PARADIGM pathway analysis of mRNASeq expression data
Lung Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1Z60NB5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1Z60NB5
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 42 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
Glypican 2 network 193
Angiopoietin receptor Tie2-mediated signaling 153
Aurora B signaling 127
FOXM1 transcription factor network 125
Signaling events mediated by the Hedgehog family 103
Aurora C signaling 77
Endothelins 74
HIF-1-alpha transcription factor network 70
Visual signal transduction: Cones 68
PLK1 signaling events 68
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 515 . 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 ( 515 ).

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
Glypican 2 network 0.3748 193 773 4 -0.2 -0.13 1000 -1000 -0.027 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2971 153 13499 88 -0.62 0.061 1000 -1000 -0.09 -1000
Aurora B signaling 0.2466 127 8518 67 -0.4 0.01 1000 -1000 -0.059 -1000
FOXM1 transcription factor network 0.2427 125 6395 51 -0.55 0.01 1000 -1000 -0.2 -1000
Signaling events mediated by the Hedgehog family 0.2000 103 5401 52 -0.37 0.18 1000 -1000 -0.071 -1000
Aurora C signaling 0.1495 77 544 7 -0.26 0.004 1000 -1000 -0.033 -1000
Endothelins 0.1437 74 7126 96 -0.3 0.025 1000 -1000 -0.073 -1000
HIF-1-alpha transcription factor network 0.1359 70 5331 76 -0.48 0.016 1000 -1000 -0.16 -1000
Visual signal transduction: Cones 0.1320 68 2590 38 -0.17 0.01 1000 -1000 -0.054 -1000
PLK1 signaling events 0.1320 68 5820 85 -0.29 0.057 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 0.1146 59 4888 82 -0.16 0.01 1000 -1000 -0.073 -1000
IL4-mediated signaling events 0.1087 56 5125 91 -0.78 0.51 1000 -1000 -0.18 -1000
Fc-epsilon receptor I signaling in mast cells 0.1029 53 5187 97 -0.15 0.028 1000 -1000 -0.072 -1000
amb2 Integrin signaling 0.1010 52 4286 82 -0.46 0.01 1000 -1000 -0.073 -1000
Signaling mediated by p38-alpha and p38-beta 0.1010 52 2303 44 -0.12 0.01 1000 -1000 -0.047 -1000
BMP receptor signaling 0.0990 51 4175 81 -0.34 0.027 1000 -1000 -0.075 -1000
FOXA2 and FOXA3 transcription factor networks 0.0951 49 2266 46 -0.5 0.015 1000 -1000 -0.094 -1000
TCGA08_retinoblastoma 0.0932 48 389 8 -0.15 0.049 1000 -1000 -0.017 -1000
Osteopontin-mediated events 0.0913 47 1792 38 -0.35 0.011 1000 -1000 -0.087 -1000
Glucocorticoid receptor regulatory network 0.0874 45 5139 114 -0.41 0.24 1000 -1000 -0.072 -1000
Visual signal transduction: Rods 0.0874 45 2355 52 -0.15 0.01 1000 -1000 -0.066 -1000
Syndecan-1-mediated signaling events 0.0854 44 1509 34 -0.33 0.01 1000 -1000 -0.053 -1000
TCGA08_p53 0.0854 44 308 7 -0.1 0.052 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 0.0738 38 457 12 -0.12 0.012 1000 -1000 -0.018 -1000
Arf6 signaling events 0.0738 38 2373 62 -0.19 0.012 1000 -1000 -0.056 -1000
p75(NTR)-mediated signaling 0.0738 38 4774 125 -0.3 0.018 1000 -1000 -0.085 -1000
Canonical Wnt signaling pathway 0.0718 37 1919 51 -0.34 0.15 1000 -1000 -0.053 -1000
Thromboxane A2 receptor signaling 0.0699 36 3851 105 -0.09 0.028 1000 -1000 -0.061 -1000
Glypican 1 network 0.0699 36 1749 48 -0.12 0.017 1000 -1000 -0.045 -1000
Effects of Botulinum toxin 0.0660 34 901 26 -0.089 0.01 1000 -1000 -0.054 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0660 34 4100 120 -0.26 0.2 1000 -1000 -0.062 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0641 33 1746 52 -0.25 0.042 1000 -1000 -0.046 -1000
Integrins in angiogenesis 0.0641 33 2774 84 -0.35 0.024 1000 -1000 -0.08 -1000
Ephrin B reverse signaling 0.0621 32 1574 48 -0.095 0.054 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.0621 32 682 21 -0.09 0.01 1000 -1000 -0.06 -1000
ErbB4 signaling events 0.0602 31 2152 69 -0.19 0.21 1000 -1000 -0.074 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0583 30 2095 68 -0.15 0.036 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.0583 30 1854 60 -0.28 0.015 1000 -1000 -0.16 -1000
Aurora A signaling 0.0544 28 1710 60 -0.29 0.015 1000 -1000 -0.051 -1000
Syndecan-3-mediated signaling events 0.0544 28 1001 35 -0.21 0.01 1000 -1000 -0.053 -1000
IL6-mediated signaling events 0.0544 28 2173 75 -0.33 0.041 1000 -1000 -0.085 -1000
Presenilin action in Notch and Wnt signaling 0.0524 27 1683 61 -0.34 0.02 1000 -1000 -0.067 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0485 25 839 33 -0.14 0.024 1000 -1000 -0.046 -1000
Reelin signaling pathway 0.0466 24 1345 56 -0.096 0.01 1000 -1000 -0.063 -1000
Nongenotropic Androgen signaling 0.0466 24 1250 52 -0.062 0.01 1000 -1000 -0.049 -1000
PDGFR-alpha signaling pathway 0.0447 23 1023 44 -0.31 0.027 1000 -1000 -0.052 -1000
Class IB PI3K non-lipid kinase events 0.0427 22 66 3 -0.012 -1000 1000 -1000 -0.011 -1000
Wnt signaling 0.0408 21 150 7 -0.057 0.009 1000 -1000 -0.028 -1000
HIF-2-alpha transcription factor network 0.0388 20 867 43 -0.12 0.046 1000 -1000 -0.09 -1000
Regulation of Androgen receptor activity 0.0388 20 1425 70 -0.26 0.026 1000 -1000 -0.06 -1000
Syndecan-2-mediated signaling events 0.0369 19 1316 69 -0.097 0.031 1000 -1000 -0.051 -1000
Coregulation of Androgen receptor activity 0.0350 18 1391 76 -0.14 0.018 1000 -1000 -0.042 -1000
PLK2 and PLK4 events 0.0350 18 56 3 -0.017 -0.003 1000 -1000 -0.02 -1000
Nectin adhesion pathway 0.0350 18 1145 63 -0.045 0.01 1000 -1000 -0.06 -1000
Syndecan-4-mediated signaling events 0.0350 18 1248 67 -0.16 0.016 1000 -1000 -0.076 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0311 16 875 54 -0.13 0.021 1000 -1000 -0.081 -1000
IL1-mediated signaling events 0.0291 15 969 62 -0.15 0.048 1000 -1000 -0.072 -1000
FAS signaling pathway (CD95) 0.0291 15 726 47 -0.25 0.011 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.0291 15 1578 102 -0.12 0.03 1000 -1000 -0.073 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0291 15 1207 78 -0.042 0.036 1000 -1000 -0.072 -1000
Caspase cascade in apoptosis 0.0272 14 1037 74 -0.038 0.031 1000 -1000 -0.05 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0272 14 497 34 -0.041 0.01 1000 -1000 -0.05 -1000
IL12-mediated signaling events 0.0272 14 1276 87 -0.095 0.039 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 0.0272 14 387 26 -0.057 0.01 1000 -1000 -0.074 -1000
Signaling events mediated by PTP1B 0.0272 14 1109 76 -0.092 0.016 1000 -1000 -0.068 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0272 14 1763 125 -0.31 0.034 1000 -1000 -0.087 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0252 13 1156 85 -0.045 0.029 1000 -1000 -0.06 -1000
Signaling events mediated by HDAC Class III 0.0252 13 548 40 -0.12 0.018 1000 -1000 -0.032 -1000
S1P1 pathway 0.0252 13 470 36 -0.058 0.012 1000 -1000 -0.051 -1000
EPHB forward signaling 0.0252 13 1117 85 -0.066 0.049 1000 -1000 -0.079 -1000
Signaling events mediated by PRL 0.0252 13 443 34 -0.18 0.022 1000 -1000 -0.033 -1000
BARD1 signaling events 0.0214 11 683 57 -0.18 0.03 1000 -1000 -0.051 -1000
Ephrin A reverse signaling 0.0214 11 82 7 -0.01 0.008 1000 -1000 -0.026 -1000
S1P5 pathway 0.0214 11 200 17 -0.031 0.029 1000 -1000 -0.047 -1000
TCR signaling in naïve CD8+ T cells 0.0214 11 1102 93 -0.072 0.041 1000 -1000 -0.071 -1000
Calcium signaling in the CD4+ TCR pathway 0.0214 11 351 31 -0.1 0.012 1000 -1000 -0.078 -1000
BCR signaling pathway 0.0214 11 1145 99 -0.14 0.025 1000 -1000 -0.076 -1000
ErbB2/ErbB3 signaling events 0.0194 10 668 65 -0.1 0.02 1000 -1000 -0.062 -1000
Regulation of p38-alpha and p38-beta 0.0194 10 565 54 -0.08 0.017 1000 -1000 -0.055 -1000
S1P4 pathway 0.0194 10 258 25 -0.031 0.011 1000 -1000 -0.045 -1000
IL2 signaling events mediated by STAT5 0.0175 9 206 22 -0.11 0.054 1000 -1000 -0.052 -1000
Regulation of nuclear SMAD2/3 signaling 0.0155 8 1199 136 -0.1 0.054 1000 -1000 -0.069 -1000
Plasma membrane estrogen receptor signaling 0.0155 8 764 86 -0.036 0.03 1000 -1000 -0.07 -1000
IL27-mediated signaling events 0.0136 7 386 51 -0.11 0.011 1000 -1000 -0.072 -1000
Regulation of Telomerase 0.0136 7 775 102 -0.092 0.03 1000 -1000 -0.082 -1000
Ras signaling in the CD4+ TCR pathway 0.0136 7 129 17 -0.014 0.023 1000 -1000 -0.037 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0117 6 184 28 -0.031 0.021 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 0.0117 6 235 39 -0.046 0.015 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0117 6 434 65 -0.18 0.053 1000 -1000 -0.06 -1000
Signaling mediated by p38-gamma and p38-delta 0.0117 6 94 15 0 0.022 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 0.0117 6 383 58 -0.17 0.031 1000 -1000 -0.061 -1000
Arf6 trafficking events 0.0117 6 475 71 -0.081 0.034 1000 -1000 -0.066 -1000
Insulin Pathway 0.0117 6 489 74 -0.15 0.029 1000 -1000 -0.072 -1000
VEGFR1 specific signals 0.0117 6 388 56 -0.31 0.043 1000 -1000 -0.065 -1000
p38 MAPK signaling pathway 0.0117 6 298 44 -0.08 0.026 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class II 0.0097 5 410 75 -0.044 0.027 1000 -1000 -0.053 -1000
JNK signaling in the CD4+ TCR pathway 0.0097 5 93 17 -0.013 0.031 1000 -1000 -0.059 -1000
Ceramide signaling pathway 0.0097 5 403 76 -0.09 0.036 1000 -1000 -0.058 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0097 5 453 83 -0.063 0.039 1000 -1000 -0.07 -1000
FoxO family signaling 0.0097 5 323 64 -0.12 0.055 1000 -1000 -0.076 -1000
IL2 signaling events mediated by PI3K 0.0097 5 293 58 -0.15 0.065 1000 -1000 -0.069 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0097 5 411 74 -0.11 0.059 1000 -1000 -0.076 -1000
Class I PI3K signaling events 0.0097 5 418 73 -0.08 0.022 1000 -1000 -0.06 -1000
IFN-gamma pathway 0.0078 4 337 68 -0.08 0.046 1000 -1000 -0.088 -1000
Signaling events mediated by HDAC Class I 0.0078 4 516 104 -0.049 0.043 1000 -1000 -0.052 -1000
TCGA08_rtk_signaling 0.0078 4 111 26 -0.024 0.036 1000 -1000 -0.021 -1000
Circadian rhythm pathway 0.0058 3 73 22 -0.026 0.034 1000 -1000 -0.071 -1000
Arf6 downstream pathway 0.0058 3 168 43 -0.036 0.025 1000 -1000 -0.032 -1000
TRAIL signaling pathway 0.0058 3 149 48 -0.009 0.039 1000 -1000 -0.057 -1000
IGF1 pathway 0.0058 3 225 57 -0.037 0.04 1000 -1000 -0.075 -1000
S1P3 pathway 0.0058 3 155 42 -0.03 0.021 1000 -1000 -0.054 -1000
Rapid glucocorticoid signaling 0.0058 3 63 20 -0.007 0.01 1000 -1000 -0.034 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0039 2 119 45 -0.011 0.06 1000 -1000 -0.081 -1000
E-cadherin signaling in the nascent adherens junction 0.0039 2 183 76 -0.037 0.049 1000 -1000 -0.069 -1000
PDGFR-beta signaling pathway 0.0039 2 227 97 -0.036 0.048 1000 -1000 -0.073 -1000
Canonical NF-kappaB pathway 0.0019 1 44 39 -0.013 0.066 1000 -1000 -0.07 -1000
a4b1 and a4b7 Integrin signaling 0.0019 1 8 5 -0.002 0.009 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0019 1 89 55 -0.005 0.058 1000 -1000 -0.075 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0019 1 41 37 -0.005 0.037 1000 -1000 -0.052 -1000
ceramide signaling pathway 0.0019 1 57 49 -0.011 0.039 1000 -1000 -0.042 -1000
E-cadherin signaling events 0.0019 1 8 5 -0.002 0.01 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 12 23 -0.003 0.036 1000 -1000 -0.059 -1000
Insulin-mediated glucose transport 0.0000 0 25 32 -0.003 0.034 1000 -1000 -0.064 -1000
mTOR signaling pathway 0.0000 0 17 53 -0.001 0.026 1000 -1000 -0.048 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 29 68 -0.033 0.045 1000 -1000 -0.05 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 19 36 -0.003 0.018 1000 -1000 -0.062 -1000
Atypical NF-kappaB pathway 0.0000 0 17 31 -0.002 0.038 1000 -1000 -0.052 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 11 27 -0.001 0.023 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 0.0000 0 29 43 -0.007 0.037 1000 -1000 -0.056 -1000
Arf1 pathway 0.0000 0 20 54 -0.006 0.024 1000 -1000 -0.042 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.01 1000 -1000 -0.052 -1000
Total NA 3099 179615 7203 -18 -1000 131000 -131000 -8.2 -131000
Glypican 2 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
MDK -0.15 0.24 -9999 0 -0.51 157 157
GPC2 -0.13 0.23 -9999 0 -0.51 136 136
GPC2/Midkine -0.2 0.23 -9999 0 -0.43 240 240
neuron projection morphogenesis -0.2 0.23 -9999 0 -0.43 240 240
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.43 0.52 -10000 0 -0.95 248 248
NCK1/PAK1/Dok-R -0.21 0.22 -10000 0 -0.44 248 248
NCK1/Dok-R -0.56 0.61 -10000 0 -1.2 248 248
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.061 0.1 0.24 128 -10000 0 128
RELA 0.01 0 -10000 0 -10000 0 0
SHC1 0.003 0.033 -10000 0 -0.51 2 2
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.012 0.2 0.25 124 -0.51 53 177
TNIP2 0.01 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.5 0.55 -10000 0 -1 248 248
FN1 0.005 0.05 -10000 0 -0.5 5 5
PLD2 -0.54 0.67 -10000 0 -1.2 248 248
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB14 -0.025 0.13 -10000 0 -0.51 35 35
ELK1 -0.47 0.58 -10000 0 -1 248 248
GRB7 0.004 0.055 -10000 0 -0.5 6 6
PAK1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.53 0.59 -10000 0 -1.1 248 248
CDKN1A -0.29 0.35 -10000 0 -0.65 245 245
ITGA5 0.008 0.032 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.56 0.61 -10000 0 -1.2 248 248
CRK 0.01 0 -10000 0 -10000 0 0
mol:NO -0.3 0.38 -10000 0 -0.68 248 248
PLG -0.55 0.67 -10000 0 -1.2 248 248
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.41 0.48 -10000 0 -0.9 248 248
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.005 0.023 -10000 0 -0.5 1 1
ANGPT2 -0.22 0.3 -10000 0 -0.62 156 156
BMX -0.62 0.7 -10000 0 -1.3 248 248
ANGPT1 -0.32 0.55 -10000 0 -1.3 128 128
tube development -0.33 0.4 -10000 0 -0.74 246 246
ANGPT4 -0.26 0.25 -10000 0 -0.5 264 264
response to hypoxia -0.03 0.035 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.58 0.7 -10000 0 -1.3 248 248
alpha5/beta1 Integrin -0.001 0.022 -10000 0 -0.36 2 2
FGF2 -0.065 0.18 -10000 0 -0.5 74 74
STAT5A (dimer) -0.38 0.46 -10000 0 -0.85 246 246
mol:L-citrulline -0.3 0.38 -10000 0 -0.68 248 248
AGTR1 -0.16 0.24 -10000 0 -0.5 167 167
MAPK14 -0.57 0.68 -10000 0 -1.2 248 248
Tie2/SHP2 -0.49 0.55 -10000 0 -1.1 218 218
TEK -0.53 0.62 -10000 0 -1.2 218 218
RPS6KB1 -0.41 0.5 -10000 0 -0.91 248 248
Angiotensin II/AT1 -0.11 0.17 -10000 0 -0.36 167 167
Tie2/Ang1/GRB2 -0.57 0.7 -10000 0 -1.2 248 248
MAPK3 -0.48 0.6 -10000 0 -1.1 248 248
MAPK1 -0.48 0.6 -10000 0 -1.1 248 248
Tie2/Ang1/GRB7 -0.57 0.7 -10000 0 -1.2 248 248
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.54 0.67 -10000 0 -1.2 248 248
PI3K -0.51 0.61 -10000 0 -1.1 248 248
FES -0.57 0.67 -10000 0 -1.2 248 248
Crk/Dok-R -0.56 0.61 -10000 0 -1.2 248 248
Tie2/Ang1/ABIN2 -0.57 0.7 -10000 0 -1.2 248 248
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.37 0.46 -10000 0 -0.84 248 248
STAT5A 0.009 0.022 -10000 0 -0.5 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.41 0.5 -10000 0 -0.91 248 248
Tie2/Ang2 -0.49 0.57 -10000 0 -1.1 246 246
Tie2/Ang1 -0.61 0.76 -10000 0 -1.3 248 248
FOXO1 -0.38 0.46 -10000 0 -0.84 248 248
ELF1 -0.029 0.051 -10000 0 -10000 0 0
ELF2 -0.55 0.68 -10000 0 -1.2 248 248
mol:Choline -0.51 0.62 -10000 0 -1.1 248 248
cell migration -0.12 0.12 -10000 0 -0.24 248 248
FYN -0.39 0.46 -10000 0 -0.86 246 246
DOK2 -0.033 0.14 -10000 0 -0.5 43 43
negative regulation of cell cycle -0.26 0.32 -10000 0 -0.58 246 246
ETS1 -0.049 0.1 -10000 0 -0.26 22 22
PXN -0.32 0.4 -10000 0 -0.73 248 248
ITGB1 0.01 0 -10000 0 -10000 0 0
NOS3 -0.35 0.43 -10000 0 -0.79 248 248
RAC1 0.01 0 -10000 0 -10000 0 0
TNF -0.067 0.14 -10000 0 -0.39 40 40
MAPKKK cascade -0.51 0.62 -10000 0 -1.1 248 248
RASA1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.58 0.69 -10000 0 -1.2 248 248
NCK1 0.01 0 -10000 0 -10000 0 0
vasculogenesis -0.26 0.34 -10000 0 -0.6 248 248
mol:Phosphatidic acid -0.51 0.62 -10000 0 -1.1 248 248
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.3 0.38 -10000 0 -0.68 248 248
Rac1/GTP -0.41 0.42 -10000 0 -0.84 248 248
MMP2 -0.55 0.67 -10000 0 -1.2 248 248
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 -0.14 0.16 -9999 0 -0.32 212 212
STMN1 -0.18 0.19 -9999 0 -0.36 267 267
Aurora B/RasGAP/Survivin -0.3 0.26 -9999 0 -0.5 320 320
Chromosomal passenger complex/Cul3 protein complex -0.13 0.14 -9999 0 -0.29 165 165
BIRC5 -0.29 0.26 -9999 0 -0.52 297 297
DES -0.38 0.37 -9999 0 -0.74 260 260
Aurora C/Aurora B/INCENP -0.14 0.14 -9999 0 -0.27 271 271
Aurora B/TACC1 -0.16 0.17 -9999 0 -0.31 274 274
Aurora B/PP2A -0.18 0.18 -9999 0 -0.35 267 267
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.032 0.044 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.004 -9999 0 -10000 0 0
NDC80 -0.33 0.31 -9999 0 -0.58 301 301
Cul3 protein complex -0.015 0.067 -9999 0 -0.3 26 26
KIF2C -0.12 0.11 -9999 0 -0.21 276 276
PEBP1 0.004 0.005 -9999 0 -10000 0 0
KIF20A -0.27 0.26 -9999 0 -0.51 277 277
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.18 0.18 -9999 0 -0.35 267 267
SEPT1 0.009 0.022 -9999 0 -0.5 1 1
SMC2 0.01 0 -9999 0 -10000 0 0
SMC4 0.01 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.059 0.072 -9999 0 -10000 0 0
PSMA3 0.01 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.003 -9999 0 -10000 0 0
H3F3B -0.086 0.097 -9999 0 -0.18 267 267
AURKB -0.26 0.26 -9999 0 -0.51 267 267
AURKC 0.004 0.055 -9999 0 -0.5 6 6
CDCA8 -0.17 0.25 -9999 0 -0.52 170 170
cytokinesis -0.22 0.2 -9999 0 -0.42 223 223
Aurora B/Septin1 -0.2 0.2 -9999 0 -0.43 190 190
AURKA -0.091 0.21 -9999 0 -0.51 100 100
INCENP 0.003 0.007 -9999 0 -10000 0 0
KLHL13 -0.014 0.11 -9999 0 -0.5 24 24
BUB1 -0.13 0.23 -9999 0 -0.51 133 133
hSgo1/Aurora B/Survivin -0.4 0.35 -9999 0 -0.64 327 327
EVI5 0.009 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.21 0.22 -9999 0 -0.46 180 180
SGOL1 -0.23 0.26 -9999 0 -0.51 237 237
CENPA -0.16 0.15 -9999 0 -0.3 260 260
NCAPG -0.2 0.26 -9999 0 -0.51 213 213
Aurora B/HC8 Proteasome -0.18 0.18 -9999 0 -0.35 267 267
NCAPD2 0.009 0.023 -9999 0 -0.51 1 1
Aurora B/PP1-gamma -0.18 0.18 -9999 0 -0.35 267 267
RHOA 0.01 0 -9999 0 -10000 0 0
NCAPH -0.21 0.26 -9999 0 -0.51 223 223
NPM1 -0.081 0.079 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
KLHL9 0.007 0.039 -9999 0 -0.5 3 3
mitotic prometaphase -0.008 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.18 -9999 0 -0.35 267 267
PPP1CC 0.01 0 -9999 0 -10000 0 0
Centraspindlin -0.23 0.24 -9999 0 -0.46 226 226
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.081 0.079 -9999 0 -10000 0 0
MYLK -0.098 0.12 -9999 0 -0.2 270 270
KIF23 -0.1 0.21 -9999 0 -0.52 108 108
VIM -0.18 0.19 -9999 0 -0.36 267 267
RACGAP1 0 0.052 -9999 0 -0.52 5 5
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.081 0.079 -9999 0 -10000 0 0
Chromosomal passenger complex -0.19 0.19 -9999 0 -0.36 257 257
Chromosomal passenger complex/EVI5 -0.32 0.31 -9999 0 -0.62 256 256
TACC1 -0.013 0.1 -9999 0 -0.5 23 23
PPP2R5D 0.01 0 -9999 0 -10000 0 0
CUL3 0.01 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.42 0.53 -9999 0 -1 156 156
PLK1 -0.15 0.19 -9999 0 -10000 0 0
BIRC5 -0.19 0.2 -9999 0 -10000 0 0
HSPA1B -0.42 0.53 -9999 0 -1 154 154
MAP2K1 -0.002 0.034 -9999 0 -10000 0 0
BRCA2 -0.42 0.53 -9999 0 -1 153 153
FOXM1 -0.54 0.68 -9999 0 -1.3 183 183
XRCC1 -0.42 0.53 -9999 0 -1 153 153
FOXM1B/p19 -0.5 0.48 -9999 0 -1 181 181
Cyclin D1/CDK4 -0.43 0.5 -9999 0 -0.98 165 165
CDC2 -0.45 0.56 -9999 0 -1.1 181 181
TGFA -0.42 0.49 -9999 0 -0.96 158 158
SKP2 -0.43 0.53 -9999 0 -1.1 146 146
CCNE1 -0.19 0.26 -9999 0 -0.52 190 190
CKS1B -0.43 0.54 -9999 0 -1.1 158 158
RB1 -0.22 0.18 -9999 0 -0.47 16 16
FOXM1C/SP1 -0.48 0.6 -9999 0 -1.2 176 176
AURKB -0.17 0.2 -9999 0 -0.36 144 144
CENPF -0.48 0.58 -9999 0 -1.1 173 173
CDK4 0.001 0.053 -9999 0 -0.53 5 5
MYC -0.37 0.47 -9999 0 -0.9 162 162
CHEK2 -0.007 0.064 -9999 0 -0.56 5 5
ONECUT1 -0.47 0.54 -9999 0 -1.1 177 177
CDKN2A -0.14 0.23 -9999 0 -0.5 152 152
LAMA4 -0.43 0.54 -9999 0 -1.1 156 156
FOXM1B/HNF6 -0.55 0.63 -9999 0 -1.2 180 180
FOS -0.44 0.56 -9999 0 -1.1 157 157
SP1 0.01 0.001 -9999 0 -10000 0 0
CDC25B -0.42 0.53 -9999 0 -1 156 156
response to radiation -0.013 0.031 -9999 0 -10000 0 0
CENPB -0.42 0.53 -9999 0 -1 156 156
CENPA -0.5 0.59 -9999 0 -1.1 197 197
NEK2 -0.5 0.58 -9999 0 -1.1 205 205
HIST1H2BA -0.43 0.53 -9999 0 -1 159 159
CCNA2 -0.12 0.22 -9999 0 -0.52 119 119
EP300 0.01 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.5 0.62 -9999 0 -1.2 167 167
CCNB2 -0.49 0.58 -9999 0 -1.1 196 196
CCNB1 -0.47 0.58 -9999 0 -1.1 168 168
ETV5 -0.43 0.54 -9999 0 -1.1 147 147
ESR1 -0.44 0.54 -9999 0 -1.1 161 161
CCND1 -0.44 0.51 -9999 0 -1 167 167
GSK3A 0.002 0.027 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.18 0.25 -9999 0 -0.44 220 220
CDK2 0.006 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.016 0.037 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.53 0.49 -9999 0 -1.1 189 189
GAS1 -0.44 0.54 -9999 0 -1.1 166 166
MMP2 -0.42 0.53 -9999 0 -1 159 159
RB1/FOXM1C -0.46 0.54 -9999 0 -1.1 182 182
CREBBP 0.01 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.21 0.25 -10000 0 -0.66 91 91
IHH -0.31 0.27 -10000 0 -0.54 296 296
SHH Np/Cholesterol/GAS1 -0.043 0.1 -10000 0 -0.28 77 77
LRPAP1 0.01 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.042 0.1 0.28 77 -10000 0 77
SMO/beta Arrestin2 -0.21 0.22 -10000 0 -0.51 105 105
SMO -0.23 0.23 -10000 0 -0.54 106 106
AKT1 -0.095 0.11 -10000 0 -0.3 21 21
ARRB2 0.01 0 -10000 0 -10000 0 0
BOC 0.008 0.032 -10000 0 -0.5 2 2
ADRBK1 0.01 0 -10000 0 -10000 0 0
heart looping -0.23 0.23 -10000 0 -0.53 106 106
STIL -0.2 0.22 -10000 0 -0.53 112 112
DHH N/PTCH2 -0.026 0.092 -10000 0 -0.35 38 38
DHH N/PTCH1 -0.19 0.2 -10000 0 -0.5 95 95
PIK3CA 0.01 0 -10000 0 -10000 0 0
DHH -0.027 0.13 -10000 0 -0.5 37 37
PTHLH -0.28 0.29 -10000 0 -0.77 91 91
determination of left/right symmetry -0.23 0.23 -10000 0 -0.53 106 106
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
skeletal system development -0.28 0.29 -10000 0 -0.76 91 91
IHH N/Hhip -0.37 0.26 -10000 0 -0.5 386 386
DHH N/Hhip -0.22 0.2 -10000 0 -0.38 293 293
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.23 0.23 -10000 0 -0.53 106 106
pancreas development -0.27 0.25 -10000 0 -0.5 280 280
HHAT 0.008 0.032 -10000 0 -0.5 2 2
PI3K -0.001 0.016 -10000 0 -0.35 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.005 0.086 -10000 0 -0.5 15 15
somite specification -0.23 0.23 -10000 0 -0.53 106 106
SHH Np/Cholesterol/PTCH1 -0.18 0.2 -10000 0 -0.47 115 115
SHH Np/Cholesterol/PTCH2 -0.035 0.09 -10000 0 -0.26 69 69
SHH Np/Cholesterol/Megalin -0.11 0.15 -10000 0 -0.3 190 190
SHH -0.032 0.13 -10000 0 -0.35 68 68
catabolic process -0.2 0.2 -10000 0 -0.53 81 81
SMO/Vitamin D3 -0.2 0.22 -10000 0 -0.53 108 108
SHH Np/Cholesterol/Hhip -0.18 0.17 -10000 0 -0.3 302 302
LRP2 -0.13 0.23 -10000 0 -0.5 144 144
receptor-mediated endocytosis -0.26 0.23 -10000 0 -0.56 155 155
SHH Np/Cholesterol/BOC -0.036 0.09 -10000 0 -0.26 70 70
SHH Np/Cholesterol/CDO -0.042 0.1 -10000 0 -0.28 76 76
mesenchymal cell differentiation 0.18 0.16 0.3 302 -10000 0 302
mol:Vitamin D3 -0.18 0.2 -10000 0 -0.48 115 115
IHH N/PTCH2 -0.18 0.16 -10000 0 -0.32 296 296
CDON -0.004 0.083 -10000 0 -0.5 14 14
IHH N/PTCH1 -0.2 0.21 -10000 0 -0.54 81 81
Megalin/LRPAP1 -0.099 0.16 -10000 0 -0.35 144 144
PTCH2 0.009 0.022 -10000 0 -0.5 1 1
SHH Np/Cholesterol -0.036 0.092 -10000 0 -0.27 68 68
PTCH1 -0.2 0.2 -10000 0 -0.53 81 81
HHIP -0.27 0.25 -10000 0 -0.5 280 280
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.01 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.14 0.14 -9999 0 -0.27 271 271
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.041 0.039 -9999 0 -10000 0 0
AURKB -0.26 0.26 -9999 0 -0.51 267 267
AURKC 0.004 0.055 -9999 0 -0.5 6 6
Endothelins

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
AKT1 -0.048 0.2 0.26 1 -0.45 64 65
PTK2B 0.008 0.032 -10000 0 -0.5 2 2
mol:Ca2+ -0.053 0.28 -10000 0 -0.95 42 42
EDN1 -0.066 0.23 -10000 0 -0.54 82 82
EDN3 -0.14 0.22 -10000 0 -0.5 142 142
EDN2 -0.14 0.23 -10000 0 -0.51 147 147
HRAS/GDP -0.079 0.2 -10000 0 -0.48 66 66
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.005 0.13 -10000 0 -0.39 29 29
ADCY4 -0.065 0.17 -10000 0 -0.47 48 48
ADCY5 -0.088 0.2 -10000 0 -0.51 67 67
ADCY6 -0.054 0.16 -10000 0 -0.45 47 47
ADCY7 -0.055 0.16 -10000 0 -0.45 46 46
ADCY1 -0.059 0.16 -10000 0 -0.46 46 46
ADCY2 -0.083 0.19 -10000 0 -0.49 58 58
ADCY3 -0.054 0.16 -10000 0 -0.48 38 38
ADCY8 -0.16 0.19 -10000 0 -0.44 103 103
ADCY9 -0.059 0.16 -10000 0 -0.46 46 46
arachidonic acid secretion -0.065 0.2 -10000 0 -0.5 63 63
ETB receptor/Endothelin-1/Gq/GTP -0.16 0.2 -10000 0 -0.39 139 139
GNAO1 0.003 0.06 -10000 0 -0.51 7 7
HRAS 0.009 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.025 0.22 0.23 183 -0.48 43 226
ETA receptor/Endothelin-1/Gs/GTP 0.015 0.22 0.21 180 -0.41 68 248
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.097 0.26 -10000 0 -0.47 128 128
EDNRB -0.28 0.25 -10000 0 -0.5 296 296
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.057 0.22 -10000 0 -0.6 45 45
CYSLTR1 -0.063 0.23 -10000 0 -0.64 47 47
SLC9A1 -0.022 0.11 0.18 1 -0.29 34 35
mol:GDP -0.091 0.21 -10000 0 -0.5 72 72
SLC9A3 -0.3 0.36 -10000 0 -0.54 303 303
RAF1 -0.087 0.2 -10000 0 -0.52 62 62
JUN -0.019 0.19 -10000 0 -0.65 28 28
JAK2 -0.05 0.2 0.26 1 -0.46 65 66
mol:IP3 -0.089 0.18 -10000 0 -0.41 74 74
ETA receptor/Endothelin-1 -0.021 0.28 0.26 184 -0.51 73 257
PLCB1 0.007 0.032 -10000 0 -0.5 2 2
PLCB2 0 0.071 -10000 0 -0.5 10 10
ETA receptor/Endothelin-3 -0.095 0.18 -10000 0 -0.37 144 144
FOS -0.078 0.24 -10000 0 -0.88 32 32
Gai/GDP -0.008 0.082 -10000 0 -0.58 3 3
CRK 0.01 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.25 -10000 0 -0.56 103 103
BCAR1 0.009 0.022 -10000 0 -0.5 1 1
PRKCB1 -0.085 0.17 -10000 0 -0.4 74 74
GNAQ 0.01 0.023 -10000 0 -0.5 1 1
GNAZ -0.031 0.14 -10000 0 -0.5 41 41
GNAL -0.002 0.077 -10000 0 -0.5 12 12
Gs family/GDP -0.11 0.17 -10000 0 -0.45 76 76
ETA receptor/Endothelin-1/Gq/GTP -0.009 0.14 -10000 0 -0.35 47 47
MAPK14 -0.12 0.18 -10000 0 -0.42 84 84
TRPC6 -0.06 0.31 -10000 0 -1 42 42
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.19 -10000 0 -0.4 111 111
ETB receptor/Endothelin-2 -0.3 0.23 -10000 0 -0.43 350 350
ETB receptor/Endothelin-3 -0.29 0.22 -10000 0 -0.43 353 353
ETB receptor/Endothelin-1 -0.25 0.26 -10000 0 -0.44 304 304
MAPK3 -0.085 0.24 -10000 0 -0.78 40 40
MAPK1 -0.085 0.24 -10000 0 -0.79 39 39
Rac1/GDP -0.079 0.2 -10000 0 -0.48 65 65
cAMP biosynthetic process -0.1 0.19 -10000 0 -0.46 77 77
MAPK8 -0.03 0.21 -10000 0 -0.6 44 44
SRC 0.01 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.15 0.18 -10000 0 -0.39 123 123
p130Cas/CRK/Src/PYK2 -0.09 0.23 -10000 0 -0.59 65 65
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.079 0.2 -10000 0 -0.48 65 65
COL1A2 -0.2 0.28 -10000 0 -0.64 108 108
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.099 0.18 -10000 0 -0.38 149 149
mol:DAG -0.089 0.18 -10000 0 -0.41 74 74
MAP2K2 -0.081 0.21 -10000 0 -0.6 50 50
MAP2K1 -0.081 0.21 -10000 0 -0.62 47 47
EDNRA 0.011 0.1 0.2 1 -0.37 9 10
positive regulation of muscle contraction -0.035 0.17 0.23 1 -0.48 37 38
Gq family/GDP -0.076 0.17 -10000 0 -0.5 44 44
HRAS/GTP -0.094 0.2 -10000 0 -0.47 69 69
PRKCH -0.079 0.17 -10000 0 -0.46 48 48
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.08 0.17 -10000 0 -0.46 50 50
PRKCB -0.086 0.19 -10000 0 -0.49 54 54
PRKCE -0.082 0.18 -10000 0 -0.47 52 52
PRKCD -0.08 0.17 -10000 0 -0.46 49 49
PRKCG -0.11 0.19 -10000 0 -0.46 78 78
regulation of vascular smooth muscle contraction -0.092 0.28 -10000 0 -1 32 32
PRKCQ -0.12 0.21 -10000 0 -0.45 102 102
PLA2G4A -0.072 0.22 -10000 0 -0.54 63 63
GNA14 -0.003 0.084 -10000 0 -0.51 14 14
GNA15 0.01 0.004 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
GNA11 0.008 0.032 -10000 0 -0.5 2 2
Rac1/GTP 0.025 0.22 0.23 183 -0.48 43 226
MMP1 -0.22 0.2 -10000 0 -0.37 287 287
HIF-1-alpha transcription factor network

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
PKM2 -0.33 0.46 -9999 0 -1.1 95 95
HDAC7 0.008 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.27 0.36 -9999 0 -0.83 92 92
SMAD4 0.011 0.003 -9999 0 -10000 0 0
ID2 -0.33 0.46 -9999 0 -1.1 96 96
AP1 -0.023 0.085 -9999 0 -0.36 30 30
ABCG2 -0.35 0.49 -9999 0 -1.1 103 103
HIF1A -0.04 0.071 -9999 0 -10000 0 0
TFF3 -0.38 0.51 -9999 0 -1.1 117 117
GATA2 -0.033 0.14 -9999 0 -0.51 41 41
AKT1 -0.045 0.08 -9999 0 -10000 0 0
response to hypoxia -0.062 0.083 -9999 0 -0.24 8 8
MCL1 -0.33 0.46 -9999 0 -1.1 96 96
NDRG1 -0.33 0.46 -9999 0 -1.1 96 96
SERPINE1 -0.33 0.47 -9999 0 -1.1 98 98
FECH -0.33 0.46 -9999 0 -1.1 96 96
FURIN -0.33 0.47 -9999 0 -1.1 97 97
NCOA2 0.006 0.05 -9999 0 -0.5 5 5
EP300 -0.045 0.11 -9999 0 -0.33 13 13
HMOX1 -0.33 0.46 -9999 0 -1.1 96 96
BHLHE40 -0.33 0.46 -9999 0 -1 99 99
BHLHE41 -0.33 0.47 -9999 0 -1.1 99 99
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.038 0.07 -9999 0 -0.4 4 4
ENG -0.011 0.1 -9999 0 -0.58 6 6
JUN 0.005 0.039 -9999 0 -0.5 3 3
RORA -0.33 0.47 -9999 0 -1.1 98 98
ABCB1 -0.12 0.25 -9999 0 -1.2 23 23
TFRC -0.33 0.46 -9999 0 -1 101 101
CXCR4 -0.33 0.46 -9999 0 -1 101 101
TF -0.38 0.51 -9999 0 -1.1 121 121
CITED2 -0.33 0.46 -9999 0 -1 103 103
HIF1A/ARNT -0.37 0.55 -9999 0 -1.2 110 110
LDHA -0.045 0.058 -9999 0 -0.44 2 2
ETS1 -0.33 0.46 -9999 0 -1.1 95 95
PGK1 -0.33 0.46 -9999 0 -1.1 96 96
NOS2 -0.35 0.49 -9999 0 -1.1 114 114
ITGB2 -0.33 0.47 -9999 0 -1.1 98 98
ALDOA -0.33 0.46 -9999 0 -1.1 96 96
Cbp/p300/CITED2 -0.32 0.48 -9999 0 -1.1 95 95
FOS -0.019 0.12 -9999 0 -0.51 27 27
HK2 -0.33 0.46 -9999 0 -1 102 102
SP1 0.015 0.014 -9999 0 -10000 0 0
GCK -0.1 0.26 -9999 0 -1.2 16 16
HK1 -0.33 0.46 -9999 0 -1.1 96 96
NPM1 -0.33 0.46 -9999 0 -1.1 96 96
EGLN1 -0.33 0.46 -9999 0 -1.1 96 96
CREB1 0.016 0.001 -9999 0 -10000 0 0
PGM1 -0.33 0.46 -9999 0 -1.1 96 96
SMAD3 0.011 0.003 -9999 0 -10000 0 0
EDN1 -0.2 0.45 -9999 0 -1.2 82 82
IGFBP1 -0.36 0.49 -9999 0 -1.1 112 112
VEGFA -0.24 0.35 -9999 0 -0.78 77 77
HIF1A/JAB1 -0.025 0.032 -9999 0 -10000 0 0
CP -0.44 0.52 -9999 0 -1.1 147 147
CXCL12 -0.34 0.48 -9999 0 -1.1 98 98
COPS5 0.01 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.33 0.46 -9999 0 -1 99 99
EGLN3 -0.38 0.51 -9999 0 -1.1 125 125
CA9 -0.48 0.51 -9999 0 -1.1 152 152
TERT -0.39 0.51 -9999 0 -1.1 119 119
ENO1 -0.33 0.46 -9999 0 -1.1 96 96
PFKL -0.33 0.46 -9999 0 -1 99 99
NCOA1 0.01 0 -9999 0 -10000 0 0
ADM -0.33 0.47 -9999 0 -1.1 96 96
ARNT -0.041 0.071 -9999 0 -10000 0 0
HNF4A -0.1 0.21 -9999 0 -0.51 112 112
ADFP -0.33 0.46 -9999 0 -1 109 109
SLC2A1 -0.32 0.42 -9999 0 -0.87 117 117
LEP -0.35 0.48 -9999 0 -1.1 105 105
HIF1A/ARNT/Cbp/p300 -0.28 0.38 -9999 0 -0.86 98 98
EPO -0.14 0.26 -9999 0 -0.77 6 6
CREBBP -0.045 0.11 -9999 0 -0.33 13 13
HIF1A/ARNT/Cbp/p300/HDAC7 -0.3 0.39 -9999 0 -0.9 92 92
PFKFB3 -0.33 0.46 -9999 0 -1 101 101
NT5E -0.34 0.47 -9999 0 -1 104 104
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.022 0.071 -9999 0 -0.25 45 45
RGS9BP -0.066 0.18 -9999 0 -0.5 76 76
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.03 0.13 -9999 0 -0.51 35 35
mol:Na + -0.16 0.18 -9999 0 -0.34 242 242
mol:ADP -0.015 0.094 -9999 0 -0.36 35 35
GNAT2 0.007 0.023 -9999 0 -0.51 1 1
RGS9-1/Gbeta5/R9AP -0.13 0.17 -9999 0 -0.33 210 210
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.019 -9999 0 -0.31 2 2
GRK7 0.006 0.005 -9999 0 -10000 0 0
CNGB3 -0.092 0.2 -9999 0 -0.51 97 97
Cone Metarhodopsin II/X-Arrestin -0.002 0.028 -9999 0 -0.37 3 3
mol:Ca2+ -0.16 0.18 -9999 0 -0.32 265 265
Cone PDE6 -0.11 0.15 -9999 0 -0.5 27 27
Cone Metarhodopsin II -0.019 0.07 -9999 0 -0.28 35 35
Na + (4 Units) -0.16 0.18 -9999 0 -0.32 265 265
GNAT2/GDP -0.11 0.14 -9999 0 -0.27 210 210
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.018 -9999 0 -0.28 2 2
Cone Transducin -0.024 0.076 -9999 0 -0.27 45 45
SLC24A2 -0.033 0.14 -9999 0 -0.51 40 40
GNB3/GNGT2 -0.031 0.1 -9999 0 -0.36 44 44
GNB3 -0.023 0.13 -9999 0 -0.51 33 33
GNAT2/GTP -0.001 0.016 -9999 0 -0.37 1 1
CNGA3 -0.17 0.25 -9999 0 -0.51 177 177
ARR3 -0.001 0.039 -9999 0 -0.51 3 3
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.16 0.18 -9999 0 -0.34 242 242
mol:Pi -0.13 0.17 -9999 0 -0.32 210 210
Cone CNG Channel -0.13 0.15 -9999 0 -0.5 33 33
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.033 0.14 -9999 0 -0.51 40 40
RGS9 -0.15 0.24 -9999 0 -0.5 160 160
PDE6C 0.003 0.004 -9999 0 -10000 0 0
GNGT2 -0.001 0.074 -9999 0 -0.5 11 11
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.023 -9999 0 -0.51 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.057 0.069 0.13 237 -10000 0 237
BUB1B -0.11 0.12 -10000 0 -0.2 303 303
PLK1 -0.024 0.048 -10000 0 -0.11 88 88
PLK1S1 -0.008 0.025 -10000 0 -0.11 1 1
KIF2A -0.015 0.043 -10000 0 -0.18 1 1
regulation of mitotic centrosome separation -0.024 0.047 -10000 0 -0.11 88 88
GOLGA2 0.01 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.21 0.25 -10000 0 -0.43 262 262
WEE1 -0.02 0.052 -10000 0 -0.18 1 1
cytokinesis -0.11 0.12 -10000 0 -0.25 159 159
PP2A-alpha B56 -0.012 0.032 -10000 0 -10000 0 0
AURKA -0.018 0.042 -10000 0 -0.1 78 78
PICH/PLK1 -0.13 0.21 -10000 0 -0.39 195 195
CENPE -0.072 0.14 -10000 0 -0.34 107 107
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.015 0.043 -10000 0 -0.17 1 1
PPP2CA 0.01 0 -10000 0 -10000 0 0
FZR1 0.01 0 -10000 0 -10000 0 0
TPX2 -0.042 0.05 -10000 0 -0.11 70 70
PAK1 0.008 0.004 -10000 0 -10000 0 0
SPC24 -0.14 0.24 -10000 0 -0.51 152 152
FBXW11 0.01 0 -10000 0 -10000 0 0
CLSPN -0.034 0.056 -10000 0 -0.13 72 72
GORASP1 0.01 0 -10000 0 -10000 0 0
metaphase -0.002 0.004 -10000 0 -0.011 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.012 0.025 -10000 0 -0.058 78 78
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.01 3 3
STAG2 0.01 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.011 -10000 0 -10000 0 0
spindle elongation -0.024 0.047 -10000 0 -0.11 88 88
ODF2 0.008 0.004 -10000 0 -10000 0 0
BUB1 -0.02 0.038 -10000 0 -10000 0 0
TPT1 -0.008 0.025 -10000 0 -0.11 1 1
CDC25C -0.061 0.058 -10000 0 -0.14 78 78
CDC25B 0.008 0.003 -10000 0 -10000 0 0
SGOL1 -0.057 0.069 -10000 0 -0.13 237 237
RHOA 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.063 0.1 -10000 0 -0.23 134 134
CDC14B 0.007 0.003 -10000 0 -10000 0 0
CDC20 -0.29 0.26 -10000 0 -0.51 301 301
PLK1/PBIP1 -0.044 0.085 -10000 0 -0.33 36 36
mitosis -0.003 0.008 0.019 22 -0.018 78 100
FBXO5 -0.015 0.042 -10000 0 -0.17 1 1
CDC2 -0.002 0.005 -10000 0 -0.011 105 105
NDC80 -0.24 0.26 -10000 0 -0.51 248 248
metaphase plate congression -0.013 0.031 -10000 0 -10000 0 0
ERCC6L -0.14 0.19 -10000 0 -0.37 180 180
NLP/gamma Tubulin -0.01 0.026 -10000 0 -0.11 2 2
microtubule cytoskeleton organization -0.008 0.025 -10000 0 -0.11 1 1
G2/M transition DNA damage checkpoint -0.001 0.002 -10000 0 -0.01 1 1
PPP1R12A 0.009 0.001 -10000 0 -10000 0 0
interphase -0.001 0.002 -10000 0 -0.01 1 1
PLK1/PRC1-2 -0.19 0.21 -10000 0 -0.36 277 277
GRASP65/GM130/RAB1/GTP/PLK1 -0.016 0.026 -10000 0 -10000 0 0
RAB1A 0.01 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.014 0.044 -10000 0 -0.36 1 1
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.034 -10000 0 -10000 0 0
microtubule-based process -0.16 0.17 -10000 0 -0.32 277 277
Golgi organization -0.024 0.047 -10000 0 -0.11 88 88
Cohesin/SA2 -0.027 0.035 -10000 0 -0.16 1 1
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.27 0.26 -10000 0 -0.51 277 277
APC/C/CDC20 -0.18 0.17 -10000 0 -0.32 301 301
PPP2R1A 0.01 0 -10000 0 -10000 0 0
chromosome segregation -0.043 0.083 -10000 0 -0.32 36 36
PRC1 -0.062 0.18 -10000 0 -0.51 71 71
ECT2 -0.03 0.088 -10000 0 -0.35 30 30
C13orf34 -0.014 0.042 -10000 0 -0.36 1 1
NUDC -0.013 0.031 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.11 0.11 -10000 0 -0.2 303 303
spindle assembly -0.017 0.038 -10000 0 -0.088 70 70
spindle stabilization -0.008 0.025 -10000 0 -0.11 1 1
APC/C/HCDH1 0.012 0.005 -10000 0 -10000 0 0
MKLP2/PLK1 -0.16 0.17 -10000 0 -0.32 277 277
CCNB1 -0.13 0.23 -10000 0 -0.51 140 140
PPP1CB 0.009 0.001 -10000 0 -10000 0 0
BTRC 0.01 0 -10000 0 -10000 0 0
ROCK2 -0.007 0.032 -10000 0 -10000 0 0
TUBG1 -0.008 0.025 -10000 0 -0.11 2 2
G2/M transition of mitotic cell cycle -0.063 0.099 -10000 0 -0.23 134 134
MLF1IP -0.021 0.098 -10000 0 -0.38 36 36
INCENP 0.009 0.001 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.033 0.042 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.085 0.12 -9999 0 -0.36 33 33
JUN -0.052 0.12 -9999 0 -0.34 27 27
HRAS 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.12 0.16 -9999 0 -0.3 206 206
RAP1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.008 0.032 -9999 0 -0.51 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.16 -9999 0 -0.31 145 145
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.084 0.13 -9999 0 -0.27 158 158
RHOA 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.1 0.14 -9999 0 -0.47 27 27
GRB7 0.004 0.055 -9999 0 -0.5 6 6
RET51/GFRalpha1/GDNF -0.12 0.16 -9999 0 -0.41 50 50
MAPKKK cascade -0.095 0.13 -9999 0 -0.43 30 30
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.084 0.13 -9999 0 -0.27 158 158
lamellipodium assembly -0.082 0.11 -9999 0 -0.33 33 33
RET51/GFRalpha1/GDNF/SHC -0.12 0.16 -9999 0 -0.41 52 52
PIK3CA 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.085 0.13 -9999 0 -0.28 158 158
RET9/GFRalpha1/GDNF/Shank3 -0.087 0.14 -9999 0 -0.28 159 159
MAPK3 -0.078 0.14 -9999 0 -0.45 27 27
DOK1 0.01 0 -9999 0 -10000 0 0
DOK6 -0.043 0.16 -9999 0 -0.5 53 53
PXN 0.01 0 -9999 0 -10000 0 0
neurite development -0.075 0.15 -9999 0 -0.37 59 59
DOK5 -0.065 0.18 -9999 0 -0.51 74 74
GFRA1 -0.14 0.23 -9999 0 -0.5 152 152
MAPK8 -0.059 0.12 -9999 0 -0.35 25 25
HRAS/GTP -0.11 0.14 -9999 0 -0.47 27 27
tube development -0.08 0.12 -9999 0 -0.26 159 159
MAPK1 -0.078 0.14 -9999 0 -0.45 27 27
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.055 0.12 -9999 0 -0.23 151 151
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PDLIM7 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.18 -9999 0 -0.53 59 59
SHC1 0.008 0.032 -9999 0 -0.51 2 2
RET51/GFRalpha1/GDNF/Dok4 -0.12 0.16 -9999 0 -0.3 206 206
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.18 -9999 0 -0.32 257 257
PRKCA 0.008 0.032 -9999 0 -0.5 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.071 0.14 -9999 0 -0.28 151 151
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.056 0.12 -9999 0 -0.24 151 151
RET51/GFRalpha1/GDNF/Grb7 -0.12 0.16 -9999 0 -0.32 149 149
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.063 0.18 -9999 0 -0.51 72 72
DOK4 0.01 0 -9999 0 -10000 0 0
JNK cascade -0.051 0.12 -9999 0 -0.34 27 27
RET9/GFRalpha1/GDNF/FRS2 -0.085 0.13 -9999 0 -0.27 160 160
SHANK3 0.003 0.059 -9999 0 -0.5 7 7
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.055 0.12 -9999 0 -0.24 151 151
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.071 0.13 -9999 0 -0.27 91 91
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.07 0.13 -9999 0 -0.37 26 26
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.073 0.14 -9999 0 -0.41 28 28
PI3K -0.09 0.19 -9999 0 -0.36 151 151
SOS1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.08 0.12 -9999 0 -0.26 159 159
GRB10 0.01 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.065 0.12 -9999 0 -0.34 26 26
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.16 -9999 0 -0.3 208 208
GAB1 0.008 0.032 -9999 0 -0.5 2 2
IRS1 0.009 0.022 -9999 0 -0.5 1 1
IRS2 0.009 0.022 -9999 0 -0.5 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.074 0.14 -9999 0 -0.42 30 30
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.16 -9999 0 -0.3 207 207
GRB2 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GDNF -0.004 0.067 -9999 0 -0.51 9 9
RAC1 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.16 -9999 0 -0.3 206 206
Rac1/GTP -0.095 0.13 -9999 0 -0.4 33 33
RET9/GFRalpha1/GDNF -0.094 0.14 -9999 0 -0.31 158 158
GFRalpha1/GDNF -0.11 0.17 -9999 0 -0.36 158 158
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.45 0.52 -10000 0 -1.2 120 120
STAT6 (cleaved dimer) -0.49 0.49 -10000 0 -1.2 147 147
IGHG1 -0.15 0.17 -10000 0 -0.37 27 27
IGHG3 -0.44 0.5 -10000 0 -1.1 132 132
AKT1 -0.18 0.24 -10000 0 -0.73 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.19 -10000 0 -0.82 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.19 0.24 -10000 0 -0.65 26 26
THY1 -0.46 0.52 -10000 0 -1.2 124 124
MYB 0.003 0.059 -10000 0 -0.5 7 7
HMGA1 -0.037 0.15 -10000 0 -0.51 46 46
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.28 -10000 0 -0.63 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.24 -10000 0 -0.64 30 30
SP1 0.015 0.004 -10000 0 -10000 0 0
INPP5D 0.007 0.039 -10000 0 -0.5 3 3
SOCS5 0.021 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.49 -10000 0 -1.2 130 130
SOCS1 -0.27 0.33 -10000 0 -0.75 104 104
SOCS3 -0.2 0.26 -10000 0 -0.93 13 13
FCER2 -0.35 0.43 -10000 0 -1 82 82
PARP14 0.01 0.003 -10000 0 -10000 0 0
CCL17 -0.5 0.6 -10000 0 -1.4 127 127
GRB2 0.01 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.2 -10000 0 -0.66 11 11
T cell proliferation -0.44 0.53 -10000 0 -1.2 124 124
IL4R/JAK1 -0.45 0.52 -10000 0 -1.2 126 126
EGR2 -0.48 0.56 -10000 0 -1.3 125 125
JAK2 -0.013 0.045 -10000 0 -0.54 2 2
JAK3 0.014 0.004 -10000 0 -10000 0 0
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
JAK1 0.006 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.19 -10000 0 -0.78 10 10
CCL26 -0.47 0.53 -10000 0 -1.2 125 125
IL4R -0.48 0.56 -10000 0 -1.3 124 124
PTPN6 0.02 0.013 -10000 0 -10000 0 0
IL13RA2 -0.5 0.57 -10000 0 -1.3 136 136
IL13RA1 -0.011 0.03 -10000 0 -10000 0 0
IRF4 -0.11 0.24 -10000 0 -0.99 24 24
ARG1 -0.12 0.18 -10000 0 -0.72 20 20
CBL -0.22 0.26 -10000 0 -0.6 76 76
GTF3A 0.005 0.03 -10000 0 -0.5 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.015 0.049 -10000 0 -0.4 2 2
IRF4/BCL6 -0.094 0.22 -10000 0 -0.91 24 24
CD40LG -0.009 0.11 -10000 0 -0.5 24 24
MAPK14 -0.22 0.27 -10000 0 -0.63 60 60
mitosis -0.17 0.23 -10000 0 -0.7 13 13
STAT6 -0.53 0.62 -10000 0 -1.4 130 130
SPI1 -0.012 0.11 -10000 0 -0.5 25 25
RPS6KB1 -0.16 0.22 -10000 0 -0.68 12 12
STAT6 (dimer) -0.53 0.62 -10000 0 -1.4 130 130
STAT6 (dimer)/PARP14 -0.49 0.57 -10000 0 -1.3 127 127
mast cell activation 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.26 -10000 0 -0.76 31 31
FRAP1 -0.18 0.24 -10000 0 -0.73 14 14
LTA -0.45 0.52 -10000 0 -1.3 109 109
FES 0.009 0.022 -10000 0 -0.5 1 1
T-helper 1 cell differentiation 0.51 0.6 1.4 130 -10000 0 130
CCL11 -0.46 0.53 -10000 0 -1.2 128 128
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.18 0.24 -10000 0 -0.81 12 12
IL2RG 0.009 0.05 -10000 0 -0.49 5 5
IL10 -0.46 0.53 -10000 0 -1.2 120 120
IRS1 0.009 0.022 -10000 0 -0.5 1 1
IRS2 0.009 0.022 -10000 0 -0.5 1 1
IL4 -0.099 0.12 -10000 0 -10000 0 0
IL5 -0.46 0.52 -10000 0 -1.2 116 116
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.4 -10000 0 -0.91 122 122
COL1A1 -0.23 0.24 -10000 0 -0.62 70 70
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.54 -10000 0 -1.3 121 121
IL2R gamma/JAK3 0.014 0.036 -10000 0 -0.34 5 5
TFF3 -0.5 0.56 -10000 0 -1.3 132 132
ALOX15 -0.78 0.72 -10000 0 -1.4 271 271
MYBL1 0 0.071 -10000 0 -0.51 10 10
T-helper 2 cell differentiation -0.36 0.4 -10000 0 -0.92 125 125
SHC1 0.008 0.032 -10000 0 -0.51 2 2
CEBPB 0.012 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.24 -10000 0 -0.77 13 13
mol:PI-3-4-5-P3 -0.18 0.24 -10000 0 -0.73 14 14
PI3K -0.18 0.25 -10000 0 -0.81 13 13
DOK2 -0.033 0.14 -10000 0 -0.5 43 43
ETS1 0.019 0.025 -10000 0 -0.46 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.19 -10000 0 -0.67 9 9
ITGB3 -0.46 0.53 -10000 0 -1.2 120 120
PIGR -0.6 0.68 -10000 0 -1.5 169 169
IGHE 0.034 0.041 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.19 -10000 0 -0.66 9 9
BCL6 0.01 0.003 -10000 0 -10000 0 0
OPRM1 -0.46 0.52 -10000 0 -1.2 121 121
RETNLB -0.46 0.52 -10000 0 -1.2 116 116
SELP -0.58 0.68 -10000 0 -1.5 156 156
AICDA -0.47 0.54 -10000 0 -1.2 133 133
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.023 -9999 0 -0.51 1 1
LAT2 -0.093 0.2 -9999 0 -0.47 83 83
AP1 -0.13 0.21 -9999 0 -0.5 102 102
mol:PIP3 -0.099 0.22 -9999 0 -0.5 92 92
IKBKB -0.044 0.13 -9999 0 -0.27 86 86
AKT1 -0.065 0.16 -9999 0 -0.38 81 81
IKBKG -0.044 0.13 -9999 0 -0.27 86 86
MS4A2 -0.11 0.22 -9999 0 -0.5 122 122
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.002 -9999 0 -10000 0 0
MAP3K1 -0.067 0.18 -9999 0 -0.4 92 92
mol:Ca2+ -0.07 0.17 -9999 0 -0.37 92 92
LYN 0.008 0.005 -9999 0 -10000 0 0
CBLB -0.088 0.19 -9999 0 -0.44 85 85
SHC1 0.008 0.032 -9999 0 -0.51 2 2
RasGAP/p62DOK -0.025 0.077 -9999 0 -0.26 48 48
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0.039 -9999 0 -0.5 3 3
PLD2 -0.097 0.19 -9999 0 -0.46 79 79
PTPN13 -0.11 0.22 -9999 0 -0.5 102 102
PTPN11 0.006 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.045 0.15 -9999 0 -0.32 82 82
SYK 0.005 0.041 -9999 0 -0.53 3 3
GRB2 0.009 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.2 -9999 0 -0.52 93 93
LAT -0.088 0.19 -9999 0 -0.45 83 83
PAK2 -0.082 0.2 -9999 0 -0.46 92 92
NFATC2 -0.073 0.16 -9999 0 -0.75 23 23
HRAS -0.096 0.22 -9999 0 -0.5 93 93
GAB2 0.005 0.05 -9999 0 -0.5 5 5
PLA2G1B -0.001 0.031 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.22 -9999 0 -0.4 192 192
Antigen/IgE/Fc epsilon R1 -0.14 0.2 -9999 0 -0.37 192 192
mol:GDP -0.11 0.24 -9999 0 -0.54 96 96
JUN 0.007 0.039 -9999 0 -0.5 3 3
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.023 -9999 0 -0.5 1 1
FOS -0.017 0.11 -9999 0 -0.5 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.12 0.18 -9999 0 -0.39 127 127
CHUK -0.044 0.13 -9999 0 -0.27 86 86
KLRG1 -0.084 0.18 -9999 0 -0.42 82 82
VAV1 -0.091 0.19 -9999 0 -0.46 83 83
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.088 0.19 -9999 0 -0.37 127 127
negative regulation of mast cell degranulation -0.074 0.17 -9999 0 -0.4 81 81
BTK -0.12 0.27 -9999 0 -0.59 96 96
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.22 -9999 0 -0.58 78 78
GAB2/PI3K/SHP2 -0.1 0.16 -9999 0 -0.42 81 81
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.099 0.2 -9999 0 -0.49 82 82
RAF1 0.021 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.19 -9999 0 -0.5 78 78
FCER1G -0.002 0.085 -9999 0 -0.51 14 14
FCER1A -0.13 0.23 -9999 0 -0.51 139 139
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.18 -9999 0 -0.38 145 145
MAPK3 0.028 0.02 -9999 0 -10000 0 0
MAPK1 0.028 0.02 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.061 -9999 0 -10000 0 0
DUSP1 -0.038 0.15 -9999 0 -0.5 48 48
NF-kappa-B/RelA -0.043 0.062 -9999 0 -0.23 7 7
actin cytoskeleton reorganization -0.096 0.2 -9999 0 -0.48 82 82
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.18 -9999 0 -0.45 90 90
FER -0.088 0.19 -9999 0 -0.37 127 127
RELA 0.01 0 -9999 0 -10000 0 0
ITK -0.038 0.089 -9999 0 -0.53 13 13
SOS1 0.01 0 -9999 0 -10000 0 0
PLCG1 -0.11 0.24 -9999 0 -0.54 93 93
cytokine secretion -0.032 0.045 -9999 0 -10000 0 0
SPHK1 -0.09 0.19 -9999 0 -0.45 84 84
PTK2 -0.1 0.21 -9999 0 -0.5 82 82
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.22 -9999 0 -0.54 93 93
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.095 0.22 -9999 0 -0.49 93 93
MAP2K2 0.025 0.02 -9999 0 -10000 0 0
MAP2K1 0.025 0.02 -9999 0 -10000 0 0
MAP2K7 0.01 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.093 0.15 -9999 0 -0.38 81 81
MAP2K4 0.011 0.011 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.2 -9999 0 -0.52 81 81
mol:Choline -0.096 0.18 -9999 0 -0.45 79 79
SHC/Grb2/SOS1 -0.1 0.16 -9999 0 -0.42 80 80
FYN 0.009 0.022 -9999 0 -0.5 1 1
DOK1 0.01 0 -9999 0 -10000 0 0
PXN -0.088 0.19 -9999 0 -0.46 80 80
HCLS1 -0.09 0.19 -9999 0 -0.45 83 83
PRKCB -0.072 0.17 -9999 0 -0.38 93 93
FCGR2B 0.009 0.022 -9999 0 -0.5 1 1
IGHE -0.002 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.075 0.17 -9999 0 -0.4 81 81
LCP2 0.006 0.039 -9999 0 -0.5 3 3
PLA2G4A -0.12 0.21 -9999 0 -0.38 167 167
RASA1 0.01 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.096 0.18 -9999 0 -0.45 79 79
IKK complex -0.021 0.098 -9999 0 -0.23 26 26
WIPF1 0.01 0 -9999 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.022 0.092 -9999 0 -0.41 24 24
alphaM/beta2 Integrin/GPIbA -0.027 0.1 -9999 0 -0.39 32 32
alphaM/beta2 Integrin/proMMP-9 -0.086 0.15 -9999 0 -0.32 133 133
PLAUR 0.01 0 -9999 0 -10000 0 0
HMGB1 0.005 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.022 0.095 -9999 0 -0.43 23 23
AGER -0.46 0.15 -9999 0 -0.51 466 466
RAP1A 0.01 0 -9999 0 -10000 0 0
SELPLG -0.008 0.094 -9999 0 -0.5 18 18
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.29 0.16 -9999 0 -0.5 134 134
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.1 0.21 -9999 0 -0.51 112 112
CYR61 -0.017 0.11 -9999 0 -0.5 27 27
TLN1 0.009 0.022 -9999 0 -0.5 1 1
Rap1/GTP -0.084 0.14 -9999 0 -0.42 50 50
RHOA 0.01 0 -9999 0 -10000 0 0
P-selectin oligomer -0.1 0.21 -9999 0 -0.5 115 115
MYH2 -0.15 0.2 -9999 0 -0.47 108 108
MST1R 0.008 0.032 -9999 0 -0.5 2 2
leukocyte activation during inflammatory response -0.044 0.11 -9999 0 -0.31 67 67
APOB -0.042 0.15 -9999 0 -0.5 51 51
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.023 -9999 0 -0.51 1 1
JAM3 0.005 0.05 -9999 0 -0.5 5 5
GP1BA 0 0.071 -9999 0 -0.5 10 10
alphaM/beta2 Integrin/CTGF -0.038 0.12 -9999 0 -0.4 45 45
alphaM/beta2 Integrin -0.088 0.18 -9999 0 -0.44 67 67
JAM3 homodimer 0.005 0.05 -9999 0 -0.5 5 5
ICAM2 0.005 0.05 -9999 0 -0.5 5 5
ICAM1 0.003 0.059 -9999 0 -0.5 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.087 0.18 -9999 0 -0.43 67 67
cell adhesion -0.027 0.1 -9999 0 -0.39 32 32
NFKB1 -0.3 0.22 -9999 0 -0.62 134 134
THY1 -0.003 0.081 -9999 0 -0.51 13 13
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.032 0.094 -9999 0 -0.31 54 54
alphaM/beta2 Integrin/LRP/tPA -0.05 0.13 -9999 0 -0.42 35 35
IL6 -0.35 0.33 -9999 0 -0.85 141 141
ITGB2 -0.005 0.072 -9999 0 -0.51 10 10
elevation of cytosolic calcium ion concentration -0.065 0.13 -9999 0 -0.29 105 105
alphaM/beta2 Integrin/JAM2/JAM3 -0.05 0.14 -9999 0 -0.47 35 35
JAM2 -0.049 0.16 -9999 0 -0.5 59 59
alphaM/beta2 Integrin/ICAM1 -0.029 0.11 -9999 0 -0.51 15 15
alphaM/beta2 Integrin/uPA/Plg -0.074 0.13 -9999 0 -0.3 120 120
RhoA/GTP -0.1 0.19 -9999 0 -0.48 66 66
positive regulation of phagocytosis -0.079 0.16 -9999 0 -0.64 30 30
Ron/MSP -0.017 0.076 -9999 0 -0.36 24 24
alphaM/beta2 Integrin/uPAR/uPA -0.066 0.13 -9999 0 -0.3 105 105
alphaM/beta2 Integrin/uPAR -0.022 0.091 -9999 0 -0.42 23 23
PLAU -0.084 0.2 -9999 0 -0.51 93 93
PLAT -0.049 0.16 -9999 0 -0.51 58 58
actin filament polymerization -0.15 0.19 -9999 0 -0.45 108 108
MST1 -0.012 0.1 -9999 0 -0.51 22 22
alphaM/beta2 Integrin/lipoprotein(a) -0.045 0.11 -9999 0 -0.31 66 66
TNF -0.28 0.23 -9999 0 -0.6 134 134
RAP1B 0.01 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.075 0.14 -9999 0 -0.33 114 114
fibrinolysis -0.073 0.13 -9999 0 -0.3 120 120
HCK -0.014 0.11 -9999 0 -0.5 24 24
dendritic cell antigen processing and presentation -0.087 0.18 -9999 0 -0.43 67 67
VTN -0.084 0.2 -9999 0 -0.5 95 95
alphaM/beta2 Integrin/CYR61 -0.037 0.12 -9999 0 -0.4 45 45
LPA 0 0.039 -9999 0 -0.5 3 3
LRP1 0.006 0.045 -9999 0 -0.5 4 4
cell migration -0.076 0.13 -9999 0 -0.38 34 34
FN1 0.005 0.05 -9999 0 -0.5 5 5
alphaM/beta2 Integrin/Thy1 -0.029 0.1 -9999 0 -0.38 36 36
MPO -0.006 0.088 -9999 0 -0.5 16 16
KNG1 -0.03 0.13 -9999 0 -0.51 35 35
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.093 0.18 -9999 0 -0.46 62 62
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.009 0.074 -9999 0 -0.51 11 11
CTGF -0.019 0.12 -9999 0 -0.5 29 29
alphaM/beta2 Integrin/Hck -0.034 0.14 -9999 0 -0.53 31 31
ITGAM -0.017 0.1 -9999 0 -0.51 22 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.085 0.18 -9999 0 -0.54 41 41
HP -0.14 0.23 -9999 0 -0.5 146 146
leukocyte adhesion -0.27 0.19 -9999 0 -0.47 174 174
SELP -0.1 0.21 -9999 0 -0.5 115 115
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.093 0.32 -9999 0 -1 49 49
MKNK1 0.01 0 -9999 0 -10000 0 0
MAPK14 -0.031 0.12 -9999 0 -0.42 9 9
ATF2/c-Jun -0.014 0.12 -9999 0 -0.53 10 10
MAPK11 -0.034 0.13 -9999 0 -0.47 12 12
MITF -0.036 0.16 -9999 0 -0.36 94 94
MAPKAPK5 -0.03 0.15 -9999 0 -0.34 89 89
KRT8 -0.031 0.15 -9999 0 -0.35 89 89
MAPKAPK3 0.01 0 -9999 0 -10000 0 0
MAPKAPK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.048 0.18 -9999 0 -0.43 89 89
CEBPB -0.03 0.15 -9999 0 -0.34 89 89
SLC9A1 -0.03 0.15 -9999 0 -0.34 89 89
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.026 0.15 -9999 0 -0.34 89 89
p38alpha-beta/MNK1 -0.029 0.15 -9999 0 -0.52 12 12
JUN -0.013 0.12 -9999 0 -0.52 10 10
PPARGC1A -0.12 0.22 -9999 0 -0.46 91 91
USF1 -0.03 0.15 -9999 0 -0.34 89 89
RAB5/GDP/GDI1 -0.044 0.096 -9999 0 -0.38 12 12
NOS2 -0.092 0.32 -9999 0 -1 47 47
DDIT3 -0.032 0.15 -9999 0 -0.35 89 89
RAB5A 0.01 0 -9999 0 -10000 0 0
HSPB1 -0.019 0.12 -9999 0 -0.45 13 13
p38alpha-beta/HBP1 -0.029 0.15 -9999 0 -0.52 12 12
CREB1 -0.031 0.16 -9999 0 -0.37 89 89
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.02 0.13 -9999 0 -0.49 10 10
RPS6KA4 -0.03 0.15 -9999 0 -0.34 89 89
PLA2G4A -0.057 0.16 -9999 0 -0.52 20 20
GDI1 -0.03 0.15 -9999 0 -0.34 89 89
TP53 -0.041 0.18 -9999 0 -0.42 89 89
RPS6KA5 -0.032 0.15 -9999 0 -0.35 89 89
ESR1 -0.045 0.17 -9999 0 -0.38 95 95
HBP1 0.01 0 -9999 0 -10000 0 0
MEF2C -0.03 0.15 -9999 0 -0.34 89 89
MEF2A -0.03 0.15 -9999 0 -0.34 89 89
EIF4EBP1 -0.033 0.16 -9999 0 -0.37 89 89
KRT19 -0.034 0.15 -9999 0 -0.34 92 92
ELK4 -0.03 0.15 -9999 0 -0.34 89 89
ATF6 -0.03 0.15 -9999 0 -0.34 89 89
ATF1 -0.031 0.16 -9999 0 -0.37 89 89
p38alpha-beta/MAPKAPK2 -0.029 0.15 -9999 0 -0.52 12 12
p38alpha-beta/MAPKAPK3 -0.029 0.15 -9999 0 -0.52 12 12
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.078 0.13 -9999 0 -0.5 19 19
SMAD6-7/SMURF1 -0.038 0.1 -9999 0 -0.3 67 67
NOG -0.026 0.13 -9999 0 -0.5 36 36
SMAD9 -0.12 0.2 -9999 0 -0.48 114 114
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD5 -0.027 0.12 -9999 0 -0.36 26 26
BMP7/USAG1 -0.28 0.19 -9999 0 -0.39 369 369
SMAD5/SKI -0.02 0.11 -9999 0 -0.43 11 11
SMAD1 0.023 0.029 -9999 0 -10000 0 0
BMP2 -0.061 0.18 -9999 0 -0.5 71 71
SMAD1/SMAD1/SMAD4 -0.025 0.065 -9999 0 -0.41 1 1
BMPR1A 0.01 0 -9999 0 -10000 0 0
BMPR1B -0.044 0.16 -9999 0 -0.5 54 54
BMPR1A-1B/BAMBI -0.043 0.11 -9999 0 -0.31 72 72
AHSG -0.034 0.14 -9999 0 -0.51 39 39
CER1 -0.004 0.055 -9999 0 -0.51 6 6
BMP2-4/CER1 -0.053 0.12 -9999 0 -0.32 85 85
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.019 0.12 -9999 0 -0.4 23 23
BMP2-4 (homodimer) -0.059 0.14 -9999 0 -0.38 81 81
RGMB 0.01 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.065 0.13 -9999 0 -0.52 18 18
RGMA 0.001 0.068 -9999 0 -0.51 9 9
SMURF1 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.026 0.11 -9999 0 -0.37 24 24
BMP2-4/USAG1 -0.24 0.18 -9999 0 -0.34 363 363
SMAD6/SMURF1/SMAD5 -0.02 0.11 -9999 0 -0.43 11 11
SOSTDC1 -0.33 0.24 -9999 0 -0.5 346 346
BMP7/BMPR2/BMPR1A-1B -0.061 0.12 -9999 0 -0.49 9 9
SKI 0.01 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.064 0.18 -9999 0 -0.5 75 75
HFE2 -0.006 0.078 -9999 0 -0.51 12 12
ZFYVE16 0.01 0 -9999 0 -10000 0 0
MAP3K7 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.063 0.14 -9999 0 -0.32 101 101
SMAD5/SMAD5/SMAD4 -0.02 0.11 -9999 0 -0.43 11 11
MAPK1 0.01 0 -9999 0 -10000 0 0
TAK1/TAB family -0.041 0.083 -9999 0 -0.35 16 16
BMP7 (homodimer) -0.057 0.17 -9999 0 -0.5 67 67
NUP214 0.01 0 -9999 0 -10000 0 0
BMP6/FETUA -0.079 0.16 -9999 0 -0.37 109 109
SMAD1/SKI 0.027 0.027 -9999 0 -10000 0 0
SMAD6 -0.057 0.17 -9999 0 -0.5 67 67
CTDSP2 0.01 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.072 0.14 -9999 0 -0.32 114 114
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.34 0.24 -9999 0 -0.51 349 349
BMPR2 (homodimer) 0.01 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.018 -9999 0 -0.29 2 2
BMPR1A-1B (homodimer) -0.037 0.11 -9999 0 -0.35 54 54
CHRDL1 -0.18 0.24 -9999 0 -0.5 187 187
ENDOFIN/SMAD1 0.027 0.027 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.029 0.074 -9999 0 -0.46 1 1
SMAD6/SMURF1 0.01 0 -9999 0 -10000 0 0
BAMBI -0.012 0.1 -9999 0 -0.51 22 22
SMURF2 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.2 -9999 0 -0.37 215 215
BMP2-4/GREM1 -0.25 0.18 -9999 0 -0.34 375 375
SMAD7 0.009 0.022 -9999 0 -0.5 1 1
SMAD8A/SMAD8A/SMAD4 -0.092 0.2 -9999 0 -0.45 114 114
SMAD1/SMAD6 0.027 0.027 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.057 0.17 -9999 0 -0.5 67 67
BMP6 -0.064 0.18 -9999 0 -0.5 75 75
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.02 0.11 -9999 0 -0.34 24 24
PPM1A 0.01 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.027 0.027 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.016 -9999 0 -0.35 1 1
CTDSPL 0.01 0 -9999 0 -10000 0 0
PPP1CA 0.01 0 -9999 0 -10000 0 0
XIAP 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.01 0 -9999 0 -10000 0 0
PPP1R15A 0.008 0.032 -9999 0 -0.5 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.04 0.13 -9999 0 -0.38 37 37
CHRD -0.015 0.11 -9999 0 -0.51 25 25
BMPR2 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.12 -9999 0 -0.4 24 24
BMP4 -0.006 0.089 -9999 0 -0.5 16 16
FST -0.036 0.15 -9999 0 -0.5 46 46
BMP2-4/NOG -0.069 0.15 -9999 0 -0.34 104 104
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.056 0.11 -9999 0 -0.49 8 8
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.22 0.32 -10000 0 -0.81 60 60
PCK1 -0.17 0.23 -10000 0 -0.66 41 41
HNF4A -0.4 0.49 -10000 0 -1 156 156
KCNJ11 -0.19 0.33 -10000 0 -0.89 53 53
AKT1 -0.074 0.14 -10000 0 -0.41 11 11
response to starvation -0.028 0.047 -10000 0 -10000 0 0
DLK1 -0.21 0.32 -10000 0 -0.87 51 51
NKX2-1 -0.11 0.38 0.46 1 -1.3 38 39
ACADM -0.22 0.32 -10000 0 -0.84 54 54
TAT -0.16 0.22 -10000 0 -0.66 36 36
CEBPB 0.009 0.005 -10000 0 -10000 0 0
CEBPA -0.016 0.11 -10000 0 -0.5 26 26
TTR -0.2 0.25 -10000 0 -0.74 52 52
PKLR -0.22 0.32 -10000 0 -0.88 50 50
APOA1 -0.5 0.63 -10000 0 -1.3 173 173
CPT1C -0.22 0.32 -10000 0 -0.87 54 54
ALAS1 -0.075 0.16 -10000 0 -10000 0 0
TFRC -0.16 0.25 -10000 0 -0.73 32 32
FOXF1 -0.1 0.21 0.22 2 -0.48 119 121
NF1 0.015 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.11 0.23 -10000 0 -0.56 105 105
CPT1A -0.22 0.32 -10000 0 -0.83 55 55
HMGCS1 -0.22 0.32 -10000 0 -0.81 62 62
NR3C1 0.004 0.032 -10000 0 -10000 0 0
CPT1B -0.22 0.32 -10000 0 -0.84 58 58
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.001 0.025 -10000 0 -10000 0 0
GCK -0.23 0.34 -10000 0 -0.84 70 70
CREB1 0.005 0.02 -10000 0 -10000 0 0
IGFBP1 -0.13 0.19 -10000 0 -0.57 29 29
PDX1 -0.16 0.25 -10000 0 -0.67 55 55
UCP2 -0.22 0.32 -10000 0 -0.82 57 57
ALDOB -0.2 0.34 -10000 0 -0.85 63 63
AFP -0.071 0.14 -10000 0 -0.47 25 25
BDH1 -0.22 0.32 -10000 0 -0.83 58 58
HADH -0.18 0.31 -10000 0 -0.86 43 43
F2 -0.32 0.43 -10000 0 -1 82 82
HNF1A -0.11 0.23 -10000 0 -0.56 105 105
G6PC -0.08 0.15 -10000 0 -0.58 15 15
SLC2A2 -0.15 0.23 -10000 0 -0.67 28 28
INS 0 0.027 -10000 0 -10000 0 0
FOXA1 -0.012 0.11 0.26 6 -0.54 12 18
FOXA3 -0.16 0.27 -10000 0 -0.57 146 146
FOXA2 -0.21 0.36 -10000 0 -0.9 61 61
ABCC8 -0.25 0.41 -10000 0 -0.96 92 92
ALB -0.082 0.16 -10000 0 -0.48 30 30
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.024 0.13 -10000 0 -0.47 38 38
CDKN2C 0.022 0.031 -10000 0 -0.45 1 1
CDKN2A -0.15 0.24 -10000 0 -0.52 152 152
CCND2 0.041 0.066 0.2 38 -0.12 5 43
RB1 -0.045 0.068 -10000 0 -0.2 39 39
CDK4 0.049 0.071 0.21 39 -10000 0 39
CDK6 0.047 0.071 0.22 38 -10000 0 38
G1/S progression 0.037 0.073 0.2 39 -10000 0 39
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.17 0.14 -9999 0 -0.51 22 22
NF kappa B1 p50/RelA/I kappa B alpha -0.15 0.11 -9999 0 -0.45 22 22
alphaV/beta3 Integrin/Osteopontin/Src -0.25 0.16 -9999 0 -0.36 359 359
AP1 -0.16 0.12 -9999 0 -0.45 42 42
ILK -0.18 0.15 -9999 0 -0.53 22 22
bone resorption -0.15 0.11 -9999 0 -0.43 27 27
PTK2B 0.008 0.032 -9999 0 -0.5 2 2
PYK2/p130Cas -0.17 0.12 -9999 0 -0.48 25 25
ITGAV 0.011 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.006 0.046 -9999 0 -0.35 9 9
alphaV/beta3 Integrin/Osteopontin -0.22 0.15 -9999 0 -0.39 89 89
MAP3K1 -0.18 0.15 -9999 0 -0.36 88 88
JUN 0.007 0.039 -9999 0 -0.5 3 3
MAPK3 -0.17 0.15 -9999 0 -0.38 88 88
MAPK1 -0.17 0.15 -9999 0 -0.38 88 88
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.16 0.14 -9999 0 -0.5 22 22
ITGB3 -0.017 0.12 -9999 0 -0.51 28 28
NFKBIA -0.15 0.15 -9999 0 -0.36 88 88
FOS -0.017 0.11 -9999 0 -0.5 27 27
CD44 0.001 0.067 -9999 0 -0.5 9 9
CHUK 0.01 0 -9999 0 -10000 0 0
PLAU -0.16 0.18 -9999 0 -0.5 78 78
NF kappa B1 p50/RelA -0.15 0.12 -9999 0 -0.47 22 22
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
RELA 0.01 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.019 0.081 -9999 0 -0.36 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.18 0.15 -9999 0 -0.35 88 88
VAV3 -0.17 0.14 -9999 0 -0.51 26 26
MAP3K14 -0.19 0.16 -9999 0 -0.38 88 88
ROCK2 0.01 0 -9999 0 -10000 0 0
SPP1 -0.35 0.24 -9999 0 -0.5 359 359
RAC1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.16 0.12 -9999 0 -0.46 26 26
MMP2 -0.12 0.13 -9999 0 -0.43 16 16
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.029 0.085 0.32 6 -10000 0 6
SMARCC2 0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.011 0.005 -10000 0 -10000 0 0
TBX21 -0.1 0.22 -10000 0 -0.58 58 58
SUMO2 0.009 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0 -10000 0 -10000 0 0
FKBP4 0.009 0.023 -10000 0 -0.51 1 1
FKBP5 0.008 0.032 -10000 0 -0.5 2 2
GR alpha/HSP90/FKBP51/HSP90 0.089 0.11 0.28 71 -10000 0 71
PRL -0.067 0.13 -10000 0 -0.59 5 5
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.53 157 -10000 0 157
RELA -0.034 0.089 -10000 0 -10000 0 0
FGG 0 0.33 0.46 73 -0.48 106 179
GR beta/TIF2 0.092 0.12 0.31 65 -10000 0 65
IFNG -0.23 0.28 -10000 0 -0.66 104 104
apoptosis -0.011 0.15 0.47 11 -0.57 13 24
CREB1 -0.006 0.048 -10000 0 -10000 0 0
histone acetylation -0.029 0.14 0.28 5 -0.36 36 41
BGLAP -0.064 0.13 -10000 0 -0.46 14 14
GR/PKAc 0.088 0.1 0.28 50 -10000 0 50
NF kappa B1 p50/RelA -0.059 0.16 -10000 0 -0.43 30 30
SMARCD1 0.011 0.005 -10000 0 -10000 0 0
MDM2 0.076 0.097 0.25 75 -0.23 1 76
GATA3 0.012 0.039 -10000 0 -0.5 3 3
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.13 0.32 -10000 0 -1.1 46 46
GSK3B 0.009 0.005 -10000 0 -10000 0 0
NR1I3 0.012 0.14 0.47 9 -0.58 5 14
CSN2 0.12 0.17 0.39 65 -10000 0 65
BRG1/BAF155/BAF170/BAF60A 0.02 0.025 -10000 0 -0.32 1 1
NFATC1 0.007 0.05 -10000 0 -0.5 5 5
POU2F1 0.01 0.014 -10000 0 -10000 0 0
CDKN1A 0.024 0.059 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.005 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.51 10 10
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.087 0.1 0.27 63 -10000 0 63
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.014 0.21 0.45 9 -0.81 28 37
JUN -0.17 0.18 -10000 0 -0.44 107 107
IL4 -0.078 0.15 -10000 0 -0.49 24 24
CDK5R1 -0.007 0.09 -10000 0 -0.51 16 16
PRKACA 0.01 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.12 0.22 0.21 1 -0.48 87 88
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.091 0.1 0.27 68 -10000 0 68
cortisol/GR alpha (monomer) 0.24 0.32 0.63 159 -10000 0 159
NCOA2 0.005 0.05 -10000 0 -0.5 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.069 0.13 -10000 0 -0.57 27 27
AP-1/NFAT1-c-4 -0.28 0.28 -10000 0 -0.64 150 150
AFP -0.14 0.16 -10000 0 -0.55 28 28
SUV420H1 0.01 0 -10000 0 -10000 0 0
IRF1 0.13 0.15 0.41 54 -10000 0 54
TP53 0.026 0.022 -10000 0 -0.48 1 1
PPP5C 0.01 0 -10000 0 -10000 0 0
KRT17 -0.26 0.33 -10000 0 -0.76 118 118
KRT14 -0.18 0.2 -10000 0 -0.51 75 75
TBP 0.017 0 -10000 0 -10000 0 0
CREBBP 0.053 0.062 -10000 0 -0.26 1 1
HDAC1 0.007 0.004 -10000 0 -10000 0 0
HDAC2 0.015 0.024 -10000 0 -10000 0 0
AP-1 -0.28 0.28 -10000 0 -0.65 150 150
MAPK14 0.009 0.005 -10000 0 -10000 0 0
MAPK10 -0.046 0.16 -10000 0 -0.5 56 56
MAPK11 0.006 0.039 -10000 0 -0.5 3 3
KRT5 -0.41 0.5 -10000 0 -1.1 158 158
interleukin-1 receptor activity 0.006 0.024 -10000 0 -10000 0 0
NCOA1 0.012 0.001 -10000 0 -10000 0 0
STAT1 0.016 0 -10000 0 -10000 0 0
CGA -0.11 0.19 -10000 0 -0.51 60 60
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.19 0.45 87 -10000 0 87
MAPK3 0.009 0.005 -10000 0 -10000 0 0
MAPK1 0.009 0.005 -10000 0 -10000 0 0
ICAM1 -0.14 0.24 -10000 0 -0.6 64 64
NFKB1 -0.034 0.089 -10000 0 -0.25 16 16
MAPK8 -0.15 0.17 -10000 0 -0.4 112 112
MAPK9 0.009 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.015 0.15 0.47 11 -0.6 13 24
BAX 0.026 0.021 -10000 0 -10000 0 0
POMC -0.18 0.31 -10000 0 -0.87 53 53
EP300 0.053 0.062 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.22 0.26 0.54 158 -10000 0 158
proteasomal ubiquitin-dependent protein catabolic process 0.052 0.075 0.22 29 -0.2 1 30
SGK1 0.097 0.092 -10000 0 -1.1 1 1
IL13 -0.16 0.19 -10000 0 -0.58 41 41
IL6 -0.3 0.45 -10000 0 -0.96 146 146
PRKACG 0.002 0.004 -10000 0 -10000 0 0
IL5 -0.14 0.16 -10000 0 -0.6 11 11
IL2 -0.21 0.23 -10000 0 -0.57 104 104
CDK5 0.009 0.003 -10000 0 -10000 0 0
PRKACB 0.009 0.023 -10000 0 -0.51 1 1
HSP90AA1 0.01 0 -10000 0 -10000 0 0
IL8 -0.14 0.23 -10000 0 -0.56 74 74
CDK5R1/CDK5 -0.01 0.063 -10000 0 -0.36 16 16
NF kappa B1 p50/RelA/PKAc -0.026 0.12 -10000 0 -0.38 11 11
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.24 0.5 161 -10000 0 161
SMARCA4 0.01 0.023 -10000 0 -0.5 1 1
chromatin remodeling 0.14 0.15 0.36 103 -10000 0 103
NF kappa B1 p50/RelA/Cbp 0.009 0.15 0.36 8 -0.38 13 21
JUN (dimer) -0.17 0.18 -10000 0 -0.44 107 107
YWHAH 0.01 0 -10000 0 -10000 0 0
VIPR1 -0.34 0.43 -10000 0 -0.85 210 210
NR3C1 0.14 0.19 0.45 90 -10000 0 90
NR4A1 -0.1 0.22 -10000 0 -0.5 117 117
TIF2/SUV420H1 -0.003 0.035 -10000 0 -0.35 5 5
MAPKKK cascade -0.011 0.15 0.47 11 -0.57 13 24
cortisol/GR alpha (dimer)/Src-1 0.22 0.26 0.53 158 -10000 0 158
PBX1 -0.005 0.087 -10000 0 -0.5 15 15
POU1F1 0.002 0.031 -10000 0 -0.6 1 1
SELE -0.26 0.43 -10000 0 -1 112 112
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.36 103 -10000 0 103
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.24 0.5 161 -10000 0 161
mol:cortisol 0.13 0.19 0.36 161 -0.21 13 174
MMP1 -0.26 0.19 -10000 0 -0.46 151 151
Visual signal transduction: Rods

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
mol:K + 0.01 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.051 -9999 0 -0.37 10 10
Metarhodopsin II/Arrestin -0.001 0.014 -9999 0 -0.31 1 1
PDE6G/GNAT1/GTP -0.009 0.058 -9999 0 -0.34 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.007 0.071 -9999 0 -0.51 10 10
GRK1 -0.03 0.13 -9999 0 -0.51 35 35
CNG Channel -0.1 0.15 -9999 0 -0.48 40 40
mol:Na + -0.12 0.15 -9999 0 -0.48 41 41
mol:ADP -0.03 0.13 -9999 0 -0.51 35 35
RGS9-1/Gbeta5/R9AP -0.13 0.17 -9999 0 -0.33 210 210
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.15 -9999 0 -0.5 41 41
CNGB1 -0.086 0.2 -9999 0 -0.51 95 95
RDH5 0.002 0.064 -9999 0 -0.51 8 8
SAG 0.001 0.023 -9999 0 -0.51 1 1
mol:Ca2+ -0.092 0.16 -9999 0 -0.47 41 41
Na + (4 Units) -0.11 0.14 -9999 0 -0.45 41 41
RGS9 -0.15 0.24 -9999 0 -0.5 160 160
GNB1/GNGT1 -0.073 0.14 -9999 0 -0.36 104 104
GNAT1/GDP -0.12 0.15 -9999 0 -0.28 215 215
GUCY2D -0.001 0.071 -9999 0 -0.5 10 10
GNGT1 -0.098 0.21 -9999 0 -0.51 104 104
GUCY2F 0 0.032 -9999 0 -0.51 2 2
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.014 0.095 -9999 0 -0.26 63 63
mol:11-cis-retinal 0.002 0.064 -9999 0 -0.51 8 8
mol:cGMP -0.053 0.11 -9999 0 -0.42 9 9
GNB1 0.01 0 -9999 0 -10000 0 0
Rhodopsin -0.006 0.045 -9999 0 -0.36 8 8
SLC24A1 0.01 0 -9999 0 -10000 0 0
CNGA1 -0.059 0.18 -9999 0 -0.51 68 68
Metarhodopsin II -0.019 0.07 -9999 0 -0.28 35 35
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.055 0.12 -9999 0 -0.28 100 100
RGS9BP -0.066 0.18 -9999 0 -0.5 76 76
Metarhodopsin II/Transducin -0.021 0.061 -9999 0 -0.22 3 3
GCAP Family/Ca ++ -0.051 0.11 -9999 0 -0.29 91 91
PDE6A/B -0.035 0.1 -9999 0 -0.35 51 51
mol:Pi -0.13 0.17 -9999 0 -0.32 210 210
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.061 0.12 -9999 0 -0.28 111 111
PDE6B 0.001 0.067 -9999 0 -0.5 9 9
PDE6A -0.032 0.14 -9999 0 -0.5 42 42
PDE6G 0.004 0.055 -9999 0 -0.5 6 6
RHO 0.004 0.005 -9999 0 -10000 0 0
PDE6 -0.13 0.16 -9999 0 -0.48 58 58
GUCA1A -0.08 0.19 -9999 0 -0.51 88 88
GC2/GCAP Family -0.052 0.11 -9999 0 -0.29 93 93
GUCA1C -0.001 0.022 -9999 0 -0.51 1 1
GUCA1B 0.003 0.06 -9999 0 -0.51 7 7
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0 -9999 0 -10000 0 0
CCL5 0.005 0.05 -9999 0 -0.5 5 5
SDCBP 0.01 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.11 -9999 0 -0.27 81 81
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 -0.1 0.1 -9999 0 -0.31 37 37
Syndecan-1/Syntenin -0.1 0.1 -9999 0 -0.31 34 34
MAPK3 -0.082 0.095 -9999 0 -0.49 2 2
HGF/MET -0.044 0.12 -9999 0 -0.37 62 62
TGFB1/TGF beta receptor Type II 0.01 0 -9999 0 -10000 0 0
BSG 0.01 0 -9999 0 -10000 0 0
keratinocyte migration -0.1 0.1 -9999 0 -0.31 37 37
Syndecan-1/RANTES -0.1 0.1 -9999 0 -0.32 38 38
Syndecan-1/CD147 -0.092 0.099 -9999 0 -0.29 35 35
Syndecan-1/Syntenin/PIP2 -0.11 0.086 -9999 0 -0.3 34 34
LAMA5 0.007 0.039 -9999 0 -0.5 3 3
positive regulation of cell-cell adhesion -0.1 0.085 -9999 0 -0.29 34 34
MMP7 -0.09 0.2 -9999 0 -0.51 99 99
HGF -0.021 0.12 -9999 0 -0.5 31 31
Syndecan-1/CASK -0.11 0.1 -9999 0 -0.26 81 81
Syndecan-1/HGF/MET -0.12 0.13 -9999 0 -0.36 77 77
regulation of cell adhesion -0.074 0.092 -9999 0 -0.47 2 2
HPSE 0.008 0.032 -9999 0 -0.51 2 2
positive regulation of cell migration -0.11 0.11 -9999 0 -0.27 81 81
SDC1 -0.11 0.11 -9999 0 -0.27 81 81
Syndecan-1/Collagen -0.11 0.11 -9999 0 -0.27 81 81
PPIB 0.009 0.023 -9999 0 -0.51 1 1
MET -0.024 0.13 -9999 0 -0.5 34 34
PRKACA 0.01 0 -9999 0 -10000 0 0
MMP9 -0.1 0.21 -9999 0 -0.51 112 112
MAPK1 -0.082 0.095 -9999 0 -0.49 2 2
homophilic cell adhesion -0.11 0.11 -9999 0 -0.27 81 81
MMP1 -0.33 0.24 -9999 0 -0.51 342 342
TCGA08_p53

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
CDKN2A -0.1 0.17 -10000 0 -0.37 152 152
TP53 -0.027 0.044 0.17 1 -10000 0 1
Senescence -0.027 0.044 0.17 1 -10000 0 1
Apoptosis -0.027 0.044 0.17 1 -10000 0 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.052 0.086 0.18 151 -0.33 2 153
MDM4 0.01 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.001 0.073 -9999 0 -0.31 27 27
ADCY5 -0.031 0.12 -9999 0 -0.31 73 73
ADCY6 0.011 0.036 -9999 0 -0.3 7 7
ADCY7 0.011 0.039 -9999 0 -0.3 8 8
ADCY1 0.006 0.055 -9999 0 -0.3 16 16
ADCY2 -0.024 0.11 -9999 0 -0.3 63 63
ADCY3 0.012 0.034 -9999 0 -0.3 6 6
ADCY8 -0.12 0.15 -9999 0 -0.3 207 207
PRKCE 0.005 0.04 -9999 0 -0.36 6 6
ADCY9 0.006 0.055 -9999 0 -0.3 16 16
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.061 0.098 -9999 0 -0.35 28 28
Arf6 signaling events

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.002 0.023 -9999 0 -0.3 3 3
ARNO/beta Arrestin1-2 -0.095 0.11 -9999 0 -0.36 22 22
EGFR -0.006 0.089 -9999 0 -0.5 16 16
EPHA2 0 0.07 -9999 0 -0.5 10 10
USP6 0.01 0 -9999 0 -10000 0 0
IQSEC1 0.009 0.022 -9999 0 -0.5 1 1
EGFR/EGFR/EGF/EGF -0.08 0.15 -9999 0 -0.37 111 111
ARRB2 -0.007 0.056 -9999 0 -0.18 46 46
mol:GTP 0.012 0.021 -9999 0 -0.13 2 2
ARRB1 0.004 0.055 -9999 0 -0.5 6 6
FBXO8 0.01 0 -9999 0 -10000 0 0
TSHR -0.045 0.16 -9999 0 -0.51 54 54
EGF -0.09 0.2 -9999 0 -0.51 99 99
somatostatin receptor activity 0 0 -9999 0 -0.001 94 94
ARAP2 -0.008 0.094 -9999 0 -0.5 18 18
mol:GDP -0.089 0.12 -9999 0 -0.26 125 125
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 57 57
ITGA2B -0.044 0.16 -9999 0 -0.5 54 54
ARF6 0.01 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.037 -9999 0 -0.26 11 11
ADAP1 0.009 0.022 -9999 0 -0.5 1 1
KIF13B 0.008 0.032 -9999 0 -0.5 2 2
HGF/MET -0.044 0.12 -9999 0 -0.37 62 62
PXN 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.084 0.11 -9999 0 -0.26 93 93
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.067 0.13 -9999 0 -0.31 111 111
ADRB2 -0.19 0.25 -9999 0 -0.5 201 201
receptor agonist activity 0 0 -9999 0 0 128 128
actin filament binding 0 0 -9999 0 0 131 131
SRC 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.12 -9999 0 -0.51 28 28
GNAQ 0.009 0.022 -9999 0 -0.5 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 89 89
ARF6/GDP -0.011 0.074 -9999 0 -0.33 12 12
ARF6/GDP/GULP/ACAP1 -0.082 0.099 -9999 0 -0.3 48 48
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.041 0.096 -9999 0 -0.27 31 31
ACAP1 0.008 0.032 -9999 0 -0.5 2 2
ACAP2 0.009 0.023 -9999 0 -0.51 1 1
LHCGR/beta Arrestin2 -0.022 0.077 -9999 0 -0.27 46 46
EFNA1 0.009 0.022 -9999 0 -0.5 1 1
HGF -0.021 0.12 -9999 0 -0.5 31 31
CYTH3 0.007 0.023 -9999 0 -0.37 2 2
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 76 76
endosomal lumen acidification 0 0 -9999 0 0 35 35
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.006 0.045 -9999 0 -0.5 4 4
GNAQ/ARNO 0.006 0.013 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 25 25
MET -0.024 0.13 -9999 0 -0.5 34 34
GNA14 -0.004 0.083 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 89 89
GNA11 0.008 0.032 -9999 0 -0.5 2 2
LHCGR -0.041 0.15 -9999 0 -0.51 46 46
AGTR1 -0.16 0.24 -9999 0 -0.5 167 167
desensitization of G-protein coupled receptor protein signaling pathway -0.021 0.077 -9999 0 -0.27 46 46
IPCEF1/ARNO -0.044 0.1 -9999 0 -0.46 4 4
alphaIIb/beta3 Integrin -0.056 0.13 -9999 0 -0.36 81 81
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.022 -9999 0 -0.35 2 2
Necdin/E2F1 -0.01 0.058 -9999 0 -0.36 14 14
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.029 0.078 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.16 -9999 0 -0.32 182 182
NT-4/5 (dimer)/p75(NTR) -0.031 0.1 -9999 0 -0.38 42 42
IKBKB 0.01 0 -9999 0 -10000 0 0
AKT1 0.002 0.083 -9999 0 -10000 0 0
IKBKG 0.01 0 -9999 0 -10000 0 0
BDNF -0.26 0.25 -9999 0 -0.5 269 269
MGDIs/NGR/p75(NTR)/LINGO1 -0.048 0.12 -9999 0 -0.31 79 79
FURIN -0.004 0.084 -9999 0 -0.51 14 14
proBDNF (dimer)/p75(NTR)/Sortilin -0.16 0.16 -9999 0 -0.3 278 278
LINGO1 -0.055 0.17 -9999 0 -0.51 64 64
Sortilin/TRAF6/NRIF -0.002 0.019 -9999 0 -10000 0 0
proBDNF (dimer) -0.26 0.25 -9999 0 -0.5 269 269
NTRK1 -0.01 0.099 -9999 0 -0.5 20 20
RTN4R 0.008 0.032 -9999 0 -0.5 2 2
neuron apoptosis -0.11 0.14 -9999 0 -0.41 32 32
IRAK1 0.009 0.023 -9999 0 -0.51 1 1
SHC1 -0.013 0.099 -9999 0 -0.29 57 57
ARHGDIA 0.01 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.018 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.029 0.082 -9999 0 -0.26 32 32
MAGEH1 0.01 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.032 0.088 -9999 0 -0.52 2 2
Mammalian IAPs/DIABLO -0.004 0.03 -9999 0 -10000 0 0
proNGF (dimer) -0.028 0.13 -9999 0 -0.5 38 38
MAGED1 0.009 0.023 -9999 0 -0.51 1 1
APP 0.01 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.12 -9999 0 -0.5 28 28
ZNF274 0.01 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.026 0.075 -9999 0 -0.25 1 1
NGF -0.028 0.14 -9999 0 -0.5 38 38
cell cycle arrest 0.01 0.11 -9999 0 -0.28 24 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.062 -9999 0 -0.22 24 24
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.025 0.088 -9999 0 -0.31 42 42
NCSTN 0.01 0 -9999 0 -10000 0 0
mol:GTP -0.032 0.092 -9999 0 -0.29 56 56
PSENEN 0.009 0.023 -9999 0 -0.51 1 1
mol:ceramide -0.005 0.089 -9999 0 -0.26 57 57
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.015 0.056 -9999 0 -0.39 1 1
p75(NTR)/beta APP -0.012 0.064 -9999 0 -0.36 17 17
BEX1 -0.14 0.23 -9999 0 -0.5 146 146
mol:GDP -0.02 0.097 -9999 0 -0.3 55 55
NGF (dimer) -0.084 0.14 -9999 0 -0.28 152 152
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.042 0.1 -9999 0 -0.28 79 79
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
RAC1/GTP -0.027 0.077 -9999 0 -0.25 55 55
MYD88 0.01 0 -9999 0 -10000 0 0
CHUK 0.01 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.032 0.092 -9999 0 -0.3 56 56
RHOB 0.009 0.022 -9999 0 -0.5 1 1
RHOA 0.01 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.006 0.044 -9999 0 -0.36 8 8
NT3 (dimer) -0.018 0.12 -9999 0 -0.5 28 28
TP53 -0.11 0.14 -9999 0 -0.46 10 10
PRDM4 -0.005 0.09 -9999 0 -0.26 57 57
BDNF (dimer) -0.3 0.22 -9999 0 -0.39 392 392
PIK3CA 0.01 0 -9999 0 -10000 0 0
SORT1 0.008 0.032 -9999 0 -0.5 2 2
activation of caspase activity -0.028 0.077 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.029 0.082 -9999 0 -0.26 57 57
RHOC 0.01 0 -9999 0 -10000 0 0
XIAP 0.01 0 -9999 0 -10000 0 0
MAPK10 -0.098 0.15 -9999 0 -0.41 54 54
DIABLO 0.01 0 -9999 0 -10000 0 0
SMPD2 -0.005 0.09 -9999 0 -0.26 57 57
APH1B 0.008 0.032 -9999 0 -0.5 2 2
APH1A 0.01 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.033 0.093 -9999 0 -0.3 57 57
PSEN1 0.01 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.031 0.11 -9999 0 -0.38 41 41
MAPK8 -0.075 0.12 -9999 0 -0.37 30 30
MAPK9 -0.075 0.12 -9999 0 -0.36 32 32
APAF1 0.01 0 -9999 0 -10000 0 0
NTF3 -0.018 0.12 -9999 0 -0.5 28 28
NTF4 -0.018 0.12 -9999 0 -0.5 28 28
NDN 0.004 0.055 -9999 0 -0.5 6 6
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.024 0.068 -9999 0 -10000 0 0
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.016 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.032 0.091 -9999 0 -0.29 56 56
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.13 0.13 -9999 0 -0.49 10 10
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.14 0.14 -9999 0 -0.27 278 278
PRKACB 0.009 0.023 -9999 0 -0.51 1 1
proBDNF (dimer)/p75 ECD -0.18 0.18 -9999 0 -0.35 269 269
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.003 0.06 -9999 0 -0.51 7 7
BIRC2 0.01 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.018 0.11 -9999 0 -0.32 2 2
BAD -0.077 0.13 -9999 0 -0.38 33 33
RIPK2 0.01 0 -9999 0 -10000 0 0
NGFR -0.007 0.092 -9999 0 -0.5 17 17
CYCS 0.001 0.086 -9999 0 -0.49 1 1
ADAM17 0.01 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.028 0.081 -9999 0 -0.26 55 55
BCL2L11 -0.077 0.13 -9999 0 -0.38 33 33
BDNF (dimer)/p75(NTR) -0.2 0.18 -9999 0 -0.36 278 278
PI3K -0.028 0.081 -9999 0 -0.26 56 56
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.029 0.082 -9999 0 -10000 0 0
NDNL2 0.01 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
PRKCI 0.01 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.038 0.11 -9999 0 -0.36 55 55
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.029 0.084 -9999 0 -0.27 57 57
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCZ 0.007 0.039 -9999 0 -0.5 3 3
PLG -0.009 0.074 -9999 0 -0.51 11 11
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.14 0.16 -9999 0 -0.47 36 36
SQSTM1 0.009 0.023 -9999 0 -0.51 1 1
NGFRAP1 0.005 0.05 -9999 0 -0.5 5 5
CASP3 -0.071 0.12 -9999 0 -0.38 25 25
E2F1 0.002 0.064 -9999 0 -0.51 8 8
CASP9 0.01 0 -9999 0 -10000 0 0
IKK complex -0.025 0.067 -9999 0 -0.39 3 3
NGF (dimer)/TRKA -0.04 0.11 -9999 0 -0.36 57 57
MMP7 -0.09 0.2 -9999 0 -0.51 99 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.026 0.075 -9999 0 -10000 0 0
MMP3 -0.19 0.25 -9999 0 -0.51 195 195
APAF-1/Caspase 9 -0.021 0.057 -9999 0 -0.37 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.019 0.18 1 -10000 0 1
AES 0.003 0.016 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.01 0 -10000 0 -10000 0 0
DKK2 -0.097 0.21 -10000 0 -0.5 108 108
TLE1 0.003 0.016 -10000 0 -10000 0 0
MACF1 0.006 0.045 -10000 0 -0.5 4 4
CTNNB1 0.088 0.08 0.24 18 -0.28 1 19
WIF1 -0.34 0.24 -10000 0 -0.5 356 356
beta catenin/RanBP3 0.013 0.088 0.38 25 -10000 0 25
KREMEN2 -0.12 0.22 -10000 0 -0.51 128 128
DKK1 -0.12 0.23 -10000 0 -0.5 135 135
beta catenin/beta TrCP1 0.089 0.075 0.23 17 -10000 0 17
FZD1 0.01 0.001 -10000 0 -10000 0 0
AXIN2 -0.026 0.24 -10000 0 -1.3 18 18
AXIN1 0.011 0.001 -10000 0 -10000 0 0
RAN 0.009 0.023 -10000 0 -0.51 1 1
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.073 0.06 0.27 1 -10000 0 1
Axin1/APC/GSK3 0.021 0.061 0.2 46 -10000 0 46
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.046 -10000 0 -10000 0 0
HNF1A -0.1 0.21 -10000 0 -0.51 105 105
CTBP1 0.004 0.017 -10000 0 -10000 0 0
MYC 0.006 0.1 -10000 0 -1.4 2 2
RANBP3 0.01 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.13 0.19 -10000 0 -0.36 194 194
NKD1 -0.053 0.17 -10000 0 -0.5 63 63
TCF4 0.002 0.036 -10000 0 -0.5 2 2
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.006 0.039 -10000 0 -0.26 12 12
Ran/GTP 0 0.016 -10000 0 -0.37 1 1
CtBP/CBP/TCF/TLE1/AES 0.002 0.11 0.44 25 -10000 0 25
LEF1 0.003 0.028 -10000 0 -0.51 1 1
DVL1 0.074 0.052 0.19 1 -0.27 1 2
CSNK2A1 0.01 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.075 0.066 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.15 0.19 -10000 0 -0.35 223 223
LRP6 0.01 0.001 -10000 0 -10000 0 0
CSNK1A1 0.004 0.019 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.005 0.16 -10000 0 -1.3 7 7
WNT1 -0.002 0.078 -10000 0 -0.51 12 12
GSK3A 0.011 0.001 -10000 0 -10000 0 0
GSK3B 0.01 0.001 -10000 0 -10000 0 0
FRAT1 0.009 0.002 -10000 0 -10000 0 0
PPP2R5D 0.073 0.087 0.3 63 -10000 0 63
APC 0.024 0.041 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.15 0.1 0.22 348 -10000 0 348
CREBBP 0.004 0.017 -10000 0 -10000 0 0
Thromboxane A2 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
TGM2 0.004 0.045 -10000 0 -0.5 4 4
GNB1/GNG2 -0.04 0.072 -10000 0 -0.18 102 102
AKT1 -0.006 0.1 -10000 0 -0.2 59 59
EGF -0.09 0.2 -10000 0 -0.51 99 99
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.011 0.085 -10000 0 -0.42 10 10
mol:Ca2+ -0.026 0.14 -10000 0 -0.3 104 104
LYN 0.028 0.049 -10000 0 -0.36 5 5
RhoA/GTP -0.027 0.048 -10000 0 -0.14 11 11
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.03 0.16 -10000 0 -0.34 104 104
GNG2 0.008 0.032 -10000 0 -0.5 2 2
ARRB2 0.01 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.024 0.041 -10000 0 -0.33 3 3
G beta5/gamma2 -0.052 0.094 -10000 0 -0.23 102 102
PRKCH -0.032 0.16 -10000 0 -0.34 104 104
DNM1 0.002 0.064 -10000 0 -0.51 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.018 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.002 0.077 -10000 0 -0.5 12 12
G12 family/GTP -0.066 0.12 -10000 0 -0.29 104 104
ADRBK1 0.01 0 -10000 0 -10000 0 0
ADRBK2 0.008 0.032 -10000 0 -0.5 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.096 0.34 11 -10000 0 11
mol:NADP -0.001 0.074 -10000 0 -0.5 11 11
RAB11A 0.01 0 -10000 0 -10000 0 0
PRKG1 -0.056 0.17 -10000 0 -0.5 66 66
mol:IP3 -0.039 0.18 -10000 0 -0.37 104 104
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.062 0.23 -10000 0 -0.5 104 104
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.012 0.096 -10000 0 -0.36 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.018 0.075 -10000 0 -0.41 9 9
RHOA 0.01 0 -10000 0 -10000 0 0
PTGIR 0.001 0.067 -10000 0 -0.5 9 9
PRKCB1 -0.039 0.17 -10000 0 -0.37 104 104
GNAQ 0.009 0.022 -10000 0 -0.5 1 1
mol:L-citrulline -0.001 0.074 -10000 0 -0.5 11 11
TXA2/TXA2-R family -0.064 0.24 -10000 0 -0.51 104 104
LCK 0.026 0.055 -10000 0 -0.36 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.051 -10000 0 -0.5 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.021 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.008 0.048 -10000 0 -0.49 3 3
MAPK14 -0.01 0.11 -10000 0 -0.22 102 102
TGM2/GTP -0.046 0.19 -10000 0 -0.41 104 104
MAPK11 -0.011 0.11 -10000 0 -0.22 102 102
ARHGEF1 -0.009 0.087 -10000 0 -0.19 23 23
GNAI2 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.039 0.18 -10000 0 -0.38 104 104
RAB11/GDP 0.01 0.001 -10000 0 -10000 0 0
ICAM1 -0.024 0.14 -10000 0 -0.28 102 102
cAMP biosynthetic process -0.038 0.16 -10000 0 -0.34 104 104
Gq family/GTP/EBP50 0.015 0.046 -10000 0 -0.34 4 4
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.028 0.049 -10000 0 -0.36 5 5
GNB5 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
EGF/EGFR 0.006 0.079 -10000 0 -0.32 14 14
VCAM1 -0.026 0.14 -10000 0 -0.29 102 102
TP beta/Gq family/GDP/G beta5/gamma2 0.024 0.041 -10000 0 -0.33 3 3
platelet activation -0.014 0.15 -10000 0 -0.29 104 104
PGI2/IP -0.006 0.047 -10000 0 -0.36 9 9
PRKACA 0.005 0.064 -10000 0 -0.3 18 18
Gq family/GDP/G beta5/gamma2 0.022 0.043 -10000 0 -0.28 6 6
TXA2/TP beta/beta Arrestin2 -0.003 0.015 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.012 0.061 -10000 0 -0.29 15 15
mol:DAG -0.045 0.19 -10000 0 -0.41 104 104
EGFR -0.006 0.089 -10000 0 -0.5 16 16
TXA2/TP alpha -0.057 0.22 -10000 0 -0.47 104 104
Gq family/GTP -0.007 0.048 -10000 0 -0.24 16 16
YES1 0.028 0.049 -10000 0 -0.36 5 5
GNAI2/GTP -0.009 0.049 -10000 0 -0.42 5 5
PGD2/DP -0.008 0.054 -10000 0 -0.36 12 12
SLC9A3R1 0.008 0.032 -10000 0 -0.51 2 2
FYN 0.027 0.05 -10000 0 -0.36 5 5
mol:NO -0.001 0.074 -10000 0 -0.5 11 11
GNA15 0.01 0 -10000 0 -10000 0 0
PGK/cGMP -0.045 0.11 -10000 0 -0.3 76 76
RhoA/GDP 0.01 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.055 -10000 0 -0.46 5 5
NOS3 -0.001 0.074 -10000 0 -0.5 11 11
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.033 0.16 -10000 0 -0.34 105 105
PRKCB -0.035 0.17 -10000 0 -0.35 106 106
PRKCE -0.032 0.16 -10000 0 -0.34 104 104
PRKCD -0.037 0.17 -10000 0 -0.37 104 104
PRKCG -0.05 0.19 -10000 0 -0.39 104 104
muscle contraction -0.057 0.22 -10000 0 -0.48 104 104
PRKCZ -0.03 0.16 -10000 0 -0.34 103 103
ARR3 -0.001 0.039 -10000 0 -0.51 3 3
TXA2/TP beta -0.01 0.055 -10000 0 -0.47 5 5
PRKCQ -0.054 0.18 -10000 0 -0.38 104 104
MAPKKK cascade -0.054 0.21 -10000 0 -0.45 104 104
SELE -0.047 0.18 -10000 0 -0.39 102 102
TP beta/GNAI2/GDP/G beta/gamma -0.009 0.051 -10000 0 -0.47 4 4
ROCK1 0.01 0 -10000 0 -10000 0 0
GNA14 -0.004 0.083 -10000 0 -0.5 14 14
chemotaxis -0.078 0.27 -10000 0 -0.6 102 102
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.008 0.032 -10000 0 -0.5 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
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 -0.045 0.11 -10000 0 -0.31 76 76
fibroblast growth factor receptor signaling pathway -0.045 0.11 -10000 0 -0.3 76 76
LAMA1 -0.017 0.12 -10000 0 -0.51 27 27
PRNP 0.007 0.039 -10000 0 -0.5 3 3
GPC1/SLIT2 -0.094 0.16 -10000 0 -0.36 137 137
SMAD2 0.017 0.049 -10000 0 -0.26 16 16
GPC1/PrPc/Cu2+ -0.003 0.032 -10000 0 -0.3 6 6
GPC1/Laminin alpha1 -0.021 0.086 -10000 0 -0.37 29 29
TDGF1 -0.019 0.12 -10000 0 -0.5 28 28
CRIPTO/GPC1 -0.021 0.085 -10000 0 -0.36 31 31
APP/GPC1 -0.002 0.027 -10000 0 -0.35 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.002 0.075 -10000 0 -0.29 31 31
FLT1 0.01 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.009 0.051 -10000 0 -0.29 16 16
SERPINC1 -0.003 0.075 -10000 0 -0.51 11 11
FYN 0.001 0.078 -10000 0 -0.3 31 31
FGR -0.021 0.12 -10000 0 -0.32 65 65
positive regulation of MAPKKK cascade -0.018 0.12 -10000 0 -0.37 35 35
SLIT2 -0.12 0.22 -10000 0 -0.5 135 135
GPC1/NRG -0.078 0.15 -10000 0 -0.36 112 112
NRG1 -0.1 0.21 -10000 0 -0.5 111 111
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.022 -10000 0 -0.29 3 3
LYN 0.002 0.075 -10000 0 -0.29 31 31
mol:Spermine 0.007 0.028 -10000 0 -0.36 3 3
cell growth -0.045 0.11 -10000 0 -0.3 76 76
BMP signaling pathway -0.007 0.039 0.5 3 -10000 0 3
SRC 0.002 0.075 -10000 0 -0.29 31 31
TGFBR1 0.009 0.023 -10000 0 -0.51 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.08 0.19 -10000 0 -0.5 90 90
GPC1 0.007 0.039 -10000 0 -0.5 3 3
TGFBR1 (dimer) 0.009 0.023 -10000 0 -0.51 1 1
VEGFA 0.01 0 -10000 0 -10000 0 0
BLK -0.053 0.14 -10000 0 -0.3 117 117
HCK -0.012 0.1 -10000 0 -0.31 52 52
FGF2 -0.063 0.18 -10000 0 -0.5 74 74
FGFR1 0.007 0.039 -10000 0 -0.5 3 3
VEGFR1 homodimer 0.01 0 -10000 0 -10000 0 0
TGFBR2 -0.002 0.077 -10000 0 -0.5 12 12
cell death -0.002 0.027 -10000 0 -0.35 3 3
ATIII/GPC1 -0.01 0.058 -10000 0 -0.36 14 14
PLA2G2A/GPC1 -0.064 0.14 -10000 0 -0.36 92 92
LCK 0 0.078 -10000 0 -0.29 34 34
neuron differentiation -0.078 0.15 -10000 0 -0.36 112 112
PrPc/Cu2+ -0.002 0.027 -10000 0 -0.36 3 3
APP 0.01 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.002 0.077 -10000 0 -0.5 12 12
Effects of Botulinum toxin

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
STX1A -0.089 0.16 -9999 0 -0.37 134 134
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.042 0.12 -9999 0 -0.36 61 61
STXBP1 0.007 0.039 -9999 0 -0.5 3 3
ACh/CHRNA1 -0.033 0.098 -9999 0 -0.34 43 43
RAB3GAP2/RIMS1/UNC13B -0.035 0.095 -9999 0 -0.29 61 61
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 -0.051 0.16 -9999 0 -0.5 60 60
mol:ACh -0.017 0.04 -9999 0 -0.078 138 138
RAB3GAP2 0.01 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.082 0.11 -9999 0 -0.35 27 27
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.033 0.097 -9999 0 -0.34 43 43
UNC13B 0.009 0.022 -9999 0 -0.5 1 1
CHRNA1 -0.033 0.14 -9999 0 -0.51 43 43
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.037 0.11 -9999 0 -0.36 49 49
SNAP25 -0.003 0.041 -9999 0 -0.18 25 25
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.039 0.15 -9999 0 -0.51 49 49
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.071 0.14 -9999 0 -0.3 137 137
STX1A/SNAP25 fragment 1/VAMP2 -0.082 0.11 -9999 0 -0.35 27 27
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.01 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.039 0.079 -10000 0 -0.29 21 21
NT3 (dimer)/TRKC -0.086 0.17 -10000 0 -0.39 114 114
NT3 (dimer)/TRKB -0.13 0.17 -10000 0 -0.32 212 212
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.021 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
BDNF -0.26 0.25 -10000 0 -0.5 269 269
PIK3CA 0.01 0 -10000 0 -10000 0 0
DYNLT1 0.01 0 -10000 0 -10000 0 0
NTRK1 -0.01 0.099 -10000 0 -0.5 20 20
NTRK2 -0.18 0.25 -10000 0 -0.5 191 191
NTRK3 -0.089 0.2 -10000 0 -0.5 100 100
NT-4/5 (dimer)/TRKB -0.13 0.17 -10000 0 -0.33 209 209
neuron apoptosis 0.2 0.2 0.49 124 -10000 0 124
SHC 2-3/Grb2 -0.22 0.22 -10000 0 -0.54 124 124
SHC1 0.008 0.032 -10000 0 -0.51 2 2
SHC2 -0.14 0.14 -10000 0 -0.44 57 57
SHC3 -0.22 0.26 -10000 0 -0.64 119 119
STAT3 (dimer) 0.011 0.04 -10000 0 -0.33 7 7
NT3 (dimer)/TRKA -0.037 0.11 -10000 0 -0.32 60 60
RIN/GDP -0.024 0.076 -10000 0 -0.25 9 9
GIPC1 0.01 0 -10000 0 -10000 0 0
KRAS 0.008 0.032 -10000 0 -0.51 2 2
DNAJA3 -0.026 0.069 -10000 0 -0.31 11 11
RIN/GTP -0.002 0.028 -10000 0 -0.37 3 3
CCND1 0.014 0.087 -10000 0 -0.73 7 7
MAGED1 0.009 0.023 -10000 0 -0.51 1 1
PTPN11 0.01 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.12 -10000 0 -0.5 28 28
SHC/GRB2/SOS1 -0.001 0.019 -10000 0 -0.3 2 2
GRB2 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.046 0.12 -10000 0 -0.33 71 71
TRKA/NEDD4-2 -0.014 0.068 -10000 0 -0.35 20 20
ELMO1 0.005 0.05 -10000 0 -0.5 5 5
RhoG/GTP/ELMO1/DOCK1 -0.003 0.029 -10000 0 -0.3 5 5
NGF -0.028 0.14 -10000 0 -0.5 38 38
HRAS 0.01 0 -10000 0 -10000 0 0
DOCK1 0.01 0 -10000 0 -10000 0 0
GAB2 0.005 0.05 -10000 0 -0.5 5 5
RIT2 -0.002 0.039 -10000 0 -0.51 3 3
RIT1 0.01 0 -10000 0 -10000 0 0
FRS2 0.008 0.032 -10000 0 -0.51 2 2
DNM1 0.002 0.064 -10000 0 -0.51 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.028 0.074 -10000 0 -0.32 14 14
mol:GDP -0.035 0.11 -10000 0 -0.33 13 13
NGF (dimer) -0.028 0.13 -10000 0 -0.5 38 38
RhoG/GDP -0.004 0.035 -10000 0 -0.36 5 5
RIT1/GDP -0.019 0.074 -10000 0 -0.23 8 8
TIAM1 0 0.07 -10000 0 -0.5 10 10
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
BDNF (dimer)/TRKB -0.26 0.21 -10000 0 -0.38 347 347
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.022 -10000 0 -0.36 2 2
FRS2 family/SHP2 -0.002 0.023 -10000 0 -0.3 3 3
SHC/GRB2/SOS1/GAB1 -0.002 0.023 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.12 -10000 0 -0.5 28 28
RAP1/GDP -0.031 0.052 -10000 0 -0.22 3 3
KIDINS220/CRKL 0.01 0 -10000 0 -10000 0 0
BDNF (dimer) -0.26 0.25 -10000 0 -0.5 269 269
ubiquitin-dependent protein catabolic process -0.033 0.094 -10000 0 -0.3 57 57
Schwann cell development -0.047 0.034 -10000 0 -10000 0 0
EHD4 0.01 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.002 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.023 -10000 0 -10000 0 0
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.21 -10000 0 -0.5 177 177
ABL1 0.01 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.093 0.075 -10000 0 -10000 0 0
STAT3 0.011 0.039 -10000 0 -0.32 7 7
axon guidance -0.23 0.2 -10000 0 -0.48 177 177
MAPK3 -0.018 0.12 -10000 0 -0.3 71 71
MAPK1 -0.018 0.12 -10000 0 -0.3 71 71
CDC42/GDP -0.019 0.074 -10000 0 -0.23 7 7
NTF3 -0.018 0.12 -10000 0 -0.5 28 28
NTF4 -0.018 0.12 -10000 0 -0.5 28 28
NGF (dimer)/TRKA/FAIM -0.033 0.095 -10000 0 -0.3 57 57
PI3K -0.001 0.016 -10000 0 -0.35 1 1
FRS3 0.009 0.023 -10000 0 -0.51 1 1
FAIM 0.01 0 -10000 0 -10000 0 0
GAB1 0.008 0.032 -10000 0 -0.5 2 2
RASGRF1 -0.13 0.14 -10000 0 -0.43 46 46
SOS1 0.01 0 -10000 0 -10000 0 0
MCF2L -0.058 0.15 -10000 0 -0.33 117 117
RGS19 0.01 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.011 0.065 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.074 -10000 0 -0.23 7 7
NGF (dimer)/TRKA/GRIT -0.034 0.097 -10000 0 -0.31 57 57
neuron projection morphogenesis -0.001 0.08 -10000 0 -0.45 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.033 0.095 -10000 0 -0.3 57 57
MAP2K1 0.029 0.024 -10000 0 -10000 0 0
NGFR -0.007 0.092 -10000 0 -0.5 17 17
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.07 -10000 0 -0.36 1 1
RAS family/GTP/PI3K 0.023 0.014 -10000 0 -0.23 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.018 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.039 -10000 0 -0.5 3 3
MAPKKK cascade -0.083 0.16 -10000 0 -0.65 33 33
RASA1 0.01 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.014 0.068 -10000 0 -0.35 20 20
SQSTM1 0.009 0.023 -10000 0 -0.51 1 1
BDNF (dimer)/TRKB/GIPC -0.23 0.19 -10000 0 -0.34 347 347
NGF (dimer)/TRKA/p62/Atypical PKCs -0.029 0.081 -10000 0 -0.49 2 2
MATK -0.013 0.1 -10000 0 -0.5 23 23
NEDD4L 0.01 0 -10000 0 -10000 0 0
RAS family/GDP -0.026 0.049 -10000 0 -0.24 2 2
NGF (dimer)/TRKA -0.028 0.075 -10000 0 -0.25 41 41
Rac1/GTP -0.086 0.098 -10000 0 -0.3 49 49
FRS2 family/SHP2/CRK family -0.001 0.018 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.026 0.024 -9999 0 -10000 0 0
VDR 0.008 0.032 -9999 0 -0.5 2 2
FAM120B 0.01 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.091 0.14 -9999 0 -0.46 10 10
RXRs/LXRs/DNA/Oxysterols -0.073 0.14 -9999 0 -0.47 20 20
MED1 0.01 0 -9999 0 -10000 0 0
mol:9cRA 0.003 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.003 0.078 -9999 0 -0.23 53 53
RXRs/NUR77 -0.17 0.18 -9999 0 -0.48 65 65
RXRs/PPAR -0.13 0.16 -9999 0 -0.44 53 53
NCOR2 0.01 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.023 -9999 0 -0.36 2 2
RARs/VDR/DNA/Vit D3 -0.002 0.021 -9999 0 -0.24 4 4
RARA 0.01 0 -9999 0 -10000 0 0
NCOA1 0.01 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.008 0.032 -9999 0 -0.5 2 2
RARs/RARs/DNA/9cRA -0.001 0.016 -9999 0 -0.25 2 2
RARG 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.042 0.04 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.003 0.078 -9999 0 -0.46 1 1
THRA 0.01 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.023 -9999 0 -0.36 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.14 -9999 0 -0.26 267 267
NR1H4 -0.03 0.13 -9999 0 -0.51 36 36
RXRs/LXRs/DNA -0.095 0.14 -9999 0 -0.39 10 10
NR1H2 0.013 0.007 -9999 0 -10000 0 0
NR1H3 0.013 0.008 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.14 -9999 0 -0.32 12 12
NR4A1 -0.093 0.2 -9999 0 -0.5 104 104
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.097 0.12 -9999 0 -0.31 30 30
RXRG -0.25 0.25 -9999 0 -0.5 267 267
RXR alpha/CCPG 0.017 0.004 -9999 0 -10000 0 0
RXRA 0.013 0.007 -9999 0 -10000 0 0
RXRB 0.013 0.008 -9999 0 -10000 0 0
THRB -0.042 0.15 -9999 0 -0.5 52 52
PPARG -0.061 0.18 -9999 0 -0.5 71 71
PPARD 0.01 0 -9999 0 -10000 0 0
TNF -0.082 0.21 -9999 0 -1 19 19
mol:Oxysterols 0.003 0.009 -9999 0 -10000 0 0
cholesterol transport -0.072 0.13 -9999 0 -0.47 20 20
PPARA 0.01 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.008 0.032 -9999 0 -0.5 2 2
RXRs/NUR77/BCL2 -0.15 0.16 -9999 0 -0.26 318 318
SREBF1 -0.06 0.12 -9999 0 -0.53 10 10
RXRs/RXRs/DNA/9cRA -0.12 0.14 -9999 0 -0.26 267 267
ABCA1 -0.062 0.14 -9999 0 -0.62 11 11
RARs/THRs -0.025 0.074 -9999 0 -0.49 1 1
RXRs/FXR -0.14 0.16 -9999 0 -0.46 30 30
BCL2 0.007 0.039 -9999 0 -0.5 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.055 -9999 0 -0.35 13 13
alphaV beta3 Integrin -0.058 0.12 -9999 0 -0.3 98 98
PTK2 -0.058 0.15 -9999 0 -0.43 39 39
IGF1R 0.009 0.022 -9999 0 -0.5 1 1
PI4KB 0.01 0 -9999 0 -10000 0 0
MFGE8 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
CDKN1B -0.1 0.2 -9999 0 -0.5 88 88
VEGFA 0.01 0 -9999 0 -10000 0 0
ILK -0.1 0.2 -9999 0 -0.5 88 88
ROCK1 0.01 0 -9999 0 -10000 0 0
AKT1 -0.094 0.18 -9999 0 -0.47 87 87
PTK2B 0.009 0.077 -9999 0 -0.49 2 2
alphaV/beta3 Integrin/JAM-A -0.092 0.15 -9999 0 -0.51 31 31
CBL 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.032 0.092 -9999 0 -0.3 55 55
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.045 -9999 0 -0.28 13 13
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.018 0.097 -9999 0 -0.37 9 9
alphaV/beta3 Integrin/Syndecan-1 -0.016 0.067 -9999 0 -0.3 28 28
PI4KA 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.05 0.11 -9999 0 -0.53 11 11
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.22 0.15 -9999 0 -0.32 365 365
RPS6KB1 -0.01 0.12 -9999 0 -0.49 11 11
TLN1 0.009 0.022 -9999 0 -0.5 1 1
MAPK3 -0.096 0.19 -9999 0 -0.51 77 77
GPR124 0.007 0.039 -9999 0 -0.5 3 3
MAPK1 -0.096 0.19 -9999 0 -0.51 77 77
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
alphaV/beta3 Integrin/Tumstatin -0.095 0.14 -9999 0 -0.3 161 161
cell adhesion -0.024 0.069 -9999 0 -0.28 2 2
ANGPTL3 -0.021 0.12 -9999 0 -0.51 27 27
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.046 -9999 0 -0.29 13 13
IGF-1R heterotetramer 0.009 0.022 -9999 0 -0.5 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.002 0.077 -9999 0 -0.5 12 12
ITGB3 -0.018 0.12 -9999 0 -0.51 28 28
IGF1 -0.002 0.077 -9999 0 -0.5 12 12
RAC1 0.01 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.074 -9999 0 -0.31 29 29
apoptosis 0.01 0 -9999 0 -10000 0 0
CD47 0.008 0.032 -9999 0 -0.5 2 2
alphaV/beta3 Integrin/CD47 -0.017 0.069 -9999 0 -0.3 30 30
VCL 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.043 0.11 -9999 0 -0.31 70 70
CSF1 0.005 0.05 -9999 0 -0.5 5 5
PIK3C2A -0.1 0.2 -9999 0 -0.5 88 88
PI4 Kinase/Pyk2 -0.08 0.13 -9999 0 -0.44 34 34
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.021 0.072 -9999 0 -0.52 1 1
FAK1/Vinculin -0.041 0.12 -9999 0 -0.36 30 30
alphaV beta3/Integrin/ppsTEM5 -0.018 0.075 -9999 0 -0.32 29 29
RHOA 0.01 0 -9999 0 -10000 0 0
VTN -0.084 0.2 -9999 0 -0.5 95 95
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
FGF2 -0.063 0.18 -9999 0 -0.5 74 74
F11R -0.036 0.13 -9999 0 -0.35 75 75
alphaV/beta3 Integrin/Lactadherin -0.016 0.067 -9999 0 -0.3 28 28
alphaV/beta3 Integrin/TGFBR2 -0.023 0.079 -9999 0 -0.3 40 40
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.028 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.015 0.064 -9999 0 -0.28 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.005 0.05 -9999 0 -0.5 5 5
alphaV/beta3 Integrin/Pyk2 -0.02 0.07 -9999 0 -0.49 2 2
SDC1 0.01 0 -9999 0 -10000 0 0
VAV3 0.024 0.045 -9999 0 -0.49 1 1
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.009 0.022 -9999 0 -0.5 1 1
FAK1/Paxillin -0.041 0.12 -9999 0 -0.35 32 32
cell migration -0.031 0.12 -9999 0 -0.38 13 13
ITGAV 0.01 0 -9999 0 -10000 0 0
PI3K -0.082 0.13 -9999 0 -0.46 31 31
SPP1 -0.35 0.24 -9999 0 -0.51 359 359
KDR -0.003 0.08 -9999 0 -0.5 13 13
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0 -9999 0 -10000 0 0
COL4A3 -0.13 0.23 -9999 0 -0.5 139 139
angiogenesis -0.075 0.21 -9999 0 -0.51 77 77
Rac1/GTP -0.005 0.036 -9999 0 -0.45 1 1
EDIL3 -0.037 0.15 -9999 0 -0.5 47 47
cell proliferation -0.023 0.079 -9999 0 -0.29 40 40
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.002 0.063 -10000 0 -0.5 8 8
EPHB2 -0.046 0.16 -10000 0 -0.51 56 56
EFNB1 0.01 0.054 -10000 0 -0.36 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.058 0.12 -10000 0 -0.48 17 17
Ephrin B2/EPHB1-2 -0.062 0.13 -10000 0 -0.29 113 113
neuron projection morphogenesis -0.056 0.11 -10000 0 -0.46 17 17
Ephrin B1/EPHB1-2/Tiam1 -0.059 0.13 -10000 0 -0.52 17 17
DNM1 0.002 0.064 -10000 0 -0.51 8 8
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.046 0.18 -10000 0 -0.58 54 54
YES1 -0.083 0.25 -10000 0 -0.8 54 54
Ephrin B1/EPHB1-2/NCK2 -0.054 0.12 -10000 0 -0.49 14 14
PI3K -0.047 0.19 -10000 0 -0.58 54 54
mol:GDP -0.059 0.13 -10000 0 -0.51 17 17
ITGA2B -0.044 0.16 -10000 0 -0.5 54 54
endothelial cell proliferation -0.004 0.037 -10000 0 -0.3 8 8
FYN -0.083 0.25 -10000 0 -0.8 54 54
MAP3K7 -0.064 0.19 -10000 0 -0.62 54 54
FGR -0.095 0.25 -10000 0 -0.82 54 54
TIAM1 0 0.07 -10000 0 -0.5 10 10
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
RGS3 0.01 0 -10000 0 -10000 0 0
cell adhesion -0.071 0.2 -10000 0 -0.58 54 54
LYN -0.083 0.25 -10000 0 -0.8 54 54
Ephrin B1/EPHB1-2/Src Family Kinases -0.078 0.23 -10000 0 -0.74 54 54
Ephrin B1/EPHB1-2 -0.073 0.21 -10000 0 -0.67 54 54
SRC -0.083 0.24 -10000 0 -0.8 54 54
ITGB3 -0.018 0.12 -10000 0 -0.51 28 28
EPHB1 -0.051 0.17 -10000 0 -0.51 60 60
EPHB4 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.004 0.037 -10000 0 -0.3 8 8
alphaIIb/beta3 Integrin -0.056 0.13 -10000 0 -0.36 81 81
BLK -0.088 0.25 -10000 0 -0.8 54 54
HCK -0.089 0.25 -10000 0 -0.82 54 54
regulation of stress fiber formation 0.054 0.12 0.49 14 -10000 0 14
MAPK8 -0.038 0.18 -10000 0 -0.55 54 54
Ephrin B1/EPHB1-2/RGS3 -0.054 0.12 -10000 0 -0.49 14 14
endothelial cell migration -0.055 0.17 -10000 0 -0.53 55 55
NCK2 0.01 0 -10000 0 -10000 0 0
PTPN13 -0.058 0.19 -10000 0 -0.61 54 54
regulation of focal adhesion formation 0.054 0.12 0.49 14 -10000 0 14
chemotaxis 0.054 0.12 0.49 14 -10000 0 14
PIK3CA 0.01 0 -10000 0 -10000 0 0
Rac1/GTP -0.057 0.12 -10000 0 -0.48 17 17
angiogenesis -0.072 0.2 -10000 0 -0.66 54 54
LCK -0.083 0.25 -10000 0 -0.8 54 54
EGFR-dependent Endothelin signaling 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
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR -0.006 0.089 -9999 0 -0.5 16 16
EGF/EGFR -0.088 0.14 -9999 0 -0.27 167 167
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.055 0.11 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.008 0.032 -9999 0 -0.5 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.09 0.2 -9999 0 -0.51 99 99
EGF/EGFR dimer/SHC -0.067 0.13 -9999 0 -0.31 113 113
mol:GDP -0.054 0.1 -9999 0 -0.49 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.064 0.18 -9999 0 -0.5 75 75
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.049 0.095 -9999 0 -0.45 4 4
SHC1 0.008 0.032 -9999 0 -0.51 2 2
HRAS/GDP -0.05 0.097 -9999 0 -0.46 4 4
FRAP1 -0.029 0.11 -9999 0 -0.47 4 4
EGF/EGFR dimer -0.08 0.15 -9999 0 -0.37 111 111
SOS1 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.053 0.13 -9999 0 -0.35 77 77
ErbB4 signaling events

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.073 0.14 -10000 0 -0.41 47 47
epithelial cell differentiation -0.077 0.12 -10000 0 -0.44 22 22
ITCH 0.023 0.018 -10000 0 -10000 0 0
WWP1 -0.019 0.068 -10000 0 -10000 0 0
FYN 0.009 0.022 -10000 0 -0.5 1 1
EGFR -0.006 0.089 -10000 0 -0.5 16 16
PRL -0.01 0.08 -10000 0 -0.51 13 13
neuron projection morphogenesis -0.029 0.11 -10000 0 -0.44 2 2
PTPRZ1 -0.11 0.22 -10000 0 -0.5 117 117
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.069 0.1 -10000 0 -0.49 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.07 0.14 -10000 0 -0.36 54 54
ADAM17 0.023 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.033 0.088 -10000 0 -0.38 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.14 0.17 -10000 0 -0.41 90 90
NCOR1 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.079 0.12 -10000 0 -0.34 54 54
GRIN2B -0.06 0.13 -10000 0 -0.34 56 56
ErbB4/ErbB2/betacellulin -0.034 0.062 -10000 0 -0.34 12 12
STAT1 0.01 0 -10000 0 -10000 0 0
HBEGF -0.076 0.19 -10000 0 -0.5 87 87
PRLR -0.052 0.17 -10000 0 -0.5 62 62
E4ICDs/ETO2 -0.042 0.11 -10000 0 -0.42 19 19
axon guidance 0 0.076 -10000 0 -10000 0 0
NEDD4 0.022 0.028 -10000 0 -0.48 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.053 0.13 -10000 0 -0.37 74 74
CBFA2T3 -0.022 0.12 -10000 0 -0.5 32 32
ErbB4/ErbB2/HBEGF -0.069 0.11 -10000 0 -0.34 49 49
MAPK3 -0.036 0.12 -10000 0 -0.46 2 2
STAT1 (dimer) -0.024 0.074 -10000 0 -0.32 1 1
MAPK1 -0.036 0.12 -10000 0 -0.46 2 2
JAK2 0.008 0.032 -10000 0 -0.5 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.08 0.12 -10000 0 -0.34 57 57
NRG1 -0.056 0.16 -10000 0 -0.35 111 111
NRG3 -0.19 0.25 -10000 0 -0.5 202 202
NRG2 -0.049 0.16 -10000 0 -0.5 59 59
NRG4 -0.037 0.15 -10000 0 -0.51 46 46
heart development 0 0.076 -10000 0 -10000 0 0
neural crest cell migration -0.079 0.12 -10000 0 -0.34 57 57
ERBB2 0.024 0.031 -10000 0 -0.36 3 3
WWOX/E4ICDs -0.024 0.074 -10000 0 -0.33 1 1
SHC1 0.008 0.032 -10000 0 -0.51 2 2
ErbB4/EGFR/neuregulin 4 -0.068 0.11 -10000 0 -0.4 31 31
apoptosis 0.21 0.23 0.45 201 -10000 0 201
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.058 0.12 -10000 0 -0.4 32 32
ErbB4/ErbB2/epiregulin -0.1 0.13 -10000 0 -0.34 72 72
ErbB4/ErbB4/betacellulin/betacellulin -0.032 0.092 -10000 0 -0.4 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.1 0.14 -10000 0 -0.4 65 65
MDM2 -0.022 0.077 -10000 0 -0.33 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.072 0.11 -10000 0 -0.32 54 54
STAT5A 0.005 0.073 -10000 0 -0.3 1 1
ErbB4/EGFR/neuregulin 1 beta -0.086 0.13 -10000 0 -0.37 59 59
DLG4 0.01 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.022 -10000 0 -0.36 2 2
E4ICDs/TAB2/NCoR1 -0.039 0.055 -10000 0 -0.3 1 1
STAT5A (dimer) -0.082 0.13 -10000 0 -0.47 22 22
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.004 0.069 -10000 0 -10000 0 0
LRIG1 0.007 0.039 -10000 0 -0.5 3 3
EREG -0.15 0.24 -10000 0 -0.5 163 163
BTC -0.004 0.083 -10000 0 -0.5 14 14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.003 0.075 -10000 0 -10000 0 0
ERBB4 -0.033 0.088 -10000 0 -0.38 1 1
STAT5B 0.01 0 -10000 0 -10000 0 0
YAP1 -0.001 0.024 -10000 0 -0.53 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.049 0.086 -10000 0 -0.34 23 23
glial cell differentiation 0.039 0.055 0.3 1 -10000 0 1
WWOX 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.071 0.16 -10000 0 -0.46 38 38
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.064 0.19 -10000 0 -0.52 75 75
NFATC2 0.003 0.17 -10000 0 -0.67 15 15
NFATC3 -0.011 0.082 -10000 0 -0.3 9 9
CD40LG -0.074 0.36 -10000 0 -0.96 56 56
ITCH -0.011 0.099 -10000 0 -10000 0 0
CBLB -0.011 0.099 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.23 -10000 0 -0.87 28 28
JUNB 0.007 0.039 -10000 0 -0.5 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.051 0.11 -10000 0 -10000 0 0
T cell anergy -0.061 0.16 -10000 0 -0.38 98 98
TLE4 0.019 0.15 -10000 0 -0.8 9 9
Jun/NFAT1-c-4/p21SNFT -0.12 0.31 -10000 0 -0.92 56 56
AP-1/NFAT1-c-4 -0.086 0.41 -10000 0 -1.1 55 55
IKZF1 0.019 0.15 -10000 0 -0.82 9 9
T-helper 2 cell differentiation 0.005 0.19 -10000 0 -0.75 17 17
AP-1/NFAT1 -0.046 0.12 -10000 0 -0.49 20 20
CALM1 -0.011 0.066 -10000 0 -10000 0 0
EGR2 -0.058 0.4 -10000 0 -1.1 53 53
EGR3 -0.1 0.48 -10000 0 -1.3 62 62
NFAT1/FOXP3 -0.043 0.18 -10000 0 -0.57 16 16
EGR1 -0.017 0.12 -10000 0 -0.5 28 28
JUN 0.005 0.042 -10000 0 -0.5 3 3
EGR4 -0.044 0.16 -10000 0 -0.51 53 53
mol:Ca2+ -0.022 0.07 -10000 0 -10000 0 0
GBP3 0.007 0.18 -10000 0 -0.71 22 22
FOSL1 -0.011 0.1 -10000 0 -0.51 21 21
NFAT1-c-4/MAF/IRF4 -0.12 0.3 -10000 0 -0.84 64 64
DGKA 0.024 0.12 -10000 0 -0.71 5 5
CREM 0.009 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.15 0.34 -10000 0 -0.93 67 67
CTLA4 -0.028 0.16 -10000 0 -0.64 13 13
NFAT1-c-4 (dimer)/EGR1 -0.12 0.34 -10000 0 -0.94 65 65
NFAT1-c-4 (dimer)/EGR4 -0.14 0.32 -10000 0 -0.89 65 65
FOS -0.019 0.12 -10000 0 -0.51 27 27
IFNG -0.091 0.23 -10000 0 -0.9 27 27
T cell activation 0.009 0.2 -10000 0 -0.65 22 22
MAF 0.009 0.022 -10000 0 -0.5 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.036 0.29 0.72 63 -10000 0 63
TNF -0.075 0.34 -10000 0 -0.92 57 57
FASLG -0.12 0.49 -10000 0 -1.3 68 68
TBX21 -0.013 0.1 -10000 0 -0.5 22 22
BATF3 0.01 0 -10000 0 -10000 0 0
PRKCQ -0.061 0.18 -10000 0 -0.5 74 74
PTPN1 0.025 0.12 -10000 0 -0.71 5 5
NFAT1-c-4/ICER1 -0.12 0.31 -10000 0 -0.88 64 64
GATA3 0.008 0.039 -10000 0 -0.5 3 3
T-helper 1 cell differentiation -0.053 0.24 -10000 0 -0.88 27 27
IL2RA -0.12 0.22 -10000 0 -0.79 30 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.025 0.12 -10000 0 -0.71 5 5
E2F1 0.006 0.064 -10000 0 -0.5 8 8
PPARG -0.06 0.18 -10000 0 -0.5 71 71
SLC3A2 0.025 0.12 -10000 0 -0.71 5 5
IRF4 -0.006 0.09 -10000 0 -0.51 16 16
PTGS2 -0.088 0.38 -10000 0 -0.99 59 59
CSF2 -0.085 0.37 -10000 0 -0.97 57 57
JunB/Fra1/NFAT1-c-4 -0.12 0.3 -10000 0 -0.86 64 64
IL4 0.003 0.2 -10000 0 -0.84 15 15
IL5 -0.068 0.34 -10000 0 -0.93 54 54
IL2 0.009 0.2 -10000 0 -0.66 22 22
IL3 -0.026 0.047 -10000 0 -10000 0 0
RNF128 -0.08 0.24 -10000 0 -0.57 98 98
NFATC1 -0.036 0.29 -10000 0 -0.73 63 63
CDK4 0.011 0.17 0.56 21 -10000 0 21
PTPRK 0.025 0.12 -10000 0 -0.71 5 5
IL8 -0.073 0.35 -10000 0 -0.92 55 55
POU2F1 0.01 0.001 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.13 0.4 -10000 0 -1.1 46 46
IL23A -0.15 0.43 -10000 0 -1.2 41 41
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.35 -10000 0 -1.1 49 49
positive regulation of T cell mediated cytotoxicity -0.15 0.45 -10000 0 -1.2 50 50
ITGA3 -0.14 0.4 -10000 0 -1.1 48 48
IL17F -0.07 0.28 -10000 0 -0.72 38 38
IL12B 0.01 0.064 -10000 0 -0.53 6 6
STAT1 (dimer) -0.14 0.43 -10000 0 -1.2 49 49
CD4 -0.13 0.4 -10000 0 -1.1 44 44
IL23 -0.15 0.41 -10000 0 -1.2 43 43
IL23R -0.001 0.083 -10000 0 -10000 0 0
IL1B -0.16 0.46 -10000 0 -1.3 52 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.12 0.39 -10000 0 -1.1 47 47
TYK2 0.01 0.019 -10000 0 -10000 0 0
STAT4 0.01 0 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
IL18RAP -0.01 0.098 -10000 0 -0.5 20 20
IL12RB1 -0.005 0.093 -10000 0 -0.53 15 15
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.001 0.071 -10000 0 -0.39 15 15
IL23R/JAK2 0.001 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.15 0.45 -10000 0 -1.2 50 50
natural killer cell activation 0.001 0.007 0.035 1 -10000 0 1
JAK2 0.015 0.041 -10000 0 -0.52 2 2
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
NFKB1 0.009 0.003 -10000 0 -10000 0 0
RELA 0.009 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.15 0.39 -10000 0 -1.1 43 43
ALOX12B -0.14 0.4 -10000 0 -1.1 49 49
CXCL1 -0.14 0.43 -10000 0 -1.3 44 44
T cell proliferation -0.15 0.45 -10000 0 -1.2 50 50
NFKBIA 0.009 0.003 -10000 0 -10000 0 0
IL17A -0.049 0.23 -10000 0 -0.58 27 27
PI3K -0.21 0.36 -10000 0 -1.1 50 50
IFNG -0.007 0.033 -10000 0 -0.12 12 12
STAT3 (dimer) -0.2 0.34 -10000 0 -1.1 49 49
IL18R1 -0.013 0.1 -10000 0 -0.5 23 23
IL23/IL23R/JAK2/TYK2/SOCS3 -0.06 0.25 -10000 0 -0.68 31 31
IL18/IL18R -0.017 0.11 -10000 0 -0.35 43 43
macrophage activation -0.013 0.016 -10000 0 -0.044 39 39
TNF -0.15 0.44 -10000 0 -1.2 49 49
STAT3/STAT4 -0.21 0.36 -10000 0 -1.1 50 50
STAT4 (dimer) -0.14 0.43 -10000 0 -1.2 49 49
IL18 0 0.07 -10000 0 -0.5 10 10
IL19 -0.13 0.39 -10000 0 -1.1 47 47
STAT5A (dimer) -0.14 0.43 -10000 0 -1.2 49 49
STAT1 0.01 0 -10000 0 -10000 0 0
SOCS3 0.006 0.045 -10000 0 -0.5 4 4
CXCL9 -0.15 0.42 -10000 0 -1.1 53 53
MPO -0.14 0.42 -10000 0 -1.1 54 54
positive regulation of humoral immune response -0.15 0.45 -10000 0 -1.2 50 50
IL23/IL23R/JAK2/TYK2 -0.16 0.48 -10000 0 -1.3 50 50
IL6 -0.28 0.58 -10000 0 -1.2 132 132
STAT5A 0.009 0.022 -10000 0 -0.5 1 1
IL2 0.007 0.009 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.007 0.035 1 -10000 0 1
CD3E -0.13 0.4 -10000 0 -1.1 48 48
keratinocyte proliferation -0.15 0.45 -10000 0 -1.2 50 50
NOS2 -0.18 0.48 -10000 0 -1.1 80 80
Aurora A 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
Aurora A/GADD45A -0.011 0.067 -9999 0 -0.3 2 2
BIRC5 -0.29 0.26 -9999 0 -0.51 297 297
NFKBIA -0.008 0.065 -9999 0 -10000 0 0
CPEB1 -0.064 0.18 -9999 0 -0.5 74 74
AKT1 -0.008 0.065 -9999 0 -10000 0 0
NDEL1 0.01 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.017 0.061 -9999 0 -0.36 3 3
NDEL1/TACC3 -0.012 0.057 -9999 0 -0.38 3 3
GADD45A 0.008 0.032 -9999 0 -0.5 2 2
GSK3B 0.011 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.01 0.065 -9999 0 -10000 0 0
MDM2 0.008 0.032 -9999 0 -0.51 2 2
JUB 0.008 0.032 -9999 0 -0.5 2 2
TPX2 -0.19 0.19 -9999 0 -0.36 280 280
TP53 0.002 0.043 -9999 0 -10000 0 0
DLG7 -0.016 0.065 -9999 0 -10000 0 0
AURKAIP1 0.009 0.022 -9999 0 -0.5 1 1
ARHGEF7 0.01 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.013 0.062 -9999 0 -0.4 3 3
G2/M transition of mitotic cell cycle -0.017 0.061 -9999 0 -0.36 3 3
AURKA -0.018 0.08 -9999 0 -10000 0 0
AURKB -0.054 0.052 -9999 0 -0.13 91 91
CDC25B -0.011 0.052 -9999 0 -0.22 1 1
G2/M transition checkpoint -0.016 0.058 -9999 0 -0.33 2 2
mRNA polyadenylation -0.055 0.12 -9999 0 -0.3 74 74
Aurora A/CPEB -0.055 0.12 -9999 0 -0.31 74 74
Aurora A/TACC1/TRAP/chTOG -0.018 0.075 -9999 0 -0.36 7 7
BRCA1 0.007 0.039 -9999 0 -0.51 3 3
centrosome duplication -0.01 0.065 -9999 0 -10000 0 0
regulation of centrosome cycle -0.013 0.057 -9999 0 -0.37 3 3
spindle assembly -0.019 0.074 -9999 0 -0.36 7 7
TDRD7 0.01 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.16 0.14 -9999 0 -0.36 95 95
CENPA -0.05 0.05 -9999 0 -0.14 91 91
Aurora A/PP2A -0.01 0.065 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.005 0.049 -9999 0 -10000 0 0
negative regulation of DNA binding 0.002 0.043 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.016 0.059 -9999 0 -0.33 2 2
mitotic prometaphase 0.015 0.015 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.018 0.08 -9999 0 -10000 0 0
TACC1 -0.013 0.1 -9999 0 -0.5 23 23
TACC3 0.007 0.039 -9999 0 -0.51 3 3
Aurora A/Antizyme1 -0.012 0.056 -9999 0 -0.26 1 1
Aurora A/RasGAP -0.01 0.065 -9999 0 -10000 0 0
OAZ1 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.023 -9999 0 -0.51 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.011 0.003 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.19 0.19 -9999 0 -0.36 280 280
PPP2R5D 0.01 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.16 0.17 -9999 0 -0.31 280 280
PAK1 0.01 0 -9999 0 -10000 0 0
CKAP5 0.01 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.01 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.029 0.073 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.008 0.043 -9999 0 -0.25 16 16
POMC -0.014 0.11 -9999 0 -0.5 24 24
EGFR -0.006 0.089 -9999 0 -0.5 16 16
Syndecan-3/EGFR -0.008 0.042 -9999 0 -0.24 16 16
AGRP -0.21 0.25 -9999 0 -0.5 219 219
NCSTN 0.01 0 -9999 0 -10000 0 0
PSENEN 0.009 0.023 -9999 0 -0.51 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.008 0.032 -9999 0 -0.5 2 2
APH1A 0.01 0 -9999 0 -10000 0 0
NCAN -0.01 0.089 -9999 0 -0.51 16 16
long-term memory -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.01 0.047 -9999 0 -0.24 20 20
PSEN1 0.01 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.009 0.022 -9999 0 -0.5 1 1
limb bud formation 0 0.004 -9999 0 -10000 0 0
MC4R -0.03 0.13 -9999 0 -0.51 37 37
SRC 0.01 0 -9999 0 -10000 0 0
PTN -0.06 0.18 -9999 0 -0.5 70 70
FGFR/FGF/Syndecan-3 0 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.034 0.081 -9999 0 -0.44 4 4
Syndecan-3/AgRP -0.1 0.12 -9999 0 -0.24 219 219
Syndecan-3/AgRP/MC4R -0.11 0.13 -9999 0 -0.24 241 241
Fyn/Cortactin -0.001 0.016 -9999 0 -0.35 1 1
SDC3 0 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.01 0.046 -9999 0 -0.24 20 20
IL8 -0.01 0.1 -9999 0 -0.51 20 20
Syndecan-3/Fyn/Cortactin -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.042 0.12 -9999 0 -0.37 58 58
Gamma Secretase -0.001 0.018 -9999 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.22 -10000 0 -0.63 22 22
CRP -0.15 0.23 -10000 0 -0.62 28 28
cell cycle arrest -0.17 0.25 -10000 0 -0.57 91 91
TIMP1 -0.12 0.19 -10000 0 -0.56 21 21
IL6ST -0.014 0.1 -10000 0 -0.5 21 21
Rac1/GDP -0.07 0.15 -10000 0 -0.45 25 25
AP1 0.003 0.088 -10000 0 -0.54 4 4
GAB2 0.007 0.05 -10000 0 -0.5 5 5
TNFSF11 -0.19 0.25 -10000 0 -0.64 51 51
HSP90B1 -0.005 0.044 -10000 0 -10000 0 0
GAB1 0.009 0.032 -10000 0 -0.5 2 2
MAPK14 -0.047 0.14 -10000 0 -0.54 18 18
AKT1 0.036 0.033 -10000 0 -10000 0 0
FOXO1 0.04 0.033 -10000 0 -10000 0 0
MAP2K6 -0.065 0.15 -10000 0 -0.5 21 21
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
MAP2K4 -0.083 0.16 -10000 0 -0.48 24 24
MITF -0.073 0.15 -10000 0 -0.36 69 69
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0 -10000 0 -10000 0 0
A2M -0.086 0.35 -10000 0 -1.3 41 41
CEBPB 0.015 0.003 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.011 0.083 0.22 2 -0.47 5 7
STAT3 -0.17 0.26 -10000 0 -0.6 91 91
STAT1 -0.003 0.012 -10000 0 -10000 0 0
CEBPD -0.15 0.23 -10000 0 -0.68 23 23
PIK3CA 0.011 0 -10000 0 -10000 0 0
PI3K 0.015 0.017 -10000 0 -0.35 1 1
JUN 0.007 0.039 -10000 0 -0.5 3 3
PIAS3/MITF -0.062 0.14 -10000 0 -0.48 21 21
MAPK11 -0.048 0.14 -10000 0 -0.55 19 19
STAT3 (dimer)/FOXO1 -0.12 0.24 -10000 0 -0.63 37 37
GRB2/SOS1/GAB family -0.061 0.12 -10000 0 -0.45 23 23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.068 0.16 -10000 0 -0.35 79 79
GRB2 0.011 0.004 -10000 0 -10000 0 0
JAK2 0.008 0.032 -10000 0 -0.5 2 2
LBP -0.13 0.2 -10000 0 -0.59 18 18
PIK3R1 0.01 0.022 -10000 0 -0.5 1 1
JAK1 0.009 0.004 -10000 0 -10000 0 0
MYC -0.14 0.23 -10000 0 -0.64 25 25
FGG -0.33 0.46 -10000 0 -0.98 157 157
macrophage differentiation -0.17 0.25 -10000 0 -0.57 91 91
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.074 0.13 -10000 0 -0.46 15 15
JUNB -0.14 0.22 -10000 0 -0.69 19 19
FOS -0.017 0.11 -10000 0 -0.5 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.079 0.15 -10000 0 -0.35 78 78
STAT1/PIAS1 -0.082 0.14 -10000 0 -0.36 67 67
GRB2/SOS1/GAB family/SHP2/PI3K 0.017 0.037 -10000 0 -0.25 3 3
STAT3 (dimer) -0.17 0.26 -10000 0 -0.59 91 91
PRKCD -0.098 0.19 -10000 0 -0.54 22 22
IL6R -0.002 0.074 -10000 0 -0.5 11 11
SOCS3 -0.036 0.16 -10000 0 -0.69 14 14
gp130 (dimer)/JAK1/JAK1/LMO4 -0.001 0.065 -10000 0 -0.29 22 22
Rac1/GTP -0.084 0.15 -10000 0 -0.4 43 43
HCK -0.014 0.11 -10000 0 -0.5 24 24
MAPKKK cascade 0.008 0.081 -10000 0 -0.56 5 5
bone resorption -0.18 0.24 -10000 0 -0.61 51 51
IRF1 -0.14 0.22 -10000 0 -0.63 22 22
mol:GDP -0.073 0.15 -10000 0 -0.36 67 67
SOS1 0.012 0.006 -10000 0 -10000 0 0
VAV1 -0.075 0.15 -10000 0 -0.36 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.043 0.14 -10000 0 -0.5 23 23
PTPN11 -0.001 0.01 -10000 0 -10000 0 0
IL6/IL6RA -0.084 0.16 -10000 0 -0.36 128 128
gp130 (dimer)/TYK2/TYK2/LMO4 -0.003 0.063 -10000 0 -0.29 22 22
gp130 (dimer)/JAK2/JAK2/LMO4 -0.004 0.066 -10000 0 -0.29 24 24
IL6 -0.11 0.22 -10000 0 -0.5 120 120
PIAS3 0.01 0 -10000 0 -10000 0 0
PTPRE 0.012 0.033 -10000 0 -0.49 2 2
PIAS1 0.01 0 -10000 0 -10000 0 0
RAC1 0.009 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.069 0.14 -10000 0 -0.3 94 94
LMO4 0.006 0.024 -10000 0 -0.5 1 1
STAT3 (dimer)/PIAS3 -0.2 0.22 -10000 0 -0.59 70 70
MCL1 0.041 0.03 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.061 -10000 0 -0.54 5 5
HDAC1 0.002 0.007 -10000 0 -10000 0 0
AES 0.009 0.002 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
DTX1 0.007 0.039 -10000 0 -0.51 3 3
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.009 0.002 -10000 0 -10000 0 0
AP1 -0.028 0.12 -10000 0 -0.29 79 79
NCSTN 0.01 0 -10000 0 -10000 0 0
ADAM10 0.01 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.01 0.056 -10000 0 -0.36 1 1
NICD/RBPSUH -0.005 0.053 -10000 0 -0.54 5 5
WIF1 -0.34 0.24 -10000 0 -0.5 356 356
NOTCH1 -0.006 0.056 -10000 0 -0.57 5 5
PSENEN 0.009 0.023 -10000 0 -0.51 1 1
KREMEN2 -0.12 0.22 -10000 0 -0.51 128 128
DKK1 -0.12 0.23 -10000 0 -0.5 135 135
beta catenin/beta TrCP1 0.018 0.052 -10000 0 -10000 0 0
APH1B 0.008 0.032 -10000 0 -0.5 2 2
APH1A 0.01 0 -10000 0 -10000 0 0
AXIN1 -0.005 0.026 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES -0.012 0.064 0.27 1 -10000 0 1
PSEN1 0.01 0 -10000 0 -10000 0 0
FOS -0.017 0.11 -10000 0 -0.5 27 27
JUN 0.007 0.039 -10000 0 -0.5 3 3
MAP3K7 0.009 0.002 -10000 0 -10000 0 0
CTNNB1 0.013 0.055 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.13 0.19 -10000 0 -0.36 194 194
HNF1A -0.097 0.21 -10000 0 -0.51 105 105
CTBP1 0.009 0.002 -10000 0 -10000 0 0
MYC 0.015 0.084 -10000 0 -1.3 2 2
NKD1 -0.053 0.17 -10000 0 -0.5 63 63
FZD1 0.01 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.007 0.056 -10000 0 -0.54 5 5
apoptosis -0.028 0.12 -10000 0 -0.29 79 79
Delta 1/NOTCHprecursor -0.01 0.061 -10000 0 -0.54 5 5
DLL1 0.001 0.067 -10000 0 -0.5 9 9
PPARD 0.02 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.018 -10000 0 -10000 0 0
APC -0.005 0.026 -10000 0 -10000 0 0
DVL1 -0.032 0.032 -10000 0 -0.43 2 2
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.15 0.19 -10000 0 -0.35 223 223
LRP6 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.01 0.006 -10000 0 -10000 0 0
CCND1 0.004 0.15 -10000 0 -1.3 7 7
WNT1 -0.003 0.078 -10000 0 -0.51 12 12
Axin1/APC/beta catenin 0.012 0.04 -10000 0 -0.28 1 1
DKK2 -0.097 0.21 -10000 0 -0.5 108 108
NOTCH1 precursor/DVL1 -0.017 0.054 -10000 0 -0.49 6 6
GSK3B 0.009 0 -10000 0 -10000 0 0
FRAT1 0.009 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.056 -10000 0 -0.54 5 5
PPP2R5D 0.015 0.085 0.24 63 -10000 0 63
MAPK1 0.01 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.12 -10000 0 -0.31 43 43
RBPJ 0.01 0 -10000 0 -10000 0 0
CREBBP 0.012 0.002 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.22 -9999 0 -0.5 137 137
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0 -9999 0 -10000 0 0
TCEB1 0.009 0.023 -9999 0 -0.51 1 1
HIF1A/p53 0.005 0.034 -9999 0 -10000 0 0
HIF1A -0.001 0.036 -9999 0 -10000 0 0
COPS5 0.01 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0.011 -9999 0 -10000 0 0
FIH (dimer) 0.01 0 -9999 0 -10000 0 0
CDKN2A -0.14 0.24 -9999 0 -0.51 152 152
ARNT/IPAS -0.094 0.16 -9999 0 -0.35 137 137
HIF1AN 0.01 0 -9999 0 -10000 0 0
GNB2L1 0.01 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.005 0.034 -9999 0 -10000 0 0
CUL2 0.01 0 -9999 0 -10000 0 0
OS9 0.01 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.013 -9999 0 -0.3 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.005 0.034 -9999 0 -10000 0 0
PHD1-3/OS9 -0.066 0.11 -9999 0 -0.26 129 129
HIF1A/RACK1/Elongin B/Elongin C -0.011 0.019 -9999 0 -10000 0 0
VHL 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.005 0.034 -9999 0 -10000 0 0
EGLN3 -0.12 0.22 -9999 0 -0.51 130 130
EGLN2 0.01 0 -9999 0 -10000 0 0
EGLN1 0.01 0 -9999 0 -10000 0 0
TP53 0.01 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.009 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.068 0.12 -9999 0 -0.25 152 152
Reelin signaling pathway

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
CDK5R1/CDK5 -0.011 0.062 -9999 0 -0.36 16 16
VLDLR -0.002 0.077 -9999 0 -0.5 12 12
CRKL 0.01 0 -9999 0 -10000 0 0
LRPAP1 0.01 0 -9999 0 -10000 0 0
FYN 0.009 0.022 -9999 0 -0.5 1 1
ITGA3 0.005 0.05 -9999 0 -0.5 5 5
RELN/VLDLR/Fyn -0.052 0.12 -9999 0 -0.31 86 86
MAPK8IP1/MKK7/MAP3K11/JNK1 0 0.01 -9999 0 -10000 0 0
AKT1 -0.016 0.098 -9999 0 -0.39 9 9
MAP2K7 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
DAB1 -0.003 0.067 -9999 0 -0.51 9 9
RELN/LRP8/DAB1 -0.053 0.11 -9999 0 -0.28 96 96
LRPAP1/LRP8 -0.009 0.056 -9999 0 -0.36 13 13
RELN/LRP8/DAB1/Fyn -0.049 0.1 -9999 0 -0.26 97 97
DAB1/alpha3/beta1 Integrin -0.049 0.1 -9999 0 -0.47 12 12
long-term memory -0.096 0.14 -9999 0 -0.5 29 29
DAB1/LIS1 -0.049 0.11 -9999 0 -0.49 10 10
DAB1/CRLK/C3G -0.047 0.1 -9999 0 -0.48 10 10
PIK3CA 0.01 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.05 0.11 -9999 0 -0.49 10 10
ARHGEF2 0.01 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.092 0.2 -9999 0 -0.5 101 101
CDK5R1 -0.006 0.09 -9999 0 -0.51 16 16
RELN -0.069 0.18 -9999 0 -0.5 79 79
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
RELN/LRP8/Fyn -0.053 0.11 -9999 0 -0.3 92 92
GRIN2A/RELN/LRP8/DAB1/Fyn -0.096 0.14 -9999 0 -0.52 25 25
MAPK8 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.052 0.12 -9999 0 -0.29 91 91
ITGB1 0.01 0 -9999 0 -10000 0 0
MAP1B -0.034 0.13 -9999 0 -0.31 51 51
RELN/LRP8 -0.052 0.11 -9999 0 -0.3 91 91
GRIN2B/RELN/LRP8/DAB1/Fyn -0.053 0.11 -9999 0 -0.5 10 10
PI3K -0.001 0.016 -9999 0 -0.35 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.035 -9999 0 -0.35 5 5
RAP1A -0.009 0.11 -9999 0 -0.44 10 10
PAFAH1B1 0.01 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.008 0.07 -9999 0 -0.51 10 10
NCK2 0.01 0 -9999 0 -10000 0 0
neuron differentiation 0.001 0.071 -9999 0 -0.26 3 3
neuron adhesion 0 0.11 -9999 0 -0.41 12 12
LRP8 -0.003 0.081 -9999 0 -0.51 13 13
GSK3B -0.009 0.093 -9999 0 -0.39 8 8
RELN/VLDLR/DAB1/Fyn -0.048 0.11 -9999 0 -0.27 92 92
MAP3K11 0.009 0.022 -9999 0 -0.5 1 1
RELN/VLDLR/DAB1/P13K -0.024 0.1 -9999 0 -0.25 80 80
CDK5 0.01 0 -9999 0 -10000 0 0
MAPT -0.017 0.11 -9999 0 -0.46 28 28
neuron migration -0.011 0.13 -9999 0 -0.45 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0 0.071 -9999 0 -0.26 3 3
RELN/VLDLR -0.052 0.11 -9999 0 -0.28 97 97
Nongenotropic Androgen signaling

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
PTK2 0.009 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.038 0.094 -10000 0 -0.27 73 73
regulation of S phase of mitotic cell cycle -0.011 0.088 -10000 0 -0.23 70 70
GNAO1 0.003 0.06 -10000 0 -0.51 7 7
HRAS 0.01 0.001 -10000 0 -10000 0 0
SHBG/T-DHT 0 0.001 -10000 0 -10000 0 0
PELP1 0.01 0.001 -10000 0 -10000 0 0
AKT1 0.009 0 -10000 0 -10000 0 0
MAP2K1 0 0.091 -10000 0 -0.32 13 13
T-DHT/AR -0.051 0.12 -10000 0 -0.36 72 72
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 27 27
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
mol:GDP -0.054 0.14 -10000 0 -0.4 70 70
cell proliferation 0.002 0.13 -10000 0 -0.44 27 27
PIK3CA 0.01 0 -10000 0 -10000 0 0
FOS -0.011 0.19 -10000 0 -0.8 27 27
mol:Ca2+ -0.01 0.021 -10000 0 -0.063 51 51
MAPK3 0.002 0.11 -10000 0 -0.45 13 13
MAPK1 0.006 0.065 -10000 0 -0.26 13 13
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
mol:IP3 0 0.001 -10000 0 -0.004 27 27
cAMP biosynthetic process 0.009 0.019 -10000 0 -10000 0 0
GNG2 0.008 0.032 -10000 0 -0.5 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 27 27
HRAS/GTP -0.034 0.083 -10000 0 -0.24 72 72
actin cytoskeleton reorganization 0 0.01 -10000 0 -0.23 1 1
SRC 0.01 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 27 27
PI3K -0.001 0.013 -10000 0 -0.3 1 1
apoptosis -0.003 0.12 0.45 27 -10000 0 27
T-DHT/AR/PELP1 -0.042 0.1 -10000 0 -0.3 72 72
HRAS/GDP -0.051 0.13 -10000 0 -0.37 70 70
CREB1 0.001 0.13 -10000 0 -0.48 27 27
RAC1-CDC42/GTP 0 0.01 -10000 0 -0.23 1 1
AR -0.062 0.18 -10000 0 -0.5 72 72
GNB1 0.01 0 -10000 0 -10000 0 0
RAF1 -0.006 0.091 -10000 0 -0.3 13 13
RAC1-CDC42/GDP -0.048 0.12 -10000 0 -0.35 70 70
T-DHT/AR/PELP1/Src -0.037 0.093 -10000 0 -0.27 72 72
MAP2K2 0 0.091 -10000 0 -0.32 13 13
T-DHT/AR/PELP1/Src/PI3K -0.011 0.088 -10000 0 -0.23 70 70
GNAZ -0.031 0.14 -10000 0 -0.5 41 41
SHBG 0.009 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.004 0.077 -10000 0 -0.29 17 17
mol:T-DHT 0 0 -10000 0 -0.003 14 14
RAC1 0.01 0 -10000 0 -10000 0 0
GNRH1 0.006 0.032 -10000 0 -0.36 4 4
Gi family/GTP -0.035 0.081 -10000 0 -0.25 44 44
CDC42 0.01 0 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.005 0.045 -9999 0 -0.5 4 4
PDGF/PDGFRA/CRKL -0.003 0.03 -9999 0 -0.34 4 4
positive regulation of JUN kinase activity -0.003 0.027 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.079 0.15 -9999 0 -0.36 112 112
AP1 -0.048 0.19 -9999 0 -0.87 27 27
mol:IP3 0.015 0.035 -9999 0 -0.35 4 4
PLCG1 0.015 0.035 -9999 0 -0.35 4 4
PDGF/PDGFRA/alphaV Integrin -0.003 0.03 -9999 0 -0.34 4 4
RAPGEF1 0.01 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0.015 0.035 -9999 0 -0.35 4 4
CAV3 -0.1 0.2 -9999 0 -0.5 108 108
CAV1 -0.31 0.25 -9999 0 -0.5 326 326
SHC/Grb2/SOS1 -0.003 0.027 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.004 0.037 -9999 0 -0.35 6 6
FOS -0.013 0.2 -9999 0 -0.86 27 27
JUN -0.005 0.03 -9999 0 -0.36 3 3
oligodendrocyte development -0.003 0.03 -9999 0 -0.34 4 4
GRB2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
mol:DAG 0.015 0.035 -9999 0 -0.35 4 4
PDGF/PDGFRA 0.005 0.045 -9999 0 -0.5 4 4
actin cytoskeleton reorganization -0.004 0.034 -9999 0 -0.35 5 5
SRF 0.017 0.006 -9999 0 -10000 0 0
SHC1 0.008 0.032 -9999 0 -0.51 2 2
PI3K -0.003 0.028 -9999 0 -0.28 5 5
PDGF/PDGFRA/Crk/C3G -0.002 0.024 -9999 0 -0.28 4 4
JAK1 0.015 0.032 -9999 0 -0.34 4 4
ELK1/SRF 0.027 0.027 -9999 0 -10000 0 0
SHB 0.009 0.022 -9999 0 -0.5 1 1
SHF 0.008 0.032 -9999 0 -0.51 2 2
CSNK2A1 0.003 0.012 -9999 0 -10000 0 0
GO:0007205 0.015 0.038 -9999 0 -0.37 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.003 0.027 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB -0.004 0.034 -9999 0 -0.35 5 5
PDGF/PDGFRA/Caveolin-1 -0.23 0.18 -9999 0 -0.36 327 327
ITGAV 0.01 0 -9999 0 -10000 0 0
ELK1 0.019 0.038 -9999 0 -0.32 4 4
PIK3CA 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.003 0.03 -9999 0 -0.34 4 4
JAK-STAT cascade 0.015 0.032 -9999 0 -0.34 4 4
cell proliferation -0.004 0.037 -9999 0 -0.35 6 6
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.012 0.1 0.5 22 -10000 0 22
PI3K Class IB/PDE3B -0.012 0.1 -10000 0 -0.5 22 22
PDE3B -0.012 0.1 -10000 0 -0.5 22 22
Wnt signaling

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
Noncanonical Wnts/FZD -0.03 0.12 -9999 0 -0.47 14 14
FZD6 0.009 0.022 -9999 0 -0.5 1 1
WNT6 -0.023 0.12 -9999 0 -0.51 32 32
WNT4 -0.019 0.12 -9999 0 -0.5 29 29
FZD3 0.009 0.023 -9999 0 -0.51 1 1
WNT5A 0.004 0.055 -9999 0 -0.5 6 6
WNT11 -0.057 0.17 -9999 0 -0.5 67 67
HIF-2-alpha transcription factor network

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
MMP14 -0.009 0.035 -10000 0 -10000 0 0
oxygen homeostasis 0 0.013 -10000 0 -10000 0 0
TCEB2 0.01 0 -10000 0 -10000 0 0
TCEB1 0.009 0.023 -10000 0 -0.51 1 1
VHL/Elongin B/Elongin C/HIF2A -0.065 0.11 -10000 0 -0.37 37 37
EPO -0.026 0.22 -10000 0 -0.66 15 15
FIH (dimer) 0.011 0.012 -10000 0 -10000 0 0
APEX1 0.012 0.012 -10000 0 -10000 0 0
SERPINE1 -0.047 0.26 -10000 0 -0.69 27 27
FLT1 -0.009 0.052 -10000 0 -0.89 1 1
ADORA2A -0.042 0.24 -10000 0 -0.65 26 26
germ cell development -0.06 0.26 -10000 0 -0.65 32 32
SLC11A2 -0.045 0.25 -10000 0 -0.67 26 26
BHLHE40 -0.045 0.25 -10000 0 -0.67 26 26
HIF1AN 0.011 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.086 0.14 -10000 0 -0.44 43 43
ETS1 0.02 0.024 -10000 0 -0.52 1 1
CITED2 -0.011 0.071 -10000 0 -1.1 2 2
KDR -0.033 0.19 -10000 0 -1.2 13 13
PGK1 -0.045 0.25 -10000 0 -0.67 26 26
SIRT1 0.01 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.047 0.29 -10000 0 -0.74 33 33
EPAS1 -0.043 0.16 -10000 0 -0.39 53 53
SP1 0.016 0.001 -10000 0 -10000 0 0
ABCG2 -0.071 0.3 -10000 0 -0.73 50 50
EFNA1 -0.045 0.25 -10000 0 -0.68 26 26
FXN -0.042 0.24 -10000 0 -0.65 26 26
POU5F1 -0.063 0.27 -10000 0 -0.68 32 32
neuron apoptosis 0.046 0.28 0.71 33 -10000 0 33
EP300 0.01 0 -10000 0 -10000 0 0
EGLN3 -0.12 0.23 -10000 0 -0.52 130 130
EGLN2 0.01 0.012 -10000 0 -10000 0 0
EGLN1 0.011 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.001 0.013 -10000 0 -0.3 1 1
VHL 0.01 0 -10000 0 -10000 0 0
ARNT 0.012 0.012 -10000 0 -10000 0 0
SLC2A1 -0.12 0.31 -10000 0 -0.64 84 84
TWIST1 -0.081 0.29 -10000 0 -0.67 56 56
ELK1 0.016 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.084 0.14 -10000 0 -0.44 41 41
VEGFA -0.045 0.25 -10000 0 -0.67 26 26
CREBBP 0.01 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.001 -9999 0 -10000 0 0
SMARCC1 0.003 0.007 -9999 0 -10000 0 0
REL 0.01 0.001 -9999 0 -10000 0 0
HDAC7 0.023 0.089 -9999 0 -0.47 3 3
JUN 0.007 0.039 -9999 0 -0.5 3 3
EP300 0.01 0 -9999 0 -10000 0 0
KAT2B 0.01 0 -9999 0 -10000 0 0
KAT5 0.01 0 -9999 0 -10000 0 0
MAPK14 0.006 0.069 -9999 0 -0.36 17 17
FOXO1 0.009 0.022 -9999 0 -0.5 1 1
T-DHT/AR 0.02 0.094 -9999 0 -0.44 5 5
MAP2K6 -0.007 0.093 -9999 0 -0.51 17 17
BRM/BAF57 -0.003 0.031 -9999 0 -0.35 4 4
MAP2K4 0.01 0.004 -9999 0 -10000 0 0
SMARCA2 0.006 0.045 -9999 0 -0.5 4 4
PDE9A -0.043 0.17 -9999 0 -1.2 8 8
NCOA2 0.005 0.05 -9999 0 -0.5 5 5
CEBPA -0.016 0.11 -9999 0 -0.5 26 26
EHMT2 0.01 0.001 -9999 0 -10000 0 0
cell proliferation 0.021 0.13 -9999 0 -0.45 20 20
NR0B1 -0.1 0.21 -9999 0 -0.51 107 107
EGR1 -0.018 0.12 -9999 0 -0.5 28 28
RXRs/9cRA -0.14 0.13 -9999 0 -0.26 267 267
AR/RACK1/Src -0.001 0.065 -9999 0 -0.36 3 3
AR/GR -0.008 0.096 -9999 0 -0.3 25 25
GNB2L1 0.01 0.001 -9999 0 -10000 0 0
PKN1 0.01 0 -9999 0 -10000 0 0
RCHY1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.018 0.009 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.002 0.068 -9999 0 -0.38 3 3
SRC 0.023 0.054 -9999 0 -0.3 3 3
NR3C1 0.01 0 -9999 0 -10000 0 0
KLK3 -0.06 0.097 -9999 0 -0.46 5 5
APPBP2 0.01 0.003 -9999 0 -10000 0 0
TRIM24 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.013 0.069 -9999 0 -0.37 4 4
TMPRSS2 -0.099 0.3 -9999 0 -1.1 42 42
RXRG -0.26 0.25 -9999 0 -0.5 267 267
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.01 0 -9999 0 -10000 0 0
RXRB 0.01 0 -9999 0 -10000 0 0
CARM1 0.009 0.002 -9999 0 -10000 0 0
NR2C2 0.01 0 -9999 0 -10000 0 0
KLK2 0.013 0.096 -9999 0 -0.4 7 7
AR -0.013 0.11 -9999 0 -0.27 70 70
SENP1 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
MDM2 0.008 0.032 -9999 0 -0.51 2 2
SRY 0.001 0.004 -9999 0 -10000 0 0
GATA2 -0.031 0.14 -9999 0 -0.5 41 41
MYST2 0.01 0 -9999 0 -10000 0 0
HOXB13 -0.17 0.24 -9999 0 -0.51 179 179
T-DHT/AR/RACK1/Src 0.019 0.068 -9999 0 -0.38 3 3
positive regulation of transcription -0.031 0.14 -9999 0 -0.5 41 41
DNAJA1 0.01 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.008 -9999 0 -10000 0 0
NCOA1 0.012 0.003 -9999 0 -10000 0 0
SPDEF -0.16 0.24 -9999 0 -0.51 169 169
T-DHT/AR/TIF2 0.026 0.051 -9999 0 -0.25 1 1
T-DHT/AR/Hsp90 0.013 0.069 -9999 0 -0.37 4 4
GSK3B 0.01 0.003 -9999 0 -10000 0 0
NR2C1 0.01 0 -9999 0 -10000 0 0
mol:T-DHT 0.019 0.058 -9999 0 -0.31 5 5
SIRT1 0.01 0 -9999 0 -10000 0 0
ZMIZ2 0.01 0.002 -9999 0 -10000 0 0
POU2F1 0.016 0.023 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.06 0.12 -9999 0 -0.36 36 36
CREBBP 0.01 0 -9999 0 -10000 0 0
SMARCE1 0.01 0.001 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.013 0.046 -9999 0 -0.32 9 9
EPHB2 -0.047 0.16 -9999 0 -0.51 56 56
Syndecan-2/TACI -0.013 0.095 -9999 0 -0.3 52 52
LAMA1 -0.017 0.12 -9999 0 -0.51 27 27
Syndecan-2/alpha2 ITGB1 -0.058 0.11 -9999 0 -0.49 5 5
HRAS 0.01 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.029 -9999 0 -0.3 5 5
ITGA5 0.008 0.032 -9999 0 -0.5 2 2
BAX 0.029 0.027 -9999 0 -10000 0 0
EPB41 0.01 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.003 0.026 -9999 0 -0.26 5 5
LAMA3 -0.093 0.2 -9999 0 -0.5 104 104
EZR 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.097 0.21 -9999 0 -0.5 108 108
Syndecan-2/MMP2 0.015 0.033 -9999 0 -0.29 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.011 0.062 -9999 0 -0.36 16 16
dendrite morphogenesis -0.019 0.1 -9999 0 -0.3 61 61
Syndecan-2/GM-CSF -0.014 0.096 -9999 0 -0.3 52 52
determination of left/right symmetry 0.012 0.036 -9999 0 -0.35 5 5
Syndecan-2/PKC delta 0.016 0.03 -9999 0 -0.29 5 5
GNB2L1 0.01 0 -9999 0 -10000 0 0
MAPK3 -0.004 0.088 -9999 0 -0.26 52 52
MAPK1 -0.004 0.088 -9999 0 -0.26 52 52
Syndecan-2/RACK1 -0.002 0.024 -9999 0 -0.24 5 5
NF1 0.01 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.036 -9999 0 -0.35 5 5
ITGA2 -0.006 0.09 -9999 0 -0.51 16 16
MAPK8 0.024 0.031 -9999 0 -0.29 5 5
Syndecan-2/alpha2/beta1 Integrin -0.023 0.079 -9999 0 -0.5 5 5
Syndecan-2/Kininogen -0.015 0.083 -9999 0 -0.3 40 40
ITGB1 0.01 0 -9999 0 -10000 0 0
SRC 0.026 0.025 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.003 0.026 -9999 0 -0.26 5 5
extracellular matrix organization 0.016 0.03 -9999 0 -0.29 5 5
actin cytoskeleton reorganization 0.013 0.046 -9999 0 -0.32 9 9
Syndecan-2/Caveolin-2/Ras -0.057 0.11 -9999 0 -0.26 113 113
Syndecan-2/Laminin alpha3 -0.047 0.13 -9999 0 -0.29 109 109
Syndecan-2/RasGAP -0.002 0.022 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.001 0.022 -9999 0 -0.36 2 2
PRKCD 0.01 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.019 0.1 -9999 0 -0.3 61 61
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.031 0.024 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
TNFRSF13B -0.038 0.15 -9999 0 -0.51 47 47
RASA1 0.01 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.011 0.062 -9999 0 -0.36 16 16
Syndecan-2/Synbindin 0.016 0.03 -9999 0 -0.29 5 5
TGFB1 0.01 0 -9999 0 -10000 0 0
CASP3 0.023 0.028 -9999 0 -0.26 5 5
FN1 0.005 0.05 -9999 0 -0.5 5 5
Syndecan-2/IL8 0.004 0.068 -9999 0 -0.3 25 25
SDC2 0.012 0.036 -9999 0 -0.35 5 5
KNG1 -0.03 0.13 -9999 0 -0.51 35 35
Syndecan-2/Neurofibromin 0.016 0.03 -9999 0 -0.29 5 5
TRAPPC4 0.01 0 -9999 0 -10000 0 0
CSF2 -0.038 0.15 -9999 0 -0.5 48 48
Syndecan-2/TGFB1 0.016 0.03 -9999 0 -0.29 5 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.003 0.026 -9999 0 -0.26 5 5
Syndecan-2/Ezrin -0.002 0.025 -9999 0 -0.26 5 5
PRKACA 0.023 0.028 -9999 0 -0.26 5 5
angiogenesis 0.004 0.068 -9999 0 -0.3 25 25
MMP2 0.009 0.023 -9999 0 -0.51 1 1
IL8 -0.01 0.1 -9999 0 -0.51 20 20
calcineurin-NFAT signaling pathway -0.013 0.095 -9999 0 -0.3 52 52
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.001 -9999 0 -10000 0 0
SVIL 0.01 0.001 -9999 0 -10000 0 0
ZNF318 0.009 0.007 -9999 0 -10000 0 0
JMJD2C -0.001 0.018 -9999 0 -0.078 26 26
T-DHT/AR/Ubc9 -0.046 0.12 -9999 0 -0.32 72 72
CARM1 0.01 0 -9999 0 -10000 0 0
PRDX1 0.009 0.023 -9999 0 -0.51 1 1
PELP1 0.01 0.001 -9999 0 -10000 0 0
CTNNB1 0.01 0.001 -9999 0 -10000 0 0
AKT1 0.01 0.002 -9999 0 -10000 0 0
PTK2B 0.008 0.032 -9999 0 -0.5 2 2
MED1 0.01 0.002 -9999 0 -10000 0 0
MAK -0.008 0.091 -9999 0 -0.5 17 17
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.005 0.05 -9999 0 -0.5 5 5
GSN 0.01 0.001 -9999 0 -10000 0 0
NCOA2 0.005 0.05 -9999 0 -0.5 5 5
NCOA6 0.01 0.001 -9999 0 -10000 0 0
DNA-PK 0.001 0.008 -9999 0 -10000 0 0
NCOA4 0.01 0 -9999 0 -10000 0 0
PIAS3 0.01 0.001 -9999 0 -10000 0 0
cell proliferation -0.036 0.13 -9999 0 -0.72 17 17
XRCC5 0.01 0.001 -9999 0 -10000 0 0
UBE3A 0.01 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.057 0.13 -9999 0 -0.33 89 89
FHL2 -0.05 0.13 -9999 0 -0.43 21 21
RANBP9 0.01 0.001 -9999 0 -10000 0 0
JMJD1A 0 0.04 -9999 0 -0.13 47 47
CDK6 0.008 0.032 -9999 0 -0.5 2 2
TGFB1I1 0.007 0.039 -9999 0 -0.5 3 3
T-DHT/AR/CyclinD1 -0.049 0.12 -9999 0 -0.33 77 77
XRCC6 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.04 0.14 -9999 0 -0.34 80 80
CTDSP1 0.01 0.001 -9999 0 -10000 0 0
CTDSP2 0.01 0.004 -9999 0 -10000 0 0
BRCA1 0.007 0.039 -9999 0 -0.51 3 3
TCF4 0.008 0.032 -9999 0 -0.5 2 2
CDKN2A -0.14 0.24 -9999 0 -0.51 152 152
SRF 0.006 0.026 -9999 0 -10000 0 0
NKX3-1 -0.046 0.12 -9999 0 -0.47 24 24
KLK3 0.016 0.045 -9999 0 -10000 0 0
TMF1 0.01 0.001 -9999 0 -10000 0 0
HNRNPA1 0.01 0.002 -9999 0 -10000 0 0
AOF2 0 0.003 -9999 0 -10000 0 0
APPL1 0.018 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.048 0.12 -9999 0 -0.32 73 73
AR -0.068 0.18 -9999 0 -0.52 72 72
UBA3 0.01 0.001 -9999 0 -10000 0 0
PATZ1 0.01 0.002 -9999 0 -10000 0 0
PAWR 0.01 0.001 -9999 0 -10000 0 0
PRKDC 0.01 0.001 -9999 0 -10000 0 0
PA2G4 0.01 0.003 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.034 0.11 -9999 0 -0.29 72 72
RPS6KA3 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.045 0.12 -9999 0 -0.32 72 72
LATS2 0.01 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.036 0.11 -9999 0 -0.3 72 72
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0.003 0.059 -9999 0 -0.5 7 7
KLK2 -0.042 0.089 -9999 0 -0.36 26 26
CASP8 0.009 0.022 -9999 0 -0.5 1 1
T-DHT/AR/TIF2/CARM1 -0.038 0.11 -9999 0 -0.29 76 76
TMPRSS2 -0.096 0.27 -9999 0 -0.96 43 43
CCND1 0.003 0.059 -9999 0 -0.5 7 7
PIAS1 0.01 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.007 0.026 -9999 0 -0.076 36 36
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.01 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.048 0.12 -9999 0 -0.32 74 74
CMTM2 -0.084 0.2 -9999 0 -0.5 95 95
SNURF -0.009 0.096 -9999 0 -0.5 19 19
ZMIZ1 0.005 0.022 -9999 0 -10000 0 0
CCND3 0.01 0 -9999 0 -10000 0 0
TGIF1 0.01 0.002 -9999 0 -10000 0 0
FKBP4 0.009 0.023 -9999 0 -0.51 1 1
PLK2 and PLK4 events

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
PLK2 0.009 0.022 -9999 0 -0.5 1 1
PLK4 -0.017 0.12 -9999 0 -0.51 27 27
regulation of centriole replication -0.003 0.086 -9999 0 -0.36 28 28
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.022 -9999 0 -0.5 1 1
alphaV beta3 Integrin -0.019 0.081 -9999 0 -0.36 28 28
PTK2 -0.039 0.11 -9999 0 -0.38 41 41
positive regulation of JNK cascade -0.023 0.077 -9999 0 -0.28 41 41
CDC42/GDP 0.009 0.12 -9999 0 -0.38 41 41
Rac1/GDP 0.01 0.11 -9999 0 -0.37 41 41
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.028 0.094 -9999 0 -0.34 41 41
nectin-3/I-afadin -0.029 0.097 -9999 0 -0.35 42 42
RAPGEF1 0.003 0.12 -9999 0 -0.42 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.005 0.14 -9999 0 -0.47 41 41
PDGFB-D/PDGFRB 0.009 0.022 -9999 0 -0.5 1 1
TLN1 0.002 0.084 -9999 0 -0.39 15 15
Rap1/GTP -0.024 0.081 -9999 0 -0.3 41 41
IQGAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.029 0.097 -9999 0 -0.35 42 42
PVR 0.01 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.01 0 -9999 0 -10000 0 0
mol:GDP 0.002 0.14 -9999 0 -0.46 41 41
MLLT4 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.02 0.069 -9999 0 -0.49 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.008 0.052 -9999 0 -0.36 11 11
positive regulation of lamellipodium assembly -0.025 0.081 -9999 0 -0.3 42 42
PVRL1 -0.001 0.075 -9999 0 -0.51 11 11
PVRL3 -0.032 0.14 -9999 0 -0.5 42 42
PVRL2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
CLDN1 -0.009 0.097 -9999 0 -0.51 19 19
JAM-A/CLDN1 -0.031 0.09 -9999 0 -0.52 4 4
SRC -0.045 0.14 -9999 0 -0.53 41 41
ITGB3 -0.018 0.12 -9999 0 -0.51 28 28
nectin-1(dimer)/I-afadin/I-afadin -0.008 0.052 -9999 0 -0.36 11 11
FARP2 -0.002 0.13 -9999 0 -0.45 41 41
RAC1 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.024 0.08 -9999 0 -0.29 42 42
nectin-1/I-afadin -0.008 0.052 -9999 0 -0.36 11 11
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.03 0.091 -9999 0 -0.3 52 52
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.009 0.022 -9999 0 -0.5 1 1
positive regulation of filopodium formation -0.023 0.077 -9999 0 -0.28 41 41
alphaV/beta3 Integrin/Talin -0.001 0.096 -9999 0 -0.48 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.004 0.088 -9999 0 -0.43 14 14
VAV2 -0.003 0.14 -9999 0 -0.46 42 42
RAP1/GDP -0.028 0.095 -9999 0 -0.35 41 41
ITGAV 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.024 0.08 -9999 0 -0.29 42 42
nectin-3(dimer)/I-afadin/I-afadin -0.029 0.097 -9999 0 -0.35 42 42
Rac1/GTP -0.03 0.098 -9999 0 -0.36 42 42
PTPRM -0.026 0.092 -9999 0 -0.47 14 14
E-cadherin/beta catenin/alpha catenin -0.006 0.035 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
Syndecan-4-mediated 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
PTK2 0.01 0.047 -9999 0 -0.48 4 4
Syndecan-4/Syndesmos -0.024 0.084 -9999 0 -0.52 2 2
positive regulation of JNK cascade -0.053 0.081 -9999 0 -0.44 4 4
Syndecan-4/ADAM12 -0.11 0.16 -9999 0 -0.37 96 96
CCL5 0.005 0.05 -9999 0 -0.5 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.01 0 -9999 0 -10000 0 0
ITGA5 0.008 0.032 -9999 0 -0.5 2 2
SDCBP 0.01 0 -9999 0 -10000 0 0
PLG -0.007 0.076 -9999 0 -0.52 11 11
ADAM12 -0.16 0.24 -9999 0 -0.51 174 174
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.05 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.037 0.1 -9999 0 -0.4 14 14
Syndecan-4/CXCL12/CXCR4 -0.036 0.098 -9999 0 -0.46 4 4
Syndecan-4/Laminin alpha3 -0.073 0.13 -9999 0 -0.36 43 43
MDK -0.15 0.24 -9999 0 -0.51 157 157
Syndecan-4/FZD7 -0.024 0.085 -9999 0 -0.46 3 3
Syndecan-4/Midkine -0.099 0.14 -9999 0 -0.37 62 62
FZD7 0.009 0.022 -9999 0 -0.5 1 1
Syndecan-4/FGFR1/FGF -0.072 0.1 -9999 0 -0.47 10 10
THBS1 0.007 0.039 -9999 0 -0.5 3 3
integrin-mediated signaling pathway -0.04 0.1 -9999 0 -0.4 11 11
positive regulation of MAPKKK cascade -0.053 0.081 -9999 0 -0.44 4 4
Syndecan-4/TACI -0.046 0.12 -9999 0 -0.38 28 28
CXCR4 0.01 0 -9999 0 -10000 0 0
cell adhesion 0.006 0.038 -9999 0 -0.33 4 4
Syndecan-4/Dynamin -0.024 0.084 -9999 0 -0.52 2 2
Syndecan-4/TSP1 -0.025 0.089 -9999 0 -0.63 2 2
Syndecan-4/GIPC -0.024 0.084 -9999 0 -0.52 2 2
Syndecan-4/RANTES -0.026 0.086 -9999 0 -0.52 2 2
ITGB1 0.01 0 -9999 0 -10000 0 0
LAMA1 -0.017 0.12 -9999 0 -0.51 27 27
LAMA3 -0.093 0.2 -9999 0 -0.5 104 104
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.016 0.039 -9999 0 -0.46 2 2
Syndecan-4/alpha-Actinin -0.024 0.084 -9999 0 -0.52 2 2
TFPI -0.012 0.1 -9999 0 -0.5 22 22
F2 -0.071 0.18 -9999 0 -0.51 74 74
alpha5/beta1 Integrin -0.001 0.022 -9999 0 -0.36 2 2
positive regulation of cell adhesion -0.077 0.14 -9999 0 -0.49 10 10
ACTN1 0.01 0 -9999 0 -10000 0 0
TNC -0.026 0.13 -9999 0 -0.51 36 36
Syndecan-4/CXCL12 -0.039 0.1 -9999 0 -0.39 13 13
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CXCL12 -0.022 0.12 -9999 0 -0.5 32 32
TNFRSF13B -0.038 0.15 -9999 0 -0.51 47 47
FGF2 -0.063 0.18 -9999 0 -0.5 74 74
FGFR1 0.007 0.039 -9999 0 -0.5 3 3
Syndecan-4/PI-4-5-P2 -0.03 0.084 -9999 0 -0.52 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.007 0.05 -9999 0 -0.49 5 5
cell migration -0.016 0.021 -9999 0 -10000 0 0
PRKCD 0.012 0.006 -9999 0 -10000 0 0
vasculogenesis -0.024 0.086 -9999 0 -0.6 2 2
SDC4 -0.031 0.088 -9999 0 -0.55 2 2
Syndecan-4/Tenascin C -0.041 0.1 -9999 0 -0.41 11 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.029 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.084 -9999 0 -0.52 2 2
MMP9 -0.1 0.21 -9999 0 -0.51 112 112
Rac1/GTP 0.006 0.039 -9999 0 -0.34 4 4
cytoskeleton organization -0.023 0.082 -9999 0 -0.5 2 2
GIPC1 0.01 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.034 0.098 -9999 0 -0.42 8 8
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.01 0 -9999 0 -10000 0 0
VLDLR -0.002 0.077 -9999 0 -0.5 12 12
LRPAP1 0.01 0 -9999 0 -10000 0 0
NUDC 0.01 0 -9999 0 -10000 0 0
RELN/LRP8 -0.052 0.11 -9999 0 -0.3 91 91
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.01 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.024 0.11 -9999 0 -0.26 91 91
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.003 0.067 -9999 0 -0.51 9 9
IQGAP1 0.01 0 -9999 0 -10000 0 0
PLA2G7 0 0.071 -9999 0 -0.51 10 10
CALM1 0.01 0 -9999 0 -10000 0 0
DYNLT1 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.009 0.056 -9999 0 -0.36 13 13
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.01 0 -9999 0 -10000 0 0
CDK5R1 -0.006 0.09 -9999 0 -0.51 16 16
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.13 0.23 -9999 0 -0.51 141 141
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.057 0.13 -9999 0 -0.32 91 91
YWHAE 0.01 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.038 0.11 -9999 0 -0.33 29 29
MAP1B -0.002 0.019 -9999 0 -0.28 1 1
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.017 0.11 -9999 0 -0.58 2 2
RELN -0.069 0.18 -9999 0 -0.5 79 79
PAFAH/LIS1 0.014 0.044 -9999 0 -0.3 10 10
LIS1/CLIP170 0.021 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.047 0.072 -9999 0 -0.4 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.02 0.11 -9999 0 -0.36 18 18
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.046 0.12 -9999 0 -0.36 29 29
LIS1/IQGAP1 0.021 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 -0.014 0.11 -9999 0 -0.51 24 24
PAFAH1B2 0.01 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.014 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.061 0.089 -9999 0 -0.32 29 29
LRP8 -0.003 0.081 -9999 0 -0.51 13 13
NDEL1/Katanin 60 -0.038 0.11 -9999 0 -0.33 29 29
P39/CDK5 -0.081 0.15 -9999 0 -0.48 29 29
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0 -9999 0 -10000 0 0
CDK5 -0.016 0.1 -9999 0 -0.49 1 1
PPP2R5D 0.01 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.047 0.11 -9999 0 -0.49 9 9
RELN/VLDLR -0.052 0.11 -9999 0 -0.28 97 97
CDC42 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A -0.001 0.022 -10000 0 -0.36 2 2
PRKCZ 0.007 0.039 -10000 0 -0.5 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.039 -10000 0 -0.26 1 1
IRAK/TOLLIP 0.02 0.022 -10000 0 -0.26 3 3
IKBKB 0.01 0 -10000 0 -10000 0 0
IKBKG 0.01 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.18 -10000 0 -0.36 178 178
IL1A -0.15 0.24 -10000 0 -0.5 158 158
IL1B -0.009 0.096 -10000 0 -0.35 37 37
IRAK/TRAF6/p62/Atypical PKCs -0.003 0.025 -10000 0 -10000 0 0
IL1R2 -0.015 0.11 -10000 0 -0.51 25 25
IL1R1 0.008 0.032 -10000 0 -0.5 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.049 0.19 10 -0.38 1 11
TOLLIP 0.01 0 -10000 0 -10000 0 0
TICAM2 0.006 0.045 -10000 0 -0.5 4 4
MAP3K3 0.009 0.022 -10000 0 -0.5 1 1
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.048 0.018 -10000 0 -10000 0 0
JUN 0.025 0.049 -10000 0 -0.42 1 1
MAP3K7 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.061 -10000 0 -0.47 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.08 0.12 -10000 0 -0.26 159 159
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.073 0.11 -10000 0 -0.49 1 1
IL1 beta fragment/IL1R1/IL1RAP -0.019 0.07 -10000 0 -0.26 38 38
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.022 0.046 -10000 0 -10000 0 0
IRAK1 0.015 0.024 -10000 0 -0.3 3 3
IL1RN/IL1R1 -0.007 0.049 -10000 0 -0.35 10 10
IRAK4 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
PI3K -0.001 0.016 -10000 0 -0.35 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.052 -10000 0 -0.39 1 1
CHUK 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.019 0.07 -10000 0 -0.26 38 38
IL1 beta/IL1R2 -0.035 0.1 -10000 0 -0.31 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.015 0.054 -10000 0 -0.42 1 1
IRAK3 -0.004 0.083 -10000 0 -0.5 14 14
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.063 -10000 0 -0.47 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.12 -10000 0 -0.46 1 1
IL1 alpha/IL1R1/IL1RAP -0.091 0.14 -10000 0 -0.29 159 159
RELA 0.01 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.009 0.023 -10000 0 -0.51 1 1
MYD88 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.013 0.026 -10000 0 -10000 0 0
IL1RAP 0.01 0 -10000 0 -10000 0 0
UBE2N 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.016 0.052 -10000 0 -0.39 1 1
CASP1 0.004 0.055 -10000 0 -0.5 6 6
IL1RN/IL1R2 -0.023 0.089 -10000 0 -0.37 32 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.018 0.064 -10000 0 -0.49 1 1
TMEM189-UBE2V1 0.002 0.032 -10000 0 -0.51 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.04 0.091 -10000 0 -0.39 2 2
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL1RN 0.002 0.063 -10000 0 -0.5 8 8
TRAF6/TAK1/TAB1/TAB2 -0.001 0.015 -10000 0 -0.24 2 2
MAP2K6 0.016 0.048 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.02 0.19 3 -10000 0 3
RFC1 0.002 0.02 0.19 3 -10000 0 3
PRKDC 0.002 0.02 0.18 5 -0.2 1 6
RIPK1 0.011 0.004 -10000 0 -10000 0 0
CASP7 -0.016 0.04 0.23 2 -0.5 1 3
FASLG/FAS/FADD/FAF1 0.006 0.075 0.21 37 -0.26 10 47
MAP2K4 -0.026 0.13 -10000 0 -0.46 7 7
mol:ceramide -0.01 0.091 -10000 0 -0.37 10 10
GSN 0.002 0.02 0.19 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 8 0.011 0.077 0.19 36 -0.33 8 44
FAS 0.002 0.055 -10000 0 -0.5 6 6
BID 0.001 0.023 0.28 2 -0.3 1 3
MAP3K1 -0.007 0.082 0.19 2 -0.29 7 9
MAP3K7 0.008 0.004 -10000 0 -10000 0 0
RB1 0.002 0.02 0.19 3 -10000 0 3
CFLAR 0.011 0.004 -10000 0 -10000 0 0
HGF/MET -0.067 0.15 -10000 0 -0.35 99 99
ARHGDIB 0.002 0.02 0.19 3 -0.2 1 4
FADD 0.008 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.02 -10000 0 -0.19 3 3
NFKB1 -0.048 0.085 -10000 0 -0.26 6 6
MAPK8 -0.058 0.2 -10000 0 -0.42 121 121
DFFA 0.002 0.02 0.19 3 -10000 0 3
DNA fragmentation during apoptosis 0.002 0.02 0.18 4 -0.2 1 5
FAS/FADD/MET -0.023 0.081 -10000 0 -0.3 39 39
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.007 0.045 -10000 0 -0.5 4 4
FAF1 0.008 0.005 -10000 0 -10000 0 0
PARP1 0.002 0.02 0.19 3 -10000 0 3
DFFB 0.002 0.02 0.19 3 -0.2 1 4
CHUK -0.042 0.075 -10000 0 -10000 0 0
FASLG 0.002 0.056 -10000 0 -0.51 6 6
FAS/FADD -0.006 0.039 -10000 0 -0.36 6 6
HGF -0.021 0.12 -10000 0 -0.5 31 31
LMNA 0.002 0.018 0.2 1 -10000 0 1
CASP6 0.002 0.02 0.19 3 -10000 0 3
CASP10 0.006 0.032 -10000 0 -0.51 2 2
CASP3 0.002 0.024 0.21 5 -0.23 1 6
PTPN13 -0.044 0.16 -10000 0 -0.5 54 54
CASP8 0.001 0.03 0.28 4 -0.36 1 5
IL6 -0.25 0.51 -10000 0 -1.2 120 120
MET -0.024 0.13 -10000 0 -0.5 34 34
ICAD/CAD 0.002 0.019 0.2 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.01 0.092 -10000 0 -0.38 10 10
activation of caspase activity by cytochrome c 0.001 0.023 0.28 2 -0.3 1 3
PAK2 0.002 0.02 0.19 3 -10000 0 3
BCL2 0.007 0.039 -10000 0 -0.5 3 3
LPA receptor mediated events

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
GNB1/GNG2 -0.002 0.021 -9999 0 -0.26 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.069 -9999 0 -0.36 3 3
AP1 -0.036 0.086 -9999 0 -0.45 5 5
mol:PIP3 -0.028 0.073 -9999 0 -0.41 4 4
AKT1 -0.002 0.016 -9999 0 -10000 0 0
PTK2B 0.018 0.032 -9999 0 -0.27 2 2
RHOA 0.024 0.024 -9999 0 -10000 0 0
PIK3CB 0.009 0 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.085 -9999 0 -0.37 4 4
MAGI3 0.004 0.055 -9999 0 -0.5 6 6
RELA 0.01 0 -9999 0 -10000 0 0
apoptosis -0.006 0.085 -9999 0 -0.25 52 52
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.015 0.064 -9999 0 -0.26 10 10
NF kappa B1 p50/RelA -0.026 0.071 -9999 0 -0.36 3 3
endothelial cell migration 0.021 0.024 -9999 0 -0.36 2 2
ADCY4 0.012 0.068 -9999 0 -0.36 6 6
ADCY5 -0.003 0.085 -9999 0 -0.3 20 20
ADCY6 0.019 0.053 -9999 0 -0.35 2 2
ADCY7 0.019 0.054 -9999 0 -0.35 2 2
ADCY1 0.017 0.057 -9999 0 -0.32 4 4
ADCY2 0.002 0.079 -9999 0 -0.32 11 11
ADCY3 0.02 0.053 -9999 0 -0.35 2 2
ADCY8 -0.052 0.1 -9999 0 -0.3 23 23
ADCY9 0.016 0.062 -9999 0 -0.33 6 6
GSK3B 0.023 0.031 -9999 0 -0.25 2 2
arachidonic acid secretion 0.023 0.05 -9999 0 -0.32 2 2
GNG2 0.008 0.032 -9999 0 -0.5 2 2
TRIP6 0.017 0.029 -9999 0 -0.36 3 3
GNAO1 0.017 0.04 -9999 0 -0.29 8 8
HRAS 0.01 0 -9999 0 -10000 0 0
NFKBIA 0.011 0.096 -9999 0 -0.42 3 3
GAB1 0.008 0.032 -9999 0 -0.5 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.025 0.15 -9999 0 -0.86 15 15
JUN 0.007 0.039 -9999 0 -0.5 3 3
LPA/LPA2/NHERF2 -0.004 0.032 -9999 0 -0.3 6 6
TIAM1 -0.029 0.17 -9999 0 -1 15 15
PIK3R1 0.008 0.022 -9999 0 -0.5 1 1
mol:IP3 0.004 0.086 -9999 0 -0.38 4 4
PLCB3 0.019 0.031 -9999 0 -0.26 6 6
FOS -0.017 0.11 -9999 0 -0.5 27 27
positive regulation of mitosis 0.023 0.05 -9999 0 -0.32 2 2
LPA/LPA1-2-3 -0.029 0.081 -9999 0 -0.26 57 57
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
stress fiber formation 0.016 0.052 -9999 0 -10000 0 0
GNAZ -0.004 0.086 -9999 0 -0.29 42 42
EGFR/PI3K-beta/Gab1 -0.029 0.075 -9999 0 -0.43 4 4
positive regulation of dendritic cell cytokine production -0.029 0.08 -9999 0 -0.26 57 57
LPA/LPA2/MAGI-3 -0.004 0.034 -9999 0 -0.3 7 7
ARHGEF1 0.03 0.018 -9999 0 -10000 0 0
GNAI2 0.021 0.016 -9999 0 -0.29 1 1
GNAI3 0.021 0.016 -9999 0 -0.29 1 1
GNAI1 0.02 0.025 -9999 0 -0.29 3 3
LPA/LPA3 -0.038 0.11 -9999 0 -0.36 55 55
LPA/LPA2 -0.001 0.016 -9999 0 -0.36 1 1
LPA/LPA1 -0.001 0.018 -9999 0 -0.29 2 2
HB-EGF/EGFR -0.11 0.18 -9999 0 -0.33 189 189
HBEGF -0.12 0.2 -9999 0 -0.38 185 185
mol:DAG 0.004 0.086 -9999 0 -0.38 4 4
cAMP biosynthetic process 0.006 0.063 -9999 0 -0.33 3 3
NFKB1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
GNB1 0.009 0 -9999 0 -10000 0 0
LYN 0.011 0.096 -9999 0 -0.42 3 3
GNAQ -0.011 0.088 -9999 0 -0.26 56 56
LPAR2 0.009 0.023 -9999 0 -0.51 1 1
LPAR3 -0.045 0.16 -9999 0 -0.5 55 55
LPAR1 0.012 0.023 -9999 0 -0.49 1 1
IL8 -0.041 0.14 -9999 0 -0.37 38 38
PTK2 0.002 0.083 -9999 0 -0.23 57 57
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.007 0.085 -9999 0 -0.25 52 52
EGFR -0.006 0.089 -9999 0 -0.5 16 16
PLCG1 -0.008 0.097 -9999 0 -0.28 52 52
PLD2 0.002 0.083 -9999 0 -0.24 9 9
G12/G13 -0.001 0.013 -9999 0 -0.26 1 1
PI3K-beta -0.003 0.018 -9999 0 -10000 0 0
cell migration -0.016 0.049 -9999 0 -0.25 15 15
SLC9A3R2 0.005 0.05 -9999 0 -0.5 5 5
PXN 0.016 0.053 -9999 0 -10000 0 0
HRAS/GTP 0.023 0.051 -9999 0 -0.32 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
MMP9 -0.1 0.21 -9999 0 -0.51 112 112
PRKCE 0.004 0.055 -9999 0 -0.5 6 6
PRKCD 0.01 0.083 -9999 0 -0.39 3 3
Gi(beta/gamma) 0.021 0.053 -9999 0 -0.33 2 2
mol:LPA 0.003 0.007 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.023 0.064 -9999 0 -10000 0 0
MAPKKK cascade 0.023 0.05 -9999 0 -0.32 2 2
contractile ring contraction involved in cytokinesis 0.024 0.024 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.018 0.098 -9999 0 -0.26 68 68
GNA15 -0.01 0.085 -9999 0 -0.25 56 56
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
MAPT 0.015 0.065 -9999 0 -0.26 10 10
GNA11 -0.011 0.09 -9999 0 -0.26 56 56
Rac1/GTP -0.026 0.16 -9999 0 -0.92 15 15
MMP2 0.021 0.024 -9999 0 -0.36 2 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.018 0.099 -10000 0 -0.4 24 24
CRKL 0.014 0.099 -10000 0 -0.41 24 24
HRAS 0.026 0.11 -10000 0 -0.49 11 11
mol:PIP3 0.003 0.093 0.22 1 -0.41 23 24
SPRED1 0.01 0 -10000 0 -10000 0 0
SPRED2 0.01 0 -10000 0 -10000 0 0
GAB1 0.008 0.1 -10000 0 -0.44 24 24
FOXO3 0.019 0.09 -10000 0 -0.38 23 23
AKT1 0.013 0.096 -10000 0 -0.41 23 23
BAD 0.019 0.09 -10000 0 -0.38 23 23
megakaryocyte differentiation -0.015 0.13 -10000 0 -0.47 29 29
GSK3B 0.019 0.09 -10000 0 -0.38 23 23
RAF1 0.032 0.088 -10000 0 -0.39 11 11
SHC1 0.008 0.032 -10000 0 -0.51 2 2
STAT3 0.009 0.1 -10000 0 -0.44 23 23
STAT1 0.004 0.22 -10000 0 -0.95 24 24
HRAS/SPRED1 -0.02 0.074 -10000 0 -0.39 11 11
cell proliferation 0.01 0.1 -10000 0 -0.44 23 23
PIK3CA 0.01 0 -10000 0 -10000 0 0
TEC 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.1 -10000 0 -0.44 23 23
HRAS/SPRED2 -0.02 0.074 -10000 0 -0.39 11 11
LYN/TEC/p62DOK -0.02 0.087 -10000 0 -0.41 23 23
MAPK3 0.036 0.066 -10000 0 -0.28 9 9
STAP1 0.002 0.11 -10000 0 -0.44 27 27
GRAP2 -0.006 0.088 -10000 0 -0.5 16 16
JAK2 -0.042 0.18 -10000 0 -0.8 25 25
STAT1 (dimer) 0.005 0.21 -10000 0 -0.93 24 24
mol:Gleevec -0.002 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.023 0.09 -10000 0 -0.41 24 24
actin filament polymerization 0.009 0.1 -10000 0 -0.44 23 23
LYN 0.01 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) 0.009 0.15 -10000 0 -0.59 26 26
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
CBL/CRKL/GRB2 -0.019 0.08 -10000 0 -0.37 23 23
PI3K -0.007 0.095 -10000 0 -0.42 23 23
PTEN 0.01 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.001 0.26 -10000 0 -1.2 23 23
MAPK8 0.009 0.1 -10000 0 -0.44 23 23
STAT3 (dimer) 0.01 0.1 -10000 0 -0.44 23 23
positive regulation of transcription 0.034 0.056 -10000 0 -0.23 6 6
mol:GDP -0.026 0.096 -10000 0 -0.41 26 26
PIK3C2B 0.009 0.1 -10000 0 -0.45 23 23
CBL/CRKL 0.02 0.094 -10000 0 -0.38 24 24
FER 0.009 0.1 -10000 0 -0.44 23 23
SH2B3 0.009 0.1 -10000 0 -0.44 24 24
PDPK1 0.009 0.087 -10000 0 -0.37 23 23
SNAI2 0.007 0.11 -10000 0 -0.46 24 24
positive regulation of cell proliferation 0.01 0.17 -10000 0 -0.72 24 24
KITLG 0.009 0.048 -10000 0 -0.53 4 4
cell motility 0.01 0.17 -10000 0 -0.72 24 24
PTPN6 0.002 0.007 -10000 0 -10000 0 0
EPOR 0.029 0.066 -10000 0 -10000 0 0
STAT5A (dimer) 0.012 0.14 -10000 0 -0.6 24 24
SOCS1 0.008 0.032 -10000 0 -0.51 2 2
cell migration 0.001 0.12 0.46 24 -10000 0 24
SOS1 0.01 0 -10000 0 -10000 0 0
EPO 0.004 0.046 -10000 0 -0.51 4 4
VAV1 0.005 0.05 -10000 0 -0.5 5 5
GRB10 0.009 0.1 -10000 0 -0.44 23 23
PTPN11 0.009 0.004 -10000 0 -10000 0 0
SCF/KIT 0.003 0.11 -10000 0 -0.46 24 24
GO:0007205 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 0.035 0.071 -10000 0 -0.31 9 9
CBL 0.01 0 -10000 0 -10000 0 0
KIT -0.015 0.26 -10000 0 -1.2 23 23
MAP2K2 0.035 0.071 -10000 0 -0.31 9 9
SHC/Grb2/SOS1 -0.021 0.092 -10000 0 -0.43 23 23
STAT5A 0.012 0.14 -10000 0 -0.62 24 24
GRB2 0.01 0 -10000 0 -10000 0 0
response to radiation 0.007 0.11 -10000 0 -0.45 24 24
SHC/GRAP2 -0.012 0.068 -10000 0 -0.37 17 17
PTPRO -0.015 0.14 -10000 0 -0.48 29 29
SH2B2 0.009 0.1 -10000 0 -0.44 23 23
DOK1 0.01 0 -10000 0 -10000 0 0
MATK -0.002 0.12 -10000 0 -0.46 24 24
CREBBP 0.029 0.007 -10000 0 -10000 0 0
BCL2 0.027 0.086 -10000 0 -0.8 2 2
Caspase cascade in apoptosis

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
TOP1 0.003 0.084 -10000 0 -0.29 36 36
ACTA1 -0.007 0.1 -10000 0 -0.36 36 36
NUMA1 0.003 0.084 -10000 0 -0.29 36 36
SPTAN1 -0.004 0.1 -10000 0 -0.36 36 36
LIMK1 -0.004 0.1 -10000 0 -0.36 36 36
BIRC3 0.003 0.06 -10000 0 -0.5 7 7
BIRC2 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
CASP10 -0.003 0.095 -10000 0 -0.33 38 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
PTK2 0.003 0.084 -10000 0 -0.29 36 36
DIABLO 0.01 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.1 -10000 0 -0.35 36 36
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.008 0.032 -10000 0 -0.5 2 2
GSN -0.004 0.1 -10000 0 -0.36 36 36
MADD 0.01 0 -10000 0 -10000 0 0
TFAP2A -0.038 0.12 -10000 0 -0.66 18 18
BID 0.004 0.057 -10000 0 -0.2 37 37
MAP3K1 0.004 0.037 -10000 0 -0.2 5 5
TRADD 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.1 -10000 0 -0.36 36 36
CASP9 0.01 0 -10000 0 -10000 0 0
DNA repair -0.002 0.028 0.15 3 -10000 0 3
neuron apoptosis 0.017 0.021 -10000 0 -0.35 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.1 -10000 0 -0.34 36 36
APAF1 0.01 0 -10000 0 -10000 0 0
CASP6 0.016 0.054 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
ICAD/CAD 0.002 0.1 -10000 0 -0.34 35 35
CASP7 -0.005 0.028 0.29 2 -10000 0 2
KRT18 0.011 0.017 -10000 0 -10000 0 0
apoptosis 0.006 0.09 -10000 0 -0.52 6 6
DFFA -0.004 0.1 -10000 0 -0.36 36 36
DFFB -0.004 0.1 -10000 0 -0.36 36 36
PARP1 0.002 0.029 -10000 0 -0.15 3 3
actin filament polymerization -0.002 0.096 0.33 36 -10000 0 36
TNF -0.009 0.096 -10000 0 -0.5 19 19
CYCS 0.007 0.041 -10000 0 -0.22 5 5
SATB1 0.016 0.066 -10000 0 -0.41 3 3
SLK -0.004 0.1 -10000 0 -0.36 36 36
p15 BID/BAX 0.009 0.051 -10000 0 -0.28 5 5
CASP2 0.03 0.043 -10000 0 -10000 0 0
JNK cascade -0.004 0.037 0.2 5 -10000 0 5
CASP3 -0.011 0.11 -10000 0 -0.38 36 36
LMNB2 0.029 0.038 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
CASP4 0.01 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.004 0.03 -10000 0 -10000 0 0
negative regulation of DNA binding -0.037 0.12 -10000 0 -0.65 18 18
stress fiber formation -0.004 0.1 -10000 0 -0.35 36 36
GZMB -0.011 0.11 -10000 0 -0.4 36 36
CASP1 0.01 0.035 -10000 0 -0.31 6 6
LMNB1 0.028 0.039 -10000 0 -10000 0 0
APP 0.017 0.021 -10000 0 -0.35 1 1
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.016 -10000 0 -0.36 1 1
VIM 0.002 0.089 -10000 0 -0.3 35 35
LMNA 0.029 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.025 0.045 -10000 0 -10000 0 0
LRDD 0.008 0.032 -10000 0 -0.5 2 2
SREBF1 -0.004 0.1 -10000 0 -0.36 36 36
APAF-1/Caspase 9 -0.003 0.017 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.003 0.083 -10000 0 -0.28 36 36
CFL2 0.002 0.099 -10000 0 -0.34 36 36
GAS2 -0.017 0.12 -10000 0 -0.37 37 37
positive regulation of apoptosis 0.031 0.038 -10000 0 -10000 0 0
PRF1 -0.013 0.1 -10000 0 -0.5 23 23
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.041 0.11 0.35 59 -10000 0 59
KIRREL -0.01 0.092 -10000 0 -0.5 17 17
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.041 0.11 -10000 0 -0.36 59 59
PLCG1 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0 -10000 0 -10000 0 0
WASL 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.028 0.079 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.005 0.058 -10000 0 -10000 0 0
FYN -0.012 0.076 -10000 0 -0.24 17 17
mol:Ca2+ -0.028 0.078 -10000 0 -10000 0 0
mol:DAG -0.028 0.079 -10000 0 -10000 0 0
NPHS2 -0.002 0.015 -10000 0 -10000 0 0
mol:IP3 -0.028 0.079 -10000 0 -10000 0 0
regulation of endocytosis -0.023 0.065 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol -0.029 0.081 -10000 0 -0.25 59 59
establishment of cell polarity -0.041 0.11 -10000 0 -0.35 59 59
Nephrin/NEPH1/podocin/NCK1-2 -0.025 0.07 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 -0.011 0.071 -10000 0 -10000 0 0
NPHS1 -0.035 0.14 -10000 0 -0.5 42 42
Nephrin/NEPH1/podocin -0.026 0.071 -10000 0 -0.25 17 17
TJP1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
NCK2 0.01 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.028 0.079 -10000 0 -10000 0 0
CD2AP 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.028 0.079 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.031 0.11 -10000 0 -0.28 50 50
cytoskeleton organization 0.007 0.067 -10000 0 -10000 0 0
Nephrin/NEPH1 -0.028 0.078 -10000 0 -0.25 59 59
Nephrin/NEPH1/ZO-1 -0.031 0.087 -10000 0 -0.27 59 59
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.025 0.092 -10000 0 -0.35 11 11
TBX21 -0.004 0.34 -10000 0 -1.2 30 30
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.002 0.091 -10000 0 -0.52 15 15
GADD45B 0.016 0.27 -10000 0 -1 20 20
IL12RB2 -0.024 0.14 -10000 0 -0.5 42 42
GADD45G 0.014 0.27 -10000 0 -1 21 21
natural killer cell activation 0.008 0.016 -10000 0 -10000 0 0
RELB 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL18 0.004 0.071 -10000 0 -0.5 10 10
IL2RA -0.026 0.13 -10000 0 -0.51 36 36
IFNG -0.032 0.14 -10000 0 -0.51 41 41
STAT3 (dimer) 0.026 0.23 -10000 0 -0.78 22 22
HLA-DRB5 -0.043 0.16 -10000 0 -0.5 54 54
FASLG 0.014 0.29 -10000 0 -1 23 23
NF kappa B2 p52/RelB -0.082 0.22 -10000 0 -0.91 24 24
CD4 0 0.07 -10000 0 -0.5 10 10
SOCS1 0.008 0.032 -10000 0 -0.51 2 2
EntrezGene:6955 0.001 0.008 -10000 0 -10000 0 0
CD3D 0.008 0.04 -10000 0 -0.51 3 3
CD3E 0.006 0.05 -10000 0 -0.5 5 5
CD3G 0.001 0.071 -10000 0 -0.5 10 10
IL12Rbeta2/JAK2 -0.003 0.11 -10000 0 -0.35 44 44
CCL3 0.017 0.27 -10000 0 -0.98 23 23
CCL4 0.016 0.28 -10000 0 -1 22 22
HLA-A 0.011 0.005 -10000 0 -10000 0 0
IL18/IL18R 0.016 0.12 -10000 0 -0.36 43 43
NOS2 -0.045 0.41 -10000 0 -1.2 55 55
IL12/IL12R/TYK2/JAK2/SPHK2 0.025 0.092 -10000 0 -0.35 11 11
IL1R1 0.018 0.27 -10000 0 -0.98 22 22
IL4 -0.004 0.016 -10000 0 -10000 0 0
JAK2 0.015 0.035 -10000 0 -0.5 2 2
EntrezGene:6957 0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.014 0.16 -10000 0 -0.96 10 10
RAB7A 0.036 0.22 -10000 0 -0.82 15 15
lysosomal transport 0.038 0.22 -10000 0 -0.77 15 15
FOS -0.031 0.32 -10000 0 -1.1 36 36
STAT4 (dimer) 0.035 0.25 -10000 0 -0.91 20 20
STAT5A (dimer) -0.095 0.23 -10000 0 -0.82 33 33
GZMA 0.015 0.28 -10000 0 -1.1 21 21
GZMB -0.001 0.32 -10000 0 -1.2 28 28
HLX 0.005 0.05 -10000 0 -0.5 5 5
LCK 0.015 0.29 -10000 0 -1 24 24
TCR/CD3/MHC II/CD4 -0.019 0.16 -10000 0 -0.56 29 29
IL2/IL2R -0.022 0.078 -10000 0 -0.28 41 41
MAPK14 0.022 0.27 -10000 0 -0.94 21 21
CCR5 0.016 0.26 -10000 0 -1 18 18
IL1B -0.014 0.13 -10000 0 -0.51 31 31
STAT6 0.029 0.086 -10000 0 -0.26 1 1
STAT4 0.01 0 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
NFKB2 0.01 0 -10000 0 -10000 0 0
IL12B 0.013 0.059 -10000 0 -0.52 6 6
CD8A 0.005 0.056 -10000 0 -0.5 6 6
CD8B 0.003 0.064 -10000 0 -0.5 8 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.025 0.091 0.35 11 -10000 0 11
IL2RB 0.008 0.032 -10000 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.23 -10000 0 -0.81 20 20
IL2RG 0.005 0.05 -10000 0 -0.5 5 5
IL12 0.021 0.064 -10000 0 -0.36 12 12
STAT5A 0.009 0.022 -10000 0 -0.5 1 1
CD247 0.005 0.055 -10000 0 -0.5 6 6
IL2 0.006 0.005 -10000 0 -10000 0 0
SPHK2 0.009 0.022 -10000 0 -0.5 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.011 0.058 -10000 0 -0.51 6 6
IL12/IL12R/TYK2/JAK2 0.011 0.31 -10000 0 -1 27 27
MAP2K3 0.019 0.27 -10000 0 -0.94 22 22
RIPK2 0.01 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.27 -10000 0 -0.91 24 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.009 0.096 -10000 0 -0.5 19 19
IL18RAP -0.006 0.1 -10000 0 -0.5 20 20
IL12Rbeta1/TYK2 0.014 0.071 -10000 0 -0.38 15 15
EOMES -0.009 0.14 -10000 0 -1.2 7 7
STAT1 (dimer) 0.02 0.23 -10000 0 -0.77 23 23
T cell proliferation 0.03 0.21 -10000 0 -0.67 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.009 0.11 -10000 0 -0.5 23 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.078 0.18 -10000 0 -0.72 22 22
ATF2 0.03 0.25 -10000 0 -0.85 21 21
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 -0.013 0.1 -9999 0 -0.5 23 23
GNB1/GNG2 -0.045 0.097 -9999 0 -0.44 14 14
mol:DAG -0.008 0.1 -9999 0 -0.4 14 14
PLCG1 -0.009 0.11 -9999 0 -0.41 14 14
YES1 -0.021 0.11 -9999 0 -0.44 14 14
FZD3 0.009 0.023 -9999 0 -0.51 1 1
FZD6 0.009 0.022 -9999 0 -0.5 1 1
G protein -0.04 0.092 -9999 0 -0.41 14 14
MAP3K7 -0.017 0.12 -9999 0 -0.39 28 28
mol:Ca2+ -0.008 0.1 -9999 0 -0.38 14 14
mol:IP3 -0.008 0.1 -9999 0 -0.4 14 14
NLK -0.002 0.006 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.025 0.13 -9999 0 -0.42 29 29
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.03 0.12 -9999 0 -0.47 14 14
CSNK1A1 0.01 0 -9999 0 -10000 0 0
GNAS -0.021 0.11 -9999 0 -0.44 14 14
GO:0007205 -0.008 0.1 -9999 0 -0.39 14 14
WNT6 -0.023 0.12 -9999 0 -0.51 32 32
WNT4 -0.019 0.12 -9999 0 -0.5 29 29
NFAT1/CK1 alpha -0.048 0.097 -9999 0 -0.42 15 15
GNG2 0.008 0.032 -9999 0 -0.5 2 2
WNT5A 0.004 0.055 -9999 0 -0.5 6 6
WNT11 -0.057 0.17 -9999 0 -0.5 67 67
CDC42 -0.014 0.11 -9999 0 -0.41 14 14
Signaling events mediated by PTP1B

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
PDGFRB 0.009 0.022 -10000 0 -0.5 1 1
Jak2/Leptin Receptor -0.039 0.094 0.18 1 -0.35 21 22
PTP1B/AKT1 0.01 0.037 -10000 0 -0.22 1 1
FYN 0.009 0.022 -10000 0 -0.5 1 1
p210 bcr-abl/PTP1B 0.006 0.041 -10000 0 -0.23 2 2
EGFR -0.007 0.089 -10000 0 -0.51 16 16
EGF/EGFR -0.049 0.091 -10000 0 -0.29 25 25
CSF1 0.005 0.05 -10000 0 -0.5 5 5
AKT1 0.01 0.001 -10000 0 -10000 0 0
INSR 0.01 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.019 0.093 -10000 0 -0.26 59 59
Insulin Receptor/Insulin -0.007 0.021 -10000 0 -10000 0 0
HCK -0.014 0.11 -10000 0 -0.5 24 24
CRK 0.01 0 -10000 0 -10000 0 0
TYK2 0.011 0.039 -10000 0 -0.23 1 1
EGF -0.089 0.2 -10000 0 -0.5 99 99
YES1 0.01 0 -10000 0 -10000 0 0
CAV1 -0.092 0.099 -10000 0 -0.25 80 80
TXN 0.005 0.039 -10000 0 -0.5 3 3
PTP1B/IRS1/GRB2 0.016 0.039 -10000 0 -0.3 1 1
cell migration -0.006 0.041 0.23 2 -10000 0 2
STAT3 0.01 0.001 -10000 0 -10000 0 0
PRLR -0.053 0.17 -10000 0 -0.5 62 62
ITGA2B -0.044 0.16 -10000 0 -0.5 54 54
CSF1R 0.003 0.059 -10000 0 -0.5 7 7
Prolactin Receptor/Prolactin -0.052 0.13 -10000 0 -0.37 74 74
FGR -0.029 0.14 -10000 0 -0.5 39 39
PTP1B/p130 Cas 0.01 0.041 -10000 0 -0.25 2 2
Crk/p130 Cas 0.016 0.039 -10000 0 -0.26 1 1
DOK1 0.016 0.038 -10000 0 -0.25 1 1
JAK2 -0.005 0.064 -10000 0 -0.3 12 12
Jak2/Leptin Receptor/Leptin -0.027 0.065 -10000 0 -0.41 5 5
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
PTPN1 0.006 0.041 -10000 0 -0.23 2 2
LYN 0.01 0 -10000 0 -10000 0 0
CDH2 -0.048 0.16 -10000 0 -0.51 58 58
SRC 0.015 0.018 -10000 0 -10000 0 0
ITGB3 -0.019 0.12 -10000 0 -0.51 28 28
CAT1/PTP1B -0.031 0.13 -10000 0 -0.48 24 24
CAPN1 0.01 0.001 -10000 0 -10000 0 0
CSK 0.01 0 -10000 0 -10000 0 0
PI3K -0.003 0.02 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.022 0.063 -10000 0 -0.42 5 5
negative regulation of transcription -0.005 0.063 -10000 0 -0.3 12 12
FCGR2A 0.002 0.063 -10000 0 -0.5 8 8
FER 0.008 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.056 0.13 -10000 0 -0.36 81 81
BLK -0.08 0.2 -10000 0 -0.51 89 89
Insulin Receptor/Insulin/Shc -0.001 0.019 -10000 0 -0.31 2 2
RHOA 0.01 0.001 -10000 0 -10000 0 0
LEPR -0.047 0.16 -10000 0 -0.5 57 57
BCAR1 0.009 0.022 -10000 0 -0.5 1 1
p210 bcr-abl/Grb2 0.01 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.039 0.14 -10000 0 -0.49 28 28
PRL -0.01 0.08 -10000 0 -0.51 13 13
SOCS3 0.001 0.11 -10000 0 -1.2 4 4
SPRY2 0.006 0.032 -10000 0 -0.5 2 2
Insulin Receptor/Insulin/IRS1 -0.001 0.013 -10000 0 -0.3 1 1
CSF1/CSF1R 0.01 0.06 -10000 0 -0.36 6 6
Ras protein signal transduction 0.01 0.014 -10000 0 -10000 0 0
IRS1 0.009 0.022 -10000 0 -0.5 1 1
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.044 0.16 -10000 0 -0.51 52 52
STAT5B 0.004 0.044 -10000 0 -0.23 2 2
STAT5A 0.003 0.045 -10000 0 -0.23 3 3
GRB2 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.041 -10000 0 -0.29 1 1
CSN2 -0.014 0.044 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
LAT 0.007 0.06 -10000 0 -0.45 8 8
YBX1 0.015 0.001 -10000 0 -10000 0 0
LCK 0.007 0.039 -10000 0 -0.5 3 3
SHC1 0.008 0.032 -10000 0 -0.51 2 2
NOX4 -0.008 0.089 -10000 0 -0.5 16 16
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.019 0.081 -9999 0 -0.36 28 28
AKT1 0.028 0.12 -9999 0 -0.52 14 14
PTK2B -0.01 0.13 -9999 0 -0.58 15 15
VEGFR2 homodimer/Frs2 -0.022 0.14 -9999 0 -0.71 13 13
CAV1 -0.31 0.25 -9999 0 -0.5 326 326
CALM1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.041 0.12 -9999 0 -0.65 13 13
endothelial cell proliferation 0.034 0.12 -9999 0 -0.49 14 14
mol:Ca2+ 0.003 0.12 -9999 0 -0.56 14 14
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.037 0.11 -9999 0 -0.6 13 13
RP11-342D11.1 -0.003 0.12 -9999 0 -0.57 14 14
CDH5 -0.055 0.17 -9999 0 -0.5 65 65
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0.008 0.032 -9999 0 -0.51 2 2
SHC2 0.001 0.067 -9999 0 -0.5 9 9
HRAS/GDP -0.031 0.092 -9999 0 -0.48 14 14
SH2D2A 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.032 0.095 -9999 0 -0.48 16 16
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.04 0.12 -9999 0 -0.63 13 13
VEGFR1 homodimer 0.01 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.034 0.1 -9999 0 -0.53 14 14
GRB10 0.003 0.12 -9999 0 -0.56 14 14
PTPN11 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
PAK1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.064 0.16 -9999 0 -0.56 35 35
HRAS 0.01 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.006 0.085 -9999 0 -0.35 14 14
HIF1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.008 0.032 -9999 0 -0.51 2 2
oxygen and reactive oxygen species metabolic process -0.037 0.11 -9999 0 -0.59 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.003 0.08 -9999 0 -0.5 13 13
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.041 0.12 -9999 0 -0.63 13 13
mol:GDP -0.033 0.099 -9999 0 -0.52 14 14
mol:NADP 0.024 0.1 -9999 0 -0.41 18 18
eNOS/Hsp90 0.028 0.098 -9999 0 -0.39 15 15
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
mol:IP3 0.003 0.12 -9999 0 -0.57 14 14
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.009 0.022 -9999 0 -0.5 1 1
VEGFA 0.011 0 -9999 0 -10000 0 0
VEGFC 0.006 0.045 -9999 0 -0.5 4 4
FAK1/Vinculin 0.005 0.14 -9999 0 -0.6 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.05 0.12 -9999 0 -0.61 14 14
PTPN6 0.01 0 -9999 0 -10000 0 0
EPAS1 -0.046 0.17 -9999 0 -0.49 65 65
mol:L-citrulline 0.024 0.1 -9999 0 -0.41 18 18
ITGAV 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.038 0.12 -9999 0 -0.62 13 13
VEGFR2 homodimer/VEGFA homodimer -0.04 0.12 -9999 0 -0.62 14 14
VEGFR2/3 heterodimer -0.028 0.16 -9999 0 -0.69 18 18
VEGFB 0.01 0 -9999 0 -10000 0 0
MAPK11 0.004 0.13 -9999 0 -0.57 15 15
VEGFR2 homodimer -0.029 0.16 -9999 0 -0.42 65 65
FLT1 0.01 0 -9999 0 -10000 0 0
NEDD4 0.01 0.022 -9999 0 -0.5 1 1
MAPK3 0.008 0.12 -9999 0 -0.54 14 14
MAPK1 0.008 0.12 -9999 0 -0.54 14 14
VEGFA145/NRP2 -0.002 0.027 -9999 0 -0.35 3 3
VEGFR1/2 heterodimer -0.02 0.14 -9999 0 -0.69 13 13
KDR -0.029 0.16 -9999 0 -0.42 65 65
VEGFA165/NRP1/VEGFR2 homodimer -0.037 0.11 -9999 0 -0.57 15 15
SRC 0.01 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.008 0.12 -9999 0 -0.55 14 14
PI3K -0.036 0.11 -9999 0 -0.59 14 14
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.04 0.12 -9999 0 -0.63 13 13
FES 0.002 0.12 -9999 0 -0.58 14 14
GAB1 -0.038 0.11 -9999 0 -0.61 13 13
VEGFR2 homodimer/VEGFA homodimer/Src -0.04 0.12 -9999 0 -0.63 13 13
CTNNB1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.14 -9999 0 -0.4 52 52
VEGFR2 homodimer/VEGFA homodimer/Yes -0.04 0.12 -9999 0 -0.63 13 13
PI3K/GAB1 0.027 0.12 -9999 0 -0.54 14 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.036 0.11 -9999 0 -0.59 13 13
PRKACA 0.01 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.049 0.14 -9999 0 -0.63 19 19
HSP90AA1 0.01 0 -9999 0 -10000 0 0
CDC42 0.003 0.12 -9999 0 -0.58 14 14
actin cytoskeleton reorganization -0.04 0.12 -9999 0 -0.63 13 13
PTK2 -0.001 0.15 -9999 0 -0.66 15 15
EDG1 -0.003 0.12 -9999 0 -0.57 14 14
mol:DAG 0.003 0.12 -9999 0 -0.57 14 14
CaM/Ca2+ -0.033 0.1 -9999 0 -0.52 14 14
MAP2K3 0.01 0.12 -9999 0 -0.55 14 14
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.037 0.11 -9999 0 -0.58 14 14
PLCG1 0.003 0.12 -9999 0 -0.58 14 14
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.038 0.11 -9999 0 -0.59 14 14
IQGAP1 0.01 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.04 0.12 -9999 0 -0.63 13 13
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.04 0.12 -9999 0 -0.63 13 13
cell migration 0.012 0.14 -9999 0 -0.59 14 14
mol:PI-3-4-5-P3 -0.034 0.1 -9999 0 -0.53 15 15
FYN 0.009 0.022 -9999 0 -0.5 1 1
VEGFB/NRP1 -0.034 0.1 -9999 0 -0.54 14 14
mol:NO 0.024 0.1 -9999 0 -0.41 18 18
PXN 0.01 0 -9999 0 -10000 0 0
HRAS/GTP -0.03 0.092 -9999 0 -0.48 14 14
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.002 0.13 -9999 0 -0.58 14 14
VHL 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.12 -9999 0 -0.51 28 28
NOS3 0.023 0.11 -9999 0 -0.46 18 18
VEGFR2 homodimer/VEGFA homodimer/Sck -0.045 0.13 -9999 0 -0.64 16 16
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.009 0.12 -9999 0 -0.53 14 14
PRKCB 0.003 0.13 -9999 0 -0.56 16 16
VCL 0.01 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.004 0.12 -9999 0 -0.57 14 14
VEGFR1/2 heterodimer/VEGFA homodimer -0.04 0.12 -9999 0 -0.63 13 13
VEGFA165/NRP2 -0.002 0.027 -9999 0 -0.35 3 3
MAPKKK cascade -0.03 0.09 -9999 0 -0.49 13 13
NRP2 0.007 0.039 -9999 0 -0.5 3 3
VEGFC homodimer 0.006 0.045 -9999 0 -0.5 4 4
NCK1 0.01 0 -9999 0 -10000 0 0
ROCK1 0.01 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.005 0.14 -9999 0 -0.6 15 15
MAP3K13 0.003 0.12 -9999 0 -0.58 14 14
PDPK1 0.026 0.11 -9999 0 -0.48 14 14
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.023 0.088 -9999 0 -0.36 34 34
CRKL 0.004 0.081 -9999 0 -0.4 6 6
mol:PIP3 -0.016 0.005 -9999 0 -10000 0 0
AKT1 0.001 0.004 -9999 0 -10000 0 0
PTK2B 0.008 0.032 -9999 0 -0.5 2 2
RAPGEF1 0.01 0.077 -9999 0 -0.4 5 5
RANBP10 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.037 0.1 -9999 0 -0.31 62 62
MAP3K5 0.016 0.079 -9999 0 -0.41 6 6
HGF/MET/CIN85/CBL/ENDOPHILINS -0.033 0.091 -9999 0 -0.27 62 62
AP1 -0.024 0.078 -9999 0 -0.32 30 30
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.008 0.032 -9999 0 -0.51 2 2
apoptosis -0.03 0.17 -9999 0 -0.71 30 30
STAT3 (dimer) 0.006 0.079 -9999 0 -0.39 4 4
GAB1/CRKL/SHP2/PI3K -0.02 0.063 -9999 0 -0.44 4 4
INPP5D 0.007 0.039 -9999 0 -0.5 3 3
CBL/CRK 0.01 0.077 -9999 0 -0.4 5 5
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
ELK1 -0.011 0.047 -9999 0 -0.19 34 34
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.015 0.044 -9999 0 -0.25 4 4
PAK1 0.007 0.004 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.037 0.1 -9999 0 -0.31 62 62
HRAS -0.011 0.13 -9999 0 -0.56 21 21
DOCK1 0.01 0.077 -9999 0 -0.4 5 5
GAB1 -0.002 0.085 -9999 0 -0.3 23 23
CRK 0.004 0.081 -9999 0 -0.4 6 6
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.045 0.14 -9999 0 -0.48 45 45
JUN 0.007 0.039 -9999 0 -0.5 3 3
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.024 0.067 -9999 0 -0.22 45 45
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
cell morphogenesis 0.026 0.087 -9999 0 -0.43 4 4
GRB2/SHC -0.001 0.066 -9999 0 -0.32 5 5
FOS -0.017 0.11 -9999 0 -0.5 27 27
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.011 0.047 -9999 0 -0.19 34 34
HGF/MET/MUC20 -0.038 0.1 -9999 0 -0.31 62 62
cell migration -0.02 0.058 -9999 0 -0.31 5 5
GRB2 0.01 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
MET/RANBP10 -0.023 0.088 -9999 0 -0.36 34 34
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.081 -9999 0 -0.41 4 4
MET/MUC20 -0.024 0.09 -9999 0 -0.36 34 34
RAP1B 0.016 0.073 -9999 0 -0.46 3 3
RAP1A 0.016 0.073 -9999 0 -0.46 3 3
HGF/MET/RANBP9 -0.037 0.1 -9999 0 -0.31 62 62
RAF1 -0.004 0.12 -9999 0 -0.52 21 21
STAT3 0.006 0.08 -9999 0 -0.4 4 4
cell proliferation 0.006 0.11 -9999 0 -0.33 45 45
RPS6KB1 0.001 0.028 -9999 0 -10000 0 0
MAPK3 -0.014 0.043 -9999 0 -10000 0 0
MAPK1 -0.014 0.043 -9999 0 -0.18 15 15
RANBP9 0.01 0 -9999 0 -10000 0 0
MAPK8 0.029 0.068 -9999 0 -0.36 4 4
SRC 0.007 0.076 -9999 0 -0.38 4 4
PI3K 0 0.065 -9999 0 -0.23 22 22
MET/Glomulin -0.012 0.081 -9999 0 -0.32 34 34
SOS1 0.01 0 -9999 0 -10000 0 0
MAP2K1 0.003 0.12 -9999 0 -0.48 21 21
MET -0.024 0.13 -9999 0 -0.5 34 34
MAP4K1 0.01 0.084 -9999 0 -0.45 6 6
PTK2 0.01 0 -9999 0 -10000 0 0
MAP2K2 0.003 0.12 -9999 0 -0.48 21 21
BAD 0.007 0.004 -9999 0 -10000 0 0
MAP2K4 0.021 0.074 -9999 0 -0.4 5 5
SHP2/GRB2/SOS1/GAB1 -0.025 0.078 -9999 0 -0.34 22 22
INPPL1 0.01 0 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0 -9999 0 -10000 0 0
HGS -0.005 0.066 -9999 0 -0.24 21 21
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.021 0.12 -9999 0 -0.5 31 31
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
PTPRJ 0.01 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.001 0.066 -9999 0 -0.33 3 3
PDPK1 -0.006 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.039 0.11 -9999 0 -0.32 62 62
Signaling events mediated by HDAC Class III

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
EP300 0.01 0 -10000 0 -10000 0 0
HDAC4 0.009 0.023 -10000 0 -0.51 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.003 0.083 0.36 26 -10000 0 26
CDKN1A -0.001 0.03 -10000 0 -0.68 1 1
KAT2B 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.009 0.022 -10000 0 -0.5 1 1
FOXO4 0.018 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
TAT -0.038 0.15 -10000 0 -0.51 47 47
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.007 0.028 -10000 0 -0.36 3 3
PPARGC1A -0.12 0.22 -10000 0 -0.5 127 127
FHL2 -0.056 0.17 -10000 0 -0.51 65 65
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.006 -10000 0 -10000 0 0
HIST2H4A -0.003 0.083 -10000 0 -0.36 26 26
SIRT1/FOXO3a 0 0.006 -10000 0 -10000 0 0
SIRT1 0 0.008 0.19 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.014 -10000 0 -0.3 1 1
SIRT1/Histone H1b -0.009 0.032 -10000 0 -10000 0 0
apoptosis 0 0.006 -10000 0 -10000 0 0
SIRT1/PGC1A -0.074 0.13 -10000 0 -0.3 127 127
p53/SIRT1 0.001 0.017 0.38 1 -10000 0 1
SIRT1/FOXO4 0 0.006 0.15 1 -10000 0 1
FOXO1/FHL2/SIRT1 -0.034 0.091 -10000 0 -0.27 66 66
HIST1H1E 0.004 0.044 -10000 0 -10000 0 0
SIRT1/p300 0 0.006 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.023 0.3 3 -10000 0 3
TP53 0 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.006 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
MEF2D 0.01 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.033 0.1 -10000 0 -0.36 47 47
ACSS2 0.015 0.017 -10000 0 -0.35 1 1
SIRT1/PCAF/MYOD -0.001 0.024 -10000 0 -0.3 3 3
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.056 -9999 0 -0.36 13 13
PDGFRB 0.008 0.023 -9999 0 -0.5 1 1
SPHK1 -0.009 0.02 -9999 0 -10000 0 0
mol:S1P -0.011 0.026 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.011 0.13 -9999 0 -0.35 49 49
GNAO1 0.003 0.06 -9999 0 -0.51 7 7
PDGFB-D/PDGFRB/PLCgamma1 -0.003 0.12 -9999 0 -0.44 11 11
PLCG1 -0.006 0.13 -9999 0 -0.34 47 47
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.023 -9999 0 -0.5 1 1
GNAI2 0.01 0.003 -9999 0 -10000 0 0
GNAI3 0.01 0.003 -9999 0 -10000 0 0
GNAI1 0.008 0.032 -9999 0 -0.51 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.005 0.051 -9999 0 -0.31 13 13
S1P1/S1P -0.019 0.053 -9999 0 -0.35 5 5
negative regulation of cAMP metabolic process -0.01 0.13 -9999 0 -0.35 49 49
MAPK3 -0.02 0.18 -9999 0 -0.53 47 47
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.004 0.081 -9999 0 -0.5 13 13
PLCB2 0.01 0.07 -9999 0 -0.34 8 8
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.016 0.045 -9999 0 -0.3 5 5
receptor internalization -0.019 0.051 -9999 0 -0.33 5 5
PTGS2 -0.058 0.3 -9999 0 -0.98 47 47
Rac1/GTP -0.016 0.045 -9999 0 -0.3 5 5
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFA 0.009 0.003 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.01 0.13 -9999 0 -0.35 49 49
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.031 0.14 -9999 0 -0.5 41 41
MAPK1 -0.02 0.18 -9999 0 -0.53 47 47
S1P1/S1P/PDGFB-D/PDGFRB 0.012 0.073 -9999 0 -0.37 5 5
ABCC1 0.01 0.002 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.037 0.1 -10000 0 -0.32 60 60
cell-cell adhesion 0.049 0.096 0.42 13 -10000 0 13
Ephrin B/EPHB2/RasGAP -0.034 0.087 -10000 0 -0.49 2 2
ITSN1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
SHC1 0.008 0.032 -10000 0 -0.51 2 2
Ephrin B1/EPHB3 -0.006 0.044 -10000 0 -0.3 11 11
Ephrin B1/EPHB1 -0.037 0.1 -10000 0 -0.31 62 62
HRAS/GDP -0.036 0.085 -10000 0 -0.48 5 5
Ephrin B/EPHB1/GRB7 -0.039 0.099 -10000 0 -0.54 6 6
Endophilin/SYNJ1 -0.006 0.091 -10000 0 -0.46 2 2
KRAS 0.008 0.032 -10000 0 -0.51 2 2
Ephrin B/EPHB1/Src -0.036 0.094 -10000 0 -0.55 4 4
endothelial cell migration -0.004 0.031 -10000 0 -0.24 9 9
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.004 0.055 -10000 0 -0.5 6 6
PAK1 -0.002 0.095 -10000 0 -0.46 3 3
HRAS 0.01 0 -10000 0 -10000 0 0
RRAS -0.008 0.096 -10000 0 -0.47 4 4
DNM1 0.002 0.064 -10000 0 -0.51 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.008 0.099 -10000 0 -0.53 4 4
lamellipodium assembly -0.049 0.096 -10000 0 -0.42 13 13
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.006 0.071 -10000 0 -0.43 5 5
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
EPHB2 -0.047 0.16 -10000 0 -0.51 56 56
EPHB3 0.002 0.064 -10000 0 -0.51 8 8
EPHB1 -0.051 0.17 -10000 0 -0.51 60 60
EPHB4 0.01 0 -10000 0 -10000 0 0
mol:GDP -0.033 0.085 -10000 0 -0.39 10 10
Ephrin B/EPHB2 -0.035 0.089 -10000 0 -0.5 2 2
Ephrin B/EPHB3 -0.012 0.055 -10000 0 -0.27 12 12
JNK cascade -0.031 0.12 -10000 0 -0.49 9 9
Ephrin B/EPHB1 -0.037 0.096 -10000 0 -0.27 61 61
RAP1/GDP -0.027 0.073 -10000 0 -0.43 5 5
EFNB2 0.002 0.063 -10000 0 -0.5 8 8
EFNB3 0.004 0.055 -10000 0 -0.5 6 6
EFNB1 0.007 0.039 -10000 0 -0.5 3 3
Ephrin B2/EPHB1-2 -0.065 0.13 -10000 0 -0.3 113 113
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.048 0.096 -10000 0 -0.43 13 13
Rap1/GTP -0.048 0.095 -10000 0 -0.42 13 13
axon guidance -0.037 0.1 -10000 0 -0.32 60 60
MAPK3 0.018 0.064 -10000 0 -0.38 5 5
MAPK1 0.018 0.064 -10000 0 -0.38 5 5
Rac1/GDP 0.001 0.09 -10000 0 -0.45 5 5
actin cytoskeleton reorganization -0.04 0.08 -10000 0 -0.36 13 13
CDC42/GDP 0.001 0.09 -10000 0 -0.45 5 5
PI3K -0.004 0.032 -10000 0 -0.24 9 9
EFNA5 0.003 0.06 -10000 0 -0.5 7 7
Ephrin B2/EPHB4 -0.005 0.037 -10000 0 -0.3 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.005 0.063 -10000 0 -0.41 2 2
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.048 0.095 -10000 0 -0.42 13 13
PTK2 0.014 0.028 -10000 0 -10000 0 0
MAP4K4 -0.031 0.12 -10000 0 -0.49 9 9
SRC 0.01 0 -10000 0 -10000 0 0
KALRN 0.007 0.039 -10000 0 -0.5 3 3
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.009 0.094 -10000 0 -0.36 6 6
MAP2K1 0.012 0.067 -10000 0 -0.4 5 5
WASL 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.061 0.12 -10000 0 -0.29 106 106
cell migration 0.018 0.071 -10000 0 -0.43 5 5
NRAS 0.01 0 -10000 0 -10000 0 0
SYNJ1 -0.007 0.092 -10000 0 -0.47 2 2
PXN 0.01 0 -10000 0 -10000 0 0
TF -0.066 0.14 -10000 0 -0.46 20 20
HRAS/GTP -0.053 0.1 -10000 0 -0.45 13 13
Ephrin B1/EPHB1-2 -0.062 0.12 -10000 0 -0.29 110 110
cell adhesion mediated by integrin 0.002 0.052 0.27 13 -10000 0 13
RAC1 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.057 0.11 -10000 0 -0.48 13 13
RAC1-CDC42/GTP -0.051 0.097 -10000 0 -0.41 14 14
RASA1 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.027 0.073 -10000 0 -0.46 4 4
ruffle organization -0.011 0.12 -10000 0 -0.42 13 13
NCK1 0.01 0 -10000 0 -10000 0 0
receptor internalization -0.004 0.095 -10000 0 -0.45 4 4
Ephrin B/EPHB2/KALRN -0.036 0.089 -10000 0 -0.49 3 3
ROCK1 0.014 0.041 -10000 0 -0.27 11 11
RAS family/GDP -0.038 0.076 -10000 0 -0.35 13 13
Rac1/GTP -0.051 0.1 -10000 0 -0.44 13 13
Ephrin B/EPHB1/Src/Paxillin 0.004 0.071 -10000 0 -0.47 4 4
Signaling events mediated by PRL

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
CCNE1 -0.18 0.25 -10000 0 -0.51 190 190
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.008 0.032 -10000 0 -0.5 2 2
CDKN1A 0.018 0.04 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin -0.001 0.022 -10000 0 -0.36 2 2
mol:Ca2+ -0.06 0.14 0.2 2 -0.37 85 87
AGT -0.076 0.19 -10000 0 -0.51 85 85
CCNA2 -0.044 0.14 -10000 0 -0.49 14 14
TUBA1B 0.01 0 -10000 0 -10000 0 0
EGR1 -0.001 0.083 -10000 0 -0.35 28 28
CDK2/Cyclin E1 -0.07 0.14 -10000 0 -0.36 18 18
MAPK3 0.016 0.023 -10000 0 -0.36 2 2
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.023 -10000 0 -0.36 2 2
PTP4A1 0.014 0.064 -10000 0 -10000 0 0
PTP4A3 0.008 0.032 -10000 0 -0.51 2 2
PTP4A2 0.01 0 -10000 0 -10000 0 0
ITGB1 0.016 0.023 -10000 0 -0.36 2 2
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.019 0.03 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.017 0.06 -10000 0 -10000 0 0
RABGGTA 0.01 0 -10000 0 -10000 0 0
BCAR1 0 0.02 0.2 2 -0.36 1 3
RHOC 0.019 0.03 -10000 0 -10000 0 0
RHOA 0.019 0.03 -10000 0 -10000 0 0
cell motility 0.022 0.033 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.018 0.059 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.003 0.031 -10000 0 -0.36 4 4
ROCK1 0.022 0.033 -10000 0 -10000 0 0
RABGGTB 0.01 0 -10000 0 -10000 0 0
CDK2 0.01 0 -10000 0 -10000 0 0
mitosis 0.014 0.063 -10000 0 -10000 0 0
ATF5 0.009 0.023 -10000 0 -0.51 1 1
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.002 0.027 -10000 0 -0.36 3 3
ATM 0.01 0 -10000 0 -10000 0 0
UBE2D3 0.01 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
ATR 0.01 0 -10000 0 -10000 0 0
UBE2L3 0.01 0 -10000 0 -10000 0 0
FANCD2 0.019 0.015 -10000 0 -10000 0 0
protein ubiquitination -0.091 0.12 -10000 0 -0.49 4 4
XRCC5 0.01 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.01 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.006 0.02 -10000 0 -10000 0 0
FANCF 0.01 0 -10000 0 -10000 0 0
BRCA1 0.007 0.039 -10000 0 -0.51 3 3
CCNE1 -0.18 0.25 -10000 0 -0.51 190 190
CDK2/Cyclin E1 -0.13 0.17 -10000 0 -0.36 190 190
FANCG 0.01 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.038 -10000 0 -0.36 6 6
FANCE 0.01 0 -10000 0 -10000 0 0
FANCC 0.01 0 -10000 0 -10000 0 0
NBN 0.01 0 -10000 0 -10000 0 0
FANCA -0.011 0.1 -10000 0 -0.51 21 21
DNA repair -0.014 0.12 -10000 0 -0.39 13 13
BRCA1/BARD1/ubiquitin -0.004 0.038 -10000 0 -0.36 6 6
BARD1/DNA-PK -0.002 0.02 -10000 0 -0.26 3 3
FANCL 0.01 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.002 0.027 0.35 3 -10000 0 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.03 0.018 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.003 0.032 -10000 0 -0.3 6 6
BRCA1/BARD1/P53 -0.003 0.028 -10000 0 -0.26 4 4
BARD1/CSTF1/BRCA1 -0.003 0.032 -10000 0 -0.3 6 6
BRCA1/BACH1 0.007 0.039 -10000 0 -0.51 3 3
BARD1 0.007 0.039 -10000 0 -0.5 3 3
PCNA 0.008 0.032 -10000 0 -0.51 2 2
BRCA1/BARD1/UbcH5C -0.003 0.032 -10000 0 -0.3 6 6
BRCA1/BARD1/UbcH7 -0.003 0.032 -10000 0 -0.3 6 6
BRCA1/BARD1/RAD51/PCNA -0.048 0.11 -10000 0 -0.28 89 89
BARD1/DNA-PK/P53 -0.001 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.038 -10000 0 -0.36 6 6
BRCA1/BARD1/CTIP -0.003 0.028 -10000 0 -0.26 4 4
FA complex 0.026 0.029 -10000 0 -10000 0 0
BARD1/EWS -0.002 0.027 -10000 0 -0.36 3 3
RBBP8 0.018 0 -10000 0 -10000 0 0
TP53 0.01 0 -10000 0 -10000 0 0
TOPBP1 0.01 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.028 0.26 4 -10000 0 4
BRCA1/BARD1 -0.092 0.12 -10000 0 -0.5 4 4
CSTF1 0.01 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.002 0.028 -10000 0 -0.36 3 3
CDK2 0.01 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.077 0.19 -10000 0 -0.51 86 86
RAD50 0.01 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.038 -10000 0 -0.36 6 6
EWSR1 0.01 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.01 0.057 -9999 0 -0.32 16 16
EFNA5 0.003 0.06 -9999 0 -0.5 7 7
FYN 0.008 0.055 -9999 0 -0.28 17 17
neuron projection morphogenesis -0.01 0.057 -9999 0 -0.32 16 16
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.01 0.057 -9999 0 -0.32 16 16
EPHA5 -0.004 0.071 -9999 0 -0.51 10 10
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.029 0.072 0.4 5 -10000 0 5
GNAI2 0.01 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.02 0.074 -10000 0 -0.3 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.06 -10000 0 -0.51 7 7
RhoA/GTP -0.029 0.073 -10000 0 -0.41 5 5
negative regulation of cAMP metabolic process -0.01 0.091 -10000 0 -0.25 36 36
GNAZ -0.031 0.14 -10000 0 -0.5 41 41
GNAI3 0.01 0 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
S1PR5 -0.024 0.13 -10000 0 -0.5 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.01 0.092 -10000 0 -0.26 36 36
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.019 0.082 -10000 0 -0.51 11 11
FYN 0.03 0.13 -10000 0 -0.65 13 13
LAT/GRAP2/SLP76 -0.016 0.1 -10000 0 -0.52 16 16
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.037 0.092 -10000 0 -0.43 13 13
B2M 0.011 0.003 -10000 0 -10000 0 0
IKBKG -0.008 0.023 -10000 0 -0.14 6 6
MAP3K8 0.008 0.032 -10000 0 -0.5 2 2
mol:Ca2+ -0.01 0.025 -10000 0 -0.11 14 14
integrin-mediated signaling pathway -0.001 0.018 -10000 0 -0.3 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.034 0.13 -10000 0 -0.63 14 14
TRPV6 -0.072 0.18 -10000 0 -0.51 73 73
CD28 0.009 0.023 -10000 0 -0.51 1 1
SHC1 0.03 0.12 -10000 0 -0.58 14 14
receptor internalization 0.023 0.12 -10000 0 -0.56 15 15
PRF1 -0.014 0.25 -10000 0 -1.1 25 25
KRAS 0.008 0.032 -10000 0 -0.51 2 2
GRB2 0.01 0 -10000 0 -10000 0 0
COT/AKT1 0.038 0.077 -10000 0 -0.36 13 13
LAT 0.03 0.12 -10000 0 -0.62 12 12
EntrezGene:6955 0 0.005 -10000 0 -10000 0 0
CD3D 0.008 0.04 -10000 0 -0.51 3 3
CD3E 0.006 0.052 -10000 0 -0.52 5 5
CD3G 0.001 0.071 -10000 0 -0.51 10 10
RASGRP2 0.002 0.04 -10000 0 -0.16 27 27
RASGRP1 0.036 0.1 -10000 0 -0.42 16 16
HLA-A 0.011 0.003 -10000 0 -10000 0 0
RASSF5 0.008 0.032 -10000 0 -0.5 2 2
RAP1A/GTP/RAPL -0.001 0.019 -10000 0 -0.3 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.029 0.036 -10000 0 -0.12 14 14
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.041 -10000 0 -0.23 9 9
PRKCA -0.005 0.051 -10000 0 -0.27 11 11
GRAP2 -0.006 0.088 -10000 0 -0.5 16 16
mol:IP3 0.01 0.11 0.21 63 -0.44 11 74
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.016 0.11 -10000 0 -0.59 11 11
ORAI1 0.041 0.099 0.28 73 -10000 0 73
CSK 0.03 0.12 -10000 0 -0.66 11 11
B7 family/CD28 -0.033 0.14 -10000 0 -0.67 17 17
CHUK 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.024 0.14 -10000 0 -0.67 14 14
PTPN6 0.027 0.12 -10000 0 -0.64 12 12
VAV1 0.029 0.12 -10000 0 -0.62 14 14
Monovalent TCR/CD3 0.008 0.086 -10000 0 -0.38 17 17
CBL 0.01 0 -10000 0 -10000 0 0
LCK 0.028 0.13 -10000 0 -0.69 12 12
PAG1 0.029 0.12 -10000 0 -0.66 11 11
RAP1A 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.023 0.14 -10000 0 -0.73 12 12
CD80 -0.003 0.081 -10000 0 -0.5 13 13
CD86 0 0.071 -10000 0 -0.5 10 10
PDK1/CARD11/BCL10/MALT1 -0.017 0.05 -10000 0 -0.28 9 9
HRAS 0.01 0 -10000 0 -10000 0 0
GO:0035030 0.024 0.12 -10000 0 -0.55 17 17
CD8A 0.005 0.056 -10000 0 -0.51 6 6
CD8B 0.003 0.064 -10000 0 -0.51 8 8
PTPRC -0.007 0.092 -10000 0 -0.5 17 17
PDK1/PKC theta 0.033 0.12 -10000 0 -0.48 18 18
CSK/PAG1 0.033 0.12 -10000 0 -0.66 10 10
SOS1 0.01 0 -10000 0 -10000 0 0
peptide-MHC class I 0.016 0.007 -10000 0 -10000 0 0
GRAP2/SLP76 -0.02 0.12 -10000 0 -0.6 16 16
STIM1 0.021 0.049 -10000 0 -10000 0 0
RAS family/GTP 0.038 0.041 -10000 0 -0.17 7 7
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.022 0.13 -10000 0 -0.61 15 15
mol:DAG -0.005 0.074 -10000 0 -0.37 13 13
RAP1A/GDP 0.013 0.016 -10000 0 -0.062 3 3
PLCG1 0.01 0 -10000 0 -10000 0 0
CD247 0.005 0.056 -10000 0 -0.51 6 6
cytotoxic T cell degranulation -0.01 0.24 -10000 0 -1.1 25 25
RAP1A/GTP -0.004 0.013 -10000 0 -0.063 12 12
mol:PI-3-4-5-P3 0.036 0.11 -10000 0 -0.51 14 14
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.007 0.12 0.23 62 -0.56 12 74
NRAS 0.01 0 -10000 0 -10000 0 0
ZAP70 0.004 0.055 -10000 0 -0.5 6 6
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.015 0.1 -10000 0 -0.55 13 13
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
CD8 heterodimer 0.006 0.07 -10000 0 -0.45 11 11
CARD11 -0.02 0.12 -10000 0 -0.51 30 30
PRKCB -0.008 0.065 -10000 0 -0.3 18 18
PRKCE -0.006 0.054 -10000 0 -0.3 9 9
PRKCQ 0.025 0.14 -10000 0 -0.54 20 20
LCP2 0.007 0.039 -10000 0 -0.5 3 3
BCL10 0.01 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.037 0.08 -10000 0 -0.36 13 13
IKK complex 0.036 0.033 -10000 0 -0.11 9 9
RAS family/GDP -0.002 0.007 -10000 0 -0.076 1 1
MAP3K14 0.038 0.06 -10000 0 -0.27 12 12
PDPK1 0.039 0.088 -10000 0 -0.41 13 13
TCR/CD3/MHC I/CD8/Fyn 0.022 0.13 -10000 0 -0.7 12 12
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.008 0.041 -9999 0 -0.31 5 5
NFATC2 -0.003 0.072 -9999 0 -0.31 23 23
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.03 0.22 -9999 0 -0.71 24 24
PTGS2 -0.044 0.24 -9999 0 -0.66 34 34
JUNB 0.007 0.039 -9999 0 -0.5 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.009 -9999 0 -10000 0 0
CALM1 0.009 0.007 -9999 0 -10000 0 0
JUN 0.006 0.04 -9999 0 -0.5 3 3
mol:Ca2+ -0.005 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.011 0.1 -9999 0 -0.51 21 21
CREM 0.009 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.049 0.096 -9999 0 -0.47 13 13
FOS -0.018 0.12 -9999 0 -0.51 27 27
IFNG -0.037 0.23 -9999 0 -0.63 38 38
AP-1/NFAT1-c-4 -0.1 0.18 -9999 0 -0.64 31 31
FASLG -0.022 0.2 -9999 0 -0.64 21 21
NFAT1-c-4/ICER1 -0.032 0.072 -9999 0 -0.39 12 12
IL2RA -0.034 0.22 -9999 0 -0.62 32 32
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.041 0.23 -9999 0 -0.69 31 31
JunB/Fra1/NFAT1-c-4 -0.04 0.086 -9999 0 -0.4 13 13
IL4 -0.024 0.19 -9999 0 -0.61 20 20
IL2 -0.001 0.01 -9999 0 -10000 0 0
IL3 -0.01 0.016 -9999 0 -10000 0 0
FKBP1A 0.01 0 -9999 0 -10000 0 0
BATF3 0.01 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.01 0.001 -9999 0 -10000 0 0
BCR signaling pathway

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
JUN -0.019 0.085 -10000 0 -0.41 5 5
IKBKB -0.004 0.047 -10000 0 -0.25 3 3
AKT1 -0.033 0.08 -10000 0 -0.26 4 4
IKBKG -0.002 0.049 -10000 0 -0.26 4 4
CALM1 -0.015 0.078 0.23 1 -0.59 5 6
PIK3CA 0.01 0 -10000 0 -10000 0 0
MAP3K1 -0.039 0.11 -10000 0 -0.56 4 4
MAP3K7 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.083 0.23 1 -0.63 5 6
DOK1 0.01 0 -10000 0 -10000 0 0
AP-1 -0.005 0.056 0.15 3 -0.25 6 9
LYN 0.01 0 -10000 0 -10000 0 0
BLNK 0.008 0.032 -10000 0 -0.5 2 2
SHC1 0.008 0.032 -10000 0 -0.51 2 2
BCR complex -0.082 0.16 -10000 0 -0.38 110 110
CD22 -0.052 0.11 -10000 0 -0.55 11 11
CAMK2G -0.009 0.073 0.22 1 -0.54 5 6
CSNK2A1 0.01 0 -10000 0 -10000 0 0
INPP5D 0.007 0.039 -10000 0 -0.5 3 3
SHC/GRB2/SOS1 -0.05 0.099 -10000 0 -0.43 12 12
GO:0007205 -0.023 0.084 0.23 1 -0.65 5 6
SYK 0.007 0.039 -10000 0 -0.5 3 3
ELK1 -0.016 0.08 0.23 1 -0.6 5 6
NFATC1 -0.06 0.12 -10000 0 -0.39 16 16
B-cell antigen/BCR complex -0.082 0.16 -10000 0 -0.38 110 110
PAG1/CSK -0.001 0.016 -10000 0 -0.35 1 1
NFKBIB 0.006 0.019 -10000 0 -10000 0 0
HRAS -0.015 0.078 0.21 1 -0.54 5 6
NFKBIA 0.006 0.018 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.01 0.015 -10000 0 -10000 0 0
RasGAP/Csk -0.056 0.11 -10000 0 -0.5 10 10
mol:GDP -0.023 0.082 0.24 1 -0.63 5 6
PTEN 0.01 0 -10000 0 -10000 0 0
CD79B 0 0.071 -10000 0 -0.51 10 10
NF-kappa-B/RelA/I kappa B alpha 0.01 0.015 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.07 0.13 -10000 0 -0.61 5 5
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
mol:IP3 -0.028 0.084 0.23 1 -0.66 5 6
CSK 0.01 0 -10000 0 -10000 0 0
FOS -0.021 0.092 0.22 1 -0.46 10 11
CHUK -0.002 0.049 -10000 0 -0.26 4 4
IBTK 0.01 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.033 0.075 -10000 0 -0.5 6 6
PTPN6 -0.048 0.099 -10000 0 -0.51 11 11
RELA 0.01 0 -10000 0 -10000 0 0
BCL2A1 0.009 0.021 -10000 0 -0.095 8 8
VAV2 -0.12 0.15 -10000 0 -0.36 107 107
ubiquitin-dependent protein catabolic process 0.009 0.018 -10000 0 -10000 0 0
BTK -0.072 0.26 0.32 1 -1 35 36
CD19 -0.14 0.17 -10000 0 -0.41 107 107
MAP4K1 0.005 0.05 -10000 0 -0.5 5 5
CD72 0.009 0.022 -10000 0 -0.5 1 1
PAG1 0.009 0.022 -10000 0 -0.5 1 1
MAPK14 -0.029 0.1 -10000 0 -0.47 4 4
SH3BP5 0.004 0.055 -10000 0 -0.5 6 6
PIK3AP1 -0.017 0.1 0.21 4 -0.52 13 17
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.013 0.11 -10000 0 -0.79 6 6
RAF1 -0.008 0.074 0.21 1 -0.5 5 6
RasGAP/p62DOK/SHIP -0.054 0.11 -10000 0 -0.47 11 11
CD79A -0.1 0.21 -10000 0 -0.51 109 109
re-entry into mitotic cell cycle -0.005 0.055 0.15 3 -0.25 6 9
RASA1 0.01 0 -10000 0 -10000 0 0
MAPK3 0.005 0.064 -10000 0 -0.41 5 5
MAPK1 0.005 0.064 -10000 0 -0.41 5 5
CD72/SHP1 -0.018 0.1 -10000 0 -0.47 11 11
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.029 0.1 -10000 0 -0.47 4 4
actin cytoskeleton organization -0.079 0.15 -10000 0 -0.45 12 12
NF-kappa-B/RelA 0.025 0.028 -10000 0 -10000 0 0
Calcineurin -0.021 0.057 -10000 0 -0.48 5 5
PI3K -0.1 0.12 -10000 0 -0.42 13 13
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.028 0.082 0.22 4 -0.68 5 9
SOS1 0.01 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.011 0.098 -10000 0 -0.69 6 6
DAPP1 -0.03 0.093 -10000 0 -0.85 4 4
cytokine secretion -0.056 0.12 -10000 0 -0.37 16 16
mol:DAG -0.028 0.084 0.23 1 -0.66 5 6
PLCG2 0.007 0.039 -10000 0 -0.5 3 3
MAP2K1 -0.002 0.069 -10000 0 -0.46 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.069 0.14 -10000 0 -0.32 110 110
mol:PI-3-4-5-P3 -0.077 0.092 -10000 0 -0.3 13 13
ETS1 -0.003 0.069 0.22 1 -0.46 6 7
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.058 0.12 -10000 0 -0.5 12 12
B-cell antigen/BCR complex/LYN -0.042 0.091 -10000 0 -0.75 3 3
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 -0.084 0.15 -10000 0 -0.48 12 12
B-cell antigen/BCR complex/LYN/SYK -0.058 0.11 -10000 0 -0.48 12 12
CARD11 -0.03 0.099 0.23 1 -0.49 10 11
FCGR2B 0.009 0.022 -10000 0 -0.5 1 1
PPP3CA 0.01 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
IKK complex 0.003 0.024 -10000 0 -10000 0 0
PTPRC -0.007 0.091 -10000 0 -0.5 17 17
PDPK1 -0.035 0.079 -10000 0 -0.25 4 4
PPP3CB 0.01 0 -10000 0 -10000 0 0
PPP3CC 0.01 0 -10000 0 -10000 0 0
POU2F2 0.011 0.012 -10000 0 -0.1 1 1
ErbB2/ErbB3 signaling events

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
USP8 0.014 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.042 0.079 -9999 0 -0.33 2 2
NFATC4 -0.009 0.089 -9999 0 -0.35 2 2
ERBB2IP 0.01 0.002 -9999 0 -10000 0 0
HSP90 (dimer) 0.01 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.049 0.093 -9999 0 -0.42 1 1
JUN 0.02 0.062 -9999 0 -0.17 3 3
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 -0.019 0.1 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.057 0.11 -9999 0 -0.5 2 2
AKT1 0.008 0.003 -9999 0 -10000 0 0
BAD 0.015 0.002 -9999 0 -10000 0 0
MAPK10 -0.041 0.071 -9999 0 -0.27 24 24
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.028 0.11 -9999 0 -0.45 1 1
RAF1 0 0.098 -9999 0 -0.3 2 2
ErbB2/ErbB3/neuregulin 2 -0.034 0.089 -9999 0 -0.27 64 64
STAT3 0.001 0.002 -9999 0 -10000 0 0
cell migration -0.004 0.079 -9999 0 -0.22 23 23
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.004 0.16 -9999 0 -0.59 17 17
FOS -0.001 0.15 -9999 0 -0.44 40 40
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.049 0.093 -9999 0 -0.42 1 1
MAPK3 0 0.14 -9999 0 -0.51 13 13
MAPK1 0 0.14 -9999 0 -0.51 13 13
JAK2 -0.02 0.1 -9999 0 -0.4 2 2
NF2 -0.002 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.035 0.11 -9999 0 -0.24 112 112
NRG1 -0.1 0.21 -9999 0 -0.5 111 111
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.021 0.11 -9999 0 -0.34 1 1
MAPK9 -0.024 0.046 -9999 0 -0.2 1 1
ERBB2 -0.002 0.028 -9999 0 -0.37 3 3
ERBB3 0.006 0.032 -9999 0 -0.5 2 2
SHC1 0.008 0.032 -9999 0 -0.51 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
apoptosis 0.001 0.007 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.017 0.009 -9999 0 -10000 0 0
FRAP1 0.007 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.034 0.063 -9999 0 -0.28 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.023 -9999 0 -0.31 3 3
CHRNA1 0 0.14 -9999 0 -0.56 15 15
myelination -0.007 0.088 -9999 0 -0.32 2 2
PPP3CB -0.018 0.097 -9999 0 -0.37 1 1
KRAS 0.008 0.032 -9999 0 -0.51 2 2
RAC1-CDC42/GDP -0.042 0.085 -9999 0 -0.32 2 2
NRG2 -0.049 0.16 -9999 0 -0.5 59 59
mol:GDP -0.035 0.11 -9999 0 -0.24 112 112
SOS1 0.01 0.001 -9999 0 -10000 0 0
MAP2K2 0.007 0.097 -9999 0 -0.31 7 7
SRC 0.01 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.001 -9999 0 -10000 0 0
PTPN11 -0.02 0.1 -9999 0 -0.4 1 1
MAP2K1 -0.014 0.14 -9999 0 -0.5 13 13
heart morphogenesis -0.049 0.093 -9999 0 -0.42 1 1
RAS family/GDP -0.042 0.081 -9999 0 -0.34 2 2
GRB2 0.01 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.007 -9999 0 -10000 0 0
CHRNE 0.012 0.02 -9999 0 -0.16 3 3
HSP90AA1 0.01 0 -9999 0 -10000 0 0
activation of caspase activity -0.008 0.003 -9999 0 -10000 0 0
nervous system development -0.049 0.093 -9999 0 -0.42 1 1
CDC42 0.01 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 -0.001 0.013 -9999 0 -0.3 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.007 0.092 -9999 0 -0.51 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.005 0.043 -9999 0 -0.2 5 5
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.01 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 0.009 0.022 -9999 0 -0.5 1 1
FYN 0.009 0.022 -9999 0 -0.5 1 1
MAP3K12 0.01 0 -9999 0 -10000 0 0
FGR -0.029 0.14 -9999 0 -0.5 39 39
p38 alpha/TAB1 -0.016 0.051 -9999 0 -0.34 6 6
PRKG1 -0.056 0.17 -9999 0 -0.5 66 66
DUSP8 0 0.07 -9999 0 -0.5 10 10
PGK/cGMP/p38 alpha -0.039 0.098 -9999 0 -0.37 28 28
apoptosis -0.015 0.049 -9999 0 -0.35 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.01 0 -9999 0 -10000 0 0
DUSP1 -0.038 0.15 -9999 0 -0.5 48 48
PAK1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.011 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 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 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.008 0.093 -9999 0 -0.36 20 20
BLK -0.08 0.2 -9999 0 -0.51 89 89
HCK -0.014 0.11 -9999 0 -0.5 24 24
MAP2K3 0.01 0 -9999 0 -10000 0 0
DUSP16 0.01 0 -9999 0 -10000 0 0
DUSP10 0.008 0.032 -9999 0 -0.5 2 2
TRAF6/MEKK3 -0.001 0.012 -9999 0 -0.27 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0.067 -9999 0 -0.4 5 5
positive regulation of innate immune response 0.013 0.098 -9999 0 -0.38 19 19
LCK 0.007 0.039 -9999 0 -0.5 3 3
p38alpha-beta/MKP7 0.017 0.094 -9999 0 -0.41 12 12
p38alpha-beta/MKP5 0.017 0.098 -9999 0 -0.42 13 13
PGK/cGMP -0.046 0.12 -9999 0 -0.36 66 66
PAK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.003 0.12 -9999 0 -0.44 17 17
CDC42 0.01 0 -9999 0 -10000 0 0
RALB 0.01 0 -9999 0 -10000 0 0
RALA 0.01 0 -9999 0 -10000 0 0
PAK3 -0.058 0.17 -9999 0 -0.51 67 67
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.003 0.06 -9999 0 -0.51 7 7
CDC42/GTP -0.026 0.068 -9999 0 -0.4 4 4
PLCG1 0 0.082 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.026 0.067 -9999 0 -0.39 4 4
S1PR5 -0.024 0.13 -9999 0 -0.5 34 34
S1PR4 -0.017 0.11 -9999 0 -0.5 27 27
MAPK3 0 0.082 -9999 0 -0.41 4 4
MAPK1 0 0.082 -9999 0 -0.41 4 4
S1P/S1P5/Gi -0.01 0.092 -9999 0 -0.26 36 36
GNAI1 0.008 0.032 -9999 0 -0.5 2 2
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.02 0.074 -9999 0 -0.3 34 34
RHOA 0.011 0.059 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.007 0.087 -9999 0 -0.25 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.031 0.14 -9999 0 -0.5 41 41
S1P/S1P4/G12/G13 -0.014 0.059 -9999 0 -0.26 27 27
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.005 0.05 -9999 0 -0.5 5 5
ELF1 0.001 0.057 -9999 0 -0.33 1 1
CCNA2 -0.11 0.22 -9999 0 -0.51 119 119
PIK3CA 0.01 0 -9999 0 -10000 0 0
JAK3 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
JAK1 0.01 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.051 0.047 -9999 0 -0.51 1 1
SHC1 0.008 0.032 -9999 0 -0.51 2 2
SP1 0.01 0.045 -9999 0 -0.33 9 9
IL2RA -0.004 0.11 -9999 0 -0.39 36 36
IL2RB 0.008 0.032 -9999 0 -0.5 2 2
SOS1 0.01 0 -9999 0 -10000 0 0
IL2RG 0.005 0.05 -9999 0 -0.5 5 5
G1/S transition of mitotic cell cycle -0.012 0.12 -9999 0 -0.68 10 10
PTPN11 0.01 0 -9999 0 -10000 0 0
CCND2 0.011 0.098 -9999 0 -0.73 9 9
LCK 0.007 0.039 -9999 0 -0.5 3 3
GRB2 0.01 0 -9999 0 -10000 0 0
IL2 0.006 0.005 -9999 0 -10000 0 0
CDK6 0.008 0.032 -9999 0 -0.5 2 2
CCND3 0.054 0.043 -9999 0 -0.43 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.007 -10000 0 -10000 0 0
HSPA8 0.008 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.012 0.075 0.19 1 -0.32 24 25
AKT1 0.007 0.02 -10000 0 -10000 0 0
GSC -0.023 0.098 -10000 0 -0.38 5 5
NKX2-5 -0.029 0.13 -10000 0 -0.5 34 34
muscle cell differentiation 0.021 0.053 0.34 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.044 0.056 -10000 0 -10000 0 0
SMAD4 0.018 0.024 -10000 0 -10000 0 0
CBFB 0.01 0 -10000 0 -10000 0 0
SAP18 0.009 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.011 0.075 -10000 0 -0.29 32 32
SMAD3/SMAD4/VDR 0.009 0.031 -10000 0 -0.32 1 1
MYC 0.011 0.038 -10000 0 -0.5 2 2
CDKN2B -0.065 0.34 -10000 0 -1.3 38 38
AP1 0.03 0.076 -10000 0 -0.51 3 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.044 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.095 -10000 0 -0.3 38 38
SP3 0.012 0 -10000 0 -10000 0 0
CREB1 0.01 0 -10000 0 -10000 0 0
FOXH1 -0.06 0.18 -10000 0 -0.51 69 69
SMAD3/SMAD4/GR 0.002 0.023 -10000 0 -10000 0 0
GATA3 0.008 0.043 -10000 0 -0.5 3 3
SKI/SIN3/HDAC complex/NCoR1 0.031 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.045 0.1 -10000 0 -0.47 8 8
endothelial cell migration -0.005 0.067 1.3 1 -10000 0 1
MAX 0.008 0.003 -10000 0 -10000 0 0
RBBP7 0.009 0.001 -10000 0 -10000 0 0
RBBP4 0.009 0.001 -10000 0 -10000 0 0
RUNX2 0.003 0.06 -10000 0 -0.51 7 7
RUNX3 0.007 0.039 -10000 0 -0.5 3 3
RUNX1 0.01 0 -10000 0 -10000 0 0
CTBP1 0.01 0 -10000 0 -10000 0 0
NR3C1 0.008 0.003 -10000 0 -10000 0 0
VDR 0.008 0.032 -10000 0 -0.5 2 2
CDKN1A 0.05 0.067 -10000 0 -1.2 1 1
KAT2B 0.011 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.044 0.1 -10000 0 -0.3 69 69
DCP1A 0.01 0 -10000 0 -10000 0 0
SKI 0.009 0.001 -10000 0 -10000 0 0
SERPINE1 0.005 0.067 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.002 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.011 0.066 -10000 0 -0.31 20 20
SAP30 0.009 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.011 0.026 -10000 0 -10000 0 0
JUN 0.031 0.075 -10000 0 -0.51 3 3
SMAD3/SMAD4/IRF7 -0.001 0.04 -10000 0 -0.39 3 3
TFE3 0.015 0.003 -10000 0 -10000 0 0
COL1A2 -0.009 0.088 -10000 0 -0.87 2 2
mesenchymal cell differentiation 0.003 0.042 0.31 7 -10000 0 7
DLX1 -0.024 0.12 -10000 0 -0.51 31 31
TCF3 0.01 0 -10000 0 -10000 0 0
FOS -0.012 0.11 -10000 0 -0.5 27 27
SMAD3/SMAD4/Max 0.002 0.023 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.005 0.013 -10000 0 -10000 0 0
ZBTB17 0.012 0.015 -10000 0 -10000 0 0
LAMC1 0.044 0.027 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.002 0.022 -10000 0 -10000 0 0
IRF7 0.007 0.043 -10000 0 -0.55 3 3
ESR1 -0.016 0.11 -10000 0 -0.5 25 25
HNF4A -0.1 0.21 -10000 0 -0.51 112 112
MEF2C -0.018 0.12 -10000 0 -0.45 7 7
SMAD2-3/SMAD4 -0.006 0.028 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.008 0.018 -10000 0 -10000 0 0
IGHV3OR16-13 -0.001 0.006 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0 -10000 0 -10000 0 0
CREBBP 0.012 0.005 -10000 0 -10000 0 0
SKIL 0.01 0 -10000 0 -10000 0 0
HDAC1 0.009 0.001 -10000 0 -10000 0 0
HDAC2 0.009 0.001 -10000 0 -10000 0 0
SNIP1 0.008 0.003 -10000 0 -10000 0 0
GCN5L2 0.002 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.004 0.024 -10000 0 -10000 0 0
MSG1/HSC70 -0.023 0.087 -10000 0 -0.36 33 33
SMAD2 0.007 0.022 -10000 0 -10000 0 0
SMAD3 0.019 0.023 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.036 0.025 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.016 0.012 -10000 0 -10000 0 0
NCOR1 0.009 0.001 -10000 0 -10000 0 0
NCOA2 0.005 0.05 -10000 0 -0.5 5 5
NCOA1 0.01 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.027 -10000 0 -0.36 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.05 0.054 -10000 0 -10000 0 0
IFNB1 0.031 0.054 -10000 0 -0.52 3 3
SMAD3/SMAD4/MEF2C -0.005 0.12 -10000 0 -0.48 5 5
CITED1 -0.024 0.12 -10000 0 -0.5 33 33
SMAD2-3/SMAD4/ARC105 -0.004 0.023 -10000 0 -10000 0 0
RBL1 0.01 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.015 0.14 -10000 0 -0.46 38 38
RUNX1-3/PEBPB2 -0.002 0.022 -10000 0 -0.29 3 3
SMAD7 0.054 0.086 -10000 0 -0.58 3 3
MYC/MIZ-1 0.01 0.045 -10000 0 -0.36 2 2
SMAD3/SMAD4 0.024 0.063 0.28 2 -0.38 1 3
IL10 0.033 0.08 -10000 0 -0.49 10 10
PIASy/HDAC complex 0.008 0.004 -10000 0 -10000 0 0
PIAS3 0.011 0.003 -10000 0 -10000 0 0
CDK2 0.012 0.005 -10000 0 -10000 0 0
IL5 0.033 0.046 -10000 0 -10000 0 0
CDK4 0.007 0.051 -10000 0 -0.51 5 5
PIAS4 0.008 0.004 -10000 0 -10000 0 0
ATF3 -0.012 0.1 -10000 0 -0.5 22 22
SMAD3/SMAD4/SP1 -0.001 0.034 -10000 0 -10000 0 0
FOXG1 -0.055 0.16 -10000 0 -0.51 58 58
FOXO3 0.014 0.026 -10000 0 -10000 0 0
FOXO1 0.014 0.03 -10000 0 -0.35 1 1
FOXO4 0.014 0.026 -10000 0 -10000 0 0
heart looping -0.018 0.12 -10000 0 -0.45 7 7
CEBPB 0.008 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.018 0.08 -10000 0 -0.32 31 31
MYOD1 -0.002 0.039 -10000 0 -0.51 3 3
SMAD3/SMAD4/HNF4 -0.066 0.13 -10000 0 -0.31 112 112
SMAD3/SMAD4/GATA3 -0.002 0.045 -10000 0 -0.34 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.003 0.03 -10000 0 -0.32 2 2
SMAD3/SMAD4/SP1-3 0.021 0.041 -10000 0 -10000 0 0
MED15 0.01 0 -10000 0 -10000 0 0
SP1 0.013 0.02 -10000 0 -10000 0 0
SIN3B 0.009 0.001 -10000 0 -10000 0 0
SIN3A 0.009 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.04 0.12 -10000 0 -0.36 28 28
ITGB5 0.05 0.035 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.035 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.041 0.11 -10000 0 -0.31 71 71
AR -0.062 0.18 -10000 0 -0.5 72 72
negative regulation of cell growth 0.036 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.002 0.033 -10000 0 -0.32 3 3
E2F5 0.006 0.045 -10000 0 -0.51 4 4
E2F4 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.032 0.082 -10000 0 -0.32 6 6
SMAD2-3/SMAD4/FOXO1-3a-4 0.022 0.097 -10000 0 -0.31 38 38
TFDP1 0.009 0.023 -10000 0 -0.51 1 1
SMAD3/SMAD4/AP1 0.034 0.077 -10000 0 -0.51 3 3
SMAD3/SMAD4/RUNX2 -0.003 0.043 -10000 0 -0.31 7 7
TGIF2 0.01 0 -10000 0 -10000 0 0
TGIF1 0.01 0 -10000 0 -10000 0 0
ATF2 0.01 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.014 0.059 -10000 0 -0.26 15 15
ER alpha/Gai/GDP/Gbeta gamma 0.006 0.088 -10000 0 -0.37 14 14
AKT1 0.009 0.11 -10000 0 -0.72 12 12
PIK3CA 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.006 0.12 -10000 0 -0.73 12 12
mol:Ca2+ 0.014 0.087 -10000 0 -0.41 15 15
IGF1R 0.009 0.022 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/Striatin -0.015 0.066 -10000 0 -0.3 26 26
SHC1 0.008 0.032 -10000 0 -0.51 2 2
apoptosis -0.009 0.11 0.69 12 -10000 0 12
RhoA/GTP -0.011 0.047 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.024 0.073 -10000 0 -0.38 14 14
regulation of stress fiber formation -0.03 0.049 0.36 1 -10000 0 1
E2/ERA-ERB (dimer) -0.016 0.067 -10000 0 -0.3 27 27
KRAS 0.008 0.032 -10000 0 -0.51 2 2
G13/GTP -0.013 0.059 -10000 0 -0.27 25 25
pseudopodium formation 0.03 0.049 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1 -0.015 0.065 -10000 0 -0.3 25 25
GRB2 0.01 0 -10000 0 -10000 0 0
GNG2 0.008 0.032 -10000 0 -0.5 2 2
GNAO1 0.003 0.06 -10000 0 -0.51 7 7
HRAS 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.088 -10000 0 -0.43 14 14
E2/ER beta (dimer) -0.001 0.023 -10000 0 -0.36 2 2
mol:GDP -0.013 0.059 -10000 0 -0.34 13 13
mol:NADP 0.014 0.088 -10000 0 -0.43 14 14
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
mol:IP3 0.014 0.091 -10000 0 -0.43 15 15
IGF-1R heterotetramer 0.009 0.022 -10000 0 -0.5 1 1
PLCB1 0.013 0.081 -10000 0 -0.42 14 14
PLCB2 0.009 0.092 -10000 0 -0.45 15 15
IGF1 -0.002 0.077 -10000 0 -0.5 12 12
mol:L-citrulline 0.014 0.088 -10000 0 -0.43 14 14
RHOA 0.01 0 -10000 0 -10000 0 0
Gai/GDP -0.02 0.072 -10000 0 -0.66 3 3
JNK cascade -0.001 0.023 -10000 0 -0.36 2 2
BCAR1 0.009 0.022 -10000 0 -0.5 1 1
ESR2 0.008 0.032 -10000 0 -0.5 2 2
GNAQ 0.009 0.022 -10000 0 -0.5 1 1
ESR1 -0.015 0.11 -10000 0 -0.5 25 25
Gq family/GDP/Gbeta gamma 0.023 0.054 -10000 0 -0.43 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.046 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.024 0.072 -10000 0 -0.39 13 13
GNAZ -0.031 0.14 -10000 0 -0.5 41 41
E2/ER alpha (dimer) -0.018 0.078 -10000 0 -0.36 25 25
STRN 0.009 0.022 -10000 0 -0.5 1 1
GNAL -0.002 0.077 -10000 0 -0.5 12 12
PELP1 0.01 0 -10000 0 -10000 0 0
MAPK11 0.012 0.031 -10000 0 -0.3 5 5
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
HBEGF -0.032 0.11 -10000 0 -0.37 23 23
cAMP biosynthetic process -0.018 0.066 -10000 0 -0.25 37 37
SRC 0.012 0.084 -10000 0 -0.36 13 13
PI3K -0.001 0.016 -10000 0 -0.35 1 1
GNB1 0.01 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.012 0.055 -10000 0 -0.32 12 12
SOS1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.069 -10000 0 -0.4 8 8
Gs family/GTP -0.018 0.067 -10000 0 -0.25 37 37
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.017 -10000 0 -0.27 2 2
vasodilation 0.014 0.085 -10000 0 -0.41 14 14
mol:DAG 0.014 0.091 -10000 0 -0.43 15 15
Gs family/GDP/Gbeta gamma -0.016 0.061 -10000 0 -0.34 12 12
MSN 0.03 0.052 -10000 0 -0.39 1 1
Gq family/GTP -0.017 0.078 -10000 0 -0.45 14 14
mol:PI-3-4-5-P3 0.006 0.11 -10000 0 -0.7 12 12
NRAS 0.01 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.014 0.085 0.41 14 -10000 0 14
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.012 0.055 -10000 0 -0.33 12 12
NOS3 0.013 0.092 -10000 0 -0.45 14 14
GNA11 0.008 0.032 -10000 0 -0.5 2 2
MAPKKK cascade 0.021 0.094 -10000 0 -0.53 12 12
E2/ER alpha (dimer)/PELP1/Src -0.025 0.076 -10000 0 -0.41 13 13
ruffle organization 0.03 0.049 -10000 0 -0.36 1 1
ROCK2 0.026 0.051 -10000 0 -10000 0 0
GNA14 -0.004 0.083 -10000 0 -0.5 14 14
GNA15 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
MMP9 -0.036 0.13 -10000 0 -0.44 14 14
MMP2 0.017 0.081 -10000 0 -0.51 3 3
IL27-mediated signaling events

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.022 -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 -0.001 0.08 0.52 2 -10000 0 2
IL27/IL27R/JAK1 -0.028 0.085 -10000 0 -1.1 1 1
TBX21 0 0.14 -10000 0 -0.58 12 12
IL12B 0.003 0.056 -10000 0 -0.51 6 6
IL12A 0.004 0.04 -10000 0 -0.36 6 6
IL6ST -0.011 0.1 -10000 0 -0.5 21 21
IL27RA/JAK1 0.011 0.055 -10000 0 -1.2 1 1
IL27 -0.006 0.084 -10000 0 -0.51 14 14
TYK2 0.01 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.065 0.12 -10000 0 -0.57 1 1
T-helper 2 cell differentiation -0.001 0.08 0.52 2 -10000 0 2
T cell proliferation during immune response -0.001 0.08 0.52 2 -10000 0 2
MAPKKK cascade 0.001 0.08 -10000 0 -0.52 2 2
STAT3 0.01 0 -10000 0 -10000 0 0
STAT2 0.01 0 -10000 0 -10000 0 0
STAT1 0.01 0.002 -10000 0 -10000 0 0
IL12RB1 -0.006 0.086 -10000 0 -0.5 15 15
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.008 0.16 -10000 0 -0.52 18 18
IL27/IL27R/JAK2/TYK2 0 0.08 -10000 0 -0.53 2 2
positive regulation of T cell mediated cytotoxicity 0.001 0.08 -10000 0 -0.52 2 2
STAT1 (dimer) -0.047 0.12 0.48 1 -0.79 4 5
JAK2 0.008 0.032 -10000 0 -0.5 2 2
JAK1 0.01 0.002 -10000 0 -10000 0 0
STAT2 (dimer) 0.005 0.076 -10000 0 -0.5 2 2
T cell proliferation -0.053 0.14 -10000 0 -0.45 20 20
IL12/IL12R/TYK2/JAK2 0.009 0.078 -10000 0 -0.6 2 2
IL17A -0.065 0.12 -10000 0 -0.57 1 1
mast cell activation -0.001 0.08 0.52 2 -10000 0 2
IFNG 0 0.027 -10000 0 -0.12 10 10
T cell differentiation -0.003 0.005 -10000 0 -0.02 22 22
STAT3 (dimer) 0.005 0.076 -10000 0 -0.5 2 2
STAT5A (dimer) 0.005 0.08 -10000 0 -0.62 2 2
STAT4 (dimer) 0.005 0.076 -10000 0 -0.5 2 2
STAT4 0.01 0 -10000 0 -10000 0 0
T cell activation -0.006 0.006 0.12 1 -10000 0 1
IL27R/JAK2/TYK2 -0.017 0.073 -10000 0 -1.1 1 1
GATA3 0.004 0.08 -10000 0 -1.2 2 2
IL18 0.002 0.051 -10000 0 -0.36 10 10
positive regulation of mast cell cytokine production 0.005 0.075 -10000 0 -0.49 2 2
IL27/EBI3 -0.005 0.064 -10000 0 -0.36 16 16
IL27RA 0.001 0.056 -10000 0 -1.2 1 1
IL6 -0.11 0.22 -10000 0 -0.5 120 120
STAT5A 0.009 0.022 -10000 0 -0.5 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.003 0.021 0.46 1 -10000 0 1
IL1B -0.013 0.088 -10000 0 -0.36 31 31
EBI3 0.007 0.032 -10000 0 -0.51 2 2
TNF -0.005 0.07 -10000 0 -0.36 19 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.063 0.17 -9999 0 -0.57 16 16
RAD9A 0.01 0 -9999 0 -10000 0 0
AP1 -0.011 0.087 -9999 0 -0.36 30 30
IFNAR2 0.008 0.005 -9999 0 -10000 0 0
AKT1 0.002 0.043 -9999 0 -0.21 12 12
ER alpha/Oestrogen -0.018 0.079 -9999 0 -0.37 25 25
NFX1/SIN3/HDAC complex 0.027 0.018 -9999 0 -10000 0 0
EGF -0.092 0.2 -9999 0 -0.51 99 99
SMG5 0.01 0 -9999 0 -10000 0 0
SMG6 0.01 0 -9999 0 -10000 0 0
SP3/HDAC2 0.012 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.085 0.14 -9999 0 -0.54 15 15
SAP18 0.007 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.037 0.14 -9999 0 -0.51 44 44
WRN 0.01 0 -9999 0 -10000 0 0
SP1 0.009 0.006 -9999 0 -10000 0 0
SP3 0.007 0.005 -9999 0 -10000 0 0
TERF2IP 0.01 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.079 0.12 -9999 0 -0.6 8 8
Mad/Max 0.01 0.008 -9999 0 -10000 0 0
TERT -0.065 0.18 -9999 0 -0.59 16 16
CCND1 -0.059 0.2 -9999 0 -1.1 8 8
MAX 0.007 0.005 -9999 0 -10000 0 0
RBBP7 0.007 0.004 -9999 0 -10000 0 0
RBBP4 0.007 0.004 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.01 0 -9999 0 -10000 0 0
SIN3A 0.007 0.004 -9999 0 -10000 0 0
Telomerase/911 0.021 0.029 -9999 0 -10000 0 0
CDKN1B -0.003 0.084 -9999 0 -10000 0 0
RAD1 0.01 0 -9999 0 -10000 0 0
XRCC5 0.01 0 -9999 0 -10000 0 0
XRCC6 0.01 0 -9999 0 -10000 0 0
SAP30 0.007 0.004 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.007 0.005 -9999 0 -10000 0 0
JUN 0.005 0.039 -9999 0 -0.5 3 3
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.005 -9999 0 -10000 0 0
FOS -0.019 0.11 -9999 0 -0.5 27 27
IFN-gamma/IRF1 -0.028 0.095 -9999 0 -0.35 41 41
PARP2 0.01 0 -9999 0 -10000 0 0
BLM -0.041 0.15 -9999 0 -0.51 50 50
Telomerase -0.022 0.057 -9999 0 -10000 0 0
IRF1 0.01 0.007 -9999 0 -10000 0 0
ESR1 -0.017 0.11 -9999 0 -0.5 25 25
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.02 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.03 0.02 -9999 0 -10000 0 0
HDAC1 0.007 0.004 -9999 0 -10000 0 0
HDAC2 0.008 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.02 0.004 -9999 0 -10000 0 0
ABL1 0.01 0 -9999 0 -10000 0 0
MXD1 0.007 0.005 -9999 0 -10000 0 0
MRE11A 0.01 0 -9999 0 -10000 0 0
HUS1 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.01 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.081 0.13 -9999 0 -0.63 8 8
NR2F2 0.013 0.007 -9999 0 -10000 0 0
MAPK3 0.011 0.008 -9999 0 -10000 0 0
MAPK1 0.011 0.008 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.01 0.002 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
HNRNPC 0.01 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 0.01 0 -9999 0 -10000 0 0
EGFR -0.009 0.089 -9999 0 -0.51 16 16
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.081 0.16 -9999 0 -0.37 111 111
MYC 0.006 0.032 -9999 0 -0.5 2 2
IL2 0.003 0.01 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
TGFB1 0.01 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.032 0.098 -9999 0 -0.33 50 50
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.082 0.14 -9999 0 -0.63 9 9
SP1/HDAC2 0.013 0.011 -9999 0 -10000 0 0
PINX1 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.079 0.12 -9999 0 -0.6 8 8
Smad3/Myc 0.021 0.02 -9999 0 -0.29 2 2
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.031 0.14 -9999 0 -0.5 41 41
Telomerase/PinX1 -0.079 0.12 -9999 0 -0.6 8 8
Telomerase/AKT1/mTOR/p70S6K 0.006 0.053 -9999 0 -10000 0 0
SIN3B 0.007 0.004 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.079 0.12 -9999 0 -0.6 8 8
response to DNA damage stimulus 0.003 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 -0.079 0.12 -9999 0 -0.6 8 8
E2F1 0 0.065 -9999 0 -0.52 8 8
ZNFX1 0.007 0.004 -9999 0 -10000 0 0
PIF1 -0.068 0.18 -9999 0 -0.51 77 77
NCL 0.01 0 -9999 0 -10000 0 0
DKC1 0.01 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.023 0.094 -9999 0 -0.34 27 27
MAP3K8 0.008 0.032 -9999 0 -0.5 2 2
FOS 0.023 0.067 -9999 0 -0.37 5 5
PRKCA 0.008 0.032 -9999 0 -0.5 2 2
PTPN7 0.011 0.003 -9999 0 -10000 0 0
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.004 0.083 -9999 0 -0.5 14 14
NRAS 0.01 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.017 -9999 0 -0.28 2 2
MAPK3 0.02 0.039 -9999 0 -10000 0 0
MAP2K1 0.018 0.081 -9999 0 -0.41 16 16
ELK1 0.009 0.005 -9999 0 -10000 0 0
BRAF -0.014 0.069 -9999 0 -0.39 16 16
mol:GTP 0 0.001 -9999 0 -0.005 27 27
MAPK1 0.02 0.039 -9999 0 -10000 0 0
RAF1 -0.014 0.069 -9999 0 -0.39 16 16
KRAS 0.008 0.032 -9999 0 -0.51 2 2
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.009 0.022 -9999 0 -0.5 1 1
SPHK1 0.005 0.051 -9999 0 -0.51 5 5
GNAI2 0.01 0 -9999 0 -10000 0 0
mol:S1P 0.016 0.02 -9999 0 -0.27 1 1
GNAO1 0.003 0.06 -9999 0 -0.51 7 7
mol:Sphinganine-1-P 0.013 0.04 -9999 0 -0.36 6 6
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.023 -9999 0 -0.51 1 1
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.015 -9999 0 -0.23 1 1
S1PR5 -0.024 0.13 -9999 0 -0.5 34 34
S1PR4 -0.017 0.11 -9999 0 -0.5 27 27
GNAI1 0.008 0.032 -9999 0 -0.5 2 2
S1P/S1P5/G12 -0.018 0.064 -9999 0 -0.25 34 34
S1P/S1P3/Gq 0.021 0.055 -9999 0 -0.49 2 2
S1P/S1P4/Gi -0.001 0.088 -9999 0 -0.42 5 5
GNAQ 0.009 0.022 -9999 0 -0.5 1 1
GNAZ -0.031 0.14 -9999 0 -0.5 41 41
GNA14 -0.004 0.083 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.008 0.032 -9999 0 -0.5 2 2
ABCC1 0.01 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.009 0.022 -10000 0 -0.5 1 1
ANTXR2 0.009 0.022 -10000 0 -0.5 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.004 -10000 0 -0.066 2 2
monocyte activation -0.004 0.09 -10000 0 -0.44 19 19
MAP2K2 0 0.002 -10000 0 -10000 0 0
MAP2K1 0 0.003 -10000 0 -10000 0 0
MAP2K7 0 0.003 -10000 0 -10000 0 0
MAP2K6 -0.009 0.047 -10000 0 -0.26 17 17
CYAA 0.011 0.016 -10000 0 -0.25 2 2
MAP2K4 0 0.003 -10000 0 -10000 0 0
IL1B -0.003 0.066 -10000 0 -0.26 32 32
Channel -0.001 0.017 -10000 0 -0.27 2 2
NLRP1 -0.001 0.016 -10000 0 -0.26 2 2
CALM1 0.01 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.004 0.066 2 -10000 0 2
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
PGR -0.046 0.099 -10000 0 -0.26 91 91
PA/Cellular Receptors -0.001 0.019 -10000 0 -0.3 2 2
apoptosis 0 0.004 -10000 0 -0.066 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.011 0.017 -10000 0 -0.26 2 2
macrophage activation 0.015 0.004 -10000 0 -10000 0 0
TNF -0.009 0.096 -10000 0 -0.5 19 19
VCAM1 -0.004 0.09 -10000 0 -0.44 19 19
platelet activation 0 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.013 -10000 0 -10000 0 0
IL18 0.007 0.046 -10000 0 -0.31 10 10
negative regulation of macrophage activation 0 0.004 -10000 0 -0.066 2 2
LEF 0 0.004 -10000 0 -0.066 2 2
CASP1 -0.002 0.017 -10000 0 -0.23 2 2
mol:cAMP 0 0.005 -10000 0 -10000 0 0
necrosis 0 0.004 -10000 0 -0.066 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.001 0.016 -10000 0 -0.25 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.01 0.001 -9999 0 -10000 0 0
HDAC2 0.01 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.003 0.032 -9999 0 -0.3 6 6
forebrain development -0.018 0.15 -9999 0 -0.52 23 23
GNAO1 0.002 0.06 -9999 0 -0.5 7 7
SMO/beta Arrestin2 0.012 0.034 -9999 0 -0.36 4 4
SMO 0.005 0.046 -9999 0 -0.51 4 4
ARRB2 0.009 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.034 0.036 -9999 0 -10000 0 0
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
GSK3B 0.01 0 -9999 0 -10000 0 0
GNAI2 0.009 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0.006 0.013 -9999 0 -10000 0 0
GNAI1 0.007 0.032 -9999 0 -0.5 2 2
XPO1 0.01 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.048 0.11 -9999 0 -0.54 14 14
SAP30 0.01 0.001 -9999 0 -10000 0 0
mol:GDP 0.005 0.046 -9999 0 -0.51 4 4
MIM/GLI2A 0.002 0.04 -9999 0 -0.53 1 1
IFT88 0.01 0 -9999 0 -10000 0 0
GNAI3 0.009 0.004 -9999 0 -10000 0 0
GLI2 0.035 0.012 -9999 0 -10000 0 0
GLI3 0.03 0.038 -9999 0 -0.24 7 7
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
SAP18 0.01 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.01 0 -9999 0 -10000 0 0
GNG2 0.008 0.032 -9999 0 -0.5 2 2
Gi family/GTP 0.001 0.078 -9999 0 -0.27 21 21
SIN3B 0.01 0.001 -9999 0 -10000 0 0
SIN3A 0.01 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.037 0.033 -9999 0 -10000 0 0
GLI2/Su(fu) 0.04 0.026 -9999 0 -0.27 1 1
FOXA2 -0.18 0.39 -9999 0 -1 87 87
neural tube patterning -0.018 0.15 -9999 0 -0.52 23 23
SPOP 0.01 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.017 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CSNK1G2 0.01 0 -9999 0 -10000 0 0
CSNK1G3 0.01 0 -9999 0 -10000 0 0
MTSS1 0.002 0.04 -9999 0 -0.53 1 1
embryonic limb morphogenesis -0.018 0.15 -9999 0 -0.52 23 23
SUFU 0.019 0.018 -9999 0 -10000 0 0
LGALS3 0.01 0 -9999 0 -10000 0 0
catabolic process 0.053 0.035 -9999 0 -0.3 1 1
GLI3A/CBP 0.004 0.059 -9999 0 -0.33 15 15
KIF3A 0.01 0 -9999 0 -10000 0 0
GLI1 -0.019 0.15 -9999 0 -0.54 23 23
RAB23 0.01 0 -9999 0 -10000 0 0
CSNK1A1 0.01 0 -9999 0 -10000 0 0
IFT172 0.01 0 -9999 0 -10000 0 0
RBBP7 0.01 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.017 -9999 0 -10000 0 0
GNAZ -0.032 0.14 -9999 0 -0.5 41 41
RBBP4 0.01 0.001 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.011 -9999 0 -10000 0 0
STK36 0.01 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.008 0.072 -9999 0 -0.36 4 4
PTCH1 -0.02 0.19 -9999 0 -0.95 14 14
MIM/GLI1 -0.049 0.22 -9999 0 -0.5 91 91
CREBBP 0.004 0.059 -9999 0 -0.33 15 15
Su(fu)/SIN3/HDAC complex 0.04 0.007 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.023 0 -9999 0 -10000 0 0
SNTA1 0.006 0.045 -9999 0 -0.51 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.022 0.024 -9999 0 -0.3 3 3
MAPK12 0.014 0.052 -9999 0 -0.26 18 18
CCND1 0.007 0.056 -9999 0 -0.43 7 7
p38 gamma/SNTA1 0.016 0.054 -9999 0 -10000 0 0
MAP2K3 0.01 0 -9999 0 -10000 0 0
PKN1 0.01 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.014 0.052 -9999 0 -0.26 18 18
MAP2K6 0.008 0.057 -9999 0 -0.29 18 18
MAPT 0.007 0.071 -9999 0 -0.29 25 25
MAPK13 0.018 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.013 0.014 -9999 0 -0.31 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.01 0 -10000 0 -10000 0 0
HDAC3 0.01 0 -10000 0 -10000 0 0
VDR 0.008 0.032 -10000 0 -0.5 2 2
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.031 0.02 -10000 0 -10000 0 0
KAT2B 0.01 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
AKT1 0.015 0.026 0.2 1 -0.23 2 3
RAR alpha/9cRA/Cyclin H -0.007 0.024 -10000 0 -0.26 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.029 0.021 -10000 0 -10000 0 0
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.007 0.03 -10000 0 -10000 0 0
NCOR2 0.01 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.023 -10000 0 -0.36 2 2
RXRs/RARs/NRIP1/9cRA -0.012 0.068 -10000 0 -0.55 2 2
NCOA2 0.005 0.05 -10000 0 -0.5 5 5
NCOA3 0.01 0 -10000 0 -10000 0 0
NCOA1 0.01 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.008 0.032 -10000 0 -0.5 2 2
RARG 0.01 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
MAPK1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.044 0.058 -10000 0 -0.5 3 3
RARA 0.009 0.041 -10000 0 -0.23 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.027 0.03 -10000 0 -0.22 1 1
PRKCA 0.01 0.032 -10000 0 -0.5 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.026 0.076 -10000 0 -0.49 3 3
RXRG -0.17 0.18 -10000 0 -0.33 267 267
RXRA 0.016 0.039 -10000 0 -0.22 2 2
RXRB 0.001 0.063 -10000 0 -0.31 2 2
VDR/Vit D3/DNA -0.001 0.023 -10000 0 -0.36 2 2
RBP1 0.005 0.051 -10000 0 -0.51 5 5
CRBP1/9-cic-RA -0.004 0.036 -10000 0 -0.37 5 5
RARB 0.01 0.032 -10000 0 -0.5 2 2
PRKCG -0.043 0.16 -10000 0 -0.5 53 53
MNAT1 0.01 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.067 -10000 0 -0.59 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.06 -10000 0 -0.45 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.03 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.076 -10000 0 -0.49 3 3
positive regulation of DNA binding -0.007 0.023 -10000 0 -0.24 2 2
NRIP1 -0.024 0.072 -10000 0 -0.54 2 2
RXRs/RARs -0.034 0.078 -10000 0 -0.49 3 3
RXRs/RXRs/DNA/9cRA -0.048 0.06 -10000 0 -0.61 2 2
PRKACA 0.01 0 -10000 0 -10000 0 0
CDK7 0.01 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.016 -10000 0 -10000 0 0
CCNH 0.01 0 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.005 0.05 -10000 0 -0.5 5 5
CLTC 0.011 0.045 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.02 0.003 -10000 0 -10000 0 0
Dynamin 2/GTP -0.025 0.078 -10000 0 -0.27 47 47
EXOC4 0.01 0 -10000 0 -10000 0 0
CD59 0.013 0.03 -10000 0 -10000 0 0
CPE 0.003 0.06 -10000 0 -0.3 19 19
CTNNB1 0.01 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0 0.078 -10000 0 -0.25 47 47
DNM2 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.021 -10000 0 -10000 0 0
TSHR -0.019 0.098 -10000 0 -0.3 54 54
INS 0.007 0.008 -10000 0 -10000 0 0
BIN1 0.01 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.092 -10000 0 -0.3 47 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.077 -10000 0 -0.27 47 47
JUP 0.013 0.03 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.012 -10000 0 -0.26 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.013 0.032 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.008 0.032 -10000 0 -0.51 2 2
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.01 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.034 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.01 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.017 0.053 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.015 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.001 0.019 -10000 0 -0.3 2 2
ACAP1 0.02 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.025 0.086 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.016 0.042 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.01 0 -10000 0 -10000 0 0
exocyst 0.034 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0 0.078 -10000 0 -10000 0 0
NME1 -0.015 0.092 -10000 0 -0.3 47 47
clathrin coat assembly 0.011 0.045 -10000 0 -10000 0 0
IL2RA 0.004 0.045 -10000 0 -10000 0 0
VAMP3 0.015 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.012 0.041 -10000 0 -0.34 3 3
EXOC6 0.01 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.01 0 -10000 0 -10000 0 0
PIP5K1C 0.019 0.021 -10000 0 -10000 0 0
SDC1 0.013 0.03 -10000 0 -10000 0 0
ARF6/GDP -0.015 0.091 -10000 0 -0.3 47 47
EXOC7 0.01 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.018 0.055 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.012 0.26 1 -10000 0 1
SCAMP2 0.01 0 -10000 0 -10000 0 0
ADRB2 -0.081 0.14 -10000 0 -0.36 31 31
EXOC3 0.01 0 -10000 0 -10000 0 0
ASAP2 0.009 0.022 -10000 0 -0.5 1 1
Dynamin 2/GDP -0.007 0.083 -10000 0 -0.27 47 47
KLC1 0.01 0 -10000 0 -10000 0 0
AVPR2 -0.04 0.12 -10000 0 -0.36 17 17
RALA 0.01 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.049 -10000 0 -10000 0 0
Insulin Pathway

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.013 0.052 -9999 0 -10000 0 0
TC10/GTP -0.012 0.049 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.012 -9999 0 -0.27 1 1
HRAS 0.01 0 -9999 0 -10000 0 0
APS homodimer 0.009 0.022 -9999 0 -0.5 1 1
GRB14 -0.025 0.13 -9999 0 -0.51 35 35
FOXO3 -0.003 0.025 -9999 0 -0.52 1 1
AKT1 0.023 0.061 -9999 0 -10000 0 0
INSR 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0 -9999 0 -10000 0 0
SORBS1 -0.019 0.12 -9999 0 -0.5 29 29
CRK 0.01 0 -9999 0 -10000 0 0
PTPN1 0.028 0 -9999 0 -10000 0 0
CAV1 -0.15 0.13 -9999 0 -0.25 326 326
CBL/APS/CAP/Crk-II/C3G -0.014 0.055 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.001 0.012 -9999 0 -0.27 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.014 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.029 0.013 -9999 0 -10000 0 0
RPS6KB1 0.029 0.057 -9999 0 -10000 0 0
PARD6A 0.009 0.022 -9999 0 -0.5 1 1
CBL 0.01 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.044 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.021 -9999 0 -10000 0 0
Insulin Receptor 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.001 0.019 -9999 0 -10000 0 0
PRKCI -0.004 0.013 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.015 0.055 -9999 0 -10000 0 0
SHC1 0.008 0.032 -9999 0 -0.51 2 2
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.001 0.014 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
RHOQ 0.01 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.023 0.061 -9999 0 -10000 0 0
PRKCZ -0.006 0.036 -9999 0 -0.45 3 3
SH2B2 0.009 0.022 -9999 0 -0.5 1 1
SHC/SHIP 0.023 0.028 -9999 0 -10000 0 0
F2RL2 -0.029 0.14 -9999 0 -0.51 39 39
TRIP10 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.018 -9999 0 -0.28 2 2
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.016 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.015 0.06 -9999 0 -0.26 30 30
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.017 -9999 0 -0.28 2 2
INPP5D 0.019 0.024 -9999 0 -0.25 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
SGK1 -0.003 0.035 -9999 0 -0.79 1 1
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.009 0.022 -9999 0 -0.5 1 1
p62DOK/RasGAP 0 0.002 -9999 0 -10000 0 0
INS 0.002 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.024 -9999 0 -0.25 4 4
GRB2 0.01 0 -9999 0 -10000 0 0
EIF4EBP1 0.021 0.073 -9999 0 -0.41 3 3
PTPRA 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.025 0.014 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.001 0.012 -9999 0 -0.28 1 1
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.019 0.066 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.022 0.051 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ 0.026 0.048 -9999 0 -10000 0 0
HIF1A 0.016 0 -9999 0 -10000 0 0
GAB1 0.008 0.032 -9999 0 -0.5 2 2
AKT1 0.038 0.042 -9999 0 -10000 0 0
PLCG1 0.022 0.052 -9999 0 -10000 0 0
NOS3 0.039 0.049 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
mol:NO 0.039 0.048 -9999 0 -10000 0 0
FLT1 0.024 0 -9999 0 -10000 0 0
PGF -0.007 0.093 -9999 0 -0.51 17 17
VEGFR1 homodimer/NRP2/VEGFR121 -0.001 0.019 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.043 0.047 -9999 0 -10000 0 0
endothelial cell proliferation 0.029 0.058 -9999 0 -0.37 3 3
mol:Ca2+ 0.022 0.051 -9999 0 -10000 0 0
MAPK3 0.031 0.05 -9999 0 -0.46 1 1
MAPK1 0.031 0.05 -9999 0 -0.46 1 1
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
PLGF homodimer -0.007 0.092 -9999 0 -0.51 17 17
PRKACA 0.01 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.31 0.25 -9999 0 -0.5 326 326
VEGFA homodimer 0.01 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.025 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.036 0.049 -9999 0 -0.44 1 1
PI3K -0.008 0.043 -9999 0 -10000 0 0
PRKCA 0.026 0.053 -9999 0 -0.49 1 1
PRKCB 0.02 0.068 -9999 0 -0.49 2 2
VEGFR1 homodimer/PLGF homodimer 0.015 0.057 -9999 0 -10000 0 0
VEGFA 0.01 0 -9999 0 -10000 0 0
VEGFB 0.01 0 -9999 0 -10000 0 0
mol:IP3 0.022 0.051 -9999 0 -10000 0 0
RASA1 0.031 0 -9999 0 -10000 0 0
NRP2 0.007 0.039 -9999 0 -0.5 3 3
VEGFR1 homodimer 0.024 0 -9999 0 -10000 0 0
VEGFB homodimer 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.12 -9999 0 -0.4 13 13
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.043 -9999 0 -10000 0 0
mol:L-citrulline 0.039 0.048 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0.01 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.008 0.042 -9999 0 -10000 0 0
PDPK1 0.031 0.047 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.039 0.048 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.023 0.024 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.01 0 -10000 0 -10000 0 0
MAP2K3 0.021 0.025 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.029 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.003 0.059 -10000 0 -0.5 7 7
TXN 0.006 0.015 -10000 0 -0.19 3 3
CALM1 0.01 0 -10000 0 -10000 0 0
GADD45A 0.008 0.032 -10000 0 -0.5 2 2
GADD45B 0.006 0.045 -10000 0 -0.5 4 4
MAP3K1 0.01 0 -10000 0 -10000 0 0
MAP3K6 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.01 0 -10000 0 -10000 0 0
MAP3K4 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0 0 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.013 0.17 3 -10000 0 3
RAC1/OSM/MEKK3 -0.001 0.012 -10000 0 -0.26 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.009 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.08 0.2 -10000 0 -0.51 89 89
CCM2 0.01 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.053 0.12 -10000 0 -0.3 89 89
MAPK11 0.007 0.039 -10000 0 -0.5 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.047 0.1 -10000 0 -0.27 89 89
OSM/MEKK3 -0.001 0.016 -10000 0 -0.35 1 1
TAOK1 0.013 0.014 -10000 0 -0.31 1 1
TAOK2 0.013 0 -10000 0 -10000 0 0
TAOK3 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
MAP3K10 0.007 0.039 -10000 0 -0.5 3 3
MAP3K3 0.009 0.022 -10000 0 -0.5 1 1
TRX/ASK1 0.011 0.013 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.006 0.044 -10000 0 -0.5 2 2
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.016 -9999 0 -0.26 2 2
HDAC3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.014 -9999 0 -0.22 2 2
GATA1/HDAC4 -0.037 0.11 -9999 0 -0.35 54 54
GATA1/HDAC5 -0.036 0.11 -9999 0 -0.35 53 53
GATA2/HDAC5 -0.028 0.095 -9999 0 -0.35 41 41
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.002 0.077 -9999 0 -0.5 12 12
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.013 -9999 0 -0.3 1 1
HDAC4/ANKRA2 -0.001 0.016 -9999 0 -0.36 1 1
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
GATA2 -0.031 0.14 -9999 0 -0.5 41 41
HDAC4/RFXANK -0.001 0.016 -9999 0 -0.36 1 1
BCOR 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.009 0.022 -9999 0 -0.5 1 1
HDAC5 0.01 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.022 -9999 0 -0.35 2 2
Histones 0.027 0.03 -9999 0 -10000 0 0
ADRBK1 0.01 0 -9999 0 -10000 0 0
HDAC4 0.009 0.023 -9999 0 -0.51 1 1
XPO1 0.01 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.016 -9999 0 -0.36 1 1
HDAC7 0.01 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.01 0 -9999 0 -10000 0 0
HDAC6 0.009 0.023 -9999 0 -0.51 1 1
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 0.001 0.067 -9999 0 -0.5 9 9
Tubulin/HDAC6 -0.009 0.052 -9999 0 -0.3 16 16
SUMO1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
GATA1 -0.044 0.15 -9999 0 -0.5 53 53
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
NR3C1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.023 0.012 -9999 0 -0.24 1 1
SRF 0.01 0 -9999 0 -10000 0 0
HDAC4/YWHAB -0.001 0.016 -9999 0 -0.36 1 1
Tubulin -0.01 0.06 -9999 0 -0.36 15 15
HDAC4/14-3-3 E -0.001 0.016 -9999 0 -0.36 1 1
GNB1 0.01 0 -9999 0 -10000 0 0
RANGAP1 0.01 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.013 -9999 0 -0.3 1 1
HDAC4/SRF -0.006 0.04 -9999 0 -0.29 10 10
HDAC4/ER alpha -0.018 0.078 -9999 0 -0.36 26 26
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.03 -9999 0 -10000 0 0
cell motility -0.009 0.051 -9999 0 -0.3 16 16
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.01 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.009 0.023 -9999 0 -0.51 1 1
Hsp90/HDAC6 -0.001 0.016 -9999 0 -0.36 1 1
ESR1 -0.015 0.11 -9999 0 -0.5 25 25
HDAC6/HDAC11 -0.001 0.016 -9999 0 -0.36 1 1
Ran/GTP/Exportin 1 0 0.01 -9999 0 -0.22 1 1
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.023 -9999 0 -0.51 1 1
HDAC4/MEF2C 0 0.011 -9999 0 -10000 0 0
GNG2 0.008 0.032 -9999 0 -0.5 2 2
NCOR2 0.01 0 -9999 0 -10000 0 0
TUBB2A -0.005 0.087 -9999 0 -0.51 15 15
HDAC11 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
ANKRA2 0.01 0 -9999 0 -10000 0 0
RFXANK 0.01 0 -9999 0 -10000 0 0
nuclear import 0 0.008 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.013 0.072 -9999 0 -0.65 4 4
MAP4K1 0.005 0.05 -9999 0 -0.5 5 5
MAP3K8 0.008 0.032 -9999 0 -0.5 2 2
PRKCB -0.004 0.083 -9999 0 -0.5 14 14
DBNL 0.01 0 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
MAP3K1 0.025 0.068 -9999 0 -0.6 4 4
JUN 0.011 0.11 -9999 0 -0.62 14 14
MAP3K7 0.025 0.068 -9999 0 -0.6 4 4
GRAP2 -0.006 0.088 -9999 0 -0.5 16 16
CRK 0.01 0 -9999 0 -10000 0 0
MAP2K4 0.031 0.074 -9999 0 -0.67 4 4
LAT 0.009 0.023 -9999 0 -0.51 1 1
LCP2 0.007 0.039 -9999 0 -0.5 3 3
MAPK8 0.007 0.11 -9999 0 -0.64 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.019 0.072 -9999 0 -0.64 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.012 0.067 -9999 0 -0.61 4 4
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.049 -10000 0 -0.35 9 9
MAP4K4 0.029 0.042 -10000 0 -10000 0 0
BAG4 0.009 0.023 -10000 0 -0.51 1 1
PKC zeta/ceramide -0.012 0.032 -10000 0 -0.25 2 2
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 0.003 0.06 -10000 0 -0.51 7 7
BAX -0.003 0.015 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AKT1 0.017 0.007 -10000 0 -10000 0 0
BAD -0.01 0.03 0.14 4 -10000 0 4
SMPD1 0.017 0.035 -10000 0 -0.16 18 18
RB1 -0.01 0.03 0.14 4 -10000 0 4
FADD/Caspase 8 0.036 0.045 -10000 0 -0.45 1 1
MAP2K4 -0.004 0.028 -10000 0 -10000 0 0
NSMAF 0.01 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.004 0.028 -10000 0 -10000 0 0
EGF -0.09 0.2 -10000 0 -0.51 99 99
mol:ceramide -0.018 0.032 0.14 4 -10000 0 4
MADD 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.011 0.049 -10000 0 -0.35 9 9
ASAH1 0.009 0.022 -10000 0 -0.5 1 1
negative regulation of cell cycle -0.01 0.03 0.14 4 -10000 0 4
cell proliferation -0.01 0.03 -10000 0 -10000 0 0
BID 0.019 0.033 -10000 0 -10000 0 0
MAP3K1 -0.01 0.03 0.14 4 -10000 0 4
EIF2A 0.002 0.027 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
CRADD 0.008 0.032 -10000 0 -0.5 2 2
MAPK3 0.005 0.027 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.005 0.027 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.011 0.029 -10000 0 -10000 0 0
FADD 0.029 0.042 -10000 0 -10000 0 0
KSR1 -0.01 0.03 0.14 4 -10000 0 4
MAPK8 -0.001 0.03 -10000 0 -0.2 2 2
PRKRA -0.01 0.03 -10000 0 -10000 0 0
PDGFA 0.002 0.063 -10000 0 -0.5 8 8
TRAF2 0.01 0 -10000 0 -10000 0 0
IGF1 -0.002 0.077 -10000 0 -0.5 12 12
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.018 0.032 0.14 4 -10000 0 4
CTSD 0.01 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.008 0.039 -10000 0 -10000 0 0
PRKCD 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.039 -10000 0 -0.5 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.011 0.049 -10000 0 -0.35 9 9
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.024 0.045 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.056 -10000 0 -0.29 20 20
mol:Sphingosine-1-phosphate 0.011 0.048 -10000 0 -0.35 9 9
MAP2K1 0.002 0.027 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
CYCS -0.005 0.022 0.15 1 -10000 0 1
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.016 -10000 0 -0.36 1 1
EIF2AK2 -0.004 0.028 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.011 0.055 -10000 0 -0.29 19 19
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.038 -10000 0 -0.58 1 1
MAP2K2 0.002 0.027 -10000 0 -10000 0 0
SMPD3 0.016 0.042 -10000 0 -0.18 19 19
TNF -0.009 0.096 -10000 0 -0.5 19 19
PKC zeta/PAR4 -0.002 0.027 -10000 0 -0.35 3 3
mol:PHOSPHOCHOLINE 0.022 0.065 0.15 96 -10000 0 96
NF kappa B1/RelA/I kappa B alpha -0.001 0.018 -10000 0 -10000 0 0
AIFM1 -0.005 0.022 0.15 1 -10000 0 1
BCL2 0.007 0.039 -10000 0 -0.5 3 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.01 0 -10000 0 -10000 0 0
NFATC1 0.035 0.041 -10000 0 -0.4 1 1
NFATC2 0.012 0.045 -10000 0 -0.26 2 2
NFATC3 0.013 0.03 -10000 0 -0.37 3 3
YWHAE 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.015 0.095 -10000 0 -0.36 18 18
Exportin 1/Ran/NUP214 -0.001 0.013 -10000 0 -0.3 1 1
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.034 0.08 -10000 0 -0.39 15 15
BCL2/BAX -0.002 0.027 -10000 0 -0.36 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.005 0.007 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
MAPK14 0.008 0.004 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.015 0.089 -10000 0 -0.34 18 18
Calcineurin A alpha-beta B1/BCL2 0.007 0.039 -10000 0 -0.5 3 3
FKBP8 0.009 0.022 -10000 0 -0.5 1 1
activation-induced cell death of T cells 0.014 0.088 0.34 18 -10000 0 18
KPNB1 0.01 0 -10000 0 -10000 0 0
KPNA2 0.002 0.064 -10000 0 -0.51 8 8
XPO1 0.009 0.001 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.51 10 10
MAP3K8 0.006 0.032 -10000 0 -0.5 2 2
NFAT4/CK1 alpha -0.001 0.016 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.053 0.1 -10000 0 -0.38 6 6
CABIN1 -0.016 0.096 -10000 0 -0.37 18 18
CALM1 0.008 0.004 -10000 0 -10000 0 0
RAN 0.008 0.023 -10000 0 -0.51 1 1
MAP3K1 0.01 0 -10000 0 -10000 0 0
CAMK4 0.001 0.067 -10000 0 -0.5 9 9
mol:Ca2+ -0.003 0.007 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.027 -10000 0 -0.35 3 3
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 0.008 0.004 -10000 0 -10000 0 0
MAPK9 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.004 0.036 -10000 0 -0.34 3 3
PRKCH 0.01 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.004 -10000 0 -10000 0 0
PIM1 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.013 0.21 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.016 -10000 0 -10000 0 0
PRKCB -0.004 0.083 -10000 0 -0.5 14 14
PRKCE 0.004 0.055 -10000 0 -0.5 6 6
JNK2/NFAT4 0.016 0.028 -10000 0 -0.33 3 3
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.01 0 -10000 0 -10000 0 0
NUP214 0.009 0.001 -10000 0 -10000 0 0
PRKCZ 0.005 0.039 -10000 0 -0.5 3 3
PRKCA 0.008 0.032 -10000 0 -0.5 2 2
PRKCG -0.045 0.16 -10000 0 -0.51 53 53
PRKCQ -0.063 0.18 -10000 0 -0.5 74 74
FKBP38/BCL2 -0.003 0.031 -10000 0 -0.36 4 4
EP300 0.008 0.005 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
NFATc/JNK1 0.034 0.042 -10000 0 -0.38 1 1
CaM/Ca2+/FKBP38 -0.001 0.014 -10000 0 -0.31 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.012 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.039 -10000 0 -0.3 9 9
NFATc/ERK1 0.039 0.039 -10000 0 -0.37 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.034 0.08 -10000 0 -0.39 15 15
NR4A1 -0.056 0.21 -10000 0 -0.48 104 104
GSK3B 0.008 0.004 -10000 0 -10000 0 0
positive T cell selection 0.013 0.03 -10000 0 -0.37 3 3
NFAT1/CK1 alpha -0.011 0.026 -10000 0 -0.26 1 1
RCH1/ KPNB1 -0.006 0.044 -10000 0 -0.36 8 8
YWHAQ 0.01 0 -10000 0 -10000 0 0
PRKACA 0.008 0.004 -10000 0 -10000 0 0
AKAP5 0.007 0.039 -10000 0 -0.5 3 3
MEF2D 0.008 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.034 0.042 -10000 0 -0.38 1 1
CREBBP 0.008 0.005 -10000 0 -10000 0 0
BCL2 0.007 0.039 -10000 0 -0.5 3 3
FoxO family signaling

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
G6PC 0.016 0.046 -9999 0 -10000 0 0
PLK1 -0.12 0.24 -9999 0 -0.59 42 42
CDKN1B 0.015 0.11 -9999 0 -10000 0 0
FOXO3 -0.069 0.2 -9999 0 -0.5 42 42
KAT2B 0.004 0.019 -9999 0 -10000 0 0
FOXO1/SIRT1 0.014 0.03 -9999 0 -10000 0 0
CAT -0.065 0.22 -9999 0 -1.1 9 9
CTNNB1 0.01 0 -9999 0 -10000 0 0
AKT1 0.005 0.02 -9999 0 -10000 0 0
FOXO1 0.021 0.03 -9999 0 -10000 0 0
MAPK10 -0.004 0.087 -9999 0 -0.25 56 56
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.052 0.063 -9999 0 -10000 0 0
response to oxidative stress -0.007 0.023 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.11 0.15 -9999 0 -0.47 41 41
XPO1 0.01 0 -9999 0 -10000 0 0
EP300 0.01 0.004 -9999 0 -10000 0 0
BCL2L11 0.009 0.031 -9999 0 -10000 0 0
FOXO1/SKP2 0.021 0.037 -9999 0 -10000 0 0
mol:GDP -0.007 0.023 -9999 0 -10000 0 0
RAN 0.01 0.023 -9999 0 -0.51 1 1
GADD45A 0.009 0.11 -9999 0 -0.71 2 2
YWHAQ 0.01 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.055 0.016 -9999 0 -10000 0 0
MST1 -0.018 0.11 -9999 0 -0.52 22 22
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.02 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
MAPK8 0.025 0.01 -9999 0 -10000 0 0
MAPK9 0.025 0.009 -9999 0 -10000 0 0
YWHAG 0.01 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
SIRT1 0.007 0.008 -9999 0 -10000 0 0
SOD2 0.013 0.13 -9999 0 -10000 0 0
RBL2 -0.02 0.14 -9999 0 -10000 0 0
RAL/GDP 0.013 0.014 -9999 0 -10000 0 0
CHUK 0.004 0.019 -9999 0 -10000 0 0
Ran/GTP 0.01 0.017 -9999 0 -0.36 1 1
CSNK1G2 0.01 0 -9999 0 -10000 0 0
RAL/GTP 0.019 0.015 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
FASLG -0.006 0.14 -9999 0 -1.3 6 6
SKP2 0.006 0.045 -9999 0 -0.51 4 4
USP7 0.011 0.001 -9999 0 -10000 0 0
IKBKB 0.004 0.019 -9999 0 -10000 0 0
CCNB1 -0.094 0.24 -9999 0 -0.58 41 41
FOXO1-3a-4/beta catenin -0.033 0.07 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.037 -9999 0 -10000 0 0
CSNK1A1 0.01 0 -9999 0 -10000 0 0
SGK1 0.003 0.03 -9999 0 -0.52 1 1
CSNK1G3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.014 -9999 0 -0.3 1 1
ZFAND5 0.055 0.056 -9999 0 -10000 0 0
SFN 0 0.071 -9999 0 -0.51 10 10
CDK2 0.01 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.022 0.045 -9999 0 -0.37 1 1
CREBBP 0.01 0.005 -9999 0 -10000 0 0
FBXO32 -0.075 0.22 -9999 0 -0.57 39 39
BCL6 -0.02 0.14 -9999 0 -0.49 4 4
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
YWHAH 0.01 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.047 0.036 -10000 0 -0.44 1 1
UGCG -0.002 0.028 -10000 0 -0.62 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.04 0.054 -10000 0 -0.3 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.021 0.03 -10000 0 -0.61 1 1
mol:DAG 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.037 -10000 0 -0.34 5 5
FRAP1 0.063 0.058 -10000 0 -0.39 5 5
FOXO3 0.065 0.052 -10000 0 -0.35 4 4
AKT1 0.061 0.054 -10000 0 -0.38 4 4
GAB2 0.006 0.05 -10000 0 -0.5 5 5
SMPD1 -0.001 0.007 -10000 0 -10000 0 0
SGMS1 -0.001 0.007 -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 0.017 0.014 -10000 0 -0.29 1 1
CALM1 0.01 0 -10000 0 -10000 0 0
cell proliferation 0.039 0.032 -10000 0 -0.27 3 3
EIF3A 0.01 0 -10000 0 -10000 0 0
PI3K 0.019 0.017 -10000 0 -0.35 1 1
RPS6KB1 0.021 0.022 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.001 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -0.011 2 2
JAK3 0.012 0.001 -10000 0 -10000 0 0
PIK3R1 0.011 0.022 -10000 0 -0.5 1 1
JAK1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MYC 0.062 0.074 -10000 0 -0.73 3 3
MYB 0.016 0.11 -10000 0 -1.2 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.054 0.05 -10000 0 -0.35 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.054 0.049 -10000 0 -0.34 3 3
Rac1/GDP 0.022 0.013 -10000 0 -0.26 1 1
T cell proliferation 0.056 0.051 -10000 0 -0.37 2 2
SHC1 0.008 0.032 -10000 0 -0.51 2 2
RAC1 0.01 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.007 -10000 0 -0.051 7 7
PRKCZ 0.057 0.053 -10000 0 -0.38 2 2
NF kappa B1 p50/RelA -0.004 0.037 -10000 0 -0.34 5 5
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.042 0.039 -10000 0 -0.43 2 2
HSP90AA1 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL2RA -0.026 0.13 -10000 0 -0.51 36 36
IL2RB 0.01 0.032 -10000 0 -0.5 2 2
TERT -0.15 0.24 -10000 0 -0.51 157 157
E2F1 0.019 0.043 -10000 0 -0.42 4 4
SOS1 0.01 0.001 -10000 0 -10000 0 0
RPS6 0.01 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.003 0.024 7 -10000 0 7
PTPN11 0.011 0.001 -10000 0 -10000 0 0
IL2RG 0.007 0.05 -10000 0 -0.5 5 5
actin cytoskeleton organization 0.056 0.051 -10000 0 -0.37 2 2
GRB2 0.01 0.001 -10000 0 -10000 0 0
IL2 0.008 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.013 -10000 0 -0.24 1 1
LCK 0.009 0.039 -10000 0 -0.5 3 3
BCL2 0.064 0.063 -10000 0 -0.53 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.023 0.015 -9999 0 -0.22 2 2
epithelial cell differentiation -0.001 0.015 -9999 0 -10000 0 0
CYFIP2 0.003 0.059 -9999 0 -0.5 7 7
ENAH 0.048 0.031 -9999 0 -0.29 1 1
EGFR -0.006 0.089 -9999 0 -0.5 16 16
EPHA2 0 0.07 -9999 0 -0.5 10 10
MYO6 0.029 0.016 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.004 0.034 -9999 0 -0.29 7 7
AQP5 -0.1 0.17 -9999 0 -0.42 114 114
CTNND1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.016 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.13 -9999 0 -0.46 1 1
EGF -0.09 0.2 -9999 0 -0.51 99 99
NCKAP1 0.01 0 -9999 0 -10000 0 0
AQP3 -0.018 0.087 -9999 0 -0.44 21 21
cortical microtubule organization -0.001 0.015 -9999 0 -10000 0 0
GO:0000145 0.028 0.015 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.015 -9999 0 -10000 0 0
MLLT4 0.01 0 -9999 0 -10000 0 0
ARF6/GDP -0.005 0.031 -9999 0 -0.39 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.037 -9999 0 -0.26 11 11
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.037 0.02 -9999 0 -10000 0 0
PVRL2 0.01 0 -9999 0 -10000 0 0
ZYX 0.028 0.019 -9999 0 -10000 0 0
ARF6/GTP -0.005 0.034 -9999 0 -10000 0 0
CDH1 0.008 0.032 -9999 0 -0.5 2 2
EGFR/EGFR/EGF/EGF -0.05 0.096 -9999 0 -0.46 4 4
RhoA/GDP -0.001 0.014 -9999 0 -10000 0 0
actin cytoskeleton organization 0.034 0.015 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.009 0.022 -9999 0 -0.5 1 1
GIT1 0.01 0 -9999 0 -10000 0 0
IGF1R 0.009 0.022 -9999 0 -0.5 1 1
IGF1 -0.002 0.077 -9999 0 -0.5 12 12
DIAPH1 -0.008 0.065 -9999 0 -0.56 7 7
Wnt receptor signaling pathway 0.001 0.015 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.031 -9999 0 -0.39 1 1
CTNNA1 0.01 0 -9999 0 -10000 0 0
VCL 0.034 0.016 -9999 0 -10000 0 0
EFNA1 0.009 0.022 -9999 0 -0.5 1 1
LPP 0.034 0.019 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.005 0.037 -9999 0 -0.45 1 1
SEC6/SEC8 -0.001 0.012 -9999 0 -10000 0 0
MGAT3 -0.11 0.13 -9999 0 -0.47 1 1
HGF/MET -0.028 0.078 -9999 0 -0.46 4 4
HGF -0.021 0.12 -9999 0 -0.5 31 31
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.023 0.016 -9999 0 -0.23 2 2
actin cable formation 0.059 0.03 -9999 0 -10000 0 0
KIAA1543 0.033 0.026 -9999 0 -0.45 1 1
KIFC3 0.028 0.019 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
EXOC3 0.01 0 -9999 0 -10000 0 0
ACTN1 0.029 0.016 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.001 0.015 -9999 0 -10000 0 0
EXOC4 0.01 0 -9999 0 -10000 0 0
STX4 0.029 0.016 -9999 0 -10000 0 0
PIP5K1C 0.029 0.016 -9999 0 -10000 0 0
LIMA1 0.01 0 -9999 0 -10000 0 0
ABI1 0.01 0 -9999 0 -10000 0 0
ROCK1 -0.004 0.027 -9999 0 -0.34 1 1
adherens junction assembly 0.045 0.037 -9999 0 -0.52 2 2
IGF-1R heterotetramer/IGF1 -0.006 0.036 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.024 0.13 -9999 0 -0.5 34 34
PLEKHA7 0.029 0.016 -9999 0 -10000 0 0
mol:GTP -0.005 0.037 -9999 0 -0.26 11 11
establishment of epithelial cell apical/basal polarity 0.048 0.014 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.023 0.015 -9999 0 -0.22 2 2
regulation of cell-cell adhesion 0.034 0.015 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.023 0.016 -9999 0 -0.23 2 2
Class I PI3K signaling events

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
ARF5/GTP -0.003 0.023 -9999 0 -10000 0 0
DAPP1 -0.005 0.11 -9999 0 -0.48 19 19
Src family/SYK family/BLNK-LAT/BTK-ITK -0.005 0.16 -9999 0 -0.59 26 26
mol:DAG 0.021 0.069 -9999 0 -0.24 20 20
HRAS 0.01 0.001 -9999 0 -10000 0 0
RAP1A 0.01 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.02 0.072 -9999 0 -0.4 11 11
PLCG2 0.007 0.039 -9999 0 -0.5 3 3
PLCG1 0.01 0 -9999 0 -10000 0 0
ARF5 0.01 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.022 -9999 0 -10000 0 0
ARF1/GTP -0.003 0.022 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.022 -9999 0 -10000 0 0
ADAP1 -0.003 0.026 -9999 0 -0.43 1 1
ARAP3 -0.002 0.022 -9999 0 -10000 0 0
INPPL1 0.01 0 -9999 0 -10000 0 0
PREX1 0.004 0.055 -9999 0 -0.5 6 6
ARHGEF6 -0.009 0.096 -9999 0 -0.5 19 19
ARHGEF7 0.01 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
NRAS 0.01 0.001 -9999 0 -10000 0 0
FYN 0.009 0.022 -9999 0 -0.5 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
FGR -0.029 0.14 -9999 0 -0.5 39 39
mol:Ca2+ 0.019 0.037 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0 0.07 -9999 0 -0.5 10 10
ZAP70 0.004 0.055 -9999 0 -0.5 6 6
mol:IP3 0.022 0.05 -9999 0 -0.21 7 7
LYN 0.01 0 -9999 0 -10000 0 0
ARF1/GDP 0.02 0.072 -9999 0 -0.4 11 11
RhoA/GDP -0.007 0.037 -9999 0 -0.36 2 2
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK 0.008 0.032 -9999 0 -0.5 2 2
actin cytoskeleton reorganization 0.038 0.064 -9999 0 -0.43 5 5
SRC 0.01 0 -9999 0 -10000 0 0
PLEKHA2 0.021 0.028 -9999 0 -0.29 4 4
RAC1 0.01 0 -9999 0 -10000 0 0
PTEN 0 0.003 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.019 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.02 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.003 0.12 -9999 0 -0.48 19 19
BLK -0.08 0.2 -9999 0 -0.51 89 89
PDPK1 0.01 0 -9999 0 -10000 0 0
CYTH1 -0.002 0.02 -9999 0 -10000 0 0
HCK -0.014 0.11 -9999 0 -0.5 24 24
CYTH3 -0.003 0.024 -9999 0 -10000 0 0
CYTH2 -0.002 0.02 -9999 0 -10000 0 0
KRAS 0.008 0.032 -9999 0 -0.5 2 2
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.002 0.027 -9999 0 -0.57 1 1
SGK1 -0.002 0.029 -9999 0 -0.62 1 1
INPP5D 0.007 0.039 -9999 0 -0.5 3 3
mol:GDP 0.015 0.076 -9999 0 -0.42 11 11
SOS1 0.01 0 -9999 0 -10000 0 0
SYK 0.007 0.039 -9999 0 -0.5 3 3
ARF6/GDP -0.007 0.037 -9999 0 -0.37 2 2
mol:PI-3-4-5-P3 -0.002 0.022 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.022 -9999 0 -10000 0 0
VAV1 0.005 0.05 -9999 0 -0.5 5 5
mol:PI-3-4-P2 0.016 0.028 -9999 0 -0.35 3 3
RAS family/GTP/PI3K Class I -0.002 0.022 -9999 0 -10000 0 0
PLEKHA1 0.022 0.024 -9999 0 -0.29 3 3
Rac1/GDP 0.02 0.072 -9999 0 -0.4 11 11
LAT 0.009 0.023 -9999 0 -0.51 1 1
Rac1/GTP 0.011 0.11 -9999 0 -0.45 22 22
ITK -0.008 0.039 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.093 -9999 0 -0.35 20 20
LCK 0.007 0.039 -9999 0 -0.5 3 3
BTK -0.017 0.063 -9999 0 -0.43 3 3
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.008 0.066 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.013 0.044 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.004 0.021 -9999 0 -0.3 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.014 0.045 -9999 0 -0.33 4 4
CaM/Ca2+ -0.016 0.053 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.017 0.063 -9999 0 -10000 0 0
AKT1 0.026 0.059 -9999 0 -10000 0 0
MAP2K1 0.024 0.062 -9999 0 -10000 0 0
MAP3K11 0.017 0.064 -9999 0 -10000 0 0
IFNGR1 0.009 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.054 0.11 -9999 0 -0.38 50 50
Rap1/GTP -0.012 0.038 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.019 0.063 -9999 0 -10000 0 0
CEBPB 0.043 0.086 -9999 0 -0.41 11 11
STAT3 0.01 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.017 0.056 -9999 0 -10000 0 0
STAT1 0.017 0.063 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.03 0.14 -9999 0 -0.5 41 41
PIK3CA 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.022 0.061 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.011 0.041 -9999 0 -0.35 2 2
mol:Ca2+ -0.017 0.057 -9999 0 -10000 0 0
MAPK3 0.033 0.061 -9999 0 -10000 0 0
STAT1 (dimer) -0.017 0.061 -9999 0 -0.47 4 4
MAPK1 0.033 0.061 -9999 0 -0.34 1 1
JAK2 0.007 0.032 -9999 0 -0.5 2 2
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
JAK1 0.009 0.007 -9999 0 -10000 0 0
CAMK2D 0.01 0 -9999 0 -10000 0 0
DAPK1 0.038 0.1 -9999 0 -0.6 11 11
SMAD7 0.027 0.041 -9999 0 -0.26 1 1
CBL/CRKL/C3G -0.014 0.047 -9999 0 -10000 0 0
PI3K -0.015 0.051 -9999 0 -10000 0 0
IFNG -0.03 0.14 -9999 0 -0.5 41 41
apoptosis 0.027 0.077 -9999 0 -0.43 11 11
CAMK2G 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.041 0.15 -9999 0 -0.5 51 51
CAMK2B -0.08 0.2 -9999 0 -0.51 89 89
FRAP1 0.026 0.056 -9999 0 -10000 0 0
PRKCD 0.027 0.06 -9999 0 -10000 0 0
RAP1B 0.01 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.014 0.045 -9999 0 -0.33 4 4
PTPN2 0.01 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
IRF1 0.046 0.051 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.015 0.05 -9999 0 -10000 0 0
SOCS1 0.001 0.02 -9999 0 -10000 0 0
mol:GDP -0.014 0.045 -9999 0 -10000 0 0
CASP1 0.026 0.05 -9999 0 -0.3 6 6
PTGES2 0.01 0 -9999 0 -10000 0 0
IRF9 0.04 0.03 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.05 -9999 0 -10000 0 0
RAP1/GDP -0.012 0.039 -9999 0 -10000 0 0
CBL 0.016 0.063 -9999 0 -10000 0 0
MAP3K1 0.017 0.064 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
PIAS4 0.009 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.014 0.045 -9999 0 -0.33 4 4
PTPN11 0.01 0.066 -9999 0 -0.25 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.01 0.053 -9999 0 -0.29 18 18
Ran/GTP/Exportin 1/HDAC1 0 0.01 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.05 -9999 0 -0.27 18 18
SUMO1 0.01 0 -9999 0 -10000 0 0
ZFPM1 0.009 0.023 -9999 0 -0.51 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.009 0.023 -9999 0 -0.51 1 1
Histones -0.005 0.024 -9999 0 -10000 0 0
YY1/LSF 0.024 0 -9999 0 -10000 0 0
SMG5 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.023 -9999 0 -0.51 1 1
I kappa B alpha/HDAC3 0.017 0.048 -9999 0 -0.23 18 18
I kappa B alpha/HDAC1 0.019 0.034 -9999 0 -10000 0 0
SAP18 0.01 0 -9999 0 -10000 0 0
RELA 0.021 0.046 -9999 0 -0.22 18 18
HDAC1/Smad7 -0.001 0.013 -9999 0 -0.29 1 1
RANGAP1 0.01 0 -9999 0 -10000 0 0
HDAC3/TR2 0.019 0.034 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.012 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.024 0.042 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.031 0.14 -9999 0 -0.5 41 41
GATA1 -0.044 0.15 -9999 0 -0.5 53 53
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.024 0.062 -9999 0 -0.28 1 1
RBBP7 0.01 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.01 0 -9999 0 -10000 0 0
MAX 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.01 0 -9999 0 -10000 0 0
NFKBIA 0.015 0.038 -9999 0 -10000 0 0
KAT2B 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.034 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0.01 0 -9999 0 -10000 0 0
CHD3 0.01 0 -9999 0 -10000 0 0
SAP30 0.01 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.01 0 -9999 0 -10000 0 0
YY1/HDAC3 0.028 0.032 -9999 0 -10000 0 0
YY1/HDAC2 0.024 0 -9999 0 -10000 0 0
YY1/HDAC1 0.024 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.037 0 -9999 0 -10000 0 0
PPARG -0.049 0.12 -9999 0 -0.3 83 83
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.034 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.013 -9999 0 -0.29 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.039 0.012 -9999 0 -10000 0 0
HDAC1 0.01 0 -9999 0 -10000 0 0
HDAC3 0.015 0.038 -9999 0 -10000 0 0
HDAC2 0.01 0 -9999 0 -10000 0 0
YY1 0.024 0 -9999 0 -10000 0 0
HDAC8 0.01 0 -9999 0 -10000 0 0
SMAD7 0.009 0.022 -9999 0 -0.5 1 1
NCOR2 0.01 0 -9999 0 -10000 0 0
MXD1 0.01 0 -9999 0 -10000 0 0
STAT3 0.02 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.038 -9999 0 -10000 0 0
histone deacetylation 0.037 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.026 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GATAD2B 0.01 0 -9999 0 -10000 0 0
GATAD2A 0.01 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.004 0.086 -9999 0 -0.27 41 41
GATA1/HDAC1 -0.036 0.11 -9999 0 -0.35 53 53
GATA1/HDAC3 -0.013 0.091 -9999 0 -0.26 53 53
CHD4 0.01 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.013 0.067 -9999 0 -0.35 19 19
SIN3/HDAC complex/Mad/Max 0.037 0 -9999 0 -10000 0 0
NuRD Complex 0.043 0.012 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.024 -9999 0 -10000 0 0
SIN3B 0.01 0 -9999 0 -10000 0 0
MTA2 0.01 0 -9999 0 -10000 0 0
SIN3A 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.023 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.037 0.11 -9999 0 -0.36 53 53
FKBP25/HDAC1/HDAC2 -0.001 0.013 -9999 0 -0.3 1 1
TNF -0.009 0.096 -9999 0 -0.5 19 19
negative regulation of cell growth 0.037 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.037 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0.01 -9999 0 -0.22 1 1
NF kappa B/RelA/I kappa B alpha -0.01 0.054 -9999 0 -0.29 18 18
SIN3/HDAC complex/NCoR1 0.036 0 -9999 0 -10000 0 0
TFCP2 0.01 0 -9999 0 -10000 0 0
NR2C1 0.01 0 -9999 0 -10000 0 0
MBD3 0.008 0.032 -9999 0 -0.5 2 2
MBD2 0.01 0 -9999 0 -10000 0 0
TCGA08_rtk_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
PDGFRA 0.006 0.045 -10000 0 -0.5 4 4
HRAS 0.01 0 -10000 0 -10000 0 0
EGFR -0.006 0.089 -10000 0 -0.5 16 16
AKT 0.028 0.034 -10000 0 -0.33 4 4
FOXO3 0.01 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
FOXO1 0.009 0.022 -10000 0 -0.5 1 1
AKT3 0.006 0.045 -10000 0 -0.5 4 4
FOXO4 0.01 0 -10000 0 -10000 0 0
MET -0.024 0.13 -10000 0 -0.5 34 34
PIK3CA 0.01 0 -10000 0 -10000 0 0
PIK3CB 0.01 0 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
PIK3CG -0.008 0.094 -10000 0 -0.5 18 18
PIK3R3 0.009 0.022 -10000 0 -0.5 1 1
PIK3R2 0.01 0 -10000 0 -10000 0 0
NF1 0.01 0 -10000 0 -10000 0 0
RAS 0.007 0.046 -10000 0 -0.25 5 5
ERBB2 0.007 0.039 -10000 0 -0.51 3 3
proliferation/survival/translation -0.019 0.033 0.19 7 -10000 0 7
PI3K 0.012 0.052 -10000 0 -0.22 11 11
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
KRAS 0.008 0.032 -10000 0 -0.51 2 2
FOXO 0.036 0.014 -10000 0 -10000 0 0
AKT2 0.01 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
Circadian rhythm pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.019 0.072 -9999 0 -0.49 5 5
CLOCK 0.012 0.002 -9999 0 -10000 0 0
TIMELESS/CRY2 0.03 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0 0.001 -9999 0 -10000 0 0
ATR 0.01 0 -9999 0 -10000 0 0
NR1D1 0.031 0.02 -9999 0 -10000 0 0
ARNTL 0.012 0.002 -9999 0 -10000 0 0
TIMELESS 0.029 0.038 -9999 0 -10000 0 0
NPAS2 0.009 0.039 -9999 0 -0.5 3 3
CRY2 0.01 0 -9999 0 -10000 0 0
mol:CO -0.01 0.009 -9999 0 -10000 0 0
CHEK1 -0.026 0.13 -9999 0 -0.51 36 36
mol:HEME 0.01 0.009 -9999 0 -10000 0 0
PER1 -0.01 0.098 -9999 0 -0.5 20 20
BMAL/CLOCK/NPAS2 0.031 0.026 -9999 0 -0.29 3 3
BMAL1/CLOCK 0.034 0.033 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.019 0.072 -9999 0 -0.49 5 5
TIMELESS/CHEK1/ATR -0.02 0.073 -9999 0 -10000 0 0
mol:NADPH 0.01 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.019 0.065 -9999 0 -0.52 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.002 0.004 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.03 0.011 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.004 -10000 0 -10000 0 0
myoblast fusion -0.015 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.1 0.29 54 -10000 0 54
ARF1/GTP 0 0.001 -10000 0 -10000 0 0
mol:GM1 0.008 0.003 -10000 0 -10000 0 0
mol:Choline 0.023 0.002 -10000 0 -10000 0 0
lamellipodium assembly 0.009 0.028 -10000 0 -10000 0 0
MAPK3 0.021 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.006 0.1 -10000 0 -0.29 54 54
ARF1 0.01 0 -10000 0 -10000 0 0
ARF6/GDP 0.001 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.016 -10000 0 -10000 0 0
ARF6 0.009 0.002 -10000 0 -10000 0 0
RAB11A 0.01 0 -10000 0 -10000 0 0
TIAM1 0.001 0.07 -10000 0 -0.5 10 10
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.007 -10000 0 -10000 0 0
actin filament bundle formation 0 0.005 -10000 0 -10000 0 0
KALRN 0.005 0.028 -10000 0 -0.26 3 3
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0 0.005 -10000 0 -10000 0 0
NME1 -0.036 0.15 -10000 0 -0.5 47 47
Rac1/GDP 0 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.009 0.028 -10000 0 -10000 0 0
RAC1 0.01 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 0.007 0.024 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
PLD1 0.017 0.003 -10000 0 -10000 0 0
RAB11FIP3 0.01 0 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.028 -10000 0 -10000 0 0
ruffle organization 0.023 0.004 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.003 -10000 0 -10000 0 0
PLD2 0.017 0.003 -10000 0 -10000 0 0
PIP5K1A 0.023 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.028 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.004 0.055 -10000 0 -0.5 6 6
positive regulation of NF-kappaB transcription factor activity -0.005 0.047 -10000 0 -0.4 7 7
MAP2K4 0.034 0.028 -10000 0 -0.33 1 1
IKBKB 0.01 0 -10000 0 -10000 0 0
TNFRSF10B 0.01 0 -10000 0 -10000 0 0
TNFRSF10A 0.008 0.032 -10000 0 -0.5 2 2
SMPD1 -0.002 0.02 -10000 0 -0.19 5 5
IKBKG 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.008 0.032 -10000 0 -0.5 2 2
TRAIL/TRAILR2 -0.004 0.038 -10000 0 -0.35 6 6
TRAIL/TRAILR3 -0.009 0.063 -10000 0 -0.4 12 12
TRAIL/TRAILR1 -0.005 0.048 -10000 0 -0.4 7 7
TRAIL/TRAILR4 -0.005 0.048 -10000 0 -0.4 7 7
TRAIL/TRAILR1/DAP3/GTP -0.004 0.037 -10000 0 -0.3 7 7
IKK complex -0.001 0.013 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.013 0.04 -10000 0 -0.35 6 6
MAP3K1 -0.003 0.026 -10000 0 -0.36 1 1
TRAILR4 (trimer) 0.008 0.032 -10000 0 -0.5 2 2
TRADD 0.01 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.032 -10000 0 -0.5 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.025 0.033 -10000 0 -0.46 1 1
CFLAR 0.01 0 -10000 0 -10000 0 0
MAPK1 0.013 0.04 -10000 0 -0.35 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP -0.004 0.033 -10000 0 -0.49 1 1
mol:ceramide -0.002 0.02 -10000 0 -0.19 5 5
FADD 0.01 0 -10000 0 -10000 0 0
MAPK8 0.039 0.027 -10000 0 -0.31 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.002 0.063 -10000 0 -0.5 8 8
CHUK 0.01 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.005 0.04 -10000 0 -0.33 7 7
DAP3 0.01 0 -10000 0 -10000 0 0
CASP10 -0.004 0.044 0.24 1 -0.35 6 7
JNK cascade -0.005 0.047 -10000 0 -0.4 7 7
TRAIL (trimer) 0.004 0.055 -10000 0 -0.5 6 6
TNFRSF10C 0.002 0.063 -10000 0 -0.5 8 8
TRAIL/TRAILR1/DAP3/GTP/FADD -0.004 0.034 -10000 0 -0.28 7 7
TRAIL/TRAILR2/FADD -0.003 0.031 -10000 0 -0.29 6 6
cell death -0.002 0.019 -10000 0 -0.19 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.026 0.025 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.01 0 -10000 0 -10000 0 0
CASP8 -0.001 0.039 -10000 0 -0.86 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.003 0.025 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.01 0 -10000 0 -10000 0 0
PTK2 0.01 0 -10000 0 -10000 0 0
CRKL 0.014 0.044 -10000 0 -0.26 12 12
GRB2/SOS1/SHC -0.001 0.019 -10000 0 -0.3 2 2
HRAS 0.01 0 -10000 0 -10000 0 0
IRS1/Crk 0.014 0.044 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/PTP1B -0.007 0.044 -10000 0 -0.28 13 13
AKT1 0.03 0.039 -10000 0 -0.38 1 1
BAD 0.035 0.038 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.044 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.006 0.041 -10000 0 -0.26 12 12
RAF1 0.037 0.037 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.038 -10000 0 -0.44 1 1
YWHAZ 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.007 0.045 -10000 0 -0.29 12 12
PIK3CA 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.03 0.039 -10000 0 -0.38 1 1
GNB2L1 0.01 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.032 0.033 -10000 0 -0.29 1 1
PXN 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.006 0.038 -10000 0 -0.41 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.039 -10000 0 -0.47 1 1
IGF-1R heterotetramer 0.008 0.025 -10000 0 -0.51 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.006 0.041 -10000 0 -0.26 12 12
Crk/p130 Cas/Paxillin -0.006 0.037 -10000 0 -0.41 1 1
IGF1R 0.008 0.025 -10000 0 -0.51 1 1
IGF1 -0.002 0.079 -10000 0 -0.51 12 12
IRS2/Crk 0.019 0.043 -10000 0 -0.33 2 2
PI3K -0.006 0.039 -10000 0 -0.33 2 2
apoptosis -0.037 0.034 0.31 1 -10000 0 1
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD 0.024 0.057 -10000 0 -0.35 11 11
RAF1/14-3-3 E 0.04 0.033 -10000 0 -0.29 1 1
BAD/14-3-3 0.039 0.035 -10000 0 -0.33 1 1
PRKCZ 0.028 0.043 -10000 0 -0.38 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.005 0.028 -10000 0 -0.32 1 1
PTPN1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.019 0.06 -10000 0 -0.36 12 12
BCAR1 0.009 0.022 -10000 0 -0.5 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.007 0.043 -10000 0 -0.36 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0 -10000 0 -10000 0 0
IRS1/NCK2 0.014 0.043 -10000 0 -0.26 12 12
GRB10 0.01 0 -10000 0 -10000 0 0
PTPN11 0.014 0.044 -10000 0 -0.26 12 12
IRS1 0.008 0.047 -10000 0 -0.28 13 13
IRS2 0.014 0.045 -10000 0 -0.26 13 13
IGF-1R heterotetramer/IGF1 -0.009 0.059 -10000 0 -0.37 13 13
GRB2 0.01 0 -10000 0 -10000 0 0
PDPK1 0.024 0.041 -10000 0 -0.41 1 1
YWHAE 0.01 0 -10000 0 -10000 0 0
PRKD1 0.012 0.079 -10000 0 -0.37 11 11
SHC1 0.008 0.032 -10000 0 -0.51 2 2
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.022 -9999 0 -0.5 1 1
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.075 -9999 0 -0.23 43 43
GNAO1 0.004 0.06 -9999 0 -0.51 7 7
S1P/S1P3/G12/G13 -0.001 0.012 -9999 0 -0.27 1 1
AKT1 -0.008 0.034 -9999 0 -0.62 1 1
AKT3 0.021 0.11 -9999 0 -1.1 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.022 -9999 0 -0.5 1 1
GNAI2 0.011 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GNAI1 0.009 0.032 -9999 0 -0.5 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.023 -9999 0 -0.51 1 1
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.013 0.071 -9999 0 -0.47 2 2
MAPK3 0.018 0.067 -9999 0 -0.45 2 2
MAPK1 0.018 0.067 -9999 0 -0.45 2 2
JAK2 0.021 0.068 -9999 0 -0.4 3 3
CXCR4 0.018 0.067 -9999 0 -0.45 2 2
FLT1 0.012 0.003 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.067 -9999 0 -0.45 2 2
S1P/S1P3/Gi 0.013 0.071 -9999 0 -0.48 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.017 0.054 -9999 0 -0.43 2 2
VEGFA 0.012 0.003 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.011 0.068 -9999 0 -0.35 3 3
VEGFR1 homodimer/VEGFA homodimer 0.021 0.006 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.016 0.051 -9999 0 -0.26 14 14
GNAQ 0.009 0.022 -9999 0 -0.5 1 1
GNAZ -0.03 0.14 -9999 0 -0.5 41 41
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.004 0.083 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.008 0.032 -9999 0 -0.5 2 2
Rac1/GTP -0.017 0.054 -9999 0 -0.43 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.007 0.041 -10000 0 -0.25 14 14
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.028 -10000 0 -0.37 3 3
GNB1/GNG2 -0.001 0.019 -10000 0 -0.3 2 2
GNB1 0.01 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 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.006 0.042 -10000 0 -0.28 12 12
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 0.002 0.011 0.074 12 -10000 0 12
GNAL -0.002 0.077 -10000 0 -0.5 12 12
GNG2 0.008 0.032 -10000 0 -0.5 2 2
CRH 0 0.039 -10000 0 -0.51 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.005 0.025 -10000 0 -0.32 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.009 0.023 -9999 0 -0.51 1 1
Caspase 8 (4 units) -0.006 0.039 -9999 0 -0.34 4 4
NEF 0.002 0.018 -9999 0 -10000 0 0
NFKBIA 0.011 0.011 -9999 0 -10000 0 0
BIRC3 0.028 0.059 -9999 0 -0.47 7 7
CYCS 0.035 0.044 -9999 0 -0.3 4 4
RIPK1 0.01 0 -9999 0 -10000 0 0
CD247 0.006 0.06 -9999 0 -0.52 6 6
MAP2K7 0.036 0.037 -9999 0 -0.33 1 1
protein ubiquitination 0.05 0.033 -9999 0 -10000 0 0
CRADD 0.008 0.032 -9999 0 -0.5 2 2
DAXX 0.01 0 -9999 0 -10000 0 0
FAS 0.004 0.055 -9999 0 -0.5 6 6
BID 0.031 0.046 -9999 0 -0.32 4 4
NF-kappa-B/RelA/I kappa B alpha -0.003 0.028 -9999 0 -10000 0 0
TRADD 0.01 0 -9999 0 -10000 0 0
MAP3K5 0.01 0 -9999 0 -10000 0 0
CFLAR 0.01 0 -9999 0 -10000 0 0
FADD 0.01 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.003 0.028 -9999 0 -10000 0 0
MAPK8 0.041 0.035 -9999 0 -0.31 1 1
APAF1 0.01 0 -9999 0 -10000 0 0
TRAF1 0.01 0 -9999 0 -10000 0 0
TRAF2 0.01 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.025 0.048 -9999 0 -0.29 10 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.043 0.038 -9999 0 -10000 0 0
CHUK 0.051 0.034 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.003 0.032 -9999 0 -0.49 1 1
TCRz/NEF -0.007 0.052 -9999 0 -0.35 11 11
TNF -0.009 0.096 -9999 0 -0.5 19 19
FASLG 0.012 0.076 -9999 0 -0.48 11 11
NFKB1 0.011 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.056 -9999 0 -0.29 20 20
CASP6 -0.004 0.035 -9999 0 -0.6 1 1
CASP7 0.06 0.056 -9999 0 -0.48 3 3
RELA 0.011 0.011 -9999 0 -10000 0 0
CASP2 0.01 0 -9999 0 -10000 0 0
CASP3 0.06 0.056 -9999 0 -0.48 3 3
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.016 -9999 0 -0.36 1 1
CASP8 0.009 0.022 -9999 0 -0.5 1 1
CASP9 0.01 0 -9999 0 -10000 0 0
MAP3K14 0.047 0.037 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.007 0.042 -9999 0 -0.48 1 1
BCL2 0.043 0.04 -9999 0 -0.37 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.031 0.028 -9999 0 -0.42 2 2
KLHL20 -0.011 0.034 -9999 0 -0.25 2 2
CYFIP2 0.003 0.059 -9999 0 -0.5 7 7
Rac1/GDP 0.049 0.02 -9999 0 -10000 0 0
ENAH 0.031 0.028 -9999 0 -0.42 2 2
AP1M1 0.01 0 -9999 0 -10000 0 0
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.01 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.024 -9999 0 -0.17 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.002 0.02 -9999 0 -10000 0 0
RAPGEF1 0.041 0.025 -9999 0 -0.35 2 2
CTNND1 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.002 0.027 -9999 0 -0.43 2 2
CRK 0.036 0.027 -9999 0 -0.39 2 2
E-cadherin/gamma catenin/alpha catenin -0.002 0.022 -9999 0 -0.29 3 3
alphaE/beta7 Integrin -0.001 0.016 -9999 0 -0.35 1 1
IQGAP1 0.01 0 -9999 0 -10000 0 0
NCKAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.031 0.028 -9999 0 -0.42 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.009 -9999 0 -10000 0 0
MLLT4 0.01 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.03 0.089 -9999 0 -0.28 54 54
PI3K -0.001 0.011 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.027 -9999 0 -0.36 3 3
TIAM1 0 0.07 -9999 0 -0.5 10 10
E-cadherin(dimer)/Ca2+ -0.001 0.015 -9999 0 -10000 0 0
AKT1 0 0.006 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
RhoA/GDP 0.049 0.02 -9999 0 -10000 0 0
actin cytoskeleton organization -0.008 0.025 -9999 0 -0.18 2 2
CDC42/GDP 0.049 0.02 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.017 -9999 0 -0.23 2 2
ITGB7 0.009 0.022 -9999 0 -0.5 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.001 0.016 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.001 0.015 -9999 0 -0.25 2 2
mol:GDP 0.048 0.022 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.009 0.023 -9999 0 -0.51 1 1
p120 catenin/RhoA/GDP -0.001 0.015 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.018 0.034 -9999 0 -0.21 7 7
NME1 -0.037 0.15 -9999 0 -0.51 47 47
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.031 0.028 -9999 0 -0.42 2 2
regulation of cell-cell adhesion -0.001 0.009 -9999 0 -10000 0 0
WASF2 -0.004 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.012 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.002 0.021 -9999 0 -10000 0 0
CCND1 0.021 0.042 -9999 0 -0.26 7 7
VAV2 0.038 0.04 -9999 0 -0.47 3 3
RAP1/GDP 0 0.013 -9999 0 -10000 0 0
adherens junction assembly 0.031 0.027 -9999 0 -0.4 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.002 0.019 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.001 0.021 -9999 0 -0.34 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.031 0.028 -9999 0 -0.42 2 2
PIK3CA 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.017 0.053 -9999 0 -0.42 2 2
E-cadherin/beta catenin/alpha catenin -0.001 0.018 -9999 0 -0.29 2 2
ITGAE 0.01 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.028 -9999 0 -0.44 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.003 0.034 -9999 0 -0.55 1 1
PDGFB-D/PDGFRB/SLAP -0.009 0.059 -9999 0 -0.38 12 12
PDGFB-D/PDGFRB/APS/CBL -0.001 0.018 -9999 0 -0.29 2 2
AKT1 0.044 0.029 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.023 0.042 -9999 0 -0.59 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
FGR -0.036 0.14 -9999 0 -0.51 39 39
mol:Ca2+ 0.021 0.038 -9999 0 -0.63 1 1
MYC 0.031 0.07 -9999 0 -0.68 3 3
SHC1 0.008 0.032 -9999 0 -0.51 2 2
HRAS/GDP 0.002 0.013 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.006 0.054 -9999 0 -0.4 8 8
GRB10 0.01 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0.021 0.039 -9999 0 -0.65 1 1
PTEN 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
GRB7 0.004 0.055 -9999 0 -0.5 6 6
PDGFB-D/PDGFRB/SHP2 0 0.016 -9999 0 -0.36 1 1
PDGFB-D/PDGFRB/GRB10 0 0.016 -9999 0 -0.36 1 1
cell cycle arrest -0.009 0.059 -9999 0 -0.38 12 12
HRAS 0.01 0 -9999 0 -10000 0 0
HIF1A 0.048 0.027 -9999 0 -10000 0 0
GAB1 0.019 0.049 -9999 0 -0.64 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.023 0.045 -9999 0 -0.57 1 1
PDGFB-D/PDGFRB 0.006 0.018 -9999 0 -0.31 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0.016 -9999 0 -0.36 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.004 0.034 -9999 0 -0.51 1 1
positive regulation of MAPKKK cascade 0 0.016 -9999 0 -0.36 1 1
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
mol:IP3 0.021 0.039 -9999 0 -0.65 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.009 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.004 0.042 -9999 0 -0.36 7 7
SHB 0.009 0.022 -9999 0 -0.5 1 1
BLK -0.015 0.052 -9999 0 -0.47 5 5
PTPN2 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0.016 -9999 0 -0.36 1 1
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
VAV2 0.019 0.066 -9999 0 -0.55 2 2
CBL 0.01 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0.016 -9999 0 -0.36 1 1
LCK 0 0.036 -9999 0 -0.45 3 3
PDGFRB 0.01 0.023 -9999 0 -0.51 1 1
ACP1 0.01 0 -9999 0 -10000 0 0
HCK -0.021 0.12 -9999 0 -0.53 24 24
ABL1 0.017 0.051 -9999 0 -0.6 1 1
PDGFB-D/PDGFRB/CBL 0.017 0.055 -9999 0 -0.73 1 1
PTPN1 0.01 0.001 -9999 0 -10000 0 0
SNX15 0.01 0 -9999 0 -10000 0 0
STAT3 0.01 0 -9999 0 -10000 0 0
STAT1 0.01 0 -9999 0 -10000 0 0
cell proliferation 0.031 0.064 -9999 0 -0.6 3 3
SLA -0.002 0.077 -9999 0 -0.5 12 12
actin cytoskeleton reorganization 0.039 0.02 -9999 0 -10000 0 0
SRC 0.002 0.017 -9999 0 -0.34 1 1
PI3K -0.003 0.026 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.005 0.039 -9999 0 -0.3 9 9
SH2B2 0.009 0.022 -9999 0 -0.5 1 1
PLCgamma1/SPHK1 0.024 0.043 -9999 0 -0.62 1 1
LYN 0.003 0.017 -9999 0 -0.34 1 1
LRP1 0.006 0.045 -9999 0 -0.5 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
STAT5B 0.01 0 -9999 0 -10000 0 0
STAT5A 0.009 0.022 -9999 0 -0.5 1 1
NCK1-2/p130 Cas 0.002 0.017 -9999 0 -10000 0 0
SPHK1 0.005 0.051 -9999 0 -0.5 5 5
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.021 0.039 -9999 0 -0.65 1 1
PLCG1 0.021 0.04 -9999 0 -0.67 1 1
NHERF/PDGFRB -0.005 0.036 -9999 0 -0.29 8 8
YES1 0.003 0.017 -9999 0 -0.34 1 1
cell migration -0.005 0.036 -9999 0 -0.29 8 8
SHC/Grb2/SOS1 0.001 0.02 -9999 0 -10000 0 0
SLC9A3R2 0.005 0.05 -9999 0 -0.5 5 5
SLC9A3R1 0.008 0.032 -9999 0 -0.51 2 2
NHERF1-2/PDGFRB/PTEN -0.004 0.032 -9999 0 -10000 0 0
FYN 0.002 0.028 -9999 0 -0.43 2 2
DOK1 0.026 0.013 -9999 0 -10000 0 0
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.004 0.055 -9999 0 -0.5 6 6
RAC1 0.028 0.066 -9999 0 -0.53 3 3
PRKCD 0.026 0.013 -9999 0 -10000 0 0
FER 0.026 0.013 -9999 0 -0.27 1 1
MAPKKK cascade -0.001 0.017 -9999 0 -10000 0 0
RASA1 0.026 0.013 -9999 0 -0.27 1 1
NCK1 0.01 0 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
p62DOK/Csk 0.008 0.017 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.022 -9999 0 -0.36 2 2
chemotaxis 0.017 0.049 -9999 0 -0.58 1 1
STAT1-3-5/STAT1-3-5 -0.001 0.013 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0.016 -9999 0 -0.37 1 1
PTPRJ 0.01 0 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.066 0.012 -9999 0 -10000 0 0
ERC1 0.01 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.001 0.016 -9999 0 -0.35 1 1
NFKBIA 0.036 0 -9999 0 -10000 0 0
BIRC2 0.01 0 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
RIPK2 0.01 0 -9999 0 -10000 0 0
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.007 0.036 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
NEMO/ATM 0.039 0.009 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.009 0.023 -9999 0 -0.51 1 1
Exportin 1/RanGTP -0.001 0.013 -9999 0 -0.3 1 1
IKK complex/ELKS 0 0.006 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.009 0.022 -9999 0 -0.5 1 1
NFKB1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
MALT1 0.01 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.01 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.013 0.067 -9999 0 -0.35 19 19
TRAF6 0.01 0 -9999 0 -10000 0 0
PRKCA 0.008 0.032 -9999 0 -0.5 2 2
CHUK 0.01 0 -9999 0 -10000 0 0
UBE2D3 0.01 0 -9999 0 -10000 0 0
TNF -0.009 0.096 -9999 0 -0.5 19 19
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.01 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
IKK complex 0 0.007 -9999 0 -10000 0 0
CYLD 0.01 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.001 0.013 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.01 0 -9999 0 -10000 0 0
ITGB7 0.009 0.022 -9999 0 -0.5 1 1
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
alpha4/beta1 Integrin -0.001 0.022 -9999 0 -0.35 2 2
EPO 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
BCL2L1 0.059 0.031 -10000 0 -10000 0 0
CRKL 0.034 0.033 -10000 0 -0.43 1 1
mol:DAG 0.039 0.026 -10000 0 -0.31 1 1
HRAS 0.05 0.038 -10000 0 -0.54 1 1
MAPK8 0.027 0.025 -10000 0 -0.28 1 1
RAP1A 0.034 0.033 -10000 0 -0.43 1 1
GAB1 0.033 0.042 -10000 0 -0.67 1 1
MAPK14 0.027 0.025 -10000 0 -0.28 1 1
EPO 0.005 0.046 -10000 0 -0.51 4 4
PLCG1 0.04 0.026 -10000 0 -0.31 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.003 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.005 0.037 -10000 0 -0.3 8 8
GAB1/SHC/GRB2/SOS1 -0.004 0.034 -10000 0 -0.58 1 1
EPO/EPOR (dimer) 0.014 0.034 -10000 0 -0.36 4 4
IRS2 0.034 0.037 -10000 0 -0.43 2 2
STAT1 0.047 0.029 -10000 0 -0.31 1 1
STAT5B 0.044 0.028 -10000 0 -0.31 1 1
cell proliferation 0.032 0.023 -10000 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.037 -10000 0 -0.46 2 2
TEC 0.034 0.033 -10000 0 -0.43 1 1
SOCS3 0.006 0.045 -10000 0 -0.5 4 4
STAT1 (dimer) 0.047 0.028 -10000 0 -0.3 1 1
JAK2 0.009 0.033 -10000 0 -0.51 2 2
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2 0.039 0.035 -10000 0 -0.46 1 1
EPO/EPOR 0.014 0.034 -10000 0 -0.36 4 4
LYN 0.011 0.001 -10000 0 -10000 0 0
TEC/VAV2 0.04 0.034 -10000 0 -0.41 1 1
elevation of cytosolic calcium ion concentration 0.012 0.003 -10000 0 -10000 0 0
SHC1 0.008 0.032 -10000 0 -0.51 2 2
EPO/EPOR (dimer)/LYN 0.025 0.028 -10000 0 -0.29 4 4
mol:IP3 0.039 0.026 -10000 0 -0.31 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.005 0.036 -10000 0 -0.4 3 3
SH2B3 0.009 0.032 -10000 0 -0.5 2 2
NFKB1 0.027 0.025 -10000 0 -0.28 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.034 0.24 2 -0.34 2 4
PTPN6 0.029 0.034 -10000 0 -0.45 1 1
TEC/VAV2/GRB2 0.043 0.033 -10000 0 -0.4 1 1
EPOR 0.012 0.003 -10000 0 -10000 0 0
INPP5D 0.007 0.039 -10000 0 -0.5 3 3
mol:GDP -0.004 0.034 -10000 0 -0.59 1 1
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG2 0.007 0.039 -10000 0 -0.5 3 3
CRKL/CBL/C3G 0.043 0.031 -10000 0 -0.4 1 1
VAV2 0.034 0.034 -10000 0 -0.43 1 1
CBL 0.034 0.033 -10000 0 -0.43 1 1
SHC/Grb2/SOS1 -0.004 0.028 -10000 0 -0.4 1 1
STAT5A 0.043 0.035 -10000 0 -0.4 2 2
GRB2 0.01 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.057 0.039 -10000 0 -0.39 2 2
LYN/PLCgamma2 -0.002 0.027 -10000 0 -0.35 3 3
PTPN11 0.01 0 -10000 0 -10000 0 0
BTK 0.017 0.079 -10000 0 -0.46 5 5
BCL2 0.058 0.05 -10000 0 -0.81 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.022 0.026 -9999 0 -0.34 2 2
CRKL 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.01 0 -9999 0 -10000 0 0
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.005 0.036 -9999 0 -10000 0 0
EPO 0.002 0.045 -9999 0 -0.51 4 4
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.022 -9999 0 -0.35 2 2
EPO/EPOR (dimer) -0.003 0.032 -9999 0 -0.36 4 4
lamellipodium assembly 0 0.012 -9999 0 -0.25 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
JAK2 0.004 0.036 -9999 0 -0.43 2 2
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
MADCAM1 0.002 0.06 -9999 0 -0.51 7 7
cell adhesion -0.005 0.036 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.01 0 -9999 0 -10000 0 0
SRC 0.023 0.03 -9999 0 -10000 0 0
ITGB7 0.009 0.022 -9999 0 -0.5 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.003 0.031 -9999 0 -0.29 6 6
p130Cas/Crk/Dock1 0.037 0.028 -9999 0 -10000 0 0
VCAM1 0.006 0.045 -9999 0 -0.5 4 4
RHOA 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.016 -9999 0 -10000 0 0
BCAR1 0.028 0.031 -9999 0 -10000 0 0
EPOR 0.01 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.012 -9999 0 -0.26 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.033 0.041 -10000 0 -10000 0 0
BAG4 0.009 0.023 -10000 0 -0.51 1 1
BAD 0.023 0.017 -10000 0 -10000 0 0
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 0.003 0.06 -10000 0 -0.51 7 7
BAX 0.023 0.017 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.013 -10000 0 -10000 0 0
IKBKB 0.038 0.04 -10000 0 -10000 0 0
MAP2K2 0.032 0.02 -10000 0 -10000 0 0
MAP2K1 0.032 0.02 -10000 0 -10000 0 0
SMPD1 0.015 0.013 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.038 0.042 -10000 0 -0.29 1 1
MAP2K4 0.028 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.039 0.04 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.036 0.023 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.029 0.02 -10000 0 -10000 0 0
CRADD 0.008 0.032 -10000 0 -0.5 2 2
mol:ceramide 0.018 0.018 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.01 0 -10000 0 -10000 0 0
MAP3K1 0.024 0.018 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
RELA/p50 0.01 0 -10000 0 -10000 0 0
MAPK3 0.034 0.02 -10000 0 -10000 0 0
MAPK1 0.034 0.02 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.033 0.041 -10000 0 -10000 0 0
KSR1 0.024 0.019 -10000 0 -10000 0 0
MAPK8 0.033 0.017 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.038 0.04 -10000 0 -10000 0 0
TNF R/SODD -0.001 0.016 -10000 0 -0.36 1 1
TNF -0.009 0.096 -10000 0 -0.5 19 19
CYCS 0.025 0.018 0.13 1 -10000 0 1
IKBKG 0.038 0.04 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.043 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AIFM1 0.025 0.018 0.13 1 -10000 0 1
TNF/TNF R/SODD -0.011 0.056 -10000 0 -0.29 20 20
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.021 0.033 -10000 0 -0.68 1 1
NSMAF 0.033 0.041 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0.007 0.039 -10000 0 -0.5 3 3
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.002 0.022 -9999 0 -0.29 3 3
E-cadherin/beta catenin -0.001 0.022 -9999 0 -0.35 2 2
CTNNB1 0.01 0 -9999 0 -10000 0 0
JUP 0.009 0.023 -9999 0 -0.51 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD2 0.011 0 -9999 0 -10000 0 0
SMAD3 0.033 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.036 0.008 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.003 0.027 -9999 0 -10000 0 0
PPM1A 0.01 0 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.01 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.022 -9999 0 -0.35 2 2
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0.01 0 -9999 0 -10000 0 0
NUP214 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.01 0 -9999 0 -10000 0 0
CTDSP2 0.01 0 -9999 0 -10000 0 0
CTDSPL 0.01 0 -9999 0 -10000 0 0
KPNB1 0.01 0 -9999 0 -10000 0 0
TGFBRAP1 0.008 0.032 -9999 0 -0.5 2 2
UBE2I 0.01 0 -9999 0 -10000 0 0
NUP153 0.01 0 -9999 0 -10000 0 0
KPNA2 0.002 0.064 -9999 0 -0.51 8 8
PIAS4 0.01 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.003 0.027 -10000 0 -0.29 3 3
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
AKT2 0.01 0 -10000 0 -10000 0 0
STXBP4 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.032 0.036 0.2 1 -0.32 3 4
YWHAZ 0.01 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.018 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
ASIP 0.005 0.023 -10000 0 -0.51 1 1
PRKCI 0.01 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.01 0 -10000 0 -10000 0 0
GYS1 0.025 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.039 -10000 0 -0.5 3 3
TRIP10 0.01 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.034 0.018 -10000 0 -10000 0 0
VAMP2 0.01 0 -10000 0 -10000 0 0
SLC2A4 0.032 0.039 0.21 1 -0.36 3 4
STX4 0.01 0 -10000 0 -10000 0 0
GSK3B 0.02 0 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.51 10 10
LNPEP 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
mTOR signaling pathway

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.01 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.016 -10000 0 -0.25 2 2
FRAP1 0.012 0.005 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -0.22 2 2
INSR 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.004 -10000 0 -10000 0 0
TSC2 0.01 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.013 -10000 0 -10000 0 0
TSC1 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.012 0.015 -10000 0 -0.32 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.009 -10000 0 -10000 0 0
MAP3K5 0.008 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.022 -10000 0 -0.5 1 1
apoptosis 0.008 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.026 0.009 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0.006 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.002 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.018 -10000 0 -0.26 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.009 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.013 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.001 0.014 -10000 0 -0.23 2 2
EIF4E 0.01 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.003 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.013 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.012 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.01 0 -10000 0 -10000 0 0
PPP5C 0.01 0 -10000 0 -10000 0 0
EIF4G1 0.01 0 -10000 0 -10000 0 0
IRS1 0.006 0.016 -10000 0 -0.35 1 1
INS 0 0 -10000 0 -10000 0 0
PTEN 0.009 0 -10000 0 -10000 0 0
PDK2 -0.001 0.014 -10000 0 -0.23 2 2
EIF4EBP1 0.007 0.01 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
PPP2R5D 0.017 0.005 -10000 0 -10000 0 0
peptide biosynthetic process 0.013 0 -10000 0 -10000 0 0
RHEB 0.009 0.023 -10000 0 -0.51 1 1
EIF4A1 0.01 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.013 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.013 0.009 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.029 0 -9999 0 -10000 0 0
CDKN1A 0.029 0.011 -9999 0 -0.22 1 1
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.01 0 -9999 0 -10000 0 0
FOXO3 0.029 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.01 0 -9999 0 -10000 0 0
AKT3 0.011 0.029 -9999 0 -0.31 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.029 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.01 0 -9999 0 -10000 0 0
RAF1 0.01 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.029 0 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
AKT1/RAF1 0.029 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.029 0 -9999 0 -10000 0 0
YWHAQ 0.01 0 -9999 0 -10000 0 0
TBC1D4 0.019 0 -9999 0 -10000 0 0
MAP3K5 0.01 0 -9999 0 -10000 0 0
MAPKAP1 0.01 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.033 0.012 -9999 0 -10000 0 0
YWHAH 0.01 0 -9999 0 -10000 0 0
AKT1S1 0.029 0 -9999 0 -10000 0 0
CASP9 0.029 0 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.034 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0.009 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.003 -9999 0 -10000 0 0
CHUK 0.029 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.039 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.045 0.013 -9999 0 -10000 0 0
PDPK1 0.01 0 -9999 0 -10000 0 0
MDM2 0.028 0.016 -9999 0 -0.23 2 2
MAPKKK cascade -0.028 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.037 0.015 -9999 0 -10000 0 0
TSC1/TSC2 0.034 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.012 -9999 0 -10000 0 0
glucose import 0.021 0.027 -9999 0 -0.26 5 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.003 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.021 0.028 -9999 0 -0.26 5 5
GSK3A 0.029 0 -9999 0 -10000 0 0
FOXO1 0.029 0.011 -9999 0 -0.22 1 1
GSK3B 0.029 0 -9999 0 -10000 0 0
SFN 0 0.071 -9999 0 -0.51 10 10
G1/S transition of mitotic cell cycle 0.034 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.036 0.016 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
KPNA1 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
YWHAG 0.01 0 -9999 0 -10000 0 0
RHEB 0.009 0.023 -9999 0 -0.51 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0.01 0 -9999 0 -10000 0 0
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.018 -9999 0 -0.29 2 2
alpha4/beta7 Integrin/Paxillin -0.002 0.02 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.018 -9999 0 -0.34 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
TLN1 0.009 0.022 -9999 0 -0.5 1 1
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
ARF6/GTP -0.001 0.013 -9999 0 -10000 0 0
cell adhesion -0.001 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.016 -9999 0 -10000 0 0
ITGB1 0.01 0 -9999 0 -10000 0 0
ITGB7 0.009 0.022 -9999 0 -0.5 1 1
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.025 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 -0.001 0.013 -9999 0 -0.29 1 1
VCAM1 0.006 0.045 -9999 0 -0.5 4 4
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.015 -9999 0 -10000 0 0
BCAR1 0.009 0.022 -9999 0 -0.5 1 1
mol:GDP 0.001 0.015 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.018 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.02 -9999 0 -0.38 1 1
Atypical NF-kappaB pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.016 -9999 0 -0.35 1 1
FBXW11 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.019 -9999 0 -10000 0 0
NFKBIA 0.021 0.022 -9999 0 -0.2 5 5
MAPK14 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0 -9999 0 -10000 0 0
ARRB2 0.013 0 -9999 0 -10000 0 0
REL 0.01 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.014 -9999 0 -0.29 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
NFKB1 0.018 0 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.026 0.022 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.038 0.019 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
NF kappa B1 p50/RelA 0.026 0.022 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
SYK 0.007 0.039 -9999 0 -0.5 3 3
I kappa B alpha/PIK3R1 0.024 0.024 -9999 0 -0.23 1 1
cell death -0.002 0.014 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.021 0 -9999 0 -10000 0 0
LCK 0.007 0.039 -9999 0 -0.5 3 3
BCL3 0.009 0.022 -9999 0 -0.5 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.012 -9999 0 -10000 0 0
MDM2/SUMO1 0.022 0.016 -9999 0 -0.24 2 2
HDAC4 0.009 0.023 -9999 0 -0.51 1 1
Ran/GTP/Exportin 1/HDAC1 0 0.009 -9999 0 -10000 0 0
SUMO1 0.01 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.022 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.009 0.023 -9999 0 -0.51 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.023 0.012 -9999 0 -0.24 1 1
SUMO1/HDAC1 0.023 0 -9999 0 -10000 0 0
RANGAP1 0.01 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.016 -9999 0 -0.26 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -10000 0 0
Ran/GTP 0 0.01 -9999 0 -0.24 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.032 -9999 0 -0.51 2 2
UBE2I 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0.01 -9999 0 -0.22 1 1
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.038 0.016 -9999 0 -10000 0 0
adherens junction organization 0.031 0.025 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.035 0.043 -9999 0 -10000 0 0
FMN1 0.024 0.05 -9999 0 -10000 0 0
mol:IP3 -0.001 0.012 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.018 -9999 0 -10000 0 0
CTNNB1 0.009 0.001 -9999 0 -10000 0 0
AKT1 0.037 0.016 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.027 -9999 0 -0.36 2 2
CTNND1 0.011 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.017 -9999 0 -10000 0 0
VASP 0.033 0.017 -9999 0 -10000 0 0
ZYX 0.033 0.02 -9999 0 -10000 0 0
JUB 0.033 0.023 -9999 0 -10000 0 0
EGFR(dimer) 0.025 0.048 -9999 0 -0.32 1 1
E-cadherin/beta catenin-gamma catenin -0.002 0.022 -9999 0 -0.28 3 3
mol:PI-3-4-5-P3 -0.001 0.014 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.014 -9999 0 -10000 0 0
FYN 0.021 0.062 -9999 0 -0.28 1 1
mol:Ca2+ -0.001 0.012 -9999 0 -10000 0 0
JUP 0.008 0.023 -9999 0 -0.51 1 1
PIK3R1 0.009 0.022 -9999 0 -0.5 1 1
mol:DAG -0.001 0.012 -9999 0 -10000 0 0
CDH1 0.007 0.032 -9999 0 -0.5 2 2
RhoA/GDP 0.035 0.043 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.033 0.017 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
EGFR -0.006 0.089 -9999 0 -0.5 16 16
CASR 0.011 0.075 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.011 -9999 0 -10000 0 0
AKT2 0.037 0.016 -9999 0 -10000 0 0
actin cable formation 0.029 0.049 -9999 0 -10000 0 0
apoptosis 0.001 0.013 -9999 0 -10000 0 0
CTNNA1 0.011 0.001 -9999 0 -10000 0 0
mol:GDP 0.031 0.046 -9999 0 -0.29 1 1
PIP5K1A 0.033 0.017 -9999 0 -10000 0 0
PLCG1 -0.001 0.012 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.038 -9999 0 -0.29 1 1
homophilic cell adhesion 0.001 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 0.016 0 -9999 0 -10000 0 0
AP2 0 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 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0 -9999 0 -10000 0 0
CD4 0 0.07 -9999 0 -0.5 10 10
CLTA 0.01 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 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 0.022 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 0.01 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.01 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 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 0.024 0.031 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 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 0.009 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 -0.006 0.04 -9999 0 -0.29 10 10
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 0 -9999 0 -9999 0 0
FBXW11 0.01 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 0.01 0 -9999 0 -9999 0 0
CHUK 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.01 0 -9999 0 -9999 0 0
MAP3K14 0.01 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -9999 0 0
RELB 0.01 0 -9999 0 -9999 0 0
NFKB2 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 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 515 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.S2.AA1A TCGA.O1.A52J TCGA.NJ.A7XG TCGA.NJ.A55R
109_MAP3K5 0.043 0.043 -0.15 0.043
47_PPARGC1A 0.0097 0.0097 -0.5 0.0097
105_BMP4 0.0097 0.0097 0.0097 0.0097
105_BMP6 0.0097 -0.5 -0.5 0.0097
105_BMP7 -0.51 0.0097 0.0097 0.0097
105_BMP2 0.0097 0.0097 0.0097 0.0097
131_RELN/VLDLR 0 -0.26 -0.26 0
30_TGFB1/TGF beta receptor Type II 0.0093 0.0092 0.0092 0.013
84_STAT5B 0.035 0.035 -0.057 0.037
84_STAT5A 0.035 0.035 -0.057 0.037
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/LUAD-TP/19438942/LUAD-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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