PARADIGM pathway analysis of mRNASeq expression and copy number data
Brain Lower Grade Glioma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C19022NZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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/C19022NZ
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 58 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 92
IL23-mediated signaling events 83
Signaling mediated by p38-alpha and p38-beta 68
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 65
IL12-mediated signaling events 64
FOXM1 transcription factor network 61
Aurora B signaling 61
Syndecan-1-mediated signaling events 58
Signaling events regulated by Ret tyrosine kinase 56
TCR signaling in naïve CD8+ T cells 55
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 513 . 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 ( 513 ).

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 0.1793 92 648 7 -0.063 0 1000 -1000 -0.005 -1000
IL23-mediated signaling events 0.1618 83 5002 60 -0.49 0.026 1000 -1000 -0.092 -1000
Signaling mediated by p38-alpha and p38-beta 0.1326 68 3003 44 -0.1 0.026 1000 -1000 -0.028 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1267 65 4442 68 -0.3 0.18 1000 -1000 -0.076 -1000
IL12-mediated signaling events 0.1248 64 5653 87 -0.4 0.072 1000 -1000 -0.053 -1000
FOXM1 transcription factor network 0.1189 61 3141 51 -0.28 0.026 1000 -1000 -0.1 -1000
Aurora B signaling 0.1189 61 4150 67 -0.26 0.046 1000 -1000 -0.035 -1000
Syndecan-1-mediated signaling events 0.1131 58 1980 34 -0.074 0.026 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 0.1092 56 4672 82 -0.074 0.026 1000 -1000 -0.044 -1000
TCR signaling in naïve CD8+ T cells 0.1072 55 5186 93 -0.18 0.21 1000 -1000 -0.042 -1000
Endothelins 0.1014 52 5070 96 -0.13 0.026 1000 -1000 -0.041 -1000
Thromboxane A2 receptor signaling 0.0975 50 5348 105 -0.13 0.034 1000 -1000 -0.032 -1000
Syndecan-4-mediated signaling events 0.0936 48 3232 67 -0.095 0.035 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 0.0877 45 2363 52 -0.092 0.047 1000 -1000 -0.03 -1000
Reelin signaling pathway 0.0877 45 2571 56 -0.1 0.06 1000 -1000 -0.029 -1000
TCGA08_retinoblastoma 0.0858 44 359 8 -0.023 0.043 1000 -1000 -0.004 -1000
Effects of Botulinum toxin 0.0819 42 1093 26 -0.087 0.026 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0.0799 41 2672 65 -0.11 0.037 1000 -1000 -0.047 -1000
Syndecan-3-mediated signaling events 0.0799 41 1469 35 -0.061 0.063 1000 -1000 -0.022 -1000
FOXA2 and FOXA3 transcription factor networks 0.0780 40 1866 46 -0.22 0.03 1000 -1000 -0.097 -1000
Arf6 signaling events 0.0760 39 2423 62 -0.14 0.054 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 0.0721 37 2814 76 -0.11 0.056 1000 -1000 -0.053 -1000
IL4-mediated signaling events 0.0721 37 3441 91 -0.42 0.27 1000 -1000 -0.11 -1000
amb2 Integrin signaling 0.0721 37 3055 82 -0.15 0.028 1000 -1000 -0.027 -1000
Visual signal transduction: Rods 0.0721 37 1957 52 -0.1 0.026 1000 -1000 -0.016 -1000
E-cadherin signaling events 0.0721 37 187 5 -0.046 0.026 1000 -1000 0.003 -1000
Ras signaling in the CD4+ TCR pathway 0.0721 37 631 17 -0.054 0.034 1000 -1000 -0.018 -1000
Caspase cascade in apoptosis 0.0702 36 2690 74 -0.13 0.05 1000 -1000 -0.033 -1000
Aurora C signaling 0.0702 36 255 7 -0.074 0.01 1000 -1000 -0.011 -1000
BCR signaling pathway 0.0702 36 3631 99 -0.095 0.044 1000 -1000 -0.052 -1000
EGFR-dependent Endothelin signaling events 0.0702 36 765 21 -0.035 0.037 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 0.0682 35 4496 125 -0.072 0.063 1000 -1000 -0.048 -1000
Nongenotropic Androgen signaling 0.0682 35 1830 52 -0.076 0.036 1000 -1000 -0.023 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0682 35 2625 74 -0.062 0.059 1000 -1000 -0.056 -1000
Fc-epsilon receptor I signaling in mast cells 0.0663 34 3335 97 -0.06 0.042 1000 -1000 -0.053 -1000
LPA receptor mediated events 0.0663 34 3533 102 -0.1 0.03 1000 -1000 -0.067 -1000
a4b1 and a4b7 Integrin signaling 0.0624 32 161 5 -0.007 0.012 1000 -1000 0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0624 32 2791 85 -0.17 0.039 1000 -1000 -0.047 -1000
PDGFR-alpha signaling pathway 0.0604 31 1386 44 -0.1 0.032 1000 -1000 -0.028 -1000
IL1-mediated signaling events 0.0604 31 1942 62 -0.075 0.044 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0604 31 1637 52 -0.16 0.067 1000 -1000 -0.04 -1000
Retinoic acid receptors-mediated signaling 0.0585 30 1776 58 -0.087 0.051 1000 -1000 -0.03 -1000
Osteopontin-mediated events 0.0565 29 1127 38 -0.05 0.027 1000 -1000 -0.031 -1000
PLK1 signaling events 0.0565 29 2485 85 -0.078 0.038 1000 -1000 -0.024 -1000
Ceramide signaling pathway 0.0565 29 2264 76 -0.068 0.045 1000 -1000 -0.042 -1000
Glypican 2 network 0.0565 29 116 4 -0.002 0.003 1000 -1000 0.006 -1000
Visual signal transduction: Cones 0.0546 28 1093 38 -0.053 0.034 1000 -1000 -0.01 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0546 28 1520 54 -0.072 0.033 1000 -1000 -0.036 -1000
Noncanonical Wnt signaling pathway 0.0546 28 735 26 -0.048 0.026 1000 -1000 -0.028 -1000
Wnt signaling 0.0546 28 196 7 -0.008 0.01 1000 -1000 -0.009 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0546 28 2538 88 -0.091 0.029 1000 -1000 -0.06 -1000
BMP receptor signaling 0.0526 27 2237 81 -0.077 0.044 1000 -1000 -0.032 -1000
Glypican 1 network 0.0526 27 1306 48 -0.08 0.05 1000 -1000 -0.018 -1000
Calcium signaling in the CD4+ TCR pathway 0.0526 27 861 31 -0.094 0.026 1000 -1000 -0.04 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0507 26 886 34 -0.017 0.04 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 0.0507 26 453 17 -0.024 0.026 1000 -1000 -0.029 -1000
S1P5 pathway 0.0507 26 450 17 -0.052 0.026 1000 -1000 -0.011 -1000
Ephrin B reverse signaling 0.0507 26 1277 48 -0.026 0.027 1000 -1000 -0.015 -1000
Canonical Wnt signaling pathway 0.0487 25 1289 51 -0.13 0.065 1000 -1000 -0.039 -1000
Rapid glucocorticoid signaling 0.0487 25 507 20 -0.075 0.027 1000 -1000 -0.003 -1000
Glucocorticoid receptor regulatory network 0.0468 24 2837 114 -0.27 0.14 1000 -1000 -0.047 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0468 24 901 37 -0.034 0.046 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 0.0468 24 1838 76 -0.046 0.048 1000 -1000 -0.046 -1000
Regulation of nuclear SMAD2/3 signaling 0.0448 23 3149 136 -0.19 0.16 1000 -1000 -0.035 -1000
FAS signaling pathway (CD95) 0.0448 23 1087 47 -0.096 0.039 1000 -1000 -0.048 -1000
EPHB forward signaling 0.0448 23 2017 85 -0.027 0.054 1000 -1000 -0.046 -1000
IL6-mediated signaling events 0.0448 23 1748 75 -0.1 0.04 1000 -1000 -0.058 -1000
Presenilin action in Notch and Wnt signaling 0.0429 22 1353 61 -0.13 0.063 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 0.0429 22 580 26 -0.046 0.062 1000 -1000 -0.004 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0429 22 2663 120 -0.12 0.074 1000 -1000 -0.039 -1000
Coregulation of Androgen receptor activity 0.0409 21 1663 76 -0.083 0.05 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 0.0409 21 1509 69 -0.061 0.038 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.0409 21 906 43 -0.046 0.027 1000 -1000 -0.03 -1000
EPO signaling pathway 0.0390 20 1123 55 -0.028 0.07 1000 -1000 -0.027 -1000
TCGA08_p53 0.0390 20 140 7 -0.017 0.025 1000 -1000 -0.006 -1000
IL2 signaling events mediated by PI3K 0.0390 20 1199 58 -0.073 0.042 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0390 20 457 22 -0.027 0.027 1000 -1000 -0.03 -1000
Cellular roles of Anthrax toxin 0.0370 19 779 39 -0.13 0.029 1000 -1000 -0.018 -1000
Signaling events mediated by PTP1B 0.0370 19 1467 76 -0.07 0.04 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 0.0370 19 784 40 -0.064 0.05 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0351 18 1449 78 -0.017 0.037 1000 -1000 -0.044 -1000
S1P1 pathway 0.0331 17 628 36 -0.095 0.026 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 0.0331 17 940 54 -0.054 0.056 1000 -1000 -0.041 -1000
IL27-mediated signaling events 0.0331 17 903 51 -0.085 0.026 1000 -1000 -0.046 -1000
ceramide signaling pathway 0.0312 16 800 49 -0.06 0.037 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0312 16 1360 83 -0.093 0.051 1000 -1000 -0.026 -1000
Plasma membrane estrogen receptor signaling 0.0312 16 1406 86 -0.039 0.038 1000 -1000 -0.045 -1000
S1P4 pathway 0.0312 16 401 25 -0.052 0.045 1000 -1000 -0.02 -1000
LPA4-mediated signaling events 0.0292 15 180 12 -0.03 0.005 1000 -1000 -0.02 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0292 15 444 28 -0.052 0.032 1000 -1000 -0.013 -1000
Class I PI3K signaling events 0.0292 15 1134 73 -0.075 0.048 1000 -1000 -0.027 -1000
Paxillin-dependent events mediated by a4b1 0.0273 14 522 36 -0.038 0.047 1000 -1000 -0.03 -1000
Integrins in angiogenesis 0.0273 14 1205 84 -0.025 0.057 1000 -1000 -0.033 -1000
ErbB4 signaling events 0.0253 13 903 69 -0.07 0.045 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0253 13 589 45 -0.06 0.061 1000 -1000 -0.042 -1000
Signaling events mediated by PRL 0.0253 13 456 34 -0.06 0.033 1000 -1000 -0.034 -1000
Regulation of Androgen receptor activity 0.0253 13 969 70 -0.065 0.036 1000 -1000 -0.039 -1000
BARD1 signaling events 0.0234 12 708 57 -0.041 0.052 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 0.0234 12 390 31 -0.019 0.038 1000 -1000 -0.013 -1000
Regulation of Telomerase 0.0234 12 1306 102 -0.13 0.065 1000 -1000 -0.042 -1000
VEGFR1 specific signals 0.0234 12 703 56 -0.038 0.055 1000 -1000 -0.037 -1000
PLK2 and PLK4 events 0.0214 11 34 3 0.001 -1000 1000 -1000 -0.01 -1000
Aurora A signaling 0.0214 11 661 60 -0.057 0.058 1000 -1000 -0.017 -1000
Nectin adhesion pathway 0.0214 11 744 63 -0.046 0.066 1000 -1000 -0.044 -1000
TRAIL signaling pathway 0.0214 11 569 48 -0.001 0.062 1000 -1000 -0.029 -1000
PDGFR-beta signaling pathway 0.0214 11 1084 97 -0.072 0.072 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 0.0195 10 154 15 -0.017 0.026 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0175 9 309 32 -0.041 0.051 1000 -1000 -0.029 -1000
Insulin Pathway 0.0175 9 707 74 -0.071 0.062 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0156 8 580 68 -0.032 0.048 1000 -1000 -0.029 -1000
S1P3 pathway 0.0156 8 343 42 0 0.038 1000 -1000 -0.03 -1000
IFN-gamma pathway 0.0136 7 540 68 -0.099 0.056 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0136 7 314 43 -0.058 0.059 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class I 0.0136 7 805 104 -0.06 0.059 1000 -1000 -0.026 -1000
FoxO family signaling 0.0136 7 500 64 -0.033 0.08 1000 -1000 -0.054 -1000
IGF1 pathway 0.0136 7 455 57 -0.014 0.064 1000 -1000 -0.033 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0136 7 239 33 -0.029 0.065 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 0.0136 7 345 44 -0.018 0.042 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0117 6 781 125 -0.02 0.065 1000 -1000 -0.036 -1000
Class IB PI3K non-lipid kinase events 0.0117 6 18 3 -0.02 0.02 1000 -1000 -0.009 -1000
Canonical NF-kappaB pathway 0.0097 5 233 39 -0.06 0.059 1000 -1000 -0.027 -1000
Circadian rhythm pathway 0.0097 5 111 22 -0.007 0.038 1000 -1000 -0.042 -1000
Hedgehog signaling events mediated by Gli proteins 0.0097 5 381 65 -0.006 0.059 1000 -1000 -0.045 -1000
Arf6 downstream pathway 0.0097 5 246 43 -0.043 0.049 1000 -1000 -0.026 -1000
mTOR signaling pathway 0.0097 5 268 53 -0.018 0.041 1000 -1000 -0.031 -1000
Arf6 trafficking events 0.0097 5 424 71 -0.05 0.049 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 0.0078 4 351 75 -0.093 0.071 1000 -1000 -0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 40 23 -0.001 0.05 1000 -1000 -0.027 -1000
Arf1 pathway 0.0019 1 70 54 -0.001 0.039 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0019 1 18 13 0 0.059 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.061 1000 -1000 -0.025 -1000
Total NA 3300 189557 7203 -10 -990 131000 -131000 -4.3 -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 -0.052 0.14 -10000 0 -0.28 126 126
EFNA5 -0.027 0.13 -10000 0 -0.29 86 86
FYN -0.056 0.13 0.18 6 -0.29 99 105
neuron projection morphogenesis -0.052 0.14 -10000 0 -0.28 126 126
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.052 0.14 -10000 0 -0.28 126 126
EPHA5 -0.063 0.16 -10000 0 -0.43 79 79
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 -0.42 0.54 -9999 0 -1.2 131 131
IL23A -0.44 0.55 -9999 0 -1.3 122 122
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.53 -9999 0 -1.2 128 128
positive regulation of T cell mediated cytotoxicity -0.45 0.6 -9999 0 -1.3 130 130
ITGA3 -0.4 0.5 -9999 0 -1.2 113 113
IL17F -0.26 0.32 -9999 0 -0.72 121 121
IL12B -0.02 0.044 -9999 0 -0.16 5 5
STAT1 (dimer) -0.43 0.57 -9999 0 -1.3 131 131
CD4 -0.37 0.49 -9999 0 -1.1 111 111
IL23 -0.42 0.53 -9999 0 -1.2 123 123
IL23R -0.2 0.38 -9999 0 -1.1 76 76
IL1B -0.47 0.59 -9999 0 -1.4 132 132
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.38 0.48 -9999 0 -1.1 120 120
TYK2 -0.007 0.035 -9999 0 -10000 0 0
STAT4 -0.061 0.15 -9999 0 -0.26 158 158
STAT3 0.026 0.003 -9999 0 -10000 0 0
IL18RAP -0.024 0.13 -9999 0 -0.43 41 41
IL12RB1 -0.033 0.1 -9999 0 -0.34 40 40
PIK3CA 0.025 0.02 -9999 0 -0.43 1 1
IL12Rbeta1/TYK2 -0.023 0.083 -9999 0 -0.31 28 28
IL23R/JAK2 -0.19 0.36 -9999 0 -1.1 65 65
positive regulation of chronic inflammatory response -0.45 0.6 -9999 0 -1.3 130 130
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 0.024 0.005 -9999 0 -10000 0 0
RELA 0.023 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.49 -9999 0 -1.1 124 124
ALOX12B -0.45 0.55 -9999 0 -1.2 152 152
CXCL1 -0.43 0.54 -9999 0 -1.2 137 137
T cell proliferation -0.45 0.6 -9999 0 -1.3 130 130
NFKBIA 0.024 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.25 -9999 0 -0.56 109 109
PI3K -0.4 0.54 -9999 0 -1.2 128 128
IFNG -0.018 0.031 -9999 0 -0.11 20 20
STAT3 (dimer) -0.38 0.51 -9999 0 -1.1 125 125
IL18R1 -0.006 0.11 -9999 0 -0.27 58 58
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.36 -9999 0 -0.82 101 101
IL18/IL18R -0.003 0.13 -9999 0 -0.27 89 89
macrophage activation -0.019 0.02 -9999 0 -0.045 110 110
TNF -0.46 0.59 -9999 0 -1.4 126 126
STAT3/STAT4 -0.43 0.55 -9999 0 -1.2 139 139
STAT4 (dimer) -0.45 0.58 -9999 0 -1.3 139 139
IL18 0.002 0.093 -9999 0 -0.29 39 39
IL19 -0.38 0.48 -9999 0 -1.1 118 118
STAT5A (dimer) -0.43 0.57 -9999 0 -1.3 130 130
STAT1 0.021 0.027 -9999 0 -0.13 16 16
SOCS3 -0.028 0.12 -9999 0 -0.43 29 29
CXCL9 -0.45 0.55 -9999 0 -1.2 145 145
MPO -0.46 0.56 -9999 0 -1.2 153 153
positive regulation of humoral immune response -0.45 0.6 -9999 0 -1.3 130 130
IL23/IL23R/JAK2/TYK2 -0.49 0.68 -9999 0 -1.5 130 130
IL6 -0.4 0.54 -9999 0 -1.3 114 114
STAT5A 0.016 0.066 -9999 0 -0.43 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 -0.43 0.55 -9999 0 -1.2 137 137
keratinocyte proliferation -0.45 0.6 -9999 0 -1.3 130 130
NOS2 -0.41 0.51 -9999 0 -1.2 127 127
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.33 -10000 0 -0.97 62 62
MKNK1 0.022 0.01 -10000 0 -10000 0 0
MAPK14 -0.015 0.12 -10000 0 -0.29 76 76
ATF2/c-Jun -0.021 0.1 -10000 0 -0.44 10 10
MAPK11 -0.024 0.13 -10000 0 -0.31 83 83
MITF -0.026 0.14 0.3 1 -0.33 83 84
MAPKAPK5 -0.027 0.14 -10000 0 -0.34 83 83
KRT8 -0.064 0.18 -10000 0 -0.37 114 114
MAPKAPK3 0.025 0.021 -10000 0 -0.43 1 1
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.03 0.18 -10000 0 -0.42 83 83
CEBPB -0.034 0.16 -10000 0 -0.37 84 84
SLC9A1 -0.04 0.16 0.3 1 -0.39 81 82
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.024 0.15 -10000 0 -0.33 85 85
p38alpha-beta/MNK1 -0.011 0.14 -10000 0 -0.33 81 81
JUN -0.019 0.097 -10000 0 -0.44 10 10
PPARGC1A -0.04 0.17 -10000 0 -0.38 91 91
USF1 -0.025 0.14 0.3 1 -0.34 81 82
RAB5/GDP/GDI1 -0.012 0.11 -10000 0 -0.25 83 83
NOS2 -0.054 0.23 -10000 0 -0.52 77 77
DDIT3 -0.027 0.14 0.22 1 -0.34 82 83
RAB5A 0.026 0.004 -10000 0 -10000 0 0
HSPB1 0.007 0.15 0.28 68 -0.28 75 143
p38alpha-beta/HBP1 -0.008 0.14 -10000 0 -0.33 71 71
CREB1 -0.031 0.15 -10000 0 -0.36 82 82
RAB5/GDP 0.019 0.003 -10000 0 -10000 0 0
EIF4E -0.033 0.12 0.24 4 -0.3 75 79
RPS6KA4 -0.025 0.14 -10000 0 -0.34 80 80
PLA2G4A -0.04 0.13 0.2 1 -0.33 76 77
GDI1 -0.027 0.14 -10000 0 -0.34 83 83
TP53 -0.053 0.17 -10000 0 -0.43 82 82
RPS6KA5 -0.034 0.15 -10000 0 -0.35 89 89
ESR1 -0.035 0.15 -10000 0 -0.35 89 89
HBP1 0.02 0.011 -10000 0 -10000 0 0
MEF2C -0.028 0.14 -10000 0 -0.34 82 82
MEF2A -0.028 0.14 -10000 0 -0.35 82 82
EIF4EBP1 -0.035 0.15 -10000 0 -0.36 83 83
KRT19 -0.062 0.18 -10000 0 -0.37 116 116
ELK4 -0.025 0.14 0.3 1 -0.34 81 82
ATF6 -0.025 0.14 0.3 1 -0.34 81 82
ATF1 -0.034 0.15 -10000 0 -0.37 84 84
p38alpha-beta/MAPKAPK2 0 0.15 -10000 0 -0.33 81 81
p38alpha-beta/MAPKAPK3 -0.002 0.15 -10000 0 -0.34 82 82
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.004 0.076 -10000 0 -0.23 36 36
NFATC2 -0.084 0.23 -10000 0 -0.57 60 60
NFATC3 -0.035 0.11 -10000 0 -0.27 64 64
CD40LG -0.24 0.4 -10000 0 -0.95 106 106
ITCH -0.024 0.091 -10000 0 -0.22 85 85
CBLB -0.023 0.093 -10000 0 -0.22 83 83
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.36 -10000 0 -0.88 82 82
JUNB 0.006 0.072 -10000 0 -0.43 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.11 -10000 0 -0.26 88 88
T cell anergy -0.066 0.16 0.26 1 -0.39 87 88
TLE4 -0.06 0.17 -10000 0 -0.53 37 37
Jun/NFAT1-c-4/p21SNFT -0.2 0.44 -10000 0 -0.98 105 105
AP-1/NFAT1-c-4 -0.24 0.5 -10000 0 -1.1 106 106
IKZF1 -0.064 0.18 -10000 0 -0.54 46 46
T-helper 2 cell differentiation -0.14 0.28 -10000 0 -0.83 45 45
AP-1/NFAT1 -0.062 0.19 -10000 0 -0.43 68 68
CALM1 -0.01 0.072 -10000 0 -0.16 86 86
EGR2 -0.24 0.51 -10000 0 -1.3 82 82
EGR3 -0.26 0.55 -10000 0 -1.3 93 93
NFAT1/FOXP3 -0.054 0.19 -10000 0 -0.47 57 57
EGR1 -0.044 0.14 -10000 0 -0.27 112 112
JUN 0.009 0.03 -10000 0 -10000 0 0
EGR4 -0.087 0.17 -10000 0 -0.28 181 181
mol:Ca2+ -0.025 0.06 -10000 0 -0.15 87 87
GBP3 -0.079 0.22 -10000 0 -0.61 65 65
FOSL1 -0.028 0.13 -10000 0 -0.25 98 98
NFAT1-c-4/MAF/IRF4 -0.19 0.43 -10000 0 -0.97 105 105
DGKA -0.057 0.16 -10000 0 -0.48 38 38
CREM 0.023 0.022 -10000 0 -0.28 2 2
NFAT1-c-4/PPARG -0.2 0.44 -10000 0 -0.99 105 105
CTLA4 -0.08 0.19 -10000 0 -0.52 63 63
NFAT1-c-4 (dimer)/EGR1 -0.22 0.47 -10000 0 -1.1 105 105
NFAT1-c-4 (dimer)/EGR4 -0.24 0.46 -10000 0 -1.1 105 105
FOS -0.04 0.14 -10000 0 -0.32 80 80
IFNG -0.1 0.21 -10000 0 -0.62 42 42
T cell activation -0.11 0.23 -10000 0 -0.67 42 42
MAF 0.024 0.035 -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 0.18 0.38 0.84 105 -10000 0 105
TNF -0.3 0.44 -10000 0 -1 119 119
FASLG -0.26 0.55 -10000 0 -1.3 100 100
TBX21 -0.004 0.1 -10000 0 -0.26 54 54
BATF3 0 0.091 -10000 0 -0.43 19 19
PRKCQ 0.015 0.061 -10000 0 -0.43 9 9
PTPN1 -0.058 0.16 -10000 0 -0.48 36 36
NFAT1-c-4/ICER1 -0.19 0.43 -10000 0 -0.97 105 105
GATA3 -0.038 0.14 -10000 0 -0.28 101 101
T-helper 1 cell differentiation -0.1 0.2 -10000 0 -0.62 42 42
IL2RA -0.17 0.32 -10000 0 -0.81 71 71
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.056 0.16 -10000 0 -0.46 42 42
E2F1 0.017 0.057 -10000 0 -0.36 8 8
PPARG 0.009 0.081 -10000 0 -0.43 16 16
SLC3A2 -0.055 0.16 -10000 0 -0.47 39 39
IRF4 -0.005 0.1 -10000 0 -0.43 25 25
PTGS2 -0.26 0.43 -10000 0 -1 108 108
CSF2 -0.24 0.4 -10000 0 -0.95 106 106
JunB/Fra1/NFAT1-c-4 -0.2 0.43 -10000 0 -0.97 104 104
IL4 -0.15 0.3 -10000 0 -0.9 42 42
IL5 -0.23 0.4 -10000 0 -0.94 106 106
IL2 -0.12 0.23 -10000 0 -0.68 42 42
IL3 -0.023 0.079 -10000 0 -0.69 3 3
RNF128 -0.084 0.2 -10000 0 -0.52 87 87
NFATC1 -0.18 0.38 -10000 0 -0.85 105 105
CDK4 0.11 0.21 0.63 32 -10000 0 32
PTPRK -0.057 0.16 -10000 0 -0.47 43 43
IL8 -0.26 0.42 -10000 0 -0.98 113 113
POU2F1 0.026 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.073 0.14 -10000 0 -0.35 62 62
TBX21 -0.33 0.46 -10000 0 -0.99 139 139
B2M 0.025 0.016 -10000 0 -0.13 5 5
TYK2 -0.002 0.035 -10000 0 -10000 0 0
IL12RB1 -0.028 0.1 -10000 0 -0.34 40 40
GADD45B -0.24 0.36 -10000 0 -0.81 98 98
IL12RB2 -0.047 0.12 -10000 0 -0.3 60 60
GADD45G -0.25 0.38 -10000 0 -0.85 107 107
natural killer cell activation -0.012 0.02 -10000 0 -0.04 113 113
RELB 0.02 0.025 -10000 0 -0.2 4 4
RELA 0.025 0.005 -10000 0 -10000 0 0
IL18 -0.005 0.096 -10000 0 -0.3 38 38
IL2RA -0.013 0.068 -10000 0 -0.16 65 65
IFNG -0.008 0.021 -10000 0 -0.13 5 5
STAT3 (dimer) -0.24 0.33 -10000 0 -0.71 138 138
HLA-DRB5 -0.002 0.006 -10000 0 -0.02 44 44
FASLG -0.3 0.42 0.48 1 -0.94 125 126
NF kappa B2 p52/RelB -0.29 0.43 -10000 0 -0.86 149 149
CD4 0.018 0.029 -10000 0 -0.28 2 2
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
EntrezGene:6955 -0.001 0.007 -10000 0 -0.023 44 44
CD3D -0.035 0.12 -10000 0 -0.23 107 107
CD3E -0.052 0.14 -10000 0 -0.26 129 129
CD3G 0.004 0.044 -10000 0 -0.14 27 27
IL12Rbeta2/JAK2 -0.027 0.094 -10000 0 -0.32 31 31
CCL3 -0.4 0.56 -10000 0 -1.2 140 140
CCL4 -0.39 0.56 -10000 0 -1.2 144 144
HLA-A 0 0.003 -10000 0 -0.049 1 1
IL18/IL18R -0.021 0.14 -10000 0 -0.29 87 87
NOS2 -0.28 0.42 -10000 0 -0.87 136 136
IL12/IL12R/TYK2/JAK2/SPHK2 -0.067 0.13 -10000 0 -0.36 59 59
IL1R1 -0.32 0.44 0.48 1 -0.98 125 126
IL4 0.017 0.034 -10000 0 -10000 0 0
JAK2 -0.003 0.035 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -0.021 45 45
TCR/CD3/MHC I/CD8 -0.046 0.12 -10000 0 -0.41 34 34
RAB7A -0.19 0.3 0.52 1 -0.67 95 96
lysosomal transport -0.18 0.28 0.51 1 -0.63 96 97
FOS -0.23 0.44 -10000 0 -1.2 72 72
STAT4 (dimer) -0.28 0.38 0.5 1 -0.78 151 152
STAT5A (dimer) -0.3 0.44 -10000 0 -0.86 156 156
GZMA -0.37 0.5 -10000 0 -1.1 145 145
GZMB -0.36 0.49 -10000 0 -1.1 135 135
HLX 0.018 0.046 -10000 0 -0.43 4 4
LCK -0.34 0.47 -10000 0 -0.94 158 158
TCR/CD3/MHC II/CD4 -0.039 0.1 -10000 0 -0.25 59 59
IL2/IL2R 0.003 0.11 -10000 0 -0.24 67 67
MAPK14 -0.24 0.36 -10000 0 -0.78 116 116
CCR5 -0.28 0.42 0.45 1 -0.91 120 121
IL1B -0.095 0.16 -10000 0 -0.36 110 110
STAT6 -0.072 0.11 -10000 0 -0.44 5 5
STAT4 -0.061 0.15 -10000 0 -0.26 158 158
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.027 -10000 0 -0.13 16 16
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.03 -10000 0 -0.33 3 3
IL12B -0.012 0.038 -10000 0 -0.15 6 6
CD8A -0.023 0.13 -10000 0 -0.28 82 82
CD8B -0.001 0.1 -10000 0 -0.34 38 38
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.072 0.13 0.35 61 -10000 0 61
IL2RB -0.028 0.13 -10000 0 -0.25 100 100
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.34 0.49 1 -0.7 151 152
IL2RG 0 0.087 -10000 0 -0.43 16 16
IL12 -0.019 0.085 -10000 0 -0.34 22 22
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
CD247 0.008 0.065 -10000 0 -0.32 13 13
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 -0.024 0.1 -10000 0 -0.44 24 24
IL12/IL12R/TYK2/JAK2 -0.36 0.52 -10000 0 -1 155 155
MAP2K3 -0.24 0.37 -10000 0 -0.76 123 123
RIPK2 0.024 0.007 -10000 0 -10000 0 0
MAP2K6 -0.24 0.37 -10000 0 -0.75 130 130
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.007 -10000 0 -0.023 44 44
IL18RAP -0.032 0.13 -10000 0 -0.39 49 49
IL12Rbeta1/TYK2 -0.017 0.087 -10000 0 -0.33 26 26
EOMES 0.022 0.097 -10000 0 -0.8 5 5
STAT1 (dimer) -0.23 0.33 -10000 0 -0.7 135 135
T cell proliferation -0.2 0.28 0.49 1 -0.56 151 152
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.014 0.11 -10000 0 -0.28 58 58
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 -0.62 152 152
ATF2 -0.22 0.33 0.51 1 -0.72 115 116
FOXM1 transcription factor network

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
NFATC3 -0.18 0.49 -9999 0 -1.2 78 78
PLK1 0.009 0.14 -9999 0 -1.3 5 5
BIRC5 -0.18 0.51 -9999 0 -1.4 74 74
HSPA1B -0.19 0.5 -9999 0 -1.2 82 82
MAP2K1 0.01 0.045 -9999 0 -0.18 1 1
BRCA2 -0.2 0.51 -9999 0 -1.2 84 84
FOXM1 -0.28 0.71 -9999 0 -1.7 85 85
XRCC1 -0.18 0.49 -9999 0 -1.2 77 77
FOXM1B/p19 -0.19 0.5 -9999 0 -1.2 84 84
Cyclin D1/CDK4 -0.18 0.45 -9999 0 -1.1 82 82
CDC2 -0.19 0.52 -9999 0 -1.2 86 86
TGFA -0.16 0.44 -9999 0 -1 84 84
SKP2 -0.19 0.5 -9999 0 -1.2 82 82
CCNE1 0.016 0.022 -9999 0 -0.14 2 2
CKS1B -0.18 0.49 -9999 0 -1.1 86 86
RB1 -0.11 0.32 -9999 0 -0.9 51 51
FOXM1C/SP1 -0.22 0.59 -9999 0 -1.4 87 87
AURKB -0.23 0.56 -9999 0 -1.4 92 92
CENPF -0.2 0.53 -9999 0 -1.3 77 77
CDK4 0.014 0.026 -9999 0 -10000 0 0
MYC -0.16 0.43 -9999 0 -0.99 87 87
CHEK2 0.004 0.066 -9999 0 -0.24 14 14
ONECUT1 -0.18 0.48 -9999 0 -1.1 86 86
CDKN2A -0.012 0.11 -9999 0 -0.42 31 31
LAMA4 -0.18 0.49 -9999 0 -1.2 79 79
FOXM1B/HNF6 -0.23 0.59 -9999 0 -1.4 83 83
FOS -0.26 0.56 -9999 0 -1.2 124 124
SP1 0.025 0.009 -9999 0 -10000 0 0
CDC25B -0.18 0.49 -9999 0 -1.2 80 80
response to radiation 0 0.026 -9999 0 -10000 0 0
CENPB -0.18 0.49 -9999 0 -1.2 77 77
CENPA -0.21 0.54 -9999 0 -1.3 82 82
NEK2 -0.23 0.56 -9999 0 -1.3 91 91
HIST1H2BA -0.19 0.49 -9999 0 -1.2 78 78
CCNA2 -0.012 0.1 -9999 0 -0.24 62 62
EP300 0.022 0.04 -9999 0 -0.43 4 4
CCNB1/CDK1 -0.22 0.59 -9999 0 -1.5 78 78
CCNB2 -0.23 0.57 -9999 0 -1.4 89 89
CCNB1 -0.19 0.52 -9999 0 -1.3 78 78
ETV5 -0.19 0.5 -9999 0 -1.2 84 84
ESR1 -0.2 0.5 -9999 0 -1.2 87 87
CCND1 -0.18 0.46 -9999 0 -1.1 83 83
GSK3A 0.012 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.013 0.091 -9999 0 -0.3 26 26
CDK2 0.014 0.049 -9999 0 -0.32 7 7
G2/M transition of mitotic cell cycle -0.003 0.03 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.2 0.55 -9999 0 -1.3 86 86
GAS1 -0.18 0.49 -9999 0 -1.2 80 80
MMP2 -0.19 0.5 -9999 0 -1.2 80 80
RB1/FOXM1C -0.2 0.49 -9999 0 -1.1 86 86
CREBBP 0.026 0.003 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.072 0.19 -10000 0 -0.44 93 93
STMN1 -0.048 0.12 0.19 3 -0.31 78 81
Aurora B/RasGAP/Survivin -0.057 0.19 -10000 0 -0.34 136 136
Chromosomal passenger complex/Cul3 protein complex -0.07 0.15 -10000 0 -0.34 94 94
BIRC5 -0.063 0.17 -10000 0 -0.32 127 127
DES -0.26 0.45 -10000 0 -0.86 168 168
Aurora C/Aurora B/INCENP -0.014 0.11 -10000 0 -0.24 97 97
Aurora B/TACC1 -0.027 0.11 -10000 0 -0.26 88 88
Aurora B/PP2A -0.035 0.13 -10000 0 -0.31 89 89
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.02 0.06 -10000 0 -0.15 93 93
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.096 0.19 0.2 6 -0.36 146 152
Cul3 protein complex 0.046 0.028 -10000 0 -0.26 2 2
KIF2C -0.094 0.25 -10000 0 -0.49 102 102
PEBP1 0.015 0.04 -10000 0 -0.44 3 3
KIF20A -0.078 0.17 -10000 0 -0.3 162 162
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.036 0.13 -10000 0 -0.31 90 90
SEPT1 0.024 0.024 -10000 0 -0.43 1 1
SMC2 0.026 0.004 -10000 0 -10000 0 0
SMC4 0.017 0.036 -10000 0 -0.13 29 29
NSUN2/NPM1/Nucleolin -0.13 0.3 -10000 0 -0.76 92 92
PSMA3 0.026 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.044 0.12 -10000 0 -0.3 90 90
AURKB -0.075 0.18 -10000 0 -0.32 147 147
AURKC 0.01 0.054 -10000 0 -0.43 5 5
CDCA8 -0.01 0.075 -10000 0 -0.46 8 8
cytokinesis -0.16 0.33 0.22 2 -0.73 109 111
Aurora B/Septin1 -0.13 0.32 0.27 2 -0.71 105 107
AURKA 0.018 0.038 -10000 0 -0.44 1 1
INCENP 0.015 0.029 -10000 0 -0.44 1 1
KLHL13 0.025 0.028 -10000 0 -0.43 2 2
BUB1 -0.043 0.15 -10000 0 -0.28 116 116
hSgo1/Aurora B/Survivin -0.083 0.22 -10000 0 -0.37 162 162
EVI5 0.021 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.11 0.29 0.19 1 -0.61 107 108
SGOL1 -0.047 0.15 -10000 0 -0.28 122 122
CENPA -0.1 0.26 0.23 1 -0.56 104 105
NCAPG -0.062 0.16 -10000 0 -0.43 77 77
Aurora B/HC8 Proteasome -0.036 0.13 -10000 0 -0.31 90 90
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.036 0.13 -10000 0 -0.31 90 90
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH -0.015 0.12 -10000 0 -0.43 32 32
NPM1 -0.085 0.2 -10000 0 -0.51 94 94
RASA1 0.026 0.003 -10000 0 -10000 0 0
KLHL9 0.024 0.008 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.13 -10000 0 -0.31 90 90
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin -0.13 0.31 0.2 1 -0.66 110 111
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.085 0.2 -10000 0 -0.51 93 93
MYLK -0.05 0.12 -10000 0 -0.29 100 100
KIF23 -0.036 0.13 -10000 0 -0.25 104 104
VIM -0.082 0.15 0.18 6 -0.32 130 136
RACGAP1 0.017 0.022 -10000 0 -0.13 5 5
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.087 0.21 -10000 0 -0.53 92 92
Chromosomal passenger complex -0.13 0.29 0.19 1 -0.63 112 113
Chromosomal passenger complex/EVI5 -0.043 0.19 -10000 0 -0.33 139 139
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
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CCL5 -0.026 0.13 -10000 0 -0.26 93 93
SDCBP 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.065 0.14 0.24 6 -0.31 83 89
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 -0.056 0.14 0.2 12 -0.33 64 76
Syndecan-1/Syntenin -0.048 0.14 0.23 18 -0.34 62 80
MAPK3 -0.052 0.13 0.19 14 -0.37 41 55
HGF/MET -0.039 0.12 -10000 0 -0.28 81 81
TGFB1/TGF beta receptor Type II 0.021 0.022 -10000 0 -0.43 1 1
BSG 0.025 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.055 0.14 0.2 12 -0.33 64 76
Syndecan-1/RANTES -0.068 0.16 0.24 17 -0.34 90 107
Syndecan-1/CD147 -0.043 0.14 0.24 4 -0.37 46 50
Syndecan-1/Syntenin/PIP2 -0.047 0.14 0.22 16 -0.34 54 70
LAMA5 0.024 0.022 -10000 0 -0.43 1 1
positive regulation of cell-cell adhesion -0.047 0.14 0.22 16 -0.34 54 70
MMP7 -0.072 0.16 -10000 0 -0.29 148 148
HGF -0.009 0.091 -10000 0 -0.2 68 68
Syndecan-1/CASK -0.069 0.13 -10000 0 -0.3 84 84
Syndecan-1/HGF/MET -0.074 0.16 0.24 4 -0.35 87 91
regulation of cell adhesion -0.043 0.14 0.29 18 -0.36 40 58
HPSE -0.015 0.12 -10000 0 -0.43 40 40
positive regulation of cell migration -0.065 0.14 0.24 6 -0.31 83 89
SDC1 -0.063 0.14 0.19 2 -0.27 127 129
Syndecan-1/Collagen -0.065 0.14 0.24 6 -0.31 83 89
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.046 0.14 -10000 0 -0.43 50 50
PRKACA 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.22 133 133
MAPK1 -0.051 0.13 0.2 13 -0.36 41 54
homophilic cell adhesion -0.061 0.14 0.22 15 -0.31 81 96
MMP1 -0.008 0.048 -10000 0 -0.43 1 1
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 -0.008 0.071 -10000 0 -0.39 11 11
Crk/p130 Cas/Paxillin -0.05 0.12 -10000 0 -0.28 75 75
JUN -0.06 0.13 -10000 0 -0.4 43 43
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.017 0.15 -10000 0 -0.28 108 108
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 -0.28 130 130
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 -0.003 0.12 -10000 0 -0.26 85 85
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.037 0.15 -10000 0 -0.26 134 134
GRB7 0.002 0.043 -10000 0 -0.13 40 40
RET51/GFRalpha1/GDNF -0.018 0.15 -10000 0 -0.28 118 118
MAPKKK cascade -0.049 0.14 -10000 0 -0.28 123 123
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.002 0.12 -10000 0 -0.26 83 83
lamellipodium assembly -0.036 0.1 -10000 0 -0.25 65 65
RET51/GFRalpha1/GDNF/SHC -0.023 0.16 -10000 0 -0.28 126 126
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC -0.002 0.12 -10000 0 -0.26 82 82
RET9/GFRalpha1/GDNF/Shank3 -0.005 0.12 -10000 0 -0.26 87 87
MAPK3 -0.074 0.12 0.17 5 -0.26 122 127
DOK1 0.025 0.021 -10000 0 -0.43 1 1
DOK6 -0.017 0.13 -10000 0 -0.38 53 53
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.067 0.13 -10000 0 -0.36 51 51
DOK5 0.015 0.066 -10000 0 -0.43 11 11
GFRA1 -0.014 0.12 -10000 0 -0.3 60 60
MAPK8 -0.061 0.14 -10000 0 -0.27 132 132
HRAS/GTP -0.034 0.17 -10000 0 -0.3 128 128
tube development 0 0.12 0.2 14 -0.25 81 95
MAPK1 -0.074 0.12 0.17 5 -0.26 123 128
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.1 -10000 0 -0.25 81 81
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
PDLIM7 0.023 0.021 -10000 0 -0.13 9 9
RET51/GFRalpha1/GDNF/Dok6 -0.027 0.18 -10000 0 -0.31 132 132
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RET51/GFRalpha1/GDNF/Dok4 -0.031 0.17 -10000 0 -0.29 135 135
RET51/GFRalpha1/GDNF/Dok5 -0.025 0.16 -10000 0 -0.28 130 130
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
CREB1 -0.041 0.14 -10000 0 -0.31 84 84
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.11 -10000 0 -0.26 80 80
RET51/GFRalpha1/GDNF/Grb7 -0.027 0.16 -10000 0 -0.29 129 129
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.044 0.15 -10000 0 -0.3 108 108
DOK4 0.012 0.079 -10000 0 -0.43 16 16
JNK cascade -0.062 0.13 0.19 1 -0.4 42 43
RET9/GFRalpha1/GDNF/FRS2 -0.003 0.12 -10000 0 -0.26 85 85
SHANK3 0.021 0.034 -10000 0 -0.19 10 10
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.1 -10000 0 -0.25 80 80
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.15 -10000 0 -0.28 129 129
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.055 0.15 -10000 0 -0.28 133 133
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.05 0.15 -10000 0 -0.28 122 122
PI3K -0.058 0.16 0.23 1 -0.38 80 81
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.007 0.12 -10000 0 -0.25 81 81
GRB10 0.021 0.03 -10000 0 -0.43 2 2
activation of MAPKK activity -0.051 0.14 -10000 0 -0.34 82 82
RET51/GFRalpha1/GDNF/FRS2 -0.024 0.16 -10000 0 -0.28 131 131
GAB1 0.025 0.021 -10000 0 -0.43 1 1
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.15 -10000 0 -0.28 122 122
RET51/GFRalpha1/GDNF/PKC alpha -0.024 0.16 -10000 0 -0.28 128 128
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GDNF -0.034 0.14 -10000 0 -0.38 72 72
RAC1 0.023 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.023 0.16 -10000 0 -0.28 128 128
Rac1/GTP -0.037 0.12 -10000 0 -0.3 63 63
RET9/GFRalpha1/GDNF -0.027 0.12 -10000 0 -0.28 85 85
GFRalpha1/GDNF -0.034 0.14 -10000 0 -0.33 85 85
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 0.16 0.24 11 -0.37 71 82
FYN -0.072 0.2 0.25 18 -0.43 89 107
LAT/GRAP2/SLP76 -0.074 0.17 0.23 5 -0.39 79 84
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.15 0.22 20 -0.33 85 105
B2M 0.021 0.021 -10000 0 -0.14 4 4
IKBKG -0.013 0.051 0.091 18 -0.12 29 47
MAP3K8 0.016 0.047 -10000 0 -0.2 18 18
mol:Ca2+ -0.017 0.027 0.089 12 -0.07 42 54
integrin-mediated signaling pathway 0.023 0.036 -10000 0 -0.24 7 7
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.081 0.2 0.25 17 -0.44 87 104
TRPV6 0.21 0.52 1.1 116 -0.45 38 154
CD28 -0.023 0.12 -10000 0 -0.43 39 39
SHC1 -0.073 0.19 0.23 25 -0.41 92 117
receptor internalization -0.059 0.15 0.24 2 -0.39 62 64
PRF1 -0.11 0.33 -10000 0 -0.96 55 55
KRAS 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.042 0.13 0.21 18 -0.28 76 94
LAT -0.084 0.19 0.23 16 -0.41 94 110
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.037 0.12 -10000 0 -0.24 102 102
CD3E -0.052 0.15 -10000 0 -0.27 128 128
CD3G 0.001 0.044 -10000 0 -0.13 14 14
RASGRP2 -0.003 0.019 0.13 1 -0.16 2 3
RASGRP1 -0.065 0.16 0.26 17 -0.34 86 103
HLA-A -0.002 0.006 -10000 0 -10000 0 0
RASSF5 0.017 0.056 -10000 0 -0.43 7 7
RAP1A/GTP/RAPL 0.023 0.036 -10000 0 -0.24 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.065 0.17 28 -0.13 14 42
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.067 -10000 0 -0.18 68 68
PRKCA -0.045 0.088 0.14 9 -0.21 68 77
GRAP2 -0.006 0.1 -10000 0 -0.26 57 57
mol:IP3 -0.064 0.14 0.19 15 -0.31 82 97
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.055 0.13 -10000 0 -0.36 59 59
ORAI1 -0.18 0.43 0.59 5 -0.95 114 119
CSK -0.075 0.19 0.22 18 -0.42 91 109
B7 family/CD28 -0.064 0.21 0.27 8 -0.45 85 93
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.09 0.2 0.26 1 -0.44 98 99
PTPN6 -0.085 0.19 0.22 4 -0.42 95 99
VAV1 -0.077 0.2 0.22 23 -0.42 100 123
Monovalent TCR/CD3 -0.045 0.11 -10000 0 -0.27 90 90
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.089 0.22 0.25 19 -0.45 105 124
PAG1 -0.072 0.19 0.21 27 -0.4 95 122
RAP1A 0.021 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.088 0.2 0.26 1 -0.44 96 97
CD80 -0.001 0.073 -10000 0 -0.18 55 55
CD86 0.001 0.097 -10000 0 -0.43 23 23
PDK1/CARD11/BCL10/MALT1 -0.04 0.084 -10000 0 -0.21 70 70
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.078 0.17 0.2 18 -0.38 89 107
CD8A -0.027 0.13 -10000 0 -0.29 82 82
CD8B -0.005 0.1 -10000 0 -0.36 35 35
PTPRC -0.004 0.1 -10000 0 -0.36 31 31
PDK1/PKC theta -0.065 0.18 0.29 15 -0.39 81 96
CSK/PAG1 -0.074 0.18 0.22 16 -0.41 88 104
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.072 0.19 0.25 5 -0.42 88 93
STIM1 -0.008 0.2 1.2 10 -0.89 2 12
RAS family/GTP -0.011 0.08 0.17 24 -0.17 37 61
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.063 0.15 -10000 0 -0.4 63 63
mol:DAG -0.071 0.11 0.13 2 -0.27 93 95
RAP1A/GDP 0.004 0.027 0.084 17 -0.066 2 19
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.008 0.065 -10000 0 -0.4 9 9
cytotoxic T cell degranulation -0.11 0.31 -10000 0 -0.89 56 56
RAP1A/GTP 0 0.007 -10000 0 -0.062 2 2
mol:PI-3-4-5-P3 -0.067 0.17 0.24 17 -0.37 87 104
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.078 0.17 0.23 8 -0.39 82 90
NRAS 0.021 0.01 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.43 22 22
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.087 0.16 0.2 1 -0.38 85 86
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
CD8 heterodimer -0.022 0.13 -10000 0 -0.3 77 77
CARD11 0.012 0.067 -10000 0 -0.36 14 14
PRKCB -0.053 0.093 0.14 10 -0.22 78 88
PRKCE -0.047 0.09 0.15 6 -0.22 68 74
PRKCQ -0.073 0.2 0.28 14 -0.43 85 99
LCP2 0.02 0.033 -10000 0 -0.15 15 15
BCL10 0.021 0.01 -10000 0 -10000 0 0
regulation of survival gene product expression -0.048 0.13 0.21 22 -0.28 82 104
IKK complex -0.003 0.057 0.15 28 -0.11 11 39
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.034 0.1 0.17 20 -0.22 68 88
PDPK1 -0.054 0.14 0.23 20 -0.31 82 102
TCR/CD3/MHC I/CD8/Fyn -0.09 0.22 0.24 1 -0.51 85 86
Endothelins

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
AKT1 -0.056 0.13 0.24 1 -0.27 110 111
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
mol:Ca2+ -0.044 0.22 -10000 0 -0.75 34 34
EDN1 -0.036 0.11 0.21 1 -0.24 80 81
EDN3 0.006 0.091 -10000 0 -0.4 23 23
EDN2 -0.006 0.031 -10000 0 -0.13 20 20
HRAS/GDP -0.051 0.17 0.26 9 -0.43 51 60
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.13 0.17 1 -0.33 52 53
ADCY4 -0.068 0.14 -10000 0 -0.3 91 91
ADCY5 -0.072 0.14 -10000 0 -0.32 88 88
ADCY6 -0.066 0.13 -10000 0 -0.3 82 82
ADCY7 -0.066 0.13 -10000 0 -0.3 84 84
ADCY1 -0.071 0.14 -10000 0 -0.3 107 107
ADCY2 -0.07 0.14 -10000 0 -0.31 89 89
ADCY3 -0.067 0.13 -10000 0 -0.28 98 98
ADCY8 -0.08 0.14 -10000 0 -0.3 120 120
ADCY9 -0.066 0.13 -10000 0 -0.28 104 104
arachidonic acid secretion -0.066 0.2 0.29 9 -0.46 82 91
ETB receptor/Endothelin-1/Gq/GTP -0.027 0.12 -10000 0 -0.28 70 70
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.013 0.13 -10000 0 -0.25 101 101
ETA receptor/Endothelin-1/Gs/GTP -0.04 0.16 -10000 0 -0.26 154 154
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.099 0.2 0.23 1 -0.48 95 96
EDNRB -0.015 0.12 -10000 0 -0.39 44 44
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.065 0.16 0.24 1 -0.33 98 99
CYSLTR1 -0.064 0.15 0.24 1 -0.47 38 39
SLC9A1 -0.034 0.098 0.17 1 -0.25 61 62
mol:GDP -0.063 0.18 0.27 10 -0.43 59 69
SLC9A3 -0.075 0.25 -10000 0 -0.65 63 63
RAF1 -0.072 0.19 0.26 10 -0.43 78 88
JUN -0.036 0.19 -10000 0 -0.64 26 26
JAK2 -0.055 0.13 0.24 1 -0.27 108 109
mol:IP3 -0.042 0.14 -10000 0 -0.35 57 57
ETA receptor/Endothelin-1 -0.04 0.17 0.41 1 -0.32 115 116
PLCB1 0.009 0.081 -10000 0 -0.43 17 17
PLCB2 0.011 0.073 -10000 0 -0.36 17 17
ETA receptor/Endothelin-3 -0.017 0.11 0.17 1 -0.29 50 51
FOS -0.11 0.31 0.34 6 -0.87 65 71
Gai/GDP 0.002 0.14 -10000 0 -0.71 15 15
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca ++ -0.072 0.17 0.22 1 -0.41 72 73
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
PRKCB1 -0.042 0.14 -10000 0 -0.34 56 56
GNAQ 0.024 0.011 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.026 0.14 -10000 0 -0.42 59 59
Gs family/GDP -0.073 0.18 0.27 4 -0.4 74 78
ETA receptor/Endothelin-1/Gq/GTP -0.028 0.12 0.19 1 -0.3 55 56
MAPK14 -0.034 0.12 -10000 0 -0.34 44 44
TRPC6 -0.048 0.24 -10000 0 -0.81 34 34
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.13 0.17 1 -0.32 56 57
ETB receptor/Endothelin-2 -0.005 0.09 -10000 0 -0.28 42 42
ETB receptor/Endothelin-3 -0.004 0.12 -10000 0 -0.33 51 51
ETB receptor/Endothelin-1 -0.027 0.13 -10000 0 -0.31 71 71
MAPK3 -0.1 0.28 0.33 8 -0.74 67 75
MAPK1 -0.1 0.28 0.33 8 -0.75 67 75
Rac1/GDP -0.053 0.16 0.28 2 -0.44 46 48
cAMP biosynthetic process -0.072 0.16 0.22 1 -0.37 73 74
MAPK8 -0.048 0.21 0.32 1 -0.64 43 44
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.022 0.098 0.16 1 -0.29 42 43
p130Cas/CRK/Src/PYK2 -0.049 0.18 0.32 10 -0.52 39 49
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.053 0.16 0.34 1 -0.44 46 47
COL1A2 -0.059 0.16 -10000 0 -0.44 49 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.017 0.089 -10000 0 -0.25 37 37
mol:DAG -0.042 0.14 -10000 0 -0.35 57 57
MAP2K2 -0.081 0.23 0.34 14 -0.57 69 83
MAP2K1 -0.089 0.23 0.26 8 -0.57 72 80
EDNRA -0.032 0.12 0.21 1 -0.3 45 46
positive regulation of muscle contraction -0.024 0.13 0.21 38 -0.28 56 94
Gq family/GDP -0.043 0.17 0.24 1 -0.43 52 53
HRAS/GTP -0.061 0.17 0.25 10 -0.42 57 67
PRKCH -0.042 0.14 -10000 0 -0.38 43 43
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.04 0.14 0.23 8 -0.38 44 52
PRKCB -0.052 0.14 -10000 0 -0.37 54 54
PRKCE -0.043 0.14 0.22 1 -0.38 45 46
PRKCD -0.052 0.15 -10000 0 -0.43 47 47
PRKCG -0.075 0.15 -10000 0 -0.37 70 70
regulation of vascular smooth muscle contraction -0.13 0.36 0.39 5 -1 64 69
PRKCQ -0.036 0.15 0.22 21 -0.39 47 68
PLA2G4A -0.073 0.22 0.31 7 -0.5 82 89
GNA14 0.008 0.081 -10000 0 -0.34 23 23
GNA15 0.012 0.071 -10000 0 -0.43 12 12
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA11 0.016 0.06 -10000 0 -0.43 9 9
Rac1/GTP -0.012 0.13 -10000 0 -0.25 101 101
MMP1 0.018 0.1 0.41 13 -0.83 1 14
Thromboxane A2 receptor signaling

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
TGM2 0.023 0.016 -10000 0 -0.13 5 5
GNB1/GNG2 -0.054 0.077 -10000 0 -0.18 124 124
AKT1 -0.031 0.12 0.3 8 -0.26 31 39
EGF -0.01 0.11 -10000 0 -0.31 54 54
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.075 0.33 18 -0.25 1 19
mol:Ca2+ -0.05 0.16 0.33 7 -0.29 125 132
LYN 0.009 0.081 0.32 19 -0.24 4 23
RhoA/GTP -0.025 0.062 -10000 0 -0.13 111 111
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.066 0.18 0.31 11 -0.35 127 138
GNG2 0.022 0.04 -10000 0 -0.43 4 4
ARRB2 0.026 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.002 0.099 -10000 0 -0.4 21 21
G beta5/gamma2 -0.064 0.1 -10000 0 -0.24 122 122
PRKCH -0.063 0.17 0.34 7 -0.34 123 130
DNM1 -0.026 0.12 -10000 0 -0.22 106 106
TXA2/TP beta/beta Arrestin3 -0.007 0.045 -10000 0 -0.25 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.004 0.063 -10000 0 -0.43 5 5
G12 family/GTP -0.066 0.14 -10000 0 -0.3 116 116
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
ADRBK2 0.024 0.029 -10000 0 -0.43 2 2
RhoA/GTP/ROCK1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP 0.022 0.11 0.29 21 -0.31 9 30
mol:NADP 0.017 0.034 -10000 0 -0.28 4 4
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
mol:IP3 -0.067 0.19 0.35 7 -0.37 125 132
cell morphogenesis 0.033 0.007 -10000 0 -10000 0 0
PLCB2 -0.099 0.25 0.39 6 -0.49 125 131
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.088 0.31 16 -0.21 12 28
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.071 0.3 9 -0.25 9 18
RHOA 0.026 0.004 -10000 0 -10000 0 0
PTGIR 0.012 0.049 -10000 0 -0.18 22 22
PRKCB1 -0.069 0.18 0.33 6 -0.36 127 133
GNAQ 0.026 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.034 -10000 0 -0.28 4 4
TXA2/TXA2-R family -0.11 0.25 0.4 5 -0.52 128 133
LCK -0.001 0.085 0.34 16 -0.2 8 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.048 -10000 0 -0.2 9 9
TXA2-R family/G12 family/GDP/G beta/gamma -0.048 0.17 -10000 0 -0.44 80 80
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.049 -10000 0 -0.2 9 9
MAPK14 -0.04 0.12 0.26 11 -0.23 123 134
TGM2/GTP -0.079 0.2 0.38 3 -0.41 123 126
MAPK11 -0.042 0.12 0.26 11 -0.23 125 136
ARHGEF1 -0.035 0.083 0.14 1 -0.18 113 114
GNAI2 0.025 0.005 -10000 0 -10000 0 0
JNK cascade -0.074 0.19 0.35 7 -0.38 128 135
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.054 0.15 0.3 6 -0.28 130 136
cAMP biosynthetic process -0.065 0.18 0.35 7 -0.34 125 132
Gq family/GTP/EBP50 0.005 0.07 0.24 8 -0.22 34 42
actin cytoskeleton reorganization 0.033 0.007 -10000 0 -10000 0 0
SRC 0.004 0.063 0.3 9 -0.23 2 11
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.012 0.12 0.33 26 -0.26 33 59
VCAM1 -0.075 0.18 0.3 6 -0.36 130 136
TP beta/Gq family/GDP/G beta5/gamma2 -0.002 0.099 -10000 0 -0.4 21 21
platelet activation -0.052 0.16 0.32 12 -0.3 127 139
PGI2/IP 0.01 0.034 -10000 0 -0.12 22 22
PRKACA 0.004 0.037 -10000 0 -0.23 8 8
Gq family/GDP/G beta5/gamma2 -0.001 0.094 -10000 0 -0.37 22 22
TXA2/TP beta/beta Arrestin2 -0.02 0.12 -10000 0 -0.48 32 32
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.036 -10000 0 -0.22 9 9
mol:DAG -0.077 0.2 0.37 6 -0.4 125 131
EGFR -0.017 0.12 -10000 0 -0.4 46 46
TXA2/TP alpha -0.091 0.23 0.41 6 -0.46 125 131
Gq family/GTP -0.002 0.063 0.21 5 -0.21 35 40
YES1 0.009 0.078 0.34 16 -0.23 4 20
GNAI2/GTP 0.003 0.045 -10000 0 -0.22 4 4
PGD2/DP 0.005 0.043 -10000 0 -0.3 5 5
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
FYN 0.01 0.077 0.32 18 -0.22 2 20
mol:NO 0.017 0.034 -10000 0 -0.28 4 4
GNA15 0.013 0.07 -10000 0 -0.43 12 12
PGK/cGMP 0.007 0.069 -10000 0 -0.25 31 31
RhoA/GDP 0.025 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.055 -10000 0 -0.21 9 9
NOS3 0.017 0.034 -10000 0 -0.28 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.06 0.18 0.31 9 -0.34 122 131
PRKCB -0.074 0.18 0.35 5 -0.36 128 133
PRKCE -0.065 0.18 0.32 8 -0.35 123 131
PRKCD -0.076 0.19 0.32 7 -0.38 128 135
PRKCG -0.085 0.19 0.36 7 -0.38 129 136
muscle contraction -0.099 0.24 0.39 5 -0.48 129 134
PRKCZ -0.069 0.17 0.33 7 -0.34 130 137
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
TXA2/TP beta 0.011 0.052 -10000 0 -0.21 11 11
PRKCQ -0.062 0.18 0.29 11 -0.35 120 131
MAPKKK cascade -0.087 0.22 0.37 6 -0.44 127 133
SELE -0.065 0.16 0.3 6 -0.32 127 133
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.054 -10000 0 -0.21 9 9
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
chemotaxis -0.13 0.29 0.39 5 -0.61 129 134
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.016 0.007 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.013 0.069 0.25 1 -0.4 6 7
Syndecan-4/Syndesmos -0.059 0.2 0.32 1 -0.46 92 93
positive regulation of JNK cascade -0.053 0.2 0.31 1 -0.44 93 94
Syndecan-4/ADAM12 -0.068 0.2 0.34 1 -0.46 93 94
CCL5 -0.026 0.13 -10000 0 -0.26 93 93
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.025 0.006 -10000 0 -10000 0 0
ITGA5 0.017 0.042 -10000 0 -0.16 24 24
SDCBP 0.025 0.006 -10000 0 -10000 0 0
PLG 0.001 0.025 -10000 0 -0.15 3 3
ADAM12 -0.002 0.078 -10000 0 -0.43 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.003 -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 -0.08 0.22 0.32 1 -0.49 95 96
Syndecan-4/CXCL12/CXCR4 -0.056 0.21 0.32 1 -0.46 93 94
Syndecan-4/Laminin alpha3 -0.07 0.21 0.32 1 -0.48 94 95
MDK -0.002 0.097 -10000 0 -0.43 22 22
Syndecan-4/FZD7 -0.078 0.22 -10000 0 -0.5 96 96
Syndecan-4/Midkine -0.067 0.21 0.32 1 -0.47 90 91
FZD7 -0.018 0.13 -10000 0 -0.4 53 53
Syndecan-4/FGFR1/FGF -0.044 0.19 0.3 1 -0.44 85 86
THBS1 -0.017 0.1 -10000 0 -0.2 98 98
integrin-mediated signaling pathway -0.066 0.2 0.32 1 -0.46 92 93
positive regulation of MAPKKK cascade -0.053 0.2 0.31 1 -0.44 93 94
Syndecan-4/TACI -0.063 0.2 0.31 1 -0.46 93 94
CXCR4 0.012 0.073 -10000 0 -0.43 12 12
cell adhesion 0.017 0.036 0.2 14 -0.17 2 16
Syndecan-4/Dynamin -0.063 0.2 -10000 0 -0.46 93 93
Syndecan-4/TSP1 -0.07 0.21 0.32 1 -0.48 93 94
Syndecan-4/GIPC -0.063 0.2 -10000 0 -0.46 92 92
Syndecan-4/RANTES -0.077 0.21 0.32 1 -0.48 94 95
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
LAMA3 -0.004 0.1 -10000 0 -0.29 49 49
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.035 0.16 0.85 18 -0.4 1 19
Syndecan-4/alpha-Actinin -0.061 0.2 0.32 1 -0.46 93 94
TFPI -0.023 0.12 -10000 0 -0.43 33 33
F2 0.007 0.031 -10000 0 -0.13 7 7
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
positive regulation of cell adhesion -0.095 0.22 0.31 1 -0.49 103 104
ACTN1 0.014 0.043 -10000 0 -0.14 34 34
TNC -0.005 0.1 -10000 0 -0.26 55 55
Syndecan-4/CXCL12 -0.062 0.2 0.32 1 -0.46 93 94
FGF6 -0.013 0.01 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CXCL12 0.021 0.038 -10000 0 -0.24 8 8
TNFRSF13B -0.003 0.028 -10000 0 -10000 0 0
FGF2 0.024 0.029 -10000 0 -0.33 3 3
FGFR1 0.025 0.005 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.079 0.19 -10000 0 -0.46 93 93
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.034 -10000 0 -0.14 18 18
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.001 0.096 -10000 0 -0.41 26 26
vasculogenesis -0.067 0.2 0.32 1 -0.46 94 95
SDC4 -0.077 0.2 -10000 0 -0.48 93 93
Syndecan-4/Tenascin C -0.069 0.21 0.32 1 -0.48 92 93
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.058 0.2 0.32 1 -0.46 89 90
MMP9 -0.045 0.13 -10000 0 -0.23 133 133
Rac1/GTP 0.017 0.036 0.2 14 -0.17 2 16
cytoskeleton organization -0.056 0.2 0.32 1 -0.44 92 93
GIPC1 0.025 0.009 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.074 0.21 0.34 1 -0.48 93 94
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.19 -10000 0 -0.58 53 53
IHH 0.011 0.056 0.18 1 -0.2 6 7
SHH Np/Cholesterol/GAS1 -0.012 0.084 0.16 12 -0.24 53 65
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.012 0.083 0.24 53 -0.16 12 65
SMO/beta Arrestin2 -0.005 0.12 -10000 0 -0.4 18 18
SMO -0.02 0.11 -10000 0 -0.41 20 20
AKT1 -0.003 0.11 -10000 0 -0.53 13 13
ARRB2 0.026 0.002 -10000 0 -10000 0 0
BOC 0.023 0.036 -10000 0 -0.31 5 5
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
heart looping -0.02 0.11 -10000 0 -0.41 20 20
STIL -0.012 0.13 0.25 2 -0.3 37 39
DHH N/PTCH2 0.005 0.085 -10000 0 -0.31 31 31
DHH N/PTCH1 -0.02 0.12 -10000 0 -0.3 58 58
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DHH -0.007 0.1 -10000 0 -0.43 27 27
PTHLH -0.061 0.26 -10000 0 -0.78 53 53
determination of left/right symmetry -0.02 0.11 -10000 0 -0.41 20 20
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
skeletal system development -0.06 0.25 -10000 0 -0.77 53 53
IHH N/Hhip -0.039 0.14 -10000 0 -0.34 76 76
DHH N/Hhip -0.048 0.14 -10000 0 -0.31 99 99
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.02 0.11 -10000 0 -0.41 20 20
pancreas development -0.057 0.16 -10000 0 -0.29 133 133
HHAT 0.012 0.077 -10000 0 -0.39 17 17
PI3K 0.038 0.007 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.016 0.047 -10000 0 -0.16 26 26
somite specification -0.02 0.11 -10000 0 -0.41 20 20
SHH Np/Cholesterol/PTCH1 -0.036 0.11 -10000 0 -0.28 67 67
SHH Np/Cholesterol/PTCH2 -0.017 0.082 0.15 2 -0.24 56 58
SHH Np/Cholesterol/Megalin -0.059 0.12 0.15 8 -0.27 114 122
SHH -0.03 0.097 -10000 0 -0.31 52 52
catabolic process -0.018 0.12 -10000 0 -0.34 52 52
SMO/Vitamin D3 -0.033 0.12 0.34 1 -0.38 21 22
SHH Np/Cholesterol/Hhip -0.047 0.12 0.16 8 -0.27 97 105
LRP2 -0.092 0.18 -10000 0 -0.31 181 181
receptor-mediated endocytosis -0.066 0.14 -10000 0 -0.42 42 42
SHH Np/Cholesterol/BOC -0.014 0.08 -10000 0 -0.24 54 54
SHH Np/Cholesterol/CDO -0.02 0.089 0.17 1 -0.25 59 60
mesenchymal cell differentiation 0.047 0.12 0.27 97 -0.15 8 105
mol:Vitamin D3 -0.002 0.15 0.32 3 -0.28 66 69
IHH N/PTCH2 0.023 0.051 -10000 0 -0.37 5 5
CDON 0.001 0.096 -10000 0 -0.43 23 23
IHH N/PTCH1 -0.011 0.12 -10000 0 -0.34 52 52
Megalin/LRPAP1 -0.051 0.14 -10000 0 -0.3 107 107
PTCH2 0.016 0.048 -10000 0 -0.28 10 10
SHH Np/Cholesterol -0.019 0.075 0.2 1 -0.23 52 53
PTCH1 -0.019 0.12 -10000 0 -0.34 52 52
HHIP -0.057 0.16 -10000 0 -0.29 133 133
Reelin signaling pathway

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
CDK5R1/CDK5 0.016 0.069 -10000 0 -0.3 21 21
VLDLR 0.014 0.067 -10000 0 -0.43 11 11
CRKL 0.026 0.008 -10000 0 -0.13 1 1
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ITGA3 0.017 0.046 -10000 0 -0.17 23 23
RELN/VLDLR/Fyn 0 0.1 -10000 0 -0.25 68 68
MAPK8IP1/MKK7/MAP3K11/JNK1 0.06 0.054 -10000 0 -0.22 14 14
AKT1 -0.047 0.11 -10000 0 -0.26 97 97
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
DAB1 -0.038 0.15 -10000 0 -0.35 80 80
RELN/LRP8/DAB1 -0.024 0.12 -10000 0 -0.25 95 95
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
RELN/LRP8/DAB1/Fyn -0.017 0.11 -10000 0 -0.23 95 95
DAB1/alpha3/beta1 Integrin -0.021 0.11 -10000 0 -0.24 75 75
long-term memory -0.1 0.17 -10000 0 -0.31 165 165
DAB1/LIS1 -0.014 0.12 -10000 0 -0.23 96 96
DAB1/CRLK/C3G -0.02 0.11 -10000 0 -0.24 80 80
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DAB1/NCK2 -0.014 0.12 -10000 0 -0.24 82 82
ARHGEF2 0.025 0.021 -10000 0 -0.43 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.068 0.17 -10000 0 -0.29 152 152
CDK5R1 0.001 0.1 -10000 0 -0.43 28 28
RELN -0.046 0.14 -10000 0 -0.43 58 58
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.001 0.095 -10000 0 -0.25 58 58
GRIN2A/RELN/LRP8/DAB1/Fyn -0.051 0.16 -10000 0 -0.28 131 131
MAPK8 0.015 0.069 -10000 0 -0.43 12 12
RELN/VLDLR/DAB1 -0.031 0.12 -10000 0 -0.25 102 102
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
MAP1B -0.032 0.12 0.16 5 -0.25 99 104
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
GRIN2B/RELN/LRP8/DAB1/Fyn -0.057 0.15 -10000 0 -0.27 140 140
PI3K 0.038 0.007 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.037 -10000 0 -0.27 4 4
RAP1A -0.022 0.12 0.31 9 -0.35 14 23
PAFAH1B1 0.026 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.04 -10000 0 -0.43 4 4
CRLK/C3G 0.037 0.01 -10000 0 -10000 0 0
GRIN2B -0.076 0.16 -10000 0 -0.43 82 82
NCK2 0.026 0.002 -10000 0 -10000 0 0
neuron differentiation -0.028 0.13 -10000 0 -0.36 44 44
neuron adhesion -0.014 0.13 0.34 12 -0.37 10 22
LRP8 0.02 0.03 -10000 0 -0.43 2 2
GSK3B -0.051 0.11 -10000 0 -0.25 90 90
RELN/VLDLR/DAB1/Fyn -0.024 0.12 -10000 0 -0.24 101 101
MAP3K11 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.049 0.12 -10000 0 -0.27 102 102
CDK5 0.02 0.011 -10000 0 -10000 0 0
MAPT 0.006 0.098 0.77 6 -0.39 8 14
neuron migration -0.041 0.16 0.23 53 -0.33 70 123
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.028 0.13 -10000 0 -0.36 44 44
RELN/VLDLR 0.005 0.098 -10000 0 -0.23 65 65
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.078 -10000 0 -0.38 18 18
CDKN2C 0.01 0.041 -10000 0 -0.14 16 16
CDKN2A -0.014 0.1 -10000 0 -0.33 42 42
CCND2 0.017 0.069 0.21 48 -0.13 3 51
RB1 -0.023 0.079 0.12 1 -0.24 50 51
CDK4 0.021 0.077 0.24 47 -0.17 1 48
CDK6 0.017 0.081 0.25 43 -0.16 10 53
G1/S progression 0.043 0.1 0.26 76 -0.22 4 80
Effects of Botulinum toxin

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
STX1A -0.01 0.044 -10000 0 -0.3 6 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.02 0.12 -10000 0 -0.31 69 69
STXBP1 0.016 0.044 -10000 0 -0.43 2 2
ACh/CHRNA1 -0.042 0.11 0.13 8 -0.24 91 99
RAB3GAP2/RIMS1/UNC13B 0.01 0.11 -10000 0 -0.26 67 67
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 -0.05 0.16 -10000 0 -0.32 113 113
mol:ACh -0.008 0.057 0.098 60 -0.12 70 130
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.03 0.12 -10000 0 -0.27 70 70
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.11 0.13 8 -0.24 91 99
UNC13B 0.025 0.021 -10000 0 -0.43 1 1
CHRNA1 -0.064 0.15 -10000 0 -0.43 68 68
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.055 0.13 0.13 2 -0.31 89 91
SNAP25 -0.043 0.098 -10000 0 -0.26 85 85
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.087 0.17 -10000 0 -0.43 91 91
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.051 -10000 0 -0.16 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.03 0.12 -10000 0 -0.27 70 70
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.12 -10000 0 -0.3 47 47
NFATC4 -0.057 0.089 0.22 2 -0.23 49 51
ERBB2IP 0.026 0.02 -10000 0 -0.42 1 1
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.048 0.11 0.2 1 -0.24 115 116
JUN -0.022 0.084 0.19 4 -0.36 10 14
HRAS 0.024 0.006 -10000 0 -10000 0 0
DOCK7 -0.065 0.098 -10000 0 -0.24 112 112
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.034 0.13 -10000 0 -0.25 119 119
AKT1 0.003 0.007 -10000 0 -10000 0 0
BAD -0.006 0.004 -10000 0 -10000 0 0
MAPK10 -0.03 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 0.22 1 -0.26 115 116
RAF1 -0.044 0.13 0.26 7 -0.33 41 48
ErbB2/ErbB3/neuregulin 2 -0.003 0.08 0.16 2 -0.25 40 42
STAT3 0.028 0.044 -10000 0 -0.91 1 1
cell migration -0.022 0.077 0.22 13 -0.2 11 24
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.11 0.26 0.36 1 -0.62 77 78
FOS -0.083 0.2 0.28 3 -0.41 118 121
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.11 0.2 1 -0.24 115 116
MAPK3 -0.081 0.21 0.36 2 -0.52 65 67
MAPK1 -0.083 0.21 0.36 2 -0.53 65 67
JAK2 -0.067 0.097 -10000 0 -0.24 110 110
NF2 0.005 0.033 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.12 0.18 1 -0.26 116 117
NRG1 -0.081 0.18 -10000 0 -0.42 101 101
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
MAPK8 -0.053 0.12 -10000 0 -0.27 112 112
MAPK9 -0.029 0.063 0.17 3 -0.21 5 8
ERBB2 -0.022 0.017 -10000 0 -0.32 1 1
ERBB3 -0.017 0.12 -10000 0 -0.36 55 55
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
apoptosis 0.003 0.013 -10000 0 -0.2 1 1
STAT3 (dimer) 0.029 0.042 -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 0.075 -10000 0 -0.18 96 96
ErbB2/ErbB2/HSP90 (dimer) 0 0.025 -10000 0 -0.27 1 1
CHRNA1 -0.091 0.24 0.33 2 -0.63 71 73
myelination -0.054 0.089 0.23 3 -0.26 22 25
PPP3CB -0.065 0.091 -10000 0 -0.22 111 111
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.11 -10000 0 -0.23 98 98
NRG2 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.053 0.12 0.17 2 -0.26 117 119
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.048 0.13 0.27 6 -0.34 41 47
SRC 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.068 0.097 -10000 0 -0.24 114 114
MAP2K1 -0.088 0.21 -10000 0 -0.59 36 36
heart morphogenesis -0.048 0.11 0.2 1 -0.24 115 116
RAS family/GDP -0.027 0.13 0.23 1 -0.29 46 47
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.035 -10000 0 -0.74 1 1
CHRNE -0.002 0.031 0.1 1 -0.17 10 11
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 -0.048 0.11 0.2 1 -0.24 115 116
CDC42 0.022 0.01 -10000 0 -10000 0 0
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 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.012 0.14 -10000 0 -0.35 64 64
Syndecan-3/Neurocan -0.042 0.15 -10000 0 -0.37 77 77
POMC 0.015 0.063 -10000 0 -0.43 9 9
EGFR -0.017 0.12 -10000 0 -0.4 46 46
Syndecan-3/EGFR -0.051 0.15 -10000 0 -0.38 74 74
AGRP 0.012 0.024 -10000 0 -10000 0 0
NCSTN 0.026 0.004 -10000 0 -10000 0 0
PSENEN 0.022 0.01 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
NCAN -0.001 0.1 -10000 0 -0.4 31 31
long-term memory -0.014 0.14 -10000 0 -0.35 72 72
Syndecan-3/IL8 -0.054 0.16 -10000 0 -0.4 77 77
PSEN1 0.025 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.036 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
limb bud formation -0.046 0.14 -10000 0 -0.38 77 77
MC4R -0.051 0.16 -10000 0 -0.33 106 106
SRC 0.025 0.005 -10000 0 -10000 0 0
PTN 0.019 0.03 -10000 0 -0.43 2 2
FGFR/FGF/Syndecan-3 -0.046 0.14 -10000 0 -0.38 77 77
neuron projection morphogenesis -0.015 0.15 0.26 1 -0.35 65 66
Syndecan-3/AgRP -0.03 0.14 -10000 0 -0.37 77 77
Syndecan-3/AgRP/MC4R -0.045 0.16 -10000 0 -0.38 77 77
Fyn/Cortactin 0.036 0.01 -10000 0 -10000 0 0
SDC3 -0.047 0.14 -10000 0 -0.39 77 77
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.053 0.16 -10000 0 -0.39 77 77
IL8 -0.061 0.15 -10000 0 -0.25 158 158
Syndecan-3/Fyn/Cortactin -0.014 0.14 -10000 0 -0.36 72 72
Syndecan-3/CASK -0.045 0.14 -10000 0 -0.37 77 77
alpha-MSH/MC4R -0.026 0.13 -10000 0 -0.32 76 76
Gamma Secretase 0.063 0.032 -10000 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 -0.84 49 49
PCK1 -0.18 0.39 -10000 0 -1.2 55 55
HNF4A -0.14 0.33 -10000 0 -0.9 55 55
KCNJ11 -0.18 0.4 -10000 0 -1 72 72
AKT1 -0.066 0.18 -10000 0 -0.43 46 46
response to starvation -0.003 0.026 -10000 0 -0.31 2 2
DLK1 -0.16 0.35 -10000 0 -0.91 65 65
NKX2-1 -0.057 0.15 0.3 3 -0.38 39 42
ACADM -0.13 0.3 -10000 0 -0.8 56 56
TAT -0.18 0.39 -10000 0 -1.2 53 53
CEBPB 0.012 0.074 -10000 0 -0.43 13 13
CEBPA 0.015 0.051 -10000 0 -0.32 8 8
TTR -0.12 0.27 0.52 3 -0.84 38 41
PKLR -0.13 0.3 -10000 0 -0.85 48 48
APOA1 -0.18 0.4 -10000 0 -1.1 57 57
CPT1C -0.12 0.3 0.46 1 -0.84 48 49
ALAS1 -0.06 0.18 -10000 0 -0.76 3 3
TFRC -0.14 0.3 -10000 0 -0.93 38 38
FOXF1 0.019 0.042 -10000 0 -0.19 16 16
NF1 0.03 0.02 -10000 0 -0.43 1 1
HNF1A (dimer) 0.025 0.026 -10000 0 -0.44 1 1
CPT1A -0.13 0.3 -10000 0 -0.83 51 51
HMGCS1 -0.13 0.3 -10000 0 -0.84 50 50
NR3C1 -0.017 0.089 -10000 0 -0.2 87 87
CPT1B -0.15 0.32 -10000 0 -0.85 61 61
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.024 0.013 -10000 0 -10000 0 0
GCK -0.16 0.37 0.48 2 -0.89 81 83
CREB1 0.008 0.058 -10000 0 -0.18 36 36
IGFBP1 -0.22 0.48 0.35 1 -1.2 85 86
PDX1 -0.057 0.17 -10000 0 -0.64 5 5
UCP2 -0.14 0.32 -10000 0 -0.86 58 58
ALDOB -0.14 0.35 -10000 0 -0.91 58 58
AFP -0.034 0.1 -10000 0 -0.43 9 9
BDH1 -0.16 0.35 -10000 0 -0.96 59 59
HADH -0.13 0.32 -10000 0 -0.86 53 53
F2 -0.15 0.35 -10000 0 -0.98 47 47
HNF1A 0.025 0.026 -10000 0 -0.44 1 1
G6PC -0.036 0.17 -10000 0 -0.84 13 13
SLC2A2 -0.063 0.19 -10000 0 -0.57 10 10
INS 0.008 0.087 0.21 55 -0.4 4 59
FOXA1 -0.007 0.086 -10000 0 -0.29 30 30
FOXA3 -0.041 0.14 -10000 0 -0.37 61 61
FOXA2 -0.15 0.37 -10000 0 -0.93 61 61
ABCC8 -0.19 0.41 -10000 0 -0.98 86 86
ALB -0.07 0.23 -10000 0 -0.92 32 32
Arf6 signaling events

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
CENTA1/KIF3B 0.024 0.035 -10000 0 -0.26 5 5
ARNO/beta Arrestin1-2 -0.1 0.31 -10000 0 -0.8 82 82
EGFR -0.017 0.12 -10000 0 -0.4 46 46
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
USP6 0.023 0.022 -10000 0 -10000 0 0
IQSEC1 0.023 0.027 -10000 0 -0.17 8 8
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.32 69 69
ARRB2 0.011 0.007 -10000 0 -10000 0 0
mol:GTP 0.008 0.042 0.18 5 -0.17 10 15
ARRB1 0.012 0.077 -10000 0 -0.43 15 15
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR -0.086 0.17 -10000 0 -0.43 92 92
EGF -0.01 0.11 -10000 0 -0.31 54 54
somatostatin receptor activity 0 0 0.001 60 -0.001 26 86
ARAP2 0.011 0.079 -10000 0 -0.43 16 16
mol:GDP -0.016 0.13 0.19 46 -0.28 47 93
mol:PI-3-4-5-P3 0 0 0.001 78 -0.001 12 90
ITGA2B -0.013 0.12 -10000 0 -0.37 50 50
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.037 -10000 0 -0.25 3 3
ADAP1 0.013 0.052 -10000 0 -0.2 20 20
KIF13B 0.025 0.005 -10000 0 -10000 0 0
HGF/MET -0.039 0.12 -10000 0 -0.28 81 81
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.13 0.25 55 -0.26 33 88
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.002 0.11 -10000 0 -0.28 70 70
ADRB2 0.005 0.094 -10000 0 -0.43 23 23
receptor agonist activity 0 0 0 29 0 26 55
actin filament binding 0 0 0.001 61 0 29 90
SRC 0.025 0.005 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
GNAQ 0.026 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 76 -0.001 19 95
ARF6/GDP -0.027 0.14 0.25 3 -0.46 30 33
ARF6/GDP/GULP/ACAP1 -0.012 0.16 0.22 31 -0.35 49 80
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.094 -10000 0 -0.24 51 51
ACAP1 0.01 0.06 -10000 0 -0.43 5 5
ACAP2 0.026 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.023 0.007 -10000 0 -10000 0 0
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
HGF -0.009 0.091 -10000 0 -0.2 68 68
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.14 0.38 -10000 0 -1 81 81
NCK1 0.025 0.02 -10000 0 -0.43 1 1
fibronectin binding 0 0 0.001 66 0 27 93
endosomal lumen acidification 0 0 0.001 61 0 37 98
microtubule-based process 0 0 -10000 0 0 12 12
GULP1 -0.016 0.13 -10000 0 -0.37 55 55
GNAQ/ARNO -0.12 0.35 -10000 0 -0.93 81 81
mol:Phosphatidic acid 0 0 0 18 -10000 0 18
PIP3-E 0 0 0 42 0 15 57
MET -0.046 0.14 -10000 0 -0.43 50 50
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 64 -0.001 20 84
GNA11 0.017 0.06 -10000 0 -0.43 9 9
LHCGR 0.009 0.031 -10000 0 -0.13 15 15
AGTR1 0.002 0.092 -10000 0 -0.43 20 20
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.007 -10000 0 -10000 0 0
IPCEF1/ARNO -0.13 0.33 -10000 0 -0.88 81 81
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
HIF-1-alpha transcription factor network

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
PKM2 -0.079 0.31 -10000 0 -0.8 45 45
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.04 0.34 -10000 0 -0.76 53 53
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.066 0.31 -10000 0 -0.8 44 44
AP1 -0.011 0.1 -10000 0 -0.28 56 56
ABCG2 -0.067 0.32 -10000 0 -0.81 44 44
HIF1A 0.005 0.071 -10000 0 -0.35 2 2
TFF3 -0.07 0.32 -10000 0 -0.8 45 45
GATA2 0.014 0.066 -10000 0 -0.33 15 15
AKT1 -0.005 0.085 -10000 0 -0.22 20 20
response to hypoxia -0.021 0.074 -10000 0 -0.18 44 44
MCL1 -0.065 0.31 -10000 0 -0.8 44 44
NDRG1 -0.077 0.31 -10000 0 -0.81 46 46
SERPINE1 -0.091 0.32 -10000 0 -0.79 55 55
FECH -0.067 0.31 -10000 0 -0.8 44 44
FURIN -0.065 0.31 -10000 0 -0.8 44 44
NCOA2 -0.004 0.11 -10000 0 -0.43 34 34
EP300 -0.014 0.13 -10000 0 -0.32 53 53
HMOX1 -0.069 0.32 -10000 0 -0.82 45 45
BHLHE40 -0.07 0.32 -10000 0 -0.81 46 46
BHLHE41 -0.071 0.32 -10000 0 -0.84 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.056 0.1 -10000 0 -0.31 1 1
ENG 0.012 0.078 0.27 2 -0.29 1 3
JUN 0.018 0.024 -10000 0 -10000 0 0
RORA -0.065 0.31 -10000 0 -0.8 45 45
ABCB1 -0.021 0.12 -10000 0 -0.71 10 10
TFRC -0.065 0.31 -10000 0 -0.81 44 44
CXCR4 -0.071 0.32 -10000 0 -0.84 45 45
TF -0.083 0.34 -10000 0 -0.83 53 53
CITED2 -0.065 0.31 -10000 0 -0.81 44 44
HIF1A/ARNT -0.034 0.4 -10000 0 -0.94 41 41
LDHA -0.012 0.14 -10000 0 -0.82 10 10
ETS1 -0.07 0.31 -10000 0 -0.81 43 43
PGK1 -0.066 0.31 -10000 0 -0.81 43 43
NOS2 -0.074 0.33 -10000 0 -0.82 48 48
ITGB2 -0.073 0.33 -10000 0 -0.86 44 44
ALDOA -0.065 0.31 -10000 0 -0.8 44 44
Cbp/p300/CITED2 -0.087 0.37 -10000 0 -0.87 57 57
FOS -0.032 0.14 -10000 0 -0.29 92 92
HK2 -0.073 0.33 -10000 0 -0.83 47 47
SP1 0.031 0.007 -10000 0 -10000 0 0
GCK -0.1 0.42 -10000 0 -1.3 50 50
HK1 -0.064 0.31 -10000 0 -0.81 44 44
NPM1 -0.065 0.31 -10000 0 -0.81 43 43
EGLN1 -0.065 0.31 -10000 0 -0.8 44 44
CREB1 0.03 0.008 -10000 0 -10000 0 0
PGM1 -0.067 0.31 -10000 0 -0.8 43 43
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.075 0.27 -10000 0 -0.77 49 49
IGFBP1 -0.099 0.33 -10000 0 -0.79 58 58
VEGFA -0.053 0.28 -10000 0 -0.68 48 48
HIF1A/JAB1 0.02 0.057 -10000 0 -0.36 1 1
CP -0.11 0.35 -10000 0 -0.85 57 57
CXCL12 -0.067 0.32 -10000 0 -0.8 46 46
COPS5 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.008 -10000 0 -10000 0 0
BNIP3 -0.066 0.31 -10000 0 -0.8 44 44
EGLN3 -0.069 0.32 -10000 0 -0.82 46 46
CA9 -0.081 0.32 -10000 0 -0.82 47 47
TERT -0.09 0.33 -10000 0 -0.82 51 51
ENO1 -0.066 0.31 -10000 0 -0.8 44 44
PFKL -0.065 0.31 -10000 0 -0.8 44 44
NCOA1 0.026 0.003 -10000 0 -10000 0 0
ADM -0.076 0.32 -10000 0 -0.8 50 50
ARNT 0.005 0.069 -10000 0 -0.27 1 1
HNF4A -0.004 0.054 -10000 0 -0.13 64 64
ADFP -0.079 0.31 -10000 0 -0.8 45 45
SLC2A1 -0.056 0.27 -10000 0 -0.66 48 48
LEP -0.067 0.29 -10000 0 -0.79 42 42
HIF1A/ARNT/Cbp/p300 -0.051 0.34 -10000 0 -0.78 54 54
EPO -0.047 0.24 -10000 0 -0.73 24 24
CREBBP -0.012 0.12 -10000 0 -0.31 51 51
HIF1A/ARNT/Cbp/p300/HDAC7 -0.037 0.34 -10000 0 -0.78 49 49
PFKFB3 -0.07 0.31 -10000 0 -0.82 42 42
NT5E -0.068 0.32 -10000 0 -0.8 46 46
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.36 -10000 0 -1.1 36 36
STAT6 (cleaved dimer) -0.28 0.39 -10000 0 -1 80 80
IGHG1 -0.1 0.2 -10000 0 -0.96 14 14
IGHG3 -0.24 0.34 -10000 0 -0.93 59 59
AKT1 -0.18 0.31 -10000 0 -0.89 58 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.31 -10000 0 -0.96 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.96 57 57
THY1 -0.26 0.39 -10000 0 -1.2 45 45
MYB -0.015 0.12 -10000 0 -0.28 66 66
HMGA1 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.31 -10000 0 -0.81 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.33 -10000 0 -0.96 59 59
SP1 0.024 0.02 -10000 0 -0.12 2 2
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
SOCS5 0.032 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.38 -10000 0 -1 67 67
SOCS1 -0.21 0.28 -10000 0 -0.73 59 59
SOCS3 -0.22 0.36 -10000 0 -1 59 59
FCER2 -0.26 0.4 -10000 0 -1.1 58 58
PARP14 0.017 0.046 -10000 0 -0.43 4 4
CCL17 -0.25 0.36 -10000 0 -1.1 40 40
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.24 -10000 0 -0.71 47 47
T cell proliferation -0.27 0.38 -10000 0 -1.1 60 60
IL4R/JAK1 -0.25 0.36 -10000 0 -1 45 45
EGR2 -0.34 0.5 -10000 0 -1.3 77 77
JAK2 -0.008 0.041 -10000 0 -10000 0 0
JAK3 -0.011 0.1 -10000 0 -0.31 40 40
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.023 -10000 0 -10000 0 0
COL1A2 -0.09 0.2 -10000 0 -1.2 10 10
CCL26 -0.22 0.37 -10000 0 -1.1 35 35
IL4R -0.26 0.38 -10000 0 -1.1 43 43
PTPN6 0.019 0.065 -10000 0 -0.35 13 13
IL13RA2 -0.42 0.56 -10000 0 -1.3 129 129
IL13RA1 -0.013 0.071 -10000 0 -0.42 9 9
IRF4 -0.11 0.31 -10000 0 -1.3 29 29
ARG1 -0.09 0.21 -10000 0 -0.95 18 18
CBL -0.19 0.29 -10000 0 -0.77 69 69
GTF3A 0.002 0.052 -10000 0 -0.15 22 22
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL13RA1/JAK2 -0.009 0.071 -10000 0 -0.32 8 8
IRF4/BCL6 -0.097 0.3 -10000 0 -1.2 29 29
CD40LG 0.003 0.053 -10000 0 -0.14 9 9
MAPK14 -0.21 0.32 -10000 0 -0.83 73 73
mitosis -0.17 0.29 -10000 0 -0.82 58 58
STAT6 -0.28 0.4 -10000 0 -1.1 55 55
SPI1 0.015 0.064 -10000 0 -0.4 10 10
RPS6KB1 -0.16 0.28 -10000 0 -0.79 57 57
STAT6 (dimer) -0.28 0.4 -10000 0 -1.1 55 55
STAT6 (dimer)/PARP14 -0.26 0.39 -10000 0 -1 60 60
mast cell activation 0.007 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.31 -10000 0 -0.9 53 53
FRAP1 -0.18 0.31 -10000 0 -0.89 58 58
LTA -0.28 0.42 -10000 0 -1.3 52 52
FES 0.024 0.024 -10000 0 -0.2 4 4
T-helper 1 cell differentiation 0.27 0.39 1.1 55 -10000 0 55
CCL11 -0.25 0.34 -10000 0 -1 40 40
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.3 -10000 0 -0.9 47 47
IL2RG -0.002 0.087 -10000 0 -0.39 18 18
IL10 -0.33 0.5 -10000 0 -1.4 78 78
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
IL4 -0.063 0.12 -10000 0 -1 3 3
IL5 -0.25 0.36 -10000 0 -1.1 37 37
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.32 -10000 0 -0.88 53 53
COL1A1 -0.26 0.5 -10000 0 -1.4 79 79
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.36 -10000 0 -1.1 36 36
IL2R gamma/JAK3 -0.009 0.1 -10000 0 -0.27 53 53
TFF3 -0.25 0.36 -10000 0 -1.1 42 42
ALOX15 -0.26 0.36 -10000 0 -1.1 38 38
MYBL1 0.024 0.011 -10000 0 -0.13 2 2
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.91 70 70
SHC1 0.024 0.014 -10000 0 -0.13 4 4
CEBPB 0.013 0.074 -10000 0 -0.41 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.33 -10000 0 -0.93 62 62
mol:PI-3-4-5-P3 -0.18 0.31 -10000 0 -0.89 58 58
PI3K -0.19 0.34 -10000 0 -0.97 58 58
DOK2 -0.017 0.11 -10000 0 -0.25 77 77
ETS1 0.023 0.048 -10000 0 -0.41 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 0.34 1 -0.67 46 47
ITGB3 -0.27 0.39 -10000 0 -1.1 50 50
PIGR -0.33 0.5 -10000 0 -1.4 75 75
IGHE 0.011 0.057 0.16 9 -0.2 13 22
MAPKKK cascade -0.13 0.22 0.34 1 -0.66 46 47
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.26 0.36 -10000 0 -1.1 43 43
RETNLB -0.26 0.36 -10000 0 -1.1 36 36
SELP -0.25 0.36 -10000 0 -1.1 39 39
AICDA -0.24 0.35 -10000 0 -1 39 39
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.011 0.13 -10000 0 -0.33 54 54
alphaM/beta2 Integrin/GPIbA -0.012 0.13 -10000 0 -0.33 54 54
alphaM/beta2 Integrin/proMMP-9 -0.036 0.14 -10000 0 -0.31 90 90
PLAUR 0.012 0.041 -10000 0 -0.43 1 1
HMGB1 0.009 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.003 0.12 -10000 0 -0.35 40 40
AGER -0.008 0.092 -10000 0 -0.43 20 20
RAP1A 0.021 0.01 -10000 0 -10000 0 0
SELPLG -0.001 0.11 -10000 0 -0.4 32 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.033 0.16 -10000 0 -0.28 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.22 133 133
CYR61 -0.015 0.1 -10000 0 -0.24 70 70
TLN1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.024 0.12 -10000 0 -0.36 32 32
RHOA 0.026 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.003 0.041 -10000 0 -0.13 36 36
MYH2 -0.039 0.12 -10000 0 -0.39 25 25
MST1R 0.02 0.05 -10000 0 -0.43 6 6
leukocyte activation during inflammatory response -0.019 0.13 -10000 0 -0.3 72 72
APOB -0.025 0.13 -10000 0 -0.43 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.013 0.067 -10000 0 -0.26 24 24
JAM3 0.024 0.007 -10000 0 -10000 0 0
GP1BA 0.014 0.072 -10000 0 -0.43 13 13
alphaM/beta2 Integrin/CTGF -0.017 0.13 -10000 0 -0.33 60 60
alphaM/beta2 Integrin -0.045 0.13 -10000 0 -0.4 36 36
JAM3 homodimer 0.024 0.007 -10000 0 -10000 0 0
ICAM2 0.025 0.005 -10000 0 -10000 0 0
ICAM1 0.01 0.065 -10000 0 -0.2 33 33
phagocytosis triggered by activation of immune response cell surface activating receptor -0.044 0.13 -10000 0 -0.41 33 33
cell adhesion -0.012 0.12 -10000 0 -0.33 54 54
NFKB1 -0.1 0.19 -10000 0 -0.42 109 109
THY1 0.015 0.062 -10000 0 -0.32 14 14
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.005 0.083 -10000 0 -0.25 44 44
alphaM/beta2 Integrin/LRP/tPA 0.006 0.12 -10000 0 -0.34 40 40
IL6 -0.12 0.23 -10000 0 -0.65 57 57
ITGB2 -0.014 0.097 -10000 0 -0.3 39 39
elevation of cytosolic calcium ion concentration -0.008 0.12 -10000 0 -0.31 55 55
alphaM/beta2 Integrin/JAM2/JAM3 0.012 0.11 -10000 0 -0.33 38 38
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.002 0.13 -10000 0 -0.28 74 74
alphaM/beta2 Integrin/uPA/Plg -0.012 0.12 -10000 0 -0.32 54 54
RhoA/GTP -0.037 0.12 -10000 0 -0.36 35 35
positive regulation of phagocytosis -0.04 0.14 -10000 0 -0.39 52 52
Ron/MSP 0.015 0.083 -10000 0 -0.3 31 31
alphaM/beta2 Integrin/uPAR/uPA -0.007 0.12 -10000 0 -0.31 55 55
alphaM/beta2 Integrin/uPAR -0.012 0.12 -10000 0 -0.34 44 44
PLAU -0.001 0.081 -10000 0 -0.43 12 12
PLAT 0.005 0.058 -10000 0 -0.43 2 2
actin filament polymerization -0.036 0.11 0.19 2 -0.38 24 26
MST1 0.001 0.099 -10000 0 -0.36 32 32
alphaM/beta2 Integrin/lipoprotein(a) -0.016 0.14 -10000 0 -0.3 73 73
TNF -0.15 0.27 -10000 0 -0.69 86 86
RAP1B 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.02 0.13 -10000 0 -0.32 61 61
fibrinolysis -0.014 0.12 -10000 0 -0.31 54 54
HCK 0.014 0.063 -10000 0 -0.27 19 19
dendritic cell antigen processing and presentation -0.044 0.13 -10000 0 -0.41 33 33
VTN 0.012 0.075 -10000 0 -0.43 14 14
alphaM/beta2 Integrin/CYR61 -0.031 0.13 -10000 0 -0.32 72 72
LPA 0.005 0.039 -10000 0 -0.13 31 31
LRP1 0.026 0.004 -10000 0 -10000 0 0
cell migration -0.05 0.13 -10000 0 -0.3 91 91
FN1 0.021 0.029 -10000 0 -0.13 18 18
alphaM/beta2 Integrin/Thy1 -0.008 0.12 -10000 0 -0.32 52 52
MPO -0.051 0.15 -10000 0 -0.29 122 122
KNG1 -0.009 0.032 -10000 0 -0.13 22 22
RAP1/GDP 0.028 0.015 -10000 0 -10000 0 0
ROCK1 -0.035 0.12 -10000 0 -0.39 25 25
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.01 0.018 -10000 0 -0.13 3 3
CTGF 0.003 0.088 -10000 0 -0.27 39 39
alphaM/beta2 Integrin/Hck -0.009 0.14 -10000 0 -0.36 50 50
ITGAM -0.02 0.12 -10000 0 -0.43 34 34
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.006 0.15 -10000 0 -0.39 51 51
HP -0.033 0.13 -10000 0 -0.24 112 112
leukocyte adhesion -0.031 0.14 -10000 0 -0.35 56 56
SELP 0.003 0.041 -10000 0 -0.13 36 36
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.031 -10000 0 -0.3 2 2
Metarhodopsin II/Arrestin 0.014 0.048 -10000 0 -0.26 11 11
PDE6G/GNAT1/GTP 0.009 0.07 -10000 0 -0.26 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.047 -10000 0 -0.43 2 2
GRK1 0.021 0.015 -10000 0 -10000 0 0
CNG Channel -0.046 0.14 -10000 0 -0.25 138 138
mol:Na + -0.068 0.13 -10000 0 -0.24 159 159
mol:ADP 0.021 0.015 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.26 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.058 0.14 -10000 0 -0.25 159 159
CNGB1 -0.072 0.14 -10000 0 -0.43 61 61
RDH5 0.016 0.038 -10000 0 -0.13 31 31
SAG -0.009 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.11 0.31 3 -0.31 45 48
Na + (4 Units) -0.079 0.12 -10000 0 -0.23 153 153
RGS9 -0.012 0.12 -10000 0 -0.4 45 45
GNB1/GNGT1 0.02 0.016 -10000 0 -10000 0 0
GNAT1/GDP 0.026 0.081 -10000 0 -0.23 40 40
GUCY2D 0.007 0.032 -10000 0 -0.13 16 16
GNGT1 -0.013 0.011 -10000 0 -0.13 2 2
GUCY2F 0.011 0.024 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.087 0.15 2 -0.24 58 60
mol:11-cis-retinal 0.016 0.038 -10000 0 -0.13 31 31
mol:cGMP -0.006 0.11 -10000 0 -0.24 80 80
GNB1 0.022 0.01 -10000 0 -10000 0 0
Rhodopsin 0.014 0.061 -10000 0 -0.29 11 11
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.018 0.12 -10000 0 -0.32 63 63
Metarhodopsin II 0.018 0.044 -10000 0 -0.23 11 11
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.003 0.12 -10000 0 -0.25 82 82
RGS9BP 0.017 0.046 -10000 0 -0.38 6 6
Metarhodopsin II/Transducin -0.001 0.04 -10000 0 -0.24 10 10
GCAP Family/Ca ++ -0.007 0.11 -10000 0 -0.23 93 93
PDE6A/B 0.001 0.094 -10000 0 -0.3 37 37
mol:Pi 0.018 0.088 -10000 0 -0.26 41 41
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.023 0.03 -10000 0 -0.18 2 2
PDE6B 0.002 0.092 -10000 0 -0.28 40 40
PDE6A 0.001 0.086 -10000 0 -0.23 47 47
PDE6G -0.002 0.1 -10000 0 -0.43 25 25
RHO -0.003 0.075 -10000 0 -0.2 46 46
PDE6 0.009 0.12 -10000 0 -0.24 87 87
GUCA1A -0.061 0.15 -10000 0 -0.28 137 137
GC2/GCAP Family 0.006 0.12 -10000 0 -0.25 82 82
GUCA1C -0.007 0.029 -10000 0 -0.13 16 16
GUCA1B 0.012 0.079 -10000 0 -0.43 16 16
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 63 63
E-cadherin/beta catenin -0.017 0.11 -9999 0 -0.3 59 59
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
JUP 0.02 0.049 -9999 0 -0.43 6 6
CDH1 -0.046 0.15 -9999 0 -0.43 59 59
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.043 0.2 -9999 0 -0.43 90 90
MAP3K8 0.015 0.048 -9999 0 -0.2 18 18
FOS -0.041 0.18 -9999 0 -0.44 73 73
PRKCA 0.02 0.024 -9999 0 -0.43 1 1
PTPN7 -0.054 0.15 -9999 0 -0.29 124 124
HRAS 0.024 0.006 -9999 0 -10000 0 0
PRKCB -0.011 0.098 -9999 0 -0.22 68 68
NRAS 0.021 0.01 -9999 0 -10000 0 0
RAS family/GTP 0.034 0.026 -9999 0 -10000 0 0
MAPK3 -0.032 0.16 -9999 0 -0.43 67 67
MAP2K1 0.003 0.1 -9999 0 -0.44 20 20
ELK1 0.021 0.017 -9999 0 -10000 0 0
BRAF -0.006 0.085 -9999 0 -0.39 22 22
mol:GTP 0 0.001 -9999 0 -0.004 59 59
MAPK1 -0.036 0.17 -9999 0 -0.43 70 70
RAF1 -0.002 0.086 -9999 0 -0.41 19 19
KRAS 0.025 0.005 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.027 0.11 -10000 0 -0.38 21 21
ACTA1 -0.054 0.13 0.22 2 -0.33 70 72
NUMA1 -0.027 0.11 -10000 0 -0.39 21 21
SPTAN1 -0.049 0.13 0.21 7 -0.33 66 73
LIMK1 -0.028 0.14 0.22 13 -0.33 62 75
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
CASP10 -0.055 0.098 0.16 1 -0.28 71 72
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
PTK2 -0.03 0.12 -10000 0 -0.34 32 32
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.048 0.13 0.21 7 -0.33 66 73
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
GSN -0.054 0.13 0.34 1 -0.33 70 71
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.13 0.29 -10000 0 -0.59 135 135
BID -0.024 0.066 -10000 0 -0.18 70 70
MAP3K1 -0.011 0.066 -10000 0 -0.44 5 5
TRADD 0.025 0.02 -10000 0 -0.43 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.016 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.048 0.13 0.19 4 -0.33 68 72
CASP9 0.022 0.012 -10000 0 -0.13 1 1
DNA repair 0.011 0.056 0.23 9 -0.15 13 22
neuron apoptosis 0.016 0.064 -10000 0 -0.62 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.038 0.13 0.21 2 -0.31 71 73
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.013 0.16 -10000 0 -0.88 13 13
TRAF2 0.026 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.13 0.31 8 -0.32 70 78
CASP7 -0.009 0.096 0.24 21 -0.3 17 38
KRT18 -0.065 0.21 -10000 0 -0.57 71 71
apoptosis -0.052 0.14 0.29 2 -0.43 35 37
DFFA -0.05 0.13 0.19 6 -0.33 70 76
DFFB -0.05 0.13 0.19 6 -0.33 70 76
PARP1 -0.011 0.057 0.15 12 -0.23 9 21
actin filament polymerization 0.025 0.13 0.31 62 -0.26 9 71
TNF -0.06 0.16 -10000 0 -0.43 68 68
CYCS -0.011 0.056 0.19 4 -0.2 10 14
SATB1 -0.014 0.16 -10000 0 -0.86 12 12
SLK -0.053 0.13 0.33 1 -0.33 70 71
p15 BID/BAX -0.011 0.063 -10000 0 -0.27 8 8
CASP2 0.024 0.11 0.21 86 -0.32 14 100
JNK cascade 0.011 0.065 0.43 5 -10000 0 5
CASP3 -0.055 0.13 0.19 2 -0.34 71 73
LMNB2 0.025 0.11 0.23 11 -0.42 12 23
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CASP4 0.016 0.044 -10000 0 -0.15 26 26
Mammalian IAPs/DIABLO 0.05 0.065 -10000 0 -0.24 23 23
negative regulation of DNA binding -0.13 0.29 -10000 0 -0.58 135 135
stress fiber formation -0.052 0.13 0.33 1 -0.32 70 71
GZMB -0.052 0.12 -10000 0 -0.28 98 98
CASP1 0.003 0.049 -10000 0 -0.29 13 13
LMNB1 0.019 0.13 0.23 11 -0.41 18 29
APP 0.016 0.065 -10000 0 -0.63 4 4
TNFRSF1A 0.017 0.054 -10000 0 -0.43 7 7
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.02 -10000 0 -0.3 1 1
VIM -0.049 0.15 0.32 1 -0.43 36 37
LMNA 0.027 0.11 0.22 12 -0.38 12 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.095 -10000 0 -0.35 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.059 0.13 -10000 0 -0.32 76 76
APAF-1/Caspase 9 -0.072 0.22 -10000 0 -0.62 70 70
nuclear fragmentation during apoptosis -0.026 0.11 -10000 0 -0.36 24 24
CFL2 -0.026 0.14 0.26 9 -0.31 62 71
GAS2 -0.054 0.13 0.18 2 -0.32 75 77
positive regulation of apoptosis 0.028 0.12 0.22 16 -0.39 15 31
PRF1 -0.015 0.12 -10000 0 -0.28 66 66
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.021 -9999 0 -0.43 1 1
Aurora C/Aurora B/INCENP -0.012 0.11 -9999 0 -0.23 97 97
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.031 -9999 0 -10000 0 0
AURKB -0.074 0.17 -9999 0 -0.31 152 152
AURKC 0.01 0.054 -9999 0 -0.43 5 5
BCR signaling pathway

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
JUN -0.059 0.18 0.3 5 -0.42 82 87
IKBKB 0.016 0.09 0.25 16 -0.31 3 19
AKT1 -0.022 0.1 0.26 24 -0.21 37 61
IKBKG 0.004 0.093 0.25 10 -0.27 12 22
CALM1 -0.04 0.14 0.24 2 -0.46 36 38
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.034 0.18 0.3 16 -0.48 50 66
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.16 0.23 2 -0.4 55 57
DOK1 0.025 0.021 -10000 0 -0.43 1 1
AP-1 -0.044 0.12 0.24 3 -0.27 74 77
LYN 0.021 0.035 -10000 0 -0.43 2 2
BLNK -0.021 0.13 -10000 0 -0.38 59 59
SHC1 0.024 0.014 -10000 0 -0.13 4 4
BCR complex -0.006 0.096 -10000 0 -0.27 51 51
CD22 -0.066 0.15 -10000 0 -0.43 54 54
CAMK2G -0.037 0.14 0.26 4 -0.44 34 38
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
SHC/GRB2/SOS1 -0.027 0.11 -10000 0 -0.25 68 68
GO:0007205 -0.042 0.16 0.23 2 -0.41 55 57
SYK 0.009 0.083 -10000 0 -0.43 17 17
ELK1 -0.039 0.15 0.24 1 -0.48 35 36
NFATC1 -0.044 0.14 0.27 6 -0.42 47 53
B-cell antigen/BCR complex -0.006 0.096 -10000 0 -0.27 51 51
PAG1/CSK 0.036 0.01 -10000 0 -10000 0 0
NFKBIB 0.017 0.047 0.13 21 -0.13 13 34
HRAS -0.031 0.14 0.26 6 -0.44 31 37
NFKBIA 0.016 0.047 0.13 23 -0.13 12 35
NF-kappa-B/RelA/I kappa B beta 0.022 0.041 0.13 22 -10000 0 22
RasGAP/Csk -0.002 0.13 -10000 0 -0.24 96 96
mol:GDP -0.037 0.15 0.22 2 -0.44 44 46
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.005 0.099 -10000 0 -0.26 54 54
NF-kappa-B/RelA/I kappa B alpha 0.022 0.041 0.13 21 -10000 0 21
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.059 0.18 0.34 4 -0.51 50 54
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.044 0.16 0.25 1 -0.41 57 58
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.059 0.16 0.22 2 -0.45 44 46
CHUK -0.006 0.098 0.24 11 -0.3 18 29
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.002 0.15 0.24 10 -0.46 28 38
PTPN6 -0.067 0.15 0.22 2 -0.45 51 53
RELA 0.025 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.038 0.12 4 -0.12 2 6
VAV2 -0.053 0.15 0.23 1 -0.47 47 48
ubiquitin-dependent protein catabolic process 0.019 0.046 0.13 21 -0.13 13 34
BTK -0.018 0.21 -10000 0 -1.1 18 18
CD19 -0.056 0.14 -10000 0 -0.39 60 60
MAP4K1 0.013 0.061 -10000 0 -0.43 9 9
CD72 0.017 0.048 -10000 0 -0.19 20 20
PAG1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.026 0.16 0.28 17 -0.41 49 66
SH3BP5 0.024 0.029 -10000 0 -0.33 3 3
PIK3AP1 -0.041 0.16 -10000 0 -0.43 55 55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.06 0.23 -10000 0 -0.56 61 61
RAF1 -0.028 0.13 0.26 5 -0.42 29 34
RasGAP/p62DOK/SHIP -0.002 0.12 -10000 0 -0.24 89 89
CD79A -0.002 0.086 -10000 0 -0.25 42 42
re-entry into mitotic cell cycle -0.044 0.12 0.24 3 -0.27 74 77
RASA1 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.11 0.26 4 -0.41 20 24
MAPK1 -0.024 0.11 0.25 4 -0.4 20 24
CD72/SHP1 -0.055 0.16 0.27 13 -0.42 56 69
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.031 0.16 0.28 17 -0.4 53 70
actin cytoskeleton organization -0.027 0.15 0.3 19 -0.43 39 58
NF-kappa-B/RelA 0.044 0.079 0.24 23 -0.21 7 30
Calcineurin -0.012 0.14 0.22 1 -0.42 31 32
PI3K -0.066 0.13 -10000 0 -0.37 55 55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.17 -10000 0 -0.44 56 56
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.068 0.27 -10000 0 -0.8 55 55
DAPP1 -0.095 0.31 -10000 0 -0.91 56 56
cytokine secretion -0.04 0.14 0.26 6 -0.4 47 53
mol:DAG -0.044 0.16 0.25 1 -0.41 57 58
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
MAP2K1 -0.026 0.12 0.26 4 -0.41 25 29
B-cell antigen/BCR complex/FcgammaRIIB -0.024 0.13 -10000 0 -0.25 117 117
mol:PI-3-4-5-P3 -0.055 0.095 0.19 2 -0.29 45 47
ETS1 -0.026 0.13 0.26 9 -0.42 30 39
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.13 -10000 0 -0.26 89 89
B-cell antigen/BCR complex/LYN -0.048 0.15 -10000 0 -0.42 56 56
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 -0.033 0.15 0.28 15 -0.46 38 53
B-cell antigen/BCR complex/LYN/SYK -0.048 0.17 0.28 1 -0.43 60 61
CARD11 -0.022 0.18 0.26 21 -0.52 35 56
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
PPP3CA 0.025 0.011 -10000 0 -0.13 2 2
BCL10 0.021 0.01 -10000 0 -10000 0 0
IKK complex 0.01 0.051 0.15 24 -0.12 5 29
PTPRC -0.003 0.1 -10000 0 -0.43 24 24
PDPK1 -0.034 0.079 0.19 14 -0.21 38 52
PPP3CB 0.024 0.013 -10000 0 -0.13 3 3
PPP3CC 0.025 0.005 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.15 18 -10000 0 18
EGFR-dependent Endothelin signaling 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
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.017 0.12 -10000 0 -0.4 46 46
EGF/EGFR -0.008 0.11 -10000 0 -0.24 88 88
EGF/EGFR dimer/SHC/GRB2/SOS1 0.022 0.1 -10000 0 -0.24 64 64
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.007 0.081 -10000 0 -0.28 31 31
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.01 0.11 -10000 0 -0.31 54 54
EGF/EGFR dimer/SHC 0 0.11 -10000 0 -0.27 67 67
mol:GDP 0.016 0.1 -10000 0 -0.23 64 64
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.002 0.086 -10000 0 -0.23 48 48
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.088 -10000 0 -0.22 63 63
SHC1 0.024 0.014 -10000 0 -0.13 4 4
HRAS/GDP 0.015 0.096 -10000 0 -0.22 63 63
FRAP1 -0.035 0.075 0.11 7 -0.22 64 71
EGF/EGFR dimer -0.02 0.12 -10000 0 -0.32 69 69
SOS1 0.026 0.002 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.005 0.087 -10000 0 -0.3 33 33
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.029 0.025 -10000 0 -0.28 2 2
Necdin/E2F1 0.013 0.082 -10000 0 -0.31 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.016 0.11 -10000 0 -0.24 72 72
NGF (dimer)/p75(NTR)/BEX1 -0.018 0.13 -10000 0 -0.28 90 90
NT-4/5 (dimer)/p75(NTR) -0.005 0.088 -10000 0 -0.29 38 38
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.092 0.18 9 -0.24 70 79
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.18 88 88
MGDIs/NGR/p75(NTR)/LINGO1 -0.002 0.13 -10000 0 -0.3 77 77
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.011 0.096 -10000 0 -0.25 53 53
LINGO1 0.001 0.1 -10000 0 -0.43 28 28
Sortilin/TRAF6/NRIF 0.025 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.01 0.089 -10000 0 -0.18 88 88
NTRK1 0.015 0.058 -10000 0 -0.43 7 7
RTN4R -0.006 0.11 -10000 0 -0.34 44 44
neuron apoptosis -0.066 0.16 0.29 9 -0.41 49 58
IRAK1 0.026 0.003 -10000 0 -10000 0 0
SHC1 -0.038 0.1 0.19 1 -0.28 72 73
ARHGDIA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.063 0.032 -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 0.06 -10000 0 -0.43 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.14 -10000 0 -0.27 97 97
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.24 23 23
proNGF (dimer) -0.026 0.13 -10000 0 -0.34 64 64
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 0.032 -10000 0 -0.43 1 1
ZNF274 0.021 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.017 0.094 -10000 0 -0.24 68 68
NGF -0.026 0.13 -10000 0 -0.34 64 64
cell cycle arrest -0.036 0.089 0.26 10 -0.21 70 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.099 -10000 0 -0.25 70 70
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.013 0.08 -10000 0 -0.25 35 35
NCSTN 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.007 0.12 -10000 0 -0.27 75 75
PSENEN 0.022 0.01 -10000 0 -10000 0 0
mol:ceramide -0.032 0.097 0.18 7 -0.25 72 79
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.021 0.094 -10000 0 -0.27 36 36
p75(NTR)/beta APP 0.006 0.089 -10000 0 -0.3 34 34
BEX1 0.01 0.084 -10000 0 -0.43 18 18
mol:GDP -0.044 0.1 -10000 0 -0.27 75 75
NGF (dimer) -0.026 0.13 -10000 0 -0.25 118 118
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.014 0.13 -10000 0 -0.28 75 75
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.006 0.094 -10000 0 -0.23 66 66
MYD88 0.019 0.054 -10000 0 -0.36 9 9
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.006 0.12 -10000 0 -0.27 75 75
RHOB 0.025 0.012 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.028 0.044 -10000 0 -0.3 6 6
NT3 (dimer) 0.006 0.032 -10000 0 -0.13 17 17
TP53 -0.021 0.1 0.3 11 -0.28 21 32
PRDM4 -0.032 0.099 0.18 7 -0.25 73 80
BDNF (dimer) -0.016 0.12 -10000 0 -0.23 111 111
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SORT1 0.02 0.022 -10000 0 -0.43 1 1
activation of caspase activity 0.011 0.11 -10000 0 -0.24 72 72
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.005 0.11 -10000 0 -0.25 73 73
RHOC 0.02 0.023 -10000 0 -0.28 2 2
XIAP 0.026 0.001 -10000 0 -10000 0 0
MAPK10 -0.017 0.13 0.3 25 -0.32 39 64
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.032 0.098 0.18 7 -0.25 72 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 -0.007 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 0.016 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.001 0.09 -10000 0 -0.3 37 37
MAPK8 -0.026 0.13 0.31 14 -0.32 41 55
MAPK9 -0.014 0.13 0.3 26 -0.32 36 62
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.032 -10000 0 -0.13 17 17
NTF4 -0.003 0.032 -10000 0 -0.43 1 1
NDN -0.003 0.11 -10000 0 -0.43 33 33
RAC1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.011 0.1 -10000 0 -0.23 70 70
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.045 -10000 0 -0.24 6 6
RhoA-B-C/GTP -0.007 0.12 -10000 0 -0.27 75 75
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.094 -10000 0 -0.23 46 46
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.096 -10000 0 -0.25 47 47
PRKACB 0.021 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.007 0.077 -10000 0 -0.32 18 18
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.1 0.16 3 -0.28 71 74
BAD -0.018 0.13 0.29 28 -0.32 38 66
RIPK2 0.024 0.007 -10000 0 -10000 0 0
NGFR -0.016 0.12 -10000 0 -0.43 34 34
CYCS -0.026 0.09 0.22 8 -0.24 63 71
ADAM17 0.022 0.045 -10000 0 -0.43 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.005 0.11 -10000 0 -0.26 65 65
BCL2L11 -0.02 0.13 0.28 25 -0.32 39 64
BDNF (dimer)/p75(NTR) -0.02 0.11 -10000 0 -0.3 53 53
PI3K 0.007 0.11 -10000 0 -0.25 71 71
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.006 0.11 -10000 0 -0.25 73 73
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) -0.034 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 0.007 0.11 -10000 0 -0.26 72 72
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
PLG -0.01 0.018 -10000 0 -0.13 3 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.044 0.11 0.24 2 -0.27 81 83
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.002 -10000 0 -10000 0 0
CASP3 -0.018 0.13 0.28 26 -0.31 40 66
E2F1 0.014 0.056 -10000 0 -0.2 24 24
CASP9 0.022 0.012 -10000 0 -0.13 1 1
IKK complex -0.021 0.13 -10000 0 -0.31 43 43
NGF (dimer)/TRKA -0.013 0.1 -10000 0 -0.3 54 54
MMP7 -0.072 0.16 -10000 0 -0.29 148 148
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.11 -10000 0 -0.24 70 70
MMP3 -0.004 0.046 -10000 0 -0.14 42 42
APAF-1/Caspase 9 -0.029 0.082 -10000 0 -0.29 17 17
Nongenotropic Androgen signaling

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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.004 0.097 -10000 0 -0.22 75 75
regulation of S phase of mitotic cell cycle -0.011 0.084 -10000 0 -0.22 69 69
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.012 0.036 -10000 0 -0.25 9 9
PELP1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.035 0.096 0.18 27 -0.29 18 45
T-DHT/AR -0.034 0.11 -10000 0 -0.23 107 107
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 55 55
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
mol:GDP -0.05 0.13 -10000 0 -0.38 71 71
cell proliferation -0.044 0.16 0.29 7 -0.42 53 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FOS -0.076 0.26 0.27 1 -0.79 56 57
mol:Ca2+ -0.008 0.019 -10000 0 -0.055 50 50
MAPK3 -0.036 0.13 0.27 8 -0.32 51 59
MAPK1 -0.015 0.089 0.22 1 -0.3 17 18
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 55 55
cAMP biosynthetic process -0.001 0.036 0.23 1 -0.24 9 10
GNG2 0.022 0.04 -10000 0 -0.43 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 55 55
HRAS/GTP 0 0.095 -10000 0 -0.22 70 70
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 55 55
PI3K 0.035 0.007 -10000 0 -10000 0 0
apoptosis 0.034 0.15 0.42 55 -0.24 6 61
T-DHT/AR/PELP1 -0.014 0.1 -10000 0 -0.26 71 71
HRAS/GDP -0.037 0.13 0.13 2 -0.36 71 73
CREB1 -0.037 0.16 0.25 6 -0.45 55 61
RAC1-CDC42/GTP 0.036 0.024 -10000 0 -10000 0 0
AR -0.049 0.16 -10000 0 -0.33 107 107
GNB1 0.022 0.01 -10000 0 -10000 0 0
RAF1 -0.021 0.098 0.18 28 -0.22 70 98
RAC1-CDC42/GDP -0.021 0.13 -10000 0 -0.33 70 70
T-DHT/AR/PELP1/Src 0.006 0.1 -10000 0 -0.24 71 71
MAP2K2 -0.036 0.092 0.18 23 -0.22 67 90
T-DHT/AR/PELP1/Src/PI3K -0.011 0.084 -10000 0 -0.22 69 69
GNAZ 0.026 0.004 -10000 0 -10000 0 0
SHBG 0.017 0.061 -10000 0 -0.43 9 9
Gi family/GNB1/GNG2/GDP -0.031 0.12 -10000 0 -0.35 37 37
mol:T-DHT 0 0.001 -10000 0 -0.002 37 37
RAC1 0.023 0.009 -10000 0 -10000 0 0
GNRH1 0.002 0.035 -10000 0 -0.3 6 6
Gi family/GTP -0.021 0.068 -10000 0 -0.21 37 37
CDC42 0.022 0.01 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.084 -10000 0 -0.23 62 62
epithelial cell differentiation 0.024 0.086 -10000 0 -0.22 55 55
CYFIP2 0.022 0.037 -10000 0 -0.43 3 3
ENAH -0.025 0.061 0.27 3 -10000 0 3
EGFR -0.017 0.12 -10000 0 -0.4 46 46
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
MYO6 -0.014 0.08 0.18 21 -0.21 51 72
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.045 0.028 -10000 0 -0.23 3 3
AQP5 -0.062 0.16 0.22 4 -0.44 67 71
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.014 0.078 0.18 20 -0.21 51 71
regulation of calcium-dependent cell-cell adhesion -0.016 0.081 0.18 19 -0.21 56 75
EGF -0.01 0.11 -10000 0 -0.31 54 54
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.019 0.1 0.22 3 -0.45 17 20
cortical microtubule organization 0.024 0.086 -10000 0 -0.22 55 55
GO:0000145 -0.027 0.07 0.16 20 -0.2 51 71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.089 -10000 0 -0.22 55 55
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GDP -0.038 0.056 -10000 0 -0.23 6 6
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.037 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.085 0.17 8 -0.34 18 26
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
ZYX -0.013 0.069 0.18 11 -0.21 43 54
ARF6/GTP 0.059 0.038 -10000 0 -0.24 3 3
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.24 105 105
RhoA/GDP 0.026 0.083 -10000 0 -0.21 55 55
actin cytoskeleton organization -0.028 0.075 0.16 21 -0.21 49 70
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
IGF1R 0.026 0.004 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
DIAPH1 0.02 0.12 -10000 0 -0.61 7 7
Wnt receptor signaling pathway -0.024 0.086 0.22 55 -10000 0 55
RHOA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.038 0.056 -10000 0 -0.23 6 6
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.029 0.077 0.17 21 -0.22 49 70
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
LPP -0.036 0.077 0.17 19 -0.21 60 79
Ephrin A1/EPHA2 0.013 0.08 -10000 0 -0.2 54 54
SEC6/SEC8 -0.015 0.06 -10000 0 -0.21 26 26
MGAT3 -0.016 0.082 0.18 19 -0.21 56 75
HGF/MET -0.025 0.12 -10000 0 -0.25 93 93
HGF -0.009 0.091 -10000 0 -0.2 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.085 -10000 0 -0.23 62 62
actin cable formation -0.005 0.096 0.28 18 -0.26 9 27
KIAA1543 -0.032 0.076 0.16 15 -0.22 55 70
KIFC3 -0.016 0.079 0.18 16 -0.21 54 70
NCK1 0.025 0.02 -10000 0 -0.43 1 1
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.019 0.081 0.18 19 -0.21 52 71
NCK1/GIT1 0.038 0.016 -10000 0 -0.3 1 1
mol:GDP 0.024 0.086 -10000 0 -0.22 55 55
EXOC4 0.02 0.011 -10000 0 -10000 0 0
STX4 -0.014 0.08 0.18 20 -0.21 53 73
PIP5K1C -0.014 0.078 0.18 20 -0.21 51 71
LIMA1 0.019 0.056 -10000 0 -0.43 8 8
ABI1 0.023 0.008 -10000 0 -10000 0 0
ROCK1 -0.022 0.082 0.39 6 -10000 0 6
adherens junction assembly -0.01 0.09 0.27 10 -0.41 5 15
IGF-1R heterotetramer/IGF1 0.014 0.09 -10000 0 -0.22 62 62
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
MET -0.046 0.14 -10000 0 -0.43 50 50
PLEKHA7 -0.019 0.085 0.18 16 -0.23 55 71
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 27 -0.37 1 28
cortical actin cytoskeleton stabilization -0.01 0.084 -10000 0 -0.23 62 62
regulation of cell-cell adhesion -0.028 0.075 0.16 21 -0.21 49 70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.085 -10000 0 -0.23 62 62
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.008 -10000 0 -0.13 1 1
LAT2 -0.023 0.12 0.17 5 -0.43 25 30
AP1 -0.015 0.17 0.25 1 -0.55 29 30
mol:PIP3 -0.009 0.17 0.29 37 -0.48 28 65
IKBKB 0.005 0.11 0.25 37 -0.27 20 57
AKT1 -0.031 0.11 0.31 22 -0.32 11 33
IKBKG 0.001 0.1 0.23 27 -0.26 22 49
MS4A2 -0.006 0.037 -10000 0 -0.13 25 25
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.007 0.13 0.32 10 -0.48 23 33
mol:Ca2+ -0.001 0.14 0.27 38 -0.35 28 66
LYN 0.021 0.035 -10000 0 -0.45 2 2
CBLB -0.019 0.1 -10000 0 -0.37 25 25
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RasGAP/p62DOK 0.042 0.047 -10000 0 -0.23 14 14
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
PLD2 -0.042 0.1 0.26 18 -0.24 73 91
PTPN13 -0.007 0.13 -10000 0 -0.51 20 20
PTPN11 0.021 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.005 0.1 0.26 23 -0.3 19 42
SYK 0.009 0.085 -10000 0 -0.4 20 20
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.03 0.14 0.21 6 -0.35 57 63
LAT -0.029 0.11 -10000 0 -0.31 44 44
PAK2 -0.009 0.15 0.29 10 -0.53 24 34
NFATC2 -0.051 0.15 -10000 0 -0.53 43 43
HRAS -0.014 0.16 0.24 10 -0.55 27 37
GAB2 0.025 0.005 -10000 0 -10000 0 0
PLA2G1B 0.025 0.094 -10000 0 -0.82 5 5
Fc epsilon R1 -0.016 0.13 -10000 0 -0.27 87 87
Antigen/IgE/Fc epsilon R1 -0.008 0.12 -10000 0 -0.25 87 87
mol:GDP -0.016 0.16 0.22 8 -0.56 30 38
JUN 0.019 0.022 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.29 92 92
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.26 65 65
CHUK 0 0.1 0.23 26 -0.26 22 48
KLRG1 -0.023 0.098 0.16 3 -0.24 65 68
VAV1 -0.026 0.13 0.16 3 -0.3 58 61
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.11 0.18 5 -0.37 24 29
negative regulation of mast cell degranulation -0.003 0.11 0.2 9 -0.4 18 27
BTK -0.022 0.17 -10000 0 -0.68 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.14 -10000 0 -0.29 108 108
GAB2/PI3K/SHP2 -0.047 0.081 -10000 0 -0.24 64 64
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 0.19 1 -0.26 75 76
RAF1 0.02 0.099 -10000 0 -0.93 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.016 0.16 -10000 0 -0.28 122 122
FCER1G 0.006 0.09 -10000 0 -0.35 27 27
FCER1A -0.06 0.16 -10000 0 -0.28 137 137
Antigen/IgE/Fc epsilon R1/Fyn 0.009 0.11 -10000 0 -0.23 86 86
MAPK3 0.024 0.093 -10000 0 -0.82 5 5
MAPK1 0.023 0.096 -10000 0 -0.85 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.004 0.14 -10000 0 -0.53 28 28
DUSP1 0.008 0.077 -10000 0 -0.25 32 32
NF-kappa-B/RelA 0.004 0.059 0.13 15 -0.17 16 31
actin cytoskeleton reorganization -0.005 0.13 -10000 0 -0.5 20 20
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.006 0.14 0.23 6 -0.48 27 33
FER -0.027 0.11 -10000 0 -0.32 40 40
RELA 0.025 0.005 -10000 0 -10000 0 0
ITK -0.024 0.093 -10000 0 -0.35 35 35
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.007 0.17 0.26 24 -0.57 28 52
cytokine secretion -0.003 0.038 -10000 0 -0.14 6 6
SPHK1 -0.028 0.12 0.2 1 -0.36 33 34
PTK2 -0.006 0.13 -10000 0 -0.54 19 19
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.15 0.25 10 -0.35 65 75
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.004 0.16 0.29 32 -0.45 28 60
MAP2K2 0.023 0.098 -10000 0 -0.82 5 5
MAP2K1 0.015 0.093 -10000 0 -0.87 5 5
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.1 0.18 20 -0.34 20 40
MAP2K4 0.032 0.063 -10000 0 -1.4 1 1
Fc epsilon R1/FcgammaRIIB -0.031 0.16 -10000 0 -0.26 147 147
mol:Choline -0.041 0.1 0.26 18 -0.23 73 91
SHC/Grb2/SOS1 0.019 0.12 -10000 0 -0.37 22 22
FYN 0.025 0.005 -10000 0 -10000 0 0
DOK1 0.025 0.021 -10000 0 -0.43 1 1
PXN -0.003 0.12 -10000 0 -0.49 20 20
HCLS1 -0.026 0.12 0.14 1 -0.42 29 30
PRKCB -0.005 0.13 0.27 24 -0.34 28 52
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.003 0.11 0.2 9 -0.41 18 27
LCP2 0.021 0.033 -10000 0 -0.15 15 15
PLA2G4A -0.027 0.12 -10000 0 -0.37 36 36
RASA1 0.026 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.041 0.1 0.26 18 -0.23 73 91
IKK complex 0.009 0.093 0.23 37 -0.21 16 53
WIPF1 0.026 0.002 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.014 0.089 -10000 0 -0.22 60 60
NF kappa B1 p50/RelA/I kappa B alpha 0 0.11 0.24 15 -0.34 23 38
AP1 -0.029 0.1 -10000 0 -0.23 92 92
mol:PIP3 -0.036 0.088 -10000 0 -0.22 81 81
AKT1 0.001 0.1 0.27 17 -0.25 21 38
PTK2B -0.005 0.09 0.18 7 -0.28 19 26
RHOA 0.004 0.079 0.22 16 -0.36 7 23
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.072 0.21 20 -0.28 10 30
MAGI3 0.02 0.022 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.02 0.087 -10000 0 -0.27 51 51
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.088 0.22 6 -0.27 17 23
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.32 38 38
endothelial cell migration -0.022 0.11 -10000 0 -0.3 56 56
ADCY4 -0.014 0.12 -10000 0 -0.37 44 44
ADCY5 -0.015 0.12 -10000 0 -0.34 51 51
ADCY6 -0.013 0.12 -10000 0 -0.34 51 51
ADCY7 -0.013 0.12 -10000 0 -0.34 51 51
ADCY1 -0.032 0.12 -10000 0 -0.36 49 49
ADCY2 -0.017 0.12 -10000 0 -0.35 53 53
ADCY3 -0.013 0.12 -10000 0 -0.34 51 51
ADCY8 -0.034 0.14 -10000 0 -0.39 58 58
ADCY9 -0.013 0.12 -10000 0 -0.34 51 51
GSK3B -0.006 0.087 0.2 3 -0.28 17 20
arachidonic acid secretion -0.019 0.12 -10000 0 -0.33 54 54
GNG2 0.022 0.04 -10000 0 -0.43 4 4
TRIP6 0.013 0.031 -10000 0 -0.34 2 2
GNAO1 -0.018 0.089 -10000 0 -0.26 60 60
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA -0.019 0.12 0.24 17 -0.34 33 50
GAB1 0.025 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.11 -10000 0 -0.84 7 7
JUN 0.019 0.022 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.028 0.039 -10000 0 -0.25 7 7
TIAM1 0.017 0.13 -10000 0 -1 7 7
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 -0.009 0.066 0.2 14 -0.29 10 24
PLCB3 0.017 0.049 0.18 24 -0.23 7 31
FOS -0.031 0.14 -10000 0 -0.29 92 92
positive regulation of mitosis -0.019 0.12 -10000 0 -0.33 54 54
LPA/LPA1-2-3 0.007 0.094 -10000 0 -0.23 62 62
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
stress fiber formation 0.003 0.095 0.2 11 -0.26 20 31
GNAZ -0.014 0.084 -10000 0 -0.25 53 53
EGFR/PI3K-beta/Gab1 -0.03 0.095 -10000 0 -0.23 81 81
positive regulation of dendritic cell cytokine production 0.006 0.093 -10000 0 -0.23 62 62
LPA/LPA2/MAGI-3 0.021 0.042 -10000 0 -0.25 8 8
ARHGEF1 0.015 0.097 0.2 59 -0.2 47 106
GNAI2 -0.015 0.085 -10000 0 -0.25 54 54
GNAI3 -0.003 0.062 -10000 0 -0.26 25 25
GNAI1 -0.015 0.082 -10000 0 -0.25 52 52
LPA/LPA3 0.002 0.036 -10000 0 -0.13 17 17
LPA/LPA2 0.012 0.042 -10000 0 -0.2 15 15
LPA/LPA1 -0.016 0.1 -10000 0 -0.3 56 56
HB-EGF/EGFR -0.035 0.11 -10000 0 -0.26 82 82
HBEGF -0.034 0.09 -10000 0 -0.29 48 48
mol:DAG -0.009 0.066 0.2 14 -0.29 10 24
cAMP biosynthetic process -0.016 0.14 0.33 8 -0.36 49 57
NFKB1 0.026 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 -0.015 0.12 0.24 19 -0.36 31 50
GNAQ 0.002 0.037 -10000 0 -0.25 7 7
LPAR2 0.018 0.054 -10000 0 -0.43 7 7
LPAR3 -0.009 0.043 -10000 0 -0.13 48 48
LPAR1 -0.024 0.14 -10000 0 -0.39 56 56
IL8 -0.1 0.21 0.32 12 -0.44 112 124
PTK2 -0.014 0.089 0.19 25 -0.22 59 84
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.021 0.087 -10000 0 -0.27 51 51
EGFR -0.017 0.12 -10000 0 -0.4 46 46
PLCG1 -0.013 0.06 0.15 6 -0.22 23 29
PLD2 -0.013 0.094 0.19 29 -0.22 62 91
G12/G13 0.018 0.083 -10000 0 -0.23 47 47
PI3K-beta -0.021 0.085 -10000 0 -0.27 30 30
cell migration 0.01 0.052 0.24 1 -0.24 5 6
SLC9A3R2 0.025 0.01 -10000 0 -10000 0 0
PXN 0.002 0.097 0.2 10 -0.27 20 30
HRAS/GTP -0.02 0.12 -10000 0 -0.34 54 54
RAC1 0.023 0.009 -10000 0 -10000 0 0
MMP9 -0.042 0.13 -10000 0 -0.22 133 133
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
PRKCD -0.008 0.097 0.22 30 -0.3 27 57
Gi(beta/gamma) -0.019 0.13 -10000 0 -0.36 58 58
mol:LPA -0.001 0.022 -10000 0 -0.16 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.093 0.33 1 -0.36 8 9
MAPKKK cascade -0.019 0.12 -10000 0 -0.33 54 54
contractile ring contraction involved in cytokinesis 0.001 0.087 0.22 21 -0.37 8 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.007 0.06 0.12 1 -0.22 31 32
GNA15 -0.005 0.057 -10000 0 -0.27 19 19
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.008 0.09 0.22 6 -0.28 17 23
GNA11 -0.002 0.049 -10000 0 -0.25 15 15
Rac1/GTP 0.03 0.11 -10000 0 -0.9 7 7
MMP2 -0.022 0.11 -10000 0 -0.3 56 56
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.023 0.012 -9999 0 -0.13 2 2
ITGB7 0.002 0.091 -9999 0 -0.43 19 19
ITGA4 -0.007 0.1 -9999 0 -0.26 60 60
alpha4/beta7 Integrin -0.004 0.1 -9999 0 -0.28 55 55
alpha4/beta1 Integrin 0.012 0.076 -9999 0 -0.29 25 25
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.021 0.1 -10000 0 -0.3 50 50
CRKL 0.012 0.14 0.27 15 -0.45 20 35
mol:PIP3 0.001 0.039 -10000 0 -0.84 1 1
AKT1 -0.004 0.043 0.28 1 -0.73 1 2
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
RAPGEF1 0.015 0.14 0.29 15 -0.44 19 34
RANBP10 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
HGF/MET/SHIP2 -0.003 0.11 -10000 0 -0.24 79 79
MAP3K5 -0.008 0.16 0.26 16 -0.45 30 46
HGF/MET/CIN85/CBL/ENDOPHILINS 0.008 0.1 -10000 0 -0.26 53 53
AP1 -0.01 0.1 -10000 0 -0.25 52 52
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
apoptosis -0.17 0.38 -10000 0 -0.8 130 130
STAT3 (dimer) -0.005 0.09 0.22 5 -0.23 50 55
GAB1/CRKL/SHP2/PI3K 0.039 0.14 0.29 5 -0.42 19 24
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
CBL/CRK 0.022 0.14 0.27 15 -0.44 19 34
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 0.038 0.16 0.32 116 -0.35 1 117
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.064 -10000 0 -0.28 12 12
PAK1 -0.005 0.059 -10000 0 -0.7 1 1
HGF/MET/RANBP10 -0.003 0.11 -10000 0 -0.28 58 58
HRAS -0.044 0.19 -10000 0 -0.6 51 51
DOCK1 0.009 0.14 0.26 18 -0.44 19 37
GAB1 0.001 0.14 0.24 6 -0.49 18 24
CRK 0.011 0.14 0.26 22 -0.46 20 42
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.043 0.18 -10000 0 -0.53 61 61
JUN 0.019 0.022 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.025 0.08 -10000 0 -0.24 58 58
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.02 0.14 0.31 31 -0.46 10 41
GRB2/SHC 0.006 0.087 0.2 8 -0.22 49 57
FOS -0.031 0.14 -10000 0 -0.29 92 92
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.038 0.16 0.31 116 -0.35 1 117
HGF/MET/MUC20 -0.031 0.1 -10000 0 -0.24 81 81
cell migration 0.006 0.085 0.19 8 -0.22 49 57
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.021 0.1 -10000 0 -0.3 50 50
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.083 -10000 0 -0.24 52 52
MET/MUC20 -0.03 0.096 -10000 0 -0.3 50 50
RAP1B 0.016 0.14 0.29 18 -0.41 19 37
RAP1A 0.014 0.13 0.28 17 -0.4 19 36
HGF/MET/RANBP9 -0.003 0.11 -10000 0 -0.28 58 58
RAF1 -0.021 0.2 0.35 2 -0.56 51 53
STAT3 -0.005 0.09 0.22 5 -0.24 50 55
cell proliferation 0.002 0.15 0.29 16 -0.36 52 68
RPS6KB1 -0.004 0.043 -10000 0 -0.17 16 16
MAPK3 0.026 0.15 0.51 7 -10000 0 7
MAPK1 0.032 0.16 0.58 12 -10000 0 12
RANBP9 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.008 0.15 0.3 6 -0.45 26 32
SRC -0.018 0.077 0.16 1 -0.22 52 53
PI3K 0.006 0.089 0.19 9 -0.23 49 58
MET/Glomulin -0.038 0.091 -10000 0 -0.28 51 51
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 -0.02 0.19 0.33 4 -0.52 51 55
MET -0.046 0.14 -10000 0 -0.43 50 50
MAP4K1 -0.005 0.17 0.27 17 -0.49 28 45
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.013 0.19 0.33 17 -0.52 51 68
BAD 0 0.051 -10000 0 -0.7 1 1
MAP2K4 -0.006 0.15 0.29 12 -0.42 28 40
SHP2/GRB2/SOS1/GAB1 -0.005 0.13 -10000 0 -0.35 53 53
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.024 0.073 0.17 2 -0.22 55 57
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.009 0.091 -10000 0 -0.2 68 68
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.006 0.092 0.19 10 -0.22 60 70
PDPK1 -0.002 0.045 0.32 1 -0.78 1 2
HGF/MET/SHIP -0.006 0.11 -10000 0 -0.28 62 62
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.027 0.14 -10000 0 -0.41 54 54
PDGF/PDGFRA/CRKL -0.003 0.099 -10000 0 -0.29 50 50
positive regulation of JUN kinase activity 0.03 0.083 -10000 0 -0.23 45 45
CRKL 0.026 0.008 -10000 0 -0.13 1 1
PDGF/PDGFRA/Caveolin-3 -0.009 0.1 -10000 0 -0.3 52 52
AP1 -0.094 0.25 -10000 0 -0.79 54 54
mol:IP3 -0.024 0.091 -10000 0 -0.31 43 43
PLCG1 -0.024 0.091 -10000 0 -0.31 43 43
PDGF/PDGFRA/alphaV Integrin -0.003 0.1 -10000 0 -0.3 51 51
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.091 -10000 0 -0.31 43 43
CAV3 0.002 0.03 -10000 0 -0.13 14 14
CAV1 0.006 0.051 -10000 0 -0.43 2 2
SHC/Grb2/SOS1 0.032 0.084 -10000 0 -0.23 45 45
PDGF/PDGFRA/Shf -0.005 0.11 -10000 0 -0.31 51 51
FOS -0.1 0.25 0.31 2 -0.78 54 56
JUN -0.02 0.025 0.16 1 -10000 0 1
oligodendrocyte development -0.003 0.1 -10000 0 -0.29 51 51
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:DAG -0.024 0.091 -10000 0 -0.31 43 43
PDGF/PDGFRA -0.027 0.14 -10000 0 -0.41 54 54
actin cytoskeleton reorganization -0.003 0.098 -10000 0 -0.3 49 49
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
PI3K 0.02 0.087 -10000 0 -0.25 47 47
PDGF/PDGFRA/Crk/C3G 0.018 0.089 -10000 0 -0.25 50 50
JAK1 -0.021 0.087 -10000 0 -0.3 45 45
ELK1/SRF -0.011 0.08 0.15 28 -0.25 40 68
SHB 0.026 0.004 -10000 0 -10000 0 0
SHF 0.022 0.04 -10000 0 -0.43 4 4
CSNK2A1 0.029 0.018 -10000 0 -10000 0 0
GO:0007205 -0.027 0.1 0.23 6 -0.34 42 48
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.03 0.083 -10000 0 -0.23 45 45
PDGF/PDGFRA/SHB -0.003 0.099 -10000 0 -0.3 49 49
PDGF/PDGFRA/Caveolin-1 -0.005 0.084 -10000 0 -0.31 30 30
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.034 0.087 0.2 5 -0.3 42 47
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PDGF/PDGFRA/Crk -0.003 0.1 -10000 0 -0.3 50 50
JAK-STAT cascade -0.021 0.087 -10000 0 -0.3 45 45
cell proliferation -0.005 0.11 -10000 0 -0.31 51 51
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
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 -0.02 0.099 -10000 0 -0.33 31 31
IRAK/TOLLIP 0.028 0.008 -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 -0.31 102 102
IL1A -0.033 0.14 -10000 0 -0.28 97 97
IL1B -0.058 0.12 -10000 0 -0.32 77 77
IRAK/TRAF6/p62/Atypical PKCs 0.044 0.052 -10000 0 -0.2 15 15
IL1R2 -0.047 0.14 -10000 0 -0.25 129 129
IL1R1 0.006 0.077 -10000 0 -0.21 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.094 -10000 0 -0.33 27 27
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.016 0.064 -10000 0 -0.43 10 10
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.03 0.048 -10000 0 -10000 0 0
JUN -0.009 0.035 0.16 6 -0.22 9 15
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.12 -10000 0 -0.25 83 83
IL1 alpha/IL1R1/IL1RAP/MYD88 0.019 0.12 -10000 0 -0.26 66 66
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.028 0.12 -10000 0 -0.24 66 66
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.12 0.17 1 -0.26 91 92
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.042 0.17 10 -0.22 12 22
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -10000 0 -0.28 68 68
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.025 0.11 -10000 0 -0.36 30 30
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.12 0.17 1 -0.26 91 92
IL1 beta/IL1R2 -0.075 0.14 -10000 0 -0.3 115 115
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.015 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA -0.024 0.11 -10000 0 -0.24 79 79
IRAK3 0.022 0.041 -10000 0 -0.43 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.023 0.13 -10000 0 -0.26 90 90
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.099 -10000 0 -0.25 65 65
IL1 alpha/IL1R1/IL1RAP 0.009 0.12 -10000 0 -0.25 78 78
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 0.019 0.054 -10000 0 -0.36 9 9
IRAK/TRAF6/MEKK3 0.042 0.018 -10000 0 -0.22 1 1
IL1RAP 0.007 0.066 -10000 0 -0.43 7 7
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.041 0.1 -10000 0 -0.34 24 24
CASP1 0.01 0.071 -10000 0 -0.43 11 11
IL1RN/IL1R2 -0.057 0.14 -10000 0 -0.29 116 116
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.029 0.13 -10000 0 -0.26 94 94
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.1 -10000 0 -0.36 28 28
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL1RN -0.035 0.13 -10000 0 -0.24 116 116
TRAF6/TAK1/TAB1/TAB2 0.036 0.015 -10000 0 -0.21 1 1
MAP2K6 0.015 0.028 0.18 11 -0.2 2 13
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.17 0.37 1 -1.1 9 10
VDR -0.013 0.11 -10000 0 -0.26 70 70
FAM120B 0.025 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.33 90 90
RXRs/LXRs/DNA/Oxysterols -0.074 0.21 -10000 0 -0.5 85 85
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 0.023 0.041 -10000 0 -0.22 14 14
RXRs/NUR77 0.011 0.11 -10000 0 -0.25 58 58
RXRs/PPAR -0.013 0.098 -10000 0 -0.26 56 56
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.008 0.079 -10000 0 -0.18 72 72
RARs/VDR/DNA/Vit D3 0.043 0.07 -10000 0 -0.22 31 31
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.013 0.11 -10000 0 -0.26 70 70
RARs/RARs/DNA/9cRA 0.035 0.032 -10000 0 -0.22 3 3
RARG 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.028 0.12 0.58 17 -0.43 9 26
RARs/THRs/DNA/SMRT 0.022 0.041 -10000 0 -0.22 13 13
THRA 0.023 0.035 -10000 0 -0.43 3 3
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.008 0.079 -10000 0 -0.18 72 72
RXRs/PPAR/9cRA/PGJ2/DNA -0.004 0.11 -10000 0 -0.25 59 59
NR1H4 -0.043 0.13 -10000 0 -0.24 130 130
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.27 43 43
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 -0.002 0.12 -10000 0 -0.24 76 76
NR4A1 0.012 0.062 -10000 0 -0.2 32 32
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.037 0.11 -10000 0 -0.26 82 82
RXRG -0.036 0.14 -10000 0 -0.41 61 61
RXR alpha/CCPG 0.027 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 0.059 -10000 0 -0.43 7 7
PPARG 0.009 0.081 -10000 0 -0.43 16 16
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF -0.16 0.37 -10000 0 -0.96 80 80
mol:Oxysterols -0.006 0.019 -10000 0 -10000 0 0
cholesterol transport -0.073 0.21 -10000 0 -0.49 85 85
PPARA 0.026 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.035 -10000 0 -0.43 3 3
RXRs/NUR77/BCL2 -0.016 0.094 -10000 0 -0.25 59 59
SREBF1 -0.084 0.24 -10000 0 -0.85 31 31
RXRs/RXRs/DNA/9cRA -0.004 0.11 -10000 0 -0.25 59 59
ABCA1 -0.086 0.24 -10000 0 -0.82 33 33
RARs/THRs 0.067 0.05 -10000 0 -0.22 13 13
RXRs/FXR -0.011 0.14 -10000 0 -0.27 89 89
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR -0.013 0.11 -10000 0 -0.26 70 70
Cbp/p300/PCAF 0.048 0.03 -10000 0 -0.26 4 4
EP300 0.022 0.04 -10000 0 -0.43 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.072 -10000 0 -0.37 10 10
KAT2B 0.025 0.008 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.012 0.075 0.19 7 -0.36 8 15
RAR alpha/9cRA/Cyclin H -0.007 0.11 0.22 1 -0.37 10 11
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.062 0.18 1 -0.31 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.025 0.1 -10000 0 -0.22 76 76
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.008 0.079 -10000 0 -0.18 72 72
RXRs/RARs/NRIP1/9cRA -0.074 0.19 0.28 1 -0.43 83 84
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA3 0.025 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.013 0.11 -10000 0 -0.26 70 70
RARG 0.026 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.009 -10000 0 -10000 0 0
MAPK3 0.027 0.002 -10000 0 -10000 0 0
MAPK1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.015 0.069 -10000 0 -0.43 12 12
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.086 0.2 -10000 0 -0.41 113 113
RARA -0.024 0.094 -10000 0 -0.24 74 74
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.089 0.18 1 -0.34 20 21
PRKCA 0.026 0.021 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.08 0.2 0.27 1 -0.45 83 84
RXRG -0.061 0.16 -10000 0 -0.38 92 92
RXRA -0.021 0.086 -10000 0 -0.21 71 71
RXRB -0.027 0.099 -10000 0 -0.28 64 64
VDR/Vit D3/DNA -0.008 0.079 -10000 0 -0.18 72 72
RBP1 -0.006 0.081 -10000 0 -0.43 10 10
CRBP1/9-cic-RA -0.002 0.056 -10000 0 -0.27 12 12
RARB 0.024 0.035 -10000 0 -0.43 3 3
PRKCG -0.064 0.15 -10000 0 -0.25 157 157
MNAT1 0.025 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.079 0.19 -10000 0 -0.42 103 103
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.059 0.16 0.21 1 -0.37 81 82
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.094 0.21 2 -0.32 19 21
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.075 0.19 0.27 1 -0.44 82 83
positive regulation of DNA binding -0.014 0.099 -10000 0 -0.35 10 10
NRIP1 -0.066 0.18 -10000 0 -0.57 27 27
RXRs/RARs -0.075 0.2 -10000 0 -0.44 87 87
RXRs/RXRs/DNA/9cRA -0.087 0.18 -10000 0 -0.41 108 108
PRKACA 0.025 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.003 -10000 0 -10000 0 0
TFIIH 0.051 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.007 0.091 -10000 0 -0.31 8 8
CCNH 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.017 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.007 0.085 -10000 0 -0.21 51 51
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.093 0.3 5 -0.52 1 6
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.096 -10000 0 -0.3 40 40
AP1 -0.023 0.12 -10000 0 -0.4 19 19
ILK -0.015 0.081 0.19 3 -0.22 48 51
bone resorption -0.032 0.13 0.32 2 -0.36 38 40
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
PYK2/p130Cas 0.019 0.11 -10000 0 -0.25 56 56
ITGAV 0.027 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.005 0.11 -10000 0 -0.31 53 53
alphaV/beta3 Integrin/Osteopontin 0.018 0.1 -10000 0 -0.25 53 53
MAP3K1 -0.019 0.084 0.19 5 -0.22 52 57
JUN 0.019 0.022 -10000 0 -10000 0 0
MAPK3 -0.027 0.081 0.19 4 -0.24 13 17
MAPK1 -0.026 0.079 0.19 3 -0.22 24 27
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.029 0.084 0.19 4 -0.23 54 58
ITGB3 0 0.082 -10000 0 -0.18 64 64
NFKBIA -0.025 0.08 -10000 0 -0.28 12 12
FOS -0.031 0.14 -10000 0 -0.29 92 92
CD44 -0.015 0.12 -10000 0 -0.43 37 37
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU -0.044 0.18 -10000 0 -1.1 12 12
NF kappa B1 p50/RelA 0.003 0.099 -10000 0 -0.34 11 11
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.02 0.064 -10000 0 -0.3 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.026 0.1 0.19 7 -0.27 56 63
VAV3 -0.05 0.098 0.19 4 -0.25 65 69
MAP3K14 -0.02 0.084 0.19 4 -0.22 53 57
ROCK2 0.008 0.088 -10000 0 -0.43 20 20
SPP1 -0.024 0.13 -10000 0 -0.42 40 40
RAC1 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.093 0.18 3 -0.23 61 64
MMP2 -0.046 0.11 -10000 0 -0.4 23 23
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.023 0.076 0.22 66 -0.092 6 72
BUB1B -0.03 0.1 0.12 2 -0.27 71 73
PLK1 0.003 0.031 0.091 12 -0.12 9 21
PLK1S1 0.007 0.029 0.11 3 -0.18 5 8
KIF2A 0 0.039 0.21 5 -0.2 5 10
regulation of mitotic centrosome separation 0.003 0.031 0.091 12 -0.12 9 21
GOLGA2 0.025 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.034 0.14 -10000 0 -0.28 105 105
WEE1 -0.003 0.084 -10000 0 -0.35 25 25
cytokinesis -0.066 0.16 0.2 2 -0.38 100 102
PP2A-alpha B56 -0.03 0.22 -10000 0 -0.63 61 61
AURKA 0.009 0.025 0.11 1 -0.34 1 2
PICH/PLK1 -0.007 0.061 0.16 6 -0.22 24 30
CENPE -0.018 0.061 -10000 0 -0.24 28 28
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.039 0.21 5 -0.2 5 10
PPP2CA 0.026 0.003 -10000 0 -10000 0 0
FZR1 0.025 0.006 -10000 0 -10000 0 0
TPX2 -0.006 0.072 0.11 11 -0.27 32 43
PAK1 0.008 0.062 -10000 0 -0.44 5 5
SPC24 -0.044 0.14 -10000 0 -0.27 114 114
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.049 0.12 0.13 2 -0.26 118 120
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 3 -0.018 4 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.017 0.047 23 -0.06 10 33
G2 phase of mitotic cell cycle 0 0.002 0.013 3 -0.01 1 4
STAG2 0.026 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.068 -10000 0 -0.52 8 8
spindle elongation 0.003 0.031 0.091 12 -0.12 9 21
ODF2 0.026 0.005 -10000 0 -10000 0 0
BUB1 -0.051 0.23 -10000 0 -0.69 60 60
TPT1 0 0.043 -10000 0 -0.19 21 21
CDC25C -0.03 0.12 0.15 1 -0.36 59 60
CDC25B 0.026 0.006 -10000 0 -10000 0 0
SGOL1 -0.023 0.076 0.092 6 -0.22 66 72
RHOA 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.041 -10000 0 -0.2 8 8
CDC14B 0.006 0.002 -10000 0 -10000 0 0
CDC20 -0.028 0.12 -10000 0 -0.25 93 93
PLK1/PBIP1 -0.013 0.06 0.087 1 -0.22 33 34
mitosis -0.002 0.004 0.023 2 -10000 0 2
FBXO5 0 0.031 0.097 5 -0.14 6 11
CDC2 0.001 0.002 0.011 1 -0.014 1 2
NDC80 -0.056 0.16 -10000 0 -0.43 72 72
metaphase plate congression -0.024 0.089 -10000 0 -0.23 76 76
ERCC6L -0.002 0.062 0.26 1 -0.22 25 26
NLP/gamma Tubulin 0.003 0.02 0.069 8 -0.087 6 14
microtubule cytoskeleton organization 0 0.043 -10000 0 -0.19 21 21
G2/M transition DNA damage checkpoint 0 0.002 0.012 3 -10000 0 3
PPP1R12A 0.026 0.02 -10000 0 -0.43 1 1
interphase 0 0.002 0.012 3 -10000 0 3
PLK1/PRC1-2 -0.016 0.11 -10000 0 -0.22 96 96
GRASP65/GM130/RAB1/GTP/PLK1 0.037 0.035 -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 0.026 0.077 26 -0.097 6 32
mitotic prometaphase 0.002 0.007 0.018 76 -0.012 3 79
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.06 0.21 1 -0.47 2 3
microtubule-based process -0.032 0.1 0.11 3 -0.24 94 97
Golgi organization 0.003 0.031 0.091 12 -0.12 9 21
Cohesin/SA2 0.017 0.028 0.1 1 -0.12 5 6
PPP1CB/MYPT1 0.038 0.016 -10000 0 -0.31 1 1
KIF20A -0.078 0.17 -10000 0 -0.3 162 162
APC/C/CDC20 -0.004 0.074 0.12 2 -0.23 40 42
PPP2R1A 0.021 0.01 -10000 0 -10000 0 0
chromosome segregation -0.013 0.06 0.086 1 -0.22 33 34
PRC1 0.02 0.031 -10000 0 -10000 0 0
ECT2 0.001 0.038 0.22 6 -0.17 3 9
C13orf34 0.003 0.026 0.073 23 -0.097 9 32
NUDC -0.024 0.089 -10000 0 -0.23 76 76
regulation of attachment of spindle microtubules to kinetochore -0.029 0.099 0.12 2 -0.26 71 73
spindle assembly 0.002 0.027 0.081 13 -0.1 8 21
spindle stabilization 0.007 0.029 0.11 3 -0.18 5 8
APC/C/HCDH1 0.023 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 -0.032 0.1 0.11 3 -0.24 94 97
CCNB1 0.017 0.038 -10000 0 -0.13 33 33
PPP1CB 0.027 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 -0.004 0.085 -10000 0 -0.39 22 22
TUBG1 0.008 0.021 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle -0.003 0.034 -10000 0 -0.21 6 6
MLF1IP -0.018 0.076 -10000 0 -0.31 30 30
INCENP 0.024 0.021 -10000 0 -0.44 1 1
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.006 0.023 -10000 0 -0.3 1 1
MAP4K4 -0.01 0.095 -10000 0 -0.37 16 16
BAG4 0.014 0.072 -10000 0 -0.43 13 13
PKC zeta/ceramide -0.032 0.13 0.14 1 -0.29 74 75
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX -0.063 0.14 -10000 0 -0.35 93 93
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.003 0.046 0.68 2 -10000 0 2
BAD -0.036 0.12 0.19 13 -0.27 70 83
SMPD1 -0.009 0.077 0.16 7 -0.17 66 73
RB1 -0.041 0.12 0.18 1 -0.27 71 72
FADD/Caspase 8 -0.003 0.091 -10000 0 -0.38 13 13
MAP2K4 -0.041 0.11 0.23 1 -0.27 64 65
NSMAF 0.025 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.038 0.11 0.18 6 -0.27 60 66
EGF -0.01 0.11 -10000 0 -0.31 54 54
mol:ceramide -0.042 0.12 0.14 1 -0.28 73 74
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 0.007 0.023 -10000 0 -0.3 1 1
ASAH1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.12 0.18 1 -0.26 71 72
cell proliferation -0.021 0.11 -10000 0 -0.32 40 40
BID -0.006 0.11 -10000 0 -0.69 6 6
MAP3K1 -0.041 0.12 0.25 1 -0.27 70 71
EIF2A -0.041 0.11 0.34 1 -0.37 29 30
TRADD 0.025 0.02 -10000 0 -0.43 1 1
CRADD 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.029 0.093 0.17 6 -0.41 17 23
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.03 0.094 0.17 6 -0.43 16 22
Cathepsin D/ceramide -0.028 0.12 0.14 1 -0.27 71 72
FADD -0.01 0.091 -10000 0 -0.36 15 15
KSR1 -0.041 0.12 -10000 0 -0.27 70 70
MAPK8 -0.068 0.16 -10000 0 -0.4 55 55
PRKRA -0.041 0.12 0.13 1 -0.27 71 72
PDGFA 0.016 0.036 -10000 0 -0.15 19 19
TRAF2 0.026 0.005 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.042 0.12 0.14 1 -0.28 73 74
CTSD 0.025 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.037 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 -0.34 40 40
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.023 -10000 0 -0.3 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 0.003 0.087 -10000 0 -0.43 17 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.096 -10000 0 -0.34 21 21
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
mol:Sphingosine-1-phosphate 0.006 0.023 -10000 0 -0.3 1 1
MAP2K1 -0.037 0.11 0.18 6 -0.4 24 30
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
CYCS -0.033 0.084 -10000 0 -0.2 83 83
TNFRSF1A 0.017 0.054 -10000 0 -0.43 7 7
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
EIF2AK2 -0.042 0.11 0.16 3 -0.26 68 71
TNF-alpha/TNFR1A/FAN 0.008 0.11 -10000 0 -0.27 66 66
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.08 -10000 0 -0.51 6 6
MAP2K2 -0.032 0.088 0.17 7 -0.32 24 31
SMPD3 -0.02 0.1 0.19 1 -0.28 41 42
TNF -0.06 0.16 -10000 0 -0.43 68 68
PKC zeta/PAR4 0.004 0.085 -10000 0 -0.31 31 31
mol:PHOSPHOCHOLINE -0.009 0.089 0.2 33 -0.19 52 85
NF kappa B1/RelA/I kappa B alpha 0.045 0.074 -10000 0 -0.22 29 29
AIFM1 -0.044 0.095 -10000 0 -0.22 82 82
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Glypican 2 network

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
MDK -0.002 0.097 -9999 0 -0.43 22 22
GPC2 0.003 0.084 -9999 0 -0.37 22 22
GPC2/Midkine 0.002 0.091 -9999 0 -0.31 36 36
neuron projection morphogenesis 0.002 0.091 -9999 0 -0.31 36 36
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.077 -10000 0 -0.22 50 50
RGS9BP 0.017 0.046 -10000 0 -0.38 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.021 0.015 -10000 0 -10000 0 0
mol:Na + -0.019 0.088 -10000 0 -0.25 51 51
mol:ADP 0.005 0.016 -10000 0 -10000 0 0
GNAT2 0.015 0.018 -10000 0 -0.13 2 2
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.26 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.02 0.025 -10000 0 -0.13 1 1
GRK7 0.017 0.023 -10000 0 -0.13 6 6
CNGB3 0.004 0.031 -10000 0 -0.13 16 16
Cone Metarhodopsin II/X-Arrestin 0.013 0.006 -10000 0 -0.083 1 1
mol:Ca2+ -0.053 0.11 0.18 18 -0.26 91 109
Cone PDE6 0.034 0.085 -10000 0 -0.23 40 40
Cone Metarhodopsin II 0.029 0.013 -10000 0 -10000 0 0
Na + (4 Units) -0.023 0.12 -10000 0 -0.24 106 106
GNAT2/GDP 0.024 0.078 -10000 0 -0.22 40 40
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.004 0.03 0.18 8 -10000 0 8
Cone Transducin 0.009 0.083 -10000 0 -0.23 50 50
SLC24A2 -0.039 0.14 -10000 0 -0.3 100 100
GNB3/GNGT2 -0.001 0.1 -10000 0 -0.31 51 51
GNB3 -0.008 0.12 -10000 0 -0.43 35 35
GNAT2/GTP 0.014 0.01 -10000 0 -0.083 2 2
CNGA3 -0.049 0.14 -10000 0 -0.43 54 54
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.089 -10000 0 -0.26 51 51
mol:Pi 0.018 0.088 -10000 0 -0.26 41 41
Cone CNG Channel 0.009 0.082 -10000 0 -0.21 47 47
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.039 0.14 -10000 0 -0.3 100 100
RGS9 -0.012 0.12 -10000 0 -0.4 45 45
PDE6C 0.004 0.025 -10000 0 -10000 0 0
GNGT2 0.008 0.082 -10000 0 -0.43 16 16
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.005 0.035 -10000 0 -0.13 23 23
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.014 0.067 -10000 0 -0.43 11 11
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.022 0.01 -10000 0 -10000 0 0
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
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 0.007 0.11 0.18 82 -0.23 53 135
IQGAP1/CaM 0.033 0.033 -10000 0 -0.28 4 4
DAB1 -0.038 0.15 -10000 0 -0.35 80 80
IQGAP1 0.02 0.043 -10000 0 -0.43 4 4
PLA2G7 -0.005 0.11 -10000 0 -0.31 47 47
CALM1 0.025 0.009 -10000 0 -0.13 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0.001 0.1 -10000 0 -0.43 28 28
LIS1/Poliovirus Protein 3A 0.01 0.002 -10000 0 -10000 0 0
CDK5R2 -0.05 0.16 -10000 0 -0.43 77 77
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.036 0.13 -10000 0 -0.28 102 102
YWHAE 0.026 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.014 0.18 0.32 81 -0.44 28 109
MAP1B 0.005 0.012 -10000 0 -0.26 1 1
RAC1 0.011 0.016 -10000 0 -0.15 4 4
p35/CDK5 -0.021 0.092 0.18 8 -0.25 46 54
RELN -0.046 0.14 -10000 0 -0.43 58 58
PAFAH/LIS1 0.011 0.065 0.17 1 -0.26 26 27
LIS1/CLIP170 0.028 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.03 0.11 -10000 0 -0.37 27 27
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.072 0.16 -10000 0 -0.36 86 86
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.036 0.14 0.28 20 -0.44 32 52
LIS1/IQGAP1 0.025 0.029 0.17 2 -0.26 4 6
RHOA 0.012 0.016 -10000 0 -0.15 4 4
PAFAH1B1 0.013 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.01 -10000 0 -10000 0 0
PAFAH1B2 0.012 0.074 -10000 0 -0.43 14 14
MAP1B/LIS1/Dynein heavy chain 0.025 0.019 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.019 0.18 0.32 78 -0.43 27 105
LRP8 0.02 0.03 -10000 0 -0.43 2 2
NDEL1/Katanin 60 0.013 0.18 0.32 81 -0.44 28 109
P39/CDK5 -0.038 0.11 0.21 11 -0.26 72 83
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.029 0.072 0.18 9 -0.22 52 61
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.007 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.024 0.12 -10000 0 -0.24 99 99
RELN/VLDLR 0.005 0.098 -10000 0 -0.23 65 65
CDC42 0.008 0.042 -10000 0 -0.46 4 4
Noncanonical Wnt signaling pathway

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
NFATC2 -0.023 0.13 -10000 0 -0.43 45 45
GNB1/GNG2 0.02 0.097 -10000 0 -0.27 33 33
mol:DAG 0.003 0.089 0.21 13 -0.26 25 38
PLCG1 0.003 0.091 0.21 13 -0.27 25 38
YES1 -0.014 0.082 -10000 0 -0.27 41 41
FZD3 0.023 0.035 -10000 0 -0.43 3 3
FZD6 0.014 0.041 -10000 0 -0.14 29 29
G protein 0.025 0.1 0.26 3 -0.27 26 29
MAP3K7 -0.047 0.1 0.21 15 -0.28 33 48
mol:Ca2+ 0.003 0.088 0.21 13 -0.26 25 38
mol:IP3 0.003 0.089 0.21 13 -0.26 25 38
NLK 0.01 0.044 -10000 0 -0.95 1 1
GNB1 0.022 0.01 -10000 0 -10000 0 0
CAMK2A -0.048 0.11 0.21 13 -0.27 48 61
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.008 0.087 -10000 0 -0.27 44 44
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
GNAS -0.013 0.08 0.16 2 -0.26 41 43
GO:0007205 -0.005 0.088 0.21 13 -0.27 25 38
WNT6 0.003 0.087 -10000 0 -0.25 43 43
WNT4 0.008 0.057 -10000 0 -0.17 35 35
NFAT1/CK1 alpha -0.002 0.12 0.33 3 -0.32 27 30
GNG2 0.022 0.04 -10000 0 -0.43 4 4
WNT5A 0.01 0.079 -10000 0 -0.43 15 15
WNT11 0.009 0.075 -10000 0 -0.27 27 27
CDC42 0.001 0.064 -10000 0 -0.27 14 14
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.008 0.087 -9999 0 -0.27 44 44
FZD6 0.014 0.041 -9999 0 -0.14 29 29
WNT6 0.003 0.087 -9999 0 -0.25 43 43
WNT4 0.008 0.057 -9999 0 -0.17 35 35
FZD3 0.023 0.035 -9999 0 -0.43 3 3
WNT5A 0.01 0.079 -9999 0 -0.43 15 15
WNT11 0.009 0.075 -9999 0 -0.27 27 27
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.061 0.25 -10000 0 -0.85 38 38
NCK1/PAK1/Dok-R -0.056 0.12 -10000 0 -0.4 41 41
NCK1/Dok-R -0.057 0.29 -10000 0 -1 36 36
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
mol:beta2-estradiol 0.011 0.058 0.23 31 -10000 0 31
RELA 0.025 0.005 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
F2 0.012 0.064 0.25 27 -0.14 4 31
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.03 0.27 -10000 0 -0.96 36 36
FN1 0.021 0.029 -10000 0 -0.13 18 18
PLD2 -0.065 0.28 -10000 0 -1.1 36 36
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 -0.071 0.16 -10000 0 -0.43 70 70
ELK1 -0.057 0.26 -10000 0 -0.95 36 36
GRB7 0.002 0.043 -10000 0 -0.13 40 40
PAK1 0.008 0.061 -10000 0 -0.16 47 47
Tie2/Ang1/alpha5/beta1 Integrin -0.036 0.28 -10000 0 -1 36 36
CDKN1A -0.072 0.25 -10000 0 -0.66 68 68
ITGA5 0.017 0.042 -10000 0 -0.16 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.057 0.28 -10000 0 -1 36 36
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:NO -0.012 0.21 0.35 1 -0.6 38 39
PLG -0.068 0.28 -10000 0 -1.1 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.053 0.24 -10000 0 -0.81 37 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ANGPT2 -0.068 0.25 -10000 0 -1 25 25
BMX -0.073 0.28 -10000 0 -1.1 36 36
ANGPT1 -0.083 0.31 -10000 0 -1.2 32 32
tube development -0.065 0.23 -10000 0 -0.66 54 54
ANGPT4 -0.008 0.1 -10000 0 -0.41 27 27
response to hypoxia -0.006 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.086 0.31 -10000 0 -1.2 36 36
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
FGF2 0.024 0.03 -10000 0 -0.33 3 3
STAT5A (dimer) -0.076 0.28 -10000 0 -0.74 65 65
mol:L-citrulline -0.012 0.21 0.35 1 -0.6 38 39
AGTR1 0 0.092 -10000 0 -0.43 20 20
MAPK14 -0.06 0.28 -10000 0 -1 37 37
Tie2/SHP2 -0.02 0.2 -10000 0 -1.1 14 14
TEK -0.022 0.21 -10000 0 -1.2 14 14
RPS6KB1 -0.049 0.24 -10000 0 -0.81 37 37
Angiotensin II/AT1 0.001 0.066 -10000 0 -0.29 21 21
Tie2/Ang1/GRB2 -0.056 0.3 -10000 0 -1.1 36 36
MAPK3 -0.062 0.26 -10000 0 -0.98 36 36
MAPK1 -0.061 0.26 -10000 0 -0.97 36 36
Tie2/Ang1/GRB7 -0.06 0.3 -10000 0 -1.1 36 36
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.068 0.29 -10000 0 -1.1 36 36
PI3K -0.064 0.28 -10000 0 -0.97 37 37
FES -0.063 0.29 -10000 0 -1 37 37
Crk/Dok-R -0.057 0.28 -10000 0 -1 36 36
Tie2/Ang1/ABIN2 -0.056 0.3 -10000 0 -1.1 36 36
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.053 0.23 -10000 0 -0.76 38 38
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.039 0.25 -10000 0 -0.81 37 37
Tie2/Ang2 -0.091 0.31 -10000 0 -0.92 52 52
Tie2/Ang1 -0.066 0.31 -10000 0 -1.1 36 36
FOXO1 -0.061 0.24 -10000 0 -0.72 54 54
ELF1 0.026 0.022 -10000 0 -0.12 4 4
ELF2 -0.061 0.28 -10000 0 -1 36 36
mol:Choline -0.062 0.27 -10000 0 -1 36 36
cell migration -0.029 0.067 -10000 0 -0.23 39 39
FYN -0.076 0.26 -10000 0 -0.76 54 54
DOK2 -0.017 0.11 -10000 0 -0.25 77 77
negative regulation of cell cycle -0.063 0.22 -10000 0 -0.59 68 68
ETS1 0.004 0.08 -10000 0 -0.27 34 34
PXN -0.024 0.22 0.4 3 -0.67 37 40
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
NOS3 -0.021 0.23 -10000 0 -0.69 38 38
RAC1 0.023 0.009 -10000 0 -10000 0 0
TNF -0.074 0.17 -10000 0 -0.41 90 90
MAPKKK cascade -0.062 0.27 -10000 0 -1 36 36
RASA1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.058 0.3 -10000 0 -1.1 36 36
NCK1 0.025 0.02 -10000 0 -0.43 1 1
vasculogenesis -0.006 0.19 0.34 2 -0.54 39 41
mol:Phosphatidic acid -0.062 0.27 -10000 0 -1 36 36
mol:Angiotensin II -0.001 0.006 -10000 0 -10000 0 0
mol:NADP -0.012 0.21 0.35 1 -0.6 38 39
Rac1/GTP -0.045 0.22 -10000 0 -0.75 37 37
MMP2 -0.07 0.28 -10000 0 -1.1 36 36
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.034 0.1 -10000 0 -0.23 61 61
SMAD6-7/SMURF1 0.039 0.03 -10000 0 -0.26 2 2
NOG -0.028 0.14 -10000 0 -0.39 66 66
SMAD9 -0.047 0.18 -10000 0 -0.49 60 60
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.022 0.11 0.19 1 -0.39 22 23
BMP7/USAG1 -0.009 0.093 -10000 0 -0.3 37 37
SMAD5/SKI -0.013 0.11 -10000 0 -0.36 26 26
SMAD1 0.019 0.05 -10000 0 -0.36 3 3
BMP2 -0.033 0.15 -10000 0 -0.43 65 65
SMAD1/SMAD1/SMAD4 0.022 0.053 -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 26 26
BMPR1A-1B/BAMBI 0.031 0.069 -10000 0 -0.26 25 25
AHSG -0.029 0.14 -10000 0 -0.31 80 80
CER1 -0.001 0.032 -10000 0 -0.13 19 19
BMP2-4/CER1 -0.005 0.13 -10000 0 -0.31 68 68
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.13 -10000 0 -0.43 33 33
BMP2-4 (homodimer) -0.017 0.14 -10000 0 -0.36 68 68
RGMB 0.02 0.047 -10000 0 -0.3 9 9
BMP6/BMPR2/BMPR1A-1B 0.044 0.074 -10000 0 -0.24 29 29
RGMA 0.016 0.066 -10000 0 -0.4 12 12
SMURF1 0.021 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.025 0.12 -10000 0 -0.39 38 38
BMP2-4/USAG1 -0.01 0.13 -10000 0 -0.3 81 81
SMAD6/SMURF1/SMAD5 -0.011 0.1 -10000 0 -0.38 20 20
SOSTDC1 -0.028 0.12 -10000 0 -0.23 102 102
BMP7/BMPR2/BMPR1A-1B 0.043 0.073 -10000 0 -0.23 30 30
SKI 0.022 0.01 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.054 -10000 0 -0.43 6 6
HFE2 0.012 0.025 -10000 0 -0.13 7 7
ZFYVE16 0.026 0.003 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0 0.13 -10000 0 -0.3 71 71
SMAD5/SMAD5/SMAD4 -0.015 0.11 -10000 0 -0.36 26 26
MAPK1 0.026 0.003 -10000 0 -10000 0 0
TAK1/TAB family -0.011 0.1 -10000 0 -0.36 24 24
BMP7 (homodimer) 0.02 0.049 -10000 0 -0.43 6 6
NUP214 0.025 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.008 0.11 -10000 0 -0.32 52 52
SMAD1/SKI 0.025 0.057 -10000 0 -0.37 3 3
SMAD6 0.022 0.041 -10000 0 -0.33 6 6
CTDSP2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.023 0.15 -10000 0 -0.32 100 100
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.077 0.17 -10000 0 -0.3 161 161
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.023 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.02 0.074 -10000 0 -0.3 25 25
CHRDL1 -0.037 0.15 -10000 0 -0.43 65 65
ENDOFIN/SMAD1 0.029 0.06 0.3 1 -0.37 3 4
SMAD6-7/SMURF1/SMAD1 0.036 0.065 -10000 0 -0.35 4 4
SMAD6/SMURF1 0.021 0.011 -10000 0 -10000 0 0
BAMBI 0.022 0.019 -10000 0 -0.13 6 6
SMURF2 0.023 0.035 -10000 0 -0.43 3 3
BMP2-4/CHRDL1 -0.035 0.16 -10000 0 -0.3 124 124
BMP2-4/GREM1 -0.052 0.17 -10000 0 -0.3 150 150
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.18 -10000 0 -0.47 61 61
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 0.049 -10000 0 -0.43 6 6
BMP6 0.017 0.054 -10000 0 -0.43 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.028 0.11 -10000 0 -0.35 37 37
PPM1A 0.025 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.028 0.061 0.3 1 -0.36 3 4
SMAD7/SMURF1 0.03 0.017 -10000 0 -10000 0 0
CTDSPL 0.025 0.02 -10000 0 -0.43 1 1
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.019 0.021 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 -10000 0 -0.41 47 47
CHRD 0.021 0.045 -10000 0 -0.43 5 5
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.13 -10000 0 -0.42 38 38
BMP4 0.007 0.089 -10000 0 -0.4 22 22
FST -0.016 0.12 -10000 0 -0.27 71 71
BMP2-4/NOG -0.023 0.17 -10000 0 -0.39 82 82
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.044 0.07 -10000 0 -0.22 25 25
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.025 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.047 0.025 -10000 0 -0.26 2 2
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
PRNP 0.025 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.016 0.11 -10000 0 -0.3 56 56
SMAD2 0.018 0.032 0.18 14 -0.23 1 15
GPC1/PrPc/Cu2+ 0.032 0.013 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.001 0.1 -10000 0 -0.3 51 51
TDGF1 -0.029 0.14 -10000 0 -0.34 75 75
CRIPTO/GPC1 -0.005 0.11 -10000 0 -0.31 54 54
APP/GPC1 0.036 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.019 0.088 -10000 0 -0.27 54 54
FLT1 0.024 0.021 -10000 0 -0.43 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.022 -10000 0 -0.2 2 2
SERPINC1 0.015 0.028 -10000 0 -0.13 13 13
FYN -0.016 0.083 -10000 0 -0.26 51 51
FGR -0.014 0.077 -10000 0 -0.26 43 43
positive regulation of MAPKKK cascade -0.051 0.15 0.34 4 -0.39 55 59
SLIT2 -0.045 0.14 -10000 0 -0.43 56 56
GPC1/NRG -0.044 0.13 -10000 0 -0.3 99 99
NRG1 -0.08 0.18 -10000 0 -0.43 98 98
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.018 -10000 0 -10000 0 0
LYN -0.02 0.087 -10000 0 -0.26 54 54
mol:Spermine 0.006 0.008 -10000 0 -10000 0 0
cell growth 0.047 0.025 -10000 0 -0.26 2 2
BMP signaling pathway -0.024 0.015 -10000 0 -10000 0 0
SRC -0.015 0.081 -10000 0 -0.26 48 48
TGFBR1 0.024 0.022 -10000 0 -0.28 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.032 0.087 -10000 0 -0.19 84 84
GPC1 0.024 0.015 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.024 0.022 -10000 0 -0.28 2 2
VEGFA 0.019 0.032 -10000 0 -10000 0 0
BLK -0.048 0.11 -10000 0 -0.28 76 76
HCK -0.021 0.092 -10000 0 -0.28 53 53
FGF2 0.024 0.029 -10000 0 -0.33 3 3
FGFR1 0.025 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
TGFBR2 0.024 0.016 -10000 0 -0.13 5 5
cell death 0.036 0.014 -10000 0 -10000 0 0
ATIII/GPC1 0.032 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 0 0.07 -10000 0 -0.28 20 20
LCK -0.037 0.1 -10000 0 -0.28 70 70
neuron differentiation -0.043 0.13 -10000 0 -0.3 99 99
PrPc/Cu2+ 0.019 0.004 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.016 -10000 0 -0.13 5 5
Calcium 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
NFATC1 -0.009 0.057 -10000 0 -0.25 22 22
NFATC2 -0.022 0.075 -10000 0 -0.26 40 40
NFATC3 0.002 0.023 -10000 0 -0.14 1 1
CD40LG -0.073 0.14 0.31 3 -0.38 51 54
PTGS2 -0.094 0.18 0.36 1 -0.46 74 75
JUNB 0.006 0.072 -10000 0 -0.43 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.018 -10000 0 -0.086 2 2
CaM/Ca2+ 0.011 0.018 -10000 0 -0.086 2 2
CALM1 0.021 0.016 -10000 0 -0.13 1 1
JUN 0.016 0.025 -10000 0 -10000 0 0
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 -0.25 98 98
CREM 0.023 0.022 -10000 0 -0.28 2 2
Jun/NFAT1-c-4/p21SNFT -0.029 0.12 -10000 0 -0.36 32 32
FOS -0.035 0.14 -10000 0 -0.32 77 77
IFNG -0.072 0.14 0.28 2 -0.38 49 51
AP-1/NFAT1-c-4 -0.056 0.17 -10000 0 -0.42 50 50
FASLG -0.073 0.14 0.36 1 -0.38 50 51
NFAT1-c-4/ICER1 -0.024 0.097 -10000 0 -0.25 54 54
IL2RA -0.073 0.15 0.31 3 -0.39 56 59
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.072 0.14 0.33 2 -0.38 46 48
JunB/Fra1/NFAT1-c-4 -0.038 0.13 0.2 2 -0.33 47 49
IL4 -0.071 0.14 0.33 2 -0.38 46 48
IL2 -0.011 0.14 -10000 0 -0.93 12 12
IL3 0.01 0.06 -10000 0 -0.64 4 4
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
BATF3 0 0.091 -10000 0 -0.43 19 19
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.004 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.002 0.094 0.32 37 -10000 0 37
KIRREL -0.008 0.12 -10000 0 -0.42 39 39
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.002 0.095 -10000 0 -0.32 37 37
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 0.03 0.08 -10000 0 -0.24 37 37
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.069 -10000 0 -0.25 31 31
FYN -0.009 0.075 0.18 23 -0.23 38 61
mol:Ca2+ 0.027 0.079 -10000 0 -0.24 38 38
mol:DAG 0.028 0.08 -10000 0 -0.24 38 38
NPHS2 0.001 0.033 -10000 0 -0.28 2 2
mol:IP3 0.028 0.08 -10000 0 -0.24 38 38
regulation of endocytosis 0.024 0.072 -10000 0 -0.21 38 38
Nephrin/NEPH1/podocin/Cholesterol 0.017 0.075 -10000 0 -0.24 38 38
establishment of cell polarity -0.002 0.094 -10000 0 -0.32 37 37
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.081 -10000 0 -0.22 37 37
Nephrin/NEPH1/beta Arrestin2 0.025 0.073 -10000 0 -0.22 38 38
NPHS1 -0.001 0.053 -10000 0 -0.15 39 39
Nephrin/NEPH1/podocin 0.018 0.073 -10000 0 -0.23 38 38
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -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 0.028 0.081 -10000 0 -0.24 38 38
CD2AP 0.026 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.028 0.08 -10000 0 -0.24 37 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.086 0.19 25 -0.23 45 70
cytoskeleton organization -0.017 0.082 0.2 12 -0.27 31 43
Nephrin/NEPH1 0.01 0.066 -10000 0 -0.22 37 37
Nephrin/NEPH1/ZO-1 0.022 0.081 -10000 0 -0.25 37 37
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.018 0.1 -10000 0 -0.26 52 52
MAP4K1 0.013 0.061 -10000 0 -0.43 9 9
MAP3K8 0.016 0.047 -10000 0 -0.2 18 18
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
DBNL 0.023 0.009 -10000 0 -10000 0 0
CRKL 0.026 0.008 -10000 0 -0.13 1 1
MAP3K1 -0.007 0.082 0.17 1 -0.35 11 12
JUN -0.024 0.17 -10000 0 -0.57 41 41
MAP3K7 -0.007 0.082 -10000 0 -0.27 24 24
GRAP2 -0.006 0.1 -10000 0 -0.26 57 57
CRK 0.026 0.002 -10000 0 -10000 0 0
MAP2K4 -0.002 0.091 0.26 4 -0.35 12 16
LAT 0.003 0.1 -10000 0 -0.43 26 26
LCP2 0.02 0.033 -10000 0 -0.15 15 15
MAPK8 -0.022 0.18 -10000 0 -0.6 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.002 0.088 -10000 0 -0.28 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.097 -10000 0 -0.24 47 47
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.009 0.095 0.22 65 -10000 0 65
GNAI2 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.015 0.093 -10000 0 -0.26 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
RhoA/GTP -0.009 0.097 -10000 0 -0.23 65 65
negative regulation of cAMP metabolic process -0.018 0.099 -10000 0 -0.24 65 65
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNA12 0.022 0.009 -10000 0 -10000 0 0
S1PR5 -0.052 0.16 -10000 0 -0.3 122 122
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.018 0.1 -10000 0 -0.25 65 65
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
Ephrin B reverse 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
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EPHB2 0.017 0.04 -10000 0 -0.36 4 4
EFNB1 -0.022 0.081 -10000 0 -0.31 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.093 -10000 0 -0.25 45 45
Ephrin B2/EPHB1-2 0.016 0.081 -10000 0 -0.25 40 40
neuron projection morphogenesis -0.008 0.084 -10000 0 -0.24 45 45
Ephrin B1/EPHB1-2/Tiam1 -0.007 0.1 -10000 0 -0.26 60 60
DNM1 -0.026 0.12 -10000 0 -0.22 105 105
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.01 0.086 0.21 2 -0.51 13 15
YES1 -0.005 0.13 -10000 0 -0.77 13 13
Ephrin B1/EPHB1-2/NCK2 -0.007 0.11 -10000 0 -0.26 61 61
PI3K 0.027 0.091 -10000 0 -0.52 13 13
mol:GDP -0.008 0.1 -10000 0 -0.26 60 60
ITGA2B -0.013 0.12 -10000 0 -0.37 50 50
endothelial cell proliferation 0.025 0.022 -10000 0 -0.26 1 1
FYN -0.003 0.12 -10000 0 -0.75 13 13
MAP3K7 -0.01 0.089 0.22 1 -0.54 13 14
FGR -0.008 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 -0.012 0.11 -10000 0 -0.4 21 21
LYN -0.003 0.12 -10000 0 -0.75 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.11 -10000 0 -0.69 13 13
Ephrin B1/EPHB1-2 -0.01 0.096 -10000 0 -0.58 13 13
SRC -0.004 0.12 -10000 0 -0.74 13 13
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
EPHB1 -0.008 0.12 -10000 0 -0.43 38 38
EPHB4 0.021 0.011 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
alphaIIb/beta3 Integrin -0.011 0.11 -10000 0 -0.31 53 53
BLK -0.01 0.13 -10000 0 -0.74 13 13
HCK -0.004 0.13 -10000 0 -0.76 13 13
regulation of stress fiber formation 0.008 0.1 0.26 61 -10000 0 61
MAPK8 -0.014 0.09 0.2 1 -0.5 13 14
Ephrin B1/EPHB1-2/RGS3 -0.007 0.11 -10000 0 -0.26 61 61
endothelial cell migration 0.026 0.11 0.2 82 -0.41 13 95
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTPN13 0.023 0.053 -10000 0 -0.56 4 4
regulation of focal adhesion formation 0.008 0.1 0.26 61 -10000 0 61
chemotaxis 0.008 0.1 0.26 61 -10000 0 61
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.003 0.089 -10000 0 -0.24 45 45
angiogenesis -0.009 0.095 -10000 0 -0.58 13 13
LCK -0.019 0.13 -10000 0 -0.76 13 13
Canonical Wnt signaling pathway

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
HDAC1 0.024 0.024 0.19 4 -10000 0 4
AES 0.026 0.019 0.17 3 -10000 0 3
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
SMAD4 0.026 0.004 -10000 0 -10000 0 0
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
TLE1 0.025 0.035 0.18 4 -0.43 2 6
MACF1 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.044 0.099 0.29 26 -0.31 4 30
WIF1 -0.13 0.18 -10000 0 -0.27 265 265
beta catenin/RanBP3 0.016 0.1 0.4 27 -0.3 1 28
KREMEN2 -0.007 0.1 -10000 0 -0.25 58 58
DKK1 -0.035 0.13 -10000 0 -0.24 113 113
beta catenin/beta TrCP1 0.052 0.097 0.29 24 -0.28 4 28
FZD1 0.021 0.01 -10000 0 -10000 0 0
AXIN2 0.003 0.16 0.58 18 -0.89 5 23
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 0.021 0.076 -10000 0 -0.53 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.065 0.09 0.3 15 -0.58 3 18
Axin1/APC/GSK3 0.03 0.073 0.26 10 -0.29 1 11
Axin1/APC/GSK3/beta catenin/Macf1 0.042 0.075 0.26 9 -0.42 2 11
HNF1A 0.027 0.029 0.19 4 -0.43 1 5
CTBP1 0.027 0.022 0.19 4 -10000 0 4
MYC 0.01 0.35 0.55 62 -1.5 20 82
RANBP3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.009 0.11 -10000 0 -0.27 68 68
NKD1 0.016 0.059 -10000 0 -0.43 8 8
TCF4 0.026 0.027 0.18 4 -0.38 1 5
TCF3 0.025 0.032 0.18 3 -0.37 2 5
WNT1/LRP6/FZD1/Axin1 0.052 0.03 -10000 0 -10000 0 0
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.13 0.5 29 -0.36 1 30
LEF1 0.026 0.026 0.18 3 -10000 0 3
DVL1 0.027 0.037 -10000 0 -0.26 1 1
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.061 0.11 0.3 16 -0.73 3 19
DKK1/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.25 71 71
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.028 0.022 0.19 4 -10000 0 4
NLK 0.024 0.013 -10000 0 -0.16 1 1
CCND1 -0.021 0.26 0.56 19 -1.5 12 31
WNT1 0.008 0.042 -10000 0 -0.13 39 39
GSK3A 0.022 0.01 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.28 4 4
PPP2R5D 0.027 0.055 0.28 8 -0.24 3 11
APC 0.037 0.08 0.19 99 -10000 0 99
WNT1/LRP6/FZD1 0.042 0.08 0.2 75 -0.21 1 76
CREBBP 0.028 0.021 0.19 4 -10000 0 4
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.008 0.085 -10000 0 -0.22 57 57
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.058 0.11 -10000 0 -0.3 79 79
GNB1/GNG2 0.027 0.029 -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 -0.011 0.078 -10000 0 -0.23 59 59
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 0.008 0.02 0.063 59 -10000 0 59
GNAL -0.026 0.14 -10000 0 -0.42 59 59
GNG2 0.022 0.04 -10000 0 -0.43 4 4
CRH -0.075 0.16 -10000 0 -0.27 166 166
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.046 -10000 0 -0.3 12 12
MAPK11 0.002 0.038 -10000 0 -0.3 8 8
Glucocorticoid receptor regulatory network

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
PCK2 0.046 0.091 -10000 0 -0.84 3 3
SMARCC2 0.025 0.016 -10000 0 -10000 0 0
SMARCC1 0.024 0.016 -10000 0 -10000 0 0
TBX21 -0.067 0.18 -10000 0 -0.64 34 34
SUMO2 0.023 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.032 -10000 0 -0.16 10 10
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 -0.038 0.15 -10000 0 -0.43 62 62
GR alpha/HSP90/FKBP51/HSP90 0.049 0.12 0.27 16 -0.24 43 59
PRL -0.033 0.067 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.11 0.19 0.48 53 -0.35 1 54
RELA -0.03 0.091 -10000 0 -0.26 21 21
FGG 0.089 0.14 0.4 43 -10000 0 43
GR beta/TIF2 0.055 0.12 0.27 31 -0.3 31 62
IFNG -0.13 0.18 -10000 0 -0.54 39 39
apoptosis 0.015 0.17 0.58 18 -0.53 6 24
CREB1 0.026 0.009 -10000 0 -10000 0 0
histone acetylation -0.047 0.1 0.23 1 -0.33 34 35
BGLAP -0.039 0.097 -10000 0 -0.78 2 2
GR/PKAc 0.075 0.068 0.28 11 -10000 0 11
NF kappa B1 p50/RelA -0.048 0.15 -10000 0 -0.31 96 96
SMARCD1 0.025 0.016 -10000 0 -10000 0 0
MDM2 0.046 0.063 0.2 44 -10000 0 44
GATA3 -0.032 0.14 -10000 0 -0.42 49 49
AKT1 0.022 0.013 0.18 3 -10000 0 3
CSF2 -0.055 0.084 -10000 0 -0.43 1 1
GSK3B 0.022 0.026 -10000 0 -0.43 1 1
NR1I3 0.021 0.17 0.57 17 -0.62 3 20
CSN2 0.072 0.12 0.35 29 -10000 0 29
BRG1/BAF155/BAF170/BAF60A 0.06 0.047 -10000 0 -0.22 11 11
NFATC1 0.004 0.095 -10000 0 -0.43 23 23
POU2F1 0.026 0.005 -10000 0 -10000 0 0
CDKN1A -0.047 0.29 -10000 0 -1.4 21 21
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.01 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.43 28 28
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.032 0.12 0.28 9 -0.25 38 47
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.04 0.27 0.54 16 -0.77 53 69
JUN -0.076 0.13 0.27 2 -0.38 40 42
IL4 -0.061 0.12 -10000 0 -0.53 12 12
CDK5R1 0.001 0.1 -10000 0 -0.43 28 28
PRKACA 0.025 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.092 0.1 -10000 0 -0.31 55 55
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.05 0.11 0.28 10 -0.22 31 41
cortisol/GR alpha (monomer) 0.14 0.2 0.55 54 -10000 0 54
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.07 0.14 -10000 0 -0.41 61 61
AP-1/NFAT1-c-4 -0.16 0.23 -10000 0 -0.51 121 121
AFP -0.075 0.12 -10000 0 -0.54 1 1
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.083 0.096 0.39 12 -10000 0 12
TP53 0.002 0.13 -10000 0 -0.47 33 33
PPP5C 0.022 0.01 -10000 0 -10000 0 0
KRT17 -0.27 0.42 -10000 0 -1.1 99 99
KRT14 -0.056 0.086 -10000 0 -10000 0 0
TBP 0.03 0.016 -10000 0 -0.29 1 1
CREBBP 0.025 0.044 -10000 0 -0.24 13 13
HDAC1 0.02 0.009 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
AP-1 -0.16 0.23 -10000 0 -0.51 121 121
MAPK14 0.024 0.015 -10000 0 -10000 0 0
MAPK10 0.021 0.038 -10000 0 -0.43 3 3
MAPK11 0.016 0.058 -10000 0 -0.43 8 8
KRT5 -0.24 0.39 -10000 0 -1 87 87
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.027 0.01 -10000 0 -10000 0 0
STAT1 0.024 0.032 -10000 0 -0.16 10 10
CGA -0.047 0.085 -10000 0 -0.35 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.044 0.091 0.31 9 -0.36 5 14
MAPK3 0.024 0.016 -10000 0 -10000 0 0
MAPK1 0.024 0.015 -10000 0 -10000 0 0
ICAM1 -0.098 0.2 -10000 0 -0.63 35 35
NFKB1 -0.03 0.089 -10000 0 -0.24 26 26
MAPK8 -0.077 0.12 0.31 1 -0.34 53 54
MAPK9 0.023 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.012 0.18 0.58 18 -0.56 6 24
BAX -0.025 0.12 -10000 0 -0.44 8 8
POMC -0.085 0.22 -10000 0 -1.5 9 9
EP300 0.021 0.06 -10000 0 -0.29 17 17
cortisol/GR alpha (dimer)/p53 0.12 0.18 0.49 46 -0.46 1 47
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.053 0.19 20 -10000 0 20
SGK1 0.004 0.23 -10000 0 -1.4 13 13
IL13 -0.13 0.19 -10000 0 -0.6 32 32
IL6 -0.13 0.28 -10000 0 -0.95 45 45
PRKACG 0.01 0.024 -10000 0 -10000 0 0
IL5 -0.099 0.15 -10000 0 -0.63 10 10
IL2 -0.13 0.18 -10000 0 -0.57 27 27
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 -0.19 0.35 -10000 0 -0.91 85 85
CDK5R1/CDK5 0.015 0.069 -10000 0 -0.3 21 21
NF kappa B1 p50/RelA/PKAc -0.006 0.12 -10000 0 -0.32 19 19
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.12 0.16 0.47 45 -10000 0 45
SMARCA4 0.024 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.078 0.12 0.33 38 -0.36 7 45
NF kappa B1 p50/RelA/Cbp -0.012 0.15 -10000 0 -0.38 32 32
JUN (dimer) -0.076 0.13 0.27 2 -0.38 40 42
YWHAH 0.019 0.033 -10000 0 -0.13 23 23
VIPR1 -0.072 0.18 -10000 0 -0.67 35 35
NR3C1 0.081 0.12 0.35 45 -10000 0 45
NR4A1 0.008 0.087 -10000 0 -0.45 15 15
TIF2/SUV420H1 0.014 0.083 -10000 0 -0.3 32 32
MAPKKK cascade 0.015 0.17 0.58 18 -0.53 6 24
cortisol/GR alpha (dimer)/Src-1 0.14 0.17 0.48 55 -10000 0 55
PBX1 0.025 0.021 -10000 0 -0.43 1 1
POU1F1 0 0.022 -10000 0 -10000 0 0
SELE -0.14 0.28 -10000 0 -0.9 48 48
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.078 0.12 0.33 37 -0.36 7 44
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.12 0.16 0.47 45 -10000 0 45
mol:cortisol 0.065 0.11 0.32 51 -10000 0 51
MMP1 -0.04 0.09 -10000 0 -0.94 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.084 -10000 0 -0.28 40 40
CRKL 0.026 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.007 0.1 -10000 0 -0.26 60 60
alpha4/beta7 Integrin/MAdCAM1 0.011 0.12 -10000 0 -0.26 78 78
EPO 0.013 0.03 -10000 0 -0.17 7 7
alpha4/beta7 Integrin -0.004 0.1 -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 0.012 0.076 -10000 0 -0.29 25 25
EPO/EPOR (dimer) 0.027 0.025 -10000 0 -0.3 1 1
lamellipodium assembly 0.014 0.035 -10000 0 -0.26 3 3
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.007 0.05 -10000 0 -0.22 21 21
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
MADCAM1 -0.033 0.13 -10000 0 -0.43 41 41
cell adhesion 0.009 0.12 -10000 0 -0.25 78 78
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
SRC -0.023 0.099 0.18 29 -0.24 66 95
ITGB7 0.002 0.091 -10000 0 -0.43 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.009 0.11 -10000 0 -0.26 74 74
p130Cas/Crk/Dock1 -0.006 0.099 0.2 26 -0.21 68 94
VCAM1 -0.033 0.13 -10000 0 -0.3 84 84
RHOA 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.046 0.065 -10000 0 -0.23 22 22
BCAR1 -0.034 0.092 0.19 28 -0.23 66 94
EPOR 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.036 -10000 0 -0.27 3 3
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.14 -10000 0 -0.42 55 55
KLHL20 0.011 0.071 0.16 7 -0.22 6 13
CYFIP2 0.022 0.037 -10000 0 -0.43 3 3
Rac1/GDP -0.004 0.095 0.26 4 -0.26 48 52
ENAH -0.032 0.15 -10000 0 -0.42 59 59
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 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.004 0.066 -10000 0 -0.24 1 1
ABI1/Sra1/Nap1 -0.014 0.036 -10000 0 -0.15 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.021 0.12 -10000 0 -0.26 70 70
RAPGEF1 -0.02 0.14 0.24 5 -0.37 55 60
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.028 0.15 -10000 0 -0.43 62 62
CRK -0.031 0.14 0.22 1 -0.4 56 57
E-cadherin/gamma catenin/alpha catenin 0.014 0.1 -10000 0 -0.26 63 63
alphaE/beta7 Integrin 0.019 0.069 -10000 0 -0.3 19 19
IQGAP1 0.02 0.043 -10000 0 -0.43 4 4
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
DLG1 -0.031 0.14 -10000 0 -0.42 60 60
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.045 -10000 0 -0.18 1 1
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.012 -10000 0 -10000 0 0
PI3K -0.015 0.058 -10000 0 -0.23 1 1
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.021 0.12 -10000 0 -0.31 63 63
TIAM1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.029 0.089 -10000 0 -0.22 55 55
AKT1 -0.003 0.043 0.12 2 -0.14 1 3
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
RhoA/GDP 0.004 0.1 0.25 8 -0.26 52 60
actin cytoskeleton organization 0.014 0.06 0.16 19 -0.16 6 25
CDC42/GDP 0 0.1 0.26 5 -0.25 52 57
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.078 -10000 0 -0.22 60 60
ITGB7 0.002 0.091 -10000 0 -0.43 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.031 0.095 -10000 0 -0.23 55 55
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.086 -10000 0 -0.22 59 59
mol:GDP -0.012 0.11 0.26 9 -0.3 52 61
CDC42/GTP/IQGAP1 0.027 0.028 -10000 0 -0.23 4 4
JUP 0.02 0.049 -10000 0 -0.43 6 6
p120 catenin/RhoA/GDP 0.008 0.1 0.26 6 -0.26 51 57
RAC1/GTP/IQGAP1 0.027 0.03 -10000 0 -0.26 4 4
PIP5K1C/AP1M1 0.037 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.052 0.14 21 -0.17 15 36
NME1 0.026 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.032 0.15 -10000 0 -0.42 61 61
regulation of cell-cell adhesion -0.009 0.055 -10000 0 -0.21 1 1
WASF2 0.009 0.029 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.082 0.24 2 -0.26 1 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.12 -10000 0 -0.25 74 74
CCND1 0.012 0.061 0.16 17 -0.21 15 32
VAV2 -0.013 0.15 -10000 0 -0.56 8 8
RAP1/GDP 0.007 0.091 0.27 4 -0.25 7 11
adherens junction assembly -0.03 0.14 -10000 0 -0.41 61 61
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.023 0.008 -10000 0 -10000 0 0
PIP5K1C 0.025 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.016 0.11 -10000 0 -0.24 71 71
E-cadherin/beta catenin -0.029 0.1 -10000 0 -0.32 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.032 0.14 -10000 0 -0.42 59 59
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.017 0.084 -10000 0 -0.34 7 7
E-cadherin/beta catenin/alpha catenin 0.016 0.1 -10000 0 -0.26 59 59
ITGAE 0.026 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.029 0.16 -10000 0 -0.44 62 62
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 0.018 0.048 -10000 0 -0.43 4 4
HSPA8 0.023 0.023 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.017 0.092 0.21 3 -0.28 18 21
AKT1 0.015 0.035 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 67 67
NKX2-5 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.062 0.17 0.37 95 -10000 0 95
SMAD2-3/SMAD4/SP1 0.02 0.12 -10000 0 -0.29 27 27
SMAD4 -0.009 0.07 -10000 0 -0.23 13 13
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.031 0.078 -10000 0 -0.26 22 22
SMAD3/SMAD4/VDR 0.038 0.11 -10000 0 -0.25 33 33
MYC 0.009 0.085 -10000 0 -0.41 19 19
CDKN2B -0.19 0.49 -10000 0 -1.5 59 59
AP1 0 0.092 -10000 0 -0.29 19 19
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.004 0.083 -10000 0 -0.31 18 18
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.038 0.14 -10000 0 -0.37 62 62
SP3 0.027 0.01 -10000 0 -10000 0 0
CREB1 0.026 0.002 -10000 0 -10000 0 0
FOXH1 -0.003 0.076 -10000 0 -0.24 27 27
SMAD3/SMAD4/GR 0.038 0.084 -10000 0 -0.24 6 6
GATA3 -0.053 0.15 -10000 0 -0.4 62 62
SKI/SIN3/HDAC complex/NCoR1 0.012 0.062 -10000 0 -0.3 15 15
MEF2C/TIF2 -0.02 0.13 0.31 3 -0.33 30 33
endothelial cell migration 0.16 0.46 1.3 71 -10000 0 71
MAX 0.032 0.019 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
RUNX2 0.016 0.058 -10000 0 -0.43 7 7
RUNX3 -0.001 0.091 -10000 0 -0.3 36 36
RUNX1 -0.007 0.1 -10000 0 -0.24 62 62
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.033 0.019 -10000 0 -10000 0 0
VDR -0.013 0.11 -10000 0 -0.26 70 70
CDKN1A -0.044 0.26 -10000 0 -1.3 21 21
KAT2B 0.021 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.01 0.13 -10000 0 -0.3 70 70
DCP1A 0.026 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 71 71
SMAD3/SMAD4/ATF2 0.019 0.086 -10000 0 -0.26 16 16
SMAD3/SMAD4/ATF3 0.015 0.091 -10000 0 -0.29 14 14
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.06 0.2 5 -0.26 4 9
JUN -0.014 0.082 -10000 0 -0.29 17 17
SMAD3/SMAD4/IRF7 0.019 0.084 -10000 0 -0.29 9 9
TFE3 0.014 0.035 -10000 0 -10000 0 0
COL1A2 0.003 0.1 -10000 0 -0.87 6 6
mesenchymal cell differentiation -0.02 0.087 0.28 14 -10000 0 14
DLX1 -0.066 0.16 -10000 0 -0.28 157 157
TCF3 0.023 0.029 -10000 0 -0.43 2 2
FOS -0.03 0.14 -10000 0 -0.39 57 57
SMAD3/SMAD4/Max 0.038 0.084 0.21 1 -0.24 7 8
Cbp/p300/SNIP1 0.036 0.043 -10000 0 -0.26 4 4
ZBTB17 0.023 0.014 -10000 0 -10000 0 0
LAMC1 -0.01 0.061 -10000 0 -0.41 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.083 -10000 0 -0.31 9 9
IRF7 0.016 0.052 -10000 0 -0.35 7 7
ESR1 0.009 0.071 -10000 0 -0.41 12 12
HNF4A -0.007 0.041 -10000 0 -0.13 40 40
MEF2C -0.01 0.12 0.32 3 -0.32 31 34
SMAD2-3/SMAD4 0.008 0.1 -10000 0 -0.26 23 23
Cbp/p300/Src-1 0.043 0.049 -10000 0 -0.26 4 4
IGHV3OR16-13 0.001 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.02 0.045 -10000 0 -0.43 5 5
CREBBP 0.021 0.023 -10000 0 -10000 0 0
SKIL 0.021 0.049 -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 -0.26 5 5
MSG1/HSC70 0.016 0.07 -10000 0 -0.3 19 19
SMAD2 0 0.059 -10000 0 -0.18 11 11
SMAD3 0.006 0.056 -10000 0 -0.21 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.061 -10000 0 -0.25 15 15
SMAD2/SMAD2/SMAD4 -0.005 0.044 0.18 1 -0.22 2 3
NCOR1 0.024 0.029 -10000 0 -0.43 2 2
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA1 0.026 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.044 0.13 -10000 0 -0.3 90 90
SMAD2-3/SMAD4/SP1/MIZ-1 0.019 0.12 -10000 0 -0.29 28 28
IFNB1 -0.01 0.06 -10000 0 -0.32 4 4
SMAD3/SMAD4/MEF2C 0.005 0.13 -10000 0 -0.33 31 31
CITED1 0 0.091 -10000 0 -0.24 51 51
SMAD2-3/SMAD4/ARC105 0.023 0.1 -10000 0 -0.26 15 15
RBL1 0.011 0.079 -10000 0 -0.41 17 17
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.05 0.19 -10000 0 -0.55 58 58
RUNX1-3/PEBPB2 0.02 0.087 -10000 0 -0.24 48 48
SMAD7 -0.017 0.11 -10000 0 -0.39 18 18
MYC/MIZ-1 0.02 0.066 0.18 6 -0.29 17 23
SMAD3/SMAD4 -0.024 0.18 0.28 37 -0.44 64 101
IL10 -0.063 0.19 0.25 3 -0.5 63 66
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 0.049 -10000 0 -0.44 4 4
IL5 -0.039 0.13 0.23 3 -0.36 38 41
CDK4 0.021 0.024 -10000 0 -10000 0 0
PIAS4 0.022 0.023 -10000 0 -10000 0 0
ATF3 0.006 0.071 -10000 0 -0.43 9 9
SMAD3/SMAD4/SP1 0.023 0.099 -10000 0 -0.26 19 19
FOXG1 0 0.1 -10000 0 -0.42 30 30
FOXO3 0.002 0.037 -10000 0 -10000 0 0
FOXO1 0.001 0.038 -10000 0 -0.3 1 1
FOXO4 0.001 0.041 -10000 0 -0.39 1 1
heart looping -0.01 0.12 0.32 3 -0.32 31 34
CEBPB 0.007 0.076 -10000 0 -0.44 13 13
SMAD3/SMAD4/DLX1 -0.026 0.14 -10000 0 -0.28 86 86
MYOD1 -0.089 0.17 -10000 0 -0.43 94 94
SMAD3/SMAD4/HNF4 0.021 0.079 -10000 0 -0.23 12 12
SMAD3/SMAD4/GATA3 -0.025 0.15 -10000 0 -0.32 83 83
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.049 -10000 0 -0.43 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.11 -10000 0 -0.25 40 40
SMAD3/SMAD4/SP1-3 0.042 0.097 -10000 0 -0.28 11 11
MED15 0.026 0.004 -10000 0 -10000 0 0
SP1 0.013 0.039 -10000 0 -0.14 7 7
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 -0.005 0.12 -10000 0 -0.27 71 71
ITGB5 -0.007 0.08 -10000 0 -0.44 7 7
TGIF/SIN3/HDAC complex/CtBP 0.011 0.075 -10000 0 -0.46 10 10
SMAD3/SMAD4/AR -0.02 0.13 -10000 0 -0.29 77 77
AR -0.049 0.16 -10000 0 -0.33 107 107
negative regulation of cell growth -0.003 0.094 -10000 0 -0.38 18 18
SMAD3/SMAD4/MYOD -0.036 0.14 -10000 0 -0.29 100 100
E2F5 0.023 0.029 -10000 0 -0.43 2 2
E2F4 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.25 45 45
SMAD2-3/SMAD4/FOXO1-3a-4 -0.029 0.14 -10000 0 -0.4 54 54
TFDP1 0.025 0.021 -10000 0 -0.43 1 1
SMAD3/SMAD4/AP1 0.021 0.1 -10000 0 -0.29 19 19
SMAD3/SMAD4/RUNX2 0.021 0.087 -10000 0 -0.28 14 14
TGIF2 0.021 0.045 -10000 0 -0.43 5 5
TGIF1 0.016 0.06 -10000 0 -0.43 8 8
ATF2 0.016 0.069 -10000 0 -0.43 12 12
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.053 0.2 30 -0.2 2 32
RFC1 0 0.038 0.18 18 -0.2 2 20
PRKDC 0.008 0.054 0.2 35 -0.2 2 37
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CASP7 -0.016 0.14 -10000 0 -0.57 29 29
FASLG/FAS/FADD/FAF1 0.004 0.054 0.19 15 -0.26 8 23
MAP2K4 -0.027 0.11 0.22 1 -0.32 40 41
mol:ceramide 0.003 0.068 -10000 0 -0.26 19 19
GSN -0.001 0.062 0.2 26 -0.3 9 35
FASLG/FAS/FADD/FAF1/Caspase 8 0.005 0.055 0.17 1 -0.24 10 11
FAS 0.011 0.064 -10000 0 -0.28 18 18
BID -0.01 0.052 0.26 17 -10000 0 17
MAP3K1 -0.024 0.11 0.22 1 -0.35 33 34
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
RB1 0.001 0.039 0.18 19 -0.2 2 21
CFLAR 0.026 0.008 -10000 0 -0.13 1 1
HGF/MET -0.005 0.12 -10000 0 -0.24 84 84
ARHGDIB 0.006 0.052 0.2 32 -0.22 1 33
FADD 0.022 0.014 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.067 0.24 19 -0.19 26 45
NFKB1 -0.011 0.12 -10000 0 -0.74 11 11
MAPK8 -0.044 0.15 -10000 0 -0.47 42 42
DFFA 0 0.034 0.17 16 -0.2 2 18
DNA fragmentation during apoptosis -0.003 0.045 0.18 17 -0.18 12 29
FAS/FADD/MET -0.003 0.1 -10000 0 -0.26 55 55
CFLAR/RIP1 0.039 0.009 -10000 0 -10000 0 0
FAIM3 0.004 0.088 -10000 0 -0.43 18 18
FAF1 0.019 0.016 -10000 0 -10000 0 0
PARP1 0.001 0.039 0.18 19 -0.2 2 21
DFFB 0 0.034 0.17 16 -0.2 2 18
CHUK -0.011 0.12 -10000 0 -0.7 11 11
FASLG 0.007 0.041 -10000 0 -0.13 33 33
FAS/FADD 0.024 0.049 -10000 0 -0.31 8 8
HGF -0.009 0.091 -10000 0 -0.2 68 68
LMNA -0.001 0.047 0.2 12 -0.21 1 13
CASP6 0.001 0.042 0.18 20 -0.22 3 23
CASP10 0.022 0.015 -10000 0 -0.13 1 1
CASP3 0.003 0.046 0.22 18 -0.22 2 20
PTPN13 0.022 0.041 -10000 0 -0.37 5 5
CASP8 -0.01 0.066 0.34 17 -10000 0 17
IL6 -0.096 0.36 -10000 0 -1.3 42 42
MET -0.046 0.14 -10000 0 -0.43 50 50
ICAD/CAD 0.001 0.044 0.2 19 -0.21 1 20
FASLG/FAS/FADD/FAF1/Caspase 10 0.003 0.069 -10000 0 -0.26 19 19
activation of caspase activity by cytochrome c -0.01 0.052 0.26 17 -10000 0 17
PAK2 0.002 0.042 0.19 22 -0.22 1 23
BCL2 0.021 0.045 -10000 0 -0.43 5 5
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.006 0.088 -10000 0 -0.26 47 47
cell-cell adhesion 0.02 0.05 0.22 24 -10000 0 24
Ephrin B/EPHB2/RasGAP 0.054 0.058 -10000 0 -0.24 12 12
ITSN1 0.026 0.003 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Ephrin B1/EPHB3 0.033 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.013 0.076 -10000 0 -0.26 37 37
HRAS/GDP 0.018 0.064 -10000 0 -0.27 10 10
Ephrin B/EPHB1/GRB7 0.043 0.097 -10000 0 -0.26 44 44
Endophilin/SYNJ1 0.012 0.056 0.18 26 -0.23 11 37
KRAS 0.025 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.046 0.088 -10000 0 -0.24 37 37
endothelial cell migration 0.042 0.028 -10000 0 -0.22 1 1
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.002 0.043 -10000 0 -0.13 40 40
PAK1 -0.012 0.065 0.19 21 -0.23 14 35
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS 0.009 0.055 0.18 24 -0.23 11 35
DNM1 -0.026 0.12 -10000 0 -0.22 106 106
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.005 0.08 0.19 17 -0.23 44 61
lamellipodium assembly -0.02 0.05 -10000 0 -0.22 24 24
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.074 -10000 0 -0.24 30 30
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPHB2 0.017 0.04 -10000 0 -0.43 3 3
EPHB3 0.025 0.01 -10000 0 -0.13 2 2
EPHB1 -0.008 0.12 -10000 0 -0.43 38 38
EPHB4 0.021 0.011 -10000 0 -10000 0 0
mol:GDP -0.002 0.057 0.23 3 -0.3 7 10
Ephrin B/EPHB2 0.042 0.054 -10000 0 -0.24 13 13
Ephrin B/EPHB3 0.052 0.045 -10000 0 -0.23 11 11
JNK cascade -0.003 0.078 0.22 15 -0.23 39 54
Ephrin B/EPHB1 0.032 0.089 -10000 0 -0.24 44 44
RAP1/GDP 0.044 0.095 0.23 64 -0.28 8 72
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EFNB3 0.016 0.064 -10000 0 -0.34 14 14
EFNB1 0.025 0.012 -10000 0 -0.13 3 3
Ephrin B2/EPHB1-2 0.017 0.082 -10000 0 -0.25 40 40
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.077 -10000 0 -0.32 11 11
Rap1/GTP -0.001 0.073 -10000 0 -0.29 12 12
axon guidance -0.006 0.087 -10000 0 -0.26 47 47
MAPK3 0.002 0.066 0.19 1 -0.29 8 9
MAPK1 0.002 0.065 0.19 1 -0.28 9 10
Rac1/GDP 0.024 0.084 0.23 41 -0.28 8 49
actin cytoskeleton reorganization -0.004 0.047 -10000 0 -0.27 7 7
CDC42/GDP 0.04 0.098 0.23 71 -0.28 8 79
PI3K 0.046 0.03 -10000 0 -0.22 1 1
EFNA5 -0.027 0.13 -10000 0 -0.29 86 86
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.013 0.045 -10000 0 -0.29 8 8
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.069 -10000 0 -0.22 42 42
PTK2 0.054 0.16 0.54 52 -10000 0 52
MAP4K4 -0.003 0.079 0.22 15 -0.23 39 54
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.02 0.038 -10000 0 -0.17 16 16
Intersectin/N-WASP 0.03 0.017 -10000 0 -10000 0 0
neuron projection morphogenesis 0.032 0.12 0.3 69 -0.34 4 73
MAP2K1 0.006 0.068 -10000 0 -0.29 10 10
WASL 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.031 0.086 -10000 0 -0.25 39 39
cell migration 0.004 0.087 0.3 2 -0.35 9 11
NRAS 0.021 0.01 -10000 0 -10000 0 0
SYNJ1 0.012 0.056 0.18 26 -0.23 11 37
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.022 0.075 0.17 20 -0.24 33 53
HRAS/GTP 0.016 0.081 -10000 0 -0.23 43 43
Ephrin B1/EPHB1-2 0.019 0.079 -10000 0 -0.25 38 38
cell adhesion mediated by integrin 0.003 0.048 0.21 11 -0.19 16 27
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0.02 0.087 -10000 0 -0.24 44 44
RAC1-CDC42/GTP -0.004 0.058 -10000 0 -0.3 8 8
RASA1 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.08 0.23 35 -0.27 8 43
ruffle organization 0.039 0.13 0.34 52 -0.35 5 57
NCK1 0.025 0.02 -10000 0 -0.43 1 1
receptor internalization -0.024 0.075 0.17 20 -0.24 30 50
Ephrin B/EPHB2/KALRN 0.053 0.061 -10000 0 -0.24 14 14
ROCK1 0.02 0.031 0.18 17 -10000 0 17
RAS family/GDP -0.007 0.044 -10000 0 -0.28 7 7
Rac1/GTP -0.001 0.058 -10000 0 -0.24 24 24
Ephrin B/EPHB1/Src/Paxillin 0.006 0.074 -10000 0 -0.24 38 38
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.007 0.2 0.51 3 -0.7 10 13
CRP -0.015 0.2 0.59 5 -0.69 12 17
cell cycle arrest -0.019 0.22 0.52 2 -0.76 16 18
TIMP1 -0.012 0.2 0.47 1 -0.77 11 12
IL6ST -0.009 0.11 -10000 0 -0.42 34 34
Rac1/GDP -0.05 0.16 -10000 0 -0.42 58 58
AP1 0.033 0.1 -10000 0 -0.58 2 2
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.016 0.19 0.52 1 -0.68 12 13
HSP90B1 0.012 0.17 -10000 0 -0.91 14 14
GAB1 0.025 0.021 -10000 0 -0.43 1 1
MAPK14 -0.072 0.19 -10000 0 -0.54 54 54
AKT1 0.035 0.049 -10000 0 -0.7 1 1
FOXO1 0.035 0.051 -10000 0 -0.66 1 1
MAP2K6 -0.058 0.16 0.2 1 -0.44 56 57
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.048 0.16 0.29 3 -0.44 49 52
MITF -0.05 0.15 -10000 0 -0.41 53 53
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.006 -10000 0 -10000 0 0
A2M 0.017 0.082 -10000 0 -1.2 2 2
CEBPB 0.017 0.074 -10000 0 -0.43 13 13
GRB2/SOS1/GAB family/SHP2 0.008 0.081 -10000 0 -0.43 6 6
STAT3 -0.025 0.23 0.52 2 -0.82 16 18
STAT1 0.017 0.045 -10000 0 -0.9 1 1
CEBPD -0.043 0.3 0.52 2 -1 32 34
PIK3CA 0.026 0.02 -10000 0 -0.43 1 1
PI3K 0.04 0.007 -10000 0 -10000 0 0
JUN 0.019 0.022 -10000 0 -10000 0 0
PIAS3/MITF -0.031 0.16 -10000 0 -0.43 42 42
MAPK11 -0.075 0.19 -10000 0 -0.55 53 53
STAT3 (dimer)/FOXO1 -0.006 0.16 -10000 0 -0.57 14 14
GRB2/SOS1/GAB family -0.012 0.15 -10000 0 -0.43 32 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.045 0.15 -10000 0 -0.41 53 53
GRB2 0.025 0.006 -10000 0 -10000 0 0
JAK2 0.025 0.006 -10000 0 -10000 0 0
LBP 0.003 0.19 0.45 6 -0.64 15 21
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.016 -10000 0 -10000 0 0
MYC -0.019 0.28 0.52 2 -0.91 29 31
FGG -0.018 0.19 0.49 2 -0.67 13 15
macrophage differentiation -0.019 0.22 0.52 2 -0.76 16 18
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.12 -10000 0 -0.27 61 61
JUNB -0.019 0.23 0.49 3 -0.91 15 18
FOS -0.031 0.14 -10000 0 -0.29 92 92
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.05 0.16 0.23 1 -0.42 56 57
STAT1/PIAS1 -0.021 0.16 0.24 1 -0.44 36 37
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.049 -10000 0 -0.36 5 5
STAT3 (dimer) -0.022 0.23 0.52 2 -0.8 16 18
PRKCD -0.025 0.23 0.42 25 -0.55 46 71
IL6R 0.005 0.082 -10000 0 -0.34 23 23
SOCS3 -0.093 0.3 0.39 2 -1.1 37 39
gp130 (dimer)/JAK1/JAK1/LMO4 0.019 0.078 -10000 0 -0.24 33 33
Rac1/GTP -0.049 0.16 -10000 0 -0.43 57 57
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAPKKK cascade 0.032 0.08 0.3 1 -0.96 1 2
bone resorption -0.014 0.19 0.48 2 -0.65 12 14
IRF1 -0.014 0.19 0.51 2 -0.68 12 14
mol:GDP -0.057 0.16 0.2 1 -0.42 62 63
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.058 0.16 0.2 1 -0.43 62 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.25 -10000 0 -0.61 65 65
PTPN11 0.009 0.079 -10000 0 -0.69 6 6
IL6/IL6RA -0.023 0.11 -10000 0 -0.32 50 50
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.075 -10000 0 -0.25 31 31
gp130 (dimer)/JAK2/JAK2/LMO4 0.019 0.076 -10000 0 -0.25 32 32
IL6 -0.037 0.12 -10000 0 -0.43 37 37
PIAS3 0.024 0.008 -10000 0 -10000 0 0
PTPRE 0.023 0.024 -10000 0 -0.43 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.12 0.21 1 -0.31 64 65
LMO4 0.018 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.025 0.21 -10000 0 -0.75 16 16
MCL1 0.039 0.057 -10000 0 -0.62 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.14 -10000 0 -0.55 26 26
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 0.019 0.053 -10000 0 -0.39 8 8
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
TLE1 0.024 0.029 -10000 0 -0.43 2 2
AP1 -0.027 0.091 -10000 0 -0.26 53 53
NCSTN 0.026 0.004 -10000 0 -10000 0 0
ADAM10 0.015 0.069 -10000 0 -0.43 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.066 -10000 0 -10000 0 0
NICD/RBPSUH 0.016 0.12 -10000 0 -0.49 26 26
WIF1 -0.13 0.18 -10000 0 -0.27 265 265
NOTCH1 -0.001 0.12 -10000 0 -0.52 26 26
PSENEN 0.022 0.01 -10000 0 -10000 0 0
KREMEN2 -0.007 0.1 -10000 0 -0.43 23 23
DKK1 -0.035 0.13 -10000 0 -0.24 113 113
beta catenin/beta TrCP1 0.011 0.072 0.28 6 -0.31 2 8
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
AXIN1 0.007 0.049 0.34 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.019 0.049 0.29 4 -0.26 3 7
PSEN1 0.025 0.005 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.29 92 92
JUN 0.019 0.022 -10000 0 -10000 0 0
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.002 0.072 0.29 7 -0.33 2 9
MAPK3 0.026 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.009 0.11 -10000 0 -0.27 68 68
HNF1A 0.025 0.021 -10000 0 -0.43 1 1
CTBP1 0.026 0.006 -10000 0 -10000 0 0
MYC -0.031 0.28 -10000 0 -1.4 20 20
NKD1 0.016 0.059 -10000 0 -0.43 8 8
FZD1 0.021 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.013 0.12 -10000 0 -0.5 26 26
apoptosis -0.027 0.09 -10000 0 -0.26 53 53
Delta 1/NOTCHprecursor -0.001 0.14 -10000 0 -0.55 26 26
DLL1 -0.009 0.12 -10000 0 -0.43 38 38
PPARD 0.022 0.058 -10000 0 -1.1 1 1
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
APC 0.003 0.069 0.34 1 -0.47 4 5
DVL1 -0.013 0.07 -10000 0 -0.26 31 31
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 -0.25 71 71
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
NLK 0.014 0.011 -10000 0 -10000 0 0
CCND1 -0.011 0.22 -10000 0 -1.4 13 13
WNT1 0.005 0.043 -10000 0 -0.13 39 39
Axin1/APC/beta catenin 0.004 0.094 0.3 6 -0.42 3 9
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
NOTCH1 precursor/DVL1 -0.019 0.14 -10000 0 -0.53 24 24
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.28 4 4
NOTCH/Deltex homolog 1 0.015 0.13 -10000 0 -0.51 26 26
PPP2R5D 0.01 0.051 0.25 8 -0.3 3 11
MAPK1 0.026 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.013 0.12 -10000 0 -0.24 95 95
RBPJ 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.021 0.14 -10000 0 -0.41 54 54
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.017 0.12 -10000 0 -0.4 46 46
AKT 0.039 0.11 0.26 49 -0.22 11 60
FOXO3 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
AKT3 0.022 0.04 -10000 0 -0.43 4 4
FOXO4 0.025 0.02 -10000 0 -0.43 1 1
MET -0.046 0.14 -10000 0 -0.43 50 50
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
PIK3CG -0.01 0.1 -10000 0 -0.27 53 53
PIK3R3 0.02 0.024 -10000 0 -0.23 3 3
PIK3R2 0.025 0.005 -10000 0 -10000 0 0
NF1 0.025 0.02 -10000 0 -0.43 1 1
RAS -0.008 0.07 0.16 3 -0.15 72 75
ERBB2 0.023 0.027 -10000 0 -0.43 1 1
proliferation/survival/translation -0.025 0.081 0.33 14 -0.23 11 25
PI3K 0.021 0.11 0.25 61 -0.14 65 126
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
FOXO 0.062 0.087 0.22 78 -10000 0 78
AKT2 0.022 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.026 0.008 -10000 0 -0.13 1 1
RAS family/GTP/Tiam1 0.011 0.032 -10000 0 -0.26 2 2
NT3 (dimer)/TRKC 0.028 0.033 -10000 0 -0.34 2 2
NT3 (dimer)/TRKB 0.011 0.097 -10000 0 -0.26 54 54
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.026 -10000 0 -0.48 1 1
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.18 88 88
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
NTRK1 0.015 0.058 -10000 0 -0.43 7 7
NTRK2 0.006 0.092 -10000 0 -0.43 22 22
NTRK3 0.022 0.04 -10000 0 -0.43 4 4
NT-4/5 (dimer)/TRKB 0.005 0.093 -10000 0 -0.26 46 46
neuron apoptosis 0.058 0.15 0.36 76 -10000 0 76
SHC 2-3/Grb2 -0.063 0.16 -10000 0 -0.39 76 76
SHC1 0.024 0.014 -10000 0 -0.13 4 4
SHC2 -0.029 0.099 -10000 0 -0.39 14 14
SHC3 -0.099 0.2 -10000 0 -0.5 89 89
STAT3 (dimer) 0.02 0.057 -10000 0 -0.33 12 12
NT3 (dimer)/TRKA 0.018 0.088 -10000 0 -0.25 46 46
RIN/GDP -0.004 0.081 0.23 6 -0.3 2 8
GIPC1 0.025 0.009 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
DNAJA3 -0.047 0.099 -10000 0 -0.26 76 76
RIN/GTP -0.072 0.13 -10000 0 -0.3 118 118
CCND1 0.001 0.11 -10000 0 -0.7 12 12
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 0.032 -10000 0 -0.43 1 1
SHC/GRB2/SOS1 0.05 0.014 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.015 0.12 -10000 0 -0.28 85 85
TRKA/NEDD4-2 0.024 0.056 -10000 0 -0.31 11 11
ELMO1 0.017 0.049 -10000 0 -0.43 6 6
RhoG/GTP/ELMO1/DOCK1 0.024 0.038 -10000 0 -0.25 8 8
NGF -0.026 0.13 -10000 0 -0.34 64 64
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
GAB2 0.025 0.005 -10000 0 -10000 0 0
RIT2 -0.1 0.19 -10000 0 -0.43 118 118
RIT1 0.026 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
DNM1 -0.026 0.12 -10000 0 -0.22 106 106
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 -0.032 0.1 -10000 0 -0.25 70 70
mol:GDP 0.03 0.073 0.28 7 -0.62 1 8
NGF (dimer) -0.026 0.13 -10000 0 -0.34 64 64
RhoG/GDP 0.013 0.035 -10000 0 -0.3 6 6
RIT1/GDP 0.027 0.053 0.2 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 0.03 0.083 -10000 0 -0.26 36 36
KIDINS220/CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 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 0.032 -10000 0 -0.13 17 17
RAP1/GDP 0.023 0.04 -10000 0 -0.31 1 1
KIDINS220/CRKL 0.025 0.008 -10000 0 -0.13 1 1
BDNF (dimer) -0.01 0.089 -10000 0 -0.18 88 88
ubiquitin-dependent protein catabolic process 0.005 0.099 -10000 0 -0.26 56 56
Schwann cell development -0.014 0.019 -10000 0 -10000 0 0
EHD4 0.024 0.018 -10000 0 -0.13 7 7
FRS2 family/GRB2/SOS1 0.063 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 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 0.016 0.069 -10000 0 -0.22 27 27
ABL1 0.025 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.009 0.089 -10000 0 -0.32 9 9
STAT3 0.02 0.057 -10000 0 -0.33 12 12
axon guidance -0.003 0.064 -10000 0 -0.22 27 27
MAPK3 -0.038 0.11 0.18 11 -0.26 79 90
MAPK1 -0.037 0.11 0.18 11 -0.26 78 89
CDC42/GDP 0.032 0.052 0.22 6 -0.37 1 7
NTF3 0.006 0.032 -10000 0 -0.13 17 17
NTF4 -0.003 0.032 -10000 0 -0.43 1 1
NGF (dimer)/TRKA/FAIM 0.007 0.097 -10000 0 -0.26 56 56
PI3K 0.038 0.007 -10000 0 -10000 0 0
FRS3 0.026 0.002 -10000 0 -10000 0 0
FAIM 0.022 0.04 -10000 0 -0.43 4 4
GAB1 0.025 0.021 -10000 0 -0.43 1 1
RASGRF1 -0.07 0.12 -10000 0 -0.26 120 120
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L 0.002 0.028 -10000 0 -0.28 3 3
RGS19 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.069 -10000 0 -0.61 2 2
Rac1/GDP 0.025 0.053 0.22 5 -0.36 1 6
NGF (dimer)/TRKA/GRIT -0.009 0.089 -10000 0 -0.25 54 54
neuron projection morphogenesis -0.03 0.12 0.35 1 -0.53 7 8
NGF (dimer)/TRKA/NEDD4-2 0.005 0.099 -10000 0 -0.26 56 56
MAP2K1 0.024 0.05 0.2 35 -0.23 1 36
NGFR -0.016 0.12 -10000 0 -0.43 34 34
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.096 -10000 0 -0.24 73 73
RAS family/GTP/PI3K 0.019 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.072 0.022 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.009 -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 0.007 0.076 -10000 0 -0.31 23 23
MAPKKK cascade -0.12 0.23 -10000 0 -0.47 137 137
RASA1 0.026 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.045 -10000 0 -0.3 7 7
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.043 0.075 -10000 0 -0.25 27 27
NGF (dimer)/TRKA/p62/Atypical PKCs 0.021 0.1 -10000 0 -0.24 59 59
MATK -0.027 0.13 -10000 0 -0.43 46 46
NEDD4L 0.02 0.044 -10000 0 -0.43 4 4
RAS family/GDP -0.006 0.02 -10000 0 -0.28 1 1
NGF (dimer)/TRKA -0.036 0.1 -10000 0 -0.27 76 76
Rac1/GTP -0.04 0.077 -10000 0 -0.25 27 27
FRS2 family/SHP2/CRK family 0.074 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.026 0.004 -9999 0 -10000 0 0
SVIL 0.015 0.042 -9999 0 -0.16 23 23
ZNF318 0.026 0.003 -9999 0 -10000 0 0
JMJD2C 0 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.021 0.11 -9999 0 -0.26 78 78
CARM1 0.025 0.006 -9999 0 -10000 0 0
PRDX1 0.012 0.066 -9999 0 -0.43 11 11
PELP1 0.026 0.002 -9999 0 -10000 0 0
CTNNB1 0.026 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 22 22
MED1 0.026 0.003 -9999 0 -10000 0 0
MAK 0.008 0.062 -9999 0 -0.43 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.011 0.069 -9999 0 -0.43 12 12
GSN 0.017 0.061 -9999 0 -0.37 11 11
NCOA2 -0.005 0.11 -9999 0 -0.43 34 34
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 10 10
XRCC5 0.026 0.003 -9999 0 -10000 0 0
UBE3A 0.026 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.031 0.12 -9999 0 -0.27 92 92
FHL2 -0.02 0.16 -9999 0 -0.98 12 12
RANBP9 0.026 0.003 -9999 0 -10000 0 0
JMJD1A -0.009 0.038 -9999 0 -0.13 42 42
CDK6 0.004 0.083 -9999 0 -0.35 23 23
TGFB1I1 0.022 0.039 -9999 0 -0.43 3 3
T-DHT/AR/CyclinD1 -0.029 0.12 -9999 0 -0.27 88 88
XRCC6 0.026 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.026 0.12 -9999 0 -0.25 107 107
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
BRCA1 0.025 0.012 -9999 0 -10000 0 0
TCF4 0.025 0.02 -9999 0 -0.43 1 1
CDKN2A -0.013 0.11 -9999 0 -0.43 31 31
SRF 0.024 0.027 -9999 0 -0.13 12 12
NKX3-1 -0.036 0.077 -9999 0 -0.17 105 105
KLK3 0.003 0.046 -9999 0 -10000 0 0
TMF1 0.025 0.02 -9999 0 -0.43 1 1
HNRNPA1 0.026 0.004 -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 -0.024 0.11 -9999 0 -0.26 80 80
AR -0.057 0.16 -9999 0 -0.34 108 108
UBA3 0.026 0.004 -9999 0 -10000 0 0
PATZ1 0.026 0.004 -9999 0 -10000 0 0
PAWR 0.003 0.087 -9999 0 -0.43 17 17
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 -0.22 88 88
RPS6KA3 0.025 0.02 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.022 0.11 -9999 0 -0.26 79 79
LATS2 0.018 0.046 -9999 0 -0.21 15 15
T-DHT/AR/PRX1 -0.023 0.1 -9999 0 -0.24 86 86
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -0.083 1 1
VAV3 -0.03 0.11 -9999 0 -0.2 114 114
KLK2 -0.044 0.12 -9999 0 -0.43 36 36
CASP8 0.021 0.033 -9999 0 -0.43 1 1
T-DHT/AR/TIF2/CARM1 -0.017 0.13 -9999 0 -0.27 87 87
TMPRSS2 -0.083 0.25 -9999 0 -0.89 43 43
CCND1 0.011 0.073 -9999 0 -0.43 12 12
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
mol:T-DHT -0.006 0.019 -9999 0 -0.065 41 41
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.025 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.029 0.12 -9999 0 -0.28 81 81
CMTM2 0.013 0.073 -9999 0 -0.33 19 19
SNURF 0.011 0.08 -9999 0 -0.4 18 18
ZMIZ1 0.016 0.029 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -0.13 1 1
TGIF1 0.016 0.06 -9999 0 -0.43 8 8
FKBP4 0.024 0.007 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.015 0.048 0.16 1 -0.25 13 14
EPHB2 0.017 0.04 -10000 0 -0.43 3 3
Syndecan-2/TACI 0.012 0.046 -10000 0 -0.26 13 13
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
Syndecan-2/alpha2 ITGB1 0.021 0.093 0.18 1 -0.26 43 44
HRAS 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.041 -10000 0 -0.25 13 13
ITGA5 0.017 0.042 -10000 0 -0.16 24 24
BAX 0 0.036 -10000 0 -10000 0 0
EPB41 0.021 0.023 -10000 0 -0.28 2 2
positive regulation of cell-cell adhesion 0.016 0.04 -10000 0 -0.22 13 13
LAMA3 -0.004 0.1 -10000 0 -0.29 49 49
EZR 0.017 0.06 -10000 0 -0.43 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.041 -10000 0 -0.16 20 20
Syndecan-2/MMP2 0.009 0.06 -10000 0 -0.25 23 23
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.069 -10000 0 -0.3 19 19
dendrite morphogenesis 0.011 0.049 -10000 0 -0.24 16 16
Syndecan-2/GM-CSF 0.011 0.045 -10000 0 -0.26 13 13
determination of left/right symmetry 0.002 0.049 -10000 0 -0.3 13 13
Syndecan-2/PKC delta 0.004 0.081 -10000 0 -0.29 32 32
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.02 0.066 0.19 49 -0.23 13 62
MAPK1 0.02 0.063 0.19 46 -0.23 11 57
Syndecan-2/RACK1 0.028 0.043 -10000 0 -0.21 13 13
NF1 0.025 0.02 -10000 0 -0.43 1 1
FGFR/FGF/Syndecan-2 0.002 0.049 -10000 0 -0.3 13 13
ITGA2 0.002 0.09 -10000 0 -0.27 41 41
MAPK8 -0.003 0.055 -10000 0 -0.25 24 24
Syndecan-2/alpha2/beta1 Integrin 0.008 0.11 0.2 1 -0.26 62 63
Syndecan-2/Kininogen 0.009 0.047 -10000 0 -0.25 13 13
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
SRC 0.025 0.064 0.19 50 -0.2 13 63
Syndecan-2/CASK/Protein 4.1 0.012 0.041 -10000 0 -0.21 14 14
extracellular matrix organization 0.013 0.045 -10000 0 -0.24 14 14
actin cytoskeleton reorganization 0.015 0.048 0.16 1 -0.25 13 14
Syndecan-2/Caveolin-2/Ras 0.023 0.046 -10000 0 -0.23 13 13
Syndecan-2/Laminin alpha3 0.002 0.077 0.16 1 -0.28 31 32
Syndecan-2/RasGAP 0.038 0.045 -10000 0 -0.2 13 13
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
Syndecan-2 dimer 0.011 0.049 -10000 0 -0.24 16 16
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.045 0.18 9 -0.2 13 22
RHOA 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.025 0.006 -10000 0 -10000 0 0
TNFRSF13B -0.003 0.028 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.069 -10000 0 -0.3 19 19
Syndecan-2/Synbindin 0.016 0.045 -10000 0 -0.25 13 13
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CASP3 0.013 0.089 0.19 46 -0.27 30 76
FN1 0.021 0.029 -10000 0 -0.13 18 18
Syndecan-2/IL8 -0.029 0.1 0.17 4 -0.26 68 72
SDC2 0.002 0.049 -10000 0 -0.3 13 13
KNG1 -0.009 0.032 -10000 0 -0.13 22 22
Syndecan-2/Neurofibromin 0.018 0.045 -10000 0 -0.25 13 13
TRAPPC4 0.025 0.007 -10000 0 -10000 0 0
CSF2 -0.014 0.009 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.013 0.046 -10000 0 -0.24 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.041 -10000 0 -0.23 13 13
Syndecan-2/Ezrin 0.026 0.063 -10000 0 -0.29 17 17
PRKACA 0.025 0.066 0.19 48 -0.23 13 61
angiogenesis -0.028 0.099 0.17 4 -0.26 68 72
MMP2 0.013 0.067 -10000 0 -0.26 24 24
IL8 -0.061 0.15 -10000 0 -0.25 158 158
calcineurin-NFAT signaling pathway 0.012 0.046 -10000 0 -0.25 13 13
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.053 0.19 1 -0.29 3 4
adherens junction organization -0.019 0.09 -10000 0 -0.25 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.082 0.24 1 -0.29 8 9
FMN1 -0.032 0.11 -10000 0 -0.27 60 60
mol:IP3 0.004 0.053 -10000 0 -0.25 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.09 -10000 0 -0.24 56 56
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.008 0.064 0.18 2 -0.27 4 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.36 55 55
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.083 -10000 0 -0.23 55 55
VASP -0.011 0.081 -10000 0 -0.24 40 40
ZYX -0.012 0.078 -10000 0 -0.24 48 48
JUB -0.009 0.085 -10000 0 -0.23 56 56
EGFR(dimer) -0.017 0.1 -10000 0 -0.25 56 56
E-cadherin/beta catenin-gamma catenin -0.001 0.1 -10000 0 -0.25 63 63
mol:PI-3-4-5-P3 0.023 0.074 0.21 2 -0.28 4 6
PIK3CA 0.026 0.02 -10000 0 -0.41 1 1
PI3K 0.024 0.075 0.21 2 -0.29 4 6
FYN 0.002 0.05 -10000 0 -0.26 4 4
mol:Ca2+ 0.004 0.052 -10000 0 -0.24 3 3
JUP 0.021 0.05 -10000 0 -0.43 6 6
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG 0.004 0.053 -10000 0 -0.25 3 3
CDH1 -0.046 0.15 -10000 0 -0.41 63 63
RhoA/GDP 0.012 0.095 0.23 6 -0.29 8 14
establishment of polarity of embryonic epithelium -0.011 0.08 -10000 0 -0.23 40 40
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
EGFR -0.017 0.12 -10000 0 -0.4 46 46
CASR -0.005 0.049 -10000 0 -0.3 1 1
RhoA/GTP 0.016 0.053 -10000 0 -0.3 1 1
AKT2 0.009 0.056 0.18 2 -0.26 4 6
actin cable formation -0.03 0.098 0.18 1 -0.28 45 46
apoptosis -0.003 0.064 0.28 5 -0.2 4 9
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.017 0.077 0.16 5 -0.3 9 14
PIP5K1A -0.01 0.084 -10000 0 -0.23 55 55
PLCG1 0.004 0.053 -10000 0 -0.25 3 3
Rac1/GTP -0.007 0.1 -10000 0 -0.33 12 12
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.06 0.08 0.36 1 -0.48 4 5
CRKL 0.052 0.081 0.23 42 -0.38 1 43
mol:DAG 0.028 0.049 -10000 0 -0.32 4 4
HRAS 0.049 0.086 0.27 36 -0.3 1 37
MAPK8 0.033 0.07 0.16 80 -0.24 11 91
RAP1A 0.047 0.08 0.23 39 -0.36 1 40
GAB1 0.051 0.083 0.23 42 -0.35 2 44
MAPK14 0.04 0.063 0.16 89 -0.26 2 91
EPO 0.019 0.03 -10000 0 -0.18 6 6
PLCG1 0.028 0.05 -10000 0 -0.32 4 4
EPOR/TRPC2/IP3 Receptors 0.029 0.013 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.074 -10000 0 -0.27 23 23
GAB1/SHC/GRB2/SOS1 0.07 0.073 0.26 21 -0.33 2 23
EPO/EPOR (dimer) 0.031 0.03 -10000 0 -0.34 1 1
IRS2 0.049 0.081 0.23 35 -0.35 2 37
STAT1 0.035 0.059 -10000 0 -0.35 5 5
STAT5B 0.03 0.053 -10000 0 -0.34 4 4
cell proliferation 0.028 0.095 0.2 100 -0.23 10 110
GAB1/SHIP/PIK3R1/SHP2/SHC 0.047 0.056 0.22 1 -0.33 3 4
TEC 0.047 0.085 0.24 36 -0.24 6 42
SOCS3 -0.028 0.12 -10000 0 -0.43 29 29
STAT1 (dimer) 0.034 0.058 -10000 0 -0.34 5 5
JAK2 0.03 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.056 0.06 0.21 21 -0.21 7 28
EPO/EPOR 0.031 0.03 -10000 0 -0.34 1 1
LYN 0.022 0.036 -10000 0 -0.44 2 2
TEC/VAV2 0.047 0.071 0.21 20 -0.23 6 26
elevation of cytosolic calcium ion concentration 0.029 0.013 -10000 0 -10000 0 0
SHC1 0.024 0.014 -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 0.069 0.08 0.28 18 -0.33 3 21
SH2B3 0.03 0.016 -10000 0 -10000 0 0
NFKB1 0.039 0.062 0.16 86 -0.26 2 88
EPO/EPOR (dimer)/JAK2/SOCS3 -0.002 0.05 -10000 0 -0.21 23 23
PTPN6 0.048 0.082 0.29 20 -0.21 7 27
TEC/VAV2/GRB2 0.056 0.073 0.27 9 -0.23 6 15
EPOR 0.029 0.013 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
mol:GDP 0.07 0.074 0.26 21 -0.33 2 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
CRKL/CBL/C3G 0.06 0.067 0.27 10 -0.2 1 11
VAV2 0.05 0.081 0.23 41 -0.38 1 42
CBL 0.05 0.079 0.23 40 -0.21 1 41
SHC/Grb2/SOS1 0.028 0.04 -10000 0 -0.36 1 1
STAT5A 0.025 0.074 -10000 0 -0.36 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.079 -10000 0 -0.39 9 9
LYN/PLCgamma2 0.029 0.051 -10000 0 -0.28 11 11
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK 0.046 0.096 0.23 43 -0.28 14 57
BCL2 0.056 0.12 0.36 1 -0.74 9 10
TCGA08_p53

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
CDKN2A -0.017 0.075 -10000 0 -0.3 31 31
TP53 -0.015 0.07 -10000 0 -0.29 25 25
Senescence -0.015 0.07 -10000 0 -0.29 25 25
Apoptosis -0.015 0.07 -10000 0 -0.29 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.056 0.21 34 -10000 0 34
MDM4 0.025 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.032 0.13 -10000 0 -0.56 10 10
UGCG -0.018 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.036 0.15 0.24 2 -0.42 32 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.018 0.14 -10000 0 -0.66 23 23
mol:DAG -0.016 0.16 -10000 0 -0.82 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.15 0.25 1 -0.42 35 36
FRAP1 -0.027 0.17 0.27 2 -0.48 36 38
FOXO3 -0.026 0.15 0.26 3 -0.42 40 43
AKT1 -0.028 0.16 0.26 2 -0.45 41 43
GAB2 0.025 0.006 -10000 0 -10000 0 0
SMPD1 -0.012 0.12 -10000 0 -0.58 21 21
SGMS1 -0.008 0.11 -10000 0 -0.56 18 18
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 -0.13 1 1
cell proliferation -0.01 0.14 0.25 3 -0.46 19 22
EIF3A 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.012 -10000 0 -10000 0 0
RPS6KB1 0.002 0.075 -10000 0 -1.1 1 1
mol:sphingomyelin -0.016 0.16 -10000 0 -0.82 18 18
natural killer cell activation 0 0.002 -10000 0 -0.011 13 13
JAK3 -0.008 0.1 -10000 0 -0.42 26 26
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 -0.023 0.23 0.35 3 -0.87 25 28
MYB -0.073 0.32 -10000 0 -1.2 39 39
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.14 -10000 0 -0.36 47 47
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.077 -10000 0 -1 1 1
mol:PI-3-4-5-P3 -0.026 0.13 -10000 0 -0.35 47 47
Rac1/GDP 0.019 0.013 -10000 0 -10000 0 0
T cell proliferation -0.018 0.12 0.22 1 -0.36 34 35
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.018 -10000 0 -0.064 37 37
PRKCZ -0.015 0.12 0.22 1 -0.38 31 32
NF kappa B1 p50/RelA -0.008 0.15 0.27 2 -0.43 32 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.033 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 -0.005 0.07 -10000 0 -0.16 65 65
IL2RB -0.027 0.13 -10000 0 -0.25 100 100
TERT -0.042 0.13 -10000 0 -0.32 74 74
E2F1 -0.013 0.13 -10000 0 -0.45 41 41
SOS1 0.026 0.004 -10000 0 -10000 0 0
RPS6 0.024 0.01 -10000 0 -10000 0 0
mol:cAMP 0.001 0.009 0.031 37 -10000 0 37
PTPN11 0.025 0.008 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.43 16 16
actin cytoskeleton organization -0.018 0.12 0.22 1 -0.36 34 35
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.021 -10000 0 -0.43 1 1
Rac1/GTP 0.042 0.025 -10000 0 -10000 0 0
LCK -0.019 0.11 -10000 0 -0.24 77 77
BCL2 -0.023 0.16 -10000 0 -0.62 18 18
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.014 0.049 -10000 0 -0.33 7 7
CCNA2 -0.007 0.099 -10000 0 -0.24 63 63
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
JAK3 -0.009 0.1 -10000 0 -0.25 64 64
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 -0.016 0.13 0.23 1 -0.39 29 30
SHC1 0.025 0.014 -10000 0 -0.13 4 4
SP1 0.027 0.034 -10000 0 -0.33 4 4
IL2RA -0.013 0.089 0.2 3 -0.7 7 10
IL2RB -0.027 0.13 -10000 0 -0.25 100 100
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.43 16 16
G1/S transition of mitotic cell cycle 0.004 0.17 0.29 2 -0.48 40 42
PTPN11 0.026 0.004 -10000 0 -10000 0 0
CCND2 0.013 0.066 -10000 0 -0.7 4 4
LCK -0.019 0.11 -10000 0 -0.25 77 77
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.016 0.004 -10000 0 -10000 0 0
CDK6 0.004 0.083 -10000 0 -0.35 23 23
CCND3 -0.012 0.12 0.32 1 -0.42 11 12
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.04 -10000 0 -0.43 4 4
ANTXR2 0.021 0.035 -10000 0 -0.18 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.006 -10000 0 -0.058 6 6
monocyte activation -0.13 0.23 -10000 0 -0.43 176 176
MAP2K2 0.013 0.039 -10000 0 -0.61 2 2
MAP2K1 -0.003 0.007 -10000 0 -0.11 1 1
MAP2K7 -0.003 0.006 -10000 0 -10000 0 0
MAP2K6 -0.004 0.011 -10000 0 -0.22 1 1
CYAA -0.007 0.023 -10000 0 -0.21 6 6
MAP2K4 -0.003 0.008 -10000 0 -0.11 2 2
IL1B -0.043 0.079 0.17 2 -0.22 77 79
Channel 0.028 0.031 -10000 0 -0.23 6 6
NLRP1 -0.004 0.014 -10000 0 -0.22 2 2
CALM1 0.025 0.009 -10000 0 -0.13 1 1
negative regulation of phagocytosis -0.005 0.078 -10000 0 -0.39 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.006 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 -0.023 0.062 -10000 0 -0.22 46 46
PA/Cellular Receptors 0.029 0.034 -10000 0 -0.25 6 6
apoptosis -0.001 0.006 -10000 0 -0.058 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.028 -10000 0 -0.22 6 6
macrophage activation -0.005 0.005 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.43 68 68
VCAM1 -0.13 0.23 -10000 0 -0.43 174 174
platelet activation -0.005 0.078 -10000 0 -0.39 20 20
MAPKKK cascade -0.005 0.024 0.082 2 -0.077 42 44
IL18 -0.013 0.051 0.16 3 -0.23 22 25
negative regulation of macrophage activation -0.001 0.006 -10000 0 -0.058 6 6
LEF -0.001 0.006 -10000 0 -0.058 6 6
CASP1 -0.002 0.018 -10000 0 -0.084 17 17
mol:cAMP -0.005 0.079 -10000 0 -0.39 20 20
necrosis -0.001 0.006 -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) 0.028 0.029 -10000 0 -0.21 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.012 -10000 0 -0.13 3 3
Jak2/Leptin Receptor 0.005 0.12 0.24 3 -0.38 31 34
PTP1B/AKT1 0.013 0.092 0.21 3 -0.32 12 15
FYN 0.025 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.002 0.094 0.21 5 -0.31 15 20
EGFR -0.019 0.13 -10000 0 -0.41 46 46
EGF/EGFR -0.019 0.12 -10000 0 -0.29 66 66
CSF1 0.017 0.045 -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 0.097 0.21 3 -0.33 13 16
Insulin Receptor/Insulin 0.017 0.086 -10000 0 -0.36 7 7
HCK 0.014 0.063 -10000 0 -0.27 19 19
CRK 0.026 0.002 -10000 0 -10000 0 0
TYK2 0.008 0.1 0.31 19 -0.33 11 30
EGF -0.012 0.12 -10000 0 -0.31 54 54
YES1 0.022 0.04 -10000 0 -0.43 4 4
CAV1 0.016 0.12 0.26 35 -0.32 19 54
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.02 0.094 0.22 1 -0.33 10 11
cell migration -0.002 0.094 0.31 15 -0.21 5 20
STAT3 0.026 0.003 -10000 0 -10000 0 0
PRLR 0.007 0.088 -10000 0 -0.32 29 29
ITGA2B -0.012 0.12 -10000 0 -0.37 50 50
CSF1R 0.002 0.099 -10000 0 -0.43 25 25
Prolactin Receptor/Prolactin 0.019 0.066 -10000 0 -0.31 18 18
FGR 0.021 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.011 0.095 0.21 3 -0.3 15 18
Crk/p130 Cas 0.022 0.097 0.22 2 -0.32 12 14
DOK1 0.008 0.093 0.21 11 -0.35 10 21
JAK2 0 0.13 -10000 0 -0.39 32 32
Jak2/Leptin Receptor/Leptin -0.02 0.1 -10000 0 -0.32 23 23
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PTPN1 0.002 0.095 0.21 5 -0.32 15 20
LYN 0.021 0.035 -10000 0 -0.43 2 2
CDH2 0.025 0.02 -10000 0 -0.43 1 1
SRC 0.024 0.052 -10000 0 -0.37 4 4
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
CAT1/PTP1B -0.016 0.16 0.3 32 -0.38 38 70
CAPN1 0.025 0.021 -10000 0 -0.43 1 1
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.085 -10000 0 -0.39 5 5
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.02 0.099 -10000 0 -0.35 21 21
negative regulation of transcription 0.001 0.12 -10000 0 -0.38 33 33
FCGR2A 0.001 0.092 -10000 0 -0.43 20 20
FER 0.008 0.09 -10000 0 -0.42 21 21
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
BLK -0.031 0.11 -10000 0 -0.21 109 109
Insulin Receptor/Insulin/Shc 0.039 0.032 -10000 0 -0.26 4 4
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.017 0.04 -10000 0 -0.21 11 11
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
p210 bcr-abl/Grb2 0.025 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.033 0.17 0.26 19 -0.42 46 65
PRL 0.004 0.02 -10000 0 -10000 0 0
SOCS3 -0.07 0.31 -10000 0 -1.3 32 32
SPRY2 0.024 0.028 -10000 0 -0.16 8 8
Insulin Receptor/Insulin/IRS1 0.04 0.03 -10000 0 -0.26 4 4
CSF1/CSF1R 0.004 0.11 0.22 2 -0.31 25 27
Ras protein signal transduction 0.018 0.12 0.51 24 -10000 0 24
IRS1 0.026 0.003 -10000 0 -10000 0 0
INS 0.005 0.042 -10000 0 -0.37 5 5
LEP 0.007 0.02 -10000 0 -0.13 4 4
STAT5B 0.008 0.1 0.2 5 -0.33 16 21
STAT5A 0.005 0.11 0.21 4 -0.33 19 23
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.095 0.21 2 -0.3 15 17
CSN2 -0.01 0.06 -10000 0 -0.56 2 2
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
LAT -0.016 0.14 -10000 0 -0.45 46 46
YBX1 0.026 0.031 -10000 0 -0.43 2 2
LCK -0.019 0.11 -10000 0 -0.25 77 77
SHC1 0.024 0.014 -10000 0 -0.13 4 4
NOX4 -0.01 0.1 -10000 0 -0.36 31 31
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.04 -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 -0.012 0.026 -10000 0 -0.13 19 19
CDKN1A -0.035 0.13 -10000 0 -0.65 21 21
KAT2B 0.025 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
FOXO3 -0.003 0.033 0.37 4 -10000 0 4
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
FOXO4 0.013 0.026 -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 -0.025 0.12 -10000 0 -0.26 90 90
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.064 0.12 -10000 0 -0.3 92 92
PPARGC1A 0.009 0.082 -10000 0 -0.37 21 21
FHL2 0.006 0.077 -10000 0 -0.22 42 42
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.026 0.16 19 -10000 0 19
HIST2H4A 0.012 0.026 0.13 19 -10000 0 19
SIRT1/FOXO3a 0.02 0.038 0.26 4 -0.19 4 8
SIRT1 0.03 0.034 0.2 19 -10000 0 19
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 0.023 0.057 0.23 1 -0.22 19 20
apoptosis -0.045 0.031 -10000 0 -10000 0 0
SIRT1/PGC1A 0.026 0.057 0.14 18 -0.25 17 35
p53/SIRT1 0.038 0.087 0.39 19 -0.31 12 31
SIRT1/FOXO4 0.032 0.038 -10000 0 -0.22 5 5
FOXO1/FHL2/SIRT1 0.042 0.051 -10000 0 -0.23 13 13
HIST1H1E 0.004 0.05 -10000 0 -0.25 18 18
SIRT1/p300 0.038 0.04 -10000 0 -0.31 4 4
muscle cell differentiation 0.029 0.12 0.25 92 -0.22 10 102
TP53 0.02 0.078 0.2 20 -0.43 12 32
KU70/SIRT1/BAX 0.045 0.032 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
MEF2D 0.025 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.003 0.096 0.18 1 -0.3 37 38
ACSS2 0.014 0.025 0.13 19 -10000 0 19
SIRT1/PCAF/MYOD -0.029 0.12 0.22 10 -0.25 92 102
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.002 0.099 0.23 9 -0.41 18 27
CRKL 0 0.098 -10000 0 -0.43 20 20
HRAS 0.007 0.11 -10000 0 -0.38 20 20
mol:PIP3 0.012 0.1 0.32 7 -0.38 18 25
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.012 -10000 0 -10000 0 0
GAB1 0.002 0.1 -10000 0 -0.44 21 21
FOXO3 0.017 0.13 0.28 11 -0.4 28 39
AKT1 0.018 0.14 0.29 11 -0.43 29 40
BAD 0.021 0.14 0.31 12 -0.4 29 41
megakaryocyte differentiation 0 0.1 -10000 0 -0.42 22 22
GSK3B 0.017 0.13 0.3 11 -0.4 28 39
RAF1 0.006 0.093 0.26 1 -0.32 16 17
SHC1 0.024 0.014 -10000 0 -0.13 4 4
STAT3 0.003 0.1 -10000 0 -0.43 21 21
STAT1 -0.013 0.22 -10000 0 -0.9 27 27
HRAS/SPRED1 0.018 0.099 0.25 1 -0.33 16 17
cell proliferation -0.003 0.11 -10000 0 -0.45 22 22
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TEC 0.015 0.063 -10000 0 -0.43 9 9
RPS6KB1 0.014 0.12 0.26 3 -0.44 23 26
HRAS/SPRED2 0.018 0.099 0.25 1 -0.33 16 17
LYN/TEC/p62DOK 0.028 0.12 -10000 0 -0.43 23 23
MAPK3 0.014 0.082 0.22 18 -0.29 6 24
STAP1 -0.001 0.1 -10000 0 -0.42 23 23
GRAP2 -0.006 0.1 -10000 0 -0.26 57 57
JAK2 -0.014 0.2 -10000 0 -0.83 24 24
STAT1 (dimer) -0.011 0.22 -10000 0 -0.88 27 27
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.023 0.12 -10000 0 -0.42 25 25
actin filament polymerization -0.005 0.099 0.32 5 -0.42 18 23
LYN 0.021 0.035 -10000 0 -0.43 2 2
STAP1/STAT5A (dimer) -0.012 0.16 -10000 0 -0.61 27 27
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.021 0.099 -10000 0 -0.4 19 19
PI3K 0.036 0.12 0.27 3 -0.42 20 23
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.008 0.25 -10000 0 -1.2 20 20
MAPK8 -0.003 0.11 -10000 0 -0.46 22 22
STAT3 (dimer) 0.003 0.1 -10000 0 -0.42 21 21
positive regulation of transcription 0.015 0.071 0.2 20 -0.23 6 26
mol:GDP 0.003 0.11 -10000 0 -0.39 22 22
PIK3C2B 0.002 0.1 -10000 0 -0.43 20 20
CBL/CRKL 0.011 0.099 -10000 0 -0.41 19 19
FER -0.005 0.12 -10000 0 -0.45 24 24
SH2B3 0.003 0.1 -10000 0 -0.43 21 21
PDPK1 0.011 0.1 0.32 8 -0.38 17 25
SNAI2 -0.003 0.11 0.38 1 -0.42 24 25
positive regulation of cell proliferation -0.007 0.18 -10000 0 -0.72 26 26
KITLG 0.017 0.067 -10000 0 -0.44 10 10
cell motility -0.007 0.18 -10000 0 -0.72 26 26
PTPN6 0.013 0.064 -10000 0 -0.34 14 14
EPOR 0.031 0.085 -10000 0 -1.2 1 1
STAT5A (dimer) -0.004 0.16 -10000 0 -0.62 26 26
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
cell migration 0.017 0.11 0.42 25 -10000 0 25
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.016 0.03 -10000 0 -0.2 5 5
VAV1 0.005 0.09 -10000 0 -0.34 29 29
GRB10 -0.001 0.095 0.24 1 -0.42 19 20
PTPN11 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT 0.005 0.11 -10000 0 -0.45 21 21
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.008 0.081 0.22 5 -0.26 15 20
CBL 0.025 0.007 -10000 0 -10000 0 0
KIT -0.012 0.26 -10000 0 -1.3 19 19
MAP2K2 0.013 0.086 0.26 16 -0.26 14 30
SHC/Grb2/SOS1 0.037 0.11 -10000 0 -0.42 19 19
STAT5A -0.004 0.16 -10000 0 -0.64 26 26
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.003 0.1 0.37 1 -0.42 24 25
SHC/GRAP2 0.013 0.077 -10000 0 -0.3 25 25
PTPRO 0 0.1 -10000 0 -0.42 22 22
SH2B2 -0.007 0.097 0.23 2 -0.42 19 21
DOK1 0.025 0.021 -10000 0 -0.43 1 1
MATK -0.017 0.11 -10000 0 -0.43 25 25
CREBBP 0.034 0.033 -10000 0 -10000 0 0
BCL2 0.011 0.19 -10000 0 -1.4 8 8
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.023 0.042 -10000 0 -0.25 5 5
PDGFRB 0.025 0.013 -10000 0 -0.14 3 3
SPHK1 -0.02 0.14 -10000 0 -0.72 19 19
mol:S1P -0.019 0.13 -10000 0 -0.63 19 19
S1P1/S1P/Gi -0.028 0.13 -10000 0 -0.37 51 51
GNAO1 0.017 0.047 -10000 0 -0.43 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.014 0.13 0.28 10 -0.34 51 61
PLCG1 -0.028 0.12 -10000 0 -0.36 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.14 3 3
GNAI2 0.021 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.038 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.028 -10000 0 -0.2 5 5
S1P1/S1P -0.017 0.1 -10000 0 -0.47 18 18
negative regulation of cAMP metabolic process -0.027 0.13 -10000 0 -0.36 51 51
MAPK3 -0.05 0.18 -10000 0 -0.53 58 58
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 0.017 0.04 -10000 0 -0.23 9 9
PLCB2 -0.012 0.11 0.31 3 -0.44 19 22
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.088 -10000 0 -0.4 18 18
receptor internalization -0.017 0.096 -10000 0 -0.43 18 18
PTGS2 -0.095 0.33 -10000 0 -1 58 58
Rac1/GTP -0.015 0.083 -10000 0 -0.38 17 17
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.033 -10000 0 -0.14 1 1
negative regulation of T cell proliferation -0.027 0.13 -10000 0 -0.36 51 51
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.016 -10000 0 -10000 0 0
MAPK1 -0.051 0.18 -10000 0 -0.54 59 59
S1P1/S1P/PDGFB-D/PDGFRB -0.006 0.1 0.22 1 -0.4 18 19
ABCC1 0.025 0.015 -10000 0 -0.13 4 4
Regulation of p38-alpha and p38-beta

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
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 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -0.13 2 2
RAC1-CDC42/GTP/PAK family -0.02 0.069 -10000 0 -0.19 60 60
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
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 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.004 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.034 0.071 -10000 0 -0.27 23 23
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
DUSP8 0.02 0.04 -10000 0 -0.21 11 11
PGK/cGMP/p38 alpha -0.011 0.11 0.16 2 -0.29 30 32
apoptosis -0.033 0.068 -10000 0 -0.26 23 23
RAL/GTP 0.031 0.012 -10000 0 -10000 0 0
LYN 0.021 0.035 -10000 0 -0.43 2 2
DUSP1 0.008 0.077 -10000 0 -0.25 32 32
PAK1 0.008 0.061 -10000 0 -0.16 47 47
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.056 0.026 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -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 0.13 0.28 25 -0.33 23 48
BLK -0.031 0.11 -10000 0 -0.21 109 109
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAP2K3 0.026 0.01 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.015 0.065 -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 0.008 0.11 0.24 26 -0.31 20 46
positive regulation of innate immune response 0.003 0.14 0.3 27 -0.38 22 49
LCK -0.019 0.11 -10000 0 -0.25 77 77
p38alpha-beta/MKP7 0.013 0.14 0.31 25 -0.36 22 47
p38alpha-beta/MKP5 0.005 0.14 0.29 23 -0.36 27 50
PGK/cGMP -0.005 0.083 -10000 0 -0.3 36 36
PAK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.007 0.15 0.31 24 -0.37 24 48
CDC42 0.022 0.01 -10000 0 -10000 0 0
RALB 0.026 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
PAK3 -0.054 0.16 -10000 0 -0.34 113 113
IL27-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
TGFB1 0.021 0.022 -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 0.002 0.089 0.37 5 -0.48 2 7
IL27/IL27R/JAK1 0.022 0.12 0.88 2 -10000 0 2
TBX21 -0.018 0.16 0.44 16 -0.4 20 36
IL12B -0.001 0.024 -10000 0 -0.13 6 6
IL12A -0.008 0.065 -10000 0 -0.3 23 23
IL6ST -0.003 0.11 -10000 0 -0.43 34 34
IL27RA/JAK1 0.024 0.051 0.37 2 -10000 0 2
IL27 0.014 0.038 -10000 0 -0.13 25 25
TYK2 0.025 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.01 0.12 -10000 0 -0.54 1 1
T-helper 2 cell differentiation 0.002 0.089 0.37 5 -0.48 2 7
T cell proliferation during immune response 0.002 0.089 0.37 5 -0.48 2 7
MAPKKK cascade -0.002 0.089 0.48 2 -0.37 5 7
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT2 0.025 0.014 -10000 0 -0.13 4 4
STAT1 0.021 0.029 -10000 0 -0.13 16 16
IL12RB1 -0.002 0.1 -10000 0 -0.32 40 40
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.033 0.16 0.45 13 -0.4 28 41
IL27/IL27R/JAK2/TYK2 -0.002 0.09 0.48 2 -0.37 5 7
positive regulation of T cell mediated cytotoxicity -0.002 0.089 0.48 2 -0.37 5 7
STAT1 (dimer) 0.01 0.19 0.55 27 -0.48 4 31
JAK2 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.021 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.018 0.098 0.39 3 -0.35 5 8
T cell proliferation -0.021 0.1 0.39 3 -0.37 11 14
IL12/IL12R/TYK2/JAK2 0 0.13 -10000 0 -0.78 10 10
IL17A -0.008 0.11 -10000 0 -10000 0 0
mast cell activation 0.002 0.089 0.37 5 -0.48 2 7
IFNG 0.005 0.026 0.12 4 -0.1 6 10
T cell differentiation -0.002 0.004 -10000 0 -0.015 5 5
STAT3 (dimer) 0.018 0.098 0.39 3 -0.36 5 8
STAT5A (dimer) 0.013 0.11 0.39 3 -0.41 8 11
STAT4 (dimer) -0.011 0.13 0.39 3 -0.37 18 21
STAT4 -0.061 0.15 -10000 0 -0.26 158 158
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.025 0.075 -10000 0 -10000 0 0
GATA3 -0.085 0.44 0.61 40 -1.3 49 89
IL18 -0.009 0.063 -10000 0 -0.3 21 21
positive regulation of mast cell cytokine production 0.017 0.097 0.39 3 -0.35 5 8
IL27/EBI3 0.019 0.067 0.24 2 -0.28 18 20
IL27RA 0.009 0.033 -10000 0 -10000 0 0
IL6 -0.034 0.12 -10000 0 -0.43 36 36
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.015 0.023 -10000 0 -10000 0 0
IL1B -0.056 0.11 -10000 0 -0.3 76 76
EBI3 0.011 0.078 -10000 0 -0.38 18 18
TNF -0.049 0.1 -10000 0 -0.3 68 68
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 -0.47 17 18
BAG4 0.014 0.072 -10000 0 -0.43 13 13
BAD 0.005 0.058 0.24 15 -0.15 11 26
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX 0.007 0.05 0.18 18 -0.14 9 27
EnzymeConsortium:3.1.4.12 0 0.03 0.065 5 -0.098 19 24
IKBKB -0.003 0.12 0.24 5 -0.46 16 21
MAP2K2 0.003 0.058 0.18 23 -0.2 1 24
MAP2K1 -0.001 0.051 0.18 9 -0.19 2 11
SMPD1 0.001 0.038 0.13 8 -0.13 10 18
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.12 0.3 7 -0.45 16 23
MAP2K4 -0.001 0.048 0.17 9 -0.17 5 14
protein ubiquitination -0.005 0.12 0.22 1 -0.47 16 17
EnzymeConsortium:2.7.1.37 -0.001 0.059 0.19 10 -0.19 4 14
response to UV 0 0.001 0.002 9 -0.002 4 13
RAF1 0 0.051 0.18 9 -0.19 2 11
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.002 0.046 0.12 8 -0.14 20 28
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 0.048 0.16 8 -0.15 14 22
TRADD 0.025 0.02 -10000 0 -0.43 1 1
RELA/p50 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.005 0.055 0.18 10 -0.2 2 12
MAPK1 0.004 0.056 0.18 11 -0.23 2 13
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD -0.006 0.12 0.26 7 -0.46 16 23
KSR1 0 0.047 0.15 5 -0.15 13 18
MAPK8 -0.006 0.05 0.19 4 -0.2 9 13
TRAF2 0.025 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.007 0.11 0.23 2 -0.46 16 18
TNF R/SODD 0.023 0.063 -10000 0 -0.31 17 17
TNF -0.06 0.16 -10000 0 -0.43 68 68
CYCS 0.016 0.061 0.17 36 -0.14 6 42
IKBKG -0.007 0.11 0.22 1 -0.46 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.006 0.12 -10000 0 -0.44 22 22
RELA 0.025 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AIFM1 0.008 0.052 0.16 27 -0.15 4 31
TNF/TNF R/SODD 0 0.12 -10000 0 -0.27 77 77
TNFRSF1A 0.017 0.054 -10000 0 -0.43 7 7
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.023 0.079 -10000 0 -0.85 3 3
NSMAF -0.002 0.12 0.22 13 -0.45 17 30
response to hydrogen peroxide 0 0.001 0.002 9 -0.002 4 13
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.009 -10000 0 -10000 0 0
NFATC1 0.002 0.11 0.25 4 -0.37 24 28
NFATC2 -0.011 0.082 0.14 2 -0.23 41 43
NFATC3 0.007 0.059 -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 3 -0.42 47 50
Exportin 1/Ran/NUP214 0.051 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.064 0.17 -10000 0 -0.38 72 72
BCL2/BAX 0.029 0.035 -10000 0 -0.28 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.008 -10000 0 -0.088 1 1
CaM/Ca2+ 0.018 0.008 -10000 0 -0.088 1 1
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 -0.4 46 46
Calcineurin A alpha-beta B1/BCL2 0.021 0.045 -10000 0 -0.43 5 5
FKBP8 0.025 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.03 0.14 0.4 46 -10000 0 46
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -0.13 1 1
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.43 28 28
MAP3K8 0.016 0.048 -10000 0 -0.2 18 18
NFAT4/CK1 alpha 0.017 0.041 -10000 0 -0.19 13 13
MEF2D/NFAT1/Cbp/p300 0.019 0.1 -10000 0 -0.27 28 28
CABIN1 -0.044 0.15 0.17 3 -0.42 47 50
CALM1 0.025 0.009 -10000 0 -0.13 1 1
RAN 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
CAMK4 -0.093 0.19 -10000 0 -0.43 119 119
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.002 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -0.13 23 23
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.04 -10000 0 -0.3 2 2
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.015 0.069 -10000 0 -0.43 12 12
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -10000 0 0
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.13 0.26 1 -0.35 37 38
PRKCH 0.025 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.035 0.032 -10000 0 -0.3 4 4
CASP3 0.025 0.009 -10000 0 -0.13 1 1
PIM1 0.024 0.017 -10000 0 -0.13 6 6
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 -0.22 2 2
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
JNK2/NFAT4 -0.001 0.079 -10000 0 -0.31 14 14
BAD/BCL-XL 0.036 0.01 -10000 0 -10000 0 0
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
NUP214 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
PRKCG -0.065 0.15 -10000 0 -0.26 157 157
PRKCQ 0.015 0.061 -10000 0 -0.43 9 9
FKBP38/BCL2 0.033 0.035 -10000 0 -0.3 5 5
EP300 0.022 0.04 -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 0.008 0.11 0.26 1 -0.35 25 26
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 -0.043 0.12 -10000 0 -0.26 120 120
NFATc/ERK1 0.015 0.11 0.25 4 -0.35 23 27
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.066 0.17 -10000 0 -0.37 76 76
NR4A1 -0.001 0.099 0.21 4 -0.34 20 24
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
positive T cell selection 0.007 0.059 -10000 0 -0.34 14 14
NFAT1/CK1 alpha -0.003 0.06 -10000 0 -0.19 22 22
RCH1/ KPNB1 0.037 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
AKAP5 0.01 0.054 -10000 0 -0.15 43 43
MEF2D 0.024 0.012 -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 0.014 0.11 0.25 4 -0.35 24 28
CREBBP 0.026 0.006 -10000 0 -10000 0 0
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.036 0.063 -10000 0 -0.22 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.024 0.12 -10000 0 -0.42 14 14
AKT1 -0.01 0.17 -10000 0 -0.67 30 30
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.006 0.18 -10000 0 -0.69 30 30
mol:Ca2+ -0.018 0.094 -10000 0 -0.38 23 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.077 -10000 0 -0.26 35 35
SHC1 0.024 0.014 -10000 0 -0.13 4 4
apoptosis 0.008 0.16 0.64 30 -10000 0 30
RhoA/GTP 0.012 0.033 -10000 0 -0.2 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0 0.12 -10000 0 -0.4 14 14
regulation of stress fiber formation 0.003 0.066 0.39 2 -0.17 17 19
E2/ERA-ERB (dimer) 0.019 0.059 -10000 0 -0.24 22 22
KRAS 0.025 0.005 -10000 0 -10000 0 0
G13/GTP 0.024 0.041 -10000 0 -0.23 11 11
pseudopodium formation -0.003 0.066 0.17 17 -0.39 2 19
E2/ER alpha (dimer)/PELP1 0.025 0.046 -10000 0 -0.26 11 11
GRB2 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.022 0.04 -10000 0 -0.43 4 4
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.004 0.13 0.26 3 -0.4 25 28
E2/ER beta (dimer) 0.012 0.043 -10000 0 -0.3 9 9
mol:GDP 0.001 0.067 -10000 0 -0.28 21 21
mol:NADP 0.004 0.13 0.26 3 -0.4 25 28
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.019 0.097 -10000 0 -0.4 23 23
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
PLCB1 -0.01 0.09 -10000 0 -0.38 20 20
PLCB2 -0.01 0.096 -10000 0 -0.4 22 22
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:L-citrulline 0.004 0.13 0.26 3 -0.4 25 28
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP 0.008 0.11 -10000 0 -0.6 15 15
JNK cascade 0.012 0.043 -10000 0 -0.3 9 9
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
ESR2 0.016 0.062 -10000 0 -0.32 14 14
GNAQ 0.026 0.004 -10000 0 -10000 0 0
ESR1 0.011 0.07 -10000 0 -0.43 11 11
Gq family/GDP/Gbeta gamma -0.024 0.17 -10000 0 -0.59 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.029 0.071 -10000 0 -1.2 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.001 0.12 -10000 0 -0.4 13 13
GNAZ 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.009 0.049 -10000 0 -0.3 11 11
STRN 0.004 0.098 -10000 0 -0.42 26 26
GNAL -0.026 0.14 -10000 0 -0.42 59 59
PELP1 0.026 0.002 -10000 0 -10000 0 0
MAPK11 0.004 0.049 -10000 0 -0.26 17 17
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
HBEGF -0.019 0.14 0.35 21 -0.38 16 37
cAMP biosynthetic process -0.01 0.087 -10000 0 -0.21 76 76
SRC -0.026 0.12 -10000 0 -0.37 19 19
PI3K 0.038 0.007 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.022 0.072 -10000 0 -0.26 22 22
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.09 -10000 0 -0.31 21 21
Gs family/GTP -0.004 0.091 -10000 0 -0.21 76 76
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.023 -10000 0 -10000 0 0
vasodilation 0.005 0.12 0.25 4 -0.37 28 32
mol:DAG -0.019 0.097 -10000 0 -0.4 23 23
Gs family/GDP/Gbeta gamma -0.014 0.087 -10000 0 -0.28 24 24
MSN -0.003 0.069 0.18 16 -0.42 2 18
Gq family/GTP 0.001 0.089 -10000 0 -0.3 34 34
mol:PI-3-4-5-P3 -0.004 0.17 -10000 0 -0.66 30 30
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 0.37 28 -0.25 4 32
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.072 -10000 0 -0.29 18 18
NOS3 0.003 0.14 0.29 2 -0.42 25 27
GNA11 0.017 0.06 -10000 0 -0.43 9 9
MAPKKK cascade -0.007 0.15 0.37 3 -0.44 38 41
E2/ER alpha (dimer)/PELP1/Src 0.003 0.12 0.26 9 -0.41 14 23
ruffle organization -0.003 0.066 0.17 17 -0.39 2 19
ROCK2 0.002 0.07 0.19 16 -0.28 2 18
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.039 0.13 0.33 4 -0.36 25 29
MMP2 -0.015 0.13 0.27 14 -0.36 17 31
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
CDC42/GTP 0.026 0.051 -10000 0 -0.24 7 7
PLCG1 0.004 0.054 -10000 0 -0.24 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 0.015 -10000 0 -10000 0 0
cell migration 0.025 0.05 -10000 0 -0.24 7 7
S1PR5 -0.052 0.16 -10000 0 -0.3 122 122
S1PR4 0.019 0.042 -10000 0 -0.2 14 14
MAPK3 0.006 0.055 -10000 0 -0.24 8 8
MAPK1 0.007 0.05 -10000 0 -0.21 7 7
S1P/S1P5/Gi -0.018 0.1 -10000 0 -0.25 65 65
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
CDC42/GDP 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.015 0.093 -10000 0 -0.26 60 60
RHOA 0.045 0.087 0.22 81 -0.22 3 84
S1P/S1P4/Gi 0.011 0.058 -10000 0 -0.26 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.04 0.029 -10000 0 -0.23 3 3
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.009 0.027 -10000 0 -0.26 5 5
ADCY5 -0.014 0.046 -10000 0 -0.27 15 15
ADCY6 -0.007 0.017 -10000 0 -0.26 2 2
ADCY7 -0.007 0.017 -10000 0 -0.26 2 2
ADCY1 -0.03 0.069 -10000 0 -0.24 46 46
ADCY2 -0.012 0.04 -10000 0 -0.26 13 13
ADCY3 -0.007 0.017 -10000 0 -0.26 2 2
ADCY8 -0.03 0.075 -10000 0 -0.26 50 50
PRKCE 0.005 0.022 -10000 0 -0.3 2 2
ADCY9 -0.008 0.023 -10000 0 -0.26 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.076 0.18 22 -0.22 17 39
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 0.086 -9999 0 -0.43 17 17
GNAI2 0.025 0.005 -9999 0 -10000 0 0
mol:S1P 0 0.064 -9999 0 -0.34 16 16
GNAO1 0.022 0.045 -9999 0 -0.43 5 5
mol:Sphinganine-1-P 0.003 0.041 -9999 0 -0.3 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.022 0.074 -9999 0 -0.28 16 16
GNAI3 0.021 0.01 -9999 0 -10000 0 0
G12/G13 0.032 0.015 -9999 0 -10000 0 0
S1PR3 0.005 0.075 -9999 0 -0.2 45 45
S1PR2 0.022 0.036 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.063 -9999 0 -0.29 17 17
S1PR5 -0.052 0.16 -9999 0 -0.3 122 122
S1PR4 0.019 0.042 -9999 0 -0.2 14 14
GNAI1 0.019 0.036 -9999 0 -0.43 3 3
S1P/S1P5/G12 -0.015 0.11 -9999 0 -0.26 70 70
S1P/S1P3/Gq -0.007 0.11 -9999 0 -0.32 42 42
S1P/S1P4/Gi 0.002 0.084 -9999 0 -0.28 17 17
GNAQ 0.026 0.004 -9999 0 -10000 0 0
GNAZ 0.026 0.004 -9999 0 -10000 0 0
GNA14 0.009 0.081 -9999 0 -0.34 23 23
GNA15 0.013 0.07 -9999 0 -0.43 12 12
GNA12 0.022 0.009 -9999 0 -10000 0 0
GNA13 0.025 0.005 -9999 0 -10000 0 0
GNA11 0.017 0.06 -9999 0 -0.43 9 9
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 0.04 0.2 8 -10000 0 8
DAPP1 -0.033 0.14 0.26 6 -0.4 38 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.075 0.22 0.32 7 -0.5 70 77
mol:DAG -0.021 0.099 0.29 13 -0.26 23 36
HRAS 0.025 0.008 -10000 0 -10000 0 0
RAP1A 0.022 0.011 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.06 0.19 4 -0.31 6 10
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.051 0.18 28 -10000 0 28
ARF1/GTP 0.003 0.035 0.22 6 -10000 0 6
RHOA 0.026 0.004 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
RAP1A/GTP -0.003 0.041 0.17 19 -10000 0 19
ADAP1 -0.006 0.045 0.19 12 -0.21 4 16
ARAP3 0 0.05 0.18 28 -10000 0 28
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PREX1 0.016 0.063 -10000 0 -0.43 10 10
ARHGEF6 0.023 0.04 -10000 0 -0.43 4 4
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
ARF1 0.026 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 0.004 -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 14 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.004 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.43 22 22
mol:IP3 -0.017 0.076 0.27 11 -0.2 18 29
LYN 0.021 0.035 -10000 0 -0.43 2 2
ARF1/GDP 0.033 0.07 0.2 6 -0.3 9 15
RhoA/GDP 0.037 0.06 0.24 14 -10000 0 14
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
BLNK -0.022 0.13 -10000 0 -0.38 59 59
actin cytoskeleton reorganization 0.022 0.1 0.27 27 -0.38 9 36
SRC 0.025 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.02 -10000 0 -0.26 3 3
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 0.043 0.22 7 -10000 0 7
RhoA/GTP 0.005 0.054 0.19 27 -10000 0 27
Src family/SYK family/BLNK-LAT -0.067 0.17 -10000 0 -0.42 64 64
BLK -0.031 0.11 -10000 0 -0.21 109 109
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
CYTH1 -0.004 0.043 0.19 11 -10000 0 11
HCK 0.014 0.063 -10000 0 -0.27 19 19
CYTH3 -0.003 0.041 0.19 12 -10000 0 12
CYTH2 -0.004 0.043 0.21 9 -10000 0 9
KRAS 0.026 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.008 0.078 0.21 2 -0.4 15 17
SGK1 0 0.098 -10000 0 -0.38 29 29
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
mol:GDP 0.022 0.072 0.2 11 -0.31 9 20
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.009 0.083 -10000 0 -0.43 17 17
ARF6/GDP 0.033 0.064 0.25 19 -0.22 1 20
mol:PI-3-4-5-P3 -0.011 0.026 0.19 6 -10000 0 6
ARAP3/RAP1A/GTP -0.003 0.041 0.17 19 -10000 0 19
VAV1 0.005 0.09 -10000 0 -0.34 29 29
mol:PI-3-4-P2 0.01 0.026 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.032 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.021 -10000 0 -0.26 3 3
Rac1/GDP 0.024 0.063 0.2 3 -0.3 7 10
LAT 0.003 0.1 -10000 0 -0.43 26 26
Rac1/GTP 0.019 0.075 -10000 0 -0.4 10 10
ITK -0.022 0.065 0.2 9 -0.21 19 28
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.036 0.12 0.35 8 -0.37 25 33
LCK -0.019 0.11 -10000 0 -0.25 77 77
BTK -0.01 0.055 0.19 12 -0.21 2 14
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.022 0.014 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.007 0.1 -10000 0 -0.26 60 60
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.004 0.1 -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 0.034 0.066 -10000 0 -0.25 24 24
alpha4/beta7 Integrin/Paxillin 0.01 0.082 0.18 3 -0.24 41 44
lamellipodium assembly 0.023 0.049 0.27 1 -0.43 3 4
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.005 -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 0.038 0.056 -10000 0 -0.21 21 21
cell adhesion 0.037 0.059 -10000 0 -0.22 21 21
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.021 0.061 0.17 1 -0.24 21 22
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
ITGB7 0.002 0.091 -10000 0 -0.43 19 19
ARF6/GDP 0.024 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0 0.097 0.18 2 -0.23 66 68
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.26 4 4
VCAM1 -0.033 0.13 -10000 0 -0.3 84 84
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.06 -10000 0 -0.22 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.04 0.06 -10000 0 -0.22 21 21
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.038 0.059 0.22 21 -10000 0 21
CBL 0.025 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 0.039 0.06 -10000 0 -0.22 21 21
Rac1/GTP 0.023 0.054 0.28 1 -0.48 3 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.039 -10000 0 -0.25 5 5
alphaV beta3 Integrin 0.044 0.053 -10000 0 -0.26 14 14
PTK2 0.01 0.11 0.27 19 -0.38 15 34
IGF1R 0.026 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.036 -10000 0 -0.43 3 3
SRC 0.025 0.005 -10000 0 -10000 0 0
CDKN1B 0.005 0.08 -10000 0 -0.41 17 17
VEGFA 0.019 0.032 -10000 0 -10000 0 0
ILK 0.005 0.079 -10000 0 -0.38 18 18
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.002 0.072 0.18 1 -0.37 17 18
PTK2B 0 0.061 0.18 21 -0.22 14 35
alphaV/beta3 Integrin/JAM-A 0.04 0.069 0.19 2 -0.23 27 29
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.029 0.054 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.057 0.048 -10000 0 -0.23 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.056 -10000 0 -0.28 6 6
alphaV/beta3 Integrin/Syndecan-1 0.035 0.071 -10000 0 -0.2 38 38
PI4KA 0.023 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.038 0.068 -10000 0 -0.21 26 26
PI4 Kinase 0.035 0.018 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
alphaV/beta3 Integrin/Osteopontin 0.013 0.1 -10000 0 -0.22 75 75
RPS6KB1 -0.021 0.062 0.38 3 -0.25 2 5
TLN1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.002 0.085 -10000 0 -0.38 17 17
GPR124 0.024 0.015 -10000 0 -10000 0 0
MAPK1 -0.001 0.084 -10000 0 -0.39 17 17
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.032 0.086 -10000 0 -0.25 40 40
cell adhesion 0.029 0.056 -10000 0 -0.25 15 15
ANGPTL3 0.002 0.019 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.028 -10000 0 -0.2 4 4
IGF-1R heterotetramer 0.026 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 -0.13 5 5
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
IGF1 0.012 0.076 -10000 0 -0.34 20 20
RAC1 0.023 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.044 0.05 -10000 0 -0.24 14 14
apoptosis 0.026 0.002 -10000 0 -10000 0 0
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.047 0.049 -10000 0 -0.26 12 12
VCL 0.022 0.032 -10000 0 -0.43 2 2
alphaV/beta3 Integrin/Del1 0.015 0.11 -10000 0 -0.28 59 59
CSF1 0.017 0.045 -10000 0 -0.43 5 5
PIK3C2A 0.003 0.085 -10000 0 -0.41 19 19
PI4 Kinase/Pyk2 0.006 0.069 -10000 0 -0.26 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.061 -10000 0 -0.23 15 15
FAK1/Vinculin 0.019 0.094 0.24 19 -0.31 16 35
alphaV beta3/Integrin/ppsTEM5 0.045 0.05 -10000 0 -0.24 14 14
RHOA 0.026 0.004 -10000 0 -10000 0 0
VTN 0.012 0.075 -10000 0 -0.43 14 14
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
FGF2 0.024 0.029 -10000 0 -0.33 3 3
F11R 0.01 0.024 -10000 0 -0.3 2 2
alphaV/beta3 Integrin/Lactadherin 0.045 0.054 -10000 0 -0.26 15 15
alphaV/beta3 Integrin/TGFBR2 0.045 0.051 -10000 0 -0.23 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.043 -10000 0 -0.24 5 5
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.044 0.045 -10000 0 -0.23 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.029 -10000 0 -0.13 18 18
alphaV/beta3 Integrin/Pyk2 0.032 0.064 0.18 16 -0.22 15 31
SDC1 0.007 0.071 -10000 0 -0.19 44 44
VAV3 -0.008 0.074 0.18 26 -0.23 31 57
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.02 0.095 0.26 19 -0.31 15 34
cell migration 0.015 0.088 0.23 20 -0.29 15 35
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.05 0.067 -10000 0 -0.21 25 25
SPP1 -0.025 0.13 -10000 0 -0.43 40 40
KDR 0.021 0.039 -10000 0 -0.23 9 9
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 -0.01 0.099 -10000 0 -0.43 21 21
angiogenesis 0 0.097 0.24 1 -0.41 17 18
Rac1/GTP 0.003 0.068 -10000 0 -0.21 29 29
EDIL3 -0.025 0.14 -10000 0 -0.43 53 53
cell proliferation 0.044 0.051 -10000 0 -0.23 15 15
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.026 0.056 -10000 0 -10000 0 0
epithelial cell differentiation -0.014 0.086 -10000 0 -0.36 6 6
ITCH 0.03 0.013 -10000 0 -10000 0 0
WWP1 0.017 0.063 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
EGFR -0.017 0.12 -10000 0 -0.4 46 46
PRL -0.011 0.016 -10000 0 -0.13 2 2
neuron projection morphogenesis -0.02 0.11 0.28 18 -0.4 2 20
PTPRZ1 0.015 0.05 -10000 0 -0.43 6 6
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.11 -10000 0 -0.32 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.04 0.1 -10000 0 -0.32 14 14
ADAM17 0.025 0.046 -10000 0 -0.42 5 5
ErbB4/ErbB4 0.006 0.051 -10000 0 -0.36 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.013 0.082 -10000 0 -0.34 10 10
NCOR1 0.024 0.028 -10000 0 -0.43 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.028 0.1 -10000 0 -0.3 14 14
GRIN2B -0.068 0.13 0.24 10 -0.36 41 51
ErbB4/ErbB2/betacellulin -0.001 0.097 -10000 0 -0.34 12 12
STAT1 0.021 0.027 -10000 0 -0.13 16 16
HBEGF 0.023 0.022 -10000 0 -10000 0 0
PRLR 0.006 0.088 -10000 0 -0.32 30 30
E4ICDs/ETO2 0.022 0.066 -10000 0 -0.35 3 3
axon guidance -0.024 0.079 -10000 0 -0.38 8 8
NEDD4 0.025 0.041 -10000 0 -0.22 10 10
Prolactin receptor/Prolactin receptor/Prolactin 0.016 0.065 -10000 0 -0.31 18 18
CBFA2T3 0.02 0.053 -10000 0 -0.43 7 7
ErbB4/ErbB2/HBEGF 0.027 0.052 -10000 0 -0.28 3 3
MAPK3 -0.018 0.11 0.26 15 -0.33 5 20
STAT1 (dimer) 0.025 0.059 -10000 0 -0.32 1 1
MAPK1 -0.017 0.11 0.26 15 -0.33 5 20
JAK2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.1 -10000 0 -0.29 17 17
NRG1 -0.062 0.13 -10000 0 -0.31 101 101
NRG3 0.001 0.1 -10000 0 -0.43 27 27
NRG2 0.025 0.02 -10000 0 -0.43 1 1
NRG4 0.002 0.075 -10000 0 -0.19 51 51
heart development -0.024 0.079 -10000 0 -0.38 8 8
neural crest cell migration -0.037 0.099 -10000 0 -0.29 17 17
ERBB2 0.01 0.036 -10000 0 -0.3 6 6
WWOX/E4ICDs 0.025 0.058 -10000 0 -0.32 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
ErbB4/EGFR/neuregulin 4 0.005 0.1 -10000 0 -0.32 21 21
apoptosis -0.001 0.11 0.37 32 -10000 0 32
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.026 0.057 -10000 0 -0.37 1 1
ErbB4/ErbB2/epiregulin 0.025 0.056 -10000 0 -0.3 5 5
ErbB4/ErbB4/betacellulin/betacellulin -0.005 0.1 -10000 0 -0.38 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.076 -10000 0 -0.32 1 1
MDM2 0.01 0.055 0.25 4 -0.32 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.1 -10000 0 -0.29 12 12
STAT5A -0.028 0.084 -10000 0 -0.4 7 7
ErbB4/EGFR/neuregulin 1 beta -0.045 0.12 -10000 0 -0.34 32 32
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 0.021 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.008 0.098 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.013 0.083 -10000 0 -0.38 6 6
LRIG1 0.015 0.069 -10000 0 -0.43 12 12
EREG 0.009 0.036 -10000 0 -0.13 24 24
BTC -0.041 0.14 -10000 0 -0.33 87 87
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.075 -10000 0 -0.38 8 8
ERBB4 0.006 0.051 -10000 0 -0.36 1 1
STAT5B 0.026 0.003 -10000 0 -10000 0 0
YAP1 -0.015 0.13 -10000 0 -0.55 27 27
GRB2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.022 0.065 -10000 0 -0.31 5 5
glial cell differentiation -0.021 0.056 0.5 1 -10000 0 1
WWOX 0.026 0.003 -10000 0 -10000 0 0
cell proliferation -0.07 0.14 -10000 0 -0.43 26 26
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 0.014 0.072 -10000 0 -0.43 13 13
Caspase 8 (4 units) 0.031 0.06 -10000 0 -0.3 4 4
NEF -0.001 0.011 -10000 0 -10000 0 0
NFKBIA 0.02 0.029 -10000 0 -10000 0 0
BIRC3 -0.005 0.1 -10000 0 -0.45 24 24
CYCS 0.006 0.049 0.18 9 -0.33 2 11
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CD247 0.01 0.068 -10000 0 -0.25 25 25
MAP2K7 0.025 0.086 -10000 0 -0.61 4 4
protein ubiquitination 0.018 0.089 0.22 12 -0.33 9 21
CRADD 0.026 0.003 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.014 0.063 -10000 0 -0.28 18 18
BID 0.01 0.048 0.18 6 -0.26 5 11
NF-kappa-B/RelA/I kappa B alpha 0.038 0.069 -10000 0 -0.24 24 24
TRADD 0.025 0.02 -10000 0 -0.43 1 1
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
CFLAR 0.026 0.007 -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 0.038 0.069 -10000 0 -0.25 24 24
MAPK8 0.019 0.082 -10000 0 -0.55 4 4
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.019 0.053 -10000 0 -0.43 7 7
TRAF2 0.026 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.047 -10000 0 -0.23 11 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.089 -10000 0 -0.4 11 11
CHUK 0.017 0.094 0.23 12 -0.36 9 21
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.061 0.054 -10000 0 -0.22 13 13
TCRz/NEF 0.009 0.052 -10000 0 -0.19 25 25
TNF -0.06 0.16 -10000 0 -0.43 68 68
FASLG -0.006 0.051 -10000 0 -0.26 8 8
NFKB1 0.021 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
CASP6 0.027 0.099 -10000 0 -0.57 8 8
CASP7 0.007 0.13 0.29 14 -0.47 26 40
RELA 0.019 0.03 -10000 0 -10000 0 0
CASP2 0.02 0.011 -10000 0 -10000 0 0
CASP3 0.007 0.13 0.29 14 -0.46 29 43
TNFRSF1A 0.017 0.054 -10000 0 -0.43 7 7
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
CASP8 0.021 0.033 -10000 0 -0.43 1 1
CASP9 0.022 0.012 -10000 0 -0.13 1 1
MAP3K14 0.014 0.095 0.21 5 -0.39 10 15
APAF-1/Caspase 9 0.003 0.083 -10000 0 -0.32 22 22
BCL2 0.016 0.082 0.27 1 -0.7 2 3
Signaling events mediated by PRL

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
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
mol:Halofuginone 0.003 0.009 -10000 0 -0.2 1 1
ITGA1 0.015 0.059 -10000 0 -0.43 7 7
CDKN1A -0.06 0.16 -10000 0 -0.37 96 96
PRL-3/alpha Tubulin 0.033 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.06 -10000 0 -0.32 21 21
AGT 0.006 0.093 -10000 0 -0.43 22 22
CCNA2 -0.039 0.079 -10000 0 -0.59 1 1
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
EGR1 -0.028 0.095 -10000 0 -0.3 53 53
CDK2/Cyclin E1 -0.03 0.15 -10000 0 -0.37 57 57
MAPK3 0.012 0.008 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.032 0.015 -10000 0 -10000 0 0
MAPK1 0.011 0.008 -10000 0 -10000 0 0
PTP4A1 -0.025 0.074 -10000 0 -0.62 1 1
PTP4A3 0.023 0.013 -10000 0 -10000 0 0
PTP4A2 0.022 0.01 -10000 0 -10000 0 0
ITGB1 0.01 0.01 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.006 0.036 -10000 0 -0.31 2 2
Rab GGTase beta/Rab GGTase alpha 0.031 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.008 0.08 -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 -0.058 0.15 -10000 0 -0.36 95 95
RHOA 0.002 0.055 -10000 0 -0.32 10 10
cell motility -0.014 0.095 0.28 1 -0.28 33 34
PRL-1/alpha Tubulin -0.004 0.084 -10000 0 -0.59 1 1
PRL-3/alpha1 Integrin 0.027 0.042 -10000 0 -0.28 6 6
ROCK1 -0.017 0.094 0.28 1 -0.28 33 34
RABGGTB 0.022 0.01 -10000 0 -10000 0 0
CDK2 0.02 0.044 -10000 0 -0.43 4 4
mitosis -0.025 0.074 -10000 0 -0.61 1 1
ATF5 0.02 0.018 -10000 0 -0.13 5 5
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.014 0.032 -10000 0 -0.69 1 1
REL 0.007 0.086 -10000 0 -0.32 28 28
HDAC7 -0.017 0.078 -10000 0 -0.29 16 16
JUN 0.019 0.022 -10000 0 -10000 0 0
EP300 0.022 0.04 -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 0.02 -10000 0 -0.3 1 1
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
T-DHT/AR 0.002 0.092 -10000 0 -0.3 17 17
MAP2K6 0.021 0.024 -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 2 2
SMARCA2 0.025 0.006 -10000 0 -10000 0 0
PDE9A 0.01 0.086 -10000 0 -0.83 3 3
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
CEBPA 0.015 0.049 -10000 0 -0.26 12 12
EHMT2 0.026 0.003 -10000 0 -10000 0 0
cell proliferation 0.002 0.11 0.36 9 -0.4 10 19
NR0B1 -0.042 0.15 -10000 0 -0.31 102 102
EGR1 -0.039 0.14 -10000 0 -0.27 112 112
RXRs/9cRA 0.019 0.086 -10000 0 -0.23 52 52
AR/RACK1/Src 0.001 0.073 0.22 1 -0.28 7 8
AR/GR -0.011 0.1 0.23 2 -0.24 69 71
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
PKN1 0.025 0.005 -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 0.05 -10000 0 -0.31 12 12
T-DHT/AR/TIF2/CARM1 -0.002 0.1 0.35 1 -0.38 19 20
SRC -0.013 0.044 0.2 8 -0.22 11 19
NR3C1 0.026 0.004 -10000 0 -10000 0 0
KLK3 -0.042 0.1 -10000 0 -0.58 1 1
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 0.073 0.27 2 -0.31 9 11
TMPRSS2 -0.065 0.29 -10000 0 -1 44 44
RXRG -0.027 0.14 -10000 0 -0.4 63 63
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.025 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.025 0.006 -10000 0 -10000 0 0
NR2C2 0.018 0.06 -10000 0 -0.43 9 9
KLK2 -0.019 0.1 0.44 1 -0.39 13 14
AR -0.029 0.099 0.13 3 -0.26 72 75
SENP1 0.026 0.004 -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 0.015 0.065 -10000 0 -0.33 15 15
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.009 0.047 -10000 0 -0.13 57 57
T-DHT/AR/RACK1/Src 0.003 0.079 0.37 2 -0.28 9 11
positive regulation of transcription 0.015 0.065 -10000 0 -0.33 15 15
DNAJA1 0.022 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.03 0.011 -10000 0 -10000 0 0
SPDEF -0.005 0.1 -10000 0 -0.43 25 25
T-DHT/AR/TIF2 -0.003 0.1 0.23 3 -0.37 21 24
T-DHT/AR/Hsp90 -0.004 0.071 0.35 1 -0.3 10 11
GSK3B 0.025 0.021 -10000 0 -0.43 1 1
NR2C1 0.026 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.039 -10000 0 -0.24 12 12
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.023 0.009 -10000 0 -10000 0 0
POU2F1 0.022 0.038 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.032 0.1 0.25 3 -0.27 42 45
CREBBP 0.026 0.003 -10000 0 -10000 0 0
SMARCE1 0.026 0.003 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.02 0.074 -10000 0 -0.3 25 25
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 0.004 -10000 0 -10000 0 0
FANCD2 0.016 0.029 -10000 0 -0.29 4 4
protein ubiquitination 0.04 0.069 -10000 0 -0.22 26 26
XRCC5 0.026 0.003 -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 0.006 -10000 0 -10000 0 0
DNA-PK 0.05 0.014 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.024 0.062 -10000 0 -0.48 4 4
FANCF 0.025 0.005 -10000 0 -10000 0 0
BRCA1 0.025 0.012 -10000 0 -10000 0 0
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
CDK2/Cyclin E1 0.027 0.037 -10000 0 -0.28 5 5
FANCG 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.02 0.075 -10000 0 -0.3 26 26
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.024 0.022 -10000 0 -0.28 2 2
NBN 0.024 0.007 -10000 0 -10000 0 0
FANCA 0.009 0.069 -10000 0 -0.2 38 38
DNA repair 0.01 0.09 0.27 9 -0.4 7 16
BRCA1/BARD1/ubiquitin 0.02 0.075 -10000 0 -0.3 26 26
BARD1/DNA-PK 0.049 0.064 -10000 0 -0.24 23 23
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.02 0.074 0.3 25 -10000 0 25
BRCA1/BARD1/CTIP/M/R/N Complex 0.018 0.057 -10000 0 -0.22 22 22
BRCA1/BACH1/BARD1/TopBP1 0.036 0.071 -10000 0 -0.26 26 26
BRCA1/BARD1/P53 0.043 0.082 -10000 0 -0.25 36 36
BARD1/CSTF1/BRCA1 0.035 0.068 -10000 0 -0.26 25 25
BRCA1/BACH1 0.025 0.012 -10000 0 -10000 0 0
BARD1 0.003 0.098 -10000 0 -0.41 27 27
PCNA 0.025 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.036 0.068 -10000 0 -0.25 26 26
BRCA1/BARD1/UbcH7 0.036 0.067 -10000 0 -0.25 25 25
BRCA1/BARD1/RAD51/PCNA 0.041 0.085 -10000 0 -0.25 38 38
BARD1/DNA-PK/P53 0.052 0.08 -10000 0 -0.23 33 33
BRCA1/BARD1/Ubiquitin 0.02 0.075 -10000 0 -0.3 26 26
BRCA1/BARD1/CTIP 0.029 0.06 0.21 1 -0.24 23 24
FA complex 0.024 0.037 -10000 0 -0.21 8 8
BARD1/EWS 0.021 0.073 -10000 0 -0.3 24 24
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.41 14 14
TOPBP1 0.025 0.02 -10000 0 -0.43 1 1
G1/S transition of mitotic cell cycle -0.041 0.081 0.24 36 -10000 0 36
BRCA1/BARD1 0.046 0.072 -10000 0 -0.22 26 26
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.07 -10000 0 -0.3 25 25
CDK2 0.02 0.044 -10000 0 -0.43 4 4
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.001 0.085 -10000 0 -0.43 14 14
RAD50 0.026 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.02 0.075 -10000 0 -0.3 26 26
EWSR1 0.026 0.004 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.028 0.023 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.016 0.055 -10000 0 -0.26 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.082 0.19 3 -0.29 15 18
NFKBIA -0.014 0.073 -10000 0 -0.23 46 46
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 0.007 0.086 -10000 0 -0.32 28 28
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.018 -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 0.025 0.02 -10000 0 -0.43 1 1
NF kappa B1 p50 dimer 0.02 0.011 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 41 41
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.009 0.082 0.19 3 -0.29 14 17
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 41 41
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 0.009 0.083 -10000 0 -0.43 17 17
I kappa B alpha/PIK3R1 -0.001 0.088 0.19 4 -0.22 46 50
cell death 0.008 0.079 0.18 3 -0.28 14 17
NF kappa B1 p105/c-Rel 0.016 0.055 -10000 0 -0.26 18 18
LCK -0.019 0.11 -10000 0 -0.25 77 77
BCL3 0.018 0.024 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.37 -10000 0 -1.1 58 58
RAD9A 0.025 0.005 -10000 0 -10000 0 0
AP1 -0.016 0.1 -10000 0 -0.28 56 56
IFNAR2 0.02 0.018 -10000 0 -10000 0 0
AKT1 0.004 0.035 -10000 0 -0.18 11 11
ER alpha/Oestrogen 0.005 0.05 -10000 0 -0.25 15 15
NFX1/SIN3/HDAC complex -0.005 0.072 -10000 0 -0.22 16 16
EGF -0.014 0.11 -10000 0 -0.31 54 54
SMG5 0.025 0.005 -10000 0 -10000 0 0
SMG6 0.026 0.002 -10000 0 -10000 0 0
SP3/HDAC2 0.029 0.027 -10000 0 -10000 0 0
TERT/c-Abl -0.1 0.34 -10000 0 -1 58 58
SAP18 0.025 0.006 -10000 0 -10000 0 0
MRN complex 0.046 0.018 -10000 0 -10000 0 0
WT1 0.001 0.045 -10000 0 -0.16 5 5
WRN 0.023 0.035 -10000 0 -0.43 3 3
SP1 0.019 0.022 -10000 0 -10000 0 0
SP3 0.022 0.015 -10000 0 -10000 0 0
TERF2IP 0.026 0.003 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.073 0.31 -10000 0 -0.9 58 58
Mad/Max 0.03 0.024 -10000 0 -10000 0 0
TERT -0.13 0.39 -10000 0 -1.2 58 58
CCND1 -0.11 0.34 -10000 0 -0.99 64 64
MAX 0.021 0.015 -10000 0 -10000 0 0
RBBP7 0.025 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
TERF2 0.021 0.006 -10000 0 -10000 0 0
PTGES3 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.025 0.003 -10000 0 -10000 0 0
Telomerase/911 0.031 0.057 0.22 2 -0.32 3 5
CDKN1B 0.009 0.024 -10000 0 -10000 0 0
RAD1 0.026 0.003 -10000 0 -10000 0 0
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
SAP30 0.025 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.036 0.007 -10000 0 -10000 0 0
UBE3A 0.022 0.014 -10000 0 -10000 0 0
JUN 0.015 0.025 -10000 0 -10000 0 0
E6 -0.001 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.015 -10000 0 -10000 0 0
FOS -0.035 0.14 -10000 0 -0.29 92 92
IFN-gamma/IRF1 0.025 0.035 -10000 0 -0.15 2 2
PARP2 0.026 0.004 -10000 0 -10000 0 0
BLM -0.009 0.1 -10000 0 -0.43 26 26
Telomerase -0.017 0.099 -10000 0 -0.33 32 32
IRF1 0.017 0.036 -10000 0 -10000 0 0
ESR1 0.01 0.07 -10000 0 -0.35 15 15
KU/TER 0.038 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.073 -10000 0 -0.25 12 12
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.001 0.074 -10000 0 -0.25 12 12
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.019 0.022 -10000 0 -10000 0 0
ATM 0.01 0.002 -10000 0 -10000 0 0
SMAD3 0.012 0.016 -10000 0 -0.3 1 1
ABL1 0.025 0.005 -10000 0 -10000 0 0
MXD1 0.021 0.015 -10000 0 -10000 0 0
MRE11A 0.025 0.006 -10000 0 -10000 0 0
HUS1 0.023 0.009 -10000 0 -10000 0 0
RPS6KB1 0.025 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.087 0.34 -10000 0 -1 54 54
NR2F2 0.017 0.061 -10000 0 -0.22 24 24
MAPK3 -0.014 0.01 -10000 0 -10000 0 0
MAPK1 -0.014 0.01 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.022 -10000 0 -0.42 1 1
NFKB1 0.026 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -10000 0 -10000 0 0
NBN 0.024 0.007 -10000 0 -10000 0 0
EGFR -0.02 0.12 -10000 0 -0.41 46 46
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.025 0.12 -10000 0 -0.32 71 71
MYC 0.002 0.087 -10000 0 -0.43 19 19
IL2 0.007 0.024 -10000 0 -10000 0 0
KU 0.038 0.007 -10000 0 -10000 0 0
RAD50 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.022 -10000 0 -0.42 1 1
TRF2/BLM 0.012 0.073 -10000 0 -0.28 25 25
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.092 0.35 -10000 0 -1 58 58
SP1/HDAC2 0.028 0.032 -10000 0 -10000 0 0
PINX1 0.025 0.005 -10000 0 -10000 0 0
Telomerase/EST1A -0.072 0.31 -10000 0 -0.9 58 58
Smad3/Myc 0.01 0.057 -10000 0 -0.27 18 18
911 complex 0.044 0.021 -10000 0 -10000 0 0
IFNG 0.015 0.021 -10000 0 -0.13 5 5
Telomerase/PinX1 -0.074 0.31 -10000 0 -0.9 58 58
Telomerase/AKT1/mTOR/p70S6K -0.01 0.1 -10000 0 -0.41 12 12
SIN3B 0.025 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Telomerase/EST1B -0.073 0.31 -10000 0 -0.9 58 58
response to DNA damage stimulus 0.006 0.009 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.065 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.033 0.025 -10000 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.072 0.31 -10000 0 -0.9 58 58
E2F1 0.008 0.058 -10000 0 -0.21 24 24
ZNFX1 0.025 0.005 -10000 0 -10000 0 0
PIF1 -0.009 0.11 -10000 0 -0.28 59 59
NCL 0.026 0.004 -10000 0 -10000 0 0
DKC1 0.026 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0.023 -10000 0 -0.3 2 2
VEGFR1 homodimer/NRP1 0.012 0.02 -10000 0 -0.3 2 2
mol:DAG -0.014 0.074 0.19 2 -0.23 49 51
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.027 -10000 0 -0.27 2 2
CaM/Ca2+ 0 0.076 -10000 0 -0.22 48 48
HIF1A 0.03 0.021 -10000 0 -0.42 1 1
GAB1 0.025 0.021 -10000 0 -0.43 1 1
AKT1 -0.015 0.082 -10000 0 -0.49 1 1
PLCG1 -0.014 0.075 -10000 0 -0.23 49 49
NOS3 -0.009 0.07 -10000 0 -0.31 2 2
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.005 0.081 0.28 1 -0.3 2 3
FLT1 0.017 0.024 -10000 0 -0.35 2 2
PGF -0.034 0.14 -10000 0 -0.31 90 90
VEGFR1 homodimer/NRP2/VEGFR121 0.042 0.035 -10000 0 -0.23 6 6
CALM1 0.025 0.009 -10000 0 -0.13 1 1
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Hsp90 0.021 0.089 0.28 3 -0.3 1 4
endothelial cell proliferation -0.026 0.097 0.27 1 -0.32 16 17
mol:Ca2+ -0.014 0.074 0.19 2 -0.23 49 51
MAPK3 -0.027 0.061 0.17 3 -0.26 1 4
MAPK1 -0.027 0.061 0.17 3 -0.26 1 4
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PLGF homodimer -0.034 0.14 -10000 0 -0.31 90 90
PRKACA 0.025 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.006 0.051 -10000 0 -0.43 2 2
VEGFA homodimer 0.019 0.032 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.027 0.03 -10000 0 -0.3 2 2
platelet activating factor biosynthetic process -0.028 0.059 -10000 0 -0.26 1 1
PI3K 0.028 0.088 -10000 0 -0.22 55 55
PRKCA -0.027 0.064 0.18 3 -0.28 1 4
PRKCB -0.038 0.074 0.18 3 -0.28 12 15
VEGFR1 homodimer/PLGF homodimer -0.008 0.092 -10000 0 -0.26 57 57
VEGFA 0.019 0.032 -10000 0 -10000 0 0
VEGFB 0.025 0.005 -10000 0 -10000 0 0
mol:IP3 -0.014 0.074 0.19 2 -0.23 49 51
RASA1 0.014 0.021 -10000 0 -0.32 1 1
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFR1 homodimer 0.016 0.024 -10000 0 -0.35 2 2
VEGFB homodimer 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Caveolin-1 0.002 0.077 -10000 0 -0.3 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.026 0.087 -10000 0 -0.22 55 55
mol:L-citrulline 0.005 0.081 0.28 1 -0.3 2 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.055 0.031 -10000 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.044 0.021 -10000 0 -0.23 1 1
CD2AP 0.026 0.002 -10000 0 -10000 0 0
PI3K/GAB1 0.035 0.09 -10000 0 -0.23 1 1
PDPK1 -0.012 0.076 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.025 -10000 0 -0.27 2 2
mol:NADP 0.005 0.081 0.28 1 -0.3 2 3
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.053 0.03 -10000 0 -0.3 1 1
VEGFR1 homodimer/NRP2 0.027 0.034 -10000 0 -0.25 6 6
PLK2 and PLK4 events

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
PLK2 0.017 0.044 -9999 0 -0.43 2 2
PLK4 0.015 0.054 -9999 0 -0.19 25 25
regulation of centriole replication 0.001 0.044 -9999 0 -0.28 7 7
Aurora A signaling

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
Aurora A/GADD45A 0.025 0.045 0.21 3 -0.27 3 6
BIRC5 -0.057 0.16 -10000 0 -0.3 128 128
NFKBIA 0.013 0.035 0.25 3 -0.24 2 5
CPEB1 0.013 0.074 -10000 0 -0.43 14 14
AKT1 0.013 0.033 0.23 2 -0.24 2 4
NDEL1 0.026 0.002 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.031 -10000 0 -0.22 2 2
NDEL1/TACC3 0.043 0.043 0.2 2 -0.23 4 6
GADD45A 0.012 0.041 -10000 0 -0.14 29 29
GSK3B 0.028 0.025 -10000 0 -0.44 1 1
PAK1/Aurora A 0.023 0.05 -10000 0 -0.25 7 7
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.014 0.079 -10000 0 -0.3 31 31
TP53 0.017 0.052 -10000 0 -0.24 17 17
DLG7 0.013 0.03 -10000 0 -0.24 2 2
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 0.046 0.046 0.21 2 -0.25 4 6
G2/M transition of mitotic cell cycle 0.028 0.031 -10000 0 -0.22 2 2
AURKA 0.022 0.04 -10000 0 -0.29 2 2
AURKB -0.044 0.13 -10000 0 -0.29 99 99
CDC25B 0.021 0.029 -10000 0 -0.23 2 2
G2/M transition checkpoint 0.012 0.026 -10000 0 -0.22 2 2
mRNA polyadenylation 0.022 0.051 -10000 0 -0.25 12 12
Aurora A/CPEB 0.022 0.051 -10000 0 -0.25 12 12
Aurora A/TACC1/TRAP/chTOG 0.058 0.039 -10000 0 -0.24 3 3
BRCA1 0.025 0.012 -10000 0 -10000 0 0
centrosome duplication 0.023 0.05 -10000 0 -0.25 7 7
regulation of centrosome cycle 0.042 0.042 0.19 2 -0.23 4 6
spindle assembly 0.056 0.039 -10000 0 -0.24 3 3
TDRD7 0.025 0.021 -10000 0 -0.43 1 1
Aurora A/RasGAP/Survivin 0.019 0.089 -10000 0 -0.21 37 37
CENPA -0.03 0.12 -10000 0 -0.38 49 49
Aurora A/PP2A 0.032 0.034 -10000 0 -0.24 2 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.016 0.036 0.18 1 -0.24 2 3
negative regulation of DNA binding 0.017 0.053 -10000 0 -0.24 17 17
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 0.012 0.027 -10000 0 -0.22 2 2
mitotic prometaphase 0.012 0.036 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.039 -10000 0 -0.29 2 2
TACC1 0.025 0.005 -10000 0 -10000 0 0
TACC3 0.012 0.052 -10000 0 -0.15 38 38
Aurora A/Antizyme1 0.04 0.035 -10000 0 -0.22 2 2
Aurora A/RasGAP 0.033 0.032 -10000 0 -0.24 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 0.015 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.032 -10000 0 -0.26 4 4
Importin alpha/Importin beta/TPX2 -0.014 0.078 -10000 0 -0.3 31 31
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.003 0.064 -10000 0 -0.24 17 17
PAK1 0.008 0.061 -10000 0 -0.16 47 47
CKAP5 0.025 0.005 -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 0.012 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
PTK2 0.009 0.088 -10000 0 -0.34 18 18
positive regulation of JNK cascade -0.007 0.092 -10000 0 -0.32 12 12
CDC42/GDP 0.02 0.12 -10000 0 -0.41 13 13
Rac1/GDP 0.003 0.12 -10000 0 -0.42 10 10
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.002 0.11 -10000 0 -0.4 12 12
nectin-3/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
RAPGEF1 0 0.12 0.27 3 -0.35 26 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0.12 -10000 0 -0.39 26 26
PDGFB-D/PDGFRB 0.025 0.012 -10000 0 -0.13 3 3
TLN1 0.002 0.017 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.083 -10000 0 -0.26 26 26
IQGAP1 0.02 0.043 -10000 0 -0.43 4 4
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
PVR 0.022 0.01 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.01 -10000 0 -10000 0 0
mol:GDP -0.002 0.14 -10000 0 -0.49 14 14
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.066 0.044 -10000 0 -0.22 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
positive regulation of lamellipodium assembly -0.004 0.088 -10000 0 -0.3 13 13
PVRL1 0.011 0.077 -10000 0 -0.43 15 15
PVRL3 0.019 0.056 -10000 0 -0.43 8 8
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
CLDN1 0.01 0.073 -10000 0 -0.26 28 28
JAM-A/CLDN1 0.049 0.063 -10000 0 -0.24 20 20
SRC -0.015 0.13 -10000 0 -0.42 29 29
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
FARP2 -0.01 0.15 -10000 0 -0.56 12 12
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) 0.037 0.042 -10000 0 -0.26 7 7
nectin-1/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
nectin-2/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.027 0.03 -10000 0 -0.26 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.067 -10000 0 -0.27 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.028 -10000 0 -0.23 4 4
F11R 0.022 0.03 -10000 0 -0.16 11 11
positive regulation of filopodium formation -0.007 0.092 -10000 0 -0.32 12 12
alphaV/beta3 Integrin/Talin 0.035 0.062 0.2 23 -0.22 13 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
PIP5K1C 0.005 0.02 -10000 0 -0.16 7 7
VAV2 0.001 0.14 -10000 0 -0.48 15 15
RAP1/GDP 0.01 0.11 -10000 0 -0.37 13 13
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.044 -10000 0 -0.26 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
Rac1/GTP -0.002 0.11 -10000 0 -0.37 13 13
PTPRM 0.01 0.025 -10000 0 -0.17 9 9
E-cadherin/beta catenin/alpha catenin 0.022 0.1 -10000 0 -0.23 60 60
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
TRAIL 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
TNFSF10 0.011 0.073 -10000 0 -0.43 12 12
positive regulation of NF-kappaB transcription factor activity 0.021 0.062 -10000 0 -0.3 14 14
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 0.036 -10000 0 -0.43 3 3
TNFRSF10A 0 0.098 -10000 0 -0.43 24 24
SMPD1 0.007 0.032 -10000 0 -0.18 14 14
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.038 -10000 0 -0.43 2 2
TRAIL/TRAILR2 0.023 0.063 -10000 0 -0.32 14 14
TRAIL/TRAILR3 0.014 0.082 -10000 0 -0.32 23 23
TRAIL/TRAILR1 0.007 0.091 -10000 0 -0.29 39 39
TRAIL/TRAILR4 0.021 0.062 -10000 0 -0.3 14 14
TRAIL/TRAILR1/DAP3/GTP 0.027 0.074 -10000 0 -0.23 36 36
IKK complex 0.014 0.045 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -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 0.05 -10000 0 -0.3 12 12
MAP3K1 0.019 0.05 -10000 0 -0.24 3 3
TRAILR4 (trimer) 0.019 0.038 -10000 0 -0.43 2 2
TRADD 0.025 0.02 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0 0.098 -10000 0 -0.43 24 24
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.06 -10000 0 -0.21 32 32
CFLAR 0.026 0.007 -10000 0 -0.13 1 1
MAPK1 0.003 0.05 -10000 0 -0.3 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP 0.049 0.078 -10000 0 -0.22 34 34
mol:ceramide 0.007 0.032 -10000 0 -0.18 14 14
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.059 -10000 0 -0.28 4 4
TRAF2 0.026 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.009 0.074 -10000 0 -0.25 31 31
CHUK 0.025 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.028 0.079 -10000 0 -0.25 37 37
DAP3 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.001 0.063 0.21 1 -0.27 12 13
JNK cascade 0.021 0.062 -10000 0 -0.3 14 14
TRAIL (trimer) 0.011 0.073 -10000 0 -0.43 12 12
TNFRSF10C 0.009 0.074 -10000 0 -0.25 31 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.037 0.073 -10000 0 -0.22 34 34
TRAIL/TRAILR2/FADD 0.041 0.053 -10000 0 -0.26 14 14
cell death 0.007 0.032 -10000 0 -0.18 14 14
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.02 0.042 -10000 0 -0.22 14 14
TRAILR2 (trimer) 0.022 0.036 -10000 0 -0.43 3 3
CASP8 0.013 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 0.062 0.054 -10000 0 -0.22 14 14
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.015 0.075 0.31 7 -0.29 12 19
PDGFB-D/PDGFRB/SLAP 0.021 0.061 -10000 0 -0.3 15 15
PDGFB-D/PDGFRB/APS/CBL 0.034 0.043 -10000 0 -0.26 7 7
AKT1 0.007 0.071 0.31 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.083 0.32 10 -0.3 10 20
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FGR -0.041 0.14 0.34 2 -0.37 72 74
mol:Ca2+ 0.019 0.074 0.29 15 -0.29 4 19
MYC 0.033 0.2 0.41 30 -0.77 20 50
SHC1 0.024 0.014 -10000 0 -0.13 4 4
HRAS/GDP 0.03 0.029 0.17 15 -10000 0 15
LRP1/PDGFRB/PDGFB 0.051 0.014 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.018 0.074 0.29 15 -0.3 4 19
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.002 0.043 -10000 0 -0.13 40 40
PDGFB-D/PDGFRB/SHP2 0.038 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.031 0.027 -10000 0 -0.31 2 2
cell cycle arrest 0.021 0.06 -10000 0 -0.3 15 15
HRAS 0.025 0.006 -10000 0 -10000 0 0
HIF1A 0.004 0.067 0.26 17 -10000 0 17
GAB1 0.012 0.091 0.31 14 -0.34 6 20
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.096 0.34 18 -0.32 6 24
PDGFB-D/PDGFRB 0.049 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.011 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.015 0.078 0.22 2 -0.33 11 13
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 0.018 0.074 0.3 15 -0.3 4 19
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.026 0.036 -10000 0 -0.18 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
BLK -0.019 0.12 0.31 1 -0.47 32 33
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 0.02 -10000 0 -0.43 1 1
VAV2 0.015 0.1 0.34 13 -0.36 10 23
CBL 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.012 -10000 0 -10000 0 0
LCK -0.072 0.18 0.34 2 -0.41 104 106
PDGFRB 0.025 0.014 -10000 0 -0.14 3 3
ACP1 0.026 0.004 -10000 0 -10000 0 0
HCK 0.003 0.084 0.31 1 -0.58 9 10
ABL1 0.006 0.094 0.29 17 -0.34 10 27
PDGFB-D/PDGFRB/CBL 0.015 0.093 0.3 13 -0.39 5 18
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 -0.13 16 16
cell proliferation 0.036 0.19 0.4 31 -0.66 21 52
SLA 0.006 0.078 -10000 0 -0.28 28 28
actin cytoskeleton reorganization 0.033 0.047 0.33 4 -10000 0 4
SRC 0.011 0.025 -10000 0 -10000 0 0
PI3K 0.004 0.025 -10000 0 -0.21 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.028 -10000 0 -0.17 2 2
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
PLCgamma1/SPHK1 0.02 0.084 0.33 10 -0.31 10 20
LYN 0.01 0.054 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 0.066 -10000 0 -0.43 11 11
NCK1-2/p130 Cas 0.072 0.032 -10000 0 -0.22 2 2
SPHK1 0.005 0.086 -10000 0 -0.43 17 17
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.018 0.074 0.3 15 -0.3 4 19
PLCG1 0.018 0.075 0.3 15 -0.3 4 19
NHERF/PDGFRB 0.048 0.031 -10000 0 -0.26 4 4
YES1 0.001 0.086 -10000 0 -0.49 13 13
cell migration 0.047 0.031 -10000 0 -0.26 4 4
SHC/Grb2/SOS1 0.07 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.01 -10000 0 -10000 0 0
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
NHERF1-2/PDGFRB/PTEN 0.059 0.034 -10000 0 -0.24 4 4
FYN 0.002 0.078 0.3 1 -0.4 15 16
DOK1 0.015 0.024 0.18 7 -0.24 1 8
HRAS/GTP 0.018 0.005 -10000 0 -10000 0 0
PDGFB 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.032 0.15 0.4 26 -0.44 19 45
PRKCD 0.006 0.066 0.18 17 -0.24 26 43
FER 0.009 0.06 0.19 16 -0.24 20 36
MAPKKK cascade 0.006 0.067 0.35 8 -10000 0 8
RASA1 0.019 0.033 0.19 16 -10000 0 16
NCK1 0.025 0.02 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.033 0.026 0.18 5 -0.22 1 6
PDGFB-D/PDGFRB/SHB 0.037 0.011 -10000 0 -10000 0 0
chemotaxis 0.006 0.093 0.29 17 -0.33 10 27
STAT1-3-5/STAT1-3-5 0.055 0.045 -10000 0 -0.21 11 11
Bovine Papilomavirus E5/PDGFRB 0.017 0.012 -10000 0 -0.095 1 1
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.041 -10000 0 -0.26 13 13
SNTA1 -0.001 0.1 -10000 0 -0.36 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.012 0.032 -10000 0 -0.26 7 7
MAPK12 -0.003 0.017 -10000 0 -0.22 3 3
CCND1 0 0.064 -10000 0 -0.41 12 12
p38 gamma/SNTA1 0.013 0.062 0.19 18 -0.21 25 43
MAP2K3 0.026 0.01 -10000 0 -10000 0 0
PKN1 0.025 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.017 -10000 0 -0.22 3 3
MAP2K6 0.003 0.011 -10000 0 -0.24 1 1
MAPT 0.004 0.06 0.24 5 -0.24 18 23
MAPK13 0.001 0.054 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.004 0.15 0.24 5 -0.38 22 27
CaM/Ca2+ 0.018 0.006 -10000 0 -0.083 1 1
AKT1 0.025 0.005 -10000 0 -10000 0 0
AKT2 0.022 0.01 -10000 0 -10000 0 0
STXBP4 0.025 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.013 0.15 0.23 24 -0.35 41 65
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -0.13 1 1
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 0.033 -10000 0 -0.13 23 23
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 -10000 0 0
ASIP -0.041 0.15 -10000 0 -0.43 59 59
PRKCI 0.026 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 -0.083 1 1
RHOQ 0.026 0.002 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 1 -0.25 1 2
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
AS160/14-3-3 0.01 0.054 -10000 0 -0.51 1 1
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 -0.018 0.16 0.26 6 -0.38 41 47
STX4 0.026 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.016 -10000 0 -0.29 1 1
SFN -0.023 0.11 -10000 0 -0.43 28 28
LNPEP 0.008 0.088 -10000 0 -0.43 20 20
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.031 0.045 -10000 0 -0.21 11 11
TC10/GTP 0.031 0.039 -10000 0 -0.21 8 8
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.033 -10000 0 -0.22 4 4
HRAS 0.025 0.006 -10000 0 -10000 0 0
APS homodimer 0.014 0.057 -10000 0 -0.43 8 8
GRB14 -0.071 0.16 -10000 0 -0.43 70 70
FOXO3 -0.019 0.15 -10000 0 -0.61 31 31
AKT1 -0.034 0.089 0.34 7 -0.29 2 9
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.03 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
SORBS1 0.023 0.035 -10000 0 -0.43 3 3
CRK 0.026 0.002 -10000 0 -10000 0 0
PTPN1 0.01 0.035 -10000 0 -10000 0 0
CAV1 0.005 0.039 0.18 11 -0.23 4 15
CBL/APS/CAP/Crk-II/C3G 0.05 0.051 -10000 0 -0.22 9 9
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.032 -10000 0 -0.22 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.028 -10000 0 -0.2 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.036 -10000 0 -0.42 1 1
RPS6KB1 -0.033 0.082 0.33 7 -0.33 1 8
PARD6A 0.026 0.002 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.04 -10000 0 -0.6 2 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.078 -10000 0 -0.34 1 1
HRAS/GTP 0.014 0.025 -10000 0 -0.21 3 3
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.061 0.037 -10000 0 -0.21 4 4
PRKCI 0.019 0.049 -10000 0 -0.44 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.084 -10000 0 -0.21 69 69
SHC1 0.024 0.014 -10000 0 -0.13 4 4
negative regulation of MAPKKK cascade 0.038 0.045 -10000 0 -0.5 2 2
PI3K 0.055 0.031 -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 -0.037 0.082 0.47 3 -0.29 2 5
PRKCZ -0.042 0.15 -10000 0 -0.36 88 88
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
SHC/SHIP 0.032 0.049 0.21 13 -0.21 7 20
F2RL2 -0.018 0.1 -10000 0 -0.19 103 103
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
Insulin Receptor/Insulin/Shc 0.039 0.029 -10000 0 -0.22 4 4
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.037 -10000 0 -0.21 4 4
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
CBL/APS/CAP/Crk-II 0.044 0.048 -10000 0 -0.23 9 9
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.038 -10000 0 -0.23 5 5
INPP5D 0.018 0.051 0.18 30 -0.22 7 37
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.034 0.18 -10000 0 -0.75 31 31
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
p62DOK/RasGAP 0.039 0.045 -10000 0 -0.51 2 2
INS 0.015 0.041 -10000 0 -0.43 4 4
mol:PI-3-4-P2 0.018 0.05 0.18 30 -0.22 7 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.035 0.086 0.33 7 -0.25 8 15
PTPRA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TC10/GTP/CIP4 0.032 0.024 -10000 0 -0.26 3 3
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.022 0.024 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS1 0.04 0.028 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS3 0.029 0.033 -10000 0 -0.31 4 4
Par3/Par6 0.047 0.061 -10000 0 -0.22 24 24
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.018 -10000 0 -10000 0 0
CDKN1B 0.014 0.063 -10000 0 -0.28 17 17
CDKN1A 0.001 0.067 -10000 0 -0.29 15 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
FOXO3 0.015 0.044 -10000 0 -0.28 9 9
AKT1 0.007 0.058 -10000 0 -0.3 18 18
BAD 0.025 0.005 -10000 0 -10000 0 0
AKT3 0.01 0.046 -10000 0 -0.48 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.062 -10000 0 -0.28 18 18
AKT1/ASK1 0.027 0.064 -10000 0 -0.27 18 18
BAD/YWHAZ 0.044 0.02 -10000 0 -10000 0 0
RICTOR 0.026 0.003 -10000 0 -10000 0 0
RAF1 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.063 0.26 18 -10000 0 18
TSC1 0.009 0.057 -10000 0 -0.28 17 17
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.06 -10000 0 -0.28 15 15
EP300 0.022 0.04 -10000 0 -0.43 4 4
mol:GDP 0.011 0.06 -10000 0 -0.29 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.01 0.059 -10000 0 -0.28 18 18
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.005 0.016 -10000 0 -0.25 2 2
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
MAPKAP1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.068 0.46 2 -0.19 7 9
YWHAH 0.019 0.033 -10000 0 -0.13 23 23
AKT1S1 0.016 0.037 -10000 0 -0.28 4 4
CASP9 0.011 0.05 0.2 1 -0.28 12 13
YWHAB 0.025 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.066 0.24 2 -0.27 16 18
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
YWHAE 0.026 0.002 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.001 0.062 0.2 1 -0.26 14 15
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.018 -10000 0 -10000 0 0
CHUK 0.01 0.056 -10000 0 -0.28 16 16
BAD/BCL-XL 0.032 0.062 -10000 0 -0.27 17 17
mTORC2 0.032 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.02 -10000 0 -0.29 2 2
FOXO1-3a-4/14-3-3 family 0.023 0.08 0.23 1 -0.36 5 6
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
MDM2 0.013 0.061 0.26 1 -0.28 17 18
MAPKKK cascade -0.032 0.06 0.28 15 -10000 0 15
MDM2/Cbp/p300 0.043 0.065 0.26 1 -0.27 15 16
TSC1/TSC2 0.014 0.068 0.24 15 -0.28 17 32
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.062 0.25 1 -0.26 15 16
glucose import -0.016 0.064 0.21 2 -0.24 35 37
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.047 0.2 14 -10000 0 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.051 -10000 0 -0.22 27 27
GSK3A 0.016 0.041 -10000 0 -0.28 5 5
FOXO1 0.01 0.059 -10000 0 -0.28 17 17
GSK3B 0.011 0.057 -10000 0 -0.28 16 16
SFN -0.023 0.11 -10000 0 -0.43 28 28
G1/S transition of mitotic cell cycle 0.02 0.051 0.26 10 -0.28 4 14
p27Kip1/14-3-3 family 0.024 0.066 -10000 0 -0.94 1 1
PRKACA 0.025 0.005 -10000 0 -10000 0 0
KPNA1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -10000 0 0
RHEB 0.02 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.025 0.012 -10000 0 -0.13 3 3
mol:S1P 0.001 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.039 -10000 0 -0.25 8 8
GNAO1 0.022 0.046 -10000 0 -0.44 5 5
S1P/S1P3/G12/G13 0.038 0.043 -10000 0 -0.23 9 9
AKT1 0.015 0.074 -10000 0 -0.38 14 14
AKT3 0.013 0.13 -10000 0 -0.86 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.012 -10000 0 -0.13 3 3
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.022 0.012 -10000 0 -10000 0 0
GNAI1 0.02 0.036 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.006 0.075 -10000 0 -0.2 45 45
S1PR2 0.022 0.036 -10000 0 -0.31 5 5
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.074 -10000 0 -0.27 19 19
MAPK3 0.006 0.07 -10000 0 -0.28 15 15
MAPK1 0.008 0.065 -10000 0 -0.26 14 14
JAK2 0.008 0.076 0.2 3 -0.3 13 16
CXCR4 0.001 0.078 -10000 0 -0.28 20 20
FLT1 0.026 0.024 -10000 0 -0.49 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 -0.29 13 13
S1P/S1P3/Gi 0.011 0.075 -10000 0 -0.28 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.073 -10000 0 -0.27 15 15
VEGFA 0.021 0.033 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.014 0.062 -10000 0 -0.27 9 9
VEGFR1 homodimer/VEGFA homodimer 0.036 0.034 -10000 0 -0.4 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.001 0.081 -10000 0 -0.25 41 41
GNAQ 0.026 0.004 -10000 0 -10000 0 0
GNAZ 0.026 0.008 -10000 0 -10000 0 0
G12/G13 0.032 0.015 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.011 0.068 -10000 0 -0.28 13 13
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.033 0.2 1 -10000 0 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.008 -10000 0 -0.13 1 1
STAT1 (dimer)/Cbp/p300 0.038 0.05 0.29 2 -0.23 2 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.025 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.075 -10000 0 -0.23 24 24
CaM/Ca2+ 0.046 0.034 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.019 0.033 -10000 0 -10000 0 0
AKT1 0.002 0.039 0.24 3 -10000 0 3
MAP2K1 -0.002 0.036 0.25 3 -10000 0 3
MAP3K11 0.011 0.032 0.28 2 -10000 0 2
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.059 0.19 -10000 0 -0.42 100 100
Rap1/GTP 0.012 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.056 0.035 -10000 0 -10000 0 0
CEBPB 0.016 0.11 0.29 2 -0.48 16 18
STAT3 0.026 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.031 0.15 -10000 0 -1.1 8 8
STAT1 0.01 0.036 0.26 3 -10000 0 3
CALM1 0.025 0.009 -10000 0 -0.13 1 1
IFN-gamma (dimer) 0.011 0.021 -10000 0 -0.13 5 5
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
STAT1 (dimer)/PIAS1 0.022 0.043 0.26 3 -0.2 4 7
CEBPB/PTGES2/Cbp/p300 0.027 0.075 -10000 0 -0.32 15 15
mol:Ca2+ 0.042 0.031 -10000 0 -10000 0 0
MAPK3 0.016 0.065 -10000 0 -0.74 2 2
STAT1 (dimer) -0.021 0.1 -10000 0 -0.32 22 22
MAPK1 0.011 0.089 -10000 0 -0.69 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 0.025 0.02 -10000 0 -0.43 1 1
DAPK1 0.011 0.12 0.32 3 -0.59 18 21
SMAD7 -0.009 0.046 0.17 3 -0.15 6 9
CBL/CRKL/C3G 0.035 0.032 0.29 1 -10000 0 1
PI3K 0.044 0.035 -10000 0 -10000 0 0
IFNG 0.011 0.021 -10000 0 -0.13 5 5
apoptosis 0.006 0.11 0.31 2 -0.44 23 25
CAMK2G 0.024 0.021 -10000 0 -0.43 1 1
STAT3 (dimer) 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.099 0.17 -10000 0 -0.43 97 97
CAMK2B -0.018 0.12 -10000 0 -0.43 33 33
FRAP1 -0.002 0.036 0.18 8 -10000 0 8
PRKCD -0.008 0.056 0.24 3 -0.22 3 6
RAP1B 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.075 -10000 0 -0.23 24 24
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.022 0.04 -10000 0 -0.43 4 4
IRF1 -0.001 0.062 0.26 4 -0.31 7 11
STAT1 (dimer)/PIASy 0.021 0.041 0.28 3 -10000 0 3
SOCS1 0.001 0.17 -10000 0 -1.4 8 8
mol:GDP 0.032 0.03 0.27 1 -10000 0 1
CASP1 -0.012 0.058 0.2 3 -0.25 13 16
PTGES2 0.025 0.005 -10000 0 -10000 0 0
IRF9 0.022 0.041 0.17 5 -0.19 1 6
mol:PI-3-4-5-P3 0.031 0.028 -10000 0 -10000 0 0
RAP1/GDP 0.028 0.025 -10000 0 -10000 0 0
CBL 0.01 0.031 0.28 2 -10000 0 2
MAP3K1 0.01 0.033 0.28 2 -10000 0 2
PIAS1 0.022 0.04 -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 -0.023 0.075 -10000 0 -0.23 24 24
PTPN11 0.013 0.029 0.23 2 -10000 0 2
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.21 -10000 0 -0.9 24 24
oxygen homeostasis 0.002 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.035 0.09 0.23 1 -0.32 5 6
EPO 0.027 0.13 -10000 0 -0.5 6 6
FIH (dimer) 0.022 0.021 -10000 0 -10000 0 0
APEX1 0.022 0.024 -10000 0 -10000 0 0
SERPINE1 -0.011 0.19 -10000 0 -0.45 59 59
FLT1 0.014 0.14 -10000 0 -0.7 12 12
ADORA2A 0.017 0.15 0.34 3 -0.51 6 9
germ cell development 0.016 0.16 -10000 0 -0.49 16 16
SLC11A2 0.023 0.15 -10000 0 -0.52 6 6
BHLHE40 0.017 0.16 -10000 0 -0.55 13 13
HIF1AN 0.022 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.036 0.12 -10000 0 -0.37 7 7
ETS1 0.027 0.05 -10000 0 -0.43 5 5
CITED2 0.017 0.12 -10000 0 -0.62 11 11
KDR 0.017 0.14 -10000 0 -0.81 12 12
PGK1 0.023 0.15 -10000 0 -0.52 6 6
SIRT1 0.025 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.059 0.18 -10000 0 -0.56 8 8
EPAS1 0.012 0.073 -10000 0 -0.29 9 9
SP1 0.025 0.024 -10000 0 -0.1 10 10
ABCG2 0.022 0.16 -10000 0 -0.6 6 6
EFNA1 0.023 0.15 -10000 0 -0.5 8 8
FXN 0.018 0.14 0.34 3 -0.55 4 7
POU5F1 0.015 0.17 -10000 0 -0.5 17 17
neuron apoptosis -0.058 0.18 0.54 8 -10000 0 8
EP300 0.022 0.04 -10000 0 -0.43 4 4
EGLN3 0.012 0.069 -10000 0 -0.43 11 11
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 0.049 0.015 -10000 0 -10000 0 0
VHL 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.021 0.025 -10000 0 -10000 0 0
SLC2A1 0.014 0.14 0.35 2 -0.52 6 8
TWIST1 0.011 0.15 0.34 2 -0.5 13 15
ELK1 0.031 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.042 0.12 -10000 0 -0.39 5 5
VEGFA 0.022 0.15 -10000 0 -0.51 6 6
CREBBP 0.026 0.003 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.016 0.12 -9999 0 -0.28 70 70
Ran/GTP/Exportin 1/HDAC1 0.006 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.12 -9999 0 -0.28 65 65
SUMO1 0.026 0.002 -9999 0 -10000 0 0
ZFPM1 0.025 0.02 -9999 0 -0.43 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
FKBP3 0.026 0.004 -9999 0 -10000 0 0
Histones 0.026 0.075 -9999 0 -0.23 4 4
YY1/LSF 0.027 0.04 -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 -0.017 0.087 -9999 0 -0.23 67 67
I kappa B alpha/HDAC1 0.009 0.073 -9999 0 -0.34 7 7
SAP18 0.025 0.005 -9999 0 -10000 0 0
RELA -0.006 0.084 -9999 0 -0.21 64 64
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 -0.25 5 5
NuRD/MBD3 Complex 0.019 0.023 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.008 0.088 -9999 0 -0.31 7 7
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.015 0.065 -9999 0 -0.33 15 15
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 0.015 0.066 -9999 0 -0.36 1 1
RBBP7 0.026 0.003 -9999 0 -10000 0 0
NPC 0.016 0.001 -9999 0 -10000 0 0
RBBP4 0.021 0.022 -9999 0 -0.43 1 1
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 -0.013 0.075 -9999 0 -0.38 7 7
KAT2B 0.025 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.021 0.017 -9999 0 -10000 0 0
SIN3 complex 0.059 0.023 -9999 0 -10000 0 0
SMURF1 0.021 0.011 -9999 0 -10000 0 0
CHD3 0.025 0.02 -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 0.024 0.028 -9999 0 -0.43 2 2
YY1/HDAC3 0.002 0.063 -9999 0 -0.22 9 9
YY1/HDAC2 0.028 0.036 -9999 0 -0.2 7 7
YY1/HDAC1 0.022 0.038 -9999 0 -0.21 7 7
NuRD/MBD2 Complex (MeCP1) 0.019 0.029 -9999 0 -0.34 1 1
PPARG -0.026 0.12 -9999 0 -0.29 78 78
HDAC8/hEST1B 0.049 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 0.017 0.054 -9999 0 -0.43 7 7
HDAC3/SMRT (N-CoR2) 0.01 0.071 -9999 0 -0.27 4 4
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 0.003 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.014 0.063 -9999 0 -10000 0 0
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC3 -0.01 0.065 -9999 0 -0.17 68 68
HDAC2 0.025 0.005 -9999 0 -10000 0 0
YY1 0.017 0.024 -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 0.027 -9999 0 -0.28 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 0.042 -9999 0 -0.23 5 5
YY1/SAP30/HDAC1 0.034 0.039 -9999 0 -0.19 7 7
EP300 0.022 0.04 -9999 0 -0.43 4 4
STAT3 (dimer non-phopshorylated) 0.018 0.027 -9999 0 -0.28 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.075 -9999 0 -0.38 7 7
histone deacetylation 0.03 0.037 -9999 0 -0.34 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.061 -9999 0 -0.22 8 8
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 0.005 -9999 0 -10000 0 0
GATA2/HDAC3 0.006 0.08 -9999 0 -0.26 15 15
GATA1/HDAC1 0.029 0.02 -9999 0 -10000 0 0
GATA1/HDAC3 0.007 0.072 -9999 0 -0.25 6 6
CHD4 0.025 0.007 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.031 0.12 -9999 0 -0.32 69 69
SIN3/HDAC complex/Mad/Max 0.017 0.034 -9999 0 -10000 0 0
NuRD Complex 0.016 0.067 -9999 0 -0.22 6 6
positive regulation of chromatin silencing 0.024 0.074 -9999 0 -0.23 4 4
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 0.031 -9999 0 -0.24 1 1
GATA1/Fog1 0.034 0.022 -9999 0 -0.31 1 1
FKBP25/HDAC1/HDAC2 0.042 0.023 -9999 0 -10000 0 0
TNF -0.06 0.16 -9999 0 -0.43 68 68
negative regulation of cell growth 0.019 0.047 -9999 0 -0.24 6 6
NuRD/MBD2/PRMT5 Complex 0.019 0.029 -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 69 69
SIN3/HDAC complex/NCoR1 0.02 0.047 -9999 0 -0.25 9 9
TFCP2 0.025 0.02 -9999 0 -0.43 1 1
NR2C1 0.026 0.003 -9999 0 -10000 0 0
MBD3 0.025 0.006 -9999 0 -10000 0 0
MBD2 0.026 0.004 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC -0.005 0.15 -10000 0 -1.3 6 6
PLK1 0.027 0.15 -10000 0 -1.3 4 4
CDKN1B 0.052 0.11 -10000 0 -0.34 8 8
FOXO3 0.044 0.096 -10000 0 -0.52 5 5
KAT2B 0.03 0.014 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.078 -10000 0 -0.49 7 7
CAT 0.037 0.11 -10000 0 -1.2 1 1
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.016 -10000 0 -10000 0 0
FOXO1 0.007 0.082 -10000 0 -0.47 9 9
MAPK10 0.044 0.061 0.19 67 -0.21 2 69
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.06 0.064 0.29 2 -0.36 1 3
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 0.027 0.002 -10000 0 -10000 0 0
EP300 0.022 0.042 -10000 0 -0.43 4 4
BCL2L11 0.024 0.12 -10000 0 -1.3 4 4
FOXO1/SKP2 0.017 0.084 -10000 0 -0.4 12 12
mol:GDP 0.008 0.01 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A -0.033 0.22 -10000 0 -0.49 84 84
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.07 -10000 0 -0.57 2 2
MST1 0.006 0.1 -10000 0 -0.36 32 32
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 -0.001 0.094 -10000 0 -0.66 2 2
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.036 0.063 0.19 54 -0.22 10 64
MAPK9 0.046 0.059 0.19 70 -10000 0 70
YWHAG 0.019 0.024 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
SIRT1 0.024 0.007 -10000 0 -10000 0 0
SOD2 0.054 0.1 -10000 0 -0.69 2 2
RBL2 0.058 0.094 -10000 0 -1.1 1 1
RAL/GDP 0.037 0.019 -10000 0 -10000 0 0
CHUK 0.03 0.013 -10000 0 -10000 0 0
Ran/GTP 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
RAL/GTP 0.04 0.019 -10000 0 -10000 0 0
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
FASLG 0.025 0.023 -10000 0 -10000 0 0
SKP2 0.021 0.046 -10000 0 -0.32 8 8
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 -0.52 3 3
FOXO1-3a-4/beta catenin 0.08 0.091 -10000 0 -0.39 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.083 -10000 0 -0.4 12 12
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
SGK1 0.02 0.067 -10000 0 -0.4 12 12
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.006 -10000 0 -10000 0 0
ZFAND5 0.059 0.064 0.35 3 -10000 0 3
SFN -0.023 0.11 -10000 0 -0.43 28 28
CDK2 0.02 0.046 -10000 0 -0.43 4 4
FOXO3A/14-3-3 0.008 0.086 -10000 0 -0.68 2 2
CREBBP 0.026 0.015 -10000 0 -10000 0 0
FBXO32 0.052 0.15 -10000 0 -1.2 3 3
BCL6 0.052 0.11 -10000 0 -0.72 4 4
RALB 0.027 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -0.13 23 23
IGF1 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
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTK2 0.023 0.008 -10000 0 -10000 0 0
CRKL 0.01 0.037 0.14 3 -0.22 11 14
GRB2/SOS1/SHC 0.05 0.014 -10000 0 -10000 0 0
HRAS 0.025 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.02 0.039 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.042 0.046 -10000 0 -0.24 12 12
AKT1 -0.009 0.041 0.16 8 -0.2 12 20
BAD -0.009 0.038 0.16 7 -0.19 9 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.038 0.16 2 -0.22 12 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.026 0.041 0.2 1 -0.22 12 13
RAF1 0.008 0.059 -10000 0 -0.42 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.052 0.045 -10000 0 -0.21 11 11
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.043 -10000 0 -0.24 12 12
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RPS6KB1 -0.008 0.043 0.19 7 -0.2 12 19
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.002 0.05 -10000 0 -0.34 4 4
PXN 0.026 0.004 -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 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.034 -10000 0 -0.2 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.064 0.047 -10000 0 -0.19 12 12
IGF-1R heterotetramer 0.025 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.042 0.044 -10000 0 -0.22 12 12
Crk/p130 Cas/Paxillin 0.051 0.046 0.21 2 -0.2 13 15
IGF1R 0.025 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.077 -10000 0 -0.36 19 19
IRS2/Crk 0.019 0.039 0.16 2 -0.21 13 15
PI3K 0.054 0.045 -10000 0 -0.21 12 12
apoptosis -0.014 0.04 0.2 1 -0.16 6 7
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
PRKCD -0.001 0.086 -10000 0 -0.42 16 16
RAF1/14-3-3 E 0.025 0.058 -10000 0 -0.37 5 5
BAD/14-3-3 0.015 0.042 0.17 6 -0.21 1 7
PRKCZ -0.013 0.05 0.17 6 -0.21 17 23
Crk/p130 Cas/Paxillin/FAK1 0.028 0.041 -10000 0 -0.21 1 1
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 15 15
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.046 0.051 -10000 0 -0.21 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 0.027 0.042 -10000 0 -0.22 12 12
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.01 0.038 0.16 2 -0.22 12 14
IRS1 0.011 0.043 0.12 11 -0.24 12 23
IRS2 0.009 0.039 0.16 2 -0.22 13 15
IGF-1R heterotetramer/IGF1 0.027 0.058 -10000 0 -0.32 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDPK1 0.012 0.045 0.19 8 -0.2 13 21
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKD1 0.008 0.061 -10000 0 -0.32 15 15
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.029 0.13 -10000 0 -0.31 78 78
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.058 -10000 0 -0.27 7 7
HIF1A 0.009 0.034 -10000 0 -0.26 5 5
COPS5 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.03 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A -0.013 0.11 -10000 0 -0.43 31 31
ARNT/IPAS -0.006 0.097 -10000 0 -0.3 43 43
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 -0.27 7 7
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 0.047 -10000 0 -0.26 7 7
PHD1-3/OS9 0.047 0.046 -10000 0 -0.22 9 9
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 0.29 1 -0.26 6 7
VHL 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.047 -10000 0 -0.27 6 6
EGLN3 0.016 0.066 -10000 0 -0.43 11 11
EGLN2 0.022 0.01 -10000 0 -10000 0 0
EGLN1 0.026 0.004 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.41 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.065 -10000 0 -0.53 6 6
ARNT 0.025 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.006 0.07 0.32 1 -0.29 7 8
p38 MAPK signaling 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
TRAF6/ASK1 0.015 0.032 -10000 0 -0.21 8 8
TRAF2/ASK1 0.03 0.033 -10000 0 -0.26 6 6
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 0.011 0.072 -10000 0 -0.34 6 6
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.092 0.2 4 -0.32 16 20
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 -0.43 19 19
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -0.13 1 1
GADD45A 0.012 0.041 -10000 0 -0.14 29 29
GADD45B 0.009 0.07 -10000 0 -0.22 33 33
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
MAP3K6 0.02 0.02 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -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 0.026 0.042 -10000 0 -0.3 6 6
TAK1/TAB family -0.002 0.025 0.16 7 -0.13 5 12
RAC1/OSM/MEKK3 0.042 0.02 -10000 0 -10000 0 0
TRAF2 0.026 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.059 -10000 0 -0.28 5 5
TRAF6 0.006 0.013 -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 0.12 -10000 0 -0.43 33 33
CCM2 0.022 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.074 -10000 0 -0.25 34 34
MAPK11 0.018 0.057 -10000 0 -0.43 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.021 0.08 -10000 0 -0.25 36 36
OSM/MEKK3 0.032 0.015 -10000 0 -10000 0 0
TAOK1 -0.012 0.085 -10000 0 -0.29 43 43
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.004 -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 0.02 0.049 -10000 0 -0.43 6 6
MAP3K10 0.019 0.022 -10000 0 -0.13 9 9
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.02 0.028 -10000 0 -0.24 5 5
GADD45/MTK1/MTK1 0.027 0.068 -10000 0 -0.22 25 25
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
AKT1 0.034 0.078 0.32 5 -0.52 4 9
PTK2B 0.005 0.073 0.35 2 -0.45 4 6
VEGFR2 homodimer/Frs2 0.028 0.052 -10000 0 -0.61 3 3
CAV1 0.006 0.051 -10000 0 -0.43 2 2
CALM1 0.025 0.009 -10000 0 -0.13 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.044 0.053 -10000 0 -0.57 3 3
endothelial cell proliferation 0.043 0.084 0.29 14 -0.45 4 18
mol:Ca2+ 0.019 0.06 0.36 1 -0.38 5 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.047 0.061 -10000 0 -0.54 3 3
RP11-342D11.1 0.008 0.058 0.18 15 -0.41 5 20
CDH5 0.025 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.063 0.024 -10000 0 -0.23 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
SHC2 0.025 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.049 -10000 0 -0.42 3 3
SH2D2A -0.02 0.12 -10000 0 -0.43 36 36
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.059 0.082 0.29 4 -0.41 6 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.089 -10000 0 -0.26 37 37
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
SHC/GRB2/SOS1 0.065 0.058 -10000 0 -0.45 3 3
GRB10 0.015 0.067 0.36 1 -0.52 5 6
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
PAK1 0.008 0.061 -10000 0 -0.16 47 47
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.063 0.062 -10000 0 -0.53 3 3
HRAS 0.025 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.019 0.052 -10000 0 -0.36 5 5
HIF1A 0.025 0.021 -10000 0 -0.43 1 1
FRS2 0.026 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.045 0.06 -10000 0 -0.54 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.039 -10000 0 -0.23 9 9
Nck/Pak 0.023 0.05 -10000 0 -0.3 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.053 -10000 0 -0.57 3 3
mol:GDP 0.051 0.054 -10000 0 -0.44 3 3
mol:NADP 0.042 0.071 0.27 6 -0.38 5 11
eNOS/Hsp90 0.053 0.068 0.28 5 -0.36 5 10
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.06 0.36 1 -0.38 5 6
HIF1A/ARNT 0.036 0.018 -10000 0 -0.3 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.02 0.032 -10000 0 -10000 0 0
VEGFC 0.017 0.05 -10000 0 -0.43 5 5
FAK1/Vinculin 0.038 0.082 0.29 3 -0.53 5 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.071 -10000 0 -0.28 14 14
PTPN6 0.014 0.064 -10000 0 -0.34 14 14
EPAS1 0.03 0.03 -10000 0 -0.33 3 3
mol:L-citrulline 0.042 0.071 0.27 6 -0.38 5 11
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.055 0.051 -10000 0 -0.49 3 3
VEGFR2 homodimer/VEGFA homodimer 0.047 0.06 -10000 0 -0.45 5 5
VEGFR2/3 heterodimer 0.026 0.058 -10000 0 -0.47 5 5
VEGFB 0.025 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.072 0.32 5 -0.52 4 9
VEGFR2 homodimer 0.015 0.056 -10000 0 -0.69 3 3
FLT1 0.024 0.021 -10000 0 -0.43 1 1
NEDD4 0.022 0.04 -10000 0 -0.22 10 10
MAPK3 0.004 0.064 0.28 4 -0.38 4 8
MAPK1 0.005 0.064 0.27 5 -0.38 4 9
VEGFA145/NRP2 0.03 0.043 -10000 0 -0.28 6 6
VEGFR1/2 heterodimer 0.028 0.052 -10000 0 -0.61 3 3
KDR 0.015 0.056 -10000 0 -0.7 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.043 0.062 -10000 0 -0.41 5 5
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.005 0.068 0.28 5 -0.4 4 9
PI3K 0.041 0.063 -10000 0 -0.54 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.045 0.053 -10000 0 -0.57 3 3
FES 0.017 0.062 0.2 2 -0.42 5 7
GAB1 0.028 0.059 -10000 0 -0.5 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.05 -10000 0 -0.51 3 3
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.066 0.31 2 -0.39 5 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.055 -10000 0 -0.36 7 7
PI3K/GAB1 0.046 0.066 -10000 0 -0.47 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.063 0.063 -10000 0 -0.53 3 3
PRKACA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.063 -10000 0 -0.34 10 10
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.014 0.062 0.36 1 -0.42 5 6
actin cytoskeleton reorganization 0.023 0.089 -10000 0 -0.26 37 37
PTK2 0.016 0.065 -10000 0 -0.58 3 3
EDG1 0.008 0.058 0.18 15 -0.41 5 20
mol:DAG 0.019 0.06 0.36 1 -0.38 5 6
CaM/Ca2+ 0.028 0.056 -10000 0 -0.44 3 3
MAP2K3 0.004 0.069 0.36 1 -0.51 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.065 0.089 -10000 0 -0.53 5 5
PLCG1 0.019 0.061 0.36 1 -0.39 5 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.055 0.052 -10000 0 -0.49 3 3
IQGAP1 0.02 0.043 -10000 0 -0.43 4 4
YES1 0.022 0.04 -10000 0 -0.43 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.045 0.053 -10000 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.037 0.065 -10000 0 -0.32 11 11
cell migration 0.046 0.09 0.27 10 -0.51 6 16
mol:PI-3-4-5-P3 0.04 0.06 -10000 0 -0.5 3 3
FYN 0.025 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.022 0.058 -10000 0 -0.39 5 5
mol:NO 0.042 0.071 0.27 6 -0.38 5 11
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.046 -10000 0 -0.42 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.066 -10000 0 -0.53 5 5
VHL 0.026 0.004 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
NOS3 0.043 0.076 0.3 3 -0.43 5 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.054 -10000 0 -0.57 3 3
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.01 0.055 0.36 1 -0.39 3 4
PRKCB -0.001 0.071 0.36 2 -0.35 7 9
VCL 0.022 0.032 -10000 0 -0.43 2 2
VEGFA165/NRP1 0.029 0.06 0.21 1 -0.41 5 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.053 -10000 0 -0.57 3 3
VEGFA165/NRP2 0.03 0.043 -10000 0 -0.28 6 6
MAPKKK cascade 0.034 0.069 0.3 4 -0.42 5 9
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFC homodimer 0.017 0.05 -10000 0 -0.43 5 5
NCK1 0.025 0.02 -10000 0 -0.43 1 1
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.08 0.28 4 -0.56 4 8
MAP3K13 0.013 0.072 0.36 1 -0.4 6 7
PDPK1 0.025 0.061 0.27 2 -0.5 3 5
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.02 0.045 0.38 6 -10000 0 6
PI3K Class IB/PDE3B 0.02 0.045 -10000 0 -0.38 6 6
PDE3B 0.02 0.046 -10000 0 -0.38 6 6
Canonical NF-kappaB pathway

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
FBXW11 0.028 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 0.053 0.061 0.21 9 -0.28 1 10
ERC1 0.024 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.051 -10000 0 -0.3 9 9
NFKBIA 0.019 0.034 0.21 15 -10000 0 15
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 0.02 0.033 -10000 0 -10000 0 0
IKK complex/A20 0.03 0.099 -10000 0 -0.36 5 5
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 0.045 -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 0.045 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.041 0.025 -10000 0 -0.23 1 1
NOD2 0.011 0.069 -10000 0 -0.23 29 29
NFKB1 0.028 0.004 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
MALT1 0.026 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.037 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 69 69
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
CHUK 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.43 68 68
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 0.018 0.034 0.21 15 -10000 0 15
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.017 0.054 -10000 0 -0.43 7 7
IKK complex 0.052 0.05 0.25 1 -10000 0 1
CYLD 0.026 0.003 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.054 0.25 1 -0.37 1 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.037 0.05 -10000 0 -0.41 1 1
CLOCK 0.002 0.1 -10000 0 -0.43 28 28
TIMELESS/CRY2 0.026 0.047 -10000 0 -0.38 1 1
DEC1/BMAL1 0.031 0.022 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
NR1D1 0.009 0.1 -10000 0 -1.3 3 3
ARNTL 0.025 0.015 -10000 0 -0.13 3 3
TIMELESS 0.013 0.041 -10000 0 -0.42 1 1
NPAS2 0.021 0.052 -10000 0 -0.31 10 10
CRY2 0.023 0.035 -10000 0 -0.43 3 3
mol:CO -0.007 0.011 0.13 3 -10000 0 3
CHEK1 0.023 0.018 -10000 0 -0.13 6 6
mol:HEME 0.007 0.011 -10000 0 -0.13 3 3
PER1 0.018 0.06 -10000 0 -0.43 9 9
BMAL/CLOCK/NPAS2 0.037 0.079 -10000 0 -0.26 31 31
BMAL1/CLOCK 0.005 0.11 -10000 0 -0.86 3 3
S phase of mitotic cell cycle 0.037 0.05 -10000 0 -0.41 1 1
TIMELESS/CHEK1/ATR 0.038 0.05 -10000 0 -0.42 1 1
mol:NADPH 0.007 0.011 -10000 0 -0.13 3 3
PER1/TIMELESS 0.025 0.054 -10000 0 -0.38 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.008 0.029 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.038 -10000 0 -0.25 5 5
forebrain development 0.018 0.14 0.46 2 -0.52 14 16
GNAO1 0.022 0.046 -10000 0 -0.43 5 5
SMO/beta Arrestin2 0.029 0.031 -10000 0 -0.3 3 3
SMO 0.018 0.036 -10000 0 -0.43 3 3
ARRB2 0.026 0.004 -10000 0 -10000 0 0
GLI3/SPOP 0.016 0.087 -10000 0 -0.36 12 12
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.023 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
XPO1 0.027 0.007 -10000 0 -10000 0 0
GLI1/Su(fu) 0.011 0.11 -10000 0 -0.76 5 5
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.036 -10000 0 -0.43 3 3
MIM/GLI2A 0.017 0.043 -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 0.048 0.27 2 -10000 0 2
GLI3 0.006 0.088 0.22 2 -0.36 14 16
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 0.04 -10000 0 -0.43 4 4
Gi family/GTP 0.002 0.055 -10000 0 -0.3 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) 0.013 0.073 -10000 0 -0.44 5 5
GLI2/Su(fu) 0.027 0.049 -10000 0 -0.37 3 3
FOXA2 0.012 0.093 -10000 0 -0.75 5 5
neural tube patterning 0.018 0.14 0.46 2 -0.52 14 16
SPOP 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.046 -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 0.043 -10000 0 -0.37 5 5
embryonic limb morphogenesis 0.018 0.14 0.46 2 -0.52 14 16
SUFU 0.018 0.018 -10000 0 -0.16 3 3
LGALS3 0.012 0.053 -10000 0 -0.15 39 39
catabolic process 0.042 0.09 0.29 1 -0.58 3 4
GLI3A/CBP 0.003 0.087 -10000 0 -0.32 31 31
KIF3A 0.025 0.02 -10000 0 -0.43 1 1
GLI1 0.018 0.14 0.46 2 -0.54 14 16
RAB23 0.025 0.02 -10000 0 -0.43 1 1
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.035 -10000 0 -0.43 3 3
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.045 0.048 -10000 0 -0.24 4 4
GNAZ 0.026 0.006 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.04 0.051 -10000 0 -0.52 1 1
STK36 0.026 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.011 0.053 -10000 0 -0.37 6 6
PTCH1 0.015 0.16 0.57 1 -1.1 7 8
MIM/GLI1 0.022 0.14 0.55 1 -0.63 8 9
CREBBP 0.003 0.087 -10000 0 -0.32 31 31
Su(fu)/SIN3/HDAC complex -0.006 0.11 0.24 2 -0.25 70 72
Arf6 downstream 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
PLAUR 0.013 0.066 -10000 0 -0.97 2 2
regulation of axonogenesis 0.001 0.055 0.28 9 -10000 0 9
myoblast fusion -0.008 0.041 0.35 4 -10000 0 4
mol:GTP 0.019 0.025 -10000 0 -0.16 7 7
regulation of calcium-dependent cell-cell adhesion -0.043 0.027 0.2 2 -10000 0 2
ARF1/GTP 0.035 0.024 -10000 0 -0.15 2 2
mol:GM1 0.008 0.018 -10000 0 -0.15 2 2
mol:Choline -0.009 0.064 -10000 0 -0.24 34 34
lamellipodium assembly 0.003 0.047 -10000 0 -0.37 6 6
MAPK3 0.02 0.026 -10000 0 -0.3 2 2
ARF6/GTP/NME1/Tiam1 0.044 0.027 -10000 0 -0.2 2 2
ARF1 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.008 0.041 -10000 0 -0.35 4 4
ARF1/GDP 0.012 0.048 -10000 0 -0.28 7 7
ARF6 0.032 0.012 -10000 0 -10000 0 0
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 0.026 -10000 0 -0.3 2 2
actin filament bundle formation -0.016 0.047 0.31 5 -10000 0 5
KALRN 0.005 0.028 -10000 0 -0.25 4 4
RAB11FIP3/RAB11A 0.038 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.047 -10000 0 -0.31 5 5
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.045 -10000 0 -0.25 6 6
substrate adhesion-dependent cell spreading 0.019 0.025 -10000 0 -0.16 7 7
cortical actin cytoskeleton organization 0.003 0.048 -10000 0 -0.37 6 6
RAC1 0.023 0.009 -10000 0 -10000 0 0
liver development 0.019 0.025 -10000 0 -0.16 7 7
ARF6/GTP 0.019 0.025 -10000 0 -0.16 7 7
RhoA/GTP 0.035 0.023 -10000 0 -0.15 2 2
mol:GDP 0.008 0.032 -10000 0 -0.32 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.049 0.025 -10000 0 -0.15 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
PLD1 -0.003 0.074 -10000 0 -0.27 34 34
RAB11FIP3 0.026 0.002 -10000 0 -10000 0 0
tube morphogenesis 0.003 0.047 -10000 0 -0.37 6 6
ruffle organization -0.001 0.055 -10000 0 -0.28 9 9
regulation of epithelial cell migration 0.019 0.025 -10000 0 -0.16 7 7
PLD2 0.016 0.026 -10000 0 -0.22 2 2
PIP5K1A -0.001 0.055 -10000 0 -0.28 9 9
mol:Phosphatidic acid -0.009 0.064 -10000 0 -0.24 34 34
Rac1/GTP 0.003 0.048 -10000 0 -0.37 6 6
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 0.016 -10000 0 -0.17 2 2
FRAP1 0.021 0.045 0.27 2 -0.31 2 4
AKT1 0.009 0.034 0.17 15 -0.18 1 16
INSR 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.027 -10000 0 -0.26 4 4
mol:GTP 0.032 0.038 0.17 10 -10000 0 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.014 0.018 -10000 0 -10000 0 0
TSC2 0.026 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.015 0.025 -10000 0 -10000 0 0
TSC1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.017 -10000 0 -0.18 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.023 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.007 -10000 0 -10000 0 0
RPS6KB1 0.026 0.05 0.26 9 -0.32 1 10
MAP3K5 -0.005 0.051 -10000 0 -0.22 25 25
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
apoptosis -0.005 0.051 -10000 0 -0.22 25 25
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.024 0.048 0.25 10 -0.28 1 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.033 0.19 3 -0.25 1 4
eIF4E/eIF4G1/eIF4A1 0.016 0.023 -10000 0 -0.2 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.041 0.019 -10000 0 -0.17 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.022 0.13 4 -10000 0 4
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.032 0.18 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.003 0.022 0.18 2 -0.23 1 3
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.14 -10000 0 -0.57 25 25
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.045 -10000 0 -0.25 3 3
TSC1/TSC2 0.039 0.048 0.22 15 -10000 0 15
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 0.018 -10000 0 -0.2 3 3
INS -0.018 0.037 -10000 0 -0.37 5 5
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.003 0.021 0.18 2 -0.19 1 3
EIF4EBP1 0.003 0.15 -10000 0 -1.1 9 9
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PPP2R5D 0.02 0.043 0.26 2 -0.28 2 4
peptide biosynthetic process -0.008 0.033 0.18 10 -0.23 4 14
RHEB 0.02 0.011 -10000 0 -10000 0 0
EIF4A1 0.026 0.003 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 26 -10000 0 26
EEF2 -0.008 0.033 0.18 10 -0.23 4 14
eIF4E/4E-BP1 0.016 0.14 -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 -0.019 0.13 -10000 0 -0.31 68 68
CLTC 0.024 0.054 -10000 0 -0.36 6 6
calcium ion-dependent exocytosis 0.013 0.05 -10000 0 -0.27 3 3
Dynamin 2/GTP 0.025 0.008 -10000 0 -10000 0 0
EXOC4 0.02 0.011 -10000 0 -10000 0 0
CD59 0.015 0.048 -10000 0 -0.31 8 8
CPE 0.007 0.041 -10000 0 -0.26 12 12
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
membrane fusion 0.015 0.053 -10000 0 -0.26 3 3
CTNND1 0.014 0.024 0.18 10 -10000 0 10
DNM2 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.039 -10000 0 -0.25 2 2
TSHR -0.05 0.1 -10000 0 -0.26 92 92
INS -0.008 0.11 -10000 0 -0.45 27 27
BIN1 0.025 0.02 -10000 0 -0.43 1 1
mol:Choline 0.015 0.053 -10000 0 -0.26 3 3
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 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.007 -10000 0 -10000 0 0
JUP 0.012 0.055 -10000 0 -0.31 10 10
ASAP2/amphiphysin II 0.049 0.016 -10000 0 -0.23 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.008 0.08 -10000 0 -0.28 18 18
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 0.026 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.018 0.022 -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 -0.016 0.071 0.3 7 -10000 0 7
positive regulation of phagocytosis 0.012 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.006 -10000 0 -10000 0 0
ACAP1 0.02 0.05 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.01 0.07 -10000 0 -0.31 11 11
clathrin heavy chain/ACAP1 0.027 0.058 0.2 18 -0.28 6 24
JIP4/KLC1 0.048 0.012 -10000 0 -10000 0 0
EXOC1 0.025 0.006 -10000 0 -10000 0 0
exocyst 0.02 0.019 -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 0.007 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.014 0.023 0.18 9 -10000 0 9
NME1 0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.057 0.25 2 -0.36 6 8
IL2RA 0.007 0.054 -10000 0 -0.31 9 9
VAMP3 0.012 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.07 -10000 0 -0.28 10 10
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.003 0.065 -10000 0 -0.26 30 30
PLD2 0.012 0.013 -10000 0 -0.25 1 1
EXOC5 0.026 0.004 -10000 0 -10000 0 0
PIP5K1C 0.016 0.037 -10000 0 -0.26 2 2
SDC1 0.011 0.053 -10000 0 -0.31 8 8
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 0.018 0.073 -10000 0 -0.31 7 7
mol:Phosphatidic acid 0.015 0.053 -10000 0 -0.26 3 3
endocytosis -0.047 0.015 0.23 1 -10000 0 1
SCAMP2 0.026 0.003 -10000 0 -10000 0 0
ADRB2 0.015 0.074 0.27 3 -0.35 8 11
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ASAP2 0.026 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.009 -10000 0 -10000 0 0
KLC1 0.025 0.005 -10000 0 -10000 0 0
AVPR2 0.022 0.061 0.24 3 -0.34 7 10
RALA 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.073 -10000 0 -0.32 5 5
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 0.052 0.037 -9999 0 -0.22 4 4
HDAC3 0.026 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.034 0.016 -9999 0 -10000 0 0
GATA1/HDAC5 0.035 0.015 -9999 0 -10000 0 0
GATA2/HDAC5 0.03 0.049 -9999 0 -0.3 10 10
HDAC5/BCL6/BCoR 0.052 0.01 -9999 0 -10000 0 0
HDAC9 0.015 0.055 -9999 0 -0.3 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.013 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.009 -9999 0 -10000 0 0
HDAC5/YWHAB 0.037 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
GATA2 0.015 0.065 -9999 0 -0.33 15 15
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 0.03 0.033 -9999 0 -0.3 4 4
Histones 0.03 0.044 -9999 0 -0.19 8 8
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 0.004 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.005 -9999 0 -10000 0 0
TUBA1B 0.026 0.004 -9999 0 -10000 0 0
HDAC6 0.026 0.002 -9999 0 -10000 0 0
HDAC5/RFXANK 0.037 0.011 -9999 0 -10000 0 0
CAMK4 -0.093 0.19 -9999 0 -0.43 119 119
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 0.004 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.021 -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 0.038 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 0.014 -9999 0 -10000 0 0
HDAC4/SRF -0.018 0.13 -9999 0 -0.26 117 117
HDAC4/ER alpha 0.025 0.054 -9999 0 -0.3 11 11
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.03 0.044 -9999 0 -0.19 8 8
cell motility 0.05 0.012 -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 0.004 -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 0.011 0.07 -9999 0 -0.43 11 11
HDAC6/HDAC11 0.037 0.017 -9999 0 -0.3 1 1
Ran/GTP/Exportin 1 0.042 0.019 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
MEF2C 0.018 0.041 -9999 0 -0.16 21 21
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 0.04 -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 0.025 0.02 -9999 0 -0.43 1 1
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 0.025 0.009 -9999 0 -0.13 1 1
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 0.026 0.004 -9999 0 -10000 0 0
SMAD2 -0.001 0.035 -9999 0 -0.25 2 2
SMAD3 0.024 0.026 -9999 0 -10000 0 0
SMAD3/SMAD4 0.038 0.044 -9999 0 -0.71 1 1
SMAD4/Ubc9/PIASy 0.05 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 -0.13 1 1
SMAD2/SMAD4 0.014 0.036 -9999 0 -0.23 2 2
MAP3K1 0.024 0.019 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.06 -9999 0 -0.3 16 16
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 0.025 0.02 -9999 0 -0.43 1 1
KPNB1 0.026 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.012 0.079 -9999 0 -0.43 16 16
UBE2I 0.026 0.002 -9999 0 -10000 0 0
NUP153 0.026 0.003 -9999 0 -10000 0 0
KPNA2 0.025 0.009 -9999 0 -0.13 1 1
PIAS4 0.025 0.005 -9999 0 -10000 0 0
Arf1 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
coatomer protein complex 0.013 0.028 0.15 21 -10000 0 21
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.027 0.13 7 -10000 0 7
AP2 0.031 0.016 -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 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.007 -10000 0 -10000 0 0
CD4 0.022 0.025 -10000 0 -0.43 1 1
CLTA 0.026 0.005 -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 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP 0.025 0.015 -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 0.004 0.017 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.015 -10000 0 -10000 0 0
DDEF1 0.003 0.017 -10000 0 -0.17 1 1
ARF1/GDP 0.002 0.018 -10000 0 -0.088 4 4
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.007 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 0.021 -10000 0 -10000 0 0
ARFIP2 0.023 0.008 -10000 0 -10000 0 0
COPA 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.023 -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 0.019 -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 0.015 -10000 0 -0.14 4 4
ARF1/GDP/Membrin 0.022 0.02 -10000 0 -0.21 1 1
Arfaptin 2/Rac/GDP 0.029 0.014 -10000 0 -10000 0 0
CYTH2 0.022 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.019 -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 0.04 -10000 0 -0.18 5 5
PLD2 0.004 0.017 -10000 0 -0.17 1 1
ARF-GAP1/v-SNARE 0.007 0.004 -10000 0 -10000 0 0
PIP5K1A 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP/Membrin/GBF1/p115 0.014 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.017 -10000 0 -0.17 1 1
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 0.046 -10000 0 -0.33 9 9
GBF1 0.004 0.046 -10000 0 -0.32 10 10
ARF1/GTP/Arfaptin 2 0.027 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.026 -10000 0 -0.23 1 1
Alternative NF-kappaB pathway

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
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 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.04 -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 0.025 -9999 0 -0.2 4 4
NFKB2 0.023 0.03 -9999 0 -0.33 3 3
NF kappa B2 p52/RelB 0.026 0.027 -9999 0 -0.22 4 4
regulation of B cell activation 0.026 0.027 -9999 0 -0.22 4 4
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.022 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.005 -9999 0 -10000 0 0
MDM2/SUMO1 0.041 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 0.012 -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 0.021 -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 0.033 -9999 0 -0.24 5 5
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 0.016 0.001 -9999 0 -10000 0 0
PIAS2 0.025 0.02 -9999 0 -0.43 1 1
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 511 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.16 -0.16 0.064 -0.19
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 0.068 -0.23 0
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.026 0.026
84_STAT5B 0.097 0.033 0.066 0.033
84_STAT5A 0.097 0.033 0.066 0.033
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/11493537/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LGG-TP/11541546/Gistic2_Analysis_11541946/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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