 -0.26 5 5
ADCY5 -0.014 0.049 -10000 0 -0.27 15 15
ADCY6 -0.007 0.018 -10000 0 -0.26 2 2
ADCY7 -0.007 0.018 -10000 0 -0.26 2 2
ADCY1 -0.03 0.069 -10000 0 -0.24 42 42
ADCY2 -0.012 0.041 -10000 0 -0.26 12 12
ADCY3 -0.007 0.018 -10000 0 -0.26 2 2
ADCY8 -0.031 0.076 -10000 0 -0.26 46 46
PRKCE 0.004 0.023 -10000 0 -0.3 2 2
ADCY9 -0.007 0.022 -10000 0 -0.26 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.078 0.18 21 -0.22 16 37
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.009 0.11 0.23 1 -0.45 16 17
BAG4 0.015 0.067 -10000 0 -0.43 10 10
BAD 0.005 0.057 0.24 13 -0.14 12 25
NFKBIA 0.026 0.003 -10000 0 -10000 0 0
BIRC3 -0.004 0.1 -10000 0 -0.43 23 23
BAX 0.008 0.051 0.18 17 -0.16 4 21
EnzymeConsortium:3.1.4.12 0 0.03 0.064 5 -0.094 18 23
IKBKB -0.004 0.12 0.22 10 -0.44 14 24
MAP2K2 0.003 0.058 0.18 22 -0.2 1 23
MAP2K1 -0.001 0.051 0.17 11 -0.19 2 13
SMPD1 0.002 0.038 0.12 10 -0.14 7 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.002 0.12 0.3 6 -0.44 15 21
MAP2K4 -0.001 0.048 0.2 4 -0.18 3 7
protein ubiquitination -0.006 0.11 0.22 1 -0.44 15 16
EnzymeConsortium:2.7.1.37 -0.001 0.059 0.19 9 -0.19 4 13
response to UV 0 0.001 0.002 9 -0.002 4 13
RAF1 0.001 0.051 0.17 12 -0.18 3 15
CRADD 0.026 0.002 -10000 0 -10000 0 0
mol:ceramide 0.001 0.046 0.12 8 -0.14 18 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.008 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.047 0.16 6 -0.18 4 10
TRADD 0.025 0.021 -10000 0 -0.43 1 1
RELA/p50 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.005 0.055 0.18 9 -0.2 1 10
MAPK1 0.004 0.056 0.18 9 -0.23 2 11
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD -0.007 0.11 0.26 6 -0.4 20 26
KSR1 0 0.047 0.15 6 -0.15 12 18
MAPK8 -0.006 0.049 0.2 3 -0.2 8 11
TRAF2 0.025 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.008 0.11 0.22 1 -0.44 14 15
TNF R/SODD 0.024 0.058 -10000 0 -0.31 13 13
TNF -0.061 0.16 -10000 0 -0.43 62 62
CYCS 0.017 0.061 0.19 27 -0.14 2 29
IKBKG -0.008 0.11 0.21 2 -0.43 15 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.007 0.12 -10000 0 -0.38 26 26
RELA 0.025 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AIFM1 0.008 0.052 0.16 23 -0.16 2 25
TNF/TNF R/SODD 0.001 0.12 -10000 0 -0.27 68 68
TNFRSF1A 0.019 0.049 -10000 0 -0.34 7 7
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.021 0.084 -10000 0 -0.85 3 3
NSMAF -0.003 0.12 0.22 11 -0.43 16 27
response to hydrogen peroxide 0 0.001 0.002 9 -0.002 4 13
BCL2 0.021 0.043 -10000 0 -0.43 4 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.036 -10000 0 -0.23 4 4
alphaV beta3 Integrin 0.042 0.059 -10000 0 -0.26 16 16
PTK2 0.009 0.11 0.27 15 -0.37 17 32
IGF1R 0.025 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.037 -10000 0 -0.43 3 3
SRC 0.025 0.005 -10000 0 -10000 0 0
CDKN1B 0.004 0.082 -10000 0 -0.41 16 16
VEGFA 0.019 0.032 -10000 0 -0.13 21 21
ILK 0.003 0.081 -10000 0 -0.38 17 17
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.004 0.073 -10000 0 -0.37 16 16
PTK2B -0.001 0.062 0.18 18 -0.23 15 33
alphaV/beta3 Integrin/JAM-A 0.037 0.073 0.2 1 -0.23 28 29
CBL 0.024 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.028 0.058 -10000 0 -0.26 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.056 0.05 -10000 0 -0.23 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.01 0.059 -10000 0 -0.32 4 4
alphaV/beta3 Integrin/Syndecan-1 0.035 0.073 -10000 0 -0.21 33 33
PI4KA 0.023 0.02 -10000 0 -0.13 8 8
IGF-1R heterotetramer/IGF1/IRS1 0.035 0.071 -10000 0 -0.21 28 28
PI4 Kinase 0.035 0.017 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.011 0.1 -10000 0 -0.22 70 70
RPS6KB1 -0.022 0.066 0.38 3 -0.25 1 4
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.005 0.091 -10000 0 -0.38 19 19
GPR124 0.024 0.015 -10000 0 -0.13 4 4
MAPK1 -0.004 0.09 -10000 0 -0.39 18 18
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.09 -10000 0 -0.26 39 39
cell adhesion 0.027 0.061 -10000 0 -0.25 17 17
ANGPTL3 0.002 0.019 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.025 -10000 0 -0.26 1 1
IGF-1R heterotetramer 0.025 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
TGFBR2 0.024 0.016 -10000 0 -10000 0 0
ITGB3 -0.003 0.088 -10000 0 -0.2 59 59
IGF1 0.012 0.075 -10000 0 -0.43 12 12
RAC1 0.023 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.041 0.056 -10000 0 -0.24 16 16
apoptosis 0.026 0.002 -10000 0 -10000 0 0
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.044 0.055 -10000 0 -0.26 14 14
VCL 0.021 0.04 -10000 0 -0.43 3 3
alphaV/beta3 Integrin/Del1 0.016 0.11 -10000 0 -0.3 49 49
CSF1 0.016 0.048 -10000 0 -0.43 5 5
PIK3C2A 0.002 0.085 -10000 0 -0.41 17 17
PI4 Kinase/Pyk2 0.005 0.07 -10000 0 -0.25 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.064 -10000 0 -0.23 16 16
FAK1/Vinculin 0.018 0.098 0.25 13 -0.34 12 25
alphaV beta3/Integrin/ppsTEM5 0.042 0.056 -10000 0 -0.24 16 16
RHOA 0.025 0.004 -10000 0 -10000 0 0
VTN 0.011 0.078 -10000 0 -0.43 13 13
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
FGF2 0.023 0.031 -10000 0 -0.43 2 2
F11R 0.009 0.025 -10000 0 -0.31 2 2
alphaV/beta3 Integrin/Lactadherin 0.042 0.06 -10000 0 -0.26 17 17
alphaV/beta3 Integrin/TGFBR2 0.042 0.057 -10000 0 -0.24 17 17
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.043 -10000 0 -0.24 5 5
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.041 0.05 -10000 0 -0.24 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.029 -10000 0 -0.13 17 17
alphaV/beta3 Integrin/Pyk2 0.03 0.066 0.18 14 -0.22 16 30
SDC1 0.009 0.064 -10000 0 -0.17 39 39
VAV3 -0.008 0.073 0.18 22 -0.23 28 50
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.025 0.021 -10000 0 -0.43 1 1
FAK1/Paxillin 0.019 0.098 0.26 15 -0.3 16 31
cell migration 0.014 0.091 0.23 18 -0.31 12 30
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.048 0.07 -10000 0 -0.21 26 26
SPP1 -0.023 0.12 -10000 0 -0.43 35 35
KDR 0.021 0.034 -10000 0 -0.43 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.002 -10000 0 -10000 0 0
COL4A3 -0.009 0.1 -10000 0 -0.43 20 20
angiogenesis -0.004 0.1 0.24 1 -0.42 17 18
Rac1/GTP 0.003 0.068 0.17 19 -0.21 27 46
EDIL3 -0.022 0.14 -10000 0 -0.38 54 54
cell proliferation 0.041 0.057 -10000 0 -0.24 17 17
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.022 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.019 0.068 -10000 0 -0.19 52 52
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.037 -10000 0 -0.43 3 3
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.004 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.003 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.034 0.073 -10000 0 -0.29 19 19
PRKG1 -0.01 0.12 -10000 0 -0.43 33 33
DUSP8 0.019 0.041 -10000 0 -0.22 10 10
PGK/cGMP/p38 alpha -0.011 0.11 -10000 0 -0.31 22 22
apoptosis -0.033 0.069 -10000 0 -0.28 19 19
RAL/GTP 0.03 0.013 -10000 0 -10000 0 0
LYN 0.02 0.036 -10000 0 -0.43 2 2
DUSP1 0.008 0.077 -10000 0 -0.25 29 29
PAK1 0.007 0.063 -10000 0 -0.43 5 5
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.055 0.026 -10000 0 -10000 0 0
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0.016 -10000 0 -10000 0 0
MAPK11 0.002 0.13 0.27 24 -0.34 21 45
BLK -0.03 0.11 -10000 0 -0.2 99 99
HCK 0.013 0.067 -10000 0 -0.43 9 9
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.013 0.069 -10000 0 -0.32 16 16
TRAF6/MEKK3 0.031 0.015 -10000 0 -0.23 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.11 0.23 24 -0.34 15 39
positive regulation of innate immune response 0.004 0.14 0.3 25 -0.38 20 45
LCK -0.022 0.12 -10000 0 -0.25 73 73
p38alpha-beta/MKP7 0.015 0.14 0.3 25 -0.37 19 44
p38alpha-beta/MKP5 0.007 0.14 0.29 21 -0.37 23 44
PGK/cGMP -0.006 0.084 -10000 0 -0.3 33 33
PAK2 0.025 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.009 0.15 0.3 23 -0.38 21 44
CDC42 0.022 0.009 -10000 0 -10000 0 0
RALB 0.026 0.002 -10000 0 -10000 0 0
RALA 0.022 0.009 -10000 0 -10000 0 0
PAK3 -0.052 0.16 -10000 0 -0.34 98 98
Wnt signaling

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
Noncanonical Wnts/FZD -0.01 0.091 -9999 0 -0.28 43 43
FZD6 0.015 0.039 -9999 0 -0.43 1 1
WNT6 0.001 0.091 -9999 0 -0.43 17 17
WNT4 0.009 0.055 -9999 0 -0.43 4 4
FZD3 0.022 0.037 -9999 0 -0.43 3 3
WNT5A 0.008 0.083 -9999 0 -0.33 22 22
WNT11 0.008 0.081 -9999 0 -0.43 14 14
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.052 -10000 0 -0.43 6 6
CDC42/GTP 0.025 0.054 -10000 0 -0.26 8 8
PLCG1 0.004 0.057 -10000 0 -0.27 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
G12/G13 0.032 0.014 -10000 0 -10000 0 0
cell migration 0.025 0.053 -10000 0 -0.25 8 8
S1PR5 -0.054 0.16 -10000 0 -0.29 114 114
S1PR4 0.02 0.032 -10000 0 -0.15 12 12
MAPK3 0.006 0.058 -10000 0 -0.28 7 7
MAPK1 0.008 0.053 -10000 0 -0.24 7 7
S1P/S1P5/Gi -0.02 0.1 -10000 0 -0.25 61 61
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
CDC42/GDP 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.093 -10000 0 -0.26 53 53
RHOA 0.044 0.084 0.22 71 -0.22 1 72
S1P/S1P4/Gi 0.011 0.061 -10000 0 -0.28 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
S1P/S1P4/G12/G13 0.041 0.024 -10000 0 -0.24 1 1
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.009 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.021 0.01 -9999 0 -10000 0 0
SPHK1 0.004 0.087 -9999 0 -0.43 16 16
GNAI2 0.025 0.005 -9999 0 -10000 0 0
mol:S1P 0 0.064 -9999 0 -0.32 16 16
GNAO1 0.02 0.052 -9999 0 -0.43 6 6
mol:Sphinganine-1-P 0.002 0.042 -9999 0 -0.31 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.023 0.074 -9999 0 -0.27 15 15
GNAI3 0.021 0.01 -9999 0 -10000 0 0
G12/G13 0.032 0.014 -9999 0 -10000 0 0
S1PR3 0.006 0.071 -9999 0 -0.43 8 8
S1PR2 0.022 0.038 -9999 0 -0.36 4 4
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.013 0.063 -9999 0 -0.29 16 16
S1PR5 -0.054 0.16 -9999 0 -0.29 114 114
S1PR4 0.02 0.032 -9999 0 -0.15 12 12
GNAI1 0.019 0.038 -9999 0 -0.43 3 3
S1P/S1P5/G12 -0.015 0.11 -9999 0 -0.26 63 63
S1P/S1P3/Gq -0.008 0.11 -9999 0 -0.37 28 28
S1P/S1P4/Gi 0.002 0.086 -9999 0 -0.29 16 16
GNAQ 0.025 0.004 -9999 0 -10000 0 0
GNAZ 0.025 0.022 -9999 0 -0.43 1 1
GNA14 0.007 0.087 -9999 0 -0.35 23 23
GNA15 0.011 0.077 -9999 0 -0.36 17 17
GNA12 0.022 0.009 -9999 0 -10000 0 0
GNA13 0.025 0.004 -9999 0 -10000 0 0
GNA11 0.018 0.056 -9999 0 -0.43 7 7
ABCC1 0.025 0.014 -9999 0 -0.13 4 4
Class I PI3K signaling events

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
ARF5/GTP 0 0.041 0.29 2 -10000 0 2
DAPP1 -0.033 0.14 0.26 6 -0.41 33 39
Src family/SYK family/BLNK-LAT/BTK-ITK -0.075 0.22 0.32 7 -0.5 61 68
mol:DAG -0.021 0.099 0.3 12 -0.26 20 32
HRAS 0.025 0.007 -10000 0 -10000 0 0
RAP1A 0.022 0.011 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.061 0.19 4 -0.31 6 10
PLCG2 0.019 0.05 -10000 0 -0.43 5 5
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0.001 0.052 0.21 16 -10000 0 16
ARF1/GTP 0.001 0.03 0.28 1 -10000 0 1
RHOA 0.025 0.004 -10000 0 -10000 0 0
YES1 0.022 0.037 -10000 0 -0.43 3 3
RAP1A/GTP -0.003 0.042 0.17 17 -10000 0 17
ADAP1 -0.007 0.042 0.2 9 -0.22 3 12
ARAP3 0 0.052 0.21 16 -10000 0 16
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PREX1 0.015 0.067 -10000 0 -0.43 10 10
ARHGEF6 0.022 0.042 -10000 0 -0.43 4 4
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
ARF1 0.025 0.004 -10000 0 -10000 0 0
NRAS 0.022 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.003 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.059 0.23 11 -0.14 12 23
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.004 -10000 0 -10000 0 0
ZAP70 -0.007 0.1 -10000 0 -0.25 55 55
mol:IP3 -0.017 0.076 0.25 12 -0.2 15 27
LYN 0.02 0.036 -10000 0 -0.43 2 2
ARF1/GDP 0.032 0.072 0.2 6 -0.3 9 15
RhoA/GDP 0.036 0.06 0.24 13 -10000 0 13
PDK1/Src/Hsp90 0.048 0.021 -10000 0 -0.26 1 1
BLNK -0.02 0.13 -10000 0 -0.38 51 51
actin cytoskeleton reorganization 0.022 0.1 0.28 23 -0.38 9 32
SRC 0.025 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.017 -10000 0 -0.26 2 2
RAC1 0.023 0.009 -10000 0 -10000 0 0
PTEN 0.022 0.013 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.044 0.22 7 -10000 0 7
RhoA/GTP 0.006 0.055 0.21 15 -10000 0 15
Src family/SYK family/BLNK-LAT -0.068 0.17 -10000 0 -0.43 55 55
BLK -0.03 0.11 -10000 0 -0.2 99 99
PDPK1 0.025 0.021 -10000 0 -0.43 1 1
CYTH1 -0.005 0.041 0.19 10 -10000 0 10
HCK 0.013 0.067 -10000 0 -0.43 9 9
CYTH3 -0.004 0.038 0.28 3 -10000 0 3
CYTH2 -0.005 0.041 0.22 8 -10000 0 8
KRAS 0.025 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.078 0.21 2 -0.4 14 16
SGK1 0.001 0.097 -10000 0 -0.38 26 26
INPP5D 0.022 0.033 -10000 0 -0.43 2 2
mol:GDP 0.021 0.074 0.19 14 -0.31 9 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.01 0.08 -10000 0 -0.43 14 14
ARF6/GDP 0.034 0.066 0.25 19 -0.22 1 20
mol:PI-3-4-5-P3 -0.01 0.026 0.2 5 -10000 0 5
ARAP3/RAP1A/GTP -0.003 0.042 0.17 17 -10000 0 17
VAV1 0.004 0.09 -10000 0 -0.43 18 18
mol:PI-3-4-P2 0.011 0.023 -10000 0 -0.31 2 2
RAS family/GTP/PI3K Class I 0.031 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.008 0.019 -10000 0 -0.26 2 2
Rac1/GDP 0.023 0.064 0.2 3 -0.3 7 10
LAT 0 0.11 -10000 0 -0.43 26 26
Rac1/GTP 0.018 0.077 -10000 0 -0.4 10 10
ITK -0.024 0.065 0.2 9 -0.22 18 27
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.036 0.12 0.32 9 -0.38 21 30
LCK -0.022 0.12 -10000 0 -0.25 73 73
BTK -0.011 0.051 0.2 9 -0.2 11 20
Signaling events mediated by PRL

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
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
mol:Halofuginone 0.003 0.009 -10000 0 -0.2 1 1
ITGA1 0.017 0.05 -10000 0 -0.2 18 18
CDKN1A -0.057 0.15 -10000 0 -0.37 85 85
PRL-3/alpha Tubulin 0.033 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.054 -10000 0 -0.32 15 15
AGT 0.009 0.084 -10000 0 -0.4 18 18
CCNA2 -0.035 0.081 -10000 0 -0.59 1 1
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
EGR1 -0.024 0.091 -10000 0 -0.3 42 42
CDK2/Cyclin E1 -0.028 0.15 -10000 0 -0.32 85 85
MAPK3 0.012 0.006 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.032 0.015 -10000 0 -10000 0 0
MAPK1 0.012 0.006 -10000 0 -10000 0 0
PTP4A1 -0.022 0.072 -10000 0 -0.62 1 1
PTP4A3 0.023 0.011 -10000 0 -10000 0 0
PTP4A2 0.022 0.01 -10000 0 -10000 0 0
ITGB1 0.011 0.009 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.006 0.035 -10000 0 -0.3 2 2
Rab GGTase beta/Rab GGTase alpha 0.031 0.015 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.005 0.078 -10000 0 -0.57 1 1
RABGGTA 0.026 0.004 -10000 0 -10000 0 0
BCAR1 -0.017 0.019 0.24 1 -0.32 1 2
RHOC -0.055 0.15 -10000 0 -0.35 84 84
RHOA 0.003 0.054 -10000 0 -0.32 9 9
cell motility -0.013 0.096 0.28 1 -0.29 29 30
PRL-1/alpha Tubulin -0.001 0.083 -10000 0 -0.59 1 1
PRL-3/alpha1 Integrin 0.027 0.04 -10000 0 -0.28 5 5
ROCK1 -0.016 0.094 0.28 1 -0.29 29 30
RABGGTB 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.019 0.047 -10000 0 -0.43 4 4
mitosis -0.022 0.072 -10000 0 -0.62 1 1
ATF5 0.02 0.018 -10000 0 -0.13 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.009 -10000 0 -0.13 1 1
NFATC1 0.003 0.11 0.26 3 -0.37 19 22
NFATC2 -0.01 0.079 -10000 0 -0.23 36 36
NFATC3 0.006 0.062 -10000 0 -0.34 14 14
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.044 0.15 0.17 2 -0.44 40 42
Exportin 1/Ran/NUP214 0.051 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.063 0.17 -10000 0 -0.39 60 60
BCL2/BAX 0.029 0.033 -10000 0 -0.29 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.018 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
BAD 0.025 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D -0.03 0.15 -10000 0 -0.42 39 39
Calcineurin A alpha-beta B1/BCL2 0.021 0.043 -10000 0 -0.43 4 4
FKBP8 0.025 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.03 0.14 0.41 39 -10000 0 39
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.025 0.008 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN -0.022 0.11 -10000 0 -0.43 24 24
MAP3K8 0.017 0.04 -10000 0 -0.17 16 16
NFAT4/CK1 alpha 0.016 0.043 -10000 0 -0.2 13 13
MEF2D/NFAT1/Cbp/p300 0.019 0.1 -10000 0 -0.27 24 24
CABIN1 -0.044 0.15 0.17 2 -0.44 40 42
CALM1 0.025 0.009 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.016 -10000 0 -10000 0 0
CAMK4 -0.09 0.19 -10000 0 -0.43 105 105
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.002 -10000 0 -10000 0 0
YWHAH 0.019 0.032 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.038 -10000 0 -0.31 1 1
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.015 0.067 -10000 0 -0.43 10 10
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 10 10
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.002 0.12 0.23 1 -0.35 29 30
PRKCH 0.025 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.034 0.034 -10000 0 -0.31 4 4
CASP3 0.025 0.009 -10000 0 -0.13 1 1
PIM1 0.024 0.018 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.004 -10000 0 -10000 0 0
apoptosis 0.015 0.019 -10000 0 -0.31 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.046 -10000 0 -0.23 1 1
PRKCB -0.008 0.1 -10000 0 -0.22 64 64
PRKCE 0.022 0.035 -10000 0 -0.43 2 2
JNK2/NFAT4 -0.002 0.08 -10000 0 -0.31 14 14
BAD/BCL-XL 0.036 0.01 -10000 0 -10000 0 0
PRKCD 0.005 0.095 -10000 0 -0.43 21 21
NUP214 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
PRKCA 0.024 0.022 -10000 0 -0.43 1 1
PRKCG -0.064 0.15 -10000 0 -0.43 57 57
PRKCQ 0.013 0.067 -10000 0 -0.38 12 12
FKBP38/BCL2 0.033 0.033 -10000 0 -0.3 4 4
EP300 0.021 0.043 -10000 0 -0.43 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.009 0.11 0.26 1 -0.35 19 20
CaM/Ca2+/FKBP38 0.032 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.012 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.041 0.12 -10000 0 -0.26 106 106
NFATc/ERK1 0.016 0.11 0.26 3 -0.35 18 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.066 0.17 -10000 0 -0.38 64 64
NR4A1 -0.001 0.1 0.22 3 -0.36 17 20
GSK3B 0.026 0.003 -10000 0 -10000 0 0
positive T cell selection 0.006 0.062 -10000 0 -0.34 14 14
NFAT1/CK1 alpha -0.002 0.059 -10000 0 -0.19 18 18
RCH1/ KPNB1 0.037 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
AKAP5 0.011 0.051 -10000 0 -0.43 2 2
MEF2D 0.024 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha 0.015 0.11 0.26 3 -0.35 19 22
CREBBP 0.025 0.006 -10000 0 -10000 0 0
BCL2 0.021 0.043 -10000 0 -0.43 4 4
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.014 -10000 0 -10000 0 0
DOCK1 0.022 0.031 -10000 0 -0.43 2 2
ITGA4 -0.01 0.11 -10000 0 -0.43 25 25
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.11 -10000 0 -0.28 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.069 -10000 0 -0.25 24 24
alpha4/beta7 Integrin/Paxillin 0.014 0.085 0.18 2 -0.24 42 44
lamellipodium assembly 0.023 0.049 0.27 1 -0.43 3 4
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.003 -10000 0 -10000 0 0
TLN1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.013 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.037 0.06 -10000 0 -0.21 22 22
cell adhesion 0.036 0.063 -10000 0 -0.22 22 22
CRKL/CBL 0.036 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.026 0.062 0.17 1 -0.24 22 23
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
ITGB7 0 0.095 -10000 0 -0.43 19 19
ARF6/GDP 0.025 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.1 -10000 0 -0.23 65 65
p130Cas/Crk/Dock1 0.047 0.029 -10000 0 -0.26 3 3
VCAM1 -0.037 0.14 -10000 0 -0.43 47 47
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.064 -10000 0 -0.22 22 22
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.064 -10000 0 -0.22 22 22
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
mol:GDP -0.037 0.063 0.22 22 -10000 0 22
CBL 0.024 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.064 -10000 0 -0.22 22 22
Rac1/GTP 0.024 0.053 0.28 1 -0.48 3 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.015 0.067 -10000 0 -0.43 10 10
Caspase 8 (4 units) 0.029 0.062 -10000 0 -0.22 14 14
NEF -0.001 0.011 -10000 0 -0.11 1 1
NFKBIA 0.019 0.03 -10000 0 -0.14 1 1
BIRC3 -0.007 0.11 -10000 0 -0.46 23 23
CYCS 0.005 0.049 0.18 6 -0.34 2 8
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CD247 0.01 0.067 -10000 0 -0.24 23 23
MAP2K7 0.023 0.089 -10000 0 -0.61 4 4
protein ubiquitination 0.017 0.088 0.24 4 -0.33 9 13
CRADD 0.026 0.002 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.012 0.069 -10000 0 -0.3 18 18
BID 0.009 0.051 0.18 6 -0.22 12 18
NF-kappa-B/RelA/I kappa B alpha 0.037 0.07 -10000 0 -0.25 22 22
TRADD 0.025 0.021 -10000 0 -0.43 1 1
MAP3K5 0.021 0.043 -10000 0 -0.43 4 4
CFLAR 0.026 0.008 -10000 0 -0.13 1 1
FADD 0.025 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.037 0.071 -10000 0 -0.25 22 22
MAPK8 0.019 0.085 -10000 0 -0.55 4 4
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.018 0.056 -10000 0 -0.43 7 7
TRAF2 0.025 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.012 0.05 -10000 0 -0.23 13 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.09 -10000 0 -0.38 13 13
CHUK 0.016 0.093 0.24 4 -0.36 9 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.06 0.055 -10000 0 -0.22 13 13
TCRz/NEF 0.008 0.052 -10000 0 -0.19 23 23
TNF -0.061 0.16 -10000 0 -0.43 62 62
FASLG -0.007 0.051 -10000 0 -0.26 7 7
NFKB1 0.02 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.001 0.12 -10000 0 -0.27 68 68
CASP6 0.026 0.1 -10000 0 -0.54 9 9
CASP7 0.005 0.14 0.29 12 -0.49 24 36
RELA 0.018 0.03 -10000 0 -0.14 1 1
CASP2 0.02 0.011 -10000 0 -10000 0 0
CASP3 0.006 0.14 0.29 12 -0.49 25 37
TNFRSF1A 0.019 0.049 -10000 0 -0.34 7 7
TNFR1A/BAG4 0.024 0.058 -10000 0 -0.31 13 13
CASP8 0.02 0.034 -10000 0 -0.43 1 1
CASP9 0.022 0.012 -10000 0 -0.13 1 1
MAP3K14 0.014 0.095 0.2 4 -0.4 9 13
APAF-1/Caspase 9 0.002 0.087 -10000 0 -0.33 22 22
BCL2 0.015 0.084 0.28 1 -0.52 4 5
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.027 0.057 -10000 0 -0.32 1 1
epithelial cell differentiation -0.016 0.088 -10000 0 -0.34 8 8
ITCH 0.029 0.012 -10000 0 -10000 0 0
WWP1 0.018 0.064 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
EGFR -0.013 0.12 -10000 0 -0.43 34 34
PRL -0.011 0.016 -10000 0 -0.13 2 2
neuron projection morphogenesis -0.019 0.11 0.28 18 -0.29 5 23
PTPRZ1 0.014 0.053 -10000 0 -0.43 6 6
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.11 -10000 0 -0.28 9 9
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.1 -10000 0 -0.3 14 14
ADAM17 0.025 0.044 -10000 0 -0.43 4 4
ErbB4/ErbB4 0.006 0.05 -10000 0 -0.36 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.012 0.084 -10000 0 -0.34 11 11
NCOR1 0.025 0.021 -10000 0 -0.43 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.1 -10000 0 -0.29 13 13
GRIN2B -0.069 0.13 0.24 9 -0.35 43 52
ErbB4/ErbB2/betacellulin 0.001 0.095 -10000 0 -0.32 12 12
STAT1 0.021 0.027 -10000 0 -10000 0 0
HBEGF 0.022 0.022 -10000 0 -0.13 10 10
PRLR 0.004 0.091 -10000 0 -0.32 29 29
E4ICDs/ETO2 0.023 0.064 -10000 0 -0.35 2 2
axon guidance -0.024 0.08 -10000 0 -0.39 7 7
NEDD4 0.024 0.042 -10000 0 -0.43 3 3
Prolactin receptor/Prolactin receptor/Prolactin 0.015 0.067 -10000 0 -0.31 17 17
CBFA2T3 0.02 0.052 -10000 0 -0.39 7 7
ErbB4/ErbB2/HBEGF 0.028 0.053 -10000 0 -0.31 4 4
MAPK3 -0.017 0.11 0.26 13 -0.28 7 20
STAT1 (dimer) 0.026 0.058 -10000 0 -0.32 1 1
MAPK1 -0.017 0.11 0.26 13 -0.28 7 20
JAK2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.098 -10000 0 -0.28 15 15
NRG1 -0.062 0.13 -10000 0 -0.31 92 92
NRG3 -0.002 0.11 -10000 0 -0.43 27 27
NRG2 0.025 0.022 -10000 0 -0.43 1 1
NRG4 -0.002 0.087 -10000 0 -0.43 14 14
heart development -0.024 0.08 -10000 0 -0.39 7 7
neural crest cell migration -0.036 0.098 -10000 0 -0.28 15 15
ERBB2 0.011 0.032 -10000 0 -0.3 4 4
WWOX/E4ICDs 0.026 0.057 -10000 0 -0.32 1 1
SHC1 0.024 0.015 -10000 0 -0.13 4 4
ErbB4/EGFR/neuregulin 4 0.005 0.1 -10000 0 -0.33 18 18
apoptosis 0 0.12 0.36 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.026 0.059 -10000 0 -0.35 2 2
ErbB4/ErbB2/epiregulin 0.026 0.054 -10000 0 -0.32 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.003 0.1 -10000 0 -0.34 12 12
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.044 0.077 -10000 0 -0.28 4 4
MDM2 0.011 0.055 0.25 4 -0.32 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.099 -10000 0 -0.27 12 12
STAT5A -0.028 0.086 -10000 0 -0.38 9 9
ErbB4/EGFR/neuregulin 1 beta -0.043 0.12 -10000 0 -0.35 26 26
DLG4 0.023 0.021 -10000 0 -0.13 9 9
GRB2/SHC 0.036 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.023 0.053 -10000 0 -0.3 1 1
STAT5A (dimer) -0.009 0.1 -10000 0 -0.38 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.013 0.085 -10000 0 -0.37 7 7
LRIG1 0.014 0.073 -10000 0 -0.43 12 12
EREG 0.009 0.035 -10000 0 -0.13 22 22
BTC -0.04 0.14 -10000 0 -0.43 51 51
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.077 -10000 0 -0.39 7 7
ERBB4 0.006 0.05 -10000 0 -0.36 1 1
STAT5B 0.026 0.003 -10000 0 -10000 0 0
YAP1 -0.013 0.12 -10000 0 -0.55 23 23
GRB2 0.025 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.021 0.069 -10000 0 -0.31 6 6
glial cell differentiation -0.022 0.053 0.3 1 -10000 0 1
WWOX 0.026 0.003 -10000 0 -10000 0 0
cell proliferation -0.069 0.14 0.24 3 -0.38 34 37
BARD1 signaling events

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
BARD1/CSTF1 0.022 0.071 -10000 0 -0.31 20 20
ATM 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
UBE2L3 0.026 0.003 -10000 0 -10000 0 0
FANCD2 0.017 0.026 -10000 0 -0.29 3 3
protein ubiquitination 0.042 0.067 -10000 0 -0.23 21 21
XRCC5 0.026 0.002 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.018 -10000 0 -10000 0 0
MRE11A 0.025 0.005 -10000 0 -10000 0 0
DNA-PK 0.05 0.013 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.024 0.063 -10000 0 -0.48 4 4
FANCF 0.025 0.005 -10000 0 -10000 0 0
BRCA1 0.025 0.013 -10000 0 -0.13 3 3
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
CDK2/Cyclin E1 0.027 0.038 -10000 0 -0.28 5 5
FANCG 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.022 0.071 -10000 0 -0.3 21 21
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.024 0.023 -10000 0 -0.43 1 1
NBN 0.024 0.007 -10000 0 -10000 0 0
FANCA 0.008 0.071 -10000 0 -0.2 35 35
DNA repair 0.011 0.09 0.27 9 -0.4 7 16
BRCA1/BARD1/ubiquitin 0.022 0.071 -10000 0 -0.3 21 21
BARD1/DNA-PK 0.05 0.063 -10000 0 -0.24 20 20
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.021 0.071 0.31 20 -10000 0 20
BRCA1/BARD1/CTIP/M/R/N Complex 0.018 0.056 -10000 0 -0.23 19 19
BRCA1/BACH1/BARD1/TopBP1 0.038 0.065 -10000 0 -0.25 21 21
BRCA1/BARD1/P53 0.045 0.08 -10000 0 -0.25 30 30
BARD1/CSTF1/BRCA1 0.037 0.064 -10000 0 -0.26 20 20
BRCA1/BACH1 0.025 0.013 -10000 0 -0.13 3 3
BARD1 0.005 0.094 -10000 0 -0.43 20 20
PCNA 0.024 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.037 0.065 -10000 0 -0.25 21 21
BRCA1/BARD1/UbcH7 0.038 0.065 -10000 0 -0.25 21 21
BRCA1/BARD1/RAD51/PCNA 0.042 0.084 -10000 0 -0.25 33 33
BARD1/DNA-PK/P53 0.052 0.079 -10000 0 -0.24 29 29
BRCA1/BARD1/Ubiquitin 0.022 0.071 -10000 0 -0.3 21 21
BRCA1/BARD1/CTIP 0.031 0.056 0.21 1 -0.24 18 19
FA complex 0.023 0.038 -10000 0 -0.21 8 8
BARD1/EWS 0.022 0.071 -10000 0 -0.31 20 20
RBBP8 0.013 0.006 -10000 0 -10000 0 0
TP53 0.014 0.073 -10000 0 -0.41 13 13
TOPBP1 0.026 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.079 0.25 30 -10000 0 30
BRCA1/BARD1 0.048 0.069 -10000 0 -0.23 21 21
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.005 0.066 -10000 0 -0.3 20 20
CDK2 0.019 0.047 -10000 0 -0.43 4 4
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.002 0.088 -10000 0 -0.2 57 57
RAD50 0.026 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.022 0.071 -10000 0 -0.3 21 21
EWSR1 0.026 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.007 0.15 0.24 5 -0.37 23 28
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
AKT1 0.025 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.01 -10000 0 -10000 0 0
STXBP4 0.025 0.022 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.016 0.15 0.22 32 -0.31 68 100
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.019 0.032 -10000 0 -10000 0 0
YWHAB 0.025 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.051 0.017 -10000 0 -0.26 1 1
YWHAG 0.019 0.024 -10000 0 -0.13 10 10
ASIP -0.038 0.14 -10000 0 -0.43 52 52
PRKCI 0.026 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
GYS1 0.01 0.012 0.24 1 -10000 0 1
PRKCZ 0.005 0.08 -10000 0 -0.32 22 22
TRIP10 0.02 0.044 -10000 0 -0.33 6 6
TC10/GTP/CIP4/Exocyst 0.031 0.026 -10000 0 -0.26 3 3
AS160/14-3-3 0.01 0.055 -10000 0 -0.3 3 3
VAMP2 0.026 0.002 -10000 0 -10000 0 0
SLC2A4 -0.021 0.17 0.24 22 -0.34 68 90
STX4 0.026 0.002 -10000 0 -10000 0 0
GSK3B 0.018 0.009 -10000 0 -10000 0 0
SFN -0.022 0.11 -10000 0 -0.43 24 24
LNPEP 0.007 0.091 -10000 0 -0.43 19 19
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.37 -9999 0 -1.2 48 48
RAD9A 0.025 0.005 -9999 0 -10000 0 0
AP1 -0.015 0.1 -9999 0 -0.28 50 50
IFNAR2 0.02 0.018 -9999 0 -10000 0 0
AKT1 0.003 0.036 -9999 0 -0.18 11 11
ER alpha/Oestrogen 0.005 0.052 -9999 0 -0.25 15 15
NFX1/SIN3/HDAC complex -0.003 0.07 -9999 0 -0.22 13 13
EGF -0.01 0.11 -9999 0 -0.34 37 37
SMG5 0.025 0.005 -9999 0 -10000 0 0
SMG6 0.026 0.002 -9999 0 -10000 0 0
SP3/HDAC2 0.029 0.027 -9999 0 -10000 0 0
TERT/c-Abl -0.096 0.34 -9999 0 -1.1 48 48
SAP18 0.025 0.005 -9999 0 -10000 0 0
MRN complex 0.046 0.018 -9999 0 -10000 0 0
WT1 0.001 0.044 -9999 0 -0.14 11 11
WRN 0.023 0.03 -9999 0 -0.43 2 2
SP1 0.019 0.022 -9999 0 -10000 0 0
SP3 0.022 0.014 -9999 0 -10000 0 0
TERF2IP 0.026 0.002 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.069 0.31 -9999 0 -0.94 48 48
Mad/Max 0.03 0.023 -9999 0 -10000 0 0
TERT -0.12 0.39 -9999 0 -1.2 48 48
CCND1 -0.11 0.34 -9999 0 -1 57 57
MAX 0.021 0.015 -9999 0 -10000 0 0
RBBP7 0.025 0.003 -9999 0 -10000 0 0
RBBP4 0.022 0.009 -9999 0 -10000 0 0
TERF2 0.021 0.005 -9999 0 -10000 0 0
PTGES3 0.026 0.003 -9999 0 -10000 0 0
SIN3A 0.025 0.003 -9999 0 -10000 0 0
Telomerase/911 0.031 0.056 -9999 0 -0.32 2 2
CDKN1B 0.009 0.023 -9999 0 -10000 0 0
RAD1 0.026 0.003 -9999 0 -10000 0 0
XRCC5 0.026 0.002 -9999 0 -10000 0 0
XRCC6 0.026 0.004 -9999 0 -10000 0 0
SAP30 0.025 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0.036 0.007 -9999 0 -10000 0 0
UBE3A 0.022 0.014 -9999 0 -10000 0 0
JUN 0.015 0.024 -9999 0 -0.13 8 8
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.014 -9999 0 -10000 0 0
FOS -0.034 0.14 -9999 0 -0.29 82 82
IFN-gamma/IRF1 0.026 0.034 -9999 0 -10000 0 0
PARP2 0.026 0.003 -9999 0 -10000 0 0
BLM -0.008 0.1 -9999 0 -0.25 56 56
Telomerase -0.015 0.097 -9999 0 -0.33 28 28
IRF1 0.018 0.034 -9999 0 -0.13 1 1
ESR1 0.009 0.074 -9999 0 -0.28 23 23
KU/TER 0.038 0.006 -9999 0 -10000 0 0
ATM/TRF2 0.037 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.001 0.072 -9999 0 -0.23 15 15
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.001 0.073 -9999 0 -0.24 15 15
HDAC1 0.021 0.01 -9999 0 -10000 0 0
HDAC2 0.019 0.022 -9999 0 -10000 0 0
ATM 0.01 0.002 -9999 0 -10000 0 0
SMAD3 0.012 0.016 -9999 0 -0.3 1 1
ABL1 0.025 0.004 -9999 0 -10000 0 0
MXD1 0.021 0.014 -9999 0 -10000 0 0
MRE11A 0.025 0.005 -9999 0 -10000 0 0
HUS1 0.022 0.009 -9999 0 -10000 0 0
RPS6KB1 0.025 0.004 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.083 0.34 -9999 0 -1 48 48
NR2F2 0.016 0.063 -9999 0 -0.22 23 23
MAPK3 -0.013 0.009 -9999 0 -10000 0 0
MAPK1 -0.013 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.023 -9999 0 -0.43 1 1
NFKB1 0.026 0.004 -9999 0 -10000 0 0
HNRNPC 0.026 0.003 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -9999 0 -10000 0 0
NBN 0.024 0.007 -9999 0 -10000 0 0
EGFR -0.016 0.12 -9999 0 -0.43 34 34
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.02 0.12 -9999 0 -0.33 54 54
MYC -0.001 0.091 -9999 0 -0.43 19 19
IL2 0.007 0.023 -9999 0 -10000 0 0
KU 0.038 0.006 -9999 0 -10000 0 0
RAD50 0.026 0.003 -9999 0 -10000 0 0
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
TGFB1 0.021 0.023 -9999 0 -0.43 1 1
TRF2/BLM 0.011 0.074 -9999 0 -0.28 23 23
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.088 0.35 -9999 0 -1.1 48 48
SP1/HDAC2 0.029 0.031 -9999 0 -10000 0 0
PINX1 0.025 0.005 -9999 0 -10000 0 0
Telomerase/EST1A -0.068 0.31 -9999 0 -0.93 48 48
Smad3/Myc 0.009 0.06 -9999 0 -0.27 18 18
911 complex 0.043 0.021 -9999 0 -10000 0 0
IFNG 0.015 0.02 -9999 0 -0.14 2 2
Telomerase/PinX1 -0.071 0.31 -9999 0 -0.93 48 48
Telomerase/AKT1/mTOR/p70S6K -0.008 0.097 -9999 0 -0.45 7 7
SIN3B 0.024 0.006 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
Telomerase/EST1B -0.07 0.31 -9999 0 -0.93 48 48
response to DNA damage stimulus 0.006 0.009 -9999 0 -0.1 1 1
MRN complex/TRF2/Rap1 0.064 0.026 -9999 0 -10000 0 0
TRF2/WRN 0.033 0.022 -9999 0 -0.28 2 2
Telomerase/hnRNP C1/C2 -0.068 0.31 -9999 0 -0.93 48 48
E2F1 0.009 0.057 -9999 0 -0.2 22 22
ZNFX1 0.025 0.005 -9999 0 -10000 0 0
PIF1 -0.009 0.11 -9999 0 -0.27 54 54
NCL 0.026 0.004 -9999 0 -10000 0 0
DKC1 0.026 0.003 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.014 0.034 -10000 0 -0.69 1 1
REL 0.003 0.095 -10000 0 -0.43 20 20
HDAC7 -0.015 0.078 -10000 0 -0.27 17 17
JUN 0.019 0.022 -10000 0 -0.13 8 8
EP300 0.022 0.043 -10000 0 -0.43 4 4
KAT2B 0.025 0.008 -10000 0 -10000 0 0
KAT5 0.025 0.005 -10000 0 -10000 0 0
MAPK14 0.007 0.021 -10000 0 -0.31 1 1
FOXO1 0.023 0.023 -10000 0 -0.43 1 1
T-DHT/AR 0.003 0.091 -10000 0 -0.29 17 17
MAP2K6 0.021 0.025 -10000 0 -0.43 1 1
BRM/BAF57 0.036 0.01 -10000 0 -10000 0 0
MAP2K4 0.022 0.018 -10000 0 -0.14 1 1
SMARCA2 0.024 0.006 -10000 0 -10000 0 0
PDE9A 0.009 0.09 -10000 0 -0.83 3 3
NCOA2 -0.004 0.11 -10000 0 -0.43 29 29
CEBPA 0.016 0.047 -10000 0 -0.24 11 11
EHMT2 0.026 0.003 -10000 0 -10000 0 0
cell proliferation 0.002 0.11 0.36 8 -0.39 10 18
NR0B1 -0.041 0.15 -10000 0 -0.31 89 89
EGR1 -0.033 0.13 -10000 0 -0.43 41 41
RXRs/9cRA 0.019 0.085 -10000 0 -0.23 46 46
AR/RACK1/Src 0.002 0.072 -10000 0 -0.31 5 5
AR/GR -0.012 0.099 0.23 2 -0.24 62 64
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
PKN1 0.025 0.006 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.001 0.049 -10000 0 -0.31 10 10
T-DHT/AR/TIF2/CARM1 -0.001 0.1 0.35 1 -0.38 15 16
SRC -0.014 0.036 0.19 2 -0.22 9 11
NR3C1 0.026 0.003 -10000 0 -10000 0 0
KLK3 -0.038 0.1 0.32 1 -0.45 3 4
APPBP2 0.022 0.014 -10000 0 -10000 0 0
TRIM24 0.02 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.002 0.069 0.22 5 -0.3 8 13
TMPRSS2 -0.067 0.29 -10000 0 -1 40 40
RXRG -0.026 0.14 -10000 0 -0.43 50 50
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.025 0.004 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.025 0.005 -10000 0 -10000 0 0
NR2C2 0.02 0.052 -10000 0 -0.43 6 6
KLK2 -0.017 0.096 0.44 1 -0.42 9 10
AR -0.029 0.096 -10000 0 -0.26 62 62
SENP1 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 0.014 0.068 -10000 0 -0.34 14 14
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.008 0.046 -10000 0 -0.13 50 50
T-DHT/AR/RACK1/Src 0.003 0.078 0.52 1 -0.32 5 6
positive regulation of transcription 0.014 0.068 -10000 0 -0.34 14 14
DNAJA1 0.022 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.03 0.012 -10000 0 -10000 0 0
SPDEF -0.006 0.1 -10000 0 -0.28 47 47
T-DHT/AR/TIF2 -0.002 0.097 0.23 3 -0.4 15 18
T-DHT/AR/Hsp90 -0.003 0.069 0.22 5 -0.29 9 14
GSK3B 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.026 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.038 -10000 0 -0.24 10 10
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.022 0.009 -10000 0 -10000 0 0
POU2F1 0.022 0.037 -10000 0 -0.12 3 3
T-DHT/AR/DAX-1 -0.031 0.1 0.22 7 -0.25 53 60
CREBBP 0.026 0.002 -10000 0 -10000 0 0
SMARCE1 0.026 0.003 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.01 0.074 -10000 0 -0.43 11 11
positive regulation of NF-kappaB transcription factor activity 0.02 0.063 -10000 0 -0.31 13 13
MAP2K4 0.015 0.049 0.21 1 -0.24 2 3
IKBKB 0.025 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.022 0.038 -10000 0 -0.36 4 4
TNFRSF10A 0.003 0.091 -10000 0 -0.32 29 29
SMPD1 0.007 0.033 -10000 0 -0.18 13 13
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.039 -10000 0 -0.43 2 2
TRAIL/TRAILR2 0.022 0.065 -10000 0 -0.33 13 13
TRAIL/TRAILR3 0.012 0.084 -10000 0 -0.33 22 22
TRAIL/TRAILR1 0.009 0.087 -10000 0 -0.29 32 32
TRAIL/TRAILR4 0.02 0.063 -10000 0 -0.31 13 13
TRAIL/TRAILR1/DAP3/GTP 0.028 0.071 -10000 0 -0.24 29 29
IKK complex 0.013 0.046 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.003 -10000 0 -10000 0 0
MAPK3 0.003 0.051 -10000 0 -0.31 11 11
MAP3K1 0.019 0.051 -10000 0 -0.24 3 3
TRAILR4 (trimer) 0.019 0.039 -10000 0 -0.43 2 2
TRADD 0.025 0.021 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0.003 0.091 -10000 0 -0.32 29 29
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.059 -10000 0 -0.22 27 27
CFLAR 0.026 0.008 -10000 0 -0.13 1 1
MAPK1 0.003 0.051 -10000 0 -0.31 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP 0.052 0.075 -10000 0 -0.22 28 28
mol:ceramide 0.007 0.033 -10000 0 -0.18 13 13
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.06 0.2 2 -0.29 4 6
TRAF2 0.025 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.007 0.077 -10000 0 -0.43 12 12
CHUK 0.025 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.029 0.077 -10000 0 -0.25 31 31
DAP3 0.025 0.004 -10000 0 -10000 0 0
CASP10 -0.001 0.063 0.21 1 -0.28 11 12
JNK cascade 0.02 0.063 -10000 0 -0.31 13 13
TRAIL (trimer) 0.01 0.074 -10000 0 -0.43 11 11
TNFRSF10C 0.007 0.077 -10000 0 -0.43 12 12
TRAIL/TRAILR1/DAP3/GTP/FADD 0.038 0.07 -10000 0 -0.22 28 28
TRAIL/TRAILR2/FADD 0.04 0.054 -10000 0 -0.26 13 13
cell death 0.007 0.033 -10000 0 -0.18 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.02 0.042 -10000 0 -0.22 13 13
TRAILR2 (trimer) 0.022 0.038 -10000 0 -0.36 4 4
CASP8 0.014 0.043 -10000 0 -0.77 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.061 0.055 -10000 0 -0.23 13 13
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.043 -10000 0 -0.26 13 13
SNTA1 0.002 0.097 -10000 0 -0.36 28 28
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.013 0.035 -10000 0 -0.26 8 8
MAPK12 0.001 0.022 -10000 0 -0.23 4 4
CCND1 0.004 0.068 -10000 0 -0.41 11 11
p38 gamma/SNTA1 0.014 0.061 0.19 13 -0.21 22 35
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.043 0.21 15 -0.23 4 19
MAP2K6 0.006 0.017 -10000 0 -0.25 2 2
MAPT 0.004 0.061 0.26 4 -0.23 18 22
MAPK13 0 0.056 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.013 0.015 -10000 0 -0.29 1 1
Atypical NF-kappaB pathway

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
BCL3/RelA 0.028 0.024 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.013 0.06 -10000 0 -0.26 20 20
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.081 0.19 3 -0.29 12 15
NFKBIA -0.014 0.074 -10000 0 -0.23 42 42
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.008 -10000 0 -10000 0 0
ARRB2 0.014 0.002 -10000 0 -10000 0 0
REL 0.003 0.095 -10000 0 -0.43 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.019 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.02 0.012 0.25 1 -10000 0 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.009 0.077 -10000 0 -0.22 37 37
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.01 0.081 0.19 3 -0.29 12 15
SRC 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.038 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.077 -10000 0 -0.22 37 37
IKBKB 0.025 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.01 0.08 -10000 0 -0.43 14 14
I kappa B alpha/PIK3R1 0 0.087 0.19 4 -0.3 14 18
cell death 0.009 0.078 0.18 3 -0.28 12 15
NF kappa B1 p105/c-Rel 0.013 0.06 -10000 0 -0.26 20 20
LCK -0.022 0.12 -10000 0 -0.25 73 73
BCL3 0.018 0.026 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.016 0.068 -10000 0 -0.31 14 14
PTK2 0.006 0.092 -10000 0 -0.36 16 16
positive regulation of JNK cascade -0.006 0.092 -10000 0 -0.33 11 11
CDC42/GDP 0.019 0.12 -10000 0 -0.42 13 13
Rac1/GDP 0.004 0.12 -10000 0 -0.43 9 9
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.002 0.11 -10000 0 -0.41 11 11
nectin-3/I-afadin 0.031 0.043 -10000 0 -0.31 7 7
RAPGEF1 0 0.12 0.28 2 -0.4 12 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.015 0.12 -10000 0 -0.44 14 14
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
TLN1 0.002 0.016 -10000 0 -0.15 5 5
Rap1/GTP -0.005 0.083 -10000 0 -0.31 9 9
IQGAP1 0.022 0.033 -10000 0 -0.23 6 6
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.24 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.031 0.043 -10000 0 -0.31 7 7
PVR 0.022 0.01 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.01 -10000 0 -10000 0 0
mol:GDP -0.003 0.14 -10000 0 -0.51 13 13
MLLT4 0.024 0.022 -10000 0 -0.43 1 1
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.066 0.043 -10000 0 -0.22 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.023 0.064 -10000 0 -0.31 16 16
positive regulation of lamellipodium assembly -0.003 0.088 -10000 0 -0.31 11 11
PVRL1 0.009 0.081 -10000 0 -0.43 15 15
PVRL3 0.02 0.052 -10000 0 -0.43 6 6
PVRL2 0.02 0.024 -10000 0 -0.28 2 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.044 0.15 -10000 0 -0.43 52 52
CLDN1 0.013 0.065 -10000 0 -0.24 22 22
JAM-A/CLDN1 0.051 0.057 -10000 0 -0.24 14 14
SRC -0.015 0.13 -10000 0 -0.48 14 14
ITGB3 -0.003 0.088 -10000 0 -0.2 59 59
nectin-1(dimer)/I-afadin/I-afadin 0.023 0.064 -10000 0 -0.31 16 16
FARP2 -0.009 0.15 -10000 0 -0.57 11 11
RAC1 0.023 0.009 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.039 -10000 0 -0.26 5 5
nectin-1/I-afadin 0.023 0.064 -10000 0 -0.31 16 16
nectin-2/I-afadin 0.029 0.028 -10000 0 -0.31 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.028 0.024 -10000 0 -0.26 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.069 -10000 0 -0.27 21 21
CDC42/GTP/IQGAP1/filamentous actin 0.028 0.023 -10000 0 -0.23 2 2
F11R 0.021 0.031 -10000 0 -0.16 11 11
positive regulation of filopodium formation -0.006 0.092 -10000 0 -0.33 11 11
alphaV/beta3 Integrin/Talin 0.032 0.064 0.2 19 -0.22 14 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.029 0.028 -10000 0 -0.31 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.029 0.028 -10000 0 -0.31 2 2
PIP5K1C 0.005 0.023 -10000 0 -0.18 6 6
VAV2 0.001 0.14 -10000 0 -0.51 12 12
RAP1/GDP 0.011 0.11 -10000 0 -0.38 12 12
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.038 0.041 -10000 0 -0.26 6 6
nectin-3(dimer)/I-afadin/I-afadin 0.031 0.043 -10000 0 -0.31 7 7
Rac1/GTP -0.001 0.11 -10000 0 -0.38 11 11
PTPRM 0.009 0.029 -10000 0 -0.19 8 8
E-cadherin/beta catenin/alpha catenin 0.022 0.1 -10000 0 -0.23 56 56
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.009 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.015 0.075 0.31 7 -0.3 9 16
PDGFB-D/PDGFRB/SLAP 0.02 0.062 -10000 0 -0.3 14 14
PDGFB-D/PDGFRB/APS/CBL 0.034 0.044 -10000 0 -0.26 7 7
AKT1 0.006 0.07 0.31 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.082 0.31 10 -0.3 9 19
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
FGR -0.04 0.14 0.34 2 -0.38 63 65
mol:Ca2+ 0.019 0.072 0.29 14 -0.28 2 16
MYC 0.03 0.21 0.4 29 -0.75 21 50
SHC1 0.024 0.015 -10000 0 -0.13 4 4
HRAS/GDP 0.03 0.029 0.17 13 -10000 0 13
LRP1/PDGFRB/PDGFB 0.051 0.012 -10000 0 -10000 0 0
GRB10 0.021 0.023 -10000 0 -0.43 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.018 0.072 0.29 14 -0.29 2 16
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.003 0.042 -10000 0 -0.13 36 36
PDGFB-D/PDGFRB/SHP2 0.037 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.032 0.023 -10000 0 -0.31 1 1
cell cycle arrest 0.02 0.062 -10000 0 -0.3 14 14
HRAS 0.025 0.006 -10000 0 -10000 0 0
HIF1A 0.004 0.066 0.27 14 -10000 0 14
GAB1 0.011 0.091 0.3 13 -0.37 4 17
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.014 0.095 0.32 18 -0.34 4 22
PDGFB-D/PDGFRB 0.048 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.037 0.011 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.015 0.079 0.22 2 -0.34 10 12
positive regulation of MAPKKK cascade 0.037 0.012 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.072 0.29 14 -0.29 2 16
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.026 0.035 -10000 0 -0.17 1 1
SHB 0.025 0.004 -10000 0 -10000 0 0
BLK -0.017 0.12 0.3 1 -0.46 27 28
PTPN2 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.012 -10000 0 -10000 0 0
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
VAV2 0.014 0.1 0.34 12 -0.36 9 21
CBL 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.036 0.019 -10000 0 -0.28 1 1
LCK -0.073 0.18 0.34 2 -0.41 95 97
PDGFRB 0.025 0.014 -10000 0 -0.13 3 3
ACP1 0.026 0.004 -10000 0 -10000 0 0
HCK 0.001 0.088 0.3 1 -0.59 9 10
ABL1 0.005 0.095 0.28 16 -0.34 11 27
PDGFB-D/PDGFRB/CBL 0.014 0.091 0.29 12 -0.38 4 16
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.025 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.027 -10000 0 -10000 0 0
cell proliferation 0.033 0.19 0.38 30 -0.66 21 51
SLA 0.006 0.079 -10000 0 -0.28 26 26
actin cytoskeleton reorganization 0.033 0.048 0.28 6 -0.21 1 7
SRC 0.011 0.023 -10000 0 -10000 0 0
PI3K 0.008 0.022 -10000 0 -0.21 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.028 -10000 0 -0.16 2 2
SH2B2 0.014 0.056 -10000 0 -0.43 7 7
PLCgamma1/SPHK1 0.02 0.083 0.32 10 -0.31 9 19
LYN 0.01 0.056 0.3 1 -0.5 4 5
LRP1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
STAT5B 0.026 0.003 -10000 0 -10000 0 0
STAT5A 0.016 0.067 -10000 0 -0.4 11 11
NCK1-2/p130 Cas 0.071 0.033 -10000 0 -0.22 2 2
SPHK1 0.004 0.088 -10000 0 -0.43 16 16
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.019 0.072 0.29 14 -0.29 2 16
PLCG1 0.018 0.073 0.29 14 -0.3 2 16
NHERF/PDGFRB 0.049 0.028 -10000 0 -0.26 3 3
YES1 0 0.089 -10000 0 -0.51 12 12
cell migration 0.048 0.028 -10000 0 -0.26 3 3
SHC/Grb2/SOS1 0.07 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.025 0.01 -10000 0 -0.13 2 2
SLC9A3R1 0.022 0.037 -10000 0 -0.43 3 3
NHERF1-2/PDGFRB/PTEN 0.06 0.031 -10000 0 -0.24 3 3
FYN 0.003 0.074 0.3 1 -0.39 13 14
DOK1 0.014 0.022 0.18 4 -0.24 1 5
HRAS/GTP 0.018 0.005 -10000 0 -10000 0 0
PDGFB 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.03 0.15 0.4 23 -0.44 19 42
PRKCD 0.007 0.062 0.18 13 -0.24 21 34
FER 0.009 0.058 0.19 14 -0.24 17 31
MAPKKK cascade 0.005 0.065 0.33 8 -10000 0 8
RASA1 0.018 0.032 0.19 14 -10000 0 14
NCK1 0.025 0.022 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.032 0.025 0.18 2 -0.22 1 3
PDGFB-D/PDGFRB/SHB 0.037 0.011 -10000 0 -10000 0 0
chemotaxis 0.006 0.093 0.28 16 -0.33 11 27
STAT1-3-5/STAT1-3-5 0.054 0.046 -10000 0 -0.22 10 10
Bovine Papilomavirus E5/PDGFRB 0.017 0.012 -10000 0 -0.093 1 1
PTPRJ 0.024 0.022 -10000 0 -0.43 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.004 0.21 -10000 0 -0.95 20 20
oxygen homeostasis 0.002 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.002 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.037 0.091 -10000 0 -0.33 6 6
EPO 0.028 0.14 -10000 0 -0.5 8 8
FIH (dimer) 0.022 0.021 -10000 0 -10000 0 0
APEX1 0.022 0.024 -10000 0 -10000 0 0
SERPINE1 -0.009 0.2 -10000 0 -0.46 57 57
FLT1 0.014 0.14 -10000 0 -0.71 10 10
ADORA2A 0.018 0.15 0.33 4 -0.47 12 16
germ cell development 0.017 0.17 -10000 0 -0.47 22 22
SLC11A2 0.024 0.16 -10000 0 -0.49 11 11
BHLHE40 0.018 0.17 -10000 0 -0.54 16 16
HIF1AN 0.022 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.037 0.12 -10000 0 -0.37 9 9
ETS1 0.028 0.047 -10000 0 -0.44 4 4
CITED2 0.018 0.11 -10000 0 -0.62 9 9
KDR 0.02 0.13 -10000 0 -0.81 9 9
PGK1 0.024 0.16 -10000 0 -0.48 12 12
SIRT1 0.025 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.062 0.19 -10000 0 -0.54 12 12
EPAS1 0.012 0.077 -10000 0 -0.32 8 8
SP1 0.024 0.025 -10000 0 -10000 0 0
ABCG2 0.023 0.16 -10000 0 -0.55 10 10
EFNA1 0.025 0.16 -10000 0 -0.49 11 11
FXN 0.02 0.15 0.33 4 -0.47 10 14
POU5F1 0.016 0.17 -10000 0 -0.49 22 22
neuron apoptosis -0.06 0.18 0.53 12 -10000 0 12
EP300 0.022 0.043 -10000 0 -0.43 4 4
EGLN3 0.014 0.063 -10000 0 -0.44 8 8
EGLN2 0.018 0.022 -10000 0 -10000 0 0
EGLN1 0.022 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.048 0.015 -10000 0 -10000 0 0
VHL 0.025 0.004 -10000 0 -10000 0 0
ARNT 0.021 0.025 -10000 0 -0.14 1 1
SLC2A1 0.015 0.15 0.35 2 -0.47 12 14
TWIST1 0.012 0.15 0.34 2 -0.5 16 18
ELK1 0.03 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.043 0.13 -10000 0 -0.36 10 10
VEGFA 0.023 0.16 -10000 0 -0.47 12 12
CREBBP 0.026 0.002 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.029 0.048 -10000 0 -0.2 13 13
TC10/GTP 0.03 0.04 -10000 0 -0.21 8 8
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.034 -10000 0 -0.23 4 4
HRAS 0.025 0.006 -10000 0 -10000 0 0
APS homodimer 0.014 0.056 -10000 0 -0.43 7 7
GRB14 -0.07 0.16 -10000 0 -0.43 63 63
FOXO3 -0.017 0.15 -10000 0 -0.61 27 27
AKT1 -0.033 0.09 0.35 6 -0.3 2 8
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.027 -10000 0 -0.2 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.023 -10000 0 -0.43 1 1
SORBS1 0.021 0.043 -10000 0 -0.43 4 4
CRK 0.026 0.002 -10000 0 -10000 0 0
PTPN1 0.01 0.035 -10000 0 -10000 0 0
CAV1 0.005 0.042 0.18 11 -0.24 5 16
CBL/APS/CAP/Crk-II/C3G 0.049 0.052 -10000 0 -0.22 9 9
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.034 -10000 0 -0.23 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.029 -10000 0 -0.2 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.027 0.037 -10000 0 -0.42 1 1
RPS6KB1 -0.032 0.083 0.34 6 -0.28 2 8
PARD6A 0.026 0.002 -10000 0 -10000 0 0
CBL 0.024 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.042 -10000 0 -0.6 2 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.079 -10000 0 -0.29 2 2
HRAS/GTP 0.013 0.027 -10000 0 -0.2 6 6
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.062 0.038 -10000 0 -0.21 4 4
PRKCI 0.018 0.05 -10000 0 -0.44 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.018 0.084 -10000 0 -0.21 62 62
SHC1 0.024 0.015 -10000 0 -0.13 4 4
negative regulation of MAPKKK cascade 0.037 0.046 -10000 0 -0.5 2 2
PI3K 0.054 0.032 -10000 0 -0.2 4 4
NCK2 0.026 0.002 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
AKT2 -0.036 0.084 0.47 3 -0.3 2 5
PRKCZ -0.043 0.15 -10000 0 -0.36 80 80
SH2B2 0.014 0.056 -10000 0 -0.43 7 7
SHC/SHIP 0.032 0.049 0.21 11 -0.21 6 17
F2RL2 -0.02 0.11 -10000 0 -0.19 95 95
TRIP10 0.02 0.044 -10000 0 -0.33 6 6
Insulin Receptor/Insulin/Shc 0.039 0.028 -10000 0 -0.22 3 3
TC10/GTP/CIP4/Exocyst 0.031 0.026 -10000 0 -0.26 3 3
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.063 0.035 -10000 0 -0.21 3 3
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.022 -10000 0 -0.43 1 1
CBL/APS/CAP/Crk-II 0.043 0.05 -10000 0 -0.24 9 9
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.037 -10000 0 -0.23 4 4
INPP5D 0.019 0.051 0.18 27 -0.22 6 33
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.032 0.18 -10000 0 -0.74 27 27
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.025 0.021 -10000 0 -0.43 1 1
p62DOK/RasGAP 0.037 0.047 -10000 0 -0.51 2 2
INS 0.016 0.038 -10000 0 -0.43 3 3
mol:PI-3-4-P2 0.018 0.051 0.18 27 -0.22 6 33
GRB2 0.025 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.035 0.087 0.34 6 -0.25 9 15
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.031 0.026 -10000 0 -0.26 3 3
PDPK1 0.025 0.021 -10000 0 -0.43 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.022 0.025 -10000 0 -0.21 4 4
Insulin Receptor/Insulin/IRS1 0.04 0.03 -10000 0 -0.23 4 4
Insulin Receptor/Insulin/IRS3 0.029 0.031 -10000 0 -0.31 3 3
Par3/Par6 0.045 0.064 -10000 0 -0.22 22 22
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.032 0.14 -10000 0 -0.31 73 73
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.002 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.06 -10000 0 -0.22 20 20
HIF1A 0.006 0.03 -10000 0 -0.26 5 5
COPS5 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.066 0.029 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A -0.015 0.12 -10000 0 -0.43 30 30
ARNT/IPAS -0.008 0.099 -10000 0 -0.31 41 41
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.018 0.048 -10000 0 -0.26 8 8
CUL2 0.024 0.007 -10000 0 -10000 0 0
OS9 0.025 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.049 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.02 0.048 -10000 0 -0.26 7 7
PHD1-3/OS9 0.048 0.044 -10000 0 -0.22 7 7
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 -10000 0 -0.26 6 6
VHL 0.025 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.048 -10000 0 -0.27 6 6
EGLN3 0.018 0.06 -10000 0 -0.43 8 8
EGLN2 0.022 0.01 -10000 0 -10000 0 0
EGLN1 0.025 0.004 -10000 0 -10000 0 0
TP53 0.014 0.073 -10000 0 -0.41 13 13
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.067 -10000 0 -0.58 5 5
ARNT 0.025 0.008 -10000 0 -0.13 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.005 0.071 0.18 1 -0.21 37 38
Aurora A signaling

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
Aurora A/GADD45A 0.027 0.042 0.21 3 -0.25 2 5
BIRC5 -0.059 0.16 -10000 0 -0.43 68 68
NFKBIA 0.014 0.033 0.25 2 -0.25 1 3
CPEB1 0.016 0.067 -10000 0 -0.43 10 10
AKT1 0.013 0.031 0.25 1 -0.25 1 2
NDEL1 0.026 0.002 -10000 0 -10000 0 0
Aurora A/BRCA1 0.029 0.028 -10000 0 -0.22 1 1
NDEL1/TACC3 0.044 0.04 0.19 1 -0.41 1 2
GADD45A 0.012 0.041 -10000 0 -0.43 1 1
GSK3B 0.028 0.015 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.05 -10000 0 -0.26 6 6
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.015 0.081 -10000 0 -0.31 30 30
TP53 0.017 0.053 -10000 0 -0.25 14 14
DLG7 0.014 0.029 -10000 0 -0.24 1 1
AURKAIP1 0.022 0.01 -10000 0 -10000 0 0
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.047 0.043 0.2 1 -0.44 1 2
G2/M transition of mitotic cell cycle 0.029 0.028 -10000 0 -0.22 1 1
AURKA 0.023 0.037 -10000 0 -0.29 1 1
AURKB -0.046 0.13 -10000 0 -0.28 94 94
CDC25B 0.022 0.027 -10000 0 -0.23 1 1
G2/M transition checkpoint 0.013 0.024 -10000 0 -0.22 1 1
mRNA polyadenylation 0.024 0.044 -10000 0 -0.24 8 8
Aurora A/CPEB 0.024 0.044 -10000 0 -0.24 8 8
Aurora A/TACC1/TRAP/chTOG 0.059 0.037 -10000 0 -0.25 2 2
BRCA1 0.025 0.013 -10000 0 -0.13 3 3
centrosome duplication 0.024 0.049 -10000 0 -0.25 6 6
regulation of centrosome cycle 0.043 0.039 0.19 1 -0.41 1 2
spindle assembly 0.057 0.036 -10000 0 -0.25 2 2
TDRD7 0.024 0.022 -10000 0 -0.43 1 1
Aurora A/RasGAP/Survivin 0.019 0.091 -10000 0 -0.21 35 35
CENPA -0.032 0.12 -10000 0 -0.37 45 45
Aurora A/PP2A 0.033 0.031 -10000 0 -0.25 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.017 0.035 0.18 1 -0.24 1 2
negative regulation of DNA binding 0.017 0.052 -10000 0 -0.25 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
Ajuba/Aurora A 0.013 0.024 -10000 0 -0.22 1 1
mitotic prometaphase 0.013 0.037 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.037 -10000 0 -0.29 1 1
TACC1 0.025 0.005 -10000 0 -10000 0 0
TACC3 0.014 0.047 -10000 0 -0.43 2 2
Aurora A/Antizyme1 0.041 0.033 -10000 0 -0.22 1 1
Aurora A/RasGAP 0.033 0.031 -10000 0 -0.25 1 1
OAZ1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.028 0.016 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.033 -10000 0 -0.26 4 4
Importin alpha/Importin beta/TPX2 -0.015 0.081 -10000 0 -0.31 30 30
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.066 -10000 0 -0.24 16 16
PAK1 0.007 0.063 -10000 0 -0.43 5 5
CKAP5 0.025 0.005 -10000 0 -10000 0 0
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 0.045 0.032 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.039 0.049 0.29 2 -0.22 1 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.021 0.075 -10000 0 -0.24 20 20
CaM/Ca2+ 0.046 0.033 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.02 0.033 -10000 0 -10000 0 0
AKT1 0.004 0.039 0.26 2 -10000 0 2
MAP2K1 -0.001 0.036 0.25 3 -10000 0 3
MAP3K11 0.011 0.032 0.28 2 -10000 0 2
IFNGR1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.057 0.19 -10000 0 -0.42 90 90
Rap1/GTP 0.013 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.055 0.034 -10000 0 -10000 0 0
CEBPB 0.017 0.11 0.29 2 -0.49 13 15
STAT3 0.026 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.029 0.16 -10000 0 -1.1 8 8
STAT1 0.01 0.036 0.26 3 -10000 0 3
CALM1 0.025 0.009 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.011 0.02 -10000 0 -0.13 4 4
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.022 0.043 0.26 3 -0.2 4 7
CEBPB/PTGES2/Cbp/p300 0.028 0.074 -10000 0 -0.34 9 9
mol:Ca2+ 0.042 0.03 -10000 0 -10000 0 0
MAPK3 0.018 0.056 -10000 0 -0.72 1 1
STAT1 (dimer) -0.018 0.11 -10000 0 -0.33 20 20
MAPK1 0.01 0.094 -10000 0 -0.71 6 6
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.011 -10000 0 -10000 0 0
CAMK2D 0.024 0.022 -10000 0 -0.43 1 1
DAPK1 0.013 0.12 0.32 3 -0.6 15 18
SMAD7 -0.008 0.046 0.2 2 -0.17 3 5
CBL/CRKL/C3G 0.036 0.032 0.29 1 -10000 0 1
PI3K 0.044 0.034 -10000 0 -10000 0 0
IFNG 0.011 0.02 -10000 0 -0.13 4 4
apoptosis 0.008 0.1 0.31 2 -0.44 19 21
CAMK2G 0.024 0.022 -10000 0 -0.43 1 1
STAT3 (dimer) 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.097 0.17 -10000 0 -0.43 86 86
CAMK2B -0.018 0.11 -10000 0 -0.27 63 63
FRAP1 -0.001 0.036 0.22 3 -10000 0 3
PRKCD -0.005 0.055 0.27 2 -0.23 1 3
RAP1B 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.021 0.075 -10000 0 -0.24 20 20
PTPN2 0.025 0.004 -10000 0 -10000 0 0
EP300 0.022 0.043 -10000 0 -0.43 4 4
IRF1 -0.001 0.062 0.26 4 -0.31 7 11
STAT1 (dimer)/PIASy 0.023 0.041 0.28 3 -10000 0 3
SOCS1 -0.001 0.18 -10000 0 -1.4 8 8
mol:GDP 0.033 0.029 0.27 1 -10000 0 1
CASP1 -0.011 0.058 0.2 3 -0.25 12 15
PTGES2 0.025 0.004 -10000 0 -10000 0 0
IRF9 0.022 0.04 0.16 6 -0.19 1 7
mol:PI-3-4-5-P3 0.032 0.027 -10000 0 -10000 0 0
RAP1/GDP 0.028 0.024 -10000 0 -10000 0 0
CBL 0.011 0.031 0.28 2 -10000 0 2
MAP3K1 0.011 0.033 0.28 2 -10000 0 2
PIAS1 0.022 0.042 -10000 0 -0.43 4 4
PIAS4 0.025 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.021 0.075 -10000 0 -0.24 20 20
PTPN11 0.014 0.029 0.23 2 -10000 0 2
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.025 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.015 0.12 -9999 0 -0.28 63 63
Ran/GTP/Exportin 1/HDAC1 0.006 0.004 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.11 -9999 0 -0.28 58 58
SUMO1 0.026 0.002 -9999 0 -10000 0 0
ZFPM1 0.025 0.021 -9999 0 -0.43 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
FKBP3 0.026 0.003 -9999 0 -10000 0 0
Histones 0.027 0.075 -9999 0 -0.24 3 3
YY1/LSF 0.027 0.041 -9999 0 -0.25 5 5
SMG5 0.025 0.005 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.016 0.085 -9999 0 -0.23 60 60
I kappa B alpha/HDAC1 0.011 0.067 -9999 0 -0.3 5 5
SAP18 0.025 0.005 -9999 0 -10000 0 0
RELA -0.006 0.083 -9999 0 -0.2 59 59
HDAC1/Smad7 0.034 0.026 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
HDAC3/TR2 0.01 0.071 -9999 0 -0.28 3 3
NuRD/MBD3 Complex 0.022 0.018 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.008 0.088 -9999 0 -0.28 7 7
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.014 0.068 -9999 0 -0.34 14 14
GATA1 0.013 0.025 -9999 0 -10000 0 0
Mad/Max 0.037 0.008 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.016 0.064 -9999 0 -0.36 1 1
RBBP7 0.026 0.003 -9999 0 -10000 0 0
NPC 0.015 0.001 -9999 0 -10000 0 0
RBBP4 0.022 0.01 -9999 0 -10000 0 0
MAX 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
NFKBIA -0.012 0.07 -9999 0 -0.18 61 61
KAT2B 0.025 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.021 0.015 -9999 0 -10000 0 0
SIN3 complex 0.058 0.023 -9999 0 -10000 0 0
SMURF1 0.021 0.011 -9999 0 -10000 0 0
CHD3 0.025 0.021 -9999 0 -0.43 1 1
SAP30 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.025 0.021 -9999 0 -0.43 1 1
YY1/HDAC3 0.002 0.062 -9999 0 -0.22 6 6
YY1/HDAC2 0.028 0.036 -9999 0 -0.21 5 5
YY1/HDAC1 0.022 0.039 -9999 0 -0.21 6 6
NuRD/MBD2 Complex (MeCP1) 0.021 0.026 -9999 0 -0.34 1 1
PPARG -0.026 0.12 -9999 0 -0.3 69 69
HDAC8/hEST1B 0.048 0.016 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.019 0.049 -9999 0 -0.34 7 7
HDAC3/SMRT (N-CoR2) 0.01 0.071 -9999 0 -0.28 3 3
MBD3L2 -0.015 0.005 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.026 -9999 0 -10000 0 0
CREBBP 0.026 0.002 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.015 0.06 -9999 0 -10000 0 0
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC3 -0.01 0.064 -9999 0 -0.17 61 61
HDAC2 0.025 0.005 -9999 0 -10000 0 0
YY1 0.017 0.025 -9999 0 -0.24 4 4
HDAC8 0.026 0.003 -9999 0 -10000 0 0
SMAD7 0.026 0.004 -9999 0 -10000 0 0
NCOR2 0.026 0.003 -9999 0 -10000 0 0
MXD1 0.026 0.002 -9999 0 -10000 0 0
STAT3 0.018 0.029 -9999 0 -0.29 4 4
NFKB1 0.026 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.033 0.043 -9999 0 -0.4 1 1
YY1/SAP30/HDAC1 0.034 0.04 -9999 0 -0.19 3 3
EP300 0.022 0.043 -9999 0 -0.43 4 4
STAT3 (dimer non-phopshorylated) 0.018 0.029 -9999 0 -0.29 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.07 -9999 0 -0.18 61 61
histone deacetylation 0.031 0.036 -9999 0 -0.33 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.061 -9999 0 -0.23 7 7
nuclear export -0.048 0.015 -9999 0 -10000 0 0
PRKACA 0.025 0.005 -9999 0 -10000 0 0
GATAD2B 0.026 0.004 -9999 0 -10000 0 0
GATAD2A 0.025 0.006 -9999 0 -10000 0 0
GATA2/HDAC3 0.005 0.081 -9999 0 -0.26 13 13
GATA1/HDAC1 0.029 0.019 -9999 0 -10000 0 0
GATA1/HDAC3 0.007 0.071 -9999 0 -0.26 4 4
CHD4 0.024 0.007 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.031 0.12 -9999 0 -0.32 62 62
SIN3/HDAC complex/Mad/Max 0.02 0.029 -9999 0 -10000 0 0
NuRD Complex 0.016 0.065 -9999 0 -0.25 1 1
positive regulation of chromatin silencing 0.025 0.073 -9999 0 -0.24 3 3
SIN3B 0.025 0.006 -9999 0 -10000 0 0
MTA2 0.025 0.005 -9999 0 -10000 0 0
SIN3A 0.026 0.003 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
HDAC complex 0.053 0.028 -9999 0 -10000 0 0
GATA1/Fog1 0.034 0.022 -9999 0 -0.31 1 1
FKBP25/HDAC1/HDAC2 0.042 0.022 -9999 0 -10000 0 0
TNF -0.061 0.16 -9999 0 -0.43 62 62
negative regulation of cell growth 0.02 0.046 -9999 0 -0.24 5 5
NuRD/MBD2/PRMT5 Complex 0.021 0.026 -9999 0 -0.34 1 1
Ran/GTP/Exportin 1 0.042 0.019 -9999 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.019 0.11 -9999 0 -0.29 62 62
SIN3/HDAC complex/NCoR1 0.022 0.043 -9999 0 -0.24 7 7
TFCP2 0.025 0.022 -9999 0 -0.43 1 1
NR2C1 0.026 0.002 -9999 0 -10000 0 0
MBD3 0.025 0.006 -9999 0 -10000 0 0
MBD2 0.025 0.004 -9999 0 -10000 0 0
S1P3 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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
mol:S1P 0.001 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.01 0.045 -10000 0 -0.28 9 9
GNAO1 0.021 0.053 -10000 0 -0.44 6 6
S1P/S1P3/G12/G13 0.039 0.041 -10000 0 -0.23 7 7
AKT1 0.018 0.067 -10000 0 -0.38 10 10
AKT3 0.014 0.12 -10000 0 -0.99 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.011 -10000 0 -10000 0 0
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.007 0.071 -10000 0 -0.43 8 8
S1PR2 0.022 0.038 -10000 0 -0.36 4 4
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.076 -10000 0 -0.3 14 14
MAPK3 0.006 0.072 -10000 0 -0.29 14 14
MAPK1 0.008 0.067 -10000 0 -0.27 13 13
JAK2 0.008 0.074 0.2 3 -0.3 9 12
CXCR4 0.001 0.076 -10000 0 -0.27 19 19
FLT1 0.025 0.025 -10000 0 -0.48 1 1
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.005 0.067 -10000 0 -0.31 11 11
S1P/S1P3/Gi 0.011 0.077 -10000 0 -0.31 14 14
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.075 -10000 0 -0.28 13 13
VEGFA 0.02 0.032 -10000 0 -0.12 21 21
S1P/S1P2/Gi 0.013 0.066 -10000 0 -0.28 10 10
VEGFR1 homodimer/VEGFA homodimer 0.035 0.033 -10000 0 -0.38 1 1
RHOA 0.025 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0 0.081 -10000 0 -0.25 39 39
GNAQ 0.025 0.004 -10000 0 -10000 0 0
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
G12/G13 0.032 0.014 -10000 0 -10000 0 0
GNA14 0.007 0.087 -10000 0 -0.35 23 23
GNA15 0.011 0.077 -10000 0 -0.36 17 17
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.004 -10000 0 -10000 0 0
GNA11 0.018 0.056 -10000 0 -0.43 7 7
Rac1/GTP 0.011 0.069 -10000 0 -0.29 11 11
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.037 -10000 0 -0.25 4 4
forebrain development 0.018 0.15 0.62 1 -0.44 29 30
GNAO1 0.02 0.052 -10000 0 -0.44 6 6
SMO/beta Arrestin2 0.029 0.028 -10000 0 -0.31 2 2
SMO 0.018 0.032 -10000 0 -0.43 2 2
ARRB2 0.026 0.005 -10000 0 -10000 0 0
GLI3/SPOP 0.016 0.089 -10000 0 -0.38 10 10
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.026 0.003 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GNAI1 0.019 0.038 -10000 0 -0.43 3 3
XPO1 0.026 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0.01 0.11 -10000 0 -0.81 5 5
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.032 -10000 0 -0.43 2 2
MIM/GLI2A 0.017 0.045 -10000 0 -0.37 5 5
IFT88 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.011 -10000 0 -10000 0 0
GLI2 0.031 0.046 0.27 2 -10000 0 2
GLI3 0.006 0.09 0.22 1 -0.38 11 12
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.043 -10000 0 -0.43 4 4
Gi family/GTP 0.001 0.058 -10000 0 -0.32 9 9
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.073 -10000 0 -0.47 4 4
GLI2/Su(fu) 0.026 0.048 -10000 0 -0.37 3 3
FOXA2 0.011 0.097 -10000 0 -0.67 7 7
neural tube patterning 0.018 0.15 0.62 1 -0.44 29 30
SPOP 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.043 0.047 -10000 0 -0.22 4 4
GNB1 0.022 0.01 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
MTSS1 0.017 0.045 -10000 0 -0.37 5 5
embryonic limb morphogenesis 0.018 0.15 0.62 1 -0.44 29 30
SUFU 0.018 0.017 -10000 0 -0.17 1 1
LGALS3 0.014 0.048 -10000 0 -0.43 2 2
catabolic process 0.041 0.092 0.29 1 -0.58 3 4
GLI3A/CBP 0.003 0.087 -10000 0 -0.32 28 28
KIF3A 0.025 0.022 -10000 0 -0.43 1 1
GLI1 0.017 0.15 0.62 1 -0.46 29 30
RAB23 0.025 0.021 -10000 0 -0.43 1 1
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.037 -10000 0 -0.43 3 3
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.045 0.047 -10000 0 -0.29 2 2
GNAZ 0.025 0.022 -10000 0 -0.43 1 1
RBBP4 0.022 0.01 -10000 0 -10000 0 0
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
PIAS1 0.022 0.042 -10000 0 -0.43 4 4
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.04 0.05 -10000 0 -0.52 1 1
STK36 0.026 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.058 -10000 0 -0.36 8 8
PTCH1 0.015 0.17 0.57 1 -0.98 8 9
MIM/GLI1 0.021 0.14 0.55 1 -0.44 25 26
CREBBP 0.003 0.087 -10000 0 -0.32 28 28
Su(fu)/SIN3/HDAC complex -0.004 0.11 0.22 3 -0.26 61 64
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.018 -10000 0 -10000 0 0
CDKN1B 0.016 0.059 -10000 0 -0.28 12 12
CDKN1A 0.003 0.064 -10000 0 -0.28 11 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
FOXO3 0.017 0.039 -10000 0 -0.28 6 6
AKT1 0.009 0.054 -10000 0 -0.29 14 14
BAD 0.025 0.005 -10000 0 -10000 0 0
AKT3 0.011 0.037 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.058 -10000 0 -0.28 13 13
AKT1/ASK1 0.029 0.06 -10000 0 -0.27 14 14
BAD/YWHAZ 0.044 0.02 -10000 0 -10000 0 0
RICTOR 0.026 0.003 -10000 0 -10000 0 0
RAF1 0.025 0.004 -10000 0 -10000 0 0
JNK cascade -0.028 0.058 0.26 14 -10000 0 14
TSC1 0.011 0.053 -10000 0 -0.28 13 13
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.033 0.056 -10000 0 -0.28 11 11
EP300 0.022 0.043 -10000 0 -0.43 4 4
mol:GDP 0.013 0.056 -10000 0 -0.29 14 14
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.012 0.056 -10000 0 -0.28 13 13
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.006 0.012 -10000 0 -0.25 1 1
MAP3K5 0.021 0.043 -10000 0 -0.43 4 4
MAPKAP1 0.025 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.025 0.067 0.46 2 -0.19 6 8
YWHAH 0.019 0.032 -10000 0 -10000 0 0
AKT1S1 0.016 0.038 -10000 0 -0.28 4 4
CASP9 0.011 0.05 -10000 0 -0.28 11 11
YWHAB 0.025 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.035 0.062 0.24 2 -0.27 12 14
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.021 -10000 0 -0.26 1 1
YWHAE 0.026 0.002 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.002 0.059 0.2 1 -0.26 4 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.017 -10000 0 -10000 0 0
CHUK 0.013 0.05 -10000 0 -0.28 11 11
BAD/BCL-XL 0.033 0.057 -10000 0 -0.27 13 13
mTORC2 0.032 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.015 -10000 0 -0.29 1 1
FOXO1-3a-4/14-3-3 family 0.024 0.078 0.23 1 -0.38 4 5
PDPK1 0.025 0.021 -10000 0 -0.43 1 1
MDM2 0.015 0.057 0.26 1 -0.28 12 13
MAPKKK cascade -0.033 0.055 0.28 11 -10000 0 11
MDM2/Cbp/p300 0.044 0.063 0.26 1 -0.27 11 12
TSC1/TSC2 0.015 0.064 0.24 12 -0.28 13 25
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.061 0.25 1 -0.26 12 13
glucose import -0.016 0.064 0.21 2 -0.24 32 34
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.023 0.044 0.2 13 -10000 0 13
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.013 0.053 -10000 0 -0.22 26 26
GSK3A 0.017 0.042 -10000 0 -0.28 5 5
FOXO1 0.012 0.055 -10000 0 -0.28 12 12
GSK3B 0.013 0.052 -10000 0 -0.28 12 12
SFN -0.022 0.11 -10000 0 -0.43 24 24
G1/S transition of mitotic cell cycle 0.02 0.05 0.26 8 -0.28 4 12
p27Kip1/14-3-3 family 0.024 0.069 -10000 0 -0.93 1 1
PRKACA 0.025 0.005 -10000 0 -10000 0 0
KPNA1 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 10 10
RHEB 0.02 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.002 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTK2 0.023 0.008 -10000 0 -10000 0 0
CRKL 0.009 0.039 0.16 2 -0.22 11 13
GRB2/SOS1/SHC 0.05 0.013 -10000 0 -10000 0 0
HRAS 0.025 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.019 0.04 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.041 0.047 -10000 0 -0.24 11 11
AKT1 -0.008 0.042 0.17 7 -0.2 11 18
BAD -0.008 0.038 0.16 7 -0.19 8 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.039 0.16 2 -0.22 11 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.026 0.041 -10000 0 -0.22 12 12
RAF1 0.01 0.055 -10000 0 -0.42 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.052 0.045 -10000 0 -0.21 10 10
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.027 0.044 -10000 0 -0.23 12 12
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.007 0.043 0.19 7 -0.2 8 15
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.003 0.047 -10000 0 -0.34 3 3
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.034 -10000 0 -0.2 8 8
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.064 0.047 -10000 0 -0.19 11 11
IGF-1R heterotetramer 0.025 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.041 0.045 -10000 0 -0.22 12 12
Crk/p130 Cas/Paxillin 0.05 0.047 0.21 2 -0.21 12 14
IGF1R 0.025 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.077 -10000 0 -0.44 12 12
IRS2/Crk 0.018 0.04 0.16 2 -0.21 12 14
PI3K 0.053 0.046 -10000 0 -0.21 11 11
apoptosis -0.015 0.04 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
PRKCD 0 0.086 -10000 0 -0.42 14 14
RAF1/14-3-3 E 0.026 0.055 -10000 0 -0.36 4 4
BAD/14-3-3 0.016 0.041 -10000 0 -10000 0 0
PRKCZ -0.013 0.051 0.17 6 -0.21 16 22
Crk/p130 Cas/Paxillin/FAK1 0.027 0.04 -10000 0 -10000 0 0
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.012 0.062 -10000 0 -0.34 13 13
BCAR1 0.025 0.021 -10000 0 -0.43 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.046 0.05 -10000 0 -0.21 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 0.027 0.044 -10000 0 -0.21 12 12
GRB10 0.021 0.023 -10000 0 -0.43 1 1
PTPN11 0.01 0.039 0.16 2 -0.22 11 13
IRS1 0.011 0.044 0.13 1 -0.23 12 13
IRS2 0.008 0.04 0.16 2 -0.22 12 14
IGF-1R heterotetramer/IGF1 0.026 0.059 -10000 0 -0.32 12 12
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDPK1 0.013 0.045 0.19 8 -0.2 11 19
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKD1 0.009 0.061 -10000 0 -0.33 13 13
SHC1 0.024 0.015 -10000 0 -0.13 4 4
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.029 -10000 0 -0.21 5 5
TRAF2/ASK1 0.031 0.028 -10000 0 -0.26 4 4
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 0.011 0.071 -10000 0 -0.37 5 5
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.003 0.089 0.2 4 -0.34 11 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.002 0.09 -10000 0 -0.27 36 36
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
GADD45A 0.012 0.041 -10000 0 -0.43 1 1
GADD45B 0.01 0.067 -10000 0 -0.43 8 8
MAP3K1 0.024 0.016 -10000 0 -10000 0 0
MAP3K6 0.02 0.019 -10000 0 -0.13 6 6
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
MAP3K4 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.027 0.037 -10000 0 -0.31 4 4
TAK1/TAB family -0.003 0.019 0.16 3 -0.13 3 6
RAC1/OSM/MEKK3 0.042 0.019 -10000 0 -10000 0 0
TRAF2 0.025 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.059 -10000 0 -0.29 5 5
TRAF6 0.006 0.014 -10000 0 -0.3 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.018 0.11 -10000 0 -0.27 63 63
CCM2 0.022 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.073 -10000 0 -0.25 30 30
MAPK11 0.023 0.037 -10000 0 -0.43 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.022 0.078 -10000 0 -0.25 31 31
OSM/MEKK3 0.032 0.015 -10000 0 -10000 0 0
TAOK1 -0.011 0.083 -10000 0 -0.29 37 37
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.021 0.043 -10000 0 -0.43 4 4
MAP3K10 0.019 0.022 -10000 0 -0.13 8 8
MAP3K3 0.025 0.004 -10000 0 -10000 0 0
TRX/ASK1 0.021 0.024 -10000 0 -0.25 3 3
GADD45/MTK1/MTK1 0.027 0.068 -10000 0 -0.22 22 22
Canonical NF-kappaB 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
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.061 0.19 19 -0.28 1 20
ERC1 0.024 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.025 0.052 -10000 0 -0.31 9 9
NFKBIA 0.019 0.034 0.21 14 -10000 0 14
BIRC2 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
RIPK2 0.024 0.007 -10000 0 -10000 0 0
IKBKG 0.019 0.034 -10000 0 -10000 0 0
IKK complex/A20 0.03 0.099 -10000 0 -0.38 4 4
NEMO/A20/RIP2 0.024 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.038 0.046 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.046 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.041 0.026 -10000 0 -0.24 1 1
NOD2 0.011 0.072 -10000 0 -0.24 26 26
NFKB1 0.027 0.004 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
MALT1 0.025 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.036 0.01 -10000 0 -10000 0 0
ATM 0.025 0.005 -10000 0 -10000 0 0
TNF/TNFR1A -0.031 0.12 -10000 0 -0.32 62 62
TRAF6 0.024 0.022 -10000 0 -0.43 1 1
PRKCA 0.024 0.022 -10000 0 -0.43 1 1
CHUK 0.025 0.006 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF -0.061 0.16 -10000 0 -0.43 62 62
NF kappa B1 p50/RelA 0.056 0.016 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.034 0.21 14 -10000 0 14
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.049 -10000 0 -0.34 7 7
IKK complex 0.052 0.051 0.25 1 -10000 0 1
CYLD 0.026 0.002 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.055 0.25 1 -0.37 1 2
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 0.012 0.069 -10000 0 -0.97 2 2
regulation of axonogenesis 0 0.048 0.24 6 -10000 0 6
myoblast fusion -0.009 0.039 0.35 3 -10000 0 3
mol:GTP 0.019 0.025 -10000 0 -0.16 6 6
regulation of calcium-dependent cell-cell adhesion -0.043 0.027 0.2 2 -10000 0 2
ARF1/GTP 0.035 0.023 -10000 0 -0.15 2 2
mol:GM1 0.008 0.018 -10000 0 -0.15 2 2
mol:Choline -0.008 0.063 -10000 0 -0.24 30 30
lamellipodium assembly 0.004 0.044 -10000 0 -0.36 5 5
MAPK3 0.02 0.027 -10000 0 -0.3 2 2
ARF6/GTP/NME1/Tiam1 0.044 0.027 -10000 0 -0.2 2 2
ARF1 0.025 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.009 0.039 -10000 0 -0.36 3 3
ARF1/GDP 0.014 0.045 -10000 0 -0.27 7 7
ARF6 0.032 0.012 -10000 0 -0.14 1 1
RAB11A 0.026 0.003 -10000 0 -10000 0 0
TIAM1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.027 -10000 0 -0.3 2 2
actin filament bundle formation -0.018 0.044 0.27 6 -10000 0 6
KALRN 0.006 0.025 -10000 0 -0.27 2 2
RAB11FIP3/RAB11A 0.038 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.045 -10000 0 -0.27 6 6
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.041 -10000 0 -0.23 6 6
substrate adhesion-dependent cell spreading 0.019 0.025 -10000 0 -0.16 6 6
cortical actin cytoskeleton organization 0.004 0.045 -10000 0 -0.36 5 5
RAC1 0.023 0.009 -10000 0 -10000 0 0
liver development 0.019 0.025 -10000 0 -0.16 6 6
ARF6/GTP 0.019 0.025 -10000 0 -0.16 6 6
RhoA/GTP 0.035 0.021 -10000 0 -0.15 2 2
mol:GDP 0.008 0.033 -10000 0 -0.32 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.05 0.024 -10000 0 -0.15 1 1
RHOA 0.025 0.004 -10000 0 -10000 0 0
PLD1 -0.004 0.074 -10000 0 -0.27 31 31
RAB11FIP3 0.026 0.002 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.044 -10000 0 -0.36 5 5
ruffle organization 0 0.048 -10000 0 -0.24 6 6
regulation of epithelial cell migration 0.019 0.025 -10000 0 -0.16 6 6
PLD2 0.017 0.022 -10000 0 -0.17 1 1
PIP5K1A 0 0.048 -10000 0 -0.24 6 6
mol:Phosphatidic acid -0.008 0.063 -10000 0 -0.24 30 30
Rac1/GTP 0.004 0.045 -10000 0 -0.36 5 5
FoxO family signaling

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
G6PC -0.004 0.14 -10000 0 -1.3 5 5
PLK1 0.026 0.15 -10000 0 -1.3 4 4
CDKN1B 0.053 0.11 -10000 0 -0.34 8 8
FOXO3 0.044 0.098 -10000 0 -0.52 5 5
KAT2B 0.03 0.014 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.08 -10000 0 -0.57 5 5
CAT 0.037 0.12 -10000 0 -1.2 1 1
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.032 0.016 -10000 0 -10000 0 0
FOXO1 0.007 0.084 -10000 0 -0.42 10 10
MAPK10 0.045 0.061 0.19 63 -0.22 2 65
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.062 0.062 0.29 2 -10000 0 2
response to oxidative stress 0.008 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.045 0.1 -10000 0 -0.47 6 6
XPO1 0.026 0.002 -10000 0 -10000 0 0
EP300 0.022 0.044 -10000 0 -0.43 4 4
BCL2L11 0.026 0.1 -10000 0 -1.2 3 3
FOXO1/SKP2 0.017 0.087 -10000 0 -0.44 10 10
mol:GDP 0.008 0.01 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A -0.03 0.22 -10000 0 -0.57 19 19
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.073 -10000 0 -0.57 2 2
MST1 0.004 0.1 -10000 0 -0.43 24 24
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0 0.093 -10000 0 -0.94 1 1
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.037 0.063 0.19 51 -0.21 8 59
MAPK9 0.047 0.06 0.19 66 -10000 0 66
YWHAG 0.019 0.024 -10000 0 -0.13 10 10
YWHAE 0.026 0.002 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
SIRT1 0.024 0.006 -10000 0 -10000 0 0
SOD2 0.054 0.1 -10000 0 -0.69 2 2
RBL2 0.06 0.079 -10000 0 -10000 0 0
RAL/GDP 0.037 0.018 -10000 0 -10000 0 0
CHUK 0.03 0.013 -10000 0 -10000 0 0
Ran/GTP 0.022 0.003 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
RAL/GTP 0.04 0.018 -10000 0 -10000 0 0
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
FASLG 0.024 0.024 -10000 0 -10000 0 0
SKP2 0.02 0.049 -10000 0 -0.43 5 5
USP7 0.027 0.002 -10000 0 -10000 0 0
IKBKB 0.03 0.013 -10000 0 -10000 0 0
CCNB1 0.033 0.1 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.082 0.089 0.28 2 -0.35 2 4
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.086 -10000 0 -0.43 10 10
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
SGK1 0.02 0.068 -10000 0 -0.43 10 10
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.005 -10000 0 -10000 0 0
ZFAND5 0.061 0.061 0.35 2 -10000 0 2
SFN -0.022 0.11 -10000 0 -0.43 24 24
CDK2 0.019 0.048 -10000 0 -0.43 4 4
FOXO3A/14-3-3 0.009 0.087 -10000 0 -0.66 2 2
CREBBP 0.025 0.014 -10000 0 -0.13 1 1
FBXO32 0.052 0.16 -10000 0 -1.2 3 3
BCL6 0.055 0.11 -10000 0 -0.76 3 3
RALB 0.027 0.002 -10000 0 -10000 0 0
RALA 0.023 0.01 -10000 0 -10000 0 0
YWHAH 0.019 0.032 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.016 0.068 -10000 0 -0.31 14 14
AKT1 0.035 0.069 0.31 4 -0.45 3 7
PTK2B 0.005 0.072 0.35 2 -0.44 3 5
VEGFR2 homodimer/Frs2 0.029 0.047 -10000 0 -0.64 2 2
CAV1 0.007 0.049 -10000 0 -0.14 35 35
CALM1 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.048 -10000 0 -0.59 2 2
endothelial cell proliferation 0.043 0.08 0.28 11 -0.43 3 14
mol:Ca2+ 0.02 0.055 0.36 1 -0.39 3 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.049 0.055 -10000 0 -0.39 4 4
RP11-342D11.1 0.009 0.054 -10000 0 -0.44 3 3
CDH5 0.025 0.012 -10000 0 -0.13 3 3
VEGFA homodimer 0.063 0.02 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
SHC2 0.025 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.039 0.044 -10000 0 -0.41 2 2
SH2D2A -0.018 0.12 -10000 0 -0.25 70 70
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.06 0.079 0.28 3 -0.4 5 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.027 0.083 -10000 0 -0.25 29 29
VEGFR1 homodimer 0.024 0.022 -10000 0 -0.43 1 1
SHC/GRB2/SOS1 0.067 0.052 -10000 0 -0.38 3 3
GRB10 0.017 0.06 0.36 1 -0.53 3 4
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.007 0.063 -10000 0 -0.43 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.066 0.054 -10000 0 -0.55 2 2
HRAS 0.025 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.055 -10000 0 -0.38 4 4
HIF1A 0.025 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.047 0.054 -10000 0 -0.39 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.041 -10000 0 -0.23 9 9
Nck/Pak 0.022 0.051 -10000 0 -0.31 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.045 0.048 -10000 0 -0.59 2 2
mol:GDP 0.053 0.048 -10000 0 -0.37 3 3
mol:NADP 0.042 0.068 0.28 4 -0.38 4 8
eNOS/Hsp90 0.053 0.066 0.28 4 -0.36 4 8
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.02 0.055 0.36 1 -0.39 3 4
HIF1A/ARNT 0.036 0.01 -10000 0 -10000 0 0
SHB 0.025 0.004 -10000 0 -10000 0 0
VEGFA 0.02 0.032 -10000 0 -0.12 21 21
VEGFC 0.017 0.052 -10000 0 -0.43 5 5
FAK1/Vinculin 0.038 0.081 0.3 2 -0.5 5 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.053 0.068 -10000 0 -0.56 2 2
PTPN6 0.015 0.061 -10000 0 -0.43 8 8
EPAS1 0.03 0.038 -10000 0 -0.5 2 2
mol:L-citrulline 0.042 0.068 0.28 4 -0.38 4 8
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.057 0.045 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer 0.048 0.055 -10000 0 -0.48 3 3
VEGFR2/3 heterodimer 0.026 0.058 -10000 0 -0.5 4 4
VEGFB 0.025 0.005 -10000 0 -10000 0 0
MAPK11 0.006 0.065 0.32 4 -0.6 2 6
VEGFR2 homodimer 0.017 0.05 -10000 0 -0.72 2 2
FLT1 0.024 0.022 -10000 0 -0.43 1 1
NEDD4 0.022 0.04 -10000 0 -0.43 3 3
MAPK3 0.004 0.058 0.36 1 -0.4 2 3
MAPK1 0.005 0.058 0.29 2 -0.4 2 4
VEGFA145/NRP2 0.029 0.044 -10000 0 -0.28 6 6
VEGFR1/2 heterodimer 0.029 0.047 -10000 0 -0.64 2 2
KDR 0.017 0.05 -10000 0 -0.72 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.045 0.058 -10000 0 -0.44 3 3
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.006 0.062 0.31 2 -0.42 2 4
PI3K 0.042 0.058 -10000 0 -0.53 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.046 0.048 -10000 0 -0.59 2 2
FES 0.018 0.058 -10000 0 -0.46 3 3
GAB1 0.029 0.055 -10000 0 -0.49 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.044 -10000 0 -0.5 2 2
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.008 -10000 0 -0.13 1 1
eNOS/Caveolin-1 0.033 0.064 0.31 2 -0.4 4 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.044 0.049 -10000 0 -0.34 5 5
PI3K/GAB1 0.047 0.061 -10000 0 -0.45 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.065 0.059 -10000 0 -0.55 2 2
PRKACA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.064 -10000 0 -0.34 9 9
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.016 0.057 0.36 1 -0.46 3 4
actin cytoskeleton reorganization 0.026 0.083 -10000 0 -0.25 29 29
PTK2 0.016 0.061 -10000 0 -0.59 2 2
EDG1 0.009 0.054 -10000 0 -0.44 3 3
mol:DAG 0.02 0.055 0.36 1 -0.39 3 4
CaM/Ca2+ 0.029 0.05 -10000 0 -0.43 2 2
MAP2K3 0.007 0.064 0.36 1 -0.53 2 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.068 0.084 -10000 0 -0.55 3 3
PLCG1 0.02 0.056 0.36 1 -0.4 3 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.056 0.046 -10000 0 -0.48 2 2
IQGAP1 0.022 0.033 -10000 0 -0.23 6 6
YES1 0.022 0.037 -10000 0 -0.43 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.048 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.06 -10000 0 -0.31 9 9
cell migration 0.047 0.089 0.27 8 -0.54 5 13
mol:PI-3-4-5-P3 0.041 0.055 -10000 0 -0.49 2 2
FYN 0.025 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.023 0.054 -10000 0 -0.42 3 3
mol:NO 0.042 0.068 0.28 4 -0.38 4 8
PXN 0.026 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.041 -10000 0 -0.41 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.059 -10000 0 -0.55 3 3
VHL 0.025 0.004 -10000 0 -10000 0 0
ITGB3 -0.003 0.088 -10000 0 -0.2 59 59
NOS3 0.043 0.073 0.31 2 -0.42 4 6
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.049 -10000 0 -0.59 2 2
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.012 0.05 0.36 1 -0.36 2 3
PRKCB 0 0.066 0.36 1 -0.3 9 10
VCL 0.021 0.04 -10000 0 -0.43 3 3
VEGFA165/NRP1 0.03 0.055 -10000 0 -0.44 3 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.048 -10000 0 -0.59 2 2
VEGFA165/NRP2 0.029 0.044 -10000 0 -0.28 6 6
MAPKKK cascade 0.036 0.064 0.3 4 -0.42 3 7
NRP2 0.02 0.048 -10000 0 -0.34 7 7
VEGFC homodimer 0.017 0.052 -10000 0 -0.43 5 5
NCK1 0.025 0.022 -10000 0 -0.43 1 1
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.078 0.29 3 -0.58 3 6
MAP3K13 0.016 0.066 0.36 1 -0.41 4 5
PDPK1 0.027 0.053 0.27 2 -0.44 2 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.03 0.02 -10000 0 -0.35 1 1
VEGFR1 homodimer/NRP1 0.013 0.017 -10000 0 -0.35 1 1
mol:DAG -0.013 0.073 -10000 0 -0.3 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.025 -10000 0 -0.32 1 1
CaM/Ca2+ 0 0.074 -10000 0 -0.26 2 2
HIF1A 0.031 0.006 -10000 0 -10000 0 0
GAB1 0.024 0.022 -10000 0 -0.43 1 1
AKT1 -0.014 0.079 -10000 0 -10000 0 0
PLCG1 -0.013 0.073 -10000 0 -0.3 1 1
NOS3 -0.008 0.069 -10000 0 -0.32 1 1
CBL 0.024 0.007 -10000 0 -10000 0 0
mol:NO 0.006 0.078 0.28 1 -0.31 1 2
FLT1 0.017 0.02 -10000 0 -0.41 1 1
PGF -0.034 0.14 -10000 0 -0.43 49 49
VEGFR1 homodimer/NRP2/VEGFR121 0.042 0.035 -10000 0 -0.23 5 5
CALM1 0.025 0.009 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.022 0.087 0.28 3 -10000 0 3
endothelial cell proliferation -0.026 0.097 -10000 0 -0.41 5 5
mol:Ca2+ -0.013 0.073 -10000 0 -0.29 1 1
MAPK3 -0.027 0.06 -10000 0 -0.26 1 1
MAPK1 -0.026 0.06 -10000 0 -0.26 1 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PLGF homodimer -0.034 0.14 -10000 0 -0.43 49 49
PRKACA 0.025 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.007 0.049 -10000 0 -0.14 35 35
VEGFA homodimer 0.019 0.032 -10000 0 -0.13 21 21
VEGFR1 homodimer/VEGFA homodimer 0.027 0.028 -10000 0 -0.35 1 1
platelet activating factor biosynthetic process -0.027 0.058 -10000 0 -10000 0 0
PI3K 0.028 0.087 -10000 0 -10000 0 0
PRKCA -0.027 0.063 0.19 1 -0.28 1 2
PRKCB -0.037 0.074 0.19 1 -0.28 11 12
VEGFR1 homodimer/PLGF homodimer -0.007 0.091 -10000 0 -0.26 50 50
VEGFA 0.019 0.032 -10000 0 -0.13 21 21
VEGFB 0.025 0.005 -10000 0 -10000 0 0
mol:IP3 -0.013 0.073 -10000 0 -0.3 1 1
RASA1 0.014 0.02 -10000 0 -0.32 1 1
NRP2 0.02 0.048 -10000 0 -0.34 7 7
VEGFR1 homodimer 0.017 0.02 -10000 0 -0.41 1 1
VEGFB homodimer 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.022 -10000 0 -0.43 1 1
eNOS/Caveolin-1 0.005 0.073 -10000 0 -0.3 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.086 -10000 0 -10000 0 0
mol:L-citrulline 0.006 0.078 0.28 1 -0.31 1 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.055 0.029 -10000 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.017 -10000 0 -10000 0 0
CD2AP 0.026 0.002 -10000 0 -10000 0 0
PI3K/GAB1 0.036 0.089 -10000 0 -10000 0 0
PDPK1 -0.011 0.073 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.023 -10000 0 -0.32 1 1
mol:NADP 0.006 0.078 0.28 1 -0.31 1 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.053 0.028 -10000 0 -0.3 1 1
VEGFR1 homodimer/NRP2 0.027 0.033 -10000 0 -0.26 5 5
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.019 0.048 0.43 5 -10000 0 5
PI3K Class IB/PDE3B 0.019 0.048 -10000 0 -0.43 5 5
PDE3B 0.019 0.048 -10000 0 -0.43 5 5
PLK2 and PLK4 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
PLK2 0.016 0.048 -9999 0 -0.43 3 3
PLK4 0.016 0.047 -9999 0 -0.43 3 3
regulation of centriole replication 0.001 0.045 -9999 0 -0.29 7 7
Circadian rhythm 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
chromatin modification 0.038 0.046 -10000 0 -0.41 1 1
CLOCK 0.004 0.099 -10000 0 -0.43 23 23
TIMELESS/CRY2 0.027 0.043 -10000 0 -10000 0 0
DEC1/BMAL1 0.031 0.022 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
NR1D1 0.011 0.09 -10000 0 -1.3 2 2
ARNTL 0.025 0.015 -10000 0 -10000 0 0
TIMELESS 0.014 0.037 -10000 0 -10000 0 0
NPAS2 0.021 0.054 -10000 0 -0.44 6 6
CRY2 0.023 0.03 -10000 0 -0.43 2 2
mol:CO -0.007 0.01 0.13 2 -10000 0 2
CHEK1 0.022 0.018 -10000 0 -0.13 6 6
mol:HEME 0.007 0.01 -10000 0 -0.13 2 2
PER1 0.016 0.067 -10000 0 -0.43 10 10
BMAL/CLOCK/NPAS2 0.038 0.077 -10000 0 -0.26 26 26
BMAL1/CLOCK 0.008 0.1 -10000 0 -0.72 3 3
S phase of mitotic cell cycle 0.038 0.046 -10000 0 -0.41 1 1
TIMELESS/CHEK1/ATR 0.039 0.047 -10000 0 -0.42 1 1
mol:NADPH 0.007 0.01 -10000 0 -0.13 2 2
PER1/TIMELESS 0.025 0.053 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.007 0.029 -10000 0 -0.13 11 11
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.01 -10000 0 -10000 0 0
mol:PIP3 0.009 0.02 -10000 0 -0.2 3 3
FRAP1 0.022 0.043 0.27 2 -0.31 2 4
AKT1 0.01 0.034 0.17 14 -0.23 1 15
INSR 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.025 -10000 0 -0.26 3 3
mol:GTP 0.034 0.038 0.18 10 -0.19 1 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.017 -10000 0 -0.16 1 1
TSC2 0.026 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.016 0.023 -10000 0 -0.17 1 1
TSC1 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.022 -10000 0 -0.23 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.022 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.007 -10000 0 -10000 0 0
RPS6KB1 0.027 0.049 0.25 8 -0.32 1 9
MAP3K5 -0.004 0.047 -10000 0 -0.21 21 21
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
apoptosis -0.004 0.047 -10000 0 -0.21 21 21
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.025 0.048 0.24 9 -0.28 1 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.033 0.19 3 -0.25 1 4
eIF4E/eIF4G1/eIF4A1 0.016 0.022 -10000 0 -0.2 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.21 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.024 0.15 5 -10000 0 5
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.026 0.031 0.18 1 -0.17 1 2
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.002 0.023 0.18 2 -0.21 2 4
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.007 0.13 -10000 0 -0.57 21 21
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.046 -10000 0 -0.25 4 4
TSC1/TSC2 0.039 0.045 0.21 13 -0.2 1 14
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.024 0.01 -10000 0 -10000 0 0
PPP5C 0.022 0.01 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.008 0.022 -10000 0 -0.25 3 3
INS -0.017 0.034 -10000 0 -0.43 3 3
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.002 0.023 0.18 2 -0.23 2 4
EIF4EBP1 0.001 0.16 -10000 0 -1.1 9 9
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PPP2R5D 0.021 0.042 0.26 2 -0.28 2 4
peptide biosynthetic process -0.007 0.032 0.18 9 -0.23 3 12
RHEB 0.02 0.011 -10000 0 -10000 0 0
EIF4A1 0.026 0.002 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 23 -10000 0 23
EEF2 -0.007 0.033 0.18 9 -0.23 3 12
eIF4E/4E-BP1 0.014 0.15 -10000 0 -1 9 9
Arf6 trafficking events

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
SLC2A4 -0.02 0.13 -10000 0 -0.31 64 64
CLTC 0.026 0.049 -10000 0 -0.35 4 4
calcium ion-dependent exocytosis 0.013 0.049 -10000 0 -0.32 1 1
Dynamin 2/GTP 0.025 0.007 -10000 0 -10000 0 0
EXOC4 0.02 0.011 -10000 0 -10000 0 0
CD59 0.016 0.04 -10000 0 -0.29 5 5
CPE 0.006 0.044 -10000 0 -0.26 12 12
CTNNB1 0.025 0.004 -10000 0 -10000 0 0
membrane fusion 0.002 0.039 -10000 0 -0.31 1 1
CTNND1 0.014 0.023 0.18 8 -10000 0 8
DNM2 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.017 0.035 0.15 2 -10000 0 2
TSHR -0.051 0.1 -10000 0 -0.26 83 83
INS -0.005 0.1 -10000 0 -0.45 21 21
BIN1 0.026 0.002 -10000 0 -10000 0 0
mol:Choline 0.002 0.039 -10000 0 -0.31 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.007 -10000 0 -10000 0 0
JUP 0.014 0.048 -10000 0 -0.28 8 8
ASAP2/amphiphysin II 0.049 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.006 0.072 -10000 0 -0.26 14 14
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.002 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.025 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.021 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.064 0.27 4 -10000 0 4
positive regulation of phagocytosis 0.012 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.005 -10000 0 -10000 0 0
ACAP1 0.021 0.048 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.006 0.058 -10000 0 -0.27 7 7
clathrin heavy chain/ACAP1 0.027 0.054 0.2 16 -0.26 4 20
JIP4/KLC1 0.048 0.011 -10000 0 -10000 0 0
EXOC1 0.025 0.005 -10000 0 -10000 0 0
exocyst 0.019 0.022 -10000 0 -10000 0 0
RALA/GTP 0.017 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.006 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.014 0.021 0.18 7 -10000 0 7
NME1 0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.051 0.25 2 -0.34 4 6
IL2RA 0.007 0.048 -10000 0 -0.3 5 5
VAMP3 0.012 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.067 -10000 0 -0.28 7 7
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.004 0.065 -10000 0 -0.26 28 28
PLD2 0.013 0.006 -10000 0 -10000 0 0
EXOC5 0.026 0.003 -10000 0 -10000 0 0
PIP5K1C 0.016 0.033 -10000 0 -10000 0 0
SDC1 0.013 0.045 -10000 0 -0.29 5 5
ARF6/GDP 0.024 0.005 -10000 0 -10000 0 0
EXOC7 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.02 0.067 -10000 0 -0.28 4 4
mol:Phosphatidic acid 0.002 0.039 -10000 0 -0.31 1 1
endocytosis -0.047 0.008 -10000 0 -10000 0 0
SCAMP2 0.026 0.003 -10000 0 -10000 0 0
ADRB2 0.014 0.071 0.28 2 -0.34 6 8
EXOC3 0.025 0.004 -10000 0 -10000 0 0
ASAP2 0.026 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.008 -10000 0 -10000 0 0
KLC1 0.025 0.004 -10000 0 -10000 0 0
AVPR2 0.023 0.056 0.24 2 -0.33 5 7
RALA 0.022 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.066 -10000 0 -0.27 3 3
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.051 0.038 -9999 0 -0.23 4 4
HDAC3 0.026 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.033 0.016 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.015 -9999 0 -10000 0 0
GATA2/HDAC5 0.029 0.052 -9999 0 -0.31 10 10
HDAC5/BCL6/BCoR 0.051 0.01 -9999 0 -10000 0 0
HDAC9 0.016 0.05 -9999 0 -0.3 9 9
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.012 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.009 -9999 0 -10000 0 0
HDAC5/YWHAB 0.037 0.009 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
GATA2 0.014 0.068 -9999 0 -0.34 14 14
HDAC4/RFXANK 0.036 0.011 -9999 0 -10000 0 0
BCOR 0.026 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.004 -9999 0 -10000 0 0
HDAC5 0.026 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.029 0.035 -9999 0 -0.31 4 4
Histones 0.032 0.041 -9999 0 -0.26 1 1
ADRBK1 0.025 0.005 -9999 0 -10000 0 0
HDAC4 0.025 0.005 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.006 -9999 0 -10000 0 0
HDAC4/Ubc9 0.037 0.008 -9999 0 -10000 0 0
HDAC7 0.026 0.003 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.005 -9999 0 -10000 0 0
TUBA1B 0.026 0.003 -9999 0 -10000 0 0
HDAC6 0.026 0.002 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.011 -9999 0 -10000 0 0
CAMK4 -0.09 0.19 -9999 0 -0.43 105 105
Tubulin/HDAC6 0.051 0.012 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.025 0.005 -9999 0 -10000 0 0
GATA1 0.013 0.025 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
NR3C1 0.026 0.003 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.02 -9999 0 -0.21 1 1
SRF 0.026 0.002 -9999 0 -10000 0 0
HDAC4/YWHAB 0.036 0.011 -9999 0 -10000 0 0
Tubulin 0.037 0.007 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.037 0.008 -9999 0 -10000 0 0
GNB1 0.022 0.01 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.038 0.007 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.013 -9999 0 -10000 0 0
HDAC4/SRF -0.017 0.13 -9999 0 -0.26 103 103
HDAC4/ER alpha 0.025 0.056 -9999 0 -0.31 11 11
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.041 -9999 0 -0.26 1 1
cell motility 0.05 0.011 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
HDAC7/HDAC3 0.038 0.007 -9999 0 -10000 0 0
BCL6 0.026 0.003 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.025 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.008 -9999 0 -10000 0 0
ESR1 0.01 0.073 -9999 0 -0.27 23 23
HDAC6/HDAC11 0.038 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.019 -9999 0 -0.21 1 1
NPC 0.015 0.001 -9999 0 -10000 0 0
MEF2C 0.018 0.041 -9999 0 -0.43 2 2
RAN 0.026 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.071 0.029 -9999 0 -0.22 2 2
GNG2 0.022 0.043 -9999 0 -0.43 4 4
NCOR2 0.026 0.003 -9999 0 -10000 0 0
TUBB2A 0.026 0.004 -9999 0 -10000 0 0
HDAC11 0.026 0.004 -9999 0 -10000 0 0
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
ANKRA2 0.026 0.003 -9999 0 -10000 0 0
RFXANK 0.024 0.009 -9999 0 -10000 0 0
nuclear import -0.032 0.01 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.004 -9999 0 -10000 0 0
SMAD2 -0.001 0.035 -9999 0 -0.25 2 2
SMAD3 0.025 0.026 -9999 0 -10000 0 0
SMAD3/SMAD4 0.037 0.046 -9999 0 -0.43 3 3
SMAD4/Ubc9/PIASy 0.049 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.047 0.044 -9999 0 -10000 0 0
PPM1A 0.025 0.005 -9999 0 -10000 0 0
CALM1 0.025 0.009 -9999 0 -10000 0 0
SMAD2/SMAD4 0.014 0.036 -9999 0 -0.23 2 2
MAP3K1 0.024 0.016 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.028 0.057 -9999 0 -0.3 13 13
MAPK3 0.026 0.002 -9999 0 -10000 0 0
MAPK1 0.026 0.003 -9999 0 -10000 0 0
NUP214 0.025 0.005 -9999 0 -10000 0 0
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
CTDSPL 0.024 0.022 -9999 0 -0.43 1 1
KPNB1 0.026 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.013 0.076 -9999 0 -0.43 13 13
UBE2I 0.026 0.002 -9999 0 -10000 0 0
NUP153 0.026 0.003 -9999 0 -10000 0 0
KPNA2 0.025 0.008 -9999 0 -10000 0 0
PIAS4 0.025 0.005 -9999 0 -10000 0 0
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 0.037 0.009 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
CHUK 0.025 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.039 -9999 0 -0.22 3 3
NFKB1 0.026 0.004 -9999 0 -10000 0 0
MAP3K14 0.026 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.018 -9999 0 -10000 0 0
RELB 0.02 0.026 -9999 0 -0.2 4 4
NFKB2 0.023 0.031 -9999 0 -0.43 2 2
NF kappa B2 p52/RelB 0.026 0.028 -9999 0 -0.22 4 4
regulation of B cell activation 0.025 0.028 -9999 0 -0.22 4 4
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 0.022 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.004 -9999 0 -10000 0 0
MDM2/SUMO1 0.04 0.02 -9999 0 -0.23 1 1
HDAC4 0.025 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.006 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.013 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.011 0.002 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.02 -9999 0 -0.21 1 1
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.032 -9999 0 -0.24 4 4
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.003 -9999 0 -10000 0 0
Ran/GTP 0.029 0.019 -9999 0 -0.24 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.026 0.004 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.017 -9999 0 -0.21 1 1
NPC 0.015 0.001 -9999 0 -10000 0 0
PIAS2 0.026 0.004 -9999 0 -10000 0 0
PIAS1 0.022 0.042 -9999 0 -0.43 4 4
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 0.013 0.028 0.15 9 -10000 0 9
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.011 0.027 0.13 6 -0.14 1 7
AP2 0.031 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.028 0.015 -10000 0 -10000 0 0
CLTB 0.026 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.007 -10000 0 -10000 0 0
CD4 0.021 0.034 -10000 0 -0.23 6 6
CLTA 0.025 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.007 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.026 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.01 0.005 -10000 0 -10000 0 0
mol:Choline 0.005 0.015 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.014 -10000 0 -10000 0 0
DDEF1 0.004 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.003 0.016 -10000 0 -10000 0 0
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.008 0.009 -10000 0 -10000 0 0
Rac/GTP 0.014 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.02 -10000 0 -10000 0 0
ARFIP2 0.023 0.008 -10000 0 -10000 0 0
COPA 0.025 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.021 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.014 0.011 -10000 0 -10000 0 0
GGA3 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.019 0.018 -10000 0 -0.16 1 1
AP2A1 0.021 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.014 0.014 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.022 0.019 -10000 0 -0.21 1 1
Arfaptin 2/Rac/GDP 0.028 0.014 -10000 0 -10000 0 0
CYTH2 0.022 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.018 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.009 0.042 -10000 0 -0.2 5 5
PLD2 0.002 0.008 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.004 -10000 0 -10000 0 0
PIP5K1A 0.003 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.023 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.015 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.004 -10000 0 -10000 0 0
GOSR2 0.012 0.009 -10000 0 -10000 0 0
USO1 0.006 0.045 -10000 0 -0.33 8 8
GBF1 0.005 0.046 -10000 0 -0.31 9 9
ARF1/GTP/Arfaptin 2 0.028 0.021 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.029 -10000 0 -0.24 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 461 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.VW.A7QS TCGA.TQ.A7RW TCGA.TQ.A7RV TCGA.TQ.A7RU
109_MAP3K5 -0.27 0.063 -0.12 -0.37
47_PPARGC1A 0.026 0.026 0.026 0.026
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0.026 0.026 0.026
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0 0.067 0.067 -0.21
30_TGFB1/TGF beta receptor Type II 0 0.026 0.026 0
84_STAT5B -0.0012 0.11 0.034 -0.031
84_STAT5A -0.15 0.11 0.034 -0.031
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/LGG-TP/8100485/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LGG-TP/8266086/Gistic2_Analysis_8266119/all_data_by_genes.txt

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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