PARADIGM pathway analysis of mRNA expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
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 (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1FQ9TS0
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 32 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
TCGA08_retinoblastoma 88
Signaling events mediated by Stem cell factor receptor (c-Kit) 43
Fc-epsilon receptor I signaling in mast cells 35
BCR signaling pathway 34
HIF-1-alpha transcription factor network 33
IGF1 pathway 28
FAS signaling pathway (CD95) 23
Syndecan-1-mediated signaling events 21
Visual signal transduction: Rods 18
Arf6 signaling events 16
Results
Summary Table

The following list describes the columns found in ##REF##406.

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

  • 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.

Pathway.Name 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
TCGA08_retinoblastoma 88 704 8 -0.37 0.21 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 43 3420 78 -0.99 0.26 1000 -1000 -0.063 -1000
Fc-epsilon receptor I signaling in mast cells 35 3469 97 -0.33 0.042 1000 -1000 -0.059 -1000
BCR signaling pathway 34 3463 99 -0.36 0.034 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 33 2534 76 -0.75 0.041 1000 -1000 -0.068 -1000
IGF1 pathway 28 1649 57 -0.3 0.096 1000 -1000 -0.047 -1000
FAS signaling pathway (CD95) 23 1115 47 -0.17 0.12 1000 -1000 -0.065 -1000
Syndecan-1-mediated signaling events 21 746 34 -0.3 0.033 1000 -1000 -0.049 -1000
Visual signal transduction: Rods 18 970 52 -0.41 0.069 1000 -1000 -0.035 -1000
Arf6 signaling events 16 995 62 -0.14 0.081 1000 -1000 -0.02 -1000
EGFR-dependent Endothelin signaling events 15 323 21 -0.11 0.048 1000 -1000 -0.049 -1000
HIF-2-alpha transcription factor network 14 631 43 -0.57 0.33 1000 -1000 -0.049 -1000
Wnt signaling 14 102 7 -0.05 0.034 1000 -1000 -0.027 -1000
TRAIL signaling pathway 13 628 48 -0.11 0.034 1000 -1000 -0.038 -1000
Endothelins 13 1286 96 -0.42 0.092 1000 -1000 -0.049 -1000
IL6-mediated signaling events 13 995 75 -0.3 0.068 1000 -1000 -0.056 -1000
BMP receptor signaling 12 1014 81 -0.23 0.066 1000 -1000 -0.054 -1000
Glypican 1 network 12 597 48 -0.23 0.053 1000 -1000 -0.031 -1000
Reelin signaling pathway 12 727 56 -0.27 0.091 1000 -1000 -0.035 -1000
TCGA08_p53 11 80 7 -0.062 0.033 1000 -1000 -0.003 -1000
IL12-mediated signaling events 10 920 87 -0.38 0.068 1000 -1000 -0.077 -1000
IL4-mediated signaling events 10 946 91 -0.52 0.32 1000 -1000 -0.12 -1000
IL1-mediated signaling events 10 681 62 -0.24 0.064 1000 -1000 -0.045 -1000
RXR and RAR heterodimerization with other nuclear receptor 10 533 52 -0.42 0.11 1000 -1000 -0.044 -1000
Visual signal transduction: Cones 9 370 38 -0.12 0.055 1000 -1000 -0.009 -1000
FOXA2 and FOXA3 transcription factor networks 9 458 46 -0.73 0.038 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 9 341 35 -0.3 0.058 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 9 309 34 -0.063 0.097 1000 -1000 -0.042 -1000
PLK2 and PLK4 events 8 26 3 -0.001 0.019 1000 -1000 -0.009 -1000
Ceramide signaling pathway 8 634 76 -0.29 0.078 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 8 488 58 -0.54 0.041 1000 -1000 -0.044 -1000
FOXM1 transcription factor network 8 432 51 -0.34 0.033 1000 -1000 -0.12 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 7 407 54 -0.27 0.041 1000 -1000 -0.051 -1000
Signaling events mediated by the Hedgehog family 7 408 52 -0.077 0.056 1000 -1000 -0.048 -1000
Thromboxane A2 receptor signaling 7 832 105 -0.35 0.081 1000 -1000 -0.048 -1000
Syndecan-2-mediated signaling events 7 525 69 -0.3 0.054 1000 -1000 -0.039 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 7 618 85 -0.13 0.067 1000 -1000 -0.049 -1000
p75(NTR)-mediated signaling 7 944 125 -0.3 0.078 1000 -1000 -0.053 -1000
Canonical Wnt signaling pathway 7 389 51 -0.22 0.18 1000 -1000 -0.057 -1000
Regulation of nuclear SMAD2/3 signaling 6 914 136 -1.2 0.1 1000 -1000 -0.041 -1000
Osteopontin-mediated events 6 259 38 -0.22 0.047 1000 -1000 -0.047 -1000
Presenilin action in Notch and Wnt signaling 6 387 61 -0.22 0.12 1000 -1000 -0.045 -1000
PLK1 signaling events 6 549 85 -0.097 0.067 1000 -1000 -0.034 -1000
amb2 Integrin signaling 6 518 82 -0.24 0.048 1000 -1000 -0.048 -1000
Glucocorticoid receptor regulatory network 6 732 114 -0.31 0.23 1000 -1000 -0.06 -1000
Ephrin B reverse signaling 6 293 48 -0.084 0.048 1000 -1000 -0.035 -1000
Integrins in angiogenesis 6 514 84 -0.29 0.083 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 6 609 93 -0.067 0.049 1000 -1000 -0.056 -1000
Glypican 2 network 6 24 4 0 0.011 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 6 419 68 -0.37 0.06 1000 -1000 -0.084 -1000
Regulation of Androgen receptor activity 6 432 70 -0.52 0.063 1000 -1000 -0.059 -1000
Aurora B signaling 6 424 67 -0.13 0.046 1000 -1000 -0.044 -1000
Noncanonical Wnt signaling pathway 5 136 26 -0.05 0.034 1000 -1000 -0.052 -1000
a4b1 and a4b7 Integrin signaling 5 25 5 0.001 0.042 1000 -1000 0.007 -1000
EPO signaling pathway 5 285 55 -0.48 0.034 1000 -1000 -0.05 -1000
PDGFR-alpha signaling pathway 5 254 44 -0.034 0.074 1000 -1000 -0.042 -1000
Paxillin-independent events mediated by a4b1 and a4b7 5 196 37 -0.12 0.075 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 5 156 31 -0.15 0.039 1000 -1000 -0.046 -1000
IL23-mediated signaling events 5 349 60 -0.28 0.034 1000 -1000 -0.1 -1000
VEGFR1 specific signals 5 304 56 -0.004 0.1 1000 -1000 -0.044 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 5 167 33 -0.12 0.078 1000 -1000 -0.035 -1000
Sphingosine 1-phosphate (S1P) pathway 4 128 28 -0.03 0.043 1000 -1000 -0.016 -1000
Cellular roles of Anthrax toxin 4 174 39 -0.051 0.034 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 4 367 76 -0.28 0.055 1000 -1000 -0.044 -1000
Nectin adhesion pathway 4 280 63 -0.3 0.082 1000 -1000 -0.059 -1000
ceramide signaling pathway 4 196 49 -0.17 0.063 1000 -1000 -0.044 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 335 83 -0.17 0.092 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 202 45 -0.098 0.06 1000 -1000 -0.058 -1000
EPHB forward signaling 4 349 85 -0.085 0.11 1000 -1000 -0.069 -1000
Regulation of p38-alpha and p38-beta 4 256 54 -0.079 0.062 1000 -1000 -0.053 -1000
IL27-mediated signaling events 4 250 51 -0.15 0.034 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 4 122 26 -0.13 0.066 1000 -1000 -0.013 -1000
Class I PI3K signaling events 4 298 73 -0.24 0.061 1000 -1000 -0.048 -1000
Syndecan-4-mediated signaling events 4 310 67 -0.36 0.1 1000 -1000 -0.05 -1000
Plasma membrane estrogen receptor signaling 4 398 86 -0.29 0.1 1000 -1000 -0.067 -1000
ErbB4 signaling events 3 214 69 -0.2 0.099 1000 -1000 -0.05 -1000
Class I PI3K signaling events mediated by Akt 3 204 68 -0.057 0.082 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 3 155 40 -0.2 0.063 1000 -1000 -0.018 -1000
S1P5 pathway 3 60 17 -0.03 0.034 1000 -1000 -0.013 -1000
FoxO family signaling 3 201 64 -0.18 0.063 1000 -1000 -0.046 -1000
Signaling mediated by p38-gamma and p38-delta 3 59 15 -0.032 0.031 1000 -1000 -0.028 -1000
Signaling mediated by p38-alpha and p38-beta 3 143 44 -0.16 0.033 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 3 79 26 -0.019 0.064 1000 -1000 -0.006 -1000
Nongenotropic Androgen signaling 3 156 52 -0.038 0.08 1000 -1000 -0.039 -1000
Stabilization and expansion of the E-cadherin adherens junction 3 293 74 -0.29 0.064 1000 -1000 -0.067 -1000
Arf6 trafficking events 3 252 71 -0.096 0.054 1000 -1000 -0.031 -1000
Regulation of Telomerase 3 362 102 -0.14 0.078 1000 -1000 -0.06 -1000
S1P3 pathway 3 152 42 -0.029 0.049 1000 -1000 -0.032 -1000
S1P4 pathway 3 89 25 -0.03 0.043 1000 -1000 -0.027 -1000
E-cadherin signaling events 3 16 5 0.019 0.052 1000 -1000 0.005 -1000
Ras signaling in the CD4+ TCR pathway 3 66 17 0 0.056 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 2 173 74 -0.081 0.049 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 2 176 76 -0.082 0.067 1000 -1000 -0.025 -1000
Canonical NF-kappaB pathway 2 95 39 -0.024 0.075 1000 -1000 -0.036 -1000
BARD1 signaling events 2 143 57 -0.054 0.068 1000 -1000 -0.045 -1000
JNK signaling in the CD4+ TCR pathway 2 35 17 -0.006 0.074 1000 -1000 -0.035 -1000
Aurora A signaling 2 122 60 -0.011 0.085 1000 -1000 -0.02 -1000
Arf6 downstream pathway 2 118 43 -0.05 0.051 1000 -1000 -0.03 -1000
mTOR signaling pathway 2 129 53 -0.066 0.046 1000 -1000 -0.041 -1000
IFN-gamma pathway 2 153 68 -0.044 0.055 1000 -1000 -0.061 -1000
S1P1 pathway 2 107 36 -0.039 0.034 1000 -1000 -0.044 -1000
E-cadherin signaling in the nascent adherens junction 2 196 76 -0.03 0.099 1000 -1000 -0.074 -1000
Insulin Pathway 2 153 74 -0.033 0.098 1000 -1000 -0.045 -1000
PDGFR-beta signaling pathway 2 201 97 -0.11 0.1 1000 -1000 -0.055 -1000
LPA4-mediated signaling events 1 18 12 -0.005 0.031 1000 -1000 -0.017 -1000
ErbB2/ErbB3 signaling events 1 76 65 -0.009 0.061 1000 -1000 -0.07 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 26 23 0.011 0.044 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class II 1 76 75 -0.022 0.066 1000 -1000 -0.031 -1000
Ephrin A reverse signaling 1 13 7 0 0.037 1000 -1000 -0.005 -1000
Hedgehog signaling events mediated by Gli proteins 1 127 65 -0.052 0.077 1000 -1000 -0.046 -1000
Insulin-mediated glucose transport 1 32 32 -0.029 0.053 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 1 79 58 -0.011 0.067 1000 -1000 -0.056 -1000
Paxillin-dependent events mediated by a4b1 1 65 36 -0.067 0.071 1000 -1000 -0.038 -1000
Signaling events mediated by VEGFR1 and VEGFR2 1 221 125 -0.03 0.12 1000 -1000 -0.066 -1000
LPA receptor mediated events 1 193 102 -0.1 0.046 1000 -1000 -0.061 -1000
IL2 signaling events mediated by STAT5 1 37 22 -0.019 0.073 1000 -1000 -0.048 -1000
Angiopoietin receptor Tie2-mediated signaling 1 133 88 -0.09 0.12 1000 -1000 -0.069 -1000
Neurotrophic factor-mediated Trk receptor signaling 1 141 120 -0.026 0.091 1000 -1000 -0.051 -1000
Arf1 pathway 1 97 54 0 0.08 1000 -1000 -0.02 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0 17 34 -0.046 0.092 1000 -1000 -0.036 -1000
Circadian rhythm pathway 0 20 22 -0.012 0.077 1000 -1000 -0.038 -1000
Aurora C signaling 0 3 7 0 0.047 1000 -1000 -0.012 -1000
Signaling events regulated by Ret tyrosine kinase 0 40 82 0 0.071 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class I 0 68 104 -0.064 0.08 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0 2 31 0 0.07 1000 -1000 -0.034 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 6 27 0 0.059 1000 -1000 -0.043 -1000
Rapid glucocorticoid signaling 0 3 20 0 0.038 1000 -1000 -0.005 -1000
E-cadherin signaling in keratinocytes 0 16 43 -0.054 0.1 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.033 0.033 1000 -1000 -0.01 -1000
p38 MAPK signaling pathway 0 16 44 -0.001 0.067 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.089 1000 -1000 0 -1000
Total 893 53150 7203 -22 9.5 131000 -131000 -5.6 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.37 0.21 -10000 0 -0.48 117 117
CDKN2C 0.04 0.051 -10000 0 -0.48 1 1
CDKN2A -0.085 0.17 -10000 0 -0.32 48 48
CCND2 0.19 0.092 0.23 116 -10000 0 116
RB1 -0.16 0.1 0.2 1 -0.23 92 93
CDK4 0.19 0.092 0.23 116 -10000 0 116
CDK6 0.21 0.1 0.25 116 -10000 0 116
G1/S progression 0.17 0.11 0.23 95 -0.26 2 97
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.24 0.2 0.28 1 -0.42 69 70
CRKL -0.26 0.2 -10000 0 -0.44 70 70
HRAS -0.2 0.19 -10000 0 -0.39 55 55
mol:PIP3 -0.23 0.19 -10000 0 -0.41 64 64
SPRED1 0.026 0.041 -10000 0 -0.32 2 2
SPRED2 0.034 0 -10000 0 -10000 0 0
GAB1 -0.27 0.22 -10000 0 -0.46 70 70
FOXO3 -0.25 0.22 -10000 0 -0.45 65 65
AKT1 -0.27 0.24 -10000 0 -0.48 68 68
BAD -0.25 0.22 -10000 0 -0.45 64 64
megakaryocyte differentiation -0.28 0.21 -10000 0 -0.46 75 75
GSK3B -0.24 0.22 -10000 0 -0.45 63 63
RAF1 -0.17 0.15 -10000 0 -0.34 29 29
SHC1 0.033 0.006 -10000 0 -10000 0 0
STAT3 -0.26 0.21 -10000 0 -0.46 69 69
STAT1 -0.71 0.55 -10000 0 -1.2 73 73
HRAS/SPRED1 -0.17 0.16 -10000 0 -0.39 15 15
cell proliferation -0.26 0.21 -10000 0 -0.45 70 70
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
TEC 0.033 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.27 0.23 -10000 0 -0.47 72 72
HRAS/SPRED2 -0.17 0.16 -10000 0 -0.39 14 14
LYN/TEC/p62DOK -0.23 0.21 -10000 0 -0.44 61 61
MAPK3 -0.12 0.11 -10000 0 -0.29 9 9
STAP1 -0.38 0.27 -10000 0 -0.57 89 89
GRAP2 0.031 0.009 -10000 0 -10000 0 0
JAK2 -0.55 0.43 -10000 0 -0.93 72 72
STAT1 (dimer) -0.69 0.53 -10000 0 -1.2 73 73
mol:Gleevec 0.011 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.24 -10000 0 -0.46 71 71
actin filament polymerization -0.26 0.21 -10000 0 -0.45 71 71
LYN 0.029 0.012 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.48 0.33 -10000 0 -0.72 88 88
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.22 0.2 -10000 0 -0.41 67 67
PI3K -0.24 0.23 -10000 0 -0.44 70 70
PTEN 0.024 0.063 -10000 0 -0.51 2 2
SCF/KIT/EPO/EPOR -0.78 0.68 -10000 0 -1.5 70 70
MAPK8 -0.27 0.21 -10000 0 -0.46 70 70
STAT3 (dimer) -0.26 0.21 -10000 0 -0.45 69 69
positive regulation of transcription -0.099 0.09 -10000 0 -0.25 5 5
mol:GDP -0.22 0.2 -10000 0 -0.4 67 67
PIK3C2B -0.26 0.22 -10000 0 -0.46 70 70
CBL/CRKL -0.24 0.2 -10000 0 -0.42 69 69
FER -0.27 0.21 -10000 0 -0.46 70 70
SH2B3 -0.26 0.21 -10000 0 -0.46 70 70
PDPK1 -0.21 0.18 -10000 0 -0.38 62 62
SNAI2 -0.25 0.21 -10000 0 -0.45 68 68
positive regulation of cell proliferation -0.47 0.36 -10000 0 -0.79 73 73
KITLG -0.02 0.06 -10000 0 -0.45 2 2
cell motility -0.47 0.36 -10000 0 -0.79 73 73
PTPN6 0.048 0.013 -10000 0 -10000 0 0
EPOR -0.19 0.19 -10000 0 -1.1 2 2
STAT5A (dimer) -0.38 0.29 -10000 0 -0.64 71 71
SOCS1 0.034 0.003 -10000 0 -10000 0 0
cell migration 0.26 0.21 0.45 70 -10000 0 70
SOS1 0.034 0 -10000 0 -10000 0 0
EPO -0.007 0.037 -10000 0 -0.34 1 1
VAV1 -0.003 0.14 -10000 0 -0.51 10 10
GRB10 -0.26 0.21 -10000 0 -0.46 68 68
PTPN11 0.042 0.031 -10000 0 -0.32 1 1
SCF/KIT -0.28 0.22 -10000 0 -0.48 71 71
GO:0007205 0.015 0.01 -10000 0 -10000 0 0
MAP2K1 -0.13 0.12 -10000 0 -0.31 11 11
CBL 0.033 0.005 -10000 0 -10000 0 0
KIT -0.73 0.71 -10000 0 -1.5 70 70
MAP2K2 -0.13 0.12 -10000 0 -0.32 10 10
SHC/Grb2/SOS1 -0.23 0.22 -10000 0 -0.44 67 67
STAT5A -0.39 0.3 -10000 0 -0.66 71 71
GRB2 0.032 0.007 -10000 0 -10000 0 0
response to radiation -0.25 0.21 -10000 0 -0.44 68 68
SHC/GRAP2 0.045 0.015 -10000 0 -10000 0 0
PTPRO -0.28 0.22 -10000 0 -0.47 75 75
SH2B2 -0.27 0.21 -10000 0 -0.46 71 71
DOK1 0.032 0.029 -10000 0 -0.32 1 1
MATK -0.26 0.21 -10000 0 -0.46 71 71
CREBBP -0.071 0.082 -10000 0 -10000 0 0
BCL2 -0.99 0.74 -10000 0 -1.6 92 92
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.033 0.18 -10000 0 -0.51 18 18
LAT2 -0.21 0.21 -10000 0 -0.41 65 65
AP1 -0.26 0.3 -10000 0 -0.56 58 58
mol:PIP3 -0.26 0.25 0.28 1 -0.52 62 63
IKBKB -0.13 0.15 0.2 7 -0.27 57 64
AKT1 -0.2 0.18 0.3 1 -0.41 49 50
IKBKG -0.14 0.14 0.19 2 -0.28 59 61
MS4A2 -0.28 0.27 -10000 0 -0.51 84 84
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.004 -10000 0 -10000 0 0
MAP3K1 -0.21 0.21 -10000 0 -0.43 59 59
mol:Ca2+ -0.2 0.19 0.25 1 -0.38 61 62
LYN 0.025 0.012 -10000 0 -10000 0 0
CBLB -0.21 0.2 -10000 0 -0.37 80 80
SHC1 0.033 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.04 0.089 -10000 0 -0.29 10 10
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.23 0.21 0.34 1 -0.43 68 69
PTPN13 -0.25 0.24 -10000 0 -0.58 25 25
PTPN11 0.006 0.042 -10000 0 -0.34 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.16 0.15 -10000 0 -0.33 47 47
SYK 0.029 0.008 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.26 0.27 -10000 0 -0.53 63 63
LAT -0.21 0.21 -10000 0 -0.38 80 80
PAK2 -0.23 0.24 -10000 0 -0.48 59 59
NFATC2 -0.06 0.066 -10000 0 -10000 0 0
HRAS -0.26 0.26 -10000 0 -0.52 62 62
GAB2 0.033 0.005 -10000 0 -10000 0 0
PLA2G1B 0.037 0.14 -10000 0 -0.88 3 3
Fc epsilon R1 -0.28 0.27 -10000 0 -0.46 95 95
Antigen/IgE/Fc epsilon R1 -0.25 0.25 -10000 0 -0.42 95 95
mol:GDP -0.28 0.29 -10000 0 -0.56 63 63
JUN 0.021 0.063 -10000 0 -0.32 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.005 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.22 0.22 -10000 0 -0.39 83 83
CHUK -0.14 0.14 0.22 1 -0.28 59 60
KLRG1 -0.19 0.19 -10000 0 -0.39 56 56
VAV1 -0.22 0.22 -10000 0 -0.4 80 80
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.21 0.2 -10000 0 -0.38 80 80
negative regulation of mast cell degranulation -0.18 0.17 -10000 0 -0.37 57 57
BTK -0.29 0.33 -10000 0 -0.62 60 60
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.33 0.33 -10000 0 -0.62 72 72
GAB2/PI3K/SHP2 -0.21 0.2 -10000 0 -0.43 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.23 0.22 -10000 0 -0.48 57 57
RAF1 0.04 0.15 -10000 0 -1 3 3
Fc epsilon R1/FcgammaRIIB/SHIP -0.28 0.3 -10000 0 -0.46 97 97
FCER1G 0.042 0.013 -10000 0 -10000 0 0
FCER1A -0.22 0.28 -10000 0 -0.52 68 68
Antigen/IgE/Fc epsilon R1/Fyn -0.23 0.24 -10000 0 -0.39 95 95
MAPK3 0.037 0.14 -10000 0 -0.88 3 3
MAPK1 0.031 0.14 -10000 0 -0.92 3 3
NFKB1 0.033 0.005 -10000 0 -10000 0 0
MAPK8 -0.19 0.35 -10000 0 -0.83 30 30
DUSP1 0 0.13 -10000 0 -0.51 9 9
NF-kappa-B/RelA -0.078 0.092 -10000 0 -0.2 2 2
actin cytoskeleton reorganization -0.22 0.22 -10000 0 -0.61 7 7
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.22 0.24 -10000 0 -0.47 59 59
FER -0.21 0.21 -10000 0 -0.38 80 80
RELA 0.033 0.005 -10000 0 -10000 0 0
ITK -0.046 0.061 -10000 0 -0.34 2 2
SOS1 0.034 0 -10000 0 -10000 0 0
PLCG1 -0.23 0.29 0.28 1 -0.52 60 61
cytokine secretion -0.06 0.062 -10000 0 -10000 0 0
SPHK1 -0.23 0.2 -10000 0 -0.39 83 83
PTK2 -0.22 0.23 -10000 0 -0.65 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.27 0.28 -10000 0 -0.56 62 62
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.28 0.27 0.29 1 -0.54 63 64
MAP2K2 0.032 0.14 -10000 0 -0.88 3 3
MAP2K1 0.031 0.14 -10000 0 -0.93 3 3
MAP2K7 0.034 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.16 0.18 -10000 0 -0.36 55 55
MAP2K4 -0.2 0.43 -10000 0 -0.96 35 35
Fc epsilon R1/FcgammaRIIB -0.3 0.31 -10000 0 -0.49 97 97
mol:Choline -0.22 0.21 0.34 1 -0.42 68 69
SHC/Grb2/SOS1 -0.18 0.22 -10000 0 -0.42 53 53
FYN 0.031 0.029 -10000 0 -0.32 1 1
DOK1 0.032 0.029 -10000 0 -0.32 1 1
PXN -0.21 0.21 -10000 0 -0.59 7 7
HCLS1 -0.22 0.22 -10000 0 -0.46 56 56
PRKCB -0.2 0.19 0.25 1 -0.38 64 65
FCGR2B -0.077 0.22 -10000 0 -0.51 30 30
IGHE -0.007 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.18 0.18 -10000 0 -0.37 57 57
LCP2 0.024 0.06 -10000 0 -0.38 3 3
PLA2G4A -0.27 0.24 -10000 0 -0.48 72 72
RASA1 0.031 0.029 -10000 0 -0.32 1 1
mol:Phosphatidic acid -0.22 0.21 0.34 1 -0.42 68 69
IKK complex -0.093 0.12 0.19 7 -0.21 41 48
WIPF1 0.034 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.2 0.26 -10000 0 -0.51 53 53
IKBKB -0.09 0.13 -10000 0 -0.3 12 12
AKT1 -0.11 0.14 -10000 0 -0.28 45 45
IKBKG -0.098 0.14 -10000 0 -0.29 20 20
CALM1 -0.28 0.32 -10000 0 -0.61 63 63
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
MAP3K1 -0.24 0.35 -10000 0 -0.68 51 51
MAP3K7 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.3 0.34 -10000 0 -0.63 68 68
DOK1 0.032 0.029 -10000 0 -0.32 1 1
AP-1 -0.13 0.14 -10000 0 -0.29 54 54
LYN 0.029 0.012 -10000 0 -10000 0 0
BLNK 0.017 0.088 -10000 0 -0.51 4 4
SHC1 0.033 0.006 -10000 0 -10000 0 0
BCR complex -0.24 0.3 -10000 0 -0.53 73 73
CD22 -0.27 0.38 -10000 0 -0.76 50 50
CAMK2G -0.26 0.29 -10000 0 -0.55 64 64
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.15 0.21 -10000 0 -0.44 38 38
GO:0007205 -0.31 0.36 -10000 0 -0.64 68 68
SYK 0.033 0.005 -10000 0 -10000 0 0
ELK1 -0.29 0.33 -10000 0 -0.61 65 65
NFATC1 -0.29 0.35 -10000 0 -0.67 61 61
B-cell antigen/BCR complex -0.24 0.3 -10000 0 -0.53 73 73
PAG1/CSK -0.089 0.19 -10000 0 -0.37 46 46
NFKBIB -0.015 0.055 -10000 0 -0.14 4 4
HRAS -0.24 0.28 -10000 0 -0.54 62 62
NFKBIA -0.013 0.053 -10000 0 -0.14 2 2
NF-kappa-B/RelA/I kappa B beta -0.005 0.046 -10000 0 -10000 0 0
RasGAP/Csk -0.2 0.31 -10000 0 -0.59 47 47
mol:GDP -0.29 0.33 -10000 0 -0.6 68 68
PTEN 0.024 0.063 -10000 0 -0.51 2 2
CD79B -0.12 0.24 -10000 0 -0.51 42 42
NF-kappa-B/RelA/I kappa B alpha -0.004 0.045 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.29 0.34 -10000 0 -0.65 63 63
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.31 0.36 -10000 0 -0.66 68 68
CSK 0.032 0.008 -10000 0 -10000 0 0
FOS -0.28 0.3 -10000 0 -0.58 64 64
CHUK -0.11 0.15 -10000 0 -0.33 25 25
IBTK 0.033 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.22 0.28 -10000 0 -0.53 58 58
PTPN6 -0.26 0.35 -10000 0 -0.72 49 49
RELA 0.033 0.005 -10000 0 -10000 0 0
BCL2A1 -0.002 0.033 -10000 0 -10000 0 0
VAV2 -0.35 0.44 -10000 0 -0.82 62 62
ubiquitin-dependent protein catabolic process -0.011 0.054 -10000 0 -0.14 4 4
BTK -0.18 0.45 -10000 0 -1.2 24 24
CD19 -0.35 0.45 -10000 0 -0.83 62 62
MAP4K1 0.033 0.006 -10000 0 -10000 0 0
CD72 0.029 0.041 -10000 0 -0.32 2 2
PAG1 -0.14 0.25 -10000 0 -0.51 46 46
MAPK14 -0.2 0.29 -10000 0 -0.57 49 49
SH3BP5 0.033 0.005 -10000 0 -10000 0 0
PIK3AP1 -0.3 0.36 -10000 0 -0.68 62 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.36 0.41 -10000 0 -0.76 66 66
RAF1 -0.22 0.26 -10000 0 -0.5 60 60
RasGAP/p62DOK/SHIP -0.2 0.29 -10000 0 -0.46 75 75
CD79A -0.23 0.27 -10000 0 -0.51 71 71
re-entry into mitotic cell cycle -0.14 0.14 -10000 0 -0.29 54 54
RASA1 0.031 0.029 -10000 0 -0.32 1 1
MAPK3 -0.19 0.21 -10000 0 -0.45 50 50
MAPK1 -0.18 0.21 -10000 0 -0.44 50 50
CD72/SHP1 -0.22 0.34 -10000 0 -0.68 48 48
NFKB1 0.033 0.005 -10000 0 -10000 0 0
MAPK8 -0.2 0.29 -10000 0 -0.57 49 49
actin cytoskeleton organization -0.26 0.36 0.28 3 -0.66 60 63
NF-kappa-B/RelA -0.002 0.088 -10000 0 -10000 0 0
Calcineurin -0.22 0.27 -10000 0 -0.5 63 63
PI3K -0.24 0.28 -10000 0 -0.54 62 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.33 0.39 -10000 0 -0.71 65 65
SOS1 0.034 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.26 0.4 -10000 0 -0.81 46 46
DAPP1 -0.32 0.46 -10000 0 -0.94 47 47
cytokine secretion -0.26 0.31 -10000 0 -0.6 61 61
mol:DAG -0.31 0.36 -10000 0 -0.66 68 68
PLCG2 -0.24 0.27 -10000 0 -0.51 75 75
MAP2K1 -0.21 0.24 -10000 0 -0.49 51 51
B-cell antigen/BCR complex/FcgammaRIIB -0.25 0.33 -10000 0 -0.54 76 76
mol:PI-3-4-5-P3 -0.16 0.19 -10000 0 -0.38 53 53
ETS1 -0.23 0.26 -10000 0 -0.5 62 62
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.15 0.25 -10000 0 -0.4 68 68
B-cell antigen/BCR complex/LYN -0.29 0.41 -10000 0 -0.8 51 51
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 -0.29 0.39 -10000 0 -0.73 60 60
B-cell antigen/BCR complex/LYN/SYK -0.23 0.35 -10000 0 -0.69 48 48
CARD11 -0.28 0.33 -10000 0 -0.62 64 64
FCGR2B -0.077 0.22 -10000 0 -0.51 30 30
PPP3CA 0.033 0.005 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex -0.028 0.057 0.12 1 -0.13 3 4
PTPRC 0.018 0.088 -10000 0 -0.51 4 4
PDPK1 -0.1 0.13 -10000 0 -0.26 43 43
PPP3CB 0.033 0.005 -10000 0 -10000 0 0
PPP3CC 0.023 0.046 -10000 0 -0.51 1 1
POU2F2 0 0.032 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.53 0.37 -9999 0 -0.94 50 50
HDAC7 -0.001 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.43 0.29 -9999 0 -0.82 30 30
SMAD4 0.024 0.016 -9999 0 -10000 0 0
ID2 -0.53 0.36 -9999 0 -0.94 49 49
AP1 0.008 0.1 -9999 0 -0.3 12 12
ABCG2 -0.75 0.38 -9999 0 -1 86 86
HIF1A -0.082 0.067 -9999 0 -0.34 2 2
TFF3 -0.54 0.37 -9999 0 -0.96 49 49
GATA2 0.031 0.017 -9999 0 -10000 0 0
AKT1 -0.076 0.062 -9999 0 -10000 0 0
response to hypoxia -0.093 0.048 -9999 0 -0.23 1 1
MCL1 -0.53 0.36 -9999 0 -0.94 49 49
NDRG1 -0.55 0.39 -9999 0 -1 51 51
SERPINE1 -0.56 0.37 -9999 0 -0.95 54 54
FECH -0.53 0.36 -9999 0 -0.94 49 49
FURIN -0.53 0.36 -9999 0 -0.94 49 49
NCOA2 0.03 0.012 -9999 0 -10000 0 0
EP300 -0.09 0.088 -9999 0 -0.3 7 7
HMOX1 -0.56 0.4 -9999 0 -0.99 53 53
BHLHE40 -0.54 0.35 -9999 0 -0.93 51 51
BHLHE41 -0.54 0.35 -9999 0 -0.93 51 51
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.096 0.096 -9999 0 -10000 0 0
ENG -0.095 0.078 -9999 0 -10000 0 0
JUN 0.019 0.064 -9999 0 -0.32 5 5
RORA -0.54 0.37 -9999 0 -0.95 49 49
ABCB1 -0.58 0.6 -9999 0 -1.3 64 64
TFRC -0.53 0.36 -9999 0 -0.94 50 50
CXCR4 -0.54 0.37 -9999 0 -0.95 50 50
TF -0.53 0.36 -9999 0 -0.94 49 49
CITED2 -0.53 0.36 -9999 0 -0.94 49 49
HIF1A/ARNT -0.6 0.41 -9999 0 -1.1 49 49
LDHA -0.056 0.13 -9999 0 -0.93 3 3
ETS1 -0.53 0.36 -9999 0 -0.94 49 49
PGK1 -0.54 0.36 -9999 0 -0.93 51 51
NOS2 -0.54 0.35 -9999 0 -0.93 51 51
ITGB2 -0.53 0.37 -9999 0 -0.95 48 48
ALDOA -0.53 0.36 -9999 0 -0.94 48 48
Cbp/p300/CITED2 -0.54 0.37 -9999 0 -0.98 43 43
FOS 0.001 0.11 -9999 0 -0.46 8 8
HK2 -0.53 0.36 -9999 0 -0.94 49 49
SP1 -0.019 0.07 -9999 0 -10000 0 0
GCK -0.1 0.12 -9999 0 -10000 0 0
HK1 -0.53 0.36 -9999 0 -0.94 49 49
NPM1 -0.53 0.36 -9999 0 -0.94 49 49
EGLN1 -0.53 0.36 -9999 0 -0.94 49 49
CREB1 0.041 0.001 -9999 0 -10000 0 0
PGM1 -0.56 0.38 -9999 0 -0.97 53 53
SMAD3 0.032 0.009 -9999 0 -10000 0 0
EDN1 -0.15 0.3 -9999 0 -1.3 8 8
IGFBP1 -0.53 0.37 -9999 0 -0.94 51 51
VEGFA -0.39 0.26 -9999 0 -0.73 34 34
HIF1A/JAB1 -0.042 0.052 -9999 0 -0.32 1 1
CP -0.57 0.4 -9999 0 -0.99 56 56
CXCL12 -0.71 0.41 -9999 0 -0.99 85 85
COPS5 0.03 0.012 -9999 0 -10000 0 0
SMAD3/SMAD4 0.033 0.03 -9999 0 -10000 0 0
BNIP3 -0.55 0.38 -9999 0 -0.96 52 52
EGLN3 -0.6 0.41 -9999 0 -1 61 61
CA9 -0.59 0.36 -9999 0 -0.95 57 57
TERT -0.53 0.36 -9999 0 -0.94 49 49
ENO1 -0.53 0.36 -9999 0 -0.93 50 50
PFKL -0.53 0.36 -9999 0 -0.94 48 48
NCOA1 0.027 0.063 -9999 0 -0.51 2 2
ADM -0.53 0.36 -9999 0 -0.94 49 49
ARNT -0.089 0.056 -9999 0 -10000 0 0
HNF4A 0.013 0.064 -9999 0 -0.51 2 2
ADFP -0.54 0.35 -9999 0 -0.93 51 51
SLC2A1 -0.4 0.26 -9999 0 -0.71 38 38
LEP -0.53 0.36 -9999 0 -0.94 50 50
HIF1A/ARNT/Cbp/p300 -0.44 0.29 -9999 0 -0.82 34 34
EPO -0.29 0.23 -9999 0 -0.83 12 12
CREBBP -0.086 0.08 -9999 0 -0.28 3 3
HIF1A/ARNT/Cbp/p300/HDAC7 -0.44 0.28 -9999 0 -0.83 33 33
PFKFB3 -0.54 0.37 -9999 0 -0.94 51 51
NT5E -0.55 0.37 -9999 0 -0.96 49 49
IGF1 pathway

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
NCK2 0.034 0 -10000 0 -10000 0 0
PTK2 0.027 0.013 -10000 0 -10000 0 0
CRKL -0.15 0.14 -10000 0 -0.27 86 86
GRB2/SOS1/SHC 0.064 0.018 -10000 0 -10000 0 0
HRAS 0.033 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.14 0.15 -10000 0 -0.27 86 86
IGF-1R heterotetramer/IGF1/PTP1B -0.091 0.14 -10000 0 -0.3 43 43
AKT1 -0.13 0.12 -10000 0 -0.34 3 3
BAD -0.12 0.11 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.15 0.14 -10000 0 -0.27 86 86
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.16 -10000 0 -0.27 86 86
RAF1 -0.12 0.13 -10000 0 -0.57 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.16 -10000 0 -0.26 83 83
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.17 -10000 0 -0.29 86 86
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.13 0.12 -10000 0 -0.34 3 3
GNB2L1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.082 0.11 -10000 0 -0.45 2 2
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.14 -10000 0 -0.34 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.094 0.16 -10000 0 -0.28 3 3
IGF-1R heterotetramer -0.03 0.056 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.13 0.16 -10000 0 -0.27 86 86
Crk/p130 Cas/Paxillin -0.11 0.16 -10000 0 -0.35 4 4
IGF1R -0.03 0.056 -10000 0 -10000 0 0
IGF1 -0.3 0.28 -10000 0 -0.52 87 87
IRS2/Crk -0.098 0.13 -10000 0 -0.26 57 57
PI3K -0.12 0.16 -10000 0 -0.26 84 84
apoptosis 0.096 0.11 0.29 3 -10000 0 3
HRAS/GDP 0.024 0.004 -10000 0 -10000 0 0
PRKCD -0.2 0.19 -10000 0 -0.36 86 86
RAF1/14-3-3 E -0.094 0.12 -10000 0 -0.48 3 3
BAD/14-3-3 -0.1 0.11 -10000 0 -0.3 3 3
PRKCZ -0.13 0.12 -10000 0 -0.34 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.094 0.12 -10000 0 -10000 0 0
PTPN1 0.018 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.2 0.2 -10000 0 -0.37 87 87
BCAR1 0.033 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.12 0.16 -10000 0 -0.27 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.14 0.15 -10000 0 -0.27 86 86
GRB10 0.014 0.074 -10000 0 -0.32 7 7
PTPN11 -0.15 0.14 -10000 0 -0.27 86 86
IRS1 -0.16 0.15 -10000 0 -0.29 86 86
IRS2 -0.098 0.14 -10000 0 -0.27 57 57
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.39 86 86
GRB2 0.032 0.007 -10000 0 -10000 0 0
PDPK1 -0.13 0.13 -10000 0 -0.36 3 3
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKD1 -0.2 0.19 -10000 0 -0.36 82 82
SHC1 0.033 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.091 0.1 0.21 50 -10000 0 50
RFC1 0.088 0.1 0.21 49 -10000 0 49
PRKDC 0.11 0.14 0.4 11 -10000 0 11
RIPK1 0.036 0.004 -10000 0 -10000 0 0
CASP7 -0.12 0.27 -10000 0 -0.72 24 24
FASLG/FAS/FADD/FAF1 -0.045 0.16 0.19 1 -0.35 25 26
MAP2K4 -0.1 0.18 -10000 0 -0.47 21 21
mol:ceramide -0.08 0.16 -10000 0 -0.39 26 26
GSN 0.056 0.14 0.21 48 -0.3 4 52
FASLG/FAS/FADD/FAF1/Caspase 8 -0.057 0.16 -10000 0 -0.41 20 20
FAS -0.02 0.15 -10000 0 -0.51 13 13
BID -0.024 0.035 -10000 0 -0.21 5 5
MAP3K1 -0.066 0.19 -10000 0 -0.5 18 18
MAP3K7 0.031 0.005 -10000 0 -10000 0 0
RB1 0.11 0.15 0.28 54 -10000 0 54
CFLAR 0.036 0.002 -10000 0 -10000 0 0
HGF/MET -0.11 0.16 -10000 0 -0.35 27 27
ARHGDIB 0.089 0.1 0.21 49 -10000 0 49
FADD 0.029 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.054 0.14 0.29 4 -0.21 48 52
NFKB1 -0.042 0.14 -10000 0 -1 3 3
MAPK8 -0.12 0.17 -10000 0 -0.5 17 17
DFFA 0.085 0.1 0.21 48 -10000 0 48
DNA fragmentation during apoptosis 0.086 0.11 0.21 49 -10000 0 49
FAS/FADD/MET -0.087 0.14 -10000 0 -0.36 14 14
CFLAR/RIP1 0.053 0.006 -10000 0 -10000 0 0
FAIM3 0.031 0.03 -10000 0 -0.32 1 1
FAF1 0.027 0.008 -10000 0 -10000 0 0
PARP1 0.089 0.1 0.21 49 -10000 0 49
DFFB 0.083 0.11 0.21 47 -10000 0 47
CHUK -0.039 0.13 -10000 0 -0.93 3 3
FASLG -0.054 0.19 -10000 0 -0.51 22 22
FAS/FADD 0.003 0.12 -10000 0 -0.37 13 13
HGF 0.032 0.008 -10000 0 -10000 0 0
LMNA 0.078 0.092 -10000 0 -10000 0 0
CASP6 0.089 0.1 0.21 49 -10000 0 49
CASP10 0.026 0.044 -10000 0 -0.51 1 1
CASP3 0.12 0.12 0.26 49 -10000 0 49
PTPN13 -0.08 0.17 -10000 0 -0.33 46 46
CASP8 -0.022 0.013 -10000 0 -10000 0 0
IL6 -0.11 0.16 -10000 0 -0.98 3 3
MET -0.13 0.17 -10000 0 -0.32 68 68
ICAD/CAD 0.056 0.098 0.22 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.081 0.16 -10000 0 -0.4 26 26
activation of caspase activity by cytochrome c -0.024 0.035 -10000 0 -0.21 5 5
PAK2 0.093 0.11 0.22 50 -10000 0 50
BCL2 -0.17 0.25 -10000 0 -0.51 53 53
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.033 0.005 -10000 0 -10000 0 0
CCL5 -0.07 0.21 -10000 0 -0.51 28 28
SDCBP 0.029 0.012 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.11 0.4 1 -0.31 23 24
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.088 0.1 -10000 0 -0.36 9 9
Syndecan-1/Syntenin -0.099 0.1 0.36 1 -0.36 10 11
MAPK3 -0.11 0.099 0.34 1 -0.36 2 3
HGF/MET -0.076 0.13 -10000 0 -0.22 68 68
TGFB1/TGF beta receptor Type II 0.033 0.005 -10000 0 -10000 0 0
BSG 0.033 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.087 0.1 -10000 0 -0.36 9 9
Syndecan-1/RANTES -0.16 0.16 0.36 1 -0.4 33 34
Syndecan-1/CD147 -0.11 0.1 0.36 1 -0.34 10 11
Syndecan-1/Syntenin/PIP2 -0.096 0.1 0.33 1 -0.34 10 11
LAMA5 0.004 0.068 -10000 0 -0.32 6 6
positive regulation of cell-cell adhesion -0.095 0.099 0.33 1 -0.34 10 11
MMP7 -0.3 0.075 -10000 0 -0.32 141 141
HGF 0.032 0.008 -10000 0 -10000 0 0
Syndecan-1/CASK -0.11 0.097 -10000 0 -0.3 24 24
Syndecan-1/HGF/MET -0.17 0.12 -10000 0 -0.4 17 17
regulation of cell adhesion -0.1 0.098 0.32 1 -0.37 1 2
HPSE -0.044 0.19 -10000 0 -0.51 21 21
positive regulation of cell migration -0.11 0.11 0.4 1 -0.31 23 24
SDC1 -0.11 0.11 0.4 1 -0.31 23 24
Syndecan-1/Collagen -0.11 0.11 0.4 1 -0.31 23 24
PPIB 0.025 0.05 -10000 0 -0.32 3 3
MET -0.13 0.17 -10000 0 -0.32 68 68
PRKACA 0.033 0.005 -10000 0 -10000 0 0
MMP9 0.005 0.071 -10000 0 -0.36 5 5
MAPK1 -0.1 0.099 0.34 1 -0.33 9 10
homophilic cell adhesion -0.11 0.11 0.4 1 -0.31 23 24
MMP1 -0.29 0.1 -10000 0 -0.32 134 134
Visual signal transduction: Rods

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
mol:K + 0.032 0.008 -10000 0 -10000 0 0
GNAT1/GTP 0.025 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin -0.25 0.14 -10000 0 -0.31 119 119
PDE6G/GNAT1/GTP 0.043 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.004 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.23 0.2 -10000 0 -0.47 39 39
mol:Na + -0.11 0.15 -10000 0 -0.37 3 3
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.057 0.17 -10000 0 -0.32 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.11 0.16 -10000 0 -0.38 3 3
CNGB1 0.034 0 -10000 0 -10000 0 0
RDH5 -0.12 0.24 -10000 0 -0.51 42 42
SAG -0.41 0.21 -10000 0 -0.51 120 120
mol:Ca2+ -0.12 0.14 0.34 2 -0.36 3 5
Na + (4 Units) -0.11 0.14 -10000 0 -0.36 3 3
RGS9 -0.12 0.24 -10000 0 -0.51 40 40
GNB1/GNGT1 -0.05 0.12 -10000 0 -10000 0 0
GNAT1/GDP -0.037 0.15 -10000 0 -0.27 40 40
GUCY2D 0.027 0.014 -10000 0 -10000 0 0
GNGT1 -0.094 0.17 -10000 0 -0.32 53 53
GUCY2F 0.026 0.063 -10000 0 -0.51 2 2
GNB5 0.022 0.057 -10000 0 -0.32 4 4
mol:GMP (4 units) -0.1 0.15 -10000 0 -0.27 69 69
mol:11-cis-retinal -0.12 0.24 -10000 0 -0.51 42 42
mol:cGMP 0.047 0.066 -10000 0 -0.27 3 3
GNB1 0.031 0.009 -10000 0 -10000 0 0
Rhodopsin -0.07 0.19 -10000 0 -0.37 42 42
SLC24A1 0.032 0.008 -10000 0 -10000 0 0
CNGA1 -0.26 0.27 -10000 0 -0.51 79 79
Metarhodopsin II 0.021 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.058 0.059 -10000 0 -0.29 1 1
RGS9BP 0.02 0.063 -10000 0 -0.32 5 5
Metarhodopsin II/Transducin -0.006 0.056 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.054 0.048 -10000 0 -0.28 1 1
PDE6A/B -0.15 0.21 -10000 0 -0.37 69 69
mol:Pi -0.057 0.17 -10000 0 -0.32 40 40
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.023 0.1 -10000 0 -10000 0 0
PDE6B 0.032 0.008 -10000 0 -10000 0 0
PDE6A -0.22 0.27 -10000 0 -0.51 69 69
PDE6G 0.032 0.007 -10000 0 -10000 0 0
RHO 0.033 0.004 -10000 0 -10000 0 0
PDE6 -0.16 0.22 -10000 0 -0.48 29 29
GUCA1A 0.033 0.005 -10000 0 -10000 0 0
GC2/GCAP Family 0.069 0.067 -10000 0 -0.29 3 3
GUCA1C 0.025 0.06 -10000 0 -0.38 3 3
GUCA1B 0.028 0.041 -10000 0 -0.32 2 2
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.039 -10000 0 -0.31 2 2
ARNO/beta Arrestin1-2 -0.063 0.13 -10000 0 -0.24 51 51
EGFR 0.02 0.077 -10000 0 -0.51 3 3
EPHA2 0.014 0.074 -10000 0 -0.32 7 7
USP6 0.027 0.014 -10000 0 -10000 0 0
IQSEC1 0.033 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.069 0.17 -10000 0 -0.37 30 30
ARRB2 0.015 0.013 -10000 0 -10000 0 0
mol:GTP 0.007 0.021 0.12 3 -10000 0 3
ARRB1 0.022 0.077 -10000 0 -0.51 3 3
FBXO8 0.032 0.008 -10000 0 -10000 0 0
TSHR 0.029 0.011 -10000 0 -10000 0 0
EGF -0.11 0.22 -10000 0 -0.44 45 45
somatostatin receptor activity 0 0 0.001 5 -0.001 27 32
ARAP2 0 0 0 6 0 21 27
mol:GDP -0.072 0.11 0.16 2 -0.26 26 28
mol:PI-3-4-5-P3 0 0 0 5 -0.001 26 31
ITGA2B 0.032 0.007 -10000 0 -10000 0 0
ARF6 0.03 0.01 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.059 -10000 0 -10000 0 0
ADAP1 0 0 0 3 0 5 8
KIF13B 0.019 0.063 -10000 0 -0.51 2 2
HGF/MET -0.076 0.13 -10000 0 -0.22 68 68
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.067 0.12 0.21 3 -0.24 27 30
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.043 0.16 -10000 0 -0.31 30 30
ADRB2 -0.14 0.25 -10000 0 -0.51 48 48
receptor agonist activity 0 0 0 5 0 23 28
actin filament binding 0 0 0 5 0 29 34
SRC 0.019 0.017 -10000 0 -10000 0 0
ITGB3 0.032 0.007 -10000 0 -10000 0 0
GNAQ 0 0 0.001 6 -0.001 14 20
EFA6/PI-4-5-P2 0 0.001 0.001 7 -0.001 14 21
ARF6/GDP -0.045 0.12 0.2 1 -0.32 16 17
ARF6/GDP/GULP/ACAP1 -0.071 0.14 -10000 0 -0.31 24 24
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.023 -10000 0 -10000 0 0
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 5 0 19 24
LHCGR/beta Arrestin2 0.015 0.036 -10000 0 -10000 0 0
EFNA1 0.033 0.006 -10000 0 -10000 0 0
HGF 0.032 0.008 -10000 0 -10000 0 0
CYTH3 0 0 0.001 6 -0.001 24 30
CYTH2 -0.001 0.002 -10000 0 -0.004 29 29
NCK1 0.033 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0 5 0 18 23
endosomal lumen acidification 0 0 0 11 0 14 25
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.15 -10000 0 -0.5 13 13
GNAQ/ARNO -0.001 0.003 0.008 6 -0.006 14 20
mol:Phosphatidic acid 0 0 0 5 0 19 24
PIP3-E 0 0 0 2 0 31 33
MET -0.13 0.17 -10000 0 -0.32 68 68
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.023 0.057 -10000 0 -0.32 4 4
GIT1 0.032 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 6 -0.001 23 29
GNA11 0 0.13 -10000 0 -0.51 9 9
LHCGR 0.031 0.029 -10000 0 -0.32 1 1
AGTR1 -0.085 0.22 -10000 0 -0.5 33 33
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.036 -10000 0 -10000 0 0
IPCEF1/ARNO -0.041 0.11 -10000 0 -0.24 31 31
alphaIIb/beta3 Integrin 0.048 0.01 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.033 0.005 -9999 0 -10000 0 0
EGFR 0.02 0.077 -9999 0 -0.51 3 3
EGF/EGFR -0.087 0.17 -9999 0 -0.32 38 38
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.014 0.15 -9999 0 -0.27 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.061 0.16 -9999 0 -0.32 40 40
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.22 -9999 0 -0.44 45 45
EGF/EGFR dimer/SHC -0.042 0.15 -9999 0 -0.31 29 29
mol:GDP -0.018 0.14 -9999 0 -0.27 28 28
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.004 0.12 -9999 0 -0.51 8 8
GRB2/SOS1 0.048 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.028 0.13 -9999 0 -10000 0 0
SHC1 0.033 0.006 -9999 0 -10000 0 0
HRAS/GDP -0.016 0.14 -9999 0 -10000 0 0
FRAP1 -0.069 0.1 -9999 0 -0.26 28 28
EGF/EGFR dimer -0.069 0.17 -9999 0 -0.37 30 30
SOS1 0.034 0 -9999 0 -10000 0 0
GRB2 0.032 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.044 0.15 -9999 0 -0.25 46 46
HIF-2-alpha transcription factor network

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
MMP14 -0.069 0.21 -10000 0 -0.74 12 12
oxygen homeostasis -0.013 0.009 -10000 0 -10000 0 0
TCEB2 0.033 0.005 -10000 0 -10000 0 0
TCEB1 0.029 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.13 0.13 -10000 0 -0.42 10 10
EPO -0.26 0.17 -10000 0 -0.56 13 13
FIH (dimer) 0.003 0.025 -10000 0 -10000 0 0
APEX1 -0.001 0.029 -10000 0 -10000 0 0
SERPINE1 -0.32 0.23 -10000 0 -0.65 32 32
FLT1 -0.03 0.13 -10000 0 -0.71 4 4
ADORA2A -0.29 0.19 -10000 0 -0.6 20 20
germ cell development -0.3 0.19 -10000 0 -0.6 20 20
SLC11A2 -0.32 0.2 -10000 0 -0.62 25 25
BHLHE40 -0.3 0.2 -10000 0 -0.56 34 34
HIF1AN 0.003 0.025 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.2 0.15 -10000 0 -0.43 25 25
ETS1 0.038 0.035 -10000 0 -0.31 1 1
CITED2 -0.017 0.14 -10000 0 -0.94 3 3
KDR -0.021 0.16 -10000 0 -0.91 4 4
PGK1 -0.31 0.2 -10000 0 -0.61 25 25
SIRT1 0.033 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.34 0.24 -10000 0 -0.65 33 33
EPAS1 -0.16 0.14 -10000 0 -0.35 42 42
SP1 0.035 0.019 -10000 0 -10000 0 0
ABCG2 -0.57 0.25 -10000 0 -0.71 93 93
EFNA1 -0.3 0.2 -10000 0 -0.62 20 20
FXN -0.29 0.19 -10000 0 -0.6 20 20
POU5F1 -0.3 0.2 -10000 0 -0.62 20 20
neuron apoptosis 0.33 0.23 0.64 32 -10000 0 32
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 -0.14 0.23 -10000 0 -0.52 40 40
EGLN2 0.006 0.026 -10000 0 -10000 0 0
EGLN1 0.004 0.026 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.056 0.027 -10000 0 -10000 0 0
VHL 0.033 0.005 -10000 0 -10000 0 0
ARNT 0 0.03 -10000 0 -10000 0 0
SLC2A1 -0.31 0.21 -10000 0 -0.62 27 27
TWIST1 -0.3 0.21 -10000 0 -0.63 28 28
ELK1 0.038 0.029 -10000 0 -0.31 1 1
HIF2A/ARNT/Cbp/p300 -0.2 0.15 -10000 0 -0.44 22 22
VEGFA -0.31 0.21 -10000 0 -0.62 25 25
CREBBP 0.033 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.043 0.11 -9999 0 -0.33 11 11
FZD6 0.019 0.057 -9999 0 -0.32 4 4
WNT6 0.034 0.003 -9999 0 -10000 0 0
WNT4 -0.001 0.12 -9999 0 -0.49 9 9
FZD3 -0.05 0.14 -9999 0 -0.32 32 32
WNT5A -0.007 0.11 -9999 0 -0.32 17 17
WNT11 -0.036 0.14 -9999 0 -0.32 29 29
TRAIL signaling pathway

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
TNFSF10 -0.029 0.17 -9999 0 -0.51 17 17
positive regulation of NF-kappaB transcription factor activity -0.013 0.13 -9999 0 -0.34 20 20
MAP2K4 -0.014 0.099 -9999 0 -0.34 8 8
IKBKB 0.03 0.011 -9999 0 -10000 0 0
TNFRSF10B -0.033 0.13 -9999 0 -0.32 25 25
TNFRSF10A -0.014 0.11 -9999 0 -0.32 17 17
SMPD1 -0.11 0.2 -9999 0 -0.4 40 40
IKBKG 0.033 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.05 -9999 0 -0.32 3 3
TRAIL/TRAILR2 -0.049 0.16 -9999 0 -0.31 36 36
TRAIL/TRAILR3 -0.038 0.15 -9999 0 -0.3 33 33
TRAIL/TRAILR1 -0.036 0.15 -9999 0 -0.32 30 30
TRAIL/TRAILR4 -0.013 0.13 -9999 0 -0.34 20 20
TRAIL/TRAILR1/DAP3/GTP -0.012 0.13 -9999 0 -0.32 17 17
IKK complex -0.008 0.09 -9999 0 -0.53 2 2
RIPK1 0.034 0.003 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.024 0.005 -9999 0 -10000 0 0
MAPK3 -0.03 0.14 -9999 0 -0.38 18 18
MAP3K1 -0.013 0.11 -9999 0 -0.35 9 9
TRAILR4 (trimer) 0.019 0.05 -9999 0 -0.32 3 3
TRADD 0.034 0 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.014 0.11 -9999 0 -0.32 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.013 0.11 -9999 0 -0.34 9 9
CFLAR 0.034 0 -9999 0 -10000 0 0
MAPK1 -0.021 0.12 -9999 0 -0.37 15 15
TRAIL/TRAILR1/FADD/TRADD/RIP 0.012 0.14 -9999 0 -0.3 17 17
mol:ceramide -0.11 0.2 -9999 0 -0.4 40 40
FADD 0.033 0.005 -9999 0 -10000 0 0
MAPK8 -0.016 0.096 -9999 0 -0.37 4 4
TRAF2 0.033 0.004 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.11 -9999 0 -0.32 17 17
CHUK 0.032 0.008 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.015 0.14 -9999 0 -0.34 17 17
DAP3 0.033 0.006 -9999 0 -10000 0 0
CASP10 -0.049 0.13 -9999 0 -0.43 12 12
JNK cascade -0.013 0.13 -9999 0 -0.34 20 20
TRAIL (trimer) -0.029 0.17 -9999 0 -0.51 17 17
TNFRSF10C -0.014 0.11 -9999 0 -0.32 17 17
TRAIL/TRAILR1/DAP3/GTP/FADD 0 0.13 -9999 0 -0.3 17 17
TRAIL/TRAILR2/FADD -0.027 0.15 -9999 0 -0.36 17 17
cell death -0.11 0.2 -9999 0 -0.4 40 40
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.017 0.11 -9999 0 -0.32 12 12
TRAILR2 (trimer) -0.033 0.13 -9999 0 -0.32 25 25
CASP8 0.03 0.034 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.001 0.14 -9999 0 -0.31 17 17
Endothelins

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
AKT1 -0.022 0.15 -10000 0 -0.36 10 10
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.016 0.18 -10000 0 -0.72 3 3
EDN1 0.036 0.15 -10000 0 -0.51 8 8
EDN3 -0.18 0.25 -10000 0 -0.51 53 53
EDN2 -0.38 0.23 -10000 0 -0.51 113 113
HRAS/GDP 0.01 0.18 0.31 2 -0.52 7 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.005 0.14 -10000 0 -0.39 8 8
ADCY4 -0.025 0.11 -10000 0 -0.38 3 3
ADCY5 -0.026 0.11 -10000 0 -0.38 3 3
ADCY6 -0.025 0.11 -10000 0 -0.34 2 2
ADCY7 -0.026 0.11 -10000 0 -0.38 3 3
ADCY1 -0.023 0.11 -10000 0 -0.38 3 3
ADCY2 -0.026 0.11 -10000 0 -0.38 3 3
ADCY3 -0.035 0.12 -10000 0 -0.36 4 4
ADCY8 -0.028 0.11 -10000 0 -0.38 3 3
ADCY9 -0.025 0.11 -10000 0 -0.38 3 3
arachidonic acid secretion -0.056 0.21 0.29 1 -0.54 16 17
ETB receptor/Endothelin-1/Gq/GTP -0.039 0.16 -10000 0 -0.43 14 14
GNAO1 0.034 0 -10000 0 -10000 0 0
HRAS 0.033 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.09 0.18 -10000 0 -0.33 9 9
ETA receptor/Endothelin-1/Gs/GTP 0.06 0.17 -10000 0 -0.35 5 5
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.022 0.15 -10000 0 -0.48 4 4
EDNRB -0.045 0.17 -10000 0 -0.52 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.016 0.13 -10000 0 -0.42 4 4
CYSLTR1 -0.023 0.16 -10000 0 -0.48 4 4
SLC9A1 0.002 0.093 -10000 0 -0.26 5 5
mol:GDP -0.005 0.18 0.31 2 -0.49 10 12
SLC9A3 -0.42 0.32 -10000 0 -0.74 50 50
RAF1 -0.026 0.19 0.3 2 -0.55 10 12
JUN 0.014 0.17 -10000 0 -0.67 2 2
JAK2 -0.025 0.15 -10000 0 -0.38 9 9
mol:IP3 -0.017 0.16 0.24 4 -0.46 10 14
ETA receptor/Endothelin-1 0.092 0.22 -10000 0 -0.42 10 10
PLCB1 -0.042 0.14 -10000 0 -0.32 28 28
PLCB2 0.031 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.15 0.21 -10000 0 -0.4 59 59
FOS -0.063 0.3 -10000 0 -0.9 14 14
Gai/GDP 0.017 0.13 -10000 0 -0.85 2 2
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:Ca ++ -0.03 0.19 -10000 0 -0.54 10 10
BCAR1 0.033 0.004 -10000 0 -10000 0 0
PRKCB1 -0.014 0.16 0.23 4 -0.44 10 14
GNAQ 0.001 0.004 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNAL 0.026 0.014 -10000 0 -10000 0 0
Gs family/GDP -0.002 0.16 0.27 1 -0.47 8 9
ETA receptor/Endothelin-1/Gq/GTP -0.004 0.14 -10000 0 -0.36 11 11
MAPK14 -0.038 0.14 -10000 0 -0.41 11 11
TRPC6 0.014 0.18 -10000 0 -0.76 3 3
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNAI1 -0.03 0.17 -10000 0 -0.51 17 17
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.037 0.14 -10000 0 -0.41 13 13
ETB receptor/Endothelin-2 -0.25 0.2 -10000 0 -0.42 79 79
ETB receptor/Endothelin-3 -0.15 0.22 -10000 0 -0.45 49 49
ETB receptor/Endothelin-1 -0.024 0.17 -10000 0 -0.42 20 20
MAPK3 -0.045 0.25 -10000 0 -0.72 14 14
MAPK1 -0.053 0.26 -10000 0 -0.73 15 15
Rac1/GDP -0.005 0.17 0.29 1 -0.47 9 10
cAMP biosynthetic process 0.002 0.1 -10000 0 -0.31 2 2
MAPK8 0.014 0.18 -10000 0 -0.59 7 7
SRC 0.019 0.017 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.017 0.13 -10000 0 -0.35 11 11
p130Cas/CRK/Src/PYK2 0.018 0.19 0.33 5 -0.53 7 12
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.005 0.17 0.29 1 -0.47 9 10
COL1A2 -0.014 0.22 -10000 0 -0.64 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.32 0.2 -10000 0 -0.41 117 117
mol:DAG -0.017 0.16 0.24 4 -0.46 10 14
MAP2K2 -0.034 0.21 0.32 1 -0.56 13 14
MAP2K1 -0.037 0.22 0.32 1 -0.58 14 15
EDNRA -0.03 0.18 -10000 0 -0.32 40 40
positive regulation of muscle contraction 0.003 0.14 0.27 8 -0.36 4 12
Gq family/GDP -0.015 0.17 -10000 0 -0.49 10 10
HRAS/GTP -0.018 0.18 0.28 1 -0.48 10 11
PRKCH -0.015 0.16 0.23 3 -0.47 9 12
RAC1 0.03 0.01 -10000 0 -10000 0 0
PRKCA -0.009 0.17 0.34 3 -0.47 9 12
PRKCB -0.016 0.16 0.23 4 -0.44 10 14
PRKCE -0.014 0.16 -10000 0 -0.48 8 8
PRKCD -0.013 0.15 0.23 1 -0.46 8 9
PRKCG -0.016 0.16 0.28 1 -0.47 9 10
regulation of vascular smooth muscle contraction -0.078 0.34 -10000 0 -1.1 14 14
PRKCQ -0.017 0.15 -10000 0 -0.46 8 8
PLA2G4A -0.062 0.23 0.3 1 -0.59 16 17
GNA14 0.012 0.11 -10000 0 -0.52 6 6
GNA15 0.024 0.057 -10000 0 -0.31 4 4
GNA12 0.03 0.01 -10000 0 -10000 0 0
GNA11 0.001 0.13 -10000 0 -0.51 9 9
Rac1/GTP 0.09 0.18 -10000 0 -0.33 9 9
MMP1 -0.23 0.097 0.41 1 -0.28 74 75
IL6-mediated signaling events

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
BCL2L1 -0.07 0.14 -10000 0 -10000 0 0
CRP -0.13 0.14 -10000 0 -0.65 1 1
cell cycle arrest -0.14 0.15 -10000 0 -0.76 1 1
TIMP1 -0.16 0.15 -10000 0 -0.94 1 1
IL6ST 0.031 0.01 -10000 0 -10000 0 0
Rac1/GDP -0.18 0.16 -10000 0 -0.39 33 33
AP1 0.009 0.13 -10000 0 -0.55 3 3
GAB2 0.037 0.01 -10000 0 -10000 0 0
TNFSF11 -0.11 0.17 -10000 0 -0.74 1 1
HSP90B1 0.011 0.044 -10000 0 -10000 0 0
GAB1 0.032 0.045 -10000 0 -0.51 1 1
MAPK14 -0.18 0.17 -10000 0 -0.49 16 16
AKT1 0.041 0.048 -10000 0 -10000 0 0
FOXO1 0.068 0.095 -10000 0 -10000 0 0
MAP2K6 -0.19 0.17 -10000 0 -0.39 41 41
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.18 0.15 -10000 0 -0.44 18 18
MITF -0.18 0.15 -10000 0 -0.34 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.005 -10000 0 -10000 0 0
A2M -0.18 0.52 -10000 0 -1.4 22 22
CEBPB 0.019 0.035 -10000 0 -0.32 1 1
GRB2/SOS1/GAB family/SHP2 -0.008 0.098 0.29 1 -0.49 2 3
STAT3 -0.15 0.15 -10000 0 -0.81 1 1
STAT1 0.005 0.022 -10000 0 -10000 0 0
CEBPD -0.12 0.14 -10000 0 -0.65 1 1
PIK3CA 0.035 0.004 -10000 0 -10000 0 0
PI3K 0.051 0.01 -10000 0 -10000 0 0
JUN 0.021 0.063 -10000 0 -0.32 5 5
PIAS3/MITF -0.17 0.15 -10000 0 -0.35 28 28
MAPK11 -0.17 0.17 -10000 0 -0.5 16 16
STAT3 (dimer)/FOXO1 -0.092 0.16 0.4 1 -0.6 1 2
GRB2/SOS1/GAB family -0.098 0.18 -10000 0 -0.44 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.16 -10000 0 -0.37 37 37
GRB2 0.035 0.009 -10000 0 -10000 0 0
JAK2 0.026 0.05 -10000 0 -0.32 3 3
LBP -0.02 0.14 -10000 0 -0.51 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.03 0.012 -10000 0 -10000 0 0
MYC -0.14 0.17 -10000 0 -0.74 1 1
FGG -0.13 0.13 -10000 0 -0.64 1 1
macrophage differentiation -0.14 0.15 -10000 0 -0.76 1 1
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.18 -10000 0 -0.38 67 67
JUNB -0.13 0.14 -10000 0 -0.72 1 1
FOS 0.003 0.11 -10000 0 -0.46 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.19 0.16 -10000 0 -0.34 56 56
STAT1/PIAS1 -0.14 0.13 -10000 0 -0.35 14 14
GRB2/SOS1/GAB family/SHP2/PI3K 0.047 0.044 -10000 0 -10000 0 0
STAT3 (dimer) -0.15 0.15 -10000 0 -0.79 1 1
PRKCD -0.18 0.17 0.37 1 -0.47 13 14
IL6R -0.28 0.27 -10000 0 -0.51 85 85
SOCS3 -0.16 0.17 -10000 0 -0.56 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 0.048 0.06 -10000 0 -0.29 1 1
Rac1/GTP -0.19 0.16 -10000 0 -0.41 28 28
HCK -0.002 0.1 -10000 0 -0.51 6 6
MAPKKK cascade 0.028 0.1 -10000 0 -0.56 2 2
bone resorption -0.11 0.17 -10000 0 -0.7 1 1
IRF1 -0.14 0.15 -10000 0 -0.86 2 2
mol:GDP -0.2 0.17 -10000 0 -0.37 48 48
SOS1 0.037 0.009 -10000 0 -10000 0 0
VAV1 -0.2 0.17 -10000 0 -0.38 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.26 0.22 -10000 0 -0.49 48 48
PTPN11 0.008 0.076 -10000 0 -0.88 1 1
IL6/IL6RA -0.3 0.2 -10000 0 -0.39 109 109
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.058 -10000 0 -0.29 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.073 -10000 0 -0.33 4 4
IL6 -0.16 0.17 -10000 0 -0.32 79 79
PIAS3 0.031 0.029 -10000 0 -0.32 1 1
PTPRE 0.033 0.03 -10000 0 -0.3 1 1
PIAS1 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.15 -10000 0 -0.31 64 64
LMO4 0.015 0.077 -10000 0 -0.35 6 6
STAT3 (dimer)/PIAS3 -0.15 0.15 -10000 0 -0.78 1 1
MCL1 0.043 0.06 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.025 0.12 -9999 0 -10000 0 0
SMAD6-7/SMURF1 0.043 0.038 -9999 0 -10000 0 0
NOG 0.032 0.007 -9999 0 -10000 0 0
SMAD9 -0.078 0.21 -9999 0 -0.52 24 24
SMAD4 0.023 0.016 -9999 0 -10000 0 0
SMAD5 -0.1 0.16 -9999 0 -0.49 12 12
BMP7/USAG1 -0.15 0.19 -9999 0 -0.36 57 57
SMAD5/SKI -0.097 0.16 -9999 0 -0.5 10 10
SMAD1 -0.019 0.1 -9999 0 -0.49 4 4
BMP2 -0.044 0.18 -9999 0 -0.51 19 19
SMAD1/SMAD1/SMAD4 0.009 0.089 -9999 0 -0.43 3 3
BMPR1A 0.032 0.009 -9999 0 -10000 0 0
BMPR1B 0.031 0.029 -9999 0 -0.32 1 1
BMPR1A-1B/BAMBI 0.03 0.085 -9999 0 -10000 0 0
AHSG 0.033 0.004 -9999 0 -10000 0 0
CER1 0.031 0.029 -9999 0 -0.32 1 1
BMP2-4/CER1 -0.066 0.17 -9999 0 -0.38 24 24
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.024 0.12 -9999 0 -0.38 7 7
BMP2-4 (homodimer) -0.087 0.18 -9999 0 -0.32 49 49
RGMB 0.023 0.057 -9999 0 -0.32 4 4
BMP6/BMPR2/BMPR1A-1B -0.1 0.18 -9999 0 -0.29 71 71
RGMA 0.024 0.063 -9999 0 -0.51 2 2
SMURF1 0.032 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.033 0.11 -9999 0 -0.33 8 8
BMP2-4/USAG1 -0.18 0.22 -9999 0 -0.41 63 63
SMAD6/SMURF1/SMAD5 -0.097 0.15 -9999 0 -0.48 10 10
SOSTDC1 -0.18 0.26 -9999 0 -0.51 58 58
BMP7/BMPR2/BMPR1A-1B -0.022 0.092 -9999 0 -10000 0 0
SKI 0.031 0.009 -9999 0 -10000 0 0
BMP6 (homodimer) -0.23 0.27 -9999 0 -0.51 72 72
HFE2 0.033 0.005 -9999 0 -10000 0 0
ZFYVE16 0.033 0.005 -9999 0 -10000 0 0
MAP3K7 0.033 0.005 -9999 0 -10000 0 0
BMP2-4/CHRD -0.062 0.16 -9999 0 -0.38 23 23
SMAD5/SMAD5/SMAD4 -0.09 0.15 -9999 0 -0.49 10 10
MAPK1 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.021 0.11 -9999 0 -0.31 4 4
BMP7 (homodimer) -0.074 0.14 -9999 0 -0.32 39 39
NUP214 0.033 0.004 -9999 0 -10000 0 0
BMP6/FETUA -0.15 0.21 -9999 0 -0.37 70 70
SMAD1/SKI -0.012 0.1 -9999 0 -0.51 3 3
SMAD6 0.027 0.041 -9999 0 -0.32 2 2
CTDSP2 0.026 0.063 -9999 0 -0.51 2 2
BMP2-4/FETUA -0.062 0.16 -9999 0 -0.38 23 23
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.002 0.095 -9999 0 -0.32 12 12
BMPR2 (homodimer) 0.034 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.066 0.015 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.044 0.026 -9999 0 -0.22 1 1
CHRDL1 0.028 0.053 -9999 0 -0.41 2 2
ENDOFIN/SMAD1 -0.01 0.1 -9999 0 -0.51 3 3
SMAD6-7/SMURF1/SMAD1 0.016 0.1 -9999 0 -0.48 3 3
SMAD6/SMURF1 0.032 0.008 -9999 0 -10000 0 0
BAMBI -0.014 0.12 -9999 0 -0.32 20 20
SMURF2 0.006 0.092 -9999 0 -0.32 11 11
BMP2-4/CHRDL1 -0.068 0.17 -9999 0 -0.38 25 25
BMP2-4/GREM1 -0.08 0.18 -9999 0 -0.41 25 25
SMAD7 0.024 0.016 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.078 0.21 -9999 0 -0.49 25 25
SMAD1/SMAD6 -0.012 0.1 -9999 0 -0.51 3 3
TAK1/SMAD6 0.047 0.013 -9999 0 -10000 0 0
BMP7 -0.074 0.15 -9999 0 -0.32 39 39
BMP6 -0.23 0.27 -9999 0 -0.51 72 72
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.036 0.13 -9999 0 -0.38 11 11
PPM1A 0.03 0.011 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.02 0.11 -9999 0 -0.55 3 3
SMAD7/SMURF1 0.033 0.024 -9999 0 -10000 0 0
CTDSPL 0.03 0.045 -9999 0 -0.51 1 1
PPP1CA 0.033 0.005 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.003 -9999 0 -10000 0 0
PPP1R15A 0.033 0.004 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.025 0.11 -9999 0 -0.35 6 6
CHRD 0.033 0.004 -9999 0 -10000 0 0
BMPR2 0.034 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.12 -9999 0 -0.35 8 8
BMP4 -0.08 0.17 -9999 0 -0.33 45 45
FST 0.033 0.004 -9999 0 -10000 0 0
BMP2-4/NOG -0.063 0.16 -9999 0 -0.37 24 24
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.024 0.12 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.046 0.058 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.045 0.058 -10000 0 -10000 0 0
LAMA1 0.026 0.015 -10000 0 -10000 0 0
PRNP 0.026 0.014 -10000 0 -10000 0 0
GPC1/SLIT2 -0.17 0.2 -10000 0 -0.36 77 77
SMAD2 0.011 0.044 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.025 0.046 -10000 0 -0.18 5 5
GPC1/Laminin alpha1 0.025 0.058 -10000 0 -0.22 7 7
TDGF1 -0.19 0.17 -10000 0 -0.32 94 94
CRIPTO/GPC1 -0.13 0.14 -10000 0 -0.23 97 97
APP/GPC1 0.033 0.058 -10000 0 -0.22 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.11 0.1 -10000 0 -0.33 7 7
FLT1 0 0.087 -10000 0 -0.32 10 10
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.055 -10000 0 -10000 0 0
SERPINC1 0.03 0.029 -10000 0 -0.32 1 1
FYN -0.12 0.11 -10000 0 -0.33 7 7
FGR -0.12 0.1 -10000 0 -0.33 7 7
positive regulation of MAPKKK cascade -0.022 0.12 0.29 2 -0.35 6 8
SLIT2 -0.23 0.27 -10000 0 -0.51 71 71
GPC1/NRG 0.029 0.057 -10000 0 -0.21 7 7
NRG1 0.028 0.013 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.011 0.089 -10000 0 -0.34 2 2
LYN -0.098 0.11 -10000 0 -0.33 7 7
mol:Spermine -0.001 0.048 -10000 0 -0.22 7 7
cell growth 0.045 0.058 -10000 0 -10000 0 0
BMP signaling pathway -0.016 0.074 0.32 7 -10000 0 7
SRC -0.053 0.097 -10000 0 -0.32 5 5
TGFBR1 0.033 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.064 0.19 -10000 0 -0.43 30 30
GPC1 0.016 0.074 -10000 0 -0.32 7 7
TGFBR1 (dimer) 0.033 0.005 -10000 0 -10000 0 0
VEGFA -0.003 0.11 -10000 0 -0.32 15 15
BLK -0.15 0.15 -10000 0 -0.4 27 27
HCK -0.068 0.12 -10000 0 -0.37 11 11
FGF2 0.031 0.029 -10000 0 -0.32 1 1
FGFR1 0.03 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer 0 0.086 -10000 0 -0.32 10 10
TGFBR2 0.033 0.004 -10000 0 -10000 0 0
cell death 0.033 0.057 -10000 0 -0.22 7 7
ATIII/GPC1 0.033 0.061 -10000 0 -0.22 8 8
PLA2G2A/GPC1 -0.042 0.16 -10000 0 -0.31 34 34
LCK -0.12 0.1 -10000 0 -0.33 7 7
neuron differentiation 0.029 0.057 -10000 0 -0.21 7 7
PrPc/Cu2+ 0.019 0.011 -10000 0 -10000 0 0
APP 0.032 0.009 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.033 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.045 0.025 -10000 0 -0.22 1 1
VLDLR -0.083 0.22 -10000 0 -0.5 32 32
CRKL 0.032 0.008 -10000 0 -10000 0 0
LRPAP1 0.032 0.008 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
ITGA3 0.03 0.029 -10000 0 -0.32 1 1
RELN/VLDLR/Fyn -0.017 0.15 -10000 0 -0.32 28 28
MAPK8IP1/MKK7/MAP3K11/JNK1 0.091 0.034 -10000 0 -10000 0 0
AKT1 -0.023 0.094 -10000 0 -10000 0 0
MAP2K7 0.034 0.003 -10000 0 -10000 0 0
RAPGEF1 0.033 0.004 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.12 0.083 -10000 0 -0.19 2 2
LRPAP1/LRP8 -0.18 0.092 -10000 0 -0.22 127 127
RELN/LRP8/DAB1/Fyn -0.11 0.082 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin -0.16 0.13 -10000 0 -0.38 26 26
long-term memory -0.13 0.1 -10000 0 -0.28 20 20
DAB1/LIS1 -0.16 0.13 -10000 0 -0.39 26 26
DAB1/CRLK/C3G -0.16 0.13 -10000 0 -0.38 24 24
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.14 -10000 0 -0.39 26 26
ARHGEF2 0.03 0.029 -10000 0 -0.32 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.034 0.003 -10000 0 -10000 0 0
CDK5R1 0.033 0.006 -10000 0 -10000 0 0
RELN 0.032 0.008 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.14 0.09 -10000 0 -0.22 2 2
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.091 -10000 0 -10000 0 0
MAPK8 0.033 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.012 0.14 -10000 0 -0.28 28 28
ITGB1 0.031 0.029 -10000 0 -0.32 1 1
MAP1B -0.15 0.12 -10000 0 -0.36 31 31
RELN/LRP8 -0.14 0.091 -10000 0 -0.22 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn -0.13 0.11 -10000 0 -0.3 20 20
PI3K 0.049 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.044 0.033 -10000 0 -0.22 2 2
RAP1A -0.15 0.12 -10000 0 -0.36 24 24
PAFAH1B1 0.027 0.014 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.029 -10000 0 -0.32 1 1
CRLK/C3G 0.047 0.013 -10000 0 -10000 0 0
GRIN2B -0.026 0.13 -10000 0 -0.32 25 25
NCK2 0.034 0 -10000 0 -10000 0 0
neuron differentiation -0.023 0.054 -10000 0 -0.35 2 2
neuron adhesion -0.14 0.12 -10000 0 -0.35 25 25
LRP8 -0.27 0.12 -10000 0 -0.32 127 127
GSK3B -0.023 0.093 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/Fyn 0 0.14 -10000 0 -0.27 28 28
MAP3K11 0.033 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.11 -10000 0 -0.24 28 28
CDK5 0.03 0.029 -10000 0 -0.32 1 1
MAPT 0.017 0.11 0.79 3 -10000 0 3
neuron migration -0.12 0.12 -10000 0 -0.34 26 26
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.023 0.055 -10000 0 -0.36 2 2
RELN/VLDLR -0.18 0.14 -10000 0 -0.39 34 34
TCGA08_p53

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
CDKN2A -0.062 0.11 0.22 1 -0.22 48 49
TP53 -0.028 0.066 -10000 0 -0.25 10 10
Senescence -0.028 0.067 -10000 0 -0.25 10 10
Apoptosis -0.028 0.067 -10000 0 -0.25 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.057 0.29 1 -10000 0 1
MDM4 0.033 0.006 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 0.008 0.086 -10000 0 -0.31 1 1
TBX21 -0.38 0.66 -10000 0 -1.3 46 46
B2M 0.01 0.11 -10000 0 -0.51 6 6
TYK2 0.015 0.039 -10000 0 -10000 0 0
IL12RB1 0.015 0.039 -10000 0 -10000 0 0
GADD45B -0.14 0.36 -10000 0 -0.92 19 19
IL12RB2 0.013 0.05 -10000 0 -0.36 1 1
GADD45G -0.13 0.35 -10000 0 -0.91 18 18
natural killer cell activation -0.006 0.023 -10000 0 -10000 0 0
RELB 0.033 0.004 -10000 0 -10000 0 0
RELA 0.033 0.005 -10000 0 -10000 0 0
IL18 -0.017 0.16 -10000 0 -0.5 14 14
IL2RA 0.021 0.063 -10000 0 -0.32 5 5
IFNG -0.045 0.15 -10000 0 -0.32 33 33
STAT3 (dimer) -0.11 0.32 -10000 0 -0.73 23 23
HLA-DRB5 0.01 0.11 -10000 0 -0.51 6 6
FASLG -0.24 0.55 -10000 0 -1.4 24 24
NF kappa B2 p52/RelB -0.14 0.37 -10000 0 -0.8 27 27
CD4 0.031 0.013 -10000 0 -10000 0 0
SOCS1 0.034 0.003 -10000 0 -10000 0 0
EntrezGene:6955 0.001 0.006 -10000 0 -10000 0 0
CD3D 0.014 0.099 -10000 0 -0.51 5 5
CD3E 0.032 0.013 -10000 0 -10000 0 0
CD3G 0.012 0.1 -10000 0 -0.48 6 6
IL12Rbeta2/JAK2 0.019 0.07 -10000 0 -0.28 1 1
CCL3 -0.15 0.36 -10000 0 -0.88 20 20
CCL4 -0.15 0.38 -10000 0 -0.92 20 20
HLA-A 0.02 0.088 -10000 0 -0.51 4 4
IL18/IL18R -0.032 0.21 -10000 0 -0.36 38 38
NOS2 -0.16 0.37 -10000 0 -0.78 30 30
IL12/IL12R/TYK2/JAK2/SPHK2 0.005 0.089 -10000 0 -0.31 1 1
IL1R1 -0.15 0.38 -10000 0 -0.93 20 20
IL4 0.039 0.025 -10000 0 -10000 0 0
JAK2 0.008 0.06 -10000 0 -0.31 3 3
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.15 -10000 0 -0.63 6 6
RAB7A -0.11 0.31 -10000 0 -0.77 18 18
lysosomal transport -0.11 0.3 -10000 0 -0.73 18 18
FOS -0.19 0.48 -10000 0 -1.2 24 24
STAT4 (dimer) -0.13 0.35 -10000 0 -0.82 22 22
STAT5A (dimer) -0.15 0.36 -10000 0 -0.81 26 26
GZMA -0.15 0.36 -10000 0 -0.8 27 27
GZMB -0.15 0.36 -10000 0 -0.88 21 21
HLX 0.033 0.006 -10000 0 -10000 0 0
LCK -0.16 0.38 -10000 0 -0.86 27 27
TCR/CD3/MHC II/CD4 -0.015 0.19 -10000 0 -0.72 8 8
IL2/IL2R 0.068 0.059 -10000 0 -0.29 1 1
MAPK14 -0.15 0.39 -10000 0 -0.96 20 20
CCR5 -0.2 0.49 -10000 0 -1.2 23 23
IL1B -0.093 0.16 -10000 0 -0.32 47 47
STAT6 -0.017 0.1 -10000 0 -10000 0 0
STAT4 0.03 0.045 -10000 0 -0.51 1 1
STAT3 0.033 0.005 -10000 0 -10000 0 0
STAT1 0.001 0.1 -10000 0 -0.32 14 14
NFKB1 0.033 0.005 -10000 0 -10000 0 0
NFKB2 0.029 0.03 -10000 0 -0.32 1 1
IL12B 0.014 0.048 -10000 0 -0.3 1 1
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.035 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.008 0.086 0.31 1 -10000 0 1
IL2RB 0.032 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.32 -10000 0 -0.75 22 22
IL2RG 0.03 0.045 -10000 0 -0.51 1 1
IL12 0.016 0.074 -10000 0 -0.24 2 2
STAT5A 0.033 0.005 -10000 0 -10000 0 0
CD247 0.007 0.12 -10000 0 -0.51 7 7
IL2 0.033 0.005 -10000 0 -10000 0 0
SPHK2 0.03 0.045 -10000 0 -0.51 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.071 -10000 0 -0.32 5 5
IL12/IL12R/TYK2/JAK2 -0.17 0.41 -10000 0 -0.91 27 27
MAP2K3 -0.17 0.42 -10000 0 -0.99 22 22
RIPK2 -0.014 0.11 -10000 0 -0.32 18 18
MAP2K6 -0.16 0.39 -10000 0 -0.95 21 21
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.017 0.089 -10000 0 -0.51 4 4
IL18RAP -0.073 0.22 -10000 0 -0.52 29 29
IL12Rbeta1/TYK2 0.025 0.054 -10000 0 -10000 0 0
EOMES 0.023 0.08 -10000 0 -0.64 1 1
STAT1 (dimer) -0.12 0.3 -10000 0 -0.72 21 21
T cell proliferation -0.098 0.27 -10000 0 -0.63 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.03 0.047 -10000 0 -0.52 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.31 -10000 0 -0.7 21 21
ATF2 -0.14 0.35 -10000 0 -0.87 20 20
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.22 0.45 -10000 0 -1.1 15 15
STAT6 (cleaved dimer) -0.34 0.45 -10000 0 -1.1 26 26
IGHG1 -0.082 0.17 -10000 0 -10000 0 0
IGHG3 -0.29 0.42 -10000 0 -1.1 22 22
AKT1 -0.14 0.25 -10000 0 -0.85 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.21 -10000 0 -0.77 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.24 -10000 0 -0.95 3 3
THY1 -0.31 0.44 -10000 0 -1.2 18 18
MYB 0.03 0.045 -10000 0 -0.51 1 1
HMGA1 0.034 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.23 0.32 -10000 0 -0.85 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.24 -10000 0 -0.92 3 3
SP1 0.023 0.034 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.049 0.025 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.46 -10000 0 -1.1 25 25
SOCS1 -0.22 0.31 -10000 0 -0.74 18 18
SOCS3 -0.2 0.27 -10000 0 -0.76 9 9
FCER2 -0.26 0.39 -10000 0 -1.1 12 12
PARP14 0.03 0.041 -10000 0 -0.32 2 2
CCL17 -0.3 0.44 -10000 0 -1.1 18 18
GRB2 0.032 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.18 -10000 0 -0.57 3 3
T cell proliferation -0.29 0.44 -10000 0 -1.1 20 20
IL4R/JAK1 -0.3 0.44 -10000 0 -1.1 19 19
EGR2 -0.32 0.48 -10000 0 -1.3 18 18
JAK2 -0.014 0.069 -10000 0 -0.35 3 3
JAK3 0.018 0.035 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
JAK1 0.009 0.029 -10000 0 -10000 0 0
COL1A2 -0.096 0.17 -10000 0 -10000 0 0
CCL26 -0.31 0.44 -10000 0 -1.2 18 18
IL4R -0.32 0.46 -10000 0 -1.2 19 19
PTPN6 0.039 0.016 -10000 0 -10000 0 0
IL13RA2 -0.33 0.44 -10000 0 -1.1 20 20
IL13RA1 -0.006 0.05 -10000 0 -10000 0 0
IRF4 -0.38 0.64 -10000 0 -1.4 39 39
ARG1 -0.017 0.16 -10000 0 -10000 0 0
CBL -0.22 0.3 -10000 0 -0.82 14 14
GTF3A -0.1 0.15 -10000 0 -0.36 35 35
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.008 0.08 -10000 0 -0.31 2 2
IRF4/BCL6 -0.35 0.6 -10000 0 -1.3 39 39
CD40LG -0.003 0.08 -10000 0 -0.51 1 1
MAPK14 -0.22 0.3 -10000 0 -0.81 14 14
mitosis -0.14 0.24 -10000 0 -0.79 4 4
STAT6 -0.33 0.49 -10000 0 -1.3 21 21
SPI1 0.036 0.017 -10000 0 -10000 0 0
RPS6KB1 -0.13 0.24 -10000 0 -0.81 3 3
STAT6 (dimer) -0.33 0.49 -10000 0 -1.3 21 21
STAT6 (dimer)/PARP14 -0.3 0.46 -10000 0 -1.2 21 21
mast cell activation 0.008 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.25 -10000 0 -0.77 7 7
FRAP1 -0.14 0.25 -10000 0 -0.84 4 4
LTA -0.3 0.43 -10000 0 -1.1 19 19
FES 0.028 0.045 -10000 0 -0.51 1 1
T-helper 1 cell differentiation 0.32 0.48 1.2 21 -10000 0 21
CCL11 -0.4 0.6 -10000 0 -1.4 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.25 -10000 0 -0.8 5 5
IL2RG 0.015 0.057 -10000 0 -0.54 1 1
IL10 -0.29 0.43 -10000 0 -1.1 18 18
IRS1 0.026 0.05 -10000 0 -0.32 3 3
IRS2 0.023 0.016 -10000 0 -10000 0 0
IL4 -0.048 0.12 -10000 0 -10000 0 0
IL5 -0.3 0.43 -10000 0 -1.1 18 18
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.23 0.34 -10000 0 -0.86 15 15
COL1A1 -0.21 0.23 -10000 0 -1.1 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.3 0.44 -10000 0 -1.2 17 17
IL2R gamma/JAK3 0.024 0.062 -10000 0 -0.44 1 1
TFF3 -0.31 0.47 -10000 0 -1.2 20 20
ALOX15 -0.3 0.44 -10000 0 -1.2 19 19
MYBL1 0.024 0.042 -10000 0 -0.32 2 2
T-helper 2 cell differentiation -0.24 0.36 -10000 0 -0.86 21 21
SHC1 0.033 0.006 -10000 0 -10000 0 0
CEBPB 0.017 0.035 -10000 0 -0.31 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.24 -10000 0 -1.1 2 2
mol:PI-3-4-5-P3 -0.14 0.25 -10000 0 -0.84 4 4
PI3K -0.15 0.26 -10000 0 -0.91 4 4
DOK2 0.023 0.046 -10000 0 -0.51 1 1
ETS1 0.038 0.032 -10000 0 -0.28 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.18 -10000 0 -0.58 4 4
ITGB3 -0.29 0.43 -10000 0 -1.1 18 18
PIGR -0.33 0.51 -10000 0 -1.3 23 23
IGHE 0.069 0.072 0.18 13 -10000 0 13
MAPKKK cascade -0.1 0.18 -10000 0 -0.57 4 4
BCL6 0.03 0.029 -10000 0 -0.32 1 1
OPRM1 -0.3 0.43 -10000 0 -1.1 19 19
RETNLB -0.52 0.69 -10000 0 -1.5 47 47
SELP -0.37 0.56 -10000 0 -1.4 27 27
AICDA -0.31 0.46 -10000 0 -1.2 22 22
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.025 0.004 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.033 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.06 -9999 0 -10000 0 0
IRAK/TOLLIP 0.039 0.01 -9999 0 -10000 0 0
IKBKB 0.03 0.011 -9999 0 -10000 0 0
IKBKG 0.033 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.19 -9999 0 -0.33 115 115
IL1A -0.15 0.18 -9999 0 -0.32 79 79
IL1B -0.08 0.14 -9999 0 -0.38 10 10
IRAK/TRAF6/p62/Atypical PKCs 0.064 0.027 -9999 0 -10000 0 0
IL1R2 -0.18 0.26 -9999 0 -0.51 58 58
IL1R1 0.027 0.063 -9999 0 -0.51 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.06 -9999 0 -10000 0 0
TOLLIP 0.033 0.005 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.041 0.057 -9999 0 -10000 0 0
JUN -0.025 0.065 -9999 0 -10000 0 0
MAP3K7 0.033 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.016 0.14 -9999 0 -0.39 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.054 0.13 -9999 0 -0.33 6 6
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.043 0.14 -9999 0 -0.31 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.043 0.13 -9999 0 -0.3 15 15
NFKB1 0.033 0.005 -9999 0 -10000 0 0
MAPK8 -0.009 0.07 -9999 0 -0.24 12 12
IRAK1 0.02 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.062 0.14 -9999 0 -0.22 61 61
IRAK4 0.034 0.003 -9999 0 -10000 0 0
PRKCI 0.031 0.029 -9999 0 -0.32 1 1
TRAF6 0.033 0.006 -9999 0 -10000 0 0
PI3K 0.049 0.009 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.07 -9999 0 -10000 0 0
CHUK 0.032 0.008 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.043 0.13 -9999 0 -0.3 15 15
IL1 beta/IL1R2 -0.18 0.19 -9999 0 -0.36 61 61
IRAK/TRAF6/TAK1/TAB1/TAB2 0.047 0.013 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.12 -9999 0 -0.37 1 1
IRAK3 0.024 0.057 -9999 0 -0.32 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.028 0.13 -9999 0 -0.28 15 15
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.065 -9999 0 -0.3 2 2
IL1 alpha/IL1R1/IL1RAP -0.072 0.14 -9999 0 -0.36 6 6
RELA 0.033 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.033 0.004 -9999 0 -10000 0 0
MYD88 0.033 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.056 0.022 -9999 0 -10000 0 0
IL1RAP 0.024 0.057 -9999 0 -0.32 4 4
UBE2N 0.033 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.038 0.1 -9999 0 -0.35 1 1
CASP1 -0.002 0.13 -9999 0 -0.47 10 10
IL1RN/IL1R2 -0.21 0.18 -9999 0 -0.32 107 107
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.027 0.13 -9999 0 -0.29 15 15
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.066 -9999 0 -0.34 3 3
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
IL1RN -0.11 0.17 -9999 0 -0.32 59 59
TRAF6/TAK1/TAB1/TAB2 0.047 0.012 -9999 0 -10000 0 0
MAP2K6 -0.001 0.075 -9999 0 -0.25 12 12
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.056 -10000 0 -10000 0 0
VDR 0.012 0.11 -10000 0 -0.51 6 6
FAM120B 0.033 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.056 0.03 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.065 0.033 -10000 0 -10000 0 0
MED1 0.032 0.008 -10000 0 -10000 0 0
mol:9cRA 0.006 0.002 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.072 -10000 0 -0.26 8 8
RXRs/NUR77 0.092 0.033 -10000 0 -10000 0 0
RXRs/PPAR 0.029 0.064 -10000 0 -10000 0 0
NCOR2 0.033 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.078 -10000 0 -0.37 6 6
RARs/VDR/DNA/Vit D3 0.057 0.075 -10000 0 -0.27 6 6
RARA 0.032 0.008 -10000 0 -10000 0 0
NCOA1 0.027 0.063 -10000 0 -0.51 2 2
VDR/VDR/DNA 0.012 0.11 -10000 0 -0.51 6 6
RARs/RARs/DNA/9cRA 0.056 0.03 -10000 0 -10000 0 0
RARG 0.029 0.041 -10000 0 -0.32 2 2
RPS6KB1 0.02 0.073 0.53 3 -10000 0 3
RARs/THRs/DNA/SMRT 0.027 0.06 -10000 0 -10000 0 0
THRA 0.032 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0.078 -10000 0 -0.37 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.078 0.022 -10000 0 -10000 0 0
NR1H4 -0.42 0.2 -10000 0 -0.51 123 123
RXRs/LXRs/DNA 0.11 0.05 -10000 0 -10000 0 0
NR1H2 0.039 0.005 -10000 0 -10000 0 0
NR1H3 0.035 0.045 -10000 0 -0.5 1 1
RXRs/VDR/DNA/Vit D3 0.073 0.072 -10000 0 -0.26 6 6
NR4A1 0.031 0.029 -10000 0 -0.32 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.18 0.1 -10000 0 -0.23 112 112
RXRG 0.038 0.007 -10000 0 -10000 0 0
RXR alpha/CCPG 0.052 0.01 -10000 0 -10000 0 0
RXRA 0.039 0.005 -10000 0 -10000 0 0
RXRB 0.039 0.007 -10000 0 -10000 0 0
THRB 0.004 0.12 -10000 0 -0.51 8 8
PPARG 0.004 0.12 -10000 0 -0.51 8 8
PPARD 0.034 0 -10000 0 -10000 0 0
TNF 0.058 0.031 -10000 0 -10000 0 0
mol:Oxysterols 0.006 0.002 -10000 0 -10000 0 0
cholesterol transport 0.065 0.033 -10000 0 -10000 0 0
PPARA 0.028 0.045 -10000 0 -0.51 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.033 0.004 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.095 0.12 -10000 0 -0.23 50 50
SREBF1 0.048 0.036 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.078 0.023 -10000 0 -10000 0 0
ABCA1 0.057 0.031 -10000 0 -10000 0 0
RARs/THRs 0.073 0.087 -10000 0 -0.27 7 7
RXRs/FXR -0.21 0.14 -10000 0 -0.28 118 118
BCL2 -0.17 0.25 -10000 0 -0.51 53 53
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.051 0.03 -9999 0 -10000 0 0
RGS9BP 0.02 0.063 -9999 0 -0.32 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.031 0.13 -9999 0 -0.31 25 25
mol:ADP 0.009 0.019 -9999 0 -0.22 1 1
GNAT2 0.028 0.041 -9999 0 -0.32 2 2
RGS9-1/Gbeta5/R9AP -0.057 0.17 -9999 0 -0.32 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.04 0.028 -9999 0 -0.18 2 2
GRK7 0.031 0.029 -9999 0 -0.32 1 1
CNGB3 0.019 0.057 -9999 0 -0.32 4 4
Cone Metarhodopsin II/X-Arrestin 0.025 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.14 -9999 0 -0.28 24 24
Cone PDE6 -0.025 0.16 -9999 0 -0.27 39 39
Cone Metarhodopsin II 0.02 0.015 -9999 0 -0.16 1 1
Na + (4 Units) -0.012 0.13 -9999 0 -0.28 24 24
GNAT2/GDP -0.041 0.15 -9999 0 -0.27 40 40
GNB5 0.022 0.057 -9999 0 -0.32 4 4
mol:GMP (4 units) 0.019 0.026 -9999 0 -10000 0 0
Cone Transducin 0.055 0.033 -9999 0 -10000 0 0
SLC24A2 0.033 0.005 -9999 0 -10000 0 0
GNB3/GNGT2 0.047 0.013 -9999 0 -10000 0 0
GNB3 0.033 0.005 -9999 0 -10000 0 0
GNAT2/GTP 0.021 0.028 -9999 0 -0.22 2 2
CNGA3 -0.069 0.21 -9999 0 -0.51 28 28
ARR3 0.034 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.031 0.13 -9999 0 -0.31 25 25
mol:Pi -0.057 0.17 -9999 0 -0.32 40 40
Cone CNG Channel -0.006 0.13 -9999 0 -0.26 23 23
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.033 0.005 -9999 0 -10000 0 0
RGS9 -0.12 0.24 -9999 0 -0.51 40 40
PDE6C 0.032 0.009 -9999 0 -10000 0 0
GNGT2 0.032 0.007 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.033 0.004 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.096 0.27 -10000 0 -0.84 10 10
PCK1 -0.73 0.66 -10000 0 -1.3 88 88
HNF4A -0.072 0.32 0.59 5 -1.3 4 9
KCNJ11 -0.083 0.29 -10000 0 -1.1 4 4
AKT1 -0.035 0.14 -10000 0 -0.45 2 2
response to starvation -0.014 0.028 -10000 0 -0.22 1 1
DLK1 -0.078 0.29 -10000 0 -1 5 5
NKX2-1 0.011 0.19 -10000 0 -10000 0 0
ACADM -0.11 0.29 -10000 0 -0.98 8 8
TAT -0.13 0.22 -10000 0 -0.88 5 5
CEBPB -0.006 0.038 -10000 0 -0.32 1 1
CEBPA -0.005 0.043 -10000 0 -10000 0 0
TTR -0.71 0.67 -10000 0 -1.3 80 80
PKLR -0.099 0.28 -10000 0 -0.87 9 9
APOA1 -0.085 0.36 -10000 0 -1.4 6 6
CPT1C -0.1 0.28 -10000 0 -0.87 9 9
ALAS1 -0.025 0.16 -10000 0 -0.71 1 1
TFRC -0.13 0.29 -10000 0 -1.2 4 4
FOXF1 0.02 0.079 -10000 0 -0.51 3 3
NF1 0.038 0.009 -10000 0 -10000 0 0
HNF1A (dimer) 0.035 0.038 -10000 0 -10000 0 0
CPT1A -0.1 0.29 -10000 0 -0.92 9 9
HMGCS1 -0.096 0.28 0.59 1 -0.93 6 7
NR3C1 -0.013 0.16 -10000 0 -0.5 13 13
CPT1B -0.096 0.27 -10000 0 -0.95 6 6
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.024 -10000 0 -10000 0 0
GCK -0.085 0.28 -10000 0 -0.95 6 6
CREB1 -0.12 0.14 -10000 0 -0.27 50 50
IGFBP1 -0.06 0.17 -10000 0 -0.62 3 3
PDX1 -0.014 0.14 -10000 0 -10000 0 0
UCP2 -0.095 0.27 -10000 0 -0.88 8 8
ALDOB -0.12 0.37 -10000 0 -1.2 10 10
AFP -0.12 0.14 -10000 0 -0.48 6 6
BDH1 -0.1 0.3 -10000 0 -1.1 6 6
HADH -0.086 0.29 -10000 0 -0.97 6 6
F2 -0.071 0.33 -10000 0 -1.3 4 4
HNF1A 0.035 0.038 -10000 0 -10000 0 0
G6PC -0.079 0.18 -10000 0 -1.4 1 1
SLC2A2 -0.04 0.2 -10000 0 -1.1 1 1
INS 0.027 0.021 -10000 0 -10000 0 0
FOXA1 -0.096 0.2 -10000 0 -0.51 28 28
FOXA3 -0.14 0.17 -10000 0 -0.39 24 24
FOXA2 -0.1 0.33 -10000 0 -1 7 7
ABCC8 -0.12 0.36 -10000 0 -1.1 11 11
ALB -0.13 0.14 -10000 0 -0.48 7 7
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.033 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.058 0.15 -9999 0 -0.5 5 5
Syndecan-3/Neurocan 0.012 0.1 -9999 0 -0.37 9 9
POMC 0.03 0.045 -9999 0 -0.51 1 1
EGFR 0.02 0.077 -9999 0 -0.51 3 3
Syndecan-3/EGFR 0.004 0.11 -9999 0 -0.36 9 9
AGRP 0.034 0 -9999 0 -10000 0 0
NCSTN 0.033 0.006 -9999 0 -10000 0 0
PSENEN 0.032 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.029 0.03 -9999 0 -0.32 1 1
APH1A 0.003 0.12 -9999 0 -0.51 8 8
NCAN 0.033 0.004 -9999 0 -10000 0 0
long-term memory 0.027 0.1 -9999 0 -0.35 9 9
Syndecan-3/IL8 -0.14 0.11 -9999 0 -0.49 10 10
PSEN1 0.03 0.011 -9999 0 -10000 0 0
Src/Cortactin 0.028 0.025 -9999 0 -10000 0 0
FYN 0.031 0.029 -9999 0 -0.32 1 1
limb bud formation -0.01 0.096 -9999 0 -0.38 9 9
MC4R 0.023 0.016 -9999 0 -10000 0 0
SRC 0.019 0.017 -9999 0 -10000 0 0
PTN -0.17 0.26 -9999 0 -0.51 56 56
FGFR/FGF/Syndecan-3 -0.01 0.097 -9999 0 -0.38 9 9
neuron projection morphogenesis -0.023 0.17 -9999 0 -0.49 5 5
Syndecan-3/AgRP 0.012 0.1 -9999 0 -0.37 9 9
Syndecan-3/AgRP/MC4R 0.018 0.1 -9999 0 -0.34 9 9
Fyn/Cortactin 0.046 0.024 -9999 0 -0.22 1 1
SDC3 -0.01 0.098 -9999 0 -0.39 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.14 0.1 -9999 0 -0.49 10 10
IL8 -0.3 0.074 -9999 0 -0.32 141 141
Syndecan-3/Fyn/Cortactin 0.028 0.1 -9999 0 -0.36 9 9
Syndecan-3/CASK -0.012 0.094 -9999 0 -0.37 9 9
alpha-MSH/MC4R 0.032 0.039 -9999 0 -0.35 1 1
Gamma Secretase 0.058 0.09 -9999 0 -0.27 8 8
Signaling events mediated by PRL

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
CCNE1 0.019 0.069 -10000 0 -0.32 6 6
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.031 0.029 -10000 0 -0.32 1 1
CDKN1A 0.012 0.049 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.017 0.11 -10000 0 -0.22 32 32
mol:Ca2+ -0.057 0.12 0.39 1 -0.25 23 24
AGT -0.063 0.16 -10000 0 -0.32 40 40
CCNA2 0.057 0.11 -10000 0 -10000 0 0
TUBA1B 0.031 0.029 -10000 0 -0.32 1 1
EGR1 0.01 0.048 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.05 0.11 -10000 0 -10000 0 0
MAPK3 -0.006 0.14 0.24 19 -0.37 2 21
PRL-2 /Rab GGTase beta 0.047 0.013 -10000 0 -10000 0 0
MAPK1 -0.005 0.13 0.24 18 -0.22 29 47
PTP4A1 0.004 0.024 -10000 0 -10000 0 0
PTP4A3 -0.046 0.14 -10000 0 -0.32 31 31
PTP4A2 0.032 0.008 -10000 0 -10000 0 0
ITGB1 -0.005 0.13 0.24 19 -0.22 32 51
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1 0.019 0.044 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.044 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 0.097 0.09 0.37 1 -10000 0 1
RABGGTA 0.031 0.01 -10000 0 -10000 0 0
BCAR1 0.013 0.057 -10000 0 -10000 0 0
RHOC 0.013 0.07 -10000 0 -0.41 1 1
RHOA 0.022 0.046 -10000 0 -10000 0 0
cell motility 0.047 0.11 -10000 0 -0.44 1 1
PRL-1/alpha Tubulin 0.097 0.092 0.37 1 -10000 0 1
PRL-3/alpha1 Integrin -0.014 0.11 -10000 0 -0.22 30 30
ROCK1 0.047 0.11 -10000 0 -0.44 1 1
RABGGTB 0.032 0.007 -10000 0 -10000 0 0
CDK2 -0.014 0.12 -10000 0 -0.32 20 20
mitosis 0.004 0.024 -10000 0 -10000 0 0
ATF5 0.033 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.074 -9999 0 -0.32 7 7
PLK4 0.019 0.069 -9999 0 -0.32 6 6
regulation of centriole replication -0.001 0.067 -9999 0 -0.22 13 13
Ceramide signaling pathway

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
SPHK2 0.007 0.063 -10000 0 -0.37 4 4
MAP4K4 0.016 0.068 -10000 0 -0.32 3 3
BAG4 0.03 0.011 -10000 0 -10000 0 0
PKC zeta/ceramide -0.04 0.068 0.15 1 -0.2 16 17
NFKBIA 0.03 0.011 -10000 0 -10000 0 0
BIRC3 0.013 0.096 -10000 0 -0.44 6 6
BAX -0.006 0.045 -10000 0 -0.39 1 1
RIPK1 0.034 0.003 -10000 0 -10000 0 0
AKT1 0.006 0.012 -10000 0 -10000 0 0
BAD -0.039 0.069 0.16 1 -0.2 16 17
SMPD1 -0.028 0.12 -10000 0 -0.26 28 28
RB1 0.016 0.098 0.19 24 -0.2 6 30
FADD/Caspase 8 0.036 0.043 -10000 0 -10000 0 0
MAP2K4 -0.034 0.067 -10000 0 -0.23 6 6
NSMAF 0.029 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.032 0.072 0.19 2 -0.22 6 8
EGF -0.11 0.22 -10000 0 -0.44 45 45
mol:ceramide -0.042 0.074 0.16 3 -0.21 16 19
MADD 0.033 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.007 0.055 -10000 0 -0.37 3 3
ASAH1 0.026 0.014 -10000 0 -10000 0 0
negative regulation of cell cycle 0.017 0.098 0.19 24 -0.2 6 30
cell proliferation -0.14 0.13 -10000 0 -0.3 26 26
BID -0.012 0.18 -10000 0 -0.7 9 9
MAP3K1 -0.04 0.069 0.16 1 -0.2 16 17
EIF2A -0.052 0.074 -10000 0 -0.24 1 1
TRADD 0.034 0 -10000 0 -10000 0 0
CRADD 0.03 0.045 -10000 0 -0.51 1 1
MAPK3 -0.027 0.069 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.032 0.073 -10000 0 -0.27 2 2
Cathepsin D/ceramide -0.031 0.087 0.17 1 -0.22 17 18
FADD 0.026 0.044 -10000 0 -10000 0 0
KSR1 -0.035 0.074 0.2 1 -0.21 12 13
MAPK8 -0.034 0.071 -10000 0 -0.23 5 5
PRKRA -0.04 0.069 0.16 1 -0.2 16 17
PDGFA 0.019 0.077 -10000 0 -0.51 3 3
TRAF2 0.033 0.004 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 87 87
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.042 0.073 0.16 3 -0.21 16 19
CTSD 0.026 0.063 -10000 0 -0.51 2 2
regulation of nitric oxide biosynthetic process 0.048 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.15 0.14 -10000 0 -0.32 26 26
PRKCD 0.033 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.055 -10000 0 -0.37 3 3
RelA/NF kappa B1 0.049 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.033 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.032 0.053 -10000 0 -0.29 2 2
TNFR1A/BAG4/TNF-alpha 0.059 0.024 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.063 -10000 0 -0.37 4 4
MAP2K1 -0.03 0.069 -10000 0 -0.24 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.033 0.005 -10000 0 -10000 0 0
CYCS 0.078 0.076 0.16 30 -10000 0 30
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
NFKB1 0.033 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.018 -10000 0 -10000 0 0
EIF2AK2 -0.041 0.068 -10000 0 -0.22 7 7
TNF-alpha/TNFR1A/FAN 0.057 0.026 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.037 0.077 -10000 0 -0.38 4 4
MAP2K2 -0.031 0.069 -10000 0 -0.24 1 1
SMPD3 0.02 0.078 -10000 0 -0.32 6 6
TNF 0.034 0.003 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.046 0.1 0.23 29 -10000 0 29
NF kappa B1/RelA/I kappa B alpha 0.07 0.028 -10000 0 -10000 0 0
AIFM1 0.071 0.081 0.17 31 -10000 0 31
BCL2 -0.17 0.25 -10000 0 -0.51 53 53
IL2 signaling events mediated by PI3K

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
BCL2L1 0.078 0.095 -10000 0 -10000 0 0
UGCG -0.009 0.067 -10000 0 -0.75 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.19 0.21 -10000 0 -0.49 31 31
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.01 0.066 -10000 0 -0.74 1 1
mol:DAG 0.041 0.11 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.25 0.22 -10000 0 -0.47 62 62
FRAP1 -0.3 0.26 -10000 0 -0.52 69 69
FOXO3 -0.17 0.17 -10000 0 -0.43 21 21
AKT1 -0.18 0.18 -10000 0 -0.44 28 28
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 -0.17 0.33 -10000 0 -0.78 32 32
SGMS1 -0.012 0.079 -10000 0 -0.64 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.012 -10000 0 -10000 0 0
CALM1 0.029 0.012 -10000 0 -10000 0 0
cell proliferation -0.025 0.098 -10000 0 -0.44 2 2
EIF3A 0.033 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.024 0.17 -10000 0 -1 4 4
mol:sphingomyelin 0.041 0.11 -10000 0 -0.64 2 2
natural killer cell activation -0.007 0.005 -10000 0 -0.013 21 21
JAK3 0.029 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.008 -10000 0 -10000 0 0
JAK1 0.029 0.008 -10000 0 -10000 0 0
NFKB1 0.033 0.005 -10000 0 -10000 0 0
MYC -0.17 0.17 -10000 0 -0.47 13 13
MYB 0.019 0.12 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.084 0.12 -10000 0 -0.41 6 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.16 -10000 0 -0.92 4 4
mol:PI-3-4-5-P3 -0.083 0.11 -10000 0 -0.4 6 6
Rac1/GDP 0.008 0.022 -10000 0 -10000 0 0
T cell proliferation -0.079 0.11 -10000 0 -0.38 6 6
SHC1 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.006 -10000 0 -0.065 1 1
PRKCZ -0.081 0.11 -10000 0 -0.39 6 6
NF kappa B1 p50/RelA -0.25 0.23 -10000 0 -0.47 60 60
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.05 -10000 0 -0.41 1 1
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
RELA 0.033 0.005 -10000 0 -10000 0 0
IL2RA 0.016 0.063 -10000 0 -0.32 5 5
IL2RB 0.028 0.01 -10000 0 -10000 0 0
TERT 0.032 0.008 -10000 0 -10000 0 0
E2F1 0.018 0.062 -10000 0 -0.43 1 1
SOS1 0.028 0.004 -10000 0 -10000 0 0
RPS6 0.033 0.005 -10000 0 -10000 0 0
mol:cAMP -0.002 0.003 0.031 1 -10000 0 1
PTPN11 0.024 0.029 -10000 0 -0.32 1 1
IL2RG 0.025 0.045 -10000 0 -0.51 1 1
actin cytoskeleton organization -0.079 0.11 -10000 0 -0.38 6 6
GRB2 0.027 0.007 -10000 0 -10000 0 0
IL2 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.034 -10000 0 -10000 0 0
LCK 0.025 0.03 -10000 0 -0.32 1 1
BCL2 -0.54 0.44 -10000 0 -0.89 90 90
FOXM1 transcription factor network

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
NFATC3 -0.23 0.33 -9999 0 -1.1 5 5
PLK1 0.004 0.15 -9999 0 -0.99 3 3
BIRC5 -0.04 0.23 -9999 0 -1.2 5 5
HSPA1B -0.23 0.33 -9999 0 -0.95 11 11
MAP2K1 0.001 0.04 -9999 0 -10000 0 0
BRCA2 -0.2 0.35 -9999 0 -1.1 8 8
FOXM1 -0.26 0.38 -9999 0 -1.2 10 10
XRCC1 -0.22 0.33 -9999 0 -1 7 7
FOXM1B/p19 -0.28 0.36 -9999 0 -1 13 13
Cyclin D1/CDK4 -0.23 0.32 -9999 0 -0.95 8 8
CDC2 -0.24 0.34 -9999 0 -1 11 11
TGFA -0.23 0.32 -9999 0 -1 7 7
SKP2 -0.23 0.34 -9999 0 -1.1 5 5
CCNE1 0.016 0.071 -9999 0 -0.33 6 6
CKS1B -0.22 0.34 -9999 0 -1 7 7
RB1 -0.083 0.17 -9999 0 -0.98 1 1
FOXM1C/SP1 -0.27 0.38 -9999 0 -1.1 13 13
AURKB -0.18 0.42 -9999 0 -1 29 29
CENPF -0.22 0.33 -9999 0 -1.1 5 5
CDK4 -0.007 0.098 -9999 0 -0.33 12 12
MYC -0.26 0.32 -9999 0 -0.89 16 16
CHEK2 0.001 0.04 -9999 0 -10000 0 0
ONECUT1 -0.23 0.33 -9999 0 -0.98 9 9
CDKN2A -0.082 0.16 -9999 0 -0.32 48 48
LAMA4 -0.22 0.33 -9999 0 -1.1 5 5
FOXM1B/HNF6 -0.26 0.37 -9999 0 -1.1 10 10
FOS -0.28 0.42 -9999 0 -1.2 15 15
SP1 0.029 0.016 -9999 0 -10000 0 0
CDC25B -0.24 0.34 -9999 0 -1 7 7
response to radiation -0.012 0.02 -9999 0 -10000 0 0
CENPB -0.2 0.32 -9999 0 -1.1 4 4
CENPA -0.24 0.35 -9999 0 -1.1 9 9
NEK2 -0.26 0.35 -9999 0 -1.1 8 8
HIST1H2BA -0.23 0.33 -9999 0 -1.1 5 5
CCNA2 -0.022 0.13 -9999 0 -0.33 22 22
EP300 0.032 0.009 -9999 0 -10000 0 0
CCNB1/CDK1 -0.26 0.37 -9999 0 -1.2 7 7
CCNB2 -0.22 0.33 -9999 0 -1.1 4 4
CCNB1 -0.24 0.35 -9999 0 -1.1 8 8
ETV5 -0.24 0.33 -9999 0 -1.1 5 5
ESR1 -0.23 0.35 -9999 0 -1.3 5 5
CCND1 -0.23 0.32 -9999 0 -0.96 8 8
GSK3A 0.003 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.025 0.13 -9999 0 -0.39 7 7
CDK2 -0.017 0.12 -9999 0 -0.32 20 20
G2/M transition of mitotic cell cycle -0.014 0.025 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.23 0.35 -9999 0 -1 10 10
GAS1 -0.34 0.49 -9999 0 -1.3 23 23
MMP2 -0.23 0.33 -9999 0 -1.1 4 4
RB1/FOXM1C -0.22 0.32 -9999 0 -1 7 7
CREBBP 0.033 0.005 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.011 -9999 0 -10000 0 0
VLDLR -0.083 0.22 -9999 0 -0.5 32 32
LRPAP1 0.032 0.008 -9999 0 -10000 0 0
NUDC 0.03 0.011 -9999 0 -10000 0 0
RELN/LRP8 -0.14 0.091 -9999 0 -0.22 2 2
CaM/Ca2+ 0.022 0.009 -9999 0 -10000 0 0
KATNA1 0.033 0.005 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.12 0.076 -9999 0 -10000 0 0
IQGAP1/CaM 0.041 0.019 -9999 0 -10000 0 0
DAB1 0.033 0.006 -9999 0 -10000 0 0
IQGAP1 0.032 0.009 -9999 0 -10000 0 0
PLA2G7 0.008 0.12 -9999 0 -0.51 7 7
CALM1 0.029 0.012 -9999 0 -10000 0 0
DYNLT1 0.033 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.18 0.092 -9999 0 -0.22 127 127
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.034 0.003 -9999 0 -10000 0 0
CDK5R1 0.033 0.006 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.007 -9999 0 -10000 0 0
CDK5R2 0.034 0.003 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.015 0.15 -9999 0 -0.31 28 28
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.09 0.086 -9999 0 -10000 0 0
MAP1B 0.007 0.004 -9999 0 -10000 0 0
RAC1 0.012 0.011 -9999 0 -10000 0 0
p35/CDK5 -0.11 0.069 -9999 0 -10000 0 0
RELN 0.032 0.008 -9999 0 -10000 0 0
PAFAH/LIS1 0.011 0.071 -9999 0 -0.3 7 7
LIS1/CLIP170 0.026 0.019 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.064 0.07 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.027 0.13 -9999 0 -0.34 5 5
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.094 0.082 -9999 0 -10000 0 0
LIS1/IQGAP1 0.026 0.019 -9999 0 -10000 0 0
RHOA 0.014 0.01 -9999 0 -10000 0 0
PAFAH1B1 0.013 0.01 -9999 0 -10000 0 0
PAFAH1B3 0.005 0.096 -9999 0 -0.32 12 12
PAFAH1B2 0.033 0.005 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.038 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.089 0.087 -9999 0 -10000 0 0
LRP8 -0.27 0.12 -9999 0 -0.32 127 127
NDEL1/Katanin 60 -0.093 0.088 -9999 0 -10000 0 0
P39/CDK5 -0.11 0.068 -9999 0 -10000 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.019 -9999 0 -10000 0 0
CDK5 -0.12 0.064 -9999 0 -10000 0 0
PPP2R5D 0.033 0.005 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.017 -9999 0 -10000 0 0
CSNK2A1 0.026 0.014 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0 0.14 -9999 0 -0.27 26 26
RELN/VLDLR -0.18 0.14 -9999 0 -0.39 34 34
CDC42 0.013 0.01 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.027 0.091 -10000 0 -0.71 1 1
IHH 0.033 0.062 -10000 0 -0.62 1 1
SHH Np/Cholesterol/GAS1 -0.054 0.15 -10000 0 -0.32 30 30
LRPAP1 0.032 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.15 0.32 30 -10000 0 30
SMO/beta Arrestin2 0.038 0.084 -10000 0 -0.53 1 1
SMO 0.027 0.07 -10000 0 -0.56 1 1
AKT1 0.014 0.11 -10000 0 -0.39 2 2
ARRB2 0.027 0.014 -10000 0 -10000 0 0
BOC 0.033 0.004 -10000 0 -10000 0 0
ADRBK1 0.033 0.005 -10000 0 -10000 0 0
heart looping 0.027 0.069 -10000 0 -0.55 1 1
STIL -0.011 0.12 -10000 0 -0.36 7 7
DHH N/PTCH2 0.049 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.045 0.069 -10000 0 -0.49 1 1
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
DHH 0.034 0.003 -10000 0 -10000 0 0
PTHLH 0.026 0.096 -10000 0 -0.87 1 1
determination of left/right symmetry 0.027 0.069 -10000 0 -0.55 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
skeletal system development 0.026 0.096 -10000 0 -0.86 1 1
IHH N/Hhip -0.043 0.19 -10000 0 -0.41 30 30
DHH N/Hhip -0.037 0.17 -10000 0 -0.37 30 30
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.069 -10000 0 -0.55 1 1
pancreas development -0.077 0.22 -10000 0 -0.51 30 30
HHAT -0.015 0.15 -10000 0 -0.51 13 13
PI3K 0.049 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.072 0.2 -10000 0 -0.46 32 32
somite specification 0.027 0.069 -10000 0 -0.55 1 1
SHH Np/Cholesterol/PTCH1 0.009 0.098 -10000 0 -0.37 3 3
SHH Np/Cholesterol/PTCH2 0.003 0.092 -10000 0 -0.28 13 13
SHH Np/Cholesterol/Megalin 0.003 0.092 -10000 0 -0.28 13 13
SHH -0.016 0.11 0.24 1 -0.36 14 15
catabolic process 0.03 0.071 -10000 0 -0.54 1 1
SMO/Vitamin D3 0.011 0.1 -10000 0 -0.49 1 1
SHH Np/Cholesterol/Hhip -0.056 0.16 -10000 0 -0.32 36 36
LRP2 0.034 0.003 -10000 0 -10000 0 0
receptor-mediated endocytosis 0.007 0.098 -10000 0 -0.46 1 1
SHH Np/Cholesterol/BOC 0.005 0.089 -10000 0 -0.28 12 12
SHH Np/Cholesterol/CDO 0.003 0.092 -10000 0 -0.28 13 13
mesenchymal cell differentiation 0.056 0.15 0.31 36 -10000 0 36
mol:Vitamin D3 0.016 0.11 -10000 0 -0.37 3 3
IHH N/PTCH2 0.049 0.039 -10000 0 -0.39 1 1
CDON 0.033 0.005 -10000 0 -10000 0 0
IHH N/PTCH1 0.039 0.073 -10000 0 -0.55 1 1
Megalin/LRPAP1 0.047 0.012 -10000 0 -10000 0 0
PTCH2 0.033 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.009 0.087 -10000 0 -0.28 13 13
PTCH1 0.03 0.071 -10000 0 -0.55 1 1
HHIP -0.077 0.22 -10000 0 -0.51 30 30
Thromboxane A2 receptor 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
TGM2 0.004 0.068 -10000 0 -0.32 6 6
GNB1/GNG2 -0.058 0.053 -10000 0 -0.18 6 6
AKT1 -0.039 0.11 -10000 0 -0.31 8 8
EGF -0.11 0.22 -10000 0 -0.44 45 45
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.12 0.086 -10000 0 -0.27 3 3
mol:Ca2+ -0.039 0.11 -10000 0 -0.32 5 5
LYN -0.11 0.092 -10000 0 -0.27 3 3
RhoA/GTP -0.014 0.047 -10000 0 -0.14 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.041 0.11 -10000 0 -0.36 4 4
GNG2 0.03 0.01 -10000 0 -10000 0 0
ARRB2 0.027 0.014 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.08 0.17 -10000 0 -0.53 15 15
G beta5/gamma2 -0.073 0.071 -10000 0 -0.25 6 6
PRKCH -0.049 0.12 -10000 0 -0.43 4 4
DNM1 0.024 0.057 -10000 0 -0.32 4 4
TXA2/TP beta/beta Arrestin3 -0.007 0.028 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.35 0.24 -10000 0 -0.51 104 104
G12 family/GTP -0.042 0.095 -10000 0 -0.32 3 3
ADRBK1 0.033 0.005 -10000 0 -10000 0 0
ADRBK2 0.032 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.019 -10000 0 -10000 0 0
mol:GDP 0.081 0.1 0.34 10 -10000 0 10
mol:NADP 0.03 0.029 -10000 0 -0.32 1 1
RAB11A 0.032 0.008 -10000 0 -10000 0 0
PRKG1 0.033 0.006 -10000 0 -10000 0 0
mol:IP3 -0.05 0.13 -10000 0 -0.41 5 5
cell morphogenesis 0.035 0.019 -10000 0 -10000 0 0
PLCB2 -0.07 0.17 -10000 0 -0.55 6 6
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.15 0.12 -10000 0 -0.36 19 19
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.083 0.1 -10000 0 -0.37 5 5
RHOA 0.033 0.004 -10000 0 -10000 0 0
PTGIR 0.033 0.005 -10000 0 -10000 0 0
PRKCB1 -0.046 0.12 -10000 0 -0.39 5 5
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.029 -10000 0 -0.32 1 1
TXA2/TXA2-R family -0.066 0.16 -10000 0 -0.54 5 5
LCK -0.13 0.087 -10000 0 -0.28 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.15 0.11 -10000 0 -0.3 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.053 0.14 -10000 0 -0.53 11 11
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.15 0.1 -10000 0 -0.29 4 4
MAPK14 -0.026 0.082 -10000 0 -0.25 3 3
TGM2/GTP -0.055 0.14 -10000 0 -0.46 3 3
MAPK11 -0.027 0.082 -10000 0 -0.25 3 3
ARHGEF1 -0.016 0.071 -10000 0 -0.2 2 2
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
JNK cascade -0.048 0.12 -10000 0 -0.41 4 4
RAB11/GDP 0.032 0.008 -10000 0 -10000 0 0
ICAM1 -0.03 0.097 -10000 0 -0.29 4 4
cAMP biosynthetic process -0.051 0.12 -10000 0 -0.38 4 4
Gq family/GTP/EBP50 -0.005 0.078 -10000 0 -0.22 15 15
actin cytoskeleton reorganization 0.035 0.019 -10000 0 -10000 0 0
SRC -0.072 0.092 -10000 0 -0.28 1 1
GNB5 0.022 0.057 -10000 0 -0.32 4 4
GNB1 0.031 0.009 -10000 0 -10000 0 0
EGF/EGFR -0.095 0.11 0.2 1 -0.31 13 14
VCAM1 -0.032 0.1 -10000 0 -0.41 4 4
TP beta/Gq family/GDP/G beta5/gamma2 -0.08 0.17 -10000 0 -0.53 15 15
platelet activation -0.038 0.11 -10000 0 -0.33 3 3
PGI2/IP 0.025 0.004 -10000 0 -10000 0 0
PRKACA -0.18 0.12 -10000 0 -0.26 101 101
Gq family/GDP/G beta5/gamma2 -0.091 0.16 -10000 0 -0.49 16 16
TXA2/TP beta/beta Arrestin2 -0.036 0.065 -10000 0 -0.42 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.17 0.11 -10000 0 -0.24 99 99
mol:DAG -0.053 0.14 -10000 0 -0.43 6 6
EGFR 0.02 0.077 -10000 0 -0.51 3 3
TXA2/TP alpha -0.068 0.16 -10000 0 -0.53 4 4
Gq family/GTP -0.011 0.081 0.23 1 -0.21 18 19
YES1 -0.12 0.089 -10000 0 -0.27 3 3
GNAI2/GTP -0.14 0.098 -10000 0 -0.29 5 5
PGD2/DP -0.26 0.16 -10000 0 -0.37 104 104
SLC9A3R1 0.029 0.045 -10000 0 -0.51 1 1
FYN -0.13 0.086 -10000 0 -0.27 3 3
mol:NO 0.03 0.029 -10000 0 -0.32 1 1
GNA15 0.023 0.057 -10000 0 -0.32 4 4
PGK/cGMP 0.041 0.022 -10000 0 -0.18 1 1
RhoA/GDP 0.034 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.1 0.11 -10000 0 -0.33 4 4
NOS3 0.03 0.029 -10000 0 -0.32 1 1
RAC1 0.03 0.01 -10000 0 -10000 0 0
PRKCA -0.042 0.12 -10000 0 -0.36 5 5
PRKCB -0.044 0.12 -10000 0 -0.37 5 5
PRKCE -0.043 0.12 -10000 0 -0.38 4 4
PRKCD -0.046 0.12 -10000 0 -0.39 5 5
PRKCG -0.047 0.13 -10000 0 -0.4 5 5
muscle contraction -0.059 0.15 -10000 0 -0.5 5 5
PRKCZ -0.043 0.11 -10000 0 -0.36 4 4
ARR3 0.034 0 -10000 0 -10000 0 0
TXA2/TP beta -0.15 0.11 -10000 0 -0.31 4 4
PRKCQ -0.047 0.12 -10000 0 -0.36 6 6
MAPKKK cascade -0.061 0.14 -10000 0 -0.47 6 6
SELE -0.044 0.11 -10000 0 -0.31 6 6
TP beta/GNAI2/GDP/G beta/gamma -0.15 0.12 -10000 0 -0.31 5 5
ROCK1 0.027 0.014 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
chemotaxis -0.063 0.16 -10000 0 -0.64 4 4
GNA12 0.03 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -10000 0 0
GNA11 0 0.13 -10000 0 -0.51 9 9
Rac1/GTP 0.022 0.008 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.002 0.077 -10000 0 -10000 0 0
EPHB2 0.022 0.06 -10000 0 -0.38 3 3
Syndecan-2/TACI 0.025 0.019 -10000 0 -10000 0 0
LAMA1 0.026 0.015 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.022 0.098 -10000 0 -0.29 1 1
HRAS 0.033 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.01 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.049 -10000 0 -0.32 3 3
BAX 0.009 0.02 -10000 0 -10000 0 0
EPB41 0.031 0.01 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.028 0.015 -10000 0 -10000 0 0
LAMA3 0.02 0.042 -10000 0 -0.32 2 2
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.016 0.074 -10000 0 -0.32 7 7
Syndecan-2/MMP2 0.03 0.023 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.047 0.13 -10000 0 -0.22 53 53
dendrite morphogenesis 0.023 0.04 -10000 0 -0.31 1 1
Syndecan-2/GM-CSF -0.067 0.11 -10000 0 -0.22 1 1
determination of left/right symmetry 0.014 0.01 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.031 0.017 -10000 0 -10000 0 0
GNB2L1 0.033 0.004 -10000 0 -10000 0 0
MAPK3 -0.046 0.13 0.2 17 -0.35 2 19
MAPK1 -0.041 0.12 0.2 17 -10000 0 17
Syndecan-2/RACK1 0.043 0.023 -10000 0 -10000 0 0
NF1 0.032 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.01 -10000 0 -10000 0 0
ITGA2 -0.092 0.17 -10000 0 -0.32 53 53
MAPK8 0.014 0.014 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.017 0.098 -10000 0 -0.29 1 1
Syndecan-2/Kininogen 0.021 0.057 -10000 0 -0.31 4 4
ITGB1 0.031 0.029 -10000 0 -0.32 1 1
SRC 0.021 0.04 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.026 0.016 -10000 0 -10000 0 0
extracellular matrix organization 0.03 0.017 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.002 0.077 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.034 0.049 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.02 0.03 -10000 0 -10000 0 0
Syndecan-2/RasGAP 0.054 0.034 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.042 0.044 -10000 0 -0.22 4 4
PRKCD 0.033 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.023 0.04 -10000 0 -0.31 1 1
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.03 -10000 0 -10000 0 0
RHOA 0.033 0.004 -10000 0 -10000 0 0
SDCBP 0.029 0.012 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.046 -10000 0 -0.51 1 1
RASA1 0.031 0.029 -10000 0 -0.32 1 1
alpha2/beta1 Integrin -0.047 0.13 -10000 0 -0.22 53 53
Syndecan-2/Synbindin 0.03 0.017 -10000 0 -10000 0 0
TGFB1 0.033 0.005 -10000 0 -10000 0 0
CASP3 0.048 0.064 0.2 22 -10000 0 22
FN1 -0.026 0.13 -10000 0 -0.32 25 25
Syndecan-2/IL8 -0.12 0.1 -10000 0 -0.22 2 2
SDC2 0.014 0.01 -10000 0 -10000 0 0
KNG1 0.019 0.088 -10000 0 -0.51 4 4
Syndecan-2/Neurofibromin 0.03 0.017 -10000 0 -10000 0 0
TRAPPC4 0.033 0.005 -10000 0 -10000 0 0
CSF2 -0.15 0.18 -10000 0 -0.32 79 79
Syndecan-2/TGFB1 0.031 0.017 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.028 0.015 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.015 -10000 0 -10000 0 0
PRKACA 0.049 0.065 0.2 23 -10000 0 23
angiogenesis -0.12 0.1 -10000 0 -0.22 2 2
MMP2 0.032 0.029 -10000 0 -0.32 1 1
IL8 -0.3 0.074 -10000 0 -0.32 141 141
calcineurin-NFAT signaling pathway 0.025 0.019 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.075 0.13 -10000 0 -0.22 67 67
CRKL 0.02 0.098 -10000 0 -0.48 3 3
mol:PIP3 0.004 0.06 0.45 2 -10000 0 2
AKT1 0.001 0.045 0.31 2 -10000 0 2
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 0.021 0.096 0.3 1 -0.45 3 4
RANBP10 0.034 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.05 0.12 -10000 0 -10000 0 0
MAP3K5 0.033 0.097 -10000 0 -0.57 2 2
HGF/MET/CIN85/CBL/ENDOPHILINS -0.041 0.13 -10000 0 -0.4 4 4
AP1 -0.035 0.11 -10000 0 -0.32 10 10
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.098 0.29 -10000 0 -0.76 23 23
STAT3 (dimer) 0.014 0.061 0.23 2 -10000 0 2
GAB1/CRKL/SHP2/PI3K 0.067 0.095 -10000 0 -0.49 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.039 0.098 -10000 0 -0.51 2 2
PTPN11 0.031 0.029 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.018 0.017 -10000 0 -10000 0 0
PTEN 0.024 0.063 -10000 0 -0.51 2 2
ELK1 -0.045 0.11 0.29 6 -10000 0 6
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.049 -10000 0 -0.34 1 1
PAK1 0 0.043 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.05 0.12 -10000 0 -10000 0 0
HRAS 0.016 0.07 -10000 0 -0.41 1 1
DOCK1 0.018 0.097 -10000 0 -0.5 2 2
GAB1 0.01 0.094 -10000 0 -0.5 3 3
CRK 0.019 0.097 -10000 0 -0.48 3 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.053 -10000 0 -10000 0 0
JUN 0.021 0.063 -10000 0 -0.32 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.048 0.057 -10000 0 -0.22 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.059 0.099 0.28 5 -10000 0 5
GRB2/SHC -0.021 0.077 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
GLMN 0.002 0.013 -10000 0 -0.16 1 1
cell motility -0.045 0.11 0.29 6 -10000 0 6
HGF/MET/MUC20 -0.06 0.11 -10000 0 -0.18 68 68
cell migration -0.021 0.076 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
CBL 0.033 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.075 0.13 -10000 0 -0.22 68 68
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.062 -10000 0 -0.28 1 1
MET/MUC20 -0.087 0.12 -10000 0 -0.22 68 68
RAP1B 0.022 0.093 0.29 1 -0.48 2 3
RAP1A 0.019 0.091 0.29 1 -0.48 2 3
HGF/MET/RANBP9 -0.05 0.12 -10000 0 -10000 0 0
RAF1 0.015 0.066 -10000 0 -10000 0 0
STAT3 0.014 0.061 0.23 2 -10000 0 2
cell proliferation 0.032 0.073 -10000 0 -10000 0 0
RPS6KB1 -0.021 0.058 -10000 0 -0.32 3 3
MAPK3 -0.058 0.12 0.7 2 -10000 0 2
MAPK1 -0.024 0.2 0.66 9 -10000 0 9
RANBP9 0.034 0.003 -10000 0 -10000 0 0
MAPK8 0.037 0.1 -10000 0 -0.5 2 2
SRC 0.018 0.068 -10000 0 -10000 0 0
PI3K -0.023 0.078 -10000 0 -10000 0 0
MET/Glomulin -0.1 0.11 -10000 0 -0.21 71 71
SOS1 0.034 0 -10000 0 -10000 0 0
MAP2K1 0.016 0.066 -10000 0 -10000 0 0
MET -0.13 0.17 -10000 0 -0.32 68 68
MAP4K1 0.033 0.1 -10000 0 -0.62 2 2
PTK2 0.027 0.013 -10000 0 -10000 0 0
MAP2K2 0.015 0.066 -10000 0 -10000 0 0
BAD 0 0.043 -10000 0 -10000 0 0
MAP2K4 0.022 0.088 -10000 0 -0.51 2 2
SHP2/GRB2/SOS1/GAB1 0.034 0.098 -10000 0 -0.48 2 2
INPPL1 0.033 0.005 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.019 0.088 -10000 0 -0.51 4 4
HGS -0.042 0.055 -10000 0 -0.2 1 1
PLCgamma1/PKC 0.014 0.012 -10000 0 -10000 0 0
HGF 0.032 0.008 -10000 0 -10000 0 0
RASA1 0.031 0.029 -10000 0 -0.32 1 1
NCK1 0.033 0.004 -10000 0 -10000 0 0
PTPRJ 0.033 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.004 0.056 -10000 0 -10000 0 0
PDPK1 0.001 0.051 0.35 2 -10000 0 2
HGF/MET/SHIP -0.06 0.11 -10000 0 -0.18 68 68
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.044 0.036 -10000 0 -0.37 1 1
Necdin/E2F1 -0.026 0.13 -10000 0 -0.37 15 15
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.053 0.058 -10000 0 -0.27 3 3
NGF (dimer)/p75(NTR)/BEX1 0.041 0.031 -10000 0 -0.31 1 1
NT-4/5 (dimer)/p75(NTR) 0.024 0.005 -10000 0 -10000 0 0
IKBKB 0.03 0.011 -10000 0 -10000 0 0
AKT1 0.021 0.021 -10000 0 -10000 0 0
IKBKG 0.033 0.004 -10000 0 -10000 0 0
BDNF 0.007 0.092 -10000 0 -0.32 11 11
MGDIs/NGR/p75(NTR)/LINGO1 0.04 0.073 -10000 0 -0.34 1 1
FURIN 0.032 0.009 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.042 0.072 -10000 0 -0.31 1 1
LINGO1 0.024 0.05 -10000 0 -0.32 3 3
Sortilin/TRAF6/NRIF 0.018 0.071 -10000 0 -10000 0 0
proBDNF (dimer) 0.007 0.092 -10000 0 -0.32 11 11
NTRK1 0.033 0.006 -10000 0 -10000 0 0
RTN4R 0.008 0.088 -10000 0 -0.32 10 10
neuron apoptosis 0.016 0.081 -10000 0 -0.37 1 1
IRAK1 0.033 0.004 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
ARHGDIA 0.032 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.058 0.09 -10000 0 -0.27 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.08 -10000 0 -0.28 8 8
MAGEH1 0.008 0.12 -10000 0 -0.51 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.003 0.13 -10000 0 -0.3 23 23
Mammalian IAPs/DIABLO 0.049 0.064 -10000 0 -0.28 4 4
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.031 0.029 -10000 0 -0.32 1 1
APP 0.032 0.009 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.045 0.012 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.006 0.035 0.21 2 -0.28 1 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.03 0.047 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.043 0.011 -10000 0 -10000 0 0
NCSTN 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.094 0.17 -10000 0 -0.31 55 55
PSENEN 0.032 0.007 -10000 0 -10000 0 0
mol:ceramide 0.021 0.032 -10000 0 -0.28 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.026 0.043 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.046 0.014 -10000 0 -10000 0 0
BEX1 0.03 0.045 -10000 0 -0.51 1 1
mol:GDP 0.004 0.001 -10000 0 -10000 0 0
NGF (dimer) -0.15 0.05 -10000 0 -0.21 2 2
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.056 0.074 -10000 0 -0.31 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.035 0.014 -10000 0 -10000 0 0
MYD88 0.033 0.004 -10000 0 -10000 0 0
CHUK 0.032 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.094 0.17 -10000 0 -0.31 55 55
RHOB 0.01 0.088 -10000 0 -0.32 10 10
RHOA 0.033 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.021 0.042 -10000 0 -0.22 3 3
NT3 (dimer) 0.031 0.029 -10000 0 -0.32 1 1
TP53 -0.002 0.053 -10000 0 -10000 0 0
PRDM4 0.021 0.032 0.19 2 -0.28 1 3
BDNF (dimer) -0.3 0.066 -10000 0 -0.32 131 131
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
SORT1 0.029 0.045 -10000 0 -0.51 1 1
activation of caspase activity 0.048 0.055 -10000 0 -0.27 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.034 -10000 0 -0.28 1 1
RHOC 0.032 0.008 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.019 0.071 0.24 2 -10000 0 2
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 0.021 0.033 -10000 0 -0.28 1 1
APH1B 0.029 0.03 -10000 0 -0.32 1 1
APH1A 0.003 0.12 -10000 0 -0.51 8 8
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.032 -10000 0 -0.31 1 1
PSEN1 0.03 0.011 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.015 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.045 0.025 -10000 0 -0.22 1 1
MAPK8 0.022 0.064 0.24 1 -10000 0 1
MAPK9 0.022 0.063 0.24 1 -10000 0 1
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 0.031 0.029 -10000 0 -0.32 1 1
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.054 0.2 -10000 0 -0.51 23 23
RAC1/GDP 0.023 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.066 0.16 -10000 0 -0.26 55 55
p75 CTF/Sortilin/TRAF6/NRIF 0.078 0.038 -10000 0 -0.29 1 1
RhoA-B-C/GTP -0.093 0.17 -10000 0 -0.31 55 55
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.075 -10000 0 -0.27 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.059 0.073 -10000 0 -0.29 1 1
PRKACB -0.17 0.26 -10000 0 -0.51 55 55
proBDNF (dimer)/p75 ECD 0.029 0.07 -10000 0 -0.22 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.013 0.096 -10000 0 -0.44 6 6
BIRC2 0.032 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.12 0.14 -10000 0 -0.38 18 18
BAD 0.017 0.069 0.23 1 -10000 0 1
RIPK2 -0.014 0.11 -10000 0 -0.32 18 18
NGFR 0.032 0.007 -10000 0 -10000 0 0
CYCS 0.014 0.039 -10000 0 -0.27 2 2
ADAM17 0.034 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.074 -10000 0 -10000 0 0
BCL2L11 0.018 0.07 0.23 1 -10000 0 1
BDNF (dimer)/p75(NTR) 0.028 0.07 -10000 0 -0.22 11 11
PI3K 0.06 0.017 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.052 0.04 -10000 0 -0.28 1 1
NDNL2 0.029 0.03 -10000 0 -0.32 1 1
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKCI 0.031 0.029 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR) 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.038 -10000 0 -0.28 1 1
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.033 0.005 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.015 0.049 -10000 0 -0.31 1 1
SQSTM1 0.033 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.063 -10000 0 -0.51 2 2
CASP3 0.016 0.068 -10000 0 -10000 0 0
E2F1 0.014 0.042 -10000 0 -0.32 2 2
CASP9 0.031 0.01 -10000 0 -10000 0 0
IKK complex 0.056 0.044 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.024 0.005 -10000 0 -10000 0 0
MMP7 -0.3 0.075 -10000 0 -0.32 141 141
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.038 -10000 0 -0.27 1 1
MMP3 -0.29 0.092 -10000 0 -0.32 137 137
APAF-1/Caspase 9 0.006 0.052 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.055 0.026 -10000 0 -10000 0 0
AES 0.053 0.021 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.046 0.014 -10000 0 -10000 0 0
SMAD4 0.023 0.016 -10000 0 -10000 0 0
DKK2 -0.13 0.18 -10000 0 -0.32 67 67
TLE1 0.053 0.019 -10000 0 -10000 0 0
MACF1 0.033 0.006 -10000 0 -10000 0 0
CTNNB1 0.062 0.065 -10000 0 -10000 0 0
WIF1 -0.033 0.14 -10000 0 -0.32 28 28
beta catenin/RanBP3 0.18 0.12 0.33 36 -10000 0 36
KREMEN2 -0.024 0.13 -10000 0 -0.32 24 24
DKK1 -0.043 0.14 -10000 0 -0.32 32 32
beta catenin/beta TrCP1 0.08 0.064 -10000 0 -10000 0 0
FZD1 0.032 0.008 -10000 0 -10000 0 0
AXIN2 -0.15 0.18 -10000 0 -1.6 1 1
AXIN1 0.034 0.005 -10000 0 -10000 0 0
RAN 0.035 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.055 0.064 -10000 0 -0.5 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.001 0.16 -10000 0 -0.65 4 4
Axin1/APC/GSK3 0.07 0.062 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.066 -10000 0 -10000 0 0
HNF1A 0.054 0.019 -10000 0 -10000 0 0
CTBP1 0.052 0.022 -10000 0 -10000 0 0
MYC -0.046 0.24 0.58 7 -10000 0 7
RANBP3 0.034 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.073 0.15 -10000 0 -0.34 14 14
NKD1 -0.22 0.16 -10000 0 -0.32 108 108
TCF4 0.038 0.031 -10000 0 -10000 0 0
TCF3 0.052 0.022 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.079 0.028 -10000 0 -10000 0 0
Ran/GTP 0.027 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.13 0.15 0.44 10 -0.44 1 11
LEF1 -0.023 0.15 -10000 0 -0.3 33 33
DVL1 0.053 0.065 -10000 0 -0.47 1 1
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.01 0.099 -10000 0 -0.52 3 3
DKK1/LRP6/Kremen 2 -0.024 0.13 -10000 0 -0.34 8 8
LRP6 0.033 0.005 -10000 0 -10000 0 0
CSNK1A1 0.058 0.023 -10000 0 -10000 0 0
NLK 0.028 0.008 -10000 0 -10000 0 0
CCND1 -0.088 0.11 -10000 0 -10000 0 0
WNT1 0.034 0.003 -10000 0 -10000 0 0
GSK3A 0.033 0.005 -10000 0 -10000 0 0
GSK3B 0.033 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.045 -10000 0 -0.51 1 1
PPP2R5D 0.13 0.075 0.24 7 -10000 0 7
APC 0.03 0.062 -10000 0 -0.26 3 3
WNT1/LRP6/FZD1 0.05 0.047 -10000 0 -10000 0 0
CREBBP 0.053 0.02 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.045 0.017 -10000 0 -10000 0 0
HSPA8 0.03 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.002 0.083 -10000 0 -0.38 2 2
AKT1 -0.056 0.056 -10000 0 -10000 0 0
GSC -0.06 0.16 -10000 0 -0.6 4 4
NKX2-5 0.023 0.043 -10000 0 -0.31 1 1
muscle cell differentiation 0.097 0.16 0.56 7 -10000 0 7
SMAD2-3/SMAD4/SP1 -0.097 0.11 -10000 0 -0.34 2 2
SMAD4 -0.02 0.045 -10000 0 -10000 0 0
CBFB 0.027 0.049 -10000 0 -0.32 3 3
SAP18 0.023 0.015 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.053 0.092 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.052 0.1 -10000 0 -10000 0 0
MYC -0.049 0.14 -10000 0 -0.19 64 64
CDKN2B -1.2 0.58 -10000 0 -1.4 121 121
AP1 -0.011 0.097 -10000 0 -0.35 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.037 0.14 -10000 0 -0.41 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.32 0.22 -10000 0 -0.45 91 91
SP3 0.036 0.003 -10000 0 -10000 0 0
CREB1 0.034 0 -10000 0 -10000 0 0
FOXH1 0.02 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.034 0.12 -10000 0 -0.37 13 13
GATA3 0.031 0.031 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.021 0.073 -10000 0 -0.46 1 1
MEF2C/TIF2 -0.044 0.15 -10000 0 -0.52 11 11
endothelial cell migration -0.01 0.11 -10000 0 -10000 0 0
MAX 0.033 0.014 -10000 0 -10000 0 0
RBBP7 0.032 0.003 -10000 0 -10000 0 0
RBBP4 0.031 0.008 -10000 0 -10000 0 0
RUNX2 0.033 0.004 -10000 0 -10000 0 0
RUNX3 0.004 0.11 -10000 0 -0.46 8 8
RUNX1 -0.071 0.16 -10000 0 -0.32 43 43
CTBP1 0.032 0.008 -10000 0 -10000 0 0
NR3C1 -0.012 0.16 -10000 0 -0.51 13 13
VDR 0.012 0.11 -10000 0 -0.51 6 6
CDKN1A -0.062 0.17 -10000 0 -1.5 2 2
KAT2B 0.004 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.034 0.071 -10000 0 -10000 0 0
DCP1A 0.033 0.004 -10000 0 -10000 0 0
SKI 0.03 0.009 -10000 0 -10000 0 0
SERPINE1 0.01 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.008 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.015 0.071 -10000 0 -0.3 1 1
SAP30 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.093 0.051 -10000 0 -0.2 1 1
JUN -0.026 0.089 -10000 0 -0.35 4 4
SMAD3/SMAD4/IRF7 0.001 0.06 -10000 0 -10000 0 0
TFE3 0.035 0.007 -10000 0 -10000 0 0
COL1A2 -0.034 0.1 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.009 0.06 -10000 0 -10000 0 0
DLX1 0.029 0.041 -10000 0 -0.32 2 2
TCF3 0.032 0.007 -10000 0 -10000 0 0
FOS -0.001 0.12 -10000 0 -0.48 8 8
SMAD3/SMAD4/Max -0.003 0.066 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.072 0.026 -10000 0 -10000 0 0
ZBTB17 0.074 0.035 -10000 0 -10000 0 0
LAMC1 -0.017 0.039 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.058 -10000 0 -10000 0 0
IRF7 0.036 0.006 -10000 0 -10000 0 0
ESR1 0.027 0.063 -10000 0 -0.51 2 2
HNF4A 0.011 0.063 -10000 0 -0.51 2 2
MEF2C -0.051 0.16 -10000 0 -0.54 11 11
SMAD2-3/SMAD4 -0.067 0.086 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.077 0.054 -10000 0 -0.3 2 2
IGHV3OR16-13 -0.006 0.027 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.009 0.057 -10000 0 -0.32 4 4
CREBBP 0.043 0.01 -10000 0 -10000 0 0
SKIL 0.024 0.057 -10000 0 -0.32 4 4
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC2 0.032 0.005 -10000 0 -10000 0 0
SNIP1 0.03 0.006 -10000 0 -10000 0 0
GCN5L2 0.012 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.002 0.059 -10000 0 -10000 0 0
MSG1/HSC70 0.009 0.087 -10000 0 -0.22 14 14
SMAD2 -0.04 0.053 -10000 0 -10000 0 0
SMAD3 -0.024 0.042 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.012 0.066 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4 -0.059 0.074 -10000 0 -0.2 15 15
NCOR1 0.025 0.014 -10000 0 -10000 0 0
NCOA2 0.029 0.012 -10000 0 -10000 0 0
NCOA1 0.027 0.063 -10000 0 -0.51 2 2
MYOD/E2A 0.045 0.025 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.096 0.11 -10000 0 -0.32 2 2
IFNB1 -0.015 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.065 0.16 -10000 0 -0.54 11 11
CITED1 -0.012 0.12 -10000 0 -0.32 19 19
SMAD2-3/SMAD4/ARC105 -0.053 0.084 -10000 0 -10000 0 0
RBL1 0.012 0.05 -10000 0 -0.32 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.39 0.27 -10000 0 -0.56 99 99
RUNX1-3/PEBPB2 -0.032 0.13 -10000 0 -0.34 6 6
SMAD7 -0.07 0.14 -10000 0 -0.47 6 6
MYC/MIZ-1 0.1 0.12 0.22 1 -0.22 8 9
SMAD3/SMAD4 0.056 0.12 0.33 2 -0.31 1 3
IL10 -0.014 0.053 -10000 0 -10000 0 0
PIASy/HDAC complex 0.004 0.026 -10000 0 -10000 0 0
PIAS3 0.036 0.03 -10000 0 -0.32 1 1
CDK2 -0.005 0.12 -10000 0 -0.31 20 20
IL5 -0.025 0.085 -10000 0 -10000 0 0
CDK4 0.017 0.096 -10000 0 -0.3 12 12
PIAS4 0.004 0.026 -10000 0 -10000 0 0
ATF3 0.021 0.063 -10000 0 -0.32 5 5
SMAD3/SMAD4/SP1 -0.047 0.082 -10000 0 -0.33 1 1
FOXG1 -0.017 0.12 -10000 0 -0.32 20 20
FOXO3 -0.075 0.064 -10000 0 -10000 0 0
FOXO1 -0.062 0.093 -10000 0 -0.46 5 5
FOXO4 -0.073 0.063 -10000 0 -10000 0 0
heart looping -0.05 0.16 -10000 0 -0.53 11 11
CEBPB -0.018 0.042 -10000 0 -0.37 1 1
SMAD3/SMAD4/DLX1 -0.011 0.066 -10000 0 -10000 0 0
MYOD1 0.031 0.029 -10000 0 -0.32 1 1
SMAD3/SMAD4/HNF4 -0.003 0.055 -10000 0 -0.31 2 2
SMAD3/SMAD4/GATA3 0.001 0.073 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.024 0.057 -10000 0 -0.32 4 4
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.05 0.12 -10000 0 -0.36 4 4
SMAD3/SMAD4/SP1-3 -0.031 0.08 -10000 0 -10000 0 0
MED15 0.032 0.008 -10000 0 -10000 0 0
SP1 -0.029 0.038 -10000 0 -10000 0 0
SIN3B 0.032 0.005 -10000 0 -10000 0 0
SIN3A 0.031 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.035 0.094 -10000 0 -0.33 5 5
ITGB5 -0.043 0.055 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.025 0.08 -10000 0 -0.49 2 2
SMAD3/SMAD4/AR -0.01 0.064 -10000 0 -10000 0 0
AR 0.032 0.029 -10000 0 -0.32 1 1
negative regulation of cell growth -0.03 0.091 -10000 0 -0.35 4 4
SMAD3/SMAD4/MYOD -0.009 0.063 -10000 0 -10000 0 0
E2F5 -0.064 0.15 -10000 0 -0.32 39 39
E2F4 0.032 0.029 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.021 0.073 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.33 0.24 -10000 0 -0.46 108 108
TFDP1 0.016 0.05 -10000 0 -0.32 3 3
SMAD3/SMAD4/AP1 -0.005 0.1 -10000 0 -0.35 4 4
SMAD3/SMAD4/RUNX2 -0.008 0.061 -10000 0 -10000 0 0
TGIF2 0.009 0.057 -10000 0 -0.32 4 4
TGIF1 -0.015 0.11 -10000 0 -0.33 17 17
ATF2 0.034 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.1 0.097 -9999 0 -0.33 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.098 0.11 -9999 0 -0.37 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.12 -9999 0 -0.23 49 49
AP1 -0.1 0.11 -9999 0 -0.41 1 1
ILK -0.1 0.094 -9999 0 -0.33 1 1
bone resorption -0.089 0.093 -9999 0 -10000 0 0
PTK2B 0.027 0.014 -9999 0 -10000 0 0
PYK2/p130Cas -0.08 0.1 -9999 0 -10000 0 0
ITGAV 0.032 0.03 -9999 0 -0.32 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.036 0.057 -9999 0 -0.22 7 7
alphaV/beta3 Integrin/Osteopontin -0.11 0.12 -9999 0 -0.36 1 1
MAP3K1 -0.1 0.095 -9999 0 -0.33 1 1
JUN 0.021 0.063 -9999 0 -0.32 5 5
MAPK3 -0.12 0.1 -9999 0 -0.4 3 3
MAPK1 -0.11 0.098 -9999 0 -0.35 1 1
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
NFKB1 0.033 0.005 -9999 0 -10000 0 0
MAPK8 -0.096 0.088 -9999 0 -0.31 1 1
ITGB3 0.033 0.008 -9999 0 -10000 0 0
NFKBIA -0.1 0.094 -9999 0 -0.34 2 2
FOS 0.003 0.11 -9999 0 -0.46 8 8
CD44 0.016 0.074 -9999 0 -0.32 7 7
CHUK 0.032 0.008 -9999 0 -10000 0 0
PLAU -0.14 0.15 -9999 0 -0.58 2 2
NF kappa B1 p50/RelA -0.1 0.12 -9999 0 -0.44 1 1
BCAR1 0.033 0.004 -9999 0 -10000 0 0
RELA 0.033 0.005 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.026 -9999 0 -0.23 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.1 0.095 -9999 0 -0.33 1 1
VAV3 -0.15 0.15 -9999 0 -0.42 28 28
MAP3K14 -0.11 0.097 -9999 0 -0.35 1 1
ROCK2 0.034 0 -9999 0 -10000 0 0
SPP1 -0.22 0.16 -9999 0 -0.32 107 107
RAC1 0.03 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.14 -9999 0 -0.39 27 27
MMP2 -0.098 0.086 -9999 0 -0.42 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.032 0.11 -10000 0 -10000 0 0
HDAC1 0.038 0.012 -10000 0 -10000 0 0
AES 0.034 0.007 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
DTX1 0.033 0.004 -10000 0 -10000 0 0
LRP6/FZD1 0.046 0.014 -10000 0 -10000 0 0
TLE1 0.035 0.005 -10000 0 -10000 0 0
AP1 -0.083 0.1 -10000 0 -0.28 23 23
NCSTN 0.033 0.006 -10000 0 -10000 0 0
ADAM10 0.032 0.009 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.002 0.094 -10000 0 -0.67 2 2
NICD/RBPSUH 0.027 0.11 -10000 0 -10000 0 0
WIF1 -0.033 0.14 -10000 0 -0.32 28 28
NOTCH1 0.006 0.1 -10000 0 -0.39 1 1
PSENEN 0.032 0.007 -10000 0 -10000 0 0
KREMEN2 -0.024 0.13 -10000 0 -0.32 24 24
DKK1 -0.043 0.14 -10000 0 -0.32 32 32
beta catenin/beta TrCP1 0.077 0.068 -10000 0 -10000 0 0
APH1B 0.029 0.03 -10000 0 -0.32 1 1
APH1A 0.003 0.12 -10000 0 -0.51 8 8
AXIN1 -0.02 0.074 -10000 0 -0.66 1 1
CtBP/CBP/TCF1/TLE1/AES 0.058 0.04 -10000 0 -10000 0 0
PSEN1 0.03 0.01 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
JUN 0.021 0.063 -10000 0 -0.32 5 5
MAP3K7 0.036 0.006 -10000 0 -10000 0 0
CTNNB1 0.061 0.07 0.25 1 -10000 0 1
MAPK3 0.026 0.063 -10000 0 -0.51 2 2
DKK2/LRP6/Kremen 2 -0.074 0.15 -10000 0 -0.34 14 14
HNF1A 0.035 0.004 -10000 0 -10000 0 0
CTBP1 0.034 0.008 -10000 0 -10000 0 0
MYC -0.092 0.11 -10000 0 -10000 0 0
NKD1 -0.22 0.16 -10000 0 -0.32 108 108
FZD1 0.032 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.029 0.11 -10000 0 -10000 0 0
apoptosis -0.083 0.1 -10000 0 -0.28 23 23
Delta 1/NOTCHprecursor 0.028 0.11 -10000 0 -10000 0 0
DLL1 0.033 0.005 -10000 0 -10000 0 0
PPARD 0.022 0.02 -10000 0 -10000 0 0
Gamma Secretase 0.057 0.09 -10000 0 -0.27 8 8
APC -0.039 0.11 -10000 0 -0.41 9 9
DVL1 0.011 0.079 -10000 0 -0.58 2 2
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP1 0.003 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.024 0.13 -10000 0 -0.34 8 8
LRP6 0.033 0.005 -10000 0 -10000 0 0
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
NLK 0.026 0.011 -10000 0 -10000 0 0
CCND1 -0.029 0.14 -10000 0 -0.81 3 3
WNT1 0.034 0.003 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.014 0.11 -10000 0 -0.46 2 2
DKK2 -0.13 0.18 -10000 0 -0.32 67 67
NOTCH1 precursor/DVL1 0.013 0.15 -10000 0 -0.52 6 6
GSK3B 0.034 0.004 -10000 0 -10000 0 0
FRAT1 0.029 0.045 -10000 0 -0.51 1 1
NOTCH/Deltex homolog 1 0.033 0.11 -10000 0 -10000 0 0
PPP2R5D 0.12 0.073 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.036 0.093 -10000 0 -10000 0 0
RBPJ 0.032 0.007 -10000 0 -10000 0 0
CREBBP 0.028 0.007 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.009 0.025 -10000 0 -0.12 1 1
BUB1B -0.011 0.065 -10000 0 -0.14 8 8
PLK1 0.019 0.032 0.08 1 -10000 0 1
PLK1S1 0.008 0.017 0.043 1 -10000 0 1
KIF2A 0.016 0.028 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.019 0.032 0.08 1 -10000 0 1
GOLGA2 0.033 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.026 0.033 -10000 0 -0.18 1 1
WEE1 0.014 0.074 -10000 0 -0.41 3 3
cytokinesis 0.016 0.055 -10000 0 -10000 0 0
PP2A-alpha B56 0.031 0.13 -10000 0 -0.63 5 5
AURKA 0.028 0.032 0.11 1 -10000 0 1
PICH/PLK1 -0.075 0.14 0.19 7 -0.28 32 39
CENPE 0.011 0.041 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.016 0.027 -10000 0 -10000 0 0
PPP2CA 0.033 0.004 -10000 0 -10000 0 0
FZR1 0.033 0.006 -10000 0 -10000 0 0
TPX2 0.044 0.052 0.13 23 -10000 0 23
PAK1 0.034 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
CLSPN 0.011 0.051 -10000 0 -0.22 6 6
GORASP1 0.033 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.018 2 -0.011 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.017 0.043 1 -10000 0 1
G2 phase of mitotic cell cycle 0.001 0.004 0.018 2 -10000 0 2
STAG2 0.029 0.041 -10000 0 -0.32 2 2
GRASP65/GM130/RAB1/GTP 0.011 0.062 -10000 0 -0.5 2 2
spindle elongation 0.019 0.032 0.08 1 -10000 0 1
ODF2 0.036 0.005 -10000 0 -10000 0 0
BUB1 -0.011 0.13 -10000 0 -0.68 5 5
TPT1 0.028 0.041 -10000 0 -0.19 2 2
CDC25C 0.018 0.037 -10000 0 -0.24 2 2
CDC25B -0.097 0.16 -10000 0 -0.32 52 52
SGOL1 0.009 0.025 0.12 1 -10000 0 1
RHOA 0.033 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 -0.031 0.092 -10000 0 -0.21 13 13
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 0.023 0.057 -10000 0 -0.32 4 4
PLK1/PBIP1 0.005 0.048 -10000 0 -0.15 8 8
mitosis -0.002 0.003 -10000 0 -10000 0 0
FBXO5 0.002 0.046 -10000 0 -0.14 5 5
CDC2 -0.001 0.006 0.01 14 -0.011 14 28
NDC80 0.024 0.031 -10000 0 -0.32 1 1
metaphase plate congression -0.003 0.079 -10000 0 -0.22 16 16
ERCC6L -0.071 0.13 0.18 7 -0.27 29 36
NLP/gamma Tubulin 0.009 0.017 0.087 1 -10000 0 1
microtubule cytoskeleton organization 0.028 0.041 -10000 0 -0.19 2 2
G2/M transition DNA damage checkpoint 0 0.003 0.016 4 -10000 0 4
PPP1R12A 0.034 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.016 4 -10000 0 4
PLK1/PRC1-2 0.03 0.079 -10000 0 -0.21 8 8
GRASP65/GM130/RAB1/GTP/PLK1 0.067 0.029 -10000 0 -10000 0 0
RAB1A 0.034 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.025 0.034 0.075 23 -10000 0 23
mitotic prometaphase 0.001 0.006 0.018 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.054 -10000 0 -0.39 2 2
microtubule-based process 0.019 0.066 -10000 0 -0.17 12 12
Golgi organization 0.019 0.032 0.08 1 -10000 0 1
Cohesin/SA2 0.032 0.031 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.05 0.008 -10000 0 -10000 0 0
KIF20A -0.002 0.11 -10000 0 -0.32 15 15
APC/C/CDC20 0.032 0.043 -10000 0 -0.17 3 3
PPP2R1A 0.033 0.004 -10000 0 -10000 0 0
chromosome segregation 0.005 0.047 -10000 0 -0.15 8 8
PRC1 0.022 0.057 -10000 0 -0.32 4 4
ECT2 -0.085 0.087 0.23 1 -0.16 62 63
C13orf34 0.019 0.029 0.073 2 -10000 0 2
NUDC -0.003 0.079 -10000 0 -0.22 16 16
regulation of attachment of spindle microtubules to kinetochore -0.01 0.065 -10000 0 -0.14 8 8
spindle assembly 0.014 0.027 0.13 1 -10000 0 1
spindle stabilization 0.008 0.017 0.043 1 -10000 0 1
APC/C/HCDH1 0.031 0.008 -10000 0 -10000 0 0
MKLP2/PLK1 0.019 0.067 -10000 0 -0.17 12 12
CCNB1 -0.028 0.13 -10000 0 -0.32 26 26
PPP1CB 0.035 0.001 -10000 0 -10000 0 0
BTRC 0.032 0.008 -10000 0 -10000 0 0
ROCK2 0.03 0.026 -10000 0 -10000 0 0
TUBG1 0.018 0.018 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.027 0.1 0.17 14 -0.21 11 25
MLF1IP -0.009 0.063 -10000 0 -0.22 12 12
INCENP 0.028 0.041 -10000 0 -0.32 2 2
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.027 0.079 -9999 0 -0.34 4 4
alphaM/beta2 Integrin/GPIbA 0.024 0.072 -9999 0 -0.33 4 4
alphaM/beta2 Integrin/proMMP-9 0.015 0.059 -9999 0 -0.25 2 2
PLAUR 0.033 0.005 -9999 0 -10000 0 0
HMGB1 -0.002 0.026 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.029 0.076 -9999 0 -0.34 4 4
AGER -0.002 0.034 -9999 0 -10000 0 0
RAP1A 0.032 0.008 -9999 0 -10000 0 0
SELPLG 0.019 0.088 -9999 0 -0.51 4 4
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.018 0.08 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 0.005 0.071 -9999 0 -0.36 5 5
CYR61 -0.001 0.1 -9999 0 -0.32 14 14
TLN1 0.033 0.004 -9999 0 -10000 0 0
Rap1/GTP 0.016 0.099 -9999 0 -0.47 3 3
RHOA 0.033 0.004 -9999 0 -10000 0 0
P-selectin oligomer -0.022 0.16 -9999 0 -0.51 15 15
MYH2 -0.006 0.098 -9999 0 -0.5 3 3
MST1R 0.033 0.004 -9999 0 -10000 0 0
leukocyte activation during inflammatory response 0.043 0.068 -9999 0 -0.29 4 4
APOB 0.032 0.029 -9999 0 -0.32 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.032 0.029 -9999 0 -0.32 1 1
JAM3 0.032 0.007 -9999 0 -10000 0 0
GP1BA 0.027 0.014 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.026 0.079 -9999 0 -0.34 4 4
alphaM/beta2 Integrin -0.003 0.1 -9999 0 -0.52 3 3
JAM3 homodimer 0.032 0.007 -9999 0 -10000 0 0
ICAM2 0.026 0.053 -9999 0 -0.41 2 2
ICAM1 0.014 0.079 -9999 0 -0.32 8 8
phagocytosis triggered by activation of immune response cell surface activating receptor -0.002 0.099 -9999 0 -0.52 3 3
cell adhesion 0.024 0.072 -9999 0 -0.33 4 4
NFKB1 -0.012 0.13 -9999 0 -10000 0 0
THY1 -0.015 0.12 -9999 0 -0.32 20 20
RhoA/GDP 0.025 0.003 -9999 0 -10000 0 0
Lipoprotein(a) 0.043 0.02 -9999 0 -0.18 1 1
alphaM/beta2 Integrin/LRP/tPA 0.044 0.075 -9999 0 -0.3 4 4
IL6 -0.072 0.16 -9999 0 -10000 0 0
ITGB2 -0.009 0.066 -9999 0 -0.5 2 2
elevation of cytosolic calcium ion concentration -0.035 0.13 -9999 0 -0.31 4 4
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.18 -9999 0 -0.31 71 71
JAM2 -0.24 0.27 -9999 0 -0.51 73 73
alphaM/beta2 Integrin/ICAM1 0.039 0.11 -9999 0 -0.3 6 6
alphaM/beta2 Integrin/uPA/Plg -0.034 0.13 -9999 0 -0.31 4 4
RhoA/GTP -0.003 0.099 -9999 0 -0.47 3 3
positive regulation of phagocytosis -0.009 0.092 -9999 0 -0.39 3 3
Ron/MSP 0.033 0.064 -9999 0 -0.22 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.034 0.13 -9999 0 -0.31 4 4
alphaM/beta2 Integrin/uPAR 0.028 0.076 -9999 0 -0.34 4 4
PLAU -0.095 0.17 -9999 0 -0.32 54 54
PLAT 0.023 0.054 -9999 0 -0.41 2 2
actin filament polymerization -0.006 0.094 -9999 0 -0.47 3 3
MST1 0.012 0.084 -9999 0 -0.32 9 9
alphaM/beta2 Integrin/lipoprotein(a) 0.048 0.07 -9999 0 -0.29 4 4
TNF -0.013 0.12 -9999 0 -10000 0 0
RAP1B 0.034 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.053 0.13 -9999 0 -0.25 18 18
fibrinolysis -0.035 0.13 -9999 0 -0.31 4 4
HCK -0.003 0.1 -9999 0 -0.51 6 6
dendritic cell antigen processing and presentation -0.002 0.099 -9999 0 -0.52 3 3
VTN 0.032 0.007 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.009 0.1 -9999 0 -0.24 17 17
LPA 0.033 0.005 -9999 0 -10000 0 0
LRP1 0.034 0.003 -9999 0 -10000 0 0
cell migration 0.012 0.058 -9999 0 -0.3 2 2
FN1 -0.026 0.13 -9999 0 -0.32 25 25
alphaM/beta2 Integrin/Thy1 0 0.11 -9999 0 -0.3 7 7
MPO 0.009 0.088 -9999 0 -0.32 10 10
KNG1 0.019 0.088 -9999 0 -0.51 4 4
RAP1/GDP 0.043 0.011 -9999 0 -10000 0 0
ROCK1 0 0.093 -9999 0 -0.5 2 2
ELA2 0 0 -9999 0 -10000 0 0
PLG 0.033 0.005 -9999 0 -10000 0 0
CTGF 0.031 0.029 -9999 0 -0.32 1 1
alphaM/beta2 Integrin/Hck 0.006 0.082 -9999 0 -0.31 7 7
ITGAM -0.009 0.069 -9999 0 -0.52 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.011 0.15 -9999 0 -0.34 19 19
HP 0.033 0.004 -9999 0 -10000 0 0
leukocyte adhesion -0.14 0.14 -9999 0 -0.39 8 8
SELP -0.022 0.16 -9999 0 -0.51 15 15
Glucocorticoid receptor regulatory network

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
PCK2 0.055 0.098 -10000 0 -0.75 1 1
SMARCC2 0.034 0.003 -10000 0 -10000 0 0
SMARCC1 0.026 0.05 -10000 0 -0.32 3 3
TBX21 -0.3 0.38 -10000 0 -0.85 46 46
SUMO2 0.033 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.006 0.1 -10000 0 -0.31 14 14
FKBP4 0.033 0.006 -10000 0 -10000 0 0
FKBP5 0.034 0.003 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.093 0.13 0.31 4 -0.3 6 10
PRL -0.036 0.096 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.2 0.22 0.51 31 -10000 0 31
RELA -0.09 0.055 -10000 0 -10000 0 0
FGG 0.14 0.17 0.45 12 -10000 0 12
GR beta/TIF2 0.092 0.13 0.3 12 -0.34 6 18
IFNG -0.15 0.18 -10000 0 -0.62 6 6
apoptosis 0.052 0.1 0.52 1 -10000 0 1
CREB1 0.042 0 -10000 0 -10000 0 0
histone acetylation -0.056 0.096 -10000 0 -0.3 5 5
BGLAP -0.053 0.1 -10000 0 -10000 0 0
GR/PKAc -0.026 0.21 0.32 3 -0.34 20 23
NF kappa B1 p50/RelA -0.15 0.092 -10000 0 -0.38 3 3
SMARCD1 0.034 0.003 -10000 0 -10000 0 0
MDM2 0.078 0.064 0.23 9 -10000 0 9
GATA3 0.039 0.025 -10000 0 -10000 0 0
AKT1 0.026 0.02 0.24 1 -10000 0 1
CSF2 -0.13 0.13 -10000 0 -0.53 1 1
GSK3B 0.034 0.006 -10000 0 -10000 0 0
NR1I3 0.056 0.1 0.5 1 -10000 0 1
CSN2 0.11 0.14 0.37 9 -10000 0 9
BRG1/BAF155/BAF170/BAF60A 0.079 0.038 -10000 0 -10000 0 0
NFATC1 0.027 0.034 -10000 0 -0.31 1 1
POU2F1 0.038 0.011 -10000 0 -10000 0 0
CDKN1A -0.032 0.21 -10000 0 -1.7 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.005 -10000 0 -10000 0 0
SFN 0.026 0.045 -10000 0 -0.51 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.13 0.32 3 -0.29 5 8
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.042 0.099 0.48 1 -10000 0 1
JUN -0.1 0.12 -10000 0 -0.4 7 7
IL4 -0.05 0.097 -10000 0 -0.45 1 1
CDK5R1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.014 0.13 -10000 0 -0.32 10 10
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.13 0.32 3 -0.29 5 8
cortisol/GR alpha (monomer) 0.23 0.26 0.58 35 -10000 0 35
NCOA2 0.029 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.03 0.12 -10000 0 -0.48 8 8
AP-1/NFAT1-c-4 -0.14 0.14 -10000 0 -0.57 4 4
AFP -0.069 0.098 -10000 0 -10000 0 0
SUV420H1 0.033 0.005 -10000 0 -10000 0 0
IRF1 0.11 0.15 0.43 2 -1 1 3
TP53 0.026 0.074 -10000 0 -0.39 1 1
PPP5C 0.033 0.005 -10000 0 -10000 0 0
KRT17 -0.13 0.16 -10000 0 -0.61 5 5
KRT14 -0.069 0.099 -10000 0 -10000 0 0
TBP 0.041 0.006 -10000 0 -10000 0 0
CREBBP 0.035 0.015 -10000 0 -10000 0 0
HDAC1 0.03 0.016 -10000 0 -10000 0 0
HDAC2 0.042 0.012 -10000 0 -10000 0 0
AP-1 -0.14 0.14 -10000 0 -0.57 4 4
MAPK14 0.034 0.004 -10000 0 -10000 0 0
MAPK10 0.024 0.069 -10000 0 -0.44 3 3
MAPK11 0.03 0.03 -10000 0 -0.32 1 1
KRT5 -0.12 0.15 -10000 0 -0.54 5 5
interleukin-1 receptor activity 0.009 0.01 -10000 0 -10000 0 0
NCOA1 0.028 0.064 -10000 0 -0.51 2 2
STAT1 0.006 0.1 -10000 0 -0.31 14 14
CGA -0.056 0.1 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.083 0.14 0.35 11 -10000 0 11
MAPK3 0.027 0.063 -10000 0 -0.51 2 2
MAPK1 0.032 0.009 -10000 0 -10000 0 0
ICAM1 -0.18 0.16 -10000 0 -0.59 6 6
NFKB1 -0.09 0.055 -10000 0 -10000 0 0
MAPK8 -0.1 0.13 -10000 0 -0.4 9 9
MAPK9 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.053 0.1 0.53 1 -10000 0 1
BAX -0.012 0.083 -10000 0 -10000 0 0
POMC -0.085 0.16 -10000 0 -1.3 1 1
EP300 0.035 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.18 0.22 0.54 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.087 0.34 9 -10000 0 9
SGK1 0.036 0.06 -10000 0 -0.22 1 1
IL13 -0.096 0.13 -10000 0 -10000 0 0
IL6 -0.24 0.2 -10000 0 -0.6 9 9
PRKACG 0.033 0.004 -10000 0 -10000 0 0
IL5 -0.091 0.13 -10000 0 -10000 0 0
IL2 -0.13 0.15 -10000 0 -0.62 1 1
CDK5 0.03 0.029 -10000 0 -0.32 1 1
PRKACB -0.17 0.26 -10000 0 -0.51 55 55
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
IL8 -0.31 0.15 -10000 0 -0.55 23 23
CDK5R1/CDK5 0.045 0.026 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/PKAc -0.2 0.16 -10000 0 -0.42 38 38
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 24 -10000 0 24
SMARCA4 0.033 0.004 -10000 0 -10000 0 0
chromatin remodeling 0.12 0.13 0.34 16 -10000 0 16
NF kappa B1 p50/RelA/Cbp -0.1 0.075 -10000 0 -0.34 1 1
JUN (dimer) -0.1 0.12 -10000 0 -0.4 7 7
YWHAH 0.032 0.009 -10000 0 -10000 0 0
VIPR1 -0.16 0.27 -10000 0 -0.84 18 18
NR3C1 0.12 0.2 0.41 17 -0.44 11 28
NR4A1 0.033 0.068 -10000 0 -0.51 2 2
TIF2/SUV420H1 0.042 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.052 0.1 0.52 1 -10000 0 1
cortisol/GR alpha (dimer)/Src-1 0.22 0.23 0.52 34 -0.45 1 35
PBX1 0.024 0.089 -10000 0 -0.5 4 4
POU1F1 0.035 0.046 -10000 0 -0.5 1 1
SELE -0.22 0.2 -10000 0 -0.66 9 9
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.13 0.34 16 -10000 0 16
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 24 -10000 0 24
mol:cortisol 0.13 0.12 0.32 32 -10000 0 32
MMP1 -0.22 0.13 -10000 0 -0.78 4 4
Ephrin B reverse signaling

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
EFNB2 0.019 0.046 -10000 0 -0.51 1 1
EPHB2 0.022 0.061 -10000 0 -0.38 3 3
EFNB1 0.013 0.039 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.11 -10000 0 -0.27 3 3
Ephrin B2/EPHB1-2 -0.015 0.091 -10000 0 -0.29 2 2
neuron projection morphogenesis -0.015 0.093 -10000 0 -0.26 3 3
Ephrin B1/EPHB1-2/Tiam1 -0.014 0.11 -10000 0 -0.28 5 5
DNM1 0.024 0.057 -10000 0 -0.32 4 4
cell-cell signaling -0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.013 0.073 -10000 0 -0.42 4 4
YES1 -0.03 0.12 -10000 0 -0.68 4 4
Ephrin B1/EPHB1-2/NCK2 -0.013 0.12 -10000 0 -0.29 5 5
PI3K 0.02 0.088 -10000 0 -0.38 5 5
mol:GDP -0.015 0.11 -10000 0 -0.28 5 5
ITGA2B 0.032 0.007 -10000 0 -10000 0 0
endothelial cell proliferation -0.005 0.08 -10000 0 -0.18 23 23
FYN -0.02 0.12 -10000 0 -0.65 5 5
MAP3K7 -0.019 0.076 -10000 0 -0.45 4 4
FGR -0.014 0.098 -10000 0 -0.65 3 3
TIAM1 0.032 0.008 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RGS3 0.033 0.004 -10000 0 -10000 0 0
cell adhesion 0.014 0.076 -10000 0 -0.37 3 3
LYN -0.016 0.11 -10000 0 -0.66 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.017 0.1 -10000 0 -0.59 4 4
Ephrin B1/EPHB1-2 -0.017 0.065 -10000 0 -0.53 2 2
SRC -0.017 0.11 -10000 0 -0.63 4 4
ITGB3 0.032 0.007 -10000 0 -10000 0 0
EPHB1 -0.084 0.16 -10000 0 -0.32 50 50
EPHB4 -0.037 0.14 -10000 0 -0.32 29 29
RAC1 0.03 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.081 -10000 0 -0.18 23 23
alphaIIb/beta3 Integrin 0.048 0.01 -10000 0 -10000 0 0
BLK -0.042 0.12 -10000 0 -0.7 3 3
HCK -0.017 0.09 -10000 0 -0.7 2 2
regulation of stress fiber formation 0.014 0.11 0.28 5 -10000 0 5
MAPK8 -0.011 0.07 -10000 0 -0.43 3 3
Ephrin B1/EPHB1-2/RGS3 -0.014 0.11 -10000 0 -0.29 5 5
endothelial cell migration 0.013 0.14 0.38 5 -0.47 3 8
NCK2 0.034 0 -10000 0 -10000 0 0
PTPN13 -0.075 0.16 -10000 0 -0.3 46 46
regulation of focal adhesion formation 0.014 0.11 0.28 5 -10000 0 5
chemotaxis 0.015 0.11 0.28 5 -10000 0 5
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.009 0.1 -10000 0 -0.27 3 3
angiogenesis -0.017 0.065 -10000 0 -0.53 2 2
LCK -0.018 0.11 -10000 0 -0.66 4 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.021 0.08 -10000 0 -0.22 14 14
alphaV beta3 Integrin 0.061 0.033 -10000 0 -10000 0 0
PTK2 0.068 0.096 0.35 2 -10000 0 2
IGF1R 0.032 0.008 -10000 0 -10000 0 0
PI4KB 0.033 0.006 -10000 0 -10000 0 0
MFGE8 0.032 0.009 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
CDKN1B 0.031 0.014 -10000 0 -10000 0 0
VEGFA -0.003 0.11 -10000 0 -0.32 15 15
ILK 0.032 0.014 -10000 0 -10000 0 0
ROCK1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.023 0.014 -10000 0 -10000 0 0
PTK2B 0.007 0.053 -10000 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A 0.072 0.041 -10000 0 -10000 0 0
CBL 0.033 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.062 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.18 -10000 0 -0.29 86 86
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.021 0.066 -10000 0 -0.35 3 3
alphaV/beta3 Integrin/Syndecan-1 0.064 0.025 -10000 0 -10000 0 0
PI4KA 0.032 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.17 -10000 0 -0.4 17 17
PI4 Kinase 0.046 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.11 0.11 -10000 0 -0.26 3 3
RPS6KB1 -0.16 0.14 -10000 0 -0.38 17 17
TLN1 0.033 0.004 -10000 0 -10000 0 0
MAPK3 -0.043 0.11 -10000 0 -0.44 6 6
GPR124 0.024 0.042 -10000 0 -0.32 2 2
MAPK1 -0.043 0.11 -10000 0 -0.44 7 7
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.06 0.038 -10000 0 -10000 0 0
cell adhesion 0.054 0.029 -10000 0 -10000 0 0
ANGPTL3 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.062 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
TGFBR2 0.033 0.004 -10000 0 -10000 0 0
ITGB3 0.032 0.007 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 87 87
RAC1 0.03 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.051 0.042 -10000 0 -10000 0 0
apoptosis 0.031 0.029 -10000 0 -0.32 1 1
CD47 0.033 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.063 0.026 -10000 0 -10000 0 0
VCL 0.033 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.021 0.12 -10000 0 -0.31 16 16
CSF1 0.032 0.007 -10000 0 -10000 0 0
PIK3C2A 0.026 0.028 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.022 0.059 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.054 0.076 -10000 0 -10000 0 0
FAK1/Vinculin 0.079 0.093 0.3 4 -10000 0 4
alphaV beta3/Integrin/ppsTEM5 0.052 0.042 -10000 0 -10000 0 0
RHOA 0.033 0.004 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -10000 0 0
BCAR1 0.033 0.004 -10000 0 -10000 0 0
FGF2 0.031 0.029 -10000 0 -0.32 1 1
F11R 0.017 0.02 -10000 0 -0.22 1 1
alphaV/beta3 Integrin/Lactadherin 0.059 0.03 -10000 0 -10000 0 0
alphaV/beta3 Integrin/TGFBR2 0.063 0.026 -10000 0 -10000 0 0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.08 0.03 -10000 0 -10000 0 0
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.06 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.026 0.13 -10000 0 -0.32 25 25
alphaV/beta3 Integrin/Pyk2 0.033 0.069 -10000 0 -10000 0 0
SDC1 0.034 0 -10000 0 -10000 0 0
VAV3 -0.039 0.12 -10000 0 -0.28 30 30
PTPN11 0.031 0.029 -10000 0 -0.32 1 1
IRS1 0.026 0.05 -10000 0 -0.32 3 3
FAK1/Paxillin 0.079 0.093 0.29 5 -10000 0 5
cell migration 0.073 0.089 0.27 7 -10000 0 7
ITGAV 0.031 0.029 -10000 0 -0.32 1 1
PI3K 0.083 0.043 -10000 0 -10000 0 0
SPP1 -0.22 0.16 -10000 0 -0.32 107 107
KDR 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.031 0.029 -10000 0 -0.32 1 1
COL4A3 0.029 0.041 -10000 0 -0.32 2 2
angiogenesis -0.031 0.11 -10000 0 -0.46 6 6
Rac1/GTP -0.022 0.11 -10000 0 -0.26 28 28
EDIL3 -0.026 0.17 -10000 0 -0.51 16 16
cell proliferation 0.062 0.026 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.011 0.15 0.29 3 -0.49 8 11
FYN -0.033 0.18 -10000 0 -0.57 10 10
LAT/GRAP2/SLP76 0.001 0.15 -10000 0 -0.5 8 8
IKBKB 0.03 0.011 -10000 0 -10000 0 0
AKT1 -0.024 0.14 -10000 0 -0.4 12 12
B2M 0.009 0.11 -10000 0 -0.51 6 6
IKBKG 0.003 0.05 0.12 3 -0.14 1 4
MAP3K8 0 0.1 -10000 0 -0.32 14 14
mol:Ca2+ -0.009 0.016 0.09 1 -0.084 2 3
integrin-mediated signaling pathway 0.042 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.19 -10000 0 -0.59 11 11
TRPV6 0.049 0.26 1.2 7 -10000 0 7
CD28 -0.032 0.18 -10000 0 -0.51 18 18
SHC1 -0.021 0.18 0.3 3 -0.62 8 11
receptor internalization -0.022 0.19 -10000 0 -0.55 13 13
PRF1 -0.013 0.2 -10000 0 -0.94 4 4
KRAS 0.034 0.003 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.018 0.12 -10000 0 -0.34 12 12
LAT -0.025 0.17 -10000 0 -0.62 8 8
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.015 0.099 -10000 0 -0.51 5 5
CD3E 0.033 0.006 -10000 0 -10000 0 0
CD3G 0.013 0.1 -10000 0 -0.48 6 6
RASGRP2 0.005 0.035 -10000 0 -0.14 6 6
RASGRP1 0.002 0.14 -10000 0 -0.43 8 8
HLA-A 0.019 0.089 -10000 0 -0.52 4 4
RASSF5 0.033 0.006 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.042 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.06 0.15 4 -0.14 3 7
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.023 0.061 -10000 0 -0.22 8 8
PRKCA 0.026 0.099 0.17 12 -0.26 6 18
GRAP2 0.031 0.009 -10000 0 -10000 0 0
mol:IP3 -0.023 0.11 -10000 0 -0.36 10 10
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.16 -10000 0 -0.53 9 9
ORAI1 -0.041 0.22 -10000 0 -1 7 7
CSK -0.025 0.17 -10000 0 -0.56 10 10
B7 family/CD28 -0.02 0.22 -10000 0 -0.65 12 12
CHUK 0.032 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.029 0.2 -10000 0 -0.61 11 11
PTPN6 -0.026 0.17 -10000 0 -0.63 8 8
VAV1 -0.04 0.19 -10000 0 -0.66 10 10
Monovalent TCR/CD3 -0.007 0.15 -10000 0 -0.49 10 10
CBL 0.033 0.005 -10000 0 -10000 0 0
LCK -0.034 0.18 -10000 0 -0.58 10 10
PAG1 -0.067 0.21 -10000 0 -0.58 12 12
RAP1A 0.032 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.028 0.2 -10000 0 -0.62 11 11
CD80 0.026 0.05 -10000 0 -0.32 3 3
CD86 0.008 0.12 -10000 0 -0.51 7 7
PDK1/CARD11/BCL10/MALT1 -0.015 0.082 -10000 0 -0.27 8 8
HRAS 0.033 0.005 -10000 0 -10000 0 0
GO:0035030 -0.042 0.18 -10000 0 -0.53 12 12
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.034 0.003 -10000 0 -10000 0 0
PTPRC 0.018 0.089 -10000 0 -0.51 4 4
PDK1/PKC theta -0.017 0.16 -10000 0 -0.5 10 10
CSK/PAG1 -0.061 0.2 -10000 0 -0.57 11 11
SOS1 0.034 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.12 -10000 0 -0.5 7 7
GRAP2/SLP76 0.001 0.17 -10000 0 -0.6 8 8
STIM1 0.002 0.1 1.2 1 -10000 0 1
RAS family/GTP 0.03 0.07 0.19 2 -0.19 3 5
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.026 0.21 -10000 0 -0.59 13 13
mol:DAG -0.033 0.089 -10000 0 -0.33 10 10
RAP1A/GDP 0.016 0.029 0.086 2 -10000 0 2
PLCG1 0.018 0.017 -10000 0 -10000 0 0
CD247 0.007 0.12 -10000 0 -0.51 7 7
cytotoxic T cell degranulation -0.011 0.19 -10000 0 -0.89 4 4
RAP1A/GTP 0.002 0.013 -10000 0 -0.064 3 3
mol:PI-3-4-5-P3 -0.026 0.16 -10000 0 -0.48 11 11
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.024 0.14 -10000 0 -0.46 10 10
NRAS 0.027 0.041 -10000 0 -0.32 2 2
ZAP70 0.034 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.018 0.16 0.24 1 -0.52 10 11
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.025 0.008 -10000 0 -10000 0 0
CARD11 0.004 0.092 -10000 0 -0.32 11 11
PRKCB -0.022 0.064 -10000 0 -0.23 10 10
PRKCE 0.028 0.1 0.17 12 -0.26 6 18
PRKCQ -0.021 0.18 -10000 0 -0.57 10 10
LCP2 0.025 0.06 -10000 0 -0.38 3 3
BCL10 0.032 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.019 0.12 -10000 0 -0.34 12 12
IKK complex 0.036 0.066 0.13 33 -0.12 2 35
RAS family/GDP -0.001 0.011 -10000 0 -0.058 1 1
MAP3K14 -0.014 0.096 0.19 1 -0.28 8 9
PDPK1 -0.018 0.13 -10000 0 -0.41 9 9
TCR/CD3/MHC I/CD8/Fyn -0.028 0.19 -10000 0 -0.67 8 8
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.014 0.079 -9999 0 -0.32 8 8
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.011 0.054 -9999 0 -0.22 8 8
neuron projection morphogenesis 0.011 0.054 -9999 0 -0.22 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.036 0.024 -10000 0 -10000 0 0
NFATC2 -0.01 0.12 -10000 0 -10000 0 0
NFATC3 -0.028 0.088 -10000 0 -0.3 5 5
CD40LG -0.26 0.25 -10000 0 -0.74 12 12
ITCH 0.014 0.047 -10000 0 -10000 0 0
CBLB 0.032 0.042 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.17 -10000 0 -0.7 2 2
JUNB 0.024 0.057 -10000 0 -0.32 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.056 -10000 0 -0.27 4 4
T cell anergy 0.039 0.093 -10000 0 -0.42 3 3
TLE4 -0.003 0.078 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -10000 0 -0.74 3 3
AP-1/NFAT1-c-4 -0.27 0.28 -10000 0 -0.82 11 11
IKZF1 -0.003 0.077 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.072 0.13 -10000 0 -0.83 1 1
AP-1/NFAT1 -0.05 0.12 -10000 0 -0.41 2 2
CALM1 0.034 0.038 -10000 0 -10000 0 0
EGR2 -0.07 0.28 -10000 0 -1.4 5 5
EGR3 -0.056 0.16 -10000 0 -0.67 2 2
NFAT1/FOXP3 0.007 0.09 -10000 0 -10000 0 0
EGR1 0.018 0.074 -10000 0 -0.32 7 7
JUN -0.049 0.067 -10000 0 -0.34 5 5
EGR4 0.001 0 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.029 -10000 0 -10000 0 0
GBP3 -0.067 0.25 -10000 0 -0.74 17 17
FOSL1 0.005 0.096 -10000 0 -0.32 12 12
NFAT1-c-4/MAF/IRF4 -0.2 0.25 -10000 0 -0.86 9 9
DGKA -0.003 0.078 -10000 0 -10000 0 0
CREM 0.033 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.078 0.18 -10000 0 -0.69 4 4
CTLA4 0.034 0.11 -10000 0 -10000 0 0
NFAT1-c-4 (dimer)/EGR1 -0.065 0.17 -10000 0 -0.76 2 2
NFAT1-c-4 (dimer)/EGR4 -0.068 0.16 -10000 0 -0.71 3 3
FOS -0.061 0.11 -10000 0 -0.49 8 8
IFNG -0.2 0.26 -10000 0 -0.69 16 16
T cell activation -0.049 0.14 -10000 0 -10000 0 0
MAF -0.17 0.26 -10000 0 -0.51 56 56
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.06 0.15 0.6 5 -10000 0 5
TNF -0.063 0.15 -10000 0 -0.81 1 1
FASLG -0.23 0.57 -10000 0 -1.5 22 22
TBX21 -0.14 0.24 -10000 0 -0.51 42 42
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.011 0.069 -10000 0 -0.31 4 4
PTPN1 -0.003 0.078 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.066 0.17 -10000 0 -0.77 2 2
GATA3 0.036 0.005 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.19 0.26 -10000 0 -0.68 16 16
IL2RA -0.12 0.17 -10000 0 -0.73 2 2
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.002 0.074 -10000 0 -10000 0 0
E2F1 0.013 0.046 -10000 0 -0.31 2 2
PPARG 0.004 0.12 -10000 0 -0.51 8 8
SLC3A2 -0.001 0.079 -10000 0 -10000 0 0
IRF4 -0.1 0.24 -10000 0 -0.51 37 37
PTGS2 -0.29 0.28 -10000 0 -0.76 18 18
CSF2 -0.32 0.28 -10000 0 -0.77 19 19
JunB/Fra1/NFAT1-c-4 -0.066 0.18 -10000 0 -0.86 1 1
IL4 -0.073 0.14 -10000 0 -0.87 1 1
IL5 -0.26 0.26 -10000 0 -0.76 11 11
IL2 -0.05 0.14 -10000 0 -10000 0 0
IL3 -0.016 0.09 -10000 0 -0.86 1 1
RNF128 0.017 0.11 -10000 0 -0.6 4 4
NFATC1 -0.06 0.15 -10000 0 -0.6 5 5
CDK4 0.026 0.11 -10000 0 -10000 0 0
PTPRK -0.002 0.076 -10000 0 -10000 0 0
IL8 -0.37 0.26 -10000 0 -0.76 25 25
POU2F1 0.039 0.007 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.019 0.005 -10000 0 -10000 0 0
SMARCC1 0.006 0.085 -10000 0 -0.87 1 1
REL 0.033 0 -10000 0 -10000 0 0
HDAC7 -0.1 0.14 -10000 0 -0.44 11 11
JUN 0.022 0.063 -10000 0 -0.32 5 5
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.033 0.11 -10000 0 -0.39 12 12
FOXO1 0.005 0.097 -10000 0 -0.51 5 5
T-DHT/AR -0.083 0.17 -10000 0 -0.46 11 11
MAP2K6 -0.018 0.15 -10000 0 -0.52 12 12
BRM/BAF57 0.048 0.014 -10000 0 -10000 0 0
MAP2K4 0.022 0.016 -10000 0 -10000 0 0
SMARCA2 0.034 0.005 -10000 0 -10000 0 0
PDE9A -0.52 0.58 -10000 0 -1.1 73 73
NCOA2 0.029 0.012 -10000 0 -10000 0 0
CEBPA 0.032 0.007 -10000 0 -10000 0 0
EHMT2 0.034 0.003 -10000 0 -10000 0 0
cell proliferation -0.006 0.18 0.34 2 -0.39 9 11
NR0B1 0.029 0.041 -10000 0 -0.32 2 2
EGR1 0.017 0.074 -10000 0 -0.32 7 7
RXRs/9cRA 0.063 0.016 -10000 0 -10000 0 0
AR/RACK1/Src 0.037 0.14 -10000 0 -0.34 9 9
AR/GR -0.036 0.11 -10000 0 -0.33 7 7
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
PKN1 0.031 0.029 -10000 0 -0.32 1 1
RCHY1 0.033 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.024 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.027 0.11 -10000 0 -0.35 9 9
SRC 0.002 0.12 -10000 0 -0.32 9 9
NR3C1 -0.014 0.15 -10000 0 -0.51 13 13
KLK3 -0.062 0.097 -10000 0 -10000 0 0
APPBP2 0.011 0.027 -10000 0 -10000 0 0
TRIM24 0.033 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.056 0.1 -10000 0 -0.35 12 12
TMPRSS2 -0.071 0.18 -10000 0 -0.78 6 6
RXRG 0.033 0.006 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.004 -10000 0 -10000 0 0
RXRB 0.034 0.004 -10000 0 -10000 0 0
CARM1 0.034 0.005 -10000 0 -10000 0 0
NR2C2 0.033 0.005 -10000 0 -10000 0 0
KLK2 0.021 0.1 -10000 0 -10000 0 0
AR -0.013 0.067 -10000 0 -0.26 3 3
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
MDM2 0.032 0.003 -10000 0 -10000 0 0
SRY -0.001 0 -10000 0 -10000 0 0
GATA2 0.033 0.004 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.25 0.14 -10000 0 -0.32 118 118
T-DHT/AR/RACK1/Src 0.034 0.14 -10000 0 -0.35 9 9
positive regulation of transcription 0.033 0.004 -10000 0 -10000 0 0
DNAJA1 0.01 0.039 -10000 0 -0.34 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.029 0.074 -10000 0 -0.59 2 2
SPDEF -0.13 0.25 -10000 0 -0.51 45 45
T-DHT/AR/TIF2 -0.007 0.085 -10000 0 -0.42 2 2
T-DHT/AR/Hsp90 -0.042 0.11 -10000 0 -0.37 10 10
GSK3B 0.031 0.005 -10000 0 -10000 0 0
NR2C1 0.024 0.057 -10000 0 -0.32 4 4
mol:T-DHT -0.042 0.094 -10000 0 -0.33 12 12
SIRT1 0.033 0.006 -10000 0 -10000 0 0
ZMIZ2 0.03 0.01 -10000 0 -10000 0 0
POU2F1 -0.023 0.071 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.048 0.11 -10000 0 -0.37 10 10
CREBBP 0.033 0.005 -10000 0 -10000 0 0
SMARCE1 0.033 0.008 -10000 0 -10000 0 0
Aurora B signaling

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.004 0.055 -9999 0 -0.24 1 1
STMN1 0.012 0.029 -9999 0 -0.22 2 2
Aurora B/RasGAP/Survivin 0.023 0.082 -9999 0 -0.22 2 2
Chromosomal passenger complex/Cul3 protein complex -0.061 0.13 -9999 0 -0.32 16 16
BIRC5 -0.011 0.12 -9999 0 -0.33 18 18
DES -0.13 0.31 -9999 0 -0.69 34 34
Aurora C/Aurora B/INCENP 0.046 0.036 -9999 0 -10000 0 0
Aurora B/TACC1 0.034 0.02 -9999 0 -10000 0 0
Aurora B/PP2A 0.039 0.021 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.011 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.002 0.004 -9999 0 -10000 0 0
NDC80 0.013 0.021 -9999 0 -0.22 1 1
Cul3 protein complex -0.046 0.17 -9999 0 -0.31 37 37
KIF2C -0.001 0.052 -9999 0 -0.26 2 2
PEBP1 0.034 0.004 -9999 0 -10000 0 0
KIF20A 0.001 0.11 -9999 0 -0.31 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.037 0.03 -9999 0 -0.22 1 1
SEPT1 0.034 0.003 -9999 0 -10000 0 0
SMC2 0.017 0.074 -9999 0 -0.32 7 7
SMC4 0.033 0.004 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.081 0.22 -9999 0 -0.49 31 31
PSMA3 0.03 0.011 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B 0.016 0.008 -9999 0 -10000 0 0
AURKB 0.027 0.014 -9999 0 -10000 0 0
AURKC 0.033 0.005 -9999 0 -10000 0 0
CDCA8 0.03 0.03 -9999 0 -0.32 1 1
cytokinesis -0.026 0.13 -9999 0 -0.4 11 11
Aurora B/Septin1 -0.024 0.14 -9999 0 -0.41 8 8
AURKA 0.012 0.05 -9999 0 -0.32 3 3
INCENP 0.028 0.041 -9999 0 -0.32 2 2
KLHL13 -0.13 0.24 -9999 0 -0.47 47 47
BUB1 -0.078 0.16 -9999 0 -0.32 48 48
hSgo1/Aurora B/Survivin 0.019 0.083 -9999 0 -0.26 4 4
EVI5 0.032 0.006 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.13 -9999 0 -0.35 7 7
SGOL1 0.023 0.057 -9999 0 -0.32 4 4
CENPA 0.007 0.081 -9999 0 -0.27 3 3
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.039 0.021 -9999 0 -10000 0 0
NCAPD2 0.032 0.007 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.039 0.021 -9999 0 -10000 0 0
RHOA 0.033 0.004 -9999 0 -10000 0 0
NCAPH 0.017 0.074 -9999 0 -0.32 7 7
NPM1 -0.043 0.14 -9999 0 -0.62 2 2
RASA1 0.031 0.029 -9999 0 -0.32 1 1
KLHL9 0.033 0.005 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.021 -9999 0 -10000 0 0
PPP1CC 0.033 0.004 -9999 0 -10000 0 0
Centraspindlin -0.018 0.13 -9999 0 -0.33 12 12
RhoA/GDP 0.025 0.003 -9999 0 -10000 0 0
NSUN2 -0.039 0.14 -9999 0 -0.29 29 29
MYLK -0.011 0.1 -9999 0 -0.39 10 10
KIF23 -0.021 0.13 -9999 0 -0.32 22 22
VIM 0.013 0.033 -9999 0 -0.38 1 1
RACGAP1 0.019 0.07 -9999 0 -0.32 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.043 0.14 -9999 0 -0.31 22 22
Chromosomal passenger complex -0.014 0.083 -9999 0 -0.29 6 6
Chromosomal passenger complex/EVI5 0.042 0.091 -9999 0 -0.29 1 1
TACC1 0.029 0.012 -9999 0 -10000 0 0
PPP2R5D 0.033 0.005 -9999 0 -10000 0 0
CUL3 0.034 0.003 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.018 0.017 -10000 0 -10000 0 0
GNB1/GNG2 -0.027 0.11 -10000 0 -0.34 4 4
mol:DAG -0.021 0.077 -10000 0 -0.32 1 1
PLCG1 -0.022 0.079 -10000 0 -0.33 1 1
YES1 -0.027 0.091 -10000 0 -0.3 7 7
FZD3 -0.05 0.14 -10000 0 -0.32 32 32
FZD6 0.019 0.057 -10000 0 -0.32 4 4
G protein 0.033 0.13 0.3 4 -0.33 1 5
MAP3K7 -0.016 0.07 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.075 -10000 0 -0.31 1 1
mol:IP3 -0.021 0.077 -10000 0 -0.32 1 1
NLK -0.008 0.13 -10000 0 -0.76 4 4
GNB1 0.031 0.009 -10000 0 -10000 0 0
CAMK2A -0.019 0.073 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.043 0.11 -10000 0 -0.33 11 11
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
GNAS -0.006 0.094 0.24 1 -0.3 7 8
GO:0007205 -0.023 0.074 -10000 0 -0.31 1 1
WNT6 0.034 0.003 -10000 0 -10000 0 0
WNT4 -0.001 0.12 -10000 0 -0.49 9 9
NFAT1/CK1 alpha -0.015 0.084 -10000 0 -10000 0 0
GNG2 0.03 0.01 -10000 0 -10000 0 0
WNT5A -0.007 0.11 -10000 0 -0.32 17 17
WNT11 -0.036 0.14 -10000 0 -0.32 29 29
CDC42 -0.028 0.082 -10000 0 -0.34 1 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.031 0.029 -9999 0 -0.32 1 1
ITGB7 0.001 0.13 -9999 0 -0.51 9 9
ITGA4 0.026 0.063 -9999 0 -0.51 2 2
alpha4/beta7 Integrin 0.019 0.12 -9999 0 -0.4 10 10
alpha4/beta1 Integrin 0.042 0.053 -9999 0 -0.32 3 3
EPO signaling pathway

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
BCL2L1 -0.11 0.15 -10000 0 -10000 0 0
CRKL -0.03 0.074 -10000 0 -10000 0 0
mol:DAG -0.015 0.063 -10000 0 -10000 0 0
HRAS -0.023 0.078 -10000 0 -10000 0 0
MAPK8 0.023 0.076 -10000 0 -10000 0 0
RAP1A -0.033 0.074 -10000 0 -10000 0 0
GAB1 -0.033 0.079 -10000 0 -0.36 1 1
MAPK14 0.024 0.077 -10000 0 -10000 0 0
EPO 0.01 0.039 -10000 0 -0.33 1 1
PLCG1 -0.016 0.064 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.013 0.027 -10000 0 -10000 0 0
RAPGEF1 0.033 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.023 0.069 -10000 0 -0.21 5 5
GAB1/SHC/GRB2/SOS1 -0.011 0.091 -10000 0 -0.33 1 1
EPO/EPOR (dimer) 0.013 0.043 -10000 0 -0.23 1 1
IRS2 -0.02 0.063 -10000 0 -10000 0 0
STAT1 -0.08 0.13 -10000 0 -0.36 6 6
STAT5B -0.049 0.1 -10000 0 -10000 0 0
cell proliferation 0.02 0.076 0.2 1 -10000 0 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.074 -10000 0 -0.32 1 1
TEC -0.033 0.074 -10000 0 -10000 0 0
SOCS3 0.008 0.088 -10000 0 -0.32 10 10
STAT1 (dimer) -0.079 0.13 -10000 0 -0.36 6 6
JAK2 0.021 0.051 -10000 0 -0.32 3 3
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.017 0.096 -10000 0 -10000 0 0
EPO/EPOR 0.013 0.043 -10000 0 -0.23 1 1
LYN 0.009 0.025 -10000 0 -10000 0 0
TEC/VAV2 -0.031 0.081 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.013 0.027 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.007 0.055 -10000 0 -10000 0 0
mol:IP3 -0.015 0.063 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.013 0.065 -10000 0 -10000 0 0
SH2B3 0.027 0.015 -10000 0 -10000 0 0
NFKB1 0.023 0.076 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.036 -10000 0 -10000 0 0
PTPN6 -0.035 0.075 -10000 0 -10000 0 0
TEC/VAV2/GRB2 -0.022 0.089 -10000 0 -10000 0 0
EPOR 0.013 0.027 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.091 -10000 0 -0.34 1 1
SOS1 0.034 0 -10000 0 -10000 0 0
PLCG2 -0.24 0.27 -10000 0 -0.51 75 75
CRKL/CBL/C3G -0.017 0.085 -10000 0 -10000 0 0
VAV2 -0.038 0.078 -10000 0 -10000 0 0
CBL -0.033 0.074 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.023 0.076 -10000 0 -10000 0 0
STAT5A -0.049 0.1 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
STAT5 (dimer) -0.11 0.16 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.15 0.2 -10000 0 -0.37 64 64
PTPN11 0.031 0.029 -10000 0 -0.32 1 1
BTK -0.074 0.12 -10000 0 -0.33 17 17
BCL2 -0.48 0.44 -10000 0 -0.83 90 90
PDGFR-alpha signaling pathway

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
PDGFRA 0.022 0.08 -10000 0 -0.51 3 3
PDGF/PDGFRA/CRKL 0.04 0.059 -10000 0 -0.36 3 3
positive regulation of JUN kinase activity 0.071 0.055 -10000 0 -0.27 3 3
CRKL 0.032 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.042 0.059 -10000 0 -0.36 3 3
AP1 -0.017 0.2 -10000 0 -0.75 7 7
mol:IP3 0.021 0.076 0.23 10 -0.37 2 12
PLCG1 0.021 0.077 0.23 10 -0.37 2 12
PDGF/PDGFRA/alphaV Integrin 0.041 0.063 -10000 0 -0.32 4 4
RAPGEF1 0.033 0.004 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.076 0.23 10 -0.37 2 12
CAV3 0.033 0.005 -10000 0 -10000 0 0
CAV1 0.025 0.05 -10000 0 -0.32 3 3
SHC/Grb2/SOS1 0.074 0.056 -10000 0 -0.27 3 3
PDGF/PDGFRA/Shf -0.008 0.12 -10000 0 -0.24 25 25
FOS -0.034 0.18 0.32 3 -0.74 7 10
JUN -0.014 0.043 -10000 0 -0.22 4 4
oligodendrocyte development 0.041 0.063 -10000 0 -0.32 4 4
GRB2 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:DAG 0.021 0.076 0.23 10 -0.37 2 12
PDGF/PDGFRA 0.022 0.08 -10000 0 -0.51 3 3
actin cytoskeleton reorganization 0.037 0.069 -10000 0 -0.3 5 5
SRF 0.011 0.014 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.062 0.047 -10000 0 -0.3 2 2
PDGF/PDGFRA/Crk/C3G 0.046 0.059 -10000 0 -0.3 3 3
JAK1 0.013 0.055 -10000 0 -0.36 3 3
ELK1/SRF 0.035 0.072 -10000 0 -0.29 2 2
SHB 0.026 0.05 -10000 0 -0.32 3 3
SHF -0.03 0.13 -10000 0 -0.32 26 26
CSNK2A1 0.019 0.023 -10000 0 -10000 0 0
GO:0007205 0.019 0.083 0.25 12 -0.39 2 14
SOS1 0.034 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.071 0.055 -10000 0 -0.27 3 3
PDGF/PDGFRA/SHB 0.037 0.069 -10000 0 -0.3 5 5
PDGF/PDGFRA/Caveolin-1 0.035 0.07 -10000 0 -0.29 6 6
ITGAV 0.031 0.029 -10000 0 -0.32 1 1
ELK1 0.036 0.095 0.22 25 -0.34 2 27
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.033 0.06 -10000 0 -0.36 3 3
JAK-STAT cascade 0.013 0.055 -10000 0 -0.35 3 3
cell proliferation -0.008 0.12 -10000 0 -0.24 25 25
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.082 -9999 0 -0.3 9 9
CRKL 0.032 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
DOCK1 0.026 0.063 -9999 0 -0.51 2 2
ITGA4 0.026 0.063 -9999 0 -0.51 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.045 0.2 -9999 0 -0.32 46 46
EPO 0.03 0.03 -9999 0 -0.32 1 1
alpha4/beta7 Integrin 0.019 0.12 -9999 0 -0.4 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.014 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.053 -9999 0 -0.32 3 3
EPO/EPOR (dimer) 0.045 0.025 -9999 0 -0.22 1 1
lamellipodium assembly 0.006 0.095 -9999 0 -0.56 1 1
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
PI3K 0.049 0.009 -9999 0 -10000 0 0
ARF6 0.03 0.01 -9999 0 -10000 0 0
JAK2 0.028 0.041 -9999 0 -0.24 2 2
PXN 0.034 0.003 -9999 0 -10000 0 0
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
MADCAM1 -0.12 0.24 -9999 0 -0.51 42 42
cell adhesion -0.046 0.19 -9999 0 -0.32 46 46
CRKL/CBL 0.047 0.013 -9999 0 -10000 0 0
ITGB1 0.031 0.029 -9999 0 -0.32 1 1
SRC 0.003 0.055 -9999 0 -0.31 4 4
ITGB7 0.001 0.13 -9999 0 -0.51 9 9
RAC1 0.03 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.048 0.085 -9999 0 -0.37 5 5
p130Cas/Crk/Dock1 0.057 0.09 -9999 0 -0.31 1 1
VCAM1 0.018 0.088 -9999 0 -0.51 4 4
RHOA 0.033 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.075 0.051 -9999 0 -0.29 2 2
BCAR1 -0.003 0.05 -9999 0 -0.29 4 4
EPOR 0.033 0.005 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.033 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.005 0.098 -9999 0 -0.58 1 1
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.017 0.039 -9999 0 -0.2 1 1
NFATC2 -0.012 0.028 -9999 0 -10000 0 0
NFATC3 -0.02 0.041 -9999 0 -10000 0 0
CD40LG -0.086 0.21 -9999 0 -0.52 6 6
PTGS2 -0.12 0.24 -9999 0 -0.53 21 21
JUNB 0.024 0.057 -9999 0 -0.32 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.031 -9999 0 -10000 0 0
CaM/Ca2+ -0.007 0.031 -9999 0 -10000 0 0
CALM1 0.011 0.028 -9999 0 -10000 0 0
JUN 0.004 0.066 -9999 0 -0.32 5 5
mol:Ca2+ -0.012 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -9999 0 -10000 0 0
FOSL1 0.005 0.096 -9999 0 -0.32 12 12
CREM 0.033 0.003 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.05 0.11 -9999 0 -0.3 2 2
FOS -0.013 0.11 -9999 0 -0.46 8 8
IFNG -0.11 0.24 -9999 0 -0.53 19 19
AP-1/NFAT1-c-4 -0.099 0.23 -9999 0 -0.48 20 20
FASLG -0.12 0.23 -9999 0 -0.51 16 16
NFAT1-c-4/ICER1 -0.029 0.069 -9999 0 -10000 0 0
IL2RA -0.088 0.21 -9999 0 -0.58 5 5
FKBP12/FK506 0.019 0.011 -9999 0 -10000 0 0
CSF2 -0.15 0.24 -9999 0 -0.52 25 25
JunB/Fra1/NFAT1-c-4 0.002 0.12 -9999 0 -0.35 2 2
IL4 -0.085 0.2 -9999 0 -0.51 5 5
IL2 0 0.14 -9999 0 -0.98 3 3
IL3 0.024 0.086 -9999 0 -0.67 2 2
FKBP1A 0.026 0.014 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.039 0.007 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.25 0.36 -10000 0 -1.2 13 13
IL23A -0.28 0.31 -10000 0 -1.2 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.3 -10000 0 -1.1 6 6
positive regulation of T cell mediated cytotoxicity -0.23 0.31 -10000 0 -1.2 6 6
ITGA3 -0.23 0.29 -10000 0 -1.1 6 6
IL17F -0.15 0.21 -10000 0 -0.7 6 6
IL12B -0.005 0.048 -10000 0 -0.34 1 1
STAT1 (dimer) -0.24 0.32 -10000 0 -1.2 6 6
CD4 -0.21 0.28 -10000 0 -1 6 6
IL23 -0.27 0.3 -10000 0 -1.1 6 6
IL23R -0.081 0.29 -10000 0 -1.1 9 9
IL1B -0.27 0.31 -10000 0 -1.2 6 6
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.22 0.3 -10000 0 -1.1 6 6
TYK2 -0.002 0.032 -10000 0 -10000 0 0
STAT4 0.03 0.045 -10000 0 -0.51 1 1
STAT3 0.034 0.005 -10000 0 -10000 0 0
IL18RAP -0.073 0.22 -10000 0 -0.51 29 29
IL12RB1 -0.002 0.032 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.005 0.043 -10000 0 -10000 0 0
IL23R/JAK2 -0.084 0.28 -10000 0 -1.1 8 8
positive regulation of chronic inflammatory response -0.23 0.31 -10000 0 -1.2 6 6
natural killer cell activation 0.005 0.014 0.081 4 -10000 0 4
JAK2 -0.01 0.062 -10000 0 -0.35 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
NFKB1 0.031 0.005 -10000 0 -10000 0 0
RELA 0.031 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.29 -10000 0 -1.1 6 6
ALOX12B -0.21 0.28 -10000 0 -1 6 6
CXCL1 -0.28 0.3 -10000 0 -1.1 6 6
T cell proliferation -0.23 0.31 -10000 0 -1.2 6 6
NFKBIA 0.028 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -0.56 4 4
PI3K -0.2 0.3 -10000 0 -1.1 6 6
IFNG -0.021 0.04 0.14 3 -0.11 2 5
STAT3 (dimer) -0.18 0.3 -10000 0 -1.1 6 6
IL18R1 0.03 0.044 -10000 0 -0.51 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.2 -10000 0 -0.8 4 4
IL18/IL18R -0.056 0.19 -10000 0 -0.35 38 38
macrophage activation -0.019 0.015 -10000 0 -0.045 2 2
TNF -0.25 0.3 -10000 0 -1.1 6 6
STAT3/STAT4 -0.21 0.3 -10000 0 -1.1 6 6
STAT4 (dimer) -0.22 0.31 -10000 0 -1.2 6 6
IL18 -0.018 0.16 -10000 0 -0.5 14 14
IL19 -0.21 0.28 -10000 0 -1.1 5 5
STAT5A (dimer) -0.22 0.31 -10000 0 -1.2 6 6
STAT1 0.001 0.1 -10000 0 -0.32 14 14
SOCS3 0.008 0.088 -10000 0 -0.32 10 10
CXCL9 -0.28 0.37 -10000 0 -1.2 14 14
MPO -0.22 0.28 -10000 0 -1.1 5 5
positive regulation of humoral immune response -0.23 0.31 -10000 0 -1.2 6 6
IL23/IL23R/JAK2/TYK2 -0.24 0.32 -10000 0 -1.3 6 6
IL6 -0.26 0.31 -10000 0 -1.2 5 5
STAT5A 0.033 0.005 -10000 0 -10000 0 0
IL2 0.032 0.014 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.014 0.081 4 -10000 0 4
CD3E -0.21 0.28 -10000 0 -1 6 6
keratinocyte proliferation -0.23 0.31 -10000 0 -1.2 6 6
NOS2 -0.21 0.28 -10000 0 -1 6 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.01 0.071 -10000 0 -0.39 1 1
VEGFR1 homodimer/NRP1 -0.004 0.064 -10000 0 -0.39 1 1
mol:DAG 0.011 0.078 -10000 0 -0.35 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.003 0.081 -10000 0 -0.42 2 2
CaM/Ca2+ 0.025 0.081 -10000 0 -0.33 2 2
HIF1A 0.024 0.059 -10000 0 -0.46 1 1
GAB1 0.03 0.045 -10000 0 -0.51 1 1
AKT1 0.045 0.095 -10000 0 -10000 0 0
PLCG1 0.011 0.079 -10000 0 -0.35 2 2
NOS3 0.09 0.12 0.31 24 -10000 0 24
CBL 0.033 0.005 -10000 0 -10000 0 0
mol:NO 0.09 0.12 0.3 24 -10000 0 24
FLT1 -0.003 0.077 -10000 0 -0.37 2 2
PGF 0.018 0.064 -10000 0 -0.32 5 5
VEGFR1 homodimer/NRP2/VEGFR121 0.015 0.095 -10000 0 -0.49 2 2
CALM1 0.029 0.012 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.1 0.13 0.31 23 -0.38 1 24
endothelial cell proliferation 0.09 0.14 0.34 24 -10000 0 24
mol:Ca2+ 0.011 0.078 -10000 0 -0.35 2 2
MAPK3 0.019 0.1 0.35 5 -0.37 2 7
MAPK1 0.02 0.096 0.35 5 -0.31 2 7
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.018 0.063 -10000 0 -0.32 5 5
PRKACA 0.033 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.05 -10000 0 -0.32 3 3
VEGFA homodimer -0.003 0.11 -10000 0 -0.32 15 15
VEGFR1 homodimer/VEGFA homodimer 0.003 0.09 -10000 0 -0.46 2 2
platelet activating factor biosynthetic process 0.072 0.15 0.34 21 -0.41 1 22
PI3K 0.072 0.1 -10000 0 -0.33 2 2
PRKCA 0.025 0.1 0.36 5 -0.32 2 7
PRKCB 0.022 0.099 0.36 5 -0.32 2 7
VEGFR1 homodimer/PLGF homodimer 0.006 0.08 -10000 0 -0.38 2 2
VEGFA -0.003 0.11 -10000 0 -0.32 15 15
VEGFB 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.078 -10000 0 -0.35 2 2
RASA1 0.045 0.11 -10000 0 -0.36 1 1
NRP2 0.032 0.029 -10000 0 -0.32 1 1
VEGFR1 homodimer -0.003 0.077 -10000 0 -0.37 2 2
VEGFB homodimer 0.033 0.005 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.096 0.13 0.3 21 -0.4 1 22
PTPN11 0.031 0.029 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 0.028 0.081 -10000 0 -0.33 2 2
mol:L-citrulline 0.09 0.12 0.3 24 -10000 0 24
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.064 0.11 -10000 0 -0.4 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.015 0.089 -10000 0 -0.42 2 2
CD2AP 0.03 0.045 -10000 0 -0.51 1 1
PI3K/GAB1 0.079 0.11 -10000 0 -0.32 1 1
PDPK1 0.045 0.1 -10000 0 -0.32 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.016 0.089 -10000 0 -0.42 2 2
mol:NADP 0.09 0.12 0.3 24 -10000 0 24
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.023 0.092 -10000 0 -0.4 2 2
VEGFR1 homodimer/NRP2 0.01 0.077 -10000 0 -0.54 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.033 0.005 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.033 0.005 -9999 0 -10000 0 0
TCEB1 0.029 0.012 -9999 0 -10000 0 0
HIF1A/p53 -0.014 0.093 -9999 0 -0.42 4 4
HIF1A -0.025 0.091 -9999 0 -0.36 8 8
COPS5 0.029 0.012 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.078 0.043 -9999 0 -10000 0 0
FIH (dimer) 0.032 0.008 -9999 0 -10000 0 0
CDKN2A -0.081 0.16 -9999 0 -0.32 48 48
ARNT/IPAS 0.048 0.011 -9999 0 -10000 0 0
HIF1AN 0.032 0.008 -9999 0 -10000 0 0
GNB2L1 0.033 0.004 -9999 0 -10000 0 0
HIF1A/ARNT -0.02 0.095 -9999 0 -0.43 4 4
CUL2 0.034 0.003 -9999 0 -10000 0 0
OS9 0.034 0.003 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.057 0.026 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.011 0.092 -9999 0 -0.42 4 4
PHD1-3/OS9 -0.032 0.16 -9999 0 -0.28 37 37
HIF1A/RACK1/Elongin B/Elongin C 0.005 0.099 -9999 0 -0.41 4 4
VHL 0.033 0.005 -9999 0 -10000 0 0
HSP90AA1 0.03 0.011 -9999 0 -10000 0 0
HIF1A/JAB1 -0.017 0.093 -9999 0 -0.43 4 4
EGLN3 -0.12 0.24 -9999 0 -0.51 40 40
EGLN2 0.033 0.005 -9999 0 -10000 0 0
EGLN1 0.032 0.008 -9999 0 -10000 0 0
TP53 0.015 0.064 -9999 0 -0.32 5 5
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.096 -9999 0 -0.52 4 4
ARNT 0.033 0.006 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.032 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF -0.068 0.11 -9999 0 -0.44 5 5
Sphingosine 1-phosphate (S1P) pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.03 0.045 -10000 0 -0.51 1 1
SPHK1 -0.022 0.13 -10000 0 -0.32 23 23
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
mol:S1P -0.006 0.057 0.16 1 -0.25 3 4
GNAO1 0.034 0 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.02 0.094 -10000 0 -0.23 23 23
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.02 0.059 -10000 0 -0.28 1 1
GNAI3 0.032 0.007 -10000 0 -10000 0 0
G12/G13 0.043 0.018 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.011 0.048 -10000 0 -0.25 2 2
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.03 0.17 -10000 0 -0.51 17 17
S1P/S1P5/G12 0.006 0.054 -10000 0 -0.3 1 1
S1P/S1P3/Gq -0.013 0.1 -10000 0 -0.29 14 14
S1P/S1P4/Gi -0.013 0.11 -10000 0 -0.33 7 7
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.023 0.057 -10000 0 -0.32 4 4
GNA12 0.03 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -10000 0 0
GNA11 0 0.13 -10000 0 -0.51 9 9
ABCC1 -0.002 0.11 -10000 0 -0.32 15 15
Cellular roles of Anthrax toxin

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
ANTXR1 0.015 0.079 -10000 0 -0.32 8 8
ANTXR2 0.029 0.045 -10000 0 -0.51 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.068 1 1
monocyte activation -0.001 0.1 -10000 0 -0.33 12 12
MAP2K2 0.004 0.096 -10000 0 -0.57 4 4
MAP2K1 -0.003 0.009 -10000 0 -10000 0 0
MAP2K7 -0.003 0.009 -10000 0 -10000 0 0
MAP2K6 -0.024 0.074 -10000 0 -0.27 12 12
CYAA -0.012 0.039 -10000 0 -0.27 1 1
MAP2K4 -0.002 0.009 -10000 0 -10000 0 0
IL1B -0.051 0.072 -10000 0 -0.19 10 10
Channel 0.029 0.053 -10000 0 -0.17 9 9
NLRP1 -0.004 0.015 -10000 0 -0.15 1 1
CALM1 0.029 0.012 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.04 0.14 -10000 0 -0.39 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.068 1 -10000 0 1
MAPK3 -0.007 0.032 -10000 0 -0.27 2 2
MAPK1 -0.003 0.009 -10000 0 -10000 0 0
PGR -0.003 0.009 -10000 0 -10000 0 0
PA/Cellular Receptors 0.03 0.058 -10000 0 -0.19 9 9
apoptosis -0.002 0.01 -10000 0 -0.068 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.048 -10000 0 -0.27 1 1
macrophage activation -0.007 0.03 -10000 0 -0.26 2 2
TNF 0.034 0.003 -10000 0 -10000 0 0
VCAM1 -0.002 0.1 -10000 0 -0.34 12 12
platelet activation -0.04 0.14 -10000 0 -0.39 20 20
MAPKKK cascade 0.006 0.024 0.1 1 -10000 0 1
IL18 -0.028 0.078 -10000 0 -0.26 14 14
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.068 1 1
LEF -0.002 0.01 -10000 0 -0.069 1 1
CASP1 -0.004 0.02 -10000 0 -10000 0 0
mol:cAMP -0.041 0.14 -10000 0 -0.39 20 20
necrosis -0.002 0.01 -10000 0 -0.068 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.029 0.05 -10000 0 -0.16 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.044 0.07 -10000 0 -10000 0 0
PTP1B/AKT1 0.009 0.084 -10000 0 -0.29 3 3
FYN 0.031 0.029 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.002 0.091 0.23 1 -0.29 4 5
EGFR 0.01 0.079 -10000 0 -0.52 3 3
EGF/EGFR -0.044 0.15 -10000 0 -0.32 23 23
CSF1 0.032 0.007 -10000 0 -10000 0 0
AKT1 0.03 0.011 -10000 0 -10000 0 0
INSR 0.023 0.077 -10000 0 -0.51 3 3
PTP1B/N-cadherin 0.001 0.086 0.23 1 -0.31 2 3
Insulin Receptor/Insulin 0.031 0.093 -10000 0 -0.35 3 3
HCK -0.003 0.1 -10000 0 -0.51 6 6
CRK 0.027 0.014 -10000 0 -10000 0 0
TYK2 0.003 0.091 0.27 2 -0.32 2 4
EGF -0.11 0.23 -10000 0 -0.44 45 45
YES1 0.027 0.014 -10000 0 -10000 0 0
CAV1 0.012 0.12 0.28 3 -0.34 2 5
TXN 0.032 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.024 0.099 -10000 0 -0.31 2 2
cell migration -0.002 0.091 0.29 4 -0.23 1 5
STAT3 0.033 0.005 -10000 0 -10000 0 0
PRLR 0.033 0.03 -10000 0 -0.31 1 1
ITGA2B 0.032 0.007 -10000 0 -10000 0 0
CSF1R 0.033 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.053 0.034 -10000 0 -10000 0 0
FGR 0.03 0.01 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.011 0.093 0.23 1 -0.31 2 3
Crk/p130 Cas 0.015 0.089 -10000 0 -0.3 2 2
DOK1 0.01 0.085 -10000 0 -0.3 3 3
JAK2 0.03 0.072 -10000 0 -10000 0 0
Jak2/Leptin Receptor/Leptin 0.022 0.11 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
PTPN1 0.002 0.091 0.23 1 -0.29 4 5
LYN 0.029 0.012 -10000 0 -10000 0 0
CDH2 0.016 0.054 -10000 0 -0.34 3 3
SRC 0.021 0.086 -10000 0 -0.37 3 3
ITGB3 0.032 0.007 -10000 0 -10000 0 0
CAT1/PTP1B 0.018 0.18 0.28 10 -0.52 7 17
CAPN1 0.032 0.005 -10000 0 -10000 0 0
CSK 0.032 0.009 -10000 0 -10000 0 0
PI3K 0.044 0.092 -10000 0 -0.35 2 2
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.1 -10000 0 -10000 0 0
negative regulation of transcription 0.03 0.071 -10000 0 -10000 0 0
FCGR2A 0.009 0.088 -10000 0 -0.32 10 10
FER 0.02 0.063 -10000 0 -0.32 5 5
alphaIIb/beta3 Integrin 0.046 0.01 -10000 0 -10000 0 0
BLK -0.04 0.18 -10000 0 -0.51 18 18
Insulin Receptor/Insulin/Shc 0.055 0.057 -10000 0 -0.32 3 3
RHOA 0.032 0.004 -10000 0 -10000 0 0
LEPR 0.032 0.007 -10000 0 -10000 0 0
BCAR1 0.033 0.004 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.007 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.037 0.22 0.24 1 -0.53 16 17
PRL 0.035 0.029 -10000 0 -0.31 1 1
SOCS3 -0.024 0.2 -10000 0 -1.1 5 5
SPRY2 0.017 0.054 -10000 0 -0.42 2 2
Insulin Receptor/Insulin/IRS1 0.052 0.065 -10000 0 -0.32 3 3
CSF1/CSF1R 0.028 0.096 -10000 0 -0.3 2 2
Ras protein signal transduction 0.001 0.061 0.46 2 -10000 0 2
IRS1 0.026 0.05 -10000 0 -0.32 3 3
INS 0.032 0.008 -10000 0 -10000 0 0
LEP 0.025 0.063 -10000 0 -0.51 2 2
STAT5B 0.02 0.083 0.22 1 -0.31 2 3
STAT5A 0.02 0.083 0.22 1 -0.31 2 3
GRB2 0.032 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.093 0.23 1 -0.32 2 3
CSN2 0.026 0.042 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
LAT 0.026 0.077 -10000 0 -0.53 2 2
YBX1 0.042 0.01 -10000 0 -10000 0 0
LCK 0.029 0.03 -10000 0 -0.32 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
NOX4 -0.28 0.11 -10000 0 -0.32 132 132
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.004 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.046 0.024 -9999 0 -0.22 1 1
PTK2 0.006 0.11 -9999 0 -0.39 9 9
positive regulation of JNK cascade 0.02 0.1 -9999 0 -0.36 1 1
CDC42/GDP 0.055 0.14 -9999 0 -0.41 1 1
Rac1/GDP 0.05 0.14 -9999 0 -0.4 1 1
RAP1B 0.034 0.003 -9999 0 -10000 0 0
RAP1A 0.032 0.008 -9999 0 -10000 0 0
CTNNB1 0.029 0.041 -9999 0 -0.32 2 2
CDC42/GTP 0.043 0.13 -9999 0 -0.45 1 1
nectin-3/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
RAPGEF1 0.024 0.13 -9999 0 -0.44 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.007 0.14 -9999 0 -0.5 4 4
PDGFB-D/PDGFRB 0.033 0.004 -9999 0 -10000 0 0
TLN1 -0.004 0.05 -9999 0 -0.38 1 1
Rap1/GTP 0.015 0.095 -9999 0 -0.32 4 4
IQGAP1 0.032 0.009 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.06 0.018 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
PVR 0.033 0.004 -9999 0 -10000 0 0
Necl-5(dimer) 0.033 0.004 -9999 0 -10000 0 0
mol:GDP 0.044 0.15 -9999 0 -0.48 5 5
MLLT4 0.033 0.005 -9999 0 -10000 0 0
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
PI3K 0.073 0.09 -9999 0 -0.27 9 9
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.048 0.01 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0.024 0.11 -9999 0 -10000 0 0
PVRL1 0.033 0.005 -9999 0 -10000 0 0
PVRL3 0 0.13 -9999 0 -0.51 9 9
PVRL2 0.033 0.004 -9999 0 -10000 0 0
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
CDH1 0.019 0.088 -9999 0 -0.51 4 4
CLDN1 -0.3 0.067 -9999 0 -0.32 142 142
JAM-A/CLDN1 -0.16 0.082 -9999 0 -0.41 9 9
SRC -0.008 0.14 -9999 0 -0.53 5 5
ITGB3 0.032 0.007 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.048 0.01 -9999 0 -10000 0 0
FARP2 0.042 0.16 -9999 0 -0.68 1 1
RAC1 0.03 0.01 -9999 0 -10000 0 0
CTNNA1 0.033 0.004 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.042 0.092 -9999 0 -0.31 9 9
nectin-1/I-afadin 0.048 0.01 -9999 0 -10000 0 0
nectin-2/I-afadin 0.049 0.009 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.017 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.042 0.092 -9999 0 -0.31 9 9
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.016 -9999 0 -10000 0 0
F11R 0.033 0.006 -9999 0 -10000 0 0
positive regulation of filopodium formation 0.02 0.1 -9999 0 -0.36 1 1
alphaV/beta3 Integrin/Talin 0.004 0.085 -9999 0 -0.36 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.049 0.009 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.049 0.009 -9999 0 -10000 0 0
PIP5K1C -0.002 0.054 -9999 0 -0.41 1 1
VAV2 0.038 0.16 -9999 0 -10000 0 0
RAP1/GDP 0.06 0.13 -9999 0 -10000 0 0
ITGAV 0.031 0.029 -9999 0 -0.32 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.042 0.092 -9999 0 -0.31 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
Rac1/GTP 0.032 0.13 -9999 0 -10000 0 0
PTPRM 0.001 0.061 -9999 0 -0.22 9 9
E-cadherin/beta catenin/alpha catenin 0.082 0.068 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.031 0.01 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.02 0.09 -10000 0 -0.41 3 3
BAG4 0.03 0.011 -10000 0 -10000 0 0
BAD -0.003 0.056 -10000 0 -0.19 2 2
NFKBIA 0.03 0.011 -10000 0 -10000 0 0
BIRC3 0.013 0.096 -10000 0 -0.44 6 6
BAX -0.005 0.059 -10000 0 -0.2 3 3
EnzymeConsortium:3.1.4.12 0.01 0.021 -10000 0 -0.1 1 1
IKBKB 0.033 0.095 -10000 0 -0.39 3 3
MAP2K2 0.003 0.056 0.21 3 -10000 0 3
MAP2K1 0.004 0.055 0.21 3 -10000 0 3
SMPD1 -0.033 0.098 -10000 0 -0.22 32 32
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.031 0.087 -10000 0 -0.52 1 1
MAP2K4 0 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.026 0.089 -10000 0 -0.4 3 3
EnzymeConsortium:2.7.1.37 0.005 0.057 0.22 3 -10000 0 3
response to UV 0 0 0.002 3 -10000 0 3
RAF1 0.003 0.059 0.22 3 -10000 0 3
CRADD 0.03 0.045 -10000 0 -0.51 1 1
mol:ceramide -0.004 0.059 -10000 0 -0.18 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.015 -10000 0 -10000 0 0
MADD 0.033 0.006 -10000 0 -10000 0 0
MAP3K1 -0.003 0.056 -10000 0 -0.18 2 2
TRADD 0.034 0.001 -10000 0 -10000 0 0
RELA/p50 0.033 0.005 -10000 0 -10000 0 0
MAPK3 0.007 0.059 0.21 3 -10000 0 3
MAPK1 0.003 0.064 0.22 2 -0.25 1 3
p50/RELA/I-kappa-B-alpha 0.044 0.016 -10000 0 -10000 0 0
FADD 0.026 0.079 -10000 0 -0.48 1 1
KSR1 0 0.06 0.23 2 -0.19 2 4
MAPK8 -0.003 0.049 -10000 0 -10000 0 0
TRAF2 0.033 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.018 0.085 -10000 0 -0.41 2 2
TNF R/SODD 0.043 0.018 -10000 0 -10000 0 0
TNF 0.034 0.003 -10000 0 -10000 0 0
CYCS 0.063 0.08 0.17 20 -0.17 1 21
IKBKG 0.021 0.087 -10000 0 -0.42 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.086 -10000 0 -0.42 2 2
RELA 0.033 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.003 -10000 0 -10000 0 0
AIFM1 0.058 0.076 0.16 13 -0.17 1 14
TNF/TNF R/SODD 0.059 0.024 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.029 0.12 -10000 0 -0.7 4 4
NSMAF 0.047 0.1 0.26 3 -0.48 1 4
response to hydrogen peroxide 0 0 0.002 3 -10000 0 3
BCL2 -0.17 0.25 -10000 0 -0.51 53 53
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.017 -10000 0 -10000 0 0
NFATC1 -0.019 0.14 0.25 1 -0.39 11 12
NFATC2 0.043 0.047 0.16 1 -10000 0 1
NFATC3 0.015 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.005 0.068 -10000 0 -0.26 3 3
Exportin 1/Ran/NUP214 0.068 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.042 0.072 -10000 0 -10000 0 0
BCL2/BAX -0.15 0.18 -10000 0 -0.37 54 54
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.01 -10000 0 -10000 0 0
BAX 0.031 0.029 -10000 0 -0.32 1 1
MAPK14 0.034 0.003 -10000 0 -10000 0 0
BAD 0.033 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.021 0.071 -10000 0 -0.25 3 3
Calcineurin A alpha-beta B1/BCL2 -0.17 0.25 -10000 0 -0.51 53 53
FKBP8 0.033 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.021 0.07 0.25 3 -10000 0 3
KPNB1 0.023 0.057 -10000 0 -0.32 4 4
KPNA2 0.011 0.084 -10000 0 -0.32 9 9
XPO1 0.034 0 -10000 0 -10000 0 0
SFN 0.026 0.045 -10000 0 -0.51 1 1
MAP3K8 0.001 0.1 -10000 0 -0.32 14 14
NFAT4/CK1 alpha 0.033 0.028 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.092 0.054 -10000 0 -10000 0 0
CABIN1 0.004 0.068 -10000 0 -0.27 3 3
CALM1 0.03 0.012 -10000 0 -10000 0 0
RAN 0.034 0.003 -10000 0 -10000 0 0
MAP3K1 0.033 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.026 0.063 -10000 0 -0.51 2 2
YWHAH 0.032 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.083 -10000 0 -0.37 6 6
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.033 0.006 -10000 0 -10000 0 0
MAPK9 0.033 0.004 -10000 0 -10000 0 0
YWHAG 0.032 0.008 -10000 0 -10000 0 0
FKBP1A 0.026 0.014 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.012 0.14 -10000 0 -0.37 7 7
PRKCH 0.023 0.063 -10000 0 -0.51 2 2
CABIN1/Cbp/p300 0.047 0.014 -10000 0 -10000 0 0
CASP3 0.032 0.009 -10000 0 -10000 0 0
PIM1 0.033 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.01 -10000 0 -10000 0 0
apoptosis -0.016 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.038 0.045 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.033 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.029 0.025 -10000 0 -10000 0 0
PRKCD 0.033 0.004 -10000 0 -10000 0 0
NUP214 0.033 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.008 -10000 0 -10000 0 0
PRKCG 0.024 0.057 -10000 0 -0.32 4 4
PRKCQ 0.024 0.057 -10000 0 -0.32 4 4
FKBP38/BCL2 -0.14 0.18 -10000 0 -0.37 53 53
EP300 0.032 0.009 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
NFATc/JNK1 -0.002 0.14 -10000 0 -0.39 8 8
CaM/Ca2+/FKBP38 0.04 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.011 -10000 0 -10000 0 0
CSNK1A1 0.018 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.039 0.017 -10000 0 -10000 0 0
NFATc/ERK1 -0.007 0.14 -10000 0 -0.4 7 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.042 0.073 -10000 0 -10000 0 0
NR4A1 0.059 0.053 -10000 0 -10000 0 0
GSK3B 0.034 0.004 -10000 0 -10000 0 0
positive T cell selection 0.015 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.037 0.036 -10000 0 -10000 0 0
RCH1/ KPNB1 0.026 0.084 -10000 0 -0.27 10 10
YWHAQ 0.034 0 -10000 0 -10000 0 0
PRKACA 0.033 0.006 -10000 0 -10000 0 0
AKAP5 0.008 0.11 -10000 0 -0.51 6 6
MEF2D 0.033 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
NFATc/p38 alpha -0.004 0.14 0.26 1 -0.37 11 12
CREBBP 0.034 0.005 -10000 0 -10000 0 0
BCL2 -0.17 0.25 -10000 0 -0.51 53 53
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.03 0.011 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.008 0.14 -10000 0 -0.4 10 10
NEF -0.019 0.058 -10000 0 -10000 0 0
NFKBIA 0.027 0.028 -10000 0 -10000 0 0
BIRC3 0.009 0.1 -10000 0 -0.56 4 4
CYCS -0.026 0.15 -10000 0 -0.46 9 9
RIPK1 0.034 0.003 -10000 0 -10000 0 0
CD247 -0.019 0.15 -10000 0 -0.62 7 7
MAP2K7 -0.001 0.16 -10000 0 -0.79 3 3
protein ubiquitination 0.036 0.056 0.22 1 -0.31 1 2
CRADD 0.03 0.045 -10000 0 -0.51 1 1
DAXX 0.033 0.004 -10000 0 -10000 0 0
FAS -0.016 0.15 -10000 0 -0.51 13 13
BID -0.039 0.15 0.2 4 -0.46 10 14
NF-kappa-B/RelA/I kappa B alpha 0.055 0.069 -10000 0 -0.28 4 4
TRADD 0.034 0 -10000 0 -10000 0 0
MAP3K5 0.033 0.005 -10000 0 -10000 0 0
CFLAR 0.034 0 -10000 0 -10000 0 0
FADD 0.033 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.055 0.069 -10000 0 -0.28 4 4
MAPK8 0 0.15 -10000 0 -0.71 3 3
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.033 0.004 -10000 0 -10000 0 0
TRAF2 0.033 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.03 0.16 0.21 5 -0.34 24 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.042 0.065 -10000 0 -0.38 2 2
CHUK 0.039 0.053 0.23 1 -0.33 1 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.06 0.11 -10000 0 -0.27 13 13
TCRz/NEF -0.033 0.16 -10000 0 -0.37 24 24
TNF 0.034 0.003 -10000 0 -10000 0 0
FASLG -0.079 0.25 -10000 0 -0.63 24 24
NFKB1 0.03 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.059 0.024 -10000 0 -10000 0 0
CASP6 0.018 0.14 -10000 0 -0.66 3 3
CASP7 -0.053 0.19 -10000 0 -0.49 14 14
RELA 0.03 0.026 -10000 0 -10000 0 0
CASP2 0.032 0.007 -10000 0 -10000 0 0
CASP3 -0.018 0.16 -10000 0 -0.53 8 8
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.018 -10000 0 -10000 0 0
CASP8 0.034 0 -10000 0 -10000 0 0
CASP9 0.031 0.01 -10000 0 -10000 0 0
MAP3K14 0.042 0.067 -10000 0 -0.38 1 1
APAF-1/Caspase 9 -0.011 0.14 -10000 0 -0.47 4 4
BCL2 -0.098 0.16 -10000 0 -0.61 4 4
EPHB forward signaling

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
Ephrin A5/EPHB2 0.032 0.05 -10000 0 -0.25 4 4
cell-cell adhesion 0.048 0.075 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.051 0.065 -10000 0 -0.26 2 2
ITSN1 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.027 0.067 -10000 0 -0.2 11 11
Ephrin B1/EPHB1 -0.031 0.11 -10000 0 -0.18 50 50
HRAS/GDP -0.041 0.11 -10000 0 -0.43 2 2
Ephrin B/EPHB1/GRB7 0.011 0.099 -10000 0 -0.26 1 1
Endophilin/SYNJ1 0.061 0.082 -10000 0 -0.25 1 1
KRAS 0.034 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.016 0.079 -10000 0 -10000 0 0
endothelial cell migration 0.012 0.08 -10000 0 -0.27 1 1
GRB2 0.032 0.007 -10000 0 -10000 0 0
GRB7 0.031 0.009 -10000 0 -10000 0 0
PAK1 0.068 0.085 -10000 0 -10000 0 0
HRAS 0.033 0.005 -10000 0 -10000 0 0
RRAS 0.069 0.086 -10000 0 -0.26 1 1
DNM1 0.024 0.057 -10000 0 -0.32 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.009 0.095 -10000 0 -0.31 1 1
lamellipodium assembly -0.048 0.075 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.021 0.057 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.06 -10000 0 -0.38 3 3
EPHB3 0.005 0.1 -10000 0 -0.35 11 11
EPHB1 -0.085 0.17 -10000 0 -0.32 50 50
EPHB4 -0.037 0.14 -10000 0 -0.32 29 29
mol:GDP -0.026 0.11 0.24 3 -0.45 2 5
Ephrin B/EPHB2 0.04 0.053 -10000 0 -0.26 2 2
Ephrin B/EPHB3 0.032 0.068 -10000 0 -0.26 3 3
JNK cascade -0.041 0.1 0.35 2 -0.31 5 7
Ephrin B/EPHB1 -0.002 0.09 -10000 0 -0.26 1 1
RAP1/GDP -0.01 0.13 0.33 2 -0.4 2 4
EFNB2 0.019 0.046 -10000 0 -0.51 1 1
EFNB3 0.027 0.014 -10000 0 -10000 0 0
EFNB1 0.034 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.014 0.093 -10000 0 -0.28 2 2
RAP1B 0.034 0.003 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.009 0.09 -10000 0 -0.31 1 1
Rap1/GTP -0.018 0.071 -10000 0 -10000 0 0
axon guidance 0.032 0.05 -10000 0 -0.24 4 4
MAPK3 0.019 0.062 -10000 0 -10000 0 0
MAPK1 0.021 0.054 -10000 0 -10000 0 0
Rac1/GDP -0.027 0.11 0.3 1 -0.41 2 3
actin cytoskeleton reorganization -0.051 0.075 -10000 0 -0.3 2 2
CDC42/GDP -0.016 0.12 0.33 2 -0.41 2 4
PI3K 0.015 0.083 -10000 0 -0.27 1 1
EFNA5 0.029 0.045 -10000 0 -0.51 1 1
Ephrin B2/EPHB4 -0.005 0.081 -10000 0 -0.18 23 23
Ephrin B/EPHB2/Intersectin/N-WASP 0.018 0.047 -10000 0 -0.32 1 1
CDC42 0.031 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.068 -10000 0 -10000 0 0
PTK2 0.11 0.22 0.59 26 -10000 0 26
MAP4K4 -0.041 0.1 0.35 2 -0.31 5 7
SRC 0.019 0.017 -10000 0 -10000 0 0
KALRN 0.033 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.043 0.037 -10000 0 -0.37 1 1
neuron projection morphogenesis -0.009 0.11 0.29 6 -10000 0 6
MAP2K1 0.018 0.051 -10000 0 -10000 0 0
WASL 0.029 0.045 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/NCK1 -0.007 0.12 -10000 0 -0.3 3 3
cell migration 0.05 0.089 0.24 1 -10000 0 1
NRAS 0.027 0.041 -10000 0 -0.32 2 2
SYNJ1 0.062 0.083 -10000 0 -0.26 1 1
PXN 0.034 0.003 -10000 0 -10000 0 0
TF 0.054 0.083 -10000 0 -10000 0 0
HRAS/GTP -0.006 0.085 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 -0.019 0.11 -10000 0 -0.3 3 3
cell adhesion mediated by integrin -0.061 0.099 0.25 1 -0.2 43 44
RAC1 0.03 0.01 -10000 0 -10000 0 0
mol:GTP -0.005 0.089 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.032 0.078 -10000 0 -0.35 2 2
RASA1 0.031 0.029 -10000 0 -0.32 1 1
RAC1-CDC42/GDP -0.02 0.11 0.3 1 -0.4 2 3
ruffle organization 0 0.14 0.36 7 -10000 0 7
NCK1 0.033 0.004 -10000 0 -10000 0 0
receptor internalization 0.052 0.085 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.052 0.063 -10000 0 -0.26 2 2
ROCK1 0.006 0.054 -10000 0 -0.28 2 2
RAS family/GDP -0.05 0.071 -10000 0 -0.35 1 1
Rac1/GTP -0.047 0.081 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.009 0.041 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.043 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.012 0.15 -10000 0 -0.51 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.014 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.022 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
MAP3K12 0.034 0.003 -10000 0 -10000 0 0
FGR 0.03 0.01 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.079 0.15 -10000 0 -0.38 22 22
PRKG1 0.033 0.005 -10000 0 -10000 0 0
DUSP8 0.026 0.063 -10000 0 -0.51 2 2
PGK/cGMP/p38 alpha -0.021 0.18 0.2 1 -0.42 16 17
apoptosis -0.076 0.14 -10000 0 -0.36 22 22
RAL/GTP 0.041 0.014 -10000 0 -10000 0 0
LYN 0.029 0.012 -10000 0 -10000 0 0
DUSP1 0 0.13 -10000 0 -0.51 9 9
PAK1 0.033 0.005 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.062 0.039 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.031 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.037 0.018 -10000 0 -10000 0 0
MAPK11 -0.006 0.19 0.3 6 -0.46 12 18
BLK -0.04 0.18 -10000 0 -0.51 18 18
HCK -0.003 0.1 -10000 0 -0.51 6 6
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
DUSP16 0.033 0.005 -10000 0 -10000 0 0
DUSP10 -0.003 0.11 -10000 0 -0.32 15 15
TRAF6/MEKK3 0.04 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.025 0.21 0.22 10 -0.47 17 27
positive regulation of innate immune response -0.02 0.22 0.32 6 -0.53 14 20
LCK 0.029 0.03 -10000 0 -0.32 1 1
p38alpha-beta/MKP7 -0.007 0.22 0.32 6 -0.5 14 20
p38alpha-beta/MKP5 -0.019 0.22 0.32 6 -0.52 14 20
PGK/cGMP 0.024 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.02 0.24 0.32 6 -0.48 20 26
CDC42 0.031 0.01 -10000 0 -10000 0 0
RALB 0.034 0 -10000 0 -10000 0 0
RALA 0.03 0.011 -10000 0 -10000 0 0
PAK3 0.034 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.039 0.013 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.015 0.082 0.45 1 -10000 0 1
IL27/IL27R/JAK1 -0.016 0.11 -10000 0 -0.46 1 1
TBX21 -0.14 0.2 -10000 0 -0.44 42 42
IL12B 0.03 0.029 -10000 0 -0.32 1 1
IL12A 0 0.042 -10000 0 -0.22 5 5
IL6ST 0.029 0.008 -10000 0 -10000 0 0
IL27RA/JAK1 0.005 0.045 -10000 0 -10000 0 0
IL27 -0.002 0.12 -10000 0 -0.48 9 9
TYK2 0.022 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.006 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.015 0.082 0.45 1 -10000 0 1
T cell proliferation during immune response 0.015 0.082 0.45 1 -10000 0 1
MAPKKK cascade -0.015 0.082 -10000 0 -0.45 1 1
STAT3 0.033 0.005 -10000 0 -10000 0 0
STAT2 0.034 0.003 -10000 0 -10000 0 0
STAT1 -0.001 0.1 -10000 0 -0.32 14 14
IL12RB1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.083 0.13 -10000 0 -0.45 3 3
IL27/IL27R/JAK2/TYK2 -0.015 0.083 -10000 0 -0.45 1 1
positive regulation of T cell mediated cytotoxicity -0.015 0.082 -10000 0 -0.45 1 1
STAT1 (dimer) -0.079 0.17 -10000 0 -0.59 2 2
JAK2 0.023 0.051 -10000 0 -0.33 3 3
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.008 0.091 -10000 0 -0.43 1 1
T cell proliferation -0.085 0.12 -10000 0 -0.46 3 3
IL12/IL12R/TYK2/JAK2 0.01 0.14 -10000 0 -0.75 4 4
IL17A -0.006 0.11 -10000 0 -10000 0 0
mast cell activation 0.015 0.082 0.45 1 -10000 0 1
IFNG -0.002 0.029 -10000 0 -10000 0 0
T cell differentiation -0.005 0.005 -10000 0 -0.02 1 1
STAT3 (dimer) -0.007 0.091 -10000 0 -0.43 1 1
STAT5A (dimer) -0.008 0.091 -10000 0 -0.43 1 1
STAT4 (dimer) -0.009 0.094 -10000 0 -0.43 1 1
STAT4 0.03 0.045 -10000 0 -0.51 1 1
T cell activation -0.007 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.007 0.072 -10000 0 -10000 0 0
GATA3 0.003 0.023 -10000 0 -10000 0 0
IL18 -0.025 0.11 -10000 0 -0.36 14 14
positive regulation of mast cell cytokine production -0.007 0.09 -10000 0 -0.42 1 1
IL27/EBI3 0.016 0.094 -10000 0 -0.35 9 9
IL27RA 0 0.044 -10000 0 -10000 0 0
IL6 -0.15 0.17 -10000 0 -0.31 79 79
STAT5A 0.033 0.005 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.008 0.017 -10000 0 -10000 0 0
IL1B -0.062 0.11 -10000 0 -0.22 47 47
EBI3 0.028 0.007 -10000 0 -10000 0 0
TNF 0.01 0.001 -10000 0 -10000 0 0
TCGA08_rtk_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
PDGFRA 0.022 0.077 -10000 0 -0.51 3 3
HRAS 0.033 0.005 -10000 0 -10000 0 0
EGFR 0.02 0.077 -10000 0 -0.51 3 3
AKT 0.052 0.068 0.27 4 -10000 0 4
FOXO3 0.033 0.005 -10000 0 -10000 0 0
AKT1 0.03 0.011 -10000 0 -10000 0 0
FOXO1 0.005 0.097 -10000 0 -0.51 5 5
AKT3 0.032 0.008 -10000 0 -10000 0 0
FOXO4 0.034 0 -10000 0 -10000 0 0
MET -0.13 0.17 -10000 0 -0.32 68 68
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
PIK3CB 0.033 0.004 -10000 0 -10000 0 0
NRAS 0.027 0.041 -10000 0 -0.32 2 2
PIK3CG 0.003 0.12 -10000 0 -0.51 8 8
PIK3R3 0.033 0.005 -10000 0 -10000 0 0
PIK3R2 0.033 0.004 -10000 0 -10000 0 0
NF1 0.032 0.007 -10000 0 -10000 0 0
RAS 0.004 0.067 0.22 4 -0.21 3 7
ERBB2 0.031 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.029 0.079 0.28 3 -0.25 1 4
PI3K 0.021 0.081 0.25 8 -0.27 1 9
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
KRAS 0.034 0.003 -10000 0 -10000 0 0
FOXO 0.066 0.07 0.25 7 -10000 0 7
AKT2 0.032 0.007 -10000 0 -10000 0 0
PTEN 0.024 0.063 -10000 0 -0.51 2 2
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.018 0.032 -10000 0 -10000 0 0
DAPP1 0.009 0.18 0.25 8 -0.52 9 17
Src family/SYK family/BLNK-LAT/BTK-ITK -0.037 0.23 0.31 1 -0.63 12 13
mol:DAG -0.02 0.11 0.2 16 -0.26 5 21
HRAS 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.033 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.061 0.085 -10000 0 -0.29 3 3
PLCG2 -0.24 0.27 -10000 0 -0.51 75 75
PLCG1 0.018 0.017 -10000 0 -10000 0 0
ARF5 0.032 0.008 -10000 0 -10000 0 0
mol:GTP -0.009 0.031 0.19 2 -10000 0 2
ARF1/GTP -0.002 0.026 0.19 2 -10000 0 2
RHOA 0.033 0.004 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
RAP1A/GTP 0.018 0.036 0.21 2 -10000 0 2
ADAP1 -0.009 0.029 0.18 2 -10000 0 2
ARAP3 -0.009 0.031 0.19 2 -10000 0 2
INPPL1 0.033 0.005 -10000 0 -10000 0 0
PREX1 0.019 0.017 -10000 0 -10000 0 0
ARHGEF6 0.026 0.063 -10000 0 -0.51 2 2
ARHGEF7 0.023 0.016 -10000 0 -10000 0 0
ARF1 0.032 0.007 -10000 0 -10000 0 0
NRAS 0.029 0.042 -10000 0 -0.32 2 2
FYN 0.031 0.029 -10000 0 -0.32 1 1
ARF6 0.03 0.01 -10000 0 -10000 0 0
FGR 0.03 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.063 0.16 4 -10000 0 4
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.032 0.008 -10000 0 -10000 0 0
ZAP70 0.034 0 -10000 0 -10000 0 0
mol:IP3 -0.011 0.082 0.16 16 -0.19 3 19
LYN 0.029 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.058 0.087 -10000 0 -0.29 3 3
RhoA/GDP 0.057 0.062 0.24 3 -10000 0 3
PDK1/Src/Hsp90 0.036 0.034 -10000 0 -10000 0 0
BLNK 0.017 0.088 -10000 0 -0.51 4 4
actin cytoskeleton reorganization 0.054 0.084 0.28 1 -0.34 1 2
SRC 0.019 0.017 -10000 0 -10000 0 0
PLEKHA2 0.004 0.027 0.21 1 -0.18 2 3
RAC1 0.03 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.06 -10000 0 -0.48 2 2
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.018 0.032 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.041 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.021 0.12 -10000 0 -0.42 7 7
BLK -0.04 0.18 -10000 0 -0.51 18 18
PDPK1 0.033 0.005 -10000 0 -10000 0 0
CYTH1 -0.009 0.029 0.18 2 -10000 0 2
HCK -0.003 0.1 -10000 0 -0.51 6 6
CYTH3 -0.009 0.029 0.18 2 -10000 0 2
CYTH2 -0.009 0.029 0.18 2 -10000 0 2
KRAS 0.035 0.005 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.032 0.19 1 -10000 0 1
SGK1 0.01 0.032 0.2 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.049 0.086 0.19 1 -0.31 3 4
SOS1 0.034 0 -10000 0 -10000 0 0
SYK 0.033 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.039 0.058 0.23 2 -10000 0 2
mol:PI-3-4-5-P3 -0.009 0.036 0.24 2 -10000 0 2
ARAP3/RAP1A/GTP 0.018 0.036 0.21 2 -10000 0 2
VAV1 -0.003 0.14 -10000 0 -0.51 10 10
mol:PI-3-4-P2 0.01 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.047 -10000 0 -10000 0 0
PLEKHA1 0.006 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.056 0.084 -10000 0 -0.29 3 3
LAT 0.031 0.029 -10000 0 -0.32 1 1
Rac1/GTP 0.009 0.061 -10000 0 -0.38 2 2
ITK -0.01 0.023 0.19 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.035 0.14 0.22 15 -0.33 9 24
LCK 0.029 0.03 -10000 0 -0.32 1 1
BTK -0.048 0.097 -10000 0 -0.26 22 22
Syndecan-4-mediated signaling events

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
PTK2 0.032 0.052 -10000 0 -10000 0 0
Syndecan-4/Syndesmos 0.1 0.12 -10000 0 -0.43 1 1
positive regulation of JNK cascade -0.071 0.15 -10000 0 -0.57 2 2
Syndecan-4/ADAM12 0.055 0.16 -10000 0 -0.45 3 3
CCL5 -0.07 0.21 -10000 0 -0.51 28 28
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
DNM2 0.033 0.005 -10000 0 -10000 0 0
ITGA5 0.027 0.049 -10000 0 -0.32 3 3
SDCBP 0.029 0.012 -10000 0 -10000 0 0
PLG 0.007 0.029 -10000 0 -10000 0 0
ADAM12 -0.12 0.17 -10000 0 -0.32 64 64
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.033 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.027 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.074 0.11 -10000 0 -0.42 1 1
Syndecan-4/CXCL12/CXCR4 -0.074 0.16 -10000 0 -0.61 2 2
Syndecan-4/Laminin alpha3 0.07 0.11 -10000 0 -0.42 1 1
MDK 0.014 0.079 -10000 0 -0.32 8 8
Syndecan-4/FZD7 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/Midkine 0.1 0.12 -10000 0 -0.43 1 1
FZD7 0.017 0.074 -10000 0 -0.32 7 7
Syndecan-4/FGFR1/FGF 0.099 0.12 -10000 0 -10000 0 0
THBS1 0.031 0.009 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.098 0.12 -10000 0 -0.42 1 1
positive regulation of MAPKKK cascade -0.071 0.15 -10000 0 -0.57 2 2
Syndecan-4/TACI 0.076 0.11 -10000 0 -0.42 1 1
CXCR4 0.012 0.084 -10000 0 -0.32 9 9
cell adhesion 0.002 0.051 0.2 3 -10000 0 3
Syndecan-4/Dynamin 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/TSP1 0.096 0.12 -10000 0 -0.42 1 1
Syndecan-4/GIPC 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/RANTES 0.058 0.15 -10000 0 -0.66 1 1
ITGB1 0.031 0.029 -10000 0 -0.32 1 1
LAMA1 0.026 0.015 -10000 0 -10000 0 0
LAMA3 0.02 0.042 -10000 0 -0.32 2 2
RAC1 0.03 0.01 -10000 0 -10000 0 0
PRKCA 0.016 0.11 0.67 4 -10000 0 4
Syndecan-4/alpha-Actinin 0.089 0.11 -10000 0 -0.43 1 1
TFPI 0.032 0.029 -10000 0 -0.32 1 1
F2 0.053 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.042 0.044 -10000 0 -0.22 4 4
positive regulation of cell adhesion 0.062 0.11 -10000 0 -10000 0 0
ACTN1 0.03 0.011 -10000 0 -10000 0 0
TNC 0.024 0.057 -10000 0 -0.32 4 4
Syndecan-4/CXCL12 -0.065 0.15 -10000 0 -0.62 2 2
FGF6 0.032 0.007 -10000 0 -10000 0 0
RHOA 0.033 0.004 -10000 0 -10000 0 0
CXCL12 -0.36 0.24 -10000 0 -0.51 107 107
TNFRSF13B 0.023 0.046 -10000 0 -0.51 1 1
FGF2 0.031 0.029 -10000 0 -0.32 1 1
FGFR1 0.03 0.011 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.013 0.072 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.052 0.13 -10000 0 -0.33 25 25
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.008 0.03 -10000 0 -10000 0 0
vasculogenesis 0.094 0.11 -10000 0 -0.41 1 1
SDC4 0.018 0.067 -10000 0 -0.45 1 1
Syndecan-4/Tenascin C 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.022 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.083 0.11 -10000 0 -10000 0 0
MMP9 0.006 0.07 -10000 0 -0.35 5 5
Rac1/GTP 0.002 0.051 0.2 3 -10000 0 3
cytoskeleton organization 0.1 0.11 -10000 0 -0.42 1 1
GIPC1 0.029 0.045 -10000 0 -0.51 1 1
Syndecan-4/TFPI 0.1 0.12 -10000 0 -0.43 1 1
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.062 0.047 -10000 0 -0.25 2 2
ER alpha/Gai/GDP/Gbeta gamma -0.012 0.14 -10000 0 -0.6 5 5
AKT1 0.019 0.16 -10000 0 -0.76 6 6
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.023 0.17 -10000 0 -0.76 6 6
mol:Ca2+ -0.015 0.12 -10000 0 -0.36 8 8
IGF1R 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.037 0.049 -10000 0 -0.25 4 4
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.02 0.16 0.72 6 -10000 0 6
RhoA/GTP 0.025 0.037 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.063 0.13 0.27 4 -0.42 3 7
regulation of stress fiber formation -0.01 0.039 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) 0.036 0.042 -10000 0 -0.3 2 2
KRAS 0.034 0.003 -10000 0 -10000 0 0
G13/GTP 0.036 0.038 -10000 0 -0.28 2 2
pseudopodium formation 0.01 0.039 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 0.031 0.044 -10000 0 -0.3 2 2
GRB2 0.032 0.007 -10000 0 -10000 0 0
GNG2 0.03 0.01 -10000 0 -10000 0 0
GNAO1 0.034 0 -10000 0 -10000 0 0
HRAS 0.033 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.008 0.14 -10000 0 -0.58 5 5
E2/ER beta (dimer) 0.022 0.008 -10000 0 -10000 0 0
mol:GDP 0.014 0.059 -10000 0 -0.38 2 2
mol:NADP 0.008 0.14 -10000 0 -0.58 5 5
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.027 0.12 -10000 0 -0.37 8 8
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
PLCB1 -0.03 0.12 -10000 0 -0.37 10 10
PLCB2 -0.017 0.1 -10000 0 -0.42 6 6
IGF1 -0.29 0.27 -10000 0 -0.51 87 87
mol:L-citrulline 0.008 0.14 -10000 0 -0.58 5 5
RHOA 0.033 0.004 -10000 0 -10000 0 0
Gai/GDP 0.017 0.12 -10000 0 -0.75 2 2
JNK cascade 0.022 0.008 -10000 0 -10000 0 0
BCAR1 0.033 0.004 -10000 0 -10000 0 0
ESR2 0.03 0.011 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 0.026 0.063 -10000 0 -0.51 2 2
Gq family/GDP/Gbeta gamma -0.036 0.18 -10000 0 -0.5 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.12 -10000 0 -0.65 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.062 0.12 0.27 4 -0.43 3 7
GNAZ 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.019 0.046 -10000 0 -0.37 2 2
STRN 0.029 0.04 -10000 0 -0.32 2 2
GNAL 0.026 0.014 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
MAPK11 0.016 0.018 -10000 0 -0.18 1 1
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNAI1 -0.03 0.17 -10000 0 -0.51 17 17
HBEGF 0.1 0.16 0.34 33 -0.4 2 35
cAMP biosynthetic process 0.026 0.035 -10000 0 -0.23 2 2
SRC 0.052 0.12 -10000 0 -0.56 1 1
PI3K 0.049 0.009 -10000 0 -10000 0 0
GNB1 0.031 0.009 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.046 0.064 -10000 0 -0.32 2 2
SOS1 0.034 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.092 0.12 -10000 0 -0.39 10 10
Gs family/GTP 0.033 0.038 -10000 0 -0.24 2 2
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.057 0.031 -10000 0 -10000 0 0
vasodilation 0.009 0.14 -10000 0 -0.55 5 5
mol:DAG -0.027 0.12 -10000 0 -0.37 8 8
Gs family/GDP/Gbeta gamma 0.02 0.053 -10000 0 -0.33 1 1
MSN 0.01 0.041 -10000 0 -10000 0 0
Gq family/GTP -0.012 0.11 -10000 0 -0.32 14 14
mol:PI-3-4-5-P3 0.024 0.16 -10000 0 -0.73 6 6
NRAS 0.027 0.041 -10000 0 -0.32 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.009 0.14 0.55 5 -10000 0 5
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.066 -10000 0 -0.36 2 2
NOS3 0.006 0.15 -10000 0 -0.61 5 5
GNA11 0 0.13 -10000 0 -0.51 9 9
MAPKKK cascade 0.044 0.14 -10000 0 -0.55 5 5
E2/ER alpha (dimer)/PELP1/Src 0.062 0.13 0.28 4 -0.42 4 8
ruffle organization 0.01 0.039 -10000 0 -10000 0 0
ROCK2 0.018 0.043 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.023 0.057 -10000 0 -0.32 4 4
GNA13 0.032 0.007 -10000 0 -10000 0 0
MMP9 0.087 0.16 0.39 29 -10000 0 29
MMP2 0.049 0.13 0.29 4 -0.45 3 7
ErbB4 signaling events

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.069 0.049 -10000 0 -10000 0 0
epithelial cell differentiation 0.06 0.061 -10000 0 -10000 0 0
ITCH 0.02 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.041 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
EGFR 0.02 0.077 -10000 0 -0.51 3 3
PRL 0.031 0.029 -10000 0 -0.32 1 1
neuron projection morphogenesis 0.051 0.056 0.29 1 -10000 0 1
PTPRZ1 0.008 0.11 -10000 0 -0.48 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.07 0.053 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.045 0.034 -10000 0 -10000 0 0
ADAM17 0.03 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4 0.022 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.071 0.039 -10000 0 -10000 0 0
NCOR1 0.026 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.058 0.039 -10000 0 -10000 0 0
GRIN2B 0.02 0.064 -10000 0 -10000 0 0
ErbB4/ErbB2/betacellulin 0.065 0.052 -10000 0 -10000 0 0
STAT1 0.001 0.1 -10000 0 -0.32 14 14
HBEGF 0.026 0.05 -10000 0 -0.32 3 3
PRLR 0.029 0.03 -10000 0 -0.32 1 1
E4ICDs/ETO2 -0.035 0.15 -10000 0 -10000 0 0
axon guidance 0.015 0.045 -10000 0 -10000 0 0
NEDD4 0.015 0.064 -10000 0 -0.32 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.044 0.033 -10000 0 -0.22 2 2
CBFA2T3 -0.16 0.26 -10000 0 -0.51 54 54
ErbB4/ErbB2/HBEGF 0.067 0.046 -10000 0 -10000 0 0
MAPK3 0.046 0.055 -10000 0 -10000 0 0
STAT1 (dimer) 0.056 0.072 -10000 0 -10000 0 0
MAPK1 0.048 0.043 -10000 0 -10000 0 0
JAK2 0.026 0.05 -10000 0 -0.32 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.038 0.035 -10000 0 -10000 0 0
NRG1 0.015 0.008 -10000 0 -10000 0 0
NRG3 0.032 0.007 -10000 0 -10000 0 0
NRG2 0.03 0.045 -10000 0 -0.51 1 1
NRG4 0.007 0.11 -10000 0 -0.48 7 7
heart development 0.015 0.045 -10000 0 -10000 0 0
neural crest cell migration 0.037 0.035 -10000 0 -10000 0 0
ERBB2 0.024 0.036 0.24 4 -10000 0 4
WWOX/E4ICDs 0.073 0.039 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.06 0.081 -10000 0 -10000 0 0
apoptosis -0.059 0.063 0.37 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.07 0.048 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.023 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.067 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.099 0.063 -10000 0 -10000 0 0
MDM2 0.02 0.03 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.025 0.026 -10000 0 -10000 0 0
STAT5A 0.037 0.058 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.049 0.054 -10000 0 -10000 0 0
DLG4 0.027 0.014 -10000 0 -10000 0 0
GRB2/SHC 0.047 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.05 0.039 -10000 0 -10000 0 0
STAT5A (dimer) 0.079 0.073 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.061 -10000 0 -10000 0 0
LRIG1 0.019 0.088 -10000 0 -0.51 4 4
EREG -0.2 0.17 -10000 0 -0.32 96 96
BTC 0.026 0.063 -10000 0 -0.51 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.015 0.045 -10000 0 -10000 0 0
ERBB4 0.022 0.026 -10000 0 -10000 0 0
STAT5B 0.033 0.005 -10000 0 -10000 0 0
YAP1 0.004 0.073 -10000 0 -0.42 4 4
GRB2 0.032 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.054 0.071 -10000 0 -10000 0 0
glial cell differentiation -0.049 0.039 -10000 0 -10000 0 0
WWOX 0.033 0.005 -10000 0 -10000 0 0
cell proliferation 0.045 0.069 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.021 0.24 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.033 0.032 -10000 0 -10000 0 0
CDKN1B 0.037 0.087 0.28 1 -0.63 1 2
CDKN1A 0.034 0.089 -10000 0 -0.63 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.042 -10000 0 -0.32 2 2
FOXO3 0.041 0.068 0.28 1 -10000 0 1
AKT1 0.025 0.085 -10000 0 -0.66 1 1
BAD 0.033 0.005 -10000 0 -10000 0 0
AKT3 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.034 0.089 -10000 0 -0.63 1 1
AKT1/ASK1 0.046 0.11 -10000 0 -0.6 1 1
BAD/YWHAZ 0.054 0.028 -10000 0 -10000 0 0
RICTOR 0.032 0.009 -10000 0 -10000 0 0
RAF1 0.033 0.005 -10000 0 -10000 0 0
JNK cascade -0.044 0.11 0.57 1 -10000 0 1
TSC1 0.033 0.089 -10000 0 -0.63 1 1
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
AKT1/RAF1 0.051 0.12 -10000 0 -0.63 1 1
EP300 0.032 0.009 -10000 0 -10000 0 0
mol:GDP 0.027 0.085 -10000 0 -0.65 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.034 0.089 -10000 0 -0.63 1 1
YWHAQ 0.034 0 -10000 0 -10000 0 0
TBC1D4 0.082 0.11 0.24 45 -10000 0 45
MAP3K5 0.033 0.005 -10000 0 -10000 0 0
MAPKAP1 0.031 0.029 -10000 0 -0.32 1 1
negative regulation of cell cycle -0.057 0.1 0.29 3 -0.23 12 15
YWHAH 0.032 0.009 -10000 0 -10000 0 0
AKT1S1 0.037 0.086 -10000 0 -0.63 1 1
CASP9 0.033 0.081 -10000 0 -0.63 1 1
YWHAB 0.018 0.017 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.049 0.11 -10000 0 -0.6 1 1
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.036 0.034 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
AKT2/p21CIP1 0.03 0.095 -10000 0 -0.57 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.036 -10000 0 -10000 0 0
CHUK 0.039 0.066 -10000 0 -10000 0 0
BAD/BCL-XL 0.022 0.085 -10000 0 -0.59 1 1
mTORC2 0.039 0.02 -10000 0 -0.16 1 1
AKT2 0.019 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.068 0.14 0.29 10 -0.43 2 12
PDPK1 0.033 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.085 -10000 0 -0.63 1 1
MAPKKK cascade -0.05 0.11 0.61 1 -10000 0 1
MDM2/Cbp/p300 0.058 0.11 -10000 0 -0.58 1 1
TSC1/TSC2 0.031 0.086 -10000 0 -0.61 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.11 -10000 0 -0.55 1 1
glucose import 0.028 0.12 0.21 30 -0.27 10 40
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.04 0.063 0.21 2 -0.35 1 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.028 0.12 0.21 30 -0.27 10 40
GSK3A 0.038 0.087 -10000 0 -0.63 1 1
FOXO1 0.059 0.13 0.28 17 -0.63 1 18
GSK3B 0.035 0.09 -10000 0 -0.63 1 1
SFN 0.026 0.045 -10000 0 -0.51 1 1
G1/S transition of mitotic cell cycle 0.037 0.1 -10000 0 -0.61 1 1
p27Kip1/14-3-3 family 0.056 0.059 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
KPNA1 0.033 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.011 -10000 0 -10000 0 0
YWHAG 0.032 0.008 -10000 0 -10000 0 0
RHEB 0.032 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.033 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.009 0.011 -10000 0 -10000 0 0
CDKN1A -0.009 0.045 -10000 0 -0.55 1 1
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.031 0.029 -10000 0 -0.32 1 1
FOXO3 -0.007 0.004 -10000 0 -10000 0 0
FOXO1 0.005 0.097 -10000 0 -0.51 5 5
FOXO4 0.021 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.034 0.003 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.019 -10000 0 -0.22 1 1
PPARGC1A -0.2 0.27 -10000 0 -0.51 64 64
FHL2 0.032 0.029 -10000 0 -0.32 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.015 -10000 0 -10000 0 0
HIST2H4A 0.009 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.022 0.025 0.19 1 -10000 0 1
SIRT1 0.03 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.063 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.028 0.04 -10000 0 -10000 0 0
apoptosis -0.058 0.028 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.18 -10000 0 -0.31 64 64
p53/SIRT1 0.021 0.048 -10000 0 -10000 0 0
SIRT1/FOXO4 0.031 0.037 0.2 1 -0.21 1 2
FOXO1/FHL2/SIRT1 0.031 0.072 -10000 0 -0.32 5 5
HIST1H1E 0.02 0.013 -10000 0 -10000 0 0
SIRT1/p300 0.044 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.019 0.019 0.18 1 -10000 0 1
TP53 0.011 0.063 -10000 0 -0.32 5 5
KU70/SIRT1/BAX 0.059 0.029 -10000 0 -10000 0 0
CREBBP 0.033 0.005 -10000 0 -10000 0 0
MEF2D 0.033 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.047 0.013 -10000 0 -10000 0 0
ACSS2 0.002 0.054 -10000 0 -0.37 3 3
SIRT1/PCAF/MYOD 0.02 0.019 -10000 0 -0.18 1 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.01 0.089 0.31 3 -10000 0 3
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.021 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0 -10000 0 -10000 0 0
RhoA/GTP 0.011 0.091 -10000 0 -0.31 3 3
negative regulation of cAMP metabolic process -0.005 0.092 -10000 0 -0.22 18 18
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNA12 0.03 0.01 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.093 -10000 0 -0.23 18 18
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
RHOA 0.033 0.004 -10000 0 -10000 0 0
GNAI1 -0.03 0.17 -10000 0 -0.51 17 17
FoxO family signaling

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
G6PC 0.023 0.14 -10000 0 -1.4 1 1
PLK1 -0.008 0.18 -10000 0 -0.78 3 3
CDKN1B 0.054 0.14 0.34 1 -0.39 1 2
FOXO3 -0.011 0.2 -10000 0 -0.58 10 10
KAT2B 0 0.018 -10000 0 -0.052 4 4
FOXO1/SIRT1 0.042 0.097 -10000 0 -0.35 3 3
CAT -0.008 0.18 -10000 0 -0.73 3 3
CTNNB1 0.029 0.041 -10000 0 -0.32 2 2
AKT1 0.028 0.031 -10000 0 -10000 0 0
FOXO1 0.031 0.1 -10000 0 -0.37 3 3
MAPK10 0.041 0.065 0.2 15 -0.26 2 17
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.063 0.071 -10000 0 -10000 0 0
response to oxidative stress 0.004 0.018 -10000 0 -0.052 4 4
FOXO3A/SIRT1 0.03 0.16 -10000 0 -0.52 8 8
XPO1 0.034 0 -10000 0 -10000 0 0
EP300 0.033 0.012 -10000 0 -10000 0 0
BCL2L11 0.034 0.034 -10000 0 -10000 0 0
FOXO1/SKP2 0.015 0.11 -10000 0 -0.33 2 2
mol:GDP 0.004 0.018 -10000 0 -0.052 4 4
RAN 0.035 0.003 -10000 0 -10000 0 0
GADD45A 0.049 0.16 -10000 0 -0.61 5 5
YWHAQ 0.034 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.054 0.13 -10000 0 -0.47 4 4
MST1 0.006 0.087 -10000 0 -0.32 9 9
CSNK1D 0.032 0.007 -10000 0 -10000 0 0
CSNK1E 0.031 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.01 0.12 -10000 0 -0.52 2 2
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.048 0.054 0.2 11 -10000 0 11
MAPK9 0.048 0.054 0.2 11 -10000 0 11
YWHAG 0.032 0.008 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
SIRT1 0.037 0.021 -10000 0 -10000 0 0
SOD2 0.047 0.14 -10000 0 -10000 0 0
RBL2 0.036 0.14 -10000 0 -0.56 1 1
RAL/GDP 0.046 0.023 -10000 0 -10000 0 0
CHUK 0.027 0.03 -10000 0 -10000 0 0
Ran/GTP 0.028 0.003 -10000 0 -10000 0 0
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
RAL/GTP 0.049 0.024 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
FASLG -0.18 0.53 -10000 0 -1.5 22 22
SKP2 -0.025 0.13 -10000 0 -0.32 24 24
USP7 0.031 0.045 -10000 0 -0.51 1 1
IKBKB 0.025 0.03 -10000 0 -10000 0 0
CCNB1 -0.025 0.2 -10000 0 -0.87 3 3
FOXO1-3a-4/beta catenin 0.062 0.15 0.34 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.11 -10000 0 -0.32 2 2
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
SGK1 0 0.018 -10000 0 -0.052 4 4
CSNK1G3 0.033 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.05 0.005 -10000 0 -10000 0 0
ZFAND5 0.06 0.067 -10000 0 -10000 0 0
SFN 0.026 0.045 -10000 0 -0.51 1 1
CDK2 -0.012 0.12 -10000 0 -0.31 20 20
FOXO3A/14-3-3 -0.007 0.12 -10000 0 -0.66 2 2
CREBBP 0.035 0.012 -10000 0 -10000 0 0
FBXO32 -0.026 0.37 -10000 0 -1.4 9 9
BCL6 0.035 0.14 -10000 0 -10000 0 0
RALB 0.035 0.001 -10000 0 -10000 0 0
RALA 0.031 0.011 -10000 0 -10000 0 0
YWHAH 0.032 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.019 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.005 0.022 -10000 0 -10000 0 0
MAPK12 -0.03 0.091 0.21 2 -0.29 11 13
CCND1 -0.009 0.047 -10000 0 -10000 0 0
p38 gamma/SNTA1 -0.013 0.086 -10000 0 -0.28 11 11
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
PKN1 0.031 0.029 -10000 0 -0.32 1 1
G2/M transition checkpoint -0.032 0.092 0.21 2 -0.29 12 14
MAP2K6 -0.027 0.097 0.24 2 -0.3 13 15
MAPT -0.007 0.055 0.21 1 -0.26 2 3
MAPK13 0.017 0.008 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.006 0.057 -10000 0 -0.28 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.042 0.12 -10000 0 -10000 0 0
MKNK1 0.033 0.005 -10000 0 -10000 0 0
MAPK14 -0.005 0.07 -10000 0 -10000 0 0
ATF2/c-Jun -0.007 0.071 -10000 0 -0.43 1 1
MAPK11 -0.007 0.071 -10000 0 -0.3 1 1
MITF -0.006 0.065 -10000 0 -0.27 1 1
MAPKAPK5 -0.007 0.067 -10000 0 -0.27 1 1
KRT8 -0.01 0.073 -10000 0 -0.29 3 3
MAPKAPK3 0.033 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.033 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.007 0.092 -10000 0 -10000 0 0
CEBPB -0.003 0.052 -10000 0 -10000 0 0
SLC9A1 -0.009 0.066 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.006 0.07 -10000 0 -0.32 1 1
p38alpha-beta/MNK1 0.01 0.084 -10000 0 -10000 0 0
JUN -0.009 0.069 -10000 0 -0.42 1 1
PPARGC1A -0.16 0.19 -10000 0 -0.36 65 65
USF1 -0.012 0.076 -10000 0 -0.27 1 1
RAB5/GDP/GDI1 0.005 0.054 -10000 0 -10000 0 0
NOS2 -0.009 0.057 -10000 0 -0.27 1 1
DDIT3 -0.008 0.067 -10000 0 -0.27 1 1
RAB5A 0.033 0.005 -10000 0 -10000 0 0
HSPB1 0.003 0.086 0.29 7 -0.26 1 8
p38alpha-beta/HBP1 0.01 0.083 -10000 0 -10000 0 0
CREB1 -0.002 0.065 -10000 0 -0.37 1 1
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.011 0.056 -10000 0 -10000 0 0
RPS6KA4 -0.004 0.061 -10000 0 -10000 0 0
PLA2G4A -0.084 0.13 -10000 0 -0.3 27 27
GDI1 -0.005 0.065 -10000 0 -0.27 1 1
TP53 -0.024 0.066 -10000 0 -10000 0 0
RPS6KA5 -0.011 0.071 -10000 0 -0.34 2 2
ESR1 -0.01 0.072 -10000 0 -0.28 2 2
HBP1 0.032 0.008 -10000 0 -10000 0 0
MEF2C -0.037 0.12 -10000 0 -0.33 15 15
MEF2A -0.006 0.065 -10000 0 -0.27 1 1
EIF4EBP1 -0.009 0.074 -10000 0 -0.37 2 2
KRT19 -0.015 0.085 -10000 0 -0.34 5 5
ELK4 -0.005 0.069 -10000 0 -0.27 1 1
ATF6 -0.003 0.064 -10000 0 -10000 0 0
ATF1 -0.002 0.065 -10000 0 -0.37 1 1
p38alpha-beta/MAPKAPK2 0.015 0.082 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.011 0.085 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.002 0.048 0.22 1 -0.22 6 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.049 0.009 -10000 0 -10000 0 0
STXBP1 0.017 0.074 -10000 0 -0.32 7 7
ACh/CHRNA1 0.021 0.039 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.064 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.033 0.005 -10000 0 -10000 0 0
mol:ACh 0.005 0.044 0.097 7 -0.11 5 12
RAB3GAP2 0.033 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.075 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.021 0.039 -10000 0 -10000 0 0
UNC13B 0.033 0.004 -10000 0 -10000 0 0
CHRNA1 0.034 0.003 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.01 0.081 -10000 0 -0.2 17 17
SNAP25 0.006 0.003 -10000 0 -10000 0 0
VAMP2 0.006 0.003 -10000 0 -10000 0 0
SYT1 -0.019 0.12 -10000 0 -0.32 22 22
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.061 0.18 1 -0.18 13 14
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.075 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.008 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.054 0.029 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.018 0.018 -10000 0 -10000 0 0
GNAO1 0.034 0 -10000 0 -10000 0 0
HRAS 0.033 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.018 0.009 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.009 0.003 -10000 0 -10000 0 0
MAP2K1 0.067 0.085 0.22 1 -10000 0 1
T-DHT/AR 0.023 0.02 -10000 0 -0.22 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 14 14
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNAI1 -0.03 0.17 -10000 0 -0.51 17 17
mol:GDP 0.007 0.007 -10000 0 -10000 0 0
cell proliferation 0.046 0.14 -10000 0 -0.41 5 5
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
FOS -0.003 0.24 -10000 0 -0.8 12 12
mol:Ca2+ -0.004 0.025 -10000 0 -0.064 17 17
MAPK3 0.058 0.11 0.31 1 -10000 0 1
MAPK1 0.021 0.11 -10000 0 -0.39 5 5
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 14 14
cAMP biosynthetic process 0.003 0.02 -10000 0 -10000 0 0
GNG2 0.03 0.01 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 14 14
HRAS/GTP 0.031 0.036 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.042 0.022 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 14 14
PI3K 0.044 0.008 -10000 0 -10000 0 0
apoptosis -0.038 0.13 0.36 11 -10000 0 11
T-DHT/AR/PELP1 0.035 0.024 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.021 -10000 0 -10000 0 0
CREB1 0.038 0.14 -10000 0 -0.4 9 9
RAC1-CDC42/GTP 0.052 0.027 -10000 0 -10000 0 0
AR 0.031 0.029 -10000 0 -0.32 1 1
GNB1 0.031 0.009 -10000 0 -10000 0 0
RAF1 0.08 0.085 0.23 1 -10000 0 1
RAC1-CDC42/GDP 0.065 0.046 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.032 0.033 -10000 0 -10000 0 0
MAP2K2 0.069 0.086 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.018 0.019 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
SHBG 0.027 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.008 0.094 -10000 0 -0.48 2 2
mol:T-DHT 0 0.001 -10000 0 -0.004 11 11
RAC1 0.03 0.01 -10000 0 -10000 0 0
GNRH1 0.008 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.007 0.089 -10000 0 -0.28 5 5
CDC42 0.031 0.01 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.004 0.1 -10000 0 -0.48 2 2
epithelial cell differentiation 0.058 0.062 -10000 0 -0.27 4 4
CYFIP2 0.022 0.077 -10000 0 -0.51 3 3
ENAH -0.012 0.049 -10000 0 -10000 0 0
EGFR 0.02 0.077 -10000 0 -0.51 3 3
EPHA2 0.014 0.074 -10000 0 -0.32 7 7
MYO6 0.011 0.049 -10000 0 -10000 0 0
CTNNB1 0.029 0.041 -10000 0 -0.32 2 2
ABI1/Sra1/Nap1 0.058 0.058 -10000 0 -0.31 3 3
AQP5 0.007 0.05 -10000 0 -10000 0 0
CTNND1 0.033 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.048 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.068 -10000 0 -10000 0 0
EGF -0.11 0.22 -10000 0 -0.44 45 45
NCKAP1 0.032 0.029 -10000 0 -0.32 1 1
AQP3 0.009 0.052 -10000 0 -10000 0 0
cortical microtubule organization 0.058 0.062 -10000 0 -0.27 4 4
GO:0000145 -0.012 0.042 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.064 0.064 -10000 0 -0.27 4 4
MLLT4 0.033 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.056 -10000 0 -0.35 2 2
ARF6 0.03 0.01 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.059 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.005 0.043 -10000 0 -10000 0 0
PVRL2 0.033 0.004 -10000 0 -10000 0 0
ZYX 0.009 0.05 -10000 0 -10000 0 0
ARF6/GTP 0.064 0.062 -10000 0 -10000 0 0
CDH1 0.019 0.088 -10000 0 -0.51 4 4
EGFR/EGFR/EGF/EGF -0.035 0.14 -10000 0 -0.49 1 1
RhoA/GDP 0.06 0.06 -10000 0 -0.25 4 4
actin cytoskeleton organization 0.003 0.046 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
GIT1 0.032 0.007 -10000 0 -10000 0 0
IGF1R 0.032 0.008 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 87 87
DIAPH1 0.048 0.13 -10000 0 -0.66 3 3
Wnt receptor signaling pathway -0.058 0.062 0.27 4 -10000 0 4
RHOA 0.033 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.057 -10000 0 -0.35 2 2
CTNNA1 0.033 0.004 -10000 0 -10000 0 0
VCL 0.003 0.047 -10000 0 -10000 0 0
EFNA1 0.033 0.006 -10000 0 -10000 0 0
LPP 0 0.045 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.038 0.077 -10000 0 -0.38 2 2
SEC6/SEC8 0.009 0.045 -10000 0 -10000 0 0
MGAT3 0 0.069 -10000 0 -10000 0 0
HGF/MET -0.043 0.11 -10000 0 -0.33 2 2
HGF 0.032 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.004 0.1 -10000 0 -0.48 2 2
actin cable formation 0.014 0.071 0.25 4 -0.31 1 5
KIAA1543 -0.013 0.042 -10000 0 -10000 0 0
KIFC3 0.01 0.05 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ACTN1 0.009 0.049 -10000 0 -10000 0 0
NCK1/GIT1 0.047 0.012 -10000 0 -10000 0 0
mol:GDP 0.058 0.062 -10000 0 -0.27 4 4
EXOC4 0.032 0.007 -10000 0 -10000 0 0
STX4 0.011 0.049 -10000 0 -10000 0 0
PIP5K1C 0.01 0.049 -10000 0 -10000 0 0
LIMA1 -0.025 0.17 -10000 0 -0.51 16 16
ABI1 0.033 0.004 -10000 0 -10000 0 0
ROCK1 0.004 0.066 0.31 1 -10000 0 1
adherens junction assembly 0.006 0.05 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.13 0.16 -10000 0 -0.45 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.049 0.009 -10000 0 -10000 0 0
MET -0.13 0.17 -10000 0 -0.32 68 68
PLEKHA7 0.01 0.049 -10000 0 -10000 0 0
mol:GTP 0.059 0.058 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.022 0.068 0.33 1 -10000 0 1
cortical actin cytoskeleton stabilization -0.004 0.1 -10000 0 -0.48 2 2
regulation of cell-cell adhesion 0.003 0.046 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.004 0.1 -10000 0 -0.48 2 2
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.014 0.14 -10000 0 -0.51 11 11
CLTC -0.015 0.13 -10000 0 -0.4 14 14
calcium ion-dependent exocytosis -0.015 0.097 -10000 0 -0.32 7 7
Dynamin 2/GTP 0.03 0.02 -10000 0 -10000 0 0
EXOC4 0.032 0.007 -10000 0 -10000 0 0
CD59 -0.005 0.097 -10000 0 -0.34 10 10
CPE -0.006 0.083 -10000 0 -0.28 12 12
CTNNB1 0.029 0.041 -10000 0 -0.32 2 2
membrane fusion 0.005 0.07 -10000 0 -0.34 2 2
CTNND1 0.02 0.028 -10000 0 -10000 0 0
DNM2 0.033 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.081 -10000 0 -0.29 5 5
TSHR 0.018 0.007 -10000 0 -10000 0 0
INS 0.009 0.069 -10000 0 -0.54 2 2
BIN1 0.034 0 -10000 0 -10000 0 0
mol:Choline 0.005 0.07 -10000 0 -0.34 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.018 -10000 0 -0.18 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.03 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.02 -10000 0 -10000 0 0
JUP -0.006 0.096 -10000 0 -0.34 10 10
ASAP2/amphiphysin II 0.039 0.013 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.008 -10000 0 -10000 0 0
CDH1 -0.012 0.1 -10000 0 -0.33 12 12
clathrin-independent pinocytosis 0.022 0.008 -10000 0 -10000 0 0
MAPK8IP3 0.033 0.005 -10000 0 -10000 0 0
positive regulation of endocytosis 0.022 0.008 -10000 0 -10000 0 0
EXOC2 0.033 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.029 0.057 -10000 0 -0.31 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.011 0.12 0.33 13 -10000 0 13
positive regulation of phagocytosis 0.017 0.008 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.041 0.015 -10000 0 -10000 0 0
ACAP1 0.004 0.069 -10000 0 -0.28 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.096 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 -0.015 0.12 -10000 0 -0.34 12 12
JIP4/KLC1 0.054 0.024 -10000 0 -10000 0 0
EXOC1 0.033 0.006 -10000 0 -10000 0 0
exocyst 0.034 0.051 -10000 0 -0.31 2 2
RALA/GTP 0.022 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.04 0.016 -10000 0 -10000 0 0
receptor recycling 0.022 0.008 -10000 0 -10000 0 0
CTNNA1 0.02 0.028 -10000 0 -10000 0 0
NME1 0.016 0.018 -10000 0 -0.18 1 1
clathrin coat assembly -0.013 0.13 -10000 0 -0.39 14 14
IL2RA -0.008 0.097 -10000 0 -0.34 10 10
VAMP3 0.017 0.008 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.023 0.13 -10000 0 -0.35 9 9
EXOC6 0.032 0.008 -10000 0 -10000 0 0
PLD1 -0.029 0.11 -10000 0 -0.3 21 21
PLD2 0.015 0.011 -10000 0 -10000 0 0
EXOC5 0.03 0.011 -10000 0 -10000 0 0
PIP5K1C -0.001 0.073 -10000 0 -0.28 3 3
SDC1 -0.006 0.096 -10000 0 -0.34 10 10
ARF6/GDP 0.028 0.024 0.18 1 -0.18 1 2
EXOC7 0.032 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.012 0.13 -10000 0 -0.35 12 12
mol:Phosphatidic acid 0.005 0.07 -10000 0 -0.34 2 2
endocytosis -0.038 0.013 -10000 0 -10000 0 0
SCAMP2 0.032 0.009 -10000 0 -10000 0 0
ADRB2 -0.096 0.19 -10000 0 -0.5 17 17
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.022 -10000 0 -10000 0 0
KLC1 0.03 0.011 -10000 0 -10000 0 0
AVPR2 -0.012 0.13 -10000 0 -0.38 14 14
RALA 0.03 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.01 0.12 -10000 0 -0.39 4 4
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.01 0.11 -9999 0 -10000 0 0
RAD9A 0.033 0.005 -9999 0 -10000 0 0
AP1 0.012 0.1 -9999 0 -0.3 12 12
IFNAR2 0.033 0.008 -9999 0 -10000 0 0
AKT1 0.023 0.043 -9999 0 -0.44 1 1
ER alpha/Oestrogen 0.019