PARADIGM pathway analysis of mRNA expression data
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1NP22XJ
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1NP22XJ
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 54 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
Signaling events mediated by Stem cell factor receptor (c-Kit) 241
Signaling mediated by p38-alpha and p38-beta 227
Endothelins 162
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 159
EGFR-dependent Endothelin signaling events 141
Class IB PI3K non-lipid kinase events 137
IGF1 pathway 135
Arf6 signaling events 131
Nongenotropic Androgen signaling 103
HIF-1-alpha transcription factor network 98
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 526 . 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 ( 526 ).

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
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.4582 241 18810 78 -1.1 0.35 1000 -1000 -0.052 -1000
Signaling mediated by p38-alpha and p38-beta 0.4316 227 10030 44 -0.73 0.016 1000 -1000 -0.041 -1000
Endothelins 0.3080 162 15577 96 -0.83 0.03 1000 -1000 -0.047 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.3023 159 10868 68 -1 0.47 1000 -1000 -0.069 -1000
EGFR-dependent Endothelin signaling events 0.2681 141 2964 21 -0.45 0.016 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.2605 137 411 3 -0.18 -1000 1000 -1000 -0.007 -1000
IGF1 pathway 0.2567 135 7741 57 -0.37 0.15 1000 -1000 -0.063 -1000
Arf6 signaling events 0.2490 131 8158 62 -0.45 0.018 1000 -1000 -0.039 -1000
Nongenotropic Androgen signaling 0.1958 103 5381 52 -0.59 0.28 1000 -1000 -0.04 -1000
HIF-1-alpha transcription factor network 0.1863 98 7494 76 -0.51 0.054 1000 -1000 -0.039 -1000
Signaling events mediated by PTP1B 0.1844 97 7424 76 -0.48 0.21 1000 -1000 -0.058 -1000
Calcium signaling in the CD4+ TCR pathway 0.1844 97 3024 31 -0.54 0.026 1000 -1000 -0.054 -1000
S1P1 pathway 0.1806 95 3428 36 -0.67 0.016 1000 -1000 -0.053 -1000
FOXM1 transcription factor network 0.1768 93 4789 51 -0.84 0.017 1000 -1000 -0.084 -1000
Glucocorticoid receptor regulatory network 0.1692 89 10248 114 -1.2 0.3 1000 -1000 -0.056 -1000
Ras signaling in the CD4+ TCR pathway 0.1445 76 1308 17 -0.23 0.013 1000 -1000 -0.032 -1000
PDGFR-alpha signaling pathway 0.1426 75 3316 44 -0.84 0.046 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.1350 71 3438 48 -0.26 0.14 1000 -1000 -0.044 -1000
IL6-mediated signaling events 0.1350 71 5391 75 -0.52 0.052 1000 -1000 -0.047 -1000
BMP receptor signaling 0.1331 70 5721 81 -0.6 0.04 1000 -1000 -0.064 -1000
FAS signaling pathway (CD95) 0.1331 70 3303 47 -0.97 0.072 1000 -1000 -0.035 -1000
Fc-epsilon receptor I signaling in mast cells 0.1217 64 6256 97 -0.51 0.039 1000 -1000 -0.061 -1000
IL23-mediated signaling events 0.1141 60 3620 60 -0.93 0.019 1000 -1000 -0.099 -1000
Integrins in angiogenesis 0.1084 57 4843 84 -0.57 0.053 1000 -1000 -0.068 -1000
Plasma membrane estrogen receptor signaling 0.1084 57 4946 86 -0.35 0.16 1000 -1000 -0.064 -1000
Signaling events mediated by PRL 0.1065 56 1927 34 -0.44 0.025 1000 -1000 -0.036 -1000
IL4-mediated signaling events 0.1046 55 5061 91 -0.63 0.23 1000 -1000 -0.15 -1000
E-cadherin signaling in keratinocytes 0.1008 53 2313 43 -0.38 0.044 1000 -1000 -0.049 -1000
p75(NTR)-mediated signaling 0.0913 48 6010 125 -0.25 0.016 1000 -1000 -0.064 -1000
Glypican 1 network 0.0913 48 2348 48 -0.55 0.061 1000 -1000 -0.037 -1000
Nectin adhesion pathway 0.0798 42 2702 63 -0.1 0.016 1000 -1000 -0.057 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0798 42 3148 74 -0.38 0.08 1000 -1000 -0.072 -1000
ErbB4 signaling events 0.0779 41 2830 69 -0.5 0.12 1000 -1000 -0.06 -1000
Signaling events regulated by Ret tyrosine kinase 0.0760 40 3290 82 -0.18 0.018 1000 -1000 -0.065 -1000
Insulin Pathway 0.0760 40 2962 74 -0.39 0.046 1000 -1000 -0.068 -1000
Visual signal transduction: Rods 0.0760 40 2094 52 -0.58 0.029 1000 -1000 -0.056 -1000
EPHB forward signaling 0.0741 39 3337 85 -0.26 0.12 1000 -1000 -0.068 -1000
ErbB2/ErbB3 signaling events 0.0703 37 2448 65 -0.48 0.03 1000 -1000 -0.049 -1000
Presenilin action in Notch and Wnt signaling 0.0684 36 2209 61 -0.53 0.04 1000 -1000 -0.049 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0665 35 3050 85 -0.54 0.035 1000 -1000 -0.062 -1000
Signaling events mediated by the Hedgehog family 0.0646 34 1798 52 -0.22 0.14 1000 -1000 -0.062 -1000
S1P5 pathway 0.0646 34 587 17 -0.25 0.078 1000 -1000 -0.028 -1000
TCGA08_retinoblastoma 0.0646 34 277 8 -0.043 0.021 1000 -1000 -0.008 -1000
Syndecan-3-mediated signaling events 0.0589 31 1097 35 -0.51 0.016 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0589 31 3833 120 -0.42 0.18 1000 -1000 -0.05 -1000
S1P4 pathway 0.0589 31 786 25 -0.25 0.03 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 0.0570 30 802 26 -0.38 0.028 1000 -1000 -0.015 -1000
Syndecan-2-mediated signaling events 0.0551 29 2002 69 -0.46 0.046 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.0532 28 2900 102 -0.51 0.045 1000 -1000 -0.052 -1000
S1P3 pathway 0.0532 28 1217 42 -0.25 0.041 1000 -1000 -0.032 -1000
Regulation of nuclear SMAD2/3 signaling 0.0513 27 3749 136 -0.52 0.065 1000 -1000 -0.042 -1000
Ceramide signaling pathway 0.0513 27 2113 76 -0.35 0.098 1000 -1000 -0.041 -1000
Reelin signaling pathway 0.0513 27 1526 56 -0.1 0.044 1000 -1000 -0.054 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0513 27 1443 52 -0.53 0.089 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.0494 26 1207 46 -0.84 0.075 1000 -1000 -0.02 -1000
IL27-mediated signaling events 0.0494 26 1353 51 -0.52 0.04 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0475 25 710 28 -0.25 0.03 1000 -1000 -0.033 -1000
amb2 Integrin signaling 0.0456 24 2043 82 -0.62 0.049 1000 -1000 -0.053 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0456 24 2164 88 -0.55 0.068 1000 -1000 -0.071 -1000
mTOR signaling pathway 0.0437 23 1256 53 -0.072 0.042 1000 -1000 -0.052 -1000
Wnt signaling 0.0437 23 164 7 -0.029 0.012 1000 -1000 -0.019 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0418 22 2850 125 -0.52 0.059 1000 -1000 -0.081 -1000
E-cadherin signaling events 0.0418 22 113 5 -0.039 0.014 1000 -1000 -0.029 -1000
Thromboxane A2 receptor signaling 0.0399 21 2244 105 -0.38 0.098 1000 -1000 -0.056 -1000
IL1-mediated signaling events 0.0399 21 1319 62 -0.12 0.082 1000 -1000 -0.065 -1000
Canonical Wnt signaling pathway 0.0399 21 1073 51 -0.53 0.2 1000 -1000 -0.04 -1000
Regulation of Telomerase 0.0399 21 2213 102 -0.51 0.067 1000 -1000 -0.078 -1000
Aurora B signaling 0.0399 21 1443 67 -0.52 0.077 1000 -1000 -0.055 -1000
IL12-mediated signaling events 0.0380 20 1818 87 -0.88 0.027 1000 -1000 -0.073 -1000
Osteopontin-mediated events 0.0380 20 791 38 -0.51 0.062 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0380 20 1455 70 -0.6 0.061 1000 -1000 -0.048 -1000
Coregulation of Androgen receptor activity 0.0361 19 1509 76 -0.25 0.026 1000 -1000 -0.034 -1000
Insulin-mediated glucose transport 0.0361 19 608 32 -0.11 0.049 1000 -1000 -0.044 -1000
Regulation of p38-alpha and p38-beta 0.0361 19 1075 54 -0.43 0.051 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.0323 17 1184 67 -0.55 0.05 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 0.0304 16 1191 74 -0.22 0.074 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0.0285 15 46 3 -0.019 -0.009 1000 -1000 -0.008 -1000
Noncanonical Wnt signaling pathway 0.0285 15 409 26 -0.042 0.032 1000 -1000 -0.055 -1000
Hedgehog signaling events mediated by Gli proteins 0.0285 15 1014 65 -0.25 0.08 1000 -1000 -0.058 -1000
IL2 signaling events mediated by PI3K 0.0266 14 851 58 -0.11 0.04 1000 -1000 -0.065 -1000
E-cadherin signaling in the nascent adherens junction 0.0266 14 1129 76 -0.055 0.046 1000 -1000 -0.066 -1000
Arf6 trafficking events 0.0266 14 1035 71 -0.41 0.054 1000 -1000 -0.055 -1000
BCR signaling pathway 0.0266 14 1405 99 -0.24 0.076 1000 -1000 -0.066 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0247 13 618 45 -0.049 0.07 1000 -1000 -0.062 -1000
Class I PI3K signaling events mediated by Akt 0.0228 12 845 68 -0.24 0.069 1000 -1000 -0.046 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0190 10 586 54 -0.1 0.044 1000 -1000 -0.073 -1000
JNK signaling in the CD4+ TCR pathway 0.0190 10 177 17 -0.083 0.057 1000 -1000 -0.04 -1000
EPO signaling pathway 0.0190 10 591 55 -0.13 0.064 1000 -1000 -0.057 -1000
TRAIL signaling pathway 0.0190 10 526 48 -0.024 0.047 1000 -1000 -0.054 -1000
VEGFR1 specific signals 0.0190 10 564 56 -0.52 0.071 1000 -1000 -0.054 -1000
Cellular roles of Anthrax toxin 0.0171 9 372 39 -0.14 0.023 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class III 0.0171 9 385 40 -0.1 0.029 1000 -1000 -0.025 -1000
FoxO family signaling 0.0171 9 605 64 -0.027 0.11 1000 -1000 -0.032 -1000
Signaling mediated by p38-gamma and p38-delta 0.0171 9 138 15 0 0.03 1000 -1000 -0.013 -1000
Signaling events mediated by HDAC Class II 0.0152 8 602 75 -0.18 0.043 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0152 8 491 58 -0.1 0.042 1000 -1000 -0.054 -1000
Syndecan-1-mediated signaling events 0.0133 7 263 34 -0.1 0.016 1000 -1000 -0.054 -1000
IFN-gamma pathway 0.0133 7 506 68 -0.055 0.086 1000 -1000 -0.063 -1000
TCR signaling in naïve CD8+ T cells 0.0133 7 690 93 -0.083 0.089 1000 -1000 -0.05 -1000
Visual signal transduction: Cones 0.0114 6 231 38 -0.03 0.026 1000 -1000 -0.044 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0114 6 254 37 -0.055 0.051 1000 -1000 -0.036 -1000
ceramide signaling pathway 0.0114 6 336 49 -0.13 0.06 1000 -1000 -0.033 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0114 6 555 83 -0.13 0.066 1000 -1000 -0.057 -1000
Paxillin-dependent events mediated by a4b1 0.0114 6 236 36 -0.055 0.029 1000 -1000 -0.05 -1000
p38 MAPK signaling pathway 0.0114 6 305 44 -0.036 0.039 1000 -1000 -0.052 -1000
HIF-2-alpha transcription factor network 0.0095 5 244 43 -0.21 0.22 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 0.0076 4 154 31 -0.055 0.063 1000 -1000 -0.034 -1000
IL2 signaling events mediated by STAT5 0.0076 4 92 22 -0.054 0.087 1000 -1000 -0.019 -1000
Class I PI3K signaling events 0.0076 4 294 73 -0.027 0.089 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0076 4 455 97 -0.19 0.045 1000 -1000 -0.069 -1000
Aurora A signaling 0.0057 3 208 60 -0.087 0.047 1000 -1000 -0.045 -1000
Arf6 downstream pathway 0.0057 3 132 43 -0.039 0.04 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 0.0057 3 412 104 -0.24 0.074 1000 -1000 -0.052 -1000
LPA4-mediated signaling events 0.0019 1 13 12 0 0.042 1000 -1000 -0.007 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0019 1 40 34 -0.004 0.057 1000 -1000 -0.042 -1000
Ephrin A reverse signaling 0.0019 1 7 7 0 0.03 1000 -1000 -0.02 -1000
Effects of Botulinum toxin 0.0019 1 29 26 -0.046 0.024 1000 -1000 -0.038 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 18 23 -0.029 0.063 1000 -1000 -0.046 -1000
Canonical NF-kappaB pathway 0.0000 0 4 39 -0.018 0.11 1000 -1000 -0.06 -1000
BARD1 signaling events 0.0000 0 12 57 -0.078 0.052 1000 -1000 -0.044 -1000
Circadian rhythm pathway 0.0000 0 13 22 -0.053 0.065 1000 -1000 -0.053 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 -0.003 0.016 1000 -1000 -0.036 -1000
Aurora C signaling 0.0000 0 1 7 -0.014 0.021 1000 -1000 -0.028 -1000
PLK1 signaling events 0.0000 0 45 85 -0.09 0.067 1000 -1000 -0.033 -1000
TCGA08_p53 0.0000 0 0 7 -0.004 0.015 1000 -1000 -0.012 -1000
Glypican 2 network 0.0000 0 0 4 -0.007 -1000 1000 -1000 -0.02 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.042 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0000 0 18 33 -0.017 0.05 1000 -1000 -0.048 -1000
Rapid glucocorticoid signaling 0.0000 0 16 20 -0.003 0.016 1000 -1000 -0.024 -1000
Arf1 pathway 0.0000 0 6 54 -0.001 0.045 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 -0.002 0.016 1000 -1000 -0.046 -1000
Total NA 4535 276112 7203 -41 -2000 131000 -131000 -6.3 -131000
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.3 0.16 -10000 0 -0.39 414 414
CRKL -0.33 0.18 -10000 0 -0.42 414 414
HRAS -0.25 0.15 -10000 0 -0.38 28 28
mol:PIP3 -0.33 0.18 -10000 0 -0.42 411 411
SPRED1 0.013 0.045 -10000 0 -0.72 2 2
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.36 0.18 -10000 0 -0.45 415 415
FOXO3 -0.3 0.16 -10000 0 -0.38 413 413
AKT1 -0.33 0.18 -10000 0 -0.41 414 414
BAD -0.3 0.16 -10000 0 -0.38 413 413
megakaryocyte differentiation -0.35 0.18 -10000 0 -0.44 414 414
GSK3B -0.3 0.16 -10000 0 -0.38 413 413
RAF1 -0.2 0.13 -10000 0 -0.36 5 5
SHC1 0.016 0 -10000 0 -10000 0 0
STAT3 -0.36 0.18 -10000 0 -0.44 414 414
STAT1 -0.87 0.45 -10000 0 -1 442 442
HRAS/SPRED1 -0.21 0.11 -10000 0 -0.42 6 6
cell proliferation -0.35 0.18 -10000 0 -0.44 414 414
PIK3CA 0.015 0.007 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.35 0.18 -10000 0 -0.44 414 414
HRAS/SPRED2 -0.21 0.1 -10000 0 -0.31 16 16
LYN/TEC/p62DOK -0.33 0.16 -10000 0 -0.41 413 413
MAPK3 -0.14 0.098 -10000 0 -0.29 2 2
STAP1 -0.36 0.18 -10000 0 -0.45 419 419
GRAP2 0.014 0.019 -10000 0 -10000 0 0
JAK2 -0.72 0.34 -10000 0 -0.87 423 423
STAT1 (dimer) -0.85 0.43 -10000 0 -1 442 442
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.33 0.16 -10000 0 -0.41 413 413
actin filament polymerization -0.36 0.18 -10000 0 -0.44 421 421
LYN 0.016 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.49 0.25 -10000 0 -0.61 420 420
PIK3R1 -0.056 0.22 -10000 0 -0.72 51 51
CBL/CRKL/GRB2 -0.3 0.15 -10000 0 -0.37 414 414
PI3K -0.36 0.21 -10000 0 -0.45 416 416
PTEN -0.002 0.12 -10000 0 -0.72 13 13
SCF/KIT/EPO/EPOR -1 0.55 -10000 0 -1.3 413 413
MAPK8 -0.36 0.18 -10000 0 -0.45 414 414
STAT3 (dimer) -0.35 0.18 -10000 0 -0.44 414 414
positive regulation of transcription -0.11 0.084 -10000 0 -0.23 2 2
mol:GDP -0.28 0.13 -10000 0 -0.37 129 129
PIK3C2B -0.36 0.18 -10000 0 -0.45 414 414
CBL/CRKL -0.3 0.17 -10000 0 -0.38 414 414
FER -0.36 0.18 -10000 0 -0.44 414 414
SH2B3 -0.36 0.18 -10000 0 -0.44 414 414
PDPK1 -0.3 0.16 -10000 0 -0.38 410 410
SNAI2 -0.41 0.23 -10000 0 -0.5 427 427
positive regulation of cell proliferation -0.61 0.31 -10000 0 -0.74 442 442
KITLG -0.019 0.077 -10000 0 -0.75 3 3
cell motility -0.61 0.31 -10000 0 -0.74 442 442
PTPN6 0.032 0.018 -10000 0 -10000 0 0
EPOR -0.22 0.14 -10000 0 -0.62 1 1
STAT5A (dimer) -0.5 0.26 -10000 0 -0.6 443 443
SOCS1 0.015 0.012 -10000 0 -10000 0 0
cell migration 0.35 0.18 0.44 416 -10000 0 416
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.02 0.058 -10000 0 -10000 0 0
VAV1 0.012 0.027 -10000 0 -10000 0 0
GRB10 -0.36 0.19 -10000 0 -0.45 414 414
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.38 0.19 -10000 0 -0.48 417 417
GO:0007205 0.018 0.01 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.32 2 2
CBL 0.016 0 -10000 0 -10000 0 0
KIT -1.1 0.58 -10000 0 -1.4 414 414
MAP2K2 -0.15 0.11 -10000 0 -0.32 2 2
SHC/Grb2/SOS1 -0.33 0.16 -10000 0 -0.41 413 413
STAT5A -0.51 0.26 -10000 0 -0.62 443 443
GRB2 0.013 0.022 -10000 0 -10000 0 0
response to radiation -0.4 0.22 -10000 0 -0.49 427 427
SHC/GRAP2 -0.001 0.009 -10000 0 -10000 0 0
PTPRO -0.36 0.18 -10000 0 -0.45 414 414
SH2B2 -0.36 0.18 -10000 0 -0.45 421 421
DOK1 0.014 0.019 -10000 0 -10000 0 0
MATK -0.36 0.18 -10000 0 -0.45 416 416
CREBBP 0.006 0.037 -10000 0 -0.72 1 1
BCL2 -0.44 0.55 -10000 0 -1.5 105 105
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.73 0.63 -9999 0 -1.2 317 317
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.18 0.16 -9999 0 -0.37 78 78
ATF2/c-Jun -0.26 0.38 -9999 0 -1 97 97
MAPK11 -0.18 0.16 -9999 0 -0.31 317 317
MITF -0.21 0.21 -9999 0 -0.37 319 319
MAPKAPK5 -0.2 0.2 -9999 0 -0.37 317 317
KRT8 -0.21 0.21 -9999 0 -0.37 317 317
MAPKAPK3 0.015 0.012 -9999 0 -10000 0 0
MAPKAPK2 0.016 0.01 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.27 0.25 -9999 0 -0.47 317 317
CEBPB -0.21 0.21 -9999 0 -0.37 317 317
SLC9A1 -0.2 0.2 -9999 0 -0.37 317 317
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.22 0.23 -9999 0 -0.38 317 317
p38alpha-beta/MNK1 -0.22 0.18 -9999 0 -0.37 317 317
JUN -0.26 0.38 -9999 0 -1 97 97
PPARGC1A -0.27 0.3 -9999 0 -0.45 328 328
USF1 -0.21 0.2 -9999 0 -0.37 317 317
RAB5/GDP/GDI1 -0.16 0.13 -9999 0 -0.33 82 82
NOS2 -0.22 0.2 -9999 0 -0.38 317 317
DDIT3 -0.21 0.2 -9999 0 -0.37 317 317
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.17 0.18 -9999 0 -0.36 125 125
p38alpha-beta/HBP1 -0.22 0.18 -9999 0 -0.37 317 317
CREB1 -0.22 0.21 -9999 0 -0.38 317 317
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.17 0.18 -9999 0 -0.4 78 78
RPS6KA4 -0.2 0.2 -9999 0 -0.37 317 317
PLA2G4A -0.43 0.34 -9999 0 -0.66 328 328
GDI1 -0.21 0.2 -9999 0 -0.37 317 317
TP53 -0.26 0.25 -9999 0 -0.46 317 317
RPS6KA5 -0.22 0.22 -9999 0 -0.38 330 330
ESR1 -0.32 0.27 -9999 0 -0.45 390 390
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.24 0.26 -9999 0 -0.41 325 325
MEF2A -0.2 0.2 -9999 0 -0.37 317 317
EIF4EBP1 -0.22 0.21 -9999 0 -0.38 317 317
KRT19 -0.22 0.22 -9999 0 -0.39 319 319
ELK4 -0.2 0.2 -9999 0 -0.37 317 317
ATF6 -0.2 0.2 -9999 0 -0.37 317 317
ATF1 -0.22 0.21 -9999 0 -0.38 317 317
p38alpha-beta/MAPKAPK2 -0.22 0.18 -9999 0 -0.46 79 79
p38alpha-beta/MAPKAPK3 -0.22 0.18 -9999 0 -0.46 81 81
Endothelins

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
AKT1 -0.11 0.24 -9999 0 -0.46 172 172
PTK2B 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.3 -9999 0 -0.75 76 76
EDN1 -0.21 0.35 -9999 0 -0.72 169 169
EDN3 -0.6 0.28 -9999 0 -0.72 437 437
EDN2 -0.061 0.09 -9999 0 -0.72 2 2
HRAS/GDP -0.24 0.25 -9999 0 -0.5 199 199
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.11 0.19 -9999 0 -0.38 133 133
ADCY4 -0.096 0.21 -9999 0 -0.38 174 174
ADCY5 -0.094 0.2 -9999 0 -0.38 173 173
ADCY6 -0.092 0.2 -9999 0 -0.38 172 172
ADCY7 -0.092 0.2 -9999 0 -0.38 172 172
ADCY1 -0.093 0.2 -9999 0 -0.38 172 172
ADCY2 -0.098 0.21 -9999 0 -0.39 176 176
ADCY3 -0.092 0.2 -9999 0 -0.38 172 172
ADCY8 -0.092 0.2 -9999 0 -0.38 172 172
ADCY9 -0.092 0.2 -9999 0 -0.38 172 172
arachidonic acid secretion -0.53 0.37 -9999 0 -0.7 399 399
ETB receptor/Endothelin-1/Gq/GTP -0.26 0.25 -9999 0 -0.43 322 322
GNAO1 0.016 0 -9999 0 -10000 0 0
HRAS 0.009 0.014 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.095 0.24 -9999 0 -0.42 171 171
ETA receptor/Endothelin-1/Gs/GTP -0.093 0.23 -9999 0 -0.41 172 172
mol:GTP -0.007 0.009 -9999 0 -10000 0 0
COL3A1 -0.11 0.24 -9999 0 -0.46 161 161
EDNRB -0.35 0.37 -9999 0 -0.72 260 260
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.11 0.24 -9999 0 -0.47 133 133
CYSLTR1 -0.11 0.25 -9999 0 -0.46 173 173
SLC9A1 -0.063 0.14 -9999 0 -0.27 81 81
mol:GDP -0.27 0.27 -9999 0 -0.54 211 211
SLC9A3 -0.4 0.41 -9999 0 -0.68 314 314
RAF1 -0.36 0.29 -9999 0 -0.56 303 303
JUN -0.24 0.47 -9999 0 -1.1 109 109
JAK2 -0.11 0.25 -9999 0 -0.46 171 171
mol:IP3 -0.23 0.24 -9999 0 -0.47 210 210
ETA receptor/Endothelin-1 -0.12 0.29 -9999 0 -0.54 171 171
PLCB1 -0.1 0.25 -9999 0 -0.73 74 74
PLCB2 0.005 0.008 -9999 0 -10000 0 0
ETA receptor/Endothelin-3 -0.44 0.21 -9999 0 -0.54 437 437
FOS -0.71 0.47 -9999 0 -1 374 374
Gai/GDP -0.1 0.16 -9999 0 -0.35 47 47
CRK 0.014 0.032 -9999 0 -0.72 1 1
mol:Ca ++ -0.3 0.33 -9999 0 -0.66 202 202
BCAR1 0.017 0.001 -9999 0 -10000 0 0
PRKCB1 -0.22 0.24 -9999 0 -0.48 188 188
GNAQ -0.008 0.01 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
GNAL 0.012 0.056 -9999 0 -0.72 3 3
Gs family/GDP -0.25 0.22 -9999 0 -0.48 208 208
ETA receptor/Endothelin-1/Gq/GTP -0.085 0.17 -9999 0 -0.32 151 151
MAPK14 -0.24 0.25 -9999 0 -0.49 208 208
TRPC6 -0.15 0.32 -9999 0 -0.8 76 76
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.27 0.27 -9999 0 -0.46 298 298
ETB receptor/Endothelin-2 -0.29 0.29 -9999 0 -0.58 262 262
ETB receptor/Endothelin-3 -0.67 0.34 -9999 0 -0.78 455 455
ETB receptor/Endothelin-1 -0.41 0.38 -9999 0 -0.68 329 329
MAPK3 -0.62 0.42 -9999 0 -0.86 380 380
MAPK1 -0.62 0.42 -9999 0 -0.86 380 380
Rac1/GDP -0.24 0.25 -9999 0 -0.5 203 203
cAMP biosynthetic process -0.039 0.19 -9999 0 -0.33 104 104
MAPK8 -0.16 0.29 -9999 0 -0.62 118 118
SRC 0.016 0.007 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.3 0.32 -9999 0 -0.58 245 245
p130Cas/CRK/Src/PYK2 -0.24 0.29 -9999 0 -0.56 189 189
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.24 0.25 -9999 0 -0.5 198 198
COL1A2 -0.32 0.35 -9999 0 -0.69 193 193
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 0.03 0.077 -9999 0 -0.53 4 4
mol:DAG -0.23 0.24 -9999 0 -0.46 216 216
MAP2K2 -0.47 0.34 -9999 0 -0.66 381 381
MAP2K1 -0.47 0.34 -9999 0 -0.66 381 381
EDNRA 0.024 0.053 -9999 0 -0.71 2 2
positive regulation of muscle contraction -0.089 0.21 -9999 0 -0.39 172 172
Gq family/GDP -0.22 0.21 -9999 0 -0.48 157 157
HRAS/GTP -0.28 0.26 -9999 0 -0.44 309 309
PRKCH -0.22 0.24 -9999 0 -0.47 194 194
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.22 0.24 -9999 0 -0.47 194 194
PRKCB -0.23 0.24 -9999 0 -0.46 221 221
PRKCE -0.22 0.24 -9999 0 -0.47 192 192
PRKCD -0.22 0.24 -9999 0 -0.47 196 196
PRKCG -0.22 0.24 -9999 0 -0.47 194 194
regulation of vascular smooth muscle contraction -0.83 0.55 -9999 0 -1.2 374 374
PRKCQ -0.23 0.24 -9999 0 -0.48 192 192
PLA2G4A -0.6 0.44 -9999 0 -0.8 399 399
GNA14 -0.018 0.09 -9999 0 -0.73 6 6
GNA15 0.006 0.021 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA11 0.009 0.008 -9999 0 -10000 0 0
Rac1/GTP -0.094 0.24 -9999 0 -0.42 171 171
MMP1 0.026 0.14 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.022 0.012 -10000 0 -10000 0 0
NFATC2 -0.065 0.22 -10000 0 -0.54 80 80
NFATC3 -0.17 0.14 -10000 0 -0.31 157 157
CD40LG -0.79 0.56 -10000 0 -1.1 363 363
ITCH -0.056 0.15 -10000 0 -0.59 1 1
CBLB -0.057 0.15 -10000 0 -1.1 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.24 -10000 0 -0.68 80 80
JUNB 0.012 0.056 -10000 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.15 -10000 0 -0.31 197 197
T cell anergy -0.13 0.24 -10000 0 -0.43 197 197
TLE4 -0.048 0.23 -10000 0 -0.56 61 61
Jun/NFAT1-c-4/p21SNFT -0.7 0.54 -10000 0 -1 352 352
AP-1/NFAT1-c-4 -1 0.74 -10000 0 -1.4 362 362
IKZF1 -0.029 0.16 -10000 0 -0.52 21 21
T-helper 2 cell differentiation -0.15 0.29 -10000 0 -0.74 65 65
AP-1/NFAT1 -0.47 0.35 -10000 0 -0.65 376 376
CALM1 -0.039 0.095 -10000 0 -0.3 1 1
EGR2 -0.89 0.85 -10000 0 -1.7 256 256
EGR3 -0.98 0.85 -10000 0 -1.6 319 319
NFAT1/FOXP3 -0.035 0.16 -10000 0 -0.38 61 61
EGR1 -0.6 0.28 -10000 0 -0.72 436 436
JUN -0.12 0.29 -10000 0 -0.72 97 97
EGR4 0.001 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.062 0.1 -10000 0 -0.34 1 1
GBP3 -0.073 0.28 -10000 0 -0.81 52 52
FOSL1 0.016 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.64 0.51 -10000 0 -0.96 344 344
DGKA -0.028 0.16 -10000 0 -0.61 12 12
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.92 0.57 -10000 0 -1.3 363 363
CTLA4 -0.02 0.14 -10000 0 -0.53 11 11
NFAT1-c-4 (dimer)/EGR1 -0.95 0.58 -10000 0 -1.3 362 362
NFAT1-c-4 (dimer)/EGR4 -0.64 0.52 -10000 0 -0.96 362 362
FOS -0.51 0.34 -10000 0 -0.72 374 374
IFNG -0.19 0.26 -10000 0 -0.92 40 40
T cell activation -0.48 0.39 -10000 0 -0.78 285 285
MAF -0.051 0.21 -10000 0 -0.72 48 48
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.47 0.43 0.75 353 -10000 0 353
TNF -0.76 0.52 -10000 0 -1.1 359 359
FASLG -0.95 0.82 -10000 0 -1.4 362 362
TBX21 -0.034 0.19 -10000 0 -0.72 35 35
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.01 0.047 -10000 0 -0.72 1 1
PTPN1 -0.03 0.16 -10000 0 -0.53 24 24
NFAT1-c-4/ICER1 -0.64 0.51 -10000 0 -0.96 360 360
GATA3 -0.076 0.19 -10000 0 -0.72 38 38
T-helper 1 cell differentiation -0.19 0.25 -10000 0 -0.89 41 41
IL2RA -0.34 0.24 -10000 0 -0.57 189 189
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.027 0.16 -10000 0 -0.52 21 21
E2F1 0.004 0.055 -10000 0 -10000 0 0
PPARG -0.53 0.32 -10000 0 -0.72 388 388
SLC3A2 -0.028 0.16 -10000 0 -0.52 21 21
IRF4 0.011 0.03 -10000 0 -10000 0 0
PTGS2 -0.96 0.64 -10000 0 -1.3 387 387
CSF2 -0.79 0.56 -10000 0 -1.1 361 361
JunB/Fra1/NFAT1-c-4 -0.61 0.49 -10000 0 -0.92 352 352
IL4 -0.16 0.31 -10000 0 -0.78 63 63
IL5 -0.79 0.56 -10000 0 -1.1 360 360
IL2 -0.48 0.4 -10000 0 -0.81 280 280
IL3 -0.085 0.051 -10000 0 -10000 0 0
RNF128 -0.26 0.4 -10000 0 -0.78 197 197
NFATC1 -0.47 0.43 -10000 0 -0.75 353 353
CDK4 0.28 0.26 0.53 163 -10000 0 163
PTPRK -0.081 0.3 -10000 0 -0.9 54 54
IL8 -0.8 0.57 -10000 0 -1.1 366 366
POU2F1 0.026 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.015 0.012 -9999 0 -10000 0 0
EGFR -0.38 0.37 -9999 0 -0.72 277 277
EGF/EGFR -0.45 0.34 -9999 0 -0.6 393 393
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.33 0.26 -9999 0 -0.47 372 372
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.013 0.046 -9999 0 -0.72 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.24 0.35 -9999 0 -0.72 178 178
EGF/EGFR dimer/SHC -0.39 0.29 -9999 0 -0.55 372 372
mol:GDP -0.33 0.25 -9999 0 -0.46 372 372
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.22 0.34 -9999 0 -0.72 169 169
GRB2/SOS1 -0.001 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.3 0.23 -9999 0 -0.67 96 96
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.3 0.24 -9999 0 -0.68 96 96
FRAP1 -0.29 0.26 -9999 0 -0.7 94 94
EGF/EGFR dimer -0.45 0.33 -9999 0 -0.64 372 372
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.18 0.25 -9999 0 -0.54 171 171
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.18 0.32 0.72 137 -10000 0 137
PI3K Class IB/PDE3B -0.18 0.32 -10000 0 -0.72 137 137
PDE3B -0.18 0.32 -10000 0 -0.72 137 137
IGF1 pathway

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
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTK2 0.015 0.014 -10000 0 -10000 0 0
CRKL -0.23 0.29 -10000 0 -0.46 280 280
GRB2/SOS1/SHC 0.002 0.011 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
IRS1/Crk -0.23 0.29 -10000 0 -0.47 280 280
IGF-1R heterotetramer/IGF1/PTP1B -0.25 0.26 -10000 0 -0.49 265 265
AKT1 -0.21 0.28 -10000 0 -0.62 118 118
BAD -0.18 0.26 -10000 0 -0.61 100 100
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.23 0.29 -10000 0 -0.46 280 280
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.23 0.29 -10000 0 -0.47 280 280
RAF1 -0.17 0.24 -10000 0 -0.58 95 95
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.23 0.26 -10000 0 -0.45 266 266
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.31 -10000 0 -0.51 280 280
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.21 0.28 -10000 0 -0.62 119 119
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.14 0.21 -10000 0 -0.48 95 95
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.2 0.23 -10000 0 -0.62 78 78
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.19 0.21 -10000 0 -0.38 265 265
IGF-1R heterotetramer -0.074 0.18 -10000 0 -0.62 37 37
IGF-1R heterotetramer/IGF1/IRS/Nck -0.25 0.28 -10000 0 -0.47 280 280
Crk/p130 Cas/Paxillin -0.22 0.25 -10000 0 -0.42 265 265
IGF1R -0.074 0.18 -10000 0 -0.62 37 37
IGF1 -0.37 0.38 -10000 0 -0.75 262 262
IRS2/Crk -0.31 0.37 -10000 0 -0.57 307 307
PI3K -0.27 0.3 -10000 0 -0.5 276 276
apoptosis 0.15 0.22 0.52 95 -10000 0 95
HRAS/GDP -0.001 0.007 -10000 0 -10000 0 0
PRKCD -0.23 0.3 -10000 0 -0.51 265 265
RAF1/14-3-3 E -0.14 0.21 -10000 0 -0.48 95 95
BAD/14-3-3 -0.16 0.24 -10000 0 -0.56 95 95
PRKCZ -0.22 0.28 -10000 0 -0.44 276 276
Crk/p130 Cas/Paxillin/FAK1 -0.19 0.21 -10000 0 -0.57 95 95
PTPN1 0.008 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.26 0.31 -10000 0 -0.54 265 265
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.22 0.24 -10000 0 -0.43 265 265
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.23 0.29 -10000 0 -0.46 280 280
GRB10 0.011 0.064 -10000 0 -0.72 4 4
PTPN11 -0.23 0.29 -10000 0 -0.46 280 280
IRS1 -0.26 0.31 -10000 0 -0.51 280 280
IRS2 -0.34 0.38 -10000 0 -0.6 307 307
IGF-1R heterotetramer/IGF1 -0.31 0.32 -10000 0 -0.62 265 265
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDPK1 -0.23 0.3 -10000 0 -0.46 276 276
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
PRKD1 -0.3 0.36 -10000 0 -0.6 281 281
SHC1 0.016 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.001 0.021 -9999 0 -0.48 1 1
ARNO/beta Arrestin1-2 -0.19 0.18 -9999 0 -0.35 285 285
EGFR -0.38 0.37 -9999 0 -0.72 277 277
EPHA2 0.005 0.09 -9999 0 -0.72 8 8
USP6 0.015 0.016 -9999 0 -10000 0 0
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.45 0.33 -9999 0 -0.64 372 372
ARRB2 0.018 0.037 -9999 0 -0.41 4 4
mol:GTP 0.008 0.005 -9999 0 -10000 0 0
ARRB1 0.014 0.035 -9999 0 -0.72 1 1
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR 0.01 0.064 -9999 0 -0.72 4 4
EGF -0.24 0.35 -9999 0 -0.72 178 178
somatostatin receptor activity 0 0 -9999 0 -0.001 314 314
ARAP2 0 0 -9999 0 0 313 313
mol:GDP -0.16 0.14 -9999 0 -0.29 232 232
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 313 313
ITGA2B 0.016 0.01 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -9999 0 -0.41 8 8
ADAP1 0 0 -9999 0 0 279 279
KIF13B 0.015 0.032 -9999 0 -0.72 1 1
HGF/MET -0.054 0.16 -9999 0 -0.54 52 52
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.18 0.13 -9999 0 -0.27 313 313
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.39 0.29 -9999 0 -0.55 372 372
ADRB2 -0.38 0.37 -9999 0 -0.72 284 284
receptor agonist activity 0 0 -9999 0 0 314 314
actin filament binding 0 0 -9999 0 -0.001 315 315
SRC 0.016 0.007 -9999 0 -10000 0 0
ITGB3 0.014 0.02 -9999 0 -10000 0 0
GNAQ 0 0 -9999 0 -0.001 306 306
EFA6/PI-4-5-P2 -0.001 0 -9999 0 -0.001 313 313
ARF6/GDP -0.029 0.057 -9999 0 -0.25 4 4
ARF6/GDP/GULP/ACAP1 -0.2 0.2 -9999 0 -0.42 189 189
alphaIIb/beta3 Integrin/paxillin/GIT1 0.002 0.015 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 0 6 6
ACAP2 0 0 -9999 0 0 314 314
LHCGR/beta Arrestin2 0.015 0.054 -9999 0 -0.6 4 4
EFNA1 0.013 0.022 -9999 0 -10000 0 0
HGF 0.015 0.01 -9999 0 -10000 0 0
CYTH3 0 0 -9999 0 -0.001 314 314
CYTH2 -0.003 0.002 -9999 0 -0.004 315 315
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 276 276
endosomal lumen acidification 0 0 -9999 0 0 181 181
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.12 0.29 -9999 0 -0.72 97 97
GNAQ/ARNO -0.004 0.003 -9999 0 -0.006 306 306
mol:Phosphatidic acid 0 0 -9999 0 0 314 314
PIP3-E 0.011 0.049 -9999 0 -0.72 2 2
MET -0.057 0.22 -9999 0 -0.72 52 52
GNA14 -0.008 0.09 -9999 0 -0.72 6 6
GNA15 0.014 0.02 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 314 314
GNA11 0.016 0 -9999 0 -10000 0 0
LHCGR 0.009 0.066 -9999 0 -0.72 4 4
AGTR1 -0.32 0.35 -9999 0 -0.72 224 224
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.053 -9999 0 -0.59 4 4
IPCEF1/ARNO -0.31 0.24 -9999 0 -0.44 373 373
alphaIIb/beta3 Integrin -0.001 0.011 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.009 -10000 0 -10000 0 0
GNB1/GNG2 -0.049 0.15 -10000 0 -0.43 70 70
regulation of S phase of mitotic cell cycle -0.044 0.15 -10000 0 -0.33 112 112
GNAO1 0.016 0 -10000 0 -10000 0 0
HRAS 0.013 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.006 0.005 -10000 0 -10000 0 0
PELP1 0.014 0.002 -10000 0 -10000 0 0
AKT1 0.014 0.013 -10000 0 -10000 0 0
MAP2K1 -0.08 0.15 -10000 0 -0.43 69 69
T-DHT/AR -0.07 0.19 -10000 0 -0.56 69 69
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.004 -10000 0 -0.007 374 374
GNAI2 0.016 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
mol:GDP -0.098 0.21 -10000 0 -0.51 90 90
cell proliferation -0.26 0.23 -10000 0 -0.4 374 374
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
FOS -0.59 0.42 -10000 0 -0.85 374 374
mol:Ca2+ -0.036 0.039 -10000 0 -0.076 244 244
MAPK3 -0.18 0.19 -10000 0 -0.56 61 61
MAPK1 -0.13 0.12 -10000 0 -0.29 64 64
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 -0.003 0.002 -10000 0 -0.005 374 374
cAMP biosynthetic process 0.03 0.032 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.005 374 374
HRAS/GTP -0.067 0.14 -10000 0 -0.42 69 69
actin cytoskeleton reorganization -0.036 0.11 -10000 0 -0.37 51 51
SRC 0.014 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.005 374 374
PI3K -0.045 0.14 -10000 0 -0.47 51 51
apoptosis 0.28 0.22 0.41 374 -10000 0 374
T-DHT/AR/PELP1 -0.056 0.17 -10000 0 -0.48 69 69
HRAS/GDP -0.082 0.2 -10000 0 -0.57 69 69
CREB1 -0.3 0.24 -10000 0 -0.44 374 374
RAC1-CDC42/GTP -0.036 0.11 -10000 0 -0.38 51 51
AR -0.085 0.25 -10000 0 -0.73 69 69
GNB1 0.016 0.01 -10000 0 -10000 0 0
RAF1 -0.067 0.15 -10000 0 -0.43 69 69
RAC1-CDC42/GDP -0.086 0.19 -10000 0 -0.53 69 69
T-DHT/AR/PELP1/Src -0.051 0.15 -10000 0 -0.44 69 69
MAP2K2 -0.08 0.15 -10000 0 -0.43 69 69
T-DHT/AR/PELP1/Src/PI3K -0.044 0.15 -10000 0 -0.33 112 112
GNAZ 0.007 0.078 -10000 0 -0.72 6 6
SHBG 0.016 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.061 0.13 -10000 0 -0.38 14 14
mol:T-DHT -0.002 0.002 -10000 0 -0.003 313 313
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.014 0.12 -10000 0 -0.55 26 26
Gi family/GTP -0.11 0.13 -10000 0 -0.26 193 193
CDC42 0.016 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.1 0.47 -10000 0 -0.75 127 127
HDAC7 0.002 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.3 0.56 1 -0.64 82 83
SMAD4 0.015 0.045 -10000 0 -0.72 2 2
ID2 -0.1 0.47 -10000 0 -0.77 121 121
AP1 -0.47 0.35 -10000 0 -0.67 375 375
ABCG2 -0.12 0.5 -10000 0 -0.82 126 126
HIF1A 0.001 0.12 -10000 0 -0.55 7 7
TFF3 -0.18 0.54 -10000 0 -0.85 156 156
GATA2 0.003 0.043 -10000 0 -10000 0 0
AKT1 0.006 0.1 -10000 0 -0.25 7 7
response to hypoxia -0.014 0.11 -10000 0 -0.16 43 43
MCL1 -0.1 0.47 -10000 0 -0.74 132 132
NDRG1 -0.11 0.48 -10000 0 -0.74 133 133
SERPINE1 -0.1 0.48 -10000 0 -0.77 122 122
FECH -0.1 0.47 -10000 0 -0.76 125 125
FURIN -0.1 0.47 -10000 0 -0.77 121 121
NCOA2 0.017 0.014 -10000 0 -10000 0 0
EP300 0.032 0.15 -10000 0 -0.2 2 2
HMOX1 -0.1 0.48 -10000 0 -0.76 123 123
BHLHE40 -0.12 0.47 -10000 0 -0.72 146 146
BHLHE41 -0.12 0.47 -10000 0 -0.72 146 146
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.029 0.083 -10000 0 -0.5 7 7
ENG 0.052 0.14 -10000 0 -0.45 7 7
JUN -0.12 0.29 -10000 0 -0.73 97 97
RORA -0.11 0.49 -10000 0 -0.79 125 125
ABCB1 -0.41 0.57 -10000 0 -1.2 169 169
TFRC -0.11 0.48 -10000 0 -0.76 132 132
CXCR4 -0.11 0.48 -10000 0 -0.75 129 129
TF -0.12 0.49 -10000 0 -0.79 130 130
CITED2 -0.11 0.48 -10000 0 -0.78 121 121
HIF1A/ARNT -0.23 0.44 0.65 20 -0.88 118 138
LDHA -0.022 0.038 -10000 0 -10000 0 0
ETS1 -0.1 0.47 -10000 0 -0.76 123 123
PGK1 -0.1 0.47 -10000 0 -0.76 125 125
NOS2 -0.12 0.47 -10000 0 -0.72 146 146
ITGB2 -0.1 0.48 -10000 0 -0.76 126 126
ALDOA -0.1 0.47 -10000 0 -0.75 127 127
Cbp/p300/CITED2 -0.12 0.47 -10000 0 -0.81 105 105
FOS -0.51 0.34 -10000 0 -0.73 374 374
HK2 -0.1 0.47 -10000 0 -0.76 125 125
SP1 0.004 0.049 -10000 0 -10000 0 0
GCK 0.054 0.2 -10000 0 -10000 0 0
HK1 -0.1 0.47 -10000 0 -0.76 125 125
NPM1 -0.1 0.47 -10000 0 -0.77 121 121
EGLN1 -0.1 0.47 -10000 0 -0.76 125 125
CREB1 0.026 0.002 -10000 0 -10000 0 0
PGM1 -0.11 0.48 -10000 0 -0.76 128 128
SMAD3 0.017 0.033 -10000 0 -0.72 1 1
EDN1 -0.46 0.64 -10000 0 -1.4 169 169
IGFBP1 -0.1 0.47 -10000 0 -0.77 122 122
VEGFA -0.033 0.37 -10000 0 -0.59 83 83
HIF1A/JAB1 -0.013 0.061 -10000 0 -0.6 4 4
CP -0.22 0.56 -10000 0 -0.85 180 180
CXCL12 -0.22 0.6 -10000 0 -0.94 176 176
COPS5 0.018 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.04 -10000 0 -0.54 3 3
BNIP3 -0.11 0.48 -10000 0 -0.76 127 127
EGLN3 -0.11 0.48 -10000 0 -0.78 125 125
CA9 -0.11 0.48 -10000 0 -0.76 132 132
TERT -0.1 0.47 -10000 0 -0.76 123 123
ENO1 -0.1 0.47 -10000 0 -0.76 125 125
PFKL -0.1 0.47 -10000 0 -0.77 122 122
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
ADM -0.25 0.55 -10000 0 -0.84 190 190
ARNT 0.008 0.09 -10000 0 -10000 0 0
HNF4A 0.022 0 -10000 0 -10000 0 0
ADFP -0.12 0.5 -10000 0 -0.81 131 131
SLC2A1 -0.03 0.36 -10000 0 -0.58 81 81
LEP -0.3 0.6 -10000 0 -0.87 233 233
HIF1A/ARNT/Cbp/p300 -0.13 0.34 -10000 0 -0.66 85 85
EPO 0.004 0.32 -10000 0 -0.5 43 43
CREBBP 0.032 0.15 -10000 0 -0.3 3 3
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.3 0.56 1 -0.64 88 89
PFKFB3 -0.11 0.48 -10000 0 -0.77 122 122
NT5E -0.11 0.49 -10000 0 -0.79 122 122
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.34 0.22 -10000 0 -0.5 338 338
PTP1B/AKT1 -0.17 0.13 -10000 0 -0.28 297 297
FYN 0.013 0.045 -10000 0 -0.72 2 2
p210 bcr-abl/PTP1B -0.21 0.15 -10000 0 -0.32 298 298
EGFR -0.39 0.37 -10000 0 -0.74 277 277
EGF/EGFR -0.48 0.32 -10000 0 -0.66 372 372
CSF1 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.013 0.02 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.2 0.15 -10000 0 -0.31 312 312
Insulin Receptor/Insulin -0.12 0.084 -10000 0 -10000 0 0
HCK 0.013 0.024 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
TYK2 -0.19 0.14 -10000 0 -0.3 297 297
EGF -0.25 0.35 -10000 0 -0.74 178 178
YES1 0.015 0.032 -10000 0 -0.72 1 1
CAV1 -0.43 0.26 -10000 0 -0.57 385 385
TXN 0.004 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.22 0.19 -10000 0 -0.35 299 299
cell migration 0.21 0.15 0.32 298 -10000 0 298
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.021 0.07 -10000 0 -10000 0 0
ITGA2B 0.013 0.01 -10000 0 -10000 0 0
CSF1R 0.016 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.05 0.024 -10000 0 -10000 0 0
FGR 0.016 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.19 0.14 -10000 0 -0.3 297 297
Crk/p130 Cas -0.17 0.14 -10000 0 -0.28 297 297
DOK1 -0.15 0.12 -10000 0 -0.28 70 70
JAK2 -0.094 0.088 -10000 0 -0.78 1 1
Jak2/Leptin Receptor/Leptin -0.36 0.23 -10000 0 -0.5 347 347
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
PTPN1 -0.21 0.15 -10000 0 -0.33 298 298
LYN 0.016 0.01 -10000 0 -10000 0 0
CDH2 -0.013 0.062 -10000 0 -10000 0 0
SRC -0.057 0.055 -10000 0 -10000 0 0
ITGB3 0.011 0.02 -10000 0 -10000 0 0
CAT1/PTP1B -0.15 0.14 -10000 0 -0.41 25 25
CAPN1 0.003 0.016 -10000 0 -10000 0 0
CSK 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.14 0.14 -10000 0 -0.5 51 51
mol:H2O2 -0.007 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.21 -10000 0 -0.44 343 343
negative regulation of transcription -0.093 0.088 -10000 0 -0.76 1 1
FCGR2A 0.013 0.023 -10000 0 -10000 0 0
FER 0.004 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.002 0.011 -10000 0 -10000 0 0
BLK 0.002 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.005 0.007 -10000 0 -10000 0 0
LEPR -0.47 0.35 -10000 0 -0.72 344 344
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0.022 -10000 0 -10000 0 0
mol:NADPH -0.007 0.004 -10000 0 -10000 0 0
TRPV6 0.026 0.059 -10000 0 -0.37 3 3
PRL 0.021 0.003 -10000 0 -10000 0 0
SOCS3 0.003 0.25 -10000 0 -1.4 15 15
SPRY2 -0.48 0.35 -10000 0 -0.73 350 350
Insulin Receptor/Insulin/IRS1 -0.061 0.16 -10000 0 -0.46 69 69
CSF1/CSF1R -0.17 0.14 -10000 0 -0.28 297 297
Ras protein signal transduction 0.076 0.044 -10000 0 -10000 0 0
IRS1 -0.081 0.25 -10000 0 -0.72 69 69
INS 0.016 0.001 -10000 0 -10000 0 0
LEP -0.35 0.37 -10000 0 -0.72 258 258
STAT5B -0.16 0.12 -10000 0 -0.25 292 292
STAT5A -0.16 0.12 -10000 0 -0.26 293 293
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.19 0.14 -10000 0 -0.3 297 297
CSN2 0.071 0.031 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
LAT -0.056 0.056 -10000 0 -10000 0 0
YBX1 0.018 0.017 -10000 0 -10000 0 0
LCK 0 0.049 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
NOX4 -0.019 0.069 -10000 0 -0.74 1 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.016 0.036 -9999 0 -0.47 2 2
NFATC2 0.018 0.029 -9999 0 -0.47 1 1
NFATC3 0.018 0.02 -9999 0 -10000 0 0
CD40LG -0.34 0.32 -9999 0 -0.58 298 298
PTGS2 -0.54 0.44 -9999 0 -0.82 343 343
JUNB 0.012 0.056 -9999 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.006 -9999 0 -10000 0 0
CaM/Ca2+ 0.002 0.006 -9999 0 -10000 0 0
CALM1 0.015 0.005 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.73 97 97
mol:Ca2+ -0.006 0.006 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.005 -9999 0 -10000 0 0
FOSL1 0.016 0.01 -9999 0 -10000 0 0
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.084 0.16 -9999 0 -0.4 98 98
FOS -0.51 0.34 -9999 0 -0.73 374 374
IFNG -0.35 0.33 -9999 0 -0.59 303 303
AP-1/NFAT1-c-4 -0.41 0.39 -9999 0 -0.7 303 303
FASLG -0.34 0.32 -9999 0 -0.58 299 299
NFAT1-c-4/ICER1 0.001 0.035 -9999 0 -0.37 3 3
IL2RA -0.34 0.32 -9999 0 -0.58 299 299
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.34 0.32 -9999 0 -0.58 297 297
JunB/Fra1/NFAT1-c-4 0.01 0.046 -9999 0 -0.35 6 6
IL4 -0.34 0.32 -9999 0 -0.57 297 297
IL2 -0.011 0.067 -9999 0 -1.5 1 1
IL3 -0.009 0.019 -9999 0 -10000 0 0
FKBP1A 0.016 0.01 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0 -9999 0 -10000 0 0
S1P1 pathway

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.097 0.17 -9999 0 -0.36 147 147
PDGFRB 0.007 0.008 -9999 0 -10000 0 0
SPHK1 -0.049 0.098 -9999 0 -1.1 4 4
mol:S1P -0.059 0.095 -9999 0 -1 4 4
S1P1/S1P/Gi -0.34 0.34 -9999 0 -0.69 215 215
GNAO1 0.007 0.009 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.28 0.29 -9999 0 -0.59 204 204
PLCG1 -0.31 0.31 -9999 0 -0.64 206 206
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.008 -9999 0 -10000 0 0
GNAI2 0.007 0.012 -9999 0 -10000 0 0
GNAI3 0.007 0.009 -9999 0 -10000 0 0
GNAI1 -0.26 0.36 -9999 0 -0.73 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.22 0.38 -9999 0 -0.83 147 147
S1P1/S1P -0.24 0.31 -9999 0 -0.73 147 147
negative regulation of cAMP metabolic process -0.33 0.33 -9999 0 -0.66 215 215
MAPK3 -0.43 0.4 -9999 0 -0.71 323 323
calcium-dependent phospholipase C activity -0.005 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.037 0.09 -9999 0 -10000 0 0
PLCB2 -0.19 0.28 -9999 0 -0.62 147 147
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.19 0.25 -9999 0 -0.58 147 147
receptor internalization -0.22 0.28 -9999 0 -0.66 147 147
PTGS2 -0.67 0.57 -9999 0 -1.1 318 318
Rac1/GTP -0.19 0.25 -9999 0 -0.58 147 147
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.06 0.12 -9999 0 -0.36 30 30
negative regulation of T cell proliferation -0.33 0.33 -9999 0 -0.66 215 215
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.079 -9999 0 -0.73 6 6
MAPK1 -0.43 0.4 -9999 0 -0.71 323 323
S1P1/S1P/PDGFB-D/PDGFRB -0.24 0.34 -9999 0 -0.77 147 147
ABCC1 0.008 0.027 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.29 0.46 -10000 0 -0.86 135 135
PLK1 0.01 0.055 -10000 0 -10000 0 0
BIRC5 -0.025 0.071 -10000 0 -10000 0 0
HSPA1B -0.3 0.46 -10000 0 -0.8 192 192
MAP2K1 0.011 0.036 -10000 0 -10000 0 0
BRCA2 -0.3 0.47 -10000 0 -0.89 127 127
FOXM1 -0.36 0.55 -10000 0 -0.99 165 165
XRCC1 -0.29 0.46 -10000 0 -0.86 135 135
FOXM1B/p19 -0.41 0.42 0.5 1 -0.88 194 195
Cyclin D1/CDK4 -0.29 0.45 -10000 0 -0.85 130 130
CDC2 -0.32 0.49 -10000 0 -0.89 155 155
TGFA -0.32 0.5 -10000 0 -0.99 122 122
SKP2 -0.29 0.46 -10000 0 -0.91 110 110
CCNE1 -0.023 0.071 -10000 0 -10000 0 0
CKS1B -0.29 0.46 -10000 0 -0.92 102 102
RB1 -0.13 0.14 -10000 0 -1.2 2 2
FOXM1C/SP1 -0.33 0.51 -10000 0 -0.92 168 168
AURKB 0.003 0.062 -10000 0 -10000 0 0
CENPF -0.31 0.47 -10000 0 -0.88 144 144
CDK4 0.009 0.024 -10000 0 -10000 0 0
MYC -0.28 0.45 -10000 0 -0.85 130 130
CHEK2 0.009 0.044 -10000 0 -10000 0 0
ONECUT1 -0.3 0.47 -10000 0 -0.86 150 150
CDKN2A -0.015 0.06 -10000 0 -10000 0 0
LAMA4 -0.3 0.47 -10000 0 -0.95 100 100
FOXM1B/HNF6 -0.35 0.55 -10000 0 -1 147 147
FOS -0.84 0.7 -10000 0 -1.3 378 378
SP1 0.017 0.003 -10000 0 -10000 0 0
CDC25B -0.3 0.46 -10000 0 -0.89 121 121
response to radiation -0.01 0.036 -10000 0 -10000 0 0
CENPB -0.29 0.46 -10000 0 -0.91 108 108
CENPA -0.31 0.47 -10000 0 -0.92 115 115
NEK2 -0.32 0.47 -10000 0 -0.97 94 94
HIST1H2BA -0.29 0.46 -10000 0 -0.9 110 110
CCNA2 -0.045 0.082 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.34 0.52 -10000 0 -1.1 100 100
CCNB2 -0.31 0.47 -10000 0 -0.87 145 145
CCNB1 -0.32 0.49 -10000 0 -0.9 146 146
ETV5 -0.31 0.49 -10000 0 -0.93 132 132
ESR1 -0.44 0.63 -10000 0 -1.2 174 174
CCND1 -0.29 0.47 -10000 0 -0.88 127 127
GSK3A 0.015 0.029 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.023 0.088 -10000 0 -10000 0 0
CDK2 0.007 0.027 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.013 0.042 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.38 0.39 -10000 0 -0.83 194 194
GAS1 -0.5 0.67 -10000 0 -1.3 181 181
MMP2 -0.3 0.47 -10000 0 -0.91 116 116
RB1/FOXM1C -0.29 0.47 -10000 0 -0.87 138 138
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.016 0.071 0.39 1 -10000 0 1
SMARCC2 0.016 0 -10000 0 -10000 0 0
SMARCC1 0.014 0.02 -10000 0 -10000 0 0
TBX21 -0.091 0.27 -10000 0 -1 36 36
SUMO2 0.003 0.009 -10000 0 -10000 0 0
STAT1 (dimer) -0.001 0.064 -10000 0 -10000 0 0
FKBP4 0.01 0.031 -10000 0 -10000 0 0
FKBP5 -0.002 0.11 -10000 0 -0.72 11 11
GR alpha/HSP90/FKBP51/HSP90 0.09 0.15 0.33 29 -0.43 6 35
PRL -0.037 0.1 -10000 0 -0.48 1 1
cortisol/GR alpha (dimer)/TIF2 0.26 0.25 0.48 275 -10000 0 275
RELA -0.1 0.081 -10000 0 -0.3 9 9
FGG 0.26 0.21 0.45 229 -10000 0 229
GR beta/TIF2 0.11 0.15 0.31 60 -0.44 7 67
IFNG -0.51 0.32 -10000 0 -0.75 293 293
apoptosis -0.25 0.15 0.56 1 -0.53 19 20
CREB1 0.026 0.004 -10000 0 -10000 0 0
histone acetylation 0.05 0.15 0.45 45 -0.32 13 58
BGLAP -0.05 0.13 -10000 0 -0.52 2 2
GR/PKAc 0.11 0.14 0.32 23 -0.39 8 31
NF kappa B1 p50/RelA -0.18 0.15 -10000 0 -0.36 84 84
SMARCD1 0.016 0 -10000 0 -10000 0 0
MDM2 0.13 0.091 0.22 209 -10000 0 209
GATA3 -0.063 0.19 -10000 0 -0.71 38 38
AKT1 -0.002 0.02 -10000 0 -10000 0 0
CSF2 0.001 0.11 -10000 0 -0.46 1 1
GSK3B 0.002 0.012 -10000 0 -10000 0 0
NR1I3 -0.2 0.16 0.54 1 -0.6 1 2
CSN2 0.22 0.18 0.39 216 -10000 0 216
BRG1/BAF155/BAF170/BAF60A 0.002 0.013 -10000 0 -10000 0 0
NFATC1 0.024 0.046 -10000 0 -0.71 2 2
POU2F1 0.026 0 -10000 0 -10000 0 0
CDKN1A 0.058 0.099 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.012 0.006 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 26 -0.4 4 30
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.7 0.37 0.52 1 -0.87 436 437
JUN -0.24 0.27 -10000 0 -0.56 182 182
IL4 -0.052 0.13 -10000 0 -0.45 14 14
CDK5R1 0.001 0.019 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.64 0.36 -10000 0 -0.77 420 420
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.14 0.33 29 -0.38 7 36
cortisol/GR alpha (monomer) 0.3 0.3 0.56 274 -0.47 1 275
NCOA2 0.015 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.59 0.34 -10000 0 -0.8 374 374
AP-1/NFAT1-c-4 -0.86 0.48 -10000 0 -1.1 404 404
AFP -0.18 0.22 -10000 0 -0.6 58 58
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.5 25 -10000 0 25
TP53 0.043 0.032 -10000 0 -0.47 2 2
PPP5C 0.014 0.02 -10000 0 -10000 0 0
KRT17 -1.1 0.75 -10000 0 -1.7 338 338
KRT14 -0.94 0.72 -10000 0 -1.5 334 334
TBP 0.028 0.001 -10000 0 -10000 0 0
CREBBP 0.17 0.14 0.28 303 -0.46 1 304
HDAC1 0.003 0.005 -10000 0 -10000 0 0
HDAC2 0.011 0.017 -10000 0 -10000 0 0
AP-1 -0.87 0.5 -10000 0 -1.1 404 404
MAPK14 0.003 0.007 -10000 0 -10000 0 0
MAPK10 -0.016 0.11 -10000 0 -0.73 12 12
MAPK11 0.003 0.007 -10000 0 -10000 0 0
KRT5 -1.2 0.73 -10000 0 -1.7 365 365
interleukin-1 receptor activity -0.003 0.002 -10000 0 -10000 0 0
NCOA1 0.019 0.032 -10000 0 -0.71 1 1
STAT1 -0.001 0.064 -10000 0 -10000 0 0
CGA -0.068 0.14 -10000 0 -0.56 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.18 0.33 269 -0.37 4 273
MAPK3 0.003 0.007 -10000 0 -10000 0 0
MAPK1 0.003 0.007 -10000 0 -10000 0 0
ICAM1 -0.28 0.23 -10000 0 -0.55 124 124
NFKB1 -0.1 0.081 -10000 0 -0.24 28 28
MAPK8 -0.13 0.18 -10000 0 -0.41 88 88
MAPK9 0.003 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.15 0.56 1 -0.56 19 20
BAX 0.063 0.035 -10000 0 -10000 0 0
POMC -0.14 0.2 -10000 0 -0.76 15 15
EP300 0.17 0.14 0.29 249 -10000 0 249
cortisol/GR alpha (dimer)/p53 0.28 0.26 0.5 274 -10000 0 274
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.078 0.23 25 -10000 0 25
SGK1 0.25 0.16 0.37 333 -10000 0 333
IL13 -0.36 0.24 -10000 0 -0.79 58 58
IL6 -0.88 0.53 -10000 0 -1.2 391 391
PRKACG 0.015 0.032 -10000 0 -0.72 1 1
IL5 -0.31 0.2 -10000 0 -0.64 50 50
IL2 -0.5 0.32 -10000 0 -0.75 288 288
CDK5 -0.001 0.027 -10000 0 -10000 0 0
PRKACB -0.007 0.099 -10000 0 -0.72 8 8
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
IL8 -0.28 0.23 -10000 0 -0.48 245 245
CDK5R1/CDK5 -0.003 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.1 0.13 -10000 0 -0.52 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.47 254 -10000 0 254
SMARCA4 0.015 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.16 0.34 234 -10000 0 234
NF kappa B1 p50/RelA/Cbp -0.014 0.16 0.38 10 -0.43 2 12
JUN (dimer) -0.24 0.27 -10000 0 -0.56 182 182
YWHAH 0.015 0.012 -10000 0 -10000 0 0
VIPR1 -0.053 0.17 -10000 0 -0.62 28 28
NR3C1 0.18 0.2 0.36 204 -0.54 10 214
NR4A1 -0.01 0.16 -10000 0 -0.72 26 26
TIF2/SUV420H1 -0.001 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.15 0.56 1 -0.53 19 20
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.49 273 -10000 0 273
PBX1 0.008 0.065 -10000 0 -0.72 2 2
POU1F1 0.025 0.032 -10000 0 -0.72 1 1
SELE -0.35 0.38 -10000 0 -0.92 101 101
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.34 232 -10000 0 232
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.47 254 -10000 0 254
mol:cortisol 0.19 0.17 0.32 287 -10000 0 287
MMP1 -0.17 0.08 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.23 0.2 -9999 0 -0.36 374 374
MAP3K8 -0.093 0.25 -9999 0 -0.73 70 70
FOS -0.12 0.12 -9999 0 -0.3 58 58
PRKCA 0.005 0.013 -9999 0 -10000 0 0
PTPN7 -0.003 0.038 -9999 0 -10000 0 0
HRAS 0.013 0.012 -9999 0 -10000 0 0
PRKCB -0.013 0.01 -9999 0 -0.019 374 374
NRAS 0.012 0.019 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.052 0.065 -9999 0 -10000 0 0
MAP2K1 -0.055 0.091 -9999 0 -0.27 58 58
ELK1 0 0.018 -9999 0 -10000 0 0
BRAF -0.018 0.015 -9999 0 -10000 0 0
mol:GTP -0.004 0.003 -9999 0 -0.006 374 374
MAPK1 -0.052 0.065 -9999 0 -10000 0 0
RAF1 -0.018 0.015 -9999 0 -10000 0 0
KRAS 0.01 0.026 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.099 0.25 -9999 0 -0.76 64 64
PDGF/PDGFRA/CRKL -0.068 0.18 -9999 0 -0.56 64 64
positive regulation of JUN kinase activity -0.05 0.14 -9999 0 -0.42 64 64
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.071 0.19 -9999 0 -0.57 65 65
AP1 -0.84 0.54 -9999 0 -1.2 375 375
mol:IP3 -0.084 0.19 -9999 0 -0.6 64 64
PLCG1 -0.084 0.19 -9999 0 -0.6 64 64
PDGF/PDGFRA/alphaV Integrin -0.07 0.18 -9999 0 -0.56 65 65
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
mol:Ca2+ -0.084 0.19 -9999 0 -0.59 64 64
CAV3 0.013 0.046 -9999 0 -0.72 2 2
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
SHC/Grb2/SOS1 -0.05 0.14 -9999 0 -0.42 64 64
PDGF/PDGFRA/Shf -0.068 0.18 -9999 0 -0.56 64 64
FOS -0.8 0.55 -9999 0 -1.1 376 376
JUN -0.15 0.23 -9999 0 -0.62 97 97
oligodendrocyte development -0.07 0.18 -9999 0 -0.56 65 65
GRB2 0.013 0.022 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:DAG -0.084 0.19 -9999 0 -0.6 64 64
PDGF/PDGFRA -0.099 0.25 -9999 0 -0.76 64 64
actin cytoskeleton reorganization -0.07 0.18 -9999 0 -0.56 65 65
SRF 0.046 0.012 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
PI3K -0.1 0.23 -9999 0 -0.56 95 95
PDGF/PDGFRA/Crk/C3G -0.058 0.16 -9999 0 -0.48 64 64
JAK1 -0.058 0.19 -9999 0 -0.56 66 66
ELK1/SRF -0.024 0.16 -9999 0 -0.45 64 64
SHB 0.013 0.037 -9999 0 -0.72 1 1
SHF 0.015 0.012 -9999 0 -10000 0 0
CSNK2A1 0.046 0.028 -9999 0 -10000 0 0
GO:0007205 -0.091 0.2 -9999 0 -0.62 64 64
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.05 0.14 -9999 0 -0.42 64 64
PDGF/PDGFRA/SHB -0.07 0.18 -9999 0 -0.56 65 65
PDGF/PDGFRA/Caveolin-1 -0.47 0.31 -9999 0 -0.64 387 387
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
ELK1 -0.099 0.18 -9999 0 -0.57 64 64
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.069 0.19 -9999 0 -0.57 64 64
JAK-STAT cascade -0.058 0.19 -9999 0 -0.56 66 66
cell proliferation -0.068 0.18 -9999 0 -0.56 64 64
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.008 0.079 -10000 0 -0.72 6 6
EPHB2 0.005 0.04 -10000 0 -10000 0 0
EFNB1 0.027 0.036 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.18 -10000 0 -0.35 197 197
Ephrin B2/EPHB1-2 -0.15 0.22 -10000 0 -0.43 198 198
neuron projection morphogenesis -0.12 0.17 -10000 0 -0.33 197 197
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.2 -10000 0 -0.38 197 197
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.046 0.22 -10000 0 -0.65 58 58
YES1 -0.084 0.28 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/NCK2 -0.13 0.2 -10000 0 -0.38 197 197
PI3K -0.082 0.25 -10000 0 -0.58 95 95
mol:GDP -0.14 0.19 -10000 0 -0.38 197 197
ITGA2B 0.016 0.01 -10000 0 -10000 0 0
endothelial cell proliferation -0.005 0.055 -10000 0 -0.47 7 7
FYN -0.084 0.27 -10000 0 -0.91 52 52
MAP3K7 -0.065 0.22 -10000 0 -0.72 52 52
FGR -0.085 0.27 -10000 0 -0.91 52 52
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.057 0.23 -10000 0 -0.65 55 55
LYN -0.084 0.27 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.081 0.26 -10000 0 -0.85 52 52
Ephrin B1/EPHB1-2 -0.076 0.23 -10000 0 -0.78 52 52
SRC -0.085 0.27 -10000 0 -0.91 52 52
ITGB3 0.014 0.02 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 197 197
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
alphaIIb/beta3 Integrin -0.001 0.011 -10000 0 -10000 0 0
BLK -0.084 0.27 -10000 0 -0.91 52 52
HCK -0.085 0.27 -10000 0 -0.91 52 52
regulation of stress fiber formation 0.14 0.19 0.38 197 -10000 0 197
MAPK8 -0.035 0.21 -10000 0 -0.62 58 58
Ephrin B1/EPHB1-2/RGS3 -0.13 0.2 -10000 0 -0.38 197 197
endothelial cell migration -0.058 0.2 -10000 0 -0.6 57 57
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTPN13 -0.073 0.25 -10000 0 -0.83 52 52
regulation of focal adhesion formation 0.14 0.19 0.38 197 -10000 0 197
chemotaxis 0.14 0.19 0.38 197 -10000 0 197
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.12 0.17 -10000 0 -0.34 197 197
angiogenesis -0.076 0.23 -10000 0 -0.77 52 52
LCK -0.083 0.27 -10000 0 -0.91 52 52
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.082 0.26 -10000 0 -0.77 27 27
CRP -0.082 0.26 -10000 0 -0.78 26 26
cell cycle arrest -0.099 0.3 -10000 0 -0.62 105 105
TIMP1 -0.099 0.23 -10000 0 -0.52 76 76
IL6ST -0.01 0.15 -10000 0 -0.72 21 21
Rac1/GDP -0.16 0.22 -10000 0 -0.47 117 117
AP1 -0.29 0.26 -10000 0 -0.48 291 291
GAB2 0.019 0.018 -10000 0 -10000 0 0
TNFSF11 -0.089 0.26 -10000 0 -0.74 32 32
HSP90B1 0.02 0.065 -10000 0 -0.96 1 1
GAB1 0.017 0.034 -10000 0 -0.72 1 1
MAPK14 -0.2 0.24 -10000 0 -0.76 56 56
AKT1 0.044 0.079 -10000 0 -10000 0 0
FOXO1 -0.004 0.17 -10000 0 -0.41 50 50
MAP2K6 -0.21 0.24 -10000 0 -0.52 124 124
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.12 0.23 -10000 0 -0.48 114 114
MITF -0.19 0.24 -10000 0 -0.51 117 117
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0 -10000 0 -10000 0 0
A2M -0.16 0.5 -10000 0 -1.5 65 65
CEBPB 0.025 0.033 -10000 0 -0.72 1 1
GRB2/SOS1/GAB family/SHP2 -0.025 0.093 0.3 1 -10000 0 1
STAT3 -0.11 0.32 -10000 0 -0.66 106 106
STAT1 -0.001 0.034 -10000 0 -10000 0 0
CEBPD -0.16 0.42 -10000 0 -1.1 71 71
PIK3CA 0.018 0.007 -10000 0 -10000 0 0
PI3K -0.028 0.17 -10000 0 -0.54 51 51
JUN -0.12 0.29 -10000 0 -0.72 97 97
PIAS3/MITF -0.18 0.23 -10000 0 -0.55 84 84
MAPK11 -0.2 0.24 -10000 0 -0.76 56 56
STAT3 (dimer)/FOXO1 -0.12 0.32 -10000 0 -0.68 94 94
GRB2/SOS1/GAB family -0.17 0.17 -10000 0 -0.64 42 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.22 0.23 -10000 0 -0.48 126 126
GRB2 0.016 0.023 -10000 0 -10000 0 0
JAK2 0.015 0.033 -10000 0 -0.72 1 1
LBP -0.088 0.22 -10000 0 -0.65 25 25
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
JAK1 0.017 0.046 -10000 0 -0.73 2 2
MYC -0.11 0.34 -10000 0 -1.1 38 38
FGG -0.083 0.26 -10000 0 -0.77 27 27
macrophage differentiation -0.099 0.3 -10000 0 -0.62 105 105
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.3 0.22 -10000 0 -0.4 396 396
JUNB -0.092 0.26 -10000 0 -0.69 38 38
FOS -0.51 0.34 -10000 0 -0.72 374 374
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.21 0.24 -10000 0 -0.53 120 120
STAT1/PIAS1 -0.17 0.23 -10000 0 -0.51 108 108
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.082 -10000 0 -10000 0 0
STAT3 (dimer) -0.1 0.31 -10000 0 -0.65 105 105
PRKCD -0.092 0.24 -10000 0 -0.48 111 111
IL6R 0.018 0.033 -10000 0 -0.72 1 1
SOCS3 -0.2 0.27 -10000 0 -0.86 55 55
gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.15 -10000 0 -0.47 44 44
Rac1/GTP -0.15 0.23 -10000 0 -0.48 115 115
HCK 0.013 0.024 -10000 0 -10000 0 0
MAPKKK cascade 0.005 0.083 -10000 0 -10000 0 0
bone resorption -0.093 0.25 -10000 0 -0.68 34 34
IRF1 -0.084 0.26 -10000 0 -0.76 28 28
mol:GDP -0.18 0.23 -10000 0 -0.5 118 118
SOS1 0.02 0.008 -10000 0 -10000 0 0
VAV1 -0.19 0.24 -10000 0 -0.5 118 118
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.24 -10000 0 -0.78 56 56
PTPN11 -0.009 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.38 0.25 -10000 0 -0.53 391 391
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.14 -10000 0 -0.47 43 43
gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.15 -10000 0 -0.48 43 43
IL6 -0.52 0.32 -10000 0 -0.72 391 391
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE 0.002 0.045 -10000 0 -0.72 2 2
PIAS1 0.016 0.007 -10000 0 -10000 0 0
RAC1 0.017 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.23 0.21 -10000 0 -0.33 372 372
LMO4 -0.017 0.15 -10000 0 -0.72 22 22
STAT3 (dimer)/PIAS3 -0.17 0.26 -10000 0 -0.64 105 105
MCL1 0.052 0.073 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.036 0.077 -9999 0 -0.42 9 9
SMAD6-7/SMURF1 0 0.004 -9999 0 -10000 0 0
NOG 0.014 0.035 -9999 0 -0.72 1 1
SMAD9 -0.084 0.18 -9999 0 -0.91 20 20
SMAD4 0.013 0.045 -9999 0 -0.72 2 2
SMAD5 -0.15 0.21 -9999 0 -0.56 69 69
BMP7/USAG1 -0.4 0.24 -9999 0 -0.55 377 377
SMAD5/SKI -0.13 0.2 -9999 0 -0.56 61 61
SMAD1 0.025 0.045 -9999 0 -10000 0 0
BMP2 -0.34 0.37 -9999 0 -0.72 252 252
SMAD1/SMAD1/SMAD4 -0.002 0.021 -9999 0 -10000 0 0
BMPR1A 0.009 0.072 -9999 0 -0.72 5 5
BMPR1B -0.046 0.079 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI -0.012 0.16 -9999 0 -0.51 41 41
AHSG 0.016 0 -9999 0 -10000 0 0
CER1 0.016 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.28 0.28 -9999 0 -0.51 289 289
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.21 -9999 0 -0.5 97 97
BMP2-4 (homodimer) -0.33 0.32 -9999 0 -0.6 289 289
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.14 0.23 -9999 0 -0.45 182 182
RGMA -0.097 0.27 -9999 0 -0.72 81 81
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.22 -9999 0 -0.54 95 95
BMP2-4/USAG1 -0.6 0.34 -9999 0 -0.7 444 444
SMAD6/SMURF1/SMAD5 -0.13 0.2 -9999 0 -0.56 61 61
SOSTDC1 -0.51 0.33 -9999 0 -0.72 377 377
BMP7/BMPR2/BMPR1A-1B 0.038 0.065 -9999 0 -0.44 5 5
SKI 0.016 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.24 0.35 -9999 0 -0.72 180 180
HFE2 0.011 0.056 -9999 0 -0.72 3 3
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD -0.28 0.28 -9999 0 -0.51 289 289
SMAD5/SMAD5/SMAD4 -0.14 0.2 -9999 0 -0.56 62 62
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.16 -9999 0 -0.46 76 76
BMP7 (homodimer) -0.002 0.051 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.18 0.26 -9999 0 -0.54 180 180
SMAD1/SKI 0.033 0.043 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.28 0.28 -9999 0 -0.51 289 289
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
GREM1 -0.002 0.051 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.001 0.032 -9999 0 -0.46 2 2
BMPR1A-1B (homodimer) -0.035 0.065 -9999 0 -0.57 5 5
CHRDL1 -0.42 0.36 -9999 0 -0.72 309 309
ENDOFIN/SMAD1 0.033 0.043 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.014 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.064 0.19 -9999 0 -0.72 37 37
SMURF2 0.015 0.012 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.53 0.4 -9999 0 -0.74 378 378
BMP2-4/GREM1 -0.28 0.28 -9999 0 -0.52 289 289
SMAD7 0.016 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.06 0.18 -9999 0 -0.85 21 21
SMAD1/SMAD6 0.033 0.043 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.005 -9999 0 -10000 0 0
BMP7 -0.002 0.051 -9999 0 -10000 0 0
BMP6 -0.24 0.35 -9999 0 -0.72 180 180
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.14 0.21 -9999 0 -0.51 95 95
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.033 0.043 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0.003 -9999 0 -10000 0 0
CTDSPL 0.013 0.045 -9999 0 -0.72 2 2
PPP1CA 0.01 0.032 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.045 -9999 0 -0.72 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.15 0.22 -9999 0 -0.51 97 97
CHRD 0.013 0.022 -9999 0 -10000 0 0
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.19 0.25 -9999 0 -0.64 95 95
BMP4 -0.088 0.26 -9999 0 -0.72 73 73
FST 0.009 0.066 -9999 0 -0.72 4 4
BMP2-4/NOG -0.28 0.28 -9999 0 -0.51 290 290
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.04 0.064 -9999 0 -0.4 5 5
FAS signaling pathway (CD95)

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
SPTAN1 0.054 0.11 0.27 104 -10000 0 104
RFC1 0.054 0.11 0.27 104 -10000 0 104
PRKDC 0.052 0.11 0.27 99 -10000 0 99
RIPK1 0.023 0.004 -10000 0 -10000 0 0
CASP7 -0.047 0.054 -10000 0 -0.99 1 1
FASLG/FAS/FADD/FAF1 -0.033 0.1 0.25 11 -0.37 25 36
MAP2K4 -0.17 0.16 -10000 0 -0.38 70 70
mol:ceramide -0.1 0.13 -10000 0 -0.45 34 34
GSN -0.073 0.23 0.28 76 -0.46 115 191
FASLG/FAS/FADD/FAF1/Caspase 8 -0.047 0.097 -10000 0 -0.35 22 22
FAS -0.045 0.18 -10000 0 -0.74 35 35
BID -0.002 0.008 -10000 0 -10000 0 0
MAP3K1 -0.074 0.11 -10000 0 -0.32 25 25
MAP3K7 0.004 0.012 -10000 0 -10000 0 0
RB1 0.053 0.11 0.27 103 -0.45 1 104
CFLAR 0.02 0.044 -10000 0 -0.69 2 2
HGF/MET -0.089 0.2 -10000 0 -0.49 97 97
ARHGDIB 0.052 0.11 0.28 102 -0.45 1 103
FADD -0.01 0.049 -10000 0 -10000 0 0
actin filament polymerization 0.072 0.23 0.45 115 -0.27 76 191
NFKB1 -0.15 0.093 -10000 0 -0.27 30 30
MAPK8 -0.29 0.23 -10000 0 -0.42 391 391
DFFA 0.054 0.11 0.27 104 -10000 0 104
DNA fragmentation during apoptosis 0.054 0.11 0.27 104 -10000 0 104
FAS/FADD/MET -0.083 0.19 -10000 0 -0.52 80 80
CFLAR/RIP1 -0.002 0.031 -10000 0 -0.5 2 2
FAIM3 0.015 0.03 -10000 0 -10000 0 0
FAF1 0.005 0.008 -10000 0 -10000 0 0
PARP1 0.047 0.11 0.28 87 -10000 0 87
DFFB 0.054 0.11 0.27 104 -10000 0 104
CHUK -0.13 0.084 -10000 0 -0.59 1 1
FASLG -0.011 0.056 -10000 0 -0.73 1 1
FAS/FADD -0.044 0.14 -10000 0 -0.57 35 35
HGF 0.016 0.01 -10000 0 -10000 0 0
LMNA 0.05 0.1 0.25 101 -10000 0 101
CASP6 0.054 0.11 0.27 102 -10000 0 102
CASP10 0.004 0.011 -10000 0 -10000 0 0
CASP3 0.064 0.13 0.33 104 -10000 0 104
PTPN13 -0.057 0.22 -10000 0 -0.72 52 52
CASP8 -0.002 0.009 -10000 0 -10000 0 0
IL6 -0.97 0.6 -10000 0 -1.3 391 391
MET -0.057 0.22 -10000 0 -0.72 52 52
ICAD/CAD 0.051 0.1 0.26 104 -10000 0 104
FASLG/FAS/FADD/FAF1/Caspase 10 -0.1 0.13 -10000 0 -0.47 32 32
activation of caspase activity by cytochrome c -0.002 0.008 -10000 0 -10000 0 0
PAK2 0.054 0.11 0.27 104 -10000 0 104
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.089 0.26 -9999 0 -0.72 75 75
LAT2 -0.048 0.18 -9999 0 -0.4 92 92
AP1 -0.32 0.25 -9999 0 -0.58 215 215
mol:PIP3 -0.047 0.23 -9999 0 -0.46 101 101
IKBKB -0.016 0.14 -9999 0 -0.28 68 68
AKT1 -0.07 0.24 -9999 0 -0.62 58 58
IKBKG -0.016 0.14 -9999 0 -0.28 72 72
MS4A2 -0.12 0.28 -9999 0 -0.72 92 92
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.007 -9999 0 -10000 0 0
MAP3K1 -0.013 0.16 -9999 0 -0.42 47 47
mol:Ca2+ -0.027 0.18 -9999 0 -0.34 101 101
LYN 0.014 0.012 -9999 0 -10000 0 0
CBLB -0.047 0.18 -9999 0 -0.4 92 92
SHC1 0.016 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.18 0.21 -9999 0 -0.42 225 225
positive regulation of cell migration -0.14 0.25 -9999 0 -0.55 147 147
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.085 0.24 -9999 0 -0.46 139 139
PTPN13 -0.072 0.22 -9999 0 -0.58 54 54
PTPN11 0.015 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.017 0.18 -9999 0 -0.39 57 57
SYK 0.009 0.031 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.2 -9999 0 -0.47 101 101
LAT -0.048 0.18 -9999 0 -0.39 93 93
PAK2 -0.021 0.17 -9999 0 -0.44 49 49
NFATC2 -0.041 0.073 -9999 0 -0.61 1 1
HRAS -0.034 0.18 -9999 0 -0.48 51 51
GAB2 0.015 0.016 -9999 0 -10000 0 0
PLA2G1B 0.039 0.021 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.27 -9999 0 -0.58 138 138
Antigen/IgE/Fc epsilon R1 -0.14 0.25 -9999 0 -0.53 138 138
mol:GDP -0.043 0.19 -9999 0 -0.5 51 51
JUN -0.12 0.29 -9999 0 -0.72 97 97
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 51 51
FOS -0.51 0.34 -9999 0 -0.72 374 374
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.092 0.17 -9999 0 -0.41 100 100
CHUK -0.016 0.14 -9999 0 -0.29 69 69
KLRG1 -0.047 0.17 -9999 0 -0.36 92 92
VAV1 -0.051 0.18 -9999 0 -0.4 93 93
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.047 0.18 -9999 0 -0.39 92 92
negative regulation of mast cell degranulation -0.076 0.14 -9999 0 -0.34 92 92
BTK -0.048 0.19 -9999 0 -0.49 53 53
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.087 0.26 -9999 0 -0.46 138 138
GAB2/PI3K/SHP2 -0.14 0.23 -9999 0 -0.7 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.064 0.21 -9999 0 -0.37 138 138
RAF1 0.023 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.24 -9999 0 -0.5 138 138
FCER1G 0.016 0.017 -9999 0 -10000 0 0
FCER1A -0.11 0.28 -9999 0 -0.74 88 88
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.24 -9999 0 -0.5 138 138
MAPK3 0.037 0.021 -9999 0 -10000 0 0
MAPK1 0.037 0.021 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.011 0.077 -9999 0 -0.42 8 8
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
NF-kappa-B/RelA -0.037 0.06 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.046 0.18 -9999 0 -0.51 44 44
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.1 0.18 -9999 0 -0.51 63 63
FER -0.047 0.18 -9999 0 -0.39 92 92
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.021 0.049 -9999 0 -0.56 2 2
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.039 0.2 -9999 0 -0.51 51 51
cytokine secretion -0.027 0.044 -9999 0 -10000 0 0
SPHK1 -0.052 0.19 -9999 0 -0.41 96 96
PTK2 -0.049 0.19 -9999 0 -0.54 43 43
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -9999 0 -0.49 101 101
EDG1 -0.14 0.25 -9999 0 -0.55 147 147
mol:DAG -0.082 0.26 -9999 0 -0.52 112 112
MAP2K2 0.032 0.022 -9999 0 -10000 0 0
MAP2K1 0.032 0.022 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.074 0.14 -9999 0 -0.46 42 42
MAP2K4 0.011 0.11 -9999 0 -0.92 7 7
Fc epsilon R1/FcgammaRIIB -0.14 0.26 -9999 0 -0.53 138 138
mol:Choline -0.084 0.24 -9999 0 -0.45 139 139
SHC/Grb2/SOS1 -0.07 0.15 -9999 0 -0.48 42 42
FYN 0.013 0.045 -9999 0 -0.72 2 2
DOK1 0.014 0.019 -9999 0 -10000 0 0
PXN -0.035 0.18 -9999 0 -0.49 42 42
HCLS1 -0.047 0.18 -9999 0 -0.39 92 92
PRKCB -0.041 0.18 -9999 0 -0.36 106 106
FCGR2B 0.01 0.065 -9999 0 -0.72 4 4
IGHE -0.001 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.078 0.14 -9999 0 -0.43 53 53
LCP2 0.012 0.024 -9999 0 -10000 0 0
PLA2G4A -0.29 0.26 -9999 0 -0.44 354 354
RASA1 0.015 0.012 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.084 0.24 -9999 0 -0.45 139 139
IKK complex 0.007 0.11 -9999 0 -0.22 45 45
WIPF1 0.013 0.024 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.35 0.46 -10000 0 -1.4 48 48
IL23A -0.31 0.38 -10000 0 -1 40 40
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.3 -10000 0 -0.76 102 102
positive regulation of T cell mediated cytotoxicity -0.35 0.41 -10000 0 -0.77 153 153
ITGA3 -0.31 0.38 -10000 0 -1 41 41
IL17F -0.22 0.3 -10000 0 -0.64 71 71
IL12B 0.012 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.34 0.4 -10000 0 -0.75 157 157
CD4 -0.31 0.37 -10000 0 -0.98 40 40
IL23 -0.3 0.37 -10000 0 -0.98 40 40
IL23R -0.04 0.13 -10000 0 -1.6 2 2
IL1B -0.32 0.39 -10000 0 -1.1 40 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.31 0.37 -10000 0 -0.98 40 40
TYK2 0.009 0.019 -10000 0 -10000 0 0
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.017 0 -10000 0 -10000 0 0
IL18RAP -0.046 0.21 -10000 0 -0.72 45 45
IL12RB1 0.009 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.006 0.026 -10000 0 -10000 0 0
IL23R/JAK2 -0.048 0.14 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.35 0.41 -10000 0 -0.77 153 153
natural killer cell activation 0.003 0.009 0.079 2 -10000 0 2
JAK2 0.011 0.043 -10000 0 -0.76 1 1
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
NFKB1 0.014 0.004 -10000 0 -10000 0 0
RELA 0.014 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.29 0.36 -10000 0 -0.94 40 40
ALOX12B -0.31 0.37 -10000 0 -0.98 40 40
CXCL1 -0.77 0.7 -10000 0 -1.4 303 303
T cell proliferation -0.35 0.41 -10000 0 -0.77 153 153
NFKBIA 0.013 0.033 -10000 0 -0.73 1 1
IL17A -0.15 0.25 -10000 0 -0.49 57 57
PI3K -0.39 0.34 -10000 0 -0.84 117 117
IFNG -0.012 0.03 0.15 2 -0.11 6 8
STAT3 (dimer) -0.36 0.32 -10000 0 -0.91 80 80
IL18R1 0.015 0.035 -10000 0 -0.72 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.25 -10000 0 -0.55 50 50
IL18/IL18R -0.01 0.15 -10000 0 -0.47 45 45
macrophage activation -0.021 0.016 -10000 0 -0.042 40 40
TNF -0.32 0.38 -10000 0 -1 40 40
STAT3/STAT4 -0.36 0.32 0.36 1 -0.71 158 159
STAT4 (dimer) -0.34 0.4 -10000 0 -0.76 150 150
IL18 0.003 0.055 -10000 0 -0.72 1 1
IL19 -0.32 0.37 -10000 0 -0.97 43 43
STAT5A (dimer) -0.34 0.39 -10000 0 -0.82 101 101
STAT1 -0.011 0.061 -10000 0 -10000 0 0
SOCS3 -0.005 0.12 -10000 0 -0.72 15 15
CXCL9 -0.33 0.39 -10000 0 -1 47 47
MPO -0.31 0.37 -10000 0 -0.98 40 40
positive regulation of humoral immune response -0.35 0.41 -10000 0 -0.77 153 153
IL23/IL23R/JAK2/TYK2 -0.36 0.43 -10000 0 -0.8 151 151
IL6 -0.93 0.66 -10000 0 -1.3 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
IL2 0.019 0.034 -10000 0 -0.72 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.079 2 -10000 0 2
CD3E -0.31 0.37 -10000 0 -0.98 41 41
keratinocyte proliferation -0.35 0.41 -10000 0 -0.77 153 153
NOS2 -0.32 0.37 -10000 0 -0.69 159 159
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.026 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.35 0.2 -9999 0 -0.46 403 403
PTK2 -0.096 0.11 -9999 0 -0.56 1 1
IGF1R -0.023 0.15 -9999 0 -0.72 23 23
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 -0.023 0.16 -9999 0 -0.72 26 26
SRC 0.016 0.007 -9999 0 -10000 0 0
CDKN1B -0.14 0.12 -9999 0 -0.93 9 9
VEGFA -0.005 0.054 -9999 0 -10000 0 0
ILK -0.12 0.068 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.095 0.078 -9999 0 -10000 0 0
PTK2B 0.04 0.032 -9999 0 -0.38 1 1
alphaV/beta3 Integrin/JAM-A -0.29 0.16 -9999 0 -0.38 403 403
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.023 -9999 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.28 0.31 -9999 0 -0.52 280 280
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.053 0.013 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 0.021 0.043 -9999 0 -0.46 1 1
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.54 0.34 -9999 0 -0.66 412 412
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.028 0.062 -9999 0 -0.46 4 4
RPS6KB1 -0.49 0.3 -9999 0 -0.61 412 412
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.57 0.33 -9999 0 -0.74 403 403
GPR124 -0.015 0.15 -9999 0 -0.72 22 22
MAPK1 -0.57 0.33 -9999 0 -0.74 403 403
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
alphaV/beta3 Integrin/Tumstatin 0.001 0.023 -9999 0 -0.46 1 1
cell adhesion -0.023 0.096 -9999 0 -0.36 37 37
ANGPTL3 0.016 0.001 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.011 0.027 -9999 0 -10000 0 0
IGF-1R heterotetramer -0.023 0.15 -9999 0 -0.72 23 23
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
ITGB3 0.014 0.02 -9999 0 -10000 0 0
IGF1 -0.35 0.37 -9999 0 -0.72 262 262
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.094 -9999 0 -0.46 23 23
apoptosis 0.014 0.034 -9999 0 -0.72 1 1
CD47 0.001 0.11 -9999 0 -0.72 11 11
alphaV/beta3 Integrin/CD47 -0.009 0.069 -9999 0 -0.46 12 12
VCL 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.012 0.1 -9999 0 -0.46 25 25
CSF1 0.016 0.007 -9999 0 -10000 0 0
PIK3C2A -0.12 0.068 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.24 0.14 -9999 0 -0.46 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.012 0.036 -9999 0 -0.41 1 1
FAK1/Vinculin -0.073 0.091 -9999 0 -0.43 1 1
alphaV beta3/Integrin/ppsTEM5 -0.018 0.095 -9999 0 -0.46 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
VTN 0.015 0.012 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
F11R -0.41 0.24 -9999 0 -0.54 403 403
alphaV/beta3 Integrin/Lactadherin -0.021 0.1 -9999 0 -0.46 27 27
alphaV/beta3 Integrin/TGFBR2 -0.033 0.12 -9999 0 -0.46 39 39
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0 0.019 -9999 0 -0.41 1 1
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.001 0.021 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.098 0.074 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.041 0.032 -9999 0 -0.38 1 1
SDC1 -0.027 0.072 -9999 0 -10000 0 0
VAV3 0.037 0.089 -9999 0 -0.38 22 22
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
FAK1/Paxillin -0.073 0.091 -9999 0 -0.43 1 1
cell migration -0.06 0.087 -9999 0 -0.39 1 1
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PI3K -0.29 0.19 -9999 0 -0.63 64 64
SPP1 -0.057 0.094 -9999 0 -0.72 3 3
KDR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.034 -9999 0 -0.72 1 1
COL4A3 0.016 0 -9999 0 -10000 0 0
angiogenesis -0.55 0.33 -9999 0 -0.71 403 403
Rac1/GTP -0.004 0.077 -9999 0 -0.34 22 22
EDIL3 -0.036 0.16 -9999 0 -0.72 24 24
cell proliferation -0.033 0.12 -9999 0 -0.46 39 39
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.07 0.18 -10000 0 -0.39 118 118
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.2 -10000 0 -0.42 120 120
AKT1 -0.18 0.35 -10000 0 -0.82 117 117
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.36 -10000 0 -0.83 117 117
mol:Ca2+ -0.05 0.16 -10000 0 -0.39 77 77
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
E2/ER alpha (dimer)/Striatin -0.091 0.21 -10000 0 -0.47 118 118
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.16 0.34 0.77 117 -10000 0 117
RhoA/GTP -0.069 0.15 -10000 0 -0.34 117 117
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.15 0.2 -10000 0 -0.48 120 120
regulation of stress fiber formation 0.02 0.13 0.33 3 -10000 0 3
E2/ERA-ERB (dimer) -0.089 0.2 -10000 0 -0.47 117 117
KRAS 0.012 0.025 -10000 0 -10000 0 0
G13/GTP -0.081 0.19 -10000 0 -0.43 117 117
pseudopodium formation -0.02 0.13 -10000 0 -0.33 3 3
E2/ER alpha (dimer)/PELP1 -0.089 0.2 -10000 0 -0.47 117 117
GRB2 0.013 0.022 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
GNAO1 0.016 0 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.22 -10000 0 -0.51 118 118
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.092 0.21 -10000 0 -0.49 117 117
mol:NADP -0.12 0.22 -10000 0 -0.51 118 118
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 -0.053 0.17 -10000 0 -0.41 77 77
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
PLCB1 -0.064 0.17 -10000 0 -0.43 77 77
PLCB2 -0.006 0.095 -10000 0 -0.63 6 6
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
mol:L-citrulline -0.12 0.22 -10000 0 -0.51 118 118
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.096 0.13 -10000 0 -0.77 2 2
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.016 0 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
Gq family/GDP/Gbeta gamma 0.032 0.052 -10000 0 -0.78 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.043 0.13 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.15 0.2 -10000 0 -0.48 120 120
GNAZ 0.008 0.078 -10000 0 -0.72 6 6
E2/ER alpha (dimer) -0.14 0.22 -10000 0 -0.55 117 117
STRN 0.014 0.034 -10000 0 -0.72 1 1
GNAL 0.012 0.056 -10000 0 -0.72 3 3
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.024 0 -10000 0 -10000 0 0
GNAI2 0.016 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
HBEGF -0.12 0.18 -10000 0 -0.4 87 87
cAMP biosynthetic process -0.076 0.17 -10000 0 -0.38 119 119
SRC -0.12 0.19 -10000 0 -0.39 120 120
PI3K -0.052 0.16 -10000 0 -0.54 51 51
GNB1 0.016 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.077 0.19 -10000 0 -0.42 118 118
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.27 0.24 -10000 0 -0.49 247 247
Gs family/GTP -0.075 0.17 -10000 0 -0.38 119 119
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.016 -10000 0 -10000 0 0
vasodilation -0.12 0.22 -10000 0 -0.48 118 118
mol:DAG -0.053 0.17 -10000 0 -0.41 77 77
Gs family/GDP/Gbeta gamma -0.079 0.17 -10000 0 -0.39 117 117
MSN -0.023 0.14 -10000 0 -0.36 3 3
Gq family/GTP -0.032 0.094 -10000 0 -0.68 6 6
mol:PI-3-4-5-P3 -0.17 0.34 -10000 0 -0.79 117 117
NRAS 0.014 0.019 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.22 0.48 118 -10000 0 118
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.083 0.2 -10000 0 -0.45 117 117
NOS3 -0.13 0.24 -10000 0 -0.53 118 118
GNA11 0.016 0 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.27 -10000 0 -0.6 118 118
E2/ER alpha (dimer)/PELP1/Src -0.16 0.21 -10000 0 -0.51 120 120
ruffle organization -0.02 0.13 -10000 0 -0.33 3 3
ROCK2 -0.036 0.15 -10000 0 -0.37 16 16
GNA14 -0.008 0.09 -10000 0 -0.72 6 6
GNA15 0.014 0.02 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.43 84 84
MMP2 -0.11 0.18 -10000 0 -0.56 22 22
Signaling events mediated by PRL

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
CCNE1 -0.018 0.066 -9999 0 -10000 0 0
mol:Halofuginone 0.004 0.002 -9999 0 -10000 0 0
ITGA1 0.013 0.045 -9999 0 -0.72 2 2
CDKN1A -0.12 0.079 -9999 0 -0.59 2 2
PRL-3/alpha Tubulin -0.003 0.016 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.04 -9999 0 -10000 0 0
AGT -0.013 0.062 -9999 0 -10000 0 0
CCNA2 -0.32 0.17 -9999 0 -0.43 169 169
TUBA1B 0.015 0.012 -9999 0 -10000 0 0
EGR1 -0.44 0.21 -9999 0 -0.53 436 436
CDK2/Cyclin E1 -0.098 0.082 -9999 0 -0.55 2 2
MAPK3 0.025 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta -0.001 0.011 -9999 0 -10000 0 0
MAPK1 0.025 0.02 -9999 0 -10000 0 0
PTP4A1 -0.32 0.17 -9999 0 -0.4 436 436
PTP4A3 0.01 0.031 -9999 0 -10000 0 0
PTP4A2 0.013 0.022 -9999 0 -10000 0 0
ITGB1 0.025 0.02 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1 -0.12 0.072 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.29 0.16 -9999 0 -0.37 436 436
RABGGTA 0.016 0 -9999 0 -10000 0 0
BCAR1 -0.001 0.008 -9999 0 -10000 0 0
RHOC -0.12 0.072 -9999 0 -10000 0 0
RHOA -0.12 0.072 -9999 0 -10000 0 0
cell motility -0.12 0.078 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.29 0.16 -9999 0 -0.44 6 6
PRL-3/alpha1 Integrin -0.005 0.036 -9999 0 -0.54 2 2
ROCK1 -0.12 0.078 -9999 0 -10000 0 0
RABGGTB 0.016 0 -9999 0 -10000 0 0
CDK2 0.013 0.024 -9999 0 -10000 0 0
mitosis -0.32 0.17 -9999 0 -0.4 436 436
ATF5 0.015 0.012 -9999 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.21 0.48 -10000 0 -0.97 102 102
STAT6 (cleaved dimer) -0.3 0.38 -10000 0 -0.93 112 112
IGHG1 -0.046 0.22 -10000 0 -0.34 61 61
IGHG3 -0.22 0.46 -10000 0 -0.92 108 108
AKT1 -0.069 0.28 -10000 0 -0.52 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.009 0.2 -10000 0 -0.47 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.084 0.3 -10000 0 -0.58 64 64
THY1 -0.21 0.48 -10000 0 -0.97 100 100
MYB -0.049 0.2 -10000 0 -0.72 41 41
HMGA1 0.011 0.028 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.083 0.3 -10000 0 -0.51 95 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.058 0.26 -10000 0 -0.49 36 36
SP1 0.023 0.01 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.018 0.036 -10000 0 -0.72 1 1
STAT6 (dimer)/ETS1 -0.28 0.37 -10000 0 -0.92 107 107
SOCS1 -0.098 0.34 -10000 0 -0.62 98 98
SOCS3 -0.07 0.33 -10000 0 -1.3 16 16
FCER2 -0.21 0.42 -10000 0 -0.78 81 81
PARP14 0.011 0.033 -10000 0 -10000 0 0
CCL17 -0.21 0.48 -10000 0 -0.97 100 100
GRB2 0.013 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.032 0.22 -10000 0 -0.45 15 15
T cell proliferation -0.24 0.49 -10000 0 -0.95 122 122
IL4R/JAK1 -0.22 0.48 -10000 0 -0.99 103 103
EGR2 -0.63 0.81 -10000 0 -1.4 264 264
JAK2 0.014 0.054 -10000 0 -0.76 1 1
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
JAK1 0.016 0.051 -10000 0 -0.72 2 2
COL1A2 -0.041 0.22 -10000 0 -1.6 3 3
CCL26 -0.21 0.48 -10000 0 -0.97 102 102
IL4R -0.23 0.52 -10000 0 -1 103 103
PTPN6 0.02 0.021 -10000 0 -10000 0 0
IL13RA2 -0.22 0.5 -10000 0 -1 107 107
IL13RA1 0.016 0.043 -10000 0 -10000 0 0
IRF4 0.017 0.13 -10000 0 -10000 0 0
ARG1 -0.007 0.2 -10000 0 -1.3 4 4
CBL -0.068 0.28 -10000 0 -0.47 94 94
GTF3A 0.012 0.015 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.072 -10000 0 -0.58 1 1
IRF4/BCL6 -0.027 0.17 -10000 0 -0.52 25 25
CD40LG 0.025 0.022 -10000 0 -10000 0 0
MAPK14 -0.069 0.29 -10000 0 -0.6 39 39
mitosis -0.064 0.27 -10000 0 -0.5 52 52
STAT6 -0.24 0.55 -10000 0 -1.1 104 104
SPI1 0.019 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.055 0.26 -10000 0 -0.5 40 40
STAT6 (dimer) -0.24 0.55 -10000 0 -1.1 104 104
STAT6 (dimer)/PARP14 -0.23 0.49 -10000 0 -1 104 104
mast cell activation 0.001 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.041 0.25 -10000 0 -0.48 26 26
FRAP1 -0.069 0.28 -10000 0 -0.52 51 51
LTA -0.21 0.48 -10000 0 -0.97 102 102
FES 0.013 0.045 -10000 0 -0.72 2 2
T-helper 1 cell differentiation 0.23 0.54 1.1 104 -10000 0 104
CCL11 -0.22 0.46 -10000 0 -0.94 102 102
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.041 0.25 -10000 0 -0.48 25 25
IL2RG 0.011 0.041 -10000 0 -10000 0 0
IL10 -0.21 0.48 -10000 0 -0.97 100 100
IRS1 -0.081 0.25 -10000 0 -0.72 69 69
IRS2 -0.18 0.32 -10000 0 -0.72 137 137
IL4 -0.007 0.16 -10000 0 -10000 0 0
IL5 -0.21 0.48 -10000 0 -0.97 102 102
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.41 -10000 0 -0.77 99 99
COL1A1 -0.053 0.21 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.22 0.49 -10000 0 -1 103 103
IL2R gamma/JAK3 0.033 0.021 -10000 0 -10000 0 0
TFF3 -0.36 0.67 -10000 0 -1.3 151 151
ALOX15 -0.21 0.49 -10000 0 -0.97 103 103
MYBL1 -0.022 0.069 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.16 0.42 -10000 0 -0.76 111 111
SHC1 0.016 0 -10000 0 -10000 0 0
CEBPB 0.022 0.035 -10000 0 -0.72 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.1 0.29 -10000 0 -0.52 92 92
mol:PI-3-4-5-P3 -0.069 0.28 -10000 0 -0.52 51 51
PI3K -0.074 0.29 -10000 0 -0.55 51 51
DOK2 0.013 0.046 -10000 0 -0.72 2 2
ETS1 0.017 0.038 -10000 0 -0.68 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.023 0.21 -10000 0 -0.53 6 6
ITGB3 -0.21 0.48 -10000 0 -0.97 102 102
PIGR -0.57 0.8 -10000 0 -1.4 223 223
IGHE 0.001 0.064 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.21 -10000 0 -0.52 6 6
BCL6 -0.06 0.22 -10000 0 -0.72 53 53
OPRM1 -0.21 0.48 -10000 0 -0.97 101 101
RETNLB -0.21 0.48 -10000 0 -0.97 102 102
SELP -0.44 0.78 -10000 0 -1.5 160 160
AICDA -0.21 0.46 -10000 0 -0.94 102 102
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.008 0.13 -10000 0 -0.37 51 51
adherens junction organization 0.013 0.096 -10000 0 -0.28 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.17 0.22 -10000 0 -0.57 58 58
FMN1 0.011 0.09 -10000 0 -0.28 38 38
mol:IP3 -0.041 0.1 -10000 0 -0.34 51 51
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.094 -10000 0 -0.29 38 38
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
AKT1 0.009 0.12 -10000 0 -0.33 51 51
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.016 0.13 -10000 0 -0.46 37 37
CTNND1 0.015 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.02 0.089 -10000 0 -0.49 1 1
VASP 0.016 0.091 -10000 0 -0.27 38 38
ZYX 0.02 0.091 -10000 0 -0.27 39 39
JUB 0.006 0.12 -10000 0 -0.42 21 21
EGFR(dimer) -0.19 0.23 -10000 0 -0.39 277 277
E-cadherin/beta catenin-gamma catenin -0.026 0.12 -10000 0 -0.44 38 38
mol:PI-3-4-5-P3 -0.046 0.11 -10000 0 -0.35 51 51
PIK3CA 0.015 0.009 -10000 0 -10000 0 0
PI3K -0.046 0.11 -10000 0 -0.36 51 51
FYN 0.023 0.11 -10000 0 -0.48 3 3
mol:Ca2+ 0.003 0.12 -10000 0 -0.33 51 51
JUP 0.014 0.035 -10000 0 -0.72 1 1
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
mol:DAG -0.041 0.1 -10000 0 -0.34 51 51
CDH1 -0.033 0.18 -10000 0 -0.72 33 33
RhoA/GDP -0.17 0.22 -10000 0 -0.55 62 62
establishment of polarity of embryonic epithelium 0.016 0.09 -10000 0 -0.27 38 38
SRC 0.016 0.007 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.38 0.37 -10000 0 -0.72 277 277
CASR 0.013 0.12 -10000 0 -0.31 51 51
RhoA/GTP -0.036 0.092 -10000 0 -0.3 51 51
AKT2 0.009 0.12 -10000 0 -0.33 51 51
actin cable formation 0.015 0.089 -10000 0 -0.26 38 38
apoptosis 0.044 0.11 0.35 51 -10000 0 51
CTNNA1 0.016 0.005 -10000 0 -10000 0 0
mol:GDP -0.19 0.24 -10000 0 -0.39 293 293
PIP5K1A 0.019 0.09 -10000 0 -0.5 1 1
PLCG1 -0.042 0.11 -10000 0 -0.34 51 51
Rac1/GTP -0.19 0.18 -10000 0 -0.35 277 277
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0 0.003 -9999 0 -10000 0 0
Necdin/E2F1 -0.15 0.24 -9999 0 -0.56 135 135
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.087 0.18 -9999 0 -0.42 110 110
NGF (dimer)/p75(NTR)/BEX1 -0.078 0.19 -9999 0 -0.48 94 94
NT-4/5 (dimer)/p75(NTR) -0.098 0.21 -9999 0 -0.55 94 94
IKBKB 0.014 0.02 -9999 0 -10000 0 0
AKT1 -0.076 0.21 -9999 0 -0.43 131 131
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF 0.006 0.057 -9999 0 -0.72 2 2
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.19 -9999 0 -0.47 94 94
FURIN 0.013 0.024 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.081 0.18 -9999 0 -0.46 96 96
LINGO1 -0.01 0.059 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.002 0.016 -9999 0 -10000 0 0
proBDNF (dimer) 0.006 0.057 -9999 0 -0.72 2 2
NTRK1 0.014 0.019 -9999 0 -10000 0 0
RTN4R 0.007 0.037 -9999 0 -10000 0 0
neuron apoptosis -0.015 0.17 -9999 0 -0.38 94 94
IRAK1 0.014 0.02 -9999 0 -10000 0 0
SHC1 -0.064 0.19 -9999 0 -0.47 94 94
ARHGDIA 0.015 0.014 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.086 0.18 -9999 0 -0.44 103 103
MAGEH1 -0.003 0.12 -9999 0 -0.72 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.27 -9999 0 -0.52 186 186
Mammalian IAPs/DIABLO -0.025 0.11 -9999 0 -0.42 35 35
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.006 0.04 -9999 0 -10000 0 0
APP 0.006 0.074 -9999 0 -0.72 5 5
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.015 0.014 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.045 0.16 -9999 0 -0.4 94 94
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.062 0.15 -9999 0 -0.38 94 94
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.02 0.13 -9999 0 -0.3 94 94
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.084 0.18 -9999 0 -0.47 94 94
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.086 0.2 -9999 0 -0.5 96 96
PSENEN 0.014 0.019 -9999 0 -10000 0 0
mol:ceramide -0.047 0.17 -9999 0 -0.42 94 94
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.009 0.11 -9999 0 -0.26 5 5
p75(NTR)/beta APP -0.1 0.22 -9999 0 -0.55 97 97
BEX1 -0.006 0.056 -9999 0 -10000 0 0
mol:GDP -0.076 0.19 -9999 0 -0.48 94 94
NGF (dimer) -0.068 0.16 -9999 0 -0.42 86 86
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.059 0.17 -9999 0 -0.42 94 94
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RAC1/GTP -0.073 0.16 -9999 0 -0.41 94 94
MYD88 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
NGF (dimer)/p75(NTR)/PKA -0.087 0.2 -9999 0 -0.5 96 96
RHOB 0.013 0.046 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.01 0.026 -9999 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -9999 0 -0.72 150 150
TP53 -0.02 0.16 -9999 0 -0.36 96 96
PRDM4 -0.048 0.17 -9999 0 -0.42 94 94
BDNF (dimer) -0.032 0.2 -9999 0 -0.46 89 89
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
SORT1 0.016 0.007 -9999 0 -10000 0 0
activation of caspase activity -0.086 0.17 -9999 0 -0.41 110 110
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.16 -9999 0 -0.42 94 94
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.17 -9999 0 -0.36 94 94
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.048 0.17 -9999 0 -0.42 94 94
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.01 0.032 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.084 0.18 -9999 0 -0.47 94 94
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.003 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.25 0.31 -9999 0 -0.6 216 216
MAPK8 -0.008 0.17 -9999 0 -0.36 94 94
MAPK9 -0.007 0.17 -9999 0 -0.36 94 94
APAF1 0.016 0.007 -9999 0 -10000 0 0
NTF3 -0.2 0.33 -9999 0 -0.72 150 150
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.17 0.32 -9999 0 -0.72 135 135
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.067 0.16 -9999 0 -0.39 97 97
p75 CTF/Sortilin/TRAF6/NRIF 0.001 0.009 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.086 0.2 -9999 0 -0.5 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.065 0.15 -9999 0 -0.38 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.072 0.16 -9999 0 -0.41 96 96
PRKACB -0.007 0.099 -9999 0 -0.72 8 8
proBDNF (dimer)/p75 ECD -0.006 0.037 -9999 0 -0.54 2 2
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.038 0.18 -9999 0 -0.72 35 35
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.23 -9999 0 -0.54 107 107
BAD -0.003 0.17 -9999 0 -0.36 94 94
RIPK2 0.014 0.02 -9999 0 -10000 0 0
NGFR -0.12 0.28 -9999 0 -0.72 94 94
CYCS -0.04 0.16 -9999 0 -0.39 94 94
ADAM17 0.016 0.007 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.075 0.16 -9999 0 -0.42 94 94
BCL2L11 -0.003 0.17 -9999 0 -0.36 94 94
BDNF (dimer)/p75(NTR) -0.1 0.21 -9999 0 -0.54 96 96
PI3K -0.12 0.21 -9999 0 -0.46 131 131
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.075 0.16 -9999 0 -0.42 94 94
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
PRKCI 0.013 0.022 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.098 0.21 -9999 0 -0.55 94 94
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.072 0.17 -9999 0 -0.43 94 94
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.048 0.18 -9999 0 -0.43 96 96
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
NGFRAP1 -0.016 0.15 -9999 0 -0.72 23 23
CASP3 0.001 0.16 -9999 0 -0.33 94 94
E2F1 -0.006 0.055 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.03 0.07 -9999 0 -0.37 1 1
NGF (dimer)/TRKA -0.001 0.011 -9999 0 -10000 0 0
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.069 0.15 -9999 0 -0.39 94 94
MMP3 -0.078 0.11 -9999 0 -0.72 8 8
APAF-1/Caspase 9 -0.068 0.14 -9999 0 -0.59 10 10
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.36 0.21 -9999 0 -0.47 407 407
fibroblast growth factor receptor signaling pathway -0.36 0.21 -9999 0 -0.47 407 407
LAMA1 0.016 0.01 -9999 0 -10000 0 0
PRNP -0.003 0.12 -9999 0 -0.72 14 14
GPC1/SLIT2 -0.071 0.18 -9999 0 -0.54 69 69
SMAD2 0.009 0.12 -9999 0 -0.41 38 38
GPC1/PrPc/Cu2+ -0.012 0.076 -9999 0 -0.47 14 14
GPC1/Laminin alpha1 -0.001 0.008 -9999 0 -10000 0 0
TDGF1 0.016 0 -9999 0 -10000 0 0
CRIPTO/GPC1 0 0.006 -9999 0 -10000 0 0
APP/GPC1 -0.007 0.053 -9999 0 -0.54 5 5
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.034 0.022 -9999 0 -0.46 1 1
FLT1 0.016 0.01 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.032 0.12 -9999 0 -0.46 38 38
SERPINC1 0.012 0.025 -9999 0 -10000 0 0
FYN 0.033 0.031 -9999 0 -0.46 2 2
FGR 0.035 0.006 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.061 0.021 -9999 0 -10000 0 0
SLIT2 -0.081 0.25 -9999 0 -0.72 69 69
GPC1/NRG -0.07 0.18 -9999 0 -0.54 67 67
NRG1 -0.079 0.25 -9999 0 -0.72 67 67
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.011 0.028 -9999 0 -10000 0 0
LYN 0.035 0.008 -9999 0 -10000 0 0
mol:Spermine 0.014 0.008 -9999 0 -10000 0 0
cell growth -0.36 0.21 -9999 0 -0.47 407 407
BMP signaling pathway -0.015 0.012 -9999 0 -10000 0 0
SRC 0.035 0.007 -9999 0 -10000 0 0
TGFBR1 0.014 0.017 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.1 0.26 -9999 0 -0.72 79 79
GPC1 0.015 0.012 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.014 0.017 -9999 0 -10000 0 0
VEGFA -0.005 0.054 -9999 0 -10000 0 0
BLK 0.028 0.025 -9999 0 -10000 0 0
HCK 0.033 0.014 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
VEGFR1 homodimer 0.016 0.01 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
cell death -0.007 0.053 -9999 0 -0.54 5 5
ATIII/GPC1 -0.002 0.013 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.086 0.19 -9999 0 -0.54 79 79
LCK 0.027 0.026 -9999 0 -10000 0 0
neuron differentiation -0.069 0.18 -9999 0 -0.54 67 67
PrPc/Cu2+ -0.015 0.089 -9999 0 -0.55 14 14
APP 0.006 0.074 -9999 0 -0.72 5 5
TGFBR2 (dimer) -0.037 0.19 -9999 0 -0.72 38 38
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.026 -9999 0 -0.54 1 1
PTK2 -0.083 0.19 -9999 0 -0.49 89 89
positive regulation of JNK cascade -0.054 0.12 -9999 0 -0.32 89 89
CDC42/GDP -0.008 0.19 -9999 0 -0.43 89 89
Rac1/GDP -0.006 0.19 -9999 0 -0.42 89 89
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
CDC42/GTP -0.066 0.15 -9999 0 -0.39 89 89
nectin-3/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
RAPGEF1 -0.022 0.21 -9999 0 -0.48 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.04 0.24 -9999 0 -0.56 89 89
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 -0.02 0.16 -9999 0 -0.64 23 23
Rap1/GTP -0.056 0.13 -9999 0 -0.33 89 89
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
PVR 0.014 0.017 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0.017 -9999 0 -10000 0 0
mol:GDP -0.025 0.23 -9999 0 -0.53 89 89
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.1 0.2 -9999 0 -0.44 124 124
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
positive regulation of lamellipodium assembly -0.056 0.12 -9999 0 -0.33 89 89
PVRL1 0.016 0.01 -9999 0 -10000 0 0
PVRL3 -0.1 0.27 -9999 0 -0.72 83 83
PVRL2 0.01 0.032 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
CLDN1 -0.055 0.2 -9999 0 -0.72 42 42
JAM-A/CLDN1 -0.1 0.22 -9999 0 -0.48 116 116
SRC -0.1 0.24 -9999 0 -0.63 89 89
ITGB3 0.014 0.02 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
FARP2 -0.03 0.22 -9999 0 -0.52 89 89
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.08 0.18 -9999 0 -0.48 89 89
nectin-1/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
nectin-2/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
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 -0.081 0.18 -9999 0 -0.48 89 89
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.012 0.027 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.054 0.12 -9999 0 -0.32 89 89
alphaV/beta3 Integrin/Talin 0 0.15 -9999 0 -0.61 21 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
nectin-2(dimer)/I-afadin/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
PIP5K1C -0.032 0.17 -9999 0 -0.68 23 23
VAV2 -0.032 0.23 -9999 0 -0.53 89 89
RAP1/GDP -0.066 0.15 -9999 0 -0.39 89 89
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.079 0.19 -9999 0 -0.48 89 89
nectin-3(dimer)/I-afadin/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
Rac1/GTP -0.068 0.15 -9999 0 -0.4 89 89
PTPRM -0.048 0.19 -9999 0 -0.37 96 96
E-cadherin/beta catenin/alpha catenin -0.027 0.11 -9999 0 -0.37 46 46
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.002 0.11 -10000 0 -0.29 60 60
epithelial cell differentiation -0.026 0.1 -10000 0 -0.39 37 37
CYFIP2 -0.002 0.051 -10000 0 -10000 0 0
ENAH 0.058 0.085 -10000 0 -0.43 2 2
EGFR -0.38 0.37 -10000 0 -0.72 277 277
EPHA2 0.005 0.09 -10000 0 -0.72 8 8
MYO6 0.019 0.11 -10000 0 -0.37 38 38
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
ABI1/Sra1/Nap1 0.009 0.026 -10000 0 -10000 0 0
AQP5 -0.18 0.26 -10000 0 -0.55 157 157
CTNND1 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.1 -10000 0 -0.36 37 37
regulation of calcium-dependent cell-cell adhesion -0.015 0.15 -10000 0 -0.37 79 79
EGF -0.24 0.35 -10000 0 -0.72 178 178
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.081 0.2 -10000 0 -0.56 65 65
cortical microtubule organization -0.026 0.1 -10000 0 -0.39 37 37
GO:0000145 0.019 0.099 -10000 0 -0.34 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.026 0.1 -10000 0 -0.39 37 37
MLLT4 0.002 0.1 -10000 0 -0.72 10 10
ARF6/GDP -0.025 0.085 -10000 0 -0.64 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -10000 0 -0.41 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.034 0.1 -10000 0 -0.33 37 37
PVRL2 0.01 0.032 -10000 0 -10000 0 0
ZYX 0.018 0.11 -10000 0 -0.36 38 38
ARF6/GTP -0.003 0.048 -10000 0 -0.37 8 8
CDH1 -0.032 0.18 -10000 0 -0.72 33 33
EGFR/EGFR/EGF/EGF -0.33 0.26 -10000 0 -0.46 382 382
RhoA/GDP -0.024 0.092 -10000 0 -0.36 37 37
actin cytoskeleton organization 0.026 0.1 -10000 0 -0.34 38 38
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
GIT1 0.015 0.016 -10000 0 -10000 0 0
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
DIAPH1 0.012 0.026 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.026 0.1 0.39 37 -10000 0 37
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.086 -10000 0 -0.64 2 2
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.026 0.11 -10000 0 -0.35 38 38
EFNA1 0.013 0.022 -10000 0 -10000 0 0
LPP 0.029 0.1 -10000 0 -0.34 37 37
Ephrin A1/EPHA2 -0.028 0.1 -10000 0 -0.36 43 43
SEC6/SEC8 -0.027 0.091 -10000 0 -0.44 4 4
MGAT3 -0.015 0.15 -10000 0 -0.38 79 79
HGF/MET -0.057 0.14 -10000 0 -0.37 84 84
HGF 0.016 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.002 0.11 -10000 0 -0.3 60 60
actin cable formation 0.08 0.081 -10000 0 -0.32 3 3
KIAA1543 0.028 0.1 -10000 0 -0.34 37 37
KIFC3 0.019 0.1 -10000 0 -0.36 37 37
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.019 0.1 -10000 0 -0.36 37 37
NCK1/GIT1 -0.001 0.008 -10000 0 -10000 0 0
mol:GDP -0.026 0.1 -10000 0 -0.39 37 37
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.019 0.1 -10000 0 -0.36 37 37
PIP5K1C 0.019 0.1 -10000 0 -0.36 37 37
LIMA1 -0.016 0.15 -10000 0 -0.72 23 23
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 -0.02 0.075 -10000 0 -0.54 2 2
adherens junction assembly 0.05 0.097 -10000 0 -0.37 1 1
IGF-1R heterotetramer/IGF1 -0.21 0.22 -10000 0 -0.39 290 290
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.014 0.075 -10000 0 -0.54 10 10
MET -0.057 0.22 -10000 0 -0.72 52 52
PLEKHA7 0.019 0.1 -10000 0 -0.36 37 37
mol:GTP -0.004 0.052 -10000 0 -0.41 8 8
establishment of epithelial cell apical/basal polarity 0.044 0.11 -10000 0 -0.41 4 4
cortical actin cytoskeleton stabilization 0.002 0.11 -10000 0 -0.29 60 60
regulation of cell-cell adhesion 0.026 0.1 -10000 0 -0.34 38 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.002 0.11 -10000 0 -0.3 60 60
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.003 0.09 -10000 0 -0.42 8 8
epithelial cell differentiation 0.026 0.08 -10000 0 -10000 0 0
ITCH 0.025 0.02 -10000 0 -10000 0 0
WWP1 0.008 0.077 -10000 0 -10000 0 0
FYN 0.013 0.045 -10000 0 -0.72 2 2
EGFR -0.38 0.37 -10000 0 -0.72 277 277
PRL 0.016 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.012 0.14 -10000 0 -0.41 10 10
PTPRZ1 -0.5 0.34 -10000 0 -0.72 370 370
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.12 -10000 0 -0.45 13 13
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.04 0.16 -10000 0 -0.43 70 70
ADAM17 0.024 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.097 -10000 0 -0.46 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.087 -10000 0 -0.41 6 6
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.031 0.16 -10000 0 -0.41 67 67
GRIN2B -0.028 0.16 -10000 0 -0.38 79 79
ErbB4/ErbB2/betacellulin 0 0.11 -10000 0 -0.42 26 26
STAT1 -0.011 0.061 -10000 0 -10000 0 0
HBEGF 0.011 0.064 -10000 0 -0.72 4 4
PRLR -0.026 0.071 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.054 0.19 -10000 0 -0.5 71 71
axon guidance 0.12 0.12 -10000 0 -0.3 7 7
NEDD4 0.017 0.073 -10000 0 -0.7 5 5
Prolactin receptor/Prolactin receptor/Prolactin -0.02 0.034 -10000 0 -10000 0 0
CBFA2T3 -0.084 0.25 -10000 0 -0.72 70 70
ErbB4/ErbB2/HBEGF 0.017 0.075 -10000 0 -0.4 6 6
MAPK3 0.002 0.14 -10000 0 -0.43 11 11
STAT1 (dimer) 0.007 0.095 -10000 0 -0.4 4 4
MAPK1 0.002 0.14 -10000 0 -0.43 11 11
JAK2 0.015 0.033 -10000 0 -0.72 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.038 0.16 -10000 0 -0.41 69 69
NRG1 -0.04 0.19 -10000 0 -0.55 67 67
NRG3 0.009 0.052 -10000 0 -0.72 2 2
NRG2 -0.48 0.35 -10000 0 -0.72 353 353
NRG4 0.015 0.014 -10000 0 -10000 0 0
heart development 0.12 0.12 -10000 0 -0.3 7 7
neural crest cell migration -0.037 0.16 -10000 0 -0.4 69 69
ERBB2 0.021 0.044 -10000 0 -0.53 1 1
WWOX/E4ICDs 0.007 0.083 -10000 0 -0.4 4 4
SHC1 0.016 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.23 0.18 -10000 0 -0.4 281 281
apoptosis 0.017 0.066 0.36 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.31 0.22 -10000 0 -0.45 354 354
ErbB4/ErbB2/epiregulin 0.019 0.076 -10000 0 -0.42 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.13 -10000 0 -0.45 28 28
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.004 0.083 -10000 0 -0.41 4 4
MDM2 0.009 0.084 -10000 0 -0.4 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.14 -10000 0 -0.41 67 67
STAT5A 0.12 0.11 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.25 0.26 -10000 0 -0.46 290 290
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.061 -10000 0 -0.38 6 6
STAT5A (dimer) 0.032 0.093 -10000 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -10000 0 -0.72 1 1
STAT5B (dimer) 0.11 0.1 -10000 0 -10000 0 0
LRIG1 -0.019 0.16 -10000 0 -0.72 25 25
EREG -0.001 0.064 -10000 0 -0.72 2 2
BTC -0.019 0.16 -10000 0 -0.72 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.12 0.12 -10000 0 -0.3 7 7
ERBB4 0 0.097 -10000 0 -0.47 4 4
STAT5B 0.016 0.007 -10000 0 -10000 0 0
YAP1 -0.011 0.058 -10000 0 -0.63 4 4
GRB2 0.013 0.022 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.02 0.069 -10000 0 -0.46 2 2
glial cell differentiation 0.024 0.061 0.38 6 -10000 0 6
WWOX 0.009 0.033 -10000 0 -10000 0 0
cell proliferation 0.022 0.16 -10000 0 -0.45 16 16
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.038 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.17 -9999 0 -0.47 82 82
JUN -0.074 0.19 -9999 0 -0.42 98 98
HRAS 0.015 0.012 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.01 0.18 -9999 0 -0.43 72 72
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.011 0.039 -9999 0 -0.72 1 1
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.013 0.18 -9999 0 -0.42 68 68
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
RET9/GFRalpha1/GDNF/Enigma -0.017 0.16 -9999 0 -0.42 68 68
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP 0.01 0.15 -9999 0 -0.37 68 68
GRB7 0.001 0.048 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.015 0.18 -9999 0 -0.42 68 68
MAPKKK cascade -0.003 0.13 -9999 0 -0.38 14 14
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.074 0.25 -9999 0 -0.53 109 109
lamellipodium assembly -0.12 0.17 -9999 0 -0.4 103 103
RET51/GFRalpha1/GDNF/SHC 0.015 0.18 -9999 0 -0.42 68 68
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.017 0.16 -9999 0 -0.42 68 68
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.16 -9999 0 -0.42 68 68
MAPK3 -0.057 0.12 -9999 0 -0.35 68 68
DOK1 0.014 0.019 -9999 0 -10000 0 0
DOK6 0.009 0.06 -9999 0 -0.72 3 3
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.034 0.12 -9999 0 -0.38 15 15
DOK5 -0.018 0.15 -9999 0 -0.72 23 23
GFRA1 -0.16 0.23 -9999 0 -0.72 68 68
MAPK8 -0.005 0.1 -9999 0 -0.3 14 14
HRAS/GTP 0.01 0.16 -9999 0 -0.39 68 68
tube development -0.013 0.15 -9999 0 -0.39 68 68
MAPK1 -0.057 0.12 -9999 0 -0.35 68 68
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PDLIM7 0.016 0.007 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.018 0.17 -9999 0 -0.41 69 69
SHC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.015 0.18 -9999 0 -0.42 68 68
RET51/GFRalpha1/GDNF/Dok5 -0.009 0.21 -9999 0 -0.45 88 88
PRKCA 0.016 0.01 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
CREB1 -0.011 0.12 -9999 0 -0.32 68 68
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/Grb7 0.011 0.18 -9999 0 -0.44 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.062 0.081 -9999 0 -10000 0 0
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.072 0.19 -9999 0 -0.41 98 98
RET9/GFRalpha1/GDNF/FRS2 -0.017 0.16 -9999 0 -0.42 69 69
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.009 0.11 -9999 0 -0.3 68 68
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.007 0.11 -9999 0 -0.29 68 68
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.11 -9999 0 -0.29 68 68
PI3K -0.16 0.3 -9999 0 -0.68 103 103
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.01 0.15 -9999 0 -0.39 68 68
GRB10 0.011 0.064 -9999 0 -0.72 4 4
activation of MAPKK activity -0.012 0.1 -9999 0 -0.3 13 13
RET51/GFRalpha1/GDNF/FRS2 0.012 0.18 -9999 0 -0.42 69 69
GAB1 0.014 0.034 -9999 0 -0.72 1 1
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
IRS2 -0.18 0.32 -9999 0 -0.72 137 137
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/PKC alpha 0.015 0.18 -9999 0 -0.42 68 68
GRB2 0.013 0.022 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.016 0.007 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.044 0.27 -9999 0 -0.54 109 109
Rac1/GTP -0.14 0.21 -9999 0 -0.5 103 103
RET9/GFRalpha1/GDNF -0.027 0.17 -9999 0 -0.47 68 68
GFRalpha1/GDNF -0.11 0.17 -9999 0 -0.54 68 68
Insulin Pathway

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
CBL/APS/CAP -0.25 0.23 -9999 0 -0.42 311 311
TC10/GTP -0.2 0.18 -9999 0 -0.35 292 292
Insulin Receptor/Insulin/IRS1/Shp2 -0.053 0.14 -9999 0 -0.42 69 69
HRAS 0.015 0.012 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.091 0.23 -9999 0 -0.72 57 57
FOXO3 -0.016 0.031 -9999 0 -10000 0 0
AKT1 -0.06 0.2 -9999 0 -0.57 30 30
INSR 0.019 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.064 -9999 0 -0.72 4 4
SORBS1 -0.39 0.37 -9999 0 -0.72 292 292
CRK 0.015 0.032 -9999 0 -0.72 1 1
PTPN1 0.045 0.036 -9999 0 -10000 0 0
CAV1 -0.33 0.25 -9999 0 -0.46 394 394
CBL/APS/CAP/Crk-II/C3G -0.22 0.2 -9999 0 -0.39 292 292
Insulin Receptor/Insulin/IRS1/NCK2 -0.054 0.14 -9999 0 -0.42 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.083 0.16 -9999 0 -0.38 113 113
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.016 0.098 -9999 0 -10000 0 0
RPS6KB1 -0.046 0.19 -9999 0 -0.55 25 25
PARD6A 0.015 0.016 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.002 0.012 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.093 0.16 -9999 0 -0.57 24 24
HRAS/GTP -0.04 0.1 -9999 0 -0.37 3 3
Insulin Receptor 0.018 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.047 0.13 -9999 0 -0.38 69 69
PRKCI -0.02 0.058 -9999 0 -0.63 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.11 0.19 -9999 0 -0.57 39 39
SHC1 0.016 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.002 0.013 -9999 0 -10000 0 0
PI3K -0.084 0.17 -9999 0 -0.39 113 113
NCK2 0.016 0.01 -9999 0 -10000 0 0
RHOQ 0.015 0.032 -9999 0 -0.72 1 1
mol:H2O2 -0.001 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
AKT2 -0.06 0.2 -9999 0 -0.63 24 24
PRKCZ -0.026 0.059 -9999 0 -0.64 2 2
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.014 0.14 -9999 0 -0.37 69 69
F2RL2 -0.007 0.075 -9999 0 -0.72 3 3
TRIP10 0.015 0.032 -9999 0 -0.72 1 1
Insulin Receptor/Insulin/Shc 0.001 0.005 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst -0.002 0.029 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.004 0.015 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.23 0.21 -9999 0 -0.42 292 292
TC10/GDP -0.001 0.024 -9999 0 -0.55 1 1
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.037 -9999 0 -0.42 4 4
INPP5D -0.026 0.15 -9999 0 -0.4 69 69
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.01 0.016 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
p62DOK/RasGAP 0.002 0.013 -9999 0 -10000 0 0
INS 0.019 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.025 0.14 -9999 0 -0.4 69 69
GRB2 0.013 0.022 -9999 0 -10000 0 0
EIF4EBP1 -0.049 0.19 -9999 0 -0.54 28 28
PTPRA 0.019 0.002 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.002 0.029 -9999 0 -0.47 2 2
PDPK1 0.016 0.007 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.11 -9999 0 -0.31 2 2
Insulin Receptor/Insulin/IRS1 -0.055 0.14 -9999 0 -0.43 69 69
Insulin Receptor/Insulin/IRS3 0.001 0.003 -9999 0 -10000 0 0
Par3/Par6 0.007 0.047 -9999 0 -0.39 5 5
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0.004 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.009 0.039 -9999 0 -0.47 2 2
PDE6G/GNAT1/GTP 0.001 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.016 0.007 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.16 0.18 -9999 0 -0.36 238 238
mol:Na + -0.15 0.18 -9999 0 -0.57 11 11
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.018 0.13 -9999 0 -0.47 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.18 -9999 0 -0.6 11 11
CNGB1 0.016 0 -9999 0 -10000 0 0
RDH5 -0.58 0.29 -9999 0 -0.72 428 428
SAG -0.013 0.074 -9999 0 -0.72 2 2
mol:Ca2+ -0.11 0.2 -9999 0 -0.55 11 11
Na + (4 Units) -0.14 0.16 -9999 0 -0.53 11 11
RGS9 -0.03 0.18 -9999 0 -0.72 32 32
GNB1/GNGT1 -0.018 0.034 -9999 0 -10000 0 0
GNAT1/GDP -0.013 0.11 -9999 0 -0.4 35 35
GUCY2D 0.016 0 -9999 0 -10000 0 0
GNGT1 -0.022 0.068 -9999 0 -10000 0 0
GUCY2F 0.012 0.047 -9999 0 -0.72 2 2
GNB5 0.015 0.032 -9999 0 -0.72 1 1
mol:GMP (4 units) 0.029 0.069 -9999 0 -0.39 14 14
mol:11-cis-retinal -0.58 0.29 -9999 0 -0.72 428 428
mol:cGMP -0.01 0.073 -9999 0 -0.44 13 13
GNB1 0.016 0.01 -9999 0 -10000 0 0
Rhodopsin -0.44 0.21 -9999 0 -0.54 428 428
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.31 0.36 -9999 0 -0.72 230 230
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.009 0.069 -9999 0 -0.44 12 12
RGS9BP -0.015 0.076 -9999 0 -0.72 2 2
Metarhodopsin II/Transducin 0.029 0.005 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.009 0.071 -9999 0 -0.46 12 12
PDE6A/B -0.015 0.087 -9999 0 -0.54 14 14
mol:Pi -0.018 0.12 -9999 0 -0.47 35 35
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.018 0.033 -9999 0 -10000 0 0
PDE6B -0.005 0.12 -9999 0 -0.72 14 14
PDE6A 0.016 0.01 -9999 0 -10000 0 0
PDE6G 0.015 0.012 -9999 0 -10000 0 0
RHO 0.016 0 -9999 0 -10000 0 0
PDE6 -0.02 0.12 -9999 0 -0.39 47 47
GUCA1A 0.003 0.096 -9999 0 -0.72 9 9
GC2/GCAP Family -0.01 0.078 -9999 0 -0.47 13 13
GUCA1C 0.011 0.057 -9999 0 -0.72 3 3
GUCA1B 0.015 0.033 -9999 0 -0.72 1 1
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.003 0.028 -10000 0 -0.47 1 1
cell-cell adhesion 0.12 0.16 0.45 21 -10000 0 21
Ephrin B/EPHB2/RasGAP 0.001 0.053 -10000 0 -0.38 8 8
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.001 0.03 -10000 0 -0.47 2 2
Ephrin B1/EPHB1 -0.18 0.23 -10000 0 -0.47 197 197
HRAS/GDP -0.12 0.16 -10000 0 -0.52 15 15
Ephrin B/EPHB1/GRB7 -0.15 0.2 -10000 0 -0.4 198 198
Endophilin/SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
KRAS 0.012 0.025 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.15 0.2 -10000 0 -0.39 198 198
endothelial cell migration -0.041 0.13 -10000 0 -0.4 56 56
GRB2 0.013 0.022 -10000 0 -10000 0 0
GRB7 0.001 0.048 -10000 0 -10000 0 0
PAK1 0.053 0.059 -10000 0 -0.38 8 8
HRAS 0.015 0.012 -10000 0 -10000 0 0
RRAS 0.038 0.052 -10000 0 -0.36 8 8
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.11 0.21 -10000 0 -0.37 199 199
lamellipodium assembly -0.12 0.16 -10000 0 -0.45 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.08 0.18 -10000 0 -0.3 198 198
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
EPHB2 0.006 0.04 -10000 0 -10000 0 0
EPHB3 0.014 0.017 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 197 197
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
mol:GDP -0.1 0.14 -10000 0 -0.62 10 10
Ephrin B/EPHB2 0 0.052 -10000 0 -0.39 8 8
Ephrin B/EPHB3 -0.005 0.049 -10000 0 -0.39 8 8
JNK cascade -0.12 0.21 -10000 0 -0.38 197 197
Ephrin B/EPHB1 -0.15 0.2 -10000 0 -0.4 198 198
RAP1/GDP -0.083 0.12 -10000 0 -0.52 10 10
EFNB2 0.008 0.079 -10000 0 -0.72 6 6
EFNB3 0.016 0 -10000 0 -10000 0 0
EFNB1 0.013 0.045 -10000 0 -0.72 2 2
Ephrin B2/EPHB1-2 -0.16 0.22 -10000 0 -0.43 198 198
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.16 -10000 0 -0.62 9 9
Rap1/GTP -0.12 0.15 -10000 0 -0.47 16 16
axon guidance 0.003 0.028 -10000 0 -0.47 1 1
MAPK3 -0.053 0.16 -10000 0 -0.66 7 7
MAPK1 -0.053 0.16 -10000 0 -0.66 7 7
Rac1/GDP -0.054 0.16 -10000 0 -0.55 10 10
actin cytoskeleton reorganization -0.088 0.12 -10000 0 -0.46 9 9
CDC42/GDP -0.054 0.16 -10000 0 -0.55 10 10
PI3K -0.041 0.13 -10000 0 -0.4 56 56
EFNA5 0.014 0.034 -10000 0 -0.72 1 1
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.041 0.043 -10000 0 -0.29 9 9
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.15 -10000 0 -0.57 8 8
PTK2 0.039 0.051 -10000 0 -10000 0 0
MAP4K4 -0.12 0.21 -10000 0 -0.38 197 197
SRC 0.016 0.007 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.001 0.023 -10000 0 -0.54 1 1
neuron projection morphogenesis -0.032 0.16 -10000 0 -0.46 9 9
MAP2K1 -0.066 0.17 -10000 0 -0.7 7 7
WASL 0.015 0.032 -10000 0 -0.72 1 1
Ephrin B1/EPHB1-2/NCK1 -0.15 0.21 -10000 0 -0.42 197 197
cell migration -0.07 0.18 -10000 0 -0.72 7 7
NRAS 0.014 0.019 -10000 0 -10000 0 0
SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
PXN 0.016 0 -10000 0 -10000 0 0
TF 0.033 0.088 -10000 0 -0.35 26 26
HRAS/GTP -0.12 0.17 -10000 0 -0.5 16 16
Ephrin B1/EPHB1-2 -0.16 0.21 -10000 0 -0.43 197 197
cell adhesion mediated by integrin -0.028 0.063 0.36 8 -10000 0 8
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.13 0.18 -10000 0 -0.36 198 198
RAC1-CDC42/GTP -0.11 0.15 -10000 0 -0.47 15 15
RASA1 0.015 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.083 0.12 -10000 0 -0.52 10 10
ruffle organization -0.072 0.19 -10000 0 -0.45 21 21
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.047 0.051 -10000 0 -0.34 8 8
Ephrin B/EPHB2/KALRN 0 0.052 -10000 0 -0.38 8 8
ROCK1 0.03 0.029 -10000 0 -0.42 2 2
RAS family/GDP -0.074 0.1 -10000 0 -0.47 8 8
Rac1/GTP -0.12 0.17 -10000 0 -0.48 21 21
Ephrin B/EPHB1/Src/Paxillin -0.085 0.18 -10000 0 -0.3 198 198
ErbB2/ErbB3 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
USP8 0.023 0.013 -9999 0 -10000 0 0
RAS family/GTP -0.022 0.11 -9999 0 -0.34 10 10
NFATC4 -0.019 0.098 -9999 0 -0.3 14 14
ERBB2IP 0.017 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.016 0.01 -9999 0 -10000 0 0
mammary gland morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
JUN -0.035 0.083 -9999 0 -10000 0 0
HRAS 0.014 0.012 -9999 0 -10000 0 0
DOCK7 -0.029 0.12 -9999 0 -0.37 15 15
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.056 0.14 -9999 0 -0.41 68 68
AKT1 0.012 0.014 -9999 0 -10000 0 0
BAD 0.024 0.011 -9999 0 -10000 0 0
MAPK10 -0.025 0.07 -9999 0 -0.3 12 12
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.14 -9999 0 -0.38 68 68
RAF1 -0.022 0.11 -9999 0 -0.34 18 18
ErbB2/ErbB3/neuregulin 2 -0.3 0.21 -9999 0 -0.44 354 354
STAT3 0.004 0.009 -9999 0 -10000 0 0
cell migration 0.017 0.078 -9999 0 -0.29 4 4
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.24 0.28 -9999 0 -0.62 133 133
FOS -0.34 0.29 -9999 0 -0.52 375 375
NRAS 0.013 0.019 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.13 -9999 0 -0.35 68 68
MAPK3 -0.15 0.21 -9999 0 -0.49 99 99
MAPK1 -0.15 0.21 -9999 0 -0.48 101 101
JAK2 -0.029 0.12 -9999 0 -0.34 54 54
NF2 0.001 0.008 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.015 0.12 -9999 0 -0.33 67 67
NRG1 -0.08 0.25 -9999 0 -0.72 67 67
GRB2/SOS1 -0.001 0.011 -9999 0 -10000 0 0
MAPK8 -0.023 0.11 -9999 0 -0.31 55 55
MAPK9 -0.02 0.056 -9999 0 -10000 0 0
ERBB2 -0.013 0.041 -9999 0 -0.56 1 1
ERBB3 0.008 0.03 -9999 0 -10000 0 0
SHC1 0.015 0.001 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.013 0.014 -9999 0 -10000 0 0
STAT3 (dimer) 0.004 0.009 -9999 0 -10000 0 0
RNF41 0.03 0.013 -9999 0 -10000 0 0
FRAP1 0.024 0.011 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.079 -9999 0 -0.26 14 14
ErbB2/ErbB2/HSP90 (dimer) -0.009 0.03 -9999 0 -0.47 1 1
CHRNA1 -0.11 0.17 -9999 0 -0.36 96 96
myelination 0.011 0.1 -9999 0 -0.32 2 2
PPP3CB -0.027 0.11 -9999 0 -0.35 15 15
KRAS 0.011 0.025 -9999 0 -10000 0 0
RAC1-CDC42/GDP 0.006 0.1 -9999 0 -0.28 12 12
NRG2 -0.48 0.35 -9999 0 -0.72 353 353
mol:GDP -0.015 0.12 -9999 0 -0.32 67 67
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.026 0.12 -9999 0 -0.37 16 16
SRC 0.016 0.007 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.029 0.12 -9999 0 -0.37 15 15
MAP2K1 -0.16 0.2 -9999 0 -0.48 65 65
heart morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
RAS family/GDP -0.016 0.1 -9999 0 -0.34 5 5
GRB2 0.012 0.022 -9999 0 -10000 0 0
PRKACA -0.002 0.008 -9999 0 -10000 0 0
CHRNE 0.007 0.02 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.014 -9999 0 -10000 0 0
nervous system development -0.034 0.13 -9999 0 -0.35 68 68
CDC42 0.016 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.002 0.01 -10000 0 -10000 0 0
HDAC1 0.014 0.011 -10000 0 -10000 0 0
AES 0.016 0.004 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 0.012 0.056 -10000 0 -0.72 3 3
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
TLE1 -0.009 0.13 -10000 0 -0.72 18 18
AP1 -0.26 0.2 -10000 0 -0.38 374 374
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.015 0.012 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.094 -10000 0 -0.58 2 2
NICD/RBPSUH 0.002 0.009 -10000 0 -10000 0 0
WIF1 -0.53 0.32 -10000 0 -0.72 392 392
NOTCH1 0.002 0.008 -10000 0 -10000 0 0
PSENEN 0.014 0.019 -10000 0 -10000 0 0
KREMEN2 -0.076 0.08 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 -0.004 0.053 -10000 0 -0.48 4 4
APH1B 0.015 0.033 -10000 0 -0.72 1 1
APH1A 0.01 0.032 -10000 0 -10000 0 0
AXIN1 0.006 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.027 0.074 0.3 2 -0.3 18 20
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 374 374
JUN -0.12 0.29 -10000 0 -0.72 97 97
MAP3K7 0.015 0.011 -10000 0 -10000 0 0
CTNNB1 -0.015 0.055 -10000 0 -0.51 4 4
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
HNF1A 0.015 0.012 -10000 0 -10000 0 0
CTBP1 0.015 0.008 -10000 0 -10000 0 0
MYC -0.055 0.34 -10000 0 -1.5 29 29
NKD1 0.014 0.018 -10000 0 -10000 0 0
FZD1 0.015 0.032 -10000 0 -0.72 1 1
NOTCH1 precursor/Deltex homolog 1 0 0.03 -10000 0 -0.38 3 3
apoptosis -0.26 0.2 -10000 0 -0.38 374 374
Delta 1/NOTCHprecursor 0.002 0.009 -10000 0 -10000 0 0
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.022 0.027 -10000 0 -10000 0 0
Gamma Secretase 0.004 0.027 -10000 0 -0.38 1 1
APC 0.006 0.006 -10000 0 -10000 0 0
DVL1 -0.041 0.025 -10000 0 -10000 0 0
CSNK2A1 0.016 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.015 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.027 0.16 -10000 0 -0.5 46 46
LRP6 0.015 0.012 -10000 0 -10000 0 0
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
NLK 0.029 0.015 -10000 0 -10000 0 0
CCND1 -0.02 0.23 -10000 0 -1.5 12 12
WNT1 0.016 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.006 0.045 -10000 0 -0.33 1 1
DKK2 0.007 0.074 -10000 0 -0.72 5 5
NOTCH1 precursor/DVL1 -0.008 0.012 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0 0.03 -10000 0 -0.38 3 3
PPP2R5D -0.021 0.016 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.31 0.18 -10000 0 -0.41 392 392
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.018 0.033 -10000 0 -0.73 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.054 0.16 -10000 0 -0.54 52 52
CRKL 0.018 0.1 -10000 0 -0.29 53 53
mol:PIP3 -0.014 0.1 0.62 13 -10000 0 13
AKT1 0.008 0.068 0.42 13 -10000 0 13
PTK2B 0.016 0 -10000 0 -10000 0 0
RAPGEF1 0.027 0.098 -10000 0 -0.37 1 1
RANBP10 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.044 0.14 -10000 0 -0.46 52 52
MAP3K5 0.013 0.14 -10000 0 -0.38 35 35
HGF/MET/CIN85/CBL/ENDOPHILINS -0.041 0.12 -10000 0 -0.41 53 53
AP1 -0.42 0.32 -10000 0 -0.6 375 375
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis -0.54 0.37 -10000 0 -0.76 375 375
STAT3 (dimer) 0.023 0.097 -10000 0 -0.28 2 2
GAB1/CRKL/SHP2/PI3K -0.054 0.12 -10000 0 -0.59 7 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.026 0.099 -10000 0 -0.35 2 2
PTPN11 0.016 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.007 -10000 0 -10000 0 0
PTEN -0.002 0.12 -10000 0 -0.72 13 13
ELK1 -0.022 0.076 -10000 0 -0.25 52 52
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.017 0.052 -10000 0 -10000 0 0
PAK1 0.005 0.067 0.39 13 -10000 0 13
HGF/MET/RANBP10 -0.045 0.14 -10000 0 -0.46 52 52
HRAS -0.022 0.22 -10000 0 -0.68 52 52
DOCK1 0.024 0.1 -10000 0 -0.35 5 5
GAB1 0.008 0.11 -10000 0 -0.31 53 53
CRK 0.017 0.1 -10000 0 -0.29 54 54
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.062 0.19 -10000 0 -0.64 52 52
JUN -0.12 0.29 -10000 0 -0.72 97 97
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.098 -10000 0 -0.33 52 52
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
cell morphogenesis 0.022 0.15 -10000 0 -0.57 7 7
GRB2/SHC 0.007 0.094 -10000 0 -0.28 52 52
FOS -0.51 0.34 -10000 0 -0.72 374 374
GLMN 0 0.002 -10000 0 -10000 0 0
cell motility -0.022 0.076 -10000 0 -0.25 52 52
HGF/MET/MUC20 -0.046 0.14 -10000 0 -0.47 52 52
cell migration 0.007 0.093 -10000 0 -0.27 52 52
GRB2 0.013 0.022 -10000 0 -10000 0 0
CBL 0.016 0 -10000 0 -10000 0 0
MET/RANBP10 -0.053 0.16 -10000 0 -0.54 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.1 -10000 0 -0.29 52 52
MET/MUC20 -0.055 0.16 -10000 0 -0.55 52 52
RAP1B 0.035 0.093 -10000 0 -0.34 1 1
RAP1A 0.035 0.093 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.045 0.14 -10000 0 -0.46 52 52
RAF1 -0.01 0.21 -10000 0 -0.63 52 52
STAT3 0.023 0.098 -10000 0 -0.28 2 2
cell proliferation 0.023 0.14 -10000 0 -0.41 52 52
RPS6KB1 0.005 0.04 -10000 0 -10000 0 0
MAPK3 -0.027 0.069 -10000 0 -10000 0 0
MAPK1 -0.027 0.069 -10000 0 -0.24 52 52
RANBP9 0.016 0.007 -10000 0 -10000 0 0
MAPK8 0.027 0.12 -10000 0 -0.42 10 10
SRC 0.025 0.095 -10000 0 -10000 0 0
PI3K -0.033 0.16 -10000 0 -0.35 96 96
MET/Glomulin -0.035 0.15 -10000 0 -0.49 52 52
SOS1 0.016 0 -10000 0 -10000 0 0
MAP2K1 0.002 0.19 -10000 0 -0.57 52 52
MET -0.057 0.22 -10000 0 -0.72 52 52
MAP4K1 0.03 0.098 -10000 0 -0.37 1 1
PTK2 0.015 0.014 -10000 0 -10000 0 0
MAP2K2 0.002 0.19 -10000 0 -0.57 52 52
BAD 0.016 0.062 0.4 13 -10000 0 13
MAP2K4 0.018 0.14 -10000 0 -0.43 16 16
SHP2/GRB2/SOS1/GAB1 -0.041 0.13 -10000 0 -0.42 52 52
INPPL1 0.015 0.012 -10000 0 -10000 0 0
PXN 0.016 0 -10000 0 -10000 0 0
SH3KBP1 0.015 0.033 -10000 0 -0.72 1 1
HGS -0.003 0.097 -10000 0 -0.3 52 52
PLCgamma1/PKC 0 0.004 -10000 0 -10000 0 0
HGF 0.016 0.01 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
PTPRJ 0.014 0.019 -10000 0 -10000 0 0
NCK/PLCgamma1 0.01 0.092 -10000 0 -10000 0 0
PDPK1 -0.002 0.078 0.48 13 -10000 0 13
HGF/MET/SHIP -0.046 0.14 -10000 0 -0.47 52 52
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.055 0.26 -10000 0 -0.55 103 103
IHH 0.009 0.047 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.14 0.2 -10000 0 -0.43 169 169
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.2 0.42 169 -10000 0 169
SMO/beta Arrestin2 -0.003 0.16 -10000 0 -0.65 8 8
SMO -0.012 0.17 -10000 0 -0.66 9 9
AKT1 -0.014 0.17 -10000 0 -0.56 29 29
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.15 0.31 -10000 0 -0.72 117 117
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.011 0.17 -10000 0 -0.65 9 9
STIL 0.011 0.12 -10000 0 -0.43 6 6
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.001 0.12 -10000 0 -0.39 3 3
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DHH 0.016 0 -10000 0 -10000 0 0
PTHLH -0.15 0.47 -10000 0 -1.1 103 103
determination of left/right symmetry -0.011 0.17 -10000 0 -0.65 9 9
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
skeletal system development -0.15 0.46 -10000 0 -1.1 103 103
IHH N/Hhip 0.023 0.023 -10000 0 -10000 0 0
DHH N/Hhip 0 0.006 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.011 0.17 -10000 0 -0.65 9 9
pancreas development 0.015 0.012 -10000 0 -10000 0 0
HHAT 0.006 0.074 -10000 0 -0.72 5 5
PI3K -0.052 0.16 -10000 0 -0.54 51 51
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.22 0.34 -10000 0 -0.72 166 166
somite specification -0.011 0.17 -10000 0 -0.65 9 9
SHH Np/Cholesterol/PTCH1 0.008 0.12 -10000 0 -0.6 1 1
SHH Np/Cholesterol/PTCH2 -0.005 0.041 -10000 0 -0.42 5 5
SHH Np/Cholesterol/Megalin -0.12 0.2 -10000 0 -0.43 149 149
SHH 0.022 0.057 -10000 0 -0.54 5 5
catabolic process -0.009 0.14 -10000 0 -0.4 6 6
SMO/Vitamin D3 0.004 0.14 -10000 0 -0.52 9 9
SHH Np/Cholesterol/Hhip -0.004 0.041 -10000 0 -0.42 5 5
LRP2 -0.19 0.33 -10000 0 -0.72 147 147
receptor-mediated endocytosis -0.12 0.17 -10000 0 -0.54 42 42
SHH Np/Cholesterol/BOC -0.098 0.18 -10000 0 -0.43 121 121
SHH Np/Cholesterol/CDO -0.007 0.057 -10000 0 -0.48 7 7
mesenchymal cell differentiation 0.004 0.041 0.42 5 -10000 0 5
mol:Vitamin D3 0.012 0.12 -10000 0 -0.6 1 1
IHH N/PTCH2 0.023 0.022 -10000 0 -10000 0 0
CDON 0.012 0.056 -10000 0 -0.72 3 3
IHH N/PTCH1 -0.007 0.14 -10000 0 -0.4 6 6
Megalin/LRPAP1 -0.15 0.24 -10000 0 -0.54 147 147
PTCH2 0.016 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.003 0.043 -10000 0 -0.43 5 5
PTCH1 -0.009 0.14 -10000 0 -0.4 6 6
HHIP 0.015 0.012 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.078 0.11 0.48 3 -10000 0 3
GNAI2 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.08 0.11 -10000 0 -0.49 3 3
negative regulation of cAMP metabolic process -0.067 0.14 -10000 0 -0.25 193 193
GNAZ 0.008 0.078 -10000 0 -0.72 6 6
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.068 0.14 -10000 0 -0.25 193 193
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
TCGA08_retinoblastoma

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
CDKN2B 0.007 0.061 -10000 0 -0.69 3 3
CDKN2C -0.043 0.2 -10000 0 -0.7 44 44
CDKN2A -0.008 0.066 -10000 0 -10000 0 0
CCND2 0.016 0.059 0.2 42 -0.17 7 49
RB1 -0.018 0.063 0.18 3 -0.22 42 45
CDK4 0.021 0.066 0.23 45 -10000 0 45
CDK6 0.017 0.067 0.22 42 -0.26 4 46
G1/S progression 0.002 0.068 0.22 42 -0.18 3 45
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.009 0.034 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.25 0.18 -9999 0 -0.45 48 48
Syndecan-3/Neurocan -0.004 0.073 -9999 0 -0.66 6 6
POMC 0.012 0.038 -9999 0 -0.72 1 1
EGFR -0.38 0.37 -9999 0 -0.72 277 277
Syndecan-3/EGFR -0.21 0.21 -9999 0 -0.4 278 278
AGRP 0.016 0.01 -9999 0 -10000 0 0
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.014 0.019 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.01 0.032 -9999 0 -10000 0 0
NCAN 0.01 0.03 -9999 0 -10000 0 0
long-term memory -0.003 0.072 -9999 0 -0.55 8 8
Syndecan-3/IL8 0.003 0.079 -9999 0 -0.63 7 7
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin -0.004 0.016 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
limb bud formation -0.007 0.073 -9999 0 -0.69 6 6
MC4R 0.015 0.012 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PTN -0.51 0.34 -9999 0 -0.72 373 373
FGFR/FGF/Syndecan-3 -0.008 0.074 -9999 0 -0.7 6 6
neuron projection morphogenesis -0.24 0.17 -9999 0 -0.46 40 40
Syndecan-3/AgRP -0.006 0.071 -9999 0 -0.66 6 6
Syndecan-3/AgRP/MC4R -0.005 0.069 -9999 0 -0.64 6 6
Fyn/Cortactin -0.006 0.037 -9999 0 -0.54 2 2
SDC3 -0.008 0.075 -9999 0 -0.71 6 6
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.077 -9999 0 -0.62 7 7
IL8 -0.006 0.063 -9999 0 -0.72 1 1
Syndecan-3/Fyn/Cortactin -0.003 0.074 -9999 0 -0.57 8 8
Syndecan-3/CASK -0.007 0.072 -9999 0 -0.67 6 6
alpha-MSH/MC4R -0.003 0.026 -9999 0 -0.54 1 1
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.059 0.094 -10000 0 -0.31 5 5
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.55 161 161
NT3 (dimer)/TRKB -0.42 0.39 -10000 0 -0.67 329 329
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.1 -10000 0 -0.3 4 4
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF 0.006 0.057 -10000 0 -0.72 2 2
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.014 0.019 -10000 0 -10000 0 0
NTRK2 -0.34 0.37 -10000 0 -0.72 252 252
NTRK3 -0.006 0.13 -10000 0 -0.72 16 16
NT-4/5 (dimer)/TRKB -0.3 0.32 -10000 0 -0.58 274 274
neuron apoptosis 0.18 0.23 0.54 124 -10000 0 124
SHC 2-3/Grb2 -0.2 0.26 -10000 0 -0.6 124 124
SHC1 0.016 0 -10000 0 -10000 0 0
SHC2 -0.2 0.27 -10000 0 -0.63 121 121
SHC3 -0.17 0.24 -10000 0 -0.6 105 105
STAT3 (dimer) 0.019 0.059 -10000 0 -0.36 12 12
NT3 (dimer)/TRKA -0.21 0.27 -10000 0 -0.51 216 216
RIN/GDP -0.002 0.099 -10000 0 -0.26 5 5
GIPC1 0.015 0.012 -10000 0 -10000 0 0
KRAS 0.012 0.025 -10000 0 -10000 0 0
DNAJA3 -0.09 0.18 -10000 0 -0.44 94 94
RIN/GTP -0.001 0.024 -10000 0 -0.55 1 1
CCND1 -0.001 0.15 -10000 0 -0.94 12 12
MAGED1 0.006 0.04 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0.012 0.026 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.011 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.003 0.015 -10000 0 -10000 0 0
TRKA/NEDD4-2 -0.017 0.09 -10000 0 -0.54 15 15
ELMO1 0.016 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.004 0.041 -10000 0 -0.47 4 4
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
DOCK1 0.011 0.064 -10000 0 -0.72 4 4
GAB2 0.015 0.016 -10000 0 -10000 0 0
RIT2 0.015 0.032 -10000 0 -0.72 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.011 0.039 -10000 0 -0.72 1 1
DNM1 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.087 0.18 -10000 0 -0.43 94 94
mol:GDP -0.017 0.14 -10000 0 -0.37 10 10
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.002 0.098 -10000 0 -0.24 8 8
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
BDNF (dimer)/TRKB -0.22 0.23 -10000 0 -0.46 254 254
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0.006 -10000 0 -10000 0 0
FRS2 family/SHP2 0.001 0.023 -10000 0 -0.46 1 1
SHC/GRB2/SOS1/GAB1 0.001 0.022 -10000 0 -0.41 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -10000 0 -0.72 150 150
RAP1/GDP -0.035 0.057 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) 0.006 0.057 -10000 0 -0.72 2 2
ubiquitin-dependent protein catabolic process -0.012 0.078 -10000 0 -0.47 15 15
Schwann cell development -0.044 0.037 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.003 0.025 -10000 0 -0.41 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.05 0.018 -10000 0 -10000 0 0
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.26 -10000 0 -0.68 110 110
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.07 0.075 -10000 0 -10000 0 0
STAT3 0.02 0.059 -10000 0 -0.36 12 12
axon guidance -0.26 0.25 -10000 0 -0.64 110 110
MAPK3 0.029 0.016 -10000 0 -10000 0 0
MAPK1 0.029 0.016 -10000 0 -10000 0 0
CDC42/GDP -0.002 0.098 -10000 0 -0.26 4 4
NTF3 -0.2 0.33 -10000 0 -0.72 150 150
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.001 0.009 -10000 0 -10000 0 0
PI3K -0.052 0.16 -10000 0 -0.54 51 51
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0.007 -10000 0 -10000 0 0
GAB1 0.014 0.034 -10000 0 -0.72 1 1
RASGRF1 -0.092 0.18 -10000 0 -0.44 96 96
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.12 0.24 -10000 0 -0.47 161 161
RGS19 0.012 0.027 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.07 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.098 -10000 0 -0.24 8 8
NGF (dimer)/TRKA/GRIT 0.003 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.053 0.19 -10000 0 -0.42 89 89
NGF (dimer)/TRKA/NEDD4-2 -0.012 0.079 -10000 0 -0.47 15 15
MAP2K1 0.048 0.022 -10000 0 -0.38 1 1
NGFR -0.12 0.28 -10000 0 -0.72 94 94
NGF (dimer)/TRKA/GIPC/GAIP 0.039 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.007 0.099 -10000 0 -0.3 51 51
FRS2 family/SHP2/GRB2/SOS1 0.003 0.024 -10000 0 -0.38 1 1
NRAS 0.014 0.019 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
PRKCI 0.013 0.022 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.047 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
TRKA/c-Abl -0.001 0.009 -10000 0 -10000 0 0
SQSTM1 0.016 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.2 0.21 -10000 0 -0.41 254 254
NGF (dimer)/TRKA/p62/Atypical PKCs 0.002 0.013 -10000 0 -10000 0 0
MATK 0.011 0.029 -10000 0 -10000 0 0
NEDD4L -0.005 0.12 -10000 0 -0.72 15 15
RAS family/GDP -0.033 0.053 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.097 0.2 -10000 0 -0.47 94 94
Rac1/GTP -0.073 0.1 -10000 0 -0.34 40 40
FRS2 family/SHP2/CRK family 0 0.028 -10000 0 -0.41 2 2
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.08 0.11 -9999 0 -0.49 3 3
PLCG1 -0.054 0.13 -9999 0 -0.53 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
cell migration -0.078 0.11 -9999 0 -0.48 3 3
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.054 0.13 -9999 0 -0.51 3 3
MAPK1 -0.054 0.13 -9999 0 -0.22 193 193
S1P/S1P5/Gi -0.068 0.14 -9999 0 -0.25 193 193
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0 0 -9999 0 -10000 0 0
RHOA 0.03 0.006 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.068 0.14 -9999 0 -0.25 193 193
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
S1P/S1P4/G12/G13 0.001 0.006 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.074 0.24 -10000 0 -0.72 64 64
HRAS 0.015 0.012 -10000 0 -10000 0 0
EGFR -0.38 0.37 -10000 0 -0.72 277 277
AKT 0.023 0.044 -10000 0 -0.26 2 2
FOXO3 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
FOXO1 -0.085 0.25 -10000 0 -0.72 72 72
AKT3 0.014 0.017 -10000 0 -10000 0 0
FOXO4 0.016 0 -10000 0 -10000 0 0
MET -0.057 0.22 -10000 0 -0.72 52 52
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PIK3CB 0.016 0.01 -10000 0 -10000 0 0
NRAS 0.014 0.019 -10000 0 -10000 0 0
PIK3CG 0.013 0.023 -10000 0 -10000 0 0
PIK3R3 0.006 0.039 -10000 0 -10000 0 0
PIK3R2 0.014 0.019 -10000 0 -10000 0 0
NF1 0.016 0 -10000 0 -10000 0 0
RAS -0.11 0.15 -10000 0 -0.38 87 87
ERBB2 -0.004 0.06 -10000 0 -0.72 1 1
proliferation/survival/translation -0.009 0.073 0.23 22 -0.19 4 26
PI3K -0.1 0.16 0.22 9 -0.31 142 151
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
KRAS 0.012 0.025 -10000 0 -10000 0 0
FOXO 0.028 0.04 0.2 5 -0.23 1 6
AKT2 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.12 -10000 0 -0.72 13 13
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.046 0.11 -9999 0 -0.47 20 20
EPHB2 0.006 0.04 -9999 0 -10000 0 0
Syndecan-2/TACI 0.012 0.093 -9999 0 -0.46 20 20
LAMA1 0.016 0.01 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.16 0.22 -9999 0 -0.42 196 196
HRAS 0.015 0.012 -9999 0 -10000 0 0
Syndecan-2/CASK -0.018 0.089 -9999 0 -0.47 20 20
ITGA5 0.016 0.007 -9999 0 -10000 0 0
BAX 0.033 0.087 -9999 0 -10000 0 0
EPB41 0.016 0.007 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.017 0.081 -9999 0 -0.42 21 21
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.46 0.35 -9999 0 -0.72 338 338
Syndecan-2/MMP2 0.008 0.12 -9999 0 -0.54 21 21
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.02 0.1 -9999 0 -0.54 19 19
dendrite morphogenesis 0.015 0.094 -9999 0 -0.45 20 20
Syndecan-2/GM-CSF 0.013 0.096 -9999 0 -0.46 20 20
determination of left/right symmetry 0.003 0.11 -9999 0 -0.54 20 20
Syndecan-2/PKC delta 0.012 0.094 -9999 0 -0.46 20 20
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 0.021 0.088 -9999 0 -0.41 20 20
MAPK1 0.021 0.088 -9999 0 -0.41 20 20
Syndecan-2/RACK1 -0.015 0.075 -9999 0 -0.39 20 20
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.003 0.11 -9999 0 -0.54 20 20
ITGA2 -0.011 0.14 -9999 0 -0.72 19 19
MAPK8 0.024 0.097 -9999 0 -0.45 21 21
Syndecan-2/alpha2/beta1 Integrin -0.027 0.11 -9999 0 -0.43 35 35
Syndecan-2/Kininogen 0.012 0.093 -9999 0 -0.46 20 20
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.031 0.078 -9999 0 -0.36 20 20
Syndecan-2/CASK/Protein 4.1 -0.016 0.08 -9999 0 -0.42 20 20
extracellular matrix organization 0.012 0.093 -9999 0 -0.45 20 20
actin cytoskeleton reorganization 0.046 0.11 -9999 0 -0.46 20 20
Syndecan-2/Caveolin-2/Ras -0.28 0.22 -9999 0 -0.44 338 338
Syndecan-2/Laminin alpha3 -0.15 0.25 -9999 0 -0.48 189 189
Syndecan-2/RasGAP -0.013 0.071 -9999 0 -0.36 20 20
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
PRKCD 0.014 0.019 -9999 0 -10000 0 0
Syndecan-2 dimer 0.015 0.095 -9999 0 -0.46 20 20
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.077 -9999 0 -0.35 20 20
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.02 0.1 -9999 0 -0.54 19 19
Syndecan-2/Synbindin 0.012 0.093 -9999 0 -0.46 20 20
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CASP3 0.023 0.087 -9999 0 -0.41 20 20
FN1 -0.098 0.074 -9999 0 -10000 0 0
Syndecan-2/IL8 0.017 0.1 -9999 0 -0.46 21 21
SDC2 0.003 0.11 -9999 0 -0.54 20 20
KNG1 0.016 0.007 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.012 0.093 -9999 0 -0.46 20 20
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 0.01 0.03 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.012 0.093 -9999 0 -0.46 20 20
Syndecan-2/Syntenin/PI-4-5-P2 -0.017 0.082 -9999 0 -0.42 21 21
Syndecan-2/Ezrin -0.016 0.08 -9999 0 -0.42 20 20
PRKACA 0.024 0.086 -9999 0 -0.41 20 20
angiogenesis 0.017 0.099 -9999 0 -0.46 21 21
MMP2 0.009 0.072 -9999 0 -0.72 5 5
IL8 -0.006 0.063 -9999 0 -0.72 1 1
calcineurin-NFAT signaling pathway 0.012 0.093 -9999 0 -0.45 20 20
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.003 0.037 -9999 0 -0.34 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.026 -9999 0 -0.31 1 1
AP1 -0.34 0.25 -9999 0 -0.47 376 376
mol:PIP3 -0.21 0.2 -9999 0 -0.38 294 294
AKT1 0.028 0.1 -9999 0 -0.39 5 5
PTK2B 0.024 0.023 -9999 0 -0.2 5 5
RHOA 0.027 0.025 -9999 0 -0.21 3 3
PIK3CB 0.015 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0.032 0.027 -9999 0 -0.37 1 1
MAGI3 0.003 0.066 -9999 0 -0.72 3 3
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis 0.018 0.027 -9999 0 -0.25 5 5
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.038 0.036 -9999 0 -0.34 3 3
NF kappa B1 p50/RelA -0.003 0.024 -9999 0 -0.29 2 2
endothelial cell migration 0.017 0.081 -9999 0 -0.81 5 5
ADCY4 -0.038 0.12 -9999 0 -0.4 11 11
ADCY5 -0.036 0.12 -9999 0 -0.42 8 8
ADCY6 -0.036 0.12 -9999 0 -0.42 8 8
ADCY7 -0.036 0.12 -9999 0 -0.42 8 8
ADCY1 -0.036 0.12 -9999 0 -0.42 8 8
ADCY2 -0.039 0.12 -9999 0 -0.41 12 12
ADCY3 -0.036 0.12 -9999 0 -0.42 8 8
ADCY8 -0.036 0.12 -9999 0 -0.42 8 8
ADCY9 -0.036 0.12 -9999 0 -0.42 8 8
GSK3B 0.032 0.022 -9999 0 -0.21 1 1
arachidonic acid secretion -0.024 0.11 -9999 0 -0.42 7 7
GNG2 0.015 0.032 -9999 0 -0.72 1 1
TRIP6 0.024 0.023 -9999 0 -0.48 1 1
GNAO1 0.022 0.032 -9999 0 -0.3 5 5
HRAS 0.015 0.012 -9999 0 -10000 0 0
NFKBIA 0.044 0.033 -9999 0 -0.32 2 2
GAB1 0.014 0.034 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.003 0.009 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.72 97 97
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.47 1 1
TIAM1 0.003 0.008 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 51 51
mol:IP3 0.033 0.028 -9999 0 -0.38 1 1
PLCB3 0.025 0.023 -9999 0 -0.42 1 1
FOS -0.51 0.34 -9999 0 -0.72 374 374
positive regulation of mitosis -0.024 0.11 -9999 0 -0.42 7 7
LPA/LPA1-2-3 -0.003 0.027 -9999 0 -0.28 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation 0.031 0.024 -9999 0 -0.2 5 5
GNAZ 0.016 0.061 -9999 0 -0.39 11 11
EGFR/PI3K-beta/Gab1 -0.22 0.22 -9999 0 -0.39 294 294
positive regulation of dendritic cell cytokine production -0.003 0.027 -9999 0 -0.28 5 5
LPA/LPA2/MAGI-3 -0.007 0.04 -9999 0 -0.47 3 3
ARHGEF1 0.038 0.028 -9999 0 -10000 0 0
GNAI2 0.022 0.032 -9999 0 -0.3 5 5
GNAI3 0.022 0.032 -9999 0 -0.3 5 5
GNAI1 -0.16 0.24 -9999 0 -0.47 190 190
LPA/LPA3 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA2 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA1 -0.004 0.036 -9999 0 -0.36 5 5
HB-EGF/EGFR -0.26 0.25 -9999 0 -0.49 277 277
HBEGF -0.024 0.07 -9999 0 -0.54 4 4
mol:DAG 0.033 0.028 -9999 0 -0.38 1 1
cAMP biosynthetic process -0.03 0.12 -9999 0 -0.42 8 8
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
GNB1 0.015 0.01 -9999 0 -10000 0 0
LYN 0.045 0.027 -9999 0 -0.27 1 1
GNAQ 0.004 0.011 -9999 0 -0.1 5 5
LPAR2 0 0 -9999 0 -10000 0 0
LPAR3 0 0 -9999 0 -10000 0 0
LPAR1 0.004 0.021 -9999 0 -0.2 5 5
IL8 -0.27 0.18 -9999 0 -0.4 318 318
PTK2 0.02 0.027 -9999 0 -0.25 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 0.018 0.027 -9999 0 -0.26 5 5
EGFR -0.38 0.37 -9999 0 -0.72 277 277
PLCG1 0.018 0.021 -9999 0 -0.15 6 6
PLD2 0.019 0.032 -9999 0 -0.28 6 6
G12/G13 -0.002 0.026 -9999 0 -0.26 5 5
PI3K-beta -0.033 0.097 -9999 0 -0.32 51 51
cell migration 0.004 0.016 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.72 1 1
PXN 0.031 0.024 -9999 0 -0.21 5 5
HRAS/GTP -0.059 0.085 -9999 0 -0.43 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
PRKCE 0.016 0 -9999 0 -10000 0 0
PRKCD 0.04 0.028 -9999 0 -0.35 1 1
Gi(beta/gamma) -0.031 0.12 -9999 0 -0.48 7 7
mol:LPA 0.004 0.021 -9999 0 -0.2 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.023 -9999 0 -10000 0 0
MAPKKK cascade -0.024 0.11 -9999 0 -0.42 7 7
contractile ring contraction involved in cytokinesis 0.027 0.025 -9999 0 -0.21 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 0.004 0.048 -9999 0 -0.37 7 7
GNA15 0.013 0.012 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
MAPT 0.038 0.037 -9999 0 -0.36 3 3
GNA11 0.014 0.011 -9999 0 -10000 0 0
Rac1/GTP 0.004 0.011 -9999 0 -10000 0 0
MMP2 0.017 0.082 -9999 0 -0.82 5 5
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.15 0.22 -9999 0 -0.35 259 259
GNAO1 0.018 0.001 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.025 0.005 -9999 0 -10000 0 0
AKT1 -0.022 0.042 -9999 0 -10000 0 0
AKT3 0.005 0.08 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0.007 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.36 -9999 0 -0.72 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.002 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
mol:Ca2+ -0.054 0.14 -9999 0 -0.23 193 193
MAPK3 -0.041 0.13 -9999 0 -0.62 2 2
MAPK1 -0.041 0.13 -9999 0 -0.62 2 2
JAK2 -0.038 0.13 -9999 0 -0.52 3 3
CXCR4 -0.046 0.13 -9999 0 -0.33 12 12
FLT1 0.019 0.01 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.041 0.13 -9999 0 -0.62 2 2
S1P/S1P3/Gi -0.054 0.14 -9999 0 -0.24 193 193
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.075 0.1 -9999 0 -0.6 2 2
VEGFA -0.001 0.054 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.059 0.14 -9999 0 -0.24 193 193
VEGFR1 homodimer/VEGFA homodimer 0.041 0.02 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.036 -9999 0 -0.31 6 6
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.078 -9999 0 -0.72 6 6
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
GNA14 -0.008 0.09 -9999 0 -0.72 6 6
GNA15 0.014 0.02 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.075 0.1 -9999 0 -0.6 2 2
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.011 -10000 0 -10000 0 0
HSPA8 0.016 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.13 0.23 0.3 1 -0.52 121 122
AKT1 0.017 0.02 -10000 0 -10000 0 0
GSC -0.097 0.43 -10000 0 -1.5 46 46
NKX2-5 -0.003 0.057 -10000 0 -10000 0 0
muscle cell differentiation 0.035 0.11 0.45 22 -10000 0 22
SMAD2-3/SMAD4/SP1 0.026 0.094 -10000 0 -0.45 6 6
SMAD4 -0.013 0.082 -10000 0 -0.38 11 11
CBFB 0.016 0.01 -10000 0 -10000 0 0
SAP18 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.26 0.23 -10000 0 -0.46 302 302
SMAD3/SMAD4/VDR 0 0.065 -10000 0 -0.45 6 6
MYC -0.028 0.17 -10000 0 -0.73 29 29
CDKN2B 0.023 0.13 -10000 0 -1.5 3 3
AP1 -0.35 0.39 -10000 0 -0.73 185 185
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.065 0.04 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.016 0.11 -10000 0 -0.33 19 19
SP3 0.019 0.005 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.058 0.17 -10000 0 -0.55 49 49
GATA3 -0.067 0.19 -10000 0 -0.7 38 38
SKI/SIN3/HDAC complex/NCoR1 0.056 0.021 -10000 0 -10000 0 0
MEF2C/TIF2 -0.012 0.2 -10000 0 -0.71 34 34
endothelial cell migration -0.032 0.047 -10000 0 -10000 0 0
MAX 0.014 0.002 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
RUNX2 0.013 0.022 -10000 0 -10000 0 0
RUNX3 -0.045 0.2 -10000 0 -0.72 42 42
RUNX1 -0.006 0.12 -10000 0 -0.72 15 15
CTBP1 0.016 0.007 -10000 0 -10000 0 0
NR3C1 -0.051 0.21 -10000 0 -0.73 46 46
VDR 0.013 0.046 -10000 0 -0.72 2 2
CDKN1A 0.033 0.11 -10000 0 -1.4 2 2
KAT2B 0 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.019 0.1 -10000 0 -0.39 18 18
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.016 0.007 -10000 0 -10000 0 0
SERPINE1 0.03 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.013 0.067 -10000 0 -0.46 5 5
SMAD3/SMAD4/ATF3 -0.18 0.25 -10000 0 -0.52 175 175
SAP30 0.016 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.01 0.039 -10000 0 -0.42 1 1
JUN -0.34 0.38 -10000 0 -0.76 170 170
SMAD3/SMAD4/IRF7 -0.011 0.068 -10000 0 -0.45 5 5
TFE3 0.015 0.036 -10000 0 -10000 0 0
COL1A2 0.043 0.12 -10000 0 -1.1 3 3
mesenchymal cell differentiation 0.014 0.068 0.46 5 -10000 0 5
DLX1 0.006 0.04 -10000 0 -10000 0 0
TCF3 0.014 0.019 -10000 0 -10000 0 0
FOS -0.52 0.35 -10000 0 -0.74 374 374
SMAD3/SMAD4/Max -0.015 0.067 -10000 0 -0.46 5 5
Cbp/p300/SNIP1 0.004 0.026 -10000 0 -0.44 1 1
ZBTB17 0.014 0.005 -10000 0 -10000 0 0
LAMC1 -0.009 0.21 -10000 0 -0.75 37 37
TGIF2/HDAC complex/SMAD3/SMAD4 -0.014 0.067 -10000 0 -0.46 5 5
IRF7 0.018 0.023 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.73 117 117
HNF4A 0.016 0 -10000 0 -10000 0 0
MEF2C -0.004 0.21 -10000 0 -0.76 34 34
SMAD2-3/SMAD4 -0.02 0.081 -10000 0 -0.41 10 10
Cbp/p300/Src-1 0.006 0.036 -10000 0 -0.44 2 2
IGHV3OR16-13 -0.011 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0.01 -10000 0 -10000 0 0
CREBBP 0.016 0.032 -10000 0 -0.7 1 1
SKIL -0.001 0.049 -10000 0 -10000 0 0
HDAC1 0.016 0.001 -10000 0 -10000 0 0
HDAC2 0.014 0.017 -10000 0 -10000 0 0
SNIP1 0.015 0.004 -10000 0 -10000 0 0
GCN5L2 0.018 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.02 0.1 -10000 0 -0.4 29 29
MSG1/HSC70 -0.31 0.27 -10000 0 -0.54 302 302
SMAD2 0.014 0.035 -10000 0 -10000 0 0
SMAD3 -0.003 0.058 -10000 0 -0.78 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.055 -10000 0 -0.35 3 3
SMAD2/SMAD2/SMAD4 0.011 0.041 -10000 0 -0.42 2 2
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
NCOA2 0.015 0.014 -10000 0 -10000 0 0
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
MYOD/E2A -0.004 0.035 -10000 0 -0.54 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.089 -10000 0 -0.41 6 6
IFNB1 0.026 0.073 -10000 0 -0.46 3 3
SMAD3/SMAD4/MEF2C -0.027 0.21 -10000 0 -0.75 35 35
CITED1 -0.41 0.36 -10000 0 -0.72 302 302
SMAD2-3/SMAD4/ARC105 -0.013 0.071 -10000 0 -0.42 6 6
RBL1 0.007 0.037 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.12 -10000 0 -0.38 15 15
RUNX1-3/PEBPB2 -0.048 0.15 -10000 0 -0.48 55 55
SMAD7 -0.18 0.24 -10000 0 -0.54 115 115
MYC/MIZ-1 -0.029 0.13 -10000 0 -0.55 29 29
SMAD3/SMAD4 0.03 0.076 0.28 20 -10000 0 20
IL10 -0.013 0.14 -10000 0 -0.47 38 38
PIASy/HDAC complex 0.014 0.016 -10000 0 -10000 0 0
PIAS3 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.015 0.024 -10000 0 -10000 0 0
IL5 -0.013 0.14 -10000 0 -0.46 38 38
CDK4 0.017 0.018 -10000 0 -10000 0 0
PIAS4 0.014 0.016 -10000 0 -10000 0 0
ATF3 -0.22 0.34 -10000 0 -0.72 170 170
SMAD3/SMAD4/SP1 -0.006 0.073 -10000 0 -0.47 6 6
FOXG1 0.004 0.041 -10000 0 -10000 0 0
FOXO3 0.033 0.015 -10000 0 -10000 0 0
FOXO1 -0.045 0.2 -10000 0 -0.54 72 72
FOXO4 0.033 0.015 -10000 0 -10000 0 0
heart looping -0.003 0.21 -10000 0 -0.74 34 34
CEBPB 0.016 0.033 -10000 0 -0.72 1 1
SMAD3/SMAD4/DLX1 -0.016 0.072 -10000 0 -0.48 5 5
MYOD1 0.011 0.049 -10000 0 -0.72 2 2
SMAD3/SMAD4/HNF4 -0.013 0.067 -10000 0 -0.46 5 5
SMAD3/SMAD4/GATA3 -0.028 0.16 -10000 0 -0.53 40 40
SnoN/SIN3/HDAC complex/NCoR1 -0.001 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.046 0.15 -10000 0 -0.45 58 58
SMAD3/SMAD4/SP1-3 0.002 0.071 -10000 0 -0.46 6 6
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.026 0.014 -10000 0 -10000 0 0
SIN3B 0.015 0.016 -10000 0 -10000 0 0
SIN3A 0.016 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.13 -10000 0 -0.42 30 30
ITGB5 0.045 0.093 -10000 0 -0.68 5 5
TGIF/SIN3/HDAC complex/CtBP 0.059 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.079 0.19 -10000 0 -0.53 71 71
AR -0.082 0.25 -10000 0 -0.72 69 69
negative regulation of cell growth -0.041 0.12 -10000 0 -0.42 9 9
SMAD3/SMAD4/MYOD -0.016 0.073 -10000 0 -0.47 7 7
E2F5 -0.002 0.051 -10000 0 -10000 0 0
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.075 -10000 0 -0.37 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.017 0.12 -10000 0 -0.34 21 21
TFDP1 0.012 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.35 0.4 -10000 0 -0.77 174 174
SMAD3/SMAD4/RUNX2 -0.014 0.068 -10000 0 -0.46 5 5
TGIF2 0.016 0.01 -10000 0 -10000 0 0
TGIF1 0.015 0.032 -10000 0 -0.72 1 1
ATF2 0.016 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.026 0.17 -10000 0 -0.54 51 51
MAP4K4 0.044 0.066 -10000 0 -10000 0 0
BAG4 0.011 0.029 -10000 0 -10000 0 0
PKC zeta/ceramide -0.03 0.073 0.16 36 -10000 0 36
NFKBIA 0.015 0.032 -10000 0 -0.72 1 1
BIRC3 -0.038 0.18 -10000 0 -0.72 35 35
BAX -0.003 0.039 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.028 0.024 -10000 0 -10000 0 0
BAD -0.018 0.076 0.19 36 -10000 0 36
SMPD1 0.032 0.027 -10000 0 -0.23 1 1
RB1 -0.019 0.078 0.19 35 -0.3 2 37
FADD/Caspase 8 0.052 0.066 -10000 0 -10000 0 0
MAP2K4 -0.019 0.093 -10000 0 -0.42 11 11
NSMAF 0.012 0.056 -10000 0 -0.72 3 3
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.072 -10000 0 -10000 0 0
EGF -0.24 0.35 -10000 0 -0.72 178 178
mol:ceramide -0.03 0.082 0.2 36 -10000 0 36
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.034 0.19 -10000 0 -0.57 54 54
ASAH1 0.005 0.086 -10000 0 -0.72 7 7
negative regulation of cell cycle -0.02 0.077 0.19 35 -0.3 2 37
cell proliferation -0.17 0.16 -10000 0 -0.34 224 224
BID 0.031 0.052 -10000 0 -10000 0 0
MAP3K1 -0.024 0.085 0.19 35 -0.43 4 39
EIF2A -0.003 0.071 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.007 0.068 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.068 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.026 0.076 0.18 36 -0.17 4 40
FADD 0.038 0.07 -10000 0 -10000 0 0
KSR1 -0.018 0.076 0.19 36 -10000 0 36
MAPK8 -0.015 0.08 0.18 35 -0.27 11 46
PRKRA -0.018 0.076 0.19 36 -10000 0 36
PDGFA -0.055 0.22 -10000 0 -0.72 51 51
TRAF2 0.015 0.012 -10000 0 -10000 0 0
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.03 0.081 0.19 36 -10000 0 36
CTSD 0.001 0.047 -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 -0.17 0.19 -10000 0 -0.37 224 224
PRKCD 0.014 0.019 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.034 0.19 -10000 0 -0.57 54 54
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0.037 -10000 0 -0.72 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.036 0.069 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.004 0.019 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.026 0.17 -10000 0 -0.54 51 51
MAP2K1 0.002 0.069 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS 0.026 0.087 0.2 66 -10000 0 66
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.074 0.19 33 -10000 0 33
TNF-alpha/TNFR1A/FAN 0 0.037 -10000 0 -0.46 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.046 0.041 -10000 0 -10000 0 0
MAP2K2 0.002 0.069 -10000 0 -10000 0 0
SMPD3 0.035 0.03 -10000 0 -0.22 1 1
TNF 0.012 0.025 -10000 0 -10000 0 0
PKC zeta/PAR4 -0.002 0.026 -10000 0 -0.55 1 1
mol:PHOSPHOCHOLINE 0.098 0.14 0.26 214 -10000 0 214
NF kappa B1/RelA/I kappa B alpha 0 0.026 -10000 0 -0.39 2 2
AIFM1 0.026 0.087 0.2 66 -10000 0 66
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
Reelin signaling pathway

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
CDK5R1/CDK5 -0.003 0.016 -9999 0 -10000 0 0
VLDLR -0.1 0.27 -9999 0 -0.72 83 83
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
ITGA3 0.013 0.046 -9999 0 -0.72 2 2
RELN/VLDLR/Fyn -0.09 0.19 -9999 0 -0.48 100 100
MAPK8IP1/MKK7/MAP3K11/JNK1 0.002 0.022 -9999 0 -0.38 1 1
AKT1 -0.05 0.19 -9999 0 -0.34 133 133
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 0.004 0.095 -9999 0 -0.44 20 20
LRPAP1/LRP8 -0.022 0.035 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.005 0.093 -9999 0 -0.41 22 22
DAB1/alpha3/beta1 Integrin -0.056 0.16 -9999 0 -0.46 30 30
long-term memory 0.001 0.11 -9999 0 -0.41 31 31
DAB1/LIS1 -0.053 0.17 -9999 0 -0.39 98 98
DAB1/CRLK/C3G -0.054 0.16 -9999 0 -0.46 28 28
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
DAB1/NCK2 -0.053 0.17 -9999 0 -0.39 98 98
ARHGEF2 0.012 0.026 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.016 0.007 -9999 0 -10000 0 0
CDK5R1 0.014 0.019 -9999 0 -10000 0 0
RELN -0.013 0.14 -9999 0 -0.72 20 20
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RELN/LRP8/Fyn 0.001 0.11 -9999 0 -0.48 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.008 0.094 -9999 0 -0.4 22 22
MAPK8 0.015 0.032 -9999 0 -0.72 1 1
RELN/VLDLR/DAB1 -0.082 0.18 -9999 0 -0.44 98 98
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.087 0.22 -9999 0 -0.44 133 133
RELN/LRP8 0.003 0.1 -9999 0 -0.48 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn -0.001 0.12 -9999 0 -0.43 31 31
PI3K -0.052 0.16 -9999 0 -0.54 51 51
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.034 -9999 0 -0.54 2 2
RAP1A -0.019 0.16 -9999 0 -0.42 28 28
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.016 0.007 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.002 0.11 -9999 0 -0.72 12 12
NCK2 0.016 0.01 -9999 0 -10000 0 0
neuron differentiation 0.044 0.049 -9999 0 -10000 0 0
neuron adhesion -0.001 0.16 -9999 0 -0.63 6 6
LRP8 -0.029 0.072 -9999 0 -10000 0 0
GSK3B -0.038 0.18 -9999 0 -0.64 23 23
RELN/VLDLR/DAB1/Fyn -0.077 0.16 -9999 0 -0.41 100 100
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.063 0.2 -9999 0 -0.37 133 133
CDK5 0.012 0.027 -9999 0 -10000 0 0
MAPT 0.014 0.06 -9999 0 -0.66 3 3
neuron migration -0.018 0.18 -9999 0 -0.52 24 24
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.044 0.049 -9999 0 -10000 0 0
RELN/VLDLR -0.063 0.19 -9999 0 -0.45 98 98
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0 0.013 -9999 0 -10000 0 0
VDR 0.013 0.046 -9999 0 -0.72 2 2
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.074 0.041 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.084 0.043 -9999 0 -0.36 2 2
MED1 0.006 0.039 -9999 0 -10000 0 0
mol:9cRA 0.008 0.004 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.035 0.17 -9999 0 -0.32 117 117
RXRs/NUR77 0.034 0.11 -9999 0 -0.4 31 31
RXRs/PPAR -0.19 0.16 -9999 0 -0.32 63 63
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.034 -9999 0 -0.55 2 2
RARs/VDR/DNA/Vit D3 -0.064 0.15 -9999 0 -0.39 86 86
RARA 0.015 0.016 -9999 0 -10000 0 0
NCOA1 0.015 0.032 -9999 0 -0.72 1 1
VDR/VDR/DNA 0.013 0.046 -9999 0 -0.72 2 2
RARs/RARs/DNA/9cRA -0.063 0.15 -9999 0 -0.4 85 85
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.023 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.034 0.16 -9999 0 -0.32 117 117
THRA -0.031 0.18 -9999 0 -0.72 33 33
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.034 -9999 0 -0.55 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.048 0.049 -9999 0 -0.4 5 5
NR1H4 0.016 0.01 -9999 0 -10000 0 0
RXRs/LXRs/DNA 0.08 0.049 -9999 0 -0.35 6 6
NR1H2 0.024 0.003 -9999 0 -10000 0 0
NR1H3 0.024 0.032 -9999 0 -0.71 1 1
RXRs/VDR/DNA/Vit D3 0.051 0.05 -9999 0 -0.38 7 7
NR4A1 -0.02 0.16 -9999 0 -0.72 26 26
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.049 0.029 -9999 0 -0.23 5 5
RXRG 0.016 0.072 -9999 0 -0.72 5 5
RXR alpha/CCPG 0.027 0.01 -9999 0 -10000 0 0
RXRA 0.024 0.003 -9999 0 -10000 0 0
RXRB 0.025 0.004 -9999 0 -10000 0 0
THRB 0.006 0.085 -9999 0 -0.72 7 7
PPARG -0.53 0.32 -9999 0 -0.72 388 388
PPARD 0.016 0.01 -9999 0 -10000 0 0
TNF 0.089 0.041 -9999 0 -10000 0 0
mol:Oxysterols 0.008 0.004 -9999 0 -10000 0 0
cholesterol transport 0.084 0.043 -9999 0 -0.36 2 2
PPARA 0.015 0.032 -9999 0 -0.72 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.1 0.27 -9999 0 -0.72 85 85
RXRs/NUR77/BCL2 -0.04 0.16 -9999 0 -0.3 129 129
SREBF1 0.088 0.042 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.048 0.049 -9999 0 -0.4 5 5
ABCA1 0.087 0.082 -9999 0 -1.1 2 2
RARs/THRs -0.09 0.18 -9999 0 -0.41 117 117
RXRs/FXR 0.057 0.045 -9999 0 -0.4 5 5
BCL2 -0.13 0.29 -9999 0 -0.72 104 104
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.032 0.16 -9999 0 -0.54 2 2
PCK1 -0.84 0.6 -9999 0 -1.2 400 400
HNF4A 0.042 0.16 -9999 0 -10000 0 0
KCNJ11 0.034 0.18 -9999 0 -0.6 2 2
AKT1 0.014 0.11 -9999 0 -0.33 3 3
response to starvation 0.008 0.002 -9999 0 -10000 0 0
DLK1 0.034 0.18 -9999 0 -0.6 2 2
NKX2-1 0.075 0.11 -9999 0 -10000 0 0
ACADM 0.024 0.2 -9999 0 -0.98 7 7
TAT -0.023 0.2 -9999 0 -0.81 10 10
CEBPB 0.021 0.033 -9999 0 -0.72 1 1
CEBPA 0.02 0.056 -9999 0 -0.72 3 3
TTR -0.035 0.24 -9999 0 -0.59 62 62
PKLR 0.032 0.16 -9999 0 -0.54 2 2
APOA1 0.041 0.19 -9999 0 -10000 0 0
CPT1C 0.032 0.16 -9999 0 -0.55 1 1
ALAS1 0.034 0.12 -9999 0 -10000 0 0
TFRC -0.004 0.19 -9999 0 -10000 0 0
FOXF1 -0.002 0.018 -9999 0 -10000 0 0
NF1 0.026 0 -9999 0 -10000 0 0
HNF1A (dimer) 0.041 0.016 -9999 0 -10000 0 0
CPT1A 0.033 0.16 -9999 0 -0.54 2 2
HMGCS1 0.032 0.16 -9999 0 -0.54 2 2
NR3C1 -0.031 0.21 -9999 0 -0.71 46 46
CPT1B 0.032 0.16 -9999 0 -0.54 2 2
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.025 0.008 -9999 0 -10000 0 0
GCK 0.032 0.16 -9999 0 -0.54 2 2
CREB1 -0.16 0.11 -9999 0 -0.24 285 285
IGFBP1 0.008 0.15 -9999 0 -0.94 2 2
PDX1 0.043 0.14 -9999 0 -1.5 1 1
UCP2 0.033 0.16 -9999 0 -0.54 2 2
ALDOB 0.033 0.18 -9999 0 -0.6 2 2
AFP -0.095 0.15 -9999 0 -0.43 69 69
BDH1 0.032 0.16 -9999 0 -0.54 2 2
HADH 0.029 0.2 -9999 0 -0.99 4 4
F2 0.041 0.19 -9999 0 -10000 0 0
HNF1A 0.041 0.016 -9999 0 -10000 0 0
G6PC -0.083 0.11 -9999 0 -0.54 2 2
SLC2A2 0.04 0.15 -9999 0 -1.3 1 1
INS 0 0.009 -9999 0 -10000 0 0
FOXA1 -0.12 0.26 -9999 0 -0.71 80 80
FOXA3 -0.13 0.13 -9999 0 -0.38 39 39
FOXA2 0.038 0.23 -9999 0 -0.6 5 5
ABCC8 -0.1 0.43 -9999 0 -1 91 91
ALB -0.098 0.16 -9999 0 -0.45 73 73
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.01 -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 0.04 0.18 0.69 21 -0.51 1 22
IL27/IL27R/JAK1 -0.082 0.27 -10000 0 -1 26 26
TBX21 -0.059 0.24 -10000 0 -0.66 54 54
IL12B 0.013 0.024 -10000 0 -10000 0 0
IL12A 0.002 0.082 -10000 0 -0.55 11 11
IL6ST -0.02 0.15 -10000 0 -0.73 21 21
IL27RA/JAK1 -0.029 0.25 -10000 0 -1.3 19 19
IL27 -0.067 0.23 -10000 0 -0.73 58 58
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.22 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.04 0.18 0.69 21 -0.51 1 22
T cell proliferation during immune response 0.04 0.18 0.69 21 -0.51 1 22
MAPKKK cascade -0.04 0.18 0.51 1 -0.69 21 22
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.061 -10000 0 -10000 0 0
IL12RB1 0.017 0.001 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.047 0.21 -10000 0 -0.62 39 39
IL27/IL27R/JAK2/TYK2 -0.041 0.18 0.51 1 -0.7 21 22
positive regulation of T cell mediated cytotoxicity -0.04 0.18 0.51 1 -0.69 21 22
STAT1 (dimer) -0.075 0.31 0.49 23 -1 30 53
JAK2 0.011 0.034 -10000 0 -0.73 1 1
JAK1 0.013 0.046 -10000 0 -0.72 2 2
STAT2 (dimer) -0.031 0.17 0.44 1 -0.66 21 22
T cell proliferation -0.33 0.25 0.47 1 -0.53 186 187
IL12/IL12R/TYK2/JAK2 0.035 0.047 -10000 0 -10000 0 0
IL17A -0.22 0.15 -10000 0 -10000 0 0
mast cell activation 0.04 0.18 0.69 21 -0.51 1 22
IFNG 0.002 0.027 0.12 1 -0.09 10 11
T cell differentiation -0.004 0.007 0.034 1 -0.025 21 22
STAT3 (dimer) -0.031 0.17 0.44 1 -0.66 21 22
STAT5A (dimer) -0.032 0.17 0.44 1 -0.66 22 23
STAT4 (dimer) -0.036 0.18 0.44 1 -0.62 27 28
STAT4 0.005 0.086 -10000 0 -0.72 7 7
T cell activation -0.006 0.026 0.13 18 -10000 0 18
IL27R/JAK2/TYK2 -0.048 0.24 -10000 0 -1.2 19 19
GATA3 -0.094 0.37 -10000 0 -1.4 38 38
IL18 0.005 0.038 -10000 0 -0.55 1 1
positive regulation of mast cell cytokine production -0.03 0.16 0.44 1 -0.64 21 22
IL27/EBI3 -0.058 0.17 -10000 0 -0.55 58 58
IL27RA -0.053 0.26 0.44 1 -1.4 18 19
IL6 -0.52 0.32 -10000 0 -0.71 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.019 0.11 0.5 18 -1.4 1 19
IL1B 0.006 0.062 -10000 0 -0.55 6 6
EBI3 0.013 0.013 -10000 0 -10000 0 0
TNF 0.012 0.017 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0 -9999 0 -10000 0 0
SPHK1 0.004 0.071 -9999 0 -0.72 4 4
GNAI2 0.016 0.007 -9999 0 -10000 0 0
mol:S1P 0.025 0.032 -9999 0 -0.34 4 4
GNAO1 0.016 0 -9999 0 -10000 0 0
mol:Sphinganine-1-P 0.021 0.053 -9999 0 -0.54 4 4
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.023 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
S1P1/S1P -0.1 0.22 -9999 0 -0.46 147 147
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
S1P/S1P5/G12 -0.001 0.023 -9999 0 -0.26 4 4
S1P/S1P3/Gq 0.03 0.041 -9999 0 -0.32 6 6
S1P/S1P4/Gi -0.057 0.14 -9999 0 -0.24 193 193
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
GNA14 -0.008 0.09 -9999 0 -0.72 6 6
GNA15 0.014 0.02 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
ABCC1 0.012 0.026 -9999 0 -10000 0 0
amb2 Integrin signaling

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.056 -9999 0 -0.51 5 5
alphaM/beta2 Integrin/GPIbA -0.023 0.036 -9999 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 -0.04 0.073 -9999 0 -10000 0 0
PLAUR -0.022 0.069 -9999 0 -10000 0 0
HMGB1 -0.017 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.023 0.029 -9999 0 -10000 0 0
AGER -0.018 0.04 -9999 0 -0.78 1 1
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG 0.014 0.034 -9999 0 -0.72 1 1
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.089 -9999 0 -0.63 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
CYR61 -0.21 0.34 -9999 0 -0.72 161 161
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.002 0.027 -9999 0 -0.36 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.33 -9999 0 -0.72 150 150
MYH2 0.047 0.057 -9999 0 -0.37 5 5
MST1R 0.005 0.041 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.011 0.022 -9999 0 -10000 0 0
APOB 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.072 -9999 0 -0.72 5 5
JAM3 -0.038 0.19 -9999 0 -0.72 39 39
GP1BA 0.011 0.029 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.042 0.1 -9999 0 -0.52 22 22
alphaM/beta2 Integrin 0.027 0.039 -9999 0 -0.43 1 1
JAM3 homodimer -0.038 0.19 -9999 0 -0.72 39 39
ICAM2 0.004 0.096 -9999 0 -0.72 9 9
ICAM1 0.008 0.045 -9999 0 -0.72 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor 0.027 0.039 -9999 0 -0.43 1 1
cell adhesion -0.023 0.036 -9999 0 -10000 0 0
NFKB1 -0.22 0.18 -9999 0 -0.41 25 25
THY1 0.013 0.024 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.11 0.19 -9999 0 -0.45 118 118
IL6 -0.62 0.41 -9999 0 -0.86 391 391
ITGB2 -0.026 0.041 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration -0.022 0.069 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.17 0.27 -9999 0 -0.56 152 152
JAM2 -0.19 0.33 -9999 0 -0.72 150 150
alphaM/beta2 Integrin/ICAM1 -0.005 0.04 -9999 0 -0.43 1 1
alphaM/beta2 Integrin/uPA/Plg -0.019 0.047 -9999 0 -0.46 1 1
RhoA/GTP 0.043 0.05 -9999 0 -0.34 7 7
positive regulation of phagocytosis 0.001 0.029 -9999 0 -10000 0 0
Ron/MSP -0.005 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA -0.022 0.071 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR -0.028 0.058 -9999 0 -10000 0 0
PLAU -0.009 0.059 -9999 0 -10000 0 0
PLAT -0.15 0.31 -9999 0 -0.72 118 118
actin filament polymerization 0.046 0.055 -9999 0 -0.36 5 5
MST1 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.023 -9999 0 -10000 0 0
TNF -0.2 0.17 -9999 0 -0.67 1 1
RAP1B 0.016 0.01 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.049 -9999 0 -10000 0 0
fibrinolysis -0.019 0.047 -9999 0 -0.46 1 1
HCK 0.013 0.024 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation 0.027 0.039 -9999 0 -0.43 1 1
VTN 0.015 0.012 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.17 0.23 -9999 0 -0.51 161 161
LPA 0.016 0 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.044 0.063 -9999 0 -0.46 5 5
FN1 -0.098 0.074 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.024 0.033 -9999 0 -10000 0 0
MPO 0.015 0.016 -9999 0 -10000 0 0
KNG1 0.016 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
ROCK1 0.049 0.048 -9999 0 -0.49 1 1
ELA2 0.016 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
CTGF -0.015 0.15 -9999 0 -0.72 22 22
alphaM/beta2 Integrin/Hck -0.024 0.034 -9999 0 -10000 0 0
ITGAM -0.017 0.025 -9999 0 -0.2 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.21 -9999 0 -0.46 150 150
HP 0.016 0 -9999 0 -10000 0 0
leukocyte adhesion -0.21 0.23 -9999 0 -0.56 138 138
SELP -0.19 0.33 -9999 0 -0.72 150 150
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.051 0.24 -10000 0 -0.94 24 24
NCK1/PAK1/Dok-R -0.029 0.093 -10000 0 -0.43 24 24
NCK1/Dok-R -0.048 0.23 -10000 0 -1.1 24 24
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol -0.008 0.041 0.24 14 -10000 0 14
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.018 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.008 0.042 0.26 13 -10000 0 13
TNIP2 0.015 0.012 -10000 0 -10000 0 0
NF kappa B/RelA -0.045 0.21 -10000 0 -1 24 24
FN1 -0.098 0.074 -10000 0 -10000 0 0
PLD2 0.039 0.26 -10000 0 -1.1 24 24
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.091 0.23 -10000 0 -0.72 57 57
ELK1 0.054 0.24 -10000 0 -1 24 24
GRB7 0.001 0.048 -10000 0 -10000 0 0
PAK1 -0.01 0.06 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.051 0.26 -10000 0 -1.1 24 24
CDKN1A 0.05 0.19 -10000 0 -0.68 19 19
ITGA5 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.047 0.23 -10000 0 -1.1 24 24
CRK 0.015 0.032 -10000 0 -0.72 1 1
mol:NO 0.066 0.19 -10000 0 -0.67 24 24
PLG 0.039 0.26 -10000 0 -1.1 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.003 0.21 -10000 0 -0.9 24 24
GRB2 0.013 0.022 -10000 0 -10000 0 0
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
ANGPT2 -0.027 0.2 -10000 0 -0.63 17 17
BMX -0.21 0.34 -10000 0 -1.4 24 24
ANGPT1 0.015 0.23 -10000 0 -1.4 14 14
tube development 0.042 0.21 -10000 0 -0.68 25 25
ANGPT4 0.016 0.001 -10000 0 -10000 0 0
response to hypoxia 0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.001 0.31 -10000 0 -1.3 24 24
alpha5/beta1 Integrin 0 0.003 -10000 0 -10000 0 0
FGF2 -0.55 0.31 -10000 0 -0.72 403 403
STAT5A (dimer) 0.045 0.23 -10000 0 -0.84 21 21
mol:L-citrulline 0.066 0.19 -10000 0 -0.67 24 24
AGTR1 -0.31 0.35 -10000 0 -0.72 224 224
MAPK14 0.035 0.27 -10000 0 -1.2 24 24
Tie2/SHP2 -0.032 0.18 -10000 0 -1.2 12 12
TEK 0.027 0.21 -10000 0 -1.3 12 12
RPS6KB1 0.048 0.23 -10000 0 -0.9 24 24
Angiotensin II/AT1 -0.23 0.27 -10000 0 -0.55 224 224
Tie2/Ang1/GRB2 0.036 0.27 -10000 0 -1.2 24 24
MAPK3 0.049 0.24 -10000 0 -1 24 24
MAPK1 0.049 0.24 -10000 0 -1 24 24
Tie2/Ang1/GRB7 0.039 0.27 -10000 0 -1.2 24 24
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.039 0.26 -10000 0 -1.1 24 24
PI3K 0.034 0.27 -10000 0 -1.1 24 24
FES 0.033 0.27 -10000 0 -1.2 24 24
Crk/Dok-R -0.048 0.23 -10000 0 -1.1 24 24
Tie2/Ang1/ABIN2 0.035 0.27 -10000 0 -1.2 24 24
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.055 0.22 -10000 0 -0.83 24 24
STAT5A 0.014 0.045 -10000 0 -0.72 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.049 0.23 -10000 0 -0.9 24 24
Tie2/Ang2 0.024 0.26 -10000 0 -0.97 24 24
Tie2/Ang1 0.028 0.28 -10000 0 -1.2 24 24
FOXO1 0.04 0.26 -10000 0 -0.87 25 25
ELF1 0.026 0.018 -10000 0 -10000 0 0
ELF2 0.036 0.26 -10000 0 -1.1 24 24
mol:Choline 0.041 0.25 -10000 0 -1.1 24 24
cell migration -0.013 0.054 -10000 0 -0.24 24 24
FYN 0.037 0.23 -10000 0 -0.8 24 24
DOK2 0.013 0.046 -10000 0 -0.72 2 2
negative regulation of cell cycle 0.052 0.18 -10000 0 -0.61 19 19
ETS1 0.022 0.057 -10000 0 -0.89 1 1
PXN 0.061 0.2 -10000 0 -0.73 24 24
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.063 0.21 -10000 0 -0.78 24 24
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.02 0.046 -10000 0 -10000 0 0
MAPKKK cascade 0.041 0.25 -10000 0 -1.1 24 24
RASA1 0.015 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.033 0.27 -10000 0 -1.2 24 24
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.068 0.17 -10000 0 -0.6 24 24
mol:Phosphatidic acid 0.041 0.25 -10000 0 -1.1 24 24
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.066 0.19 -10000 0 -0.67 24 24
Rac1/GTP -0.053 0.18 -10000 0 -0.83 24 24
MMP2 0.036 0.27 -10000 0 -1.2 24 24
mTOR signaling pathway

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
GBL 0.016 0.007 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.072 0.16 0.32 6 -0.36 106 112
FRAP1 0.009 0.049 -10000 0 -10000 0 0
AKT1 -0.032 0.15 0.25 6 -0.32 106 112
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.049 0.1 -10000 0 -0.31 52 52
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.014 0.033 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.042 0.092 0.18 1 -0.4 8 9
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.033 0.14 -10000 0 -0.39 69 69
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.017 0.039 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 0.002 0.091 -10000 0 -0.31 7 7
MAP3K5 -0.015 0.11 -10000 0 -0.42 35 35
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
apoptosis -0.015 0.11 -10000 0 -0.42 35 35
mol:LY294002 0 0.001 -10000 0 -0.002 62 62
EIF4B 0.012 0.083 -10000 0 -0.27 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.026 0.058 -10000 0 -0.4 1 1
eIF4E/eIF4G1/eIF4A1 -0.005 0.015 -10000 0 -10000 0 0
KIAA1303 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.057 0.18 -10000 0 -0.38 113 113
mTOR/RHEB/GTP/Raptor/GBL 0.031 0.071 -10000 0 -10000 0 0
FKBP1A 0.016 0.01 -10000 0 -10000 0 0
RHEB/GTP -0.042 0.091 0.23 1 -0.39 8 9
mol:Amino Acids 0 0.001 -10000 0 -0.002 62 62
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.066 0.14 0.26 6 -0.33 106 112
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C -0.02 0.16 -10000 0 -0.62 35 35
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.042 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.052 0.11 -10000 0 -0.33 52 52
tumor necrosis factor receptor activity 0 0.001 0.002 62 -10000 0 62
RPS6 0.015 0.032 -10000 0 -0.72 1 1
PPP5C 0.014 0.02 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 -0.046 0.15 -10000 0 -0.42 69 69
INS 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.11 -10000 0 -0.72 13 13
PDK2 -0.066 0.14 0.26 6 -0.34 106 112
EIF4EBP1 0.022 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PPP2R5D 0.017 0.046 -10000 0 -10000 0 0
peptide biosynthetic process 0.032 0 -10000 0 -10000 0 0
RHEB 0.016 0.007 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 13 -0.003 51 64
EEF2 0.033 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.029 0.014 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.002 0.026 -9999 0 -0.54 1 1
AKT1 -0.006 0.2 -9999 0 -0.54 31 31
PTK2B 0.001 0.14 -9999 0 -0.52 23 23
VEGFR2 homodimer/Frs2 -0.006 0.14 -9999 0 -0.52 32 32
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.057 0.15 -9999 0 -0.58 26 26
endothelial cell proliferation 0.015 0.19 -9999 0 -0.5 29 29
mol:Ca2+ -0.043 0.22 -9999 0 -0.69 29 29
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.05 0.13 -9999 0 -0.54 25 25
RP11-342D11.1 -0.054 0.22 -9999 0 -0.69 30 30
CDH5 0.016 0 -9999 0 -10000 0 0
VEGFA homodimer 0.003 0.053 -9999 0 -0.44 4 4
SHC1 0.016 0 -9999 0 -10000 0 0
SHC2 -0.023 0.17 -9999 0 -0.72 28 28
HRAS/GDP -0.078 0.16 -9999 0 -0.58 29 29
SH2D2A -0.006 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.063 0.15 -9999 0 -0.52 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.05 0.16 -9999 0 -0.58 26 26
VEGFR1 homodimer 0.016 0.01 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.084 0.18 -9999 0 -0.65 29 29
GRB10 -0.046 0.23 -9999 0 -0.73 30 30
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
PAK1 -0.01 0.06 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.047 0.13 -9999 0 -0.51 28 28
HRAS 0.015 0.012 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.085 -9999 0 -0.29 4 4
HIF1A 0.008 0.067 -9999 0 -0.72 4 4
FRS2 0.011 0.039 -9999 0 -0.72 1 1
oxygen and reactive oxygen species metabolic process -0.049 0.13 -9999 0 -0.54 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.013 0.029 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.059 0.15 -9999 0 -0.58 27 27
mol:GDP -0.083 0.17 -9999 0 -0.63 29 29
mol:NADP 0.007 0.16 -9999 0 -0.45 27 27
eNOS/Hsp90 0.015 0.16 -9999 0 -0.42 27 27
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:IP3 -0.044 0.22 -9999 0 -0.7 29 29
HIF1A/ARNT -0.005 0.048 -9999 0 -0.54 4 4
SHB 0.013 0.037 -9999 0 -0.72 1 1
VEGFA -0.018 0.068 -9999 0 -10000 0 0
VEGFC -0.002 0.12 -9999 0 -0.72 13 13
FAK1/Vinculin 0.027 0.14 -9999 0 -0.49 23 23
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.14 -9999 0 -0.54 25 25
PTPN6 0.015 0.014 -9999 0 -10000 0 0
EPAS1 -0.03 0.18 -9999 0 -0.76 31 31
mol:L-citrulline 0.007 0.16 -9999 0 -0.45 27 27
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.049 0.14 -9999 0 -0.54 26 26
VEGFR2 homodimer/VEGFA homodimer -0.11 0.21 -9999 0 -0.75 30 30
VEGFR2/3 heterodimer -0.006 0.14 -9999 0 -0.52 31 31
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.04 0.22 -9999 0 -0.69 30 30
VEGFR2 homodimer -0.016 0.16 -9999 0 -0.61 31 31
FLT1 0.016 0.01 -9999 0 -10000 0 0
NEDD4 -0.004 0.079 -9999 0 -0.74 5 5
MAPK3 -0.032 0.2 -9999 0 -0.63 29 29
MAPK1 -0.032 0.2 -9999 0 -0.63 29 29
VEGFA145/NRP2 -0.005 0.041 -9999 0 -10000 0 0
VEGFR1/2 heterodimer -0.005 0.14 -9999 0 -0.52 31 31
KDR -0.016 0.16 -9999 0 -0.61 31 31
VEGFA165/NRP1/VEGFR2 homodimer -0.092 0.19 -9999 0 -0.69 29 29
SRC 0.016 0.007 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.031 0.21 -9999 0 -0.64 29 29
PI3K -0.098 0.19 -9999 0 -0.65 33 33
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.057 0.14 -9999 0 -0.58 25 25
FES -0.047 0.23 -9999 0 -0.71 31 31
GAB1 -0.066 0.15 -9999 0 -0.6 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.057 0.14 -9999 0 -0.58 25 25
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.23 0.24 -9999 0 -0.52 149 149
VEGFR2 homodimer/VEGFA homodimer/Yes -0.058 0.14 -9999 0 -0.58 26 26
PI3K/GAB1 -0.015 0.22 -9999 0 -0.55 47 47
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.037 0.14 -9999 0 -0.54 23 23
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.046 0.13 -9999 0 -0.51 36 36
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
CDC42 -0.045 0.22 -9999 0 -0.71 29 29
actin cytoskeleton reorganization -0.05 0.15 -9999 0 -0.58 26 26
PTK2 0.019 0.15 -9999 0 -0.53 23 23
EDG1 -0.17 0.4 -9999 0 -0.79 149 149
mol:DAG -0.044 0.22 -9999 0 -0.7 29 29
CaM/Ca2+ -0.09 0.17 -9999 0 -0.64 29 29
MAP2K3 -0.033 0.21 -9999 0 -0.67 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.099 0.21 -9999 0 -0.76 30 30
PLCG1 -0.045 0.22 -9999 0 -0.71 29 29
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.05 0.14 -9999 0 -0.54 26 26
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.057 0.14 -9999 0 -0.58 25 25
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.056 0.14 -9999 0 -0.57 27 27
cell migration 0.059 0.13 -9999 0 -0.4 23 23
mol:PI-3-4-5-P3 -0.025 0.22 -9999 0 -0.59 35 35
FYN 0.013 0.045 -9999 0 -0.72 2 2
VEGFB/NRP1 -0.095 0.18 -9999 0 -0.65 29 29
mol:NO 0.007 0.16 -9999 0 -0.45 27 27
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.084 0.15 -9999 0 -0.58 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.042 0.24 -9999 0 -0.75 30 30
VHL 0.012 0.027 -9999 0 -10000 0 0
ITGB3 0.014 0.02 -9999 0 -10000 0 0
NOS3 0.003 0.18 -9999 0 -0.51 27 27
VEGFR2 homodimer/VEGFA homodimer/Sck -0.08 0.18 -9999 0 -0.61 39 39
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.031 0.21 -9999 0 -0.65 29 29
PRKCB -0.041 0.21 -9999 0 -0.66 29 29
VCL 0.016 0.007 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.048 0.22 -9999 0 -0.69 30 30
VEGFR1/2 heterodimer/VEGFA homodimer -0.056 0.14 -9999 0 -0.58 25 25
VEGFA165/NRP2 -0.005 0.041 -9999 0 -10000 0 0
MAPKKK cascade -0.072 0.17 -9999 0 -0.61 30 30
NRP2 0.015 0.016 -9999 0 -10000 0 0
VEGFC homodimer -0.002 0.11 -9999 0 -0.72 13 13
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.028 0.14 -9999 0 -0.49 23 23
MAP3K13 -0.045 0.22 -9999 0 -0.71 29 29
PDPK1 -0.011 0.2 -9999 0 -0.53 30 30
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.032 0.12 -9999 0 -0.46 38 38
E-cadherin/beta catenin -0.039 0.14 -9999 0 -0.54 37 37
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
JUP 0.014 0.035 -9999 0 -0.72 1 1
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.002 0.048 -10000 0 -10000 0 0
GNB1/GNG2 -0.017 0.051 -10000 0 -0.17 52 52
AKT1 0.072 0.088 -10000 0 -0.19 51 51
EGF -0.24 0.35 -10000 0 -0.72 178 178
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.06 0.036 -10000 0 -10000 0 0
mol:Ca2+ 0.075 0.12 -10000 0 -0.28 52 52
LYN 0.06 0.036 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.035 -10000 0 -0.13 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.08 0.14 -10000 0 -0.32 52 52
GNG2 0.015 0.032 -10000 0 -0.72 1 1
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.041 0.037 -10000 0 -0.45 2 2
G beta5/gamma2 -0.022 0.066 -10000 0 -0.22 51 51
PRKCH 0.073 0.14 -10000 0 -0.34 52 52
DNM1 0.016 0.007 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.001 0.005 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.006 0.081 -10000 0 -0.72 6 6
G12 family/GTP -0.027 0.086 -10000 0 -0.28 52 52
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.014 0.045 -10000 0 -0.72 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.064 0.079 0.35 5 -10000 0 5
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0.01 -10000 0 -10000 0 0
PRKG1 0.016 0 -10000 0 -10000 0 0
mol:IP3 0.077 0.14 -10000 0 -0.35 52 52
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.076 0.18 -10000 0 -0.47 52 52
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.063 0.038 -10000 0 -10000 0 0
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.061 0.036 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.016 0 -10000 0 -10000 0 0
PRKCB1 0.074 0.14 -10000 0 -0.35 52 52
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.076 0.19 -10000 0 -0.5 52 52
LCK 0.064 0.038 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.002 0.028 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.04 0.014 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.002 0.028 -10000 0 -10000 0 0
MAPK14 0.076 0.098 -10000 0 -0.21 52 52
TGM2/GTP 0.082 0.16 -10000 0 -0.38 52 52
MAPK11 0.076 0.098 -10000 0 -0.21 52 52
ARHGEF1 0.061 0.076 -10000 0 -0.16 52 52
GNAI2 0.016 0.007 -10000 0 -10000 0 0
JNK cascade 0.078 0.15 -10000 0 -0.37 52 52
RAB11/GDP 0.014 0.01 -10000 0 -10000 0 0
ICAM1 0.071 0.12 -10000 0 -0.28 52 52
cAMP biosynthetic process 0.074 0.13 -10000 0 -0.32 52 52
Gq family/GTP/EBP50 0.021 0.027 -10000 0 -0.22 6 6
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.06 0.036 -10000 0 -10000 0 0
GNB5 0.015 0.032 -10000 0 -0.72 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.038 0.096 -10000 0 -0.32 6 6
VCAM1 0.068 0.13 -10000 0 -0.31 52 52
TP beta/Gq family/GDP/G beta5/gamma2 0.041 0.037 -10000 0 -0.45 2 2
platelet activation 0.098 0.13 -10000 0 -0.28 52 52
PGI2/IP 0 0.001 -10000 0 -10000 0 0
PRKACA 0.024 0.039 -10000 0 -0.34 6 6
Gq family/GDP/G beta5/gamma2 0.039 0.037 -10000 0 -0.43 2 2
TXA2/TP beta/beta Arrestin2 0 0.003 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.034 0.037 -10000 0 -0.31 6 6
mol:DAG 0.075 0.16 -10000 0 -0.4 52 52
EGFR -0.38 0.37 -10000 0 -0.72 277 277
TXA2/TP alpha 0.084 0.17 -10000 0 -0.43 52 52
Gq family/GTP -0.003 0.03 -10000 0 -0.28 6 6
YES1 0.06 0.043 -10000 0 -0.53 1 1
GNAI2/GTP -0.004 0.032 -10000 0 -10000 0 0
PGD2/DP -0.008 0.059 -10000 0 -0.55 6 6
SLC9A3R1 -0.022 0.069 -10000 0 -10000 0 0
FYN 0.059 0.043 -10000 0 -0.31 2 2
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 0.014 0.02 -10000 0 -10000 0 0
PGK/cGMP 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.007 0.043 -10000 0 -10000 0 0
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.075 0.14 -10000 0 -0.33 52 52
PRKCB 0.068 0.14 -10000 0 -0.34 52 52
PRKCE 0.076 0.14 -10000 0 -0.34 52 52
PRKCD 0.073 0.15 -10000 0 -0.37 52 52
PRKCG 0.074 0.15 -10000 0 -0.36 52 52
muscle contraction 0.081 0.18 -10000 0 -0.46 52 52
PRKCZ 0.074 0.14 -10000 0 -0.33 52 52
ARR3 0.016 0 -10000 0 -10000 0 0
TXA2/TP beta -0.004 0.035 -10000 0 -0.34 2 2
PRKCQ 0.073 0.14 -10000 0 -0.34 52 52
MAPKKK cascade 0.076 0.16 -10000 0 -0.41 52 52
SELE 0.058 0.16 -10000 0 -0.4 52 52
TP beta/GNAI2/GDP/G beta/gamma -0.003 0.032 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.008 0.09 -10000 0 -0.72 6 6
chemotaxis 0.071 0.23 -10000 0 -0.6 52 52
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
GNA11 0.016 0 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.006 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
ERC1 0.013 0.022 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.037 0.086 -9999 0 -0.35 21 21
IRAK/TOLLIP 0.031 0.012 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.008 0.045 -9999 0 -0.54 3 3
IL1A 0.014 0.02 -9999 0 -10000 0 0
IL1B -0.043 0.2 -9999 0 -0.57 62 62
IRAK/TRAF6/p62/Atypical PKCs 0.002 0.013 -9999 0 -10000 0 0
IL1R2 0.004 0.065 -9999 0 -0.72 3 3
IL1R1 -0.067 0.23 -9999 0 -0.72 59 59
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.14 -9999 0 -0.46 19 19
TOLLIP 0.016 0.007 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 -0.001 0.021 -9999 0 -0.46 1 1
IKK complex/ELKS 0.082 0.02 -9999 0 -10000 0 0
JUN -0.01 0.16 -9999 0 -0.59 5 5
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.12 0.24 -9999 0 -0.54 99 99
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.13 -9999 0 -0.41 59 59
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.04 0.12 -9999 0 -0.38 59 59
IL1 beta fragment/IL1R1/IL1RAP -0.098 0.21 -9999 0 -0.49 104 104
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.054 0.062 -9999 0 -10000 0 0
IRAK1 0.022 0.012 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.071 0.17 -9999 0 -0.55 59 59
IRAK4 0.016 0.01 -9999 0 -10000 0 0
PRKCI 0.013 0.022 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.017 0.15 -9999 0 -0.48 23 23
CHUK 0.015 0.032 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.098 0.21 -9999 0 -0.49 104 104
IL1 beta/IL1R2 -0.057 0.17 -9999 0 -0.49 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 0.001 0.018 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.21 -9999 0 -0.67 45 45
IRAK3 0.012 0.039 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.087 0.19 -9999 0 -0.44 104 104
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.11 -9999 0 -0.3 1 1
IL1 alpha/IL1R1/IL1RAP -0.05 0.14 -9999 0 -0.46 59 59
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
MYD88 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.004 -9999 0 -10000 0 0
IL1RAP 0.016 0 -9999 0 -10000 0 0
UBE2N 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6 -0.07 0.16 -9999 0 -0.61 21 21
CASP1 -0.068 0.24 -9999 0 -0.72 60 60
IL1RN/IL1R2 -0.018 0.052 -9999 0 -0.54 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.09 0.2 -9999 0 -0.46 104 104
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.12 -9999 0 -0.34 59 59
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
IL1RN -0.006 0.056 -9999 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0 0.017 -9999 0 -0.36 1 1
MAP2K6 0.047 0.063 -9999 0 -0.35 13 13
Canonical Wnt signaling pathway

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
HDAC1 0.011 0.028 -10000 0 -10000 0 0
AES 0.01 0.023 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
SMAD4 0.013 0.045 -10000 0 -0.72 2 2
DKK2 0.007 0.074 -10000 0 -0.72 5 5
TLE1 -0.016 0.14 -10000 0 -0.72 18 18
MACF1 0.017 0 -10000 0 -10000 0 0
CTNNB1 0.16 0.077 0.3 1 -10000 0 1
WIF1 -0.53 0.32 -10000 0 -0.72 392 392
beta catenin/RanBP3 0.04 0.13 0.46 46 -10000 0 46
KREMEN2 -0.076 0.08 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 0.16 0.072 -10000 0 -10000 0 0
FZD1 0.016 0.032 -10000 0 -0.72 1 1
AXIN2 -0.018 0.21 -10000 0 -1.5 9 9
AXIN1 0.017 0.01 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.042 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.13 0.1 0.33 3 -0.48 4 7
Axin1/APC/GSK3 0.002 0.014 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.11 0.033 -10000 0 -10000 0 0
HNF1A 0.01 0.028 0.27 1 -10000 0 1
CTBP1 0.01 0.026 -10000 0 -10000 0 0
MYC -0.068 0.36 -10000 0 -1.5 29 29
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
NKD1 0.013 0.019 -10000 0 -10000 0 0
TCF4 0 0.086 -10000 0 -0.71 7 7
TCF3 0.009 0.03 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.02 -10000 0 -0.4 1 1
Ran/GTP 0.002 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.032 0.15 0.47 44 -0.41 1 45
LEF1 -0.015 0.068 -10000 0 -10000 0 0
DVL1 0.11 0.062 0.23 3 -10000 0 3
CSNK2A1 0.017 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.12 0.11 -10000 0 -0.46 3 3
DKK1/LRP6/Kremen 2 -0.025 0.16 -10000 0 -0.5 46 46
LRP6 0.016 0.012 -10000 0 -10000 0 0
CSNK1A1 0.011 0.028 -10000 0 -10000 0 0
NLK 0.005 0.041 -10000 0 -10000 0 0
CCND1 -0.033 0.24 -10000 0 -1.6 12 12
WNT1 0.017 0.002 -10000 0 -10000 0 0
GSK3A 0.018 0.001 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
PPP2R5D 0.065 0.029 -10000 0 -10000 0 0
APC 0.054 0.02 -10000 0 -0.37 1 1
WNT1/LRP6/FZD1 0.2 0.12 0.27 391 -10000 0 391
CREBBP 0.009 0.041 -10000 0 -0.73 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.067 0.13 -10000 0 -0.66 9 9
RAD9A 0.016 0 -10000 0 -10000 0 0
AP1 -0.46 0.35 -10000 0 -0.65 375 375
IFNAR2 0.018 0.003 -10000 0 -10000 0 0
AKT1 -0.034 0.12 -10000 0 -0.25 118 118
ER alpha/Oestrogen -0.14 0.22 -10000 0 -0.55 117 117
NFX1/SIN3/HDAC complex 0.06 0.01 -10000 0 -10000 0 0
EGF -0.23 0.35 -10000 0 -0.72 178 178
SMG5 0.014 0.02 -10000 0 -10000 0 0
SMG6 0.016 0 -10000 0 -10000 0 0
SP3/HDAC2 0.023 0.015 -10000 0 -10000 0 0
TERT/c-Abl -0.063 0.11 -10000 0 -0.64 7 7
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0 0.004 -10000 0 -10000 0 0
WT1 -0.04 0.077 -10000 0 -10000 0 0
WRN 0.016 0.01 -10000 0 -10000 0 0
SP1 0.019 0.003 -10000 0 -10000 0 0
SP3 0.017 0.003 -10000 0 -10000 0 0
TERF2IP 0.016 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.091 -10000 0 -0.61 5 5
Mad/Max 0.022 0.011 -10000 0 -10000 0 0
TERT -0.07 0.13 -10000 0 -0.7 8 8
CCND1 -0.072 0.2 -10000 0 -1.2 13 13
MAX 0.017 0.003 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
TERF2 -0.001 0.029 -10000 0 -0.66 1 1
PTGES3 0.015 0.032 -10000 0 -0.72 1 1
SIN3A 0.017 0.001 -10000 0 -10000 0 0
Telomerase/911 0.037 0.025 -10000 0 -10000 0 0
CDKN1B 0.011 0.12 -10000 0 -0.76 10 10
RAD1 0.015 0.012 -10000 0 -10000 0 0
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
SAP30 0.016 0.007 -10000 0 -10000 0 0
TRF2/PARP2 -0.001 0.023 -10000 0 -0.53 1 1
UBE3A 0.017 0.003 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.72 97 97
E6 0.001 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.006 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 374 374
IFN-gamma/IRF1 0 0.073 -10000 0 -0.35 10 10
PARP2 0.016 0 -10000 0 -10000 0 0
BLM -0.033 0.074 -10000 0 -10000 0 0
Telomerase 0.008 0.026 -10000 0 -10000 0 0
IRF1 0.01 0.046 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
KU/TER 0 0 -10000 0 -10000 0 0
ATM/TRF2 -0.001 0.019 -10000 0 -0.43 1 1
ubiquitin-dependent protein catabolic process 0.067 0.01 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.067 0.01 -10000 0 -10000 0 0
HDAC1 0.017 0.001 -10000 0 -10000 0 0
HDAC2 0.017 0.018 -10000 0 -10000 0 0
ATM 0 0.011 0.25 1 -10000 0 1
SMAD3 0.026 0.026 -10000 0 -0.54 1 1
ABL1 0.016 0 -10000 0 -10000 0 0
MXD1 0.017 0.008 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
HUS1 0.015 0.012 -10000 0 -10000 0 0
RPS6KB1 0.013 0.024 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.056 0.12 -10000 0 -0.62 10 10
NR2F2 -0.007 0.12 -10000 0 -0.72 14 14
MAPK3 0.03 0.026 -10000 0 -0.54 1 1
MAPK1 0.03 0.026 -10000 0 -0.54 1 1
TGFB1/TGF beta receptor Type II 0.015 0.01 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
HNRNPC 0.016 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0.011 0.25 1 -10000 0 1
NBN 0.016 0.007 -10000 0 -10000 0 0
EGFR -0.37 0.37 -10000 0 -0.72 277 277
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.45 0.33 -10000 0 -0.64 372 372
MYC -0.023 0.17 -10000 0 -0.72 29 29
IL2 0.018 0.033 -10000 0 -0.72 1 1
KU 0 0 -10000 0 -10000 0 0
RAD50 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
TGFB1 0.015 0.01 -10000 0 -10000 0 0
TRF2/BLM 0.022 0.042 -10000 0 -0.53 1 1
FRAP1 0.016 0 -10000 0 -10000 0 0
KU/TERT -0.056 0.11 -10000 0 -0.63 7 7
SP1/HDAC2 0.026 0.016 -10000 0 -10000 0 0
PINX1 0.016 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.052 0.091 -10000 0 -0.64 4 4
Smad3/Myc 0.004 0.11 -10000 0 -0.46 30 30
911 complex 0 0.009 -10000 0 -10000 0 0
IFNG -0.016 0.074 -10000 0 -0.71 1 1
Telomerase/PinX1 -0.052 0.091 -10000 0 -0.61 5 5
Telomerase/AKT1/mTOR/p70S6K 0.015 0.062 -10000 0 -0.48 2 2
SIN3B 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Telomerase/EST1B -0.053 0.092 -10000 0 -0.61 5 5
response to DNA damage stimulus 0.004 0.003 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.018 -10000 0 -0.4 1 1
TRF2/WRN -0.001 0.024 -10000 0 -0.53 1 1
Telomerase/hnRNP C1/C2 -0.052 0.091 -10000 0 -0.61 5 5
E2F1 -0.004 0.056 -10000 0 -10000 0 0
ZNFX1 0.014 0.022 -10000 0 -10000 0 0
PIF1 0.01 0.032 -10000 0 -10000 0 0
NCL 0.016 0 -10000 0 -10000 0 0
DKC1 0.015 0.014 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.024 0.024 -9999 0 -10000 0 0
STMN1 -0.008 0.068 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.018 0.077 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.18 0.13 -9999 0 -0.26 384 384
BIRC5 -0.087 0.078 -9999 0 -10000 0 0
DES 0.006 0.1 -9999 0 -0.61 13 13
Aurora C/Aurora B/INCENP 0.028 0.036 -9999 0 -10000 0 0
Aurora B/TACC1 -0.011 0.12 -9999 0 -0.49 31 31
Aurora B/PP2A 0.022 0.031 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.017 0.011 -9999 0 -0.19 1 1
mitotic metaphase/anaphase transition -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.053 0.078 -9999 0 -10000 0 0
Cul3 protein complex -0.34 0.22 -9999 0 -0.47 384 384
KIF2C 0.017 0.012 -9999 0 -10000 0 0
PEBP1 0.013 0.033 -9999 0 -0.74 1 1
KIF20A -0.091 0.077 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.023 0.03 -9999 0 -10000 0 0
SEPT1 0.013 0.023 -9999 0 -10000 0 0
SMC2 0.009 0.034 -9999 0 -10000 0 0
SMC4 -0.002 0.051 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.036 0.012 -9999 0 -10000 0 0
PSMA3 0.016 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.001 -9999 0 -10000 0 0
H3F3B 0.014 0.024 -9999 0 -0.41 1 1
AURKB -0.015 0.064 -9999 0 -10000 0 0
AURKC 0.013 0.022 -9999 0 -10000 0 0
CDCA8 -0.064 0.081 -9999 0 -10000 0 0
cytokinesis -0.009 0.03 -9999 0 -10000 0 0
Aurora B/Septin1 0.009 0.035 -9999 0 -10000 0 0
AURKA -0.05 0.08 -9999 0 -10000 0 0
INCENP 0 0.046 -9999 0 -10000 0 0
KLHL13 -0.52 0.33 -9999 0 -0.72 382 382
BUB1 -0.12 0.059 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.009 0.098 -9999 0 -10000 0 0
EVI5 0.015 0.032 -9999 0 -0.73 1 1
RhoA/GTP 0.018 0.069 -9999 0 -10000 0 0
SGOL1 -0.029 0.073 -9999 0 -10000 0 0
CENPA 0.012 0.019 -9999 0 -10000 0 0
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.023 0.029 -9999 0 -10000 0 0
NCAPD2 0.009 0.034 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.023 0.029 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.036 0.076 -9999 0 -10000 0 0
NPM1 0.017 0.009 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
KLHL9 0.004 0.096 -9999 0 -0.72 9 9
mitotic prometaphase -0.002 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.029 -9999 0 -10000 0 0
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.003 0.079 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.017 0.009 -9999 0 -10000 0 0
MYLK -0.11 0.19 -9999 0 -0.41 151 151
KIF23 -0.081 0.08 -9999 0 -10000 0 0
VIM -0.044 0.17 -9999 0 -0.56 49 49
RACGAP1 -0.029 0.074 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.009 -9999 0 -10000 0 0
Chromosomal passenger complex 0.004 0.031 -9999 0 -0.23 1 1
Chromosomal passenger complex/EVI5 0.077 0.091 -9999 0 -0.59 1 1
TACC1 -0.028 0.17 -9999 0 -0.72 31 31
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
CUL3 0.012 0.056 -9999 0 -0.72 3 3
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.012 0.074 -10000 0 -0.28 7 7
TBX21 -0.095 0.39 -10000 0 -1.3 39 39
B2M 0.016 0.033 -10000 0 -0.72 1 1
TYK2 0.009 0.017 -10000 0 -10000 0 0
IL12RB1 0.009 0.017 -10000 0 -10000 0 0
GADD45B -0.036 0.25 -10000 0 -0.78 34 34
IL12RB2 -0.018 0.076 -10000 0 -0.72 2 2
GADD45G -0.03 0.22 -10000 0 -0.7 32 32
natural killer cell activation -0.004 0.019 -10000 0 -10000 0 0
RELB 0.013 0.024 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.007 0.055 -10000 0 -0.73 1 1
IL2RA 0.006 0.039 -10000 0 -10000 0 0
IFNG -0.021 0.074 -10000 0 -0.72 1 1
STAT3 (dimer) -0.019 0.21 -10000 0 -0.55 36 36
HLA-DRB5 0.005 0.008 -10000 0 -10000 0 0
FASLG -0.045 0.24 -10000 0 -0.78 21 21
NF kappa B2 p52/RelB -0.09 0.19 -10000 0 -0.52 73 73
CD4 0.005 0.008 -10000 0 -10000 0 0
SOCS1 0.015 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.017 0.014 -10000 0 -10000 0 0
CD3D -0.002 0.037 -10000 0 -10000 0 0
CD3E 0.005 0.011 -10000 0 -10000 0 0
CD3G -0.022 0.11 -10000 0 -0.73 10 10
IL12Rbeta2/JAK2 -0.002 0.065 -10000 0 -0.55 3 3
CCL3 -0.042 0.24 -10000 0 -0.78 19 19
CCL4 -0.042 0.24 -10000 0 -0.78 19 19
HLA-A 0.014 0.025 -10000 0 -10000 0 0
IL18/IL18R 0.027 0.16 -10000 0 -0.49 45 45
NOS2 -0.045 0.24 -10000 0 -0.53 76 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.012 0.074 -10000 0 -0.27 11 11
IL1R1 -0.14 0.46 -10000 0 -1.3 64 64
IL4 0.022 0.017 -10000 0 -10000 0 0
JAK2 0.008 0.037 -10000 0 -0.74 1 1
EntrezGene:6957 -0.015 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.076 -10000 0 -0.44 7 7
RAB7A 0.009 0.21 -10000 0 -0.69 18 18
lysosomal transport 0.011 0.2 -10000 0 -0.6 27 27
FOS -0.88 0.64 -10000 0 -1.3 374 374
STAT4 (dimer) -0.006 0.24 -10000 0 -0.67 39 39
STAT5A (dimer) -0.089 0.21 -10000 0 -0.54 75 75
GZMA -0.051 0.23 -10000 0 -0.54 74 74
GZMB -0.046 0.24 -10000 0 -0.67 36 36
HLX 0.013 0.045 -10000 0 -0.72 2 2
LCK -0.053 0.25 -10000 0 -0.56 74 74
TCR/CD3/MHC II/CD4 -0.12 0.13 -10000 0 -0.35 44 44
IL2/IL2R 0.007 0.039 -10000 0 -0.41 1 1
MAPK14 -0.008 0.24 -10000 0 -0.72 34 34
CCR5 -0.033 0.22 -10000 0 -0.71 32 32
IL1B -0.001 0.083 -10000 0 -0.74 6 6
STAT6 -0.028 0.16 -10000 0 -0.45 39 39
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.061 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.015 0.012 -10000 0 -10000 0 0
IL12B 0.007 0.029 -10000 0 -10000 0 0
CD8A 0.002 0.002 -10000 0 -10000 0 0
CD8B 0.014 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.073 0.28 7 -10000 0 7
IL2RB 0.013 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.23 -10000 0 -0.62 39 39
IL2RG 0.006 0.039 -10000 0 -10000 0 0
IL12 0 0.087 -10000 0 -0.55 11 11
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
CD247 -0.041 0.16 -10000 0 -0.73 25 25
IL2 0.015 0.033 -10000 0 -0.72 1 1
SPHK2 0.016 0 -10000 0 -10000 0 0
FRAP1 0.016 0 -10000 0 -10000 0 0
IL12A -0.008 0.11 -10000 0 -0.73 11 11
IL12/IL12R/TYK2/JAK2 -0.053 0.26 -10000 0 -0.6 74 74
MAP2K3 -0.013 0.24 -10000 0 -0.72 35 35
RIPK2 0.014 0.02 -10000 0 -10000 0 0
MAP2K6 -0.017 0.24 -10000 0 -0.71 37 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.033 -10000 0 -0.74 1 1
IL18RAP -0.043 0.21 -10000 0 -0.73 45 45
IL12Rbeta1/TYK2 0.011 0.025 -10000 0 -10000 0 0
EOMES 0.016 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.011 0.21 -10000 0 -0.55 36 36
T cell proliferation -0.004 0.2 -10000 0 -0.55 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.036 -10000 0 -0.73 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.07 0.18 -10000 0 -0.64 37 37
ATF2 0.003 0.23 -10000 0 -0.66 34 34
Osteopontin-mediated events

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
IKK alpha homodimer 0.039 0.052 -9999 0 -0.36 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.036 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src 0.033 0.066 -9999 0 -0.52 4 4
AP1 -0.29 0.25 -9999 0 -0.68 106 106
ILK 0.031 0.051 -9999 0 -0.38 4 4
bone resorption 0.062 0.049 -9999 0 -10000 0 0
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.047 0.065 -9999 0 -10000 0 0
ITGAV 0.02 0.033 -9999 0 -0.71 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.034 -9999 0 -0.54 2 2
alphaV/beta3 Integrin/Osteopontin 0.041 0.065 -9999 0 -0.43 4 4
MAP3K1 0.028 0.066 -9999 0 -0.41 8 8
JUN -0.12 0.29 -9999 0 -0.72 97 97
MAPK3 0.044 0.052 -9999 0 -0.34 4 4
MAPK1 0.044 0.052 -9999 0 -0.34 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.034 0.065 -9999 0 -0.37 9 9
ITGB3 0.019 0.019 -9999 0 -10000 0 0
NFKBIA 0.056 0.052 -9999 0 -10000 0 0
FOS -0.51 0.34 -9999 0 -0.72 374 374
CD44 0.014 0.034 -9999 0 -0.72 1 1
CHUK 0.015 0.032 -9999 0 -0.72 1 1
PLAU 0.033 0.058 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.018 0.04 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.026 -9999 0 -0.52 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.027 0.055 -9999 0 -0.38 4 4
VAV3 0.013 0.1 -9999 0 -0.4 25 25
MAP3K14 0.035 0.051 -9999 0 -0.38 4 4
ROCK2 0.015 0.033 -9999 0 -0.72 1 1
SPP1 -0.049 0.092 -9999 0 -0.71 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.081 -9999 0 -0.36 25 25
MMP2 -0.22 0.22 -9999 0 -0.54 104 104
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.03 0 -9999 0 -10000 0 0
SMARCC1 0.011 0.026 -9999 0 -10000 0 0
REL 0.011 0.027 -9999 0 -10000 0 0
HDAC7 -0.003 0.14 -9999 0 -0.58 8 8
JUN -0.12 0.29 -9999 0 -0.72 97 97
EP300 0.016 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.088 -9999 0 -0.55 12 12
FOXO1 -0.085 0.25 -9999 0 -0.72 72 72
T-DHT/AR 0.002 0.15 -9999 0 -0.61 8 8
MAP2K6 -0.003 0.11 -9999 0 -0.73 12 12
BRM/BAF57 0 0.005 -9999 0 -10000 0 0
MAP2K4 0.005 0.085 -9999 0 -0.72 7 7
SMARCA2 0.017 0 -9999 0 -10000 0 0
PDE9A -0.093 0.28 -9999 0 -1.2 30 30
NCOA2 0.016 0.014 -9999 0 -10000 0 0
CEBPA 0.012 0.056 -9999 0 -0.72 3 3
EHMT2 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.061 0.14 -9999 0 -0.45 6 6
NR0B1 -0.17 0.31 -9999 0 -0.72 124 124
EGR1 -0.6 0.28 -9999 0 -0.72 436 436
RXRs/9cRA -0.004 0.041 -9999 0 -0.42 5 5
AR/RACK1/Src 0.032 0.1 -9999 0 -0.46 9 9
AR/GR -0.043 0.17 -9999 0 -0.42 61 61
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.016 0.012 -9999 0 -10000 0 0
RCHY1 0.011 0.064 -9999 0 -0.72 4 4
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.018 0.072 -9999 0 -0.54 8 8
T-DHT/AR/TIF2/CARM1 0.029 0.1 -9999 0 -0.47 9 9
SRC 0.032 0.093 -9999 0 -0.41 19 19
NR3C1 -0.048 0.21 -9999 0 -0.72 46 46
KLK3 -0.068 0.09 -9999 0 -10000 0 0
APPBP2 0.012 0.016 -9999 0 -10000 0 0
TRIM24 0.016 0.014 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.034 0.087 -9999 0 -0.44 19 19
TMPRSS2 -0.28 0.5 -9999 0 -1.2 126 126
RXRG 0.009 0.072 -9999 0 -0.72 5 5
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.016 0 -9999 0 -10000 0 0
RXRB 0.016 0 -9999 0 -10000 0 0
CARM1 0.015 0.017 -9999 0 -10000 0 0
NR2C2 0.014 0.019 -9999 0 -10000 0 0
KLK2 0.05 0.088 -9999 0 -0.53 1 1
AR -0.011 0.13 -9999 0 -0.29 77 77
SENP1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
MDM2 0.01 0.025 -9999 0 -10000 0 0
SRY 0.006 0.073 -9999 0 -0.72 5 5
GATA2 0.007 0.037 -9999 0 -10000 0 0
MYST2 0.012 0.037 -9999 0 -0.72 1 1
HOXB13 -0.04 0.077 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.027 0.1 -9999 0 -0.47 9 9
positive regulation of transcription 0.007 0.037 -9999 0 -10000 0 0
DNAJA1 0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.034 -9999 0 -0.36 4 4
NCOA1 0.022 0.034 -9999 0 -0.75 1 1
SPDEF -0.06 0.22 -9999 0 -0.72 54 54
T-DHT/AR/TIF2 0.038 0.066 -9999 0 -0.38 1 1
T-DHT/AR/Hsp90 0.013 0.1 -9999 0 -0.43 19 19
GSK3B 0.015 0.011 -9999 0 -10000 0 0
NR2C1 0.014 0.032 -9999 0 -0.72 1 1
mol:T-DHT 0.02 0.1 -9999 0 -0.45 19 19
SIRT1 0.016 0.007 -9999 0 -10000 0 0
ZMIZ2 0.015 0 -9999 0 -10000 0 0
POU2F1 0.024 0.024 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.086 0.21 -9999 0 -0.42 136 136
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
SMARCE1 0.017 0.01 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.003 0.1 -9999 0 -0.72 10 10
SVIL 0.001 0.11 -9999 0 -0.72 12 12
ZNF318 0.007 0.006 -9999 0 -10000 0 0
JMJD2C 0.026 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.061 0.17 -9999 0 -0.48 69 69
CARM1 0.015 0.017 -9999 0 -10000 0 0
PRDX1 0.014 0.016 -9999 0 -10000 0 0
PELP1 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.065 -9999 0 -0.72 4 4
AKT1 0.013 0.02 -9999 0 -10000 0 0
PTK2B 0.017 0 -9999 0 -10000 0 0
MED1 0.005 0.039 -9999 0 -10000 0 0
MAK -0.001 0.034 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.007 -9999 0 -10000 0 0
GSN -0.18 0.33 -9999 0 -0.72 143 143
NCOA2 0.015 0.014 -9999 0 -10000 0 0
NCOA6 0.018 0.007 -9999 0 -10000 0 0
DNA-PK 0.003 0.014 -9999 0 -10000 0 0
NCOA4 0.014 0.045 -9999 0 -0.72 2 2
PIAS3 0.018 0 -9999 0 -10000 0 0
cell proliferation -0.02 0.033 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
UBE3A 0.019 0.001 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.072 0.17 -9999 0 -0.42 88 88
FHL2 -0.15 0.36 -9999 0 -1.1 58 58
RANBP9 0.018 0.007 -9999 0 -10000 0 0
JMJD1A -0.008 0.062 -9999 0 -10000 0 0
CDK6 0.005 0.086 -9999 0 -0.72 7 7
TGFB1I1 0.014 0.056 -9999 0 -0.72 3 3
T-DHT/AR/CyclinD1 -0.07 0.2 -9999 0 -0.5 81 81
XRCC6 0.015 0 -9999 0 -10000 0 0
T-DHT/AR -0.076 0.2 -9999 0 -0.46 88 88
CTDSP1 0.017 0 -9999 0 -10000 0 0
CTDSP2 0.013 0.001 -9999 0 -10000 0 0
BRCA1 0.014 0.025 -9999 0 -10000 0 0
TCF4 0.004 0.085 -9999 0 -0.72 7 7
CDKN2A -0.013 0.061 -9999 0 -10000 0 0
SRF 0.01 0.043 -9999 0 -10000 0 0
NKX3-1 -0.08 0.11 -9999 0 -0.25 126 126
KLK3 0.013 0.038 -9999 0 -10000 0 0
TMF1 0.017 0 -9999 0 -10000 0 0
HNRNPA1 0.015 0 -9999 0 -10000 0 0
AOF2 0.018 0.007 -9999 0 -10000 0 0
APPL1 0.025 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.084 0.16 -9999 0 -0.48 69 69
AR -0.096 0.25 -9999 0 -0.73 69 69
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.014 0.007 -9999 0 -10000 0 0
PAWR 0.013 0.037 -9999 0 -0.72 1 1
PRKDC 0.009 0.03 -9999 0 -10000 0 0
PA2G4 0.014 0.007 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.056 0.16 -9999 0 -0.45 69 69
RPS6KA3 0.015 0.046 -9999 0 -0.72 2 2
T-DHT/AR/ARA70 -0.062 0.18 -9999 0 -0.48 71 71
LATS2 0.001 0.1 -9999 0 -0.72 10 10
T-DHT/AR/PRX1 -0.077 0.15 -9999 0 -0.45 69 69
Cyclin D3/CDK11 p58 0 0.004 -9999 0 -10000 0 0
VAV3 -0.031 0.15 -9999 0 -0.72 21 21
KLK2 0.001 0.076 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.043 0.16 -9999 0 -0.44 69 69
TMPRSS2 -0.25 0.49 -9999 0 -1.1 126 126
CCND1 -0.027 0.12 -9999 0 -0.72 12 12
PIAS1 0.019 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.018 0.041 -9999 0 -0.081 146 146
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.019 0.016 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.09 0.17 -9999 0 -0.49 76 76
CMTM2 0.016 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.001 0.037 -9999 0 -10000 0 0
CCND3 0.016 0.007 -9999 0 -10000 0 0
TGIF1 0.013 0.032 -9999 0 -0.72 1 1
FKBP4 0.012 0.031 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.11 0.099 0.18 1 -0.34 1 2
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.014 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.1 0.14 -10000 0 -0.22 289 289
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.005 0.11 -10000 0 -0.54 21 21
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.012 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
SNARE/Synip 0.001 0.01 -10000 0 -10000 0 0
YWHAG 0.016 0.01 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0.022 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.015 0.032 -10000 0 -0.72 1 1
GYS1 0.04 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.015 0.032 -10000 0 -0.72 1 1
TC10/GTP/CIP4/Exocyst -0.002 0.029 -10000 0 -0.47 2 2
AS160/14-3-3 0.049 0.047 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 -0.11 0.15 -10000 0 -0.24 289 289
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.033 0.002 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
LNPEP 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.11 -9999 0 -0.72 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.006 0.085 -9999 0 -0.72 7 7
RAC1-CDC42/GTP/PAK family -0.14 0.14 -9999 0 -0.25 321 321
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
MAP3K12 0.016 0 -9999 0 -10000 0 0
FGR 0.016 0 -9999 0 -10000 0 0
p38 alpha/TAB1 0.02 0.04 -9999 0 -0.35 1 1
PRKG1 0.016 0 -9999 0 -10000 0 0
DUSP8 0.016 0.007 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.005 0.028 -9999 0 -0.34 1 1
apoptosis -0.005 0.028 -9999 0 -0.34 1 1
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0.01 -9999 0 -10000 0 0
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
PAK1 -0.01 0.06 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.004 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.036 0.06 -9999 0 -0.28 12 12
BLK 0.002 0.045 -9999 0 -10000 0 0
HCK 0.013 0.024 -9999 0 -10000 0 0
MAP2K3 0.016 0.007 -9999 0 -10000 0 0
DUSP16 0.014 0.034 -9999 0 -0.72 1 1
DUSP10 0.013 0.037 -9999 0 -0.72 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.045 0.047 -9999 0 -0.38 1 1
positive regulation of innate immune response 0.044 0.066 -9999 0 -0.3 12 12
LCK 0 0.049 -9999 0 -10000 0 0
p38alpha-beta/MKP7 0.051 0.066 -9999 0 -0.34 2 2
p38alpha-beta/MKP5 0.051 0.066 -9999 0 -0.32 3 3
PGK/cGMP 0 0 -9999 0 -10000 0 0
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.1 0.19 -9999 0 -0.34 151 151
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.43 0.36 -9999 0 -0.72 321 321
Syndecan-4-mediated signaling events

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
PTK2 0.027 0.01 -9999 0 -10000 0 0
Syndecan-4/Syndesmos 0.043 0.02 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.073 0.17 -9999 0 -0.39 8 8
Syndecan-4/ADAM12 0.05 0.03 -9999 0 -10000 0 0
CCL5 0.006 0.08 -9999 0 -0.72 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0.007 -9999 0 -10000 0 0
ITGA5 0.016 0.007 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
PLG 0.003 0.031 -9999 0 -0.7 1 1
ADAM12 -0.013 0.069 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.025 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.07 0.18 -9999 0 -0.41 8 8
Syndecan-4/Laminin alpha3 -0.091 0.19 -9999 0 -0.38 3 3
MDK 0.004 0.043 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.076 0.18 -9999 0 -0.38 4 4
Syndecan-4/Midkine 0.046 0.025 -9999 0 -10000 0 0
FZD7 -0.2 0.34 -9999 0 -0.72 156 156
Syndecan-4/FGFR1/FGF -0.25 0.16 -9999 0 -0.65 13 13
THBS1 0.012 0.027 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.042 0.026 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.073 0.17 -9999 0 -0.39 8 8
Syndecan-4/TACI 0.042 0.02 -9999 0 -10000 0 0
CXCR4 0.004 0.043 -9999 0 -10000 0 0
cell adhesion 0.032 0.008 -9999 0 -10000 0 0
Syndecan-4/Dynamin 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.044 0.021 -9999 0 -10000 0 0
Syndecan-4/GIPC 0.043 0.02 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.038 0.046 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 0.016 0.01 -9999 0 -10000 0 0
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.017 0.014 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin 0.042 0.02 -9999 0 -10000 0 0
TFPI -0.28 0.36 -9999 0 -0.72 207 207
F2 0.018 0.001 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.079 0.19 -9999 0 -0.4 2 2
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC 0.01 0.042 -9999 0 -0.72 1 1
Syndecan-4/CXCL12 -0.082 0.18 -9999 0 -0.38 2 2
FGF6 0.013 0.045 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.21 0.34 -9999 0 -0.72 164 164
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
Syndecan-4/PI-4-5-P2 0.031 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.1 0.077 -9999 0 -10000 0 0
cell migration -0.02 0.012 -9999 0 -10000 0 0
PRKCD 0.002 0.019 -9999 0 -10000 0 0
vasculogenesis 0.043 0.021 -9999 0 -10000 0 0
SDC4 0.034 0.021 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.043 0.027 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.02 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.042 0.027 -9999 0 -10000 0 0
MMP9 -0.057 0.081 -9999 0 -10000 0 0
Rac1/GTP 0.025 0.014 -9999 0 -10000 0 0
cytoskeleton organization 0.042 0.02 -9999 0 -10000 0 0
GIPC1 0.015 0.012 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.11 0.19 -9999 0 -0.38 3 3
Caspase cascade in apoptosis

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
TOP1 0.052 0.046 0.23 15 -10000 0 15
ACTA1 -0.005 0.088 0.27 4 -0.35 1 5
NUMA1 0.052 0.048 0.23 15 -10000 0 15
SPTAN1 0.048 0.057 0.3 2 -10000 0 2
LIMK1 0.038 0.063 0.28 14 -10000 0 14
BIRC3 -0.038 0.18 -10000 0 -0.72 35 35
BIRC2 0.016 0 -10000 0 -10000 0 0
BAX 0.015 0.014 -10000 0 -10000 0 0
CASP10 0.031 0.04 -10000 0 -0.46 2 2
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.053 0.047 0.23 15 -10000 0 15
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.048 0.057 0.28 11 -10000 0 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.067 0.19 -10000 0 -0.38 126 126
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A 0.041 0.01 -10000 0 -10000 0 0
BID 0.029 0.02 -10000 0 -0.24 2 2
MAP3K1 0.026 0.05 -10000 0 -0.42 4 4
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.006 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.046 0.06 0.27 15 -0.32 1 16
CASP9 0.017 0.001 -10000 0 -10000 0 0
DNA repair -0.032 0.052 -10000 0 -0.23 33 33
neuron apoptosis 0.031 0.065 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.056 0.053 0.29 2 -10000 0 2
APAF1 0.016 0.007 -10000 0 -10000 0 0
CASP6 0.057 0.025 -10000 0 -10000 0 0
TRAF2 0.015 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.056 0.054 0.3 2 -10000 0 2
CASP7 0.018 0.085 0.32 35 -0.56 1 36
KRT18 0.035 0.014 -10000 0 -10000 0 0
apoptosis 0.038 0.098 0.31 10 -0.31 4 14
DFFA 0.048 0.057 0.27 15 -10000 0 15
DFFB 0.048 0.057 0.28 11 -10000 0 11
PARP1 0.032 0.052 0.23 33 -10000 0 33
actin filament polymerization 0.031 0.16 0.36 91 -0.3 2 93
TNF 0.012 0.025 -10000 0 -10000 0 0
CYCS 0.041 0.032 -10000 0 -0.18 2 2
SATB1 0.016 0.13 -10000 0 -0.35 51 51
SLK 0.047 0.06 0.27 15 -0.38 1 16
p15 BID/BAX 0.034 0.018 -10000 0 -10000 0 0
CASP2 0.05 0.056 -10000 0 -10000 0 0
JNK cascade -0.026 0.05 0.42 4 -10000 0 4
CASP3 0.041 0.062 0.29 15 -10000 0 15
LMNB2 0.063 0.026 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.005 0.09 -10000 0 -0.72 8 8
Mammalian IAPs/DIABLO -0.025 0.11 -10000 0 -0.42 35 35
negative regulation of DNA binding 0.041 0.01 -10000 0 -10000 0 0
stress fiber formation 0.047 0.06 0.27 15 -0.38 1 16
GZMB 0.021 0.046 -10000 0 -0.54 2 2
CASP1 -0.036 0.18 -10000 0 -0.49 60 60
LMNB1 0.074 0.028 -10000 0 -10000 0 0
APP 0.031 0.066 -10000 0 -0.63 5 5
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM 0.031 0.1 0.29 16 -0.28 11 27
LMNA 0.06 0.026 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.042 0.059 -10000 0 -10000 0 0
LRDD 0.016 0 -10000 0 -10000 0 0
SREBF1 0.041 0.061 0.28 14 -10000 0 14
APAF-1/Caspase 9 0.012 0.043 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.052 0.048 0.23 15 -10000 0 15
CFL2 -0.032 0.17 0.3 2 -0.37 91 93
GAS2 -0.22 0.2 0.27 4 -0.38 318 322
positive regulation of apoptosis 0.072 0.028 -10000 0 -10000 0 0
PRF1 0.012 0.025 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.019 0.15 -9999 0 -0.72 23 23
PLK4 -0.009 0.059 -9999 0 -10000 0 0
regulation of centriole replication -0.014 0.12 -9999 0 -0.56 23 23
Noncanonical Wnt signaling pathway

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
NFATC2 0.015 0.032 -9999 0 -0.72 1 1
GNB1/GNG2 -0.042 0.15 -9999 0 -0.68 19 19
mol:DAG 0.013 0.15 -9999 0 -0.6 19 19
PLCG1 0.012 0.16 -9999 0 -0.63 19 19
YES1 -0.006 0.17 -9999 0 -0.73 18 18
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
G protein 0.011 0.16 -9999 0 -0.64 19 19
MAP3K7 0.032 0.13 -9999 0 -0.48 19 19
mol:Ca2+ 0.014 0.14 -9999 0 -0.58 19 19
mol:IP3 0.013 0.15 -9999 0 -0.6 19 19
NLK 0.031 0.016 -9999 0 -10000 0 0
GNB1 0.016 0.01 -9999 0 -10000 0 0
CAMK2A 0.023 0.14 -9999 0 -0.53 19 19
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.007 0.17 -9999 0 -0.71 18 18
GO:0007205 0.013 0.15 -9999 0 -0.59 19 19
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
NFAT1/CK1 alpha -0.036 0.14 -9999 0 -0.64 18 18
GNG2 0.015 0.032 -9999 0 -0.72 1 1
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
CDC42 0.004 0.16 -9999 0 -0.68 18 18
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC2 0.014 0.017 -9999 0 -10000 0 0
GNB1/GNG2 -0.018 0.095 -9999 0 -0.46 23 23
forebrain development -0.018 0.19 -9999 0 -0.52 53 53
GNAO1 0.017 0 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.006 0.11 -9999 0 -0.54 22 22
SMO -0.015 0.15 -9999 0 -0.72 22 22
ARRB2 0.018 0 -9999 0 -10000 0 0
GLI3/SPOP 0.051 0.074 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
GSK3B 0.016 0.01 -9999 0 -10000 0 0
GNAI2 0.017 0.007 -9999 0 -10000 0 0
SIN3/HDAC complex 0.001 0.009 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
XPO1 0.021 0.001 -9999 0 -10000 0 0
GLI1/Su(fu) -0.048 0.14 -9999 0 -0.86 8 8
SAP30 0.016 0.007 -9999 0 -10000 0 0
mol:GDP -0.015 0.15 -9999 0 -0.72 22 22
MIM/GLI2A 0.017 0.04 -9999 0 -10000 0 0
IFT88 0.015 0.032 -9999 0 -0.72 1 1
GNAI3 0.017 0 -9999 0 -10000 0 0
GLI2 0.053 0.038 -9999 0 -10000 0 0
GLI3 0.045 0.078 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.015 0.032 -9999 0 -0.72 1 1
GNG2 0.015 0.032 -9999 0 -0.72 1 1
Gi family/GTP -0.066 0.16 -9999 0 -0.25 204 204
SIN3B 0.014 0.016 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.067 0.059 -9999 0 -0.39 1 1
GLI2/Su(fu) 0.066 0.059 -9999 0 -0.34 1 1
FOXA2 0.009 0.028 -9999 0 -10000 0 0
neural tube patterning -0.018 0.19 -9999 0 -0.52 53 53
SPOP 0.016 0.007 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.033 0.055 -9999 0 -0.41 1 1
GNB1 0.016 0.01 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.017 0.04 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.018 0.19 -9999 0 -0.52 53 53
SUFU 0.027 0.061 -9999 0 -0.46 1 1
LGALS3 -0.074 0.24 -9999 0 -0.72 64 64
catabolic process 0.08 0.073 -9999 0 -10000 0 0
GLI3A/CBP -0.012 0.12 -9999 0 -0.37 54 54
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.012 0.19 -9999 0 -0.53 53 53
RAB23 0.014 0.017 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.015 0.032 -9999 0 -0.72 1 1
RBBP7 0.012 0.026 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.022 0.16 -9999 0 -0.43 65 65
GNAZ 0.009 0.078 -9999 0 -0.72 6 6
RBBP4 0.016 0.007 -9999 0 -10000 0 0
CSNK1G1 0.016 0.01 -9999 0 -10000 0 0
PIAS1 0.016 0.007 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.057 0.036 -9999 0 -10000 0 0
STK36 0.019 0.032 -9999 0 -0.72 1 1
Gi family/GNB1/GNG2/GDP -0.057 0.15 -9999 0 -0.52 14 14
PTCH1 -0.004 0.17 -9999 0 -0.82 7 7
MIM/GLI1 0.001 0.19 -9999 0 -0.55 39 39
CREBBP -0.012 0.12 -9999 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.058 0.017 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.047 0.08 -10000 0 -10000 0 0
UGCG 0.009 0.046 -10000 0 -0.75 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.17 -10000 0 -0.37 40 40
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.028 0.047 -10000 0 -0.74 1 1
mol:DAG -0.005 0.075 -10000 0 -0.99 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.087 0.15 -10000 0 -0.46 40 40
FRAP1 -0.012 0.23 -10000 0 -0.53 42 42
FOXO3 0.027 0.16 -10000 0 -0.45 20 20
AKT1 0.017 0.17 -10000 0 -0.43 35 35
GAB2 0.012 0.017 -10000 0 -10000 0 0
SMPD1 -0.001 0.018 -10000 0 -10000 0 0
SGMS1 -0.005 0.053 -10000 0 -0.66 3 3
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 -0.025 0.14 -10000 0 -0.46 51 51
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.026 0.091 -10000 0 -0.26 27 27
EIF3A 0.016 0.007 -10000 0 -10000 0 0
PI3K -0.03 0.17 -10000 0 -0.54 51 51
RPS6KB1 0.009 0.071 -10000 0 -10000 0 0
mol:sphingomyelin -0.005 0.075 -10000 0 -0.99 3 3
natural killer cell activation -0.001 0.005 -10000 0 -0.013 28 28
JAK3 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 51 51
JAK1 0.013 0.046 -10000 0 -0.72 2 2
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC -0.006 0.27 -10000 0 -1 29 29
MYB -0.062 0.36 -10000 0 -1.3 41 41
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.04 0.11 -10000 0 -0.35 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.07 -10000 0 -0.59 1 1
mol:PI-3-4-5-P3 0.04 0.11 -10000 0 -0.34 2 2
Rac1/GDP -0.015 0.13 -10000 0 -0.41 51 51
T cell proliferation 0.039 0.1 -10000 0 -0.32 2 2
SHC1 0.014 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.02 -10000 0 -0.067 41 41
PRKCZ 0.038 0.1 -10000 0 -0.34 2 2
NF kappa B1 p50/RelA -0.084 0.15 -10000 0 -0.45 40 40
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.032 0.087 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA 0.004 0.039 -10000 0 -10000 0 0
IL2RB 0.014 0.024 -10000 0 -10000 0 0
TERT 0.013 0.036 -10000 0 -0.72 1 1
E2F1 0.001 0.13 -10000 0 -0.44 41 41
SOS1 0.013 0.008 -10000 0 -10000 0 0
RPS6 0.015 0.032 -10000 0 -0.72 1 1
mol:cAMP -0.001 0.009 0.031 41 -10000 0 41
PTPN11 0.014 0.008 -10000 0 -10000 0 0
IL2RG 0.006 0.039 -10000 0 -10000 0 0
actin cytoskeleton organization 0.039 0.1 -10000 0 -0.32 2 2
GRB2 0.01 0.023 -10000 0 -10000 0 0
IL2 0.014 0.034 -10000 0 -0.72 1 1
PIK3CA 0.016 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.13 -10000 0 -0.39 51 51
LCK 0 0.049 -10000 0 -10000 0 0
BCL2 -0.11 0.41 -10000 0 -0.91 104 104
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.15 -9999 0 -0.53 37 37
KLHL20 -0.014 0.049 -9999 0 -0.25 4 4
CYFIP2 -0.002 0.051 -9999 0 -10000 0 0
Rac1/GDP 0.046 0.1 -9999 0 -0.31 37 37
ENAH 0.01 0.15 -9999 0 -0.53 37 37
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
CDC42/GTP -0.019 0.064 -9999 0 -0.45 1 1
ABI1/Sra1/Nap1 -0.011 0.032 -9999 0 -0.18 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.028 0.11 -9999 0 -0.41 37 37
RAPGEF1 0.03 0.13 -9999 0 -0.44 37 37
CTNND1 0.016 0.007 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.14 -9999 0 -0.55 37 37
CRK 0.02 0.14 -9999 0 -0.49 37 37
E-cadherin/gamma catenin/alpha catenin -0.028 0.11 -9999 0 -0.46 34 34
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
DLG1 0.01 0.15 -9999 0 -0.53 37 37
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.064 -9999 0 -0.31 3 3
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
ARF6/GTP/NME1/Tiam1 0.003 0.015 -9999 0 -10000 0 0
PI3K -0.038 0.083 -9999 0 -0.42 3 3
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.036 0.13 -9999 0 -0.54 34 34
TIAM1 0.015 0.012 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.026 0.1 -9999 0 -0.39 37 37
AKT1 -0.02 0.048 -9999 0 -0.22 3 3
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
RhoA/GDP 0.046 0.1 -9999 0 -0.31 37 37
actin cytoskeleton organization -0.007 0.039 -9999 0 -0.18 4 4
CDC42/GDP 0.046 0.1 -9999 0 -0.31 37 37
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.01 0.083 -9999 0 -0.3 34 34
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.11 -9999 0 -0.41 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.1 -9999 0 -0.4 37 37
mol:GDP 0.039 0.12 -9999 0 -0.36 37 37
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.014 0.035 -9999 0 -0.72 1 1
p120 catenin/RhoA/GDP -0.023 0.081 -9999 0 -0.38 3 3
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0.003 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.018 0.059 -9999 0 -0.22 17 17
NME1 0.011 0.029 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.009 0.15 -9999 0 -0.53 38 38
regulation of cell-cell adhesion -0.017 0.056 -9999 0 -0.38 1 1
WASF2 -0.004 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.021 0.075 -9999 0 -0.53 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.023 0.095 -9999 0 -0.38 34 34
CCND1 0.019 0.072 -9999 0 -0.27 17 17
VAV2 0.024 0.14 -9999 0 -0.47 37 37
RAP1/GDP -0.015 0.081 -9999 0 -0.52 1 1
adherens junction assembly 0.01 0.15 -9999 0 -0.51 38 38
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0.007 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.024 0.093 -9999 0 -0.36 38 38
E-cadherin/beta catenin -0.029 0.11 -9999 0 -0.45 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.003 0.15 -9999 0 -0.53 37 37
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
Rac1/GTP -0.025 0.077 -9999 0 -0.35 10 10
E-cadherin/beta catenin/alpha catenin -0.031 0.12 -9999 0 -0.46 37 37
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.14 -9999 0 -0.56 37 37
Arf6 trafficking events

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
SLC2A4 -0.41 0.36 -10000 0 -0.72 302 302
CLTC 0.038 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.026 0.04 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.009 -10000 0 -10000 0 0
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.029 0.041 -10000 0 -0.32 3 3
CPE -0.065 0.19 -10000 0 -0.47 95 95
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
membrane fusion 0.025 0.043 -10000 0 -10000 0 0
CTNND1 0.039 0.013 -10000 0 -10000 0 0
DNM2 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.023 -10000 0 -10000 0 0
TSHR 0.02 0.043 -10000 0 -0.47 4 4
INS 0.024 0.008 -10000 0 -10000 0 0
BIN1 0.016 0.007 -10000 0 -10000 0 0
mol:Choline 0.025 0.043 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.015 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
JUP 0.032 0.022 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.015 0.069 -10000 0 -0.34 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.046 -10000 0 -0.72 2 2
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.008 0.036 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.054 0.015 -10000 0 -0.29 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.012 0.049 0.36 4 -10000 0 4
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.002 0.029 -10000 0 -0.47 2 2
ACAP1 0.023 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.031 0.02 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.041 0.027 -10000 0 -10000 0 0
JIP4/KLC1 0 0.003 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.054 0.015 -10000 0 -0.3 1 1
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0.003 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.039 0.013 -10000 0 -10000 0 0
NME1 0.021 0.015 -10000 0 -10000 0 0
clathrin coat assembly 0.038 0.014 -10000 0 -10000 0 0
IL2RA 0.031 0.019 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.2 0.17 -10000 0 -0.34 302 302
EXOC6 0.014 0.034 -10000 0 -0.72 1 1
PLD1 -0.013 0.062 -10000 0 -0.32 21 21
PLD2 -0.001 0.014 -10000 0 -0.32 1 1
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.037 0.023 -10000 0 -10000 0 0
SDC1 0.026 0.021 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.015 -10000 0 -10000 0 0
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.012 0.05 -10000 0 -0.37 4 4
mol:Phosphatidic acid 0.025 0.043 -10000 0 -10000 0 0
endocytosis 0 0.003 -10000 0 -10000 0 0
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 -0.17 0.2 -10000 0 -0.36 284 284
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.014 -10000 0 -10000 0 0
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.044 0.028 -10000 0 -0.36 2 2
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.009 0.044 -10000 0 -0.37 1 1
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.002 0.13 -10000 0 -0.4 15 15
IKBKB 0.047 0.045 0.23 1 -10000 0 1
AKT1 0.032 0.082 0.26 13 -0.24 9 22
IKBKG 0.051 0.045 0.23 1 -10000 0 1
CALM1 0.028 0.074 -10000 0 -0.36 12 12
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
MAP3K1 0.049 0.1 -10000 0 -0.56 13 13
MAP3K7 0.016 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.078 0.24 15 -0.39 12 27
DOK1 0.014 0.019 -10000 0 -10000 0 0
AP-1 -0.11 0.12 -10000 0 -0.26 114 114
LYN 0.016 0.01 -10000 0 -10000 0 0
BLNK 0.011 0.029 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
BCR complex -0.018 0.086 -10000 0 -0.54 13 13
CD22 -0.019 0.11 -10000 0 -0.69 13 13
CAMK2G 0.036 0.071 -10000 0 -0.33 12 12
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.052 -10000 0 -0.37 1 1
GO:0007205 0.019 0.079 0.24 15 -0.4 12 27
SYK 0.01 0.03 -10000 0 -10000 0 0
ELK1 0.027 0.075 -10000 0 -0.37 12 12
NFATC1 0.037 0.085 -10000 0 -0.43 15 15
B-cell antigen/BCR complex -0.018 0.086 -10000 0 -0.54 13 13
PAG1/CSK -0.002 0.015 -10000 0 -10000 0 0
NFKBIB 0.033 0.019 0.12 1 -10000 0 1
HRAS 0.033 0.068 -10000 0 -0.35 12 12
NFKBIA 0.033 0.019 0.12 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.036 0.018 0.13 1 -10000 0 1
RasGAP/Csk -0.007 0.088 -10000 0 -0.5 13 13
mol:GDP 0.018 0.074 0.23 15 -0.37 12 27
PTEN -0.002 0.12 -10000 0 -0.72 13 13
CD79B -0.003 0.12 -10000 0 -0.72 13 13
NF-kappa-B/RelA/I kappa B alpha 0.036 0.018 0.13 1 -10000 0 1
GRB2 0.013 0.022 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.013 0.14 -10000 0 -0.54 15 15
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 0.019 0.08 0.24 15 -0.4 12 27
CSK 0.016 0.01 -10000 0 -10000 0 0
FOS -0.24 0.19 -10000 0 -0.36 361 361
CHUK 0.05 0.049 -10000 0 -0.44 1 1
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.008 0.049 -10000 0 -0.4 4 4
PTPN6 -0.017 0.1 -10000 0 -0.64 13 13
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.032 0.015 -10000 0 -10000 0 0
VAV2 -0.015 0.1 -10000 0 -0.65 13 13
ubiquitin-dependent protein catabolic process 0.037 0.019 0.13 1 -10000 0 1
BTK 0.005 0.014 -10000 0 -10000 0 0
CD19 -0.023 0.11 -10000 0 -0.69 13 13
MAP4K1 0.013 0.023 -10000 0 -10000 0 0
CD72 -0.017 0.065 -10000 0 -10000 0 0
PAG1 0.012 0.026 -10000 0 -10000 0 0
MAPK14 0.056 0.09 -10000 0 -0.46 13 13
SH3BP5 -0.006 0.13 -10000 0 -0.72 16 16
PIK3AP1 0.026 0.086 0.27 13 -0.44 12 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.038 0.073 -10000 0 -0.62 4 4
RAF1 0.041 0.065 -10000 0 -0.38 5 5
RasGAP/p62DOK/SHIP -0.007 0.084 -10000 0 -0.49 13 13
CD79A 0.007 0.037 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.1 0.12 -10000 0 -0.25 112 112
RASA1 0.015 0.012 -10000 0 -10000 0 0
MAPK3 0.056 0.057 -10000 0 -0.33 4 4
MAPK1 0.056 0.057 -10000 0 -0.33 4 4
CD72/SHP1 0.042 0.11 -10000 0 -0.59 13 13
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.055 0.091 -10000 0 -0.46 13 13
actin cytoskeleton organization 0.038 0.098 -10000 0 -0.54 13 13
NF-kappa-B/RelA 0.076 0.035 0.24 1 -10000 0 1
Calcineurin -0.014 0.062 -10000 0 -0.37 5 5
PI3K -0.037 0.1 -10000 0 -0.47 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.003 0.089 0.27 15 -0.47 12 27
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 0.033 0.12 -10000 0 -0.72 13 13
DAPP1 -0.005 0.14 -10000 0 -0.83 13 13
cytokine secretion 0.037 0.08 -10000 0 -0.4 15 15
mol:DAG 0.019 0.08 0.24 15 -0.4 12 27
PLCG2 0 0.11 -10000 0 -0.72 11 11
MAP2K1 0.049 0.062 -10000 0 -0.37 4 4
B-cell antigen/BCR complex/FcgammaRIIB -0.012 0.099 -10000 0 -0.59 13 13
mol:PI-3-4-5-P3 -0.021 0.094 0.34 13 -0.33 14 27
ETS1 0.043 0.068 -10000 0 -0.38 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.069 -10000 0 -0.38 13 13
B-cell antigen/BCR complex/LYN -0.016 0.12 -10000 0 -0.73 13 13
MALT1 0.016 0.007 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 0.038 0.1 -10000 0 -0.59 13 13
B-cell antigen/BCR complex/LYN/SYK -0.012 0.1 -10000 0 -0.62 13 13
CARD11 0.025 0.076 -10000 0 -0.37 12 12
FCGR2B 0.01 0.065 -10000 0 -0.72 4 4
PPP3CA 0.01 0.065 -10000 0 -0.72 4 4
BCL10 0.016 0.007 -10000 0 -10000 0 0
IKK complex 0.036 0.027 0.14 2 -0.12 1 3
PTPRC 0.006 0.057 -10000 0 -0.72 2 2
PDPK1 0.022 0.076 0.23 13 -0.25 6 19
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.006 0.085 -10000 0 -0.72 7 7
POU2F2 0.033 0.013 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.011 0.029 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.039 0.13 -9999 0 -0.56 16 16
NEF 0.002 0.015 -9999 0 -10000 0 0
NFKBIA 0.01 0.048 -9999 0 -0.85 1 1
BIRC3 0 0.2 -9999 0 -0.74 35 35
CYCS 0.013 0.13 -9999 0 -0.52 15 15
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.027 0.16 -9999 0 -0.72 25 25
MAP2K7 0.022 0.12 -9999 0 -0.48 12 12
protein ubiquitination 0.068 0.068 -9999 0 -0.37 1 1
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0.007 -9999 0 -10000 0 0
FAS -0.033 0.18 -9999 0 -0.72 35 35
BID 0.003 0.14 -9999 0 -0.54 16 16
NF-kappa-B/RelA/I kappa B alpha -0.023 0.083 -9999 0 -0.32 35 35
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 -0.033 0.18 -9999 0 -0.72 35 35
CFLAR 0.013 0.045 -9999 0 -0.72 2 2
FADD 0.002 0.046 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.023 0.084 -9999 0 -0.32 35 35
MAPK8 0.03 0.11 -9999 0 -0.49 10 10
APAF1 0.016 0.007 -9999 0 -10000 0 0
TRAF1 0.015 0.016 -9999 0 -10000 0 0
TRAF2 0.015 0.012 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.006 0.14 -9999 0 -0.35 64 64
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.056 0.076 -9999 0 -0.34 1 1
CHUK 0.07 0.071 -9999 0 -0.41 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.044 0.15 -9999 0 -0.42 64 64
TCRz/NEF -0.031 0.12 -9999 0 -0.55 25 25
TNF 0.012 0.025 -9999 0 -10000 0 0
FASLG -0.004 0.12 -9999 0 -0.48 25 25
NFKB1 0.012 0.03 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.004 0.019 -9999 0 -10000 0 0
CASP6 -0.03 0.096 -9999 0 -0.61 7 7
CASP7 0.028 0.2 -9999 0 -0.58 41 41
RELA 0.012 0.03 -9999 0 -10000 0 0
CASP2 0.016 0.007 -9999 0 -10000 0 0
CASP3 0.029 0.19 -9999 0 -0.58 41 41
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.014 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.064 0.073 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.049 0.13 -9999 0 -0.48 40 40
BCL2 -0.036 0.18 -9999 0 -0.42 36 36
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.029 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.001 0.01 -10000 0 -10000 0 0
CDKN1B 0.047 0.053 -10000 0 -0.36 9 9
CDKN1A 0.052 0.026 -10000 0 -0.36 2 2
FRAP1 0.016 0 -10000 0 -10000 0 0
PRKDC 0.01 0.03 -10000 0 -10000 0 0
FOXO3 0.054 0.003 -10000 0 -10000 0 0
AKT1 0.003 0.011 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
AKT3 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.054 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.02 0.088 -10000 0 -0.35 35 35
BAD/YWHAZ 0.001 0.009 -10000 0 -10000 0 0
RICTOR 0.016 0 -10000 0 -10000 0 0
RAF1 0.016 0.007 -10000 0 -10000 0 0
JNK cascade 0.02 0.085 0.34 35 -10000 0 35
TSC1 0.054 0.002 -10000 0 -10000 0 0
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
AKT1/RAF1 0.053 0.003 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.011 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.054 0.002 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.012 0.095 -10000 0 -0.45 21 21
MAP3K5 -0.033 0.18 -10000 0 -0.72 35 35
MAPKAP1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.055 0.017 -10000 0 -10000 0 0
YWHAH 0.015 0.012 -10000 0 -10000 0 0
AKT1S1 0.053 0.007 -10000 0 -10000 0 0
CASP9 0.054 0.002 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.054 0.051 -10000 0 -0.33 9 9
GBL 0.016 0.007 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.001 0.007 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
SRC 0.016 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.002 0.025 -10000 0 -0.34 2 2
KIAA1303 0.016 0.01 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.048 0.001 -10000 0 -10000 0 0
CHUK 0.053 0.018 -10000 0 -0.36 1 1
BAD/BCL-XL 0.069 0.002 -10000 0 -10000 0 0
mTORC2 0 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.062 0.048 -10000 0 -10000 0 0
PDPK1 0.016 0.007 -10000 0 -10000 0 0
MDM2 0.052 0.011 -10000 0 -10000 0 0
MAPKKK cascade -0.052 0.003 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.066 0.019 -10000 0 -10000 0 0
TSC1/TSC2 0.062 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.02 -10000 0 -10000 0 0
glucose import -0.23 0.24 -10000 0 -0.42 310 310
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.062 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.24 0.24 -10000 0 -0.43 310 310
GSK3A 0.054 0.002 -10000 0 -10000 0 0
FOXO1 -0.002 0.14 -10000 0 -0.36 72 72
GSK3B 0.054 0.005 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
G1/S transition of mitotic cell cycle 0.062 0.004 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.061 0.021 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
KPNA1 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
YWHAG 0.016 0.01 -10000 0 -10000 0 0
RHEB 0.016 0.007 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR -0.1 0.27 -9999 0 -0.72 83 83
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 0.003 0.1 -9999 0 -0.48 20 20
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.005 0.093 -9999 0 -0.43 20 20
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.016 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.023 0.11 -9999 0 -0.72 10 10
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.022 0.035 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.015 0.033 -9999 0 -0.72 1 1
CDK5R1 0.014 0.019 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.022 0 -9999 0 -10000 0 0
CDK5R2 0.016 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.089 0.19 -9999 0 -0.48 98 98
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
NDEL1/14-3-3 E 0.043 0.079 -9999 0 -0.37 1 1
MAP1B -0.035 0.11 -9999 0 -0.36 52 52
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 0.022 0.085 -9999 0 -0.37 20 20
RELN -0.013 0.14 -9999 0 -0.72 20 20
PAFAH/LIS1 0.033 0.071 -9999 0 -0.46 10 10
LIS1/CLIP170 0.033 0.022 -9999 0 -0.46 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.009 0.045 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.012 0.14 -9999 0 -0.58 5 5
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.035 0.081 -9999 0 -0.38 7 7
LIS1/IQGAP1 0.034 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.029 0 -9999 0 -10000 0 0
PAFAH1B3 -0.039 0.077 -9999 0 -10000 0 0
PAFAH1B2 0.016 0.007 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.008 0.075 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.004 0.06 -9999 0 -10000 0 0
LRP8 -0.029 0.072 -9999 0 -10000 0 0
NDEL1/Katanin 60 0.044 0.077 -9999 0 -10000 0 0
P39/CDK5 0.023 0.084 -9999 0 -0.37 20 20
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.034 0 -9999 0 -10000 0 0
CDK5 0.014 0.089 -9999 0 -0.4 20 20
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.018 -9999 0 -0.4 1 1
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.074 0.16 -9999 0 -0.4 98 98
RELN/VLDLR -0.063 0.19 -9999 0 -0.45 98 98
CDC42 0 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.001 0.03 -9999 0 -10000 0 0
MAP4K1 0.013 0.023 -9999 0 -10000 0 0
MAP3K8 -0.083 0.25 -9999 0 -0.72 70 70
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.015 0.012 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.052 0.042 -9999 0 -0.36 4 4
JUN -0.046 0.17 -9999 0 -0.39 98 98
MAP3K7 0.057 0.015 -9999 0 -10000 0 0
GRAP2 0.014 0.019 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
MAP2K4 0.038 0.074 -9999 0 -0.48 3 3
LAT 0.012 0.026 -9999 0 -10000 0 0
LCP2 0.013 0.024 -9999 0 -10000 0 0
MAPK8 0.023 0.034 -9999 0 -0.57 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.05 0.015 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 0.004 0.03 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.026 0.16 -9999 0 -0.48 1 1
CRKL 0.036 0.055 -9999 0 -0.42 1 1
mol:DAG 0.039 0.069 -9999 0 -0.34 1 1
HRAS 0.064 0.053 -9999 0 -0.35 1 1
MAPK8 0.031 0.038 -9999 0 -0.42 1 1
RAP1A 0.036 0.055 -9999 0 -0.42 1 1
GAB1 0.035 0.059 -9999 0 -0.44 2 2
MAPK14 0.031 0.033 -9999 0 -10000 0 0
EPO -0.005 0.056 -9999 0 -10000 0 0
PLCG1 0.039 0.07 -9999 0 -0.35 1 1
EPOR/TRPC2/IP3 Receptors 0.016 0.008 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.007 0.087 -9999 0 -0.48 15 15
GAB1/SHC/GRB2/SOS1 -0.001 0.034 -9999 0 -0.37 2 2
EPO/EPOR (dimer) 0.027 0.037 -9999 0 -10000 0 0
IRS2 -0.071 0.2 -9999 0 -0.4 138 138
STAT1 0.032 0.12 -9999 0 -0.45 1 1
STAT5B 0.034 0.094 -9999 0 -0.4 1 1
cell proliferation 0.038 0.037 -9999 0 -0.38 1 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.036 0.092 -9999 0 -0.35 18 18
TEC 0.036 0.055 -9999 0 -0.42 1 1
SOCS3 -0.005 0.12 -9999 0 -0.72 15 15
STAT1 (dimer) 0.032 0.12 -9999 0 -0.38 2 2
JAK2 0.014 0.034 -9999 0 -0.73 1 1
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
EPO/EPOR (dimer)/JAK2 0.05 0.068 -9999 0 -0.45 1 1
EPO/EPOR 0.027 0.037 -9999 0 -10000 0 0
LYN 0.015 0.014 -9999 0 -10000 0 0
TEC/VAV2 0.047 0.055 -9999 0 -0.4 1 1
elevation of cytosolic calcium ion concentration 0.016 0.008 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.041 0.039 -9999 0 -10000 0 0
mol:IP3 0.039 0.069 -9999 0 -0.34 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.19 -9999 0 -0.38 178 178
SH2B3 0.015 0.008 -9999 0 -10000 0 0
NFKB1 0.031 0.033 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.046 -9999 0 -0.26 16 16
PTPN6 0.027 0.057 -9999 0 -0.45 1 1
TEC/VAV2/GRB2 0.054 0.054 -9999 0 -0.38 1 1
EPOR 0.016 0.008 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.001 0.035 -9999 0 -0.37 2 2
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0 0.11 -9999 0 -0.72 11 11
CRKL/CBL/C3G 0.053 0.052 -9999 0 -0.38 1 1
VAV2 0.036 0.056 -9999 0 -0.42 1 1
CBL 0.036 0.055 -9999 0 -0.42 1 1
SHC/Grb2/SOS1 -0.001 0.034 -9999 0 -0.38 1 1
STAT5A 0.032 0.097 -9999 0 -0.38 3 3
GRB2 0.013 0.022 -9999 0 -10000 0 0
STAT5 (dimer) 0.031 0.15 -9999 0 -0.55 1 1
LYN/PLCgamma2 -0.012 0.078 -9999 0 -0.54 11 11
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK 0.037 0.057 -9999 0 -0.42 1 1
BCL2 -0.1 0.42 -9999 0 -0.94 104 104
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.015 0.15 -9999 0 -0.72 22 22
positive regulation of NF-kappaB transcription factor activity -0.022 0.11 -9999 0 -0.54 22 22
MAP2K4 0.039 0.081 -9999 0 -0.36 8 8
IKBKB 0.014 0.02 -9999 0 -10000 0 0
TNFRSF10B 0.015 0.033 -9999 0 -0.72 1 1
TNFRSF10A 0.014 0.034 -9999 0 -0.72 1 1
SMPD1 0.013 0.058 -9999 0 -0.26 23 23
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.024 0.11 -9999 0 -0.54 23 23
TRAIL/TRAILR3 -0.023 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1 -0.024 0.11 -9999 0 -0.54 23 23
TRAIL/TRAILR4 -0.023 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1/DAP3/GTP -0.018 0.087 -9999 0 -0.42 23 23
IKK complex -0.005 0.047 -9999 0 -0.77 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP -0.001 0.008 -9999 0 -10000 0 0
MAPK3 0.006 0.11 -9999 0 -0.54 22 22
MAP3K1 0.037 0.07 -9999 0 -0.34 3 3
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.034 -9999 0 -0.72 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.032 0.069 -9999 0 -0.29 23 23
CFLAR 0.013 0.045 -9999 0 -0.72 2 2
MAPK1 0.006 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1/FADD/TRADD/RIP -0.009 0.085 -9999 0 -0.39 23 23
mol:ceramide 0.013 0.058 -9999 0 -0.26 23 23
FADD 0.002 0.046 -9999 0 -10000 0 0
MAPK8 0.047 0.082 -9999 0 -0.37 9 9
TRAF2 0.015 0.012 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
TRAIL/TRAILR1/FADD -0.013 0.1 -9999 0 -0.47 23 23
DAP3 0.015 0.014 -9999 0 -10000 0 0
CASP10 -0.021 0.09 -9999 0 -0.45 22 22
JNK cascade -0.022 0.11 -9999 0 -0.54 22 22
TRAIL (trimer) -0.015 0.15 -9999 0 -0.72 22 22
TNFRSF10C 0.016 0.01 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD -0.01 0.086 -9999 0 -0.4 23 23
TRAIL/TRAILR2/FADD -0.013 0.098 -9999 0 -0.46 23 23
cell death 0.013 0.058 -9999 0 -0.26 23 23
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.032 0.069 -9999 0 -0.29 23 23
TRAILR2 (trimer) 0.015 0.033 -9999 0 -0.72 1 1
CASP8 0.005 0.034 -9999 0 -0.3 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.009 0.084 -9999 0 -0.38 23 23
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.036 0.043 -9999 0 -0.44 4 4
VEGFR1 homodimer/NRP1 -0.004 0.04 -9999 0 -0.45 4 4
mol:DAG 0.046 0.04 -9999 0 -0.39 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.047 -9999 0 -0.42 4 4
CaM/Ca2+ 0.053 0.037 -9999 0 -10000 0 0
HIF1A 0.019 0.066 -9999 0 -0.7 4 4
GAB1 0.014 0.034 -9999 0 -0.72 1 1
AKT1 0.03 0.13 -9999 0 -0.7 1 1
PLCG1 0.046 0.04 -9999 0 -0.39 4 4
NOS3 0.064 0.056 -9999 0 -0.44 1 1
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO 0.063 0.055 -9999 0 -0.42 1 1
FLT1 0.033 0.05 -9999 0 -0.52 4 4
PGF 0.016 0.01 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.01 0.05 -9999 0 -0.46 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
eNOS/Hsp90 0.071 0.053 -9999 0 -10000 0 0
endothelial cell proliferation 0.053 0.041 -9999 0 -0.4 1 1
mol:Ca2+ 0.046 0.039 -9999 0 -0.38 4 4
MAPK3 0.062 0.035 -9999 0 -10000 0 0
MAPK1 0.062 0.035 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
PLGF homodimer 0.016 0.01 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
VEGFA homodimer -0.005 0.054 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.043 0.049 -9999 0 -0.46 4 4
platelet activating factor biosynthetic process 0.069 0.034 -9999 0 -10000 0 0
PI3K -0.038 0.12 -9999 0 -0.6 2 2
PRKCA 0.054 0.037 -9999 0 -10000 0 0
PRKCB 0.044 0.037 -9999 0 -0.36 4 4
VEGFR1 homodimer/PLGF homodimer 0.036 0.043 -9999 0 -0.44 4 4
VEGFA -0.005 0.054 -9999 0 -10000 0 0
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.046 0.04 -9999 0 -0.39 4 4
RASA1 0.047 0.04 -9999 0 -0.39 4 4
NRP2 0.015 0.016 -9999 0 -10000 0 0
VEGFR1 homodimer 0.033 0.05 -9999 0 -0.52 4 4
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.21 0.18 -9999 0 -0.45 50 50
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.037 0.12 -9999 0 -0.59 2 2
mol:L-citrulline 0.063 0.055 -9999 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.011 0.049 -9999 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.009 0.049 -9999 0 -0.46 1 1
CD2AP 0.016 0.01 -9999 0 -10000 0 0
PI3K/GAB1 -0.036 0.11 -9999 0 -0.72 1 1
PDPK1 0.021 0.13 -9999 0 -0.7 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.009 0.049 -9999 0 -0.46 1 1
mol:NADP 0.063 0.055 -9999 0 -0.42 1 1
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.01 0.047 -9999 0 -0.42 1 1
VEGFR1 homodimer/NRP2 0.037 0.043 -9999 0 -0.44 4 4
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.037 -10000 0 -0.72 1 1
ANTXR2 0.002 0.1 -10000 0 -0.72 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.091 11 11
monocyte activation 0.012 0.069 -10000 0 -0.45 11 11
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.002 0.011 -10000 0 -10000 0 0
MAP2K7 -0.002 0.011 -10000 0 -10000 0 0
MAP2K6 -0.011 0.065 -10000 0 -0.43 12 12
CYAA 0.01 0.061 -10000 0 -0.4 11 11
MAP2K4 -0.007 0.05 -10000 0 -0.43 7 7
IL1B 0.004 0.068 -10000 0 -0.39 12 12
Channel -0.008 0.062 -10000 0 -0.43 11 11
NLRP1 -0.006 0.047 -10000 0 -0.43 6 6
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.091 11 -10000 0 11
MAPK3 -0.002 0.011 -10000 0 -10000 0 0
MAPK1 -0.002 0.011 -10000 0 -10000 0 0
PGR -0.14 0.18 -10000 0 -0.42 160 160
PA/Cellular Receptors -0.009 0.068 -10000 0 -0.47 11 11
apoptosis -0.002 0.013 -10000 0 -0.091 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.012 0.061 -10000 0 -0.4 11 11
macrophage activation 0.023 0.012 -10000 0 -10000 0 0
TNF 0.012 0.025 -10000 0 -10000 0 0
VCAM1 0.012 0.069 -10000 0 -0.46 11 11
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.027 0.19 4 -10000 0 4
IL18 0.003 0.053 -10000 0 -0.34 7 7
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.091 11 11
LEF -0.002 0.013 -10000 0 -0.092 11 11
CASP1 -0.012 0.046 -10000 0 -0.27 10 10
mol:cAMP -0.002 0.015 -10000 0 -10000 0 0
necrosis -0.002 0.013 -10000 0 -0.091 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.059 -10000 0 -0.41 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.009 -10000 0 -10000 0 0
CDKN1A -0.004 0.055 -10000 0 -0.88 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.015 0.014 -10000 0 -10000 0 0
FOXO3 0 0.002 -10000 0 -10000 0 0
FOXO1 -0.085 0.25 -10000 0 -0.72 72 72
FOXO4 0.029 0.016 -10000 0 -0.33 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT 0.008 0.06 -10000 0 -0.72 3 3
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.037 -10000 0 -0.55 2 2
PPARGC1A -0.066 0.23 -10000 0 -0.72 57 57
FHL2 -0.067 0.23 -10000 0 -0.72 58 58
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.011 -10000 0 -10000 0 0
HIST2H4A 0.011 0.009 -10000 0 -10000 0 0
SIRT1/FOXO3a 0 0.01 -10000 0 -10000 0 0
SIRT1 0.001 0.015 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.011 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.005 0.018 -10000 0 -0.28 1 1
apoptosis -0.002 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.049 0.15 -10000 0 -0.47 57 57
p53/SIRT1 0.002 0.028 0.43 2 -10000 0 2
SIRT1/FOXO4 0.001 0.017 -10000 0 -0.28 1 1
FOXO1/FHL2/SIRT1 -0.1 0.2 -10000 0 -0.47 116 116
HIST1H1E 0.022 0.018 -10000 0 -0.33 1 1
SIRT1/p300 0.001 0.011 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.031 0.47 2 -10000 0 2
TP53 0 0.016 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.002 0.012 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.004 0.044 -10000 0 -0.54 3 3
ACSS2 0.026 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.002 0.032 -10000 0 -0.47 2 2
FoxO family signaling

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
G6PC 0.023 0.12 -9999 0 -10000 0 0
PLK1 0.072 0.17 -9999 0 -0.53 13 13
CDKN1B 0.094 0.16 -9999 0 -0.49 11 11
FOXO3 0.069 0.18 -9999 0 -0.44 35 35
KAT2B 0.007 0.02 -9999 0 -0.043 61 61
FOXO1/SIRT1 -0.027 0.1 -9999 0 -0.31 2 2
CAT 0.009 0.37 -9999 0 -1.2 42 42
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
AKT1 0.029 0.026 -9999 0 -0.21 1 1
FOXO1 0.014 0.13 -9999 0 -0.31 73 73
MAPK10 0.036 0.07 -9999 0 -0.39 12 12
mol:GTP 0.002 0.004 -9999 0 -10000 0 0
FOXO4 0.1 0.1 -9999 0 -0.38 2 2
response to oxidative stress 0.013 0.022 -9999 0 -0.041 41 41
FOXO3A/SIRT1 -0.025 0.14 -9999 0 -0.48 20 20
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.02 0.002 -9999 0 -10000 0 0
BCL2L11 0.043 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.018 0.12 -9999 0 -0.33 7 7
mol:GDP 0.013 0.022 -9999 0 -0.041 41 41
RAN 0.017 0.004 -9999 0 -10000 0 0
GADD45A 0.086 0.18 -9999 0 -0.94 10 10
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.086 0.04 -9999 0 -10000 0 0
MST1 0.024 0.017 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.072 0.028 -9999 0 -10000 0 0
YWHAB 0.015 0.012 -9999 0 -10000 0 0
MAPK8 0.046 0.029 -9999 0 -0.38 1 1
MAPK9 0.046 0.022 -9999 0 -10000 0 0
YWHAG 0.016 0.01 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
YWHAZ 0.014 0.017 -9999 0 -10000 0 0
SIRT1 0.006 0.011 -9999 0 -10000 0 0
SOD2 0.11 0.17 -9999 0 -0.49 8 8
RBL2 0.093 0.14 -9999 0 -0.55 1 1
RAL/GDP 0.036 0.02 -9999 0 -10000 0 0
CHUK 0.023 0.038 -9999 0 -0.75 1 1
Ran/GTP 0.016 0.006 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.043 0.025 -9999 0 -10000 0 0
CSNK1G1 0.016 0.01 -9999 0 -10000 0 0
FASLG 0.035 0.077 -9999 0 -1.6 1 1
SKP2 0.012 0.025 -9999 0 -10000 0 0
USP7 0.017 0.005 -9999 0 -10000 0 0
IKBKB 0.022 0.028 -9999 0 -10000 0 0
CCNB1 0.064 0.17 -9999 0 -0.58 9 9
FOXO1-3a-4/beta catenin 0.006 0.18 -9999 0 -0.4 54 54
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.12 -9999 0 -0.33 7 7
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.007 0.02 -9999 0 -0.043 61 61
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.01 -9999 0 -10000 0 0
ZFAND5 0.1 0.092 -9999 0 -10000 0 0
SFN 0.012 0.048 -9999 0 -0.72 2 2
CDK2 0.018 0.024 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.078 0.044 -9999 0 -0.34 1 1
CREBBP 0.02 0.032 -9999 0 -0.72 1 1
FBXO32 0.028 0.33 -9999 0 -1.2 29 29
BCL6 -0.014 0.41 -9999 0 -1.2 53 53
RALB 0.017 0.002 -9999 0 -10000 0 0
RALA 0.017 0.002 -9999 0 -10000 0 0
YWHAH 0.015 0.012 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.034 0.028 -9999 0 -0.46 1 1
SNTA1 0.015 0.032 -9999 0 -0.72 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.02 0.043 -9999 0 -0.46 1 1
MAPK12 0.016 0.09 -9999 0 -0.35 29 29
CCND1 0.01 0.093 -9999 0 -0.54 12 12
p38 gamma/SNTA1 0.022 0.086 -9999 0 -0.38 14 14
MAP2K3 0.016 0.007 -9999 0 -10000 0 0
PKN1 0.015 0.012 -9999 0 -10000 0 0
G2/M transition checkpoint 0.016 0.09 -9999 0 -0.35 29 29
MAP2K6 0.008 0.097 -9999 0 -0.39 29 29
MAPT 0.03 0.044 -9999 0 -0.34 4 4
MAPK13 0.025 0.032 -9999 0 -0.54 1 1
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.008 0.076 -9999 0 -0.41 17 17
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0 0.019 -10000 0 -0.41 1 1
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC5 0 0 -10000 0 -10000 0 0
GATA2/HDAC5 -0.004 0.018 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR -0.046 0.14 -10000 0 -0.46 53 53
HDAC9 0.014 0.017 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.04 0.13 -10000 0 -0.46 46 46
HDAC4/ANKRA2 -0.003 0.041 -10000 0 -0.54 3 3
HDAC5/YWHAB 0 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.003 -10000 0 -10000 0 0
GATA2 0.007 0.037 -10000 0 -10000 0 0
HDAC4/RFXANK 0 0.003 -10000 0 -10000 0 0
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.034 -10000 0 -0.72 1 1
HDAC5 0.016 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.024 -10000 0 -0.54 1 1
Histones 0.043 0.012 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.003 0.041 -10000 0 -0.54 3 3
HDAC4/Ubc9 0 0 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.023 -10000 0 -0.54 1 1
TUBA1B 0.015 0.012 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0 0.003 -10000 0 -10000 0 0
CAMK4 0.014 0.017 -10000 0 -10000 0 0
Tubulin/HDAC6 -0.007 0.06 -10000 0 -0.46 9 9
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
GATA1 0.016 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
NR3C1 -0.048 0.21 -10000 0 -0.72 46 46
SUMO1/HDAC4 0.038 0.002 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0 0.006 -10000 0 -10000 0 0
Tubulin -0.01 0.07 -10000 0 -0.54 9 9
HDAC4/14-3-3 E -0.001 0.023 -10000 0 -0.54 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
RANGAP1 0.01 0.031 -10000 0 -10000 0 0
BCL6/BCoR -0.054 0.16 -10000 0 -0.54 53 53
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -10000 0 -10000 0 0
HDAC4/SRF 0.001 0.009 -10000 0 -10000 0 0
HDAC4/ER alpha -0.14 0.22 -10000 0 -0.54 117 117
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.043 0.012 -10000 0 -10000 0 0
cell motility -0.007 0.06 -10000 0 -0.46 9 9
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.058 0.22 -10000 0 -0.72 53 53
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0 0.005 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
HDAC6/HDAC11 -0.003 0.014 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.001 0.006 -10000 0 -10000 0 0
NPC 0 0.003 -10000 0 -10000 0 0
MEF2C -0.029 0.18 -10000 0 -0.72 32 32
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.023 0.091 -10000 0 -0.38 32 32
GNG2 0.015 0.032 -10000 0 -0.72 1 1
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.003 0.096 -10000 0 -0.72 9 9
HDAC11 0.01 0.03 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
RANBP2 0.016 0.007 -10000 0 -10000 0 0
ANKRA2 0.012 0.056 -10000 0 -0.72 3 3
RFXANK 0.016 0.007 -10000 0 -10000 0 0
nuclear import -0.036 0.018 0.39 1 -10000 0 1
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.013 0.046 -10000 0 -0.72 2 2
Cbp/p300/PCAF -0.001 0.02 -10000 0 -0.47 1 1
EP300 0.016 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.09 -10000 0 -0.41 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 -0.009 0.13 0.24 20 -0.3 79 99
RAR alpha/9cRA/Cyclin H -0.003 0.024 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.004 0.11 -10000 0 -0.24 85 85
CDC2 -0.066 0.081 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.026 -10000 0 -0.57 1 1
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.034 -10000 0 -0.55 2 2
RXRs/RARs/NRIP1/9cRA 0.024 0.13 -10000 0 -0.51 11 11
NCOA2 0.015 0.014 -10000 0 -10000 0 0
NCOA3 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
VDR/VDR/DNA 0.013 0.046 -10000 0 -0.72 2 2
RARG 0.017 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.002 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.016 0.032 -10000 0 -0.72 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.007 0.045 -10000 0 -10000 0 0
RARA 0.038 0.02 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.1 -10000 0 -0.23 85 85
PRKCA 0.019 0.012 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.018 0.13 -10000 0 -0.55 12 12
RXRG 0.033 0.044 -10000 0 -0.39 5 5
RXRA 0.042 0.032 -10000 0 -10000 0 0
RXRB 0.037 0.013 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.034 -10000 0 -0.55 2 2
RBP1 -0.023 0.16 -10000 0 -0.72 26 26
CRBP1/9-cic-RA -0.029 0.12 -10000 0 -0.55 26 26
RARB -0.1 0.27 -10000 0 -0.72 85 85
PRKCG 0.02 0.007 -10000 0 -10000 0 0
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.022 0.12 -10000 0 -0.45 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.11 -10000 0 -0.33 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.088 -10000 0 -0.44 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.018 0.13 -10000 0 -0.55 12 12
positive regulation of DNA binding -0.003 0.022 -10000 0 -10000 0 0
NRIP1 0.009 0.2 -10000 0 -1.3 10 10
RXRs/RARs 0.017 0.11 -10000 0 -0.4 13 13
RXRs/RXRs/DNA/9cRA 0.016 0.052 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0.007 -10000 0 -10000 0 0
TFIIH 0 0.004 -10000 0 -10000 0 0
RAR alpha/9cRA 0 0.008 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
RAR gamma2/9cRA 0 0.002 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CCL5 0.006 0.08 -9999 0 -0.72 6 6
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
FGFR/FGF2/Syndecan-1 -0.026 0.099 -9999 0 -0.29 1 1
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 -0.015 0.094 -9999 0 -10000 0 0
Syndecan-1/Syntenin -0.016 0.095 -9999 0 -0.39 1 1
MAPK3 0.004 0.087 -9999 0 -10000 0 0
HGF/MET -0.054 0.16 -9999 0 -0.54 52 52
TGFB1/TGF beta receptor Type II 0.016 0.01 -9999 0 -10000 0 0
BSG 0.015 0.014 -9999 0 -10000 0 0
keratinocyte migration -0.014 0.093 -9999 0 -10000 0 0
Syndecan-1/RANTES -0.019 0.11 -9999 0 -0.55 6 6
Syndecan-1/CD147 -0.004 0.091 -9999 0 -10000 0 0
Syndecan-1/Syntenin/PIP2 -0.023 0.087 -9999 0 -0.38 1 1
LAMA5 0.015 0.014 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.086 -9999 0 -0.37 1 1
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
HGF 0.016 0.01 -9999 0 -10000 0 0
Syndecan-1/CASK -0.026 0.093 -9999 0 -0.27 1 1
Syndecan-1/HGF/MET -0.044 0.16 -9999 0 -0.46 52 52
regulation of cell adhesion 0.014 0.085 -9999 0 -10000 0 0
HPSE 0.003 0.044 -9999 0 -10000 0 0
positive regulation of cell migration -0.026 0.099 -9999 0 -0.29 1 1
SDC1 -0.026 0.099 -9999 0 -0.29 1 1
Syndecan-1/Collagen -0.026 0.099 -9999 0 -0.29 1 1
PPIB 0.016 0.01 -9999 0 -10000 0 0
MET -0.057 0.22 -9999 0 -0.72 52 52
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
MAPK1 0.004 0.087 -9999 0 -10000 0 0
homophilic cell adhesion -0.026 0.098 -9999 0 -0.28 1 1
MMP1 -0.089 0.077 -9999 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.047 0.07 -9999 0 -0.35 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.004 0.065 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.004 0.07 -9999 0 -0.46 12 12
antigen processing and presentation of peptide antigen via MHC class I -0.033 0.096 -9999 0 -0.35 26 26
CaM/Ca2+ 0.012 0.065 -9999 0 -0.33 7 7
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.027 0.074 -9999 0 -0.33 13 13
AKT1 0.015 0.13 -9999 0 -0.46 17 17
MAP2K1 0.045 0.07 -9999 0 -0.36 1 1
MAP3K11 0.038 0.063 -9999 0 -0.33 13 13
IFNGR1 0.005 0.095 -9999 0 -0.72 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII 0.006 0.07 -9999 0 -0.5 5 5
Rap1/GTP -0.006 0.036 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.014 0.074 -9999 0 -0.37 13 13
CEBPB 0.086 0.073 -9999 0 -0.46 1 1
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.072 -9999 0 -10000 0 0
STAT1 0.031 0.075 -9999 0 -0.33 13 13
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.018 0.072 -9999 0 -0.72 1 1
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.046 0.068 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.004 0.032 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.07 -9999 0 -0.35 13 13
MAPK3 0.061 0.07 -9999 0 -10000 0 0
STAT1 (dimer) -0.038 0.14 -9999 0 -0.52 26 26
MAPK1 0.061 0.07 -9999 0 -10000 0 0
JAK2 0.015 0.033 -9999 0 -0.72 1 1
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
JAK1 0.014 0.046 -9999 0 -0.72 2 2
CAMK2D 0.01 0.065 -9999 0 -0.72 4 4
DAPK1 0.083 0.054 -9999 0 -10000 0 0
SMAD7 0.043 0.074 -9999 0 -0.17 22 22
CBL/CRKL/C3G -0.001 0.047 -9999 0 -10000 0 0
PI3K -0.025 0.13 -9999 0 -0.45 25 25
IFNG -0.018 0.072 -9999 0 -0.72 1 1
apoptosis 0.059 0.052 -9999 0 -10000 0 0
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A 0.016 0 -9999 0 -10000 0 0
CAMK2B -0.006 0.094 -9999 0 -0.72 7 7
FRAP1 0.025 0.13 -9999 0 -0.48 10 10
PRKCD 0.016 0.14 -9999 0 -0.45 19 19
RAP1B 0.016 0.01 -9999 0 -10000 0 0
negative regulation of cell growth -0.033 0.096 -9999 0 -0.35 26 26
PTPN2 0.016 0.01 -9999 0 -10000 0 0
EP300 0.017 0 -9999 0 -10000 0 0
IRF1 0.066 0.073 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.008 0.06 -9999 0 -10000 0 0
SOCS1 0.009 0.015 -9999 0 -10000 0 0
mol:GDP -0.002 0.045 -9999 0 -10000 0 0
CASP1 0.018 0.14 -9999 0 -0.34 60 60
PTGES2 0.016 0.007 -9999 0 -10000 0 0
IRF9 0.071 0.03 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.13 -9999 0 -0.43 25 25
RAP1/GDP -0.005 0.037 -9999 0 -10000 0 0
CBL 0.037 0.063 -9999 0 -0.33 13 13
MAP3K1 0.036 0.073 -9999 0 -0.34 17 17
PIAS1 0.016 0.007 -9999 0 -10000 0 0
PIAS4 0.014 0.016 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.033 0.096 -9999 0 -0.35 26 26
PTPN11 0.026 0.066 -9999 0 -0.35 13 13
CREBBP 0.016 0.032 -9999 0 -0.72 1 1
RAPGEF1 0.016 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.008 0.055 -10000 0 -0.36 8 8
FYN 0.068 0.08 -10000 0 -0.42 9 9
LAT/GRAP2/SLP76 -0.009 0.059 -10000 0 -0.36 8 8
IKBKB 0.014 0.02 -10000 0 -10000 0 0
AKT1 0.075 0.068 -10000 0 -0.29 9 9
B2M 0.017 0.033 -10000 0 -0.73 1 1
IKBKG -0.002 0.012 -10000 0 -10000 0 0
MAP3K8 -0.083 0.25 -10000 0 -0.72 70 70
mol:Ca2+ -0.004 0.018 -10000 0 -0.095 18 18
integrin-mediated signaling pathway 0.001 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.078 0.085 -10000 0 -0.39 9 9
TRPV6 -0.03 0.14 -10000 0 -0.74 18 18
CD28 -0.003 0.11 -10000 0 -0.72 11 11
SHC1 0.065 0.084 -10000 0 -0.43 9 9
receptor internalization 0.047 0.11 -10000 0 -0.36 28 28
PRF1 0.053 0.067 -10000 0 -10000 0 0
KRAS 0.012 0.025 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -10000 0 0
COT/AKT1 0.03 0.12 -10000 0 -0.25 75 75
LAT 0.063 0.087 -10000 0 -0.43 9 9
EntrezGene:6955 0.002 0.001 -10000 0 -10000 0 0
CD3D 0.011 0.034 -10000 0 -10000 0 0
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G -0.009 0.11 -10000 0 -0.72 10 10
RASGRP2 0.016 0.031 -10000 0 -0.17 13 13
RASGRP1 0.084 0.07 -10000 0 -0.28 7 7
HLA-A 0.015 0.025 -10000 0 -10000 0 0
RASSF5 0.013 0.021 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.001 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.056 0.031 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.004 0.02 -10000 0 -10000 0 0
PRKCA -0.004 0.034 -10000 0 -0.18 7 7
GRAP2 0.014 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.07 0.27 18 -0.29 7 25
EntrezGene:6957 0.003 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.037 0.072 -10000 0 -0.37 9 9
ORAI1 0.018 0.07 0.37 18 -10000 0 18
CSK 0.063 0.082 -10000 0 -0.42 9 9
B7 family/CD28 -0.012 0.094 -10000 0 -0.5 13 13
CHUK 0.015 0.032 -10000 0 -0.72 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.057 0.091 -10000 0 -0.48 9 9
PTPN6 0.06 0.082 -10000 0 -0.42 9 9
VAV1 0.063 0.086 -10000 0 -0.43 9 9
Monovalent TCR/CD3 0.013 0.098 -10000 0 -0.37 28 28
CBL 0.016 0 -10000 0 -10000 0 0
LCK 0.064 0.076 -10000 0 -0.39 9 9
PAG1 0.062 0.082 -10000 0 -0.42 9 9
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.054 0.092 -10000 0 -0.42 13 13
CD80 0.006 0.041 -10000 0 -10000 0 0
CD86 0.016 0.012 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.005 0.026 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
GO:0035030 0.056 0.097 -10000 0 -0.43 13 13
CD8A 0.003 0.002 -10000 0 -10000 0 0
CD8B 0.014 0.026 -10000 0 -10000 0 0
PTPRC 0.006 0.057 -10000 0 -0.73 2 2
PDK1/PKC theta 0.089 0.081 -10000 0 -0.33 9 9
CSK/PAG1 0.067 0.077 -10000 0 -0.4 7 7
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.025 0.029 -10000 0 -0.55 1 1
GRAP2/SLP76 -0.01 0.066 -10000 0 -0.4 9 9
STIM1 0.01 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.072 0.037 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.047 0.11 -10000 0 -0.38 28 28
mol:DAG -0.006 0.047 -10000 0 -0.26 7 7
RAP1A/GDP 0.027 0.013 -10000 0 -10000 0 0
PLCG1 0.016 0.007 -10000 0 -10000 0 0
CD247 -0.028 0.16 -10000 0 -0.72 25 25
cytotoxic T cell degranulation 0.053 0.066 -10000 0 -10000 0 0
RAP1A/GTP -0.002 0.009 -10000 0 -0.061 13 13
mol:PI-3-4-5-P3 0.076 0.077 -10000 0 -0.34 9 9
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.002 0.08 0.29 17 -0.35 7 24
NRAS 0.014 0.019 -10000 0 -10000 0 0
ZAP70 0.012 0.026 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.01 0.06 -10000 0 -0.36 7 7
MALT1 0.016 0.007 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer 0.013 0.018 -10000 0 -10000 0 0
CARD11 0.011 0.029 -10000 0 -10000 0 0
PRKCB -0.005 0.034 -10000 0 -0.19 7 7
PRKCE -0.004 0.033 -10000 0 -0.18 7 7
PRKCQ 0.083 0.086 -10000 0 -0.37 9 9
LCP2 0.012 0.024 -10000 0 -10000 0 0
BCL10 0.016 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.072 0.062 -10000 0 -0.25 9 9
IKK complex 0.064 0.03 -10000 0 -0.11 1 1
RAS family/GDP 0 0.003 -10000 0 -10000 0 0
MAP3K14 0.037 0.1 -10000 0 -0.28 7 7
PDPK1 0.077 0.066 -10000 0 -0.28 8 8
TCR/CD3/MHC I/CD8/Fyn 0.05 0.086 -10000 0 -0.52 8 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.003 0.035 -9999 0 -0.4 4 4
RGS9BP -0.015 0.076 -9999 0 -0.72 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.006 0.037 -9999 0 -0.47 2 2
mol:ADP 0.013 0.025 -9999 0 -0.55 1 1
GNAT2 0.01 0.065 -9999 0 -0.72 4 4
RGS9-1/Gbeta5/R9AP -0.018 0.13 -9999 0 -0.47 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.046 -9999 0 -0.47 5 5
GRK7 0.015 0.033 -9999 0 -0.72 1 1
CNGB3 0.008 0.034 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.022 0.037 -9999 0 -0.42 2 2
Cone PDE6 -0.011 0.11 -9999 0 -0.39 37 37
Cone Metarhodopsin II -0.001 0.019 -9999 0 -0.44 1 1
Na + (4 Units) 0.008 0.036 -9999 0 -0.42 2 2
GNAT2/GDP -0.016 0.11 -9999 0 -0.4 39 39
GNB5 0.015 0.032 -9999 0 -0.72 1 1
mol:GMP (4 units) 0.026 0.05 -9999 0 -0.43 6 6
Cone Transducin -0.003 0.037 -9999 0 -0.42 4 4
SLC24A2 0.016 0.01 -9999 0 -10000 0 0
GNB3/GNGT2 0 0.003 -9999 0 -10000 0 0
GNB3 0.016 0.007 -9999 0 -10000 0 0
GNAT2/GTP -0.005 0.048 -9999 0 -0.55 4 4
CNGA3 0.002 0.061 -9999 0 -0.72 2 2
ARR3 0.016 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.006 0.037 -9999 0 -0.47 2 2
mol:Pi -0.018 0.12 -9999 0 -0.47 35 35
Cone CNG Channel 0.004 0.055 -9999 0 -0.39 8 8
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.016 0.01 -9999 0 -10000 0 0
RGS9 -0.03 0.18 -9999 0 -0.72 32 32
PDE6C 0.014 0.034 -9999 0 -0.72 1 1
GNGT2 0.016 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.013 0.036 -9999 0 -0.72 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.039 0.003 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.064 -9999 0 -0.72 4 4
ITGA4 0.01 0.032 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.004 0.019 -9999 0 -10000 0 0
EPO -0.006 0.056 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
alpha4/beta1 Integrin -0.003 0.015 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.011 0.027 -9999 0 -10000 0 0
lamellipodium assembly -0.031 0.11 -9999 0 -0.35 51 51
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 0.04 0.023 -9999 0 -0.44 1 1
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
MADCAM1 0.015 0.014 -9999 0 -10000 0 0
cell adhesion 0.004 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.03 0.067 -9999 0 -0.41 11 11
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.069 -9999 0 -0.46 11 11
p130Cas/Crk/Dock1 0.051 0.069 -9999 0 -10000 0 0
VCAM1 -0.001 0.11 -9999 0 -0.72 11 11
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.004 0.019 -9999 0 -10000 0 0
BCAR1 0.039 0.063 -9999 0 -0.37 11 11
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
Rac1/GTP -0.033 0.11 -9999 0 -0.36 51 51
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.085 -10000 0 -10000 0 0
BAG4 0.011 0.029 -10000 0 -10000 0 0
BAD 0.037 0.029 -10000 0 -10000 0 0
NFKBIA 0.015 0.032 -10000 0 -0.72 1 1
BIRC3 -0.039 0.18 -10000 0 -0.72 35 35
BAX 0.036 0.029 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.016 0.021 -10000 0 -10000 0 0
IKBKB 0.053 0.083 -10000 0 -10000 0 0
MAP2K2 0.053 0.025 -10000 0 -10000 0 0
MAP2K1 0.053 0.025 -10000 0 -10000 0 0
SMPD1 0.024 0.021 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.086 -10000 0 -10000 0 0
MAP2K4 0.036 0.062 -10000 0 -0.34 11 11
protein ubiquitination 0.055 0.084 -10000 0 -0.37 1 1
EnzymeConsortium:2.7.1.37 0.057 0.029 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAF1 0.046 0.026 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
mol:ceramide 0.028 0.03 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.02 -10000 0 -0.47 1 1
MADD 0.017 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.047 -10000 0 -0.37 4 4
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.056 0.024 -10000 0 -10000 0 0
MAPK1 0.056 0.024 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha -0.001 0.023 -10000 0 -0.54 1 1
FADD 0.04 0.089 -10000 0 -10000 0 0
KSR1 0.038 0.028 -10000 0 -10000 0 0
MAPK8 0.043 0.06 -10000 0 -0.31 12 12
TRAF2 0.015 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.053 0.086 -10000 0 -0.62 1 1
TNF R/SODD -0.001 0.014 -10000 0 -10000 0 0
TNF 0.013 0.025 -10000 0 -10000 0 0
CYCS 0.06 0.052 0.16 86 -10000 0 86
IKBKG 0.054 0.082 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.037 0.089 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0.001 -10000 0 -10000 0 0
AIFM1 0.06 0.052 0.16 78 -10000 0 78
TNF/TNF R/SODD 0.004 0.02 -10000 0 -10000 0 0
TNFRSF1A 0.016 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.024 -10000 0 -10000 0 0
NSMAF 0.044 0.091 -10000 0 -0.65 1 1
response to hydrogen peroxide 0.001 0 -10000 0 -10000 0 0
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -9999 0 -10000 0 0
NFATC1 0.059 0.026 -9999 0 -10000 0 0
NFATC2 0.024 0.062 -9999 0 -0.21 5 5
NFATC3 0.019 0.004 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
Calcineurin A alpha-beta B1/CABIN1 0.049 0.027 -9999 0 -0.23 4 4
Exportin 1/Ran/NUP214 0 0 -9999 0 -10000 0 0
mol:DAG 0 0.002 -9999 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.001 0.018 -9999 0 -10000 0 0
BCL2/BAX -0.11 0.22 -9999 0 -0.54 104 104
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.005 -9999 0 -10000 0 0
CaM/Ca2+ 0.014 0.005 -9999 0 -10000 0 0
BAX 0.015 0.014 -9999 0 -10000 0 0
MAPK14 0.016 0.004 -9999 0 -10000 0 0
BAD 0.016 0 -9999 0 -10000 0 0
CABIN1/MEF2D 0.054 0.025 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/BCL2 -0.13 0.29 -9999 0 -0.72 104 104
FKBP8 0.016 0.007 -9999 0 -10000 0 0
activation-induced cell death of T cells -0.054 0.025 -9999 0 -10000 0 0
KPNB1 0.016 0.007 -9999 0 -10000 0 0
KPNA2 -0.029 0.072 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SFN 0.012 0.048 -9999 0 -0.72 2 2
MAP3K8 -0.083 0.25 -9999 0 -0.72 70 70
NFAT4/CK1 alpha 0 0.037 -9999 0 -0.38 4 4
MEF2D/NFAT1/Cbp/p300 -0.023 0.073 -9999 0 -0.43 6 6
CABIN1 0.049 0.027 -9999 0 -0.23 4 4
CALM1 0.016 0.004 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
CAMK4 0.014 0.017 -9999 0 -10000 0 0
mol:Ca2+ 0.001 0.004 -9999 0 -10000 0 0
MAPK3 0.016 0 -9999 0 -10000 0 0
YWHAH 0.015 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.007 0.038 -9999 0 -0.54 2 2
YWHAB 0.015 0.012 -9999 0 -10000 0 0
MAPK8 0.015 0.032 -9999 0 -0.72 1 1
MAPK9 0.016 0.007 -9999 0 -10000 0 0
YWHAG 0.016 0.01 -9999 0 -10000 0 0
FKBP1A 0.016 0.01 -9999 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.002 0.02 -9999 0 -10000 0 0
PRKCH 0.011 0.064 -9999 0 -0.72 4 4
CABIN1/Cbp/p300 -0.001 0.023 -9999 0 -0.54 1 1
CASP3 0.016 0.004 -9999 0 -10000 0 0
PIM1 0.015 0.016 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
apoptosis -0.032 0.065 -9999 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.054 0.018 -9999 0 -10000 0 0
PRKCB 0 0 -9999 0 -10000 0 0
PRKCE 0.016 0 -9999 0 -10000 0 0
JNK2/NFAT4 0.027 0.005 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
PRKCD 0.014 0.019 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
PRKCZ 0 0.002 -9999 0 -10000 0 0
PRKCA 0.016 0.01 -9999 0 -10000 0 0
PRKCG 0.016 0 -9999 0 -10000 0 0
PRKCQ 0.008 0.046 -9999 0 -0.72 1 1
FKBP38/BCL2 -0.11 0.22 -9999 0 -0.54 104 104
EP300 0.017 0.003 -9999 0 -10000 0 0
PRKCB1 0.008 0.036 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
NFATc/JNK1 0.064 0.033 -9999 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0.003 -9999 0 -10000 0 0
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSNK1A1 0.025 0.006 -9999 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.001 0.008 -9999 0 -10000 0 0
NFATc/ERK1 0.066 0.025 -9999 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.001 0.018 -9999 0 -10000 0 0
NR4A1 0.034 0.16 -9999 0 -0.65 27 27
GSK3B 0.016 0.011 -9999 0 -10000 0 0
positive T cell selection 0.019 0.004 -9999 0 -10000 0 0
NFAT1/CK1 alpha -0.014 0.033 -9999 0 -10000 0 0
RCH1/ KPNB1 -0.022 0.035 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0.004 -9999 0 -10000 0 0
AKAP5 0.004 0.059 -9999 0 -0.72 2 2
MEF2D 0.017 0.003 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
YWHAZ 0.014 0.017 -9999 0 -10000 0 0
NFATc/p38 alpha 0.064 0.028 -9999 0 -10000 0 0
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
BCL2 -0.13 0.29 -9999 0 -0.72 104 104
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.004 -9999 0 -10000 0 0
DOCK1 0.011 0.064 -9999 0 -0.72 4 4
ITGA4 0.01 0.032 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
alpha4/beta1 Integrin 0.003 0.016 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.004 0.018 -9999 0 -10000 0 0
lamellipodium assembly -0.041 0.13 -9999 0 -0.42 51 51
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
ARF6 0.016 0 -9999 0 -10000 0 0
TLN1 0.016 0 -9999 0 -10000 0 0
PXN 0.029 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
ARF6/GTP 0.004 0.017 -9999 0 -10000 0 0
cell adhesion 0.004 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.004 0.018 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ARF6/GDP 0.001 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.059 -9999 0 -0.38 11 11
p130Cas/Crk/Dock1 -0.004 0.044 -9999 0 -0.46 5 5
VCAM1 -0.001 0.11 -9999 0 -0.72 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.004 0.019 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.005 0.021 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
mol:GDP -0.005 0.02 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.004 0.019 -9999 0 -10000 0 0
Rac1/GTP -0.046 0.14 -9999 0 -0.47 51 51
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.027 0.1 -9999 0 -0.4 36 36
TRAF2/ASK1 -0.031 0.12 -9999 0 -0.47 35 35
ATM 0.016 0 -9999 0 -10000 0 0
MAP2K3 0.039 0.073 -9999 0 -0.36 4 4
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.028 0.12 -9999 0 -0.37 35 35
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.014 0.019 -9999 0 -10000 0 0
TXN 0.011 0.002 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A 0.004 0.096 -9999 0 -0.72 9 9
GADD45B 0.01 0.065 -9999 0 -0.72 4 4
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
MAP3K6 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.036 0.13 -9999 0 -0.54 35 35
TAK1/TAB family -0.001 0.021 -9999 0 -0.49 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.015 0.012 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.011 0.04 -9999 0 -10000 0 0
TRAF6 0.021 0.019 -9999 0 -0.41 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.006 0.094 -9999 0 -0.72 7 7
CCM2 0.016 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.001 0.057 -9999 0 -0.47 7 7
MAPK11 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.029 0.12 -9999 0 -0.43 42 42
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.021 0.007 -9999 0 -10000 0 0
TAOK2 0.022 0 -9999 0 -10000 0 0
TAOK3 0.022 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
MAP3K5 -0.033 0.18 -9999 0 -0.72 35 35
MAP3K10 0.012 0.047 -9999 0 -0.72 2 2
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 -0.012 0.12 -9999 0 -0.46 35 35
GADD45/MTK1/MTK1 -0.008 0.066 -9999 0 -0.42 12 12
HIF-2-alpha transcription factor network

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
MMP14 0.005 0.018 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.014 -10000 0 -10000 0 0
TCEB2 0.016 0.01 -10000 0 -10000 0 0
TCEB1 0.014 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.008 0.072 -10000 0 -0.35 10 10
EPO 0.19 0.18 -10000 0 -0.54 5 5
FIH (dimer) 0.031 0.014 -10000 0 -10000 0 0
APEX1 0.032 0.015 -10000 0 -10000 0 0
SERPINE1 0.19 0.18 -10000 0 -0.65 5 5
FLT1 0.005 0.046 -10000 0 -0.94 1 1
ADORA2A 0.17 0.18 -10000 0 -0.6 6 6
germ cell development 0.18 0.18 -10000 0 -0.59 6 6
SLC11A2 0.19 0.18 -10000 0 -0.58 7 7
BHLHE40 0.18 0.18 -10000 0 -0.51 12 12
HIF1AN 0.031 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.051 0.13 -10000 0 -0.41 11 11
ETS1 0.034 0.036 -10000 0 -0.72 1 1
CITED2 -0.011 0.14 -10000 0 -1.2 7 7
KDR 0.005 0.047 -10000 0 -0.94 1 1
PGK1 0.19 0.18 -10000 0 -0.61 6 6
SIRT1 0.016 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.22 0.21 -10000 0 -0.59 12 12
EPAS1 0.098 0.12 -10000 0 -0.39 16 16
SP1 0.025 0.006 -10000 0 -10000 0 0
ABCG2 0.16 0.25 -10000 0 -0.71 27 27
EFNA1 0.18 0.19 -10000 0 -0.62 6 6
FXN 0.18 0.18 -10000 0 -0.6 6 6
POU5F1 0.19 0.19 -10000 0 -0.62 6 6
neuron apoptosis -0.21 0.21 0.57 12 -10000 0 12
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 0.012 0.072 -10000 0 -0.73 1 1
EGLN2 0.031 0.02 -10000 0 -10000 0 0
EGLN1 0.029 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.004 0.017 -10000 0 -10000 0 0
VHL 0.012 0.027 -10000 0 -10000 0 0
ARNT 0.033 0.012 -10000 0 -10000 0 0
SLC2A1 0.18 0.18 -10000 0 -0.58 7 7
TWIST1 0.13 0.28 -10000 0 -0.62 56 56
ELK1 0.025 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.043 0.12 -10000 0 -0.46 9 9
VEGFA 0.18 0.19 -10000 0 -0.6 7 7
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Atypical NF-kappaB 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
BCL3/RelA -0.001 0.007 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.034 0.014 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.058 0.013 -9999 0 -10000 0 0
NFKBIA 0.035 0.015 -9999 0 -0.24 1 1
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.033 0.01 -9999 0 -10000 0 0
ARRB2 0.022 0 -9999 0 -10000 0 0
REL 0.012 0.027 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.033 0.011 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.01 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.027 0.007 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
NFKB1 0.028 0.013 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.044 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.063 0.013 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
NF kappa B1 p50/RelA 0.044 0.007 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.01 0.03 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.001 0.12 -9999 0 -0.38 51 51
cell death 0.06 0.012 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.034 0.014 -9999 0 -10000 0 0
LCK 0 0.049 -9999 0 -10000 0 0
BCL3 0.015 0.014 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.016 0.016 -9999 0 -10000 0 0
ELF1 0.027 0.007 -9999 0 -10000 0 0
CCNA2 -0.04 0.077 -9999 0 -10000 0 0
PIK3CA 0.017 0.007 -9999 0 -10000 0 0
JAK3 0.017 0 -9999 0 -10000 0 0
PIK3R1 -0.054 0.22 -9999 0 -0.72 51 51
JAK1 0.015 0.045 -9999 0 -0.72 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.081 0.066 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
SP1 0.02 0.051 -9999 0 -0.36 9 9
IL2RA 0.034 0.026 -9999 0 -10000 0 0
IL2RB 0.014 0.023 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG 0.008 0.039 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.033 0.14 -9999 0 -0.76 13 13
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.023 0.13 -9999 0 -0.94 9 9
LCK 0.001 0.049 -9999 0 -10000 0 0
GRB2 0.014 0.022 -9999 0 -10000 0 0
IL2 0.016 0.033 -9999 0 -0.72 1 1
CDK6 0.005 0.086 -9999 0 -0.72 7 7
CCND3 0.087 0.061 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.006 0.042 0.27 13 -10000 0 13
DAPP1 0.055 0.022 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK 0.084 0.024 -10000 0 -10000 0 0
mol:DAG 0.077 0.036 0.22 10 -10000 0 10
HRAS 0.016 0.012 -10000 0 -10000 0 0
RAP1A 0.017 0.002 -10000 0 -10000 0 0
ARF5/GDP 0.041 0.047 -10000 0 -0.29 1 1
PLCG2 0 0.11 -10000 0 -0.72 11 11
PLCG1 0.016 0.007 -10000 0 -10000 0 0
ARF5 0.016 0 -10000 0 -10000 0 0
mol:GTP 0.005 0.039 0.26 10 -10000 0 10
ARF1/GTP 0.005 0.038 0.26 10 -10000 0 10
RHOA 0.016 0 -10000 0 -10000 0 0
YES1 0.015 0.032 -10000 0 -0.72 1 1
RAP1A/GTP 0.005 0.037 0.24 10 -10000 0 10
ADAP1 0.005 0.036 0.24 10 -10000 0 10
ARAP3 0.005 0.038 0.26 10 -10000 0 10
INPPL1 0.015 0.012 -10000 0 -10000 0 0
PREX1 -0.027 0.091 -10000 0 -0.72 4 4
ARHGEF6 -0.013 0.14 -10000 0 -0.72 21 21
ARHGEF7 0.015 0.012 -10000 0 -10000 0 0
ARF1 0.016 0.01 -10000 0 -10000 0 0
NRAS 0.015 0.018 -10000 0 -10000 0 0
FYN 0.013 0.045 -10000 0 -0.72 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
FGR 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0.052 0.024 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.012 -10000 0 -10000 0 0
ZAP70 0.012 0.026 -10000 0 -10000 0 0
mol:IP3 0.064 0.031 -10000 0 -10000 0 0
LYN 0.016 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.041 0.047 -10000 0 -0.29 1 1
RhoA/GDP 0.004 0.041 0.26 9 -10000 0 9
PDK1/Src/Hsp90 0.001 0.007 -10000 0 -10000 0 0
BLNK 0.011 0.029 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.062 0.047 -10000 0 -10000 0 0
SRC 0.016 0.007 -10000 0 -10000 0 0
PLEKHA2 0.025 0.009 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PTEN -0.017 0.11 -10000 0 -0.7 13 13
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.006 0.042 0.28 10 -10000 0 10
RhoA/GTP 0.005 0.037 0.25 10 -10000 0 10
Src family/SYK family/BLNK-LAT 0.069 0.023 -10000 0 -10000 0 0
BLK 0.002 0.045 -10000 0 -10000 0 0
PDPK1 0.016 0.007 -10000 0 -10000 0 0
CYTH1 0.005 0.036 0.24 10 -10000 0 10
HCK 0.013 0.024 -10000 0 -10000 0 0
CYTH3 0.005 0.036 0.24 10 -10000 0 10
CYTH2 0.005 0.036 0.24 10 -10000 0 10
KRAS 0.013 0.025 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.005 0.031 0.21 10 -10000 0 10
SGK1 0.005 0.032 0.21 13 -10000 0 13
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.05 -10000 0 -0.24 3 3
SOS1 0.016 0 -10000 0 -10000 0 0
SYK 0.01 0.03 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.043 0.26 12 -10000 0 12
mol:PI-3-4-5-P3 0.007 0.052 0.33 13 -10000 0 13
ARAP3/RAP1A/GTP 0.005 0.037 0.24 10 -10000 0 10
VAV1 0.012 0.027 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.034 0.019 -10000 0 -10000 0 0
PLEKHA1 0.021 0.044 -10000 0 -0.47 4 4
Rac1/GDP 0.041 0.047 -10000 0 -0.29 1 1
LAT 0.012 0.026 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.075 -10000 0 -0.32 20 20
ITK 0.003 0.044 0.25 10 -0.36 2 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.089 0.043 -10000 0 -10000 0 0
LCK 0 0.049 -10000 0 -10000 0 0
BTK 0.004 0.038 0.25 10 -10000 0 10
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.065 0.2 -9999 0 -0.44 39 39
PDGFB-D/PDGFRB/SLAP 0.001 0.011 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0 0 -9999 0 -10000 0 0
AKT1 0.014 0.12 -9999 0 -0.4 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.018 0.079 -9999 0 -0.49 4 4
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
FGR -0.011 0.025 -9999 0 -10000 0 0
mol:Ca2+ 0.023 0.05 -9999 0 -10000 0 0
MYC -0.002 0.22 -9999 0 -0.85 29 29
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP 0 0.011 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.001 0.008 -9999 0 -10000 0 0
GRB10 0.011 0.064 -9999 0 -0.72 4 4
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.022 0.051 -9999 0 -10000 0 0
PTEN -0.002 0.12 -9999 0 -0.72 13 13
GRB2 0.013 0.022 -9999 0 -10000 0 0
GRB7 0.001 0.048 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 -0.004 0.047 -9999 0 -0.54 4 4
cell cycle arrest 0.001 0.011 -9999 0 -10000 0 0
HRAS 0.015 0.012 -9999 0 -10000 0 0
HIF1A 0.021 0.12 -9999 0 -0.38 7 7
GAB1 0.008 0.088 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.002 0.1 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.034 -9999 0 -0.55 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.11 0.18 -9999 0 -0.47 36 36
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:IP3 0.023 0.051 -9999 0 -10000 0 0
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.015 0.01 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0 0.025 -9999 0 -10000 0 0
SHB 0.013 0.037 -9999 0 -0.72 1 1
BLK -0.006 0.029 -9999 0 -10000 0 0
PTPN2 0.015 0.011 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 0.008 0.1 -9999 0 -0.37 10 10
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0.009 -9999 0 -10000 0 0
LCK -0.007 0.03 -9999 0 -10000 0 0
PDGFRB 0.013 0.009 -9999 0 -10000 0 0
ACP1 0.013 0.045 -9999 0 -0.72 2 2
HCK -0.009 0.024 -9999 0 -10000 0 0
ABL1 0.019 0.064 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.013 0.079 -9999 0 -10000 0 0
PTPN1 0.007 0.037 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 -0.011 0.061 -9999 0 -10000 0 0
cell proliferation 0.003 0.19 -9999 0 -0.74 29 29
SLA 0.013 0.022 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.045 0.037 -9999 0 -10000 0 0
SRC -0.01 0.023 -9999 0 -10000 0 0
PI3K -0.041 0.11 -9999 0 -0.4 12 12
PDGFB-D/PDGFRB/GRB7/SHC 0.008 0.023 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.018 0.08 -9999 0 -0.5 4 4
LYN -0.011 0.024 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0.007 -9999 0 -10000 0 0
STAT5A 0.013 0.045 -9999 0 -0.72 2 2
NCK1-2/p130 Cas 0.005 0.019 -9999 0 -10000 0 0
SPHK1 0.001 0.072 -9999 0 -0.73 4 4
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
mol:DAG 0.023 0.051 -9999 0 -10000 0 0
PLCG1 0.023 0.052 -9999 0 -10000 0 0
NHERF/PDGFRB 0.018 0.04 -9999 0 -0.46 1 1
YES1 -0.013 0.041 -9999 0 -0.78 1 1
cell migration 0.018 0.04 -9999 0 -0.46 1 1
SHC/Grb2/SOS1 0.006 0.021 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.72 1 1
SLC9A3R1 -0.022 0.069 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.009 0.08 -9999 0 -0.42 14 14
FYN -0.013 0.057 -9999 0 -0.85 2 2
DOK1 0.036 0.021 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.007 -9999 0 -10000 0 0
PDGFB 0.015 0.016 -9999 0 -10000 0 0
RAC1 0.012 0.14 -9999 0 -0.44 29 29
PRKCD 0.036 0.022 -9999 0 -10000 0 0
FER 0.036 0.022 -9999 0 -10000 0 0
MAPKKK cascade 0 0.01 -9999 0 -10000 0 0
RASA1 0.036 0.022 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0.01 -9999 0 -10000 0 0
p62DOK/Csk 0.016 0.026 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.025 -9999 0 -0.54 1 1
chemotaxis 0.019 0.063 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 0.012 0.035 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.008 0.007 -9999 0 -10000 0 0
PTPRJ 0.014 0.019 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.015 0.067 -9999 0 -0.49 9 9
BIRC5 -0.087 0.078 -9999 0 -10000 0 0
NFKBIA 0.017 0.03 -9999 0 -0.5 1 1
CPEB1 -0.003 0.12 -9999 0 -0.72 13 13
AKT1 0.017 0.023 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.008 0.016 -9999 0 -10000 0 0
NDEL1/TACC3 0.02 0.047 -9999 0 -10000 0 0
GADD45A 0.004 0.096 -9999 0 -0.72 9 9
GSK3B 0.011 0.01 -9999 0 -10000 0 0
PAK1/Aurora A 0.023 0.035 -9999 0 -10000 0 0
MDM2 0.012 0.025 -9999 0 -10000 0 0
JUB -0.01 0.14 -9999 0 -0.72 19 19
TPX2 -0.052 0.046 -9999 0 -10000 0 0
TP53 0.026 0.011 -9999 0 -10000 0 0
DLG7 -0.046 0.053 -9999 0 -10000 0 0
AURKAIP1 0.015 0.012 -9999 0 -10000 0 0
ARHGEF7 0.015 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.021 0.05 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.008 0.016 -9999 0 -10000 0 0
AURKA 0.006 0.025 -9999 0 -10000 0 0
AURKB 0.018 0.015 -9999 0 -10000 0 0
CDC25B 0.004 0.029 -9999 0 -10000 0 0
G2/M transition checkpoint -0.006 0.083 -9999 0 -0.44 19 19
mRNA polyadenylation -0.001 0.07 -9999 0 -0.44 13 13
Aurora A/CPEB -0.001 0.07 -9999 0 -0.44 13 13
Aurora A/TACC1/TRAP/chTOG -0.001 0.1 -9999 0 -0.39 31 31
BRCA1 0.012 0.025 -9999 0 -10000 0 0
centrosome duplication 0.023 0.035 -9999 0 -10000 0 0
regulation of centrosome cycle 0.017 0.046 -9999 0 -10000 0 0
spindle assembly -0.009 0.097 -9999 0 -0.39 31 31
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.047 0.044 -9999 0 -10000 0 0
CENPA 0.025 0.021 -9999 0 -10000 0 0
Aurora A/PP2A 0.023 0.011 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.001 0.033 -9999 0 -10000 0 0
negative regulation of DNA binding 0.026 0.011 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.009 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
Ajuba/Aurora A -0.006 0.084 -9999 0 -0.44 19 19
mitotic prometaphase -0.003 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.025 -9999 0 -10000 0 0
TACC1 -0.028 0.17 -9999 0 -0.72 31 31
TACC3 -0.058 0.08 -9999 0 -10000 0 0
Aurora A/Antizyme1 0.017 0.014 -9999 0 -10000 0 0
Aurora A/RasGAP 0.024 0.009 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.002 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.014 0.031 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.052 0.045 -9999 0 -10000 0 0
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
Aurora A/TPX2 -0.033 0.044 -9999 0 -10000 0 0
PAK1 -0.01 0.06 -9999 0 -10000 0 0
CKAP5 0.014 0.019 -9999 0 -10000 0 0
Arf6 downstream pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.037 0.033 -10000 0 -10000 0 0
regulation of axonogenesis -0.021 0.061 0.27 22 -10000 0 22
myoblast fusion -0.016 0.016 -10000 0 -10000 0 0
mol:GTP -0.003 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.018 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.009 0.009 -10000 0 -10000 0 0
mol:Choline 0.013 0.095 -10000 0 -0.44 22 22
lamellipodium assembly 0.001 0.01 -10000 0 -10000 0 0
MAPK3 0.03 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.04 0.018 -10000 0 -10000 0 0
ARF1 0.016 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.015 -10000 0 -10000 0 0
ARF6 0.013 0.004 -10000 0 -10000 0 0
RAB11A 0.016 0.01 -10000 0 -10000 0 0
TIAM1 0.017 0.012 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.03 0.014 -10000 0 -10000 0 0
actin filament bundle formation -0.002 0.004 -10000 0 -10000 0 0
KALRN -0.001 0.002 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.004 -10000 0 -10000 0 0
NME1 0.013 0.029 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.003 0.005 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.01 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.003 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.003 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.003 0.004 -10000 0 -10000 0 0
mol:GDP -0.001 0.009 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.006 0.011 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.002 0.1 -10000 0 -0.5 21 21
RAB11FIP3 0.015 0.012 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.01 -10000 0 -10000 0 0
ruffle organization 0.021 0.061 -10000 0 -0.27 22 22
regulation of epithelial cell migration -0.003 0.005 -10000 0 -10000 0 0
PLD2 0.022 0.024 -10000 0 -0.5 1 1
PIP5K1A 0.021 0.061 -10000 0 -0.27 22 22
mol:Phosphatidic acid 0.013 0.095 -10000 0 -0.44 22 22
Rac1/GTP 0.001 0.01 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.002 0.015 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.016 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.016 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.003 -9999 0 -10000 0 0
FKBP3 0.016 0.007 -9999 0 -10000 0 0
Histones 0.002 0.012 -9999 0 -10000 0 0
YY1/LSF 0.03 0.038 -9999 0 -0.4 4 4
SMG5 0.014 0.02 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.043 0.016 -9999 0 -0.32 1 1
I kappa B alpha/HDAC1 0.04 0.02 -9999 0 -0.41 1 1
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.048 0.013 -9999 0 -10000 0 0
HDAC1/Smad7 0 0.004 -9999 0 -10000 0 0
RANGAP1 0.01 0.031 -9999 0 -10000 0 0
HDAC3/TR2 0.04 0.02 -9999 0 -0.41 1 1
NuRD/MBD3 Complex 0.06 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.051 0.012 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.007 0.037 -9999 0 -10000 0 0
GATA1 0.016 0 -9999 0 -10000 0 0
Mad/Max 0 0.003 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.074 0.004 -9999 0 -10000 0 0
RBBP7 0.012 0.026 -9999 0 -10000 0 0
NPC 0 0.003 -9999 0 -10000 0 0
RBBP4 0.016 0.007 -9999 0 -10000 0 0
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.035 0.022 -9999 0 -0.46 1 1
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.055 0.003 -9999 0 -10000 0 0
SIN3 complex 0.001 0.009 -9999 0 -10000 0 0
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.015 0.012 -9999 0 -10000 0 0
SAP30 0.016 0.007 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0.032 -9999 0 -0.72 1 1
YY1/HDAC3 0.049 0.012 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0.015 -9999 0 -0.28 1 1
YY1/HDAC1 0.032 0.013 -9999 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.06 0.003 -9999 0 -10000 0 0
PPARG -0.24 0.15 -9999 0 -0.33 388 388
HDAC8/hEST1B 0.001 0.01 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.041 0.003 -9999 0 -10000 0 0
MBD3L2 0.015 0.032 -9999 0 -0.72 1 1
ubiquitin-dependent protein catabolic process 0 0.003 -9999 0 -10000 0 0
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
NuRD/MBD3/MBD3L2 Complex 0.07 0.011 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.036 0.004 -9999 0 -10000 0 0
HDAC2 0.014 0.017 -9999 0 -10000 0 0
YY1 0.029 0.016 -9999 0 -0.33 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0.007 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0.007 -9999 0 -10000 0 0
STAT3 0.032 0.019 -9999 0 -0.39 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.007 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.003 0.032 -9999 0 -0.4 3 3
YY1/SAP30/HDAC1 0 0.011 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.032 0.019 -9999 0 -0.39 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.022 -9999 0 -0.46 1 1
histone deacetylation 0.06 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.052 0.014 -9999 0 -10000 0 0
nuclear export -0.001 0.01 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.012 0.026 -9999 0 -10000 0 0
GATA2/HDAC3 0.044 0.012 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 0.041 0.003 -9999 0 -10000 0 0
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.002 0.012 -9999 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.061 0.003 -9999 0 -10000 0 0
NuRD Complex 0.071 0.003 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.002 0.011 -9999 0 -10000 0 0
SIN3B 0.015 0.016 -9999 0 -10000 0 0
MTA2 0.016 0.007 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.038 0.002 -9999 0 -10000 0 0
HDAC complex 0.003 0.017 -9999 0 -10000 0 0
GATA1/Fog1 0 0.003 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.001 0.009 -9999 0 -10000 0 0
TNF 0.012 0.025 -9999 0 -10000 0 0
negative regulation of cell growth 0.061 0.003 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.06 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.001 0.006 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0 0.014 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.058 0.011 -9999 0 -10000 0 0
TFCP2 0.012 0.056 -9999 0 -0.72 3 3
NR2C1 0.015 0.032 -9999 0 -0.72 1 1
MBD3 0.016 0 -9999 0 -10000 0 0
MBD2 0.016 0.01 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.021 0.048 -9999 0 -0.47 5 5
ADCY5 0.023 0.024 -9999 0 -0.47 1 1
ADCY6 0.025 0 -9999 0 -10000 0 0
ADCY7 0.023 0.014 -9999 0 -10000 0 0
ADCY1 0.025 0.007 -9999 0 -10000 0 0
ADCY2 0.017 0.058 -9999 0 -0.47 7 7
ADCY3 0.025 0.005 -9999 0 -10000 0 0
ADCY8 0.024 0.013 -9999 0 -10000 0 0
PRKCE 0.015 0 -9999 0 -10000 0 0
ADCY9 0.024 0.012 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.042 0.03 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.004 0.019 -9999 0 -10000 0 0
KIRREL 0.018 0.003 -9999 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.004 0.019 -9999 0 -10000 0 0
PLCG1 0.016 0.007 -9999 0 -10000 0 0
ARRB2 0.016 0 -9999 0 -10000 0 0
WASL 0.015 0.032 -9999 0 -0.72 1 1
Nephrin/NEPH1/podocin/CD2AP 0.005 0.021 -9999 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.048 0.015 -9999 0 -0.28 1 1
FYN 0.031 0.025 -9999 0 -0.34 2 2
mol:Ca2+ 0.004 0.02 -9999 0 -10000 0 0
mol:DAG 0.004 0.02 -9999 0 -10000 0 0
NPHS2 0.018 0.003 -9999 0 -10000 0 0
mol:IP3 0.004 0.02 -9999 0 -10000 0 0
regulation of endocytosis 0.003 0.027 -9999 0 -0.3 2 2
Nephrin/NEPH1/podocin/Cholesterol 0.004 0.018 -9999 0 -10000 0 0
establishment of cell polarity 0.004 0.019 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.005 0.022 -9999 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.045 0.024 -9999 0 -0.31 2 2
NPHS1 0.011 0.032 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin 0.003 0.028 -9999 0 -0.33 2 2
TJP1 0.013 0.045 -9999 0 -0.72 2 2
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0.01 -9999 0 -10000 0 0
heterophilic cell adhesion 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.004 0.021 -9999 0 -10000 0 0
CD2AP 0.016 0.01 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.006 0.023 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
TRPC6 0.015 0.099 -9999 0 -0.42 26 26
cytoskeleton organization 0.057 0.016 -9999 0 -10000 0 0
Nephrin/NEPH1 0.003 0.016 -9999 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.002 0.036 -9999 0 -0.49 2 2
Ephrin A reverse signaling

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
MAPKKK cascade 0 0.021 -9999 0 -0.47 1 1
EFNA5 0.014 0.034 -9999 0 -0.72 1 1
FYN 0.03 0.035 -9999 0 -0.42 3 3
neuron projection morphogenesis 0 0.021 -9999 0 -0.47 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0 0.021 -9999 0 -0.47 1 1
EPHA5 0.016 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.012 0.017 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.005 0.02 -9999 0 -10000 0 0
STXBP1 0.016 0 -9999 0 -10000 0 0
ACh/CHRNA1 0.019 0.012 -9999 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.006 0.021 -9999 0 -10000 0 0
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 0.006 0.039 -9999 0 -10000 0 0
mol:ACh 0.01 0.016 -9999 0 -0.14 5 5
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.003 0.025 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.019 0.012 -9999 0 -10000 0 0
UNC13B 0.015 0.014 -9999 0 -10000 0 0
CHRNA1 0.015 0.012 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 0.024 0.075 -9999 0 -0.41 11 11
SNAP25 0.005 0.036 -9999 0 -0.35 5 5
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.046 0.11 -9999 0 -0.72 8 8
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.021 0.014 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.003 0.025 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.013 0.045 -9999 0 -0.72 2 2
SMAD2 0.018 0.022 -9999 0 -0.28 2 2
SMAD3 0.052 0.021 -9999 0 -10000 0 0
SMAD3/SMAD4 0.063 0.022 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.029 -9999 0 -0.46 2 2
SMAD2/SMAD2/SMAD4 0.023 0.048 -9999 0 -0.34 2 2
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.025 0.033 -9999 0 -0.41 2 2
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
TRAP-1/SMAD4 -0.002 0.033 -9999 0 -0.54 2 2
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.013 0.045 -9999 0 -0.72 2 2
KPNB1 0.016 0.007 -9999 0 -10000 0 0
TGFBRAP1 0.016 0.007 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.015 0.012 -9999 0 -10000 0 0
KPNA2 -0.029 0.072 -9999 0 -10000 0 0
PIAS4 0.015 0.016 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.02 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.021 -9999 0 -10000 0 0
ERC1 0.013 0.022 -9999 0 -10000 0 0
RIP2/NOD2 -0.018 0.035 -9999 0 -10000 0 0
NFKBIA 0.058 0.034 -9999 0 -0.73 1 1
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
RIPK2 0.014 0.02 -9999 0 -10000 0 0
IKBKG 0.009 0.017 -9999 0 -10000 0 0
IKK complex/A20 0.005 0.023 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.014 0.02 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.062 0.007 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.003 0.022 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0.005 -9999 0 -10000 0 0
NOD2 -0.018 0.066 -9999 0 -10000 0 0
NFKB1 0.02 0.005 -9999 0 -10000 0 0
RELA 0.02 0.005 -9999 0 -10000 0 0
MALT1 0.016 0.007 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.002 0.012 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.012 0.025 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.014 -9999 0 -0.31 1 1
BCL10 0.016 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.034 -9999 0 -0.72 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex 0.013 0.03 -9999 0 -10000 0 0
CYLD 0.016 0.007 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.002 0.021 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.003 0.014 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
PRKDC 0.01 0.03 -9999 0 -10000 0 0
ATR 0.016 0 -9999 0 -10000 0 0
UBE2L3 0.016 0 -9999 0 -10000 0 0
FANCD2 0.033 0.002 -9999 0 -10000 0 0
protein ubiquitination 0.022 0.039 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
M/R/N Complex 0 0.004 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
DNA-PK 0.003 0.015 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.016 0.031 -9999 0 -0.41 1 1
FANCF 0.015 0.032 -9999 0 -0.72 1 1
BRCA1 0.012 0.025 -9999 0 -10000 0 0
CCNE1 -0.018 0.066 -9999 0 -10000 0 0
CDK2/Cyclin E1 -0.019 0.038 -9999 0 -10000 0 0
FANCG 0.014 0.017 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.016 -9999 0 -10000 0 0
FANCE 0.015 0.033 -9999 0 -0.72 1 1
FANCC 0.014 0.017 -9999 0 -10000 0 0
NBN 0.016 0.007 -9999 0 -10000 0 0
FANCA -0.024 0.07 -9999 0 -10000 0 0
DNA repair 0.046 0.05 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.004 0.016 -9999 0 -10000 0 0
BARD1/DNA-PK 0.005 0.021 -9999 0 -10000 0 0
FANCL 0.016 0 -9999 0 -10000 0 0
mRNA polyadenylation 0.003 0.014 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.05 0.02 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.004 0.018 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.004 0.019 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.005 0.019 -9999 0 -10000 0 0
BRCA1/BACH1 0.012 0.025 -9999 0 -10000 0 0
BARD1 0.013 0.024 -9999 0 -10000 0 0
PCNA 0.01 0.031 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.004 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.004 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.052 0.051 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.006 0.022 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.016 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.001 0.041 -9999 0 -0.41 4 4
FA complex 0.048 0.02 -9999 0 -0.28 1 1
BARD1/EWS -0.002 0.012 -9999 0 -10000 0 0
RBBP8 0.025 0.05 -9999 0 -0.54 4 4
TP53 0.016 0.01 -9999 0 -10000 0 0
TOPBP1 0.015 0.012 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.004 0.019 -9999 0 -10000 0 0
BRCA1/BARD1 0.024 0.042 -9999 0 -10000 0 0
CSTF1 0.015 0.016 -9999 0 -10000 0 0
BARD1/EWS-Fli1 -0.002 0.014 -9999 0 -10000 0 0
CDK2 0.013 0.024 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.078 0.08 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.016 -9999 0 -10000 0 0
EWSR1 0.016 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.051 -9999 0 -10000 0 0
CLOCK 0.02 0.002 -9999 0 -10000 0 0
TIMELESS/CRY2 0.051 0.016 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.024 -9999 0 -0.53 1 1
ATR 0.016 0 -9999 0 -10000 0 0
NR1D1 0.052 0.012 -9999 0 -10000 0 0
ARNTL 0.019 0.032 -9999 0 -0.72 1 1
TIMELESS 0.049 0.021 -9999 0 -10000 0 0
NPAS2 0.017 0.022 -9999 0 -10000 0 0
CRY2 0.016 0 -9999 0 -10000 0 0
mol:CO -0.016 0.006 -9999 0 -10000 0 0
CHEK1 -0.053 0.08 -9999 0 -10000 0 0
mol:HEME 0.016 0.006 -9999 0 -10000 0 0
PER1 0.002 0.1 -9999 0 -0.72 10 10
BMAL/CLOCK/NPAS2 0.05 0.028 -9999 0 -0.44 1 1
BMAL1/CLOCK 0.065 0.032 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.051 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.052 -9999 0 -10000 0 0
mol:NADPH 0.016 0.006 -9999 0 -10000 0 0
PER1/TIMELESS 0.043 0.063 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.015 0.012 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.016 0 -9999 0 -9999 0 0
ITGB7 0.016 0 -9999 0 -9999 0 0
ITGA4 0.01 0.032 -9999 0 -9999 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -9999 0 0
alpha4/beta1 Integrin -0.003 0.015 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.002 0.046 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.021 0.038 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.002 0.028 -9999 0 -0.64 1 1
AURKB -0.014 0.063 -9999 0 -10000 0 0
AURKC 0.013 0.022 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.005 0.011 -9999 0 -10000 0 0
BUB1B 0.005 0.023 -9999 0 -10000 0 0
PLK1 0.017 0.011 -9999 0 -10000 0 0
PLK1S1 0.008 0.007 -9999 0 -10000 0 0
KIF2A 0.026 0.01 -9999 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.011 -9999 0 -10000 0 0
GOLGA2 0.016 0.01 -9999 0 -10000 0 0
Hec1/SPC24 0.031 0.042 -9999 0 -10000 0 0
WEE1 0.019 0.052 -9999 0 -0.55 4 4
cytokinesis 0.016 0.023 -9999 0 -10000 0 0
PP2A-alpha B56 0.067 0.027 -9999 0 -10000 0 0
AURKA 0.02 0.005 -9999 0 -10000 0 0
PICH/PLK1 -0.032 0.088 -9999 0 -0.32 3 3
CENPE -0.011 0.045 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.026 0.01 -9999 0 -10000 0 0
PPP2CA 0.016 0 -9999 0 -10000 0 0
FZR1 0.016 0.007 -9999 0 -10000 0 0
TPX2 0.019 0.006 -9999 0 -10000 0 0
PAK1 -0.011 0.058 -9999 0 -10000 0 0
SPC24 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
CLSPN 0.018 0.006 -9999 0 -10000 0 0
GORASP1 0.016 0 -9999 0 -10000 0 0
metaphase -0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.008 0.007 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
STAG2 0.016 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.015 0.013 -9999 0 -10000 0 0
spindle elongation 0.017 0.011 -9999 0 -10000 0 0
ODF2 0.013 0.015 -9999 0 -10000 0 0
BUB1 0.057 0.027 -9999 0 -10000 0 0
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.025 0.005 -9999 0 -10000 0 0
CDC25B 0.005 0.045 -9999 0 -10000 0 0
SGOL1 0.005 0.011 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.065 0.071 -9999 0 -0.32 4 4
CDC14B 0 0.089 -9999 0 -0.56 13 13
CDC20 -0.04 0.077 -9999 0 -10000 0 0
PLK1/PBIP1 -0.024 0.027 -9999 0 -10000 0 0
mitosis -0.004 0.005 -9999 0 -10000 0 0
FBXO5 0.017 0.017 -9999 0 -10000 0 0
CDC2 -0.064 0.08 -9999 0 -10000 0 0
NDC80 -0.077 0.08 -9999 0 -10000 0 0
metaphase plate congression 0.016 0.007 -9999 0 -10000 0 0
ERCC6L -0.027 0.069 -9999 0 -0.37 3 3
NLP/gamma Tubulin 0.013 0.007 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0.016 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 0.061 0.075 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.002 0.008 -9999 0 -10000 0 0
RAB1A 0.016 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.012 -9999 0 -10000 0 0
mitotic prometaphase 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.04 -9999 0 -10000 0 0
microtubule-based process 0.046 0.042 -9999 0 -10000 0 0
Golgi organization 0.017 0.011 -9999 0 -10000 0 0
Cohesin/SA2 0 0.002 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -9999 0 -10000 0 0
KIF20A -0.09 0.077 -9999 0 -10000 0 0
APC/C/CDC20 0.032 0.036 -9999 0 -10000 0 0
PPP2R1A 0.016 0.007 -9999 0 -10000 0 0
chromosome segregation -0.024 0.026 -9999 0 -10000 0 0
PRC1 -0.065 0.081 -9999 0 -10000 0 0
ECT2 0.003 0.041 -9999 0 -10000 0 0
C13orf34 0.02 0.011 -9999 0 -10000 0 0
NUDC 0.016 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.005 0.023 -9999 0 -10000 0 0
spindle assembly 0.016 0.01 -9999 0 -10000 0 0
spindle stabilization 0.008 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.01 0.077 -9999 0 -0.47 13 13
MKLP2/PLK1 0.047 0.042 -9999 0 -10000 0 0
CCNB1 -0.046 0.078 -9999 0 -10000 0 0
PPP1CB 0.016 0 -9999 0 -10000 0 0
BTRC 0.013 0.023 -9999 0 -10000 0 0
ROCK2 0.026 0.024 -9999 0 -0.49 1 1
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.018 0.034 -9999 0 -0.32 4 4
MLF1IP -0.041 0.055 -9999 0 -10000 0 0
INCENP 0.002 0.046 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.004 0.04 -9999 0 -9999 0 0
TP53 -0.003 0.013 -9999 0 -9999 0 0
Senescence -0.003 0.013 -9999 0 -9999 0 0
Apoptosis -0.003 0.013 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.007 0.026 -9999 0 -9999 0 0
MDM4 0.015 0.016 -9999 0 -9999 0 0
Glypican 2 network

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
MDK 0.004 0.043 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.007 0.025 -9999 0 -9999 0 0
neuron projection morphogenesis -0.007 0.025 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -9999 0 -9999 0 0
MDM2/SUMO1 0.039 0.008 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.022 0.002 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.036 0.003 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0.007 -9999 0 -9999 0 0
SUMO1/HDAC4 0.038 0.002 -9999 0 -9999 0 0
SUMO1/HDAC1 0.038 0.002 -9999 0 -9999 0 0
RANGAP1 0.01 0.031 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.002 0.014 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.027 0.003 -9999 0 -9999 0 0
Ran/GTP 0.001 0.004 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.012 0.025 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.001 0.006 -9999 0 -9999 0 0
NPC 0 0.003 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0.007 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.016 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.016 0.01 -9999 0 -10000 0 0
TCEB1 0.014 0.019 -9999 0 -10000 0 0
HIF1A/p53 0.041 0.029 -9999 0 -0.26 4 4
HIF1A 0.032 0.03 -9999 0 -0.28 4 4
COPS5 0.016 0.007 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.004 0.019 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.011 0.061 -9999 0 -10000 0 0
ARNT/IPAS 0 0 -9999 0 -10000 0 0
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.041 0.029 -9999 0 -0.27 2 2
CUL2 0.016 0.007 -9999 0 -10000 0 0
OS9 0.016 0.01 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.001 0.01 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.041 0.029 -9999 0 -0.27 2 2
PHD1-3/OS9 0.018 0.041 -9999 0 -0.41 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.001 0.024 -9999 0 -10000 0 0
VHL 0.012 0.027 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
HIF1A/JAB1 0.041 0.029 -9999 0 -0.27 2 2
EGLN3 -0.017 0.071 -9999 0 -0.72 1 1
EGLN2 0.014 0.017 -9999 0 -10000 0 0
EGLN1 0.015 0.016 -9999 0 -10000 0 0
TP53 0.016 0.01 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.05 0.009 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0.015 0.012 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF 0.048 0.035 -9999 0 -0.27 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.003 0.035 -10000 0 -0.4 4 4
MAPK9 0.011 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.013 0.015 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.021 -10000 0 -0.47 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
Gs family/GTP -0.003 0.033 -10000 0 -0.44 3 3
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 0.001 0.008 0.1 3 -10000 0 3
GNAL 0.012 0.056 -10000 0 -0.72 3 3
GNG2 0.015 0.032 -10000 0 -0.72 1 1
CRH 0.013 0.022 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.01 0.019 -10000 0 -0.42 1 1
MAPK11 0.011 0 -10000 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 0.001 0.005 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.006 -9999 0 -10000 0 0
AP2 -0.001 0.01 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.008 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.032 0.001 -9999 0 -10000 0 0
CD4 0.016 0 -9999 0 -10000 0 0
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
ARFGAP1 0.013 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.011 -9999 0 -0.23 1 1
ARF1/GTP -0.001 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.034 0.006 -9999 0 -10000 0 0
mol:Choline 0 0.011 -9999 0 -0.24 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0.01 -9999 0 -10000 0 0
DDEF1 0 0.011 -9999 0 -0.24 1 1
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.016 0.01 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.004 -9999 0 -10000 0 0
Rac/GTP 0 0.002 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.009 -9999 0 -10000 0 0
ARFIP2 0.013 0.017 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.03 0.004 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.004 -9999 0 -10000 0 0
GGA3 0.016 0.007 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.005 -9999 0 -10000 0 0
AP2A1 0.015 0.014 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.034 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.006 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP -0.001 0.007 -9999 0 -10000 0 0
CYTH2 0.001 0.002 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.001 0.006 -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 0.045 0.002 -9999 0 -10000 0 0
PLD2 0 0.011 -9999 0 -0.24 1 1
ARF-GAP1/v-SNARE 0.013 0.012 -9999 0 -10000 0 0
PIP5K1A 0 0.011 -9999 0 -0.23 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.007 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.011 -9999 0 -0.24 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.013 0.012 -9999 0 -10000 0 0
GOSR2 0 0.005 -9999 0 -10000 0 0
USO1 0 0.005 -9999 0 -10000 0 0
GBF1 0 0.005 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.01 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0.009 -9999 0 -10000 0 0
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 -0.001 0.023 -9999 0 -0.54 1 1
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
NF kappa B2 p100/RelB 0.002 0.022 -9999 0 -0.38 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.012 -9999 0 -10000 0 0
RELB 0.013 0.024 -9999 0 -10000 0 0
NFKB2 0.015 0.012 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.001 0.013 -9999 0 -10000 0 0
regulation of B cell activation 0.001 0.012 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 526 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.E2.A1BD TCGA.E2.A1BC TCGA.E2.A1B6 TCGA.E2.A1B5
109_MAP3K5 0.07 0.07 0.073 0.073
47_PPARGC1A 0.016 0.016 0.016 -0.15
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 0.016 0.016 0.016
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0 0 -0.41 0.087
30_TGFB1/TGF beta receptor Type II 0.016 0.015 0.015 0.016
84_STAT5B -0.25 -0.045 -0.037 -0.25
84_STAT5A -0.25 -0.045 -0.037 -0.25
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/5948102/GDAC_MergeDataFiles_3799172/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.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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