PARADIGM pathway analysis of mRNASeq expression data
Testicular Germ Cell Tumors (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1222SQ2
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 39 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXA2 and FOXA3 transcription factor networks 32
Signaling events mediated by the Hedgehog family 26
IL23-mediated signaling events 25
IL4-mediated signaling events 24
Syndecan-1-mediated signaling events 22
Ephrin A reverse signaling 22
Wnt signaling 20
Syndecan-4-mediated signaling events 18
amb2 Integrin signaling 17
Osteopontin-mediated events 16
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 150 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 150 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXA2 and FOXA3 transcription factor networks 0.2133 32 1477 46 -0.96 0.017 1000 -1000 -0.077 -1000
Signaling events mediated by the Hedgehog family 0.1733 26 1368 52 -0.39 0.24 1000 -1000 -0.097 -1000
IL23-mediated signaling events 0.1667 25 1512 60 -0.5 0.022 1000 -1000 -0.16 -1000
IL4-mediated signaling events 0.1600 24 2226 91 -0.66 0.57 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 0.1467 22 761 34 -0.31 0.011 1000 -1000 -0.078 -1000
Ephrin A reverse signaling 0.1467 22 160 7 -0.16 0 1000 -1000 -0.039 -1000
Wnt signaling 0.1333 20 146 7 -0.14 0.009 1000 -1000 -0.056 -1000
Syndecan-4-mediated signaling events 0.1200 18 1206 67 -0.3 0.042 1000 -1000 -0.11 -1000
amb2 Integrin signaling 0.1133 17 1418 82 -0.35 0.011 1000 -1000 -0.1 -1000
Osteopontin-mediated events 0.1067 16 642 38 -0.23 0.011 1000 -1000 -0.12 -1000
Glypican 1 network 0.1067 16 774 48 -0.33 0.025 1000 -1000 -0.058 -1000
Glucocorticoid receptor regulatory network 0.1067 16 1861 114 -0.7 0.3 1000 -1000 -0.078 -1000
Reelin signaling pathway 0.1067 16 899 56 -0.26 0.011 1000 -1000 -0.097 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1000 15 533 34 -0.12 0.011 1000 -1000 -0.071 -1000
Endothelins 0.1000 15 1440 96 -0.23 0.011 1000 -1000 -0.097 -1000
Calcium signaling in the CD4+ TCR pathway 0.1000 15 476 31 -0.4 0.011 1000 -1000 -0.12 -1000
E-cadherin signaling events 0.1000 15 77 5 -0.14 0.011 1000 -1000 -0.052 -1000
IL12-mediated signaling events 0.0933 14 1280 87 -0.33 0.11 1000 -1000 -0.14 -1000
p75(NTR)-mediated signaling 0.0933 14 1813 125 -0.44 0.011 1000 -1000 -0.13 -1000
Integrins in angiogenesis 0.0933 14 1204 84 -0.34 0.022 1000 -1000 -0.1 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0933 14 1058 74 -0.16 0.087 1000 -1000 -0.11 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0933 14 1126 78 -0.2 0.1 1000 -1000 -0.099 -1000
BMP receptor signaling 0.0867 13 1077 81 -0.29 0.045 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0867 13 935 68 -0.42 0.053 1000 -1000 -0.14 -1000
Signaling events regulated by Ret tyrosine kinase 0.0800 12 1062 82 -0.18 0.011 1000 -1000 -0.097 -1000
IL27-mediated signaling events 0.0800 12 615 51 -0.25 0.12 1000 -1000 -0.1 -1000
Caspase cascade in apoptosis 0.0733 11 875 74 -0.23 0.085 1000 -1000 -0.073 -1000
Noncanonical Wnt signaling pathway 0.0733 11 301 26 -0.16 0.011 1000 -1000 -0.095 -1000
TCR signaling in naïve CD8+ T cells 0.0733 11 1068 93 -0.15 0.027 1000 -1000 -0.093 -1000
IL6-mediated signaling events 0.0733 11 875 75 -0.25 0.049 1000 -1000 -0.099 -1000
LPA receptor mediated events 0.0667 10 1040 102 -0.18 0.011 1000 -1000 -0.1 -1000
IGF1 pathway 0.0600 9 527 57 -0.12 0.018 1000 -1000 -0.1 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0600 9 1164 120 -0.33 0.26 1000 -1000 -0.093 -1000
HIF-1-alpha transcription factor network 0.0533 8 618 76 -0.2 0.058 1000 -1000 -0.15 -1000
Arf6 signaling events 0.0533 8 497 62 -0.24 0.011 1000 -1000 -0.07 -1000
Nectin adhesion pathway 0.0533 8 546 63 -0.21 0.019 1000 -1000 -0.077 -1000
Nongenotropic Androgen signaling 0.0533 8 458 52 -0.13 0.021 1000 -1000 -0.069 -1000
E-cadherin signaling in the nascent adherens junction 0.0533 8 672 76 -0.14 0.011 1000 -1000 -0.1 -1000
BCR signaling pathway 0.0533 8 805 99 -0.15 0.03 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 0.0467 7 585 76 -0.58 0.023 1000 -1000 -0.059 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0467 7 415 54 -0.28 0.022 1000 -1000 -0.12 -1000
Presenilin action in Notch and Wnt signaling 0.0467 7 445 61 -0.26 0.018 1000 -1000 -0.079 -1000
IFN-gamma pathway 0.0467 7 494 68 -0.18 0.029 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 0.0467 7 262 35 -0.15 0.011 1000 -1000 -0.069 -1000
Effects of Botulinum toxin 0.0467 7 187 26 -0.1 0.011 1000 -1000 -0.068 -1000
EGFR-dependent Endothelin signaling events 0.0467 7 157 21 -0.096 0.011 1000 -1000 -0.078 -1000
Regulation of Androgen receptor activity 0.0467 7 494 70 -0.6 0.028 1000 -1000 -0.08 -1000
LPA4-mediated signaling events 0.0400 6 75 12 -0.12 0.016 1000 -1000 -0.022 -1000
ErbB4 signaling events 0.0400 6 437 69 -0.39 0.087 1000 -1000 -0.099 -1000
JNK signaling in the CD4+ TCR pathway 0.0400 6 117 17 -0.089 0.011 1000 -1000 -0.068 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0400 6 512 85 -0.14 0.011 1000 -1000 -0.083 -1000
FAS signaling pathway (CD95) 0.0400 6 328 47 -0.14 0.02 1000 -1000 -0.051 -1000
Canonical Wnt signaling pathway 0.0400 6 334 51 -0.26 0.041 1000 -1000 -0.063 -1000
Regulation of nuclear SMAD2/3 signaling 0.0333 5 753 136 -0.29 0.1 1000 -1000 -0.097 -1000
BARD1 signaling events 0.0333 5 336 57 -0.077 0.068 1000 -1000 -0.084 -1000
Visual signal transduction: Cones 0.0333 5 227 38 -0.086 0.011 1000 -1000 -0.081 -1000
Thromboxane A2 receptor signaling 0.0333 5 591 105 -0.092 0.035 1000 -1000 -0.081 -1000
Syndecan-2-mediated signaling events 0.0333 5 408 69 -0.15 0.036 1000 -1000 -0.071 -1000
a4b1 and a4b7 Integrin signaling 0.0333 5 26 5 -0.051 -0.009 1000 -1000 -0.036 -1000
Signaling events mediated by PTP1B 0.0333 5 453 76 -0.16 0.04 1000 -1000 -0.09 -1000
Fc-epsilon receptor I signaling in mast cells 0.0333 5 494 97 -0.12 0.026 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.0333 5 227 44 -0.2 0.025 1000 -1000 -0.071 -1000
Ephrin B reverse signaling 0.0333 5 281 48 -0.1 0.071 1000 -1000 -0.091 -1000
Retinoic acid receptors-mediated signaling 0.0333 5 291 58 -0.086 0.025 1000 -1000 -0.093 -1000
IL2 signaling events mediated by PI3K 0.0333 5 290 58 -0.1 0.029 1000 -1000 -0.096 -1000
Signaling mediated by p38-alpha and p38-beta 0.0333 5 242 44 -0.23 0.011 1000 -1000 -0.061 -1000
EPHB forward signaling 0.0333 5 443 85 -0.16 0.059 1000 -1000 -0.11 -1000
TCGA08_retinoblastoma 0.0333 5 43 8 -0.026 0.012 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.0333 5 307 52 -0.11 0.011 1000 -1000 -0.094 -1000
Ras signaling in the CD4+ TCR pathway 0.0333 5 89 17 -0.038 0.01 1000 -1000 -0.053 -1000
ErbB2/ErbB3 signaling events 0.0267 4 297 65 -0.077 0.026 1000 -1000 -0.078 -1000
EPO signaling pathway 0.0267 4 261 55 -0.065 0.041 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0267 4 177 37 -0.12 0.012 1000 -1000 -0.088 -1000
IL1-mediated signaling events 0.0267 4 271 62 -0.15 0.059 1000 -1000 -0.13 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0267 4 228 52 -0.1 0.019 1000 -1000 -0.08 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0267 4 223 45 -0.12 0.02 1000 -1000 -0.099 -1000
Regulation of p38-alpha and p38-beta 0.0267 4 260 54 -0.16 0.011 1000 -1000 -0.061 -1000
IL2 signaling events mediated by STAT5 0.0267 4 109 22 -0.086 0.012 1000 -1000 -0.054 -1000
Regulation of Telomerase 0.0267 4 456 102 -0.18 0.039 1000 -1000 -0.12 -1000
E-cadherin signaling in keratinocytes 0.0267 4 181 43 -0.15 0.036 1000 -1000 -0.09 -1000
Cellular roles of Anthrax toxin 0.0200 3 132 39 -0.056 0.015 1000 -1000 -0.038 -1000
Aurora A signaling 0.0200 3 201 60 -0.35 0.035 1000 -1000 -0.07 -1000
Ceramide signaling pathway 0.0200 3 292 76 -0.12 0.025 1000 -1000 -0.076 -1000
TRAIL signaling pathway 0.0200 3 178 48 -0.035 0.024 1000 -1000 -0.078 -1000
HIF-2-alpha transcription factor network 0.0200 3 141 43 -0.086 0.028 1000 -1000 -0.098 -1000
Plasma membrane estrogen receptor signaling 0.0200 3 294 86 -0.12 0.046 1000 -1000 -0.098 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0200 3 330 88 -0.19 0.081 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 0.0200 3 122 34 -0.24 0.033 1000 -1000 -0.068 -1000
FOXM1 transcription factor network 0.0200 3 169 51 -0.1 0.14 1000 -1000 -0.18 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0133 2 80 28 -0.077 0.019 1000 -1000 -0.075 -1000
PLK2 and PLK4 events 0.0133 2 8 3 -0.012 0.011 1000 -1000 -0.028 -1000
Hedgehog signaling events mediated by Gli proteins 0.0133 2 130 65 -0.26 0.05 1000 -1000 -0.075 -1000
Aurora C signaling 0.0133 2 15 7 -0.026 0.005 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class III 0.0133 2 108 40 -0.091 0.025 1000 -1000 -0.05 -1000
ceramide signaling pathway 0.0133 2 136 49 -0.059 0.028 1000 -1000 -0.063 -1000
FoxO family signaling 0.0133 2 167 64 -0.16 0.093 1000 -1000 -0.084 -1000
Paxillin-dependent events mediated by a4b1 0.0133 2 74 36 -0.051 0.022 1000 -1000 -0.083 -1000
Atypical NF-kappaB pathway 0.0133 2 62 31 -0.042 0.022 1000 -1000 -0.087 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0133 2 336 125 -0.1 0.066 1000 -1000 -0.11 -1000
TCGA08_rtk_signaling 0.0133 2 58 26 -0.054 0.037 1000 -1000 -0.023 -1000
Class I PI3K signaling events 0.0133 2 181 73 -0.16 0.026 1000 -1000 -0.087 -1000
Insulin Pathway 0.0133 2 208 74 -0.068 0.034 1000 -1000 -0.1 -1000
S1P3 pathway 0.0133 2 94 42 -0.077 0.035 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0133 2 58 20 -0.05 0.011 1000 -1000 -0.051 -1000
Class IB PI3K non-lipid kinase events 0.0133 2 6 3 0 -1000 1000 -1000 -0.018 -1000
S1P4 pathway 0.0133 2 70 25 -0.035 0.011 1000 -1000 -0.06 -1000
p38 MAPK signaling pathway 0.0133 2 113 44 -0.076 0.016 1000 -1000 -0.071 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0067 1 28 23 -0.054 0.041 1000 -1000 -0.078 -1000
Signaling events mediated by HDAC Class II 0.0067 1 75 75 -0.11 0.017 1000 -1000 -0.071 -1000
PLK1 signaling events 0.0067 1 92 85 -0.03 0.028 1000 -1000 -0.076 -1000
mTOR signaling pathway 0.0067 1 89 53 -0.022 0.024 1000 -1000 -0.074 -1000
Class I PI3K signaling events mediated by Akt 0.0067 1 87 68 -0.064 0.04 1000 -1000 -0.082 -1000
S1P5 pathway 0.0067 1 27 17 -0.021 0.018 1000 -1000 -0.06 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0067 1 98 83 -0.064 0.059 1000 -1000 -0.086 -1000
S1P1 pathway 0.0067 1 50 36 -0.027 0.026 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class I 0.0067 1 171 104 -0.11 0.046 1000 -1000 -0.088 -1000
TCGA08_p53 0.0067 1 11 7 -0.011 0.011 1000 -1000 -0.014 -1000
Glypican 2 network 0.0067 1 6 4 -0.009 0.005 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0067 1 50 33 -0.066 0.029 1000 -1000 -0.082 -1000
Aurora B signaling 0.0067 1 109 67 -0.077 0.027 1000 -1000 -0.075 -1000
Canonical NF-kappaB pathway 0.0000 0 34 39 -0.059 0.078 1000 -1000 -0.096 -1000
Circadian rhythm pathway 0.0000 0 12 22 -0.014 0.043 1000 -1000 -0.075 -1000
Arf6 downstream pathway 0.0000 0 13 43 -0.026 0.028 1000 -1000 -0.053 -1000
Insulin-mediated glucose transport 0.0000 0 25 32 -0.064 0.04 1000 -1000 -0.073 -1000
Signaling mediated by p38-gamma and p38-delta 0.0000 0 13 15 -0.007 0.032 1000 -1000 -0.04 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 -0.001 0.028 1000 -1000 -0.063 -1000
Arf6 trafficking events 0.0000 0 27 71 -0.037 0.037 1000 -1000 -0.092 -1000
VEGFR1 specific signals 0.0000 0 52 56 -0.035 0.061 1000 -1000 -0.095 -1000
PDGFR-beta signaling pathway 0.0000 0 94 97 -0.098 0.058 1000 -1000 -0.11 -1000
Arf1 pathway 0.0000 0 6 54 -0.007 0.031 1000 -1000 -0.05 -1000
Alternative NF-kappaB pathway 0.0000 0 5 13 -0.005 0.011 1000 -1000 -0.066 -1000
Total NA 863 54336 7203 -22 -990 131000 -131000 -11 -131000
FOXA2 and FOXA3 transcription factor networks

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.54 0.4 -9999 0 -0.92 60 60
PCK1 -0.32 0.22 -9999 0 -0.78 12 12
HNF4A -0.87 0.61 -9999 0 -1.3 87 87
KCNJ11 -0.51 0.42 -9999 0 -1.1 34 34
AKT1 -0.15 0.15 -9999 0 -0.42 1 1
response to starvation -0.028 0.036 -9999 0 -10000 0 0
DLK1 -0.78 0.62 -9999 0 -1.3 72 72
NKX2-1 -0.074 0.22 -9999 0 -10000 0 0
ACADM -0.54 0.4 -9999 0 -1 40 40
TAT -0.4 0.4 -9999 0 -1.2 20 20
CEBPB -0.002 0.038 -9999 0 -0.38 1 1
CEBPA -0.014 0.11 -9999 0 -0.71 3 3
TTR -0.64 0.5 -9999 0 -1 72 72
PKLR -0.57 0.44 -9999 0 -1 57 57
APOA1 -0.96 0.7 -9999 0 -1.5 86 86
CPT1C -0.55 0.41 -9999 0 -1 47 47
ALAS1 -0.21 0.21 -9999 0 -1.8 1 1
TFRC -0.37 0.28 -9999 0 -0.77 24 24
FOXF1 -0.14 0.25 -9999 0 -0.53 34 34
NF1 0.017 0.01 -9999 0 -10000 0 0
HNF1A (dimer) -0.12 0.19 -9999 0 -0.5 26 26
CPT1A -0.54 0.41 -9999 0 -0.98 48 48
HMGCS1 -0.54 0.4 -9999 0 -0.97 49 49
NR3C1 0.009 0.038 -9999 0 -10000 0 0
CPT1B -0.54 0.4 -9999 0 -0.99 44 44
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.006 0.045 -9999 0 -10000 0 0
GCK -0.54 0.4 -9999 0 -0.99 47 47
CREB1 0.007 0.022 -9999 0 -10000 0 0
IGFBP1 -0.23 0.2 -9999 0 -0.82 5 5
PDX1 -0.47 0.54 -9999 0 -1.3 37 37
UCP2 -0.54 0.41 -9999 0 -1 45 45
ALDOB -0.52 0.43 -9999 0 -1.1 32 32
AFP -0.52 0.56 -9999 0 -1.2 51 51
BDH1 -0.54 0.4 -9999 0 -1 44 44
HADH -0.51 0.42 -9999 0 -1.1 31 31
F2 -0.8 0.61 -9999 0 -1.4 66 66
HNF1A -0.12 0.19 -9999 0 -0.5 26 26
G6PC -0.26 0.48 -9999 0 -1.6 17 17
SLC2A2 -0.54 0.53 -9999 0 -1.2 43 43
INS -0.013 0.048 -9999 0 -0.4 2 2
FOXA1 -0.35 0.33 -9999 0 -0.66 64 64
FOXA3 -0.15 0.22 -9999 0 -0.73 11 11
FOXA2 -0.59 0.47 -9999 0 -1 58 58
ABCC8 -0.57 0.48 -9999 0 -1.1 51 51
ALB -0.34 0.38 -9999 0 -0.9 29 29
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.31 0.38 -10000 0 -0.79 41 41
IHH -0.26 0.36 -10000 0 -0.74 46 46
SHH Np/Cholesterol/GAS1 -0.12 0.21 -10000 0 -0.54 29 29
LRPAP1 0.011 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.12 0.21 0.54 29 -10000 0 29
SMO/beta Arrestin2 -0.2 0.24 -10000 0 -0.6 28 28
SMO -0.2 0.27 -10000 0 -0.64 29 29
AKT1 -0.076 0.12 -10000 0 -0.7 1 1
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.094 0.23 -10000 0 -0.52 30 30
ADRBK1 0.011 0 -10000 0 -10000 0 0
heart looping -0.2 0.26 -10000 0 -0.62 29 29
STIL -0.24 0.26 -10000 0 -0.75 16 16
DHH N/PTCH2 -0.063 0.18 -10000 0 -0.76 7 7
DHH N/PTCH1 -0.24 0.26 -10000 0 -0.62 36 36
PIK3CA 0.011 0 -10000 0 -10000 0 0
DHH -0.061 0.2 -10000 0 -0.53 20 20
PTHLH -0.39 0.51 -10000 0 -1.2 37 37
determination of left/right symmetry -0.2 0.26 -10000 0 -0.62 29 29
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
skeletal system development -0.39 0.5 -10000 0 -1.2 37 37
IHH N/Hhip -0.34 0.38 -10000 0 -0.75 61 61
DHH N/Hhip -0.23 0.3 -10000 0 -0.71 36 36
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.2 0.26 -10000 0 -0.62 29 29
pancreas development -0.23 0.36 -10000 0 -0.66 54 54
HHAT 0.011 0 -10000 0 -10000 0 0
PI3K -0.005 0.055 -10000 0 -0.68 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.019 0.13 -10000 0 -0.49 9 9
somite specification -0.2 0.26 -10000 0 -0.62 29 29
SHH Np/Cholesterol/PTCH1 -0.27 0.26 -10000 0 -0.64 33 33
SHH Np/Cholesterol/PTCH2 -0.11 0.21 -10000 0 -0.55 28 28
SHH Np/Cholesterol/Megalin -0.26 0.28 -10000 0 -0.6 54 54
SHH -0.11 0.27 -10000 0 -0.68 26 26
catabolic process -0.21 0.26 -10000 0 -0.61 34 34
SMO/Vitamin D3 -0.25 0.28 -10000 0 -0.82 16 16
SHH Np/Cholesterol/Hhip -0.24 0.31 -10000 0 -0.64 51 51
LRP2 -0.27 0.35 -10000 0 -0.61 67 67
receptor-mediated endocytosis -0.34 0.29 -10000 0 -0.76 35 35
SHH Np/Cholesterol/BOC -0.16 0.24 -10000 0 -0.58 34 34
SHH Np/Cholesterol/CDO -0.11 0.21 -10000 0 -0.55 27 27
mesenchymal cell differentiation 0.24 0.31 0.63 51 -10000 0 51
mol:Vitamin D3 -0.26 0.28 -10000 0 -0.64 33 33
IHH N/PTCH2 -0.18 0.25 -10000 0 -0.65 30 30
CDON 0.003 0.079 -10000 0 -0.63 2 2
IHH N/PTCH1 -0.22 0.27 -10000 0 -0.62 34 34
Megalin/LRPAP1 -0.2 0.26 -10000 0 -0.68 31 31
PTCH2 -0.006 0.11 -10000 0 -0.63 4 4
SHH Np/Cholesterol -0.1 0.21 -10000 0 -0.56 26 26
PTCH1 -0.22 0.27 -10000 0 -0.61 34 34
HHIP -0.23 0.36 -10000 0 -0.67 54 54
IL23-mediated signaling events

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.33 0.55 -10000 0 -1.2 36 36
IL23A -0.34 0.57 -10000 0 -1.2 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.41 0.52 -10000 0 -1.2 37 37
positive regulation of T cell mediated cytotoxicity -0.41 0.68 -10000 0 -1.4 39 39
ITGA3 -0.33 0.56 -10000 0 -1.2 35 35
IL17F -0.2 0.37 -10000 0 -0.74 34 34
IL12B -0.25 0.33 -10000 0 -0.55 71 71
STAT1 (dimer) -0.38 0.64 -10000 0 -1.3 38 38
CD4 -0.33 0.55 -10000 0 -1.2 35 35
IL23 -0.39 0.6 -10000 0 -1.2 41 41
IL23R -0.05 0.22 -10000 0 -1.7 2 2
IL1B -0.36 0.59 -10000 0 -1.3 35 35
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.36 0.59 -10000 0 -1.3 36 36
TYK2 0.01 0.019 -10000 0 -10000 0 0
STAT4 0.005 0.072 -10000 0 -0.88 1 1
STAT3 0.006 0.072 -10000 0 -0.88 1 1
IL18RAP -0.11 0.29 -10000 0 -0.73 25 25
IL12RB1 -0.088 0.28 -10000 0 -0.83 18 18
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.068 0.22 -10000 0 -0.72 15 15
IL23R/JAK2 -0.041 0.22 -10000 0 -1.6 2 2
positive regulation of chronic inflammatory response -0.41 0.68 -10000 0 -1.4 39 39
natural killer cell activation 0.004 0.013 0.05 6 -10000 0 6
JAK2 0.022 0.028 -10000 0 -10000 0 0
PIK3R1 0.006 0.072 -10000 0 -0.88 1 1
NFKB1 0.007 0.007 -10000 0 -10000 0 0
RELA 0.007 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.36 0.55 -10000 0 -1.1 41 41
ALOX12B -0.38 0.6 -10000 0 -1.2 41 41
CXCL1 -0.44 0.64 -10000 0 -1.3 49 49
T cell proliferation -0.41 0.68 -10000 0 -1.4 39 39
NFKBIA 0.007 0.007 -10000 0 -10000 0 0
IL17A -0.14 0.3 -10000 0 -0.58 26 26
PI3K -0.43 0.54 -10000 0 -1.2 40 40
IFNG -0.026 0.061 0.16 1 -0.13 34 35
STAT3 (dimer) -0.4 0.5 -10000 0 -1.2 39 39
IL18R1 -0.007 0.12 -10000 0 -0.88 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.46 -10000 0 -0.95 35 35
IL18/IL18R -0.13 0.3 -10000 0 -0.69 28 28
macrophage activation -0.017 0.02 -10000 0 -0.044 36 36
TNF -0.37 0.61 -10000 0 -1.3 36 36
STAT3/STAT4 -0.43 0.54 -10000 0 -1.2 38 38
STAT4 (dimer) -0.38 0.64 -10000 0 -1.3 38 38
IL18 -0.055 0.21 -10000 0 -0.65 15 15
IL19 -0.41 0.64 -10000 0 -1.3 43 43
STAT5A (dimer) -0.39 0.64 -10000 0 -1.3 38 38
STAT1 0.011 0 -10000 0 -10000 0 0
SOCS3 0 0.1 -10000 0 -0.88 2 2
CXCL9 -0.42 0.67 -10000 0 -1.4 39 39
MPO -0.35 0.58 -10000 0 -1.2 36 36
positive regulation of humoral immune response -0.41 0.68 -10000 0 -1.4 39 39
IL23/IL23R/JAK2/TYK2 -0.5 0.96 -10000 0 -1.8 39 39
IL6 -0.39 0.62 -10000 0 -1.3 39 39
STAT5A 0.005 0.072 -10000 0 -0.88 1 1
IL2 0.004 0.013 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.013 0.05 6 -10000 0 6
CD3E -0.35 0.59 -10000 0 -1.3 33 33
keratinocyte proliferation -0.41 0.68 -10000 0 -1.4 39 39
NOS2 -0.37 0.59 -10000 0 -1.2 39 39
IL4-mediated signaling events

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
BCL2L1 -0.5 0.56 -10000 0 -1.2 46 46
STAT6 (cleaved dimer) -0.56 0.55 -10000 0 -1.1 60 60
IGHG1 -0.15 0.19 -10000 0 -0.37 22 22
IGHG3 -0.49 0.54 -10000 0 -1.1 57 57
AKT1 -0.25 0.36 -10000 0 -1 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.41 -10000 0 -1.2 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.29 0.42 -10000 0 -1.2 17 17
THY1 -0.5 0.56 -10000 0 -1.2 47 47
MYB 0 0.1 -10000 0 -0.88 2 2
HMGA1 -0.015 0.15 -10000 0 -0.78 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.48 -10000 0 -0.94 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.42 -10000 0 -1.1 19 19
SP1 0.017 0.007 -10000 0 -10000 0 0
INPP5D 0.005 0.072 -10000 0 -0.88 1 1
SOCS5 0.021 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.54 -10000 0 -1.1 58 58
SOCS1 -0.3 0.36 -10000 0 -0.75 41 41
SOCS3 -0.26 0.38 -10000 0 -1.1 17 17
FCER2 -0.44 0.56 -10000 0 -1.3 33 33
PARP14 0.011 0.004 -10000 0 -10000 0 0
CCL17 -0.58 0.66 -10000 0 -1.3 56 56
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.34 -10000 0 -1 14 14
T cell proliferation -0.5 0.59 -10000 0 -1.2 51 51
IL4R/JAK1 -0.5 0.56 -10000 0 -1.2 49 49
EGR2 -0.52 0.59 -10000 0 -1.3 45 45
JAK2 -0.007 0.032 -10000 0 -10000 0 0
JAK3 0.004 0.099 -10000 0 -0.85 2 2
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
JAK1 0.007 0.014 -10000 0 -10000 0 0
COL1A2 -0.17 0.26 -10000 0 -1.6 2 2
CCL26 -0.63 0.73 -10000 0 -1.5 55 55
IL4R -0.53 0.61 -10000 0 -1.3 49 49
PTPN6 0.022 0.013 -10000 0 -10000 0 0
IL13RA2 -0.66 0.69 -10000 0 -1.4 60 60
IL13RA1 -0.019 0.11 -10000 0 -0.92 2 2
IRF4 -0.26 0.55 -10000 0 -1.5 21 21
ARG1 -0.12 0.18 -10000 0 -0.61 5 5
CBL -0.31 0.43 -10000 0 -1 24 24
GTF3A 0.009 0.024 -10000 0 -10000 0 0
PIK3CA 0.011 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.018 0.095 -10000 0 -0.72 2 2
IRF4/BCL6 -0.25 0.48 -10000 0 -1.4 21 21
CD40LG -0.11 0.29 -10000 0 -0.71 26 26
MAPK14 -0.31 0.44 -10000 0 -1.1 23 23
mitosis -0.23 0.33 -10000 0 -0.92 17 17
STAT6 -0.6 0.71 -10000 0 -1.4 54 54
SPI1 -0.003 0.096 -10000 0 -0.48 5 5
RPS6KB1 -0.22 0.32 -10000 0 -0.9 16 16
STAT6 (dimer) -0.6 0.71 -10000 0 -1.4 54 54
STAT6 (dimer)/PARP14 -0.55 0.64 -10000 0 -1.3 51 51
mast cell activation 0.011 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.43 -10000 0 -1.2 18 18
FRAP1 -0.25 0.36 -10000 0 -1 17 17
LTA -0.52 0.6 -10000 0 -1.2 48 48
FES 0.011 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.66 1.3 55 -10000 0 55
CCL11 -0.57 0.64 -10000 0 -1.3 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.43 -10000 0 -1.2 18 18
IL2RG -0.083 0.26 -10000 0 -0.72 20 20
IL10 -0.5 0.58 -10000 0 -1.2 49 49
IRS1 -0.037 0.18 -10000 0 -0.65 11 11
IRS2 0.003 0.079 -10000 0 -0.63 2 2
IL4 -0.1 0.14 -10000 0 -10000 0 0
IL5 -0.5 0.56 -10000 0 -1.2 49 49
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.44 -10000 0 -0.9 49 49
COL1A1 -0.3 0.46 -10000 0 -1.3 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.51 0.58 -10000 0 -1.2 46 46
IL2R gamma/JAK3 -0.072 0.23 -10000 0 -0.75 14 14
TFF3 -0.63 0.67 -10000 0 -1.4 59 59
ALOX15 -0.54 0.61 -10000 0 -1.3 51 51
MYBL1 0.011 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.44 0.52 -10000 0 -1 52 52
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.011 0.034 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.41 -10000 0 -1.2 17 17
mol:PI-3-4-5-P3 -0.25 0.36 -10000 0 -1 17 17
PI3K -0.27 0.41 -10000 0 -1.2 17 17
DOK2 0.005 0.072 -10000 0 -0.88 1 1
ETS1 0.016 0.072 -10000 0 -0.84 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.33 -10000 0 -1 14 14
ITGB3 -0.56 0.62 -10000 0 -1.3 56 56
PIGR -0.59 0.65 -10000 0 -1.3 56 56
IGHE 0.034 0.043 -10000 0 -10000 0 0
MAPKKK cascade -0.2 0.32 -10000 0 -0.97 14 14
BCL6 0.01 0.005 -10000 0 -10000 0 0
OPRM1 -0.5 0.56 -10000 0 -1.2 49 49
RETNLB -0.5 0.56 -10000 0 -1.2 47 47
SELP -0.57 0.66 -10000 0 -1.3 54 54
AICDA -0.57 0.64 -10000 0 -1.3 53 53
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.005 0.072 -9999 0 -0.88 1 1
CCL5 -0.067 0.24 -9999 0 -0.78 15 15
SDCBP 0.011 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.29 -9999 0 -0.58 41 41
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.2 0.28 -9999 0 -0.71 24 24
Syndecan-1/Syntenin -0.2 0.28 -9999 0 -0.68 26 26
MAPK3 -0.17 0.25 -9999 0 -0.65 22 22
HGF/MET -0.13 0.23 -9999 0 -0.7 17 17
TGFB1/TGF beta receptor Type II 0.005 0.072 -9999 0 -0.87 1 1
BSG 0.011 0 -9999 0 -10000 0 0
keratinocyte migration -0.2 0.27 -9999 0 -0.69 24 24
Syndecan-1/RANTES -0.25 0.32 -9999 0 -0.7 35 35
Syndecan-1/CD147 -0.2 0.26 -9999 0 -0.69 23 23
Syndecan-1/Syntenin/PIP2 -0.21 0.26 -9999 0 -0.66 26 26
LAMA5 0.011 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.2 0.24 -9999 0 -0.64 26 26
MMP7 -0.31 0.38 -9999 0 -0.67 71 71
HGF -0.14 0.27 -9999 0 -0.54 41 41
Syndecan-1/CASK -0.21 0.28 -9999 0 -0.56 41 41
Syndecan-1/HGF/MET -0.29 0.32 -9999 0 -0.73 37 37
regulation of cell adhesion -0.16 0.24 -9999 0 -0.62 22 22
HPSE -0.012 0.14 -9999 0 -0.88 4 4
positive regulation of cell migration -0.22 0.29 -9999 0 -0.58 41 41
SDC1 -0.22 0.3 -9999 0 -0.59 41 41
Syndecan-1/Collagen -0.22 0.29 -9999 0 -0.58 41 41
PPIB 0.011 0 -9999 0 -10000 0 0
MET -0.02 0.15 -9999 0 -0.66 7 7
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.069 0.24 -9999 0 -0.7 17 17
MAPK1 -0.17 0.25 -9999 0 -0.65 22 22
homophilic cell adhesion -0.22 0.28 -9999 0 -0.57 41 41
MMP1 -0.22 0.34 -9999 0 -0.64 54 54
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.12 0.21 -9999 0 -0.55 27 27
EFNA5 -0.16 0.31 -9999 0 -0.61 41 41
FYN -0.096 0.2 -9999 0 -0.5 27 27
neuron projection morphogenesis -0.12 0.21 -9999 0 -0.55 27 27
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.12 0.21 -9999 0 -0.55 27 27
EPHA5 -0.023 0.1 -9999 0 -0.38 11 11
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.14 0.22 -9999 0 -0.5 28 28
FZD6 0.009 0.032 -9999 0 -0.38 1 1
WNT6 -0.075 0.24 -9999 0 -0.67 19 19
WNT4 -0.076 0.17 -9999 0 -0.4 32 32
FZD3 0.005 0.072 -9999 0 -0.88 1 1
WNT5A -0.076 0.2 -9999 0 -0.48 27 27
WNT11 -0.14 0.28 -9999 0 -0.56 38 38
Syndecan-4-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
PTK2 -0.083 0.22 -9999 0 -0.76 13 13
Syndecan-4/Syndesmos -0.21 0.32 -9999 0 -0.78 30 30
positive regulation of JNK cascade -0.22 0.28 -9999 0 -0.69 33 33
Syndecan-4/ADAM12 -0.24 0.35 -9999 0 -0.8 35 35
CCL5 -0.067 0.24 -9999 0 -0.78 15 15
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.011 0 -9999 0 -10000 0 0
ITGA5 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
PLG -0.14 0.28 -9999 0 -0.56 39 39
ADAM12 -0.046 0.21 -9999 0 -0.71 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.059 0.059 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.23 0.34 -9999 0 -0.82 30 30
Syndecan-4/CXCL12/CXCR4 -0.23 0.3 -9999 0 -0.75 33 33
Syndecan-4/Laminin alpha3 -0.22 0.33 -9999 0 -0.8 31 31
MDK 0.005 0.072 -9999 0 -0.88 1 1
Syndecan-4/FZD7 -0.3 0.37 -9999 0 -0.83 38 38
Syndecan-4/Midkine -0.22 0.32 -9999 0 -0.78 30 30
FZD7 -0.16 0.31 -9999 0 -0.62 42 42
Syndecan-4/FGFR1/FGF -0.26 0.3 -9999 0 -0.75 34 34
THBS1 -0.035 0.16 -9999 0 -0.49 14 14
integrin-mediated signaling pathway -0.24 0.34 -9999 0 -0.81 33 33
positive regulation of MAPKKK cascade -0.22 0.28 -9999 0 -0.69 33 33
Syndecan-4/TACI -0.27 0.35 -9999 0 -0.8 36 36
CXCR4 0.011 0 -9999 0 -10000 0 0
cell adhesion -0.047 0.12 -9999 0 -0.41 14 14
Syndecan-4/Dynamin -0.21 0.32 -9999 0 -0.78 30 30
Syndecan-4/TSP1 -0.24 0.34 -9999 0 -0.8 33 33
Syndecan-4/GIPC -0.21 0.32 -9999 0 -0.78 30 30
Syndecan-4/RANTES -0.25 0.36 -9999 0 -0.82 36 36
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.02 0.15 -9999 0 -0.66 7 7
LAMA3 -0.016 0.13 -9999 0 -0.51 8 8
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.042 0.1 -9999 0 -0.51 3 3
Syndecan-4/alpha-Actinin -0.21 0.32 -9999 0 -0.78 30 30
TFPI -0.038 0.19 -9999 0 -0.73 10 10
F2 -0.18 0.3 -9999 0 -0.56 50 50
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.22 0.34 -9999 0 -0.79 32 32
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC -0.075 0.25 -9999 0 -0.71 18 18
Syndecan-4/CXCL12 -0.22 0.33 -9999 0 -0.78 33 33
FGF6 0.002 0.004 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CXCL12 -0.006 0.12 -9999 0 -0.88 3 3
TNFRSF13B -0.095 0.26 -9999 0 -0.65 24 24
FGF2 -0.12 0.28 -9999 0 -0.63 30 30
FGFR1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.22 0.32 -9999 0 -0.79 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.26 -9999 0 -0.55 35 35
cell migration -0.016 0.023 -9999 0 -10000 0 0
PRKCD 0.009 0.016 -9999 0 -10000 0 0
vasculogenesis -0.22 0.32 -9999 0 -0.75 33 33
SDC4 -0.24 0.35 -9999 0 -0.86 30 30
Syndecan-4/Tenascin C -0.26 0.37 -9999 0 -0.87 33 33
Syndecan-4/PI-4-5-P2/PKC alpha -0.047 0.046 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.21 0.32 -9999 0 -0.78 30 30
MMP9 -0.071 0.24 -9999 0 -0.7 17 17
Rac1/GTP -0.053 0.13 -9999 0 -0.42 14 14
cytoskeleton organization -0.2 0.3 -9999 0 -0.74 30 30
GIPC1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.24 0.35 -9999 0 -0.84 31 31
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.086 0.21 -9999 0 -0.63 17 17
alphaM/beta2 Integrin/GPIbA -0.1 0.21 -9999 0 -0.63 18 18
alphaM/beta2 Integrin/proMMP-9 -0.1 0.25 -9999 0 -0.71 19 19
PLAUR 0.011 0 -9999 0 -10000 0 0
HMGB1 0.006 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.05 0.14 -9999 0 -0.55 10 10
AGER 0.006 0.02 -9999 0 -10000 0 0
RAP1A 0.011 0 -9999 0 -10000 0 0
SELPLG -0.006 0.11 -9999 0 -0.63 4 4
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.073 0.15 -9999 0 -0.55 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.069 0.24 -9999 0 -0.7 17 17
CYR61 -0.12 0.31 -9999 0 -0.8 25 25
TLN1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP -0.21 0.26 -9999 0 -0.6 34 34
RHOA 0.011 0 -9999 0 -10000 0 0
P-selectin oligomer -0.092 0.28 -9999 0 -0.85 18 18
MYH2 -0.3 0.33 -9999 0 -0.78 39 39
MST1R 0 0.1 -9999 0 -0.88 2 2
leukocyte activation during inflammatory response -0.24 0.24 -9999 0 -0.56 47 47
APOB -0.35 0.36 -9999 0 -0.62 86 86
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.044 0.21 -9999 0 -0.83 10 10
JAM3 0.005 0.072 -9999 0 -0.88 1 1
GP1BA -0.077 0.21 -9999 0 -0.5 26 26
alphaM/beta2 Integrin/CTGF -0.11 0.22 -9999 0 -0.6 21 21
alphaM/beta2 Integrin -0.25 0.32 -9999 0 -0.63 46 46
JAM3 homodimer 0.005 0.072 -9999 0 -0.87 1 1
ICAM2 0.011 0 -9999 0 -10000 0 0
ICAM1 -0.003 0.11 -9999 0 -0.71 3 3
phagocytosis triggered by activation of immune response cell surface activating receptor -0.25 0.31 -9999 0 -0.61 46 46
cell adhesion -0.099 0.21 -9999 0 -0.62 18 18
NFKB1 -0.056 0.23 -9999 0 -0.92 4 4
THY1 0.011 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.25 0.25 -9999 0 -0.58 48 48
alphaM/beta2 Integrin/LRP/tPA -0.079 0.15 -9999 0 -0.58 7 7
IL6 -0.11 0.37 -9999 0 -1.1 17 17
ITGB2 -0.043 0.18 -9999 0 -0.59 12 12
elevation of cytosolic calcium ion concentration -0.047 0.15 -9999 0 -0.62 7 7
alphaM/beta2 Integrin/JAM2/JAM3 -0.076 0.19 -9999 0 -0.62 14 14
JAM2 -0.036 0.2 -9999 0 -0.88 8 8
alphaM/beta2 Integrin/ICAM1 -0.055 0.19 -9999 0 -0.71 9 9
alphaM/beta2 Integrin/uPA/Plg -0.13 0.21 -9999 0 -0.57 24 24
RhoA/GTP -0.32 0.38 -9999 0 -0.78 47 47
positive regulation of phagocytosis -0.19 0.24 -9999 0 -0.7 18 18
Ron/MSP -0.011 0.081 -9999 0 -0.68 2 2
alphaM/beta2 Integrin/uPAR/uPA -0.047 0.15 -9999 0 -0.62 7 7
alphaM/beta2 Integrin/uPAR -0.05 0.14 -9999 0 -0.55 10 10
PLAU 0.005 0.072 -9999 0 -0.88 1 1
PLAT -0.062 0.15 -9999 0 -0.38 28 28
actin filament polymerization -0.28 0.3 -9999 0 -0.71 40 40
MST1 0.009 0.032 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.25 0.25 -9999 0 -0.57 47 47
TNF -0.083 0.33 -9999 0 -1 12 12
RAP1B 0.009 0.032 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/uPA -0.054 0.16 -9999 0 -0.61 10 10
fibrinolysis -0.13 0.21 -9999 0 -0.57 24 24
HCK -0.005 0.096 -9999 0 -0.48 5 5
dendritic cell antigen processing and presentation -0.25 0.31 -9999 0 -0.61 46 46
VTN -0.34 0.37 -9999 0 -0.63 82 82
alphaM/beta2 Integrin/CYR61 -0.14 0.26 -9999 0 -0.66 27 27
LPA -0.017 0.098 -9999 0 -0.38 10 10
LRP1 0.011 0 -9999 0 -10000 0 0
cell migration -0.12 0.28 -9999 0 -0.72 23 23
FN1 -0.12 0.27 -9999 0 -0.57 35 35
alphaM/beta2 Integrin/Thy1 -0.05 0.14 -9999 0 -0.55 10 10
MPO -0.062 0.22 -9999 0 -0.6 18 18
KNG1 -0.14 0.31 -9999 0 -0.71 32 32
RAP1/GDP -0.001 0.017 -9999 0 -10000 0 0
ROCK1 -0.28 0.34 -9999 0 -0.76 40 40
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.15 0.28 -9999 0 -0.57 39 39
CTGF -0.078 0.25 -9999 0 -0.69 19 19
alphaM/beta2 Integrin/Hck -0.059 0.17 -9999 0 -0.64 11 11
ITGAM -0.017 0.12 -9999 0 -0.55 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.12 0.24 -9999 0 -0.62 25 25
HP -0.22 0.34 -9999 0 -0.63 54 54
leukocyte adhesion -0.082 0.17 -9999 0 -0.84 3 3
SELP -0.092 0.28 -9999 0 -0.85 18 18
Osteopontin-mediated 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
IKK alpha homodimer -0.14 0.25 -9999 0 -0.58 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.22 -9999 0 -0.76 8 8
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.26 -9999 0 -0.67 27 27
AP1 -0.23 0.35 -9999 0 -1 20 20
ILK -0.12 0.28 -9999 0 -0.61 32 32
bone resorption -0.13 0.22 -9999 0 -0.77 9 9
PTK2B 0.005 0.072 -9999 0 -0.88 1 1
PYK2/p130Cas -0.14 0.24 -9999 0 -0.56 34 34
ITGAV 0.006 0.078 -9999 0 -0.62 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.062 -9999 0 -0.68 1 1
alphaV/beta3 Integrin/Osteopontin -0.17 0.29 -9999 0 -0.67 33 33
MAP3K1 -0.12 0.28 -9999 0 -0.62 32 32
JUN -0.065 0.22 -9999 0 -0.63 18 18
MAPK3 -0.099 0.27 -9999 0 -0.57 32 32
MAPK1 -0.099 0.27 -9999 0 -0.57 32 32
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.011 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.31 -9999 0 -0.64 32 32
ITGB3 -0.065 0.23 -9999 0 -0.65 18 18
NFKBIA -0.085 0.27 -9999 0 -0.56 32 32
FOS -0.11 0.29 -9999 0 -0.73 24 24
CD44 0 0.085 -9999 0 -0.55 3 3
CHUK 0.011 0 -9999 0 -10000 0 0
PLAU -0.075 0.26 -9999 0 -0.84 7 7
NF kappa B1 p50/RelA -0.11 0.21 -9999 0 -0.74 8 8
BCAR1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.064 0.18 -9999 0 -0.67 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.12 0.28 -9999 0 -0.62 33 33
VAV3 -0.11 0.27 -9999 0 -0.57 33 33
MAP3K14 -0.12 0.28 -9999 0 -0.62 32 32
ROCK2 0.011 0 -9999 0 -10000 0 0
SPP1 -0.17 0.34 -9999 0 -0.7 39 39
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.23 -9999 0 -0.52 33 33
MMP2 -0.16 0.31 -9999 0 -0.76 24 24
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.08 0.18 -9999 0 -0.59 15 15
fibroblast growth factor receptor signaling pathway -0.079 0.18 -9999 0 -0.59 15 15
LAMA1 -0.02 0.15 -9999 0 -0.66 7 7
PRNP 0 0.1 -9999 0 -0.88 2 2
GPC1/SLIT2 -0.12 0.22 -9999 0 -0.68 17 17
SMAD2 0.025 0.065 -9999 0 -0.54 2 2
GPC1/PrPc/Cu2+ -0.008 0.069 -9999 0 -0.6 2 2
GPC1/Laminin alpha1 -0.023 0.11 -9999 0 -0.68 4 4
TDGF1 -0.33 0.34 -9999 0 -0.58 87 87
CRIPTO/GPC1 -0.25 0.26 -9999 0 -0.68 35 35
APP/GPC1 0 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.2 0.24 -9999 0 -0.59 35 35
FLT1 0.011 0 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.008 0.068 -9999 0 -0.59 2 2
SERPINC1 -0.07 0.16 -9999 0 -0.38 30 30
FYN -0.2 0.24 -9999 0 -0.59 35 35
FGR -0.21 0.25 -9999 0 -0.62 36 36
positive regulation of MAPKKK cascade -0.22 0.29 -9999 0 -0.64 42 42
SLIT2 -0.15 0.3 -9999 0 -0.6 39 39
GPC1/NRG -0.039 0.14 -9999 0 -0.68 6 6
NRG1 -0.043 0.19 -9999 0 -0.61 13 13
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.004 0.029 -9999 0 -10000 0 0
LYN -0.2 0.24 -9999 0 -0.59 35 35
mol:Spermine 0.011 0 -9999 0 -10000 0 0
cell growth -0.079 0.18 -9999 0 -0.59 15 15
BMP signaling pathway -0.011 0 -9999 0 -10000 0 0
SRC -0.2 0.24 -9999 0 -0.59 35 35
TGFBR1 0.011 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.23 0.35 -9999 0 -0.63 57 57
GPC1 0.011 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.011 0 -9999 0 -10000 0 0
VEGFA 0.003 0.055 -9999 0 -0.38 3 3
BLK -0.3 0.32 -9999 0 -0.68 56 56
HCK -0.21 0.25 -9999 0 -0.6 36 36
FGF2 -0.12 0.28 -9999 0 -0.63 30 30
FGFR1 0.011 0 -9999 0 -10000 0 0
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
TGFBR2 0 0.1 -9999 0 -0.88 2 2
cell death 0 0 -9999 0 -10000 0 0
ATIII/GPC1 -0.051 0.1 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.18 0.26 -9999 0 -0.68 29 29
LCK -0.23 0.27 -9999 0 -0.63 42 42
neuron differentiation -0.039 0.14 -9999 0 -0.68 6 6
PrPc/Cu2+ -0.009 0.079 -9999 0 -0.69 2 2
APP 0.011 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0 0.1 -9999 0 -0.87 2 2
Glucocorticoid receptor regulatory 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
PCK2 0.038 0.11 -10000 0 -10000 0 0
SMARCC2 0.013 0 -10000 0 -10000 0 0
SMARCC1 0.013 0 -10000 0 -10000 0 0
TBX21 -0.18 0.42 -10000 0 -1.1 22 22
SUMO2 0.008 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0.029 -10000 0 -0.34 1 1
FKBP4 0.011 0 -10000 0 -10000 0 0
FKBP5 0.011 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.38 14 -10000 0 14
PRL -0.099 0.2 -10000 0 -0.72 8 8
cortisol/GR alpha (dimer)/TIF2 0.17 0.38 0.66 36 -0.61 11 47
RELA -0.017 0.074 -10000 0 -10000 0 0
FGG 0.05 0.43 0.59 22 -0.83 22 44
GR beta/TIF2 0.036 0.28 0.4 19 -0.64 16 35
IFNG -0.57 0.67 -10000 0 -1.5 42 42
apoptosis -0.099 0.29 0.5 12 -0.65 12 24
CREB1 -0.049 0.11 -10000 0 -0.38 9 9
histone acetylation -0.052 0.18 0.35 1 -0.45 15 16
BGLAP -0.075 0.18 -10000 0 -0.6 5 5
GR/PKAc 0.06 0.19 0.36 11 -0.5 7 18
NF kappa B1 p50/RelA -0.029 0.13 -10000 0 -10000 0 0
SMARCD1 0.013 0 -10000 0 -10000 0 0
MDM2 0.098 0.12 0.33 20 -10000 0 20
GATA3 -0.034 0.17 -10000 0 -0.52 14 14
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.18 0.37 -10000 0 -1 18 18
GSK3B 0.008 0.013 -10000 0 -10000 0 0
NR1I3 -0.069 0.27 0.51 9 -0.6 10 19
CSN2 0.15 0.2 0.45 23 -10000 0 23
BRG1/BAF155/BAF170/BAF60A 0.001 0.006 -10000 0 -10000 0 0
NFATC1 0.012 0.016 -10000 0 -10000 0 0
POU2F1 -0.009 0.13 -10000 0 -0.89 3 3
CDKN1A -0.036 0.36 -10000 0 -1.6 7 7
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.012 -10000 0 -10000 0 0
SFN -0.064 0.23 -10000 0 -0.69 16 16
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.061 0.18 0.39 7 -0.52 5 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.068 0.26 0.49 9 -0.58 10 19
JUN -0.4 0.34 -10000 0 -0.71 67 67
IL4 -0.099 0.18 -10000 0 -0.62 6 6
CDK5R1 0.002 0.046 -10000 0 -0.39 2 2
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.39 0.4 0.27 2 -0.8 59 61
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.12 0.38 10 -10000 0 10
cortisol/GR alpha (monomer) 0.3 0.4 0.8 43 -0.46 2 45
NCOA2 -0.086 0.28 -10000 0 -0.85 17 17
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.8 24 24
AP-1/NFAT1-c-4 -0.6 0.5 -10000 0 -0.99 77 77
AFP -0.62 0.67 -10000 0 -1.4 52 52
SUV420H1 0.011 0 -10000 0 -10000 0 0
IRF1 0.15 0.21 0.55 14 -1 1 15
TP53 0.009 0.11 -10000 0 -0.48 7 7
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.7 0.66 -10000 0 -1.3 70 70
KRT14 -0.19 0.32 -10000 0 -0.93 15 15
TBP 0.02 0.001 -10000 0 -10000 0 0
CREBBP 0.041 0.059 0.31 3 -10000 0 3
HDAC1 0.008 0.007 -10000 0 -10000 0 0
HDAC2 0.013 0.025 -10000 0 -10000 0 0
AP-1 -0.61 0.51 -10000 0 -1 77 77
MAPK14 0.008 0.011 -10000 0 -10000 0 0
MAPK10 -0.1 0.24 -10000 0 -0.55 30 30
MAPK11 0.002 0.073 -10000 0 -0.88 1 1
KRT5 -0.49 0.53 -10000 0 -1.2 44 44
interleukin-1 receptor activity 0.007 0.023 -10000 0 -10000 0 0
NCOA1 0.015 0.001 -10000 0 -10000 0 0
STAT1 0.017 0.029 -10000 0 -0.34 1 1
CGA -0.31 0.52 -10000 0 -1.2 31 31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.19 0.45 34 -10000 0 34
MAPK3 0.008 0.012 -10000 0 -10000 0 0
MAPK1 0.008 0.011 -10000 0 -10000 0 0
ICAM1 -0.16 0.29 -10000 0 -0.78 17 17
NFKB1 -0.017 0.074 -10000 0 -10000 0 0
MAPK8 -0.25 0.26 -10000 0 -0.58 43 43
MAPK9 0.008 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.11 0.3 0.52 11 -0.69 12 23
BAX 0.023 0.091 -10000 0 -10000 0 0
POMC -0.28 0.56 -10000 0 -1.8 17 17
EP300 0.041 0.06 0.31 4 -10000 0 4
cortisol/GR alpha (dimer)/p53 0.25 0.31 0.68 37 -10000 0 37
proteasomal ubiquitin-dependent protein catabolic process 0.067 0.09 0.27 9 -10000 0 9
SGK1 0.11 0.083 -10000 0 -10000 0 0
IL13 -0.29 0.29 -10000 0 -0.91 17 17
IL6 -0.25 0.48 -10000 0 -1.3 21 21
PRKACG -0.062 0.23 -10000 0 -0.71 15 15
IL5 -0.24 0.23 -10000 0 -0.7 19 19
IL2 -0.35 0.33 -10000 0 -0.85 31 31
CDK5 0.007 0.008 -10000 0 -10000 0 0
PRKACB 0.011 0 -10000 0 -10000 0 0
HSP90AA1 0.011 0 -10000 0 -10000 0 0
IL8 -0.3 0.49 -10000 0 -1 39 39
CDK5R1/CDK5 0.002 0.034 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.054 0.16 -10000 0 -0.53 10 10
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.28 0.63 36 -10000 0 36
SMARCA4 0.013 0 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.18 0.45 29 -10000 0 29
NF kappa B1 p50/RelA/Cbp 0.027 0.12 0.36 1 -10000 0 1
JUN (dimer) -0.4 0.34 -10000 0 -0.7 67 67
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 -0.12 0.27 -10000 0 -0.75 17 17
NR3C1 0.18 0.26 0.58 32 -10000 0 32
NR4A1 -0.039 0.15 -10000 0 -0.48 12 12
TIF2/SUV420H1 -0.074 0.21 -10000 0 -0.68 16 16
MAPKKK cascade -0.099 0.29 0.5 12 -0.65 12 24
cortisol/GR alpha (dimer)/Src-1 0.25 0.31 0.67 38 -10000 0 38
PBX1 0.009 0.019 -10000 0 -10000 0 0
POU1F1 -0.003 0.021 -10000 0 -10000 0 0
SELE -0.18 0.33 -10000 0 -0.9 18 18
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.18 0.45 29 -10000 0 29
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.28 0.63 36 -10000 0 36
mol:cortisol 0.17 0.26 0.52 39 -0.26 2 41
MMP1 -0.42 0.6 -10000 0 -1.3 38 38
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.003 0.029 -9999 0 -10000 0 0
VLDLR -0.11 0.29 -9999 0 -0.75 24 24
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
ITGA3 -0.004 0.077 -9999 0 -0.38 6 6
RELN/VLDLR/Fyn -0.18 0.27 -9999 0 -0.63 33 33
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.082 -9999 0 -0.51 4 4
AKT1 -0.15 0.25 -9999 0 -0.46 45 45
MAP2K7 0.011 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
DAB1 -0.16 0.32 -9999 0 -0.66 39 39
RELN/LRP8/DAB1 -0.19 0.25 -9999 0 -0.55 44 44
LRPAP1/LRP8 0 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.18 0.24 -9999 0 -0.56 35 35
DAB1/alpha3/beta1 Integrin -0.22 0.28 -9999 0 -0.68 24 24
long-term memory -0.21 0.25 -9999 0 -0.54 48 48
DAB1/LIS1 -0.23 0.29 -9999 0 -0.59 48 48
DAB1/CRLK/C3G -0.22 0.28 -9999 0 -0.81 15 15
PIK3CA 0.011 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.23 0.29 -9999 0 -0.6 48 48
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.037 0.18 -9999 0 -0.65 11 11
CDK5R1 0.006 0.045 -9999 0 -0.38 2 2
RELN -0.15 0.29 -9999 0 -0.55 44 44
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
RELN/LRP8/Fyn -0.099 0.18 -9999 0 -0.59 15 15
GRIN2A/RELN/LRP8/DAB1/Fyn -0.2 0.25 -9999 0 -0.56 42 42
MAPK8 -0.012 0.14 -9999 0 -0.88 4 4
RELN/VLDLR/DAB1 -0.26 0.32 -9999 0 -0.63 56 56
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.23 0.29 -9999 0 -0.6 48 48
RELN/LRP8 -0.099 0.18 -9999 0 -0.59 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn -0.19 0.24 -9999 0 -0.55 41 41
PI3K -0.005 0.055 -9999 0 -0.68 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.01 0.05 -9999 0 -10000 0 0
RAP1A -0.2 0.26 -9999 0 -0.81 12 12
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.029 0.11 -9999 0 -0.38 14 14
NCK2 0.011 0 -9999 0 -10000 0 0
neuron differentiation -0.059 0.14 -9999 0 -0.42 6 6
neuron adhesion -0.16 0.26 -9999 0 -0.76 12 12
LRP8 0.011 0 -9999 0 -10000 0 0
GSK3B -0.13 0.24 -9999 0 -0.73 13 13
RELN/VLDLR/DAB1/Fyn -0.25 0.3 -9999 0 -0.63 48 48
MAP3K11 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.18 0.26 -9999 0 -0.5 45 45
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT 0.004 0.12 -9999 0 -0.46 8 8
neuron migration -0.13 0.24 -9999 0 -0.64 13 13
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.078 0.13 -9999 0 -0.43 6 6
RELN/VLDLR -0.16 0.25 -9999 0 -0.61 29 29
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.12 0.28 0.73 25 -10000 0 25
KIRREL -0.094 0.28 -10000 0 -0.89 17 17
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.12 0.28 -10000 0 -0.73 25 25
PLCG1 0.011 0 -10000 0 -10000 0 0
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.098 0.22 -10000 0 -0.57 25 25
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.044 0.18 -10000 0 -0.42 25 25
FYN -0.073 0.22 -10000 0 -0.54 25 25
mol:Ca2+ -0.096 0.22 -10000 0 -0.57 25 25
mol:DAG -0.097 0.22 -10000 0 -0.57 25 25
NPHS2 -0.013 0.064 -10000 0 -0.41 3 3
mol:IP3 -0.097 0.22 -10000 0 -0.57 25 25
regulation of endocytosis -0.086 0.2 -10000 0 -0.51 25 25
Nephrin/NEPH1/podocin/Cholesterol -0.099 0.23 -10000 0 -0.58 25 25
establishment of cell polarity -0.12 0.28 -10000 0 -0.73 25 25
Nephrin/NEPH1/podocin/NCK1-2 -0.09 0.21 -10000 0 -0.53 25 25
Nephrin/NEPH1/beta Arrestin2 -0.087 0.2 -10000 0 -0.52 25 25
NPHS1 -0.056 0.22 -10000 0 -0.89 10 10
Nephrin/NEPH1/podocin -0.093 0.21 -10000 0 -0.55 25 25
TJP1 0.011 0 -10000 0 -10000 0 0
NCK1 0.011 0 -10000 0 -10000 0 0
NCK2 0.011 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.098 0.22 -10000 0 -0.57 25 25
CD2AP 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.098 0.22 -10000 0 -0.57 25 25
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.086 0.23 -10000 0 -0.55 28 28
cytoskeleton organization -0.06 0.23 -10000 0 -0.55 25 25
Nephrin/NEPH1 -0.094 0.22 -10000 0 -0.56 25 25
Nephrin/NEPH1/ZO-1 -0.1 0.24 -10000 0 -0.61 25 25
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 -0.1 0.29 -10000 0 -0.61 25 25
PTK2B 0.005 0.072 -10000 0 -0.88 1 1
mol:Ca2+ -0.065 0.27 -10000 0 -0.7 15 15
EDN1 -0.03 0.18 -10000 0 -0.53 9 9
EDN3 -0.17 0.3 -10000 0 -0.56 46 46
EDN2 -0.08 0.22 -10000 0 -0.52 25 25
HRAS/GDP -0.043 0.22 -10000 0 -0.58 12 12
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.051 0.21 -10000 0 -0.57 11 11
ADCY4 -0.12 0.28 -10000 0 -0.66 22 22
ADCY5 -0.18 0.34 -10000 0 -0.7 37 37
ADCY6 -0.12 0.27 -10000 0 -0.64 23 23
ADCY7 -0.12 0.27 -10000 0 -0.64 22 22
ADCY1 -0.14 0.3 -10000 0 -0.69 23 23
ADCY2 -0.19 0.31 -10000 0 -0.62 42 42
ADCY3 -0.12 0.27 -10000 0 -0.64 22 22
ADCY8 -0.23 0.33 -10000 0 -0.67 39 39
ADCY9 -0.12 0.27 -10000 0 -0.65 21 21
arachidonic acid secretion -0.073 0.28 -10000 0 -0.66 22 22
ETB receptor/Endothelin-1/Gq/GTP -0.028 0.14 -10000 0 -0.44 9 9
GNAO1 -0.015 0.15 -10000 0 -0.78 5 5
HRAS 0.01 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.08 0.3 0.39 19 -0.6 20 39
ETA receptor/Endothelin-1/Gs/GTP -0.11 0.32 0.36 19 -0.6 31 50
mol:GTP 0 0.006 -10000 0 -10000 0 0
COL3A1 -0.2 0.42 -10000 0 -0.82 36 36
EDNRB 0.002 0.059 -10000 0 -0.39 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.16 0.38 -10000 0 -0.88 23 23
CYSLTR1 -0.11 0.3 -10000 0 -0.79 13 13
SLC9A1 -0.046 0.14 -10000 0 -0.37 7 7
mol:GDP -0.053 0.24 -10000 0 -0.6 15 15
SLC9A3 -0.035 0.2 -10000 0 -0.96 4 4
RAF1 -0.065 0.24 -10000 0 -0.57 20 20
JUN -0.1 0.35 -10000 0 -0.99 15 15
JAK2 -0.1 0.29 -10000 0 -0.6 26 26
mol:IP3 -0.05 0.21 -10000 0 -0.65 8 8
ETA receptor/Endothelin-1 -0.11 0.36 0.48 19 -0.69 26 45
PLCB1 0.01 0.005 -10000 0 -10000 0 0
PLCB2 0.004 0.072 -10000 0 -0.88 1 1
ETA receptor/Endothelin-3 -0.2 0.3 -10000 0 -0.63 44 44
FOS -0.11 0.37 -10000 0 -1 19 19
Gai/GDP -0.008 0.16 -10000 0 -0.93 4 4
CRK 0.011 0.003 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.3 -10000 0 -0.71 18 18
BCAR1 0.011 0.003 -10000 0 -10000 0 0
PRKCB1 -0.049 0.2 -10000 0 -0.59 9 9
GNAQ 0.011 0.006 -10000 0 -10000 0 0
GNAZ 0 0.1 -10000 0 -0.88 2 2
GNAL -0.05 0.22 -10000 0 -0.83 11 11
Gs family/GDP -0.12 0.21 -10000 0 -0.57 21 21
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.22 -10000 0 -0.57 14 14
MAPK14 -0.009 0.13 -10000 0 -0.56 3 3
TRPC6 -0.072 0.29 -10000 0 -0.8 13 13
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.072 -10000 0 -0.88 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.018 0.14 -10000 0 -0.46 7 7
ETB receptor/Endothelin-2 -0.07 0.17 -10000 0 -0.66 8 8
ETB receptor/Endothelin-3 -0.13 0.23 -10000 0 -0.66 19 19
ETB receptor/Endothelin-1 -0.025 0.14 -10000 0 -0.59 3 3
MAPK3 -0.095 0.33 -10000 0 -0.87 19 19
MAPK1 -0.095 0.33 -10000 0 -0.87 19 19
Rac1/GDP -0.042 0.22 -10000 0 -0.6 11 11
cAMP biosynthetic process -0.17 0.29 -10000 0 -0.7 25 25
MAPK8 -0.084 0.31 -10000 0 -0.74 18 18
SRC 0.011 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.006 0.083 -10000 0 -0.34 2 2
p130Cas/CRK/Src/PYK2 -0.054 0.26 -10000 0 -0.61 18 18
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.042 0.22 -10000 0 -0.6 11 11
COL1A2 -0.11 0.28 -10000 0 -0.71 14 14
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.14 0.28 -10000 0 -0.65 28 28
mol:DAG -0.05 0.21 -10000 0 -0.65 8 8
MAP2K2 -0.074 0.27 -10000 0 -0.67 20 20
MAP2K1 -0.074 0.27 -10000 0 -0.67 20 20
EDNRA -0.11 0.28 -10000 0 -0.62 27 27
positive regulation of muscle contraction -0.082 0.26 -10000 0 -0.68 12 12
Gq family/GDP -0.11 0.24 -10000 0 -0.7 16 16
HRAS/GTP -0.06 0.23 -10000 0 -0.55 17 17
PRKCH -0.041 0.2 -10000 0 -0.61 8 8
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.048 0.21 -10000 0 -0.61 10 10
PRKCB -0.062 0.24 -10000 0 -0.65 13 13
PRKCE -0.044 0.21 -10000 0 -0.67 8 8
PRKCD -0.042 0.2 -10000 0 -0.61 8 8
PRKCG -0.083 0.25 -10000 0 -0.65 18 18
regulation of vascular smooth muscle contraction -0.13 0.42 -10000 0 -1.2 19 19
PRKCQ -0.048 0.21 -10000 0 -0.61 10 10
PLA2G4A -0.086 0.32 -10000 0 -0.74 22 22
GNA14 -0.077 0.21 -10000 0 -0.5 26 26
GNA15 -0.019 0.15 -10000 0 -0.72 6 6
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 -0.007 0.12 -10000 0 -0.88 3 3
Rac1/GTP -0.08 0.3 0.39 19 -0.57 25 44
MMP1 -0.23 0.5 -10000 0 -1.2 28 28
Calcium signaling in the CD4+ TCR pathway

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.006 0.035 -9999 0 -10000 0 0
NFATC2 -0.077 0.21 -9999 0 -0.62 19 19
NFATC3 0.006 0.035 -9999 0 -10000 0 0
CD40LG -0.29 0.45 -9999 0 -0.98 34 34
PTGS2 -0.26 0.41 -9999 0 -0.91 33 33
JUNB 0.003 0.079 -9999 0 -0.63 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.008 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.01 -9999 0 -10000 0 0
JUN -0.07 0.23 -9999 0 -0.64 18 18
mol:Ca2+ -0.008 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.12 0.24 -9999 0 -0.48 39 39
CREM 0.011 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.2 0.26 -9999 0 -0.76 18 18
FOS -0.11 0.29 -9999 0 -0.74 24 24
IFNG -0.32 0.48 -9999 0 -0.98 44 44
AP-1/NFAT1-c-4 -0.4 0.51 -9999 0 -1.1 39 39
FASLG -0.28 0.45 -9999 0 -0.98 35 35
NFAT1-c-4/ICER1 -0.1 0.18 -9999 0 -0.54 19 19
IL2RA -0.28 0.44 -9999 0 -0.9 39 39
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.29 0.42 -9999 0 -0.83 46 46
JunB/Fra1/NFAT1-c-4 -0.15 0.23 -9999 0 -0.66 19 19
IL4 -0.26 0.39 -9999 0 -0.84 36 36
IL2 -0.006 0.021 -9999 0 -10000 0 0
IL3 -0.045 0.16 -9999 0 -1.2 3 3
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 -0.024 0.17 -9999 0 -0.88 6 6
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 -0.003 0.12 -9999 0 -0.88 3 3
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.1 0.22 -9999 0 -0.59 25 25
E-cadherin/beta catenin -0.12 0.25 -9999 0 -0.68 25 25
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.011 0 -9999 0 -10000 0 0
CDH1 -0.14 0.33 -9999 0 -0.84 27 27
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.31 -10000 0 -0.65 26 26
TBX21 -0.21 0.59 -10000 0 -1.5 23 23
B2M 0.004 0.073 -10000 0 -0.88 1 1
TYK2 0.016 0.019 -10000 0 -10000 0 0
IL12RB1 -0.082 0.28 -10000 0 -0.82 18 18
GADD45B -0.15 0.5 -10000 0 -1.2 22 22
IL12RB2 -0.016 0.18 -10000 0 -0.88 6 6
GADD45G -0.14 0.48 -10000 0 -1.2 22 22
natural killer cell activation 0.006 0.023 -10000 0 -10000 0 0
RELB 0.005 0.072 -10000 0 -0.88 1 1
RELA 0.011 0 -10000 0 -10000 0 0
IL18 -0.052 0.22 -10000 0 -0.65 15 15
IL2RA -0.079 0.26 -10000 0 -0.79 17 17
IFNG -0.18 0.36 -10000 0 -0.82 35 35
STAT3 (dimer) -0.13 0.42 -10000 0 -0.98 24 24
HLA-DRB5 -0.053 0.21 -10000 0 -0.66 14 14
FASLG -0.21 0.61 -10000 0 -1.6 22 22
NF kappa B2 p52/RelB -0.27 0.49 -10000 0 -1.3 26 26
CD4 -0.001 0.085 -10000 0 -0.55 3 3
SOCS1 0.005 0.072 -10000 0 -0.88 1 1
EntrezGene:6955 -0.004 0.013 -10000 0 -10000 0 0
CD3D -0.069 0.24 -10000 0 -0.78 15 15
CD3E -0.081 0.26 -10000 0 -0.79 17 17
CD3G -0.085 0.27 -10000 0 -0.82 17 17
IL12Rbeta2/JAK2 0.001 0.15 -10000 0 -0.7 6 6
CCL3 -0.2 0.57 -10000 0 -1.4 23 23
CCL4 -0.19 0.57 -10000 0 -1.4 22 22
HLA-A -0.001 0.1 -10000 0 -0.88 2 2
IL18/IL18R -0.084 0.32 -10000 0 -0.68 28 28
NOS2 -0.21 0.58 -10000 0 -1.4 27 27
IL12/IL12R/TYK2/JAK2/SPHK2 -0.12 0.3 -10000 0 -0.65 26 26
IL1R1 -0.19 0.55 -10000 0 -1.4 23 23
IL4 -0.009 0.062 -10000 0 -0.42 3 3
JAK2 0.016 0.019 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.2 0.58 -10000 0 -1.4 24 24
RAB7A -0.084 0.38 -10000 0 -0.91 20 20
lysosomal transport -0.075 0.36 -10000 0 -0.84 20 20
FOS -0.25 0.57 -10000 0 -1.3 33 33
STAT4 (dimer) -0.16 0.5 -10000 0 -1.2 23 23
STAT5A (dimer) -0.33 0.53 -10000 0 -1.2 33 33
GZMA -0.19 0.57 -10000 0 -1.5 20 20
GZMB -0.24 0.65 -10000 0 -1.6 26 26
HLX 0.003 0.055 -10000 0 -0.38 3 3
LCK -0.22 0.65 -10000 0 -1.5 25 25
TCR/CD3/MHC II/CD4 -0.14 0.4 -10000 0 -0.86 25 25
IL2/IL2R -0.12 0.31 -10000 0 -0.85 20 20
MAPK14 -0.14 0.5 -10000 0 -1.1 24 24
CCR5 -0.17 0.54 -10000 0 -1.4 21 21
IL1B -0.028 0.19 -10000 0 -0.73 9 9
STAT6 -0.013 0.13 0.26 1 -0.26 17 18
STAT4 0.005 0.072 -10000 0 -0.88 1 1
STAT3 0.005 0.072 -10000 0 -0.88 1 1
STAT1 0.011 0 -10000 0 -10000 0 0
NFKB1 0.011 0 -10000 0 -10000 0 0
NFKB2 0.011 0 -10000 0 -10000 0 0
IL12B -0.25 0.32 -10000 0 -0.54 71 71
CD8A -0.075 0.26 -10000 0 -0.84 15 15
CD8B -0.036 0.19 -10000 0 -0.77 9 9
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.3 0.64 26 -10000 0 26
IL2RB -0.015 0.15 -10000 0 -0.78 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.44 -10000 0 -1 23 23
IL2RG -0.087 0.26 -10000 0 -0.73 20 20
IL12 -0.18 0.28 -10000 0 -0.73 24 24
STAT5A 0.005 0.072 -10000 0 -0.88 1 1
CD247 -0.046 0.21 -10000 0 -0.83 10 10
IL2 0.006 0.006 -10000 0 -10000 0 0
SPHK2 0.003 0.055 -10000 0 -0.38 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.11 -10000 0 -0.9 2 2
IL12/IL12R/TYK2/JAK2 -0.31 0.91 0.48 1 -1.9 27 28
MAP2K3 -0.15 0.51 -10000 0 -1.2 24 24
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 -0.15 0.51 -10000 0 -1.2 24 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.027 0.17 -10000 0 -0.69 8 8
IL18RAP -0.11 0.29 -10000 0 -0.73 25 25
IL12Rbeta1/TYK2 -0.055 0.23 -10000 0 -0.72 15 15
EOMES -0.11 0.39 -10000 0 -1.5 10 10
STAT1 (dimer) -0.18 0.48 -10000 0 -1 32 32
T cell proliferation -0.073 0.34 -10000 0 -0.77 22 22
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.003 0.13 -10000 0 -0.88 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.32 -10000 0 -0.85 25 25
ATF2 -0.12 0.44 -10000 0 -1 24 24
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0 0 -9999 0 -10000 0 0
Necdin/E2F1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.16 0.3 -9999 0 -0.63 36 36
NGF (dimer)/p75(NTR)/BEX1 -0.23 0.35 -9999 0 -0.72 42 42
NT-4/5 (dimer)/p75(NTR) -0.084 0.22 -9999 0 -0.68 17 17
IKBKB 0.011 0 -9999 0 -10000 0 0
AKT1 -0.069 0.24 -9999 0 -0.61 22 22
IKBKG 0.011 0 -9999 0 -10000 0 0
BDNF -0.25 0.39 -9999 0 -0.78 49 49
MGDIs/NGR/p75(NTR)/LINGO1 -0.063 0.18 -9999 0 -0.59 16 16
FURIN 0.011 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.23 0.33 -9999 0 -0.67 48 48
LINGO1 0.011 0 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.023 0.098 -9999 0 -10000 0 0
proBDNF (dimer) -0.24 0.38 -9999 0 -0.77 49 49
NTRK1 0.003 0.055 -9999 0 -0.38 3 3
RTN4R 0.011 0 -9999 0 -10000 0 0
neuron apoptosis -0.16 0.3 -9999 0 -0.85 15 15
IRAK1 0.005 0.072 -9999 0 -0.88 1 1
SHC1 -0.093 0.26 -9999 0 -0.68 22 22
ARHGDIA 0.011 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.027 0.11 -9999 0 -0.51 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.24 -9999 0 -0.63 22 22
MAGEH1 0.006 0.045 -9999 0 -0.38 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.1 0.24 -9999 0 -0.63 22 22
Mammalian IAPs/DIABLO -0.038 0.14 -9999 0 -0.54 10 10
proNGF (dimer) -0.074 0.24 -9999 0 -0.63 20 20
MAGED1 0.003 0.079 -9999 0 -0.63 2 2
APP 0.011 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.005 0.095 -9999 0 -0.48 5 5
ZNF274 0.011 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.098 0.22 -9999 0 -0.6 22 22
NGF -0.074 0.24 -9999 0 -0.63 20 20
cell cycle arrest -0.067 0.24 -9999 0 -0.58 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.068 0.16 -9999 0 -0.71 5 5
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.073 0.19 -9999 0 -0.59 17 17
NCSTN 0.011 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.25 -9999 0 -0.68 22 22
PSENEN 0.011 0 -9999 0 -10000 0 0
mol:ceramide -0.077 0.24 -9999 0 -0.62 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.055 0.14 -9999 0 -0.62 5 5
p75(NTR)/beta APP -0.073 0.21 -9999 0 -0.68 16 16
BEX1 -0.17 0.32 -9999 0 -0.66 41 41
mol:GDP -0.1 0.26 -9999 0 -0.69 22 22
NGF (dimer) -0.32 0.31 -9999 0 -0.66 56 56
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.058 0.17 -9999 0 -0.54 16 16
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
RAC1/GTP -0.1 0.23 -9999 0 -0.61 22 22
MYD88 0.011 0 -9999 0 -10000 0 0
CHUK 0.011 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.26 -9999 0 -0.69 22 22
RHOB -0.002 0.071 -9999 0 -0.38 5 5
RHOA 0.011 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.16 0.3 -9999 0 -0.57 44 44
TP53 -0.16 0.29 -9999 0 -0.91 8 8
PRDM4 -0.078 0.25 -9999 0 -0.63 22 22
BDNF (dimer) -0.44 0.38 -9999 0 -0.77 71 71
PIK3CA 0.011 0 -9999 0 -10000 0 0
SORT1 0.011 0 -9999 0 -10000 0 0
activation of caspase activity -0.16 0.29 -9999 0 -0.62 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.24 -9999 0 -0.63 22 22
RHOC 0.011 0 -9999 0 -10000 0 0
XIAP 0.011 0 -9999 0 -10000 0 0
MAPK10 -0.15 0.27 -9999 0 -0.73 19 19
DIABLO 0.011 0 -9999 0 -10000 0 0
SMPD2 -0.078 0.25 -9999 0 -0.63 22 22
APH1B -0.036 0.2 -9999 0 -0.88 8 8
APH1A 0.011 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.12 0.26 -9999 0 -0.69 22 22
PSEN1 0.011 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.19 0.3 -9999 0 -0.74 30 30
MAPK8 -0.13 0.27 -9999 0 -0.72 17 17
MAPK9 -0.12 0.26 -9999 0 -0.73 15 15
APAF1 0.011 0 -9999 0 -10000 0 0
NTF3 -0.16 0.3 -9999 0 -0.57 44 44
NTF4 -0.005 0.096 -9999 0 -0.48 5 5
NDN 0.011 0 -9999 0 -10000 0 0
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.095 0.21 -9999 0 -0.55 22 22
p75 CTF/Sortilin/TRAF6/NRIF -0.011 0.076 -9999 0 -0.54 3 3
RhoA-B-C/GTP -0.11 0.25 -9999 0 -0.68 22 22
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.2 0.29 -9999 0 -0.58 48 48
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.21 0.3 -9999 0 -0.62 48 48
PRKACB 0.011 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.21 0.3 -9999 0 -0.68 42 42
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.053 0.22 -9999 0 -0.79 12 12
BIRC2 0.011 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.055 0.24 -9999 0 -0.61 17 17
BAD -0.13 0.26 -9999 0 -0.68 17 17
RIPK2 0.011 0 -9999 0 -10000 0 0
NGFR -0.083 0.27 -9999 0 -0.88 16 16
CYCS -0.071 0.24 -9999 0 -0.59 23 23
ADAM17 -0.006 0.12 -9999 0 -0.88 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.1 0.24 -9999 0 -0.63 22 22
BCL2L11 -0.13 0.26 -9999 0 -0.68 17 17
BDNF (dimer)/p75(NTR) -0.26 0.37 -9999 0 -0.76 48 48
PI3K -0.11 0.24 -9999 0 -0.65 22 22
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.1 0.24 -9999 0 -0.63 22 22
NDNL2 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
PRKCI 0.011 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.13 0.29 -9999 0 -0.78 22 22
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.11 0.24 -9999 0 -0.63 23 23
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCZ 0.011 0 -9999 0 -10000 0 0
PLG -0.15 0.28 -9999 0 -0.57 39 39
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.23 0.34 -9999 0 -0.91 21 21
SQSTM1 0.011 0 -9999 0 -10000 0 0
NGFRAP1 -0.1 0.3 -9999 0 -0.85 20 20
CASP3 -0.11 0.23 -9999 0 -0.61 17 17
E2F1 0.011 0 -9999 0 -10000 0 0
CASP9 0.011 0 -9999 0 -10000 0 0
IKK complex -0.067 0.16 -9999 0 -0.6 11 11
NGF (dimer)/TRKA -0.067 0.18 -9999 0 -0.65 12 12
MMP7 -0.31 0.38 -9999 0 -0.67 71 71
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.098 0.22 -9999 0 -0.6 22 22
MMP3 -0.032 0.11 -9999 0 -0.38 14 14
APAF-1/Caspase 9 -0.099 0.18 -9999 0 -0.71 5 5
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.018 0.09 -9999 0 -0.68 2 2
alphaV beta3 Integrin -0.13 0.24 -9999 0 -0.64 25 25
PTK2 -0.2 0.25 -9999 0 -0.6 28 28
IGF1R 0.011 0 -9999 0 -10000 0 0
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.005 0.072 -9999 0 -0.88 1 1
SRC 0.011 0 -9999 0 -10000 0 0
CDKN1B -0.27 0.34 -9999 0 -0.79 41 41
VEGFA 0.003 0.055 -9999 0 -0.38 3 3
ILK -0.27 0.34 -9999 0 -0.79 41 41
ROCK1 0.011 0 -9999 0 -10000 0 0
AKT1 -0.25 0.32 -9999 0 -0.73 41 41
PTK2B -0.029 0.17 -9999 0 -0.54 13 13
alphaV/beta3 Integrin/JAM-A -0.3 0.31 -9999 0 -0.65 56 56
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.069 0.16 -9999 0 -0.6 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.1 0.2 -9999 0 -0.54 25 25
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.18 -9999 0 -0.57 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.085 0.2 -9999 0 -0.61 16 16
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.34 -9999 0 -0.83 29 29
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.17 0.29 -9999 0 -0.68 33 33
RPS6KB1 -0.23 0.3 -9999 0 -0.79 26 26
TLN1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.26 0.36 -9999 0 -0.99 26 26
GPR124 -0.023 0.11 -9999 0 -0.38 13 13
MAPK1 -0.26 0.36 -9999 0 -0.99 26 26
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
alphaV/beta3 Integrin/Tumstatin -0.14 0.27 -9999 0 -0.64 31 31
cell adhesion -0.069 0.17 -9999 0 -0.56 14 14
ANGPTL3 -0.017 0.093 -9999 0 -0.38 9 9
VEGFR2 homodimer/VEGFA homodimer/Src -0.015 0.076 -9999 0 -0.59 2 2
IGF-1R heterotetramer 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0 0.1 -9999 0 -0.88 2 2
ITGB3 -0.069 0.23 -9999 0 -0.66 18 18
IGF1 -0.12 0.3 -9999 0 -0.76 25 25
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.073 0.16 -9999 0 -0.56 13 13
apoptosis 0.003 0.078 -9999 0 -0.63 2 2
CD47 -0.006 0.12 -9999 0 -0.88 3 3
alphaV/beta3 Integrin/CD47 -0.067 0.18 -9999 0 -0.59 14 14
VCL 0.006 0.045 -9999 0 -0.38 2 2
alphaV/beta3 Integrin/Del1 -0.18 0.29 -9999 0 -0.65 37 37
CSF1 0 0.1 -9999 0 -0.88 2 2
PIK3C2A -0.27 0.34 -9999 0 -0.79 41 41
PI4 Kinase/Pyk2 -0.25 0.28 -9999 0 -0.81 20 20
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.063 0.17 -9999 0 -0.57 13 13
FAK1/Vinculin -0.15 0.19 -9999 0 -0.49 21 21
alphaV beta3/Integrin/ppsTEM5 -0.073 0.17 -9999 0 -0.56 13 13
RHOA 0.011 0 -9999 0 -10000 0 0
VTN -0.34 0.37 -9999 0 -0.63 82 82
BCAR1 0.011 0 -9999 0 -10000 0 0
FGF2 -0.12 0.28 -9999 0 -0.63 30 30
F11R -0.081 0.22 -9999 0 -0.68 16 16
alphaV/beta3 Integrin/Lactadherin -0.059 0.18 -9999 0 -0.64 11 11
alphaV/beta3 Integrin/TGFBR2 -0.063 0.18 -9999 0 -0.64 12 12
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.012 0.077 -9999 0 -0.54 3 3
HSP90AA1 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.051 0.15 -9999 0 -0.55 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.27 -9999 0 -0.57 35 35
alphaV/beta3 Integrin/Pyk2 -0.062 0.16 -9999 0 -0.55 13 13
SDC1 -0.037 0.18 -9999 0 -0.59 12 12
VAV3 0.022 0.083 -9999 0 -0.5 3 3
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.037 0.18 -9999 0 -0.65 11 11
FAK1/Paxillin -0.15 0.19 -9999 0 -0.49 21 21
cell migration -0.13 0.18 -9999 0 -0.46 15 15
ITGAV 0.003 0.079 -9999 0 -0.63 2 2
PI3K -0.27 0.29 -9999 0 -0.84 20 20
SPP1 -0.18 0.34 -9999 0 -0.71 39 39
KDR -0.006 0.11 -9999 0 -0.63 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.003 0.079 -9999 0 -0.63 2 2
COL4A3 -0.13 0.32 -9999 0 -0.82 25 25
angiogenesis -0.27 0.36 -9999 0 -0.84 36 36
Rac1/GTP -0.014 0.068 -9999 0 -0.46 3 3
EDIL3 -0.18 0.35 -9999 0 -0.76 37 37
cell proliferation -0.063 0.18 -9999 0 -0.63 12 12
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.06 0.13 -10000 0 -0.35 25 25
epithelial cell differentiation -0.087 0.19 -10000 0 -0.51 25 25
CYFIP2 0.011 0 -10000 0 -10000 0 0
ENAH -0.037 0.17 -10000 0 -0.51 4 4
EGFR -0.043 0.19 -10000 0 -0.61 13 13
EPHA2 -0.1 0.29 -10000 0 -0.83 20 20
MYO6 -0.052 0.19 -10000 0 -0.48 25 25
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -10000 0 -10000 0 0
AQP5 -0.093 0.19 -10000 0 -0.7 5 5
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.05 0.19 -10000 0 -0.47 25 25
regulation of calcium-dependent cell-cell adhesion -0.051 0.19 -10000 0 -0.48 25 25
EGF -0.021 0.16 -10000 0 -0.79 6 6
NCKAP1 0.011 0 -10000 0 -10000 0 0
AQP3 -0.076 0.16 -10000 0 -0.63 1 1
cortical microtubule organization -0.087 0.19 -10000 0 -0.51 25 25
GO:0000145 -0.047 0.18 -10000 0 -0.45 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.088 0.19 -10000 0 -0.51 25 25
MLLT4 0.011 0 -10000 0 -10000 0 0
ARF6/GDP -0.12 0.2 -10000 0 -0.74 5 5
ARF6 0.011 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.07 0.18 -10000 0 -0.54 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.037 0.18 -10000 0 -0.44 25 25
PVRL2 0.011 0 -10000 0 -10000 0 0
ZYX -0.052 0.19 -10000 0 -0.48 25 25
ARF6/GTP -0.064 0.16 -10000 0 -0.5 18 18
CDH1 -0.14 0.33 -10000 0 -0.84 27 27
EGFR/EGFR/EGF/EGF -0.12 0.23 -10000 0 -0.55 31 31
RhoA/GDP -0.081 0.18 -10000 0 -0.48 25 25
actin cytoskeleton organization -0.044 0.19 -10000 0 -0.45 25 25
IGF-1R heterotetramer 0.011 0 -10000 0 -10000 0 0
GIT1 0.011 0 -10000 0 -10000 0 0
IGF1R 0.011 0 -10000 0 -10000 0 0
IGF1 -0.12 0.3 -10000 0 -0.76 25 25
DIAPH1 -0.008 0.015 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.087 0.19 0.51 25 -10000 0 25
RHOA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP -0.12 0.2 -10000 0 -0.74 5 5
CTNNA1 0.011 0 -10000 0 -10000 0 0
VCL -0.046 0.19 -10000 0 -0.47 25 25
EFNA1 0.006 0.045 -10000 0 -0.38 2 2
LPP -0.043 0.19 -10000 0 -0.45 25 25
Ephrin A1/EPHA2 -0.14 0.24 -10000 0 -0.52 39 39
SEC6/SEC8 -0.072 0.16 -10000 0 -10000 0 0
MGAT3 -0.053 0.2 -10000 0 -0.49 25 25
HGF/MET -0.16 0.24 -10000 0 -0.54 36 36
HGF -0.14 0.27 -10000 0 -0.54 41 41
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.06 0.13 -10000 0 -0.36 25 25
actin cable formation -0.009 0.15 -10000 0 -0.42 4 4
KIAA1543 -0.055 0.2 -10000 0 -0.46 29 29
KIFC3 -0.055 0.2 -10000 0 -0.48 26 26
NCK1 0.011 0 -10000 0 -10000 0 0
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 -0.052 0.19 -10000 0 -0.48 25 25
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.087 0.19 -10000 0 -0.51 25 25
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 -0.052 0.19 -10000 0 -0.48 25 25
PIP5K1C -0.052 0.19 -10000 0 -0.48 25 25
LIMA1 0.011 0 -10000 0 -10000 0 0
ABI1 0.011 0 -10000 0 -10000 0 0
ROCK1 -0.1 0.17 -10000 0 -0.61 5 5
adherens junction assembly -0.039 0.19 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.14 0.21 -10000 0 -0.46 44 44
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.02 0.15 -10000 0 -0.66 7 7
PLEKHA7 -0.066 0.21 -10000 0 -0.48 29 29
mol:GTP -0.069 0.18 -10000 0 -0.54 18 18
establishment of epithelial cell apical/basal polarity -0.017 0.17 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.06 0.13 -10000 0 -0.35 25 25
regulation of cell-cell adhesion -0.044 0.19 -10000 0 -0.45 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.06 0.13 -10000 0 -0.36 25 25
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.11 0.22 -10000 0 -0.54 19 19
CRKL -0.062 0.17 -10000 0 -0.43 17 17
HRAS -0.05 0.18 -10000 0 -0.57 5 5
mol:PIP3 -0.074 0.16 -10000 0 -0.42 19 19
SPRED1 0.011 0 -10000 0 -10000 0 0
SPRED2 0.011 0 -10000 0 -10000 0 0
GAB1 -0.073 0.17 -10000 0 -0.42 27 27
FOXO3 -0.051 0.15 -10000 0 -0.38 18 18
AKT1 -0.063 0.16 -10000 0 -0.39 27 27
BAD -0.051 0.15 -10000 0 -0.38 18 18
megakaryocyte differentiation -0.083 0.18 -10000 0 -0.42 29 29
GSK3B -0.051 0.15 -10000 0 -0.38 18 18
RAF1 -0.031 0.14 -10000 0 -0.51 3 3
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.076 0.18 -10000 0 -0.42 28 28
STAT1 -0.13 0.35 -10000 0 -1 17 17
HRAS/SPRED1 -0.069 0.12 -10000 0 -0.51 3 3
cell proliferation -0.085 0.19 -10000 0 -0.45 29 29
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
TEC -0.065 0.25 -10000 0 -0.88 13 13
RPS6KB1 -0.07 0.17 -10000 0 -0.42 27 27
HRAS/SPRED2 -0.069 0.12 -10000 0 -0.51 3 3
LYN/TEC/p62DOK -0.13 0.2 -10000 0 -0.55 17 17
MAPK3 -0.009 0.11 -10000 0 -0.34 3 3
STAP1 -0.14 0.23 -10000 0 -0.49 40 40
GRAP2 -0.018 0.15 -10000 0 -0.71 6 6
JAK2 -0.15 0.28 -10000 0 -0.86 17 17
STAT1 (dimer) -0.13 0.34 -10000 0 -1 17 17
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.11 0.18 -10000 0 -0.46 24 24
actin filament polymerization -0.1 0.22 -10000 0 -0.47 35 35
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.14 0.27 -10000 0 -0.59 32 32
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
CBL/CRKL/GRB2 -0.076 0.13 -10000 0 -0.43 4 4
PI3K -0.087 0.16 -10000 0 -0.44 18 18
PTEN 0.011 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.2 0.45 -10000 0 -1.4 15 15
MAPK8 -0.087 0.2 -10000 0 -0.46 29 29
STAT3 (dimer) -0.075 0.17 -10000 0 -0.41 28 28
positive regulation of transcription -0.004 0.092 -10000 0 -0.29 2 2
mol:GDP -0.096 0.17 -10000 0 -0.58 6 6
PIK3C2B -0.076 0.18 -10000 0 -0.47 19 19
CBL/CRKL -0.052 0.16 -10000 0 -0.45 4 4
FER -0.073 0.17 -10000 0 -0.42 27 27
SH2B3 -0.073 0.17 -10000 0 -0.42 27 27
PDPK1 -0.062 0.15 -10000 0 -0.38 19 19
SNAI2 -0.1 0.2 -10000 0 -0.46 27 27
positive regulation of cell proliferation -0.1 0.27 -10000 0 -0.73 18 18
KITLG -0.13 0.27 -10000 0 -0.53 39 39
cell motility -0.1 0.27 -10000 0 -0.73 18 18
PTPN6 0.009 0.012 -10000 0 -10000 0 0
EPOR -0.006 0.1 -10000 0 -10000 0 0
STAT5A (dimer) -0.085 0.23 -10000 0 -0.62 18 18
SOCS1 0.005 0.072 -10000 0 -0.88 1 1
cell migration 0.1 0.21 0.45 35 -10000 0 35
SOS1 0.011 0 -10000 0 -10000 0 0
EPO -0.047 0.21 -10000 0 -0.71 12 12
VAV1 -0.024 0.17 -10000 0 -0.88 6 6
GRB10 -0.073 0.17 -10000 0 -0.42 27 27
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.1 0.17 -10000 0 -0.45 27 27
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.015 0.12 -10000 0 -0.38 3 3
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.14 0.46 -10000 0 -1.5 15 15
MAP2K2 -0.015 0.12 -10000 0 -0.38 3 3
SHC/Grb2/SOS1 -0.085 0.15 -10000 0 -0.42 17 17
STAT5A -0.088 0.23 -10000 0 -0.64 18 18
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.1 0.19 -10000 0 -0.45 27 27
SHC/GRAP2 -0.022 0.11 -10000 0 -0.68 4 4
PTPRO -0.085 0.18 -10000 0 -0.43 29 29
SH2B2 -0.11 0.23 -10000 0 -0.48 35 35
DOK1 0.005 0.072 -10000 0 -0.88 1 1
MATK -0.1 0.21 -10000 0 -0.46 35 35
CREBBP 0.028 0.014 -10000 0 -10000 0 0
BCL2 -0.013 0.16 -10000 0 -1.5 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.21 0.32 -9999 0 -0.7 38 38
SMAD6-7/SMURF1 -0.008 0.068 -9999 0 -0.59 2 2
NOG -0.25 0.36 -9999 0 -0.66 58 58
SMAD9 -0.11 0.18 -9999 0 -0.51 25 25
SMAD4 0.011 0 -9999 0 -10000 0 0
SMAD5 -0.014 0.12 -9999 0 -0.69 1 1
BMP7/USAG1 -0.18 0.3 -9999 0 -0.68 39 39
SMAD5/SKI -0.007 0.11 -9999 0 -0.65 1 1
SMAD1 0.04 0.024 -9999 0 -10000 0 0
BMP2 -0.12 0.26 -9999 0 -0.56 33 33
SMAD1/SMAD1/SMAD4 -0.006 0.043 -9999 0 -10000 0 0
BMPR1A 0.011 0 -9999 0 -10000 0 0
BMPR1B -0.024 0.17 -9999 0 -0.88 6 6
BMPR1A-1B/BAMBI -0.028 0.12 -9999 0 -0.59 7 7
AHSG -0.25 0.34 -9999 0 -0.62 60 60
CER1 -0.29 0.36 -9999 0 -0.63 71 71
BMP2-4/CER1 -0.29 0.32 -9999 0 -0.61 65 65
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.064 0.13 -9999 0 -0.52 5 5
BMP2-4 (homodimer) -0.13 0.25 -9999 0 -0.68 21 21
RGMB 0.003 0.079 -9999 0 -0.63 2 2
BMP6/BMPR2/BMPR1A-1B -0.035 0.13 -9999 0 -0.54 9 9
RGMA -0.009 0.13 -9999 0 -0.75 4 4
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.065 0.14 -9999 0 -0.54 6 6
BMP2-4/USAG1 -0.2 0.29 -9999 0 -0.61 45 45
SMAD6/SMURF1/SMAD5 -0.007 0.11 -9999 0 -0.65 1 1
SOSTDC1 -0.13 0.32 -9999 0 -0.88 24 24
BMP7/BMPR2/BMPR1A-1B -0.081 0.2 -9999 0 -0.57 20 20
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.012 0.13 -9999 0 -0.68 5 5
HFE2 -0.024 0.16 -9999 0 -0.74 7 7
ZFYVE16 0.011 0 -9999 0 -10000 0 0
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.12 0.23 -9999 0 -0.61 23 23
SMAD5/SMAD5/SMAD4 -0.007 0.11 -9999 0 -0.65 1 1
MAPK1 0.011 0 -9999 0 -10000 0 0
TAK1/TAB family -0.052 0.11 -9999 0 -0.52 4 4
BMP7 (homodimer) -0.09 0.27 -9999 0 -0.75 20 20
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA -0.2 0.28 -9999 0 -0.7 31 31
SMAD1/SKI 0.045 0.023 -9999 0 -10000 0 0
SMAD6 0.005 0.072 -9999 0 -0.88 1 1
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.26 0.31 -9999 0 -0.59 63 63
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.12 0.27 -9999 0 -0.58 33 33
BMPR2 (homodimer) 0.011 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.027 0.13 -9999 0 -0.68 6 6
CHRDL1 -0.14 0.3 -9999 0 -0.66 34 34
ENDOFIN/SMAD1 0.045 0.023 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.007 0.049 -9999 0 -10000 0 0
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI 0.005 0.072 -9999 0 -0.88 1 1
SMURF2 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.3 -9999 0 -0.66 38 38
BMP2-4/GREM1 -0.18 0.29 -9999 0 -0.66 33 33
SMAD7 0.005 0.072 -9999 0 -0.88 1 1
SMAD8A/SMAD8A/SMAD4 -0.078 0.18 -9999 0 -0.47 25 25
SMAD1/SMAD6 0.045 0.023 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.09 0.27 -9999 0 -0.75 20 20
BMP6 -0.012 0.13 -9999 0 -0.68 5 5
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.03 0.13 -9999 0 -0.51 5 5
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.045 0.023 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.005 0.055 -9999 0 -0.68 1 1
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.011 0 -9999 0 -10000 0 0
CTDSP1 0.011 0 -9999 0 -10000 0 0
PPP1R15A 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.15 0.23 -9999 0 -0.68 19 19
CHRD -0.006 0.11 -9999 0 -0.63 4 4
BMPR2 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.075 0.15 -9999 0 -0.56 7 7
BMP4 -0.042 0.18 -9999 0 -0.56 14 14
FST -0.25 0.36 -9999 0 -0.65 60 60
BMP2-4/NOG -0.26 0.36 -9999 0 -0.68 53 53
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.076 0.18 -9999 0 -0.53 20 20
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.041 0.21 -10000 0 -0.97 7 7
NFATC2 -0.12 0.36 -10000 0 -0.89 22 22
NFATC3 0.007 0.063 -10000 0 -10000 0 0
CD40LG -0.35 0.52 -10000 0 -1.3 28 28
ITCH -0.052 0.12 -10000 0 -10000 0 0
CBLB -0.052 0.12 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.36 0.56 -10000 0 -1.4 28 28
JUNB 0.003 0.079 -10000 0 -0.63 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.1 0.13 -10000 0 -10000 0 0
T cell anergy -0.11 0.18 -10000 0 -0.46 25 25
TLE4 -0.072 0.28 -10000 0 -0.81 12 12
Jun/NFAT1-c-4/p21SNFT -0.24 0.38 -10000 0 -1.1 17 17
AP-1/NFAT1-c-4 -0.41 0.55 -10000 0 -1.4 28 28
IKZF1 -0.086 0.33 -10000 0 -0.96 12 12
T-helper 2 cell differentiation -0.11 0.31 -10000 0 -0.8 19 19
AP-1/NFAT1 -0.25 0.35 -10000 0 -0.75 40 40
CALM1 -0.038 0.08 -10000 0 -10000 0 0
EGR2 -0.076 0.33 -10000 0 -1.5 4 4
EGR3 -0.091 0.37 -10000 0 -1.4 7 7
NFAT1/FOXP3 -0.17 0.35 -10000 0 -0.86 23 23
EGR1 -0.002 0.09 -10000 0 -0.5 4 4
JUN -0.078 0.23 -10000 0 -0.65 18 18
EGR4 -0.079 0.25 -10000 0 -0.69 19 19
mol:Ca2+ -0.057 0.085 -10000 0 -10000 0 0
GBP3 -0.1 0.35 -10000 0 -0.87 19 19
FOSL1 -0.12 0.24 -10000 0 -0.48 39 39
NFAT1-c-4/MAF/IRF4 -0.19 0.38 -10000 0 -1.1 16 16
DGKA -0.082 0.3 -10000 0 -0.84 14 14
CREM 0.011 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.16 0.32 -10000 0 -1.1 9 9
CTLA4 -0.16 0.45 -10000 0 -1.1 23 23
NFAT1-c-4 (dimer)/EGR1 -0.16 0.33 -10000 0 -1.1 10 10
NFAT1-c-4 (dimer)/EGR4 -0.2 0.35 -10000 0 -1.1 12 12
FOS -0.12 0.29 -10000 0 -0.74 24 24
IFNG -0.42 0.68 -10000 0 -1.5 37 37
T cell activation -0.093 0.26 -10000 0 -0.76 8 8
MAF 0.005 0.072 -10000 0 -0.88 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.043 0.2 0.77 4 -10000 0 4
TNF -0.18 0.41 -10000 0 -1.1 17 17
FASLG -0.23 0.62 -10000 0 -1.7 20 20
TBX21 -0.088 0.28 -10000 0 -0.92 15 15
BATF3 -0.024 0.17 -10000 0 -0.88 6 6
PRKCQ -0.003 0.11 -10000 0 -0.92 2 2
PTPN1 -0.072 0.28 -10000 0 -0.83 11 11
NFAT1-c-4/ICER1 -0.15 0.31 -10000 0 -1.1 8 8
GATA3 -0.038 0.17 -10000 0 -0.52 14 14
T-helper 1 cell differentiation -0.39 0.63 -10000 0 -1.4 37 37
IL2RA -0.32 0.49 -10000 0 -1.2 28 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.072 0.28 -10000 0 -0.72 17 17
E2F1 0.017 0 -10000 0 -10000 0 0
PPARG 0 0.1 -10000 0 -0.88 2 2
SLC3A2 -0.072 0.28 -10000 0 -0.83 11 11
IRF4 -0.068 0.25 -10000 0 -0.84 14 14
PTGS2 -0.32 0.48 -10000 0 -1.2 26 26
CSF2 -0.34 0.49 -10000 0 -1.1 32 32
JunB/Fra1/NFAT1-c-4 -0.19 0.34 -10000 0 -1.2 9 9
IL4 -0.11 0.33 -10000 0 -0.88 17 17
IL5 -0.3 0.46 -10000 0 -1.1 28 28
IL2 -0.095 0.27 -10000 0 -0.78 8 8
IL3 -0.074 0.16 -10000 0 -1.1 3 3
RNF128 -0.21 0.36 -10000 0 -0.93 25 25
NFATC1 -0.043 0.2 -10000 0 -0.78 4 4
CDK4 0.053 0.18 0.72 2 -10000 0 2
PTPRK -0.1 0.33 -10000 0 -0.92 14 14
IL8 -0.38 0.51 -10000 0 -1.2 31 31
POU2F1 -0.003 0.12 -10000 0 -0.88 3 3
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.031 0.053 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.085 0.15 -9999 0 -0.51 6 6
JUN -0.093 0.21 -9999 0 -0.55 16 16
HRAS 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.13 0.23 -9999 0 -0.61 24 24
RAP1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.009 0.032 -9999 0 -0.38 1 1
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.14 0.24 -9999 0 -0.61 25 25
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.2 -9999 0 -0.53 25 25
RHOA 0.011 0 -9999 0 -10000 0 0
RAP1A/GTP -0.12 0.21 -9999 0 -0.55 24 24
GRB7 -0.02 0.15 -9999 0 -0.66 7 7
RET51/GFRalpha1/GDNF -0.13 0.23 -9999 0 -0.61 24 24
MAPKKK cascade -0.1 0.19 -9999 0 -0.51 17 17
BCAR1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.15 0.23 -9999 0 -0.54 33 33
lamellipodium assembly -0.081 0.14 -9999 0 -0.37 24 24
RET51/GFRalpha1/GDNF/SHC -0.13 0.23 -9999 0 -0.61 24 24
PIK3CA 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.12 0.2 -9999 0 -0.53 25 25
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.2 -9999 0 -0.53 25 25
MAPK3 -0.085 0.21 -9999 0 -0.51 24 24
DOK1 0.005 0.072 -9999 0 -0.88 1 1
DOK6 -0.052 0.16 -9999 0 -0.4 23 23
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.11 0.18 -9999 0 -0.7 5 5
DOK5 -0.029 0.13 -9999 0 -0.42 14 14
GFRA1 -0.18 0.32 -9999 0 -0.62 46 46
MAPK8 -0.062 0.17 -9999 0 -0.59 7 7
HRAS/GTP -0.12 0.22 -9999 0 -0.56 25 25
tube development -0.11 0.19 -9999 0 -0.52 22 22
MAPK1 -0.085 0.21 -9999 0 -0.51 24 24
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.07 0.13 -9999 0 -0.36 22 22
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.032 -9999 0 -0.38 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.24 -9999 0 -0.58 28 28
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.14 0.23 -9999 0 -0.61 24 24
RET51/GFRalpha1/GDNF/Dok5 -0.15 0.24 -9999 0 -0.55 36 36
PRKCA -0.002 0.09 -9999 0 -0.51 4 4
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.077 0.15 -9999 0 -0.43 22 22
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.069 0.13 -9999 0 -0.36 22 22
RET51/GFRalpha1/GDNF/Grb7 -0.15 0.24 -9999 0 -0.61 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.018 0.16 -9999 0 -0.88 5 5
DOK4 0.006 0.045 -9999 0 -0.38 2 2
JNK cascade -0.091 0.2 -9999 0 -0.54 16 16
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.2 -9999 0 -0.53 26 26
SHANK3 0.011 0 -9999 0 -10000 0 0
RASA1 0.011 0 -9999 0 -10000 0 0
NCK1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.069 0.13 -9999 0 -0.36 22 22
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.08 0.15 -9999 0 -0.42 17 17
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.081 0.15 -9999 0 -0.4 25 25
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.086 0.18 -9999 0 -0.44 24 24
PI3K -0.13 0.23 -9999 0 -0.59 24 24
SOS1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.19 -9999 0 -0.52 22 22
GRB10 0.011 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.074 0.14 -9999 0 -0.6 3 3
RET51/GFRalpha1/GDNF/FRS2 -0.13 0.23 -9999 0 -0.61 24 24
GAB1 0.011 0 -9999 0 -10000 0 0
IRS1 -0.037 0.18 -9999 0 -0.65 11 11
IRS2 0.003 0.079 -9999 0 -0.63 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.086 0.18 -9999 0 -0.44 24 24
RET51/GFRalpha1/GDNF/PKC alpha -0.14 0.24 -9999 0 -0.61 27 27
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF -0.007 0.07 -9999 0 -0.38 5 5
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.16 0.26 -9999 0 -0.62 30 30
Rac1/GTP -0.097 0.17 -9999 0 -0.45 24 24
RET9/GFRalpha1/GDNF -0.13 0.22 -9999 0 -0.58 25 25
GFRalpha1/GDNF -0.15 0.25 -9999 0 -0.66 25 25
IL27-mediated signaling events

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
TGFB1 0.006 0.073 -10000 0 -0.88 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.12 0.22 0.58 18 -10000 0 18
IL27/IL27R/JAK1 -0.18 0.3 -10000 0 -0.89 12 12
TBX21 -0.13 0.32 -10000 0 -0.86 17 17
IL12B -0.25 0.32 -10000 0 -0.54 71 71
IL12A 0 0.08 -10000 0 -0.69 2 2
IL6ST -0.15 0.34 -10000 0 -0.86 27 27
IL27RA/JAK1 0.003 0.031 -10000 0 -10000 0 0
IL27 -0.059 0.24 -10000 0 -0.85 12 12
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.038 0.13 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.12 0.22 0.58 18 -10000 0 18
T cell proliferation during immune response 0.12 0.22 0.58 18 -10000 0 18
MAPKKK cascade -0.12 0.22 -10000 0 -0.58 18 18
STAT3 0.005 0.072 -10000 0 -0.88 1 1
STAT2 0.011 0 -10000 0 -10000 0 0
STAT1 0.012 0.001 -10000 0 -10000 0 0
IL12RB1 -0.086 0.27 -10000 0 -0.8 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.12 0.29 -10000 0 -0.74 17 17
IL27/IL27R/JAK2/TYK2 -0.12 0.22 -10000 0 -0.59 18 18
positive regulation of T cell mediated cytotoxicity -0.12 0.22 -10000 0 -0.58 18 18
STAT1 (dimer) -0.22 0.39 0.52 1 -1.2 13 14
JAK2 0.01 0.006 -10000 0 -10000 0 0
JAK1 0.012 0.001 -10000 0 -10000 0 0
STAT2 (dimer) -0.11 0.21 -10000 0 -0.56 17 17
T cell proliferation -0.16 0.3 -10000 0 -0.69 28 28
IL12/IL12R/TYK2/JAK2 -0.22 0.45 -10000 0 -1.1 29 29
IL17A -0.039 0.13 -10000 0 -10000 0 0
mast cell activation 0.12 0.22 0.58 18 -10000 0 18
IFNG -0.03 0.058 -10000 0 -0.13 32 32
T cell differentiation -0.007 0.01 -10000 0 -0.025 27 27
STAT3 (dimer) -0.12 0.22 -10000 0 -0.57 18 18
STAT5A (dimer) -0.12 0.22 -10000 0 -0.6 16 16
STAT4 (dimer) -0.12 0.22 -10000 0 -0.59 17 17
STAT4 0.005 0.072 -10000 0 -0.88 1 1
T cell activation -0.011 0.007 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.11 0.2 -10000 0 -0.61 4 4
GATA3 -0.022 0.26 -10000 0 -1.5 4 4
IL18 -0.04 0.16 -10000 0 -0.49 15 15
positive regulation of mast cell cytokine production -0.12 0.21 -10000 0 -0.56 18 18
IL27/EBI3 -0.099 0.28 -10000 0 -0.83 17 17
IL27RA -0.007 0.031 -10000 0 -10000 0 0
IL6 -0.094 0.28 -10000 0 -0.82 19 19
STAT5A 0.005 0.072 -10000 0 -0.88 1 1
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.01 0.016 -10000 0 -10000 0 0
IL1B -0.023 0.14 -10000 0 -0.55 9 9
EBI3 -0.055 0.23 -10000 0 -0.8 12 12
TNF -0.042 0.18 -10000 0 -0.59 13 13
Caspase cascade in apoptosis

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
TOP1 -0.072 0.23 -10000 0 -0.59 23 23
ACTA1 -0.16 0.29 -10000 0 -0.79 23 23
NUMA1 -0.072 0.23 -10000 0 -0.59 23 23
SPTAN1 -0.097 0.29 -10000 0 -0.76 22 22
LIMK1 -0.097 0.29 -10000 0 -0.76 22 22
BIRC3 -0.053 0.22 -10000 0 -0.79 12 12
BIRC2 0.009 0.004 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
CASP10 -0.12 0.34 -10000 0 -0.83 26 26
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.003 -10000 0 -10000 0 0
PTK2 -0.072 0.23 -10000 0 -0.59 23 23
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.094 0.28 -10000 0 -0.74 22 22
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.006 0.12 -10000 0 -0.88 3 3
GSN -0.1 0.3 -10000 0 -0.76 23 23
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A -0.074 0.29 -10000 0 -0.93 14 14
BID -0.042 0.16 -10000 0 -0.36 25 25
MAP3K1 -0.02 0.081 -10000 0 -0.24 5 5
TRADD 0 0.1 -10000 0 -0.88 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.1 0.3 -10000 0 -0.76 24 24
CASP9 0.012 0 -10000 0 -10000 0 0
DNA repair 0.003 0.051 0.18 5 -10000 0 5
neuron apoptosis 0.006 0.065 -10000 0 -0.69 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.088 0.28 -10000 0 -0.74 22 22
APAF1 0.011 0 -10000 0 -10000 0 0
CASP6 -0.036 0.17 -10000 0 -0.58 9 9
TRAF2 0.011 0 -10000 0 -10000 0 0
ICAD/CAD -0.086 0.28 -10000 0 -0.73 22 22
CASP7 0.024 0.11 0.42 10 -10000 0 10
KRT18 -0.23 0.29 -10000 0 -0.63 52 52
apoptosis -0.067 0.24 -10000 0 -0.61 23 23
DFFA -0.097 0.29 -10000 0 -0.76 22 22
DFFB -0.097 0.29 -10000 0 -0.76 22 22
PARP1 -0.003 0.052 -10000 0 -0.18 5 5
actin filament polymerization 0.085 0.27 0.68 23 -10000 0 23
TNF -0.056 0.23 -10000 0 -0.76 13 13
CYCS -0.025 0.11 -10000 0 -0.26 25 25
SATB1 -0.03 0.16 -10000 0 -0.55 9 9
SLK -0.097 0.29 -10000 0 -0.76 22 22
p15 BID/BAX -0.033 0.14 -10000 0 -0.4 12 12
CASP2 -0.002 0.13 -10000 0 -0.48 7 7
JNK cascade 0.02 0.081 0.24 5 -10000 0 5
CASP3 -0.11 0.31 -10000 0 -0.79 23 23
LMNB2 -0.008 0.13 -10000 0 -0.47 8 8
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0 0.1 -10000 0 -0.88 2 2
Mammalian IAPs/DIABLO -0.038 0.14 -10000 0 -0.54 10 10
negative regulation of DNA binding -0.072 0.28 -10000 0 -0.91 14 14
stress fiber formation -0.094 0.28 -10000 0 -0.74 22 22
GZMB -0.14 0.38 -10000 0 -0.93 26 26
CASP1 0 0.14 -10000 0 -1.2 2 2
LMNB1 -0.008 0.13 -10000 0 -0.45 9 9
APP 0.006 0.066 -10000 0 -0.7 1 1
TNFRSF1A 0 0.1 -10000 0 -0.88 2 2
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.057 -10000 0 -0.69 1 1
VIM -0.069 0.23 -10000 0 -0.59 23 23
LMNA -0.008 0.13 -10000 0 -0.45 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.048 0.13 -10000 0 -0.52 7 7
LRDD 0.011 0 -10000 0 -10000 0 0
SREBF1 -0.097 0.29 -10000 0 -0.76 22 22
APAF-1/Caspase 9 -0.003 0.038 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.07 0.23 -10000 0 -0.58 23 23
CFL2 -0.089 0.28 -10000 0 -0.71 23 23
GAS2 -0.15 0.33 -10000 0 -0.82 25 25
positive regulation of apoptosis -0.004 0.13 -10000 0 -0.46 8 8
PRF1 -0.065 0.24 -10000 0 -0.8 14 14
Noncanonical Wnt signaling pathway

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
NFATC2 -0.11 0.3 -9999 0 -0.83 21 21
GNB1/GNG2 -0.12 0.2 -9999 0 -0.8 8 8
mol:DAG -0.075 0.2 -9999 0 -0.71 8 8
PLCG1 -0.079 0.2 -9999 0 -0.74 8 8
YES1 -0.1 0.22 -9999 0 -0.84 8 8
FZD3 0.005 0.072 -9999 0 -0.88 1 1
FZD6 0.009 0.032 -9999 0 -0.38 1 1
G protein -0.12 0.21 -9999 0 -0.79 9 9
MAP3K7 -0.098 0.2 -9999 0 -0.55 12 12
mol:Ca2+ -0.073 0.19 -9999 0 -0.68 8 8
mol:IP3 -0.075 0.2 -9999 0 -0.71 8 8
NLK -0.007 0.011 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.22 -9999 0 -0.53 24 24
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.22 -9999 0 -0.5 28 28
CSNK1A1 0.011 0 -9999 0 -10000 0 0
GNAS -0.11 0.24 -9999 0 -0.89 9 9
GO:0007205 -0.073 0.19 -9999 0 -0.69 8 8
WNT6 -0.075 0.24 -9999 0 -0.67 19 19
WNT4 -0.076 0.17 -9999 0 -0.4 32 32
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.69 15 15
GNG2 0.009 0.032 -9999 0 -0.38 1 1
WNT5A -0.076 0.2 -9999 0 -0.48 27 27
WNT11 -0.14 0.28 -9999 0 -0.56 38 38
CDC42 -0.087 0.21 -9999 0 -0.78 8 8
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.095 0.22 -10000 0 -0.65 18 18
FYN -0.073 0.34 -10000 0 -0.92 18 18
LAT/GRAP2/SLP76 -0.096 0.24 -10000 0 -0.68 19 19
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 -0.019 0.2 -10000 0 -0.51 19 19
B2M 0.005 0.073 -10000 0 -0.88 1 1
IKBKG -0.022 0.048 -10000 0 -0.18 5 5
MAP3K8 -0.006 0.12 -10000 0 -0.88 3 3
mol:Ca2+ -0.02 0.04 -10000 0 -0.12 16 16
integrin-mediated signaling pathway -0.012 0.084 -10000 0 -0.6 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.056 0.31 -10000 0 -0.76 21 21
TRPV6 -0.067 0.21 -10000 0 -0.58 19 19
CD28 -0.001 0.086 -10000 0 -0.55 3 3
SHC1 -0.072 0.33 -10000 0 -0.88 19 19
receptor internalization -0.094 0.37 -10000 0 -0.99 19 19
PRF1 -0.12 0.45 -10000 0 -1.3 17 17
KRAS 0.006 0.045 -10000 0 -0.38 2 2
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 -0.01 0.17 -10000 0 -0.42 19 19
LAT -0.072 0.33 -10000 0 -0.87 19 19
EntrezGene:6955 0 0.005 -10000 0 -10000 0 0
CD3D -0.068 0.25 -10000 0 -0.79 15 15
CD3E -0.079 0.26 -10000 0 -0.8 17 17
CD3G -0.083 0.27 -10000 0 -0.82 17 17
RASGRP2 0.001 0.038 -10000 0 -0.19 4 4
RASGRP1 -0.011 0.21 -10000 0 -0.52 18 18
HLA-A -0.001 0.1 -10000 0 -0.88 2 2
RASSF5 -0.006 0.12 -10000 0 -0.88 3 3
RAP1A/GTP/RAPL -0.012 0.084 -10000 0 -0.6 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.062 -10000 0 -0.13 13 13
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.04 0.087 -10000 0 -0.29 11 11
PRKCA -0.044 0.11 -10000 0 -0.3 18 18
GRAP2 -0.018 0.15 -10000 0 -0.71 6 6
mol:IP3 -0.055 0.19 0.29 7 -0.48 20 27
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.49 -10000 0 -1.2 19 19
ORAI1 0.026 0.14 0.4 7 -0.69 3 10
CSK -0.077 0.34 -10000 0 -0.9 19 19
B7 family/CD28 -0.15 0.35 -10000 0 -0.93 22 22
CHUK 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.41 -10000 0 -1.1 19 19
PTPN6 -0.083 0.35 -10000 0 -0.93 19 19
VAV1 -0.082 0.35 -10000 0 -0.88 21 21
Monovalent TCR/CD3 -0.13 0.45 -10000 0 -1.1 22 22
CBL 0.011 0 -10000 0 -10000 0 0
LCK -0.088 0.37 -10000 0 -1 18 18
PAG1 -0.08 0.34 -10000 0 -0.91 19 19
RAP1A 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.11 0.42 -10000 0 -1.1 19 19
CD80 -0.06 0.24 -10000 0 -0.8 13 13
CD86 -0.014 0.14 -10000 0 -0.88 4 4
PDK1/CARD11/BCL10/MALT1 -0.05 0.11 -10000 0 -0.34 13 13
HRAS 0.011 0 -10000 0 -10000 0 0
GO:0035030 -0.064 0.29 -10000 0 -0.71 22 22
CD8A -0.074 0.26 -10000 0 -0.85 15 15
CD8B -0.035 0.19 -10000 0 -0.77 9 9
PTPRC -0.037 0.19 -10000 0 -0.77 9 9
PDK1/PKC theta -0.025 0.25 -10000 0 -0.64 19 19
CSK/PAG1 -0.072 0.33 -10000 0 -0.87 19 19
SOS1 0.011 0 -10000 0 -10000 0 0
peptide-MHC class I -0.013 0.12 -10000 0 -0.96 2 2
GRAP2/SLP76 -0.12 0.29 -10000 0 -0.82 20 20
STIM1 0.018 0.093 -10000 0 -0.89 1 1
RAS family/GTP 0.024 0.084 -10000 0 -0.19 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.11 0.42 -10000 0 -1.1 19 19
mol:DAG -0.06 0.16 -10000 0 -0.43 20 20
RAP1A/GDP 0.01 0.027 -10000 0 -10000 0 0
PLCG1 0.011 0 -10000 0 -10000 0 0
CD247 -0.045 0.21 -10000 0 -0.83 10 10
cytotoxic T cell degranulation -0.11 0.41 -10000 0 -1.2 17 17
RAP1A/GTP -0.004 0.012 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.24 -10000 0 -0.6 21 21
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.079 0.25 0.3 7 -0.65 20 27
NRAS 0.011 0 -10000 0 -10000 0 0
ZAP70 -0.021 0.14 -10000 0 -0.57 8 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.098 0.23 -10000 0 -0.66 20 20
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
CD8 heterodimer -0.097 0.28 -10000 0 -0.84 17 17
CARD11 -0.031 0.17 -10000 0 -0.63 10 10
PRKCB -0.049 0.13 -10000 0 -0.38 17 17
PRKCE -0.043 0.11 -10000 0 -0.3 18 18
PRKCQ -0.045 0.29 -10000 0 -0.74 20 20
LCP2 0 0.1 -10000 0 -0.88 2 2
BCL10 0.011 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.009 0.17 -10000 0 -0.42 19 19
IKK complex 0.027 0.062 -10000 0 -0.13 9 9
RAS family/GDP -0.004 0.01 -10000 0 -10000 0 0
MAP3K14 0.005 0.13 -10000 0 -0.32 16 16
PDPK1 -0.013 0.19 -10000 0 -0.48 19 19
TCR/CD3/MHC I/CD8/Fyn -0.12 0.43 -10000 0 -1.1 21 21
IL6-mediated signaling events

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
BCL2L1 -0.11 0.27 -9999 0 -0.76 8 8
CRP -0.12 0.27 -9999 0 -0.72 11 11
cell cycle arrest -0.14 0.3 -9999 0 -0.75 16 16
TIMP1 -0.12 0.29 -9999 0 -0.72 16 16
IL6ST -0.14 0.34 -9999 0 -0.86 27 27
Rac1/GDP -0.12 0.27 -9999 0 -0.7 17 17
AP1 -0.085 0.24 -9999 0 -0.6 20 20
GAB2 -0.003 0.11 -9999 0 -0.71 3 3
TNFSF11 -0.17 0.37 -9999 0 -0.96 18 18
HSP90B1 0.011 0.053 -9999 0 -10000 0 0
GAB1 0.012 0.002 -9999 0 -10000 0 0
MAPK14 -0.088 0.22 -9999 0 -0.66 11 11
AKT1 0.042 0.047 -9999 0 -10000 0 0
FOXO1 0.049 0.045 -9999 0 -10000 0 0
MAP2K6 -0.1 0.23 -9999 0 -0.56 19 19
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.1 0.27 -9999 0 -0.69 17 17
MITF -0.11 0.23 -9999 0 -0.56 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.011 0 -9999 0 -10000 0 0
A2M 0.019 0.03 -9999 0 -10000 0 0
CEBPB 0.016 0.032 -9999 0 -0.38 1 1
GRB2/SOS1/GAB family/SHP2 -0.031 0.11 -9999 0 -0.52 2 2
STAT3 -0.15 0.32 -9999 0 -0.81 16 16
STAT1 -0.012 0.019 -9999 0 -10000 0 0
CEBPD -0.11 0.28 -9999 0 -0.81 8 8
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K -0.005 0.055 -9999 0 -0.68 1 1
JUN -0.066 0.22 -9999 0 -0.63 18 18
PIAS3/MITF -0.1 0.22 -9999 0 -0.63 12 12
MAPK11 -0.091 0.23 -9999 0 -0.67 12 12
STAT3 (dimer)/FOXO1 -0.062 0.24 -9999 0 -0.62 9 9
GRB2/SOS1/GAB family -0.12 0.19 -9999 0 -0.63 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.24 -9999 0 -0.5 30 30
GRB2 0.012 0.002 -9999 0 -10000 0 0
JAK2 0.011 0 -9999 0 -10000 0 0
LBP -0.13 0.34 -9999 0 -0.98 14 14
PIK3R1 0.007 0.072 -9999 0 -0.87 1 1
JAK1 0.011 0.007 -9999 0 -10000 0 0
MYC -0.13 0.31 -9999 0 -0.9 11 11
FGG -0.25 0.45 -9999 0 -1 30 30
macrophage differentiation -0.14 0.3 -9999 0 -0.75 16 16
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.2 0.31 -9999 0 -0.61 48 48
JUNB -0.11 0.27 -9999 0 -0.77 9 9
FOS -0.11 0.29 -9999 0 -0.73 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.25 -9999 0 -0.53 28 28
STAT1/PIAS1 -0.11 0.22 -9999 0 -0.56 18 18
GRB2/SOS1/GAB family/SHP2/PI3K 0.017 0.051 -9999 0 -0.31 1 1
STAT3 (dimer) -0.15 0.32 -9999 0 -0.79 16 16
PRKCD -0.097 0.28 -9999 0 -0.75 13 13
IL6R -0.071 0.26 -9999 0 -0.88 14 14
SOCS3 -0.084 0.24 -9999 0 -0.71 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 -0.094 0.23 -9999 0 -0.58 26 26
Rac1/GTP -0.16 0.24 -9999 0 -0.72 17 17
HCK -0.005 0.096 -9999 0 -0.48 5 5
MAPKKK cascade -0.003 0.1 -9999 0 -0.67 2 2
bone resorption -0.15 0.34 -9999 0 -0.83 21 21
IRF1 -0.11 0.28 -9999 0 -0.8 8 8
mol:GDP -0.13 0.28 -9999 0 -0.67 21 21
SOS1 0.011 0.004 -9999 0 -10000 0 0
VAV1 -0.13 0.29 -9999 0 -0.69 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.25 -9999 0 -0.66 16 16
PTPN11 -0.012 0.018 -9999 0 -10000 0 0
IL6/IL6RA -0.14 0.32 -9999 0 -0.8 26 26
gp130 (dimer)/TYK2/TYK2/LMO4 -0.1 0.22 -9999 0 -0.59 26 26
gp130 (dimer)/JAK2/JAK2/LMO4 -0.1 0.22 -9999 0 -0.59 26 26
IL6 -0.093 0.28 -9999 0 -0.82 19 19
PIAS3 0.011 0 -9999 0 -10000 0 0
PTPRE 0.004 0.073 -9999 0 -0.87 1 1
PIAS1 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.23 -9999 0 -0.44 47 47
LMO4 0.012 0.011 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.2 0.25 -9999 0 -0.76 16 16
MCL1 0.049 0.043 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.058 0.15 -9999 0 -0.53 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.13 -9999 0 -0.48 7 7
AP1 -0.18 0.34 -9999 0 -0.76 32 32
mol:PIP3 -0.1 0.2 -9999 0 -0.75 6 6
AKT1 -0.041 0.1 -9999 0 -0.58 1 1
PTK2B -0.03 0.14 -9999 0 -0.37 17 17
RHOA 0.005 0.067 -9999 0 -10000 0 0
PIK3CB 0.011 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.022 0.15 -9999 0 -0.48 13 13
MAGI3 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.077 0.18 -9999 0 -0.49 19 19
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.025 0.14 -9999 0 -0.48 8 8
NF kappa B1 p50/RelA -0.084 0.18 -9999 0 -0.57 9 9
endothelial cell migration -0.078 0.27 -9999 0 -0.74 20 20
ADCY4 -0.037 0.2 -9999 0 -0.62 14 14
ADCY5 -0.066 0.23 -9999 0 -0.72 14 14
ADCY6 -0.036 0.19 -9999 0 -0.59 14 14
ADCY7 -0.035 0.19 -9999 0 -0.59 14 14
ADCY1 -0.046 0.22 -9999 0 -0.64 15 15
ADCY2 -0.062 0.22 -9999 0 -0.6 18 18
ADCY3 -0.035 0.19 -9999 0 -0.59 14 14
ADCY8 -0.086 0.23 -9999 0 -0.64 17 17
ADCY9 -0.035 0.19 -9999 0 -0.59 14 14
GSK3B -0.021 0.13 -9999 0 -0.4 11 11
arachidonic acid secretion -0.028 0.18 -9999 0 -0.56 14 14
GNG2 0.009 0.032 -9999 0 -0.38 1 1
TRIP6 -0.015 0.066 -9999 0 -0.35 5 5
GNAO1 -0.056 0.21 -9999 0 -0.55 21 21
HRAS 0.011 0 -9999 0 -10000 0 0
NFKBIA -0.027 0.17 -9999 0 -0.51 13 13
GAB1 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.017 0.14 -9999 0 -1 3 3
JUN -0.066 0.22 -9999 0 -0.63 18 18
LPA/LPA2/NHERF2 -0.022 0.098 -9999 0 -0.6 4 4
TIAM1 -0.022 0.17 -9999 0 -1.2 3 3
PIK3R1 0.005 0.072 -9999 0 -0.87 1 1
mol:IP3 -0.023 0.15 -9999 0 -0.49 13 13
PLCB3 0.006 0.094 -9999 0 -0.54 4 4
FOS -0.11 0.29 -9999 0 -0.73 24 24
positive regulation of mitosis -0.028 0.18 -9999 0 -0.56 14 14
LPA/LPA1-2-3 -0.1 0.21 -9999 0 -0.57 23 23
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.011 0 -9999 0 -10000 0 0
stress fiber formation -0.036 0.16 -9999 0 -0.42 17 17
GNAZ -0.048 0.18 -9999 0 -0.59 13 13
EGFR/PI3K-beta/Gab1 -0.11 0.21 -9999 0 -0.81 6 6
positive regulation of dendritic cell cytokine production -0.1 0.21 -9999 0 -0.57 23 23
LPA/LPA2/MAGI-3 -0.022 0.098 -9999 0 -0.6 4 4
ARHGEF1 -0.02 0.15 -9999 0 -0.5 11 11
GNAI2 -0.039 0.17 -9999 0 -0.58 11 11
GNAI3 -0.039 0.17 -9999 0 -0.58 11 11
GNAI1 -0.044 0.18 -9999 0 -0.56 13 13
LPA/LPA3 -0.05 0.17 -9999 0 -0.7 9 9
LPA/LPA2 -0.027 0.11 -9999 0 -0.68 4 4
LPA/LPA1 -0.074 0.19 -9999 0 -0.54 20 20
HB-EGF/EGFR -0.096 0.24 -9999 0 -0.69 19 19
HBEGF -0.054 0.23 -9999 0 -0.75 13 13
mol:DAG -0.023 0.15 -9999 0 -0.49 13 13
cAMP biosynthetic process -0.051 0.21 -9999 0 -0.65 15 15
NFKB1 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
GNB1 0.011 0.001 -9999 0 -10000 0 0
LYN -0.027 0.17 -9999 0 -0.51 13 13
GNAQ -0.045 0.13 -9999 0 -0.46 13 13
LPAR2 -0.012 0.14 -9999 0 -0.88 4 4
LPAR3 -0.042 0.21 -9999 0 -0.88 9 9
LPAR1 -0.062 0.23 -9999 0 -0.87 11 11
IL8 -0.15 0.26 -9999 0 -0.52 41 41
PTK2 -0.066 0.21 -9999 0 -0.53 23 23
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.078 0.18 -9999 0 -0.5 19 19
EGFR -0.044 0.19 -9999 0 -0.61 13 13
PLCG1 -0.039 0.16 -9999 0 -0.52 13 13
PLD2 -0.066 0.21 -9999 0 -0.53 23 23
G12/G13 -0.057 0.15 -9999 0 -0.53 11 11
PI3K-beta -0.048 0.12 -9999 0 -0.7 1 1
cell migration -0.035 0.076 -9999 0 -0.29 4 4
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
PXN -0.037 0.16 -9999 0 -0.43 17 17
HRAS/GTP -0.071 0.17 -9999 0 -0.58 14 14
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.071 0.24 -9999 0 -0.7 17 17
PRKCE 0.004 0.072 -9999 0 -0.87 1 1
PRKCD -0.014 0.15 -9999 0 -0.53 7 7
Gi(beta/gamma) -0.07 0.17 -9999 0 -0.56 14 14
mol:LPA -0.011 0.055 -9999 0 -0.22 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.087 0.19 -9999 0 -0.52 17 17
MAPKKK cascade -0.028 0.18 -9999 0 -0.56 14 14
contractile ring contraction involved in cytokinesis 0.005 0.066 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.082 0.18 -9999 0 -0.52 18 18
GNA15 -0.059 0.15 -9999 0 -0.47 17 17
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
MAPT -0.027 0.14 -9999 0 -0.5 8 8
GNA11 -0.055 0.16 -9999 0 -0.5 15 15
Rac1/GTP -0.019 0.15 -9999 0 -1.1 3 3
MMP2 -0.079 0.27 -9999 0 -0.75 20 20
IGF1 pathway

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
NCK2 0.011 0 -9999 0 -10000 0 0
PTK2 0.011 0 -9999 0 -10000 0 0
CRKL -0.067 0.18 -9999 0 -0.46 25 25
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.011 0 -9999 0 -10000 0 0
IRS1/Crk -0.087 0.17 -9999 0 -0.46 25 25
IGF-1R heterotetramer/IGF1/PTP1B -0.081 0.19 -9999 0 -0.56 19 19
AKT1 -0.039 0.16 -9999 0 -0.44 1 1
BAD -0.028 0.16 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.067 0.18 -9999 0 -0.46 25 25
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.17 -9999 0 -0.47 25 25
RAF1 -0.022 0.15 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.082 0.16 -9999 0 -0.44 25 25
YWHAZ 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.19 -9999 0 -0.5 26 26
PIK3CA 0.011 0 -9999 0 -10000 0 0
RPS6KB1 -0.039 0.16 -9999 0 -0.44 1 1
GNB2L1 0.011 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.02 0.13 -9999 0 -10000 0 0
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.072 0.14 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.063 0.15 -9999 0 -0.45 19 19
IGF-1R heterotetramer -0.008 0.039 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.088 0.17 -9999 0 -0.47 25 25
Crk/p130 Cas/Paxillin -0.077 0.16 -9999 0 -0.43 19 19
IGF1R -0.008 0.039 -9999 0 -10000 0 0
IGF1 -0.12 0.3 -9999 0 -0.76 25 25
IRS2/Crk -0.061 0.19 -9999 0 -0.46 25 25
PI3K -0.085 0.17 -9999 0 -0.46 20 20
apoptosis 0.018 0.14 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD -0.047 0.2 -9999 0 -0.54 19 19
RAF1/14-3-3 E -0.012 0.13 -9999 0 -10000 0 0
BAD/14-3-3 -0.019 0.14 -9999 0 -10000 0 0
PRKCZ -0.039 0.16 -9999 0 -0.44 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.06 0.12 -9999 0 -10000 0 0
PTPN1 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.058 0.2 -9999 0 -0.58 19 19
BCAR1 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.07 0.16 -9999 0 -0.49 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.011 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.087 0.17 -9999 0 -0.46 25 25
GRB10 0.011 0 -9999 0 -10000 0 0
PTPN11 -0.067 0.18 -9999 0 -0.46 25 25
IRS1 -0.081 0.2 -9999 0 -0.5 26 26
IRS2 -0.072 0.19 -9999 0 -0.48 25 25
IGF-1R heterotetramer/IGF1 -0.1 0.23 -9999 0 -0.7 19 19
GRB2 0.011 0 -9999 0 -10000 0 0
PDPK1 -0.049 0.17 -9999 0 -0.43 20 20
YWHAE 0.011 0 -9999 0 -10000 0 0
PRKD1 -0.098 0.26 -9999 0 -0.64 23 23
SHC1 0.011 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.058 0.095 -10000 0 -0.43 2 2
NT3 (dimer)/TRKC -0.17 0.25 -10000 0 -0.71 21 21
NT3 (dimer)/TRKB -0.27 0.35 -10000 0 -0.69 51 51
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.029 -10000 0 -0.35 1 1
RAPGEF1 0.011 0 -10000 0 -10000 0 0
BDNF -0.25 0.39 -10000 0 -0.78 49 49
PIK3CA 0.011 0 -10000 0 -10000 0 0
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 0.003 0.055 -10000 0 -0.38 3 3
NTRK2 -0.16 0.31 -10000 0 -0.61 41 41
NTRK3 -0.054 0.18 -10000 0 -0.48 20 20
NT-4/5 (dimer)/TRKB -0.17 0.3 -10000 0 -0.72 30 30
neuron apoptosis 0.26 0.33 0.74 43 -10000 0 43
SHC 2-3/Grb2 -0.3 0.39 -10000 0 -0.87 43 43
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.24 0.41 -10000 0 -0.98 31 31
SHC3 -0.26 0.39 -10000 0 -0.94 34 34
STAT3 (dimer) -0.02 0.12 -10000 0 -0.45 8 8
NT3 (dimer)/TRKA -0.17 0.26 -10000 0 -0.64 32 32
RIN/GDP -0.026 0.1 -10000 0 -0.32 3 3
GIPC1 0.011 0 -10000 0 -10000 0 0
KRAS 0.006 0.045 -10000 0 -0.38 2 2
DNAJA3 -0.077 0.19 0.29 1 -0.56 16 17
RIN/GTP -0.009 0.048 -10000 0 -0.27 5 5
CCND1 -0.053 0.25 -10000 0 -1 8 8
MAGED1 0.003 0.079 -10000 0 -0.63 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.005 0.095 -10000 0 -0.48 5 5
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.094 0.21 -10000 0 -0.61 20 20
TRKA/NEDD4-2 -0.06 0.19 -10000 0 -0.68 12 12
ELMO1 0.011 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.004 0.049 -10000 0 -0.6 1 1
NGF -0.074 0.24 -10000 0 -0.63 20 20
HRAS 0.011 0 -10000 0 -10000 0 0
DOCK1 0.005 0.072 -10000 0 -0.88 1 1
GAB2 -0.003 0.11 -10000 0 -0.71 3 3
RIT2 -0.007 0.07 -10000 0 -0.38 5 5
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.009 0.032 -10000 0 -0.38 1 1
DNM1 -0.008 0.12 -10000 0 -0.58 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.075 0.18 0.28 1 -0.55 16 17
mol:GDP -0.039 0.14 -10000 0 -0.42 7 7
NGF (dimer) -0.074 0.24 -10000 0 -0.63 20 20
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.019 0.099 -10000 0 -0.31 2 2
TIAM1 0 0.1 -10000 0 -0.88 2 2
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
BDNF (dimer)/TRKB -0.27 0.33 -10000 0 -0.68 51 51
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.16 0.3 -10000 0 -0.57 44 44
RAP1/GDP -0.038 0.068 -10000 0 -10000 0 0
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.24 0.38 -10000 0 -0.77 49 49
ubiquitin-dependent protein catabolic process -0.1 0.24 -10000 0 -0.65 21 21
Schwann cell development -0.044 0.042 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.004 0.032 -10000 0 -10000 0 0
RAP1B 0.009 0.032 -10000 0 -0.38 1 1
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.33 0.37 -10000 0 -0.91 35 35
ABL1 0.011 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.084 0.1 -10000 0 -10000 0 0
STAT3 -0.02 0.12 -10000 0 -0.45 8 8
axon guidance -0.31 0.34 -10000 0 -0.83 35 35
MAPK3 -0.058 0.2 -10000 0 -0.57 19 19
MAPK1 -0.058 0.2 -10000 0 -0.57 19 19
CDC42/GDP -0.019 0.099 -10000 0 -0.31 2 2
NTF3 -0.16 0.3 -10000 0 -0.57 44 44
NTF4 -0.005 0.096 -10000 0 -0.48 5 5
NGF (dimer)/TRKA/FAIM -0.057 0.16 -10000 0 -0.56 12 12
PI3K -0.005 0.055 -10000 0 -0.68 1 1
FRS3 0.011 0 -10000 0 -10000 0 0
FAIM 0.011 0 -10000 0 -10000 0 0
GAB1 0.011 0 -10000 0 -10000 0 0
RASGRF1 -0.1 0.21 0.29 1 -0.55 22 23
SOS1 0.011 0 -10000 0 -10000 0 0
MCF2L -0.16 0.28 -10000 0 -0.67 29 29
RGS19 0.011 0 -10000 0 -10000 0 0
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.075 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.099 -10000 0 -0.31 2 2
NGF (dimer)/TRKA/GRIT -0.058 0.16 -10000 0 -0.57 12 12
neuron projection morphogenesis -0.059 0.21 -10000 0 -0.74 8 8
NGF (dimer)/TRKA/NEDD4-2 -0.1 0.24 -10000 0 -0.65 21 21
MAP2K1 0.039 0 -10000 0 -10000 0 0
NGFR -0.083 0.27 -10000 0 -0.88 16 16
NGF (dimer)/TRKA/GIPC/GAIP -0.037 0.1 -10000 0 -0.36 12 12
RAS family/GTP/PI3K -0.003 0.03 -10000 0 -0.36 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.013 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.011 0 -10000 0 -10000 0 0
MAPKKK cascade -0.1 0.23 -10000 0 -0.95 10 10
RASA1 0.011 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.005 0.036 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.24 0.31 -10000 0 -0.64 49 49
NGF (dimer)/TRKA/p62/Atypical PKCs -0.048 0.13 -10000 0 -0.51 10 10
MATK -0.044 0.21 -10000 0 -0.83 10 10
NEDD4L -0.06 0.24 -10000 0 -0.88 12 12
RAS family/GDP -0.033 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.083 0.2 0.32 1 -0.53 22 23
Rac1/GTP -0.075 0.12 -10000 0 -0.38 12 12
FRS2 family/SHP2/CRK family -0.001 0.013 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.09 0.42 -9999 0 -1.2 8 8
HDAC7 0.012 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.098 0.27 -9999 0 -0.81 6 6
SMAD4 0.013 0 -9999 0 -10000 0 0
ID2 -0.098 0.43 -9999 0 -1.3 8 8
AP1 -0.14 0.31 -9999 0 -0.78 24 24
ABCG2 -0.14 0.45 -9999 0 -1.2 10 10
HIF1A 0 0.074 -9999 0 -10000 0 0
TFF3 -0.19 0.49 -9999 0 -1.2 14 14
GATA2 -0.11 0.25 -9999 0 -0.53 33 33
AKT1 0.009 0.078 -9999 0 -10000 0 0
response to hypoxia -0.007 0.085 -9999 0 -10000 0 0
MCL1 -0.09 0.42 -9999 0 -1.2 8 8
NDRG1 -0.093 0.42 -9999 0 -1.2 8 8
SERPINE1 -0.13 0.46 -9999 0 -1.3 12 12
FECH -0.09 0.42 -9999 0 -1.2 8 8
FURIN -0.09 0.42 -9999 0 -1.2 9 9
NCOA2 -0.086 0.28 -9999 0 -0.85 17 17
EP300 0.037 0.11 -9999 0 -10000 0 0
HMOX1 -0.094 0.43 -9999 0 -1.3 8 8
BHLHE40 -0.09 0.42 -9999 0 -1.2 8 8
BHLHE41 -0.12 0.46 -9999 0 -1.3 10 10
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.007 0.055 -9999 0 -10000 0 0
ENG 0.058 0.099 -9999 0 -10000 0 0
JUN -0.065 0.22 -9999 0 -0.63 18 18
RORA -0.09 0.42 -9999 0 -1.2 8 8
ABCB1 -0.095 0.28 -9999 0 -1.4 6 6
TFRC -0.09 0.42 -9999 0 -1.2 8 8
CXCR4 -0.09 0.42 -9999 0 -1.2 8 8
TF -0.13 0.46 -9999 0 -1.2 12 12
CITED2 -0.091 0.42 -9999 0 -1.2 9 9
HIF1A/ARNT -0.14 0.45 -9999 0 -1.3 10 10
LDHA -0.033 0.16 -9999 0 -1.4 2 2
ETS1 -0.092 0.42 -9999 0 -1.3 8 8
PGK1 -0.09 0.42 -9999 0 -1.2 9 9
NOS2 -0.12 0.44 -9999 0 -1.3 8 8
ITGB2 -0.11 0.45 -9999 0 -1.3 11 11
ALDOA -0.09 0.42 -9999 0 -1.2 8 8
Cbp/p300/CITED2 -0.076 0.42 -9999 0 -1.2 8 8
FOS -0.11 0.29 -9999 0 -0.73 24 24
HK2 -0.093 0.42 -9999 0 -1.2 9 9
SP1 0.016 0.02 -9999 0 -10000 0 0
GCK -0.004 0.22 -9999 0 -1.5 1 1
HK1 -0.093 0.42 -9999 0 -1.2 8 8
NPM1 -0.09 0.42 -9999 0 -1.2 8 8
EGLN1 -0.09 0.42 -9999 0 -1.2 8 8
CREB1 0.018 0.01 -9999 0 -10000 0 0
PGM1 -0.11 0.44 -9999 0 -1.2 11 11
SMAD3 0.013 0 -9999 0 -10000 0 0
EDN1 -0.049 0.28 -9999 0 -1 6 6
IGFBP1 -0.098 0.43 -9999 0 -1.3 8 8
VEGFA -0.028 0.3 -9999 0 -0.85 2 2
HIF1A/JAB1 -0.01 0.025 -9999 0 -10000 0 0
CP -0.19 0.5 -9999 0 -1.2 15 15
CXCL12 -0.097 0.44 -9999 0 -1.3 8 8
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.099 0.44 -9999 0 -1.3 8 8
EGLN3 -0.097 0.43 -9999 0 -1.3 8 8
CA9 -0.12 0.44 -9999 0 -1.2 9 9
TERT -0.15 0.5 -9999 0 -1.2 16 16
ENO1 -0.092 0.42 -9999 0 -1.2 9 9
PFKL -0.09 0.42 -9999 0 -1.2 8 8
NCOA1 0.011 0.005 -9999 0 -10000 0 0
ADM -0.1 0.43 -9999 0 -1.3 8 8
ARNT -0.001 0.073 -9999 0 -10000 0 0
HNF4A -0.2 0.32 -9999 0 -0.59 54 54
ADFP -0.097 0.42 -9999 0 -1.2 9 9
SLC2A1 -0.042 0.31 -9999 0 -0.85 2 2
LEP -0.14 0.47 -9999 0 -1.2 15 15
HIF1A/ARNT/Cbp/p300 -0.078 0.3 -9999 0 -0.83 7 7
EPO -0.094 0.37 -9999 0 -1 10 10
CREBBP 0.037 0.11 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.11 0.26 -9999 0 -0.86 4 4
PFKFB3 -0.092 0.42 -9999 0 -1.3 8 8
NT5E -0.11 0.45 -9999 0 -1.2 11 11
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.007 0.04 -9999 0 -0.45 1 1
EGFR -0.043 0.19 -9999 0 -0.61 13 13
EPHA2 -0.1 0.29 -9999 0 -0.83 20 20
USP6 -0.066 0.22 -9999 0 -0.63 18 18
IQSEC1 0.011 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.064 0.18 -9999 0 -0.68 11 11
ARRB2 0.004 0.035 -9999 0 -10000 0 0
mol:GTP 0.005 0.039 -9999 0 -0.15 1 1
ARRB1 0.005 0.072 -9999 0 -0.88 1 1
FBXO8 0.011 0 -9999 0 -10000 0 0
TSHR -0.068 0.24 -9999 0 -0.78 15 15
EGF -0.021 0.16 -9999 0 -0.79 6 6
somatostatin receptor activity 0 0 -9999 0 -0.001 6 6
ARAP2 -0.045 0.21 -9999 0 -0.83 10 10
mol:GDP -0.027 0.091 -9999 0 -0.34 4 4
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 4 4
ITGA2B -0.045 0.21 -9999 0 -0.83 10 10
ARF6 0.011 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.07 0.18 -9999 0 -0.54 18 18
ADAP1 0.011 0 -9999 0 -10000 0 0
KIF13B 0.011 0 -9999 0 -10000 0 0
HGF/MET -0.13 0.23 -9999 0 -0.7 17 17
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.028 0.1 -9999 0 -0.34 6 6
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.054 0.16 -9999 0 -0.59 11 11
ADRB2 0.011 0 -9999 0 -10000 0 0
receptor agonist activity 0 0 -9999 0 0 8 8
actin filament binding 0 0 -9999 0 -0.001 6 6
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.069 0.23 -9999 0 -0.66 18 18
GNAQ 0.011 0.003 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 4 4
ARF6/GDP -0.029 0.16 -9999 0 -0.46 11 11
ARF6/GDP/GULP/ACAP1 -0.18 0.24 -9999 0 -0.51 47 47
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.079 0.19 -9999 0 -0.58 18 18
ACAP1 -0.038 0.19 -9999 0 -0.73 10 10
ACAP2 0.011 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.012 0.046 -9999 0 -10000 0 0
EFNA1 0.006 0.045 -9999 0 -0.38 2 2
HGF -0.14 0.27 -9999 0 -0.54 41 41
CYTH3 0.006 0.057 -9999 0 -0.69 1 1
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.011 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 6 6
endosomal lumen acidification 0 0 -9999 0 -0.001 6 6
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.24 0.39 -9999 0 -0.79 47 47
GNAQ/ARNO 0.009 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 1 1
MET -0.02 0.15 -9999 0 -0.66 7 7
GNA14 -0.077 0.21 -9999 0 -0.5 26 26
GNA15 -0.018 0.15 -9999 0 -0.71 6 6
GIT1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 5 5
GNA11 -0.006 0.12 -9999 0 -0.88 3 3
LHCGR -0.017 0.093 -9999 0 -0.38 9 9
AGTR1 -0.039 0.17 -9999 0 -0.52 14 14
desensitization of G-protein coupled receptor protein signaling pathway -0.012 0.046 -9999 0 -10000 0 0
IPCEF1/ARNO -0.042 0.13 -9999 0 -0.47 11 11
alphaIIb/beta3 Integrin -0.1 0.24 -9999 0 -0.72 18 18
Nectin adhesion pathway

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
PDGFRB 0.003 0.055 -9999 0 -0.38 3 3
alphaV beta3 Integrin -0.065 0.18 -9999 0 -0.68 11 11
PTK2 -0.13 0.25 -9999 0 -0.56 33 33
positive regulation of JNK cascade -0.038 0.088 -9999 0 -0.39 7 7
CDC42/GDP -0.009 0.13 -9999 0 -0.56 6 6
Rac1/GDP -0.007 0.13 -9999 0 -0.55 6 6
RAP1B 0.009 0.032 -9999 0 -0.38 1 1
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.046 0.11 -9999 0 -0.49 7 7
nectin-3/I-afadin -0.037 0.14 -9999 0 -0.68 6 6
RAPGEF1 -0.017 0.15 -9999 0 -0.65 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.03 0.18 -9999 0 -0.78 6 6
PDGFB-D/PDGFRB 0.003 0.055 -9999 0 -0.38 3 3
TLN1 0.019 0.057 -9999 0 -10000 0 0
Rap1/GTP -0.038 0.093 -9999 0 -0.44 6 6
IQGAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.015 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.037 0.14 -9999 0 -0.68 6 6
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP -0.02 0.17 -9999 0 -0.72 6 6
MLLT4 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.011 0 -9999 0 -10000 0 0
PI3K -0.033 0.11 -9999 0 -0.5 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.13 0.27 -9999 0 -0.68 29 29
positive regulation of lamellipodium assembly -0.039 0.09 -9999 0 -0.4 7 7
PVRL1 -0.16 0.35 -9999 0 -0.88 29 29
PVRL3 -0.04 0.19 -9999 0 -0.63 12 12
PVRL2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
CDH1 -0.14 0.33 -9999 0 -0.84 27 27
CLDN1 -0.21 0.35 -9999 0 -0.66 49 49
JAM-A/CLDN1 -0.16 0.23 -9999 0 -0.53 39 39
SRC -0.075 0.19 -9999 0 -0.91 6 6
ITGB3 -0.069 0.23 -9999 0 -0.66 18 18
nectin-1(dimer)/I-afadin/I-afadin -0.13 0.27 -9999 0 -0.68 29 29
FARP2 -0.027 0.17 -9999 0 -0.69 7 7
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.032 0.12 -9999 0 -0.59 6 6
nectin-1/I-afadin -0.13 0.27 -9999 0 -0.68 29 29
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.14 0.26 -9999 0 -0.62 33 33
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.005 0.072 -9999 0 -0.88 1 1
positive regulation of filopodium formation -0.038 0.088 -9999 0 -0.39 7 7
alphaV/beta3 Integrin/Talin -0.054 0.15 -9999 0 -0.55 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.014 0.055 -9999 0 -10000 0 0
VAV2 -0.027 0.17 -9999 0 -0.69 7 7
RAP1/GDP -0.044 0.11 -9999 0 -0.52 6 6
ITGAV 0.003 0.079 -9999 0 -0.63 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.032 0.12 -9999 0 -0.59 6 6
nectin-3(dimer)/I-afadin/I-afadin -0.037 0.14 -9999 0 -0.68 6 6
Rac1/GTP -0.047 0.11 -9999 0 -0.5 7 7
PTPRM -0.016 0.062 -9999 0 -0.31 6 6
E-cadherin/beta catenin/alpha catenin -0.18 0.28 -9999 0 -0.57 46 46
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.044 0.14 -10000 0 -0.55 9 9
regulation of S phase of mitotic cell cycle -0.025 0.091 -10000 0 -0.36 10 10
GNAO1 -0.015 0.15 -10000 0 -0.78 5 5
HRAS 0.011 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.086 0.18 -10000 0 -0.35 37 37
PELP1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.005 0.13 -10000 0 -0.45 9 9
T-DHT/AR -0.055 0.17 -10000 0 -0.49 17 17
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.006 23 23
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0.001 -10000 0 -10000 0 0
GNAI1 0.005 0.072 -10000 0 -0.88 1 1
mol:GDP -0.048 0.16 -10000 0 -0.66 9 9
cell proliferation -0.019 0.18 -10000 0 -0.59 4 4
PIK3CA 0.011 0 -10000 0 -10000 0 0
FOS -0.073 0.3 -10000 0 -0.89 17 17
mol:Ca2+ -0.009 0.022 -10000 0 -0.083 8 8
MAPK3 -0.011 0.15 -10000 0 -0.46 9 9
MAPK1 -0.004 0.086 -10000 0 -0.29 3 3
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
mol:IP3 0 0.002 -10000 0 -0.004 24 24
cAMP biosynthetic process -0.076 0.17 -10000 0 -0.36 30 30
GNG2 0.009 0.032 -10000 0 -0.38 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 24 24
HRAS/GTP -0.041 0.12 -10000 0 -0.5 9 9
actin cytoskeleton reorganization -0.003 0.039 -10000 0 -0.48 1 1
SRC 0.011 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 24 24
PI3K -0.004 0.049 -10000 0 -0.6 1 1
apoptosis 0.021 0.16 0.42 17 -10000 0 17
T-DHT/AR/PELP1 -0.048 0.15 -10000 0 -0.6 9 9
HRAS/GDP -0.044 0.15 -10000 0 -0.62 9 9
CREB1 -0.025 0.17 -10000 0 -0.46 17 17
RAC1-CDC42/GTP -0.003 0.04 -10000 0 -0.49 1 1
AR -0.064 0.22 -10000 0 -0.64 17 17
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.011 0.13 -10000 0 -0.48 9 9
RAC1-CDC42/GDP -0.042 0.14 -10000 0 -0.59 9 9
T-DHT/AR/PELP1/Src -0.043 0.14 -10000 0 -0.55 9 9
MAP2K2 -0.005 0.13 -10000 0 -0.45 9 9
T-DHT/AR/PELP1/Src/PI3K -0.025 0.091 -10000 0 -0.36 10 10
GNAZ -0.001 0.1 -10000 0 -0.88 2 2
SHBG -0.13 0.26 -10000 0 -0.54 37 37
Gi family/GNB1/GNG2/GDP -0.023 0.09 -10000 0 -0.49 4 4
mol:T-DHT 0 0.001 0.002 2 -0.003 14 16
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.011 0 -10000 0 -10000 0 0
Gi family/GTP -0.031 0.091 -10000 0 -0.35 7 7
CDC42 0.011 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.1 0.23 -9999 0 -0.62 25 25
KLHL20 -0.049 0.081 -9999 0 -0.34 2 2
CYFIP2 0.011 0 -9999 0 -10000 0 0
Rac1/GDP -0.017 0.16 -9999 0 -10000 0 0
ENAH -0.1 0.23 -9999 0 -0.62 25 25
AP1M1 0.011 0 -9999 0 -10000 0 0
RAP1B 0.009 0.032 -9999 0 -0.38 1 1
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.004 -9999 0 -10000 0 0
CDC42/GTP -0.053 0.12 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.032 0.054 -9999 0 -0.22 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.12 0.23 -9999 0 -0.56 32 32
RAPGEF1 -0.044 0.21 -9999 0 -0.51 25 25
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.24 -9999 0 -0.64 25 25
CRK -0.059 0.23 -9999 0 -0.57 25 25
E-cadherin/gamma catenin/alpha catenin -0.1 0.22 -9999 0 -0.59 25 25
alphaE/beta7 Integrin -0.038 0.15 -9999 0 -0.68 8 8
IQGAP1 0.011 0 -9999 0 -10000 0 0
NCKAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.015 -9999 0 -10000 0 0
DLG1 -0.1 0.23 -9999 0 -0.62 25 25
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.039 0.084 -9999 0 -10000 0 0
MLLT4 0.011 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.007 0.063 -9999 0 -0.55 2 2
PI3K -0.051 0.11 -9999 0 -10000 0 0
ARF6 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.12 0.25 -9999 0 -0.68 25 25
TIAM1 -0.001 0.1 -9999 0 -0.88 2 2
E-cadherin(dimer)/Ca2+ -0.088 0.19 -9999 0 -0.51 25 25
AKT1 -0.028 0.06 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
CDH1 -0.14 0.33 -9999 0 -0.84 27 27
RhoA/GDP -0.016 0.16 -9999 0 -10000 0 0
actin cytoskeleton organization -0.036 0.06 -9999 0 -0.24 2 2
CDC42/GDP -0.016 0.16 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.062 0.14 -9999 0 -0.36 25 25
ITGB7 -0.039 0.2 -9999 0 -0.82 9 9
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.092 0.2 -9999 0 -0.54 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin -0.089 0.19 -9999 0 -0.52 25 25
mol:GDP -0.03 0.18 -9999 0 -0.44 24 24
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.064 0.14 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.013 0.086 -9999 0 -0.26 9 9
NME1 0.011 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.1 0.23 -9999 0 -0.62 25 25
regulation of cell-cell adhesion -0.046 0.1 -9999 0 -10000 0 0
WASF2 -0.017 0.028 -9999 0 -10000 0 0
Rap1/GTP -0.061 0.13 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.12 0.22 -9999 0 -0.53 32 32
CCND1 -0.048 0.09 -9999 0 -0.34 9 9
VAV2 -0.059 0.23 -9999 0 -0.55 26 26
RAP1/GDP -0.061 0.13 -9999 0 -10000 0 0
adherens junction assembly -0.071 0.23 -9999 0 -0.59 25 25
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.011 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.11 0.21 -9999 0 -0.5 32 32
E-cadherin/beta catenin -0.091 0.2 -9999 0 -0.53 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.1 0.23 -9999 0 -0.62 25 25
PIK3CA 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.079 0.13 -9999 0 -0.62 2 2
E-cadherin/beta catenin/alpha catenin -0.1 0.22 -9999 0 -0.59 25 25
ITGAE 0.011 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.11 0.25 -9999 0 -0.66 25 25
BCR 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
JUN -0.06 0.18 -10000 0 -0.49 14 14
IKBKB -0.007 0.08 -10000 0 -0.3 3 3
AKT1 -0.027 0.12 -10000 0 -0.29 13 13
IKBKG -0.006 0.085 -10000 0 -0.32 3 3
CALM1 -0.046 0.17 -10000 0 -0.74 6 6
PIK3CA 0.011 0 -10000 0 -10000 0 0
MAP3K1 -0.073 0.25 -10000 0 -0.66 17 17
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ -0.058 0.18 -10000 0 -0.81 6 6
DOK1 0.005 0.072 -10000 0 -0.88 1 1
AP-1 -0.04 0.12 -10000 0 -0.28 16 16
LYN 0.011 0 -10000 0 -10000 0 0
BLNK -0.033 0.19 -10000 0 -0.81 8 8
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.14 0.29 -10000 0 -0.7 28 28
CD22 -0.15 0.34 -10000 0 -0.76 25 25
CAMK2G -0.035 0.15 -10000 0 -0.67 6 6
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D 0.005 0.072 -10000 0 -0.88 1 1
SHC/GRB2/SOS1 -0.11 0.24 -10000 0 -1 6 6
GO:0007205 -0.059 0.18 -10000 0 -0.84 6 6
SYK 0.005 0.072 -10000 0 -0.88 1 1
ELK1 -0.048 0.17 -10000 0 -0.76 6 6
NFATC1 -0.06 0.2 -10000 0 -0.68 10 10
B-cell antigen/BCR complex -0.14 0.29 -10000 0 -0.7 28 28
PAG1/CSK -0.009 0.078 -10000 0 -0.68 2 2
NFKBIB 0.007 0.029 -10000 0 -10000 0 0
HRAS -0.049 0.18 -10000 0 -0.79 6 6
NFKBIA 0.007 0.028 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.013 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.12 0.26 -10000 0 -0.65 23 23
mol:GDP -0.055 0.17 -10000 0 -0.77 6 6
PTEN 0.011 0 -10000 0 -10000 0 0
CD79B -0.033 0.16 -10000 0 -0.55 12 12
NF-kappa-B/RelA/I kappa B alpha 0.013 0.023 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.079 0.23 -10000 0 -0.57 20 20
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
mol:IP3 -0.069 0.19 -10000 0 -0.86 6 6
CSK 0.011 0 -10000 0 -10000 0 0
FOS -0.099 0.22 -10000 0 -0.55 24 24
CHUK -0.006 0.085 -10000 0 -0.3 5 5
IBTK 0.011 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.064 0.16 -10000 0 -0.58 10 10
PTPN6 -0.14 0.3 -10000 0 -0.89 15 15
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 0.001 0.045 -10000 0 -0.14 10 10
VAV2 -0.14 0.31 -10000 0 -1.1 10 10
ubiquitin-dependent protein catabolic process 0.011 0.028 -10000 0 -10000 0 0
BTK -0.018 0.15 0.46 1 -1.3 2 3
CD19 -0.15 0.34 -10000 0 -0.72 27 27
MAP4K1 -0.089 0.28 -10000 0 -0.88 17 17
CD72 -0.002 0.09 -10000 0 -0.51 4 4
PAG1 0 0.1 -10000 0 -0.88 2 2
MAPK14 -0.05 0.2 -10000 0 -0.56 14 14
SH3BP5 0.011 0 -10000 0 -10000 0 0
PIK3AP1 -0.056 0.2 -10000 0 -0.79 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.071 0.26 -10000 0 -0.63 20 20
RAF1 -0.038 0.17 -10000 0 -0.71 6 6
RasGAP/p62DOK/SHIP -0.12 0.28 -10000 0 -0.74 15 15
CD79A -0.14 0.31 -10000 0 -0.7 31 31
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.28 16 16
RASA1 0.011 0 -10000 0 -10000 0 0
MAPK3 -0.015 0.14 -10000 0 -0.55 6 6
MAPK1 -0.015 0.14 -10000 0 -0.55 6 6
CD72/SHP1 -0.13 0.27 -10000 0 -0.79 16 16
NFKB1 0.011 0 -10000 0 -10000 0 0
MAPK8 -0.061 0.21 -10000 0 -0.55 18 18
actin cytoskeleton organization -0.079 0.25 -10000 0 -0.82 10 10
NF-kappa-B/RelA 0.03 0.045 -10000 0 -10000 0 0
Calcineurin -0.047 0.13 -10000 0 -0.59 6 6
PI3K -0.13 0.22 -10000 0 -0.69 13 13
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.073 0.2 -10000 0 -0.94 6 6
SOS1 0.011 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.31 -10000 0 -1 13 13
DAPP1 -0.12 0.31 -10000 0 -1.3 9 9
cytokine secretion -0.053 0.19 -10000 0 -0.61 10 10
mol:DAG -0.069 0.19 -10000 0 -0.86 6 6
PLCG2 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.026 0.15 -10000 0 -0.63 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.3 -10000 0 -0.66 31 31
mol:PI-3-4-5-P3 -0.089 0.14 -10000 0 -0.44 13 13
ETS1 -0.027 0.15 -10000 0 -0.65 6 6
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.29 -10000 0 -0.68 24 24
B-cell antigen/BCR complex/LYN -0.12 0.32 -10000 0 -0.76 20 20
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 -0.089 0.28 -10000 0 -0.93 10 10
B-cell antigen/BCR complex/LYN/SYK -0.15 0.31 -10000 0 -0.81 20 20
CARD11 -0.069 0.21 -10000 0 -0.74 10 10
FCGR2B -0.023 0.16 -10000 0 -0.74 7 7
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.011 0 -10000 0 -10000 0 0
IKK complex 0.007 0.038 -10000 0 -10000 0 0
PTPRC -0.035 0.19 -10000 0 -0.77 9 9
PDPK1 -0.03 0.11 -10000 0 -0.28 13 13
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.011 0 -10000 0 -10000 0 0
POU2F2 0.014 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.003 -9999 0 -10000 0 0
SVIL -0.013 0.094 -9999 0 -0.38 9 9
ZNF318 0.005 0.073 -9999 0 -0.88 1 1
JMJD2C -0.016 0.053 -9999 0 -0.13 25 25
T-DHT/AR/Ubc9 -0.11 0.17 -9999 0 -0.55 16 16
CARM1 0.011 0 -9999 0 -10000 0 0
PRDX1 0.006 0.072 -9999 0 -0.88 1 1
PELP1 0.012 0.002 -9999 0 -10000 0 0
CTNNB1 0.011 0.003 -9999 0 -10000 0 0
AKT1 0.012 0.003 -9999 0 -10000 0 0
PTK2B 0.005 0.072 -9999 0 -0.88 1 1
MED1 0.009 0.006 -9999 0 -10000 0 0
MAK -0.031 0.16 -9999 0 -0.56 11 11
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 -0.001 0.1 -9999 0 -0.88 2 2
GSN 0.005 0.072 -9999 0 -0.88 1 1
NCOA2 -0.086 0.28 -9999 0 -0.85 17 17
NCOA6 0.011 0.003 -9999 0 -10000 0 0
DNA-PK 0 0.051 -9999 0 -0.59 1 1
NCOA4 0.011 0.002 -9999 0 -10000 0 0
PIAS3 0.011 0.003 -9999 0 -10000 0 0
cell proliferation -0.071 0.19 -9999 0 -1.2 4 4
XRCC5 0.012 0.002 -9999 0 -10000 0 0
UBE3A 0.011 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.12 0.19 -9999 0 -0.58 19 19
FHL2 -0.081 0.22 -9999 0 -1.4 4 4
RANBP9 0.011 0.003 -9999 0 -10000 0 0
JMJD1A -0.081 0.092 -9999 0 -0.18 65 65
CDK6 -0.012 0.14 -9999 0 -0.88 4 4
TGFB1I1 -0.021 0.12 -9999 0 -0.43 11 11
T-DHT/AR/CyclinD1 -0.15 0.22 -9999 0 -0.58 26 26
XRCC6 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.16 0.22 -9999 0 -0.61 18 18
CTDSP1 0.011 0.003 -9999 0 -10000 0 0
CTDSP2 0.009 0.009 -9999 0 -10000 0 0
BRCA1 0.011 0.003 -9999 0 -10000 0 0
TCF4 0.009 0.008 -9999 0 -10000 0 0
CDKN2A -0.02 0.15 -9999 0 -0.71 6 6
SRF 0.017 0.019 -9999 0 -10000 0 0
NKX3-1 -0.36 0.52 -9999 0 -1.4 27 27
KLK3 -0.006 0.073 -9999 0 -10000 0 0
TMF1 0.011 0.003 -9999 0 -10000 0 0
HNRNPA1 0.009 0.006 -9999 0 -10000 0 0
AOF2 -0.001 0.004 -9999 0 -10000 0 0
APPL1 0.023 0.006 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.11 0.18 -9999 0 -0.56 17 17
AR -0.11 0.24 -9999 0 -0.72 17 17
UBA3 0.011 0.003 -9999 0 -10000 0 0
PATZ1 0.009 0.006 -9999 0 -10000 0 0
PAWR 0.011 0.003 -9999 0 -10000 0 0
PRKDC 0.006 0.072 -9999 0 -0.88 1 1
PA2G4 0.009 0.007 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.096 0.16 -9999 0 -0.56 13 13
RPS6KA3 0.005 0.072 -9999 0 -0.88 1 1
T-DHT/AR/ARA70 -0.11 0.17 -9999 0 -0.55 16 16
LATS2 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.099 0.17 -9999 0 -0.58 14 14
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0 0.064 -9999 0 -0.38 4 4
KLK2 -0.23 0.42 -9999 0 -1.2 21 21
CASP8 0.006 0.072 -9999 0 -0.88 1 1
T-DHT/AR/TIF2/CARM1 -0.15 0.24 -9999 0 -0.67 23 23
TMPRSS2 -0.58 0.61 -9999 0 -1.3 58 58
CCND1 -0.062 0.21 -9999 0 -0.56 19 19
PIAS1 0.011 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.048 0.045 -9999 0 -0.087 79 79
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.01 0.008 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.21 -9999 0 -0.6 19 19
CMTM2 -0.016 0.11 -9999 0 -0.44 9 9
SNURF -0.013 0.14 -9999 0 -0.88 4 4
ZMIZ1 -0.029 0.04 -9999 0 -10000 0 0
CCND3 0.011 0 -9999 0 -10000 0 0
TGIF1 0.009 0.006 -9999 0 -10000 0 0
FKBP4 0.011 0.003 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR -0.11 0.29 -9999 0 -0.75 24 24
LRPAP1 0.011 0 -9999 0 -10000 0 0
NUDC 0.011 0 -9999 0 -10000 0 0
RELN/LRP8 -0.099 0.18 -9999 0 -0.59 15 15
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.011 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.064 0.18 -9999 0 -0.54 15 15
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.16 0.32 -9999 0 -0.66 39 39
IQGAP1 0.011 0 -9999 0 -10000 0 0
PLA2G7 -0.062 0.22 -9999 0 -0.6 18 18
CALM1 0.011 0 -9999 0 -10000 0 0
DYNLT1 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0 -9999 0 -10000 0 0
CDK5R1 0.006 0.045 -9999 0 -0.38 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.029 0.18 -9999 0 -0.75 8 8
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.28 0.34 -9999 0 -0.67 56 56
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.076 0.14 -9999 0 -0.71 1 1
MAP1B 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.076 0.14 -9999 0 -0.47 15 15
RELN -0.15 0.29 -9999 0 -0.55 44 44
PAFAH/LIS1 -0.045 0.14 -9999 0 -0.59 8 8
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.057 0.11 -9999 0 -0.54 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.17 0.25 -9999 0 -0.47 47 47
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.083 0.16 -9999 0 -0.58 3 3
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0 -9999 0 -10000 0 0
PAFAH1B2 -0.018 0.16 -9999 0 -0.88 5 5
MAP1B/LIS1/Dynein heavy chain 0 0 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.072 0.14 -9999 0 -0.68 1 1
LRP8 0.011 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.076 0.14 -9999 0 -0.71 1 1
P39/CDK5 -0.096 0.18 -9999 0 -0.51 20 20
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.051 0.17 -9999 0 -0.5 15 15
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.24 0.3 -9999 0 -0.62 48 48
RELN/VLDLR -0.16 0.25 -9999 0 -0.61 29 29
CDC42 0 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.02 0.1 -10000 0 -0.7 3 3
HDAC1 0.005 0.012 -10000 0 -10000 0 0
AES 0.003 0.007 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 -0.012 0.14 -10000 0 -0.88 4 4
LRP6/FZD1 -0.021 0.07 -10000 0 -10000 0 0
TLE1 0.004 0.072 -10000 0 -0.88 1 1
AP1 -0.068 0.16 -10000 0 -0.46 18 18
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0 0.1 -10000 0 -0.88 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.031 0.086 -10000 0 -0.66 1 1
NICD/RBPSUH -0.014 0.089 -10000 0 -0.76 2 2
WIF1 -0.16 0.28 -10000 0 -0.55 45 45
NOTCH1 -0.016 0.095 -10000 0 -0.81 2 2
PSENEN 0.011 0 -10000 0 -10000 0 0
KREMEN2 -0.061 0.23 -10000 0 -0.71 15 15
DKK1 -0.26 0.35 -10000 0 -0.61 66 66
beta catenin/beta TrCP1 0.014 0.046 -10000 0 -10000 0 0
APH1B -0.036 0.2 -10000 0 -0.88 8 8
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 0.003 0.051 0.33 2 -0.31 1 3
CtBP/CBP/TCF1/TLE1/AES -0.003 0.058 -10000 0 -10000 0 0
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.11 0.29 -10000 0 -0.73 24 24
JUN -0.066 0.22 -10000 0 -0.63 18 18
MAP3K7 0.003 0.008 -10000 0 -10000 0 0
CTNNB1 0.008 0.049 0.25 1 -10000 0 1
MAPK3 0.011 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.099 0.19 -10000 0 -0.6 15 15
HNF1A -0.068 0.16 -10000 0 -0.4 26 26
CTBP1 0.003 0.007 -10000 0 -10000 0 0
MYC -0.025 0.26 -10000 0 -1.6 4 4
NKD1 -0.003 0.09 -10000 0 -0.51 4 4
FZD1 -0.02 0.11 -10000 0 -0.38 12 12
NOTCH1 precursor/Deltex homolog 1 -0.028 0.14 -10000 0 -0.72 5 5
apoptosis -0.067 0.16 -10000 0 -0.46 18 18
Delta 1/NOTCHprecursor -0.02 0.098 -10000 0 -0.68 3 3
DLL1 0 0.085 -10000 0 -0.55 3 3
PPARD 0.016 0.024 -10000 0 -10000 0 0
Gamma Secretase -0.027 0.11 -10000 0 -0.51 8 8
APC 0.003 0.051 0.33 2 -0.31 1 3
DVL1 -0.019 0.032 -10000 0 -10000 0 0
CSNK2A1 0.01 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.21 0.29 -10000 0 -0.68 35 35
LRP6 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.004 -10000 0 -10000 0 0
NLK 0.016 0.011 -10000 0 -10000 0 0
CCND1 -0.073 0.34 -10000 0 -1.6 7 7
WNT1 -0.043 0.19 -10000 0 -0.61 13 13
Axin1/APC/beta catenin 0.018 0.059 0.32 2 -10000 0 2
DKK2 -0.084 0.2 -10000 0 -0.45 31 31
NOTCH1 precursor/DVL1 -0.019 0.081 -10000 0 -0.69 2 2
GSK3B 0.011 0.001 -10000 0 -10000 0 0
FRAT1 -0.001 0.1 -10000 0 -0.88 2 2
NOTCH/Deltex homolog 1 -0.028 0.14 -10000 0 -0.73 5 5
PPP2R5D -0.004 0.041 0.36 1 -10000 0 1
MAPK1 0.011 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.22 -10000 0 -0.52 33 33
RBPJ 0.011 0 -10000 0 -10000 0 0
CREBBP 0.013 0.005 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.1 0.19 -10000 0 -0.47 31 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.084 0.16 -10000 0 -0.79 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.015 0.03 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.065 0.095 -10000 0 -0.41 2 2
CaM/Ca2+ -0.093 0.18 -10000 0 -0.44 31 31
RAP1A 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.095 0.18 -10000 0 -0.45 30 30
AKT1 -0.086 0.16 -10000 0 -0.47 1 1
MAP2K1 -0.046 0.19 -10000 0 -0.5 1 1
MAP3K11 -0.059 0.2 -10000 0 -0.44 30 30
IFNGR1 0.004 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.12 0.2 -10000 0 -0.61 16 16
Rap1/GTP -0.071 0.13 -10000 0 -10000 0 0
CRKL/C3G 0 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.11 0.2 -10000 0 -0.49 31 31
CEBPB -0.006 0.17 -10000 0 -10000 0 0
STAT3 0.005 0.072 -10000 0 -0.88 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.1 0.22 -10000 0 -1.6 1 1
STAT1 -0.059 0.2 -10000 0 -0.44 30 30
CALM1 0.011 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.18 0.36 -10000 0 -0.81 35 35
PIK3CA 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.088 0.17 -10000 0 -0.42 30 30
CEBPB/PTGES2/Cbp/p300 -0.044 0.086 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.19 -10000 0 -0.47 31 31
MAPK3 -0.024 0.17 -10000 0 -10000 0 0
STAT1 (dimer) -0.085 0.13 -10000 0 -0.62 2 2
MAPK1 -0.024 0.17 -10000 0 -10000 0 0
JAK2 0.004 0.018 -10000 0 -10000 0 0
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
JAK1 0.004 0.018 -10000 0 -10000 0 0
CAMK2D 0.011 0 -10000 0 -10000 0 0
DAPK1 0.016 0.12 -10000 0 -10000 0 0
SMAD7 0.005 0.081 -10000 0 -0.36 1 1
CBL/CRKL/C3G -0.085 0.16 -10000 0 -0.48 1 1
PI3K -0.093 0.17 -10000 0 -0.48 2 2
IFNG -0.18 0.36 -10000 0 -0.82 35 35
apoptosis 0.005 0.11 0.37 1 -10000 0 1
CAMK2G 0.011 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.005 0.072 -10000 0 -0.87 1 1
CAMK2A -0.086 0.28 -10000 0 -0.85 17 17
CAMK2B -0.076 0.23 -10000 0 -0.58 22 22
FRAP1 -0.038 0.17 -10000 0 -0.43 1 1
PRKCD -0.042 0.18 -10000 0 -0.47 1 1
RAP1B 0.009 0.032 -10000 0 -0.38 1 1
negative regulation of cell growth -0.065 0.095 -10000 0 -0.41 2 2
PTPN2 0.011 0 -10000 0 -10000 0 0
EP300 0.012 0 -10000 0 -10000 0 0
IRF1 -0.007 0.17 -10000 0 -0.78 2 2
STAT1 (dimer)/PIASy -0.089 0.17 -10000 0 -0.49 2 2
SOCS1 -0.003 0.13 -10000 0 -1.6 1 1
mol:GDP -0.081 0.15 -10000 0 -0.46 1 1
CASP1 0.004 0.086 -10000 0 -0.4 2 2
PTGES2 0.011 0 -10000 0 -10000 0 0
IRF9 0.029 0.062 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.091 0.17 -10000 0 -0.47 2 2
RAP1/GDP -0.071 0.13 -10000 0 -10000 0 0
CBL -0.06 0.2 -10000 0 -0.44 30 30
MAP3K1 -0.058 0.2 -10000 0 -0.44 31 31
PIAS1 0.011 0 -10000 0 -10000 0 0
PIAS4 0.011 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.065 0.095 -10000 0 -0.41 2 2
PTPN11 -0.07 0.2 -10000 0 -0.47 31 31
CREBBP 0.012 0 -10000 0 -10000 0 0
RAPGEF1 0.011 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.048 0.12 -9999 0 -0.46 9 9
Syndecan-3/Neurocan -0.07 0.16 -9999 0 -0.51 17 17
POMC -0.12 0.28 -9999 0 -0.66 28 28
EGFR -0.043 0.19 -9999 0 -0.61 13 13
Syndecan-3/EGFR -0.032 0.1 -9999 0 -0.51 6 6
AGRP 0.006 0.006 -9999 0 -10000 0 0
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.011 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.036 0.2 -9999 0 -0.88 8 8
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.11 0.29 -9999 0 -0.73 24 24
long-term memory -0.004 0.016 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.091 0.18 -9999 0 -0.51 23 23
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
limb bud formation -0.005 0.022 -9999 0 -10000 0 0
MC4R -0.001 0.055 -9999 0 -0.38 3 3
SRC 0.011 0 -9999 0 -10000 0 0
PTN -0.089 0.24 -9999 0 -0.55 27 27
FGFR/FGF/Syndecan-3 -0.005 0.022 -9999 0 -10000 0 0
neuron projection morphogenesis -0.1 0.18 -9999 0 -0.47 26 26
Syndecan-3/AgRP -0.005 0.019 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.007 0.027 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.005 0.022 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.09 0.18 -9999 0 -0.5 23 23
IL8 -0.15 0.32 -9999 0 -0.75 31 31
Syndecan-3/Fyn/Cortactin -0.004 0.016 -9999 0 -10000 0 0
Syndecan-3/CASK -0.005 0.021 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.099 0.22 -9999 0 -0.68 16 16
Gamma Secretase -0.027 0.11 -9999 0 -0.51 8 8
Effects of Botulinum toxin

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
STX1A 0.011 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.076 0.17 -9999 0 -0.68 8 8
STXBP1 0.011 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.072 0.2 -9999 0 -0.49 24 24
RAB3GAP2/RIMS1/UNC13B -0.063 0.14 -9999 0 -0.59 8 8
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.098 0.23 -9999 0 -0.51 31 31
mol:ACh 0 0.033 -9999 0 -0.16 5 5
RAB3GAP2 0.011 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.053 0.12 -9999 0 -0.48 8 8
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.071 0.2 -9999 0 -0.49 24 24
UNC13B 0.011 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.27 -9999 0 -0.69 24 24
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.18 -9999 0 -0.62 12 12
SNAP25 -0.016 0.078 -9999 0 -0.2 17 17
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.072 0.24 -9999 0 -0.68 18 18
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.053 0.12 -9999 0 -0.48 8 8
EGFR-dependent Endothelin signaling events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.011 0 -9999 0 -10000 0 0
EGFR -0.043 0.19 -9999 0 -0.61 13 13
EGF/EGFR -0.096 0.19 -9999 0 -0.56 17 17
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.045 0.13 -9999 0 -0.51 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.076 0.2 -9999 0 -0.48 27 27
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.021 0.16 -9999 0 -0.79 6 6
EGF/EGFR dimer/SHC -0.054 0.16 -9999 0 -0.59 11 11
mol:GDP -0.045 0.13 -9999 0 -0.5 11 11
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.013 0.11 -9999 0 -0.44 8 8
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.041 0.12 -9999 0 -0.46 11 11
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.042 0.12 -9999 0 -0.47 11 11
FRAP1 -0.043 0.13 -9999 0 -0.48 11 11
EGF/EGFR dimer -0.064 0.18 -9999 0 -0.68 11 11
SOS1 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.076 0.17 -9999 0 -0.62 9 9
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.001 -9999 0 -10000 0 0
SMARCC1 0.011 0.011 -9999 0 -10000 0 0
REL -0.021 0.16 -9999 0 -0.88 5 5
HDAC7 -0.063 0.16 -9999 0 -0.76 3 3
JUN -0.066 0.22 -9999 0 -0.63 18 18
EP300 0.011 0.002 -9999 0 -10000 0 0
KAT2B 0.005 0.072 -9999 0 -0.88 1 1
KAT5 0.011 0 -9999 0 -10000 0 0
MAPK14 0.007 0.017 -9999 0 -10000 0 0
FOXO1 0.011 0 -9999 0 -10000 0 0
T-DHT/AR -0.072 0.17 -9999 0 -0.72 4 4
MAP2K6 0.005 0.008 -9999 0 -10000 0 0
BRM/BAF57 -0.018 0.11 -9999 0 -0.68 4 4
MAP2K4 0.005 0.008 -9999 0 -10000 0 0
SMARCA2 -0.013 0.14 -9999 0 -0.88 4 4
PDE9A -0.19 0.37 -9999 0 -1.2 14 14
NCOA2 -0.087 0.27 -9999 0 -0.85 17 17
CEBPA -0.003 0.11 -9999 0 -0.71 3 3
EHMT2 0.011 0.003 -9999 0 -10000 0 0
cell proliferation -0.11 0.19 -9999 0 -0.59 10 10
NR0B1 -0.09 0.26 -9999 0 -0.71 21 21
EGR1 -0.003 0.091 -9999 0 -0.51 4 4
RXRs/9cRA -0.041 0.13 -9999 0 -0.55 9 9
AR/RACK1/Src -0.032 0.12 -9999 0 -0.6 4 4
AR/GR -0.017 0.11 -9999 0 -0.41 8 8
GNB2L1 0.01 0.004 -9999 0 -10000 0 0
PKN1 0.011 0.003 -9999 0 -10000 0 0
RCHY1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.004 -9999 0 -10000 0 0
MAPK8 -0.012 0.12 -9999 0 -0.71 4 4
T-DHT/AR/TIF2/CARM1 -0.082 0.2 -9999 0 -0.63 12 12
SRC -0.008 0.1 -9999 0 -0.56 4 4
NR3C1 0.011 0 -9999 0 -10000 0 0
KLK3 -0.1 0.19 -9999 0 -0.52 13 13
APPBP2 0.006 0.007 -9999 0 -10000 0 0
TRIM24 0.011 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.045 0.11 -9999 0 -0.63 4 4
TMPRSS2 -0.6 0.63 -9999 0 -1.3 61 61
RXRG -0.06 0.22 -9999 0 -0.66 16 16
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.011 0 -9999 0 -10000 0 0
RXRB 0.011 0 -9999 0 -10000 0 0
CARM1 0.01 0.004 -9999 0 -10000 0 0
NR2C2 0.005 0.072 -9999 0 -0.88 1 1
KLK2 -0.15 0.31 -9999 0 -0.81 23 23
AR -0.027 0.12 -9999 0 -0.42 11 11
SENP1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
MDM2 0.006 0.033 -9999 0 -0.38 1 1
SRY -0.11 0.29 -9999 0 -0.79 22 22
GATA2 -0.11 0.25 -9999 0 -0.53 33 33
MYST2 0.011 0 -9999 0 -10000 0 0
HOXB13 -0.18 0.31 -9999 0 -0.58 48 48
T-DHT/AR/RACK1/Src -0.025 0.12 -9999 0 -0.61 4 4
positive regulation of transcription -0.11 0.25 -9999 0 -0.53 33 33
DNAJA1 0.006 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.008 -9999 0 -10000 0 0
NCOA1 0.017 0.005 -9999 0 -10000 0 0
SPDEF -0.17 0.32 -9999 0 -0.65 41 41
T-DHT/AR/TIF2 -0.022 0.12 -9999 0 -0.45 5 5
T-DHT/AR/Hsp90 -0.047 0.11 -9999 0 -0.63 4 4
GSK3B 0.005 0.006 -9999 0 -10000 0 0
NR2C1 0.011 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.015 0.1 -9999 0 -0.6 4 4
SIRT1 0.011 0.002 -9999 0 -10000 0 0
ZMIZ2 0.009 0.007 -9999 0 -10000 0 0
POU2F1 -0.011 0.13 -9999 0 -0.9 3 3
T-DHT/AR/DAX-1 -0.1 0.18 -9999 0 -0.58 18 18
CREBBP 0.011 0.003 -9999 0 -10000 0 0
SMARCE1 0.011 0.003 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.011 0.071 -9999 0 -0.6 2 2
ADCY5 -0.063 0.2 -9999 0 -0.64 15 15
ADCY6 0.013 0.057 -9999 0 -0.6 1 1
ADCY7 0.016 0.05 -9999 0 -0.6 1 1
ADCY1 -0.004 0.11 -9999 0 -0.6 5 5
ADCY2 -0.064 0.18 -9999 0 -0.6 12 12
ADCY3 0.016 0.05 -9999 0 -0.6 1 1
ADCY8 -0.12 0.23 -9999 0 -0.6 26 26
PRKCE 0.006 0.057 -9999 0 -0.69 1 1
ADCY9 0.016 0.05 -9999 0 -0.6 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.071 0.15 -9999 0 -0.46 10 10
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.023 0.13 -10000 0 -0.71 3 3
epithelial cell differentiation -0.043 0.11 -10000 0 -0.62 3 3
ITCH 0.023 0.019 -10000 0 -10000 0 0
WWP1 -0.008 0.079 -10000 0 -10000 0 0
FYN 0.011 0 -10000 0 -10000 0 0
EGFR -0.043 0.19 -10000 0 -0.61 13 13
PRL -0.038 0.12 -10000 0 -0.38 17 17
neuron projection morphogenesis 0.004 0.14 -10000 0 -0.65 3 3
PTPRZ1 -0.39 0.39 -10000 0 -0.7 85 85
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.048 0.14 -10000 0 -0.57 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.17 -10000 0 -0.66 8 8
ADAM17 0.004 0.12 -10000 0 -0.86 3 3
ErbB4/ErbB4 -0.018 0.098 -10000 0 -0.55 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.22 -10000 0 -0.57 23 23
NCOR1 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.056 0.15 -10000 0 -0.62 8 8
GRIN2B -0.039 0.17 -10000 0 -0.59 8 8
ErbB4/ErbB2/betacellulin -0.052 0.12 -10000 0 -0.57 5 5
STAT1 0.011 0 -10000 0 -10000 0 0
HBEGF -0.009 0.13 -10000 0 -0.75 4 4
PRLR -0.028 0.16 -10000 0 -0.58 10 10
E4ICDs/ETO2 -0.03 0.13 -10000 0 -0.58 6 6
axon guidance 0.079 0.12 -10000 0 -0.37 1 1
NEDD4 0.01 0.1 -10000 0 -0.87 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.058 0.14 -10000 0 -0.65 5 5
CBFA2T3 -0.018 0.16 -10000 0 -0.88 5 5
ErbB4/ErbB2/HBEGF -0.037 0.13 -10000 0 -0.66 5 5
MAPK3 -0.005 0.14 -10000 0 -0.63 4 4
STAT1 (dimer) -0.01 0.083 -10000 0 -0.48 1 1
MAPK1 -0.005 0.14 -10000 0 -0.63 4 4
JAK2 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.055 0.15 -10000 0 -0.62 8 8
NRG1 -0.026 0.19 -10000 0 -0.74 8 8
NRG3 -0.13 0.31 -10000 0 -0.71 30 30
NRG2 -0.077 0.27 -10000 0 -0.88 15 15
NRG4 0 0.1 -10000 0 -0.88 2 2
heart development 0.079 0.12 -10000 0 -0.37 1 1
neural crest cell migration -0.055 0.15 -10000 0 -0.61 8 8
ERBB2 0.015 0.097 -10000 0 -0.66 3 3
WWOX/E4ICDs -0.01 0.083 -10000 0 -0.48 1 1
SHC1 0.011 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.064 0.15 -10000 0 -0.59 9 9
apoptosis 0.087 0.16 0.44 21 -10000 0 21
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.068 0.2 -10000 0 -0.62 16 16
ErbB4/ErbB2/epiregulin -0.034 0.097 -10000 0 -0.61 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.049 0.12 -10000 0 -0.5 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.069 0.14 -10000 0 -0.58 7 7
MDM2 -0.008 0.087 -10000 0 -0.48 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.05 0.15 -10000 0 -0.62 8 8
STAT5A 0.077 0.12 -10000 0 -0.5 1 1
ErbB4/EGFR/neuregulin 1 beta -0.084 0.21 -10000 0 -0.7 12 12
DLG4 0.009 0.032 -10000 0 -0.38 1 1
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.03 0.066 -10000 0 -0.45 1 1
STAT5A (dimer) -0.046 0.12 -10000 0 -0.69 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.074 0.1 -10000 0 -10000 0 0
LRIG1 0.011 0 -10000 0 -10000 0 0
EREG -0.011 0.083 -10000 0 -0.38 7 7
BTC -0.044 0.15 -10000 0 -0.44 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.079 0.12 -10000 0 -0.38 1 1
ERBB4 -0.018 0.098 -10000 0 -0.55 1 1
STAT5B 0.011 0 -10000 0 -10000 0 0
YAP1 -0.01 0.021 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.033 0.11 -10000 0 -0.57 5 5
glial cell differentiation 0.03 0.066 0.45 1 -10000 0 1
WWOX 0.011 0 -10000 0 -10000 0 0
cell proliferation 0.002 0.18 -10000 0 -0.67 7 7
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.085 0.23 -9999 0 -0.65 19 19
MAP4K1 -0.089 0.28 -9999 0 -0.88 17 17
MAP3K8 -0.006 0.12 -9999 0 -0.88 3 3
PRKCB -0.027 0.18 -9999 0 -0.8 7 7
DBNL 0.011 0 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 -0.008 0.16 -9999 0 -0.78 4 4
JUN -0.067 0.25 -9999 0 -0.7 18 18
MAP3K7 -0.008 0.16 -9999 0 -0.78 4 4
GRAP2 -0.018 0.15 -9999 0 -0.71 6 6
CRK 0.011 0 -9999 0 -10000 0 0
MAP2K4 -0.003 0.17 -9999 0 -0.81 4 4
LAT 0.011 0 -9999 0 -10000 0 0
LCP2 0 0.1 -9999 0 -0.88 2 2
MAPK8 -0.034 0.22 -9999 0 -0.82 10 10
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.051 0.16 -9999 0 -0.84 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.08 0.22 -9999 0 -0.61 19 19
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.023 0.11 -9999 0 -0.68 4 4
CRKL -0.015 0.11 -9999 0 -0.4 5 5
mol:PIP3 -0.019 0.005 -9999 0 -10000 0 0
AKT1 0.002 0.004 -9999 0 -10000 0 0
PTK2B 0.005 0.072 -9999 0 -0.88 1 1
RAPGEF1 -0.006 0.11 -9999 0 -0.58 1 1
RANBP10 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.011 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.11 0.2 -9999 0 -0.61 17 17
MAP3K5 -0.053 0.17 -9999 0 -0.51 9 9
HGF/MET/CIN85/CBL/ENDOPHILINS -0.097 0.18 -9999 0 -0.57 16 16
AP1 -0.13 0.29 -9999 0 -0.73 24 24
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
apoptosis -0.11 0.31 -9999 0 -0.88 20 20
STAT3 (dimer) -0.023 0.13 -9999 0 -0.37 16 16
GAB1/CRKL/SHP2/PI3K -0.035 0.099 -9999 0 -0.61 2 2
INPP5D 0.005 0.072 -9999 0 -0.88 1 1
CBL/CRK -0.007 0.11 -9999 0 -0.58 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.011 0 -9999 0 -10000 0 0
PTEN 0.011 0 -9999 0 -10000 0 0
ELK1 -0.014 0.051 -9999 0 -0.29 4 4
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.03 0.069 -9999 0 -0.44 1 1
PAK1 0.009 0.004 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.11 0.2 -9999 0 -0.61 17 17
HRAS -0.046 0.19 -9999 0 -0.54 16 16
DOCK1 -0.01 0.11 -9999 0 -0.46 3 3
GAB1 -0.023 0.12 -9999 0 -0.33 16 16
CRK -0.015 0.11 -9999 0 -0.4 5 5
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.082 0.21 -9999 0 -0.67 16 16
JUN -0.066 0.22 -9999 0 -0.63 18 18
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.049 0.1 -9999 0 -0.32 16 16
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
cell morphogenesis 0.006 0.14 -9999 0 -0.62 3 3
GRB2/SHC -0.039 0.087 -9999 0 -0.39 4 4
FOS -0.11 0.29 -9999 0 -0.73 24 24
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.014 0.051 -9999 0 -0.29 4 4
HGF/MET/MUC20 -0.11 0.2 -9999 0 -0.62 17 17
cell migration -0.038 0.086 -9999 0 -0.38 4 4
GRB2 0.011 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
MET/RANBP10 -0.023 0.11 -9999 0 -0.68 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.058 0.13 -9999 0 -0.4 16 16
MET/MUC20 -0.024 0.12 -9999 0 -0.51 7 7
RAP1B 0.001 0.1 -9999 0 -0.53 1 1
RAP1A 0.002 0.1 -9999 0 -0.53 1 1
HGF/MET/RANBP9 -0.11 0.2 -9999 0 -0.61 17 17
RAF1 -0.035 0.18 -9999 0 -0.72 5 5
STAT3 -0.052 0.12 -9999 0 -0.38 16 16
cell proliferation -0.024 0.17 -9999 0 -0.5 16 16
RPS6KB1 -0.016 0.034 -9999 0 -10000 0 0
MAPK3 -0.017 0.046 -9999 0 -10000 0 0
MAPK1 -0.017 0.046 -9999 0 -0.26 4 4
RANBP9 0.011 0 -9999 0 -10000 0 0
MAPK8 -0.035 0.16 -9999 0 -0.54 7 7
SRC -0.022 0.13 -9999 0 -0.37 16 16
PI3K -0.042 0.1 -9999 0 -0.65 2 2
MET/Glomulin -0.011 0.11 -9999 0 -0.45 7 7
SOS1 0.011 0 -9999 0 -10000 0 0
MAP2K1 -0.024 0.16 -9999 0 -0.72 4 4
MET -0.02 0.15 -9999 0 -0.66 7 7
MAP4K1 -0.041 0.14 -9999 0 -0.37 12 12
PTK2 0.011 0 -9999 0 -10000 0 0
MAP2K2 -0.024 0.16 -9999 0 -0.72 4 4
BAD 0.009 0.004 -9999 0 -10000 0 0
MAP2K4 -0.041 0.16 -9999 0 -0.46 9 9
SHP2/GRB2/SOS1/GAB1 -0.041 0.11 -9999 0 -0.59 4 4
INPPL1 0.011 0 -9999 0 -10000 0 0
PXN 0.011 0 -9999 0 -10000 0 0
SH3KBP1 0.011 0 -9999 0 -10000 0 0
HGS -0.043 0.093 -9999 0 -0.42 4 4
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.14 0.27 -9999 0 -0.54 41 41
RASA1 0.011 0 -9999 0 -10000 0 0
NCK1 0.011 0 -9999 0 -10000 0 0
PTPRJ 0.011 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.042 0.094 -9999 0 -0.39 4 4
PDPK1 -0.008 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.11 0.2 -9999 0 -0.61 18 18
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.063 0.49 1 -0.33 1 2
RFC1 0.011 0.063 0.49 1 -0.33 1 2
PRKDC 0.007 0.079 0.49 1 -0.45 2 3
RIPK1 0.01 0.004 -10000 0 -10000 0 0
CASP7 -0.008 0.089 0.28 3 -0.74 1 4
FASLG/FAS/FADD/FAF1 -0.031 0.15 0.29 4 -0.42 15 19
MAP2K4 -0.018 0.18 -10000 0 -0.45 16 16
mol:ceramide -0.036 0.2 -10000 0 -0.54 18 18
GSN 0.007 0.079 0.49 1 -0.45 2 3
FASLG/FAS/FADD/FAF1/Caspase 8 -0.053 0.17 -10000 0 -0.49 18 18
FAS -0.001 0.1 -10000 0 -0.88 2 2
BID 0.012 0.083 0.33 6 -0.61 1 7
MAP3K1 0.005 0.12 0.23 3 -0.35 8 11
MAP3K7 0.01 0.004 -10000 0 -10000 0 0
RB1 0.011 0.063 0.49 1 -0.33 1 2
CFLAR 0.01 0.004 -10000 0 -10000 0 0
HGF/MET -0.13 0.21 -10000 0 -0.58 22 22
ARHGDIB 0.002 0.071 -10000 0 -0.45 2 2
FADD 0.011 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.079 0.45 2 -0.49 1 3
NFKB1 -0.037 0.081 -10000 0 -10000 0 0
MAPK8 -0.038 0.22 -10000 0 -0.5 23 23
DFFA 0.011 0.063 0.49 1 -0.33 1 2
DNA fragmentation during apoptosis 0.011 0.063 0.49 1 -0.33 1 2
FAS/FADD/MET -0.028 0.12 -10000 0 -0.59 6 6
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.037 0.18 -10000 0 -0.65 11 11
FAF1 0.011 0.004 -10000 0 -10000 0 0
PARP1 0.011 0.063 0.49 1 -0.33 1 2
DFFB 0.011 0.063 0.49 1 -0.33 1 2
CHUK -0.032 0.071 -10000 0 -10000 0 0
FASLG -0.098 0.29 -10000 0 -0.86 19 19
FAS/FADD -0.009 0.078 -10000 0 -0.68 2 2
HGF -0.14 0.27 -10000 0 -0.54 41 41
LMNA 0.01 0.057 0.43 1 -10000 0 1
CASP6 0.011 0.063 0.49 1 -0.33 1 2
CASP10 0.011 0.004 -10000 0 -10000 0 0
CASP3 0.013 0.078 0.32 6 -0.38 1 7
PTPN13 -0.026 0.13 -10000 0 -0.42 13 13
CASP8 0.02 0.11 0.48 6 -0.7 1 7
IL6 -0.14 0.47 -10000 0 -1.4 17 17
MET -0.02 0.15 -10000 0 -0.66 7 7
ICAD/CAD 0.01 0.058 0.44 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.037 0.2 -10000 0 -0.55 18 18
activation of caspase activity by cytochrome c 0.012 0.083 0.33 6 -0.6 1 7
PAK2 0.011 0.063 0.49 1 -0.34 1 2
BCL2 0.003 0.079 -10000 0 -0.63 2 2
Canonical 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
HDAC1 0.009 0.027 -10000 0 -10000 0 0
AES 0.008 0.023 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.021 0.07 -10000 0 -10000 0 0
SMAD4 0.011 0 -10000 0 -10000 0 0
DKK2 -0.084 0.2 -10000 0 -0.45 31 31
TLE1 0.002 0.077 -10000 0 -0.88 1 1
MACF1 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 0.016 0.097 -10000 0 -10000 0 0
WIF1 -0.16 0.28 -10000 0 -0.55 45 45
beta catenin/RanBP3 0.012 0.13 0.46 8 -10000 0 8
KREMEN2 -0.061 0.23 -10000 0 -0.71 15 15
DKK1 -0.26 0.35 -10000 0 -0.61 66 66
beta catenin/beta TrCP1 0.022 0.091 -10000 0 -10000 0 0
FZD1 -0.021 0.11 -10000 0 -0.38 12 12
AXIN2 -0.008 0.16 -10000 0 -1.8 1 1
AXIN1 0.011 0.003 -10000 0 -10000 0 0
RAN 0.011 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.026 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.078 -10000 0 -10000 0 0
Axin1/APC/GSK3 0 0.045 0.27 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.016 0.12 -10000 0 -0.52 4 4
HNF1A -0.062 0.15 -10000 0 -0.4 25 25
CTBP1 0.009 0.028 -10000 0 -10000 0 0
MYC -0.036 0.28 -10000 0 -1.7 4 4
RANBP3 0.011 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.099 0.19 -10000 0 -0.6 15 15
NKD1 -0.004 0.09 -10000 0 -0.51 4 4
TCF4 0.008 0.025 -10000 0 -10000 0 0
TCF3 0.009 0.028 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.044 0.14 -10000 0 -0.6 6 6
Ran/GTP 0 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.028 0.14 0.51 9 -10000 0 9
LEF1 -0.012 0.13 -10000 0 -0.74 4 4
DVL1 0.024 0.05 -10000 0 -10000 0 0
CSNK2A1 0.011 0.002 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.034 0.11 -10000 0 -0.49 2 2
DKK1/LRP6/Kremen 2 -0.21 0.29 -10000 0 -0.68 35 35
LRP6 0.011 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.027 -10000 0 -10000 0 0
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 -0.082 0.36 -10000 0 -1.7 7 7
WNT1 -0.043 0.19 -10000 0 -0.61 13 13
GSK3A 0.01 0.004 -10000 0 -10000 0 0
GSK3B 0.009 0.005 -10000 0 -10000 0 0
FRAT1 -0.002 0.1 -10000 0 -0.88 2 2
PPP2R5D 0.024 0.046 0.42 1 -10000 0 1
APC -0.021 0.13 -10000 0 -0.56 6 6
WNT1/LRP6/FZD1 0.039 0.11 0.28 15 -0.31 2 17
CREBBP 0.009 0.028 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.012 0.013 -10000 0 -10000 0 0
HSPA8 -0.019 0.16 -10000 0 -0.87 5 5
SMAD3/SMAD4/ER alpha -0.01 0.094 -10000 0 -0.61 2 2
AKT1 0.013 0.009 -10000 0 -10000 0 0
GSC -0.14 0.43 -10000 0 -1.6 11 11
NKX2-5 -0.29 0.4 -10000 0 -0.77 58 58
muscle cell differentiation 0.1 0.13 0.42 2 -10000 0 2
SMAD2-3/SMAD4/SP1 -0.007 0.09 -10000 0 -10000 0 0
SMAD4 -0.002 0.059 -10000 0 -10000 0 0
CBFB 0.011 0 -10000 0 -10000 0 0
SAP18 0.01 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.03 0.12 -10000 0 -0.59 5 5
SMAD3/SMAD4/VDR -0.003 0.073 -10000 0 -0.52 2 2
MYC -0.022 0.14 -10000 0 -0.88 4 4
CDKN2B 0.01 0.19 -10000 0 -1.6 2 2
AP1 -0.095 0.33 -10000 0 -0.77 23 23
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.004 0.037 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.004 0.068 -10000 0 -0.36 1 1
SP3 0.006 0.027 -10000 0 -10000 0 0
CREB1 0.011 0 -10000 0 -10000 0 0
FOXH1 -0.12 0.29 -10000 0 -0.74 25 25
SMAD3/SMAD4/GR -0.01 0.052 -10000 0 -10000 0 0
GATA3 -0.036 0.17 -10000 0 -0.52 14 14
SKI/SIN3/HDAC complex/NCoR1 0.04 0.02 -10000 0 -10000 0 0
MEF2C/TIF2 -0.28 0.29 -10000 0 -0.71 28 28
endothelial cell migration 0.099 0.39 1.5 10 -10000 0 10
MAX 0.014 0.014 -10000 0 -10000 0 0
RBBP7 0.01 0.005 -10000 0 -10000 0 0
RBBP4 0.01 0.005 -10000 0 -10000 0 0
RUNX2 -0.008 0.12 -10000 0 -0.58 5 5
RUNX3 -0.003 0.11 -10000 0 -0.71 3 3
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.011 0 -10000 0 -10000 0 0
NR3C1 0.014 0.014 -10000 0 -10000 0 0
VDR -0.003 0.11 -10000 0 -0.71 3 3
CDKN1A -0.03 0.33 -10000 0 -1.5 7 7
KAT2B 0.005 0.071 -10000 0 -0.86 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.1 0.21 -10000 0 -0.63 18 18
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.01 0.005 -10000 0 -10000 0 0
SERPINE1 -0.1 0.4 -10000 0 -1.6 10 10
SMAD3/SMAD4/ATF2 -0.021 0.084 -10000 0 -0.6 2 2
SMAD3/SMAD4/ATF3 -0.017 0.079 -10000 0 -0.78 1 1
SAP30 0.01 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.013 0.034 -10000 0 -10000 0 0
JUN -0.087 0.33 -10000 0 -0.76 23 23
SMAD3/SMAD4/IRF7 -0.016 0.069 -10000 0 -0.61 1 1
TFE3 0.014 0.013 -10000 0 -10000 0 0
COL1A2 -0.052 0.17 -10000 0 -1.2 2 2
mesenchymal cell differentiation 0.026 0.096 0.67 2 -10000 0 2
DLX1 -0.04 0.19 -10000 0 -0.63 12 12
TCF3 0.011 0 -10000 0 -10000 0 0
FOS -0.11 0.3 -10000 0 -0.76 24 24
SMAD3/SMAD4/Max -0.01 0.052 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.003 0.012 -10000 0 -10000 0 0
ZBTB17 0.002 0.009 -10000 0 -10000 0 0
LAMC1 0.029 0.058 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.013 0.05 -10000 0 -10000 0 0
IRF7 0.007 0.072 -10000 0 -0.88 1 1
ESR1 -0.007 0.1 -10000 0 -0.88 2 2
HNF4A -0.21 0.32 -10000 0 -0.59 54 54
MEF2C -0.22 0.3 -10000 0 -0.63 30 30
SMAD2-3/SMAD4 -0.019 0.059 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.01 0.023 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.016 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0 -10000 0 -10000 0 0
CREBBP 0.012 0.008 -10000 0 -10000 0 0
SKIL 0 0.1 -10000 0 -0.88 2 2
HDAC1 0.01 0.005 -10000 0 -10000 0 0
HDAC2 0.01 0.005 -10000 0 -10000 0 0
SNIP1 0.01 0.005 -10000 0 -10000 0 0
GCN5L2 0 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.008 0.053 -10000 0 -10000 0 0
MSG1/HSC70 -0.068 0.18 -10000 0 -0.68 10 10
SMAD2 0.007 0.029 -10000 0 -10000 0 0
SMAD3 0.004 0.05 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.022 0.069 -10000 0 -0.37 3 3
SMAD2/SMAD2/SMAD4 0.008 0.051 -10000 0 -0.5 1 1
NCOR1 0.01 0.005 -10000 0 -10000 0 0
NCOA2 -0.086 0.28 -10000 0 -0.85 17 17
NCOA1 0.011 0 -10000 0 -10000 0 0
MYOD/E2A -0.022 0.084 -10000 0 -0.68 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.021 0.093 -10000 0 -10000 0 0
IFNB1 0.019 0.073 -10000 0 -0.54 1 1
SMAD3/SMAD4/MEF2C -0.22 0.28 -10000 0 -0.66 25 25
CITED1 -0.06 0.19 -10000 0 -0.51 20 20
SMAD2-3/SMAD4/ARC105 -0.012 0.05 -10000 0 -10000 0 0
RBL1 0.005 0.072 -10000 0 -0.88 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.037 0.085 -10000 0 -0.53 2 2
RUNX1-3/PEBPB2 -0.009 0.07 -10000 0 -0.59 2 2
SMAD7 -0.029 0.24 -10000 0 -0.77 9 9
MYC/MIZ-1 -0.016 0.11 -10000 0 -0.69 4 4
SMAD3/SMAD4 -0.001 0.13 0.3 3 -0.45 7 10
IL10 -0.012 0.18 -10000 0 -0.75 7 7
PIASy/HDAC complex 0.012 0.01 -10000 0 -10000 0 0
PIAS3 0.011 0.005 -10000 0 -10000 0 0
CDK2 0.012 0.008 -10000 0 -10000 0 0
IL5 -0.007 0.14 -10000 0 -0.64 4 4
CDK4 0.013 0.009 -10000 0 -10000 0 0
PIAS4 0.012 0.01 -10000 0 -10000 0 0
ATF3 0.005 0.072 -10000 0 -0.88 1 1
SMAD3/SMAD4/SP1 -0.032 0.081 -10000 0 -10000 0 0
FOXG1 -0.026 0.17 -10000 0 -0.69 8 8
FOXO3 0.025 0.012 -10000 0 -10000 0 0
FOXO1 0.025 0.012 -10000 0 -10000 0 0
FOXO4 0.02 0.059 -10000 0 -0.69 1 1
heart looping -0.21 0.29 -10000 0 -0.62 31 31
CEBPB 0.01 0.032 -10000 0 -0.38 1 1
SMAD3/SMAD4/DLX1 -0.046 0.14 -10000 0 -0.67 6 6
MYOD1 -0.023 0.12 -10000 0 -0.43 11 11
SMAD3/SMAD4/HNF4 -0.15 0.22 -10000 0 -0.63 23 23
SMAD3/SMAD4/GATA3 -0.045 0.14 -10000 0 -0.66 5 5
SnoN/SIN3/HDAC complex/NCoR1 0 0.1 -10000 0 -0.87 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.011 0.077 -10000 0 -0.58 2 2
SMAD3/SMAD4/SP1-3 -0.033 0.1 -10000 0 -0.44 1 1
MED15 0.011 0 -10000 0 -10000 0 0
SP1 0.001 0.038 -10000 0 -10000 0 0
SIN3B 0.01 0.005 -10000 0 -10000 0 0
SIN3A 0.01 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.26 0.3 -10000 0 -0.61 60 60
ITGB5 -0.023 0.24 -10000 0 -0.83 11 11
TGIF/SIN3/HDAC complex/CtBP 0.038 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.062 0.16 -10000 0 -0.6 10 10
AR -0.063 0.22 -10000 0 -0.64 17 17
negative regulation of cell growth 0.028 0.072 -10000 0 -0.39 1 1
SMAD3/SMAD4/MYOD -0.031 0.089 -10000 0 -0.59 1 1
E2F5 0 0.1 -10000 0 -0.88 2 2
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.08 0.18 -10000 0 -0.53 18 18
SMAD2-3/SMAD4/FOXO1-3a-4 0.03 0.074 -10000 0 -0.42 2 2
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.13 0.33 -10000 0 -0.78 23 23
SMAD3/SMAD4/RUNX2 -0.026 0.097 -10000 0 -0.68 2 2
TGIF2 0.011 0 -10000 0 -10000 0 0
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0 0.1 -10000 0 -0.88 2 2
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.068 0.2 -10000 0 -0.68 15 15
ATM 0.011 0 -10000 0 -10000 0 0
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.005 0.072 -10000 0 -0.88 1 1
ATR 0.011 0 -10000 0 -10000 0 0
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.018 0.056 -10000 0 -0.46 2 2
protein ubiquitination -0.053 0.16 -10000 0 -0.5 16 16
XRCC5 0.011 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.011 0 -10000 0 -10000 0 0
DNA-PK -0.004 0.048 -10000 0 -0.59 1 1
FA complex/FANCD2/Ubiquitin -0.005 0.02 -10000 0 -10000 0 0
FANCF 0.011 0 -10000 0 -10000 0 0
BRCA1 0.011 0 -10000 0 -10000 0 0
CCNE1 0.005 0.072 -10000 0 -0.88 1 1
CDK2/Cyclin E1 -0.005 0.055 -10000 0 -0.68 1 1
FANCG 0.011 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.068 0.2 -10000 0 -0.68 15 15
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN 0.011 0 -10000 0 -10000 0 0
FANCA 0.011 0 -10000 0 -10000 0 0
DNA repair 0.006 0.17 -10000 0 -0.63 1 1
BRCA1/BARD1/ubiquitin -0.068 0.2 -10000 0 -0.68 15 15
BARD1/DNA-PK -0.058 0.18 -10000 0 -0.57 15 15
FANCL 0.011 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.068 0.2 0.68 15 -10000 0 15
BRCA1/BARD1/CTIP/M/R/N Complex -0.034 0.1 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.059 0.18 -10000 0 -0.59 15 15
BRCA1/BARD1/P53 -0.054 0.16 -10000 0 -0.54 15 15
BARD1/CSTF1/BRCA1 -0.059 0.18 -10000 0 -0.59 15 15
BRCA1/BACH1 0.011 0 -10000 0 -10000 0 0
BARD1 -0.077 0.27 -10000 0 -0.88 15 15
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.059 0.18 -10000 0 -0.59 15 15
BRCA1/BARD1/UbcH7 -0.059 0.18 -10000 0 -0.59 15 15
BRCA1/BARD1/RAD51/PCNA -0.076 0.19 -10000 0 -0.54 21 21
BARD1/DNA-PK/P53 -0.054 0.17 -10000 0 -0.54 15 15
BRCA1/BARD1/Ubiquitin -0.068 0.2 -10000 0 -0.68 15 15
BRCA1/BARD1/CTIP -0.054 0.16 -10000 0 -0.54 15 15
FA complex 0 0 -10000 0 -10000 0 0
BARD1/EWS -0.068 0.2 -10000 0 -0.68 15 15
RBBP8 0.022 0 -10000 0 -10000 0 0
TP53 0.011 0 -10000 0 -10000 0 0
TOPBP1 0.011 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.054 0.16 0.54 15 -10000 0 15
BRCA1/BARD1 -0.054 0.16 -10000 0 -0.51 16 16
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.069 0.21 -10000 0 -0.69 15 15
CDK2 0.011 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.024 0.17 -10000 0 -0.88 6 6
RAD50 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.068 0.2 -10000 0 -0.68 15 15
EWSR1 0.011 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.066 0.16 -9999 0 -0.57 11 11
RGS9BP -0.006 0.077 -9999 0 -0.38 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.006 0.07 -9999 0 -0.38 5 5
mol:Na + -0.07 0.18 -9999 0 -0.57 15 15
mol:ADP 0.007 0.05 -9999 0 -10000 0 0
GNAT2 -0.03 0.13 -9999 0 -0.42 14 14
RGS9-1/Gbeta5/R9AP -0.033 0.099 -9999 0 -0.5 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.03 0.085 -9999 0 -0.61 1 1
GRK7 0.009 0.005 -9999 0 -10000 0 0
CNGB3 -0.007 0.077 -9999 0 -0.38 6 6
Cone Metarhodopsin II/X-Arrestin -0.009 0.048 -9999 0 -10000 0 0
mol:Ca2+ -0.046 0.17 -9999 0 -0.52 15 15
Cone PDE6 -0.039 0.099 -9999 0 -0.52 2 2
Cone Metarhodopsin II -0.007 0.035 -9999 0 -10000 0 0
Na + (4 Units) -0.063 0.16 -9999 0 -0.52 15 15
GNAT2/GDP -0.045 0.1 -9999 0 -0.57 3 3
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.022 0.092 -9999 0 -0.44 3 3
Cone Transducin -0.07 0.16 -9999 0 -0.6 11 11
SLC24A2 0.01 0.004 -9999 0 -10000 0 0
GNB3/GNGT2 -0.064 0.18 -9999 0 -0.68 10 10
GNB3 -0.06 0.22 -9999 0 -0.62 17 17
GNAT2/GTP -0.028 0.093 -9999 0 -0.69 1 1
CNGA3 -0.084 0.26 -9999 0 -0.7 20 20
ARR3 -0.006 0.07 -9999 0 -0.38 5 5
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.071 0.18 -9999 0 -0.58 15 15
mol:Pi -0.032 0.099 -9999 0 -0.5 4 4
Cone CNG Channel -0.086 0.17 -9999 0 -0.52 15 15
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.01 0.004 -9999 0 -10000 0 0
RGS9 -0.032 0.14 -9999 0 -0.45 14 14
PDE6C -0.011 0.076 -9999 0 -0.38 6 6
GNGT2 -0.006 0.11 -9999 0 -0.63 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.008 0.07 -9999 0 -0.38 5 5
Thromboxane A2 receptor signaling

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
TGM2 -0.012 0.088 -10000 0 -0.38 8 8
GNB1/GNG2 -0.027 0.057 -10000 0 -0.2 7 7
AKT1 0.03 0.085 -10000 0 -0.21 6 6
EGF -0.021 0.16 -10000 0 -0.79 6 6
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.031 0.093 -10000 0 -0.48 3 3
mol:Ca2+ 0.018 0.12 -10000 0 -0.31 10 10
LYN -0.02 0.078 -10000 0 -0.6 1 1
RhoA/GTP -0.014 0.036 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.021 0.13 -10000 0 -0.37 10 10
GNG2 0.009 0.032 -10000 0 -0.38 1 1
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.14 -10000 0 -0.56 7 7
G beta5/gamma2 -0.034 0.075 -10000 0 -0.27 7 7
PRKCH 0.018 0.13 -10000 0 -0.36 9 9
DNM1 -0.008 0.12 -10000 0 -0.58 5 5
TXA2/TP beta/beta Arrestin3 -0.01 0.04 -10000 0 -0.32 2 2
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.017 0.15 -10000 0 -0.71 6 6
G12 family/GTP -0.037 0.086 -10000 0 -0.31 10 10
ADRBK1 0.011 0 -10000 0 -10000 0 0
ADRBK2 0.011 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.015 0.091 0.43 2 -10000 0 2
mol:NADP 0.011 0 -10000 0 -10000 0 0
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.085 0.24 -10000 0 -0.59 24 24
mol:IP3 0.014 0.14 -10000 0 -0.39 10 10
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.004 0.18 -10000 0 -0.54 10 10
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.092 0.16 -10000 0 -0.44 23 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.026 0.087 -10000 0 -0.51 2 2
RHOA 0.011 0 -10000 0 -10000 0 0
PTGIR -0.02 0.15 -10000 0 -0.66 7 7
PRKCB1 0.014 0.14 -10000 0 -0.38 10 10
GNAQ 0.011 0 -10000 0 -10000 0 0
mol:L-citrulline 0.011 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.007 0.18 -10000 0 -0.54 11 11
LCK -0.044 0.13 -10000 0 -0.47 9 9
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.032 0.12 -10000 0 -0.63 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.031 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.027 0.11 -10000 0 -0.58 3 3
MAPK14 0.028 0.095 -10000 0 -0.25 6 6
TGM2/GTP 0.009 0.16 -10000 0 -0.43 11 11
MAPK11 0.026 0.1 -10000 0 -0.29 6 6
ARHGEF1 0.02 0.073 -10000 0 -10000 0 0
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade 0.016 0.14 -10000 0 -0.39 11 11
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 0.019 0.12 -10000 0 -0.31 10 10
cAMP biosynthetic process 0.009 0.14 -10000 0 -0.36 11 11
Gq family/GTP/EBP50 -0.011 0.096 -10000 0 -0.35 8 8
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.02 0.078 -10000 0 -0.6 1 1
GNB5 0.011 0 -10000 0 -10000 0 0
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR -0.009 0.12 -10000 0 -0.34 10 10
VCAM1 0.016 0.12 -10000 0 -0.34 12 12
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.14 -10000 0 -0.56 7 7
platelet activation 0.035 0.12 -10000 0 -0.32 10 10
PGI2/IP -0.024 0.12 -10000 0 -0.51 7 7
PRKACA -0.027 0.12 -10000 0 -0.5 7 7
Gq family/GDP/G beta5/gamma2 -0.011 0.13 -10000 0 -0.54 7 7
TXA2/TP beta/beta Arrestin2 -0.012 0.081 -10000 0 -0.7 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.13 -10000 0 -0.48 9 9
mol:DAG 0.013 0.15 -10000 0 -0.43 10 10
EGFR -0.043 0.19 -10000 0 -0.61 13 13
TXA2/TP alpha 0.005 0.18 -10000 0 -0.5 11 11
Gq family/GTP -0.034 0.087 -10000 0 -0.3 13 13
YES1 -0.02 0.078 -10000 0 -0.6 1 1
GNAI2/GTP -0.024 0.093 -10000 0 -0.51 3 3
PGD2/DP -0.022 0.12 -10000 0 -0.55 6 6
SLC9A3R1 0.009 0.032 -10000 0 -0.38 1 1
FYN -0.02 0.078 -10000 0 -0.6 1 1
mol:NO 0.011 0 -10000 0 -10000 0 0
GNA15 -0.018 0.15 -10000 0 -0.71 6 6
PGK/cGMP -0.06 0.16 -10000 0 -0.6 10 10
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.034 0.11 -10000 0 -0.58 3 3
NOS3 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA 0.014 0.14 -10000 0 -0.36 12 12
PRKCB 0.007 0.15 -10000 0 -0.43 12 12
PRKCE 0.018 0.13 -10000 0 -0.39 9 9
PRKCD 0.018 0.13 -10000 0 -0.39 9 9
PRKCG 0 0.17 -10000 0 -0.4 20 20
muscle contraction 0.012 0.18 -10000 0 -0.51 11 11
PRKCZ 0.022 0.13 -10000 0 -0.35 10 10
ARR3 -0.006 0.07 -10000 0 -0.38 5 5
TXA2/TP beta -0.027 0.11 -10000 0 -0.59 3 3
PRKCQ 0.016 0.14 -10000 0 -0.38 11 11
MAPKKK cascade 0.009 0.16 -10000 0 -0.48 11 11
SELE 0.014 0.13 -10000 0 -0.36 10 10
TP beta/GNAI2/GDP/G beta/gamma -0.027 0.1 -10000 0 -0.58 3 3
ROCK1 0.011 0 -10000 0 -10000 0 0
GNA14 -0.077 0.21 -10000 0 -0.5 26 26
chemotaxis 0.005 0.2 -10000 0 -0.61 11 11
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.011 0 -10000 0 -10000 0 0
GNA11 -0.006 0.12 -10000 0 -0.88 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.082 0.17 -9999 0 -0.6 13 13
EPHB2 0.005 0.072 -9999 0 -0.88 1 1
Syndecan-2/TACI -0.067 0.17 -9999 0 -0.59 13 13
LAMA1 -0.02 0.15 -9999 0 -0.66 7 7
Syndecan-2/alpha2 ITGB1 -0.034 0.11 -9999 0 -0.51 7 7
HRAS 0.011 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 0.011 0 -9999 0 -10000 0 0
BAX 0.025 0.091 -9999 0 -0.52 4 4
EPB41 0.011 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 -0.016 0.13 -9999 0 -0.51 8 8
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.068 0.25 -9999 0 -0.84 14 14
Syndecan-2/MMP2 -0.037 0.14 -9999 0 -0.59 9 9
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.029 0.13 -9999 0 -0.68 5 5
dendrite morphogenesis -0.004 0.048 -9999 0 -0.59 1 1
Syndecan-2/GM-CSF -0.062 0.15 -9999 0 -0.59 9 9
determination of left/right symmetry 0.019 0.001 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0 0 -9999 0 -10000 0 0
GNB2L1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.03 0.15 -9999 0 -0.54 9 9
MAPK1 -0.03 0.15 -9999 0 -0.54 9 9
Syndecan-2/RACK1 0 0 -9999 0 -10000 0 0
NF1 0.011 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.019 0.001 -9999 0 -10000 0 0
ITGA2 -0.029 0.17 -9999 0 -0.66 9 9
MAPK8 0.017 0.1 -9999 0 -0.59 4 4
Syndecan-2/alpha2/beta1 Integrin -0.038 0.13 -9999 0 -0.55 9 9
Syndecan-2/Kininogen -0.098 0.21 -9999 0 -0.59 21 21
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.036 0.001 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.004 0.048 -9999 0 -0.6 1 1
actin cytoskeleton reorganization -0.081 0.17 -9999 0 -0.59 13 13
Syndecan-2/Caveolin-2/Ras -0.048 0.15 -9999 0 -0.54 13 13
Syndecan-2/Laminin alpha3 -0.016 0.078 -9999 0 -0.59 2 2
Syndecan-2/RasGAP 0 0 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.004 0.048 -9999 0 -0.59 1 1
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
TNFRSF13B -0.095 0.26 -9999 0 -0.65 24 24
RASA1 0.011 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.029 0.13 -9999 0 -0.68 5 5
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.005 0.072 -9999 0 -0.88 1 1
CASP3 0.032 0.001 -9999 0 -10000 0 0
FN1 -0.12 0.27 -9999 0 -0.57 35 35
Syndecan-2/IL8 -0.1 0.21 -9999 0 -0.59 23 23
SDC2 0.019 0.001 -9999 0 -10000 0 0
KNG1 -0.14 0.31 -9999 0 -0.71 32 32
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 -0.094 0.24 -9999 0 -0.54 28 28
Syndecan-2/TGFB1 -0.004 0.049 -9999 0 -0.6 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.032 0.001 -9999 0 -10000 0 0
angiogenesis -0.1 0.21 -9999 0 -0.59 23 23
MMP2 -0.044 0.21 -9999 0 -0.83 10 10
IL8 -0.15 0.32 -9999 0 -0.75 31 31
calcineurin-NFAT signaling pathway -0.066 0.17 -9999 0 -0.59 13 13
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 -0.039 0.2 -9999 0 -0.82 9 9
ITGA4 -0.009 0.13 -9999 0 -0.75 4 4
alpha4/beta7 Integrin -0.051 0.2 -9999 0 -0.77 10 10
alpha4/beta1 Integrin -0.015 0.097 -9999 0 -0.68 3 3
Signaling events mediated by PTP1B

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
PDGFRB 0.003 0.055 -10000 0 -0.38 3 3
Jak2/Leptin Receptor -0.039 0.091 -10000 0 -0.45 4 4
PTP1B/AKT1 -0.03 0.098 -10000 0 -0.32 5 5
FYN 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.04 0.11 -10000 0 -0.37 5 5
EGFR -0.043 0.19 -10000 0 -0.61 13 13
EGF/EGFR -0.087 0.15 -10000 0 -0.54 12 12
CSF1 0 0.1 -10000 0 -0.88 2 2
AKT1 0.011 0.001 -10000 0 -10000 0 0
INSR 0.011 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.086 0.18 -10000 0 -0.48 19 19
Insulin Receptor/Insulin -0.04 0.066 -10000 0 -10000 0 0
HCK -0.005 0.096 -10000 0 -0.48 5 5
CRK 0.011 0 -10000 0 -10000 0 0
TYK2 -0.03 0.1 -10000 0 -0.34 5 5
EGF -0.022 0.16 -10000 0 -0.8 6 6
YES1 0.011 0 -10000 0 -10000 0 0
CAV1 -0.04 0.13 -10000 0 -0.38 10 10
TXN 0.008 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.075 0.14 -10000 0 -0.51 10 10
cell migration 0.04 0.11 0.37 5 -10000 0 5
STAT3 0.004 0.072 -10000 0 -0.88 1 1
PRLR -0.033 0.16 -10000 0 -0.58 10 10
ITGA2B -0.047 0.21 -10000 0 -0.83 10 10
CSF1R -0.009 0.13 -10000 0 -0.75 4 4
Prolactin Receptor/Prolactin -0.056 0.14 -10000 0 -0.65 5 5
FGR -0.019 0.13 -10000 0 -0.49 9 9
PTP1B/p130 Cas -0.031 0.1 -10000 0 -0.34 5 5
Crk/p130 Cas -0.05 0.083 -10000 0 -0.36 1 1
DOK1 -0.023 0.096 -10000 0 -0.31 4 4
JAK2 -0.028 0.1 -10000 0 -0.48 4 4
Jak2/Leptin Receptor/Leptin -0.089 0.16 -10000 0 -0.52 13 13
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
PTPN1 -0.04 0.11 -10000 0 -0.37 5 5
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.082 0.26 -10000 0 -0.77 18 18
SRC -0.001 0.044 -10000 0 -10000 0 0
ITGB3 -0.071 0.23 -10000 0 -0.66 18 18
CAT1/PTP1B -0.077 0.16 -10000 0 -0.5 10 10
CAPN1 0.002 0.073 -10000 0 -0.88 1 1
CSK 0.011 0 -10000 0 -10000 0 0
PI3K -0.037 0.076 -10000 0 -0.68 1 1
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.08 0.14 -10000 0 -0.5 11 11
negative regulation of transcription -0.027 0.098 -10000 0 -0.48 4 4
FCGR2A -0.006 0.11 -10000 0 -0.63 4 4
FER 0.008 0.006 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.1 0.24 -10000 0 -0.72 18 18
BLK -0.16 0.32 -10000 0 -0.64 40 40
Insulin Receptor/Insulin/Shc -0.003 0.023 -10000 0 -10000 0 0
RHOA 0.008 0.006 -10000 0 -10000 0 0
LEPR 0.001 0.046 -10000 0 -0.39 2 2
BCAR1 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.071 0.2 -10000 0 -0.67 11 11
PRL -0.04 0.12 -10000 0 -0.38 17 17
SOCS3 -0.007 0.18 -10000 0 -1.6 2 2
SPRY2 -0.037 0.2 -10000 0 -0.88 8 8
Insulin Receptor/Insulin/IRS1 -0.034 0.12 -10000 0 -0.6 6 6
CSF1/CSF1R -0.067 0.14 -10000 0 -0.73 4 4
Ras protein signal transduction 0.027 0.033 -10000 0 -10000 0 0
IRS1 -0.037 0.18 -10000 0 -0.65 11 11
INS -0.004 0.044 -10000 0 -0.38 2 2
LEP -0.098 0.24 -10000 0 -0.55 29 29
STAT5B -0.032 0.1 -10000 0 -0.31 8 8
STAT5A -0.033 0.1 -10000 0 -0.31 9 9
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.1 -10000 0 -0.34 5 5
CSN2 -0.003 0.048 -10000 0 -10000 0 0
PIK3CA 0.011 0 -10000 0 -10000 0 0
LAT -0.008 0.071 -10000 0 -0.49 2 2
YBX1 0.017 0.006 -10000 0 -10000 0 0
LCK -0.042 0.21 -10000 0 -0.88 9 9
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 -0.14 0.32 -10000 0 -0.79 27 27
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.011 0 -9999 0 -10000 0 0
LAT2 -0.039 0.1 -9999 0 -0.49 4 4
AP1 -0.12 0.22 -9999 0 -0.56 23 23
mol:PIP3 -0.014 0.17 -9999 0 -0.58 6 6
IKBKB 0.004 0.1 -9999 0 -0.33 6 6
AKT1 -0.067 0.14 -9999 0 -0.74 2 2
IKBKG 0.004 0.1 -9999 0 -0.33 6 6
MS4A2 -0.048 0.16 -9999 0 -0.49 15 15
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.004 -9999 0 -10000 0 0
MAP3K1 0.008 0.12 -9999 0 -0.49 5 5
mol:Ca2+ -0.005 0.13 -9999 0 -0.41 6 6
LYN 0.01 0.005 -9999 0 -10000 0 0
CBLB -0.038 0.1 -9999 0 -0.53 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.009 0.065 -9999 0 -0.55 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.005 0.072 -9999 0 -0.88 1 1
PLD2 -0.049 0.18 -9999 0 -0.56 11 11
PTPN13 -0.015 0.12 -9999 0 -0.47 5 5
PTPN11 0.011 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.015 0.11 -9999 0 -0.43 2 2
SYK 0.004 0.073 -9999 0 -0.88 1 1
GRB2 0.011 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.067 0.15 -9999 0 -0.61 6 6
LAT -0.038 0.1 -9999 0 -0.53 3 3
PAK2 -0.001 0.14 -9999 0 -0.52 6 6
NFATC2 -0.12 0.25 -9999 0 -0.77 19 19
HRAS -0.011 0.15 -9999 0 -0.58 6 6
GAB2 -0.003 0.11 -9999 0 -0.71 3 3
PLA2G1B 0.026 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.098 0.21 -9999 0 -0.57 19 19
Antigen/IgE/Fc epsilon R1 -0.09 0.19 -9999 0 -0.53 19 19
mol:GDP -0.019 0.16 -9999 0 -0.57 9 9
JUN -0.066 0.22 -9999 0 -0.63 18 18
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.004 0.072 -9999 0 -0.88 1 1
FOS -0.11 0.29 -9999 0 -0.73 24 24
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.11 -9999 0 -0.49 5 5
CHUK 0.004 0.1 -9999 0 -0.33 6 6
KLRG1 -0.032 0.1 -9999 0 -0.51 3 3
VAV1 -0.03 0.15 -9999 0 -0.52 10 10
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.038 0.1 -9999 0 -0.53 3 3
negative regulation of mast cell degranulation -0.039 0.1 -9999 0 -0.6 3 3
BTK -0.045 0.14 -9999 0 -0.75 4 4
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.068 0.18 -9999 0 -0.54 13 13
GAB2/PI3K/SHP2 -0.075 0.16 -9999 0 -0.84 2 2
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.05 0.13 -9999 0 -0.59 5 5
RAF1 0.014 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.21 -9999 0 -0.64 15 15
FCER1G -0.025 0.12 -9999 0 -0.5 8 8
FCER1A -0.081 0.23 -9999 0 -0.54 25 25
Antigen/IgE/Fc epsilon R1/Fyn -0.082 0.18 -9999 0 -0.6 11 11
MAPK3 0.025 0.017 -9999 0 -10000 0 0
MAPK1 0.025 0.017 -9999 0 -10000 0 0
NFKB1 0.011 0 -9999 0 -10000 0 0
MAPK8 0.002 0.1 -9999 0 -0.57 4 4
DUSP1 0.003 0.079 -9999 0 -0.63 2 2
NF-kappa-B/RelA -0.02 0.048 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.005 0.11 -9999 0 -0.45 5 5
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.051 0.13 -9999 0 -0.54 7 7
FER -0.038 0.1 -9999 0 -0.49 4 4
RELA 0.011 0 -9999 0 -10000 0 0
ITK -0.044 0.14 -9999 0 -0.54 10 10
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG1 -0.015 0.16 -9999 0 -0.63 6 6
cytokine secretion -0.015 0.035 -9999 0 -10000 0 0
SPHK1 -0.039 0.1 -9999 0 -0.49 4 4
PTK2 -0.006 0.11 -9999 0 -0.47 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.07 0.16 -9999 0 -0.53 12 12
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.011 0.17 -9999 0 -0.56 6 6
MAP2K2 0.022 0.018 -9999 0 -10000 0 0
MAP2K1 0.022 0.018 -9999 0 -10000 0 0
MAP2K7 0.011 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.04 0.092 -9999 0 -0.55 2 2
MAP2K4 0.018 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.64 15 15
mol:Choline -0.048 0.18 -9999 0 -0.55 11 11
SHC/Grb2/SOS1 -0.033 0.092 -9999 0 -0.57 2 2
FYN 0.011 0 -9999 0 -10000 0 0
DOK1 0.005 0.072 -9999 0 -0.88 1 1
PXN 0.002 0.1 -9999 0 -0.5 3 3
HCLS1 -0.043 0.12 -9999 0 -0.7 3 3
PRKCB -0.011 0.14 -9999 0 -0.44 9 9
FCGR2B -0.023 0.16 -9999 0 -0.74 7 7
IGHE -0.001 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.04 0.11 -9999 0 -0.62 3 3
LCP2 -0.001 0.1 -9999 0 -0.88 2 2
PLA2G4A -0.066 0.14 -9999 0 -0.5 11 11
RASA1 0.011 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.048 0.18 -9999 0 -0.55 11 11
IKK complex 0.019 0.082 -9999 0 -0.25 4 4
WIPF1 0.005 0.072 -9999 0 -0.88 1 1
PDGFR-alpha signaling 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
PDGFRA -0.059 0.19 -9999 0 -0.49 20 20
PDGF/PDGFRA/CRKL -0.045 0.13 -9999 0 -0.7 4 4
positive regulation of JUN kinase activity -0.032 0.1 -9999 0 -0.55 4 4
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.063 0.15 -9999 0 -0.6 8 8
AP1 -0.2 0.45 -9999 0 -1.3 19 19
mol:IP3 -0.033 0.15 -9999 0 -0.74 4 4
PLCG1 -0.033 0.15 -9999 0 -0.74 4 4
PDGF/PDGFRA/alphaV Integrin -0.052 0.14 -9999 0 -0.7 5 5
RAPGEF1 0.011 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.15 -9999 0 -0.74 4 4
CAV3 -0.02 0.097 -9999 0 -0.38 10 10
CAV1 -0.035 0.18 -9999 0 -0.68 10 10
SHC/Grb2/SOS1 -0.032 0.1 -9999 0 -0.55 4 4
PDGF/PDGFRA/Shf -0.045 0.13 -9999 0 -0.7 4 4
FOS -0.16 0.44 -9999 0 -1.3 19 19
JUN -0.068 0.18 -9999 0 -0.53 17 17
oligodendrocyte development -0.052 0.14 -9999 0 -0.7 5 5
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
mol:DAG -0.033 0.15 -9999 0 -0.74 4 4
PDGF/PDGFRA -0.059 0.19 -9999 0 -0.49 20 20
actin cytoskeleton reorganization -0.045 0.13 -9999 0 -0.7 4 4
SRF 0.025 0.009 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K -0.041 0.12 -9999 0 -0.61 5 5
PDGF/PDGFRA/Crk/C3G -0.037 0.11 -9999 0 -0.61 4 4
JAK1 -0.028 0.14 -9999 0 -0.7 4 4
ELK1/SRF -0.028 0.1 -9999 0 -0.58 4 4
SHB 0.011 0 -9999 0 -10000 0 0
SHF 0.011 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0.021 -9999 0 -10000 0 0
GO:0007205 -0.03 0.14 -9999 0 -0.76 4 4
SOS1 0.011 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.032 0.1 -9999 0 -0.55 4 4
PDGF/PDGFRA/SHB -0.045 0.13 -9999 0 -0.7 4 4
PDGF/PDGFRA/Caveolin-1 -0.079 0.2 -9999 0 -0.74 10 10
ITGAV 0.003 0.079 -9999 0 -0.63 2 2
ELK1 -0.023 0.14 -9999 0 -0.71 4 4
PIK3CA 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.045 0.13 -9999 0 -0.7 4 4
JAK-STAT cascade -0.028 0.14 -9999 0 -0.7 4 4
cell proliferation -0.045 0.13 -9999 0 -0.7 4 4
Ephrin B reverse signaling

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
EFNB2 0.003 0.079 -10000 0 -0.63 2 2
EPHB2 0.004 0.073 -10000 0 -0.88 1 1
EFNB1 -0.015 0.12 -10000 0 -0.63 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.073 0.17 -10000 0 -0.54 11 11
Ephrin B2/EPHB1-2 -0.057 0.16 -10000 0 -0.58 12 12
neuron projection morphogenesis -0.069 0.16 -10000 0 -0.5 16 16
Ephrin B1/EPHB1-2/Tiam1 -0.079 0.18 -10000 0 -0.56 16 16
DNM1 -0.009 0.12 -10000 0 -0.58 5 5
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 0.01 0.064 -10000 0 -0.73 1 1
YES1 -0.01 0.082 -10000 0 -0.99 1 1
Ephrin B1/EPHB1-2/NCK2 -0.072 0.18 -10000 0 -0.56 14 14
PI3K -0.011 0.074 -10000 0 -0.63 2 2
mol:GDP -0.078 0.18 -10000 0 -0.55 16 16
ITGA2B -0.044 0.21 -10000 0 -0.83 10 10
endothelial cell proliferation -0.005 0.052 -10000 0 -0.6 1 1
FYN -0.01 0.082 -10000 0 -0.99 1 1
MAP3K7 -0.01 0.065 -10000 0 -0.78 1 1
FGR -0.014 0.084 -10000 0 -0.98 1 1
TIAM1 0 0.1 -10000 0 -0.88 2 2
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.055 0.2 -10000 0 -0.56 19 19
LYN -0.01 0.082 -10000 0 -0.99 1 1
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.077 -10000 0 -0.93 1 1
Ephrin B1/EPHB1-2 -0.015 0.071 -10000 0 -0.84 1 1
SRC -0.01 0.081 -10000 0 -0.98 1 1
ITGB3 -0.069 0.23 -10000 0 -0.66 18 18
EPHB1 -0.075 0.24 -10000 0 -0.63 20 20
EPHB4 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.052 -10000 0 -0.6 1 1
alphaIIb/beta3 Integrin -0.1 0.24 -10000 0 -0.72 18 18
BLK -0.038 0.1 -10000 0 -0.98 1 1
HCK -0.012 0.082 -10000 0 -0.98 1 1
regulation of stress fiber formation 0.071 0.17 0.55 14 -10000 0 14
MAPK8 0.003 0.1 -10000 0 -0.55 5 5
Ephrin B1/EPHB1-2/RGS3 -0.072 0.18 -10000 0 -0.56 14 14
endothelial cell migration -0.011 0.072 -10000 0 -0.58 2 2
NCK2 0.011 0 -10000 0 -10000 0 0
PTPN13 -0.026 0.12 -10000 0 -0.98 1 1
regulation of focal adhesion formation 0.071 0.17 0.55 14 -10000 0 14
chemotaxis 0.071 0.17 0.55 14 -10000 0 14
PIK3CA 0.011 0 -10000 0 -10000 0 0
Rac1/GTP -0.071 0.17 -10000 0 -0.52 15 15
angiogenesis -0.015 0.07 -10000 0 -0.84 1 1
LCK -0.021 0.094 -10000 0 -0.98 1 1
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR -0.003 0.11 -10000 0 -0.71 3 3
Cbp/p300/PCAF -0.004 0.048 -10000 0 -0.59 1 1
EP300 0.011 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.025 0.055 -10000 0 -10000 0 0
KAT2B 0.005 0.072 -10000 0 -0.88 1 1
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.023 0.086 0.25 9 -0.36 1 10
RAR alpha/9cRA/Cyclin H -0.033 0.093 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.058 -10000 0 -10000 0 0
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.042 0.14 -10000 0 -0.6 6 6
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.011 0.082 -10000 0 -0.55 3 3
RXRs/RARs/NRIP1/9cRA -0.007 0.19 -10000 0 -0.6 12 12
NCOA2 -0.086 0.28 -10000 0 -0.85 17 17
NCOA3 0.011 0 -10000 0 -10000 0 0
NCOA1 0.011 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.003 0.11 -10000 0 -0.71 3 3
RARG -0.001 0.071 -10000 0 -0.38 5 5
RAR gamma1/9cRA -0.007 0.038 -10000 0 -10000 0 0
MAPK3 0.012 0 -10000 0 -10000 0 0
MAPK1 0.011 0 -10000 0 -10000 0 0
MAPK8 -0.011 0.14 -10000 0 -0.87 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.072 0.2 -10000 0 -0.67 13 13
RARA -0.011 0.11 -10000 0 -0.33 16 16
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.11 -10000 0 -0.28 17 17
PRKCA 0.001 0.091 -10000 0 -0.5 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.015 0.18 -10000 0 -0.59 12 12
RXRG -0.056 0.21 -10000 0 -0.55 19 19
RXRA -0.002 0.11 -10000 0 -0.38 4 4
RXRB -0.016 0.14 -10000 0 -0.48 12 12
VDR/Vit D3/DNA -0.011 0.082 -10000 0 -0.55 3 3
RBP1 -0.079 0.23 -10000 0 -0.58 23 23
CRBP1/9-cic-RA -0.066 0.18 -10000 0 -0.43 23 23
RARB 0.008 0.072 -10000 0 -0.88 1 1
PRKCG -0.061 0.24 -10000 0 -0.74 15 15
MNAT1 0.011 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.2 -10000 0 -0.64 12 12
RXRs/RARs/SMRT(N-CoR2)/9cRA 0 0.16 -10000 0 -0.52 12 12
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.089 -10000 0 -0.28 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.015 0.18 -10000 0 -0.59 12 12
positive regulation of DNA binding -0.031 0.088 -10000 0 -10000 0 0
NRIP1 -0.01 0.16 -10000 0 -0.77 2 2
RXRs/RARs -0.02 0.18 -10000 0 -0.59 12 12
RXRs/RXRs/DNA/9cRA -0.069 0.19 -10000 0 -0.68 12 12
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.011 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.022 0.064 -10000 0 -10000 0 0
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.005 0.024 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.004 0.2 -10000 0 -0.96 4 4
UGCG -0.065 0.2 -10000 0 -0.74 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT -0.01 0.19 -10000 0 -0.51 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.041 0.2 -10000 0 -0.73 11 11
mol:DAG -0.002 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.06 0.16 -10000 0 -0.6 10 10
FRAP1 0.004 0.22 -10000 0 -0.72 10 10
FOXO3 0.007 0.21 -10000 0 -0.69 10 10
AKT1 -0.004 0.23 -10000 0 -0.76 10 10
GAB2 -0.003 0.11 -10000 0 -0.71 3 3
SMPD1 -0.011 0.029 -10000 0 -10000 0 0
SGMS1 -0.011 0.028 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.052 -10000 0 -0.61 1 1
CALM1 0.011 0 -10000 0 -10000 0 0
cell proliferation -0.017 0.18 -10000 0 -0.38 19 19
EIF3A 0.011 0 -10000 0 -10000 0 0
PI3K -0.005 0.056 -10000 0 -0.69 1 1
RPS6KB1 0.018 0.037 -10000 0 -0.27 1 1
mol:sphingomyelin -0.002 0.005 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.002 -10000 0 -0.012 2 2
JAK3 0.002 0.1 -10000 0 -0.88 2 2
PIK3R1 0.008 0.073 -10000 0 -0.88 1 1
JAK1 0.014 0.003 -10000 0 -10000 0 0
NFKB1 0.011 0 -10000 0 -10000 0 0
MYC -0.003 0.25 -10000 0 -0.8 11 11
MYB 0.013 0.16 -10000 0 -1.4 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.017 0.25 -10000 0 -0.74 13 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.026 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.24 -10000 0 -0.71 13 13
Rac1/GDP 0.018 0.049 -10000 0 -0.56 1 1
T cell proliferation -0.003 0.22 -10000 0 -0.66 12 12
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.011 0.002 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.005 0.008 -10000 0 -0.065 2 2
PRKCZ -0.007 0.23 -10000 0 -0.7 12 12
NF kappa B1 p50/RelA -0.059 0.16 -10000 0 -0.59 10 10
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.22 -10000 0 -0.84 8 8
HSP90AA1 0.011 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
IL2RA -0.079 0.26 -10000 0 -0.79 17 17
IL2RB -0.012 0.15 -10000 0 -0.78 5 5
TERT -0.1 0.29 -10000 0 -0.75 23 23
E2F1 0.021 0.058 -10000 0 -0.47 2 2
SOS1 0.012 0.002 -10000 0 -10000 0 0
RPS6 0.011 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.031 2 -10000 0 2
PTPN11 0.012 0.002 -10000 0 -10000 0 0
IL2RG -0.084 0.26 -10000 0 -0.72 20 20
actin cytoskeleton organization -0.003 0.22 -10000 0 -0.66 12 12
GRB2 0.012 0.002 -10000 0 -10000 0 0
IL2 0.008 0.006 -10000 0 -10000 0 0
PIK3CA 0.014 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.047 -10000 0 -0.54 1 1
LCK -0.039 0.21 -10000 0 -0.88 9 9
BCL2 0.019 0.18 -10000 0 -0.62 7 7
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.037 0.25 -9999 0 -1.4 4 4
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.011 0.095 -9999 0 -0.38 2 2
ATF2/c-Jun -0.069 0.27 -9999 0 -1 9 9
MAPK11 -0.017 0.12 -9999 0 -0.55 3 3
MITF -0.005 0.12 -9999 0 -0.47 3 3
MAPKAPK5 -0.004 0.12 -9999 0 -0.47 3 3
KRT8 -0.16 0.31 -9999 0 -0.58 45 45
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.1 -9999 0 -0.88 2 2
p38alpha-beta/CK2 -0.019 0.15 -9999 0 -0.62 3 3
CEBPB -0.005 0.12 -9999 0 -0.47 3 3
SLC9A1 -0.004 0.12 -9999 0 -0.47 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.017 0.14 -9999 0 -0.5 5 5
p38alpha-beta/MNK1 -0.003 0.12 -9999 0 -0.51 3 3
JUN -0.068 0.27 -9999 0 -1 9 9
PPARGC1A -0.044 0.16 -9999 0 -0.46 11 11
USF1 -0.004 0.12 -9999 0 -0.47 3 3
RAB5/GDP/GDI1 -0.027 0.076 -9999 0 -0.35 2 2
NOS2 -0.05 0.3 -9999 0 -1.4 7 7
DDIT3 -0.005 0.12 -9999 0 -0.47 3 3
RAB5A 0.011 0 -9999 0 -10000 0 0
HSPB1 0.007 0.099 -9999 0 -0.39 2 2
p38alpha-beta/HBP1 -0.003 0.12 -9999 0 -0.51 3 3
CREB1 -0.003 0.13 -9999 0 -0.48 3 3
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.004 0.11 -9999 0 -0.48 1 1
RPS6KA4 -0.004 0.12 -9999 0 -0.47 3 3
PLA2G4A -0.028 0.19 -9999 0 -0.66 9 9
GDI1 -0.004 0.12 -9999 0 -0.47 3 3
TP53 -0.009 0.15 -9999 0 -0.59 3 3
RPS6KA5 -0.011 0.13 -9999 0 -0.46 4 4
ESR1 -0.01 0.13 -9999 0 -0.45 5 5
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.004 0.12 -9999 0 -0.47 3 3
MEF2A -0.004 0.12 -9999 0 -0.47 3 3
EIF4EBP1 -0.003 0.13 -9999 0 -0.48 3 3
KRT19 -0.23 0.3 -9999 0 -0.55 58 58
ELK4 -0.004 0.12 -9999 0 -0.47 3 3
ATF6 -0.004 0.12 -9999 0 -0.47 3 3
ATF1 -0.003 0.13 -9999 0 -0.48 3 3
p38alpha-beta/MAPKAPK2 -0.012 0.15 -9999 0 -0.67 4 4
p38alpha-beta/MAPKAPK3 -0.003 0.12 -9999 0 -0.51 3 3
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.11 0.22 -10000 0 -0.63 19 19
cell-cell adhesion 0.059 0.14 0.77 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.03 0.1 -10000 0 -0.51 5 5
ITSN1 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.011 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.028 0.1 -10000 0 -0.53 5 5
Ephrin B1/EPHB1 -0.071 0.18 -10000 0 -0.54 17 17
HRAS/GDP -0.059 0.14 -10000 0 -0.49 4 4
Ephrin B/EPHB1/GRB7 -0.089 0.2 -10000 0 -0.59 17 17
Endophilin/SYNJ1 0.003 0.12 -10000 0 -0.57 5 5
KRAS 0.006 0.045 -10000 0 -0.38 2 2
Ephrin B/EPHB1/Src -0.072 0.16 -10000 0 -0.51 15 15
endothelial cell migration -0.008 0.059 -10000 0 -0.51 2 2
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 -0.02 0.15 -10000 0 -0.66 7 7
PAK1 0.009 0.13 -10000 0 -0.56 6 6
HRAS 0.011 0 -10000 0 -10000 0 0
RRAS 0.004 0.11 -10000 0 -0.48 5 5
DNM1 -0.008 0.12 -10000 0 -0.58 5 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.038 0.17 -10000 0 -0.48 15 15
lamellipodium assembly -0.059 0.14 -10000 0 -0.77 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.042 0.1 -10000 0 -0.35 11 11
PIK3R1 0.005 0.072 -10000 0 -0.88 1 1
EPHB2 0.005 0.072 -10000 0 -0.88 1 1
EPHB3 -0.006 0.11 -10000 0 -0.63 4 4
EPHB1 -0.074 0.24 -10000 0 -0.63 20 20
EPHB4 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.05 0.13 -10000 0 -0.5 4 4
Ephrin B/EPHB2 -0.03 0.1 -10000 0 -0.51 5 5
Ephrin B/EPHB3 -0.036 0.12 -10000 0 -0.51 6 6
JNK cascade -0.028 0.17 -10000 0 -0.54 11 11
Ephrin B/EPHB1 -0.073 0.17 -10000 0 -0.52 15 15
RAP1/GDP -0.044 0.11 -10000 0 -0.45 3 3
EFNB2 0.003 0.079 -10000 0 -0.63 2 2
EFNB3 -0.006 0.11 -10000 0 -0.63 4 4
EFNB1 -0.018 0.12 -10000 0 -0.43 10 10
Ephrin B2/EPHB1-2 -0.057 0.16 -10000 0 -0.58 12 12
RAP1B 0.009 0.032 -10000 0 -0.38 1 1
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.15 -10000 0 -0.54 5 5
Rap1/GTP -0.06 0.14 -10000 0 -0.68 2 2
axon guidance -0.11 0.21 -10000 0 -0.62 19 19
MAPK3 0.007 0.1 -10000 0 -10000 0 0
MAPK1 0.007 0.1 -10000 0 -10000 0 0
Rac1/GDP -0.045 0.12 -10000 0 -0.45 4 4
actin cytoskeleton reorganization -0.047 0.11 -10000 0 -0.59 1 1
CDC42/GDP -0.045 0.12 -10000 0 -0.45 4 4
PI3K -0.008 0.06 -10000 0 -0.51 2 2
EFNA5 -0.16 0.31 -10000 0 -0.61 41 41
Ephrin B2/EPHB4 -0.005 0.052 -10000 0 -0.6 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.018 0.066 -10000 0 -0.35 5 5
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.059 0.14 -10000 0 -0.76 1 1
PTK2 0.014 0.034 -10000 0 -10000 0 0
MAP4K4 -0.028 0.17 -10000 0 -0.55 11 11
SRC 0.011 0 -10000 0 -10000 0 0
KALRN 0.003 0.079 -10000 0 -0.63 2 2
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.045 0.11 -10000 0 -0.69 1 1
MAP2K1 -0.001 0.11 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.066 0.17 -10000 0 -0.59 11 11
cell migration 0.003 0.12 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
SYNJ1 0.002 0.13 -10000 0 -0.58 5 5
PXN 0.011 0 -10000 0 -10000 0 0
TF -0.033 0.17 -10000 0 -0.54 10 10
HRAS/GTP -0.064 0.15 -10000 0 -0.65 2 2
Ephrin B1/EPHB1-2 -0.067 0.17 -10000 0 -0.52 17 17
cell adhesion mediated by integrin 0.023 0.1 0.51 4 -10000 0 4
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.069 0.16 -10000 0 -0.5 15 15
RAC1-CDC42/GTP -0.066 0.15 -10000 0 -0.78 1 1
RASA1 0.011 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.043 0.11 -10000 0 -0.45 2 2
ruffle organization -0.008 0.16 -10000 0 -0.8 1 1
NCK1 0.011 0 -10000 0 -10000 0 0
receptor internalization 0 0.14 -10000 0 -0.52 8 8
Ephrin B/EPHB2/KALRN -0.034 0.13 -10000 0 -0.59 6 6
ROCK1 -0.002 0.1 -10000 0 -0.48 5 5
RAS family/GDP -0.043 0.1 -10000 0 -0.57 1 1
Rac1/GTP -0.063 0.15 -10000 0 -0.85 1 1
Ephrin B/EPHB1/Src/Paxillin -0.045 0.11 -10000 0 -0.35 14 14
TCGA08_retinoblastoma

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
CDKN2B -0.014 0.097 -10000 0 -0.66 3 3
CDKN2C -0.002 0.059 -10000 0 -0.71 1 1
CDKN2A -0.026 0.14 -10000 0 -0.68 6 6
CCND2 0.007 0.086 0.35 5 -0.18 4 9
RB1 -0.008 0.09 -10000 0 -0.38 5 5
CDK4 0.012 0.092 0.4 5 -10000 0 5
CDK6 0.007 0.097 0.4 5 -0.19 4 9
G1/S progression -0.006 0.092 0.38 5 -10000 0 5
Visual signal transduction: Rods

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
mol:K + 0.011 0 -9999 0 -10000 0 0
GNAT1/GTP -0.004 0.031 -9999 0 -0.27 2 2
Metarhodopsin II/Arrestin -0.009 0.043 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.064 0.17 -9999 0 -0.6 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.045 -9999 0 -0.38 2 2
GRK1 -0.006 0.07 -9999 0 -0.38 5 5
CNG Channel -0.1 0.2 -9999 0 -0.52 24 24
mol:Na + -0.07 0.18 -9999 0 -0.54 17 17
mol:ADP -0.006 0.07 -9999 0 -0.38 5 5
RGS9-1/Gbeta5/R9AP -0.033 0.099 -9999 0 -0.5 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.072 0.19 -9999 0 -0.6 12 12
CNGB1 -0.025 0.15 -9999 0 -0.53 10 10
RDH5 -0.002 0.071 -9999 0 -0.38 5 5
SAG -0.008 0.07 -9999 0 -0.38 5 5
mol:Ca2+ -0.028 0.19 -9999 0 -0.72 5 5
Na + (4 Units) -0.065 0.17 -9999 0 -0.69 5 5
RGS9 -0.032 0.14 -9999 0 -0.45 14 14
GNB1/GNGT1 -0.007 0.041 -9999 0 -10000 0 0
GNAT1/GDP -0.03 0.089 -9999 0 -0.52 2 2
GUCY2D -0.007 0.12 -9999 0 -0.88 3 3
GNGT1 -0.002 0.063 -9999 0 -0.38 4 4
GUCY2F -0.004 0.055 -9999 0 -0.38 3 3
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.089 0.18 -9999 0 -0.52 19 19
mol:11-cis-retinal -0.002 0.071 -9999 0 -0.38 5 5
mol:cGMP -0.054 0.16 -9999 0 -0.53 14 14
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin -0.011 0.052 -9999 0 -10000 0 0
SLC24A1 0.011 0 -9999 0 -10000 0 0
CNGA1 -0.003 0.11 -9999 0 -0.71 3 3
Metarhodopsin II -0.008 0.038 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.053 0.16 -9999 0 -0.56 14 14
RGS9BP -0.006 0.077 -9999 0 -0.38 6 6
Metarhodopsin II/Transducin -0.004 0.02 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.043 0.15 -9999 0 -0.57 11 11
PDE6A/B -0.049 0.16 -9999 0 -0.66 8 8
mol:Pi -0.032 0.099 -9999 0 -0.5 4 4
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.008 0.037 -9999 0 -10000 0 0
PDE6B 0.009 0.032 -9999 0 -0.38 1 1
PDE6A -0.054 0.2 -9999 0 -0.6 16 16
PDE6G -0.083 0.25 -9999 0 -0.66 21 21
RHO 0.003 0.032 -9999 0 -0.38 1 1
PDE6 -0.11 0.2 -9999 0 -0.56 21 21
GUCA1A -0.054 0.23 -9999 0 -0.88 11 11
GC2/GCAP Family -0.046 0.15 -9999 0 -0.57 11 11
GUCA1C 0 0.032 -9999 0 -0.38 1 1
GUCA1B 0.009 0.032 -9999 0 -0.38 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.038 0.22 -9999 0 -0.83 7 7
MAP3K8 -0.008 0.12 -9999 0 -0.88 3 3
FOS -0.024 0.2 -9999 0 -0.79 7 7
PRKCA -0.003 0.091 -9999 0 -0.51 4 4
PTPN7 -0.021 0.16 -9999 0 -0.79 6 6
HRAS 0.01 0.004 -9999 0 -10000 0 0
PRKCB -0.027 0.18 -9999 0 -0.81 7 7
NRAS 0.01 0.004 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.021 -9999 0 -10000 0 0
MAPK3 -0.015 0.17 -9999 0 -0.83 5 5
MAP2K1 -0.005 0.14 -9999 0 -0.62 7 7
ELK1 0.009 0.007 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.57 7 7
mol:GTP -0.001 0.002 -9999 0 -0.006 22 22
MAPK1 -0.015 0.17 -9999 0 -0.83 5 5
RAF1 -0.032 0.12 -9999 0 -0.57 7 7
KRAS 0.005 0.045 -9999 0 -0.38 2 2
ErbB2/ErbB3 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
USP8 0.02 0.004 -9999 0 -10000 0 0
RAS family/GTP -0.025 0.072 -9999 0 -0.42 1 1
NFATC4 0.013 0.089 -9999 0 -0.4 1 1
ERBB2IP 0.005 0.007 -9999 0 -10000 0 0
HSP90 (dimer) 0.011 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.028 0.1 -9999 0 -0.44 8 8
JUN 0.023 0.071 -9999 0 -10000 0 0
HRAS 0.011 0.001 -9999 0 -10000 0 0
DOCK7 0.005 0.11 -9999 0 -0.45 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.036 0.13 -9999 0 -0.54 8 8
AKT1 0.011 0.002 -9999 0 -10000 0 0
BAD 0.02 0.002 -9999 0 -10000 0 0
MAPK10 -0.047 0.095 -9999 0 -0.31 13 13
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.11 -9999 0 -0.48 8 8
RAF1 0.015 0.094 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 2 -0.064 0.18 -9999 0 -0.56 17 17
STAT3 -0.007 0.09 -9999 0 -1.1 1 1
cell migration 0.009 0.08 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.065 0.27 -9999 0 -0.63 23 23
FOS -0.049 0.23 -9999 0 -0.46 31 31
NRAS 0.011 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.028 0.1 -9999 0 -0.44 8 8
MAPK3 -0.038 0.21 -9999 0 -0.47 23 23
MAPK1 -0.038 0.21 -9999 0 -0.46 24 24
JAK2 0.005 0.11 -9999 0 -0.42 8 8
NF2 -0.001 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.096 -9999 0 -0.39 8 8
NRG1 -0.045 0.19 -9999 0 -0.61 13 13
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.002 0.11 -9999 0 -0.36 12 12
MAPK9 -0.013 0.046 -9999 0 -10000 0 0
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.006 0.11 -9999 0 -0.71 3 3
SHC1 0.008 0.005 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) -0.007 0.087 -9999 0 -1.1 1 1
RNF41 0.026 0.007 -9999 0 -10000 0 0
FRAP1 0.01 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.066 -9999 0 -0.36 1 1
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.056 0.25 -9999 0 -0.61 21 21
myelination 0.021 0.088 -9999 0 -0.4 1 1
PPP3CB 0.005 0.099 -9999 0 -0.39 8 8
KRAS 0.006 0.045 -9999 0 -0.38 2 2
RAC1-CDC42/GDP -0.02 0.075 -9999 0 -0.42 1 1
NRG2 -0.077 0.27 -9999 0 -0.88 15 15
mol:GDP -0.003 0.096 -9999 0 -0.39 8 8
SOS1 0.009 0.005 -9999 0 -10000 0 0
MAP2K2 0.016 0.1 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.004 0.11 -9999 0 -0.45 3 3
MAP2K1 -0.03 0.18 -9999 0 -0.45 5 5
heart morphogenesis -0.028 0.1 -9999 0 -0.44 8 8
RAS family/GDP -0.021 0.073 -9999 0 -0.41 1 1
GRB2 0.009 0.005 -9999 0 -10000 0 0
PRKACA -0.002 0.007 -9999 0 -10000 0 0
CHRNE 0.016 0.017 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
activation of caspase activity -0.011 0.002 -9999 0 -10000 0 0
nervous system development -0.028 0.1 -9999 0 -0.44 8 8
CDC42 0.011 0 -9999 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.047 0.12 -9999 0 -10000 0 0
CRKL 0.019 0.11 -9999 0 -0.44 8 8
mol:DAG -0.028 0.11 -9999 0 -0.48 8 8
HRAS -0.021 0.08 -9999 0 -10000 0 0
MAPK8 -0.012 0.15 -9999 0 -0.52 12 12
RAP1A 0.019 0.11 -9999 0 -10000 0 0
GAB1 0.019 0.11 -9999 0 -0.44 8 8
MAPK14 0.004 0.12 -9999 0 -0.51 8 8
EPO -0.043 0.21 -9999 0 -0.7 12 12
PLCG1 -0.029 0.11 -9999 0 -0.5 8 8
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.043 0.15 -9999 0 -0.58 10 10
GAB1/SHC/GRB2/SOS1 -0.022 0.085 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.043 0.16 -9999 0 -0.68 8 8
IRS2 0.015 0.12 -9999 0 -0.44 9 9
STAT1 0.03 0.13 -9999 0 -0.49 8 8
STAT5B 0.026 0.13 -9999 0 -0.49 8 8
cell proliferation -0.002 0.14 -9999 0 -0.48 12 12
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.091 -9999 0 -10000 0 0
TEC -0.026 0.19 -9999 0 -0.48 20 20
SOCS3 0 0.1 -9999 0 -0.88 2 2
STAT1 (dimer) 0.03 0.12 -9999 0 -0.48 8 8
JAK2 0.011 0.01 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
EPO/EPOR (dimer)/JAK2 0.021 0.12 -9999 0 -0.47 8 8
EPO/EPOR -0.043 0.16 -9999 0 -0.68 8 8
LYN 0.013 0.002 -9999 0 -10000 0 0
TEC/VAV2 -0.021 0.19 -9999 0 -0.52 13 13
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.002 0.14 -9999 0 -0.57 8 8
mol:IP3 -0.028 0.11 -9999 0 -0.48 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.033 0.11 -9999 0 -10000 0 0
SH2B3 0.011 0.01 -9999 0 -10000 0 0
NFKB1 0.004 0.12 -9999 0 -0.51 8 8
EPO/EPOR (dimer)/JAK2/SOCS3 -0.027 0.094 -9999 0 -0.37 10 10
PTPN6 0.012 0.12 -9999 0 -0.46 8 8
TEC/VAV2/GRB2 -0.065 0.17 -9999 0 -0.87 2 2
EPOR 0.012 0.01 -9999 0 -10000 0 0
INPP5D 0.005 0.072 -9999 0 -0.88 1 1
mol:GDP -0.023 0.086 -9999 0 -10000 0 0
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG2 0.011 0 -9999 0 -10000 0 0
CRKL/CBL/C3G -0.024 0.091 -9999 0 -10000 0 0
VAV2 0.016 0.12 -9999 0 -0.44 9 9
CBL 0.019 0.11 -9999 0 -0.44 8 8
SHC/Grb2/SOS1 -0.024 0.091 -9999 0 -10000 0 0
STAT5A 0.022 0.13 -9999 0 -0.49 9 9
GRB2 0.011 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.041 0.13 -9999 0 -10000 0 0
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
BTK 0.012 0.13 -9999 0 -0.46 10 10
BCL2 0.041 0.14 -9999 0 -1 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.039 0.16 -9999 0 -0.61 9 9
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.005 0.072 -9999 0 -0.88 1 1
ITGA4 -0.009 0.13 -9999 0 -0.75 4 4
alpha4/beta7 Integrin/MAdCAM1 -0.12 0.25 -9999 0 -0.63 24 24
EPO -0.046 0.21 -9999 0 -0.71 12 12
alpha4/beta7 Integrin -0.051 0.2 -9999 0 -0.77 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.015 0.097 -9999 0 -0.68 3 3
EPO/EPOR (dimer) -0.043 0.16 -9999 0 -0.68 8 8
lamellipodium assembly -0.002 0.044 -9999 0 -0.53 1 1
PIK3CA 0.011 0 -9999 0 -10000 0 0
PI3K -0.005 0.055 -9999 0 -0.68 1 1
ARF6 0.011 0 -9999 0 -10000 0 0
JAK2 -0.032 0.11 -9999 0 -0.4 11 11
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
MADCAM1 -0.12 0.29 -9999 0 -0.68 28 28
cell adhesion -0.11 0.25 -9999 0 -0.62 24 24
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.003 0.15 -9999 0 -0.74 5 5
ITGB7 -0.039 0.2 -9999 0 -0.82 9 9
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.031 0.15 -9999 0 -0.8 5 5
p130Cas/Crk/Dock1 -0.026 0.12 -9999 0 -0.6 6 6
VCAM1 -0.018 0.15 -9999 0 -0.71 6 6
RHOA 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.012 0.077 -9999 0 -0.54 3 3
BCAR1 0.012 0.14 -9999 0 -0.69 5 5
EPOR 0.011 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.045 -9999 0 -0.55 1 1
IL1-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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.011 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.011 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.018 0.069 -9999 0 -0.58 1 1
IRAK/TOLLIP -0.004 0.044 -9999 0 -0.55 1 1
IKBKB 0.011 0 -9999 0 -10000 0 0
IKBKG 0.011 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.15 0.29 -9999 0 -0.76 24 24
IL1A -0.1 0.27 -9999 0 -0.69 24 24
IL1B -0.02 0.17 -9999 0 -0.76 7 7
IRAK/TRAF6/p62/Atypical PKCs -0.003 0.038 -9999 0 -10000 0 0
IL1R2 -0.089 0.25 -9999 0 -0.64 23 23
IL1R1 -0.012 0.13 -9999 0 -0.68 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.017 0.081 -9999 0 -0.67 1 1
TOLLIP 0.011 0 -9999 0 -10000 0 0
TICAM2 0.011 0 -9999 0 -10000 0 0
MAP3K3 0.011 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.059 0.028 -9999 0 -10000 0 0
JUN -0.008 0.15 -9999 0 -0.49 9 9
MAP3K7 0.011 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.043 0.16 -9999 0 -0.57 10 10
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.078 0.18 -9999 0 -0.54 18 18
PIK3R1 0.005 0.072 -9999 0 -0.88 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.072 0.17 -9999 0 -0.51 18 18
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.17 -9999 0 -0.65 9 9
NFKB1 0.011 0 -9999 0 -10000 0 0
MAPK8 0.024 0.081 -9999 0 -0.46 4 4
IRAK1 0.015 0.051 -9999 0 -0.6 1 1
IL1RN/IL1R1 -0.054 0.17 -9999 0 -0.68 10 10
IRAK4 0.011 0 -9999 0 -10000 0 0
PRKCI 0.011 0 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
PI3K -0.005 0.055 -9999 0 -0.68 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.023 0.09 -9999 0 -0.77 1 1
CHUK 0.011 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.17 -9999 0 -0.65 9 9
IL1 beta/IL1R2 -0.097 0.24 -9999 0 -0.65 19 19
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.039 -9999 0 -0.48 1 1
NF kappa B1 p50/RelA -0.038 0.14 -9999 0 -1.2 1 1
IRAK3 0 0.085 -9999 0 -0.55 3 3
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.04 0.16 -9999 0 -0.6 8 8
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.11 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.086 0.2 -9999 0 -0.58 19 19
RELA 0.011 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.011 0 -9999 0 -10000 0 0
MYD88 0.011 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.003 0.042 -9999 0 -0.51 1 1
IL1RAP 0.011 0 -9999 0 -10000 0 0
UBE2N 0.011 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.034 0.12 -9999 0 -1 1 1
CASP1 0 0.1 -9999 0 -0.88 2 2
IL1RN/IL1R2 -0.11 0.26 -9999 0 -0.76 17 17
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.042 0.16 -9999 0 -0.61 9 9
TMEM189-UBE2V1 0.002 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.038 0.094 -9999 0 -0.4 3 3
PIK3CA 0.011 0 -9999 0 -10000 0 0
IL1RN -0.038 0.19 -9999 0 -0.73 10 10
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.031 0.003 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0 0.12 -10000 0 -1.4 1 1
VDR -0.003 0.11 -10000 0 -0.71 3 3
FAM120B 0.011 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.008 0.13 -10000 0 -0.59 2 2
RXRs/LXRs/DNA/Oxysterols 0.011 0.15 -10000 0 -0.71 2 2
MED1 0.011 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.015 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.033 0.072 -10000 0 -0.35 5 5
RXRs/NUR77 -0.042 0.13 -10000 0 -0.55 9 9
RXRs/PPAR 0.006 0.1 -10000 0 -0.36 9 9
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.011 0.082 -10000 0 -0.55 3 3
RARs/VDR/DNA/Vit D3 -0.017 0.078 -10000 0 -0.51 3 3
RARA 0.011 0 -10000 0 -10000 0 0
NCOA1 0.011 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.003 0.11 -10000 0 -0.71 3 3
RARs/RARs/DNA/9cRA -0.009 0.052 -10000 0 -0.52 1 1
RARG -0.002 0.071 -10000 0 -0.38 5 5
RPS6KB1 0.011 0.049 -10000 0 -0.43 1 1
RARs/THRs/DNA/SMRT -0.033 0.072 -10000 0 -10000 0 0
THRA 0.009 0.032 -10000 0 -0.38 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.011 0.082 -10000 0 -0.55 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.045 0.14 0.3 1 -0.56 9 10
NR1H4 -0.067 0.19 -10000 0 -0.47 24 24
RXRs/LXRs/DNA -0.05 0.13 -10000 0 -0.53 9 9
NR1H2 0.015 0.01 -10000 0 -10000 0 0
NR1H3 0.002 0.073 -10000 0 -0.39 5 5
RXRs/VDR/DNA/Vit D3 -0.048 0.14 -10000 0 -0.53 11 11
NR4A1 0.011 0 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.016 0.11 -10000 0 -0.41 6 6
RXRG -0.057 0.22 -10000 0 -0.66 16 16
RXR alpha/CCPG 0 0.003 -10000 0 -10000 0 0
RXRA 0.015 0.01 -10000 0 -10000 0 0
RXRB 0.015 0.012 -10000 0 -10000 0 0
THRB -0.1 0.21 -10000 0 -0.43 39 39
PPARG 0 0.1 -10000 0 -0.88 2 2
PPARD 0.011 0 -10000 0 -10000 0 0
TNF -0.042 0.34 -10000 0 -1.3 10 10
mol:Oxysterols 0.003 0.013 -10000 0 -10000 0 0
cholesterol transport 0.011 0.15 -10000 0 -0.7 2 2
PPARA 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.005 0.072 -10000 0 -0.88 1 1
RXRs/NUR77/BCL2 -0.03 0.12 -10000 0 -0.44 9 9
SREBF1 0.019 0.14 -10000 0 -0.64 2 2
RXRs/RXRs/DNA/9cRA -0.045 0.14 0.3 1 -0.56 9 10
ABCA1 0.019 0.14 -10000 0 -0.64 2 2
RARs/THRs -0.061 0.12 -10000 0 -0.51 5 5
RXRs/FXR -0.072 0.18 -10000 0 -0.6 12 12
BCL2 0.003 0.079 -10000 0 -0.63 2 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0 0.1 -9999 0 -0.88 2 2
Caspase 8 (4 units) -0.051 0.14 -9999 0 -0.61 6 6
NEF -0.013 0.056 -9999 0 -10000 0 0
NFKBIA 0.005 0.033 -9999 0 -10000 0 0
BIRC3 -0.022 0.23 -9999 0 -0.88 10 10
CYCS -0.009 0.16 -9999 0 -0.62 6 6
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 -0.066 0.26 -9999 0 -1 10 10
MAP2K7 -0.009 0.15 -9999 0 -0.53 7 7
protein ubiquitination 0.02 0.12 -9999 0 -0.52 3 3
CRADD -0.006 0.12 -9999 0 -0.88 3 3
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0 0.1 -9999 0 -0.88 2 2
BID -0.018 0.17 -9999 0 -0.66 6 6
NF-kappa-B/RelA/I kappa B alpha -0.026 0.089 -9999 0 -10000 0 0
TRADD 0 0.1 -9999 0 -0.88 2 2
MAP3K5 -0.03 0.19 -9999 0 -0.88 7 7
CFLAR 0.011 0 -9999 0 -10000 0 0
FADD 0.011 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.026 0.09 -9999 0 -10000 0 0
MAPK8 -0.013 0.16 -9999 0 -0.48 11 11
APAF1 0.011 0 -9999 0 -10000 0 0
TRAF1 0.011 0 -9999 0 -10000 0 0
TRAF2 0.011 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.062 0.16 -9999 0 -0.46 17 17
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.16 -9999 0 -0.7 4 4
CHUK 0.018 0.14 -9999 0 -0.59 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.034 0.13 -9999 0 -0.51 10 10
TCRz/NEF -0.09 0.26 -9999 0 -0.72 18 18
TNF -0.056 0.23 -9999 0 -0.76 13 13
FASLG -0.12 0.41 -9999 0 -1.2 18 18
NFKB1 0.005 0.033 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.059 0.18 -9999 0 -0.63 13 13
CASP6 -0.037 0.1 -9999 0 -0.53 3 3
CASP7 0.006 0.21 -9999 0 -0.7 10 10
RELA 0.005 0.033 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.006 0.21 -9999 0 -0.7 10 10
TNFRSF1A 0 0.1 -9999 0 -0.88 2 2
TNFR1A/BAG4 -0.018 0.11 -9999 0 -0.68 4 4
CASP8 0.005 0.072 -9999 0 -0.88 1 1
CASP9 0.011 0 -9999 0 -10000 0 0
MAP3K14 0.009 0.15 -9999 0 -0.62 4 4
APAF-1/Caspase 9 -0.063 0.16 -9999 0 -0.62 10 10
BCL2 -0.007 0.16 -9999 0 -0.52 8 8
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.011 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.011 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.02 0.07 -9999 0 -0.29 9 9
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
MAP3K12 0 0.1 -9999 0 -0.88 2 2
FGR -0.019 0.13 -9999 0 -0.49 9 9
p38 alpha/TAB1 -0.044 0.081 -9999 0 -0.27 11 11
PRKG1 -0.085 0.24 -9999 0 -0.59 24 24
DUSP8 -0.092 0.28 -9999 0 -0.85 18 18
PGK/cGMP/p38 alpha -0.083 0.14 -9999 0 -0.39 20 20
apoptosis -0.042 0.078 -9999 0 -0.3 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 0.003 0.079 -9999 0 -0.63 2 2
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.011 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.028 0.14 -9999 0 -0.43 11 11
BLK -0.16 0.32 -9999 0 -0.64 40 40
HCK -0.005 0.096 -9999 0 -0.48 5 5
MAP2K3 0.011 0 -9999 0 -10000 0 0
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.005 0.072 -9999 0 -0.88 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.012 0.11 -9999 0 -0.3 11 11
positive regulation of innate immune response -0.026 0.16 -9999 0 -0.46 11 11
LCK -0.042 0.21 -9999 0 -0.88 9 9
p38alpha-beta/MKP7 -0.019 0.15 -9999 0 -0.43 11 11
p38alpha-beta/MKP5 -0.022 0.15 -9999 0 -0.42 12 12
PGK/cGMP -0.071 0.18 -9999 0 -0.44 24 24
PAK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.022 0.16 -9999 0 -0.47 11 11
CDC42 0.011 0 -9999 0 -10000 0 0
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 -0.055 0.22 -9999 0 -0.7 14 14
IL2 signaling events mediated by STAT5

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 -0.002 0.11 -9999 0 -0.71 3 3
ELF1 -0.023 0.12 -9999 0 -0.39 14 14
CCNA2 0.005 0.072 -9999 0 -0.88 1 1
PIK3CA 0.012 0 -9999 0 -10000 0 0
JAK3 0 0.1 -9999 0 -0.88 2 2
PIK3R1 0.006 0.072 -9999 0 -0.88 1 1
JAK1 0.012 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.016 0.24 -9999 0 -0.74 12 12
SHC1 0.012 0 -9999 0 -10000 0 0
SP1 0.008 0.066 -9999 0 -0.39 4 4
IL2RA -0.08 0.33 -9999 0 -1.1 14 14
IL2RB -0.014 0.15 -9999 0 -0.78 5 5
SOS1 0.012 0 -9999 0 -10000 0 0
IL2RG -0.086 0.26 -9999 0 -0.73 20 20
G1/S transition of mitotic cell cycle -0.002 0.17 -9999 0 -0.67 9 9
PTPN11 0.012 0 -9999 0 -10000 0 0
CCND2 0 0.18 -9999 0 -1.1 4 4
LCK -0.041 0.21 -9999 0 -0.88 9 9
GRB2 0.012 0 -9999 0 -10000 0 0
IL2 0.006 0.006 -9999 0 -10000 0 0
CDK6 -0.012 0.14 -9999 0 -0.88 4 4
CCND3 0.002 0.2 -9999 0 -0.73 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex -0.16 0.43 -9999 0 -1.2 21 21
RAD9A 0.011 0 -9999 0 -10000 0 0
AP1 -0.14 0.31 -9999 0 -0.79 24 24
IFNAR2 0.01 0.006 -9999 0 -10000 0 0
AKT1 0.008 0.045 -9999 0 -0.34 2 2
ER alpha/Oestrogen -0.009 0.08 -9999 0 -0.69 2 2
NFX1/SIN3/HDAC complex 0.036 0.021 -9999 0 -10000 0 0
EGF -0.023 0.16 -9999 0 -0.79 6 6
SMG5 0.011 0 -9999 0 -10000 0 0
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 -0.001 0.003 -9999 0 -10000 0 0
TERT/c-Abl -0.18 0.37 -9999 0 -1.1 19 19
SAP18 0.009 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.047 0.19 -9999 0 -0.6 14 14
WRN 0.011 0 -9999 0 -10000 0 0
SP1 0.01 0.008 -9999 0 -10000 0 0
SP3 0.009 0.005 -9999 0 -10000 0 0
TERF2IP 0.011 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.16 0.32 -9999 0 -1 17 17
Mad/Max -0.002 0.021 -9999 0 -10000 0 0
TERT -0.17 0.47 -9999 0 -1.3 19 19
CCND1 -0.17 0.44 -9999 0 -1.1 24 24
MAX 0.009 0.005 -9999 0 -10000 0 0
RBBP7 0.009 0.005 -9999 0 -10000 0 0
RBBP4 0.009 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.011 0 -9999 0 -10000 0 0
SIN3A 0.009 0.005 -9999 0 -10000 0 0
Telomerase/911 0.013 0.078 -9999 0 -0.79 1 1
CDKN1B -0.1 0.26 -9999 0 -0.59 31 31
RAD1 0.011 0 -9999 0 -10000 0 0
XRCC5 0.011 0 -9999 0 -10000 0 0
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.009 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.009 0.005 -9999 0 -10000 0 0
JUN -0.067 0.23 -9999 0 -0.63 18 18
E6 -0.002 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP -0.001 0.002 -9999 0 -10000 0 0
FOS -0.11 0.29 -9999 0 -0.73 24 24
IFN-gamma/IRF1 -0.15 0.28 -9999 0 -0.69 31 31
PARP2 0.011 0 -9999 0 -10000 0 0
BLM -0.006 0.12 -9999 0 -0.88 3 3
Telomerase -0.008 0.14 -9999 0 -0.64 6 6
IRF1 0.008 0.073 -9999 0 -0.88 1 1
ESR1 -0.003 0.1 -9999 0 -0.88 2 2
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.023 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
HDAC1 0.009 0.005 -9999 0 -10000 0 0
HDAC2 0.01 0.008 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.019 0.057 -9999 0 -0.68 1 1
ABL1 0.011 0 -9999 0 -10000 0 0
MXD1 0.007 0.032 -9999 0 -0.38 1 1
MRE11A 0.011 0 -9999 0 -10000 0 0
HUS1 0.005 0.072 -9999 0 -0.88 1 1
RPS6KB1 0.011 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.36 -9999 0 -1.1 17 17
NR2F2 -0.017 0.11 -9999 0 -0.48 5 5
MAPK3 0.015 0.01 -9999 0 -10000 0 0
MAPK1 0.015 0.01 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.006 0.072 -9999 0 -0.87 1 1
NFKB1 0.011 0 -9999 0 -10000 0 0
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.011 0 -9999 0 -10000 0 0
EGFR -0.044 0.19 -9999 0 -0.61 13 13
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.064 0.18 -9999 0 -0.68 11 11
MYC -0.014 0.14 -9999 0 -0.88 4 4
IL2 0.003 0.015 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
TGFB1 0.006 0.072 -9999 0 -0.87 1 1
TRF2/BLM -0.013 0.09 -9999 0 -0.64 3 3
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.18 0.37 -9999 0 -1.1 19 19
SP1/HDAC2 0.014 0.016 -9999 0 -10000 0 0
PINX1 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.16 0.32 -9999 0 -1 17 17
Smad3/Myc -0.011 0.12 -9999 0 -0.72 4 4
911 complex -0.004 0.048 -9999 0 -0.59 1 1
IFNG -0.18 0.36 -9999 0 -0.81 35 35
Telomerase/PinX1 -0.16 0.32 -9999 0 -1 17 17
Telomerase/AKT1/mTOR/p70S6K 0.006 0.077 -9999 0 -10000 0 0
SIN3B 0.009 0.005 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.16 0.32 -9999 0 -1 17 17
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.16 0.32 -9999 0 -1 17 17
E2F1 0.01 0.006 -9999 0 -10000 0 0
ZNFX1 0.009 0.005 -9999 0 -10000 0 0
PIF1 -0.024 0.17 -9999 0 -0.88 6 6
NCL 0.011 0 -9999 0 -10000 0 0
DKC1 0.011 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.09 -10000 0 -0.48 1 1
adherens junction organization -0.033 0.14 -10000 0 -0.47 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.051 0.12 -10000 0 -0.6 3 3
FMN1 -0.066 0.2 -10000 0 -0.53 13 13
mol:IP3 -0.033 0.074 -10000 0 -0.45 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.058 0.13 -10000 0 -0.34 25 25
CTNNB1 0.004 0.009 -10000 0 -10000 0 0
AKT1 0.002 0.1 -10000 0 -0.44 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.06 0.22 -10000 0 -0.55 25 25
CTNND1 0.01 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.018 0.13 -10000 0 -10000 0 0
VASP -0.019 0.13 -10000 0 -10000 0 0
ZYX -0.019 0.13 -10000 0 -10000 0 0
JUB -0.023 0.14 -10000 0 -10000 0 0
EGFR(dimer) -0.08 0.16 -10000 0 -0.64 6 6
E-cadherin/beta catenin-gamma catenin -0.098 0.21 -10000 0 -0.57 25 25
mol:PI-3-4-5-P3 -0.04 0.089 -10000 0 -0.47 1 1
PIK3CA 0.012 0.002 -10000 0 -10000 0 0
PI3K -0.041 0.091 -10000 0 -0.48 1 1
FYN 0.007 0.084 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.073 -10000 0 -0.44 1 1
JUP 0.004 0.009 -10000 0 -10000 0 0
PIK3R1 0.006 0.072 -10000 0 -0.88 1 1
mol:DAG -0.033 0.074 -10000 0 -0.45 1 1
CDH1 -0.15 0.33 -10000 0 -0.84 27 27
RhoA/GDP -0.051 0.12 -10000 0 -0.6 3 3
establishment of polarity of embryonic epithelium -0.018 0.13 -10000 0 -10000 0 0
SRC 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
EGFR -0.043 0.19 -10000 0 -0.61 13 13
CASR -0.006 0.094 -10000 0 -0.42 1 1
RhoA/GTP -0.029 0.065 -10000 0 -0.4 1 1
AKT2 0.002 0.1 -10000 0 -0.44 1 1
actin cable formation -0.056 0.19 -10000 0 -0.51 13 13
apoptosis 0.036 0.081 0.45 1 -10000 0 1
CTNNA1 0.01 0.005 -10000 0 -10000 0 0
mol:GDP -0.057 0.13 -10000 0 -0.54 7 7
PIP5K1A -0.019 0.13 -10000 0 -10000 0 0
PLCG1 -0.033 0.076 -10000 0 -0.46 1 1
Rac1/GTP -0.072 0.15 -10000 0 -0.58 6 6
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.029 0.13 -10000 0 -0.42 14 14
ANTXR2 -0.002 0.09 -10000 0 -0.51 4 4
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.019 -10000 0 -0.095 4 4
monocyte activation -0.037 0.17 -10000 0 -0.54 13 13
MAP2K2 -0.002 0.007 -10000 0 -10000 0 0
MAP2K1 -0.004 0.016 -10000 0 -10000 0 0
MAP2K7 -0.004 0.016 -10000 0 -10000 0 0
MAP2K6 -0.004 0.016 -10000 0 -10000 0 0
CYAA -0.012 0.11 -10000 0 -0.53 4 4
MAP2K4 -0.004 0.016 -10000 0 -10000 0 0
IL1B -0.016 0.13 -10000 0 -0.62 6 6
Channel -0.028 0.11 -10000 0 -0.56 4 4
NLRP1 -0.008 0.046 -10000 0 -0.54 1 1
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.006 0.023 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.019 0.095 4 -10000 0 4
MAPK3 -0.004 0.016 -10000 0 -10000 0 0
MAPK1 -0.004 0.016 -10000 0 -10000 0 0
PGR -0.04 0.13 -10000 0 -0.45 12 12
PA/Cellular Receptors -0.03 0.12 -10000 0 -0.6 4 4
apoptosis -0.005 0.019 -10000 0 -0.095 4 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.024 0.1 -10000 0 -0.5 4 4
macrophage activation 0.015 0.018 -10000 0 -10000 0 0
TNF -0.056 0.23 -10000 0 -0.76 13 13
VCAM1 -0.05 0.17 -10000 0 -0.55 13 13
platelet activation -0.006 0.023 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.019 0.13 1 -10000 0 1
IL18 -0.029 0.13 -10000 0 -0.53 9 9
negative regulation of macrophage activation -0.005 0.019 -10000 0 -0.095 4 4
LEF -0.005 0.019 -10000 0 -0.095 4 4
CASP1 -0.009 0.05 -10000 0 -0.36 2 2
mol:cAMP -0.006 0.023 -10000 0 -10000 0 0
necrosis -0.005 0.019 -10000 0 -0.095 4 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.026 0.11 -10000 0 -0.53 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.01 0.089 -9999 0 -0.59 3 3
BIRC5 0.005 0.072 -9999 0 -0.88 1 1
NFKBIA 0.03 0.034 -9999 0 -10000 0 0
CPEB1 -0.35 0.35 -9999 0 -0.6 90 90
AKT1 0.03 0.034 -9999 0 -0.33 1 1
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.001 0.03 -9999 0 -10000 0 0
NDEL1/TACC3 -0.002 0.067 -9999 0 -0.79 1 1
GADD45A -0.006 0.12 -9999 0 -0.88 3 3
GSK3B 0.003 0.013 -9999 0 -10000 0 0
PAK1/Aurora A 0.001 0.033 -9999 0 -10000 0 0
MDM2 0.009 0.032 -9999 0 -0.38 1 1
JUB 0.001 0.064 -9999 0 -0.38 4 4
TPX2 0.022 0 -9999 0 -10000 0 0
TP53 0.002 0.026 -9999 0 -10000 0 0
DLG7 0.001 0.034 -9999 0 -0.34 1 1
AURKAIP1 0.011 0 -9999 0 -10000 0 0
ARHGEF7 0.011 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.002 0.07 -9999 0 -0.83 1 1
G2/M transition of mitotic cell cycle 0.001 0.03 -9999 0 -10000 0 0
AURKA 0.002 0.042 -9999 0 -0.4 1 1
AURKB -0.01 0.071 -9999 0 -0.81 1 1
CDC25B 0.001 0.032 -9999 0 -10000 0 0
G2/M transition checkpoint -0.004 0.04 -9999 0 -10000 0 0
mRNA polyadenylation -0.2 0.22 -9999 0 -0.54 39 39
Aurora A/CPEB -0.2 0.22 -9999 0 -0.54 39 39
Aurora A/TACC1/TRAP/chTOG -0.005 0.046 -9999 0 -0.51 1 1
BRCA1 0.011 0 -9999 0 -10000 0 0
centrosome duplication 0.001 0.033 -9999 0 -10000 0 0
regulation of centrosome cycle -0.005 0.063 -9999 0 -0.78 1 1
spindle assembly -0.005 0.046 -9999 0 -0.5 1 1
TDRD7 0.005 0.072 -9999 0 -0.88 1 1
Aurora A/RasGAP/Survivin -0.005 0.062 -9999 0 -0.76 1 1
CENPA -0.014 0.082 -9999 0 -0.36 6 6
Aurora A/PP2A 0.001 0.033 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.035 0.031 -9999 0 -0.29 1 1
negative regulation of DNA binding 0.002 0.026 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.011 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.004 0.04 -9999 0 -10000 0 0
mitotic prometaphase 0 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.042 -9999 0 -0.4 1 1
TACC1 0.011 0 -9999 0 -10000 0 0
TACC3 0.005 0.072 -9999 0 -0.88 1 1
Aurora A/Antizyme1 0.001 0.03 -9999 0 -10000 0 0
Aurora A/RasGAP 0.001 0.033 -9999 0 -0.33 1 1
OAZ1 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.003 0.013 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.022 0 -9999 0 -10000 0 0
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.033 0.03 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.013 0.13 -10000 0 -0.68 4 4
MAP4K4 -0.016 0.18 -10000 0 -0.72 7 7
BAG4 0 0.1 -10000 0 -0.88 2 2
PKC zeta/ceramide 0.006 0.046 0.2 4 -10000 0 4
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.053 0.22 -10000 0 -0.79 12 12
BAX 0.007 0.026 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.018 0.007 -10000 0 -10000 0 0
BAD 0.007 0.049 0.21 4 -10000 0 4
SMPD1 -0.005 0.094 -10000 0 -0.31 11 11
RB1 0.007 0.049 0.21 4 -10000 0 4
FADD/Caspase 8 -0.007 0.18 -10000 0 -0.74 7 7
MAP2K4 0.014 0.046 -10000 0 -10000 0 0
NSMAF 0.005 0.072 -10000 0 -0.88 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.014 0.046 -10000 0 -10000 0 0
EGF -0.021 0.16 -10000 0 -0.79 6 6
mol:ceramide -0.001 0.053 0.22 4 -10000 0 4
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.008 0.12 -10000 0 -0.68 4 4
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.007 0.049 0.21 4 -10000 0 4
cell proliferation -0.056 0.13 -10000 0 -0.39 19 19
BID -0.002 0.1 -10000 0 -0.38 6 6
MAP3K1 0.007 0.049 0.21 4 -10000 0 4
EIF2A 0.021 0.044 -10000 0 -10000 0 0
TRADD 0 0.1 -10000 0 -0.88 2 2
CRADD -0.006 0.12 -10000 0 -0.88 3 3
MAPK3 0.025 0.044 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.044 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.002 0.063 0.2 2 -0.54 1 3
FADD -0.016 0.18 -10000 0 -0.72 7 7
KSR1 0.007 0.049 0.21 4 -10000 0 4
MAPK8 0.01 0.066 0.21 4 -0.28 4 8
PRKRA 0.007 0.049 0.21 4 -10000 0 4
PDGFA -0.028 0.16 -10000 0 -0.58 10 10
TRAF2 0.011 0 -10000 0 -10000 0 0
IGF1 -0.12 0.3 -10000 0 -0.76 25 25
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.053 0.22 4 -10000 0 4
CTSD 0 0.085 -10000 0 -0.55 3 3
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.06 0.14 -10000 0 -0.42 19 19
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.011 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.008 0.12 -10000 0 -0.68 4 4
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.061 0.18 -10000 0 -0.77 7 7
TNFR1A/BAG4/TNF-alpha -0.059 0.18 -10000 0 -0.63 13 13
mol:Sphingosine-1-phosphate -0.013 0.13 -10000 0 -0.68 4 4
MAP2K1 0.021 0.044 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS 0.009 0.041 0.18 5 -10000 0 5
TNFRSF1A 0 0.1 -10000 0 -0.88 2 2
NFKB1 0.011 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.018 0.11 -10000 0 -0.68 4 4
EIF2AK2 0.014 0.046 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.055 0.18 -10000 0 -0.64 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.034 0.12 -10000 0 -0.48 6 6
MAP2K2 0.021 0.044 -10000 0 -10000 0 0
SMPD3 -0.007 0.1 -10000 0 -0.34 11 11
TNF -0.056 0.23 -10000 0 -0.76 13 13
PKC zeta/