PARADIGM pathway analysis of mRNASeq expression and copy number data
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 61 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 119
IL23-mediated signaling events 114
Aurora B signaling 97
TCGA08_retinoblastoma 89
FOXM1 transcription factor network 83
Signaling events regulated by Ret tyrosine kinase 80
IL12-mediated signaling events 78
TCR signaling in naïve CD8+ T cells 78
Syndecan-1-mediated signaling events 77
Signaling mediated by p38-alpha and p38-beta 76
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 669 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 669 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 0.1779 119 839 7 -0.051 0 1000 -1000 -0.006 -1000
IL23-mediated signaling events 0.1704 114 6878 60 -0.55 0.027 1000 -1000 -0.075 -1000
Aurora B signaling 0.1450 97 6554 67 -0.31 0.042 1000 -1000 -0.031 -1000
TCGA08_retinoblastoma 0.1330 89 717 8 -0.039 0.057 1000 -1000 -0.001 -1000
FOXM1 transcription factor network 0.1241 83 4277 51 -0.33 0.026 1000 -1000 -0.1 -1000
Signaling events regulated by Ret tyrosine kinase 0.1196 80 6617 82 -0.096 0.027 1000 -1000 -0.053 -1000
IL12-mediated signaling events 0.1166 78 6840 87 -0.38 0.07 1000 -1000 -0.074 -1000
TCR signaling in naïve CD8+ T cells 0.1166 78 7288 93 -0.18 0.18 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 0.1151 77 2637 34 -0.12 0.027 1000 -1000 -0.031 -1000
Signaling mediated by p38-alpha and p38-beta 0.1136 76 3354 44 -0.11 0.027 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.1106 74 1947 26 -0.094 0.027 1000 -1000 -0.007 -1000
Syndecan-4-mediated signaling events 0.1076 72 4836 67 -0.13 0.037 1000 -1000 -0.039 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1046 70 4790 68 -0.28 0.13 1000 -1000 -0.077 -1000
E-cadherin signaling events 0.1046 70 350 5 -0.051 0.027 1000 -1000 0.011 -1000
a4b1 and a4b7 Integrin signaling 0.1016 68 343 5 -0.022 0.002 1000 -1000 0.008 -1000
Glypican 2 network 0.1016 68 272 4 -0.02 0.006 1000 -1000 0.01 -1000
Reelin signaling pathway 0.0957 64 3590 56 -0.12 0.062 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 0.0942 63 6662 105 -0.14 0.035 1000 -1000 -0.04 -1000
Endothelins 0.0942 63 6100 96 -0.14 0.027 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.0912 61 4699 76 -0.16 0.051 1000 -1000 -0.055 -1000
Osteopontin-mediated events 0.0867 58 2220 38 -0.1 0.027 1000 -1000 -0.027 -1000
Signaling events mediated by the Hedgehog family 0.0852 57 2980 52 -0.1 0.049 1000 -1000 -0.036 -1000
amb2 Integrin signaling 0.0807 54 4456 82 -0.14 0.03 1000 -1000 -0.034 -1000
IL4-mediated signaling events 0.0777 52 4766 91 -0.55 0.35 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0762 51 3166 62 -0.12 0.049 1000 -1000 -0.023 -1000
FOXA2 and FOXA3 transcription factor networks 0.0762 51 2356 46 -0.23 0.029 1000 -1000 -0.096 -1000
Aurora C signaling 0.0747 50 352 7 -0.09 0.011 1000 -1000 -0.012 -1000
Caspase cascade in apoptosis 0.0732 49 3678 74 -0.13 0.041 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0717 48 3127 65 -0.12 0.038 1000 -1000 -0.055 -1000
p75(NTR)-mediated signaling 0.0703 47 5993 125 -0.1 0.068 1000 -1000 -0.048 -1000
PLK1 signaling events 0.0703 47 4030 85 -0.12 0.039 1000 -1000 -0.032 -1000
IL1-mediated signaling events 0.0703 47 2955 62 -0.099 0.046 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0703 47 3509 74 -0.1 0.054 1000 -1000 -0.053 -1000
Rapid glucocorticoid signaling 0.0688 46 925 20 -0.075 0.029 1000 -1000 -0.005 -1000
Glypican 1 network 0.0673 45 2178 48 -0.11 0.048 1000 -1000 -0.024 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0673 45 2340 52 -0.12 0.062 1000 -1000 -0.035 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0673 45 4023 88 -0.13 0.027 1000 -1000 -0.061 -1000
Ras signaling in the CD4+ TCR pathway 0.0673 45 777 17 -0.056 0.041 1000 -1000 -0.023 -1000
Visual signal transduction: Cones 0.0658 44 1689 38 -0.069 0.029 1000 -1000 -0.008 -1000
PDGFR-alpha signaling pathway 0.0658 44 1955 44 -0.084 0.029 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0658 44 2563 58 -0.11 0.051 1000 -1000 -0.051 -1000
Calcium signaling in the CD4+ TCR pathway 0.0658 44 1365 31 -0.14 0.025 1000 -1000 -0.037 -1000
Visual signal transduction: Rods 0.0658 44 2334 52 -0.082 0.027 1000 -1000 -0.025 -1000
Syndecan-3-mediated signaling events 0.0643 43 1524 35 -0.1 0.068 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0628 42 3580 85 -0.13 0.032 1000 -1000 -0.045 -1000
BCR signaling pathway 0.0613 41 4107 99 -0.098 0.051 1000 -1000 -0.044 -1000
LPA receptor mediated events 0.0598 40 4145 102 -0.14 0.03 1000 -1000 -0.057 -1000
Ceramide signaling pathway 0.0583 39 3036 76 -0.07 0.039 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 0.0583 39 839 21 -0.026 0.038 1000 -1000 -0.033 -1000
Fc-epsilon receptor I signaling in mast cells 0.0568 38 3701 97 -0.098 0.039 1000 -1000 -0.054 -1000
Glucocorticoid receptor regulatory network 0.0568 38 4355 114 -0.28 0.18 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 0.0568 38 2008 52 -0.053 0.039 1000 -1000 -0.027 -1000
Wnt signaling 0.0568 38 271 7 -0.011 0.014 1000 -1000 -0.012 -1000
IL6-mediated signaling events 0.0568 38 2917 75 -0.16 0.044 1000 -1000 -0.045 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0553 37 2016 54 -0.065 0.034 1000 -1000 -0.034 -1000
BMP receptor signaling 0.0553 37 3028 81 -0.081 0.047 1000 -1000 -0.039 -1000
Ephrin B reverse signaling 0.0538 36 1736 48 -0.032 0.032 1000 -1000 -0.022 -1000
TCGA08_p53 0.0523 35 251 7 -0.023 0.026 1000 -1000 -0.006 -1000
IL2 signaling events mediated by STAT5 0.0523 35 781 22 -0.093 0.029 1000 -1000 -0.039 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0508 34 1283 37 -0.037 0.039 1000 -1000 -0.019 -1000
E-cadherin signaling in the nascent adherens junction 0.0508 34 2587 76 -0.051 0.047 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 0.0478 32 560 17 -0.052 0.027 1000 -1000 -0.038 -1000
Regulation of nuclear SMAD2/3 signaling 0.0463 31 4250 136 -0.3 0.22 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0463 31 3737 120 -0.11 0.074 1000 -1000 -0.042 -1000
IL2 signaling events mediated by PI3K 0.0448 30 1771 58 -0.069 0.044 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 0.0448 30 1318 43 -0.051 0.028 1000 -1000 -0.024 -1000
EPHB forward signaling 0.0433 29 2468 85 -0.032 0.057 1000 -1000 -0.047 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0419 28 967 34 -0.012 0.037 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 0.0419 28 1997 69 -0.1 0.044 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 0.0419 28 1323 47 -0.15 0.041 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 0.0404 27 333 12 -0.022 0.006 1000 -1000 -0.013 -1000
Coregulation of Androgen receptor activity 0.0404 27 2105 76 -0.085 0.052 1000 -1000 -0.019 -1000
PLK2 and PLK4 events 0.0404 27 81 3 0.005 -1000 1000 -1000 -0.002 -1000
Presenilin action in Notch and Wnt signaling 0.0404 27 1669 61 -0.14 0.068 1000 -1000 -0.037 -1000
S1P1 pathway 0.0404 27 1006 36 -0.1 0.027 1000 -1000 -0.037 -1000
Integrins in angiogenesis 0.0404 27 2293 84 -0.05 0.055 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 0.0404 27 725 26 -0.06 0.071 1000 -1000 -0.008 -1000
Signaling events mediated by PTP1B 0.0389 26 1981 76 -0.16 0.038 1000 -1000 -0.03 -1000
Canonical Wnt signaling pathway 0.0389 26 1342 51 -0.14 0.081 1000 -1000 -0.055 -1000
Noncanonical Wnt signaling pathway 0.0374 25 671 26 -0.052 0.027 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0374 25 1994 78 -0.015 0.046 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 0.0359 24 945 39 -0.1 0.032 1000 -1000 -0.018 -1000
S1P5 pathway 0.0359 24 417 17 -0.041 0.027 1000 -1000 -0.015 -1000
Paxillin-dependent events mediated by a4b1 0.0344 23 849 36 -0.031 0.047 1000 -1000 -0.032 -1000
IL27-mediated signaling events 0.0344 23 1218 51 -0.1 0.027 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class III 0.0329 22 885 40 -0.054 0.049 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.0329 22 1909 86 -0.075 0.042 1000 -1000 -0.053 -1000
S1P4 pathway 0.0329 22 560 25 -0.041 0.05 1000 -1000 -0.021 -1000
EPO signaling pathway 0.0314 21 1182 55 -0.077 0.073 1000 -1000 -0.04 -1000
Nectin adhesion pathway 0.0314 21 1381 63 -0.051 0.062 1000 -1000 -0.047 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0299 20 1735 83 -0.089 0.053 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0284 19 626 32 -0.039 0.053 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0269 18 527 28 -0.041 0.033 1000 -1000 -0.017 -1000
ceramide signaling pathway 0.0269 18 891 49 -0.054 0.038 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 0.0269 18 1009 54 -0.068 0.055 1000 -1000 -0.044 -1000
Regulation of Androgen receptor activity 0.0269 18 1316 70 -0.077 0.036 1000 -1000 -0.047 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0254 17 564 33 -0.034 0.066 1000 -1000 -0.033 -1000
BARD1 signaling events 0.0239 16 924 57 -0.045 0.056 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0239 16 784 48 0 0.064 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0239 16 720 45 -0.054 0.052 1000 -1000 -0.047 -1000
ErbB4 signaling events 0.0224 15 1087 69 -0.067 0.035 1000 -1000 -0.036 -1000
Signaling mediated by p38-gamma and p38-delta 0.0224 15 230 15 -0.008 0.026 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0224 15 485 31 -0.031 0.039 1000 -1000 -0.015 -1000
Regulation of Telomerase 0.0224 15 1554 102 -0.11 0.07 1000 -1000 -0.046 -1000
Insulin Pathway 0.0209 14 1101 74 -0.11 0.063 1000 -1000 -0.034 -1000
S1P3 pathway 0.0209 14 604 42 -0.013 0.033 1000 -1000 -0.037 -1000
Signaling events mediated by PRL 0.0209 14 490 34 -0.038 0.035 1000 -1000 -0.024 -1000
Aurora A signaling 0.0194 13 820 60 -0.092 0.061 1000 -1000 -0.018 -1000
Arf6 downstream pathway 0.0194 13 590 43 -0.03 0.039 1000 -1000 -0.019 -1000
Class I PI3K signaling events mediated by Akt 0.0194 13 892 68 -0.033 0.049 1000 -1000 -0.024 -1000
Class I PI3K signaling events 0.0194 13 1010 73 -0.05 0.048 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 0.0179 12 526 43 -0.05 0.052 1000 -1000 -0.05 -1000
IGF1 pathway 0.0179 12 687 57 -0.02 0.059 1000 -1000 -0.043 -1000
IFN-gamma pathway 0.0164 11 815 68 -0.1 0.059 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 0.0164 11 1096 97 -0.05 0.074 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0164 11 494 44 -0.019 0.042 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 0.0149 10 397 39 -0.054 0.061 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0149 10 667 65 -0.017 0.061 1000 -1000 -0.046 -1000
VEGFR1 specific signals 0.0149 10 594 56 -0.025 0.038 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.0135 9 478 53 -0.005 0.048 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class I 0.0135 9 965 104 -0.054 0.061 1000 -1000 -0.03 -1000
FoxO family signaling 0.0135 9 590 64 -0.032 0.085 1000 -1000 -0.045 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0135 9 1146 125 -0.032 0.064 1000 -1000 -0.045 -1000
Arf6 trafficking events 0.0120 8 604 71 -0.067 0.049 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class II 0.0090 6 454 75 -0.07 0.069 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0090 6 133 22 -0.009 0.047 1000 -1000 -0.024 -1000
Class IB PI3K non-lipid kinase events 0.0090 6 18 3 -0.022 0.022 1000 -1000 -0.007 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0030 2 56 23 0 0.051 1000 -1000 -0.021 -1000
Arf1 pathway 0.0015 1 101 54 -0.01 0.043 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 0.0015 1 19 13 0 0.062 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 14 27 0 0.063 1000 -1000 -0.026 -1000
Total NA 4593 255242 7203 -12 -990 131000 -131000 -4.4 -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 -0.042 0.14 -10000 0 -0.26 168 168
EFNA5 -0.022 0.14 -10000 0 -0.37 82 82
FYN -0.046 0.13 0.18 1 -0.28 125 126
neuron projection morphogenesis -0.042 0.14 -10000 0 -0.26 168 168
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.042 0.14 -10000 0 -0.27 168 168
EPHA5 -0.051 0.17 -10000 0 -0.38 127 127
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 -0.49 0.53 -9999 0 -1.2 177 177
IL23A -0.48 0.52 -9999 0 -1.2 181 181
NF kappa B1 p50/RelA/I kappa B alpha -0.44 0.51 -9999 0 -1.2 174 174
positive regulation of T cell mediated cytotoxicity -0.51 0.58 -9999 0 -1.3 176 176
ITGA3 -0.45 0.48 -9999 0 -1.2 156 156
IL17F -0.3 0.3 -9999 0 -0.71 166 166
IL12B -0.026 0.042 -9999 0 -0.26 4 4
STAT1 (dimer) -0.49 0.55 -9999 0 -1.3 176 176
CD4 -0.43 0.47 -9999 0 -1.1 154 154
IL23 -0.46 0.5 -9999 0 -1.2 179 179
IL23R -0.17 0.34 -9999 0 -1.1 72 72
IL1B -0.52 0.57 -9999 0 -1.3 185 185
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.44 0.47 -9999 0 -1.1 157 157
TYK2 -0.011 0.03 -9999 0 -10000 0 0
STAT4 -0.059 0.16 -9999 0 -0.33 160 160
STAT3 0.027 0.002 -9999 0 -10000 0 0
IL18RAP -0.027 0.14 -9999 0 -0.33 101 101
IL12RB1 -0.033 0.1 -9999 0 -0.45 34 34
PIK3CA 0.026 0.004 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.025 0.082 -9999 0 -0.34 32 32
IL23R/JAK2 -0.16 0.33 -9999 0 -1.1 63 63
positive regulation of chronic inflammatory response -0.51 0.58 -9999 0 -1.3 176 176
natural killer cell activation 0.007 0.007 -9999 0 -10000 0 0
JAK2 -0.014 0.037 -9999 0 -10000 0 0
PIK3R1 0.027 0.003 -9999 0 -10000 0 0
NFKB1 0.024 0.004 -9999 0 -10000 0 0
RELA 0.024 0.004 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.44 0.46 -9999 0 -1.1 184 184
ALOX12B -0.51 0.54 -9999 0 -1.2 215 215
CXCL1 -0.49 0.52 -9999 0 -1.2 184 184
T cell proliferation -0.51 0.58 -9999 0 -1.3 176 176
NFKBIA 0.024 0.005 -9999 0 -10000 0 0
IL17A -0.23 0.24 -9999 0 -0.55 153 153
PI3K -0.46 0.52 -9999 0 -1.2 173 173
IFNG -0.018 0.03 -9999 0 -0.11 22 22
STAT3 (dimer) -0.43 0.49 -9999 0 -1.1 170 170
IL18R1 -0.007 0.11 -9999 0 -0.32 66 66
IL23/IL23R/JAK2/TYK2/SOCS3 -0.3 0.36 -9999 0 -0.8 147 147
IL18/IL18R -0.015 0.14 -9999 0 -0.3 107 107
macrophage activation -0.023 0.019 -9999 0 -0.044 167 167
TNF -0.5 0.55 -9999 0 -1.3 179 179
STAT3/STAT4 -0.49 0.53 -9999 0 -1.2 185 185
STAT4 (dimer) -0.52 0.56 -9999 0 -1.3 185 185
IL18 0.001 0.1 -9999 0 -0.37 44 44
IL19 -0.44 0.47 -9999 0 -1.1 154 154
STAT5A (dimer) -0.49 0.55 -9999 0 -1.3 176 176
STAT1 0.021 0.037 -9999 0 -0.22 15 15
SOCS3 -0.077 0.16 -9999 0 -0.3 206 206
CXCL9 -0.53 0.55 -9999 0 -1.2 204 204
MPO -0.5 0.53 -9999 0 -1.2 187 187
positive regulation of humoral immune response -0.51 0.58 -9999 0 -1.3 176 176
IL23/IL23R/JAK2/TYK2 -0.55 0.68 -9999 0 -1.5 172 172
IL6 -0.47 0.54 -9999 0 -1.2 171 171
STAT5A 0.019 0.063 -9999 0 -0.46 11 11
IL2 0.015 0.015 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.007 -9999 0 -10000 0 0
CD3E -0.5 0.54 -9999 0 -1.2 185 185
keratinocyte proliferation -0.51 0.58 -9999 0 -1.3 176 176
NOS2 -0.46 0.49 -9999 0 -1.2 165 165
Aurora B signaling

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.091 0.22 -10000 0 -0.56 104 104
STMN1 -0.06 0.13 -10000 0 -0.32 113 113
Aurora B/RasGAP/Survivin -0.088 0.21 -10000 0 -0.37 206 206
Chromosomal passenger complex/Cul3 protein complex -0.09 0.16 -10000 0 -0.35 152 152
BIRC5 -0.099 0.19 -10000 0 -0.36 214 214
DES -0.31 0.49 -10000 0 -0.92 228 228
Aurora C/Aurora B/INCENP -0.034 0.12 -10000 0 -0.26 123 123
Aurora B/TACC1 -0.037 0.12 -10000 0 -0.22 185 185
Aurora B/PP2A -0.047 0.14 -10000 0 -0.26 191 191
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.021 0.063 -10000 0 -0.15 116 116
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.12 0.22 0.13 1 -0.39 231 232
Cul3 protein complex 0.042 0.034 -10000 0 -0.28 2 2
KIF2C -0.13 0.3 -10000 0 -0.59 142 142
PEBP1 0.018 0.025 -10000 0 -0.48 1 1
KIF20A -0.12 0.2 -10000 0 -0.35 253 253
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.047 0.14 -10000 0 -0.25 199 199
SEPT1 0.026 0.014 -10000 0 -0.22 2 2
SMC2 0.026 0.004 -10000 0 -10000 0 0
SMC4 0.016 0.051 -10000 0 -0.22 29 29
NSUN2/NPM1/Nucleolin -0.14 0.32 -10000 0 -0.81 118 118
PSMA3 0.026 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.049 0.12 -10000 0 -0.31 112 112
AURKB -0.091 0.2 -10000 0 -0.37 201 201
AURKC 0.011 0.064 -10000 0 -0.29 26 26
CDCA8 -0.036 0.12 -10000 0 -0.28 117 117
cytokinesis -0.21 0.38 0.2 1 -0.82 151 152
Aurora B/Septin1 -0.18 0.36 -10000 0 -0.78 143 143
AURKA 0.007 0.067 -10000 0 -0.23 48 48
INCENP 0.015 0.034 -10000 0 -0.48 2 2
KLHL13 0.025 0.027 -10000 0 -0.46 2 2
BUB1 -0.066 0.17 -10000 0 -0.34 166 166
hSgo1/Aurora B/Survivin -0.13 0.26 -10000 0 -0.43 237 237
EVI5 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.16 0.33 -10000 0 -0.64 168 168
SGOL1 -0.073 0.17 -10000 0 -0.33 183 183
CENPA -0.14 0.28 -10000 0 -0.63 136 136
NCAPG -0.078 0.18 -10000 0 -0.36 176 176
Aurora B/HC8 Proteasome -0.048 0.14 -10000 0 -0.26 190 190
NCAPD2 0.026 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.048 0.14 -10000 0 -0.33 113 113
RHOA 0.027 0.003 -10000 0 -10000 0 0
NCAPH -0.036 0.15 -10000 0 -0.34 111 111
NPM1 -0.096 0.22 -10000 0 -0.54 120 120
RASA1 0.027 0.003 -10000 0 -10000 0 0
KLHL9 0.023 0.01 -10000 0 -10000 0 0
mitotic prometaphase -0.005 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.048 0.14 -10000 0 -0.26 190 190
PPP1CC 0.027 0.003 -10000 0 -10000 0 0
Centraspindlin -0.18 0.37 -10000 0 -0.67 185 185
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
NSUN2 -0.096 0.21 -10000 0 -0.53 122 122
MYLK -0.055 0.13 -10000 0 -0.31 122 122
KIF23 -0.076 0.17 -10000 0 -0.33 188 188
VIM -0.1 0.18 -10000 0 -0.32 230 230
RACGAP1 0.02 0.019 -10000 0 -0.23 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.096 0.22 -10000 0 -0.55 119 119
Chromosomal passenger complex -0.17 0.34 -10000 0 -0.63 177 177
Chromosomal passenger complex/EVI5 -0.086 0.23 -10000 0 -0.39 206 206
TACC1 0.026 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.002 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.082 -10000 0 -0.31 37 37
CDKN2C -0.001 0.072 -10000 0 -0.2 68 68
CDKN2A -0.025 0.11 -10000 0 -0.28 94 94
CCND2 0.022 0.073 0.2 82 -0.11 3 85
RB1 -0.039 0.097 0.13 1 -0.24 114 115
CDK4 0.026 0.082 0.22 82 -10000 0 82
CDK6 0.023 0.083 0.22 81 -0.15 10 91
G1/S progression 0.057 0.11 0.25 143 -0.21 2 145
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 -0.21 0.52 -9999 0 -1.2 106 106
PLK1 -0.004 0.18 -9999 0 -1.3 11 11
BIRC5 -0.23 0.55 -9999 0 -1.5 105 105
HSPA1B -0.22 0.52 -9999 0 -1.2 106 106
MAP2K1 0.011 0.046 -9999 0 -10000 0 0
BRCA2 -0.23 0.54 -9999 0 -1.2 109 109
FOXM1 -0.33 0.76 -9999 0 -1.8 113 113
XRCC1 -0.21 0.52 -9999 0 -1.2 102 102
FOXM1B/p19 -0.24 0.51 -9999 0 -1.2 104 104
Cyclin D1/CDK4 -0.2 0.47 -9999 0 -1.1 113 113
CDC2 -0.23 0.55 -9999 0 -1.3 113 113
TGFA -0.19 0.46 -9999 0 -1 116 116
SKP2 -0.22 0.52 -9999 0 -1.2 108 108
CCNE1 0.022 0.021 -9999 0 -0.23 3 3
CKS1B -0.22 0.52 -9999 0 -1.2 116 116
RB1 -0.11 0.34 -9999 0 -0.94 63 63
FOXM1C/SP1 -0.26 0.62 -9999 0 -1.4 115 115
AURKB -0.25 0.58 -9999 0 -1.5 118 118
CENPF -0.23 0.55 -9999 0 -1.3 112 112
CDK4 0.016 0.026 -9999 0 -0.23 1 1
MYC -0.19 0.45 -9999 0 -1 112 112
CHEK2 0.003 0.072 -9999 0 -0.3 19 19
ONECUT1 -0.21 0.5 -9999 0 -1.1 116 116
CDKN2A -0.024 0.12 -9999 0 -0.29 94 94
LAMA4 -0.22 0.52 -9999 0 -1.2 106 106
FOXM1B/HNF6 -0.26 0.62 -9999 0 -1.4 116 116
FOS -0.27 0.57 -9999 0 -1.2 145 145
SP1 0.026 0.008 -9999 0 -10000 0 0
CDC25B -0.21 0.52 -9999 0 -1.2 104 104
response to radiation -0.001 0.029 -9999 0 -10000 0 0
CENPB -0.21 0.52 -9999 0 -1.2 105 105
CENPA -0.26 0.57 -9999 0 -1.3 116 116
NEK2 -0.27 0.59 -9999 0 -1.3 125 125
HIST1H2BA -0.22 0.52 -9999 0 -1.2 104 104
CCNA2 -0.021 0.12 -9999 0 -0.31 93 93
EP300 0.024 0.033 -9999 0 -0.46 3 3
CCNB1/CDK1 -0.27 0.63 -9999 0 -1.5 110 110
CCNB2 -0.28 0.6 -9999 0 -1.4 128 128
CCNB1 -0.23 0.55 -9999 0 -1.3 112 112
ETV5 -0.23 0.53 -9999 0 -1.2 120 120
ESR1 -0.22 0.53 -9999 0 -1.2 112 112
CCND1 -0.2 0.48 -9999 0 -1.1 114 114
GSK3A 0.013 0.039 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.007 0.11 -9999 0 -0.33 34 34
CDK2 0.019 0.051 -9999 0 -0.33 12 12
G2/M transition of mitotic cell cycle -0.003 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.24 0.58 -9999 0 -1.3 114 114
GAS1 -0.22 0.52 -9999 0 -1.2 108 108
MMP2 -0.22 0.52 -9999 0 -1.2 106 106
RB1/FOXM1C -0.22 0.51 -9999 0 -1.2 114 114
CREBBP 0.026 0.019 -9999 0 -0.46 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.013 0.075 -10000 0 -0.47 10 10
Crk/p130 Cas/Paxillin -0.083 0.12 -10000 0 -0.3 125 125
JUN -0.068 0.14 -10000 0 -0.42 65 65
HRAS 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.058 0.16 -10000 0 -0.31 143 143
RAP1A 0.024 0.009 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.018 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.072 0.17 -10000 0 -0.32 178 178
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.14 -10000 0 -0.29 131 131
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.067 0.15 -10000 0 -0.29 170 170
GRB7 0.004 0.066 -10000 0 -0.22 52 52
RET51/GFRalpha1/GDNF -0.068 0.17 -10000 0 -0.31 169 169
MAPKKK cascade -0.075 0.15 -10000 0 -0.3 160 160
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.04 0.14 -10000 0 -0.29 134 134
lamellipodium assembly -0.052 0.12 -10000 0 -0.27 109 109
RET51/GFRalpha1/GDNF/SHC -0.072 0.17 -10000 0 -0.32 174 174
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.039 0.14 -10000 0 -0.29 129 129
RET9/GFRalpha1/GDNF/Shank3 -0.041 0.14 -10000 0 -0.29 133 133
MAPK3 -0.077 0.14 -10000 0 -0.33 91 91
DOK1 0.026 0.019 -10000 0 -0.46 1 1
DOK6 -0.06 0.18 -10000 0 -0.43 125 125
PXN 0.027 0.003 -10000 0 -10000 0 0
neurite development -0.085 0.15 -10000 0 -0.37 98 98
DOK5 0.017 0.065 -10000 0 -0.46 12 12
GFRA1 -0.059 0.17 -10000 0 -0.37 138 138
MAPK8 -0.069 0.15 -10000 0 -0.29 173 173
HRAS/GTP -0.077 0.18 -10000 0 -0.33 170 170
tube development -0.033 0.13 0.21 13 -0.27 131 144
MAPK1 -0.077 0.14 -10000 0 -0.33 91 91
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.12 -10000 0 -0.27 122 122
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.024 0.027 -10000 0 -0.46 2 2
PDLIM7 0.022 0.035 -10000 0 -0.22 13 13
RET51/GFRalpha1/GDNF/Dok6 -0.096 0.21 -10000 0 -0.36 201 201
SHC1 0.022 0.035 -10000 0 -0.22 13 13
RET51/GFRalpha1/GDNF/Dok4 -0.074 0.17 -10000 0 -0.32 180 180
RET51/GFRalpha1/GDNF/Dok5 -0.073 0.17 -10000 0 -0.32 178 178
PRKCA 0.025 0.027 -10000 0 -0.46 2 2
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
CREB1 -0.067 0.16 -10000 0 -0.37 108 108
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.044 0.12 -10000 0 -0.28 123 123
RET51/GFRalpha1/GDNF/Grb7 -0.083 0.18 -10000 0 -0.33 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.05 0.16 -10000 0 -0.36 128 128
DOK4 0.022 0.05 -10000 0 -0.46 7 7
JNK cascade -0.067 0.14 -10000 0 -0.41 66 66
RET9/GFRalpha1/GDNF/FRS2 -0.037 0.14 -10000 0 -0.29 127 127
SHANK3 0.02 0.047 -10000 0 -0.3 12 12
RASA1 0.027 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.043 0.12 -10000 0 -0.27 124 124
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.076 0.16 -10000 0 -0.3 188 188
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.079 0.16 -10000 0 -0.3 200 200
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.071 0.17 -10000 0 -0.32 166 166
PI3K -0.09 0.19 -10000 0 -0.42 132 132
SOS1 0.027 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.029 0.14 -10000 0 -0.27 131 131
GRB10 0.02 0.033 -10000 0 -0.32 5 5
activation of MAPKK activity -0.066 0.16 -10000 0 -0.34 129 129
RET51/GFRalpha1/GDNF/FRS2 -0.07 0.17 -10000 0 -0.31 173 173
GAB1 0.026 0.019 -10000 0 -0.46 1 1
IRS1 0.022 0.05 -10000 0 -0.46 7 7
IRS2 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.073 0.17 -10000 0 -0.32 166 166
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.17 -10000 0 -0.32 176 176
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GDNF -0.027 0.15 -10000 0 -0.42 78 78
RAC1 0.023 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.074 0.18 -10000 0 -0.32 180 180
Rac1/GTP -0.057 0.14 -10000 0 -0.32 108 108
RET9/GFRalpha1/GDNF -0.055 0.14 -10000 0 -0.31 131 131
GFRalpha1/GDNF -0.063 0.17 -10000 0 -0.37 131 131
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 -0.071 0.13 -10000 0 -0.37 64 64
TBX21 -0.32 0.43 -10000 0 -0.99 150 150
B2M 0.021 0.038 -10000 0 -0.24 12 12
TYK2 -0.002 0.032 -10000 0 -10000 0 0
IL12RB1 -0.024 0.1 -10000 0 -0.44 34 34
GADD45B -0.23 0.34 -10000 0 -0.83 98 98
IL12RB2 -0.047 0.12 -10000 0 -0.3 104 104
GADD45G -0.26 0.39 -10000 0 -0.96 112 112
natural killer cell activation -0.013 0.02 0.05 2 -0.041 125 127
RELB 0.021 0.03 -10000 0 -0.26 6 6
RELA 0.027 0.003 -10000 0 -10000 0 0
IL18 -0.006 0.11 -10000 0 -0.38 44 44
IL2RA -0.066 0.16 -10000 0 -0.32 166 166
IFNG 0.016 0.022 -10000 0 -0.22 5 5
STAT3 (dimer) -0.25 0.32 -10000 0 -0.71 163 163
HLA-DRB5 -0.001 0.005 -10000 0 -0.021 31 31
FASLG -0.3 0.39 -10000 0 -0.96 121 121
NF kappa B2 p52/RelB -0.29 0.4 -10000 0 -0.83 176 176
CD4 0.02 0.031 -10000 0 -0.26 6 6
SOCS1 -0.009 0.099 -10000 0 -0.26 81 81
EntrezGene:6955 -0.001 0.008 -10000 0 -0.026 39 39
CD3D -0.067 0.16 -10000 0 -0.33 164 164
CD3E -0.07 0.17 -10000 0 -0.34 170 170
CD3G -0.002 0.07 -10000 0 -0.23 56 56
IL12Rbeta2/JAK2 -0.033 0.096 -10000 0 -0.26 64 64
CCL3 -0.38 0.52 -10000 0 -1.2 169 169
CCL4 -0.37 0.51 -10000 0 -1.2 153 153
HLA-A 0 0.005 -10000 0 -0.044 6 6
IL18/IL18R -0.031 0.15 -10000 0 -0.32 107 107
NOS2 -0.28 0.4 -10000 0 -0.95 124 124
IL12/IL12R/TYK2/JAK2/SPHK2 -0.059 0.12 -10000 0 -0.36 53 53
IL1R1 -0.31 0.41 -10000 0 -0.96 139 139
IL4 0.021 0.035 -10000 0 -0.19 3 3
JAK2 -0.001 0.032 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -0.025 36 36
TCR/CD3/MHC I/CD8 -0.074 0.18 -10000 0 -0.48 65 65
RAB7A -0.19 0.29 -10000 0 -0.73 82 82
lysosomal transport -0.18 0.28 -10000 0 -0.69 85 85
FOS -0.23 0.42 -10000 0 -1.2 80 80
STAT4 (dimer) -0.28 0.36 -10000 0 -0.78 170 170
STAT5A (dimer) -0.29 0.4 -10000 0 -0.85 177 177
GZMA -0.38 0.5 -10000 0 -1.1 171 171
GZMB -0.35 0.47 -10000 0 -1 170 170
HLX 0.021 0.045 -10000 0 -0.32 10 10
LCK -0.34 0.44 -10000 0 -0.91 188 188
TCR/CD3/MHC II/CD4 -0.059 0.12 -10000 0 -0.26 110 110
IL2/IL2R -0.065 0.15 -10000 0 -0.28 190 190
MAPK14 -0.24 0.35 -10000 0 -0.8 129 129
CCR5 -0.29 0.42 -10000 0 -1.1 109 109
IL1B -0.1 0.18 -10000 0 -0.37 189 189
STAT6 -0.076 0.11 -10000 0 -0.45 9 9
STAT4 -0.059 0.16 -10000 0 -0.33 160 160
STAT3 0.027 0.002 -10000 0 -10000 0 0
STAT1 0.021 0.037 -10000 0 -0.22 15 15
NFKB1 0.027 0.003 -10000 0 -10000 0 0
NFKB2 0.023 0.021 -10000 0 -0.46 1 1
IL12B -0.012 0.038 -10000 0 -0.26 4 4
CD8A -0.023 0.14 -10000 0 -0.35 87 87
CD8B -0.002 0.1 -10000 0 -0.35 51 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.07 0.13 0.36 64 -10000 0 64
IL2RB -0.048 0.15 -10000 0 -0.33 136 136
proteasomal ubiquitin-dependent protein catabolic process -0.25 0.33 0.38 1 -0.71 170 171
IL2RG -0.003 0.1 -10000 0 -0.32 57 57
IL12 -0.015 0.07 -10000 0 -0.31 19 19
STAT5A 0.019 0.063 -10000 0 -0.46 11 11
CD247 0.007 0.077 -10000 0 -0.31 33 33
IL2 0.015 0.003 -10000 0 -10000 0 0
SPHK2 0.024 0.009 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.013 0.079 -10000 0 -0.42 19 19
IL12/IL12R/TYK2/JAK2 -0.34 0.48 -10000 0 -0.97 183 183
MAP2K3 -0.24 0.35 -10000 0 -0.79 136 136
RIPK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K6 -0.24 0.35 -10000 0 -0.79 136 136
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.023 35 35
IL18RAP -0.035 0.14 -10000 0 -0.34 101 101
IL12Rbeta1/TYK2 -0.015 0.087 -10000 0 -0.34 31 31
EOMES 0.005 0.16 -10000 0 -1.1 10 10
STAT1 (dimer) -0.24 0.31 -10000 0 -0.7 153 153
T cell proliferation -0.2 0.27 -10000 0 -0.58 159 159
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.014 0.11 -10000 0 -0.33 66 66
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.23 0.29 -10000 0 -0.65 158 158
ATF2 -0.22 0.32 -10000 0 -0.75 127 127
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 -0.07 0.18 0.22 7 -0.4 105 112
FYN -0.1 0.21 0.22 11 -0.47 124 135
LAT/GRAP2/SLP76 -0.095 0.19 0.2 3 -0.41 129 132
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.076 0.16 0.2 15 -0.34 126 141
B2M 0.018 0.039 -10000 0 -0.25 12 12
IKBKG -0.017 0.05 0.088 13 -0.12 50 63
MAP3K8 0.015 0.05 -10000 0 -0.24 21 21
mol:Ca2+ -0.017 0.027 0.087 12 -0.076 56 68
integrin-mediated signaling pathway 0.027 0.037 -10000 0 -0.26 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.21 0.23 10 -0.46 131 141
TRPV6 0.18 0.51 1.1 135 -0.47 47 182
CD28 -0.034 0.14 -10000 0 -0.33 108 108
SHC1 -0.1 0.21 0.22 11 -0.45 129 140
receptor internalization -0.081 0.17 0.2 1 -0.4 108 109
PRF1 -0.18 0.36 -10000 0 -0.86 116 116
KRAS 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.059 0.13 0.2 9 -0.29 110 119
LAT -0.11 0.21 0.21 9 -0.46 129 138
EntrezGene:6955 -0.002 0.005 -10000 0 -10000 0 0
CD3D -0.069 0.16 -10000 0 -0.33 164 164
CD3E -0.071 0.17 -10000 0 -0.34 170 170
CD3G -0.005 0.07 -10000 0 -0.23 56 56
RASGRP2 -0.003 0.018 -10000 0 -0.15 2 2
RASGRP1 -0.082 0.17 0.24 15 -0.35 130 145
HLA-A -0.003 0.006 -10000 0 -10000 0 0
RASSF5 0.018 0.06 -10000 0 -0.39 13 13
RAP1A/GTP/RAPL 0.027 0.038 -10000 0 -0.26 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.061 0.14 36 -0.11 34 70
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.047 0.068 -10000 0 -0.19 86 86
PRKCA -0.05 0.096 0.17 7 -0.23 93 100
GRAP2 -0.003 0.1 -10000 0 -0.34 51 51
mol:IP3 -0.076 0.15 0.2 25 -0.34 117 142
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.078 0.16 -10000 0 -0.39 96 96
ORAI1 -0.16 0.41 0.61 3 -0.96 133 136
CSK -0.1 0.21 0.22 9 -0.44 140 149
B7 family/CD28 -0.11 0.24 0.24 2 -0.47 156 158
CHUK 0.024 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.12 0.23 -10000 0 -0.48 143 143
PTPN6 -0.11 0.21 0.21 3 -0.47 127 130
VAV1 -0.1 0.22 0.21 17 -0.46 133 150
Monovalent TCR/CD3 -0.07 0.14 -10000 0 -0.28 169 169
CBL 0.026 0.019 -10000 0 -0.46 1 1
LCK -0.12 0.24 0.22 11 -0.5 134 145
PAG1 -0.1 0.21 0.22 12 -0.45 132 144
RAP1A 0.024 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.12 0.23 -10000 0 -0.47 144 144
CD80 -0.038 0.14 -10000 0 -0.33 113 113
CD86 0.005 0.097 -10000 0 -0.41 32 32
PDK1/CARD11/BCL10/MALT1 -0.046 0.088 -10000 0 -0.22 86 86
HRAS 0.026 0.006 -10000 0 -10000 0 0
GO:0035030 -0.11 0.19 0.21 8 -0.4 160 168
CD8A -0.027 0.14 -10000 0 -0.36 87 87
CD8B -0.006 0.11 -10000 0 -0.35 51 51
PTPRC 0.001 0.1 -10000 0 -0.37 42 42
PDK1/PKC theta -0.089 0.19 0.24 17 -0.42 116 133
CSK/PAG1 -0.1 0.2 0.25 7 -0.45 125 132
SOS1 0.027 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.01 0.03 -10000 0 -0.17 12 12
GRAP2/SLP76 -0.099 0.21 0.22 3 -0.45 133 136
STIM1 -0.009 0.14 1.1 6 -0.89 2 8
RAS family/GTP -0.017 0.075 0.16 14 -0.17 54 68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.085 0.18 -10000 0 -0.42 108 108
mol:DAG -0.083 0.12 0.12 1 -0.29 131 132
RAP1A/GDP 0.002 0.028 0.078 20 -0.064 3 23
PLCG1 0.026 0.006 -10000 0 -10000 0 0
CD247 0.007 0.077 -10000 0 -0.31 33 33
cytotoxic T cell degranulation -0.18 0.34 -10000 0 -0.81 116 116
RAP1A/GTP 0 0.007 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.09 0.18 0.22 11 -0.39 131 142
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.093 0.19 0.23 16 -0.42 115 131
NRAS 0.024 0.009 -10000 0 -10000 0 0
ZAP70 -0.004 0.1 -10000 0 -0.33 56 56
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.1 0.18 0.22 2 -0.41 130 132
MALT1 0.026 0.005 -10000 0 -10000 0 0
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
CD8 heterodimer -0.022 0.13 -10000 0 -0.32 100 100
CARD11 0.015 0.059 -10000 0 -0.4 12 12
PRKCB -0.062 0.1 0.15 6 -0.24 110 116
PRKCE -0.052 0.097 0.17 8 -0.23 103 111
PRKCQ -0.1 0.21 0.24 12 -0.45 128 140
LCP2 0.022 0.043 -10000 0 -0.34 8 8
BCL10 0.024 0.009 -10000 0 -10000 0 0
regulation of survival gene product expression -0.064 0.14 0.19 16 -0.3 120 136
IKK complex -0.009 0.053 0.14 23 -0.1 25 48
RAS family/GDP -0.006 0.01 -10000 0 -10000 0 0
MAP3K14 -0.046 0.1 0.17 10 -0.23 94 104
PDPK1 -0.071 0.15 0.21 17 -0.34 111 128
TCR/CD3/MHC I/CD8/Fyn -0.12 0.24 -10000 0 -0.55 121 121
Syndecan-1-mediated signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.03 -10000 0 -0.38 3 3
CCL5 -0.037 0.15 -10000 0 -0.34 115 115
SDCBP 0.026 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 0.22 3 -0.41 83 86
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 -0.1 0.15 0.21 2 -0.41 77 79
Syndecan-1/Syntenin -0.091 0.16 0.26 9 -0.41 76 85
MAPK3 -0.086 0.14 0.21 6 -0.39 70 76
HGF/MET -0.053 0.14 -10000 0 -0.34 108 108
TGFB1/TGF beta receptor Type II 0.022 0.03 -10000 0 -0.38 3 3
BSG 0.026 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.099 0.15 0.21 2 -0.41 77 79
Syndecan-1/RANTES -0.12 0.18 0.26 9 -0.42 117 126
Syndecan-1/CD147 -0.085 0.16 0.32 1 -0.41 70 71
Syndecan-1/Syntenin/PIP2 -0.088 0.15 0.25 9 -0.4 76 85
LAMA5 0.024 0.029 -10000 0 -0.38 3 3
positive regulation of cell-cell adhesion -0.087 0.15 0.23 8 -0.39 76 84
MMP7 -0.1 0.18 -10000 0 -0.33 241 241
HGF -0.02 0.11 -10000 0 -0.29 87 87
Syndecan-1/CASK -0.11 0.15 -10000 0 -0.39 85 85
Syndecan-1/HGF/MET -0.12 0.18 0.28 1 -0.4 132 133
regulation of cell adhesion -0.079 0.15 0.29 17 -0.39 62 79
HPSE -0.013 0.13 -10000 0 -0.4 62 62
positive regulation of cell migration -0.1 0.16 0.22 3 -0.41 83 86
SDC1 -0.11 0.15 -10000 0 -0.41 83 83
Syndecan-1/Collagen -0.1 0.16 0.22 3 -0.41 83 86
PPIB 0.027 0.003 -10000 0 -10000 0 0
MET -0.06 0.16 -10000 0 -0.33 151 151
PRKACA 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.097 0.17 -10000 0 -0.29 255 255
MAPK1 -0.085 0.14 0.21 7 -0.39 69 76
homophilic cell adhesion -0.1 0.16 0.23 9 -0.41 85 94
MMP1 -0.032 0.12 -10000 0 -0.28 116 116
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.34 -10000 0 -1 71 71
MKNK1 0.024 0.008 -10000 0 -10000 0 0
MAPK14 -0.022 0.12 -10000 0 -0.3 92 92
ATF2/c-Jun -0.021 0.1 -10000 0 -0.52 8 8
MAPK11 -0.024 0.12 -10000 0 -0.3 94 94
MITF -0.028 0.13 -10000 0 -0.34 93 93
MAPKAPK5 -0.028 0.13 -10000 0 -0.34 94 94
KRT8 -0.068 0.18 -10000 0 -0.39 128 128
MAPKAPK3 0.026 0.019 -10000 0 -0.46 1 1
MAPKAPK2 0.027 0.003 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.034 0.17 -10000 0 -0.43 95 95
CEBPB -0.033 0.15 -10000 0 -0.37 92 92
SLC9A1 -0.038 0.15 -10000 0 -0.38 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.026 0.14 -10000 0 -0.33 99 99
p38alpha-beta/MNK1 -0.018 0.14 -10000 0 -0.34 94 94
JUN -0.02 0.098 -10000 0 -0.52 8 8
PPARGC1A -0.036 0.15 -10000 0 -0.37 101 101
USF1 -0.026 0.13 -10000 0 -0.34 93 93
RAB5/GDP/GDI1 -0.016 0.1 -10000 0 -0.25 92 92
NOS2 -0.061 0.23 -10000 0 -0.98 28 28
DDIT3 -0.028 0.13 -10000 0 -0.34 91 91
RAB5A 0.027 0.003 -10000 0 -10000 0 0
HSPB1 0.01 0.15 0.27 87 -0.28 88 175
p38alpha-beta/HBP1 -0.013 0.14 -10000 0 -0.34 81 81
CREB1 -0.033 0.15 -10000 0 -0.36 94 94
RAB5/GDP 0.02 0.002 -10000 0 -10000 0 0
EIF4E -0.031 0.12 0.24 1 -0.3 90 91
RPS6KA4 -0.027 0.13 -10000 0 -0.34 93 93
PLA2G4A -0.039 0.13 0.24 1 -0.33 94 95
GDI1 -0.028 0.13 -10000 0 -0.34 94 94
TP53 -0.051 0.16 -10000 0 -0.43 95 95
RPS6KA5 -0.039 0.15 -10000 0 -0.36 109 109
ESR1 -0.036 0.15 -10000 0 -0.36 101 101
HBP1 0.021 0.011 -10000 0 -10000 0 0
MEF2C -0.031 0.14 -10000 0 -0.35 93 93
MEF2A -0.029 0.14 -10000 0 -0.35 94 94
EIF4EBP1 -0.036 0.15 -10000 0 -0.37 94 94
KRT19 -0.067 0.18 -10000 0 -0.4 110 110
ELK4 -0.027 0.14 -10000 0 -0.34 94 94
ATF6 -0.026 0.13 -10000 0 -0.34 93 93
ATF1 -0.035 0.15 -10000 0 -0.37 96 96
p38alpha-beta/MAPKAPK2 -0.01 0.15 -10000 0 -0.34 92 92
p38alpha-beta/MAPKAPK3 -0.012 0.15 -10000 0 -0.35 91 91
Effects of Botulinum toxin

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.012 0.054 -10000 0 -0.16 77 77
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.022 0.12 -10000 0 -0.33 79 79
STXBP1 0.014 0.059 -10000 0 -0.25 30 30
ACh/CHRNA1 -0.061 0.12 -10000 0 -0.22 190 190
RAB3GAP2/RIMS1/UNC13B -0.003 0.11 -10000 0 -0.28 77 77
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 -0.054 0.17 -10000 0 -0.36 136 136
mol:ACh -0.003 0.058 0.099 92 -0.12 68 160
RAB3GAP2 0.027 0.003 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.029 0.12 -10000 0 -0.26 113 113
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.061 0.12 -10000 0 -0.22 190 190
UNC13B 0.025 0.02 -10000 0 -0.46 1 1
CHRNA1 -0.094 0.18 -10000 0 -0.32 227 227
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.06 0.13 -10000 0 -0.23 218 218
SNAP25 -0.038 0.092 -10000 0 -0.27 84 84
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 -0.094 0.18 -10000 0 -0.33 221 221
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.001 0.065 -10000 0 -0.24 31 31
STX1A/SNAP25 fragment 1/VAMP2 -0.029 0.12 -10000 0 -0.26 113 113
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.004 0.063 -10000 0 -0.55 3 3
Syndecan-4/Syndesmos -0.089 0.22 -10000 0 -0.49 127 127
positive regulation of JNK cascade -0.089 0.21 -10000 0 -0.46 128 128
Syndecan-4/ADAM12 -0.12 0.22 -10000 0 -0.51 127 127
CCL5 -0.037 0.15 -10000 0 -0.34 115 115
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.026 0.005 -10000 0 -10000 0 0
ITGA5 0.007 0.071 -10000 0 -0.24 46 46
SDCBP 0.026 0.005 -10000 0 -10000 0 0
PLG 0.013 0.025 -10000 0 -0.23 4 4
ADAM12 -0.039 0.12 -10000 0 -0.26 143 143
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.035 0.025 -10000 0 -0.13 1 1
Syndecan-4/Laminin alpha1 -0.11 0.24 -10000 0 -0.52 133 133
Syndecan-4/CXCL12/CXCR4 -0.095 0.22 -10000 0 -0.49 128 128
Syndecan-4/Laminin alpha3 -0.11 0.23 -10000 0 -0.51 129 129
MDK -0.02 0.12 -10000 0 -0.32 88 88
Syndecan-4/FZD7 -0.11 0.24 -10000 0 -0.53 130 130
Syndecan-4/Midkine -0.11 0.23 -10000 0 -0.51 126 126
FZD7 -0.017 0.14 -10000 0 -0.42 65 65
Syndecan-4/FGFR1/FGF -0.076 0.21 -10000 0 -0.46 121 121
THBS1 -0.059 0.16 -10000 0 -0.3 172 172
integrin-mediated signaling pathway -0.1 0.22 -10000 0 -0.5 129 129
positive regulation of MAPKKK cascade -0.089 0.21 -10000 0 -0.46 128 128
Syndecan-4/TACI -0.095 0.22 -10000 0 -0.5 128 128
CXCR4 0.007 0.09 -10000 0 -0.37 33 33
cell adhesion 0.015 0.042 0.21 14 -0.23 1 15
Syndecan-4/Dynamin -0.092 0.22 -10000 0 -0.49 128 128
Syndecan-4/TSP1 -0.12 0.23 -10000 0 -0.53 129 129
Syndecan-4/GIPC -0.092 0.22 -10000 0 -0.49 127 127
Syndecan-4/RANTES -0.12 0.24 -10000 0 -0.53 129 129
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
LAMA1 -0.032 0.15 -10000 0 -0.42 85 85
LAMA3 -0.014 0.12 -10000 0 -0.35 70 70
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCA 0.037 0.15 0.9 17 -0.4 2 19
Syndecan-4/alpha-Actinin -0.095 0.22 -10000 0 -0.5 129 129
TFPI -0.06 0.17 -10000 0 -0.36 150 150
F2 0.003 0.033 -10000 0 -0.22 6 6
alpha5/beta1 Integrin 0.021 0.055 -10000 0 -0.31 7 7
positive regulation of cell adhesion -0.13 0.23 -10000 0 -0.52 139 139
ACTN1 0.008 0.068 -10000 0 -0.24 44 44
TNC -0.011 0.12 -10000 0 -0.33 69 69
Syndecan-4/CXCL12 -0.095 0.22 -10000 0 -0.49 128 128
FGF6 0.015 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CXCL12 0.019 0.046 -10000 0 -0.31 11 11
TNFRSF13B 0.016 0.029 -10000 0 -0.22 9 9
FGF2 0.025 0.022 -10000 0 -0.34 2 2
FGFR1 0.026 0.004 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.1 0.21 -10000 0 -0.49 128 128
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.066 -10000 0 -0.22 46 46
cell migration -0.013 0.016 -10000 0 -10000 0 0
PRKCD 0.009 0.087 -10000 0 -0.44 23 23
vasculogenesis -0.12 0.22 -10000 0 -0.5 129 129
SDC4 -0.11 0.23 -10000 0 -0.52 128 128
Syndecan-4/Tenascin C -0.1 0.23 -10000 0 -0.52 129 129
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.02 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.088 0.22 -10000 0 -0.49 124 124
MMP9 -0.1 0.16 -10000 0 -0.29 255 255
Rac1/GTP 0.015 0.042 0.21 14 -0.24 1 15
cytoskeleton organization -0.085 0.21 -10000 0 -0.47 127 127
GIPC1 0.026 0.011 -10000 0 -0.22 1 1
Syndecan-4/TFPI -0.13 0.23 -10000 0 -0.53 128 128
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.002 0.077 -10000 0 -0.26 36 36
NFATC2 -0.073 0.22 -10000 0 -0.57 60 60
NFATC3 -0.026 0.1 -10000 0 -0.27 55 55
CD40LG -0.23 0.36 -10000 0 -0.94 110 110
ITCH -0.018 0.093 -10000 0 -0.22 97 97
CBLB -0.017 0.092 -10000 0 -0.22 94 94
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.27 0.38 -10000 0 -0.86 144 144
JUNB 0.003 0.089 -10000 0 -0.3 47 47
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.11 -10000 0 -0.26 105 105
T cell anergy -0.056 0.16 -10000 0 -0.39 103 103
TLE4 -0.046 0.16 -10000 0 -0.55 31 31
Jun/NFAT1-c-4/p21SNFT -0.18 0.38 -10000 0 -0.98 100 100
AP-1/NFAT1-c-4 -0.25 0.46 -10000 0 -1.1 110 110
IKZF1 -0.049 0.17 -10000 0 -0.62 33 33
T-helper 2 cell differentiation -0.14 0.26 -10000 0 -0.81 48 48
AP-1/NFAT1 -0.07 0.18 -10000 0 -0.44 67 67
CALM1 -0.006 0.072 -10000 0 -10000 0 0
EGR2 -0.19 0.46 -10000 0 -1.2 95 95
EGR3 -0.19 0.47 -10000 0 -1.2 93 93
NFAT1/FOXP3 -0.053 0.18 -10000 0 -0.48 58 58
EGR1 -0.042 0.15 -10000 0 -0.37 104 104
JUN 0.001 0.036 -10000 0 -0.22 5 5
EGR4 -0.081 0.17 -10000 0 -0.33 187 187
mol:Ca2+ -0.026 0.062 -10000 0 -0.16 99 99
GBP3 -0.086 0.24 -10000 0 -0.66 83 83
FOSL1 -0.06 0.16 -10000 0 -0.34 158 158
NFAT1-c-4/MAF/IRF4 -0.15 0.38 -10000 0 -0.96 98 98
DGKA -0.043 0.15 -10000 0 -0.47 34 34
CREM 0.023 0.016 -10000 0 -0.22 2 2
NFAT1-c-4/PPARG -0.16 0.38 -10000 0 -0.98 99 99
CTLA4 -0.072 0.19 -10000 0 -0.54 64 64
NFAT1-c-4 (dimer)/EGR1 -0.19 0.42 -10000 0 -1.1 100 100
NFAT1-c-4 (dimer)/EGR4 -0.21 0.4 -10000 0 -1 104 104
FOS -0.045 0.14 -10000 0 -0.37 86 86
IFNG -0.093 0.19 -10000 0 -0.65 31 31
T cell activation -0.1 0.21 -10000 0 -0.67 39 39
MAF 0.024 0.033 -10000 0 -0.46 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.13 0.34 0.84 96 -10000 0 96
TNF -0.26 0.4 -10000 0 -0.95 134 134
FASLG -0.21 0.46 -10000 0 -1.3 93 93
TBX21 -0.005 0.11 -10000 0 -0.31 64 64
BATF3 -0.008 0.1 -10000 0 -0.29 72 72
PRKCQ 0.007 0.085 -10000 0 -0.44 22 22
PTPN1 -0.044 0.15 -10000 0 -0.49 31 31
NFAT1-c-4/ICER1 -0.16 0.38 -10000 0 -0.96 99 99
GATA3 -0.041 0.14 -10000 0 -0.33 119 119
T-helper 1 cell differentiation -0.092 0.19 -10000 0 -0.64 32 32
IL2RA -0.24 0.35 -10000 0 -0.81 138 138
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.042 0.15 -10000 0 -0.48 35 35
E2F1 0.015 0.068 -10000 0 -0.31 24 24
PPARG 0.008 0.086 -10000 0 -0.36 31 31
SLC3A2 -0.044 0.15 -10000 0 -0.49 31 31
IRF4 -0.002 0.1 -10000 0 -0.32 54 54
PTGS2 -0.26 0.4 -10000 0 -0.98 121 121
CSF2 -0.23 0.36 -10000 0 -0.94 110 110
JunB/Fra1/NFAT1-c-4 -0.19 0.39 -10000 0 -0.99 102 102
IL4 -0.15 0.27 -10000 0 -0.87 46 46
IL5 -0.23 0.36 -10000 0 -0.93 110 110
IL2 -0.1 0.21 -10000 0 -0.71 32 32
IL3 -0.036 0.12 -10000 0 -0.73 14 14
RNF128 -0.086 0.21 -10000 0 -0.55 105 105
NFATC1 -0.13 0.34 -10000 0 -0.85 96 96
CDK4 0.088 0.19 0.61 32 -10000 0 32
PTPRK -0.043 0.15 -10000 0 -0.5 30 30
IL8 -0.28 0.4 -10000 0 -0.96 126 126
POU2F1 0.02 0.057 -10000 0 -0.46 9 9
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.002 0.12 -9999 0 -0.28 80 80
E-cadherin/beta catenin -0.019 0.12 -9999 0 -0.25 131 131
CTNNB1 0.027 0.003 -9999 0 -10000 0 0
JUP 0.022 0.044 -9999 0 -0.39 7 7
CDH1 -0.051 0.16 -9999 0 -0.36 132 132
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.019 -9999 0 -0.22 3 3
ITGB7 0.002 0.097 -9999 0 -0.35 42 42
ITGA4 -0.022 0.13 -9999 0 -0.33 90 90
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.24 125 125
alpha4/beta1 Integrin 0 0.096 -9999 0 -0.23 83 83
Glypican 2 network

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
MDK -0.02 0.12 -9999 0 -0.32 88 88
GPC2 0.006 0.084 -9999 0 -0.41 24 24
GPC2/Midkine -0.006 0.1 -9999 0 -0.26 80 80
neuron projection morphogenesis -0.006 0.1 -9999 0 -0.26 80 80
Reelin signaling pathway

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
CDK5R1/CDK5 0.011 0.083 -10000 0 -0.32 37 37
VLDLR 0.015 0.065 -10000 0 -0.4 15 15
CRKL 0.026 0.011 -10000 0 -0.22 1 1
LRPAP1 0.027 0.003 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
ITGA3 0.007 0.072 -10000 0 -0.24 48 48
RELN/VLDLR/Fyn -0.022 0.11 -10000 0 -0.28 88 88
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.053 -10000 0 -0.23 14 14
AKT1 -0.051 0.12 -10000 0 -0.26 132 132
MAP2K7 0.025 0.019 -10000 0 -0.46 1 1
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
DAB1 -0.045 0.16 -10000 0 -0.41 104 104
RELN/LRP8/DAB1 -0.047 0.13 -10000 0 -0.28 131 131
LRPAP1/LRP8 0.034 0.024 -10000 0 -0.33 2 2
RELN/LRP8/DAB1/Fyn -0.037 0.13 -10000 0 -0.26 130 130
DAB1/alpha3/beta1 Integrin -0.044 0.13 -10000 0 -0.35 55 55
long-term memory -0.12 0.18 -10000 0 -0.33 217 217
DAB1/LIS1 -0.033 0.13 -10000 0 -0.27 115 115
DAB1/CRLK/C3G -0.038 0.12 -10000 0 -0.26 111 111
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.033 0.13 -10000 0 -0.27 115 115
ARHGEF2 0.026 0.019 -10000 0 -0.46 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.076 0.18 -10000 0 -0.34 187 187
CDK5R1 -0.011 0.13 -10000 0 -0.46 52 52
RELN -0.065 0.16 -10000 0 -0.35 153 153
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.019 0.11 -10000 0 -0.28 77 77
GRIN2A/RELN/LRP8/DAB1/Fyn -0.074 0.16 -10000 0 -0.28 197 197
MAPK8 0.018 0.057 -10000 0 -0.46 9 9
RELN/VLDLR/DAB1 -0.052 0.13 -10000 0 -0.28 139 139
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
MAP1B -0.056 0.12 0.17 12 -0.28 130 142
RELN/LRP8 -0.019 0.11 -10000 0 -0.28 78 78
GRIN2B/RELN/LRP8/DAB1/Fyn -0.08 0.16 -10000 0 -0.28 205 205
PI3K 0.039 0.008 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.021 0.055 -10000 0 -0.31 6 6
RAP1A -0.021 0.14 0.42 6 -0.35 30 36
PAFAH1B1 0.027 0.003 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.046 -10000 0 -0.46 6 6
CRLK/C3G 0.037 0.023 -10000 0 -0.27 3 3
GRIN2B -0.078 0.17 -10000 0 -0.33 190 190
NCK2 0.027 0.002 -10000 0 -10000 0 0
neuron differentiation -0.029 0.12 -10000 0 -0.35 52 52
neuron adhesion -0.021 0.14 0.42 7 -0.34 39 46
LRP8 0.023 0.028 -10000 0 -0.46 2 2
GSK3B -0.046 0.11 0.18 1 -0.28 87 88
RELN/VLDLR/DAB1/Fyn -0.043 0.13 -10000 0 -0.26 138 138
MAP3K11 0.027 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.055 0.13 -10000 0 -0.28 137 137
CDK5 0.021 0.011 -10000 0 -10000 0 0
MAPT -0.01 0.12 0.8 5 -0.41 35 40
neuron migration -0.042 0.16 0.24 54 -0.36 92 146
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.12 -10000 0 -0.36 52 52
RELN/VLDLR -0.014 0.11 -10000 0 -0.25 87 87
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.022 0.026 -10000 0 -0.22 7 7
GNB1/GNG2 -0.059 0.076 -10000 0 -0.18 159 159
AKT1 -0.038 0.13 0.28 14 -0.23 106 120
EGF -0.006 0.11 -10000 0 -0.38 53 53
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.015 0.067 0.3 18 -10000 0 18
mol:Ca2+ -0.055 0.16 0.3 12 -0.29 158 170
LYN 0.013 0.072 0.3 19 -0.29 2 21
RhoA/GTP -0.027 0.062 0.099 2 -0.13 132 134
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.073 0.18 0.32 10 -0.35 159 169
GNG2 0.022 0.043 -10000 0 -0.46 5 5
ARRB2 0.027 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.098 -10000 0 -0.4 27 27
G beta5/gamma2 -0.073 0.099 -10000 0 -0.24 155 155
PRKCH -0.068 0.17 0.34 9 -0.34 153 162
DNM1 -0.022 0.12 -10000 0 -0.29 101 101
TXA2/TP beta/beta Arrestin3 -0.006 0.043 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.004 0.07 -10000 0 -0.23 52 52
G12 family/GTP -0.076 0.13 -10000 0 -0.3 143 143
ADRBK1 0.026 0.003 -10000 0 -10000 0 0
ADRBK2 0.024 0.029 -10000 0 -0.38 3 3
RhoA/GTP/ROCK1 0.035 0.007 -10000 0 -10000 0 0
mol:GDP 0.026 0.11 0.3 21 -0.29 13 34
mol:NADP 0.019 0.03 -10000 0 -0.38 3 3
RAB11A 0.026 0.004 -10000 0 -10000 0 0
PRKG1 -0.004 0.11 -10000 0 -0.42 42 42
mol:IP3 -0.074 0.19 0.35 9 -0.36 158 167
cell morphogenesis 0.034 0.007 -10000 0 -10000 0 0
PLCB2 -0.11 0.24 0.4 7 -0.49 156 163
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0 0.079 0.3 19 -0.25 4 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.067 0.27 10 -0.26 7 17
RHOA 0.027 0.003 -10000 0 -10000 0 0
PTGIR 0.001 0.08 -10000 0 -0.26 51 51
PRKCB1 -0.075 0.18 0.33 8 -0.36 158 166
GNAQ 0.026 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.019 0.03 -10000 0 -0.38 3 3
TXA2/TXA2-R family -0.12 0.25 0.39 7 -0.52 160 167
LCK -0.005 0.087 0.3 18 -0.28 6 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.009 0.052 -10000 0 -0.23 3 3
TXA2-R family/G12 family/GDP/G beta/gamma -0.021 0.14 -10000 0 -0.43 68 68
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.014 0.053 -10000 0 -0.23 2 2
MAPK14 -0.043 0.12 0.25 13 -0.23 155 168
TGM2/GTP -0.086 0.2 0.39 4 -0.41 153 157
MAPK11 -0.044 0.12 0.25 13 -0.23 155 168
ARHGEF1 -0.039 0.084 0.14 3 -0.18 140 143
GNAI2 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.082 0.19 0.35 9 -0.38 160 169
RAB11/GDP 0.026 0.004 -10000 0 -10000 0 0
ICAM1 -0.061 0.15 0.29 8 -0.29 162 170
cAMP biosynthetic process -0.072 0.18 0.34 9 -0.34 158 167
Gq family/GTP/EBP50 0.01 0.06 0.25 5 -0.21 35 40
actin cytoskeleton reorganization 0.034 0.007 -10000 0 -10000 0 0
SRC 0.008 0.06 0.27 10 -10000 0 10
GNB5 0.027 0.003 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.002 0.11 0.3 31 -0.3 19 50
VCAM1 -0.079 0.18 0.29 9 -0.36 162 171
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.098 -10000 0 -0.4 27 27
platelet activation -0.055 0.16 0.32 14 -0.3 157 171
PGI2/IP 0.002 0.055 -10000 0 -0.18 51 51
PRKACA 0.002 0.044 -10000 0 -0.23 10 10
Gq family/GDP/G beta5/gamma2 0.003 0.091 -10000 0 -0.36 29 29
TXA2/TP beta/beta Arrestin2 -0.017 0.1 -10000 0 -0.49 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.045 -10000 0 -0.23 15 15
mol:DAG -0.083 0.2 0.36 8 -0.4 158 166
EGFR -0.019 0.13 -10000 0 -0.46 53 53
TXA2/TP alpha -0.1 0.23 0.4 8 -0.46 157 165
Gq family/GTP 0.004 0.058 0.22 4 -0.21 38 42
YES1 0.013 0.072 0.3 19 -0.24 1 20
GNAI2/GTP 0.005 0.048 -10000 0 -0.22 1 1
PGD2/DP 0.005 0.047 -10000 0 -0.15 52 52
SLC9A3R1 0.025 0.019 -10000 0 -0.46 1 1
FYN 0.014 0.069 0.31 18 -10000 0 18
mol:NO 0.019 0.03 -10000 0 -0.38 3 3
GNA15 0.011 0.08 -10000 0 -0.38 25 25
PGK/cGMP 0.01 0.069 -10000 0 -0.28 33 33
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.063 -10000 0 -0.3 2 2
NOS3 0.019 0.03 -10000 0 -0.38 3 3
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCA -0.067 0.17 0.32 10 -0.34 152 162
PRKCB -0.081 0.18 0.32 9 -0.36 161 170
PRKCE -0.07 0.18 0.31 10 -0.35 155 165
PRKCD -0.08 0.19 0.33 8 -0.38 157 165
PRKCG -0.096 0.2 0.34 10 -0.39 170 180
muscle contraction -0.11 0.24 0.37 8 -0.48 159 167
PRKCZ -0.08 0.18 0.32 9 -0.34 174 183
ARR3 0.018 0.011 -10000 0 -0.22 1 1
TXA2/TP beta 0.013 0.057 -10000 0 -0.26 1 1
PRKCQ -0.075 0.17 0.31 9 -0.35 157 166
MAPKKK cascade -0.095 0.22 0.36 8 -0.44 162 170
SELE -0.073 0.17 0.29 9 -0.33 161 170
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.061 -10000 0 -0.29 2 2
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.013 0.074 -10000 0 -0.35 24 24
chemotaxis -0.14 0.29 0.4 6 -0.62 159 165
GNA12 0.023 0.01 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.06 -10000 0 -0.46 10 10
Rac1/GTP 0.016 0.007 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.064 0.16 0.27 19 -0.37 71 90
PTK2B 0.018 0.044 -10000 0 -0.22 21 21
mol:Ca2+ -0.064 0.23 -10000 0 -0.69 52 52
EDN1 -0.044 0.13 0.23 20 -0.35 49 69
EDN3 -0.018 0.14 -10000 0 -0.44 63 63
EDN2 0.005 0.055 -10000 0 -0.22 36 36
HRAS/GDP -0.052 0.16 0.27 9 -0.42 57 66
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.03 0.13 0.18 17 -0.33 51 68
ADCY4 -0.096 0.17 0.21 1 -0.34 152 153
ADCY5 -0.11 0.19 0.21 1 -0.4 161 162
ADCY6 -0.095 0.16 0.21 2 -0.34 150 152
ADCY7 -0.096 0.17 0.21 1 -0.34 149 150
ADCY1 -0.099 0.16 0.21 1 -0.36 133 134
ADCY2 -0.11 0.18 0.21 2 -0.38 161 163
ADCY3 -0.096 0.17 -10000 0 -0.34 149 149
ADCY8 -0.11 0.17 -10000 0 -0.36 159 159
ADCY9 -0.095 0.17 0.21 1 -0.34 148 149
arachidonic acid secretion -0.064 0.19 0.29 8 -0.46 80 88
ETB receptor/Endothelin-1/Gq/GTP -0.021 0.11 -10000 0 -0.29 65 65
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
HRAS 0.025 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.027 0.16 0.36 20 -0.37 50 70
ETA receptor/Endothelin-1/Gs/GTP -0.083 0.2 0.34 23 -0.36 156 179
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.14 0.24 0.27 20 -0.56 126 146
EDNRB -0.013 0.12 -10000 0 -0.43 43 43
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.073 0.18 0.27 20 -0.48 62 82
CYSLTR1 -0.072 0.17 0.27 20 -0.47 58 78
SLC9A1 -0.035 0.1 0.19 18 -0.28 57 75
mol:GDP -0.064 0.17 0.27 9 -0.44 63 72
SLC9A3 -0.086 0.26 -10000 0 -0.68 80 80
RAF1 -0.067 0.18 0.25 9 -0.44 74 83
JUN -0.056 0.2 -10000 0 -0.63 39 39
JAK2 -0.063 0.16 0.27 19 -0.39 59 78
mol:IP3 -0.037 0.13 -10000 0 -0.39 43 43
ETA receptor/Endothelin-1 -0.06 0.2 0.41 24 -0.42 78 102
PLCB1 -0.001 0.11 -10000 0 -0.46 36 36
PLCB2 0.018 0.058 -10000 0 -0.42 11 11
ETA receptor/Endothelin-3 -0.039 0.14 -10000 0 -0.36 83 83
FOS -0.097 0.29 0.37 6 -0.9 63 69
Gai/GDP -0.02 0.2 -10000 0 -0.77 39 39
CRK 0.027 0.003 -10000 0 -10000 0 0
mol:Ca ++ -0.074 0.18 0.24 17 -0.44 73 90
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
PRKCB1 -0.037 0.13 -10000 0 -0.38 42 42
GNAQ 0.026 0.009 -10000 0 -10000 0 0
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
GNAL -0.075 0.2 -10000 0 -0.46 139 139
Gs family/GDP -0.094 0.19 0.25 2 -0.41 117 119
ETA receptor/Endothelin-1/Gq/GTP -0.027 0.12 0.21 19 -0.33 49 68
MAPK14 -0.027 0.12 -10000 0 -0.38 36 36
TRPC6 -0.068 0.25 -10000 0 -0.76 48 48
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 0.012 0.07 -10000 0 -0.46 14 14
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.026 0.12 -10000 0 -0.35 48 48
ETB receptor/Endothelin-2 -0.008 0.094 -10000 0 -0.3 46 46
ETB receptor/Endothelin-3 -0.021 0.14 -10000 0 -0.36 84 84
ETB receptor/Endothelin-1 -0.037 0.14 -10000 0 -0.34 71 71
MAPK3 -0.087 0.25 0.35 8 -0.74 68 76
MAPK1 -0.089 0.25 0.35 8 -0.75 67 75
Rac1/GDP -0.047 0.16 0.26 2 -0.42 52 54
cAMP biosynthetic process -0.11 0.19 0.25 6 -0.4 149 155
MAPK8 -0.069 0.23 -10000 0 -0.62 69 69
SRC 0.024 0.027 -10000 0 -0.46 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.023 0.11 0.17 4 -0.35 43 47
p130Cas/CRK/Src/PYK2 -0.055 0.18 0.34 8 -0.52 45 53
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.047 0.16 0.26 2 -0.43 49 51
COL1A2 -0.077 0.2 0.27 14 -0.56 58 72
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.026 0.1 -10000 0 -0.29 42 42
mol:DAG -0.037 0.13 -10000 0 -0.39 43 43
MAP2K2 -0.073 0.21 0.38 11 -0.56 72 83
MAP2K1 -0.078 0.21 0.29 4 -0.56 73 77
EDNRA -0.04 0.13 0.23 20 -0.35 49 69
positive regulation of muscle contraction -0.027 0.15 0.25 42 -0.35 49 91
Gq family/GDP -0.044 0.17 -10000 0 -0.44 56 56
HRAS/GTP -0.061 0.16 0.25 10 -0.41 69 79
PRKCH -0.035 0.13 -10000 0 -0.41 33 33
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCA -0.035 0.13 0.25 6 -0.41 36 42
PRKCB -0.054 0.14 -10000 0 -0.4 51 51
PRKCE -0.039 0.13 0.2 1 -0.4 38 39
PRKCD -0.044 0.14 -10000 0 -0.42 48 48
PRKCG -0.082 0.16 0.2 1 -0.39 87 88
regulation of vascular smooth muscle contraction -0.12 0.34 0.4 6 -1.1 61 67
PRKCQ -0.038 0.14 0.24 10 -0.41 41 51
PLA2G4A -0.07 0.21 0.31 6 -0.51 79 85
GNA14 0.012 0.075 -10000 0 -0.35 24 24
GNA15 0.01 0.08 -10000 0 -0.38 25 25
GNA12 0.023 0.01 -10000 0 -10000 0 0
GNA11 0.018 0.06 -10000 0 -0.46 10 10
Rac1/GTP -0.026 0.16 0.36 20 -0.35 56 76
MMP1 -0.028 0.21 0.45 4 -0.85 30 34
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.14 0.34 -10000 0 -0.78 88 88
HDAC7 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.098 0.36 -10000 0 -0.78 77 77
SMAD4 0.027 0.005 -10000 0 -10000 0 0
ID2 -0.12 0.36 -10000 0 -0.79 84 84
AP1 -0.004 0.1 -10000 0 -0.32 52 52
ABCG2 -0.12 0.36 -10000 0 -0.82 81 81
HIF1A -0.004 0.077 -10000 0 -0.29 3 3
TFF3 -0.13 0.36 -10000 0 -0.8 90 90
GATA2 0.015 0.069 -10000 0 -0.35 20 20
AKT1 -0.015 0.089 -10000 0 -0.23 24 24
response to hypoxia -0.03 0.082 -10000 0 -0.22 35 35
MCL1 -0.12 0.36 -10000 0 -0.8 83 83
NDRG1 -0.12 0.36 -10000 0 -0.81 84 84
SERPINE1 -0.14 0.37 -10000 0 -0.81 96 96
FECH -0.12 0.36 -10000 0 -0.81 80 80
FURIN -0.12 0.36 -10000 0 -0.8 80 80
NCOA2 0.001 0.11 -10000 0 -0.46 35 35
EP300 -0.024 0.14 -10000 0 -0.31 78 78
HMOX1 -0.12 0.37 -10000 0 -0.82 88 88
BHLHE40 -0.12 0.36 -10000 0 -0.81 83 83
BHLHE41 -0.12 0.36 -10000 0 -0.83 81 81
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.051 0.11 -10000 0 -0.28 2 2
ENG 0.016 0.089 0.32 3 -0.31 5 8
JUN 0.022 0.024 -10000 0 -0.22 5 5
RORA -0.12 0.36 -10000 0 -0.8 84 84
ABCB1 -0.046 0.18 -10000 0 -1.1 15 15
TFRC -0.12 0.36 -10000 0 -0.81 81 81
CXCR4 -0.12 0.37 -10000 0 -0.82 86 86
TF -0.14 0.38 -10000 0 -0.84 100 100
CITED2 -0.12 0.35 -10000 0 -0.8 80 80
HIF1A/ARNT -0.12 0.42 -10000 0 -0.91 79 79
LDHA -0.028 0.13 -10000 0 -0.91 9 9
ETS1 -0.12 0.36 -10000 0 -0.8 81 81
PGK1 -0.12 0.36 -10000 0 -0.81 82 82
NOS2 -0.13 0.37 -10000 0 -0.81 91 91
ITGB2 -0.12 0.37 -10000 0 -0.83 87 87
ALDOA -0.12 0.36 -10000 0 -0.8 83 83
Cbp/p300/CITED2 -0.14 0.4 -10000 0 -0.91 81 81
FOS -0.025 0.14 -10000 0 -0.36 86 86
HK2 -0.12 0.37 -10000 0 -0.83 82 82
SP1 0.032 0.014 -10000 0 -10000 0 0
GCK -0.12 0.43 -10000 0 -1.4 62 62
HK1 -0.12 0.35 -10000 0 -0.8 80 80
NPM1 -0.12 0.36 -10000 0 -0.8 81 81
EGLN1 -0.12 0.36 -10000 0 -0.8 81 81
CREB1 0.029 0.014 -10000 0 -10000 0 0
PGM1 -0.12 0.35 -10000 0 -0.79 82 82
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.071 0.26 -10000 0 -0.86 37 37
IGFBP1 -0.14 0.36 -10000 0 -0.81 94 94
VEGFA -0.11 0.32 0.45 1 -0.69 88 89
HIF1A/JAB1 0.017 0.06 -10000 0 -0.36 1 1
CP -0.16 0.39 -10000 0 -0.82 109 109
CXCL12 -0.12 0.36 -10000 0 -0.81 80 80
COPS5 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.04 0.01 -10000 0 -10000 0 0
BNIP3 -0.12 0.35 -10000 0 -0.8 81 81
EGLN3 -0.12 0.36 -10000 0 -0.81 84 84
CA9 -0.15 0.38 -10000 0 -0.8 102 102
TERT -0.14 0.37 -10000 0 -0.8 98 98
ENO1 -0.12 0.35 -10000 0 -0.8 80 80
PFKL -0.12 0.35 -10000 0 -0.81 80 80
NCOA1 0.027 0.003 -10000 0 -10000 0 0
ADM -0.14 0.38 -10000 0 -0.81 101 101
ARNT -0.003 0.075 -10000 0 -10000 0 0
HNF4A -0.007 0.067 -10000 0 -0.22 39 39
ADFP -0.14 0.34 -10000 0 -0.78 88 88
SLC2A1 -0.1 0.31 0.45 1 -0.67 77 78
LEP -0.11 0.34 -10000 0 -0.82 71 71
HIF1A/ARNT/Cbp/p300 -0.12 0.36 -10000 0 -0.8 79 79
EPO -0.074 0.28 -10000 0 -0.75 42 42
CREBBP -0.023 0.13 -10000 0 -0.3 73 73
HIF1A/ARNT/Cbp/p300/HDAC7 -0.1 0.37 -10000 0 -0.79 78 78
PFKFB3 -0.12 0.35 -10000 0 -0.81 79 79
NT5E -0.12 0.36 -10000 0 -0.8 86 86
Osteopontin-mediated 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
IKK alpha homodimer -0.035 0.11 -10000 0 -0.23 111 111
NF kappa B1 p50/RelA/I kappa B alpha -0.03 0.12 0.3 3 -0.42 11 14
alphaV/beta3 Integrin/Osteopontin/Src -0.018 0.12 -10000 0 -0.26 86 86
AP1 -0.051 0.15 -10000 0 -0.4 45 45
ILK -0.043 0.11 -10000 0 -0.25 86 86
bone resorption -0.054 0.15 -10000 0 -0.37 68 68
PTK2B 0.018 0.044 -10000 0 -0.22 21 21
PYK2/p130Cas -0.017 0.13 -10000 0 -0.37 28 28
ITGAV 0.026 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.004 0.12 -10000 0 -0.29 86 86
alphaV/beta3 Integrin/Osteopontin -0.031 0.13 -10000 0 -0.27 125 125
MAP3K1 -0.045 0.11 0.2 1 -0.24 121 122
JUN 0.022 0.023 -10000 0 -0.22 5 5
MAPK3 -0.054 0.11 0.2 1 -0.24 119 120
MAPK1 -0.053 0.11 0.2 1 -0.24 120 121
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.047 0.11 0.2 1 -0.25 85 86
ITGB3 -0.03 0.13 -10000 0 -0.28 120 120
NFKBIA -0.052 0.12 0.2 1 -0.3 41 42
FOS -0.024 0.14 -10000 0 -0.36 86 86
CD44 -0.019 0.13 -10000 0 -0.38 72 72
CHUK 0.024 0.008 -10000 0 -10000 0 0
PLAU -0.1 0.26 -10000 0 -1.2 31 31
NF kappa B1 p50/RelA -0.03 0.13 -10000 0 -0.36 32 32
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
RELA 0.027 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.003 0.097 -10000 0 -0.25 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.05 0.12 0.19 3 -0.26 129 132
VAV3 -0.091 0.13 0.2 2 -0.28 139 141
MAP3K14 -0.048 0.12 0.2 1 -0.25 121 122
ROCK2 0.014 0.077 -10000 0 -0.46 17 17
SPP1 -0.05 0.15 -10000 0 -0.31 149 149
RAC1 0.023 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.064 0.12 0.19 2 -0.33 49 51
MMP2 -0.062 0.13 -10000 0 -0.39 46 46
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.066 0.22 -10000 0 -0.61 83 83
IHH -0.001 0.068 -10000 0 -0.23 15 15
SHH Np/Cholesterol/GAS1 -0.014 0.09 -10000 0 -0.26 64 64
LRPAP1 0.027 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.014 0.09 0.25 64 -10000 0 64
SMO/beta Arrestin2 -0.019 0.14 -10000 0 -0.47 31 31
SMO -0.031 0.14 -10000 0 -0.48 33 33
AKT1 -0.005 0.11 -10000 0 -0.47 22 22
ARRB2 0.027 0.002 -10000 0 -10000 0 0
BOC 0.023 0.037 -10000 0 -0.34 6 6
ADRBK1 0.027 0.003 -10000 0 -10000 0 0
heart looping -0.03 0.13 -10000 0 -0.48 33 33
STIL -0.026 0.15 0.24 1 -0.36 59 60
DHH N/PTCH2 0 0.096 -10000 0 -0.33 39 39
DHH N/PTCH1 -0.038 0.15 -10000 0 -0.34 85 85
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DHH -0.014 0.12 -10000 0 -0.32 75 75
PTHLH -0.079 0.27 -10000 0 -0.75 80 80
determination of left/right symmetry -0.03 0.13 -10000 0 -0.48 33 33
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
skeletal system development -0.077 0.27 -10000 0 -0.74 80 80
IHH N/Hhip -0.045 0.14 -10000 0 -0.35 98 98
DHH N/Hhip -0.052 0.15 -10000 0 -0.35 112 112
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.03 0.13 -10000 0 -0.48 33 33
pancreas development -0.058 0.17 -10000 0 -0.36 144 144
HHAT 0.016 0.071 -10000 0 -0.44 15 15
PI3K 0.039 0.008 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.008 0.069 -10000 0 -0.24 46 46
somite specification -0.03 0.13 -10000 0 -0.48 33 33
SHH Np/Cholesterol/PTCH1 -0.047 0.13 -10000 0 -0.38 56 56
SHH Np/Cholesterol/PTCH2 -0.017 0.088 -10000 0 -0.26 66 66
SHH Np/Cholesterol/Megalin -0.067 0.13 -10000 0 -0.29 132 132
SHH -0.03 0.1 -10000 0 -0.33 60 60
catabolic process -0.031 0.14 -10000 0 -0.37 80 80
SMO/Vitamin D3 -0.044 0.14 -10000 0 -0.42 46 46
SHH Np/Cholesterol/Hhip -0.049 0.12 -10000 0 -0.28 117 117
LRP2 -0.1 0.2 -10000 0 -0.36 219 219
receptor-mediated endocytosis -0.079 0.17 -10000 0 -0.47 65 65
SHH Np/Cholesterol/BOC -0.014 0.086 -10000 0 -0.26 63 63
SHH Np/Cholesterol/CDO -0.02 0.096 -10000 0 -0.27 73 73
mesenchymal cell differentiation 0.049 0.12 0.28 117 -10000 0 117
mol:Vitamin D3 -0.02 0.16 -10000 0 -0.38 56 56
IHH N/PTCH2 0.017 0.062 -10000 0 -0.35 10 10
CDON 0.006 0.093 -10000 0 -0.4 31 31
IHH N/PTCH1 -0.025 0.15 -10000 0 -0.37 80 80
Megalin/LRPAP1 -0.057 0.15 -10000 0 -0.33 129 129
PTCH2 0.017 0.057 -10000 0 -0.38 12 12
SHH Np/Cholesterol -0.02 0.081 -10000 0 -0.25 60 60
PTCH1 -0.031 0.14 -10000 0 -0.37 80 80
HHIP -0.058 0.17 -10000 0 -0.36 144 144
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.016 0.13 -10000 0 -0.36 61 61
alphaM/beta2 Integrin/GPIbA -0.01 0.13 -10000 0 -0.36 62 62
alphaM/beta2 Integrin/proMMP-9 -0.079 0.15 -10000 0 -0.33 130 130
PLAUR -0.012 0.092 -10000 0 -0.24 89 89
HMGB1 0.009 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.003 0.12 -10000 0 -0.38 46 46
AGER -0.003 0.081 -10000 0 -0.46 17 17
RAP1A 0.024 0.009 -10000 0 -10000 0 0
SELPLG 0.006 0.096 -10000 0 -0.44 29 29
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.051 0.16 -10000 0 -0.38 77 77
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.097 0.17 -10000 0 -0.29 255 255
CYR61 -0.021 0.12 -10000 0 -0.32 85 85
TLN1 0.026 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.029 0.12 -10000 0 -0.37 41 41
RHOA 0.027 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.005 0.065 -10000 0 -0.22 50 50
MYH2 -0.049 0.12 -10000 0 -0.38 40 40
MST1R 0.014 0.076 -10000 0 -0.44 18 18
leukocyte activation during inflammatory response -0.029 0.13 -10000 0 -0.31 83 83
APOB -0.028 0.14 -10000 0 -0.34 97 97
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.007 0.082 -10000 0 -0.29 42 42
JAM3 0.026 0.011 -10000 0 -0.22 1 1
GP1BA 0.016 0.067 -10000 0 -0.41 15 15
alphaM/beta2 Integrin/CTGF -0.016 0.13 -10000 0 -0.36 64 64
alphaM/beta2 Integrin -0.052 0.13 -10000 0 -0.38 60 60
JAM3 homodimer 0.026 0.011 -10000 0 -0.22 1 1
ICAM2 0.026 0.004 -10000 0 -10000 0 0
ICAM1 -0.005 0.097 -10000 0 -0.28 68 68
phagocytosis triggered by activation of immune response cell surface activating receptor -0.052 0.13 -10000 0 -0.38 58 58
cell adhesion -0.01 0.13 -10000 0 -0.35 62 62
NFKB1 -0.11 0.2 -10000 0 -0.44 134 134
THY1 0.018 0.063 -10000 0 -0.44 12 12
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
Lipoprotein(a) -0.009 0.09 -10000 0 -0.23 72 72
alphaM/beta2 Integrin/LRP/tPA -0.019 0.13 -10000 0 -0.36 50 50
IL6 -0.14 0.26 -10000 0 -0.68 96 96
ITGB2 -0.014 0.1 -10000 0 -0.42 35 35
elevation of cytosolic calcium ion concentration -0.047 0.15 -10000 0 -0.3 131 131
alphaM/beta2 Integrin/JAM2/JAM3 0.014 0.12 -10000 0 -0.35 46 46
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.017 0.15 -10000 0 -0.32 98 98
alphaM/beta2 Integrin/uPA/Plg -0.038 0.14 -10000 0 -0.34 79 79
RhoA/GTP -0.047 0.13 -10000 0 -0.39 45 45
positive regulation of phagocytosis -0.039 0.15 -10000 0 -0.42 59 59
Ron/MSP 0.009 0.1 -10000 0 -0.34 45 45
alphaM/beta2 Integrin/uPAR/uPA -0.046 0.15 -10000 0 -0.3 131 131
alphaM/beta2 Integrin/uPAR -0.026 0.13 -10000 0 -0.36 56 56
PLAU -0.033 0.13 -10000 0 -0.28 121 121
PLAT -0.025 0.1 -10000 0 -0.23 131 131
actin filament polymerization -0.045 0.12 0.2 1 -0.37 39 40
MST1 -0.001 0.11 -10000 0 -0.4 43 43
alphaM/beta2 Integrin/lipoprotein(a) -0.026 0.14 -10000 0 -0.32 83 83
TNF -0.14 0.26 -10000 0 -0.59 132 132
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
alphaM/beta2 Integrin/uPA -0.047 0.14 -10000 0 -0.34 90 90
fibrinolysis -0.039 0.14 -10000 0 -0.34 79 79
HCK 0.016 0.064 -10000 0 -0.37 16 16
dendritic cell antigen processing and presentation -0.052 0.13 -10000 0 -0.38 58 58
VTN 0.007 0.094 -10000 0 -0.41 30 30
alphaM/beta2 Integrin/CYR61 -0.036 0.14 -10000 0 -0.35 83 83
LPA 0.011 0.05 -10000 0 -0.22 28 28
LRP1 0.024 0.027 -10000 0 -0.46 2 2
cell migration -0.079 0.15 -10000 0 -0.31 139 139
FN1 0.009 0.063 -10000 0 -0.22 46 46
alphaM/beta2 Integrin/Thy1 -0.009 0.12 -10000 0 -0.36 61 61
MPO -0.047 0.16 -10000 0 -0.34 130 130
KNG1 0.009 0.045 -10000 0 -0.22 24 24
RAP1/GDP 0.03 0.016 -10000 0 -10000 0 0
ROCK1 -0.044 0.12 -10000 0 -0.38 38 38
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.014 0.019 -10000 0 -0.22 4 4
CTGF 0.006 0.088 -10000 0 -0.36 33 33
alphaM/beta2 Integrin/Hck -0.009 0.14 -10000 0 -0.42 50 50
ITGAM -0.016 0.11 -10000 0 -0.46 35 35
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.009 0.15 -10000 0 -0.41 57 57
HP -0.049 0.15 -10000 0 -0.31 146 146
leukocyte adhesion -0.043 0.14 -10000 0 -0.38 65 65
SELP 0.005 0.065 -10000 0 -0.22 50 50
IL4-mediated 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
BCL2L1 -0.31 0.37 -10000 0 -1.2 53 53
STAT6 (cleaved dimer) -0.35 0.4 -10000 0 -1 114 114
IGHG1 -0.13 0.19 -10000 0 -0.96 15 15
IGHG3 -0.31 0.35 -10000 0 -0.98 86 86
AKT1 -0.21 0.3 -10000 0 -0.87 73 73
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.18 0.31 -10000 0 -0.97 60 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.31 -10000 0 -0.95 68 68
THY1 -0.33 0.39 -10000 0 -1.2 65 65
MYB -0.025 0.13 -10000 0 -0.31 98 98
HMGA1 0.024 0.029 -10000 0 -0.26 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.32 -10000 0 -0.85 96 96
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.32 -10000 0 -0.94 73 73
SP1 0.02 0.028 -10000 0 -10000 0 0
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
SOCS5 0.038 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.34 0.4 -10000 0 -1.1 102 102
SOCS1 -0.26 0.28 -10000 0 -0.74 92 92
SOCS3 -0.32 0.42 -10000 0 -1.1 112 112
FCER2 -0.3 0.36 -10000 0 -1 72 72
PARP14 0.02 0.039 -10000 0 -0.27 10 10
CCL17 -0.32 0.37 -10000 0 -1.1 58 58
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.24 -10000 0 -0.75 55 55
T cell proliferation -0.33 0.39 -10000 0 -1.1 84 84
IL4R/JAK1 -0.32 0.37 -10000 0 -1.1 63 63
EGR2 -0.39 0.47 -10000 0 -1.3 94 94
JAK2 -0.014 0.036 -10000 0 -10000 0 0
JAK3 -0.016 0.12 -10000 0 -0.31 77 77
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.02 -10000 0 -10000 0 0
COL1A2 -0.14 0.26 -10000 0 -1.4 19 19
CCL26 -0.29 0.38 -10000 0 -1.1 56 56
IL4R -0.34 0.39 -10000 0 -1.2 57 57
PTPN6 0.026 0.061 -10000 0 -0.43 11 11
IL13RA2 -0.55 0.58 -10000 0 -1.4 187 187
IL13RA1 -0.018 0.065 -10000 0 -0.49 8 8
IRF4 -0.12 0.29 -10000 0 -1.3 29 29
ARG1 -0.12 0.21 -10000 0 -0.97 21 21
CBL -0.24 0.3 -10000 0 -0.8 93 93
GTF3A -0.003 0.053 -10000 0 -0.17 11 11
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.019 0.063 -10000 0 -0.35 8 8
IRF4/BCL6 -0.1 0.27 -10000 0 -1.2 29 29
CD40LG 0.004 0.069 -10000 0 -0.23 46 46
MAPK14 -0.28 0.34 -10000 0 -0.86 116 116
mitosis -0.2 0.28 -10000 0 -0.81 73 73
STAT6 -0.36 0.42 -10000 0 -1.2 77 77
SPI1 0.013 0.077 -10000 0 -0.4 20 20
RPS6KB1 -0.19 0.27 -10000 0 -0.77 72 72
STAT6 (dimer) -0.36 0.42 -10000 0 -1.2 77 77
STAT6 (dimer)/PARP14 -0.34 0.39 -10000 0 -1.1 85 85
mast cell activation 0.01 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.31 -10000 0 -0.89 77 77
FRAP1 -0.21 0.3 -10000 0 -0.87 73 73
LTA -0.34 0.41 -10000 0 -1.2 72 72
FES 0.024 0.03 -10000 0 -0.34 4 4
T-helper 1 cell differentiation 0.35 0.41 1.2 78 -10000 0 78
CCL11 -0.31 0.35 -10000 0 -1.1 56 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.3 -10000 0 -0.87 70 70
IL2RG -0.007 0.1 -10000 0 -0.32 57 57
IL10 -0.4 0.5 -10000 0 -1.4 103 103
IRS1 0.022 0.05 -10000 0 -0.46 7 7
IRS2 0.026 0.005 -10000 0 -10000 0 0
IL4 -0.084 0.12 -10000 0 -0.85 6 6
IL5 -0.32 0.37 -10000 0 -1.1 56 56
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.28 0.32 -10000 0 -0.94 61 61
COL1A1 -0.33 0.52 -10000 0 -1.4 109 109
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.31 0.37 -10000 0 -1.2 50 50
IL2R gamma/JAK3 -0.019 0.12 -10000 0 -0.33 61 61
TFF3 -0.32 0.37 -10000 0 -1.2 55 55
ALOX15 -0.32 0.37 -10000 0 -1.1 59 59
MYBL1 0.025 0.017 -10000 0 -0.22 3 3
T-helper 2 cell differentiation -0.3 0.34 -10000 0 -0.94 88 88
SHC1 0.022 0.035 -10000 0 -0.22 13 13
CEBPB 0.013 0.073 -10000 0 -0.38 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.31 -10000 0 -0.89 78 78
mol:PI-3-4-5-P3 -0.21 0.3 -10000 0 -0.87 73 73
PI3K -0.23 0.33 -10000 0 -0.96 72 72
DOK2 -0.029 0.14 -10000 0 -0.32 104 104
ETS1 0.031 0.042 -10000 0 -0.33 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.22 -10000 0 -0.7 53 53
ITGB3 -0.36 0.43 -10000 0 -1.3 70 70
PIGR -0.38 0.46 -10000 0 -1.4 87 87
IGHE 0.02 0.054 0.16 12 -0.22 13 25
MAPKKK cascade -0.15 0.22 -10000 0 -0.68 53 53
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.32 0.37 -10000 0 -1.1 61 61
RETNLB -0.32 0.37 -10000 0 -1.1 58 58
SELP -0.32 0.37 -10000 0 -1.2 53 53
AICDA -0.3 0.36 -10000 0 -1.1 65 65
Arf6 signaling events

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
CENTA1/KIF3B 0.02 0.05 -10000 0 -0.28 12 12
ARNO/beta Arrestin1-2 -0.05 0.26 -10000 0 -0.77 72 72
EGFR -0.019 0.13 -10000 0 -0.46 53 53
EPHA2 0.009 0.064 -10000 0 -0.25 35 35
USP6 0.02 0.046 -10000 0 -0.27 14 14
IQSEC1 0.025 0.017 -10000 0 -0.22 3 3
EGFR/EGFR/EGF/EGF -0.019 0.12 -10000 0 -0.34 79 79
ARRB2 0.013 0.013 -10000 0 -10000 0 0
mol:GTP 0.009 0.041 0.15 4 -0.18 13 17
ARRB1 0.017 0.068 -10000 0 -0.46 13 13
FBXO8 0.026 0.005 -10000 0 -10000 0 0
TSHR -0.12 0.2 -10000 0 -0.35 249 249
EGF -0.006 0.11 -10000 0 -0.38 53 53
somatostatin receptor activity 0 0 0.001 67 -0.001 44 111
ARAP2 0.018 0.065 -10000 0 -0.46 12 12
mol:GDP -0.016 0.12 0.19 49 -0.27 57 106
mol:PI-3-4-5-P3 0 0 0.001 79 -0.001 13 92
ITGA2B -0.003 0.11 -10000 0 -0.4 46 46
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.049 0.051 -10000 0 -0.25 6 6
ADAP1 0.007 0.076 -10000 0 -0.32 30 30
KIF13B 0.025 0.027 -10000 0 -0.46 2 2
HGF/MET -0.053 0.14 -10000 0 -0.34 108 108
PXN 0.027 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0.12 0.24 60 -0.24 49 109
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.005 0.11 -10000 0 -0.29 78 78
ADRB2 0.008 0.092 -10000 0 -0.45 25 25
receptor agonist activity 0 0 0 34 0 45 79
actin filament binding 0 0 0.001 68 0 45 113
SRC 0.024 0.027 -10000 0 -0.46 2 2
ITGB3 -0.029 0.12 -10000 0 -0.28 120 120
GNAQ 0.026 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 90 -0.001 23 113
ARF6/GDP -0.012 0.13 0.21 6 -0.42 31 37
ARF6/GDP/GULP/ACAP1 -0.019 0.15 0.22 18 -0.33 63 81
alphaIIb/beta3 Integrin/paxillin/GIT1 0.012 0.11 -10000 0 -0.27 62 62
ACAP1 -0.001 0.087 -10000 0 -0.25 65 65
ACAP2 0.026 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.019 0.02 -10000 0 -10000 0 0
EFNA1 0.025 0.024 -10000 0 -0.3 3 3
HGF -0.02 0.11 -10000 0 -0.29 87 87
CYTH3 0.008 0.003 -10000 0 -10000 0 0
CYTH2 -0.086 0.31 -10000 0 -1 67 67
NCK1 0.027 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 65 0 36 101
endosomal lumen acidification 0 0 0.001 74 0 46 120
microtubule-based process 0 0 -10000 0 0 6 6
GULP1 -0.022 0.14 -10000 0 -0.41 74 74
GNAQ/ARNO -0.064 0.29 -10000 0 -0.93 67 67
mol:Phosphatidic acid 0 0 0 22 -10000 0 22
PIP3-E 0 0 0 44 0 20 64
MET -0.06 0.16 -10000 0 -0.33 151 151
GNA14 0.013 0.074 -10000 0 -0.35 24 24
GNA15 0.011 0.08 -10000 0 -0.38 25 25
GIT1 0.026 0.019 -10000 0 -0.46 1 1
mol:PI-4-5-P2 0 0 0.001 74 -0.001 34 108
GNA11 0.019 0.06 -10000 0 -0.46 10 10
LHCGR 0.016 0.037 -10000 0 -0.22 15 15
AGTR1 -0.018 0.12 -10000 0 -0.28 94 94
desensitization of G-protein coupled receptor protein signaling pathway 0.019 0.02 -10000 0 -10000 0 0
IPCEF1/ARNO -0.085 0.28 -10000 0 -0.86 69 69
alphaIIb/beta3 Integrin -0.023 0.12 -10000 0 -0.35 61 61
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.15 0.3 -10000 0 -0.84 59 59
PCK1 -0.17 0.36 -10000 0 -1.1 60 60
HNF4A -0.17 0.32 -10000 0 -0.95 55 55
KCNJ11 -0.21 0.4 -10000 0 -1 102 102
AKT1 -0.076 0.18 -10000 0 -0.44 46 46
response to starvation -0.002 0.021 -10000 0 -0.33 1 1
DLK1 -0.2 0.37 -10000 0 -0.92 100 100
NKX2-1 -0.059 0.15 0.29 8 -0.37 49 57
ACADM -0.15 0.3 -10000 0 -0.83 59 59
TAT -0.19 0.37 -10000 0 -1.1 66 66
CEBPB 0.014 0.072 -10000 0 -0.39 19 19
CEBPA 0.017 0.056 -10000 0 -0.36 12 12
TTR -0.13 0.26 0.46 3 -0.83 46 49
PKLR -0.15 0.3 -10000 0 -0.79 74 74
APOA1 -0.19 0.39 -10000 0 -1.1 62 62
CPT1C -0.15 0.3 -10000 0 -0.85 58 58
ALAS1 -0.065 0.18 -10000 0 -0.79 3 3
TFRC -0.14 0.28 -10000 0 -0.88 42 42
FOXF1 0.015 0.061 -10000 0 -0.28 24 24
NF1 0.029 0.038 -10000 0 -0.46 4 4
HNF1A (dimer) 0.023 0.031 -10000 0 -0.49 1 1
CPT1A -0.15 0.3 -10000 0 -0.83 63 63
HMGCS1 -0.15 0.3 -10000 0 -0.84 58 58
NR3C1 -0.013 0.086 -10000 0 -0.21 74 74
CPT1B -0.16 0.32 -10000 0 -0.86 75 75
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.022 0.021 -10000 0 -10000 0 0
GCK -0.18 0.37 -10000 0 -0.92 99 99
CREB1 0.011 0.056 -10000 0 -0.21 25 25
IGFBP1 -0.21 0.47 -10000 0 -1.3 93 93
PDX1 -0.071 0.17 -10000 0 -0.61 8 8
UCP2 -0.16 0.33 -10000 0 -0.9 69 69
ALDOB -0.17 0.36 -10000 0 -0.94 78 78
AFP -0.053 0.12 -10000 0 -0.4 24 24
BDH1 -0.18 0.36 -10000 0 -0.93 87 87
HADH -0.15 0.32 -10000 0 -0.85 67 67
F2 -0.17 0.34 -10000 0 -1 45 45
HNF1A 0.023 0.031 -10000 0 -0.49 1 1
G6PC -0.022 0.11 -10000 0 -0.58 6 6
SLC2A2 -0.078 0.19 -10000 0 -0.68 6 6
INS 0.005 0.082 0.22 48 -0.39 5 53
FOXA1 -0.023 0.11 -10000 0 -0.26 98 98
FOXA3 -0.058 0.15 -10000 0 -0.34 104 104
FOXA2 -0.18 0.37 -10000 0 -0.89 89 89
ABCC8 -0.23 0.43 -10000 0 -1 122 122
ALB -0.1 0.27 -10000 0 -0.93 59 59
Aurora C 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
INCENP 0.025 0.027 -9999 0 -0.46 2 2
Aurora C/Aurora B/INCENP -0.033 0.12 -9999 0 -0.25 123 123
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.008 0.034 -9999 0 -10000 0 0
AURKB -0.09 0.19 -9999 0 -0.36 201 201
AURKC 0.011 0.064 -9999 0 -0.29 26 26
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.033 0.12 -10000 0 -0.43 26 26
ACTA1 -0.064 0.14 0.18 1 -0.35 97 98
NUMA1 -0.035 0.12 -10000 0 -0.34 56 56
SPTAN1 -0.06 0.14 0.2 3 -0.35 96 99
LIMK1 -0.031 0.15 0.22 13 -0.36 86 99
BIRC3 -0.014 0.12 -10000 0 -0.31 79 79
BIRC2 0.026 0.004 -10000 0 -10000 0 0
BAX 0.024 0.009 -10000 0 -10000 0 0
CASP10 -0.055 0.12 -10000 0 -0.28 117 117
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
PTK2 -0.036 0.12 -10000 0 -0.37 41 41
DIABLO 0.027 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.059 0.14 0.2 3 -0.35 96 99
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
GSN -0.063 0.14 0.19 1 -0.35 97 98
MADD 0.024 0.033 -10000 0 -0.46 3 3
TFAP2A -0.13 0.28 -10000 0 -0.58 167 167
BID -0.028 0.073 -10000 0 -0.19 92 92
MAP3K1 -0.014 0.071 -10000 0 -0.33 13 13
TRADD 0.026 0.019 -10000 0 -0.46 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.015 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.057 0.14 0.19 10 -0.35 96 106
CASP9 0.024 0.013 -10000 0 -0.22 1 1
DNA repair 0.014 0.06 0.24 10 -0.16 14 24
neuron apoptosis 0.017 0.063 -10000 0 -0.63 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.047 0.14 -10000 0 -0.33 97 97
APAF1 0.027 0.003 -10000 0 -10000 0 0
CASP6 -0.011 0.15 -10000 0 -0.89 12 12
TRAF2 0.026 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.056 0.14 0.25 5 -0.34 95 100
CASP7 -0.011 0.1 0.25 22 -0.34 13 35
KRT18 -0.067 0.21 -10000 0 -0.59 88 88
apoptosis -0.065 0.14 0.32 1 -0.47 39 40
DFFA -0.059 0.14 0.2 3 -0.35 97 100
DFFB -0.059 0.14 0.2 3 -0.35 97 100
PARP1 -0.014 0.06 0.16 14 -0.24 10 24
actin filament polymerization 0.027 0.14 0.33 85 -0.23 11 96
TNF -0.054 0.16 -10000 0 -0.33 149 149
CYCS -0.013 0.059 0.16 2 -0.21 16 18
SATB1 -0.017 0.14 -10000 0 -0.86 11 11
SLK -0.058 0.14 -10000 0 -0.35 94 94
p15 BID/BAX -0.018 0.075 -10000 0 -0.27 19 19
CASP2 0 0.081 0.18 17 -0.32 15 32
JNK cascade 0.014 0.071 0.33 13 -10000 0 13
CASP3 -0.065 0.15 0.19 3 -0.36 101 104
LMNB2 0.024 0.11 0.22 10 -0.4 15 25
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CASP4 -0.005 0.092 -10000 0 -0.25 74 74
Mammalian IAPs/DIABLO 0.041 0.077 -10000 0 -0.25 28 28
negative regulation of DNA binding -0.13 0.28 -10000 0 -0.58 167 167
stress fiber formation -0.057 0.14 -10000 0 -0.35 94 94
GZMB -0.062 0.14 -10000 0 -0.28 175 175
CASP1 -0.006 0.077 -10000 0 -0.27 37 37
LMNB1 0.018 0.12 0.26 5 -0.45 19 24
APP 0.017 0.064 -10000 0 -0.64 5 5
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.024 -10000 0 -0.16 12 12
VIM -0.066 0.14 0.34 1 -0.47 39 40
LMNA 0.026 0.1 0.25 6 -0.41 12 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.007 0.091 -10000 0 -0.33 21 21
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.065 0.14 -10000 0 -0.35 100 100
APAF-1/Caspase 9 -0.047 0.19 -10000 0 -0.62 64 64
nuclear fragmentation during apoptosis -0.035 0.12 -10000 0 -0.32 62 62
CFL2 -0.028 0.15 0.23 11 -0.34 85 96
GAS2 -0.067 0.14 0.2 2 -0.35 107 109
positive regulation of apoptosis 0.027 0.11 0.2 37 -0.42 16 53
PRF1 -0.031 0.13 -10000 0 -0.32 107 107
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.003 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.13 -10000 0 -0.32 60 60
NFATC4 -0.047 0.091 0.3 2 -0.24 55 57
ERBB2IP 0.027 0.019 -10000 0 -0.46 1 1
HSP90 (dimer) 0.026 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.049 0.11 -10000 0 -0.26 130 130
JUN -0.017 0.08 0.19 1 -0.34 13 14
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK7 -0.053 0.11 -10000 0 -0.25 124 124
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.045 0.14 -10000 0 -0.28 139 139
AKT1 0.006 0.007 -10000 0 -10000 0 0
BAD 0.004 0.005 -10000 0 -10000 0 0
MAPK10 -0.017 0.066 0.16 2 -0.2 11 13
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.051 0.12 -10000 0 -0.27 130 130
RAF1 -0.048 0.12 0.23 5 -0.34 53 58
ErbB2/ErbB3/neuregulin 2 -0.005 0.096 -10000 0 -0.28 63 63
STAT3 0.026 0.072 -10000 0 -1 3 3
cell migration -0.017 0.069 0.22 7 -0.19 17 24
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.12 0.26 0.48 1 -0.62 109 110
FOS -0.081 0.19 0.42 1 -0.4 143 144
NRAS 0.023 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.11 -10000 0 -0.26 130 130
MAPK3 -0.088 0.21 0.52 1 -0.5 103 104
MAPK1 -0.092 0.21 0.52 1 -0.5 106 107
JAK2 -0.053 0.1 -10000 0 -0.25 115 115
NF2 0.008 0.03 -10000 0 -0.66 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.05 0.13 0.18 2 -0.29 130 132
NRG1 -0.074 0.18 -10000 0 -0.36 171 171
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
MAPK8 -0.044 0.11 -10000 0 -0.27 116 116
MAPK9 -0.017 0.065 0.16 2 -0.19 12 14
ERBB2 -0.02 0.021 -10000 0 -0.21 4 4
ERBB3 -0.029 0.15 -10000 0 -0.41 82 82
SHC1 0.021 0.035 -10000 0 -0.22 13 13
RAC1 0.023 0.01 -10000 0 -10000 0 0
apoptosis -0.002 0.015 -10000 0 -0.2 2 2
STAT3 (dimer) 0.027 0.07 -10000 0 -0.99 3 3
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.034 0.074 -10000 0 -0.2 46 46
ErbB2/ErbB2/HSP90 (dimer) 0.009 0.024 -10000 0 -0.29 1 1
CHRNA1 -0.11 0.25 0.44 1 -0.64 100 101
myelination -0.048 0.089 0.27 4 -0.26 29 33
PPP3CB -0.05 0.097 -10000 0 -0.23 120 120
KRAS 0.025 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.023 0.12 -10000 0 -0.31 48 48
NRG2 0.023 0.042 -10000 0 -0.46 5 5
mol:GDP -0.05 0.13 0.18 2 -0.29 130 132
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.053 0.13 0.23 7 -0.34 51 58
SRC 0.024 0.027 -10000 0 -0.46 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.053 0.11 -10000 0 -0.25 129 129
MAP2K1 -0.092 0.21 0.46 1 -0.57 53 54
heart morphogenesis -0.049 0.11 -10000 0 -0.26 130 130
RAS family/GDP -0.024 0.13 -10000 0 -0.33 53 53
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.009 0.031 -10000 0 -0.71 1 1
CHRNE 0 0.03 -10000 0 -0.14 20 20
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.007 -10000 0 -10000 0 0
nervous system development -0.049 0.11 -10000 0 -0.26 130 130
CDC42 0.024 0.008 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.032 0.031 -10000 0 -0.32 4 4
Necdin/E2F1 -0.006 0.12 -10000 0 -0.31 82 82
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.01 0.12 -10000 0 -0.26 78 78
NGF (dimer)/p75(NTR)/BEX1 -0.027 0.14 -10000 0 -0.31 110 110
NT-4/5 (dimer)/p75(NTR) -0.011 0.1 -10000 0 -0.22 106 106
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.022 0.099 0.19 14 -0.25 79 93
IKBKG 0.027 0.003 -10000 0 -10000 0 0
BDNF -0.017 0.11 -10000 0 -0.26 102 102
MGDIs/NGR/p75(NTR)/LINGO1 -0.02 0.14 -10000 0 -0.32 100 100
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.012 0.11 -10000 0 -0.29 65 65
LINGO1 -0.004 0.12 -10000 0 -0.46 41 41
Sortilin/TRAF6/NRIF 0.028 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.017 0.11 -10000 0 -0.26 102 102
NTRK1 0.011 0.07 -10000 0 -0.27 34 34
RTN4R -0.005 0.11 -10000 0 -0.38 51 51
neuron apoptosis -0.05 0.15 0.31 4 -0.44 47 51
IRAK1 0.027 0.003 -10000 0 -10000 0 0
SHC1 -0.037 0.11 -10000 0 -0.3 84 84
ARHGDIA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.068 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.006 0.13 -10000 0 -0.28 94 94
MAGEH1 0.014 0.077 -10000 0 -0.46 17 17
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.036 0.16 -10000 0 -0.29 152 152
Mammalian IAPs/DIABLO 0.041 0.077 -10000 0 -0.25 28 28
proNGF (dimer) -0.02 0.13 -10000 0 -0.38 70 70
MAGED1 0.027 0 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.009 0.048 -10000 0 -0.23 23 23
ZNF274 0.024 0.009 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.012 0.1 -10000 0 -0.26 79 79
NGF -0.02 0.13 -10000 0 -0.38 70 70
cell cycle arrest -0.028 0.1 0.33 9 -0.24 79 88
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.014 0.1 -10000 0 -0.27 80 80
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.005 0.092 -10000 0 -0.28 47 47
NCSTN 0.027 0.003 -10000 0 -10000 0 0
mol:GTP -0.014 0.12 -10000 0 -0.3 82 82
PSENEN 0.024 0.008 -10000 0 -10000 0 0
mol:ceramide -0.029 0.1 0.18 5 -0.27 84 89
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.02 0.1 -10000 0 -0.34 28 28
p75(NTR)/beta APP 0.002 0.099 -10000 0 -0.23 90 90
BEX1 0.005 0.1 -10000 0 -0.46 30 30
mol:GDP -0.044 0.11 -10000 0 -0.3 83 83
NGF (dimer) -0.057 0.13 -10000 0 -0.27 156 156
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.004 0.13 -10000 0 -0.29 98 98
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.009 0.098 -10000 0 -0.25 74 74
MYD88 0.021 0.053 -10000 0 -0.46 8 8
CHUK 0.024 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.013 0.12 -10000 0 -0.3 82 82
RHOB 0.026 0.01 -10000 0 -0.22 1 1
RHOA 0.027 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.029 0.05 -10000 0 -0.21 24 24
NT3 (dimer) 0.013 0.043 -10000 0 -0.22 21 21
TP53 -0.016 0.1 0.21 20 -0.27 55 75
PRDM4 -0.029 0.1 0.18 5 -0.28 84 89
BDNF (dimer) -0.067 0.14 -10000 0 -0.26 174 174
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
SORT1 0.022 0.028 -10000 0 -0.46 2 2
activation of caspase activity 0.006 0.12 -10000 0 -0.26 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.001 0.12 -10000 0 -0.28 84 84
RHOC 0.022 0.025 -10000 0 -0.3 3 3
XIAP 0.027 0.001 -10000 0 -10000 0 0
MAPK10 -0.01 0.12 0.31 13 -0.33 47 60
DIABLO 0.027 0.003 -10000 0 -10000 0 0
SMPD2 -0.029 0.1 0.18 5 -0.27 84 89
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.014 0.12 -10000 0 -0.3 84 84
PSEN1 0.026 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.015 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.007 0.1 -10000 0 -0.23 102 102
MAPK8 -0.022 0.12 0.34 5 -0.32 48 53
MAPK9 -0.01 0.12 0.32 13 -0.32 45 58
APAF1 0.027 0.003 -10000 0 -10000 0 0
NTF3 0.013 0.043 -10000 0 -0.22 21 21
NTF4 0.009 0.048 -10000 0 -0.23 23 23
NDN -0.035 0.16 -10000 0 -0.46 83 83
RAC1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.008 0.11 -10000 0 -0.24 76 76
p75 CTF/Sortilin/TRAF6/NRIF 0.052 0.044 -10000 0 -0.24 9 9
RhoA-B-C/GTP -0.014 0.12 -10000 0 -0.3 82 82
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.009 0.11 -10000 0 -0.25 65 65
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.001 0.11 -10000 0 -0.27 67 67
PRKACB 0.024 0.009 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.004 0.087 -10000 0 -0.18 104 104
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.014 0.12 -10000 0 -0.31 79 79
BIRC2 0.026 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.053 0.12 0.37 5 -0.3 93 98
BAD -0.01 0.12 0.3 15 -0.32 47 62
RIPK2 0.026 0.006 -10000 0 -10000 0 0
NGFR -0.023 0.13 -10000 0 -0.33 91 91
CYCS -0.022 0.095 0.25 7 -0.26 67 74
ADAM17 0.023 0.042 -10000 0 -0.46 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0 0.12 -10000 0 -0.28 78 78
BCL2L11 -0.011 0.12 0.31 12 -0.32 48 60
BDNF (dimer)/p75(NTR) -0.027 0.12 -10000 0 -0.22 165 165
PI3K 0.001 0.12 -10000 0 -0.27 81 81
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 0.12 -10000 0 -0.28 84 84
NDNL2 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.027 0.003 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.033 0.14 -10000 0 -0.34 89 89
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.001 0.12 -10000 0 -0.28 84 84
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
PLG 0.014 0.019 -10000 0 -0.22 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.043 0.12 -10000 0 -0.3 89 89
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.027 0.001 -10000 0 -10000 0 0
CASP3 -0.009 0.12 0.28 15 -0.31 46 61
E2F1 0.014 0.065 -10000 0 -0.3 24 24
CASP9 0.024 0.013 -10000 0 -0.22 1 1
IKK complex -0.013 0.13 -10000 0 -0.34 49 49
NGF (dimer)/TRKA -0.009 0.11 -10000 0 -0.31 63 63
MMP7 -0.1 0.18 -10000 0 -0.33 241 241
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.12 -10000 0 -0.26 79 79
MMP3 -0.003 0.075 -10000 0 -0.23 66 66
APAF-1/Caspase 9 -0.028 0.088 -10000 0 -0.37 15 15
PLK1 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
regulation of centriole-centriole cohesion 0.031 0.081 0.23 87 -0.097 3 90
BUB1B -0.042 0.11 0.13 2 -0.29 101 103
PLK1 0 0.031 0.082 16 -0.12 13 29
PLK1S1 0.007 0.026 0.094 9 -0.17 5 14
KIF2A 0.001 0.034 0.21 5 -0.19 3 8
regulation of mitotic centrosome separation 0 0.031 0.082 16 -0.12 13 29
GOLGA2 0.026 0.019 -10000 0 -0.46 1 1
Hec1/SPC24 -0.071 0.16 -10000 0 -0.29 201 201
WEE1 -0.006 0.084 -10000 0 -0.37 28 28
cytokinesis -0.086 0.17 0.2 2 -0.4 138 140
PP2A-alpha B56 -0.043 0.24 -10000 0 -0.64 90 90
AURKA 0.005 0.025 0.1 2 -0.34 1 3
PICH/PLK1 -0.019 0.083 0.13 1 -0.22 71 72
CENPE -0.025 0.074 -10000 0 -0.22 62 62
RhoA/GTP 0.02 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.034 0.21 5 -0.19 3 8
PPP2CA 0.027 0.003 -10000 0 -10000 0 0
FZR1 0.026 0.005 -10000 0 -10000 0 0
TPX2 -0.014 0.081 0.096 14 -0.27 54 68
PAK1 0.012 0.066 -10000 0 -0.26 34 34
SPC24 -0.074 0.17 -10000 0 -0.33 183 183
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.044 0.11 -10000 0 -0.27 119 119
GORASP1 0.027 0.003 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 5 -0.018 8 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.001 0.017 0.048 17 -0.064 12 29
G2 phase of mitotic cell cycle 0 0.002 0.014 6 -0.01 1 7
STAG2 0.027 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.019 0.055 -10000 0 -0.53 6 6
spindle elongation 0 0.031 0.082 16 -0.12 13 29
ODF2 0.027 0.004 -10000 0 -10000 0 0
BUB1 -0.072 0.25 -10000 0 -0.7 90 90
TPT1 -0.001 0.043 -10000 0 -0.18 28 28
CDC25C -0.043 0.13 -10000 0 -0.38 83 83
CDC25B 0.026 0.006 -10000 0 -10000 0 0
SGOL1 -0.031 0.081 0.097 3 -0.23 87 90
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.014 0.058 -10000 0 -0.23 10 10
CDC14B 0.009 0.002 -10000 0 -10000 0 0
CDC20 -0.063 0.15 -10000 0 -0.3 178 178
PLK1/PBIP1 -0.022 0.073 0.091 1 -0.18 91 92
mitosis -0.002 0.004 0.02 4 -10000 0 4
FBXO5 -0.001 0.032 0.15 3 -0.14 6 9
CDC2 0 0.003 -10000 0 -0.009 8 8
NDC80 -0.082 0.18 -10000 0 -0.36 183 183
metaphase plate congression -0.014 0.075 -10000 0 -0.23 64 64
ERCC6L -0.014 0.082 -10000 0 -0.22 63 63
NLP/gamma Tubulin 0.002 0.019 0.068 6 -0.082 9 15
microtubule cytoskeleton organization -0.001 0.043 -10000 0 -0.18 28 28
G2/M transition DNA damage checkpoint 0 0.002 0.01 7 -10000 0 7
PPP1R12A 0.027 0.004 -10000 0 -10000 0 0
interphase 0 0.002 0.01 7 -10000 0 7
PLK1/PRC1-2 -0.049 0.12 -10000 0 -0.24 167 167
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.035 -10000 0 -0.2 2 2
RAB1A 0.027 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.001 0.026 0.076 23 -0.083 12 35
mitotic prometaphase 0.001 0.006 0.017 63 -0.012 5 68
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.076 -10000 0 -0.24 37 37
microtubule-based process -0.059 0.12 0.12 1 -0.23 179 180
Golgi organization 0 0.031 0.082 16 -0.12 13 29
Cohesin/SA2 0.013 0.031 0.1 1 -0.12 8 9
PPP1CB/MYPT1 0.039 0.012 -10000 0 -10000 0 0
KIF20A -0.12 0.2 -10000 0 -0.35 253 253
APC/C/CDC20 -0.027 0.091 0.12 1 -0.18 140 141
PPP2R1A 0.024 0.009 -10000 0 -10000 0 0
chromosome segregation -0.022 0.072 0.09 1 -0.18 91 92
PRC1 0.015 0.054 -10000 0 -0.23 30 30
ECT2 -0.001 0.041 0.2 8 -0.15 13 21
C13orf34 0.001 0.026 0.074 18 -0.092 13 31
NUDC -0.014 0.075 -10000 0 -0.24 64 64
regulation of attachment of spindle microtubules to kinetochore -0.041 0.11 0.13 2 -0.28 101 103
spindle assembly 0.001 0.026 0.079 12 -0.098 13 25
spindle stabilization 0.007 0.026 0.094 9 -0.17 5 14
APC/C/HCDH1 0.025 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 -0.06 0.12 0.12 1 -0.23 179 180
CCNB1 -0.004 0.083 -10000 0 -0.22 84 84
PPP1CB 0.026 0.014 -10000 0 -0.22 2 2
BTRC 0.024 0.008 -10000 0 -10000 0 0
ROCK2 0.002 0.074 -10000 0 -0.39 20 20
TUBG1 0.007 0.019 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle -0.008 0.047 -10000 0 -0.24 9 9
MLF1IP -0.028 0.092 -10000 0 -0.22 106 106
INCENP 0.024 0.027 -10000 0 -0.47 2 2
IL1-mediated signaling events

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
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.024 0.027 -10000 0 -0.46 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.029 0.11 -10000 0 -0.35 41 41
IRAK/TOLLIP 0.032 0.008 -10000 0 -10000 0 0
IKBKB 0.026 0.004 -10000 0 -10000 0 0
IKBKG 0.027 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.078 0.16 -10000 0 -0.34 138 138
IL1A -0.036 0.15 -10000 0 -0.34 111 111
IL1B -0.067 0.14 -10000 0 -0.25 205 205
IRAK/TRAF6/p62/Atypical PKCs 0.039 0.074 -10000 0 -0.22 41 41
IL1R2 -0.071 0.16 -10000 0 -0.31 191 191
IL1R1 0.001 0.089 -10000 0 -0.28 55 55
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.03 0.099 0.18 1 -0.37 30 31
TOLLIP 0.026 0.006 -10000 0 -10000 0 0
TICAM2 0.017 0.063 -10000 0 -0.38 15 15
MAP3K3 0.026 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.025 0.069 -10000 0 -0.4 4 4
JUN 0.004 0.031 0.17 3 -0.21 11 14
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.039 0.14 -10000 0 -0.27 122 122
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.13 -10000 0 -0.27 104 104
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.13 -10000 0 -0.26 84 84
IL1 beta fragment/IL1R1/IL1RAP -0.061 0.14 -10000 0 -0.29 148 148
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.009 0.034 0.18 6 -0.21 12 18
IRAK1 0.017 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.05 0.14 -10000 0 -0.33 103 103
IRAK4 0.026 0.005 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
PI3K 0.039 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.032 0.12 -10000 0 -0.37 41 41
CHUK 0.024 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.061 0.14 -10000 0 -0.29 148 148
IL1 beta/IL1R2 -0.098 0.16 -10000 0 -0.31 186 186
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.018 -10000 0 -0.22 2 2
NF kappa B1 p50/RelA -0.041 0.12 -10000 0 -0.34 39 39
IRAK3 0.022 0.04 -10000 0 -0.38 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.044 0.14 -10000 0 -0.28 132 132
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.1 -10000 0 -0.26 81 81
IL1 alpha/IL1R1/IL1RAP -0.029 0.13 -10000 0 -0.29 100 100
RELA 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.021 0.053 -10000 0 -0.46 8 8
IRAK/TRAF6/MEKK3 0.046 0.02 -10000 0 -0.23 2 2
IL1RAP -0.01 0.1 -10000 0 -0.26 84 84
UBE2N 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.05 0.12 -10000 0 -0.33 48 48
CASP1 0.007 0.085 -10000 0 -0.33 35 35
IL1RN/IL1R2 -0.099 0.17 -10000 0 -0.34 181 181
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.051 0.15 -10000 0 -0.27 150 150
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.1 -10000 0 -0.38 30 30
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
IL1RN -0.07 0.17 -10000 0 -0.31 188 188
TRAF6/TAK1/TAB1/TAB2 0.036 0.017 -10000 0 -0.22 2 2
MAP2K6 0.02 0.025 0.18 9 -0.22 3 12
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.008 0.086 -10000 0 -0.23 79 79
epithelial cell differentiation 0.01 0.097 -10000 0 -0.23 75 75
CYFIP2 0.022 0.041 -10000 0 -0.36 7 7
ENAH -0.009 0.069 0.36 4 -0.23 7 11
EGFR -0.019 0.13 -10000 0 -0.46 53 53
EPHA2 0.009 0.064 -10000 0 -0.25 35 35
MYO6 -0.013 0.084 0.18 12 -0.22 74 86
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.045 0.033 -10000 0 -0.27 4 4
AQP5 -0.1 0.19 -10000 0 -0.46 126 126
CTNND1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.014 0.082 0.18 11 -0.22 74 85
regulation of calcium-dependent cell-cell adhesion -0.02 0.094 0.18 12 -0.23 89 101
EGF -0.006 0.11 -10000 0 -0.38 53 53
NCKAP1 0.027 0.001 -10000 0 -10000 0 0
AQP3 -0.026 0.12 -10000 0 -0.46 29 29
cortical microtubule organization 0.01 0.097 -10000 0 -0.23 75 75
GO:0000145 -0.022 0.075 0.17 11 -0.21 74 85
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.014 0.1 -10000 0 -0.23 75 75
MLLT4 0.025 0.02 -10000 0 -0.46 1 1
ARF6/GDP -0.027 0.068 -10000 0 -0.26 10 10
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.049 0.051 -10000 0 -0.25 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.022 0.084 0.18 3 -0.3 27 30
PVRL2 0.023 0.021 -10000 0 -0.46 1 1
ZYX -0.013 0.076 0.18 7 -0.22 63 70
ARF6/GTP 0.054 0.051 -10000 0 -0.23 6 6
CDH1 -0.051 0.16 -10000 0 -0.36 132 132
EGFR/EGFR/EGF/EGF -0.028 0.12 -10000 0 -0.26 120 120
RhoA/GDP 0.013 0.093 -10000 0 -0.22 75 75
actin cytoskeleton organization -0.017 0.08 0.18 12 -0.22 74 86
IGF-1R heterotetramer 0.02 0.057 -10000 0 -0.46 9 9
GIT1 0.026 0.019 -10000 0 -0.46 1 1
IGF1R 0.02 0.057 -10000 0 -0.46 9 9
IGF1 0.013 0.077 -10000 0 -0.38 22 22
DIAPH1 -0.002 0.17 -10000 0 -0.61 9 9
Wnt receptor signaling pathway -0.01 0.097 0.23 75 -10000 0 75
RHOA 0.027 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.028 0.069 -10000 0 -0.29 7 7
CTNNA1 0.027 0.003 -10000 0 -10000 0 0
VCL -0.018 0.082 0.18 11 -0.22 74 85
EFNA1 0.025 0.024 -10000 0 -0.3 3 3
LPP -0.026 0.084 0.18 10 -0.22 80 90
Ephrin A1/EPHA2 -0.001 0.091 -10000 0 -0.22 78 78
SEC6/SEC8 -0.016 0.066 -10000 0 -0.21 45 45
MGAT3 -0.021 0.096 0.18 12 -0.24 89 101
HGF/MET -0.053 0.13 -10000 0 -0.27 131 131
HGF -0.02 0.11 -10000 0 -0.29 87 87
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.008 0.087 -10000 0 -0.23 79 79
actin cable formation 0.001 0.081 0.26 10 -0.28 9 19
KIAA1543 -0.025 0.081 0.17 8 -0.22 77 85
KIFC3 -0.015 0.084 0.18 8 -0.22 75 83
NCK1 0.027 0.003 -10000 0 -10000 0 0
EXOC3 0.026 0.004 -10000 0 -10000 0 0
ACTN1 -0.022 0.089 0.18 11 -0.23 80 91
NCK1/GIT1 0.039 0.015 -10000 0 -0.33 1 1
mol:GDP 0.01 0.097 -10000 0 -0.23 75 75
EXOC4 0.021 0.011 -10000 0 -10000 0 0
STX4 -0.014 0.084 0.18 12 -0.22 75 87
PIP5K1C -0.014 0.083 0.18 11 -0.22 74 85
LIMA1 0.021 0.05 -10000 0 -0.46 7 7
ABI1 0.024 0.009 -10000 0 -10000 0 0
ROCK1 -0.008 0.078 0.37 4 -0.26 7 11
adherens junction assembly -0.011 0.088 0.28 8 -0.36 10 18
IGF-1R heterotetramer/IGF1 -0.002 0.1 -10000 0 -0.24 89 89
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.033 0.025 -10000 0 -0.33 2 2
MET -0.06 0.16 -10000 0 -0.33 151 151
PLEKHA7 -0.017 0.088 0.18 8 -0.23 77 85
mol:GTP 0.047 0.05 -10000 0 -0.25 6 6
establishment of epithelial cell apical/basal polarity 0.03 0.11 0.32 21 -0.39 2 23
cortical actin cytoskeleton stabilization -0.008 0.086 -10000 0 -0.23 79 79
regulation of cell-cell adhesion -0.017 0.08 0.18 12 -0.22 74 86
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.008 0.087 -10000 0 -0.23 79 79
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.018 0.12 -10000 0 -0.24 137 137
MAPK9 0.009 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.057 0.12 -10000 0 -0.23 175 175
GNB1/GNG2 0.029 0.029 -10000 0 -0.28 5 5
GNB1 0.024 0.008 -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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.039 0.11 -10000 0 -0.25 139 139
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 0.014 0.028 0.067 139 -10000 0 139
GNAL -0.075 0.2 -10000 0 -0.46 139 139
GNG2 0.022 0.043 -10000 0 -0.46 5 5
CRH -0.071 0.17 -10000 0 -0.33 175 175
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.037 -10000 0 -0.31 9 9
MAPK11 0.007 0.018 -10000 0 -0.31 2 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.049 0.024 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.048 0.024 -10000 0 -10000 0 0
LAMA1 -0.032 0.15 -10000 0 -0.42 85 85
PRNP 0.025 0.02 -10000 0 -0.46 1 1
GPC1/SLIT2 -0.023 0.12 -10000 0 -0.33 62 62
SMAD2 0.021 0.03 0.19 10 -0.25 2 12
GPC1/PrPc/Cu2+ 0.032 0.028 -10000 0 -0.52 1 1
GPC1/Laminin alpha1 -0.007 0.12 -10000 0 -0.33 74 74
TDGF1 -0.041 0.16 -10000 0 -0.39 105 105
CRIPTO/GPC1 -0.014 0.12 -10000 0 -0.34 75 75
APP/GPC1 0.035 0.025 -10000 0 -0.33 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.021 0.1 -10000 0 -0.28 76 76
FLT1 0.025 0.02 -10000 0 -0.46 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.03 -10000 0 -0.28 2 2
SERPINC1 0.019 0.039 -10000 0 -0.22 17 17
FYN -0.02 0.098 -10000 0 -0.28 75 75
FGR -0.022 0.098 -10000 0 -0.28 74 74
positive regulation of MAPKKK cascade -0.044 0.14 0.31 2 -0.38 74 76
SLIT2 -0.053 0.16 -10000 0 -0.32 153 153
GPC1/NRG -0.038 0.13 -10000 0 -0.33 97 97
NRG1 -0.073 0.18 -10000 0 -0.36 171 171
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.021 0.068 -10000 0 -0.24 7 7
LYN -0.021 0.1 -10000 0 -0.29 74 74
mol:Spermine 0.007 0.021 -10000 0 -0.17 8 8
cell growth 0.048 0.024 -10000 0 -10000 0 0
BMP signaling pathway -0.023 0.032 0.25 8 -10000 0 8
SRC -0.02 0.098 -10000 0 -0.28 72 72
TGFBR1 0.026 0.019 -10000 0 -0.46 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.11 0.19 -10000 0 -0.34 229 229
GPC1 0.023 0.032 -10000 0 -0.25 8 8
TGFBR1 (dimer) 0.026 0.019 -10000 0 -0.46 1 1
VEGFA -0.015 0.093 -10000 0 -0.22 110 110
BLK -0.041 0.11 -10000 0 -0.29 81 81
HCK -0.024 0.11 -10000 0 -0.3 76 76
FGF2 0.025 0.022 -10000 0 -0.34 2 2
FGFR1 0.026 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.46 1 1
TGFBR2 0.025 0.017 -10000 0 -0.22 3 3
cell death 0.035 0.025 -10000 0 -0.33 1 1
ATIII/GPC1 0.031 0.035 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.067 0.14 -10000 0 -0.32 124 124
LCK -0.053 0.12 -10000 0 -0.29 113 113
neuron differentiation -0.038 0.13 -10000 0 -0.32 97 97
PrPc/Cu2+ 0.019 0.014 -10000 0 -0.33 1 1
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.025 0.017 -10000 0 -0.22 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.014 0.15 0.44 7 -1.1 9 16
VDR -0.039 0.14 -10000 0 -0.31 127 127
FAM120B 0.026 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.039 0.14 -10000 0 -0.32 96 96
RXRs/LXRs/DNA/Oxysterols -0.056 0.18 -10000 0 -0.47 84 84
MED1 0.027 0.002 -10000 0 -10000 0 0
mol:9cRA -0.004 0.018 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.025 0.048 -10000 0 -0.22 21 21
RXRs/NUR77 0.001 0.12 -10000 0 -0.26 94 94
RXRs/PPAR -0.018 0.11 -10000 0 -0.25 104 104
NCOR2 0.025 0.027 -10000 0 -0.46 2 2
VDR/VDR/Vit D3 -0.026 0.1 -10000 0 -0.22 127 127
RARs/VDR/DNA/Vit D3 0.02 0.09 -10000 0 -0.24 49 49
RARA 0.027 0.002 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.039 0.14 -10000 0 -0.31 127 127
RARs/RARs/DNA/9cRA 0.04 0.027 -10000 0 -0.22 2 2
RARG 0.025 0.017 -10000 0 -0.22 3 3
RPS6KB1 0.031 0.1 0.56 17 -0.43 9 26
RARs/THRs/DNA/SMRT 0.024 0.051 -10000 0 -0.23 24 24
THRA 0.016 0.073 -10000 0 -0.46 15 15
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.026 0.1 -10000 0 -0.22 127 127
RXRs/PPAR/9cRA/PGJ2/DNA -0.012 0.12 0.31 4 -0.26 97 101
NR1H4 -0.047 0.15 -10000 0 -0.31 141 141
RXRs/LXRs/DNA 0.001 0.13 -10000 0 -0.33 24 24
NR1H2 0.019 0.023 -10000 0 -10000 0 0
NR1H3 0.02 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.03 0.14 -10000 0 -0.26 136 136
NR4A1 0.015 0.057 -10000 0 -0.25 27 27
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.044 0.12 -10000 0 -0.26 126 126
RXRG -0.055 0.18 -10000 0 -0.44 108 108
RXR alpha/CCPG 0.031 0.027 -10000 0 -0.33 1 1
RXRA 0.019 0.031 -10000 0 -0.46 1 1
RXRB 0.02 0.026 -10000 0 -10000 0 0
THRB 0.015 0.063 -10000 0 -0.3 23 23
PPARG 0.008 0.086 -10000 0 -0.36 31 31
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.12 0.34 -10000 0 -1 77 77
mol:Oxysterols -0.003 0.016 -10000 0 -10000 0 0
cholesterol transport -0.055 0.18 -10000 0 -0.45 90 90
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.025 0.025 -10000 0 -0.28 4 4
RXRs/NUR77/BCL2 -0.018 0.1 -10000 0 -0.25 96 96
SREBF1 -0.059 0.2 -10000 0 -0.81 25 25
RXRs/RXRs/DNA/9cRA -0.012 0.12 0.3 4 -0.26 97 101
ABCA1 -0.062 0.21 -10000 0 -0.83 28 28
RARs/THRs 0.062 0.066 -10000 0 -0.25 21 21
RXRs/FXR -0.034 0.15 -10000 0 -0.29 132 132
BCL2 0.024 0.033 -10000 0 -0.46 3 3
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.088 0.27 -10000 0 -0.86 57 57
NCK1/PAK1/Dok-R -0.069 0.12 -10000 0 -0.4 61 61
NCK1/Dok-R -0.08 0.3 -10000 0 -1 52 52
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol 0.014 0.061 0.24 42 -10000 0 42
RELA 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.021 0.035 -10000 0 -0.22 13 13
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
F2 0.021 0.066 0.25 36 -0.24 4 40
TNIP2 0.026 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.043 0.28 -10000 0 -0.97 52 52
FN1 0.009 0.063 -10000 0 -0.22 46 46
PLD2 -0.076 0.3 -10000 0 -1.1 52 52
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
GRB14 -0.11 0.19 -10000 0 -0.33 246 246
ELK1 -0.065 0.27 -10000 0 -0.97 52 52
GRB7 0.004 0.066 -10000 0 -0.22 52 52
PAK1 0.012 0.066 -10000 0 -0.26 34 34
Tie2/Ang1/alpha5/beta1 Integrin -0.061 0.3 -10000 0 -1 52 52
CDKN1A -0.095 0.26 -10000 0 -0.66 100 100
ITGA5 0.007 0.071 -10000 0 -0.24 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.08 0.3 -10000 0 -1 52 52
CRK 0.027 0.003 -10000 0 -10000 0 0
mol:NO -0.034 0.22 0.36 1 -0.61 57 58
PLG -0.08 0.3 -10000 0 -1.1 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.069 0.25 -10000 0 -0.84 52 52
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
ANGPT2 -0.1 0.28 -10000 0 -0.93 51 51
BMX -0.084 0.3 -10000 0 -1.1 52 52
ANGPT1 -0.096 0.32 -10000 0 -1.3 42 42
tube development -0.091 0.25 -10000 0 -0.68 81 81
ANGPT4 -0.01 0.11 -10000 0 -0.33 58 58
response to hypoxia -0.008 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.13 0.33 -10000 0 -1.2 52 52
alpha5/beta1 Integrin 0.021 0.055 -10000 0 -0.31 7 7
FGF2 0.026 0.022 -10000 0 -0.34 2 2
STAT5A (dimer) -0.11 0.3 -10000 0 -0.75 102 102
mol:L-citrulline -0.034 0.22 0.36 1 -0.61 57 58
AGTR1 -0.021 0.12 -10000 0 -0.29 94 94
MAPK14 -0.081 0.3 -10000 0 -1.1 53 53
Tie2/SHP2 -0.032 0.21 -10000 0 -1 21 21
TEK -0.033 0.22 -10000 0 -1.1 21 21
RPS6KB1 -0.073 0.26 -10000 0 -0.84 53 53
Angiotensin II/AT1 -0.017 0.081 -10000 0 -0.2 96 96
Tie2/Ang1/GRB2 -0.072 0.31 -10000 0 -1.1 52 52
MAPK3 -0.071 0.28 -10000 0 -0.99 52 52
MAPK1 -0.071 0.28 -10000 0 -0.98 52 52
Tie2/Ang1/GRB7 -0.082 0.31 -10000 0 -1.1 52 52
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.077 0.3 -10000 0 -1.1 52 52
PI3K -0.091 0.3 -10000 0 -1 53 53
FES -0.085 0.31 -10000 0 -1.1 53 53
Crk/Dok-R -0.08 0.3 -10000 0 -1 52 52
Tie2/Ang1/ABIN2 -0.072 0.31 -10000 0 -1.1 52 52
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.078 0.25 -10000 0 -0.76 57 57
STAT5A 0.019 0.063 -10000 0 -0.46 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.066 0.26 -10000 0 -0.84 53 53
Tie2/Ang2 -0.13 0.34 -10000 0 -0.94 81 81
Tie2/Ang1 -0.079 0.32 -10000 0 -1.1 52 52
FOXO1 -0.086 0.26 -10000 0 -0.72 82 82
ELF1 0.027 0.023 -10000 0 -10000 0 0
ELF2 -0.073 0.29 -10000 0 -1 52 52
mol:Choline -0.072 0.29 -10000 0 -1 52 52
cell migration -0.04 0.07 -10000 0 -0.22 61 61
FYN -0.1 0.28 -10000 0 -0.78 81 81
DOK2 -0.029 0.14 -10000 0 -0.32 104 104
negative regulation of cell cycle -0.085 0.24 -10000 0 -0.59 100 100
ETS1 0.006 0.077 -10000 0 -0.25 45 45
PXN -0.05 0.22 0.48 1 -0.69 53 54
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
NOS3 -0.046 0.24 -10000 0 -0.7 57 57
RAC1 0.023 0.01 -10000 0 -10000 0 0
TNF -0.071 0.18 -10000 0 -0.34 174 174
MAPKKK cascade -0.072 0.29 -10000 0 -1 52 52
RASA1 0.027 0.003 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.076 0.31 -10000 0 -1.1 52 52
NCK1 0.027 0.003 -10000 0 -10000 0 0
vasculogenesis -0.027 0.2 0.34 2 -0.55 57 59
mol:Phosphatidic acid -0.072 0.29 -10000 0 -1 52 52
mol:Angiotensin II -0.002 0.007 -10000 0 -10000 0 0
mol:NADP -0.034 0.22 0.36 1 -0.61 57 58
Rac1/GTP -0.061 0.24 -10000 0 -0.77 53 53
MMP2 -0.083 0.3 -10000 0 -1.1 52 52
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.043 0.21 -9999 0 -0.48 90 90
MAP3K8 0.015 0.05 -9999 0 -0.25 21 21
FOS -0.045 0.18 -9999 0 -0.46 91 91
PRKCA 0.022 0.029 -9999 0 -0.46 2 2
PTPN7 -0.056 0.17 -9999 0 -0.37 132 132
HRAS 0.025 0.006 -9999 0 -10000 0 0
PRKCB -0.019 0.12 -9999 0 -0.31 86 86
NRAS 0.024 0.009 -9999 0 -10000 0 0
RAS family/GTP 0.041 0.022 -9999 0 -10000 0 0
MAPK3 -0.037 0.17 -9999 0 -0.44 87 87
MAP2K1 0.003 0.1 -9999 0 -0.41 31 31
ELK1 0.024 0.013 -9999 0 -10000 0 0
BRAF -0.002 0.08 -9999 0 -0.37 26 26
mol:GTP 0 0.001 -9999 0 -0.003 88 88
MAPK1 -0.041 0.17 -9999 0 -0.44 93 93
RAF1 -0.001 0.089 -9999 0 -0.39 30 30
KRAS 0.026 0.006 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.016 0.076 -10000 0 -0.23 50 50
RGS9BP 0.017 0.058 -10000 0 -0.44 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.023 0.02 -10000 0 -0.22 4 4
mol:Na + -0.031 0.1 -10000 0 -0.21 125 125
mol:ADP 0.012 0.019 -10000 0 -0.28 1 1
GNAT2 0.021 0.021 -10000 0 -0.22 4 4
RGS9-1/Gbeta5/R9AP 0.007 0.11 -10000 0 -0.29 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.022 0.03 -10000 0 -0.18 2 2
GRK7 0.024 0.017 -10000 0 -0.22 3 3
CNGB3 0.015 0.038 -10000 0 -0.22 16 16
Cone Metarhodopsin II/X-Arrestin 0.013 0.007 -10000 0 -0.15 1 1
mol:Ca2+ -0.067 0.12 0.18 1 -0.28 141 142
Cone PDE6 0.016 0.1 -10000 0 -0.25 68 68
Cone Metarhodopsin II 0.029 0.017 -10000 0 -0.21 1 1
Na + (4 Units) -0.057 0.13 -10000 0 -0.27 151 151
GNAT2/GDP 0.016 0.099 -10000 0 -0.25 68 68
GNB5 0.027 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.002 0.025 -10000 0 -0.21 1 1
Cone Transducin 0.018 0.081 -10000 0 -0.25 50 50
SLC24A2 -0.046 0.16 -10000 0 -0.35 122 122
GNB3/GNGT2 0.007 0.1 -10000 0 -0.33 49 49
GNB3 0 0.11 -10000 0 -0.44 37 37
GNAT2/GTP 0.015 0.014 -10000 0 -0.15 4 4
CNGA3 -0.069 0.17 -10000 0 -0.32 182 182
ARR3 0.018 0.011 -10000 0 -0.22 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.031 0.1 -10000 0 -0.21 125 125
mol:Pi 0.006 0.11 -10000 0 -0.29 70 70
Cone CNG Channel -0.016 0.096 -10000 0 -0.22 80 80
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.046 0.16 -10000 0 -0.35 122 122
RGS9 -0.032 0.15 -10000 0 -0.43 84 84
PDE6C 0.018 0.018 -10000 0 -0.22 3 3
GNGT2 0.011 0.08 -10000 0 -0.38 25 25
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.015 0.04 -10000 0 -0.22 18 18
PDGFR-alpha signaling pathway

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
PDGFRA -0.03 0.15 -10000 0 -0.44 72 72
PDGF/PDGFRA/CRKL -0.003 0.11 -10000 0 -0.3 72 72
positive regulation of JUN kinase activity 0.027 0.09 -10000 0 -0.24 58 58
CRKL 0.026 0.011 -10000 0 -0.22 1 1
PDGF/PDGFRA/Caveolin-3 -0.012 0.11 -10000 0 -0.32 67 67
AP1 -0.076 0.24 0.32 1 -0.82 55 56
mol:IP3 -0.023 0.1 -10000 0 -0.33 60 60
PLCG1 -0.023 0.1 -10000 0 -0.33 60 60
PDGF/PDGFRA/alphaV Integrin -0.003 0.11 -10000 0 -0.32 66 66
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
CRK 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.1 -10000 0 -0.33 60 60
CAV3 0.012 0.046 -10000 0 -0.22 24 24
CAV1 -0.003 0.077 -10000 0 -0.23 63 63
SHC/Grb2/SOS1 0.029 0.092 -10000 0 -0.24 58 58
PDGF/PDGFRA/Shf -0.006 0.11 -10000 0 -0.32 69 69
FOS -0.084 0.23 -10000 0 -0.81 55 55
JUN -0.017 0.025 -10000 0 -0.18 3 3
oligodendrocyte development -0.003 0.11 -10000 0 -0.32 66 66
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:DAG -0.023 0.1 -10000 0 -0.33 60 60
PDGF/PDGFRA -0.03 0.15 -10000 0 -0.44 72 72
actin cytoskeleton reorganization -0.005 0.11 -10000 0 -0.31 66 66
SRF 0.019 0.009 -10000 0 -10000 0 0
SHC1 0.022 0.035 -10000 0 -0.22 13 13
PI3K 0.016 0.094 -10000 0 -0.26 63 63
PDGF/PDGFRA/Crk/C3G 0.015 0.096 -10000 0 -0.27 64 64
JAK1 -0.018 0.095 -10000 0 -0.31 63 63
ELK1/SRF -0.003 0.087 0.16 38 -0.25 56 94
SHB 0.025 0.02 -10000 0 -0.46 1 1
SHF 0.024 0.038 -10000 0 -0.46 4 4
CSNK2A1 0.028 0.018 -10000 0 -10000 0 0
GO:0007205 -0.026 0.11 0.23 10 -0.35 60 70
SOS1 0.027 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.027 0.09 -10000 0 -0.24 58 58
PDGF/PDGFRA/SHB -0.005 0.11 -10000 0 -0.31 66 66
PDGF/PDGFRA/Caveolin-1 -0.011 0.1 -10000 0 -0.26 82 82
ITGAV 0.027 0.002 -10000 0 -10000 0 0
ELK1 -0.027 0.095 0.2 9 -0.3 60 69
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.003 0.11 -10000 0 -0.32 66 66
JAK-STAT cascade -0.018 0.095 -10000 0 -0.31 63 63
cell proliferation -0.006 0.11 -10000 0 -0.32 69 69
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC3 0.027 0.003 -10000 0 -10000 0 0
VDR -0.039 0.14 -10000 0 -0.31 127 127
Cbp/p300/PCAF 0.048 0.034 -10000 0 -0.28 6 6
EP300 0.024 0.033 -10000 0 -0.46 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.007 0.067 -10000 0 -0.35 11 11
KAT2B 0.025 0.029 -10000 0 -0.38 3 3
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.07 0.2 16 -0.32 8 24
RAR alpha/9cRA/Cyclin H -0.009 0.11 -10000 0 -0.34 17 17
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.058 -10000 0 -0.34 9 9
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.027 0.093 -10000 0 -0.36 22 22
NCOR2 0.025 0.027 -10000 0 -0.46 2 2
VDR/VDR/Vit D3 -0.026 0.1 -10000 0 -0.22 127 127
RXRs/RARs/NRIP1/9cRA -0.068 0.18 -10000 0 -0.47 75 75
NCOA2 0 0.11 -10000 0 -0.46 35 35
NCOA3 0.026 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.039 0.14 -10000 0 -0.31 127 127
RARG 0.026 0.017 -10000 0 -0.22 3 3
RAR gamma1/9cRA 0.034 0.013 -10000 0 -10000 0 0
MAPK3 0.027 0.002 -10000 0 -10000 0 0
MAPK1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.019 0.057 -10000 0 -0.46 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.2 -10000 0 -0.47 126 126
RARA -0.031 0.096 -10000 0 -0.24 103 103
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.079 -10000 0 -0.31 23 23
PRKCA 0.027 0.027 -10000 0 -0.46 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.076 0.19 -10000 0 -0.54 57 57
RXRG -0.088 0.18 -10000 0 -0.38 160 160
RXRA -0.026 0.085 -10000 0 -0.21 102 102
RXRB -0.038 0.11 -10000 0 -0.29 101 101
VDR/Vit D3/DNA -0.026 0.1 -10000 0 -0.22 127 127
RBP1 -0.057 0.13 -10000 0 -0.25 202 202
CRBP1/9-cic-RA -0.037 0.091 -10000 0 -0.16 204 204
RARB 0.026 0.026 -10000 0 -0.28 4 4
PRKCG -0.087 0.18 -10000 0 -0.33 207 207
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.071 0.19 -10000 0 -0.46 107 107
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.054 0.16 -10000 0 -0.38 94 94
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.087 -10000 0 -0.34 17 17
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.073 0.19 -10000 0 -0.54 55 55
positive regulation of DNA binding -0.014 0.099 -10000 0 -0.33 17 17
NRIP1 -0.063 0.18 -10000 0 -0.67 9 9
RXRs/RARs -0.075 0.19 -10000 0 -0.44 109 109
RXRs/RXRs/DNA/9cRA -0.092 0.19 -10000 0 -0.45 123 123
PRKACA 0.026 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.004 -10000 0 -10000 0 0
TFIIH 0.051 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.008 0.087 -10000 0 -0.26 13 13
CCNH 0.027 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
RAR gamma2/9cRA 0.048 0.019 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.056 -10000 0 -0.28 21 21
NFATC2 -0.026 0.081 -10000 0 -0.26 59 59
NFATC3 -0.001 0.028 -10000 0 -10000 0 0
CD40LG -0.1 0.17 0.36 1 -0.42 83 84
PTGS2 -0.12 0.21 0.43 2 -0.48 115 117
JUNB 0.003 0.089 -10000 0 -0.3 47 47
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.022 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.022 -10000 0 -10000 0 0
CALM1 0.02 0.014 -10000 0 -10000 0 0
JUN 0.017 0.026 -10000 0 -0.22 5 5
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.008 -10000 0 -0.12 1 1
FOSL1 -0.06 0.16 -10000 0 -0.34 158 158
CREM 0.023 0.016 -10000 0 -0.22 2 2
Jun/NFAT1-c-4/p21SNFT -0.055 0.13 -10000 0 -0.36 50 50
FOS -0.03 0.14 -10000 0 -0.36 86 86
IFNG -0.1 0.16 -10000 0 -0.43 68 68
AP-1/NFAT1-c-4 -0.1 0.19 -10000 0 -0.46 81 81
FASLG -0.1 0.17 0.36 1 -0.43 75 76
NFAT1-c-4/ICER1 -0.033 0.097 -10000 0 -0.29 33 33
IL2RA -0.14 0.2 0.36 1 -0.45 140 141
FKBP12/FK506 0.019 0.008 -10000 0 -0.15 1 1
CSF2 -0.1 0.16 0.36 1 -0.42 74 75
JunB/Fra1/NFAT1-c-4 -0.071 0.14 -10000 0 -0.34 82 82
IL4 -0.1 0.16 0.36 1 -0.42 70 71
IL2 -0.008 0.13 -10000 0 -1 11 11
IL3 -0.005 0.12 -10000 0 -0.77 14 14
FKBP1A 0.025 0.011 -10000 0 -0.22 1 1
BATF3 -0.008 0.1 -10000 0 -0.29 72 72
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.02 0.057 -10000 0 -0.46 9 9
Visual signal transduction: Rods

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
mol:K + 0.026 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.034 -10000 0 -0.15 29 29
Metarhodopsin II/Arrestin 0.019 0.034 -10000 0 -0.12 35 35
PDE6G/GNAT1/GTP 0.008 0.075 -10000 0 -0.28 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.013 0.051 -10000 0 -0.22 29 29
GRK1 0.023 0.02 -10000 0 -0.22 4 4
CNG Channel -0.064 0.14 -10000 0 -0.29 132 132
mol:Na + -0.068 0.13 -10000 0 -0.27 129 129
mol:ADP 0.023 0.02 -10000 0 -0.22 4 4
RGS9-1/Gbeta5/R9AP 0.007 0.11 -10000 0 -0.29 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.064 0.14 -10000 0 -0.28 112 112
CNGB1 -0.052 0.14 -10000 0 -0.27 167 167
RDH5 0.008 0.065 -10000 0 -0.23 46 46
SAG 0.017 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.082 0.12 0.32 4 -0.33 47 51
Na + (4 Units) -0.066 0.12 -10000 0 -0.32 47 47
RGS9 -0.032 0.15 -10000 0 -0.43 84 84
GNB1/GNGT1 0.021 0.019 -10000 0 -0.15 4 4
GNAT1/GDP 0.011 0.1 -10000 0 -0.25 68 68
GUCY2D 0.016 0.039 -10000 0 -0.22 17 17
GNGT1 0.011 0.019 -10000 0 -0.22 4 4
GUCY2F 0.021 0.022 -10000 0 -0.22 5 5
GNB5 0.027 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.026 0.1 -10000 0 -0.25 91 91
mol:11-cis-retinal 0.008 0.065 -10000 0 -0.23 46 46
mol:cGMP -0.017 0.11 -10000 0 -0.25 100 100
GNB1 0.024 0.008 -10000 0 -10000 0 0
Rhodopsin 0.014 0.061 -10000 0 -0.19 5 5
SLC24A1 0.026 0.004 -10000 0 -10000 0 0
CNGA1 -0.008 0.12 -10000 0 -0.38 55 55
Metarhodopsin II 0.022 0.033 -10000 0 -0.11 2 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family -0.013 0.12 -10000 0 -0.26 101 101
RGS9BP 0.017 0.058 -10000 0 -0.44 10 10
Metarhodopsin II/Transducin 0.006 0.024 -10000 0 -0.16 2 2
GCAP Family/Ca ++ -0.019 0.11 -10000 0 -0.26 97 97
PDE6A/B -0.012 0.11 -10000 0 -0.34 53 53
mol:Pi 0.006 0.11 -10000 0 -0.29 70 70
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.024 0.034 -10000 0 -0.21 1 1
PDE6B -0.001 0.11 -10000 0 -0.39 44 44
PDE6A -0.014 0.11 -10000 0 -0.29 84 84
PDE6G -0.004 0.11 -10000 0 -0.37 49 49
RHO 0.011 0.056 -10000 0 -0.22 35 35
PDE6 -0.023 0.14 -10000 0 -0.27 128 128
GUCA1A -0.063 0.16 -10000 0 -0.33 164 164
GC2/GCAP Family -0.011 0.12 -10000 0 -0.26 97 97
GUCA1C 0.013 0.035 -10000 0 -0.22 14 14
GUCA1B 0.014 0.078 -10000 0 -0.45 18 18
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.003 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.01 0.12 -9999 0 -0.35 56 56
Syndecan-3/Neurocan -0.02 0.13 -9999 0 -0.37 65 65
POMC 0.014 0.071 -9999 0 -0.36 21 21
EGFR -0.019 0.13 -9999 0 -0.46 53 53
Syndecan-3/EGFR -0.032 0.13 -9999 0 -0.37 61 61
AGRP 0.019 0.035 -9999 0 -0.22 13 13
NCSTN 0.027 0.003 -9999 0 -10000 0 0
PSENEN 0.024 0.008 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.004 -9999 0 -10000 0 0
APH1A 0.027 0.003 -9999 0 -10000 0 0
NCAN -0.003 0.11 -9999 0 -0.44 41 41
long-term memory 0.01 0.12 -9999 0 -0.34 62 62
Syndecan-3/IL8 -0.064 0.15 -9999 0 -0.41 65 65
PSEN1 0.026 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.037 0.022 -9999 0 -0.33 2 2
FYN 0.026 0.005 -9999 0 -10000 0 0
limb bud formation -0.022 0.12 -9999 0 -0.38 64 64
MC4R -0.047 0.16 -9999 0 -0.36 121 121
SRC 0.024 0.027 -9999 0 -0.46 2 2
PTN 0.018 0.037 -9999 0 -0.37 5 5
FGFR/FGF/Syndecan-3 -0.022 0.12 -9999 0 -0.38 64 64
neuron projection morphogenesis 0.006 0.13 -9999 0 -0.35 58 58
Syndecan-3/AgRP -0.009 0.12 -9999 0 -0.36 65 65
Syndecan-3/AgRP/MC4R -0.031 0.14 -9999 0 -0.36 67 67
Fyn/Cortactin 0.038 0.009 -9999 0 -10000 0 0
SDC3 -0.022 0.12 -9999 0 -0.38 64 64
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.063 0.14 -9999 0 -0.41 65 65
IL8 -0.1 0.18 -9999 0 -0.31 247 247
Syndecan-3/Fyn/Cortactin 0.01 0.12 -9999 0 -0.35 62 62
Syndecan-3/CASK -0.022 0.11 -9999 0 -0.36 65 65
alpha-MSH/MC4R -0.024 0.13 -9999 0 -0.26 136 136
Gamma Secretase 0.068 0.029 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.03 0.12 -10000 0 -0.33 67 67
CRKL 0.007 0.14 0.29 14 -0.44 22 36
mol:PIP3 -0.003 0.034 -10000 0 -0.84 1 1
AKT1 -0.002 0.04 -10000 0 -0.73 1 1
PTK2B 0.018 0.044 -10000 0 -0.22 21 21
RAPGEF1 0.01 0.14 0.32 12 -0.42 21 33
RANBP10 0.027 0.003 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.034 0.13 -10000 0 -0.28 106 106
MAP3K5 0 0.15 0.29 12 -0.46 30 42
HGF/MET/CIN85/CBL/ENDOPHILINS -0.021 0.12 -10000 0 -0.26 106 106
AP1 -0.01 0.11 -10000 0 -0.28 54 54
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.035 -10000 0 -0.22 13 13
apoptosis -0.13 0.34 -10000 0 -0.8 130 130
STAT3 (dimer) -0.013 0.095 0.22 7 -0.39 13 20
GAB1/CRKL/SHP2/PI3K 0.032 0.13 0.3 6 -0.42 19 25
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
CBL/CRK 0.018 0.14 0.29 9 -0.42 21 30
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.024 0.009 -10000 0 -10000 0 0
ELK1 0.032 0.17 0.32 144 -0.2 12 156
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.011 0.066 -10000 0 -0.28 16 16
PAK1 -0.005 0.05 -10000 0 -0.7 1 1
HGF/MET/RANBP10 -0.034 0.13 -10000 0 -0.28 108 108
HRAS -0.05 0.2 -10000 0 -0.61 69 69
DOCK1 0.007 0.13 0.29 13 -0.42 21 34
GAB1 -0.001 0.13 0.24 3 -0.45 22 25
CRK 0.007 0.14 0.28 13 -0.45 21 34
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.053 0.19 -10000 0 -0.53 84 84
JUN 0.022 0.023 -10000 0 -0.22 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.033 0.088 -10000 0 -0.25 81 81
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.019 0.14 0.34 31 -0.44 13 44
GRB2/SHC -0.006 0.094 0.19 4 -0.23 64 68
FOS -0.024 0.14 -10000 0 -0.36 86 86
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.031 0.16 0.32 144 -0.2 13 157
HGF/MET/MUC20 -0.043 0.12 -10000 0 -0.28 108 108
cell migration -0.01 0.09 0.18 4 -0.23 64 68
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.026 0.019 -10000 0 -0.46 1 1
MET/RANBP10 -0.03 0.12 -10000 0 -0.33 67 67
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.021 0.091 -10000 0 -0.25 70 70
MET/MUC20 -0.041 0.11 -10000 0 -0.23 151 151
RAP1B 0.014 0.13 0.34 19 -0.4 20 39
RAP1A 0.011 0.13 0.32 12 -0.4 19 31
HGF/MET/RANBP9 -0.034 0.13 -10000 0 -0.28 108 108
RAF1 -0.032 0.2 -10000 0 -0.57 69 69
STAT3 -0.019 0.088 -10000 0 -0.39 12 12
cell proliferation -0.007 0.15 0.32 7 -0.37 65 72
RPS6KB1 -0.006 0.043 -10000 0 -0.18 18 18
MAPK3 0.019 0.15 0.35 50 -10000 0 50
MAPK1 0.026 0.17 0.38 67 -10000 0 67
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.014 0.14 0.29 7 -0.43 28 35
SRC -0.021 0.085 -10000 0 -0.35 14 14
PI3K -0.007 0.095 0.19 6 -0.23 65 71
MET/Glomulin -0.041 0.1 -10000 0 -0.3 69 69
SOS1 0.027 0.002 -10000 0 -10000 0 0
MAP2K1 -0.025 0.19 0.34 2 -0.53 69 71
MET -0.06 0.16 -10000 0 -0.33 151 151
MAP4K1 0 0.16 0.3 11 -0.49 29 40
PTK2 0.025 0.007 -10000 0 -10000 0 0
MAP2K2 -0.02 0.2 0.32 11 -0.53 69 80
BAD 0.001 0.042 -10000 0 -0.7 1 1
MAP2K4 0.003 0.14 0.29 12 -0.43 28 40
SHP2/GRB2/SOS1/GAB1 -0.014 0.13 -10000 0 -0.35 62 62
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PXN 0.027 0.003 -10000 0 -10000 0 0
SH3KBP1 0.027 0.002 -10000 0 -10000 0 0
HGS -0.029 0.079 0.14 2 -0.23 74 76
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.02 0.11 -10000 0 -0.29 87 87
RASA1 0.027 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
PTPRJ 0.026 0.019 -10000 0 -0.46 1 1
NCK/PLCgamma1 -0.009 0.094 0.19 7 -0.23 66 73
PDPK1 -0.002 0.04 -10000 0 -0.78 1 1
HGF/MET/SHIP -0.037 0.13 -10000 0 -0.28 113 113
BCR 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
JUN -0.04 0.16 0.26 4 -0.43 77 81
IKBKB 0.019 0.087 0.24 20 -0.29 8 28
AKT1 -0.019 0.098 0.28 26 -0.22 38 64
IKBKG 0.011 0.085 0.24 10 -0.27 13 23
CALM1 -0.035 0.13 -10000 0 -0.48 33 33
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 -0.027 0.17 0.29 9 -0.49 56 65
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.038 0.14 -10000 0 -0.4 58 58
DOK1 0.026 0.019 -10000 0 -0.46 1 1
AP-1 -0.031 0.1 0.22 3 -0.27 68 71
LYN 0.024 0.032 -10000 0 -0.32 5 5
BLNK -0.011 0.12 -10000 0 -0.44 50 50
SHC1 0.022 0.035 -10000 0 -0.22 13 13
BCR complex -0.009 0.11 -10000 0 -0.24 102 102
CD22 -0.081 0.15 -10000 0 -0.38 93 93
CAMK2G -0.029 0.12 -10000 0 -0.44 33 33
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
SHC/GRB2/SOS1 -0.022 0.1 -10000 0 -0.41 20 20
GO:0007205 -0.04 0.14 -10000 0 -0.41 59 59
SYK 0.013 0.077 -10000 0 -0.42 19 19
ELK1 -0.037 0.14 -10000 0 -0.42 47 47
NFATC1 -0.043 0.14 0.27 2 -0.45 52 54
B-cell antigen/BCR complex -0.009 0.11 -10000 0 -0.24 102 102
PAG1/CSK 0.038 0.009 -10000 0 -10000 0 0
NFKBIB 0.02 0.041 0.13 18 -0.13 12 30
HRAS -0.027 0.12 0.24 5 -0.43 34 39
NFKBIA 0.02 0.041 0.13 16 -0.13 11 27
NF-kappa-B/RelA/I kappa B beta 0.025 0.036 0.13 16 -10000 0 16
RasGAP/Csk -0.041 0.14 -10000 0 -0.24 166 166
mol:GDP -0.034 0.14 -10000 0 -0.44 44 44
PTEN 0.024 0.009 -10000 0 -10000 0 0
CD79B -0.013 0.12 -10000 0 -0.31 76 76
NF-kappa-B/RelA/I kappa B alpha 0.025 0.036 0.13 16 -10000 0 16
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.054 0.17 0.37 3 -0.53 54 57
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 -0.039 0.14 -10000 0 -0.41 58 58
CSK 0.027 0.003 -10000 0 -10000 0 0
FOS -0.052 0.14 0.23 1 -0.44 47 48
CHUK -0.016 0.11 0.28 5 -0.3 33 38
IBTK 0.026 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.008 0.13 0.23 3 -0.44 29 32
PTPN6 -0.08 0.15 -10000 0 -0.43 72 72
RELA 0.027 0.003 -10000 0 -10000 0 0
BCL2A1 0.006 0.039 0.12 6 -0.12 4 10
VAV2 -0.055 0.15 -10000 0 -0.51 50 50
ubiquitin-dependent protein catabolic process 0.023 0.041 0.13 17 -0.13 12 29
BTK -0.02 0.21 -10000 0 -1.2 21 21
CD19 -0.057 0.14 -10000 0 -0.42 67 67
MAP4K1 0.015 0.062 -10000 0 -0.41 13 13
CD72 0.011 0.065 -10000 0 -0.25 36 36
PAG1 0.026 0.005 -10000 0 -10000 0 0
MAPK14 -0.019 0.15 0.28 9 -0.42 54 63
SH3BP5 0.025 0.029 -10000 0 -0.38 3 3
PIK3AP1 -0.033 0.15 -10000 0 -0.44 57 57
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.043 0.2 -10000 0 -0.56 59 59
RAF1 -0.024 0.12 0.23 5 -0.41 33 38
RasGAP/p62DOK/SHIP -0.04 0.14 -10000 0 -0.25 134 134
CD79A 0 0.092 -10000 0 -0.32 46 46
re-entry into mitotic cell cycle -0.031 0.1 0.21 4 -0.27 68 72
RASA1 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.017 0.1 0.22 6 -0.4 22 28
MAPK1 -0.016 0.1 0.22 6 -0.39 22 28
CD72/SHP1 -0.07 0.16 0.26 7 -0.43 69 76
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.023 0.15 0.28 10 -0.42 56 66
actin cytoskeleton organization -0.025 0.15 0.28 9 -0.45 44 53
NF-kappa-B/RelA 0.051 0.07 0.24 15 -0.21 7 22
Calcineurin -0.005 0.12 -10000 0 -0.42 31 31
PI3K -0.069 0.13 -10000 0 -0.39 63 63
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.033 0.15 -10000 0 -0.45 57 57
SOS1 0.027 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.061 0.25 -10000 0 -0.8 62 62
DAPP1 -0.083 0.29 -10000 0 -0.92 62 62
cytokine secretion -0.04 0.13 0.27 2 -0.42 52 54
mol:DAG -0.039 0.14 -10000 0 -0.41 58 58
PLCG2 0.019 0.054 -10000 0 -0.36 12 12
MAP2K1 -0.02 0.11 0.23 6 -0.39 30 36
B-cell antigen/BCR complex/FcgammaRIIB -0.068 0.15 -10000 0 -0.29 166 166
mol:PI-3-4-5-P3 -0.053 0.092 0.22 1 -0.29 55 56
ETS1 -0.025 0.12 0.32 2 -0.4 33 35
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.001 0.13 -10000 0 -0.27 98 98
B-cell antigen/BCR complex/LYN -0.05 0.15 -10000 0 -0.45 63 63
MALT1 0.026 0.005 -10000 0 -10000 0 0
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
RAC1 -0.03 0.15 0.35 1 -0.48 43 44
B-cell antigen/BCR complex/LYN/SYK -0.06 0.17 -10000 0 -0.46 67 67
CARD11 -0.017 0.16 0.25 8 -0.5 37 45
FCGR2B -0.098 0.18 -10000 0 -0.32 237 237
PPP3CA 0.026 0.014 -10000 0 -0.22 2 2
BCL10 0.024 0.009 -10000 0 -10000 0 0
IKK complex 0.01 0.047 0.16 20 -0.12 9 29
PTPRC 0.002 0.1 -10000 0 -0.36 42 42
PDPK1 -0.033 0.072 0.22 5 -0.21 45 50
PPP3CB 0.024 0.016 -10000 0 -0.22 2 2
PPP3CC 0.026 0.005 -10000 0 -10000 0 0
POU2F2 0.022 0.028 0.14 14 -10000 0 14
LPA receptor mediated events

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
GNB1/GNG2 0.012 0.093 -10000 0 -0.24 68 68
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.1 0.25 10 -0.33 28 38
AP1 -0.033 0.11 -10000 0 -0.26 84 84
mol:PIP3 -0.033 0.092 -10000 0 -0.32 29 29
AKT1 0.015 0.091 0.26 12 -0.34 6 18
PTK2B -0.003 0.088 0.19 9 -0.26 42 51
RHOA 0.009 0.067 0.2 7 -0.33 9 16
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.062 0.21 15 -0.3 8 23
MAGI3 0.022 0.028 -10000 0 -0.46 2 2
RELA 0.026 0.003 -10000 0 -10000 0 0
apoptosis -0.019 0.091 -10000 0 -0.28 61 61
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.094 0.23 7 -0.3 17 24
NF kappa B1 p50/RelA -0.022 0.1 -10000 0 -0.36 35 35
endothelial cell migration -0.022 0.12 -10000 0 -0.33 65 65
ADCY4 -0.026 0.12 -10000 0 -0.34 73 73
ADCY5 -0.038 0.14 -10000 0 -0.37 91 91
ADCY6 -0.025 0.12 -10000 0 -0.34 74 74
ADCY7 -0.026 0.12 -10000 0 -0.34 74 74
ADCY1 -0.033 0.13 -10000 0 -0.37 68 68
ADCY2 -0.036 0.13 -10000 0 -0.35 86 86
ADCY3 -0.025 0.12 -10000 0 -0.35 67 67
ADCY8 -0.04 0.14 -10000 0 -0.39 80 80
ADCY9 -0.026 0.12 -10000 0 -0.35 69 69
GSK3B -0.002 0.085 0.23 4 -0.3 18 22
arachidonic acid secretion -0.019 0.12 -10000 0 -0.34 67 67
GNG2 0.022 0.042 -10000 0 -0.46 5 5
TRIP6 0.015 0.039 -10000 0 -0.35 5 5
GNAO1 -0.025 0.11 -10000 0 -0.28 92 92
HRAS 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.011 0.11 0.25 11 -0.35 32 43
GAB1 0.026 0.019 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.11 -10000 0 -0.9 8 8
JUN 0.022 0.023 -10000 0 -0.22 5 5
LPA/LPA2/NHERF2 0.029 0.037 -10000 0 -0.27 6 6
TIAM1 0.018 0.12 -10000 0 -1.1 8 8
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.001 0.059 0.2 10 -0.3 8 18
PLCB3 0.014 0.032 -10000 0 -0.25 7 7
FOS -0.025 0.14 -10000 0 -0.36 86 86
positive regulation of mitosis -0.019 0.12 -10000 0 -0.34 67 67
LPA/LPA1-2-3 -0.002 0.1 -10000 0 -0.26 69 69
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
stress fiber formation 0.003 0.094 0.29 1 -0.35 13 14
GNAZ -0.013 0.093 -10000 0 -0.27 66 66
EGFR/PI3K-beta/Gab1 -0.028 0.099 -10000 0 -0.35 27 27
positive regulation of dendritic cell cytokine production -0.003 0.1 -10000 0 -0.26 69 69
LPA/LPA2/MAGI-3 0.024 0.042 -10000 0 -0.27 8 8
ARHGEF1 0.022 0.098 0.2 83 -0.22 53 136
GNAI2 -0.013 0.091 -10000 0 -0.27 65 65
GNAI3 -0.013 0.087 -10000 0 -0.26 64 64
GNAI1 -0.015 0.093 -10000 0 -0.28 69 69
LPA/LPA3 -0.001 0.049 -10000 0 -0.16 49 49
LPA/LPA2 0.013 0.04 -10000 0 -0.28 8 8
LPA/LPA1 -0.017 0.11 -10000 0 -0.32 66 66
HB-EGF/EGFR -0.054 0.13 -10000 0 -0.3 124 124
HBEGF -0.068 0.12 -10000 0 -0.32 80 80
mol:DAG -0.001 0.059 0.2 10 -0.3 8 18
cAMP biosynthetic process -0.019 0.14 0.25 9 -0.36 74 83
NFKB1 0.027 0.003 -10000 0 -10000 0 0
SRC 0.024 0.027 -10000 0 -0.46 2 2
GNB1 0.024 0.008 -10000 0 -10000 0 0
LYN -0.006 0.11 0.26 10 -0.39 27 37
GNAQ 0.004 0.04 -10000 0 -0.21 13 13
LPAR2 0.021 0.048 -10000 0 -0.4 8 8
LPAR3 -0.001 0.064 -10000 0 -0.22 49 49
LPAR1 -0.022 0.14 -10000 0 -0.39 73 73
IL8 -0.14 0.21 0.34 4 -0.46 161 165
PTK2 -0.013 0.092 0.19 20 -0.24 65 85
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.019 0.092 -10000 0 -0.29 61 61
EGFR -0.019 0.13 -10000 0 -0.46 53 53
PLCG1 -0.004 0.056 0.16 5 -0.22 21 26
PLD2 -0.012 0.095 0.19 22 -0.25 65 87
G12/G13 0.016 0.087 -10000 0 -0.25 54 54
PI3K-beta -0.01 0.08 -10000 0 -0.29 24 24
cell migration 0.014 0.055 -10000 0 -0.24 8 8
SLC9A3R2 0.027 0.003 -10000 0 -10000 0 0
PXN 0.003 0.096 0.29 1 -0.36 13 14
HRAS/GTP -0.029 0.12 -10000 0 -0.35 67 67
RAC1 0.023 0.01 -10000 0 -10000 0 0
MMP9 -0.097 0.17 -10000 0 -0.29 255 255
PRKCE 0.022 0.037 -10000 0 -0.24 12 12
PRKCD -0.002 0.086 0.24 22 -0.3 26 48
Gi(beta/gamma) -0.017 0.13 -10000 0 -0.36 67 67
mol:LPA -0.003 0.026 -10000 0 -0.16 11 11
TRIP6/p130 Cas/FAK1/Paxillin 0.001 0.099 -10000 0 -0.4 12 12
MAPKKK cascade -0.019 0.12 -10000 0 -0.34 67 67
contractile ring contraction involved in cytokinesis 0.012 0.072 0.21 12 -0.33 9 21
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.003 0.057 -10000 0 -0.24 26 26
GNA15 -0.005 0.062 -10000 0 -0.26 29 29
GNA12 0.023 0.01 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.012 0.096 0.24 6 -0.3 17 23
GNA11 0 0.052 -10000 0 -0.23 23 23
Rac1/GTP 0.03 0.11 -10000 0 -0.96 8 8
MMP2 -0.022 0.12 -10000 0 -0.33 65 65
Ceramide signaling pathway

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
SPHK2 0.008 0.031 -10000 0 -0.33 1 1
MAP4K4 -0.01 0.087 -10000 0 -0.32 24 24
BAG4 0.017 0.068 -10000 0 -0.46 13 13
PKC zeta/ceramide -0.039 0.12 -10000 0 -0.25 126 126
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.014 0.12 -10000 0 -0.31 79 79
BAX -0.043 0.12 -10000 0 -0.37 76 76
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.01 0.049 0.67 3 -10000 0 3
BAD -0.036 0.099 0.18 5 -0.22 104 109
SMPD1 -0.008 0.069 0.15 4 -0.17 79 83
RB1 -0.036 0.098 0.18 2 -0.22 104 106
FADD/Caspase 8 0.002 0.09 -10000 0 -0.38 15 15
MAP2K4 -0.035 0.092 0.21 1 -0.23 70 71
NSMAF 0.026 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.035 0.098 0.19 7 -0.24 72 79
EGF -0.006 0.11 -10000 0 -0.38 53 53
mol:ceramide -0.04 0.1 -10000 0 -0.23 107 107
MADD 0.024 0.033 -10000 0 -0.46 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.031 -10000 0 -0.16 21 21
ASAH1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.036 0.097 0.18 2 -0.22 104 106
cell proliferation -0.013 0.1 -10000 0 -0.34 34 34
BID -0.008 0.13 -10000 0 -0.75 12 12
MAP3K1 -0.037 0.097 0.23 1 -0.22 107 108
EIF2A -0.033 0.091 0.17 4 -0.34 24 28
TRADD 0.026 0.019 -10000 0 -0.46 1 1
CRADD 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.025 0.087 0.18 6 -0.34 21 27
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.026 0.089 0.18 6 -0.35 24 30
Cathepsin D/ceramide -0.024 0.1 -10000 0 -0.22 103 103
FADD -0.009 0.087 -10000 0 -0.32 24 24
KSR1 -0.038 0.1 0.26 1 -0.23 106 107
MAPK8 -0.07 0.15 0.21 1 -0.34 99 100
PRKRA -0.037 0.098 -10000 0 -0.22 103 103
PDGFA 0.014 0.047 -10000 0 -0.23 21 21
TRAF2 0.026 0.004 -10000 0 -10000 0 0
IGF1 0.013 0.077 -10000 0 -0.38 22 22
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.04 0.1 -10000 0 -0.23 107 107
CTSD 0.025 0.011 -10000 0 -0.22 1 1
regulation of nitric oxide biosynthetic process 0.039 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.11 -10000 0 -0.38 31 31
PRKCD 0.009 0.09 -10000 0 -0.46 23 23
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.031 -10000 0 -0.16 21 21
RelA/NF kappa B1 0.039 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.001 0.092 -10000 0 -0.29 54 54
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.093 -10000 0 -0.34 24 24
TNFR1A/BAG4/TNF-alpha -0.011 0.12 -10000 0 -0.29 81 81
mol:Sphingosine-1-phosphate 0.008 0.031 -10000 0 -0.33 1 1
MAP2K1 -0.032 0.093 0.18 7 -0.36 23 30
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.003 -10000 0 -10000 0 0
CYCS -0.022 0.075 0.17 2 -0.21 71 73
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
NFKB1 0.027 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.025 0.064 -10000 0 -0.33 20 20
EIF2AK2 -0.035 0.095 0.16 3 -0.23 77 80
TNF-alpha/TNFR1A/FAN -0.006 0.11 -10000 0 -0.28 70 70
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.077 -10000 0 -0.53 7 7
MAP2K2 -0.028 0.087 0.18 9 -0.35 20 29
SMPD3 -0.032 0.12 0.14 1 -0.32 76 77
TNF -0.054 0.16 -10000 0 -0.33 149 149
PKC zeta/PAR4 -0.008 0.11 -10000 0 -0.35 54 54
mol:PHOSPHOCHOLINE -0.017 0.08 0.2 31 -0.16 87 118
NF kappa B1/RelA/I kappa B alpha 0.03 0.096 -10000 0 -0.25 53 53
AIFM1 -0.035 0.085 0.17 2 -0.23 71 73
BCL2 0.024 0.033 -10000 0 -0.46 3 3
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.006 -9999 0 -10000 0 0
EGFR -0.019 0.13 -9999 0 -0.46 53 53
EGF/EGFR -0.015 0.11 -9999 0 -0.24 99 99
EGF/EGFR dimer/SHC/GRB2/SOS1 0.015 0.11 -9999 0 -0.25 75 75
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.011 0.08 -9999 0 -0.37 26 26
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.006 0.11 -9999 0 -0.38 53 53
EGF/EGFR dimer/SHC -0.006 0.11 -9999 0 -0.3 78 78
mol:GDP 0.011 0.1 -9999 0 -0.25 75 75
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.006 0.084 -9999 0 -0.31 40 40
GRB2/SOS1 0.038 0.008 -9999 0 -10000 0 0
HRAS/GTP 0 0.09 -9999 0 -0.23 70 70
SHC1 0.022 0.035 -9999 0 -0.22 13 13
HRAS/GDP 0.01 0.098 -9999 0 -0.24 70 70
FRAP1 -0.026 0.08 -9999 0 -0.24 75 75
EGF/EGFR dimer -0.019 0.12 -9999 0 -0.34 79 79
SOS1 0.027 0.002 -9999 0 -10000 0 0
GRB2 0.026 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.011 0.087 -9999 0 -0.32 33 33
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.01 -10000 0 -0.22 1 1
LAT2 -0.025 0.12 -10000 0 -0.43 35 35
AP1 -0.029 0.17 -10000 0 -0.54 37 37
mol:PIP3 -0.012 0.17 0.31 29 -0.54 30 59
IKBKB 0 0.11 0.24 35 -0.28 28 63
AKT1 -0.031 0.11 0.32 12 -0.37 12 24
IKBKG -0.001 0.1 0.24 29 -0.28 27 56
MS4A2 0.001 0.054 -10000 0 -0.22 32 32
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 -0.009 0.13 0.29 9 -0.49 27 36
mol:Ca2+ -0.003 0.13 0.27 33 -0.39 30 63
LYN 0.023 0.033 -10000 0 -0.33 5 5
CBLB -0.022 0.1 -10000 0 -0.39 29 29
SHC1 0.022 0.035 -10000 0 -0.22 13 13
RasGAP/p62DOK 0.039 0.052 -10000 0 -0.25 14 14
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
PLD2 -0.044 0.11 0.34 7 -0.26 78 85
PTPN13 -0.011 0.13 -10000 0 -0.57 19 19
PTPN11 0.02 0.032 -10000 0 -0.48 2 2
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.008 0.1 0.29 13 -0.33 16 29
SYK 0.013 0.079 -10000 0 -0.44 19 19
GRB2 0.026 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.038 0.15 0.21 4 -0.48 39 43
LAT -0.03 0.11 -10000 0 -0.38 35 35
PAK2 -0.013 0.14 0.26 9 -0.56 27 36
NFATC2 -0.053 0.15 -10000 0 -0.56 49 49
HRAS -0.019 0.15 0.24 8 -0.62 27 35
GAB2 0.025 0.027 -10000 0 -0.46 2 2
PLA2G1B 0.035 0.078 -10000 0 -0.86 4 4
Fc epsilon R1 -0.046 0.14 -10000 0 -0.3 124 124
Antigen/IgE/Fc epsilon R1 -0.039 0.13 -10000 0 -0.27 124 124
mol:GDP -0.02 0.16 0.25 5 -0.61 33 38
JUN 0.022 0.023 -10000 0 -0.22 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
FOS -0.024 0.14 -10000 0 -0.36 86 86
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.024 0.11 -10000 0 -0.4 30 30
CHUK -0.003 0.1 0.23 28 -0.28 27 55
KLRG1 -0.026 0.1 -10000 0 -0.34 33 33
VAV1 -0.029 0.13 -10000 0 -0.46 34 34
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.022 0.11 -10000 0 -0.39 30 30
negative regulation of mast cell degranulation -0.012 0.11 0.18 13 -0.4 22 35
BTK -0.026 0.17 -10000 0 -0.69 31 31
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.077 0.16 -10000 0 -0.32 144 144
GAB2/PI3K/SHP2 -0.045 0.095 -10000 0 -0.26 54 54
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.03 0.11 -10000 0 -0.37 35 35
RAF1 0.03 0.081 -10000 0 -0.95 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.087 0.17 -10000 0 -0.31 180 180
FCER1G -0.003 0.11 -10000 0 -0.35 52 52
FCER1A -0.078 0.17 -10000 0 -0.32 196 196
Antigen/IgE/Fc epsilon R1/Fyn -0.026 0.12 -10000 0 -0.25 122 122
MAPK3 0.034 0.078 -10000 0 -0.86 4 4
MAPK1 0.033 0.081 -10000 0 -0.89 4 4
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.025 0.18 -10000 0 -0.54 66 66
DUSP1 0.008 0.081 -10000 0 -0.31 37 37
NF-kappa-B/RelA 0.002 0.06 0.13 3 -0.18 21 24
actin cytoskeleton reorganization -0.01 0.13 -10000 0 -0.55 21 21
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.14 0.27 2 -0.56 26 28
FER -0.026 0.11 -10000 0 -0.37 37 37
RELA 0.027 0.003 -10000 0 -10000 0 0
ITK -0.045 0.12 -10000 0 -0.38 68 68
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG1 -0.011 0.17 0.28 18 -0.66 28 46
cytokine secretion -0.006 0.038 -10000 0 -0.16 1 1
SPHK1 -0.031 0.12 -10000 0 -0.38 40 40
PTK2 -0.011 0.13 -10000 0 -0.62 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.026 0.16 0.22 8 -0.53 35 43
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.008 0.16 0.3 26 -0.53 28 54
MAP2K2 0.032 0.082 -10000 0 -0.88 4 4
MAP2K1 0.026 0.076 -10000 0 -0.89 4 4
MAP2K7 0.025 0.019 -10000 0 -0.46 1 1
KLRG1/SHP2 -0.014 0.1 0.19 14 -0.37 23 37
MAP2K4 0.03 0.084 -10000 0 -1 4 4
Fc epsilon R1/FcgammaRIIB -0.098 0.18 -10000 0 -0.3 229 229
mol:Choline -0.044 0.11 0.34 7 -0.25 78 85
SHC/Grb2/SOS1 0.013 0.12 -10000 0 -0.43 20 20
FYN 0.026 0.005 -10000 0 -10000 0 0
DOK1 0.026 0.019 -10000 0 -0.46 1 1
PXN -0.008 0.13 0.37 1 -0.56 16 17
HCLS1 -0.029 0.12 -10000 0 -0.44 34 34
PRKCB -0.01 0.13 0.26 28 -0.36 36 64
FCGR2B -0.098 0.18 -10000 0 -0.32 237 237
IGHE -0.001 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.012 0.11 0.18 13 -0.41 22 35
LCP2 0.022 0.043 -10000 0 -0.34 8 8
PLA2G4A -0.029 0.12 -10000 0 -0.39 40 40
RASA1 0.027 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.11 0.34 7 -0.25 78 85
IKK complex 0.008 0.091 0.23 36 -0.21 24 60
WIPF1 0.026 0.01 -10000 0 -0.22 1 1
Glucocorticoid receptor regulatory 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
PCK2 0.057 0.087 -10000 0 -0.83 3 3
SMARCC2 0.026 0.022 -10000 0 -0.46 1 1
SMARCC1 0.027 0.011 -10000 0 -10000 0 0
TBX21 -0.073 0.17 -10000 0 -0.61 45 45
SUMO2 0.024 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.046 -10000 0 -0.26 15 15
FKBP4 0.026 0.006 -10000 0 -10000 0 0
FKBP5 -0.03 0.15 -10000 0 -0.41 87 87
GR alpha/HSP90/FKBP51/HSP90 0.065 0.12 0.28 34 -0.25 45 79
PRL -0.046 0.076 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.15 0.19 0.49 90 -10000 0 90
RELA -0.056 0.094 -10000 0 -0.23 63 63
FGG 0.12 0.14 0.42 61 -10000 0 61
GR beta/TIF2 0.074 0.12 0.28 47 -0.3 34 81
IFNG -0.15 0.19 -10000 0 -0.61 41 41
apoptosis 0.015 0.17 0.54 22 -0.6 6 28
CREB1 0.026 0.018 -10000 0 -10000 0 0
histone acetylation -0.05 0.097 -10000 0 -0.31 43 43
BGLAP -0.049 0.099 -10000 0 -0.47 10 10
GR/PKAc 0.093 0.071 0.28 24 -10000 0 24
NF kappa B1 p50/RelA -0.094 0.16 -10000 0 -0.31 181 181
SMARCD1 0.027 0.011 -10000 0 -10000 0 0
MDM2 0.058 0.065 0.2 65 -10000 0 65
GATA3 -0.036 0.14 -10000 0 -0.32 119 119
AKT1 0.021 0.012 0.19 3 -10000 0 3
CSF2 -0.057 0.083 -10000 0 -0.41 4 4
GSK3B 0.025 0.013 -10000 0 -10000 0 0
NR1I3 0.026 0.16 0.52 22 -0.68 2 24
CSN2 0.096 0.12 0.35 51 -10000 0 51
BRG1/BAF155/BAF170/BAF60A 0.066 0.043 -10000 0 -0.27 7 7
NFATC1 0.011 0.086 -10000 0 -0.46 21 21
POU2F1 0.02 0.057 -10000 0 -0.46 9 9
CDKN1A -0.044 0.3 -10000 0 -1.5 26 26
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.009 -10000 0 -10000 0 0
SFN -0.032 0.13 -10000 0 -0.3 114 114
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.04 0.14 0.28 24 -0.26 62 86
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.036 0.27 0.49 22 -0.79 65 87
JUN -0.1 0.14 -10000 0 -0.38 78 78
IL4 -0.071 0.11 -10000 0 -0.52 17 17
CDK5R1 -0.011 0.13 -10000 0 -0.46 52 52
PRKACA 0.026 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.082 0.12 0.21 16 -0.33 64 80
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.067 0.11 0.28 23 -0.23 30 53
cortisol/GR alpha (monomer) 0.18 0.2 0.56 90 -10000 0 90
NCOA2 0 0.11 -10000 0 -0.46 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.073 0.14 -10000 0 -0.38 87 87
AP-1/NFAT1-c-4 -0.19 0.23 -10000 0 -0.56 122 122
AFP -0.096 0.12 -10000 0 -0.52 4 4
SUV420H1 0.026 0.004 -10000 0 -10000 0 0
IRF1 0.1 0.1 0.41 17 -10000 0 17
TP53 0.009 0.12 -10000 0 -0.49 37 37
PPP5C 0.024 0.009 -10000 0 -10000 0 0
KRT17 -0.28 0.41 -10000 0 -1.1 113 113
KRT14 -0.084 0.097 -10000 0 -10000 0 0
TBP 0.032 0.014 -10000 0 -0.24 1 1
CREBBP 0.033 0.039 -10000 0 -0.27 8 8
HDAC1 0.022 0.008 -10000 0 -10000 0 0
HDAC2 0.026 0.006 -10000 0 -10000 0 0
AP-1 -0.19 0.23 -10000 0 -0.57 123 123
MAPK14 0.026 0.01 -10000 0 -10000 0 0
MAPK10 0.023 0.035 -10000 0 -0.46 3 3
MAPK11 0.023 0.03 -10000 0 -0.46 2 2
KRT5 -0.27 0.4 -10000 0 -1 123 123
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.028 0.009 -10000 0 -10000 0 0
STAT1 0.024 0.047 -10000 0 -0.26 15 15
CGA -0.063 0.09 -10000 0 -0.38 11 11
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.057 0.085 0.3 17 -0.34 2 19
MAPK3 0.025 0.012 -10000 0 -10000 0 0
MAPK1 0.025 0.011 -10000 0 -10000 0 0
ICAM1 -0.15 0.23 -10000 0 -0.59 89 89
NFKB1 -0.056 0.095 -10000 0 -0.23 56 56
MAPK8 -0.093 0.12 -10000 0 -0.35 74 74
MAPK9 0.025 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.014 0.17 0.54 22 -0.64 6 28
BAX -0.011 0.1 -10000 0 -0.62 1 1
POMC -0.096 0.23 1.1 1 -1.6 12 13
EP300 0.031 0.048 -10000 0 -0.31 10 10
cortisol/GR alpha (dimer)/p53 0.16 0.18 0.51 74 -10000 0 74
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.057 0.19 38 -10000 0 38
SGK1 0.034 0.16 -10000 0 -1.3 8 8
IL13 -0.16 0.2 -10000 0 -0.74 25 25
IL6 -0.2 0.34 -10000 0 -0.89 101 101
PRKACG 0.02 0.02 -10000 0 -0.22 4 4
IL5 -0.13 0.16 -10000 0 -0.65 17 17
IL2 -0.15 0.18 -10000 0 -0.59 39 39
CDK5 0.021 0.011 -10000 0 -10000 0 0
PRKACB 0.024 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
IL8 -0.26 0.38 -10000 0 -0.86 149 149
CDK5R1/CDK5 0.011 0.084 -10000 0 -0.32 37 37
NF kappa B1 p50/RelA/PKAc -0.039 0.14 -10000 0 -0.3 53 53
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.16 0.46 86 -10000 0 86
SMARCA4 0.024 0.039 -10000 0 -0.46 4 4
chromatin remodeling 0.11 0.11 0.33 60 -0.41 4 64
NF kappa B1 p50/RelA/Cbp -0.04 0.15 -10000 0 -0.35 54 54
JUN (dimer) -0.1 0.14 -10000 0 -0.38 77 77
YWHAH 0.022 0.032 -10000 0 -0.22 11 11
VIPR1 -0.078 0.19 -10000 0 -0.62 53 53
NR3C1 0.11 0.12 0.38 62 -10000 0 62
NR4A1 0.012 0.083 -10000 0 -0.44 15 15
TIF2/SUV420H1 0.019 0.083 -10000 0 -0.33 35 35
MAPKKK cascade 0.015 0.17 0.54 22 -0.6 6 28
cortisol/GR alpha (dimer)/Src-1 0.18 0.17 0.5 89 -10000 0 89
PBX1 0.026 0.021 -10000 0 -0.46 1 1
POU1F1 0.019 0.009 -10000 0 -10000 0 0
SELE -0.19 0.3 -10000 0 -0.68 130 130
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.11 0.33 60 -0.41 4 64
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.16 0.46 86 -10000 0 86
mol:cortisol 0.088 0.12 0.31 91 -10000 0 91
MMP1 -0.11 0.26 -10000 0 -1.2 31 31
Nongenotropic Androgen 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
PTK2 0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.004 0.1 -10000 0 -0.24 86 86
regulation of S phase of mitotic cell cycle -0.006 0.089 -10000 0 -0.23 81 81
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
HRAS 0.025 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.046 -10000 0 -0.26 18 18
PELP1 0.025 0.027 -10000 0 -0.46 2 2
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.018 0.098 0.19 11 -0.32 20 31
T-DHT/AR -0.029 0.12 -10000 0 -0.29 101 101
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 57 57
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 0.012 0.07 -10000 0 -0.46 14 14
mol:GDP -0.043 0.13 -10000 0 -0.4 82 82
cell proliferation -0.027 0.15 0.28 10 -0.42 58 68
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
FOS -0.053 0.24 0.36 2 -0.8 56 58
mol:Ca2+ -0.006 0.022 -10000 0 -0.063 63 63
MAPK3 -0.023 0.12 0.27 10 -0.32 50 60
MAPK1 -0.009 0.09 0.19 6 -0.31 25 31
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 57 57
cAMP biosynthetic process -0.004 0.044 -10000 0 -0.25 17 17
GNG2 0.022 0.043 -10000 0 -0.46 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 57 57
HRAS/GTP 0.002 0.1 -10000 0 -0.24 81 81
actin cytoskeleton reorganization 0.031 0.019 -10000 0 -10000 0 0
SRC 0.024 0.027 -10000 0 -0.46 2 2
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 57 57
PI3K 0.035 0.009 -10000 0 -10000 0 0
apoptosis 0.019 0.14 0.41 59 -0.24 9 68
T-DHT/AR/PELP1 -0.009 0.11 -10000 0 -0.28 82 82
HRAS/GDP -0.029 0.13 -10000 0 -0.38 81 81
CREB1 -0.022 0.15 0.25 8 -0.44 59 67
RAC1-CDC42/GTP 0.039 0.024 -10000 0 -10000 0 0
AR -0.041 0.16 -10000 0 -0.42 101 101
GNB1 0.024 0.008 -10000 0 -10000 0 0
RAF1 -0.012 0.1 0.2 7 -0.24 80 87
RAC1-CDC42/GDP -0.012 0.13 -10000 0 -0.35 74 74
T-DHT/AR/PELP1/Src 0.004 0.11 -10000 0 -0.26 82 82
MAP2K2 -0.019 0.096 0.18 25 -0.33 19 44
T-DHT/AR/PELP1/Src/PI3K -0.006 0.09 -10000 0 -0.23 81 81
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
SHBG 0.014 0.076 -10000 0 -0.44 18 18
Gi family/GNB1/GNG2/GDP -0.023 0.13 -10000 0 -0.38 51 51
mol:T-DHT 0 0.001 -10000 0 -0.003 40 40
RAC1 0.023 0.01 -10000 0 -10000 0 0
GNRH1 0.003 0.046 -10000 0 -0.32 13 13
Gi family/GTP -0.021 0.083 -10000 0 -0.24 61 61
CDC42 0.024 0.008 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.011 0.094 -9999 0 -0.27 62 62
FZD6 0.006 0.067 -9999 0 -0.23 49 49
WNT6 0.003 0.093 -9999 0 -0.32 45 45
WNT4 0.001 0.084 -9999 0 -0.27 51 51
FZD3 0.024 0.033 -9999 0 -0.46 3 3
WNT5A 0.014 0.072 -9999 0 -0.38 20 20
WNT11 0.002 0.1 -9999 0 -0.37 41 41
IL6-mediated signaling events

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.015 0.21 0.5 6 -0.67 21 27
CRP -0.025 0.2 0.47 1 -0.66 22 23
cell cycle arrest -0.03 0.22 0.51 1 -0.69 34 35
TIMP1 -0.06 0.24 -10000 0 -0.73 47 47
IL6ST -0.015 0.12 -10000 0 -0.46 45 45
Rac1/GDP -0.064 0.18 -10000 0 -0.45 79 79
AP1 0.011 0.1 -10000 0 -0.53 6 6
GAB2 0.025 0.027 -10000 0 -0.46 2 2
TNFSF11 -0.027 0.2 0.48 1 -0.63 27 28
HSP90B1 0.017 0.16 -10000 0 -0.98 14 14
GAB1 0.026 0.019 -10000 0 -0.46 1 1
MAPK14 -0.11 0.23 0.24 1 -0.58 103 104
AKT1 0.04 0.057 -10000 0 -0.7 2 2
FOXO1 0.04 0.056 -10000 0 -0.66 2 2
MAP2K6 -0.088 0.19 0.24 2 -0.46 104 106
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.058 0.18 0.34 3 -0.47 69 72
MITF -0.07 0.16 -10000 0 -0.44 77 77
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.005 -10000 0 -10000 0 0
A2M 0.014 0.1 -10000 0 -1.2 5 5
CEBPB 0.019 0.072 -10000 0 -0.38 19 19
GRB2/SOS1/GAB family/SHP2 0.007 0.084 -10000 0 -0.46 8 8
STAT3 -0.037 0.23 0.51 1 -0.72 35 36
STAT1 0.014 0.041 -10000 0 -0.9 1 1
CEBPD -0.058 0.31 0.5 2 -1 46 48
PIK3CA 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.008 -10000 0 -10000 0 0
JUN 0.022 0.023 -10000 0 -0.22 5 5
PIAS3/MITF -0.043 0.17 0.23 4 -0.43 73 77
MAPK11 -0.11 0.23 0.25 2 -0.58 103 105
STAT3 (dimer)/FOXO1 -0.018 0.16 -10000 0 -0.54 27 27
GRB2/SOS1/GAB family -0.018 0.16 -10000 0 -0.41 55 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.058 0.16 -10000 0 -0.35 110 110
GRB2 0.026 0.005 -10000 0 -10000 0 0
JAK2 0.025 0.007 -10000 0 -10000 0 0
LBP -0.008 0.19 0.44 8 -0.61 24 32
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.019 -10000 0 -10000 0 0
MYC -0.025 0.25 0.51 3 -0.81 38 41
FGG -0.027 0.2 0.47 1 -0.66 23 24
macrophage differentiation -0.03 0.22 0.51 1 -0.69 34 35
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.031 0.13 -10000 0 -0.29 87 87
JUNB -0.03 0.24 0.47 8 -0.82 30 38
FOS -0.025 0.14 -10000 0 -0.36 86 86
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.17 0.24 1 -0.44 85 86
STAT1/PIAS1 -0.041 0.16 0.26 1 -0.43 59 60
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.058 -10000 0 -0.44 6 6
STAT3 (dimer) -0.035 0.23 0.51 1 -0.72 34 35
PRKCD -0.035 0.23 0.39 34 -0.59 57 91
IL6R 0.006 0.075 -10000 0 -0.4 19 19
SOCS3 -0.16 0.39 -10000 0 -1.1 88 88
gp130 (dimer)/JAK1/JAK1/LMO4 0.011 0.087 -10000 0 -0.27 44 44
Rac1/GTP -0.064 0.18 -10000 0 -0.46 77 77
HCK 0.016 0.064 -10000 0 -0.37 16 16
MAPKKK cascade 0.031 0.085 -10000 0 -0.62 5 5
bone resorption -0.024 0.19 0.48 1 -0.6 27 28
IRF1 -0.024 0.2 0.49 2 -0.65 23 25
mol:GDP -0.076 0.18 0.23 2 -0.45 88 90
SOS1 0.027 0.002 -10000 0 -10000 0 0
VAV1 -0.078 0.18 0.22 1 -0.46 88 89
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.12 0.29 -10000 0 -0.59 128 128
PTPN11 0.006 0.091 -10000 0 -0.75 9 9
IL6/IL6RA -0.046 0.13 -10000 0 -0.29 116 116
gp130 (dimer)/TYK2/TYK2/LMO4 0.017 0.084 -10000 0 -0.27 43 43
gp130 (dimer)/JAK2/JAK2/LMO4 0.016 0.083 -10000 0 -0.27 43 43
IL6 -0.07 0.16 -10000 0 -0.32 167 167
PIAS3 0.025 0.007 -10000 0 -10000 0 0
PTPRE 0.024 0.037 -10000 0 -0.46 3 3
PIAS1 0.025 0.027 -10000 0 -0.46 2 2
RAC1 0.023 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.05 0.13 0.23 1 -0.31 101 102
LMO4 0.017 0.021 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.047 0.21 -10000 0 -0.69 34 34
MCL1 0.044 0.057 -10000 0 -0.62 2 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.023 0.033 -10000 0 -0.46 3 3
VLDLR 0.015 0.065 -10000 0 -0.4 15 15
LRPAP1 0.027 0.003 -10000 0 -10000 0 0
NUDC 0.024 0.008 -10000 0 -10000 0 0
RELN/LRP8 -0.019 0.11 -10000 0 -0.28 78 78
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.004 0.12 0.19 90 -0.25 76 166
IQGAP1/CaM 0.034 0.031 -10000 0 -0.31 4 4
DAB1 -0.045 0.16 -10000 0 -0.41 104 104
IQGAP1 0.022 0.041 -10000 0 -0.36 7 7
PLA2G7 -0.006 0.11 -10000 0 -0.37 54 54
CALM1 0.026 0.006 -10000 0 -10000 0 0
DYNLT1 0.023 0.033 -10000 0 -0.3 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.024 -10000 0 -0.33 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.019 -10000 0 -0.46 1 1
CDK5R1 -0.011 0.13 -10000 0 -0.46 52 52
LIS1/Poliovirus Protein 3A 0.013 0.003 -10000 0 -10000 0 0
CDK5R2 -0.046 0.16 -10000 0 -0.38 119 119
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.059 0.14 -10000 0 -0.31 139 139
YWHAE 0.027 0.003 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.005 0.19 0.32 92 -0.46 46 138
MAP1B 0.007 0.011 -10000 0 -0.27 1 1
RAC1 0.014 0.015 -10000 0 -0.15 4 4
p35/CDK5 -0.028 0.11 0.19 8 -0.27 82 90
RELN -0.065 0.16 -10000 0 -0.35 153 153
PAFAH/LIS1 0.013 0.067 -10000 0 -0.28 28 28
LIS1/CLIP170 0.031 0.014 -10000 0 -0.28 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.032 0.12 -10000 0 -0.4 42 42
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.065 0.16 -10000 0 -0.44 64 64
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.05 0.15 0.21 12 -0.49 46 58
LIS1/IQGAP1 0.029 0.027 -10000 0 -0.28 4 4
RHOA 0.016 0.015 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.009 -10000 0 -10000 0 0
PAFAH1B2 0.017 0.068 -10000 0 -0.46 13 13
MAP1B/LIS1/Dynein heavy chain 0.027 0.025 -10000 0 -0.22 4 4
NDEL1/Katanin 60/Dynein heavy chain 0.004 0.19 0.32 78 -0.46 45 123
LRP8 0.023 0.028 -10000 0 -0.46 2 2
NDEL1/Katanin 60 0.001 0.19 0.32 86 -0.46 46 132
P39/CDK5 -0.039 0.12 0.22 8 -0.27 96 104
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.012 -10000 0 -10000 0 0
CDK5 -0.027 0.082 0.19 8 -0.23 73 81
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.012 -10000 0 -0.24 1 1
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.041 0.13 -10000 0 -0.26 132 132
RELN/VLDLR -0.014 0.11 -10000 0 -0.25 87 87
CDC42 0.013 0.039 -10000 0 -0.48 4 4
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.02 0.11 -9999 0 -0.25 81 81
SMAD6-7/SMURF1 0.04 0.031 -9999 0 -0.28 2 2
NOG -0.049 0.17 -9999 0 -0.4 115 115
SMAD9 -0.051 0.19 -9999 0 -0.51 83 83
SMAD4 0.026 0.005 -9999 0 -10000 0 0
SMAD5 -0.014 0.1 -9999 0 -0.36 34 34
BMP7/USAG1 -0.012 0.1 -9999 0 -0.34 43 43
SMAD5/SKI -0.01 0.11 -9999 0 -0.34 37 37
SMAD1 0.028 0.053 -9999 0 -0.39 4 4
BMP2 -0.047 0.17 -9999 0 -0.45 101 101
SMAD1/SMAD1/SMAD4 0.028 0.05 -9999 0 -0.32 4 4
BMPR1A 0.024 0.008 -9999 0 -10000 0 0
BMPR1B 0.004 0.1 -9999 0 -0.46 30 30
BMPR1A-1B/BAMBI 0.031 0.072 -9999 0 -0.28 31 31
AHSG -0.025 0.14 -9999 0 -0.37 83 83
CER1 0.004 0.06 -9999 0 -0.22 43 43
BMP2-4/CER1 -0.019 0.14 -9999 0 -0.32 101 101
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.021 0.12 -9999 0 -0.4 39 39
BMP2-4 (homodimer) -0.027 0.15 -9999 0 -0.36 101 101
RGMB 0.023 0.038 -9999 0 -0.32 7 7
BMP6/BMPR2/BMPR1A-1B 0.039 0.083 -9999 0 -0.26 38 38
RGMA 0.017 0.066 -9999 0 -0.44 13 13
SMURF1 0.021 0.011 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.024 0.12 -9999 0 -0.34 56 56
BMP2-4/USAG1 -0.035 0.14 -9999 0 -0.32 109 109
SMAD6/SMURF1/SMAD5 -0.005 0.096 -9999 0 -0.35 23 23
SOSTDC1 -0.033 0.13 -9999 0 -0.3 111 111
BMP7/BMPR2/BMPR1A-1B 0.042 0.078 -9999 0 -0.26 36 36
SKI 0.024 0.008 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.071 -9999 0 -0.33 24 24
HFE2 0.019 0.028 -9999 0 -0.22 8 8
ZFYVE16 0.027 0.003 -9999 0 -10000 0 0
MAP3K7 0.026 0.005 -9999 0 -10000 0 0
BMP2-4/CHRD -0.011 0.14 -9999 0 -0.3 109 109
SMAD5/SMAD5/SMAD4 -0.012 0.11 -9999 0 -0.35 37 37
MAPK1 0.026 0.004 -9999 0 -10000 0 0
TAK1/TAB family -0.005 0.096 -9999 0 -0.32 27 27
BMP7 (homodimer) 0.018 0.062 -9999 0 -0.46 11 11
NUP214 0.026 0.004 -9999 0 -10000 0 0
BMP6/FETUA -0.008 0.11 -9999 0 -0.33 62 62
SMAD1/SKI 0.035 0.06 -9999 0 -0.41 3 3
SMAD6 0.024 0.036 -9999 0 -0.37 5 5
CTDSP2 0.025 0.007 -9999 0 -10000 0 0
BMP2-4/FETUA -0.038 0.16 -9999 0 -0.32 140 140
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.081 0.18 -9999 0 -0.36 184 184
BMPR2 (homodimer) 0.027 0.001 -9999 0 -10000 0 0
GADD34/PP1CA 0.045 0.027 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.019 0.076 -9999 0 -0.32 30 30
CHRDL1 -0.032 0.15 -9999 0 -0.42 88 88
ENDOFIN/SMAD1 0.038 0.061 -9999 0 -0.38 4 4
SMAD6-7/SMURF1/SMAD1 0.047 0.063 -9999 0 -0.36 4 4
SMAD6/SMURF1 0.021 0.011 -9999 0 -10000 0 0
BAMBI 0.021 0.03 -9999 0 -0.26 6 6
SMURF2 0.026 0.004 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.044 0.17 -9999 0 -0.33 157 157
BMP2-4/GREM1 -0.074 0.17 -9999 0 -0.32 186 186
SMAD7 0.025 0.027 -9999 0 -0.46 2 2
SMAD8A/SMAD8A/SMAD4 -0.043 0.19 -9999 0 -0.48 91 91
SMAD1/SMAD6 0.031 0.054 -9999 0 -0.34 4 4
TAK1/SMAD6 0.031 0.017 -9999 0 -10000 0 0
BMP7 0.018 0.063 -9999 0 -0.46 11 11
BMP6 0.013 0.071 -9999 0 -0.33 24 24
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.018 0.11 -9999 0 -0.33 44 44
PPM1A 0.026 0.005 -9999 0 -10000 0 0
SMAD1/SMURF2 0.038 0.061 -9999 0 -0.38 4 4
SMAD7/SMURF1 0.031 0.017 -9999 0 -10000 0 0
CTDSPL 0.026 0.019 -9999 0 -0.46 1 1
PPP1CA 0.026 0.01 -9999 0 -0.22 1 1
XIAP 0.027 0.001 -9999 0 -10000 0 0
CTDSP1 0.027 0.002 -9999 0 -10000 0 0
PPP1R15A 0.021 0.028 -9999 0 -0.22 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 -9999 0 -0.37 72 72
CHRD 0.019 0.06 -9999 0 -0.46 10 10
BMPR2 0.027 0.001 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.029 0.13 -9999 0 -0.37 55 55
BMP4 0.011 0.083 -9999 0 -0.43 22 22
FST -0.029 0.14 -9999 0 -0.34 101 101
BMP2-4/NOG -0.047 0.18 -9999 0 -0.38 137 137
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.045 0.072 -9999 0 -0.24 31 31
Ephrin B reverse 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
EFNB2 0.022 0.035 -10000 0 -0.25 10 10
EPHB2 0.02 0.038 -10000 0 -0.34 6 6
EFNB1 -0.016 0.085 -10000 0 -0.33 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.1 -10000 0 -0.25 64 64
Ephrin B2/EPHB1-2 0.005 0.1 -10000 0 -0.26 80 80
neuron projection morphogenesis -0.009 0.091 -10000 0 -0.24 64 64
Ephrin B1/EPHB1-2/Tiam1 -0.012 0.12 -10000 0 -0.26 97 97
DNM1 -0.022 0.12 -10000 0 -0.29 101 101
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.001 0.073 -10000 0 -0.54 11 11
YES1 0.004 0.11 -10000 0 -0.8 11 11
Ephrin B1/EPHB1-2/NCK2 -0.011 0.12 -10000 0 -0.25 99 99
PI3K 0.032 0.079 -10000 0 -0.52 12 12
mol:GDP -0.012 0.12 -10000 0 -0.26 97 97
ITGA2B -0.003 0.11 -10000 0 -0.4 46 46
endothelial cell proliferation 0.025 0.026 -10000 0 -0.14 9 9
FYN 0.004 0.11 -10000 0 -0.79 11 11
MAP3K7 -0.003 0.077 -10000 0 -0.57 11 11
FGR 0.002 0.1 -10000 0 -0.81 10 10
TIAM1 0.025 0.019 -10000 0 -0.46 1 1
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
RGS3 0.025 0.02 -10000 0 -0.22 4 4
cell adhesion -0.012 0.11 -10000 0 -0.42 22 22
LYN 0.004 0.1 -10000 0 -0.78 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.002 0.097 -10000 0 -0.73 11 11
Ephrin B1/EPHB1-2 -0.002 0.079 -10000 0 -0.66 9 9
SRC 0.003 0.1 -10000 0 -0.78 11 11
ITGB3 -0.029 0.12 -10000 0 -0.28 120 120
EPHB1 -0.032 0.16 -10000 0 -0.46 79 79
EPHB4 0.021 0.017 -10000 0 -0.22 2 2
RAC1 0.023 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.026 -10000 0 -0.14 9 9
alphaIIb/beta3 Integrin -0.023 0.12 -10000 0 -0.35 61 61
BLK 0.002 0.11 -10000 0 -0.78 11 11
HCK 0.004 0.11 -10000 0 -0.8 11 11
regulation of stress fiber formation 0.012 0.12 0.25 99 -10000 0 99
MAPK8 -0.003 0.077 -10000 0 -0.53 11 11
Ephrin B1/EPHB1-2/RGS3 -0.012 0.12 -10000 0 -0.26 99 99
endothelial cell migration 0.031 0.098 0.2 99 -0.44 11 110
NCK2 0.027 0.002 -10000 0 -10000 0 0
PTPN13 0.024 0.049 -10000 0 -0.51 5 5
regulation of focal adhesion formation 0.012 0.12 0.25 99 -10000 0 99
chemotaxis 0.013 0.12 0.26 99 -10000 0 99
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.096 -10000 0 -0.24 64 64
angiogenesis -0.003 0.082 -10000 0 -0.61 11 11
LCK -0.009 0.11 -10000 0 -0.81 10 10
TCGA08_p53

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
CDKN2A -0.023 0.078 -10000 0 -0.2 94 94
TP53 -0.018 0.07 -10000 0 -0.28 37 37
Senescence -0.019 0.071 -10000 0 -0.27 39 39
Apoptosis -0.019 0.071 -10000 0 -0.27 39 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.021 0.075 0.28 42 -10000 0 42
MDM4 0.026 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.027 -10000 0 -0.46 2 2
ELF1 -0.035 0.12 -10000 0 -0.35 74 74
CCNA2 -0.019 0.12 -10000 0 -0.3 93 93
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
JAK3 -0.013 0.12 -10000 0 -0.31 77 77
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
JAK1 0.024 0.009 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.044 0.14 -10000 0 -0.42 40 40
SHC1 0.022 0.035 -10000 0 -0.22 13 13
SP1 0.029 0.036 -10000 0 -0.28 8 8
IL2RA -0.093 0.23 -10000 0 -0.72 68 68
IL2RB -0.047 0.15 -10000 0 -0.33 136 136
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG -0.003 0.1 -10000 0 -0.32 57 57
G1/S transition of mitotic cell cycle 0.003 0.16 0.36 4 -0.48 48 52
PTPN11 0.026 0.027 -10000 0 -0.46 2 2
CCND2 0.017 0.067 -10000 0 -0.73 5 5
LCK -0.03 0.13 -10000 0 -0.3 112 112
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.016 0.004 -10000 0 -10000 0 0
CDK6 0.004 0.084 -10000 0 -0.38 28 28
CCND3 -0.036 0.13 -10000 0 -0.47 14 14
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.017 0.098 -10000 0 -0.31 58 58
CRKL 0.026 0.011 -10000 0 -0.22 1 1
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.023 0.021 -10000 0 -0.46 1 1
ITGA4 -0.022 0.13 -10000 0 -0.33 90 90
alpha4/beta7 Integrin/MAdCAM1 -0.02 0.13 -10000 0 -0.28 94 94
EPO 0.011 0.055 -10000 0 -0.28 19 19
alpha4/beta7 Integrin -0.014 0.12 -10000 0 -0.24 125 125
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0 0.096 -10000 0 -0.23 83 83
EPO/EPOR (dimer) 0.024 0.043 -10000 0 -0.2 18 18
lamellipodium assembly 0.018 0.047 -10000 0 -0.26 9 9
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
JAK2 0.001 0.065 -10000 0 -0.22 41 41
PXN 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
MADCAM1 -0.035 0.13 -10000 0 -0.29 126 126
cell adhesion -0.021 0.13 -10000 0 -0.28 94 94
CRKL/CBL 0.037 0.018 -10000 0 -0.24 2 2
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
SRC -0.036 0.11 0.19 14 -0.26 101 115
ITGB7 0.002 0.097 -10000 0 -0.35 42 42
RAC1 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.03 0.12 -10000 0 -0.29 102 102
p130Cas/Crk/Dock1 -0.015 0.1 -10000 0 -0.34 11 11
VCAM1 -0.031 0.15 -10000 0 -0.4 86 86
RHOA 0.027 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.029 0.086 -10000 0 -0.25 42 42
BCAR1 -0.037 0.099 0.19 14 -0.25 96 110
EPOR 0.026 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.019 -10000 0 -0.46 1 1
GIT1 0.026 0.019 -10000 0 -0.46 1 1
Rac1/GTP 0.019 0.046 -10000 0 -0.26 9 9
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 -0.027 0.15 -10000 0 -0.42 80 80
KLHL20 0.016 0.073 0.16 2 -0.25 9 11
CYFIP2 0.022 0.041 -10000 0 -0.36 7 7
Rac1/GDP 0.001 0.099 0.27 3 -0.27 65 68
ENAH -0.028 0.15 -10000 0 -0.43 78 78
AP1M1 0.026 0.005 -10000 0 -10000 0 0
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
RAP1A 0.024 0.009 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0 0.073 -10000 0 -0.4 3 3
ABI1/Sra1/Nap1 -0.015 0.038 -10000 0 -0.17 12 12
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.001 0.13 -10000 0 -0.28 89 89
RAPGEF1 -0.017 0.14 0.25 4 -0.39 73 77
CTNND1 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.028 0.16 -10000 0 -0.44 82 82
CRK -0.026 0.14 -10000 0 -0.41 75 75
E-cadherin/gamma catenin/alpha catenin -0.002 0.12 -10000 0 -0.28 80 80
alphaE/beta7 Integrin 0.02 0.074 -10000 0 -0.33 23 23
IQGAP1 0.022 0.041 -10000 0 -0.36 7 7
NCKAP1 0.027 0.001 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.025 -10000 0 -0.25 1 1
DLG1 -0.028 0.15 -10000 0 -0.43 77 77
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.012 0.049 -10000 0 -0.27 3 3
MLLT4 0.025 0.02 -10000 0 -0.46 1 1
ARF6/GTP/NME1/Tiam1 0.047 0.021 -10000 0 -0.25 1 1
PI3K -0.012 0.064 -10000 0 -0.37 3 3
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.021 0.13 -10000 0 -0.26 134 134
TIAM1 0.025 0.019 -10000 0 -0.46 1 1
E-cadherin(dimer)/Ca2+ 0.014 0.1 -10000 0 -0.23 75 75
AKT1 0.003 0.045 0.11 20 -0.2 3 23
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
CDH1 -0.051 0.16 -10000 0 -0.36 132 132
RhoA/GDP 0.007 0.11 0.27 5 -0.27 71 76
actin cytoskeleton organization 0.019 0.063 0.16 23 -0.18 9 32
CDC42/GDP 0.005 0.11 0.27 5 -0.26 71 76
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.012 0.084 -10000 0 -0.23 79 79
ITGB7 0.002 0.097 -10000 0 -0.35 42 42
RAC1 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.016 0.11 -10000 0 -0.25 75 75
E-cadherin/Ca2+/beta catenin/alpha catenin 0.002 0.094 -10000 0 -0.23 76 76
mol:GDP -0.008 0.12 0.27 5 -0.31 71 76
CDC42/GTP/IQGAP1 0.03 0.027 -10000 0 -0.25 4 4
JUP 0.022 0.044 -10000 0 -0.39 7 7
p120 catenin/RhoA/GDP 0.011 0.11 0.28 3 -0.27 71 74
RAC1/GTP/IQGAP1 0.028 0.029 -10000 0 -0.28 4 4
PIP5K1C/AP1M1 0.038 0.017 -10000 0 -0.33 1 1
RHOA 0.027 0.003 -10000 0 -10000 0 0
CDC42 0.024 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.003 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.017 0.053 0.14 27 -0.17 17 44
NME1 0.025 0.02 -10000 0 -0.22 4 4
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.028 0.15 -10000 0 -0.43 78 78
regulation of cell-cell adhesion -0.005 0.062 -10000 0 -0.34 3 3
WASF2 0.008 0.028 -10000 0 -0.12 3 3
Rap1/GTP 0.005 0.089 0.22 3 -0.34 6 9
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.01 0.13 -10000 0 -0.27 92 92
CCND1 0.019 0.062 0.16 24 -0.21 17 41
VAV2 -0.014 0.17 -10000 0 -0.6 18 18
RAP1/GDP 0.008 0.098 0.27 3 -0.26 27 30
adherens junction assembly -0.026 0.15 -10000 0 -0.41 80 80
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.009 -10000 0 -10000 0 0
PIP5K1C 0.025 0.02 -10000 0 -0.46 1 1
regulation of heterotypic cell-cell adhesion 0.003 0.12 -10000 0 -0.26 92 92
E-cadherin/beta catenin -0.031 0.11 -10000 0 -0.33 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.029 0.15 -10000 0 -0.44 76 76
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.031 0.084 -10000 0 -0.38 12 12
E-cadherin/beta catenin/alpha catenin 0.001 0.11 -10000 0 -0.28 76 76
ITGAE 0.026 0.017 -10000 0 -0.22 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.029 0.16 -10000 0 -0.44 82 82
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.019 0.11 -10000 0 -0.27 63 63
MAP4K1 0.015 0.062 -10000 0 -0.41 13 13
MAP3K8 0.015 0.05 -10000 0 -0.24 21 21
PRKCB -0.017 0.12 -10000 0 -0.31 86 86
DBNL 0.023 0.01 -10000 0 -10000 0 0
CRKL 0.026 0.011 -10000 0 -0.22 1 1
MAP3K1 0.007 0.08 -10000 0 -0.36 11 11
JUN -0.051 0.2 -10000 0 -0.54 81 81
MAP3K7 0.007 0.079 -10000 0 -0.35 11 11
GRAP2 -0.003 0.1 -10000 0 -0.34 51 51
CRK 0.027 0.003 -10000 0 -10000 0 0
MAP2K4 0.006 0.082 0.22 4 -0.35 13 17
LAT 0.007 0.094 -10000 0 -0.44 27 27
LCP2 0.022 0.043 -10000 0 -0.34 8 8
MAPK8 -0.052 0.21 -10000 0 -0.56 86 86
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.01 0.086 -10000 0 -0.28 28 28
LAT/GRAP2/SLP76/HPK1/HIP-55 0.024 0.099 -10000 0 -0.26 56 56
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.018 0.042 -10000 0 -0.46 3 3
HSPA8 0.026 0.02 -10000 0 -0.46 1 1
SMAD3/SMAD4/ER alpha 0.016 0.094 0.23 6 -0.29 15 21
AKT1 0.009 0.041 -10000 0 -10000 0 0
GSC -0.18 0.5 -10000 0 -1.4 89 89
NKX2-5 0 0.006 -10000 0 -10000 0 0
muscle cell differentiation 0.055 0.16 0.37 95 -10000 0 95
SMAD2-3/SMAD4/SP1 -0.001 0.13 -10000 0 -0.3 37 37
SMAD4 -0.014 0.07 -10000 0 -0.25 9 9
CBFB 0.027 0.002 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.018 0.086 -10000 0 -0.28 28 28
SMAD3/SMAD4/VDR 0.013 0.12 -10000 0 -0.26 48 48
MYC 0.018 0.077 -10000 0 -0.41 18 18
CDKN2B -0.3 0.63 -10000 0 -1.6 117 117
AP1 0.001 0.095 -10000 0 -0.31 23 23
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.014 0.07 -10000 0 -0.28 13 13
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.055 0.17 -10000 0 -0.38 120 120
SP3 0.028 0.009 -10000 0 -10000 0 0
CREB1 0.027 0.001 -10000 0 -10000 0 0
FOXH1 0 0.073 -10000 0 -0.31 19 19
SMAD3/SMAD4/GR 0.036 0.087 0.21 3 -0.36 2 5
GATA3 -0.06 0.16 -10000 0 -0.35 121 121
SKI/SIN3/HDAC complex/NCoR1 0.029 0.041 -10000 0 -0.29 6 6
MEF2C/TIF2 -0.017 0.12 0.26 4 -0.3 48 52
endothelial cell migration 0.22 0.5 1.4 104 -10000 0 104
MAX 0.035 0.02 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.008 -10000 0 -10000 0 0
RUNX2 0.018 0.056 -10000 0 -0.31 17 17
RUNX3 -0.002 0.1 -10000 0 -0.39 41 41
RUNX1 -0.013 0.12 -10000 0 -0.31 76 76
CTBP1 0.027 0.003 -10000 0 -10000 0 0
NR3C1 0.036 0.019 -10000 0 -10000 0 0
VDR -0.039 0.14 -10000 0 -0.31 127 127
CDKN1A -0.046 0.26 -10000 0 -1.3 26 26
KAT2B 0.021 0.031 -10000 0 -0.38 3 3
SMAD2/SMAD2/SMAD4/FOXH1 -0.013 0.13 -10000 0 -0.29 89 89
DCP1A 0.027 0.003 -10000 0 -10000 0 0
SKI 0.024 0.009 -10000 0 -10000 0 0
SERPINE1 -0.22 0.51 -10000 0 -1.4 104 104
SMAD3/SMAD4/ATF2 0.013 0.087 -10000 0 -0.27 16 16
SMAD3/SMAD4/ATF3 0 0.11 -10000 0 -0.3 32 32
SAP30 0.026 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.059 0.19 6 -0.27 4 10
JUN -0.009 0.088 0.23 1 -0.31 23 24
SMAD3/SMAD4/IRF7 0.01 0.09 -10000 0 -0.32 12 12
TFE3 0.011 0.037 -10000 0 -10000 0 0
COL1A2 -0.02 0.14 -10000 0 -0.88 15 15
mesenchymal cell differentiation -0.013 0.088 0.27 20 -10000 0 20
DLX1 -0.071 0.18 -10000 0 -0.35 170 170
TCF3 0.025 0.02 -10000 0 -0.46 1 1
FOS -0.023 0.14 -10000 0 -0.36 86 86
SMAD3/SMAD4/Max 0.037 0.086 0.21 3 -0.31 3 6
Cbp/p300/SNIP1 0.039 0.04 -10000 0 -0.27 4 4
ZBTB17 0.025 0.024 -10000 0 -0.47 1 1
LAMC1 -0.013 0.075 -10000 0 -0.3 8 8
TGIF2/HDAC complex/SMAD3/SMAD4 0.017 0.083 -10000 0 -0.29 10 10
IRF7 0.013 0.065 -10000 0 -0.29 26 26
ESR1 0.014 0.071 -10000 0 -0.34 23 23
HNF4A 0.005 0.057 -10000 0 -0.22 39 39
MEF2C -0.014 0.12 0.22 24 -0.3 45 69
SMAD2-3/SMAD4 -0.003 0.1 -10000 0 -0.27 24 24
Cbp/p300/Src-1 0.042 0.047 -10000 0 -0.27 4 4
IGHV3OR16-13 0.002 0.027 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.022 0.039 -10000 0 -0.41 5 5
CREBBP 0.021 0.029 -10000 0 -0.46 1 1
SKIL 0.024 0.033 -10000 0 -0.46 3 3
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC2 0.026 0.006 -10000 0 -10000 0 0
SNIP1 0.024 0.009 -10000 0 -10000 0 0
GCN5L2 -0.001 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.005 0.09 -10000 0 -0.3 9 9
MSG1/HSC70 0.01 0.085 -10000 0 -0.32 26 26
SMAD2 -0.005 0.059 -10000 0 -0.19 8 8
SMAD3 0 0.06 -10000 0 -0.22 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.012 0.059 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 -0.008 0.045 0.17 2 -0.22 5 7
NCOR1 0.025 0.027 -10000 0 -0.46 2 2
NCOA2 0 0.11 -10000 0 -0.46 35 35
NCOA1 0.027 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.036 0.13 -10000 0 -0.33 88 88
SMAD2-3/SMAD4/SP1/MIZ-1 0.003 0.13 -10000 0 -0.31 30 30
IFNB1 -0.009 0.066 0.21 1 -0.33 8 9
SMAD3/SMAD4/MEF2C -0.004 0.13 -10000 0 -0.34 31 31
CITED1 -0.011 0.11 -10000 0 -0.3 77 77
SMAD2-3/SMAD4/ARC105 0.012 0.1 -10000 0 -0.28 11 11
RBL1 0.015 0.073 -10000 0 -0.46 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.076 0.22 -10000 0 -0.53 117 117
RUNX1-3/PEBPB2 0.006 0.1 -10000 0 -0.28 55 55
SMAD7 -0.019 0.12 -10000 0 -0.46 18 18
MYC/MIZ-1 0.032 0.066 0.18 8 -0.31 17 25
SMAD3/SMAD4 -0.033 0.2 0.28 50 -0.44 96 146
IL10 -0.084 0.2 0.23 10 -0.48 104 114
PIASy/HDAC complex 0.023 0.029 -10000 0 -0.46 1 1
PIAS3 0.021 0.016 -10000 0 -10000 0 0
CDK2 0.015 0.053 -10000 0 -0.32 12 12
IL5 -0.052 0.13 0.24 3 -0.38 44 47
CDK4 0.02 0.025 -10000 0 -0.22 1 1
PIAS4 0.023 0.029 -10000 0 -0.46 1 1
ATF3 -0.005 0.1 -10000 0 -0.3 63 63
SMAD3/SMAD4/SP1 0.005 0.11 -10000 0 -0.31 21 21
FOXG1 -0.003 0.12 -10000 0 -0.46 40 40
FOXO3 0 0.045 -10000 0 -0.2 3 3
FOXO1 0 0.044 -10000 0 -0.33 1 1
FOXO4 -0.002 0.051 -10000 0 -0.39 3 3
heart looping -0.014 0.12 0.22 24 -0.29 46 70
CEBPB 0.004 0.076 -10000 0 -0.39 19 19
SMAD3/SMAD4/DLX1 -0.046 0.14 -10000 0 -0.29 110 110
MYOD1 -0.075 0.17 -10000 0 -0.35 170 170
SMAD3/SMAD4/HNF4 0.004 0.085 -10000 0 -0.25 13 13
SMAD3/SMAD4/GATA3 -0.049 0.16 -10000 0 -0.34 98 98
SnoN/SIN3/HDAC complex/NCoR1 0.024 0.033 -10000 0 -0.46 3 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.005 0.12 -10000 0 -0.28 55 55
SMAD3/SMAD4/SP1-3 0.024 0.11 -10000 0 -0.3 12 12
MED15 0.026 0.004 -10000 0 -10000 0 0
SP1 0.007 0.047 -10000 0 -0.2 3 3
SIN3B 0.025 0.02 -10000 0 -0.46 1 1
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.007 0.12 -10000 0 -0.26 92 92
ITGB5 -0.006 0.087 0.32 1 -0.42 9 10
TGIF/SIN3/HDAC complex/CtBP 0.023 0.073 -10000 0 -0.49 11 11
SMAD3/SMAD4/AR -0.027 0.14 -10000 0 -0.32 82 82
AR -0.041 0.16 -10000 0 -0.41 101 101
negative regulation of cell growth -0.004 0.097 -10000 0 -0.44 14 14
SMAD3/SMAD4/MYOD -0.049 0.13 -10000 0 -0.31 100 100
E2F5 0.025 0.02 -10000 0 -0.46 1 1
E2F4 0.027 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.015 0.11 -10000 0 -0.26 43 43
SMAD2-3/SMAD4/FOXO1-3a-4 -0.046 0.16 -10000 0 -0.39 110 110
TFDP1 0.024 0.033 -10000 0 -0.46 3 3
SMAD3/SMAD4/AP1 0.016 0.1 -10000 0 -0.31 24 24
SMAD3/SMAD4/RUNX2 0.013 0.089 -10000 0 -0.27 20 20
TGIF2 0.022 0.039 -10000 0 -0.41 5 5
TGIF1 0.014 0.073 -10000 0 -0.41 18 18
ATF2 0.018 0.065 -10000 0 -0.46 12 12
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.026 0.011 -10000 0 -0.22 1 1
RAS family/GTP/Tiam1 0.02 0.029 -10000 0 -0.28 2 2
NT3 (dimer)/TRKC 0.025 0.051 -10000 0 -0.21 24 24
NT3 (dimer)/TRKB -0.016 0.13 -10000 0 -0.29 99 99
SHC/Grb2/SOS1/GAB1/PI3K 0.032 0.027 -10000 0 -0.54 1 1
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
BDNF -0.017 0.11 -10000 0 -0.26 102 102
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.033 -10000 0 -0.3 6 6
NTRK1 0.011 0.07 -10000 0 -0.27 34 34
NTRK2 -0.017 0.14 -10000 0 -0.46 59 59
NTRK3 0.021 0.053 -10000 0 -0.46 8 8
NT-4/5 (dimer)/TRKB -0.019 0.12 -10000 0 -0.29 97 97
neuron apoptosis 0.049 0.14 0.37 67 -10000 0 67
SHC 2-3/Grb2 -0.053 0.15 -10000 0 -0.4 66 66
SHC1 0.022 0.035 -10000 0 -0.22 13 13
SHC2 -0.029 0.11 -10000 0 -0.43 20 20
SHC3 -0.077 0.18 -10000 0 -0.52 74 74
STAT3 (dimer) 0.025 0.046 -10000 0 -0.33 8 8
NT3 (dimer)/TRKA 0.003 0.099 -10000 0 -0.27 55 55
RIN/GDP -0.009 0.088 0.19 10 -0.25 12 22
GIPC1 0.026 0.011 -10000 0 -0.22 1 1
KRAS 0.026 0.006 -10000 0 -10000 0 0
DNAJA3 -0.037 0.1 -10000 0 -0.27 85 85
RIN/GTP -0.075 0.14 -10000 0 -0.26 224 224
CCND1 0.011 0.088 -10000 0 -0.73 8 8
MAGED1 0.027 0 -10000 0 -10000 0 0
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.009 0.048 -10000 0 -0.23 23 23
SHC/GRB2/SOS1 0.049 0.025 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.029 0.13 -10000 0 -0.3 99 99
TRKA/NEDD4-2 0.023 0.062 -10000 0 -0.2 43 43
ELMO1 0.017 0.051 -10000 0 -0.46 7 7
RhoG/GTP/ELMO1/DOCK1 0.025 0.034 -10000 0 -0.26 7 7
NGF -0.02 0.13 -10000 0 -0.38 70 70
HRAS 0.026 0.006 -10000 0 -10000 0 0
DOCK1 0.023 0.021 -10000 0 -0.46 1 1
GAB2 0.025 0.027 -10000 0 -0.46 2 2
RIT2 -0.11 0.2 -10000 0 -0.37 224 224
RIT1 0.027 0.003 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
DNM1 -0.022 0.12 -10000 0 -0.29 101 101
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.003 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.025 0.1 -10000 0 -0.27 79 79
mol:GDP 0.028 0.082 0.26 10 -0.39 7 17
NGF (dimer) -0.02 0.13 -10000 0 -0.38 70 70
RhoG/GDP 0.013 0.036 -10000 0 -0.33 7 7
RIT1/GDP 0.032 0.062 0.2 15 -0.26 6 21
TIAM1 0.025 0.019 -10000 0 -0.46 1 1
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.006 0.12 -10000 0 -0.3 71 71
KIDINS220/CRKL/C3G 0.037 0.023 -10000 0 -0.27 3 3
SHC/RasGAP 0.035 0.026 -10000 0 -0.15 13 13
FRS2 family/SHP2 0.051 0.021 -10000 0 -0.28 2 2
SHC/GRB2/SOS1/GAB1 0.061 0.032 -10000 0 -0.31 1 1
RIT1/GTP 0.02 0.002 -10000 0 -10000 0 0
NT3 (dimer) 0.013 0.043 -10000 0 -0.22 21 21
RAP1/GDP 0.022 0.045 -10000 0 -0.25 5 5
KIDINS220/CRKL 0.026 0.011 -10000 0 -0.22 1 1
BDNF (dimer) -0.017 0.11 -10000 0 -0.26 102 102
ubiquitin-dependent protein catabolic process 0.003 0.1 -10000 0 -0.28 61 61
Schwann cell development -0.015 0.021 -10000 0 -10000 0 0
EHD4 0.025 0.017 -10000 0 -0.22 3 3
FRS2 family/GRB2/SOS1 0.064 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.045 -10000 0 -0.45 4 4
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
RAP1A 0.024 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.11 -10000 0 -0.28 52 52
ABL1 0.026 0.019 -10000 0 -0.46 1 1
SH2B family/GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.095 -10000 0 -0.4 14 14
STAT3 0.026 0.046 -10000 0 -0.33 8 8
axon guidance -0.015 0.099 -10000 0 -0.26 65 65
MAPK3 -0.038 0.11 0.19 14 -0.27 99 113
MAPK1 -0.037 0.11 0.19 15 -0.27 98 113
CDC42/GDP 0.032 0.059 0.18 14 -0.28 5 19
NTF3 0.013 0.043 -10000 0 -0.22 21 21
NTF4 0.009 0.048 -10000 0 -0.23 23 23
NGF (dimer)/TRKA/FAIM 0.006 0.1 -10000 0 -0.27 60 60
PI3K 0.039 0.008 -10000 0 -10000 0 0
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.024 0.038 -10000 0 -0.46 4 4
GAB1 0.026 0.019 -10000 0 -0.46 1 1
RASGRF1 -0.08 0.13 -10000 0 -0.27 179 179
SOS1 0.027 0.002 -10000 0 -10000 0 0
MCF2L 0.007 0.055 -10000 0 -0.34 13 13
RGS19 0.026 0.006 -10000 0 -10000 0 0
CDC42 0.024 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.009 0.071 -10000 0 -0.54 3 3
Rac1/GDP 0.03 0.056 0.2 12 -0.28 3 15
NGF (dimer)/TRKA/GRIT -0.006 0.092 -10000 0 -0.26 63 63
neuron projection morphogenesis -0.017 0.11 -10000 0 -0.55 7 7
NGF (dimer)/TRKA/NEDD4-2 0.003 0.1 -10000 0 -0.28 61 61
MAP2K1 0.027 0.041 0.19 29 -0.29 1 30
NGFR -0.023 0.13 -10000 0 -0.33 91 91
NGF (dimer)/TRKA/GIPC/GAIP -0.017 0.095 -10000 0 -0.26 70 70
RAS family/GTP/PI3K 0.024 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.073 0.025 -10000 0 -0.23 1 1
NRAS 0.024 0.009 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
MAPKKK cascade -0.073 0.21 -10000 0 -0.51 100 100
RASA1 0.027 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.026 0.054 -10000 0 -0.19 35 35
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.009 0.11 -10000 0 -0.27 62 62
NGF (dimer)/TRKA/p62/Atypical PKCs 0.011 0.12 -10000 0 -0.26 79 79
MATK -0.035 0.15 -10000 0 -0.35 106 106
NEDD4L 0.021 0.045 -10000 0 -0.32 10 10
RAS family/GDP -0.006 0.028 -10000 0 -0.22 5 5
NGF (dimer)/TRKA -0.031 0.11 -10000 0 -0.28 86 86
Rac1/GTP -0.035 0.078 -10000 0 -0.26 33 33
FRS2 family/SHP2/CRK family 0.074 0.028 -10000 0 -0.23 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.03 0.14 -10000 0 -0.56 15 15
UGCG -0.02 0.14 -10000 0 -0.68 27 27
AKT1/mTOR/p70S6K/Hsp90/TERT -0.046 0.14 0.24 2 -0.39 52 54
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.02 0.14 -10000 0 -0.67 27 27
mol:DAG -0.066 0.25 -10000 0 -0.83 62 62
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.13 0.26 1 -0.41 33 34
FRAP1 -0.036 0.15 0.28 1 -0.46 36 37
FOXO3 -0.035 0.14 0.26 3 -0.43 43 46
AKT1 -0.04 0.16 0.27 2 -0.46 44 46
GAB2 0.025 0.027 -10000 0 -0.46 2 2
SMPD1 -0.011 0.12 -10000 0 -0.61 21 21
SGMS1 -0.046 0.18 -10000 0 -0.58 61 61
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.005 -10000 0 -10000 0 0
CALM1 0.026 0.006 -10000 0 -10000 0 0
cell proliferation -0.034 0.14 0.21 2 -0.36 67 69
EIF3A 0.024 0.009 -10000 0 -10000 0 0
PI3K 0.042 0.009 -10000 0 -10000 0 0
RPS6KB1 0 0.075 -10000 0 -0.92 2 2
mol:sphingomyelin -0.066 0.25 -10000 0 -0.83 62 62
natural killer cell activation 0 0.002 -10000 0 -0.011 7 7
JAK3 -0.012 0.12 -10000 0 -0.31 77 77
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MYC -0.031 0.2 0.32 2 -0.8 25 27
MYB -0.069 0.31 -10000 0 -1.2 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.044 0.14 -10000 0 -0.38 61 61
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.023 0.076 -10000 0 -0.82 2 2
mol:PI-3-4-5-P3 -0.043 0.14 -10000 0 -0.37 61 61
Rac1/GDP 0.023 0.013 -10000 0 -10000 0 0
T cell proliferation -0.048 0.14 -10000 0 -0.4 45 45
SHC1 0.022 0.035 -10000 0 -0.22 13 13
RAC1 0.023 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.017 -10000 0 -0.062 42 42
PRKCZ -0.046 0.14 -10000 0 -0.42 42 42
NF kappa B1 p50/RelA -0.016 0.14 0.27 1 -0.43 26 27
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.038 0.15 -10000 0 -0.45 56 56
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.003 -10000 0 -10000 0 0
IL2RA -0.067 0.16 -10000 0 -0.32 166 166
IL2RB -0.046 0.15 -10000 0 -0.33 136 136
TERT -0.033 0.15 -10000 0 -0.4 87 87
E2F1 -0.015 0.13 -10000 0 -0.46 45 45
SOS1 0.027 0.002 -10000 0 -10000 0 0
RPS6 0.024 0.015 -10000 0 -0.22 2 2
mol:cAMP 0.001 0.008 0.031 42 -10000 0 42
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
IL2RG -0.002 0.1 -10000 0 -0.32 57 57
actin cytoskeleton organization -0.048 0.14 -10000 0 -0.4 45 45
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.016 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.044 0.024 -10000 0 -10000 0 0
LCK -0.029 0.13 -10000 0 -0.3 112 112
BCL2 -0.025 0.13 0.42 1 -0.61 9 10
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.058 0.2 3 -0.31 4 7
adherens junction organization -0.013 0.092 0.16 1 -0.25 74 75
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.092 0.23 2 -0.29 15 17
FMN1 -0.024 0.11 -10000 0 -0.24 106 106
mol:IP3 0.007 0.054 -10000 0 -0.28 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.093 -10000 0 -0.24 76 76
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.012 0.066 0.19 2 -0.29 4 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.012 0.14 -10000 0 -0.37 77 77
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.085 -10000 0 -0.23 74 74
VASP -0.005 0.085 -10000 0 -0.23 75 75
ZYX -0.006 0.081 -10000 0 -0.23 66 66
JUB -0.005 0.088 0.16 2 -0.23 76 78
EGFR(dimer) -0.014 0.11 -10000 0 -0.27 67 67
E-cadherin/beta catenin-gamma catenin -0.001 0.11 -10000 0 -0.27 80 80
mol:PI-3-4-5-P3 0.027 0.076 0.21 2 -0.27 6 8
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.077 0.21 2 -0.27 6 8
FYN 0.009 0.051 -10000 0 -0.26 4 4
mol:Ca2+ 0.007 0.053 -10000 0 -0.28 3 3
JUP 0.024 0.045 -10000 0 -0.39 7 7
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG 0.007 0.054 -10000 0 -0.28 3 3
CDH1 -0.051 0.16 -10000 0 -0.36 132 132
RhoA/GDP 0.026 0.1 0.23 2 -0.3 14 16
establishment of polarity of embryonic epithelium -0.005 0.083 -10000 0 -0.22 75 75
SRC 0.024 0.027 -10000 0 -0.46 2 2
RAC1 0.023 0.01 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
EGFR -0.019 0.13 -10000 0 -0.46 53 53
CASR 0.003 0.053 0.16 3 -0.29 2 5
RhoA/GTP 0.02 0.054 -10000 0 -0.29 2 2
AKT2 0.014 0.06 0.19 2 -0.3 3 5
actin cable formation -0.022 0.1 0.19 1 -0.26 64 65
apoptosis -0.007 0.065 0.3 6 -0.19 3 9
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
mol:GDP -0.011 0.08 0.17 1 -0.3 18 19
PIP5K1A -0.003 0.086 -10000 0 -0.23 73 73
PLCG1 0.007 0.055 -10000 0 -0.29 3 3
Rac1/GTP -0.005 0.1 -10000 0 -0.35 19 19
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0 0.09 -10000 0 -0.28 50 50
cell-cell adhesion 0.011 0.064 0.32 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.057 0.061 -10000 0 -0.26 13 13
ITSN1 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.022 0.035 -10000 0 -0.22 13 13
Ephrin B1/EPHB3 0.033 0.023 -10000 0 -0.28 2 2
Ephrin B1/EPHB1 -0.002 0.1 -10000 0 -0.28 78 78
HRAS/GDP 0.012 0.074 -10000 0 -0.28 17 17
Ephrin B/EPHB1/GRB7 0.016 0.12 -10000 0 -0.27 85 85
Endophilin/SYNJ1 0.014 0.049 -10000 0 -0.24 13 13
KRAS 0.026 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.031 0.11 -10000 0 -0.26 73 73
endothelial cell migration 0.041 0.033 -10000 0 -0.23 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.004 0.066 -10000 0 -0.22 52 52
PAK1 0.008 0.066 0.36 2 -0.24 15 17
HRAS 0.026 0.006 -10000 0 -10000 0 0
RRAS 0.012 0.052 0.36 1 -0.26 12 13
DNM1 -0.022 0.12 -10000 0 -0.29 101 101
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.094 0.36 1 -0.24 84 85
lamellipodium assembly -0.011 0.064 -10000 0 -0.32 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.004 0.093 -10000 0 -0.33 20 20
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
EPHB2 0.021 0.037 -10000 0 -0.34 6 6
EPHB3 0.024 0.03 -10000 0 -0.34 4 4
EPHB1 -0.032 0.16 -10000 0 -0.46 79 79
EPHB4 0.021 0.017 -10000 0 -0.22 2 2
mol:GDP -0.003 0.063 0.32 1 -0.3 11 12
Ephrin B/EPHB2 0.044 0.056 -10000 0 -0.26 13 13
Ephrin B/EPHB3 0.049 0.054 -10000 0 -0.28 12 12
JNK cascade -0.008 0.094 0.26 12 -0.24 78 90
Ephrin B/EPHB1 0.017 0.11 -10000 0 -0.25 85 85
RAP1/GDP 0.041 0.094 0.24 63 -0.33 5 68
EFNB2 0.022 0.035 -10000 0 -0.25 10 10
EFNB3 0.017 0.063 -10000 0 -0.38 15 15
EFNB1 0.025 0.019 -10000 0 -0.22 4 4
Ephrin B2/EPHB1-2 0.005 0.1 -10000 0 -0.26 80 80
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
RAP1A 0.024 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.088 -10000 0 -0.33 16 16
Rap1/GTP -0.006 0.086 -10000 0 -0.32 16 16
axon guidance 0 0.089 -10000 0 -0.28 50 50
MAPK3 -0.001 0.082 -10000 0 -0.3 20 20
MAPK1 0.001 0.08 -10000 0 -0.3 19 19
Rac1/GDP 0.021 0.083 0.24 35 -0.32 7 42
actin cytoskeleton reorganization -0.006 0.054 -10000 0 -0.3 7 7
CDC42/GDP 0.037 0.098 0.24 74 -0.32 7 81
PI3K 0.045 0.035 -10000 0 -0.23 1 1
EFNA5 -0.022 0.14 -10000 0 -0.37 82 82
Ephrin B2/EPHB4 0.025 0.026 -10000 0 -0.14 10 10
Ephrin B/EPHB2/Intersectin/N-WASP 0.018 0.047 -10000 0 -0.27 12 12
CDC42 0.024 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.082 -10000 0 -0.32 15 15
PTK2 0.044 0.13 0.54 42 -10000 0 42
MAP4K4 -0.008 0.095 0.26 12 -0.24 78 90
SRC 0.024 0.027 -10000 0 -0.46 2 2
KALRN 0.02 0.038 -10000 0 -0.22 16 16
Intersectin/N-WASP 0.031 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis 0.034 0.12 0.32 72 -0.33 7 79
MAP2K1 0.001 0.086 -10000 0 -0.32 20 20
WASL 0.021 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.021 0.11 -10000 0 -0.26 78 78
cell migration -0.003 0.1 -10000 0 -0.35 22 22
NRAS 0.024 0.009 -10000 0 -10000 0 0
SYNJ1 0.014 0.049 -10000 0 -0.24 13 13
PXN 0.027 0.003 -10000 0 -10000 0 0
TF -0.016 0.083 0.18 9 -0.24 61 70
HRAS/GTP 0.01 0.098 -10000 0 -0.23 78 78
Ephrin B1/EPHB1-2 0.007 0.1 -10000 0 -0.26 78 78
cell adhesion mediated by integrin -0.001 0.044 0.24 12 -0.19 9 21
RAC1 0.023 0.01 -10000 0 -10000 0 0
mol:GTP 0.013 0.1 -10000 0 -0.24 84 84
RAC1-CDC42/GTP -0.009 0.071 -10000 0 -0.34 11 11
RASA1 0.027 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.027 0.081 0.24 32 -0.33 5 37
ruffle organization 0.048 0.13 0.35 61 -0.34 10 71
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization -0.011 0.074 0.18 11 -0.25 30 41
Ephrin B/EPHB2/KALRN 0.052 0.065 -10000 0 -0.25 14 14
ROCK1 0.017 0.019 -10000 0 -0.25 2 2
RAS family/GDP -0.009 0.049 -10000 0 -0.31 6 6
Rac1/GTP -0.005 0.07 -10000 0 -0.34 11 11
Ephrin B/EPHB1/Src/Paxillin 0 0.092 -10000 0 -0.24 74 74
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0 0.1 0.34 44 -10000 0 44
KIRREL -0.006 0.12 -10000 0 -0.45 45 45
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0 0.1 -10000 0 -0.34 44 44
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.002 -10000 0 -10000 0 0
WASL 0.021 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.025 0.085 -10000 0 -0.26 42 42
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.003 0.065 -10000 0 -0.24 36 36
FYN -0.003 0.075 0.27 4 -0.24 43 47
mol:Ca2+ 0.022 0.084 -10000 0 -0.25 43 43
mol:DAG 0.023 0.085 -10000 0 -0.26 43 43
NPHS2 0.009 0.032 -10000 0 -0.3 3 3
mol:IP3 0.023 0.085 -10000 0 -0.26 43 43
regulation of endocytosis 0.021 0.075 -10000 0 -0.23 43 43
Nephrin/NEPH1/podocin/Cholesterol 0.012 0.08 -10000 0 -0.26 43 43
establishment of cell polarity 0 0.1 -10000 0 -0.34 44 44
Nephrin/NEPH1/podocin/NCK1-2 0.037 0.084 -10000 0 -0.23 43 43
Nephrin/NEPH1/beta Arrestin2 0.022 0.076 -10000 0 -0.23 43 43
NPHS1 0.005 0.058 -10000 0 -0.23 34 34
Nephrin/NEPH1/podocin 0.014 0.076 -10000 0 -0.24 43 43
TJP1 0.026 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.024 0.086 -10000 0 -0.26 43 43
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.024 0.085 -10000 0 -0.26 43 43
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.09 0.21 9 -0.26 56 65
cytoskeleton organization -0.002 0.076 0.21 13 -0.27 36 49
Nephrin/NEPH1 0.005 0.071 -10000 0 -0.24 42 42
Nephrin/NEPH1/ZO-1 0.017 0.086 -10000 0 -0.27 42 42
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.058 -10000 0 -0.26 16 16
EPHB2 0.021 0.037 -10000 0 -0.34 6 6
Syndecan-2/TACI 0.015 0.049 -10000 0 -0.27 15 15
LAMA1 -0.032 0.15 -10000 0 -0.42 85 85
Syndecan-2/alpha2 ITGB1 0.007 0.1 -10000 0 -0.26 70 70
HRAS 0.026 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.003 0.043 -10000 0 -0.27 14 14
ITGA5 0.007 0.071 -10000 0 -0.24 46 46
BAX 0.005 0.038 -10000 0 -10000 0 0
EPB41 0.021 0.04 -10000 0 -0.41 5 5
positive regulation of cell-cell adhesion 0.019 0.042 -10000 0 -0.24 14 14
LAMA3 -0.014 0.12 -10000 0 -0.35 70 70
EZR 0.021 0.047 -10000 0 -0.46 6 6
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.006 0.063 -10000 0 -0.24 39 39
Syndecan-2/MMP2 0.01 0.068 -10000 0 -0.26 31 31
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.013 0.08 -10000 0 -0.24 51 51
dendrite morphogenesis 0.017 0.05 -10000 0 -0.26 17 17
Syndecan-2/GM-CSF 0.012 0.048 -10000 0 -0.27 15 15
determination of left/right symmetry 0.005 0.051 -10000 0 -0.25 23 23
Syndecan-2/PKC delta 0.011 0.076 -10000 0 -0.31 31 31
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.059 0.19 37 -0.24 15 52
MAPK1 0.017 0.058 0.19 35 -0.24 14 49
Syndecan-2/RACK1 0.033 0.043 -10000 0 -0.23 14 14
NF1 0.024 0.038 -10000 0 -0.46 4 4
FGFR/FGF/Syndecan-2 0.005 0.051 -10000 0 -0.25 23 23
ITGA2 -0.004 0.11 -10000 0 -0.35 53 53
MAPK8 0.004 0.053 -10000 0 -0.27 22 22
Syndecan-2/alpha2/beta1 Integrin -0.003 0.12 -10000 0 -0.26 96 96
Syndecan-2/Kininogen 0.01 0.052 -10000 0 -0.27 14 14
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
SRC 0.023 0.056 0.19 33 -0.23 16 49
Syndecan-2/CASK/Protein 4.1 0.016 0.047 -10000 0 -0.24 18 18
extracellular matrix organization 0.017 0.05 -10000 0 -0.27 17 17
actin cytoskeleton reorganization 0.012 0.058 -10000 0 -0.26 16 16
Syndecan-2/Caveolin-2/Ras 0.02 0.056 -10000 0 -0.23 18 18
Syndecan-2/Laminin alpha3 -0.001 0.088 -10000 0 -0.29 47 47
Syndecan-2/RasGAP 0.044 0.045 -10000 0 -0.22 14 14
alpha5/beta1 Integrin 0.021 0.055 -10000 0 -0.31 7 7
PRKCD 0.009 0.09 -10000 0 -0.46 23 23
Syndecan-2 dimer 0.017 0.051 -10000 0 -0.26 17 17
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.032 0.046 0.18 5 -0.22 16 21
RHOA 0.027 0.003 -10000 0 -10000 0 0
SDCBP 0.026 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.016 0.029 -10000 0 -0.22 9 9
RASA1 0.027 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.013 0.08 -10000 0 -0.24 51 51
Syndecan-2/Synbindin 0.021 0.047 -10000 0 -0.27 14 14
TGFB1 0.022 0.03 -10000 0 -0.38 3 3
CASP3 0.014 0.078 0.2 33 -0.28 29 62
FN1 0.009 0.063 -10000 0 -0.22 46 46
Syndecan-2/IL8 -0.05 0.12 -10000 0 -0.28 103 103
SDC2 0.005 0.052 -10000 0 -0.25 23 23
KNG1 0.009 0.045 -10000 0 -0.22 24 24
Syndecan-2/Neurofibromin 0.02 0.05 -10000 0 -0.27 17 17
TRAPPC4 0.026 0.004 -10000 0 -10000 0 0
CSF2 0.014 0.025 -10000 0 -0.22 7 7
Syndecan-2/TGFB1 0.017 0.05 -10000 0 -0.27 17 17
Syndecan-2/Syntenin/PI-4-5-P2 0.019 0.042 -10000 0 -0.24 14 14
Syndecan-2/Ezrin 0.031 0.057 -10000 0 -0.29 16 16
PRKACA 0.022 0.06 0.2 36 -0.24 17 53
angiogenesis -0.05 0.12 -10000 0 -0.28 103 103
MMP2 0.007 0.082 -10000 0 -0.29 42 42
IL8 -0.1 0.18 -10000 0 -0.31 247 247
calcineurin-NFAT signaling pathway 0.015 0.049 -10000 0 -0.27 15 15
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.034 0.18 20 -0.26 1 21
RFC1 0.001 0.031 0.17 18 -10000 0 18
PRKDC 0.002 0.033 0.18 20 -10000 0 20
RIPK1 0.028 0.005 -10000 0 -10000 0 0
CASP7 -0.055 0.2 -10000 0 -0.58 76 76
FASLG/FAS/FADD/FAF1 -0.004 0.059 0.2 14 -0.26 12 26
MAP2K4 -0.047 0.13 0.22 1 -0.36 44 45
mol:ceramide -0.01 0.081 -10000 0 -0.28 16 16
GSN -0.001 0.048 0.18 20 -0.34 6 26
FASLG/FAS/FADD/FAF1/Caspase 8 -0.009 0.064 -10000 0 -0.28 8 8
FAS 0.002 0.079 -10000 0 -0.31 35 35
BID -0.006 0.053 0.29 18 -10000 0 18
MAP3K1 -0.049 0.14 -10000 0 -0.38 74 74
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
RB1 0.002 0.032 0.18 19 -10000 0 19
CFLAR 0.028 0.004 -10000 0 -10000 0 0
HGF/MET -0.036 0.13 -10000 0 -0.29 110 110
ARHGDIB 0.001 0.032 0.18 18 -10000 0 18
FADD 0.022 0.014 -10000 0 -10000 0 0
actin filament polymerization 0 0.051 0.34 6 -0.19 24 30
NFKB1 -0.019 0.11 -10000 0 -0.78 8 8
MAPK8 -0.067 0.17 -10000 0 -0.46 78 78
DFFA 0.001 0.029 0.18 16 -10000 0 16
DNA fragmentation during apoptosis 0.002 0.031 0.18 18 -10000 0 18
FAS/FADD/MET -0.026 0.12 -10000 0 -0.29 81 81
CFLAR/RIP1 0.041 0.008 -10000 0 -10000 0 0
FAIM3 0.008 0.088 -10000 0 -0.36 33 33
FAF1 0.019 0.016 -10000 0 -10000 0 0
PARP1 0.002 0.031 0.18 19 -10000 0 19
DFFB 0.001 0.029 0.18 16 -10000 0 16
CHUK -0.017 0.1 -10000 0 -0.74 8 8
FASLG 0.004 0.055 -10000 0 -0.23 32 32
FAS/FADD 0.016 0.061 -10000 0 -0.34 11 11
HGF -0.02 0.11 -10000 0 -0.29 87 87
LMNA -0.001 0.04 0.19 6 -10000 0 6
CASP6 0.001 0.033 0.18 19 -0.17 1 20
CASP10 0.022 0.014 -10000 0 -10000 0 0
CASP3 0.002 0.038 0.21 19 -10000 0 19
PTPN13 0.023 0.039 -10000 0 -0.41 5 5
CASP8 -0.007 0.064 0.35 18 -10000 0 18
IL6 -0.15 0.41 -10000 0 -1.3 75 75
MET -0.06 0.16 -10000 0 -0.33 151 151
ICAD/CAD 0.003 0.034 0.23 6 -10000 0 6
FASLG/FAS/FADD/FAF1/Caspase 10 -0.01 0.082 -10000 0 -0.29 16 16
activation of caspase activity by cytochrome c -0.006 0.053 0.29 18 -10000 0 18
PAK2 0.001 0.032 0.18 19 -10000 0 19
BCL2 0.024 0.033 -10000 0 -0.46 3 3
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.003 0.025 -10000 0 -0.28 2 2
ADCY5 -0.018 0.08 -10000 0 -0.25 63 63
ADCY6 0.005 0.02 -10000 0 -0.13 12 12
ADCY7 0.004 0.022 -10000 0 -0.28 2 2
ADCY1 -0.022 0.077 -10000 0 -0.2 87 87
ADCY2 -0.013 0.07 -10000 0 -0.24 53 53
ADCY3 0.005 0.02 -10000 0 -0.28 1 1
ADCY8 -0.019 0.078 -10000 0 -0.28 51 51
PRKCE 0.006 0.024 -10000 0 -0.16 12 12
ADCY9 0.004 0.023 -10000 0 -0.24 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0 0.078 0.19 21 -0.23 26 47
Coregulation of Androgen receptor activity

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
NRIP1 0.026 0.006 -9999 0 -10000 0 0
SVIL 0.013 0.053 -9999 0 -0.24 25 25
ZNF318 0.028 0.007 -9999 0 -10000 0 0
JMJD2C -0.001 0.009 -9999 0 -0.043 14 14
T-DHT/AR/Ubc9 -0.023 0.11 -9999 0 -0.28 86 86
CARM1 0.026 0.005 -9999 0 -10000 0 0
PRDX1 0.013 0.073 -9999 0 -0.46 15 15
PELP1 0.025 0.027 -9999 0 -0.46 2 2
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
AKT1 0.026 0.006 -9999 0 -10000 0 0
PTK2B 0.018 0.044 -9999 0 -0.22 21 21
MED1 0.027 0.003 -9999 0 -10000 0 0
MAK -0.005 0.092 -9999 0 -0.25 77 77
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.016 0.054 -9999 0 -0.46 8 8
GSN 0.02 0.051 -9999 0 -0.43 8 8
NCOA2 0 0.11 -9999 0 -0.46 35 35
NCOA6 0.024 0.027 -9999 0 -0.46 2 2
DNA-PK 0.052 0.015 -9999 0 -10000 0 0
NCOA4 0.024 0.008 -9999 0 -10000 0 0
PIAS3 0.025 0.007 -9999 0 -10000 0 0
cell proliferation -0.015 0.09 -9999 0 -0.53 16 16
XRCC5 0.027 0.002 -9999 0 -10000 0 0
UBE3A 0.024 0.011 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.031 0.12 -9999 0 -0.3 100 100
FHL2 -0.021 0.15 -9999 0 -1 12 12
RANBP9 0.026 0.004 -9999 0 -10000 0 0
JMJD1A -0.01 0.038 -9999 0 -0.13 52 52
CDK6 0.004 0.084 -9999 0 -0.38 28 28
TGFB1I1 0.021 0.045 -9999 0 -0.32 10 10
T-DHT/AR/CyclinD1 -0.03 0.12 -9999 0 -0.29 97 97
XRCC6 0.026 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.034 0.13 -9999 0 -0.3 99 99
CTDSP1 0.027 0.002 -9999 0 -10000 0 0
CTDSP2 0.025 0.008 -9999 0 -10000 0 0
BRCA1 0.025 0.017 -9999 0 -0.22 3 3
TCF4 0.026 0.02 -9999 0 -0.46 1 1
CDKN2A -0.025 0.12 -9999 0 -0.29 94 94
SRF 0.025 0.029 -9999 0 -10000 0 0
NKX3-1 -0.036 0.079 -9999 0 -0.18 127 127
KLK3 0.001 0.054 -9999 0 -10000 0 0
TMF1 0.026 0.003 -9999 0 -10000 0 0
HNRNPA1 0.027 0.005 -9999 0 -10000 0 0
AOF2 0 0.003 -9999 0 -10000 0 0
APPL1 0.018 0.005 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.025 0.11 -9999 0 -0.28 91 91
AR -0.055 0.16 -9999 0 -0.42 101 101
UBA3 0.026 0.003 -9999 0 -10000 0 0
PATZ1 0.026 0.005 -9999 0 -10000 0 0
PAWR 0.001 0.092 -9999 0 -0.29 54 54
PRKDC 0.027 0.004 -9999 0 -10000 0 0
PA2G4 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.027 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.019 0.1 -9999 0 -0.26 86 86
RPS6KA3 0.025 0.019 -9999 0 -0.46 1 1
T-DHT/AR/ARA70 -0.026 0.11 -9999 0 -0.28 87 87
LATS2 0.021 0.045 -9999 0 -0.32 10 10
T-DHT/AR/PRX1 -0.027 0.11 -9999 0 -0.26 101 101
Cyclin D3/CDK11 p58 0.02 0.002 -9999 0 -10000 0 0
VAV3 -0.075 0.15 -9999 0 -0.27 218 218
KLK2 -0.037 0.11 -9999 0 -0.46 29 29
CASP8 0.022 0.037 -9999 0 -0.24 12 12
T-DHT/AR/TIF2/CARM1 -0.018 0.13 -9999 0 -0.29 100 100
TMPRSS2 -0.085 0.25 -9999 0 -0.93 50 50
CCND1 0.015 0.065 -9999 0 -0.3 23 23
PIAS1 0.023 0.029 -9999 0 -0.46 2 2
mol:T-DHT -0.008 0.021 -9999 0 -0.064 60 60
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.023 0.023 -9999 0 -0.46 1 1
T-DHT/AR/CDK6 -0.033 0.12 -9999 0 -0.29 93 93
CMTM2 0.016 0.068 -9999 0 -0.4 16 16
SNURF 0.014 0.076 -9999 0 -0.45 17 17
ZMIZ1 0.009 0.044 -9999 0 -0.46 3 3
CCND3 0.027 0.003 -9999 0 -10000 0 0
TGIF1 0.015 0.073 -9999 0 -0.41 18 18
FKBP4 0.025 0.006 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.019 0.047 -9999 0 -0.25 18 18
PLK4 0.016 0.06 -9999 0 -0.28 23 23
regulation of centriole replication 0.005 0.052 -9999 0 -0.19 40 40
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.003 0.14 -10000 0 -0.54 30 30
HDAC1 0.023 0.011 -10000 0 -10000 0 0
AES 0.026 0.006 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.02 0.057 -10000 0 -0.44 10 10
LRP6/FZD1 0.03 0.023 -10000 0 -10000 0 0
TLE1 0.025 0.027 -10000 0 -0.46 2 2
AP1 -0.021 0.094 -10000 0 -0.26 80 80
NCSTN 0.027 0.003 -10000 0 -10000 0 0
ADAM10 0.018 0.063 -10000 0 -0.46 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.033 0.065 -10000 0 -0.46 3 3
NICD/RBPSUH 0.022 0.12 -10000 0 -0.48 31 31
WIF1 -0.14 0.19 -10000 0 -0.33 311 311
NOTCH1 0.006 0.12 -10000 0 -0.5 32 32
PSENEN 0.024 0.008 -10000 0 -10000 0 0
KREMEN2 -0.002 0.096 -10000 0 -0.28 62 62
DKK1 -0.047 0.14 -10000 0 -0.3 142 142
beta catenin/beta TrCP1 0.034 0.078 0.27 18 -0.31 2 20
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.003 -10000 0 -10000 0 0
AXIN1 0.006 0.063 0.28 1 -1 1 2
CtBP/CBP/TCF1/TLE1/AES 0.024 0.039 0.3 2 -0.26 4 6
PSEN1 0.026 0.006 -10000 0 -10000 0 0
FOS -0.024 0.14 -10000 0 -0.36 86 86
JUN 0.022 0.023 -10000 0 -0.22 5 5
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.023 0.08 0.27 19 -0.33 2 21
MAPK3 0.027 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.007 0.11 -10000 0 -0.28 68 68
HNF1A 0.026 0.019 -10000 0 -0.46 1 1
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.008 0.23 -10000 0 -1.4 17 17
NKD1 0.002 0.1 -10000 0 -0.4 38 38
FZD1 0.02 0.022 -10000 0 -0.22 4 4
NOTCH1 precursor/Deltex homolog 1 0.019 0.12 -10000 0 -0.49 32 32
apoptosis -0.021 0.094 -10000 0 -0.25 80 80
Delta 1/NOTCHprecursor -0.003 0.14 -10000 0 -0.54 30 30
DLL1 -0.022 0.14 -10000 0 -0.45 66 66
PPARD 0.025 0.067 -10000 0 -0.9 3 3
Gamma Secretase 0.068 0.029 -10000 0 -10000 0 0
APC 0.005 0.054 0.26 2 -0.31 4 6
DVL1 -0.003 0.057 -10000 0 -0.27 20 20
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.019 0.11 -10000 0 -0.28 69 69
LRP6 0.026 0.006 -10000 0 -10000 0 0
CSNK1A1 0.027 0.003 -10000 0 -10000 0 0
NLK 0.015 0.009 -10000 0 -10000 0 0
CCND1 0.007 0.17 -10000 0 -1.3 10 10
WNT1 0.011 0.056 -10000 0 -0.22 35 35
Axin1/APC/beta catenin 0.021 0.087 0.3 11 -0.53 2 13
DKK2 -0.035 0.14 -10000 0 -0.33 112 112
NOTCH1 precursor/DVL1 0 0.12 -10000 0 -0.54 23 23
GSK3B 0.026 0.003 -10000 0 -10000 0 0
FRAT1 0.02 0.042 -10000 0 -0.36 7 7
NOTCH/Deltex homolog 1 0.019 0.12 -10000 0 -0.5 32 32
PPP2R5D 0.018 0.065 0.26 25 -0.32 6 31
MAPK1 0.026 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.047 0.12 -10000 0 -0.25 117 117
RBPJ 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.02 -10000 0 -0.46 1 1
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.005 0.07 -10000 0 -0.27 4 4
PDGFRB 0.025 0.022 -10000 0 -0.23 5 5
SPHK1 -0.016 0.13 -10000 0 -0.76 19 19
mol:S1P -0.014 0.12 -10000 0 -0.66 19 19
S1P1/S1P/Gi -0.036 0.14 -10000 0 -0.37 85 85
GNAO1 0.002 0.098 -10000 0 -0.46 27 27
PDGFB-D/PDGFRB/PLCgamma1 -0.017 0.14 0.24 8 -0.34 76 84
PLCG1 -0.034 0.13 -10000 0 -0.35 79 79
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.022 -10000 0 -0.23 5 5
GNAI2 0.022 0.014 -10000 0 -10000 0 0
GNAI3 0.021 0.014 -10000 0 -10000 0 0
GNAI1 0.008 0.071 -10000 0 -0.46 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.016 0.049 -10000 0 -0.23 4 4
S1P1/S1P -0.02 0.1 -10000 0 -0.47 19 19
negative regulation of cAMP metabolic process -0.035 0.14 -10000 0 -0.36 85 85
MAPK3 -0.057 0.19 -10000 0 -0.5 89 89
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 0.02 0.002 -10000 0 -10000 0 0
KDR 0.023 0.031 -10000 0 -0.34 4 4
PLCB2 -0.011 0.1 0.23 5 -0.44 20 25
RAC1 0.023 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.086 -10000 0 -0.41 18 18
receptor internalization -0.019 0.094 -10000 0 -0.44 19 19
PTGS2 -0.1 0.34 -10000 0 -0.99 76 76
Rac1/GTP -0.015 0.081 -10000 0 -0.4 17 17
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFA -0.016 0.092 -10000 0 -0.22 110 110
negative regulation of T cell proliferation -0.035 0.14 -10000 0 -0.36 85 85
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.036 -10000 0 -0.47 3 3
MAPK1 -0.058 0.19 -10000 0 -0.5 89 89
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.11 0.3 1 -0.42 18 19
ABCC1 0.025 0.017 -10000 0 -0.23 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.008 0.07 -10000 0 -0.31 3 3
alphaV beta3 Integrin 0.014 0.087 -10000 0 -0.27 30 30
PTK2 -0.016 0.13 0.31 8 -0.41 24 32
IGF1R 0.02 0.057 -10000 0 -0.46 9 9
PI4KB 0.027 0.003 -10000 0 -10000 0 0
MFGE8 0.024 0.034 -10000 0 -0.4 4 4
SRC 0.024 0.027 -10000 0 -0.46 2 2
CDKN1B -0.005 0.1 -10000 0 -0.44 31 31
VEGFA -0.015 0.093 -10000 0 -0.22 110 110
ILK -0.004 0.099 -10000 0 -0.44 28 28
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.006 0.091 0.2 1 -0.42 27 28
PTK2B -0.02 0.088 0.19 17 -0.24 29 46
alphaV/beta3 Integrin/JAM-A 0.013 0.097 -10000 0 -0.25 53 53
CBL 0.026 0.019 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.007 0.084 -10000 0 -0.27 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.05 0.082 -10000 0 -0.32 25 25
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.072 -10000 0 -0.28 14 14
alphaV/beta3 Integrin/Syndecan-1 -0.004 0.11 -10000 0 -0.27 70 70
PI4KA 0.024 0.026 -10000 0 -0.22 7 7
IGF-1R heterotetramer/IGF1/IRS1 0.007 0.1 -10000 0 -0.26 54 54
PI4 Kinase 0.037 0.02 -10000 0 -0.15 7 7
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.033 0.13 -10000 0 -0.27 125 125
RPS6KB1 -0.019 0.088 0.29 1 -0.34 14 15
TLN1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.008 0.1 -10000 0 -0.4 32 32
GPR124 0.025 0.02 -10000 0 -0.22 4 4
MAPK1 -0.008 0.1 -10000 0 -0.4 32 32
PXN 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.024 0.13 -10000 0 -0.31 82 82
cell adhesion 0.011 0.079 -10000 0 -0.27 31 31
ANGPTL3 0.017 0.012 -10000 0 -0.22 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.024 0.065 -10000 0 -0.29 5 5
IGF-1R heterotetramer 0.02 0.057 -10000 0 -0.46 9 9
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
TGFBR2 0.025 0.017 -10000 0 -0.22 3 3
ITGB3 -0.029 0.12 -10000 0 -0.28 120 120
IGF1 0.013 0.077 -10000 0 -0.38 22 22
RAC1 0.023 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.014 0.086 -10000 0 -0.27 30 30
apoptosis 0.027 0.002 -10000 0 -10000 0 0
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.016 0.086 -10000 0 -0.28 28 28
VCL 0.022 0.028 -10000 0 -0.27 5 5
alphaV/beta3 Integrin/Del1 -0.026 0.14 -10000 0 -0.32 95 95
CSF1 0.02 0.043 -10000 0 -0.46 5 5
PIK3C2A -0.003 0.098 -10000 0 -0.45 27 27
PI4 Kinase/Pyk2 -0.014 0.093 -10000 0 -0.32 10 10
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.008 0.1 -10000 0 -0.22 83 83
FAK1/Vinculin -0.003 0.11 0.26 7 -0.34 20 27
alphaV beta3/Integrin/ppsTEM5 0.015 0.086 -10000 0 -0.27 30 30
RHOA 0.027 0.003 -10000 0 -10000 0 0
VTN 0.007 0.094 -10000 0 -0.41 30 30
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
FGF2 0.025 0.022 -10000 0 -0.34 2 2
F11R 0.015 0.023 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/Lactadherin 0.014 0.088 -10000 0 -0.28 32 32
alphaV/beta3 Integrin/TGFBR2 0.015 0.086 -10000 0 -0.27 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.042 -10000 0 -0.3 5 5
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.016 0.077 -10000 0 -0.25 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.063 -10000 0 -0.22 46 46
alphaV/beta3 Integrin/Pyk2 -0.004 0.094 -10000 0 -0.24 29 29
SDC1 -0.007 0.099 -10000 0 -0.27 74 74
VAV3 -0.028 0.084 0.19 12 -0.24 49 61
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
IRS1 0.022 0.05 -10000 0 -0.46 7 7
FAK1/Paxillin -0.003 0.11 0.28 10 -0.34 21 31
cell migration -0.004 0.099 0.24 9 -0.31 19 28
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PI3K 0.024 0.094 -10000 0 -0.3 10 10
SPP1 -0.05 0.15 -10000 0 -0.31 149 149
KDR 0.023 0.031 -10000 0 -0.34 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.002 -10000 0 -10000 0 0
COL4A3 -0.036 0.14 -10000 0 -0.33 117 117
angiogenesis -0.01 0.12 -10000 0 -0.43 30 30
Rac1/GTP -0.008 0.076 -10000 0 -0.22 44 44
EDIL3 -0.04 0.16 -10000 0 -0.42 99 99
cell proliferation 0.015 0.086 -10000 0 -0.27 30 30
TCGA08_rtk_signaling

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
PDGFRA -0.026 0.15 -10000 0 -0.44 72 72
HRAS 0.026 0.006 -10000 0 -10000 0 0
EGFR -0.019 0.13 -10000 0 -0.46 53 53
AKT 0.051 0.11 0.28 77 -0.23 5 82
FOXO3 0.025 0.02 -10000 0 -0.46 1 1
AKT1 0.026 0.006 -10000 0 -10000 0 0
FOXO1 0.025 0.02 -10000 0 -0.46 1 1
AKT3 0.023 0.042 -10000 0 -0.46 5 5
FOXO4 0.025 0.033 -10000 0 -0.46 3 3
MET -0.06 0.16 -10000 0 -0.33 151 151
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.024 0.009 -10000 0 -10000 0 0
PIK3CG -0.007 0.1 -10000 0 -0.36 48 48
PIK3R3 0.023 0.025 -10000 0 -0.3 3 3
PIK3R2 0.026 0.005 -10000 0 -10000 0 0
NF1 0.024 0.038 -10000 0 -0.46 4 4
RAS -0.011 0.07 0.22 6 -0.22 24 30
ERBB2 0.023 0.035 -10000 0 -0.25 10 10
proliferation/survival/translation -0.029 0.076 0.31 17 -0.23 14 31
PI3K 0.026 0.12 0.26 88 -0.19 34 122
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
FOXO 0.071 0.088 0.23 108 -0.1 1 109
AKT2 0.024 0.009 -10000 0 -10000 0 0
PTEN 0.024 0.009 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.022 -10000 0 -0.22 5 5
Jak2/Leptin Receptor 0.014 0.13 0.25 6 -0.38 32 38
PTP1B/AKT1 0.017 0.085 0.19 4 -0.3 17 21
FYN 0.026 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.007 0.088 0.2 6 -0.32 18 24
EGFR -0.02 0.13 -10000 0 -0.46 53 53
EGF/EGFR -0.017 0.12 -10000 0 -0.3 77 77
CSF1 0.02 0.043 -10000 0 -0.46 5 5
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.026 0.02 -10000 0 -0.46 1 1
PTP1B/N-cadherin 0.017 0.091 0.2 4 -0.31 18 22
Insulin Receptor/Insulin 0.026 0.082 -10000 0 -0.32 10 10
HCK 0.016 0.064 -10000 0 -0.37 16 16
CRK 0.027 0.003 -10000 0 -10000 0 0
TYK2 0.012 0.094 0.27 19 -0.31 17 36
EGF -0.007 0.12 -10000 0 -0.38 53 53
YES1 0.024 0.027 -10000 0 -0.46 2 2
CAV1 0.022 0.12 0.24 35 -0.35 18 53
TXN 0.028 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.026 0.091 -10000 0 -0.31 14 14
cell migration -0.007 0.088 0.32 18 -0.2 6 24
STAT3 0.027 0.003 -10000 0 -10000 0 0
PRLR 0.006 0.094 -10000 0 -0.34 41 41
ITGA2B -0.003 0.11 -10000 0 -0.4 46 46
CSF1R 0.008 0.092 -10000 0 -0.42 28 28
Prolactin Receptor/Prolactin 0.02 0.073 -10000 0 -0.33 20 20
FGR 0.022 0.025 -10000 0 -0.22 6 6
PTP1B/p130 Cas 0.016 0.088 0.19 5 -0.3 18 23
Crk/p130 Cas 0.027 0.091 0.22 1 -0.34 11 12
DOK1 0.014 0.086 0.28 2 -0.36 10 12
JAK2 0.005 0.13 0.22 2 -0.37 43 45
Jak2/Leptin Receptor/Leptin -0.045 0.13 -10000 0 -0.34 60 60
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
PTPN1 0.006 0.089 0.2 6 -0.32 18 24
LYN 0.024 0.032 -10000 0 -0.32 5 5
CDH2 0.026 0.019 -10000 0 -0.46 1 1
SRC 0.025 0.059 -10000 0 -0.38 9 9
ITGB3 -0.028 0.13 -10000 0 -0.28 120 120
CAT1/PTP1B 0 0.14 0.29 32 -0.4 30 62
CAPN1 0.027 0.02 -10000 0 -0.47 1 1
CSK 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.035 0.08 -10000 0 -0.4 4 4
mol:H2O2 0.002 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.047 0.13 -10000 0 -0.36 59 59
negative regulation of transcription 0.005 0.12 0.22 2 -0.36 43 45
FCGR2A -0.011 0.12 -10000 0 -0.34 68 68
FER 0.018 0.069 -10000 0 -0.47 13 13
alphaIIb/beta3 Integrin -0.022 0.12 -10000 0 -0.35 61 61
BLK -0.01 0.088 -10000 0 -0.23 88 88
Insulin Receptor/Insulin/Shc 0.038 0.039 -10000 0 -0.28 5 5
RHOA 0.028 0.004 -10000 0 -10000 0 0
LEPR 0.02 0.045 -10000 0 -0.32 10 10
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.013 0.14 0.25 15 -0.44 33 48
PRL 0.016 0.024 -10000 0 -0.22 6 6
SOCS3 -0.16 0.41 -10000 0 -1.3 72 72
SPRY2 0.025 0.033 -10000 0 -0.25 8 8
Insulin Receptor/Insulin/IRS1 0.038 0.044 -10000 0 -0.28 11 11
CSF1/CSF1R 0.015 0.1 -10000 0 -0.32 28 28
Ras protein signal transduction 0.016 0.1 0.52 24 -10000 0 24
IRS1 0.022 0.05 -10000 0 -0.46 7 7
INS 0.01 0.039 -10000 0 -0.42 5 5
LEP 0.005 0.043 -10000 0 -0.22 20 20
STAT5B 0.013 0.096 0.2 6 -0.33 16 22
STAT5A 0.01 0.1 0.21 5 -0.34 17 22
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.09 -10000 0 -0.31 17 17
CSN2 -0.007 0.052 -10000 0 -0.56 1 1
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
LAT -0.017 0.15 -10000 0 -0.46 60 60
YBX1 0.03 0.029 -10000 0 -0.46 2 2
LCK -0.031 0.13 -10000 0 -0.3 112 112
SHC1 0.022 0.035 -10000 0 -0.22 13 13
NOX4 -0.052 0.14 -10000 0 -0.26 180 180
Canonical Wnt signaling pathway

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
HDAC1 0.024 0.019 0.19 3 -10000 0 3
AES 0.025 0.015 0.17 1 -10000 0 1
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.023 -10000 0 -10000 0 0
SMAD4 0.026 0.005 -10000 0 -10000 0 0
DKK2 -0.035 0.14 -10000 0 -0.33 112 112
TLE1 0.024 0.031 0.21 1 -0.46 2 3
MACF1 0.022 0.034 -10000 0 -0.46 3 3
CTNNB1 0.066 0.11 0.3 49 -0.36 4 53
WIF1 -0.14 0.19 -10000 0 -0.33 311 311
beta catenin/RanBP3 0.01 0.093 0.43 22 -0.4 1 23
KREMEN2 -0.002 0.096 -10000 0 -0.28 62 62
DKK1 -0.047 0.14 -10000 0 -0.3 142 142
beta catenin/beta TrCP1 0.076 0.1 0.3 49 -0.34 3 52
FZD1 0.02 0.022 -10000 0 -0.22 4 4
AXIN2 0.007 0.14 0.57 17 -1.2 3 20
AXIN1 0.027 0.019 -10000 0 -0.46 1 1
RAN 0.027 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.027 0.077 -10000 0 -0.6 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.077 0.082 0.28 16 -0.56 3 19
Axin1/APC/GSK3 0.039 0.071 0.31 9 -0.32 2 11
Axin1/APC/GSK3/beta catenin/Macf1 0.057 0.086 0.33 13 -0.44 4 17
HNF1A 0.025 0.025 0.19 3 -0.46 1 4
CTBP1 0.026 0.017 0.19 3 -10000 0 3
MYC 0.01 0.28 0.56 52 -1.4 17 69
RANBP3 0.026 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.008 0.11 -10000 0 -0.28 68 68
NKD1 0.002 0.1 -10000 0 -0.4 38 38
TCF4 0.025 0.023 0.18 2 -0.42 1 3
TCF3 0.025 0.021 0.18 2 -0.34 1 3
WNT1/LRP6/FZD1/Axin1 0.044 0.046 -10000 0 -0.26 1 1
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.016 0.098 0.49 22 -0.36 1 23
LEF1 0.023 0.032 -10000 0 -0.23 8 8
DVL1 0.032 0.042 0.26 1 -0.27 1 2
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.081 0.096 0.28 20 -0.74 3 23
DKK1/LRP6/Kremen 2 -0.018 0.11 -10000 0 -0.28 69 69
LRP6 0.026 0.006 -10000 0 -10000 0 0
CSNK1A1 0.026 0.018 0.2 2 -10000 0 2
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 -0.014 0.19 0.56 9 -1.6 8 17
WNT1 0.011 0.056 -10000 0 -0.22 35 35
GSK3A 0.024 0.009 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.02 0.042 -10000 0 -0.36 7 7
PPP2R5D 0.04 0.062 0.29 26 -0.28 2 28
APC 0.048 0.078 0.32 8 -0.24 1 9
WNT1/LRP6/FZD1 0.053 0.076 0.21 81 -0.25 1 82
CREBBP 0.025 0.025 0.19 3 -0.46 1 4
Noncanonical Wnt signaling pathway

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
NFATC2 -0.019 0.13 -10000 0 -0.39 71 71
GNB1/GNG2 0.012 0.1 -10000 0 -0.3 31 31
mol:DAG 0.003 0.088 0.21 8 -0.31 16 24
PLCG1 0.002 0.09 0.26 2 -0.32 16 18
YES1 -0.012 0.087 -10000 0 -0.32 30 30
FZD3 0.024 0.033 -10000 0 -0.46 3 3
FZD6 0.006 0.067 -10000 0 -0.23 49 49
G protein 0.019 0.1 -10000 0 -0.32 16 16
MAP3K7 -0.049 0.1 0.23 3 -0.34 25 28
mol:Ca2+ 0.003 0.086 0.21 8 -0.3 16 24
mol:IP3 0.003 0.088 0.21 8 -0.31 16 24
NLK 0.009 0.05 -10000 0 -0.88 2 2
GNB1 0.024 0.008 -10000 0 -10000 0 0
CAMK2A -0.052 0.11 0.21 2 -0.34 32 34
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.011 0.094 -10000 0 -0.27 62 62
CSNK1A1 0.027 0.003 -10000 0 -10000 0 0
GNAS -0.012 0.085 -10000 0 -0.31 29 29
GO:0007205 -0.004 0.086 0.21 8 -0.32 15 23
WNT6 0.003 0.093 -10000 0 -0.32 45 45
WNT4 0.001 0.084 -10000 0 -0.27 51 51
NFAT1/CK1 alpha 0 0.12 0.27 2 -0.36 21 23
GNG2 0.022 0.043 -10000 0 -0.46 5 5
WNT5A 0.014 0.072 -10000 0 -0.38 20 20
WNT11 0.002 0.1 -10000 0 -0.37 41 41
CDC42 -0.007 0.072 -10000 0 -0.31 18 18
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 0.007 0.1 0.24 10 -0.42 25 35
CRKL 0.008 0.11 -10000 0 -0.44 28 28
HRAS 0.01 0.11 -10000 0 -0.38 28 28
mol:PIP3 0.023 0.11 0.29 8 -0.41 24 32
SPRED1 0.026 0.004 -10000 0 -10000 0 0
SPRED2 0.024 0.03 -10000 0 -0.34 4 4
GAB1 0.009 0.11 0.21 2 -0.46 28 30
FOXO3 0.03 0.13 0.28 17 -0.39 36 53
AKT1 0.029 0.14 0.28 18 -0.43 37 55
BAD 0.031 0.14 0.28 19 -0.4 36 55
megakaryocyte differentiation 0.006 0.11 0.21 3 -0.43 32 35
GSK3B 0.03 0.14 0.28 20 -0.4 36 56
RAF1 0.013 0.094 0.23 4 -0.31 27 31
SHC1 0.022 0.035 -10000 0 -0.22 13 13
STAT3 0.009 0.11 0.21 3 -0.46 27 30
STAT1 0 0.23 -10000 0 -1 29 29
HRAS/SPRED1 0.022 0.098 -10000 0 -0.32 26 26
cell proliferation 0.004 0.11 0.21 3 -0.45 29 32
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
TEC 0.011 0.074 -10000 0 -0.31 30 30
RPS6KB1 0.023 0.12 0.28 3 -0.44 32 35
HRAS/SPRED2 0.022 0.1 -10000 0 -0.32 26 26
LYN/TEC/p62DOK 0.035 0.12 -10000 0 -0.45 29 29
MAPK3 0.018 0.079 0.22 19 -0.25 13 32
STAP1 0 0.12 -10000 0 -0.46 29 29
GRAP2 -0.003 0.1 -10000 0 -0.34 51 51
JAK2 -0.004 0.2 -10000 0 -0.9 29 29
STAT1 (dimer) -0.001 0.22 -10000 0 -0.99 29 29
mol:Gleevec -0.002 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.021 0.13 -10000 0 -0.44 29 29
actin filament polymerization 0.002 0.1 0.39 3 -0.38 28 31
LYN 0.024 0.032 -10000 0 -0.32 5 5
STAP1/STAT5A (dimer) -0.007 0.15 -10000 0 -0.64 30 30
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.034 0.1 -10000 0 -0.41 27 27
PI3K 0.046 0.12 0.28 2 -0.42 28 30
PTEN 0.024 0.009 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.002 0.25 -10000 0 -1.2 26 26
MAPK8 0.004 0.11 0.21 3 -0.46 29 32
STAT3 (dimer) 0.01 0.11 0.21 3 -0.45 28 31
positive regulation of transcription 0.019 0.069 0.19 24 -0.21 12 36
mol:GDP 0.006 0.12 -10000 0 -0.41 27 27
PIK3C2B 0.006 0.11 0.21 3 -0.46 28 31
CBL/CRKL 0.023 0.11 -10000 0 -0.42 27 27
FER 0.005 0.11 0.21 3 -0.46 29 32
SH2B3 0.009 0.11 0.21 3 -0.46 28 31
PDPK1 0.025 0.11 0.28 11 -0.38 22 33
SNAI2 -0.002 0.12 0.38 1 -0.46 30 31
positive regulation of cell proliferation 0.004 0.18 -10000 0 -0.76 30 30
KITLG 0.022 0.056 -10000 0 -0.47 8 8
cell motility 0.004 0.18 -10000 0 -0.76 30 30
PTPN6 0.016 0.06 -10000 0 -0.44 11 11
EPOR 0.036 0.087 -10000 0 -1.2 1 1
STAT5A (dimer) 0.007 0.16 -10000 0 -0.62 31 31
SOCS1 -0.009 0.099 -10000 0 -0.26 81 81
cell migration 0.015 0.12 0.44 32 -0.21 2 34
SOS1 0.027 0.002 -10000 0 -10000 0 0
EPO 0.012 0.056 -10000 0 -0.29 19 19
VAV1 0.009 0.089 -10000 0 -0.43 25 25
GRB10 0.005 0.098 -10000 0 -0.41 26 26
PTPN11 0.024 0.027 -10000 0 -0.46 2 2
SCF/KIT 0.009 0.12 0.22 3 -0.47 29 32
GO:0007205 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 0.013 0.08 0.2 10 -0.25 24 34
CBL 0.026 0.019 -10000 0 -0.46 1 1
KIT -0.011 0.27 -10000 0 -1.3 25 25
MAP2K2 0.016 0.083 0.26 16 -0.25 21 37
SHC/Grb2/SOS1 0.041 0.12 -10000 0 -0.45 26 26
STAT5A 0.008 0.16 -10000 0 -0.64 31 31
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.001 0.11 0.38 1 -0.45 30 31
SHC/GRAP2 0.014 0.081 -10000 0 -0.33 26 26
PTPRO 0.006 0.11 0.21 3 -0.44 31 34
SH2B2 0 0.099 -10000 0 -0.39 28 28
DOK1 0.026 0.019 -10000 0 -0.46 1 1
MATK -0.015 0.12 0.21 2 -0.44 31 33
CREBBP 0.038 0.037 -10000 0 -0.44 1 1
BCL2 0.025 0.14 -10000 0 -1.2 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.026 0.019 -10000 0 -0.46 1 1
ANTXR2 0.022 0.039 -10000 0 -0.27 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.005 -10000 0 -0.061 3 3
monocyte activation -0.1 0.21 -10000 0 -0.43 179 179
MAP2K2 0.014 0.042 -10000 0 -0.6 3 3
MAP2K1 0.001 0.005 -10000 0 -10000 0 0
MAP2K7 0 0.01 -10000 0 -0.24 1 1
MAP2K6 0 0.01 -10000 0 -0.24 1 1
CYAA 0 0.019 -10000 0 -0.23 3 3
MAP2K4 0.001 0.004 -10000 0 -10000 0 0
IL1B -0.046 0.086 -10000 0 -0.22 108 108
Channel 0.031 0.025 -10000 0 -0.24 3 3
NLRP1 -0.001 0.019 -10000 0 -0.24 4 4
CALM1 0.026 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.005 0.085 -10000 0 -0.38 31 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.005 0.061 3 -10000 0 3
MAPK3 0.001 0.005 -10000 0 -10000 0 0
MAPK1 0.001 0.004 -10000 0 -10000 0 0
PGR -0.034 0.084 -10000 0 -0.23 98 98
PA/Cellular Receptors 0.032 0.028 -10000 0 -0.27 3 3
apoptosis 0 0.005 -10000 0 -0.061 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.023 -10000 0 -0.23 3 3
macrophage activation 0.001 0.004 -10000 0 -10000 0 0
TNF -0.054 0.16 -10000 0 -0.33 149 149
VCAM1 -0.1 0.21 -10000 0 -0.43 178 178
platelet activation -0.005 0.085 -10000 0 -0.38 31 31
MAPKKK cascade -0.006 0.018 -10000 0 -0.076 35 35
IL18 -0.011 0.054 0.18 1 -0.24 30 31
negative regulation of macrophage activation 0 0.005 -10000 0 -0.061 3 3
LEF 0 0.005 -10000 0 -0.061 3 3
CASP1 0.001 0.016 -10000 0 -0.085 20 20
mol:cAMP -0.005 0.085 -10000 0 -0.39 31 31
necrosis 0 0.005 -10000 0 -0.061 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.024 -10000 0 -0.23 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.099 0.31 29 -10000 0 29
GNAI2 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.008 0.088 -10000 0 -0.28 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
RhoA/GTP -0.004 0.1 -10000 0 -0.31 29 29
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.26 74 74
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNA12 0.023 0.01 -10000 0 -10000 0 0
S1PR5 -0.041 0.15 -10000 0 -0.35 119 119
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.26 74 74
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.012 0.07 -10000 0 -0.46 14 14
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.011 -10000 0 -0.22 1 1
Rac1/GDP 0.023 0.014 -10000 0 -10000 0 0
DOCK1 0.023 0.021 -10000 0 -0.46 1 1
ITGA4 -0.022 0.13 -10000 0 -0.33 90 90
RAC1 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.014 0.12 -10000 0 -0.24 125 125
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.016 0.087 -10000 0 -0.27 40 40
alpha4/beta7 Integrin/Paxillin 0.004 0.094 -10000 0 -0.25 63 63
lamellipodium assembly 0.03 0.051 0.27 1 -0.42 4 5
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
TLN1 0.026 0.006 -10000 0 -10000 0 0
PXN 0.017 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.074 -10000 0 -0.22 38 38
cell adhesion 0.024 0.077 -10000 0 -0.23 40 40
CRKL/CBL 0.037 0.018 -10000 0 -0.24 2 2
alpha4/beta1 Integrin/Paxillin 0.014 0.078 -10000 0 -0.25 40 40
ITGB1 0.023 0.019 -10000 0 -0.22 3 3
ITGB7 0.002 0.097 -10000 0 -0.35 42 42
ARF6/GDP 0.026 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.016 0.11 -10000 0 -0.24 101 101
p130Cas/Crk/Dock1 0.047 0.026 -10000 0 -0.28 2 2
VCAM1 -0.031 0.15 -10000 0 -0.4 86 86
alpha4/beta1 Integrin/Paxillin/Talin 0.026 0.079 -10000 0 -0.23 40 40
alpha4/beta1 Integrin/Paxillin/GIT1 0.026 0.079 -10000 0 -0.23 41 41
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
mol:GDP -0.024 0.078 0.23 41 -10000 0 41
CBL 0.026 0.019 -10000 0 -0.46 1 1
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GIT1 0.026 0.019 -10000 0 -0.46 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.026 0.079 -10000 0 -0.23 40 40
Rac1/GTP 0.03 0.055 0.28 1 -0.46 4 5
IL27-mediated signaling events

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
TGFB1 0.022 0.03 -10000 0 -0.38 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.001 0.087 0.38 5 -10000 0 5
IL27/IL27R/JAK1 0.021 0.12 -10000 0 -10000 0 0
TBX21 -0.017 0.16 0.45 13 -0.43 28 41
IL12B 0.017 0.02 -10000 0 -0.23 4 4
IL12A 0.001 0.05 -10000 0 -0.28 19 19
IL6ST -0.006 0.12 -10000 0 -0.46 45 45
IL27RA/JAK1 0.025 0.047 -10000 0 -10000 0 0
IL27 0.013 0.051 -10000 0 -0.22 28 28
TYK2 0.026 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.013 0.13 -10000 0 -0.62 1 1
T-helper 2 cell differentiation 0.001 0.087 0.38 5 -10000 0 5
T cell proliferation during immune response 0.001 0.087 0.38 5 -10000 0 5
MAPKKK cascade -0.001 0.087 -10000 0 -0.38 5 5
STAT3 0.027 0.002 -10000 0 -10000 0 0
STAT2 0.025 0.017 -10000 0 -0.22 3 3
STAT1 0.021 0.038 -10000 0 -0.22 15 15
IL12RB1 0.003 0.1 -10000 0 -0.42 34 34
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.03 0.16 0.46 11 -0.42 38 49
IL27/IL27R/JAK2/TYK2 -0.001 0.088 -10000 0 -0.39 5 5
positive regulation of T cell mediated cytotoxicity -0.001 0.087 -10000 0 -0.38 5 5
STAT1 (dimer) 0.016 0.18 0.5 31 -0.52 7 38
JAK2 0.026 0.008 -10000 0 -10000 0 0
JAK1 0.024 0.009 -10000 0 -10000 0 0
STAT2 (dimer) 0.012 0.088 -10000 0 -0.36 3 3
T cell proliferation -0.028 0.11 -10000 0 -0.4 13 13
IL12/IL12R/TYK2/JAK2 0.011 0.11 -10000 0 -0.78 9 9
IL17A -0.013 0.13 -10000 0 -0.62 1 1
mast cell activation 0.001 0.087 0.38 5 -10000 0 5
IFNG 0.005 0.025 0.1 4 -0.11 9 13
T cell differentiation -0.002 0.004 -10000 0 -0.016 6 6
STAT3 (dimer) 0.013 0.089 -10000 0 -0.37 4 4
STAT5A (dimer) 0.009 0.097 -10000 0 -0.42 8 8
STAT4 (dimer) -0.026 0.12 -10000 0 -0.39 18 18
STAT4 -0.059 0.16 -10000 0 -0.33 160 160
T cell activation -0.006 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.027 0.082 -10000 0 -10000 0 0
GATA3 -0.1 0.4 0.62 21 -1.4 54 75
IL18 -0.009 0.072 -10000 0 -0.26 44 44
positive regulation of mast cell cytokine production 0.013 0.088 -10000 0 -0.37 4 4
IL27/EBI3 0.022 0.065 -10000 0 -0.32 14 14
IL27RA 0.01 0.032 -10000 0 -10000 0 0
IL6 -0.064 0.16 -10000 0 -0.32 167 167
STAT5A 0.019 0.063 -10000 0 -0.46 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.015 0.024 -10000 0 -10000 0 0
IL1B -0.062 0.12 -10000 0 -0.24 189 189
EBI3 0.016 0.069 -10000 0 -0.43 15 15
TNF -0.045 0.11 -10000 0 -0.23 149 149
Signaling events mediated by HDAC Class III

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
EP300 0.024 0.033 -10000 0 -0.46 3 3
HDAC4 0.025 0.019 -10000 0 -0.46 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.017 0.028 0.15 5 -0.14 23 28
CDKN1A -0.033 0.13 -10000 0 -0.69 25 25
KAT2B 0.025 0.029 -10000 0 -0.38 3 3
BAX 0.024 0.009 -10000 0 -10000 0 0
FOXO3 -0.005 0.029 0.38 3 -0.22 1 4
FOXO1 0.025 0.02 -10000 0 -0.46 1 1
FOXO4 0.016 0.034 -10000 0 -0.32 6 6
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
TAT -0.03 0.14 -10000 0 -0.32 108 108
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.054 0.12 -10000 0 -0.33 92 92
PPARGC1A 0.016 0.07 -10000 0 -0.42 16 16
FHL2 0 0.091 -10000 0 -0.27 61 61
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.027 -10000 0 -10000 0 0
HIST2H4A 0.017 0.028 0.14 23 -0.15 5 28
SIRT1/FOXO3a 0.018 0.036 0.16 26 -0.17 4 30
SIRT1 0.029 0.035 0.21 23 -10000 0 23
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.034 -10000 0 -0.28 2 2
SIRT1/Histone H1b 0.022 0.056 0.16 21 -0.23 20 41
apoptosis -0.046 0.032 -10000 0 -10000 0 0
SIRT1/PGC1A 0.028 0.05 -10000 0 -0.27 13 13
p53/SIRT1 0.037 0.086 0.4 23 -0.33 11 34
SIRT1/FOXO4 0.032 0.044 -10000 0 -0.28 6 6
FOXO1/FHL2/SIRT1 0.031 0.061 -10000 0 -0.25 13 13
HIST1H1E 0.007 0.05 -10000 0 -0.26 21 21
SIRT1/p300 0.037 0.037 -10000 0 -0.33 3 3
muscle cell differentiation 0.026 0.12 0.28 92 -0.21 2 94
TP53 0.023 0.073 0.21 23 -0.45 12 35
KU70/SIRT1/BAX 0.047 0.032 -10000 0 -10000 0 0
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
MEF2D 0.026 0.019 -10000 0 -0.46 1 1
HIV-1 Tat/SIRT1 -0.002 0.1 -10000 0 -0.22 98 98
ACSS2 0.019 0.023 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.026 0.12 0.21 2 -0.28 92 94
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.066 -10000 0 -0.23 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.017 0.13 -10000 0 -0.44 27 27
AKT1 -0.008 0.18 -10000 0 -0.66 42 42
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.006 0.18 -10000 0 -0.68 42 42
mol:Ca2+ -0.011 0.089 -10000 0 -0.36 23 23
IGF1R 0.02 0.057 -10000 0 -0.46 9 9
E2/ER alpha (dimer)/Striatin 0.015 0.074 -10000 0 -0.28 34 34
SHC1 0.022 0.035 -10000 0 -0.22 13 13
apoptosis 0.007 0.17 0.63 42 -10000 0 42
RhoA/GTP 0.015 0.034 -10000 0 -0.21 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.12 -10000 0 -0.42 24 24
regulation of stress fiber formation -0.013 0.065 0.38 3 -0.19 16 19
E2/ERA-ERB (dimer) 0.017 0.061 -10000 0 -0.27 19 19
KRAS 0.026 0.006 -10000 0 -10000 0 0
G13/GTP 0.025 0.042 -10000 0 -0.25 12 12
pseudopodium formation 0.013 0.065 0.19 16 -0.38 3 19
E2/ER alpha (dimer)/PELP1 0.025 0.049 -10000 0 -0.28 14 14
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.043 -10000 0 -0.46 5 5
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
HRAS 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.007 0.13 0.3 1 -0.46 25 26
E2/ER beta (dimer) 0.009 0.046 -10000 0 -0.18 32 32
mol:GDP 0.004 0.065 -10000 0 -0.33 17 17
mol:NADP 0.007 0.13 0.3 1 -0.46 25 26
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 -0.012 0.092 -10000 0 -0.38 23 23
IGF-1R heterotetramer 0.02 0.057 -10000 0 -0.46 9 9
PLCB1 -0.007 0.09 -10000 0 -0.35 24 24
PLCB2 0.002 0.083 -10000 0 -0.41 18 18
IGF1 0.013 0.077 -10000 0 -0.38 22 22
mol:L-citrulline 0.007 0.13 0.3 1 -0.46 25 26
RHOA 0.027 0.003 -10000 0 -10000 0 0
Gai/GDP -0.009 0.17 -10000 0 -0.65 38 38
JNK cascade 0.009 0.046 -10000 0 -0.18 32 32
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
ESR2 0.012 0.066 -10000 0 -0.27 32 32
GNAQ 0.026 0.004 -10000 0 -10000 0 0
ESR1 0.013 0.072 -10000 0 -0.35 23 23
Gq family/GDP/Gbeta gamma -0.008 0.15 -10000 0 -0.57 32 32
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.034 0.069 -10000 0 -1.2 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.006 0.12 -10000 0 -0.42 22 22
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
E2/ER alpha (dimer) 0.01 0.051 -10000 0 -0.24 23 23
STRN 0.009 0.09 -10000 0 -0.45 24 24
GNAL -0.075 0.2 -10000 0 -0.46 139 139
PELP1 0.025 0.027 -10000 0 -0.46 2 2
MAPK11 0.008 0.041 -10000 0 -0.28 8 8
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 0.012 0.07 -10000 0 -0.46 14 14
HBEGF -0.026 0.15 0.34 22 -0.42 29 51
cAMP biosynthetic process -0.035 0.11 -10000 0 -0.23 150 150
SRC -0.018 0.12 0.23 1 -0.42 27 28
PI3K 0.039 0.008 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.071 -10000 0 -0.29 19 19
SOS1 0.027 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.1 -10000 0 -0.36 30 30
Gs family/GTP -0.03 0.12 -10000 0 -0.24 150 150
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.021 -10000 0 -10000 0 0
vasodilation 0.008 0.13 0.29 1 -0.44 25 26
mol:DAG -0.012 0.092 -10000 0 -0.38 23 23
Gs family/GDP/Gbeta gamma -0.032 0.1 -10000 0 -0.28 49 49
MSN 0.013 0.068 0.32 1 -0.42 3 4
Gq family/GTP 0.008 0.079 -10000 0 -0.4 15 15
mol:PI-3-4-5-P3 -0.004 0.17 -10000 0 -0.65 42 42
NRAS 0.024 0.009 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.008 0.13 0.44 25 -0.29 1 26
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.071 -10000 0 -0.31 17 17
NOS3 0.006 0.14 0.3 1 -0.48 25 26
GNA11 0.019 0.06 -10000 0 -0.46 10 10
MAPKKK cascade 0.001 0.15 -10000 0 -0.49 34 34
E2/ER alpha (dimer)/PELP1/Src 0.008 0.13 0.26 13 -0.43 25 38
ruffle organization 0.013 0.065 0.19 16 -0.38 3 19
ROCK2 0.023 0.068 0.33 2 -0.38 2 4
GNA14 0.013 0.074 -10000 0 -0.35 24 24
GNA15 0.011 0.08 -10000 0 -0.38 25 25
GNA13 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.054 0.14 0.37 4 -0.42 42 46
MMP2 -0.01 0.13 0.27 10 -0.44 22 32
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
CDC42/GTP 0.024 0.077 -10000 0 -0.36 13 13
PLCG1 0.007 0.076 -10000 0 -0.28 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
G12/G13 0.033 0.016 -10000 0 -10000 0 0
cell migration 0.024 0.075 -10000 0 -0.35 13 13
S1PR5 -0.041 0.15 -10000 0 -0.35 119 119
S1PR4 0.018 0.051 -10000 0 -0.28 17 17
MAPK3 0.008 0.078 -10000 0 -0.28 27 27
MAPK1 0.009 0.075 -10000 0 -0.27 26 26
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.26 74 74
GNAI1 0.012 0.07 -10000 0 -0.46 14 14
CDC42/GDP 0.018 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.008 0.088 -10000 0 -0.28 48 48
RHOA 0.05 0.078 0.2 120 -0.23 3 123
S1P/S1P4/Gi 0.011 0.083 -10000 0 -0.3 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
S1P/S1P4/G12/G13 0.037 0.034 -10000 0 -0.25 3 3
GNA12 0.023 0.01 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.008 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.067 0.073 0.34 1 -0.52 2 3
CRKL 0.049 0.076 0.24 28 -0.24 5 33
mol:DAG 0.031 0.05 -10000 0 -0.3 6 6
HRAS 0.057 0.086 0.3 33 -0.35 2 35
MAPK8 0.034 0.068 0.17 79 -0.25 13 92
RAP1A 0.046 0.075 0.24 29 -0.38 1 30
GAB1 0.049 0.078 0.25 27 -0.38 2 29
MAPK14 0.046 0.067 0.17 117 -0.24 6 123
EPO 0.013 0.056 -10000 0 -0.28 19 19
PLCG1 0.031 0.051 -10000 0 -0.31 6 6
EPOR/TRPC2/IP3 Receptors 0.031 0.012 -10000 0 -10000 0 0
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
EPO/EPOR (dimer)/SOCS3 -0.017 0.11 -10000 0 -0.29 70 70
GAB1/SHC/GRB2/SOS1 0.067 0.068 0.27 3 -0.36 2 5
EPO/EPOR (dimer) 0.028 0.046 -10000 0 -0.34 5 5
IRS2 0.048 0.075 0.23 30 -0.24 5 35
STAT1 0.038 0.057 -10000 0 -0.3 7 7
STAT5B 0.034 0.053 -10000 0 -0.3 7 7
cell proliferation 0.033 0.077 0.19 93 -0.24 13 106
GAB1/SHIP/PIK3R1/SHP2/SHC 0.027 0.052 -10000 0 -0.35 3 3
TEC 0.043 0.083 0.25 27 -0.23 12 39
SOCS3 -0.077 0.16 -10000 0 -0.3 206 206
STAT1 (dimer) 0.038 0.056 -10000 0 -0.3 7 7
JAK2 0.029 0.014 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.063 -10000 0 -0.26 5 5
EPO/EPOR 0.028 0.046 -10000 0 -0.34 5 5
LYN 0.025 0.032 -10000 0 -0.32 5 5
TEC/VAV2 0.045 0.071 0.19 1 -0.32 2 3
elevation of cytosolic calcium ion concentration 0.031 0.012 -10000 0 -10000 0 0
SHC1 0.022 0.035 -10000 0 -0.22 13 13
EPO/EPOR (dimer)/LYN 0.042 0.049 -10000 0 -0.27 6 6
mol:IP3 0.031 0.05 -10000 0 -0.3 6 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.073 0.08 0.3 16 -0.33 3 19
SH2B3 0.03 0.022 -10000 0 -0.21 4 4
NFKB1 0.045 0.066 0.19 14 -0.24 6 20
EPO/EPOR (dimer)/JAK2/SOCS3 -0.018 0.071 -10000 0 -0.22 63 63
PTPN6 0.05 0.077 0.3 13 -0.26 5 18
TEC/VAV2/GRB2 0.054 0.073 0.29 2 -0.31 2 4
EPOR 0.031 0.012 -10000 0 -10000 0 0
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
mol:GDP 0.066 0.068 0.28 2 -0.37 2 4
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG2 0.02 0.054 -10000 0 -0.36 12 12
CRKL/CBL/C3G 0.061 0.067 0.29 2 -0.39 2 4
VAV2 0.049 0.077 0.25 29 -0.31 2 31
CBL 0.049 0.078 0.31 15 -0.31 2 17
SHC/Grb2/SOS1 0.028 0.046 -10000 0 -0.38 1 1
STAT5A 0.029 0.069 -10000 0 -0.32 17 17
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.047 0.072 -10000 0 -0.35 7 7
LYN/PLCgamma2 0.033 0.051 -10000 0 -0.34 11 11
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
BTK 0.043 0.093 0.32 14 -0.35 9 23
BCL2 0.067 0.091 0.34 1 -0.73 4 5
Nectin adhesion 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
PDGFRB 0.025 0.022 -10000 0 -0.22 5 5
alphaV beta3 Integrin -0.002 0.094 -10000 0 -0.19 120 120
PTK2 0 0.11 -10000 0 -0.36 41 41
positive regulation of JNK cascade -0.003 0.097 -10000 0 -0.31 27 27
CDC42/GDP 0.018 0.13 -10000 0 -0.42 30 30
Rac1/GDP 0.012 0.12 -10000 0 -0.42 16 16
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
RAP1A 0.024 0.009 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.003 0.12 -10000 0 -0.39 27 27
nectin-3/I-afadin 0.026 0.062 -10000 0 -0.31 21 21
RAPGEF1 -0.002 0.13 -10000 0 -0.45 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.012 0.14 -10000 0 -0.49 31 31
PDGFB-D/PDGFRB 0.025 0.022 -10000 0 -0.22 5 5
TLN1 0.006 0.031 -10000 0 -0.29 3 3
Rap1/GTP -0.006 0.092 -10000 0 -0.33 24 24
IQGAP1 0.022 0.041 -10000 0 -0.36 7 7
Rap1/GTP/I-afadin 0.041 0.025 -10000 0 -0.25 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.026 0.062 -10000 0 -0.31 21 21
PVR 0.024 0.009 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.009 -10000 0 -10000 0 0
mol:GDP -0.002 0.16 -10000 0 -0.52 30 30
MLLT4 0.025 0.02 -10000 0 -0.46 1 1
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.062 0.059 -10000 0 -0.24 19 19
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.023 0.07 -10000 0 -0.32 25 25
positive regulation of lamellipodium assembly 0.002 0.092 -10000 0 -0.34 15 15
PVRL1 0.008 0.091 -10000 0 -0.46 24 24
PVRL3 0.012 0.081 -10000 0 -0.44 20 20
PVRL2 0.023 0.021 -10000 0 -0.46 1 1
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
CDH1 -0.051 0.16 -10000 0 -0.36 132 132
CLDN1 0.007 0.082 -10000 0 -0.3 38 38
JAM-A/CLDN1 0.039 0.078 -10000 0 -0.25 33 33
SRC -0.017 0.15 -10000 0 -0.54 31 31
ITGB3 -0.029 0.12 -10000 0 -0.28 120 120
nectin-1(dimer)/I-afadin/I-afadin 0.023 0.07 -10000 0 -0.32 25 25
FARP2 -0.005 0.16 -10000 0 -0.52 29 29
RAC1 0.023 0.01 -10000 0 -10000 0 0
CTNNA1 0.027 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.036 0.057 -10000 0 -0.28 18 18
nectin-1/I-afadin 0.023 0.07 -10000 0 -0.32 25 25
nectin-2/I-afadin 0.033 0.025 -10000 0 -0.33 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.028 0.029 -10000 0 -0.28 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.028 0.083 -10000 0 -0.28 42 42
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.027 -10000 0 -0.25 4 4
F11R 0.023 0.033 -10000 0 -0.25 9 9
positive regulation of filopodium formation -0.003 0.097 -10000 0 -0.31 27 27
alphaV/beta3 Integrin/Talin 0.013 0.085 0.2 16 -0.23 40 56
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.033 0.025 -10000 0 -0.33 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.033 0.025 -10000 0 -0.33 2 2
PIP5K1C 0.007 0.038 -10000 0 -0.2 20 20
VAV2 -0.002 0.16 -10000 0 -0.56 27 27
RAP1/GDP 0.015 0.12 -10000 0 -0.39 27 27
ITGAV 0.027 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.036 0.058 -10000 0 -0.28 19 19
nectin-3(dimer)/I-afadin/I-afadin 0.026 0.062 -10000 0 -0.31 21 21
Rac1/GTP 0.005 0.11 -10000 0 -0.42 15 15
PTPRM 0.008 0.045 -10000 0 -0.22 22 22
E-cadherin/beta catenin/alpha catenin 0.012 0.11 -10000 0 -0.24 87 87
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.024 0.008 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.011 -10000 0 -0.22 1 1
NFATC1 0.009 0.11 0.27 1 -0.37 23 24
NFATC2 -0.015 0.084 0.17 1 -0.25 44 45
NFATC3 -0.003 0.09 -10000 0 -0.35 40 40
YWHAE 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.056 0.15 0.18 1 -0.43 65 66
Exportin 1/Ran/NUP214 0.053 0.01 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.067 0.16 -10000 0 -0.38 86 86
BCL2/BAX 0.033 0.027 -10000 0 -0.31 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.024 0.009 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
BAD 0.027 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.042 0.15 -10000 0 -0.42 62 62
Calcineurin A alpha-beta B1/BCL2 0.024 0.033 -10000 0 -0.46 3 3
FKBP8 0.026 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.041 0.15 0.41 62 -10000 0 62
KPNB1 0.027 0.002 -10000 0 -10000 0 0
KPNA2 0.026 0.011 -10000 0 -0.22 1 1
XPO1 0.027 0.001 -10000 0 -10000 0 0
SFN -0.032 0.13 -10000 0 -0.3 114 114
MAP3K8 0.015 0.05 -10000 0 -0.25 21 21
NFAT4/CK1 alpha 0.016 0.059 -10000 0 -0.23 5 5
MEF2D/NFAT1/Cbp/p300 0.02 0.099 -10000 0 -0.27 24 24
CABIN1 -0.056 0.16 0.18 1 -0.44 65 66
CALM1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 0.025 0.02 -10000 0 -0.22 4 4
CAMK4 -0.07 0.18 -10000 0 -0.36 166 166
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.002 -10000 0 -10000 0 0
YWHAH 0.022 0.032 -10000 0 -0.22 11 11
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.053 -10000 0 -0.16 46 46
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.057 -10000 0 -0.46 9 9
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.021 0.019 -10000 0 -0.22 3 3
FKBP1A 0.025 0.011 -10000 0 -0.22 1 1
NFAT1-c-4/YWHAQ 0.009 0.13 0.24 1 -0.36 33 34
PRKCH 0.026 0.006 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.036 0.03 -10000 0 -0.33 4 4
CASP3 0.025 0.015 -10000 0 -0.22 2 2
PIM1 0.024 0.024 -10000 0 -0.22 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.007 -10000 0 -0.12 1 1
apoptosis 0.019 0.019 -10000 0 -0.38 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.046 -10000 0 -0.22 3 3
PRKCB -0.017 0.12 -10000 0 -0.31 86 86
PRKCE 0.022 0.037 -10000 0 -0.24 12 12
JNK2/NFAT4 -0.003 0.095 -10000 0 -0.32 40 40
BAD/BCL-XL 0.038 0.011 -10000 0 -10000 0 0
PRKCD 0.009 0.09 -10000 0 -0.46 23 23
NUP214 0.026 0.004 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
PRKCA 0.025 0.027 -10000 0 -0.46 2 2
PRKCG -0.089 0.18 -10000 0 -0.33 207 207
PRKCQ 0.008 0.085 -10000 0 -0.44 22 22
FKBP38/BCL2 0.036 0.026 -10000 0 -0.32 3 3
EP300 0.024 0.033 -10000 0 -0.46 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.014 0.1 -10000 0 -0.35 22 22
CaM/Ca2+/FKBP38 0.034 0.01 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.008 -10000 0 -0.15 1 1
CSNK1A1 0.016 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.026 0.11 -10000 0 -0.28 92 92
NFATc/ERK1 0.022 0.11 0.27 1 -0.35 22 23
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.068 0.16 -10000 0 -0.38 89 89
NR4A1 0 0.088 -10000 0 -0.34 13 13
GSK3B 0.027 0.003 -10000 0 -10000 0 0
positive T cell selection -0.003 0.09 -10000 0 -0.35 40 40
NFAT1/CK1 alpha -0.004 0.061 -10000 0 -0.21 19 19
RCH1/ KPNB1 0.039 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
AKAP5 0.007 0.07 -10000 0 -0.24 45 45
MEF2D 0.026 0.019 -10000 0 -0.46 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.025 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.022 0.11 0.27 1 -0.35 22 23
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
BCL2 0.024 0.033 -10000 0 -0.46 3 3
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 0.005 0.15 0.23 32 -0.35 48 80
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.006 -10000 0 -10000 0 0
AKT2 0.024 0.009 -10000 0 -10000 0 0
STXBP4 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.009 0.15 0.24 39 -0.33 83 122
YWHAZ 0.025 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.006 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.017 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.032 -10000 0 -0.22 11 11
YWHAB 0.026 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.012 -10000 0 -10000 0 0
YWHAG 0.021 0.019 -10000 0 -0.22 3 3
ASIP -0.039 0.16 -10000 0 -0.4 101 101
PRKCI 0.027 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.001 -10000 0 -10000 0 0
GYS1 0.016 0.007 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.41 51 51
TRIP10 0.022 0.046 -10000 0 -0.46 6 6
TC10/GTP/CIP4/Exocyst 0.033 0.028 -10000 0 -0.28 5 5
AS160/14-3-3 0.012 0.054 -10000 0 -0.36 2 2
VAMP2 0.026 0.01 -10000 0 -0.22 1 1
SLC2A4 -0.013 0.17 0.24 34 -0.36 83 117
STX4 0.027 0.002 -10000 0 -10000 0 0
GSK3B 0.022 0.009 -10000 0 -10000 0 0
SFN -0.032 0.13 -10000 0 -0.3 114 114
LNPEP 0.017 0.068 -10000 0 -0.46 13 13
YWHAE 0.027 0.003 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.024 0.009 -9999 0 -10000 0 0
SPHK1 0.004 0.089 -9999 0 -0.32 42 42
GNAI2 0.026 0.004 -9999 0 -10000 0 0
mol:S1P 0.005 0.059 -9999 0 -0.32 19 19
GNAO1 0.007 0.097 -9999 0 -0.46 27 27
mol:Sphinganine-1-P 0.005 0.05 -9999 0 -0.33 9 9
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.031 0.065 -9999 0 -0.31 9 9
GNAI3 0.024 0.009 -9999 0 -10000 0 0
G12/G13 0.033 0.016 -9999 0 -10000 0 0
S1PR3 0.006 0.086 -9999 0 -0.32 38 38
S1PR2 0.023 0.032 -9999 0 -0.32 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.005 0.057 -9999 0 -0.27 20 20
S1PR5 -0.041 0.15 -9999 0 -0.35 119 119
S1PR4 0.018 0.051 -9999 0 -0.28 17 17
GNAI1 0.012 0.07 -9999 0 -0.46 14 14
S1P/S1P5/G12 -0.01 0.1 -9999 0 -0.27 61 61
S1P/S1P3/Gq 0.002 0.1 -9999 0 -0.28 55 55
S1P/S1P4/Gi 0.006 0.098 -9999 0 -0.33 27 27
GNAQ 0.026 0.004 -9999 0 -10000 0 0
GNAZ 0.024 0.033 -9999 0 -0.46 3 3
GNA14 0.013 0.074 -9999 0 -0.35 24 24
GNA15 0.011 0.08 -9999 0 -0.38 25 25
GNA12 0.023 0.01 -9999 0 -10000 0 0
GNA13 0.026 0.005 -9999 0 -10000 0 0
GNA11 0.019 0.06 -9999 0 -0.46 10 10
ABCC1 0.026 0.017 -9999 0 -0.22 3 3
ceramide signaling pathway

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
MAP4K4 -0.004 0.11 -10000 0 -0.42 26 26
BAG4 0.017 0.068 -10000 0 -0.46 13 13
BAD 0.005 0.045 0.21 7 -0.18 4 11
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.014 0.12 -10000 0 -0.31 79 79
BAX 0.007 0.046 0.21 12 -0.16 5 17
EnzymeConsortium:3.1.4.12 0.001 0.029 0.067 2 -0.096 22 24
IKBKB 0 0.11 0.25 3 -0.44 19 22
MAP2K2 0.005 0.054 0.18 19 -0.25 5 24
MAP2K1 0.003 0.049 0.18 7 -0.25 5 12
SMPD1 0.002 0.033 0.1 3 -0.11 17 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.004 0.11 0.3 3 -0.45 19 22
MAP2K4 0.003 0.043 0.24 3 -0.19 3 6
protein ubiquitination -0.001 0.11 -10000 0 -0.44 20 20
EnzymeConsortium:2.7.1.37 0.003 0.056 0.19 7 -0.26 6 13
response to UV 0 0.001 0.002 7 -0.002 6 13
RAF1 0.002 0.049 0.18 6 -0.25 6 12
CRADD 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide 0.002 0.042 0.099 5 -0.14 23 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.008 -10000 0 -10000 0 0
MADD 0.024 0.033 -10000 0 -0.46 3 3
MAP3K1 0.002 0.043 0.19 3 -0.16 11 14
TRADD 0.026 0.019 -10000 0 -0.46 1 1
RELA/p50 0.026 0.003 -10000 0 -10000 0 0
MAPK3 0.008 0.052 0.18 8 -0.24 6 14
MAPK1 0.007 0.054 0.18 8 -0.24 7 15
p50/RELA/I-kappa-B-alpha 0.038 0.009 -10000 0 -10000 0 0
FADD -0.002 0.11 0.25 3 -0.44 22 25
KSR1 0.001 0.048 0.2 2 -0.19 14 16
MAPK8 0 0.045 0.22 4 -0.21 8 12
TRAF2 0.026 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.003 0.1 -10000 0 -0.46 17 17
TNF R/SODD 0.025 0.064 -10000 0 -0.33 20 20
TNF -0.054 0.16 -10000 0 -0.33 149 149
CYCS 0.017 0.052 0.17 23 -0.14 2 25
IKBKG -0.002 0.11 0.23 2 -0.44 19 21
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.12 -10000 0 -0.45 24 24
RELA 0.027 0.003 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AIFM1 0.007 0.044 0.15 19 -0.16 3 22
TNF/TNF R/SODD -0.011 0.12 -10000 0 -0.29 81 81
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.025 0.077 -10000 0 -0.83 4 4
NSMAF -0.001 0.11 0.22 10 -0.41 25 35
response to hydrogen peroxide 0 0.001 0.002 7 -0.002 6 13
BCL2 0.024 0.033 -10000 0 -0.46 3 3
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.019 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.021 0.074 -10000 0 -0.2 81 81
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.027 -10000 0 -0.46 2 2
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.004 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.004 -10000 0 -10000 0 0
FGR 0.022 0.025 -10000 0 -0.22 6 6
p38 alpha/TAB1 -0.024 0.062 -10000 0 -0.3 16 16
PRKG1 -0.004 0.11 -10000 0 -0.42 42 42
DUSP8 0.014 0.07 -10000 0 -0.37 20 20
PGK/cGMP/p38 alpha 0.004 0.097 -10000 0 -0.31 25 25
apoptosis -0.023 0.06 -10000 0 -0.29 16 16
RAL/GTP 0.031 0.013 -10000 0 -10000 0 0
LYN 0.024 0.032 -10000 0 -0.32 5 5
DUSP1 0.008 0.081 -10000 0 -0.31 37 37
PAK1 0.012 0.066 -10000 0 -0.26 34 34
SRC 0.024 0.027 -10000 0 -0.46 2 2
RAC1/OSM/MEKK3/MKK3 0.055 0.029 -10000 0 -10000 0 0
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
RAC1 0.023 0.01 -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 0.023 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.016 -10000 0 -10000 0 0
MAPK11 0.021 0.11 0.22 40 -0.35 14 54
BLK -0.01 0.088 -10000 0 -0.23 88 88
HCK 0.016 0.064 -10000 0 -0.37 16 16
MAP2K3 0.026 0.01 -10000 0 -0.22 1 1
DUSP16 0.026 0.006 -10000 0 -10000 0 0
DUSP10 0.012 0.08 -10000 0 -0.41 22 22
TRAF6/MEKK3 0.032 0.017 -10000 0 -0.25 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.025 0.1 0.22 22 -0.34 14 36
positive regulation of innate immune response 0.026 0.12 0.24 50 -0.38 17 67
LCK -0.031 0.13 -10000 0 -0.3 112 112
p38alpha-beta/MKP7 0.035 0.12 0.29 20 -0.39 14 34
p38alpha-beta/MKP5 0.03 0.13 0.25 36 -0.36 23 59
PGK/cGMP -0.002 0.078 -10000 0 -0.29 42 42
PAK2 0.026 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.029 0.13 0.29 19 -0.4 15 34
CDC42 0.024 0.008 -10000 0 -10000 0 0
RALB 0.027 0.001 -10000 0 -10000 0 0
RALA 0.023 0.01 -10000 0 -10000 0 0
PAK3 -0.068 0.18 -10000 0 -0.38 153 153
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0.006 -10000 0 -10000 0 0
SMARCC1 0.019 0.029 -10000 0 -0.7 1 1
REL 0.011 0.083 -10000 0 -0.37 27 27
HDAC7 -0.002 0.075 -10000 0 -0.3 9 9
JUN 0.022 0.023 -10000 0 -0.22 5 5
EP300 0.024 0.033 -10000 0 -0.46 3 3
KAT2B 0.025 0.029 -10000 0 -0.38 3 3
KAT5 0.027 0.003 -10000 0 -10000 0 0
MAPK14 0.014 0.019 -10000 0 -0.33 1 1
FOXO1 0.025 0.02 -10000 0 -0.46 1 1
T-DHT/AR 0.014 0.088 -10000 0 -0.29 16 16
MAP2K6 0.023 0.023 -10000 0 -0.46 1 1
BRM/BAF57 0.036 0.018 -10000 0 -0.33 1 1
MAP2K4 0.024 0.013 -10000 0 -10000 0 0
SMARCA2 0.024 0.02 -10000 0 -0.46 1 1
PDE9A 0.004 0.12 -10000 0 -0.75 12 12
NCOA2 0 0.11 -10000 0 -0.46 35 35
CEBPA 0.017 0.055 -10000 0 -0.36 12 12
EHMT2 0.025 0.027 -10000 0 -0.46 2 2
cell proliferation 0.009 0.11 0.31 11 -0.39 16 27
NR0B1 -0.077 0.18 -10000 0 -0.37 171 171
EGR1 -0.036 0.15 -10000 0 -0.37 104 104
RXRs/9cRA 0.005 0.1 -10000 0 -0.25 93 93
AR/RACK1/Src 0.009 0.07 0.22 1 -0.3 8 9
AR/GR -0.004 0.094 -10000 0 -0.24 80 80
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
PKN1 0.026 0.005 -10000 0 -10000 0 0
RCHY1 0.027 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.014 1 1
MAPK8 0.009 0.042 -10000 0 -0.33 9 9
T-DHT/AR/TIF2/CARM1 0.008 0.097 -10000 0 -0.41 16 16
SRC -0.004 0.037 0.18 1 -0.24 12 13
NR3C1 0.027 0.003 -10000 0 -10000 0 0
KLK3 -0.054 0.11 -10000 0 -0.59 3 3
APPBP2 0.024 0.013 -10000 0 -10000 0 0
TRIM24 0.021 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.006 0.065 0.2 6 -0.31 9 15
TMPRSS2 -0.072 0.3 -10000 0 -1 59 59
RXRG -0.05 0.18 -10000 0 -0.44 108 108
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.025 0.019 -10000 0 -0.46 1 1
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.026 0.005 -10000 0 -10000 0 0
NR2C2 0.021 0.05 -10000 0 -0.46 7 7
KLK2 -0.005 0.095 -10000 0 -0.38 18 18
AR -0.02 0.094 0.15 1 -0.26 79 80
SENP1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.026 0.006 -10000 0 -10000 0 0
SRY 0 0.002 0.009 2 -10000 0 2
GATA2 0.015 0.068 -10000 0 -0.35 20 20
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.042 0.13 -10000 0 -0.27 142 142
T-DHT/AR/RACK1/Src 0.012 0.073 0.23 1 -0.32 7 8
positive regulation of transcription 0.015 0.068 -10000 0 -0.35 20 20
DNAJA1 0.023 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.009 -10000 0 -10000 0 0
NCOA1 0.03 0.01 -10000 0 -10000 0 0
SPDEF -0.004 0.11 -10000 0 -0.34 54 54
T-DHT/AR/TIF2 0 0.091 -10000 0 -0.39 18 18
T-DHT/AR/Hsp90 0.006 0.063 0.2 5 -0.31 9 14
GSK3B 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.027 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.038 0.2 1 -0.25 10 11
SIRT1 0.024 0.008 -10000 0 -10000 0 0
ZMIZ2 0.023 0.01 -10000 0 -10000 0 0
POU2F1 0.015 0.068 -10000 0 -0.46 9 9
T-DHT/AR/DAX-1 -0.041 0.11 0.2 4 -0.27 69 73
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
SMARCE1 0.027 0.003 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.034 0.15 -10000 0 -0.37 96 96
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.003 -10000 0 -10000 0 0
TCEB1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.007 0.081 -10000 0 -0.26 35 35
HIF1A 0.002 0.059 -10000 0 -0.27 28 28
COPS5 0.026 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.066 0.032 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.008 -10000 0 -10000 0 0
CDKN2A -0.025 0.12 -10000 0 -0.29 94 94
ARNT/IPAS -0.009 0.11 -10000 0 -0.25 98 98
HIF1AN 0.024 0.008 -10000 0 -10000 0 0
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.075 -10000 0 -0.27 34 34
CUL2 0.024 0.008 -10000 0 -10000 0 0
OS9 0.025 0.007 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.051 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.012 0.075 -10000 0 -0.26 35 35
PHD1-3/OS9 0.05 0.046 -10000 0 -0.24 10 10
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.078 -10000 0 -0.25 30 30
VHL 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.01 0.075 -10000 0 -0.26 34 34
EGLN3 0.018 0.063 -10000 0 -0.46 11 11
EGLN2 0.024 0.009 -10000 0 -10000 0 0
EGLN1 0.027 0.003 -10000 0 -10000 0 0
TP53 0.018 0.065 -10000 0 -0.46 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.055 -10000 0 -0.48 6 6
ARNT 0.027 0.003 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.025 0.015 -10000 0 -0.22 2 2
HIF1A/p19ARF -0.011 0.095 0.27 1 -0.3 38 39
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.022 0.075 -10000 0 -0.33 28 28
ATM 0.026 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.003 -10000 0 -10000 0 0
PRKDC 0.026 0.004 -10000 0 -10000 0 0
ATR 0.027 0.003 -10000 0 -10000 0 0
UBE2L3 0.026 0.004 -10000 0 -10000 0 0
FANCD2 0.019 0.04 -10000 0 -0.3 9 9
protein ubiquitination 0.045 0.072 -10000 0 -0.24 33 33
XRCC5 0.027 0.002 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.015 -10000 0 -10000 0 0
MRE11A 0.026 0.004 -10000 0 -10000 0 0
DNA-PK 0.051 0.013 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.025 0.075 -10000 0 -0.41 12 12
FANCF 0.026 0.004 -10000 0 -10000 0 0
BRCA1 0.026 0.017 -10000 0 -0.22 3 3
CCNE1 0.023 0.019 -10000 0 -0.22 3 3
CDK2/Cyclin E1 0.029 0.041 -10000 0 -0.23 13 13
FANCG 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.023 0.076 -10000 0 -0.32 31 31
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.026 0.019 -10000 0 -0.46 1 1
NBN 0.026 0.006 -10000 0 -10000 0 0
FANCA 0.007 0.079 -10000 0 -0.28 42 42
DNA repair 0.011 0.094 0.28 7 -0.4 11 18
BRCA1/BARD1/ubiquitin 0.023 0.076 -10000 0 -0.32 31 31
BARD1/DNA-PK 0.052 0.065 -10000 0 -0.25 27 27
FANCL 0.027 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.074 0.33 28 -10000 0 28
BRCA1/BARD1/CTIP/M/R/N Complex 0.023 0.057 -10000 0 -0.23 28 28
BRCA1/BACH1/BARD1/TopBP1 0.038 0.068 -10000 0 -0.28 29 29
BRCA1/BARD1/P53 0.047 0.08 -10000 0 -0.26 39 39
BARD1/CSTF1/BRCA1 0.037 0.069 -10000 0 -0.28 29 29
BRCA1/BACH1 0.026 0.017 -10000 0 -0.22 3 3
BARD1 0.006 0.099 -10000 0 -0.45 29 29
PCNA 0.024 0.02 -10000 0 -0.22 4 4
BRCA1/BARD1/UbcH5C 0.038 0.068 -10000 0 -0.28 29 29
BRCA1/BARD1/UbcH7 0.038 0.069 -10000 0 -0.28 29 29
BRCA1/BARD1/RAD51/PCNA 0.026 0.097 -10000 0 -0.26 52 52
BARD1/DNA-PK/P53 0.056 0.077 -10000 0 -0.25 36 36
BRCA1/BARD1/Ubiquitin 0.023 0.076 -10000 0 -0.32 31 31
BRCA1/BARD1/CTIP 0.033 0.063 -10000 0 -0.25 29 29
FA complex 0.027 0.042 -10000 0 -0.21 12 12
BARD1/EWS 0.023 0.075 -10000 0 -0.32 29 29
RBBP8 0.017 0.007 -10000 0 -0.15 1 1
TP53 0.018 0.065 -10000 0 -0.46 12 12
TOPBP1 0.027 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.045 0.079 0.26 39 -10000 0 39
BRCA1/BARD1 0.05 0.075 -10000 0 -0.24 33 33
CSTF1 0.026 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.005 0.071 -10000 0 -0.32 29 29
CDK2 0.02 0.049 -10000 0 -0.32 12 12
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.012 0.11 -10000 0 -0.29 80 80
RAD50 0.027 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.023 0.076 -10000 0 -0.32 31 31
EWSR1 0.026 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.012 0.075 -10000 0 -0.32 28 28
positive regulation of NF-kappaB transcription factor activity 0.023 0.064 -10000 0 -0.32 15 15
MAP2K4 0.022 0.046 -10000 0 -0.31 2 2
IKBKB 0.026 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.024 0.033 -10000 0 -0.46 3 3
TNFRSF10A 0.002 0.1 -10000 0 -0.37 41 41
SMPD1 0.011 0.032 -10000 0 -0.19 14 14
IKBKG 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.021 0.042 -10000 0 -0.26 13 13
TRAIL/TRAILR2 0.026 0.063 -10000 0 -0.24 30 30
TRAIL/TRAILR3 0.013 0.089 -10000 0 -0.35 29 29
TRAIL/TRAILR1 0.01 0.092 -10000 0 -0.26 64 64
TRAIL/TRAILR4 0.023 0.064 -10000 0 -0.32 15 15
TRAIL/TRAILR1/DAP3/GTP 0.026 0.076 -10000 0 -0.25 41 41
IKK complex 0.01 0.064 -10000 0 -0.28 4 4
RIPK1 0.026 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.002 -10000 0 -10000 0 0
MAPK3 0.007 0.052 -10000 0 -0.22 28 28
MAP3K1 0.025 0.05 -10000 0 -0.3 3 3
TRAILR4 (trimer) 0.021 0.042 -10000 0 -0.26 13 13
TRADD 0.026 0.019 -10000 0 -0.46 1 1
TRAILR1 (trimer) 0.002 0.099 -10000 0 -0.37 41 41
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.061 -10000 0 -0.22 35 35
CFLAR 0.027 0.001 -10000 0 -10000 0 0
MAPK1 0.007 0.052 -10000 0 -0.22 28 28
TRAIL/TRAILR1/FADD/TRADD/RIP 0.05 0.08 -10000 0 -0.23 39 39
mol:ceramide 0.011 0.031 -10000 0 -0.19 14 14
FADD 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.019 0.055 -10000 0 -0.31 5 5
TRAF2 0.026 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.005 0.086 -10000 0 -0.31 42 42
CHUK 0.024 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.027 0.082 -10000 0 -0.27 39 39
DAP3 0.027 0.003 -10000 0 -10000 0 0
CASP10 0 0.056 0.22 1 -0.29 12 13
JNK cascade 0.023 0.064 -10000 0 -0.32 15 15
TRAIL (trimer) 0.012 0.075 -10000 0 -0.32 28 28
TNFRSF10C 0.005 0.087 -10000 0 -0.31 42 42
TRAIL/TRAILR1/DAP3/GTP/FADD 0.037 0.075 -10000 0 -0.23 39 39
TRAIL/TRAILR2/FADD 0.041 0.055 -10000 0 -0.28 14 14
cell death 0.011 0.031 -10000 0 -0.19 14 14
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.027 0.04 -10000 0 -0.22 14 14
TRAILR2 (trimer) 0.024 0.033 -10000 0 -0.46 3 3
CASP8 0.013 0.039 -10000 0 -0.79 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.064 0.056 -10000 0 -0.24 14 14
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0.068 -10000 0 -0.46 13 13
Caspase 8 (4 units) 0.023 0.069 -10000 0 -0.32 5 5
NEF -0.001 0.017 -10000 0 -0.2 1 1
NFKBIA 0.018 0.031 -10000 0 -10000 0 0
BIRC3 -0.01 0.12 -10000 0 -0.49 28 28
CYCS 0.008 0.053 0.19 7 -0.32 4 11
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CD247 0.008 0.082 -10000 0 -0.33 33 33
MAP2K7 0.017 0.094 -10000 0 -0.56 6 6
protein ubiquitination 0.02 0.077 0.23 7 -0.34 7 14
CRADD 0.027 0.003 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.007 0.078 -10000 0 -0.3 35 35
BID 0.009 0.054 0.19 4 -0.34 4 8
NF-kappa-B/RelA/I kappa B alpha 0.033 0.079 -10000 0 -0.25 29 29
TRADD 0.026 0.019 -10000 0 -0.46 1 1
MAP3K5 0.02 0.05 -10000 0 -0.46 7 7
CFLAR 0.027 0.001 -10000 0 -10000 0 0
FADD 0.027 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.033 0.079 -10000 0 -0.26 29 29
MAPK8 0.017 0.087 -10000 0 -0.54 5 5
APAF1 0.027 0.003 -10000 0 -10000 0 0
TRAF1 0.02 0.051 -10000 0 -0.35 11 11
TRAF2 0.026 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.055 -10000 0 -0.35 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.006 0.082 -10000 0 -0.43 8 8
CHUK 0.02 0.081 0.24 6 -0.37 7 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.052 0.067 -10000 0 -0.23 18 18
TCRz/NEF 0.007 0.065 -10000 0 -0.29 24 24
TNF -0.054 0.16 -10000 0 -0.33 149 149
FASLG 0.001 0.07 -10000 0 -0.29 24 24
NFKB1 0.018 0.031 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.12 -10000 0 -0.29 81 81
CASP6 0.027 0.096 -10000 0 -0.6 7 7
CASP7 -0.002 0.14 0.31 6 -0.49 32 38
RELA 0.017 0.032 -10000 0 -10000 0 0
CASP2 0.021 0.011 -10000 0 -10000 0 0
CASP3 0.004 0.13 0.31 6 -0.49 31 37
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
TNFR1A/BAG4 0.025 0.064 -10000 0 -0.33 20 20
CASP8 0.022 0.037 -10000 0 -0.24 12 12
CASP9 0.024 0.013 -10000 0 -0.22 1 1
MAP3K14 0.02 0.086 -10000 0 -0.41 8 8
APAF-1/Caspase 9 -0.001 0.091 -10000 0 -0.34 24 24
BCL2 0.015 0.086 0.28 1 -0.56 4 5
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.021 0.063 -10000 0 -10000 0 0
epithelial cell differentiation -0.009 0.083 -10000 0 -0.37 3 3
ITCH 0.031 0.014 -10000 0 -10000 0 0
WWP1 0.015 0.057 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
EGFR -0.019 0.13 -10000 0 -0.46 53 53
PRL 0.014 0.023 -10000 0 -0.22 6 6
neuron projection morphogenesis -0.016 0.1 0.3 11 -0.38 3 14
PTPRZ1 0.017 0.047 -10000 0 -0.46 6 6
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.004 0.11 -10000 0 -0.41 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.035 0.11 -10000 0 -0.34 15 15
ADAM17 0.028 0.044 -10000 0 -0.46 5 5
ErbB4/ErbB4 0.008 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.007 0.11 -10000 0 -0.38 30 30
NCOR1 0.025 0.027 -10000 0 -0.46 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.022 0.1 -10000 0 -0.34 11 11
GRIN2B -0.067 0.13 0.25 4 -0.36 47 51
ErbB4/ErbB2/betacellulin -0.006 0.099 -10000 0 -0.34 15 15
STAT1 0.021 0.037 -10000 0 -0.22 15 15
HBEGF 0.022 0.033 -10000 0 -0.22 12 12
PRLR 0.004 0.093 -10000 0 -0.34 41 41
E4ICDs/ETO2 0.012 0.083 -10000 0 -0.37 8 8
axon guidance -0.019 0.071 -10000 0 -0.42 4 4
NEDD4 0.028 0.039 -10000 0 -0.34 6 6
Prolactin receptor/Prolactin receptor/Prolactin 0.014 0.07 -10000 0 -0.23 44 44
CBFA2T3 0.008 0.091 -10000 0 -0.43 27 27
ErbB4/ErbB2/HBEGF 0.025 0.058 -10000 0 -0.3 5 5
MAPK3 -0.014 0.11 0.29 7 -0.39 3 10
STAT1 (dimer) 0.02 0.063 -10000 0 -10000 0 0
MAPK1 -0.014 0.1 0.29 7 -0.39 3 10
JAK2 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.032 0.1 -10000 0 -0.34 12 12
NRG1 -0.052 0.13 -10000 0 -0.34 99 99
NRG3 -0.025 0.15 -10000 0 -0.46 67 67
NRG2 0.023 0.042 -10000 0 -0.46 5 5
NRG4 0.006 0.074 -10000 0 -0.25 48 48
heart development -0.019 0.071 -10000 0 -0.42 4 4
neural crest cell migration -0.031 0.1 -10000 0 -0.34 12 12
ERBB2 0.016 0.038 -10000 0 -0.32 6 6
WWOX/E4ICDs 0.022 0.061 -10000 0 -10000 0 0
SHC1 0.022 0.035 -10000 0 -0.22 13 13
ErbB4/EGFR/neuregulin 4 0.002 0.098 -10000 0 -0.36 21 21
apoptosis 0.031 0.15 0.39 78 -10000 0 78
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.021 0.067 -10000 0 -0.38 3 3
ErbB4/ErbB2/epiregulin 0.016 0.067 -10000 0 -0.3 5 5
ErbB4/ErbB4/betacellulin/betacellulin -0.013 0.11 -10000 0 -0.37 12 12
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.035 0.084 -10000 0 -0.31 2 2
MDM2 0.011 0.058 0.25 13 -10000 0 13
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.024 0.1 -10000 0 -0.32 11 11
STAT5A -0.02 0.077 -10000 0 -0.39 6 6
ErbB4/EGFR/neuregulin 1 beta -0.035 0.12 -10000 0 -0.38 26 26
DLG4 0.023 0.029 -10000 0 -0.22 9 9
GRB2/SHC 0.035 0.026 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.02 0.058 -10000 0 -0.35 2 2
STAT5A (dimer) -0.003 0.092 -10000 0 -0.42 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.008 0.077 0.32 1 -0.4 4 5
LRIG1 0.018 0.065 -10000 0 -0.46 12 12
EREG 0.004 0.068 -10000 0 -0.22 54 54
BTC -0.039 0.15 -10000 0 -0.37 105 105
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.019 0.071 -10000 0 -0.42 4 4
ERBB4 0.008 0.056 -10000 0 -10000 0 0
STAT5B 0.027 0.003 -10000 0 -10000 0 0
YAP1 -0.009 0.12 -10000 0 -0.57 29 29
GRB2 0.026 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.018 0.066 -10000 0 -0.3 2 2
glial cell differentiation -0.019 0.058 0.35 2 -10000 0 2
WWOX 0.026 0.004 -10000 0 -10000 0 0
cell proliferation -0.06 0.13 0.28 1 -0.47 21 22
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.006 0.056 -10000 0 -0.27 20 20
SNTA1 0.007 0.09 -10000 0 -0.39 30 30
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.004 0.049 -10000 0 -0.27 13 13
MAPK12 0.005 0.014 -10000 0 -0.24 2 2
CCND1 0.007 0.048 -10000 0 -0.42 8 8
p38 gamma/SNTA1 0.02 0.055 0.2 17 -0.23 20 37
MAP2K3 0.026 0.01 -10000 0 -0.22 1 1
PKN1 0.026 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.014 -10000 0 -0.24 2 2
MAP2K6 0.006 0.011 -10000 0 -0.27 1 1
MAPT -0.008 0.092 0.23 4 -0.29 53 57
MAPK13 -0.002 0.069 -10000 0 -0.21 59 59
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.008 0.002 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.024 0.044 -10000 0 -0.15 37 37
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.022 0.052 -10000 0 -0.28 17 17
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.079 0.2 1 -0.28 16 17
NFKBIA -0.009 0.071 -10000 0 -0.23 52 52
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.007 -10000 0 -10000 0 0
ARRB2 0.017 0.002 -10000 0 -10000 0 0
REL 0.01 0.083 -10000 0 -0.37 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.036 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.002 0.074 -10000 0 -0.22 49 49
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.014 0.078 0.19 1 -0.29 14 15
SRC 0.024 0.027 -10000 0 -0.46 2 2
PI3K 0.039 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.002 0.075 -10000 0 -0.22 49 49
IKBKB 0.026 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.013 0.077 -10000 0 -0.42 19 19
I kappa B alpha/PIK3R1 0.001 0.082 0.2 1 -0.29 19 20
cell death 0.014 0.075 0.19 1 -0.28 14 15
NF kappa B1 p105/c-Rel 0.022 0.052 -10000 0 -0.28 17 17
LCK -0.031 0.13 -10000 0 -0.3 112 112
BCL3 0.01 0.057 -10000 0 -0.22 37 37
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.38 -10000 0 -1.2 68 68
RAD9A 0.027 0.003 -10000 0 -10000 0 0
AP1 -0.008 0.1 -10000 0 -0.32 52 52
IFNAR2 0.022 0.016 -10000 0 -10000 0 0
AKT1 0.006 0.037 -10000 0 -0.23 4 4
ER alpha/Oestrogen 0.007 0.052 -10000 0 -0.24 23 23
NFX1/SIN3/HDAC complex 0.013 0.061 -10000 0 -0.23 6 6
EGF -0.008 0.11 -10000 0 -0.38 53 53
SMG5 0.026 0.004 -10000 0 -10000 0 0
SMG6 0.026 0.019 -10000 0 -0.46 1 1
SP3/HDAC2 0.032 0.025 -10000 0 -10000 0 0
TERT/c-Abl -0.082 0.35 -10000 0 -1.1 69 69
SAP18 0.025 0.006 -10000 0 -10000 0 0
MRN complex 0.051 0.015 -10000 0 -10000 0 0
WT1 -0.013 0.079 -10000 0 -0.22 78 78
WRN 0.026 0.019 -10000 0 -0.46 1 1
SP1 0.021 0.02 -10000 0 -10000 0 0
SP3 0.023 0.012 -10000 0 -10000 0 0
TERF2IP 0.027 0.003 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.054 0.31 -10000 0 -0.95 67 67
Mad/Max 0.032 0.021 -10000 0 -10000 0 0
TERT -0.11 0.4 -10000 0 -1.3 67 67
CCND1 -0.087 0.33 -10000 0 -1 72 72
MAX 0.022 0.013 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.008 -10000 0 -10000 0 0
TERF2 0.023 0.004 -10000 0 -10000 0 0
PTGES3 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
Telomerase/911 0.04 0.057 -10000 0 -0.33 4 4
CDKN1B 0.013 0.033 -10000 0 -10000 0 0
RAD1 0.027 0.003 -10000 0 -10000 0 0
XRCC5 0.027 0.002 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
SAP30 0.026 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.036 0.008 -10000 0 -10000 0 0
UBE3A 0.024 0.01 -10000 0 -10000 0 0
JUN 0.019 0.025 -10000 0 -0.22 5 5
E6 -0.001 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.016 0.013 -10000 0 -10000 0 0
FOS -0.027 0.14 -10000 0 -0.36 86 86
IFN-gamma/IRF1 0.026 0.045 -10000 0 -0.26 2 2
PARP2 0.026 0.005 -10000 0 -10000 0 0
BLM -0.003 0.11 -10000 0 -0.41 44 44
Telomerase -0.017 0.11 0.23 1 -0.36 44 45
IRF1 0.018 0.052 -10000 0 -0.22 31 31
ESR1 0.012 0.072 -10000 0 -0.35 23 23
KU/TER 0.038 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.039 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.062 -10000 0 -0.3 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.018 0.063 -10000 0 -0.3 4 4
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC2 0.02 0.02 -10000 0 -10000 0 0
ATM 0.01 0.005 -10000 0 -10000 0 0
SMAD3 0.016 0.021 -10000 0 -0.32 2 2
ABL1 0.026 0.019 -10000 0 -0.46 1 1
MXD1 0.023 0.012 -10000 0 -10000 0 0
MRE11A 0.026 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.01 -10000 0 -10000 0 0
RPS6KB1 0.026 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.068 0.34 -10000 0 -1.1 67 67
NR2F2 0.018 0.063 -10000 0 -0.31 20 20
MAPK3 0.005 0.014 -10000 0 -10000 0 0
MAPK1 0.005 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.03 -10000 0 -0.38 3 3
NFKB1 0.027 0.003 -10000 0 -10000 0 0
HNRNPC 0.026 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.005 -10000 0 -10000 0 0
NBN 0.026 0.006 -10000 0 -10000 0 0
EGFR -0.021 0.13 -10000 0 -0.46 53 53
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.12 -10000 0 -0.34 80 80
MYC 0.01 0.075 -10000 0 -0.42 18 18
IL2 0.008 0.022 -10000 0 -10000 0 0
KU 0.038 0.008 -10000 0 -10000 0 0
RAD50 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
TGFB1 0.022 0.03 -10000 0 -0.38 3 3
TRF2/BLM 0.018 0.077 -10000 0 -0.27 42 42
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.072 0.35 -10000 0 -1.1 67 67
SP1/HDAC2 0.031 0.03 -10000 0 -10000 0 0
PINX1 0.026 0.004 -10000 0 -10000 0 0
Telomerase/EST1A -0.054 0.31 -10000 0 -0.94 67 67
Smad3/Myc 0.019 0.052 -10000 0 -0.29 15 15
911 complex 0.045 0.021 -10000 0 -10000 0 0
IFNG 0.016 0.025 -10000 0 -0.22 5 5
Telomerase/PinX1 -0.055 0.31 -10000 0 -0.94 67 67
Telomerase/AKT1/mTOR/p70S6K -0.002 0.1 -10000 0 -0.53 8 8
SIN3B 0.025 0.02 -10000 0 -0.46 1 1
YWHAE 0.027 0.003 -10000 0 -10000 0 0
Telomerase/EST1B -0.054 0.31 -10000 0 -0.94 67 67
response to DNA damage stimulus 0.006 0.007 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.07 0.022 -10000 0 -10000 0 0
TRF2/WRN 0.036 0.015 -10000 0 -0.31 1 1
Telomerase/hnRNP C1/C2 -0.054 0.31 -10000 0 -0.94 67 67
E2F1 0.009 0.066 -10000 0 -0.3 24 24
ZNFX1 0.025 0.006 -10000 0 -10000 0 0
PIF1 -0.013 0.12 -10000 0 -0.36 67 67
NCL 0.027 0.003 -10000 0 -10000 0 0
DKC1 0.027 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.031 0.056 -10000 0 -0.24 20 20
TC10/GTP 0.034 0.046 -10000 0 -0.25 10 10
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.051 -10000 0 -0.29 11 11
HRAS 0.026 0.006 -10000 0 -10000 0 0
APS homodimer 0.013 0.063 -10000 0 -0.46 11 11
GRB14 -0.11 0.19 -10000 0 -0.33 246 246
FOXO3 -0.013 0.15 -10000 0 -0.63 33 33
AKT1 -0.032 0.098 0.28 6 -0.3 6 12
INSR 0.028 0.021 -10000 0 -0.46 1 1
Insulin Receptor/Insulin 0.049 0.03 -10000 0 -0.21 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.02 0.033 -10000 0 -0.32 5 5
SORBS1 0.023 0.021 -10000 0 -0.46 1 1
CRK 0.027 0.003 -10000 0 -10000 0 0
PTPN1 0.015 0.032 0.31 1 -10000 0 1
CAV1 0.001 0.052 0.18 6 -0.25 12 18
CBL/APS/CAP/Crk-II/C3G 0.054 0.058 -10000 0 -0.27 11 11
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.044 -10000 0 -0.25 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.039 -10000 0 -0.22 11 11
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.032 0.048 -10000 0 -0.46 2 2
RPS6KB1 -0.032 0.089 0.25 8 -0.28 6 14
PARD6A 0.025 0.027 -10000 0 -0.46 2 2
CBL 0.026 0.019 -10000 0 -0.46 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.041 -10000 0 -0.69 2 2
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.091 -10000 0 -0.29 5 5
HRAS/GTP 0.012 0.034 -10000 0 -0.26 1 1
Insulin Receptor 0.028 0.021 -10000 0 -0.46 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.061 0.05 -10000 0 -0.23 10 10
PRKCI 0.018 0.058 -10000 0 -0.45 7 7
Insulin Receptor/Insulin/GRB14/PDK1 -0.033 0.098 -10000 0 -0.22 108 108
SHC1 0.022 0.035 -10000 0 -0.22 13 13
negative regulation of MAPKKK cascade 0.039 0.044 -10000 0 -0.58 2 2
PI3K 0.054 0.042 -10000 0 -0.22 11 11
NCK2 0.027 0.002 -10000 0 -10000 0 0
RHOQ 0.027 0.001 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
AKT2 -0.036 0.093 0.32 3 -0.3 6 9
PRKCZ -0.052 0.17 -10000 0 -0.48 73 73
SH2B2 0.013 0.063 -10000 0 -0.46 11 11
SHC/SHIP 0.03 0.051 0.19 8 -0.22 14 22
F2RL2 -0.048 0.14 -10000 0 -0.28 164 164
TRIP10 0.022 0.046 -10000 0 -0.46 6 6
Insulin Receptor/Insulin/Shc 0.039 0.036 -10000 0 -0.24 5 5
TC10/GTP/CIP4/Exocyst 0.033 0.028 -10000 0 -0.28 5 5
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.063 0.042 -10000 0 -0.22 5 5
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
RASA1 0.027 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.046 0.052 -10000 0 -0.27 11 11
TC10/GDP 0.02 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.046 -10000 0 -0.24 7 7
INPP5D 0.017 0.049 0.19 9 -0.24 15 24
SOS1 0.027 0.002 -10000 0 -10000 0 0
SGK1 -0.032 0.18 -10000 0 -0.73 39 39
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
IRS1 0.022 0.05 -10000 0 -0.46 7 7
p62DOK/RasGAP 0.039 0.044 -10000 0 -0.58 2 2
INS 0.015 0.04 -10000 0 -0.41 5 5
mol:PI-3-4-P2 0.016 0.049 0.19 9 -0.24 15 24
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.034 0.092 0.25 8 -0.29 10 18
PTPRA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.033 0.028 -10000 0 -0.28 5 5
PDPK1 0.026 0.019 -10000 0 -0.46 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.034 -10000 0 -0.22 9 9
Insulin Receptor/Insulin/IRS1 0.04 0.041 -10000 0 -0.25 11 11
Insulin Receptor/Insulin/IRS3 0.031 0.035 -10000 0 -0.33 5 5
Par3/Par6 0.012 0.09 -10000 0 -0.24 43 43
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.022 -10000 0 -0.22 5 5
mol:S1P 0.001 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.009 0.065 -10000 0 -0.27 29 29
GNAO1 0.008 0.097 -10000 0 -0.46 27 27
S1P/S1P3/G12/G13 0.032 0.053 -10000 0 -0.25 14 14
AKT1 0.017 0.079 -10000 0 -0.37 19 19
AKT3 0.013 0.13 -10000 0 -1 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.022 -10000 0 -0.22 5 5
GNAI2 0.027 0.007 -10000 0 -10000 0 0
GNAI3 0.024 0.01 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.46 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.007 0.086 -10000 0 -0.32 38 38
S1PR2 0.023 0.032 -10000 0 -0.32 5 5
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.012 0.093 -10000 0 -0.35 20 20
MAPK3 0.009 0.088 -10000 0 -0.34 20 20
MAPK1 0.01 0.084 -10000 0 -0.32 19 19
JAK2 0.004 0.1 0.19 1 -0.36 29 30
CXCR4 0.002 0.1 -10000 0 -0.35 29 29
FLT1 0.026 0.021 -10000 0 -0.46 1 1
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.007 0.088 -10000 0 -0.36 19 19
S1P/S1P3/Gi 0.012 0.093 -10000 0 -0.36 20 20
RAC1 0.023 0.01 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.09 -10000 0 -0.34 18 18
VEGFA -0.013 0.093 -10000 0 -0.22 110 110
S1P/S1P2/Gi 0.016 0.081 -10000 0 -0.29 26 26
VEGFR1 homodimer/VEGFA homodimer 0.012 0.07 -10000 0 -0.33 1 1
RHOA 0.027 0.003 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.006 0.076 -10000 0 -0.24 49 49
GNAQ 0.026 0.004 -10000 0 -10000 0 0
GNAZ 0.025 0.034 -10000 0 -0.47 3 3
G12/G13 0.033 0.016 -10000 0 -10000 0 0
GNA14 0.013 0.074 -10000 0 -0.35 24 24
GNA15 0.011 0.08 -10000 0 -0.38 25 25
GNA12 0.023 0.01 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.06 -10000 0 -0.46 10 10
Rac1/GTP 0.013 0.082 -10000 0 -0.33 17 17
Signaling events mediated by PRL

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
CCNE1 0.023 0.019 -10000 0 -0.22 3 3
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.01 0.074 -10000 0 -0.28 36 36
CDKN1A -0.038 0.14 -10000 0 -0.39 87 87
PRL-3/alpha Tubulin 0.035 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.025 0.059 -10000 0 -0.34 22 22
AGT 0.009 0.09 -10000 0 -0.45 24 24
CCNA2 -0.035 0.088 -10000 0 -0.33 9 9
TUBA1B 0.025 0.014 -10000 0 -0.22 2 2
EGR1 -0.023 0.1 -10000 0 -0.32 64 64
CDK2/Cyclin E1 -0.011 0.14 -10000 0 -0.4 58 58
MAPK3 0.016 0.01 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.035 0.013 -10000 0 -10000 0 0
MAPK1 0.016 0.01 -10000 0 -0.15 2 2
PTP4A1 -0.018 0.076 -10000 0 -10000 0 0
PTP4A3 0.024 0.015 -10000 0 -0.22 2 2
PTP4A2 0.024 0.008 -10000 0 -10000 0 0
ITGB1 0.014 0.014 -10000 0 -10000 0 0
SRC 0.024 0.027 -10000 0 -0.46 2 2
RAC1 0.01 0.036 -10000 0 -0.3 2 2
Rab GGTase beta/Rab GGTase alpha 0.034 0.014 -10000 0 -10000 0 0
PRL-1/ATF-5 0 0.084 -10000 0 -10000 0 0
RABGGTA 0.026 0.005 -10000 0 -10000 0 0
BCAR1 -0.015 0.015 -10000 0 -0.34 1 1
RHOC -0.029 0.13 -10000 0 -0.36 77 77
RHOA 0.008 0.053 -10000 0 -0.32 10 10
cell motility 0.002 0.088 0.28 1 -0.29 30 31
PRL-1/alpha Tubulin 0.003 0.086 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.052 -10000 0 -0.32 7 7
ROCK1 0 0.085 0.28 1 -0.29 29 30
RABGGTB 0.024 0.009 -10000 0 -10000 0 0
CDK2 0.02 0.049 -10000 0 -0.32 12 12
mitosis -0.018 0.076 -10000 0 -10000 0 0
ATF5 0.02 0.03 -10000 0 -0.22 9 9
Aurora A signaling

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
Aurora A/GADD45A 0.024 0.051 -10000 0 -0.26 2 2
BIRC5 -0.092 0.18 -10000 0 -0.34 214 214
NFKBIA 0.018 0.035 0.25 1 -0.25 1 2
CPEB1 0.015 0.073 -10000 0 -0.46 15 15
AKT1 0.019 0.036 0.26 2 -0.25 1 3
NDEL1 0.027 0.003 -10000 0 -10000 0 0
Aurora A/BRCA1 0.03 0.035 -10000 0 -0.23 1 1
NDEL1/TACC3 0.041 0.052 -10000 0 -0.33 2 2
GADD45A 0.009 0.06 -10000 0 -0.23 38 38
GSK3B 0.031 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.028 0.051 -10000 0 -0.27 6 6
MDM2 0.026 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.02 0.099 -10000 0 -0.33 53 53
TP53 0.024 0.048 -10000 0 -0.25 14 14
DLG7 0.017 0.034 -10000 0 -0.22 2 2
AURKAIP1 0.024 0.013 -10000 0 -0.22 1 1
ARHGEF7 0.026 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 0.055 -10000 0 -0.35 2 2
G2/M transition of mitotic cell cycle 0.029 0.034 -10000 0 -0.23 1 1
AURKA 0.026 0.045 -10000 0 -0.26 2 2
AURKB -0.053 0.14 -10000 0 -0.31 127 127
CDC25B 0.025 0.032 -10000 0 -0.24 1 1
G2/M transition checkpoint 0.014 0.029 -10000 0 -0.23 1 1
mRNA polyadenylation 0.024 0.056 -10000 0 -0.27 16 16
Aurora A/CPEB 0.024 0.056 -10000 0 -0.27 16 16
Aurora A/TACC1/TRAP/chTOG 0.061 0.044 -10000 0 -0.3 1 1
BRCA1 0.026 0.017 -10000 0 -0.22 3 3
centrosome duplication 0.028 0.051 -10000 0 -0.26 6 6
regulation of centrosome cycle 0.038 0.051 -10000 0 -0.33 2 2
spindle assembly 0.059 0.043 -10000 0 -0.3 1 1
TDRD7 0.025 0.027 -10000 0 -0.46 2 2
Aurora A/RasGAP/Survivin -0.004 0.1 -10000 0 -0.22 44 44
CENPA -0.042 0.13 -10000 0 -0.38 76 76
Aurora A/PP2A 0.035 0.038 -10000 0 -0.25 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.024 0.035 0.19 2 -0.24 1 3
negative regulation of DNA binding 0.024 0.048 -10000 0 -0.25 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.038 0.016 -10000 0 -0.33 1 1
RASA1 0.027 0.003 -10000 0 -10000 0 0
Ajuba/Aurora A 0.014 0.029 -10000 0 -0.23 1 1
mitotic prometaphase 0.015 0.035 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.045 -10000 0 -0.26 2 2
TACC1 0.026 0.004 -10000 0 -10000 0 0
TACC3 0.013 0.063 -10000 0 -0.26 30 30
Aurora A/Antizyme1 0.044 0.041 -10000 0 -0.23 1 1
Aurora A/RasGAP 0.035 0.037 -10000 0 -0.25 1 1
OAZ1 0.026 0.005 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.03 0.016 -10000 0 -10000 0 0
GIT1 0.026 0.019 -10000 0 -0.46 1 1
GIT1/beta-PIX/PAK1 0.041 0.048 -10000 0 -0.28 6 6
Importin alpha/Importin beta/TPX2 -0.02 0.099 -10000 0 -0.33 53 53
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0 0.078 -10000 0 -0.26 18 18
PAK1 0.012 0.066 -10000 0 -0.26 34 34
CKAP5 0.026 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.01 0.14 -10000 0 -0.98 10 10
regulation of axonogenesis 0.004 0.065 0.27 23 -10000 0 23
myoblast fusion 0.001 0.066 0.4 12 -10000 0 12
mol:GTP 0.008 0.045 -10000 0 -0.22 16 16
regulation of calcium-dependent cell-cell adhesion -0.03 0.055 0.22 11 -10000 0 11
ARF1/GTP 0.022 0.044 -10000 0 -0.18 13 13
mol:GM1 0 0.035 -10000 0 -0.18 13 13
mol:Choline -0.008 0.068 -10000 0 -0.27 33 33
lamellipodium assembly -0.005 0.076 -10000 0 -0.41 17 17
MAPK3 0.008 0.059 -10000 0 -0.28 15 15
ARF6/GTP/NME1/Tiam1 0.031 0.055 -10000 0 -0.22 11 11
ARF1 0.027 0.003 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.067 -10000 0 -0.41 12 12
ARF1/GDP 0.002 0.075 -10000 0 -0.32 23 23
ARF6 0.022 0.029 -10000 0 -0.18 1 1
RAB11A 0.026 0.004 -10000 0 -10000 0 0
TIAM1 0.024 0.021 -10000 0 -0.46 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.055 -10000 0 -0.26 14 14
actin filament bundle formation -0.005 0.074 0.31 22 -10000 0 22
KALRN -0.003 0.057 -10000 0 -0.3 16 16
RAB11FIP3/RAB11A 0.039 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.074 -10000 0 -0.31 22 22
NME1 0.024 0.021 -10000 0 -0.22 4 4
Rac1/GDP 0.008 0.066 -10000 0 -0.32 15 15
substrate adhesion-dependent cell spreading 0.008 0.045 -10000 0 -0.22 16 16
cortical actin cytoskeleton organization -0.005 0.077 -10000 0 -0.42 17 17
RAC1 0.023 0.01 -10000 0 -10000 0 0
liver development 0.008 0.045 -10000 0 -0.22 16 16
ARF6/GTP 0.008 0.045 -10000 0 -0.22 16 16
RhoA/GTP 0.022 0.042 -10000 0 -0.17 12 12
mol:GDP -0.006 0.071 -10000 0 -0.34 22 22
ARF6/GTP/RAB11FIP3/RAB11A 0.036 0.044 -10000 0 -0.2 2 2
RHOA 0.027 0.003 -10000 0 -10000 0 0
PLD1 -0.006 0.078 -10000 0 -0.27 42 42
RAB11FIP3 0.027 0.002 -10000 0 -10000 0 0
tube morphogenesis -0.005 0.076 -10000 0 -0.41 17 17
ruffle organization -0.004 0.065 -10000 0 -0.27 23 23
regulation of epithelial cell migration 0.008 0.045 -10000 0 -0.22 16 16
PLD2 0.01 0.04 -10000 0 -0.18 14 14
PIP5K1A -0.004 0.066 -10000 0 -0.28 23 23
mol:Phosphatidic acid -0.008 0.068 -10000 0 -0.27 33 33
Rac1/GTP -0.005 0.077 -10000 0 -0.42 17 17
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.017 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.017 -10000 0 -10000 0 0
CDKN1B 0.019 0.065 0.2 12 -0.27 25 37
CDKN1A 0.006 0.072 0.2 1 -0.27 22 23
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.026 0.004 -10000 0 -10000 0 0
FOXO3 0.02 0.05 0.2 1 -0.27 15 16
AKT1 0.022 0.019 -10000 0 -0.25 2 2
BAD 0.027 0.003 -10000 0 -10000 0 0
AKT3 0.014 0.038 -10000 0 -0.38 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.016 0.066 0.2 3 -0.28 28 31
AKT1/ASK1 0.028 0.068 -10000 0 -0.27 26 26
BAD/YWHAZ 0.049 0.017 -10000 0 -10000 0 0
RICTOR 0.025 0.027 -10000 0 -0.46 2 2
RAF1 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.027 0.066 0.26 26 -10000 0 26
TSC1 0.015 0.062 0.2 2 -0.28 23 25
YWHAZ 0.025 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.034 0.066 0.24 1 -0.27 25 26
EP300 0.024 0.033 -10000 0 -0.46 3 3
mol:GDP 0.011 0.062 -10000 0 -0.28 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.064 0.2 1 -0.27 28 29
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.011 0.012 -10000 0 -0.26 1 1
MAP3K5 0.02 0.05 -10000 0 -0.46 7 7
MAPKAP1 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.065 0.37 3 -0.18 3 6
YWHAH 0.022 0.032 -10000 0 -0.22 11 11
AKT1S1 0.019 0.049 0.2 5 -0.27 14 19
CASP9 0.015 0.058 0.2 2 -0.27 22 24
YWHAB 0.026 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.07 0.26 4 -0.26 24 28
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.027 -10000 0 -0.28 3 3
YWHAE 0.027 0.003 -10000 0 -10000 0 0
SRC 0.024 0.027 -10000 0 -0.46 2 2
AKT2/p21CIP1 0.003 0.067 0.22 2 -0.24 21 23
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.012 0.021 -10000 0 -10000 0 0
CHUK 0.014 0.053 -10000 0 -0.27 20 20
BAD/BCL-XL 0.037 0.064 -10000 0 -0.26 23 23
mTORC2 0.033 0.017 -10000 0 -0.25 2 2
AKT2 0.015 0.014 -10000 0 -0.3 1 1
FOXO1-3a-4/14-3-3 family 0.027 0.08 0.22 2 -0.31 11 13
PDPK1 0.026 0.019 -10000 0 -0.46 1 1
MDM2 0.021 0.066 0.2 16 -0.27 24 40
MAPKKK cascade -0.033 0.065 0.27 25 -0.23 1 26
MDM2/Cbp/p300 0.047 0.071 0.26 3 -0.26 22 25
TSC1/TSC2 0.018 0.068 0.26 9 -0.27 24 33
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.068 0.25 3 -0.25 22 25
glucose import -0.009 0.057 0.21 1 -0.24 28 29
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.04 0.19 11 -10000 0 11
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.009 0.057 -10000 0 -0.24 28 28
GSK3A 0.019 0.051 0.2 6 -0.27 15 21
FOXO1 0.015 0.061 0.2 1 -0.27 25 26
GSK3B 0.016 0.061 0.2 1 -0.27 25 26
SFN -0.032 0.13 -10000 0 -0.3 114 114
G1/S transition of mitotic cell cycle 0.022 0.057 0.27 9 -0.27 12 21
p27Kip1/14-3-3 family 0.03 0.068 -10000 0 -0.93 1 1
PRKACA 0.026 0.005 -10000 0 -10000 0 0
KPNA1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.021 0.019 -10000 0 -0.22 3 3
RHEB 0.021 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.019 0.034 0.3 2 -10000 0 2
DAPP1 -0.014 0.13 0.22 2 -0.43 30 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.05 0.2 0.31 3 -0.55 57 60
mol:DAG -0.01 0.089 0.27 10 -0.26 26 36
HRAS 0.027 0.008 -10000 0 -10000 0 0
RAP1A 0.025 0.01 -10000 0 -10000 0 0
ARF5/GDP 0.031 0.055 0.21 4 -0.3 5 9
PLCG2 0.02 0.054 -10000 0 -0.36 12 12
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARF5 0.021 0.011 -10000 0 -10000 0 0
mol:GTP 0.001 0.045 0.27 7 -10000 0 7
ARF1/GTP 0.008 0.037 0.36 3 -10000 0 3
RHOA 0.027 0.003 -10000 0 -10000 0 0
YES1 0.024 0.027 -10000 0 -0.46 2 2
RAP1A/GTP 0.018 0.039 0.26 2 -10000 0 2
ADAP1 -0.007 0.044 0.32 4 -0.24 5 9
ARAP3 0.001 0.045 0.27 7 -10000 0 7
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PREX1 0.019 0.057 -10000 0 -0.46 9 9
ARHGEF6 0.026 0.019 -10000 0 -0.46 1 1
ARHGEF7 0.026 0.005 -10000 0 -10000 0 0
ARF1 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.025 0.01 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
FGR 0.022 0.025 -10000 0 -0.22 6 6
mol:Ca2+ 0.001 0.058 0.18 28 -0.15 8 36
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.019 -10000 0 -0.46 1 1
ZAP70 -0.003 0.1 -10000 0 -0.33 56 56
mol:IP3 -0.006 0.07 0.2 25 -0.2 19 44
LYN 0.024 0.032 -10000 0 -0.32 5 5
ARF1/GDP 0.045 0.064 0.22 7 -0.29 8 15
RhoA/GDP 0.04 0.051 0.22 6 -10000 0 6
PDK1/Src/Hsp90 0.048 0.027 -10000 0 -0.28 3 3
BLNK -0.011 0.12 -10000 0 -0.44 50 50
actin cytoskeleton reorganization 0.042 0.095 0.27 37 -0.39 7 44
SRC 0.024 0.027 -10000 0 -0.46 2 2
PLEKHA2 0.008 0.022 -10000 0 -0.28 3 3
RAC1 0.023 0.01 -10000 0 -10000 0 0
PTEN 0.022 0.012 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.019 0.042 0.32 4 -10000 0 4
RhoA/GTP 0.024 0.046 0.31 5 -10000 0 5
Src family/SYK family/BLNK-LAT -0.042 0.16 -10000 0 -0.48 48 48
BLK -0.01 0.088 -10000 0 -0.23 88 88
PDPK1 0.026 0.019 -10000 0 -0.46 1 1
CYTH1 -0.004 0.041 0.33 4 -0.22 2 6
HCK 0.016 0.064 -10000 0 -0.37 16 16
CYTH3 -0.002 0.037 0.32 5 -10000 0 5
CYTH2 -0.003 0.039 0.32 5 -10000 0 5
KRAS 0.027 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.066 0.24 4 -0.39 11 15
SGK1 0.014 0.069 -10000 0 -0.39 14 14
INPP5D 0.022 0.044 -10000 0 -0.33 9 9
mol:GDP 0.032 0.064 0.21 12 -0.3 8 20
SOS1 0.027 0.002 -10000 0 -10000 0 0
SYK 0.013 0.077 -10000 0 -0.42 19 19
ARF6/GDP 0.033 0.054 0.29 8 -10000 0 8
mol:PI-3-4-5-P3 -0.008 0.022 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.017 0.039 0.3 1 -10000 0 1
VAV1 0.009 0.089 -10000 0 -0.43 25 25
mol:PI-3-4-P2 0.014 0.03 -10000 0 -0.33 4 4
RAS family/GTP/PI3K Class I 0.043 0.056 0.33 1 -10000 0 1
PLEKHA1 0.006 0.026 -10000 0 -0.28 4 4
Rac1/GDP 0.032 0.057 0.22 4 -0.3 6 10
LAT 0.007 0.094 -10000 0 -0.44 27 27
Rac1/GTP 0.031 0.067 0.21 1 -0.41 8 9
ITK -0.035 0.078 0.31 4 -0.22 43 47
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.021 0.12 0.31 9 -0.37 27 36
LCK -0.031 0.13 -10000 0 -0.3 112 112
BTK -0.01 0.052 0.31 4 -0.22 5 9
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 -0.04 0.27 -10000 0 -0.91 51 51
oxygen homeostasis 0 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.003 -10000 0 -10000 0 0
TCEB1 0.026 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.026 0.1 -10000 0 -0.33 4 4
EPO 0.001 0.18 -10000 0 -0.54 17 17
FIH (dimer) 0.022 0.02 -10000 0 -10000 0 0
APEX1 0.022 0.023 -10000 0 -10000 0 0
SERPINE1 -0.05 0.23 -10000 0 -0.53 39 39
FLT1 0.009 0.16 -10000 0 -0.73 19 19
ADORA2A -0.014 0.18 -10000 0 -0.53 20 20
germ cell development -0.014 0.2 -10000 0 -0.55 24 24
SLC11A2 -0.008 0.19 -10000 0 -0.53 20 20
BHLHE40 -0.013 0.2 -10000 0 -0.56 26 26
HIF1AN 0.022 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.013 0.14 -10000 0 -0.36 16 16
ETS1 0.033 0.044 -10000 0 -0.36 7 7
CITED2 0.008 0.14 -10000 0 -0.69 21 21
KDR 0.027 0.12 -10000 0 -0.75 11 11
PGK1 -0.009 0.2 -10000 0 -0.55 21 21
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.012 0.23 -10000 0 -0.61 20 20
EPAS1 0.01 0.086 -10000 0 -0.31 9 9
SP1 0.024 0.028 -10000 0 -10000 0 0
ABCG2 -0.01 0.2 -10000 0 -0.59 23 23
EFNA1 -0.007 0.19 -10000 0 -0.54 20 20
FXN -0.013 0.18 -10000 0 -0.54 18 18
POU5F1 -0.016 0.2 -10000 0 -0.57 24 24
neuron apoptosis -0.012 0.22 0.6 20 -10000 0 20
EP300 0.024 0.033 -10000 0 -0.46 3 3
EGLN3 0.015 0.065 -10000 0 -0.46 11 11
EGLN2 0.021 0.02 -10000 0 -10000 0 0
EGLN1 0.023 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.052 0.013 -10000 0 -10000 0 0
VHL 0.027 0.003 -10000 0 -10000 0 0
ARNT 0.023 0.023 -10000 0 -10000 0 0
SLC2A1 -0.016 0.18 -10000 0 -0.55 20 20
TWIST1 -0.019 0.18 -10000 0 -0.54 23 23
ELK1 0.033 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.022 0.14 -10000 0 -0.36 11 11
VEGFA -0.02 0.21 -10000 0 -0.55 27 27
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
IGF1 pathway

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
NCK2 0.027 0.002 -10000 0 -10000 0 0
PTK2 0.025 0.007 -10000 0 -10000 0 0
CRKL 0.008 0.06 -10000 0 -0.28 22 22
GRB2/SOS1/SHC 0.049 0.025 -10000 0 -10000 0 0
HRAS 0.026 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.018 0.062 -10000 0 -0.28 22 22
IGF-1R heterotetramer/IGF1/PTP1B 0.037 0.062 -10000 0 -0.29 20 20
AKT1 0.008 0.058 0.19 13 -0.44 4 17
BAD 0.005 0.055 0.18 13 -0.41 4 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.009 0.06 -10000 0 -0.28 22 22
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.022 0.069 0.21 2 -0.3 22 24
RAF1 0.016 0.064 0.28 1 -0.42 6 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.048 0.065 -10000 0 -0.26 21 21
YWHAZ 0.025 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.022 0.068 -10000 0 -0.29 25 25
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.008 0.058 0.19 12 -0.39 5 17
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.012 0.057 0.26 2 -0.34 5 7
PXN 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.054 -10000 0 -0.24 21 21
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.059 0.064 -10000 0 -0.23 20 20
IGF-1R heterotetramer 0.018 0.064 -10000 0 -0.51 9 9
IGF-1R heterotetramer/IGF1/IRS/Nck 0.037 0.067 -10000 0 -0.28 22 22
Crk/p130 Cas/Paxillin 0.048 0.068 0.22 1 -0.27 21 22
IGF1R 0.018 0.064 -10000 0 -0.51 9 9
IGF1 0.012 0.081 -10000 0 -0.4 22 22
IRS2/Crk 0.019 0.059 -10000 0 -0.27 21 21
PI3K 0.048 0.066 -10000 0 -0.27 21 21
apoptosis -0.02 0.055 0.36 4 -0.26 1 5
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
PRKCD 0.004 0.087 -10000 0 -0.37 26 26
RAF1/14-3-3 E 0.032 0.063 0.27 1 -0.36 6 7
BAD/14-3-3 0.021 0.058 0.27 1 -0.38 4 5
PRKCZ -0.008 0.083 0.18 11 -0.39 11 22
Crk/p130 Cas/Paxillin/FAK1 0.029 0.055 -10000 0 -0.42 4 4
PTPN1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.014 0.074 -10000 0 -0.34 24 24
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.041 0.061 -10000 0 -0.26 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
IRS1/NCK2 0.024 0.064 -10000 0 -0.28 22 22
GRB10 0.02 0.033 -10000 0 -0.32 5 5
PTPN11 0.008 0.065 -10000 0 -0.3 22 22
IRS1 0.008 0.065 -10000 0 -0.29 25 25
IRS2 0.008 0.059 -10000 0 -0.29 21 21
IGF-1R heterotetramer/IGF1 0.021 0.079 -10000 0 -0.37 23 23
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 0.014 0.061 0.19 13 -0.26 22 35
YWHAE 0.027 0.003 -10000 0 -10000 0 0
PRKD1 0.011 0.07 -10000 0 -0.32 24 24
SHC1 0.022 0.035 -10000 0 -0.22 13 13
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.036 -10000 0 -0.19 2 2
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.011 -10000 0 -0.22 1 1
STAT1 (dimer)/Cbp/p300 0.046 0.058 0.35 2 -0.36 1 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.016 0.076 -10000 0 -0.26 26 26
CaM/Ca2+ 0.051 0.036 -10000 0 -10000 0 0
RAP1A 0.024 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.028 0.038 -10000 0 -10000 0 0
AKT1 0.026 0.043 0.34 4 -10000 0 4
MAP2K1 0.017 0.034 0.3 2 -10000 0 2
MAP3K11 0.019 0.035 0.34 3 -10000 0 3
IFNGR1 0.027 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.058 0.17 -10000 0 -0.41 104 104
Rap1/GTP 0.017 0.03 -10000 0 -0.41 2 2
CRKL/C3G 0.037 0.023 -10000 0 -0.27 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.059 0.038 -10000 0 -10000 0 0
CEBPB 0.033 0.11 0.42 3 -0.5 15 18
STAT3 0.027 0.002 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.18 -10000 0 -1.1 15 15
STAT1 0.018 0.041 0.35 3 -10000 0 3
CALM1 0.026 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.016 0.023 -10000 0 -0.22 5 5
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.034 0.046 0.32 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.036 0.07 -10000 0 -0.34 9 9
mol:Ca2+ 0.046 0.035 -10000 0 -0.19 2 2
MAPK3 0.029 0.076 0.55 1 -0.73 4 5
STAT1 (dimer) -0.016 0.11 -10000 0 -0.37 26 26
MAPK1 0.019 0.11 0.55 1 -0.71 12 13
JAK2 0.026 0.009 -10000 0 -10000 0 0
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.025 0.01 -10000 0 -10000 0 0
CAMK2D 0.026 0.019 -10000 0 -0.46 1 1
DAPK1 0.027 0.11 0.35 5 -0.59 17 22
SMAD7 0.001 0.051 0.16 7 -0.19 10 17
CBL/CRKL/C3G 0.046 0.044 0.32 4 -0.41 2 6
PI3K 0.049 0.036 -10000 0 -10000 0 0
IFNG 0.016 0.023 -10000 0 -0.22 5 5
apoptosis 0.02 0.094 0.32 5 -0.44 20 25
CAMK2G 0.022 0.034 -10000 0 -0.46 3 3
STAT3 (dimer) 0.027 0.002 -10000 0 -10000 0 0
CAMK2A -0.1 0.18 -10000 0 -0.32 238 238
CAMK2B -0.019 0.12 -10000 0 -0.34 74 74
FRAP1 0.016 0.042 0.24 9 -10000 0 9
PRKCD 0.019 0.058 0.35 4 -10000 0 4
RAP1B 0.025 0.015 -10000 0 -0.22 2 2
negative regulation of cell growth -0.016 0.076 -10000 0 -0.26 26 26
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.024 0.033 -10000 0 -0.46 3 3
IRF1 0.003 0.079 0.34 2 -0.3 22 24
STAT1 (dimer)/PIASy 0.035 0.046 0.32 3 -0.24 1 4
SOCS1 -0.019 0.21 -10000 0 -1.4 15 15
mol:GDP 0.041 0.038 0.28 1 -0.39 2 3
CASP1 -0.003 0.069 0.18 10 -0.25 25 35
PTGES2 0.026 0.004 -10000 0 -10000 0 0
IRF9 0.03 0.039 0.19 5 -0.19 1 6
mol:PI-3-4-5-P3 0.035 0.029 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.036 -10000 0 -0.42 2 2
CBL 0.019 0.037 0.34 3 -0.4 1 4
MAP3K1 0.018 0.031 0.31 1 -10000 0 1
PIAS1 0.025 0.027 -10000 0 -0.46 2 2
PIAS4 0.026 0.019 -10000 0 -0.46 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.016 0.076 -10000 0 -0.26 26 26
PTPN11 0.021 0.032 0.31 2 -0.19 2 4
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
RAPGEF1 0.025 0.027 -10000 0 -0.46 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.074 0.32 9 -0.3 10 19
PDGFB-D/PDGFRB/SLAP 0.024 0.061 -10000 0 -0.33 14 14
PDGFB-D/PDGFRB/APS/CBL 0.036 0.052 -10000 0 -0.29 12 12
AKT1 0.036 0.06 0.27 17 -10000 0 17
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.081 0.32 10 -0.32 9 19
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
FGR -0.019 0.12 0.3 1 -0.38 60 61
mol:Ca2+ 0.027 0.068 0.29 11 -0.31 5 16
MYC 0.049 0.17 0.36 39 -0.74 18 57
SHC1 0.022 0.035 -10000 0 -0.22 13 13
HRAS/GDP 0.033 0.017 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.048 0.029 -10000 0 -0.26 3 3
GRB10 0.02 0.033 -10000 0 -0.32 5 5
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
GO:0007205 0.027 0.069 0.29 11 -0.31 5 16
PTEN 0.024 0.009 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.004 0.066 -10000 0 -0.22 52 52
PDGFB-D/PDGFRB/SHP2 0.037 0.027 -10000 0 -0.2 7 7
PDGFB-D/PDGFRB/GRB10 0.03 0.03 -10000 0 -0.33 2 2
cell cycle arrest 0.024 0.061 -10000 0 -0.33 14 14
HRAS 0.026 0.006 -10000 0 -10000 0 0
HIF1A 0.029 0.057 0.22 29 -10000 0 29
GAB1 0.022 0.084 0.32 10 -0.37 6 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.024 0.088 0.3 23 -0.36 4 27
PDGFB-D/PDGFRB 0.05 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.017 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.02 0.072 0.23 3 -0.32 10 13
positive regulation of MAPKKK cascade 0.037 0.027 -10000 0 -0.2 7 7
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 0.027 0.069 0.29 11 -0.32 5 16
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.021 0.054 -10000 0 -0.24 3 3
SHB 0.025 0.02 -10000 0 -0.46 1 1
BLK 0.007 0.056 0.3 1 -0.44 7 8
PTPN2 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.017 -10000 0 -10000 0 0
BCAR1 0.026 0.019 -10000 0 -0.46 1 1
VAV2 0.026 0.095 0.34 10 -0.38 8 18
CBL 0.026 0.019 -10000 0 -0.46 1 1
PDGFB-D/PDGFRB/DEP1 0.037 0.022 -10000 0 -0.31 1 1
LCK -0.05 0.16 0.3 1 -0.43 95 96
PDGFRB 0.026 0.023 -10000 0 -0.22 5 5
ACP1 0.027 0.003 -10000 0 -10000 0 0
HCK 0.008 0.082 0.3 1 -0.61 10 11
ABL1 0.018 0.085 0.26 20 -0.34 11 31
PDGFB-D/PDGFRB/CBL 0.024 0.086 0.3 9 -0.41 6 15
PTPN1 0.026 0.006 -10000 0 -10000 0 0
SNX15 0.027 0.003 -10000 0 -10000 0 0
STAT3 0.027 0.002 -10000 0 -10000 0 0
STAT1 0.021 0.037 -10000 0 -0.22 15 15
cell proliferation 0.051 0.16 0.34 51 -0.65 18 69
SLA 0.009 0.078 -10000 0 -0.34 28 28
actin cytoskeleton reorganization 0.042 0.043 0.25 6 -0.43 1 7
SRC 0.015 0.038 -10000 0 -0.52 2 2
PI3K 0.012 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.054 -10000 0 -0.27 3 3
SH2B2 0.013 0.063 -10000 0 -0.46 11 11
PLCgamma1/SPHK1 0.03 0.083 0.32 10 -0.33 8 18
LYN 0.016 0.05 0.3 1 -0.51 4 5
LRP1 0.024 0.027 -10000 0 -0.46 2 2
SOS1 0.027 0.002 -10000 0 -10000 0 0
STAT5B 0.027 0.003 -10000 0 -10000 0 0
STAT5A 0.019 0.063 -10000 0 -0.46 11 11
NCK1-2/p130 Cas 0.074 0.032 -10000 0 -0.23 1 1
SPHK1 0.005 0.09 -10000 0 -0.32 42 42
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.027 0.069 0.29 11 -0.32 5 16
PLCG1 0.027 0.07 0.29 11 -0.32 5 16
NHERF/PDGFRB 0.051 0.023 -10000 0 -0.28 1 1
YES1 0.007 0.081 -10000 0 -0.51 14 14
cell migration 0.05 0.023 -10000 0 -0.28 1 1
SHC/Grb2/SOS1 0.07 0.038 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.003 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.019 -10000 0 -0.46 1 1
NHERF1-2/PDGFRB/PTEN 0.057 0.032 -10000 0 -0.25 1 1
FYN 0.004 0.085 0.3 1 -0.39 25 26
DOK1 0.021 0.02 0.18 3 -0.26 1 4
HRAS/GTP 0.019 0.004 -10000 0 -10000 0 0
PDGFB 0.026 0.011 -10000 0 -0.22 1 1
RAC1 0.049 0.13 0.36 35 -0.43 16 51
PRKCD 0.012 0.054 0.19 3 -0.25 23 26
FER 0.016 0.042 0.19 3 -0.25 13 16
MAPKKK cascade 0.015 0.055 0.2 27 -10000 0 27
RASA1 0.021 0.019 0.19 3 -10000 0 3
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.029 0.19 2 -0.24 1 3
PDGFB-D/PDGFRB/SHB 0.037 0.023 -10000 0 -0.33 1 1
chemotaxis 0.019 0.083 0.26 20 -0.33 11 31
STAT1-3-5/STAT1-3-5 0.054 0.047 -10000 0 -0.23 9 9
Bovine Papilomavirus E5/PDGFRB 0.018 0.016 -10000 0 -0.15 5 5
PTPRJ 0.026 0.019 -10000 0 -0.46 1 1
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 0.016 0.033 -10000 0 -0.23 10 10
TRAF2/ASK1 0.031 0.034 -10000 0 -0.28 7 7
ATM 0.026 0.004 -10000 0 -10000 0 0
MAP2K3 0.018 0.068 0.22 2 -0.3 10 12
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.007 0.085 0.22 3 -0.33 18 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.006 0.11 -10000 0 -0.34 57 57
TXN 0.009 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.006 -10000 0 -10000 0 0
GADD45A 0.009 0.06 -10000 0 -0.23 38 38
GADD45B 0.009 0.075 -10000 0 -0.29 35 35
MAP3K1 0.025 0.02 -10000 0 -0.22 4 4
MAP3K6 0.023 0.021 -10000 0 -0.22 4 4
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
MAP3K4 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.029 0.042 -10000 0 -0.26 11 11
TAK1/TAB family -0.002 0.019 0.16 2 -0.13 4 6
RAC1/OSM/MEKK3 0.042 0.021 -10000 0 -10000 0 0
TRAF2 0.026 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.022 0.054 -10000 0 -0.28 6 6
TRAF6 0.008 0.018 -10000 0 -0.31 2 2
RAC1 0.023 0.01 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.019 0.12 -10000 0 -0.34 74 74
CCM2 0.023 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.078 -10000 0 -0.28 38 38
MAPK11 0.024 0.027 -10000 0 -0.46 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.013 0.083 -10000 0 -0.27 39 39
OSM/MEKK3 0.033 0.016 -10000 0 -10000 0 0
TAOK1 -0.009 0.088 -10000 0 -0.3 54 54
TAOK2 0.016 0.018 -10000 0 -0.3 2 2
TAOK3 0.017 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.05 -10000 0 -0.46 7 7
MAP3K10 0.021 0.033 -10000 0 -0.25 8 8
MAP3K3 0.026 0.004 -10000 0 -10000 0 0
TRX/ASK1 0.021 0.031 -10000 0 -0.27 7 7
GADD45/MTK1/MTK1 0.017 0.085 -10000 0 -0.23 50 50
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 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 0.059 0.057 0.22 6 -0.34 2 8
ERC1 0.024 0.027 -10000 0 -0.46 2 2
RIP2/NOD2 0.028 0.051 -10000 0 -0.33 9 9
NFKBIA 0.024 0.022 0.22 8 -10000 0 8
BIRC2 0.026 0.004 -10000 0 -10000 0 0
IKBKB 0.026 0.004 -10000 0 -10000 0 0
RIPK2 0.026 0.006 -10000 0 -10000 0 0
IKBKG 0.028 0.041 -10000 0 -0.68 1 1
IKK complex/A20 0.036 0.097 -10000 0 -0.4 7 7
NEMO/A20/RIP2 0.026 0.006 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
NEMO/ATM 0.046 0.053 -10000 0 -0.38 4 4
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.047 0.05 -10000 0 -0.45 1 1
BCL10/MALT1/TRAF6 0.045 0.027 -10000 0 -0.28 2 2
NOD2 0.012 0.073 -10000 0 -0.32 28 28
NFKB1 0.029 0.003 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
MALT1 0.026 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.007 -10000 0 -10000 0 0
ATM 0.026 0.004 -10000 0 -10000 0 0
TNF/TNFR1A -0.025 0.12 -10000 0 -0.24 151 151
TRAF6 0.025 0.027 -10000 0 -0.46 2 2
PRKCA 0.025 0.027 -10000 0 -0.46 2 2
CHUK 0.024 0.008 -10000 0 -10000 0 0
UBE2D3 0.027 0.003 -10000 0 -10000 0 0
TNF -0.054 0.16 -10000 0 -0.33 149 149
NF kappa B1 p50/RelA 0.061 0.013 -10000 0 -10000 0 0
BCL10 0.024 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.022 0.22 8 -10000 0 8
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
IKK complex 0.054 0.054 0.26 1 -0.48 1 2
CYLD 0.026 0.019 -10000 0 -0.46 1 1
IKK complex/PKC alpha 0.061 0.059 -10000 0 -0.66 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC2 0.026 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.035 0.04 -10000 0 -0.27 6 6
forebrain development 0.009 0.15 0.4 1 -0.43 49 50
GNAO1 0.007 0.097 -10000 0 -0.46 27 27
SMO/beta Arrestin2 0.029 0.034 -10000 0 -0.33 4 4
SMO 0.018 0.04 -10000 0 -0.41 5 5
ARRB2 0.027 0.004 -10000 0 -10000 0 0
GLI3/SPOP 0.028 0.082 -10000 0 -0.38 10 10
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.061 0.025 -10000 0 -0.24 1 1
GNAI1 0.012 0.071 -10000 0 -0.46 14 14
XPO1 0.026 0.009 -10000 0 -10000 0 0
GLI1/Su(fu) 0.006 0.12 -10000 0 -0.57 13 13
SAP30 0.026 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.04 -10000 0 -0.41 5 5
MIM/GLI2A 0.022 0.019 -10000 0 -0.22 1 1
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GLI2 0.034 0.044 0.27 3 -0.28 1 4
GLI3 0.015 0.083 -10000 0 -0.39 11 11
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.022 0.043 -10000 0 -0.46 5 5
Gi family/GTP 0.003 0.075 -10000 0 -0.31 25 25
SIN3B 0.025 0.02 -10000 0 -0.46 1 1
SIN3A 0.027 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.026 0.073 -10000 0 -0.44 5 5
GLI2/Su(fu) 0.034 0.051 -10000 0 -0.39 3 3
FOXA2 0.011 0.082 -10000 0 -0.81 3 3
neural tube patterning 0.009 0.15 0.4 1 -0.43 49 50
SPOP 0.027 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.04 0.049 -10000 0 -0.27 3 3
GNB1 0.024 0.008 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
CSNK1G3 0.027 0.003 -10000 0 -10000 0 0
MTSS1 0.023 0.019 -10000 0 -0.22 1 1
embryonic limb morphogenesis 0.009 0.15 0.4 1 -0.43 49 50
SUFU 0.02 0.026 -10000 0 -0.38 1 1
LGALS3 -0.017 0.098 -10000 0 -0.23 110 110
catabolic process 0.054 0.084 0.27 2 -0.61 3 5
GLI3A/CBP -0.006 0.099 -10000 0 -0.3 57 57
KIF3A 0.024 0.033 -10000 0 -0.46 3 3
GLI1 0.009 0.15 0.4 1 -0.45 44 45
RAB23 0.026 0.019 -10000 0 -0.46 1 1
CSNK1A1 0.027 0.003 -10000 0 -10000 0 0
IFT172 0.025 0.033 -10000 0 -0.46 3 3
RBBP7 0.027 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.069 -10000 0 -0.26 15 15
GNAZ 0.024 0.033 -10000 0 -0.46 3 3
RBBP4 0.024 0.008 -10000 0 -10000 0 0
CSNK1G1 0.026 0.01 -10000 0 -0.22 1 1
PIAS1 0.025 0.027 -10000 0 -0.46 2 2
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.045 0.047 0.23 1 -0.39 2 3
STK36 0.026 0.009 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.072 -10000 0 -0.42 11 11
PTCH1 -0.005 0.22 -10000 0 -1.1 20 20
MIM/GLI1 0.015 0.15 -10000 0 -0.59 14 14
CREBBP -0.006 0.099 -10000 0 -0.3 57 57
Su(fu)/SIN3/HDAC complex 0.012 0.092 0.21 1 -0.34 18 19
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.031 -10000 0 -0.64 1 1
VEGFR1 homodimer/NRP1 0.015 0.028 -10000 0 -0.46 2 2
mol:DAG -0.004 0.075 -10000 0 -0.59 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.01 0.055 -10000 0 -0.42 2 2
CaM/Ca2+ 0.01 0.075 -10000 0 -0.56 1 1
HIF1A 0.031 0.025 -10000 0 -0.39 2 2
GAB1 0.026 0.019 -10000 0 -0.46 1 1
AKT1 0.003 0.079 -10000 0 -0.49 2 2
PLCG1 -0.004 0.075 -10000 0 -0.6 1 1
NOS3 0.005 0.072 0.26 1 -0.44 2 3
CBL 0.026 0.019 -10000 0 -0.46 1 1
mol:NO 0.02 0.081 0.25 1 -0.42 2 3
FLT1 0.021 0.033 -10000 0 -0.52 2 2
PGF -0.022 0.13 -10000 0 -0.36 80 80
VEGFR1 homodimer/NRP2/VEGFR121 0.022 0.066 -10000 0 -0.6 1 1
CALM1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.038 0.088 0.29 3 -0.41 2 5
endothelial cell proliferation -0.013 0.1 0.28 1 -0.4 14 15
mol:Ca2+ -0.004 0.075 -10000 0 -0.58 1 1
MAPK3 -0.009 0.064 -10000 0 -0.53 1 1
MAPK1 -0.01 0.064 -10000 0 -0.53 1 1
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
PLGF homodimer -0.022 0.13 -10000 0 -0.36 80 80
PRKACA 0.026 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.003 0.077 -10000 0 -0.23 63 63
VEGFA homodimer -0.015 0.093 -10000 0 -0.22 110 110
VEGFR1 homodimer/VEGFA homodimer 0.011 0.061 -10000 0 -0.46 2 2
platelet activating factor biosynthetic process -0.011 0.061 -10000 0 -0.51 1 1
PI3K 0.029 0.085 -10000 0 -0.57 1 1
PRKCA -0.008 0.068 -10000 0 -0.55 1 1
PRKCB -0.025 0.087 -10000 0 -0.37 12 12
VEGFR1 homodimer/PLGF homodimer 0.004 0.088 -10000 0 -0.28 49 49
VEGFA -0.015 0.093 -10000 0 -0.22 110 110
VEGFB 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 -0.004 0.075 -10000 0 -0.59 1 1
RASA1 0.021 0.03 -10000 0 -0.6 1 1
NRP2 0.023 0.039 -10000 0 -0.31 8 8
VEGFR1 homodimer 0.021 0.033 -10000 0 -0.52 2 2
VEGFB homodimer 0.027 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.008 0.082 -10000 0 -0.41 2 2
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
mol:PI-3-4-5-P3 0.027 0.084 -10000 0 -0.56 1 1
mol:L-citrulline 0.02 0.081 0.25 1 -0.42 2 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.036 0.066 -10000 0 -0.45 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.061 -10000 0 -0.6 1 1
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.037 0.087 -10000 0 -0.54 1 1
PDPK1 0.004 0.076 0.34 1 -0.48 2 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.023 0.067 -10000 0 -0.58 2 2
mol:NADP 0.02 0.081 0.25 1 -0.42 2 3
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.064 -10000 0 -0.44 2 2
VEGFR1 homodimer/NRP2 0.031 0.039 -10000 0 -0.35 5 5
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.008 -10000 0 -10000 0 0
mol:PIP3 0.009 0.021 -10000 0 -0.23 3 3
FRAP1 0.029 0.048 0.26 4 -0.3 1 5
AKT1 0.013 0.035 0.19 18 -0.21 2 20
INSR 0.025 0.019 -10000 0 -0.46 1 1
Insulin Receptor/Insulin 0.024 0.028 -10000 0 -0.28 5 5
mol:GTP 0.041 0.05 0.18 34 -0.28 1 35
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.013 0.015 -10000 0 -0.15 1 1
TSC2 0.026 0.019 -10000 0 -0.46 1 1
RHEB/GDP 0.018 0.025 -10000 0 -10000 0 0
TSC1 0.025 0.027 -10000 0 -0.46 2 2
Insulin Receptor/IRS1 0.023 0.038 -10000 0 -0.28 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.022 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.009 -10000 0 -10000 0 0
RPS6KB1 0.039 0.058 0.24 21 -0.31 1 22
MAP3K5 -0.005 0.056 0.17 1 -0.22 38 39
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.005 0.055 0.17 1 -0.22 38 39
mol:LY294002 0 0 -10000 0 -0.002 9 9
EIF4B 0.039 0.058 0.25 22 -0.28 1 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.04 0.036 0.2 2 -0.25 1 3
eIF4E/eIF4G1/eIF4A1 0.018 0.019 -10000 0 -0.19 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.041 0.036 -10000 0 -0.24 9 9
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.032 0.18 12 -10000 0 12
FKBP1A 0.026 0.011 -10000 0 -0.22 1 1
RHEB/GTP 0.031 0.035 0.18 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.002 9 9
FKBP12/Rapamycin 0.019 0.008 -10000 0 -0.15 1 1
PDPK1 0.006 0.023 0.19 2 -0.24 3 5
EIF4E 0.027 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.15 -10000 0 -0.57 39 39
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.037 -10000 0 -10000 0 0
TSC1/TSC2 0.048 0.057 0.2 39 -0.3 1 40
tumor necrosis factor receptor activity 0 0 0.002 9 -10000 0 9
RPS6 0.024 0.015 -10000 0 -0.22 2 2
PPP5C 0.024 0.009 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.007 0.037 -10000 0 -0.3 9 9
INS 0.011 0.038 -10000 0 -0.41 5 5
PTEN 0.023 0.009 -10000 0 -10000 0 0
PDK2 0.007 0.021 0.19 2 -0.24 2 4
EIF4EBP1 0.007 0.14 -10000 0 -1.1 10 10
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D 0.029 0.047 0.24 7 -0.28 1 8
peptide biosynthetic process 0.011 0.024 -10000 0 -0.25 5 5
RHEB 0.021 0.011 -10000 0 -10000 0 0
EIF4A1 0.027 0.003 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 74 -10000 0 74
EEF2 0.012 0.024 -10000 0 -0.25 5 5
eIF4E/4E-BP1 0.021 0.13 -10000 0 -1 10 10
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.008 0.12 -10000 0 -0.29 74 74
Ran/GTP/Exportin 1/HDAC1 0.006 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.11 -10000 0 -0.29 70 70
SUMO1 0.027 0.001 -10000 0 -10000 0 0
ZFPM1 0.026 0.019 -10000 0 -0.46 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.004 -10000 0 -10000 0 0
FKBP3 0.026 0.005 -10000 0 -10000 0 0
Histones 0.037 0.07 -10000 0 -0.34 1 1
YY1/LSF 0.028 0.044 -10000 0 -0.24 8 8
SMG5 0.026 0.004 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.085 -10000 0 -0.24 71 71
I kappa B alpha/HDAC1 0.008 0.072 -10000 0 -0.3 11 11
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA 0 0.081 -10000 0 -0.21 72 72
HDAC1/Smad7 0.038 0.026 -10000 0 -10000 0 0
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.011 0.069 -10000 0 -0.27 4 4
NuRD/MBD3 Complex 0.03 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.009 0.086 0.19 1 -0.32 7 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.015 0.068 -10000 0 -0.35 20 20
GATA1 0.021 0.026 -10000 0 -0.22 7 7
Mad/Max 0.038 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.024 0.053 -10000 0 -10000 0 0
RBBP7 0.027 0.002 -10000 0 -10000 0 0
NPC 0.016 0.001 -10000 0 -10000 0 0
RBBP4 0.024 0.008 -10000 0 -10000 0 0
MAX 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NFKBIA -0.007 0.073 -10000 0 -0.36 9 9
KAT2B 0.025 0.029 -10000 0 -0.38 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.018 -10000 0 -10000 0 0
SIN3 complex 0.061 0.025 -10000 0 -0.25 1 1
SMURF1 0.021 0.011 -10000 0 -10000 0 0
CHD3 0.021 0.053 -10000 0 -0.46 8 8
SAP30 0.026 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.027 -10000 0 -0.46 2 2
YY1/HDAC3 0.006 0.063 -10000 0 -0.21 2 2
YY1/HDAC2 0.03 0.039 -10000 0 -0.21 5 5
YY1/HDAC1 0.026 0.042 -10000 0 -0.2 11 11
NuRD/MBD2 Complex (MeCP1) 0.03 0.025 -10000 0 -10000 0 0
PPARG -0.022 0.12 -10000 0 -0.3 88 88
HDAC8/hEST1B 0.052 0.014 -10000 0 -10000 0 0
UBE2I 0.027 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.018 0.058 -10000 0 -0.42 11 11
HDAC3/SMRT (N-CoR2) 0.01 0.071 -10000 0 -0.27 5 5
MBD3L2 0.015 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.026 -10000 0 -10000 0 0
CREBBP 0.026 0.019 -10000 0 -0.46 1 1
NuRD/MBD3/MBD3L2 Complex 0.028 0.055 -10000 0 -10000 0 0
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC3 -0.004 0.065 -10000 0 -0.26 3 3
HDAC2 0.026 0.006 -10000 0 -10000 0 0
YY1 0.022 0.027 -10000 0 -0.25 6 6
HDAC8 0.027 0.003 -10000 0 -10000 0 0
SMAD7 0.025 0.027 -10000 0 -0.46 2 2
NCOR2 0.025 0.027 -10000 0 -0.46 2 2
MXD1 0.027 0.001 -10000 0 -10000 0 0
STAT3 0.023 0.026 -10000 0 -0.3 4 4
NFKB1 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.001 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.038 0.045 -10000 0 -0.24 6 6
YY1/SAP30/HDAC1 0.038 0.043 -10000 0 -0.2 5 5
EP300 0.024 0.033 -10000 0 -0.46 3 3
STAT3 (dimer non-phopshorylated) 0.023 0.026 -10000 0 -0.3 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.073 -10000 0 -0.35 9 9
histone deacetylation 0.029 0.029 -10000 0 -0.33 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.009 0.06 -10000 0 -0.24 5 5
nuclear export -0.051 0.013 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GATAD2B 0.027 0.003 -10000 0 -10000 0 0
GATAD2A 0.026 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.006 0.076 -10000 0 -0.25 15 15
GATA1/HDAC1 0.031 0.022 -10000 0 -0.15 7 7
GATA1/HDAC3 0.007 0.07 -10000 0 -0.28 5 5
CHD4 0.026 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.025 0.12 -10000 0 -0.24 151 151
SIN3/HDAC complex/Mad/Max 0.032 0.02 -10000 0 -10000 0 0
NuRD Complex 0.03 0.059 -10000 0 -0.25 1 1
positive regulation of chromatin silencing 0.035 0.068 -10000 0 -0.34 1 1
SIN3B 0.025 0.02 -10000 0 -0.46 1 1
MTA2 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
SUMO1/HDAC1 0.038 0.026 -10000 0 -0.22 1 1
HDAC complex 0.059 0.025 -10000 0 -10000 0 0
GATA1/Fog1 0.034 0.024 -10000 0 -0.17 8 8
FKBP25/HDAC1/HDAC2 0.046 0.021 -10000 0 -10000 0 0
TNF -0.054 0.16 -10000 0 -0.33 149 149
negative regulation of cell growth 0.029 0.03 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.03 0.025 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.044 0.023 -10000 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.013 0.11 -10000 0 -0.3 73 73
SIN3/HDAC complex/NCoR1 0.029 0.04 -10000 0 -0.23 7 7
TFCP2 0.025 0.027 -10000 0 -0.46 2 2
NR2C1 0.027 0.003 -10000 0 -10000 0 0
MBD3 0.026 0.005 -10000 0 -10000 0 0
MBD2 0.026 0.004 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.013 0.051 -10000 0 -10000 0 0
PLK1 0.017 0.18 -10000 0 -1.3 7 7
CDKN1B 0.038 0.14 0.3 1 -0.35 22 23
FOXO3 0.038 0.11 -10000 0 -0.52 5 5
KAT2B 0.028 0.032 -10000 0 -0.37 3 3
FOXO1/SIRT1 0.026 0.045 -10000 0 -10000 0 0
CAT 0.031 0.12 -10000 0 -1.2 1 1
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.032 0.016 -10000 0 -10000 0 0
FOXO1 0.017 0.049 -10000 0 -0.24 4 4
MAPK10 0.053 0.061 0.19 103 -0.22 1 104
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.071 0.064 0.28 3 -0.44 1 4
response to oxidative stress 0.008 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.039 0.12 -10000 0 -0.49 5 5
XPO1 0.027 0.002 -10000 0 -10000 0 0
EP300 0.024 0.034 -10000 0 -0.46 3 3
BCL2L11 0.03 0.09 -10000 0 -1.3 3 3
FOXO1/SKP2 0.027 0.054 -10000 0 -0.28 2 2
mol:GDP 0.008 0.011 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
GADD45A -0.012 0.2 -10000 0 -0.62 13 13
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.046 0.069 0.22 1 -0.81 1 2
MST1 0.002 0.11 -10000 0 -0.39 43 43
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.089 -10000 0 -0.65 2 2
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.038 0.057 0.19 60 -0.23 8 68
MAPK9 0.054 0.06 0.19 104 -10000 0 104
YWHAG 0.021 0.019 -10000 0 -0.22 3 3
YWHAE 0.027 0.003 -10000 0 -10000 0 0
YWHAZ 0.025 0.007 -10000 0 -10000 0 0
SIRT1 0.023 0.009 -10000 0 -10000 0 0
SOD2 0.047 0.13 -10000 0 -0.53 10 10
RBL2 0.057 0.11 -10000 0 -0.81 3 3
RAL/GDP 0.038 0.019 -10000 0 -10000 0 0
CHUK 0.028 0.017 -10000 0 -10000 0 0
Ran/GTP 0.022 0.003 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
RAL/GTP 0.041 0.021 -10000 0 -10000 0 0
CSNK1G1 0.026 0.01 -10000 0 -0.22 1 1
FASLG 0.024 0.039 -10000 0 -10000 0 0
SKP2 0.022 0.044 -10000 0 -0.39 7 7
USP7 0.028 0.003 -10000 0 -10000 0 0
IKBKB 0.029 0.017 -10000 0 -10000 0 0
CCNB1 0.023 0.13 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.085 0.095 0.3 5 -0.4 2 7
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.054 -10000 0 -0.28 2 2
CSNK1A1 0.027 0.003 -10000 0 -10000 0 0
SGK1 0.024 0.052 -10000 0 -0.45 7 7
CSNK1G3 0.027 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.005 -10000 0 -10000 0 0
ZFAND5 0.069 0.061 0.38 1 -10000 0 1
SFN -0.032 0.13 -10000 0 -0.3 114 114
CDK2 0.02 0.05 -10000 0 -0.32 12 12
FOXO3A/14-3-3 0.017 0.081 -10000 0 -0.54 3 3
CREBBP 0.026 0.021 -10000 0 -0.46 1 1
FBXO32 0.04 0.15 -10000 0 -1.3 3 3
BCL6 0.05 0.13 -10000 0 -0.71 9 9
RALB 0.028 0.001 -10000 0 -10000 0 0
RALA 0.023 0.01 -10000 0 -10000 0 0
YWHAH 0.022 0.032 -10000 0 -0.22 11 11
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.002 0.094 -10000 0 -0.19 120 120
AKT1 0.04 0.077 0.34 3 -0.49 4 7
PTK2B -0.012 0.092 0.36 1 -0.41 4 5
VEGFR2 homodimer/Frs2 0.034 0.043 -10000 0 -0.52 3 3
CAV1 -0.003 0.077 -10000 0 -0.23 63 63
CALM1 0.026 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.029 0.07 -10000 0 -0.59 2 2
endothelial cell proliferation 0.045 0.093 0.31 19 -0.42 6 25
mol:Ca2+ 0.015 0.07 0.37 1 -0.42 5 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.038 0.069 -10000 0 -0.56 2 2
RP11-342D11.1 0.003 0.066 -10000 0 -0.42 5 5
CDH5 0.024 0.024 -10000 0 -0.22 6 6
VEGFA homodimer 0.038 0.065 -10000 0 -0.25 1 1
SHC1 0.022 0.035 -10000 0 -0.22 13 13
SHC2 0.024 0.027 -10000 0 -0.46 2 2
HRAS/GDP 0.024 0.065 -10000 0 -0.39 4 4
SH2D2A -0.032 0.14 -10000 0 -0.33 109 109
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.064 0.08 0.34 2 -0.43 5 7
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.003 0.11 -10000 0 -0.4 7 7
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.46 1 1
SHC/GRB2/SOS1 0.047 0.081 -10000 0 -0.42 4 4
GRB10 0.013 0.07 0.37 1 -0.46 6 7
PTPN11 0.025 0.027 -10000 0 -0.46 2 2
GRB2 0.026 0.005 -10000 0 -10000 0 0
PAK1 0.012 0.066 -10000 0 -0.26 34 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.047 0.08 -10000 0 -0.41 4 4
HRAS 0.026 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.013 0.062 -10000 0 -0.3 7 7
HIF1A 0.025 0.02 -10000 0 -0.46 1 1
FRS2 0.026 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.036 0.068 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.042 -10000 0 -0.29 10 10
Nck/Pak 0.028 0.049 -10000 0 -0.33 5 5
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.029 0.071 -10000 0 -0.5 3 3
mol:GDP 0.035 0.073 -10000 0 -0.41 4 4
mol:NADP 0.045 0.072 0.31 6 -0.4 6 12
eNOS/Hsp90 0.055 0.07 0.31 5 -0.39 5 10
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 0.015 0.071 0.37 1 -0.43 5 6
HIF1A/ARNT 0.037 0.017 -10000 0 -0.33 1 1
SHB 0.025 0.02 -10000 0 -0.46 1 1
VEGFA -0.014 0.093 -10000 0 -0.22 110 110
VEGFC 0.016 0.06 -10000 0 -0.29 22 22
FAK1/Vinculin 0.026 0.085 0.31 1 -0.6 3 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.014 0.1 -10000 0 -0.4 5 5
PTPN6 0.018 0.06 -10000 0 -0.44 11 11
EPAS1 0.032 0.03 -10000 0 -0.37 3 3
mol:L-citrulline 0.045 0.072 0.31 6 -0.4 6 12
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PIK3CA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.041 0.069 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer 0.03 0.08 -10000 0 -0.4 7 7
VEGFR2/3 heterodimer 0.032 0.05 -10000 0 -0.36 8 8
VEGFB 0.027 0.003 -10000 0 -10000 0 0
MAPK11 0.004 0.074 0.38 2 -0.56 3 5
VEGFR2 homodimer 0.022 0.046 -10000 0 -0.59 3 3
FLT1 0.025 0.02 -10000 0 -0.46 1 1
NEDD4 0.024 0.038 -10000 0 -0.34 6 6
MAPK3 0.004 0.076 0.31 6 -0.39 5 11
MAPK1 0.004 0.076 0.31 6 -0.41 4 10
VEGFA145/NRP2 0.006 0.076 -10000 0 -0.25 11 11
VEGFR1/2 heterodimer 0.033 0.047 -10000 0 -0.6 3 3
KDR 0.023 0.046 -10000 0 -0.59 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.032 0.078 -10000 0 -0.44 5 5
SRC 0.024 0.027 -10000 0 -0.46 2 2
platelet activating factor biosynthetic process 0.006 0.077 0.32 5 -0.4 5 10
PI3K 0.038 0.072 -10000 0 -0.51 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.029 0.071 -10000 0 -0.5 3 3
FES 0.013 0.073 -10000 0 -0.43 5 5
GAB1 0.026 0.07 -10000 0 -0.48 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.071 -10000 0 -0.46 4 4
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
ARNT 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.033 0.071 0.34 2 -0.4 5 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.027 0.072 -10000 0 -0.5 3 3
PI3K/GAB1 0.049 0.074 -10000 0 -0.43 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.041 0.081 -10000 0 -0.55 2 2
PRKACA 0.026 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.061 -10000 0 -0.51 3 3
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
CDC42 0.012 0.072 0.37 1 -0.43 5 6
actin cytoskeleton reorganization -0.003 0.11 -10000 0 -0.4 7 7
PTK2 0.009 0.075 -10000 0 -0.6 2 2
EDG1 0.003 0.066 -10000 0 -0.42 5 5
mol:DAG 0.015 0.071 0.37 1 -0.43 5 6
CaM/Ca2+ 0.024 0.067 -10000 0 -0.48 3 3
MAP2K3 0.005 0.077 0.37 1 -0.4 6 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.062 0.1 0.31 6 -0.47 6 12
PLCG1 0.015 0.071 0.37 1 -0.43 5 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.075 -10000 0 -0.49 4 4
IQGAP1 0.022 0.041 -10000 0 -0.36 7 7
YES1 0.024 0.027 -10000 0 -0.46 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.075 -10000 0 -0.46 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.023 0.077 -10000 0 -0.59 2 2
cell migration 0.041 0.088 0.29 4 -0.52 4 8
mol:PI-3-4-5-P3 0.037 0.069 -10000 0 -0.48 4 4
FYN 0.026 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.017 0.068 -10000 0 -0.4 5 5
mol:NO 0.045 0.072 0.31 6 -0.4 6 12
PXN 0.027 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.007 0.057 -10000 0 -0.38 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.031 0.076 -10000 0 -0.47 6 6
VHL 0.027 0.003 -10000 0 -10000 0 0
ITGB3 -0.029 0.12 -10000 0 -0.28 120 120
NOS3 0.045 0.077 0.33 5 -0.46 5 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.028 0.072 -10000 0 -0.46 4 4
RAC1 0.023 0.01 -10000 0 -10000 0 0
PRKCA 0.01 0.068 0.37 2 -0.4 4 6
PRKCB -0.007 0.086 0.37 2 -0.35 13 15
VCL 0.022 0.028 -10000 0 -0.27 5 5
VEGFA165/NRP1 0.018 0.073 -10000 0 -0.42 5 5
VEGFR1/2 heterodimer/VEGFA homodimer 0.028 0.072 -10000 0 -0.49 4 4
VEGFA165/NRP2 0.006 0.076 -10000 0 -0.25 11 11
MAPKKK cascade 0.035 0.074 0.28 4 -0.43 4 8
NRP2 0.023 0.039 -10000 0 -0.31 8 8
VEGFC homodimer 0.016 0.06 -10000 0 -0.29 22 22
NCK1 0.027 0.003 -10000 0 -10000 0 0
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.029 0.088 0.31 4 -0.58 3 7
MAP3K13 0.009 0.081 0.37 1 -0.39 8 9
PDPK1 0.029 0.065 -10000 0 -0.47 4 4
Arf6 trafficking events

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
SLC2A4 -0.016 0.12 -10000 0 -0.32 80 80
CLTC 0.024 0.062 -10000 0 -0.3 18 18
calcium ion-dependent exocytosis 0.02 0.047 -10000 0 -0.27 3 3
Dynamin 2/GTP 0.027 0.013 -10000 0 -10000 0 0
EXOC4 0.021 0.011 -10000 0 -10000 0 0
CD59 0.017 0.052 -10000 0 -0.24 19 19
CPE 0.013 0.034 -10000 0 -0.26 10 10
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.008 0.036 -10000 0 -0.26 3 3
CTNND1 0.019 0.021 0.19 8 -10000 0 8
DNM2 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.042 0.16 6 -0.24 3 9
TSHR -0.067 0.12 -10000 0 -0.28 132 132
INS -0.004 0.1 -10000 0 -0.46 30 30
BIN1 0.026 0.019 -10000 0 -0.46 1 1
mol:Choline 0.008 0.036 -10000 0 -0.26 3 3
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.011 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.013 -10000 0 -10000 0 0
JUP 0.016 0.057 -10000 0 -0.25 21 21
ASAP2/amphiphysin II 0.049 0.016 -10000 0 -0.25 1 1
ARF6/GTP 0.019 0.004 -10000 0 -10000 0 0
CDH1 -0.009 0.084 -10000 0 -0.26 31 31
clathrin-independent pinocytosis 0.019 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.02 0.057 -10000 0 -0.46 9 9
positive regulation of endocytosis 0.019 0.004 -10000 0 -10000 0 0
EXOC2 0.026 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.025 0.023 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.015 0.076 0.3 9 -10000 0 9
positive regulation of phagocytosis 0.015 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.031 0.037 -10000 0 -0.28 9 9
ACAP1 0.025 0.047 -10000 0 -0.22 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.004 0.065 -10000 0 -0.34 11 11
clathrin heavy chain/ACAP1 0.029 0.058 0.2 11 -0.27 7 18
JIP4/KLC1 0.049 0.013 -10000 0 -10000 0 0
EXOC1 0.026 0.005 -10000 0 -10000 0 0
exocyst 0.025 0.024 -10000 0 -10000 0 0
RALA/GTP 0.017 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.008 -10000 0 -10000 0 0
receptor recycling 0.019 0.004 -10000 0 -10000 0 0
CTNNA1 0.018 0.02 0.19 7 -10000 0 7
NME1 0.016 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.063 0.23 2 -0.3 18 20
IL2RA -0.016 0.077 -10000 0 -0.33 15 15
VAMP3 0.015 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.009 0.068 -10000 0 -0.27 14 14
EXOC6 0.024 0.008 -10000 0 -10000 0 0
PLD1 0.004 0.057 -10000 0 -0.27 27 27
PLD2 0.016 0.013 -10000 0 -0.26 1 1
EXOC5 0.026 0.005 -10000 0 -10000 0 0
PIP5K1C 0.022 0.036 -10000 0 -0.24 3 3
SDC1 0.008 0.064 -10000 0 -0.32 12 12
ARF6/GDP 0.025 0.013 -10000 0 -0.12 4 4
EXOC7 0.026 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.017 0.078 -10000 0 -0.31 9 9
mol:Phosphatidic acid 0.008 0.036 -10000 0 -0.26 3 3
endocytosis -0.048 0.015 0.25 1 -10000 0 1
SCAMP2 0.027 0.003 -10000 0 -10000 0 0
ADRB2 0.016 0.077 0.27 3 -0.3 21 24
EXOC3 0.026 0.004 -10000 0 -10000 0 0
ASAP2 0.027 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.031 0.014 -10000 0 -10000 0 0
KLC1 0.026 0.005 -10000 0 -10000 0 0
AVPR2 0.022 0.067 0.21 8 -0.29 19 27
RALA 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.075 -10000 0 -0.31 7 7
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.056 0.038 -10000 0 -0.24 6 6
HDAC3 0.027 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.008 -10000 0 -0.21 1 1
GATA1/HDAC4 0.034 0.024 -10000 0 -0.17 7 7
GATA1/HDAC5 0.034 0.024 -10000 0 -0.17 8 8
GATA2/HDAC5 0.03 0.056 -10000 0 -0.26 20 20
HDAC5/BCL6/BCoR 0.051 0.029 -10000 0 -0.4 2 2
HDAC9 0.016 0.055 -10000 0 -0.41 10 10
Glucocorticoid receptor/Hsp90/HDAC6 0.052 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.016 -10000 0 -0.33 1 1
HDAC5/YWHAB 0.038 0.017 -10000 0 -0.33 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.004 -10000 0 -10000 0 0
GATA2 0.015 0.068 -10000 0 -0.35 20 20
HDAC4/RFXANK 0.037 0.019 -10000 0 -0.24 2 2
BCOR 0.025 0.029 -10000 0 -0.38 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.026 0.006 -10000 0 -10000 0 0
HDAC5 0.026 0.019 -10000 0 -0.46 1 1
GNB1/GNG2 0.032 0.034 -10000 0 -0.33 5 5
Histones 0.036 0.047 -10000 0 -0.32 3 3
ADRBK1 0.027 0.003 -10000 0 -10000 0 0
HDAC4 0.025 0.019 -10000 0 -0.46 1 1
XPO1 0.027 0.001 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.015 -10000 0 -0.33 1 1
HDAC4/Ubc9 0.038 0.016 -10000 0 -0.33 1 1
HDAC7 0.026 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.015 -10000 0 -0.33 1 1
TUBA1B 0.025 0.014 -10000 0 -0.22 2 2
HDAC6 0.027 0.001 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.018 -10000 0 -0.24 2 2
CAMK4 -0.07 0.18 -10000 0 -0.36 166 166
Tubulin/HDAC6 0.051 0.02 -10000 0 -0.28 1 1
SUMO1 0.027 0.001 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
GATA1 0.021 0.026 -10000 0 -0.22 7 7
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.027 0.003 -10000 0 -10000 0 0
NR3C1 0.027 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.041 0.026 -10000 0 -0.21 2 2
SRF 0.027 0.003 -10000 0 -10000 0 0
HDAC4/YWHAB 0.037 0.017 -10000 0 -0.33 1 1
Tubulin 0.037 0.019 -10000 0 -0.33 1 1
HDAC4/14-3-3 E 0.038 0.016 -10000 0 -0.33 1 1
GNB1 0.024 0.008 -10000 0 -10000 0 0
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.037 0.023 -10000 0 -0.27 3 3
HDAC4/HDAC3/SMRT (N-CoR2) 0.051 0.025 -10000 0 -0.28 3 3
HDAC4/SRF -0.012 0.12 -10000 0 -0.28 91 91
HDAC4/ER alpha 0.027 0.056 -10000 0 -0.33 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.047 -10000 0 -0.32 3 3
cell motility 0.051 0.02 -10000 0 -0.28 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.008 -10000 0 -10000 0 0
BCL6 0.026 0.004 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.025 0.019 -10000 0 -0.46 1 1
Hsp90/HDAC6 0.038 0.009 -10000 0 -10000 0 0
ESR1 0.013 0.072 -10000 0 -0.35 23 23
HDAC6/HDAC11 0.038 0.021 -10000 0 -0.33 2 2
Ran/GTP/Exportin 1 0.044 0.023 -10000 0 -0.21 1 1
NPC 0.016 0.001 -10000 0 -10000 0 0
MEF2C 0.019 0.047 -10000 0 -0.25 18 18
RAN 0.027 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.069 0.042 -10000 0 -0.23 5 5
GNG2 0.022 0.043 -10000 0 -0.46 5 5
NCOR2 0.025 0.027 -10000 0 -0.46 2 2
TUBB2A 0.026 0.019 -10000 0 -0.46 1 1
HDAC11 0.025 0.027 -10000 0 -0.46 2 2
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
RANBP2 0.027 0.001 -10000 0 -10000 0 0
ANKRA2 0.027 0.003 -10000 0 -10000 0 0
RFXANK 0.026 0.011 -10000 0 -0.22 1 1
nuclear import -0.035 0.02 0.27 2 -10000 0 2
Circadian rhythm pathway

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
chromatin modification 0.046 0.065 -10000 0 -1.3 1 1
CLOCK 0.01 0.092 -10000 0 -0.46 24 24
TIMELESS/CRY2 0.032 0.07 -10000 0 -0.9 2 2
DEC1/BMAL1 0.029 0.038 -10000 0 -0.16 1 1
ATR 0.027 0.003 -10000 0 -10000 0 0
NR1D1 0.021 0.062 -10000 0 -1.4 1 1
ARNTL 0.028 0.006 -10000 0 -10000 0 0
TIMELESS 0.02 0.066 -10000 0 -0.97 2 2
NPAS2 0.022 0.055 -10000 0 -0.41 10 10
CRY2 0.022 0.046 -10000 0 -0.46 6 6
mol:CO -0.009 0.009 0.13 2 -10000 0 2
CHEK1 0.026 0.014 -10000 0 -0.22 2 2
mol:HEME 0.009 0.009 -10000 0 -0.13 2 2
PER1 0.02 0.057 -10000 0 -0.46 9 9
BMAL/CLOCK/NPAS2 0.045 0.074 -10000 0 -0.27 31 31
BMAL1/CLOCK 0.02 0.11 -10000 0 -0.69 6 6
S phase of mitotic cell cycle 0.046 0.065 -10000 0 -1.3 1 1
TIMELESS/CHEK1/ATR 0.047 0.068 -10000 0 -1.3 1 1
mol:NADPH 0.009 0.009 -10000 0 -0.13 2 2
PER1/TIMELESS 0.031 0.073 -10000 0 -0.9 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.012 0.05 -10000 0 -0.22 28 28
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.022 0.043 0.42 6 -10000 0 6
PI3K Class IB/PDE3B 0.022 0.043 -10000 0 -0.42 6 6
PDE3B 0.022 0.044 -10000 0 -0.42 6 6
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 0.005 -9999 0 -10000 0 0
SMAD2 0 0.038 -9999 0 -0.23 4 4
SMAD3 0.034 0.03 -9999 0 -10000 0 0
SMAD3/SMAD4 0.044 0.048 -9999 0 -0.39 6 6
SMAD4/Ubc9/PIASy 0.051 0.019 -9999 0 -0.28 1 1
SMAD2/SMAD2/SMAD4 0.05 0.045 -9999 0 -10000 0 0
PPM1A 0.026 0.005 -9999 0 -10000 0 0
CALM1 0.026 0.006 -9999 0 -10000 0 0
SMAD2/SMAD4 0.015 0.039 -9999 0 -0.22 4 4
MAP3K1 0.025 0.02 -9999 0 -0.22 4 4
TRAP-1/SMAD4 0.029 0.058 -9999 0 -0.33 17 17
MAPK3 0.027 0.002 -9999 0 -10000 0 0
MAPK1 0.026 0.004 -9999 0 -10000 0 0
NUP214 0.026 0.004 -9999 0 -10000 0 0
CTDSP1 0.027 0.002 -9999 0 -10000 0 0
CTDSP2 0.025 0.007 -9999 0 -10000 0 0
CTDSPL 0.026 0.019 -9999 0 -0.46 1 1
KPNB1 0.027 0.002 -9999 0 -10000 0 0
TGFBRAP1 0.014 0.077 -9999 0 -0.46 17 17
UBE2I 0.027 0.003 -9999 0 -10000 0 0
NUP153 0.027 0.003 -9999 0 -10000 0 0
KPNA2 0.026 0.011 -9999 0 -0.22 1 1
PIAS4 0.025 0.02 -9999 0 -0.46 1 1
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 0.017 0.026 0.15 23 -10000 0 23
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.011 0.029 0.13 3 -10000 0 3
AP2 0.035 0.014 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.015 -10000 0 -10000 0 0
CLTB 0.027 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.022 0.007 -10000 0 -10000 0 0
CD4 0.023 0.029 -10000 0 -0.26 6 6
CLTA 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.009 0.006 -10000 0 -0.15 1 1
mol:PI-4-5-P2 0.006 0.01 -10000 0 -0.17 1 1
ARF1/GTP 0.029 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.01 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.006 -10000 0 -10000 0 0
DDEF1 0.005 0.01 -10000 0 -0.18 1 1
ARF1/GDP 0.005 0.016 -10000 0 -10000 0 0
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.008 -10000 0 -10000 0 0
Rac/GTP 0.017 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.018 -10000 0 -10000 0 0
ARFIP2 0.024 0.007 -10000 0 -10000 0 0
COPA 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.023 0.01 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.017 0.025 -10000 0 -0.17 1 1
ARF1/GTP/ARHGAP10 0.016 0.008 -10000 0 -10000 0 0
GGA3 0.026 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.013 -10000 0 -10000 0 0
AP2A1 0.024 0.009 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.014 -10000 0 -0.21 1 1
ARF1/GDP/Membrin 0.026 0.016 -10000 0 -0.21 1 1
Arfaptin 2/Rac/GDP 0.03 0.014 -10000 0 -10000 0 0
CYTH2 0.025 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.032 0.015 -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 0.019 0.035 -10000 0 -0.27 1 1
PLD2 0.006 0.01 -10000 0 -0.17 1 1
ARF-GAP1/v-SNARE 0.009 0.006 -10000 0 -0.15 1 1
PIP5K1A 0.006 0.011 -10000 0 -0.17 1 1
ARF1/GTP/Membrin/GBF1/p115 0.017 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.01 -10000 0 -0.17 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.006 -10000 0 -0.15 1 1
GOSR2 0.015 0.008 -10000 0 -10000 0 0
USO1 0.011 0.036 -10000 0 -0.33 7 7
GBF1 -0.01 0.086 -10000 0 -0.32 48 48
ARF1/GTP/Arfaptin 2 0.033 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.043 0.028 -10000 0 -0.25 1 1
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.012 -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 0.024 0.008 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.062 0.038 -9999 0 -0.22 2 2
NFKB1 0.027 0.003 -9999 0 -10000 0 0
MAP3K14 0.027 0.002 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.033 0.025 -9999 0 -0.18 6 6
RELB 0.021 0.03 -9999 0 -0.26 6 6
NFKB2 0.023 0.021 -9999 0 -0.46 1 1
NF kappa B2 p52/RelB 0.027 0.025 -9999 0 -0.27 2 2
regulation of B cell activation 0.027 0.025 -9999 0 -0.26 2 2
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 0.024 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.009 -10000 0 -0.19 1 1
MDM2/SUMO1 0.042 0.023 -10000 0 -0.22 1 1
HDAC4 0.025 0.019 -10000 0 -0.46 1 1
Ran/GTP/Exportin 1/HDAC1 0.007 0.007 -10000 0 -10000 0 0
SUMO1 0.027 0.001 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.015 0.012 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.017 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.001 -10000 0 -10000 0 0
SUMO1/HDAC4 0.041 0.026 -10000 0 -0.21 2 2
SUMO1/HDAC1 0.038 0.026 -10000 0 -0.22 1 1
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.063 0.026 -10000 0 -0.25 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.004 -10000 0 -10000 0 0
Ran/GTP 0.031 0.021 -10000 0 -0.23 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.005 -10000 0 -10000 0 0
UBE2I 0.027 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.021 0.19 1 -0.21 1 2
NPC 0.016 0.001 -10000 0 -10000 0 0
PIAS2 0.026 0.004 -10000 0 -10000 0 0
PIAS1 0.025 0.027 -10000 0 -0.46 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 660 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.041 -0.19 0.074 -0.19
47_PPARGC1A 0.027 0.027 0.027 0.027
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 0.027 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 0.027
131_RELN/VLDLR 0.069 0.069 -0.25 0.069
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.01 0.041 -0.0051 0.12
84_STAT5A 0.01 0.041 -0.0051 0.12
Methods & Data
Input

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

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

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBMLGG-TP/19775186/GDAC_Gistic2Report_19791513/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.

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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