PARADIGM pathway analysis of mRNASeq expression data
Bladder Urothelial Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1WD3ZDC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1WD3ZDC
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 64 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 130
Glypican 2 network 103
Aurora B signaling 94
Signaling events regulated by Ret tyrosine kinase 72
Signaling mediated by p38-alpha and p38-beta 72
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 72
Nongenotropic Androgen signaling 61
Signaling events mediated by the Hedgehog family 60
IL4-mediated signaling events 59
Endothelins 56
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 357 . 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 ( 357 ).

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
FOXM1 transcription factor network 0.3641 130 6663 51 -0.86 0.016 1000 -1000 -0.13 -1000
Glypican 2 network 0.2885 103 412 4 -0.17 -0.13 1000 -1000 -0.011 -1000
Aurora B signaling 0.2633 94 6364 67 -0.51 0.016 1000 -1000 -0.057 -1000
Signaling events regulated by Ret tyrosine kinase 0.2017 72 5937 82 -0.32 0.016 1000 -1000 -0.073 -1000
Signaling mediated by p38-alpha and p38-beta 0.2017 72 3176 44 -0.26 0.016 1000 -1000 -0.049 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2017 72 4945 68 -0.72 0.36 1000 -1000 -0.096 -1000
Nongenotropic Androgen signaling 0.1709 61 3196 52 -0.25 0.14 1000 -1000 -0.055 -1000
Signaling events mediated by the Hedgehog family 0.1681 60 3150 52 -0.18 0.18 1000 -1000 -0.047 -1000
IL4-mediated signaling events 0.1653 59 5374 91 -0.78 0.56 1000 -1000 -0.1 -1000
Endothelins 0.1569 56 5377 96 -0.33 0.042 1000 -1000 -0.059 -1000
IGF1 pathway 0.1541 55 3158 57 -0.25 0.047 1000 -1000 -0.079 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1457 52 4092 78 -0.26 0.093 1000 -1000 -0.048 -1000
Reelin signaling pathway 0.1401 50 2801 56 -0.24 0.04 1000 -1000 -0.078 -1000
TCGA08_p53 0.1401 50 354 7 -0.17 0.078 1000 -1000 -0.011 -1000
Thromboxane A2 receptor signaling 0.1373 49 5169 105 -0.2 0.037 1000 -1000 -0.057 -1000
Aurora C signaling 0.1345 48 342 7 -0.22 0 1000 -1000 -0.024 -1000
TCGA08_retinoblastoma 0.1345 48 390 8 -0.25 0.068 1000 -1000 -0.012 -1000
Fc-epsilon receptor I signaling in mast cells 0.1289 46 4556 97 -0.2 0.042 1000 -1000 -0.072 -1000
p75(NTR)-mediated signaling 0.1261 45 5663 125 -0.17 0.046 1000 -1000 -0.085 -1000
PLK1 signaling events 0.1204 43 3735 85 -0.37 0.051 1000 -1000 -0.037 -1000
IL23-mediated signaling events 0.1204 43 2620 60 -0.62 0.016 1000 -1000 -0.11 -1000
Ephrin A reverse signaling 0.1176 42 295 7 -0.072 0 1000 -1000 -0.018 -1000
HIF-1-alpha transcription factor network 0.1176 42 3226 76 -0.36 0.033 1000 -1000 -0.064 -1000
Plasma membrane estrogen receptor signaling 0.1176 42 3636 86 -0.25 0.12 1000 -1000 -0.067 -1000
Ras signaling in the CD4+ TCR pathway 0.1176 42 721 17 -0.16 0.022 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.1148 41 3493 84 -0.28 0.032 1000 -1000 -0.076 -1000
Rapid glucocorticoid signaling 0.1148 41 837 20 -0.24 0.037 1000 -1000 -0.01 -1000
BMP receptor signaling 0.1120 40 3244 81 -0.33 0.053 1000 -1000 -0.082 -1000
Glypican 1 network 0.1064 38 1849 48 -0.26 0.036 1000 -1000 -0.025 -1000
amb2 Integrin signaling 0.1064 38 3149 82 -0.34 0.021 1000 -1000 -0.068 -1000
Calcium signaling in the CD4+ TCR pathway 0.1064 38 1181 31 -0.3 0.016 1000 -1000 -0.072 -1000
IL6-mediated signaling events 0.1064 38 2862 75 -0.25 0.07 1000 -1000 -0.063 -1000
Syndecan-1-mediated signaling events 0.1036 37 1287 34 -0.28 0.016 1000 -1000 -0.033 -1000
TCR signaling in naïve CD8+ T cells 0.1036 37 3519 93 -0.15 0.063 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.1008 36 3674 102 -0.23 0.032 1000 -1000 -0.065 -1000
Glucocorticoid receptor regulatory network 0.0980 35 4038 114 -0.6 0.27 1000 -1000 -0.069 -1000
PDGFR-alpha signaling pathway 0.0952 34 1516 44 -0.34 0.033 1000 -1000 -0.053 -1000
S1P1 pathway 0.0952 34 1253 36 -0.32 0.016 1000 -1000 -0.047 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0924 33 3997 120 -0.33 0.18 1000 -1000 -0.07 -1000
S1P5 pathway 0.0868 31 541 17 -0.17 0.11 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0868 31 1655 52 -0.32 0.028 1000 -1000 -0.048 -1000
IL12-mediated signaling events 0.0812 29 2574 87 -0.42 0.035 1000 -1000 -0.093 -1000
Visual signal transduction: Cones 0.0812 29 1130 38 -0.13 0.017 1000 -1000 -0.056 -1000
LPA4-mediated signaling events 0.0784 28 345 12 -0.17 0.023 1000 -1000 -0.015 -1000
Osteopontin-mediated events 0.0784 28 1095 38 -0.19 0.017 1000 -1000 -0.084 -1000
BCR signaling pathway 0.0784 28 2814 99 -0.19 0.037 1000 -1000 -0.076 -1000
S1P4 pathway 0.0784 28 703 25 -0.17 0.031 1000 -1000 -0.034 -1000
JNK signaling in the CD4+ TCR pathway 0.0756 27 459 17 -0.16 0.019 1000 -1000 -0.026 -1000
Coregulation of Androgen receptor activity 0.0728 26 2013 76 -0.24 0.033 1000 -1000 -0.042 -1000
Syndecan-2-mediated signaling events 0.0728 26 1835 69 -0.087 0.031 1000 -1000 -0.026 -1000
S1P3 pathway 0.0728 26 1112 42 -0.17 0.032 1000 -1000 -0.027 -1000
Aurora A signaling 0.0700 25 1554 60 -0.36 0.031 1000 -1000 -0.043 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0700 25 2287 88 -0.23 0.048 1000 -1000 -0.091 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0672 24 1338 54 -0.2 0.031 1000 -1000 -0.086 -1000
Arf6 signaling events 0.0672 24 1510 62 -0.24 0.03 1000 -1000 -0.042 -1000
Class IB PI3K non-lipid kinase events 0.0672 24 72 3 -0.024 -1000 1000 -1000 -0.008 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0616 22 755 34 -0.052 0.016 1000 -1000 -0.051 -1000
Syndecan-4-mediated signaling events 0.0616 22 1498 67 -0.19 0.02 1000 -1000 -0.067 -1000
FAS signaling pathway (CD95) 0.0588 21 1010 47 -0.57 0.019 1000 -1000 -0.026 -1000
Wnt signaling 0.0588 21 153 7 -0.058 0.016 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 0.0560 20 1262 61 -0.18 0.044 1000 -1000 -0.053 -1000
Visual signal transduction: Rods 0.0560 20 1047 52 -0.21 0.016 1000 -1000 -0.073 -1000
Canonical Wnt signaling pathway 0.0532 19 1007 51 -0.18 0.083 1000 -1000 -0.039 -1000
Noncanonical Wnt signaling pathway 0.0504 18 487 26 -0.1 0.016 1000 -1000 -0.044 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0476 17 500 28 -0.17 0.03 1000 -1000 -0.022 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0476 17 564 33 -0.29 0.046 1000 -1000 -0.047 -1000
ErbB2/ErbB3 signaling events 0.0448 16 1075 65 -0.24 0.027 1000 -1000 -0.06 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0448 16 1397 85 -0.22 0.023 1000 -1000 -0.063 -1000
Effects of Botulinum toxin 0.0448 16 416 26 -0.072 0.016 1000 -1000 -0.056 -1000
Caspase cascade in apoptosis 0.0420 15 1155 74 -0.058 0.043 1000 -1000 -0.029 -1000
ErbB4 signaling events 0.0420 15 1089 69 -0.24 0.038 1000 -1000 -0.07 -1000
FOXA2 and FOXA3 transcription factor networks 0.0420 15 725 46 -0.19 0.095 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0392 14 988 70 -0.22 0.03 1000 -1000 -0.048 -1000
Hedgehog signaling events mediated by Gli proteins 0.0364 13 863 65 -0.17 0.067 1000 -1000 -0.047 -1000
Nectin adhesion pathway 0.0364 13 881 63 -0.054 0.03 1000 -1000 -0.061 -1000
IL27-mediated signaling events 0.0364 13 713 51 -0.25 0.029 1000 -1000 -0.066 -1000
EGFR-dependent Endothelin signaling events 0.0364 13 293 21 -0.071 0.023 1000 -1000 -0.062 -1000
IL2 signaling events mediated by STAT5 0.0336 12 284 22 -0.12 0.068 1000 -1000 -0.036 -1000
Regulation of nuclear SMAD2/3 signaling 0.0308 11 1527 136 -0.2 0.069 1000 -1000 -0.063 -1000
Cellular roles of Anthrax toxin 0.0308 11 464 39 -0.1 0.018 1000 -1000 -0.019 -1000
IL2 signaling events mediated by PI3K 0.0308 11 653 58 -0.21 0.055 1000 -1000 -0.066 -1000
Signaling events mediated by PTP1B 0.0280 10 815 76 -0.14 0.036 1000 -1000 -0.065 -1000
Syndecan-3-mediated signaling events 0.0280 10 364 35 -0.13 0.046 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 0.0252 9 383 40 -0.23 0.026 1000 -1000 -0.031 -1000
IL1-mediated signaling events 0.0252 9 615 62 -0.094 0.075 1000 -1000 -0.081 -1000
Ephrin B reverse signaling 0.0252 9 468 48 -0.057 0.018 1000 -1000 -0.059 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0252 9 788 83 -0.28 0.043 1000 -1000 -0.056 -1000
Regulation of p38-alpha and p38-beta 0.0252 9 510 54 -0.15 0.043 1000 -1000 -0.05 -1000
BARD1 signaling events 0.0224 8 468 57 -0.16 0.045 1000 -1000 -0.048 -1000
a4b1 and a4b7 Integrin signaling 0.0224 8 44 5 -0.004 0.009 1000 -1000 -0.015 -1000
Class I PI3K signaling events mediated by Akt 0.0224 8 569 68 -0.21 0.061 1000 -1000 -0.044 -1000
EPHB forward signaling 0.0224 8 697 85 -0.047 0.041 1000 -1000 -0.078 -1000
Regulation of Telomerase 0.0224 8 886 102 -0.17 0.038 1000 -1000 -0.099 -1000
Signaling events mediated by PRL 0.0224 8 273 34 -0.1 0.026 1000 -1000 -0.028 -1000
E-cadherin signaling events 0.0224 8 42 5 -0.006 0.016 1000 -1000 -0.016 -1000
EPO signaling pathway 0.0196 7 403 55 -0.047 0.057 1000 -1000 -0.073 -1000
IFN-gamma pathway 0.0196 7 487 68 -0.18 0.056 1000 -1000 -0.079 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0196 7 280 37 -0.031 0.035 1000 -1000 -0.044 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0196 7 570 74 -0.25 0.077 1000 -1000 -0.077 -1000
Arf6 trafficking events 0.0196 7 533 71 -0.42 0.05 1000 -1000 -0.061 -1000
Insulin Pathway 0.0196 7 570 74 -0.26 0.042 1000 -1000 -0.082 -1000
PDGFR-beta signaling pathway 0.0196 7 754 97 -0.056 0.054 1000 -1000 -0.075 -1000
TRAIL signaling pathway 0.0168 6 316 48 -0.011 0.051 1000 -1000 -0.057 -1000
Ceramide signaling pathway 0.0140 5 384 76 -0.25 0.044 1000 -1000 -0.028 -1000
Signaling mediated by p38-gamma and p38-delta 0.0140 5 89 15 0 0.032 1000 -1000 -0.021 -1000
Retinoic acid receptors-mediated signaling 0.0140 5 315 58 -0.08 0.036 1000 -1000 -0.062 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0140 5 247 45 -0.032 0.068 1000 -1000 -0.077 -1000
TCGA08_rtk_signaling 0.0140 5 134 26 -0.069 0.048 1000 -1000 -0.014 -1000
PLK2 and PLK4 events 0.0112 4 14 3 0.005 0.019 1000 -1000 -0.009 -1000
E-cadherin signaling in the nascent adherens junction 0.0112 4 369 76 -0.02 0.058 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class II 0.0084 3 269 75 -0.086 0.039 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0084 3 147 43 -0.16 0.16 1000 -1000 -0.061 -1000
Paxillin-dependent events mediated by a4b1 0.0084 3 123 36 -0.035 0.036 1000 -1000 -0.056 -1000
Class I PI3K signaling events 0.0084 3 253 73 -0.054 0.041 1000 -1000 -0.057 -1000
E-cadherin signaling in keratinocytes 0.0084 3 129 43 -0.046 0.048 1000 -1000 -0.056 -1000
p38 MAPK signaling pathway 0.0084 3 160 44 -0.044 0.047 1000 -1000 -0.054 -1000
Canonical NF-kappaB pathway 0.0056 2 91 39 -0.021 0.092 1000 -1000 -0.069 -1000
ceramide signaling pathway 0.0056 2 99 49 -0.024 0.051 1000 -1000 -0.033 -1000
FoxO family signaling 0.0056 2 160 64 -0.067 0.098 1000 -1000 -0.048 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0056 2 310 125 -0.054 0.099 1000 -1000 -0.082 -1000
Circadian rhythm pathway 0.0028 1 36 22 -0.016 0.053 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 0.0028 1 60 32 -0.14 0.042 1000 -1000 -0.046 -1000
mTOR signaling pathway 0.0028 1 63 53 -0.006 0.042 1000 -1000 -0.056 -1000
VEGFR1 specific signals 0.0028 1 89 56 -0.051 0.071 1000 -1000 -0.041 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 12 23 0.007 0.055 1000 -1000 -0.045 -1000
Arf6 downstream pathway 0.0000 0 20 43 -0.039 0.039 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0000 0 81 104 -0.031 0.066 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0.0000 0 23 31 0 0.056 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 24 27 -0.002 0.039 1000 -1000 -0.045 -1000
Arf1 pathway 0.0000 0 6 54 0 0.04 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.046 1000 -1000 -0.026 -1000
Total NA 3095 179636 7203 -25 -990 131000 -131000 -6.8 -131000
FOXM1 transcription factor network

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
NFATC3 -0.65 0.52 -9999 0 -1.1 177 177
PLK1 -0.13 0.18 -9999 0 -10000 0 0
BIRC5 -0.25 0.19 -9999 0 -1.5 1 1
HSPA1B -0.65 0.52 -9999 0 -1.1 174 174
MAP2K1 -0.007 0.031 -9999 0 -10000 0 0
BRCA2 -0.66 0.53 -9999 0 -1.1 180 180
FOXM1 -0.86 0.73 -9999 0 -1.4 198 198
XRCC1 -0.65 0.52 -9999 0 -1.1 182 182
FOXM1B/p19 -0.76 0.51 -9999 0 -1.1 217 217
Cyclin D1/CDK4 -0.59 0.47 -9999 0 -0.98 178 178
CDC2 -0.7 0.55 -9999 0 -1.1 198 198
TGFA -0.56 0.45 -9999 0 -0.93 177 177
SKP2 -0.65 0.52 -9999 0 -1.1 179 179
CCNE1 -0.073 0.19 -9999 0 -0.52 56 56
CKS1B -0.65 0.52 -9999 0 -1.1 182 182
RB1 -0.25 0.15 -9999 0 -0.46 13 13
FOXM1C/SP1 -0.76 0.62 -9999 0 -1.2 195 195
AURKB -0.16 0.19 -9999 0 -10000 0 0
CENPF -0.73 0.56 -9999 0 -1.2 192 192
CDK4 0.004 0.03 -9999 0 -0.51 1 1
MYC -0.57 0.46 -9999 0 -0.94 184 184
CHEK2 -0.007 0.031 -9999 0 -10000 0 0
ONECUT1 -0.63 0.5 -9999 0 -1 185 185
CDKN2A -0.24 0.26 -9999 0 -0.5 174 174
LAMA4 -0.66 0.53 -9999 0 -1.1 182 182
FOXM1B/HNF6 -0.75 0.62 -9999 0 -1.2 185 185
FOS -0.77 0.61 -9999 0 -1.2 197 197
SP1 0.016 0.001 -9999 0 -10000 0 0
CDC25B -0.65 0.52 -9999 0 -1.1 180 180
response to radiation -0.023 0.03 -9999 0 -10000 0 0
CENPB -0.65 0.52 -9999 0 -1.1 182 182
CENPA -0.74 0.56 -9999 0 -1.2 196 196
NEK2 -0.73 0.56 -9999 0 -1.2 193 193
HIST1H2BA -0.66 0.52 -9999 0 -1.1 182 182
CCNA2 -0.13 0.23 -9999 0 -0.52 94 94
EP300 0.016 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.78 0.64 -9999 0 -1.3 184 184
CCNB2 -0.74 0.56 -9999 0 -1.2 197 197
CCNB1 -0.72 0.57 -9999 0 -1.2 186 186
ETV5 -0.65 0.52 -9999 0 -1.1 176 176
ESR1 -0.73 0.57 -9999 0 -1.2 194 194
CCND1 -0.61 0.49 -9999 0 -1 178 178
GSK3A 0.003 0.025 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.2 -9999 0 -0.37 128 128
CDK2 0.01 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.035 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.75 0.51 -9999 0 -1.1 200 200
GAS1 -0.78 0.56 -9999 0 -1.1 220 220
MMP2 -0.67 0.55 -9999 0 -1.1 184 184
RB1/FOXM1C -0.64 0.52 -9999 0 -1.1 182 182
CREBBP 0.016 0 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.014 0.12 -9999 0 -0.51 20 20
GPC2 -0.17 0.25 -9999 0 -0.51 124 124
GPC2/Midkine -0.13 0.2 -9999 0 -0.38 134 134
neuron projection morphogenesis -0.13 0.2 -9999 0 -0.38 134 134
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 -0.15 0.15 -9999 0 -0.32 113 113
STMN1 -0.17 0.22 -9999 0 -0.39 171 171
Aurora B/RasGAP/Survivin -0.32 0.24 -9999 0 -0.45 263 263
Chromosomal passenger complex/Cul3 protein complex -0.18 0.16 -9999 0 -0.36 127 127
BIRC5 -0.37 0.24 -9999 0 -0.51 259 259
DES -0.51 0.37 -9999 0 -0.77 233 233
Aurora C/Aurora B/INCENP -0.11 0.15 -9999 0 -0.27 169 169
Aurora B/TACC1 -0.12 0.16 -9999 0 -0.3 162 162
Aurora B/PP2A -0.14 0.19 -9999 0 -0.35 161 161
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.021 0.045 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.004 -9999 0 -10000 0 0
NDC80 -0.25 0.29 -9999 0 -0.51 184 184
Cul3 protein complex -0.063 0.17 -9999 0 -0.36 86 86
KIF2C -0.12 0.099 -9999 0 -0.2 202 202
PEBP1 0.006 0.007 -9999 0 -10000 0 0
KIF20A -0.38 0.23 -9999 0 -0.51 266 266
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.14 0.19 -9999 0 -0.35 161 161
SEPT1 0.011 0.048 -9999 0 -0.51 3 3
SMC2 0.014 0.028 -9999 0 -0.51 1 1
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.058 0.068 -9999 0 -10000 0 0
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.004 -9999 0 -10000 0 0
H3F3B -0.068 0.099 -9999 0 -0.18 161 161
AURKB -0.22 0.27 -9999 0 -0.51 161 161
AURKC -0.001 0.09 -9999 0 -0.51 11 11
CDCA8 -0.13 0.23 -9999 0 -0.52 95 95
cytokinesis -0.26 0.18 -9999 0 -0.41 191 191
Aurora B/Septin1 -0.24 0.19 -9999 0 -0.42 145 145
AURKA -0.14 0.24 -9999 0 -0.51 104 104
INCENP 0.005 0.029 -9999 0 -0.53 1 1
KLHL13 -0.11 0.24 -9999 0 -0.58 76 76
BUB1 -0.081 0.2 -9999 0 -0.51 65 65
hSgo1/Aurora B/Survivin -0.41 0.3 -9999 0 -0.53 280 280
EVI5 0.014 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.21 -9999 0 -0.46 180 180
SGOL1 -0.21 0.26 -9999 0 -0.51 152 152
CENPA -0.18 0.14 -9999 0 -0.3 172 172
NCAPG -0.21 0.26 -9999 0 -0.51 155 155
Aurora B/HC8 Proteasome -0.14 0.19 -9999 0 -0.35 161 161
NCAPD2 0.014 0.028 -9999 0 -0.51 1 1
Aurora B/PP1-gamma -0.14 0.19 -9999 0 -0.35 161 161
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.31 0.25 -9999 0 -0.51 221 221
NPM1 -0.066 0.083 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
KLHL9 -0.009 0.12 -9999 0 -0.58 15 15
mitotic prometaphase -0.009 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.19 -9999 0 -0.35 161 161
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.23 -9999 0 -0.48 193 193
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
NSUN2 -0.066 0.083 -9999 0 -10000 0 0
MYLK -0.19 0.2 -9999 0 -0.31 228 228
KIF23 -0.25 0.26 -9999 0 -0.51 178 178
VIM -0.15 0.2 -9999 0 -0.36 165 165
RACGAP1 0.008 0.04 -9999 0 -0.52 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.066 0.083 -9999 0 -10000 0 0
Chromosomal passenger complex -0.2 0.16 -9999 0 -0.33 189 189
Chromosomal passenger complex/EVI5 -0.32 0.29 -9999 0 -0.57 177 177
TACC1 0.012 0.044 -9999 0 -0.58 2 2
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.048 0.044 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.15 0.13 -9999 0 -0.4 26 26
JUN -0.11 0.15 -9999 0 -0.44 21 21
HRAS 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.18 0.19 -9999 0 -0.33 201 201
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.005 0.072 -9999 0 -0.51 7 7
RAP1A/GDP 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.19 -9999 0 -0.33 200 200
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.17 0.17 -9999 0 -0.32 199 199
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.16 0.15 -9999 0 -0.55 13 13
GRB7 -0.013 0.12 -9999 0 -0.52 19 19
RET51/GFRalpha1/GDNF -0.17 0.19 -9999 0 -0.33 200 200
MAPKKK cascade -0.15 0.14 -9999 0 -0.5 13 13
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.18 0.18 -9999 0 -0.33 201 201
lamellipodium assembly -0.15 0.13 -9999 0 -0.38 26 26
RET51/GFRalpha1/GDNF/SHC -0.17 0.19 -9999 0 -0.33 200 200
PIK3CA 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.17 0.18 -9999 0 -0.32 199 199
RET9/GFRalpha1/GDNF/Shank3 -0.17 0.17 -9999 0 -0.32 199 199
MAPK3 -0.13 0.16 -9999 0 -0.51 13 13
DOK1 0.014 0.028 -9999 0 -0.51 1 1
DOK6 -0.2 0.28 -9999 0 -0.58 130 130
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.16 0.18 -9999 0 -0.38 98 98
DOK5 -0.043 0.18 -9999 0 -0.57 35 35
GFRA1 -0.32 0.29 -9999 0 -0.58 199 199
MAPK8 -0.12 0.14 -9999 0 -0.42 16 16
HRAS/GTP -0.18 0.16 -9999 0 -0.58 13 13
tube development -0.15 0.16 -9999 0 -0.3 199 199
MAPK1 -0.13 0.16 -9999 0 -0.51 13 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.13 0.14 -9999 0 -0.26 199 199
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.27 0.25 -9999 0 -0.61 99 99
SHC1 0.014 0.028 -9999 0 -0.51 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.19 -9999 0 -0.33 200 200
RET51/GFRalpha1/GDNF/Dok5 -0.2 0.22 -9999 0 -0.36 210 210
PRKCA 0.011 0.054 -9999 0 -0.58 3 3
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
CREB1 -0.15 0.17 -9999 0 -0.29 199 199
PIK3R1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.13 0.14 -9999 0 -0.25 199 199
RET51/GFRalpha1/GDNF/Grb7 -0.19 0.2 -9999 0 -0.35 202 202
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.011 0.12 -9999 0 -0.55 17 17
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.11 0.15 -9999 0 -0.43 21 21
RET9/GFRalpha1/GDNF/FRS2 -0.17 0.18 -9999 0 -0.32 203 203
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.13 0.14 -9999 0 -0.26 199 199
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.13 0.15 -9999 0 -0.45 17 17
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.13 0.15 -9999 0 -0.27 122 122
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.14 0.17 -9999 0 -0.58 14 14
PI3K -0.19 0.23 -9999 0 -0.38 199 199
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.16 -9999 0 -0.3 199 199
GRB10 0.009 0.062 -9999 0 -0.58 4 4
activation of MAPKK activity -0.12 0.14 -9999 0 -0.4 16 16
RET51/GFRalpha1/GDNF/FRS2 -0.18 0.19 -9999 0 -0.33 201 201
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.004 0.082 -9999 0 -0.58 7 7
IRS2 -0.008 0.12 -9999 0 -0.58 14 14
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.17 -9999 0 -0.28 122 122
RET51/GFRalpha1/GDNF/PKC alpha -0.18 0.19 -9999 0 -0.33 200 200
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.003 0.048 -9999 0 -0.51 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.18 0.19 -9999 0 -0.34 202 202
Rac1/GTP -0.17 0.15 -9999 0 -0.46 26 26
RET9/GFRalpha1/GDNF -0.2 0.19 -9999 0 -0.36 199 199
GFRalpha1/GDNF -0.23 0.22 -9999 0 -0.42 199 199
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.26 0.51 -9999 0 -1.1 90 90
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.061 0.15 -9999 0 -0.29 95 95
ATF2/c-Jun -0.05 0.2 -9999 0 -0.81 15 15
MAPK11 -0.061 0.15 -9999 0 -0.29 95 95
MITF -0.093 0.22 -9999 0 -0.39 111 111
MAPKAPK5 -0.063 0.18 -9999 0 -0.35 95 95
KRT8 -0.075 0.21 -9999 0 -0.38 98 98
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.092 0.22 -9999 0 -0.44 95 95
CEBPB -0.064 0.18 -9999 0 -0.36 95 95
SLC9A1 -0.062 0.18 -9999 0 -0.35 95 95
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.058 0.18 -9999 0 -0.35 95 95
p38alpha-beta/MNK1 -0.06 0.18 -9999 0 -0.34 95 95
JUN -0.049 0.19 -9999 0 -0.8 15 15
PPARGC1A -0.22 0.28 -9999 0 -0.42 206 206
USF1 -0.063 0.18 -9999 0 -0.35 95 95
RAB5/GDP/GDI1 -0.07 0.11 -9999 0 -0.35 17 17
NOS2 -0.094 0.25 -9999 0 -0.77 22 22
DDIT3 -0.063 0.18 -9999 0 -0.35 95 95
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.042 0.15 -9999 0 -0.4 17 17
p38alpha-beta/HBP1 -0.06 0.18 -9999 0 -0.34 95 95
CREB1 -0.068 0.2 -9999 0 -0.38 95 95
RAB5/GDP 0.012 0 -9999 0 -10000 0 0
EIF4E -0.046 0.16 -9999 0 -0.43 17 17
RPS6KA4 -0.062 0.18 -9999 0 -0.35 95 95
PLA2G4A -0.066 0.19 -9999 0 -0.5 35 35
GDI1 -0.062 0.18 -9999 0 -0.35 95 95
TP53 -0.083 0.22 -9999 0 -0.43 95 95
RPS6KA5 -0.074 0.2 -9999 0 -0.38 99 99
ESR1 -0.13 0.25 -9999 0 -0.41 137 137
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.075 0.2 -9999 0 -0.36 103 103
MEF2A -0.062 0.18 -9999 0 -0.35 95 95
EIF4EBP1 -0.069 0.2 -9999 0 -0.38 96 96
KRT19 -0.081 0.21 -9999 0 -0.39 102 102
ELK4 -0.062 0.18 -9999 0 -0.35 95 95
ATF6 -0.062 0.18 -9999 0 -0.35 95 95
ATF1 -0.068 0.2 -9999 0 -0.38 96 96
p38alpha-beta/MAPKAPK2 -0.06 0.18 -9999 0 -0.34 95 95
p38alpha-beta/MAPKAPK3 -0.06 0.18 -9999 0 -0.34 95 95
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.003 0.1 -10000 0 -0.63 8 8
NFATC2 -0.11 0.28 -10000 0 -0.64 63 63
NFATC3 -0.092 0.13 -10000 0 -0.31 36 36
CD40LG -0.55 0.54 -10000 0 -1.1 165 165
ITCH 0.029 0.084 -10000 0 -0.41 1 1
CBLB 0.029 0.081 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.38 0.45 -10000 0 -1.1 77 77
JUNB 0.009 0.062 -10000 0 -0.58 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.027 0.081 -10000 0 -0.28 32 32
T cell anergy -0.007 0.13 -10000 0 -0.39 32 32
TLE4 -0.069 0.24 -10000 0 -0.63 40 40
Jun/NFAT1-c-4/p21SNFT -0.46 0.56 -10000 0 -1 152 152
AP-1/NFAT1-c-4 -0.64 0.7 -10000 0 -1.3 165 165
IKZF1 -0.067 0.24 -10000 0 -0.64 36 36
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.91 60 60
AP-1/NFAT1 -0.2 0.27 -10000 0 -0.51 125 125
CALM1 0.016 0.053 -10000 0 -10000 0 0
EGR2 -0.51 0.74 -10000 0 -1.5 108 108
EGR3 -0.72 0.84 -10000 0 -1.6 171 171
NFAT1/FOXP3 -0.081 0.22 -10000 0 -0.51 58 58
EGR1 -0.13 0.25 -10000 0 -0.58 87 87
JUN -0.012 0.11 -10000 0 -0.58 13 13
EGR4 -0.011 0.12 -10000 0 -0.55 16 16
mol:Ca2+ -0.001 0.057 -10000 0 -10000 0 0
GBP3 -0.059 0.22 -10000 0 -0.56 37 37
FOSL1 -0.024 0.15 -10000 0 -0.58 24 24
NFAT1-c-4/MAF/IRF4 -0.45 0.56 -10000 0 -0.95 173 173
DGKA -0.054 0.21 -10000 0 -0.54 34 34
CREM 0.015 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.48 0.55 -10000 0 -0.97 173 173
CTLA4 -0.069 0.23 -10000 0 -0.7 29 29
NFAT1-c-4 (dimer)/EGR1 -0.51 0.62 -10000 0 -1.1 174 174
NFAT1-c-4 (dimer)/EGR4 -0.46 0.56 -10000 0 -0.96 175 175
FOS -0.18 0.28 -10000 0 -0.59 110 110
IFNG -0.25 0.3 -10000 0 -0.78 66 66
T cell activation -0.26 0.32 -10000 0 -0.76 63 63
MAF -0.001 0.098 -10000 0 -0.58 10 10
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.36 0.5 0.79 171 -10000 0 171
TNF -0.44 0.52 -10000 0 -0.94 163 163
FASLG -0.69 0.81 -10000 0 -1.4 180 180
TBX21 -0.024 0.14 -10000 0 -0.57 21 21
BATF3 0.003 0.084 -10000 0 -0.55 8 8
PRKCQ -0.042 0.18 -10000 0 -0.57 35 35
PTPN1 -0.054 0.21 -10000 0 -0.55 32 32
NFAT1-c-4/ICER1 -0.46 0.54 -10000 0 -0.96 173 173
GATA3 -0.025 0.15 -10000 0 -0.57 25 25
T-helper 1 cell differentiation -0.23 0.31 -10000 0 -0.75 68 68
IL2RA -0.38 0.43 -10000 0 -1 82 82
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.054 0.21 -10000 0 -0.55 33 33
E2F1 -0.095 0.22 -10000 0 -0.5 81 81
PPARG -0.024 0.15 -10000 0 -0.57 24 24
SLC3A2 -0.055 0.21 -10000 0 -0.53 40 40
IRF4 -0.035 0.16 -10000 0 -0.57 31 31
PTGS2 -0.58 0.57 -10000 0 -1.1 172 172
CSF2 -0.56 0.52 -10000 0 -1 175 175
JunB/Fra1/NFAT1-c-4 -0.44 0.55 -10000 0 -0.94 173 173
IL4 -0.25 0.38 -10000 0 -0.99 58 58
IL5 -0.53 0.52 -10000 0 -1 163 163
IL2 -0.26 0.32 -10000 0 -0.77 63 63
IL3 -0.082 0.062 -10000 0 -10000 0 0
RNF128 -0.01 0.2 -10000 0 -0.63 34 34
NFATC1 -0.36 0.51 -10000 0 -0.8 171 171
CDK4 0.18 0.27 0.64 37 -10000 0 37
PTPRK -0.054 0.21 -10000 0 -0.5 48 48
IL8 -0.55 0.55 -10000 0 -1.1 167 167
POU2F1 0.016 0.002 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.1 0.17 -10000 0 -0.32 132 132
regulation of S phase of mitotic cell cycle -0.068 0.14 -10000 0 -0.25 128 128
GNAO1 -0.17 0.27 -10000 0 -0.58 110 110
HRAS 0.015 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.002 -10000 0 -10000 0 0
PELP1 0.015 0.002 -10000 0 -10000 0 0
AKT1 0.013 0.001 -10000 0 -10000 0 0
MAP2K1 -0.085 0.15 -10000 0 -0.35 48 48
T-DHT/AR -0.15 0.21 -10000 0 -0.43 128 128
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 110 110
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.01 0.054 -10000 0 -0.58 3 3
mol:GDP -0.16 0.21 -10000 0 -0.44 128 128
cell proliferation -0.16 0.24 -10000 0 -0.45 111 111
PIK3CA 0.016 0 -10000 0 -10000 0 0
FOS -0.25 0.4 -10000 0 -0.84 110 110
mol:Ca2+ -0.045 0.044 -10000 0 -0.085 166 166
MAPK3 -0.13 0.19 -10000 0 -0.49 48 48
MAPK1 -0.069 0.12 -10000 0 -0.27 47 47
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 110 110
cAMP biosynthetic process 0.039 0.037 -10000 0 -10000 0 0
GNG2 0.006 0.076 -10000 0 -0.58 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 110 110
HRAS/GTP -0.11 0.14 -10000 0 -0.29 128 128
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.015 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 110 110
PI3K 0.021 0 -10000 0 -10000 0 0
apoptosis 0.14 0.23 0.45 110 -10000 0 110
T-DHT/AR/PELP1 -0.12 0.18 -10000 0 -0.36 128 128
HRAS/GDP -0.15 0.2 -10000 0 -0.42 128 128
CREB1 -0.15 0.24 -10000 0 -0.49 110 110
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.2 0.28 -10000 0 -0.58 128 128
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 -0.088 0.15 -10000 0 -0.34 48 48
RAC1-CDC42/GDP -0.14 0.19 -10000 0 -0.39 128 128
T-DHT/AR/PELP1/Src -0.099 0.17 -10000 0 -0.32 128 128
MAP2K2 -0.085 0.15 -10000 0 -0.35 48 48
T-DHT/AR/PELP1/Src/PI3K -0.069 0.14 -10000 0 -0.25 128 128
GNAZ -0.11 0.24 -10000 0 -0.58 76 76
SHBG 0.015 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.16 0.25 -10000 0 -0.46 125 125
mol:T-DHT 0 0.001 -10000 0 -0.003 62 62
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 0.013 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.16 0.21 -10000 0 -0.41 116 116
CDC42 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.055 0.24 -10000 0 -0.63 41 41
IHH -0.061 0.19 -10000 0 -0.52 48 48
SHH Np/Cholesterol/GAS1 -0.17 0.2 -10000 0 -0.35 189 189
LRPAP1 0.014 0.028 -10000 0 -0.51 1 1
dorsoventral neural tube patterning 0.17 0.2 0.35 189 -10000 0 189
SMO/beta Arrestin2 -0.046 0.16 -10000 0 -0.5 22 22
SMO -0.057 0.17 -10000 0 -0.49 29 29
AKT1 -0.002 0.08 -10000 0 -0.29 3 3
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.037 0.17 -10000 0 -0.58 32 32
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.056 0.17 -10000 0 -0.48 29 29
STIL -0.15 0.21 -10000 0 -0.48 73 73
DHH N/PTCH2 -0.017 0.13 -10000 0 -0.43 31 31
DHH N/PTCH1 -0.036 0.16 -10000 0 -0.5 22 22
PIK3CA 0.016 0 -10000 0 -10000 0 0
DHH -0.016 0.13 -10000 0 -0.58 18 18
PTHLH -0.1 0.36 -10000 0 -1 41 41
determination of left/right symmetry -0.056 0.17 -10000 0 -0.48 29 29
PIK3R1 0.016 0 -10000 0 -10000 0 0
skeletal system development -0.1 0.36 -10000 0 -1 41 41
IHH N/Hhip -0.14 0.23 -10000 0 -0.48 104 104
DHH N/Hhip -0.11 0.21 -10000 0 -0.43 106 106
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.056 0.17 -10000 0 -0.48 29 29
pancreas development -0.14 0.26 -10000 0 -0.57 92 92
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K 0.023 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.12 0.25 -10000 0 -0.57 83 83
somite specification -0.056 0.17 -10000 0 -0.48 29 29
SHH Np/Cholesterol/PTCH1 -0.12 0.19 -10000 0 -0.45 53 53
SHH Np/Cholesterol/PTCH2 -0.11 0.17 -10000 0 -0.32 137 137
SHH Np/Cholesterol/Megalin -0.16 0.2 -10000 0 -0.35 169 169
SHH -0.14 0.21 -10000 0 -0.41 128 128
catabolic process -0.03 0.16 -10000 0 -0.54 15 15
SMO/Vitamin D3 -0.11 0.2 -10000 0 -0.47 47 47
SHH Np/Cholesterol/Hhip -0.18 0.22 -10000 0 -0.38 182 182
LRP2 -0.093 0.21 -10000 0 -0.51 73 73
receptor-mediated endocytosis -0.15 0.21 -10000 0 -0.48 63 63
SHH Np/Cholesterol/BOC -0.13 0.18 -10000 0 -0.33 150 150
SHH Np/Cholesterol/CDO -0.14 0.19 -10000 0 -0.33 167 167
mesenchymal cell differentiation 0.18 0.22 0.38 182 -10000 0 182
mol:Vitamin D3 -0.12 0.19 -10000 0 -0.45 53 53
IHH N/PTCH2 -0.04 0.14 -10000 0 -0.33 62 62
CDON -0.067 0.2 -10000 0 -0.58 50 50
IHH N/PTCH1 -0.03 0.16 -10000 0 -0.54 15 15
Megalin/LRPAP1 -0.057 0.15 -10000 0 -0.36 74 74
PTCH2 -0.008 0.12 -10000 0 -0.58 14 14
SHH Np/Cholesterol -0.11 0.16 -10000 0 -0.32 128 128
PTCH1 -0.03 0.16 -10000 0 -0.54 15 15
HHIP -0.14 0.26 -10000 0 -0.57 92 92
IL4-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
BCL2L1 -0.48 0.56 -10000 0 -1.2 109 109
STAT6 (cleaved dimer) -0.56 0.55 -10000 0 -1.1 140 140
IGHG1 -0.15 0.2 -10000 0 -0.37 71 71
IGHG3 -0.48 0.54 -10000 0 -1.1 123 123
AKT1 -0.21 0.31 -10000 0 -0.77 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.29 -10000 0 -0.76 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.32 -10000 0 -0.74 48 48
THY1 -0.49 0.56 -10000 0 -1.2 109 109
MYB -0.051 0.17 -10000 0 -0.51 45 45
HMGA1 0.007 0.067 -10000 0 -0.51 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.4 -10000 0 -0.77 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.32 -10000 0 -0.71 56 56
SP1 0.023 0.009 -10000 0 -10000 0 0
INPP5D 0.004 0.082 -10000 0 -0.58 7 7
SOCS5 0.029 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.51 0.56 -10000 0 -1.2 120 120
SOCS1 -0.29 0.36 -10000 0 -0.75 89 89
SOCS3 -0.31 0.46 -10000 0 -1.3 52 52
FCER2 -0.72 0.73 -10000 0 -1.4 174 174
PARP14 0.01 0.014 -10000 0 -10000 0 0
CCL17 -0.51 0.56 -10000 0 -1.2 107 107
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.25 -10000 0 -0.63 33 33
T cell proliferation -0.49 0.59 -10000 0 -1.2 116 116
IL4R/JAK1 -0.49 0.56 -10000 0 -1.2 113 113
EGR2 -0.67 0.72 -10000 0 -1.4 144 144
JAK2 -0.006 0.046 -10000 0 -0.61 1 1
JAK3 0.015 0.041 -10000 0 -0.52 2 2
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.009 0.016 -10000 0 -10000 0 0
COL1A2 -0.2 0.39 -10000 0 -1.6 22 22
CCL26 -0.5 0.57 -10000 0 -1.2 109 109
IL4R -0.52 0.61 -10000 0 -1.3 112 112
PTPN6 0.025 0.031 -10000 0 -0.5 1 1
IL13RA2 -0.52 0.59 -10000 0 -1.2 115 115
IL13RA1 -0.006 0.046 -10000 0 -0.62 1 1
IRF4 -0.25 0.49 -10000 0 -1.3 56 56
ARG1 -0.12 0.2 -10000 0 -0.67 19 19
CBL -0.28 0.37 -10000 0 -0.74 93 93
GTF3A 0.024 0.005 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.009 0.059 -10000 0 -0.46 2 2
IRF4/BCL6 -0.2 0.45 -10000 0 -1.2 53 53
CD40LG -0.053 0.19 -10000 0 -0.58 40 40
MAPK14 -0.3 0.42 -10000 0 -0.84 87 87
mitosis -0.2 0.29 -10000 0 -0.72 43 43
STAT6 -0.58 0.71 -10000 0 -1.4 122 122
SPI1 0 0.099 -10000 0 -0.55 11 11
RPS6KB1 -0.19 0.28 -10000 0 -0.7 40 40
STAT6 (dimer) -0.58 0.71 -10000 0 -1.4 122 122
STAT6 (dimer)/PARP14 -0.57 0.63 -10000 0 -1.2 139 139
mast cell activation 0.011 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.34 -10000 0 -0.79 49 49
FRAP1 -0.21 0.31 -10000 0 -0.77 43 43
LTA -0.5 0.59 -10000 0 -1.2 113 113
FES 0.014 0.031 -10000 0 -0.58 1 1
T-helper 1 cell differentiation 0.56 0.66 1.3 122 -10000 0 122
CCL11 -0.51 0.6 -10000 0 -1.2 115 115
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.32 -10000 0 -0.78 44 44
IL2RG -0.009 0.12 -10000 0 -0.55 17 17
IL10 -0.51 0.6 -10000 0 -1.3 110 110
IRS1 0.004 0.082 -10000 0 -0.58 7 7
IRS2 -0.008 0.12 -10000 0 -0.58 14 14
IL4 -0.1 0.14 -10000 0 -10000 0 0
IL5 -0.49 0.56 -10000 0 -1.2 106 106
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.43 -10000 0 -0.88 112 112
COL1A1 -0.17 0.32 -10000 0 -1.7 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.58 -10000 0 -1.2 106 106
IL2R gamma/JAK3 -0.002 0.099 -10000 0 -0.43 17 17
TFF3 -0.65 0.7 -10000 0 -1.4 143 143
ALOX15 -0.53 0.57 -10000 0 -1.2 124 124
MYBL1 0.01 0.055 -10000 0 -0.51 4 4
T-helper 2 cell differentiation -0.41 0.47 -10000 0 -0.96 118 118
SHC1 0.014 0.028 -10000 0 -0.51 1 1
CEBPB 0.015 0.034 -10000 0 -0.58 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.32 -10000 0 -0.71 52 52
mol:PI-3-4-5-P3 -0.21 0.31 -10000 0 -0.77 43 43
PI3K -0.23 0.34 -10000 0 -0.84 43 43
DOK2 -0.007 0.11 -10000 0 -0.57 14 14
ETS1 0.027 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.24 -10000 0 -0.63 27 27
ITGB3 -0.55 0.65 -10000 0 -1.3 117 117
PIGR -0.78 0.73 -10000 0 -1.4 182 182
IGHE 0.033 0.049 -10000 0 -0.23 1 1
MAPKKK cascade -0.15 0.23 -10000 0 -0.62 27 27
BCL6 0.02 0.01 -10000 0 -10000 0 0
OPRM1 -0.49 0.56 -10000 0 -1.2 109 109
RETNLB -0.5 0.56 -10000 0 -1.2 109 109
SELP -0.62 0.7 -10000 0 -1.4 131 131
AICDA -0.48 0.54 -10000 0 -1.2 108 108
Endothelins

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
AKT1 -0.008 0.24 -10000 0 -0.58 35 35
PTK2B 0.014 0.031 -10000 0 -0.58 1 1
mol:Ca2+ -0.012 0.22 -10000 0 -0.67 23 23
EDN1 0.042 0.11 -10000 0 -0.45 8 8
EDN3 -0.002 0.061 -10000 0 -0.51 5 5
EDN2 -0.053 0.18 -10000 0 -0.54 44 44
HRAS/GDP -0.069 0.24 -10000 0 -0.49 62 62
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.026 0.19 -10000 0 -0.43 43 43
ADCY4 -0.15 0.26 -10000 0 -0.59 62 62
ADCY5 -0.3 0.34 -10000 0 -0.65 142 142
ADCY6 -0.15 0.26 -10000 0 -0.6 60 60
ADCY7 -0.15 0.26 -10000 0 -0.6 60 60
ADCY1 -0.15 0.27 -10000 0 -0.61 63 63
ADCY2 -0.26 0.32 -10000 0 -0.65 114 114
ADCY3 -0.15 0.26 -10000 0 -0.6 60 60
ADCY8 -0.16 0.26 -10000 0 -0.61 60 60
ADCY9 -0.15 0.27 -10000 0 -0.61 61 61
arachidonic acid secretion -0.12 0.28 -10000 0 -0.53 89 89
ETB receptor/Endothelin-1/Gq/GTP -0.04 0.19 -10000 0 -0.48 40 40
GNAO1 -0.17 0.27 -10000 0 -0.58 110 110
HRAS 0.013 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.041 0.26 0.26 126 -0.54 35 161
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.32 0.24 86 -0.62 64 150
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.017 0.27 -10000 0 -0.82 24 24
EDNRB -0.053 0.19 -10000 0 -0.57 42 42
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.013 0.24 -10000 0 -0.64 27 27
CYSLTR1 -0.03 0.28 -10000 0 -0.72 38 38
SLC9A1 -0.002 0.13 -10000 0 -0.34 21 21
mol:GDP -0.083 0.25 -10000 0 -0.53 63 63
SLC9A3 -0.028 0.24 -10000 0 -0.62 37 37
RAF1 -0.13 0.28 -10000 0 -0.53 86 86
JUN -0.032 0.29 -10000 0 -0.89 27 27
JAK2 -0.009 0.24 -10000 0 -0.59 35 35
mol:IP3 -0.048 0.21 -10000 0 -0.51 44 44
ETA receptor/Endothelin-1 0.031 0.31 0.29 130 -0.63 40 170
PLCB1 -0.004 0.098 -10000 0 -0.58 10 10
PLCB2 0.009 0.045 -10000 0 -0.58 2 2
ETA receptor/Endothelin-3 -0.038 0.2 -10000 0 -0.47 57 57
FOS -0.28 0.48 -10000 0 -0.95 115 115
Gai/GDP -0.25 0.41 -10000 0 -0.84 110 110
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.074 0.29 -10000 0 -0.61 59 59
BCAR1 0.016 0.001 -10000 0 -10000 0 0
PRKCB1 -0.049 0.2 -10000 0 -0.48 48 48
GNAQ 0.014 0.009 -10000 0 -10000 0 0
GNAZ -0.11 0.24 -10000 0 -0.58 76 76
GNAL -0.24 0.29 -10000 0 -0.58 154 154
Gs family/GDP -0.22 0.25 -10000 0 -0.52 124 124
ETA receptor/Endothelin-1/Gq/GTP -0.029 0.21 -10000 0 -0.49 42 42
MAPK14 -0.025 0.17 -10000 0 -0.51 26 26
TRPC6 -0.015 0.24 -10000 0 -0.72 23 23
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.054 -10000 0 -0.58 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.034 0.18 -10000 0 -0.48 35 35
ETB receptor/Endothelin-2 -0.076 0.19 -10000 0 -0.43 79 79
ETB receptor/Endothelin-3 -0.041 0.15 -10000 0 -0.41 47 47
ETB receptor/Endothelin-1 -0.011 0.17 -10000 0 -0.41 45 45
MAPK3 -0.23 0.42 -10000 0 -0.79 119 119
MAPK1 -0.23 0.42 -10000 0 -0.79 119 119
Rac1/GDP -0.068 0.24 -10000 0 -0.49 61 61
cAMP biosynthetic process -0.24 0.29 -10000 0 -0.53 153 153
MAPK8 -0.028 0.25 -10000 0 -0.68 33 33
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.11 0.22 -10000 0 -0.43 82 82
p130Cas/CRK/Src/PYK2 -0.061 0.24 -10000 0 -0.55 50 50
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.068 0.24 -10000 0 -0.49 62 62
COL1A2 -0.058 0.35 -10000 0 -0.98 35 35
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.08 0.22 -10000 0 -0.43 94 94
mol:DAG -0.048 0.21 -10000 0 -0.51 44 44
MAP2K2 -0.17 0.33 -10000 0 -0.59 120 120
MAP2K1 -0.17 0.33 -10000 0 -0.59 120 120
EDNRA -0.037 0.26 -10000 0 -0.64 53 53
positive regulation of muscle contraction 0.001 0.21 -10000 0 -0.59 25 25
Gq family/GDP -0.13 0.2 -10000 0 -0.51 62 62
HRAS/GTP -0.098 0.24 -10000 0 -0.51 67 67
PRKCH -0.041 0.2 -10000 0 -0.5 42 42
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.043 0.2 -10000 0 -0.5 43 43
PRKCB -0.13 0.26 -10000 0 -0.5 96 96
PRKCE -0.04 0.2 -10000 0 -0.49 42 42
PRKCD -0.042 0.2 -10000 0 -0.49 44 44
PRKCG -0.055 0.2 -10000 0 -0.5 43 43
regulation of vascular smooth muscle contraction -0.33 0.56 -10000 0 -1.1 115 115
PRKCQ -0.071 0.23 -10000 0 -0.51 59 59
PLA2G4A -0.14 0.31 -10000 0 -0.58 89 89
GNA14 -0.069 0.21 -10000 0 -0.58 50 50
GNA15 0.012 0.044 -10000 0 -0.58 2 2
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.013 0.032 -10000 0 -0.58 1 1
Rac1/GTP 0.041 0.26 0.26 122 -0.57 31 153
MMP1 -0.19 0.23 0.33 2 -0.4 175 177
IGF1 pathway

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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL -0.12 0.16 -10000 0 -0.29 162 162
GRB2/SOS1/SHC 0.031 0.017 -10000 0 -0.29 1 1
HRAS 0.016 0 -10000 0 -10000 0 0
IRS1/Crk -0.11 0.16 -10000 0 -0.29 160 160
IGF-1R heterotetramer/IGF1/PTP1B -0.15 0.16 -10000 0 -0.33 160 160
AKT1 -0.074 0.14 -10000 0 -0.46 6 6
BAD -0.062 0.13 -10000 0 -0.42 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.11 0.16 -10000 0 -0.29 160 160
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.16 -10000 0 -0.29 160 160
RAF1 -0.054 0.13 -10000 0 -0.4 6 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.099 0.16 -10000 0 -0.52 6 6
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.18 -10000 0 -0.32 163 163
PIK3CA 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.074 0.14 -10000 0 -0.46 6 6
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.05 0.12 -10000 0 -0.34 6 6
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.12 -10000 0 -0.46 7 7
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.085 0.15 -10000 0 -0.4 7 7
IGF-1R heterotetramer -0.023 0.068 -10000 0 -0.63 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.16 -10000 0 -0.29 160 160
Crk/p130 Cas/Paxillin -0.087 0.15 -10000 0 -0.5 6 6
IGF1R -0.023 0.068 -10000 0 -0.64 3 3
IGF1 -0.25 0.3 -10000 0 -0.59 159 159
IRS2/Crk -0.11 0.18 -10000 0 -0.29 160 160
PI3K -0.098 0.16 -10000 0 -0.26 160 160
apoptosis 0.047 0.12 0.36 6 -10000 0 6
HRAS/GDP 0.012 0 -10000 0 -10000 0 0
PRKCD -0.14 0.21 -10000 0 -0.37 160 160
RAF1/14-3-3 E -0.04 0.12 -10000 0 -0.35 7 7
BAD/14-3-3 -0.05 0.13 -10000 0 -0.38 6 6
PRKCZ -0.076 0.14 -10000 0 -0.47 8 8
Crk/p130 Cas/Paxillin/FAK1 -0.08 0.092 -10000 0 -0.38 6 6
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.16 0.22 -10000 0 -0.4 160 160
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.16 -10000 0 -0.28 162 162
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.11 0.16 -10000 0 -0.29 160 160
GRB10 0.009 0.062 -10000 0 -0.58 4 4
PTPN11 -0.11 0.16 -10000 0 -0.29 160 160
IRS1 -0.13 0.18 -10000 0 -0.32 163 163
IRS2 -0.13 0.18 -10000 0 -0.32 160 160
IGF-1R heterotetramer/IGF1 -0.18 0.23 -10000 0 -0.44 160 160
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 -0.086 0.15 -10000 0 -0.49 6 6
YWHAE 0.014 0.031 -10000 0 -0.58 1 1
PRKD1 -0.15 0.23 -10000 0 -0.4 161 161
SHC1 0.014 0.028 -10000 0 -0.51 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.058 0.19 -10000 0 -0.4 81 81
CRKL -0.062 0.2 -10000 0 -0.42 80 80
HRAS -0.061 0.21 -10000 0 -0.5 37 37
mol:PIP3 -0.072 0.18 -10000 0 -0.4 80 80
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.072 0.2 -10000 0 -0.44 81 81
FOXO3 -0.05 0.18 -10000 0 -0.38 80 80
AKT1 -0.063 0.19 -10000 0 -0.41 80 80
BAD -0.05 0.18 -10000 0 -0.38 80 80
megakaryocyte differentiation -0.077 0.21 -10000 0 -0.43 84 84
GSK3B -0.05 0.18 -10000 0 -0.38 80 80
RAF1 -0.038 0.18 -10000 0 -0.41 31 31
SHC1 0.014 0.028 -10000 0 -0.51 1 1
STAT3 -0.072 0.2 -10000 0 -0.44 81 81
STAT1 -0.2 0.47 -10000 0 -1 87 87
HRAS/SPRED1 -0.04 0.17 -10000 0 -0.41 31 31
cell proliferation -0.072 0.21 -10000 0 -0.44 80 80
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.072 0.2 -10000 0 -0.44 81 81
HRAS/SPRED2 -0.04 0.17 -10000 0 -0.41 31 31
LYN/TEC/p62DOK -0.095 0.17 -10000 0 -0.4 80 80
MAPK3 -0.011 0.13 -10000 0 -0.29 24 24
STAP1 -0.091 0.22 -10000 0 -0.46 82 82
GRAP2 -0.057 0.19 -10000 0 -0.58 44 44
JAK2 -0.2 0.37 -10000 0 -0.84 87 87
STAT1 (dimer) -0.19 0.46 -10000 0 -0.98 87 87
mol:Gleevec 0.001 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.11 0.18 -10000 0 -0.42 83 83
actin filament polymerization -0.074 0.2 -10000 0 -0.43 82 82
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.29 -10000 0 -0.62 82 82
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.04 0.18 -10000 0 -0.37 80 80
PI3K -0.054 0.2 -10000 0 -0.41 80 80
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.25 0.57 -10000 0 -1.3 82 82
MAPK8 -0.074 0.21 -10000 0 -0.45 80 80
STAT3 (dimer) -0.07 0.2 -10000 0 -0.43 81 81
positive regulation of transcription -0.004 0.11 -10000 0 -0.24 19 19
mol:GDP -0.11 0.2 -10000 0 -0.41 90 90
PIK3C2B -0.072 0.2 -10000 0 -0.44 81 81
CBL/CRKL -0.049 0.19 -10000 0 -0.38 80 80
FER -0.074 0.21 -10000 0 -0.44 81 81
SH2B3 -0.072 0.2 -10000 0 -0.44 81 81
PDPK1 -0.059 0.17 -10000 0 -0.36 80 80
SNAI2 -0.078 0.21 -10000 0 -0.45 81 81
positive regulation of cell proliferation -0.13 0.34 -10000 0 -0.72 87 87
KITLG 0.009 0.065 -10000 0 -0.6 4 4
cell motility -0.13 0.34 -10000 0 -0.72 87 87
PTPN6 0.016 0.03 -10000 0 -0.52 1 1
EPOR -0.023 0.15 -10000 0 -0.56 2 2
STAT5A (dimer) -0.1 0.29 -10000 0 -0.6 87 87
SOCS1 0.014 0.028 -10000 0 -0.51 1 1
cell migration 0.093 0.22 0.46 85 -10000 0 85
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.033 0.14 -10000 0 -0.51 30 30
VAV1 -0.014 0.13 -10000 0 -0.57 18 18
GRB10 -0.075 0.21 -10000 0 -0.45 81 81
PTPN11 0.017 0.008 -10000 0 -10000 0 0
SCF/KIT -0.085 0.22 -10000 0 -0.46 84 84
GO:0007205 0.003 0.011 -10000 0 -10000 0 0
MAP2K1 -0.018 0.14 -10000 0 -0.31 29 29
CBL 0.016 0 -10000 0 -10000 0 0
KIT -0.26 0.59 -10000 0 -1.4 80 80
MAP2K2 -0.018 0.14 -10000 0 -0.32 24 24
SHC/Grb2/SOS1 -0.095 0.17 -10000 0 -0.4 80 80
STAT5A -0.11 0.3 -10000 0 -0.62 87 87
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation -0.076 0.21 -10000 0 -0.44 81 81
SHC/GRAP2 -0.032 0.14 -10000 0 -0.41 45 45
PTPRO -0.079 0.21 -10000 0 -0.44 84 84
SH2B2 -0.076 0.21 -10000 0 -0.44 82 82
DOK1 0.014 0.028 -10000 0 -0.51 1 1
MATK -0.096 0.22 -10000 0 -0.47 85 85
CREBBP 0.034 0.02 -10000 0 -10000 0 0
BCL2 -0.061 0.31 -10000 0 -1.4 14 14
Reelin signaling pathway

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
CDK5R1/CDK5 0.002 0.087 -9999 0 -0.36 20 20
VLDLR -0.001 0.098 -9999 0 -0.58 10 10
CRKL 0.013 0.039 -9999 0 -0.51 2 2
LRPAP1 0.014 0.028 -9999 0 -0.51 1 1
FYN 0.011 0.054 -9999 0 -0.58 3 3
ITGA3 0.008 0.061 -9999 0 -0.51 5 5
RELN/VLDLR/Fyn -0.12 0.19 -9999 0 -0.35 141 141
MAPK8IP1/MKK7/MAP3K11/JNK1 0.04 0.044 -9999 0 -10000 0 0
AKT1 -0.095 0.16 -9999 0 -0.44 24 24
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.07 0.2 -9999 0 -0.55 51 51
RELN/LRP8/DAB1 -0.2 0.23 -9999 0 -0.38 192 192
LRPAP1/LRP8 -0.048 0.15 -9999 0 -0.36 67 67
RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.39 153 153
DAB1/alpha3/beta1 Integrin -0.18 0.19 -9999 0 -0.52 63 63
long-term memory -0.23 0.27 -9999 0 -0.61 91 91
DAB1/LIS1 -0.18 0.2 -9999 0 -0.53 60 60
DAB1/CRLK/C3G -0.18 0.19 -9999 0 -0.51 61 61
PIK3CA 0.016 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.18 0.2 -9999 0 -0.54 60 60
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.12 0.24 -9999 0 -0.57 77 77
CDK5R1 -0.014 0.12 -9999 0 -0.51 20 20
RELN -0.2 0.28 -9999 0 -0.57 131 131
PIK3R1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.17 0.22 -9999 0 -0.38 169 169
GRIN2A/RELN/LRP8/DAB1/Fyn -0.24 0.27 -9999 0 -0.64 87 87
MAPK8 0.011 0.054 -9999 0 -0.58 3 3
RELN/VLDLR/DAB1 -0.15 0.2 -9999 0 -0.35 168 168
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.21 0.24 -9999 0 -0.43 160 160
RELN/LRP8 -0.16 0.22 -9999 0 -0.4 141 141
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.58 55 55
PI3K 0.023 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.044 -9999 0 -0.36 5 5
RAP1A -0.14 0.2 -9999 0 -0.48 61 61
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.061 -9999 0 -0.56 4 4
CRLK/C3G 0.021 0.028 -9999 0 -0.36 2 2
GRIN2B -0.01 0.089 -9999 0 -0.51 11 11
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.079 0.14 -9999 0 -0.32 53 53
neuron adhesion -0.12 0.2 -9999 0 -0.45 64 64
LRP8 -0.081 0.2 -9999 0 -0.51 66 66
GSK3B -0.082 0.15 -9999 0 -0.41 24 24
RELN/VLDLR/DAB1/Fyn -0.14 0.19 -9999 0 -0.34 156 156
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.11 0.16 -9999 0 -0.29 153 153
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT -0.023 0.16 -9999 0 -0.52 32 32
neuron migration -0.14 0.21 -9999 0 -0.46 64 64
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.08 0.14 -9999 0 -0.32 53 53
RELN/VLDLR -0.15 0.21 -9999 0 -0.56 38 38
TCGA08_p53

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
CDKN2A -0.17 0.19 -10000 0 -0.37 174 174
TP53 -0.041 0.061 -10000 0 -10000 0 0
Senescence -0.041 0.06 -10000 0 -10000 0 0
Apoptosis -0.041 0.06 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.078 0.12 0.19 168 -0.33 12 180
MDM4 0.016 0 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.017 0.13 -10000 0 -0.55 20 20
GNB1/GNG2 -0.079 0.09 -10000 0 -0.18 145 145
AKT1 -0.042 0.13 -10000 0 -0.2 75 75
EGF -0.018 0.12 -10000 0 -0.51 22 22
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.036 0.057 -10000 0 -0.37 1 1
mol:Ca2+ -0.085 0.18 -10000 0 -0.3 143 143
LYN 0.036 0.056 -10000 0 -0.37 1 1
RhoA/GTP -0.051 0.059 -10000 0 -0.14 20 20
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.097 0.21 -10000 0 -0.34 143 143
GNG2 0.006 0.076 -10000 0 -0.58 6 6
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.015 0.071 -10000 0 -0.36 4 4
G beta5/gamma2 -0.1 0.12 -10000 0 -0.24 145 145
PRKCH -0.099 0.21 -10000 0 -0.34 143 143
DNM1 0.001 0.093 -10000 0 -0.58 9 9
TXA2/TP beta/beta Arrestin3 -0.008 0.039 -10000 0 -0.24 9 9
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.016 0.13 -10000 0 -0.58 18 18
G12 family/GTP -0.13 0.14 -10000 0 -0.3 143 143
ADRBK1 0.015 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.042 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.012 0.011 -10000 0 -10000 0 0
mol:GDP 0.037 0.12 0.31 13 -10000 0 13
mol:NADP 0.014 0.028 -10000 0 -0.51 1 1
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.12 0.25 -10000 0 -0.58 82 82
mol:IP3 -0.11 0.22 -10000 0 -0.38 143 143
cell morphogenesis 0.01 0.011 -10000 0 -10000 0 0
PLCB2 -0.16 0.3 -10000 0 -0.51 143 143
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0 0.097 -10000 0 -0.4 3 3
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.085 -10000 0 -0.4 6 6
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.014 0.031 -10000 0 -0.58 1 1
PRKCB1 -0.11 0.22 -10000 0 -0.37 143 143
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.014 0.028 -10000 0 -0.51 1 1
TXA2/TXA2-R family -0.17 0.3 -10000 0 -0.53 143 143
LCK 0.032 0.066 -10000 0 -0.4 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.049 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.032 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.012 0.048 -10000 0 -10000 0 0
MAPK14 -0.052 0.15 -10000 0 -0.22 143 143
TGM2/GTP -0.13 0.26 -10000 0 -0.43 143 143
MAPK11 -0.052 0.15 -10000 0 -0.22 143 143
ARHGEF1 -0.04 0.11 -10000 0 -0.18 100 100
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade -0.12 0.23 -10000 0 -0.39 143 143
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.077 0.17 -10000 0 -0.28 145 145
cAMP biosynthetic process -0.11 0.21 -10000 0 -0.36 143 143
Gq family/GTP/EBP50 -0.005 0.087 -10000 0 -0.28 11 11
actin cytoskeleton reorganization 0.01 0.011 -10000 0 -10000 0 0
SRC 0.036 0.056 -10000 0 -0.37 1 1
GNB5 0.015 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR 0.035 0.075 -10000 0 -0.31 2 2
VCAM1 -0.088 0.19 -10000 0 -0.31 143 143
TP beta/Gq family/GDP/G beta5/gamma2 0.015 0.071 -10000 0 -0.36 4 4
platelet activation -0.072 0.2 -10000 0 -0.3 143 143
PGI2/IP 0.009 0.023 -10000 0 -0.42 1 1
PRKACA 0.008 0.067 -10000 0 -0.27 19 19
Gq family/GDP/G beta5/gamma2 0.013 0.072 -10000 0 -0.33 4 4
TXA2/TP beta/beta Arrestin2 -0.015 0.085 -10000 0 -0.54 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.015 0.066 -10000 0 -0.25 21 21
mol:DAG -0.13 0.25 -10000 0 -0.42 143 143
EGFR -0.008 0.11 -10000 0 -0.54 15 15
TXA2/TP alpha -0.15 0.28 -10000 0 -0.48 143 143
Gq family/GTP -0.032 0.083 -10000 0 -0.23 53 53
YES1 0.036 0.056 -10000 0 -0.37 1 1
GNAI2/GTP -0.012 0.05 -10000 0 -0.43 1 1
PGD2/DP -0.013 0.095 -10000 0 -0.42 18 18
SLC9A3R1 -0.012 0.12 -10000 0 -0.51 19 19
FYN 0.034 0.063 -10000 0 -0.4 2 2
mol:NO 0.014 0.028 -10000 0 -0.51 1 1
GNA15 0.012 0.044 -10000 0 -0.58 2 2
PGK/cGMP -0.067 0.16 -10000 0 -0.35 83 83
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.018 0.11 -10000 0 -0.55 6 6
NOS3 0.014 0.028 -10000 0 -0.51 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.1 0.21 -10000 0 -0.34 143 143
PRKCB -0.15 0.24 -10000 0 -0.42 147 147
PRKCE -0.095 0.21 -10000 0 -0.34 143 143
PRKCD -0.11 0.23 -10000 0 -0.38 143 143
PRKCG -0.12 0.23 -10000 0 -0.39 143 143
muscle contraction -0.16 0.29 -10000 0 -0.49 143 143
PRKCZ -0.097 0.21 -10000 0 -0.34 143 143
ARR3 0.003 0.006 -10000 0 -10000 0 0
TXA2/TP beta 0.011 0.066 -10000 0 -0.49 1 1
PRKCQ -0.11 0.22 -10000 0 -0.37 144 144
MAPKKK cascade -0.15 0.27 -10000 0 -0.46 143 143
SELE -0.13 0.24 -10000 0 -0.41 145 145
TP beta/GNAI2/GDP/G beta/gamma 0.033 0.071 -10000 0 -0.48 1 1
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.067 0.2 -10000 0 -0.58 50 50
chemotaxis -0.2 0.35 -10000 0 -0.62 143 143
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.031 -10000 0 -0.58 1 1
Rac1/GTP 0.007 0.006 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.014 0.028 -9999 0 -0.51 1 1
Aurora C/Aurora B/INCENP -0.11 0.15 -9999 0 -0.27 169 169
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.035 0.037 -9999 0 -10000 0 0
AURKB -0.22 0.26 -9999 0 -0.51 161 161
AURKC -0.001 0.09 -9999 0 -0.51 11 11
TCGA08_retinoblastoma

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
CDKN2B -0.034 0.16 -10000 0 -0.54 32 32
CDKN2C 0.039 0.039 -10000 0 -0.45 1 1
CDKN2A -0.25 0.27 -10000 0 -0.52 174 174
CCND2 0.053 0.081 0.23 33 -0.15 9 42
RB1 -0.051 0.088 0.16 2 -0.24 32 34
CDK4 0.068 0.082 0.24 34 -10000 0 34
CDK6 0.059 0.089 0.25 32 -0.19 7 39
G1/S progression 0.051 0.088 0.24 32 -0.16 2 34
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.014 0.031 -9999 0 -0.58 1 1
LAT2 -0.1 0.19 -9999 0 -0.35 110 110
AP1 -0.2 0.22 -9999 0 -0.52 96 96
mol:PIP3 -0.12 0.24 -9999 0 -0.5 69 69
IKBKB -0.077 0.15 -9999 0 -0.29 94 94
AKT1 -0.078 0.18 -9999 0 -0.43 50 50
IKBKG -0.077 0.15 -9999 0 -0.29 92 92
MS4A2 -0.15 0.26 -9999 0 -0.58 99 99
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.001 -9999 0 -10000 0 0
MAP3K1 -0.073 0.19 -9999 0 -0.41 61 61
mol:Ca2+ -0.084 0.18 -9999 0 -0.37 69 69
LYN 0.013 0.006 -9999 0 -10000 0 0
CBLB -0.098 0.19 -9999 0 -0.34 107 107
SHC1 0.014 0.028 -9999 0 -0.51 1 1
RasGAP/p62DOK -0.069 0.16 -9999 0 -0.32 102 102
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.004 0.082 -9999 0 -0.58 7 7
PLD2 -0.12 0.21 -9999 0 -0.4 98 98
PTPN13 -0.098 0.2 -9999 0 -0.48 52 52
PTPN11 0.012 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.048 0.16 -9999 0 -0.34 47 47
SYK 0.01 0.046 -9999 0 -0.6 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.16 0.21 -9999 0 -0.53 67 67
LAT -0.099 0.19 -9999 0 -0.44 58 58
PAK2 -0.09 0.21 -9999 0 -0.46 61 61
NFATC2 -0.16 0.26 -9999 0 -0.7 63 63
HRAS -0.11 0.23 -9999 0 -0.5 63 63
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.042 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.19 0.24 -9999 0 -0.43 158 158
Antigen/IgE/Fc epsilon R1 -0.17 0.22 -9999 0 -0.4 158 158
mol:GDP -0.12 0.24 -9999 0 -0.54 64 64
JUN -0.006 0.11 -9999 0 -0.58 13 13
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
FOS -0.17 0.27 -9999 0 -0.58 110 110
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.2 -9999 0 -0.37 107 107
CHUK -0.077 0.15 -9999 0 -0.29 93 93
KLRG1 -0.096 0.18 -9999 0 -0.42 57 57
VAV1 -0.11 0.21 -9999 0 -0.47 64 64
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.098 0.19 -9999 0 -0.44 56 56
negative regulation of mast cell degranulation -0.087 0.18 -9999 0 -0.42 56 56
BTK -0.13 0.26 -9999 0 -0.59 62 62
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.16 0.27 -9999 0 -0.48 109 109
GAB2/PI3K/SHP2 -0.13 0.17 -9999 0 -0.48 50 50
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.22 -9999 0 -0.52 61 61
RAF1 0.03 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.24 -9999 0 -0.59 69 69
FCER1G -0.005 0.11 -9999 0 -0.53 16 16
FCER1A -0.14 0.26 -9999 0 -0.59 92 92
Antigen/IgE/Fc epsilon R1/Fyn -0.16 0.21 -9999 0 -0.37 153 153
MAPK3 0.04 0.023 -9999 0 -10000 0 0
MAPK1 0.04 0.023 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.011 0.083 -9999 0 -0.59 3 3
DUSP1 -0.15 0.27 -9999 0 -0.58 102 102
NF-kappa-B/RelA -0.062 0.071 -9999 0 -0.22 11 11
actin cytoskeleton reorganization -0.1 0.2 -9999 0 -0.48 48 48
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.13 0.18 -9999 0 -0.46 58 58
FER -0.1 0.19 -9999 0 -0.45 57 57
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.085 0.17 -9999 0 -0.52 43 43
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.12 0.24 -9999 0 -0.54 64 64
cytokine secretion -0.045 0.051 -9999 0 -10000 0 0
SPHK1 -0.13 0.2 -9999 0 -0.46 71 71
PTK2 -0.11 0.2 -9999 0 -0.5 48 48
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.17 0.22 -9999 0 -0.55 68 68
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.11 0.23 -9999 0 -0.5 67 67
MAP2K2 0.036 0.024 -9999 0 -10000 0 0
MAP2K1 0.036 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.4 53 53
MAP2K4 0.019 0.012 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.2 0.24 -9999 0 -0.42 161 161
mol:Choline -0.12 0.21 -9999 0 -0.4 98 98
SHC/Grb2/SOS1 -0.11 0.16 -9999 0 -0.44 48 48
FYN 0.011 0.054 -9999 0 -0.58 3 3
DOK1 0.014 0.028 -9999 0 -0.51 1 1
PXN -0.092 0.19 -9999 0 -0.46 47 47
HCLS1 -0.1 0.19 -9999 0 -0.45 57 57
PRKCB -0.12 0.21 -9999 0 -0.4 102 102
FCGR2B -0.032 0.16 -9999 0 -0.57 29 29
IGHE -0.003 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.088 0.18 -9999 0 -0.43 56 56
LCP2 0.012 0.044 -9999 0 -0.58 2 2
PLA2G4A -0.12 0.21 -9999 0 -0.44 77 77
RASA1 0.016 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.12 0.21 -9999 0 -0.4 98 98
IKK complex -0.043 0.12 -9999 0 -0.22 56 56
WIPF1 -0.003 0.1 -9999 0 -0.58 11 11
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.023 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.12 0.21 -10000 0 -0.41 113 113
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.074 0.19 -10000 0 -0.6 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.24 -10000 0 -0.42 133 133
NT-4/5 (dimer)/p75(NTR) -0.11 0.22 -10000 0 -0.45 99 99
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.071 0.18 -10000 0 -0.57 18 18
IKBKG 0.016 0 -10000 0 -10000 0 0
BDNF -0.099 0.23 -10000 0 -0.58 69 69
MGDIs/NGR/p75(NTR)/LINGO1 -0.12 0.2 -10000 0 -0.36 135 135
FURIN 0.014 0.028 -10000 0 -0.51 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.13 0.22 -10000 0 -0.39 133 133
LINGO1 -0.008 0.11 -10000 0 -0.51 16 16
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.099 0.23 -10000 0 -0.57 69 69
NTRK1 0.006 0.061 -10000 0 -0.51 5 5
RTN4R -0.061 0.18 -10000 0 -0.51 52 52
neuron apoptosis -0.12 0.22 -10000 0 -0.52 54 54
IRAK1 0.016 0 -10000 0 -10000 0 0
SHC1 -0.1 0.21 -10000 0 -0.4 113 113
ARHGDIA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP 0.012 0 -10000 0 -10000 0 0
Gamma Secretase 0.046 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.086 0.2 -10000 0 -0.36 109 109
MAGEH1 0.012 0.044 -10000 0 -0.58 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.12 0.24 -10000 0 -0.41 129 129
Mammalian IAPs/DIABLO 0.014 0.095 -10000 0 -0.33 22 22
proNGF (dimer) -0.063 0.2 -10000 0 -0.57 47 47
MAGED1 0.016 0 -10000 0 -10000 0 0
APP 0.012 0.044 -10000 0 -0.58 2 2
NT-4/5 (dimer) -0.026 0.15 -10000 0 -0.57 25 25
ZNF274 0.016 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.079 0.18 -10000 0 -0.33 109 109
NGF -0.063 0.2 -10000 0 -0.58 47 47
cell cycle arrest -0.085 0.17 -10000 0 -0.45 29 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.058 0.16 -10000 0 -0.43 25 25
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.081 0.19 -10000 0 -0.38 99 99
NCSTN 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.1 0.21 -10000 0 -0.39 115 115
PSENEN 0.016 0 -10000 0 -10000 0 0
mol:ceramide -0.084 0.19 -10000 0 -0.35 109 109
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.038 0.14 -10000 0 -0.42 19 19
p75(NTR)/beta APP -0.081 0.19 -10000 0 -0.42 85 85
BEX1 -0.045 0.17 -10000 0 -0.56 36 36
mol:GDP -0.11 0.21 -10000 0 -0.4 113 113
NGF (dimer) -0.09 0.17 -10000 0 -0.31 127 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.095 0.18 -10000 0 -0.35 86 86
PIK3R1 0.016 0 -10000 0 -10000 0 0
RAC1/GTP -0.089 0.18 -10000 0 -0.34 113 113
MYD88 0.016 0 -10000 0 -10000 0 0
CHUK 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.21 -10000 0 -0.39 115 115
RHOB 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.063 0.16 -10000 0 -0.36 81 81
NT3 (dimer) -0.092 0.23 -10000 0 -0.57 65 65
TP53 -0.078 0.18 -10000 0 -0.55 20 20
PRDM4 -0.085 0.19 -10000 0 -0.35 109 109
BDNF (dimer) -0.17 0.23 -10000 0 -0.37 171 171
PIK3CA 0.016 0 -10000 0 -10000 0 0
SORT1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.17 -10000 0 -0.59 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.084 0.19 -10000 0 -0.36 109 109
RHOC 0.016 0 -10000 0 -10000 0 0
XIAP 0.012 0.042 -10000 0 -0.54 2 2
MAPK10 -0.1 0.22 -10000 0 -0.53 50 50
DIABLO 0.016 0 -10000 0 -10000 0 0
SMPD2 -0.085 0.19 -10000 0 -0.35 109 109
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.21 -10000 0 -0.39 113 113
PSEN1 0.016 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.25 -10000 0 -0.47 128 128
MAPK8 -0.085 0.21 -10000 0 -0.52 41 41
MAPK9 -0.083 0.21 -10000 0 -0.52 41 41
APAF1 0.016 0 -10000 0 -10000 0 0
NTF3 -0.093 0.23 -10000 0 -0.57 65 65
NTF4 -0.026 0.15 -10000 0 -0.58 25 25
NDN -0.059 0.2 -10000 0 -0.58 45 45
RAC1/GDP 0.012 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.095 0.15 -10000 0 -0.54 18 18
p75 CTF/Sortilin/TRAF6/NRIF 0.04 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.12 0.2 -10000 0 -0.39 115 115
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.091 0.19 -10000 0 -0.58 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.2 -10000 0 -0.35 129 129
PRKACB 0.012 0.044 -10000 0 -0.58 2 2
proBDNF (dimer)/p75 ECD -0.061 0.17 -10000 0 -0.41 69 69
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.024 0.15 -10000 0 -0.57 24 24
BIRC2 0.013 0.039 -10000 0 -0.51 2 2
neuron projection morphogenesis -0.12 0.21 0.2 13 -0.4 101 114
BAD -0.086 0.21 -10000 0 -0.5 47 47
RIPK2 0.016 0 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.57 84 84
CYCS -0.071 0.18 -10000 0 -0.57 18 18
ADAM17 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.084 0.19 -10000 0 -0.36 109 109
BCL2L11 -0.086 0.21 -10000 0 -0.5 47 47
BDNF (dimer)/p75(NTR) -0.16 0.25 -10000 0 -0.46 133 133
PI3K -0.084 0.19 -10000 0 -0.36 109 109
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.084 0.19 -10000 0 -0.36 109 109
NDNL2 0.016 0 -10000 0 -10000 0 0
YWHAE 0.014 0.031 -10000 0 -0.58 1 1
PRKCI 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.13 0.24 -10000 0 -0.47 113 113
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.084 0.19 -10000 0 -0.36 109 109
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.044 -10000 0 -0.58 2 2
PLG -0.003 0.06 -10000 0 -0.51 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.14 0.25 -10000 0 -0.48 91 91
SQSTM1 0.016 0 -10000 0 -10000 0 0
NGFRAP1 0.012 0.044 -10000 0 -0.58 2 2
CASP3 -0.077 0.2 -10000 0 -0.45 47 47
E2F1 -0.1 0.22 -10000 0 -0.51 81 81
CASP9 0.016 0 -10000 0 -10000 0 0
IKK complex -0.076 0.13 -10000 0 -0.49 19 19
NGF (dimer)/TRKA -0.042 0.15 -10000 0 -0.41 52 52
MMP7 -0.11 0.23 -10000 0 -0.52 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.071 0.18 -10000 0 -0.58 18 18
MMP3 -0.1 0.23 -10000 0 -0.55 74 74
APAF-1/Caspase 9 -0.085 0.13 -10000 0 -0.44 28 28
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.051 0.066 0.13 152 -10000 0 152
BUB1B -0.078 0.12 -10000 0 -0.23 114 114
PLK1 -0.019 0.05 -10000 0 -0.11 64 64
PLK1S1 -0.003 0.026 -10000 0 -10000 0 0
KIF2A -0.008 0.045 -10000 0 -0.18 1 1
regulation of mitotic centrosome separation -0.019 0.05 -10000 0 -0.11 64 64
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.24 -10000 0 -0.41 165 165
WEE1 -0.016 0.054 -10000 0 -10000 0 0
cytokinesis -0.14 0.11 -10000 0 -0.24 126 126
PP2A-alpha B56 0.018 0.038 -10000 0 -10000 0 0
AURKA -0.018 0.047 -10000 0 -0.13 2 2
PICH/PLK1 -0.11 0.19 -10000 0 -0.37 97 97
CENPE -0.068 0.14 -10000 0 -0.33 77 77
RhoA/GTP 0.012 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.045 -10000 0 -0.18 1 1
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.016 0 -10000 0 -10000 0 0
TPX2 -0.037 0.051 -10000 0 -0.1 79 79
PAK1 0.013 0.032 -10000 0 -0.59 1 1
SPC24 -0.17 0.25 -10000 0 -0.51 126 126
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.033 0.057 -10000 0 -0.13 54 54
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.002 0.004 -10000 0 -0.011 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.009 0.026 -10000 0 -0.054 64 64
G2 phase of mitotic cell cycle -0.002 0.003 -10000 0 -0.009 1 1
STAG2 0.012 0.044 -10000 0 -0.58 2 2
GRASP65/GM130/RAB1/GTP 0.006 0.011 -10000 0 -10000 0 0
spindle elongation -0.019 0.05 -10000 0 -0.11 64 64
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.015 0.034 -10000 0 -10000 0 0
TPT1 -0.003 0.026 -10000 0 -0.097 1 1
CDC25C -0.056 0.059 -10000 0 -10000 0 0
CDC25B 0.005 0.068 -10000 0 -0.51 6 6
SGOL1 -0.051 0.066 -10000 0 -0.13 152 152
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.074 0.11 -10000 0 -0.26 42 42
CDC14B 0.011 0.024 -10000 0 -0.43 1 1
CDC20 -0.28 0.26 -10000 0 -0.51 204 204
PLK1/PBIP1 -0.03 0.057 -10000 0 -0.28 12 12
mitosis -0.001 0.01 0.021 21 -0.019 7 28
FBXO5 -0.011 0.047 -10000 0 -0.23 3 3
CDC2 -0.003 0.005 -10000 0 -0.012 44 44
NDC80 -0.15 0.24 -10000 0 -0.51 115 115
metaphase plate congression -0.008 0.032 -10000 0 -10000 0 0
ERCC6L -0.093 0.17 -10000 0 -0.44 49 49
NLP/gamma Tubulin -0.005 0.027 -10000 0 -0.097 2 2
microtubule cytoskeleton organization -0.003 0.026 -10000 0 -0.097 1 1
G2/M transition DNA damage checkpoint -0.001 0.002 -10000 0 -10000 0 0
PPP1R12A 0.015 0.001 -10000 0 -10000 0 0
interphase -0.001 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.25 0.2 -10000 0 -0.34 268 268
GRASP65/GM130/RAB1/GTP/PLK1 -0.009 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.013 0.048 -10000 0 -0.22 2 2
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.051 -10000 0 -0.3 1 1
microtubule-based process -0.22 0.15 -10000 0 -0.3 266 266
Golgi organization -0.019 0.05 -10000 0 -0.11 64 64
Cohesin/SA2 -0.025 0.039 -10000 0 -0.25 3 3
PPP1CB/MYPT1 0.017 0.009 -10000 0 -10000 0 0
KIF20A -0.37 0.23 -10000 0 -0.51 266 266
APC/C/CDC20 -0.17 0.17 -10000 0 -0.31 204 204
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.03 0.057 -10000 0 -0.28 12 12
PRC1 -0.084 0.2 -10000 0 -0.51 68 68
ECT2 -0.037 0.11 -10000 0 -0.34 38 38
C13orf34 -0.01 0.045 -10000 0 -0.22 2 2
NUDC -0.008 0.032 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.077 0.12 -10000 0 -0.23 114 114
spindle assembly -0.011 0.04 -10000 0 -0.099 8 8
spindle stabilization -0.003 0.026 -10000 0 -10000 0 0
APC/C/HCDH1 0.019 0.02 -10000 0 -0.36 1 1
MKLP2/PLK1 -0.22 0.15 -10000 0 -0.3 266 266
CCNB1 -0.16 0.25 -10000 0 -0.5 123 123
PPP1CB 0.015 0.001 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 -0.008 0.069 -10000 0 -0.43 7 7
TUBG1 -0.003 0.026 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.075 0.1 -10000 0 -0.26 34 34
MLF1IP -0.003 0.067 -10000 0 -0.38 11 11
INCENP 0.014 0.028 -10000 0 -0.51 1 1
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.34 0.54 -10000 0 -1.2 74 74
IL23A -0.29 0.46 -10000 0 -1.1 60 60
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.4 -10000 0 -1 73 73
positive regulation of T cell mediated cytotoxicity -0.32 0.5 -10000 0 -1.1 74 74
ITGA3 -0.28 0.44 -10000 0 -1 65 65
IL17F -0.18 0.31 -10000 0 -0.67 65 65
IL12B -0.012 0.095 -10000 0 -0.51 11 11
STAT1 (dimer) -0.31 0.48 -10000 0 -1.1 72 72
CD4 -0.28 0.44 -10000 0 -1 65 65
IL23 -0.29 0.44 -10000 0 -1.1 62 62
IL23R -0.03 0.089 -10000 0 -10000 0 0
IL1B -0.31 0.49 -10000 0 -1.1 66 66
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.3 0.44 -10000 0 -1 68 68
TYK2 0.008 0.021 -10000 0 -10000 0 0
STAT4 -0.016 0.13 -10000 0 -0.58 19 19
STAT3 0.016 0 -10000 0 -10000 0 0
IL18RAP -0.018 0.13 -10000 0 -0.57 19 19
IL12RB1 -0.029 0.14 -10000 0 -0.55 24 24
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.02 0.11 -10000 0 -0.4 24 24
IL23R/JAK2 -0.035 0.11 -10000 0 -0.47 1 1
positive regulation of chronic inflammatory response -0.32 0.5 -10000 0 -1.1 74 74
natural killer cell activation 0.003 0.008 -10000 0 -10000 0 0
JAK2 0.012 0.041 -10000 0 -0.61 1 1
PIK3R1 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.004 -10000 0 -10000 0 0
RELA 0.014 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.28 0.42 -10000 0 -0.99 63 63
ALOX12B -0.29 0.44 -10000 0 -1 62 62
CXCL1 -0.34 0.52 -10000 0 -1.2 77 77
T cell proliferation -0.32 0.5 -10000 0 -1.1 74 74
NFKBIA 0.014 0.004 -10000 0 -10000 0 0
IL17A -0.12 0.25 -10000 0 -0.54 51 51
PI3K -0.32 0.42 -10000 0 -1 74 74
IFNG -0.017 0.035 0.1 1 -0.097 2 3
STAT3 (dimer) -0.31 0.38 -10000 0 -0.98 70 70
IL18R1 0.009 0.054 -10000 0 -0.57 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.31 -10000 0 -0.73 53 53
IL18/IL18R 0.002 0.11 -10000 0 -0.38 24 24
macrophage activation -0.018 0.017 -10000 0 -0.043 67 67
TNF -0.29 0.46 -10000 0 -1.1 68 68
STAT3/STAT4 -0.34 0.43 -10000 0 -1 75 75
STAT4 (dimer) -0.32 0.49 -10000 0 -1.1 74 74
IL18 0.006 0.069 -10000 0 -0.57 5 5
IL19 -0.29 0.44 -10000 0 -1 69 69
STAT5A (dimer) -0.3 0.48 -10000 0 -1.1 74 74
STAT1 0.01 0.055 -10000 0 -0.51 4 4
SOCS3 -0.047 0.18 -10000 0 -0.58 38 38
CXCL9 -0.33 0.46 -10000 0 -1.1 70 70
MPO -0.27 0.43 -10000 0 -1 65 65
positive regulation of humoral immune response -0.32 0.5 -10000 0 -1.1 74 74
IL23/IL23R/JAK2/TYK2 -0.34 0.54 -10000 0 -1.2 74 74
IL6 -0.62 0.68 -10000 0 -1.3 174 174
STAT5A 0.014 0.031 -10000 0 -0.58 1 1
IL2 0.005 0.013 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.008 -10000 0 -10000 0 0
CD3E -0.33 0.53 -10000 0 -1.2 73 73
keratinocyte proliferation -0.32 0.5 -10000 0 -1.1 74 74
NOS2 -0.3 0.46 -10000 0 -1 70 70
Ephrin A reverse signaling

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
MAPKKK cascade -0.046 0.14 -9999 0 -0.36 58 58
EFNA5 -0.003 0.1 -9999 0 -0.58 11 11
FYN -0.034 0.13 -9999 0 -0.32 61 61
neuron projection morphogenesis -0.046 0.14 -9999 0 -0.36 58 58
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.046 0.14 -9999 0 -0.36 58 58
EPHA5 -0.072 0.2 -9999 0 -0.57 49 49
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.44 -9999 0 -0.94 53 53
HDAC7 0.018 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.13 0.36 -9999 0 -0.78 46 46
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.2 0.44 -9999 0 -0.94 58 58
AP1 -0.12 0.23 -9999 0 -0.45 111 111
ABCG2 -0.21 0.45 -9999 0 -0.96 56 56
HIF1A -0.015 0.083 -9999 0 -0.65 1 1
TFF3 -0.28 0.5 -9999 0 -1 80 80
GATA2 -0.005 0.11 -9999 0 -0.53 15 15
AKT1 -0.015 0.091 -9999 0 -10000 0 0
response to hypoxia -0.039 0.096 -9999 0 -0.23 15 15
MCL1 -0.2 0.44 -9999 0 -0.93 56 56
NDRG1 -0.2 0.44 -9999 0 -0.95 54 54
SERPINE1 -0.2 0.45 -9999 0 -0.96 54 54
FECH -0.2 0.44 -9999 0 -0.94 54 54
FURIN -0.2 0.44 -9999 0 -0.93 56 56
NCOA2 -0.022 0.14 -9999 0 -0.57 23 23
EP300 -0.007 0.14 -9999 0 -0.33 23 23
HMOX1 -0.2 0.44 -9999 0 -0.93 56 56
BHLHE40 -0.2 0.44 -9999 0 -0.94 57 57
BHLHE41 -0.2 0.45 -9999 0 -0.96 56 56
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.001 0.081 -9999 0 -0.41 1 1
ENG 0.033 0.098 -9999 0 -10000 0 0
JUN -0.005 0.11 -9999 0 -0.57 13 13
RORA -0.2 0.45 -9999 0 -0.94 57 57
ABCB1 -0.19 0.39 -9999 0 -1.2 44 44
TFRC -0.2 0.45 -9999 0 -0.94 57 57
CXCR4 -0.2 0.45 -9999 0 -0.96 54 54
TF -0.23 0.46 -9999 0 -0.95 67 67
CITED2 -0.2 0.44 -9999 0 -0.94 54 54
HIF1A/ARNT -0.2 0.52 -9999 0 -1 67 67
LDHA -0.024 0.044 -9999 0 -10000 0 0
ETS1 -0.2 0.44 -9999 0 -0.94 54 54
PGK1 -0.2 0.44 -9999 0 -0.93 56 56
NOS2 -0.22 0.46 -9999 0 -0.98 61 61
ITGB2 -0.21 0.45 -9999 0 -0.95 58 58
ALDOA -0.2 0.44 -9999 0 -0.94 53 53
Cbp/p300/CITED2 -0.18 0.46 -9999 0 -1 48 48
FOS -0.17 0.27 -9999 0 -0.57 110 110
HK2 -0.2 0.44 -9999 0 -0.94 56 56
SP1 0.017 0.029 -9999 0 -10000 0 0
GCK -0.086 0.4 -9999 0 -1.5 24 24
HK1 -0.2 0.44 -9999 0 -0.94 54 54
NPM1 -0.2 0.44 -9999 0 -0.93 56 56
EGLN1 -0.2 0.44 -9999 0 -0.94 53 53
CREB1 0.025 0 -9999 0 -10000 0 0
PGM1 -0.2 0.44 -9999 0 -0.94 54 54
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.054 0.22 -9999 0 -0.76 10 10
IGFBP1 -0.22 0.45 -9999 0 -0.94 62 62
VEGFA -0.086 0.34 -9999 0 -0.74 26 26
HIF1A/JAB1 -0.007 0.043 -9999 0 -0.48 1 1
CP -0.29 0.5 -9999 0 -0.99 85 85
CXCL12 -0.28 0.52 -9999 0 -1 88 88
COPS5 0.016 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0.025 0.005 -9999 0 -10000 0 0
BNIP3 -0.2 0.44 -9999 0 -0.93 56 56
EGLN3 -0.2 0.44 -9999 0 -0.94 56 56
CA9 -0.36 0.5 -9999 0 -1 85 85
TERT -0.29 0.48 -9999 0 -1 74 74
ENO1 -0.2 0.44 -9999 0 -0.93 56 56
PFKL -0.2 0.44 -9999 0 -0.93 55 55
NCOA1 0.016 0.002 -9999 0 -10000 0 0
ADM -0.2 0.44 -9999 0 -0.94 56 56
ARNT -0.013 0.076 -9999 0 -10000 0 0
HNF4A -0.04 0.16 -9999 0 -0.51 35 35
ADFP -0.21 0.44 -9999 0 -0.89 67 67
SLC2A1 -0.089 0.34 -9999 0 -0.77 26 26
LEP -0.24 0.47 -9999 0 -0.97 69 69
HIF1A/ARNT/Cbp/p300 -0.14 0.38 -9999 0 -0.8 48 48
EPO -0.097 0.3 -9999 0 -0.8 11 11
CREBBP -0.007 0.14 -9999 0 -0.34 22 22
HIF1A/ARNT/Cbp/p300/HDAC7 -0.12 0.37 -9999 0 -0.79 43 43
PFKFB3 -0.2 0.44 -9999 0 -0.95 53 53
NT5E -0.22 0.48 -9999 0 -0.97 67 67
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.025 0.13 -10000 0 -0.3 65 65
ER alpha/Gai/GDP/Gbeta gamma -0.18 0.34 -10000 0 -0.66 93 93
AKT1 -0.13 0.35 -10000 0 -0.9 61 61
PIK3CA 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.14 0.36 -10000 0 -0.93 61 61
mol:Ca2+ -0.04 0.18 -10000 0 -0.43 53 53
IGF1R 0.011 0.054 -10000 0 -0.58 3 3
E2/ER alpha (dimer)/Striatin -0.043 0.14 -10000 0 -0.35 61 61
SHC1 0.014 0.028 -10000 0 -0.51 1 1
apoptosis 0.12 0.33 0.85 61 -10000 0 61
RhoA/GTP -0.042 0.093 -10000 0 -0.48 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.17 0.25 -10000 0 -0.54 93 93
regulation of stress fiber formation -0.011 0.1 0.4 4 -10000 0 4
E2/ERA-ERB (dimer) -0.045 0.14 -10000 0 -0.35 63 63
KRAS 0.014 0.028 -10000 0 -0.51 1 1
G13/GTP -0.038 0.13 -10000 0 -0.32 61 61
pseudopodium formation 0.011 0.1 -10000 0 -0.4 4 4
E2/ER alpha (dimer)/PELP1 -0.043 0.14 -10000 0 -0.35 61 61
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.006 0.076 -10000 0 -0.58 6 6
GNAO1 -0.17 0.27 -10000 0 -0.58 110 110
HRAS 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.29 -10000 0 -0.69 62 62
E2/ER beta (dimer) 0.009 0.028 -10000 0 -0.37 2 2
mol:GDP -0.069 0.15 -10000 0 -0.4 61 61
mol:NADP -0.12 0.29 -10000 0 -0.69 62 62
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.043 0.19 -10000 0 -0.45 53 53
IGF-1R heterotetramer 0.011 0.054 -10000 0 -0.57 3 3
PLCB1 -0.051 0.19 -10000 0 -0.46 53 53
PLCB2 -0.044 0.18 -10000 0 -0.45 52 52
IGF1 -0.25 0.29 -10000 0 -0.58 159 159
mol:L-citrulline -0.12 0.29 -10000 0 -0.69 62 62
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.25 0.41 -10000 0 -0.84 110 110
JNK cascade 0.009 0.028 -10000 0 -0.36 2 2
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.013 0.039 -10000 0 -0.51 2 2
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 -0.086 0.22 -10000 0 -0.58 61 61
Gq family/GDP/Gbeta gamma -0.001 0.11 -10000 0 -0.51 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.026 0.12 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.17 0.25 -10000 0 -0.54 94 94
GNAZ -0.11 0.24 -10000 0 -0.58 76 76
E2/ER alpha (dimer) -0.063 0.16 -10000 0 -0.42 61 61
STRN 0.016 0 -10000 0 -10000 0 0
GNAL -0.24 0.29 -10000 0 -0.58 154 154
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.02 0.024 -10000 0 -0.3 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.054 -10000 0 -0.58 3 3
HBEGF -0.19 0.29 -10000 0 -0.6 98 98
cAMP biosynthetic process -0.17 0.19 -10000 0 -0.34 180 180
SRC -0.16 0.32 -10000 0 -0.62 93 93
PI3K 0.023 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.062 0.13 -10000 0 -0.35 61 61
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.22 0.24 -10000 0 -0.5 132 132
Gs family/GTP -0.17 0.19 -10000 0 -0.34 180 180
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.016 -10000 0 -0.26 1 1
vasodilation -0.11 0.27 -10000 0 -0.65 62 62
mol:DAG -0.043 0.19 -10000 0 -0.45 53 53
Gs family/GDP/Gbeta gamma -0.15 0.18 -10000 0 -0.46 64 64
MSN 0.01 0.11 -10000 0 -0.43 4 4
Gq family/GTP -0.054 0.19 -10000 0 -0.47 52 52
mol:PI-3-4-5-P3 -0.13 0.34 -10000 0 -0.88 61 61
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.11 0.27 0.65 62 -10000 0 62
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
RhoA/GDP -0.064 0.14 -10000 0 -0.37 61 61
NOS3 -0.13 0.31 -10000 0 -0.74 62 62
GNA11 0.014 0.031 -10000 0 -0.58 1 1
MAPKKK cascade -0.11 0.29 -10000 0 -0.7 61 61
E2/ER alpha (dimer)/PELP1/Src -0.18 0.27 -10000 0 -0.58 93 93
ruffle organization 0.011 0.1 -10000 0 -0.4 4 4
ROCK2 0.002 0.11 -10000 0 -0.47 3 3
GNA14 -0.067 0.2 -10000 0 -0.58 50 50
GNA15 0.012 0.044 -10000 0 -0.58 2 2
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.21 0.29 -10000 0 -0.62 93 93
MMP2 -0.17 0.31 -10000 0 -0.59 102 102
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.13 0.23 -9999 0 -0.41 116 116
MAP3K8 0.007 0.054 -9999 0 -0.58 3 3
FOS -0.092 0.18 -9999 0 -0.45 46 46
PRKCA 0.007 0.054 -9999 0 -0.58 3 3
PTPN7 -0.003 0.095 -9999 0 -0.56 10 10
HRAS 0.015 0.002 -9999 0 -10000 0 0
PRKCB -0.16 0.27 -9999 0 -0.58 103 103
NRAS 0.015 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.022 0.022 -9999 0 -0.28 1 1
MAPK3 -0.048 0.12 -9999 0 -0.51 9 9
MAP2K1 -0.11 0.23 -9999 0 -0.46 103 103
ELK1 0.01 0.01 -9999 0 -10000 0 0
BRAF -0.11 0.22 -9999 0 -0.44 103 103
mol:GTP -0.001 0.003 -9999 0 -0.005 109 109
MAPK1 -0.048 0.12 -9999 0 -0.46 11 11
RAF1 -0.11 0.22 -9999 0 -0.44 103 103
KRAS 0.013 0.028 -9999 0 -0.51 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.022 0.023 -9999 0 -0.41 1 1
alphaV beta3 Integrin -0.13 0.24 -9999 0 -0.43 126 126
PTK2 -0.11 0.24 -9999 0 -0.55 62 62
IGF1R 0.011 0.054 -9999 0 -0.58 3 3
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.012 0.044 -9999 0 -0.58 2 2
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.14 0.29 -9999 0 -0.72 62 62
VEGFA 0.016 0 -9999 0 -10000 0 0
ILK -0.14 0.29 -9999 0 -0.72 62 62
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.12 0.27 -9999 0 -0.67 62 62
PTK2B 0.005 0.11 -9999 0 -0.29 43 43
alphaV/beta3 Integrin/JAM-A -0.15 0.27 -9999 0 -0.65 62 62
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.021 0.13 -9999 0 -0.36 46 46
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.18 -9999 0 -0.32 163 163
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.022 0.14 -9999 0 -0.43 18 18
alphaV/beta3 Integrin/Syndecan-1 -0.019 0.13 -9999 0 -0.35 47 47
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.29 -9999 0 -0.63 115 115
PI4 Kinase 0.023 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.14 0.18 -9999 0 -0.31 179 179
RPS6KB1 -0.21 0.29 -9999 0 -0.58 115 115
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.28 0.41 -9999 0 -0.79 126 126
GPR124 -0.049 0.18 -9999 0 -0.58 39 39
MAPK1 -0.28 0.41 -9999 0 -0.79 126 126
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.12 0.21 -9999 0 -0.39 132 132
cell adhesion -0.035 0.12 -9999 0 -0.34 43 43
ANGPTL3 0.004 0.061 -9999 0 -0.51 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.031 0.02 -9999 0 -0.34 1 1
IGF-1R heterotetramer 0.011 0.054 -9999 0 -0.57 3 3
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.044 -9999 0 -0.58 2 2
ITGB3 -0.054 0.19 -9999 0 -0.58 42 42
IGF1 -0.25 0.29 -9999 0 -0.58 159 159
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.052 0.19 -9999 0 -0.45 61 61
apoptosis 0.014 0.031 -9999 0 -0.57 1 1
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.013 0.12 -9999 0 -0.35 42 42
VCL 0.014 0.031 -9999 0 -0.58 1 1
alphaV/beta3 Integrin/Del1 -0.062 0.2 -9999 0 -0.45 70 70
CSF1 -0.006 0.11 -9999 0 -0.58 13 13
PIK3C2A -0.14 0.29 -9999 0 -0.72 62 62
PI4 Kinase/Pyk2 -0.15 0.21 -9999 0 -0.55 62 62
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.002 0.12 -9999 0 -0.32 42 42
FAK1/Vinculin -0.078 0.19 -9999 0 -0.42 63 63
alphaV beta3/Integrin/ppsTEM5 -0.052 0.2 -9999 0 -0.46 61 61
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.093 0.23 -9999 0 -0.57 66 66
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.18 0.28 -9999 0 -0.58 116 116
F11R -0.12 0.21 -9999 0 -0.42 116 116
alphaV/beta3 Integrin/Lactadherin -0.015 0.13 -9999 0 -0.36 43 43
alphaV/beta3 Integrin/TGFBR2 -0.015 0.13 -9999 0 -0.36 43 43
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.027 0.067 -9999 0 -0.3 14 14
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.011 0.11 -9999 0 -0.32 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.035 0.16 -9999 0 -0.53 33 33
alphaV/beta3 Integrin/Pyk2 0.006 0.11 -9999 0 -0.29 43 43
SDC1 0.007 0.07 -9999 0 -0.58 5 5
VAV3 0.026 0.075 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.004 0.082 -9999 0 -0.58 7 7
FAK1/Paxillin -0.077 0.19 -9999 0 -0.42 62 62
cell migration -0.061 0.17 -9999 0 -0.4 47 47
ITGAV 0.014 0.031 -9999 0 -0.58 1 1
PI3K -0.16 0.22 -9999 0 -0.58 62 62
SPP1 -0.19 0.26 -9999 0 -0.51 141 141
KDR 0.014 0.031 -9999 0 -0.58 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.031 -9999 0 -0.57 1 1
COL4A3 -0.16 0.27 -9999 0 -0.57 107 107
angiogenesis -0.27 0.4 -9999 0 -0.77 127 127
Rac1/GTP 0.032 0.069 -9999 0 -10000 0 0
EDIL3 -0.066 0.2 -9999 0 -0.58 49 49
cell proliferation -0.015 0.13 -9999 0 -0.36 43 43
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.12 0.17 -10000 0 -0.3 156 156
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.1 0.17 -10000 0 -0.37 102 102
GNB1/GNG2 0.015 0.048 -10000 0 -0.35 6 6
GNB1 0.016 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
Gs family/GTP -0.14 0.17 -10000 0 -0.33 154 154
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 0.037 0.042 0.085 154 -10000 0 154
GNAL -0.24 0.29 -10000 0 -0.58 154 154
GNG2 0.006 0.076 -10000 0 -0.58 6 6
CRH -0.14 0.24 -10000 0 -0.51 102 102
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.034 -10000 0 -0.36 3 3
MAPK11 0.01 0 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.21 -9999 0 -0.35 143 143
SMAD6-7/SMURF1 0.027 0.041 -9999 0 -0.31 5 5
NOG -0.028 0.14 -9999 0 -0.51 28 28
SMAD9 -0.15 0.25 -9999 0 -0.54 95 95
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.035 0.11 -9999 0 -0.31 16 16
BMP7/USAG1 -0.27 0.27 -9999 0 -0.49 203 203
SMAD5/SKI -0.025 0.1 -9999 0 -0.37 5 5
SMAD1 0.046 0.022 -9999 0 -10000 0 0
BMP2 -0.047 0.18 -9999 0 -0.58 38 38
SMAD1/SMAD1/SMAD4 -0.002 0.02 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.066 0.19 -9999 0 -0.51 54 54
BMPR1A-1B/BAMBI -0.051 0.16 -9999 0 -0.35 77 77
AHSG -0.061 0.17 -9999 0 -0.51 46 46
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.034 0.14 -9999 0 -0.35 56 56
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.067 0.15 -9999 0 -0.36 35 35
BMP2-4 (homodimer) -0.045 0.16 -9999 0 -0.41 56 56
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.008 0.11 -9999 0 -0.3 6 6
RGMA -0.16 0.27 -9999 0 -0.58 105 105
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.069 0.14 -9999 0 -0.36 37 37
BMP2-4/USAG1 -0.15 0.22 -9999 0 -0.39 156 156
SMAD6/SMURF1/SMAD5 -0.025 0.1 -9999 0 -0.37 5 5
SOSTDC1 -0.19 0.28 -9999 0 -0.57 122 122
BMP7/BMPR2/BMPR1A-1B -0.12 0.2 -9999 0 -0.34 154 154
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.011 0.05 -9999 0 -0.53 3 3
HFE2 0.002 0.048 -9999 0 -0.51 3 3
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.063 0.18 -9999 0 -0.38 83 83
SMAD5/SMAD5/SMAD4 -0.025 0.1 -9999 0 -0.37 5 5
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.072 0.096 -9999 0 -0.35 21 21
BMP7 (homodimer) -0.19 0.28 -9999 0 -0.57 123 123
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.036 0.13 -9999 0 -0.36 49 49
SMAD1/SKI 0.053 0.02 -9999 0 -10000 0 0
SMAD6 0.01 0.057 -9999 0 -0.52 4 4
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.073 0.17 -9999 0 -0.35 93 93
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.15 0.26 -9999 0 -0.54 108 108
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.032 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.036 0.14 -9999 0 -0.36 54 54
CHRDL1 -0.33 0.29 -9999 0 -0.58 208 208
ENDOFIN/SMAD1 0.053 0.02 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.001 0.026 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.038 0.17 -9999 0 -0.56 33 33
SMURF2 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.24 0.22 -9999 0 -0.39 231 231
BMP2-4/GREM1 -0.13 0.19 -9999 0 -0.34 159 159
SMAD7 0.014 0.031 -9999 0 -0.58 1 1
SMAD8A/SMAD8A/SMAD4 -0.14 0.24 -9999 0 -0.51 95 95
SMAD1/SMAD6 0.053 0.02 -9999 0 -10000 0 0
TAK1/SMAD6 0.023 0 -9999 0 -10000 0 0
BMP7 -0.19 0.28 -9999 0 -0.58 123 123
BMP6 0.011 0.05 -9999 0 -0.53 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.06 0.13 -9999 0 -0.33 37 37
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.053 0.02 -9999 0 -10000 0 0
SMAD7/SMURF1 0.022 0.023 -9999 0 -0.41 1 1
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.012 0.042 -9999 0 -0.54 2 2
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.097 0.17 -9999 0 -0.44 46 46
CHRD -0.044 0.18 -9999 0 -0.57 36 36
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.084 0.15 -9999 0 -0.4 36 36
BMP4 -0.014 0.13 -9999 0 -0.56 18 18
FST -0.028 0.15 -9999 0 -0.56 27 27
BMP2-4/NOG -0.052 0.17 -9999 0 -0.38 72 72
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.11 0.19 -9999 0 -0.32 128 128
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.17 0.28 -10000 0 -0.5 136 136
fibroblast growth factor receptor signaling pathway -0.17 0.28 -10000 0 -0.5 136 136
LAMA1 -0.087 0.21 -10000 0 -0.52 68 68
PRNP 0.002 0.088 -10000 0 -0.58 8 8
GPC1/SLIT2 -0.18 0.22 -10000 0 -0.42 168 168
SMAD2 0.036 0.03 -10000 0 -0.3 2 2
GPC1/PrPc/Cu2+ 0.012 0.058 -10000 0 -0.35 9 9
GPC1/Laminin alpha1 -0.052 0.16 -10000 0 -0.37 68 68
TDGF1 0.007 0.028 -10000 0 -0.51 1 1
CRIPTO/GPC1 0.016 0.029 -10000 0 -0.36 2 2
APP/GPC1 0.02 0.038 -10000 0 -0.39 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.026 0.025 -10000 0 -0.3 2 2
FLT1 0.016 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.029 0.033 -10000 0 -0.33 3 3
SERPINC1 -0.031 0.14 -10000 0 -0.51 30 30
FYN 0.023 0.042 -10000 0 -0.33 5 5
FGR 0.025 0.031 -10000 0 -0.31 3 3
positive regulation of MAPKKK cascade 0.023 0.075 -10000 0 -0.36 3 3
SLIT2 -0.26 0.3 -10000 0 -0.58 168 168
GPC1/NRG -0.074 0.18 -10000 0 -0.4 81 81
NRG1 -0.11 0.24 -10000 0 -0.56 80 80
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0.017 -10000 0 -0.29 1 1
LYN 0.026 0.025 -10000 0 -0.3 2 2
mol:Spermine 0.012 0.02 -10000 0 -0.37 1 1
cell growth -0.17 0.28 -10000 0 -0.5 136 136
BMP signaling pathway -0.014 0.028 0.51 1 -10000 0 1
SRC 0.026 0.025 -10000 0 -0.3 2 2
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.26 0.29 -10000 0 -0.57 165 165
GPC1 0.014 0.028 -10000 0 -0.51 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA 0.016 0 -10000 0 -10000 0 0
BLK -0.019 0.12 -10000 0 -0.33 44 44
HCK 0.009 0.081 -10000 0 -0.33 19 19
FGF2 -0.18 0.28 -10000 0 -0.58 116 116
FGFR1 -0.12 0.25 -10000 0 -0.58 83 83
VEGFR1 homodimer 0.016 0 -10000 0 -10000 0 0
TGFBR2 0.012 0.044 -10000 0 -0.58 2 2
cell death 0.02 0.038 -10000 0 -0.39 3 3
ATIII/GPC1 -0.012 0.11 -10000 0 -0.36 31 31
PLA2G2A/GPC1 -0.18 0.22 -10000 0 -0.41 165 165
LCK 0.02 0.052 -10000 0 -0.32 8 8
neuron differentiation -0.073 0.18 -10000 0 -0.4 81 81
PrPc/Cu2+ 0.002 0.064 -10000 0 -0.42 8 8
APP 0.012 0.044 -10000 0 -0.58 2 2
TGFBR2 (dimer) 0.012 0.044 -10000 0 -0.57 2 2
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.08 0.18 -9999 0 -0.46 53 53
alphaM/beta2 Integrin/GPIbA -0.055 0.13 -9999 0 -0.42 35 35
alphaM/beta2 Integrin/proMMP-9 -0.13 0.19 -9999 0 -0.38 112 112
PLAUR 0.016 0 -9999 0 -10000 0 0
HMGB1 -0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.049 0.12 -9999 0 -0.44 29 29
AGER -0.012 0.073 -9999 0 -0.54 6 6
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG 0.001 0.09 -9999 0 -0.56 9 9
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.14 -9999 0 -0.51 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.24 -9999 0 -0.51 97 97
CYR61 -0.16 0.27 -9999 0 -0.58 106 106
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.061 0.14 -9999 0 -0.51 21 21
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -9999 0 -0.57 75 75
MYH2 -0.056 0.15 -9999 0 -0.44 26 26
MST1R -0.016 0.13 -9999 0 -0.55 20 20
leukocyte activation during inflammatory response -0.12 0.18 -9999 0 -0.37 102 102
APOB -0.083 0.21 -9999 0 -0.57 58 58
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.037 0.17 -9999 0 -0.58 32 32
JAM3 -0.023 0.14 -9999 0 -0.58 23 23
GP1BA 0.004 0.074 -9999 0 -0.52 7 7
alphaM/beta2 Integrin/CTGF -0.12 0.21 -9999 0 -0.46 88 88
alphaM/beta2 Integrin -0.059 0.17 -9999 0 -0.55 25 25
JAM3 homodimer -0.023 0.14 -9999 0 -0.57 23 23
ICAM2 0.014 0.031 -9999 0 -0.58 1 1
ICAM1 0.005 0.074 -9999 0 -0.52 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.058 0.17 -9999 0 -0.54 25 25
cell adhesion -0.055 0.13 -9999 0 -0.42 35 35
NFKB1 -0.14 0.22 -9999 0 -0.62 24 24
THY1 0.013 0.039 -9999 0 -0.51 2 2
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.079 0.17 -9999 0 -0.37 86 86
alphaM/beta2 Integrin/LRP/tPA -0.036 0.16 -9999 0 -0.46 36 36
IL6 -0.34 0.42 -9999 0 -0.77 167 167
ITGB2 -0.029 0.12 -9999 0 -0.56 16 16
elevation of cytosolic calcium ion concentration -0.074 0.14 -9999 0 -0.37 44 44
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.24 -9999 0 -0.44 112 112
JAM2 -0.14 0.26 -9999 0 -0.58 96 96
alphaM/beta2 Integrin/ICAM1 -0.066 0.15 -9999 0 -0.42 37 37
alphaM/beta2 Integrin/uPA/Plg -0.079 0.15 -9999 0 -0.33 78 78
RhoA/GTP -0.049 0.15 -9999 0 -0.47 24 24
positive regulation of phagocytosis -0.071 0.17 -9999 0 -0.53 31 31
Ron/MSP -0.021 0.13 -9999 0 -0.39 38 38
alphaM/beta2 Integrin/uPAR/uPA -0.057 0.15 -9999 0 -0.37 44 44
alphaM/beta2 Integrin/uPAR -0.049 0.12 -9999 0 -0.44 29 29
PLAU -0.055 0.18 -9999 0 -0.51 48 48
PLAT -0.014 0.13 -9999 0 -0.57 18 18
actin filament polymerization -0.053 0.14 -9999 0 -0.42 26 26
MST1 -0.014 0.12 -9999 0 -0.51 20 20
alphaM/beta2 Integrin/lipoprotein(a) -0.12 0.18 -9999 0 -0.37 102 102
TNF -0.13 0.21 -9999 0 -0.56 24 24
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.089 0.15 -9999 0 -0.36 76 76
fibrinolysis -0.082 0.14 -9999 0 -0.34 73 73
HCK -0.012 0.12 -9999 0 -0.56 17 17
dendritic cell antigen processing and presentation -0.058 0.17 -9999 0 -0.54 25 25
VTN -0.093 0.23 -9999 0 -0.57 66 66
alphaM/beta2 Integrin/CYR61 -0.15 0.23 -9999 0 -0.46 114 114
LPA -0.046 0.17 -9999 0 -0.56 35 35
LRP1 0.011 0.054 -9999 0 -0.58 3 3
cell migration -0.13 0.22 -9999 0 -0.44 76 76
FN1 -0.035 0.16 -9999 0 -0.53 33 33
alphaM/beta2 Integrin/Thy1 -0.05 0.12 -9999 0 -0.43 31 31
MPO 0.01 0.039 -9999 0 -0.51 2 2
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0.021 0 -9999 0 -10000 0 0
ROCK1 -0.038 0.14 -9999 0 -0.46 20 20
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.003 0.06 -9999 0 -0.51 5 5
CTGF -0.1 0.24 -9999 0 -0.58 73 73
alphaM/beta2 Integrin/Hck -0.064 0.17 -9999 0 -0.52 35 35
ITGAM -0.037 0.14 -9999 0 -0.59 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.096 0.21 -9999 0 -0.4 92 92
HP -0.055 0.18 -9999 0 -0.51 46 46
leukocyte adhesion -0.17 0.22 -9999 0 -0.5 89 89
SELP -0.11 0.24 -9999 0 -0.58 75 75
Calcium signaling in the CD4+ TCR pathway

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.086 -9999 0 -0.38 17 17
NFATC2 -0.061 0.15 -9999 0 -0.38 62 62
NFATC3 0.007 0.028 -9999 0 -10000 0 0
CD40LG -0.26 0.33 -9999 0 -0.73 89 89
PTGS2 -0.3 0.36 -9999 0 -0.7 129 129
JUNB 0.009 0.062 -9999 0 -0.58 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 0.012 0.008 -9999 0 -10000 0 0
JUN -0.01 0.11 -9999 0 -0.58 13 13
mol:Ca2+ -0.009 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.004 -9999 0 -10000 0 0
FOSL1 -0.024 0.15 -9999 0 -0.58 24 24
CREM 0.015 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.18 -9999 0 -0.49 51 51
FOS -0.17 0.28 -9999 0 -0.59 110 110
IFNG -0.28 0.33 -9999 0 -0.71 95 95
AP-1/NFAT1-c-4 -0.29 0.38 -9999 0 -0.71 121 121
FASLG -0.25 0.32 -9999 0 -0.71 85 85
NFAT1-c-4/ICER1 -0.075 0.16 -9999 0 -0.4 52 52
IL2RA -0.25 0.33 -9999 0 -0.76 76 76
FKBP12/FK506 0.012 0 -9999 0 -10000 0 0
CSF2 -0.27 0.33 -9999 0 -0.67 108 108
JunB/Fra1/NFAT1-c-4 -0.1 0.17 -9999 0 -0.42 59 59
IL4 -0.24 0.3 -9999 0 -0.67 78 78
IL2 -0.009 0.019 -9999 0 -10000 0 0
IL3 -0.024 0.023 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 0.003 0.084 -9999 0 -0.55 8 8
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.002 -9999 0 -10000 0 0
IL6-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
BCL2L1 -0.064 0.24 -10000 0 -0.64 26 26
CRP -0.075 0.25 -10000 0 -0.68 26 26
cell cycle arrest -0.075 0.27 -10000 0 -0.65 46 46
TIMP1 -0.056 0.22 -10000 0 -0.5 38 38
IL6ST -0.073 0.22 -10000 0 -0.58 56 56
Rac1/GDP -0.14 0.27 -10000 0 -0.57 74 74
AP1 -0.056 0.18 -10000 0 -0.45 23 23
GAB2 0.019 0.007 -10000 0 -10000 0 0
TNFSF11 -0.076 0.26 -10000 0 -0.67 32 32
HSP90B1 0.022 0.056 -10000 0 -0.56 1 1
GAB1 0.018 0.004 -10000 0 -10000 0 0
MAPK14 -0.17 0.31 -10000 0 -0.72 69 69
AKT1 0.064 0.015 -10000 0 -10000 0 0
FOXO1 0.07 0.013 -10000 0 -10000 0 0
MAP2K6 -0.17 0.29 -10000 0 -0.62 76 76
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.1 0.26 -10000 0 -0.6 56 56
MITF -0.17 0.29 -10000 0 -0.56 91 91
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0 -10000 0 -10000 0 0
A2M -0.096 0.41 -10000 0 -1.4 30 30
CEBPB 0.023 0.032 -10000 0 -0.57 1 1
GRB2/SOS1/GAB family/SHP2 -0.017 0.097 0.25 1 -10000 0 1
STAT3 -0.086 0.29 -10000 0 -0.7 46 46
STAT1 -0.007 0.019 -10000 0 -10000 0 0
CEBPD -0.066 0.25 -10000 0 -0.69 23 23
PIK3CA 0.018 0 -10000 0 -10000 0 0
PI3K 0.026 0.001 -10000 0 -10000 0 0
JUN -0.006 0.11 -10000 0 -0.58 13 13
PIAS3/MITF -0.15 0.27 -10000 0 -0.55 84 84
MAPK11 -0.17 0.31 -10000 0 -0.72 69 69
STAT3 (dimer)/FOXO1 -0.035 0.24 -10000 0 -0.56 35 35
GRB2/SOS1/GAB family -0.14 0.21 0.21 4 -0.58 51 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.17 0.28 -10000 0 -0.5 101 101
GRB2 0.018 0.004 -10000 0 -10000 0 0
JAK2 0.014 0.031 -10000 0 -0.58 1 1
LBP -0.073 0.22 -10000 0 -0.57 21 21
PIK3R1 0.017 0 -10000 0 -10000 0 0
JAK1 0.017 0.007 -10000 0 -10000 0 0
MYC -0.091 0.32 -10000 0 -0.92 31 31
FGG -0.09 0.26 -10000 0 -0.66 34 34
macrophage differentiation -0.075 0.27 -10000 0 -0.65 46 46
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.24 -10000 0 -0.53 78 78
JUNB -0.067 0.25 -10000 0 -0.67 28 28
FOS -0.17 0.27 -10000 0 -0.58 110 110
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.28 -10000 0 -0.52 96 96
STAT1/PIAS1 -0.12 0.24 -10000 0 -0.54 61 61
GRB2/SOS1/GAB family/SHP2/PI3K 0.051 0.018 -10000 0 -10000 0 0
STAT3 (dimer) -0.082 0.28 -10000 0 -0.68 46 46
PRKCD -0.076 0.26 -10000 0 -0.59 50 50
IL6R -0.034 0.17 -10000 0 -0.57 31 31
SOCS3 -0.22 0.42 -10000 0 -1.1 58 58
gp130 (dimer)/JAK1/JAK1/LMO4 -0.018 0.14 -10000 0 -0.34 57 57
Rac1/GTP -0.13 0.27 -10000 0 -0.58 69 69
HCK -0.011 0.12 -10000 0 -0.56 17 17
MAPKKK cascade 0.022 0.075 -10000 0 -10000 0 0
bone resorption -0.071 0.25 -10000 0 -0.63 33 33
IRF1 -0.064 0.24 -10000 0 -0.66 23 23
mol:GDP -0.15 0.28 -10000 0 -0.58 79 79
SOS1 0.018 0.007 -10000 0 -10000 0 0
VAV1 -0.16 0.28 -10000 0 -0.6 79 79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.2 0.35 -10000 0 -0.78 72 72
PTPN11 -0.005 0.018 -10000 0 -10000 0 0
IL6/IL6RA -0.2 0.26 -10000 0 -0.46 170 170
gp130 (dimer)/TYK2/TYK2/LMO4 -0.023 0.14 -10000 0 -0.34 57 57
gp130 (dimer)/JAK2/JAK2/LMO4 -0.024 0.14 -10000 0 -0.35 57 57
IL6 -0.25 0.3 -10000 0 -0.57 162 162
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE 0.006 0.042 -10000 0 -0.52 2 2
PIAS1 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.26 -10000 0 -0.37 175 175
LMO4 0.018 0.033 -10000 0 -0.58 1 1
STAT3 (dimer)/PIAS3 -0.15 0.24 -10000 0 -0.68 46 46
MCL1 0.07 0.014 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.016 0 -9999 0 -10000 0 0
CCL5 -0.03 0.16 -9999 0 -0.55 29 29
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.12 0.14 -9999 0 -0.35 50 50
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.11 0.13 -9999 0 -0.39 21 21
Syndecan-1/Syntenin -0.11 0.13 -9999 0 -0.33 50 50
MAPK3 -0.082 0.12 -9999 0 -0.4 12 12
HGF/MET -0.081 0.18 -9999 0 -0.41 86 86
TGFB1/TGF beta receptor Type II 0.016 0 -9999 0 -10000 0 0
BSG 0.016 0 -9999 0 -10000 0 0
keratinocyte migration -0.1 0.13 -9999 0 -0.38 21 21
Syndecan-1/RANTES -0.13 0.16 -9999 0 -0.39 62 62
Syndecan-1/CD147 -0.094 0.12 -9999 0 -0.42 13 13
Syndecan-1/Syntenin/PIP2 -0.1 0.12 -9999 0 -0.32 50 50
LAMA5 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.12 0.11 -9999 0 -0.31 50 50
MMP7 -0.11 0.23 -9999 0 -0.52 85 85
HGF -0.12 0.25 -9999 0 -0.57 85 85
Syndecan-1/CASK -0.12 0.13 -9999 0 -0.34 50 50
Syndecan-1/HGF/MET -0.16 0.18 -9999 0 -0.45 71 71
regulation of cell adhesion -0.072 0.12 -9999 0 -0.44 6 6
HPSE -0.032 0.15 -9999 0 -0.51 32 32
positive regulation of cell migration -0.12 0.14 -9999 0 -0.35 50 50
SDC1 -0.12 0.14 -9999 0 -0.36 50 50
Syndecan-1/Collagen -0.12 0.14 -9999 0 -0.35 50 50
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.014 0.028 -9999 0 -0.51 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.13 0.24 -9999 0 -0.51 97 97
MAPK1 -0.082 0.12 -9999 0 -0.4 12 12
homophilic cell adhesion -0.12 0.14 -9999 0 -0.35 50 50
MMP1 -0.28 0.26 -9999 0 -0.51 204 204
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.097 0.21 -10000 0 -0.55 57 57
FYN -0.081 0.33 -10000 0 -0.74 62 62
LAT/GRAP2/SLP76 -0.11 0.25 -10000 0 -0.6 64 64
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.032 0.21 -10000 0 -0.46 59 59
B2M 0.015 0.005 -10000 0 -10000 0 0
IKBKG -0.023 0.044 -10000 0 -0.14 22 22
MAP3K8 0.011 0.054 -10000 0 -0.58 3 3
mol:Ca2+ -0.023 0.038 -10000 0 -0.11 37 37
integrin-mediated signaling pathway 0.019 0.028 -10000 0 -0.35 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.072 0.31 -10000 0 -0.7 60 60
TRPV6 -0.11 0.22 -10000 0 -0.56 70 70
CD28 -0.011 0.12 -10000 0 -0.58 16 16
SHC1 -0.074 0.3 -10000 0 -0.69 62 62
receptor internalization -0.085 0.32 -10000 0 -0.72 62 62
PRF1 -0.09 0.35 -10000 0 -0.94 41 41
KRAS 0.014 0.028 -10000 0 -0.51 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.014 0.17 -10000 0 -0.36 57 57
LAT -0.074 0.3 -10000 0 -0.69 62 62
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.047 0.18 -10000 0 -0.58 38 38
CD3E -0.051 0.19 -10000 0 -0.59 40 40
CD3G -0.055 0.19 -10000 0 -0.58 42 42
RASGRP2 -0.041 0.083 -10000 0 -0.17 97 97
RASGRP1 -0.027 0.21 -10000 0 -0.46 58 58
HLA-A 0.013 0.032 -10000 0 -0.59 1 1
RASSF5 0.012 0.044 -10000 0 -0.58 2 2
RAP1A/GTP/RAPL 0.019 0.028 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.07 -10000 0 -0.13 53 53
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.042 0.078 -10000 0 -0.22 44 44
PRKCA -0.044 0.11 -10000 0 -0.28 56 56
GRAP2 -0.057 0.19 -10000 0 -0.58 44 44
mol:IP3 -0.05 0.21 0.23 58 -0.46 56 114
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.089 0.32 -10000 0 -0.72 59 59
ORAI1 0.063 0.12 0.31 70 -0.37 1 71
CSK -0.077 0.31 -10000 0 -0.72 60 60
B7 family/CD28 -0.15 0.28 -10000 0 -0.66 66 66
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.1 0.36 -10000 0 -0.82 62 62
PTPN6 -0.081 0.31 -10000 0 -0.7 62 62
VAV1 -0.083 0.32 -10000 0 -0.72 64 64
Monovalent TCR/CD3 -0.079 0.26 -10000 0 -0.55 69 69
CBL 0.016 0 -10000 0 -10000 0 0
LCK -0.087 0.33 -10000 0 -0.75 62 62
PAG1 -0.077 0.31 -10000 0 -0.71 61 61
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.1 0.36 -10000 0 -0.8 64 64
CD80 -0.05 0.17 -10000 0 -0.51 44 44
CD86 0.009 0.061 -10000 0 -0.56 4 4
PDK1/CARD11/BCL10/MALT1 -0.051 0.095 -10000 0 -0.26 52 52
HRAS 0.016 0 -10000 0 -10000 0 0
GO:0035030 -0.069 0.25 -10000 0 -0.55 64 64
CD8A -0.047 0.18 -10000 0 -0.58 38 38
CD8B -0.042 0.18 -10000 0 -0.58 35 35
PTPRC -0.059 0.2 -10000 0 -0.58 45 45
PDK1/PKC theta -0.044 0.26 -10000 0 -0.57 61 61
CSK/PAG1 -0.068 0.3 -10000 0 -0.7 57 57
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.026 -10000 0 -0.43 1 1
GRAP2/SLP76 -0.13 0.3 -10000 0 -0.71 65 65
STIM1 0.034 0.061 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.089 -10000 0 -0.17 44 44
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.096 0.35 -10000 0 -0.79 62 62
mol:DAG -0.064 0.16 -10000 0 -0.4 59 59
RAP1A/GDP 0.004 0.031 -10000 0 -0.064 2 2
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 0.004 0.082 -10000 0 -0.57 7 7
cytotoxic T cell degranulation -0.083 0.33 -10000 0 -0.85 43 43
RAP1A/GTP -0.018 0.027 -10000 0 -0.069 31 31
mol:PI-3-4-5-P3 -0.049 0.25 -10000 0 -0.56 60 60
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.074 0.26 0.25 53 -0.61 56 109
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.008 0.12 -10000 0 -0.58 14 14
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.1 0.24 -10000 0 -0.6 59 59
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.061 0.22 -10000 0 -0.55 53 53
CARD11 0.001 0.09 -10000 0 -0.56 9 9
PRKCB -0.09 0.16 -10000 0 -0.36 74 74
PRKCE -0.043 0.11 -10000 0 -0.28 56 56
PRKCQ -0.066 0.3 -10000 0 -0.67 61 61
LCP2 0.012 0.044 -10000 0 -0.58 2 2
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.021 0.18 -10000 0 -0.39 59 59
IKK complex 0.014 0.071 -10000 0 -0.12 46 46
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 0.001 0.13 -10000 0 -0.28 52 52
PDPK1 -0.025 0.2 -10000 0 -0.44 59 59
TCR/CD3/MHC I/CD8/Fyn -0.12 0.39 -10000 0 -0.88 64 64
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.011 0.13 -9999 0 -0.39 26 26
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.11 -9999 0 -0.33 10 10
AP1 -0.15 0.21 -9999 0 -0.53 58 58
mol:PIP3 -0.06 0.13 -9999 0 -0.46 22 22
AKT1 0.032 0.097 -9999 0 -0.4 8 8
PTK2B -0.004 0.099 -9999 0 -0.23 46 46
RHOA 0.018 0.05 -9999 0 -0.26 1 1
PIK3CB 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.001 0.098 -9999 0 -0.26 32 32
MAGI3 0.015 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.036 0.15 -9999 0 -0.32 67 67
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.012 0.12 -9999 0 -0.29 45 45
NF kappa B1 p50/RelA -0.05 0.12 -9999 0 -0.44 17 17
endothelial cell migration -0.05 0.22 -9999 0 -0.59 47 47
ADCY4 -0.1 0.22 -9999 0 -0.46 75 75
ADCY5 -0.23 0.3 -9999 0 -0.57 137 137
ADCY6 -0.1 0.22 -9999 0 -0.46 75 75
ADCY7 -0.1 0.22 -9999 0 -0.46 75 75
ADCY1 -0.11 0.22 -9999 0 -0.45 79 79
ADCY2 -0.2 0.28 -9999 0 -0.54 123 123
ADCY3 -0.1 0.22 -9999 0 -0.46 75 75
ADCY8 -0.11 0.22 -9999 0 -0.46 75 75
ADCY9 -0.11 0.22 -9999 0 -0.47 76 76
GSK3B 0.005 0.094 -9999 0 -0.3 17 17
arachidonic acid secretion -0.11 0.22 -9999 0 -0.46 77 77
GNG2 0.005 0.076 -9999 0 -0.57 6 6
TRIP6 0.023 0.023 -9999 0 -10000 0 0
GNAO1 -0.13 0.23 -9999 0 -0.4 132 132
HRAS 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.002 0.12 -9999 0 -0.31 31 31
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.069 -9999 0 -0.92 2 2
JUN -0.006 0.11 -9999 0 -0.58 13 13
LPA/LPA2/NHERF2 -0.009 0.036 -9999 0 -0.33 3 3
TIAM1 -0.003 0.082 -9999 0 -1.1 2 2
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
mol:IP3 0.001 0.099 -9999 0 -0.26 32 32
PLCB3 0.023 0.038 -9999 0 -0.29 3 3
FOS -0.17 0.27 -9999 0 -0.58 110 110
positive regulation of mitosis -0.11 0.22 -9999 0 -0.46 77 77
LPA/LPA1-2-3 -0.041 0.16 -9999 0 -0.37 55 55
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation -0.005 0.12 -9999 0 -0.34 24 24
GNAZ -0.093 0.2 -9999 0 -0.38 110 110
EGFR/PI3K-beta/Gab1 -0.062 0.13 -9999 0 -0.48 22 22
positive regulation of dendritic cell cytokine production -0.069 0.15 -9999 0 -0.37 54 54
LPA/LPA2/MAGI-3 -0.007 0.037 -9999 0 -0.33 3 3
ARHGEF1 0.004 0.11 -9999 0 -0.35 21 21
GNAI2 -0.015 0.13 -9999 0 -0.33 47 47
GNAI3 -0.015 0.13 -9999 0 -0.33 47 47
GNAI1 -0.018 0.13 -9999 0 -0.33 50 50
LPA/LPA3 -0.048 0.12 -9999 0 -0.42 34 34
LPA/LPA2 -0.011 0.046 -9999 0 -0.4 3 3
LPA/LPA1 -0.052 0.14 -9999 0 -0.4 47 47
HB-EGF/EGFR -0.085 0.18 -9999 0 -0.34 111 111
HBEGF -0.093 0.19 -9999 0 -0.38 105 105
mol:DAG 0.001 0.099 -9999 0 -0.26 32 32
cAMP biosynthetic process -0.15 0.26 -9999 0 -0.46 122 122
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0.001 -9999 0 -10000 0 0
LYN 0.002 0.12 -9999 0 -0.31 31 31
GNAQ -0.01 0.096 -9999 0 -0.28 37 37
LPAR2 0.011 0.048 -9999 0 -0.51 3 3
LPAR3 -0.04 0.17 -9999 0 -0.57 34 34
LPAR1 -0.03 0.16 -9999 0 -0.62 21 21
IL8 -0.12 0.23 -9999 0 -0.48 80 80
PTK2 -0.027 0.15 -9999 0 -0.36 46 46
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
CASP3 -0.036 0.15 -9999 0 -0.32 67 67
EGFR -0.008 0.11 -9999 0 -0.54 15 15
PLCG1 -0.02 0.11 -9999 0 -0.29 43 43
PLD2 -0.027 0.15 -9999 0 -0.36 46 46
G12/G13 -0.005 0.12 -9999 0 -0.38 21 21
PI3K-beta -0.031 0.088 -9999 0 -0.46 8 8
cell migration -0.017 0.053 -9999 0 -0.21 9 9
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
PXN -0.005 0.12 -9999 0 -0.34 24 24
HRAS/GTP -0.11 0.23 -9999 0 -0.48 77 77
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.13 0.24 -9999 0 -0.51 97 97
PRKCE 0.016 0 -9999 0 -10000 0 0
PRKCD 0.009 0.095 -9999 0 -0.33 6 6
Gi(beta/gamma) -0.1 0.22 -9999 0 -0.45 77 77
mol:LPA -0.011 0.052 -9999 0 -0.19 26 26
TRIP6/p130 Cas/FAK1/Paxillin -0.048 0.12 -9999 0 -0.49 15 15
MAPKKK cascade -0.11 0.22 -9999 0 -0.46 77 77
contractile ring contraction involved in cytokinesis 0.018 0.049 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.055 0.15 -9999 0 -0.32 82 82
GNA15 -0.012 0.099 -9999 0 -0.28 39 39
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
MAPT -0.013 0.12 -9999 0 -0.29 45 45
GNA11 -0.011 0.1 -9999 0 -0.29 37 37
Rac1/GTP 0.025 0.075 -9999 0 -0.98 2 2
MMP2 -0.05 0.22 -9999 0 -0.6 47 47
Glucocorticoid receptor regulatory network

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
PCK2 0.015 0.062 0.28 4 -0.35 1 5
SMARCC2 0.015 0.015 -10000 0 -10000 0 0
SMARCC1 0.015 0.016 -10000 0 -10000 0 0
TBX21 -0.086 0.22 -10000 0 -0.74 29 29
SUMO2 0.011 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.02 0.055 -10000 0 -0.49 4 4
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 -0.013 0.13 -10000 0 -0.58 17 17
GR alpha/HSP90/FKBP51/HSP90 0.084 0.12 0.28 17 -0.38 3 20
PRL -0.059 0.12 -10000 0 -0.46 10 10
cortisol/GR alpha (dimer)/TIF2 0.22 0.22 0.48 94 -0.42 2 96
RELA -0.098 0.12 -10000 0 -0.29 19 19
FGG 0.16 0.22 0.44 54 -0.48 9 63
GR beta/TIF2 0.079 0.15 0.29 26 -0.36 20 46
IFNG -0.32 0.25 -10000 0 -0.66 87 87
apoptosis -0.07 0.18 0.44 3 -0.53 14 17
CREB1 0.014 0.031 -10000 0 -10000 0 0
histone acetylation -0.011 0.14 0.5 1 -0.44 14 15
BGLAP -0.041 0.11 -10000 0 -0.51 1 1
GR/PKAc 0.1 0.089 0.27 17 -10000 0 17
NF kappa B1 p50/RelA -0.18 0.23 -10000 0 -0.45 120 120
SMARCD1 0.015 0.016 -10000 0 -10000 0 0
MDM2 0.089 0.088 0.24 27 -0.24 3 30
GATA3 -0.02 0.15 -10000 0 -0.57 25 25
AKT1 0.002 0.006 -10000 0 -10000 0 0
CSF2 -0.078 0.13 -10000 0 -0.45 5 5
GSK3B 0.011 0.008 -10000 0 -10000 0 0
NR1I3 -0.026 0.18 0.46 1 -0.49 9 10
CSN2 0.16 0.14 0.36 49 -10000 0 49
BRG1/BAF155/BAF170/BAF60A 0.039 0.053 -10000 0 -0.32 2 2
NFATC1 -0.011 0.13 -10000 0 -0.57 17 17
POU2F1 0.017 0.011 -10000 0 -10000 0 0
CDKN1A 0.037 0.082 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.034 0.15 -10000 0 -0.52 33 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.073 0.13 0.27 16 -0.49 1 17
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.16 0.39 0.44 1 -0.84 87 88
JUN -0.17 0.17 -10000 0 -0.48 53 53
IL4 -0.085 0.15 -10000 0 -0.57 14 14
CDK5R1 -0.016 0.12 -10000 0 -0.51 20 20
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.24 0.29 0.21 1 -0.57 121 122
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.094 0.11 0.29 13 -0.49 1 14
cortisol/GR alpha (monomer) 0.27 0.24 0.55 106 -10000 0 106
NCOA2 -0.023 0.14 -10000 0 -0.58 23 23
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.23 0.28 -10000 0 -0.63 110 110
AP-1/NFAT1-c-4 -0.4 0.32 -10000 0 -0.72 146 146
AFP -0.14 0.15 -10000 0 -0.57 13 13
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.16 0.12 0.44 11 -10000 0 11
TP53 0.04 0.028 -10000 0 -0.49 1 1
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.36 0.38 -10000 0 -0.94 73 73
KRT14 -0.24 0.24 -10000 0 -0.57 67 67
TBP 0.026 0.012 -10000 0 -10000 0 0
CREBBP 0.071 0.087 0.32 2 -10000 0 2
HDAC1 0.014 0.008 -10000 0 -10000 0 0
HDAC2 0.019 0.013 -10000 0 -10000 0 0
AP-1 -0.41 0.33 -10000 0 -0.72 147 147
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.04 0.17 -10000 0 -0.58 31 31
MAPK11 0.011 0.008 -10000 0 -10000 0 0
KRT5 -0.57 0.55 -10000 0 -1.1 153 153
interleukin-1 receptor activity 0.004 0.013 -10000 0 -10000 0 0
NCOA1 0.019 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.055 -10000 0 -0.49 4 4
CGA -0.071 0.13 -10000 0 -0.58 3 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.15 0.34 67 -0.47 2 69
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.24 0.25 -10000 0 -0.55 99 99
NFKB1 -0.098 0.12 -10000 0 -0.29 20 20
MAPK8 -0.13 0.14 -10000 0 -0.39 44 44
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.081 0.18 0.44 3 -0.56 14 17
BAX 0.041 0.031 -10000 0 -10000 0 0
POMC -0.3 0.3 -10000 0 -0.82 39 39
EP300 0.071 0.087 0.29 4 -10000 0 4
cortisol/GR alpha (dimer)/p53 0.26 0.2 0.5 103 -10000 0 103
proteasomal ubiquitin-dependent protein catabolic process 0.061 0.07 0.22 5 -0.23 2 7
SGK1 0.088 0.29 -10000 0 -1.3 13 13
IL13 -0.24 0.22 -10000 0 -0.76 30 30
IL6 -0.6 0.6 -10000 0 -1.2 175 175
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.21 0.19 -10000 0 -0.7 19 19
IL2 -0.28 0.22 -10000 0 -0.63 59 59
CDK5 0.014 0.003 -10000 0 -10000 0 0
PRKACB 0.012 0.044 -10000 0 -0.58 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.35 0.45 -10000 0 -0.87 111 111
CDK5R1/CDK5 -0.005 0.087 -10000 0 -0.36 20 20
NF kappa B1 p50/RelA/PKAc -0.11 0.18 -10000 0 -0.38 46 46
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.19 0.46 103 -10000 0 103
SMARCA4 0.015 0.015 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.14 0.35 51 -0.42 4 55
NF kappa B1 p50/RelA/Cbp -0.076 0.23 0.39 1 -0.5 27 28
JUN (dimer) -0.17 0.17 -10000 0 -0.47 53 53
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.076 0.2 -10000 0 -0.67 28 28
NR3C1 0.15 0.15 0.38 51 -0.43 3 54
NR4A1 -0.32 0.3 -10000 0 -0.58 201 201
TIF2/SUV420H1 -0.005 0.11 -10000 0 -0.41 23 23
MAPKKK cascade -0.07 0.18 0.44 3 -0.53 14 17
cortisol/GR alpha (dimer)/Src-1 0.25 0.2 0.48 103 -10000 0 103
PBX1 -0.008 0.12 -10000 0 -0.57 15 15
POU1F1 0.003 0.04 -10000 0 -0.5 2 2
SELE -0.56 0.59 -10000 0 -1.2 155 155
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.14 0.35 51 -0.43 4 55
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.19 0.46 103 -10000 0 103
mol:cortisol 0.14 0.14 0.3 110 -10000 0 110
MMP1 -0.26 0.18 -10000 0 -0.47 100 100
PDGFR-alpha signaling pathway

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
PDGFRA -0.079 0.21 -9999 0 -0.59 51 51
PDGF/PDGFRA/CRKL -0.046 0.16 -9999 0 -0.42 52 52
positive regulation of JUN kinase activity -0.014 0.12 -9999 0 -0.32 22 22
CRKL 0.013 0.039 -9999 0 -0.51 2 2
PDGF/PDGFRA/Caveolin-3 -0.056 0.16 -9999 0 -0.43 53 53
AP1 -0.34 0.47 -9999 0 -1 110 110
mol:IP3 -0.053 0.16 -9999 0 -0.44 51 51
PLCG1 -0.053 0.16 -9999 0 -0.44 51 51
PDGF/PDGFRA/alphaV Integrin -0.045 0.16 -9999 0 -0.42 51 51
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.052 0.16 -9999 0 -0.44 51 51
CAV3 0 0.047 -9999 0 -0.51 3 3
CAV1 -0.013 0.13 -9999 0 -0.58 17 17
SHC/Grb2/SOS1 -0.013 0.12 -9999 0 -0.32 22 22
PDGF/PDGFRA/Shf -0.049 0.16 -9999 0 -0.44 53 53
FOS -0.3 0.48 -9999 0 -1 110 110
JUN -0.037 0.092 -9999 0 -0.49 13 13
oligodendrocyte development -0.044 0.16 -9999 0 -0.42 51 51
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:DAG -0.053 0.16 -9999 0 -0.44 51 51
PDGF/PDGFRA -0.079 0.21 -9999 0 -0.59 51 51
actin cytoskeleton reorganization -0.043 0.15 -9999 0 -0.42 51 51
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.014 0.028 -9999 0 -0.51 1 1
PI3K -0.025 0.13 -9999 0 -0.34 51 51
PDGF/PDGFRA/Crk/C3G -0.025 0.13 -9999 0 -0.34 51 51
JAK1 -0.041 0.15 -9999 0 -0.42 51 51
ELK1/SRF -0.011 0.13 -9999 0 -0.32 51 51
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.007 0.07 -9999 0 -0.58 5 5
CSNK2A1 0.022 0.028 -9999 0 -10000 0 0
GO:0007205 -0.057 0.17 -9999 0 -0.46 51 51
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.014 0.12 -9999 0 -0.32 22 22
PDGF/PDGFRA/SHB -0.044 0.15 -9999 0 -0.42 51 51
PDGF/PDGFRA/Caveolin-1 -0.062 0.19 -9999 0 -0.47 59 59
ITGAV 0.014 0.031 -9999 0 -0.58 1 1
ELK1 -0.051 0.16 -9999 0 -0.41 51 51
PIK3CA 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.044 0.15 -9999 0 -0.42 51 51
JAK-STAT cascade -0.041 0.15 -9999 0 -0.41 51 51
cell proliferation -0.049 0.16 -9999 0 -0.44 53 53
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.018 0.025 -9999 0 -0.41 1 1
PDGFRB -0.003 0.094 -9999 0 -0.58 9 9
SPHK1 -0.035 0.064 -9999 0 -1.1 1 1
mol:S1P -0.041 0.066 -9999 0 -0.67 2 2
S1P1/S1P/Gi -0.19 0.27 -9999 0 -0.48 133 133
GNAO1 -0.17 0.28 -9999 0 -0.58 110 110
PDGFB-D/PDGFRB/PLCgamma1 -0.16 0.25 -9999 0 -0.5 89 89
PLCG1 -0.17 0.25 -9999 0 -0.45 133 133
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.093 -9999 0 -0.58 9 9
GNAI2 0.012 0.007 -9999 0 -10000 0 0
GNAI3 0.012 0.007 -9999 0 -10000 0 0
GNAI1 0.007 0.055 -9999 0 -0.58 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.015 0.023 -9999 0 -0.35 1 1
S1P1/S1P -0.043 0.071 -9999 0 -0.47 3 3
negative regulation of cAMP metabolic process -0.18 0.26 -9999 0 -0.47 133 133
MAPK3 -0.22 0.32 -9999 0 -0.59 131 131
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
KDR 0.013 0.031 -9999 0 -0.58 1 1
PLCB2 -0.015 0.082 -9999 0 -0.36 5 5
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.034 0.059 -9999 0 -0.39 3 3
receptor internalization -0.041 0.067 -9999 0 -0.43 3 3
PTGS2 -0.32 0.48 -9999 0 -0.88 129 129
Rac1/GTP -0.034 0.059 -9999 0 -0.39 3 3
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA 0.014 0.004 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.18 0.26 -9999 0 -0.47 133 133
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.58 76 76
MAPK1 -0.22 0.32 -9999 0 -0.59 131 131
S1P1/S1P/PDGFB-D/PDGFRB -0.033 0.11 -9999 0 -0.45 9 9
ABCC1 0.01 0.039 -9999 0 -0.51 2 2
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0.039 -10000 0 -0.51 2 2
RAS family/GTP/Tiam1 -0.085 0.12 -10000 0 -0.27 44 44
NT3 (dimer)/TRKC -0.26 0.28 -10000 0 -0.49 198 198
NT3 (dimer)/TRKB -0.26 0.3 -10000 0 -0.49 200 200
SHC/Grb2/SOS1/GAB1/PI3K 0.043 0.008 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.099 0.23 -10000 0 -0.58 69 69
PIK3CA 0.016 0 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.006 0.061 -10000 0 -0.51 5 5
NTRK2 -0.22 0.29 -10000 0 -0.57 143 143
NTRK3 -0.28 0.29 -10000 0 -0.58 175 175
NT-4/5 (dimer)/TRKB -0.22 0.27 -10000 0 -0.45 188 188
neuron apoptosis 0.18 0.25 0.52 103 -10000 0 103
SHC 2-3/Grb2 -0.2 0.28 -10000 0 -0.58 103 103
SHC1 0.014 0.028 -10000 0 -0.51 1 1
SHC2 -0.21 0.28 -10000 0 -0.63 86 86
SHC3 -0.21 0.26 -10000 0 -0.58 98 98
STAT3 (dimer) 0.011 0.063 -10000 0 -0.34 7 7
NT3 (dimer)/TRKA -0.13 0.22 -10000 0 -0.4 131 131
RIN/GDP -0.065 0.1 -10000 0 -0.25 27 27
GIPC1 0.016 0 -10000 0 -10000 0 0
KRAS 0.014 0.028 -10000 0 -0.51 1 1
DNAJA3 -0.1 0.16 -10000 0 -0.37 80 80
RIN/GTP 0 0.02 -10000 0 -0.37 1 1
CCND1 0.007 0.14 -10000 0 -0.55 18 18
MAGED1 0.016 0 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.026 0.15 -10000 0 -0.57 25 25
SHC/GRB2/SOS1 0.031 0.017 -10000 0 -0.29 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.052 0.17 -10000 0 -0.38 72 72
TRKA/NEDD4-2 0.016 0.044 -10000 0 -0.36 5 5
ELMO1 0.012 0.044 -10000 0 -0.58 2 2
RhoG/GTP/ELMO1/DOCK1 0.018 0.042 -10000 0 -0.52 2 2
NGF -0.063 0.2 -10000 0 -0.58 47 47
HRAS 0.016 0 -10000 0 -10000 0 0
DOCK1 0.014 0.031 -10000 0 -0.58 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0 0.027 -10000 0 -0.51 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.005 0.072 -10000 0 -0.51 7 7
DNM1 0.001 0.093 -10000 0 -0.58 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.1 0.16 -10000 0 -0.36 84 84
mol:GDP -0.095 0.15 -10000 0 -0.37 33 33
NGF (dimer) -0.063 0.2 -10000 0 -0.57 47 47
RhoG/GDP 0.009 0.033 -10000 0 -0.42 2 2
RIT1/GDP -0.058 0.1 -10000 0 -0.25 24 24
TIAM1 0.012 0.044 -10000 0 -0.58 2 2
PIK3R1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.18 0.24 -10000 0 -0.41 174 174
KIDINS220/CRKL/C3G 0.021 0.028 -10000 0 -0.36 2 2
SHC/RasGAP 0.022 0.02 -10000 0 -0.36 1 1
FRS2 family/SHP2 0.025 0.045 -10000 0 -0.29 7 7
SHC/GRB2/SOS1/GAB1 0.039 0.016 -10000 0 -10000 0 0
RIT1/GTP 0.012 0 -10000 0 -10000 0 0
NT3 (dimer) -0.092 0.23 -10000 0 -0.57 65 65
RAP1/GDP -0.067 0.068 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.013 0.039 -10000 0 -0.51 2 2
BDNF (dimer) -0.099 0.23 -10000 0 -0.57 69 69
ubiquitin-dependent protein catabolic process -0.024 0.13 -10000 0 -0.34 52 52
Schwann cell development -0.054 0.036 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.034 0.041 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.044 0.02 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.33 0.28 -10000 0 -0.62 147 147
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
Rap1/GTP -0.064 0.074 -10000 0 -10000 0 0
STAT3 0.011 0.063 -10000 0 -0.34 7 7
axon guidance -0.31 0.26 -10000 0 -0.59 147 147
MAPK3 -0.038 0.16 -10000 0 -0.35 62 62
MAPK1 -0.038 0.16 -10000 0 -0.35 62 62
CDC42/GDP -0.058 0.1 -10000 0 -0.25 24 24
NTF3 -0.093 0.23 -10000 0 -0.57 65 65
NTF4 -0.026 0.15 -10000 0 -0.58 25 25
NGF (dimer)/TRKA/FAIM -0.024 0.13 -10000 0 -0.34 52 52
PI3K 0.023 0 -10000 0 -10000 0 0
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.14 0.17 -10000 0 -0.38 85 85
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.23 0.26 -10000 0 -0.43 200 200
RGS19 0.014 0.028 -10000 0 -0.51 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.073 -10000 0 -10000 0 0
Rac1/GDP -0.058 0.1 -10000 0 -0.25 24 24
NGF (dimer)/TRKA/GRIT -0.034 0.13 -10000 0 -0.35 52 52
neuron projection morphogenesis -0.073 0.18 -10000 0 -0.53 21 21
NGF (dimer)/TRKA/NEDD4-2 -0.024 0.13 -10000 0 -0.34 52 52
MAP2K1 0.045 0.014 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.57 84 84
NGF (dimer)/TRKA/GIPC/GAIP -0.004 0.11 -10000 0 -0.32 18 18
RAS family/GTP/PI3K 0.036 0.008 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.041 0.038 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.044 -10000 0 -0.58 2 2
MAPKKK cascade -0.12 0.24 -10000 0 -0.72 47 47
RASA1 0.016 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.016 0.044 -10000 0 -0.36 5 5
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.38 167 167
NGF (dimer)/TRKA/p62/Atypical PKCs -0.003 0.12 -10000 0 -0.3 16 16
MATK -0.031 0.16 -10000 0 -0.56 29 29
NEDD4L 0.016 0 -10000 0 -10000 0 0
RAS family/GDP -0.063 0.064 -10000 0 -0.23 2 2
NGF (dimer)/TRKA -0.11 0.18 -10000 0 -0.35 111 111
Rac1/GTP -0.11 0.11 -10000 0 -0.29 71 71
FRS2 family/SHP2/CRK family 0.039 0.043 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.11 0.16 0.43 50 -10000 0 50
GNAI2 0.016 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.064 -10000 0 -0.31 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.17 0.27 -10000 0 -0.58 110 110
RhoA/GTP -0.089 0.18 -10000 0 -0.44 50 50
negative regulation of cAMP metabolic process -0.1 0.19 -10000 0 -0.35 112 112
GNAZ -0.11 0.24 -10000 0 -0.58 76 76
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 -0.005 0.1 -10000 0 -0.52 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.11 0.2 -10000 0 -0.35 112 112
RhoA/GDP 0.012 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.054 -10000 0 -0.58 3 3
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.019 0.029 -9999 0 -10000 0 0
VDR 0.012 0.042 -9999 0 -0.54 2 2
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.013 0.13 -9999 0 -0.39 7 7
RXRs/LXRs/DNA/Oxysterols 0.006 0.12 -9999 0 -0.39 7 7
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.006 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.008 0.11 -9999 0 -0.28 40 40
RXRs/NUR77 -0.23 0.22 -9999 0 -0.37 241 241
RXRs/PPAR -0.047 0.14 -9999 0 -0.38 15 15
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.03 -9999 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.011 0.088 -9999 0 -0.29 28 28
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0.042 -9999 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.006 0.086 -9999 0 -0.29 27 27
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.044 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.008 0.11 -9999 0 -0.28 40 40
THRA 0.016 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0.03 -9999 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.047 0.16 -9999 0 -0.3 95 95
NR1H4 -0.12 0.24 -9999 0 -0.56 83 83
RXRs/LXRs/DNA -0.017 0.15 -9999 0 -0.38 7 7
NR1H2 0.022 0.005 -9999 0 -10000 0 0
NR1H3 0.022 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.15 -9999 0 -0.28 96 96
NR4A1 -0.32 0.29 -9999 0 -0.58 200 200
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.084 0.16 -9999 0 -0.32 77 77
RXRG -0.14 0.26 -9999 0 -0.57 95 95
RXR alpha/CCPG 0.026 0.024 -9999 0 -0.41 1 1
RXRA 0.02 0.032 -9999 0 -0.57 1 1
RXRB 0.022 0.005 -9999 0 -10000 0 0
THRB -0.016 0.13 -9999 0 -0.58 19 19
PPARG -0.024 0.15 -9999 0 -0.57 24 24
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.008 0.13 -9999 0 -0.48 6 6
mol:Oxysterols 0.007 0.006 -9999 0 -10000 0 0
cholesterol transport 0.006 0.12 -9999 0 -0.38 7 7
PPARA 0.012 0.044 -9999 0 -0.58 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.029 0.16 -9999 0 -0.58 27 27
RXRs/NUR77/BCL2 -0.21 0.2 -9999 0 -0.32 243 243
SREBF1 0.015 0.11 -9999 0 -0.47 2 2
RXRs/RXRs/DNA/9cRA -0.046 0.16 -9999 0 -0.3 95 95
ABCA1 0.016 0.11 -9999 0 -0.46 1 1
RARs/THRs 0.005 0.12 -9999 0 -0.58 6 6
RXRs/FXR -0.12 0.21 -9999 0 -0.36 141 141
BCL2 -0.008 0.12 -9999 0 -0.58 14 14
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.011 0.12 -10000 0 -0.35 19 19
TBX21 -0.15 0.5 -10000 0 -1.2 56 56
B2M 0.016 0.008 -10000 0 -10000 0 0
TYK2 0.017 0.023 -10000 0 -10000 0 0
IL12RB1 -0.02 0.15 -10000 0 -0.56 24 24
GADD45B -0.081 0.39 -10000 0 -0.96 42 42
IL12RB2 -0.071 0.2 -10000 0 -0.52 59 59
GADD45G -0.077 0.37 -10000 0 -0.9 43 43
natural killer cell activation 0.001 0.026 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.011 0.072 -10000 0 -0.59 5 5
IL2RA -0.036 0.16 -10000 0 -0.55 33 33
IFNG -0.087 0.2 -10000 0 -0.51 68 68
STAT3 (dimer) -0.078 0.36 -10000 0 -0.76 60 60
HLA-DRB5 -0.028 0.14 -10000 0 -0.55 25 25
FASLG -0.16 0.51 -10000 0 -1.2 63 63
NF kappa B2 p52/RelB -0.2 0.39 -10000 0 -0.98 61 61
CD4 0.009 0.045 -10000 0 -0.58 2 2
SOCS1 0.014 0.028 -10000 0 -0.51 1 1
EntrezGene:6955 -0.007 0.016 -10000 0 -10000 0 0
CD3D -0.051 0.18 -10000 0 -0.57 38 38
CD3E -0.055 0.19 -10000 0 -0.58 40 40
CD3G -0.059 0.19 -10000 0 -0.58 42 42
IL12Rbeta2/JAK2 -0.04 0.15 -10000 0 -0.37 60 60
CCL3 -0.15 0.5 -10000 0 -1.1 59 59
CCL4 -0.18 0.55 -10000 0 -1.3 62 62
HLA-A 0.014 0.032 -10000 0 -0.58 1 1
IL18/IL18R 0.035 0.13 -10000 0 -0.4 24 24
NOS2 -0.12 0.42 -10000 0 -1 48 48
IL12/IL12R/TYK2/JAK2/SPHK2 -0.011 0.12 -10000 0 -0.35 19 19
IL1R1 -0.12 0.44 -10000 0 -1 54 54
IL4 0.002 0.026 -10000 0 -10000 0 0
JAK2 0.015 0.039 -10000 0 -0.58 1 1
EntrezGene:6957 -0.006 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.4 -10000 0 -0.84 67 67
RAB7A -0.031 0.31 -10000 0 -0.71 42 42
lysosomal transport -0.026 0.3 -10000 0 -0.67 42 42
FOS -0.42 0.66 -10000 0 -1.2 133 133
STAT4 (dimer) -0.076 0.4 -10000 0 -0.82 63 63
STAT5A (dimer) -0.24 0.4 -10000 0 -0.91 75 75
GZMA -0.18 0.55 -10000 0 -1.3 58 58
GZMB -0.16 0.5 -10000 0 -1.2 57 57
HLX 0.016 0 -10000 0 -10000 0 0
LCK -0.15 0.5 -10000 0 -1.1 61 61
TCR/CD3/MHC II/CD4 -0.13 0.3 -10000 0 -0.63 65 65
IL2/IL2R -0.017 0.14 -10000 0 -0.42 29 29
MAPK14 -0.062 0.38 -10000 0 -0.85 50 50
CCR5 -0.1 0.42 -10000 0 -1 46 46
IL1B -0.03 0.16 -10000 0 -0.55 30 30
STAT6 -0.011 0.14 0.25 1 -0.28 39 40
STAT4 -0.016 0.13 -10000 0 -0.58 19 19
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.01 0.055 -10000 0 -0.51 4 4
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.004 0.091 -10000 0 -0.49 11 11
CD8A -0.047 0.18 -10000 0 -0.58 38 38
CD8B -0.042 0.18 -10000 0 -0.57 35 35
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.011 0.12 0.35 19 -10000 0 19
IL2RB 0.006 0.075 -10000 0 -0.56 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.061 0.36 -10000 0 -0.74 63 63
IL2RG -0.011 0.12 -10000 0 -0.54 17 17
IL12 0.004 0.088 -10000 0 -0.35 17 17
STAT5A 0.014 0.031 -10000 0 -0.58 1 1
CD247 0 0.081 -10000 0 -0.57 7 7
IL2 0.004 0.007 -10000 0 -10000 0 0
SPHK2 0.014 0.028 -10000 0 -0.51 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.071 -10000 0 -0.5 6 6
IL12/IL12R/TYK2/JAK2 -0.17 0.57 -10000 0 -1.2 64 64
MAP2K3 -0.067 0.38 -10000 0 -0.84 51 51
RIPK2 0.016 0 -10000 0 -10000 0 0
MAP2K6 -0.071 0.38 -10000 0 -0.85 51 51
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.008 0.11 -10000 0 -0.58 12 12
IL18RAP -0.013 0.14 -10000 0 -0.58 19 19
IL12Rbeta1/TYK2 -0.006 0.11 -10000 0 -0.41 24 24
EOMES -0.073 0.32 -10000 0 -1.4 19 19
STAT1 (dimer) -0.087 0.35 -10000 0 -0.74 62 62
T cell proliferation -0.04 0.3 -10000 0 -0.62 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.056 -10000 0 -0.59 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.25 -10000 0 -0.65 57 57
ATF2 -0.046 0.35 -10000 0 -0.78 47 47
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.016 0.055 -9999 0 -0.28 12 12
RGS9BP -0.011 0.12 -9999 0 -0.56 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.001 0.004 -9999 0 -10000 0 0
mol:Na + -0.11 0.18 -9999 0 -0.34 124 124
mol:ADP 0.011 0.021 -9999 0 -0.37 1 1
GNAT2 0.007 0.055 -9999 0 -0.51 4 4
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.35 89 89
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.006 0.038 -9999 0 -0.31 5 5
GRK7 0.011 0.028 -9999 0 -0.51 1 1
CNGB3 -0.13 0.23 -9999 0 -0.51 99 99
Cone Metarhodopsin II/X-Arrestin 0.002 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.11 0.18 -9999 0 -0.32 133 133
Cone PDE6 -0.053 0.14 -9999 0 -0.4 9 9
Cone Metarhodopsin II 0.008 0.016 -9999 0 -0.28 1 1
Na + (4 Units) -0.11 0.18 -9999 0 -0.32 133 133
GNAT2/GDP -0.051 0.15 -9999 0 -0.3 86 86
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.007 0.034 -9999 0 -0.28 5 5
Cone Transducin 0.017 0.058 -9999 0 -0.29 12 12
SLC24A2 -0.017 0.12 -9999 0 -0.51 19 19
GNB3/GNGT2 0.013 0.064 -9999 0 -0.41 8 8
GNB3 0.009 0.061 -9999 0 -0.56 4 4
GNAT2/GTP 0.005 0.04 -9999 0 -0.37 4 4
CNGA3 -0.049 0.18 -9999 0 -0.58 36 36
ARR3 0.003 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.11 0.18 -9999 0 -0.34 124 124
mol:Pi -0.065 0.17 -9999 0 -0.35 89 89
Cone CNG Channel -0.098 0.14 -9999 0 -0.45 16 16
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.017 0.12 -9999 0 -0.51 19 19
RGS9 -0.11 0.24 -9999 0 -0.58 76 76
PDE6C 0.003 0.006 -9999 0 -10000 0 0
GNGT2 0.009 0.062 -9999 0 -0.58 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.028 -9999 0 -0.51 1 1
LPA4-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
ADCY4 0.021 0.02 -9999 0 -0.35 1 1
ADCY5 -0.17 0.19 -9999 0 -0.35 183 183
ADCY6 0.023 0 -9999 0 -10000 0 0
ADCY7 0.023 0 -9999 0 -10000 0 0
ADCY1 0.013 0.054 -9999 0 -0.31 10 10
ADCY2 -0.12 0.18 -9999 0 -0.35 135 135
ADCY3 0.023 0 -9999 0 -10000 0 0
ADCY8 0.011 0.034 -9999 0 -0.3 4 4
PRKCE 0.013 0 -9999 0 -10000 0 0
ADCY9 0.017 0.044 -9999 0 -0.35 5 5
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.063 0.094 -9999 0 -0.28 7 7
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.089 0.16 -9999 0 -0.54 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.053 0.14 -9999 0 -0.47 5 5
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.17 -9999 0 -0.35 142 142
AP1 -0.17 0.25 -9999 0 -0.53 86 86
ILK -0.1 0.16 -9999 0 -0.47 9 9
bone resorption -0.073 0.15 -9999 0 -0.47 15 15
PTK2B 0.014 0.031 -9999 0 -0.58 1 1
PYK2/p130Cas -0.1 0.13 -9999 0 -0.52 5 5
ITGAV 0.017 0.032 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0 0.097 -9999 0 -0.41 19 19
alphaV/beta3 Integrin/Osteopontin -0.15 0.16 -9999 0 -0.34 78 78
MAP3K1 -0.1 0.16 -9999 0 -0.3 75 75
JUN -0.006 0.11 -9999 0 -0.58 13 13
MAPK3 -0.09 0.16 -9999 0 -0.36 24 24
MAPK1 -0.09 0.16 -9999 0 -0.34 37 37
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.092 0.16 -9999 0 -0.43 12 12
ITGB3 -0.051 0.19 -9999 0 -0.57 42 42
NFKBIA -0.073 0.16 -9999 0 -0.53 5 5
FOS -0.17 0.27 -9999 0 -0.58 110 110
CD44 -0.004 0.11 -9999 0 -0.57 12 12
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU -0.089 0.18 -9999 0 -0.81 1 1
NF kappa B1 p50/RelA -0.096 0.1 -9999 0 -0.46 5 5
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.038 0.14 -9999 0 -0.41 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.11 0.16 -9999 0 -0.3 76 76
VAV3 -0.096 0.16 -9999 0 -0.48 11 11
MAP3K14 -0.1 0.17 -9999 0 -0.34 44 44
ROCK2 0.004 0.082 -9999 0 -0.58 7 7
SPP1 -0.19 0.26 -9999 0 -0.5 141 141
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.081 0.15 -9999 0 -0.48 9 9
MMP2 -0.15 0.24 -9999 0 -0.56 63 63
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 -0.054 0.17 -10000 0 -0.42 45 45
IKBKB -0.006 0.076 -10000 0 -0.26 6 6
AKT1 -0.048 0.12 -10000 0 -0.24 72 72
IKBKG -0.004 0.079 -10000 0 -0.28 6 6
CALM1 -0.044 0.14 -10000 0 -0.41 29 29
PIK3CA 0.016 0 -10000 0 -10000 0 0
MAP3K1 -0.089 0.24 -10000 0 -0.54 61 61
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.14 -10000 0 -0.44 29 29
DOK1 0.014 0.028 -10000 0 -0.51 1 1
AP-1 -0.052 0.11 -10000 0 -0.25 49 49
LYN 0.016 0 -10000 0 -10000 0 0
BLNK -0.001 0.098 -10000 0 -0.58 10 10
SHC1 0.014 0.028 -10000 0 -0.51 1 1
BCR complex -0.096 0.22 -10000 0 -0.47 86 86
CD22 -0.19 0.32 -10000 0 -0.72 77 77
CAMK2G -0.033 0.13 -10000 0 -0.4 23 23
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.004 0.082 -10000 0 -0.58 7 7
SHC/GRB2/SOS1 -0.074 0.14 -10000 0 -0.49 21 21
GO:0007205 -0.057 0.15 -10000 0 -0.45 29 29
SYK 0.012 0.044 -10000 0 -0.58 2 2
ELK1 -0.045 0.14 -10000 0 -0.42 29 29
NFATC1 -0.1 0.24 -10000 0 -0.52 67 67
B-cell antigen/BCR complex -0.096 0.22 -10000 0 -0.47 86 86
PAG1/CSK 0.023 0 -10000 0 -10000 0 0
NFKBIB 0.01 0.029 -10000 0 -10000 0 0
HRAS -0.039 0.14 -10000 0 -0.39 29 29
NFKBIA 0.01 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.016 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.068 0.21 -10000 0 -0.59 35 35
mol:GDP -0.054 0.14 -10000 0 -0.42 29 29
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B -0.02 0.14 -10000 0 -0.56 22 22
NF-kappa-B/RelA/I kappa B alpha 0.016 0.024 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.12 0.24 -10000 0 -0.52 78 78
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.057 0.15 -10000 0 -0.45 29 29
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.12 0.19 -10000 0 -0.46 50 50
CHUK -0.004 0.079 -10000 0 -0.28 6 6
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.054 0.11 -10000 0 -0.47 15 15
PTPN6 -0.15 0.31 -10000 0 -0.68 74 74
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.012 0.034 -10000 0 -0.1 21 21
VAV2 -0.18 0.28 -10000 0 -0.66 70 70
ubiquitin-dependent protein catabolic process 0.015 0.028 -10000 0 -10000 0 0
BTK -0.064 0.27 0.36 5 -1.2 20 25
CD19 -0.19 0.3 -10000 0 -0.68 73 73
MAP4K1 -0.002 0.099 -10000 0 -0.56 11 11
CD72 -0.002 0.095 -10000 0 -0.51 12 12
PAG1 0.016 0 -10000 0 -10000 0 0
MAPK14 -0.065 0.2 -10000 0 -0.45 60 60
SH3BP5 0.014 0.031 -10000 0 -0.58 1 1
PIK3AP1 -0.054 0.18 -10000 0 -0.5 34 34
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.07 0.21 -10000 0 -0.43 78 78
RAF1 -0.03 0.13 -10000 0 -0.44 16 16
RasGAP/p62DOK/SHIP -0.1 0.2 -10000 0 -0.6 36 36
CD79A -0.12 0.24 -10000 0 -0.57 81 81
re-entry into mitotic cell cycle -0.051 0.11 -10000 0 -0.24 50 50
RASA1 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.009 0.11 -10000 0 -0.42 11 11
MAPK1 -0.009 0.11 -10000 0 -0.42 11 11
CD72/SHP1 -0.14 0.29 -10000 0 -0.65 72 72
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.067 0.2 -10000 0 -0.46 57 57
actin cytoskeleton organization -0.12 0.25 -10000 0 -0.57 62 62
NF-kappa-B/RelA 0.037 0.046 -10000 0 -10000 0 0
Calcineurin -0.047 0.1 -10000 0 -0.47 11 11
PI3K -0.16 0.21 -10000 0 -0.5 87 87
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.056 0.16 -10000 0 -0.45 33 33
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.28 -10000 0 -0.77 46 46
DAPP1 -0.15 0.3 -10000 0 -0.89 43 43
cytokine secretion -0.092 0.22 -10000 0 -0.48 67 67
mol:DAG -0.057 0.15 -10000 0 -0.45 29 29
PLCG2 0.009 0.057 -10000 0 -0.52 4 4
MAP2K1 -0.019 0.12 -10000 0 -0.47 11 11
B-cell antigen/BCR complex/FcgammaRIIB -0.099 0.24 -10000 0 -0.47 93 93
mol:PI-3-4-5-P3 -0.11 0.15 -10000 0 -0.34 87 87
ETS1 -0.022 0.12 -10000 0 -0.47 11 11
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.055 0.18 -10000 0 -0.57 21 21
B-cell antigen/BCR complex/LYN -0.14 0.28 -10000 0 -0.54 85 85
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.12 0.27 -10000 0 -0.63 61 61
B-cell antigen/BCR complex/LYN/SYK -0.17 0.28 -10000 0 -0.65 75 75
CARD11 -0.053 0.15 -10000 0 -0.43 33 33
FCGR2B -0.032 0.16 -10000 0 -0.57 29 29
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.006 0.039 -10000 0 -10000 0 0
PTPRC -0.059 0.2 -10000 0 -0.57 45 45
PDPK1 -0.049 0.12 -10000 0 -0.26 49 49
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0.016 0.026 -10000 0 -0.1 10 10
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.17 0.27 -9999 0 -0.58 110 110
CDC42/GTP -0.087 0.18 -9999 0 -0.44 49 49
PLCG1 -0.089 0.19 -9999 0 -0.46 49 49
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.023 0 -9999 0 -10000 0 0
cell migration -0.11 0.16 -9999 0 -0.44 49 49
S1PR5 -0.005 0.1 -9999 0 -0.52 14 14
S1PR4 0.005 0.078 -9999 0 -0.55 7 7
MAPK3 -0.089 0.19 -9999 0 -0.46 49 49
MAPK1 -0.089 0.19 -9999 0 -0.46 49 49
S1P/S1P5/Gi -0.11 0.2 -9999 0 -0.35 112 112
GNAI1 0.011 0.054 -9999 0 -0.58 3 3
CDC42/GDP 0.012 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.008 0.064 -9999 0 -0.31 14 14
RHOA 0.031 0.042 -9999 0 -0.28 4 4
S1P/S1P4/Gi -0.1 0.2 -9999 0 -0.35 111 111
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.58 76 76
S1P/S1P4/G12/G13 0.024 0.045 -9999 0 -0.29 7 7
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.014 0.14 -9999 0 -0.35 47 47
MAP4K1 -0.002 0.099 -9999 0 -0.56 11 11
MAP3K8 0.011 0.054 -9999 0 -0.58 3 3
PRKCB -0.16 0.27 -9999 0 -0.58 103 103
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.013 0.039 -9999 0 -0.51 2 2
MAP3K1 0.011 0.11 -9999 0 -0.59 5 5
JUN -0.15 0.29 -9999 0 -0.56 114 114
MAP3K7 0.011 0.11 -9999 0 -0.59 5 5
GRAP2 -0.057 0.19 -9999 0 -0.58 44 44
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 0.019 0.12 -9999 0 -0.54 6 6
LAT 0.014 0.028 -9999 0 -0.51 1 1
LCP2 0.012 0.044 -9999 0 -0.58 2 2
MAPK8 -0.16 0.3 -9999 0 -0.6 106 106
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.003 0.12 -9999 0 -0.63 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.005 0.14 -9999 0 -0.7 5 5
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.014 -9999 0 -10000 0 0
SVIL 0.008 0.056 -9999 0 -0.58 3 3
ZNF318 0.024 0.035 -9999 0 -10000 0 0
JMJD2C -0.002 0.026 -9999 0 -0.079 28 28
T-DHT/AR/Ubc9 -0.12 0.19 -9999 0 -0.38 128 128
CARM1 0.015 0.002 -9999 0 -10000 0 0
PRDX1 0.016 0.002 -9999 0 -10000 0 0
PELP1 0.017 0.006 -9999 0 -10000 0 0
CTNNB1 0.013 0.011 -9999 0 -10000 0 0
AKT1 0.018 0.009 -9999 0 -10000 0 0
PTK2B 0.012 0.032 -9999 0 -0.58 1 1
MED1 0.018 0.011 -9999 0 -10000 0 0
MAK 0.012 0.084 -9999 0 -0.49 8 8
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0.011 0.034 -9999 0 -0.57 1 1
GSN 0.002 0.077 -9999 0 -0.58 6 6
NCOA2 -0.023 0.14 -9999 0 -0.58 23 23
NCOA6 0.011 0.03 -9999 0 -0.51 1 1
DNA-PK 0.033 0.037 -9999 0 -10000 0 0
NCOA4 0.015 0.001 -9999 0 -10000 0 0
PIAS3 0.013 0.011 -9999 0 -10000 0 0
cell proliferation -0.02 0.052 -9999 0 -0.21 3 3
XRCC5 0.017 0.008 -9999 0 -10000 0 0
UBE3A 0.011 0.021 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.15 0.23 -9999 0 -0.42 138 138
FHL2 -0.019 0.11 -9999 0 -1.2 1 1
RANBP9 0.013 0.013 -9999 0 -10000 0 0
JMJD1A -0.012 0.058 -9999 0 -0.12 77 77
CDK6 -0.002 0.1 -9999 0 -0.58 11 11
TGFB1I1 -0.004 0.099 -9999 0 -0.58 10 10
T-DHT/AR/CyclinD1 -0.14 0.2 -9999 0 -0.39 140 140
XRCC6 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR -0.13 0.22 -9999 0 -0.39 130 130
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.021 0.023 -9999 0 -10000 0 0
BRCA1 0.011 0.032 -9999 0 -0.53 1 1
TCF4 0.015 0.057 -9999 0 -0.58 3 3
CDKN2A -0.24 0.26 -9999 0 -0.5 174 174
SRF 0.027 0.012 -9999 0 -10000 0 0
NKX3-1 -0.077 0.18 -9999 0 -1 7 7
KLK3 -0.059 0.31 -9999 0 -1.5 15 15
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.019 0.013 -9999 0 -10000 0 0
AOF2 -0.004 0.015 -9999 0 -0.071 15 15
APPL1 0.031 0.02 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.12 0.2 -9999 0 -0.37 128 128
AR -0.21 0.29 -9999 0 -0.59 128 128
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.019 0.013 -9999 0 -10000 0 0
PAWR 0.013 0.031 -9999 0 -0.58 1 1
PRKDC 0.017 0.008 -9999 0 -10000 0 0
PA2G4 0.019 0.016 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.11 0.18 -9999 0 -0.34 128 128
RPS6KA3 0.012 0.014 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.12 0.19 -9999 0 -0.38 128 128
LATS2 0.017 0.034 -9999 0 -0.58 1 1
T-DHT/AR/PRX1 -0.11 0.18 -9999 0 -0.34 128 128
Cyclin D3/CDK11 p58 0.012 0.003 -9999 0 -10000 0 0
VAV3 0.001 0.083 -9999 0 -0.54 8 8
KLK2 -0.092 0.13 -9999 0 -0.48 17 17
CASP8 0.016 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.2 -9999 0 -0.36 138 138
TMPRSS2 -0.22 0.43 -9999 0 -1 70 70
CCND1 -0.013 0.12 -9999 0 -0.54 18 18
PIAS1 0.011 0.021 -9999 0 -10000 0 0
mol:T-DHT -0.007 0.026 -9999 0 -0.072 31 31
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.008 0.033 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.2 -9999 0 -0.39 134 134
CMTM2 0.012 0.048 -9999 0 -0.51 3 3
SNURF -0.033 0.16 -9999 0 -0.58 28 28
ZMIZ1 0.011 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.019 0.013 -9999 0 -10000 0 0
FKBP4 0.013 0.013 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.027 0.13 -9999 0 -0.34 55 55
EPHB2 -0.018 0.13 -9999 0 -0.51 23 23
Syndecan-2/TACI -0.033 0.14 -9999 0 -0.35 56 56
LAMA1 -0.087 0.21 -9999 0 -0.52 68 68
Syndecan-2/alpha2 ITGB1 -0.03 0.15 -9999 0 -0.33 50 50
HRAS 0.016 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.007 0.092 -9999 0 -0.35 24 24
ITGA5 -0.008 0.12 -9999 0 -0.58 14 14
BAX 0.021 0.089 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.004 0.084 -9999 0 -0.31 24 24
LAMA3 -0.077 0.21 -9999 0 -0.54 59 59
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.011 0.054 -9999 0 -0.58 3 3
Syndecan-2/MMP2 -0.028 0.16 -9999 0 -0.42 45 45
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.018 0.046 -9999 0 -0.37 5 5
dendrite morphogenesis -0.017 0.12 -9999 0 -0.32 47 47
Syndecan-2/GM-CSF -0.054 0.15 -9999 0 -0.32 84 84
determination of left/right symmetry -0.006 0.11 -9999 0 -0.41 24 24
Syndecan-2/PKC delta 0.004 0.093 -9999 0 -0.34 24 24
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.038 0.14 -9999 0 -0.28 84 84
MAPK1 -0.038 0.14 -9999 0 -0.28 84 84
Syndecan-2/RACK1 0.014 0.08 -9999 0 -0.28 24 24
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.006 0.11 -9999 0 -0.41 24 24
ITGA2 0.008 0.063 -9999 0 -0.52 5 5
MAPK8 0.011 0.099 -9999 0 -0.34 27 27
Syndecan-2/alpha2/beta1 Integrin -0.035 0.14 -9999 0 -0.33 38 38
Syndecan-2/Kininogen -0.007 0.092 -9999 0 -0.35 24 24
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.022 0.076 -9999 0 -0.26 24 24
Syndecan-2/CASK/Protein 4.1 0.004 0.084 -9999 0 -0.31 24 24
extracellular matrix organization 0.004 0.092 -9999 0 -0.34 24 24
actin cytoskeleton reorganization -0.027 0.13 -9999 0 -0.33 55 55
Syndecan-2/Caveolin-2/Ras 0.011 0.093 -9999 0 -0.31 26 26
Syndecan-2/Laminin alpha3 -0.053 0.16 -9999 0 -0.36 76 76
Syndecan-2/RasGAP 0.021 0.077 -9999 0 -0.26 24 24
alpha5/beta1 Integrin 0.006 0.085 -9999 0 -0.41 14 14
PRKCD 0.016 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.017 0.12 -9999 0 -0.32 47 47
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.031 0.075 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.043 0.17 -9999 0 -0.57 34 34
RASA1 0.016 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.018 0.046 -9999 0 -0.37 5 5
Syndecan-2/Synbindin 0.004 0.093 -9999 0 -0.34 24 24
TGFB1 0.016 0 -9999 0 -10000 0 0
CASP3 0.015 0.085 -9999 0 -0.3 24 24
FN1 -0.035 0.16 -9999 0 -0.53 33 33
Syndecan-2/IL8 -0.049 0.16 -9999 0 -0.37 70 70
SDC2 -0.006 0.11 -9999 0 -0.41 24 24
KNG1 0 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.004 0.093 -9999 0 -0.34 24 24
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.078 0.2 -9999 0 -0.51 63 63
Syndecan-2/TGFB1 0.004 0.093 -9999 0 -0.34 24 24
Syndecan-2/Syntenin/PI-4-5-P2 0.004 0.084 -9999 0 -0.31 24 24
Syndecan-2/Ezrin 0.014 0.085 -9999 0 -0.3 24 24
PRKACA 0.015 0.085 -9999 0 -0.3 24 24
angiogenesis -0.048 0.16 -9999 0 -0.36 70 70
MMP2 -0.037 0.17 -9999 0 -0.58 32 32
IL8 -0.069 0.21 -9999 0 -0.57 51 51
calcineurin-NFAT signaling pathway -0.033 0.14 -9999 0 -0.35 56 56
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.001 0.093 -9999 0 -0.58 9 9
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.099 0.19 -9999 0 -0.31 141 141
GNAO1 -0.17 0.27 -9999 0 -0.58 110 110
S1P/S1P3/G12/G13 0.025 0.051 -9999 0 -0.31 8 8
AKT1 -0.035 0.16 -9999 0 -0.84 9 9
AKT3 -0.056 0.25 -9999 0 -1.3 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.001 0.093 -9999 0 -0.57 9 9
GNAI2 0.017 0.004 -9999 0 -10000 0 0
GNAI3 0.017 0.003 -9999 0 -10000 0 0
GNAI1 0.012 0.054 -9999 0 -0.57 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.004 0.087 -9999 0 -0.57 8 8
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.22 -9999 0 -0.52 56 56
MAPK3 -0.089 0.21 -9999 0 -0.49 56 56
MAPK1 -0.089 0.21 -9999 0 -0.49 56 56
JAK2 -0.088 0.21 -9999 0 -0.5 57 57
CXCR4 -0.093 0.22 -9999 0 -0.5 57 57
FLT1 0.018 0.003 -9999 0 -10000 0 0
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
SRC -0.089 0.21 -9999 0 -0.49 56 56
S1P/S1P3/Gi -0.1 0.22 -9999 0 -0.52 56 56
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.087 0.2 -9999 0 -0.47 56 56
VEGFA 0.018 0.003 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.095 0.19 -9999 0 -0.34 111 111
VEGFR1 homodimer/VEGFA homodimer 0.032 0.008 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.011 0.11 -9999 0 -0.26 58 58
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.58 76 76
G12/G13 0.023 0 -9999 0 -10000 0 0
GNA14 -0.067 0.2 -9999 0 -0.58 50 50
GNA15 0.012 0.044 -9999 0 -0.58 2 2
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.014 0.031 -9999 0 -0.58 1 1
Rac1/GTP -0.087 0.2 -9999 0 -0.47 56 56
Aurora A 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
Aurora A/GADD45A -0.013 0.076 -9999 0 -10000 0 0
BIRC5 -0.36 0.23 -9999 0 -0.51 259 259
NFKBIA -0.012 0.077 -9999 0 -10000 0 0
CPEB1 -0.28 0.29 -9999 0 -0.58 173 173
AKT1 -0.012 0.077 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.02 0.067 -9999 0 -0.4 1 1
NDEL1/TACC3 -0.021 0.1 -9999 0 -0.37 11 11
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.018 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.014 0.08 -9999 0 -0.48 1 1
MDM2 -0.002 0.094 -9999 0 -0.51 12 12
JUB 0.011 0.048 -9999 0 -0.51 3 3
TPX2 -0.18 0.19 -9999 0 -0.36 192 192
TP53 0.001 0.055 -9999 0 -10000 0 0
DLG7 -0.023 0.076 -9999 0 -10000 0 0
AURKAIP1 0.014 0.028 -9999 0 -0.51 1 1
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.023 0.11 -9999 0 -0.39 11 11
G2/M transition of mitotic cell cycle -0.02 0.067 -9999 0 -0.4 1 1
AURKA -0.026 0.095 -9999 0 -10000 0 0
AURKB -0.048 0.059 -9999 0 -10000 0 0
CDC25B -0.006 0.07 -9999 0 -0.24 6 6
G2/M transition checkpoint -0.021 0.071 -9999 0 -0.35 3 3
mRNA polyadenylation -0.18 0.18 -9999 0 -0.36 173 173
Aurora A/CPEB -0.18 0.19 -9999 0 -0.36 173 173
Aurora A/TACC1/TRAP/chTOG 0.007 0.069 -9999 0 -0.41 1 1
BRCA1 0.014 0.028 -9999 0 -0.51 1 1
centrosome duplication -0.014 0.079 -9999 0 -0.47 1 1
regulation of centrosome cycle -0.031 0.095 -9999 0 -0.36 11 11
spindle assembly 0.006 0.068 -9999 0 -0.4 1 1
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.19 0.14 -9999 0 -0.35 101 101
CENPA -0.048 0.06 -9999 0 -10000 0 0
Aurora A/PP2A -0.013 0.076 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.005 0.059 -9999 0 -10000 0 0
negative regulation of DNA binding 0.001 0.055 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.023 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.021 0.071 -9999 0 -0.35 3 3
mitotic prometaphase 0.012 0.015 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.094 -9999 0 -10000 0 0
TACC1 0.012 0.044 -9999 0 -0.58 2 2
TACC3 -0.024 0.14 -9999 0 -0.51 27 27
Aurora A/Antizyme1 -0.002 0.07 -9999 0 -10000 0 0
Aurora A/RasGAP -0.013 0.076 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.004 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.031 0.02 -9999 0 -0.34 1 1
Importin alpha/Importin beta/TPX2 -0.18 0.19 -9999 0 -0.36 192 192
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.16 0.19 -9999 0 -0.32 192 192
PAK1 0.014 0.031 -9999 0 -0.58 1 1
CKAP5 0.016 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 0.025 0.28 -10000 0 -0.81 34 34
NCK1/PAK1/Dok-R -0.042 0.12 -10000 0 -0.41 34 34
NCK1/Dok-R -0.02 0.33 -10000 0 -1 34 34
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.008 0.071 0.24 29 -10000 0 29
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.015 0.028 -10000 0 -0.5 1 1
Rac/GDP 0.012 0 -10000 0 -10000 0 0
F2 -0.023 0.16 0.26 28 -0.54 25 53
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.088 0.28 -10000 0 -0.94 34 34
FN1 -0.035 0.16 -10000 0 -0.53 33 33
PLD2 -0.017 0.34 -10000 0 -1 34 34
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.048 0.17 -10000 0 -0.51 43 43
ELK1 0.001 0.3 -10000 0 -0.93 34 34
GRB7 -0.013 0.12 -10000 0 -0.52 19 19
PAK1 0.014 0.031 -10000 0 -0.58 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.31 -10000 0 -1 34 34
CDKN1A 0.031 0.2 -10000 0 -0.58 24 24
ITGA5 -0.008 0.12 -10000 0 -0.58 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.02 0.33 -10000 0 -1 34 34
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO 0.044 0.22 -10000 0 -0.61 34 34
PLG -0.027 0.34 -10000 0 -1.1 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.005 0.27 -10000 0 -0.81 34 34
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
ANGPT2 -0.041 0.2 -10000 0 -0.66 18 18
BMX -0.11 0.36 -10000 0 -1.1 34 34
ANGPT1 -0.055 0.37 -10000 0 -1.3 29 29
tube development 0.021 0.22 -10000 0 -0.61 31 31
ANGPT4 0.002 0.067 -10000 0 -0.5 6 6
response to hypoxia -0.001 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.053 0.35 -10000 0 -1.1 34 34
alpha5/beta1 Integrin 0.006 0.085 -10000 0 -0.41 14 14
FGF2 -0.18 0.28 -10000 0 -0.58 116 116
STAT5A (dimer) 0.023 0.24 -10000 0 -0.7 28 28
mol:L-citrulline 0.044 0.22 -10000 0 -0.61 34 34
AGTR1 -0.23 0.29 -10000 0 -0.57 151 151
MAPK14 -0.014 0.33 -10000 0 -1 34 34
Tie2/SHP2 -0.034 0.15 -10000 0 -1.1 6 6
TEK 0.017 0.18 -10000 0 -1.2 6 6
RPS6KB1 0.023 0.27 -10000 0 -0.79 34 34
Angiotensin II/AT1 -0.17 0.22 -10000 0 -0.42 151 151
Tie2/Ang1/GRB2 -0.021 0.34 -10000 0 -1.1 34 34
MAPK3 -0.005 0.31 -10000 0 -0.96 34 34
MAPK1 -0.005 0.31 -10000 0 -0.96 34 34
Tie2/Ang1/GRB7 -0.036 0.35 -10000 0 -1.1 34 34
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.019 0.34 -10000 0 -1 34 34
PI3K 0.006 0.31 -10000 0 -0.93 34 34
FES -0.015 0.32 -10000 0 -1 34 34
Crk/Dok-R -0.02 0.33 -10000 0 -1 34 34
Tie2/Ang1/ABIN2 -0.021 0.34 -10000 0 -1.1 34 34
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.032 0.25 -10000 0 -0.73 34 34
STAT5A 0.014 0.031 -10000 0 -0.58 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.023 0.27 -10000 0 -0.79 34 34
Tie2/Ang2 0.003 0.27 -10000 0 -0.83 27 27
Tie2/Ang1 -0.028 0.36 -10000 0 -1.1 34 34
FOXO1 0.04 0.25 -10000 0 -0.73 34 34
ELF1 0.025 0.014 -10000 0 -10000 0 0
ELF2 -0.019 0.33 -10000 0 -1 34 34
mol:Choline -0.013 0.32 -10000 0 -1 34 34
cell migration -0.028 0.07 -10000 0 -0.23 34 34
FYN 0.016 0.24 -10000 0 -0.71 28 28
DOK2 -0.007 0.11 -10000 0 -0.57 14 14
negative regulation of cell cycle 0.033 0.19 -10000 0 -0.52 25 25
ETS1 0.008 0.067 -10000 0 -0.24 4 4
PXN 0.038 0.23 -10000 0 -0.66 34 34
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.039 0.24 -10000 0 -0.69 34 34
RAC1 0.016 0 -10000 0 -10000 0 0
TNF -0.016 0.13 -10000 0 -0.45 21 21
MAPKKK cascade -0.013 0.32 -10000 0 -1 34 34
RASA1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.02 0.34 -10000 0 -1.1 34 34
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.048 0.2 -10000 0 -0.55 34 34
mol:Phosphatidic acid -0.013 0.32 -10000 0 -1 34 34
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.044 0.22 -10000 0 -0.61 34 34
Rac1/GTP -0.071 0.22 -10000 0 -0.74 34 34
MMP2 -0.043 0.36 -10000 0 -1.1 34 34
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR -0.001 0.098 -9999 0 -0.58 10 10
LRPAP1 0.014 0.028 -9999 0 -0.51 1 1
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.22 -9999 0 -0.4 141 141
CaM/Ca2+ 0.012 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.14 0.2 -9999 0 -0.36 130 130
IQGAP1/CaM 0.023 0 -9999 0 -10000 0 0
DAB1 -0.07 0.2 -9999 0 -0.55 51 51
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.052 0.18 -9999 0 -0.51 46 46
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.048 0.15 -9999 0 -0.36 67 67
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 -0.014 0.12 -9999 0 -0.51 20 20
LIS1/Poliovirus Protein 3A 0.02 0 -9999 0 -10000 0 0
CDK5R2 -0.021 0.12 -9999 0 -0.51 22 22
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.22 -9999 0 -0.39 168 168
YWHAE 0.014 0.031 -9999 0 -0.58 1 1
NDEL1/14-3-3 E -0.096 0.18 -9999 0 -0.44 37 37
MAP1B -0.033 0.095 -9999 0 -0.31 38 38
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.2 -9999 0 -0.52 39 39
RELN -0.2 0.28 -9999 0 -0.57 131 131
PAFAH/LIS1 -0.01 0.11 -9999 0 -0.29 46 46
LIS1/CLIP170 0.031 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.094 0.11 -9999 0 -0.36 30 30
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.11 0.18 -9999 0 -0.49 31 31
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.11 0.19 -9999 0 -0.47 38 38
LIS1/IQGAP1 0.031 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.026 0 -9999 0 -10000 0 0
PAFAH1B3 -0.017 0.13 -9999 0 -0.51 22 22
PAFAH1B2 0.016 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.007 0.066 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.085 0.17 -9999 0 -0.44 32 32
LRP8 -0.081 0.2 -9999 0 -0.51 66 66
NDEL1/Katanin 60 -0.095 0.18 -9999 0 -0.44 37 37
P39/CDK5 -0.13 0.2 -9999 0 -0.51 41 41
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0 -9999 0 -10000 0 0
CDK5 -0.12 0.19 -9999 0 -0.52 31 31
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.13 0.19 -9999 0 -0.56 24 24
RELN/VLDLR -0.15 0.21 -9999 0 -0.56 38 38
CDC42 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.017 0.039 -9999 0 -0.35 4 4
ARNO/beta Arrestin1-2 -0.032 0.084 -9999 0 -0.37 1 1
EGFR -0.008 0.11 -9999 0 -0.54 15 15
EPHA2 0.011 0.054 -9999 0 -0.58 3 3
USP6 0.016 0 -9999 0 -10000 0 0
IQSEC1 0.014 0.028 -9999 0 -0.51 1 1
EGFR/EGFR/EGF/EGF -0.018 0.12 -9999 0 -0.37 37 37
ARRB2 0.011 0.015 -9999 0 -0.18 2 2
mol:GTP 0.015 0.033 -9999 0 -0.21 4 4
ARRB1 0.011 0.054 -9999 0 -0.58 3 3
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR 0.002 0.067 -9999 0 -0.51 6 6
EGF -0.018 0.12 -9999 0 -0.51 22 22
somatostatin receptor activity 0 0 -9999 0 -0.001 59 59
ARAP2 0.012 0.044 -9999 0 -0.58 2 2
mol:GDP -0.07 0.11 -9999 0 -0.23 85 85
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 53 53
ITGA2B -0.026 0.14 -9999 0 -0.51 28 28
ARF6 0.015 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.055 -9999 0 -0.3 3 3
ADAP1 0.009 0.062 -9999 0 -0.58 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.081 0.18 -9999 0 -0.41 86 86
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.064 0.12 -9999 0 -0.26 59 59
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.005 0.1 -9999 0 -0.3 38 38
ADRB2 -0.054 0.19 -9999 0 -0.58 42 42
receptor agonist activity 0 0 -9999 0 0 68 68
actin filament binding 0 0 -9999 0 0 59 59
SRC 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.19 -9999 0 -0.58 42 42
GNAQ 0.015 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 54 54
ARF6/GDP 0.008 0.095 -9999 0 -0.35 17 17
ARF6/GDP/GULP/ACAP1 -0.11 0.17 -9999 0 -0.42 65 65
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.023 0.14 -9999 0 -0.33 42 42
ACAP1 -0.017 0.13 -9999 0 -0.56 20 20
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.003 0.022 -9999 0 -0.27 2 2
EFNA1 0.002 0.082 -9999 0 -0.51 9 9
HGF -0.12 0.25 -9999 0 -0.57 85 85
CYTH3 0.013 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 45 45
endosomal lumen acidification 0 0 0 3 0 53 56
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.076 0.21 -9999 0 -0.58 55 55
GNAQ/ARNO 0.017 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 4 4
MET 0.014 0.028 -9999 0 -0.51 1 1
GNA14 -0.067 0.2 -9999 0 -0.58 50 50
GNA15 0.012 0.044 -9999 0 -0.58 2 2
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 55 55
GNA11 0.014 0.031 -9999 0 -0.58 1 1
LHCGR 0.001 0.039 -9999 0 -0.51 2 2
AGTR1 -0.24 0.29 -9999 0 -0.58 151 151
desensitization of G-protein coupled receptor protein signaling pathway 0.003 0.022 -9999 0 -0.27 2 2
IPCEF1/ARNO -0.003 0.077 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.057 0.17 -9999 0 -0.41 66 66
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.024 0.15 0.57 24 -10000 0 24
PI3K Class IB/PDE3B -0.024 0.15 -10000 0 -0.57 24 24
PDE3B -0.024 0.15 -10000 0 -0.58 24 24
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.042 0.15 0.42 45 -10000 0 45
KIRREL -0.052 0.19 -10000 0 -0.59 39 39
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.042 0.15 -10000 0 -0.42 45 45
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.016 0 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.05 0.12 -10000 0 -0.33 39 39
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.007 0.1 -10000 0 -0.4 6 6
FYN -0.03 0.12 -10000 0 -0.33 40 40
mol:Ca2+ -0.049 0.12 -10000 0 -0.33 39 39
mol:DAG -0.05 0.12 -10000 0 -0.33 39 39
NPHS2 -0.025 0.11 -10000 0 -0.51 18 18
mol:IP3 -0.05 0.12 -10000 0 -0.33 39 39
regulation of endocytosis -0.019 0.12 -10000 0 -0.34 21 21
Nephrin/NEPH1/podocin/Cholesterol -0.041 0.12 -10000 0 -0.31 59 59
establishment of cell polarity -0.042 0.15 -10000 0 -0.42 45 45
Nephrin/NEPH1/podocin/NCK1-2 -0.014 0.12 -10000 0 -0.46 6 6
Nephrin/NEPH1/beta Arrestin2 -0.018 0.12 -10000 0 -0.34 21 21
NPHS1 -0.009 0.068 -10000 0 -0.5 6 6
Nephrin/NEPH1/podocin -0.03 0.12 -10000 0 -0.33 40 40
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.05 0.12 -10000 0 -0.33 39 39
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.05 0.12 -10000 0 -0.33 39 39
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.12 -10000 0 -0.32 40 40
cytoskeleton organization -0.007 0.12 -10000 0 -0.47 6 6
Nephrin/NEPH1 -0.027 0.1 -10000 0 -0.3 45 45
Nephrin/NEPH1/ZO-1 -0.042 0.11 -10000 0 -0.34 39 39
Syndecan-4-mediated signaling events

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
PTK2 -0.004 0.11 -9999 0 -0.54 11 11
Syndecan-4/Syndesmos -0.03 0.13 -9999 0 -0.56 10 10
positive regulation of JNK cascade -0.1 0.18 -9999 0 -0.49 36 36
Syndecan-4/ADAM12 -0.056 0.16 -9999 0 -0.43 34 34
CCL5 -0.03 0.16 -9999 0 -0.55 29 29
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.008 0.12 -9999 0 -0.58 14 14
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.003 0.061 -9999 0 -0.51 5 5
ADAM12 -0.039 0.16 -9999 0 -0.51 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.051 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.18 -9999 0 -0.45 42 42
Syndecan-4/CXCL12/CXCR4 -0.11 0.19 -9999 0 -0.52 36 36
Syndecan-4/Laminin alpha3 -0.075 0.18 -9999 0 -0.44 45 45
MDK -0.014 0.12 -9999 0 -0.51 20 20
Syndecan-4/FZD7 -0.045 0.14 -9999 0 -0.49 16 16
Syndecan-4/Midkine -0.044 0.14 -9999 0 -0.5 15 15
FZD7 -0.014 0.13 -9999 0 -0.58 18 18
Syndecan-4/FGFR1/FGF -0.19 0.23 -9999 0 -0.53 89 89
THBS1 -0.004 0.11 -9999 0 -0.58 12 12
integrin-mediated signaling pathway -0.056 0.17 -9999 0 -0.5 27 27
positive regulation of MAPKKK cascade -0.1 0.18 -9999 0 -0.49 36 36
Syndecan-4/TACI -0.06 0.15 -9999 0 -0.48 20 20
CXCR4 0.007 0.07 -9999 0 -0.58 5 5
cell adhesion 0.004 0.11 -9999 0 -0.49 11 11
Syndecan-4/Dynamin -0.03 0.13 -9999 0 -0.56 10 10
Syndecan-4/TSP1 -0.04 0.14 -9999 0 -0.57 12 12
Syndecan-4/GIPC -0.03 0.13 -9999 0 -0.56 10 10
Syndecan-4/RANTES -0.052 0.16 -9999 0 -0.52 22 22
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.087 0.21 -9999 0 -0.52 68 68
LAMA3 -0.077 0.21 -9999 0 -0.54 59 59
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.02 0.061 -9999 0 -0.52 3 3
Syndecan-4/alpha-Actinin -0.03 0.13 -9999 0 -0.56 10 10
TFPI 0.002 0.088 -9999 0 -0.58 8 8
F2 -0.035 0.14 -9999 0 -0.51 29 29
alpha5/beta1 Integrin 0.006 0.085 -9999 0 -0.41 14 14
positive regulation of cell adhesion -0.11 0.2 -9999 0 -0.5 43 43
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC -0.043 0.17 -9999 0 -0.56 36 36
Syndecan-4/CXCL12 -0.12 0.19 -9999 0 -0.53 35 35
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.16 0.27 -9999 0 -0.58 105 105
TNFRSF13B -0.043 0.17 -9999 0 -0.57 34 34
FGF2 -0.18 0.28 -9999 0 -0.58 116 116
FGFR1 -0.12 0.25 -9999 0 -0.58 83 83
Syndecan-4/PI-4-5-P2 -0.04 0.13 -9999 0 -0.56 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.034 0.16 -9999 0 -0.53 33 33
cell migration -0.015 0.022 -9999 0 -10000 0 0
PRKCD 0.016 0.008 -9999 0 -10000 0 0
vasculogenesis -0.039 0.14 -9999 0 -0.55 12 12
SDC4 -0.041 0.14 -9999 0 -0.6 10 10
Syndecan-4/Tenascin C -0.058 0.17 -9999 0 -0.52 27 27
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.03 0.13 -9999 0 -0.56 10 10
MMP9 -0.13 0.24 -9999 0 -0.51 97 97
Rac1/GTP 0.003 0.11 -9999 0 -0.51 11 11
cytoskeleton organization -0.029 0.13 -9999 0 -0.53 10 10
GIPC1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.036 0.15 -9999 0 -0.6 13 13
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.05 0.24 16 -10000 0 16
RFC1 0.012 0.05 0.24 14 -10000 0 14
PRKDC 0.012 0.05 0.24 16 -10000 0 16
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CASP7 -0.029 0.044 0.25 2 -10000 0 2
FASLG/FAS/FADD/FAF1 -0.038 0.086 0.22 5 -0.31 22 27
MAP2K4 -0.088 0.17 -10000 0 -0.44 21 21
mol:ceramide -0.056 0.13 -10000 0 -0.39 28 28
GSN 0.006 0.065 0.24 14 -0.34 5 19
FASLG/FAS/FADD/FAF1/Caspase 8 -0.035 0.11 -10000 0 -0.36 22 22
FAS 0.001 0.071 -10000 0 -0.59 5 5
BID 0.003 0.034 0.3 3 -0.31 1 4
MAP3K1 -0.037 0.1 -10000 0 -0.26 12 12
MAP3K7 0.009 0.008 -10000 0 -10000 0 0
RB1 0.012 0.05 0.24 14 -10000 0 14
CFLAR 0.019 0.005 -10000 0 -10000 0 0
HGF/MET -0.066 0.17 -10000 0 -0.35 92 92
ARHGDIB 0.012 0.05 0.24 16 -10000 0 16
FADD 0 0.068 -10000 0 -0.52 6 6
actin filament polymerization -0.006 0.065 0.34 5 -0.24 14 19
NFKB1 -0.096 0.1 -10000 0 -0.27 19 19
MAPK8 -0.16 0.25 -10000 0 -0.42 162 162
DFFA 0.012 0.05 0.24 16 -10000 0 16
DNA fragmentation during apoptosis 0.012 0.05 0.24 14 -10000 0 14
FAS/FADD/MET 0.007 0.064 -10000 0 -0.32 12 12
CFLAR/RIP1 0.012 0.011 -10000 0 -10000 0 0
FAIM3 0.009 0.072 -10000 0 -0.54 6 6
FAF1 0.009 0.009 -10000 0 -10000 0 0
PARP1 0.012 0.05 0.24 14 -10000 0 14
DFFB 0.012 0.05 0.24 14 -10000 0 14
CHUK -0.083 0.09 -10000 0 -0.27 1 1
FASLG -0.037 0.16 -10000 0 -0.57 28 28
FAS/FADD 0.001 0.072 -10000 0 -0.4 11 11
HGF -0.12 0.25 -10000 0 -0.57 85 85
LMNA 0.011 0.047 0.22 14 -10000 0 14
CASP6 0.012 0.05 0.24 14 -10000 0 14
CASP10 0.009 0.008 -10000 0 -10000 0 0
CASP3 0.014 0.059 0.27 17 -10000 0 17
PTPN13 0.002 0.088 -10000 0 -0.58 8 8
CASP8 0.005 0.04 0.39 3 -10000 0 3
IL6 -0.57 0.67 -10000 0 -1.3 162 162
MET 0.014 0.028 -10000 0 -0.51 1 1
ICAD/CAD 0.011 0.047 0.23 14 -10000 0 14
FASLG/FAS/FADD/FAF1/Caspase 10 -0.057 0.14 -10000 0 -0.39 28 28
activation of caspase activity by cytochrome c 0.003 0.034 0.3 3 -0.31 1 4
PAK2 0.012 0.05 0.24 16 -10000 0 16
BCL2 -0.007 0.12 -10000 0 -0.57 14 14
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.04 0.14 -9999 0 -0.54 13 13
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.057 0.18 -9999 0 -0.53 48 48
WNT4 -0.029 0.15 -9999 0 -0.57 27 27
FZD3 0.012 0.044 -9999 0 -0.58 2 2
WNT5A -0.008 0.11 -9999 0 -0.54 15 15
WNT11 -0.058 0.19 -9999 0 -0.53 48 48
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.004 0.033 -10000 0 -10000 0 0
HDAC1 0.014 0.012 -10000 0 -10000 0 0
AES 0.015 0.004 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.007 0.11 -10000 0 -0.56 14 14
LRP6/FZD1 0.022 0.023 -10000 0 -0.42 1 1
TLE1 0.01 0.054 -10000 0 -0.58 3 3
AP1 -0.091 0.18 -10000 0 -0.32 121 121
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.015 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.031 0.075 -10000 0 -10000 0 0
NICD/RBPSUH 0.038 0.009 -10000 0 -10000 0 0
WIF1 -0.12 0.24 -10000 0 -0.57 80 80
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.18 0.25 -10000 0 -0.51 134 134
DKK1 -0.083 0.22 -10000 0 -0.56 61 61
beta catenin/beta TrCP1 0.032 0.045 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 0.005 0.015 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.031 0.052 0.28 4 -10000 0 4
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.17 0.27 -10000 0 -0.58 110 110
JUN -0.006 0.11 -10000 0 -0.58 13 13
MAP3K7 0.015 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.048 0.2 12 -10000 0 12
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.16 0.21 -10000 0 -0.35 179 179
HNF1A 0.009 0.055 -10000 0 -0.51 4 4
CTBP1 0.014 0.028 -10000 0 -0.5 1 1
MYC -0.047 0.32 -10000 0 -1.4 18 18
NKD1 -0.02 0.14 -10000 0 -0.56 22 22
FZD1 0.014 0.031 -10000 0 -0.58 1 1
NOTCH1 precursor/Deltex homolog 1 0.026 0.058 -10000 0 -10000 0 0
apoptosis -0.09 0.18 -10000 0 -0.32 121 121
Delta 1/NOTCHprecursor 0.033 0.039 -10000 0 -10000 0 0
DLL1 0.006 0.073 -10000 0 -0.55 6 6
PPARD 0.022 0.027 -10000 0 -10000 0 0
Gamma Secretase 0.044 0.011 -10000 0 -10000 0 0
APC 0.005 0.015 -10000 0 -10000 0 0
DVL1 0.01 0.032 -10000 0 -10000 0 0
CSNK2A1 0.016 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.15 0.2 -10000 0 -0.35 170 170
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.002 -10000 0 -10000 0 0
NLK 0.018 0.012 -10000 0 -10000 0 0
CCND1 -0.014 0.22 -10000 0 -1.5 7 7
WNT1 0.007 0.048 -10000 0 -0.51 3 3
Axin1/APC/beta catenin 0.043 0.033 -10000 0 -10000 0 0
DKK2 -0.1 0.22 -10000 0 -0.51 82 82
NOTCH1 precursor/DVL1 0.002 0.01 -10000 0 -10000 0 0
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.01 0.05 -10000 0 -10000 0 0
PPP2R5D 0.013 0.069 0.28 22 -10000 0 22
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.047 0.14 -10000 0 -0.31 73 73
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.018 0.006 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0.003 0.04 -9999 0 -0.37 4 4
Metarhodopsin II/Arrestin 0.002 0.004 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.003 0.067 -9999 0 -0.3 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.004 0.055 -9999 0 -0.51 4 4
GRK1 0.001 0.004 -9999 0 -10000 0 0
CNG Channel -0.15 0.16 -9999 0 -0.48 39 39
mol:Na + -0.16 0.16 -9999 0 -0.48 44 44
mol:ADP 0.001 0.004 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.35 89 89
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.16 -9999 0 -0.49 44 44
CNGB1 -0.21 0.26 -9999 0 -0.51 154 154
RDH5 0.014 0.031 -9999 0 -0.58 1 1
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.17 -9999 0 -0.46 44 44
Na + (4 Units) -0.15 0.15 -9999 0 -0.45 44 44
RGS9 -0.11 0.24 -9999 0 -0.58 76 76
GNB1/GNGT1 0.001 0.085 -9999 0 -0.36 19 19
GNAT1/GDP -0.052 0.15 -9999 0 -0.3 86 86
GUCY2D -0.049 0.17 -9999 0 -0.51 42 42
GNGT1 -0.014 0.12 -9999 0 -0.51 19 19
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.095 -9999 0 -0.32 16 16
mol:11-cis-retinal 0.014 0.031 -9999 0 -0.57 1 1
mol:cGMP -0.022 0.11 -9999 0 -0.45 4 4
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin 0.013 0.024 -9999 0 -0.42 1 1
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.053 0.18 -9999 0 -0.54 44 44
Metarhodopsin II 0.003 0.005 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.024 0.12 -9999 0 -0.48 4 4
RGS9BP -0.011 0.12 -9999 0 -0.56 16 16
Metarhodopsin II/Transducin 0.01 0.036 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.002 0.07 -9999 0 -0.29 19 19
PDE6A/B -0.002 0.1 -9999 0 -0.42 20 20
mol:Pi -0.065 0.17 -9999 0 -0.35 89 89
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.006 0.071 -9999 0 -0.26 23 23
PDE6B -0.011 0.12 -9999 0 -0.57 16 16
PDE6A 0.007 0.061 -9999 0 -0.51 5 5
PDE6G -0.002 0.094 -9999 0 -0.51 12 12
RHO 0.004 0.007 -9999 0 -10000 0 0
PDE6 -0.089 0.15 -9999 0 -0.58 13 13
GUCA1A -0.013 0.11 -9999 0 -0.51 17 17
GC2/GCAP Family 0.003 0.071 -9999 0 -0.29 19 19
GUCA1C 0 0.027 -9999 0 -0.51 1 1
GUCA1B 0.012 0.042 -9999 0 -0.54 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.033 -10000 0 -10000 0 0
AES 0.019 0.025 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.02 0.024 -10000 0 -0.41 1 1
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.1 0.22 -10000 0 -0.51 82 82
TLE1 0.014 0.06 -10000 0 -0.58 3 3
MACF1 0.016 0 -10000 0 -10000 0 0
CTNNB1 0.04 0.08 0.26 8 -10000 0 8
WIF1 -0.12 0.24 -10000 0 -0.57 80 80
beta catenin/RanBP3 0.037 0.13 0.37 44 -10000 0 44
KREMEN2 -0.18 0.25 -10000 0 -0.51 134 134
DKK1 -0.083 0.22 -10000 0 -0.56 61 61
beta catenin/beta TrCP1 0.048 0.075 0.25 8 -10000 0 8
FZD1 0.014 0.031 -10000 0 -0.58 1 1
AXIN2 -0.086 0.36 -10000 0 -1.4 24 24
AXIN1 0.016 0.001 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.035 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.083 0.059 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.017 0.046 0.2 10 -10000 0 10
Axin1/APC/GSK3/beta catenin/Macf1 0.062 0.036 -10000 0 -10000 0 0
HNF1A 0.014 0.062 -10000 0 -0.51 4 4
CTBP1 0.018 0.038 -10000 0 -0.48 1 1
MYC -0.073 0.34 -10000 0 -1.5 18 18
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.16 0.2 -10000 0 -0.35 179 179
NKD1 -0.021 0.14 -10000 0 -0.56 22 22
TCF4 0.015 0.06 -10000 0 -0.56 3 3
TCF3 0.019 0.027 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.028 0.035 -10000 0 -0.31 1 1
Ran/GTP 0.012 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.058 0.17 0.48 42 -10000 0 42
LEF1 0.012 0.067 -10000 0 -0.5 5 5
DVL1 0.059 0.038 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.066 0.086 -10000 0 -0.34 1 1
DKK1/LRP6/Kremen 2 -0.15 0.2 -10000 0 -0.35 170 170
LRP6 0.016 0.001 -10000 0 -10000 0 0
CSNK1A1 0.018 0.031 -10000 0 -10000 0 0
NLK 0.015 0.006 -10000 0 -10000 0 0
CCND1 -0.041 0.24 -10000 0 -1.3 9 9
WNT1 0.008 0.048 -10000 0 -0.51 3 3
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.048 0.071 0.31 22 -10000 0 22
APC 0.041 0.03 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.071 0.09 0.24 71 -10000 0 71
CREBBP 0.019 0.027 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.088 0.22 -9999 0 -0.58 62 62
GNB1/GNG2 -0.024 0.14 -9999 0 -0.5 13 13
mol:DAG -0.014 0.13 -9999 0 -0.45 13 13
PLCG1 -0.015 0.13 -9999 0 -0.47 13 13
YES1 -0.029 0.14 -9999 0 -0.5 13 13
FZD3 0.012 0.044 -9999 0 -0.58 2 2
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.015 0.13 -9999 0 -0.47 13 13
MAP3K7 -0.085 0.18 -9999 0 -0.39 55 55
mol:Ca2+ -0.013 0.12 -9999 0 -0.44 13 13
mol:IP3 -0.014 0.13 -9999 0 -0.45 13 13
NLK -0.003 0.008 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.1 0.19 -9999 0 -0.42 56 56
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.04 0.14 -9999 0 -0.54 13 13
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.029 0.14 -9999 0 -0.5 13 13
GO:0007205 -0.013 0.13 -9999 0 -0.44 13 13
WNT6 -0.057 0.18 -9999 0 -0.53 48 48
WNT4 -0.029 0.15 -9999 0 -0.57 27 27
NFAT1/CK1 alpha -0.055 0.16 -9999 0 -0.46 25 25
GNG2 0.006 0.076 -9999 0 -0.58 6 6
WNT5A -0.008 0.11 -9999 0 -0.54 15 15
WNT11 -0.058 0.19 -9999 0 -0.53 48 48
CDC42 -0.019 0.13 -9999 0 -0.47 13 13
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0.028 -9999 0 -0.51 1 1
SPHK1 -0.053 0.18 -9999 0 -0.51 47 47
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.004 0.057 -9999 0 -0.29 1 1
GNAO1 -0.17 0.27 -9999 0 -0.58 110 110
mol:Sphinganine-1-P -0.025 0.13 -9999 0 -0.36 48 48
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.041 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.023 0 -9999 0 -10000 0 0
S1PR3 0.002 0.086 -9999 0 -0.57 8 8
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.016 0.041 -9999 0 -0.25 1 1
S1PR5 -0.005 0.1 -9999 0 -0.52 14 14
S1PR4 0.005 0.078 -9999 0 -0.55 7 7
GNAI1 0.011 0.054 -9999 0 -0.58 3 3
S1P/S1P5/G12 0.009 0.071 -9999 0 -0.27 14 14
S1P/S1P3/Gq -0.012 0.11 -9999 0 -0.26 58 58
S1P/S1P4/Gi -0.1 0.19 -9999 0 -0.46 57 57
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.58 76 76
GNA14 -0.067 0.2 -9999 0 -0.58 50 50
GNA15 0.012 0.044 -9999 0 -0.58 2 2
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.014 0.031 -9999 0 -0.58 1 1
ABCC1 0.013 0.039 -9999 0 -0.51 2 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.29 0.3 -9999 0 -0.58 183 183
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0.028 -9999 0 -0.51 1 1
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 0.035 0.015 -9999 0 -10000 0 0
HIF1A 0.027 0.016 -9999 0 -10000 0 0
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.046 0.015 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.24 0.26 -9999 0 -0.51 174 174
ARNT/IPAS -0.2 0.22 -9999 0 -0.41 183 183
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.035 0.015 -9999 0 -10000 0 0
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.031 0.017 -9999 0 -0.29 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.035 0.015 -9999 0 -10000 0 0
PHD1-3/OS9 0.033 0.048 -9999 0 -0.3 7 7
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.012 -9999 0 -10000 0 0
VHL 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.035 0.015 -9999 0 -10000 0 0
EGLN3 0.004 0.082 -9999 0 -0.58 7 7
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.008 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.089 0.13 -9999 0 -0.28 8 8
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.021 0.12 -9999 0 -0.42 7 7
NFATC4 -0.025 0.12 -9999 0 -0.38 10 10
ERBB2IP 0.016 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.016 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.045 0.13 -9999 0 -0.46 7 7
JUN 0.004 0.084 -9999 0 -0.34 1 1
HRAS 0.015 0.001 -9999 0 -10000 0 0
DOCK7 -0.037 0.13 -9999 0 -0.43 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.066 0.15 -9999 0 -0.32 71 71
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.022 0.003 -9999 0 -10000 0 0
MAPK10 -0.016 0.095 -9999 0 -0.29 11 11
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.047 0.14 -9999 0 -0.5 7 7
RAF1 -0.012 0.12 -9999 0 -0.41 7 7
ErbB2/ErbB3/neuregulin 2 -0.15 0.18 -9999 0 -0.34 163 163
STAT3 0.003 0.005 -9999 0 -10000 0 0
cell migration -0.003 0.089 -9999 0 -0.24 11 11
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.087 0.24 -9999 0 -0.55 37 37
FOS -0.12 0.27 -9999 0 -0.51 111 111
NRAS 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.045 0.13 -9999 0 -0.46 7 7
MAPK3 -0.053 0.18 -9999 0 -0.52 18 18
MAPK1 -0.053 0.18 -9999 0 -0.52 18 18
JAK2 -0.037 0.13 -9999 0 -0.43 7 7
NF2 -0.001 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.039 0.13 -9999 0 -0.28 71 71
NRG1 -0.12 0.24 -9999 0 -0.56 80 80
GRB2/SOS1 0.023 0.001 -9999 0 -10000 0 0
MAPK8 -0.033 0.13 -9999 0 -0.29 30 30
MAPK9 0.002 0.075 -9999 0 -0.23 1 1
ERBB2 -0.014 0.07 -9999 0 -0.38 13 13
ERBB3 -0.002 0.096 -9999 0 -0.56 10 10
SHC1 0.014 0.028 -9999 0 -0.51 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.005 0.012 -9999 0 -10000 0 0
STAT3 (dimer) 0.022 0.006 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.044 0.077 -9999 0 -0.3 7 7
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.057 -9999 0 -0.31 13 13
CHRNA1 -0.05 0.17 -9999 0 -0.39 36 36
myelination -0.016 0.11 -9999 0 -0.36 10 10
PPP3CB -0.034 0.12 -9999 0 -0.4 7 7
KRAS 0.014 0.028 -9999 0 -0.51 1 1
RAC1-CDC42/GDP -0.017 0.12 -9999 0 -0.39 7 7
NRG2 -0.24 0.29 -9999 0 -0.58 152 152
mol:GDP -0.039 0.13 -9999 0 -0.28 71 71
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.008 0.12 -9999 0 -0.46 5 5
SRC 0.016 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.034 0.13 -9999 0 -0.43 7 7
MAP2K1 -0.068 0.19 -9999 0 -0.45 32 32
heart morphogenesis -0.045 0.13 -9999 0 -0.46 7 7
RAS family/GDP -0.021 0.12 -9999 0 -0.48 5 5
GRB2 0.015 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.007 -9999 0 -10000 0 0
CHRNE 0.013 0.025 -9999 0 -0.18 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.045 0.13 -9999 0 -0.46 7 7
CDC42 0.016 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.022 0.02 -9999 0 -0.36 1 1
CRKL -0.01 0.1 -9999 0 -0.36 3 3
mol:PIP3 -0.021 0.006 -9999 0 -10000 0 0
AKT1 0.002 0.005 -9999 0 -10000 0 0
PTK2B 0.014 0.031 -9999 0 -0.58 1 1
RAPGEF1 -0.001 0.099 -9999 0 -0.37 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.058 0.16 -9999 0 -0.34 86 86
MAP3K5 0.005 0.1 -9999 0 -0.36 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.042 0.14 -9999 0 -0.3 78 78
AP1 -0.11 0.2 -9999 0 -0.4 111 111
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.028 -9999 0 -0.51 1 1
apoptosis -0.22 0.36 -9999 0 -0.75 111 111
STAT3 (dimer) -0.015 0.12 -9999 0 -0.49 1 1
GAB1/CRKL/SHP2/PI3K -0.036 0.068 -9999 0 -0.34 2 2
INPP5D 0.004 0.082 -9999 0 -0.58 7 7
CBL/CRK 0.001 0.096 -9999 0 -0.33 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 -0.003 0.014 -9999 0 -0.2 1 1
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.032 0.06 -9999 0 -0.39 1 1
PAK1 0.009 0.017 -9999 0 -0.29 1 1
HGF/MET/RANBP10 -0.058 0.16 -9999 0 -0.34 86 86
HRAS -0.029 0.14 -9999 0 -0.38 1 1
DOCK1 -0.002 0.099 -9999 0 -0.37 2 2
GAB1 -0.018 0.1 -9999 0 -0.21 78 78
CRK -0.008 0.1 -9999 0 -0.32 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.1 0.19 -9999 0 -0.47 78 78
JUN -0.006 0.11 -9999 0 -0.58 13 13
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.033 0.093 -9999 0 -0.2 78 78
PIK3R1 0.016 0 -9999 0 -10000 0 0
cell morphogenesis 0.012 0.12 -9999 0 -0.42 2 2
GRB2/SHC -0.011 0.085 -9999 0 -0.42 1 1
FOS -0.17 0.27 -9999 0 -0.58 110 110
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.003 0.014 -9999 0 -0.2 1 1
HGF/MET/MUC20 -0.068 0.16 -9999 0 -0.35 86 86
cell migration -0.012 0.083 -9999 0 -0.41 1 1
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
MET/RANBP10 0.022 0.02 -9999 0 -0.36 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.023 0.12 -9999 0 -0.24 78 78
MET/MUC20 0.011 0.02 -9999 0 -0.37 1 1
RAP1B 0.008 0.094 -9999 0 -0.34 2 2
RAP1A 0.008 0.094 -9999 0 -0.34 2 2
HGF/MET/RANBP9 -0.058 0.16 -9999 0 -0.34 86 86
RAF1 -0.02 0.13 -9999 0 -0.35 1 1
STAT3 -0.015 0.12 -9999 0 -0.5 1 1
cell proliferation -0.024 0.16 -9999 0 -0.32 78 78
RPS6KB1 -0.003 0.035 -9999 0 -10000 0 0
MAPK3 -0.009 0.012 -9999 0 -10000 0 0
MAPK1 -0.009 0.012 -9999 0 -10000 0 0
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.023 0.096 -9999 0 -0.36 5 5
SRC -0.012 0.11 -9999 0 -0.47 1 1
PI3K -0.011 0.084 -9999 0 -0.42 1 1
MET/Glomulin 0.014 0.018 -9999 0 -0.32 1 1
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 -0.01 0.12 -9999 0 -10000 0 0
MET 0.014 0.028 -9999 0 -0.51 1 1
MAP4K1 -0.004 0.11 -9999 0 -0.36 5 5
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 -0.01 0.12 -9999 0 -10000 0 0
BAD 0.01 0.005 -9999 0 -10000 0 0
MAP2K4 0.014 0.095 -9999 0 -0.33 4 4
SHP2/GRB2/SOS1/GAB1 -0.037 0.068 -9999 0 -0.3 1 1
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.021 0.087 -9999 0 -0.44 1 1
PLCgamma1/PKC 0.012 0 -9999 0 -10000 0 0
HGF -0.12 0.25 -9999 0 -0.57 85 85
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
PTPRJ 0.014 0.031 -9999 0 -0.58 1 1
NCK/PLCgamma1 -0.014 0.094 -9999 0 -0.43 1 1
PDPK1 -0.008 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.065 0.17 -9999 0 -0.35 89 89
Effects of Botulinum toxin

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
STX1A 0.009 0.04 -9999 0 -0.37 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.003 0.08 -9999 0 -0.41 13 13
STXBP1 -0.008 0.12 -9999 0 -0.58 14 14
ACh/CHRNA1 -0.048 0.13 -9999 0 -0.33 59 59
RAB3GAP2/RIMS1/UNC13B 0.014 0.069 -9999 0 -0.34 13 13
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.012 0.11 -9999 0 -0.57 13 13
mol:ACh -0.002 0.039 -9999 0 -0.12 29 29
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.032 0.085 -9999 0 -0.38 11 11
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.048 0.13 -9999 0 -0.33 59 59
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.072 0.19 -9999 0 -0.51 59 59
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.031 0.13 -9999 0 -0.39 38 38
SNAP25 -0.02 0.086 -9999 0 -0.26 37 37
VAMP2 0.008 0 -9999 0 -10000 0 0
SYT1 -0.046 0.18 -9999 0 -0.56 38 38
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.003 0.08 -9999 0 -0.34 18 18
STX1A/SNAP25 fragment 1/VAMP2 -0.032 0.085 -9999 0 -0.38 11 11
Caspase cascade in apoptosis

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
TOP1 -0.007 0.13 -10000 0 -0.36 32 32
ACTA1 -0.028 0.17 -10000 0 -0.47 34 34
NUMA1 -0.007 0.13 -10000 0 -0.36 32 32
SPTAN1 -0.023 0.16 -10000 0 -0.47 32 32
LIMK1 -0.023 0.16 -10000 0 -0.47 32 32
BIRC3 -0.024 0.15 -10000 0 -0.57 24 24
BIRC2 0.013 0.039 -10000 0 -0.51 2 2
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.039 0.18 -10000 0 -0.41 59 59
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0.042 -10000 0 -0.54 2 2
PTK2 -0.007 0.13 -10000 0 -0.36 32 32
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.022 0.16 -10000 0 -0.46 32 32
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.028 0.17 -10000 0 -0.47 37 37
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A 0.018 0.042 -10000 0 -0.48 1 1
BID -0.009 0.089 -10000 0 -0.24 38 38
MAP3K1 0.001 0.058 -10000 0 -0.22 6 6
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.023 0.16 -10000 0 -0.47 32 32
CASP9 0.016 0 -10000 0 -10000 0 0
DNA repair -0.006 0.054 0.15 6 -0.2 12 18
neuron apoptosis 0.021 0.062 -10000 0 -0.77 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.013 0.16 -10000 0 -0.45 32 32
APAF1 0.016 0 -10000 0 -10000 0 0
CASP6 0.017 0.078 -10000 0 -0.35 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.014 0.16 -10000 0 -0.45 32 32
CASP7 0.011 0.081 0.31 21 -10000 0 21
KRT18 0.013 0.043 -10000 0 -0.64 1 1
apoptosis -0.007 0.15 0.28 1 -0.43 32 33
DFFA -0.023 0.16 -10000 0 -0.47 32 32
DFFB -0.023 0.16 -10000 0 -0.47 32 32
PARP1 0.006 0.055 0.2 12 -0.16 6 18
actin filament polymerization 0.015 0.16 0.44 32 -10000 0 32
TNF -0.009 0.11 -10000 0 -0.51 17 17
CYCS -0.002 0.068 -10000 0 -0.21 18 18
SATB1 0.014 0.093 -10000 0 -0.35 5 5
SLK -0.023 0.16 -10000 0 -0.47 32 32
p15 BID/BAX 0 0.08 -10000 0 -0.3 9 9
CASP2 0.041 0.052 -10000 0 -10000 0 0
JNK cascade -0.001 0.057 0.21 6 -10000 0 6
CASP3 -0.033 0.17 -10000 0 -0.51 32 32
LMNB2 0.039 0.046 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.014 0.028 -10000 0 -0.51 1 1
Mammalian IAPs/DIABLO 0.014 0.095 -10000 0 -0.33 22 22
negative regulation of DNA binding 0.018 0.041 -10000 0 -0.48 1 1
stress fiber formation -0.022 0.16 -10000 0 -0.46 32 32
GZMB -0.058 0.2 -10000 0 -0.49 59 59
CASP1 0.011 0.055 -10000 0 -0.33 9 9
LMNB1 0.039 0.046 -10000 0 -10000 0 0
APP 0.021 0.063 -10000 0 -0.78 2 2
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.013 0 -10000 0 -10000 0 0
VIM -0.012 0.15 0.23 12 -0.42 32 44
LMNA 0.039 0.046 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.034 0.055 -10000 0 -10000 0 0
LRDD 0.016 0 -10000 0 -10000 0 0
SREBF1 -0.025 0.16 -10000 0 -0.47 32 32
APAF-1/Caspase 9 0.002 0.047 0.3 3 -10000 0 3
nuclear fragmentation during apoptosis -0.007 0.13 -10000 0 -0.36 32 32
CFL2 -0.016 0.16 -10000 0 -0.45 32 32
GAS2 -0.057 0.19 -10000 0 -0.42 59 59
positive regulation of apoptosis 0.043 0.046 -10000 0 -10000 0 0
PRF1 -0.024 0.14 -10000 0 -0.55 25 25
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.07 -9999 0 -0.32 12 12
epithelial cell differentiation -0.041 0.087 -9999 0 -0.41 6 6
ITCH 0.017 0.029 -9999 0 -0.51 1 1
WWP1 0.035 0.029 -9999 0 -10000 0 0
FYN 0.011 0.054 -9999 0 -0.58 3 3
EGFR -0.008 0.11 -9999 0 -0.54 15 15
PRL -0.002 0.061 -9999 0 -0.51 5 5
neuron projection morphogenesis 0.01 0.12 -9999 0 -0.46 1 1
PTPRZ1 -0.17 0.26 -9999 0 -0.55 113 113
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.13 -9999 0 -0.52 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.14 -9999 0 -0.36 12 12
ADAM17 0.018 0.008 -9999 0 -10000 0 0
ErbB4/ErbB4 0.034 0.036 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.056 -9999 0 -0.33 1 1
NCOR1 0.016 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.029 0.14 -9999 0 -0.35 14 14
GRIN2B -0.031 0.14 -9999 0 -0.49 6 6
ErbB4/ErbB2/betacellulin -0.004 0.12 -9999 0 -0.41 4 4
STAT1 0.01 0.055 -9999 0 -0.51 4 4
HBEGF -0.004 0.11 -9999 0 -0.58 12 12
PRLR -0.045 0.17 -9999 0 -0.54 39 39
E4ICDs/ETO2 0.023 0.069 -9999 0 -0.31 12 12
axon guidance 0.033 0.1 -9999 0 -0.34 1 1
NEDD4 0.018 0.008 -9999 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.034 0.13 -9999 0 -0.38 44 44
CBFA2T3 -0.004 0.11 -9999 0 -0.58 12 12
ErbB4/ErbB2/HBEGF 0.024 0.083 -9999 0 -0.4 3 3
MAPK3 0.001 0.12 -9999 0 -0.49 1 1
STAT1 (dimer) 0.031 0.043 -9999 0 -10000 0 0
MAPK1 0.001 0.12 -9999 0 -0.49 1 1
JAK2 0.014 0.031 -9999 0 -0.58 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.14 -9999 0 -0.36 15 15
NRG1 -0.07 0.18 -9999 0 -0.41 80 80
NRG3 -0.007 0.085 -9999 0 -0.51 10 10
NRG2 -0.24 0.29 -9999 0 -0.58 152 152
NRG4 -0.038 0.17 -9999 0 -0.58 32 32
heart development 0.033 0.1 -9999 0 -0.34 1 1
neural crest cell migration -0.035 0.14 -9999 0 -0.36 15 15
ERBB2 0.014 0.073 -9999 0 -0.36 13 13
WWOX/E4ICDs 0.034 0.035 -9999 0 -10000 0 0
SHC1 0.014 0.028 -9999 0 -0.51 1 1
ErbB4/EGFR/neuregulin 4 -0.001 0.12 -9999 0 -0.47 6 6
apoptosis 0.017 0.043 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.18 -9999 0 -0.32 152 152
ErbB4/ErbB2/epiregulin -0.047 0.14 -9999 0 -0.39 12 12
ErbB4/ErbB4/betacellulin/betacellulin -0.007 0.12 -9999 0 -0.32 40 40
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.036 0.093 -9999 0 -0.46 3 3
MDM2 0.028 0.064 -9999 0 -0.33 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.057 0.12 -9999 0 -0.33 12 12
STAT5A 0.038 0.1 -9999 0 -0.4 1 1
ErbB4/EGFR/neuregulin 1 beta -0.038 0.15 -9999 0 -0.38 16 16
DLG4 0.014 0.031 -9999 0 -0.58 1 1
GRB2/SHC 0.022 0.02 -9999 0 -0.36 1 1
E4ICDs/TAB2/NCoR1 -0.004 0.017 -9999 0 -10000 0 0
STAT5A (dimer) -0.042 0.093 -9999 0 -0.44 6 6
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.037 0.095 -9999 0 -10000 0 0
LRIG1 -0.034 0.16 -9999 0 -0.58 30 30
EREG -0.13 0.25 -9999 0 -0.54 95 95
BTC -0.051 0.19 -9999 0 -0.58 40 40
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.031 0.11 -9999 0 -0.34 1 1
ERBB4 0.034 0.036 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
YAP1 -0.001 0.012 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.005 0.12 -9999 0 -0.48 7 7
glial cell differentiation 0.004 0.017 -9999 0 -10000 0 0
WWOX 0.014 0.031 -9999 0 -0.58 1 1
cell proliferation -0.053 0.17 -9999 0 -0.47 20 20
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.017 0.25 -10000 0 -0.85 11 11
PCK1 -0.025 0.18 -10000 0 -0.69 9 9
HNF4A -0.049 0.3 -10000 0 -0.98 16 16
KCNJ11 -0.041 0.32 -10000 0 -0.93 25 25
AKT1 0.016 0.11 -10000 0 -0.38 5 5
response to starvation -0.004 0.02 -10000 0 -10000 0 0
DLK1 -0.055 0.33 -10000 0 -0.95 29 29
NKX2-1 0.095 0.23 0.66 11 -0.5 1 12
ACADM -0.021 0.26 -10000 0 -0.83 15 15
TAT -0.026 0.19 -10000 0 -0.7 12 12
CEBPB 0.012 0.034 -10000 0 -0.59 1 1
CEBPA 0 0.085 -10000 0 -0.52 9 9
TTR -0.095 0.23 -10000 0 -0.67 22 22
PKLR -0.041 0.27 -10000 0 -0.82 18 18
APOA1 -0.03 0.3 -10000 0 -0.99 13 13
CPT1C -0.023 0.26 -10000 0 -0.8 15 15
ALAS1 0.031 0.14 -10000 0 -10000 0 0
TFRC -0.01 0.19 -10000 0 -0.59 9 9
FOXF1 -0.19 0.28 -10000 0 -0.57 129 129
NF1 0.024 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.02 0.072 -10000 0 -0.54 4 4
CPT1A -0.019 0.25 -10000 0 -0.89 11 11
HMGCS1 -0.017 0.25 -10000 0 -0.79 14 14
NR3C1 0.001 0.098 -10000 0 -0.57 9 9
CPT1B -0.019 0.25 -10000 0 -0.82 13 13
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.013 0.042 -10000 0 -10000 0 0
GCK -0.067 0.34 -10000 0 -0.94 33 33
CREB1 0.014 0.022 -10000 0 -10000 0 0
IGFBP1 -0.01 0.17 -10000 0 -0.59 11 11
PDX1 -0.074 0.21 -10000 0 -0.67 7 7
UCP2 -0.019 0.25 -10000 0 -0.78 15 15
ALDOB -0.028 0.29 -10000 0 -0.86 18 18
AFP -0.072 0.15 -10000 0 -0.46 21 21
BDH1 -0.018 0.25 -10000 0 -0.81 13 13
HADH -0.008 0.26 -10000 0 -0.86 11 11
F2 -0.029 0.29 -10000 0 -0.98 13 13
HNF1A -0.02 0.072 -10000 0 -0.54 4 4
G6PC -0.03 0.13 -10000 0 -0.57 3 3
SLC2A2 -0.018 0.19 -10000 0 -0.66 10 10
INS -0.006 0.029 -10000 0 -10000 0 0
FOXA1 -0.061 0.2 -10000 0 -0.58 41 41
FOXA3 -0.098 0.22 -10000 0 -0.51 69 69
FOXA2 -0.016 0.3 -10000 0 -0.83 19 19
ABCC8 -0.015 0.26 -10000 0 -0.88 11 11
ALB -0.088 0.16 -10000 0 -0.46 25 25
Regulation of Androgen receptor activity

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
HDAC1 0.026 0.002 -9999 0 -10000 0 0
SMARCC1 0.012 0.014 -9999 0 -10000 0 0
REL 0.01 0.058 -9999 0 -0.53 4 4
HDAC7 -0.015 0.14 -9999 0 -0.37 3 3
JUN -0.007 0.11 -9999 0 -0.58 13 13
EP300 0.015 0.001 -9999 0 -10000 0 0
KAT2B 0.015 0.001 -9999 0 -10000 0 0
KAT5 0.016 0.001 -9999 0 -10000 0 0
MAPK14 0.016 0.052 -9999 0 -0.4 5 5
FOXO1 0.015 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.022 0.14 -9999 0 -0.36 23 23
MAP2K6 0.005 0.068 -9999 0 -0.56 5 5
BRM/BAF57 0.021 0.008 -9999 0 -10000 0 0
MAP2K4 0.013 0.007 -9999 0 -10000 0 0
SMARCA2 0.015 0.004 -9999 0 -10000 0 0
PDE9A -0.16 0.4 -9999 0 -1.2 43 43
NCOA2 -0.023 0.14 -9999 0 -0.58 23 23
CEBPA 0.002 0.083 -9999 0 -0.51 9 9
EHMT2 0.014 0.004 -9999 0 -10000 0 0
cell proliferation -0.002 0.15 -9999 0 -0.49 7 7
NR0B1 -0.039 0.14 -9999 0 -0.51 31 31
EGR1 -0.13 0.25 -9999 0 -0.58 87 87
RXRs/9cRA -0.068 0.15 -9999 0 -0.32 95 95
AR/RACK1/Src -0.016 0.089 -9999 0 -0.38 5 5
AR/GR -0.074 0.15 -9999 0 -0.32 62 62
GNB2L1 0.015 0.001 -9999 0 -10000 0 0
PKN1 0.014 0.031 -9999 0 -0.58 1 1
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.018 0.043 -9999 0 -0.42 3 3
T-DHT/AR/TIF2/CARM1 -0.021 0.12 -9999 0 -0.43 12 12
SRC 0.027 0.056 -9999 0 -0.31 1 1
NR3C1 0.001 0.093 -9999 0 -0.58 9 9
KLK3 -0.12 0.27 -9999 0 -1 23 23
APPBP2 0.013 0.008 -9999 0 -10000 0 0
TRIM24 0.011 0.04 -9999 0 -0.51 2 2
T-DHT/AR/TIP60 -0.01 0.092 -9999 0 -0.4 5 5
TMPRSS2 -0.22 0.46 -9999 0 -1.2 64 64
RXRG -0.15 0.26 -9999 0 -0.58 95 95
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.031 -9999 0 -0.58 1 1
RXRB 0.015 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.002 -9999 0 -10000 0 0
NR2C2 0.012 0.042 -9999 0 -0.54 2 2
KLK2 -0.029 0.15 -9999 0 -0.49 11 11
AR -0.08 0.16 -9999 0 -0.29 128 128
SENP1 0.015 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0 0.094 -9999 0 -0.5 12 12
SRY -0.001 0.067 -9999 0 -0.51 6 6
GATA2 -0.007 0.11 -9999 0 -0.53 15 15
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.081 0.22 -9999 0 -0.57 58 58
T-DHT/AR/RACK1/Src -0.003 0.092 -9999 0 -0.39 5 5
positive regulation of transcription -0.007 0.11 -9999 0 -0.53 15 15
DNAJA1 0.013 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.024 -9999 0 -10000 0 0
NCOA1 0.02 0.006 -9999 0 -10000 0 0
SPDEF -0.1 0.23 -9999 0 -0.55 73 73
T-DHT/AR/TIF2 0.002 0.094 -9999 0 -0.36 8 8
T-DHT/AR/Hsp90 -0.01 0.092 -9999 0 -0.4 5 5
GSK3B 0.014 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.002 -9999 0 -10000 0 0
mol:T-DHT 0.02 0.06 -9999 0 -0.3 7 7
SIRT1 0.015 0.001 -9999 0 -10000 0 0
ZMIZ2 0.017 0.007 -9999 0 -10000 0 0
POU2F1 0.017 0.042 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.052 0.11 -9999 0 -0.4 12 12
CREBBP 0.015 0.001 -9999 0 -10000 0 0
SMARCE1 0.015 0.004 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.016 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.004 0.095 -9999 0 -0.36 22 22
forebrain development -0.084 0.24 -9999 0 -0.57 54 54
GNAO1 -0.17 0.27 -9999 0 -0.58 110 110
SMO/beta Arrestin2 0.002 0.093 -9999 0 -0.41 17 17
SMO -0.013 0.13 -9999 0 -0.58 17 17
ARRB2 0.015 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.054 0.056 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.04 0.002 -9999 0 -10000 0 0
GNAI1 0.011 0.054 -9999 0 -0.58 3 3
XPO1 0.016 0.007 -9999 0 -10000 0 0
GLI1/Su(fu) -0.089 0.19 -9999 0 -0.61 29 29
SAP30 0.016 0.001 -9999 0 -10000 0 0
mol:GDP -0.013 0.13 -9999 0 -0.57 17 17
MIM/GLI2A 0.017 0.008 -9999 0 -10000 0 0
IFT88 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0.001 -9999 0 -10000 0 0
GLI2 0.021 0.076 -9999 0 -10000 0 0
GLI3 0.048 0.059 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.016 0 -9999 0 -10000 0 0
GNG2 0.006 0.076 -9999 0 -0.58 6 6
Gi family/GTP -0.12 0.22 -9999 0 -0.4 106 106
SIN3B 0.016 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.067 0.041 -9999 0 -10000 0 0
GLI2/Su(fu) 0.028 0.087 -9999 0 -0.29 12 12
FOXA2 -0.053 0.11 -9999 0 -10000 0 0
neural tube patterning -0.084 0.24 -9999 0 -0.57 54 54
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.029 0.045 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.017 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.084 0.24 -9999 0 -0.57 54 54
SUFU 0.02 0.051 -9999 0 -10000 0 0
LGALS3 0.014 0.031 -9999 0 -0.58 1 1
catabolic process 0.059 0.076 -9999 0 -0.31 5 5
GLI3A/CBP -0.028 0.13 -9999 0 -0.34 52 52
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.086 0.25 -9999 0 -0.59 54 54
RAB23 0.014 0.031 -9999 0 -0.58 1 1
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.016 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.028 0.048 -9999 0 -0.3 1 1
GNAZ -0.11 0.24 -9999 0 -0.58 76 76
RBBP4 0.016 0.001 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.027 0.071 -9999 0 -10000 0 0
STK36 0.016 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.094 0.21 -9999 0 -0.49 57 57
PTCH1 -0.065 0.21 -9999 0 -0.72 19 19
MIM/GLI1 -0.087 0.25 -9999 0 -0.62 44 44
CREBBP -0.028 0.13 -9999 0 -0.34 52 52
Su(fu)/SIN3/HDAC complex 0.055 0.015 -9999 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.001 0.093 -9999 0 -0.58 9 9
alphaV beta3 Integrin -0.029 0.14 -9999 0 -0.42 42 42
PTK2 -0.049 0.13 -9999 0 -0.45 27 27
positive regulation of JNK cascade -0.025 0.081 -9999 0 -0.31 27 27
CDC42/GDP 0.025 0.13 -9999 0 -0.41 27 27
Rac1/GDP 0.027 0.13 -9999 0 -0.4 27 27
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.03 0.1 -9999 0 -0.38 27 27
nectin-3/I-afadin -0.012 0.12 -9999 0 -0.41 29 29
RAPGEF1 0.017 0.14 -9999 0 -0.46 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.006 0.16 -9999 0 -0.53 27 27
PDGFB-D/PDGFRB 0.001 0.093 -9999 0 -0.57 9 9
TLN1 0.016 0.07 -9999 0 -0.32 6 6
Rap1/GTP -0.025 0.085 -9999 0 -0.32 27 27
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.03 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.012 0.12 -9999 0 -0.41 29 29
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.017 0.16 -9999 0 -0.51 27 27
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.012 0.099 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.022 0.023 -9999 0 -0.41 1 1
positive regulation of lamellipodium assembly -0.027 0.087 -9999 0 -0.32 28 28
PVRL1 0.014 0.031 -9999 0 -0.58 1 1
PVRL3 -0.032 0.16 -9999 0 -0.57 29 29
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 -0.006 0.11 -9999 0 -0.58 13 13
CLDN1 -0.016 0.13 -9999 0 -0.55 20 20
JAM-A/CLDN1 -0.006 0.12 -9999 0 -0.32 39 39
SRC -0.05 0.16 -9999 0 -0.6 27 27
ITGB3 -0.054 0.19 -9999 0 -0.58 42 42
nectin-1(dimer)/I-afadin/I-afadin 0.022 0.023 -9999 0 -0.41 1 1
FARP2 0.012 0.15 -9999 0 -0.5 27 27
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.002 0.1 -9999 0 -0.34 29 29
nectin-1/I-afadin 0.022 0.023 -9999 0 -0.41 1 1
nectin-2/I-afadin 0.023 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.001 0.1 -9999 0 -0.34 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
F11R 0.014 0.031 -9999 0 -0.58 1 1
positive regulation of filopodium formation -0.025 0.081 -9999 0 -0.31 27 27
alphaV/beta3 Integrin/Talin -0.003 0.13 -9999 0 -0.43 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.023 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.023 0 -9999 0 -10000 0 0
PIP5K1C 0.008 0.074 -9999 0 -0.36 6 6
VAV2 0.008 0.16 -9999 0 -0.51 29 29
RAP1/GDP -0.029 0.1 -9999 0 -0.38 27 27
ITGAV 0.014 0.031 -9999 0 -0.58 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.002 0.1 -9999 0 -0.34 29 29
nectin-3(dimer)/I-afadin/I-afadin -0.012 0.12 -9999 0 -0.41 29 29
Rac1/GTP -0.033 0.11 -9999 0 -0.39 28 28
PTPRM -0.003 0.082 -9999 0 -0.25 33 33
E-cadherin/beta catenin/alpha catenin -0.01 0.055 -9999 0 -0.55 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.019 0.005 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.029 0.13 0.47 8 -10000 0 8
IL27/IL27R/JAK1 -0.058 0.16 -10000 0 -0.7 5 5
TBX21 -0.045 0.2 -10000 0 -0.51 32 32
IL12B -0.008 0.091 -10000 0 -0.51 11 11
IL12A 0.006 0.049 -10000 0 -0.37 6 6
IL6ST -0.08 0.22 -10000 0 -0.58 56 56
IL27RA/JAK1 0.016 0.038 -10000 0 -10000 0 0
IL27 -0.019 0.12 -10000 0 -0.51 20 20
TYK2 0.014 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.16 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.029 0.13 0.47 8 -10000 0 8
T cell proliferation during immune response 0.029 0.13 0.47 8 -10000 0 8
MAPKKK cascade -0.029 0.13 -10000 0 -0.47 8 8
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.01 0.055 -10000 0 -0.5 4 4
IL12RB1 -0.022 0.14 -10000 0 -0.54 24 24
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.068 0.22 -10000 0 -0.51 41 41
IL27/IL27R/JAK2/TYK2 -0.029 0.13 -10000 0 -0.48 8 8
positive regulation of T cell mediated cytotoxicity -0.029 0.13 -10000 0 -0.47 8 8
STAT1 (dimer) -0.085 0.21 0.48 13 -0.62 20 33
JAK2 0.012 0.032 -10000 0 -0.58 1 1
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.021 0.12 -10000 0 -0.47 7 7
T cell proliferation -0.16 0.19 -10000 0 -0.48 45 45
IL12/IL12R/TYK2/JAK2 0.001 0.082 -10000 0 -10000 0 0
IL17A -0.12 0.15 -10000 0 -10000 0 0
mast cell activation 0.029 0.13 0.47 8 -10000 0 8
IFNG -0.008 0.034 -10000 0 -0.09 9 9
T cell differentiation -0.005 0.006 -10000 0 -0.019 33 33
STAT3 (dimer) -0.021 0.12 -10000 0 -0.49 6 6
STAT5A (dimer) -0.022 0.12 -10000 0 -0.47 7 7
STAT4 (dimer) -0.037 0.14 -10000 0 -0.5 10 10
STAT4 -0.016 0.13 -10000 0 -0.58 19 19
T cell activation -0.01 0.008 0.051 4 -10000 0 4
IL27R/JAK2/TYK2 -0.029 0.13 -10000 0 -0.61 2 2
GATA3 -0.069 0.35 -10000 0 -1.4 23 23
IL18 0.007 0.051 -10000 0 -0.42 5 5
positive regulation of mast cell cytokine production -0.02 0.12 -10000 0 -0.48 6 6
IL27/EBI3 -0.015 0.11 -10000 0 -0.39 28 28
IL27RA 0.006 0.039 -10000 0 -10000 0 0
IL6 -0.25 0.29 -10000 0 -0.57 162 162
STAT5A 0.014 0.031 -10000 0 -0.58 1 1
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.004 0.023 -10000 0 -10000 0 0
IL1B -0.022 0.11 -10000 0 -0.4 30 30
EBI3 -0.002 0.09 -10000 0 -0.53 10 10
TNF -0.005 0.081 -10000 0 -0.37 17 17
EGFR-dependent Endothelin signaling events

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
HRAS 0.016 0 -9999 0 -10000 0 0
EGFR -0.008 0.11 -9999 0 -0.54 15 15
EGF/EGFR -0.07 0.12 -9999 0 -0.3 59 59
EGF/EGFR dimer/SHC/GRB2/SOS1 0.015 0.09 -9999 0 -0.49 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.071 0.21 -9999 0 -0.58 52 52
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.018 0.12 -9999 0 -0.51 22 22
EGF/EGFR dimer/SHC -0.005 0.1 -9999 0 -0.31 37 37
mol:GDP -0.025 0.076 -9999 0 -0.48 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.075 -9999 0 -0.53 7 7
GRB2/SOS1 0.023 0 -9999 0 -10000 0 0
HRAS/GTP -0.023 0.068 -9999 0 -0.45 1 1
SHC1 0.014 0.028 -9999 0 -0.51 1 1
HRAS/GDP -0.023 0.07 -9999 0 -0.45 1 1
FRAP1 0.012 0.085 -9999 0 -0.47 1 1
EGF/EGFR dimer -0.018 0.12 -9999 0 -0.37 37 37
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.048 0.16 -9999 0 -0.42 58 58
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.002 0.09 -9999 0 -0.34 18 18
CCNA2 -0.12 0.23 -9999 0 -0.51 94 94
PIK3CA 0.017 0 -9999 0 -10000 0 0
JAK3 0.014 0.039 -9999 0 -0.51 2 2
PIK3R1 0.016 0 -9999 0 -10000 0 0
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.061 0.1 -9999 0 -0.62 4 4
SHC1 0.015 0.028 -9999 0 -0.51 1 1
SP1 -0.004 0.098 -9999 0 -0.34 28 28
IL2RA -0.023 0.2 -9999 0 -0.61 33 33
IL2RB 0.007 0.075 -9999 0 -0.56 6 6
SOS1 0.016 0 -9999 0 -10000 0 0
IL2RG -0.01 0.12 -9999 0 -0.54 17 17
G1/S transition of mitotic cell cycle -0.062 0.25 -9999 0 -0.76 33 33
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 -0.03 0.23 -9999 0 -0.81 28 28
LCK 0.007 0.073 -9999 0 -0.55 6 6
GRB2 0.016 0 -9999 0 -10000 0 0
IL2 0.005 0.007 -9999 0 -10000 0 0
CDK6 -0.003 0.1 -9999 0 -0.58 11 11
CCND3 0.068 0.09 -9999 0 -0.56 3 3
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.007 -10000 0 -10000 0 0
HSPA8 0.015 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.064 0.15 0.22 3 -0.38 58 61
AKT1 0.015 0.015 -10000 0 -10000 0 0
GSC -0.007 0.087 -10000 0 -10000 0 0
NKX2-5 -0.078 0.19 -10000 0 -0.5 59 59
muscle cell differentiation 0.052 0.087 0.4 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.048 0.097 -10000 0 -0.38 5 5
SMAD4 0.01 0.051 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.028 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.001 0.039 -10000 0 -0.48 1 1
MYC -0.013 0.13 -10000 0 -0.58 18 18
CDKN2B -0.015 0.27 -10000 0 -1.4 11 11
AP1 -0.052 0.21 -10000 0 -0.66 20 20
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.069 0.023 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.026 0.078 -10000 0 -0.32 8 8
SP3 0.019 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.1 0.22 -10000 0 -0.5 83 83
SMAD3/SMAD4/GR -0.018 0.078 -10000 0 -0.44 9 9
GATA3 -0.028 0.15 -10000 0 -0.57 25 25
SKI/SIN3/HDAC complex/NCoR1 0.054 0.009 -10000 0 -10000 0 0
MEF2C/TIF2 -0.077 0.2 -10000 0 -0.57 32 32
endothelial cell migration 0.007 0.17 1.4 5 -10000 0 5
MAX 0.014 0.007 -10000 0 -10000 0 0
RBBP7 0.015 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.001 -10000 0 -10000 0 0
RUNX2 0.007 0.069 -10000 0 -0.52 6 6
RUNX3 -0.008 0.12 -10000 0 -0.58 14 14
RUNX1 0.016 0 -10000 0 -10000 0 0
CTBP1 0.014 0.028 -10000 0 -0.51 1 1
NR3C1 -0.001 0.093 -10000 0 -0.58 9 9
VDR 0.012 0.042 -10000 0 -0.54 2 2
CDKN1A 0.056 0.11 -10000 0 -1.4 1 1
KAT2B 0.016 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.042 0.15 -10000 0 -0.35 37 37
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.001 -10000 0 -10000 0 0
SERPINE1 -0.008 0.18 -10000 0 -1.4 5 5
SMAD3/SMAD4/ATF2 -0.006 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.073 0.16 -10000 0 -0.4 64 64
SAP30 0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.014 0.026 -10000 0 -10000 0 0
JUN -0.052 0.21 -10000 0 -0.66 20 20
SMAD3/SMAD4/IRF7 -0.021 0.08 -10000 0 -0.4 6 6
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.038 0.26 -10000 0 -0.99 23 23
mesenchymal cell differentiation 0.013 0.058 0.32 6 -10000 0 6
DLX1 -0.04 0.16 -10000 0 -0.51 37 37
TCF3 0.016 0 -10000 0 -10000 0 0
FOS -0.16 0.28 -10000 0 -0.58 110 110
SMAD3/SMAD4/Max -0.009 0.042 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.032 0.007 -10000 0 -10000 0 0
ZBTB17 0.017 0.012 -10000 0 -10000 0 0
LAMC1 0.046 0.062 -10000 0 -0.63 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.006 0.044 -10000 0 -10000 0 0
IRF7 -0.004 0.1 -10000 0 -0.52 13 13
ESR1 -0.084 0.22 -10000 0 -0.57 61 61
HNF4A -0.039 0.15 -10000 0 -0.51 35 35
MEF2C -0.07 0.19 -10000 0 -0.59 21 21
SMAD2-3/SMAD4 0.01 0.064 -10000 0 -0.32 1 1
Cbp/p300/Src-1 0.033 0.011 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.017 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0.005 -10000 0 -10000 0 0
SKIL 0.014 0.028 -10000 0 -0.51 1 1
HDAC1 0.015 0.001 -10000 0 -10000 0 0
HDAC2 0.015 0.001 -10000 0 -10000 0 0
SNIP1 0.015 0.001 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.066 -10000 0 -0.33 1 1
MSG1/HSC70 0.015 0.045 -10000 0 -0.36 5 5
SMAD2 0.017 0.02 -10000 0 -10000 0 0
SMAD3 0.01 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.039 0.045 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.011 0.024 -10000 0 -10000 0 0
NCOR1 0.015 0.001 -10000 0 -10000 0 0
NCOA2 -0.023 0.14 -10000 0 -0.58 23 23
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.062 0.092 -10000 0 -0.38 3 3
IFNB1 0.013 0.1 -10000 0 -0.47 8 8
SMAD3/SMAD4/MEF2C -0.068 0.19 -10000 0 -0.58 23 23
CITED1 0.008 0.061 -10000 0 -0.51 5 5
SMAD2-3/SMAD4/ARC105 0.035 0.064 -10000 0 -10000 0 0
RBL1 0.013 0.039 -10000 0 -0.51 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.041 0.11 -10000 0 -0.49 11 11
RUNX1-3/PEBPB2 0.017 0.073 -10000 0 -0.34 14 14
SMAD7 -0.002 0.18 -10000 0 -0.59 10 10
MYC/MIZ-1 -0.01 0.1 -10000 0 -0.42 18 18
SMAD3/SMAD4 0.006 0.069 0.25 1 -0.42 4 5
IL10 -0.008 0.18 -10000 0 -0.62 21 21
PIASy/HDAC complex 0.015 0.006 -10000 0 -10000 0 0
PIAS3 0.016 0.003 -10000 0 -10000 0 0
CDK2 0.016 0.004 -10000 0 -10000 0 0
IL5 -0.002 0.12 -10000 0 -0.5 6 6
CDK4 0.015 0.028 -10000 0 -0.51 1 1
PIAS4 0.015 0.006 -10000 0 -10000 0 0
ATF3 -0.09 0.23 -10000 0 -0.58 64 64
SMAD3/SMAD4/SP1 0.03 0.093 -10000 0 -0.36 7 7
FOXG1 -0.069 0.18 -10000 0 -0.51 50 50
FOXO3 0.026 0.02 -10000 0 -10000 0 0
FOXO1 0.026 0.02 -10000 0 -10000 0 0
FOXO4 0.025 0.028 -10000 0 -0.35 1 1
heart looping -0.069 0.19 -10000 0 -0.59 21 21
CEBPB 0.014 0.032 -10000 0 -0.57 1 1
SMAD3/SMAD4/DLX1 -0.038 0.1 -10000 0 -0.34 19 19
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.036 0.1 -10000 0 -0.34 19 19
SMAD3/SMAD4/GATA3 -0.041 0.12 -10000 0 -0.4 21 21
SnoN/SIN3/HDAC complex/NCoR1 0.014 0.028 -10000 0 -0.51 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.025 0.09 -10000 0 -0.39 8 8
SMAD3/SMAD4/SP1-3 0.042 0.085 -10000 0 -0.37 1 1
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.018 0.036 -10000 0 -10000 0 0
SIN3B 0.015 0.001 -10000 0 -10000 0 0
SIN3A 0.015 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.077 0.18 -10000 0 -0.45 28 28
ITGB5 0.055 0.072 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.055 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.14 0.18 -10000 0 -0.37 128 128
AR -0.2 0.28 -10000 0 -0.58 128 128
negative regulation of cell growth 0.009 0.1 -10000 0 -0.4 5 5
SMAD3/SMAD4/MYOD -0.008 0.047 -10000 0 -10000 0 0
E2F5 0.012 0.042 -10000 0 -0.54 2 2
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.014 0.13 -10000 0 -0.39 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 0.044 0.08 -10000 0 -0.34 11 11
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.051 0.21 -10000 0 -0.67 20 20
SMAD3/SMAD4/RUNX2 -0.011 0.06 -10000 0 -0.32 6 6
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.016 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.016 0 -10000 0 -10000 0 0
ANTXR2 -0.018 0.14 -10000 0 -0.58 20 20
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.017 -10000 0 -0.075 20 20
monocyte activation -0.006 0.09 -10000 0 -0.41 16 16
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.003 0.014 -10000 0 -10000 0 0
MAP2K7 -0.003 0.014 -10000 0 -10000 0 0
MAP2K6 -0.008 0.039 -10000 0 -0.31 5 5
CYAA -0.001 0.073 -10000 0 -0.3 20 20
MAP2K4 -0.003 0.014 -10000 0 -10000 0 0
IL1B -0.012 0.089 -10000 0 -0.29 31 31
Channel 0.001 0.079 -10000 0 -0.32 20 20
NLRP1 -0.008 0.038 -10000 0 -0.31 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.005 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.017 0.075 20 -10000 0 20
MAPK3 -0.003 0.014 -10000 0 -10000 0 0
MAPK1 -0.003 0.014 -10000 0 -10000 0 0
PGR -0.1 0.15 -10000 0 -0.32 115 115
PA/Cellular Receptors 0 0.086 -10000 0 -0.35 20 20
apoptosis -0.004 0.017 -10000 0 -0.075 20 20
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.074 -10000 0 -0.3 20 20
macrophage activation 0.018 0.016 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.51 17 17
VCAM1 -0.006 0.09 -10000 0 -0.41 16 16
platelet activation -0.005 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.021 0.14 1 -10000 0 1
IL18 0.008 0.052 -10000 0 -0.26 10 10
negative regulation of macrophage activation -0.004 0.017 -10000 0 -0.075 20 20
LEF -0.004 0.017 -10000 0 -0.075 20 20
CASP1 -0.008 0.031 -10000 0 -0.17 8 8
mol:cAMP -0.005 0.019 -10000 0 -10000 0 0
necrosis -0.004 0.017 -10000 0 -0.075 20 20
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.074 -10000 0 -0.3 20 20
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.053 0.082 -10000 0 -0.57 2 2
UGCG -0.018 0.17 -10000 0 -0.66 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT 0.024 0.12 -10000 0 -0.38 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.015 0.17 -10000 0 -0.65 22 22
mol:DAG 0 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.12 -10000 0 -0.4 32 32
FRAP1 0.044 0.17 -10000 0 -0.46 32 32
FOXO3 0.055 0.15 -10000 0 -0.45 21 21
AKT1 0.047 0.16 -10000 0 -0.46 25 25
GAB2 0.015 0.004 -10000 0 -10000 0 0
SMPD1 0.023 0.029 -10000 0 -10000 0 0
SGMS1 0.023 0.029 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.007 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.013 0.14 -10000 0 -0.34 31 31
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K 0.028 0.009 -10000 0 -10000 0 0
RPS6KB1 0.018 0.038 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.003 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.013 15 15
JAK3 0.015 0.039 -10000 0 -0.5 2 2
PIK3R1 0.018 0.005 -10000 0 -10000 0 0
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC 0.025 0.25 -10000 0 -0.94 21 21
MYB -0.016 0.13 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.05 0.13 -10000 0 -0.61 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.035 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.05 0.12 -10000 0 -0.59 7 7
Rac1/GDP 0.031 0.01 -10000 0 -10000 0 0
T cell proliferation 0.055 0.12 -10000 0 -0.58 6 6
SHC1 0.014 0.028 -10000 0 -0.51 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.013 -10000 0 -0.031 45 45
PRKCZ 0.055 0.12 -10000 0 -0.61 6 6
NF kappa B1 p50/RelA -0.028 0.12 -10000 0 -0.45 20 20
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.046 0.087 -10000 0 -0.49 7 7
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.036 0.16 -10000 0 -0.54 33 33
IL2RB 0.008 0.075 -10000 0 -0.56 6 6
TERT -0.21 0.26 -10000 0 -0.51 153 153
E2F1 -0.007 0.084 -10000 0 -0.25 24 24
SOS1 0.016 0.004 -10000 0 -10000 0 0
RPS6 0.016 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.015 45 -10000 0 45
PTPN11 0.016 0.004 -10000 0 -10000 0 0
IL2RG -0.008 0.12 -10000 0 -0.54 17 17
actin cytoskeleton organization 0.055 0.12 -10000 0 -0.58 6 6
GRB2 0.016 0.004 -10000 0 -10000 0 0
IL2 0.007 0.008 -10000 0 -10000 0 0
PIK3CA 0.018 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.013 -10000 0 -10000 0 0
LCK 0.009 0.073 -10000 0 -0.55 6 6
BCL2 0.035 0.22 -10000 0 -0.8 19 19
Signaling events mediated by PTP1B

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
PDGFRB 0.001 0.093 -10000 0 -0.58 9 9
Jak2/Leptin Receptor -0.005 0.093 0.2 14 -0.36 8 22
PTP1B/AKT1 0.026 0.048 -10000 0 -0.24 2 2
FYN 0.011 0.054 -10000 0 -0.58 3 3
p210 bcr-abl/PTP1B 0.02 0.053 -10000 0 -0.24 4 4
EGFR -0.007 0.11 -10000 0 -0.54 15 15
EGF/EGFR -0.026 0.073 -10000 0 -0.27 17 17
CSF1 -0.006 0.11 -10000 0 -0.58 13 13
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.002 0.1 -10000 0 -0.29 22 22
Insulin Receptor/Insulin -0.004 0.025 -10000 0 -10000 0 0
HCK -0.012 0.12 -10000 0 -0.56 17 17
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 0.028 0.05 -10000 0 -0.25 2 2
EGF -0.017 0.12 -10000 0 -0.5 22 22
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 0.023 0.067 -10000 0 -0.26 4 4
TXN 0.013 0.039 -10000 0 -0.51 2 2
PTP1B/IRS1/GRB2 0.03 0.068 -10000 0 -0.38 4 4
cell migration -0.02 0.053 0.24 4 -10000 0 4
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.044 0.17 -10000 0 -0.53 39 39
ITGA2B -0.026 0.14 -10000 0 -0.51 28 28
CSF1R -0.021 0.14 -10000 0 -0.57 22 22
Prolactin Receptor/Prolactin -0.04 0.13 -10000 0 -0.38 44 44
FGR 0.014 0.031 -10000 0 -0.58 1 1
PTP1B/p130 Cas 0.027 0.049 -10000 0 -0.25 2 2
Crk/p130 Cas 0.036 0.048 -10000 0 -0.24 1 1
DOK1 0.029 0.062 -10000 0 -0.27 5 5
JAK2 0.012 0.072 -10000 0 -0.34 5 5
Jak2/Leptin Receptor/Leptin -0.073 0.15 -10000 0 -0.43 39 39
PIK3R1 0.016 0 -10000 0 -10000 0 0
PTPN1 0.02 0.053 -10000 0 -0.24 4 4
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.041 0.16 -10000 0 -0.51 38 38
SRC 0.028 0.022 -10000 0 -10000 0 0
ITGB3 -0.054 0.19 -10000 0 -0.58 42 42
CAT1/PTP1B 0 0.11 -10000 0 -0.38 10 10
CAPN1 0.016 0.002 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0 0.021 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.072 0.15 -10000 0 -0.46 39 39
negative regulation of transcription 0.016 0.073 -10000 0 -0.33 5 5
FCGR2A -0.001 0.091 -10000 0 -0.51 11 11
FER 0.013 0.045 -10000 0 -0.58 2 2
alphaIIb/beta3 Integrin -0.061 0.17 -10000 0 -0.41 66 66
BLK -0.054 0.18 -10000 0 -0.56 42 42
Insulin Receptor/Insulin/Shc 0.021 0.017 -10000 0 -0.3 1 1
RHOA 0.016 0.002 -10000 0 -10000 0 0
LEPR -0.007 0.11 -10000 0 -0.57 14 14
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.021 0.13 -10000 0 -0.45 13 13
PRL 0 0.061 -10000 0 -0.51 5 5
SOCS3 -0.14 0.43 -10000 0 -1.4 38 38
SPRY2 0.004 0.083 -10000 0 -0.58 7 7
Insulin Receptor/Insulin/IRS1 0.014 0.052 -10000 0 -0.36 7 7
CSF1/CSF1R 0.006 0.12 -10000 0 -0.37 20 20
Ras protein signal transduction 0.011 0.018 -10000 0 -10000 0 0
IRS1 0.004 0.082 -10000 0 -0.58 7 7
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.062 0.19 -10000 0 -0.56 46 46
STAT5B 0.023 0.054 -10000 0 -0.23 4 4
STAT5A 0.023 0.054 -10000 0 -0.23 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.072 -10000 0 -0.31 9 9
CSN2 -0.012 0.047 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
LAT 0.024 0.035 -10000 0 -0.39 1 1
YBX1 0.024 0.027 -10000 0 -0.49 1 1
LCK 0.006 0.073 -10000 0 -0.55 6 6
SHC1 0.014 0.028 -10000 0 -0.51 1 1
NOX4 -0.019 0.13 -10000 0 -0.5 24 24
Syndecan-3-mediated signaling events

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
CTTN 0.014 0.028 -9999 0 -0.51 1 1
Syndecan-3/Src/Cortactin -0.064 0.11 -9999 0 -0.81 1 1
Syndecan-3/Neurocan -0.009 0.051 -9999 0 -0.27 12 12
POMC -0.006 0.11 -9999 0 -0.54 14 14
EGFR -0.008 0.11 -9999 0 -0.54 15 15
Syndecan-3/EGFR -0.012 0.06 -9999 0 -0.28 16 16
AGRP 0.005 0.039 -9999 0 -0.51 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.007 0.089 -9999 0 -0.51 11 11
long-term memory -0.004 0.048 -9999 0 -0.44 3 3
Syndecan-3/IL8 -0.042 0.11 -9999 0 -0.29 51 51
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0.022 0.02 -9999 0 -0.36 1 1
FYN 0.011 0.054 -9999 0 -0.58 3 3
limb bud formation -0.002 0.033 -9999 0 -0.62 1 1
MC4R -0.002 0.061 -9999 0 -0.51 5 5
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.13 0.25 -9999 0 -0.56 91 91
FGFR/FGF/Syndecan-3 -0.002 0.033 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.046 0.12 -9999 0 -0.6 2 2
Syndecan-3/AgRP -0.003 0.036 -9999 0 -0.36 3 3
Syndecan-3/AgRP/MC4R 0.001 0.047 -9999 0 -0.58 1 1
Fyn/Cortactin 0.018 0.045 -9999 0 -0.4 4 4
SDC3 -0.002 0.033 -9999 0 -0.63 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.041 0.11 -9999 0 -0.29 51 51
IL8 -0.069 0.21 -9999 0 -0.57 51 51
Syndecan-3/Fyn/Cortactin 0.034 0.054 -9999 0 -0.46 3 3
Syndecan-3/CASK -0.002 0.032 -9999 0 -0.6 1 1
alpha-MSH/MC4R -0.005 0.089 -9999 0 -0.38 19 19
Gamma Secretase 0.046 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.1 0.36 27 -10000 0 27
CDKN1A -0.002 0.041 -10000 0 -0.77 1 1
KAT2B 0.016 0 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.026 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.015 0.11 -10000 0 -0.51 17 17
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.013 0 -10000 0 -10000 0 0
PPARGC1A -0.23 0.29 -10000 0 -0.57 145 145
FHL2 0.014 0.031 -10000 0 -0.58 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.008 -10000 0 -10000 0 0
HIST2H4A -0.005 0.1 -10000 0 -0.36 27 27
SIRT1/FOXO3a 0 0.007 -10000 0 -10000 0 0
SIRT1 0.001 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.01 0.033 -10000 0 -10000 0 0
apoptosis 0 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.14 0.17 -10000 0 -0.35 145 145
p53/SIRT1 0.001 0.021 0.4 1 -10000 0 1
SIRT1/FOXO4 0 0.01 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0 0.018 -10000 0 -0.31 1 1
HIST1H1E 0.01 0.048 -10000 0 -10000 0 0
SIRT1/p300 0 0.008 -10000 0 -10000 0 0
muscle cell differentiation 0 0.008 -10000 0 -10000 0 0
TP53 0.001 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.017 0.077 -10000 0 -0.36 17 17
ACSS2 0.022 0.021 -10000 0 -0.36 1 1
SIRT1/PCAF/MYOD 0 0.008 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0.018 0.006 -10000 0 -10000 0 0
PRKCZ 0.012 0.044 -10000 0 -0.58 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.017 0.048 -10000 0 -0.29 2 2
IRAK/TOLLIP 0.034 0.004 -10000 0 -10000 0 0
IKBKB 0.016 0 -10000 0 -10000 0 0
IKBKG 0.016 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.094 0.19 -10000 0 -0.39 101 101
IL1A -0.092 0.22 -10000 0 -0.54 69 69
IL1B -0.018 0.13 -10000 0 -0.4 37 37
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.018 -10000 0 -10000 0 0
IL1R2 -0.04 0.16 -10000 0 -0.52 37 37
IL1R1 0.014 0.031 -10000 0 -0.58 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.031 0.062 0.22 7 -0.33 2 9
TOLLIP 0.016 0 -10000 0 -10000 0 0
TICAM2 0.014 0.031 -10000 0 -0.58 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.011 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.075 0.009 -10000 0 -10000 0 0
JUN 0.035 0.066 -10000 0 -10000 0 0
MAP3K7 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.013 0.11 -10000 0 -0.51 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.031 0.14 -10000 0 -0.33 34 34
PIK3R1 0.016 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.021 0.13 -10000 0 -0.52 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.005 0.12 -10000 0 -0.35 25 25
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.039 0.043 -10000 0 -10000 0 0
IRAK1 0.027 0.005 -10000 0 -10000 0 0
IL1RN/IL1R1 0.009 0.078 -10000 0 -0.39 12 12
IRAK4 0.016 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
PI3K 0.023 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.023 0.068 -10000 0 -0.38 2 2
CHUK 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.005 0.12 -10000 0 -0.35 25 25
IL1 beta/IL1R2 -0.041 0.15 -10000 0 -0.34 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.029 0.08 -10000 0 -0.46 4 4
IRAK3 0.001 0.093 -10000 0 -0.58 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.012 0.11 -10000 0 -0.51 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.094 -10000 0 -0.5 1 1
IL1 alpha/IL1R1/IL1RAP -0.046 0.15 -10000 0 -0.32 78 78
RELA 0.016 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.016 0 -10000 0 -10000 0 0
MYD88 0.016 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.004 -10000 0 -10000 0 0
IL1RAP -0.001 0.09 -10000 0 -0.51 11 11
UBE2N 0.016 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.026 0.072 -10000 0 -0.42 4 4
CASP1 0.002 0.088 -10000 0 -0.58 8 8
IL1RN/IL1R2 -0.03 0.14 -10000 0 -0.38 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.005 0.11 -10000 0 -0.54 4 4
TMEM189-UBE2V1 0.008 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.077 -10000 0 -0.52 1 1
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL1RN -0.002 0.096 -10000 0 -0.52 12 12
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.035 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0.039 -10000 0 -0.51 2 2
EPHB2 -0.018 0.13 -10000 0 -0.5 23 23
EFNB1 0.015 0.069 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.034 0.1 -10000 0 -0.52 4 4
Ephrin B2/EPHB1-2 -0.016 0.12 -10000 0 -0.29 52 52
neuron projection morphogenesis -0.039 0.094 -10000 0 -0.5 4 4
Ephrin B1/EPHB1-2/Tiam1 -0.006 0.12 -10000 0 -0.38 12 12
DNM1 0.001 0.093 -10000 0 -0.58 9 9
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.013 0.096 -10000 0 -0.62 8 8
YES1 -0.017 0.13 -10000 0 -0.87 8 8
Ephrin B1/EPHB1-2/NCK2 -0.004 0.12 -10000 0 -0.5 4 4
PI3K 0.014 0.097 -10000 0 -0.62 8 8
mol:GDP -0.007 0.12 -10000 0 -0.37 12 12
ITGA2B -0.026 0.14 -10000 0 -0.51 28 28
endothelial cell proliferation 0.018 0.025 -10000 0 -0.3 2 2
FYN -0.018 0.13 -10000 0 -0.89 8 8
MAP3K7 -0.01 0.099 -10000 0 -0.66 8 8
FGR -0.017 0.13 -10000 0 -0.88 8 8
TIAM1 0.012 0.044 -10000 0 -0.58 2 2
PIK3R1 0.016 0 -10000 0 -10000 0 0
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.025 0.15 -10000 0 -0.54 12 12
LYN -0.017 0.13 -10000 0 -0.87 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.018 0.12 -10000 0 -0.81 8 8
Ephrin B1/EPHB1-2 -0.017 0.11 -10000 0 -0.72 8 8
SRC -0.017 0.13 -10000 0 -0.86 8 8
ITGB3 -0.054 0.19 -10000 0 -0.58 42 42
EPHB1 -0.032 0.16 -10000 0 -0.57 29 29
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.018 0.025 -10000 0 -0.3 2 2
alphaIIb/beta3 Integrin -0.057 0.17 -10000 0 -0.41 66 66
BLK -0.032 0.13 -10000 0 -0.86 8 8
HCK -0.023 0.14 -10000 0 -0.89 8 8
regulation of stress fiber formation 0.005 0.12 0.5 4 -10000 0 4
MAPK8 0.018 0.1 -10000 0 -0.65 8 8
Ephrin B1/EPHB1-2/RGS3 -0.004 0.12 -10000 0 -0.58 3 3
endothelial cell migration -0.009 0.085 -10000 0 -0.55 8 8
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.009 0.1 -10000 0 -0.69 8 8
regulation of focal adhesion formation 0.005 0.12 0.5 4 -10000 0 4
chemotaxis 0.005 0.12 0.57 3 -10000 0 3
PIK3CA 0.016 0 -10000 0 -10000 0 0
Rac1/GTP -0.04 0.096 -10000 0 -0.52 4 4
angiogenesis -0.017 0.11 -10000 0 -0.71 8 8
LCK -0.019 0.13 -10000 0 -0.86 8 8
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.014 0.028 -10000 0 -0.51 1 1
NFATC1 0.036 0.078 -10000 0 -0.29 17 17
NFATC2 -0.025 0.078 -10000 0 -0.19 43 43
NFATC3 0.01 0.035 -10000 0 -0.42 2 2
YWHAE 0.014 0.031 -10000 0 -0.58 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.046 0.14 -10000 0 -0.44 28 28
Exportin 1/Ran/NUP214 0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.003 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.071 0.12 -10000 0 -0.4 34 34
BCL2/BAX 0.006 0.085 -10000 0 -0.41 14 14
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.01 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.007 0.008 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.04 0.14 -10000 0 -0.42 28 28
Calcineurin A alpha-beta B1/BCL2 -0.008 0.12 -10000 0 -0.57 14 14
FKBP8 0.016 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.039 0.14 0.41 28 -10000 0 28
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.013 0.039 -10000 0 -0.51 2 2
XPO1 0.015 0.001 -10000 0 -10000 0 0
SFN -0.034 0.15 -10000 0 -0.52 33 33
MAP3K8 0.002 0.054 -10000 0 -0.58 3 3
NFAT4/CK1 alpha -0.001 0.018 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.13 0.18 -10000 0 -0.38 43 43
CABIN1 -0.046 0.15 -10000 0 -0.45 28 28
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.015 0.001 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 -0.003 0.1 -10000 0 -0.57 11 11
mol:Ca2+ -0.009 0.009 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.006 0.04 -10000 0 -0.36 4 4
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.002 0.054 -10000 0 -0.58 3 3
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.029 0.083 -10000 0 -0.31 10 10
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.01 0.014 -10000 0 -10000 0 0
CASP3 0.007 0.008 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.006 -10000 0 -10000 0 0
apoptosis -0.005 0.025 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.038 -10000 0 -0.28 1 1
PRKCB -0.16 0.27 -10000 0 -0.58 103 103
PRKCE 0.016 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.024 0.031 -10000 0 -0.37 2 2
BAD/BCL-XL 0.022 0.02 -10000 0 -0.36 1 1
PRKCD 0.016 0 -10000 0 -10000 0 0
NUP214 0.015 0.001 -10000 0 -10000 0 0
PRKCZ 0.004 0.045 -10000 0 -0.58 2 2
PRKCA 0.011 0.054 -10000 0 -0.58 3 3
PRKCG -0.008 0.089 -10000 0 -0.51 11 11
PRKCQ -0.042 0.18 -10000 0 -0.57 35 35
FKBP38/BCL2 0.006 0.085 -10000 0 -0.41 14 14
EP300 0.009 0.006 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.015 0.08 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.01 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.011 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.001 0.065 -10000 0 -0.36 11 11
NFATc/ERK1 0.043 0.075 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.068 0.12 -10000 0 -0.4 33 33
NR4A1 -0.28 0.3 -10000 0 -0.54 200 200
GSK3B 0.007 0.008 -10000 0 -10000 0 0
positive T cell selection 0.01 0.035 -10000 0 -0.41 2 2
NFAT1/CK1 alpha -0.035 0.051 -10000 0 -0.29 3 3
RCH1/ KPNB1 0.021 0.028 -10000 0 -0.36 2 2
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.007 0.008 -10000 0 -10000 0 0
AKAP5 0.01 0.055 -10000 0 -0.51 4 4
MEF2D 0.009 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.017 0.077 -10000 0 -10000 0 0
CREBBP 0.009 0.006 -10000 0 -10000 0 0
BCL2 -0.008 0.12 -10000 0 -0.58 14 14
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.021 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.007 0.068 -9999 0 -0.56 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.025 0.023 -9999 0 -0.21 1 1
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.011 0.054 -9999 0 -0.58 3 3
MAP3K12 0.014 0.031 -9999 0 -0.58 1 1
FGR 0.014 0.031 -9999 0 -0.58 1 1
p38 alpha/TAB1 -0.02 0.053 -9999 0 -0.26 10 10
PRKG1 -0.12 0.25 -9999 0 -0.58 82 82
DUSP8 -0.026 0.15 -9999 0 -0.58 25 25
PGK/cGMP/p38 alpha -0.072 0.12 -9999 0 -0.38 29 29
apoptosis -0.02 0.051 -9999 0 -0.27 7 7
RAL/GTP 0.02 0.017 -9999 0 -0.3 1 1
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 -0.15 0.27 -9999 0 -0.58 102 102
PAK1 0.014 0.031 -9999 0 -0.58 1 1
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.039 0.016 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.014 0.028 -9999 0 -0.51 1 1
RAC1-CDC42/GTP 0.021 0 -9999 0 -10000 0 0
MAPK11 0.029 0.096 -9999 0 -0.32 11 11
BLK -0.054 0.18 -9999 0 -0.56 42 42
HCK -0.012 0.12 -9999 0 -0.56 17 17
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.01 0.055 -9999 0 -0.51 4 4
TRAF6/MEKK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.032 0.08 -9999 0 -0.28 10 10
positive regulation of innate immune response 0.037 0.11 -9999 0 -0.35 11 11
LCK 0.006 0.073 -9999 0 -0.55 6 6
p38alpha-beta/MKP7 0.043 0.1 -9999 0 -0.51 2 2
p38alpha-beta/MKP5 0.041 0.11 -9999 0 -0.36 8 8
PGK/cGMP -0.089 0.18 -9999 0 -0.42 82 82
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.033 0.18 -9999 0 -0.43 37 37
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.014 0.028 -9999 0 -0.51 1 1
PAK3 -0.006 0.085 -9999 0 -0.51 10 10
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.012 0.068 -10000 0 -0.41 9 9
ATM 0.016 0 -10000 0 -10000 0 0
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.029 0.019 -10000 0 -10000 0 0
protein ubiquitination -0.043 0.093 -10000 0 -0.3 9 9
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0.032 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0.032 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.045 0.036 -10000 0 -10000 0 0
FANCF 0.012 0.042 -10000 0 -0.54 2 2
BRCA1 0.014 0.028 -10000 0 -0.51 1 1
CCNE1 -0.066 0.19 -10000 0 -0.51 56 56
CDK2/Cyclin E1 -0.036 0.14 -10000 0 -0.36 56 56
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.011 0.071 -10000 0 -0.41 10 10
FANCE 0.016 0 -10000 0 -10000 0 0
FANCC 0.014 0.028 -10000 0 -0.51 1 1
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.02 0.13 -10000 0 -0.51 24 24
DNA repair -0.023 0.13 -10000 0 -0.4 4 4
BRCA1/BARD1/ubiquitin 0.011 0.071 -10000 0 -0.41 10 10
BARD1/DNA-PK 0.031 0.054 -10000 0 -0.3 9 9
FANCL 0.014 0.028 -10000 0 -0.51 1 1
mRNA polyadenylation -0.012 0.068 0.41 9 -10000 0 9
BRCA1/BARD1/CTIP/M/R/N Complex 0.04 0.044 -10000 0 -0.23 9 9
BRCA1/BACH1/BARD1/TopBP1 0.021 0.061 -10000 0 -0.34 10 10
BRCA1/BARD1/P53 0.031 0.056 -10000 0 -0.3 9 9
BARD1/CSTF1/BRCA1 0.021 0.061 -10000 0 -0.34 10 10
BRCA1/BACH1 0.014 0.028 -10000 0 -0.51 1 1
BARD1 0 0.093 -10000 0 -0.58 9 9
PCNA 0.014 0.028 -10000 0 -0.51 1 1
BRCA1/BARD1/UbcH5C 0.021 0.061 -10000 0 -0.34 10 10
BRCA1/BARD1/UbcH7 0.021 0.061 -10000 0 -0.34 10 10
BRCA1/BARD1/RAD51/PCNA -0.072 0.15 -10000 0 -0.36 9 9
BARD1/DNA-PK/P53 0.038 0.051 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.011 0.071 -10000 0 -0.41 10 10
BRCA1/BARD1/CTIP 0.03 0.056 -10000 0 -0.3 10 10
FA complex 0.035 0.043 -10000 0 -10000 0 0
BARD1/EWS 0.012 0.068 -10000 0 -0.41 9 9
RBBP8 0.026 0 -10000 0 -10000 0 0
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.029 0.055 0.3 9 -10000 0 9
BRCA1/BARD1 -0.006 0.11 -10000 0 -0.31 9 9
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0.068 -10000 0 -0.42 9 9
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.16 0.25 -10000 0 -0.51 123 123
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.071 -10000 0 -0.41 10 10
EWSR1 0.016 0 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.009 0.062 -9999 0 -0.58 4 4
ITGA4 -0.004 0.11 -9999 0 -0.57 12 12
alpha4/beta7 Integrin 0.004 0.09 -9999 0 -0.41 16 16
alpha4/beta1 Integrin 0.009 0.078 -9999 0 -0.41 12 12
Class I PI3K signaling events mediated by Akt

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 0.02 -9999 0 -0.36 1 1
BAD/BCL-XL/YWHAZ 0.038 0.016 -9999 0 -10000 0 0
CDKN1B 0.043 0 -9999 0 -10000 0 0
CDKN1A 0.042 0.016 -9999 0 -0.26 1 1
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.043 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.016 0 -9999 0 -10000 0 0
AKT3 0.009 0.063 -9999 0 -0.35 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.042 0.014 -9999 0 -10000 0 0
AKT1/ASK1 0.041 0 -9999 0 -10000 0 0
BAD/YWHAZ 0.032 0 -9999 0 -10000 0 0
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.014 0.028 -9999 0 -0.51 1 1
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.043 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0.043 0.014 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.036 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.043 0 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.028 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.044 0.027 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.043 0 -9999 0 -10000 0 0
CASP9 0.043 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.051 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0 -9999 0 -10000 0 0
YWHAE 0.014 0.031 -9999 0 -0.58 1 1
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.013 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0 -9999 0 -10000 0 0
CHUK 0.043 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.058 0.013 -9999 0 -10000 0 0
mTORC2 0.02 0 -9999 0 -10000 0 0
AKT2 0.02 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.061 0.031 -9999 0 -10000 0 0
PDPK1 0.016 0 -9999 0 -10000 0 0
MDM2 0.034 0.047 -9999 0 -10000 0 0
MAPKKK cascade -0.042 0.014 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.049 0.044 -9999 0 -10000 0 0
TSC1/TSC2 0.05 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.043 -9999 0 -10000 0 0
glucose import -0.21 0.15 -9999 0 -0.3 260 260
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.21 0.15 -9999 0 -0.3 260 260
GSK3A 0.043 0 -9999 0 -10000 0 0
FOXO1 0.043 0 -9999 0 -10000 0 0
GSK3B 0.043 0 -9999 0 -10000 0 0
SFN -0.034 0.15 -9999 0 -0.52 33 33
G1/S transition of mitotic cell cycle 0.05 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.045 0.041 -9999 0 -0.3 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.011 0.1 -10000 0 -0.32 34 34
cell-cell adhesion 0.041 0.092 0.46 6 -10000 0 6
Ephrin B/EPHB2/RasGAP 0.01 0.1 -10000 0 -0.51 2 2
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
SHC1 0.014 0.028 -10000 0 -0.51 1 1
Ephrin B1/EPHB3 0.007 0.065 -10000 0 -0.3 15 15
Ephrin B1/EPHB1 -0.009 0.1 -10000 0 -0.35 29 29
HRAS/GDP -0.027 0.087 -10000 0 -0.49 5 5
Ephrin B/EPHB1/GRB7 -0.013 0.14 -10000 0 -0.58 6 6
Endophilin/SYNJ1 0.009 0.094 -10000 0 -0.48 2 2
KRAS 0.014 0.028 -10000 0 -0.51 1 1
Ephrin B/EPHB1/Src 0.002 0.12 -10000 0 -0.59 5 5
endothelial cell migration -0.001 0.018 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 -0.013 0.12 -10000 0 -0.52 19 19
PAK1 0.013 0.1 -10000 0 -0.48 2 2
HRAS 0.016 0 -10000 0 -10000 0 0
RRAS 0.007 0.1 -10000 0 -0.51 3 3
DNM1 0.001 0.093 -10000 0 -0.58 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.002 0.12 -10000 0 -0.56 5 5
lamellipodium assembly -0.041 0.092 -10000 0 -0.46 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.014 0.094 -10000 0 -0.44 4 4
PIK3R1 0.016 0 -10000 0 -10000 0 0
EPHB2 -0.018 0.13 -10000 0 -0.51 23 23
EPHB3 -0.007 0.11 -10000 0 -0.51 15 15
EPHB1 -0.032 0.16 -10000 0 -0.57 29 29
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.1 -10000 0 -0.47 5 5
Ephrin B/EPHB2 0.001 0.1 -10000 0 -0.32 13 13
Ephrin B/EPHB3 0.007 0.097 -10000 0 -0.34 13 13
JNK cascade 0.001 0.11 -10000 0 -0.57 1 1
Ephrin B/EPHB1 -0.007 0.12 -10000 0 -0.33 36 36
RAP1/GDP 0.03 0.091 -10000 0 -0.4 5 5
EFNB2 0.013 0.039 -10000 0 -0.51 2 2
EFNB3 -0.016 0.13 -10000 0 -0.55 20 20
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.018 0.12 -10000 0 -0.3 52 52
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.04 0.094 -10000 0 -0.48 6 6
Rap1/GTP -0.04 0.091 -10000 0 -0.46 6 6
axon guidance -0.011 0.099 -10000 0 -0.32 34 34
MAPK3 0.03 0.085 -10000 0 -0.38 4 4
MAPK1 0.03 0.085 -10000 0 -0.38 4 4
Rac1/GDP 0.024 0.095 -10000 0 -0.43 5 5
actin cytoskeleton reorganization -0.029 0.067 -10000 0 -0.37 5 5
CDC42/GDP 0.024 0.095 -10000 0 -0.43 5 5
PI3K 0.035 0.021 -10000 0 -10000 0 0
EFNA5 -0.003 0.1 -10000 0 -0.58 11 11
Ephrin B2/EPHB4 0.019 0.024 -10000 0 -0.3 2 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.067 -10000 0 -0.38 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.039 0.088 -10000 0 -0.45 6 6
PTK2 0.011 0.027 -10000 0 -10000 0 0
MAP4K4 0.001 0.11 -10000 0 -0.58 1 1
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.008 0.065 -10000 0 -0.54 5 5
Intersectin/N-WASP 0.023 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.037 0.1 -10000 0 -0.38 6 6
MAP2K1 0.022 0.089 -10000 0 -0.41 4 4
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.006 0.11 -10000 0 -0.3 25 25
cell migration 0.026 0.1 -10000 0 -0.45 4 4
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.009 0.095 -10000 0 -0.49 2 2
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.018 0.13 -10000 0 -0.5 9 9
HRAS/GTP -0.044 0.099 -10000 0 -0.49 6 6
Ephrin B1/EPHB1-2 -0.016 0.11 -10000 0 -0.29 52 52
cell adhesion mediated by integrin 0.015 0.076 0.29 20 -10000 0 20
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.13 -10000 0 -0.53 6 6
RAC1-CDC42/GTP -0.047 0.1 -10000 0 -0.44 12 12
RASA1 0.016 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.091 -10000 0 -0.43 4 4
ruffle organization 0.018 0.12 -10000 0 -0.46 6 6
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.01 0.1 -10000 0 -0.46 2 2
Ephrin B/EPHB2/KALRN 0.006 0.1 -10000 0 -0.31 15 15
ROCK1 0.017 0.059 -10000 0 -0.27 15 15
RAS family/GDP -0.027 0.064 -10000 0 -0.38 4 4
Rac1/GTP -0.043 0.097 -10000 0 -0.49 6 6
Ephrin B/EPHB1/Src/Paxillin 0.009 0.099 -10000 0 -0.27 36 36
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.2 -9999 0 -0.65 8 8
RAD9A 0.007 0.067 -9999 0 -0.51 6 6
AP1 -0.13 0.23 -9999 0 -0.46 111 111
IFNAR2 0.01 0.009 -9999 0 -10000 0 0
AKT1 -0.027 0.092 -9999 0 -0.24 31 31
ER alpha/Oestrogen -0.067 0.16 -9999 0 -0.43 61 61
NFX1/SIN3/HDAC complex 0.032 0.029 -9999 0 -10000 0 0
EGF -0.02 0.13 -9999 0 -0.51 22 22
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.014 -9999 0 -10000 0 0
TERT/c-Abl -0.13 0.17 -9999 0 -0.64 6 6
SAP18 0.015 0.002 -9999 0 -10000 0 0
MRN complex 0.032 0 -9999 0 -10000 0 0
WT1 -0.061 0.17 -9999 0 -0.51 46 46
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.011 0.01 -9999 0 -10000 0 0
SP3 0.013 0.004 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.14 -9999 0 -0.63 4 4
Mad/Max 0.013 0.024 -9999 0 -0.37 1 1
TERT -0.13 0.2 -9999 0 -0.71 6 6
CCND1 -0.12 0.24 -9999 0 -1 10 10
MAX 0.013 0.004 -9999 0 -10000 0 0
RBBP7 0.015 0.002 -9999 0 -10000 0 0
RBBP4 0.015 0.002 -9999 0 -10000 0 0
TERF2 0.014 0 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.015 0.002 -9999 0 -10000 0 0
Telomerase/911 0.024 0.039 -9999 0 -10000 0 0
CDKN1B -0.022 0.12 -9999 0 -10000 0 0
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 0.015 0.002 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.014 0.004 -9999 0 -10000 0 0
JUN -0.008 0.11 -9999 0 -0.58 13 13
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -9999 0 -10000 0 0
FOS -0.17 0.27 -9999 0 -0.58 110 110
IFN-gamma/IRF1 -0.049 0.14 -9999 0 -0.34 68 68
PARP2 0.016 0 -9999 0 -10000 0 0
BLM 0.002 0.082 -9999 0 -0.51 9 9
Telomerase -0.007 0.062 -9999 0 -0.41 1 1
IRF1 0.019 0.005 -9999 0 -10000 0 0
ESR1 -0.087 0.22 -9999 0 -0.58 61 61
KU/TER 0.023 0 -9999 0 -10000 0 0
ATM/TRF2 0.024 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.03 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.032 -9999 0 -10000 0 0
HDAC1 0.015 0.002 -9999 0 -10000 0 0
HDAC2 0.01 0.01 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.029 0.005 -9999 0 -10000 0 0
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.012 0.028 -9999 0 -0.52 1 1
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.13 0.16 -9999 0 -0.65 5 5
NR2F2 0.018 0.033 -9999 0 -0.58 1 1
MAPK3 0.012 0.011 -9999 0 -10000 0 0
MAPK1 0.012 0.011 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.017 0.002 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.016 0 -9999 0 -10000 0 0
EGFR -0.01 0.11 -9999 0 -0.54 15 15
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.026 0.12 -9999 0 -0.37 37 37
MYC -0.02 0.13 -9999 0 -0.58 18 18
IL2 -0.001 0.013 -9999 0 -10000 0 0
KU 0.023 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.017 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.008 0.051 -9999 0 -0.33 9 9
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.1 0.19 -9999 0 -0.64 6 6
SP1/HDAC2 0.017 0.016 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.14 -9999 0 -0.63 4 4
Smad3/Myc 0.014 0.082 -9999 0 -0.34 18 18
911 complex 0.026 0.041 -9999 0 -0.29 6 6
IFNG -0.083 0.2 -9999 0 -0.5 68 68
Telomerase/PinX1 -0.12 0.14 -9999 0 -0.63 4 4
Telomerase/AKT1/mTOR/p70S6K -0.011 0.066 -9999 0 -10000 0 0
SIN3B 0.015 0.002 -9999 0 -10000 0 0
YWHAE 0.014 0.031 -9999 0 -0.58 1 1
Telomerase/EST1B -0.12 0.14 -9999 0 -0.63 4 4
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.12 0.14 -9999 0 -0.63 4 4
E2F1 -0.11 0.22 -9999 0 -0.51 81 81
ZNFX1 0.015 0.002 -9999 0 -10000 0 0
PIF1 -0.029 0.15 -9999 0 -0.51 30 30
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.066 0.19 -9999 0 -0.51 56 56
mol:Halofuginone 0.006 0.001 -9999 0 -10000 0 0
ITGA1 0.016 0 -9999 0 -10000 0 0
CDKN1A 0 0.075 -9999 0 -0.67 1 1
PRL-3/alpha Tubulin 0.023 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.14 -9999 0 -0.43 45 45
AGT -0.059 0.2 -9999 0 -0.57 45 45
CCNA2 -0.1 0.18 -9999 0 -0.53 22 22
TUBA1B 0.016 0 -9999 0 -10000 0 0
EGR1 -0.078 0.19 -9999 0 -0.41 87 87
CDK2/Cyclin E1 -0.024 0.12 -9999 0 -0.38 14 14
MAPK3 0.026 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.023 0 -9999 0 -10000 0 0
MAPK1 0.026 0 -9999 0 -10000 0 0
PTP4A1 -0.039 0.14 -9999 0 -10000 0 0
PTP4A3 0.016 0 -9999 0 -10000 0 0
PTP4A2 0.016 0 -9999 0 -10000 0 0
ITGB1 0.026 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1 0.002 0.066 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.023 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.031 0.14 -9999 0 -0.53 1 1
RABGGTA 0.016 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.002 0.066 -9999 0 -10000 0 0
RHOA 0.002 0.066 -9999 0 -10000 0 0
cell motility 0.005 0.071 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.029 0.14 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.023 0 -9999 0 -10000 0 0
ROCK1 0.005 0.071 -9999 0 -10000 0 0
RABGGTB 0.016 0 -9999 0 -10000 0 0
CDK2 0.016 0 -9999 0 -10000 0 0
mitosis -0.039 0.14 -9999 0 -10000 0 0
ATF5 0.013 0.039 -9999 0 -0.51 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.016 0.079 -9999 0 -0.37 14 14
E-cadherin/beta catenin 0.007 0.082 -9999 0 -0.41 13 13
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.012 0.044 -9999 0 -0.58 2 2
CDH1 -0.006 0.11 -9999 0 -0.58 13 13
EPO signaling pathway

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
BCL2L1 0.061 0.09 -9999 0 -0.42 3 3
CRKL 0.026 0.079 -9999 0 -0.29 3 3
mol:DAG 0.038 0.066 -9999 0 -0.28 1 1
HRAS 0.054 0.068 -9999 0 -10000 0 0
MAPK8 0.011 0.092 -9999 0 -0.34 6 6
RAP1A 0.028 0.077 -9999 0 -0.29 3 3
GAB1 0.028 0.077 -9999 0 -0.29 3 3
MAPK14 0.013 0.084 -9999 0 -0.28 3 3
EPO -0.028 0.14 -9999 0 -0.5 30 30
PLCG1 0.039 0.067 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.006 0.077 -9999 0 -0.5 8 8
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.038 0.16 -9999 0 -0.34 70 70
GAB1/SHC/GRB2/SOS1 -0.017 0.046 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.013 0.12 -9999 0 -0.35 38 38
IRS2 0.016 0.097 -9999 0 -0.34 6 6
STAT1 0.044 0.082 -9999 0 -0.38 3 3
STAT5B 0.042 0.074 -9999 0 -0.34 3 3
cell proliferation 0.019 0.086 -9999 0 -0.37 3 3
GAB1/SHIP/PIK3R1/SHP2/SHC -0.019 0.055 -9999 0 -0.43 2 2
TEC 0.028 0.077 -9999 0 -0.29 3 3
SOCS3 -0.047 0.18 -9999 0 -0.58 38 38
STAT1 (dimer) 0.044 0.081 -9999 0 -0.37 3 3
JAK2 0.014 0.032 -9999 0 -0.57 1 1
PIK3R1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.034 0.086 -9999 0 -0.3 4 4
EPO/EPOR -0.013 0.12 -9999 0 -0.35 38 38
LYN 0.017 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.036 0.078 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.006 0.077 -9999 0 -0.5 8 8
SHC1 0.014 0.028 -9999 0 -0.51 1 1
EPO/EPOR (dimer)/LYN 0.01 0.097 -9999 0 -0.27 38 38
mol:IP3 0.038 0.066 -9999 0 -0.28 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.025 0.1 -9999 0 -0.4 5 5
SH2B3 0.016 0.007 -9999 0 -10000 0 0
NFKB1 0.013 0.084 -9999 0 -0.28 3 3
EPO/EPOR (dimer)/JAK2/SOCS3 -0.037 0.084 -9999 0 -0.31 13 13
PTPN6 0.019 0.08 -9999 0 -0.3 4 4
TEC/VAV2/GRB2 0.042 0.076 -9999 0 -10000 0 0
EPOR 0.006 0.077 -9999 0 -0.5 8 8
INPP5D 0.004 0.082 -9999 0 -0.58 7 7
mol:GDP -0.017 0.046 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.01 0.057 -9999 0 -0.52 4 4
CRKL/CBL/C3G 0.042 0.075 -9999 0 -10000 0 0
VAV2 0.026 0.079 -9999 0 -0.29 3 3
CBL 0.028 0.077 -9999 0 -0.29 3 3
SHC/Grb2/SOS1 -0.019 0.05 -9999 0 -10000 0 0
STAT5A 0.041 0.076 -9999 0 -0.32 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.057 0.096 -9999 0 -0.47 3 3
LYN/PLCgamma2 0.02 0.042 -9999 0 -0.37 4 4
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK 0.009 0.11 -9999 0 -0.36 8 8
BCL2 0.039 0.19 -9999 0 -0.9 14 14
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.095 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.013 0.039 -9999 0 -0.51 2 2
STAT1 (dimer)/Cbp/p300 0.037 0.092 -9999 0 -0.36 4 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.02 -9999 0 -0.34 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.063 -9999 0 -0.31 7 7
CaM/Ca2+ -0.033 0.068 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.007 0.099 -9999 0 -0.42 4 4
AKT1 0.023 0.081 -9999 0 -10000 0 0
MAP2K1 0.019 0.086 -9999 0 -10000 0 0
MAP3K11 0.008 0.089 -9999 0 -10000 0 0
IFNGR1 0.014 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.19 -9999 0 -0.41 118 118
Rap1/GTP -0.023 0.048 -9999 0 -10000 0 0
CRKL/C3G 0.021 0.028 -9999 0 -0.36 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.004 0.1 -9999 0 -10000 0 0
CEBPB 0.056 0.085 -9999 0 -0.37 3 3
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.007 0.095 -9999 0 -10000 0 0
STAT1 0.006 0.098 -9999 0 -0.42 4 4
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.084 0.2 -9999 0 -0.5 68 68
PIK3CA 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.015 0.094 -9999 0 -0.4 4 4
CEBPB/PTGES2/Cbp/p300 -0.008 0.024 -9999 0 -10000 0 0
mol:Ca2+ -0.002 0.093 -9999 0 -10000 0 0
MAPK3 0.036 0.076 -9999 0 -10000 0 0
STAT1 (dimer) -0.04 0.086 -9999 0 -0.46 6 6
MAPK1 0.036 0.076 -9999 0 -10000 0 0
JAK2 0.012 0.032 -9999 0 -0.57 1 1
PIK3R1 0.016 0 -9999 0 -10000 0 0
JAK1 0.014 0.008 -9999 0 -10000 0 0
CAMK2D 0.014 0.031 -9999 0 -0.58 1 1
DAPK1 0.055 0.087 -9999 0 -0.62 3 3
SMAD7 0.018 0.061 -9999 0 -0.35 1 1
CBL/CRKL/C3G 0.021 0.086 -9999 0 -0.39 1 1
PI3K -0.031 0.063 -9999 0 -10000 0 0
IFNG -0.084 0.2 -9999 0 -0.5 68 68
apoptosis 0.035 0.068 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.18 0.28 -9999 0 -0.58 118 118
CAMK2B -0.044 0.16 -9999 0 -0.51 40 40
FRAP1 0.023 0.077 -9999 0 -10000 0 0
PRKCD 0.024 0.083 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.032 0.063 -9999 0 -0.31 7 7
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
IRF1 0.051 0.079 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy 0.011 0.094 -9999 0 -0.4 4 4
SOCS1 0.006 0.021 -9999 0 -10000 0 0
mol:GDP -0.029 0.059 -9999 0 -0.37 1 1
CASP1 0.015 0.073 -9999 0 -0.29 9 9
PTGES2 0.016 0 -9999 0 -10000 0 0
IRF9 0.055 0.035 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.03 0.062 -9999 0 -10000 0 0
RAP1/GDP -0.023 0.049 -9999 0 -10000 0 0
CBL 0.007 0.089 -9999 0 -10000 0 0
MAP3K1 0.008 0.089 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.063 -9999 0 -0.31 7 7
PTPN11 -0.002 0.093 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.081 -9999 0 -0.36 15 15
CRKL 0.013 0.039 -9999 0 -0.51 2 2
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DOCK1 0.014 0.031 -9999 0 -0.58 1 1
ITGA4 -0.004 0.11 -9999 0 -0.57 12 12
alpha4/beta7 Integrin/MAdCAM1 0.014 0.092 -9999 0 -0.34 15 15
EPO -0.031 0.14 -9999 0 -0.51 30 30
alpha4/beta7 Integrin 0.004 0.09 -9999 0 -0.41 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.009 0.078 -9999 0 -0.41 12 12
EPO/EPOR (dimer) -0.019 0.12 -9999 0 -0.36 38 38
lamellipodium assembly 0.002 0.012 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.023 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 0.009 0.08 -9999 0 -0.3 12 12
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
MADCAM1 -0.004 0.094 -9999 0 -0.51 12 12
cell adhesion 0.013 0.091 -9999 0 -0.34 15 15
CRKL/CBL 0.021 0.028 -9999 0 -0.36 2 2
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.011 0.11 -9999 0 -0.39 21 21
ITGB7 0.009 0.062 -9999 0 -0.58 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.001 0.12 -9999 0 -0.42 24 24
p130Cas/Crk/Dock1 0.035 0.097 -9999 0 -0.51 6 6
VCAM1 -0.014 0.13 -9999 0 -0.57 18 18
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.029 0.061 -9999 0 -0.3 11 11
BCAR1 0.02 0.1 -9999 0 -0.57 6 6
EPOR 0.004 0.077 -9999 0 -0.51 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.012 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.026 0.053 -10000 0 -0.24 13 13
epithelial cell differentiation -0.01 0.053 -10000 0 -0.28 13 13
CYFIP2 -0.001 0.098 -10000 0 -0.58 10 10
ENAH 0.06 0.056 -10000 0 -0.33 1 1
EGFR -0.008 0.11 -10000 0 -0.54 15 15
EPHA2 0.011 0.054 -10000 0 -0.58 3 3
MYO6 0.032 0.058 -10000 0 -10000 0 0
CTNNB1 0.016 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.021 0.062 -10000 0 -0.34 10 10
AQP5 -0.013 0.047 -10000 0 -0.35 1 1
CTNND1 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.057 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.086 -10000 0 -0.5 2 2
EGF -0.018 0.12 -10000 0 -0.51 22 22
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.093 0.2 -10000 0 -0.49 66 66
cortical microtubule organization -0.01 0.053 -10000 0 -0.28 13 13
GO:0000145 0.031 0.054 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.061 -10000 0 -0.29 13 13
MLLT4 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.013 0.052 -10000 0 -0.46 1 1
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.055 -10000 0 -0.3 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.045 0.056 -10000 0 -10000 0 0
PVRL2 0.016 0 -10000 0 -10000 0 0
ZYX 0.032 0.06 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.043 -10000 0 -10000 0 0
CDH1 -0.006 0.11 -10000 0 -0.58 13 13
EGFR/EGFR/EGF/EGF -0.032 0.085 -10000 0 -0.51 3 3
RhoA/GDP -0.01 0.049 -10000 0 -10000 0 0
actin cytoskeleton organization 0.038 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.054 -10000 0 -0.57 3 3
GIT1 0.016 0 -10000 0 -10000 0 0
IGF1R 0.011 0.054 -10000 0 -0.58 3 3
IGF1 -0.25 0.29 -10000 0 -0.58 159 159
DIAPH1 -0.015 0.097 -10000 0 -0.58 10 10
Wnt receptor signaling pathway 0.01 0.053 0.28 13 -10000 0 13
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.053 -10000 0 -0.46 1 1
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.038 0.059 -10000 0 -10000 0 0
EFNA1 0.002 0.082 -10000 0 -0.51 9 9
LPP 0.04 0.055 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.016 0.063 -10000 0 -0.54 1 1
SEC6/SEC8 -0.008 0.041 -10000 0 -10000 0 0
MGAT3 0.018 0.087 -10000 0 -0.52 2 2
HGF/MET -0.069 0.11 -10000 0 -0.49 2 2
HGF -0.12 0.25 -10000 0 -0.57 85 85
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.026 0.053 -10000 0 -0.25 13 13
actin cable formation 0.077 0.054 -10000 0 -0.26 1 1
KIAA1543 0.031 0.096 -10000 0 -0.53 8 8
KIFC3 0.032 0.058 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.032 0.058 -10000 0 -10000 0 0
NCK1/GIT1 0.023 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.053 -10000 0 -0.28 13 13
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.032 0.058 -10000 0 -10000 0 0
PIP5K1C 0.032 0.058 -10000 0 -10000 0 0
LIMA1 0.016 0 -10000 0 -10000 0 0
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 0.055 0.063 -10000 0 -0.4 1 1
adherens junction assembly 0.049 0.095 -10000 0 -0.51 8 8
IGF-1R heterotetramer/IGF1 -0.12 0.13 -10000 0 -0.54 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.023 0 -10000 0 -10000 0 0
MET 0.014 0.028 -10000 0 -0.51 1 1
PLEKHA7 0.032 0.064 -10000 0 -0.56 1 1
mol:GTP 0.029 0.055 -10000 0 -0.3 3 3
establishment of epithelial cell apical/basal polarity 0.061 0.052 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.026 0.053 -10000 0 -0.24 13 13
regulation of cell-cell adhesion 0.038 0.058 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.026 0.053 -10000 0 -0.25 13 13
Arf6 trafficking events

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
SLC2A4 -0.42 0.26 -10000 0 -0.58 260 260
CLTC 0.037 0.009 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.03 0.011 -10000 0 -10000 0 0
Dynamin 2/GTP 0.028 0.015 -10000 0 -0.26 1 1
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.033 0.008 -10000 0 -10000 0 0
CPE 0.008 0.07 -10000 0 -0.35 13 13
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0.03 0.012 -10000 0 -10000 0 0
CTNND1 0.036 0.014 -10000 0 -10000 0 0
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.008 -10000 0 -10000 0 0
TSHR 0.013 0.041 -10000 0 -0.3 6 6
INS 0.014 0.003 -10000 0 -10000 0 0
BIN1 -0.062 0.2 -10000 0 -0.58 47 47
mol:Choline 0.03 0.012 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.017 -10000 0 -0.3 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.015 -10000 0 -0.26 1 1
JUP 0.032 0.019 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.015 0.12 -10000 0 -0.31 47 47
ARF6/GTP 0.012 0 -10000 0 -10000 0 0
CDH1 0.025 0.044 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.012 0 -10000 0 -10000 0 0
MAPK8IP3 0.008 0.063 -10000 0 -0.52 5 5
positive regulation of endocytosis 0.012 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.05 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.025 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.022 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.017 0.039 -10000 0 -0.31 5 5
ACAP1 0.023 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.059 0.11 -10000 0 -0.28 2 2
clathrin heavy chain/ACAP1 0.041 0.013 -10000 0 -10000 0 0
JIP4/KLC1 0.03 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.05 0 -10000 0 -10000 0 0
RALA/GTP 0.011 0.02 -10000 0 -0.37 1 1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.021 0 -10000 0 -10000 0 0
receptor recycling 0.012 0 -10000 0 -10000 0 0
CTNNA1 0.036 0.014 -10000 0 -10000 0 0
NME1 0.021 0.017 -10000 0 -0.3 1 1
clathrin coat assembly 0.037 0.009 -10000 0 -10000 0 0
IL2RA 0.016 0.056 -10000 0 -10000 0 0
VAMP3 0.022 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.18 0.11 -10000 0 -0.28 16 16
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0.025 0.017 -10000 0 -0.28 1 1
PLD2 0.026 0.006 -10000 0 -10000 0 0
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.037 0.008 -10000 0 -10000 0 0
SDC1 0.03 0.028 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.017 -10000 0 -0.3 1 1
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.025 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.03 0.012 -10000 0 -10000 0 0
endocytosis 0.016 0.12 0.31 47 -10000 0 47
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.008 0.098 -10000 0 -0.26 42 42
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0.016 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.029 0.015 -10000 0 -0.26 1 1
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.014 0.09 -10000 0 -0.26 34 34
RALA 0.014 0.028 -10000 0 -0.51 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.021 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.13 0.13 -9999 0 -0.55 3 3
TC10/GTP -0.12 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.027 0.049 -9999 0 -0.32 7 7
HRAS 0.016 0 -9999 0 -10000 0 0
APS homodimer 0.008 0.061 -9999 0 -0.51 5 5
GRB14 -0.048 0.17 -9999 0 -0.51 43 43
FOXO3 -0.025 0.11 -9999 0 -0.59 13 13
AKT1 0.024 0.085 -9999 0 -10000 0 0
INSR 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.042 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.009 0.062 -9999 0 -0.58 4 4
SORBS1 -0.26 0.3 -9999 0 -0.58 165 165
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.04 0 -9999 0 -10000 0 0
CAV1 0.01 0.091 -9999 0 -0.34 21 21
CBL/APS/CAP/Crk-II/C3G -0.11 0.16 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.027 0.049 -9999 0 -0.32 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.038 -9999 0 -0.27 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.04 0.034 -9999 0 -10000 0 0
RPS6KB1 0.032 0.081 -9999 0 -10000 0 0
PARD6A 0.014 0.031 -9999 0 -0.58 1 1
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.012 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.022 0.056 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.044 -9999 0 -10000 0 0
Insulin Receptor 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.034 0.048 -9999 0 -10000 0 0
PRKCI -0.007 0.028 -9999 0 -0.47 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.029 0.071 -9999 0 -10000 0 0
SHC1 0.014 0.028 -9999 0 -0.51 1 1
negative regulation of MAPKKK cascade 0.001 0.01 -9999 0 -10000 0 0
PI3K -0.005 0.038 -9999 0 -0.27 7 7
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
AKT2 0.024 0.085 -9999 0 -10000 0 0
PRKCZ -0.01 0.046 -9999 0 -0.48 3 3
SH2B2 0.008 0.061 -9999 0 -0.51 5 5
SHC/SHIP 0.027 0.062 -9999 0 -0.27 14 14
F2RL2 -0.024 0.14 -9999 0 -0.54 25 25
TRIP10 0.014 0.031 -9999 0 -0.58 1 1
Insulin Receptor/Insulin/Shc 0.023 0.016 -9999 0 -0.28 1 1
TC10/GTP/CIP4/Exocyst 0.02 0.02 -9999 0 -0.35 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.04 0.015 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.17 -9999 0 -0.3 165 165
TC10/GDP 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.029 0.04 -9999 0 -0.31 5 5
INPP5D 0.019 0.064 -9999 0 -0.3 14 14
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.034 0.17 -9999 0 -0.9 13 13
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.004 0.082 -9999 0 -0.58 7 7
p62DOK/RasGAP 0.001 0.01 -9999 0 -10000 0 0
INS 0.004 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.063 -9999 0 -0.29 14 14
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.021 0.094 -9999 0 -0.39 2 2
PTPRA 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0.02 0.02 -9999 0 -0.35 1 1
PDPK1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.033 0.04 -9999 0 -0.24 7 7
Insulin Receptor/Insulin/IRS1 0.017 0.049 -9999 0 -0.33 7 7
Insulin Receptor/Insulin/IRS3 0.016 0 -9999 0 -10000 0 0
Par3/Par6 0.014 0.08 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.001 0.11 -9999 0 -0.52 9 9
PDGFB-D/PDGFRB/SLAP -0.003 0.12 -9999 0 -0.52 17 17
PDGFB-D/PDGFRB/APS/CBL 0.017 0.069 -9999 0 -0.32 14 14
AKT1 0.049 0.066 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0.12 -9999 0 -0.56 9 9
PIK3CA 0.016 0 -9999 0 -10000 0 0
FGR -0.01 0.066 -9999 0 -0.39 10 10
mol:Ca2+ 0.016 0.1 -9999 0 -0.58 9 9
MYC 0.002 0.2 -9999 0 -0.75 22 22
SHC1 0.014 0.028 -9999 0 -0.51 1 1
HRAS/GDP 0.034 0.05 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.017 0.07 -9999 0 -0.34 13 13
GRB10 0.009 0.062 -9999 0 -0.58 4 4
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.015 0.1 -9999 0 -0.59 9 9
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 -0.013 0.12 -9999 0 -0.52 19 19
PDGFB-D/PDGFRB/SHP2 0.012 0.069 -9999 0 -0.41 9 9
PDGFB-D/PDGFRB/GRB10 0.007 0.082 -9999 0 -0.41 13 13
cell cycle arrest -0.003 0.12 -9999 0 -0.52 17 17
HRAS 0.016 0 -9999 0 -10000 0 0
HIF1A 0.054 0.062 -9999 0 -10000 0 0
GAB1 0.012 0.11 -9999 0 -0.56 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0.1 -9999 0 -0.51 9 9
PDGFB-D/PDGFRB 0.019 0.062 -9999 0 -0.36 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.012 0.069 -9999 0 -0.41 9 9
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.033 0.093 -9999 0 -0.48 9 9
positive regulation of MAPKKK cascade 0.012 0.068 -9999 0 -0.41 9 9
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.015 0.1 -9999 0 -0.59 9 9
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.009 0.11 -9999 0 -0.39 28 28
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.056 0.16 -9999 0 -0.52 37 37
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.012 0.069 -9999 0 -0.41 9 9
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 0.012 0.12 -9999 0 -0.59 9 9
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.011 0.077 -9999 0 -0.45 9 9
LCK -0.015 0.094 -9999 0 -0.47 12 12
PDGFRB 0.001 0.094 -9999 0 -0.58 9 9
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.029 0.15 -9999 0 -0.64 17 17
ABL1 0.013 0.094 -9999 0 -0.5 9 9
PDGFB-D/PDGFRB/CBL 0.01 0.12 -9999 0 -0.63 9 9
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.01 0.055 -9999 0 -0.51 4 4
cell proliferation 0.007 0.18 -9999 0 -0.65 23 23
SLA -0.006 0.11 -9999 0 -0.58 13 13
actin cytoskeleton reorganization 0.049 0.049 -9999 0 -10000 0 0
SRC -0.007 0.06 -9999 0 -0.37 9 9
PI3K -0.015 0.053 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.003 0.096 -9999 0 -0.32 29 29
SH2B2 0.008 0.061 -9999 0 -0.51 5 5
PLCgamma1/SPHK1 -0.001 0.12 -9999 0 -0.58 9 9
LYN -0.007 0.06 -9999 0 -0.37 9 9
LRP1 0.011 0.054 -9999 0 -0.58 3 3
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.014 0.031 -9999 0 -0.58 1 1
NCK1-2/p130 Cas -0.001 0.045 -9999 0 -10000 0 0
SPHK1 -0.053 0.18 -9999 0 -0.5 47 47
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.015 0.1 -9999 0 -0.59 9 9
PLCG1 0.015 0.11 -9999 0 -0.61 9 9
NHERF/PDGFRB 0.004 0.092 -9999 0 -0.31 28 28
YES1 -0.008 0.06 -9999 0 -0.37 9 9
cell migration 0.001 0.091 -9999 0 -0.31 28 28
SHC/Grb2/SOS1 -0.002 0.046 -9999 0 -10000 0 0
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
SLC9A3R1 -0.012 0.12 -9999 0 -0.51 19 19
NHERF1-2/PDGFRB/PTEN 0.014 0.084 -9999 0 -0.3 9 9
FYN -0.012 0.074 -9999 0 -0.4 12 12
DOK1 0.027 0.057 -9999 0 -0.31 9 9
HRAS/GTP 0.012 0 -9999 0 -10000 0 0
PDGFB 0.014 0.028 -9999 0 -0.51 1 1
RAC1 0.016 0.14 -9999 0 -0.46 26 26
PRKCD 0.029 0.055 -9999 0 -0.31 9 9
FER 0.027 0.061 -9999 0 -0.31 11 11
MAPKKK cascade -0.007 0.042 -9999 0 -10000 0 0
RASA1 0.029 0.055 -9999 0 -0.31 9 9
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.036 0.052 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.012 0.069 -9999 0 -0.41 9 9
chemotaxis 0.013 0.092 -9999 0 -0.48 9 9
STAT1-3-5/STAT1-3-5 -0.009 0.045 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0.069 -9999 0 -0.43 9 9
PTPRJ 0.014 0.031 -9999 0 -0.58 1 1
TRAIL signaling 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
TNFSF10 -0.009 0.11 -10000 0 -0.51 17 17
positive regulation of NF-kappaB transcription factor activity 0 0.092 -10000 0 -0.37 21 21
MAP2K4 0.047 0.032 -10000 0 -10000 0 0
IKBKB 0.016 0 -10000 0 -10000 0 0
TNFRSF10B 0.016 0 -10000 0 -10000 0 0
TNFRSF10A 0.014 0.031 -10000 0 -0.58 1 1
SMPD1 0.016 0.034 -10000 0 -10000 0 0
IKBKG 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.009 0.062 -10000 0 -0.58 4 4
TRAIL/TRAILR2 0.005 0.081 -10000 0 -0.36 17 17
TRAIL/TRAILR3 -0.004 0.099 -10000 0 -0.36 25 25
TRAIL/TRAILR1 0.004 0.084 -10000 0 -0.36 18 18
TRAIL/TRAILR4 0 0.092 -10000 0 -0.37 21 21
TRAIL/TRAILR1/DAP3/GTP 0.015 0.065 -10000 0 -0.27 18 18
IKK complex -0.005 0.02 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0 -10000 0 -10000 0 0
MAPK3 0.008 0.081 -10000 0 -0.36 17 17
MAP3K1 0.04 0.034 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.009 0.062 -10000 0 -0.57 4 4
TRADD 0.016 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.031 -10000 0 -0.57 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.033 0.04 -10000 0 -10000 0 0
CFLAR 0.016 0 -10000 0 -10000 0 0
MAPK1 0.008 0.081 -10000 0 -0.36 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP 0.028 0.07 -10000 0 -10000 0 0
mol:ceramide 0.016 0.033 -10000 0 -10000 0 0
FADD 0.007 0.067 -10000 0 -0.51 6 6
MAPK8 0.051 0.041 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.082 -10000 0 -0.54 8 8
CHUK 0.016 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.01 0.081 -10000 0 -0.29 24 24
DAP3 0.016 0 -10000 0 -10000 0 0
CASP10 -0.011 0.06 0.27 4 -10000 0 4
JNK cascade 0 0.092 -10000 0 -0.37 21 21
TRAIL (trimer) -0.009 0.11 -10000 0 -0.51 17 17
TNFRSF10C 0.003 0.083 -10000 0 -0.54 8 8
TRAIL/TRAILR1/DAP3/GTP/FADD 0.018 0.07 -10000 0 -0.24 24 24
TRAIL/TRAILR2/FADD 0.011 0.079 -10000 0 -0.29 23 23
cell death 0.016 0.033 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.034 0.037 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.016 0 -10000 0 -10000 0 0
CASP8 0.004 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.029 0.068 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.029 -10000 0 -0.36 2 2
MAP4K4 0.036 0.061 -10000 0 -10000 0 0
BAG4 0.016 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.03 -10000 0 -0.32 2 2
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.024 0.15 -10000 0 -0.57 24 24
BAX 0.002 0.01 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.022 0.006 -10000 0 -10000 0 0
BAD -0.004 0.019 -10000 0 -10000 0 0
SMPD1 0.025 0.031 -10000 0 -10000 0 0
RB1 -0.004 0.019 0.14 2 -10000 0 2
FADD/Caspase 8 0.044 0.066 -10000 0 -0.28 2 2
MAP2K4 0.004 0.018 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.024 -10000 0 -0.31 1 1
EGF -0.018 0.12 -10000 0 -0.51 22 22
mol:ceramide -0.015 0.02 0.14 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.025 0.02 -10000 0 -0.36 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.005 0.019 0.14 2 -10000 0 2
cell proliferation -0.088 0.13 -10000 0 -0.26 14 14
BID 0.03 0.042 -10000 0 -10000 0 0
MAP3K1 -0.004 0.019 0.14 2 -10000 0 2
EIF2A 0.012 0.017 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.016 0.023 -10000 0 -0.28 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.023 -10000 0 -0.28 1 1
Cathepsin D/ceramide -0.003 0.019 -10000 0 -10000 0 0
FADD 0.033 0.069 -10000 0 -0.32 2 2
KSR1 -0.004 0.019 0.14 2 -10000 0 2
MAPK8 0.007 0.034 -10000 0 -0.23 5 5
PRKRA -0.004 0.019 0.14 2 -10000 0 2
PDGFA 0.014 0.028 -10000 0 -0.51 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.58 159 159
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.02 0.14 2 -10000 0 2
CTSD 0.016 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.023 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.093 0.14 -10000 0 -0.29 10 10
PRKCD 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.044 -10000 0 -0.58 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.025 0.02 -10000 0 -0.36 1 1
RelA/NF kappa B1 0.023 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.031 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.03 0.062 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.016 0.069 -10000 0 -0.29 17 17
mol:Sphingosine-1-phosphate 0.024 0.028 -10000 0 -0.36 2 2
MAP2K1 0.012 0.023 -10000 0 -0.29 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS 0.006 0.035 0.17 14 -10000 0 14
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0 -10000 0 -10000 0 0
EIF2AK2 0.004 0.018 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.016 0.069 -10000 0 -0.29 17 17
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.04 0.038 -10000 0 -10000 0 0
MAP2K2 0.012 0.023 -10000 0 -0.29 1 1
SMPD3 0.027 0.035 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.51 17 17
PKC zeta/PAR4 0.019 0.04 -10000 0 -0.41 3 3
mol:PHOSPHOCHOLINE -0.002 0.037 0.14 19 -10000 0 19
NF kappa B1/RelA/I kappa B alpha 0.044 0.029 -10000 0 -10000 0 0
AIFM1 0.006 0.035 0.17 14 -10000 0 14
BCL2 -0.008 0.12 -10000 0 -0.58 14 14
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.034 0 -9999 0 -10000 0 0
SNTA1 0.016 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.007 0.09 -9999 0 -0.29 30 30
MAPK12 0.025 0.053 -9999 0 -0.3 4 4
CCND1 0.01 0.071 -9999 0 -0.45 7 7
p38 gamma/SNTA1 0.032 0.05 -9999 0 -0.28 4 4
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.014 0.031 -9999 0 -0.58 1 1
G2/M transition checkpoint 0.025 0.053 -9999 0 -0.3 4 4
MAP2K6 0.021 0.048 -9999 0 -0.32 7 7
MAPT 0.004 0.1 -9999 0 -0.32 30 30
MAPK13 0.026 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0.027 -9999 0 -0.35 2 2
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.012 0.042 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.032 0 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.035 0.058 -10000 0 -0.26 2 2
KAT2B 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.017 0.083 0.22 15 -0.26 22 37
RAR alpha/9cRA/Cyclin H -0.006 0.032 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.067 -10000 0 -0.29 2 2
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.018 0.052 -10000 0 -0.47 3 3
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.03 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.016 0.093 -10000 0 -0.44 4 4
NCOA2 -0.023 0.14 -10000 0 -0.58 23 23
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0.042 -10000 0 -0.54 2 2
RARG 0.017 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.022 0 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.012 0.054 -10000 0 -0.57 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.002 0.068 -10000 0 -0.41 4 4
RARA 0.024 0.042 -10000 0 -0.25 6 6
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.014 0.097 -10000 0 -0.46 5 5
PRKCA 0.015 0.054 -10000 0 -0.57 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.003 0.096 -10000 0 -0.47 4 4
RXRG -0.08 0.16 -10000 0 -0.34 98 98
RXRA 0.032 0.042 -10000 0 -0.25 4 4
RXRB 0.021 0.048 -10000 0 -0.34 3 3
VDR/Vit D3/DNA 0.009 0.03 -10000 0 -0.4 2 2
RBP1 -0.019 0.14 -10000 0 -0.57 21 21
CRBP1/9-cic-RA -0.014 0.1 -10000 0 -0.42 21 21
RARB -0.026 0.16 -10000 0 -0.58 27 27
PRKCG -0.004 0.089 -10000 0 -0.5 11 11
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.016 0.095 -10000 0 -0.44 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.021 0.086 -10000 0 -0.4 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.063 -10000 0 -0.34 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.096 -10000 0 -0.47 4 4
positive regulation of DNA binding -0.005 0.03 -10000 0 -10000 0 0
NRIP1 0.005 0.09 -10000 0 -0.65 1 1
RXRs/RARs -0.005 0.097 -10000 0 -0.4 8 8
RXRs/RXRs/DNA/9cRA -0.016 0.062 -10000 0 -0.44 3 3
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0.032 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.003 0.018 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.016 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.016 0.058 -9999 0 -0.36 2 2
NEF -0.009 0.051 -9999 0 -10000 0 0
NFKBIA 0.012 0.027 -9999 0 -10000 0 0
BIRC3 0.01 0.16 -9999 0 -0.57 24 24
CYCS 0.033 0.081 -9999 0 -0.37 2 2
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.004 0.093 -9999 0 -0.57 7 7
MAP2K7 0.039 0.064 -9999 0 -0.31 1 1
protein ubiquitination 0.067 0.043 -9999 0 -10000 0 0
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.007 0.07 -9999 0 -0.58 5 5
BID 0.025 0.085 -9999 0 -0.4 2 2
NF-kappa-B/RelA/I kappa B alpha -0.018 0.067 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.007 0.067 -9999 0 -0.51 6 6
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.018 0.067 -9999 0 -10000 0 0
MAPK8 0.044 0.066 -9999 0 -0.28 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.012 0.042 -9999 0 -0.54 2 2
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.018 0.088 -9999 0 -0.28 22 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.057 0.049 -9999 0 -10000 0 0
CHUK 0.068 0.045 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.037 0.052 -9999 0 -0.28 5 5
TCRz/NEF -0.03 0.096 -9999 0 -0.32 35 35
TNF -0.009 0.11 -9999 0 -0.51 17 17
FASLG -0.025 0.18 -9999 0 -0.56 34 34
NFKB1 0.012 0.027 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.016 0.069 -9999 0 -0.29 17 17
CASP6 -0.01 0.037 -9999 0 -10000 0 0
CASP7 0.047 0.15 -9999 0 -0.52 21 21
RELA 0.012 0.027 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 0.047 0.15 -9999 0 -0.52 21 21
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.023 0 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.047 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.032 0.096 -9999 0 -0.38 21 21
BCL2 0.039 0.084 -9999 0 -0.34 2 2
TCGA08_rtk_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
PDGFRA -0.069 0.21 -10000 0 -0.58 51 51
HRAS 0.016 0 -10000 0 -10000 0 0
EGFR -0.008 0.11 -10000 0 -0.54 15 15
AKT 0.032 0.06 -10000 0 -0.28 11 11
FOXO3 0.016 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
FOXO1 0.016 0 -10000 0 -10000 0 0
AKT3 -0.003 0.1 -10000 0 -0.58 11 11
FOXO4 0.014 0.028 -10000 0 -0.51 1 1
MET 0.014 0.028 -10000 0 -0.51 1 1
PIK3CA 0.016 0 -10000 0 -10000 0 0
PIK3CB 0.016 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
PIK3CG -0.006 0.11 -10000 0 -0.56 13 13
PIK3R3 0.016 0 -10000 0 -10000 0 0
PIK3R2 0.016 0 -10000 0 -10000 0 0
NF1 0.016 0 -10000 0 -10000 0 0
RAS -0.001 0.069 -10000 0 -0.26 6 6
ERBB2 -0.003 0.098 -10000 0 -0.51 13 13
proliferation/survival/translation -0.036 0.027 0.19 1 -10000 0 1
PI3K 0.01 0.069 -10000 0 -0.22 10 10
PIK3R1 0.016 0 -10000 0 -10000 0 0
KRAS 0.014 0.028 -10000 0 -0.51 1 1
FOXO 0.048 0.028 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
PTEN 0.016 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.016 0 -9999 0 -10000 0 0
PLK4 0.005 0.072 -9999 0 -0.51 7 7
regulation of centriole replication 0.019 0.053 -9999 0 -0.36 7 7
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.095 -9999 0 -0.45 13 13
KLHL20 -0.013 0.04 -9999 0 -0.21 3 3
CYFIP2 -0.001 0.098 -9999 0 -0.58 10 10
Rac1/GDP 0.058 0.061 -9999 0 -10000 0 0
ENAH 0.031 0.094 -9999 0 -0.45 13 13
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.006 0.033 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.03 -9999 0 -0.2 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.024 0.077 -9999 0 -0.32 16 16
RAPGEF1 0.046 0.083 -9999 0 -0.38 13 13
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.02 0.096 -9999 0 -0.47 13 13
CRK 0.039 0.089 -9999 0 -0.42 13 13
E-cadherin/gamma catenin/alpha catenin 0.015 0.079 -9999 0 -0.37 14 14
alphaE/beta7 Integrin 0.018 0.046 -9999 0 -0.41 4 4
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.03 0.001 -9999 0 -10000 0 0
DLG1 0.031 0.094 -9999 0 -0.45 13 13
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.024 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.027 0.03 -9999 0 -0.3 3 3
PI3K -0.006 0.03 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.005 0.091 -9999 0 -0.44 14 14
TIAM1 0.012 0.044 -9999 0 -0.58 2 2
E-cadherin(dimer)/Ca2+ 0.024 0.061 -9999 0 -0.29 13 13
AKT1 -0.003 0.017 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 -0.006 0.11 -9999 0 -0.58 13 13
RhoA/GDP 0.057 0.061 -9999 0 -10000 0 0
actin cytoskeleton organization 0.04 0.046 -9999 0 -0.15 3 3
CDC42/GDP 0.057 0.061 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.017 0.061 -9999 0 -0.28 14 14
ITGB7 0.009 0.062 -9999 0 -0.58 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.026 0.065 -9999 0 -0.3 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.06 -9999 0 -0.29 13 13
mol:GDP 0.053 0.069 -9999 0 -0.3 12 12
CDC42/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
JUP 0.012 0.044 -9999 0 -0.58 2 2
p120 catenin/RhoA/GDP -0.01 0.048 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.023 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.026 0.056 -9999 0 -0.2 18 18
NME1 0.014 0.028 -9999 0 -0.51 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.031 0.094 -9999 0 -0.45 13 13
regulation of cell-cell adhesion -0.006 0.03 -9999 0 -10000 0 0
WASF2 -0.006 0.015 -9999 0 -10000 0 0
Rap1/GTP -0.007 0.039 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.029 0.079 -9999 0 -0.58 2 2
CCND1 0.03 0.068 -9999 0 -0.24 18 18
VAV2 0.039 0.1 -9999 0 -0.44 15 15
RAP1/GDP 0.054 0.054 -9999 0 -10000 0 0
adherens junction assembly 0.031 0.091 -9999 0 -0.44 13 13
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.037 0.077 -9999 0 -0.55 2 2
E-cadherin/beta catenin -0.014 0.071 -9999 0 -0.38 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.029 0.094 -9999 0 -0.45 13 13
PIK3CA 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.02 0.064 -9999 0 -0.34 3 3
E-cadherin/beta catenin/alpha catenin 0.017 0.07 -9999 0 -0.34 13 13
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.091 -9999 0 -0.48 13 13
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.034 0.044 -10000 0 -0.3 6 6
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.02 0.005 -10000 0 -10000 0 0
GATA1/HDAC5 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC5 0.006 0.08 -10000 0 -0.38 15 15
HDAC5/BCL6/BCoR 0.032 0 -10000 0 -10000 0 0
HDAC9 -0.026 0.15 -10000 0 -0.58 25 25
Glucocorticoid receptor/Hsp90/HDAC6 0.022 0.059 -10000 0 -0.34 9 9
HDAC4/ANKRA2 0.023 0 -10000 0 -10000 0 0
HDAC5/YWHAB 0.023 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -10000 0 -10000 0 0
GATA2 -0.007 0.11 -10000 0 -0.53 15 15
HDAC4/RFXANK 0.022 0.02 -10000 0 -0.36 1 1
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.016 0 -10000 0 -10000 0 0
HDAC5 0.016 0 -10000 0 -10000 0 0
GNB1/GNG2 0.016 0.056 -10000 0 -0.41 6 6
Histones 0.027 0.067 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.023 0 -10000 0 -10000 0 0
HDAC4/Ubc9 0.023 0 -10000 0 -10000 0 0
HDAC7 0.016 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.022 0.023 -10000 0 -0.41 1 1
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.022 0.02 -10000 0 -0.36 1 1
CAMK4 -0.003 0.1 -10000 0 -0.57 11 11
Tubulin/HDAC6 0.03 0.028 -10000 0 -0.34 2 2
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 0.011 0.007 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.014 0.031 -10000 0 -0.58 1 1
NR3C1 0.001 0.093 -10000 0 -0.58 9 9
SUMO1/HDAC4 0.036 0 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.023 0 -10000 0 -10000 0 0
Tubulin 0.021 0.033 -10000 0 -0.41 2 2
HDAC4/14-3-3 E 0.022 0.023 -10000 0 -0.41 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.016 0 -10000 0 -10000 0 0
BCL6/BCoR 0.023 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.032 0 -10000 0 -10000 0 0
HDAC4/SRF 0.02 0.064 -10000 0 -0.34 11 11
HDAC4/ER alpha -0.051 0.16 -10000 0 -0.41 61 61
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.066 -10000 0 -10000 0 0
cell motility 0.029 0.028 -10000 0 -0.34 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.023 0 -10000 0 -10000 0 0
BCL6 0.016 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.023 0 -10000 0 -10000 0 0
ESR1 -0.086 0.22 -10000 0 -0.58 61 61
HDAC6/HDAC11 0.018 0.045 -10000 0 -0.4 4 4
Ran/GTP/Exportin 1 0.039 0 -10000 0 -10000 0 0
NPC 0.009 0 -10000 0 -10000 0 0
MEF2C -0.003 0.1 -10000 0 -0.58 11 11
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.036 0.056 -10000 0 -10000 0 0
GNG2 0.006 0.076 -10000 0 -0.58 6 6
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.012 0.044 -10000 0 -0.58 2 2
HDAC11 0.009 0.061 -10000 0 -0.56 4 4
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.014 0.028 -10000 0 -0.51 1 1
nuclear import -0.033 0.018 0.31 1 -10000 0 1
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 0.009 0.024 -10000 0 -10000 0 0
oxygen homeostasis 0.01 0.017 -10000 0 -10000 0 0
TCEB2 0.014 0.028 -10000 0 -0.51 1 1
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.002 0.038 -10000 0 -10000 0 0
EPO 0.12 0.21 -10000 0 -0.58 3 3
FIH (dimer) 0.026 0.015 -10000 0 -10000 0 0
APEX1 0.025 0.017 -10000 0 -10000 0 0
SERPINE1 0.13 0.22 -10000 0 -0.7 6 6
FLT1 0.012 0.024 -10000 0 -10000 0 0
ADORA2A 0.13 0.2 -10000 0 -0.55 5 5
germ cell development 0.095 0.25 -10000 0 -0.52 21 21
SLC11A2 0.14 0.2 -10000 0 -0.56 5 5
BHLHE40 0.14 0.2 -10000 0 -0.62 6 6
HIF1AN 0.026 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.081 0.13 -10000 0 -10000 0 0
ETS1 0.034 0.002 -10000 0 -10000 0 0
CITED2 0.009 0.019 -10000 0 -10000 0 0
KDR 0.009 0.072 -10000 0 -1.3 1 1
PGK1 0.14 0.2 -10000 0 -0.56 5 5
SIRT1 0.015 0.002 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.22 -10000 0 -0.65 5 5
EPAS1 0.089 0.1 -10000 0 -0.29 2 2
SP1 0.025 0.003 -10000 0 -10000 0 0
ABCG2 0.13 0.22 -10000 0 -0.64 4 4
EFNA1 0.13 0.21 -10000 0 -0.6 5 5
FXN 0.13 0.19 -10000 0 -0.55 5 5
POU5F1 0.095 0.26 -10000 0 -0.54 21 21
neuron apoptosis -0.16 0.22 0.63 5 -10000 0 5
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 0.014 0.083 -10000 0 -0.56 7 7
EGLN2 0.026 0.016 -10000 0 -10000 0 0
EGLN1 0.026 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.031 0.017 -10000 0 -0.29 1 1
VHL 0.016 0 -10000 0 -10000 0 0
ARNT 0.025 0.017 -10000 0 -10000 0 0
SLC2A1 0.13 0.2 -10000 0 -0.54 6 6
TWIST1 0.069 0.3 -10000 0 -0.65 28 28
ELK1 0.025 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.006 0.059 -10000 0 -10000 0 0
VEGFA 0.14 0.2 -10000 0 -0.56 5 5
CREBBP 0.016 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0.039 -10000 0 -0.51 2 2
Rac1/GDP 0.002 0.01 -10000 0 -10000 0 0
DOCK1 0.014 0.031 -10000 0 -0.58 1 1
ITGA4 -0.004 0.11 -10000 0 -0.57 12 12
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.004 0.09 -10000 0 -0.41 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.019 0.067 -10000 0 -0.34 12 12
alpha4/beta7 Integrin/Paxillin 0.024 0.07 -10000 0 -0.3 16 16
lamellipodium assembly 0.001 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
PI3K 0.023 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.016 0 -10000 0 -10000 0 0
PXN 0.026 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.044 -10000 0 -10000 0 0
cell adhesion 0.035 0.057 -10000 0 -10000 0 0
CRKL/CBL 0.021 0.028 -10000 0 -0.36 2 2
alpha4/beta1 Integrin/Paxillin 0.028 0.061 -10000 0 -0.3 11 11
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 0.009 0.062 -10000 0 -0.58 4 4
ARF6/GDP 0.002 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.021 0.1 -10000 0 -0.58 6 6
p130Cas/Crk/Dock1 0.031 0.02 -10000 0 -0.34 1 1
VCAM1 -0.014 0.13 -10000 0 -0.57 18 18
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.058 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.036 0.058 -10000 0 -0.28 11 11
BCAR1 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.035 0.057 0.28 11 -10000 0 11
CBL 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.036 0.058 -10000 0 -10000 0 0
Rac1/GTP 0.001 0.02 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0 0.009 -9999 0 -10000 0 0
DAPP1 0.018 0.093 -9999 0 -0.43 6 6
Src family/SYK family/BLNK-LAT/BTK-ITK 0.012 0.15 -9999 0 -0.48 20 20
mol:DAG 0.033 0.085 -9999 0 -0.23 15 15
HRAS 0.017 0.001 -9999 0 -10000 0 0
RAP1A 0.016 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.041 0.046 -9999 0 -10000 0 0
PLCG2 0.01 0.057 -9999 0 -0.52 4 4
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.01 -9999 0 -10000 0 0
ADAP1 -0.003 0.029 -9999 0 -10000 0 0
ARAP3 -0.001 0.01 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.011 0.054 -9999 0 -0.58 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.011 0.054 -9999 0 -0.58 3 3
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.014 0.031 -9999 0 -0.58 1 1
mol:Ca2+ 0.029 0.049 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.012 0.044 -9999 0 -0.58 2 2
ZAP70 -0.008 0.12 -9999 0 -0.58 14 14
mol:IP3 0.034 0.065 -9999 0 -0.21 1 1
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.041 0.046 -9999 0 -10000 0 0
RhoA/GDP -0.002 0.01 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0 -9999 0 -10000 0 0
BLNK -0.001 0.098 -9999 0 -0.58 10 10
actin cytoskeleton reorganization 0.064 0.042 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.027 0.052 -9999 0 -0.34 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP 0 0.009 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.01 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.014 0.12 -9999 0 -0.43 12 12
BLK -0.054 0.18 -9999 0 -0.56 42 42
PDPK1 0.016 0 -9999 0 -10000 0 0
CYTH1 -0.001 0.01 -9999 0 -10000 0 0
HCK -0.012 0.12 -9999 0 -0.56 17 17
CYTH3 -0.001 0.01 -9999 0 -10000 0 0
CYTH2 -0.001 0.01 -9999 0 -10000 0 0
KRAS 0.015 0.027 -9999 0 -0.5 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.033 0.093 -9999 0 -0.44 13 13
SGK1 -0.018 0.091 -9999 0 -0.49 13 13
INPP5D 0.004 0.082 -9999 0 -0.58 7 7
mol:GDP 0.033 0.048 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.012 0.044 -9999 0 -0.58 2 2
ARF6/GDP -0.002 0.01 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.01 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.01 -9999 0 -10000 0 0
VAV1 -0.014 0.13 -9999 0 -0.57 18 18
mol:PI-3-4-P2 0.018 0.061 -9999 0 -0.41 7 7
RAS family/GTP/PI3K Class I 0.036 0.013 -9999 0 -10000 0 0
PLEKHA1 0.027 0.052 -9999 0 -0.34 7 7
Rac1/GDP 0.041 0.046 -9999 0 -10000 0 0
LAT 0.014 0.028 -9999 0 -0.51 1 1
Rac1/GTP 0.034 0.059 -9999 0 -0.27 5 5
ITK -0.032 0.085 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.034 0.11 -9999 0 -0.32 16 16
LCK 0.006 0.073 -9999 0 -0.55 6 6
BTK -0.016 0.062 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.038 -10000 0 -0.37 1 1
adherens junction organization 0.037 0.067 -10000 0 -0.27 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.047 0.064 -10000 0 -0.36 2 2
FMN1 0.029 0.079 -10000 0 -0.53 2 2
mol:IP3 0.042 0.038 -10000 0 -0.39 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.064 -10000 0 -0.27 14 14
CTNNB1 0.016 0.002 -10000 0 -10000 0 0
AKT1 0.048 0.044 -10000 0 -0.42 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.033 0.088 -10000 0 -0.41 13 13
CTNND1 0.017 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.039 0.061 -10000 0 -0.56 1 1
VASP 0.039 0.062 -10000 0 -0.58 1 1
ZYX 0.038 0.064 -10000 0 -0.42 2 2
JUB 0.037 0.068 -10000 0 -0.53 2 2
EGFR(dimer) 0.028 0.085 -10000 0 -0.33 8 8
E-cadherin/beta catenin-gamma catenin -0.014 0.069 -10000 0 -0.35 14 14
mol:PI-3-4-5-P3 0.04 0.045 -10000 0 -0.45 1 1
PIK3CA 0.017 0.001 -10000 0 -10000 0 0
PI3K 0.041 0.046 -10000 0 -0.46 1 1
FYN 0.047 0.055 -10000 0 -0.3 4 4
mol:Ca2+ 0.041 0.038 -10000 0 -0.38 1 1
JUP 0.012 0.044 -10000 0 -0.57 2 2
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
mol:DAG 0.042 0.038 -10000 0 -0.39 1 1
CDH1 -0.006 0.11 -10000 0 -0.57 13 13
RhoA/GDP 0.047 0.064 -10000 0 -0.36 2 2
establishment of polarity of embryonic epithelium 0.039 0.061 -10000 0 -0.56 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.008 0.11 -10000 0 -0.54 15 15
CASR 0.04 0.053 -10000 0 -0.35 1 1
RhoA/GTP -0.005 0.026 -10000 0 -0.34 1 1
AKT2 0.048 0.044 -10000 0 -0.42 1 1
actin cable formation 0.037 0.077 -10000 0 -0.51 2 2
apoptosis -0.046 0.042 0.41 1 -10000 0 1
CTNNA1 0.017 0.001 -10000 0 -10000 0 0
mol:GDP 0.039 0.068 -10000 0 -0.39 2 2
PIP5K1A 0.039 0.062 -10000 0 -0.58 1 1
PLCG1 0.042 0.039 -10000 0 -0.4 1 1
Rac1/GTP -0.018 0.064 -10000 0 -0.5 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
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 -9999 0 -10000 0 0
TRAF2/ASK1 0.021 0 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
MAP2K3 0.041 0.021 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.047 0.033 -9999 0 -0.22 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.006 0.076 -9999 0 -0.58 6 6
TXN 0.009 0.015 -9999 0 -0.19 2 2
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A 0.016 0 -9999 0 -10000 0 0
GADD45B -0.001 0.098 -9999 0 -0.58 10 10
MAP3K1 0.016 0 -9999 0 -10000 0 0
MAP3K6 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.023 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.029 0.016 -9999 0 -0.26 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.009 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.044 0.16 -9999 0 -0.51 40 40
CCM2 0.014 0.028 -9999 0 -0.51 1 1
CaM/Ca2+/CAMKIIB -0.015 0.1 -9999 0 -0.3 40 40
MAPK11 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.003 0.093 -9999 0 -0.26 40 40
OSM/MEKK3 0.022 0.02 -9999 0 -0.36 1 1
TAOK1 0.019 0.019 -9999 0 -0.35 1 1
TAOK2 0.02 0 -9999 0 -10000 0 0
TAOK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAP3K10 0.014 0.028 -9999 0 -0.51 1 1
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 0.018 0.013 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 0.023 0.071 -9999 0 -0.31 15 15
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 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.092 0.028 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.004 0.097 -9999 0 -0.36 25 25
NFKBIA 0.053 0 -9999 0 -10000 0 0
BIRC2 0.013 0.039 -9999 0 -0.51 2 2
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.016 0 -9999 0 -10000 0 0
IKBKG -0.005 0.019 -9999 0 -10000 0 0
IKK complex/A20 -0.012 0.045 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.051 0.031 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.021 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.003 0.011 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.032 0 -9999 0 -10000 0 0
NOD2 -0.021 0.13 -9999 0 -0.51 25 25
NFKB1 0.019 0 -9999 0 -10000 0 0
RELA 0.019 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.021 0.028 -9999 0 -0.36 2 2
ATM 0.016 0 -9999 0 -10000 0 0
TNF/TNFR1A 0.005 0.081 -9999 0 -0.36 17 17
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.011 0.054 -9999 0 -0.58 3 3
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF -0.009 0.11 -9999 0 -0.51 17 17
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.053 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex 0.058 0.031 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.005 0.023 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.038 0.076 -10000 0 -10000 0 0
BAG4 0.016 0 -10000 0 -10000 0 0
BAD 0.032 0.026 -10000 0 -10000 0 0
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.024 0.15 -10000 0 -0.57 24 24
BAX 0.032 0.026 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.014 0.019 -10000 0 -10000 0 0
IKBKB 0.045 0.073 -10000 0 -10000 0 0
MAP2K2 0.045 0.025 -10000 0 -10000 0 0
MAP2K1 0.045 0.025 -10000 0 -10000 0 0
SMPD1 0.02 0.019 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.043 0.08 -10000 0 -10000 0 0
MAP2K4 0.039 0.024 -10000 0 -10000 0 0
protein ubiquitination 0.047 0.074 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.051 0.025 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.039 0.027 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
mol:ceramide 0.024 0.027 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0.021 0 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.025 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.048 0.025 -10000 0 -10000 0 0
MAPK1 0.048 0.025 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.023 0 -10000 0 -10000 0 0
FADD 0.035 0.082 -10000 0 -0.29 2 2
KSR1 0.033 0.025 -10000 0 -10000 0 0
MAPK8 0.043 0.034 -10000 0 -0.23 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.045 0.073 -10000 0 -10000 0 0
TNF R/SODD 0.023 0 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.51 17 17
CYCS 0.037 0.032 0.15 11 -10000 0 11
IKBKG 0.045 0.073 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.032 0.078 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AIFM1 0.037 0.032 0.15 11 -10000 0 11
TNF/TNF R/SODD 0.017 0.068 -10000 0 -0.29 17 17
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.031 0.021 -10000 0 -10000 0 0
NSMAF 0.039 0.073 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.008 0.12 -10000 0 -0.58 14 14
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.023 0.077 -9999 0 -10000 0 0
PLK1 -0.053 0.22 -9999 0 -0.59 7 7
CDKN1B 0.075 0.1 -9999 0 -10000 0 0
FOXO3 -0.012 0.18 -9999 0 -0.5 7 7
KAT2B 0.014 0.019 -9999 0 -10000 0 0
FOXO1/SIRT1 0.021 0.046 -9999 0 -10000 0 0
CAT -0.002 0.17 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
AKT1 0.016 0.02 -9999 0 -10000 0 0
FOXO1 0.032 0.046 -9999 0 -10000 0 0
MAPK10 0.012 0.095 -9999 0 -0.29 32 32
mol:GTP 0.003 0 -9999 0 -10000 0 0
FOXO4 0.094 0.066 -9999 0 -10000 0 0
response to oxidative stress -0.001 0.023 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.054 0.12 -9999 0 -0.45 3 3
XPO1 0.016 0 -9999 0 -10000 0 0
EP300 0.016 0.005 -9999 0 -10000 0 0
BCL2L11 0.023 0.034 -9999 0 -10000 0 0
FOXO1/SKP2 0.031 0.054 -9999 0 -10000 0 0
mol:GDP -0.001 0.023 -9999 0 -10000 0 0
RAN 0.018 0 -9999 0 -10000 0 0
GADD45A 0.07 0.091 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.076 0.036 -9999 0 -10000 0 0
MST1 -0.016 0.12 -9999 0 -0.51 20 20
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.056 0.048 -9999 0 -0.34 1 1
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.038 0.035 -9999 0 -0.28 4 4
MAPK9 0.04 0.018 -9999 0 -0.25 1 1
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.014 0.031 -9999 0 -0.58 1 1
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.013 0.017 -9999 0 -10000 0 0
SOD2 0.08 0.12 -9999 0 -10000 0 0
RBL2 0.034 0.13 -9999 0 -10000 0 0
RAL/GDP 0.025 0.025 -9999 0 -0.31 1 1
CHUK 0.014 0.019 -9999 0 -10000 0 0
Ran/GTP 0.017 0 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.035 0.023 -9999 0 -0.28 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.067 0.35 -9999 0 -1.4 21 21
SKP2 0.007 0.067 -9999 0 -0.51 6 6
USP7 0.017 0 -9999 0 -10000 0 0
IKBKB 0.014 0.019 -9999 0 -10000 0 0
CCNB1 -0.051 0.22 -9999 0 -0.6 6 6
FOXO1-3a-4/beta catenin 0.098 0.12 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.054 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.008 0.11 -9999 0 -0.57 13 13
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.001 -9999 0 -10000 0 0
ZFAND5 0.097 0.059 -9999 0 -10000 0 0
SFN -0.034 0.15 -9999 0 -0.52 33 33
CDK2 0.015 0.01 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.043 0.065 -9999 0 -0.36 2 2
CREBBP 0.015 0.01 -9999 0 -10000 0 0
FBXO32 -0.002 0.17 -9999 0 -10000 0 0
BCL6 0.034 0.13 -9999 0 -10000 0 0
RALB 0.017 0 -9999 0 -10000 0 0
RALA 0.016 0.028 -9999 0 -0.5 1 1
YWHAH 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.029 0.14 -9999 0 -0.42 42 42
AKT1 0.097 0.045 -9999 0 -0.51 1 1
PTK2B 0.025 0.12 -9999 0 -0.54 4 4
VEGFR2 homodimer/Frs2 0.033 0.06 -9999 0 -0.7 1 1
CAV1 -0.013 0.13 -9999 0 -0.58 17 17
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.044 0.057 -9999 0 -0.65 1 1
endothelial cell proliferation 0.053 0.1 -9999 0 -0.59 1 1
mol:Ca2+ 0.061 0.047 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.058 0.039 -9999 0 -0.61 1 1
RP11-342D11.1 0.05 0.047 -9999 0 -0.59 1 1
CDH5 0.014 0.031 -9999 0 -0.58 1 1
VEGFA homodimer 0.041 0.016 -9999 0 -10000 0 0
SHC1 0.014 0.028 -9999 0 -0.51 1 1
SHC2 -0.019 0.14 -9999 0 -0.57 21 21
HRAS/GDP -0.004 0.034 -9999 0 -0.49 1 1
SH2D2A 0.011 0.048 -9999 0 -0.51 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.031 -9999 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.049 -9999 0 -0.65 1 1
VEGFR1 homodimer 0.016 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.004 0.037 -9999 0 -0.55 1 1
GRB10 0.057 0.078 -9999 0 -0.59 5 5
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.014 0.031 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.003 0.046 -9999 0 -0.86 1 1
HRAS 0.016 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.03 0.086 -9999 0 -0.39 4 4
HIF1A 0.014 0.028 -9999 0 -0.51 1 1
FRS2 0.005 0.072 -9999 0 -0.51 7 7
oxygen and reactive oxygen species metabolic process -0.003 0.033 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak 0.022 0.023 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.047 0.052 -9999 0 -0.65 1 1
mol:GDP -0.004 0.036 -9999 0 -0.53 1 1
mol:NADP 0.087 0.037 -9999 0 -0.4 1 1
eNOS/Hsp90 0.09 0.035 -9999 0 -0.38 1 1
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.061 0.047 -9999 0 -0.59 1 1
HIF1A/ARNT 0.022 0.02 -9999 0 -0.36 1 1
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA 0.017 0.008 -9999 0 -10000 0 0
VEGFC 0.011 0.054 -9999 0 -0.58 3 3
FAK1/Vinculin 0.051 0.099 -9999 0 -0.6 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.019 0.12 -9999 0 -0.57 4 4
PTPN6 0.014 0.028 -9999 0 -0.51 1 1
EPAS1 0.026 0.02 -9999 0 -0.34 1 1
mol:L-citrulline 0.087 0.037 -9999 0 -0.4 1 1
ITGAV 0.014 0.031 -9999 0 -0.58 1 1
PIK3CA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.052 0.055 -9999 0 -0.61 1 1
VEGFR2 homodimer/VEGFA homodimer 0.055 0.051 -9999 0 -0.64 1 1
VEGFR2/3 heterodimer 0.04 0.041 -9999 0 -0.7 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 0.064 0.049 -9999 0 -0.6 1 1
VEGFR2 homodimer 0.039 0.046 -9999 0 -0.8 1 1
FLT1 0.016 0 -9999 0 -10000 0 0
NEDD4 0.017 0.008 -9999 0 -10000 0 0
MAPK3 0.028 0.079 -9999 0 -0.44 3 3
MAPK1 0.028 0.079 -9999 0 -0.44 3 3
VEGFA145/NRP2 0.005 0.091 -9999 0 -0.41 16 16
VEGFR1/2 heterodimer 0.04 0.041 -9999 0 -0.7 1 1
KDR 0.039 0.046 -9999 0 -0.8 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.046 0.082 -9999 0 -0.56 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.033 0.077 -9999 0 -0.44 3 3
PI3K 0.086 0.049 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.05 0.041 -9999 0 -0.65 1 1
FES 0.06 0.051 -9999 0 -0.6 1 1
GAB1 -0.004 0.036 -9999 0 -0.61 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.041 -9999 0 -0.65 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.077 0.066 -9999 0 -0.38 1 1
VEGFR2 homodimer/VEGFA homodimer/Yes 0.05 0.041 -9999 0 -0.65 1 1
PI3K/GAB1 0.099 0.045 -9999 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.007 0.044 -9999 0 -0.58 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.049 -9999 0 -0.65 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 0.061 0.048 -9999 0 -0.6 1 1
actin cytoskeleton reorganization 0.047 0.049 -9999 0 -0.64 1 1
PTK2 0.045 0.1 -9999 0 -0.66 2 2
EDG1 0.05 0.047 -9999 0 -0.59 1 1
mol:DAG 0.061 0.047 -9999 0 -0.59 1 1
CaM/Ca2+ 0.063 0.044 -9999 0 -0.54 1 1
MAP2K3 0.065 0.051 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.059 0.079 -9999 0 -0.6 5 5
PLCG1 0.061 0.048 -9999 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.039 -9999 0 -0.61 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.05 0.041 -9999 0 -0.65 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.049 0.044 -9999 0 -0.65 1 1
cell migration 0.078 0.09 -9999 0 -0.73 1 1
mol:PI-3-4-5-P3 0.084 0.046 -9999 0 -0.54 1 1
FYN 0.011 0.054 -9999 0 -0.58 3 3
VEGFB/NRP1 0.057 0.044 -9999 0 -0.55 1 1
mol:NO 0.087 0.037 -9999 0 -0.4 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.004 0.034 -9999 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.058 0.079 -9999 0 -0.6 5 5
VHL 0.016 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.19 -9999 0 -0.58 42 42
NOS3 0.089 0.04 -9999 0 -0.45 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck 0.03 0.091 -9999 0 -0.55 2 2
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.064 0.053 -9999 0 -0.55 1 1
PRKCB -0.023 0.15 -9999 0 -0.62 3 3
VCL 0.014 0.031 -9999 0 -0.58 1 1
VEGFA165/NRP1 0.051 0.047 -9999 0 -0.59 1 1
VEGFR1/2 heterodimer/VEGFA homodimer 0.05 0.041 -9999 0 -0.65 1 1
VEGFA165/NRP2 0.005 0.091 -9999 0 -0.41 16 16
MAPKKK cascade 0.081 0.069 -9999 0 -0.49 5 5
NRP2 -0.011 0.12 -9999 0 -0.58 16 16
VEGFC homodimer 0.011 0.054 -9999 0 -0.57 3 3
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.052 0.098 -9999 0 -0.6 2 2
MAP3K13 0.059 0.054 -9999 0 -0.6 1 1
PDPK1 0.089 0.042 -9999 0 -0.48 1 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.052 0.038 -9999 0 -10000 0 0
CLOCK 0.019 0.002 -9999 0 -10000 0 0
TIMELESS/CRY2 0.049 0.028 -9999 0 -10000 0 0
DEC1/BMAL1 0.008 0.055 -9999 0 -0.35 8 8
ATR 0.016 0 -9999 0 -10000 0 0
NR1D1 0.049 0.016 -9999 0 -10000 0 0
ARNTL 0.019 0.002 -9999 0 -10000 0 0
TIMELESS 0.047 0.031 -9999 0 -10000 0 0
NPAS2 0.018 0.031 -9999 0 -0.57 1 1
CRY2 0.016 0 -9999 0 -10000 0 0
mol:CO -0.016 0.007 -9999 0 -10000 0 0
CHEK1 0.01 0.055 -9999 0 -0.51 4 4
mol:HEME 0.016 0.007 -9999 0 -10000 0 0
PER1 -0.008 0.12 -9999 0 -0.58 14 14
BMAL/CLOCK/NPAS2 0.05 0.021 -9999 0 -0.33 1 1
BMAL1/CLOCK 0.051 0.038 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.052 0.038 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.053 0.039 -9999 0 -10000 0 0
mol:NADPH 0.016 0.007 -9999 0 -10000 0 0
PER1/TIMELESS 0.036 0.071 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.009 0.076 -9999 0 -0.51 8 8
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.082 -10000 0 -0.34 4 4
CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.13 0.11 0.22 1 -0.34 6 7
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.026 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0.032 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP 0.006 0.048 -10000 0 -0.51 3 3
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.036 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.044 -10000 0 -0.58 2 2
TRIP10 0.014 0.031 -10000 0 -0.58 1 1
TC10/GTP/CIP4/Exocyst 0.02 0.02 -10000 0 -0.35 1 1
AS160/14-3-3 0.042 0.043 -10000 0 -0.3 1 1
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 -0.14 0.12 0.23 1 -0.38 6 7
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.03 0 -10000 0 -10000 0 0
SFN -0.034 0.15 -10000 0 -0.52 33 33
LNPEP 0.016 0 -10000 0 -10000 0 0
YWHAE 0.014 0.031 -10000 0 -0.58 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.04 -10000 0 -0.29 7 7
FRAP1 0.017 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.036 -10000 0 -10000 0 0
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.023 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.005 -10000 0 -10000 0 0
TSC2 0.015 0 -10000 0 -10000 0 0
RHEB/GDP -0.003 0.019 -10000 0 -10000 0 0
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.012 0.051 -10000 0 -0.35 7 7
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.03 0.019 -10000 0 -10000 0 0
MAP3K5 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.012 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 7 7
EIF4B 0.036 0.018 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.047 -10000 0 -0.31 7 7
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.012 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
RHEB/GTP -0.003 0.019 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 7 7
FKBP12/Rapamycin 0.012 0.002 -10000 0 -10000 0 0
PDPK1 -0.005 0.036 -10000 0 -0.26 7 7
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.005 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0 -10000 0 -10000 0 0
TSC1/TSC2 0.042 0.031 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 7 -10000 0 7
RPS6 0.016 0 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.002 0.054 -10000 0 -0.38 7 7
INS 0 0 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.005 0.036 -10000 0 -0.26 7 7
EIF4EBP1 0.012 0.015 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
PPP2R5D 0.024 0.007 -10000 0 -10000 0 0
peptide biosynthetic process 0.02 0 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.02 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.02 0.013 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.037 0.017 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.026 0.016 -9999 0 -0.28 1 1
mol:DAG 0.035 0.055 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.034 0.015 -9999 0 -10000 0 0
CaM/Ca2+ 0.042 0.051 -9999 0 -10000 0 0
HIF1A 0.024 0.027 -9999 0 -0.49 1 1
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.06 0.042 -9999 0 -10000 0 0
PLCG1 0.036 0.055 -9999 0 -10000 0 0
NOS3 0.065 0.042 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO 0.065 0.041 -9999 0 -10000 0 0
FLT1 0.035 0.02 -9999 0 -0.34 1 1
PGF -0.002 0.094 -9999 0 -0.51 12 12
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.072 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.071 0.04 -9999 0 -10000 0 0
endothelial cell proliferation -0.022 0.13 -9999 0 -0.42 7 7
mol:Ca2+ 0.035 0.054 -9999 0 -10000 0 0
MAPK3 0.046 0.055 -9999 0 -10000 0 0
MAPK1 0.046 0.055 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
PLGF homodimer -0.002 0.094 -9999 0 -0.51 12 12
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.013 0.13 -9999 0 -0.58 17 17
VEGFA homodimer 0.016 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.037 0.017 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.053 0.054 -9999 0 -10000 0 0
PI3K 0.043 0.052 -9999 0 -10000 0 0
PRKCA 0.04 0.058 -9999 0 -10000 0 0
PRKCB -0.051 0.16 -9999 0 -0.53 4 4
VEGFR1 homodimer/PLGF homodimer 0.027 0.06 -9999 0 -10000 0 0
VEGFA 0.016 0 -9999 0 -10000 0 0
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.035 0.055 -9999 0 -10000 0 0
RASA1 0.045 0.015 -9999 0 -10000 0 0
NRP2 -0.011 0.12 -9999 0 -0.58 16 16
VEGFR1 homodimer 0.035 0.02 -9999 0 -0.34 1 1
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.058 0.074 -9999 0 -0.41 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.051 -9999 0 -10000 0 0
mol:L-citrulline 0.065 0.041 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.053 0.014 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.015 -9999 0 -10000 0 0
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 0.049 0.049 -9999 0 -10000 0 0
PDPK1 0.048 0.049 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.045 0.015 -9999 0 -10000 0 0
mol:NADP 0.065 0.041 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.014 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.021 0.079 -9999 0 -0.34 16 16
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.016 0 -9999 0 -10000 0 0
SMAD3 0.048 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.055 0.005 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.032 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.045 0.019 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.024 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.017 0.051 -9999 0 -0.41 5 5
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.007 0.07 -9999 0 -0.58 5 5
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.013 0.039 -9999 0 -0.51 2 2
PIAS4 0.016 0 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.05 0.005 -10000 0 -10000 0 0
regulation of axonogenesis -0.034 0.014 0.22 1 -10000 0 1
myoblast fusion -0.023 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.032 0.3 3 -10000 0 3
ARF1/GTP 0 0.001 -10000 0 -10000 0 0
mol:GM1 0.013 0.004 -10000 0 -10000 0 0
mol:Choline 0.032 0.02 -10000 0 -0.35 1 1
lamellipodium assembly 0 0.014 -10000 0 -10000 0 0
MAPK3 0.035 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.039 0.032 -10000 0 -0.31 3 3
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.013 -10000 0 -10000 0 0
ARF1/GDP 0.032 0.012 -10000 0 -10000 0 0
ARF6 0.015 0.002 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.014 0.044 -10000 0 -0.57 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.035 0.003 -10000 0 -10000 0 0
actin filament bundle formation -0.03 0.011 -10000 0 -10000 0 0
KALRN -0.003 0.032 -10000 0 -0.26 5 5
RAB11FIP3/RAB11A 0.023 0 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.012 -10000 0 -10000 0 0
NME1 0.016 0.028 -10000 0 -0.5 1 1
Rac1/GDP 0.031 0.012 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0 0.014 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
liver development 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0.003 -10000 0 -10000 0 0
RhoA/GTP 0 0.001 -10000 0 -10000 0 0
mol:GDP 0 0.013 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.002 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.024 0.023 -10000 0 -0.4 1 1
RAB11FIP3 0.016 0 -10000 0 -10000 0 0
tube morphogenesis 0 0.014 -10000 0 -10000 0 0
ruffle organization 0.034 0.014 -10000 0 -0.22 1 1
regulation of epithelial cell migration 0 0.003 -10000 0 -10000 0 0
PLD2 0.025 0.004 -10000 0 -10000 0 0
PIP5K1A 0.034 0.014 -10000 0 -0.22 1 1
mol:Phosphatidic acid 0.032 0.02 -10000 0 -0.35 1 1
Rac1/GTP 0 0.015 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.008 0.037 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.048 0.034 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones 0.048 0.027 -9999 0 -10000 0 0
YY1/LSF 0.037 0 -9999 0 -10000 0 0
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.039 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.032 0.03 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.038 0.032 -9999 0 -10000 0 0
HDAC1/Smad7 0.031 0.02 -9999 0 -0.34 1 1
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 0.032 0.03 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.056 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.041 0.029 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.007 0.11 -9999 0 -0.53 15 15
GATA1 0.011 0.007 -9999 0 -10000 0 0
Mad/Max 0.022 0.02 -9999 0 -0.36 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.066 0.003 -9999 0 -10000 0 0
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
RBBP4 0.016 0 -9999 0 -10000 0 0
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.026 0.034 -9999 0 -10000 0 0
KAT2B 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.051 0 -9999 0 -10000 0 0
SIN3 complex 0.04 0 -9999 0 -10000 0 0
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 0.016 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 0.045 0.028 -9999 0 -10000 0 0
YY1/HDAC2 0.037 0 -9999 0 -10000 0 0
YY1/HDAC1 0.037 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.056 0 -9999 0 -10000 0 0
PPARG 0.016 0.096 -9999 0 -0.33 22 22
HDAC8/hEST1B 0.032 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.032 0.03 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.02 -9999 0 -0.34 1 1
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.059 0 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.026 0.034 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.035 0 -9999 0 -10000 0 0
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.014 0.031 -9999 0 -0.58 1 1
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.028 -9999 0 -0.51 1 1
STAT3 0.03 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.044 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.044 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.03 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.034 -9999 0 -10000 0 0
histone deacetylation 0.055 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.042 0.028 -9999 0 -10000 0 0
nuclear export -0.031 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.019 0.067 -9999 0 -0.3 5 5
GATA1/HDAC1 0.02 0.005 -9999 0 -10000 0 0
GATA1/HDAC3 0.02 0.033 -9999 0 -10000 0 0
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.005 0.081 -9999 0 -0.36 17 17
SIN3/HDAC complex/Mad/Max 0.055 0.005 -9999 0 -10000 0 0
NuRD Complex 0.065 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.016 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.036 0 -9999 0 -10000 0 0
HDAC complex 0.04 0 -9999 0 -10000 0 0
GATA1/Fog1 0.02 0.005 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.032 0 -9999 0 -10000 0 0
TNF -0.009 0.11 -9999 0 -0.51 17 17
negative regulation of cell growth 0.055 0.005 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.056 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.042 0.036 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.053 0 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.016 0 -9999 0 -10000 0 0
MBD2 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.022 0.023 -9999 0 -0.41 1 1
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.027 0.037 -9999 0 -0.32 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.029 -9999 0 -10000 0 0
NFKBIA 0.029 0.033 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0 -9999 0 -10000 0 0
ARRB2 0.02 0 -9999 0 -10000 0 0
REL 0.009 0.059 -9999 0 -0.54 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.02 -9999 0 -0.34 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
NFKB1 0.026 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.032 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.056 0.028 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K 0.023 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.037 0.033 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.012 0.044 -9999 0 -0.58 2 2
I kappa B alpha/PIK3R1 0.036 0.031 -9999 0 -10000 0 0
cell death 0.054 0.027 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.027 0.037 -9999 0 -0.32 4 4
LCK 0.006 0.073 -9999 0 -0.55 6 6
BCL3 0.014 0.031 -9999 0 -0.58 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.027 0.048 -9999 0 -0.23 12 12
HDAC4 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.033 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.036 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.036 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.03 0.053 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0 -9999 0 -10000 0 0
Ran/GTP 0.032 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.002 0.094 -9999 0 -0.51 12 12
UBE2I 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
PIAS2 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 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
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0 -9999 0 -10000 0 0
AP2 0.023 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.03 0 -9999 0 -10000 0 0
CD4 0.012 0.044 -9999 0 -0.58 2 2
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.032 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.02 0 -9999 0 -10000 0 0
Rac/GTP 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARFIP2 0.014 0 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.03 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.022 0 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.032 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.022 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.012 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.04 0.018 -9999 0 -0.2 2 2
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.013 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.013 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.028 -9999 0 -0.34 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.023 0 -9999 0 -9999 0 0
FBXW11 0.016 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -9999 0 0
CHUK 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.046 0 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAP3K14 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.023 0 -9999 0 -9999 0 0
RELB 0.016 0 -9999 0 -9999 0 0
NFKB2 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.021 0 -9999 0 -9999 0 0
regulation of B cell activation 0.021 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 357 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZF.AA5P TCGA.ZF.AA5H TCGA.ZF.AA56 TCGA.ZF.AA54
109_MAP3K5 0.063 -0.044 0.063 -0.036
47_PPARGC1A 0.016 -0.58 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 -0.58 0.016 -0.58
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0.04 0.04 -0.57 -0.25
30_TGFB1/TGF beta receptor Type II 0.019 0.019 0.019 0.018
84_STAT5B 0.036 0.051 0.0069 -0.013
84_STAT5A 0.036 0.051 0.0069 -0.013
Methods & Data
Input

  • Expression Data Normalization = Normal controls 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/BLCA-TP/11492168/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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