PARADIGM pathway analysis of mRNASeq expression and copy number data
Brain Lower Grade Glioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12B8X8X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12B8X8X
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 56 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 101
IL23-mediated signaling events 81
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 67
Signaling mediated by p38-alpha and p38-beta 66
FOXM1 transcription factor network 59
Aurora B signaling 59
IL12-mediated signaling events 56
TCR signaling in naïve CD8+ T cells 56
Signaling events regulated by Ret tyrosine kinase 54
Syndecan-1-mediated signaling events 52
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 516 . 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 ( 516 ).

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 0.1957 101 709 7 -0.063 0 1000 -1000 0 -1000
IL23-mediated signaling events 0.1570 81 4902 60 -0.49 0.026 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1298 67 4599 68 -0.3 0.18 1000 -1000 -0.08 -1000
Signaling mediated by p38-alpha and p38-beta 0.1279 66 2923 44 -0.1 0.026 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 0.1143 59 3021 51 -0.27 0.026 1000 -1000 -0.12 -1000
Aurora B signaling 0.1143 59 3998 67 -0.26 0.046 1000 -1000 -0.041 -1000
IL12-mediated signaling events 0.1085 56 4884 87 -0.4 0.073 1000 -1000 -0.071 -1000
TCR signaling in naïve CD8+ T cells 0.1085 56 5236 93 -0.18 0.21 1000 -1000 -0.043 -1000
Signaling events regulated by Ret tyrosine kinase 0.1047 54 4469 82 -0.074 0.026 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 0.1008 52 1771 34 -0.075 0.026 1000 -1000 -0.03 -1000
Thromboxane A2 receptor signaling 0.0988 51 5360 105 -0.13 0.034 1000 -1000 -0.034 -1000
Reelin signaling pathway 0.0969 50 2844 56 -0.1 0.059 1000 -1000 -0.025 -1000
E-cadherin signaling events 0.0969 50 250 5 -0.046 0.026 1000 -1000 0.004 -1000
Effects of Botulinum toxin 0.0930 48 1262 26 -0.088 0.026 1000 -1000 -0.002 -1000
TCGA08_retinoblastoma 0.0930 48 389 8 -0.023 0.042 1000 -1000 -0.004 -1000
Syndecan-4-mediated signaling events 0.0930 48 3229 67 -0.094 0.035 1000 -1000 -0.035 -1000
Endothelins 0.0891 46 4458 96 -0.13 0.026 1000 -1000 -0.041 -1000
Signaling events mediated by the Hedgehog family 0.0853 44 2335 52 -0.093 0.048 1000 -1000 -0.029 -1000
ErbB2/ErbB3 signaling events 0.0833 43 2853 65 -0.1 0.037 1000 -1000 -0.05 -1000
FOXA2 and FOXA3 transcription factor networks 0.0814 42 1967 46 -0.22 0.03 1000 -1000 -0.077 -1000
Syndecan-3-mediated signaling events 0.0814 42 1471 35 -0.061 0.063 1000 -1000 -0.023 -1000
IL4-mediated signaling events 0.0775 40 3702 91 -0.42 0.27 1000 -1000 -0.1 -1000
Visual signal transduction: Rods 0.0775 40 2103 52 -0.1 0.026 1000 -1000 -0.025 -1000
Arf6 signaling events 0.0736 38 2380 62 -0.14 0.054 1000 -1000 -0.036 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0736 38 2865 74 -0.063 0.059 1000 -1000 -0.057 -1000
HIF-1-alpha transcription factor network 0.0717 37 2850 76 -0.11 0.056 1000 -1000 -0.053 -1000
amb2 Integrin signaling 0.0698 36 2960 82 -0.15 0.028 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0678 35 2985 85 -0.17 0.038 1000 -1000 -0.033 -1000
p75(NTR)-mediated signaling 0.0678 35 4433 125 -0.073 0.063 1000 -1000 -0.05 -1000
BCR signaling pathway 0.0678 35 3517 99 -0.095 0.044 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.0678 35 750 21 -0.034 0.037 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.0678 35 610 17 -0.054 0.034 1000 -1000 -0.017 -1000
Caspase cascade in apoptosis 0.0659 34 2556 74 -0.13 0.05 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 0.0659 34 1794 52 -0.075 0.036 1000 -1000 -0.028 -1000
Osteopontin-mediated events 0.0640 33 1272 38 -0.05 0.027 1000 -1000 -0.027 -1000
LPA receptor mediated events 0.0640 33 3428 102 -0.1 0.03 1000 -1000 -0.052 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0620 32 1749 54 -0.072 0.033 1000 -1000 -0.025 -1000
PDGFR-alpha signaling pathway 0.0620 32 1445 44 -0.1 0.032 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.0620 32 1005 31 -0.094 0.025 1000 -1000 -0.04 -1000
Visual signal transduction: Cones 0.0601 31 1186 38 -0.055 0.034 1000 -1000 -0.01 -1000
IL1-mediated signaling events 0.0601 31 1938 62 -0.073 0.045 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0601 31 1644 52 -0.15 0.067 1000 -1000 -0.036 -1000
a4b1 and a4b7 Integrin signaling 0.0581 30 154 5 -0.008 0.012 1000 -1000 0.006 -1000
Fc-epsilon receptor I signaling in mast cells 0.0562 29 2854 97 -0.06 0.042 1000 -1000 -0.065 -1000
PLK1 signaling events 0.0562 29 2473 85 -0.078 0.038 1000 -1000 -0.04 -1000
Ceramide signaling pathway 0.0562 29 2254 76 -0.068 0.045 1000 -1000 -0.029 -1000
Retinoic acid receptors-mediated signaling 0.0562 29 1732 58 -0.088 0.051 1000 -1000 -0.044 -1000
Glypican 2 network 0.0562 29 116 4 -0.002 0.004 1000 -1000 0.007 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0562 29 2572 88 -0.087 0.029 1000 -1000 -0.069 -1000
Noncanonical Wnt signaling pathway 0.0543 28 729 26 -0.048 0.026 1000 -1000 -0.031 -1000
Glypican 1 network 0.0543 28 1368 48 -0.08 0.05 1000 -1000 -0.013 -1000
BMP receptor signaling 0.0523 27 2261 81 -0.079 0.044 1000 -1000 -0.035 -1000
Aurora C signaling 0.0504 26 182 7 -0.072 0.011 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 0.0504 26 3009 114 -0.27 0.14 1000 -1000 -0.044 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0504 26 969 37 -0.034 0.046 1000 -1000 -0.023 -1000
S1P5 pathway 0.0504 26 445 17 -0.053 0.026 1000 -1000 -0.011 -1000
Regulation of nuclear SMAD2/3 signaling 0.0484 25 3458 136 -0.18 0.16 1000 -1000 -0.026 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0484 25 872 34 -0.017 0.04 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 0.0484 25 1240 48 -0.027 0.027 1000 -1000 -0.017 -1000
TCGA08_rtk_signaling 0.0484 25 655 26 -0.047 0.061 1000 -1000 -0.003 -1000
E-cadherin signaling in the nascent adherens junction 0.0484 25 1945 76 -0.046 0.048 1000 -1000 -0.047 -1000
Rapid glucocorticoid signaling 0.0484 25 516 20 -0.075 0.027 1000 -1000 -0.002 -1000
JNK signaling in the CD4+ TCR pathway 0.0465 24 420 17 -0.025 0.026 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.0465 24 1129 47 -0.099 0.039 1000 -1000 -0.047 -1000
Canonical Wnt signaling pathway 0.0465 24 1268 51 -0.13 0.066 1000 -1000 -0.041 -1000
EPHB forward signaling 0.0465 24 2049 85 -0.029 0.054 1000 -1000 -0.045 -1000
IL6-mediated signaling events 0.0465 24 1868 75 -0.1 0.04 1000 -1000 -0.053 -1000
Wnt signaling 0.0446 23 164 7 -0.007 0.01 1000 -1000 -0.009 -1000
E-cadherin signaling in keratinocytes 0.0446 23 1018 43 -0.046 0.027 1000 -1000 -0.027 -1000
Coregulation of Androgen receptor activity 0.0426 22 1707 76 -0.082 0.05 1000 -1000 -0.017 -1000
Presenilin action in Notch and Wnt signaling 0.0426 22 1376 61 -0.13 0.063 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0407 21 1473 69 -0.061 0.038 1000 -1000 -0.033 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0407 21 2580 120 -0.11 0.074 1000 -1000 -0.035 -1000
Signaling events mediated by PTP1B 0.0388 20 1522 76 -0.072 0.04 1000 -1000 -0.027 -1000
EPO signaling pathway 0.0388 20 1127 55 -0.029 0.07 1000 -1000 -0.026 -1000
TCGA08_p53 0.0388 20 140 7 -0.017 0.025 1000 -1000 -0.008 -1000
IL2 signaling events mediated by PI3K 0.0388 20 1191 58 -0.075 0.041 1000 -1000 -0.03 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0388 20 1578 78 -0.017 0.037 1000 -1000 -0.059 -1000
PLK2 and PLK4 events 0.0368 19 57 3 0.001 -1000 1000 -1000 -0.009 -1000
Cellular roles of Anthrax toxin 0.0368 19 762 39 -0.13 0.029 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 0.0368 19 793 40 -0.064 0.05 1000 -1000 -0.016 -1000
S1P1 pathway 0.0349 18 650 36 -0.095 0.026 1000 -1000 -0.037 -1000
IL2 signaling events mediated by STAT5 0.0329 17 378 22 -0.028 0.027 1000 -1000 -0.031 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0310 16 1355 83 -0.094 0.051 1000 -1000 -0.023 -1000
Regulation of p38-alpha and p38-beta 0.0310 16 877 54 -0.055 0.056 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 0.0310 16 1404 86 -0.039 0.038 1000 -1000 -0.04 -1000
VEGFR1 specific signals 0.0310 16 934 56 -0.038 0.055 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 0.0291 15 188 12 -0.031 0.005 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0291 15 420 28 -0.053 0.032 1000 -1000 -0.018 -1000
ceramide signaling pathway 0.0291 15 777 49 -0.06 0.037 1000 -1000 -0.032 -1000
S1P4 pathway 0.0291 15 396 25 -0.053 0.045 1000 -1000 -0.022 -1000
Insulin-mediated glucose transport 0.0271 14 457 32 -0.04 0.051 1000 -1000 -0.022 -1000
Paxillin-dependent events mediated by a4b1 0.0271 14 520 36 -0.038 0.047 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.0271 14 1219 84 -0.024 0.057 1000 -1000 -0.029 -1000
IL27-mediated signaling events 0.0271 14 725 51 -0.085 0.026 1000 -1000 -0.048 -1000
Class I PI3K signaling events 0.0271 14 1092 73 -0.074 0.048 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0252 13 783 57 -0.041 0.051 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0252 13 627 48 -0.001 0.063 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0252 13 1342 102 -0.13 0.065 1000 -1000 -0.042 -1000
Signaling events mediated by PRL 0.0252 13 457 34 -0.059 0.033 1000 -1000 -0.039 -1000
Regulation of Androgen receptor activity 0.0252 13 970 70 -0.066 0.036 1000 -1000 -0.051 -1000
ErbB4 signaling events 0.0233 12 833 69 -0.071 0.045 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0233 12 581 45 -0.06 0.061 1000 -1000 -0.047 -1000
Nectin adhesion pathway 0.0213 11 730 63 -0.046 0.066 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0213 11 1072 97 -0.072 0.072 1000 -1000 -0.04 -1000
Aurora A signaling 0.0194 10 627 60 -0.058 0.058 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0194 10 153 15 -0.016 0.025 1000 -1000 -0.027 -1000
Insulin Pathway 0.0194 10 751 74 -0.071 0.062 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 0.0174 9 631 68 -0.032 0.048 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 0.0174 9 305 31 -0.019 0.038 1000 -1000 -0.016 -1000
IFN-gamma pathway 0.0155 8 558 68 -0.099 0.056 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 0.0155 8 362 43 -0.058 0.059 1000 -1000 -0.049 -1000
FoxO family signaling 0.0155 8 529 64 -0.033 0.079 1000 -1000 -0.045 -1000
S1P3 pathway 0.0155 8 367 42 0 0.038 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0155 8 268 33 -0.029 0.065 1000 -1000 -0.025 -1000
p38 MAPK signaling pathway 0.0155 8 368 44 -0.018 0.042 1000 -1000 -0.017 -1000
IGF1 pathway 0.0136 7 413 57 -0.014 0.064 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 0.0116 6 655 104 -0.06 0.059 1000 -1000 -0.029 -1000
Class IB PI3K non-lipid kinase events 0.0116 6 18 3 -0.02 0.02 1000 -1000 -0.007 -1000
Canonical NF-kappaB pathway 0.0097 5 218 39 -0.06 0.059 1000 -1000 -0.024 -1000
Circadian rhythm pathway 0.0097 5 112 22 -0.007 0.038 1000 -1000 -0.037 -1000
Hedgehog signaling events mediated by Gli proteins 0.0097 5 377 65 -0.006 0.059 1000 -1000 -0.039 -1000
Arf6 downstream pathway 0.0097 5 246 43 -0.043 0.049 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0097 5 733 125 -0.02 0.065 1000 -1000 -0.035 -1000
Arf6 trafficking events 0.0097 5 374 71 -0.05 0.048 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0078 4 358 75 -0.094 0.071 1000 -1000 -0.018 -1000
mTOR signaling pathway 0.0078 4 255 53 -0.018 0.041 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 41 23 -0.001 0.05 1000 -1000 -0.021 -1000
Arf1 pathway 0.0019 1 67 54 -0.001 0.039 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0019 1 17 13 0 0.059 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.061 1000 -1000 -0.024 -1000
Total NA 3336 189734 7203 -10 -990 131000 -131000 -4.2 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.052 0.14 -10000 0 -0.28 126 126
EFNA5 -0.029 0.14 -10000 0 -0.3 87 87
FYN -0.056 0.13 0.18 6 -0.29 100 106
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 -0.3 138 138
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 -1.2 127 127
IL23A -0.44 0.55 -9999 0 -1.3 121 121
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.53 -9999 0 -1.2 126 126
positive regulation of T cell mediated cytotoxicity -0.45 0.6 -9999 0 -1.3 128 128
ITGA3 -0.39 0.5 -9999 0 -1.2 117 117
IL17F -0.26 0.32 -9999 0 -0.72 121 121
IL12B -0.02 0.045 -9999 0 -0.16 5 5
STAT1 (dimer) -0.43 0.57 -9999 0 -1.3 128 128
CD4 -0.37 0.49 -9999 0 -1.2 110 110
IL23 -0.42 0.53 -9999 0 -1.2 123 123
IL23R -0.2 0.38 -9999 0 -1.1 72 72
IL1B -0.46 0.59 -9999 0 -1.4 131 131
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.38 0.49 -9999 0 -1.1 116 116
TYK2 -0.007 0.035 -9999 0 -10000 0 0
STAT4 -0.064 0.16 -9999 0 -0.43 69 69
STAT3 0.026 0.003 -9999 0 -10000 0 0
IL18RAP -0.023 0.13 -9999 0 -0.42 42 42
IL12RB1 -0.032 0.1 -9999 0 -0.39 31 31
PIK3CA 0.025 0.02 -9999 0 -0.43 1 1
IL12Rbeta1/TYK2 -0.022 0.082 -9999 0 -0.32 24 24
IL23R/JAK2 -0.19 0.36 -9999 0 -1.1 64 64
positive regulation of chronic inflammatory response -0.45 0.6 -9999 0 -1.3 128 128
natural killer cell activation 0.005 0.007 -9999 0 -10000 0 0
JAK2 -0.008 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 -1.2 151 151
CXCL1 -0.43 0.54 -9999 0 -1.2 133 133
T cell proliferation -0.45 0.6 -9999 0 -1.3 128 128
NFKBIA 0.024 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.25 -9999 0 -0.56 110 110
PI3K -0.4 0.54 -9999 0 -1.2 124 124
IFNG -0.018 0.031 -9999 0 -0.11 20 20
STAT3 (dimer) -0.38 0.51 -9999 0 -1.2 121 121
IL18R1 -0.006 0.11 -9999 0 -0.27 58 58
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.36 -9999 0 -0.81 102 102
IL18/IL18R -0.004 0.13 -9999 0 -0.3 73 73
macrophage activation -0.019 0.02 -9999 0 -0.045 107 107
TNF -0.46 0.59 -9999 0 -1.4 125 125
STAT3/STAT4 -0.43 0.55 -9999 0 -1.2 136 136
STAT4 (dimer) -0.45 0.58 -9999 0 -1.3 138 138
IL18 0.002 0.093 -9999 0 -0.43 21 21
IL19 -0.38 0.48 -9999 0 -1.1 117 117
STAT5A (dimer) -0.43 0.57 -9999 0 -1.3 130 130
STAT1 0.021 0.028 -9999 0 -0.13 16 16
SOCS3 -0.029 0.12 -9999 0 -0.21 118 118
CXCL9 -0.45 0.55 -9999 0 -1.2 144 144
MPO -0.45 0.56 -9999 0 -1.2 151 151
positive regulation of humoral immune response -0.45 0.6 -9999 0 -1.3 128 128
IL23/IL23R/JAK2/TYK2 -0.49 0.69 -9999 0 -1.5 126 126
IL6 -0.4 0.54 -9999 0 -1.3 116 116
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 -1.2 139 139
keratinocyte proliferation -0.45 0.6 -9999 0 -1.3 128 128
NOS2 -0.4 0.51 -9999 0 -1.2 123 123
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.004 0.075 -10000 0 -0.24 32 32
NFATC2 -0.083 0.23 -10000 0 -0.57 61 61
NFATC3 -0.036 0.11 -10000 0 -0.27 64 64
CD40LG -0.24 0.4 -10000 0 -0.94 106 106
ITCH -0.024 0.091 -10000 0 -0.22 86 86
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 -0.85 90 90
JUNB 0.007 0.071 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.11 -10000 0 -0.26 89 89
T cell anergy -0.066 0.16 0.26 1 -0.39 88 89
TLE4 -0.06 0.17 -10000 0 -0.5 42 42
Jun/NFAT1-c-4/p21SNFT -0.2 0.43 -10000 0 -0.98 105 105
AP-1/NFAT1-c-4 -0.24 0.5 -10000 0 -1.1 106 106
IKZF1 -0.063 0.18 -10000 0 -0.54 46 46
T-helper 2 cell differentiation -0.14 0.28 -10000 0 -0.74 61 61
AP-1/NFAT1 -0.063 0.18 -10000 0 -0.41 75 75
CALM1 -0.01 0.072 -10000 0 -0.16 87 87
EGR2 -0.24 0.51 -10000 0 -1.3 77 77
EGR3 -0.26 0.55 -10000 0 -1.3 94 94
NFAT1/FOXP3 -0.054 0.19 -10000 0 -0.45 61 61
EGR1 -0.043 0.14 -10000 0 -0.27 111 111
JUN 0.009 0.031 -10000 0 -0.14 8 8
EGR4 -0.088 0.17 -10000 0 -0.28 183 183
mol:Ca2+ -0.025 0.06 -10000 0 -0.15 88 88
GBP3 -0.079 0.22 -10000 0 -0.61 65 65
FOSL1 -0.028 0.13 -10000 0 -0.25 97 97
NFAT1-c-4/MAF/IRF4 -0.19 0.43 -10000 0 -0.96 106 106
DGKA -0.057 0.16 -10000 0 -0.47 39 39
CREM 0.023 0.022 -10000 0 -0.43 1 1
NFAT1-c-4/PPARG -0.2 0.44 -10000 0 -0.99 106 106
CTLA4 -0.079 0.19 -10000 0 -0.49 70 70
NFAT1-c-4 (dimer)/EGR1 -0.23 0.47 -10000 0 -1.1 106 106
NFAT1-c-4 (dimer)/EGR4 -0.24 0.46 -10000 0 -1 107 107
FOS -0.041 0.14 -10000 0 -0.3 93 93
IFNG -0.1 0.21 -10000 0 -0.65 37 37
T cell activation -0.11 0.23 -10000 0 -0.66 43 43
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 0.84 106 -10000 0 106
TNF -0.3 0.44 -10000 0 -0.99 124 124
FASLG -0.26 0.55 -10000 0 -1.3 101 101
TBX21 -0.004 0.099 -10000 0 -0.26 54 54
BATF3 0.001 0.091 -10000 0 -0.26 45 45
PRKCQ 0.015 0.061 -10000 0 -0.4 10 10
PTPN1 -0.058 0.16 -10000 0 -0.47 39 39
NFAT1-c-4/ICER1 -0.19 0.43 -10000 0 -0.97 105 105
GATA3 -0.038 0.14 -10000 0 -0.43 49 49
T-helper 1 cell differentiation -0.1 0.2 -10000 0 -0.64 37 37
IL2RA -0.17 0.32 -10000 0 -0.78 79 79
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 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 -0.054 0.16 -10000 0 -0.46 42 42
IRF4 -0.006 0.1 -10000 0 -0.28 53 53
PTGS2 -0.26 0.43 -10000 0 -1 108 108
CSF2 -0.24 0.39 -10000 0 -0.95 106 106
JunB/Fra1/NFAT1-c-4 -0.2 0.43 -10000 0 -0.96 105 105
IL4 -0.15 0.3 -10000 0 -0.81 56 56
IL5 -0.24 0.4 -10000 0 -0.94 106 106
IL2 -0.12 0.23 -10000 0 -0.68 41 41
IL3 -0.024 0.082 -10000 0 -0.65 4 4
RNF128 -0.085 0.2 -10000 0 -0.52 88 88
NFATC1 -0.18 0.38 -10000 0 -0.85 106 106
CDK4 0.11 0.21 0.57 54 -10000 0 54
PTPRK -0.057 0.16 -10000 0 -0.47 45 45
IL8 -0.26 0.42 -10000 0 -0.98 113 113
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
Signaling mediated by p38-alpha and p38-beta

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.1 0.33 -10000 0 -0.98 61 61
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 -0.38 79 79
SLC9A1 -0.04 0.16 0.3 1 -0.39 81 82
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.023 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 74 74
NOS2 -0.054 0.23 -10000 0 -0.93 24 24
DDIT3 -0.026 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 -0.03 0.15 -10000 0 -0.36 80 80
RAB5/GDP 0.019 0.003 -10000 0 -10000 0 0
EIF4E -0.033 0.12 0.25 3 -0.3 74 77
RPS6KA4 -0.025 0.14 -10000 0 -0.34 80 80
PLA2G4A -0.04 0.13 -10000 0 -0.33 76 76
GDI1 -0.026 0.14 -10000 0 -0.34 83 83
TP53 -0.053 0.17 -10000 0 -0.42 82 82
RPS6KA5 -0.033 0.15 -10000 0 -0.35 88 88
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 81 81
MEF2A -0.028 0.14 -10000 0 -0.35 82 82
EIF4EBP1 -0.034 0.15 -10000 0 -0.36 81 81
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 -0.033 0.15 -10000 0 -0.37 82 82
p38alpha-beta/MAPKAPK2 0 0.15 -10000 0 -0.33 81 81
p38alpha-beta/MAPKAPK3 -0.002 0.15 -10000 0 -0.34 81 81
FOXM1 transcription factor network

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
NFATC3 -0.18 0.49 -9999 0 -1.2 77 77
PLK1 0.006 0.15 -9999 0 -1.3 6 6
BIRC5 -0.19 0.51 -9999 0 -1.4 75 75
HSPA1B -0.19 0.5 -9999 0 -1.2 82 82
MAP2K1 0.01 0.045 -9999 0 -0.18 1 1
BRCA2 -0.19 0.51 -9999 0 -1.2 82 82
FOXM1 -0.27 0.7 -9999 0 -1.7 80 80
XRCC1 -0.18 0.49 -9999 0 -1.2 75 75
FOXM1B/p19 -0.19 0.5 -9999 0 -1.2 81 81
Cyclin D1/CDK4 -0.17 0.45 -9999 0 -1.1 80 80
CDC2 -0.19 0.52 -9999 0 -1.3 79 79
TGFA -0.16 0.44 -9999 0 -1 82 82
SKP2 -0.19 0.5 -9999 0 -1.2 80 80
CCNE1 0.016 0.022 -9999 0 -10000 0 0
CKS1B -0.18 0.49 -9999 0 -1.1 84 84
RB1 -0.11 0.32 -9999 0 -0.92 47 47
FOXM1C/SP1 -0.22 0.59 -9999 0 -1.4 82 82
AURKB -0.23 0.56 -9999 0 -1.4 90 90
CENPF -0.2 0.52 -9999 0 -1.3 76 76
CDK4 0.014 0.026 -9999 0 -10000 0 0
MYC -0.16 0.43 -9999 0 -1 81 81
CHEK2 0.004 0.066 -9999 0 -0.32 8 8
ONECUT1 -0.18 0.47 -9999 0 -1.1 79 79
CDKN2A -0.012 0.11 -9999 0 -0.33 46 46
LAMA4 -0.18 0.49 -9999 0 -1.2 78 78
FOXM1B/HNF6 -0.23 0.58 -9999 0 -1.4 79 79
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 77 77
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 0.53 -9999 0 -1.3 81 81
NEK2 -0.23 0.56 -9999 0 -1.3 90 90
HIST1H2BA -0.18 0.48 -9999 0 -1.2 77 77
CCNA2 -0.012 0.1 -9999 0 -0.44 22 22
EP300 0.022 0.04 -9999 0 -0.43 4 4
CCNB1/CDK1 -0.22 0.59 -9999 0 -1.5 77 77
CCNB2 -0.23 0.57 -9999 0 -1.4 86 86
CCNB1 -0.19 0.52 -9999 0 -1.3 77 77
ETV5 -0.19 0.49 -9999 0 -1.2 81 81
ESR1 -0.2 0.5 -9999 0 -1.2 86 86
CCND1 -0.18 0.46 -9999 0 -1.1 81 81
GSK3A 0.012 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.012 0.091 -9999 0 -0.3 25 25
CDK2 0.014 0.049 -9999 0 -0.25 11 11
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 80 80
GAS1 -0.18 0.49 -9999 0 -1.2 77 77
MMP2 -0.19 0.5 -9999 0 -1.2 78 78
RB1/FOXM1C -0.19 0.48 -9999 0 -1.2 80 80
CREBBP 0.026 0.003 -9999 0 -10000 0 0
Aurora B signaling

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.071 0.19 -10000 0 -0.48 78 78
STMN1 -0.047 0.12 0.18 3 -0.31 76 79
Aurora B/RasGAP/Survivin -0.057 0.19 -10000 0 -0.36 123 123
Chromosomal passenger complex/Cul3 protein complex -0.069 0.15 -10000 0 -0.37 78 78
BIRC5 -0.064 0.17 -10000 0 -0.33 119 119
DES -0.26 0.45 -10000 0 -0.86 166 166
Aurora C/Aurora B/INCENP -0.013 0.11 -10000 0 -0.24 89 89
Aurora B/TACC1 -0.027 0.11 -10000 0 -0.26 87 87
Aurora B/PP2A -0.034 0.13 -10000 0 -0.31 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.019 0.059 -10000 0 -0.14 91 91
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.095 0.19 0.19 6 -0.36 145 151
Cul3 protein complex 0.046 0.027 -10000 0 -0.26 2 2
KIF2C -0.093 0.25 -10000 0 -0.48 103 103
PEBP1 0.015 0.04 -10000 0 -0.44 3 3
KIF20A -0.079 0.17 -10000 0 -0.43 93 93
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.035 0.13 -10000 0 -0.31 88 88
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 -10000 0 0
NSUN2/NPM1/Nucleolin -0.12 0.3 -10000 0 -0.76 90 90
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 -0.043 0.12 -10000 0 -0.3 88 88
AURKB -0.074 0.18 -10000 0 -0.43 92 92
AURKC 0.011 0.051 -10000 0 -0.43 4 4
CDCA8 -0.01 0.075 -10000 0 -0.18 60 60
cytokinesis -0.16 0.32 0.24 1 -0.76 103 104
Aurora B/Septin1 -0.13 0.32 0.26 2 -0.71 103 105
AURKA 0.018 0.038 -10000 0 -0.15 22 22
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 -0.28 117 117
hSgo1/Aurora B/Survivin -0.083 0.22 -10000 0 -0.37 158 158
EVI5 0.021 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.11 0.29 -10000 0 -0.64 99 99
SGOL1 -0.047 0.15 -10000 0 -0.28 122 122
CENPA -0.1 0.25 0.23 1 -0.56 102 103
NCAPG -0.061 0.16 -10000 0 -0.3 137 137
Aurora B/HC8 Proteasome -0.035 0.13 -10000 0 -0.31 88 88
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.035 0.13 -10000 0 -0.31 88 88
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH -0.015 0.12 -10000 0 -0.43 32 32
NPM1 -0.083 0.2 -10000 0 -0.51 92 92
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 -0.035 0.13 -10000 0 -0.31 88 88
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin -0.13 0.31 0.2 1 -0.67 106 107
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.082 0.2 -10000 0 -0.51 90 90
MYLK -0.049 0.12 -10000 0 -0.29 98 98
KIF23 -0.036 0.13 -10000 0 -0.25 111 111
VIM -0.081 0.15 0.18 6 -0.32 128 134
RACGAP1 0.017 0.022 -10000 0 -0.14 5 5
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.085 0.21 -10000 0 -0.53 90 90
Chromosomal passenger complex -0.13 0.29 0.19 1 -0.65 106 107
Chromosomal passenger complex/EVI5 -0.043 0.19 -10000 0 -0.34 126 126
TACC1 0.025 0.005 -10000 0 -10000 0 0
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.073 0.13 -10000 0 -0.35 61 61
TBX21 -0.33 0.46 -10000 0 -1 126 126
B2M 0.025 0.016 -10000 0 -0.13 5 5
TYK2 -0.002 0.034 -10000 0 -10000 0 0
IL12RB1 -0.027 0.1 -10000 0 -0.39 30 30
GADD45B -0.24 0.36 -10000 0 -0.85 84 84
IL12RB2 -0.049 0.12 -10000 0 -0.29 71 71
GADD45G -0.25 0.38 -10000 0 -0.91 90 90
natural killer cell activation -0.012 0.02 -10000 0 -0.041 105 105
RELB 0.02 0.025 -10000 0 -0.21 4 4
RELA 0.025 0.005 -10000 0 -10000 0 0
IL18 -0.005 0.095 -10000 0 -0.4 24 24
IL2RA -0.015 0.071 -10000 0 -0.17 67 67
IFNG -0.008 0.021 -10000 0 -0.13 5 5
STAT3 (dimer) -0.24 0.33 -10000 0 -0.72 131 131
HLA-DRB5 -0.002 0.006 -10000 0 -0.021 38 38
FASLG -0.3 0.42 0.48 1 -0.96 118 119
NF kappa B2 p52/RelB -0.3 0.43 -10000 0 -0.9 138 138
CD4 0.017 0.035 -10000 0 -0.43 2 2
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
EntrezGene:6955 -0.001 0.007 -10000 0 -0.024 40 40
CD3D -0.033 0.12 -10000 0 -0.41 35 35
CD3E -0.052 0.14 -10000 0 -0.26 130 130
CD3G 0.004 0.044 -10000 0 -0.15 1 1
IL12Rbeta2/JAK2 -0.029 0.095 -10000 0 -0.28 43 43
CCL3 -0.4 0.55 -10000 0 -1.3 130 130
CCL4 -0.39 0.56 -10000 0 -1.2 136 136
HLA-A 0 0.003 -10000 0 -0.049 1 1
IL18/IL18R -0.021 0.14 -10000 0 -0.32 74 74
NOS2 -0.28 0.41 -10000 0 -0.91 119 119
IL12/IL12R/TYK2/JAK2/SPHK2 -0.068 0.13 -10000 0 -0.36 58 58
IL1R1 -0.32 0.44 -10000 0 -1 110 110
IL4 0.017 0.034 -10000 0 -10000 0 0
JAK2 -0.003 0.034 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -0.024 22 22
TCR/CD3/MHC I/CD8 -0.046 0.12 -10000 0 -0.45 22 22
RAB7A -0.19 0.3 0.52 1 -0.8 48 49
lysosomal transport -0.18 0.28 0.51 1 -0.74 51 52
FOS -0.23 0.44 -10000 0 -1.2 71 71
STAT4 (dimer) -0.28 0.38 0.5 1 -0.82 133 134
STAT5A (dimer) -0.3 0.43 -10000 0 -0.89 145 145
GZMA -0.37 0.5 -10000 0 -1.1 141 141
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 -0.97 147 147
TCR/CD3/MHC II/CD4 -0.038 0.1 -10000 0 -0.26 56 56
IL2/IL2R 0.002 0.11 -10000 0 -0.24 68 68
MAPK14 -0.24 0.36 -10000 0 -0.83 95 95
CCR5 -0.28 0.42 -10000 0 -1 96 96
IL1B -0.094 0.16 -10000 0 -0.36 113 113
STAT6 -0.072 0.11 -10000 0 -0.41 6 6
STAT4 -0.064 0.16 -10000 0 -0.43 69 69
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.028 -10000 0 -0.13 16 16
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.03 -10000 0 -0.43 2 2
IL12B -0.012 0.038 -10000 0 -0.15 6 6
CD8A -0.024 0.13 -10000 0 -0.42 45 45
CD8B -0.002 0.1 -10000 0 -0.43 27 27
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.073 0.13 0.35 61 -10000 0 61
IL2RB -0.028 0.13 -10000 0 -0.43 39 39
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.34 0.49 1 -0.74 133 134
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
IL12 -0.019 0.084 -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 -1.1 142 142
MAP2K3 -0.24 0.36 -10000 0 -0.8 108 108
RIPK2 0.024 0.007 -10000 0 -10000 0 0
MAP2K6 -0.24 0.36 -10000 0 -0.82 102 102
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.007 -10000 0 -0.024 39 39
IL18RAP -0.032 0.13 -10000 0 -0.36 54 54
IL12Rbeta1/TYK2 -0.017 0.086 -10000 0 -0.34 24 24
EOMES 0.022 0.097 -10000 0 -0.8 5 5
STAT1 (dimer) -0.24 0.32 -10000 0 -0.72 127 127
T cell proliferation -0.2 0.27 0.49 1 -0.58 130 131
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 -0.64 136 136
ATF2 -0.22 0.33 0.51 1 -0.77 95 96
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.046 0.17 0.22 19 -0.36 79 98
FYN -0.072 0.2 0.25 19 -0.44 89 108
LAT/GRAP2/SLP76 -0.074 0.17 0.23 6 -0.39 81 87
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.15 0.22 21 -0.33 86 107
B2M 0.021 0.021 -10000 0 -0.14 5 5
IKBKG -0.013 0.051 0.085 29 -0.12 36 65
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
mol:Ca2+ -0.016 0.027 0.089 12 -0.07 41 53
integrin-mediated signaling pathway 0.022 0.039 -10000 0 -0.24 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.081 0.2 0.25 17 -0.44 89 106
TRPV6 0.21 0.52 1.1 116 -0.45 39 155
CD28 -0.023 0.12 -10000 0 -0.3 71 71
SHC1 -0.074 0.19 0.23 25 -0.41 96 121
receptor internalization -0.059 0.15 0.24 2 -0.38 66 68
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 -0.043 0.13 0.21 19 -0.28 76 95
LAT -0.084 0.19 0.22 17 -0.41 101 118
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.035 0.12 -10000 0 -0.42 34 34
CD3E -0.052 0.15 -10000 0 -0.27 129 129
CD3G 0.001 0.044 -10000 0 -10000 0 0
RASGRP2 -0.003 0.019 0.13 1 -0.16 2 3
RASGRP1 -0.065 0.16 0.26 17 -0.34 88 105
HLA-A -0.002 0.006 -10000 0 -10000 0 0
RASSF5 0.016 0.062 -10000 0 -0.3 16 16
RAP1A/GTP/RAPL 0.023 0.039 -10000 0 -0.24 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.065 0.16 34 -0.12 19 53
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 71 80
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
mol:IP3 -0.063 0.14 0.19 17 -0.31 87 104
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.055 0.14 -10000 0 -0.36 62 62
ORAI1 -0.18 0.43 0.59 5 -0.95 114 119
CSK -0.076 0.19 0.22 18 -0.41 97 115
B7 family/CD28 -0.065 0.21 0.26 9 -0.45 88 97
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 0.21 5 -0.42 95 100
VAV1 -0.078 0.2 0.22 22 -0.42 100 122
Monovalent TCR/CD3 -0.044 0.11 -10000 0 -0.27 88 88
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.089 0.22 0.25 19 -0.46 102 121
PAG1 -0.073 0.19 0.21 27 -0.41 96 123
RAP1A 0.021 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.089 0.2 0.26 1 -0.44 96 97
CD80 -0.001 0.073 -10000 0 -0.18 55 55
CD86 0 0.1 -10000 0 -0.43 25 25
PDK1/CARD11/BCL10/MALT1 -0.04 0.084 -10000 0 -0.21 68 68
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.078 0.17 0.2 18 -0.38 91 109
CD8A -0.027 0.13 -10000 0 -0.42 46 46
CD8B -0.006 0.1 -10000 0 -0.43 27 27
PTPRC -0.004 0.1 -10000 0 -0.43 24 24
PDK1/PKC theta -0.065 0.18 0.28 17 -0.39 82 99
CSK/PAG1 -0.074 0.18 0.22 17 -0.4 92 109
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.019 -10000 0 -0.089 5 5
GRAP2/SLP76 -0.073 0.19 0.24 6 -0.42 89 95
STIM1 -0.008 0.2 1.2 10 -0.89 2 12
RAS family/GTP -0.011 0.08 0.18 22 -0.16 40 62
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.063 0.16 -10000 0 -0.4 66 66
mol:DAG -0.07 0.11 0.13 2 -0.27 100 102
RAP1A/GDP 0.004 0.027 0.078 21 -0.062 5 26
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.008 0.065 -10000 0 -0.25 20 20
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.9 55 55
RAP1A/GTP 0 0.007 -10000 0 -0.062 2 2
mol:PI-3-4-5-P3 -0.067 0.17 0.23 19 -0.37 88 107
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.078 0.17 0.23 8 -0.39 85 93
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 -0.088 0.16 0.2 1 -0.38 90 91
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
CD8 heterodimer -0.023 0.13 -10000 0 -0.3 79 79
CARD11 0.012 0.067 -10000 0 -0.43 11 11
PRKCB -0.053 0.093 0.15 6 -0.22 79 85
PRKCE -0.047 0.09 0.14 8 -0.21 76 84
PRKCQ -0.074 0.2 0.26 18 -0.42 88 106
LCP2 0.02 0.033 -10000 0 -0.43 1 1
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 84 106
IKK complex -0.003 0.057 0.15 27 -0.11 13 40
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.034 0.1 0.17 20 -0.22 70 90
PDPK1 -0.055 0.14 0.23 20 -0.32 80 100
TCR/CD3/MHC I/CD8/Fyn -0.09 0.22 0.23 1 -0.52 85 86
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 -0.051 0.12 -10000 0 -0.28 75 75
JUN -0.061 0.14 -10000 0 -0.4 46 46
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.15 -10000 0 -0.28 109 109
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 -0.025 0.16 -10000 0 -0.28 131 131
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.004 0.12 -10000 0 -0.26 86 86
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.038 0.15 -10000 0 -0.26 135 135
GRB7 0.001 0.044 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.019 0.15 -10000 0 -0.28 119 119
MAPKKK cascade -0.049 0.14 -10000 0 -0.28 124 124
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.003 0.12 -10000 0 -0.26 84 84
lamellipodium assembly -0.036 0.1 -10000 0 -0.26 66 66
RET51/GFRalpha1/GDNF/SHC -0.023 0.16 -10000 0 -0.28 127 127
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC -0.003 0.12 -10000 0 -0.26 83 83
RET9/GFRalpha1/GDNF/Shank3 -0.006 0.12 -10000 0 -0.26 88 88
MAPK3 -0.074 0.12 0.17 5 -0.32 61 66
DOK1 0.025 0.021 -10000 0 -0.28 2 2
DOK6 -0.017 0.13 -10000 0 -0.38 54 54
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.067 0.13 -10000 0 -0.36 52 52
DOK5 0.016 0.066 -10000 0 -0.43 11 11
GFRA1 -0.015 0.12 -10000 0 -0.31 61 61
MAPK8 -0.062 0.14 -10000 0 -0.28 133 133
HRAS/GTP -0.035 0.17 -10000 0 -0.3 129 129
tube development 0 0.12 0.2 14 -0.25 82 96
MAPK1 -0.074 0.12 -10000 0 -0.34 50 50
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.11 -10000 0 -0.25 82 82
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 -0.028 0.18 -10000 0 -0.31 133 133
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RET51/GFRalpha1/GDNF/Dok4 -0.032 0.17 -10000 0 -0.29 136 136
RET51/GFRalpha1/GDNF/Dok5 -0.026 0.16 -10000 0 -0.28 131 131
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 85 85
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.11 -10000 0 -0.26 81 81
RET51/GFRalpha1/GDNF/Grb7 -0.028 0.16 -10000 0 -0.29 129 129
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.043 0.15 -10000 0 -0.43 62 62
DOK4 0.012 0.079 -10000 0 -0.43 16 16
JNK cascade -0.062 0.13 0.19 1 -0.4 44 45
RET9/GFRalpha1/GDNF/FRS2 -0.003 0.12 -10000 0 -0.26 86 86
SHANK3 0.021 0.035 -10000 0 -0.43 2 2
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.1 -10000 0 -0.25 81 81
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.15 -10000 0 -0.28 130 130
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.15 -10000 0 -0.28 134 134
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.15 -10000 0 -0.28 123 123
PI3K -0.06 0.16 0.23 1 -0.38 80 81
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.006 0.12 -10000 0 -0.25 82 82
GRB10 0.021 0.03 -10000 0 -0.43 2 2
activation of MAPKK activity -0.052 0.14 -10000 0 -0.34 83 83
RET51/GFRalpha1/GDNF/FRS2 -0.025 0.16 -10000 0 -0.28 132 132
GAB1 0.025 0.02 -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 -0.29 123 123
RET51/GFRalpha1/GDNF/PKC alpha -0.025 0.16 -10000 0 -0.28 129 129
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GDNF -0.034 0.15 -10000 0 -0.43 60 60
RAC1 0.023 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.023 0.16 -10000 0 -0.28 129 129
Rac1/GTP -0.037 0.12 -10000 0 -0.3 63 63
RET9/GFRalpha1/GDNF -0.028 0.12 -10000 0 -0.28 86 86
GFRalpha1/GDNF -0.035 0.14 -10000 0 -0.34 86 86
Syndecan-1-mediated signaling events

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CCL5 -0.025 0.12 -10000 0 -0.43 39 39
SDCBP 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.065 0.14 0.24 6 -0.32 73 79
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 9 -0.38 45 54
Syndecan-1/Syntenin -0.048 0.14 0.24 15 -0.36 51 66
MAPK3 -0.051 0.13 0.19 14 -0.37 39 53
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
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 10 -0.38 45 55
Syndecan-1/RANTES -0.068 0.16 0.24 16 -0.39 61 77
Syndecan-1/CD147 -0.043 0.14 0.34 1 -0.39 40 41
Syndecan-1/Syntenin/PIP2 -0.047 0.14 0.24 12 -0.35 49 61
LAMA5 0.024 0.022 -10000 0 -0.43 1 1
positive regulation of cell-cell adhesion -0.047 0.14 0.23 12 -0.35 49 61
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
HGF -0.009 0.091 -10000 0 -0.2 69 69
Syndecan-1/CASK -0.069 0.13 -10000 0 -0.31 74 74
Syndecan-1/HGF/MET -0.075 0.16 0.24 4 -0.35 84 88
regulation of cell adhesion -0.043 0.14 0.3 17 -0.36 39 56
HPSE -0.014 0.12 -10000 0 -0.43 39 39
positive regulation of cell migration -0.065 0.14 0.24 6 -0.32 73 79
SDC1 -0.063 0.14 0.19 2 -0.32 78 80
Syndecan-1/Collagen -0.065 0.14 0.24 6 -0.32 73 79
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.047 0.14 -10000 0 -0.26 121 121
PRKACA 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
MAPK1 -0.051 0.13 0.2 13 -0.37 39 52
homophilic cell adhesion -0.061 0.14 0.22 15 -0.34 63 78
MMP1 -0.008 0.048 -10000 0 -0.43 1 1
Thromboxane A2 receptor signaling

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
TGM2 0.023 0.016 -10000 0 -0.13 5 5
GNB1/GNG2 -0.055 0.077 -10000 0 -0.18 125 125
AKT1 -0.032 0.12 0.29 9 -0.24 48 57
EGF -0.01 0.11 -10000 0 -0.31 54 54
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.074 0.33 18 -0.25 1 19
mol:Ca2+ -0.051 0.16 0.33 7 -0.29 126 133
LYN 0.009 0.081 0.32 19 -0.24 4 23
RhoA/GTP -0.025 0.062 -10000 0 -0.13 109 109
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.18 0.31 11 -0.35 128 139
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 -0.001 0.099 -10000 0 -0.4 21 21
G beta5/gamma2 -0.065 0.1 -10000 0 -0.24 123 123
PRKCH -0.064 0.17 0.33 7 -0.34 124 131
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
TXA2/TP beta/beta Arrestin3 -0.008 0.045 -10000 0 -0.25 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.003 0.063 -10000 0 -0.24 14 14
G12 family/GTP -0.067 0.14 -10000 0 -0.3 115 115
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
ADRBK2 0.024 0.029 -10000 0 -0.33 3 3
RhoA/GTP/ROCK1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP 0.023 0.11 0.29 21 -0.31 9 30
mol:NADP 0.017 0.034 -10000 0 -0.21 8 8
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.009 0.12 -10000 0 -0.43 36 36
mol:IP3 -0.068 0.19 0.35 7 -0.37 126 133
cell morphogenesis 0.033 0.007 -10000 0 -10000 0 0
PLCB2 -0.1 0.25 0.39 6 -0.5 125 131
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.088 0.31 16 -0.22 8 24
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 -0.19 22 22
PRKCB1 -0.07 0.18 0.33 6 -0.36 128 134
GNAQ 0.026 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.034 -10000 0 -0.21 8 8
TXA2/TXA2-R family -0.11 0.25 0.39 6 -0.52 129 135
LCK -0.001 0.085 0.34 16 -0.23 2 18
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 77 77
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.009 0.049 -10000 0 -0.2 9 9
MAPK14 -0.041 0.12 0.26 11 -0.23 125 136
TGM2/GTP -0.081 0.2 0.38 3 -0.41 125 128
MAPK11 -0.043 0.12 0.26 11 -0.23 126 137
ARHGEF1 -0.036 0.083 0.14 1 -0.18 113 114
GNAI2 0.025 0.005 -10000 0 -10000 0 0
JNK cascade -0.076 0.19 0.35 7 -0.38 129 136
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 -0.066 0.18 0.35 7 -0.34 126 133
Gq family/GTP/EBP50 0.005 0.07 0.24 8 -0.25 22 30
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 -0.011 0.12 0.31 29 -0.26 33 62
VCAM1 -0.076 0.18 0.3 6 -0.36 131 137
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.099 -10000 0 -0.4 21 21
platelet activation -0.053 0.16 0.32 12 -0.3 128 140
PGI2/IP 0.01 0.034 -10000 0 -0.3 4 4
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 -0.021 0.12 -10000 0 -0.48 33 33
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 -0.078 0.21 0.37 6 -0.41 126 132
EGFR -0.016 0.12 -10000 0 -0.4 46 46
TXA2/TP alpha -0.093 0.23 0.41 6 -0.46 126 132
Gq family/GTP -0.002 0.063 0.21 5 -0.21 35 40
YES1 0.009 0.078 0.34 16 -0.24 3 19
GNAI2/GTP 0.003 0.045 -10000 0 -0.23 3 3
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 -0.21 8 8
GNA15 0.013 0.07 -10000 0 -0.34 17 17
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 -0.29 2 2
NOS3 0.017 0.034 -10000 0 -0.21 8 8
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.061 0.18 0.3 10 -0.34 122 132
PRKCB -0.075 0.18 0.35 5 -0.36 129 134
PRKCE -0.066 0.18 0.32 8 -0.35 124 132
PRKCD -0.077 0.2 0.31 8 -0.39 129 137
PRKCG -0.086 0.19 0.35 8 -0.38 130 138
muscle contraction -0.1 0.24 0.39 5 -0.48 130 135
PRKCZ -0.07 0.17 0.33 7 -0.34 131 138
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
TXA2/TP beta 0.01 0.052 -10000 0 -0.21 9 9
PRKCQ -0.063 0.18 0.29 11 -0.35 121 132
MAPKKK cascade -0.088 0.22 0.37 6 -0.44 128 134
SELE -0.066 0.16 0.3 6 -0.32 130 136
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.053 -10000 0 -0.28 2 2
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.43 16 16
chemotaxis -0.13 0.29 0.39 5 -0.61 130 135
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
Reelin signaling pathway

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.015 0.07 -10000 0 -0.3 22 22
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
CRKL 0.025 0.008 -10000 0 -10000 0 0
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 0.059 0.055 -10000 0 -0.22 15 15
AKT1 -0.047 0.11 -10000 0 -0.26 98 98
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
DAB1 -0.039 0.15 -10000 0 -0.36 80 80
RELN/LRP8/DAB1 -0.024 0.12 -10000 0 -0.24 103 103
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
RELN/LRP8/DAB1/Fyn -0.017 0.11 -10000 0 -0.22 103 103
DAB1/alpha3/beta1 Integrin -0.02 0.11 -10000 0 -0.23 92 92
long-term memory -0.1 0.17 -10000 0 -0.29 191 191
DAB1/LIS1 -0.014 0.12 -10000 0 -0.23 100 100
DAB1/CRLK/C3G -0.02 0.11 -10000 0 -0.24 81 81
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DAB1/NCK2 -0.014 0.12 -10000 0 -0.23 100 100
ARHGEF2 0.025 0.02 -10000 0 -0.43 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.071 0.17 -10000 0 -0.29 155 155
CDK5R1 0 0.1 -10000 0 -0.42 30 30
RELN -0.046 0.14 -10000 0 -0.29 107 107
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 -0.052 0.16 -10000 0 -0.28 134 134
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
RELN/VLDLR/DAB1 -0.031 0.12 -10000 0 -0.24 109 109
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
MAP1B -0.032 0.12 0.16 60 -0.25 102 162
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
GRIN2B/RELN/LRP8/DAB1/Fyn -0.057 0.15 -10000 0 -0.28 140 140
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 -0.077 0.16 -10000 0 -0.43 83 83
NCK2 0.026 0.002 -10000 0 -10000 0 0
neuron differentiation -0.028 0.13 -10000 0 -0.34 52 52
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 -0.052 0.11 -10000 0 -0.25 94 94
RELN/VLDLR/DAB1/Fyn -0.024 0.12 -10000 0 -0.23 109 109
MAP3K11 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.049 0.12 -10000 0 -0.27 103 103
CDK5 0.02 0.011 -10000 0 -10000 0 0
MAPT 0.006 0.098 0.77 6 -0.39 8 14
neuron migration -0.042 0.16 0.23 54 -0.31 100 154
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.13 -10000 0 -0.34 52 52
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 66 66
E-cadherin 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
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 -0.28 122 122
Effects of Botulinum toxin

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
STX1A -0.011 0.046 -10000 0 -0.3 7 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.019 0.12 -10000 0 -0.31 69 69
STXBP1 0.016 0.044 -10000 0 -0.16 26 26
ACh/CHRNA1 -0.042 0.11 0.13 8 -0.24 92 100
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 -0.049 0.16 -10000 0 -0.43 70 70
mol:ACh -0.008 0.057 0.098 60 -0.11 74 134
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.031 0.12 -10000 0 -0.27 71 71
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.11 0.13 8 -0.24 92 100
UNC13B 0.025 0.021 -10000 0 -0.43 1 1
CHRNA1 -0.065 0.15 -10000 0 -0.43 68 68
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.056 0.13 0.11 9 -0.22 154 163
SNAP25 -0.043 0.098 -10000 0 -0.26 86 86
VAMP2 0.005 0 -10000 0 -10000 0 0
SYT1 -0.088 0.17 -10000 0 -0.27 197 197
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0 0.052 -10000 0 -0.16 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.031 0.12 -10000 0 -0.27 71 71
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.078 -10000 0 -0.31 25 25
CDKN2C 0.01 0.042 -10000 0 -0.13 27 27
CDKN2A -0.014 0.1 -10000 0 -0.32 46 46
CCND2 0.016 0.068 0.21 48 -0.13 3 51
RB1 -0.023 0.079 0.12 1 -0.24 53 54
CDK4 0.021 0.077 0.23 51 -0.17 1 52
CDK6 0.017 0.081 0.25 44 -0.16 10 54
G1/S progression 0.042 0.099 0.25 76 -0.22 4 80
Syndecan-4-mediated signaling events

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.069 0.25 1 -0.43 5 6
Syndecan-4/Syndesmos -0.059 0.2 0.32 1 -0.46 91 92
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 -0.025 0.12 -10000 0 -0.43 39 39
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.025 0.006 -10000 0 -10000 0 0
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
SDCBP 0.025 0.006 -10000 0 -10000 0 0
PLG 0.001 0.026 -10000 0 -0.14 4 4
ADAM12 -0.001 0.077 -10000 0 -0.18 65 65
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 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.22 0.32 1 -0.49 95 96
Syndecan-4/CXCL12/CXCR4 -0.056 0.21 0.32 1 -0.46 92 93
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 0.3 2 -0.47 90 92
FZD7 -0.018 0.13 -10000 0 -0.4 54 54
Syndecan-4/FGFR1/FGF -0.044 0.19 0.3 1 -0.44 85 86
THBS1 -0.018 0.1 -10000 0 -0.2 100 100
integrin-mediated signaling pathway -0.066 0.2 0.31 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 0.072 -10000 0 -0.27 25 25
cell adhesion 0.017 0.036 0.2 14 -0.2 1 15
Syndecan-4/Dynamin -0.063 0.2 -10000 0 -0.46 93 93
Syndecan-4/TSP1 -0.071 0.21 0.32 1 -0.48 92 93
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 93 94
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 -0.024 0.12 -10000 0 -0.43 33 33
F2 0.006 0.031 -10000 0 -0.13 8 8
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
positive regulation of cell adhesion -0.094 0.22 0.31 1 -0.49 103 104
ACTN1 0.014 0.044 -10000 0 -0.14 35 35
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 -0.13 11 11
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 -0.16 5 5
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.001 0.096 -10000 0 -0.41 26 26
vasculogenesis -0.068 0.2 0.31 1 -0.46 93 94
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 0.016 -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 -0.24 118 118
Rac1/GTP 0.017 0.036 0.2 14 -0.2 1 15
cytoskeleton organization -0.056 0.2 0.31 1 -0.44 92 93
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
Syndecan-4/TFPI -0.074 0.21 0.34 1 -0.48 93 94
Endothelins

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
AKT1 -0.056 0.13 0.24 1 -0.27 110 111
PTK2B 0.018 0.032 -10000 0 -10000 0 0
mol:Ca2+ -0.045 0.22 -10000 0 -0.74 36 36
EDN1 -0.036 0.11 0.21 1 -0.22 101 102
EDN3 0.006 0.09 -10000 0 -0.43 21 21
EDN2 -0.006 0.031 -10000 0 -0.13 20 20
HRAS/GDP -0.051 0.17 0.28 7 -0.46 43 50
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.13 -10000 0 -0.38 37 37
ADCY4 -0.069 0.14 -10000 0 -0.31 88 88
ADCY5 -0.073 0.14 -10000 0 -0.32 89 89
ADCY6 -0.067 0.13 -10000 0 -0.3 85 85
ADCY7 -0.067 0.13 -10000 0 -0.3 85 85
ADCY1 -0.072 0.14 -10000 0 -0.32 93 93
ADCY2 -0.071 0.14 -10000 0 -0.31 90 90
ADCY3 -0.067 0.13 -10000 0 -0.31 81 81
ADCY8 -0.081 0.15 -10000 0 -0.32 108 108
ADCY9 -0.067 0.14 -10000 0 -0.32 79 79
arachidonic acid secretion -0.066 0.2 0.29 9 -0.46 78 87
ETB receptor/Endothelin-1/Gq/GTP -0.026 0.12 -10000 0 -0.29 62 62
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 -0.25 102 102
ETA receptor/Endothelin-1/Gs/GTP -0.041 0.16 -10000 0 -0.26 155 155
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.099 0.2 -10000 0 -0.53 79 79
EDNRB -0.014 0.12 -10000 0 -0.39 43 43
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.065 0.16 0.24 1 -0.41 55 56
CYSLTR1 -0.064 0.15 0.24 1 -0.47 38 39
SLC9A1 -0.034 0.098 0.17 1 -0.28 45 46
mol:GDP -0.063 0.18 0.28 9 -0.48 48 57
SLC9A3 -0.075 0.25 -10000 0 -0.65 63 63
RAF1 -0.072 0.19 0.27 8 -0.46 66 74
JUN -0.037 0.19 -10000 0 -0.63 29 29
JAK2 -0.055 0.13 0.24 1 -0.27 108 109
mol:IP3 -0.042 0.14 -10000 0 -0.46 32 32
ETA receptor/Endothelin-1 -0.04 0.17 0.41 1 -0.32 114 115
PLCB1 0.01 0.081 -10000 0 -0.43 17 17
PLCB2 0.011 0.073 -10000 0 -0.36 17 17
ETA receptor/Endothelin-3 -0.018 0.11 -10000 0 -0.34 39 39
FOS -0.11 0.31 0.35 5 -0.87 65 70
Gai/GDP 0.002 0.14 -10000 0 -0.71 15 15
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca ++ -0.071 0.17 -10000 0 -0.44 59 59
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
PRKCB1 -0.042 0.14 -10000 0 -0.45 31 31
GNAQ 0.024 0.011 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.028 0.15 -10000 0 -0.42 61 61
Gs family/GDP -0.073 0.18 0.27 4 -0.44 63 67
ETA receptor/Endothelin-1/Gq/GTP -0.029 0.12 -10000 0 -0.33 41 41
MAPK14 -0.033 0.12 -10000 0 -0.44 27 27
TRPC6 -0.049 0.24 -10000 0 -0.8 35 35
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 -0.032 0.13 -10000 0 -0.4 35 35
ETB receptor/Endothelin-2 -0.004 0.09 -10000 0 -0.3 37 37
ETB receptor/Endothelin-3 -0.003 0.11 -10000 0 -0.34 49 49
ETB receptor/Endothelin-1 -0.027 0.13 0.18 1 -0.31 70 71
MAPK3 -0.1 0.27 0.34 6 -0.76 65 71
MAPK1 -0.1 0.28 0.34 7 -0.76 65 72
Rac1/GDP -0.053 0.16 0.34 1 -0.47 40 41
cAMP biosynthetic process -0.073 0.16 0.22 1 -0.37 79 80
MAPK8 -0.049 0.22 -10000 0 -0.68 39 39
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.022 0.098 0.16 1 -0.3 38 39
p130Cas/CRK/Src/PYK2 -0.049 0.18 0.32 10 -0.56 33 43
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.053 0.16 0.34 1 -0.47 40 41
COL1A2 -0.058 0.16 -10000 0 -0.45 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.018 0.089 -10000 0 -0.29 26 26
mol:DAG -0.042 0.14 -10000 0 -0.46 32 32
MAP2K2 -0.081 0.22 0.35 12 -0.58 66 78
MAP2K1 -0.089 0.23 0.28 5 -0.6 67 72
EDNRA -0.033 0.12 0.21 1 -0.35 34 35
positive regulation of muscle contraction -0.024 0.13 0.22 29 -0.29 47 76
Gq family/GDP -0.043 0.17 -10000 0 -0.48 39 39
HRAS/GTP -0.061 0.17 0.27 8 -0.46 47 55
PRKCH -0.042 0.13 -10000 0 -0.47 27 27
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.039 0.14 0.24 7 -0.47 28 35
PRKCB -0.052 0.14 -10000 0 -0.45 35 35
PRKCE -0.043 0.14 0.22 1 -0.46 29 30
PRKCD -0.052 0.15 -10000 0 -0.5 34 34
PRKCG -0.075 0.15 -10000 0 -0.41 54 54
regulation of vascular smooth muscle contraction -0.13 0.36 0.4 4 -1 64 68
PRKCQ -0.035 0.15 0.22 19 -0.49 29 48
PLA2G4A -0.073 0.22 0.31 7 -0.5 78 85
GNA14 0.008 0.081 -10000 0 -0.43 16 16
GNA15 0.012 0.071 -10000 0 -0.34 17 17
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 0.017 0.1 0.42 12 -0.83 1 13
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.19 -10000 0 -0.58 53 53
IHH 0.012 0.056 -10000 0 -0.2 6 6
SHH Np/Cholesterol/GAS1 -0.011 0.084 0.16 12 -0.24 53 65
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.011 0.083 0.24 53 -0.15 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 -0.48 17 17
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 -0.019 0.11 -10000 0 -0.41 20 20
STIL -0.012 0.13 0.23 3 -0.3 38 41
DHH N/PTCH2 0.004 0.085 -10000 0 -0.31 31 31
DHH N/PTCH1 -0.02 0.12 -10000 0 -0.3 56 56
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 -0.019 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 -0.04 0.14 -10000 0 -0.34 76 76
DHH N/Hhip -0.049 0.14 -10000 0 -0.31 101 101
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.019 0.11 -10000 0 -0.41 20 20
pancreas development -0.058 0.16 -10000 0 -0.29 135 135
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 -0.17 26 26
somite specification -0.019 0.11 -10000 0 -0.41 20 20
SHH Np/Cholesterol/PTCH1 -0.036 0.11 -10000 0 -0.28 68 68
SHH Np/Cholesterol/PTCH2 -0.016 0.082 0.15 2 -0.24 56 58
SHH Np/Cholesterol/Megalin -0.059 0.12 0.15 8 -0.27 115 123
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 -0.032 0.12 0.29 2 -0.34 34 36
SHH Np/Cholesterol/Hhip -0.048 0.12 0.15 8 -0.26 102 110
LRP2 -0.093 0.18 -10000 0 -0.43 108 108
receptor-mediated endocytosis -0.066 0.14 -10000 0 -0.4 47 47
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 0.048 0.12 0.26 102 -0.15 8 110
mol:Vitamin D3 -0.001 0.14 0.26 6 -0.28 67 73
IHH N/PTCH2 0.023 0.051 -10000 0 -0.37 5 5
CDON 0.001 0.095 -10000 0 -0.43 23 23
IHH N/PTCH1 -0.011 0.12 -10000 0 -0.34 52 52
Megalin/LRPAP1 -0.052 0.14 -10000 0 -0.3 108 108
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 -0.058 0.16 -10000 0 -0.29 135 135
ErbB2/ErbB3 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
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.12 -10000 0 -0.24 102 102
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 -0.047 0.11 0.2 1 -0.24 115 116
JUN -0.022 0.083 0.2 3 -0.38 9 12
HRAS 0.024 0.006 -10000 0 -10000 0 0
DOCK7 -0.064 0.098 -10000 0 -0.24 104 104
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.035 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 -0.21 8 10
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.12 0.21 1 -0.26 115 116
RAF1 -0.044 0.12 0.25 8 -0.32 46 54
ErbB2/ErbB3/neuregulin 2 -0.003 0.08 0.16 1 -0.25 40 41
STAT3 0.028 0.043 -10000 0 -0.91 1 1
cell migration -0.022 0.077 0.22 13 -0.21 10 23
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.1 0.25 0.36 1 -0.61 82 83
FOS -0.083 0.2 0.28 3 -0.41 118 121
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.11 0.2 1 -0.24 115 116
MAPK3 -0.08 0.21 0.36 2 -0.51 70 72
MAPK1 -0.083 0.21 0.36 2 -0.52 66 68
JAK2 -0.067 0.097 -10000 0 -0.24 106 106
NF2 0.005 0.033 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.052 0.12 0.17 2 -0.26 118 120
NRG1 -0.081 0.18 -10000 0 -0.32 156 156
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
MAPK8 -0.054 0.12 -10000 0 -0.27 112 112
MAPK9 -0.029 0.063 0.17 3 -0.19 7 10
ERBB2 -0.022 0.017 -10000 0 -0.32 1 1
ERBB3 -0.017 0.12 -10000 0 -0.4 46 46
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 -0.041 0.074 -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 23 26
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 -0.23 106 106
NRG2 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.053 0.12 0.17 2 -0.26 119 121
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.048 0.13 0.24 10 -0.34 42 52
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 0.2 -10000 0 -0.58 38 38
heart morphogenesis -0.047 0.11 0.2 1 -0.24 115 116
RAS family/GDP -0.026 0.12 0.22 2 -0.24 101 103
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 -0.18 9 10
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.007 -10000 0 -10000 0 0
nervous system development -0.047 0.11 0.2 1 -0.24 115 116
CDC42 0.022 0.01 -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 -0.79 60 60
PCK1 -0.18 0.39 -10000 0 -1.2 54 54
HNF4A -0.15 0.33 -10000 0 -0.9 57 57
KCNJ11 -0.18 0.4 -10000 0 -1 76 76
AKT1 -0.067 0.18 -10000 0 -0.41 54 54
response to starvation -0.003 0.026 -10000 0 -0.31 2 2
DLK1 -0.16 0.35 -10000 0 -0.9 70 70
NKX2-1 -0.058 0.15 0.3 3 -0.37 47 50
ACADM -0.13 0.3 -10000 0 -0.83 51 51
TAT -0.19 0.39 -10000 0 -1.2 53 53
CEBPB 0.013 0.073 -10000 0 -0.43 13 13
CEBPA 0.015 0.05 -10000 0 -0.32 8 8
TTR -0.12 0.27 0.53 3 -0.82 40 43
PKLR -0.14 0.3 -10000 0 -0.82 54 54
APOA1 -0.18 0.4 -10000 0 -1.1 64 64
CPT1C -0.13 0.3 -10000 0 -0.81 55 55
ALAS1 -0.06 0.18 0.46 1 -0.71 4 5
TFRC -0.14 0.3 -10000 0 -0.85 48 48
FOXF1 0.019 0.042 -10000 0 -0.19 16 16
NF1 0.03 0.02 -10000 0 -0.42 1 1
HNF1A (dimer) 0.025 0.026 -10000 0 -0.44 1 1
CPT1A -0.13 0.3 -10000 0 -0.81 56 56
HMGCS1 -0.13 0.3 -10000 0 -0.8 58 58
NR3C1 -0.018 0.089 -10000 0 -0.2 75 75
CPT1B -0.15 0.32 -10000 0 -0.8 74 74
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.024 0.013 -10000 0 -10000 0 0
GCK -0.16 0.37 0.5 1 -0.88 84 85
CREB1 0.008 0.058 -10000 0 -0.19 29 29
IGFBP1 -0.22 0.48 -10000 0 -1.2 85 85
PDX1 -0.058 0.17 -10000 0 -0.62 6 6
UCP2 -0.14 0.32 -10000 0 -0.82 66 66
ALDOB -0.14 0.35 -10000 0 -0.91 59 59
AFP -0.035 0.1 -10000 0 -0.43 9 9
BDH1 -0.16 0.35 -10000 0 -0.92 67 67
HADH -0.13 0.32 -10000 0 -0.84 59 59
F2 -0.15 0.35 -10000 0 -0.98 47 47
HNF1A 0.025 0.026 -10000 0 -0.44 1 1
G6PC -0.034 0.16 -10000 0 -0.77 13 13
SLC2A2 -0.064 0.19 -10000 0 -0.8 2 2
INS 0.008 0.086 0.21 61 -0.35 5 66
FOXA1 -0.007 0.087 -10000 0 -0.28 32 32
FOXA3 -0.041 0.14 -10000 0 -0.37 59 59
FOXA2 -0.15 0.37 -10000 0 -0.91 66 66
ABCC8 -0.19 0.41 -10000 0 -0.98 86 86
ALB -0.07 0.23 -10000 0 -0.91 32 32
Syndecan-3-mediated 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
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 -0.016 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 -0.13 5 5
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 -0.43 28 28
long-term memory -0.013 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 -0.013 0.14 -10000 0 -0.36 72 72
Syndecan-3/CASK -0.045 0.14 -10000 0 -0.36 77 77
alpha-MSH/MC4R -0.025 0.13 -10000 0 -0.32 76 76
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.36 -10000 0 -1 43 43
STAT6 (cleaved dimer) -0.28 0.39 -10000 0 -1 79 79
IGHG1 -0.1 0.2 -10000 0 -0.98 13 13
IGHG3 -0.24 0.34 -10000 0 -0.93 61 61
AKT1 -0.18 0.31 -10000 0 -0.88 60 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.31 -10000 0 -0.87 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.93 62 62
THY1 -0.26 0.39 -10000 0 -1.2 44 44
MYB -0.016 0.12 -10000 0 -0.28 67 67
HMGA1 0.025 0.01 -10000 0 -0.13 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.31 -10000 0 -0.8 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.33 -10000 0 -0.93 65 65
SP1 0.025 0.019 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
SOCS5 0.033 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.38 -10000 0 -1 70 70
SOCS1 -0.21 0.28 -10000 0 -0.73 61 61
SOCS3 -0.23 0.36 -10000 0 -1 67 67
FCER2 -0.26 0.4 -10000 0 -1.2 49 49
PARP14 0.017 0.046 -10000 0 -0.22 13 13
CCL17 -0.25 0.36 -10000 0 -1.1 37 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.24 -10000 0 -0.66 59 59
T cell proliferation -0.27 0.38 -10000 0 -1 63 63
IL4R/JAK1 -0.25 0.36 -10000 0 -1 46 46
EGR2 -0.34 0.5 -10000 0 -1.3 75 75
JAK2 -0.008 0.041 -10000 0 -10000 0 0
JAK3 -0.011 0.1 -10000 0 -0.24 65 65
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.022 -10000 0 -10000 0 0
COL1A2 -0.088 0.2 -10000 0 -1.1 9 9
CCL26 -0.22 0.37 -10000 0 -1.1 35 35
IL4R -0.26 0.38 -10000 0 -1.1 45 45
PTPN6 0.019 0.065 -10000 0 -0.39 11 11
IL13RA2 -0.42 0.55 -10000 0 -1.3 129 129
IL13RA1 -0.013 0.07 -10000 0 -0.42 9 9
IRF4 -0.12 0.32 -10000 0 -1.3 30 30
ARG1 -0.09 0.21 -10000 0 -0.95 18 18
CBL -0.19 0.29 -10000 0 -0.75 75 75
GTF3A 0.003 0.052 -10000 0 -0.15 16 16
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL13RA1/JAK2 -0.01 0.07 -10000 0 -0.32 8 8
IRF4/BCL6 -0.099 0.3 -10000 0 -1.2 30 30
CD40LG 0.003 0.054 -10000 0 -0.13 59 59
MAPK14 -0.22 0.32 -10000 0 -0.8 84 84
mitosis -0.17 0.29 -10000 0 -0.81 60 60
STAT6 -0.28 0.4 -10000 0 -1.1 57 57
SPI1 0.015 0.064 -10000 0 -0.27 19 19
RPS6KB1 -0.16 0.28 -10000 0 -0.78 59 59
STAT6 (dimer) -0.28 0.4 -10000 0 -1.1 57 57
STAT6 (dimer)/PARP14 -0.26 0.38 -10000 0 -1 61 61
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 -0.82 68 68
FRAP1 -0.18 0.31 -10000 0 -0.88 60 60
LTA -0.28 0.42 -10000 0 -1.2 55 55
FES 0.024 0.024 -10000 0 -0.21 4 4
T-helper 1 cell differentiation 0.27 0.39 1.1 57 -10000 0 57
CCL11 -0.25 0.34 -10000 0 -1 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.3 -10000 0 -0.83 58 58
IL2RG -0.002 0.087 -10000 0 -0.22 52 52
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 -0.064 0.12 -10000 0 -0.88 4 4
IL5 -0.25 0.36 -10000 0 -1.1 37 37
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.32 -10000 0 -0.88 52 52
COL1A1 -0.26 0.49 -10000 0 -1.4 75 75
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 37 37
IL2R gamma/JAK3 -0.009 0.1 -10000 0 -0.27 53 53
TFF3 -0.26 0.36 -10000 0 -1.1 42 42
ALOX15 -0.26 0.36 -10000 0 -1.1 37 37
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 -0.91 65 65
mol:PI-3-4-5-P3 -0.18 0.31 -10000 0 -0.88 60 60
PI3K -0.19 0.34 -10000 0 -0.96 60 60
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
ETS1 0.022 0.052 -10000 0 -0.41 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 0.34 1 -0.63 56 57
ITGB3 -0.27 0.39 -10000 0 -1.1 50 50
PIGR -0.34 0.51 -10000 0 -1.4 77 77
IGHE 0.011 0.058 0.16 9 -0.2 13 22
MAPKKK cascade -0.13 0.22 0.34 1 -0.62 56 57
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.26 0.36 -10000 0 -1.1 39 39
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 38 38
Visual signal transduction: Rods

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
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 0.013 0.05 -10000 0 -0.26 12 12
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 -0.15 31 31
GRK1 0.021 0.015 -10000 0 -10000 0 0
CNG Channel -0.047 0.14 -10000 0 -0.25 141 141
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 -0.27 40 40
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 -0.24 176 176
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 44 47
Na + (4 Units) -0.079 0.12 -10000 0 -0.23 152 152
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
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 -0.012 0.011 -10000 0 -10000 0 0
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 59 61
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 0.013 0.063 -10000 0 -0.29 12 12
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 0.045 -10000 0 -0.23 12 12
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 0.05 -10000 0 -0.39 7 7
Metarhodopsin II/Transducin -0.001 0.043 -10000 0 -0.25 11 11
GCAP Family/Ca ++ -0.007 0.11 -10000 0 -0.23 93 93
PDE6A/B 0.001 0.095 -10000 0 -0.3 38 38
mol:Pi 0.017 0.088 -10000 0 -0.27 40 40
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.023 0.03 -10000 0 -0.24 1 1
PDE6B 0.002 0.092 -10000 0 -0.28 40 40
PDE6A 0 0.088 -10000 0 -0.24 48 48
PDE6G -0.001 0.1 -10000 0 -0.32 39 39
RHO -0.003 0.077 -10000 0 -0.21 46 46
PDE6 0.009 0.12 -10000 0 -0.24 88 88
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 -10000 0 0
GUCA1B 0.012 0.079 -10000 0 -0.43 16 16
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.036 -10000 0 -0.26 6 6
ARNO/beta Arrestin1-2 -0.099 0.31 -10000 0 -0.81 81 81
EGFR -0.016 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 -0.13 10 10
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 0.007 0.042 0.18 5 -0.17 11 16
ARRB1 0.012 0.076 -10000 0 -0.43 15 15
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR -0.084 0.17 -10000 0 -0.43 90 90
EGF -0.01 0.11 -10000 0 -0.34 48 48
somatostatin receptor activity 0 0 0.001 59 -0.001 21 80
ARAP2 0.012 0.079 -10000 0 -0.43 16 16
mol:GDP -0.016 0.13 0.19 46 -0.3 40 86
mol:PI-3-4-5-P3 0 0 0.001 69 -0.001 7 76
ITGA2B -0.012 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 0.036 -10000 0 -0.25 3 3
ADAP1 0.014 0.054 -10000 0 -0.43 6 6
KIF13B 0.025 0.005 -10000 0 -10000 0 0
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.13 0.26 52 -0.27 29 81
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.005 0.11 -10000 0 -0.27 70 70
ADRB2 0.005 0.094 -10000 0 -0.43 23 23
receptor agonist activity 0 0 0 28 0 21 49
actin filament binding 0 0 0.001 59 -0.001 22 81
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 67 -0.001 16 83
ARF6/GDP -0.026 0.14 0.23 5 -0.44 34 39
ARF6/GDP/GULP/ACAP1 -0.012 0.16 0.22 29 -0.36 45 74
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.094 -10000 0 -0.24 52 52
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 -10000 0 0
HGF -0.009 0.091 -10000 0 -0.2 69 69
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 63 0 20 83
endosomal lumen acidification 0 0 0.001 61 0 26 87
microtubule-based process 0 0 -10000 0 0 12 12
GULP1 -0.016 0.13 -10000 0 -0.43 44 44
GNAQ/ARNO -0.12 0.35 -10000 0 -0.93 81 81
mol:Phosphatidic acid 0 0 0 17 -10000 0 17
PIP3-E 0 0 0 39 0 12 51
MET -0.047 0.14 -10000 0 -0.26 121 121
GNA14 0.009 0.081 -10000 0 -0.43 16 16
GNA15 0.013 0.07 -10000 0 -0.34 17 17
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 64 -0.001 17 81
GNA11 0.017 0.06 -10000 0 -0.43 9 9
LHCGR 0.009 0.031 -10000 0 -0.13 16 16
AGTR1 0.001 0.093 -10000 0 -0.43 21 21
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
Stabilization and expansion of the E-cadherin adherens junction

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
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 -0.28 6 6
ENAH -0.024 0.061 0.27 3 -10000 0 3
EGFR -0.016 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 55 76
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.045 0.028 -10000 0 -0.23 3 3
AQP5 -0.063 0.16 0.22 4 -0.44 71 75
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.077 0.18 20 -0.21 53 73
regulation of calcium-dependent cell-cell adhesion -0.015 0.081 0.18 20 -0.21 58 78
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 -10000 0 -0.45 17 17
cortical microtubule organization 0.024 0.086 -10000 0 -0.22 55 55
GO:0000145 -0.026 0.07 0.16 20 -0.2 53 73
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.088 -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 -0.2 35 35
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.036 -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 44 55
ARF6/GTP 0.059 0.038 -10000 0 -0.24 3 3
CDH1 -0.046 0.15 -10000 0 -0.28 122 122
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 0.17 21 -0.21 51 72
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 -0.2 35 35
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.029 0.077 0.17 21 -0.22 52 73
EFNA1 0.024 0.014 -10000 0 -10000 0 0
LPP -0.036 0.077 0.17 19 -0.21 61 80
Ephrin A1/EPHA2 0.013 0.079 -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 20 -0.21 58 78
HGF/MET -0.025 0.12 -10000 0 -0.25 97 97
HGF -0.009 0.091 -10000 0 -0.2 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.085 -10000 0 -0.23 62 62
actin cable formation -0.004 0.096 0.28 18 -0.26 11 29
KIAA1543 -0.032 0.076 0.16 15 -0.22 58 73
KIFC3 -0.016 0.079 0.18 16 -0.21 55 71
NCK1 0.025 0.02 -10000 0 -0.43 1 1
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.019 0.08 0.18 19 -0.21 56 75
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 0.079 0.18 20 -0.21 55 75
PIP5K1C -0.013 0.078 0.18 20 -0.21 53 73
LIMA1 0.019 0.056 -10000 0 -0.43 8 8
ABI1 0.023 0.008 -10000 0 -10000 0 0
ROCK1 -0.021 0.082 0.4 6 -10000 0 6
adherens junction assembly -0.01 0.089 0.27 10 -0.38 6 16
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 -0.047 0.14 -10000 0 -0.26 121 121
PLEKHA7 -0.019 0.085 0.18 16 -0.22 58 74
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 -0.28 3 30
cortical actin cytoskeleton stabilization -0.01 0.084 -10000 0 -0.23 62 62
regulation of cell-cell adhesion -0.028 0.075 0.17 21 -0.21 51 72
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.085 -10000 0 -0.23 62 62
HIF-1-alpha transcription factor network

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
PKM2 -0.078 0.3 -10000 0 -0.79 46 46
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.041 0.34 -10000 0 -0.75 56 56
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.065 0.31 -10000 0 -0.81 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 -0.069 0.32 -10000 0 -0.79 47 47
GATA2 0.014 0.066 -10000 0 -0.4 11 11
AKT1 -0.005 0.086 -10000 0 -0.22 21 21
response to hypoxia -0.021 0.075 -10000 0 -0.19 39 39
MCL1 -0.065 0.31 -10000 0 -0.81 44 44
NDRG1 -0.076 0.31 -10000 0 -0.82 45 45
SERPINE1 -0.092 0.32 -10000 0 -0.78 56 56
FECH -0.066 0.31 -10000 0 -0.8 44 44
FURIN -0.064 0.31 -10000 0 -0.8 44 44
NCOA2 -0.004 0.11 -10000 0 -0.43 34 34
EP300 -0.015 0.13 -10000 0 -0.32 55 55
HMOX1 -0.069 0.32 -10000 0 -0.81 46 46
BHLHE40 -0.07 0.32 -10000 0 -0.81 46 46
BHLHE41 -0.07 0.32 -10000 0 -0.84 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.056 0.1 -10000 0 -0.31 1 1
ENG 0.013 0.078 0.26 4 -0.29 1 5
JUN 0.018 0.024 -10000 0 -0.13 9 9
RORA -0.065 0.31 -10000 0 -0.8 45 45
ABCB1 -0.021 0.12 -10000 0 -0.69 10 10
TFRC -0.065 0.31 -10000 0 -0.81 44 44
CXCR4 -0.07 0.32 -10000 0 -0.83 46 46
TF -0.083 0.34 -10000 0 -0.82 53 53
CITED2 -0.065 0.31 -10000 0 -0.81 44 44
HIF1A/ARNT -0.034 0.39 -10000 0 -0.92 44 44
LDHA -0.012 0.14 -10000 0 -0.92 8 8
ETS1 -0.07 0.31 -10000 0 -0.81 43 43
PGK1 -0.065 0.31 -10000 0 -0.81 43 43
NOS2 -0.074 0.32 -10000 0 -0.82 48 48
ITGB2 -0.072 0.33 -10000 0 -0.85 45 45
ALDOA -0.064 0.31 -10000 0 -0.81 44 44
Cbp/p300/CITED2 -0.087 0.37 -10000 0 -0.85 60 60
FOS -0.032 0.14 -10000 0 -0.29 93 93
HK2 -0.072 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 51 51
HK1 -0.064 0.31 -10000 0 -0.81 44 44
NPM1 -0.064 0.31 -10000 0 -0.8 44 44
EGLN1 -0.065 0.31 -10000 0 -0.81 44 44
CREB1 0.03 0.008 -10000 0 -10000 0 0
PGM1 -0.067 0.31 -10000 0 -0.8 44 44
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.075 0.27 -10000 0 -0.72 56 56
IGFBP1 -0.099 0.33 -10000 0 -0.78 61 61
VEGFA -0.053 0.28 -10000 0 -0.66 53 53
HIF1A/JAB1 0.02 0.057 -10000 0 -0.36 1 1
CP -0.11 0.35 -10000 0 -0.84 57 57
CXCL12 -0.067 0.31 -10000 0 -0.8 46 46
COPS5 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.009 -10000 0 -10000 0 0
BNIP3 -0.066 0.31 -10000 0 -0.81 44 44
EGLN3 -0.069 0.32 -10000 0 -0.82 46 46
CA9 -0.08 0.32 -10000 0 -0.82 48 48
TERT -0.089 0.33 -10000 0 -0.82 51 51
ENO1 -0.065 0.31 -10000 0 -0.8 44 44
PFKL -0.064 0.31 -10000 0 -0.8 45 45
NCOA1 0.026 0.003 -10000 0 -10000 0 0
ADM -0.075 0.32 -10000 0 -0.8 50 50
ARNT 0.005 0.068 -10000 0 -0.27 1 1
HNF4A -0.004 0.055 -10000 0 -0.14 45 45
ADFP -0.078 0.3 -10000 0 -0.79 46 46
SLC2A1 -0.056 0.27 -10000 0 -0.64 53 53
LEP -0.067 0.29 -10000 0 -0.79 42 42
HIF1A/ARNT/Cbp/p300 -0.051 0.34 -10000 0 -0.77 57 57
EPO -0.047 0.24 -10000 0 -0.71 25 25
CREBBP -0.013 0.12 -10000 0 -0.31 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.038 0.34 -10000 0 -0.76 54 54
PFKFB3 -0.07 0.31 -10000 0 -0.83 42 42
NT5E -0.067 0.32 -10000 0 -0.8 46 46
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.01 0.13 -10000 0 -0.34 51 51
alphaM/beta2 Integrin/GPIbA -0.011 0.12 -10000 0 -0.33 54 54
alphaM/beta2 Integrin/proMMP-9 -0.035 0.14 -10000 0 -0.31 87 87
PLAUR 0.011 0.042 -10000 0 -0.14 31 31
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 0.091 -10000 0 -0.44 19 19
RAP1A 0.021 0.01 -10000 0 -10000 0 0
SELPLG -0.001 0.1 -10000 0 -0.43 29 29
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.16 -10000 0 -0.28 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
CYR61 -0.015 0.1 -10000 0 -0.24 71 71
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 0.042 -10000 0 -10000 0 0
MYH2 -0.039 0.11 -10000 0 -0.4 23 23
MST1R 0.02 0.049 -10000 0 -0.39 7 7
leukocyte activation during inflammatory response -0.021 0.13 -10000 0 -0.3 71 71
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 -0.43 10 10
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 -0.016 0.13 -10000 0 -0.33 59 59
alphaM/beta2 Integrin -0.045 0.13 -10000 0 -0.38 38 38
JAM3 homodimer 0.024 0.007 -10000 0 -10000 0 0
ICAM2 0.025 0.005 -10000 0 -10000 0 0
ICAM1 0.011 0.062 -10000 0 -0.43 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.044 0.13 -10000 0 -0.39 36 36
cell adhesion -0.011 0.12 -10000 0 -0.33 54 54
NFKB1 -0.1 0.19 -10000 0 -0.43 102 102
THY1 0.015 0.061 -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 0.007 0.12 -10000 0 -0.34 39 39
IL6 -0.12 0.23 -10000 0 -0.66 58 58
ITGB2 -0.014 0.097 -10000 0 -0.38 26 26
elevation of cytosolic calcium ion concentration -0.008 0.12 -10000 0 -0.29 61 61
alphaM/beta2 Integrin/JAM2/JAM3 0.012 0.11 -10000 0 -0.33 37 37
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.002 0.13 -10000 0 -0.28 73 73
alphaM/beta2 Integrin/uPA/Plg -0.012 0.12 -10000 0 -0.31 57 57
RhoA/GTP -0.037 0.12 -10000 0 -0.36 33 33
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 -0.006 0.12 -10000 0 -0.29 61 61
alphaM/beta2 Integrin/uPAR -0.011 0.12 -10000 0 -0.32 49 49
PLAU -0.001 0.081 -10000 0 -0.19 64 64
PLAT 0.005 0.058 -10000 0 -0.43 2 2
actin filament polymerization -0.036 0.11 0.19 2 -0.39 23 25
MST1 0.001 0.099 -10000 0 -0.36 32 32
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.14 -10000 0 -0.3 72 72
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 58 58
fibrinolysis -0.013 0.12 -10000 0 -0.3 57 57
HCK 0.014 0.063 -10000 0 -0.27 19 19
dendritic cell antigen processing and presentation -0.044 0.13 -10000 0 -0.39 36 36
VTN 0.012 0.075 -10000 0 -0.35 19 19
alphaM/beta2 Integrin/CYR61 -0.03 0.13 -10000 0 -0.32 71 71
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 0.02 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.007 0.12 -10000 0 -0.33 51 51
MPO -0.05 0.15 -10000 0 -0.29 121 121
KNG1 -0.009 0.032 -10000 0 -10000 0 0
RAP1/GDP 0.028 0.015 -10000 0 -10000 0 0
ROCK1 -0.034 0.12 0.17 1 -0.4 23 24
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.01 0.019 -10000 0 -0.13 4 4
CTGF 0.004 0.086 -10000 0 -0.26 38 38
alphaM/beta2 Integrin/Hck -0.009 0.14 -10000 0 -0.37 47 47
ITGAM -0.02 0.12 -10000 0 -0.41 36 36
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.005 0.15 -10000 0 -0.4 50 50
HP -0.034 0.13 -10000 0 -0.24 113 113
leukocyte adhesion -0.031 0.14 -10000 0 -0.4 42 42
SELP 0.003 0.042 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.022 0.1 -10000 0 -0.3 52 52
CRKL 0.011 0.14 0.27 15 -0.46 20 35
mol:PIP3 0.001 0.039 -10000 0 -0.84 1 1
AKT1 -0.003 0.043 0.28 1 -0.73 1 2
PTK2B 0.018 0.032 -10000 0 -10000 0 0
RAPGEF1 0.014 0.14 0.29 14 -0.44 20 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 -0.004 0.11 -10000 0 -0.24 81 81
MAP3K5 -0.008 0.16 0.26 16 -0.47 29 45
HGF/MET/CIN85/CBL/ENDOPHILINS 0.007 0.11 -10000 0 -0.26 55 55
AP1 -0.01 0.1 0.15 4 -0.24 56 60
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) -0.006 0.09 0.22 4 -0.23 51 55
GAB1/CRKL/SHP2/PI3K 0.038 0.14 0.29 5 -0.42 20 25
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
CBL/CRK 0.02 0.14 0.29 9 -0.44 20 29
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 0.32 115 -0.35 1 116
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.066 -10000 0 -0.3 12 12
PAK1 -0.004 0.059 -10000 0 -0.7 1 1
HGF/MET/RANBP10 -0.004 0.11 -10000 0 -0.24 83 83
HRAS -0.047 0.2 -10000 0 -0.6 53 53
DOCK1 0.008 0.14 0.26 19 -0.44 20 39
GAB1 0 0.14 0.24 6 -0.49 19 25
CRK 0.01 0.14 0.28 16 -0.46 20 36
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.045 0.19 -10000 0 -0.53 63 63
JUN 0.019 0.023 -10000 0 -0.13 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.082 -10000 0 -0.24 60 60
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.019 0.14 0.31 31 -0.45 11 42
GRB2/SHC 0.005 0.088 0.19 8 -0.22 57 65
FOS -0.031 0.14 -10000 0 -0.28 93 93
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.037 0.16 0.32 115 -0.34 1 116
HGF/MET/MUC20 -0.032 0.1 -10000 0 -0.24 83 83
cell migration 0.005 0.087 0.19 8 -0.21 57 65
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.022 0.1 -10000 0 -0.3 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.084 -10000 0 -0.24 53 53
MET/MUC20 -0.031 0.097 -10000 0 -0.3 52 52
RAP1B 0.015 0.14 0.29 17 -0.41 20 37
RAP1A 0.013 0.13 0.29 16 -0.4 20 36
HGF/MET/RANBP9 -0.004 0.11 -10000 0 -0.24 83 83
RAF1 -0.024 0.2 0.35 2 -0.56 53 55
STAT3 -0.006 0.09 0.22 4 -0.24 51 55
cell proliferation 0.001 0.15 0.29 15 -0.36 56 71
RPS6KB1 -0.005 0.043 -10000 0 -0.21 7 7
MAPK3 0.025 0.15 0.5 8 -10000 0 8
MAPK1 0.031 0.16 0.61 11 -10000 0 11
RANBP9 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.01 0.15 0.3 6 -0.46 26 32
SRC -0.018 0.078 0.16 1 -0.23 53 54
PI3K 0.005 0.09 0.19 9 -0.22 58 67
MET/Glomulin -0.038 0.092 -10000 0 -0.28 52 52
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 -0.022 0.19 0.33 4 -0.52 53 57
MET -0.047 0.14 -10000 0 -0.26 121 121
MAP4K1 -0.006 0.17 0.27 20 -0.48 29 49
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.015 0.2 0.33 17 -0.52 53 70
BAD 0 0.051 -10000 0 -0.7 1 1
MAP2K4 -0.006 0.15 0.29 12 -0.43 28 40
SHP2/GRB2/SOS1/GAB1 -0.006 0.13 -10000 0 -0.35 55 55
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 -0.025 0.074 0.17 2 -0.22 57 59
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.009 0.091 -10000 0 -0.2 69 69
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 0.005 0.094 0.19 10 -0.22 62 72
PDPK1 -0.002 0.045 0.32 1 -0.78 1 2
HGF/MET/SHIP -0.007 0.11 -10000 0 -0.24 88 88
p75(NTR)-mediated 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
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 0.015 0.11 -10000 0 -0.24 73 73
NGF (dimer)/p75(NTR)/BEX1 -0.018 0.13 -10000 0 -0.28 91 91
NT-4/5 (dimer)/p75(NTR) -0.005 0.089 -10000 0 -0.29 40 40
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.092 0.18 9 -0.24 71 80
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.43 14 14
MGDIs/NGR/p75(NTR)/LINGO1 -0.002 0.13 -10000 0 -0.3 78 78
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.01 0.098 -10000 0 -0.26 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 -0.43 14 14
NTRK1 0.016 0.055 -10000 0 -0.22 20 20
RTN4R -0.006 0.11 -10000 0 -0.34 44 44
neuron apoptosis -0.066 0.16 0.29 8 -0.45 38 46
IRAK1 0.026 0.003 -10000 0 -10000 0 0
SHC1 -0.038 0.1 0.19 1 -0.27 76 77
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 0.001 0.12 -10000 0 -0.25 81 81
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 98 98
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.23 23 23
proNGF (dimer) -0.025 0.13 -10000 0 -0.35 63 63
MAGED1 0.026 0.002 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.43 1 1
ZNF274 0.021 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.017 0.094 -10000 0 -0.24 69 69
NGF -0.025 0.13 -10000 0 -0.35 63 63
cell cycle arrest -0.037 0.089 0.26 10 -0.21 71 81
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.099 -10000 0 -0.25 71 71
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.012 0.081 -10000 0 -0.24 40 40
NCSTN 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.017 0.12 -10000 0 -0.27 76 76
PSENEN 0.022 0.01 -10000 0 -10000 0 0
mol:ceramide -0.032 0.097 0.18 7 -0.25 73 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.021 0.094 -10000 0 -0.31 23 23
p75(NTR)/beta APP 0.005 0.09 -10000 0 -0.3 35 35
BEX1 0.01 0.084 -10000 0 -0.43 18 18
mol:GDP -0.044 0.1 -10000 0 -0.27 76 76
NGF (dimer) -0.025 0.13 -10000 0 -0.25 119 119
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.12 -10000 0 -0.27 76 76
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.006 0.094 -10000 0 -0.23 67 67
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 -0.007 0.12 -10000 0 -0.27 76 76
RHOB 0.025 0.012 -10000 0 -0.13 3 3
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 -10000 0 0
TP53 -0.021 0.1 0.22 32 -0.24 49 81
PRDM4 -0.032 0.099 0.18 7 -0.25 74 81
BDNF (dimer) -0.017 0.12 -10000 0 -0.25 97 97
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 73 73
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.005 0.11 -10000 0 -0.25 77 77
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 -0.31 43 68
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.032 0.098 0.18 7 -0.25 73 80
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 77 77
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) -0.002 0.091 -10000 0 -0.3 38 38
MAPK8 -0.026 0.13 0.31 14 -0.31 45 59
MAPK9 -0.015 0.13 0.3 26 -0.32 40 66
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.032 -10000 0 -10000 0 0
NTF4 -0.003 0.033 -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 -0.22 72 72
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.045 -10000 0 -0.24 6 6
RhoA-B-C/GTP -0.017 0.12 -10000 0 -0.27 76 76
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.095 -10000 0 -0.24 46 46
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.097 -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 0.14 7 -0.27 77 84
BAD -0.018 0.14 0.29 28 -0.32 41 69
RIPK2 0.024 0.007 -10000 0 -10000 0 0
NGFR -0.017 0.12 -10000 0 -0.28 72 72
CYCS -0.026 0.09 0.22 8 -0.24 61 69
ADAM17 0.022 0.045 -10000 0 -0.43 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.005 0.11 -10000 0 -0.25 69 69
BCL2L11 -0.021 0.13 0.28 25 -0.32 41 66
BDNF (dimer)/p75(NTR) -0.02 0.11 -10000 0 -0.3 53 53
PI3K 0.007 0.11 -10000 0 -0.25 72 72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.006 0.11 -10000 0 -0.25 77 77
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 77 77
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.006 0.11 -10000 0 -0.25 73 73
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 -0.43 14 14
PLG -0.01 0.019 -10000 0 -0.13 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.044 0.11 0.19 4 -0.28 81 85
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 0.27 27 -0.31 41 68
E2F1 0.014 0.056 -10000 0 -0.43 6 6
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 -0.012 0.1 -10000 0 -0.3 53 53
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.11 -10000 0 -0.24 71 71
MMP3 -0.005 0.047 -10000 0 -0.14 42 42
APAF-1/Caspase 9 -0.029 0.082 -10000 0 -0.3 15 15
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 -0.058 0.18 0.3 5 -0.41 83 88
IKBKB 0.016 0.09 0.25 16 -0.31 3 19
AKT1 -0.022 0.1 0.27 23 -0.22 33 56
IKBKG 0.004 0.093 0.24 14 -0.26 15 29
CALM1 -0.04 0.14 0.24 2 -0.38 55 57
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.033 0.18 0.31 14 -0.48 50 64
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.15 0.22 3 -0.4 58 61
DOK1 0.025 0.021 -10000 0 -0.28 2 2
AP-1 -0.044 0.12 0.24 3 -0.27 74 77
LYN 0.021 0.035 -10000 0 -0.19 10 10
BLNK -0.021 0.13 -10000 0 -0.43 49 49
SHC1 0.024 0.014 -10000 0 -0.13 4 4
BCR complex -0.006 0.096 -10000 0 -0.27 51 51
CD22 -0.065 0.15 -10000 0 -0.43 51 51
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 -0.28 6 6
SHC/GRB2/SOS1 -0.027 0.11 -10000 0 -0.25 68 68
GO:0007205 -0.042 0.16 0.23 2 -0.4 58 60
SYK 0.009 0.083 -10000 0 -0.43 17 17
ELK1 -0.039 0.15 0.22 2 -0.43 44 46
NFATC1 -0.043 0.14 0.27 6 -0.43 46 52
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 0.046 0.13 21 -0.13 13 34
HRAS -0.031 0.14 0.26 6 -0.43 33 39
NFKBIA 0.016 0.047 0.13 21 -0.13 12 33
NF-kappa-B/RelA/I kappa B beta 0.022 0.041 0.13 20 -10000 0 20
RasGAP/Csk -0.002 0.12 -10000 0 -0.24 96 96
mol:GDP -0.037 0.15 0.22 3 -0.43 46 49
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.005 0.099 -10000 0 -0.43 23 23
NF-kappa-B/RelA/I kappa B alpha 0.022 0.041 0.13 20 -10000 0 20
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.059 0.18 0.37 3 -0.51 51 54
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.044 0.16 0.22 3 -0.41 58 61
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 12 -0.28 24 36
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 -0.068 0.15 0.22 2 -0.45 52 54
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 -10000 0 -0.5 41 41
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 -0.34 13 13
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 0.29 14 -0.41 49 63
SH3BP5 0.024 0.029 -10000 0 -0.43 2 2
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 -0.23 98 98
CD79A -0.001 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 -0.4 21 25
MAPK1 -0.023 0.11 0.27 3 -0.41 19 22
CD72/SHP1 -0.056 0.16 0.27 12 -0.43 51 63
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.031 0.16 0.28 16 -0.41 51 67
actin cytoskeleton organization -0.027 0.15 0.31 16 -0.43 38 54
NF-kappa-B/RelA 0.044 0.079 0.24 21 -0.21 7 28
Calcineurin -0.012 0.13 0.22 1 -0.42 31 32
PI3K -0.067 0.13 -10000 0 -0.4 47 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.17 -10000 0 -0.44 57 57
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.068 0.27 -10000 0 -0.79 56 56
DAPP1 -0.095 0.31 -10000 0 -0.91 56 56
cytokine secretion -0.04 0.14 0.26 6 -0.4 46 52
mol:DAG -0.044 0.16 0.22 3 -0.41 58 61
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
MAP2K1 -0.026 0.12 0.28 3 -0.4 27 30
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.13 -10000 0 -0.27 96 96
mol:PI-3-4-5-P3 -0.056 0.094 0.18 1 -0.29 43 44
ETS1 -0.026 0.13 0.26 9 -0.43 29 38
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 0.29 12 -0.46 37 49
B-cell antigen/BCR complex/LYN/SYK -0.049 0.17 0.27 1 -0.45 54 55
CARD11 -0.022 0.18 0.25 23 -0.48 40 63
FCGR2B -0.05 0.15 -10000 0 -0.43 59 59
PPP3CA 0.025 0.011 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
IKK complex 0.01 0.051 0.15 23 -0.12 5 28
PTPRC -0.003 0.1 -10000 0 -0.43 24 24
PDPK1 -0.035 0.079 0.19 14 -0.21 36 50
PPP3CB 0.024 0.013 -10000 0 -10000 0 0
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 -0.016 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 0.006 0.083 -10000 0 -0.43 16 16
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 47 47
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.087 -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 -0.034 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 0.088 -10000 0 -0.3 34 34
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.042 0.2 -9999 0 -0.43 89 89
MAP3K8 0.015 0.047 -9999 0 -0.43 4 4
FOS -0.041 0.18 -9999 0 -0.44 71 71
PRKCA 0.02 0.024 -9999 0 -0.43 1 1
PTPN7 -0.054 0.15 -9999 0 -0.29 122 122
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 -0.005 0.083 -9999 0 -0.39 21 21
mol:GTP 0 0.001 -9999 0 -0.004 59 59
MAPK1 -0.035 0.17 -9999 0 -0.43 69 69
RAF1 -0.001 0.086 -9999 0 -0.41 19 19
KRAS 0.025 0.005 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.026 0.11 -10000 0 -0.43 16 16
ACTA1 -0.054 0.13 0.22 2 -0.33 69 71
NUMA1 -0.027 0.11 -10000 0 -0.42 17 17
SPTAN1 -0.049 0.13 0.21 6 -0.33 66 72
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 0.097 0.16 1 -0.27 73 74
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 -0.42 18 18
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.048 0.13 0.21 6 -0.33 66 72
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 0.22 4 -0.33 70 74
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.13 0.29 -10000 0 -0.59 135 135
BID -0.024 0.065 0.11 1 -0.18 70 71
MAP3K1 -0.011 0.065 -10000 0 -0.49 4 4
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 6 -0.33 68 74
CASP9 0.022 0.012 -10000 0 -0.13 1 1
DNA repair 0.011 0.056 0.23 9 -0.15 14 23
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 -0.037 0.13 0.22 1 -0.47 17 18
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.013 0.16 -10000 0 -0.92 12 12
TRAF2 0.025 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.13 0.34 6 -0.31 70 76
CASP7 -0.009 0.096 0.24 21 -0.3 17 38
KRT18 -0.067 0.21 -10000 0 -0.57 73 73
apoptosis -0.051 0.14 0.29 2 -0.44 33 35
DFFA -0.049 0.13 0.2 2 -0.32 70 72
DFFB -0.049 0.13 0.2 2 -0.32 70 72
PARP1 -0.011 0.056 0.15 13 -0.23 9 22
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 -0.052 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 -0.33 13 99
JNK cascade 0.011 0.065 0.49 4 -10000 0 4
CASP3 -0.055 0.13 0.2 1 -0.34 70 71
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 -0.16 26 26
Mammalian IAPs/DIABLO 0.05 0.064 -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 -0.34 10 10
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 -0.44 35 36
LMNA 0.027 0.11 0.23 10 -0.44 8 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.094 -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 -0.41 17 17
CFL2 -0.026 0.14 0.26 9 -0.31 62 71
GAS2 -0.054 0.13 -10000 0 -0.32 75 75
positive regulation of apoptosis 0.028 0.12 0.23 15 -0.39 15 30
PRF1 -0.014 0.12 -10000 0 -0.43 33 33
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 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 -0.01 0.083 -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 30 -0.29 18 48
T-DHT/AR -0.033 0.11 -10000 0 -0.29 75 75
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 -0.043 0.16 0.29 7 -0.42 53 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FOS -0.075 0.26 0.27 1 -0.78 56 57
mol:Ca2+ -0.007 0.019 -10000 0 -0.054 50 50
MAPK3 -0.036 0.13 0.27 8 -0.32 52 60
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 0.034 0.007 -10000 0 -10000 0 0
apoptosis 0.033 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 -0.036 0.13 -10000 0 -0.36 71 71
CREB1 -0.037 0.16 0.25 6 -0.46 54 60
RAC1-CDC42/GTP 0.036 0.024 -10000 0 -10000 0 0
AR -0.048 0.16 -10000 0 -0.34 104 104
GNB1 0.022 0.01 -10000 0 -10000 0 0
RAF1 -0.02 0.098 0.18 28 -0.22 70 98
RAC1-CDC42/GDP -0.021 0.13 -10000 0 -0.34 67 67
T-DHT/AR/PELP1/Src 0.006 0.099 -10000 0 -0.24 71 71
MAP2K2 -0.036 0.092 0.18 26 -0.22 67 93
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 0.06 -10000 0 -0.43 9 9
Gi family/GNB1/GNG2/GDP -0.03 0.12 -10000 0 -0.35 37 37
mol:T-DHT 0 0.001 -10000 0 -0.002 35 35
RAC1 0.023 0.009 -10000 0 -10000 0 0
GNRH1 0.002 0.035 -10000 0 -0.3 6 6
Gi family/GTP -0.021 0.068 -10000 0 -0.2 37 37
CDC42 0.022 0.01 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.006 0.085 -10000 0 -0.21 51 51
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.092 0.3 5 -0.31 4 9
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.095 -10000 0 -0.3 39 39
AP1 -0.023 0.12 -10000 0 -0.39 19 19
ILK -0.015 0.08 -10000 0 -0.22 47 47
bone resorption -0.032 0.13 0.32 2 -0.36 40 42
PTK2B 0.018 0.032 -10000 0 -10000 0 0
PYK2/p130Cas 0.02 0.11 -10000 0 -0.25 55 55
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 52 52
MAP3K1 -0.018 0.083 0.19 6 -0.22 51 57
JUN 0.019 0.023 -10000 0 -0.13 9 9
MAPK3 -0.026 0.081 0.19 4 -0.21 62 66
MAPK1 -0.026 0.079 0.19 3 -0.21 61 64
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 -0.19 64 64
NFKBIA -0.025 0.08 0.19 2 -0.27 15 17
FOS -0.031 0.14 -10000 0 -0.28 93 93
CD44 -0.015 0.12 -10000 0 -0.31 62 62
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 0.004 0.098 -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 -0.025 0.1 0.19 7 -0.27 55 62
VAV3 -0.05 0.098 0.19 4 -0.25 64 68
MAP3K14 -0.019 0.084 0.19 4 -0.22 52 56
ROCK2 0.008 0.088 -10000 0 -0.43 20 20
SPP1 -0.023 0.12 -10000 0 -0.26 87 87
RAC1 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.092 0.18 3 -0.23 60 63
MMP2 -0.046 0.11 -10000 0 -0.4 23 23
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 0.013 0.089 -10000 0 -0.22 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.11 0.24 16 -0.33 25 41
AP1 -0.03 0.1 -10000 0 -0.23 89 89
mol:PIP3 -0.036 0.088 -10000 0 -0.24 58 58
AKT1 0 0.1 0.27 17 -0.34 5 22
PTK2B -0.005 0.09 0.17 12 -0.24 39 51
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 0.071 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 -0.021 0.087 -10000 0 -0.27 52 52
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.088 0.21 8 -0.27 17 25
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.35 30 30
endothelial cell migration -0.022 0.11 -10000 0 -0.3 57 57
ADCY4 -0.015 0.12 -10000 0 -0.35 52 52
ADCY5 -0.015 0.12 -10000 0 -0.34 52 52
ADCY6 -0.013 0.12 -10000 0 -0.34 52 52
ADCY7 -0.014 0.12 -10000 0 -0.34 52 52
ADCY1 -0.032 0.12 -10000 0 -0.36 50 50
ADCY2 -0.018 0.12 -10000 0 -0.35 54 54
ADCY3 -0.013 0.12 -10000 0 -0.34 52 52
ADCY8 -0.035 0.14 -10000 0 -0.39 59 59
ADCY9 -0.014 0.12 -10000 0 -0.34 52 52
GSK3B -0.006 0.087 0.18 6 -0.27 19 25
arachidonic acid secretion -0.02 0.12 -10000 0 -0.34 52 52
GNG2 0.022 0.04 -10000 0 -0.43 4 4
TRIP6 0.012 0.031 -10000 0 -0.21 7 7
GNAO1 -0.018 0.089 -10000 0 -0.25 61 61
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA -0.019 0.12 0.24 17 -0.34 34 51
GAB1 0.025 0.02 -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 0.023 -10000 0 -0.13 9 9
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 -0.008 0.066 0.2 14 -0.29 10 24
PLCB3 0.017 0.048 0.18 24 -0.23 7 31
FOS -0.031 0.14 -10000 0 -0.28 93 93
positive regulation of mitosis -0.02 0.12 -10000 0 -0.34 52 52
LPA/LPA1-2-3 0.007 0.094 -10000 0 -0.23 63 63
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 0.002 0.097 0.28 1 -0.36 7 8
GNAZ -0.014 0.084 -10000 0 -0.25 54 54
EGFR/PI3K-beta/Gab1 -0.03 0.095 -10000 0 -0.25 53 53
positive regulation of dendritic cell cytokine production 0.006 0.093 -10000 0 -0.23 63 63
LPA/LPA2/MAGI-3 0.021 0.042 -10000 0 -0.25 8 8
ARHGEF1 0.015 0.097 0.2 60 -0.2 48 108
GNAI2 -0.015 0.085 -10000 0 -0.25 55 55
GNAI3 -0.003 0.062 -10000 0 -0.26 26 26
GNAI1 -0.015 0.083 -10000 0 -0.25 53 53
LPA/LPA3 0.002 0.036 -10000 0 -0.18 8 8
LPA/LPA2 0.013 0.042 -10000 0 -0.19 16 16
LPA/LPA1 -0.017 0.1 -10000 0 -0.3 57 57
HB-EGF/EGFR -0.035 0.11 -10000 0 -0.26 84 84
HBEGF -0.033 0.09 -10000 0 -0.29 48 48
mol:DAG -0.008 0.066 0.2 14 -0.29 10 24
cAMP biosynthetic process -0.016 0.14 0.3 10 -0.35 52 62
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 22 -0.36 31 53
GNAQ 0.002 0.037 -10000 0 -0.25 7 7
LPAR2 0.018 0.054 -10000 0 -0.34 10 10
LPAR3 -0.009 0.044 -10000 0 -10000 0 0
LPAR1 -0.025 0.14 -10000 0 -0.39 57 57
IL8 -0.1 0.21 0.32 12 -0.44 114 126
PTK2 -0.014 0.09 0.19 25 -0.22 60 85
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.021 0.087 -10000 0 -0.27 52 52
EGFR -0.017 0.12 -10000 0 -0.4 46 46
PLCG1 -0.013 0.059 0.15 6 -0.22 23 29
PLD2 -0.013 0.094 0.19 28 -0.22 63 91
G12/G13 0.018 0.084 -10000 0 -0.23 48 48
PI3K-beta -0.022 0.085 -10000 0 -0.28 25 25
cell migration 0.009 0.052 0.24 1 -0.24 5 6
SLC9A3R2 0.025 0.01 -10000 0 -10000 0 0
PXN 0.002 0.098 0.28 1 -0.37 7 8
HRAS/GTP -0.02 0.12 -10000 0 -0.34 52 52
RAC1 0.023 0.009 -10000 0 -10000 0 0
MMP9 -0.042 0.13 -10000 0 -0.23 133 133
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
PRKCD -0.008 0.097 0.22 30 -0.29 27 57
Gi(beta/gamma) -0.019 0.13 -10000 0 -0.38 51 51
mol:LPA -0.001 0.022 -10000 0 -0.16 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.094 0.33 1 -0.35 9 10
MAPKKK cascade -0.02 0.12 -10000 0 -0.34 52 52
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 -10000 0 -0.26 23 23
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 0.21 8 -0.28 17 25
GNA11 -0.002 0.049 -10000 0 -0.25 15 15
Rac1/GTP 0.03 0.11 -10000 0 -0.9 7 7
MMP2 -0.023 0.11 -10000 0 -0.3 57 57
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
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 -0.039 0.15 -10000 0 -0.36 80 80
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
PLA2G7 -0.004 0.11 -10000 0 -0.31 46 46
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 0.1 -10000 0 -0.42 30 30
LIS1/Poliovirus Protein 3A 0.01 0.002 -10000 0 -10000 0 0
CDK5R2 -0.05 0.16 -10000 0 -0.36 102 102
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.035 0.13 -10000 0 -0.27 109 109
YWHAE 0.026 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.014 0.18 0.32 81 -0.41 32 113
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 -0.23 66 74
RELN -0.046 0.14 -10000 0 -0.29 107 107
PAFAH/LIS1 0.011 0.064 0.17 1 -0.26 25 26
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 -0.34 32 32
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.072 0.16 -10000 0 -0.3 135 135
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.037 0.14 0.28 20 -0.32 63 83
LIS1/IQGAP1 0.025 0.029 0.17 2 -0.26 4 6
RHOA 0.012 0.016 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.01 -10000 0 -10000 0 0
PAFAH1B2 0.012 0.074 -10000 0 -0.43 14 14
MAP1B/LIS1/Dynein heavy chain 0.025 0.019 -10000 0 -0.17 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.019 0.18 0.32 78 -0.4 32 110
LRP8 0.02 0.03 -10000 0 -0.43 2 2
NDEL1/Katanin 60 0.013 0.18 0.32 81 -0.41 32 113
P39/CDK5 -0.037 0.11 0.21 11 -0.24 91 102
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 54 63
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 -0.24 100 100
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 66 66
CDC42 0.008 0.042 -10000 0 -0.46 4 4
PDGFR-alpha signaling pathway

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
PDGFRA -0.028 0.14 -10000 0 -0.43 52 52
PDGF/PDGFRA/CRKL -0.003 0.099 -10000 0 -0.3 50 50
positive regulation of JUN kinase activity 0.03 0.084 -10000 0 -0.23 46 46
CRKL 0.025 0.008 -10000 0 -10000 0 0
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 44 44
PLCG1 -0.024 0.092 -10000 0 -0.31 44 44
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 44 44
CAV3 0.002 0.031 -10000 0 -0.13 14 14
CAV1 0.006 0.051 -10000 0 -0.15 44 44
SHC/Grb2/SOS1 0.032 0.085 -10000 0 -0.23 46 46
PDGF/PDGFRA/Shf -0.005 0.11 -10000 0 -0.31 53 53
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 -0.3 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 44 44
PDGF/PDGFRA -0.028 0.14 -10000 0 -0.43 52 52
actin cytoskeleton reorganization -0.003 0.099 -10000 0 -0.3 50 50
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
PI3K 0.019 0.088 -10000 0 -0.25 48 48
PDGF/PDGFRA/Crk/C3G 0.017 0.09 -10000 0 -0.25 51 51
JAK1 -0.021 0.088 -10000 0 -0.3 46 46
ELK1/SRF -0.011 0.081 0.15 28 -0.25 41 69
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 -0.028 0.1 0.23 6 -0.34 43 49
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.03 0.084 -10000 0 -0.23 46 46
PDGF/PDGFRA/SHB -0.003 0.099 -10000 0 -0.3 50 50
PDGF/PDGFRA/Caveolin-1 -0.005 0.085 -10000 0 -0.31 31 31
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.034 0.087 0.2 5 -0.3 43 48
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PDGF/PDGFRA/Crk -0.003 0.1 -10000 0 -0.3 51 51
JAK-STAT cascade -0.021 0.088 -10000 0 -0.3 46 46
cell proliferation -0.005 0.11 -10000 0 -0.31 53 53
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.009 0.057 -10000 0 -0.25 22 22
NFATC2 -0.022 0.074 -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 -0.37 53 56
PTGS2 -0.094 0.18 0.36 1 -0.45 78 79
JUNB 0.007 0.071 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.018 -10000 0 -0.088 1 1
CaM/Ca2+ 0.011 0.018 -10000 0 -0.088 1 1
CALM1 0.021 0.016 -10000 0 -0.14 1 1
JUN 0.015 0.025 -10000 0 -0.14 9 9
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 97 97
CREM 0.023 0.022 -10000 0 -0.28 2 2
Jun/NFAT1-c-4/p21SNFT -0.029 0.12 -10000 0 -0.35 34 34
FOS -0.036 0.14 -10000 0 -0.29 93 93
IFNG -0.072 0.14 0.28 2 -0.38 49 51
AP-1/NFAT1-c-4 -0.057 0.17 -10000 0 -0.42 52 52
FASLG -0.073 0.14 0.36 1 -0.37 51 52
NFAT1-c-4/ICER1 -0.024 0.097 -10000 0 -0.25 55 55
IL2RA -0.074 0.15 0.31 3 -0.38 58 61
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.072 0.14 0.33 2 -0.37 50 52
JunB/Fra1/NFAT1-c-4 -0.039 0.13 0.19 2 -0.27 90 92
IL4 -0.071 0.14 0.33 2 -0.37 50 52
IL2 -0.011 0.14 -10000 0 -0.93 12 12
IL3 0.009 0.069 -10000 0 -0.66 5 5
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
BATF3 0.001 0.091 -10000 0 -0.26 45 45
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.077 -10000 0 -0.22 50 50
RGS9BP 0.017 0.05 -10000 0 -0.39 7 7
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 -0.27 40 40
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 0.032 -10000 0 -0.13 16 16
Cone Metarhodopsin II/X-Arrestin 0.013 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 0.18 18 -0.26 94 112
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) -0.025 0.12 -10000 0 -0.24 109 109
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 0.082 -10000 0 -0.23 50 50
SLC24A2 -0.042 0.15 -10000 0 -0.3 103 103
GNB3/GNGT2 -0.001 0.1 -10000 0 -0.31 51 51
GNB3 -0.007 0.12 -10000 0 -0.4 38 38
GNAT2/GTP 0.014 0.01 -10000 0 -10000 0 0
CNGA3 -0.049 0.14 -10000 0 -0.24 143 143
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 0.017 0.088 -10000 0 -0.27 40 40
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 + -0.042 0.15 -10000 0 -0.3 103 103
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
PDE6C 0.004 0.025 -10000 0 -0.13 5 5
GNGT2 0.008 0.082 -10000 0 -0.3 28 28
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.005 0.036 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
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 -0.023 0.098 -10000 0 -0.32 34 34
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 -0.056 0.14 -10000 0 -0.31 101 101
IL1A -0.033 0.14 -10000 0 -0.28 97 97
IL1B -0.057 0.12 -10000 0 -0.32 76 76
IRAK/TRAF6/p62/Atypical PKCs 0.045 0.052 -10000 0 -0.2 15 15
IL1R2 -0.045 0.14 -10000 0 -0.25 127 127
IL1R1 0.006 0.077 -10000 0 -0.43 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.093 -10000 0 -0.34 23 23
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.016 0.064 -10000 0 -0.38 12 12
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 0.036 0.16 6 -0.22 10 16
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.12 -10000 0 -0.25 82 82
IL1 alpha/IL1R1/IL1RAP/MYD88 0.02 0.12 -10000 0 -0.26 66 66
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.029 0.12 -10000 0 -0.24 66 66
IL1 beta fragment/IL1R1/IL1RAP -0.044 0.12 0.17 1 -0.26 90 91
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.009 0.042 0.17 10 -0.21 13 23
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -10000 0 -0.28 69 69
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 -0.044 0.12 0.17 1 -0.26 90 91
IL1 beta/IL1R2 -0.073 0.14 -10000 0 -0.3 113 113
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.015 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.24 78 78
IRAK3 0.022 0.041 -10000 0 -0.33 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.023 0.13 -10000 0 -0.26 89 89
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.099 -10000 0 -0.25 65 65
IL1 alpha/IL1R1/IL1RAP 0.009 0.11 -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 0.067 -10000 0 -0.18 47 47
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.04 0.1 -10000 0 -0.23 84 84
CASP1 0.01 0.071 -10000 0 -0.25 27 27
IL1RN/IL1R2 -0.056 0.14 -10000 0 -0.29 114 114
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.028 0.13 -10000 0 -0.26 93 93
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 -0.43 44 44
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 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
TGFB1 0.008 0.17 0.36 10 -1.1 9 19
VDR -0.014 0.11 -10000 0 -0.26 71 71
FAM120B 0.025 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.32 96 96
RXRs/LXRs/DNA/Oxysterols -0.073 0.21 -10000 0 -0.47 97 97
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 58 58
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RARs/VDR/DNA/Vit D3 0.042 0.071 -10000 0 -0.22 32 32
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.014 0.11 -10000 0 -0.26 71 71
RARs/RARs/DNA/9cRA 0.035 0.032 -10000 0 -0.22 3 3
RARG 0.025 0.008 -10000 0 -0.13 1 1
RPS6KB1 0.028 0.12 0.58 17 -0.43 9 26
RARs/THRs/DNA/SMRT 0.022 0.041 -10000 0 -0.22 14 14
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 -0.009 0.08 -10000 0 -0.29 33 33
RXRs/PPAR/9cRA/PGJ2/DNA -0.004 0.11 -10000 0 -0.24 60 60
NR1H4 -0.042 0.13 -10000 0 -0.24 128 128
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.26 48 48
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 -0.003 0.12 -10000 0 -0.24 77 77
NR4A1 0.012 0.062 -10000 0 -0.2 31 31
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 -0.4 63 63
RXR alpha/CCPG 0.027 0.028 -10000 0 -10000 0 0
RXRA 0.015 0.029 -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 -0.15 0.37 -10000 0 -0.99 76 76
mol:Oxysterols -0.006 0.019 -10000 0 -10000 0 0
cholesterol transport -0.072 0.21 -10000 0 -0.46 97 97
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 -0.085 0.24 -10000 0 -0.71 46 46
RXRs/RXRs/DNA/9cRA -0.004 0.11 -10000 0 -0.24 60 60
ABCA1 -0.086 0.24 -10000 0 -0.66 54 54
RARs/THRs 0.067 0.05 -10000 0 -0.22 13 13
RXRs/FXR -0.01 0.14 -10000 0 -0.27 89 89
BCL2 0.021 0.045 -10000 0 -0.43 5 5
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.012 -9999 0 -0.13 2 2
ITGB7 0.001 0.091 -9999 0 -0.26 44 44
ITGA4 -0.008 0.1 -9999 0 -0.43 26 26
alpha4/beta7 Integrin -0.005 0.1 -9999 0 -0.28 56 56
alpha4/beta1 Integrin 0.012 0.077 -9999 0 -0.29 26 26
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.026 0.008 -10000 0 -10000 0 0
LAT2 -0.023 0.12 0.17 4 -0.43 25 29
AP1 -0.015 0.17 0.25 1 -0.56 28 29
mol:PIP3 -0.009 0.17 0.3 35 -0.48 28 63
IKBKB 0.005 0.11 0.24 40 -0.27 20 60
AKT1 -0.03 0.11 0.31 22 -0.32 11 33
IKBKG 0.001 0.1 0.22 30 -0.26 22 52
MS4A2 -0.006 0.037 -10000 0 -0.14 8 8
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 0.036 -10000 0 -0.21 8 8
CBLB -0.019 0.1 -10000 0 -0.39 22 22
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 -0.28 6 6
PLD2 -0.041 0.1 0.26 18 -0.24 69 87
PTPN13 -0.007 0.13 -10000 0 -0.53 18 18
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 21 -0.31 15 36
SYK 0.009 0.085 -10000 0 -0.44 17 17
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.14 0.21 6 -0.48 28 34
LAT -0.029 0.11 -10000 0 -0.34 36 36
PAK2 -0.009 0.15 0.3 9 -0.54 23 32
NFATC2 -0.051 0.15 -10000 0 -0.53 43 43
HRAS -0.014 0.16 0.26 8 -0.6 23 31
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 -0.29 78 78
Antigen/IgE/Fc epsilon R1 -0.008 0.12 -10000 0 -0.25 84 84
mol:GDP -0.016 0.16 0.24 4 -0.61 26 30
JUN 0.019 0.023 -10000 0 -0.13 9 9
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 -0.28 93 93
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.39 24 24
CHUK 0 0.1 0.23 26 -0.26 22 48
KLRG1 -0.023 0.098 0.16 3 -0.34 25 28
VAV1 -0.026 0.13 0.17 2 -0.45 28 30
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.018 0.1 0.18 4 -0.4 21 25
negative regulation of mast cell degranulation -0.003 0.11 0.19 15 -0.4 18 33
BTK -0.022 0.17 -10000 0 -0.68 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.14 -10000 0 -0.29 106 106
GAB2/PI3K/SHP2 -0.046 0.081 -10000 0 -0.24 61 61
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 -0.02 0.16 -10000 0 -0.28 122 122
FCER1G 0.006 0.09 -10000 0 -0.39 23 23
FCER1A -0.06 0.15 -10000 0 -0.42 70 70
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.11 -10000 0 -0.24 77 77
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 0.003 0.14 -10000 0 -0.53 28 28
DUSP1 0.008 0.076 -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 -0.52 18 18
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.006 0.14 0.26 3 -0.54 22 25
FER -0.026 0.11 -10000 0 -0.34 36 36
RELA 0.025 0.005 -10000 0 -10000 0 0
ITK -0.024 0.092 -10000 0 -0.35 35 35
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.007 0.17 0.29 17 -0.64 23 40
cytokine secretion -0.002 0.038 -10000 0 -0.14 6 6
SPHK1 -0.028 0.12 0.2 1 -0.43 24 25
PTK2 -0.006 0.13 -10000 0 -0.55 17 17
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.15 0.25 10 -0.53 26 36
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.003 0.16 0.3 30 -0.46 27 57
MAP2K2 0.023 0.098 -10000 0 -0.82 5 5
MAP2K1 0.015 0.092 -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 -0.35 19 39
MAP2K4 0.032 0.063 -10000 0 -1.4 1 1
Fc epsilon R1/FcgammaRIIB -0.031 0.16 -10000 0 -0.29 121 121
mol:Choline -0.041 0.1 0.26 18 -0.24 69 87
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 -0.28 2 2
PXN -0.003 0.12 -10000 0 -0.51 17 17
HCLS1 -0.026 0.12 -10000 0 -0.43 28 28
PRKCB -0.005 0.13 0.26 27 -0.35 25 52
FCGR2B -0.05 0.15 -10000 0 -0.43 59 59
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.003 0.11 0.19 15 -0.41 18 33
LCP2 0.021 0.033 -10000 0 -0.43 1 1
PLA2G4A -0.027 0.12 -10000 0 -0.4 30 30
RASA1 0.026 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.041 0.1 0.26 18 -0.24 69 87
IKK complex 0.009 0.093 0.23 39 -0.21 16 55
WIPF1 0.026 0.002 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.023 0.076 0.22 66 -0.092 6 72
BUB1B -0.03 0.1 0.12 2 -0.27 69 71
PLK1 0.003 0.031 0.079 23 -0.12 9 32
PLK1S1 0.007 0.029 0.11 2 -0.18 5 7
KIF2A 0 0.039 0.24 4 -0.2 5 9
regulation of mitotic centrosome separation 0.003 0.031 0.079 23 -0.12 9 32
GOLGA2 0.025 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.034 0.14 -10000 0 -0.29 101 101
WEE1 -0.003 0.084 -10000 0 -0.35 25 25
cytokinesis -0.067 0.16 0.2 2 -0.39 97 99
PP2A-alpha B56 -0.03 0.22 -10000 0 -0.63 61 61
AURKA 0.008 0.025 0.1 2 -0.34 1 3
PICH/PLK1 -0.008 0.062 0.16 6 -0.22 24 30
CENPE -0.018 0.061 0.11 1 -0.24 28 29
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.039 0.24 4 -0.2 5 9
PPP2CA 0.026 0.003 -10000 0 -10000 0 0
FZR1 0.025 0.006 -10000 0 -10000 0 0
TPX2 -0.006 0.071 0.11 11 -0.27 31 42
PAK1 0.009 0.061 -10000 0 -0.16 46 46
SPC24 -0.044 0.14 -10000 0 -0.43 55 55
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.05 0.12 0.13 2 -0.26 119 121
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 3 -0.017 5 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.018 0.046 25 -0.058 11 36
G2 phase of mitotic cell cycle 0 0.002 0.014 2 -0.01 1 3
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 0.079 23 -0.12 9 32
ODF2 0.026 0.005 -10000 0 -10000 0 0
BUB1 -0.051 0.23 -10000 0 -0.68 60 60
TPT1 0 0.043 0.087 1 -0.18 22 23
CDC25C -0.028 0.12 0.15 1 -0.36 56 57
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 -0.22 6 6
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 0.11 2 -0.14 6 8
CDC2 0.001 0.002 0.011 1 -0.014 1 2
NDC80 -0.056 0.16 -10000 0 -0.3 128 128
metaphase plate congression -0.024 0.089 -10000 0 -0.23 76 76
ERCC6L -0.003 0.063 0.26 1 -0.22 24 25
NLP/gamma Tubulin 0.003 0.02 0.067 9 -0.087 6 15
microtubule cytoskeleton organization 0 0.043 0.087 1 -0.18 22 23
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 0.14 1 -0.22 97 98
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 0.073 32 -0.089 8 40
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 -0.33 4 5
microtubule-based process -0.032 0.1 0.12 2 -0.24 95 97
Golgi organization 0.003 0.031 0.079 23 -0.12 9 32
Cohesin/SA2 0.017 0.028 0.096 2 -0.12 5 7
PPP1CB/MYPT1 0.038 0.016 -10000 0 -0.31 1 1
KIF20A -0.078 0.17 -10000 0 -0.43 93 93
APC/C/CDC20 -0.004 0.074 0.11 3 -0.23 40 43
PPP2R1A 0.021 0.01 -10000 0 -10000 0 0
chromosome segregation -0.013 0.059 0.086 1 -0.22 33 34
PRC1 0.019 0.032 -10000 0 -10000 0 0
ECT2 0.001 0.038 0.21 7 -0.17 3 10
C13orf34 0.003 0.027 0.07 27 -0.097 9 36
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 -0.27 69 71
spindle assembly 0.002 0.027 0.077 16 -0.1 8 24
spindle stabilization 0.007 0.029 0.11 2 -0.18 5 7
APC/C/HCDH1 0.023 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 -0.033 0.1 0.12 2 -0.24 95 97
CCNB1 0.017 0.038 -10000 0 -0.14 1 1
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 -0.38 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 -0.23 5 5
MLF1IP -0.018 0.076 -10000 0 -0.31 30 30
INCENP 0.024 0.021 -10000 0 -0.43 1 1
Ceramide signaling pathway

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
SPHK2 0.005 0.023 -10000 0 -0.3 1 1
MAP4K4 -0.01 0.094 -10000 0 -0.37 16 16
BAG4 0.014 0.071 -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 0.076 0.16 7 -0.23 19 26
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 -0.04 0.11 0.24 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 62 68
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 0.024 -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 -0.02 0.11 -10000 0 -0.34 34 34
BID -0.006 0.11 -10000 0 -0.64 7 7
MAP3K1 -0.041 0.12 0.25 1 -0.27 70 71
EIF2A -0.04 0.11 0.25 2 -0.27 56 58
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 -0.36 22 28
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.03 0.093 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 54 54
PRKRA -0.041 0.12 0.13 1 -0.27 71 72
PDGFA 0.016 0.036 -10000 0 -0.43 1 1
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 -0.37 34 34
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.024 -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 -0.25 44 44
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.096 -10000 0 -0.39 16 16
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
mol:Sphingosine-1-phosphate 0.005 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 -0.21 82 82
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
EIF2AK2 -0.041 0.11 0.16 3 -0.26 71 74
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 0.012 0.079 -10000 0 -0.51 6 6
MAP2K2 -0.032 0.088 0.17 8 -0.27 39 47
SMPD3 -0.02 0.1 0.19 1 -0.28 42 43
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 32 -0.19 50 82
NF kappa B1/RelA/I kappa B alpha 0.045 0.073 -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
Retinoic acid receptors-mediated signaling

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR -0.014 0.11 -10000 0 -0.26 71 71
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 0.073 -10000 0 -0.39 9 9
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 -0.35 9 16
RAR alpha/9cRA/Cyclin H -0.008 0.11 0.22 1 -0.38 11 12
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 -0.026 0.1 -10000 0 -0.4 18 18
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RXRs/RARs/NRIP1/9cRA -0.075 0.19 0.28 1 -0.44 78 79
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 -0.014 0.11 -10000 0 -0.26 71 71
RARG 0.026 0.008 -10000 0 -0.13 1 1
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 0.014 0.071 -10000 0 -0.43 13 13
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.087 0.2 -10000 0 -0.43 106 106
RARA -0.026 0.097 -10000 0 -0.24 75 75
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 -10000 0 -0.46 79 79
RXRG -0.061 0.16 -10000 0 -0.38 93 93
RXRA -0.022 0.088 -10000 0 -0.21 72 72
RXRB -0.027 0.099 -10000 0 -0.28 65 65
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.29 33 33
RBP1 -0.006 0.082 -10000 0 -0.17 85 85
CRBP1/9-cic-RA -0.002 0.056 -10000 0 -0.11 87 87
RARB 0.024 0.035 -10000 0 -0.43 3 3
PRKCG -0.065 0.15 -10000 0 -0.26 159 159
MNAT1 0.025 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.08 0.19 -10000 0 -0.44 87 87
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.059 0.16 -10000 0 -0.38 70 70
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.096 0.21 2 -0.35 17 19
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.076 0.19 -10000 0 -0.45 79 79
positive regulation of DNA binding -0.014 0.1 -10000 0 -0.36 11 11
NRIP1 -0.066 0.18 -10000 0 -0.64 15 15
RXRs/RARs -0.076 0.2 -10000 0 -0.45 82 82
RXRs/RXRs/DNA/9cRA -0.088 0.18 -10000 0 -0.41 105 105
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 0.092 -10000 0 -0.31 9 9
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
Glypican 2 network

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.002 0.097 -9999 0 -0.43 22 22
GPC2 0.004 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 0.09 -9999 0 -0.31 36 36
Angiopoietin receptor Tie2-mediated signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.06 0.25 -10000 0 -0.85 38 38
NCK1/PAK1/Dok-R -0.056 0.12 -10000 0 -0.41 39 39
NCK1/Dok-R -0.057 0.28 -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 0.015 -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 -0.15 1 28
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 0.02 0.029 -10000 0 -10000 0 0
PLD2 -0.064 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 -0.25 180 180
ELK1 -0.057 0.26 -10000 0 -0.95 36 36
GRB7 0.001 0.044 -10000 0 -10000 0 0
PAK1 0.008 0.061 -10000 0 -0.16 46 46
Tie2/Ang1/alpha5/beta1 Integrin -0.036 0.28 -10000 0 -0.99 36 36
CDKN1A -0.069 0.24 -10000 0 -0.66 66 66
ITGA5 0.017 0.043 -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 -0.01 0.21 -10000 0 -0.6 38 38
PLG -0.068 0.28 -10000 0 -1.1 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.052 0.23 -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 -0.066 0.24 -10000 0 -0.99 24 24
BMX -0.072 0.28 -10000 0 -1.1 36 36
ANGPT1 -0.083 0.3 -10000 0 -1.2 32 32
tube development -0.063 0.22 -10000 0 -0.67 52 52
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) -0.073 0.28 -10000 0 -0.74 63 63
mol:L-citrulline -0.01 0.21 -10000 0 -0.6 38 38
AGTR1 0 0.094 -10000 0 -0.35 29 29
MAPK14 -0.059 0.28 -10000 0 -1 37 37
Tie2/SHP2 -0.019 0.2 -10000 0 -1.1 14 14
TEK -0.022 0.21 -10000 0 -1.2 14 14
RPS6KB1 -0.047 0.24 -10000 0 -0.81 37 37
Angiotensin II/AT1 0 0.067 -10000 0 -0.29 22 22
Tie2/Ang1/GRB2 -0.056 0.29 -10000 0 -1.1 36 36
MAPK3 -0.061 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 -0.063 0.28 -10000 0 -0.97 37 37
FES -0.062 0.29 -10000 0 -1 36 36
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 -0.052 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 -0.038 0.25 -10000 0 -0.81 37 37
Tie2/Ang2 -0.087 0.3 -10000 0 -0.92 50 50
Tie2/Ang1 -0.065 0.3 -10000 0 -1.1 36 36
FOXO1 -0.059 0.24 -10000 0 -0.72 53 53
ELF1 0.026 0.022 -10000 0 -10000 0 0
ELF2 -0.06 0.28 -10000 0 -1 36 36
mol:Choline -0.061 0.27 -10000 0 -1 36 36
cell migration -0.029 0.066 -10000 0 -0.23 39 39
FYN -0.074 0.25 -10000 0 -0.77 51 51
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
negative regulation of cell cycle -0.06 0.22 -10000 0 -0.58 68 68
ETS1 0.003 0.082 -10000 0 -0.28 35 35
PXN -0.023 0.22 0.42 2 -0.67 37 39
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
NOS3 -0.02 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 -0.061 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 -0.005 0.19 0.34 2 -0.54 38 40
mol:Phosphatidic acid -0.061 0.27 -10000 0 -1 36 36
mol:Angiotensin II -0.001 0.006 -10000 0 -10000 0 0
mol:NADP -0.01 0.21 -10000 0 -0.6 38 38
Rac1/GTP -0.044 0.22 -10000 0 -0.75 37 37
MMP2 -0.07 0.28 -10000 0 -1.1 36 36
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.023 0.13 -10000 0 -0.43 45 45
GNB1/GNG2 0.021 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 -0.013 0.082 -10000 0 -0.27 42 42
FZD3 0.023 0.035 -10000 0 -0.43 3 3
FZD6 0.015 0.04 -10000 0 -0.14 27 27
G protein 0.025 0.099 0.26 2 -0.27 26 28
MAP3K7 -0.048 0.1 0.21 15 -0.27 34 49
mol:Ca2+ 0.003 0.087 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 -0.007 0.087 -10000 0 -0.27 44 44
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
GNAS -0.013 0.079 0.16 1 -0.26 42 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 -0.43 5 5
NFAT1/CK1 alpha -0.002 0.12 0.33 3 -0.29 41 44
GNG2 0.022 0.04 -10000 0 -0.43 4 4
WNT5A 0.01 0.078 -10000 0 -0.43 15 15
WNT11 0.009 0.075 -10000 0 -0.28 27 27
CDC42 0.001 0.064 -10000 0 -0.24 25 25
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.025 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.046 0.027 -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 -0.028 0.14 -10000 0 -0.43 53 53
CRIPTO/GPC1 -0.004 0.11 -10000 0 -0.31 53 53
APP/GPC1 0.036 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.088 -10000 0 -0.27 53 53
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 0.029 -10000 0 -0.13 14 14
FYN -0.015 0.082 -10000 0 -0.26 50 50
FGR -0.013 0.076 -10000 0 -0.26 42 42
positive regulation of MAPKKK cascade -0.05 0.15 0.34 4 -0.38 57 61
SLIT2 -0.044 0.14 -10000 0 -0.43 56 56
GPC1/NRG -0.043 0.13 -10000 0 -0.3 99 99
NRG1 -0.08 0.18 -10000 0 -0.32 156 156
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.018 -10000 0 -0.14 1 1
LYN -0.019 0.086 -10000 0 -0.26 53 53
mol:Spermine 0.006 0.008 -10000 0 -10000 0 0
cell growth 0.046 0.027 -10000 0 -0.26 2 2
BMP signaling pathway -0.024 0.015 0.13 4 -10000 0 4
SRC -0.014 0.08 -10000 0 -0.26 47 47
TGFBR1 0.024 0.022 -10000 0 -0.43 1 1
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 -0.13 4 4
TGFBR1 (dimer) 0.024 0.022 -10000 0 -0.43 1 1
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
BLK -0.048 0.11 -10000 0 -0.28 75 75
HCK -0.02 0.091 -10000 0 -0.28 52 52
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 -0.26 23 23
LCK -0.037 0.1 -10000 0 -0.28 69 69
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
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 -0.029 0.14 -10000 0 -0.39 67 67
SMAD9 -0.047 0.18 -10000 0 -0.49 61 61
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.022 0.11 -10000 0 -0.39 22 22
BMP7/USAG1 -0.009 0.093 -10000 0 -0.3 37 37
SMAD5/SKI -0.013 0.11 -10000 0 -0.37 24 24
SMAD1 0.019 0.05 -10000 0 -0.42 2 2
BMP2 -0.033 0.15 -10000 0 -0.43 66 66
SMAD1/SMAD1/SMAD4 0.022 0.053 -10000 0 -0.31 3 3
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B 0.003 0.1 -10000 0 -0.43 26 26
BMPR1A-1B/BAMBI 0.031 0.069 -10000 0 -0.26 24 24
AHSG -0.029 0.14 -10000 0 -0.31 81 81
CER1 -0.001 0.033 -10000 0 -0.13 19 19
BMP2-4/CER1 -0.005 0.13 -10000 0 -0.31 69 69
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.13 -10000 0 -0.42 35 35
BMP2-4 (homodimer) -0.017 0.14 -10000 0 -0.36 69 69
RGMB 0.02 0.047 -10000 0 -0.43 5 5
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 -0.011 0.13 -10000 0 -0.3 82 82
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 0.072 -10000 0 -0.23 30 30
SKI 0.022 0.01 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.054 -10000 0 -0.24 17 17
HFE2 0.012 0.025 -10000 0 -0.13 8 8
ZFYVE16 0.026 0.003 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD -0.001 0.13 -10000 0 -0.3 72 72
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 -0.32 101 101
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.079 0.17 -10000 0 -0.3 162 162
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 -0.036 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 0.064 -10000 0 -0.35 4 4
SMAD6/SMURF1 0.021 0.011 -10000 0 -10000 0 0
BAMBI 0.022 0.019 -10000 0 -10000 0 0
SMURF2 0.024 0.029 -10000 0 -0.43 2 2
BMP2-4/CHRDL1 -0.036 0.16 -10000 0 -0.3 125 125
BMP2-4/GREM1 -0.054 0.17 -10000 0 -0.3 153 153
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.038 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 -0.24 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.029 0.11 -10000 0 -0.37 33 33
PPM1A 0.025 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.029 0.061 0.3 1 -0.36 3 4
SMAD7/SMURF1 0.03 0.016 -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 -0.13 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 -10000 0 -0.42 46 46
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 0.088 -10000 0 -0.43 20 20
FST -0.016 0.12 -10000 0 -0.27 71 71
BMP2-4/NOG -0.024 0.17 -10000 0 -0.39 83 83
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.044 0.069 -10000 0 -0.22 25 25
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.021 -9999 0 -0.43 1 1
Aurora C/Aurora B/INCENP -0.011 0.11 -9999 0 -0.24 89 89
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 -0.072 0.17 -9999 0 -0.43 88 88
AURKC 0.011 0.051 -9999 0 -0.43 4 4
Glucocorticoid receptor regulatory network

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
PCK2 0.047 0.09 -10000 0 -0.84 3 3
SMARCC2 0.024 0.017 -10000 0 -0.13 1 1
SMARCC1 0.024 0.017 -10000 0 -0.11 1 1
TBX21 -0.067 0.17 -10000 0 -0.64 34 34
SUMO2 0.023 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.033 -10000 0 -0.16 10 10
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 -0.037 0.15 -10000 0 -0.34 89 89
GR alpha/HSP90/FKBP51/HSP90 0.049 0.12 0.26 20 -0.23 47 67
PRL -0.034 0.068 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.11 0.19 0.48 54 -0.34 1 55
RELA -0.032 0.092 -10000 0 -0.23 34 34
FGG 0.09 0.14 0.4 43 -10000 0 43
GR beta/TIF2 0.056 0.12 0.27 29 -0.29 31 60
IFNG -0.13 0.18 -10000 0 -0.57 30 30
apoptosis 0.014 0.17 0.57 19 -0.53 6 25
CREB1 0.026 0.009 -10000 0 -10000 0 0
histone acetylation -0.048 0.1 -10000 0 -0.34 34 34
BGLAP -0.039 0.097 -10000 0 -0.78 2 2
GR/PKAc 0.076 0.068 0.28 11 -10000 0 11
NF kappa B1 p50/RelA -0.05 0.15 -10000 0 -0.31 108 108
SMARCD1 0.024 0.017 -10000 0 -10000 0 0
MDM2 0.047 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 -0.056 0.084 -10000 0 -10000 0 0
GSK3B 0.023 0.026 -10000 0 -0.43 1 1
NR1I3 0.021 0.17 0.55 19 -0.57 4 23
CSN2 0.074 0.12 0.34 34 -10000 0 34
BRG1/BAF155/BAF170/BAF60A 0.06 0.047 -10000 0 -0.22 11 11
NFATC1 0.005 0.095 -10000 0 -0.43 23 23
POU2F1 0.025 0.021 -10000 0 -0.43 1 1
CDKN1A -0.044 0.28 -10000 0 -1.4 20 20
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 -0.24 45 54
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.04 0.27 0.52 18 -0.76 54 72
JUN -0.078 0.13 0.27 2 -0.37 48 50
IL4 -0.062 0.12 -10000 0 -0.45 24 24
CDK5R1 0 0.1 -10000 0 -0.42 30 30
PRKACA 0.025 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.092 0.1 -10000 0 -0.3 64 64
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.11 0.28 11 -0.22 33 44
cortisol/GR alpha (monomer) 0.14 0.19 0.54 56 -10000 0 56
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.14 -10000 0 -0.37 73 73
AP-1/NFAT1-c-4 -0.17 0.23 -10000 0 -0.51 123 123
AFP -0.077 0.12 -10000 0 -0.56 2 2
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.084 0.096 0.4 9 -10000 0 9
TP53 0.004 0.12 -10000 0 -0.47 32 32
PPP5C 0.022 0.01 -10000 0 -10000 0 0
KRT17 -0.27 0.42 -10000 0 -1.1 100 100
KRT14 -0.057 0.086 -10000 0 -10000 0 0
TBP 0.03 0.016 -10000 0 -0.29 1 1
CREBBP 0.025 0.046 -10000 0 -0.25 14 14
HDAC1 0.02 0.009 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
AP-1 -0.17 0.23 -10000 0 -0.52 123 123
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 90 90
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.027 0.009 -10000 0 -10000 0 0
STAT1 0.024 0.033 -10000 0 -0.16 10 10
CGA -0.048 0.085 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.044 0.091 0.3 10 -0.36 5 15
MAPK3 0.024 0.016 -10000 0 -10000 0 0
MAPK1 0.024 0.015 -10000 0 -10000 0 0
ICAM1 -0.098 0.19 -10000 0 -0.61 35 35
NFKB1 -0.031 0.089 -10000 0 -0.24 26 26
MAPK8 -0.079 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 0.57 19 -0.56 6 25
BAX -0.024 0.11 -10000 0 -0.6 1 1
POMC -0.086 0.22 -10000 0 -1.5 9 9
EP300 0.021 0.061 -10000 0 -0.29 18 18
cortisol/GR alpha (dimer)/p53 0.12 0.18 0.49 47 -0.46 1 48
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.053 0.19 18 -10000 0 18
SGK1 0.002 0.24 -10000 0 -1.4 14 14
IL13 -0.13 0.19 -10000 0 -0.58 39 39
IL6 -0.14 0.29 -10000 0 -0.93 48 48
PRKACG 0.01 0.024 -10000 0 -0.13 4 4
IL5 -0.1 0.15 -10000 0 -0.62 11 11
IL2 -0.13 0.18 -10000 0 -0.58 25 25
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 -0.89 88 88
CDK5R1/CDK5 0.015 0.07 -10000 0 -0.3 22 22
NF kappa B1 p50/RelA/PKAc -0.007 0.12 -10000 0 -0.31 23 23
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.46 49 -10000 0 49
SMARCA4 0.024 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.079 0.12 0.32 40 -0.35 8 48
NF kappa B1 p50/RelA/Cbp -0.014 0.15 -10000 0 -0.37 36 36
JUN (dimer) -0.077 0.13 0.27 2 -0.37 48 50
YWHAH 0.019 0.033 -10000 0 -0.13 23 23
VIPR1 -0.071 0.18 -10000 0 -0.67 35 35
NR3C1 0.083 0.12 0.35 44 -10000 0 44
NR4A1 0.008 0.087 -10000 0 -0.45 15 15
TIF2/SUV420H1 0.015 0.083 -10000 0 -0.3 32 32
MAPKKK cascade 0.014 0.17 0.57 19 -0.53 6 25
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 0.021 -10000 0 -10000 0 0
SELE -0.15 0.28 -10000 0 -0.83 61 61
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.078 0.12 0.32 39 -0.34 9 48
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.46 49 -10000 0 49
mol:cortisol 0.066 0.11 0.31 53 -10000 0 53
MMP1 -0.041 0.09 -10000 0 -0.94 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.086 -10000 0 -0.29 41 41
CRKL 0.025 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.43 26 26
alpha4/beta7 Integrin/MAdCAM1 0.01 0.12 -10000 0 -0.25 80 80
EPO 0.013 0.03 -10000 0 -0.18 7 7
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.012 0.077 -10000 0 -0.29 26 26
EPO/EPOR (dimer) 0.027 0.025 -10000 0 -0.3 1 1
lamellipodium assembly 0.014 0.035 -10000 0 -0.26 4 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
JAK2 0.006 0.051 -10000 0 -0.22 22 22
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
MADCAM1 -0.034 0.13 -10000 0 -0.24 111 111
cell adhesion 0.008 0.12 -10000 0 -0.25 80 80
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
SRC -0.024 0.099 0.18 29 -0.24 67 96
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
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 -0.007 0.099 0.2 26 -0.22 63 89
VCAM1 -0.033 0.13 -10000 0 -0.3 85 85
RHOA 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.046 0.066 -10000 0 -0.23 23 23
BCAR1 -0.034 0.092 0.19 28 -0.23 67 95
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
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.095 0.22 60 -10000 0 60
GNAI2 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.094 -10000 0 -0.26 61 61
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 60 60
negative regulation of cAMP metabolic process -0.019 0.099 -10000 0 -0.24 66 66
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 -0.053 0.16 -10000 0 -0.3 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.019 0.1 -10000 0 -0.24 66 66
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
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.048 -10000 0 -0.43 4 4
HSPA8 0.023 0.022 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.017 0.091 0.22 1 -0.27 19 20
AKT1 0.015 0.034 -10000 0 -0.11 2 2
GSC -0.17 0.49 -10000 0 -1.4 69 69
NKX2-5 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.062 0.17 0.37 97 -10000 0 97
SMAD2-3/SMAD4/SP1 0.02 0.12 -10000 0 -0.28 33 33
SMAD4 -0.009 0.069 -10000 0 -0.21 17 17
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.028 0.08 -10000 0 -0.26 23 23
SMAD3/SMAD4/VDR 0.037 0.11 -10000 0 -0.24 35 35
MYC 0.009 0.087 -10000 0 -0.38 22 22
CDKN2B -0.18 0.49 -10000 0 -1.4 62 62
AP1 0.001 0.092 -10000 0 -0.26 29 29
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 -0.23 7 7
GATA3 -0.053 0.14 -10000 0 -0.4 62 62
SKI/SIN3/HDAC complex/NCoR1 0.014 0.061 -10000 0 -0.3 15 15
MEF2C/TIF2 -0.02 0.13 0.29 4 -0.28 51 55
endothelial cell migration 0.16 0.46 1.3 73 -10000 0 73
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 0.017 0.057 -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 -0.014 0.11 -10000 0 -0.26 71 71
CDKN1A -0.041 0.25 -10000 0 -1.3 20 20
KAT2B 0.021 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.011 0.13 -10000 0 -0.3 72 72
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 73 73
SMAD3/SMAD4/ATF2 0.019 0.086 -10000 0 -0.24 21 21
SMAD3/SMAD4/ATF3 0.014 0.091 -10000 0 -0.28 16 16
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.061 0.2 4 -0.26 4 8
JUN -0.014 0.082 -10000 0 -0.27 25 25
SMAD3/SMAD4/IRF7 0.019 0.084 -10000 0 -0.26 13 13
TFE3 0.014 0.035 -10000 0 -10000 0 0
COL1A2 0.005 0.093 -10000 0 -0.88 5 5
mesenchymal cell differentiation -0.02 0.087 0.28 15 -10000 0 15
DLX1 -0.066 0.16 -10000 0 -0.43 76 76
TCF3 0.023 0.029 -10000 0 -0.43 2 2
FOS -0.03 0.14 -10000 0 -0.3 88 88
SMAD3/SMAD4/Max 0.038 0.084 0.21 4 -0.22 9 13
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 0.21 1 -0.31 2 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.082 -10000 0 -0.29 11 11
IRF7 0.016 0.052 -10000 0 -0.21 20 20
ESR1 0.009 0.071 -10000 0 -0.27 25 25
HNF4A -0.007 0.042 -10000 0 -0.13 40 40
MEF2C -0.01 0.12 0.21 35 -0.29 45 80
SMAD2-3/SMAD4 0.008 0.1 -10000 0 -0.25 29 29
Cbp/p300/Src-1 0.042 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 -0.38 6 6
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 -0.23 8 8
MSG1/HSC70 0.015 0.072 -10000 0 -0.3 20 20
SMAD2 0 0.059 -10000 0 -0.16 24 24
SMAD3 0.006 0.056 -10000 0 -0.21 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.06 -10000 0 -0.26 13 13
SMAD2/SMAD2/SMAD4 -0.005 0.044 0.18 1 -0.21 3 4
NCOR1 0.024 0.028 -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 -0.045 0.13 -10000 0 -0.3 91 91
SMAD2-3/SMAD4/SP1/MIZ-1 0.019 0.12 -10000 0 -0.27 37 37
IFNB1 -0.01 0.06 0.19 1 -0.3 5 6
SMAD3/SMAD4/MEF2C 0.005 0.13 -10000 0 -0.32 33 33
CITED1 -0.001 0.092 -10000 0 -0.24 53 53
SMAD2-3/SMAD4/ARC105 0.022 0.1 -10000 0 -0.24 22 22
RBL1 0.012 0.077 -10000 0 -0.41 16 16
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.049 0.19 -10000 0 -0.54 60 60
RUNX1-3/PEBPB2 0.02 0.086 -10000 0 -0.24 48 48
SMAD7 -0.017 0.11 -10000 0 -0.39 18 18
MYC/MIZ-1 0.02 0.067 0.18 8 -0.28 19 27
SMAD3/SMAD4 -0.024 0.18 0.27 42 -0.44 66 108
IL10 -0.062 0.19 0.26 2 -0.5 63 65
PIASy/HDAC complex 0.021 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 37 40
CDK4 0.02 0.024 -10000 0 -10000 0 0
PIAS4 0.022 0.023 -10000 0 -10000 0 0
ATF3 0.006 0.072 -10000 0 -0.19 48 48
SMAD3/SMAD4/SP1 0.024 0.099 -10000 0 -0.24 24 24
FOXG1 -0.001 0.11 -10000 0 -0.42 31 31
FOXO3 0.002 0.037 -10000 0 -0.14 1 1
FOXO1 0.002 0.038 -10000 0 -0.3 1 1
FOXO4 0.001 0.041 -10000 0 -0.16 9 9
heart looping -0.01 0.12 0.21 35 -0.29 45 80
CEBPB 0.007 0.076 -10000 0 -0.36 17 17
SMAD3/SMAD4/DLX1 -0.026 0.14 -10000 0 -0.28 86 86
MYOD1 -0.09 0.17 -10000 0 -0.43 95 95
SMAD3/SMAD4/HNF4 0.021 0.079 -10000 0 -0.23 11 11
SMAD3/SMAD4/GATA3 -0.026 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 39 39
SMAD3/SMAD4/SP1-3 0.042 0.096 -10000 0 -0.27 12 12
MED15 0.026 0.004 -10000 0 -10000 0 0
SP1 0.013 0.038 -10000 0 -0.16 3 3
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.006 0.12 -10000 0 -0.26 74 74
ITGB5 -0.007 0.08 -10000 0 -0.44 7 7
TGIF/SIN3/HDAC complex/CtBP 0.012 0.074 -10000 0 -0.46 10 10
SMAD3/SMAD4/AR -0.019 0.13 -10000 0 -0.29 76 76
AR -0.047 0.16 -10000 0 -0.33 104 104
negative regulation of cell growth -0.002 0.094 -10000 0 -0.39 17 17
SMAD3/SMAD4/MYOD -0.037 0.14 -10000 0 -0.29 103 103
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 -0.23 66 66
SMAD2-3/SMAD4/FOXO1-3a-4 -0.029 0.14 -10000 0 -0.4 55 55
TFDP1 0.025 0.021 -10000 0 -0.43 1 1
SMAD3/SMAD4/AP1 0.022 0.1 -10000 0 -0.27 26 26
SMAD3/SMAD4/RUNX2 0.021 0.087 -10000 0 -0.28 15 15
TGIF2 0.021 0.045 -10000 0 -0.38 6 6
TGIF1 0.016 0.06 -10000 0 -0.27 17 17
ATF2 0.016 0.069 -10000 0 -0.43 12 12
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.003 0.095 0.32 38 -10000 0 38
KIRREL -0.009 0.12 -10000 0 -0.43 38 38
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.003 0.095 -10000 0 -0.32 38 38
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 0.029 0.08 -10000 0 -0.24 38 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.069 -10000 0 -0.24 32 32
FYN -0.009 0.076 0.18 22 -0.22 39 61
mol:Ca2+ 0.026 0.08 -10000 0 -0.24 39 39
mol:DAG 0.027 0.081 -10000 0 -0.24 39 39
NPHS2 0.001 0.033 -10000 0 -0.28 2 2
mol:IP3 0.027 0.081 -10000 0 -0.24 39 39
regulation of endocytosis 0.023 0.072 -10000 0 -0.21 39 39
Nephrin/NEPH1/podocin/Cholesterol 0.016 0.075 -10000 0 -0.23 39 39
establishment of cell polarity -0.003 0.095 -10000 0 -0.32 38 38
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.082 -10000 0 -0.22 38 38
Nephrin/NEPH1/beta Arrestin2 0.025 0.074 -10000 0 -0.22 39 39
NPHS1 -0.001 0.053 -10000 0 -0.26 6 6
Nephrin/NEPH1/podocin 0.018 0.073 -10000 0 -0.23 39 39
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 39 39
CD2AP 0.026 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.027 0.08 -10000 0 -0.24 38 38
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.086 0.19 26 -0.23 46 72
cytoskeleton organization -0.017 0.083 0.2 12 -0.27 32 44
Nephrin/NEPH1 0.009 0.067 -10000 0 -0.22 38 38
Nephrin/NEPH1/ZO-1 0.021 0.081 -10000 0 -0.25 38 38
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EPHB2 0.017 0.04 -10000 0 -0.22 10 10
EFNB1 -0.023 0.082 -10000 0 -0.31 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.095 -10000 0 -0.25 46 46
Ephrin B2/EPHB1-2 0.016 0.082 -10000 0 -0.25 41 41
neuron projection morphogenesis -0.009 0.085 -10000 0 -0.24 46 46
Ephrin B1/EPHB1-2/Tiam1 -0.008 0.11 -10000 0 -0.26 61 61
DNM1 -0.027 0.12 -10000 0 -0.22 106 106
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.085 0.22 1 -0.51 13 14
YES1 -0.005 0.13 -10000 0 -0.77 13 13
Ephrin B1/EPHB1-2/NCK2 -0.008 0.11 -10000 0 -0.26 62 62
PI3K 0.027 0.091 -10000 0 -0.52 13 13
mol:GDP -0.009 0.1 -10000 0 -0.26 61 61
ITGA2B -0.012 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 -0.41 20 20
LYN -0.002 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 0.095 -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 -0.009 0.12 -10000 0 -0.43 39 39
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 -0.01 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 0.009 0.1 0.26 62 -10000 0 62
MAPK8 -0.014 0.09 -10000 0 -0.5 13 13
Ephrin B1/EPHB1-2/RGS3 -0.008 0.11 -10000 0 -0.26 62 62
endothelial cell migration 0.026 0.11 0.22 28 -0.41 13 41
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTPN13 0.023 0.052 -10000 0 -0.56 4 4
regulation of focal adhesion formation 0.009 0.1 0.26 62 -10000 0 62
chemotaxis 0.009 0.11 0.26 62 -10000 0 62
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.004 0.09 -10000 0 -0.24 46 46
angiogenesis -0.009 0.095 -10000 0 -0.58 13 13
LCK -0.019 0.13 -10000 0 -0.76 13 13
TCGA08_rtk_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
PDGFRA -0.022 0.14 -10000 0 -0.41 55 55
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.4 46 46
AKT 0.038 0.11 0.27 47 -0.23 10 57
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 -0.43 1 1
AKT3 0.022 0.04 -10000 0 -0.43 4 4
FOXO4 0.025 0.02 -10000 0 -0.43 1 1
MET -0.047 0.14 -10000 0 -0.26 121 121
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 -0.43 1 1
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 73 76
ERBB2 0.023 0.027 -10000 0 -0.17 8 8
proliferation/survival/translation -0.025 0.081 0.33 14 -0.23 11 25
PI3K 0.021 0.11 0.25 61 -0.14 66 127
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
FOXO 0.061 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
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.14 -10000 0 -0.42 55 55
KLHL20 0.011 0.07 0.16 6 -0.22 6 12
CYFIP2 0.022 0.037 -10000 0 -0.28 6 6
Rac1/GDP -0.004 0.095 0.26 4 -0.26 48 52
ENAH -0.032 0.14 -10000 0 -0.42 61 61
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 0.065 -10000 0 -0.24 1 1
ABI1/Sra1/Nap1 -0.014 0.035 -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 4 -0.37 55 59
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 -0.03 0.14 0.22 1 -0.4 57 58
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 -0.25 10 10
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 0.044 -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 0.057 -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 -0.02 0.12 -10000 0 -0.31 63 63
TIAM1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.029 0.088 -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 -0.28 122 122
RhoA/GDP 0.004 0.1 0.26 8 -0.26 51 59
actin cytoskeleton organization 0.014 0.06 0.16 18 -0.16 6 24
CDC42/GDP 0 0.099 0.25 5 -0.25 51 56
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.078 -10000 0 -0.22 60 60
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
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 0.085 -10000 0 -0.22 59 59
mol:GDP -0.011 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 0.009 0.1 0.26 6 -0.26 50 56
RAC1/GTP/IQGAP1 0.027 0.029 -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 0.012 0.051 0.14 19 -0.16 14 33
NME1 0.026 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.031 0.15 -10000 0 -0.42 62 62
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 0.081 0.21 3 -0.26 1 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.12 -10000 0 -0.25 74 74
CCND1 0.012 0.06 0.16 15 -0.2 14 29
VAV2 -0.013 0.15 -10000 0 -0.64 5 5
RAP1/GDP 0.004 0.091 0.27 4 -0.23 22 26
adherens junction assembly -0.03 0.14 -10000 0 -0.4 62 62
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 74 74
E-cadherin/beta catenin -0.028 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 60 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.016 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 0.15 -10000 0 -0.44 62 62
Rapid glucocorticoid signaling

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.008 0.086 -10000 0 -0.22 58 58
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 0.028 -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 -0.012 0.079 -10000 0 -0.23 61 61
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 0.062 61 -10000 0 61
GNAL -0.028 0.15 -10000 0 -0.42 61 61
GNG2 0.022 0.04 -10000 0 -0.43 4 4
CRH -0.075 0.16 -10000 0 -0.27 167 167
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.047 -10000 0 -0.3 13 13
MAPK11 0.002 0.037 -10000 0 -0.3 8 8
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.1 -10000 0 -0.25 53 53
MAP4K1 0.013 0.061 -10000 0 -0.34 13 13
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
DBNL 0.023 0.009 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -10000 0 0
MAP3K1 -0.007 0.082 0.17 1 -0.36 10 11
JUN -0.025 0.17 -10000 0 -0.57 42 42
MAP3K7 -0.007 0.081 -10000 0 -0.36 10 10
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
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 -0.42 27 27
LCP2 0.02 0.033 -10000 0 -0.43 1 1
MAPK8 -0.023 0.18 -10000 0 -0.6 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.002 0.089 -10000 0 -0.28 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.098 -10000 0 -0.24 48 48
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.052 0.2 30 -0.2 2 32
RFC1 0 0.037 0.18 18 -0.2 2 20
PRKDC 0.007 0.054 0.2 35 -0.2 2 37
RIPK1 0.027 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 14 -0.26 8 22
MAP2K4 -0.028 0.11 0.22 1 -0.33 37 38
mol:ceramide 0.003 0.068 -10000 0 -0.26 19 19
GSN -0.001 0.062 0.19 26 -0.3 9 35
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.054 -10000 0 -0.27 5 5
FAS 0.011 0.064 -10000 0 -0.43 9 9
BID -0.01 0.052 0.26 17 -10000 0 17
MAP3K1 -0.024 0.11 0.22 1 -0.36 31 32
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 -0.006 0.12 -10000 0 -0.24 86 86
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 0.066 0.24 19 -0.19 26 45
NFKB1 -0.011 0.12 -10000 0 -0.74 11 11
MAPK8 -0.045 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 11 28
FAS/FADD/MET -0.004 0.1 -10000 0 -0.27 56 56
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 -0.012 0.12 -10000 0 -0.7 11 11
FASLG 0.007 0.04 -10000 0 -0.13 32 32
FAS/FADD 0.024 0.049 -10000 0 -0.31 8 8
HGF -0.009 0.091 -10000 0 -0.2 69 69
LMNA -0.001 0.047 0.2 12 -0.21 1 13
CASP6 0 0.041 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 -0.099 0.36 -10000 0 -1.2 45 45
MET -0.047 0.14 -10000 0 -0.26 121 121
ICAD/CAD 0.001 0.044 0.3 6 -0.21 1 7
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 0.051 0.26 17 -10000 0 17
PAK2 0.002 0.041 0.18 22 -0.22 1 23
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Canonical Wnt signaling pathway

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.024 0.19 4 -10000 0 4
AES 0.026 0.019 0.17 4 -10000 0 4
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.017 -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 27 -0.31 4 31
WIF1 -0.13 0.18 -10000 0 -0.27 266 266
beta catenin/RanBP3 0.016 0.1 0.4 27 -0.3 1 28
KREMEN2 -0.007 0.1 -10000 0 -0.24 63 63
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.053 0.097 0.29 25 -0.28 4 29
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 0.075 -10000 0 -0.53 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.09 0.28 20 -0.58 3 23
Axin1/APC/GSK3 0.03 0.073 0.24 13 -0.25 2 15
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.075 0.26 9 -0.42 2 11
HNF1A 0.027 0.029 0.19 4 -0.43 1 5
CTBP1 0.027 0.021 0.19 4 -10000 0 4
MYC 0.008 0.36 0.55 64 -1.5 21 85
RANBP3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.005 0.11 -10000 0 -0.27 65 65
NKD1 0.016 0.059 -10000 0 -0.28 16 16
TCF4 0.026 0.027 0.18 3 -0.38 1 4
TCF3 0.025 0.031 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 4 -10000 0 4
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 0.062 0.11 0.3 16 -0.73 3 19
DKK1/LRP6/Kremen 2 0.002 0.11 -10000 0 -0.26 64 64
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 -0.018 0.25 0.56 19 -1.5 11 30
WNT1 0.01 0.04 -10000 0 -10000 0 0
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 0.038 0.079 0.19 100 -10000 0 100
WNT1/LRP6/FZD1 0.042 0.079 0.2 75 -0.21 1 76
CREBBP 0.028 0.021 0.19 4 -10000 0 4
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 -0.007 0.089 -10000 0 -0.26 49 49
cell-cell adhesion 0.02 0.05 0.22 26 -10000 0 26
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 0.012 0.077 -10000 0 -0.26 38 38
HRAS/GDP 0.018 0.064 -10000 0 -0.27 10 10
Ephrin B/EPHB1/GRB7 0.042 0.098 -10000 0 -0.26 45 45
Endophilin/SYNJ1 0.012 0.056 0.18 26 -0.22 13 39
KRAS 0.025 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.045 0.088 -10000 0 -0.24 38 38
endothelial cell migration 0.042 0.028 -10000 0 -0.22 1 1
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.001 0.044 -10000 0 -10000 0 0
PAK1 -0.012 0.065 0.29 3 -0.25 5 8
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS 0.01 0.054 0.18 22 -0.23 11 33
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.005 0.08 0.19 17 -0.23 45 62
lamellipodium assembly -0.02 0.05 -10000 0 -0.22 26 26
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.074 -10000 0 -0.24 31 31
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPHB2 0.017 0.04 -10000 0 -0.22 10 10
EPHB3 0.025 0.011 -10000 0 -0.13 2 2
EPHB1 -0.009 0.12 -10000 0 -0.43 39 39
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 0.053 -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 40 55
Ephrin B/EPHB1 0.031 0.089 -10000 0 -0.24 45 45
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 -0.43 10 10
EFNB1 0.025 0.012 -10000 0 -0.13 3 3
Ephrin B2/EPHB1-2 0.017 0.082 -10000 0 -0.25 41 41
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 -0.22 44 44
axon guidance -0.007 0.088 -10000 0 -0.26 49 49
MAPK3 0.001 0.066 0.19 1 -0.28 10 11
MAPK1 0.002 0.065 0.19 1 -0.28 10 11
Rac1/GDP 0.024 0.084 0.23 41 -0.28 8 49
actin cytoskeleton reorganization -0.004 0.047 -10000 0 -0.26 8 8
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 -0.029 0.14 -10000 0 -0.3 87 87
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.045 -10000 0 -0.29 8 8
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.07 -10000 0 -0.22 43 43
PTK2 0.054 0.16 0.54 52 -10000 0 52
MAP4K4 -0.003 0.079 0.22 15 -0.23 40 55
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.02 0.038 -10000 0 -0.43 2 2
Intersectin/N-WASP 0.03 0.017 -10000 0 -10000 0 0
neuron projection morphogenesis 0.031 0.12 0.3 69 -0.34 4 73
MAP2K1 0.005 0.069 -10000 0 -0.23 30 30
WASL 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.03 0.086 -10000 0 -0.25 40 40
cell migration 0.004 0.087 0.3 2 -0.34 10 12
NRAS 0.021 0.01 -10000 0 -10000 0 0
SYNJ1 0.012 0.056 0.18 26 -0.22 13 39
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.022 0.075 0.17 20 -0.23 33 53
HRAS/GTP 0.016 0.082 -10000 0 -0.22 44 44
Ephrin B1/EPHB1-2 0.018 0.08 -10000 0 -0.24 40 40
cell adhesion mediated by integrin 0.002 0.048 0.22 10 -0.19 16 26
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0.02 0.087 -10000 0 -0.23 45 45
RAC1-CDC42/GTP -0.004 0.059 -10000 0 -0.22 28 28
RASA1 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.08 0.23 36 -0.27 8 44
ruffle organization 0.039 0.13 0.35 52 -0.35 5 57
NCK1 0.025 0.02 -10000 0 -0.43 1 1
receptor internalization -0.025 0.075 0.17 20 -0.24 31 51
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 -0.23 26 26
Ephrin B/EPHB1/Src/Paxillin 0.006 0.074 -10000 0 -0.24 39 39
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 -0.009 0.2 0.48 8 -0.66 17 25
CRP -0.016 0.2 0.59 5 -0.71 14 19
cell cycle arrest -0.021 0.22 0.49 3 -0.69 26 29
TIMP1 -0.014 0.2 0.46 2 -0.67 21 23
IL6ST -0.008 0.11 -10000 0 -0.43 32 32
Rac1/GDP -0.05 0.16 -10000 0 -0.43 57 57
AP1 0.033 0.1 -10000 0 -0.81 1 1
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.018 0.2 0.5 2 -0.67 17 19
HSP90B1 0.012 0.16 -10000 0 -0.91 14 14
GAB1 0.025 0.021 -10000 0 -0.43 1 1
MAPK14 -0.073 0.19 -10000 0 -0.54 56 56
AKT1 0.035 0.049 -10000 0 -0.7 1 1
FOXO1 0.035 0.051 -10000 0 -0.66 1 1
MAP2K6 -0.059 0.16 0.2 2 -0.45 58 60
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.049 0.17 0.29 3 -0.44 53 56
MITF -0.05 0.15 -10000 0 -0.42 54 54
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 0.073 -10000 0 -0.43 13 13
GRB2/SOS1/GAB family/SHP2 0.007 0.081 -10000 0 -0.54 3 3
STAT3 -0.028 0.24 0.5 3 -0.74 26 29
STAT1 0.017 0.045 -10000 0 -0.9 1 1
CEBPD -0.044 0.3 0.49 4 -1 34 38
PIK3CA 0.026 0.02 -10000 0 -0.43 1 1
PI3K 0.04 0.007 -10000 0 -10000 0 0
JUN 0.019 0.023 -10000 0 -0.13 9 9
PIAS3/MITF -0.032 0.16 -10000 0 -0.43 44 44
MAPK11 -0.076 0.19 -10000 0 -0.55 55 55
STAT3 (dimer)/FOXO1 -0.007 0.17 -10000 0 -0.58 16 16
GRB2/SOS1/GAB family -0.012 0.15 -10000 0 -0.42 34 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.046 0.15 -10000 0 -0.45 46 46
GRB2 0.025 0.006 -10000 0 -10000 0 0
JAK2 0.025 0.006 -10000 0 -10000 0 0
LBP 0.001 0.19 0.46 6 -0.63 18 24
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.016 -10000 0 -10000 0 0
MYC -0.022 0.28 0.49 4 -0.89 34 38
FGG -0.02 0.2 0.5 2 -0.69 15 17
macrophage differentiation -0.021 0.22 0.49 3 -0.69 26 29
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.12 -10000 0 -0.28 56 56
JUNB -0.021 0.24 0.45 10 -0.81 22 32
FOS -0.031 0.14 -10000 0 -0.28 93 93
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.16 0.23 1 -0.44 55 56
STAT1/PIAS1 -0.022 0.16 -10000 0 -0.44 38 38
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.049 -10000 0 -0.51 2 2
STAT3 (dimer) -0.025 0.24 0.5 3 -0.73 26 29
PRKCD -0.026 0.23 0.39 33 -0.55 49 82
IL6R 0.005 0.082 -10000 0 -0.43 16 16
SOCS3 -0.094 0.3 0.39 2 -1 40 42
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.078 -10000 0 -0.24 32 32
Rac1/GTP -0.05 0.17 -10000 0 -0.43 58 58
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAPKKK cascade 0.032 0.08 -10000 0 -0.96 1 1
bone resorption -0.016 0.19 0.5 2 -0.63 17 19
IRF1 -0.016 0.2 0.51 3 -0.69 15 18
mol:GDP -0.058 0.16 0.2 1 -0.43 62 63
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.058 0.16 0.2 1 -0.44 62 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.25 -10000 0 -0.62 66 66
PTPN11 0.009 0.079 -10000 0 -0.69 6 6
IL6/IL6RA -0.024 0.11 -10000 0 -0.32 51 51
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.074 -10000 0 -0.25 30 30
gp130 (dimer)/JAK2/JAK2/LMO4 0.02 0.075 -10000 0 -0.25 31 31
IL6 -0.038 0.12 -10000 0 -0.43 38 38
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 -0.35 47 48
LMO4 0.018 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.028 0.22 -10000 0 -0.69 26 26
MCL1 0.039 0.057 -10000 0 -0.62 1 1
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
Noncanonical Wnts/FZD -0.007 0.087 -9999 0 -0.27 44 44
FZD6 0.015 0.04 -9999 0 -0.14 27 27
WNT6 0.003 0.087 -9999 0 -0.25 43 43
WNT4 0.008 0.057 -9999 0 -0.43 5 5
FZD3 0.023 0.035 -9999 0 -0.43 3 3
WNT5A 0.01 0.078 -9999 0 -0.43 15 15
WNT11 0.009 0.075 -9999 0 -0.28 27 27
E-cadherin signaling in keratinocytes

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
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 0.17 6 -0.28 9 15
FMN1 -0.032 0.11 -10000 0 -0.27 60 60
mol:IP3 0.004 0.052 -10000 0 -0.23 4 4
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 0.024 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 -0.25 6 6
mol:Ca2+ 0.004 0.052 -10000 0 -0.23 4 4
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 0.052 -10000 0 -0.23 4 4
CDH1 -0.046 0.15 -10000 0 -0.28 118 118
RhoA/GDP 0.011 0.094 0.23 3 -0.29 8 11
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 -0.016 0.12 -10000 0 -0.4 46 46
CASR -0.005 0.049 -10000 0 -0.24 2 2
RhoA/GTP 0.016 0.053 -10000 0 -0.3 1 1
AKT2 0.01 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 0.076 0.15 5 -0.27 12 17
PIP5K1A -0.01 0.084 -10000 0 -0.23 55 55
PLCG1 0.004 0.053 -10000 0 -0.24 4 4
Rac1/GTP -0.007 0.1 -10000 0 -0.23 56 56
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.026 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 -0.02 0.11 -9999 0 -0.26 75 75
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 -10000 0 0
MED1 0.026 0.003 -9999 0 -10000 0 0
MAK 0.007 0.063 -9999 0 -0.16 49 49
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 0.06 -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 -0.03 0.12 -9999 0 -0.27 89 89
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 -0.43 17 17
TGFB1I1 0.022 0.038 -9999 0 -0.23 9 9
T-DHT/AR/CyclinD1 -0.029 0.12 -9999 0 -0.27 86 86
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 -0.13 3 3
TCF4 0.025 0.02 -9999 0 -0.43 1 1
CDKN2A -0.012 0.11 -9999 0 -0.3 53 53
SRF 0.024 0.027 -9999 0 -0.13 11 11
NKX3-1 -0.035 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 78 78
AR -0.056 0.16 -9999 0 -0.4 83 83
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 -0.25 44 44
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 -0.017 0.099 -9999 0 -0.23 77 77
RPS6KA3 0.025 0.02 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.021 0.11 -9999 0 -0.26 76 76
LATS2 0.018 0.046 -9999 0 -0.21 15 15
T-DHT/AR/PRX1 -0.026 0.1 -9999 0 -0.24 86 86
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -10000 0 0
VAV3 -0.031 0.11 -9999 0 -0.2 115 115
KLK2 -0.044 0.12 -9999 0 -0.41 40 40
CASP8 0.021 0.033 -9999 0 -0.43 1 1
T-DHT/AR/TIF2/CARM1 -0.017 0.12 -9999 0 -0.27 87 87
TMPRSS2 -0.082 0.25 -9999 0 -0.89 43 43
CCND1 0.011 0.07 -9999 0 -0.26 25 25
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 79 79
CMTM2 0.013 0.073 -9999 0 -0.33 19 19
SNURF 0.011 0.079 -9999 0 -0.43 16 16
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 -0.29 15 15
FKBP4 0.024 0.007 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.14 -10000 0 -0.56 25 25
HDAC1 0.022 0.014 -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 -0.43 7 7
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 -0.25 60 60
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 0.065 -10000 0 -10000 0 0
NICD/RBPSUH 0.016 0.12 -10000 0 -0.5 25 25
WIF1 -0.13 0.18 -10000 0 -0.27 266 266
NOTCH1 0 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 -0.24 63 63
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.011 0.072 0.31 4 -0.31 2 6
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 0.02 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 -0.28 93 93
JUN 0.019 0.023 -10000 0 -0.13 9 9
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 0.007 0.11 -10000 0 -0.27 65 65
HNF1A 0.025 0.021 -10000 0 -0.43 1 1
CTBP1 0.026 0.006 -10000 0 -10000 0 0
MYC -0.033 0.28 -10000 0 -1.4 21 21
NKD1 0.016 0.059 -10000 0 -0.28 16 16
FZD1 0.021 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.013 0.12 -10000 0 -0.54 21 21
apoptosis -0.027 0.09 -10000 0 -0.25 60 60
Delta 1/NOTCHprecursor -0.001 0.14 -10000 0 -0.55 25 25
DLL1 -0.008 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 0.28 2 -0.47 4 6
DVL1 -0.012 0.07 -10000 0 -0.24 39 39
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.007 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 -0.008 0.21 -10000 0 -1.4 12 12
WNT1 0.007 0.04 -10000 0 -10000 0 0
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 -0.55 21 21
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 -0.011 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
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 -0.22 10 10
Syndecan-2/TACI 0.012 0.046 -10000 0 -0.25 13 13
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
Syndecan-2/alpha2 ITGB1 0.021 0.093 -10000 0 -0.26 43 43
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 0.043 -10000 0 -0.16 24 24
BAX -0.001 0.037 -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 0.01 0.06 -10000 0 -0.25 23 23
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.068 -10000 0 -0.3 19 19
dendrite morphogenesis 0.011 0.049 -10000 0 -0.24 16 16
Syndecan-2/GM-CSF 0.011 0.044 -10000 0 -0.25 13 13
determination of left/right symmetry 0.002 0.049 -10000 0 -0.3 13 13
Syndecan-2/PKC delta 0.005 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 0.056 -10000 0 -0.25 25 25
Syndecan-2/alpha2/beta1 Integrin 0.008 0.11 0.19 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 -0.13 11 11
RASA1 0.026 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.068 -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 0.02 0.029 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.028 0.099 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 -10000 0 0
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 0.045 -10000 0 -0.24 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.041 -10000 0 -0.22 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 -0.43 10 10
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
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.016 0.023 -10000 0 -0.26 2 2
NT3 (dimer)/TRKC 0.028 0.033 -10000 0 -0.34 2 2
NT3 (dimer)/TRKB 0.01 0.098 -10000 0 -0.27 52 52
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 -0.43 14 14
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
NTRK1 0.016 0.055 -10000 0 -0.22 20 20
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 0.004 0.093 -10000 0 -0.26 47 47
neuron apoptosis 0.057 0.15 0.36 80 -10000 0 80
SHC 2-3/Grb2 -0.062 0.16 -10000 0 -0.38 80 80
SHC1 0.024 0.014 -10000 0 -0.13 4 4
SHC2 -0.029 0.1 -10000 0 -0.35 21 21
SHC3 -0.099 0.21 -10000 0 -0.52 83 83
STAT3 (dimer) 0.021 0.055 -10000 0 -0.33 11 11
NT3 (dimer)/TRKA 0.018 0.087 -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 -0.13 1 1
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 -0.3 119 119
CCND1 0.002 0.11 0.2 4 -0.7 11 15
MAGED1 0.026 0.002 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.43 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 -0.014 0.12 -10000 0 -0.28 83 83
TRKA/NEDD4-2 0.025 0.054 -10000 0 -0.31 10 10
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 -0.025 0.13 -10000 0 -0.35 63 63
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 -0.11 0.19 -10000 0 -0.31 201 201
RIT1 0.026 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
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) -0.025 0.13 -10000 0 -0.35 63 63
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 -0.27 34 34
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 -10000 0 0
RAP1/GDP 0.023 0.04 -10000 0 -0.31 1 1
KIDINS220/CRKL 0.025 0.008 -10000 0 -10000 0 0
BDNF (dimer) -0.01 0.089 -10000 0 -0.43 14 14
ubiquitin-dependent protein catabolic process -0.001 0.098 -10000 0 -0.25 59 59
Schwann cell development -0.014 0.019 -10000 0 -10000 0 0
EHD4 0.024 0.019 -10000 0 -10000 0 0
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 -0.23 25 25
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 -0.008 0.089 -10000 0 -0.36 5 5
STAT3 0.021 0.055 -10000 0 -0.33 11 11
axon guidance -0.002 0.064 -10000 0 -0.22 25 25
MAPK3 -0.037 0.11 0.18 11 -0.26 78 89
MAPK1 -0.036 0.11 0.18 11 -0.26 77 88
CDC42/GDP 0.032 0.052 0.22 6 -0.37 1 7
NTF3 0.006 0.032 -10000 0 -10000 0 0
NTF4 -0.003 0.033 -10000 0 -0.43 1 1
NGF (dimer)/TRKA/FAIM 0.008 0.096 -10000 0 -0.26 55 55
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 0.02 -10000 0 -0.43 1 1
RASGRF1 -0.069 0.12 -10000 0 -0.25 120 120
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 -0.008 0.088 -10000 0 -0.25 53 53
neuron projection morphogenesis -0.029 0.12 -10000 0 -0.73 2 2
NGF (dimer)/TRKA/NEDD4-2 0.006 0.098 -10000 0 -0.25 59 59
MAP2K1 0.024 0.05 0.36 3 -0.23 1 4
NGFR -0.017 0.12 -10000 0 -0.28 72 72
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 -0.43 14 14
MAPKKK cascade -0.11 0.23 -10000 0 -0.47 135 135
RASA1 0.026 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.042 -10000 0 -0.3 6 6
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 0.022 0.1 -10000 0 -0.24 58 58
MATK -0.027 0.13 -10000 0 -0.43 46 46
NEDD4L 0.02 0.044 -10000 0 -0.23 12 12
RAS family/GDP -0.006 0.02 -10000 0 -0.28 1 1
NGF (dimer)/TRKA -0.035 0.1 -10000 0 -0.27 76 76
Rac1/GTP -0.04 0.077 -10000 0 -0.22 44 44
FRS2 family/SHP2/CRK family 0.074 0.018 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
Jak2/Leptin Receptor 0.006 0.12 0.24 3 -0.38 31 34
PTP1B/AKT1 0.014 0.091 0.2 5 -0.28 17 22
FYN 0.025 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.094 0.19 10 -0.28 22 32
EGFR -0.019 0.13 -10000 0 -0.41 46 46
EGF/EGFR -0.018 0.12 -10000 0 -0.29 68 68
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 0.013 0.096 0.2 5 -0.31 15 20
Insulin Receptor/Insulin 0.018 0.086 0.2 1 -0.33 9 10
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 0.3 20 -0.31 14 34
EGF -0.012 0.12 -10000 0 -0.43 34 34
YES1 0.022 0.04 -10000 0 -0.43 4 4
CAV1 0.017 0.12 0.24 46 -0.3 23 69
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.021 0.093 0.2 3 -0.29 15 18
cell migration -0.003 0.094 0.28 22 -0.19 10 32
STAT3 0.026 0.003 -10000 0 -10000 0 0
PRLR 0.007 0.088 -10000 0 -0.43 19 19
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 0.02 0.066 -10000 0 -0.31 18 18
FGR 0.021 0.015 -10000 0 -0.13 3 3
PTP1B/p130 Cas 0.012 0.095 0.2 5 -0.28 20 25
Crk/p130 Cas 0.023 0.097 0.21 3 -0.29 15 18
DOK1 0.008 0.092 0.2 13 -0.33 12 25
JAK2 0.001 0.12 -10000 0 -0.4 30 30
Jak2/Leptin Receptor/Leptin -0.019 0.1 -10000 0 -0.32 23 23
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PTPN1 0.003 0.095 0.19 10 -0.28 22 32
LYN 0.021 0.035 -10000 0 -0.19 10 10
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 -0.015 0.16 0.28 37 -0.36 43 80
CAPN1 0.025 0.021 -10000 0 -0.43 1 1
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.084 -10000 0 -0.36 6 6
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.02 0.099 -10000 0 -0.34 22 22
negative regulation of transcription 0.001 0.12 -10000 0 -0.4 30 30
FCGR2A 0.001 0.092 -10000 0 -0.27 42 42
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 -0.03 0.11 -10000 0 -0.21 108 108
Insulin Receptor/Insulin/Shc 0.039 0.031 -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 -0.032 0.17 0.26 20 -0.42 47 67
PRL 0.003 0.02 -10000 0 -10000 0 0
SOCS3 -0.072 0.31 -10000 0 -1.3 33 33
SPRY2 0.024 0.028 -10000 0 -0.43 1 1
Insulin Receptor/Insulin/IRS1 0.04 0.03 -10000 0 -0.26 4 4
CSF1/CSF1R 0.005 0.11 0.22 2 -0.3 29 31
Ras protein signal transduction 0.018 0.11 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 -10000 0 0
STAT5B 0.009 0.1 0.2 5 -0.33 16 21
STAT5A 0.005 0.11 0.19 6 -0.32 21 27
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.094 0.2 4 -0.28 19 23
CSN2 -0.01 0.06 -10000 0 -0.56 2 2
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
LAT -0.015 0.14 -10000 0 -0.45 47 47
YBX1 0.026 0.031 -10000 0 -0.42 2 2
LCK -0.019 0.11 -10000 0 -0.43 30 30
SHC1 0.024 0.014 -10000 0 -0.13 4 4
NOX4 -0.009 0.1 -10000 0 -0.41 24 24
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.06 0.08 0.36 1 -0.48 4 5
CRKL 0.052 0.081 0.28 22 -0.38 1 23
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 0.032 0.071 0.16 80 -0.24 12 92
RAP1A 0.047 0.08 0.28 23 -0.36 1 24
GAB1 0.051 0.083 0.24 39 -0.35 2 41
MAPK14 0.04 0.063 0.16 89 -0.26 2 91
EPO 0.018 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 0.075 -10000 0 -0.27 24 24
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 0.28 20 -0.35 2 22
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 11 111
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 -0.029 0.12 -10000 0 -0.21 118 118
STAT1 (dimer) 0.035 0.058 -10000 0 -0.32 6 6
JAK2 0.03 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.06 -10000 0 -0.21 7 7
EPO/EPOR 0.031 0.03 -10000 0 -0.34 1 1
LYN 0.022 0.036 -10000 0 -0.19 10 10
TEC/VAV2 0.047 0.071 0.26 7 -0.23 6 13
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 0.045 0.037 -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 -0.13 2 2
NFKB1 0.039 0.062 0.16 85 -0.26 2 87
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.05 -10000 0 -0.21 24 24
PTPN6 0.048 0.081 0.29 20 -0.39 1 21
TEC/VAV2/GRB2 0.055 0.072 0.27 7 -0.26 3 10
EPOR 0.029 0.013 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
mol:GDP 0.07 0.073 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 0.059 0.065 0.27 7 -10000 0 7
VAV2 0.05 0.081 0.24 38 -0.38 1 39
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 0.073 -10000 0 -0.36 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.079 -10000 0 -0.34 13 13
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 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
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 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
BCL2L1 -0.032 0.13 -10000 0 -0.47 21 21
UGCG -0.018 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.037 0.15 0.23 2 -0.4 38 40
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 -0.018 0.15 0.25 1 -0.42 36 37
FRAP1 -0.028 0.17 0.27 2 -0.47 38 40
FOXO3 -0.027 0.15 0.26 3 -0.42 42 45
AKT1 -0.029 0.16 0.26 2 -0.45 42 44
GAB2 0.025 0.006 -10000 0 -10000 0 0
SMPD1 -0.013 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 -0.011 0.14 0.25 3 -0.41 25 28
EIF3A 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.012 -10000 0 -10000 0 0
RPS6KB1 0.002 0.076 -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 -0.012 13 13
JAK3 -0.008 0.1 -10000 0 -0.24 65 65
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 -0.025 0.24 0.35 4 -0.84 28 32
MYB -0.075 0.33 -10000 0 -1.2 40 40
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.027 0.14 -10000 0 -0.36 47 47
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.078 -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 38 38
PRKCZ -0.015 0.12 0.22 1 -0.38 31 32
NF kappa B1 p50/RelA -0.009 0.15 0.27 2 -0.42 36 38
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 -0.007 0.072 -10000 0 -0.17 67 67
IL2RB -0.027 0.13 -10000 0 -0.41 42 42
TERT -0.042 0.13 -10000 0 -0.43 48 48
E2F1 -0.014 0.13 -10000 0 -0.45 42 42
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 38 -10000 0 38
PTPN11 0.025 0.008 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
actin cytoskeleton organization -0.018 0.12 0.22 1 -0.36 34 35
GRB2 0.025 0.007 -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 0.041 0.025 -10000 0 -10000 0 0
LCK -0.019 0.11 -10000 0 -0.38 36 36
BCL2 -0.023 0.16 -10000 0 -0.63 17 17
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.002 0.099 0.22 13 -0.41 18 31
CRKL 0 0.098 -10000 0 -0.43 20 20
HRAS 0.007 0.11 -10000 0 -0.36 23 23
mol:PIP3 0.012 0.1 0.31 7 -0.38 18 25
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.012 -10000 0 -0.13 3 3
GAB1 0.002 0.1 0.2 2 -0.44 21 23
FOXO3 0.017 0.13 0.28 12 -0.39 29 41
AKT1 0.018 0.14 0.29 12 -0.42 30 42
BAD 0.021 0.14 0.3 14 -0.39 30 44
megakaryocyte differentiation 0 0.1 0.2 3 -0.42 22 25
GSK3B 0.017 0.13 0.29 12 -0.4 29 41
RAF1 0.006 0.093 0.25 1 -0.31 19 20
SHC1 0.024 0.014 -10000 0 -0.13 4 4
STAT3 0.004 0.1 0.2 3 -0.43 21 24
STAT1 -0.013 0.22 -10000 0 -0.89 28 28
HRAS/SPRED1 0.018 0.099 0.25 1 -0.31 20 21
cell proliferation -0.003 0.11 0.2 3 -0.45 22 25
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TEC 0.015 0.063 -10000 0 -0.29 17 17
RPS6KB1 0.014 0.12 0.26 4 -0.44 23 27
HRAS/SPRED2 0.018 0.099 0.25 1 -0.31 20 21
LYN/TEC/p62DOK 0.029 0.12 -10000 0 -0.42 24 24
MAPK3 0.014 0.082 0.22 19 -0.27 8 27
STAP1 -0.001 0.1 0.19 2 -0.42 23 25
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
JAK2 -0.014 0.2 -10000 0 -0.78 27 27
STAT1 (dimer) -0.011 0.22 -10000 0 -0.87 28 28
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.023 0.12 -10000 0 -0.41 27 27
actin filament polymerization -0.005 0.099 0.32 5 -0.4 21 26
LYN 0.021 0.035 -10000 0 -0.19 10 10
STAP1/STAT5A (dimer) -0.011 0.16 -10000 0 -0.59 29 29
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 -0.007 0.25 -10000 0 -1.2 20 20
MAPK8 -0.003 0.11 0.2 3 -0.46 22 25
STAT3 (dimer) 0.004 0.1 0.2 3 -0.42 21 24
positive regulation of transcription 0.015 0.071 0.2 20 -0.22 8 28
mol:GDP 0.003 0.11 -10000 0 -0.38 23 23
PIK3C2B 0.002 0.1 0.2 3 -0.42 21 24
CBL/CRKL 0.011 0.099 -10000 0 -0.41 19 19
FER -0.005 0.12 0.2 3 -0.45 24 27
SH2B3 0.003 0.1 0.2 3 -0.43 21 24
PDPK1 0.011 0.1 0.32 8 -0.38 17 25
SNAI2 -0.003 0.11 0.29 2 -0.42 25 27
positive regulation of cell proliferation -0.007 0.18 -10000 0 -0.71 27 27
KITLG 0.017 0.066 -10000 0 -0.41 11 11
cell motility -0.007 0.18 -10000 0 -0.71 27 27
PTPN6 0.013 0.063 -10000 0 -0.36 13 13
EPOR 0.031 0.084 -10000 0 -1.2 1 1
STAT5A (dimer) -0.004 0.16 -10000 0 -0.59 29 29
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
cell migration 0.017 0.11 0.42 25 -0.2 2 27
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.016 0.03 -10000 0 -0.18 7 7
VAV1 0.005 0.09 -10000 0 -0.34 29 29
GRB10 -0.001 0.094 0.24 1 -0.41 20 21
PTPN11 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT 0.006 0.11 0.21 3 -0.44 22 25
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.008 0.081 0.22 5 -0.26 16 21
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 0.25 17 -0.26 15 32
SHC/Grb2/SOS1 0.037 0.11 -10000 0 -0.42 19 19
STAT5A -0.004 0.16 -10000 0 -0.61 29 29
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.002 0.1 0.28 2 -0.41 25 27
SHC/GRAP2 0.012 0.079 -10000 0 -0.3 26 26
PTPRO 0 0.1 0.2 3 -0.42 22 25
SH2B2 -0.007 0.096 0.23 2 -0.4 21 23
DOK1 0.025 0.021 -10000 0 -0.28 2 2
MATK -0.017 0.11 0.2 2 -0.43 25 27
CREBBP 0.034 0.033 -10000 0 -10000 0 0
BCL2 0.012 0.19 -10000 0 -1.4 8 8
PLK2 and PLK4 events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.044 -9999 0 -0.15 27 27
PLK4 0.016 0.05 -9999 0 -0.18 24 24
regulation of centriole replication 0.001 0.042 -9999 0 -0.28 6 6
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.04 -10000 0 -0.43 4 4
ANTXR2 0.021 0.035 -10000 0 -0.43 2 2
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 -0.42 176 176
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 -0.003 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 76 78
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 -0.004 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 -0.022 0.061 -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 0.027 -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 -0.004 0.078 -10000 0 -0.39 20 20
MAPKKK cascade -0.005 0.024 0.091 1 -0.077 42 43
IL18 -0.012 0.051 0.16 3 -0.23 21 24
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 -0.001 0.018 -10000 0 -0.098 12 12
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 HDAC Class III

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
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 0.025 -10000 0 -0.13 18 18
CDKN1A -0.034 0.13 -10000 0 -0.65 20 20
KAT2B 0.025 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
FOXO3 -0.003 0.033 0.36 4 -10000 0 4
FOXO1 0.024 0.022 -10000 0 -0.43 1 1
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 -0.43 39 39
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.064 0.12 -10000 0 -0.3 93 93
PPARGC1A 0.009 0.082 -10000 0 -0.37 21 21
FHL2 0.006 0.077 -10000 0 -0.22 43 43
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.025 -10000 0 -10000 0 0
HIST2H4A 0.012 0.025 0.13 18 -10000 0 18
SIRT1/FOXO3a 0.02 0.038 0.17 20 -0.19 4 24
SIRT1 0.03 0.033 0.2 18 -10000 0 18
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.028 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.022 0.057 0.16 17 -0.22 19 36
apoptosis -0.045 0.031 -10000 0 -10000 0 0
SIRT1/PGC1A 0.025 0.057 0.14 17 -0.25 17 34
p53/SIRT1 0.037 0.085 0.38 18 -0.31 12 30
SIRT1/FOXO4 0.031 0.037 0.16 18 -0.22 5 23
FOXO1/FHL2/SIRT1 0.042 0.05 -10000 0 -0.23 13 13
HIST1H1E 0.004 0.05 -10000 0 -0.25 18 18
SIRT1/p300 0.037 0.039 0.16 18 -0.31 4 22
muscle cell differentiation 0.03 0.12 0.25 93 -0.22 10 103
TP53 0.02 0.077 0.2 18 -0.43 12 30
KU70/SIRT1/BAX 0.045 0.031 -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 0.097 0.16 17 -0.3 38 55
ACSS2 0.013 0.024 0.13 18 -10000 0 18
SIRT1/PCAF/MYOD -0.03 0.12 0.22 10 -0.25 93 103
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 -0.027 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 -0.016 0.1 0.18 1 -0.45 19 20
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 -0.43 3 3
PLCB2 -0.012 0.11 0.28 4 -0.44 19 23
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.087 -10000 0 -0.38 19 19
receptor internalization -0.016 0.096 -10000 0 -0.42 19 19
PTGS2 -0.095 0.33 -10000 0 -1 58 58
Rac1/GTP -0.015 0.083 -10000 0 -0.37 18 18
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.034 -10000 0 -0.13 22 22
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 0.21 2 -0.4 18 20
ABCC1 0.025 0.015 -10000 0 -0.14 4 4
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.013 0.052 -10000 0 -0.33 8 8
CCNA2 -0.007 0.099 -10000 0 -0.43 22 22
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
JAK3 -0.009 0.1 -10000 0 -0.25 65 65
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 -0.017 0.13 -10000 0 -0.39 27 27
SHC1 0.025 0.015 -10000 0 -0.13 4 4
SP1 0.027 0.034 -10000 0 -0.33 4 4
IL2RA -0.015 0.093 -10000 0 -0.7 8 8
IL2RB -0.028 0.13 -10000 0 -0.43 39 39
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
G1/S transition of mitotic cell cycle 0.004 0.17 0.28 5 -0.48 38 43
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 -0.43 17 17
CCND3 -0.012 0.12 -10000 0 -0.46 7 7
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.009 -10000 0 -0.13 1 1
NFATC1 0.002 0.11 0.25 4 -0.36 24 28
NFATC2 -0.011 0.082 0.14 2 -0.24 39 41
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 -0.41 48 51
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 -0.37 73 73
BCL2/BAX 0.029 0.034 -10000 0 -0.28 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.008 -10000 0 -0.089 1 1
CaM/Ca2+ 0.018 0.008 -10000 0 -0.089 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 -0.031 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 0.39 46 -10000 0 46
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.43 28 28
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
NFAT4/CK1 alpha 0.016 0.042 -10000 0 -0.19 13 13
MEF2D/NFAT1/Cbp/p300 0.019 0.1 -10000 0 -0.28 25 25
CABIN1 -0.044 0.15 0.17 3 -0.42 48 51
CALM1 0.025 0.009 -10000 0 -0.14 1 1
RAN 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
CAMK4 -0.094 0.19 -10000 0 -0.43 121 121
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 0.024 0.043 -10000 0 -0.3 3 3
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.13 0.26 1 -0.36 34 35
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 0.004 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 0.078 -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 -0.43 14 14
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
PRKCG -0.066 0.15 -10000 0 -0.26 159 159
PRKCQ 0.015 0.061 -10000 0 -0.37 11 11
FKBP38/BCL2 0.033 0.034 -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 -0.044 0.12 -10000 0 -0.25 122 122
NFATc/ERK1 0.015 0.11 0.26 3 -0.35 23 26
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.067 0.17 -10000 0 -0.37 79 79
NR4A1 -0.001 0.099 0.21 4 -0.34 19 23
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 0.009 0.058 -10000 0 -0.16 45 45
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 0.26 3 -0.35 24 27
CREBBP 0.026 0.006 -10000 0 -10000 0 0
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Regulation of p38-alpha and p38-beta

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
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 61 61
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 -0.13 3 3
p38 alpha/TAB1 -0.034 0.071 -10000 0 -0.28 21 21
PRKG1 -0.009 0.12 -10000 0 -0.43 36 36
DUSP8 0.02 0.039 -10000 0 -0.22 10 10
PGK/cGMP/p38 alpha -0.011 0.11 -10000 0 -0.3 27 27
apoptosis -0.033 0.068 -10000 0 -0.27 21 21
RAL/GTP 0.031 0.012 -10000 0 -10000 0 0
LYN 0.021 0.035 -10000 0 -0.19 10 10
DUSP1 0.008 0.076 -10000 0 -0.25 32 32
PAK1 0.008 0.061 -10000 0 -0.16 46 46
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 26 -0.33 23 49
BLK -0.03 0.11 -10000 0 -0.21 108 108
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAP2K3 0.025 0.01 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.015 0.065 -10000 0 -0.43 10 10
TRAF6/MEKK3 0.031 0.015 -10000 0 -0.23 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.11 0.24 26 -0.32 18 44
positive regulation of innate immune response 0.003 0.14 0.3 27 -0.38 22 49
LCK -0.019 0.11 -10000 0 -0.43 30 30
p38alpha-beta/MKP7 0.013 0.14 0.31 25 -0.36 22 47
p38alpha-beta/MKP5 0.006 0.14 0.29 23 -0.36 26 49
PGK/cGMP -0.005 0.082 -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 23 -0.37 24 47
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 -0.055 0.16 -10000 0 -0.34 113 113
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.036 0.064 -10000 0 -0.22 25 25
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.12 -10000 0 -0.42 14 14
AKT1 -0.009 0.17 -10000 0 -0.66 31 31
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.005 0.18 -10000 0 -0.69 30 30
mol:Ca2+ -0.018 0.093 -10000 0 -0.38 23 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.076 -10000 0 -0.26 34 34
SHC1 0.024 0.014 -10000 0 -0.13 4 4
apoptosis 0.008 0.16 0.63 31 -10000 0 31
RhoA/GTP 0.012 0.032 -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 16 18
E2/ERA-ERB (dimer) 0.018 0.06 -10000 0 -0.24 23 23
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 16 -0.39 2 18
E2/ER alpha (dimer)/PELP1 0.025 0.045 -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 0.28 2 -0.38 28 30
E2/ER beta (dimer) 0.012 0.045 -10000 0 -0.3 10 10
mol:GDP 0 0.068 -10000 0 -0.3 19 19
mol:NADP 0.004 0.13 0.28 2 -0.38 28 30
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 0.095 -10000 0 -0.41 21 21
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:L-citrulline 0.004 0.13 0.28 2 -0.38 28 30
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP 0.008 0.11 -10000 0 -0.6 15 15
JNK cascade 0.011 0.045 -10000 0 -0.3 10 10
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
ESR2 0.015 0.065 -10000 0 -0.43 10 10
GNAQ 0.026 0.004 -10000 0 -10000 0 0
ESR1 0.011 0.07 -10000 0 -0.26 25 25
Gq family/GDP/Gbeta gamma -0.024 0.17 -10000 0 -0.6 27 27
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 0.11 -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 0.005 0.096 -10000 0 -0.42 25 25
GNAL -0.028 0.15 -10000 0 -0.42 61 61
PELP1 0.026 0.002 -10000 0 -10000 0 0
MAPK11 0.003 0.05 -10000 0 -0.26 18 18
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 -0.011 0.089 -10000 0 -0.22 76 76
SRC -0.025 0.12 0.21 1 -0.37 19 20
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 -0.27 19 19
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 -0.005 0.093 -10000 0 -0.22 76 76
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.022 -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 0.088 -10000 0 -0.3 21 21
MSN -0.003 0.069 0.18 16 -0.42 2 18
Gq family/GTP 0.001 0.089 -10000 0 -0.4 18 18
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 0.073 -10000 0 -0.29 19 19
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 -0.006 0.15 0.37 3 -0.44 40 43
E2/ER alpha (dimer)/PELP1/Src 0.003 0.12 0.26 9 -0.39 16 25
ruffle organization -0.003 0.066 0.17 16 -0.39 2 18
ROCK2 0.002 0.07 0.19 16 -0.28 2 18
GNA14 0.009 0.081 -10000 0 -0.43 16 16
GNA15 0.013 0.07 -10000 0 -0.34 17 17
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.039 0.13 0.33 4 -0.36 25 29
MMP2 -0.014 0.13 0.27 14 -0.36 17 31
VEGFR1 specific signals

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
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 3 -0.23 49 52
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.027 -10000 0 -0.27 2 2
CaM/Ca2+ 0 0.076 -10000 0 -0.22 49 49
HIF1A 0.03 0.021 -10000 0 -0.42 1 1
GAB1 0.025 0.02 -10000 0 -0.43 1 1
AKT1 -0.015 0.082 -10000 0 -0.49 1 1
PLCG1 -0.014 0.075 0.19 3 -0.23 49 52
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 -0.29 2 5
endothelial cell proliferation -0.026 0.097 0.27 1 -0.28 51 52
mol:Ca2+ -0.014 0.074 0.19 3 -0.23 49 52
MAPK3 -0.027 0.061 0.17 3 -0.26 1 4
MAPK1 -0.027 0.061 0.17 3 -0.24 2 5
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 -0.15 44 44
VEGFA homodimer 0.019 0.032 -10000 0 -0.13 22 22
VEGFR1 homodimer/VEGFA homodimer 0.027 0.03 -10000 0 -0.3 2 2
platelet activating factor biosynthetic process -0.027 0.059 0.16 2 -0.26 1 3
PI3K 0.028 0.088 -10000 0 -0.22 55 55
PRKCA -0.027 0.064 0.18 3 -0.22 48 51
PRKCB -0.038 0.073 0.18 3 -0.23 59 62
VEGFR1 homodimer/PLGF homodimer -0.007 0.091 -10000 0 -0.26 57 57
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
VEGFB 0.025 0.005 -10000 0 -10000 0 0
mol:IP3 -0.014 0.074 0.19 3 -0.23 49 52
RASA1 0.014 0.021 0.19 3 -0.32 1 4
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFR1 homodimer 0.017 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 0.076 -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 -0.26 2 2
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 0.036 0.089 -10000 0 -0.23 1 1
PDPK1 -0.012 0.075 -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 -0.26 2 2
VEGFR1 homodimer/NRP2 0.027 0.034 -10000 0 -0.25 6 6
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.031 0.075 -10000 0 -0.26 51 51
PRKCE 0.005 0.022 -10000 0 -0.13 9 9
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 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
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 -0.3 19 19
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 -0.43 3 3
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.062 -9999 0 -0.29 17 17
S1PR5 -0.053 0.16 -9999 0 -0.3 124 124
S1PR4 0.019 0.042 -9999 0 -0.43 3 3
GNAI1 0.019 0.036 -9999 0 -0.43 3 3
S1P/S1P5/G12 -0.016 0.11 -9999 0 -0.26 71 71
S1P/S1P3/Gq -0.006 0.11 -9999 0 -0.38 29 29
S1P/S1P4/Gi 0.003 0.084 -9999 0 -0.29 15 15
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 -0.43 16 16
GNA15 0.013 0.07 -9999 0 -0.34 17 17
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
ceramide signaling 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
MAP4K4 -0.008 0.11 0.23 1 -0.46 18 19
BAG4 0.014 0.071 -10000 0 -0.43 13 13
BAD 0.005 0.058 0.24 15 -0.14 14 29
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 -0.15 8 26
EnzymeConsortium:3.1.4.12 0 0.03 0.07 3 -0.097 19 22
IKBKB -0.002 0.12 0.24 5 -0.46 16 21
MAP2K2 0.003 0.057 0.18 23 -0.2 1 24
MAP2K1 -0.001 0.051 0.18 9 -0.19 2 11
SMPD1 0.001 0.038 0.12 10 -0.13 10 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.12 0.3 7 -0.44 17 24
MAP2K4 -0.001 0.048 0.21 5 -0.18 3 8
protein ubiquitination -0.005 0.11 0.22 1 -0.46 16 17
EnzymeConsortium:2.7.1.37 -0.001 0.058 0.19 10 -0.2 2 12
response to UV 0 0.001 0.002 6 -0.002 3 9
RAF1 0 0.051 0.18 9 -0.18 3 12
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.002 0.046 0.12 7 -0.14 19 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.008 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 0.001 0.048 0.17 7 -0.18 5 12
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 10 -0.23 2 12
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD -0.005 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 0.18 29 -0.14 4 33
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 -0.39 29 29
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 -0.34 10 10
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.023 0.078 -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 6 -0.002 3 9
BCL2 0.021 0.045 -10000 0 -0.43 5 5
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.23 8 8
PLCG1 0.005 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 -0.23 8 8
S1PR5 -0.053 0.16 -10000 0 -0.3 124 124
S1PR4 0.019 0.042 -10000 0 -0.43 3 3
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 -0.019 0.1 -10000 0 -0.24 66 66
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 -0.016 0.094 -10000 0 -0.26 61 61
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
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.004 0.15 0.24 5 -0.32 42 47
CaM/Ca2+ 0.018 0.006 -10000 0 -0.084 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 0.02 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.013 0.15 0.22 31 -0.31 74 105
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 -0.13 11 11
ASIP -0.04 0.14 -10000 0 -0.32 94 94
PRKCI 0.026 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 -0.084 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 -0.43 14 14
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 0.002 -10000 0 -10000 0 0
SLC2A4 -0.018 0.16 0.23 24 -0.34 74 98
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
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.014 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.43 26 26
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.067 -10000 0 -0.26 23 23
alpha4/beta7 Integrin/Paxillin 0.009 0.083 0.18 3 -0.24 42 45
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 0.037 0.057 -10000 0 -0.21 22 22
cell adhesion 0.036 0.06 -10000 0 -0.22 22 22
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.02 0.062 0.17 1 -0.23 22 23
ITGB1 0.023 0.012 -10000 0 -0.13 2 2
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
ARF6/GDP 0.024 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0 0.097 -10000 0 -0.23 67 67
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.26 4 4
VCAM1 -0.033 0.13 -10000 0 -0.3 85 85
alpha4/beta1 Integrin/Paxillin/Talin 0.038 0.061 -10000 0 -0.22 22 22
alpha4/beta1 Integrin/Paxillin/GIT1 0.039 0.061 -10000 0 -0.22 22 22
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.038 0.06 0.22 22 -10000 0 22
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 0.038 0.061 -10000 0 -0.22 22 22
Rac1/GTP 0.023 0.054 0.28 1 -0.48 3 4
Integrins in angiogenesis

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
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 0.28 16 -0.37 16 32
IGF1R 0.026 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.035 -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 -0.13 22 22
ILK 0.005 0.078 -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 0.2 1 -0.23 27 28
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 -0.32 4 4
alphaV/beta3 Integrin/Syndecan-1 0.035 0.071 -10000 0 -0.21 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 0.014 0.099 -10000 0 -0.22 74 74
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 -0.13 4 4
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 0.031 0.086 -10000 0 -0.25 40 40
cell adhesion 0.028 0.056 -10000 0 -0.25 15 15
ANGPTL3 0.002 0.02 -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 0.03 0.059 -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 0.048 -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 0.084 -10000 0 -0.4 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 0.095 0.26 14 -0.32 14 28
alphaV beta3/Integrin/ppsTEM5 0.044 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 -0.35 19 19
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 0.042 -10000 0 -0.23 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 0.02 0.029 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.032 0.064 -10000 0 -0.22 15 15
SDC1 0.007 0.07 -10000 0 -0.19 43 43
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 0.27 16 -0.3 15 31
cell migration 0.014 0.088 0.24 17 -0.31 11 28
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.05 0.067 -10000 0 -0.21 25 25
SPP1 -0.024 0.12 -10000 0 -0.26 87 87
KDR 0.021 0.039 -10000 0 -0.43 3 3
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 -0.011 0.1 -10000 0 -0.43 22 22
angiogenesis 0 0.097 -10000 0 -0.41 17 17
Rac1/GTP 0.003 0.068 -10000 0 -0.21 29 29
EDIL3 -0.024 0.14 -10000 0 -0.43 53 53
cell proliferation 0.03 0.06 -10000 0 -0.23 15 15
IL27-mediated signaling events

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
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 0.001 0.088 0.4 2 -0.48 2 4
IL27/IL27R/JAK1 0.022 0.12 0.88 2 -10000 0 2
TBX21 -0.019 0.16 0.47 13 -0.41 18 31
IL12B -0.001 0.024 -10000 0 -0.13 6 6
IL12A -0.008 0.065 -10000 0 -0.3 23 23
IL6ST -0.002 0.11 -10000 0 -0.43 32 32
IL27RA/JAK1 0.024 0.051 -10000 0 -10000 0 0
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 0.43 1 -0.5 3 4
T-helper 2 cell differentiation 0.001 0.088 0.4 2 -0.48 2 4
T cell proliferation during immune response 0.001 0.088 0.4 2 -0.48 2 4
MAPKKK cascade -0.001 0.088 0.48 2 -0.4 2 4
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT2 0.025 0.014 -10000 0 -10000 0 0
STAT1 0.021 0.029 -10000 0 -0.13 16 16
IL12RB1 -0.001 0.098 -10000 0 -0.31 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.034 0.16 0.47 11 -0.47 9 20
IL27/IL27R/JAK2/TYK2 -0.001 0.089 0.48 2 -0.4 2 4
positive regulation of T cell mediated cytotoxicity -0.001 0.088 0.48 2 -0.4 2 4
STAT1 (dimer) 0.009 0.19 0.56 26 -0.51 1 27
JAK2 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.021 0.012 -10000 0 -10000 0 0
STAT2 (dimer) 0.018 0.097 0.39 3 -0.39 2 5
T cell proliferation -0.021 0.1 0.44 2 -0.4 6 8
IL12/IL12R/TYK2/JAK2 0.001 0.13 -10000 0 -0.78 10 10
IL17A -0.009 0.11 0.43 1 -0.47 2 3
mast cell activation 0.001 0.088 0.4 2 -0.48 2 4
IFNG 0.005 0.026 0.12 4 -0.11 5 9
T cell differentiation -0.002 0.004 -10000 0 -0.015 3 3
STAT3 (dimer) 0.018 0.098 0.39 3 -0.39 2 5
STAT5A (dimer) 0.013 0.11 0.39 3 -0.47 4 7
STAT4 (dimer) -0.011 0.13 0.39 3 -0.42 8 11
STAT4 -0.064 0.16 -10000 0 -0.43 69 69
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.025 0.074 -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 0.018 0.096 0.39 3 -0.38 2 5
IL27/EBI3 0.019 0.067 0.24 2 -0.28 18 20
IL27RA 0.009 0.033 -10000 0 -10000 0 0
IL6 -0.035 0.12 -10000 0 -0.43 37 37
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 75 75
EBI3 0.011 0.078 -10000 0 -0.42 15 15
TNF -0.049 0.1 -10000 0 -0.3 68 68
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0.04 0.2 8 -10000 0 8
DAPP1 -0.033 0.14 0.26 6 -0.39 39 45
Src family/SYK family/BLNK-LAT/BTK-ITK -0.074 0.22 0.33 6 -0.51 66 72
mol:DAG -0.02 0.099 0.29 13 -0.26 24 37
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 -0.004 0.041 0.17 19 -10000 0 19
ADAP1 -0.006 0.046 0.19 10 -0.21 5 15
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 -0.13 3 3
mol:Ca2+ -0.01 0.059 0.22 12 -0.14 14 26
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 0.26 12 -0.2 18 30
LYN 0.021 0.035 -10000 0 -0.19 10 10
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 -0.021 0.13 -10000 0 -0.43 49 49
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 0.18 28 -10000 0 28
Src family/SYK family/BLNK-LAT -0.067 0.17 -10000 0 -0.42 65 65
BLK -0.03 0.11 -10000 0 -0.21 108 108
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 10 -10000 0 10
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 0.08 0.21 2 -0.4 16 18
SGK1 -0.001 0.1 -10000 0 -0.38 30 30
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
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 0.027 0.19 6 -10000 0 6
ARAP3/RAP1A/GTP -0.004 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 0.031 0.04 -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 -0.42 27 27
Rac1/GTP 0.019 0.075 -10000 0 -0.4 10 10
ITK -0.022 0.064 0.2 9 -0.21 19 28
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.035 0.12 0.35 8 -0.35 28 36
LCK -0.019 0.11 -10000 0 -0.43 30 30
BTK -0.01 0.055 0.2 10 -0.21 2 12
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.019 0.076 -10000 0 -0.3 26 26
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 0.07 -10000 0 -0.22 27 27
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 -0.13 3 3
CCNE1 0.021 0.014 -10000 0 -10000 0 0
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 0.076 -10000 0 -0.3 27 27
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 -0.38 8 17
BRCA1/BARD1/ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BARD1/DNA-PK 0.049 0.065 -10000 0 -0.23 24 24
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.019 0.075 0.3 26 -10000 0 26
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.058 -10000 0 -0.22 23 23
BRCA1/BACH1/BARD1/TopBP1 0.035 0.072 -10000 0 -0.26 27 27
BRCA1/BARD1/P53 0.043 0.083 -10000 0 -0.25 37 37
BARD1/CSTF1/BRCA1 0.035 0.069 -10000 0 -0.26 26 26
BRCA1/BACH1 0.025 0.012 -10000 0 -0.13 3 3
BARD1 0.002 0.1 -10000 0 -0.41 28 28
PCNA 0.025 0.011 -10000 0 -0.13 2 2
BRCA1/BARD1/UbcH5C 0.035 0.069 -10000 0 -0.25 27 27
BRCA1/BARD1/UbcH7 0.036 0.068 -10000 0 -0.25 26 26
BRCA1/BARD1/RAD51/PCNA 0.04 0.085 -10000 0 -0.24 39 39
BARD1/DNA-PK/P53 0.051 0.08 -10000 0 -0.23 34 34
BRCA1/BARD1/Ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BRCA1/BARD1/CTIP 0.028 0.06 0.21 1 -0.23 24 25
FA complex 0.024 0.037 -10000 0 -0.21 8 8
BARD1/EWS 0.021 0.074 -10000 0 -0.3 25 25
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.43 13 13
TOPBP1 0.025 0.02 -10000 0 -0.43 1 1
G1/S transition of mitotic cell cycle -0.041 0.082 0.24 37 -10000 0 37
BRCA1/BARD1 0.045 0.073 -10000 0 -0.22 27 27
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.071 -10000 0 -0.3 26 26
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 -0.2 61 61
RAD50 0.026 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.02 0.076 -10000 0 -0.3 27 27
EWSR1 0.026 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.012 0.07 -10000 0 -0.43 11 11
positive regulation of NF-kappaB transcription factor activity 0.022 0.06 -10000 0 -0.3 13 13
MAP2K4 0.016 0.048 0.21 1 -0.23 3 4
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 -0.33 36 36
SMPD1 0.007 0.031 -10000 0 -0.18 13 13
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.038 -10000 0 -0.17 15 15
TRAIL/TRAILR2 0.024 0.061 -10000 0 -0.32 13 13
TRAIL/TRAILR3 0.015 0.08 -10000 0 -0.32 22 22
TRAIL/TRAILR1 0.008 0.089 -10000 0 -0.29 38 38
TRAIL/TRAILR4 0.022 0.06 -10000 0 -0.3 13 13
TRAIL/TRAILR1/DAP3/GTP 0.027 0.073 -10000 0 -0.23 35 35
IKK complex 0.014 0.044 -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 0.004 0.048 -10000 0 -0.3 11 11
MAP3K1 0.02 0.049 -10000 0 -0.22 13 13
TRAILR4 (trimer) 0.019 0.038 -10000 0 -0.17 15 15
TRADD 0.025 0.02 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0 0.098 -10000 0 -0.33 36 36
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.059 -10000 0 -0.21 31 31
CFLAR 0.026 0.007 -10000 0 -0.13 1 1
MAPK1 0.004 0.048 -10000 0 -0.3 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP 0.05 0.077 -10000 0 -0.22 33 33
mol:ceramide 0.007 0.031 -10000 0 -0.18 13 13
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.059 0.2 2 -0.27 5 7
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 0.078 -10000 0 -0.25 36 36
DAP3 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.001 0.062 0.16 17 -0.27 11 28
JNK cascade 0.022 0.06 -10000 0 -0.3 13 13
TRAIL (trimer) 0.012 0.07 -10000 0 -0.43 11 11
TNFRSF10C 0.009 0.074 -10000 0 -0.25 31 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.037 0.072 -10000 0 -0.22 33 33
TRAIL/TRAILR2/FADD 0.042 0.051 -10000 0 -0.26 13 13
cell death 0.007 0.031 -10000 0 -0.18 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.22 13 13
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 0.063 0.053 -10000 0 -0.22 13 13
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.12 0.37 -10000 0 -1.2 54 54
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 -0.3 11 11
NFX1/SIN3/HDAC complex -0.004 0.072 -10000 0 -0.23 13 13
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 0.03 0.027 -10000 0 -10000 0 0
TERT/c-Abl -0.099 0.34 -10000 0 -1.1 54 54
SAP18 0.025 0.006 -10000 0 -10000 0 0
MRN complex 0.046 0.018 -10000 0 -10000 0 0
WT1 0 0.046 -10000 0 -0.14 45 45
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 -0.072 0.31 -10000 0 -0.93 54 54
Mad/Max 0.03 0.023 -10000 0 -10000 0 0
TERT -0.13 0.39 -10000 0 -1.2 54 54
CCND1 -0.11 0.34 -10000 0 -0.99 63 63
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 0.056 0.22 1 -0.32 3 4
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 -0.13 9 9
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 0.13 -10000 0 -0.29 93 93
IFN-gamma/IRF1 0.025 0.035 -10000 0 -10000 0 0
PARP2 0.026 0.004 -10000 0 -10000 0 0
BLM -0.008 0.1 -10000 0 -0.25 62 62
Telomerase -0.016 0.098 -10000 0 -0.33 32 32
IRF1 0.017 0.036 -10000 0 -10000 0 0
ESR1 0.01 0.07 -10000 0 -0.26 25 25
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 0.072 -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 -0.086 0.34 -10000 0 -1 54 54
NR2F2 0.017 0.06 -10000 0 -0.22 24 24
MAPK3 -0.014 0.01 -10000 0 -10000 0 0
MAPK1 -0.013 0.009 -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 -0.4 46 46
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.025 0.12 -10000 0 -0.32 70 70
MYC 0.001 0.088 -10000 0 -0.4 22 22
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 0.072 -10000 0 -0.28 24 24
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.09 0.35 -10000 0 -1.1 54 54
SP1/HDAC2 0.029 0.032 -10000 0 -10000 0 0
PINX1 0.025 0.005 -10000 0 -10000 0 0
Telomerase/EST1A -0.071 0.31 -10000 0 -0.93 54 54
Smad3/Myc 0.01 0.058 -10000 0 -0.27 19 19
911 complex 0.044 0.021 -10000 0 -10000 0 0
IFNG 0.015 0.021 -10000 0 -0.14 2 2
Telomerase/PinX1 -0.073 0.31 -10000 0 -0.93 54 54
Telomerase/AKT1/mTOR/p70S6K -0.01 0.1 -10000 0 -0.48 8 8
SIN3B 0.025 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Telomerase/EST1B -0.072 0.31 -10000 0 -0.93 54 54
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 -0.07 0.31 -10000 0 -0.93 54 54
E2F1 0.009 0.058 -10000 0 -0.26 14 14
ZNFX1 0.025 0.005 -10000 0 -10000 0 0
PIF1 -0.01 0.11 -10000 0 -0.27 61 61
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
Signaling events mediated by PRL

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
CCNE1 0.021 0.014 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.009 -10000 0 -0.2 1 1
ITGA1 0.015 0.059 -10000 0 -0.22 23 23
CDKN1A -0.059 0.16 -10000 0 -0.37 95 95
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 0.092 -10000 0 -0.4 24 24
CCNA2 -0.038 0.079 -10000 0 -0.58 1 1
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
EGR1 -0.027 0.095 -10000 0 -0.3 53 53
CDK2/Cyclin E1 -0.029 0.15 -10000 0 -0.32 95 95
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 0.012 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 0.032 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.008 0.079 -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 -0.057 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 -0.35 7 8
PRL-1/alpha Tubulin -0.004 0.084 -10000 0 -0.58 1 1
PRL-3/alpha1 Integrin 0.027 0.042 -10000 0 -0.28 6 6
ROCK1 -0.017 0.093 0.28 1 -0.36 7 8
RABGGTB 0.022 0.01 -10000 0 -10000 0 0
CDK2 0.02 0.044 -10000 0 -0.43 4 4
mitosis -0.025 0.073 -10000 0 -0.61 1 1
ATF5 0.02 0.018 -10000 0 -0.13 5 5
Regulation of Androgen receptor activity

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
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 0.079 -10000 0 -0.29 16 16
JUN 0.019 0.023 -10000 0 -0.13 9 9
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 -0.43 1 1
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 0.008 0.092 -10000 0 -0.92 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 0.001 0.11 0.37 8 -0.39 10 18
NR0B1 -0.041 0.15 -10000 0 -0.31 102 102
EGR1 -0.038 0.14 -10000 0 -0.27 111 111
RXRs/9cRA 0.019 0.085 -10000 0 -0.23 52 52
AR/RACK1/Src 0.001 0.074 0.22 1 -0.26 10 11
AR/GR -0.012 0.1 0.23 2 -0.24 67 69
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 0.052 -10000 0 -0.3 13 13
T-DHT/AR/TIF2/CARM1 -0.002 0.1 0.35 1 -0.37 20 21
SRC -0.013 0.044 0.2 8 -0.22 12 20
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 -0.003 0.073 0.27 2 -0.3 10 12
TMPRSS2 -0.066 0.29 -10000 0 -0.99 45 45
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 -0.02 0.1 0.44 1 -0.38 15 16
AR -0.029 0.099 -10000 0 -0.26 68 68
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 0.064 -10000 0 -0.43 10 10
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.009 0.048 -10000 0 -0.13 55 55
T-DHT/AR/RACK1/Src 0.002 0.079 0.37 2 -0.27 10 12
positive regulation of transcription 0.015 0.064 -10000 0 -0.43 10 10
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 0.072 0.35 1 -0.3 11 12
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
NR2C1 0.026 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.04 -10000 0 -0.24 13 13
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.023 0.009 -10000 0 -10000 0 0
POU2F1 0.021 0.042 -10000 0 -0.28 2 2
T-DHT/AR/DAX-1 -0.032 0.1 0.25 3 -0.27 43 46
CREBBP 0.026 0.003 -10000 0 -10000 0 0
SMARCE1 0.026 0.003 -10000 0 -10000 0 0
ErbB4 signaling 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
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 -0.016 0.12 -10000 0 -0.4 46 46
PRL -0.011 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis -0.019 0.11 0.38 6 -0.4 2 8
PTPRZ1 0.016 0.046 -10000 0 -0.43 5 5
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 -0.039 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 -0.027 0.1 -10000 0 -0.32 10 10
GRIN2B -0.068 0.13 0.24 10 -0.36 40 50
ErbB4/ErbB2/betacellulin -0.001 0.096 -10000 0 -0.34 12 12
STAT1 0.021 0.028 -10000 0 -0.13 16 16
HBEGF 0.023 0.022 -10000 0 -0.13 10 10
PRLR 0.006 0.088 -10000 0 -0.32 30 30
E4ICDs/ETO2 0.022 0.065 -10000 0 -0.35 3 3
axon guidance -0.024 0.079 -10000 0 -0.4 6 6
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 -0.017 0.11 0.27 12 -0.41 2 14
STAT1 (dimer) 0.026 0.058 -10000 0 -0.32 1 1
MAPK1 -0.017 0.11 0.27 12 -0.33 5 17
JAK2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.099 -10000 0 -0.31 11 11
NRG1 -0.061 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 0.001 0.079 -10000 0 -0.2 53 53
heart development -0.024 0.079 -10000 0 -0.4 6 6
neural crest cell migration -0.036 0.099 -10000 0 -0.3 13 13
ERBB2 0.01 0.036 -10000 0 -0.29 6 6
WWOX/E4ICDs 0.025 0.057 -10000 0 -0.32 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
ErbB4/EGFR/neuregulin 4 0.004 0.1 -10000 0 -0.34 17 17
apoptosis -0.001 0.11 0.36 35 -10000 0 35
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 -0.31 4 4
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 -0.31 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 -0.38 23 23
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 0.022 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.007 0.097 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.012 0.083 -10000 0 -0.38 6 6
LRIG1 0.015 0.069 -10000 0 -0.43 12 12
EREG 0.008 0.036 -10000 0 -10000 0 0
BTC -0.04 0.14 -10000 0 -0.33 87 87
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.075 -10000 0 -0.4 6 6
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 0.021 0.067 -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 -0.071 0.14 -10000 0 -0.44 24 24
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.071 -10000 0 -0.43 13 13
Caspase 8 (4 units) 0.031 0.059 -10000 0 -0.3 4 4
NEF -0.001 0.011 -10000 0 -10000 0 0
NFKBIA 0.02 0.029 -10000 0 -0.14 1 1
BIRC3 -0.005 0.1 -10000 0 -0.45 24 24
CYCS 0.007 0.048 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 0.25 7 -0.33 9 16
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 -0.43 9 9
BID 0.01 0.048 0.18 6 -0.35 2 8
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 -0.39 8 8
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 -0.27 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.088 -10000 0 -0.38 13 13
CHUK 0.017 0.094 0.25 7 -0.36 9 16
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 -0.2 25 25
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 -0.59 7 7
CASP7 0.007 0.13 0.29 13 -0.47 26 39
RELA 0.019 0.03 -10000 0 -0.14 1 1
CASP2 0.02 0.011 -10000 0 -10000 0 0
CASP3 0.007 0.13 0.29 13 -0.47 27 40
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
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 0.094 0.21 5 -0.39 10 15
APAF-1/Caspase 9 0.004 0.083 -10000 0 -0.32 22 22
BCL2 0.016 0.082 0.27 1 -0.7 2 3
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
PTK2 0.009 0.088 -10000 0 -0.34 17 17
positive regulation of JNK cascade -0.007 0.092 -10000 0 -0.31 14 14
CDC42/GDP 0.02 0.12 -10000 0 -0.41 13 13
Rac1/GDP 0.004 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 -0.38 14 14
nectin-3/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
RAPGEF1 0 0.12 0.28 2 -0.43 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.013 0.12 -10000 0 -0.44 13 13
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
TLN1 0.002 0.017 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.083 -10000 0 -0.31 9 9
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
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 -0.5 13 13
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 0.043 -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 -0.003 0.088 -10000 0 -0.31 12 12
PVRL1 0.011 0.076 -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 -0.28 122 122
CLDN1 0.01 0.073 -10000 0 -0.43 12 12
JAM-A/CLDN1 0.049 0.063 -10000 0 -0.24 20 20
SRC -0.014 0.12 -10000 0 -0.48 14 14
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 -0.55 13 13
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 0.029 -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 -0.31 14 14
alphaV/beta3 Integrin/Talin 0.035 0.062 0.2 23 -0.22 12 35
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 0.002 0.14 -10000 0 -0.52 10 10
RAP1/GDP 0.011 0.11 -10000 0 -0.37 12 12
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 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 -0.001 0.11 -10000 0 -0.37 12 12
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 61 61
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.015 0.075 0.31 7 -0.29 12 19
PDGFB-D/PDGFRB/SLAP 0.021 0.06 -10000 0 -0.3 15 15
PDGFB-D/PDGFRB/APS/CBL 0.034 0.044 -10000 0 -0.26 8 8
AKT1 0.007 0.071 0.33 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.082 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 75 77
mol:Ca2+ 0.019 0.073 0.29 15 -0.29 4 19
MYC 0.032 0.21 0.41 30 -0.75 22 52
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 0.001 0.044 -10000 0 -10000 0 0
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 0.005 0.066 0.31 11 -10000 0 11
GAB1 0.012 0.091 0.31 14 -0.34 6 20
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.014 0.096 0.33 20 -0.31 7 27
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 0.079 0.22 2 -0.3 17 19
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 0.025 0.036 -10000 0 -0.18 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
BLK -0.018 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 -0.35 12 25
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 -0.4 106 108
PDGFRB 0.025 0.014 -10000 0 -0.14 3 3
ACP1 0.026 0.004 -10000 0 -10000 0 0
HCK 0.003 0.083 0.31 1 -0.58 9 10
ABL1 0.006 0.094 0.29 17 -0.32 12 29
PDGFB-D/PDGFRB/CBL 0.015 0.093 0.3 13 -0.35 9 22
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 0.028 -10000 0 -0.13 16 16
cell proliferation 0.035 0.19 0.39 32 -0.66 22 54
SLA 0.006 0.077 -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 0.006 0.024 -10000 0 -0.21 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.044 0.031 -10000 0 -0.21 1 1
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 -0.33 26 26
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 0.085 -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 0.025 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 -0.39 16 17
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 0.031 0.15 0.4 26 -0.43 22 48
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 0.066 0.41 6 -10000 0 6
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 3 -0.22 1 4
PDGFB-D/PDGFRB/SHB 0.037 0.011 -10000 0 -10000 0 0
chemotaxis 0.006 0.093 0.29 17 -0.32 12 29
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 -0.096 1 1
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.025 0.045 0.21 3 -0.27 3 6
BIRC5 -0.058 0.16 -10000 0 -0.3 129 129
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 -0.31 2 4
GADD45A 0.012 0.042 -10000 0 -0.43 1 1
GSK3B 0.028 0.025 -10000 0 -0.44 1 1
PAK1/Aurora A 0.024 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 -0.013 0.077 -10000 0 -0.3 30 30
TP53 0.017 0.052 -10000 0 -0.25 15 15
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 0.043 0.048 0.21 2 -0.33 2 4
G2/M transition of mitotic cell cycle 0.028 0.031 -10000 0 -0.22 2 2
AURKA 0.022 0.039 -10000 0 -0.29 2 2
AURKB -0.043 0.13 -10000 0 -0.29 97 97
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 0.023 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 -0.13 3 3
centrosome duplication 0.024 0.05 -10000 0 -0.25 7 7
regulation of centrosome cycle 0.039 0.045 0.19 2 -0.31 2 4
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 0.018 0.09 0.2 3 -0.21 38 41
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 -0.23 2 3
negative regulation of DNA binding 0.017 0.053 -10000 0 -0.25 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
Ajuba/Aurora A 0.012 0.027 -10000 0 -0.22 2 2
mitotic prometaphase 0.011 0.035 -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 0.011 0.053 -10000 0 -0.15 40 40
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 -0.013 0.077 -10000 0 -0.3 30 30
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.064 -10000 0 -0.24 17 17
PAK1 0.008 0.061 -10000 0 -0.16 46 46
CKAP5 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 -0.016 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 0.061 -10000 0 -0.41 11 11
p38 gamma/SNTA1 0.013 0.062 0.19 18 -0.21 25 43
MAP2K3 0.025 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 0.053 -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 Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.03 0.046 -10000 0 -0.2 14 14
TC10/GTP 0.031 0.04 -10000 0 -0.2 10 10
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 -0.25 180 180
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 -0.2 4 4
CAV1 0.005 0.039 0.18 11 -0.23 4 15
CBL/APS/CAP/Crk-II/C3G 0.049 0.052 -10000 0 -0.22 10 10
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 -0.19 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 -0.27 2 2
HRAS/GTP 0.014 0.025 -10000 0 -0.19 6 6
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 0.048 -10000 0 -0.44 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.084 -10000 0 -0.21 70 70
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 -0.36 1 4
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 -0.019 0.1 -10000 0 -0.43 21 21
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 0.043 0.049 -10000 0 -0.23 10 10
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 -0.37 5 5
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 0.085 0.33 7 -0.25 9 16
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 -0.21 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 23 23
Class I PI3K signaling events mediated by Akt

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
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 0.2 10 -0.28 17 27
CDKN1A 0.002 0.066 0.2 1 -0.29 15 16
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 0.2 4 -0.28 18 22
AKT1/ASK1 0.027 0.064 -10000 0 -0.27 19 19
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 0.062 0.26 19 -10000 0 19
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 0.2 1 -0.28 18 19
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 0.2 5 -0.28 4 9
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 0.065 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 0.061 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 0.2 1 -0.28 16 17
BAD/BCL-XL 0.032 0.061 -10000 0 -0.27 18 18
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 0.22 2 -0.36 5 7
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
MDM2 0.013 0.061 0.21 6 -0.28 17 23
MAPKKK cascade -0.032 0.059 0.28 15 -10000 0 15
MDM2/Cbp/p300 0.043 0.064 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 0.017 0.041 0.2 7 -0.28 5 12
FOXO1 0.011 0.059 0.2 2 -0.28 17 19
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 -0.93 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 -0.13 11 11
RHEB 0.02 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.054 -10000 0 -0.26 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.082 0.2 2 -0.29 14 16
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 0.019 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 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 39 39
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.009 0.082 0.19 2 -0.28 14 16
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 -0.009 0.077 -10000 0 -0.23 39 39
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 0.087 0.19 4 -0.3 16 20
cell death 0.008 0.079 0.18 2 -0.27 14 16
NF kappa B1 p105/c-Rel 0.016 0.054 -10000 0 -0.26 18 18
LCK -0.019 0.11 -10000 0 -0.43 30 30
BCL3 0.018 0.024 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.033 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.038 0.05 0.29 2 -0.23 1 3
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 0.074 -10000 0 -0.24 23 23
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 0.26 2 -10000 0 2
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 -0.41 101 101
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 -0.49 15 17
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 0.028 0.074 -10000 0 -0.33 13 13
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 -0.33 21 21
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 0.35 2 -0.59 18 20
SMAD7 -0.009 0.046 0.2 2 -0.17 3 5
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 0.007 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 98 98
CAMK2B -0.018 0.12 -10000 0 -0.27 69 69
FRAP1 -0.002 0.036 0.22 3 -10000 0 3
PRKCD -0.008 0.055 0.27 2 -10000 0 2
RAP1B 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.074 -10000 0 -0.24 23 23
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 0.022 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 0.04 0.15 8 -0.16 4 12
mol:PI-3-4-5-P3 0.031 0.028 -10000 0 -10000 0 0
RAP1/GDP 0.027 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 0.074 -10000 0 -0.24 23 23
PTPN11 0.013 0.029 0.29 1 -10000 0 1
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 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
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 -0.48 7 7
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 64 64
FLT1 0.013 0.14 -10000 0 -0.69 13 13
ADORA2A 0.017 0.15 0.33 4 -0.44 12 16
germ cell development 0.016 0.16 -10000 0 -0.46 21 21
SLC11A2 0.023 0.15 -10000 0 -0.46 11 11
BHLHE40 0.018 0.16 -10000 0 -0.53 15 15
HIF1AN 0.022 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.036 0.12 -10000 0 -0.36 8 8
ETS1 0.026 0.054 -10000 0 -0.43 6 6
CITED2 0.017 0.12 -10000 0 -0.66 9 9
KDR 0.016 0.14 -10000 0 -0.79 13 13
PGK1 0.023 0.15 -10000 0 -0.5 7 7
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 -0.5 13 13
EPAS1 0.012 0.073 -10000 0 -0.3 8 8
SP1 0.025 0.024 -10000 0 -0.12 1 1
ABCG2 0.022 0.16 -10000 0 -0.55 8 8
EFNA1 0.023 0.15 -10000 0 -0.49 9 9
FXN 0.018 0.14 0.33 4 -0.46 8 12
POU5F1 0.015 0.17 -10000 0 -0.48 21 21
neuron apoptosis -0.058 0.18 0.49 13 -10000 0 13
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 0.015 0.14 0.35 2 -0.45 11 13
TWIST1 0.011 0.15 0.34 2 -0.5 14 16
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 -0.48 8 8
CREBBP 0.026 0.003 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.002 0.14 -10000 0 -1.3 5 5
PLK1 0.024 0.16 -10000 0 -1.3 5 5
CDKN1B 0.052 0.11 0.28 1 -0.34 10 11
FOXO3 0.043 0.098 -10000 0 -0.45 9 9
KAT2B 0.03 0.014 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.076 -10000 0 -0.47 7 7
CAT 0.036 0.12 -10000 0 -0.64 5 5
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.016 -10000 0 -10000 0 0
FOXO1 0.008 0.08 -10000 0 -0.42 10 10
MAPK10 0.044 0.061 0.19 68 -0.21 2 70
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.06 0.065 0.29 2 -0.36 1 3
response to oxidative stress 0.008 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.044 0.1 -10000 0 -0.42 11 11
XPO1 0.027 0.002 -10000 0 -10000 0 0
EP300 0.023 0.041 -10000 0 -0.43 4 4
BCL2L11 0.024 0.12 -10000 0 -1.3 4 4
FOXO1/SKP2 0.018 0.082 -10000 0 -0.42 10 10
mol:GDP 0.008 0.01 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A -0.033 0.22 -10000 0 -0.49 84 84
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.035 0.071 -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 0.035 0.064 0.19 54 -0.22 11 65
MAPK9 0.046 0.059 0.19 71 -10000 0 71
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
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 -0.68 2 2
RBL2 0.057 0.095 -10000 0 -1.1 1 1
RAL/GDP 0.037 0.018 -10000 0 -10000 0 0
CHUK 0.03 0.013 -10000 0 -10000 0 0
Ran/GTP 0.021 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 -10000 0 0
FASLG 0.025 0.023 -10000 0 -10000 0 0
SKP2 0.021 0.046 -10000 0 -0.43 5 5
USP7 0.027 0.002 -10000 0 -10000 0 0
IKBKB 0.03 0.013 -10000 0 -10000 0 0
CCNB1 0.032 0.1 -10000 0 -0.52 2 2
FOXO1-3a-4/beta catenin 0.079 0.092 0.28 2 -0.37 3 5
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.081 -10000 0 -0.42 10 10
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
SGK1 0.019 0.07 -10000 0 -0.4 13 13
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 -0.33 6 6
FOXO3A/14-3-3 0.008 0.086 -10000 0 -0.68 2 2
CREBBP 0.026 0.014 -10000 0 -0.13 1 1
FBXO32 0.051 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
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.013 -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 -1 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
GNAI2 0.026 0.008 -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 -0.43 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.074 -10000 0 -0.27 20 20
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 0.19 8 -0.29 14 22
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 0.066 -10000 0 -0.29 13 13
S1P/S1P3/Gi 0.011 0.075 -10000 0 -0.27 20 20
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 -0.13 22 22
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 0.002 0.08 -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 -0.43 16 16
GNA15 0.013 0.07 -10000 0 -0.34 17 17
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 0.012 0.068 -10000 0 -0.28 13 13
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
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 -0.26 8 8
HIF1A 0.009 0.034 -10000 0 -0.25 6 6
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 -0.3 55 55
ARNT/IPAS -0.006 0.096 -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 0.047 -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 0.021 0.047 -10000 0 -0.26 8 8
PHD1-3/OS9 0.047 0.046 -10000 0 -0.22 9 9
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.051 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 -0.26 7 7
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 -0.43 13 13
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 0.069 0.25 2 -0.28 8 10
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.032 -10000 0 -0.14 17 17
TRAF2/ASK1 0.03 0.032 -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 -0.31 17 21
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 0.042 -10000 0 -0.43 1 1
GADD45B 0.01 0.067 -10000 0 -0.21 33 33
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
MAP3K6 0.02 0.019 -10000 0 -0.13 6 6
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 0.041 -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 -0.3 4 4
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 -0.27 69 69
CCM2 0.022 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.073 -10000 0 -0.25 34 34
MAPK11 0.019 0.056 -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 44 44
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 0.023 -10000 0 -0.13 9 9
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.021 0.028 -10000 0 -0.24 5 5
GADD45/MTK1/MTK1 0.027 0.068 -10000 0 -0.22 24 24
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.16 2 -0.22 11 13
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 0.17 7 -0.2 10 17
BAD -0.009 0.038 0.16 7 -0.22 1 8
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 0.027 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 -0.23 1 8
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.002 0.049 -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 -0.35 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 -10000 0 -10000 0 0
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 0.041 -10000 0 -10000 0 0
PRKCZ -0.013 0.05 0.17 6 -0.21 12 18
Crk/p130 Cas/Paxillin/FAK1 0.028 0.041 -10000 0 -10000 0 0
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.012 0.062 -10000 0 -0.34 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 15 15
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 0.012 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 -0.31 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 0.06 -10000 0 -0.32 15 15
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.016 0.12 -9999 0 -0.29 64 64
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 -0.33 1 1
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 -0.016 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 0.083 -9999 0 -0.31 6 6
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 -0.27 4 4
NuRD/MBD3 Complex 0.019 0.023 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.009 0.088 -9999 0 -0.31 7 7
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.015 0.064 -9999 0 -0.43 10 10
GATA1 0.013 0.025 -9999 0 -0.13 7 7
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 0.062 -9999 0 -0.29 2 2
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 -0.34 10 10
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 0.064 -9999 0 -0.26 3 3
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 0.034 0.042 -9999 0 -0.24 4 4
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 0.031 0.037 -9999 0 -0.33 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.06 -9999 0 -0.23 7 7
nuclear export -0.048 0.015 -9999 0 -10000 0 0
PRKACA 0.025 0.005 -9999 0 -10000 0 0
GATAD2B 0.026 0.004 -9999 0 -10000 0 0
GATAD2A 0.025 0.005 -9999 0 -10000 0 0
GATA2/HDAC3 0.006 0.08 -9999 0 -0.26 14 14
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 0.066 -9999 0 -0.25 1 1
positive regulation of chromatin silencing 0.024 0.073 -9999 0 -0.33 1 1
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 -0.23 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 0.02 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 0.043 0.019 -9999 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.019 0.11 -9999 0 -0.29 65 65
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
Class IB PI3K non-lipid kinase events

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
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 0.045 -10000 0 -0.38 6 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 10 -0.28 1 11
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 0.098 -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 0.044 -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 -0.43 10 10
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 0.019 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 -0.34 10 10
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 -0.36 1 2
Circadian rhythm 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
chromatin modification 0.037 0.05 -10000 0 -0.41 1 1
CLOCK 0.002 0.1 -10000 0 -0.42 28 28
TIMELESS/CRY2 0.026 0.047 -10000 0 -10000 0 0
DEC1/BMAL1 0.031 0.022 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
NR1D1 0.009 0.1 -10000 0 -1.3 3 3
ARNTL 0.025 0.015 -10000 0 -10000 0 0
TIMELESS 0.013 0.041 -10000 0 -10000 0 0
NPAS2 0.021 0.052 -10000 0 -0.43 6 6
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 0.078 -10000 0 -0.26 31 31
BMAL1/CLOCK 0.005 0.11 -10000 0 -0.75 4 4
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 -10000 0 0
mol:NADPH 0.007 0.011 -10000 0 -0.13 3 3
PER1/TIMELESS 0.025 0.054 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.008 0.029 -10000 0 -0.13 11 11
Hedgehog signaling events mediated by Gli proteins

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
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 -0.44 27 29
GNAO1 0.022 0.045 -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) 0.012 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 -0.37 13 15
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 -0.29 9 9
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.072 -10000 0 -0.48 4 4
GLI2/Su(fu) 0.027 0.049 -10000 0 -0.62 1 1
FOXA2 0.012 0.093 -10000 0 -0.75 5 5
neural tube patterning 0.018 0.14 0.46 2 -0.44 27 29
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 -0.44 27 29
SUFU 0.018 0.018 -10000 0 -10000 0 0
LGALS3 0.012 0.053 -10000 0 -0.16 39 39
catabolic process 0.042 0.09 0.29 1 -0.58 3 4
GLI3A/CBP 0.004 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 -0.45 27 29
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 0.047 -10000 0 -0.26 3 3
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 -10000 0 0
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 -0.54 12 13
CREBBP 0.004 0.087 -10000 0 -0.32 31 31
Su(fu)/SIN3/HDAC complex -0.006 0.11 0.24 2 -0.35 19 21
Arf6 downstream pathway

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
PLAUR 0.013 0.066 -10000 0 -0.97 2 2
regulation of axonogenesis 0.002 0.055 0.28 9 -10000 0 9
myoblast fusion -0.008 0.041 0.35 4 -10000 0 4
mol:GTP 0.019 0.026 -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 0.034 0.024 -10000 0 -0.15 2 2
mol:GM1 0.008 0.018 -10000 0 -0.15 2 2
mol:Choline -0.009 0.065 -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 0.014 0.045 -10000 0 -0.24 7 7
substrate adhesion-dependent cell spreading 0.019 0.026 -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 0.026 -10000 0 -0.16 7 7
ARF6/GTP 0.019 0.026 -10000 0 -0.16 7 7
RhoA/GTP 0.035 0.023 -10000 0 -0.17 1 1
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 -0.004 0.075 -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 -0.002 0.055 -10000 0 -0.28 9 9
regulation of epithelial cell migration 0.019 0.026 -10000 0 -0.16 7 7
PLD2 0.016 0.026 -10000 0 -0.22 2 2
PIP5K1A -0.002 0.055 -10000 0 -0.28 9 9
mol:Phosphatidic acid -0.009 0.065 -10000 0 -0.24 34 34
Rac1/GTP 0.003 0.048 -10000 0 -0.37 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
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 -0.52 3 5
VEGFR2 homodimer/Frs2 0.028 0.052 -10000 0 -0.61 3 3
CAV1 0.006 0.051 -10000 0 -0.15 44 44
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 0.31 10 -0.45 4 14
mol:Ca2+ 0.019 0.06 0.36 1 -0.47 3 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.047 0.061 -10000 0 -0.54 3 3
RP11-342D11.1 0.008 0.058 -10000 0 -0.41 5 5
CDH5 0.025 0.012 -10000 0 -0.13 3 3
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 -0.27 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.059 0.081 0.29 3 -0.42 5 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.089 -10000 0 -0.59 3 3
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 0.066 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 46 46
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 0.046 0.06 -10000 0 -0.54 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.039 -10000 0 -0.43 3 3
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 0.3 3 -0.38 5 8
eNOS/Hsp90 0.053 0.068 0.29 3 -0.36 5 8
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.06 0.36 1 -0.47 3 4
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 0.033 -10000 0 -0.13 22 22
VEGFC 0.017 0.051 -10000 0 -0.21 18 18
FAK1/Vinculin 0.038 0.082 0.3 2 -0.53 5 7
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 0.048 0.072 -10000 0 -0.54 3 3
PTPN6 0.014 0.064 -10000 0 -0.34 14 14
EPAS1 0.03 0.029 -10000 0 -0.33 3 3
mol:L-citrulline 0.042 0.071 0.3 3 -0.38 5 8
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 -0.62 3 3
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 -0.41 3 8
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 -0.52 3 3
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.006 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 -10000 0 -0.54 3 3
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 -0.45 4 4
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 -0.5 4 4
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.014 0.062 0.36 1 -0.54 3 4
actin cytoskeleton reorganization 0.023 0.088 -10000 0 -0.58 3 3
PTK2 0.016 0.065 -10000 0 -0.57 3 3
EDG1 0.008 0.058 -10000 0 -0.41 5 5
mol:DAG 0.019 0.06 0.36 1 -0.47 3 4
CaM/Ca2+ 0.028 0.055 -10000 0 -0.44 3 3
MAP2K3 0.005 0.069 0.36 1 -0.51 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.065 0.088 -10000 0 -0.53 5 5
PLCG1 0.019 0.061 0.36 1 -0.48 3 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.055 0.052 -10000 0 -0.49 3 3
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
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 -0.57 3 3
cell migration 0.046 0.09 0.32 3 -0.51 6 9
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 -0.5 3 3
mol:NO 0.042 0.071 0.3 3 -0.38 5 8
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 0.075 0.32 2 -0.43 5 7
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 0.011 0.055 0.36 1 -0.39 3 4
PRKCB -0.001 0.071 0.36 2 -0.38 5 7
VCL 0.022 0.032 -10000 0 -0.43 2 2
VEGFA165/NRP1 0.029 0.059 -10000 0 -0.41 5 5
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 0.32 3 -0.42 5 8
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFC homodimer 0.017 0.051 -10000 0 -0.21 18 18
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 0.29 3 -0.56 4 7
MAP3K13 0.014 0.072 0.36 1 -0.47 4 5
PDPK1 0.026 0.061 0.27 2 -0.5 3 5
Arf6 trafficking events

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
SLC2A4 -0.019 0.13 -10000 0 -0.43 41 41
CLTC 0.024 0.054 -10000 0 -0.36 6 6
calcium ion-dependent exocytosis 0.012 0.05 -10000 0 -0.26 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 0.047 -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 90 90
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 -0.33 8 8
ASAP2/amphiphysin II 0.048 0.016 -10000 0 -0.23 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.008 0.079 -10000 0 -0.34 9 9
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 0.019 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 0.33 5 -10000 0 5
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 0.026 0.058 0.2 14 -0.28 6 20
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 0.006 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 9 9
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.004 0.065 -10000 0 -0.26 31 31
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 -0.34 5 5
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 -0.36 7 10
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 -0.34 4 4
Signaling events mediated by HDAC Class II

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
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 0.016 -9999 0 -10000 0 0
GATA2/HDAC5 0.03 0.049 -9999 0 -0.3 10 10
HDAC5/BCL6/BCoR 0.051 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 0.064 -9999 0 -0.43 10 10
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 -0.23 2 2
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 -0.094 0.19 -9999 0 -0.43 121 121
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 -0.13 7 7
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 -0.019 0.13 -9999 0 -0.26 119 119
HDAC4/ER alpha 0.026 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 -0.23 2 2
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 -0.26 25 25
HDAC6/HDAC11 0.037 0.017 -9999 0 -0.3 1 1
Ran/GTP/Exportin 1 0.043 0.019 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
MEF2C 0.019 0.04 -9999 0 -0.16 20 20
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
mTOR signaling pathway

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
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 0.044 0.24 5 -0.31 2 7
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 0.2 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.017 -10000 0 -0.16 1 1
TSC2 0.026 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.015 0.025 -10000 0 -0.16 1 1
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 0.14 3 -10000 0 3
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 -0.56 27 27
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.045 -10000 0 -10000 0 0
TSC1/TSC2 0.039 0.048 0.27 6 -10000 0 6
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 0.23 5 -0.28 2 7
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 25 -10000 0 25
EEF2 -0.008 0.033 0.18 10 -0.23 4 14
eIF4E/4E-BP1 0.016 0.14 -10000 0 -1 9 9
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 0.025 0.025 -9999 0 -10000 0 0
SMAD3/SMAD4 0.038 0.044 -9999 0 -0.43 3 3
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 -10000 0 0
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 -0.13 1 8
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 0.032 -10000 0 -0.43 2 2
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 -10000 0 0
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.007 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 -10000 0 0
ARF1/GDP/Membrin 0.022 0.019 -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 0.008 0.042 -10000 0 -0.19 7 7
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 0.045 -10000 0 -0.33 9 9
GBF1 0.004 0.046 -10000 0 -0.32 10 10
ARF1/GTP/Arfaptin 2 0.027 0.021 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.029 -10000 0 -0.23 2 2
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 -0.21 4 4
NFKB2 0.023 0.03 -9999 0 -0.43 2 2
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 -0.23 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 513 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 0.027 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/19437981/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LGG-TP/19775313/Gistic2_Analysis_19775882/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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