PARADIGM pathway analysis of mRNASeq expression data
Pancreatic Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C12806HN
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 46 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
FOXA2 and FOXA3 transcription factor networks 39
Nephrin/Neph1 signaling in the kidney podocyte 36
IL23-mediated signaling events 36
HIF-1-alpha transcription factor network 35
Signaling events mediated by the Hedgehog family 28
amb2 Integrin signaling 25
IL4-mediated signaling events 24
TCGA08_retinoblastoma 22
TCR signaling in naïve CD8+ T cells 21
BCR signaling pathway 21
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 178 . 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 ( 178 ).

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
FOXA2 and FOXA3 transcription factor networks 0.2191 39 1810 46 -0.79 0.026 1000 -1000 -0.077 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.2022 36 1239 34 -0.27 0.016 1000 -1000 -0.056 -1000
IL23-mediated signaling events 0.2022 36 2209 60 -0.78 0.018 1000 -1000 -0.17 -1000
HIF-1-alpha transcription factor network 0.1966 35 2691 76 -0.68 0.025 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.1573 28 1457 52 -0.42 0.11 1000 -1000 -0.062 -1000
amb2 Integrin signaling 0.1404 25 2076 82 -0.28 0.022 1000 -1000 -0.094 -1000
IL4-mediated signaling events 0.1348 24 2191 91 -0.73 0.54 1000 -1000 -0.14 -1000
TCGA08_retinoblastoma 0.1236 22 176 8 -0.14 0.068 1000 -1000 -0.02 -1000
TCR signaling in naïve CD8+ T cells 0.1180 21 2002 93 -0.22 0.1 1000 -1000 -0.083 -1000
BCR signaling pathway 0.1180 21 2136 99 -0.32 0.027 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.1180 21 1409 67 -0.27 0.039 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.1124 20 1817 87 -0.34 0.052 1000 -1000 -0.14 -1000
Calcium signaling in the CD4+ TCR pathway 0.1067 19 615 31 -0.46 0.016 1000 -1000 -0.095 -1000
Syndecan-1-mediated signaling events 0.1011 18 620 34 -0.24 0.016 1000 -1000 -0.068 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1011 18 1276 68 -0.55 0.12 1000 -1000 -0.14 -1000
Endothelins 0.0955 17 1676 96 -0.23 0.041 1000 -1000 -0.097 -1000
IGF1 pathway 0.0955 17 981 57 -0.22 0.033 1000 -1000 -0.11 -1000
JNK signaling in the CD4+ TCR pathway 0.0899 16 277 17 -0.11 0.016 1000 -1000 -0.044 -1000
p75(NTR)-mediated signaling 0.0899 16 2096 125 -0.45 0.049 1000 -1000 -0.12 -1000
Glypican 1 network 0.0899 16 815 48 -0.41 0.033 1000 -1000 -0.051 -1000
IL6-mediated signaling events 0.0899 16 1225 75 -0.32 0.067 1000 -1000 -0.095 -1000
Osteopontin-mediated events 0.0787 14 543 38 -0.22 0.016 1000 -1000 -0.12 -1000
Thromboxane A2 receptor signaling 0.0787 14 1499 105 -0.17 0.035 1000 -1000 -0.078 -1000
a4b1 and a4b7 Integrin signaling 0.0787 14 70 5 -0.061 0.001 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 0.0787 14 1075 76 -0.28 0.031 1000 -1000 -0.091 -1000
Glucocorticoid receptor regulatory network 0.0787 14 1656 114 -0.56 0.18 1000 -1000 -0.089 -1000
Ras signaling in the CD4+ TCR pathway 0.0730 13 237 17 -0.097 0.027 1000 -1000 -0.045 -1000
Visual signal transduction: Cones 0.0674 12 476 38 -0.16 0.016 1000 -1000 -0.074 -1000
TCGA08_p53 0.0674 12 86 7 -0.1 0.06 1000 -1000 -0.013 -1000
Integrins in angiogenesis 0.0674 12 1023 84 -0.22 0.026 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0618 11 707 62 -0.19 0.02 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.0618 11 1136 97 -0.18 0.034 1000 -1000 -0.096 -1000
Reelin signaling pathway 0.0618 11 651 56 -0.19 0.029 1000 -1000 -0.1 -1000
IL27-mediated signaling events 0.0618 11 587 51 -0.16 0.073 1000 -1000 -0.082 -1000
Wnt signaling 0.0618 11 82 7 -0.12 -0.007 1000 -1000 -0.027 -1000
Class IB PI3K non-lipid kinase events 0.0618 11 33 3 -0.026 -1000 1000 -1000 -0.015 -1000
FOXM1 transcription factor network 0.0618 11 606 51 -0.18 0.095 1000 -1000 -0.19 -1000
Noncanonical Wnt signaling pathway 0.0562 10 267 26 -0.12 0.016 1000 -1000 -0.064 -1000
Syndecan-2-mediated signaling events 0.0562 10 743 69 -0.2 0.044 1000 -1000 -0.04 -1000
BMP receptor signaling 0.0562 10 843 81 -0.24 0.06 1000 -1000 -0.11 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0562 10 521 52 -0.24 0.038 1000 -1000 -0.054 -1000
Effects of Botulinum toxin 0.0562 10 276 26 -0.098 0.016 1000 -1000 -0.076 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0562 10 1219 120 -0.45 0.066 1000 -1000 -0.1 -1000
Visual signal transduction: Rods 0.0562 10 536 52 -0.23 0.016 1000 -1000 -0.098 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0506 9 365 37 -0.17 0.024 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.0506 9 197 21 -0.17 0.024 1000 -1000 -0.078 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0449 8 440 54 -0.15 0.032 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0449 8 60 7 -0.02 0.005 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 0.0449 8 348 39 -0.16 0.017 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0449 8 549 62 -0.23 0.072 1000 -1000 -0.12 -1000
FAS signaling pathway (CD95) 0.0449 8 384 47 -0.14 0.021 1000 -1000 -0.053 -1000
LPA receptor mediated events 0.0449 8 876 102 -0.13 0.04 1000 -1000 -0.1 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0449 8 721 88 -0.14 0.066 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 0.0393 7 548 76 -0.48 0.081 1000 -1000 -0.044 -1000
ErbB4 signaling events 0.0393 7 528 69 -0.47 0.16 1000 -1000 -0.11 -1000
Presenilin action in Notch and Wnt signaling 0.0393 7 449 61 -0.37 0.05 1000 -1000 -0.092 -1000
Signaling mediated by p38-alpha and p38-beta 0.0393 7 318 44 -0.27 0.016 1000 -1000 -0.064 -1000
Canonical Wnt signaling pathway 0.0393 7 384 51 -0.37 0.046 1000 -1000 -0.069 -1000
Nongenotropic Androgen signaling 0.0393 7 386 52 -0.041 0.02 1000 -1000 -0.074 -1000
Regulation of Androgen receptor activity 0.0393 7 547 70 -0.56 0.059 1000 -1000 -0.068 -1000
LPA4-mediated signaling events 0.0337 6 81 12 -0.058 0.021 1000 -1000 -0.029 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0337 6 577 85 -0.12 0.032 1000 -1000 -0.081 -1000
EPO signaling pathway 0.0337 6 371 55 -0.14 0.016 1000 -1000 -0.11 -1000
Ceramide signaling pathway 0.0337 6 462 76 -0.22 0.044 1000 -1000 -0.049 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0337 6 498 83 -0.55 0.061 1000 -1000 -0.081 -1000
FoxO family signaling 0.0337 6 405 64 -0.55 0.12 1000 -1000 -0.078 -1000
Syndecan-3-mediated signaling events 0.0337 6 226 35 -0.11 0.049 1000 -1000 -0.051 -1000
Regulation of p38-alpha and p38-beta 0.0337 6 341 54 -0.21 0.042 1000 -1000 -0.071 -1000
Class I PI3K signaling events 0.0337 6 490 73 -0.21 0.036 1000 -1000 -0.076 -1000
Insulin Pathway 0.0337 6 504 74 -0.23 0.042 1000 -1000 -0.1 -1000
Plasma membrane estrogen receptor signaling 0.0337 6 544 86 -0.22 0.032 1000 -1000 -0.1 -1000
Rapid glucocorticoid signaling 0.0337 6 123 20 -0.17 0.016 1000 -1000 -0.025 -1000
Aurora B signaling 0.0337 6 445 67 -0.15 0.018 1000 -1000 -0.078 -1000
Caspase cascade in apoptosis 0.0281 5 377 74 -0.15 0.026 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0281 5 141 28 -0.034 0.03 1000 -1000 -0.045 -1000
Insulin-mediated glucose transport 0.0281 5 172 32 -0.55 0.037 1000 -1000 -0.067 -1000
mTOR signaling pathway 0.0281 5 272 53 -0.24 0.046 1000 -1000 -0.068 -1000
Signaling events regulated by Ret tyrosine kinase 0.0281 5 443 82 -0.058 0.016 1000 -1000 -0.1 -1000
HIF-2-alpha transcription factor network 0.0281 5 255 43 -0.081 0.031 1000 -1000 -0.083 -1000
S1P1 pathway 0.0281 5 215 36 -0.23 0.016 1000 -1000 -0.068 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0281 5 268 45 -0.15 0.038 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0281 5 509 97 -0.15 0.063 1000 -1000 -0.089 -1000
S1P4 pathway 0.0281 5 135 25 -0.034 0.024 1000 -1000 -0.048 -1000
Regulation of nuclear SMAD2/3 signaling 0.0225 4 640 136 -0.12 0.064 1000 -1000 -0.082 -1000
PLK1 signaling events 0.0225 4 352 85 -0.056 0.036 1000 -1000 -0.05 -1000
PDGFR-alpha signaling pathway 0.0225 4 189 44 -0.12 0.034 1000 -1000 -0.078 -1000
S1P5 pathway 0.0225 4 81 17 -0.034 0.016 1000 -1000 -0.048 -1000
ceramide signaling pathway 0.0225 4 217 49 -0.15 0.024 1000 -1000 -0.049 -1000
Retinoic acid receptors-mediated signaling 0.0225 4 240 58 -0.16 0.033 1000 -1000 -0.09 -1000
IL2 signaling events mediated by PI3K 0.0225 4 282 58 -0.075 0.041 1000 -1000 -0.095 -1000
EPHB forward signaling 0.0225 4 352 85 -0.069 0.049 1000 -1000 -0.11 -1000
Glypican 2 network 0.0225 4 18 4 -0.007 0.007 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0225 4 355 74 -0.22 0.07 1000 -1000 -0.11 -1000
IL2 signaling events mediated by STAT5 0.0225 4 88 22 -0.089 0.033 1000 -1000 -0.052 -1000
Regulation of Telomerase 0.0225 4 435 102 -0.2 0.059 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0225 4 149 33 -0.14 0.047 1000 -1000 -0.054 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0225 4 362 78 -0.14 0.085 1000 -1000 -0.089 -1000
ErbB2/ErbB3 signaling events 0.0169 3 219 65 -0.033 0.037 1000 -1000 -0.085 -1000
Canonical NF-kappaB pathway 0.0169 3 130 39 -0.15 0.086 1000 -1000 -0.096 -1000
BARD1 signaling events 0.0169 3 217 57 -0.036 0.056 1000 -1000 -0.068 -1000
PLK2 and PLK4 events 0.0169 3 10 3 -0.003 0.016 1000 -1000 -0.023 -1000
Arf6 downstream pathway 0.0169 3 143 43 -0.023 0.026 1000 -1000 -0.04 -1000
Aurora C signaling 0.0169 3 21 7 -0.022 0.012 1000 -1000 -0.038 -1000
TRAIL signaling pathway 0.0169 3 159 48 -0.021 0.047 1000 -1000 -0.08 -1000
Ephrin B reverse signaling 0.0169 3 162 48 -0.057 0.02 1000 -1000 -0.089 -1000
Signaling events mediated by HDAC Class I 0.0169 3 334 104 -0.15 0.062 1000 -1000 -0.072 -1000
Paxillin-dependent events mediated by a4b1 0.0169 3 108 36 -0.072 0.033 1000 -1000 -0.084 -1000
S1P3 pathway 0.0169 3 163 42 -0.032 0.031 1000 -1000 -0.058 -1000
Hedgehog signaling events mediated by Gli proteins 0.0112 2 180 65 -0.053 0.066 1000 -1000 -0.075 -1000
Aurora A signaling 0.0112 2 128 60 -0.027 0.04 1000 -1000 -0.043 -1000
Class I PI3K signaling events mediated by Akt 0.0112 2 198 68 -0.55 0.06 1000 -1000 -0.068 -1000
Nectin adhesion pathway 0.0112 2 167 63 -0.034 0.055 1000 -1000 -0.087 -1000
Atypical NF-kappaB pathway 0.0112 2 89 31 -0.034 0.041 1000 -1000 -0.052 -1000
TCGA08_rtk_signaling 0.0112 2 72 26 -0.068 0.054 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0112 2 70 34 -0.041 0.045 1000 -1000 -0.044 -1000
p38 MAPK signaling pathway 0.0112 2 125 44 -0.1 0.032 1000 -1000 -0.071 -1000
Alternative NF-kappaB pathway 0.0112 2 28 13 -0.003 0.03 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class II 0.0056 1 126 75 -0.036 0.041 1000 -1000 -0.057 -1000
Circadian rhythm pathway 0.0056 1 32 22 -0.014 0.053 1000 -1000 -0.054 -1000
IFN-gamma pathway 0.0056 1 129 68 -0.1 0.077 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class III 0.0056 1 77 40 -0.026 0.027 1000 -1000 -0.042 -1000
Signaling mediated by p38-gamma and p38-delta 0.0056 1 27 15 0 0.035 1000 -1000 -0.032 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0056 1 246 125 -0.034 0.09 1000 -1000 -0.11 -1000
Arf6 trafficking events 0.0056 1 120 71 -0.17 0.052 1000 -1000 -0.094 -1000
E-cadherin signaling events 0.0056 1 5 5 0.012 0.028 1000 -1000 -0.033 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.001 0.056 1000 -1000 -0.06 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 69 76 -0.014 0.071 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.042 1000 -1000 -0.067 -1000
VEGFR1 specific signals 0.0000 0 38 56 -0.014 0.073 1000 -1000 -0.066 -1000
E-cadherin signaling in keratinocytes 0.0000 0 22 43 -0.051 0.055 1000 -1000 -0.073 -1000
Arf1 pathway 0.0000 0 30 54 -0.041 0.033 1000 -1000 -0.04 -1000
Total NA 1113 68034 7203 -25 -990 131000 -131000 -9.8 -131000
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.55 -9999 0 -1.2 47 47
PCK1 -0.53 0.38 -9999 0 -0.91 73 73
HNF4A -0.56 0.62 -9999 0 -1.3 62 62
KCNJ11 -0.47 0.61 -9999 0 -1.3 46 46
AKT1 -0.18 0.18 -9999 0 -0.46 4 4
response to starvation -0.019 0.036 -9999 0 -10000 0 0
DLK1 -0.58 0.69 -9999 0 -1.4 64 64
NKX2-1 0.017 0.21 -9999 0 -10000 0 0
ACADM -0.46 0.55 -9999 0 -1.2 47 47
TAT -0.35 0.36 -9999 0 -0.93 31 31
CEBPB 0.001 0.028 -9999 0 -10000 0 0
CEBPA -0.066 0.2 -9999 0 -0.68 17 17
TTR -0.79 0.54 -9999 0 -1.1 109 109
PKLR -0.48 0.57 -9999 0 -1.3 50 50
APOA1 -0.61 0.65 -9999 0 -1.4 62 62
CPT1C -0.46 0.56 -9999 0 -1.2 48 48
ALAS1 -0.065 0.16 -9999 0 -10000 0 0
TFRC -0.36 0.36 -9999 0 -0.9 31 31
FOXF1 0.005 0.088 -9999 0 -0.66 3 3
NF1 0.026 0.002 -9999 0 -10000 0 0
HNF1A (dimer) -0.038 0.16 -9999 0 -0.69 8 8
CPT1A -0.46 0.55 -9999 0 -1.2 47 47
HMGCS1 -0.45 0.55 -9999 0 -1.2 50 50
NR3C1 -0.053 0.12 -9999 0 -0.69 4 4
CPT1B -0.48 0.57 -9999 0 -1.2 58 58
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.017 0.03 -9999 0 -10000 0 0
GCK -0.51 0.63 -9999 0 -1.4 52 52
CREB1 -0.047 0.063 -9999 0 -10000 0 0
IGFBP1 -0.29 0.33 -9999 0 -0.76 36 36
PDX1 -0.28 0.49 -9999 0 -1.6 17 17
UCP2 -0.46 0.55 -9999 0 -1.2 48 48
ALDOB -0.52 0.64 -9999 0 -1.4 53 53
AFP -0.4 0.27 -9999 0 -0.7 63 63
BDH1 -0.46 0.55 -9999 0 -1.2 51 51
HADH -0.44 0.56 -9999 0 -1.3 43 43
F2 -0.57 0.65 -9999 0 -1.4 58 58
HNF1A -0.038 0.16 -9999 0 -0.69 8 8
G6PC -0.39 0.53 -9999 0 -1.3 42 42
SLC2A2 -0.47 0.65 -9999 0 -1.5 45 45
INS -0.19 0.34 -9999 0 -0.63 66 66
FOXA1 -0.56 0.33 -9999 0 -0.77 124 124
FOXA3 -0.24 0.28 -9999 0 -0.77 34 34
FOXA2 -0.52 0.65 -9999 0 -1.3 54 54
ABCC8 -0.59 0.69 -9999 0 -1.4 60 60
ALB -0.65 0.53 -9999 0 -1 95 95
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.23 0.28 0.53 82 -10000 0 82
KIRREL -0.07 0.2 -10000 0 -0.69 16 16
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.24 0.28 -10000 0 -0.53 82 82
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.012 0.051 -10000 0 -0.67 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.19 0.23 -10000 0 -0.4 89 89
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.15 0.19 -10000 0 -0.58 9 9
FYN -0.18 0.22 -10000 0 -0.38 89 89
mol:Ca2+ -0.2 0.21 -10000 0 -0.42 55 55
mol:DAG -0.19 0.22 -10000 0 -0.42 55 55
NPHS2 -0.067 0.17 -10000 0 -0.68 12 12
mol:IP3 -0.19 0.22 -10000 0 -0.42 55 55
regulation of endocytosis -0.16 0.21 -10000 0 -0.65 10 10
Nephrin/NEPH1/podocin/Cholesterol -0.2 0.23 -10000 0 -0.41 91 91
establishment of cell polarity -0.23 0.28 -10000 0 -0.53 82 82
Nephrin/NEPH1/podocin/NCK1-2 -0.16 0.21 -10000 0 -0.65 9 9
Nephrin/NEPH1/beta Arrestin2 -0.16 0.21 -10000 0 -0.66 10 10
NPHS1 -0.27 0.34 -10000 0 -0.68 71 71
Nephrin/NEPH1/podocin -0.18 0.22 -10000 0 -0.38 89 89
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.19 0.23 -10000 0 -0.42 55 55
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.19 0.23 -10000 0 -0.42 55 55
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.18 0.22 -10000 0 -0.7 12 12
cytoskeleton organization -0.18 0.24 -10000 0 -0.45 46 46
Nephrin/NEPH1 -0.17 0.21 -10000 0 -0.39 82 82
Nephrin/NEPH1/ZO-1 -0.18 0.23 -10000 0 -0.42 82 82
IL23-mediated signaling events

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
CCL2 -0.7 0.76 -10000 0 -1.4 85 85
IL23A -0.54 0.69 -10000 0 -1.4 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.58 0.63 -10000 0 -1.4 60 60
positive regulation of T cell mediated cytotoxicity -0.62 0.82 -10000 0 -1.6 62 62
ITGA3 -0.5 0.65 -10000 0 -1.3 56 56
IL17F -0.3 0.41 -10000 0 -0.8 54 54
IL12B -0.036 0.18 -10000 0 -0.7 12 12
STAT1 (dimer) -0.58 0.76 -10000 0 -1.5 62 62
CD4 -0.5 0.66 -10000 0 -1.4 54 54
IL23 -0.53 0.67 -10000 0 -1.3 62 62
IL23R -0.074 0.2 -10000 0 -0.71 12 12
IL1B -0.56 0.72 -10000 0 -1.5 58 58
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.51 0.64 -10000 0 -1.3 58 58
TYK2 0.008 0.025 -10000 0 -10000 0 0
STAT4 -0.026 0.16 -10000 0 -0.67 11 11
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.087 0.24 -10000 0 -0.67 27 27
IL12RB1 -0.055 0.21 -10000 0 -0.7 16 16
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
IL12Rbeta1/TYK2 -0.038 0.16 -10000 0 -0.54 16 16
IL23R/JAK2 -0.08 0.21 -10000 0 -0.7 12 12
positive regulation of chronic inflammatory response -0.62 0.82 -10000 0 -1.6 62 62
natural killer cell activation 0.006 0.017 0.058 12 -10000 0 12
JAK2 0.018 0.03 -10000 0 -10000 0 0
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
NFKB1 0.014 0.005 -10000 0 -10000 0 0
RELA 0.014 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.49 0.62 -10000 0 -1.2 62 62
ALOX12B -0.53 0.66 -10000 0 -1.4 57 57
CXCL1 -0.53 0.69 -10000 0 -1.4 61 61
T cell proliferation -0.62 0.82 -10000 0 -1.6 62 62
NFKBIA 0.014 0.005 -10000 0 -10000 0 0
IL17A -0.21 0.33 -10000 0 -0.6 47 47
PI3K -0.6 0.64 -10000 0 -1.4 64 64
IFNG -0.014 0.044 -10000 0 -0.13 7 7
STAT3 (dimer) -0.56 0.59 -10000 0 -1.3 62 62
IL18R1 0.009 0.072 -10000 0 -0.67 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.27 0.42 -10000 0 -0.95 30 30
IL18/IL18R -0.051 0.2 -10000 0 -0.46 32 32
macrophage activation -0.024 0.02 -10000 0 -0.046 50 50
TNF -0.6 0.76 -10000 0 -1.5 63 63
STAT3/STAT4 -0.61 0.65 -10000 0 -1.4 66 66
STAT4 (dimer) -0.59 0.77 -10000 0 -1.5 62 62
IL18 -0.01 0.13 -10000 0 -0.67 7 7
IL19 -0.51 0.65 -10000 0 -1.3 56 56
STAT5A (dimer) -0.58 0.76 -10000 0 -1.5 60 60
STAT1 0.012 0.051 -10000 0 -0.67 1 1
SOCS3 0.005 0.088 -10000 0 -0.67 3 3
CXCL9 -0.62 0.75 -10000 0 -1.5 71 71
MPO -0.5 0.66 -10000 0 -1.3 59 59
positive regulation of humoral immune response -0.62 0.82 -10000 0 -1.6 62 62
IL23/IL23R/JAK2/TYK2 -0.78 1.1 -10000 0 -2.1 62 62
IL6 -0.54 0.66 -10000 0 -1.4 58 58
STAT5A 0.012 0.051 -10000 0 -0.67 1 1
IL2 0.005 0.072 -10000 0 -0.66 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.017 0.058 12 -10000 0 12
CD3E -0.52 0.68 -10000 0 -1.4 59 59
keratinocyte proliferation -0.62 0.82 -10000 0 -1.6 62 62
NOS2 -0.5 0.64 -10000 0 -1.3 54 54
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.49 0.63 -9999 0 -1.3 48 48
HDAC7 0.014 0.01 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.37 0.5 -9999 0 -1 50 50
SMAD4 0.018 0 -9999 0 -10000 0 0
ID2 -0.49 0.63 -9999 0 -1.3 49 49
AP1 -0.077 0.21 -9999 0 -0.49 36 36
ABCG2 -0.49 0.64 -9999 0 -1.4 49 49
HIF1A -0.047 0.098 -9999 0 -0.83 1 1
TFF3 -0.68 0.66 -9999 0 -1.4 67 67
GATA2 0.01 0.074 -9999 0 -0.68 2 2
AKT1 -0.054 0.092 -9999 0 -10000 0 0
response to hypoxia -0.078 0.097 -9999 0 -0.27 1 1
MCL1 -0.49 0.63 -9999 0 -1.4 46 46
NDRG1 -0.5 0.64 -9999 0 -1.4 46 46
SERPINE1 -0.5 0.64 -9999 0 -1.4 47 47
FECH -0.49 0.63 -9999 0 -1.4 46 46
FURIN -0.49 0.63 -9999 0 -1.4 46 46
NCOA2 -0.029 0.16 -9999 0 -0.67 11 11
EP300 -0.061 0.14 -9999 0 -0.38 14 14
HMOX1 -0.51 0.66 -9999 0 -1.4 53 53
BHLHE40 -0.49 0.63 -9999 0 -1.4 48 48
BHLHE41 -0.49 0.63 -9999 0 -1.4 47 47
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.037 0.088 -9999 0 -0.52 2 2
ENG 0 0.11 -9999 0 -0.52 1 1
JUN 0.013 0.052 -9999 0 -0.68 1 1
RORA -0.49 0.64 -9999 0 -1.4 47 47
ABCB1 -0.23 0.44 -9999 0 -1.4 22 22
TFRC -0.49 0.63 -9999 0 -1.3 48 48
CXCR4 -0.5 0.64 -9999 0 -1.4 49 49
TF -0.56 0.66 -9999 0 -1.4 58 58
CITED2 -0.49 0.63 -9999 0 -1.4 48 48
HIF1A/ARNT -0.66 1 -9999 0 -1.8 57 57
LDHA -0.073 0.19 -9999 0 -1.5 3 3
ETS1 -0.49 0.63 -9999 0 -1.4 48 48
PGK1 -0.49 0.63 -9999 0 -1.3 48 48
NOS2 -0.51 0.64 -9999 0 -1.4 47 47
ITGB2 -0.53 0.68 -9999 0 -1.4 55 55
ALDOA -0.49 0.63 -9999 0 -1.4 47 47
Cbp/p300/CITED2 -0.51 0.66 -9999 0 -1.4 48 48
FOS -0.12 0.27 -9999 0 -0.66 35 35
HK2 -0.51 0.66 -9999 0 -1.4 50 50
SP1 0.022 0.017 -9999 0 -10000 0 0
GCK -0.21 0.48 -9999 0 -1.3 24 24
HK1 -0.49 0.63 -9999 0 -1.4 46 46
NPM1 -0.49 0.63 -9999 0 -1.3 48 48
EGLN1 -0.49 0.63 -9999 0 -1.3 49 49
CREB1 0.025 0.003 -9999 0 -10000 0 0
PGM1 -0.49 0.63 -9999 0 -1.4 46 46
SMAD3 0.014 0.051 -9999 0 -0.67 1 1
EDN1 -0.11 0.31 -9999 0 -1.1 10 10
IGFBP1 -0.63 0.65 -9999 0 -1.3 70 70
VEGFA -0.32 0.43 -9999 0 -0.9 43 43
HIF1A/JAB1 -0.029 0.059 -9999 0 -0.63 1 1
CP -0.54 0.67 -9999 0 -1.4 58 58
CXCL12 -0.51 0.66 -9999 0 -1.4 47 47
COPS5 0.013 0.009 -9999 0 -10000 0 0
SMAD3/SMAD4 0.024 0.039 -9999 0 -0.49 1 1
BNIP3 -0.49 0.64 -9999 0 -1.3 49 49
EGLN3 -0.51 0.66 -9999 0 -1.4 50 50
CA9 -0.66 0.68 -9999 0 -1.4 74 74
TERT -0.51 0.65 -9999 0 -1.4 50 50
ENO1 -0.49 0.63 -9999 0 -1.3 51 51
PFKL -0.49 0.63 -9999 0 -1.3 51 51
NCOA1 0.016 0.003 -9999 0 -10000 0 0
ADM -0.55 0.68 -9999 0 -1.4 57 57
ARNT -0.041 0.077 -9999 0 -10000 0 0
HNF4A -0.008 0.12 -9999 0 -0.68 5 5
ADFP -0.5 0.63 -9999 0 -1.3 57 57
SLC2A1 -0.4 0.5 -9999 0 -1 56 56
LEP -0.63 0.67 -9999 0 -1.3 71 71
HIF1A/ARNT/Cbp/p300 -0.38 0.51 -9999 0 -1 49 49
EPO -0.39 0.52 -9999 0 -1.2 41 41
CREBBP -0.061 0.14 -9999 0 -0.38 14 14
HIF1A/ARNT/Cbp/p300/HDAC7 -0.39 0.52 -9999 0 -1.1 52 52
PFKFB3 -0.49 0.63 -9999 0 -1.4 47 47
NT5E -0.51 0.65 -9999 0 -1.4 52 52
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.2 0.32 -10000 0 -1.1 16 16
IHH -0.42 0.32 -10000 0 -0.64 119 119
SHH Np/Cholesterol/GAS1 -0.11 0.23 -10000 0 -0.44 52 52
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.23 0.44 52 -10000 0 52
SMO/beta Arrestin2 -0.15 0.23 -10000 0 -0.75 16 16
SMO -0.16 0.24 -10000 0 -0.78 16 16
AKT1 -0.052 0.11 -10000 0 -0.85 1 1
ARRB2 0.012 0.051 -10000 0 -0.67 1 1
BOC 0.005 0.088 -10000 0 -0.67 3 3
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.16 0.24 -10000 0 -0.76 16 16
STIL -0.2 0.25 -10000 0 -0.6 40 40
DHH N/PTCH2 -0.072 0.22 -10000 0 -0.55 30 30
DHH N/PTCH1 -0.19 0.22 -10000 0 -0.68 18 18
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
DHH -0.03 0.17 -10000 0 -0.67 12 12
PTHLH -0.2 0.34 -10000 0 -1.2 16 16
determination of left/right symmetry -0.16 0.24 -10000 0 -0.76 16 16
PIK3R1 0.016 0 -10000 0 -10000 0 0
skeletal system development -0.19 0.34 -10000 0 -1.1 16 16
IHH N/Hhip -0.3 0.25 -10000 0 -0.45 124 124
DHH N/Hhip -0.061 0.21 -10000 0 -0.56 26 26
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.16 0.24 -10000 0 -0.76 16 16
pancreas development -0.053 0.21 -10000 0 -0.67 18 18
HHAT 0.012 0.051 -10000 0 -0.67 1 1
PI3K 0.021 0.039 -10000 0 -0.49 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.057 0.21 -10000 0 -0.67 19 19
somite specification -0.16 0.24 -10000 0 -0.76 16 16
SHH Np/Cholesterol/PTCH1 -0.22 0.26 -10000 0 -0.64 40 40
SHH Np/Cholesterol/PTCH2 -0.12 0.22 -10000 0 -0.42 58 58
SHH Np/Cholesterol/Megalin -0.12 0.22 -10000 0 -0.42 59 59
SHH -0.095 0.22 -10000 0 -0.49 42 42
catabolic process -0.2 0.2 -10000 0 -0.67 14 14
SMO/Vitamin D3 -0.2 0.27 -10000 0 -0.63 40 40
SHH Np/Cholesterol/Hhip -0.11 0.21 -10000 0 -0.41 55 55
LRP2 -0.079 0.23 -10000 0 -0.66 24 24
receptor-mediated endocytosis -0.21 0.27 -10000 0 -0.76 21 21
SHH Np/Cholesterol/BOC -0.073 0.19 -10000 0 -0.4 43 43
SHH Np/Cholesterol/CDO -0.069 0.17 -10000 0 -0.38 43 43
mesenchymal cell differentiation 0.11 0.21 0.41 55 -10000 0 55
mol:Vitamin D3 -0.22 0.27 -10000 0 -0.64 41 41
IHH N/PTCH2 -0.31 0.26 -10000 0 -0.46 125 125
CDON 0.012 0.051 -10000 0 -0.67 1 1
IHH N/PTCH1 -0.2 0.21 -10000 0 -0.68 14 14
Megalin/LRPAP1 -0.047 0.17 -10000 0 -0.49 24 24
PTCH2 -0.068 0.23 -10000 0 -0.67 22 22
SHH Np/Cholesterol -0.091 0.16 -10000 0 -0.39 42 42
PTCH1 -0.2 0.2 -10000 0 -0.67 14 14
HHIP -0.053 0.21 -10000 0 -0.67 18 18
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.15 0.32 -9999 0 -0.75 34 34
alphaM/beta2 Integrin/GPIbA -0.15 0.28 -9999 0 -0.59 44 44
alphaM/beta2 Integrin/proMMP-9 -0.18 0.35 -9999 0 -0.76 41 41
PLAUR -0.011 0.13 -9999 0 -0.67 7 7
HMGB1 0.006 0.021 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.26 -9999 0 -0.63 34 34
AGER -0.03 0.16 -9999 0 -0.7 9 9
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.026 0.16 -9999 0 -0.67 11 11
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.19 0.29 -9999 0 -0.78 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.084 0.24 -9999 0 -0.67 26 26
CYR61 -0.011 0.13 -9999 0 -0.67 7 7
TLN1 0.013 0.051 -9999 0 -0.66 1 1
Rap1/GTP -0.19 0.3 -9999 0 -0.73 32 32
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.038 0.18 -9999 0 -0.67 14 14
MYH2 -0.2 0.31 -9999 0 -0.66 42 42
MST1R -0.14 0.28 -9999 0 -0.66 40 40
leukocyte activation during inflammatory response -0.23 0.3 -9999 0 -0.64 47 47
APOB -0.19 0.31 -9999 0 -0.66 54 54
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.03 0.17 -9999 0 -0.67 12 12
JAM3 0.005 0.088 -9999 0 -0.67 3 3
GP1BA -0.03 0.17 -9999 0 -0.67 12 12
alphaM/beta2 Integrin/CTGF -0.15 0.31 -9999 0 -0.73 35 35
alphaM/beta2 Integrin -0.22 0.4 -9999 0 -0.77 43 43
JAM3 homodimer 0.005 0.088 -9999 0 -0.67 3 3
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.038 0.18 -9999 0 -0.67 14 14
phagocytosis triggered by activation of immune response cell surface activating receptor -0.21 0.38 -9999 0 -0.74 43 43
cell adhesion -0.15 0.27 -9999 0 -0.59 44 44
NFKB1 -0.2 0.38 -9999 0 -0.9 32 32
THY1 -0.011 0.13 -9999 0 -0.67 7 7
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.14 0.22 -9999 0 -0.43 62 62
alphaM/beta2 Integrin/LRP/tPA -0.12 0.3 -9999 0 -0.6 42 42
IL6 -0.23 0.42 -9999 0 -0.82 49 49
ITGB2 -0.12 0.27 -9999 0 -0.69 33 33
elevation of cytosolic calcium ion concentration -0.12 0.34 -9999 0 -0.72 36 36
alphaM/beta2 Integrin/JAM2/JAM3 -0.1 0.3 -9999 0 -0.66 33 33
JAM2 -0.003 0.11 -9999 0 -0.67 5 5
alphaM/beta2 Integrin/ICAM1 -0.2 0.38 -9999 0 -0.9 29 29
alphaM/beta2 Integrin/uPA/Plg -0.17 0.35 -9999 0 -0.62 55 55
RhoA/GTP -0.21 0.34 -9999 0 -0.66 47 47
positive regulation of phagocytosis -0.23 0.35 -9999 0 -0.83 39 39
Ron/MSP -0.11 0.23 -9999 0 -0.5 47 47
alphaM/beta2 Integrin/uPAR/uPA -0.12 0.35 -9999 0 -0.73 36 36
alphaM/beta2 Integrin/uPAR -0.14 0.3 -9999 0 -0.67 35 35
PLAU -0.034 0.18 -9999 0 -0.67 13 13
PLAT -0.041 0.19 -9999 0 -0.67 15 15
actin filament polymerization -0.19 0.29 -9999 0 -0.61 42 42
MST1 -0.014 0.14 -9999 0 -0.67 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.22 0.32 -9999 0 -0.65 47 47
TNF -0.28 0.48 -9999 0 -0.97 53 53
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.15 0.32 -9999 0 -0.74 35 35
fibrinolysis -0.18 0.34 -9999 0 -0.61 55 55
HCK -0.12 0.27 -9999 0 -0.67 34 34
dendritic cell antigen processing and presentation -0.21 0.38 -9999 0 -0.74 43 43
VTN -0.15 0.29 -9999 0 -0.67 43 43
alphaM/beta2 Integrin/CYR61 -0.14 0.3 -9999 0 -0.69 34 34
LPA -0.023 0.15 -9999 0 -0.66 9 9
LRP1 0.012 0.051 -9999 0 -0.67 1 1
cell migration -0.16 0.4 -9999 0 -0.78 42 42
FN1 -0.057 0.21 -9999 0 -0.67 19 19
alphaM/beta2 Integrin/Thy1 -0.14 0.3 -9999 0 -0.71 33 33
MPO -0.038 0.18 -9999 0 -0.67 14 14
KNG1 -0.082 0.23 -9999 0 -0.66 24 24
RAP1/GDP 0.022 0 -9999 0 -10000 0 0
ROCK1 -0.18 0.3 -9999 0 -0.66 38 38
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.092 0.24 -9999 0 -0.66 27 27
CTGF -0.03 0.17 -9999 0 -0.67 12 12
alphaM/beta2 Integrin/Hck -0.2 0.38 -9999 0 -0.81 42 42
ITGAM -0.049 0.19 -9999 0 -0.69 14 14
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.35 -9999 0 -0.84 28 28
HP -0.14 0.29 -9999 0 -0.66 41 41
leukocyte adhesion -0.18 0.33 -9999 0 -0.85 28 28
SELP -0.038 0.18 -9999 0 -0.67 14 14
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.45 0.6 -10000 0 -1.3 46 46
STAT6 (cleaved dimer) -0.52 0.58 -10000 0 -1.3 54 54
IGHG1 -0.13 0.19 -10000 0 -0.45 4 4
IGHG3 -0.44 0.58 -10000 0 -1.2 50 50
AKT1 -0.2 0.38 -10000 0 -1.2 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.42 -10000 0 -1.4 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.44 -10000 0 -1.4 15 15
THY1 -0.46 0.62 -10000 0 -1.3 46 46
MYB -0.026 0.16 -10000 0 -0.66 11 11
HMGA1 -0.007 0.12 -10000 0 -0.66 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.52 -10000 0 -1.3 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.45 -10000 0 -1.4 16 16
SP1 0.024 0.007 -10000 0 -10000 0 0
INPP5D -0.003 0.11 -10000 0 -0.67 5 5
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.63 -10000 0 -1.3 48 48
SOCS1 -0.26 0.38 -10000 0 -0.84 29 29
SOCS3 -0.22 0.38 -10000 0 -1.2 15 15
FCER2 -0.73 0.75 -10000 0 -1.5 82 82
PARP14 0.004 0.054 -10000 0 -0.67 1 1
CCL17 -0.54 0.68 -10000 0 -1.4 56 56
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.18 0.36 -10000 0 -1.1 15 15
T cell proliferation -0.45 0.63 -10000 0 -1.4 46 46
IL4R/JAK1 -0.45 0.61 -10000 0 -1.3 46 46
EGR2 -0.53 0.64 -10000 0 -1.4 47 47
JAK2 -0.001 0.034 -10000 0 -10000 0 0
JAK3 -0.003 0.12 -10000 0 -0.64 6 6
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.011 0.017 -10000 0 -10000 0 0
COL1A2 -0.2 0.44 -10000 0 -1.6 13 13
CCL26 -0.47 0.63 -10000 0 -1.4 47 47
IL4R -0.49 0.67 -10000 0 -1.4 46 46
PTPN6 0.026 0.013 -10000 0 -10000 0 0
IL13RA2 -0.49 0.63 -10000 0 -1.3 50 50
IL13RA1 -0.001 0.034 -10000 0 -10000 0 0
IRF4 -0.27 0.53 -10000 0 -1.2 33 33
ARG1 -0.17 0.32 -10000 0 -0.86 25 25
CBL -0.27 0.45 -10000 0 -1.2 22 22
GTF3A 0.024 0.007 -10000 0 -10000 0 0
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
IL13RA1/JAK2 0 0.051 -10000 0 -10000 0 0
IRF4/BCL6 -0.21 0.49 -10000 0 -1.1 32 32
CD40LG -0.094 0.26 -10000 0 -0.68 28 28
MAPK14 -0.27 0.47 -10000 0 -1.4 18 18
mitosis -0.18 0.34 -10000 0 -1 15 15
STAT6 -0.62 0.97 -10000 0 -1.8 50 50
SPI1 -0.067 0.23 -10000 0 -0.67 22 22
RPS6KB1 -0.17 0.33 -10000 0 -0.99 15 15
STAT6 (dimer) -0.64 1 -10000 0 -1.9 50 50
STAT6 (dimer)/PARP14 -0.56 0.72 -10000 0 -1.5 52 52
mast cell activation 0.009 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.47 -10000 0 -1.3 20 20
FRAP1 -0.2 0.38 -10000 0 -1.2 15 15
LTA -0.48 0.64 -10000 0 -1.4 49 49
FES 0.001 0.1 -10000 0 -0.67 4 4
T-helper 1 cell differentiation 0.54 0.75 1.5 50 -10000 0 50
CCL11 -0.46 0.62 -10000 0 -1.3 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.46 -10000 0 -1.4 16 16
IL2RG -0.023 0.16 -10000 0 -0.65 11 11
IL10 -0.49 0.66 -10000 0 -1.5 42 42
IRS1 0.016 0 -10000 0 -10000 0 0
IRS2 0.016 0 -10000 0 -10000 0 0
IL4 -0.096 0.17 -10000 0 -0.81 4 4
IL5 -0.46 0.6 -10000 0 -1.3 46 46
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.33 0.43 -10000 0 -0.92 44 44
COL1A1 -0.22 0.48 -10000 0 -1.7 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.65 -10000 0 -1.4 45 45
IL2R gamma/JAK3 -0.018 0.18 -10000 0 -0.65 12 12
TFF3 -0.63 0.65 -10000 0 -1.4 59 59
ALOX15 -0.46 0.61 -10000 0 -1.3 48 48
MYBL1 0.013 0.051 -10000 0 -0.66 1 1
T-helper 2 cell differentiation -0.4 0.56 -10000 0 -1.1 48 48
SHC1 0.016 0 -10000 0 -10000 0 0
CEBPB 0.018 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.44 -10000 0 -1.3 16 16
mol:PI-3-4-5-P3 -0.2 0.38 -10000 0 -1.2 15 15
PI3K -0.22 0.43 -10000 0 -1.4 15 15
DOK2 -0.076 0.23 -10000 0 -0.67 24 24
ETS1 0.022 0.051 -10000 0 -0.63 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.34 -10000 0 -1.1 15 15
ITGB3 -0.47 0.64 -10000 0 -1.4 47 47
PIGR -0.54 0.66 -10000 0 -1.4 53 53
IGHE 0.028 0.049 -10000 0 -10000 0 0
MAPKKK cascade -0.16 0.32 -10000 0 -1 15 15
BCL6 0.012 0.09 -10000 0 -0.67 3 3
OPRM1 -0.46 0.6 -10000 0 -1.3 46 46
RETNLB -0.47 0.61 -10000 0 -1.3 46 46
SELP -0.5 0.67 -10000 0 -1.5 46 46
AICDA -0.52 0.67 -10000 0 -1.4 56 56
TCGA08_retinoblastoma

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
CDKN2B -0.055 0.2 -10000 0 -0.64 19 19
CDKN2C 0.023 0.054 -10000 0 -0.6 1 1
CDKN2A -0.14 0.28 -10000 0 -0.66 40 40
CCND2 0.06 0.11 0.28 23 -10000 0 23
RB1 -0.051 0.12 -10000 0 -0.29 23 23
CDK4 0.068 0.12 0.29 24 -10000 0 24
CDK6 0.067 0.12 0.31 23 -10000 0 23
G1/S progression 0.051 0.12 0.29 23 -10000 0 23
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.13 0.25 -10000 0 -0.63 33 33
FYN -0.13 0.42 -10000 0 -0.9 36 36
LAT/GRAP2/SLP76 -0.14 0.3 -10000 0 -0.72 34 34
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.047 0.24 -10000 0 -0.51 34 34
B2M 0.016 0.005 -10000 0 -10000 0 0
IKBKG -0.027 0.055 -10000 0 -0.18 6 6
MAP3K8 -0.022 0.16 -10000 0 -0.67 10 10
mol:Ca2+ -0.033 0.047 -10000 0 -0.13 20 20
integrin-mediated signaling pathway 0.009 0.074 -10000 0 -0.42 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.37 -10000 0 -0.81 35 35
TRPV6 -0.2 0.31 -10000 0 -0.68 52 52
CD28 -0.042 0.19 -10000 0 -0.68 15 15
SHC1 -0.12 0.38 -10000 0 -0.86 34 34
receptor internalization -0.13 0.42 -10000 0 -0.95 33 33
PRF1 -0.092 0.36 -10000 0 -0.97 22 22
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.034 0.21 -10000 0 -0.46 31 31
LAT -0.12 0.39 -10000 0 -0.86 35 35
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.049 0.2 -10000 0 -0.68 17 17
CD3E -0.072 0.23 -10000 0 -0.68 23 23
CD3G -0.061 0.22 -10000 0 -0.68 20 20
RASGRP2 -0.008 0.056 -10000 0 -0.15 18 18
RASGRP1 -0.11 0.28 -10000 0 -0.55 43 43
HLA-A 0.016 0.006 -10000 0 -10000 0 0
RASSF5 -0.003 0.11 -10000 0 -0.67 5 5
RAP1A/GTP/RAPL 0.01 0.074 -10000 0 -0.43 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.084 -10000 0 -0.14 34 34
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.051 0.098 -10000 0 -0.26 27 27
PRKCA -0.047 0.13 -10000 0 -0.31 29 29
GRAP2 -0.014 0.14 -10000 0 -0.67 8 8
mol:IP3 -0.054 0.24 0.26 34 -0.5 31 65
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.42 -10000 0 -0.97 30 30
ORAI1 0.1 0.16 0.35 52 -10000 0 52
CSK -0.12 0.39 -10000 0 -0.88 34 34
B7 family/CD28 -0.22 0.4 -10000 0 -0.97 36 36
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.48 -10000 0 -1.1 35 35
PTPN6 -0.12 0.4 -10000 0 -0.87 35 35
VAV1 -0.13 0.4 -10000 0 -0.9 35 35
Monovalent TCR/CD3 -0.11 0.35 -10000 0 -0.78 31 31
CBL 0.016 0 -10000 0 -10000 0 0
LCK -0.14 0.44 -10000 0 -0.95 36 36
PAG1 -0.12 0.4 -10000 0 -0.89 34 34
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.47 -10000 0 -1 35 35
CD80 -0.088 0.25 -10000 0 -0.68 27 27
CD86 -0.092 0.25 -10000 0 -0.67 28 28
PDK1/CARD11/BCL10/MALT1 -0.063 0.12 -10000 0 -0.32 27 27
HRAS 0.016 0 -10000 0 -10000 0 0
GO:0035030 -0.12 0.34 -10000 0 -0.74 36 36
CD8A -0.091 0.25 -10000 0 -0.68 28 28
CD8B -0.061 0.22 -10000 0 -0.68 20 20
PTPRC -0.11 0.27 -10000 0 -0.68 32 32
PDK1/PKC theta -0.068 0.3 -10000 0 -0.66 33 33
CSK/PAG1 -0.11 0.38 -10000 0 -0.87 33 33
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.023 0.012 -10000 0 -10000 0 0
GRAP2/SLP76 -0.16 0.36 -10000 0 -0.83 36 36
STIM1 0.055 0.081 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.1 -10000 0 -0.19 26 26
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.48 -10000 0 -1.1 33 33
mol:DAG -0.071 0.19 -10000 0 -0.45 31 31
RAP1A/GDP 0 0.037 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.026 0.17 -10000 0 -0.68 11 11
cytotoxic T cell degranulation -0.085 0.34 -10000 0 -0.91 22 22
RAP1A/GTP -0.007 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.07 0.29 -10000 0 -0.63 35 35
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.087 0.31 0.28 32 -0.69 31 63
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.088 0.25 -10000 0 -0.67 27 27
GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.13 0.29 -10000 0 -0.69 33 33
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.11 0.29 -10000 0 -0.69 33 33
CARD11 -0.014 0.14 -10000 0 -0.67 8 8
PRKCB -0.074 0.18 -10000 0 -0.44 32 32
PRKCE -0.047 0.13 -10000 0 -0.31 28 28
PRKCQ -0.096 0.35 -10000 0 -0.77 34 34
LCP2 -0.057 0.21 -10000 0 -0.67 19 19
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.032 0.2 -10000 0 -0.43 33 33
IKK complex 0.026 0.077 -10000 0 -0.13 22 22
RAS family/GDP -0.008 0.012 -10000 0 -10000 0 0
MAP3K14 -0.011 0.16 -10000 0 -0.35 25 25
PDPK1 -0.039 0.23 -10000 0 -0.5 31 31
TCR/CD3/MHC I/CD8/Fyn -0.16 0.48 -10000 0 -1.1 34 34
BCR signaling pathway

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
JUN -0.1 0.22 -9999 0 -0.48 36 36
IKBKB -0.03 0.1 -9999 0 -0.28 11 11
AKT1 -0.077 0.14 -9999 0 -0.28 38 38
IKBKG -0.029 0.11 -9999 0 -0.3 13 13
CALM1 -0.11 0.25 -9999 0 -0.55 33 33
PIK3CA 0.013 0.051 -9999 0 -0.67 1 1
MAP3K1 -0.18 0.32 -9999 0 -0.68 42 42
MAP3K7 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.27 -9999 0 -0.59 34 34
DOK1 0.009 0.072 -9999 0 -0.67 2 2
AP-1 -0.067 0.12 -9999 0 -0.29 23 23
LYN 0.005 0.088 -9999 0 -0.67 3 3
BLNK -0.018 0.15 -9999 0 -0.67 9 9
SHC1 0.016 0 -9999 0 -10000 0 0
BCR complex -0.15 0.32 -9999 0 -0.66 46 46
CD22 -0.26 0.43 -9999 0 -0.96 42 42
CAMK2G -0.093 0.23 -9999 0 -0.66 19 19
CSNK2A1 0.016 0 -9999 0 -10000 0 0
INPP5D -0.003 0.11 -9999 0 -0.67 5 5
SHC/GRB2/SOS1 -0.14 0.25 -9999 0 -0.7 24 24
GO:0007205 -0.13 0.28 -9999 0 -0.61 34 34
SYK -0.007 0.12 -9999 0 -0.67 6 6
ELK1 -0.11 0.25 -9999 0 -0.56 33 33
NFATC1 -0.19 0.3 -9999 0 -0.64 45 45
B-cell antigen/BCR complex -0.15 0.32 -9999 0 -0.66 46 46
PAG1/CSK 0.018 0.055 -9999 0 -0.49 2 2
NFKBIB 0.002 0.037 -9999 0 -10000 0 0
HRAS -0.1 0.25 -9999 0 -0.55 33 33
NFKBIA 0.003 0.036 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.01 0.03 -9999 0 -10000 0 0
RasGAP/Csk -0.14 0.3 -9999 0 -0.76 27 27
mol:GDP -0.12 0.26 -9999 0 -0.57 34 34
PTEN 0.016 0 -9999 0 -10000 0 0
CD79B -0.083 0.24 -9999 0 -0.67 26 26
NF-kappa-B/RelA/I kappa B alpha 0.011 0.029 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.2 0.29 -9999 0 -0.61 50 50
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.13 0.29 -9999 0 -0.62 34 34
CSK 0.016 0 -9999 0 -10000 0 0
FOS -0.16 0.25 -9999 0 -0.66 25 25
CHUK -0.029 0.11 -9999 0 -0.3 12 12
IBTK 0.016 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.11 0.21 -9999 0 -0.64 20 20
PTPN6 -0.21 0.4 -9999 0 -0.88 41 41
RELA 0.016 0 -9999 0 -10000 0 0
BCL2A1 0.001 0.048 -9999 0 -0.12 20 20
VAV2 -0.28 0.4 -9999 0 -0.84 50 50
ubiquitin-dependent protein catabolic process 0.008 0.035 -9999 0 -10000 0 0
BTK -0.19 0.42 -9999 0 -1.1 29 29
CD19 -0.32 0.41 -9999 0 -0.9 49 49
MAP4K1 -0.088 0.25 -9999 0 -0.67 27 27
CD72 -0.049 0.2 -9999 0 -0.67 17 17
PAG1 0.009 0.072 -9999 0 -0.67 2 2
MAPK14 -0.14 0.26 -9999 0 -0.58 36 36
SH3BP5 0.005 0.088 -9999 0 -0.67 3 3
PIK3AP1 -0.17 0.35 -9999 0 -0.65 46 46
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.16 0.4 -9999 0 -0.78 35 35
RAF1 -0.086 0.23 -9999 0 -0.52 30 30
RasGAP/p62DOK/SHIP -0.18 0.3 -9999 0 -0.78 29 29
CD79A -0.13 0.28 -9999 0 -0.67 39 39
re-entry into mitotic cell cycle -0.067 0.12 -9999 0 -0.29 23 23
RASA1 0.012 0.051 -9999 0 -0.67 1 1
MAPK3 -0.053 0.18 -9999 0 -0.51 17 17
MAPK1 -0.053 0.18 -9999 0 -0.51 17 17
CD72/SHP1 -0.2 0.41 -9999 0 -0.84 45 45
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.14 0.26 -9999 0 -0.59 36 36
actin cytoskeleton organization -0.22 0.32 -9999 0 -0.67 49 49
NF-kappa-B/RelA 0.027 0.056 -9999 0 -10000 0 0
Calcineurin -0.1 0.19 -9999 0 -0.59 19 19
PI3K -0.22 0.27 -9999 0 -0.62 50 50
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.14 0.32 -9999 0 -0.67 34 34
SOS1 0.016 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.21 0.41 -9999 0 -1 32 32
DAPP1 -0.24 0.43 -9999 0 -1 34 34
cytokine secretion -0.17 0.27 -9999 0 -0.58 45 45
mol:DAG -0.13 0.29 -9999 0 -0.62 34 34
PLCG2 0.001 0.1 -9999 0 -0.67 4 4
MAP2K1 -0.07 0.2 -9999 0 -0.57 18 18
B-cell antigen/BCR complex/FcgammaRIIB -0.18 0.34 -9999 0 -0.62 59 59
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.42 43 43
ETS1 -0.077 0.2 -9999 0 -0.57 20 20
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.32 -9999 0 -0.81 24 24
B-cell antigen/BCR complex/LYN -0.22 0.37 -9999 0 -0.78 42 42
MALT1 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 -0.24 0.35 -9999 0 -0.74 49 49
B-cell antigen/BCR complex/LYN/SYK -0.24 0.39 -9999 0 -0.88 42 42
CARD11 -0.12 0.29 -9999 0 -0.62 34 34
FCGR2B -0.08 0.24 -9999 0 -0.67 25 25
PPP3CA 0.016 0 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
IKK complex -0.003 0.046 -9999 0 -10000 0 0
PTPRC -0.11 0.26 -9999 0 -0.67 32 32
PDPK1 -0.076 0.13 -9999 0 -0.28 36 36
PPP3CB 0.016 0 -9999 0 -10000 0 0
PPP3CC 0.005 0.088 -9999 0 -0.67 3 3
POU2F2 0.009 0.034 -9999 0 -0.12 8 8
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.054 0.21 -9999 0 -0.66 19 19
Syndecan-4/Syndesmos -0.16 0.35 -9999 0 -0.75 37 37
positive regulation of JNK cascade -0.16 0.33 -9999 0 -0.76 32 32
Syndecan-4/ADAM12 -0.21 0.42 -9999 0 -0.87 43 43
CCL5 -0.038 0.18 -9999 0 -0.67 14 14
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 0.005 0.088 -9999 0 -0.67 3 3
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.09 0.24 -9999 0 -0.66 27 27
ADAM12 -0.12 0.27 -9999 0 -0.67 34 34
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.057 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.18 0.38 -9999 0 -0.79 41 41
Syndecan-4/CXCL12/CXCR4 -0.18 0.37 -9999 0 -0.85 32 32
Syndecan-4/Laminin alpha3 -0.27 0.35 -9999 0 -0.79 43 43
MDK 0.016 0 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.16 0.36 -9999 0 -0.78 37 37
Syndecan-4/Midkine -0.16 0.35 -9999 0 -0.75 37 37
FZD7 -0.003 0.11 -9999 0 -0.67 5 5
Syndecan-4/FGFR1/FGF -0.19 0.32 -9999 0 -0.86 25 25
THBS1 -0.049 0.2 -9999 0 -0.67 17 17
integrin-mediated signaling pathway -0.2 0.38 -9999 0 -0.76 45 45
positive regulation of MAPKKK cascade -0.16 0.33 -9999 0 -0.76 32 32
Syndecan-4/TACI -0.23 0.38 -9999 0 -0.78 44 44
CXCR4 -0.014 0.14 -9999 0 -0.67 8 8
cell adhesion -0.01 0.15 -9999 0 -0.41 19 19
Syndecan-4/Dynamin -0.16 0.35 -9999 0 -0.75 37 37
Syndecan-4/TSP1 -0.18 0.39 -9999 0 -0.81 41 41
Syndecan-4/GIPC -0.16 0.35 -9999 0 -0.75 37 37
Syndecan-4/RANTES -0.18 0.38 -9999 0 -0.8 38 38
ITGB1 0.012 0.051 -9999 0 -0.67 1 1
LAMA1 -0.034 0.18 -9999 0 -0.67 13 13
LAMA3 -0.2 0.32 -9999 0 -0.66 57 57
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.039 0.074 -9999 0 -0.54 1 1
Syndecan-4/alpha-Actinin -0.16 0.35 -9999 0 -0.75 37 37
TFPI -0.007 0.12 -9999 0 -0.67 6 6
F2 -0.12 0.26 -9999 0 -0.66 34 34
alpha5/beta1 Integrin 0.013 0.077 -9999 0 -0.49 4 4
positive regulation of cell adhesion -0.27 0.36 -9999 0 -0.83 41 41
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC -0.11 0.26 -9999 0 -0.67 32 32
Syndecan-4/CXCL12 -0.18 0.37 -9999 0 -0.79 39 39
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.045 0.2 -9999 0 -0.67 16 16
TNFRSF13B -0.12 0.27 -9999 0 -0.67 36 36
FGF2 -0.018 0.15 -9999 0 -0.67 9 9
FGFR1 0.012 0.051 -9999 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.17 0.35 -9999 0 -0.76 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.053 0.2 -9999 0 -0.63 19 19
cell migration -0.009 0.019 -9999 0 -10000 0 0
PRKCD 0.02 0.014 -9999 0 -10000 0 0
vasculogenesis -0.17 0.36 -9999 0 -0.75 41 41
SDC4 -0.18 0.38 -9999 0 -0.83 37 37
Syndecan-4/Tenascin C -0.21 0.41 -9999 0 -0.82 45 45
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.045 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.16 0.35 -9999 0 -0.75 37 37
MMP9 -0.083 0.24 -9999 0 -0.66 26 26
Rac1/GTP -0.015 0.16 -9999 0 -0.43 19 19
cytoskeleton organization -0.15 0.32 -9999 0 -0.7 37 37
GIPC1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.37 -9999 0 -0.79 37 37
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.053 0.26 -10000 0 -0.52 31 31
TBX21 -0.24 0.64 -10000 0 -1.3 43 43
B2M 0.012 0.015 -10000 0 -10000 0 0
TYK2 0.021 0.028 -10000 0 -10000 0 0
IL12RB1 -0.041 0.21 -10000 0 -0.71 16 16
GADD45B -0.14 0.49 -10000 0 -1 34 34
IL12RB2 -0.028 0.18 -10000 0 -0.68 13 13
GADD45G -0.15 0.5 -10000 0 -1.1 29 29
natural killer cell activation 0.004 0.03 -10000 0 -10000 0 0
RELB -0.003 0.11 -10000 0 -0.67 5 5
RELA 0.016 0 -10000 0 -10000 0 0
IL18 -0.007 0.14 -10000 0 -0.68 7 7
IL2RA -0.076 0.23 -10000 0 -0.67 24 24
IFNG -0.018 0.14 -10000 0 -0.67 8 8
STAT3 (dimer) -0.13 0.46 -10000 0 -0.86 43 43
HLA-DRB5 -0.09 0.24 -10000 0 -0.67 27 27
FASLG -0.29 0.7 -10000 0 -1.4 47 47
NF kappa B2 p52/RelB -0.31 0.51 -10000 0 -1.1 48 48
CD4 -0.044 0.19 -10000 0 -0.67 15 15
SOCS1 0.001 0.1 -10000 0 -0.67 4 4
EntrezGene:6955 -0.009 0.019 -10000 0 -10000 0 0
CD3D -0.056 0.2 -10000 0 -0.68 17 17
CD3E -0.079 0.23 -10000 0 -0.68 23 23
CD3G -0.068 0.22 -10000 0 -0.68 20 20
IL12Rbeta2/JAK2 -0.003 0.15 -10000 0 -0.51 13 13
CCL3 -0.24 0.65 -10000 0 -1.3 43 43
CCL4 -0.27 0.69 -10000 0 -1.4 45 45
HLA-A 0.012 0.015 -10000 0 -10000 0 0
IL18/IL18R -0.024 0.23 -10000 0 -0.48 32 32
NOS2 -0.19 0.56 -10000 0 -1.1 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 -0.045 0.24 -10000 0 -0.48 30 30
IL1R1 -0.2 0.6 -10000 0 -1.2 36 36
IL4 -0.015 0.099 -10000 0 -0.64 4 4
JAK2 0.021 0.028 -10000 0 -10000 0 0
EntrezGene:6957 -0.008 0.019 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.34 0.7 -10000 0 -1.3 51 51
RAB7A -0.08 0.41 -10000 0 -0.86 25 25
lysosomal transport -0.07 0.39 -10000 0 -0.81 25 25
FOS -0.23 0.48 -10000 0 -1 36 36
STAT4 (dimer) -0.16 0.54 -10000 0 -1 43 43
STAT5A (dimer) -0.32 0.5 -10000 0 -1.1 48 48
GZMA -0.24 0.64 -10000 0 -1.3 43 43
GZMB -0.21 0.58 -10000 0 -1.2 39 39
HLX 0.012 0.051 -10000 0 -0.67 1 1
LCK -0.25 0.65 -10000 0 -1.2 48 48
TCR/CD3/MHC II/CD4 -0.22 0.51 -10000 0 -1 38 38
IL2/IL2R -0.062 0.24 -10000 0 -0.57 29 29
MAPK14 -0.14 0.51 -10000 0 -1 35 35
CCR5 -0.26 0.67 -10000 0 -1.4 41 41
IL1B -0.045 0.21 -10000 0 -0.69 17 17
STAT6 -0.032 0.24 -10000 0 -1.4 3 3
STAT4 -0.026 0.16 -10000 0 -0.67 11 11
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.012 0.051 -10000 0 -0.67 1 1
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.001 0.1 -10000 0 -0.67 4 4
IL12B -0.027 0.18 -10000 0 -0.68 12 12
CD8A -0.096 0.25 -10000 0 -0.68 28 28
CD8B -0.065 0.22 -10000 0 -0.68 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.052 0.26 0.51 31 -10000 0 31
IL2RB -0.011 0.13 -10000 0 -0.67 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.48 -10000 0 -0.9 43 43
IL2RG -0.026 0.16 -10000 0 -0.67 11 11
IL12 -0.042 0.21 -10000 0 -0.55 24 24
STAT5A 0.012 0.051 -10000 0 -0.67 1 1
CD247 -0.033 0.16 -10000 0 -0.67 11 11
IL2 0.001 0.072 -10000 0 -0.67 2 2
SPHK2 0.016 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.034 0.19 -10000 0 -0.68 14 14
IL12/IL12R/TYK2/JAK2 -0.29 0.75 -10000 0 -1.3 49 49
MAP2K3 -0.14 0.52 -10000 0 -1 36 36
RIPK2 0.012 0.051 -10000 0 -0.67 1 1
MAP2K6 -0.15 0.53 -10000 0 -1.1 36 36
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.067 0.22 -10000 0 -0.67 21 21
IL18RAP -0.084 0.25 -10000 0 -0.67 27 27
IL12Rbeta1/TYK2 -0.017 0.17 -10000 0 -0.54 16 16
EOMES -0.32 0.62 -10000 0 -1.4 41 41
STAT1 (dimer) -0.14 0.46 -10000 0 -0.86 43 43
T cell proliferation -0.082 0.38 -10000 0 -0.71 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.075 -10000 0 -0.68 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.22 0.33 -10000 0 -0.8 37 37
ATF2 -0.11 0.47 -10000 0 -0.95 32 32
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.031 0.11 -9999 0 -0.49 9 9
NFATC2 -0.055 0.14 -9999 0 -0.47 18 18
NFATC3 -0.007 0.035 -9999 0 -10000 0 0
CD40LG -0.35 0.38 -9999 0 -0.86 49 49
PTGS2 -0.46 0.4 -9999 0 -0.85 72 72
JUNB 0.016 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.011 0.016 -9999 0 -10000 0 0
CALM1 0.008 0.011 -9999 0 -10000 0 0
JUN 0.004 0.052 -9999 0 -0.68 1 1
mol:Ca2+ -0.015 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.005 -9999 0 -10000 0 0
FOSL1 -0.31 0.34 -9999 0 -0.66 85 85
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.23 -9999 0 -0.69 21 21
FOS -0.13 0.27 -9999 0 -0.68 35 35
IFNG -0.33 0.34 -9999 0 -0.82 38 38
AP-1/NFAT1-c-4 -0.4 0.44 -9999 0 -1.1 37 37
FASLG -0.36 0.4 -9999 0 -0.91 47 47
NFAT1-c-4/ICER1 -0.1 0.18 -9999 0 -0.55 18 18
IL2RA -0.35 0.37 -9999 0 -0.85 45 45
FKBP12/FK506 0.012 0 -9999 0 -10000 0 0
CSF2 -0.36 0.38 -9999 0 -0.85 50 50
JunB/Fra1/NFAT1-c-4 -0.26 0.24 -9999 0 -0.58 43 43
IL4 -0.32 0.34 -9999 0 -0.82 37 37
IL2 -0.016 0.12 -9999 0 -1 2 2
IL3 -0.034 0.058 -9999 0 -0.74 1 1
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.007 0.12 -9999 0 -0.67 6 6
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.051 -9999 0 -0.67 1 1
Syndecan-1-mediated signaling events

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.005 0.088 -9999 0 -0.67 3 3
CCL5 -0.038 0.18 -9999 0 -0.67 14 14
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.16 0.28 -9999 0 -0.7 26 26
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 -0.15 0.28 -9999 0 -0.7 26 26
Syndecan-1/Syntenin -0.14 0.27 -9999 0 -0.66 26 26
MAPK3 -0.12 0.24 -9999 0 -0.66 19 19
HGF/MET -0.06 0.22 -9999 0 -0.57 25 25
TGFB1/TGF beta receptor Type II 0.005 0.088 -9999 0 -0.67 3 3
BSG 0.016 0 -9999 0 -10000 0 0
keratinocyte migration -0.15 0.27 -9999 0 -0.68 26 26
Syndecan-1/RANTES -0.17 0.31 -9999 0 -0.72 30 30
Syndecan-1/CD147 -0.13 0.26 -9999 0 -0.72 19 19
Syndecan-1/Syntenin/PIP2 -0.14 0.26 -9999 0 -0.64 26 26
LAMA5 0.005 0.088 -9999 0 -0.67 3 3
positive regulation of cell-cell adhesion -0.14 0.25 -9999 0 -0.62 26 26
MMP7 -0.096 0.25 -9999 0 -0.67 29 29
HGF -0.053 0.21 -9999 0 -0.67 18 18
Syndecan-1/CASK -0.16 0.27 -9999 0 -0.67 26 26
Syndecan-1/HGF/MET -0.19 0.33 -9999 0 -0.75 31 31
regulation of cell adhesion -0.1 0.23 -9999 0 -0.71 14 14
HPSE 0.009 0.072 -9999 0 -0.67 2 2
positive regulation of cell migration -0.16 0.28 -9999 0 -0.7 26 26
SDC1 -0.16 0.28 -9999 0 -0.71 26 26
Syndecan-1/Collagen -0.16 0.28 -9999 0 -0.7 26 26
PPIB 0.016 0 -9999 0 -10000 0 0
MET -0.03 0.17 -9999 0 -0.67 12 12
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.084 0.24 -9999 0 -0.67 26 26
MAPK1 -0.12 0.24 -9999 0 -0.66 19 19
homophilic cell adhesion -0.16 0.27 -9999 0 -0.68 26 26
MMP1 -0.24 0.33 -9999 0 -0.66 67 67
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.076 0.26 -10000 0 -0.72 23 23
NFATC2 -0.07 0.33 -10000 0 -0.91 17 17
NFATC3 -0.017 0.075 -10000 0 -10000 0 0
CD40LG -0.43 0.51 -10000 0 -1.2 40 40
ITCH 0.049 0.05 -10000 0 -10000 0 0
CBLB 0.049 0.05 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.37 0.56 -10000 0 -1.4 39 39
JUNB 0.016 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.05 -10000 0 -10000 0 0
T cell anergy 0.039 0.1 -10000 0 -0.58 2 2
TLE4 -0.035 0.26 -10000 0 -0.88 11 11
Jun/NFAT1-c-4/p21SNFT -0.21 0.49 -10000 0 -1.3 21 21
AP-1/NFAT1-c-4 -0.48 0.62 -10000 0 -1.4 39 39
IKZF1 -0.098 0.38 -10000 0 -0.97 25 25
T-helper 2 cell differentiation -0.14 0.32 -10000 0 -1 16 16
AP-1/NFAT1 -0.16 0.29 -10000 0 -0.64 34 34
CALM1 0.029 0.032 -10000 0 -10000 0 0
EGR2 -0.13 0.46 -10000 0 -1.6 11 11
EGR3 -0.12 0.42 -10000 0 -1.4 13 13
NFAT1/FOXP3 -0.12 0.4 -10000 0 -0.95 26 26
EGR1 0.006 0.072 -10000 0 -0.66 2 2
JUN -0.01 0.057 -10000 0 -0.67 1 1
EGR4 -0.22 0.32 -10000 0 -0.67 61 61
mol:Ca2+ 0.013 0.034 -10000 0 -10000 0 0
GBP3 -0.061 0.32 -10000 0 -1 14 14
FOSL1 -0.31 0.34 -10000 0 -0.66 85 85
NFAT1-c-4/MAF/IRF4 -0.18 0.48 -10000 0 -1.4 19 19
DGKA -0.033 0.25 -10000 0 -0.84 11 11
CREM 0.016 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.24 0.51 -10000 0 -1.3 24 24
CTLA4 -0.13 0.43 -10000 0 -1.1 25 25
NFAT1-c-4 (dimer)/EGR1 -0.18 0.48 -10000 0 -1.4 19 19
NFAT1-c-4 (dimer)/EGR4 -0.32 0.53 -10000 0 -1.3 27 27
FOS -0.14 0.28 -10000 0 -0.7 35 35
IFNG -0.21 0.42 -10000 0 -1 30 30
T cell activation -0.15 0.26 -10000 0 -0.9 8 8
MAF 0.009 0.072 -10000 0 -0.67 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.12 0.4 1.3 13 -10000 0 13
TNF -0.35 0.54 -10000 0 -1.2 44 44
FASLG -0.36 0.74 -10000 0 -1.7 40 40
TBX21 -0.052 0.21 -10000 0 -0.67 18 18
BATF3 -0.007 0.12 -10000 0 -0.67 6 6
PRKCQ -0.07 0.23 -10000 0 -0.69 21 21
PTPN1 -0.033 0.25 -10000 0 -0.84 11 11
NFAT1-c-4/ICER1 -0.17 0.46 -10000 0 -1.3 20 20
GATA3 -0.044 0.2 -10000 0 -0.67 16 16
T-helper 1 cell differentiation -0.19 0.42 -10000 0 -1 30 30
IL2RA -0.35 0.51 -10000 0 -1.3 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.033 0.25 -10000 0 -0.84 11 11
E2F1 0.016 0.071 -10000 0 -0.65 2 2
PPARG -0.12 0.27 -10000 0 -0.66 36 36
SLC3A2 -0.033 0.25 -10000 0 -0.84 11 11
IRF4 -0.049 0.2 -10000 0 -0.67 17 17
PTGS2 -0.55 0.51 -10000 0 -1.2 52 52
CSF2 -0.44 0.5 -10000 0 -1.1 45 45
JunB/Fra1/NFAT1-c-4 -0.32 0.47 -10000 0 -1.2 28 28
IL4 -0.14 0.34 -10000 0 -1.1 16 16
IL5 -0.39 0.46 -10000 0 -1.1 34 34
IL2 -0.15 0.26 -10000 0 -0.93 8 8
IL3 -0.073 0.08 -10000 0 -0.84 1 1
RNF128 0.034 0.13 -10000 0 -0.73 5 5
NFATC1 -0.12 0.41 -10000 0 -1.4 12 12
CDK4 0.064 0.21 0.68 7 -10000 0 7
PTPRK -0.037 0.27 -10000 0 -0.94 10 10
IL8 -0.44 0.51 -10000 0 -1.2 43 43
POU2F1 0.012 0.051 -10000 0 -0.67 1 1
Endothelins

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
AKT1 -0.009 0.33 -10000 0 -0.92 16 16
PTK2B 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.034 0.25 -10000 0 -0.92 8 8
EDN1 0.018 0.19 -10000 0 -0.74 7 7
EDN3 -0.068 0.22 -10000 0 -0.67 22 22
EDN2 -0.22 0.32 -10000 0 -0.67 61 61
HRAS/GDP -0.045 0.31 -10000 0 -0.77 22 22
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.022 0.3 -10000 0 -0.85 16 16
ADCY4 -0.029 0.29 -10000 0 -0.83 16 16
ADCY5 -0.08 0.35 -10000 0 -0.88 21 21
ADCY6 -0.018 0.28 -10000 0 -0.83 15 15
ADCY7 -0.026 0.31 -10000 0 -0.88 16 16
ADCY1 -0.037 0.32 -10000 0 -0.95 15 15
ADCY2 -0.031 0.32 -10000 0 -0.96 15 15
ADCY3 -0.018 0.28 -10000 0 -0.83 15 15
ADCY8 -0.04 0.3 -10000 0 -0.85 16 16
ADCY9 -0.018 0.28 -10000 0 -0.83 15 15
arachidonic acid secretion -0.032 0.26 -10000 0 -0.65 18 18
ETB receptor/Endothelin-1/Gq/GTP 0.011 0.17 -10000 0 -0.56 9 9
GNAO1 -0.033 0.18 -10000 0 -0.66 13 13
HRAS 0.016 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0 0.34 0.33 53 -0.93 14 67
ETA receptor/Endothelin-1/Gs/GTP -0.007 0.34 0.31 53 -0.9 15 68
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.039 0.41 -10000 0 -1.1 19 19
EDNRB -0.004 0.12 -10000 0 -0.67 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.028 0.37 -10000 0 -1 17 17
CYSLTR1 -0.058 0.41 -10000 0 -0.94 27 27
SLC9A1 -0.001 0.14 -10000 0 -0.41 11 11
mol:GDP -0.062 0.35 -10000 0 -0.86 23 23
SLC9A3 -0.11 0.28 -10000 0 -0.79 18 18
RAF1 -0.071 0.3 -10000 0 -0.77 22 22
JUN 0.041 0.23 -10000 0 -0.82 8 8
JAK2 -0.009 0.33 -10000 0 -0.89 17 17
mol:IP3 -0.03 0.3 -10000 0 -0.81 18 18
ETA receptor/Endothelin-1 -0.007 0.4 0.38 53 -1 17 70
PLCB1 0.012 0.051 -10000 0 -0.67 1 1
PLCB2 -0.074 0.23 -10000 0 -0.67 23 23
ETA receptor/Endothelin-3 -0.069 0.25 -10000 0 -0.61 27 27
FOS -0.081 0.28 -10000 0 -0.63 20 20
Gai/GDP 0.007 0.15 -10000 0 -0.65 7 7
CRK 0.017 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.05 0.41 -10000 0 -1.1 20 20
BCAR1 0.017 0.001 -10000 0 -10000 0 0
PRKCB1 -0.027 0.28 -10000 0 -0.76 18 18
GNAQ 0.018 0.005 -10000 0 -10000 0 0
GNAZ -0.01 0.13 -10000 0 -0.66 7 7
GNAL 0.005 0.088 -10000 0 -0.67 3 3
Gs family/GDP -0.11 0.27 -10000 0 -0.74 23 23
ETA receptor/Endothelin-1/Gq/GTP 0.02 0.23 -10000 0 -0.68 13 13
MAPK14 -0.009 0.21 -10000 0 -0.69 11 11
TRPC6 0.03 0.26 -10000 0 -1 8 8
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.005 0.088 -10000 0 -0.66 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.22 -10000 0 -0.67 13 13
ETB receptor/Endothelin-2 -0.17 0.26 -10000 0 -0.5 66 66
ETB receptor/Endothelin-3 -0.054 0.2 -10000 0 -0.52 26 26
ETB receptor/Endothelin-1 0.008 0.2 -10000 0 -0.68 10 10
MAPK3 -0.081 0.3 -10000 0 -0.77 17 17
MAPK1 -0.081 0.3 -10000 0 -0.77 17 17
Rac1/GDP -0.043 0.31 -10000 0 -0.77 22 22
cAMP biosynthetic process -0.037 0.3 -10000 0 -0.85 17 17
MAPK8 0.024 0.28 -10000 0 -0.88 12 12
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.008 0.19 -10000 0 -0.82 7 7
p130Cas/CRK/Src/PYK2 -0.043 0.32 -10000 0 -0.84 20 20
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.043 0.31 -10000 0 -0.83 19 19
COL1A2 -0.038 0.44 -10000 0 -1.3 17 17
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.18 0.3 -10000 0 -0.53 66 66
mol:DAG -0.03 0.3 -10000 0 -0.8 18 18
MAP2K2 -0.072 0.29 -10000 0 -0.71 21 21
MAP2K1 -0.072 0.29 -10000 0 -0.75 19 19
EDNRA 0.002 0.23 -10000 0 -0.87 9 9
positive regulation of muscle contraction -0.001 0.3 -10000 0 -0.88 14 14
Gq family/GDP -0.12 0.28 -10000 0 -0.85 19 19
HRAS/GTP -0.074 0.33 -10000 0 -0.82 23 23
PRKCH -0.021 0.28 -10000 0 -0.88 14 14
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.022 0.28 -10000 0 -0.89 14 14
PRKCB -0.076 0.36 -10000 0 -0.86 26 26
PRKCE -0.02 0.28 -10000 0 -0.88 14 14
PRKCD -0.02 0.28 -10000 0 -0.86 14 14
PRKCG -0.11 0.33 -10000 0 -0.74 27 27
regulation of vascular smooth muscle contraction -0.094 0.32 -10000 0 -0.79 17 17
PRKCQ -0.061 0.33 -10000 0 -0.87 21 21
PLA2G4A -0.04 0.28 -10000 0 -0.73 18 18
GNA14 -0.002 0.11 -10000 0 -0.67 5 5
GNA15 -0.006 0.12 -10000 0 -0.67 6 6
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.052 -10000 0 -0.67 1 1
Rac1/GTP 0 0.34 0.33 53 -0.86 16 69
MMP1 -0.23 0.37 -10000 0 -0.67 67 67
IGF1 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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL -0.094 0.17 -10000 0 -0.34 60 60
GRB2/SOS1/SHC 0.033 0 -10000 0 -10000 0 0
HRAS 0.016 0 -10000 0 -10000 0 0
IRS1/Crk -0.094 0.18 -10000 0 -0.34 60 60
IGF-1R heterotetramer/IGF1/PTP1B -0.11 0.2 -10000 0 -0.39 61 61
AKT1 -0.058 0.16 -10000 0 -0.59 1 1
BAD -0.047 0.15 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.094 0.17 -10000 0 -0.34 60 60
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.094 0.18 -10000 0 -0.34 60 60
RAF1 -0.038 0.14 -10000 0 -0.51 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.079 0.17 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.11 0.19 -10000 0 -0.37 61 61
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
RPS6KB1 -0.058 0.16 -10000 0 -0.59 1 1
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.036 0.13 -10000 0 -0.43 1 1
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
HRAS/GTP -0.092 0.13 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.071 0.16 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.012 0.041 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.093 0.18 -10000 0 -0.34 60 60
Crk/p130 Cas/Paxillin -0.068 0.16 -10000 0 -10000 0 0
IGF1R -0.012 0.041 -10000 0 -10000 0 0
IGF1 -0.22 0.33 -10000 0 -0.68 61 61
IRS2/Crk -0.08 0.17 -10000 0 -10000 0 0
PI3K -0.081 0.17 -10000 0 -0.67 1 1
apoptosis 0.032 0.13 0.46 1 -10000 0 1
HRAS/GDP 0.012 0 -10000 0 -10000 0 0
PRKCD -0.11 0.22 -10000 0 -0.41 60 60
RAF1/14-3-3 E -0.024 0.13 -10000 0 -0.43 1 1
BAD/14-3-3 -0.035 0.14 -10000 0 -0.49 1 1
PRKCZ -0.06 0.16 -10000 0 -0.6 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.075 0.1 -10000 0 -0.49 1 1
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.23 -10000 0 -0.44 60 60
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.09 0.18 -10000 0 -0.72 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.093 0.17 -10000 0 -0.34 60 60
GRB10 0.012 0.051 -10000 0 -0.67 1 1
PTPN11 -0.094 0.17 -10000 0 -0.34 60 60
IRS1 -0.11 0.19 -10000 0 -0.37 61 61
IRS2 -0.094 0.17 -10000 0 -0.34 60 60
IGF-1R heterotetramer/IGF1 -0.16 0.25 -10000 0 -0.51 61 61
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 -0.07 0.16 -10000 0 -0.63 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 -0.12 0.25 -10000 0 -0.45 60 60
SHC1 0.016 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.091 0.3 -9999 0 -0.65 33 33
MAP4K1 -0.088 0.25 -9999 0 -0.67 27 27
MAP3K8 -0.022 0.16 -9999 0 -0.67 10 10
PRKCB -0.095 0.25 -9999 0 -0.67 29 29
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.045 0.24 -9999 0 -0.69 18 18
JUN -0.1 0.34 -9999 0 -0.84 28 28
MAP3K7 -0.041 0.23 -9999 0 -0.65 18 18
GRAP2 -0.014 0.14 -9999 0 -0.67 8 8
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.042 0.26 -9999 0 -0.73 18 18
LAT -0.007 0.12 -9999 0 -0.67 6 6
LCP2 -0.057 0.21 -9999 0 -0.67 19 19
MAPK8 -0.11 0.36 -9999 0 -0.92 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.053 0.24 -9999 0 -0.69 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.078 0.29 -9999 0 -0.84 18 18
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.024 0 -9999 0 -10000 0 0
Necdin/E2F1 0.005 0.11 -9999 0 -0.56 6 6
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.034 0.19 -9999 0 -0.71 6 6
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.32 -9999 0 -0.57 61 61
NT-4/5 (dimer)/p75(NTR) -0.4 0.27 -9999 0 -0.54 132 132
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.037 0.19 -9999 0 -0.7 7 7
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.022 0.16 -9999 0 -0.66 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.055 0.18 -9999 0 -0.43 34 34
FURIN 0.012 0.051 -9999 0 -0.67 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.061 0.2 -9999 0 -0.46 34 34
LINGO1 0.009 0.072 -9999 0 -0.66 2 2
Sortilin/TRAF6/NRIF 0 0 -9999 0 -10000 0 0
proBDNF (dimer) -0.022 0.16 -9999 0 -0.66 10 10
NTRK1 0.005 0.088 -9999 0 -0.67 3 3
RTN4R -0.003 0.11 -9999 0 -0.67 5 5
neuron apoptosis -0.031 0.2 -9999 0 -0.65 10 10
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.061 0.21 -9999 0 -0.49 32 32
ARHGDIA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP 0.012 0 -9999 0 -10000 0 0
Gamma Secretase 0.049 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.049 0.21 -9999 0 -0.47 32 32
MAGEH1 0.009 0.072 -9999 0 -0.67 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.056 0.22 -9999 0 -0.49 33 33
Mammalian IAPs/DIABLO 0.014 0.1 -9999 0 -0.37 12 12
proNGF (dimer) -0.022 0.16 -9999 0 -0.67 10 10
MAGED1 0.016 0 -9999 0 -10000 0 0
APP 0.016 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.45 0.32 -9999 0 -0.66 121 121
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.043 0.18 -9999 0 -0.42 32 32
NGF -0.022 0.16 -9999 0 -0.67 10 10
cell cycle arrest -0.041 0.19 -9999 0 -0.69 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.023 0.15 -9999 0 -0.56 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.34 0.24 -9999 0 -0.46 132 132
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.061 0.21 -9999 0 -0.49 32 32
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.046 0.19 -9999 0 -0.44 32 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.008 0.13 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.057 0.19 -9999 0 -0.49 28 28
BEX1 -0.17 0.3 -9999 0 -0.67 48 48
mol:GDP -0.072 0.21 -9999 0 -0.5 32 32
NGF (dimer) -0.11 0.25 -9999 0 -0.45 55 55
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.039 0.17 -9999 0 -0.38 34 34
PIK3R1 0.016 0 -9999 0 -10000 0 0
RAC1/GTP -0.053 0.18 -9999 0 -0.43 32 32
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.061 0.21 -9999 0 -0.49 32 32
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.019 0.054 -9999 0 -0.49 2 2
NT3 (dimer) 0.005 0.088 -9999 0 -0.67 3 3
TP53 -0.03 0.18 -9999 0 -0.67 5 5
PRDM4 -0.047 0.19 -9999 0 -0.44 32 32
BDNF (dimer) -0.29 0.28 -9999 0 -0.47 115 115
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
SORT1 0.016 0 -9999 0 -10000 0 0
activation of caspase activity -0.073 0.17 -9999 0 -0.7 6 6
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.045 0.2 -9999 0 -0.44 32 32
RHOC 0.012 0.051 -9999 0 -0.67 1 1
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.025 0.21 -9999 0 -0.65 12 12
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.047 0.19 -9999 0 -0.44 32 32
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.061 0.21 -9999 0 -0.49 32 32
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.024 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.064 0.21 -9999 0 -0.54 28 28
MAPK8 -0.017 0.19 -9999 0 -0.58 10 10
MAPK9 -0.015 0.19 -9999 0 -0.56 10 10
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.088 -9999 0 -0.67 3 3
NTF4 -0.45 0.32 -9999 0 -0.66 121 121
NDN -0.003 0.11 -9999 0 -0.67 5 5
RAC1/GDP 0.012 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.07 0.16 -9999 0 -0.66 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.035 0.053 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.061 0.21 -9999 0 -0.48 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.034 0.18 -9999 0 -0.71 4 4
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.045 0.19 -9999 0 -0.75 4 4
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.013 0.14 -9999 0 -0.52 12 12
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.03 0.17 -9999 0 -0.67 12 12
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.038 0.2 -9999 0 -0.49 20 20
BAD -0.012 0.2 -9999 0 -0.58 11 11
RIPK2 0.012 0.051 -9999 0 -0.67 1 1
NGFR -0.092 0.25 -9999 0 -0.67 28 28
CYCS -0.035 0.18 -9999 0 -0.7 6 6
ADAM17 0.005 0.088 -9999 0 -0.67 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.047 0.2 -9999 0 -0.44 33 33
BCL2L11 -0.012 0.2 -9999 0 -0.58 11 11
BDNF (dimer)/p75(NTR) -0.084 0.23 -9999 0 -0.54 34 34
PI3K -0.047 0.2 -9999 0 -0.45 32 32
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.045 0.2 -9999 0 -0.44 32 32
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.009 0.072 -9999 0 -0.66 2 2
NGF (dimer)/p75(NTR) -0.083 0.24 -9999 0 -0.57 32 32
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.045 0.2 -9999 0 -0.44 32 32
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.013 0.051 -9999 0 -0.66 1 1
PLG -0.092 0.24 -9999 0 -0.66 27 27
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.061 0.22 -9999 0 -0.51 28 28
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.007 0.18 -9999 0 -0.53 11 11
E2F1 0.009 0.072 -9999 0 -0.66 2 2
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.053 0.13 -9999 0 -0.54 7 7
NGF (dimer)/TRKA -0.014 0.14 -9999 0 -0.5 13 13
MMP7 -0.096 0.25 -9999 0 -0.67 29 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.034 0.19 -9999 0 -0.71 6 6
MMP3 -0.29 0.34 -9999 0 -0.66 79 79
APAF-1/Caspase 9 -0.07 0.15 -9999 0 -0.52 13 13
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.002 0.15 -10000 0 -0.59 9 9
fibroblast growth factor receptor signaling pathway 0.002 0.15 -10000 0 -0.58 9 9
LAMA1 -0.034 0.18 -10000 0 -0.67 13 13
PRNP 0.012 0.051 -10000 0 -0.67 1 1
GPC1/SLIT2 -0.055 0.2 -10000 0 -0.54 25 25
SMAD2 0.033 0.053 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.012 0.078 -10000 0 -0.56 3 3
GPC1/Laminin alpha1 -0.022 0.15 -10000 0 -0.52 15 15
TDGF1 -0.069 0.22 -10000 0 -0.67 22 22
CRIPTO/GPC1 -0.047 0.19 -10000 0 -0.53 23 23
APP/GPC1 0.016 0.067 -10000 0 -0.49 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.029 0.17 -10000 0 -0.45 23 23
FLT1 0.016 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.026 0.058 -10000 0 -0.42 3 3
SERPINC1 -0.062 0.21 -10000 0 -0.66 20 20
FYN -0.031 0.17 -10000 0 -0.46 23 23
FGR -0.13 0.27 -10000 0 -0.51 52 52
positive regulation of MAPKKK cascade -0.18 0.33 -10000 0 -0.7 38 38
SLIT2 -0.08 0.24 -10000 0 -0.67 25 25
GPC1/NRG -0.007 0.13 -10000 0 -0.53 10 10
NRG1 -0.014 0.14 -10000 0 -0.66 8 8
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.023 0.067 -10000 0 -0.42 4 4
LYN -0.037 0.18 -10000 0 -0.46 25 25
mol:Spermine 0.005 0.067 -10000 0 -0.5 3 3
cell growth 0.002 0.15 -10000 0 -0.58 9 9
BMP signaling pathway -0.005 0.088 0.67 3 -10000 0 3
SRC -0.029 0.17 -10000 0 -0.45 23 23
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.41 0.33 -10000 0 -0.66 111 111
GPC1 0.005 0.088 -10000 0 -0.67 3 3
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA 0.013 0.051 -10000 0 -0.66 1 1
BLK -0.18 0.26 -10000 0 -0.46 76 76
HCK -0.11 0.26 -10000 0 -0.52 47 47
FGF2 -0.018 0.15 -10000 0 -0.67 9 9
FGFR1 0.012 0.051 -10000 0 -0.67 1 1
VEGFR1 homodimer 0.016 0 -10000 0 -10000 0 0
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death 0.016 0.067 -10000 0 -0.49 3 3
ATIII/GPC1 -0.043 0.18 -10000 0 -0.51 22 22
PLA2G2A/GPC1 -0.3 0.26 -10000 0 -0.5 111 111
LCK -0.046 0.19 -10000 0 -0.47 28 28
neuron differentiation -0.007 0.13 -10000 0 -0.53 10 10
PrPc/Cu2+ 0.009 0.039 -10000 0 -0.5 1 1
APP 0.016 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.16 0.36 -10000 0 -0.78 26 26
CRP -0.32 0.56 -10000 0 -1.1 58 58
cell cycle arrest -0.21 0.42 -10000 0 -0.85 43 43
TIMP1 -0.12 0.31 -10000 0 -0.65 26 26
IL6ST -0.057 0.21 -10000 0 -0.67 19 19
Rac1/GDP -0.09 0.26 -10000 0 -0.67 20 20
AP1 -0.044 0.16 -10000 0 -0.43 5 5
GAB2 0.018 0.004 -10000 0 -10000 0 0
TNFSF11 -0.18 0.41 -10000 0 -0.83 38 38
HSP90B1 0.015 0.065 -10000 0 -10000 0 0
GAB1 0.017 0.002 -10000 0 -10000 0 0
MAPK14 -0.052 0.24 -10000 0 -0.77 11 11
AKT1 0.061 0.03 -10000 0 -10000 0 0
FOXO1 0.063 0.047 -10000 0 -10000 0 0
MAP2K6 -0.071 0.24 -10000 0 -0.74 13 13
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.098 0.29 -10000 0 -0.66 24 24
MITF -0.089 0.28 -10000 0 -0.69 20 20
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 -0.015 0.25 -10000 0 -1.5 5 5
CEBPB 0.023 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.013 0.09 0.26 1 -10000 0 1
STAT3 -0.23 0.46 -10000 0 -0.91 43 43
STAT1 -0.015 0.091 -10000 0 -1.2 1 1
CEBPD -0.16 0.36 -10000 0 -0.73 38 38
PIK3CA 0.015 0.051 -10000 0 -0.67 1 1
PI3K 0.025 0.039 -10000 0 -0.49 1 1
JUN 0.012 0.051 -10000 0 -0.67 1 1
PIAS3/MITF -0.075 0.26 -10000 0 -0.71 16 16
MAPK11 -0.058 0.26 -10000 0 -0.79 13 13
STAT3 (dimer)/FOXO1 -0.1 0.34 -10000 0 -0.69 24 24
GRB2/SOS1/GAB family -0.12 0.21 -10000 0 -0.63 18 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.13 0.29 -10000 0 -0.71 23 23
GRB2 0.017 0.002 -10000 0 -10000 0 0
JAK2 0.016 0 -10000 0 -10000 0 0
LBP -0.21 0.36 -10000 0 -0.71 38 38
PIK3R1 0.018 0 -10000 0 -10000 0 0
JAK1 0.017 0.007 -10000 0 -10000 0 0
MYC -0.16 0.37 -10000 0 -0.81 26 26
FGG -0.3 0.54 -10000 0 -1.1 54 54
macrophage differentiation -0.21 0.42 -10000 0 -0.85 43 43
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.24 -10000 0 -0.81 11 11
JUNB -0.16 0.35 -10000 0 -0.7 37 37
FOS -0.12 0.27 -10000 0 -0.66 35 35
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.088 0.25 -10000 0 -0.56 25 25
STAT1/PIAS1 -0.088 0.24 -10000 0 -0.56 22 22
GRB2/SOS1/GAB family/SHP2/PI3K 0.047 0.032 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.46 -10000 0 -0.91 43 43
PRKCD -0.11 0.32 -10000 0 -0.74 22 22
IL6R -0.018 0.15 -10000 0 -0.68 9 9
SOCS3 -0.042 0.25 -10000 0 -1.2 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.02 0.16 -10000 0 -0.44 20 20
Rac1/GTP -0.099 0.28 -10000 0 -0.69 21 21
HCK -0.12 0.27 -10000 0 -0.67 34 34
MAPKKK cascade 0.014 0.07 -10000 0 -10000 0 0
bone resorption -0.17 0.38 -10000 0 -0.77 38 38
IRF1 -0.16 0.36 -10000 0 -0.78 26 26
mol:GDP -0.099 0.27 -10000 0 -0.68 21 21
SOS1 0.017 0.004 -10000 0 -10000 0 0
VAV1 -0.1 0.28 -10000 0 -0.71 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.062 0.27 -10000 0 -0.93 11 11
PTPN11 -0.008 0.018 -10000 0 -10000 0 0
IL6/IL6RA -0.1 0.24 -10000 0 -0.52 41 41
gp130 (dimer)/TYK2/TYK2/LMO4 -0.024 0.15 -10000 0 -0.44 20 20
gp130 (dimer)/JAK2/JAK2/LMO4 -0.024 0.15 -10000 0 -0.44 20 20
IL6 -0.12 0.27 -10000 0 -0.67 34 34
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE 0.013 0.051 -10000 0 -0.63 1 1
PIAS1 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.081 0.22 -10000 0 -0.59 17 17
LMO4 0.008 0.074 -10000 0 -0.68 2 2
STAT3 (dimer)/PIAS3 -0.27 0.36 -10000 0 -0.84 40 40
MCL1 0.067 0.028 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.097 0.26 -9999 0 -0.77 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.064 0.26 -9999 0 -0.76 13 13
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.26 -9999 0 -0.51 57 57
AP1 -0.15 0.34 -9999 0 -0.9 20 20
ILK -0.11 0.26 -9999 0 -0.74 14 14
bone resorption -0.085 0.29 -9999 0 -0.91 13 13
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.097 0.28 -9999 0 -0.99 10 10
ITGAV 0.005 0.1 -9999 0 -0.68 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.001 0.11 -9999 0 -0.49 8 8
alphaV/beta3 Integrin/Osteopontin -0.16 0.27 -9999 0 -0.49 61 61
MAP3K1 -0.12 0.28 -9999 0 -0.82 14 14
JUN 0.013 0.051 -9999 0 -0.67 1 1
MAPK3 -0.097 0.27 -9999 0 -0.83 13 13
MAPK1 -0.097 0.27 -9999 0 -0.83 13 13
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.1 0.28 -9999 0 -0.81 14 14
ITGB3 -0.03 0.18 -9999 0 -0.68 13 13
NFKBIA -0.088 0.28 -9999 0 -0.86 13 13
FOS -0.12 0.27 -9999 0 -0.66 35 35
CD44 0.001 0.1 -9999 0 -0.67 4 4
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU -0.11 0.37 -9999 0 -1.3 13 13
NF kappa B1 p50/RelA -0.12 0.22 -9999 0 -0.78 13 13
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.016 0.18 -9999 0 -0.64 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.12 0.3 -9999 0 -0.86 15 15
VAV3 -0.22 0.37 -9999 0 -0.82 36 36
MAP3K14 -0.11 0.28 -9999 0 -0.79 14 14
ROCK2 0.001 0.1 -9999 0 -0.67 4 4
SPP1 -0.19 0.32 -9999 0 -0.66 56 56
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.19 0.33 -9999 0 -0.78 32 32
MMP2 -0.12 0.28 -9999 0 -0.87 14 14
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.011 0.13 -10000 0 -0.67 7 7
GNB1/GNG2 -0.065 0.086 -10000 0 -0.22 29 29
AKT1 -0.022 0.13 -10000 0 -0.26 1 1
EGF -0.17 0.3 -10000 0 -0.67 49 49
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.036 0.18 -10000 0 -0.55 9 9
mol:Ca2+ -0.061 0.19 -10000 0 -0.33 47 47
LYN 0.029 0.093 -10000 0 -0.48 3 3
RhoA/GTP -0.042 0.055 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.068 0.21 -10000 0 -0.38 44 44
GNG2 -0.003 0.11 -10000 0 -0.67 5 5
ARRB2 0.012 0.051 -10000 0 -0.67 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.018 0.11 -10000 0 -0.46 7 7
G beta5/gamma2 -0.082 0.11 -10000 0 -0.29 27 27
PRKCH -0.07 0.2 -10000 0 -0.38 42 42
DNM1 0.005 0.088 -10000 0 -0.66 3 3
TXA2/TP beta/beta Arrestin3 -0.006 0.035 -10000 0 -0.29 2 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.019 0.15 -10000 0 -0.67 9 9
G12 family/GTP -0.1 0.14 -10000 0 -0.32 44 44
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.009 0.072 -10000 0 -0.67 2 2
RhoA/GTP/ROCK1 0.016 0.01 -10000 0 -10000 0 0
mol:GDP 0.028 0.14 0.42 9 -10000 0 9
mol:NADP 0.012 0.051 -10000 0 -0.67 1 1
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.022 0.16 -10000 0 -0.67 10 10
mol:IP3 -0.085 0.23 -10000 0 -0.42 47 47
cell morphogenesis 0.016 0.01 -10000 0 -10000 0 0
PLCB2 -0.13 0.31 -10000 0 -0.6 47 47
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.072 0.17 -10000 0 -0.54 5 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.17 -10000 0 -0.56 8 8
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.009 0.072 -10000 0 -0.67 2 2
PRKCB1 -0.08 0.22 -10000 0 -0.4 46 46
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.012 0.051 -10000 0 -0.67 1 1
TXA2/TXA2-R family -0.13 0.3 -10000 0 -0.57 46 46
LCK 0.023 0.11 -10000 0 -0.55 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.073 -10000 0 -0.67 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.042 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.081 -10000 0 -0.62 2 2
MAPK14 -0.032 0.14 -10000 0 -0.28 15 15
TGM2/GTP -0.1 0.25 -10000 0 -0.51 36 36
MAPK11 -0.035 0.15 -10000 0 -0.3 17 17
ARHGEF1 -0.023 0.11 -10000 0 -10000 0 0
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade -0.082 0.22 -10000 0 -0.41 46 46
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.058 0.18 -10000 0 -0.35 32 32
cAMP biosynthetic process -0.082 0.21 -10000 0 -0.41 37 37
Gq family/GTP/EBP50 0.018 0.068 -10000 0 -0.3 5 5
actin cytoskeleton reorganization 0.016 0.01 -10000 0 -10000 0 0
SRC 0.035 0.078 -10000 0 -0.47 2 2
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.075 0.17 -10000 0 -0.44 22 22
VCAM1 -0.069 0.2 -10000 0 -0.37 40 40
TP beta/Gq family/GDP/G beta5/gamma2 0.018 0.11 -10000 0 -0.46 7 7
platelet activation -0.044 0.19 -10000 0 -0.33 34 34
PGI2/IP 0.006 0.055 -10000 0 -0.51 2 2
PRKACA 0.003 0.097 -10000 0 -0.37 10 10
Gq family/GDP/G beta5/gamma2 0.016 0.11 -10000 0 -0.44 8 8
TXA2/TP beta/beta Arrestin2 -0.01 0.066 -10000 0 -0.43 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.012 0.092 -10000 0 -0.77 1 1
mol:DAG -0.093 0.24 -10000 0 -0.46 46 46
EGFR 0.001 0.1 -10000 0 -0.67 4 4
TXA2/TP alpha -0.12 0.29 -10000 0 -0.58 37 37
Gq family/GTP -0.012 0.059 -10000 0 -0.32 3 3
YES1 0.035 0.078 -10000 0 -0.47 2 2
GNAI2/GTP -0.018 0.077 -10000 0 -0.56 2 2
PGD2/DP -0.014 0.11 -10000 0 -0.5 9 9
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN 0.033 0.086 -10000 0 -0.48 3 3
mol:NO 0.012 0.051 -10000 0 -0.67 1 1
GNA15 -0.007 0.12 -10000 0 -0.67 6 6
PGK/cGMP -0.006 0.11 -10000 0 -0.43 11 11
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.014 0.14 -10000 0 -0.79 3 3
NOS3 0.012 0.051 -10000 0 -0.67 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.069 0.2 -10000 0 -0.38 42 42
PRKCB -0.097 0.24 -10000 0 -0.46 44 44
PRKCE -0.067 0.2 -10000 0 -0.38 36 36
PRKCD -0.073 0.21 -10000 0 -0.39 44 44
PRKCG -0.12 0.25 -10000 0 -0.46 48 48
muscle contraction -0.12 0.28 -10000 0 -0.54 47 47
PRKCZ -0.065 0.2 -10000 0 -0.36 44 44
ARR3 0.005 0.007 -10000 0 -10000 0 0
TXA2/TP beta 0.012 0.097 -10000 0 -0.64 2 2
PRKCQ -0.089 0.23 -10000 0 -0.43 46 46
MAPKKK cascade -0.11 0.27 -10000 0 -0.53 46 46
SELE -0.072 0.2 -10000 0 -0.36 41 41
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.1 -10000 0 -0.6 2 2
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.003 0.11 -10000 0 -0.67 5 5
chemotaxis -0.14 0.32 -10000 0 -0.63 45 45
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.012 0.051 -10000 0 -0.67 1 1
Rac1/GTP 0.008 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.012 0.051 -9999 0 -0.67 1 1
ITGB7 0.001 0.1 -9999 0 -0.67 4 4
ITGA4 -0.061 0.22 -9999 0 -0.67 20 20
alpha4/beta7 Integrin -0.046 0.18 -9999 0 -0.49 24 24
alpha4/beta1 Integrin -0.037 0.17 -9999 0 -0.49 21 21
Signaling events mediated by PTP1B

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
PDGFRB 0.001 0.1 -10000 0 -0.67 4 4
Jak2/Leptin Receptor -0.043 0.12 -10000 0 -0.42 10 10
PTP1B/AKT1 -0.027 0.11 -10000 0 -0.42 9 9
FYN 0.012 0.051 -10000 0 -0.67 1 1
p210 bcr-abl/PTP1B -0.031 0.12 -10000 0 -0.43 10 10
EGFR -0.003 0.1 -10000 0 -0.68 4 4
EGF/EGFR -0.12 0.2 -10000 0 -0.42 46 46
CSF1 -0.018 0.15 -10000 0 -0.67 9 9
AKT1 0.014 0.004 -10000 0 -10000 0 0
INSR 0.014 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.057 0.18 -10000 0 -0.48 23 23
Insulin Receptor/Insulin -0.14 0.19 -10000 0 -0.46 25 25
HCK -0.12 0.27 -10000 0 -0.67 34 34
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.02 0.11 -10000 0 -0.42 9 9
EGF -0.17 0.31 -10000 0 -0.67 49 49
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.067 0.18 -10000 0 -0.56 11 11
TXN 0.012 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.01 0.11 -10000 0 -0.42 7 7
cell migration 0.031 0.12 0.43 10 -10000 0 10
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.057 0.21 -10000 0 -0.66 19 19
ITGA2B -0.016 0.14 -10000 0 -0.67 8 8
CSF1R -0.092 0.25 -10000 0 -0.67 28 28
Prolactin Receptor/Prolactin -0.073 0.2 -10000 0 -0.54 26 26
FGR -0.14 0.29 -10000 0 -0.67 40 40
PTP1B/p130 Cas -0.02 0.11 -10000 0 -0.42 9 9
Crk/p130 Cas -0.01 0.11 -10000 0 -0.44 6 6
DOK1 -0.053 0.18 -10000 0 -0.6 11 11
JAK2 -0.03 0.11 -10000 0 -0.42 8 8
Jak2/Leptin Receptor/Leptin -0.16 0.19 -10000 0 -0.62 11 11
PIK3R1 0.016 0 -10000 0 -10000 0 0
PTPN1 -0.031 0.12 -10000 0 -0.43 10 10
LYN 0.005 0.088 -10000 0 -0.67 3 3
CDH2 -0.053 0.21 -10000 0 -0.67 18 18
SRC 0.009 0.042 -10000 0 -10000 0 0
ITGB3 -0.035 0.18 -10000 0 -0.67 13 13
CAT1/PTP1B -0.22 0.34 -10000 0 -0.7 46 46
CAPN1 0.012 0.007 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K -0.13 0.18 -10000 0 -0.54 10 10
mol:H2O2 -0.003 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.14 0.18 -10000 0 -0.63 9 9
negative regulation of transcription -0.03 0.11 -10000 0 -0.41 8 8
FCGR2A -0.03 0.17 -10000 0 -0.67 12 12
FER 0.012 0.006 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.046 0.17 -10000 0 -0.52 20 20
BLK -0.21 0.32 -10000 0 -0.67 59 59
Insulin Receptor/Insulin/Shc -0.13 0.22 -10000 0 -0.42 66 66
RHOA 0.012 0.007 -10000 0 -10000 0 0
LEPR 0.001 0.1 -10000 0 -0.67 4 4
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.003 0.004 -10000 0 -10000 0 0
TRPV6 -0.26 0.38 -10000 0 -0.7 59 59
PRL -0.029 0.16 -10000 0 -0.66 10 10
SOCS3 -0.006 0.19 -10000 0 -1.5 3 3
SPRY2 0.014 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.13 0.22 -10000 0 -0.42 66 66
CSF1/CSF1R -0.083 0.24 -10000 0 -0.58 25 25
Ras protein signal transduction 0.026 0.031 -10000 0 -10000 0 0
IRS1 0.016 0 -10000 0 -10000 0 0
INS -0.24 0.33 -10000 0 -0.67 66 66
LEP -0.28 0.34 -10000 0 -0.67 77 77
STAT5B -0.027 0.11 -10000 0 -0.41 10 10
STAT5A -0.028 0.11 -10000 0 -0.4 11 11
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.028 0.15 -10000 0 -0.54 10 10
CSN2 -0.012 0.055 -10000 0 -10000 0 0
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
LAT -0.053 0.26 -10000 0 -0.86 14 14
YBX1 0.024 0.003 -10000 0 -10000 0 0
LCK -0.011 0.13 -10000 0 -0.67 7 7
SHC1 0.016 0 -10000 0 -10000 0 0
NOX4 -0.029 0.17 -10000 0 -0.68 11 11
Glucocorticoid receptor regulatory network

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.02 0.097 -10000 0 -10000 0 0
SMARCC2 0.015 0.021 -10000 0 -10000 0 0
SMARCC1 0.015 0.021 -10000 0 -10000 0 0
TBX21 -0.12 0.35 -10000 0 -0.96 23 23
SUMO2 0.018 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.051 -10000 0 -0.66 1 1
FKBP4 0.001 0.1 -10000 0 -0.66 4 4
FKBP5 -0.007 0.12 -10000 0 -0.67 6 6
GR alpha/HSP90/FKBP51/HSP90 0.061 0.14 0.39 10 -0.43 3 13
PRL -0.059 0.2 -10000 0 -0.75 7 7
cortisol/GR alpha (dimer)/TIF2 0.12 0.31 0.66 26 -0.58 3 29
RELA -0.028 0.11 -10000 0 -10000 0 0
FGG -0.024 0.41 0.62 18 -0.64 41 59
GR beta/TIF2 0.046 0.19 0.4 13 -0.5 10 23
IFNG -0.28 0.41 -10000 0 -1.1 23 23
apoptosis 0.026 0.19 0.54 11 -0.86 2 13
CREB1 0.014 0.044 -10000 0 -10000 0 0
histone acetylation 0.01 0.22 0.39 8 -0.58 13 21
BGLAP -0.036 0.17 -10000 0 -0.61 6 6
GR/PKAc 0.077 0.11 0.37 11 -10000 0 11
NF kappa B1 p50/RelA -0.051 0.2 -10000 0 -0.5 9 9
SMARCD1 0.015 0.021 -10000 0 -10000 0 0
MDM2 0.071 0.12 0.34 17 -10000 0 17
GATA3 -0.042 0.2 -10000 0 -0.66 16 16
AKT1 0.004 0.004 -10000 0 -10000 0 0
CSF2 -0.13 0.32 -10000 0 -1 12 12
GSK3B 0.018 0.012 -10000 0 -10000 0 0
NR1I3 0.061 0.19 0.56 8 -0.99 2 10
CSN2 0.095 0.2 0.5 14 -10000 0 14
BRG1/BAF155/BAF170/BAF60A 0.037 0.077 -10000 0 -0.4 3 3
NFATC1 -0.019 0.16 -10000 0 -0.72 9 9
POU2F1 0.009 0.068 -10000 0 -0.78 1 1
CDKN1A 0.034 0.047 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.01 -10000 0 -10000 0 0
SFN -0.55 0.25 -10000 0 -0.66 148 148
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.28 0.19 0.42 1 -0.5 30 31
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.059 0.18 0.54 8 -0.76 3 11
JUN -0.17 0.24 -10000 0 -0.68 20 20
IL4 -0.086 0.26 -10000 0 -0.84 13 13
CDK5R1 -0.002 0.11 -10000 0 -0.66 5 5
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.29 -10000 0 -0.67 36 36
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.067 0.14 0.39 8 -0.43 1 9
cortisol/GR alpha (monomer) 0.18 0.37 0.83 29 -10000 0 29
NCOA2 -0.026 0.16 -10000 0 -0.67 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.73 35 35
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.87 56 56
AFP -0.12 0.23 -10000 0 -0.77 12 12
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.11 0.18 0.56 12 -10000 0 12
TP53 0.035 0.073 -10000 0 -0.65 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.35 0.53 -10000 0 -1.2 39 39
KRT14 -0.24 0.37 -10000 0 -0.81 40 40
TBP 0.026 0.017 -10000 0 -10000 0 0
CREBBP 0.07 0.1 0.32 3 -10000 0 3
HDAC1 0.014 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.026 -10000 0 -10000 0 0
AP-1 -0.39 0.42 -10000 0 -0.88 56 56
MAPK14 0.017 0.009 -10000 0 -10000 0 0
MAPK10 -0.013 0.14 -10000 0 -0.66 8 8
MAPK11 0.006 0.088 -10000 0 -0.66 3 3
KRT5 -0.56 0.65 -10000 0 -1.3 73 73
interleukin-1 receptor activity 0.009 0.026 -10000 0 -10000 0 0
NCOA1 0.02 0.002 -10000 0 -10000 0 0
STAT1 0.023 0.051 -10000 0 -0.66 1 1
CGA -0.07 0.22 -10000 0 -0.68 14 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.13 0.2 0.48 27 -10000 0 27
MAPK3 0.017 0.011 -10000 0 -10000 0 0
MAPK1 0.017 0.009 -10000 0 -10000 0 0
ICAM1 -0.2 0.47 -10000 0 -1.3 22 22
NFKB1 -0.028 0.11 -10000 0 -10000 0 0
MAPK8 -0.13 0.22 -10000 0 -0.65 16 16
MAPK9 0.017 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.024 0.2 0.55 11 -0.92 2 13
BAX 0.034 0.047 -10000 0 -10000 0 0
POMC -0.23 0.5 -10000 0 -1.6 19 19
EP300 0.07 0.1 0.31 5 -10000 0 5
cortisol/GR alpha (dimer)/p53 0.16 0.29 0.68 28 -10000 0 28
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.088 0.27 8 -10000 0 8
SGK1 0.075 0.28 -10000 0 -1.3 6 6
IL13 -0.23 0.33 -10000 0 -0.96 20 20
IL6 -0.24 0.47 -10000 0 -1.1 33 33
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.18 0.26 -10000 0 -0.88 12 12
IL2 -0.25 0.33 -10000 0 -0.89 25 25
CDK5 0.017 0.005 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0.051 -10000 0 -0.66 1 1
IL8 -0.29 0.56 -10000 0 -1.4 34 34
CDK5R1/CDK5 0.011 0.085 -10000 0 -0.48 5 5
NF kappa B1 p50/RelA/PKAc -0.013 0.14 -10000 0 -0.44 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.28 0.66 23 -0.76 1 24
SMARCA4 0.011 0.055 -10000 0 -0.67 1 1
chromatin remodeling 0.11 0.17 0.46 16 -0.51 2 18
NF kappa B1 p50/RelA/Cbp 0.031 0.21 0.43 6 -0.54 2 8
JUN (dimer) -0.17 0.24 -10000 0 -0.68 20 20
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.096 0.28 -10000 0 -0.77 22 22
NR3C1 0.12 0.23 0.64 19 -10000 0 19
NR4A1 -0.12 0.28 -10000 0 -0.63 39 39
TIF2/SUV420H1 -0.008 0.12 -10000 0 -0.49 11 11
MAPKKK cascade 0.026 0.19 0.54 11 -0.86 2 13
cortisol/GR alpha (dimer)/Src-1 0.16 0.29 0.68 27 -10000 0 27
PBX1 0.013 0.036 -10000 0 -10000 0 0
POU1F1 0.003 0.037 -10000 0 -10000 0 0
SELE -0.24 0.49 -10000 0 -1.1 39 39
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.17 0.46 16 -0.52 2 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.28 0.66 23 -0.76 1 24
mol:cortisol 0.11 0.24 0.48 37 -0.25 1 38
MMP1 -0.31 0.39 -10000 0 -0.75 62 62
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.089 0.28 -9999 0 -0.81 17 17
MAP3K8 -0.023 0.16 -9999 0 -0.67 10 10
FOS -0.079 0.27 -9999 0 -0.82 17 17
PRKCA 0.01 0.052 -9999 0 -0.67 1 1
PTPN7 -0.043 0.19 -9999 0 -0.67 15 15
HRAS 0.016 0.001 -9999 0 -10000 0 0
PRKCB -0.097 0.25 -9999 0 -0.67 29 29
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.027 0.013 -9999 0 -10000 0 0
MAPK3 -0.065 0.25 -9999 0 -0.85 15 15
MAP2K1 -0.056 0.21 -9999 0 -0.51 28 28
ELK1 0.014 0.008 -9999 0 -10000 0 0
BRAF -0.047 0.18 -9999 0 -0.46 28 28
mol:GTP -0.001 0.002 -9999 0 -0.005 34 34
MAPK1 -0.065 0.25 -9999 0 -0.85 15 15
RAF1 -0.047 0.18 -9999 0 -0.46 28 28
KRAS 0.016 0.001 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.027 0.15 -9999 0 -0.39 23 23
RGS9BP 0.003 0.088 -9999 0 -0.66 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.002 0.006 -9999 0 -10000 0 0
mol:Na + -0.12 0.21 -9999 0 -0.44 55 55
mol:ADP 0.005 0.054 -9999 0 -0.5 2 2
GNAT2 0.014 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0 0.12 -9999 0 -0.41 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.009 0.033 -9999 0 -0.42 1 1
GRK7 0.003 0.071 -9999 0 -0.66 2 2
CNGB3 -0.039 0.17 -9999 0 -0.66 12 12
Cone Metarhodopsin II/X-Arrestin 0.004 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.22 -9999 0 -0.42 63 63
Cone PDE6 0.004 0.11 -9999 0 -0.7 1 1
Cone Metarhodopsin II 0.004 0.043 -9999 0 -0.4 2 2
Na + (4 Units) -0.13 0.22 -9999 0 -0.41 63 63
GNAT2/GDP 0.008 0.1 -9999 0 -0.35 13 13
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.012 0.03 -9999 0 -0.38 1 1
Cone Transducin -0.028 0.15 -9999 0 -0.42 23 23
SLC24A2 -0.031 0.17 -9999 0 -0.66 12 12
GNB3/GNGT2 -0.047 0.19 -9999 0 -0.53 23 23
GNB3 -0.007 0.12 -9999 0 -0.66 6 6
GNAT2/GTP 0.01 0.004 -9999 0 -10000 0 0
CNGA3 -0.16 0.3 -9999 0 -0.66 45 45
ARR3 0.005 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.13 0.21 -9999 0 -0.44 55 55
mol:Pi -0.001 0.12 -9999 0 -0.41 13 13
Cone CNG Channel -0.11 0.17 -9999 0 -0.68 3 3
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.031 0.17 -9999 0 -0.66 12 12
RGS9 -0.022 0.16 -9999 0 -0.66 10 10
PDE6C 0.007 0.008 -9999 0 -10000 0 0
GNGT2 -0.057 0.21 -9999 0 -0.67 19 19
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.05 -9999 0 -0.66 1 1
TCGA08_p53

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
CDKN2A -0.1 0.22 -10000 0 -0.5 40 40
TP53 -0.037 0.079 -10000 0 -0.51 2 2
Senescence -0.037 0.079 -10000 0 -0.5 2 2
Apoptosis -0.037 0.079 -10000 0 -0.5 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.06 0.11 0.27 40 -10000 0 40
MDM4 0.016 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.016 0.067 -9999 0 -0.49 3 3
alphaV beta3 Integrin -0.029 0.21 -9999 0 -0.62 17 17
PTK2 -0.05 0.22 -9999 0 -0.75 9 9
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.012 0.051 -9999 0 -0.67 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.12 0.25 -9999 0 -0.55 39 39
VEGFA 0.013 0.051 -9999 0 -0.66 1 1
ILK -0.12 0.25 -9999 0 -0.53 43 43
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.099 0.23 -9999 0 -0.51 39 39
PTK2B 0.004 0.16 -9999 0 -0.83 5 5
alphaV/beta3 Integrin/JAM-A -0.1 0.25 -9999 0 -0.92 8 8
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.072 0.24 -9999 0 -0.53 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.1 0.2 -9999 0 -0.37 61 61
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.042 0.17 -9999 0 -0.68 6 6
alphaV/beta3 Integrin/Syndecan-1 -0.024 0.2 -9999 0 -0.61 16 16
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.3 -9999 0 -0.84 23 23
PI4 Kinase 0.024 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
alphaV/beta3 Integrin/Osteopontin -0.15 0.27 -9999 0 -0.49 61 61
RPS6KB1 -0.13 0.3 -9999 0 -0.75 23 23
TLN1 0.013 0.051 -9999 0 -0.66 1 1
MAPK3 -0.12 0.31 -9999 0 -0.99 16 16
GPR124 0.001 0.1 -9999 0 -0.67 4 4
MAPK1 -0.12 0.31 -9999 0 -0.99 16 16
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.06 0.22 -9999 0 -0.5 31 31
cell adhesion -0.078 0.22 -9999 0 -0.68 13 13
ANGPTL3 -0.085 0.24 -9999 0 -0.66 26 26
VEGFR2 homodimer/VEGFA homodimer/Src 0.026 0.058 -9999 0 -0.42 3 3
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 -0.034 0.18 -9999 0 -0.67 13 13
IGF1 -0.22 0.33 -9999 0 -0.67 61 61
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.017 0.18 -9999 0 -0.61 14 14
apoptosis 0.001 0.1 -9999 0 -0.67 4 4
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.008 0.16 -9999 0 -0.54 13 13
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.044 0.22 -9999 0 -0.54 24 24
CSF1 -0.018 0.15 -9999 0 -0.67 9 9
PIK3C2A -0.12 0.25 -9999 0 -0.55 39 39
PI4 Kinase/Pyk2 -0.11 0.21 -9999 0 -0.85 8 8
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.003 0.18 -9999 0 -0.57 13 13
FAK1/Vinculin -0.027 0.17 -9999 0 -0.58 7 7
alphaV beta3/Integrin/ppsTEM5 -0.017 0.19 -9999 0 -0.61 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.15 0.29 -9999 0 -0.67 43 43
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.018 0.15 -9999 0 -0.67 9 9
F11R 0.001 0.11 -9999 0 -0.49 9 9
alphaV/beta3 Integrin/Lactadherin -0.01 0.17 -9999 0 -0.56 13 13
alphaV/beta3 Integrin/TGFBR2 -0.008 0.16 -9999 0 -0.54 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.013 0.13 -9999 0 -0.75 3 3
HSP90AA1 0.013 0.051 -9999 0 -0.66 1 1
alphaV/beta3 Integrin/Talin -0.009 0.15 -9999 0 -0.49 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.057 0.21 -9999 0 -0.67 19 19
alphaV/beta3 Integrin/Pyk2 0.006 0.17 -9999 0 -0.84 5 5
SDC1 -0.011 0.13 -9999 0 -0.67 7 7
VAV3 -0.096 0.24 -9999 0 -0.83 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.027 0.17 -9999 0 -0.58 7 7
cell migration -0.014 0.16 -9999 0 -0.53 6 6
ITGAV 0.001 0.1 -9999 0 -0.67 4 4
PI3K -0.12 0.21 -9999 0 -0.86 8 8
SPP1 -0.2 0.32 -9999 0 -0.67 56 56
KDR 0.009 0.072 -9999 0 -0.67 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.001 0.1 -9999 0 -0.67 4 4
COL4A3 -0.064 0.22 -9999 0 -0.67 21 21
angiogenesis -0.13 0.31 -9999 0 -0.93 17 17
Rac1/GTP -0.081 0.22 -9999 0 -0.76 8 8
EDIL3 -0.041 0.19 -9999 0 -0.67 15 15
cell proliferation -0.008 0.16 -9999 0 -0.53 13 13
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.055 0.17 -9999 0 -0.42 31 31
ARNO/beta Arrestin1-2 -0.015 0.093 -9999 0 -0.52 1 1
EGFR 0.001 0.1 -9999 0 -0.67 4 4
EPHA2 -0.19 0.31 -9999 0 -0.66 54 54
USP6 0.012 0.051 -9999 0 -0.67 1 1
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.13 0.24 -9999 0 -0.5 52 52
ARRB2 0.011 0.031 -9999 0 -0.4 1 1
mol:GTP -0.015 0.062 -9999 0 -0.24 5 5
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.031 0.17 -9999 0 -0.66 12 12
EGF -0.17 0.31 -9999 0 -0.67 49 49
somatostatin receptor activity 0 0 -9999 0 -0.001 16 16
ARAP2 0.001 0.1 -9999 0 -0.67 4 4
mol:GDP -0.032 0.11 -9999 0 -0.3 17 17
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 10 10
ITGA2B -0.014 0.14 -9999 0 -0.66 8 8
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.087 0.19 -9999 0 -0.37 56 56
ADAP1 -0.1 0.26 -9999 0 -0.66 31 31
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.06 0.22 -9999 0 -0.57 25 25
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.031 0.12 -9999 0 -0.31 16 16
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.1 0.21 -9999 0 -0.42 52 52
ADRB2 -0.038 0.18 -9999 0 -0.67 14 14
receptor agonist activity 0 0 -9999 0 0 13 13
actin filament binding 0 0 -9999 0 -0.001 16 16
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 -0.034 0.18 -9999 0 -0.67 13 13
GNAQ 0.016 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 11 11
ARF6/GDP -0.034 0.14 -9999 0 -0.46 11 11
ARF6/GDP/GULP/ACAP1 -0.032 0.16 -9999 0 -0.49 13 13
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.006 0.14 -9999 0 -0.39 20 20
ACAP1 -0.034 0.18 -9999 0 -0.67 13 13
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.004 0.027 -9999 0 -0.34 1 1
EFNA1 0.009 0.072 -9999 0 -0.66 2 2
HGF -0.053 0.21 -9999 0 -0.67 18 18
CYTH3 0.005 0.067 -9999 0 -0.51 3 3
CYTH2 0.011 0.002 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 11 11
endosomal lumen acidification 0 0 -9999 0 -0.001 16 16
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.009 0.072 -9999 0 -0.67 2 2
GNAQ/ARNO 0.02 0.005 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 4 4
MET -0.03 0.17 -9999 0 -0.67 12 12
GNA14 -0.003 0.11 -9999 0 -0.67 5 5
GNA15 -0.007 0.12 -9999 0 -0.67 6 6
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 11 11
GNA11 0.012 0.051 -9999 0 -0.67 1 1
LHCGR 0.005 0.007 -9999 0 -10000 0 0
AGTR1 -0.076 0.23 -9999 0 -0.67 24 24
desensitization of G-protein coupled receptor protein signaling pathway 0.004 0.027 -9999 0 -0.34 1 1
IPCEF1/ARNO -0.077 0.16 -9999 0 -0.66 1 1
alphaIIb/beta3 Integrin -0.036 0.17 -9999 0 -0.51 20 20
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.062 0.27 -9999 0 -0.84 15 15
AP1 -0.18 0.27 -9999 0 -0.69 31 31
mol:PIP3 -0.065 0.28 -9999 0 -0.7 22 22
IKBKB -0.024 0.16 -9999 0 -0.37 23 23
AKT1 -0.018 0.18 -9999 0 -0.66 7 7
IKBKG -0.024 0.16 -9999 0 -0.37 23 23
MS4A2 -0.026 0.17 -9999 0 -0.67 11 11
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.052 -9999 0 -0.67 1 1
MAP3K1 -0.042 0.24 -9999 0 -0.66 19 19
mol:Ca2+ -0.035 0.2 -9999 0 -0.48 22 22
LYN 0.003 0.092 -9999 0 -0.7 3 3
CBLB -0.048 0.23 -9999 0 -0.74 13 13
SHC1 0.016 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.02 0.079 -9999 0 -0.47 4 4
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.11 -9999 0 -0.67 5 5
PLD2 -0.054 0.21 -9999 0 -0.65 10 10
PTPN13 -0.035 0.22 -9999 0 -0.76 11 11
PTPN11 0.014 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.01 0.15 -9999 0 -0.43 10 10
SYK -0.008 0.13 -9999 0 -0.69 6 6
GRB2 0.016 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.13 0.26 -9999 0 -0.73 23 23
LAT -0.058 0.26 -9999 0 -0.82 14 14
PAK2 -0.061 0.28 -9999 0 -0.73 21 21
NFATC2 -0.097 0.22 -9999 0 -0.72 18 18
HRAS -0.083 0.32 -9999 0 -0.84 22 22
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B -0.001 0.032 -9999 0 -10000 0 0
Fc epsilon R1 -0.11 0.23 -9999 0 -0.5 40 40
Antigen/IgE/Fc epsilon R1 -0.1 0.21 -9999 0 -0.46 40 40
mol:GDP -0.11 0.35 -9999 0 -0.92 23 23
JUN 0.012 0.051 -9999 0 -0.67 1 1
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.001 -9999 0 -10000 0 0
FOS -0.12 0.27 -9999 0 -0.66 35 35
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.06 0.24 -9999 0 -0.64 19 19
CHUK -0.024 0.16 -9999 0 -0.37 23 23
KLRG1 -0.055 0.23 -9999 0 -0.73 14 14
VAV1 -0.07 0.29 -9999 0 -0.82 17 17
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.048 0.23 -9999 0 -0.74 13 13
negative regulation of mast cell degranulation -0.049 0.24 -9999 0 -0.88 11 11
BTK -0.13 0.39 -9999 0 -0.9 30 30
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.091 0.3 -9999 0 -0.78 20 20
GAB2/PI3K/SHP2 -0.081 0.18 -9999 0 -0.74 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.061 0.26 -9999 0 -0.79 14 14
RAF1 0.021 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.3 -9999 0 -0.86 20 20
FCER1G -0.05 0.2 -9999 0 -0.68 17 17
FCER1A -0.062 0.22 -9999 0 -0.68 20 20
Antigen/IgE/Fc epsilon R1/Fyn -0.095 0.2 -9999 0 -0.48 28 28
MAPK3 0.034 0.021 -9999 0 -10000 0 0
MAPK1 0.034 0.021 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.003 0.11 -9999 0 -1.2 1 1
DUSP1 0.009 0.072 -9999 0 -0.67 2 2
NF-kappa-B/RelA -0.041 0.073 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.043 0.22 -9999 0 -0.81 10 10
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.26 -9999 0 -0.78 19 19
FER -0.048 0.23 -9999 0 -0.74 13 13
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.089 0.2 -9999 0 -0.56 26 26
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.097 0.35 -9999 0 -0.9 23 23
cytokine secretion -0.029 0.052 -9999 0 -10000 0 0
SPHK1 -0.069 0.27 -9999 0 -0.8 16 16
PTK2 -0.048 0.24 -9999 0 -0.87 10 10
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.27 -9999 0 -0.76 24 24
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.058 0.27 -9999 0 -0.66 23 23
MAP2K2 0.029 0.021 -9999 0 -10000 0 0
MAP2K1 0.029 0.021 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.083 0.21 -9999 0 -0.72 13 13
MAP2K4 0.023 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.15 0.29 -9999 0 -0.56 47 47
mol:Choline -0.053 0.2 -9999 0 -0.64 10 10
SHC/Grb2/SOS1 -0.077 0.2 -9999 0 -0.79 10 10
FYN 0.012 0.051 -9999 0 -0.67 1 1
DOK1 0.009 0.072 -9999 0 -0.67 2 2
PXN -0.033 0.21 -9999 0 -0.77 10 10
HCLS1 -0.083 0.3 -9999 0 -0.73 24 24
PRKCB -0.056 0.22 -9999 0 -0.57 23 23
FCGR2B -0.08 0.24 -9999 0 -0.67 25 25
IGHE -0.002 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.051 0.26 -9999 0 -0.92 11 11
LCP2 -0.057 0.21 -9999 0 -0.67 19 19
PLA2G4A -0.061 0.26 -9999 0 -0.76 16 16
RASA1 0.012 0.051 -9999 0 -0.67 1 1
mol:Phosphatidic acid -0.053 0.2 -9999 0 -0.64 10 10
IKK complex 0.002 0.12 -9999 0 -0.28 16 16
WIPF1 -0.003 0.11 -9999 0 -0.67 5 5
Reelin signaling pathway

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
CDK5R1/CDK5 0.01 0.085 -9999 0 -0.49 5 5
VLDLR 0.009 0.072 -9999 0 -0.67 2 2
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.012 0.051 -9999 0 -0.67 1 1
ITGA3 -0.003 0.11 -9999 0 -0.66 5 5
RELN/VLDLR/Fyn -0.084 0.21 -9999 0 -0.43 45 45
MAPK8IP1/MKK7/MAP3K11/JNK1 0.029 0.094 -9999 0 -0.7 1 1
AKT1 -0.046 0.15 -9999 0 -0.52 7 7
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.042 0.19 -9999 0 -0.66 15 15
RELN/LRP8/DAB1 -0.11 0.22 -9999 0 -0.43 56 56
LRPAP1/LRP8 0.013 0.076 -9999 0 -0.49 4 4
RELN/LRP8/DAB1/Fyn -0.1 0.22 -9999 0 -0.47 25 25
DAB1/alpha3/beta1 Integrin -0.12 0.19 -9999 0 -0.68 10 10
long-term memory -0.19 0.27 -9999 0 -0.74 22 22
DAB1/LIS1 -0.12 0.19 -9999 0 -0.71 7 7
DAB1/CRLK/C3G -0.11 0.18 -9999 0 -0.69 7 7
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
DAB1/NCK2 -0.12 0.19 -9999 0 -0.72 7 7
ARHGEF2 0.012 0.051 -9999 0 -0.67 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.038 0.18 -9999 0 -0.67 14 14
CDK5R1 -0.003 0.11 -9999 0 -0.66 5 5
RELN -0.15 0.29 -9999 0 -0.67 44 44
PIK3R1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.089 0.21 -9999 0 -0.43 47 47
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.24 -9999 0 -0.76 11 11
MAPK8 0.012 0.051 -9999 0 -0.67 1 1
RELN/VLDLR/DAB1 -0.11 0.22 -9999 0 -0.43 54 54
ITGB1 0.012 0.051 -9999 0 -0.67 1 1
MAP1B -0.097 0.23 -9999 0 -0.8 8 8
RELN/LRP8 -0.087 0.2 -9999 0 -0.42 47 47
GRIN2B/RELN/LRP8/DAB1/Fyn -0.17 0.26 -9999 0 -0.72 18 18
PI3K 0.021 0.039 -9999 0 -0.49 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.007 0.093 -9999 0 -0.49 6 6
RAP1A -0.059 0.19 -9999 0 -0.64 7 7
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 -0.01 0.13 -9999 0 -0.66 7 7
CRLK/C3G 0.024 0 -9999 0 -10000 0 0
GRIN2B -0.13 0.27 -9999 0 -0.67 36 36
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.028 0.15 -9999 0 -0.52 9 9
neuron adhesion -0.052 0.2 -9999 0 -0.59 10 10
LRP8 0.001 0.1 -9999 0 -0.66 4 4
GSK3B -0.035 0.15 -9999 0 -0.49 7 7
RELN/VLDLR/DAB1/Fyn -0.096 0.22 -9999 0 -0.76 7 7
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.058 0.16 -9999 0 -0.56 7 7
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT -0.03 0.16 -9999 0 -0.6 13 13
neuron migration -0.039 0.19 -9999 0 -0.52 9 9
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.15 -9999 0 -0.52 9 9
RELN/VLDLR -0.073 0.19 -9999 0 -0.39 48 48
IL27-mediated signaling events

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
TGFB1 0.003 0.093 -10000 0 -0.67 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.073 0.19 0.59 12 -10000 0 12
IL27/IL27R/JAK1 -0.12 0.26 -10000 0 -0.86 10 10
TBX21 -0.1 0.28 -10000 0 -0.65 27 27
IL12B -0.032 0.17 -10000 0 -0.67 12 12
IL12A -0.027 0.14 -10000 0 -0.5 14 14
IL6ST -0.057 0.22 -10000 0 -0.68 19 19
IL27RA/JAK1 0.005 0.15 -10000 0 -1.4 2 2
IL27 -0.08 0.23 -10000 0 -0.67 24 24
TYK2 0.017 0.009 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.15 -10000 0 -0.8 2 2
T-helper 2 cell differentiation 0.073 0.19 0.59 12 -10000 0 12
T cell proliferation during immune response 0.073 0.19 0.59 12 -10000 0 12
MAPKKK cascade -0.073 0.19 -10000 0 -0.59 12 12
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.013 0.051 -10000 0 -0.67 1 1
IL12RB1 -0.045 0.2 -10000 0 -0.67 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.093 0.27 -10000 0 -0.63 25 25
IL27/IL27R/JAK2/TYK2 -0.074 0.2 -10000 0 -0.6 12 12
positive regulation of T cell mediated cytotoxicity -0.073 0.19 -10000 0 -0.59 12 12
STAT1 (dimer) -0.16 0.3 -10000 0 -0.8 21 21
JAK2 0.019 0.009 -10000 0 -10000 0 0
JAK1 0.016 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.061 0.19 -10000 0 -0.57 11 11
T cell proliferation -0.13 0.24 -10000 0 -0.6 24 24
IL12/IL12R/TYK2/JAK2 -0.07 0.28 -10000 0 -0.93 14 14
IL17A -0.057 0.15 -10000 0 -0.81 2 2
mast cell activation 0.073 0.19 0.59 12 -10000 0 12
IFNG -0.01 0.041 -10000 0 -0.12 11 11
T cell differentiation -0.005 0.007 0.016 1 -0.023 10 11
STAT3 (dimer) -0.061 0.19 -10000 0 -0.56 12 12
STAT5A (dimer) -0.063 0.19 -10000 0 -0.57 12 12
STAT4 (dimer) -0.084 0.22 -10000 0 -0.63 15 15
STAT4 -0.026 0.16 -10000 0 -0.67 11 11
T cell activation -0.011 0.016 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.014 0.2 0.47 1 -1.4 2 3
GATA3 -0.052 0.3 -10000 0 -0.89 16 16
IL18 -0.007 0.1 -10000 0 -0.51 7 7
positive regulation of mast cell cytokine production -0.06 0.18 -10000 0 -0.55 12 12
IL27/EBI3 -0.11 0.24 -10000 0 -0.52 43 43
IL27RA -0.011 0.16 0.38 1 -1.5 2 3
IL6 -0.12 0.27 -10000 0 -0.67 34 34
STAT5A 0.012 0.051 -10000 0 -0.67 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 0.003 0.12 0.5 2 -1.3 1 3
IL1B -0.036 0.15 -10000 0 -0.5 17 17
EBI3 -0.065 0.22 -10000 0 -0.67 21 21
TNF -0.11 0.22 -10000 0 -0.51 42 42
Wnt signaling

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
Noncanonical Wnts/FZD -0.066 0.22 -9999 0 -0.68 14 14
FZD6 0.012 0.051 -9999 0 -0.67 1 1
WNT6 -0.023 0.16 -9999 0 -0.67 10 10
WNT4 -0.045 0.2 -9999 0 -0.66 16 16
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A -0.007 0.12 -9999 0 -0.67 6 6
WNT11 -0.12 0.27 -9999 0 -0.67 35 35
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.026 0.16 0.67 11 -10000 0 11
PI3K Class IB/PDE3B -0.026 0.16 -10000 0 -0.67 11 11
PDE3B -0.026 0.16 -10000 0 -0.67 11 11
FOXM1 transcription factor network

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
NFATC3 0.082 0.48 -9999 0 -1.2 14 14
PLK1 0.041 0.16 -9999 0 -0.6 9 9
BIRC5 0.015 0.29 -9999 0 -1.2 8 8
HSPA1B 0.058 0.5 -9999 0 -1.2 15 15
MAP2K1 0.047 0.042 -9999 0 -10000 0 0
BRCA2 0.079 0.48 -9999 0 -1.2 14 14
FOXM1 0.001 0.75 -9999 0 -2.1 15 15
XRCC1 0.082 0.48 -9999 0 -1.2 14 14
FOXM1B/p19 -0.18 0.42 -9999 0 -1.2 19 19
Cyclin D1/CDK4 0.025 0.49 -9999 0 -1.1 16 16
CDC2 0.072 0.5 -9999 0 -1.3 15 15
TGFA 0.032 0.49 -9999 0 -1.1 16 16
SKP2 0.082 0.48 -9999 0 -1.2 14 14
CCNE1 0 0.12 -9999 0 -0.65 6 6
CKS1B 0.081 0.48 -9999 0 -1.2 14 14
RB1 -0.082 0.19 -9999 0 -0.89 6 6
FOXM1C/SP1 0.049 0.55 -9999 0 -1.5 14 14
AURKB 0.011 0.3 -9999 0 -1.1 10 10
CENPF 0.073 0.5 -9999 0 -1.3 14 14
CDK4 0.026 0.019 -9999 0 -10000 0 0
MYC 0.095 0.43 -9999 0 -1 14 14
CHEK2 0.043 0.071 -9999 0 -0.72 1 1
ONECUT1 0.007 0.54 -9999 0 -1.3 17 17
CDKN2A -0.14 0.28 -9999 0 -0.67 40 40
LAMA4 0.073 0.49 -9999 0 -1.3 15 15
FOXM1B/HNF6 -0.035 0.66 -9999 0 -1.7 17 17
FOS 0.022 0.5 -9999 0 -1.2 15 15
SP1 0.018 0.001 -9999 0 -10000 0 0
CDC25B 0.081 0.48 -9999 0 -1.2 14 14
response to radiation 0.026 0.039 -9999 0 -10000 0 0
CENPB 0.082 0.48 -9999 0 -1.2 14 14
CENPA 0.077 0.49 -9999 0 -1.3 14 14
NEK2 0.035 0.52 -9999 0 -1.3 16 16
HIST1H2BA 0.072 0.47 -9999 0 -1.2 14 14
CCNA2 0.011 0.091 -9999 0 -0.68 3 3
EP300 0.016 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.05 0.57 -9999 0 -1.5 15 15
CCNB2 0.068 0.51 -9999 0 -1.3 16 16
CCNB1 0.073 0.51 -9999 0 -1.3 15 15
ETV5 0.081 0.48 -9999 0 -1.2 14 14
ESR1 0.047 0.54 -9999 0 -1.3 20 20
CCND1 0.027 0.5 -9999 0 -1.2 16 16
GSK3A 0.043 0.036 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.033 0.13 -9999 0 -0.45 10 10
CDK2 0.015 0.075 -9999 0 -0.68 2 2
G2/M transition of mitotic cell cycle 0.031 0.045 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.4 -9999 0 -1.3 17 17
GAS1 0.031 0.56 -9999 0 -1.3 21 21
MMP2 0.054 0.54 -9999 0 -1.3 18 18
RB1/FOXM1C 0.035 0.5 -9999 0 -1.2 15 15
CREBBP 0.016 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.053 0.21 -9999 0 -0.67 18 18
GNB1/GNG2 -0.053 0.22 -9999 0 -0.66 14 14
mol:DAG -0.039 0.2 -9999 0 -0.62 12 12
PLCG1 -0.041 0.2 -9999 0 -0.65 12 12
YES1 -0.053 0.21 -9999 0 -0.64 14 14
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.012 0.051 -9999 0 -0.67 1 1
G protein -0.046 0.22 -9999 0 -0.72 12 12
MAP3K7 -0.033 0.2 -9999 0 -0.64 12 12
mol:Ca2+ -0.037 0.19 -9999 0 -0.6 12 12
mol:IP3 -0.039 0.2 -9999 0 -0.62 12 12
NLK -0.003 0.008 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.047 0.23 -9999 0 -0.68 14 14
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.066 0.22 -9999 0 -0.68 14 14
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.059 0.24 -9999 0 -0.7 14 14
GO:0007205 -0.038 0.19 -9999 0 -0.61 12 12
WNT6 -0.023 0.16 -9999 0 -0.67 10 10
WNT4 -0.045 0.2 -9999 0 -0.66 16 16
NFAT1/CK1 alpha -0.058 0.23 -9999 0 -0.76 10 10
GNG2 -0.003 0.11 -9999 0 -0.67 5 5
WNT5A -0.007 0.12 -9999 0 -0.67 6 6
WNT11 -0.12 0.27 -9999 0 -0.67 35 35
CDC42 -0.042 0.2 -9999 0 -0.63 12 12
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.024 0.16 -9999 0 -0.48 19 19
EPHB2 -0.014 0.14 -9999 0 -0.67 8 8
Syndecan-2/TACI -0.069 0.19 -9999 0 -0.43 38 38
LAMA1 -0.034 0.18 -9999 0 -0.67 13 13
Syndecan-2/alpha2 ITGB1 -0.096 0.21 -9999 0 -0.63 5 5
HRAS 0.016 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.01 0.057 -9999 0 -0.43 3 3
ITGA5 0.005 0.088 -9999 0 -0.67 3 3
BAX 0.038 0.071 -9999 0 -0.72 1 1
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.02 0.052 -9999 0 -0.38 3 3
LAMA3 -0.2 0.32 -9999 0 -0.66 57 57
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.003 0.11 -9999 0 -0.67 5 5
Syndecan-2/MMP2 -0.007 0.14 -9999 0 -0.48 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.007 0.1 -9999 0 -0.58 5 5
dendrite morphogenesis 0.003 0.12 -9999 0 -0.5 9 9
Syndecan-2/GM-CSF -0.06 0.18 -9999 0 -0.43 35 35
determination of left/right symmetry 0.015 0.067 -9999 0 -0.49 3 3
Syndecan-2/PKC delta 0.023 0.058 -9999 0 -0.42 3 3
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.044 0.17 -9999 0 -0.38 35 35
MAPK1 -0.044 0.17 -9999 0 -0.38 35 35
Syndecan-2/RACK1 0.03 0.05 -9999 0 -0.35 3 3
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.015 0.067 -9999 0 -0.49 3 3
ITGA2 -0.003 0.11 -9999 0 -0.67 5 5
MAPK8 0.031 0.078 -9999 0 -0.54 3 3
Syndecan-2/alpha2/beta1 Integrin 0 0.16 -9999 0 -0.71 5 5
Syndecan-2/Kininogen -0.041 0.17 -9999 0 -0.44 25 25
ITGB1 0.012 0.051 -9999 0 -0.67 1 1
SRC 0.037 0.048 -9999 0 -0.33 1 1
Syndecan-2/CASK/Protein 4.1 0.021 0.053 -9999 0 -0.38 3 3
extracellular matrix organization 0.015 0.09 -9999 0 -0.49 5 5
actin cytoskeleton reorganization -0.024 0.16 -9999 0 -0.48 19 19
Syndecan-2/Caveolin-2/Ras 0.02 0.094 -9999 0 -0.43 7 7
Syndecan-2/Laminin alpha3 -0.12 0.21 -9999 0 -0.41 60 60
Syndecan-2/RasGAP 0.035 0.067 -9999 0 -0.45 3 3
alpha5/beta1 Integrin 0.013 0.077 -9999 0 -0.49 4 4
PRKCD 0.016 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.003 0.12 -9999 0 -0.5 9 9
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.044 0.065 -9999 0 -0.66 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.12 0.27 -9999 0 -0.67 36 36
RASA1 0.012 0.051 -9999 0 -0.67 1 1
alpha2/beta1 Integrin 0.007 0.1 -9999 0 -0.58 5 5
Syndecan-2/Synbindin 0.023 0.058 -9999 0 -0.42 3 3
TGFB1 0.005 0.088 -9999 0 -0.67 3 3
CASP3 0.032 0.053 -9999 0 -0.37 3 3
FN1 -0.057 0.21 -9999 0 -0.67 19 19
Syndecan-2/IL8 -0.057 0.19 -9999 0 -0.46 32 32
SDC2 0.015 0.067 -9999 0 -0.5 3 3
KNG1 -0.082 0.23 -9999 0 -0.66 24 24
Syndecan-2/Neurofibromin 0.023 0.058 -9999 0 -0.42 3 3
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.11 0.26 -9999 0 -0.66 33 33
Syndecan-2/TGFB1 0.015 0.091 -9999 0 -0.5 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.021 0.053 -9999 0 -0.38 3 3
Syndecan-2/Ezrin 0.032 0.053 -9999 0 -0.37 3 3
PRKACA 0.032 0.053 -9999 0 -0.37 3 3
angiogenesis -0.057 0.19 -9999 0 -0.45 32 32
MMP2 -0.03 0.17 -9999 0 -0.67 12 12
IL8 -0.11 0.26 -9999 0 -0.67 32 32
calcineurin-NFAT signaling pathway -0.068 0.19 -9999 0 -0.43 38 38
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.076 0.23 -9999 0 -0.74 10 10
SMAD6-7/SMURF1 0.031 0.034 -9999 0 -0.42 1 1
NOG -0.022 0.16 -9999 0 -0.67 10 10
SMAD9 -0.005 0.13 -9999 0 -0.48 10 10
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 0.025 0.1 -9999 0 -0.49 5 5
BMP7/USAG1 -0.24 0.31 -9999 0 -0.56 81 81
SMAD5/SKI 0.033 0.1 -9999 0 -0.46 5 5
SMAD1 0.053 0.016 -9999 0 -10000 0 0
BMP2 0.009 0.072 -9999 0 -0.67 2 2
SMAD1/SMAD1/SMAD4 -0.001 0.018 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.007 0.12 -9999 0 -0.67 6 6
BMPR1A-1B/BAMBI 0.016 0.088 -9999 0 -0.42 7 7
AHSG -0.14 0.28 -9999 0 -0.66 40 40
CER1 -0.001 0.071 -9999 0 -0.66 2 2
BMP2-4/CER1 -0.012 0.14 -9999 0 -0.48 14 14
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.015 0.14 -9999 0 -0.54 6 6
BMP2-4 (homodimer) -0.016 0.14 -9999 0 -0.52 13 13
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.026 0.081 -9999 0 -0.37 7 7
RGMA -0.037 0.18 -9999 0 -0.67 14 14
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.006 0.13 -9999 0 -0.49 7 7
BMP2-4/USAG1 -0.17 0.24 -9999 0 -0.44 75 75
SMAD6/SMURF1/SMAD5 0.033 0.1 -9999 0 -0.46 5 5
SOSTDC1 -0.24 0.33 -9999 0 -0.66 67 67
BMP7/BMPR2/BMPR1A-1B -0.038 0.18 -9999 0 -0.42 31 31
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.012 0.051 -9999 0 -0.67 1 1
HFE2 0.001 0.071 -9999 0 -0.66 2 2
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.011 0.16 -9999 0 -0.49 15 15
SMAD5/SMAD5/SMAD4 0.033 0.1 -9999 0 -0.46 5 5
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.03 0.094 -9999 0 -0.46 5 5
BMP7 (homodimer) -0.094 0.25 -9999 0 -0.66 29 29
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.095 0.22 -9999 0 -0.5 40 40
SMAD1/SKI 0.06 0.015 -9999 0 -10000 0 0
SMAD6 0.012 0.051 -9999 0 -0.67 1 1
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.1 0.22 -9999 0 -0.45 49 49
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.091 0.25 -9999 0 -0.66 28 28
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.031 0.033 -9999 0 -0.41 1 1
BMPR1A-1B (homodimer) 0.007 0.094 -9999 0 -0.49 6 6
CHRDL1 -0.11 0.27 -9999 0 -0.67 34 34
ENDOFIN/SMAD1 0.06 0.015 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.02 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.012 0.051 -9999 0 -0.67 1 1
SMURF2 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.086 0.22 -9999 0 -0.47 42 42
BMP2-4/GREM1 -0.07 0.22 -9999 0 -0.48 36 36
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.003 0.12 -9999 0 -0.46 9 9
SMAD1/SMAD6 0.06 0.015 -9999 0 -10000 0 0
TAK1/SMAD6 0.024 0 -9999 0 -10000 0 0
BMP7 -0.094 0.25 -9999 0 -0.66 29 29
BMP6 0.012 0.051 -9999 0 -0.67 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.014 0.12 -9999 0 -0.46 6 6
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.06 0.015 -9999 0 -10000 0 0
SMAD7/SMURF1 0.024 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.051 -9999 0 -0.66 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.026 0.19 -9999 0 -0.56 12 12
CHRD 0.001 0.1 -9999 0 -0.67 4 4
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.001 0.14 -9999 0 -0.53 7 7
BMP4 -0.03 0.17 -9999 0 -0.66 12 12
FST -0.071 0.23 -9999 0 -0.66 23 23
BMP2-4/NOG -0.026 0.17 -9999 0 -0.45 22 22
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.027 0.17 -9999 0 -0.71 4 4
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.002 0.18 -9999 0 -1.3 3 3
VDR 0.001 0.1 -9999 0 -0.67 4 4
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.057 0.2 -9999 0 -0.55 14 14
RXRs/LXRs/DNA/Oxysterols -0.077 0.25 -9999 0 -0.7 14 14
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA -0.005 0.024 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.037 0.059 -9999 0 -0.57 1 1
RXRs/NUR77 -0.1 0.23 -9999 0 -0.57 21 21
RXRs/PPAR -0.068 0.16 -9999 0 -0.43 14 14
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.001 0.077 -9999 0 -0.5 4 4
RARs/VDR/DNA/Vit D3 0.024 0.085 -9999 0 -0.41 6 6
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.001 0.1 -9999 0 -0.67 4 4
RARs/RARs/DNA/9cRA 0.02 0.053 -9999 0 -0.37 3 3
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.024 0.073 -9999 0 -0.41 3 3
RARs/THRs/DNA/SMRT 0.037 0.059 -9999 0 -0.57 1 1
THRA 0.013 0.051 -9999 0 -0.66 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.001 0.077 -9999 0 -0.5 4 4
RXRs/PPAR/9cRA/PGJ2/DNA -0.058 0.18 -9999 0 -0.4 34 34
NR1H4 -0.15 0.3 -9999 0 -0.67 44 44
RXRs/LXRs/DNA -0.049 0.21 -9999 0 -0.59 12 12
NR1H2 0.015 0.018 -9999 0 -10000 0 0
NR1H3 -0.001 0.11 -9999 0 -0.68 4 4
RXRs/VDR/DNA/Vit D3 -0.048 0.18 -9999 0 -0.43 16 16
NR4A1 -0.087 0.24 -9999 0 -0.66 27 27
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.1 0.19 -9999 0 -0.42 33 33
RXRG -0.12 0.27 -9999 0 -0.67 34 34
RXR alpha/CCPG 0.023 0.013 -9999 0 -10000 0 0
RXRA 0.015 0.018 -9999 0 -10000 0 0
RXRB 0.014 0.021 -9999 0 -10000 0 0
THRB 0.012 0.051 -9999 0 -0.67 1 1
PPARG -0.12 0.27 -9999 0 -0.66 36 36
PPARD 0.012 0.051 -9999 0 -0.67 1 1
TNF -0.24 0.54 -9999 0 -1.2 42 42
mol:Oxysterols -0.003 0.022 -9999 0 -10000 0 0
cholesterol transport -0.075 0.25 -9999 0 -0.7 14 14
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.005 0.088 -9999 0 -0.67 3 3
RXRs/NUR77/BCL2 -0.076 0.2 -9999 0 -0.48 23 23
SREBF1 -0.06 0.23 -9999 0 -0.63 14 14
RXRs/RXRs/DNA/9cRA -0.057 0.18 -9999 0 -0.4 34 34
ABCA1 -0.067 0.26 -9999 0 -0.76 12 12
RARs/THRs 0.038 0.075 -9999 0 -0.71 1 1
RXRs/FXR -0.14 0.26 -9999 0 -0.59 31 31
BCL2 -0.014 0.14 -9999 0 -0.67 8 8
Effects of Botulinum toxin

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
STX1A -0.082 0.2 -9999 0 -0.5 33 33
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.009 0.12 -9999 0 -0.49 11 11
STXBP1 0.005 0.087 -9999 0 -0.66 3 3
ACh/CHRNA1 -0.076 0.17 -9999 0 -0.47 26 26
RAB3GAP2/RIMS1/UNC13B 0.005 0.11 -9999 0 -0.41 11 11
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 -0.027 0.16 -9999 0 -0.66 11 11
mol:ACh -0.029 0.068 -9999 0 -0.16 28 28
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.098 0.16 -9999 0 -0.52 11 11
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.076 0.17 -9999 0 -0.47 26 26
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.081 0.24 -9999 0 -0.67 25 25
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.031 0.12 -9999 0 -0.49 9 9
SNAP25 -0.04 0.12 -9999 0 -0.3 28 28
VAMP2 0.007 0.016 -9999 0 -0.21 1 1
SYT1 -0.014 0.14 -9999 0 -0.67 8 8
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.067 0.19 -9999 0 -0.44 34 34
STX1A/SNAP25 fragment 1/VAMP2 -0.098 0.16 -9999 0 -0.52 11 11
Neurotrophic factor-mediated Trk receptor signaling

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.015 0.097 -10000 0 -0.5 4 4
NT3 (dimer)/TRKC -0.007 0.13 -10000 0 -0.54 10 10
NT3 (dimer)/TRKB -0.097 0.27 -10000 0 -0.6 37 37
SHC/Grb2/SOS1/GAB1/PI3K 0.043 0.024 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.022 0.16 -10000 0 -0.66 10 10
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.005 0.088 -10000 0 -0.67 3 3
NTRK2 -0.072 0.23 -10000 0 -0.67 23 23
NTRK3 -0.014 0.14 -10000 0 -0.67 8 8
NT-4/5 (dimer)/TRKB -0.38 0.31 -10000 0 -0.52 133 133
neuron apoptosis 0.066 0.21 0.54 23 -10000 0 23
SHC 2-3/Grb2 -0.075 0.24 -10000 0 -0.61 23 23
SHC1 0.016 0 -10000 0 -10000 0 0
SHC2 -0.1 0.22 -10000 0 -0.64 21 21
SHC3 -0.12 0.22 -10000 0 -0.62 25 25
STAT3 (dimer) 0.023 0.032 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.051 0.2 -10000 0 -0.47 30 30
RIN/GDP 0.039 0.071 -10000 0 -0.27 2 2
GIPC1 0.016 0 -10000 0 -10000 0 0
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.076 0.17 -10000 0 -0.43 28 28
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.03 0.067 -10000 0 -0.6 2 2
MAGED1 0.016 0 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.45 0.32 -10000 0 -0.66 121 121
SHC/GRB2/SOS1 0.033 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.12 0.24 -10000 0 -0.47 54 54
TRKA/NEDD4-2 0.015 0.067 -10000 0 -0.49 3 3
ELMO1 0.005 0.088 -10000 0 -0.67 3 3
RhoG/GTP/ELMO1/DOCK1 0.015 0.058 -10000 0 -0.43 3 3
NGF -0.022 0.16 -10000 0 -0.67 10 10
HRAS 0.016 0 -10000 0 -10000 0 0
DOCK1 0.016 0 -10000 0 -10000 0 0
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 0.005 0.088 -10000 0 -0.66 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.079 0.18 -10000 0 -0.44 29 29
mol:GDP 0.05 0.1 -10000 0 -0.4 3 3
NGF (dimer) -0.022 0.16 -10000 0 -0.67 10 10
RhoG/GDP 0.003 0.066 -10000 0 -0.5 3 3
RIT1/GDP 0.047 0.072 -10000 0 -0.28 1 1
TIAM1 -0.014 0.14 -10000 0 -0.67 8 8
PIK3R1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.049 0.18 -10000 0 -0.44 31 31
KIDINS220/CRKL/C3G 0.024 0 -10000 0 -10000 0 0
SHC/RasGAP 0.021 0.039 -10000 0 -0.49 1 1
FRS2 family/SHP2 0.033 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.042 0 -10000 0 -10000 0 0
RIT1/GTP 0.012 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.088 -10000 0 -0.67 3 3
RAP1/GDP -0.012 0.04 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.022 0.16 -10000 0 -0.66 10 10
ubiquitin-dependent protein catabolic process 0 0.12 -10000 0 -0.42 13 13
Schwann cell development -0.021 0.033 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.042 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.049 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.074 0.17 -10000 0 -0.7 8 8
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
Rap1/GTP 0.028 0.077 -10000 0 -10000 0 0
STAT3 0.023 0.032 -10000 0 -10000 0 0
axon guidance -0.071 0.16 -10000 0 -0.65 8 8
MAPK3 -0.1 0.22 -10000 0 -0.42 54 54
MAPK1 -0.1 0.22 -10000 0 -0.42 54 54
CDC42/GDP 0.047 0.072 -10000 0 -0.28 1 1
NTF3 0.005 0.088 -10000 0 -0.67 3 3
NTF4 -0.45 0.32 -10000 0 -0.66 121 121
NGF (dimer)/TRKA/FAIM 0 0.12 -10000 0 -0.42 13 13
PI3K 0.021 0.039 -10000 0 -0.49 1 1
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.24 -10000 0 -0.51 43 43
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0.006 0.12 -10000 0 -0.45 10 10
RGS19 0.005 0.088 -10000 0 -0.67 3 3
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.027 0.084 -10000 0 -10000 0 0
Rac1/GDP 0.047 0.072 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.011 0.12 -10000 0 -0.43 13 13
neuron projection morphogenesis -0.032 0.18 -10000 0 -0.62 7 7
NGF (dimer)/TRKA/NEDD4-2 0 0.12 -10000 0 -0.42 13 13
MAP2K1 0.046 0 -10000 0 -10000 0 0
NGFR -0.092 0.25 -10000 0 -0.67 28 28
NGF (dimer)/TRKA/GIPC/GAIP 0.011 0.11 -10000 0 -0.8 1 1
RAS family/GTP/PI3K 0.036 0.024 -10000 0 -0.28 1 1
FRS2 family/SHP2/GRB2/SOS1 0.049 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
PRKCI 0.009 0.072 -10000 0 -0.66 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.051 -10000 0 -0.66 1 1
MAPKKK cascade -0.062 0.18 -10000 0 -0.72 12 12
RASA1 0.012 0.051 -10000 0 -0.67 1 1
TRKA/c-Abl 0.015 0.067 -10000 0 -0.49 3 3
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.034 0.17 -10000 0 -0.4 25 25
NGF (dimer)/TRKA/p62/Atypical PKCs 0.013 0.11 -10000 0 -10000 0 0
MATK -0.17 0.3 -10000 0 -0.67 48 48
NEDD4L 0.016 0 -10000 0 -10000 0 0
RAS family/GDP -0.01 0.039 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.081 0.18 -10000 0 -0.43 33 33
Rac1/GTP -0.072 0.13 -10000 0 -0.39 19 19
FRS2 family/SHP2/CRK family 0.049 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0.001 0.038 -9999 0 -0.5 1 1
Metarhodopsin II/Arrestin 0.004 0.005 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.11 0.21 -9999 0 -0.44 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.05 -9999 0 -0.66 1 1
GRK1 0.002 0.006 -9999 0 -10000 0 0
CNG Channel -0.23 0.3 -9999 0 -0.75 35 35
mol:Na + -0.16 0.19 -9999 0 -0.66 9 9
mol:ADP 0.002 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0 0.12 -9999 0 -0.41 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.2 -9999 0 -0.69 9 9
CNGB1 -0.01 0.12 -9999 0 -0.67 6 6
RDH5 0.013 0.051 -9999 0 -0.66 1 1
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.2 -9999 0 -0.63 9 9
Na + (4 Units) -0.14 0.18 -9999 0 -0.61 9 9
RGS9 -0.022 0.16 -9999 0 -0.66 10 10
GNB1/GNGT1 0.012 0 -9999 0 -10000 0 0
GNAT1/GDP 0 0.1 -9999 0 -0.35 14 14
GUCY2D -0.008 0.12 -9999 0 -0.67 6 6
GNGT1 0 0 -9999 0 -10000 0 0
GUCY2F 0.003 0.006 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.14 0.28 -9999 0 -0.51 58 58
mol:11-cis-retinal 0.013 0.051 -9999 0 -0.66 1 1
mol:cGMP -0.067 0.18 -9999 0 -0.71 3 3
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin 0.013 0.038 -9999 0 -0.49 1 1
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.12 0.28 -9999 0 -0.67 36 36
Metarhodopsin II 0.005 0.006 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.073 0.19 -9999 0 -0.48 11 11
RGS9BP 0.003 0.088 -9999 0 -0.66 3 3
Metarhodopsin II/Transducin 0.011 0.019 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.069 0.18 -9999 0 -0.4 39 39
PDE6A/B -0.065 0.21 -9999 0 -0.52 29 29
mol:Pi -0.001 0.12 -9999 0 -0.41 13 13
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.011 0.03 -9999 0 -0.39 1 1
PDE6B -0.088 0.25 -9999 0 -0.67 27 27
PDE6A 0.001 0.1 -9999 0 -0.67 4 4
PDE6G -0.18 0.31 -9999 0 -0.67 50 50
RHO 0.006 0.008 -9999 0 -10000 0 0
PDE6 -0.18 0.28 -9999 0 -0.75 26 26
GUCA1A -0.035 0.18 -9999 0 -0.67 13 13
GC2/GCAP Family -0.067 0.18 -9999 0 -0.42 20 20
GUCA1C -0.1 0.24 -9999 0 -0.66 28 28
GUCA1B 0.016 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.029 0.17 -9999 0 -0.47 21 21
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DOCK1 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.061 0.22 -9999 0 -0.67 20 20
alpha4/beta7 Integrin/MAdCAM1 -0.13 0.24 -9999 0 -0.75 11 11
EPO -0.14 0.28 -9999 0 -0.67 40 40
alpha4/beta7 Integrin -0.046 0.18 -9999 0 -0.49 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.037 0.17 -9999 0 -0.49 21 21
EPO/EPOR (dimer) -0.097 0.22 -9999 0 -0.49 41 41
lamellipodium assembly 0.005 0.033 -9999 0 -0.37 1 1
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
PI3K 0.021 0.039 -9999 0 -0.49 1 1
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.079 0.19 -9999 0 -0.71 6 6
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
MADCAM1 -0.17 0.31 -9999 0 -0.67 49 49
cell adhesion -0.12 0.24 -9999 0 -0.74 11 11
CRKL/CBL 0.024 0 -9999 0 -10000 0 0
ITGB1 0.012 0.051 -9999 0 -0.67 1 1
SRC -0.06 0.22 -9999 0 -0.48 34 34
ITGB7 0.001 0.1 -9999 0 -0.67 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.075 0.24 -9999 0 -0.53 34 34
p130Cas/Crk/Dock1 -0.025 0.19 -9999 0 -0.63 10 10
VCAM1 -0.072 0.23 -9999 0 -0.67 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.007 0.13 -9999 0 -10000 0 0
BCAR1 -0.047 0.21 -9999 0 -0.69 10 10
EPOR 0.012 0.051 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0.005 0.034 -9999 0 -0.38 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0.016 0 -9999 0 -10000 0 0
EGFR 0.001 0.1 -9999 0 -0.67 4 4
EGF/EGFR -0.13 0.22 -9999 0 -0.8 9 9
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.068 0.18 -9999 0 -0.71 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.018 0.15 -9999 0 -0.67 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.17 0.3 -9999 0 -0.67 49 49
EGF/EGFR dimer/SHC -0.1 0.21 -9999 0 -0.42 52 52
mol:GDP -0.1 0.16 -9999 0 -0.7 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.007 0.12 -9999 0 -0.67 6 6
GRB2/SOS1 0.024 0 -9999 0 -10000 0 0
HRAS/GTP -0.092 0.15 -9999 0 -0.65 1 1
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.094 0.15 -9999 0 -0.65 1 1
FRAP1 -0.068 0.17 -9999 0 -0.67 1 1
EGF/EGFR dimer -0.13 0.24 -9999 0 -0.5 52 52
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.017 0.17 -9999 0 -0.64 11 11
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.009 0.072 -9999 0 -0.67 2 2
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.087 0.2 -9999 0 -0.42 47 47
CaM/Ca2+ 0.012 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.07 0.18 -9999 0 -0.38 47 47
IQGAP1/CaM 0.024 0 -9999 0 -10000 0 0
DAB1 -0.042 0.19 -9999 0 -0.66 15 15
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.12 0.27 -9999 0 -0.67 34 34
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 0.013 0.076 -9999 0 -0.49 4 4
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 -0.003 0.11 -9999 0 -0.66 5 5
LIS1/Poliovirus Protein 3A 0.02 0 -9999 0 -10000 0 0
CDK5R2 -0.068 0.22 -9999 0 -0.67 22 22
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.12 0.24 -9999 0 -0.46 54 54
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.056 0.19 -9999 0 -0.51 11 11
MAP1B -0.006 0.044 -9999 0 -0.34 3 3
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.055 0.18 -9999 0 -0.66 3 3
RELN -0.15 0.29 -9999 0 -0.67 44 44
PAFAH/LIS1 -0.054 0.18 -9999 0 -0.42 34 34
LIS1/CLIP170 0.032 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.077 0.12 -9999 0 -0.43 5 5
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.046 0.16 -9999 0 -0.57 7 7
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.069 0.2 -9999 0 -0.55 11 11
LIS1/IQGAP1 0.032 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.027 0 -9999 0 -10000 0 0
PAFAH1B3 0.013 0.051 -9999 0 -0.66 1 1
PAFAH1B2 0.012 0.051 -9999 0 -0.67 1 1
MAP1B/LIS1/Dynein heavy chain 0.027 0.031 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.047 0.18 -9999 0 -0.49 11 11
LRP8 0.001 0.1 -9999 0 -0.66 4 4
NDEL1/Katanin 60 -0.056 0.19 -9999 0 -0.51 11 11
P39/CDK5 -0.09 0.21 -9999 0 -0.66 9 9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.032 0 -9999 0 -10000 0 0
CDK5 -0.056 0.18 -9999 0 -0.69 1 1
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.028 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.084 0.22 -9999 0 -0.76 6 6
RELN/VLDLR -0.073 0.19 -9999 0 -0.39 48 48
CDC42 0 0 -9999 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.009 0.11 -9999 0 -0.42 12 12
EFNA5 0.005 0.088 -9999 0 -0.67 3 3
FYN 0 0.11 -9999 0 -0.41 12 12
neuron projection morphogenesis -0.009 0.11 -9999 0 -0.42 12 12
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.009 0.11 -9999 0 -0.42 12 12
EPHA5 -0.02 0.15 -9999 0 -0.66 9 9
Cellular roles of Anthrax toxin

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
ANTXR1 -0.03 0.17 -10000 0 -0.67 12 12
ANTXR2 0.009 0.072 -10000 0 -0.67 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.024 -10000 0 -0.093 12 12
monocyte activation -0.16 0.31 -10000 0 -0.58 53 53
MAP2K2 -0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.005 0.02 -10000 0 -10000 0 0
MAP2K7 -0.005 0.02 -10000 0 -10000 0 0
MAP2K6 -0.012 0.056 -10000 0 -0.41 3 3
CYAA -0.012 0.12 -10000 0 -0.43 12 12
MAP2K4 -0.005 0.02 -10000 0 -10000 0 0
IL1B -0.033 0.14 -10000 0 -0.41 21 21
Channel -0.011 0.12 -10000 0 -0.45 12 12
NLRP1 -0.016 0.075 -10000 0 -0.44 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.024 0.093 12 -10000 0 12
MAPK3 -0.005 0.02 -10000 0 -10000 0 0
MAPK1 -0.005 0.02 -10000 0 -10000 0 0
PGR -0.02 0.083 -10000 0 -0.42 7 7
PA/Cellular Receptors -0.012 0.13 -10000 0 -0.49 12 12
apoptosis -0.006 0.024 -10000 0 -0.093 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.01 0.12 -10000 0 -0.42 12 12
macrophage activation 0.017 0.022 -10000 0 -10000 0 0
TNF -0.15 0.29 -10000 0 -0.67 42 42
VCAM1 -0.16 0.31 -10000 0 -0.58 53 53
platelet activation -0.007 0.027 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.029 0.2 1 -10000 0 1
IL18 -0.011 0.13 -10000 0 -0.49 10 10
negative regulation of macrophage activation -0.006 0.024 -10000 0 -0.093 12 12
LEF -0.006 0.024 -10000 0 -0.093 12 12
CASP1 -0.018 0.079 -10000 0 -0.37 7 7
mol:cAMP -0.007 0.027 -10000 0 -10000 0 0
necrosis -0.006 0.024 -10000 0 -0.093 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.01 0.12 -10000 0 -0.43 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.016 0.006 -9999 0 -10000 0 0
PRKCZ 0.013 0.051 -9999 0 -0.66 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.009 0.072 -9999 0 -0.66 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.045 0.16 -9999 0 -0.63 9 9
IRAK/TOLLIP 0.034 0.004 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.25 -9999 0 -0.53 46 46
IL1A -0.053 0.21 -9999 0 -0.67 18 18
IL1B -0.044 0.2 -9999 0 -0.57 21 21
IRAK/TRAF6/p62/Atypical PKCs 0.028 0.05 -9999 0 -10000 0 0
IL1R2 -0.11 0.26 -9999 0 -0.66 32 32
IL1R1 -0.018 0.15 -9999 0 -0.67 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.14 -9999 0 -0.61 6 6
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.012 0.051 -9999 0 -0.67 1 1
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.011 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.072 0.031 -9999 0 -10000 0 0
JUN 0.042 0.065 -9999 0 -0.6 1 1
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.024 0.24 -9999 0 -0.92 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.028 0.2 -9999 0 -0.5 23 23
PIK3R1 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.018 0.19 -9999 0 -0.76 7 7
IL1 beta fragment/IL1R1/IL1RAP -0.043 0.25 -9999 0 -0.98 9 9
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.037 0.052 -9999 0 -10000 0 0
IRAK1 0.026 0.005 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.17 0.27 -9999 0 -0.53 63 63
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.009 0.072 -9999 0 -0.66 2 2
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K 0.021 0.039 -9999 0 -0.49 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.2 -9999 0 -0.75 9 9
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.043 0.25 -9999 0 -0.98 9 9
IL1 beta/IL1R2 -0.11 0.25 -9999 0 -0.49 48 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.2 -9999 0 -0.81 9 9
IRAK3 -0.014 0.14 -9999 0 -0.67 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.024 0.24 -9999 0 -0.93 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.16 -9999 0 -0.64 7 7
IL1 alpha/IL1R1/IL1RAP -0.042 0.21 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.004 -9999 0 -10000 0 0
IL1RAP 0.001 0.1 -9999 0 -0.67 4 4
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.057 0.17 -9999 0 -0.73 9 9
CASP1 -0.014 0.14 -9999 0 -0.67 8 8
IL1RN/IL1R2 -0.23 0.34 -9999 0 -0.62 69 69
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.031 0.24 -9999 0 -0.93 9 9
TMEM189-UBE2V1 0.006 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.15 -9999 0 -0.63 7 7
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
IL1RN -0.21 0.32 -9999 0 -0.66 60 60
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.032 0.047 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.018 0.069 0.26 7 -0.26 1 8
RFC1 0.018 0.069 0.26 7 -10000 0 7
PRKDC 0.018 0.069 0.26 7 -10000 0 7
RIPK1 0.017 0.003 -10000 0 -10000 0 0
CASP7 -0.016 0.084 0.27 2 -0.39 3 5
FASLG/FAS/FADD/FAF1 -0.046 0.13 -10000 0 -0.31 29 29
MAP2K4 -0.033 0.18 -10000 0 -0.52 10 10
mol:ceramide -0.049 0.19 -10000 0 -0.55 10 10
GSN 0.018 0.069 0.26 7 -10000 0 7
FASLG/FAS/FADD/FAF1/Caspase 8 -0.047 0.16 -10000 0 -0.38 31 31
FAS 0.011 0.052 -10000 0 -0.68 1 1
BID 0.007 0.098 0.32 4 -0.63 2 6
MAP3K1 -0.005 0.12 -10000 0 -0.47 5 5
MAP3K7 0.015 0.004 -10000 0 -10000 0 0
RB1 0.018 0.069 0.26 7 -10000 0 7
CFLAR 0.017 0.003 -10000 0 -10000 0 0
HGF/MET -0.043 0.2 -10000 0 -0.51 25 25
ARHGDIB 0.007 0.11 0.26 7 -0.51 5 12
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.018 0.069 -10000 0 -0.26 7 7
NFKB1 -0.046 0.076 -10000 0 -10000 0 0
MAPK8 -0.044 0.21 -10000 0 -0.63 10 10
DFFA 0.018 0.069 0.26 7 -10000 0 7
DNA fragmentation during apoptosis 0.018 0.069 0.26 7 -10000 0 7
FAS/FADD/MET -0.004 0.12 -10000 0 -0.45 12 12
CFLAR/RIP1 0.019 0.009 -10000 0 -10000 0 0
FAIM3 -0.037 0.18 -10000 0 -0.66 14 14
FAF1 0.015 0.007 -10000 0 -10000 0 0
PARP1 0.018 0.069 0.26 7 -10000 0 7
DFFB 0.018 0.069 0.26 7 -10000 0 7
CHUK -0.039 0.066 -10000 0 -10000 0 0
FASLG -0.11 0.27 -10000 0 -0.67 33 33
FAS/FADD 0.018 0.041 -10000 0 -0.51 1 1
HGF -0.053 0.21 -10000 0 -0.67 18 18
LMNA 0.017 0.063 -10000 0 -10000 0 0
CASP6 0.018 0.069 0.26 7 -10000 0 7
CASP10 0.003 0.089 -10000 0 -0.67 3 3
CASP3 0.021 0.081 0.32 7 -0.3 1 8
PTPN13 0.012 0.051 -10000 0 -0.67 1 1
CASP8 0.015 0.11 0.35 12 -0.44 3 15
IL6 -0.14 0.39 -10000 0 -1.3 14 14
MET -0.03 0.17 -10000 0 -0.67 12 12
ICAD/CAD 0.018 0.064 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.05 0.19 -10000 0 -0.56 10 10
activation of caspase activity by cytochrome c 0.007 0.097 0.32 4 -0.63 2 6
PAK2 0.018 0.068 0.26 7 -10000 0 7
BCL2 -0.014 0.14 -10000 0 -0.67 8 8
LPA receptor mediated events

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
GNB1/GNG2 -0.002 0.15 -9999 0 -0.6 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.14 -9999 0 -0.54 4 4
AP1 -0.13 0.2 -9999 0 -0.65 13 13
mol:PIP3 -0.067 0.16 -9999 0 -0.6 10 10
AKT1 0.04 0.1 -9999 0 -0.52 2 2
PTK2B 0.002 0.13 -9999 0 -0.5 8 8
RHOA 0.023 0.067 -9999 0 -0.41 3 3
PIK3CB 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.14 -9999 0 -0.49 8 8
MAGI3 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.034 0.15 -9999 0 -0.42 15 15
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.17 -9999 0 -0.63 10 10
NF kappa B1 p50/RelA -0.063 0.15 -9999 0 -0.63 8 8
endothelial cell migration -0.03 0.22 -9999 0 -0.77 14 14
ADCY4 -0.011 0.2 -9999 0 -0.81 9 9
ADCY5 -0.046 0.25 -9999 0 -0.96 10 10
ADCY6 -0.005 0.2 -9999 0 -0.78 9 9
ADCY7 -0.013 0.23 -9999 0 -0.89 9 9
ADCY1 -0.016 0.24 -9999 0 -0.88 10 10
ADCY2 -0.015 0.23 -9999 0 -0.92 9 9
ADCY3 -0.005 0.2 -9999 0 -0.78 9 9
ADCY8 -0.014 0.21 -9999 0 -0.8 10 10
ADCY9 -0.005 0.2 -9999 0 -0.78 9 9
GSK3B 0.01 0.12 -9999 0 -0.65 4 4
arachidonic acid secretion -0.001 0.19 -9999 0 -0.75 9 9
GNG2 -0.003 0.11 -9999 0 -0.67 5 5
TRIP6 0.001 0.14 -9999 0 -0.66 7 7
GNAO1 -0.03 0.2 -9999 0 -0.62 15 15
HRAS 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.001 0.16 -9999 0 -0.55 8 8
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.031 0.2 -9999 0 -1 7 7
JUN 0.012 0.051 -9999 0 -0.67 1 1
LPA/LPA2/NHERF2 0.009 0.067 -9999 0 -0.46 3 3
TIAM1 -0.049 0.25 -9999 0 -1.3 7 7
PIK3R1 0.016 0.001 -9999 0 -10000 0 0
mol:IP3 -0.006 0.14 -9999 0 -0.51 8 8
PLCB3 0.021 0.061 -9999 0 -0.42 3 3
FOS -0.12 0.27 -9999 0 -0.66 35 35
positive regulation of mitosis -0.001 0.19 -9999 0 -0.75 9 9
LPA/LPA1-2-3 -0.051 0.2 -9999 0 -0.46 28 28
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation -0.003 0.14 -9999 0 -0.54 8 8
GNAZ -0.016 0.17 -9999 0 -0.66 10 10
EGFR/PI3K-beta/Gab1 -0.07 0.17 -9999 0 -0.64 10 10
positive regulation of dendritic cell cytokine production -0.051 0.19 -9999 0 -0.46 28 28
LPA/LPA2/MAGI-3 0.01 0.067 -9999 0 -0.46 3 3
ARHGEF1 0.018 0.11 -9999 0 -0.62 3 3
GNAI2 0 0.12 -9999 0 -0.6 5 5
GNAI3 0 0.12 -9999 0 -0.6 5 5
GNAI1 -0.006 0.15 -9999 0 -0.67 7 7
LPA/LPA3 -0.057 0.17 -9999 0 -0.51 22 22
LPA/LPA2 -0.002 0.077 -9999 0 -0.55 3 3
LPA/LPA1 -0.018 0.14 -9999 0 -0.46 14 14
HB-EGF/EGFR -0.072 0.2 -9999 0 -0.46 37 37
HBEGF -0.081 0.22 -9999 0 -0.5 36 36
mol:DAG -0.006 0.14 -9999 0 -0.51 8 8
cAMP biosynthetic process -0.018 0.24 -9999 0 -0.86 11 11
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.016 0.001 -9999 0 -10000 0 0
LYN -0.008 0.19 -9999 0 -0.67 9 9
GNAQ -0.025 0.13 -9999 0 -0.33 25 25
LPAR2 0.005 0.088 -9999 0 -0.67 3 3
LPAR3 -0.069 0.22 -9999 0 -0.67 22 22
LPAR1 -0.01 0.14 -9999 0 -0.78 5 5
IL8 -0.12 0.25 -9999 0 -0.55 34 34
PTK2 -0.036 0.19 -9999 0 -0.66 8 8
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
CASP3 -0.035 0.15 -9999 0 -0.43 15 15
EGFR 0.001 0.1 -9999 0 -0.67 4 4
PLCG1 -0.024 0.16 -9999 0 -0.48 13 13
PLD2 -0.036 0.19 -9999 0 -0.66 8 8
G12/G13 0.01 0.12 -9999 0 -0.6 4 4
PI3K-beta -0.027 0.1 -9999 0 -0.52 5 5
cell migration -0.032 0.074 -9999 0 -0.28 10 10
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
PXN -0.004 0.15 -9999 0 -0.55 8 8
HRAS/GTP -0.003 0.2 -9999 0 -0.79 9 9
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.084 0.24 -9999 0 -0.67 26 26
PRKCE 0.012 0.051 -9999 0 -0.66 1 1
PRKCD 0.003 0.14 -9999 0 -0.51 6 6
Gi(beta/gamma) -0.005 0.2 -9999 0 -0.75 10 10
mol:LPA -0.007 0.047 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.07 0.18 -9999 0 -0.73 9 9
MAPKKK cascade -0.001 0.19 -9999 0 -0.75 9 9
contractile ring contraction involved in cytokinesis 0.023 0.067 -9999 0 -0.4 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.036 0.16 -9999 0 -0.47 14 14
GNA15 -0.038 0.17 -9999 0 -0.51 13 13
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT -0.006 0.18 -9999 0 -0.66 10 10
GNA11 -0.027 0.13 -9999 0 -0.33 26 26
Rac1/GTP -0.013 0.22 -9999 0 -1.1 7 7
MMP2 -0.03 0.23 -9999 0 -0.78 14 14
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.041 0.28 -10000 0 -1 10 10
NCK1/PAK1/Dok-R -0.049 0.12 -10000 0 -0.46 11 11
NCK1/Dok-R -0.068 0.35 -10000 0 -1.4 10 10
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
mol:beta2-estradiol -0.007 0.041 0.26 4 -10000 0 4
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.017 0.001 -10000 0 -10000 0 0
Rac/GDP 0.012 0 -10000 0 -10000 0 0
F2 -0.13 0.26 -10000 0 -0.66 34 34
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.077 0.27 -10000 0 -1.2 10 10
FN1 -0.057 0.21 -10000 0 -0.67 19 19
PLD2 -0.012 0.35 -10000 0 -1.4 10 10
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.076 0.23 -10000 0 -0.67 24 24
ELK1 0.008 0.3 -10000 0 -1.2 10 10
GRB7 0.013 0.051 -10000 0 -0.66 1 1
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.31 -10000 0 -1.2 11 11
CDKN1A 0.064 0.21 -10000 0 -0.68 10 10
ITGA5 0.005 0.088 -10000 0 -0.67 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.069 0.35 -10000 0 -1.4 10 10
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO 0.06 0.22 -10000 0 -0.73 10 10
PLG -0.07 0.36 -10000 0 -1.4 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.034 0.26 -10000 0 -0.97 10 10
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
ANGPT2 0.042 0.16 -10000 0 -0.6 2 2
BMX -0.051 0.38 -10000 0 -1.5 10 10
ANGPT1 -0.016 0.26 -10000 0 -1.5 4 4
tube development 0.055 0.23 -10000 0 -0.79 10 10
ANGPT4 -0.004 0.11 -10000 0 -0.66 5 5
response to hypoxia -0.002 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.063 0.39 -10000 0 -1.5 10 10
alpha5/beta1 Integrin 0.013 0.077 -10000 0 -0.49 4 4
FGF2 -0.02 0.15 -10000 0 -0.67 9 9
STAT5A (dimer) 0.055 0.26 -10000 0 -0.9 10 10
mol:L-citrulline 0.06 0.22 -10000 0 -0.73 10 10
AGTR1 -0.074 0.23 -10000 0 -0.67 24 24
MAPK14 -0.004 0.35 -10000 0 -1.4 10 10
Tie2/SHP2 -0.073 0.3 -10000 0 -1.3 10 10
TEK -0.042 0.35 -10000 0 -1.4 10 10
RPS6KB1 0.043 0.27 -10000 0 -0.98 10 10
Angiotensin II/AT1 -0.053 0.18 -10000 0 -0.5 24 24
Tie2/Ang1/GRB2 -0.017 0.36 -10000 0 -1.4 10 10
MAPK3 0.003 0.31 -10000 0 -1.2 10 10
MAPK1 0.003 0.31 -10000 0 -1.2 10 10
Tie2/Ang1/GRB7 -0.02 0.36 -10000 0 -1.4 10 10
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.35 -10000 0 -1.4 10 10
PI3K 0.023 0.33 -10000 0 -1.2 10 10
FES -0.01 0.36 -10000 0 -1.3 11 11
Crk/Dok-R -0.068 0.35 -10000 0 -1.4 10 10
Tie2/Ang1/ABIN2 -0.017 0.36 -10000 0 -1.4 10 10
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.047 0.25 -10000 0 -0.9 10 10
STAT5A 0.013 0.051 -10000 0 -0.67 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.043 0.27 -10000 0 -0.98 10 10
Tie2/Ang2 0.032 0.31 -10000 0 -1.1 10 10
Tie2/Ang1 -0.027 0.4 -10000 0 -1.6 10 10
FOXO1 0.051 0.26 -10000 0 -0.92 10 10
ELF1 0.018 0.06 -10000 0 -0.71 1 1
ELF2 -0.017 0.35 -10000 0 -1.4 10 10
mol:Choline -0.006 0.32 -10000 0 -1.3 10 10
cell migration -0.031 0.069 -10000 0 -0.25 8 8
FYN 0.049 0.26 -10000 0 -0.92 10 10
DOK2 -0.076 0.23 -10000 0 -0.67 24 24
negative regulation of cell cycle 0.066 0.2 -10000 0 -0.61 10 10
ETS1 0.019 0.076 -10000 0 -0.88 1 1
PXN 0.057 0.23 -10000 0 -0.78 10 10
ITGB1 0.012 0.051 -10000 0 -0.67 1 1
NOS3 0.055 0.24 -10000 0 -0.86 10 10
RAC1 0.016 0 -10000 0 -10000 0 0
TNF -0.14 0.3 -10000 0 -0.67 43 43
MAPKKK cascade -0.006 0.32 -10000 0 -1.3 10 10
RASA1 0.012 0.051 -10000 0 -0.67 1 1
Tie2/Ang1/Shc -0.016 0.36 -10000 0 -1.4 10 10
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.062 0.2 -10000 0 -0.65 10 10
mol:Phosphatidic acid -0.006 0.32 -10000 0 -1.3 10 10
mol:Angiotensin II 0.002 0.004 -10000 0 -10000 0 0
mol:NADP 0.06 0.22 -10000 0 -0.73 10 10
Rac1/GTP -0.061 0.21 -10000 0 -0.9 10 10
MMP2 -0.032 0.37 -10000 0 -1.4 10 10
Coregulation of Androgen receptor activity

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
NRIP1 -0.011 0.059 -9999 0 -0.67 1 1
SVIL -0.015 0.092 -9999 0 -0.68 3 3
ZNF318 0.07 0.074 -9999 0 -10000 0 0
JMJD2C -0.009 0.054 -9999 0 -0.12 30 30
T-DHT/AR/Ubc9 -0.013 0.13 -9999 0 -0.43 14 14
CARM1 0.013 0.004 -9999 0 -10000 0 0
PRDX1 0.02 0.005 -9999 0 -10000 0 0
PELP1 0.025 0.012 -9999 0 -10000 0 0
CTNNB1 0 0.023 -9999 0 -10000 0 0
AKT1 0.031 0.021 -9999 0 -10000 0 0
PTK2B 0.002 0.021 -9999 0 -10000 0 0
MED1 0.033 0.024 -9999 0 -10000 0 0
MAK 0.051 0.13 -9999 0 -0.61 5 5
response to oxidative stress 0.004 0.006 -9999 0 -10000 0 0
HIP1 -0.03 0.13 -9999 0 -0.67 7 7
GSN -0.007 0.033 -9999 0 -10000 0 0
NCOA2 -0.029 0.16 -9999 0 -0.67 11 11
NCOA6 -0.002 0.028 -9999 0 -10000 0 0
DNA-PK 0.081 0.072 -9999 0 -10000 0 0
NCOA4 0.014 0.004 -9999 0 -10000 0 0
PIAS3 0 0.023 -9999 0 -10000 0 0
cell proliferation 0.028 0.13 -9999 0 -0.65 4 4
XRCC5 0.028 0.017 -9999 0 -10000 0 0
UBE3A -0.016 0.046 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.028 0.16 -9999 0 -0.45 19 19
FHL2 0.052 0.12 -9999 0 -0.56 3 3
RANBP9 -0.002 0.028 -9999 0 -10000 0 0
JMJD1A 0.006 0.035 -9999 0 -0.15 8 8
CDK6 0.015 0.052 -9999 0 -0.67 1 1
TGFB1I1 -0.022 0.12 -9999 0 -0.68 5 5
T-DHT/AR/CyclinD1 -0.034 0.14 -9999 0 -0.44 16 16
XRCC6 0.028 0.017 -9999 0 -10000 0 0
T-DHT/AR -0.009 0.15 -9999 0 -0.44 14 14
CTDSP1 0.01 0.008 -9999 0 -10000 0 0
CTDSP2 0.052 0.049 -9999 0 -10000 0 0
BRCA1 -0.007 0.059 -9999 0 -0.7 1 1
TCF4 0.023 0.12 -9999 0 -0.65 5 5
CDKN2A -0.12 0.29 -9999 0 -0.65 40 40
SRF 0.04 0.03 -9999 0 -10000 0 0
NKX3-1 -0.016 0.18 -9999 0 -1.3 3 3
KLK3 -0.48 0.68 -9999 0 -1.3 66 66
TMF1 0.01 0.008 -9999 0 -10000 0 0
HNRNPA1 0.035 0.027 -9999 0 -10000 0 0
AOF2 -0.023 0.032 -9999 0 -0.073 48 48
APPL1 0.06 0.045 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.005 0.17 -9999 0 -0.49 15 15
AR -0.041 0.19 -9999 0 -0.67 14 14
UBA3 0.01 0.008 -9999 0 -10000 0 0
PATZ1 0.035 0.027 -9999 0 -10000 0 0
PAWR 0.007 0.051 -9999 0 -0.67 1 1
PRKDC 0.028 0.017 -9999 0 -10000 0 0
PA2G4 0.039 0.032 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.001 0.12 -9999 0 -0.38 14 14
RPS6KA3 -0.007 0.033 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.025 0.13 -9999 0 -0.43 14 14
LATS2 0.02 0.11 -9999 0 -0.66 4 4
T-DHT/AR/PRX1 0.014 0.13 -9999 0 -0.38 14 14
Cyclin D3/CDK11 p58 0.016 0.006 -9999 0 -10000 0 0
VAV3 -0.2 0.31 -9999 0 -0.68 53 53
KLK2 -0.13 0.31 -9999 0 -0.77 30 30
CASP8 0.008 0.1 -9999 0 -0.66 4 4
T-DHT/AR/TIF2/CARM1 -0.042 0.18 -9999 0 -0.52 19 19
TMPRSS2 -0.03 0.22 -9999 0 -1.1 6 6
CCND1 0 0.074 -9999 0 -0.68 2 2
PIAS1 -0.016 0.046 -9999 0 -10000 0 0
mol:T-DHT -0.005 0.03 -9999 0 -0.069 18 18
CDC2L1 0.002 0.003 -9999 0 -10000 0 0
PIAS4 -0.035 0.071 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.009 0.14 -9999 0 -0.45 14 14
CMTM2 -0.009 0.14 -9999 0 -0.67 8 8
SNURF -0.007 0.12 -9999 0 -0.67 6 6
ZMIZ1 0.013 0.025 -9999 0 -10000 0 0
CCND3 0.018 0.003 -9999 0 -10000 0 0
TGIF1 0.02 0.11 -9999 0 -0.66 4 4
FKBP4 -0.019 0.11 -9999 0 -0.72 4 4
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.015 0.13 -10000 0 -0.54 2 2
epithelial cell differentiation -0.059 0.11 -10000 0 -0.53 1 1
ITCH 0.025 0.018 -10000 0 -10000 0 0
WWP1 0.013 0.074 -10000 0 -10000 0 0
FYN 0.012 0.051 -10000 0 -0.67 1 1
EGFR 0.001 0.1 -10000 0 -0.67 4 4
PRL -0.028 0.16 -10000 0 -0.66 10 10
neuron projection morphogenesis 0.029 0.13 -10000 0 -0.56 3 3
PTPRZ1 -0.12 0.28 -10000 0 -0.66 37 37
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.012 0.14 -10000 0 -0.58 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.002 0.12 -10000 0 -0.51 5 5
ADAM17 0.012 0.088 -10000 0 -0.65 3 3
ErbB4/ErbB4 0.006 0.094 -10000 0 -0.45 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.068 0.19 -10000 0 -0.51 10 10
NCOR1 0.013 0.051 -10000 0 -0.66 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.004 0.13 -10000 0 -0.59 4 4
GRIN2B -0.066 0.18 -10000 0 -0.67 3 3
ErbB4/ErbB2/betacellulin -0.02 0.15 -10000 0 -0.54 5 5
STAT1 0.012 0.051 -10000 0 -0.67 1 1
HBEGF -0.026 0.16 -10000 0 -0.66 11 11
PRLR -0.056 0.21 -10000 0 -0.66 19 19
E4ICDs/ETO2 -0.008 0.12 -10000 0 -0.66 2 2
axon guidance 0.045 0.071 -10000 0 -10000 0 0
NEDD4 0.025 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.062 0.2 -10000 0 -0.54 26 26
CBFA2T3 -0.014 0.14 -10000 0 -0.67 8 8
ErbB4/ErbB2/HBEGF -0.009 0.13 -10000 0 -0.49 5 5
MAPK3 0.02 0.13 -10000 0 -0.59 3 3
STAT1 (dimer) 0.009 0.085 -10000 0 -0.39 3 3
MAPK1 0.02 0.13 -10000 0 -0.59 3 3
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.003 0.13 -10000 0 -0.52 6 6
NRG1 0 0.12 -10000 0 -0.49 11 11
NRG3 -0.11 0.27 -10000 0 -0.67 33 33
NRG2 -0.03 0.17 -10000 0 -0.67 12 12
NRG4 -0.072 0.23 -10000 0 -0.67 23 23
heart development 0.045 0.071 -10000 0 -10000 0 0
neural crest cell migration -0.002 0.13 -10000 0 -0.52 6 6
ERBB2 0.012 0.1 -10000 0 -0.48 7 7
WWOX/E4ICDs 0.009 0.085 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.04 0.16 -10000 0 -0.5 7 7
apoptosis 0.16 0.22 0.67 24 -10000 0 24
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.018 0.14 -10000 0 -0.5 6 6
ErbB4/ErbB2/epiregulin -0.26 0.19 -10000 0 -0.5 26 26
ErbB4/ErbB4/betacellulin/betacellulin -0.027 0.14 -10000 0 -0.47 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.062 0.16 -10000 0 -0.65 3 3
MDM2 0.015 0.081 -10000 0 -0.39 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.096 -10000 0 -0.47 4 4
STAT5A 0.048 0.076 -10000 0 -0.48 1 1
ErbB4/EGFR/neuregulin 1 beta -0.002 0.14 -10000 0 -0.55 7 7
DLG4 -0.007 0.12 -10000 0 -0.66 6 6
GRB2/SHC 0.024 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.026 0.064 -10000 0 -10000 0 0
STAT5A (dimer) -0.063 0.12 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.049 0.063 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.47 0.3 -10000 0 -0.66 128 128
BTC -0.045 0.19 -10000 0 -0.66 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.045 0.071 -10000 0 -10000 0 0
ERBB4 0.006 0.094 -10000 0 -0.45 2 2
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.016 0.066 -10000 0 -0.48 3 3
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.036 0.17 -10000 0 -0.51 9 9
glial cell differentiation 0.026 0.063 -10000 0 -10000 0 0
WWOX 0.013 0.051 -10000 0 -0.66 1 1
cell proliferation -0.014 0.15 -10000 0 -0.55 5 5
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.011 0.084 -10000 0 -0.65 3 3
HDAC1 0.012 0.005 -10000 0 -10000 0 0
AES 0.015 0.001 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.014 0.14 -10000 0 -0.67 8 8
LRP6/FZD1 0.022 0.039 -10000 0 -0.49 1 1
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.033 0.12 -10000 0 -0.34 5 5
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.008 0.072 -10000 0 -0.67 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.073 -10000 0 -0.42 3 3
NICD/RBPSUH 0.03 0.087 -10000 0 -0.64 3 3
WIF1 -0.083 0.23 -10000 0 -0.66 25 25
NOTCH1 -0.011 0.087 -10000 0 -0.68 3 3
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.03 0.17 -10000 0 -0.66 12 12
DKK1 -0.37 0.34 -10000 0 -0.66 101 101
beta catenin/beta TrCP1 0.035 0.048 0.26 3 -10000 0 3
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 0.005 0.045 0.29 2 -0.27 1 3
CtBP/CBP/TCF1/TLE1/AES 0.018 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.12 0.27 -10000 0 -0.66 35 35
JUN 0.012 0.051 -10000 0 -0.67 1 1
MAP3K7 0.014 0.002 -10000 0 -10000 0 0
CTNNB1 0.027 0.051 0.27 3 -10000 0 3
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.029 0.17 -10000 0 -0.45 23 23
HNF1A -0.012 0.13 -10000 0 -0.66 7 7
CTBP1 0.015 0.001 -10000 0 -10000 0 0
MYC 0.013 0.16 -10000 0 -1.5 2 2
NKD1 -0.011 0.13 -10000 0 -0.67 7 7
FZD1 0.013 0.051 -10000 0 -0.67 1 1
NOTCH1 precursor/Deltex homolog 1 0.013 0.13 -10000 0 -0.75 3 3
apoptosis -0.033 0.12 -10000 0 -0.34 5 5
Delta 1/NOTCHprecursor 0.03 0.087 -10000 0 -0.64 3 3
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.021 0.11 -10000 0 -1.5 1 1
Gamma Secretase 0.05 0.001 -10000 0 -10000 0 0
APC 0.005 0.045 0.29 2 -10000 0 2
DVL1 -0.005 0.035 -10000 0 -10000 0 0
CSNK2A1 0.017 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.25 0.25 -10000 0 -0.44 105 105
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.017 0.001 -10000 0 -10000 0 0
NLK 0.016 0.006 -10000 0 -10000 0 0
CCND1 0.023 0.063 -10000 0 -0.56 2 2
WNT1 -0.1 0.26 -10000 0 -0.67 30 30
Axin1/APC/beta catenin 0.043 0.051 0.34 2 -10000 0 2
DKK2 -0.034 0.18 -10000 0 -0.67 13 13
NOTCH1 precursor/DVL1 -0.013 0.075 -10000 0 -0.58 3 3
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.072 -10000 0 -0.67 2 2
NOTCH/Deltex homolog 1 -0.026 0.12 -10000 0 -0.76 3 3
PPP2R5D 0.005 0.064 0.32 7 -10000 0 7
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.089 0.21 -10000 0 -0.49 17 17
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.02 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.27 0.32 -9999 0 -0.57 91 91
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.087 0.12 -9999 0 -0.44 3 3
ATF2/c-Jun -0.049 0.13 -9999 0 -0.75 3 3
MAPK11 -0.099 0.15 -9999 0 -0.58 7 7
MITF -0.11 0.2 -9999 0 -0.78 7 7
MAPKAPK5 -0.091 0.15 -9999 0 -0.56 5 5
KRT8 -0.094 0.15 -9999 0 -0.56 5 5
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.13 0.19 -9999 0 -0.67 7 7
CEBPB -0.091 0.15 -9999 0 -0.56 5 5
SLC9A1 -0.091 0.15 -9999 0 -0.56 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.089 0.16 -9999 0 -0.66 5 5
p38alpha-beta/MNK1 -0.09 0.16 -9999 0 -0.63 5 5
JUN -0.048 0.13 -9999 0 -0.74 3 3
PPARGC1A -0.12 0.18 -9999 0 -0.59 13 13
USF1 -0.091 0.15 -9999 0 -0.56 5 5
RAB5/GDP/GDI1 -0.078 0.088 -9999 0 -0.46 4 4
NOS2 -0.12 0.25 -9999 0 -0.86 11 11
DDIT3 -0.095 0.16 -9999 0 -0.55 7 7
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.065 0.12 -9999 0 -0.48 5 5
p38alpha-beta/HBP1 -0.09 0.16 -9999 0 -0.63 5 5
CREB1 -0.085 0.15 -9999 0 -0.51 7 7
RAB5/GDP 0.012 0 -9999 0 -10000 0 0
EIF4E -0.07 0.14 -9999 0 -0.6 4 4
RPS6KA4 -0.091 0.15 -9999 0 -0.56 5 5
PLA2G4A -0.087 0.16 -9999 0 -0.56 8 8
GDI1 -0.091 0.15 -9999 0 -0.56 5 5
TP53 -0.12 0.18 -9999 0 -0.63 8 8
RPS6KA5 -0.091 0.15 -9999 0 -0.56 5 5
ESR1 -0.12 0.21 -9999 0 -0.76 10 10
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.11 0.2 -9999 0 -0.79 8 8
MEF2A -0.095 0.17 -9999 0 -0.68 5 5
EIF4EBP1 -0.086 0.15 -9999 0 -0.51 7 7
KRT19 -0.14 0.18 -9999 0 -0.54 18 18
ELK4 -0.091 0.15 -9999 0 -0.56 5 5
ATF6 -0.091 0.15 -9999 0 -0.56 5 5
ATF1 -0.085 0.15 -9999 0 -0.51 7 7
p38alpha-beta/MAPKAPK2 -0.09 0.16 -9999 0 -0.63 5 5
p38alpha-beta/MAPKAPK3 -0.09 0.16 -9999 0 -0.63 5 5
Canonical Wnt signaling pathway

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
HDAC1 0.011 0.009 -10000 0 -10000 0 0
AES 0.012 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.021 0.039 -10000 0 -0.5 1 1
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.034 0.18 -10000 0 -0.67 13 13
TLE1 0.012 0.007 -10000 0 -10000 0 0
MACF1 0.012 0.051 -10000 0 -0.67 1 1
CTNNB1 -0.007 0.11 -10000 0 -10000 0 0
WIF1 -0.084 0.23 -10000 0 -0.66 25 25
beta catenin/RanBP3 -0.031 0.087 0.38 1 -10000 0 1
KREMEN2 -0.03 0.17 -10000 0 -0.66 12 12
DKK1 -0.37 0.34 -10000 0 -0.66 101 101
beta catenin/beta TrCP1 0.003 0.11 -10000 0 -10000 0 0
FZD1 0.013 0.051 -10000 0 -0.67 1 1
AXIN2 0.022 0.05 -10000 0 -0.57 1 1
AXIN1 0.016 0.001 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.022 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.032 0.13 -10000 0 -0.69 3 3
Axin1/APC/GSK3 -0.005 0.056 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 -0.007 0.15 -10000 0 -0.56 1 1
HNF1A -0.016 0.13 -10000 0 -0.66 7 7
CTBP1 0.011 0.007 -10000 0 -10000 0 0
MYC 0.009 0.16 -10000 0 -1.4 2 2
RANBP3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.03 0.17 -10000 0 -0.45 23 23
NKD1 -0.011 0.13 -10000 0 -0.67 7 7
TCF4 -0.008 0.11 -10000 0 -0.66 5 5
TCF3 0.011 0.007 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.031 0.16 -10000 0 -10000 0 0
Ran/GTP 0.012 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.015 0.088 -10000 0 -0.62 2 2
LEF1 -0.02 0.14 -10000 0 -0.66 8 8
DVL1 0.03 0.044 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.046 0.14 -10000 0 -0.72 4 4
DKK1/LRP6/Kremen 2 -0.25 0.25 -10000 0 -0.44 105 105
LRP6 0.016 0.001 -10000 0 -10000 0 0
CSNK1A1 0.009 0.01 -10000 0 -10000 0 0
NLK 0.017 0.002 -10000 0 -10000 0 0
CCND1 0.02 0.064 -10000 0 -0.55 2 2
WNT1 -0.1 0.26 -10000 0 -0.67 30 30
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.009 0.072 -10000 0 -0.67 2 2
PPP2R5D 0.026 0.064 0.32 7 -10000 0 7
APC -0.021 0.15 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.003 0.12 0.22 20 -10000 0 20
CREBBP 0.011 0.007 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.012 0.14 -9999 0 -0.42 17 17
regulation of S phase of mitotic cell cycle 0.011 0.085 -9999 0 -10000 0 0
GNAO1 -0.033 0.18 -9999 0 -0.66 13 13
HRAS 0.016 0.001 -9999 0 -10000 0 0
SHBG/T-DHT 0.003 0.057 -9999 0 -0.43 3 3
PELP1 0.016 0.001 -9999 0 -10000 0 0
AKT1 0.014 0 -9999 0 -10000 0 0
MAP2K1 0.011 0.095 -9999 0 -10000 0 0
T-DHT/AR -0.029 0.14 -9999 0 -0.5 14 14
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.003 -9999 0 -0.006 35 35
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
GNAI1 0.005 0.088 -9999 0 -0.66 3 3
mol:GDP -0.039 0.13 -9999 0 -0.48 14 14
cell proliferation 0 0.13 -9999 0 -10000 0 0
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
FOS -0.041 0.2 -9999 0 -0.43 35 35
mol:Ca2+ -0.009 0.024 -9999 0 -0.11 7 7
MAPK3 0.006 0.11 -9999 0 -10000 0 0
MAPK1 0.005 0.072 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0 0.002 -9999 0 -0.004 35 35
cAMP biosynthetic process 0.001 0.057 -9999 0 -0.4 3 3
GNG2 -0.003 0.11 -9999 0 -0.67 5 5
potassium channel inhibitor activity 0 0.002 -9999 0 -0.004 35 35
HRAS/GTP -0.028 0.089 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.002 0.025 -9999 0 -0.33 1 1
SRC 0.016 0.001 -9999 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -9999 0 -0.004 35 35
PI3K 0.02 0.034 -9999 0 -0.43 1 1
apoptosis 0.005 0.12 -9999 0 -10000 0 0
T-DHT/AR/PELP1 -0.014 0.12 -9999 0 -0.42 14 14
HRAS/GDP -0.032 0.12 -9999 0 -0.47 12 12
CREB1 -0.007 0.13 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.002 0.025 -9999 0 -0.34 1 1
AR -0.038 0.18 -9999 0 -0.67 14 14
GNB1 0.016 0 -9999 0 -10000 0 0
RAF1 0.007 0.097 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.027 0.12 -9999 0 -0.44 12 12
T-DHT/AR/PELP1/Src -0.003 0.11 -9999 0 -0.38 14 14
MAP2K2 0.011 0.095 -9999 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.01 0.085 -9999 0 -10000 0 0
GNAZ -0.01 0.13 -9999 0 -0.66 7 7
SHBG 0.004 0.088 -9999 0 -0.67 3 3
Gi family/GNB1/GNG2/GDP 0.011 0.13 -9999 0 -0.57 5 5
mol:T-DHT 0 0.001 -9999 0 -0.002 34 34
RAC1 0.016 0 -9999 0 -10000 0 0
GNRH1 -0.004 0.094 -9999 0 -0.51 6 6
Gi family/GTP -0.007 0.12 -9999 0 -0.51 7 7
CDC42 0.016 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.024 0.005 -9999 0 -10000 0 0
SMARCC1 0.005 0.011 -9999 0 -10000 0 0
REL -0.029 0.18 -9999 0 -0.67 13 13
HDAC7 0.059 0.086 -9999 0 -0.55 1 1
JUN 0.007 0.051 -9999 0 -0.67 1 1
EP300 0.016 0.001 -9999 0 -10000 0 0
KAT2B 0.015 0.001 -9999 0 -10000 0 0
KAT5 0.017 0.001 -9999 0 -10000 0 0
MAPK14 0.019 0.069 -9999 0 -0.5 3 3
FOXO1 0.008 0.072 -9999 0 -0.67 2 2
T-DHT/AR 0.055 0.091 -9999 0 -0.59 1 1
MAP2K6 0.005 0.089 -9999 0 -0.68 3 3
BRM/BAF57 0.015 0.013 -9999 0 -10000 0 0
MAP2K4 0.016 0.005 -9999 0 -10000 0 0
SMARCA2 0.012 0.007 -9999 0 -10000 0 0
PDE9A 0.002 0.15 -9999 0 -1 3 3
NCOA2 -0.028 0.16 -9999 0 -0.67 11 11
CEBPA -0.048 0.2 -9999 0 -0.67 17 17
EHMT2 0.01 0.008 -9999 0 -10000 0 0
cell proliferation 0.059 0.1 -9999 0 -0.52 1 1
NR0B1 -0.15 0.29 -9999 0 -0.67 42 42
EGR1 0.004 0.073 -9999 0 -0.68 2 2
RXRs/9cRA -0.058 0.16 -9999 0 -0.39 34 34
AR/RACK1/Src 0.013 0.089 -9999 0 -0.56 1 1
AR/GR 0.01 0.12 -9999 0 -0.54 5 5
GNB2L1 0.016 0.003 -9999 0 -10000 0 0
PKN1 0.015 0.001 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.002 0.004 -9999 0 -10000 0 0
MAPK8 0.025 0.04 -9999 0 -0.49 1 1
T-DHT/AR/TIF2/CARM1 0.014 0.14 -9999 0 -0.54 4 4
SRC 0.037 0.066 -9999 0 -0.45 1 1
NR3C1 0.001 0.1 -9999 0 -0.67 4 4
KLK3 -0.49 0.55 -9999 0 -1.1 68 68
APPBP2 0.018 0.004 -9999 0 -10000 0 0
TRIM24 0.011 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.037 0.076 -9999 0 -0.49 1 1
TMPRSS2 -0.021 0.22 -9999 0 -1.1 7 7
RXRG -0.12 0.27 -9999 0 -0.67 34 34
mol:9cRA -0.002 0.003 -9999 0 -10000 0 0
RXRA 0.015 0.002 -9999 0 -10000 0 0
RXRB 0.015 0.002 -9999 0 -10000 0 0
CARM1 0.015 0.005 -9999 0 -10000 0 0
NR2C2 0.004 0.088 -9999 0 -0.67 3 3
KLK2 -0.06 0.27 -9999 0 -0.6 31 31
AR 0.013 0.099 -9999 0 -0.45 2 2
SENP1 0.015 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0.051 -9999 0 -0.66 1 1
MDM2 0.025 0.013 -9999 0 -10000 0 0
SRY -0.009 0.12 -9999 0 -0.65 6 6
GATA2 0.009 0.072 -9999 0 -0.67 2 2
MYST2 0.018 0.002 -9999 0 -10000 0 0
HOXB13 -0.29 0.34 -9999 0 -0.68 77 77
T-DHT/AR/RACK1/Src 0.036 0.081 -9999 0 -0.51 1 1
positive regulation of transcription 0.009 0.072 -9999 0 -0.67 2 2
DNAJA1 0.018 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.004 -9999 0 -10000 0 0
NCOA1 0.014 0.009 -9999 0 -10000 0 0
SPDEF -0.56 0.25 -9999 0 -0.67 150 150
T-DHT/AR/TIF2 0.029 0.092 -9999 0 -0.39 2 2
T-DHT/AR/Hsp90 0.032 0.081 -9999 0 -0.49 1 1
GSK3B 0.016 0.003 -9999 0 -10000 0 0
NR2C1 0.019 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.031 0.069 -9999 0 -0.48 1 1
SIRT1 0.016 0.001 -9999 0 -10000 0 0
ZMIZ2 0.025 0.013 -9999 0 -10000 0 0
POU2F1 0.034 0.054 -9999 0 -0.67 1 1
T-DHT/AR/DAX-1 -0.057 0.18 -9999 0 -0.43 7 7
CREBBP 0.015 0.001 -9999 0 -10000 0 0
SMARCE1 0.012 0.007 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.008 0.081 -9999 0 -0.43 6 6
ADCY5 -0.058 0.18 -9999 0 -0.44 31 31
ADCY6 0.021 0.034 -9999 0 -0.43 1 1
ADCY7 0.008 0.081 -9999 0 -0.43 6 6
ADCY1 -0.004 0.12 -9999 0 -0.46 10 10
ADCY2 0.001 0.11 -9999 0 -0.47 8 8
ADCY3 0.021 0.034 -9999 0 -0.43 1 1
ADCY8 -0.003 0.091 -9999 0 -0.42 8 8
PRKCE 0.011 0.039 -9999 0 -0.5 1 1
ADCY9 0.021 0.034 -9999 0 -0.43 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.005 0.12 -9999 0 -0.49 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.01 0.13 -9999 0 -0.49 12 12
CRKL 0.004 0.12 -9999 0 -0.44 6 6
mol:PIP3 -0.023 0.005 -9999 0 -10000 0 0
AKT1 0.001 0.004 -9999 0 -10000 0 0
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0.11 -9999 0 -0.44 5 5
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
HGF/MET/SHIP2 -0.041 0.19 -9999 0 -0.49 25 25
MAP3K5 -0.015 0.17 -9999 0 -0.52 12 12
HGF/MET/CIN85/CBL/ENDOPHILINS -0.026 0.18 -9999 0 -0.45 25 25
AP1 -0.078 0.18 -9999 0 -0.44 36 36
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
apoptosis -0.035 0.12 -9999 0 -1.1 1 1
STAT3 (dimer) 0.002 0.13 -9999 0 -0.52 6 6
GAB1/CRKL/SHP2/PI3K -0.033 0.093 -9999 0 -0.48 4 4
INPP5D -0.003 0.11 -9999 0 -0.67 5 5
CBL/CRK 0.014 0.11 -9999 0 -0.44 5 5
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 -0.016 0.061 -9999 0 -0.24 12 12
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.071 -9999 0 -0.34 5 5
PAK1 0.009 0.004 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.041 0.19 -9999 0 -0.49 25 25
HRAS -0.02 0.19 -9999 0 -0.77 7 7
DOCK1 0.013 0.11 -9999 0 -0.44 5 5
GAB1 -0.004 0.12 -9999 0 -0.43 8 8
CRK 0.004 0.12 -9999 0 -0.47 5 5
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.078 0.21 -9999 0 -0.63 20 20
JUN 0.012 0.051 -9999 0 -0.67 1 1
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.024 0.11 -9999 0 -0.29 25 25
PIK3R1 0.016 0 -9999 0 -10000 0 0
cell morphogenesis 0.032 0.14 -9999 0 -0.52 6 6
GRB2/SHC -0.002 0.1 -9999 0 -0.44 5 5
FOS -0.12 0.27 -9999 0 -0.66 35 35
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.016 0.061 -9999 0 -0.24 12 12
HGF/MET/MUC20 -0.052 0.19 -9999 0 -0.5 25 25
cell migration -0.002 0.1 -9999 0 -0.43 5 5
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
MET/RANBP10 -0.01 0.13 -9999 0 -0.49 12 12
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.007 0.14 -9999 0 -0.54 6 6
MET/MUC20 -0.022 0.13 -9999 0 -0.5 12 12
RAP1B 0.021 0.11 -9999 0 -0.44 3 3
RAP1A 0.021 0.11 -9999 0 -0.44 3 3
HGF/MET/RANBP9 -0.041 0.19 -9999 0 -0.49 25 25
RAF1 -0.009 0.18 -9999 0 -0.71 7 7
STAT3 0.001 0.13 -9999 0 -0.52 6 6
cell proliferation 0 0.18 -9999 0 -0.6 8 8
RPS6KB1 0.002 0.041 -9999 0 -10000 0 0
MAPK3 -0.021 0.055 -9999 0 -0.23 7 7
MAPK1 -0.021 0.055 -9999 0 -10000 0 0
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.014 0.14 -9999 0 -0.53 6 6
SRC 0.003 0.13 -9999 0 -0.51 6 6
PI3K -0.004 0.11 -9999 0 -0.43 7 7
MET/Glomulin -0.016 0.12 -9999 0 -0.44 12 12
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.001 0.16 -9999 0 -0.64 7 7
MET -0.03 0.17 -9999 0 -0.67 12 12
MAP4K1 -0.026 0.18 -9999 0 -0.57 12 12
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.001 0.16 -9999 0 -0.64 7 7
BAD 0.009 0.004 -9999 0 -10000 0 0
MAP2K4 -0.004 0.15 -9999 0 -0.47 11 11
SHP2/GRB2/SOS1/GAB1 -0.041 0.12 -9999 0 -0.51 7 7
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.013 0.11 -9999 0 -0.41 7 7
PLCgamma1/PKC 0.012 0 -9999 0 -10000 0 0
HGF -0.053 0.21 -9999 0 -0.67 18 18
RASA1 0.012 0.051 -9999 0 -0.67 1 1
NCK1 0.016 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.002 0.11 -9999 0 -0.46 5 5
PDPK1 -0.01 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.052 0.22 -9999 0 -0.55 26 26
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.015 0.19 -10000 0 -0.64 4 4
CRKL -0.029 0.15 -10000 0 -0.39 3 3
mol:DAG -0.038 0.18 -10000 0 -0.61 4 4
HRAS 0.006 0.13 -10000 0 -10000 0 0
MAPK8 -0.055 0.18 -10000 0 -0.51 6 6
RAP1A -0.029 0.15 -10000 0 -0.4 1 1
GAB1 -0.029 0.15 -10000 0 -10000 0 0
MAPK14 -0.053 0.18 -10000 0 -0.62 3 3
EPO -0.14 0.28 -10000 0 -0.66 40 40
PLCG1 -0.04 0.19 -10000 0 -0.63 4 4
EPOR/TRPC2/IP3 Receptors 0.008 0.053 -10000 0 -0.66 1 1
RAPGEF1 0.016 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.071 0.19 -10000 0 -0.41 43 43
GAB1/SHC/GRB2/SOS1 -0.059 0.1 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.091 0.22 -10000 0 -0.49 41 41
IRS2 -0.029 0.15 -10000 0 -0.4 1 1
STAT1 -0.035 0.2 -10000 0 -0.64 5 5
STAT5B -0.037 0.19 -10000 0 -0.66 4 4
cell proliferation -0.042 0.17 -10000 0 -0.6 3 3
GAB1/SHIP/PIK3R1/SHP2/SHC -0.063 0.11 -10000 0 -0.53 2 2
TEC -0.031 0.16 -10000 0 -0.65 1 1
SOCS3 0.005 0.088 -10000 0 -0.67 3 3
STAT1 (dimer) -0.034 0.19 -10000 0 -0.62 5 5
JAK2 0.011 0.015 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.026 0.17 -10000 0 -0.42 3 3
EPO/EPOR -0.091 0.22 -10000 0 -0.49 41 41
LYN 0.006 0.089 -10000 0 -0.67 3 3
TEC/VAV2 -0.023 0.16 -10000 0 -0.62 3 3
elevation of cytosolic calcium ion concentration 0.008 0.053 -10000 0 -0.66 1 1
SHC1 0.016 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.064 0.2 -10000 0 -0.41 42 42
mol:IP3 -0.038 0.18 -10000 0 -0.61 4 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.02 0.16 -10000 0 -0.59 2 2
SH2B3 0.003 0.074 -10000 0 -0.67 2 2
NFKB1 -0.053 0.18 -10000 0 -0.52 5 5
EPO/EPOR (dimer)/JAK2/SOCS3 -0.069 0.13 0.29 1 -0.32 32 33
PTPN6 -0.039 0.16 -10000 0 -0.41 3 3
TEC/VAV2/GRB2 -0.015 0.16 -10000 0 -0.59 3 3
EPOR 0.008 0.053 -10000 0 -0.66 1 1
INPP5D -0.003 0.11 -10000 0 -0.67 5 5
mol:GDP -0.06 0.11 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
PLCG2 0.001 0.1 -10000 0 -0.67 4 4
CRKL/CBL/C3G -0.009 0.14 -10000 0 -10000 0 0
VAV2 -0.033 0.16 -10000 0 -0.56 3 3
CBL -0.029 0.15 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 -0.064 0.11 -10000 0 -10000 0 0
STAT5A -0.039 0.19 -10000 0 -0.66 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
STAT5 (dimer) -0.016 0.19 -10000 0 -0.64 5 5
LYN/PLCgamma2 0.006 0.12 -10000 0 -0.66 5 5
PTPN11 0.016 0 -10000 0 -10000 0 0
BTK -0.088 0.22 -10000 0 -0.6 15 15
BCL2 -0.04 0.26 -10000 0 -0.95 9 9
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0 -10000 0 -10000 0 0
MAP4K4 -0.024 0.15 -10000 0 -0.58 7 7
BAG4 0.016 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.028 0.05 -10000 0 -0.37 1 1
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.03 0.17 -10000 0 -0.67 12 12
BAX -0.009 0.02 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.027 0.01 -10000 0 -10000 0 0
BAD -0.027 0.043 -10000 0 -10000 0 0
SMPD1 -0.025 0.11 -10000 0 -0.22 42 42
RB1 -0.027 0.043 -10000 0 -10000 0 0
FADD/Caspase 8 -0.017 0.17 -10000 0 -0.62 9 9
MAP2K4 -0.021 0.054 -10000 0 -0.36 2 2
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.051 -10000 0 -0.44 1 1
EGF -0.17 0.3 -10000 0 -0.67 49 49
mol:ceramide -0.039 0.045 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.027 0 -10000 0 -10000 0 0
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.027 0.042 -10000 0 -10000 0 0
cell proliferation -0.097 0.16 -10000 0 -0.37 16 16
BID -0.023 0.13 -10000 0 -0.48 7 7
MAP3K1 -0.031 0.057 -10000 0 -0.39 2 2
EIF2A -0.01 0.049 -10000 0 -0.42 1 1
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.005 0.048 -10000 0 -0.4 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.005 0.048 -10000 0 -0.4 1 1
Cathepsin D/ceramide -0.026 0.043 -10000 0 -10000 0 0
FADD -0.024 0.15 -10000 0 -0.58 7 7
KSR1 -0.029 0.054 -10000 0 -0.47 1 1
MAPK8 -0.015 0.051 -10000 0 -0.33 1 1
PRKRA -0.027 0.043 -10000 0 -10000 0 0
PDGFA 0.016 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 -0.22 0.33 -10000 0 -0.67 61 61
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.039 0.045 -10000 0 -10000 0 0
CTSD 0.016 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.024 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.1 0.17 -10000 0 -0.4 16 16
PRKCD 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.051 -10000 0 -0.66 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.027 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0.024 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0.051 -10000 0 -0.67 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.034 0.16 -10000 0 -0.62 7 7
TNFR1A/BAG4/TNF-alpha -0.073 0.19 -10000 0 -0.42 42 42
mol:Sphingosine-1-phosphate 0.027 0 -10000 0 -10000 0 0
MAP2K1 -0.01 0.049 -10000 0 -0.41 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.008 0.044 0.17 5 -10000 0 5
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.024 0 -10000 0 -10000 0 0
EIF2AK2 -0.019 0.051 -10000 0 -0.44 1 1
TNF-alpha/TNFR1A/FAN -0.073 0.19 -10000 0 -0.42 42 42
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.15 -10000 0 -0.83 4 4
MAP2K2 -0.01 0.049 -10000 0 -0.41 1 1
SMPD3 -0.039 0.14 -10000 0 -0.4 15 15
TNF -0.15 0.29 -10000 0 -0.67 42 42
PKC zeta/PAR4 0.019 0.054 -10000 0 -0.49 2 2
mol:PHOSPHOCHOLINE 0.044 0.12 0.23 48 -10000 0 48
NF kappa B1/RelA/I kappa B alpha 0.044 0.041 -10000 0 -10000 0 0
AIFM1 -0.008 0.044 0.17 5 -10000 0 5
BCL2 -0.014 0.14 -10000 0 -0.67 8 8
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.044 0.095 -10000 0 -0.7 1 1
NFATC2 0.012 0.073 -10000 0 -0.28 4 4
NFATC3 0.023 0.027 -10000 0 -0.31 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.073 0.19 -10000 0 -0.51 22 22
Exportin 1/Ran/NUP214 0.029 0.012 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.1 0.19 -10000 0 -0.57 20 20
BCL2/BAX 0.001 0.11 -10000 0 -0.49 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.008 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.014 0.006 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.062 0.18 -10000 0 -0.48 22 22
Calcineurin A alpha-beta B1/BCL2 -0.014 0.14 -10000 0 -0.67 8 8
FKBP8 0.016 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.061 0.18 0.47 22 -10000 0 22
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0.001 -10000 0 -10000 0 0
SFN -0.55 0.25 -10000 0 -0.66 148 148
MAP3K8 -0.024 0.16 -10000 0 -0.67 10 10
NFAT4/CK1 alpha 0.03 0.047 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.009 0.13 -10000 0 -0.39 1 1
CABIN1 -0.073 0.19 -10000 0 -0.51 22 22
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
MAP3K1 0.009 0.072 -10000 0 -0.67 2 2
CAMK4 -0.034 0.18 -10000 0 -0.67 13 13
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.006 0.086 -10000 0 -0.49 5 5
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.011 0.051 -10000 0 -0.67 1 1
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.056 0.088 -10000 0 -0.51 1 1
PRKCH 0.012 0.051 -10000 0 -0.67 1 1
CABIN1/Cbp/p300 0.021 0.011 -10000 0 -10000 0 0
CASP3 0.014 0.006 -10000 0 -10000 0 0
PIM1 0.012 0.051 -10000 0 -0.67 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.004 -10000 0 -10000 0 0
apoptosis -0.007 0.031 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.087 0.062 -10000 0 -10000 0 0
PRKCB -0.095 0.25 -10000 0 -0.67 29 29
PRKCE 0.012 0.051 -10000 0 -0.67 1 1
JNK2/NFAT4 0.032 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0 -10000 0 -10000 0 0
PRKCD 0.016 0 -10000 0 -10000 0 0
NUP214 0.016 0.001 -10000 0 -10000 0 0
PRKCZ 0.011 0.051 -10000 0 -0.66 1 1
PRKCA 0.012 0.051 -10000 0 -0.67 1 1
PRKCG -0.16 0.3 -10000 0 -0.66 46 46
PRKCQ -0.065 0.22 -10000 0 -0.67 21 21
FKBP38/BCL2 0.001 0.11 -10000 0 -0.49 8 8
EP300 0.015 0.004 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.043 0.1 -10000 0 -0.63 2 2
CaM/Ca2+/FKBP38 0.021 0.009 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.021 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.012 0.12 -10000 0 -0.43 13 13
NFATc/ERK1 0.052 0.09 -10000 0 -0.65 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.1 0.19 -10000 0 -0.57 20 20
NR4A1 -0.031 0.22 -10000 0 -0.54 27 27
GSK3B 0.014 0.006 -10000 0 -10000 0 0
positive T cell selection 0.023 0.027 -10000 0 -0.31 1 1
NFAT1/CK1 alpha -0.019 0.043 -10000 0 -10000 0 0
RCH1/ KPNB1 0.024 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.014 0.006 -10000 0 -10000 0 0
AKAP5 -0.003 0.11 -10000 0 -0.67 5 5
MEF2D 0.015 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.045 0.092 -10000 0 -0.65 1 1
CREBBP 0.015 0.004 -10000 0 -10000 0 0
BCL2 -0.014 0.14 -10000 0 -0.67 8 8
FoxO family signaling

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.22 0.54 -9999 0 -1.4 29 29
PLK1 0.035 0.24 -9999 0 -0.77 9 9
CDKN1B 0.093 0.15 -9999 0 -0.38 1 1
FOXO3 0.043 0.22 -9999 0 -0.66 7 7
KAT2B 0.024 0.018 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.063 0.17 -9999 0 -0.39 29 29
CAT 0.045 0.22 -9999 0 -0.88 4 4
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.017 0.028 -9999 0 -10000 0 0
FOXO1 -0.05 0.19 -9999 0 -0.44 29 29
MAPK10 0.023 0.087 -9999 0 -0.37 8 8
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.098 0.081 -9999 0 -10000 0 0
response to oxidative stress -0.001 0.032 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.01 0.16 -9999 0 -0.59 5 5
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.008 0.022 -9999 0 -10000 0 0
BCL2L11 0.031 0.043 -9999 0 -10000 0 0
FOXO1/SKP2 -0.04 0.18 -9999 0 -0.4 29 29
mol:GDP -0.001 0.032 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.096 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family -0.05 0.071 -9999 0 -10000 0 0
MST1 -0.006 0.14 -9999 0 -0.66 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family -0.1 0.083 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.039 0.035 -9999 0 -0.36 1 1
MAPK9 0.041 0.017 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.024 0.025 -9999 0 -10000 0 0
SOD2 0.047 0.29 -9999 0 -0.96 11 11
RBL2 0.075 0.16 -9999 0 -10000 0 0
RAL/GDP 0.026 0.023 -9999 0 -10000 0 0
CHUK 0.024 0.019 -9999 0 -10000 0 0
Ran/GTP 0.017 0.004 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.037 0.023 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.24 0.6 -9999 0 -1.5 33 33
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.001 -9999 0 -10000 0 0
IKBKB 0.024 0.019 -9999 0 -10000 0 0
CCNB1 0.043 0.22 -9999 0 -0.81 5 5
FOXO1-3a-4/beta catenin 0.084 0.18 -9999 0 -0.43 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.18 -9999 0 -0.39 29 29
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.001 0.13 -9999 0 -0.69 6 6
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.007 -9999 0 -10000 0 0
ZFAND5 0.1 0.071 -9999 0 -10000 0 0
SFN -0.55 0.25 -9999 0 -0.66 148 148
CDK2 -0.007 0.082 -9999 0 -0.7 2 2
FOXO3A/14-3-3 -0.079 0.092 -9999 0 -0.42 1 1
CREBBP 0.001 0.034 -9999 0 -10000 0 0
FBXO32 0.03 0.28 -9999 0 -1.1 6 6
BCL6 0.058 0.23 -9999 0 -1.3 3 3
RALB 0.018 0.001 -9999 0 -10000 0 0
RALA 0.018 0.001 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.021 0.12 -9999 0 -0.75 2 2
Syndecan-3/Neurocan 0.008 0.089 -9999 0 -0.44 6 6
POMC -0.053 0.21 -9999 0 -0.67 18 18
EGFR 0.001 0.1 -9999 0 -0.67 4 4
Syndecan-3/EGFR 0.015 0.1 -9999 0 -0.53 5 5
AGRP -0.039 0.18 -9999 0 -0.66 14 14
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.003 0.1 -9999 0 -0.66 4 4
long-term memory 0.03 0.073 -9999 0 -0.6 2 2
Syndecan-3/IL8 -0.044 0.17 -9999 0 -0.39 32 32
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0.024 0 -9999 0 -10000 0 0
FYN 0.012 0.051 -9999 0 -0.67 1 1
limb bud formation -0.008 0.071 -9999 0 -0.67 2 2
MC4R -0.017 0.13 -9999 0 -0.66 7 7
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.022 0.16 -9999 0 -0.67 10 10
FGFR/FGF/Syndecan-3 -0.008 0.072 -9999 0 -0.68 2 2
neuron projection morphogenesis 0.008 0.12 -9999 0 -0.72 2 2
Syndecan-3/AgRP -0.01 0.12 -9999 0 -0.38 16 16
Syndecan-3/AgRP/MC4R -0.027 0.14 -9999 0 -0.64 3 3
Fyn/Cortactin 0.021 0.039 -9999 0 -0.49 1 1
SDC3 -0.008 0.073 -9999 0 -0.69 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.043 0.17 -9999 0 -0.38 32 32
IL8 -0.11 0.26 -9999 0 -0.67 32 32
Syndecan-3/Fyn/Cortactin 0.031 0.075 -9999 0 -0.62 2 2
Syndecan-3/CASK -0.007 0.069 -9999 0 -0.65 2 2
alpha-MSH/MC4R -0.053 0.18 -9999 0 -0.5 25 25
Gamma Secretase 0.049 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.022 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 0.005 0.088 -9999 0 -0.67 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.081 -9999 0 -0.24 10 10
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.012 0.051 -9999 0 -0.67 1 1
MAP3K12 0.005 0.088 -9999 0 -0.67 3 3
FGR -0.14 0.29 -9999 0 -0.67 40 40
p38 alpha/TAB1 -0.077 0.15 -9999 0 -0.52 13 13
PRKG1 -0.022 0.16 -9999 0 -0.67 10 10
DUSP8 0.009 0.072 -9999 0 -0.66 2 2
PGK/cGMP/p38 alpha -0.087 0.17 -9999 0 -0.52 17 17
apoptosis -0.074 0.14 -9999 0 -0.49 13 13
RAL/GTP 0.022 0 -9999 0 -10000 0 0
LYN 0.005 0.088 -9999 0 -0.67 3 3
DUSP1 0.009 0.072 -9999 0 -0.67 2 2
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0 -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 0.022 0 -9999 0 -10000 0 0
MAPK11 -0.087 0.23 -9999 0 -0.68 16 16
BLK -0.21 0.32 -9999 0 -0.67 59 59
HCK -0.12 0.27 -9999 0 -0.67 34 34
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.009 0.072 -9999 0 -0.67 2 2
TRAF6/MEKK3 0.021 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.05 0.18 -9999 0 -0.57 13 13
positive regulation of innate immune response -0.085 0.24 -9999 0 -0.72 15 15
LCK -0.011 0.13 -9999 0 -0.67 7 7
p38alpha-beta/MKP7 -0.072 0.23 -9999 0 -0.69 14 14
p38alpha-beta/MKP5 -0.075 0.24 -9999 0 -0.72 14 14
PGK/cGMP -0.017 0.12 -9999 0 -0.5 10 10
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.074 0.23 -9999 0 -0.69 14 14
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 -0.083 0.24 -9999 0 -0.66 26 26
Class I PI3K 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
ARF5/GTP -0.007 0.055 -9999 0 -0.6 1 1
DAPP1 -0.16 0.35 -9999 0 -0.76 34 34
Src family/SYK family/BLNK-LAT/BTK-ITK -0.2 0.38 -9999 0 -0.83 40 40
mol:DAG -0.044 0.14 -9999 0 -0.32 26 26
HRAS 0.017 0.002 -9999 0 -10000 0 0
RAP1A 0.017 0.002 -9999 0 -10000 0 0
ARF5/GDP 0.014 0.15 -9999 0 -0.55 9 9
PLCG2 0.001 0.1 -9999 0 -0.67 4 4
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.022 -9999 0 -10000 0 0
ARF1/GTP -0.005 0.04 -9999 0 -0.49 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.022 -9999 0 -10000 0 0
ADAP1 -0.057 0.13 -9999 0 -0.62 1 1
ARAP3 -0.002 0.023 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 -0.007 0.12 -9999 0 -0.67 6 6
ARHGEF6 -0.011 0.13 -9999 0 -0.67 7 7
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.002 -9999 0 -10000 0 0
FYN 0.012 0.051 -9999 0 -0.67 1 1
ARF6 0.016 0 -9999 0 -10000 0 0
FGR -0.14 0.29 -9999 0 -0.67 40 40
mol:Ca2+ -0.011 0.074 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 -0.014 0.14 -9999 0 -0.67 8 8
ZAP70 -0.088 0.25 -9999 0 -0.67 27 27
mol:IP3 -0.021 0.1 -9999 0 -10000 0 0
LYN 0.005 0.088 -9999 0 -0.67 3 3
ARF1/GDP 0.014 0.15 -9999 0 -0.76 5 5
RhoA/GDP -0.018 0.089 -9999 0 -0.64 3 3
PDK1/Src/Hsp90 0.031 0.033 -9999 0 -0.41 1 1
BLNK -0.018 0.15 -9999 0 -0.67 9 9
actin cytoskeleton reorganization 0.041 0.13 -9999 0 -0.61 5 5
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.02 0.091 -9999 0 -0.49 5 5
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.003 -9999 0 -10000 0 0
HSP90AA1 0.013 0.051 -9999 0 -0.66 1 1
ARF6/GTP -0.002 0.02 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.021 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.19 0.39 -9999 0 -0.8 40 40
BLK -0.21 0.32 -9999 0 -0.67 59 59
PDPK1 0.016 0 -9999 0 -10000 0 0
CYTH1 -0.002 0.021 -9999 0 -10000 0 0
HCK -0.12 0.27 -9999 0 -0.67 34 34
CYTH3 -0.007 0.057 -9999 0 -0.62 1 1
CYTH2 -0.002 0.021 -9999 0 -10000 0 0
KRAS 0.017 0.002 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.033 0.098 -9999 0 -0.48 6 6
SGK1 -0.019 0.096 -9999 0 -0.53 6 6
INPP5D -0.003 0.11 -9999 0 -0.67 5 5
mol:GDP 0.004 0.16 -9999 0 -0.59 9 9
SOS1 0.016 0 -9999 0 -10000 0 0
SYK -0.007 0.12 -9999 0 -0.67 6 6
ARF6/GDP -0.018 0.089 -9999 0 -0.64 3 3
mol:PI-3-4-5-P3 -0.002 0.022 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.022 -9999 0 -10000 0 0
VAV1 -0.03 0.17 -9999 0 -0.67 12 12
mol:PI-3-4-P2 0.013 0.086 -9999 0 -0.49 5 5
RAS family/GTP/PI3K Class I 0.036 0.025 -9999 0 -10000 0 0
PLEKHA1 0.022 0.074 -9999 0 -0.42 5 5
Rac1/GDP 0.014 0.15 -9999 0 -0.55 9 9
LAT -0.007 0.12 -9999 0 -0.67 6 6
Rac1/GTP -0.007 0.21 -9999 0 -0.84 9 9
ITK -0.049 0.12 -9999 0 -0.62 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.074 0.2 -9999 0 -0.47 29 29
LCK -0.011 0.13 -9999 0 -0.67 7 7
BTK -0.054 0.12 -9999 0 -0.62 1 1
Insulin Pathway

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
CBL/APS/CAP -0.11 0.14 -9999 0 -0.63 2 2
TC10/GTP -0.005 0.039 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.1 0.19 -9999 0 -10000 0 0
HRAS 0.016 0 -9999 0 -10000 0 0
APS homodimer 0.016 0 -9999 0 -10000 0 0
GRB14 -0.076 0.23 -9999 0 -0.67 24 24
FOXO3 -0.045 0.15 -9999 0 -0.83 6 6
AKT1 -0.094 0.2 -9999 0 -0.58 13 13
INSR 0.006 0.017 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.082 0.18 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.051 -9999 0 -0.67 1 1
SORBS1 0.005 0.087 -9999 0 -0.66 3 3
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 -0.083 0.17 -9999 0 -10000 0 0
CAV1 -0.1 0.19 -9999 0 -0.69 3 3
CBL/APS/CAP/Crk-II/C3G 0.042 0.05 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.1 0.19 -9999 0 -0.35 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.11 0.15 -9999 0 -0.65 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.074 0.17 -9999 0 -10000 0 0
RPS6KB1 -0.078 0.19 -9999 0 -0.52 13 13
PARD6A 0.016 0 -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 0.003 0.12 -9999 0 -1.1 2 2
PIK3R1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.12 0.16 -9999 0 -0.53 13 13
HRAS/GTP -0.099 0.14 -9999 0 -0.56 4 4
Insulin Receptor 0.006 0.017 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.084 0.18 -9999 0 -10000 0 0
PRKCI -0.04 0.085 -9999 0 -0.71 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.14 0.19 -9999 0 -0.63 13 13
SHC1 0.016 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.006 0.1 -9999 0 -0.92 2 2
PI3K -0.11 0.15 -9999 0 -0.66 1 1
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 -0.015 0.019 -9999 0 -10000 0 0
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
AKT2 -0.094 0.2 -9999 0 -0.58 13 13
PRKCZ -0.038 0.092 -9999 0 -0.82 2 2
SH2B2 0.016 0 -9999 0 -10000 0 0
SHC/SHIP -0.089 0.18 -9999 0 -0.65 4 4
F2RL2 -0.018 0.15 -9999 0 -0.67 9 9
TRIP10 0.009 0.072 -9999 0 -0.67 2 2
Insulin Receptor/Insulin/Shc -0.11 0.19 -9999 0 -0.35 66 66
TC10/GTP/CIP4/Exocyst 0.017 0.047 -9999 0 -0.43 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.084 0.18 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.012 0.051 -9999 0 -0.67 1 1
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.035 0.053 -9999 0 -0.37 3 3
TC10/GDP 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.1 0.19 -9999 0 -0.73 1 1
INPP5D -0.1 0.19 -9999 0 -0.63 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.044 0.2 -9999 0 -1.1 6 6
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.016 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0.006 0.11 -9999 0 -0.93 2 2
INS -0.23 0.33 -9999 0 -0.66 66 66
mol:PI-3-4-P2 -0.1 0.19 -9999 0 -0.62 5 5
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 -0.082 0.19 -9999 0 -0.52 13 13
PTPRA 0.006 0.017 -9999 0 -10000 0 0
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
TC10/GTP/CIP4 0.017 0.047 -9999 0 -0.43 2 2
PDPK1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.067 0.15 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.11 0.19 -9999 0 -0.35 66 66
Insulin Receptor/Insulin/IRS3 -0.16 0.25 -9999 0 -0.49 66 66
Par3/Par6 0.015 0.11 -9999 0 -0.43 9 9
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.007 0.13 -10000 0 -0.48 11 11
ER alpha/Gai/GDP/Gbeta gamma -0.001 0.17 -10000 0 -0.66 7 7
AKT1 -0.008 0.22 -10000 0 -0.88 10 10
PIK3CA 0.012 0.051 -10000 0 -0.67 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.22 -10000 0 -0.9 10 10
mol:Ca2+ -0.018 0.19 -10000 0 -0.62 11 11
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.013 0.12 -10000 0 -0.43 14 14
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.005 0.2 0.83 10 -10000 0 10
RhoA/GTP -0.017 0.07 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.046 0.14 -10000 0 -0.55 10 10
regulation of stress fiber formation -0.026 0.12 0.56 4 -10000 0 4
E2/ERA-ERB (dimer) -0.003 0.1 -10000 0 -0.43 10 10
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.002 0.095 -10000 0 -0.39 10 10
pseudopodium formation 0.026 0.12 -10000 0 -0.56 4 4
E2/ER alpha (dimer)/PELP1 -0.003 0.1 -10000 0 -0.43 10 10
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 -0.003 0.11 -10000 0 -0.67 5 5
GNAO1 -0.033 0.18 -10000 0 -0.66 13 13
HRAS 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.17 -10000 0 -0.62 10 10
E2/ER beta (dimer) 0.012 0 -10000 0 -10000 0 0
mol:GDP -0.025 0.1 -10000 0 -0.45 10 10
mol:NADP 0.014 0.17 -10000 0 -0.62 10 10
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.021 0.2 -10000 0 -0.65 11 11
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 0.016 0.12 -10000 0 -0.59 5 5
PLCB2 -0.028 0.2 -10000 0 -0.66 11 11
IGF1 -0.22 0.33 -10000 0 -0.67 61 61
mol:L-citrulline 0.014 0.17 -10000 0 -0.62 10 10
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP 0.009 0.13 -10000 0 -0.73 3 3
JNK cascade 0.012 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 0.016 0 -10000 0 -10000 0 0
ESR1 -0.022 0.16 -10000 0 -0.67 10 10
Gq family/GDP/Gbeta gamma 0.016 0.13 -10000 0 -0.56 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.08 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.046 0.14 -10000 0 -0.55 10 10
GNAZ -0.01 0.13 -10000 0 -0.66 7 7
E2/ER alpha (dimer) -0.017 0.12 -10000 0 -0.5 10 10
STRN 0.001 0.1 -10000 0 -0.67 4 4
GNAL 0.005 0.088 -10000 0 -0.67 3 3
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.015 0.058 -10000 0 -0.43 3 3
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.005 0.088 -10000 0 -0.66 3 3
HBEGF -0.02 0.22 -10000 0 -0.67 14 14
cAMP biosynthetic process -0.025 0.1 -10000 0 -0.4 11 11
SRC 0.009 0.16 -10000 0 -0.61 7 7
PI3K 0.021 0.039 -10000 0 -0.49 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.03 0.12 -10000 0 -0.51 10 10
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.17 -10000 0 -0.56 15 15
Gs family/GTP -0.025 0.1 -10000 0 -0.41 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.032 0 -10000 0 -10000 0 0
vasodilation 0.016 0.16 -10000 0 -0.58 10 10
mol:DAG -0.021 0.2 -10000 0 -0.65 11 11
Gs family/GDP/Gbeta gamma -0.032 0.13 -10000 0 -0.51 10 10
MSN 0.025 0.13 -10000 0 -0.62 4 4
Gq family/GTP 0.009 0.12 -10000 0 -0.52 6 6
mol:PI-3-4-5-P3 -0.009 0.21 -10000 0 -0.86 10 10
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.016 0.16 0.58 10 -10000 0 10
GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
RhoA/GDP -0.024 0.097 -10000 0 -0.42 10 10
NOS3 0.012 0.18 -10000 0 -0.66 10 10
GNA11 0.012 0.051 -10000 0 -0.67 1 1
MAPKKK cascade 0.012 0.18 -10000 0 -0.63 12 12
E2/ER alpha (dimer)/PELP1/Src -0.049 0.15 -10000 0 -0.56 12 12
ruffle organization 0.026 0.12 -10000 0 -0.56 4 4
ROCK2 0.03 0.097 -10000 0 -0.6 1 1
GNA14 -0.003 0.11 -10000 0 -0.67 5 5
GNA15 -0.007 0.12 -10000 0 -0.67 6 6
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.032 0.23 -10000 0 -0.71 13 13
MMP2 -0.005 0.2 -10000 0 -0.67 12 12
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.012 0.097 -10000 0 -0.48 6 6
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.13 0.22 -10000 0 -0.5 47 47
GNB1/GNG2 0.01 0.074 -10000 0 -0.43 5 5
GNB1 0.016 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
Gs family/GTP 0.004 0.053 -10000 0 -0.4 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 0.002 0.013 0.098 3 -10000 0 3
GNAL 0.005 0.088 -10000 0 -0.67 3 3
GNG2 -0.003 0.11 -10000 0 -0.67 5 5
CRH -0.17 0.3 -10000 0 -0.66 47 47
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.031 -10000 0 -0.4 1 1
MAPK11 0.003 0.053 -10000 0 -0.4 3 3
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.009 0.14 -9999 0 -0.65 7 7
STMN1 -0.001 0.12 -9999 0 -0.49 10 10
Aurora B/RasGAP/Survivin -0.011 0.19 -9999 0 -0.67 12 12
Chromosomal passenger complex/Cul3 protein complex 0.006 0.13 -9999 0 -0.5 9 9
BIRC5 -0.018 0.15 -9999 0 -0.69 9 9
DES -0.15 0.29 -9999 0 -0.71 29 29
Aurora C/Aurora B/INCENP 0.009 0.11 -9999 0 -0.43 10 10
Aurora B/TACC1 -0.001 0.1 -9999 0 -0.42 10 10
Aurora B/PP2A -0.003 0.12 -9999 0 -0.49 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.041 -9999 0 -0.18 5 5
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -10000 0 0
NDC80 -0.012 0.18 -9999 0 -0.7 10 10
Cul3 protein complex 0.018 0.081 -9999 0 -0.42 6 6
KIF2C 0.001 0.13 -9999 0 -0.42 10 10
PEBP1 0.012 0.053 -9999 0 -0.68 1 1
KIF20A -0.015 0.14 -9999 0 -0.67 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.005 0.13 -9999 0 -0.54 10 10
SEPT1 -0.022 0.16 -9999 0 -0.67 10 10
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.003 0.17 -9999 0 -0.82 6 6
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B 0.001 0.085 -9999 0 -0.34 10 10
AURKB -0.02 0.16 -9999 0 -0.68 10 10
AURKC 0.012 0.051 -9999 0 -0.66 1 1
CDCA8 0.001 0.1 -9999 0 -0.67 4 4
cytokinesis -0.021 0.22 -9999 0 -0.83 10 10
Aurora B/Septin1 -0.051 0.22 -9999 0 -0.72 13 13
AURKA -0.011 0.13 -9999 0 -0.67 7 7
INCENP 0.016 0.005 -9999 0 -10000 0 0
KLHL13 -0.003 0.11 -9999 0 -0.67 5 5
BUB1 -0.015 0.14 -9999 0 -0.67 8 8
hSgo1/Aurora B/Survivin -0.072 0.23 -9999 0 -0.57 26 26
EVI5 0.017 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.046 0.19 -9999 0 -0.76 9 9
SGOL1 -0.06 0.22 -9999 0 -0.66 20 20
CENPA -0.014 0.2 -9999 0 -0.65 12 12
NCAPG 0.001 0.1 -9999 0 -0.67 4 4
Aurora B/HC8 Proteasome -0.003 0.12 -9999 0 -0.49 10 10
NCAPD2 0.009 0.072 -9999 0 -0.66 2 2
Aurora B/PP1-gamma -0.003 0.12 -9999 0 -0.49 10 10
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.007 0.12 -9999 0 -0.67 6 6
NPM1 -0.004 0.13 -9999 0 -0.51 10 10
RASA1 0.012 0.051 -9999 0 -0.67 1 1
KLHL9 0.012 0.051 -9999 0 -0.67 1 1
mitotic prometaphase 0 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.12 -9999 0 -0.49 10 10
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.017 0.22 -9999 0 -0.82 10 10
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
NSUN2 -0.004 0.13 -9999 0 -0.51 10 10
MYLK -0.024 0.15 -9999 0 -0.44 18 18
KIF23 0.001 0.1 -9999 0 -0.68 4 4
VIM -0.014 0.16 -9999 0 -0.6 12 12
RACGAP1 0.016 0.004 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.004 0.13 -9999 0 -0.51 10 10
Chromosomal passenger complex -0.011 0.21 -9999 0 -0.75 11 11
Chromosomal passenger complex/EVI5 -0.022 0.18 -9999 0 -0.73 9 9
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.02 0.096 0.23 1 -0.46 4 5
ACTA1 0.011 0.12 0.26 3 -0.55 4 7
NUMA1 0.02 0.096 0.23 1 -0.46 4 5
SPTAN1 0.019 0.11 -10000 0 -0.52 4 4
LIMK1 0.019 0.11 -10000 0 -0.52 4 4
BIRC3 -0.03 0.17 -10000 0 -0.67 12 12
BIRC2 0.016 0 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 0 0.14 -10000 0 -0.52 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.016 0 -10000 0 -10000 0 0
PTK2 0.02 0.096 0.23 1 -0.46 4 5
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.019 0.11 -10000 0 -0.51 4 4
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN 0.019 0.11 -10000 0 -0.53 4 4
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.14 0.3 -10000 0 -0.66 43 43
BID 0.005 0.11 -10000 0 -0.88 2 2
MAP3K1 0.01 0.097 -10000 0 -0.71 2 2
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.024 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.008 0.14 -10000 0 -0.58 6 6
CASP9 0.016 0 -10000 0 -10000 0 0
DNA repair -0.019 0.044 -10000 0 -0.22 6 6
neuron apoptosis 0.016 0.069 -10000 0 -0.46 3 3
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.026 0.1 -10000 0 -0.5 4 4
APAF1 0.016 0 -10000 0 -10000 0 0
CASP6 0.016 0.081 -10000 0 -0.5 2 2
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD 0.026 0.11 -10000 0 -0.5 4 4
CASP7 0.01 0.085 0.32 12 -10000 0 12
KRT18 0.017 0.022 -10000 0 -10000 0 0
apoptosis 0.026 0.096 0.29 1 -0.49 2 3
DFFA 0.019 0.11 -10000 0 -0.52 4 4
DFFB 0.019 0.11 -10000 0 -0.52 4 4
PARP1 0.019 0.044 0.22 6 -10000 0 6
actin filament polymerization -0.024 0.1 0.48 4 -10000 0 4
TNF -0.15 0.29 -10000 0 -0.67 42 42
CYCS 0.011 0.061 -10000 0 -0.3 4 4
SATB1 0.018 0.091 -10000 0 -0.43 4 4
SLK 0.019 0.11 -10000 0 -0.52 4 4
p15 BID/BAX 0.013 0.1 -10000 0 -0.82 2 2
CASP2 -0.014 0.13 -10000 0 -0.39 7 7
JNK cascade -0.01 0.095 0.7 2 -10000 0 2
CASP3 0.011 0.12 0.28 3 -0.46 7 10
LMNB2 0.007 0.097 -10000 0 -0.37 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.009 0.072 -10000 0 -0.67 2 2
Mammalian IAPs/DIABLO 0.014 0.1 -10000 0 -0.37 12 12
negative regulation of DNA binding -0.14 0.3 -10000 0 -0.65 43 43
stress fiber formation 0.019 0.11 -10000 0 -0.51 4 4
GZMB -0.004 0.13 -10000 0 -0.53 10 10
CASP1 -0.004 0.13 -10000 0 -0.53 8 8
LMNB1 0.007 0.097 -10000 0 -0.37 4 4
APP 0.016 0.07 -10000 0 -0.46 3 3
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.002 0.077 -10000 0 -0.51 4 4
VIM 0.019 0.095 0.29 1 -0.41 4 5
LMNA 0.007 0.097 -10000 0 -0.37 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.024 0.14 -10000 0 -0.42 7 7
LRDD 0.012 0.051 -10000 0 -0.67 1 1
SREBF1 0.019 0.11 -10000 0 -0.52 4 4
APAF-1/Caspase 9 0.006 0.032 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.02 0.094 0.23 1 -0.45 4 5
CFL2 0.024 0.1 -10000 0 -0.49 4 4
GAS2 0.004 0.13 -10000 0 -0.56 5 5
positive regulation of apoptosis 0.01 0.099 -10000 0 -0.37 4 4
PRF1 0.005 0.088 -10000 0 -0.67 3 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0 -9999 0 -10000 0 0
SPHK1 -0.026 0.16 -9999 0 -0.67 11 11
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.006 0.083 -9999 0 -0.32 11 11
GNAO1 -0.033 0.18 -9999 0 -0.66 13 13
mol:Sphinganine-1-P -0.005 0.13 -9999 0 -0.49 11 11
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.075 -9999 0 -0.58 1 1
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.024 0 -9999 0 -10000 0 0
S1PR3 -0.014 0.14 -9999 0 -0.67 8 8
S1PR2 0.012 0.051 -9999 0 -0.67 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.017 0.066 -9999 0 -0.28 11 11
S1PR5 -0.034 0.18 -9999 0 -0.67 13 13
S1PR4 -0.03 0.17 -9999 0 -0.67 12 12
GNAI1 0.005 0.088 -9999 0 -0.66 3 3
S1P/S1P5/G12 -0.006 0.13 -9999 0 -0.42 13 13
S1P/S1P3/Gq 0.003 0.16 -9999 0 -0.68 7 7
S1P/S1P4/Gi -0.007 0.17 -9999 0 -0.67 7 7
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ -0.01 0.13 -9999 0 -0.66 7 7
GNA14 -0.003 0.11 -9999 0 -0.67 5 5
GNA15 -0.007 0.12 -9999 0 -0.67 6 6
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.012 0.051 -9999 0 -0.67 1 1
ABCC1 0.016 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.013 0.061 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.022 0.071 0.28 2 -0.34 1 3
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.016 0.077 -10000 0 -0.5 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0.031 0.033 -10000 0 -0.41 1 1
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP 0.004 0.071 -10000 0 -0.66 2 2
PRKCI 0.009 0.072 -10000 0 -0.66 2 2
AS160/CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.037 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.051 -10000 0 -0.66 1 1
TRIP10 0.009 0.072 -10000 0 -0.67 2 2
TC10/GTP/CIP4/Exocyst 0.017 0.047 -10000 0 -0.43 2 2
AS160/14-3-3 -0.11 0.08 -10000 0 -0.4 2 2
VAMP2 0.013 0.051 -10000 0 -0.66 1 1
SLC2A4 -0.024 0.075 0.28 2 -0.38 1 3
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.031 0 -10000 0 -10000 0 0
SFN -0.55 0.25 -10000 0 -0.66 148 148
LNPEP 0.012 0.051 -10000 0 -0.67 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -9999 0 -10000 0 0
MKNK1 0.016 0 -9999 0 -10000 0 0
mol:PIP3 -0.002 0.025 -9999 0 -0.34 1 1
FRAP1 0.018 0.01 -9999 0 -10000 0 0
AKT1 0.032 0.026 -9999 0 -0.32 1 1
INSR 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.14 0.22 -9999 0 -0.43 66 66
mol:GTP -0.001 0.019 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.007 -9999 0 -10000 0 0
TSC2 0.016 0 -9999 0 -10000 0 0
RHEB/GDP -0.001 0.018 -9999 0 -10000 0 0
TSC1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/IRS1 0.02 0.001 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.008 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EIF3A 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.032 0.018 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.013 0 -9999 0 -10000 0 0
mol:LY294002 0 0 -9999 0 -10000 0 0
EIF4B 0.038 0.016 -9999 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.035 -9999 0 -0.43 1 1
eIF4E/eIF4G1/eIF4A1 0 0.004 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
PI3K 0.028 0.028 -9999 0 -0.35 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.036 0.014 -9999 0 -10000 0 0
FKBP1A 0.017 0 -9999 0 -10000 0 0
RHEB/GTP -0.001 0.018 -9999 0 -10000 0 0
mol:Amino Acids 0 0 -9999 0 -10000 0 0
FKBP12/Rapamycin 0.013 0.001 -9999 0 -10000 0 0
PDPK1 -0.002 0.024 -9999 0 -0.32 1 1
EIF4E 0.016 0 -9999 0 -10000 0 0
ASK1/PP5C 0.027 0.007 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.021 0.001 -9999 0 -10000 0 0
TSC1/TSC2 0.046 0.024 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RPS6 0.013 0.051 -9999 0 -0.66 1 1
PPP5C 0.016 0 -9999 0 -10000 0 0
EIF4G1 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.001 -9999 0 -10000 0 0
INS -0.24 0.33 -9999 0 -0.67 66 66
PTEN 0.016 0 -9999 0 -10000 0 0
PDK2 -0.002 0.024 -9999 0 -0.32 1 1
EIF4EBP1 0.012 0.036 -9999 0 -10000 0 0
PIK3CA 0.013 0.051 -9999 0 -0.67 1 1
PPP2R5D 0.025 0.01 -9999 0 -10000 0 0
peptide biosynthetic process -0.12 0.2 -9999 0 -0.38 66 66
RHEB 0.016 0 -9999 0 -10000 0 0
EIF4A1 0.016 0 -9999 0 -10000 0 0
mol:Rapamycin 0 0 -9999 0 -10000 0 0
EEF2 -0.12 0.2 -9999 0 -0.38 66 66
eIF4E/4E-BP1 0.02 0.032 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.015 0.037 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.035 0.093 -9999 0 -0.46 3 3
JUN 0.005 0.14 -9999 0 -0.52 7 7
HRAS 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.029 0.18 -9999 0 -0.51 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.031 0.18 -9999 0 -0.51 14 14
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.037 0.18 -9999 0 -0.48 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.056 0.14 -9999 0 -0.68 4 4
GRB7 0.013 0.051 -9999 0 -0.66 1 1
RET51/GFRalpha1/GDNF -0.027 0.17 -9999 0 -0.44 17 17
MAPKKK cascade -0.052 0.14 -9999 0 -0.64 5 5
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.022 0.15 -9999 0 -0.42 20 20
lamellipodium assembly -0.034 0.088 -9999 0 -0.43 3 3
RET51/GFRalpha1/GDNF/SHC -0.027 0.17 -9999 0 -0.46 13 13
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
RET9/GFRalpha1/GDNF/SHC -0.022 0.15 -9999 0 -0.42 20 20
RET9/GFRalpha1/GDNF/Shank3 -0.024 0.15 -9999 0 -0.44 20 20
MAPK3 -0.01 0.15 -9999 0 -0.63 4 4
DOK1 0.009 0.072 -9999 0 -0.67 2 2
DOK6 0.001 0.1 -9999 0 -0.67 4 4
PXN 0.016 0 -9999 0 -10000 0 0
neurite development 0.005 0.16 -9999 0 -0.68 4 4
DOK5 -0.018 0.15 -9999 0 -0.67 9 9
GFRA1 -0.041 0.19 -9999 0 -0.67 15 15
MAPK8 -0.002 0.14 -9999 0 -0.55 6 6
HRAS/GTP -0.058 0.15 -9999 0 -0.69 5 5
tube development -0.014 0.15 -9999 0 -0.72 3 3
MAPK1 -0.01 0.15 -9999 0 -0.63 4 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.001 0.1 -9999 0 -0.5 2 2
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 -0.011 0.13 -9999 0 -0.67 7 7
RET51/GFRalpha1/GDNF/Dok6 -0.025 0.19 -9999 0 -0.84 5 5
SHC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.029 0.17 -9999 0 -0.43 26 26
RET51/GFRalpha1/GDNF/Dok5 -0.047 0.21 -9999 0 -0.6 15 15
PRKCA 0.012 0.051 -9999 0 -0.67 1 1
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
CREB1 0.002 0.12 -9999 0 -0.53 3 3
PIK3R1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.001 0.1 -9999 0 -0.5 2 2
RET51/GFRalpha1/GDNF/Grb7 -0.029 0.17 -9999 0 -0.46 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.011 0.13 -9999 0 -0.67 7 7
DOK4 0.012 0.051 -9999 0 -0.67 1 1
JNK cascade 0.006 0.13 -9999 0 -0.5 7 7
RET9/GFRalpha1/GDNF/FRS2 -0.022 0.15 -9999 0 -0.42 20 20
SHANK3 0.012 0.051 -9999 0 -0.67 1 1
RASA1 0.012 0.051 -9999 0 -0.67 1 1
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.001 0.1 -9999 0 -0.51 2 2
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.003 0.12 -9999 0 -0.52 3 3
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.009 0.14 -9999 0 -0.57 5 5
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.12 -9999 0 -0.6 3 3
PI3K 0.013 0.16 -9999 0 -0.71 3 3
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.013 0.15 -9999 0 -0.72 3 3
GRB10 0.012 0.051 -9999 0 -0.67 1 1
activation of MAPKK activity -0.001 0.11 -9999 0 -0.51 3 3
RET51/GFRalpha1/GDNF/FRS2 -0.027 0.17 -9999 0 -0.44 17 17
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.016 0 -9999 0 -10000 0 0
IRS2 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.004 0.12 -9999 0 -0.6 3 3
RET51/GFRalpha1/GDNF/PKC alpha -0.029 0.17 -9999 0 -0.75 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF -0.015 0.13 -9999 0 -0.66 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.027 0.17 -9999 0 -0.44 17 17
Rac1/GTP -0.04 0.1 -9999 0 -0.53 3 3
RET9/GFRalpha1/GDNF -0.035 0.16 -9999 0 -0.47 20 20
GFRalpha1/GDNF -0.041 0.18 -9999 0 -0.54 20 20
HIF-2-alpha transcription factor network

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
MMP14 -0.074 0.32 -10000 0 -1.4 10 10
oxygen homeostasis 0.004 0.019 -10000 0 -10000 0 0
TCEB2 0.013 0.051 -10000 0 -0.66 1 1
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.033 0.1 -10000 0 -0.59 2 2
EPO -0.077 0.4 -10000 0 -0.79 24 24
FIH (dimer) 0.021 0.017 -10000 0 -10000 0 0
APEX1 0.019 0.019 -10000 0 -10000 0 0
SERPINE1 -0.005 0.34 -10000 0 -0.9 12 12
FLT1 -0.004 0.1 -10000 0 -1.3 1 1
ADORA2A 0.01 0.3 -10000 0 -0.77 8 8
germ cell development -0.034 0.36 -10000 0 -0.78 20 20
SLC11A2 0.013 0.3 -10000 0 -0.79 8 8
BHLHE40 0.01 0.31 -10000 0 -0.85 8 8
HIF1AN 0.021 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0 0.2 -10000 0 -0.56 4 4
ETS1 0.031 0.053 -10000 0 -0.68 1 1
CITED2 -0.011 0.12 -10000 0 -1 2 2
KDR -0.013 0.17 -10000 0 -1.6 2 2
PGK1 0.013 0.3 -10000 0 -0.79 8 8
SIRT1 0.015 0.004 -10000 0 -10000 0 0
response to hypoxia -0.003 0.007 -10000 0 -10000 0 0
HIF2A/ARNT 0.018 0.35 -10000 0 -0.95 9 9
EPAS1 0.031 0.16 -10000 0 -0.4 9 9
SP1 0.024 0.006 -10000 0 -10000 0 0
ABCG2 0.007 0.31 -10000 0 -0.79 10 10
EFNA1 0.009 0.31 -10000 0 -0.82 9 9
FXN 0.01 0.3 -10000 0 -0.77 8 8
POU5F1 -0.039 0.37 -10000 0 -0.82 20 20
neuron apoptosis -0.019 0.34 0.9 9 -10000 0 9
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 -0.04 0.2 -10000 0 -0.68 16 16
EGLN2 0.022 0.017 -10000 0 -10000 0 0
EGLN1 0.021 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.031 0.033 -10000 0 -0.41 1 1
VHL 0.016 0 -10000 0 -10000 0 0
ARNT 0.019 0.019 -10000 0 -10000 0 0
SLC2A1 -0.081 0.38 -10000 0 -0.73 23 23
TWIST1 -0.021 0.36 -10000 0 -0.85 17 17
ELK1 0.026 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.055 0.13 -10000 0 -0.53 4 4
VEGFA 0.011 0.31 -10000 0 -0.8 9 9
CREBBP 0.016 0 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.004 0.067 -9999 0 -0.5 3 3
PDGFRB -0.001 0.1 -9999 0 -0.68 4 4
SPHK1 -0.076 0.21 -9999 0 -0.89 11 11
mol:S1P -0.075 0.19 -9999 0 -0.79 11 11
S1P1/S1P/Gi -0.1 0.18 -9999 0 -0.61 9 9
GNAO1 -0.041 0.18 -9999 0 -0.67 13 13
PDGFB-D/PDGFRB/PLCgamma1 -0.092 0.18 -9999 0 -0.67 8 8
PLCG1 -0.095 0.17 -9999 0 -0.61 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.1 -9999 0 -0.68 4 4
GNAI2 0.009 0.009 -9999 0 -10000 0 0
GNAI3 0.008 0.009 -9999 0 -10000 0 0
GNAI1 -0.003 0.088 -9999 0 -0.67 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.004 0.057 -9999 0 -0.42 3 3
S1P1/S1P -0.075 0.15 -9999 0 -0.57 13 13
negative regulation of cAMP metabolic process -0.1 0.17 -9999 0 -0.59 9 9
MAPK3 -0.15 0.21 -9999 0 -0.59 9 9
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
KDR 0.005 0.072 -9999 0 -0.67 2 2
PLCB2 -0.078 0.2 -9999 0 -0.52 24 24
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.061 0.12 -9999 0 -0.47 13 13
receptor internalization -0.07 0.14 -9999 0 -0.52 13 13
PTGS2 -0.23 0.28 -9999 0 -0.64 7 7
Rac1/GTP -0.061 0.12 -9999 0 -0.47 13 13
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA 0.009 0.051 -9999 0 -0.66 1 1
negative regulation of T cell proliferation -0.1 0.17 -9999 0 -0.59 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.018 0.13 -9999 0 -0.67 7 7
MAPK1 -0.15 0.21 -9999 0 -0.61 8 8
S1P1/S1P/PDGFB-D/PDGFRB -0.056 0.17 -9999 0 -0.66 10 10
ABCC1 0.014 0.003 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.016 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.052 0.12 -9999 0 -0.59 4 4
NEF -0.029 0.076 -9999 0 -10000 0 0
NFKBIA 0.012 0.03 -9999 0 -10000 0 0
BIRC3 0.004 0.18 -9999 0 -0.68 12 12
CYCS -0.007 0.14 -9999 0 -0.62 3 3
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.056 0.2 -9999 0 -0.77 11 11
MAP2K7 -0.004 0.12 -9999 0 -0.6 2 2
protein ubiquitination 0.018 0.11 -9999 0 -0.43 2 2
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.012 0.051 -9999 0 -0.67 1 1
BID -0.016 0.15 -9999 0 -0.67 3 3
NF-kappa-B/RelA/I kappa B alpha -0.02 0.075 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.023 0.088 -9999 0 -10000 0 0
MAPK8 0.003 0.13 -9999 0 -0.56 3 3
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 -0.003 0.11 -9999 0 -0.67 5 5
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.025 0.15 -9999 0 -0.78 2 2
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.14 -9999 0 -0.45 5 5
CHUK 0.017 0.12 -9999 0 -0.47 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.075 -9999 0 -0.71 1 1
TCRz/NEF -0.074 0.2 -9999 0 -0.44 38 38
TNF -0.15 0.29 -9999 0 -0.67 42 42
FASLG -0.14 0.34 -9999 0 -0.76 38 38
NFKB1 0.012 0.03 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.073 0.19 -9999 0 -0.42 42 42
CASP6 -0.036 0.11 -9999 0 -0.72 4 4
CASP7 0.021 0.19 -9999 0 -0.64 12 12
RELA 0.012 0.03 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 0.021 0.19 -9999 0 -0.64 12 12
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.024 0 -9999 0 -10000 0 0
CASP8 0.001 0.1 -9999 0 -0.67 4 4
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.008 0.13 -9999 0 -0.54 2 2
APAF-1/Caspase 9 -0.056 0.13 -9999 0 -0.56 9 9
BCL2 -0.002 0.15 -9999 0 -0.52 9 9
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.019 0.17 -9999 0 -0.59 12 12
PDGFB-D/PDGFRB/SLAP -0.11 0.25 -9999 0 -0.54 44 44
PDGFB-D/PDGFRB/APS/CBL 0.022 0.068 -9999 0 -0.42 4 4
AKT1 0.058 0.064 -9999 0 -0.56 1 1
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.18 -9999 0 -0.61 12 12
PIK3CA 0.012 0.051 -9999 0 -0.67 1 1
FGR -0.15 0.3 -9999 0 -0.68 40 40
mol:Ca2+ -0.013 0.15 -9999 0 -0.94 4 4
MYC -0.012 0.16 -9999 0 -0.69 6 6
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP 0.033 0.075 -9999 0 -0.7 1 1
LRP1/PDGFRB/PDGFB 0.013 0.11 -9999 0 -0.55 6 6
GRB10 0.012 0.051 -9999 0 -0.67 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 -0.014 0.16 -9999 0 -0.97 4 4
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.013 0.051 -9999 0 -0.66 1 1
PDGFB-D/PDGFRB/SHP2 0.012 0.078 -9999 0 -0.5 4 4
PDGFB-D/PDGFRB/GRB10 0.01 0.097 -9999 0 -0.6 4 4
cell cycle arrest -0.11 0.25 -9999 0 -0.54 44 44
HRAS 0.016 0 -9999 0 -10000 0 0
HIF1A 0.063 0.073 -9999 0 -0.74 1 1
GAB1 -0.035 0.18 -9999 0 -0.79 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.026 0.17 -9999 0 -0.73 7 7
PDGFB-D/PDGFRB 0.026 0.072 -9999 0 -0.45 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.012 0.078 -9999 0 -0.5 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.049 0.18 -9999 0 -0.65 12 12
positive regulation of MAPKKK cascade 0.012 0.078 -9999 0 -0.5 4 4
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.014 0.16 -9999 0 -0.98 4 4
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.016 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.009 0.087 -9999 0 -0.5 5 5
SHB 0.009 0.072 -9999 0 -0.67 2 2
BLK -0.14 0.24 -9999 0 -0.63 28 28
PTPN2 0.017 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.012 0.078 -9999 0 -0.5 4 4
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 -0.056 0.22 -9999 0 -0.73 12 12
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.012 0.078 -9999 0 -0.5 4 4
LCK -0.032 0.19 -9999 0 -0.92 7 7
PDGFRB 0.001 0.1 -9999 0 -0.68 4 4
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.12 0.29 -9999 0 -0.69 34 34
ABL1 -0.042 0.19 -9999 0 -0.81 7 7
PDGFB-D/PDGFRB/CBL -0.047 0.2 -9999 0 -0.87 7 7
PTPN1 0.017 0.002 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.012 0.051 -9999 0 -0.67 1 1
cell proliferation -0.009 0.15 -9999 0 -0.61 6 6
SLA -0.15 0.3 -9999 0 -0.67 44 44
actin cytoskeleton reorganization 0.046 0.079 -9999 0 -0.68 1 1
SRC -0.004 0.07 -9999 0 -0.48 3 3
PI3K -0.009 0.061 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.019 0.075 -9999 0 -0.42 5 5
SH2B2 0.016 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.023 0.19 -9999 0 -0.64 12 12
LYN -0.015 0.14 -9999 0 -0.79 5 5
LRP1 0.012 0.051 -9999 0 -0.67 1 1
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.012 0.051 -9999 0 -0.67 1 1
NCK1-2/p130 Cas 0.019 0.061 -9999 0 -10000 0 0
SPHK1 -0.026 0.17 -9999 0 -0.68 11 11
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.014 0.16 -9999 0 -0.98 4 4
PLCG1 -0.016 0.17 -9999 0 -1 4 4
NHERF/PDGFRB 0.022 0.068 -9999 0 -0.42 4 4
YES1 -0.003 0.07 -9999 0 -0.48 3 3
cell migration 0.022 0.068 -9999 0 -0.42 4 4
SHC/Grb2/SOS1 0.019 0.061 -9999 0 -10000 0 0
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.033 0.062 -9999 0 -0.38 4 4
FYN -0.007 0.12 -9999 0 -0.75 3 3
DOK1 0.025 0.087 -9999 0 -0.46 5 5
HRAS/GTP 0.012 0 -9999 0 -10000 0 0
PDGFB 0.005 0.088 -9999 0 -0.67 3 3
RAC1 -0.035 0.21 -9999 0 -0.78 9 9
PRKCD 0.029 0.065 -9999 0 -0.4 4 4
FER 0.029 0.065 -9999 0 -0.4 4 4
MAPKKK cascade -0.007 0.049 -9999 0 -10000 0 0
RASA1 0.027 0.082 -9999 0 -0.49 4 4
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.034 0.08 -9999 0 -0.7 1 1
PDGFB-D/PDGFRB/SHB 0.007 0.1 -9999 0 -0.58 5 5
chemotaxis -0.04 0.18 -9999 0 -0.76 7 7
STAT1-3-5/STAT1-3-5 -0.01 0.058 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0.079 -9999 0 -0.52 4 4
PTPRJ 0.016 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.033 0.18 -9999 0 -0.66 13 13
CDC42/GTP -0.001 0.14 -9999 0 -0.55 7 7
PLCG1 0 0.14 -9999 0 -0.57 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.024 0 -9999 0 -10000 0 0
cell migration -0.001 0.14 -9999 0 -0.53 7 7
S1PR5 -0.034 0.18 -9999 0 -0.67 13 13
S1PR4 -0.03 0.17 -9999 0 -0.67 12 12
MAPK3 0 0.14 -9999 0 -0.57 7 7
MAPK1 0 0.14 -9999 0 -0.57 7 7
S1P/S1P5/Gi -0.012 0.15 -9999 0 -0.54 8 8
GNAI1 0.005 0.088 -9999 0 -0.66 3 3
CDC42/GDP 0.012 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.011 0.12 -9999 0 -0.43 13 13
RHOA 0.011 0.097 -9999 0 -0.35 12 12
S1P/S1P4/Gi -0.009 0.15 -9999 0 -0.61 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.01 0.13 -9999 0 -0.66 7 7
S1P/S1P4/G12/G13 0.004 0.1 -9999 0 -0.38 12 12
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.011 -10000 0 -10000 0 0
HSPA8 0.016 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.034 0.12 -10000 0 -0.48 11 11
AKT1 0.013 0.023 -10000 0 -10000 0 0
GSC -0.086 0.39 -10000 0 -1.5 12 12
NKX2-5 -0.042 0.18 -10000 0 -0.66 14 14
muscle cell differentiation 0.064 0.13 0.59 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.044 0.16 -10000 0 -0.65 4 4
SMAD4 0.009 0.065 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.028 0.16 -10000 0 -0.41 25 25
SMAD3/SMAD4/VDR -0.007 0.1 -10000 0 -0.58 4 4
MYC 0.014 0.063 -10000 0 -0.54 2 2
CDKN2B -0.12 0.47 -10000 0 -1.5 19 19
AP1 -0.011 0.17 -10000 0 -1.2 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.06 0.071 -10000 0 -0.63 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.016 0.14 -10000 0 -0.57 4 4
SP3 0.019 0.001 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.098 0.26 -10000 0 -0.67 29 29
SMAD3/SMAD4/GR -0.021 0.1 -10000 0 -0.55 5 5
GATA3 -0.052 0.2 -10000 0 -0.68 16 16
SKI/SIN3/HDAC complex/NCoR1 0.053 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.084 0.26 -10000 0 -0.76 13 13
endothelial cell migration 0.056 0.31 1.3 10 -10000 0 10
MAX 0.017 0.012 -10000 0 -10000 0 0
RBBP7 0.016 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.051 -10000 0 -0.67 1 1
RUNX2 -0.003 0.11 -10000 0 -0.67 5 5
RUNX3 -0.03 0.17 -10000 0 -0.67 12 12
RUNX1 -0.007 0.12 -10000 0 -0.67 6 6
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.001 0.097 -10000 0 -0.63 4 4
VDR 0.001 0.1 -10000 0 -0.67 4 4
CDKN1A 0.048 0.11 -10000 0 -0.86 1 1
KAT2B 0.017 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.05 0.21 -10000 0 -0.46 33 33
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.016 0.001 -10000 0 -10000 0 0
SERPINE1 -0.057 0.31 -10000 0 -1.3 10 10
SMAD3/SMAD4/ATF2 0.002 0.092 -10000 0 -0.68 2 2
SMAD3/SMAD4/ATF3 -0.002 0.1 -10000 0 -0.56 4 4
SAP30 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.037 0.027 -10000 0 -10000 0 0
JUN -0.011 0.16 -10000 0 -1.2 1 1
SMAD3/SMAD4/IRF7 -0.006 0.11 -10000 0 -0.51 5 5
TFE3 0.021 0.017 -10000 0 -10000 0 0
COL1A2 -0.076 0.3 -10000 0 -1.1 13 13
mesenchymal cell differentiation 0.023 0.13 0.7 5 -10000 0 5
DLX1 -0.007 0.12 -10000 0 -0.66 6 6
TCF3 0.016 0 -10000 0 -10000 0 0
FOS -0.11 0.26 -10000 0 -0.64 35 35
SMAD3/SMAD4/Max -0.011 0.071 -10000 0 -0.76 1 1
Cbp/p300/SNIP1 0.033 0.011 -10000 0 -10000 0 0
ZBTB17 0.02 0.019 -10000 0 -10000 0 0
LAMC1 0.037 0.13 -10000 0 -1 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.083 -10000 0 -0.81 1 1
IRF7 0.001 0.1 -10000 0 -0.67 4 4
ESR1 -0.02 0.15 -10000 0 -0.64 10 10
HNF4A -0.003 0.11 -10000 0 -0.67 5 5
MEF2C -0.074 0.26 -10000 0 -0.75 13 13
SMAD2-3/SMAD4 0.023 0.12 -10000 0 -0.93 1 1
Cbp/p300/Src-1 0.035 0.017 -10000 0 -10000 0 0
IGHV3OR16-13 -0.009 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.017 0.007 -10000 0 -10000 0 0
SKIL 0.005 0.088 -10000 0 -0.67 3 3
HDAC1 0.016 0.001 -10000 0 -10000 0 0
HDAC2 0.016 0.001 -10000 0 -10000 0 0
SNIP1 0.016 0.003 -10000 0 -10000 0 0
GCN5L2 0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.04 0.11 -10000 0 -1 1 1
MSG1/HSC70 -0.049 0.18 -10000 0 -0.49 25 25
SMAD2 0.01 0.044 -10000 0 -10000 0 0
SMAD3 0.01 0.083 -10000 0 -0.91 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.042 0.06 -10000 0 -0.48 1 1
SMAD2/SMAD2/SMAD4 0.013 0.031 -10000 0 -10000 0 0
NCOR1 0.012 0.051 -10000 0 -0.66 1 1
NCOA2 -0.026 0.16 -10000 0 -0.67 11 11
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A 0.013 0.003 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.053 0.16 -10000 0 -0.72 3 3
IFNB1 0.018 0.11 -10000 0 -0.65 2 2
SMAD3/SMAD4/MEF2C -0.062 0.26 -10000 0 -0.78 12 12
CITED1 -0.079 0.24 -10000 0 -0.66 25 25
SMAD2-3/SMAD4/ARC105 0.037 0.1 -10000 0 -0.85 1 1
RBL1 0.012 0.051 -10000 0 -0.67 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.009 0.2 -10000 0 -0.57 18 18
RUNX1-3/PEBPB2 -0.011 0.16 -10000 0 -0.53 14 14
SMAD7 0.037 0.16 -10000 0 -1.2 1 1
MYC/MIZ-1 0.026 0.055 -10000 0 -10000 0 0
SMAD3/SMAD4 0.001 0.12 0.32 5 -0.54 4 9
IL10 -0.045 0.27 -10000 0 -0.75 19 19
PIASy/HDAC complex 0.016 0.008 -10000 0 -10000 0 0
PIAS3 0.017 0.004 -10000 0 -10000 0 0
CDK2 0.009 0.073 -10000 0 -0.67 2 2
IL5 -0.015 0.18 -10000 0 -0.71 6 6
CDK4 0.017 0.009 -10000 0 -10000 0 0
PIAS4 0.016 0.008 -10000 0 -10000 0 0
ATF3 0.005 0.088 -10000 0 -0.66 3 3
SMAD3/SMAD4/SP1 0.034 0.14 -10000 0 -0.75 2 2
FOXG1 -0.012 0.099 -10000 0 -0.66 4 4
FOXO3 0.023 0.03 -10000 0 -10000 0 0
FOXO1 0.017 0.066 -10000 0 -0.53 2 2
FOXO4 0.023 0.03 -10000 0 -10000 0 0
heart looping -0.072 0.25 -10000 0 -0.74 13 13
CEBPB 0.014 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.01 0.12 -10000 0 -0.54 7 7
MYOD1 0.001 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.008 0.11 -10000 0 -0.53 6 6
SMAD3/SMAD4/GATA3 -0.067 0.18 -10000 0 -0.68 9 9
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.088 -10000 0 -0.67 3 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.007 0.19 -10000 0 -0.67 10 10
SMAD3/SMAD4/SP1-3 0.051 0.13 -10000 0 -1.2 1 1
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.018 0.04 -10000 0 -10000 0 0
SIN3B 0.016 0.001 -10000 0 -10000 0 0
SIN3A 0.016 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.068 0.23 -10000 0 -0.6 14 14
ITGB5 0.048 0.13 -10000 0 -1.3 1 1
TGIF/SIN3/HDAC complex/CtBP 0.051 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.03 0.16 -10000 0 -0.52 14 14
AR -0.038 0.18 -10000 0 -0.67 14 14
negative regulation of cell growth 0.046 0.078 -10000 0 -0.62 1 1
SMAD3/SMAD4/MYOD 0 0.083 -10000 0 -0.82 1 1
E2F5 0.016 0 -10000 0 -10000 0 0
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.021 0.18 -10000 0 -0.57 6 6
SMAD2-3/SMAD4/FOXO1-3a-4 0.022 0.15 -10000 0 -0.64 3 3
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.009 0.17 -10000 0 -1.3 1 1
SMAD3/SMAD4/RUNX2 -0.007 0.14 -10000 0 -0.71 5 5
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.001 0.1 -10000 0 -0.67 4 4
ATF2 0.012 0.051 -10000 0 -0.67 1 1
PLK1 signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.013 0.074 0.22 20 -10000 0 20
BUB1B 0.012 0.073 -10000 0 -0.32 7 7
PLK1 0.014 0.034 -10000 0 -0.15 5 5
PLK1S1 0.014 0.021 -10000 0 -0.17 1 1
KIF2A 0.022 0.031 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.014 0.034 -10000 0 -0.15 5 5
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.019 0.16 -10000 0 -0.43 21 21
WEE1 0.023 0.035 -10000 0 -10000 0 0
cytokinesis 0.006 0.11 -10000 0 -0.45 9 9
PP2A-alpha B56 0.021 0.11 -10000 0 -0.67 4 4
AURKA 0.01 0.041 -10000 0 -0.18 7 7
PICH/PLK1 0.013 0.13 -10000 0 -0.47 10 10
CENPE 0.011 0.075 -10000 0 -0.39 5 5
RhoA/GTP 0.012 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.022 0.03 -10000 0 -10000 0 0
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.016 0 -10000 0 -10000 0 0
TPX2 0.004 0.058 -10000 0 -0.22 10 10
PAK1 0.016 0.001 -10000 0 -10000 0 0
SPC24 -0.056 0.21 -10000 0 -0.66 19 19
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN 0 0.072 -10000 0 -0.28 10 10
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase 0 0.004 -10000 0 -0.017 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.016 -10000 0 -0.071 5 5
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.011 5 5
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.002 0.009 -10000 0 -10000 0 0
spindle elongation 0.014 0.034 -10000 0 -0.15 5 5
ODF2 0.015 0.003 -10000 0 -10000 0 0
BUB1 -0.023 0.12 -10000 0 -0.75 4 4
TPT1 0.015 0.016 -10000 0 -10000 0 0
CDC25C -0.024 0.098 -10000 0 -0.22 33 33
CDC25B 0.013 0.051 -10000 0 -0.66 1 1
SGOL1 -0.013 0.074 -10000 0 -0.22 20 20
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.011 0.061 -10000 0 -0.36 5 5
CDC14B 0.013 0.002 -10000 0 -10000 0 0
CDC20 -0.03 0.17 -10000 0 -0.66 12 12
PLK1/PBIP1 0.013 0.058 -10000 0 -0.47 2 2
mitosis 0.001 0.006 0.032 7 -10000 0 7
FBXO5 0.021 0.026 -10000 0 -10000 0 0
CDC2 0.001 0.003 -10000 0 -0.016 5 5
NDC80 -0.003 0.11 -10000 0 -0.67 5 5
metaphase plate congression 0.015 0.022 -10000 0 -10000 0 0
ERCC6L 0.012 0.12 -10000 0 -0.46 10 10
NLP/gamma Tubulin 0.013 0.017 -10000 0 -0.088 1 1
microtubule cytoskeleton organization 0.015 0.016 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.012 0.051 -10000 0 -0.67 1 1
interphase