PARADIGM pathway analysis of mRNASeq expression data
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1MP51RQ
Maintained by Dan DiCara (Broad Institute)
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/C1MP51RQ
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 47 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
IL23-mediated signaling events 95
Ephrin A reverse signaling 92
IL4-mediated signaling events 83
Signaling mediated by p38-alpha and p38-beta 80
Wnt signaling 73
amb2 Integrin signaling 64
Syndecan-4-mediated signaling events 64
Noncanonical Wnt signaling pathway 62
Glypican 1 network 61
IL12-mediated signaling events 56
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 574 . 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 ( 574 ).

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
IL23-mediated signaling events 0.1655 95 5711 60 -0.54 0.011 1000 -1000 -0.16 -1000
Ephrin A reverse signaling 0.1603 92 649 7 -0.097 0 1000 -1000 -0.023 -1000
IL4-mediated signaling events 0.1446 83 7586 91 -0.67 0.59 1000 -1000 -0.17 -1000
Signaling mediated by p38-alpha and p38-beta 0.1394 80 3559 44 -0.19 0.011 1000 -1000 -0.045 -1000
Wnt signaling 0.1272 73 512 7 -0.14 0.004 1000 -1000 -0.028 -1000
amb2 Integrin signaling 0.1115 64 5300 82 -0.16 0.015 1000 -1000 -0.066 -1000
Syndecan-4-mediated signaling events 0.1115 64 4298 67 -0.18 0.038 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 0.1080 62 1612 26 -0.14 0.011 1000 -1000 -0.046 -1000
Glypican 1 network 0.1063 61 2928 48 -0.2 0.015 1000 -1000 -0.038 -1000
IL12-mediated signaling events 0.0976 56 4908 87 -0.29 0.069 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 0.0976 56 2583 46 -0.43 0.017 1000 -1000 -0.12 -1000
EGFR-dependent Endothelin signaling events 0.0976 56 1188 21 -0.18 0.016 1000 -1000 -0.055 -1000
TCR signaling in naïve CD8+ T cells 0.0958 55 5196 93 -0.12 0.056 1000 -1000 -0.073 -1000
Syndecan-1-mediated signaling events 0.0923 53 1821 34 -0.14 0.011 1000 -1000 -0.051 -1000
BCR signaling pathway 0.0906 52 5223 99 -0.17 0.014 1000 -1000 -0.08 -1000
Signaling events mediated by the Hedgehog family 0.0889 51 2656 52 -0.13 0.077 1000 -1000 -0.046 -1000
Reelin signaling pathway 0.0871 50 2817 56 -0.12 0.021 1000 -1000 -0.064 -1000
Endothelins 0.0854 49 4781 96 -0.15 0.011 1000 -1000 -0.078 -1000
HIF-1-alpha transcription factor network 0.0836 48 3688 76 -0.32 0.016 1000 -1000 -0.19 -1000
Fc-epsilon receptor I signaling in mast cells 0.0819 47 4612 97 -0.14 0.029 1000 -1000 -0.07 -1000
TCGA08_retinoblastoma 0.0819 47 379 8 -0.069 0.027 1000 -1000 -0.021 -1000
BMP receptor signaling 0.0801 46 3772 81 -0.16 0.032 1000 -1000 -0.084 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0767 44 3057 68 -0.31 0.12 1000 -1000 -0.13 -1000
Ephrin B reverse signaling 0.0749 43 2083 48 -0.14 0.044 1000 -1000 -0.058 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0732 42 1438 34 -0.057 0.011 1000 -1000 -0.04 -1000
TCGA08_p53 0.0732 42 296 7 -0.05 0.03 1000 -1000 -0.013 -1000
Calcium signaling in the CD4+ TCR pathway 0.0732 42 1323 31 -0.2 0.011 1000 -1000 -0.057 -1000
p75(NTR)-mediated signaling 0.0679 39 4988 125 -0.18 0.031 1000 -1000 -0.093 -1000
Glucocorticoid receptor regulatory network 0.0679 39 4448 114 -0.34 0.21 1000 -1000 -0.063 -1000
Thromboxane A2 receptor signaling 0.0645 37 3984 105 -0.18 0.042 1000 -1000 -0.056 -1000
Syndecan-2-mediated signaling events 0.0645 37 2595 69 -0.11 0.023 1000 -1000 -0.028 -1000
Osteopontin-mediated events 0.0627 36 1397 38 -0.16 0.011 1000 -1000 -0.094 -1000
Signaling events regulated by Ret tyrosine kinase 0.0627 36 3016 82 -0.1 0.011 1000 -1000 -0.073 -1000
IL1-mediated signaling events 0.0592 34 2150 62 -0.1 0.019 1000 -1000 -0.075 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0592 34 4111 120 -0.18 0.14 1000 -1000 -0.063 -1000
Visual signal transduction: Cones 0.0575 33 1272 38 -0.052 0.007 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.0575 33 859 26 -0.12 0.01 1000 -1000 -0.054 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0575 33 2632 78 -0.083 0.054 1000 -1000 -0.077 -1000
LPA receptor mediated events 0.0557 32 3311 102 -0.11 0.012 1000 -1000 -0.086 -1000
JNK signaling in the CD4+ TCR pathway 0.0540 31 534 17 -0.046 0.011 1000 -1000 -0.043 -1000
Glypican 2 network 0.0540 31 127 4 -0.012 -1000 1000 -1000 -0.01 -1000
Arf6 signaling events 0.0523 30 1874 62 -0.18 0.024 1000 -1000 -0.046 -1000
Caspase cascade in apoptosis 0.0505 29 2161 74 -0.085 0.039 1000 -1000 -0.047 -1000
Cellular roles of Anthrax toxin 0.0505 29 1139 39 -0.044 0.011 1000 -1000 -0.021 -1000
Integrins in angiogenesis 0.0505 29 2462 84 -0.16 0.019 1000 -1000 -0.076 -1000
IL27-mediated signaling events 0.0505 29 1483 51 -0.2 0.025 1000 -1000 -0.051 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0505 29 2635 88 -0.12 0.045 1000 -1000 -0.096 -1000
a4b1 and a4b7 Integrin signaling 0.0488 28 141 5 -0.024 -0.004 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 0.0488 28 1451 51 -0.18 0.089 1000 -1000 -0.066 -1000
Visual signal transduction: Rods 0.0488 28 1497 52 -0.12 0.011 1000 -1000 -0.077 -1000
Signaling events mediated by PTP1B 0.0470 27 2110 76 -0.18 0.029 1000 -1000 -0.068 -1000
FAS signaling pathway (CD95) 0.0470 27 1303 47 -0.16 0.014 1000 -1000 -0.042 -1000
Presenilin action in Notch and Wnt signaling 0.0453 26 1590 61 -0.18 0.06 1000 -1000 -0.065 -1000
Retinoic acid receptors-mediated signaling 0.0453 26 1518 58 -0.14 0.019 1000 -1000 -0.068 -1000
Ras signaling in the CD4+ TCR pathway 0.0453 26 450 17 -0.051 0.01 1000 -1000 -0.04 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0436 25 1350 54 -0.13 0.022 1000 -1000 -0.084 -1000
Plasma membrane estrogen receptor signaling 0.0436 25 2186 86 -0.071 0.02 1000 -1000 -0.072 -1000
EPHB forward signaling 0.0418 24 2084 85 -0.11 0.061 1000 -1000 -0.079 -1000
IL6-mediated signaling events 0.0418 24 1802 75 -0.11 0.042 1000 -1000 -0.065 -1000
LPA4-mediated signaling events 0.0383 22 272 12 -0.057 0.015 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0383 22 847 37 -0.12 0.025 1000 -1000 -0.042 -1000
Nongenotropic Androgen signaling 0.0366 21 1139 52 -0.052 0.012 1000 -1000 -0.053 -1000
Coregulation of Androgen receptor activity 0.0348 20 1562 76 -0.16 0.04 1000 -1000 -0.034 -1000
S1P1 pathway 0.0348 20 749 36 -0.1 0.011 1000 -1000 -0.061 -1000
IGF1 pathway 0.0348 20 1191 57 -0.071 0.023 1000 -1000 -0.079 -1000
PDGFR-alpha signaling pathway 0.0331 19 856 44 -0.066 0.017 1000 -1000 -0.059 -1000
Class I PI3K signaling events 0.0314 18 1334 73 -0.11 0.022 1000 -1000 -0.059 -1000
IL2 signaling events mediated by STAT5 0.0296 17 384 22 -0.049 0.015 1000 -1000 -0.056 -1000
Regulation of Telomerase 0.0296 17 1742 102 -0.18 0.035 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.0279 16 863 51 -0.12 0.074 1000 -1000 -0.19 -1000
ErbB2/ErbB3 signaling events 0.0261 15 994 65 -0.068 0.016 1000 -1000 -0.061 -1000
ErbB4 signaling events 0.0261 15 1092 69 -0.16 0.036 1000 -1000 -0.08 -1000
IFN-gamma pathway 0.0261 15 1023 68 -0.063 0.02 1000 -1000 -0.09 -1000
Nectin adhesion pathway 0.0261 15 955 63 -0.031 0.021 1000 -1000 -0.068 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0261 15 515 33 -0.076 0.029 1000 -1000 -0.037 -1000
Signaling events mediated by PRL 0.0261 15 521 34 -0.025 0.026 1000 -1000 -0.032 -1000
S1P4 pathway 0.0261 15 382 25 -0.044 0.015 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0244 14 1920 136 -0.081 0.038 1000 -1000 -0.063 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0244 14 419 28 -0.044 0.018 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class III 0.0244 14 573 40 -0.046 0.017 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0244 14 751 52 -0.13 0.034 1000 -1000 -0.04 -1000
PLK2 and PLK4 events 0.0226 13 39 3 -0.004 0.009 1000 -1000 -0.015 -1000
Ceramide signaling pathway 0.0226 13 1029 76 -0.18 0.059 1000 -1000 -0.053 -1000
Syndecan-3-mediated signaling events 0.0226 13 484 35 -0.11 0.031 1000 -1000 -0.044 -1000
Regulation of p38-alpha and p38-beta 0.0226 13 723 54 -0.11 0.027 1000 -1000 -0.057 -1000
Paxillin-dependent events mediated by a4b1 0.0209 12 438 36 -0.024 0.02 1000 -1000 -0.059 -1000
IL2 signaling events mediated by PI3K 0.0209 12 719 58 -0.051 0.027 1000 -1000 -0.069 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0209 12 558 45 -0.062 0.039 1000 -1000 -0.08 -1000
PDGFR-beta signaling pathway 0.0209 12 1192 97 -0.096 0.032 1000 -1000 -0.077 -1000
Regulation of Androgen receptor activity 0.0209 12 903 70 -0.19 0.027 1000 -1000 -0.059 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0192 11 939 85 -0.036 0.028 1000 -1000 -0.059 -1000
S1P5 pathway 0.0192 11 191 17 -0.044 0.011 1000 -1000 -0.031 -1000
Signaling mediated by p38-gamma and p38-delta 0.0192 11 176 15 -0.023 0.017 1000 -1000 -0.031 -1000
S1P3 pathway 0.0192 11 483 42 -0.043 0.018 1000 -1000 -0.046 -1000
Class IB PI3K non-lipid kinase events 0.0192 11 33 3 0 0 1000 -1000 -0.01 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0174 10 876 83 -0.14 0.045 1000 -1000 -0.065 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0174 10 281 27 -0.018 0.015 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class II 0.0157 9 739 75 -0.038 0.026 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0157 9 604 65 -0.043 0.035 1000 -1000 -0.055 -1000
Insulin Pathway 0.0157 9 691 74 -0.12 0.027 1000 -1000 -0.079 -1000
Rapid glucocorticoid signaling 0.0157 9 188 20 -0.021 0.011 1000 -1000 -0.018 -1000
Aurora B signaling 0.0157 9 643 67 -0.11 0.028 1000 -1000 -0.058 -1000
BARD1 signaling events 0.0139 8 488 57 -0.043 0.048 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 0.0139 8 232 26 -0.044 0.035 1000 -1000 -0.018 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0139 8 650 74 -0.18 0.051 1000 -1000 -0.082 -1000
VEGFR1 specific signals 0.0139 8 485 56 -0.018 0.03 1000 -1000 -0.049 -1000
p38 MAPK signaling pathway 0.0139 8 393 44 -0.053 0.02 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0122 7 438 55 -0.025 0.041 1000 -1000 -0.078 -1000
Canonical NF-kappaB pathway 0.0105 6 234 39 -0.016 0.053 1000 -1000 -0.069 -1000
Aurora A signaling 0.0105 6 369 60 -0.051 0.029 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0105 6 258 43 -0.041 0.025 1000 -1000 -0.044 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0105 6 817 125 -0.043 0.055 1000 -1000 -0.08 -1000
Aurora C signaling 0.0087 5 37 7 -0.01 0.011 1000 -1000 -0.032 -1000
HIF-2-alpha transcription factor network 0.0087 5 252 43 -0.08 0.082 1000 -1000 -0.077 -1000
Signaling events mediated by HDAC Class I 0.0087 5 596 104 -0.022 0.04 1000 -1000 -0.065 -1000
Atypical NF-kappaB pathway 0.0087 5 159 31 -0.032 0.028 1000 -1000 -0.037 -1000
E-cadherin signaling in the nascent adherens junction 0.0087 5 448 76 -0.043 0.044 1000 -1000 -0.078 -1000
mTOR signaling pathway 0.0070 4 233 53 -0.006 0.025 1000 -1000 -0.054 -1000
Class I PI3K signaling events mediated by Akt 0.0070 4 290 68 -0.031 0.041 1000 -1000 -0.045 -1000
TRAIL signaling pathway 0.0070 4 220 48 -0.016 0.037 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0070 4 214 49 -0.016 0.029 1000 -1000 -0.057 -1000
FoxO family signaling 0.0070 4 267 64 -0.083 0.098 1000 -1000 -0.079 -1000
Arf6 trafficking events 0.0070 4 304 71 -0.039 0.027 1000 -1000 -0.069 -1000
PLK1 signaling events 0.0052 3 271 85 -0.007 0.029 1000 -1000 -0.041 -1000
Circadian rhythm pathway 0.0035 2 61 22 -0.011 0.036 1000 -1000 -0.044 -1000
Insulin-mediated glucose transport 0.0035 2 84 32 0 0.033 1000 -1000 -0.046 -1000
E-cadherin signaling in keratinocytes 0.0035 2 111 43 -0.032 0.037 1000 -1000 -0.048 -1000
Arf1 pathway 0.0035 2 140 54 -0.014 0.02 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0.0035 2 28 13 0 0.029 1000 -1000 -0.04 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0017 1 44 23 0.005 0.034 1000 -1000 -0.044 -1000
E-cadherin signaling events 0.0017 1 5 5 0.01 0.022 1000 -1000 -0.022 -1000
Total NA 3267 188777 7203 -14 -1000 131000 -131000 -7.9 -131000
IL23-mediated signaling events

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
CCL2 -0.43 0.54 -10000 0 -1.2 144 144
IL23A -0.44 0.55 -10000 0 -1.2 139 139
NF kappa B1 p50/RelA/I kappa B alpha -0.47 0.5 -10000 0 -1.2 163 163
positive regulation of T cell mediated cytotoxicity -0.48 0.62 -10000 0 -1.3 154 154
ITGA3 -0.41 0.52 -10000 0 -1.2 134 134
IL17F -0.29 0.34 -10000 0 -0.72 156 156
IL12B -0.018 0.082 -10000 0 -0.48 15 15
STAT1 (dimer) -0.46 0.59 -10000 0 -1.3 153 153
CD4 -0.42 0.52 -10000 0 -1.1 151 151
IL23 -0.42 0.52 -10000 0 -1.2 139 139
IL23R -0.1 0.3 -10000 0 -1.4 26 26
IL1B -0.46 0.58 -10000 0 -1.3 146 146
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.54 0.61 -10000 0 -1.2 205 205
TYK2 -0.002 0.034 -10000 0 -0.62 1 1
STAT4 -0.028 0.14 -10000 0 -0.56 40 40
STAT3 0.011 0.002 -10000 0 -10000 0 0
IL18RAP -0.034 0.15 -10000 0 -0.55 45 45
IL12RB1 -0.048 0.16 -10000 0 -0.57 48 48
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
IL12Rbeta1/TYK2 -0.036 0.12 -10000 0 -0.43 49 49
IL23R/JAK2 -0.12 0.3 -10000 0 -1.4 25 25
positive regulation of chronic inflammatory response -0.48 0.62 -10000 0 -1.3 154 154
natural killer cell activation 0.008 0.017 0.069 31 -10000 0 31
JAK2 -0.02 0.11 -10000 0 -0.57 21 21
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
NFKB1 0.008 0.025 -10000 0 -0.59 1 1
RELA 0.009 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.49 -10000 0 -1.1 139 139
ALOX12B -0.46 0.56 -10000 0 -1.2 168 168
CXCL1 -0.42 0.54 -10000 0 -1.2 142 142
T cell proliferation -0.48 0.62 -10000 0 -1.3 154 154
NFKBIA 0.009 0.004 -10000 0 -10000 0 0
IL17A -0.25 0.3 -10000 0 -0.6 153 153
PI3K -0.48 0.51 -10000 0 -1.2 164 164
IFNG -0.018 0.05 0.13 19 -0.12 48 67
STAT3 (dimer) -0.47 0.48 -10000 0 -1.1 174 174
IL18R1 -0.014 0.12 -10000 0 -0.55 25 25
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.32 -10000 0 -0.73 105 105
IL18/IL18R -0.025 0.14 -10000 0 -0.38 61 61
macrophage activation -0.023 0.018 -10000 0 -0.045 128 128
TNF -0.44 0.56 -10000 0 -1.3 141 141
STAT3/STAT4 -0.49 0.52 -10000 0 -1.2 160 160
STAT4 (dimer) -0.47 0.6 -10000 0 -1.3 157 157
IL18 0.002 0.069 -10000 0 -0.54 9 9
IL19 -0.41 0.51 -10000 0 -1.1 145 145
STAT5A (dimer) -0.46 0.59 -10000 0 -1.3 153 153
STAT1 0.006 0.052 -10000 0 -0.5 6 6
SOCS3 -0.002 0.08 -10000 0 -0.49 15 15
CXCL9 -0.47 0.58 -10000 0 -1.2 168 168
MPO -0.44 0.54 -10000 0 -1.2 162 162
positive regulation of humoral immune response -0.48 0.62 -10000 0 -1.3 154 154
IL23/IL23R/JAK2/TYK2 -0.53 0.75 -10000 0 -1.5 153 153
IL6 -0.48 0.58 -10000 0 -1.3 163 163
STAT5A 0.011 0 -10000 0 -10000 0 0
IL2 0.004 0.03 -10000 0 -0.46 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.017 0.069 31 -10000 0 31
CD3E -0.42 0.53 -10000 0 -1.2 142 142
keratinocyte proliferation -0.48 0.62 -10000 0 -1.3 154 154
NOS2 -0.48 0.58 -10000 0 -1.2 171 171
Ephrin A reverse signaling

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.062 0.14 -9999 0 -0.32 129 129
EFNA5 -0.097 0.22 -9999 0 -0.52 118 118
FYN -0.053 0.14 -9999 0 -0.29 131 131
neuron projection morphogenesis -0.062 0.14 -9999 0 -0.32 129 129
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.062 0.14 -9999 0 -0.32 129 129
EPHA5 -0.004 0.069 -9999 0 -0.46 13 13
IL4-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
BCL2L1 -0.52 0.56 -10000 0 -1.3 159 159
STAT6 (cleaved dimer) -0.57 0.55 -10000 0 -1.2 209 209
IGHG1 -0.16 0.18 -10000 0 -0.56 4 4
IGHG3 -0.5 0.54 -10000 0 -1.2 188 188
AKT1 -0.24 0.29 -10000 0 -0.76 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.26 -10000 0 -0.73 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.28 -10000 0 -0.72 66 66
THY1 -0.52 0.56 -10000 0 -1.3 162 162
MYB 0.002 0.074 -10000 0 -0.58 9 9
HMGA1 0.006 0.056 -10000 0 -0.54 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.35 -10000 0 -0.8 128 128
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.29 -10000 0 -0.73 70 70
SP1 0.015 0.025 -10000 0 -0.58 1 1
INPP5D -0.015 0.12 -10000 0 -0.58 26 26
SOCS5 0.026 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.54 0.58 -10000 0 -1.3 176 176
SOCS1 -0.35 0.36 -10000 0 -0.81 142 142
SOCS3 -0.26 0.31 -10000 0 -0.83 70 70
FCER2 -0.51 0.56 -10000 0 -1.3 155 155
PARP14 0.009 0.021 -10000 0 -0.46 1 1
CCL17 -0.56 0.61 -10000 0 -1.3 173 173
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.71 35 35
T cell proliferation -0.53 0.58 -10000 0 -1.3 170 170
IL4R/JAK1 -0.52 0.56 -10000 0 -1.3 165 165
EGR2 -0.57 0.6 -10000 0 -1.4 162 162
JAK2 -0.034 0.11 -10000 0 -0.58 21 21
JAK3 0.001 0.078 -10000 0 -0.53 12 12
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
JAK1 0.003 0.044 -10000 0 -0.58 3 3
COL1A2 -0.2 0.33 -10000 0 -1.2 36 36
CCL26 -0.57 0.61 -10000 0 -1.3 178 178
IL4R -0.56 0.6 -10000 0 -1.4 164 164
PTPN6 0.023 0.012 -10000 0 -10000 0 0
IL13RA2 -0.58 0.62 -10000 0 -1.4 167 167
IL13RA1 -0.017 0.058 -10000 0 -0.59 4 4
IRF4 -0.28 0.5 -10000 0 -1.4 85 85
ARG1 -0.14 0.18 -10000 0 -0.73 20 20
CBL -0.3 0.33 -10000 0 -0.78 110 110
GTF3A 0.012 0.039 -10000 0 -0.48 3 3
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
IL13RA1/JAK2 -0.033 0.098 -10000 0 -0.45 23 23
IRF4/BCL6 -0.24 0.46 -10000 0 -1.3 81 81
CD40LG -0.038 0.16 -10000 0 -0.58 47 47
MAPK14 -0.29 0.34 -10000 0 -0.84 92 92
mitosis -0.23 0.28 -10000 0 -0.71 68 68
STAT6 -0.62 0.72 -10000 0 -1.5 174 174
SPI1 -0.013 0.12 -10000 0 -0.52 27 27
RPS6KB1 -0.22 0.27 -10000 0 -0.7 65 65
STAT6 (dimer) -0.63 0.74 -10000 0 -1.5 174 174
STAT6 (dimer)/PARP14 -0.58 0.63 -10000 0 -1.4 171 171
mast cell activation 0.012 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.3 -10000 0 -0.77 73 73
FRAP1 -0.24 0.29 -10000 0 -0.76 69 69
LTA -0.55 0.6 -10000 0 -1.4 158 158
FES -0.002 0.086 -10000 0 -0.56 13 13
T-helper 1 cell differentiation 0.59 0.66 1.4 174 -10000 0 174
CCL11 -0.56 0.61 -10000 0 -1.3 178 178
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.3 -10000 0 -0.78 69 69
IL2RG 0 0.085 -10000 0 -0.55 13 13
IL10 -0.56 0.61 -10000 0 -1.4 168 168
IRS1 0.002 0.074 -10000 0 -0.58 9 9
IRS2 0.003 0.069 -10000 0 -0.54 9 9
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.52 0.56 -10000 0 -1.3 165 165
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.41 0.42 -10000 0 -0.92 168 168
COL1A1 -0.24 0.38 -10000 0 -1.3 49 49
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.54 0.58 -10000 0 -1.3 153 153
IL2R gamma/JAK3 -0.003 0.084 -10000 0 -0.39 25 25
TFF3 -0.56 0.6 -10000 0 -1.3 176 176
ALOX15 -0.61 0.64 -10000 0 -1.4 198 198
MYBL1 0 0.081 -10000 0 -0.55 12 12
T-helper 2 cell differentiation -0.43 0.44 -10000 0 -0.98 170 170
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.009 0.043 -10000 0 -0.48 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.28 -10000 0 -0.75 57 57
mol:PI-3-4-5-P3 -0.24 0.29 -10000 0 -0.76 69 69
PI3K -0.26 0.31 -10000 0 -0.82 68 68
DOK2 -0.008 0.1 -10000 0 -0.54 20 20
ETS1 0.015 0.06 -10000 0 -0.45 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.22 -10000 0 -0.68 32 32
ITGB3 -0.52 0.57 -10000 0 -1.3 164 164
PIGR -0.67 0.7 -10000 0 -1.5 223 223
IGHE 0.04 0.052 0.26 11 -0.31 1 12
MAPKKK cascade -0.18 0.22 -10000 0 -0.67 31 31
BCL6 0.01 0.039 -10000 0 -0.45 4 4
OPRM1 -0.52 0.56 -10000 0 -1.3 161 161
RETNLB -0.67 0.67 -10000 0 -1.4 228 228
SELP -0.59 0.65 -10000 0 -1.4 170 170
AICDA -0.51 0.54 -10000 0 -1.2 156 156
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.16 0.35 -9999 0 -0.95 74 74
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.063 0.14 -9999 0 -0.41 22 22
ATF2/c-Jun -0.045 0.15 -9999 0 -0.52 22 22
MAPK11 -0.079 0.17 -9999 0 -0.36 113 113
MITF -0.093 0.2 -9999 0 -0.42 125 125
MAPKAPK5 -0.074 0.18 -9999 0 -0.39 108 108
KRT8 -0.075 0.18 -9999 0 -0.4 109 109
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.11 0.23 -9999 0 -0.5 120 120
CEBPB -0.075 0.18 -9999 0 -0.39 110 110
SLC9A1 -0.076 0.18 -9999 0 -0.4 110 110
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.18 -9999 0 -0.55 33 33
p38alpha-beta/MNK1 -0.075 0.19 -9999 0 -0.4 108 108
JUN -0.045 0.14 -9999 0 -0.52 22 22
PPARGC1A -0.11 0.22 -9999 0 -0.42 157 157
USF1 -0.074 0.18 -9999 0 -0.39 108 108
RAB5/GDP/GDI1 -0.073 0.12 -9999 0 -0.42 34 34
NOS2 -0.19 0.4 -9999 0 -1.1 85 85
DDIT3 -0.075 0.18 -9999 0 -0.39 108 108
RAB5A 0.006 0.055 -9999 0 -0.58 5 5
HSPB1 -0.06 0.16 -9999 0 -0.46 37 37
p38alpha-beta/HBP1 -0.075 0.19 -9999 0 -0.41 107 107
CREB1 -0.074 0.18 -9999 0 -0.41 109 109
RAB5/GDP 0.005 0.041 -9999 0 -0.43 5 5
EIF4E -0.063 0.17 -9999 0 -0.56 31 31
RPS6KA4 -0.074 0.18 -9999 0 -0.39 109 109
PLA2G4A -0.15 0.22 -9999 0 -0.46 138 138
GDI1 -0.074 0.18 -9999 0 -0.39 108 108
TP53 -0.12 0.24 -9999 0 -0.51 122 122
RPS6KA5 -0.076 0.18 -9999 0 -0.39 110 110
ESR1 -0.1 0.21 -9999 0 -0.42 132 132
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.079 0.18 -9999 0 -0.4 114 114
MEF2A -0.075 0.18 -9999 0 -0.4 108 108
EIF4EBP1 -0.074 0.18 -9999 0 -0.41 108 108
KRT19 -0.076 0.18 -9999 0 -0.4 110 110
ELK4 -0.077 0.18 -9999 0 -0.41 108 108
ATF6 -0.074 0.18 -9999 0 -0.39 108 108
ATF1 -0.074 0.18 -9999 0 -0.41 108 108
p38alpha-beta/MAPKAPK2 -0.075 0.19 -9999 0 -0.41 107 107
p38alpha-beta/MAPKAPK3 -0.075 0.19 -9999 0 -0.41 107 107
Wnt signaling

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
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.48 101 101
FZD6 0.004 0.065 -9999 0 -0.58 7 7
WNT6 -0.1 0.21 -9999 0 -0.5 128 128
WNT4 -0.056 0.18 -9999 0 -0.54 70 70
FZD3 -0.009 0.11 -9999 0 -0.58 20 20
WNT5A -0.008 0.1 -9999 0 -0.55 20 20
WNT11 -0.14 0.24 -9999 0 -0.52 166 166
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.078 0.21 -9999 0 -0.46 109 109
alphaM/beta2 Integrin/GPIbA -0.068 0.19 -9999 0 -0.44 103 103
alphaM/beta2 Integrin/proMMP-9 -0.095 0.23 -9999 0 -0.48 124 124
PLAUR 0.01 0.031 -9999 0 -0.52 2 2
HMGB1 -0.012 0.099 -9999 0 -0.59 16 16
alphaM/beta2 Integrin/Talin -0.055 0.18 -9999 0 -0.43 88 88
AGER -0.01 0.093 -9999 0 -0.58 14 14
RAP1A 0.01 0.025 -9999 0 -0.58 1 1
SELPLG -0.006 0.098 -9999 0 -0.55 18 18
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.085 0.2 -9999 0 -0.46 98 98
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.058 0.18 -9999 0 -0.52 76 76
CYR61 -0.023 0.12 -9999 0 -0.48 40 40
TLN1 0.01 0.025 -9999 0 -0.58 1 1
Rap1/GTP -0.12 0.16 -9999 0 -0.44 83 83
RHOA 0.01 0.025 -9999 0 -0.58 1 1
P-selectin oligomer -0.078 0.21 -9999 0 -0.55 92 92
MYH2 -0.13 0.19 -9999 0 -0.46 105 105
MST1R 0.006 0.055 -9999 0 -0.58 5 5
leukocyte activation during inflammatory response -0.14 0.19 -9999 0 -0.4 144 144
APOB -0.12 0.22 -9999 0 -0.5 139 139
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.029 0.14 -9999 0 -0.52 43 43
JAM3 0.006 0.047 -9999 0 -0.46 6 6
GP1BA -0.011 0.1 -9999 0 -0.52 23 23
alphaM/beta2 Integrin/CTGF -0.065 0.19 -9999 0 -0.43 100 100
alphaM/beta2 Integrin -0.13 0.2 -9999 0 -0.45 119 119
JAM3 homodimer 0.006 0.047 -9999 0 -0.45 6 6
ICAM2 0.002 0.068 -9999 0 -0.5 10 10
ICAM1 0.007 0.048 -9999 0 -0.5 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.13 0.2 -9999 0 -0.44 119 119
cell adhesion -0.068 0.19 -9999 0 -0.44 103 103
NFKB1 -0.1 0.24 -9999 0 -0.62 63 63
THY1 0.004 0.064 -9999 0 -0.53 8 8
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Lipoprotein(a) -0.086 0.15 -9999 0 -0.31 172 172
alphaM/beta2 Integrin/LRP/tPA -0.053 0.18 -9999 0 -0.44 82 82
IL6 -0.16 0.32 -9999 0 -0.77 97 97
ITGB2 -0.036 0.14 -9999 0 -0.53 43 43
elevation of cytosolic calcium ion concentration -0.05 0.17 -9999 0 -0.44 75 75
alphaM/beta2 Integrin/JAM2/JAM3 -0.076 0.21 -9999 0 -0.48 101 101
JAM2 -0.046 0.17 -9999 0 -0.54 60 60
alphaM/beta2 Integrin/ICAM1 -0.062 0.18 -9999 0 -0.43 89 89
alphaM/beta2 Integrin/uPA/Plg -0.076 0.2 -9999 0 -0.45 103 103
RhoA/GTP -0.14 0.2 -9999 0 -0.48 107 107
positive regulation of phagocytosis -0.13 0.2 -9999 0 -0.53 92 92
Ron/MSP -0.02 0.12 -9999 0 -0.37 54 54
alphaM/beta2 Integrin/uPAR/uPA -0.05 0.17 -9999 0 -0.45 75 75
alphaM/beta2 Integrin/uPAR -0.056 0.18 -9999 0 -0.43 89 89
PLAU 0 0.076 -9999 0 -0.49 13 13
PLAT 0 0.079 -9999 0 -0.54 12 12
actin filament polymerization -0.12 0.18 -9999 0 -0.44 105 105
MST1 -0.034 0.15 -9999 0 -0.51 50 50
alphaM/beta2 Integrin/lipoprotein(a) -0.13 0.2 -9999 0 -0.4 144 144
TNF -0.1 0.26 -9999 0 -0.73 54 54
RAP1B 0.011 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.061 0.18 -9999 0 -0.44 95 95
fibrinolysis -0.076 0.2 -9999 0 -0.44 103 103
HCK -0.02 0.13 -9999 0 -0.55 32 32
dendritic cell antigen processing and presentation -0.13 0.2 -9999 0 -0.44 119 119
VTN -0.051 0.16 -9999 0 -0.5 68 68
alphaM/beta2 Integrin/CYR61 -0.074 0.2 -9999 0 -0.43 113 113
LPA -0.027 0.12 -9999 0 -0.46 41 41
LRP1 0.004 0.063 -9999 0 -0.56 7 7
cell migration -0.1 0.25 -9999 0 -0.53 114 114
FN1 -0.087 0.21 -9999 0 -0.52 106 106
alphaM/beta2 Integrin/Thy1 -0.059 0.18 -9999 0 -0.44 91 91
MPO -0.038 0.15 -9999 0 -0.52 52 52
KNG1 -0.11 0.22 -9999 0 -0.52 131 131
RAP1/GDP 0.015 0.016 -9999 0 -0.36 1 1
ROCK1 -0.13 0.2 -9999 0 -0.46 108 108
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.037 0.15 -9999 0 -0.58 41 41
CTGF -0.006 0.089 -9999 0 -0.46 21 21
alphaM/beta2 Integrin/Hck -0.072 0.22 -9999 0 -0.49 97 97
ITGAM -0.068 0.18 -9999 0 -0.52 78 78
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.1 0.24 -9999 0 -0.47 129 129
HP -0.078 0.19 -9999 0 -0.5 98 98
leukocyte adhesion -0.12 0.21 -9999 0 -0.56 81 81
SELP -0.079 0.21 -9999 0 -0.55 92 92
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.067 0.17 -9999 0 -0.55 55 55
Syndecan-4/Syndesmos -0.14 0.23 -9999 0 -0.54 112 112
positive regulation of JNK cascade -0.14 0.22 -9999 0 -0.52 118 118
Syndecan-4/ADAM12 -0.18 0.27 -9999 0 -0.58 141 141
CCL5 -0.037 0.15 -9999 0 -0.51 53 53
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DNM2 0.01 0.025 -9999 0 -0.58 1 1
ITGA5 -0.005 0.089 -9999 0 -0.48 19 19
SDCBP 0 0.081 -9999 0 -0.58 11 11
PLG -0.033 0.14 -9999 0 -0.56 41 41
ADAM12 -0.077 0.2 -9999 0 -0.51 97 97
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.027 -9999 0 -0.46 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.04 -9999 0 -0.15 5 5
Syndecan-4/Laminin alpha1 -0.17 0.25 -9999 0 -0.58 125 125
Syndecan-4/CXCL12/CXCR4 -0.15 0.24 -9999 0 -0.55 118 118
Syndecan-4/Laminin alpha3 -0.15 0.24 -9999 0 -0.55 120 120
MDK -0.008 0.1 -9999 0 -0.51 22 22
Syndecan-4/FZD7 -0.14 0.23 -9999 0 -0.55 113 113
Syndecan-4/Midkine -0.14 0.23 -9999 0 -0.55 116 116
FZD7 0 0.076 -9999 0 -0.49 13 13
Syndecan-4/FGFR1/FGF -0.17 0.22 -9999 0 -0.55 121 121
THBS1 -0.004 0.09 -9999 0 -0.51 17 17
integrin-mediated signaling pathway -0.16 0.25 -9999 0 -0.55 129 129
positive regulation of MAPKKK cascade -0.14 0.22 -9999 0 -0.52 118 118
Syndecan-4/TACI -0.17 0.25 -9999 0 -0.56 127 127
CXCR4 -0.017 0.12 -9999 0 -0.49 32 32
cell adhesion -0.026 0.11 -9999 0 -0.3 64 64
Syndecan-4/Dynamin -0.14 0.23 -9999 0 -0.55 110 110
Syndecan-4/TSP1 -0.14 0.24 -9999 0 -0.55 116 116
Syndecan-4/GIPC -0.14 0.23 -9999 0 -0.54 111 111
Syndecan-4/RANTES -0.16 0.24 -9999 0 -0.57 118 118
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.054 0.18 -9999 0 -0.54 68 68
LAMA3 -0.016 0.12 -9999 0 -0.5 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.055 -9999 0 -0.46 2 2
Syndecan-4/alpha-Actinin -0.14 0.23 -9999 0 -0.54 110 110
TFPI -0.008 0.1 -9999 0 -0.53 20 20
F2 -0.12 0.22 -9999 0 -0.5 143 143
alpha5/beta1 Integrin 0.005 0.064 -9999 0 -0.34 19 19
positive regulation of cell adhesion -0.17 0.25 -9999 0 -0.57 131 131
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC -0.055 0.18 -9999 0 -0.52 72 72
Syndecan-4/CXCL12 -0.15 0.24 -9999 0 -0.56 118 118
FGF6 -0.001 0.019 -9999 0 -0.46 1 1
RHOA 0.01 0.025 -9999 0 -0.58 1 1
CXCL12 -0.013 0.11 -9999 0 -0.49 28 28
TNFRSF13B -0.061 0.18 -9999 0 -0.52 76 76
FGF2 -0.037 0.15 -9999 0 -0.52 53 53
FGFR1 -0.009 0.1 -9999 0 -0.51 22 22
Syndecan-4/PI-4-5-P2 -0.14 0.23 -9999 0 -0.55 110 110
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.082 0.2 -9999 0 -0.51 106 106
cell migration -0.006 0.017 -9999 0 -10000 0 0
PRKCD 0.016 0.009 -9999 0 -10000 0 0
vasculogenesis -0.14 0.23 -9999 0 -0.53 116 116
SDC4 -0.15 0.24 -9999 0 -0.58 110 110
Syndecan-4/Tenascin C -0.17 0.26 -9999 0 -0.58 129 129
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.032 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.23 -9999 0 -0.54 116 116
MMP9 -0.059 0.18 -9999 0 -0.52 76 76
Rac1/GTP -0.027 0.12 -9999 0 -0.31 64 64
cytoskeleton organization -0.13 0.22 -9999 0 -0.52 112 112
GIPC1 0.007 0.049 -9999 0 -0.58 4 4
Syndecan-4/TFPI -0.14 0.24 -9999 0 -0.55 116 116
Noncanonical Wnt signaling pathway

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
NFATC2 -0.038 0.16 -9999 0 -0.56 49 49
GNB1/GNG2 -0.11 0.19 -9999 0 -0.49 82 82
mol:DAG -0.097 0.18 -9999 0 -0.45 81 81
PLCG1 -0.1 0.18 -9999 0 -0.46 81 81
YES1 -0.12 0.2 -9999 0 -0.52 82 82
FZD3 -0.009 0.11 -9999 0 -0.58 20 20
FZD6 0.004 0.065 -9999 0 -0.58 7 7
G protein -0.1 0.18 -9999 0 -0.46 81 81
MAP3K7 -0.087 0.16 -9999 0 -0.42 69 69
mol:Ca2+ -0.094 0.17 -9999 0 -0.43 81 81
mol:IP3 -0.097 0.18 -9999 0 -0.45 81 81
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.1 0.17 -9999 0 -0.45 75 75
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.48 101 101
CSNK1A1 0.009 0.035 -9999 0 -0.58 2 2
GNAS -0.12 0.2 -9999 0 -0.51 80 80
GO:0007205 -0.096 0.18 -9999 0 -0.44 81 81
WNT6 -0.1 0.21 -9999 0 -0.5 128 128
WNT4 -0.056 0.18 -9999 0 -0.54 70 70
NFAT1/CK1 alpha -0.12 0.22 -9999 0 -0.55 84 84
GNG2 0.004 0.064 -9999 0 -0.53 8 8
WNT5A -0.008 0.1 -9999 0 -0.55 20 20
WNT11 -0.14 0.24 -9999 0 -0.52 166 166
CDC42 -0.11 0.2 -9999 0 -0.5 83 83
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.026 0.14 -10000 0 -0.36 74 74
fibroblast growth factor receptor signaling pathway -0.026 0.14 -10000 0 -0.36 74 74
LAMA1 -0.054 0.18 -10000 0 -0.54 68 68
PRNP -0.003 0.09 -10000 0 -0.57 14 14
GPC1/SLIT2 -0.088 0.18 -10000 0 -0.38 150 150
SMAD2 0.015 0.063 -10000 0 -0.34 15 15
GPC1/PrPc/Cu2+ -0.001 0.075 -10000 0 -0.34 26 26
GPC1/Laminin alpha1 -0.038 0.14 -10000 0 -0.4 76 76
TDGF1 -0.072 0.2 -10000 0 -0.58 81 81
CRIPTO/GPC1 -0.053 0.16 -10000 0 -0.41 93 93
APP/GPC1 0.008 0.061 -10000 0 -0.39 13 13
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.042 0.14 -10000 0 -0.36 93 93
FLT1 0.006 0.056 -10000 0 -0.54 6 6
GPC1/TGFB/TGFBR1/TGFBR2 0.013 0.06 -10000 0 -0.33 17 17
SERPINC1 -0.011 0.089 -10000 0 -0.46 22 22
FYN -0.041 0.14 -10000 0 -0.35 98 98
FGR -0.058 0.16 -10000 0 -0.36 121 121
positive regulation of MAPKKK cascade -0.095 0.21 -10000 0 -0.46 117 117
SLIT2 -0.12 0.23 -10000 0 -0.53 141 141
GPC1/NRG -0.049 0.15 -10000 0 -0.38 94 94
NRG1 -0.068 0.19 -10000 0 -0.53 84 84
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.012 0.065 -10000 0 -0.34 18 18
LYN -0.037 0.14 -10000 0 -0.35 93 93
mol:Spermine 0.001 0.058 -10000 0 -0.39 12 12
cell growth -0.026 0.14 -10000 0 -0.36 74 74
BMP signaling pathway 0 0.079 0.54 12 -10000 0 12
SRC -0.038 0.14 -10000 0 -0.35 93 93
TGFBR1 0.007 0.049 -10000 0 -0.58 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.27 -10000 0 -0.53 224 224
GPC1 0 0.079 -10000 0 -0.54 12 12
TGFBR1 (dimer) 0.007 0.049 -10000 0 -0.58 4 4
VEGFA 0.011 0.019 -10000 0 -0.46 1 1
BLK -0.11 0.2 -10000 0 -0.37 196 196
HCK -0.056 0.16 -10000 0 -0.36 117 117
FGF2 -0.037 0.15 -10000 0 -0.52 53 53
FGFR1 -0.009 0.1 -10000 0 -0.51 22 22
VEGFR1 homodimer 0.006 0.056 -10000 0 -0.54 6 6
TGFBR2 0.011 0.019 -10000 0 -0.46 1 1
cell death 0.008 0.061 -10000 0 -0.39 13 13
ATIII/GPC1 -0.007 0.085 -10000 0 -0.34 34 34
PLA2G2A/GPC1 -0.14 0.21 -10000 0 -0.39 228 228
LCK -0.063 0.17 -10000 0 -0.37 124 124
neuron differentiation -0.049 0.15 -10000 0 -0.38 94 94
PrPc/Cu2+ -0.002 0.066 -10000 0 -0.42 14 14
APP 0.01 0.025 -10000 0 -0.58 1 1
TGFBR2 (dimer) 0.011 0.019 -10000 0 -0.45 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.069 0.19 -10000 0 -0.44 83 83
TBX21 -0.24 0.51 -10000 0 -1.1 121 121
B2M 0.005 0.039 -10000 0 -0.5 3 3
TYK2 0.007 0.034 -10000 0 -0.61 1 1
IL12RB1 -0.039 0.16 -10000 0 -0.57 48 48
GADD45B -0.15 0.37 -10000 0 -0.84 89 89
IL12RB2 -0.039 0.16 -10000 0 -0.53 53 53
GADD45G -0.16 0.38 -10000 0 -0.83 96 96
natural killer cell activation -0.003 0.023 -10000 0 -10000 0 0
RELB 0.009 0.037 -10000 0 -0.5 3 3
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.003 0.071 -10000 0 -0.55 9 9
IL2RA -0.044 0.17 -10000 0 -0.55 57 57
IFNG -0.064 0.18 -10000 0 -0.51 80 80
STAT3 (dimer) -0.16 0.36 -10000 0 -0.75 121 121
HLA-DRB5 -0.079 0.2 -10000 0 -0.52 97 97
FASLG -0.24 0.52 -10000 0 -1.1 118 118
NF kappa B2 p52/RelB -0.27 0.4 -10000 0 -0.93 127 127
CD4 -0.014 0.12 -10000 0 -0.55 26 26
SOCS1 -0.029 0.14 -10000 0 -0.49 46 46
EntrezGene:6955 -0.004 0.015 -10000 0 -10000 0 0
CD3D -0.035 0.15 -10000 0 -0.56 43 43
CD3E -0.027 0.14 -10000 0 -0.56 36 36
CD3G -0.053 0.18 -10000 0 -0.57 61 61
IL12Rbeta2/JAK2 -0.036 0.15 -10000 0 -0.4 72 72
CCL3 -0.24 0.5 -10000 0 -1.1 122 122
CCL4 -0.22 0.49 -10000 0 -1.1 98 98
HLA-A -0.001 0.07 -10000 0 -0.52 10 10
IL18/IL18R -0.012 0.15 -10000 0 -0.39 67 67
NOS2 -0.28 0.56 -10000 0 -1.2 126 126
IL12/IL12R/TYK2/JAK2/SPHK2 -0.054 0.16 -10000 0 -0.42 61 61
IL1R1 -0.21 0.46 -10000 0 -1 111 111
IL4 0.004 0.024 -10000 0 -10000 0 0
JAK2 -0.013 0.11 -10000 0 -0.57 21 21
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.17 0.44 -10000 0 -0.94 111 111
RAB7A -0.11 0.32 -10000 0 -0.79 52 52
lysosomal transport -0.11 0.3 -10000 0 -0.73 56 56
FOS -0.17 0.41 -10000 0 -1.1 75 75
STAT4 (dimer) -0.17 0.41 -10000 0 -0.88 114 114
STAT5A (dimer) -0.29 0.42 -10000 0 -0.93 145 145
GZMA -0.24 0.5 -10000 0 -1.1 109 109
GZMB -0.25 0.51 -10000 0 -1.1 120 120
HLX 0.006 0.056 -10000 0 -0.54 6 6
LCK -0.24 0.51 -10000 0 -1.1 128 128
TCR/CD3/MHC II/CD4 -0.12 0.33 -10000 0 -0.74 91 91
IL2/IL2R -0.031 0.15 -10000 0 -0.41 63 63
MAPK14 -0.15 0.38 -10000 0 -0.84 97 97
CCR5 -0.17 0.42 -10000 0 -1.1 72 72
IL1B -0.067 0.19 -10000 0 -0.53 81 81
STAT6 -0.037 0.12 -10000 0 -0.26 19 19
STAT4 -0.028 0.14 -10000 0 -0.56 40 40
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.006 0.052 -10000 0 -0.5 6 6
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
NFKB2 0.01 0.031 -10000 0 -0.52 2 2
IL12B -0.007 0.079 -10000 0 -0.47 15 15
CD8A -0.06 0.18 -10000 0 -0.54 72 72
CD8B -0.047 0.17 -10000 0 -0.56 56 56
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.069 0.19 0.43 83 -10000 0 83
IL2RB -0.016 0.12 -10000 0 -0.55 28 28
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.37 -10000 0 -0.78 114 114
IL2RG -0.002 0.086 -10000 0 -0.56 13 13
IL12 -0.029 0.13 -10000 0 -0.4 58 58
STAT5A 0.011 0 -10000 0 -10000 0 0
CD247 -0.022 0.13 -10000 0 -0.55 31 31
IL2 0.001 0.027 -10000 0 -0.46 2 2
SPHK2 0.009 0.037 -10000 0 -0.5 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.037 0.16 -10000 0 -0.57 44 44
IL12/IL12R/TYK2/JAK2 -0.26 0.57 -10000 0 -1.1 131 131
MAP2K3 -0.16 0.39 -10000 0 -0.84 101 101
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 -0.16 0.39 -10000 0 -0.85 102 102
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.041 0.16 -10000 0 -0.52 57 57
IL18RAP -0.033 0.15 -10000 0 -0.56 45 45
IL12Rbeta1/TYK2 -0.023 0.13 -10000 0 -0.42 49 49
EOMES -0.14 0.4 -10000 0 -1.3 58 58
STAT1 (dimer) -0.18 0.38 -10000 0 -0.81 120 120
T cell proliferation -0.12 0.3 0.4 1 -0.64 105 106
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.013 0.12 -10000 0 -0.56 25 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.28 -10000 0 -0.7 108 108
ATF2 -0.14 0.36 -10000 0 -0.78 93 93
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.28 0.36 -10000 0 -0.93 81 81
PCK1 -0.27 0.44 -10000 0 -1.3 73 73
HNF4A -0.37 0.45 -10000 0 -1.1 113 113
KCNJ11 -0.27 0.38 -10000 0 -0.97 78 78
AKT1 -0.14 0.16 -10000 0 -0.47 14 14
response to starvation -0.019 0.034 -10000 0 -10000 0 0
DLK1 -0.28 0.37 -10000 0 -0.92 92 92
NKX2-1 -0.18 0.34 -10000 0 -1.1 44 44
ACADM -0.29 0.38 -10000 0 -0.98 84 84
TAT -0.18 0.22 -10000 0 -0.68 43 43
CEBPB 0.004 0.043 -10000 0 -0.49 4 4
CEBPA -0.008 0.1 -10000 0 -0.58 17 17
TTR -0.3 0.41 -10000 0 -1 101 101
PKLR -0.43 0.48 -10000 0 -1 187 187
APOA1 -0.38 0.49 -10000 0 -1.2 101 101
CPT1C -0.31 0.4 -10000 0 -1 93 93
ALAS1 -0.13 0.18 -10000 0 -0.81 3 3
TFRC -0.19 0.28 -10000 0 -0.9 32 32
FOXF1 0.013 0.1 0.27 6 -0.56 15 21
NF1 0.014 0.043 -10000 0 -0.58 3 3
HNF1A (dimer) 0.002 0.073 -10000 0 -0.58 6 6
CPT1A -0.28 0.36 -10000 0 -0.93 82 82
HMGCS1 -0.29 0.37 -10000 0 -0.93 92 92
NR3C1 -0.039 0.13 -10000 0 -0.55 28 28
CPT1B -0.3 0.39 -10000 0 -1 90 90
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0.044 -10000 0 -0.58 1 1
GCK -0.3 0.38 -10000 0 -0.98 92 92
CREB1 -0.007 0.061 -10000 0 -0.6 2 2
IGFBP1 -0.28 0.41 -10000 0 -1.1 93 93
PDX1 -0.18 0.36 -10000 0 -1.4 35 35
UCP2 -0.29 0.37 -10000 0 -0.96 87 87
ALDOB -0.38 0.49 -10000 0 -1.1 130 130
AFP -0.07 0.18 -10000 0 -0.53 41 41
BDH1 -0.29 0.37 -10000 0 -1 70 70
HADH -0.27 0.36 -10000 0 -0.96 73 73
F2 -0.42 0.53 -10000 0 -1.3 116 116
HNF1A 0.002 0.073 -10000 0 -0.58 6 6
G6PC -0.032 0.14 -10000 0 -0.68 10 10
SLC2A2 -0.17 0.24 -10000 0 -0.78 24 24
INS 0.017 0.063 0.22 6 -0.47 2 8
FOXA1 -0.07 0.21 0.27 2 -0.56 77 79
FOXA3 -0.033 0.13 -10000 0 -0.51 22 22
FOXA2 -0.32 0.42 -10000 0 -1 89 89
ABCC8 -0.3 0.39 -10000 0 -1 86 86
ALB -0.078 0.18 -10000 0 -0.56 37 37
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.008 0.042 -9999 0 -0.49 4 4
EGFR 0.004 0.064 -9999 0 -0.53 8 8
EGF/EGFR -0.12 0.15 -9999 0 -0.34 122 122
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.072 0.14 -9999 0 -0.29 90 90
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.017 0.12 -9999 0 -0.51 31 31
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.5 209 209
EGF/EGFR dimer/SHC -0.099 0.16 -9999 0 -0.3 216 216
mol:GDP -0.073 0.13 -9999 0 -0.29 90 90
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.023 0.13 -9999 0 -0.51 38 38
GRB2/SOS1 0.016 0.018 -9999 0 -0.42 1 1
HRAS/GTP -0.084 0.11 -9999 0 -0.45 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.086 0.11 -9999 0 -0.46 3 3
FRAP1 -0.07 0.13 -9999 0 -0.28 90 90
EGF/EGFR dimer -0.13 0.19 -9999 0 -0.36 216 216
SOS1 0.01 0.025 -9999 0 -0.58 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.028 0.13 -9999 0 -0.38 66 66
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.092 0.19 -10000 0 -0.54 75 75
FYN -0.087 0.28 -10000 0 -0.69 84 84
LAT/GRAP2/SLP76 -0.11 0.23 -10000 0 -0.57 91 91
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
AKT1 -0.05 0.18 -10000 0 -0.45 84 84
B2M 0.008 0.037 -10000 0 -0.5 3 3
IKBKG -0.035 0.054 -10000 0 -0.16 66 66
MAP3K8 0.01 0.031 -10000 0 -0.52 2 2
mol:Ca2+ -0.024 0.04 -10000 0 -0.1 105 105
integrin-mediated signaling pathway 0.007 0.053 -10000 0 -0.32 14 14
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.087 0.28 -10000 0 -0.67 87 87
TRPV6 -0.093 0.19 -10000 0 -0.48 113 113
CD28 -0.033 0.15 -10000 0 -0.56 45 45
SHC1 -0.084 0.27 -10000 0 -0.67 82 82
receptor internalization -0.092 0.3 -10000 0 -0.75 79 79
PRF1 -0.097 0.32 -10000 0 -1 50 50
KRAS 0.005 0.058 -10000 0 -0.56 6 6
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 -0.032 0.15 -10000 0 -0.36 78 78
LAT -0.092 0.28 -10000 0 -0.68 86 86
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.032 0.15 -10000 0 -0.56 43 43
CD3E -0.025 0.14 -10000 0 -0.56 36 36
CD3G -0.05 0.18 -10000 0 -0.57 61 61
RASGRP2 -0.01 0.045 -10000 0 -0.17 34 34
RASGRP1 -0.054 0.2 -10000 0 -0.48 83 83
HLA-A 0.001 0.071 -10000 0 -0.52 10 10
RASSF5 -0.001 0.081 -10000 0 -0.53 13 13
RAP1A/GTP/RAPL 0.007 0.053 -10000 0 -0.33 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.059 -10000 0 -0.12 72 72
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.064 0.095 -10000 0 -0.27 82 82
PRKCA -0.048 0.1 -10000 0 -0.28 72 72
GRAP2 -0.023 0.14 -10000 0 -0.55 35 35
mol:IP3 -0.056 0.19 0.2 72 -0.44 81 153
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.084 0.29 -10000 0 -0.75 69 69
ORAI1 0.056 0.11 0.27 110 -0.32 2 112
CSK -0.087 0.28 -10000 0 -0.69 82 82
B7 family/CD28 -0.11 0.32 -10000 0 -0.73 101 101
CHUK 0.007 0.049 -10000 0 -0.58 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.33 -10000 0 -0.79 85 85
PTPN6 -0.088 0.28 -10000 0 -0.69 81 81
VAV1 -0.096 0.29 -10000 0 -0.7 89 89
Monovalent TCR/CD3 -0.065 0.26 -10000 0 -0.6 78 78
CBL 0.011 0 -10000 0 -10000 0 0
LCK -0.096 0.3 -10000 0 -0.71 87 87
PAG1 -0.089 0.28 -10000 0 -0.69 83 83
RAP1A 0.01 0.025 -10000 0 -0.58 1 1
TCR/CD3/MHC I/CD8/LCK -0.11 0.32 -10000 0 -0.79 83 83
CD80 -0.039 0.16 -10000 0 -0.57 50 50
CD86 -0.036 0.16 -10000 0 -0.54 49 49
PDK1/CARD11/BCL10/MALT1 -0.078 0.12 -10000 0 -0.32 88 88
HRAS 0.008 0.042 -10000 0 -0.49 4 4
GO:0035030 -0.088 0.25 -10000 0 -0.58 101 101
CD8A -0.057 0.18 -10000 0 -0.54 72 72
CD8B -0.044 0.17 -10000 0 -0.56 56 56
PTPRC -0.041 0.16 -10000 0 -0.55 54 54
PDK1/PKC theta -0.067 0.23 -10000 0 -0.56 85 85
CSK/PAG1 -0.082 0.27 -10000 0 -0.69 78 78
SOS1 0.01 0.025 -10000 0 -0.58 1 1
peptide-MHC class I 0.007 0.059 -10000 0 -0.37 13 13
GRAP2/SLP76 -0.12 0.27 -10000 0 -0.68 88 88
STIM1 0.03 0.053 0.2 1 -10000 0 1
RAS family/GTP -0.002 0.082 -10000 0 -0.19 61 61
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.1 0.33 -10000 0 -0.82 79 79
mol:DAG -0.067 0.15 0.13 1 -0.39 86 87
RAP1A/GDP 0.001 0.027 -10000 0 -0.092 3 3
PLCG1 0.01 0.025 -10000 0 -0.58 1 1
CD247 -0.019 0.13 -10000 0 -0.56 31 31
cytotoxic T cell degranulation -0.091 0.3 -10000 0 -0.94 50 50
RAP1A/GTP -0.006 0.015 -10000 0 -0.07 26 26
mol:PI-3-4-5-P3 -0.066 0.22 -10000 0 -0.54 87 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.081 0.24 0.22 64 -0.58 83 147
NRAS 0.001 0.077 -10000 0 -0.58 10 10
ZAP70 -0.037 0.16 -10000 0 -0.53 51 51
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
LAT/GRAP2/SLP76/VAV1 -0.11 0.22 -10000 0 -0.56 91 91
MALT1 0.006 0.055 -10000 0 -0.58 5 5
TRAF6 0.01 0.025 -10000 0 -0.58 1 1
CD8 heterodimer -0.071 0.2 -10000 0 -0.46 107 107
CARD11 -0.12 0.22 -10000 0 -0.49 148 148
PRKCB -0.061 0.13 -10000 0 -0.33 81 81
PRKCE -0.047 0.1 -10000 0 -0.28 71 71
PRKCQ -0.086 0.26 -10000 0 -0.64 88 88
LCP2 -0.014 0.12 -10000 0 -0.54 26 26
BCL10 0.007 0.049 -10000 0 -0.58 4 4
regulation of survival gene product expression -0.039 0.16 -10000 0 -0.38 84 84
IKK complex 0.006 0.056 -10000 0 -0.12 55 55
RAS family/GDP -0.007 0.016 -10000 0 -0.091 11 11
MAP3K14 -0.017 0.12 -10000 0 -0.28 66 66
PDPK1 -0.044 0.18 -10000 0 -0.42 84 84
TCR/CD3/MHC I/CD8/Fyn -0.1 0.33 -10000 0 -0.79 86 86
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.001 0.083 -9999 0 -0.54 13 13
CCL5 -0.037 0.15 -9999 0 -0.51 53 53
SDCBP 0 0.081 -9999 0 -0.58 11 11
FGFR/FGF2/Syndecan-1 -0.11 0.19 -9999 0 -0.51 66 66
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 -0.12 0.2 -9999 0 -0.48 92 92
Syndecan-1/Syntenin -0.11 0.18 -9999 0 -0.48 75 75
MAPK3 -0.083 0.17 -9999 0 -0.49 48 48
HGF/MET -0.019 0.12 -9999 0 -0.39 51 51
TGFB1/TGF beta receptor Type II -0.001 0.083 -9999 0 -0.54 13 13
BSG 0.01 0.025 -9999 0 -0.58 1 1
keratinocyte migration -0.12 0.2 -9999 0 -0.47 92 92
Syndecan-1/RANTES -0.12 0.2 -9999 0 -0.5 89 89
Syndecan-1/CD147 -0.092 0.18 -9999 0 -0.46 66 66
Syndecan-1/Syntenin/PIP2 -0.1 0.18 -9999 0 -0.46 75 75
LAMA5 -0.028 0.15 -9999 0 -0.57 39 39
positive regulation of cell-cell adhesion -0.1 0.17 -9999 0 -0.45 75 75
MMP7 -0.14 0.24 -9999 0 -0.51 160 160
HGF -0.036 0.16 -9999 0 -0.55 49 49
Syndecan-1/CASK -0.11 0.18 -9999 0 -0.49 66 66
Syndecan-1/HGF/MET -0.12 0.2 -9999 0 -0.5 88 88
regulation of cell adhesion -0.075 0.16 -9999 0 -0.47 48 48
HPSE -0.005 0.092 -9999 0 -0.51 18 18
positive regulation of cell migration -0.11 0.19 -9999 0 -0.51 66 66
SDC1 -0.11 0.19 -9999 0 -0.51 66 66
Syndecan-1/Collagen -0.11 0.19 -9999 0 -0.51 66 66
PPIB 0.011 0 -9999 0 -10000 0 0
MET 0.01 0.031 -9999 0 -0.52 2 2
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.058 0.18 -9999 0 -0.52 76 76
MAPK1 -0.083 0.17 -9999 0 -0.49 47 47
homophilic cell adhesion -0.11 0.18 -9999 0 -0.5 66 66
MMP1 -0.12 0.24 -9999 0 -0.53 144 144
BCR signaling pathway

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
JUN -0.062 0.16 -10000 0 -0.4 76 76
IKBKB -0.029 0.09 -10000 0 -0.25 35 35
AKT1 -0.05 0.11 0.21 1 -0.25 87 88
IKBKG -0.03 0.096 -10000 0 -0.26 41 41
CALM1 -0.04 0.15 0.25 18 -0.45 48 66
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
MAP3K1 -0.11 0.24 -10000 0 -0.57 92 92
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.16 0.25 19 -0.47 51 70
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 -0.024 0.099 0.2 15 -0.24 50 65
LYN 0.011 0 -10000 0 -10000 0 0
BLNK -0.009 0.11 -10000 0 -0.58 20 20
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.098 0.21 -10000 0 -0.46 139 139
CD22 -0.15 0.27 -10000 0 -0.68 96 96
CAMK2G -0.032 0.14 0.25 18 -0.43 44 62
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D -0.016 0.12 -10000 0 -0.58 26 26
SHC/GRB2/SOS1 -0.076 0.14 -10000 0 -0.46 38 38
GO:0007205 -0.05 0.17 0.25 19 -0.48 51 70
SYK 0.011 0.019 -10000 0 -0.45 1 1
ELK1 -0.042 0.16 0.24 17 -0.46 48 65
NFATC1 -0.099 0.21 -10000 0 -0.49 89 89
B-cell antigen/BCR complex -0.098 0.21 -10000 0 -0.46 139 139
PAG1/CSK 0.011 0.049 -10000 0 -0.4 8 8
NFKBIB -0.002 0.032 0.084 11 -0.12 2 13
HRAS -0.038 0.15 0.23 18 -0.41 53 71
NFKBIA -0.001 0.032 0.084 11 -0.12 2 13
NF-kappa-B/RelA/I kappa B beta 0.005 0.027 0.085 11 -0.17 1 12
RasGAP/Csk -0.1 0.22 -10000 0 -0.43 135 135
mol:GDP -0.045 0.16 0.26 18 -0.45 50 68
PTEN 0.005 0.06 -10000 0 -0.58 6 6
CD79B -0.026 0.14 -10000 0 -0.51 41 41
NF-kappa-B/RelA/I kappa B alpha 0.005 0.027 0.085 11 -0.17 1 12
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.22 -10000 0 -0.52 96 96
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
mol:IP3 -0.05 0.17 0.26 19 -0.48 51 70
CSK 0.01 0.025 -10000 0 -0.58 1 1
FOS -0.052 0.16 0.24 16 -0.42 64 80
CHUK -0.031 0.099 -10000 0 -0.29 30 30
IBTK 0.001 0.078 -10000 0 -0.58 10 10
CARD11/BCL10/MALT1/TAK1 -0.1 0.16 -10000 0 -0.46 72 72
PTPN6 -0.12 0.26 -10000 0 -0.64 93 93
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 -0.002 0.036 -10000 0 -0.1 33 33
VAV2 -0.15 0.28 -10000 0 -0.65 107 107
ubiquitin-dependent protein catabolic process 0.002 0.032 0.086 11 -0.11 2 13
BTK -0.05 0.26 0.36 23 -1.1 31 54
CD19 -0.16 0.27 -10000 0 -0.63 111 111
MAP4K1 -0.043 0.17 -10000 0 -0.55 56 56
CD72 -0.007 0.095 -10000 0 -0.5 20 20
PAG1 0.005 0.061 -10000 0 -0.55 7 7
MAPK14 -0.087 0.2 -10000 0 -0.48 88 88
SH3BP5 0.004 0.065 -10000 0 -0.58 7 7
PIK3AP1 -0.053 0.17 0.3 2 -0.48 56 58
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.076 0.22 -10000 0 -0.52 90 90
RAF1 -0.03 0.14 0.22 18 -0.42 38 56
RasGAP/p62DOK/SHIP -0.13 0.2 -10000 0 -0.59 64 64
CD79A -0.11 0.23 -10000 0 -0.54 132 132
re-entry into mitotic cell cycle -0.024 0.099 0.2 15 -0.25 50 65
RASA1 0.009 0.035 -10000 0 -0.58 2 2
MAPK3 -0.015 0.12 0.21 17 -0.4 24 41
MAPK1 -0.015 0.12 0.21 16 -0.4 24 40
CD72/SHP1 -0.12 0.26 -10000 0 -0.62 94 94
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 -0.088 0.2 -10000 0 -0.48 90 90
actin cytoskeleton organization -0.12 0.23 -10000 0 -0.54 105 105
NF-kappa-B/RelA 0.014 0.053 0.17 11 -0.22 2 13
Calcineurin -0.05 0.12 -10000 0 -0.45 29 29
PI3K -0.14 0.2 -10000 0 -0.52 106 106
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.054 0.17 0.31 2 -0.49 52 54
SOS1 0.01 0.025 -10000 0 -0.58 1 1
Bam32/HPK1 -0.15 0.33 -10000 0 -0.84 91 91
DAPP1 -0.17 0.36 -10000 0 -1.1 69 69
cytokine secretion -0.091 0.19 -10000 0 -0.45 89 89
mol:DAG -0.05 0.17 0.26 19 -0.48 51 70
PLCG2 -0.01 0.11 -10000 0 -0.54 22 22
MAP2K1 -0.023 0.13 0.22 17 -0.42 31 48
B-cell antigen/BCR complex/FcgammaRIIB -0.13 0.24 -10000 0 -0.42 198 198
mol:PI-3-4-5-P3 -0.1 0.14 0.28 1 -0.36 105 106
ETS1 -0.027 0.14 0.24 18 -0.45 33 51
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.064 0.18 -10000 0 -0.36 122 122
B-cell antigen/BCR complex/LYN -0.12 0.24 -10000 0 -0.52 110 110
MALT1 0.006 0.055 -10000 0 -0.58 5 5
TRAF6 0.01 0.025 -10000 0 -0.58 1 1
RAC1 -0.13 0.25 -10000 0 -0.58 104 104
B-cell antigen/BCR complex/LYN/SYK -0.14 0.25 -10000 0 -0.64 92 92
CARD11 -0.1 0.21 0.25 15 -0.5 91 106
FCGR2B -0.082 0.21 -10000 0 -0.53 99 99
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.007 0.049 -10000 0 -0.58 4 4
IKK complex -0.006 0.04 0.091 11 -0.11 11 22
PTPRC -0.041 0.16 -10000 0 -0.54 54 54
PDPK1 -0.052 0.11 0.19 1 -0.25 88 89
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.007 0.049 -10000 0 -0.58 4 4
POU2F2 0.004 0.028 -10000 0 -0.099 16 16
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.048 0.22 -10000 0 -0.63 48 48
IHH -0.039 0.17 -10000 0 -0.62 42 42
SHH Np/Cholesterol/GAS1 -0.077 0.16 -10000 0 -0.3 173 173
LRPAP1 0.01 0.025 -10000 0 -0.58 1 1
dorsoventral neural tube patterning 0.077 0.15 0.3 173 -10000 0 173
SMO/beta Arrestin2 -0.036 0.19 -10000 0 -0.63 33 33
SMO -0.044 0.2 -10000 0 -0.64 37 37
AKT1 -0.005 0.11 -10000 0 -0.49 12 12
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.034 0.14 -10000 0 -0.48 53 53
ADRBK1 0.009 0.037 -10000 0 -0.5 3 3
heart looping -0.043 0.2 -10000 0 -0.63 37 37
STIL -0.025 0.16 -10000 0 -0.59 27 27
DHH N/PTCH2 -0.04 0.15 -10000 0 -0.43 73 73
DHH N/PTCH1 -0.045 0.17 -10000 0 -0.53 29 29
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
DHH -0.03 0.14 -10000 0 -0.54 42 42
PTHLH -0.073 0.29 -10000 0 -0.91 48 48
determination of left/right symmetry -0.043 0.2 -10000 0 -0.63 37 37
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
skeletal system development -0.071 0.28 -10000 0 -0.9 48 48
IHH N/Hhip -0.082 0.2 -10000 0 -0.46 120 120
DHH N/Hhip -0.077 0.18 -10000 0 -0.41 125 125
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.043 0.2 -10000 0 -0.63 37 37
pancreas development -0.077 0.2 -10000 0 -0.54 92 92
HHAT 0.005 0.06 -10000 0 -0.58 6 6
PI3K 0.013 0.041 -10000 0 -0.42 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.23 -10000 0 -0.52 150 150
somite specification -0.043 0.2 -10000 0 -0.63 37 37
SHH Np/Cholesterol/PTCH1 -0.031 0.17 -10000 0 -0.62 28 28
SHH Np/Cholesterol/PTCH2 -0.022 0.11 -10000 0 -0.31 73 73
SHH Np/Cholesterol/Megalin -0.022 0.11 -10000 0 -0.29 72 72
SHH -0.008 0.1 -10000 0 -0.41 35 35
catabolic process -0.031 0.16 -10000 0 -0.43 51 51
SMO/Vitamin D3 -0.038 0.19 -10000 0 -0.64 36 36
SHH Np/Cholesterol/Hhip -0.05 0.15 -10000 0 -0.32 117 117
LRP2 -0.028 0.12 -10000 0 -0.46 42 42
receptor-mediated endocytosis -0.042 0.19 -10000 0 -0.61 37 37
SHH Np/Cholesterol/BOC -0.025 0.11 -10000 0 -0.29 83 83
SHH Np/Cholesterol/CDO -0.007 0.096 -10000 0 -0.33 44 44
mesenchymal cell differentiation 0.05 0.14 0.32 117 -10000 0 117
mol:Vitamin D3 -0.029 0.17 -10000 0 -0.62 28 28
IHH N/PTCH2 -0.043 0.16 -10000 0 -0.43 75 75
CDON -0.001 0.079 -10000 0 -0.51 13 13
IHH N/PTCH1 -0.031 0.16 -10000 0 -0.44 51 51
Megalin/LRPAP1 -0.012 0.087 -10000 0 -0.32 43 43
PTCH2 -0.027 0.14 -10000 0 -0.54 40 40
SHH Np/Cholesterol -0.007 0.08 -10000 0 -0.32 35 35
PTCH1 -0.031 0.16 -10000 0 -0.44 51 51
HHIP -0.077 0.2 -10000 0 -0.54 92 92
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.015 0.024 -9999 0 -0.32 3 3
VLDLR -0.042 0.16 -9999 0 -0.54 55 55
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.01 0.025 -9999 0 -0.58 1 1
FYN 0.005 0.061 -9999 0 -0.55 7 7
ITGA3 0.008 0.044 -9999 0 -0.52 4 4
RELN/VLDLR/Fyn -0.077 0.17 -9999 0 -0.34 157 157
MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.068 -9999 0 -0.34 13 13
AKT1 -0.069 0.15 -9999 0 -0.32 92 92
MAP2K7 0.01 0.025 -9999 0 -0.58 1 1
RAPGEF1 0.01 0.025 -9999 0 -0.58 1 1
DAB1 -0.081 0.2 -9999 0 -0.51 99 99
RELN/LRP8/DAB1 -0.089 0.17 -9999 0 -0.31 187 187
LRPAP1/LRP8 0.014 0.036 -9999 0 -0.42 4 4
RELN/LRP8/DAB1/Fyn -0.081 0.16 -9999 0 -0.36 108 108
DAB1/alpha3/beta1 Integrin -0.11 0.16 -9999 0 -0.5 47 47
long-term memory -0.11 0.19 -9999 0 -0.4 114 114
DAB1/LIS1 -0.11 0.16 -9999 0 -0.51 45 45
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.5 46 46
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
DAB1/NCK2 -0.11 0.16 -9999 0 -0.52 46 46
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.02 0.11 -9999 0 -0.47 33 33
CDK5R1 0.009 0.034 -9999 0 -0.46 3 3
RELN -0.091 0.21 -9999 0 -0.52 110 110
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
RELN/LRP8/Fyn -0.047 0.14 -9999 0 -0.31 119 119
GRIN2A/RELN/LRP8/DAB1/Fyn -0.091 0.18 -9999 0 -0.37 124 124
MAPK8 0.01 0.025 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1 -0.12 0.19 -9999 0 -0.34 219 219
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.11 0.19 -9999 0 -0.38 148 148
RELN/LRP8 -0.043 0.13 -9999 0 -0.31 114 114
GRIN2B/RELN/LRP8/DAB1/Fyn -0.1 0.19 -9999 0 -0.37 143 143
PI3K 0.013 0.041 -9999 0 -0.42 5 5
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.032 -9999 0 -0.37 4 4
RAP1A -0.074 0.16 -9999 0 -0.46 46 46
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 -0.01 0.1 -9999 0 -0.52 23 23
CRLK/C3G 0.016 0.018 -9999 0 -0.42 1 1
GRIN2B -0.041 0.16 -9999 0 -0.56 52 52
NCK2 0.01 0.025 -9999 0 -0.58 1 1
neuron differentiation -0.036 0.12 -9999 0 -0.38 26 26
neuron adhesion -0.062 0.16 -9999 0 -0.44 47 47
LRP8 0.008 0.043 -9999 0 -0.58 3 3
GSK3B -0.061 0.14 -9999 0 -0.44 35 35
RELN/VLDLR/DAB1/Fyn -0.11 0.18 -9999 0 -0.38 137 137
MAP3K11 0.01 0.025 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1/P13K -0.079 0.15 -9999 0 -0.32 136 136
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT -0.062 0.18 -9999 0 -0.46 96 96
neuron migration -0.064 0.16 -9999 0 -0.46 38 38
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.036 0.12 -9999 0 -0.38 26 26
RELN/VLDLR -0.061 0.16 -9999 0 -0.36 91 91
Endothelins

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
AKT1 -0.031 0.22 0.27 34 -0.6 49 83
PTK2B 0.009 0.035 -10000 0 -0.58 2 2
mol:Ca2+ -0.02 0.24 -10000 0 -0.87 33 33
EDN1 -0.022 0.17 0.22 20 -0.44 54 74
EDN3 -0.098 0.22 -10000 0 -0.55 111 111
EDN2 -0.064 0.19 -10000 0 -0.52 80 80
HRAS/GDP -0.042 0.18 -10000 0 -0.49 53 53
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.021 0.16 -10000 0 -0.45 45 45
ADCY4 -0.046 0.2 -10000 0 -0.52 56 56
ADCY5 -0.1 0.23 -10000 0 -0.52 88 88
ADCY6 -0.042 0.19 -10000 0 -0.5 56 56
ADCY7 -0.044 0.19 -10000 0 -0.51 55 55
ADCY1 -0.069 0.21 -10000 0 -0.52 68 68
ADCY2 -0.068 0.23 -10000 0 -0.58 66 66
ADCY3 -0.042 0.19 -10000 0 -0.5 55 55
ADCY8 -0.055 0.19 -10000 0 -0.52 55 55
ADCY9 -0.044 0.19 -10000 0 -0.52 52 52
arachidonic acid secretion -0.065 0.2 -10000 0 -0.54 51 51
ETB receptor/Endothelin-1/Gq/GTP -0.011 0.14 -10000 0 -0.45 31 31
GNAO1 -0.044 0.16 -10000 0 -0.49 63 63
HRAS 0.008 0.042 -10000 0 -0.49 4 4
ETA receptor/Endothelin-1/G12/GTP -0.027 0.23 0.3 95 -0.58 45 140
ETA receptor/Endothelin-1/Gs/GTP -0.043 0.23 0.28 92 -0.53 56 148
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.049 0.27 -10000 0 -0.73 58 58
EDNRB -0.009 0.1 -10000 0 -0.57 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.063 0.28 -10000 0 -0.67 76 76
CYSLTR1 -0.063 0.29 -10000 0 -0.7 73 73
SLC9A1 -0.023 0.12 0.19 47 -0.31 44 91
mol:GDP -0.05 0.2 -10000 0 -0.51 58 58
SLC9A3 -0.15 0.31 -10000 0 -0.62 144 144
RAF1 -0.047 0.18 -10000 0 -0.5 45 45
JUN -0.006 0.2 -10000 0 -0.75 24 24
JAK2 -0.043 0.24 -10000 0 -0.59 59 59
mol:IP3 -0.023 0.17 -10000 0 -0.47 41 41
ETA receptor/Endothelin-1 -0.041 0.28 0.35 98 -0.64 56 154
PLCB1 -0.033 0.15 -10000 0 -0.56 44 44
PLCB2 0.004 0.063 -10000 0 -0.52 8 8
ETA receptor/Endothelin-3 -0.095 0.21 -10000 0 -0.44 128 128
FOS -0.053 0.24 -10000 0 -0.87 31 31
Gai/GDP -0.024 0.16 -10000 0 -0.83 17 17
CRK 0.011 0.02 -10000 0 -0.46 1 1
mol:Ca ++ -0.049 0.25 -10000 0 -0.64 62 62
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
PRKCB1 -0.022 0.16 -10000 0 -0.46 40 40
GNAQ 0.006 0.061 -10000 0 -0.58 6 6
GNAZ -0.012 0.11 -10000 0 -0.54 24 24
GNAL -0.021 0.13 -10000 0 -0.5 36 36
Gs family/GDP -0.089 0.16 -10000 0 -0.46 67 67
ETA receptor/Endothelin-1/Gq/GTP -0.013 0.18 -10000 0 -0.5 39 39
MAPK14 -0.012 0.13 -10000 0 -0.46 26 26
TRPC6 -0.025 0.26 -10000 0 -0.94 33 33
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.088 -10000 0 -0.55 14 14
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.019 0.14 -10000 0 -0.42 37 37
ETB receptor/Endothelin-2 -0.052 0.15 -10000 0 -0.38 98 98
ETB receptor/Endothelin-3 -0.077 0.18 -10000 0 -0.41 127 127
ETB receptor/Endothelin-1 -0.019 0.15 -10000 0 -0.39 60 60
MAPK3 -0.052 0.22 -10000 0 -0.71 38 38
MAPK1 -0.052 0.22 -10000 0 -0.7 39 39
Rac1/GDP -0.04 0.18 -10000 0 -0.48 54 54
cAMP biosynthetic process -0.071 0.21 -10000 0 -0.52 68 68
MAPK8 -0.016 0.22 -10000 0 -0.67 39 39
SRC 0.01 0.025 -10000 0 -0.58 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.018 0.12 -10000 0 -0.41 27 27
p130Cas/CRK/Src/PYK2 -0.05 0.21 -10000 0 -0.6 45 45
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.04 0.18 -10000 0 -0.49 48 48
COL1A2 -0.055 0.3 -10000 0 -0.8 60 60
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.07 0.18 -10000 0 -0.41 103 103
mol:DAG -0.023 0.17 -10000 0 -0.47 41 41
MAP2K2 -0.046 0.19 -10000 0 -0.55 43 43
MAP2K1 -0.046 0.19 -10000 0 -0.55 44 44
EDNRA -0.019 0.18 -10000 0 -0.51 46 46
positive regulation of muscle contraction -0.021 0.2 -10000 0 -0.54 45 45
Gq family/GDP -0.079 0.17 -10000 0 -0.56 43 43
HRAS/GTP -0.05 0.18 -10000 0 -0.47 56 56
PRKCH -0.02 0.16 -10000 0 -0.47 42 42
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.47 36 36
PRKCB -0.041 0.2 -10000 0 -0.5 61 61
PRKCE -0.016 0.16 -10000 0 -0.48 33 33
PRKCD -0.017 0.16 -10000 0 -0.47 35 35
PRKCG -0.093 0.2 -10000 0 -0.47 70 70
regulation of vascular smooth muscle contraction -0.064 0.27 -10000 0 -1 31 31
PRKCQ -0.045 0.19 -10000 0 -0.5 50 50
PLA2G4A -0.072 0.21 -10000 0 -0.59 51 51
GNA14 -0.007 0.1 -10000 0 -0.56 19 19
GNA15 -0.008 0.1 -10000 0 -0.54 21 21
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 0.007 0.051 -10000 0 -0.53 5 5
Rac1/GTP -0.027 0.23 0.3 96 -0.57 46 142
MMP1 -0.15 0.36 0.34 1 -0.75 131 132
HIF-1-alpha transcription factor network

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
PKM2 -0.23 0.46 -9999 0 -1.1 65 65
HDAC7 0.011 0.025 -9999 0 -0.58 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.33 -9999 0 -0.9 49 49
SMAD4 0.006 0.06 -9999 0 -0.58 6 6
ID2 -0.24 0.46 -9999 0 -1.1 64 64
AP1 -0.017 0.11 -9999 0 -0.38 48 48
ABCG2 -0.26 0.49 -9999 0 -1.1 81 81
HIF1A -0.031 0.11 -9999 0 -0.68 9 9
TFF3 -0.26 0.49 -9999 0 -1.2 78 78
GATA2 -0.014 0.12 -9999 0 -0.55 26 26
AKT1 -0.024 0.087 -9999 0 -0.72 1 1
response to hypoxia -0.039 0.085 -9999 0 -0.25 5 5
MCL1 -0.23 0.46 -9999 0 -1.1 64 64
NDRG1 -0.24 0.46 -9999 0 -1.1 67 67
SERPINE1 -0.25 0.48 -9999 0 -1.2 75 75
FECH -0.23 0.46 -9999 0 -1.1 66 66
FURIN -0.24 0.46 -9999 0 -1.1 67 67
NCOA2 0.004 0.068 -9999 0 -0.56 8 8
EP300 -0.016 0.12 -9999 0 -0.37 17 17
HMOX1 -0.24 0.47 -9999 0 -1.2 64 64
BHLHE40 -0.24 0.46 -9999 0 -1.1 66 66
BHLHE41 -0.25 0.48 -9999 0 -1.2 71 71
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.039 0.11 -9999 0 -0.51 13 13
ENG -0.006 0.12 -9999 0 -0.52 11 11
JUN 0.006 0.053 -9999 0 -0.56 5 5
RORA -0.24 0.48 -9999 0 -1.2 72 72
ABCB1 -0.23 0.41 -9999 0 -1.1 95 95
TFRC -0.24 0.47 -9999 0 -1.2 64 64
CXCR4 -0.25 0.48 -9999 0 -1.2 75 75
TF -0.29 0.5 -9999 0 -1.1 88 88
CITED2 -0.24 0.46 -9999 0 -1.2 63 63
HIF1A/ARNT -0.3 0.51 -9999 0 -1.3 76 76
LDHA -0.037 0.078 -9999 0 -1.1 2 2
ETS1 -0.24 0.47 -9999 0 -1.2 64 64
PGK1 -0.23 0.46 -9999 0 -1.1 64 64
NOS2 -0.29 0.5 -9999 0 -1.2 88 88
ITGB2 -0.25 0.48 -9999 0 -1.2 75 75
ALDOA -0.23 0.46 -9999 0 -1.1 69 69
Cbp/p300/CITED2 -0.22 0.47 -9999 0 -1.2 62 62
FOS -0.03 0.14 -9999 0 -0.53 44 44
HK2 -0.24 0.46 -9999 0 -1.1 65 65
SP1 0.003 0.044 -9999 0 -0.58 1 1
GCK -0.052 0.28 -9999 0 -1.3 19 19
HK1 -0.23 0.46 -9999 0 -1.1 64 64
NPM1 -0.24 0.47 -9999 0 -1.2 65 65
EGLN1 -0.23 0.46 -9999 0 -1.1 64 64
CREB1 0.016 0.035 -9999 0 -0.58 2 2
PGM1 -0.24 0.46 -9999 0 -1.1 64 64
SMAD3 0.005 0.063 -9999 0 -0.56 7 7
EDN1 -0.061 0.27 -9999 0 -1.1 24 24
IGFBP1 -0.29 0.5 -9999 0 -1.1 96 96
VEGFA -0.12 0.34 -9999 0 -0.85 28 28
HIF1A/JAB1 -0.026 0.07 -9999 0 -0.49 10 10
CP -0.3 0.51 -9999 0 -1.2 93 93
CXCL12 -0.24 0.48 -9999 0 -1.1 74 74
COPS5 0.011 0.02 -9999 0 -0.46 1 1
SMAD3/SMAD4 0.009 0.064 -9999 0 -0.41 13 13
BNIP3 -0.26 0.49 -9999 0 -1.1 80 80
EGLN3 -0.24 0.47 -9999 0 -1.2 67 67
CA9 -0.32 0.52 -9999 0 -1.1 118 118
TERT -0.26 0.48 -9999 0 -1.1 80 80
ENO1 -0.23 0.46 -9999 0 -1.1 66 66
PFKL -0.24 0.47 -9999 0 -1.2 64 64
NCOA1 0.01 0.025 -9999 0 -0.58 1 1
ADM -0.24 0.47 -9999 0 -1.1 68 68
ARNT -0.022 0.078 -9999 0 -0.64 1 1
HNF4A 0.004 0.067 -9999 0 -0.58 7 7
ADFP -0.24 0.46 -9999 0 -1.1 71 71
SLC2A1 -0.12 0.34 -9999 0 -0.88 31 31
LEP -0.25 0.47 -9999 0 -1.2 68 68
HIF1A/ARNT/Cbp/p300 -0.21 0.34 -9999 0 -0.94 46 46
EPO -0.099 0.3 -9999 0 -0.98 13 13
CREBBP -0.013 0.12 -9999 0 -0.36 14 14
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.33 -9999 0 -0.94 42 42
PFKFB3 -0.23 0.46 -9999 0 -1.1 64 64
NT5E -0.25 0.48 -9999 0 -1.2 69 69
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.031 -10000 0 -0.52 2 2
LAT2 -0.061 0.16 -10000 0 -0.4 77 77
AP1 -0.1 0.19 -10000 0 -0.57 67 67
mol:PIP3 -0.079 0.21 -10000 0 -0.57 65 65
IKBKB -0.033 0.13 0.15 12 -0.31 67 79
AKT1 -0.05 0.16 -10000 0 -0.45 42 42
IKBKG -0.033 0.13 0.15 12 -0.31 68 80
MS4A2 -0.079 0.2 -10000 0 -0.54 94 94
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
MAP3K1 -0.05 0.18 -10000 0 -0.49 60 60
mol:Ca2+ -0.055 0.16 -10000 0 -0.41 65 65
LYN 0.009 0.006 -10000 0 -10000 0 0
CBLB -0.058 0.16 -10000 0 -0.39 76 76
SHC1 0.011 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.01 0.056 -10000 0 -0.25 25 25
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.015 0.12 -10000 0 -0.58 26 26
PLD2 -0.073 0.17 -10000 0 -0.37 99 99
PTPN13 -0.091 0.19 -10000 0 -0.56 51 51
PTPN11 0.003 0.057 -10000 0 -0.6 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.025 0.13 -10000 0 -0.36 38 38
SYK 0.008 0.02 -10000 0 -0.45 1 1
GRB2 0.011 0.001 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.2 -10000 0 -0.58 67 67
LAT -0.067 0.17 -10000 0 -0.4 82 82
PAK2 -0.06 0.19 -10000 0 -0.53 63 63
NFATC2 -0.081 0.18 -10000 0 -0.65 45 45
HRAS -0.072 0.21 -10000 0 -0.57 66 66
GAB2 0.009 0.035 -10000 0 -0.58 2 2
PLA2G1B 0.029 0.026 -10000 0 -10000 0 0
Fc epsilon R1 -0.12 0.19 -10000 0 -0.38 175 175
Antigen/IgE/Fc epsilon R1 -0.1 0.18 -10000 0 -0.35 175 175
mol:GDP -0.083 0.23 -10000 0 -0.62 68 68
JUN 0.006 0.053 -10000 0 -0.56 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
FOS -0.03 0.14 -10000 0 -0.53 44 44
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.065 0.16 -10000 0 -0.38 87 87
CHUK -0.034 0.13 0.15 12 -0.31 67 79
KLRG1 -0.062 0.15 -10000 0 -0.39 67 67
VAV1 -0.074 0.19 -10000 0 -0.43 93 93
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.056 0.15 -10000 0 -0.43 56 56
negative regulation of mast cell degranulation -0.065 0.16 -10000 0 -0.41 67 67
BTK -0.086 0.24 -10000 0 -0.68 63 63
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.24 -10000 0 -0.48 119 119
GAB2/PI3K/SHP2 -0.088 0.15 -10000 0 -0.5 42 42
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.058 0.16 -10000 0 -0.33 102 102
RAF1 0.023 0.025 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.24 -10000 0 -0.47 154 154
FCER1G -0.017 0.12 -10000 0 -0.53 31 31
FCER1A -0.077 0.2 -10000 0 -0.55 88 88
Antigen/IgE/Fc epsilon R1/Fyn -0.084 0.18 -10000 0 -0.37 127 127
MAPK3 0.029 0.025 -10000 0 -10000 0 0
MAPK1 0.029 0.026 -10000 0 -10000 0 0
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 -0.005 0.073 -10000 0 -0.5 5 5
DUSP1 -0.008 0.095 -10000 0 -0.47 23 23
NF-kappa-B/RelA -0.038 0.062 -10000 0 -0.22 22 22
actin cytoskeleton reorganization -0.057 0.17 -10000 0 -0.56 36 36
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.094 0.18 -10000 0 -0.53 63 63
FER -0.061 0.16 -10000 0 -0.39 78 78
RELA 0.011 0 -10000 0 -10000 0 0
ITK -0.049 0.12 -10000 0 -0.45 43 43
SOS1 0.01 0.025 -10000 0 -0.58 1 1
PLCG1 -0.08 0.23 -10000 0 -0.62 68 68
cytokine secretion -0.027 0.045 -10000 0 -10000 0 0
SPHK1 -0.076 0.18 -10000 0 -0.41 94 94
PTK2 -0.06 0.18 -10000 0 -0.6 34 34
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.2 -10000 0 -0.53 86 86
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.071 0.2 -10000 0 -0.54 65 65
MAP2K2 0.026 0.026 -10000 0 -10000 0 0
MAP2K1 0.026 0.03 -10000 0 -10000 0 0
MAP2K7 0.01 0.025 -10000 0 -0.58 1 1
KLRG1/SHP2 -0.058 0.14 -10000 0 -0.39 60 60
MAP2K4 0.007 0.08 -10000 0 -0.94 4 4
Fc epsilon R1/FcgammaRIIB -0.14 0.25 -10000 0 -0.49 152 152
mol:Choline -0.072 0.17 -10000 0 -0.37 99 99
SHC/Grb2/SOS1 -0.044 0.15 -10000 0 -0.47 38 38
FYN 0.005 0.061 -10000 0 -0.55 7 7
DOK1 0.011 0 -10000 0 -10000 0 0
PXN -0.05 0.16 -10000 0 -0.55 34 34
HCLS1 -0.062 0.17 -10000 0 -0.4 82 82
PRKCB -0.058 0.18 -10000 0 -0.43 74 74
FCGR2B -0.082 0.21 -10000 0 -0.53 99 99
IGHE -0.003 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.066 0.16 -10000 0 -0.42 67 67
LCP2 -0.014 0.12 -10000 0 -0.54 26 26
PLA2G4A -0.13 0.21 -10000 0 -0.42 147 147
RASA1 0.009 0.035 -10000 0 -0.58 2 2
mol:Phosphatidic acid -0.072 0.17 -10000 0 -0.37 99 99
IKK complex -0.014 0.1 0.15 12 -0.24 53 65
WIPF1 -0.001 0.083 -10000 0 -0.54 13 13
TCGA08_retinoblastoma

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
CDKN2B -0.012 0.1 -10000 0 -0.51 24 24
CDKN2C 0.018 0.017 -10000 0 -10000 0 0
CDKN2A -0.069 0.19 -10000 0 -0.5 90 90
CCND2 0.019 0.072 0.21 46 -0.13 25 71
RB1 -0.016 0.077 -10000 0 -0.22 51 51
CDK4 0.027 0.075 0.23 46 -10000 0 46
CDK6 0.026 0.076 0.23 46 -10000 0 46
G1/S progression 0.016 0.077 0.22 51 -10000 0 51
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.2 -9999 0 -0.38 181 181
SMAD6-7/SMURF1 0.019 0.043 -9999 0 -0.38 6 6
NOG -0.025 0.12 -9999 0 -0.47 40 40
SMAD9 -0.062 0.16 -9999 0 -0.53 52 52
SMAD4 0.005 0.06 -9999 0 -0.58 6 6
SMAD5 -0.044 0.14 -9999 0 -0.46 28 28
BMP7/USAG1 -0.16 0.24 -9999 0 -0.44 226 226
SMAD5/SKI -0.036 0.13 -9999 0 -0.44 26 26
SMAD1 0.021 0.046 -9999 0 -0.47 3 3
BMP2 -0.001 0.081 -9999 0 -0.53 13 13
SMAD1/SMAD1/SMAD4 -0.007 0.046 -9999 0 -0.48 3 3
BMPR1A 0.01 0.025 -9999 0 -0.58 1 1
BMPR1B -0.094 0.21 -9999 0 -0.51 115 115
BMPR1A-1B/BAMBI -0.079 0.16 -9999 0 -0.32 169 169
AHSG -0.041 0.14 -9999 0 -0.46 60 60
CER1 -0.005 0.063 -9999 0 -0.46 11 11
BMP2-4/CER1 -0.009 0.094 -9999 0 -0.31 47 47
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.049 0.14 -9999 0 -0.42 44 44
BMP2-4 (homodimer) -0.009 0.1 -9999 0 -0.38 37 37
RGMB -0.012 0.1 -9999 0 -0.46 29 29
BMP6/BMPR2/BMPR1A-1B -0.045 0.14 -9999 0 -0.34 66 66
RGMA -0.071 0.2 -9999 0 -0.54 86 86
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.048 0.13 -9999 0 -0.39 41 41
BMP2-4/USAG1 -0.07 0.17 -9999 0 -0.35 144 144
SMAD6/SMURF1/SMAD5 -0.036 0.13 -9999 0 -0.44 26 26
SOSTDC1 -0.1 0.23 -9999 0 -0.56 116 116
BMP7/BMPR2/BMPR1A-1B -0.11 0.18 -9999 0 -0.38 144 144
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.01 0.1 -9999 0 -0.51 23 23
HFE2 0 0.033 -9999 0 -0.46 3 3
ZFYVE16 -0.006 0.1 -9999 0 -0.58 17 17
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.018 0.12 -9999 0 -0.34 65 65
SMAD5/SMAD5/SMAD4 -0.04 0.13 -9999 0 -0.44 27 27
MAPK1 0.01 0.025 -9999 0 -0.58 1 1
TAK1/TAB family -0.056 0.097 -9999 0 -0.38 26 26
BMP7 (homodimer) -0.13 0.24 -9999 0 -0.54 144 144
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA -0.036 0.12 -9999 0 -0.34 82 82
SMAD1/SKI 0.026 0.044 -9999 0 -0.44 3 3
SMAD6 0.007 0.051 -9999 0 -0.53 5 5
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.031 0.12 -9999 0 -0.3 93 93
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.08 0.21 -9999 0 -0.54 96 96
BMPR2 (homodimer) 0.006 0.055 -9999 0 -0.58 5 5
GADD34/PP1CA 0.012 0.064 -9999 0 -0.35 17 17
BMPR1A-1B (homodimer) -0.06 0.15 -9999 0 -0.36 116 116
CHRDL1 -0.16 0.25 -9999 0 -0.52 182 182
ENDOFIN/SMAD1 0.017 0.073 -9999 0 -0.62 3 3
SMAD6-7/SMURF1/SMAD1 0.032 0.056 -9999 0 -0.54 3 3
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.049 0.17 -9999 0 -0.52 65 65
SMURF2 0.007 0.051 -9999 0 -0.53 5 5
BMP2-4/CHRDL1 -0.1 0.18 -9999 0 -0.33 207 207
BMP2-4/GREM1 -0.056 0.16 -9999 0 -0.33 127 127
SMAD7 0.009 0.035 -9999 0 -0.58 2 2
SMAD8A/SMAD8A/SMAD4 -0.056 0.16 -9999 0 -0.48 57 57
SMAD1/SMAD6 0.026 0.044 -9999 0 -0.44 3 3
TAK1/SMAD6 0.017 0 -9999 0 -10000 0 0
BMP7 -0.13 0.24 -9999 0 -0.54 144 144
BMP6 -0.01 0.1 -9999 0 -0.52 23 23
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.039 0.12 -9999 0 -0.36 42 42
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.024 0.055 -9999 0 -0.48 4 4
SMAD7/SMURF1 0.015 0.026 -9999 0 -0.42 2 2
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.01 0.025 -9999 0 -0.58 1 1
CTDSP1 0.01 0.025 -9999 0 -0.58 1 1
PPP1R15A 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.081 0.19 -9999 0 -0.5 67 67
CHRD -0.021 0.13 -9999 0 -0.55 33 33
BMPR2 0.006 0.055 -9999 0 -0.58 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.055 0.14 -9999 0 -0.43 41 41
BMP4 -0.012 0.11 -9999 0 -0.5 26 26
FST -0.052 0.18 -9999 0 -0.52 68 68
BMP2-4/NOG -0.021 0.11 -9999 0 -0.3 74 74
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.099 0.18 -9999 0 -0.35 144 144
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.038 0.17 -10000 0 -0.61 45 45
NFATC2 -0.093 0.26 -10000 0 -0.67 65 65
NFATC3 -0.02 0.077 -10000 0 -0.29 2 2
CD40LG -0.28 0.42 -10000 0 -1 101 101
ITCH 0.027 0.086 -10000 0 -0.8 5 5
CBLB 0.028 0.082 -10000 0 -0.84 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.45 -10000 0 -1.2 89 89
JUNB 0.007 0.051 -10000 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.06 -10000 0 -0.37 14 14
T cell anergy 0.004 0.1 -10000 0 -0.55 14 14
TLE4 -0.058 0.21 -10000 0 -0.7 36 36
Jun/NFAT1-c-4/p21SNFT -0.18 0.37 -10000 0 -1 58 58
AP-1/NFAT1-c-4 -0.3 0.48 -10000 0 -1.1 98 98
IKZF1 -0.075 0.26 -10000 0 -0.75 53 53
T-helper 2 cell differentiation -0.13 0.26 -10000 0 -0.84 46 46
AP-1/NFAT1 -0.097 0.21 -10000 0 -0.56 62 62
CALM1 0.018 0.034 -10000 0 -0.3 3 3
EGR2 -0.14 0.36 -10000 0 -1.2 39 39
EGR3 -0.15 0.38 -10000 0 -1.3 41 41
NFAT1/FOXP3 -0.094 0.27 -10000 0 -0.76 61 61
EGR1 -0.012 0.11 -10000 0 -0.5 27 27
JUN -0.009 0.06 -10000 0 -0.58 5 5
EGR4 -0.055 0.17 -10000 0 -0.51 71 71
mol:Ca2+ 0.007 0.035 -10000 0 -0.32 3 3
GBP3 -0.12 0.31 -10000 0 -0.8 85 85
FOSL1 -0.024 0.13 -10000 0 -0.51 39 39
NFAT1-c-4/MAF/IRF4 -0.19 0.38 -10000 0 -1.1 62 62
DGKA -0.053 0.2 -10000 0 -0.64 36 36
CREM 0.01 0.019 -10000 0 -0.46 1 1
NFAT1-c-4/PPARG -0.15 0.35 -10000 0 -1.1 48 48
CTLA4 -0.096 0.29 -10000 0 -0.83 61 61
NFAT1-c-4 (dimer)/EGR1 -0.16 0.36 -10000 0 -1.1 52 52
NFAT1-c-4 (dimer)/EGR4 -0.18 0.36 -10000 0 -1 59 59
FOS -0.046 0.15 -10000 0 -0.54 44 44
IFNG -0.23 0.4 -10000 0 -0.97 104 104
T cell activation -0.11 0.2 -10000 0 -0.71 21 21
MAF 0.001 0.075 -10000 0 -0.54 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.12 0.3 1 37 -10000 0 37
TNF -0.18 0.35 -10000 0 -0.96 65 65
FASLG -0.24 0.51 -10000 0 -1.4 73 73
TBX21 -0.059 0.18 -10000 0 -0.56 67 67
BATF3 -0.005 0.089 -10000 0 -0.5 18 18
PRKCQ -0.047 0.17 -10000 0 -0.58 54 54
PTPN1 -0.05 0.19 -10000 0 -0.64 30 30
NFAT1-c-4/ICER1 -0.15 0.35 -10000 0 -1 51 51
GATA3 -0.017 0.12 -10000 0 -0.52 31 31
T-helper 1 cell differentiation -0.21 0.4 -10000 0 -0.93 105 105
IL2RA -0.27 0.42 -10000 0 -1.1 93 93
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.19 -10000 0 -0.64 32 32
E2F1 0.014 0.037 -10000 0 -0.49 3 3
PPARG 0.004 0.065 -10000 0 -0.58 7 7
SLC3A2 -0.049 0.19 -10000 0 -0.63 30 30
IRF4 -0.079 0.2 -10000 0 -0.54 95 95
PTGS2 -0.3 0.44 -10000 0 -0.98 125 125
CSF2 -0.31 0.44 -10000 0 -0.98 128 128
JunB/Fra1/NFAT1-c-4 -0.16 0.34 -10000 0 -1 51 51
IL4 -0.14 0.27 -10000 0 -0.91 44 44
IL5 -0.26 0.4 -10000 0 -0.98 93 93
IL2 -0.11 0.21 -10000 0 -0.74 20 20
IL3 -0.064 0.1 -10000 0 -0.8 7 7
RNF128 0.024 0.093 -10000 0 -0.62 11 11
NFATC1 -0.12 0.3 -10000 0 -1 36 36
CDK4 0.083 0.18 0.66 14 -10000 0 14
PTPRK -0.05 0.19 -10000 0 -0.63 32 32
IL8 -0.31 0.45 -10000 0 -1 125 125
POU2F1 0.002 0.073 -10000 0 -0.54 10 10
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EPHB2 0 0.081 -10000 0 -0.55 12 12
EFNB1 0.006 0.066 -10000 0 -0.36 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.062 0.15 -10000 0 -0.48 32 32
Ephrin B2/EPHB1-2 -0.051 0.13 -10000 0 -0.32 54 54
neuron projection morphogenesis -0.083 0.13 -10000 0 -0.46 32 32
Ephrin B1/EPHB1-2/Tiam1 -0.071 0.16 -10000 0 -0.49 35 35
DNM1 -0.004 0.087 -10000 0 -0.5 17 17
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.077 0.23 -10000 0 -0.66 74 74
YES1 -0.12 0.3 -10000 0 -0.89 73 73
Ephrin B1/EPHB1-2/NCK2 -0.043 0.13 -10000 0 -0.44 14 14
PI3K -0.077 0.23 -10000 0 -0.65 77 77
mol:GDP -0.071 0.16 -10000 0 -0.49 35 35
ITGA2B -0.047 0.16 -10000 0 -0.5 64 64
endothelial cell proliferation 0.014 0.02 -10000 0 -0.31 2 2
FYN -0.12 0.3 -10000 0 -0.89 73 73
MAP3K7 -0.086 0.24 -10000 0 -0.7 73 73
FGR -0.12 0.3 -10000 0 -0.88 74 74
TIAM1 -0.043 0.16 -10000 0 -0.52 59 59
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.096 0.24 -10000 0 -0.62 82 82
LYN -0.12 0.3 -10000 0 -0.89 73 73
Ephrin B1/EPHB1-2/Src Family Kinases -0.11 0.28 -10000 0 -0.83 73 73
Ephrin B1/EPHB1-2 -0.1 0.25 -10000 0 -0.76 73 73
SRC -0.12 0.3 -10000 0 -0.88 73 73
ITGB3 -0.005 0.093 -10000 0 -0.54 17 17
EPHB1 -0.11 0.22 -10000 0 -0.49 135 135
EPHB4 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.02 -10000 0 -0.32 2 2
alphaIIb/beta3 Integrin -0.037 0.13 -10000 0 -0.37 80 80
BLK -0.14 0.31 -10000 0 -0.91 74 74
HCK -0.12 0.3 -10000 0 -0.89 74 74
regulation of stress fiber formation 0.044 0.13 0.43 14 -10000 0 14
MAPK8 -0.068 0.22 -10000 0 -0.62 75 75
Ephrin B1/EPHB1-2/RGS3 -0.043 0.13 -10000 0 -0.35 29 29
endothelial cell migration -0.07 0.21 -10000 0 -0.6 74 74
NCK2 0.01 0.025 -10000 0 -0.58 1 1
PTPN13 -0.089 0.24 -10000 0 -0.65 88 88
regulation of focal adhesion formation 0.044 0.13 0.43 14 -10000 0 14
chemotaxis 0.043 0.13 0.35 29 -10000 0 29
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
Rac1/GTP -0.084 0.14 -10000 0 -0.47 32 32
angiogenesis -0.1 0.25 -10000 0 -0.75 73 73
LCK -0.12 0.3 -10000 0 -0.91 73 73
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.057 0.16 0.4 97 -10000 0 97
KIRREL -0.029 0.14 -10000 0 -0.58 34 34
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.057 0.16 -10000 0 -0.4 97 97
PLCG1 0.01 0.025 -10000 0 -0.58 1 1
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.056 0.16 -10000 0 -0.38 84 84
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.022 0.11 -10000 0 -0.35 35 35
FYN -0.041 0.13 -10000 0 -0.34 62 62
mol:Ca2+ -0.039 0.13 -10000 0 -0.36 58 58
mol:DAG -0.039 0.13 -10000 0 -0.37 58 58
NPHS2 -0.021 0.091 -10000 0 -0.46 22 22
mol:IP3 -0.039 0.13 -10000 0 -0.37 58 58
regulation of endocytosis -0.031 0.12 -10000 0 -0.32 58 58
Nephrin/NEPH1/podocin/Cholesterol -0.046 0.13 -10000 0 -0.37 58 58
establishment of cell polarity -0.057 0.16 -10000 0 -0.4 97 97
Nephrin/NEPH1/podocin/NCK1-2 -0.029 0.12 -10000 0 -0.48 17 17
Nephrin/NEPH1/beta Arrestin2 -0.031 0.12 -10000 0 -0.33 58 58
NPHS1 -0.057 0.17 -10000 0 -0.51 70 70
Nephrin/NEPH1/podocin -0.04 0.13 -10000 0 -0.34 62 62
TJP1 0.01 0.025 -10000 0 -0.58 1 1
NCK1 0.009 0.035 -10000 0 -0.58 2 2
NCK2 0.01 0.025 -10000 0 -0.58 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.039 0.13 -10000 0 -0.37 58 58
CD2AP -0.018 0.13 -10000 0 -0.58 29 29
Nephrin/NEPH1/podocin/GRB2 -0.038 0.13 -10000 0 -0.36 58 58
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.049 0.15 -10000 0 -0.38 69 69
cytoskeleton organization -0.026 0.13 -10000 0 -0.4 39 39
Nephrin/NEPH1 -0.039 0.12 -10000 0 -0.28 97 97
Nephrin/NEPH1/ZO-1 -0.037 0.14 -10000 0 -0.38 58 58
TCGA08_p53

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
CDKN2A -0.05 0.14 -10000 0 -0.37 90 90
TP53 -0.047 0.11 0.21 2 -0.36 52 54
Senescence -0.047 0.11 0.21 2 -0.35 52 54
Apoptosis -0.047 0.11 0.21 2 -0.35 52 54
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.03 0.084 0.26 38 -0.34 4 42
MDM4 0.01 0.031 -10000 0 -0.52 2 2
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.019 0.084 -9999 0 -0.34 30 30
NFATC2 -0.034 0.11 -9999 0 -0.38 49 49
NFATC3 -0.001 0.032 -9999 0 -10000 0 0
CD40LG -0.18 0.32 -9999 0 -0.73 104 104
PTGS2 -0.2 0.33 -9999 0 -0.7 128 128
JUNB 0.007 0.051 -9999 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.009 0.015 -9999 0 -10000 0 0
CALM1 0.006 0.011 -9999 0 -10000 0 0
JUN 0.001 0.054 -9999 0 -0.56 5 5
mol:Ca2+ -0.009 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.007 -9999 0 -10000 0 0
FOSL1 -0.024 0.13 -9999 0 -0.51 39 39
CREM 0.01 0.019 -9999 0 -0.46 1 1
Jun/NFAT1-c-4/p21SNFT -0.098 0.2 -9999 0 -0.52 66 66
FOS -0.036 0.15 -9999 0 -0.54 44 44
IFNG -0.19 0.32 -9999 0 -0.7 127 127
AP-1/NFAT1-c-4 -0.19 0.35 -9999 0 -0.76 118 118
FASLG -0.18 0.32 -9999 0 -0.72 115 115
NFAT1-c-4/ICER1 -0.061 0.14 -9999 0 -0.41 53 53
IL2RA -0.18 0.32 -9999 0 -0.77 95 95
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.68 150 150
JunB/Fra1/NFAT1-c-4 -0.073 0.15 -9999 0 -0.4 69 69
IL4 -0.16 0.28 -9999 0 -0.68 88 88
IL2 -0.007 0.025 -9999 0 -0.36 2 2
IL3 -0.031 0.096 -9999 0 -0.85 7 7
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 -0.005 0.089 -9999 0 -0.5 18 18
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.002 0.073 -9999 0 -0.54 10 10
p75(NTR)-mediated signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.015 0.026 -9999 0 -0.42 2 2
Necdin/E2F1 0.008 0.057 -9999 0 -0.36 13 13
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.053 0.16 -9999 0 -0.49 27 27
NGF (dimer)/p75(NTR)/BEX1 -0.099 0.2 -9999 0 -0.45 109 109
NT-4/5 (dimer)/p75(NTR) -0.067 0.16 -9999 0 -0.37 118 118
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
AKT1 -0.04 0.14 -9999 0 -0.33 85 85
IKBKG 0.01 0.025 -9999 0 -0.58 1 1
BDNF -0.02 0.13 -9999 0 -0.52 34 34
MGDIs/NGR/p75(NTR)/LINGO1 -0.062 0.16 -9999 0 -0.41 61 61
FURIN 0.01 0.031 -9999 0 -0.52 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.052 0.15 -9999 0 -0.4 58 58
LINGO1 -0.024 0.12 -9999 0 -0.47 42 42
Sortilin/TRAF6/NRIF -0.008 0.051 -9999 0 -0.79 1 1
proBDNF (dimer) -0.02 0.13 -9999 0 -0.52 34 34
NTRK1 -0.039 0.16 -9999 0 -0.53 52 52
RTN4R -0.003 0.083 -9999 0 -0.48 17 17
neuron apoptosis -0.059 0.17 -9999 0 -0.58 24 24
IRAK1 0.01 0.031 -9999 0 -0.52 2 2
SHC1 -0.057 0.16 -9999 0 -0.35 123 123
ARHGDIA 0.008 0.043 -9999 0 -0.58 3 3
RhoA/GTP 0.008 0.018 -9999 0 -0.43 1 1
Gamma Secretase 0.031 0.033 -9999 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.049 0.15 -9999 0 -0.36 85 85
MAGEH1 0.003 0.068 -9999 0 -0.56 8 8
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.05 0.16 -9999 0 -0.37 84 84
Mammalian IAPs/DIABLO 0.006 0.1 -9999 0 -0.46 20 20
proNGF (dimer) -0.029 0.14 -9999 0 -0.52 43 43
MAGED1 0.011 0 -9999 0 -10000 0 0
APP 0.01 0.025 -9999 0 -0.58 1 1
NT-4/5 (dimer) -0.014 0.091 -9999 0 -0.46 23 23
ZNF274 0.001 0.077 -9999 0 -0.58 10 10
RhoA/GDP/RHOGDI -0.044 0.14 -9999 0 -0.34 83 83
NGF -0.029 0.14 -9999 0 -0.52 43 43
cell cycle arrest -0.048 0.14 -9999 0 -0.48 21 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.023 0.11 -9999 0 -0.28 30 30
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.049 0.14 -9999 0 -0.38 48 48
NCSTN 0.011 0 -9999 0 -10000 0 0
mol:GTP -0.077 0.18 -9999 0 -0.37 145 145
PSENEN 0.01 0.025 -9999 0 -0.58 1 1
mol:ceramide -0.046 0.14 -9999 0 -0.36 79 79
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.096 -9999 0 -0.44 6 6
p75(NTR)/beta APP -0.05 0.14 -9999 0 -0.36 101 101
BEX1 -0.06 0.18 -9999 0 -0.5 77 77
mol:GDP -0.065 0.16 -9999 0 -0.35 123 123
NGF (dimer) -0.1 0.18 -9999 0 -0.38 130 130
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.05 0.15 -9999 0 -0.38 62 62
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
RAC1/GTP -0.049 0.14 -9999 0 -0.3 123 123
MYD88 0.011 0 -9999 0 -10000 0 0
CHUK 0.007 0.049 -9999 0 -0.58 4 4
NGF (dimer)/p75(NTR)/PKA -0.077 0.18 -9999 0 -0.37 145 145
RHOB 0.008 0.04 -9999 0 -0.54 3 3
RHOA 0.01 0.025 -9999 0 -0.58 1 1
MAGE-G1/E2F1 0.015 0.027 -9999 0 -0.35 3 3
NT3 (dimer) -0.02 0.13 -9999 0 -0.53 33 33
TP53 -0.06 0.16 -9999 0 -0.55 19 19
PRDM4 -0.046 0.15 -9999 0 -0.36 79 79
BDNF (dimer) -0.18 0.22 -9999 0 -0.42 194 194
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
SORT1 0.01 0.025 -9999 0 -0.58 1 1
activation of caspase activity -0.055 0.15 -9999 0 -0.48 27 27
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.045 0.15 -9999 0 -0.36 80 80
RHOC 0.011 0 -9999 0 -10000 0 0
XIAP 0.01 0.025 -9999 0 -0.58 1 1
MAPK10 -0.041 0.16 -9999 0 -0.5 29 29
DIABLO 0.011 0 -9999 0 -10000 0 0
SMPD2 -0.046 0.15 -9999 0 -0.36 79 79
APH1B 0.006 0.055 -9999 0 -0.58 5 5
APH1A 0.011 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.058 0.16 -9999 0 -0.4 79 79
PSEN1 0.011 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -9999 0 -0.42 4 4
NT3 (dimer)/p75(NTR) -0.071 0.18 -9999 0 -0.39 123 123
MAPK8 -0.025 0.14 -9999 0 -0.51 15 15
MAPK9 -0.025 0.14 -9999 0 -0.51 15 15
APAF1 0.008 0.043 -9999 0 -0.58 3 3
NTF3 -0.02 0.13 -9999 0 -0.54 33 33
NTF4 -0.014 0.091 -9999 0 -0.46 23 23
NDN 0.002 0.07 -9999 0 -0.52 10 10
RAC1/GDP 0.008 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.073 0.13 -9999 0 -0.46 30 30
p75 CTF/Sortilin/TRAF6/NRIF 0.021 0.062 -9999 0 -0.37 12 12
RhoA-B-C/GTP -0.076 0.18 -9999 0 -0.37 145 145
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.14 -9999 0 -0.57 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.14 -9999 0 -0.36 59 59
PRKACB -0.021 0.13 -9999 0 -0.57 32 32
proBDNF (dimer)/p75 ECD -0.008 0.096 -9999 0 -0.38 36 36
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.016 0.12 -9999 0 -0.52 29 29
BIRC2 -0.002 0.088 -9999 0 -0.58 13 13
neuron projection morphogenesis -0.061 0.15 -9999 0 -0.37 78 78
BAD -0.026 0.14 -9999 0 -0.48 20 20
RIPK2 0.011 0 -9999 0 -10000 0 0
NGFR -0.079 0.2 -9999 0 -0.51 100 100
CYCS -0.047 0.15 -9999 0 -0.49 26 26
ADAM17 0.009 0.035 -9999 0 -0.58 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.045 0.15 -9999 0 -0.36 80 80
BCL2L11 -0.026 0.14 -9999 0 -0.48 20 20
BDNF (dimer)/p75(NTR) -0.071 0.17 -9999 0 -0.39 124 124
PI3K -0.047 0.15 -9999 0 -0.36 84 84
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.045 0.15 -9999 0 -0.36 79 79
NDNL2 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
PRKCI 0.008 0.043 -9999 0 -0.58 3 3
NGF (dimer)/p75(NTR) -0.076 0.18 -9999 0 -0.42 123 123
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.045 0.15 -9999 0 -0.36 79 79
TRAF6 0.01 0.025 -9999 0 -0.58 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCZ 0.01 0.031 -9999 0 -0.52 2 2
PLG -0.037 0.15 -9999 0 -0.58 41 41
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.055 0.16 -9999 0 -0.4 63 63
SQSTM1 0.011 0 -9999 0 -10000 0 0
NGFRAP1 -0.02 0.13 -9999 0 -0.58 30 30
CASP3 -0.022 0.14 -9999 0 -0.43 21 21
E2F1 0.009 0.037 -9999 0 -0.5 3 3
CASP9 0.01 0.025 -9999 0 -0.58 1 1
IKK complex -0.06 0.12 -9999 0 -0.51 18 18
NGF (dimer)/TRKA -0.048 0.16 -9999 0 -0.41 86 86
MMP7 -0.14 0.24 -9999 0 -0.51 160 160
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.042 0.15 -9999 0 -0.43 34 34
MMP3 -0.13 0.24 -9999 0 -0.53 147 147
APAF-1/Caspase 9 -0.066 0.14 -9999 0 -0.58 23 23
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.021 0.074 0.35 5 -10000 0 5
SMARCC2 0.012 0.006 -10000 0 -10000 0 0
SMARCC1 0.012 0.006 -10000 0 -10000 0 0
TBX21 -0.11 0.26 -10000 0 -0.67 85 85
SUMO2 0.01 0.026 -10000 0 -0.58 1 1
STAT1 (dimer) 0.012 0.055 -10000 0 -0.52 6 6
FKBP4 0.009 0.034 -10000 0 -0.46 3 3
FKBP5 0.008 0.04 -10000 0 -0.54 3 3
GR alpha/HSP90/FKBP51/HSP90 0.074 0.12 0.3 37 -0.44 7 44
PRL -0.064 0.14 -10000 0 -0.55 18 18
cortisol/GR alpha (dimer)/TIF2 0.18 0.23 0.52 115 -0.5 5 120
RELA -0.036 0.093 -10000 0 -0.31 16 16
FGG 0.12 0.2 0.48 58 -0.44 14 72
GR beta/TIF2 0.074 0.13 0.31 49 -0.46 12 61
IFNG -0.27 0.37 -10000 0 -0.93 99 99
apoptosis 0.004 0.16 0.47 19 -0.62 5 24
CREB1 0.009 0.042 -10000 0 -0.58 2 2
histone acetylation -0.028 0.12 0.34 3 -0.36 35 38
BGLAP -0.051 0.14 -10000 0 -0.7 7 7
GR/PKAc 0.056 0.13 0.29 31 -0.36 18 49
NF kappa B1 p50/RelA -0.067 0.18 -10000 0 -0.49 45 45
SMARCD1 0.011 0.026 -10000 0 -0.58 1 1
MDM2 0.073 0.086 0.25 54 -0.28 3 57
GATA3 -0.017 0.12 -10000 0 -0.52 31 31
AKT1 0.003 0.025 -10000 0 -0.59 1 1
CSF2 -0.18 0.38 -10000 0 -1 79 79
GSK3B 0.009 0.036 -10000 0 -0.58 2 2
NR1I3 0.018 0.18 0.47 13 -0.82 13 26
CSN2 0.12 0.15 0.39 57 -0.36 4 61
BRG1/BAF155/BAF170/BAF60A 0.032 0.029 -10000 0 -0.31 2 2
NFATC1 -0.015 0.12 -10000 0 -0.5 30 30
POU2F1 0 0.076 -10000 0 -0.55 10 10
CDKN1A -0.017 0.16 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
SFN 0.005 0.057 -10000 0 -0.47 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.075 0.11 0.3 31 -0.45 6 37
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.015 0.17 0.44 16 -0.79 11 27
JUN -0.16 0.19 -10000 0 -0.48 85 85
IL4 -0.075 0.14 -10000 0 -0.53 12 12
CDK5R1 0.009 0.034 -10000 0 -0.46 3 3
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.2 0.22 26 -0.47 89 115
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.078 0.11 0.3 32 -0.42 6 38
cortisol/GR alpha (monomer) 0.21 0.28 0.63 117 -0.46 4 121
NCOA2 0.003 0.068 -10000 0 -0.56 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.083 0.16 -10000 0 -0.58 44 44
AP-1/NFAT1-c-4 -0.28 0.31 -10000 0 -0.7 136 136
AFP -0.12 0.17 -10000 0 -0.71 15 15
SUV420H1 0.01 0.025 -10000 0 -0.58 1 1
IRF1 0.12 0.14 0.44 34 -0.58 1 35
TP53 -0.03 0.18 -10000 0 -0.57 56 56
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.34 0.45 -10000 0 -1 147 147
KRT14 -0.12 0.22 -10000 0 -0.68 45 45
TBP 0.017 0.026 -10000 0 -0.37 2 2
CREBBP 0.037 0.06 0.3 6 -10000 0 6
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.022 0.027 -10000 0 -10000 0 0
AP-1 -0.28 0.31 -10000 0 -0.71 136 136
MAPK14 0.011 0.006 -10000 0 -10000 0 0
MAPK10 -0.032 0.15 -10000 0 -0.55 44 44
MAPK11 -0.003 0.083 -10000 0 -0.48 17 17
KRT5 -0.32 0.42 -10000 0 -0.91 148 148
interleukin-1 receptor activity 0.011 0.028 -10000 0 -10000 0 0
NCOA1 0.013 0.025 -10000 0 -0.58 1 1
STAT1 0.012 0.055 -10000 0 -0.52 6 6
CGA -0.062 0.13 -10000 0 -0.44 31 31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.2 0.46 106 -0.52 5 111
MAPK3 0.01 0.026 -10000 0 -0.58 1 1
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
ICAM1 -0.13 0.22 -10000 0 -0.68 44 44
NFKB1 -0.037 0.098 -10000 0 -0.39 10 10
MAPK8 -0.12 0.16 -10000 0 -0.42 80 80
MAPK9 0.011 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.004 0.16 0.47 19 -0.66 5 24
BAX -0.012 0.13 -10000 0 -0.93 2 2
POMC -0.14 0.3 -10000 0 -1.3 26 26
EP300 0.034 0.078 0.28 9 -0.48 5 14
cortisol/GR alpha (dimer)/p53 0.15 0.26 0.54 101 -0.41 15 116
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.068 0.23 20 -0.24 3 23
SGK1 0.067 0.14 0.42 1 -1.4 3 4
IL13 -0.18 0.23 -10000 0 -0.67 53 53
IL6 -0.24 0.4 -10000 0 -0.91 122 122
PRKACG 0.002 0.027 -10000 0 -0.46 2 2
IL5 -0.15 0.18 -10000 0 -0.63 31 31
IL2 -0.2 0.23 -10000 0 -0.63 77 77
CDK5 0.011 0.003 -10000 0 -10000 0 0
PRKACB -0.021 0.13 -10000 0 -0.57 32 32
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
IL8 -0.24 0.41 -10000 0 -0.87 136 136
CDK5R1/CDK5 0.014 0.026 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA/PKAc -0.049 0.16 -10000 0 -0.48 40 40
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 107 -0.4 1 108
SMARCA4 0.011 0.025 -10000 0 -0.58 1 1
chromatin remodeling 0.12 0.14 0.38 63 -0.44 3 66
NF kappa B1 p50/RelA/Cbp -0.013 0.17 0.32 7 -0.51 26 33
JUN (dimer) -0.16 0.19 -10000 0 -0.48 85 85
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 -0.077 0.21 -10000 0 -0.7 44 44
NR3C1 0.12 0.18 0.43 76 -0.45 12 88
NR4A1 -0.037 0.15 -10000 0 -0.47 59 59
TIF2/SUV420H1 0.01 0.053 -10000 0 -0.41 9 9
MAPKKK cascade 0.004 0.16 0.47 19 -0.62 5 24
cortisol/GR alpha (dimer)/Src-1 0.19 0.23 0.54 115 -0.42 4 119
PBX1 -0.004 0.092 -10000 0 -0.57 14 14
POU1F1 0 0.032 -10000 0 -0.57 1 1
SELE -0.23 0.39 -10000 0 -0.89 111 111
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.14 0.38 62 -0.44 3 65
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 107 -0.4 1 108
mol:cortisol 0.12 0.16 0.37 119 -10000 0 119
MMP1 -0.27 0.45 -10000 0 -1.1 115 115
Thromboxane A2 receptor signaling

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
TGM2 -0.004 0.088 -10000 0 -0.54 15 15
GNB1/GNG2 -0.052 0.068 -10000 0 -0.2 76 76
AKT1 -0.021 0.092 -10000 0 -0.21 49 49
EGF -0.18 0.25 -10000 0 -0.5 209 209
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.031 0.12 -10000 0 -0.4 25 25
mol:Ca2+ -0.045 0.13 -10000 0 -0.3 78 78
LYN -0.016 0.092 -10000 0 -0.41 9 9
RhoA/GTP -0.03 0.045 -10000 0 -0.14 26 26
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.049 0.14 -10000 0 -0.35 73 73
GNG2 0.004 0.064 -10000 0 -0.53 8 8
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.11 -10000 0 -0.48 23 23
G beta5/gamma2 -0.066 0.091 -10000 0 -0.26 79 79
PRKCH -0.051 0.14 -10000 0 -0.36 74 74
DNM1 -0.004 0.087 -10000 0 -0.5 17 17
TXA2/TP beta/beta Arrestin3 -0.015 0.034 -10000 0 -0.25 6 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.23 -10000 0 -0.5 145 145
G12 family/GTP -0.071 0.11 -10000 0 -0.3 76 76
ADRBK1 0.009 0.037 -10000 0 -0.5 3 3
ADRBK2 -0.001 0.083 -10000 0 -0.57 12 12
RhoA/GTP/ROCK1 0.006 0.057 -10000 0 -0.39 11 11
mol:GDP 0.042 0.11 0.31 38 -10000 0 38
mol:NADP -0.007 0.099 -10000 0 -0.52 20 20
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.024 0.14 -10000 0 -0.56 36 36
mol:IP3 -0.059 0.16 -10000 0 -0.38 78 78
cell morphogenesis 0.006 0.057 -10000 0 -0.39 11 11
PLCB2 -0.083 0.2 -10000 0 -0.52 78 78
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.072 0.14 -10000 0 -0.39 49 49
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.03 0.12 -10000 0 -0.43 20 20
RHOA 0.01 0.025 -10000 0 -0.58 1 1
PTGIR -0.005 0.091 -10000 0 -0.5 19 19
PRKCB1 -0.056 0.15 -10000 0 -0.37 76 76
GNAQ 0.005 0.06 -10000 0 -0.58 6 6
mol:L-citrulline -0.007 0.099 -10000 0 -0.52 20 20
TXA2/TXA2-R family -0.086 0.21 -10000 0 -0.53 77 77
LCK -0.035 0.12 -10000 0 -0.42 23 23
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.048 0.091 -10000 0 -0.46 8 8
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.04 -10000 0 -0.3 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.045 0.089 -10000 0 -0.45 8 8
MAPK14 -0.026 0.1 -10000 0 -0.23 66 66
TGM2/GTP -0.071 0.18 -10000 0 -0.45 76 76
MAPK11 -0.031 0.1 -10000 0 -0.24 71 71
ARHGEF1 -0.022 0.079 -10000 0 -0.19 52 52
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.06 0.16 -10000 0 -0.39 79 79
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.038 0.12 -10000 0 -0.29 68 68
cAMP biosynthetic process -0.062 0.15 -10000 0 -0.37 77 77
Gq family/GTP/EBP50 0.004 0.08 -10000 0 -0.34 19 19
actin cytoskeleton reorganization 0.006 0.057 -10000 0 -0.39 11 11
SRC -0.017 0.094 -10000 0 -0.42 10 10
GNB5 0.007 0.049 -10000 0 -0.58 4 4
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR -0.062 0.12 -10000 0 -0.32 57 57
VCAM1 -0.047 0.13 -10000 0 -0.32 79 79
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.11 -10000 0 -0.48 23 23
platelet activation -0.038 0.13 -10000 0 -0.3 75 75
PGI2/IP -0.004 0.066 -10000 0 -0.36 19 19
PRKACA -0.046 0.11 -10000 0 -0.3 62 62
Gq family/GDP/G beta5/gamma2 -0.01 0.11 -10000 0 -0.45 24 24
TXA2/TP beta/beta Arrestin2 -0.015 0.062 -10000 0 -0.48 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.04 0.11 -10000 0 -0.29 65 65
mol:DAG -0.063 0.17 -10000 0 -0.42 76 76
EGFR 0.004 0.064 -10000 0 -0.53 8 8
TXA2/TP alpha -0.085 0.2 -10000 0 -0.51 76 76
Gq family/GTP -0.012 0.08 -10000 0 -0.28 34 34
YES1 -0.019 0.099 -10000 0 -0.43 11 11
GNAI2/GTP -0.048 0.09 -10000 0 -0.45 11 11
PGD2/DP -0.086 0.16 -10000 0 -0.36 145 145
SLC9A3R1 0.011 0 -10000 0 -10000 0 0
FYN -0.019 0.096 -10000 0 -0.42 10 10
mol:NO -0.007 0.099 -10000 0 -0.52 20 20
GNA15 -0.009 0.1 -10000 0 -0.54 21 21
PGK/cGMP -0.019 0.11 -10000 0 -0.34 55 55
RhoA/GDP 0.011 0.024 -10000 0 -0.57 1 1
TP alpha/TGM2/GDP/G beta/gamma -0.028 0.12 -10000 0 -0.46 14 14
NOS3 -0.007 0.099 -10000 0 -0.52 20 20
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.049 0.14 -10000 0 -0.34 74 74
PRKCB -0.062 0.16 -10000 0 -0.39 87 87
PRKCE -0.046 0.14 -10000 0 -0.35 72 72
PRKCD -0.053 0.15 -10000 0 -0.37 74 74
PRKCG -0.085 0.18 -10000 0 -0.41 99 99
muscle contraction -0.079 0.2 -10000 0 -0.5 78 78
PRKCZ -0.049 0.14 -10000 0 -0.35 74 74
ARR3 -0.001 0.043 -10000 0 -0.46 5 5
TXA2/TP beta -0.035 0.11 -10000 0 -0.51 11 11
PRKCQ -0.065 0.16 -10000 0 -0.37 85 85
MAPKKK cascade -0.075 0.19 -10000 0 -0.47 79 79
SELE -0.06 0.16 -10000 0 -0.36 93 93
TP beta/GNAI2/GDP/G beta/gamma -0.021 0.11 -10000 0 -0.46 10 10
ROCK1 0 0.081 -10000 0 -0.58 11 11
GNA14 -0.008 0.1 -10000 0 -0.56 19 19
chemotaxis -0.095 0.23 -10000 0 -0.6 76 76
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.009 0.035 -10000 0 -0.58 2 2
GNA11 0.007 0.051 -10000 0 -0.53 5 5
Rac1/GTP 0.007 0.003 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.05 0.15 -9999 0 -0.34 114 114
EPHB2 0 0.081 -9999 0 -0.55 12 12
Syndecan-2/TACI -0.035 0.13 -9999 0 -0.32 92 92
LAMA1 -0.054 0.18 -9999 0 -0.54 68 68
Syndecan-2/alpha2 ITGB1 0.005 0.089 -9999 0 -0.31 30 30
HRAS 0.008 0.042 -9999 0 -0.49 4 4
Syndecan-2/CASK 0.001 0.061 -9999 0 -0.33 18 18
ITGA5 -0.005 0.089 -9999 0 -0.48 19 19
BAX 0.02 0.074 -9999 0 -1.1 1 1
EPB41 0.007 0.049 -9999 0 -0.58 4 4
positive regulation of cell-cell adhesion 0.002 0.074 -9999 0 -0.32 27 27
LAMA3 -0.016 0.12 -9999 0 -0.5 30 30
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.004 0.088 -9999 0 -0.51 17 17
Syndecan-2/MMP2 -0.014 0.12 -9999 0 -0.38 49 49
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.012 0.045 -9999 0 -0.42 6 6
dendrite morphogenesis 0.002 0.079 -9999 0 -0.34 29 29
Syndecan-2/GM-CSF -0.058 0.14 -9999 0 -0.32 132 132
determination of left/right symmetry 0.003 0.072 -9999 0 -0.39 18 18
Syndecan-2/PKC delta 0.01 0.061 -9999 0 -0.34 17 17
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
MAPK3 -0.046 0.13 -9999 0 -0.32 74 74
MAPK1 -0.046 0.13 -9999 0 -0.32 74 74
Syndecan-2/RACK1 0.014 0.061 -9999 0 -0.32 16 16
NF1 0.008 0.043 -9999 0 -0.58 3 3
FGFR/FGF/Syndecan-2 0.003 0.072 -9999 0 -0.39 18 18
ITGA2 0.005 0.06 -9999 0 -0.58 6 6
MAPK8 0.015 0.065 -9999 0 -0.34 19 19
Syndecan-2/alpha2/beta1 Integrin -0.015 0.12 -9999 0 -0.31 62 62
Syndecan-2/Kininogen -0.067 0.15 -9999 0 -0.32 145 145
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.018 0.062 -9999 0 -0.31 16 16
Syndecan-2/CASK/Protein 4.1 0.007 0.062 -9999 0 -0.31 21 21
extracellular matrix organization 0.002 0.085 -9999 0 -0.36 28 28
actin cytoskeleton reorganization -0.05 0.15 -9999 0 -0.33 114 114
Syndecan-2/Caveolin-2/Ras 0.006 0.084 -9999 0 -0.37 19 19
Syndecan-2/Laminin alpha3 -0.007 0.092 -9999 0 -0.31 47 47
Syndecan-2/RasGAP 0.018 0.063 -9999 0 -0.31 18 18
alpha5/beta1 Integrin 0.005 0.064 -9999 0 -0.34 19 19
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.002 0.08 -9999 0 -0.34 29 29
GO:0007205 0.003 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.065 -9999 0 -0.31 18 18
RHOA 0.01 0.025 -9999 0 -0.58 1 1
SDCBP 0 0.081 -9999 0 -0.58 11 11
TNFRSF13B -0.061 0.18 -9999 0 -0.52 76 76
RASA1 0.009 0.035 -9999 0 -0.58 2 2
alpha2/beta1 Integrin 0.012 0.045 -9999 0 -0.42 6 6
Syndecan-2/Synbindin 0.01 0.061 -9999 0 -0.34 17 17
TGFB1 -0.001 0.083 -9999 0 -0.54 13 13
CASP3 0.015 0.059 -9999 0 -0.31 16 16
FN1 -0.087 0.21 -9999 0 -0.52 106 106
Syndecan-2/IL8 -0.063 0.16 -9999 0 -0.33 138 138
SDC2 0.003 0.072 -9999 0 -0.39 18 18
KNG1 -0.11 0.22 -9999 0 -0.52 131 131
Syndecan-2/Neurofibromin 0.008 0.067 -9999 0 -0.34 20 20
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 -0.097 0.22 -9999 0 -0.52 117 117
Syndecan-2/TGFB1 0.002 0.085 -9999 0 -0.36 28 28
Syndecan-2/Syntenin/PI-4-5-P2 0.002 0.074 -9999 0 -0.32 27 27
Syndecan-2/Ezrin 0.016 0.058 -9999 0 -0.32 15 15
PRKACA 0.014 0.061 -9999 0 -0.31 17 17
angiogenesis -0.063 0.16 -9999 0 -0.33 138 138
MMP2 -0.029 0.14 -9999 0 -0.52 43 43
IL8 -0.11 0.22 -9999 0 -0.52 129 129
calcineurin-NFAT signaling pathway -0.035 0.12 -9999 0 -0.32 92 92
Osteopontin-mediated events

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
IKK alpha homodimer -0.064 0.16 -9999 0 -0.54 18 18
NF kappa B1 p50/RelA/I kappa B alpha -0.038 0.15 -9999 0 -0.51 16 16
alphaV/beta3 Integrin/Osteopontin/Src -0.11 0.19 -9999 0 -0.36 198 198
AP1 -0.073 0.2 -9999 0 -0.59 40 40
ILK -0.073 0.16 -9999 0 -0.46 24 24
bone resorption -0.051 0.16 -9999 0 -0.54 20 20
PTK2B 0.009 0.035 -9999 0 -0.58 2 2
PYK2/p130Cas -0.058 0.15 -9999 0 -0.5 19 19
ITGAV 0.003 0.081 -9999 0 -0.57 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.073 -9999 0 -0.45 14 14
alphaV/beta3 Integrin/Osteopontin -0.089 0.18 -9999 0 -0.37 112 112
MAP3K1 -0.078 0.17 -9999 0 -0.35 110 110
JUN 0.006 0.053 -9999 0 -0.56 5 5
MAPK3 -0.061 0.16 -9999 0 -0.49 21 21
MAPK1 -0.061 0.16 -9999 0 -0.5 21 21
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
NFKB1 0.01 0.025 -9999 0 -0.58 1 1
MAPK8 -0.067 0.16 -9999 0 -0.46 35 35
ITGB3 -0.002 0.094 -9999 0 -0.54 17 17
NFKBIA -0.052 0.16 -9999 0 -0.52 20 20
FOS -0.03 0.14 -9999 0 -0.53 44 44
CD44 0.007 0.049 -9999 0 -0.58 4 4
CHUK 0.007 0.049 -9999 0 -0.58 4 4
PLAU -0.048 0.18 -9999 0 -0.68 20 20
NF kappa B1 p50/RelA -0.076 0.12 -9999 0 -0.52 18 18
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.002 0.093 -9999 0 -0.41 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.075 0.16 -9999 0 -0.34 109 109
VAV3 -0.1 0.19 -9999 0 -0.49 57 57
MAP3K14 -0.073 0.16 -9999 0 -0.34 112 112
ROCK2 0 0.081 -9999 0 -0.58 11 11
SPP1 -0.16 0.25 -9999 0 -0.51 188 188
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.092 0.18 -9999 0 -0.49 45 45
MMP2 -0.072 0.2 -9999 0 -0.6 50 50
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.025 0.051 -9999 0 -0.56 2 2
Crk/p130 Cas/Paxillin -0.059 0.11 -9999 0 -0.39 29 29
JUN -0.029 0.12 -9999 0 -0.44 24 24
HRAS 0.008 0.042 -9999 0 -0.49 4 4
RET51/GFRalpha1/GDNF/GRB10 -0.072 0.17 -9999 0 -0.41 81 81
RAP1A 0.01 0.025 -9999 0 -0.58 1 1
FRS2 0.009 0.035 -9999 0 -0.58 2 2
RAP1A/GDP 0.008 0.018 -9999 0 -0.43 1 1
RET51/GFRalpha1/GDNF/DOK1 -0.069 0.17 -9999 0 -0.4 80 80
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
RET9/GFRalpha1/GDNF/Enigma -0.029 0.12 -9999 0 -0.29 90 90
RHOA 0.01 0.025 -9999 0 -0.58 1 1
RAP1A/GTP -0.08 0.14 -9999 0 -0.4 54 54
GRB7 0.002 0.067 -9999 0 -0.46 12 12
RET51/GFRalpha1/GDNF -0.069 0.17 -9999 0 -0.4 80 80
MAPKKK cascade -0.072 0.13 -9999 0 -0.47 31 31
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
RET9/GFRalpha1/GDNF/IRS1 -0.031 0.12 -9999 0 -0.3 92 92
lamellipodium assembly -0.054 0.098 -9999 0 -0.3 58 58
RET51/GFRalpha1/GDNF/SHC -0.069 0.17 -9999 0 -0.4 80 80
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC -0.026 0.11 -9999 0 -0.29 85 85
RET9/GFRalpha1/GDNF/Shank3 -0.028 0.12 -9999 0 -0.3 86 86
MAPK3 -0.051 0.14 -9999 0 -0.49 26 26
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.032 0.15 -9999 0 -0.55 44 44
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.048 0.15 -9999 0 -0.48 32 32
DOK5 -0.05 0.17 -9999 0 -0.54 64 64
GFRA1 -0.067 0.19 -9999 0 -0.53 83 83
MAPK8 -0.034 0.12 -9999 0 -0.45 21 21
HRAS/GTP -0.08 0.14 -9999 0 -0.38 82 82
tube development -0.021 0.11 -9999 0 -0.32 53 53
MAPK1 -0.051 0.14 -9999 0 -0.49 26 26
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.013 0.093 -9999 0 -0.27 57 57
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC 0.01 0.025 -9999 0 -0.58 1 1
PDLIM7 0.005 0.053 -9999 0 -0.47 7 7
RET51/GFRalpha1/GDNF/Dok6 -0.082 0.19 -9999 0 -0.41 106 106
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.07 0.17 -9999 0 -0.4 80 80
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.2 -9999 0 -0.44 113 113
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
CREB1 -0.027 0.12 -9999 0 -0.35 53 53
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.086 -9999 0 -0.26 51 51
RET51/GFRalpha1/GDNF/Grb7 -0.075 0.17 -9999 0 -0.41 81 81
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.081 0.2 -9999 0 -0.5 104 104
DOK4 0.01 0.025 -9999 0 -0.58 1 1
JNK cascade -0.028 0.12 -9999 0 -0.43 24 24
RET9/GFRalpha1/GDNF/FRS2 -0.027 0.11 -9999 0 -0.33 53 53
SHANK3 0.007 0.051 -9999 0 -0.53 5 5
RASA1 0.009 0.035 -9999 0 -0.58 2 2
NCK1 0.009 0.035 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.01 0.087 -9999 0 -0.26 52 52
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.044 0.13 -9999 0 -0.42 31 31
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.042 0.13 -9999 0 -0.34 55 55
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.044 0.14 -9999 0 -0.33 81 81
PI3K -0.044 0.17 -9999 0 -0.46 58 58
SOS1 0.01 0.025 -9999 0 -0.58 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.02 0.11 -9999 0 -0.32 53 53
GRB10 0.007 0.049 -9999 0 -0.58 4 4
activation of MAPKK activity -0.034 0.12 -9999 0 -0.42 22 22
RET51/GFRalpha1/GDNF/FRS2 -0.071 0.17 -9999 0 -0.4 82 82
GAB1 0.011 0 -9999 0 -10000 0 0
IRS1 0.002 0.074 -9999 0 -0.58 9 9
IRS2 0.003 0.069 -9999 0 -0.54 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.043 0.14 -9999 0 -0.34 80 80
RET51/GFRalpha1/GDNF/PKC alpha -0.07 0.17 -9999 0 -0.4 80 80
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.006 0.037 -9999 0 -0.5 3 3
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.074 0.18 -9999 0 -0.42 83 83
Rac1/GTP -0.063 0.12 -9999 0 -0.36 58 58
RET9/GFRalpha1/GDNF -0.037 0.12 -9999 0 -0.33 85 85
GFRalpha1/GDNF -0.044 0.14 -9999 0 -0.38 85 85
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.038 0.12 -10000 0 -0.32 84 84
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.009 0.034 -10000 0 -0.46 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.015 0.083 -10000 0 -0.28 23 23
IRAK/TOLLIP -0.016 0.097 -10000 0 -0.41 7 7
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
IKBKG 0.01 0.025 -10000 0 -0.58 1 1
IL1 alpha/IL1R2 -0.1 0.2 -10000 0 -0.4 163 163
IL1A -0.09 0.21 -10000 0 -0.51 111 111
IL1B -0.058 0.17 -10000 0 -0.4 105 105
IRAK/TRAF6/p62/Atypical PKCs 0.001 0.097 -10000 0 -0.58 5 5
IL1R2 -0.055 0.18 -10000 0 -0.52 72 72
IL1R1 -0.007 0.097 -10000 0 -0.51 20 20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.092 0.2 7 -0.3 24 31
TOLLIP 0.01 0.025 -10000 0 -0.58 1 1
TICAM2 -0.011 0.11 -10000 0 -0.58 20 20
MAP3K3 0.009 0.035 -10000 0 -0.58 2 2
TAK1/TAB1/TAB2 0.008 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.019 0.088 -10000 0 -0.61 4 4
JUN -0.003 0.09 -10000 0 -0.55 4 4
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.034 0.14 -10000 0 -0.54 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.14 -10000 0 -0.34 67 67
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.035 0.13 -10000 0 -0.32 67 67
IL1 beta fragment/IL1R1/IL1RAP -0.048 0.15 -10000 0 -0.38 72 72
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 -0.007 0.09 -10000 0 -0.53 4 4
IRAK1 -0.025 0.1 -10000 0 -0.27 85 85
IL1RN/IL1R1 -0.04 0.15 -10000 0 -0.39 81 81
IRAK4 0.011 0 -10000 0 -10000 0 0
PRKCI 0.008 0.043 -10000 0 -0.58 3 3
TRAF6 0.01 0.025 -10000 0 -0.58 1 1
PI3K 0.013 0.041 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.099 -10000 0 -0.31 31 31
CHUK 0.007 0.049 -10000 0 -0.58 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.048 0.15 -10000 0 -0.38 72 72
IL1 beta/IL1R2 -0.082 0.2 -10000 0 -0.38 151 151
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.018 0.082 -10000 0 -0.36 7 7
NF kappa B1 p50/RelA -0.057 0.12 -10000 0 -0.5 20 20
IRAK3 -0.024 0.13 -10000 0 -0.53 37 37
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.042 0.15 -10000 0 -0.35 74 74
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.023 0.11 -10000 0 -0.27 68 68
IL1 alpha/IL1R1/IL1RAP -0.057 0.15 -10000 0 -0.32 134 134
RELA 0.011 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
MYD88 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.008 0.095 -10000 0 -0.36 9 9
IL1RAP 0.001 0.077 -10000 0 -0.58 10 10
UBE2N 0.01 0.025 -10000 0 -0.58 1 1
IRAK/TRAF6 -0.084 0.14 -10000 0 -0.45 47 47
CASP1 -0.02 0.13 -10000 0 -0.54 33 33
IL1RN/IL1R2 -0.073 0.19 -10000 0 -0.42 118 118
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.038 0.14 -10000 0 -0.35 72 72
TMEM189-UBE2V1 -0.064 0.16 -10000 0 -0.46 84 84
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.11 -10000 0 -0.4 22 22
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
IL1RN -0.05 0.17 -10000 0 -0.52 67 67
TRAF6/TAK1/TAB1/TAB2 -0.031 0.08 -10000 0 -0.38 5 5
MAP2K6 -0.012 0.092 -10000 0 -0.33 15 15
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.12 -10000 0 -0.33 47 47
NT3 (dimer)/TRKC -0.045 0.15 -10000 0 -0.39 85 85
NT3 (dimer)/TRKB -0.16 0.21 -10000 0 -0.35 286 286
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.033 -10000 0 -0.3 5 5
RAPGEF1 0.01 0.025 -10000 0 -0.58 1 1
BDNF -0.02 0.13 -10000 0 -0.52 34 34
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 -0.039 0.16 -10000 0 -0.53 52 52
NTRK2 -0.18 0.25 -10000 0 -0.5 209 209
NTRK3 -0.042 0.16 -10000 0 -0.51 57 57
NT-4/5 (dimer)/TRKB -0.16 0.2 -10000 0 -0.34 284 284
neuron apoptosis 0.14 0.19 0.45 115 -10000 0 115
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.5 113 113
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.13 0.2 -10000 0 -0.55 78 78
SHC3 -0.14 0.21 -10000 0 -0.57 87 87
STAT3 (dimer) 0.018 0.015 -10000 0 -0.35 1 1
NT3 (dimer)/TRKA -0.082 0.18 -10000 0 -0.43 94 94
RIN/GDP -0.003 0.07 -10000 0 -0.27 10 10
GIPC1 0.007 0.049 -10000 0 -0.58 4 4
KRAS 0.005 0.058 -10000 0 -0.56 6 6
DNAJA3 -0.057 0.14 -10000 0 -0.35 68 68
RIN/GTP -0.001 0.019 -10000 0 -0.32 2 2
CCND1 0.024 0.035 -10000 0 -0.81 1 1
MAGED1 0.011 0 -10000 0 -10000 0 0
PTPN11 0.006 0.055 -10000 0 -0.58 5 5
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.014 0.091 -10000 0 -0.46 23 23
SHC/GRB2/SOS1 0.023 0.016 -10000 0 -0.35 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.078 0.18 -10000 0 -0.37 145 145
TRKA/NEDD4-2 -0.02 0.12 -10000 0 -0.38 53 53
ELMO1 0.004 0.059 -10000 0 -0.49 8 8
RhoG/GTP/ELMO1/DOCK1 0.011 0.039 -10000 0 -0.3 9 9
NGF -0.029 0.14 -10000 0 -0.52 43 43
HRAS 0.008 0.042 -10000 0 -0.49 4 4
DOCK1 0.01 0.025 -10000 0 -0.58 1 1
GAB2 0.009 0.035 -10000 0 -0.58 2 2
RIT2 -0.001 0.027 -10000 0 -0.46 2 2
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.009 0.035 -10000 0 -0.58 2 2
DNM1 -0.004 0.087 -10000 0 -0.5 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.019 -10000 0 -0.46 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.07 0.13 -10000 0 -0.34 72 72
mol:GDP -0.006 0.1 -10000 0 -0.39 12 12
NGF (dimer) -0.029 0.14 -10000 0 -0.52 43 43
RhoG/GDP 0.003 0.042 -10000 0 -0.35 8 8
RIT1/GDP 0.002 0.07 -10000 0 -0.27 8 8
TIAM1 -0.043 0.16 -10000 0 -0.52 59 59
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
BDNF (dimer)/TRKB -0.11 0.18 -10000 0 -0.32 226 226
KIDINS220/CRKL/C3G 0.016 0.018 -10000 0 -0.42 1 1
SHC/RasGAP 0.015 0.026 -10000 0 -0.42 2 2
FRS2 family/SHP2 0.018 0.052 -10000 0 -0.44 7 7
SHC/GRB2/SOS1/GAB1 0.029 0.014 -10000 0 -0.32 1 1
RIT1/GTP 0.008 0 -10000 0 -10000 0 0
NT3 (dimer) -0.02 0.13 -10000 0 -0.53 33 33
RAP1/GDP -0.021 0.047 -10000 0 -0.27 5 5
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.02 0.13 -10000 0 -0.52 34 34
ubiquitin-dependent protein catabolic process -0.034 0.13 -10000 0 -0.38 61 61
Schwann cell development -0.032 0.032 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.027 0.031 -10000 0 -0.32 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.028 0.05 -10000 0 -0.5 4 4
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.025 -10000 0 -0.58 1 1
CDC42/GTP -0.13 0.16 -10000 0 -0.47 65 65
ABL1 0.01 0.025 -10000 0 -0.58 1 1
SH2B family/GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
Rap1/GTP -0.017 0.08 -10000 0 -0.43 2 2
STAT3 0.018 0.015 -10000 0 -0.35 1 1
axon guidance -0.12 0.16 -10000 0 -0.45 65 65
MAPK3 -0.066 0.17 -10000 0 -0.38 101 101
MAPK1 -0.066 0.17 -10000 0 -0.38 101 101
CDC42/GDP 0 0.074 -10000 0 -0.3 10 10
NTF3 -0.02 0.13 -10000 0 -0.54 33 33
NTF4 -0.014 0.091 -10000 0 -0.46 23 23
NGF (dimer)/TRKA/FAIM -0.036 0.14 -10000 0 -0.34 91 91
PI3K 0.013 0.041 -10000 0 -0.42 5 5
FRS3 0.01 0.031 -10000 0 -0.52 2 2
FAIM 0.005 0.058 -10000 0 -0.56 6 6
GAB1 0.011 0 -10000 0 -10000 0 0
RASGRF1 -0.092 0.16 -10000 0 -0.37 104 104
SOS1 0.01 0.025 -10000 0 -0.58 1 1
MCF2L -0.033 0.13 -10000 0 -0.33 89 89
RGS19 0 0.079 -10000 0 -0.54 12 12
CDC42 0.006 0.055 -10000 0 -0.58 5 5
RAS family/GTP -0.003 0.096 -10000 0 -0.54 9 9
Rac1/GDP 0.002 0.07 -10000 0 -0.26 9 9
NGF (dimer)/TRKA/GRIT -0.04 0.13 -10000 0 -0.35 86 86
neuron projection morphogenesis -0.04 0.13 -10000 0 -0.56 8 8
NGF (dimer)/TRKA/NEDD4-2 -0.033 0.14 -10000 0 -0.38 61 61
MAP2K1 0.03 0.023 -10000 0 -0.29 3 3
NGFR -0.079 0.2 -10000 0 -0.51 100 100
NGF (dimer)/TRKA/GIPC/GAIP -0.02 0.11 -10000 0 -0.5 8 8
RAS family/GTP/PI3K 0.013 0.081 -10000 0 -0.42 15 15
FRS2 family/SHP2/GRB2/SOS1 0.028 0.048 -10000 0 -0.56 2 2
NRAS 0.001 0.077 -10000 0 -0.58 10 10
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
PRKCI 0.008 0.043 -10000 0 -0.58 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAPKKK cascade -0.089 0.18 -10000 0 -0.62 56 56
RASA1 0.009 0.035 -10000 0 -0.58 2 2
TRKA/c-Abl -0.02 0.12 -10000 0 -0.38 53 53
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.096 0.16 -10000 0 -0.36 97 97
NGF (dimer)/TRKA/p62/Atypical PKCs -0.017 0.12 -10000 0 -0.33 61 61
MATK -0.064 0.19 -10000 0 -0.52 81 81
NEDD4L 0.01 0.025 -10000 0 -0.58 1 1
RAS family/GDP -0.021 0.049 -10000 0 -0.27 8 8
NGF (dimer)/TRKA -0.076 0.14 -10000 0 -0.32 111 111
Rac1/GTP -0.079 0.11 -10000 0 -0.32 62 62
FRS2 family/SHP2/CRK family 0.029 0.05 -10000 0 -0.54 3 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.016 0.098 -9999 0 -0.31 44 44
RGS9BP -0.01 0.1 -9999 0 -0.54 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.047 -9999 0 -0.46 6 6
mol:Na + -0.046 0.12 -9999 0 -0.3 102 102
mol:ADP -0.002 0.058 -9999 0 -0.34 16 16
GNAT2 -0.008 0.097 -9999 0 -0.53 19 19
RGS9-1/Gbeta5/R9AP -0.021 0.12 -9999 0 -0.33 70 70
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.061 -9999 0 -0.32 20 20
GRK7 -0.002 0.064 -9999 0 -0.46 11 11
CNGB3 -0.029 0.12 -9999 0 -0.46 41 41
Cone Metarhodopsin II/X-Arrestin -0.001 0.03 -9999 0 -0.32 5 5
mol:Ca2+ -0.049 0.12 -9999 0 -0.28 119 119
Cone PDE6 -0.016 0.1 -9999 0 -0.32 43 43
Cone Metarhodopsin II -0.002 0.045 -9999 0 -0.26 16 16
Na + (4 Units) -0.048 0.12 -9999 0 -0.28 119 119
GNAT2/GDP -0.021 0.11 -9999 0 -0.32 53 53
GNB5 0.007 0.049 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.003 0.057 -9999 0 -0.29 22 22
Cone Transducin -0.016 0.1 -9999 0 -0.32 47 47
SLC24A2 -0.013 0.095 -9999 0 -0.48 23 23
GNB3/GNGT2 -0.018 0.12 -9999 0 -0.39 49 49
GNB3 -0.017 0.12 -9999 0 -0.53 30 30
GNAT2/GTP -0.005 0.071 -9999 0 -0.38 19 19
CNGA3 -0.048 0.16 -9999 0 -0.52 62 62
ARR3 -0.001 0.043 -9999 0 -0.46 5 5
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.047 0.12 -9999 0 -0.3 102 102
mol:Pi -0.021 0.12 -9999 0 -0.33 70 70
Cone CNG Channel -0.052 0.1 -9999 0 -0.31 41 41
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.013 0.095 -9999 0 -0.48 23 23
RGS9 -0.033 0.15 -9999 0 -0.53 47 47
PDE6C 0.001 0.027 -9999 0 -0.46 2 2
GNGT2 -0.008 0.1 -9999 0 -0.56 20 20
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.019 -9999 0 -0.46 1 1
Effects of Botulinum toxin

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
STX1A 0.001 0.052 -9999 0 -0.34 13 13
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.03 0.12 -9999 0 -0.36 67 67
STXBP1 -0.006 0.099 -9999 0 -0.55 18 18
ACh/CHRNA1 -0.028 0.11 -9999 0 -0.36 50 50
RAB3GAP2/RIMS1/UNC13B -0.019 0.11 -9999 0 -0.36 32 32
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 -0.052 0.16 -9999 0 -0.51 66 66
mol:ACh -0.007 0.035 -9999 0 -0.088 81 81
RAB3GAP2 0.008 0.043 -9999 0 -0.58 3 3
STX1A/SNAP25/VAMP2 -0.05 0.1 -9999 0 -0.33 34 34
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.028 0.11 -9999 0 -0.36 50 50
UNC13B 0.01 0.031 -9999 0 -0.52 2 2
CHRNA1 -0.036 0.15 -9999 0 -0.53 50 50
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.081 0.16 -9999 0 -0.38 125 125
SNAP25 -0.022 0.074 -9999 0 -0.2 78 78
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.12 0.24 -9999 0 -0.57 125 125
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.075 -9999 0 -0.31 31 31
STX1A/SNAP25 fragment 1/VAMP2 -0.05 0.1 -9999 0 -0.33 34 34
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.031 0.14 -10000 0 -0.41 42 42
CRKL -0.011 0.12 -10000 0 -0.42 36 36
HRAS -0.024 0.15 -10000 0 -0.43 49 49
mol:PIP3 -0.02 0.12 -10000 0 -0.41 37 37
SPRED1 0.005 0.06 -10000 0 -0.58 6 6
SPRED2 0.008 0.043 -10000 0 -0.58 3 3
GAB1 -0.017 0.13 -10000 0 -0.44 37 37
FOXO3 -0.006 0.12 -10000 0 -0.38 38 38
AKT1 -0.013 0.13 -10000 0 -0.42 38 38
BAD -0.007 0.12 -10000 0 -0.39 38 38
megakaryocyte differentiation -0.082 0.18 -10000 0 -0.36 129 129
GSK3B -0.007 0.12 -10000 0 -0.39 39 39
RAF1 -0.011 0.13 -10000 0 -0.39 30 30
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.017 0.13 -10000 0 -0.44 38 38
STAT1 -0.061 0.32 -10000 0 -1 49 49
HRAS/SPRED1 -0.015 0.13 -10000 0 -0.4 35 35
cell proliferation -0.017 0.13 -10000 0 -0.43 39 39
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
TEC 0.011 0 -10000 0 -10000 0 0
RPS6KB1 -0.019 0.14 -10000 0 -0.44 43 43
HRAS/SPRED2 -0.014 0.13 -10000 0 -0.39 34 34
LYN/TEC/p62DOK -0.005 0.12 -10000 0 -0.41 36 36
MAPK3 0.002 0.095 -10000 0 -0.28 29 29
STAP1 -0.05 0.17 -10000 0 -0.43 72 72
GRAP2 -0.023 0.14 -10000 0 -0.55 35 35
JAK2 -0.054 0.29 -10000 0 -0.89 48 48
STAT1 (dimer) -0.058 0.31 -10000 0 -0.96 49 49
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.041 0.16 -10000 0 -0.47 49 49
actin filament polymerization -0.03 0.14 -10000 0 -0.41 53 53
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.056 0.22 -10000 0 -0.65 53 53
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
CBL/CRKL/GRB2 0.002 0.12 -10000 0 -0.38 32 32
PI3K -0.01 0.14 -10000 0 -0.46 38 38
PTEN 0.005 0.06 -10000 0 -0.58 6 6
SCF/KIT/EPO/EPOR -0.062 0.34 -10000 0 -1.3 35 35
MAPK8 -0.018 0.13 -10000 0 -0.43 39 39
STAT3 (dimer) -0.017 0.13 -10000 0 -0.43 39 39
positive regulation of transcription 0.005 0.08 -10000 0 -0.24 17 17
mol:GDP -0.034 0.16 -10000 0 -0.45 54 54
PIK3C2B -0.017 0.13 -10000 0 -0.44 37 37
CBL/CRKL -0.003 0.12 -10000 0 -0.39 36 36
FER -0.022 0.14 -10000 0 -0.47 39 39
SH2B3 -0.017 0.13 -10000 0 -0.44 37 37
PDPK1 -0.013 0.11 -10000 0 -0.38 36 36
SNAI2 -0.025 0.14 -10000 0 -0.43 45 45
positive regulation of cell proliferation -0.038 0.23 -10000 0 -0.72 48 48
KITLG -0.005 0.1 -10000 0 -0.6 17 17
cell motility -0.038 0.23 -10000 0 -0.72 48 48
PTPN6 0.011 0.007 -10000 0 -10000 0 0
EPOR 0.002 0.13 -10000 0 -1.1 3 3
STAT5A (dimer) -0.03 0.19 -10000 0 -0.61 46 46
SOCS1 -0.029 0.14 -10000 0 -0.49 46 46
cell migration 0.054 0.16 0.38 82 -0.21 1 83
SOS1 0.01 0.025 -10000 0 -0.58 1 1
EPO 0 0.055 -10000 0 -0.46 8 8
VAV1 -0.024 0.14 -10000 0 -0.57 35 35
GRB10 -0.02 0.13 -10000 0 -0.44 40 40
PTPN11 0.006 0.055 -10000 0 -0.57 5 5
SCF/KIT -0.025 0.14 0.22 1 -0.44 44 45
GO:0007205 0 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.1 -10000 0 -0.31 29 29
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.064 0.33 -10000 0 -1.4 31 31
MAP2K2 -0.001 0.1 -10000 0 -0.31 27 27
SHC/Grb2/SOS1 -0.006 0.12 -10000 0 -0.42 36 36
STAT5A -0.031 0.2 -10000 0 -0.64 44 44
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.024 0.14 -10000 0 -0.42 45 45
SHC/GRAP2 -0.008 0.1 -10000 0 -0.4 35 35
PTPRO -0.083 0.18 -10000 0 -0.36 129 129
SH2B2 -0.031 0.14 -10000 0 -0.42 53 53
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.055 0.16 -10000 0 -0.39 82 82
CREBBP 0.022 0.031 -10000 0 -10000 0 0
BCL2 -0.019 0.23 -10000 0 -1.2 17 17
LPA receptor mediated events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.013 0.12 -9999 0 -0.4 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.11 -9999 0 -0.4 12 12
AP1 -0.087 0.14 -9999 0 -0.51 32 32
mol:PIP3 -0.065 0.12 -9999 0 -0.49 23 23
AKT1 0.011 0.091 -9999 0 -0.42 12 12
PTK2B -0.013 0.093 -9999 0 -0.33 22 22
RHOA 0.011 0.05 -9999 0 -0.35 3 3
PIK3CB 0.007 0.047 -9999 0 -0.55 4 4
mol:Ca2+ -0.019 0.11 -9999 0 -0.44 13 13
MAGI3 0.008 0.043 -9999 0 -0.58 3 3
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.052 0.14 -9999 0 -0.35 72 72
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
positive regulation of microtubule depolymerization -0.042 0.13 -9999 0 -0.35 39 39
NF kappa B1 p50/RelA -0.064 0.12 -9999 0 -0.47 27 27
endothelial cell migration -0.041 0.18 -9999 0 -0.51 69 69
ADCY4 -0.036 0.16 -9999 0 -0.5 44 44
ADCY5 -0.068 0.19 -9999 0 -0.56 56 56
ADCY6 -0.034 0.16 -9999 0 -0.51 41 41
ADCY7 -0.035 0.16 -9999 0 -0.52 41 41
ADCY1 -0.046 0.16 -9999 0 -0.5 47 47
ADCY2 -0.052 0.18 -9999 0 -0.52 58 58
ADCY3 -0.034 0.16 -9999 0 -0.51 41 41
ADCY8 -0.039 0.16 -9999 0 -0.52 41 41
ADCY9 -0.035 0.16 -9999 0 -0.51 42 42
GSK3B -0.008 0.091 -9999 0 -0.38 14 14
arachidonic acid secretion -0.03 0.15 -9999 0 -0.48 42 42
GNG2 0.004 0.064 -9999 0 -0.53 8 8
TRIP6 -0.014 0.12 -9999 0 -0.42 39 39
GNAO1 -0.051 0.16 -9999 0 -0.34 108 108
HRAS 0.008 0.042 -9999 0 -0.49 4 4
NFKBIA -0.021 0.12 -9999 0 -0.43 16 16
GAB1 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.03 0.2 -9999 0 -0.91 28 28
JUN 0.006 0.053 -9999 0 -0.56 5 5
LPA/LPA2/NHERF2 0.007 0.046 -9999 0 -0.32 7 7
TIAM1 -0.057 0.23 -9999 0 -1.1 28 28
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
mol:IP3 -0.02 0.12 -9999 0 -0.45 13 13
PLCB3 0.012 0.056 -9999 0 -0.57 3 3
FOS -0.03 0.14 -9999 0 -0.53 44 44
positive regulation of mitosis -0.03 0.15 -9999 0 -0.48 42 42
LPA/LPA1-2-3 -0.062 0.15 -9999 0 -0.38 72 72
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
stress fiber formation -0.022 0.11 -9999 0 -0.36 25 25
GNAZ -0.032 0.14 -9999 0 -0.36 72 72
EGFR/PI3K-beta/Gab1 -0.067 0.13 -9999 0 -0.51 23 23
positive regulation of dendritic cell cytokine production -0.062 0.15 -9999 0 -0.38 72 72
LPA/LPA2/MAGI-3 0.006 0.05 -9999 0 -0.33 9 9
ARHGEF1 -0.005 0.1 -9999 0 -0.35 35 35
GNAI2 -0.018 0.12 -9999 0 -0.36 52 52
GNAI3 -0.018 0.12 -9999 0 -0.36 52 52
GNAI1 -0.026 0.14 -9999 0 -0.39 60 60
LPA/LPA3 -0.057 0.14 -9999 0 -0.37 90 90
LPA/LPA2 -0.001 0.046 -9999 0 -0.34 7 7
LPA/LPA1 -0.031 0.14 -9999 0 -0.42 52 52
HB-EGF/EGFR -0.035 0.12 -9999 0 -0.31 93 93
HBEGF -0.04 0.14 -9999 0 -0.37 87 87
mol:DAG -0.02 0.12 -9999 0 -0.45 13 13
cAMP biosynthetic process -0.048 0.17 -9999 0 -0.49 54 54
NFKB1 0.01 0.025 -9999 0 -0.58 1 1
SRC 0.01 0.025 -9999 0 -0.58 1 1
GNB1 0.011 0.001 -9999 0 -10000 0 0
LYN -0.021 0.12 -9999 0 -0.43 16 16
GNAQ -0.032 0.1 -9999 0 -0.32 47 47
LPAR2 0.005 0.053 -9999 0 -0.47 7 7
LPAR3 -0.072 0.19 -9999 0 -0.51 90 90
LPAR1 -0.032 0.15 -9999 0 -0.61 34 34
IL8 -0.11 0.21 -9999 0 -0.46 115 115
PTK2 -0.05 0.14 -9999 0 -0.35 73 73
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.052 0.14 -9999 0 -0.35 72 72
EGFR 0.003 0.064 -9999 0 -0.53 8 8
PLCG1 -0.033 0.12 -9999 0 -0.34 50 50
PLD2 -0.05 0.14 -9999 0 -0.35 72 72
G12/G13 -0.01 0.11 -9999 0 -0.37 35 35
PI3K-beta -0.03 0.087 -9999 0 -0.44 15 15
cell migration -0.018 0.088 -9999 0 -0.26 37 37
SLC9A3R2 0.01 0.025 -9999 0 -0.58 1 1
PXN -0.023 0.11 -9999 0 -0.37 25 25
HRAS/GTP -0.032 0.16 -9999 0 -0.5 42 42
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.059 0.18 -9999 0 -0.52 76 76
PRKCE 0.011 0 -9999 0 -10000 0 0
PRKCD -0.013 0.11 -9999 0 -0.46 10 10
Gi(beta/gamma) -0.031 0.15 -9999 0 -0.49 42 42
mol:LPA -0.008 0.042 -9999 0 -0.19 18 18
TRIP6/p130 Cas/FAK1/Paxillin -0.074 0.14 -9999 0 -0.5 28 28
MAPKKK cascade -0.03 0.15 -9999 0 -0.48 42 42
contractile ring contraction involved in cytokinesis 0.011 0.05 -9999 0 -0.34 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.039 0.12 -9999 0 -0.34 57 57
GNA15 -0.039 0.12 -9999 0 -0.33 54 54
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.035 -9999 0 -0.58 2 2
MAPT -0.043 0.13 -9999 0 -0.37 38 38
GNA11 -0.031 0.1 -9999 0 -0.32 45 45
Rac1/GTP -0.033 0.21 -9999 0 -0.97 28 28
MMP2 -0.041 0.19 -9999 0 -0.51 69 69
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.046 0.19 -9999 0 -0.49 70 70
MAP4K1 -0.043 0.17 -9999 0 -0.55 56 56
MAP3K8 0.01 0.031 -9999 0 -0.52 2 2
PRKCB -0.039 0.16 -9999 0 -0.54 52 52
DBNL 0.01 0.025 -9999 0 -0.58 1 1
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 -0.02 0.15 -9999 0 -0.56 32 32
JUN -0.029 0.19 -9999 0 -0.72 37 37
MAP3K7 -0.017 0.15 -9999 0 -0.55 30 30
GRAP2 -0.023 0.14 -9999 0 -0.55 35 35
CRK 0.011 0.019 -9999 0 -0.46 1 1
MAP2K4 -0.013 0.15 -9999 0 -0.54 32 32
LAT -0.01 0.1 -9999 0 -0.51 24 24
LCP2 -0.014 0.12 -9999 0 -0.54 26 26
MAPK8 -0.034 0.2 -9999 0 -0.76 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.024 0.16 -9999 0 -0.59 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.038 0.18 -9999 0 -0.46 70 70
Glypican 2 network

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
MDK -0.008 0.1 -9999 0 -0.51 22 22
GPC2 -0.009 0.1 -9999 0 -0.55 21 21
GPC2/Midkine -0.012 0.11 -9999 0 -0.38 42 42
neuron projection morphogenesis -0.012 0.1 -9999 0 -0.38 42 42
Arf6 signaling events

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
CENTA1/KIF3B 0.013 0.035 -9999 0 -0.44 3 3
ARNO/beta Arrestin1-2 -0.003 0.069 -9999 0 -10000 0 0
EGFR 0.004 0.064 -9999 0 -0.53 8 8
EPHA2 0.006 0.056 -9999 0 -0.54 6 6
USP6 0.008 0.042 -9999 0 -0.49 4 4
IQSEC1 0.011 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.13 0.19 -9999 0 -0.36 216 216
ARRB2 0.007 0.008 -9999 0 -0.19 1 1
mol:GTP 0.004 0.047 -9999 0 -0.26 12 12
ARRB1 0.009 0.035 -9999 0 -0.58 2 2
FBXO8 0.009 0.035 -9999 0 -0.58 2 2
TSHR -0.014 0.1 -9999 0 -0.46 27 27
EGF -0.18 0.25 -9999 0 -0.5 209 209
somatostatin receptor activity 0 0 -9999 0 -0.001 47 47
ARAP2 -0.006 0.1 -9999 0 -0.58 17 17
mol:GDP -0.034 0.088 -9999 0 -0.28 42 42
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 22 22
ITGA2B -0.047 0.16 -9999 0 -0.5 64 64
ARF6 0.01 0.025 -9999 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.046 -9999 0 -0.37 6 6
ADAP1 0.01 0.031 -9999 0 -0.52 2 2
KIF13B 0.009 0.035 -9999 0 -0.58 2 2
HGF/MET -0.019 0.12 -9999 0 -0.39 51 51
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.039 0.094 -9999 0 -0.27 45 45
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.099 0.16 -9999 0 -0.3 216 216
ADRB2 -0.029 0.14 -9999 0 -0.54 42 42
receptor agonist activity 0 0 -9999 0 0 46 46
actin filament binding 0 0 -9999 0 -0.001 45 45
SRC 0.01 0.025 -9999 0 -0.58 1 1
ITGB3 -0.005 0.093 -9999 0 -0.54 17 17
GNAQ 0.005 0.06 -9999 0 -0.58 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 38 38
ARF6/GDP -0.003 0.1 -9999 0 -0.36 28 28
ARF6/GDP/GULP/ACAP1 -0.06 0.14 -9999 0 -0.37 64 64
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.013 0.11 -9999 0 -0.32 37 37
ACAP1 -0.025 0.14 -9999 0 -0.53 38 38
ACAP2 0.001 0.078 -9999 0 -0.58 10 10
LHCGR/beta Arrestin2 0.001 0.012 -9999 0 -0.26 1 1
EFNA1 0.011 0.019 -9999 0 -0.46 1 1
HGF -0.036 0.16 -9999 0 -0.55 49 49
CYTH3 0.007 0.029 -9999 0 -0.39 3 3
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.035 -9999 0 -0.58 2 2
fibronectin binding 0 0 -9999 0 0 33 33
endosomal lumen acidification 0 0 -9999 0 0 35 35
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.05 0.17 -9999 0 -0.53 65 65
GNAQ/ARNO 0.01 0.032 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 24 24
MET 0.009 0.031 -9999 0 -0.52 2 2
GNA14 -0.008 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 21 21
GIT1 0.01 0.025 -9999 0 -0.58 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 39 39
GNA11 0.007 0.051 -9999 0 -0.53 5 5
LHCGR 0 0.019 -9999 0 -0.46 1 1
AGTR1 -0.095 0.21 -9999 0 -0.52 114 114
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.012 -9999 0 -0.26 1 1
IPCEF1/ARNO -0.074 0.12 -9999 0 -0.47 1 1
alphaIIb/beta3 Integrin -0.037 0.13 -9999 0 -0.37 80 80
Caspase cascade in apoptosis

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
TOP1 -0.025 0.12 0.19 2 -0.33 57 59
ACTA1 -0.046 0.15 0.23 2 -0.42 58 60
NUMA1 -0.025 0.12 0.19 2 -0.32 57 59
SPTAN1 -0.038 0.15 0.23 2 -0.4 57 59
LIMK1 -0.038 0.15 0.23 2 -0.41 55 57
BIRC3 -0.016 0.12 -10000 0 -0.52 29 29
BIRC2 -0.002 0.088 -10000 0 -0.58 13 13
BAX 0.01 0.025 -10000 0 -0.58 1 1
CASP10 -0.052 0.16 -10000 0 -0.42 59 59
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.025 -10000 0 -0.58 1 1
PTK2 -0.025 0.12 0.19 2 -0.33 55 57
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.037 0.14 0.23 2 -0.4 57 59
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0.025 -10000 0 -0.58 1 1
GSN -0.043 0.15 0.23 2 -0.41 59 61
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A -0.085 0.2 -10000 0 -0.56 82 82
BID -0.021 0.084 -10000 0 -0.23 60 60
MAP3K1 -0.013 0.07 -10000 0 -0.33 12 12
TRADD 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -10000 0 -0.42 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.039 0.15 0.23 2 -0.41 57 59
CASP9 0.01 0.025 -10000 0 -0.58 1 1
DNA repair 0.003 0.048 -10000 0 -0.19 8 8
neuron apoptosis 0.012 0.037 -10000 0 -0.49 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.03 0.14 0.22 2 -0.39 55 57
APAF1 0.008 0.043 -10000 0 -0.58 3 3
CASP6 -0.004 0.083 -10000 0 -0.53 4 4
TRAF2 0.01 0.025 -10000 0 -0.58 1 1
ICAD/CAD -0.031 0.14 -10000 0 -0.39 55 55
CASP7 0.008 0.058 0.26 19 -10000 0 19
KRT18 0.006 0.033 -10000 0 -0.55 1 1
apoptosis -0.036 0.14 0.25 2 -0.36 63 65
DFFA -0.038 0.15 0.23 2 -0.41 55 57
DFFB -0.038 0.15 0.23 2 -0.41 55 57
PARP1 -0.003 0.048 0.19 8 -10000 0 8
actin filament polymerization 0.039 0.14 0.38 57 -10000 0 57
TNF -0.016 0.12 -10000 0 -0.54 28 28
CYCS -0.021 0.086 -10000 0 -0.28 32 32
SATB1 -0.018 0.11 -10000 0 -0.41 19 19
SLK -0.049 0.16 0.23 2 -0.41 72 74
p15 BID/BAX -0.013 0.076 -10000 0 -0.29 11 11
CASP2 0.022 0.06 -10000 0 -0.4 2 2
JNK cascade 0.013 0.069 0.32 12 -10000 0 12
CASP3 -0.046 0.15 0.24 2 -0.43 58 60
LMNB2 0.017 0.06 -10000 0 -0.53 2 2
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.008 0.04 -10000 0 -0.54 3 3
Mammalian IAPs/DIABLO 0.006 0.1 -10000 0 -0.46 20 20
negative regulation of DNA binding -0.085 0.2 -10000 0 -0.55 82 82
stress fiber formation -0.049 0.16 0.23 2 -0.4 72 74
GZMB -0.069 0.18 -10000 0 -0.4 120 120
CASP1 -0.006 0.079 -10000 0 -0.3 36 36
LMNB1 0.018 0.052 -10000 0 -0.27 3 3
APP 0.012 0.037 -10000 0 -0.5 2 2
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.018 -10000 0 -0.43 1 1
VIM -0.028 0.13 0.23 5 -0.35 52 57
LMNA 0.017 0.058 -10000 0 -0.37 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.063 -10000 0 -0.43 2 2
LRDD 0.008 0.043 -10000 0 -0.58 3 3
SREBF1 -0.039 0.15 0.23 2 -0.4 58 60
APAF-1/Caspase 9 -0.003 0.066 0.4 7 -0.75 1 8
nuclear fragmentation during apoptosis -0.024 0.12 0.19 2 -0.32 57 59
CFL2 -0.041 0.15 -10000 0 -0.39 57 57
GAS2 -0.07 0.17 0.23 1 -0.4 88 89
positive regulation of apoptosis 0.02 0.058 -10000 0 -0.62 1 1
PRF1 -0.036 0.15 -10000 0 -0.5 53 53
Cellular roles of Anthrax toxin

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
ANTXR1 -0.044 0.16 -10000 0 -0.53 59 59
ANTXR2 0.005 0.059 -10000 0 -0.53 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.022 -10000 0 -0.068 65 65
monocyte activation -0.023 0.13 -10000 0 -0.49 34 34
MAP2K2 -0.004 0.033 -10000 0 -0.76 1 1
MAP2K1 -0.008 0.027 -10000 0 -0.35 2 2
MAP2K7 -0.007 0.022 -10000 0 -0.31 1 1
MAP2K6 -0.012 0.046 -10000 0 -0.33 10 10
CYAA -0.021 0.093 -10000 0 -0.28 65 65
MAP2K4 -0.008 0.029 -10000 0 -0.31 3 3
IL1B -0.04 0.11 -10000 0 -0.28 89 89
Channel -0.021 0.1 -10000 0 -0.3 65 65
NLRP1 -0.018 0.062 -10000 0 -0.28 26 26
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.009 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.022 0.068 65 -10000 0 65
MAPK3 -0.007 0.022 -10000 0 -0.31 1 1
MAPK1 -0.007 0.024 -10000 0 -0.38 1 1
PGR -0.04 0.097 -10000 0 -0.29 73 73
PA/Cellular Receptors -0.023 0.11 -10000 0 -0.33 65 65
apoptosis -0.008 0.022 -10000 0 -0.068 65 65
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.018 0.092 -10000 0 -0.27 65 65
macrophage activation 0.007 0.028 -10000 0 -0.33 2 2
TNF -0.016 0.12 -10000 0 -0.54 28 28
VCAM1 -0.023 0.13 -10000 0 -0.49 34 34
platelet activation -0.009 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.028 0.14 5 -10000 0 5
IL18 -0.007 0.054 -10000 0 -0.24 19 19
negative regulation of macrophage activation -0.008 0.022 -10000 0 -0.068 65 65
LEF -0.008 0.022 -10000 0 -0.068 65 65
CASP1 -0.015 0.039 -10000 0 -0.15 29 29
mol:cAMP -0.009 0.025 -10000 0 -10000 0 0
necrosis -0.008 0.022 -10000 0 -0.068 65 65
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.019 0.094 -10000 0 -0.28 65 65
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.042 -9999 0 -0.36 7 7
alphaV beta3 Integrin -0.024 0.13 -9999 0 -0.37 69 69
PTK2 -0.024 0.15 -9999 0 -0.53 26 26
IGF1R 0.01 0.025 -9999 0 -0.58 1 1
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0 0.076 -9999 0 -0.49 13 13
SRC 0.01 0.025 -9999 0 -0.58 1 1
CDKN1B -0.034 0.13 -9999 0 -0.5 28 28
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
ILK -0.033 0.13 -9999 0 -0.49 27 27
ROCK1 0 0.081 -9999 0 -0.58 11 11
AKT1 -0.023 0.12 -9999 0 -0.46 26 26
PTK2B 0.012 0.078 -9999 0 -0.31 25 25
alphaV/beta3 Integrin/JAM-A -0.039 0.15 -9999 0 -0.37 70 70
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.08 -9999 0 -0.35 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.026 0.12 -9999 0 -0.33 60 60
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.11 -9999 0 -0.62 11 11
alphaV/beta3 Integrin/Syndecan-1 0.005 0.081 -9999 0 -0.34 28 28
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.19 -9999 0 -0.57 63 63
PI4 Kinase 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Osteopontin -0.1 0.17 -9999 0 -0.32 204 204
RPS6KB1 -0.081 0.2 -9999 0 -0.54 66 66
TLN1 0.01 0.025 -9999 0 -0.58 1 1
MAPK3 -0.063 0.2 -9999 0 -0.64 48 48
GPR124 0.005 0.061 -9999 0 -0.55 7 7
MAPK1 -0.063 0.2 -9999 0 -0.64 48 48
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
alphaV/beta3 Integrin/Tumstatin -0.045 0.14 -9999 0 -0.32 114 114
cell adhesion 0.003 0.091 -9999 0 -0.37 26 26
ANGPTL3 0.003 0.02 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.019 0.039 -9999 0 -0.31 8 8
IGF-1R heterotetramer 0.01 0.025 -9999 0 -0.58 1 1
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.019 -9999 0 -0.46 1 1
ITGB3 -0.005 0.093 -9999 0 -0.54 17 17
IGF1 -0.071 0.19 -9999 0 -0.52 88 88
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.002 0.093 -9999 0 -0.37 31 31
apoptosis 0 0.081 -9999 0 -0.58 11 11
CD47 0.009 0.035 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/CD47 0.005 0.085 -9999 0 -0.36 28 28
VCL 0.009 0.035 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Del1 -0.025 0.15 -9999 0 -0.41 63 63
CSF1 0.006 0.056 -9999 0 -0.54 6 6
PIK3C2A -0.054 0.18 -9999 0 -0.58 49 49
PI4 Kinase/Pyk2 -0.056 0.12 -9999 0 -0.46 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.01 0.082 -9999 0 -0.34 23 23
FAK1/Vinculin -0.013 0.12 -9999 0 -0.42 26 26
alphaV beta3/Integrin/ppsTEM5 0.002 0.093 -9999 0 -0.37 31 31
RHOA 0.01 0.025 -9999 0 -0.58 1 1
VTN -0.051 0.16 -9999 0 -0.5 68 68
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
FGF2 -0.037 0.15 -9999 0 -0.52 53 53
F11R -0.017 0.11 -9999 0 -0.37 53 53
alphaV/beta3 Integrin/Lactadherin -0.001 0.096 -9999 0 -0.35 37 37
alphaV/beta3 Integrin/TGFBR2 0.005 0.08 -9999 0 -0.34 28 28
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.017 0.066 -9999 0 -0.34 17 17
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Talin 0.006 0.074 -9999 0 -0.31 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.087 0.21 -9999 0 -0.52 106 106
alphaV/beta3 Integrin/Pyk2 0.014 0.079 -9999 0 -0.32 25 25
SDC1 0.01 0.025 -9999 0 -0.58 1 1
VAV3 -0.023 0.13 -9999 0 -0.31 89 89
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
IRS1 0.002 0.074 -9999 0 -0.58 9 9
FAK1/Paxillin -0.012 0.12 -9999 0 -0.41 26 26
cell migration -0.005 0.11 -9999 0 -0.38 25 25
ITGAV 0 0.081 -9999 0 -0.58 11 11
PI3K -0.06 0.13 -9999 0 -0.5 25 25
SPP1 -0.16 0.25 -9999 0 -0.51 188 188
KDR 0.006 0.054 -9999 0 -0.52 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0.081 -9999 0 -0.58 11 11
COL4A3 -0.071 0.19 -9999 0 -0.5 90 90
angiogenesis -0.062 0.2 -9999 0 -0.64 47 47
Rac1/GTP -0.015 0.12 -9999 0 -0.56 4 4
EDIL3 -0.039 0.16 -9999 0 -0.57 49 49
cell proliferation 0.005 0.08 -9999 0 -0.34 28 28
IL27-mediated 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
TGFB1 -0.043 0.14 -10000 0 -0.42 59 59
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.13 0.48 18 -0.25 1 19
IL27/IL27R/JAK1 -0.025 0.17 -10000 0 -0.56 28 28
TBX21 -0.046 0.23 -10000 0 -0.55 73 73
IL12B -0.005 0.074 -10000 0 -0.46 15 15
IL12A -0.024 0.11 -10000 0 -0.41 44 44
IL6ST -0.005 0.095 -10000 0 -0.58 15 15
IL27RA/JAK1 0.004 0.11 -10000 0 -0.94 6 6
IL27 -0.007 0.082 -10000 0 -0.46 18 18
TYK2 0.01 0.026 -10000 0 -0.58 1 1
T-helper cell lineage commitment -0.19 0.41 -10000 0 -1.3 59 59
T-helper 2 cell differentiation 0.025 0.13 0.48 18 -0.25 1 19
T cell proliferation during immune response 0.025 0.13 0.48 18 -0.25 1 19
MAPKKK cascade -0.025 0.13 0.25 1 -0.48 18 19
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0.019 -10000 0 -0.46 1 1
STAT1 0.006 0.052 -10000 0 -0.5 6 6
IL12RB1 -0.036 0.15 -10000 0 -0.54 48 48
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.043 0.22 -10000 0 -0.57 56 56
IL27/IL27R/JAK2/TYK2 -0.025 0.13 0.26 1 -0.49 18 19
positive regulation of T cell mediated cytotoxicity -0.025 0.13 0.25 1 -0.48 18 19
STAT1 (dimer) -0.057 0.24 0.4 21 -0.73 37 58
JAK2 -0.008 0.11 -10000 0 -0.55 21 21
JAK1 0.009 0.043 -10000 0 -0.58 3 3
STAT2 (dimer) -0.019 0.13 -10000 0 -0.48 17 17
T cell proliferation -0.098 0.18 -10000 0 -0.46 69 69
IL12/IL12R/TYK2/JAK2 -0.044 0.14 -10000 0 -0.55 15 15
IL17A -0.2 0.41 -10000 0 -1.3 59 59
mast cell activation 0.025 0.13 0.48 18 -0.25 1 19
IFNG -0.011 0.043 0.066 1 -0.11 62 63
T cell differentiation -0.004 0.007 0.014 2 -0.021 64 66
STAT3 (dimer) -0.019 0.12 -10000 0 -0.48 16 16
STAT5A (dimer) -0.019 0.12 -10000 0 -0.48 16 16
STAT4 (dimer) -0.039 0.16 -10000 0 -0.49 43 43
STAT4 -0.028 0.14 -10000 0 -0.56 40 40
T cell activation -0.006 0.011 0.12 4 -10000 0 4
IL27R/JAK2/TYK2 -0.015 0.14 -10000 0 -0.77 10 10
GATA3 -0.028 0.22 -10000 0 -1.3 16 16
IL18 0.003 0.05 -10000 0 -0.39 9 9
positive regulation of mast cell cytokine production -0.018 0.12 -10000 0 -0.47 16 16
IL27/EBI3 -0.027 0.13 -10000 0 -0.39 59 59
IL27RA -0.004 0.11 -10000 0 -1.3 4 4
IL6 -0.15 0.25 -10000 0 -0.53 161 161
STAT5A 0.011 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.006 0.044 0.48 4 -10000 0 4
IL1B -0.045 0.14 -10000 0 -0.38 81 81
EBI3 -0.031 0.15 -10000 0 -0.56 43 43
TNF -0.011 0.088 -10000 0 -0.4 28 28
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.025 0.26 -10000 0 -0.87 37 37
NCK1/PAK1/Dok-R -0.038 0.11 -10000 0 -0.41 39 39
NCK1/Dok-R -0.025 0.29 -10000 0 -1.1 37 37
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
mol:beta2-estradiol 0.006 0.056 0.24 29 -10000 0 29
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.012 0.001 -10000 0 -10000 0 0
Rac/GDP 0.008 0 -10000 0 -10000 0 0
F2 -0.11 0.23 0.25 23 -0.5 139 162
TNIP2 0.01 0.025 -10000 0 -0.58 1 1
NF kappa B/RelA -0.04 0.26 -10000 0 -0.98 37 37
FN1 -0.087 0.21 -10000 0 -0.52 106 106
PLD2 -0.006 0.3 -10000 0 -1.1 37 37
PTPN11 0.006 0.055 -10000 0 -0.58 5 5
GRB14 -0.12 0.24 -10000 0 -0.54 138 138
ELK1 0.005 0.27 -10000 0 -0.97 37 37
GRB7 0.002 0.067 -10000 0 -0.46 12 12
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.085 0.29 -10000 0 -1 40 40
CDKN1A 0.042 0.2 -10000 0 -0.68 20 20
ITGA5 -0.005 0.089 -10000 0 -0.48 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.025 0.29 -10000 0 -1.1 37 37
CRK 0.011 0.019 -10000 0 -0.46 1 1
mol:NO 0.033 0.21 -10000 0 -0.64 39 39
PLG -0.031 0.3 -10000 0 -1.1 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.02 0.24 -10000 0 -0.83 37 37
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.043 -10000 0 -0.58 3 3
ANGPT2 0.019 0.19 -10000 0 -0.86 9 9
BMX -0.052 0.32 -10000 0 -1.1 39 39
ANGPT1 -0.017 0.31 -10000 0 -1.2 31 31
tube development 0.036 0.22 -10000 0 -0.67 33 33
ANGPT4 0.001 0.043 -10000 0 -0.45 5 5
response to hypoxia -0.001 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.077 0.32 -10000 0 -1.1 38 38
alpha5/beta1 Integrin 0.005 0.064 -10000 0 -0.34 19 19
FGF2 -0.038 0.15 -10000 0 -0.52 53 53
STAT5A (dimer) 0.037 0.24 -10000 0 -0.83 20 20
mol:L-citrulline 0.033 0.21 -10000 0 -0.64 39 39
AGTR1 -0.094 0.21 -10000 0 -0.51 114 114
MAPK14 0.001 0.3 -10000 0 -1.1 36 36
Tie2/SHP2 -0.037 0.18 -10000 0 -0.98 17 17
TEK -0.015 0.2 -10000 0 -1.2 14 14
RPS6KB1 0.025 0.25 -10000 0 -0.85 37 37
Angiotensin II/AT1 -0.066 0.15 -10000 0 -0.37 114 114
Tie2/Ang1/GRB2 -0.01 0.31 -10000 0 -1.1 37 37
MAPK3 0.002 0.28 -10000 0 -1 37 37
MAPK1 0.002 0.28 -10000 0 -1 37 37
Tie2/Ang1/GRB7 -0.014 0.31 -10000 0 -1.1 37 37
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 -0.007 0.3 -10000 0 -1.1 37 37
PI3K 0.014 0.29 -10000 0 -1 37 37
FES -0.006 0.31 -10000 0 -1.1 37 37
Crk/Dok-R -0.024 0.29 -10000 0 -1.1 37 37
Tie2/Ang1/ABIN2 -0.011 0.31 -10000 0 -1.1 37 37
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.031 0.23 -10000 0 -0.77 37 37
STAT5A 0.012 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.026 0.25 -10000 0 -0.83 37 37
Tie2/Ang2 0.022 0.27 -10000 0 -0.89 33 33
Tie2/Ang1 -0.014 0.33 -10000 0 -1.2 37 37
FOXO1 0.033 0.24 -10000 0 -0.77 39 39
ELF1 0.013 0.047 -10000 0 -0.59 3 3
ELF2 -0.007 0.3 -10000 0 -1.1 37 37
mol:Choline -0.003 0.28 -10000 0 -1 37 37
cell migration -0.03 0.067 -10000 0 -0.23 47 47
FYN 0.031 0.24 -10000 0 -0.76 33 33
DOK2 -0.008 0.1 -10000 0 -0.54 20 20
negative regulation of cell cycle 0.045 0.19 -10000 0 -0.6 22 22
ETS1 -0.003 0.084 -10000 0 -0.44 12 12
PXN 0.037 0.21 -10000 0 -0.68 37 37
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 0.028 0.23 -10000 0 -0.73 39 39
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.021 0.14 -10000 0 -0.53 31 31
MAPKKK cascade -0.003 0.28 -10000 0 -1 37 37
RASA1 0.009 0.035 -10000 0 -0.58 2 2
Tie2/Ang1/Shc -0.009 0.31 -10000 0 -1.1 37 37
NCK1 0.009 0.035 -10000 0 -0.58 2 2
vasculogenesis 0.037 0.19 -10000 0 -0.57 39 39
mol:Phosphatidic acid -0.003 0.28 -10000 0 -1 37 37
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP 0.033 0.21 -10000 0 -0.64 39 39
Rac1/GTP -0.06 0.2 -10000 0 -0.77 37 37
MMP2 -0.025 0.32 -10000 0 -1.1 38 38
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 -0.017 0.12 -9999 0 -0.53 30 30
ITGA4 -0.018 0.13 -9999 0 -0.56 29 29
alpha4/beta7 Integrin -0.024 0.14 -9999 0 -0.43 53 53
alpha4/beta1 Integrin -0.004 0.093 -9999 0 -0.41 29 29
Canonical Wnt signaling pathway

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
HDAC1 0.015 0.026 -10000 0 -10000 0 0
AES 0.013 0.033 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.013 0.039 -10000 0 -0.4 5 5
SMAD4 0.005 0.06 -10000 0 -0.58 6 6
DKK2 -0.085 0.21 -10000 0 -0.54 101 101
TLE1 0.01 0.054 -10000 0 -0.58 4 4
MACF1 0.012 0.001 -10000 0 -10000 0 0
CTNNB1 0.05 0.1 0.25 13 -0.95 2 15
WIF1 -0.18 0.25 -10000 0 -0.5 211 211
beta catenin/RanBP3 0.025 0.13 0.39 56 -0.7 2 58
KREMEN2 -0.039 0.15 -10000 0 -0.48 59 59
DKK1 -0.15 0.24 -10000 0 -0.51 174 174
beta catenin/beta TrCP1 0.054 0.091 0.25 9 -0.8 2 11
FZD1 0.009 0.04 -10000 0 -0.54 3 3
AXIN2 -0.12 0.42 -10000 0 -1.4 53 53
AXIN1 0.011 0.025 -10000 0 -0.58 1 1
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.083 -10000 0 -0.95 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.1 -10000 0 -0.63 6 6
Axin1/APC/GSK3 0.046 0.08 0.22 17 -0.78 2 19
Axin1/APC/GSK3/beta catenin/Macf1 0.036 0.095 -10000 0 -0.71 4 4
HNF1A 0.008 0.059 -10000 0 -0.53 6 6
CTBP1 0.013 0.034 -10000 0 -0.58 1 1
MYC -0.014 0.16 -10000 0 -1.5 5 5
RANBP3 0.01 0.025 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.38 81 81
NKD1 -0.13 0.24 -10000 0 -0.52 155 155
TCF4 0.002 0.083 -10000 0 -0.52 13 13
TCF3 0.013 0.033 -10000 0 -0.58 1 1
WNT1/LRP6/FZD1/Axin1 0.016 0.061 -10000 0 -0.36 6 6
Ran/GTP 0.009 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.16 0.46 50 -0.64 5 55
LEF1 -0.009 0.11 -10000 0 -0.52 25 25
DVL1 0.045 0.062 0.21 1 -0.5 4 5
CSNK2A1 0.012 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.042 0.11 -10000 0 -0.58 7 7
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.4 93 93
LRP6 0.01 0.035 -10000 0 -0.58 2 2
CSNK1A1 0.013 0.044 -10000 0 -0.59 2 2
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 -0.005 0.094 -10000 0 -0.73 4 4
WNT1 -0.008 0.086 -10000 0 -0.46 20 20
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.009 0.035 -10000 0 -0.58 2 2
FRAT1 0.01 0.025 -10000 0 -0.58 1 1
PPP2R5D 0.089 0.11 0.27 151 -10000 0 151
APC 0.009 0.084 -10000 0 -0.54 4 4
WNT1/LRP6/FZD1 0.07 0.1 0.23 74 -0.69 3 77
CREBBP 0.014 0.022 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.009 0.035 -9999 0 -0.58 2 2
GNAT1/GTP 0 0.019 -9999 0 -0.32 2 2
Metarhodopsin II/Arrestin 0 0.023 -9999 0 -0.27 4 4
PDE6G/GNAT1/GTP -0.015 0.088 -9999 0 -0.33 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.027 -9999 0 -0.46 2 2
GRK1 -0.003 0.047 -9999 0 -0.46 6 6
CNG Channel -0.12 0.17 -9999 0 -0.56 46 46
mol:Na + -0.066 0.13 -9999 0 -0.5 22 22
mol:ADP -0.003 0.047 -9999 0 -0.45 6 6
RGS9-1/Gbeta5/R9AP -0.021 0.12 -9999 0 -0.33 70 70
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.068 0.14 -9999 0 -0.52 22 22
CNGB1 -0.005 0.069 -9999 0 -0.46 13 13
RDH5 -0.002 0.084 -9999 0 -0.53 14 14
SAG 0.001 0.02 -9999 0 -0.46 1 1
mol:Ca2+ -0.043 0.14 -9999 0 -0.49 22 22
Na + (4 Units) -0.063 0.12 -9999 0 -0.47 22 22
RGS9 -0.033 0.15 -9999 0 -0.53 47 47
GNB1/GNGT1 -0.022 0.11 -9999 0 -0.37 54 54
GNAT1/GDP -0.017 0.1 -9999 0 -0.32 44 44
GUCY2D -0.014 0.099 -9999 0 -0.46 27 27
GNGT1 -0.042 0.16 -9999 0 -0.52 54 54
GUCY2F 0 0.019 -9999 0 -0.46 1 1
GNB5 0.007 0.049 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.082 0.17 -9999 0 -0.36 118 118
mol:11-cis-retinal -0.002 0.083 -9999 0 -0.53 14 14
mol:cGMP -0.024 0.1 -9999 0 -0.37 15 15
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin -0.002 0.065 -9999 0 -0.37 17 17
SLC24A1 0.009 0.035 -9999 0 -0.58 2 2
CNGA1 -0.052 0.18 -9999 0 -0.53 67 67
Metarhodopsin II -0.002 0.034 -9999 0 -0.27 8 8
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.026 0.11 -9999 0 -0.35 34 34
RGS9BP -0.01 0.1 -9999 0 -0.54 21 21
Metarhodopsin II/Transducin -0.012 0.07 -9999 0 -0.28 31 31
GCAP Family/Ca ++ -0.019 0.094 -9999 0 -0.33 30 30
PDE6A/B -0.095 0.2 -9999 0 -0.41 149 149
mol:Pi -0.021 0.12 -9999 0 -0.33 70 70
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.015 0.091 -9999 0 -0.29 51 51
PDE6B -0.029 0.14 -9999 0 -0.52 43 43
PDE6A -0.1 0.22 -9999 0 -0.54 120 120
PDE6G -0.026 0.14 -9999 0 -0.54 39 39
RHO -0.002 0.033 -9999 0 -0.46 3 3
PDE6 -0.12 0.17 -9999 0 -0.56 46 46
GUCA1A -0.021 0.12 -9999 0 -0.49 33 33
GC2/GCAP Family -0.019 0.095 -9999 0 -0.34 31 31
GUCA1C -0.001 0.027 -9999 0 -0.46 2 2
GUCA1B -0.015 0.12 -9999 0 -0.54 27 27
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.087 -10000 0 -0.53 15 15
Jak2/Leptin Receptor -0.055 0.13 0.19 1 -0.41 50 51
PTP1B/AKT1 -0.02 0.076 -10000 0 -0.3 16 16
FYN 0.005 0.061 -10000 0 -0.55 7 7
p210 bcr-abl/PTP1B -0.029 0.082 0.17 1 -0.29 23 24
EGFR 0.001 0.065 -10000 0 -0.54 8 8
EGF/EGFR -0.096 0.15 -10000 0 -0.33 115 115
CSF1 0.006 0.056 -10000 0 -0.54 6 6
AKT1 0.01 0.025 -10000 0 -0.59 1 1
INSR 0.009 0.035 -10000 0 -0.58 2 2
PTP1B/N-cadherin -0.068 0.14 -10000 0 -0.34 101 101
Insulin Receptor/Insulin -0.026 0.058 -10000 0 -0.36 7 7
HCK -0.02 0.13 -10000 0 -0.55 32 32
CRK 0.011 0.019 -10000 0 -0.46 1 1
TYK2 -0.022 0.08 -10000 0 -0.32 16 16
EGF -0.18 0.25 -10000 0 -0.51 209 209
YES1 0.004 0.065 -10000 0 -0.58 7 7
CAV1 -0.041 0.1 0.16 1 -0.29 36 37
TXN 0.009 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.019 0.084 -10000 0 -0.3 23 23
cell migration 0.029 0.082 0.29 23 -0.17 1 24
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.043 0.17 -10000 0 -0.57 53 53
ITGA2B -0.047 0.16 -10000 0 -0.5 64 64
CSF1R -0.029 0.14 -10000 0 -0.53 43 43
Prolactin Receptor/Prolactin -0.042 0.14 -10000 0 -0.42 69 69
FGR -0.023 0.13 -10000 0 -0.53 36 36
PTP1B/p130 Cas -0.023 0.083 -10000 0 -0.32 19 19
Crk/p130 Cas -0.017 0.082 -10000 0 -0.34 15 15
DOK1 -0.017 0.086 -10000 0 -0.36 17 17
JAK2 -0.047 0.13 -10000 0 -0.41 50 50
Jak2/Leptin Receptor/Leptin -0.054 0.12 -10000 0 -0.45 28 28
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
PTPN1 -0.029 0.082 0.17 1 -0.29 23 24
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.081 0.2 -10000 0 -0.53 98 98
SRC 0 0.06 -10000 0 -1.2 1 1
ITGB3 -0.006 0.094 -10000 0 -0.54 17 17
CAT1/PTP1B -0.081 0.17 -10000 0 -0.48 53 53
CAPN1 0.01 0.025 -10000 0 -0.59 1 1
CSK 0.01 0.025 -10000 0 -0.58 1 1
PI3K -0.021 0.064 -10000 0 -0.42 8 8
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.049 0.11 -10000 0 -0.45 25 25
negative regulation of transcription -0.046 0.13 -10000 0 -0.4 50 50
FCGR2A -0.02 0.13 -10000 0 -0.54 33 33
FER -0.001 0.072 -10000 0 -0.54 10 10
alphaIIb/beta3 Integrin -0.039 0.13 -10000 0 -0.37 80 80
BLK -0.11 0.23 -10000 0 -0.53 132 132
Insulin Receptor/Insulin/Shc 0.014 0.027 -10000 0 -0.31 4 4
RHOA 0.01 0.025 -10000 0 -0.59 1 1
LEPR 0 0.081 -10000 0 -0.55 12 12
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.083 0.19 -10000 0 -0.51 61 61
PRL -0.013 0.088 -10000 0 -0.45 22 22
SOCS3 -0.002 0.12 -10000 0 -1.3 4 4
SPRY2 0.007 0.043 -10000 0 -0.59 3 3
Insulin Receptor/Insulin/IRS1 0.008 0.054 -10000 0 -0.35 13 13
CSF1/CSF1R -0.037 0.12 -10000 0 -0.37 47 47
Ras protein signal transduction 0.021 0.025 -10000 0 -10000 0 0
IRS1 0.002 0.074 -10000 0 -0.58 9 9
INS -0.001 0.027 -10000 0 -0.45 2 2
LEP -0.025 0.12 -10000 0 -0.46 38 38
STAT5B -0.033 0.09 -10000 0 -0.29 32 32
STAT5A -0.033 0.09 -10000 0 -0.29 32 32
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.028 0.1 -10000 0 -0.38 26 26
CSN2 -0.008 0.06 -10000 0 -10000 0 0
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
LAT -0.032 0.14 -10000 0 -0.57 30 30
YBX1 0.016 0.016 -10000 0 -0.36 1 1
LCK -0.032 0.14 -10000 0 -0.51 48 48
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 -0.07 0.19 -10000 0 -0.52 87 87
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 0.058 0.24 21 -0.3 4 25
RFC1 0.011 0.062 0.23 25 -0.38 4 29
PRKDC 0.01 0.061 0.24 21 -0.3 6 27
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.01 0.051 0.24 6 -0.43 1 7
FASLG/FAS/FADD/FAF1 0.002 0.11 0.22 60 -0.3 30 90
MAP2K4 -0.027 0.13 -10000 0 -0.42 21 21
mol:ceramide -0.027 0.12 -10000 0 -0.38 43 43
GSN 0.006 0.068 0.23 24 -0.29 12 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.12 -10000 0 -0.35 34 34
FAS -0.001 0.075 -10000 0 -0.56 10 10
BID 0.008 0.051 0.29 13 -0.32 2 15
MAP3K1 -0.005 0.087 0.22 5 -0.32 10 15
MAP3K7 0.01 0.004 -10000 0 -10000 0 0
RB1 0 0.086 0.23 24 -0.35 21 45
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.062 0.17 -10000 0 -0.37 125 125
ARHGDIB 0.01 0.06 0.24 20 -0.31 5 25
FADD 0.009 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.006 0.068 0.29 12 -0.23 24 36
NFKB1 -0.043 0.085 -10000 0 -0.73 2 2
MAPK8 -0.045 0.17 -10000 0 -0.45 67 67
DFFA 0.012 0.056 0.23 25 -0.28 3 28
DNA fragmentation during apoptosis 0.012 0.056 0.24 21 -0.28 3 24
FAS/FADD/MET 0.012 0.052 -10000 0 -0.34 12 12
CFLAR/RIP1 0.013 0.007 -10000 0 -10000 0 0
FAIM3 -0.012 0.11 -10000 0 -0.52 26 26
FAF1 0.009 0.008 -10000 0 -10000 0 0
PARP1 0.012 0.056 0.23 26 -0.28 3 29
DFFB 0.012 0.056 0.24 21 -0.28 3 24
CHUK -0.039 0.081 -10000 0 -0.77 2 2
FASLG -0.054 0.18 -10000 0 -0.54 66 66
FAS/FADD 0.006 0.056 -10000 0 -0.41 10 10
HGF -0.036 0.16 -10000 0 -0.55 49 49
LMNA 0.009 0.052 0.23 14 -0.3 3 17
CASP6 0.011 0.054 0.22 24 -0.28 3 27
CASP10 0.008 0.025 -10000 0 -0.58 1 1
CASP3 0.014 0.068 0.27 29 -0.33 3 32
PTPN13 -0.076 0.21 -10000 0 -0.56 88 88
CASP8 0.013 0.067 0.3 26 -0.44 1 27
IL6 -0.16 0.41 -10000 0 -1.2 65 65
MET 0.01 0.031 -10000 0 -0.52 2 2
ICAD/CAD 0.011 0.052 0.24 15 -0.29 2 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.027 0.12 -10000 0 -0.39 43 43
activation of caspase activity by cytochrome c 0.008 0.051 0.29 13 -0.32 2 15
PAK2 0.011 0.06 0.23 25 -0.39 3 28
BCL2 -0.007 0.1 -10000 0 -0.55 19 19
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.018 0.093 -10000 0 -0.63 10 10
HDAC1 0.008 0.004 -10000 0 -10000 0 0
AES 0.01 0.025 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 -0.01 0.11 -10000 0 -0.54 22 22
LRP6/FZD1 0.013 0.039 -10000 0 -0.4 5 5
TLE1 0.007 0.049 -10000 0 -0.58 4 4
AP1 -0.063 0.14 -10000 0 -0.31 105 105
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.006 0.055 -10000 0 -0.58 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.069 -10000 0 -1.3 1 1
NICD/RBPSUH 0.015 0.087 -10000 0 -0.65 9 9
WIF1 -0.18 0.25 -10000 0 -0.5 211 211
NOTCH1 -0.012 0.08 -10000 0 -0.63 9 9
PSENEN 0.01 0.025 -10000 0 -0.58 1 1
KREMEN2 -0.039 0.15 -10000 0 -0.48 59 59
DKK1 -0.15 0.24 -10000 0 -0.51 174 174
beta catenin/beta TrCP1 0.051 0.068 0.25 2 -10000 0 2
APH1B 0.006 0.055 -10000 0 -0.58 5 5
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 -0.014 0.047 -10000 0 -0.36 5 5
CtBP/CBP/TCF1/TLE1/AES 0.013 0.054 -10000 0 -0.93 1 1
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.03 0.14 -10000 0 -0.53 44 44
JUN 0.006 0.053 -10000 0 -0.56 5 5
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.047 0.072 0.25 3 -10000 0 3
MAPK3 0.01 0.025 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.38 81 81
HNF1A 0.005 0.058 -10000 0 -0.56 6 6
CTBP1 0.01 0.025 -10000 0 -0.58 1 1
MYC 0.009 0.13 -10000 0 -1.4 5 5
NKD1 -0.13 0.24 -10000 0 -0.52 155 155
FZD1 0.009 0.04 -10000 0 -0.54 3 3
NOTCH1 precursor/Deltex homolog 1 0.005 0.098 -10000 0 -0.59 10 10
apoptosis -0.063 0.13 -10000 0 -0.31 105 105
Delta 1/NOTCHprecursor 0.009 0.097 -10000 0 -0.63 10 10
DLL1 -0.003 0.088 -10000 0 -0.52 16 16
PPARD 0.019 0.059 -10000 0 -1.4 1 1
Gamma Secretase 0.031 0.033 -10000 0 -0.3 1 1
APC -0.029 0.1 -10000 0 -0.49 22 22
DVL1 -0.01 0.053 -10000 0 -0.5 4 4
CSNK2A1 0.012 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.4 93 93
LRP6 0.009 0.035 -10000 0 -0.58 2 2
CSNK1A1 0.01 0.035 -10000 0 -0.58 2 2
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.019 0.059 -10000 0 -1.4 1 1
WNT1 -0.009 0.086 -10000 0 -0.46 20 20
Axin1/APC/beta catenin 0.025 0.08 -10000 0 -0.42 8 8
DKK2 -0.085 0.21 -10000 0 -0.54 101 101
NOTCH1 precursor/DVL1 -0.018 0.092 -10000 0 -0.66 10 10
GSK3B 0.009 0.035 -10000 0 -0.58 2 2
FRAT1 0.01 0.025 -10000 0 -0.58 1 1
NOTCH/Deltex homolog 1 -0.021 0.093 -10000 0 -0.6 10 10
PPP2R5D 0.06 0.12 0.25 151 -10000 0 151
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
WNT1/LRP6/FZD1 -0.093 0.15 -10000 0 -0.34 84 84
RBPJ 0.01 0.031 -10000 0 -0.52 2 2
CREBBP 0.014 0.002 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.01 0.025 -10000 0 -0.58 1 1
Cbp/p300/PCAF 0.01 0.073 -10000 0 -0.37 20 20
EP300 0.007 0.049 -10000 0 -0.58 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.08 -10000 0 -0.38 12 12
KAT2B -0.006 0.1 -10000 0 -0.58 17 17
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.006 0.086 0.21 12 -0.3 15 27
RAR alpha/9cRA/Cyclin H -0.045 0.083 -10000 0 -0.5 4 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.006 0.087 -10000 0 -0.38 17 17
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0.001 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.029 0.08 -10000 0 -0.47 1 1
NCOR2 0.007 0.047 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA -0.048 0.17 -10000 0 -0.42 85 85
NCOA2 0.003 0.068 -10000 0 -0.56 8 8
NCOA3 0.01 0.025 -10000 0 -0.58 1 1
NCOA1 0.01 0.025 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.025 -10000 0 -0.58 1 1
RARG 0.006 0.06 -10000 0 -0.58 6 6
RAR gamma1/9cRA 0.012 0.038 -10000 0 -0.36 6 6
MAPK3 0.011 0.025 -10000 0 -0.58 1 1
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 0.011 0.025 -10000 0 -0.58 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.056 0.16 -10000 0 -0.43 77 77
RARA -0.037 0.099 -10000 0 -0.25 79 79
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.095 -10000 0 -0.4 19 19
PRKCA 0.011 0.032 -10000 0 -0.52 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.056 0.17 -10000 0 -0.43 84 84
RXRG -0.07 0.14 -10000 0 -0.34 78 78
RXRA -0.027 0.091 -10000 0 -0.26 5 5
RXRB -0.059 0.13 -10000 0 -0.34 76 76
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RBP1 -0.086 0.2 -10000 0 -0.48 113 113
CRBP1/9-cic-RA -0.062 0.14 -10000 0 -0.35 113 113
RARB -0.004 0.097 -10000 0 -0.54 18 18
PRKCG -0.14 0.24 -10000 0 -0.51 171 171
MNAT1 0.007 0.047 -10000 0 -0.55 4 4
RAR alpha/RXRs -0.04 0.18 -10000 0 -0.43 80 80
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.039 0.15 -10000 0 -0.37 79 79
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.096 -10000 0 -0.36 18 18
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.056 0.17 -10000 0 -0.43 84 84
positive regulation of DNA binding -0.043 0.079 -10000 0 -0.47 4 4
NRIP1 -0.059 0.2 -10000 0 -0.93 14 14
RXRs/RARs -0.059 0.16 -10000 0 -0.42 84 84
RXRs/RXRs/DNA/9cRA -0.064 0.16 -10000 0 -0.44 82 82
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.008 0.043 -10000 0 -0.58 3 3
TFIIH 0.019 0.045 -10000 0 -0.39 6 6
RAR alpha/9cRA -0.033 0.061 -10000 0 -0.39 4 4
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.006 0.042 -10000 0 -0.55 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.026 0.17 -9999 0 -0.5 51 51
MAP3K8 0.009 0.031 -9999 0 -0.52 2 2
FOS -0.026 0.16 -9999 0 -0.6 30 30
PRKCA 0.01 0.032 -9999 0 -0.52 2 2
PTPN7 -0.051 0.17 -9999 0 -0.5 71 71
HRAS 0.008 0.042 -9999 0 -0.49 4 4
PRKCB -0.039 0.16 -9999 0 -0.54 52 52
NRAS 0.001 0.077 -9999 0 -0.58 10 10
RAS family/GTP 0.01 0.07 -9999 0 -0.38 16 16
MAPK3 -0.022 0.14 -9999 0 -0.59 26 26
MAP2K1 -0.006 0.12 -9999 0 -0.42 38 38
ELK1 0.01 0.025 -9999 0 -0.58 1 1
BRAF -0.012 0.12 -9999 0 -0.43 37 37
mol:GTP 0 0.001 -9999 0 -0.005 42 42
MAPK1 -0.022 0.14 -9999 0 -0.59 26 26
RAF1 -0.011 0.11 -9999 0 -0.42 36 36
KRAS 0.005 0.058 -9999 0 -0.56 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR -0.042 0.16 -9999 0 -0.54 55 55
LRPAP1 0.01 0.025 -9999 0 -0.58 1 1
NUDC 0.011 0.019 -9999 0 -0.46 1 1
RELN/LRP8 -0.043 0.13 -9999 0 -0.31 114 114
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
KATNA1 0.01 0.025 -9999 0 -0.58 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.034 0.12 -9999 0 -0.32 60 60
IQGAP1/CaM 0.015 0.029 -9999 0 -0.39 3 3
DAB1 -0.081 0.2 -9999 0 -0.51 99 99
IQGAP1 0.008 0.04 -9999 0 -0.54 3 3
PLA2G7 -0.02 0.13 -9999 0 -0.56 32 32
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 0.014 0.036 -9999 0 -0.42 4 4
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.009 0.035 -9999 0 -0.58 2 2
CDK5R1 0.009 0.034 -9999 0 -0.46 3 3
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.048 0.16 -9999 0 -0.5 65 65
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.13 0.21 -9999 0 -0.37 219 219
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.023 0.12 -9999 0 -0.42 15 15
MAP1B -0.012 0.049 -9999 0 -0.31 9 9
RAC1 0.017 0.013 -9999 0 -0.18 2 2
p35/CDK5 -0.019 0.11 -9999 0 -0.48 3 3
RELN -0.091 0.21 -9999 0 -0.52 110 110
PAFAH/LIS1 0.002 0.083 -9999 0 -0.35 26 26
LIS1/CLIP170 0.021 0.022 -9999 0 -0.35 2 2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.043 0.08 -9999 0 -0.37 8 8
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.071 0.16 -9999 0 -0.32 131 131
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.031 0.13 -9999 0 -0.41 22 22
LIS1/IQGAP1 0.02 0.025 -9999 0 -0.32 3 3
RHOA 0.016 0.036 -9999 0 -0.49 2 2
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.008 0.044 -9999 0 -0.52 4 4
PAFAH1B2 0.007 0.049 -9999 0 -0.58 4 4
MAP1B/LIS1/Dynein heavy chain 0.013 0.035 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.018 0.12 -9999 0 -0.4 16 16
LRP8 0.008 0.043 -9999 0 -0.58 3 3
NDEL1/Katanin 60 -0.023 0.12 -9999 0 -0.42 16 16
P39/CDK5 -0.047 0.14 -9999 0 -0.48 22 22
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.012 -9999 0 -0.26 1 1
CDK5 -0.025 0.12 -9999 0 -0.29 60 60
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.019 -9999 0 -0.3 2 2
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.097 0.18 -9999 0 -0.37 131 131
RELN/VLDLR -0.061 0.16 -9999 0 -0.36 91 91
CDC42 0.012 0.058 -9999 0 -0.58 5 5
Plasma membrane estrogen 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
GNB1/GNG2 -0.013 0.11 -10000 0 -0.32 49 49
ER alpha/Gai/GDP/Gbeta gamma -0.022 0.14 -10000 0 -0.44 37 37
AKT1 -0.022 0.18 -10000 0 -0.72 33 33
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.024 0.18 -10000 0 -0.77 30 30
mol:Ca2+ -0.026 0.13 -10000 0 -0.43 32 32
IGF1R 0.01 0.025 -10000 0 -0.58 1 1
E2/ER alpha (dimer)/Striatin -0.018 0.1 -10000 0 -0.32 56 56
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.02 0.17 0.69 33 -10000 0 33
RhoA/GTP -0.029 0.088 -10000 0 -0.57 5 5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.048 0.12 -10000 0 -0.46 33 33
regulation of stress fiber formation -0.007 0.096 0.47 10 -10000 0 10
E2/ERA-ERB (dimer) -0.026 0.12 -10000 0 -0.34 67 67
KRAS 0.005 0.058 -10000 0 -0.56 6 6
G13/GTP -0.013 0.088 -10000 0 -0.29 52 52
pseudopodium formation 0.007 0.096 -10000 0 -0.47 10 10
E2/ER alpha (dimer)/PELP1 -0.015 0.096 -10000 0 -0.32 51 51
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 0.004 0.064 -10000 0 -0.53 8 8
GNAO1 -0.044 0.16 -10000 0 -0.49 63 63
HRAS 0.008 0.042 -10000 0 -0.49 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.02 0.14 -10000 0 -0.49 36 36
E2/ER beta (dimer) -0.006 0.075 -10000 0 -0.4 20 20
mol:GDP -0.041 0.11 -10000 0 -0.38 48 48
mol:NADP -0.02 0.14 -10000 0 -0.49 36 36
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
mol:IP3 -0.027 0.14 -10000 0 -0.45 32 32
IGF-1R heterotetramer 0.01 0.025 -10000 0 -0.58 1 1
PLCB1 -0.03 0.14 -10000 0 -0.47 30 30
PLCB2 -0.011 0.12 -10000 0 -0.45 26 26
IGF1 -0.071 0.19 -10000 0 -0.52 88 88
mol:L-citrulline -0.02 0.14 -10000 0 -0.49 36 36
RHOA 0.01 0.025 -10000 0 -0.58 1 1
Gai/GDP -0.02 0.15 -10000 0 -0.76 17 17
JNK cascade -0.006 0.075 -10000 0 -0.4 20 20
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
ESR2 -0.008 0.1 -10000 0 -0.54 20 20
GNAQ 0.005 0.06 -10000 0 -0.58 6 6
ESR1 -0.036 0.15 -10000 0 -0.52 50 50
Gq family/GDP/Gbeta gamma 0.002 0.12 -10000 0 -0.52 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.008 0.071 -10000 0 -0.3 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.046 0.12 -10000 0 -0.46 32 32
GNAZ -0.012 0.11 -10000 0 -0.54 24 24
E2/ER alpha (dimer) -0.026 0.11 -10000 0 -0.38 50 50
STRN 0.005 0.06 -10000 0 -0.58 6 6
GNAL -0.021 0.13 -10000 0 -0.5 36 36
PELP1 0.01 0.025 -10000 0 -0.58 1 1
MAPK11 -0.006 0.084 -10000 0 -0.32 35 35
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.088 -10000 0 -0.55 14 14
HBEGF -0.035 0.15 -10000 0 -0.44 49 49
cAMP biosynthetic process -0.046 0.11 -10000 0 -0.28 96 96
SRC -0.016 0.13 -10000 0 -0.42 34 34
PI3K 0.013 0.041 -10000 0 -0.42 5 5
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.039 0.1 -10000 0 -0.37 37 37
SOS1 0.01 0.025 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1 -0.065 0.13 -10000 0 -0.41 51 51
Gs family/GTP -0.047 0.11 -10000 0 -0.28 96 96
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.07 -10000 0 -0.38 16 16
vasodilation -0.019 0.14 -10000 0 -0.46 36 36
mol:DAG -0.027 0.14 -10000 0 -0.45 32 32
Gs family/GDP/Gbeta gamma -0.048 0.11 -10000 0 -0.38 37 37
MSN 0.006 0.1 -10000 0 -0.52 10 10
Gq family/GTP -0.015 0.12 -10000 0 -0.49 24 24
mol:PI-3-4-5-P3 -0.023 0.18 -10000 0 -0.74 30 30
NRAS 0.001 0.077 -10000 0 -0.58 10 10
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.14 0.46 36 -10000 0 36
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
RhoA/GDP -0.039 0.1 -10000 0 -0.37 45 45
NOS3 -0.022 0.15 -10000 0 -0.51 36 36
GNA11 0.007 0.051 -10000 0 -0.53 5 5
MAPKKK cascade -0.008 0.15 -10000 0 -0.56 34 34
E2/ER alpha (dimer)/PELP1/Src -0.049 0.12 -10000 0 -0.47 35 35
ruffle organization 0.007 0.096 -10000 0 -0.47 10 10
ROCK2 0.001 0.11 -10000 0 -0.62 9 9
GNA14 -0.008 0.1 -10000 0 -0.56 19 19
GNA15 -0.009 0.1 -10000 0 -0.54 21 21
GNA13 0.009 0.035 -10000 0 -0.58 2 2
MMP9 -0.042 0.16 -10000 0 -0.46 47 47
MMP2 -0.028 0.15 -10000 0 -0.45 41 41
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.059 0.15 -10000 0 -0.33 124 124
cell-cell adhesion 0.061 0.1 0.42 15 -10000 0 15
Ephrin B/EPHB2/RasGAP 0.009 0.088 -10000 0 -0.32 28 28
ITSN1 0.01 0.025 -10000 0 -0.58 1 1
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.079 -10000 0 -0.34 28 28
Ephrin B1/EPHB1 -0.058 0.13 -10000 0 -0.29 136 136
HRAS/GDP -0.058 0.1 -10000 0 -0.43 13 13
Ephrin B/EPHB1/GRB7 -0.051 0.14 -10000 0 -0.35 62 62
Endophilin/SYNJ1 0.006 0.082 -10000 0 -0.3 28 28
KRAS 0.005 0.058 -10000 0 -0.56 6 6
Ephrin B/EPHB1/Src -0.047 0.14 -10000 0 -0.34 57 57
endothelial cell migration 0.021 0.038 -10000 0 -0.36 5 5
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 0.002 0.067 -10000 0 -0.46 12 12
PAK1 0.01 0.092 -10000 0 -0.6 5 5
HRAS 0.008 0.042 -10000 0 -0.49 4 4
RRAS 0.007 0.086 -10000 0 -0.32 26 26
DNM1 -0.004 0.087 -10000 0 -0.5 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.046 0.13 -10000 0 -0.32 57 57
lamellipodium assembly -0.061 0.1 -10000 0 -0.42 15 15
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.023 0.1 -10000 0 -0.42 8 8
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
EPHB2 0 0.081 -10000 0 -0.55 12 12
EPHB3 -0.016 0.12 -10000 0 -0.55 28 28
EPHB1 -0.11 0.21 -10000 0 -0.49 135 135
EPHB4 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.11 -10000 0 -0.36 21 21
Ephrin B/EPHB2 0.003 0.086 -10000 0 -0.33 26 26
Ephrin B/EPHB3 -0.005 0.1 -10000 0 -0.34 35 35
JNK cascade -0.038 0.12 -10000 0 -0.3 50 50
Ephrin B/EPHB1 -0.053 0.13 -10000 0 -0.34 57 57
RAP1/GDP -0.011 0.1 -10000 0 -0.41 8 8
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EFNB3 -0.019 0.12 -10000 0 -0.52 33 33
EFNB1 0.01 0.025 -10000 0 -0.58 1 1
Ephrin B2/EPHB1-2 -0.052 0.13 -10000 0 -0.33 49 49
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.025 -10000 0 -0.58 1 1
CDC42/GTP -0.066 0.12 -10000 0 -0.47 19 19
Rap1/GTP -0.061 0.1 -10000 0 -0.43 17 17
axon guidance -0.059 0.15 -10000 0 -0.33 124 124
MAPK3 -0.011 0.094 -10000 0 -0.39 9 9
MAPK1 -0.011 0.095 -10000 0 -0.39 10 10
Rac1/GDP -0.016 0.1 -10000 0 -0.38 12 12
actin cytoskeleton reorganization -0.053 0.091 -10000 0 -0.39 17 17
CDC42/GDP -0.019 0.11 -10000 0 -0.39 15 15
PI3K 0.023 0.039 -10000 0 -0.36 5 5
EFNA5 -0.097 0.22 -10000 0 -0.52 118 118
Ephrin B2/EPHB4 0.014 0.02 -10000 0 -0.31 2 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.073 -10000 0 -0.29 26 26
CDC42 0.006 0.055 -10000 0 -0.58 5 5
RAS family/GTP -0.067 0.12 -10000 0 -0.46 23 23
PTK2 0.016 0.038 -10000 0 -0.57 1 1
MAP4K4 -0.039 0.12 -10000 0 -0.48 4 4
SRC 0.01 0.025 -10000 0 -0.58 1 1
KALRN 0.006 0.055 -10000 0 -0.58 5 5
Intersectin/N-WASP 0.016 0.018 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.009 0.11 -10000 0 -0.4 17 17
MAP2K1 -0.017 0.097 -10000 0 -0.4 10 10
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.045 0.13 -10000 0 -0.33 49 49
cell migration -0.014 0.11 -10000 0 -0.44 10 10
NRAS 0.001 0.077 -10000 0 -0.58 10 10
SYNJ1 0.006 0.084 -10000 0 -0.31 28 28
PXN 0.011 0 -10000 0 -10000 0 0
TF -0.044 0.13 -10000 0 -0.45 19 19
HRAS/GTP -0.067 0.11 -10000 0 -0.47 17 17
Ephrin B1/EPHB1-2 -0.051 0.13 -10000 0 -0.27 145 145
cell adhesion mediated by integrin 0.01 0.079 0.32 22 -10000 0 22
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.045 0.13 -10000 0 -0.49 15 15
RAC1-CDC42/GTP -0.072 0.12 -10000 0 -0.47 29 29
RASA1 0.009 0.035 -10000 0 -0.58 2 2
RAC1-CDC42/GDP -0.013 0.1 -10000 0 -0.4 11 11
ruffle organization -0.026 0.12 -10000 0 -0.43 16 16
NCK1 0.009 0.035 -10000 0 -0.58 2 2
receptor internalization 0.004 0.094 -10000 0 -0.5 7 7
Ephrin B/EPHB2/KALRN 0.007 0.098 -10000 0 -0.35 28 28
ROCK1 -0.002 0.091 -10000 0 -0.35 35 35
RAS family/GDP -0.048 0.088 -10000 0 -0.4 16 16
Rac1/GTP -0.064 0.11 -10000 0 -0.45 15 15
Ephrin B/EPHB1/Src/Paxillin -0.027 0.1 -10000 0 -0.28 57 57
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.2 -9999 0 -0.74 11 11
CRP -0.028 0.2 -9999 0 -0.69 17 17
cell cycle arrest -0.034 0.22 -9999 0 -0.69 26 26
TIMP1 -0.01 0.18 -9999 0 -0.63 11 11
IL6ST -0.001 0.094 -9999 0 -0.58 15 15
Rac1/GDP -0.038 0.17 -9999 0 -0.49 44 44
AP1 -0.001 0.12 -9999 0 -0.53 11 11
GAB2 0.01 0.035 -9999 0 -0.58 2 2
TNFSF11 -0.076 0.33 -9999 0 -1 52 52
HSP90B1 0.008 0.14 -9999 0 -1.3 6 6
GAB1 0.012 0.001 -9999 0 -10000 0 0
MAPK14 -0.028 0.16 -9999 0 -0.54 28 28
AKT1 0.037 0.073 -9999 0 -0.73 4 4
FOXO1 0.041 0.07 -9999 0 -0.68 4 4
MAP2K6 -0.035 0.16 -9999 0 -0.48 39 39
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.029 0.18 -9999 0 -0.52 39 39
MITF -0.046 0.17 -9999 0 -0.47 47 47
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.01 0.025 -9999 0 -0.58 1 1
A2M 0.011 0.071 -9999 0 -1.4 1 1
CEBPB 0.012 0.042 -9999 0 -0.48 4 4
GRB2/SOS1/GAB family/SHP2 0 0.09 -9999 0 -0.61 5 5
STAT3 -0.038 0.23 -9999 0 -0.73 27 27
STAT1 -0.009 0.069 -9999 0 -1.1 2 2
CEBPD -0.022 0.2 -9999 0 -0.76 14 14
PIK3CA 0.011 0.035 -9999 0 -0.58 2 2
PI3K 0.015 0.041 -9999 0 -0.42 5 5
JUN 0.006 0.053 -9999 0 -0.56 5 5
PIAS3/MITF -0.039 0.16 -9999 0 -0.48 41 41
MAPK11 -0.036 0.17 -9999 0 -0.58 32 32
STAT3 (dimer)/FOXO1 0.011 0.19 -9999 0 -0.63 13 13
GRB2/SOS1/GAB family -0.059 0.13 -9999 0 -0.54 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.047 0.17 -9999 0 -0.44 58 58
GRB2 0.012 0.001 -9999 0 -10000 0 0
JAK2 -0.009 0.1 -9999 0 -0.55 21 21
LBP -0.096 0.32 -9999 0 -0.87 62 62
PIK3R1 0.009 0.043 -9999 0 -0.58 3 3
JAK1 0.01 0.043 -9999 0 -0.58 3 3
MYC -0.026 0.21 -9999 0 -0.85 15 15
FGG -0.035 0.21 -9999 0 -0.75 16 16
macrophage differentiation -0.034 0.22 -9999 0 -0.69 26 26
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.061 0.17 -9999 0 -0.41 66 66
JUNB -0.023 0.2 -9999 0 -0.79 13 13
FOS -0.03 0.14 -9999 0 -0.53 44 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.038 0.16 -9999 0 -0.45 44 44
STAT1/PIAS1 -0.028 0.15 -9999 0 -0.49 31 31
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.076 -9999 0 -0.56 7 7
STAT3 (dimer) -0.037 0.23 -9999 0 -0.74 25 25
PRKCD -0.02 0.19 -9999 0 -0.56 32 32
IL6R -0.005 0.099 -9999 0 -0.55 18 18
SOCS3 -0.032 0.18 -9999 0 -0.77 16 16
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.081 -9999 0 -0.34 26 26
Rac1/GTP -0.037 0.18 -9999 0 -0.5 45 45
HCK -0.02 0.13 -9999 0 -0.55 32 32
MAPKKK cascade 0.012 0.094 -9999 0 -0.8 5 5
bone resorption -0.067 0.31 -9999 0 -0.93 53 53
IRF1 -0.021 0.2 -9999 0 -0.7 14 14
mol:GDP -0.047 0.18 -9999 0 -0.5 46 46
SOS1 0.01 0.025 -9999 0 -0.58 1 1
VAV1 -0.048 0.18 -9999 0 -0.52 46 46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.038 0.17 -9999 0 -0.56 34 34
PTPN11 -0.011 0.088 -9999 0 -0.91 5 5
IL6/IL6RA -0.079 0.18 -9999 0 -0.38 143 143
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.074 -9999 0 -0.33 25 25
gp130 (dimer)/JAK2/JAK2/LMO4 -0.001 0.1 -9999 0 -0.36 41 41
IL6 -0.11 0.22 -9999 0 -0.52 130 130
PIAS3 0.01 0.031 -9999 0 -0.52 2 2
PTPRE 0.006 0.026 -9999 0 -0.57 1 1
PIAS1 0.011 0 -9999 0 -10000 0 0
RAC1 0.012 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.042 0.14 -9999 0 -0.33 78 78
LMO4 0.006 0.063 -9999 0 -0.49 9 9
STAT3 (dimer)/PIAS3 -0.033 0.22 -9999 0 -0.7 27 27
MCL1 0.042 0.064 -9999 0 -0.7 3 3
LPA4-mediated signaling events

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
ADCY4 0.01 0.041 -9999 0 -0.31 9 9
ADCY5 -0.057 0.14 -9999 0 -0.32 124 124
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.014 0.023 -9999 0 -0.3 3 3
ADCY1 -0.018 0.095 -9999 0 -0.29 63 63
ADCY2 -0.017 0.1 -9999 0 -0.34 52 52
ADCY3 0.015 0 -9999 0 -10000 0 0
ADCY8 0.002 0.043 -9999 0 -0.27 14 14
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.014 0.025 -9999 0 -0.33 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.014 0.067 -9999 0 -0.36 4 4
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.009 0.12 -9999 0 -0.41 39 39
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DOCK1 0.01 0.025 -9999 0 -0.58 1 1
ITGA4 -0.018 0.13 -9999 0 -0.56 29 29
alpha4/beta7 Integrin/MAdCAM1 -0.081 0.17 -9999 0 -0.36 115 115
EPO 0 0.054 -9999 0 -0.46 8 8
alpha4/beta7 Integrin -0.024 0.14 -9999 0 -0.43 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
alpha4/beta1 Integrin -0.004 0.093 -9999 0 -0.41 29 29
EPO/EPOR (dimer) 0.004 0.059 -9999 0 -0.35 15 15
lamellipodium assembly 0.025 0.05 -9999 0 -0.44 5 5
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
PI3K 0.013 0.041 -9999 0 -0.42 5 5
ARF6 0.01 0.025 -9999 0 -0.58 1 1
JAK2 -0.006 0.11 -9999 0 -0.36 39 39
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
MADCAM1 -0.12 0.23 -9999 0 -0.52 146 146
cell adhesion -0.081 0.17 -9999 0 -0.36 115 115
CRKL/CBL 0.017 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC -0.007 0.12 -9999 0 -0.42 37 37
ITGB7 -0.017 0.12 -9999 0 -0.53 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.13 -9999 0 -0.42 46 46
p130Cas/Crk/Dock1 0.01 0.11 -9999 0 -0.51 17 17
VCAM1 -0.019 0.12 -9999 0 -0.53 32 32
RHOA 0.01 0.025 -9999 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.012 0.075 -9999 0 -0.32 26 26
BCAR1 -0.002 0.12 -9999 0 -0.4 38 38
EPOR 0.004 0.059 -9999 0 -0.49 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.01 0.025 -9999 0 -0.58 1 1
Rac1/GTP -0.002 0.052 -9999 0 -0.46 5 5
Nongenotropic Androgen signaling

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
PTK2 0.008 0.018 -10000 0 -0.43 1 1
GNB1/GNG2 -0.018 0.1 -10000 0 -0.34 27 27
regulation of S phase of mitotic cell cycle -0.002 0.074 -10000 0 -0.27 27 27
GNAO1 -0.044 0.16 -10000 0 -0.49 63 63
HRAS 0.008 0.042 -10000 0 -0.49 4 4
SHBG/T-DHT -0.008 0.062 -10000 0 -0.27 30 30
PELP1 0.01 0.025 -10000 0 -0.58 1 1
AKT1 0.008 0.018 -10000 0 -0.43 1 1
MAP2K1 -0.001 0.091 -10000 0 -0.42 5 5
T-DHT/AR -0.037 0.12 -10000 0 -0.36 70 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 42 42
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.088 -10000 0 -0.55 14 14
mol:GDP -0.034 0.098 -10000 0 -0.44 23 23
cell proliferation -0.003 0.12 -10000 0 -0.39 28 28
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
FOS -0.019 0.19 -10000 0 -0.74 31 31
mol:Ca2+ -0.011 0.021 -10000 0 -0.062 63 63
MAPK3 -0.001 0.1 -10000 0 -0.46 6 6
MAPK1 0.003 0.064 -10000 0 -0.31 4 4
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
mol:IP3 0 0.001 -10000 0 -0.004 44 44
cAMP biosynthetic process -0.003 0.062 -10000 0 -0.25 30 30
GNG2 0.004 0.064 -10000 0 -0.53 8 8
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 44 44
HRAS/GTP -0.032 0.084 -10000 0 -0.31 24 24
actin cytoskeleton reorganization -0.005 0.047 -10000 0 -0.4 7 7
SRC 0.01 0.025 -10000 0 -0.58 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 44 44
PI3K 0.012 0.035 -10000 0 -0.36 5 5
apoptosis 0.002 0.11 0.39 33 -10000 0 33
T-DHT/AR/PELP1 -0.024 0.1 -10000 0 -0.3 71 71
HRAS/GDP -0.033 0.095 -10000 0 -0.42 24 24
CREB1 -0.004 0.12 -10000 0 -0.41 33 33
RAC1-CDC42/GTP -0.004 0.048 -10000 0 -0.41 7 7
AR -0.052 0.17 -10000 0 -0.49 70 70
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.005 0.09 -10000 0 -0.48 3 3
RAC1-CDC42/GDP -0.031 0.094 -10000 0 -0.4 26 26
T-DHT/AR/PELP1/Src -0.015 0.097 -10000 0 -0.32 27 27
MAP2K2 -0.001 0.092 -10000 0 -0.54 3 3
T-DHT/AR/PELP1/Src/PI3K -0.002 0.074 -10000 0 -0.27 27 27
GNAZ -0.012 0.11 -10000 0 -0.54 24 24
SHBG -0.015 0.1 -10000 0 -0.46 30 30
Gi family/GNB1/GNG2/GDP -0.007 0.097 -10000 0 -0.37 18 18
mol:T-DHT 0 0.001 -10000 0 -0.003 23 23
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.001 0.056 -10000 0 -0.4 11 11
Gi family/GTP -0.022 0.088 -10000 0 -0.24 52 52
CDC42 0.006 0.055 -10000 0 -0.58 5 5
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.073 -10000 0 -0.59 8 8
SVIL 0 0.045 -10000 0 -0.48 4 4
ZNF318 0.031 0.048 -10000 0 -10000 0 0
JMJD2C 0.003 0.02 -10000 0 -0.077 26 26
T-DHT/AR/Ubc9 -0.023 0.11 -10000 0 -0.3 70 70
CARM1 0.009 0.025 -10000 0 -0.58 1 1
PRDX1 0.012 0.025 -10000 0 -0.58 1 1
PELP1 0.014 0.026 -10000 0 -0.58 1 1
CTNNB1 0.005 0.016 -10000 0 -10000 0 0
AKT1 0.016 0.028 -10000 0 -0.58 1 1
PTK2B 0.004 0.037 -10000 0 -0.58 2 2
MED1 0.014 0.046 -10000 0 -0.5 4 4
MAK 0.008 0.12 0.2 1 -0.46 27 28
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0 0.052 -10000 0 -0.58 4 4
GSN -0.008 0.077 -10000 0 -0.51 12 12
NCOA2 0.002 0.068 -10000 0 -0.57 8 8
NCOA6 0.004 0.031 -10000 0 -0.58 1 1
DNA-PK 0.04 0.056 -10000 0 -0.64 1 1
NCOA4 0.008 0.035 -10000 0 -0.58 2 2
PIAS3 0.004 0.035 -10000 0 -0.52 2 2
cell proliferation -0.004 0.099 -10000 0 -0.47 14 14
XRCC5 0.015 0.027 -10000 0 -0.57 1 1
UBE3A -0.005 0.058 -10000 0 -0.59 4 4
T-DHT/AR/SNURF -0.079 0.16 -10000 0 -0.33 152 152
FHL2 0.022 0.09 -10000 0 -1.1 2 2
RANBP9 0.004 0.031 -10000 0 -0.58 1 1
JMJD1A -0.006 0.043 -10000 0 -0.11 71 71
CDK6 0.011 0.02 -10000 0 -0.46 1 1
TGFB1I1 -0.001 0.053 -10000 0 -0.53 5 5
T-DHT/AR/CyclinD1 -0.031 0.11 -10000 0 -0.31 71 71
XRCC6 0.016 0.011 -10000 0 -10000 0 0
T-DHT/AR -0.02 0.12 -10000 0 -0.37 34 34
CTDSP1 0.007 0.026 -10000 0 -0.58 1 1
CTDSP2 0.025 0.032 -10000 0 -10000 0 0
BRCA1 0.003 0.031 -10000 0 -0.59 1 1
TCF4 0.009 0.084 -10000 0 -0.52 13 13
CDKN2A -0.063 0.19 -10000 0 -0.5 90 90
SRF 0.022 0.033 -10000 0 -0.45 2 2
NKX3-1 -0.074 0.24 -10000 0 -0.82 44 44
KLK3 -0.16 0.41 -10000 0 -1.4 52 52
TMF1 0.003 0.06 -10000 0 -0.58 6 6
HNRNPA1 0.018 0.017 -10000 0 -10000 0 0
AOF2 -0.008 0.021 -10000 0 -0.069 50 50
APPL1 0.022 0.071 -10000 0 -0.42 12 12
T-DHT/AR/Caspase 8 -0.017 0.11 -10000 0 -0.3 67 67
AR -0.054 0.17 -10000 0 -0.5 70 70
UBA3 0.007 0.026 -10000 0 -0.59 1 1
PATZ1 0.018 0.017 -10000 0 -10000 0 0
PAWR 0.008 0.025 -10000 0 -0.58 1 1
PRKDC 0.013 0.04 -10000 0 -0.52 3 3
PA2G4 0.02 0.021 -10000 0 -10000 0 0
UBE2I 0.011 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.1 -10000 0 -0.28 66 66
RPS6KA3 -0.002 0.054 -10000 0 -0.59 4 4
T-DHT/AR/ARA70 -0.03 0.11 -10000 0 -0.31 71 71
LATS2 0.017 0.035 -10000 0 -0.49 2 2
T-DHT/AR/PRX1 -0.011 0.11 -10000 0 -0.27 67 67
Cyclin D3/CDK11 p58 0.007 0.031 -10000 0 -0.32 5 5
VAV3 -0.073 0.2 -10000 0 -0.58 77 77
KLK2 -0.027 0.093 -10000 0 -0.4 26 26
CASP8 0.013 0.026 -10000 0 -0.58 1 1
T-DHT/AR/TIF2/CARM1 -0.026 0.11 -10000 0 -0.33 41 41
TMPRSS2 -0.019 0.11 -10000 0 -0.95 4 4
CCND1 0.007 0.027 -10000 0 -0.59 1 1
PIAS1 -0.001 0.03 -10000 0 -10000 0 0
mol:T-DHT -0.003 0.023 -10000 0 -0.07 34 34
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.009 0.052 -10000 0 -0.58 1 1
T-DHT/AR/CDK6 -0.021 0.11 -10000 0 -0.3 71 71
CMTM2 -0.03 0.14 -10000 0 -0.52 46 46
SNURF -0.079 0.2 -10000 0 -0.54 91 91
ZMIZ1 0.008 0.028 -10000 0 -0.44 1 1
CCND3 0.008 0.043 -10000 0 -0.46 5 5
TGIF1 0.018 0.017 -10000 0 -10000 0 0
FKBP4 0.003 0.038 -10000 0 -0.46 3 3
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.01 0.043 -9999 0 -0.36 7 7
PDGFRB -0.004 0.087 -9999 0 -0.53 15 15
SPHK1 -0.043 0.15 -9999 0 -0.78 20 20
mol:S1P -0.043 0.13 -9999 0 -0.66 21 21
S1P1/S1P/Gi -0.044 0.15 -9999 0 -0.39 57 57
GNAO1 -0.045 0.16 -9999 0 -0.49 63 63
PDGFB-D/PDGFRB/PLCgamma1 -0.039 0.15 -9999 0 -0.48 22 22
PLCG1 -0.039 0.14 -9999 0 -0.37 58 58
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.087 -9999 0 -0.53 15 15
GNAI2 0.01 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 -0.004 0.088 -9999 0 -0.56 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.008 0.037 -9999 0 -0.31 7 7
S1P1/S1P -0.018 0.12 -9999 0 -0.47 24 24
negative regulation of cAMP metabolic process -0.043 0.15 -9999 0 -0.38 57 57
MAPK3 -0.057 0.19 -9999 0 -0.56 52 52
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
KDR 0.005 0.054 -9999 0 -0.52 6 6
PLCB2 -0.013 0.11 -9999 0 -0.42 27 27
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.036 0.088 -9999 0 -0.39 24 24
receptor internalization -0.039 0.098 -9999 0 -0.44 24 24
PTGS2 -0.1 0.31 -9999 0 -1 48 48
Rac1/GTP -0.035 0.087 -9999 0 -0.39 24 24
RHOA 0.01 0.025 -9999 0 -0.58 1 1
VEGFA 0.01 0.02 -9999 0 -0.46 1 1
negative regulation of T cell proliferation -0.043 0.15 -9999 0 -0.38 57 57
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.013 0.11 -9999 0 -0.55 24 24
MAPK1 -0.057 0.19 -9999 0 -0.56 52 52
S1P1/S1P/PDGFB-D/PDGFRB -0.018 0.12 -9999 0 -0.44 27 27
ABCC1 0.01 0.025 -9999 0 -0.59 1 1
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.01 0.025 -10000 0 -0.58 1 1
PTK2 0.01 0.025 -10000 0 -0.58 1 1
CRKL -0.021 0.1 -10000 0 -0.3 47 47
GRB2/SOS1/SHC 0.023 0.016 -10000 0 -0.35 1 1
HRAS 0.008 0.042 -10000 0 -0.49 4 4
IRS1/Crk -0.021 0.1 -10000 0 -0.3 47 47
IGF-1R heterotetramer/IGF1/PTP1B -0.027 0.12 -10000 0 -0.34 48 48
AKT1 -0.004 0.092 -10000 0 -0.48 3 3
BAD 0.001 0.091 -10000 0 -0.46 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.021 0.1 -10000 0 -0.3 47 47
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.024 0.1 -10000 0 -0.3 53 53
RAF1 0.006 0.085 -10000 0 -0.43 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.012 0.099 -10000 0 -0.29 47 47
YWHAZ 0.008 0.043 -10000 0 -0.58 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.029 0.11 -10000 0 -0.32 55 55
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
RPS6KB1 -0.007 0.099 -10000 0 -0.51 6 6
GNB2L1 0.011 0.019 -10000 0 -0.46 1 1
positive regulation of MAPKKK cascade 0.004 0.076 -10000 0 -0.37 3 3
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
HRAS/GTP -0.033 0.078 -10000 0 -0.49 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.095 -10000 0 -0.48 3 3
IGF-1R heterotetramer 0 0.037 -10000 0 -0.66 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.02 0.1 -10000 0 -0.3 48 48
Crk/p130 Cas/Paxillin -0.009 0.095 -10000 0 -0.39 4 4
IGF1R 0 0.038 -10000 0 -0.67 1 1
IGF1 -0.071 0.2 -10000 0 -0.53 88 88
IRS2/Crk -0.018 0.1 -10000 0 -0.28 52 52
PI3K -0.015 0.1 -10000 0 -0.28 51 51
apoptosis -0.006 0.087 0.44 7 -10000 0 7
HRAS/GDP 0.006 0.03 -10000 0 -0.35 4 4
PRKCD -0.013 0.12 -10000 0 -0.39 47 47
RAF1/14-3-3 E 0.013 0.077 -10000 0 -0.37 3 3
BAD/14-3-3 0.006 0.092 -10000 0 -0.48 7 7
PRKCZ -0.005 0.093 -10000 0 -0.48 4 4
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.076 -10000 0 -0.44 8 8
PTPN1 0.01 0.025 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.02 0.13 -10000 0 -0.41 47 47
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.017 0.1 -10000 0 -0.3 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0.025 -10000 0 -0.58 1 1
IRS1/NCK2 -0.021 0.1 -10000 0 -0.3 48 48
GRB10 0.007 0.049 -10000 0 -0.58 4 4
PTPN11 -0.024 0.1 -10000 0 -0.3 53 53
IRS1 -0.03 0.11 -10000 0 -0.32 55 55
IRS2 -0.026 0.11 -10000 0 -0.31 52 52
IGF-1R heterotetramer/IGF1 -0.046 0.15 -10000 0 -0.38 88 88
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.01 0.096 -10000 0 -0.38 7 7
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.033 0.16 -10000 0 -0.42 69 69
SHC1 0.011 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.011 0.11 -9999 0 -0.57 21 21
PDGF/PDGFRA/CRKL 0.001 0.079 -9999 0 -0.4 21 21
positive regulation of JUN kinase activity 0.016 0.062 -9999 0 -0.3 20 20
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.009 0.086 -9999 0 -0.41 25 25
AP1 -0.066 0.21 -9999 0 -0.9 30 30
mol:IP3 0.001 0.086 -9999 0 -0.42 22 22
PLCG1 0.001 0.086 -9999 0 -0.42 22 22
PDGF/PDGFRA/alphaV Integrin -0.007 0.1 -9999 0 -0.42 31 31
RAPGEF1 0.01 0.025 -9999 0 -0.58 1 1
CRK 0.011 0.019 -9999 0 -0.46 1 1
mol:Ca2+ 0.001 0.085 -9999 0 -0.42 22 22
CAV3 -0.002 0.043 -9999 0 -0.46 5 5
CAV1 -0.002 0.08 -9999 0 -0.49 15 15
SHC/Grb2/SOS1 0.017 0.063 -9999 0 -0.3 20 20
PDGF/PDGFRA/Shf -0.032 0.13 -9999 0 -0.37 71 71
FOS -0.034 0.22 -9999 0 -0.89 30 30
JUN -0.009 0.043 -9999 0 -0.44 5 5
oligodendrocyte development -0.007 0.1 -9999 0 -0.42 31 31
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
mol:DAG 0.001 0.086 -9999 0 -0.42 22 22
PDGF/PDGFRA -0.011 0.11 -9999 0 -0.57 21 21
actin cytoskeleton reorganization 0 0.08 -9999 0 -0.4 22 22
SRF 0.017 0.02 -9999 0 -0.31 2 2
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K 0.006 0.075 -9999 0 -0.35 24 24
PDGF/PDGFRA/Crk/C3G 0.009 0.07 -9999 0 -0.34 21 21
JAK1 0 0.085 -9999 0 -0.4 24 24
ELK1/SRF 0.015 0.069 -9999 0 -0.32 21 21
SHB 0.011 0.019 -9999 0 -0.46 1 1
SHF -0.033 0.14 -9999 0 -0.48 52 52
CSNK2A1 0.005 0.015 -9999 0 -10000 0 0
GO:0007205 0 0.089 -9999 0 -0.44 22 22
SOS1 0.01 0.025 -9999 0 -0.58 1 1
Ras protein signal transduction 0.016 0.062 -9999 0 -0.3 20 20
PDGF/PDGFRA/SHB 0 0.08 -9999 0 -0.4 22 22
PDGF/PDGFRA/Caveolin-1 -0.008 0.1 -9999 0 -0.4 34 34
ITGAV 0 0.081 -9999 0 -0.58 11 11
ELK1 0.004 0.082 -9999 0 -0.39 21 21
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
PDGF/PDGFRA/Crk 0 0.08 -9999 0 -0.4 22 22
JAK-STAT cascade 0 0.085 -9999 0 -0.4 24 24
cell proliferation -0.031 0.13 -9999 0 -0.37 71 71
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.011 0.071 0.25 6 -0.56 4 10
DAPP1 -0.065 0.19 -10000 0 -0.51 64 64
Src family/SYK family/BLNK-LAT/BTK-ITK -0.07 0.22 -10000 0 -0.6 64 64
mol:DAG -0.015 0.11 0.18 2 -0.28 49 51
HRAS 0.008 0.042 -10000 0 -0.49 4 4
RAP1A 0.01 0.027 -10000 0 -0.62 1 1
ARF5/GDP 0.001 0.1 -10000 0 -0.43 24 24
PLCG2 -0.01 0.11 -10000 0 -0.54 22 22
PLCG1 0.01 0.025 -10000 0 -0.58 1 1
ARF5 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.011 0.073 0.23 6 -0.6 4 10
ARF1/GTP -0.011 0.071 0.24 6 -0.56 4 10
RHOA 0.01 0.025 -10000 0 -0.58 1 1
YES1 0.004 0.065 -10000 0 -0.58 7 7
RAP1A/GTP 0.01 0.075 0.22 6 -0.37 13 19
ADAP1 -0.011 0.072 0.22 6 -0.55 5 11
ARAP3 -0.011 0.072 0.23 6 -0.58 4 10
INPPL1 0.01 0.025 -10000 0 -0.58 1 1
PREX1 0.006 0.056 -10000 0 -0.54 6 6
ARHGEF6 -0.005 0.093 -10000 0 -0.54 17 17
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0.019 -10000 0 -0.46 1 1
NRAS 0.001 0.079 -10000 0 -0.59 10 10
FYN 0.005 0.061 -10000 0 -0.55 7 7
ARF6 0.01 0.025 -10000 0 -0.58 1 1
FGR -0.023 0.13 -10000 0 -0.53 36 36
mol:Ca2+ -0.001 0.055 -10000 0 -0.21 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.043 0.16 -10000 0 -0.52 59 59
ZAP70 -0.037 0.16 -10000 0 -0.53 51 51
mol:IP3 -0.005 0.076 -10000 0 -0.23 18 18
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.11 -10000 0 -0.44 24 24
RhoA/GDP -0.021 0.083 0.24 3 -0.47 10 13
PDK1/Src/Hsp90 0.021 0.027 -10000 0 -0.35 3 3
BLNK -0.009 0.11 -10000 0 -0.58 20 20
actin cytoskeleton reorganization 0.014 0.11 0.23 3 -0.48 15 18
SRC 0.01 0.025 -10000 0 -0.58 1 1
PLEKHA2 0.003 0.087 -10000 0 -0.36 30 30
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.003 0.058 -10000 0 -0.56 6 6
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
ARF6/GTP -0.01 0.073 0.25 6 -0.62 4 10
RhoA/GTP 0.015 0.077 0.22 6 -0.63 4 10
Src family/SYK family/BLNK-LAT -0.066 0.2 -10000 0 -0.57 60 60
BLK -0.11 0.23 -10000 0 -0.53 132 132
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 -0.01 0.069 0.22 6 -0.56 4 10
HCK -0.02 0.13 -10000 0 -0.55 32 32
CYTH3 -0.011 0.071 0.22 6 -0.56 4 10
CYTH2 -0.01 0.069 0.22 6 -0.56 4 10
KRAS 0.005 0.06 -10000 0 -0.57 6 6
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.022 0.076 -10000 0 -0.62 5 5
SGK1 -0.012 0.08 0.19 6 -0.7 5 11
INPP5D -0.015 0.12 -10000 0 -0.58 26 26
mol:GDP -0.006 0.11 -10000 0 -0.44 25 25
SOS1 0.01 0.025 -10000 0 -0.58 1 1
SYK 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP -0.021 0.082 0.24 3 -0.46 10 13
mol:PI-3-4-5-P3 -0.01 0.075 0.29 6 -0.59 4 10
ARAP3/RAP1A/GTP 0.01 0.076 0.22 6 -0.37 13 19
VAV1 -0.024 0.14 -10000 0 -0.57 35 35
mol:PI-3-4-P2 -0.002 0.095 -10000 0 -0.44 26 26
RAS family/GTP/PI3K Class I 0.011 0.075 -10000 0 -0.38 13 13
PLEKHA1 0.004 0.086 -10000 0 -0.36 29 29
Rac1/GDP 0.001 0.1 -10000 0 -0.43 24 24
LAT -0.01 0.1 -10000 0 -0.51 24 24
Rac1/GTP -0.013 0.14 -10000 0 -0.47 36 36
ITK -0.03 0.098 0.22 5 -0.55 7 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.15 0.21 2 -0.4 51 53
LCK -0.032 0.14 -10000 0 -0.51 48 48
BTK -0.028 0.092 0.22 3 -0.55 6 9
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.035 -9999 0 -0.58 2 2
ELF1 -0.017 0.11 -9999 0 -0.36 45 45
CCNA2 0.01 0.025 -9999 0 -0.58 1 1
PIK3CA 0.01 0.035 -9999 0 -0.58 2 2
JAK3 0.001 0.078 -9999 0 -0.53 12 12
PIK3R1 0.009 0.043 -9999 0 -0.58 3 3
JAK1 0.009 0.043 -9999 0 -0.58 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.14 -9999 0 -0.46 31 31
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.008 0.094 -9999 0 -0.35 38 38
IL2RA -0.049 0.23 -9999 0 -0.69 60 60
IL2RB -0.015 0.12 -9999 0 -0.55 28 28
SOS1 0.011 0.025 -9999 0 -0.58 1 1
IL2RG -0.001 0.086 -9999 0 -0.56 13 13
G1/S transition of mitotic cell cycle -0.016 0.18 -9999 0 -0.69 39 39
PTPN11 0.007 0.055 -9999 0 -0.58 5 5
CCND2 -0.032 0.21 -9999 0 -0.77 41 41
LCK -0.031 0.14 -9999 0 -0.51 48 48
GRB2 0.012 0.001 -9999 0 -10000 0 0
IL2 0.002 0.027 -9999 0 -0.45 2 2
CDK6 0.011 0.019 -9999 0 -0.46 1 1
CCND3 0.015 0.13 -9999 0 -0.59 9 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.29 -9999 0 -1.1 38 38
RAD9A 0.01 0.025 -9999 0 -0.58 1 1
AP1 -0.017 0.11 -9999 0 -0.38 48 48
IFNAR2 0.011 0.025 -9999 0 -0.58 1 1
AKT1 -0.006 0.061 -9999 0 -0.22 29 29
ER alpha/Oestrogen -0.026 0.11 -9999 0 -0.38 50 50
NFX1/SIN3/HDAC complex 0.033 0.028 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.51 209 209
SMG5 0.01 0.025 -9999 0 -0.58 1 1
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.016 0.02 -9999 0 -0.42 1 1
TERT/c-Abl -0.089 0.27 -9999 0 -0.96 40 40
SAP18 0.01 0.019 -9999 0 -0.45 1 1
MRN complex 0.007 0.092 -9999 0 -0.46 19 19
WT1 -0.18 0.26 -9999 0 -0.52 199 199
WRN 0.004 0.063 -9999 0 -0.56 7 7
SP1 0.01 0.026 -9999 0 -0.58 1 1
SP3 0.01 0.025 -9999 0 -0.58 1 1
TERF2IP 0.01 0.025 -9999 0 -0.58 1 1
Telomerase/Nucleolin -0.096 0.22 -9999 0 -0.89 37 37
Mad/Max 0.014 0.031 -9999 0 -0.34 4 4
TERT -0.1 0.3 -9999 0 -1.1 38 38
CCND1 -0.082 0.25 -9999 0 -0.96 35 35
MAX 0.011 0.004 -9999 0 -10000 0 0
RBBP7 0.01 0.025 -9999 0 -0.58 1 1
RBBP4 0.01 0.025 -9999 0 -0.58 1 1
TERF2 0.012 0.009 -9999 0 -10000 0 0
PTGES3 0.009 0.035 -9999 0 -0.58 2 2
SIN3A 0.01 0.025 -9999 0 -0.58 1 1
Telomerase/911 0.018 0.054 -9999 0 -0.7 2 2
CDKN1B -0.019 0.12 -9999 0 -0.36 41 41
RAD1 0.011 0.019 -9999 0 -0.46 1 1
XRCC5 0.01 0.025 -9999 0 -0.58 1 1
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.009 0.035 -9999 0 -0.58 2 2
TRF2/PARP2 0.017 0.018 -9999 0 -0.38 1 1
UBE3A 0.007 0.049 -9999 0 -0.58 4 4
JUN 0.006 0.053 -9999 0 -0.56 5 5
E6 0 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.037 -9999 0 -0.43 4 4
FOS -0.03 0.14 -9999 0 -0.53 44 44
IFN-gamma/IRF1 -0.032 0.14 -9999 0 -0.36 81 81
PARP2 0.01 0.025 -9999 0 -0.58 1 1
BLM 0.005 0.058 -9999 0 -0.56 6 6
Telomerase 0 0.07 -9999 0 -0.52 6 6
IRF1 0.012 0.035 -9999 0 -0.45 3 3
ESR1 -0.036 0.15 -9999 0 -0.53 50 50
KU/TER 0.016 0.018 -9999 0 -0.42 1 1
ATM/TRF2 0.012 0.049 -9999 0 -0.38 9 9
ubiquitin-dependent protein catabolic process 0.035 0.037 -9999 0 -0.38 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.035 0.038 -9999 0 -0.39 2 2
HDAC1 0.011 0.001 -9999 0 -10000 0 0
HDAC2 0.011 0.008 -9999 0 -10000 0 0
ATM -0.007 0.054 -9999 0 -0.44 9 9
SMAD3 0.004 0.076 -9999 0 -0.39 20 20
ABL1 0.01 0.025 -9999 0 -0.58 1 1
MXD1 0.008 0.042 -9999 0 -0.48 4 4
MRE11A 0.003 0.069 -9999 0 -0.58 8 8
HUS1 0.011 0 -9999 0 -10000 0 0
RPS6KB1 0.005 0.058 -9999 0 -0.56 6 6
TERT/NF kappa B1/14-3-3 -0.092 0.25 -9999 0 -1 33 33
NR2F2 0.012 0.007 -9999 0 -10000 0 0
MAPK3 0.009 0.027 -9999 0 -0.35 3 3
MAPK1 0.009 0.027 -9999 0 -0.35 3 3
TGFB1/TGF beta receptor Type II -0.001 0.083 -9999 0 -0.54 13 13
NFKB1 0.01 0.025 -9999 0 -0.58 1 1
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.007 0.054 -9999 0 -0.44 9 9
NBN -0.005 0.098 -9999 0 -0.58 16 16
EGFR 0.004 0.064 -9999 0 -0.54 8 8
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.13 0.19 -9999 0 -0.36 216 216
MYC 0.005 0.059 -9999 0 -0.56 6 6
IL2 0.001 0.029 -9999 0 -0.45 2 2
KU 0.016 0.018 -9999 0 -0.42 1 1
RAD50 0.01 0.025 -9999 0 -0.58 1 1
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
TGFB1 -0.001 0.083 -9999 0 -0.54 13 13
TRF2/BLM 0.014 0.04 -9999 0 -0.37 6 6
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.083 0.27 -9999 0 -0.99 38 38
SP1/HDAC2 0.017 0.023 -9999 0 -0.42 1 1
PINX1 0.004 0.065 -9999 0 -0.58 7 7
Telomerase/EST1A -0.096 0.22 -9999 0 -0.89 37 37
Smad3/Myc 0.007 0.074 -9999 0 -0.33 25 25
911 complex 0.022 0.02 -9999 0 -0.31 2 2
IFNG -0.06 0.18 -9999 0 -0.51 80 80
Telomerase/PinX1 -0.099 0.23 -9999 0 -0.88 39 39
Telomerase/AKT1/mTOR/p70S6K -0.003 0.084 -9999 0 -0.99 2 2
SIN3B 0.01 0.025 -9999 0 -0.58 1 1
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.097 0.23 -9999 0 -0.88 38 38
response to DNA damage stimulus 0.001 0.017 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.019 0.082 -9999 0 -0.62 6 6
TRF2/WRN 0.013 0.042 -9999 0 -0.36 7 7
Telomerase/hnRNP C1/C2 -0.096 0.22 -9999 0 -0.89 37 37
E2F1 0.009 0.037 -9999 0 -0.5 3 3
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 0.006 0.056 -9999 0 -0.54 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
FOXM1 transcription factor network

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
NFATC3 0.073 0.32 -9999 0 -0.98 16 16
PLK1 0.042 0.074 -9999 0 -1.4 1 1
BIRC5 0.044 0.047 -9999 0 -0.41 1 1
HSPA1B 0.059 0.34 -9999 0 -1 22 22
MAP2K1 0.028 0.049 -9999 0 -0.63 2 2
BRCA2 0.055 0.37 -9999 0 -1.2 28 28
FOXM1 0.062 0.37 -9999 0 -1.3 17 17
XRCC1 0.072 0.32 -9999 0 -1 17 17
FOXM1B/p19 -0.12 0.27 -9999 0 -1 33 33
Cyclin D1/CDK4 0.07 0.3 -9999 0 -0.9 16 16
CDC2 0.068 0.33 -9999 0 -1 17 17
TGFA 0.071 0.31 -9999 0 -0.89 19 19
SKP2 0.072 0.32 -9999 0 -1 16 16
CCNE1 0.013 0.035 -9999 0 -0.45 3 3
CKS1B 0.072 0.32 -9999 0 -0.98 17 17
RB1 -0.064 0.18 -9999 0 -0.96 18 18
FOXM1C/SP1 0.062 0.34 -9999 0 -1.1 18 18
AURKB 0.044 0.043 -9999 0 -10000 0 0
CENPF 0.061 0.36 -9999 0 -1.1 24 24
CDK4 0.018 0.012 -9999 0 -10000 0 0
MYC 0.074 0.3 -9999 0 -0.89 19 19
CHEK2 0.029 0.041 -9999 0 -0.63 1 1
ONECUT1 0.067 0.31 -9999 0 -0.95 17 17
CDKN2A -0.074 0.19 -9999 0 -0.51 90 90
LAMA4 0.071 0.32 -9999 0 -1 16 16
FOXM1B/HNF6 0.062 0.34 -9999 0 -1.1 17 17
FOS 0.032 0.39 -9999 0 -1 39 39
SP1 0.011 0.025 -9999 0 -0.58 1 1
CDC25B 0.072 0.32 -9999 0 -0.98 16 16
response to radiation 0.016 0.028 -9999 0 -10000 0 0
CENPB 0.072 0.32 -9999 0 -1 18 18
CENPA 0.072 0.32 -9999 0 -1 16 16
NEK2 0.073 0.32 -9999 0 -0.99 16 16
HIST1H2BA 0.066 0.32 -9999 0 -0.99 16 16
CCNA2 0.014 0.026 -9999 0 -0.59 1 1
EP300 0.007 0.049 -9999 0 -0.58 4 4
CCNB1/CDK1 0.063 0.35 -9999 0 -1.1 17 17
CCNB2 0.07 0.32 -9999 0 -0.99 18 18
CCNB1 0.07 0.33 -9999 0 -1 17 17
ETV5 0.057 0.35 -9999 0 -1.1 23 23
ESR1 0.03 0.4 -9999 0 -1.1 40 40
CCND1 0.073 0.31 -9999 0 -0.91 17 17
GSK3A 0.028 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.049 -9999 0 -0.5 2 2
CDK2 0.014 0.026 -9999 0 -0.59 1 1
G2/M transition of mitotic cell cycle 0.018 0.033 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.089 0.24 -9999 0 -1.1 17 17
GAS1 -0.048 0.5 -9999 0 -1.1 83 83
MMP2 0.039 0.4 -9999 0 -1.2 34 34
RB1/FOXM1C 0.069 0.33 -9999 0 -0.98 22 22
CREBBP 0.011 0 -9999 0 -10000 0 0
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 0.011 0.038 -10000 0 -0.36 6 6
RAS family/GTP -0.002 0.097 -10000 0 -0.36 12 12
NFATC4 0.003 0.088 0.19 5 -0.42 4 9
ERBB2IP -0.009 0.11 -10000 0 -0.58 20 20
HSP90 (dimer) 0.009 0.035 -10000 0 -0.58 2 2
mammary gland morphogenesis -0.011 0.1 0.22 6 -0.45 3 9
JUN 0.005 0.1 0.16 3 -0.28 44 47
HRAS 0.008 0.042 -10000 0 -0.49 4 4
DOCK7 -0.004 0.1 0.21 3 -0.4 4 7
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.019 0.12 0.23 14 -0.31 50 64
AKT1 0.008 0.019 -10000 0 -0.44 1 1
BAD 0.014 0.032 -10000 0 -0.48 2 2
MAPK10 -0.007 0.081 -10000 0 -0.27 23 23
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.01 0.11 0.24 6 -0.49 3 9
RAF1 0.007 0.099 -10000 0 -0.36 11 11
ErbB2/ErbB3/neuregulin 2 0.001 0.073 0.23 12 -0.29 5 17
STAT3 0 0.045 -10000 0 -1.1 1 1
cell migration 0.008 0.075 0.16 10 -0.24 18 28
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.009 0.19 -10000 0 -0.59 40 40
FOS -0.003 0.16 -10000 0 -0.41 57 57
NRAS 0.001 0.078 -10000 0 -0.58 10 10
mol:Ca2+ -0.011 0.1 0.22 6 -0.45 3 9
MAPK3 -0.002 0.16 -10000 0 -0.5 33 33
MAPK1 -0.002 0.16 -10000 0 -0.49 33 33
JAK2 -0.011 0.11 -10000 0 -0.43 10 10
NF2 -0.001 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.01 0.093 -10000 0 -0.28 49 49
NRG1 -0.068 0.19 -10000 0 -0.53 84 84
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
MAPK8 0 0.097 0.2 6 -0.27 52 58
MAPK9 0.007 0.059 -10000 0 -0.23 6 6
ERBB2 0.005 0.087 0.39 19 -0.34 13 32
ERBB3 0.01 0.025 -10000 0 -0.58 1 1
SHC1 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.002 0.036 0.82 1 -10000 0 1
STAT3 (dimer) 0.014 0.044 -10000 0 -1 1 1
RNF41 0.016 0.035 -10000 0 -0.32 6 6
FRAP1 0.007 0.016 -10000 0 -0.37 1 1
RAC1-CDC42/GTP -0.027 0.065 -10000 0 -0.33 7 7
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.062 0.26 17 -0.28 13 30
CHRNA1 -0.009 0.18 -10000 0 -0.61 37 37
myelination 0.005 0.086 0.19 6 -0.4 4 10
PPP3CB -0.003 0.094 -10000 0 -0.4 3 3
KRAS 0.005 0.058 -10000 0 -0.56 6 6
RAC1-CDC42/GDP -0.001 0.084 -10000 0 -0.31 6 6
NRG2 -0.015 0.1 -10000 0 -0.46 29 29
mol:GDP -0.009 0.093 -10000 0 -0.28 49 49
SOS1 0.01 0.025 -10000 0 -0.58 1 1
MAP2K2 0.011 0.1 -10000 0 -0.39 11 11
SRC 0.01 0.025 -10000 0 -0.58 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.006 0.1 -10000 0 -0.42 5 5
MAP2K1 -0.005 0.15 -10000 0 -0.53 17 17
heart morphogenesis -0.011 0.1 0.22 6 -0.45 3 9
RAS family/GDP -0.002 0.097 -10000 0 -0.42 7 7
GRB2 0.011 0.001 -10000 0 -10000 0 0
PRKACA -0.003 0.006 -10000 0 -10000 0 0
CHRNE 0 0.055 -10000 0 -0.18 45 45
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
activation of caspase activity -0.008 0.019 0.44 1 -10000 0 1
nervous system development -0.011 0.1 0.22 6 -0.45 3 9
CDC42 0.006 0.055 -10000 0 -0.58 5 5
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.013 0.1 -10000 0 -0.98 4 4
epithelial cell differentiation -0.049 0.12 -10000 0 -0.54 16 16
ITCH 0.007 0.057 -10000 0 -0.59 5 5
WWP1 0.016 0.12 -10000 0 -1.5 3 3
FYN 0.005 0.061 -10000 0 -0.55 7 7
EGFR 0.004 0.064 -10000 0 -0.53 8 8
PRL -0.013 0.088 -10000 0 -0.46 22 22
neuron projection morphogenesis 0.006 0.12 -10000 0 -0.79 4 4
PTPRZ1 -0.077 0.19 -10000 0 -0.5 96 96
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.13 -10000 0 -1.1 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.024 0.14 -10000 0 -1.2 3 3
ADAM17 0.011 0.038 -10000 0 -0.63 2 2
ErbB4/ErbB4 0.017 0.1 -10000 0 -1.1 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.1 -10000 0 -1 4 4
NCOR1 0.01 0.025 -10000 0 -0.58 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.02 0.14 -10000 0 -1 4 4
GRIN2B -0.039 0.16 -10000 0 -0.66 16 16
ErbB4/ErbB2/betacellulin 0.013 0.11 -10000 0 -0.96 4 4
STAT1 0.006 0.052 -10000 0 -0.5 6 6
HBEGF 0.001 0.069 -10000 0 -0.46 13 13
PRLR -0.043 0.17 -10000 0 -0.57 53 53
E4ICDs/ETO2 -0.036 0.15 -10000 0 -0.38 51 51
axon guidance 0.014 0.13 -10000 0 -1.1 4 4
NEDD4 0.008 0.049 -10000 0 -0.57 4 4
Prolactin receptor/Prolactin receptor/Prolactin -0.04 0.14 -10000 0 -0.42 69 69
CBFA2T3 -0.082 0.2 -10000 0 -0.5 104 104
ErbB4/ErbB2/HBEGF 0.014 0.1 -10000 0 -1.1 3 3
MAPK3 0.001 0.12 -10000 0 -0.83 4 4
STAT1 (dimer) 0.016 0.11 -10000 0 -1.1 4 4
MAPK1 0.001 0.12 -10000 0 -0.94 3 3
JAK2 -0.009 0.1 -10000 0 -0.55 21 21
ErbB4/ErbB2/neuregulin 1 beta -0.023 0.14 -10000 0 -0.91 5 5
NRG1 -0.041 0.15 -10000 0 -0.39 85 85
NRG3 -0.004 0.066 -10000 0 -0.46 12 12
NRG2 -0.015 0.1 -10000 0 -0.46 29 29
NRG4 -0.022 0.12 -10000 0 -0.47 36 36
heart development 0.014 0.13 -10000 0 -1.1 4 4
neural crest cell migration -0.022 0.14 -10000 0 -0.87 5 5
ERBB2 0.009 0.061 -10000 0 -0.34 16 16
WWOX/E4ICDs 0.018 0.097 -10000 0 -0.76 6 6
SHC1 0.011 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.003 0.12 -10000 0 -0.87 6 6
apoptosis 0.036 0.097 0.99 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.002 0.12 -10000 0 -1.1 4 4
ErbB4/ErbB2/epiregulin -0.074 0.17 -10000 0 -0.54 15 15
ErbB4/ErbB4/betacellulin/betacellulin 0.011 0.11 -10000 0 -0.48 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.02 0.16 -10000 0 -0.61 20 20
MDM2 0.019 0.1 -10000 0 -0.9 5 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.14 -10000 0 -0.78 6 6
STAT5A 0.019 0.12 -10000 0 -1.1 4 4
ErbB4/EGFR/neuregulin 1 beta -0.02 0.15 -10000 0 -1.1 4 4
DLG4 0.007 0.048 -10000 0 -0.5 5 5
GRB2/SHC 0.017 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.016 0.091 -10000 0 -0.81 5 5
STAT5A (dimer) -0.053 0.13 -10000 0 -0.61 16 16
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.018 0.12 -10000 0 -1.1 4 4
LRIG1 -0.002 0.088 -10000 0 -0.58 13 13
EREG -0.16 0.26 -10000 0 -0.55 179 179
BTC -0.002 0.088 -10000 0 -0.58 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.014 0.14 -10000 0 -1.2 4 4
ERBB4 0.017 0.1 -10000 0 -1.1 4 4
STAT5B 0.011 0 -10000 0 -10000 0 0
YAP1 0.003 0.088 -10000 0 -1.1 3 3
GRB2 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.11 -10000 0 -0.96 4 4
glial cell differentiation -0.016 0.089 0.79 5 -10000 0 5
WWOX 0.009 0.035 -10000 0 -0.58 2 2
cell proliferation -0.017 0.15 -10000 0 -0.78 7 7
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.018 0.12 -9999 0 -0.31 53 53
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.003 0.12 -9999 0 -0.56 12 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.08 -9999 0 -0.37 22 22
antigen processing and presentation of peptide antigen via MHC class I -0.039 0.074 -9999 0 -0.28 19 19
CaM/Ca2+ -0.017 0.11 -9999 0 -0.45 9 9
RAP1A 0.01 0.025 -9999 0 -0.58 1 1
STAT1 (dimer)/SHP2 -0.012 0.12 -9999 0 -0.54 11 11
AKT1 -0.003 0.11 -9999 0 -0.46 12 12
MAP2K1 -0.009 0.12 -9999 0 -0.56 11 11
MAP3K11 -0.013 0.11 -9999 0 -0.42 12 12
IFNGR1 0.008 0.012 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.053 0.12 -9999 0 -0.48 31 31
Rap1/GTP -0.031 0.073 -9999 0 -0.42 5 5
CRKL/C3G 0.016 0.018 -9999 0 -0.42 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.02 0.12 -9999 0 -0.48 10 10
CEBPB -0.008 0.16 -9999 0 -0.5 26 26
STAT3 0.011 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.052 0.22 -9999 0 -0.85 26 26
STAT1 -0.012 0.12 -9999 0 -0.53 11 11
CALM1 0.011 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.063 0.18 -9999 0 -0.51 80 80
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
STAT1 (dimer)/PIAS1 -0.005 0.11 -9999 0 -0.5 11 11
CEBPB/PTGES2/Cbp/p300 -0.039 0.087 -9999 0 -0.42 13 13
mol:Ca2+ -0.02 0.11 -9999 0 -0.31 53 53
MAPK3 -0.005 0.13 -9999 0 -0.71 7 7
STAT1 (dimer) -0.051 0.1 -9999 0 -0.4 19 19
MAPK1 -0.005 0.12 -9999 0 -0.66 8 8
JAK2 -0.012 0.11 -9999 0 -0.56 21 21
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
JAK1 0.005 0.045 -9999 0 -0.6 3 3
CAMK2D 0.007 0.049 -9999 0 -0.58 4 4
DAPK1 -0.012 0.16 -9999 0 -0.54 36 36
SMAD7 0.012 0.059 -9999 0 -0.29 2 2
CBL/CRKL/C3G -0.001 0.1 -9999 0 -0.47 6 6
PI3K -0.041 0.1 -9999 0 -0.5 12 12
IFNG -0.063 0.18 -9999 0 -0.51 80 80
apoptosis -0.012 0.12 -9999 0 -0.4 34 34
CAMK2G 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.023 0.13 -9999 0 -0.53 35 35
CAMK2B -0.053 0.17 -9999 0 -0.49 72 72
FRAP1 -0.002 0.1 -9999 0 -0.42 12 12
PRKCD -0.002 0.11 -9999 0 -0.46 12 12
RAP1B 0.011 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.039 0.074 -9999 0 -0.28 19 19
PTPN2 0.008 0.043 -9999 0 -0.58 3 3
EP300 0.007 0.049 -9999 0 -0.58 4 4
IRF1 0.001 0.13 -9999 0 -0.51 15 15
STAT1 (dimer)/PIASy -0.004 0.12 -9999 0 -0.51 10 10
SOCS1 -0.046 0.22 -9999 0 -1.4 13 13
mol:GDP -0.03 0.087 -9999 0 -0.41 8 8
CASP1 0.002 0.085 -9999 0 -0.28 33 33
PTGES2 0.007 0.046 -9999 0 -0.48 5 5
IRF9 0.02 0.054 -9999 0 -0.27 2 2
mol:PI-3-4-5-P3 -0.04 0.1 -9999 0 -0.48 12 12
RAP1/GDP -0.031 0.074 -9999 0 -0.43 5 5
CBL -0.012 0.11 -9999 0 -0.46 9 9
MAP3K1 -0.016 0.12 -9999 0 -0.49 14 14
PIAS1 0.011 0 -9999 0 -10000 0 0
PIAS4 0.011 0.024 -9999 0 -0.56 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.039 0.074 -9999 0 -0.28 19 19
PTPN11 -0.019 0.11 -9999 0 -0.31 53 53
CREBBP 0.012 0.001 -9999 0 -10000 0 0
RAPGEF1 0.01 0.025 -9999 0 -0.58 1 1
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.087 -9999 0 -0.53 15 15
alphaV beta3 Integrin -0.003 0.092 -9999 0 -0.41 27 27
PTK2 -0.027 0.1 -9999 0 -0.43 27 27
positive regulation of JNK cascade -0.017 0.068 -9999 0 -0.31 27 27
CDC42/GDP 0.018 0.11 -9999 0 -0.42 27 27
Rac1/GDP 0.021 0.1 -9999 0 -0.42 26 26
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.025 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.021 0.083 -9999 0 -0.38 27 27
nectin-3/I-afadin -0.003 0.09 -9999 0 -0.42 26 26
RAPGEF1 0.019 0.11 -9999 0 -0.46 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.12 -9999 0 -0.52 26 26
PDGFB-D/PDGFRB -0.003 0.087 -9999 0 -0.53 15 15
TLN1 0.013 0.059 -9999 0 -0.54 3 3
Rap1/GTP -0.016 0.069 -9999 0 -0.32 26 26
IQGAP1 0.008 0.04 -9999 0 -0.54 3 3
Rap1/GTP/I-afadin 0.02 0.025 -9999 0 -0.32 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.003 0.09 -9999 0 -0.42 26 26
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.014 0.13 -9999 0 -0.53 26 26
MLLT4 0.009 0.035 -9999 0 -0.58 2 2
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
PI3K 0.009 0.089 -9999 0 -0.31 37 37
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
positive regulation of lamellipodium assembly -0.025 0.083 -9999 0 -0.3 46 46
PVRL1 0.009 0.035 -9999 0 -0.58 2 2
PVRL3 -0.013 0.12 -9999 0 -0.58 24 24
PVRL2 0.01 0.031 -9999 0 -0.52 2 2
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
CDH1 0.01 0.025 -9999 0 -0.58 1 1
CLDN1 -0.013 0.12 -9999 0 -0.56 24 24
JAM-A/CLDN1 0 0.095 -9999 0 -0.32 45 45
SRC 0.006 0.13 -9999 0 -0.58 26 26
ITGB3 -0.005 0.093 -9999 0 -0.54 17 17
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
FARP2 0.016 0.12 -9999 0 -0.5 26 26
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.009 0.035 -9999 0 -0.58 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.006 0.078 -9999 0 -0.35 26 26
nectin-1/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
nectin-2/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
RAC1/GTP/IQGAP1/filamentous actin 0.014 0.025 -9999 0 -0.33 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.005 0.081 -9999 0 -0.35 28 28
CDC42/GTP/IQGAP1/filamentous actin 0.011 0.051 -9999 0 -0.45 6 6
F11R 0.011 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.017 0.068 -9999 0 -0.31 27 27
alphaV/beta3 Integrin/Talin 0.012 0.09 -9999 0 -0.52 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
nectin-2(dimer)/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
PIP5K1C 0.008 0.059 -9999 0 -0.47 3 3
VAV2 -0.003 0.16 -9999 0 -0.51 46 46
RAP1/GDP -0.021 0.083 -9999 0 -0.39 26 26
ITGAV 0 0.081 -9999 0 -0.58 11 11
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.005 0.08 -9999 0 -0.35 28 28
nectin-3(dimer)/I-afadin/I-afadin -0.003 0.09 -9999 0 -0.42 26 26
Rac1/GTP -0.031 0.1 -9999 0 -0.36 46 46
PTPRM 0.002 0.062 -9999 0 -0.25 26 26
E-cadherin/beta catenin/alpha catenin -0.004 0.037 -9999 0 -0.57 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.006 0.055 -9999 0 -0.58 5 5
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.076 0.19 -9999 0 -0.5 97 97
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.005 0.057 -9999 0 -0.47 8 8
TCEB1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/p53 -0.007 0.095 -9999 0 -0.28 53 53
HIF1A 0.014 0.036 -9999 0 -0.25 9 9
COPS5 0.011 0.019 -9999 0 -0.46 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.029 0.043 -9999 0 -0.38 4 4
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.07 0.19 -9999 0 -0.51 90 90
ARNT/IPAS -0.047 0.14 -9999 0 -0.36 98 98
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/ARNT 0.019 0.04 -9999 0 -0.4 2 2
CUL2 0.011 0 -9999 0 -10000 0 0
OS9 0.011 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.018 0.041 -9999 0 -0.3 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.019 0.045 -9999 0 -0.44 3 3
PHD1-3/OS9 0.02 0.052 -9999 0 -0.32 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.026 0.055 -9999 0 -0.4 8 8
VHL 0.01 0.025 -9999 0 -0.58 1 1
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
HIF1A/JAB1 0.02 0.036 -9999 0 -0.29 1 1
EGLN3 -0.002 0.084 -9999 0 -0.51 15 15
EGLN2 0.009 0.037 -9999 0 -0.5 3 3
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 -0.043 0.17 -9999 0 -0.58 53 53
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.026 0.046 -9999 0 -0.86 1 1
ARNT 0.01 0.025 -9999 0 -0.58 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0.031 -9999 0 -0.52 2 2
HIF1A/p19ARF -0.02 0.1 -9999 0 -0.28 44 44
Signaling events mediated by PRL

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
CCNE1 0.009 0.034 -10000 0 -0.46 3 3
mol:Halofuginone 0.004 0.01 -10000 0 -0.23 1 1
ITGA1 0.006 0.055 -10000 0 -0.58 5 5
CDKN1A 0.018 0.049 -10000 0 -0.44 4 4
PRL-3/alpha Tubulin -0.006 0.093 -10000 0 -0.37 35 35
mol:Ca2+ -0.009 0.12 0.29 33 -0.39 37 70
AGT -0.025 0.14 -10000 0 -0.53 39 39
CCNA2 0.018 0.07 -10000 0 -0.89 1 1
TUBA1B 0.011 0 -10000 0 -10000 0 0
EGR1 0.002 0.08 -10000 0 -0.35 28 28
CDK2/Cyclin E1 0.026 0.048 -10000 0 -0.43 3 3
MAPK3 -0.006 0.095 -10000 0 -0.37 36 36
PRL-2 /Rab GGTase beta 0.015 0.032 -10000 0 -0.42 3 3
MAPK1 -0.006 0.095 -10000 0 -0.37 36 36
PTP4A1 0.014 0.073 -10000 0 -0.94 1 1
PTP4A3 -0.021 0.13 -10000 0 -0.52 35 35
PTP4A2 0.011 0 -10000 0 -10000 0 0
ITGB1 -0.005 0.093 -10000 0 -0.37 35 35
SRC 0.01 0.025 -10000 0 -0.58 1 1
RAC1 0.004 0.086 -10000 0 -0.41 19 19
Rab GGTase beta/Rab GGTase alpha 0.014 0.036 -10000 0 -0.42 4 4
PRL-1/ATF-5 0.018 0.069 -10000 0 -0.89 1 1
RABGGTA 0.01 0.025 -10000 0 -0.58 1 1
BCAR1 0.015 0.075 0.29 33 -0.33 2 35
RHOC 0.004 0.086 -10000 0 -0.42 18 18
RHOA 0.003 0.087 -10000 0 -0.41 20 20
cell motility 0.003 0.092 -10000 0 -0.42 20 20
PRL-1/alpha Tubulin 0.019 0.069 -10000 0 -0.89 1 1
PRL-3/alpha1 Integrin -0.01 0.1 -10000 0 -0.37 40 40
ROCK1 0.003 0.093 -10000 0 -0.43 20 20
RABGGTB 0.008 0.043 -10000 0 -0.58 3 3
CDK2 0.01 0.025 -10000 0 -0.58 1 1
mitosis 0.014 0.073 -10000 0 -0.93 1 1
ATF5 0.011 0.019 -10000 0 -0.46 1 1
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.044 0.16 -9999 0 -0.49 63 63
CDC42/GTP -0.016 0.1 -9999 0 -0.4 16 16
PLCG1 -0.014 0.11 -9999 0 -0.45 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.015 0.026 -9999 0 -0.42 2 2
cell migration -0.016 0.1 -9999 0 -0.39 16 16
S1PR5 0.001 0.075 -9999 0 -0.54 11 11
S1PR4 -0.025 0.14 -9999 0 -0.53 38 38
MAPK3 -0.014 0.11 -9999 0 -0.47 12 12
MAPK1 -0.014 0.11 -9999 0 -0.47 12 12
S1P/S1P5/Gi -0.01 0.095 -9999 0 -0.3 27 27
GNAI1 -0.002 0.088 -9999 0 -0.55 14 14
CDC42/GDP 0.005 0.041 -9999 0 -0.43 5 5
S1P/S1P5/G12 0.009 0.047 -9999 0 -0.33 11 11
RHOA 0.005 0.076 -9999 0 -0.3 26 26
S1P/S1P4/Gi -0.021 0.11 -9999 0 -0.31 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.012 0.11 -9999 0 -0.54 24 24
S1P/S1P4/G12/G13 0 0.08 -9999 0 -0.29 40 40
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.035 -9999 0 -0.58 2 2
CDC42 0.006 0.055 -9999 0 -0.58 5 5
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.007 0.049 -10000 0 -0.57 4 4
HSPA8 0.009 0.035 -10000 0 -0.58 2 2
SMAD3/SMAD4/ER alpha -0.036 0.12 0.21 6 -0.36 45 51
AKT1 0.01 0.028 -10000 0 -0.58 1 1
GSC -0.018 0.14 -10000 0 -1.1 6 6
NKX2-5 -0.012 0.08 -10000 0 -0.46 18 18
muscle cell differentiation 0.038 0.091 0.47 13 -10000 0 13
SMAD2-3/SMAD4/SP1 0.025 0.098 -10000 0 -0.42 5 5
SMAD4 0 0.072 -10000 0 -0.56 6 6
CBFB 0.007 0.049 -10000 0 -0.58 4 4
SAP18 0.011 0.019 -10000 0 -0.46 1 1
Cbp/p300/MSG1 -0.037 0.12 -10000 0 -0.29 90 90
SMAD3/SMAD4/VDR -0.007 0.058 -10000 0 -0.45 2 2
MYC 0.005 0.059 -10000 0 -0.55 6 6
CDKN2B -0.01 0.22 -10000 0 -1.4 13 13
AP1 0.009 0.11 -10000 0 -0.48 13 13
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.038 0.055 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.008 0.082 -10000 0 -0.34 10 10
SP3 0.012 0.025 -10000 0 -0.58 1 1
CREB1 0.009 0.035 -10000 0 -0.58 2 2
FOXH1 -0.056 0.17 -10000 0 -0.5 75 75
SMAD3/SMAD4/GR -0.012 0.1 -10000 0 -0.38 30 30
GATA3 -0.027 0.13 -10000 0 -0.54 31 31
SKI/SIN3/HDAC complex/NCoR1 0.036 0.024 -10000 0 -10000 0 0
MEF2C/TIF2 -0.019 0.13 -10000 0 -0.48 21 21
endothelial cell migration 0.038 0.2 1.3 11 -10000 0 11
MAX 0.013 0.01 -10000 0 -10000 0 0
RBBP7 0.01 0.025 -10000 0 -0.58 1 1
RBBP4 0.01 0.025 -10000 0 -0.58 1 1
RUNX2 -0.006 0.095 -10000 0 -0.53 18 18
RUNX3 -0.019 0.12 -10000 0 -0.51 33 33
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.01 0.025 -10000 0 -0.58 1 1
NR3C1 -0.014 0.12 -10000 0 -0.52 28 28
VDR 0.01 0.025 -10000 0 -0.58 1 1
CDKN1A 0.028 0.13 -10000 0 -1.2 4 4
KAT2B -0.007 0.1 -10000 0 -0.58 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.023 0.13 -10000 0 -0.36 43 43
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0.001 -10000 0 -10000 0 0
SERPINE1 -0.038 0.21 -10000 0 -1.3 11 11
SMAD3/SMAD4/ATF2 0.012 0.075 -10000 0 -0.35 10 10
SMAD3/SMAD4/ATF3 0.004 0.091 -10000 0 -0.35 19 19
SAP30 0.009 0.035 -10000 0 -0.58 2 2
Cbp/p300/PIAS3 0.019 0.041 -10000 0 -0.33 6 6
JUN 0.008 0.11 -10000 0 -0.47 13 13
SMAD3/SMAD4/IRF7 0.009 0.085 -10000 0 -0.36 15 15
TFE3 0.014 0.013 -10000 0 -10000 0 0
COL1A2 -0.042 0.21 -10000 0 -0.76 36 36
mesenchymal cell differentiation -0.002 0.095 0.36 25 -10000 0 25
DLX1 -0.044 0.15 -10000 0 -0.46 64 64
TCF3 0.01 0.025 -10000 0 -0.58 1 1
FOS -0.028 0.15 -10000 0 -0.53 44 44
SMAD3/SMAD4/Max 0.006 0.07 -10000 0 -0.32 11 11
Cbp/p300/SNIP1 0.02 0.032 -10000 0 -0.35 4 4
ZBTB17 0.01 0.027 -10000 0 -0.58 1 1
LAMC1 0.023 0.066 -10000 0 -0.43 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.01 0.08 -10000 0 -0.34 16 16
IRF7 0.005 0.058 -10000 0 -0.56 6 6
ESR1 -0.034 0.15 -10000 0 -0.52 50 50
HNF4A 0.004 0.065 -10000 0 -0.58 7 7
MEF2C -0.022 0.13 -10000 0 -0.48 22 22
SMAD2-3/SMAD4 0.013 0.084 -10000 0 -0.37 11 11
Cbp/p300/Src-1 0.019 0.041 -10000 0 -0.43 4 4
IGHV3OR16-13 -0.009 0.051 -10000 0 -0.8 2 2
TGIF2/HDAC complex 0.006 0.055 -10000 0 -0.58 5 5
CREBBP 0.011 0.006 -10000 0 -10000 0 0
SKIL 0 0.081 -10000 0 -0.58 11 11
HDAC1 0.011 0.001 -10000 0 -10000 0 0
HDAC2 0.011 0.001 -10000 0 -10000 0 0
SNIP1 0.012 0.002 -10000 0 -10000 0 0
GCN5L2 -0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.023 0.075 -10000 0 -0.37 3 3
MSG1/HSC70 -0.052 0.14 -10000 0 -0.34 109 109
SMAD2 0.007 0.053 -10000 0 -0.57 4 4
SMAD3 0.001 0.076 -10000 0 -0.57 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.069 -10000 0 -0.32 6 6
SMAD2/SMAD2/SMAD4 -0.004 0.076 -10000 0 -0.35 23 23
NCOR1 0.01 0.025 -10000 0 -0.58 1 1
NCOA2 0.003 0.068 -10000 0 -0.56 8 8
NCOA1 0.01 0.025 -10000 0 -0.58 1 1
MYOD/E2A 0.007 0.026 -10000 0 -0.35 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.032 0.094 -10000 0 -0.41 4 4
IFNB1 0.009 0.082 -10000 0 -0.45 8 8
SMAD3/SMAD4/MEF2C -0.018 0.14 -10000 0 -0.48 22 22
CITED1 -0.081 0.2 -10000 0 -0.48 107 107
SMAD2-3/SMAD4/ARC105 0.021 0.078 -10000 0 -0.4 5 5
RBL1 0.008 0.04 -10000 0 -0.54 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.025 0.099 -10000 0 -0.48 15 15
RUNX1-3/PEBPB2 0.002 0.081 -10000 0 -0.3 37 37
SMAD7 0.026 0.12 -10000 0 -0.85 3 3
MYC/MIZ-1 0.012 0.051 -10000 0 -0.4 7 7
SMAD3/SMAD4 -0.016 0.1 0.31 4 -0.43 14 18
IL10 -0.036 0.2 -10000 0 -0.58 56 56
PIASy/HDAC complex 0.011 0.026 -10000 0 -0.58 1 1
PIAS3 0.009 0.032 -10000 0 -0.52 2 2
CDK2 0.01 0.025 -10000 0 -0.58 1 1
IL5 -0.013 0.13 -10000 0 -0.49 17 17
CDK4 0.011 0.006 -10000 0 -10000 0 0
PIAS4 0.011 0.026 -10000 0 -0.58 1 1
ATF3 -0.003 0.083 -10000 0 -0.46 18 18
SMAD3/SMAD4/SP1 0.016 0.094 -10000 0 -0.37 8 8
FOXG1 -0.059 0.16 -10000 0 -0.48 72 72
FOXO3 0.018 0.025 -10000 0 -0.42 1 1
FOXO1 0.017 0.031 -10000 0 -0.42 2 2
FOXO4 0.017 0.031 -10000 0 -0.42 2 2
heart looping -0.022 0.13 -10000 0 -0.47 22 22
CEBPB 0.008 0.042 -10000 0 -0.48 4 4
SMAD3/SMAD4/DLX1 -0.022 0.12 -10000 0 -0.35 22 22
MYOD1 -0.001 0.027 -10000 0 -0.46 2 2
SMAD3/SMAD4/HNF4 0.009 0.087 -10000 0 -0.38 18 18
SMAD3/SMAD4/GATA3 -0.025 0.14 -10000 0 -0.45 27 27
SnoN/SIN3/HDAC complex/NCoR1 0 0.081 -10000 0 -0.58 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.009 0.097 -10000 0 -0.41 9 9
SMAD3/SMAD4/SP1-3 0.028 0.085 -10000 0 -0.4 1 1
MED15 0.01 0.025 -10000 0 -0.58 1 1
SP1 0.009 0.043 -10000 0 -0.57 1 1
SIN3B 0.01 0.025 -10000 0 -0.58 1 1
SIN3A 0.01 0.025 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.024 0.13 -10000 0 -0.36 38 38
ITGB5 0.029 0.075 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.036 0.029 -10000 0 -0.46 1 1
SMAD3/SMAD4/AR -0.028 0.13 -10000 0 -0.37 41 41
AR -0.052 0.17 -10000 0 -0.49 70 70
negative regulation of cell growth 0.02 0.08 -10000 0 -0.35 15 15
SMAD3/SMAD4/MYOD 0.005 0.072 -10000 0 -0.33 11 11
E2F5 -0.002 0.088 -10000 0 -0.58 13 13
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.007 0.11 -10000 0 -0.4 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 0.026 0.079 -10000 0 -0.34 15 15
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.01 0.11 -10000 0 -0.48 13 13
SMAD3/SMAD4/RUNX2 0.002 0.095 -10000 0 -0.36 25 25
TGIF2 0.006 0.055 -10000 0 -0.58 5 5
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.009 0.035 -10000 0 -0.58 2 2
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.009 0.037 -9999 0 -0.5 3 3
SPHK1 -0.03 0.14 -9999 0 -0.51 45 45
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.068 -9999 0 -0.3 22 22
GNAO1 -0.044 0.16 -9999 0 -0.49 63 63
mol:Sphinganine-1-P -0.013 0.11 -9999 0 -0.36 48 48
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.018 0.054 -9999 0 -0.29 2 2
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.015 0.026 -9999 0 -0.42 2 2
S1PR3 0.005 0.059 -9999 0 -0.53 7 7
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.004 0.058 -9999 0 -0.25 22 22
S1PR5 0.001 0.075 -9999 0 -0.54 11 11
S1PR4 -0.025 0.14 -9999 0 -0.53 38 38
GNAI1 -0.002 0.088 -9999 0 -0.55 14 14
S1P/S1P5/G12 0.006 0.068 -9999 0 -0.32 9 9
S1P/S1P3/Gq -0.002 0.11 -9999 0 -0.35 36 36
S1P/S1P4/Gi -0.021 0.12 -9999 0 -0.44 19 19
GNAQ 0.005 0.06 -9999 0 -0.58 6 6
GNAZ -0.012 0.11 -9999 0 -0.54 24 24
GNA14 -0.008 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 21 21
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.035 -9999 0 -0.58 2 2
GNA11 0.007 0.051 -9999 0 -0.53 5 5
ABCC1 0.01 0.025 -9999 0 -0.58 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.007 0.049 -10000 0 -0.58 4 4
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.008 0.094 0.36 37 -10000 0 37
CDKN1A 0.006 0.068 -10000 0 -0.58 5 5
KAT2B -0.006 0.1 -10000 0 -0.58 17 17
BAX 0.01 0.025 -10000 0 -0.58 1 1
FOXO3 0.004 0.042 0.49 4 -10000 0 4
FOXO1 0.01 0.025 -10000 0 -0.58 1 1
FOXO4 0.016 0.029 -10000 0 -0.3 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT -0.018 0.11 -10000 0 -0.46 32 32
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.005 0.076 -10000 0 -0.42 19 19
PPARGC1A -0.046 0.17 -10000 0 -0.56 57 57
FHL2 0.009 0.035 -10000 0 -0.58 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.011 0.042 -10000 0 -0.42 5 5
HIST2H4A -0.008 0.095 -10000 0 -0.36 37 37
SIRT1/FOXO3a 0 0.032 0.29 2 -0.36 3 5
SIRT1 0.003 0.056 0.2 2 -0.58 5 7
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.017 0.041 -10000 0 -0.34 7 7
SIRT1/Histone H1b 0.003 0.068 -10000 0 -0.31 19 19
apoptosis -0.017 0.039 0.35 6 -10000 0 6
SIRT1/PGC1A -0.036 0.11 -10000 0 -0.35 62 62
p53/SIRT1 -0.04 0.13 0.32 4 -0.43 56 60
SIRT1/FOXO4 0.014 0.049 -10000 0 -0.37 8 8
FOXO1/FHL2/SIRT1 0.015 0.041 -10000 0 -0.32 8 8
HIST1H1E 0.002 0.062 -10000 0 -0.31 16 16
SIRT1/p300 0.008 0.062 -10000 0 -0.52 7 7
muscle cell differentiation 0.001 0.081 0.41 19 -10000 0 19
TP53 -0.046 0.17 -10000 0 -0.58 53 53
KU70/SIRT1/BAX 0.017 0.039 -10000 0 -0.35 6 6
CREBBP 0.011 0 -10000 0 -10000 0 0
MEF2D 0.01 0.025 -10000 0 -0.58 1 1
HIV-1 Tat/SIRT1 -0.011 0.085 -10000 0 -0.33 37 37
ACSS2 0.012 0.045 -10000 0 -0.42 6 6
SIRT1/PCAF/MYOD -0.001 0.081 -10000 0 -0.41 19 19
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.022 0.16 -10000 0 -1.2 9 9
VDR 0.01 0.025 -10000 0 -0.58 1 1
FAM120B 0.01 0.025 -10000 0 -0.58 1 1
RXRs/LXRs/DNA/9cRA 0.026 0.084 -10000 0 -0.58 3 3
RXRs/LXRs/DNA/Oxysterols 0.025 0.11 -10000 0 -0.43 26 26
MED1 0.008 0.044 -10000 0 -0.52 4 4
mol:9cRA 0.003 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.021 0.12 -10000 0 -0.54 7 7
RXRs/NUR77 0.004 0.095 -10000 0 -0.39 9 9
RXRs/PPAR 0.021 0.059 -10000 0 -0.52 2 2
NCOR2 0.007 0.047 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RARs/VDR/DNA/Vit D3 0.012 0.071 -10000 0 -0.33 18 18
RARA 0.007 0.046 -10000 0 -0.48 5 5
NCOA1 0.01 0.025 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.025 -10000 0 -0.58 1 1
RARs/RARs/DNA/9cRA 0.007 0.068 -10000 0 -0.31 20 20
RARG 0.005 0.06 -10000 0 -0.58 6 6
RPS6KB1 -0.008 0.079 -10000 0 -0.46 15 15
RARs/THRs/DNA/SMRT -0.022 0.12 -10000 0 -0.57 7 7
THRA 0.008 0.042 -10000 0 -0.49 4 4
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0.02 0.072 0.28 6 -0.32 4 10
NR1H4 -0.13 0.23 -10000 0 -0.5 151 151
RXRs/LXRs/DNA 0.034 0.078 -10000 0 -0.41 4 4
NR1H2 0.013 0.028 -10000 0 -0.6 1 1
NR1H3 0.013 0.024 -10000 0 -0.48 1 1
RXRs/VDR/DNA/Vit D3 0.021 0.058 -10000 0 -0.3 3 3
NR4A1 -0.024 0.12 -10000 0 -0.46 43 43
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.034 0.1 -10000 0 -0.26 67 67
RXRG -0.01 0.096 -10000 0 -0.46 25 25
RXR alpha/CCPG 0.018 0.027 -10000 0 -0.42 2 2
RXRA 0.013 0.027 -10000 0 -0.59 1 1
RXRB 0.014 0.012 -10000 0 -10000 0 0
THRB -0.071 0.2 -10000 0 -0.56 83 83
PPARG 0.004 0.065 -10000 0 -0.58 7 7
PPARD 0.01 0.025 -10000 0 -0.58 1 1
TNF 0.005 0.22 -10000 0 -1.1 20 20
mol:Oxysterols 0.003 0.011 -10000 0 -10000 0 0
cholesterol transport 0.025 0.11 -10000 0 -0.43 26 26
PPARA 0.009 0.035 -10000 0 -0.58 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.006 0.096 -10000 0 -0.54 18 18
RXRs/NUR77/BCL2 -0.001 0.072 -10000 0 -0.28 21 21
SREBF1 0.029 0.12 -10000 0 -0.82 4 4
RXRs/RXRs/DNA/9cRA 0.02 0.072 0.28 6 -0.32 4 10
ABCA1 0.021 0.16 -10000 0 -1 10 10
RARs/THRs -0.027 0.13 -10000 0 -0.54 9 9
RXRs/FXR -0.055 0.14 -10000 0 -0.33 68 68
BCL2 -0.007 0.1 -10000 0 -0.55 19 19
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.004 0.085 -9999 0 -0.48 18 18
PLK4 0.009 0.035 -9999 0 -0.58 2 2
regulation of centriole replication 0.006 0.07 -9999 0 -0.36 19 19
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 0.012 0.047 -10000 0 -0.34 10 10
MAP4K4 0.02 0.065 -10000 0 -0.51 2 2
BAG4 0.009 0.035 -10000 0 -0.58 2 2
PKC zeta/ceramide -0.023 0.041 0.15 1 -0.2 2 3
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.52 29 29
BAX -0.009 0.023 -10000 0 -0.31 1 1
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.018 0.023 -10000 0 -0.51 1 1
BAD -0.024 0.041 0.16 1 -0.2 2 3
SMPD1 0.012 0.046 -10000 0 -0.2 20 20
RB1 -0.034 0.068 0.16 2 -0.32 20 22
FADD/Caspase 8 0.028 0.061 -10000 0 -0.5 1 1
MAP2K4 -0.021 0.053 -10000 0 -0.33 8 8
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.018 0.042 -10000 0 -0.31 2 2
EGF -0.18 0.25 -10000 0 -0.5 209 209
mol:ceramide -0.032 0.043 0.14 9 -10000 0 9
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.014 0.039 -10000 0 -0.33 7 7
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.034 0.067 0.16 2 -0.32 20 22
cell proliferation -0.035 0.089 -10000 0 -0.26 52 52
BID 0.01 0.047 -10000 0 -0.33 2 2
MAP3K1 -0.026 0.051 0.16 2 -0.33 6 8
EIF2A -0.021 0.064 -10000 0 -0.32 17 17
TRADD 0.011 0 -10000 0 -10000 0 0
CRADD 0.01 0.025 -10000 0 -0.58 1 1
MAPK3 -0.009 0.039 -10000 0 -0.28 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.039 -10000 0 -0.28 2 2
Cathepsin D/ceramide -0.024 0.041 0.15 1 -0.23 2 3
FADD 0.02 0.062 -10000 0 -0.52 1 1
KSR1 -0.024 0.044 0.16 2 -0.33 2 4
MAPK8 -0.016 0.045 0.15 1 -0.22 9 10
PRKRA -0.024 0.04 0.16 2 -0.2 1 3
PDGFA 0.005 0.053 -10000 0 -0.47 7 7
TRAF2 0.01 0.025 -10000 0 -0.58 1 1
IGF1 -0.071 0.19 -10000 0 -0.52 88 88
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.031 0.042 0.14 9 -10000 0 9
CTSD 0.009 0.037 -10000 0 -0.5 3 3
regulation of nitric oxide biosynthetic process 0.016 0.018 -10000 0 -0.42 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.036 0.095 -10000 0 -0.28 52 52
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.014 0.039 -10000 0 -0.33 7 7
RelA/NF kappa B1 0.016 0.018 -10000 0 -0.42 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0.025 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.065 -10000 0 -0.56 1 1
TNFR1A/BAG4/TNF-alpha 0.005 0.078 -10000 0 -0.32 30 30
mol:Sphingosine-1-phosphate 0.012 0.047 -10000 0 -0.34 10 10
MAP2K1 -0.012 0.042 -10000 0 -0.29 3 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS -0.016 0.049 0.16 7 -0.23 13 20
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
TNFR1A/BAG4 0.015 0.026 -10000 0 -0.42 2 2
EIF2AK2 -0.027 0.062 -10000 0 -0.3 19 19
TNF-alpha/TNFR1A/FAN 0.006 0.075 -10000 0 -0.32 28 28
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.047 -10000 0 -0.43 2 2
MAP2K2 -0.012 0.04 -10000 0 -0.29 2 2
SMPD3 0.006 0.071 -10000 0 -0.35 14 14
TNF -0.016 0.12 -10000 0 -0.54 28 28
PKC zeta/PAR4 0.015 0.029 -10000 0 -0.39 3 3
mol:PHOSPHOCHOLINE 0.059 0.094 0.18 201 -10000 0 201
NF kappa B1/RelA/I kappa B alpha 0.032 0.03 -10000 0 -0.36 3 3
AIFM1 -0.01 0.038 0.14 14 -0.26 1 15
BCL2 -0.007 0.1 -10000 0 -0.55 19 19
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.012 0.077 -9999 0 -0.48 3 3
Syndecan-3/Neurocan 0.002 0.049 -9999 0 -0.6 2 2
POMC -0.024 0.13 -9999 0 -0.51 38 38
EGFR 0.004 0.064 -9999 0 -0.53 8 8
Syndecan-3/EGFR 0.015 0.05 -9999 0 -0.38 7 7
AGRP -0.001 0.051 -9999 0 -0.46 7 7
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.01 0.025 -9999 0 -0.58 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.055 -9999 0 -0.58 5 5
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.004 0.066 -9999 0 -0.46 12 12
long-term memory 0.021 0.048 -9999 0 -0.37 7 7
Syndecan-3/IL8 -0.043 0.12 -9999 0 -0.31 67 67
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0.018 -9999 0 -0.42 1 1
FYN 0.005 0.061 -9999 0 -0.55 7 7
limb bud formation -0.003 0.037 -9999 0 -0.62 2 2
MC4R -0.005 0.057 -9999 0 -0.46 9 9
SRC 0.01 0.025 -9999 0 -0.58 1 1
PTN -0.024 0.14 -9999 0 -0.54 37 37
FGFR/FGF/Syndecan-3 -0.003 0.038 -9999 0 -0.63 2 2
neuron projection morphogenesis -0.006 0.076 -9999 0 -0.46 3 3
Syndecan-3/AgRP 0.002 0.045 -9999 0 -0.6 2 2
Syndecan-3/AgRP/MC4R -0.005 0.051 -9999 0 -0.46 4 4
Fyn/Cortactin 0.012 0.045 -9999 0 -0.39 7 7
SDC3 -0.003 0.038 -9999 0 -0.64 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.042 0.12 -9999 0 -0.31 67 67
IL8 -0.11 0.22 -9999 0 -0.52 129 129
Syndecan-3/Fyn/Cortactin 0.021 0.049 -9999 0 -0.38 7 7
Syndecan-3/CASK -0.003 0.036 -9999 0 -0.6 2 2
alpha-MSH/MC4R -0.02 0.11 -9999 0 -0.38 44 44
Gamma Secretase 0.031 0.033 -9999 0 -0.3 1 1
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.014 0.022 -9999 0 -0.36 2 2
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 0.001 0.077 -9999 0 -0.58 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.008 0.043 -9999 0 -0.58 3 3
RAC1-CDC42/GTP/PAK family 0.016 0.035 -9999 0 -0.29 5 5
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.004 0.065 -9999 0 -0.58 7 7
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.009 0.035 -9999 0 -0.58 2 2
FYN 0.005 0.061 -9999 0 -0.55 7 7
MAP3K12 0.003 0.069 -9999 0 -0.54 9 9
FGR -0.023 0.13 -9999 0 -0.53 36 36
p38 alpha/TAB1 -0.038 0.087 -9999 0 -0.34 28 28
PRKG1 -0.024 0.14 -9999 0 -0.56 36 36
DUSP8 0.006 0.053 -9999 0 -0.56 5 5
PGK/cGMP/p38 alpha -0.05 0.11 -9999 0 -0.36 45 45
apoptosis -0.037 0.083 -9999 0 -0.32 28 28
RAL/GTP 0.015 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.008 0.095 -9999 0 -0.47 23 23
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.01 0.025 -9999 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 0.027 0.035 -9999 0 -0.37 4 4
TRAF6 0.01 0.025 -9999 0 -0.58 1 1
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 0.01 0.031 -9999 0 -0.52 2 2
RAC1-CDC42/GTP 0.012 0.035 -9999 0 -0.36 5 5
MAPK11 -0.025 0.14 -9999 0 -0.43 38 38
BLK -0.11 0.23 -9999 0 -0.53 132 132
HCK -0.02 0.13 -9999 0 -0.55 32 32
MAP2K3 0.01 0.025 -9999 0 -0.58 1 1
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.01 0.031 -9999 0 -0.52 2 2
TRAF6/MEKK3 0.013 0.025 -9999 0 -0.33 3 3
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.01 0.11 -9999 0 -0.37 27 27
positive regulation of innate immune response -0.022 0.15 -9999 0 -0.46 36 36
LCK -0.032 0.14 -9999 0 -0.51 48 48
p38alpha-beta/MKP7 -0.015 0.14 -9999 0 -0.47 29 29
p38alpha-beta/MKP5 -0.016 0.14 -9999 0 -0.51 24 24
PGK/cGMP -0.018 0.1 -9999 0 -0.41 36 36
PAK2 0.01 0.025 -9999 0 -0.58 1 1
p38alpha-beta/MKP1 -0.023 0.15 -9999 0 -0.44 41 41
CDC42 0.006 0.055 -9999 0 -0.58 5 5
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 0 0.058 -9999 0 -0.46 9 9
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0 -10000 0 -10000 0 0
Rac1/GDP 0.003 0.011 -10000 0 -10000 0 0
DOCK1 0.01 0.025 -10000 0 -0.58 1 1
ITGA4 -0.018 0.13 -10000 0 -0.56 29 29
RAC1 0.011 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.024 0.14 -10000 0 -0.43 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.019 -10000 0 -0.46 1 1
alpha4/beta1 Integrin 0.005 0.08 -10000 0 -0.34 29 29
alpha4/beta7 Integrin/Paxillin -0.005 0.11 -10000 0 -0.36 39 39
lamellipodium assembly -0.003 0.052 -10000 0 -0.5 5 5
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
PI3K 0.013 0.041 -10000 0 -0.42 5 5
ARF6 0.01 0.025 -10000 0 -0.58 1 1
TLN1 0.01 0.025 -10000 0 -0.58 1 1
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
ARF6/GTP -0.014 0.058 -10000 0 -10000 0 0
cell adhesion 0.017 0.069 -10000 0 -0.29 26 26
CRKL/CBL 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.011 0.073 -10000 0 -0.32 25 25
ITGB1 0.011 0 -10000 0 -10000 0 0
ITGB7 -0.017 0.12 -10000 0 -0.53 30 30
ARF6/GDP 0.002 0.027 -10000 0 -0.57 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.003 0.11 -10000 0 -0.4 36 36
p130Cas/Crk/Dock1 0.02 0.038 -10000 0 -0.36 5 5
VCAM1 -0.019 0.12 -10000 0 -0.53 32 32
alpha4/beta1 Integrin/Paxillin/Talin 0.018 0.07 -10000 0 -0.29 26 26
alpha4/beta1 Integrin/Paxillin/GIT1 0.018 0.07 -10000 0 -0.29 26 26
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
mol:GDP -0.017 0.069 0.29 26 -10000 0 26
CBL 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0 -10000 0 -10000 0 0
GIT1 0.01 0.025 -10000 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.018 0.07 -10000 0 -0.29 26 26
Rac1/GTP -0.004 0.059 -10000 0 -0.56 5 5
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.014 0.1 -10000 0 -0.52 11 11
UGCG 0.01 0.07 -10000 0 -0.84 3 3
AKT1/mTOR/p70S6K/Hsp90/TERT 0.007 0.13 -10000 0 -0.44 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.01 0.069 -10000 0 -0.82 3 3
mol:DAG -0.001 0.01 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.039 0.11 -10000 0 -0.43 31 31
FRAP1 0.017 0.15 -10000 0 -0.5 32 32
FOXO3 0.023 0.13 -10000 0 -0.44 25 25
AKT1 0.017 0.14 -10000 0 -0.47 28 28
GAB2 0.01 0.035 -10000 0 -0.58 2 2
SMPD1 0.013 0.039 -10000 0 -0.6 1 1
SGMS1 0.014 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 0.014 0.035 -10000 0 -0.36 5 5
CALM1 0.011 0 -10000 0 -10000 0 0
cell proliferation 0.018 0.081 -10000 0 -0.41 7 7
EIF3A 0.01 0.025 -10000 0 -0.58 1 1
PI3K 0.017 0.041 -10000 0 -0.42 5 5
RPS6KB1 0.007 0.097 -10000 0 -0.96 5 5
mol:sphingomyelin -0.001 0.01 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 2 2
JAK3 0.002 0.078 -10000 0 -0.53 12 12
PIK3R1 0.011 0.043 -10000 0 -0.58 3 3
JAK1 0.011 0.043 -10000 0 -0.58 3 3
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
MYC 0.021 0.15 -10000 0 -0.67 13 13
MYB 0.005 0.16 -10000 0 -1.2 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.011 0.14 -10000 0 -0.42 37 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.017 0.093 -10000 0 -0.87 5 5
mol:PI-3-4-5-P3 0.012 0.13 -10000 0 -0.4 37 37
Rac1/GDP 0.02 0.032 -10000 0 -0.32 5 5
T cell proliferation 0.017 0.13 -10000 0 -0.43 25 25
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.065 9 9
PRKCZ 0.016 0.13 -10000 0 -0.45 25 25
NF kappa B1 p50/RelA -0.038 0.11 -10000 0 -0.45 27 27
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.007 0.11 -10000 0 -0.5 18 18
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
RELA 0.011 0 -10000 0 -10000 0 0
IL2RA -0.044 0.17 -10000 0 -0.55 57 57
IL2RB -0.013 0.12 -10000 0 -0.54 28 28
TERT -0.051 0.17 -10000 0 -0.51 68 68
E2F1 0.014 0.066 -10000 0 -0.44 11 11
SOS1 0.011 0.025 -10000 0 -0.58 1 1
RPS6 0.007 0.046 -10000 0 -0.48 5 5
mol:cAMP -0.002 0.004 0.031 9 -10000 0 9
PTPN11 0.007 0.055 -10000 0 -0.58 5 5
IL2RG 0.001 0.086 -10000 0 -0.56 13 13
actin cytoskeleton organization 0.017 0.13 -10000 0 -0.43 25 25
GRB2 0.012 0.002 -10000 0 -10000 0 0
IL2 0.004 0.027 -10000 0 -0.45 2 2
PIK3CA 0.012 0.035 -10000 0 -0.58 2 2
Rac1/GTP 0.027 0.032 -10000 0 -0.3 5 5
LCK -0.03 0.14 -10000 0 -0.5 48 48
BCL2 0.014 0.18 -10000 0 -0.72 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.009 0.035 -9999 0 -0.58 2 2
Caspase 8 (4 units) 0.006 0.087 -9999 0 -0.48 6 6
NEF -0.013 0.051 -9999 0 -0.19 28 28
NFKBIA 0.009 0.023 -9999 0 -10000 0 0
BIRC3 0.007 0.12 -9999 0 -0.51 29 29
CYCS -0.001 0.11 -9999 0 -0.51 10 10
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 -0.034 0.15 -9999 0 -0.64 31 31
MAP2K7 0.013 0.084 -9999 0 -0.49 5 5
protein ubiquitination 0.038 0.057 -9999 0 -0.4 3 3
CRADD 0.01 0.025 -9999 0 -0.58 1 1
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0.001 0.074 -9999 0 -0.56 10 10
BID 0.001 0.098 -9999 0 -0.3 31 31
NF-kappa-B/RelA/I kappa B alpha 0.017 0.065 -9999 0 -0.29 16 16
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.035 -9999 0 -0.58 2 2
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 0.017 0.065 -9999 0 -0.29 16 16
MAPK8 0.018 0.083 -9999 0 -0.56 4 4
APAF1 0.008 0.043 -9999 0 -0.58 3 3
TRAF1 0.008 0.039 -9999 0 -0.46 4 4
TRAF2 0.01 0.025 -9999 0 -0.58 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.005 0.1 -9999 0 -0.3 46 46
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.057 -9999 0 -10000 0 0
CHUK 0.039 0.061 -9999 0 -0.43 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.027 0.05 -9999 0 -0.32 10 10
TCRz/NEF -0.039 0.15 -9999 0 -0.39 79 79
TNF -0.016 0.12 -9999 0 -0.54 28 28
FASLG -0.062 0.23 -9999 0 -0.6 77 77
NFKB1 0.008 0.033 -9999 0 -0.58 1 1
TNFR1A/BAG4/TNF-alpha 0.005 0.078 -9999 0 -0.32 30 30
CASP6 -0.017 0.059 -9999 0 -0.5 4 4
CASP7 0.022 0.13 -9999 0 -0.54 19 19
RELA 0.009 0.023 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.021 0.13 -9999 0 -0.54 20 20
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.026 -9999 0 -0.42 2 2
CASP8 0.01 0.025 -9999 0 -0.58 1 1
CASP9 0.01 0.025 -9999 0 -0.58 1 1
MAP3K14 0.037 0.057 -9999 0 -0.42 1 1
APAF-1/Caspase 9 -0.038 0.1 -9999 0 -0.44 25 25
BCL2 0.015 0.094 -9999 0 -0.46 9 9
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.013 0.12 -9999 0 -0.45 25 25
PDGFB-D/PDGFRB/SLAP -0.011 0.11 -9999 0 -0.4 38 38
PDGFB-D/PDGFRB/APS/CBL -0.003 0.09 -9999 0 -0.34 27 27
AKT1 0.031 0.065 -9999 0 -0.48 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.013 0.12 -9999 0 -0.48 24 24
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
FGR -0.037 0.15 -9999 0 -0.56 34 34
mol:Ca2+ -0.004 0.1 -9999 0 -0.58 14 14
MYC 0.001 0.12 -9999 0 -0.6 14 14
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.018 0.065 -9999 0 -0.32 15 15
LRP1/PDGFRB/PDGFB 0.008 0.077 -9999 0 -0.39 17 17
GRB10 0.007 0.049 -9999 0 -0.58 4 4
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
GO:0007205 -0.004 0.11 -9999 0 -0.59 14 14
PTEN 0.005 0.06 -9999 0 -0.58 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 0.002 0.067 -9999 0 -0.46 12 12
PDGFB-D/PDGFRB/SHP2 0.002 0.076 -9999 0 -0.39 20 20
PDGFB-D/PDGFRB/GRB10 0.003 0.073 -9999 0 -0.39 19 19
cell cycle arrest -0.011 0.11 -9999 0 -0.4 38 38
HRAS 0.008 0.042 -9999 0 -0.49 4 4
HIF1A 0.032 0.078 -9999 0 -0.5 7 7
GAB1 -0.014 0.12 -9999 0 -0.63 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.01 0.12 -9999 0 -0.56 14 14
PDGFB-D/PDGFRB 0.013 0.066 -9999 0 -0.36 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.006 0.064 -9999 0 -0.38 15 15
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.037 0.12 -9999 0 -0.47 25 25
positive regulation of MAPKKK cascade 0.002 0.075 -9999 0 -0.39 20 20
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
mol:IP3 -0.004 0.11 -9999 0 -0.6 14 14
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.01 0.024 -9999 0 -0.57 1 1
PDGFB-D/PDGFRB/GRB7 -0.001 0.081 -9999 0 -0.36 26 26
SHB 0.011 0.019 -9999 0 -0.46 1 1
BLK -0.096 0.2 -9999 0 -0.56 85 85
PTPN2 0.008 0.043 -9999 0 -0.58 3 3
PDGFB-D/PDGFRB/SNX15 0.006 0.064 -9999 0 -0.38 15 15
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
VAV2 -0.018 0.14 -9999 0 -0.6 20 20
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.006 0.067 -9999 0 -0.38 16 16
LCK -0.036 0.13 -9999 0 -0.5 34 34
PDGFRB -0.003 0.088 -9999 0 -0.54 15 15
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.034 0.16 -9999 0 -0.61 33 33
ABL1 -0.015 0.12 -9999 0 -0.54 17 17
PDGFB-D/PDGFRB/CBL -0.017 0.13 -9999 0 -0.7 13 13
PTPN1 0.01 0.025 -9999 0 -0.59 1 1
SNX15 0.011 0 -9999 0 -10000 0 0
STAT3 0.011 0 -9999 0 -10000 0 0
STAT1 0.006 0.052 -9999 0 -0.5 6 6
cell proliferation 0.003 0.11 -9999 0 -0.53 14 14
SLA -0.013 0.11 -9999 0 -0.52 26 26
actin cytoskeleton reorganization 0.027 0.066 -9999 0 -0.5 3 3
SRC -0.011 0.066 -9999 0 -0.4 14 14
PI3K -0.013 0.058 -9999 0 -0.52 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.008 0.069 -9999 0 -0.35 12 12
SH2B2 -0.015 0.12 -9999 0 -0.52 29 29
PLCgamma1/SPHK1 -0.014 0.13 -9999 0 -0.5 24 24
LYN -0.009 0.062 -9999 0 -0.38 13 13
LRP1 0.004 0.063 -9999 0 -0.56 7 7
SOS1 0.01 0.025 -9999 0 -0.58 1 1
STAT5B 0.011 0 -9999 0 -10000 0 0
STAT5A 0.011 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.063 -9999 0 -0.54 2 2
SPHK1 -0.029 0.14 -9999 0 -0.51 45 45
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.004 0.11 -9999 0 -0.6 14 14
PLCG1 -0.005 0.11 -9999 0 -0.62 14 14
NHERF/PDGFRB 0.013 0.057 -9999 0 -0.36 10 10
YES1 -0.017 0.098 -9999 0 -0.52 17 17
cell migration 0.013 0.057 -9999 0 -0.35 10 10
SHC/Grb2/SOS1 0.003 0.053 -9999 0 -10000 0 0
SLC9A3R2 0.01 0.025 -9999 0 -0.58 1 1
SLC9A3R1 0.011 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.017 0.062 -9999 0 -0.32 16 16
FYN -0.015 0.086 -9999 0 -0.46 17 17
DOK1 0.016 0.058 -9999 0 -0.32 13 13
HRAS/GTP 0.006 0.03 -9999 0 -0.35 4 4
PDGFB 0.008 0.042 -9999 0 -0.49 4 4
RAC1 -0.008 0.13 -9999 0 -0.59 19 19
PRKCD 0.016 0.059 -9999 0 -0.33 13 13
FER 0.01 0.076 -9999 0 -0.36 17 17
MAPKKK cascade -0.008 0.047 -9999 0 -10000 0 0
RASA1 0.015 0.065 -9999 0 -0.35 14 14
NCK1 0.009 0.035 -9999 0 -0.58 2 2
NCK2 0.01 0.025 -9999 0 -0.58 1 1
p62DOK/Csk 0.021 0.055 -9999 0 -0.29 12 12
PDGFB-D/PDGFRB/SHB 0.006 0.065 -9999 0 -0.38 16 16
chemotaxis -0.014 0.11 -9999 0 -0.52 17 17
STAT1-3-5/STAT1-3-5 -0.009 0.052 -9999 0 -0.55 1 1
Bovine Papilomavirus E5/PDGFRB -0.002 0.064 -9999 0 -0.39 15 15
PTPRJ 0.01 0.025 -9999 0 -0.58 1 1
Regulation of Androgen receptor activity

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0.019 -9999 0 -0.43 1 1
SMARCC1 0.002 0.019 -9999 0 -10000 0 0
REL 0.011 0.043 -9999 0 -0.58 3 3
HDAC7 0.027 0.093 -9999 0 -0.54 7 7
JUN 0.004 0.053 -9999 0 -0.56 5 5
EP300 0.007 0.049 -9999 0 -0.58 4 4
KAT2B -0.007 0.1 -9999 0 -0.58 17 17
KAT5 0.011 0.025 -9999 0 -0.58 1 1
MAPK14 0.011 0.061 -9999 0 -0.44 10 10
FOXO1 0.01 0.025 -9999 0 -0.58 1 1
T-DHT/AR 0.024 0.099 -9999 0 -0.55 8 8
MAP2K6 0.001 0.079 -9999 0 -0.59 10 10
BRM/BAF57 0.009 0.042 -9999 0 -0.43 5 5
MAP2K4 0.008 0.043 -9999 0 -0.58 3 3
SMARCA2 0.005 0.05 -9999 0 -0.59 4 4
PDE9A -0.08 0.28 -9999 0 -1 42 42
NCOA2 0.003 0.068 -9999 0 -0.56 8 8
CEBPA -0.005 0.099 -9999 0 -0.57 17 17
EHMT2 0.007 0.032 -9999 0 -0.52 2 2
cell proliferation 0.023 0.12 -9999 0 -0.49 17 17
NR0B1 -0.001 0.051 -9999 0 -0.46 7 7
EGR1 -0.015 0.11 -9999 0 -0.5 27 27
RXRs/9cRA 0.004 0.055 -9999 0 -0.24 26 26
AR/RACK1/Src 0.015 0.075 -9999 0 -0.42 8 8
AR/GR -0.011 0.1 -9999 0 -0.35 31 31
GNB2L1 0.011 0.02 -9999 0 -0.46 1 1
PKN1 0.008 0.043 -9999 0 -0.58 3 3
RCHY1 0.01 0.025 -9999 0 -0.58 1 1
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.038 -9999 0 -0.42 4 4
T-DHT/AR/TIF2/CARM1 0.02 0.086 -9999 0 -0.43 11 11
SRC 0.023 0.061 -9999 0 -0.36 10 10
NR3C1 -0.015 0.12 -9999 0 -0.54 28 28
KLK3 -0.19 0.36 -9999 0 -0.97 78 78
APPBP2 0.008 0.049 -9999 0 -0.58 4 4
TRIM24 0.009 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.018 0.078 -9999 0 -0.48 8 8
TMPRSS2 -0.024 0.14 -9999 0 -0.84 10 10
RXRG -0.013 0.096 -9999 0 -0.46 25 25
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.01 0.025 -9999 0 -0.58 1 1
RXRB 0.011 0.001 -9999 0 -10000 0 0
CARM1 0.01 0.025 -9999 0 -0.58 1 1
NR2C2 0.01 0.025 -9999 0 -0.58 1 1
KLK2 0.015 0.11 -9999 0 -0.45 11 11
AR -0.001 0.084 -9999 0 -0.33 14 14
SENP1 0.01 0.025 -9999 0 -0.58 1 1
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
MDM2 0.012 0.046 -9999 0 -0.52 4 4
SRY 0.001 0.039 -9999 0 -0.45 4 4
GATA2 -0.014 0.12 -9999 0 -0.55 26 26
MYST2 0.011 0.025 -9999 0 -0.58 1 1
HOXB13 -0.095 0.21 -9999 0 -0.5 117 117
T-DHT/AR/RACK1/Src 0.021 0.074 -9999 0 -0.42 8 8
positive regulation of transcription -0.014 0.12 -9999 0 -0.55 26 26
DNAJA1 0.012 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.042 -9999 0 -0.47 3 3
NCOA1 0.011 0.027 -9999 0 -0.62 1 1
SPDEF -0.16 0.25 -9999 0 -0.53 178 178
T-DHT/AR/TIF2 0.013 0.11 -9999 0 -0.75 6 6
T-DHT/AR/Hsp90 0.016 0.076 -9999 0 -0.45 9 9
GSK3B 0.009 0.035 -9999 0 -0.58 2 2
NR2C1 0.011 0.025 -9999 0 -0.58 1 1
mol:T-DHT 0.02 0.064 -9999 0 -0.37 13 13
SIRT1 0.006 0.055 -9999 0 -0.58 5 5
ZMIZ2 0.014 0.027 -9999 0 -0.58 1 1
POU2F1 0.01 0.078 -9999 0 -0.54 10 10
T-DHT/AR/DAX-1 0.008 0.076 -9999 0 -0.43 9 9
CREBBP 0.011 0.001 -9999 0 -10000 0 0
SMARCE1 0.008 0.025 -9999 0 -0.58 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.015 0.036 -10000 0 -0.54 2 2
CRKL 0.014 0.061 -10000 0 -0.27 1 1
mol:PIP3 -0.01 0.055 0.52 6 -10000 0 6
AKT1 0.004 0.039 0.36 6 -0.3 1 7
PTK2B 0.009 0.035 -10000 0 -0.58 2 2
RAPGEF1 0.018 0.061 -10000 0 -0.37 1 1
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
HGF/MET/SHIP2 -0.008 0.1 -10000 0 -0.33 52 52
MAP3K5 0.004 0.099 -10000 0 -0.4 14 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0 0.094 -10000 0 -0.32 38 38
AP1 -0.014 0.098 -10000 0 -0.33 48 48
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.026 0.17 -10000 0 -0.74 29 29
STAT3 (dimer) 0.011 0.075 -10000 0 -0.25 41 41
GAB1/CRKL/SHP2/PI3K -0.017 0.067 -10000 0 -0.68 3 3
INPP5D -0.015 0.12 -10000 0 -0.58 26 26
CBL/CRK 0.019 0.061 -10000 0 -0.44 1 1
PTPN11 0.006 0.055 -10000 0 -0.58 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.01 0.025 -10000 0 -0.58 1 1
PTEN 0.005 0.06 -10000 0 -0.58 6 6
ELK1 -0.001 0.025 0.23 2 -0.31 2 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.046 -10000 0 -0.36 3 3
PAK1 0.009 0.036 0.34 6 -0.28 1 7
HGF/MET/RANBP10 -0.008 0.1 -10000 0 -0.33 51 51
HRAS 0.004 0.096 -10000 0 -1.1 1 1
DOCK1 0.018 0.062 -10000 0 -0.53 1 1
GAB1 0.008 0.064 -10000 0 -0.28 2 2
CRK 0.013 0.063 -10000 0 -0.37 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.13 -10000 0 -0.49 36 36
JUN 0.006 0.053 -10000 0 -0.56 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.004 0.057 -10000 0 -0.21 37 37
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
cell morphogenesis 0.028 0.092 -10000 0 -0.59 4 4
GRB2/SHC 0.01 0.051 -10000 0 -0.24 2 2
FOS -0.03 0.14 -10000 0 -0.53 44 44
GLMN -0.008 0.047 -10000 0 -0.27 18 18
cell motility -0.001 0.025 0.23 2 -0.31 2 4
HGF/MET/MUC20 -0.015 0.1 -10000 0 -0.33 51 51
cell migration 0.01 0.051 -10000 0 -0.24 2 2
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.016 0.023 -10000 0 -0.37 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.007 0.076 -10000 0 -0.25 41 41
MET/MUC20 0.007 0.023 -10000 0 -0.38 2 2
RAP1B 0.023 0.058 -10000 0 -0.34 1 1
RAP1A 0.023 0.059 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.008 0.1 -10000 0 -0.33 51 51
RAF1 0.01 0.09 -10000 0 -1 1 1
STAT3 0.011 0.076 -10000 0 -0.31 3 3
cell proliferation 0.015 0.097 -10000 0 -0.34 37 37
RPS6KB1 -0.001 0.043 -10000 0 -0.33 5 5
MAPK3 -0.004 0.031 0.67 1 -0.24 1 2
MAPK1 -0.004 0.031 0.67 1 -0.24 1 2
RANBP9 0.01 0.025 -10000 0 -0.58 1 1
MAPK8 0.019 0.089 -10000 0 -0.37 13 13
SRC 0.012 0.074 -10000 0 -0.53 1 1
PI3K 0.007 0.063 -10000 0 -0.39 5 5
MET/Glomulin 0.003 0.043 -10000 0 -0.22 20 20
SOS1 0.01 0.025 -10000 0 -0.58 1 1
MAP2K1 0.015 0.089 -10000 0 -1.1 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
MAP4K1 -0.001 0.1 -10000 0 -0.42 13 13
PTK2 0.01 0.025 -10000 0 -0.58 1 1
MAP2K2 0.015 0.087 -10000 0 -0.7 2 2
BAD 0.008 0.043 0.34 6 -0.58 1 7
MAP2K4 0.009 0.094 -10000 0 -0.38 12 12
SHP2/GRB2/SOS1/GAB1 -0.016 0.057 -10000 0 -0.47 3 3
INPPL1 0.01 0.025 -10000 0 -0.58 1 1
PXN 0.011 0 -10000 0 -10000 0 0
SH3KBP1 0.009 0.035 -10000 0 -0.58 2 2
HGS 0.002 0.054 -10000 0 -0.25 3 3
PLCgamma1/PKC 0.008 0.018 -10000 0 -0.43 1 1
HGF -0.036 0.16 -10000 0 -0.55 49 49
RASA1 0.009 0.035 -10000 0 -0.58 2 2
NCK1 0.009 0.035 -10000 0 -0.58 2 2
PTPRJ 0.01 0.025 -10000 0 -0.58 1 1
NCK/PLCgamma1 0.008 0.063 -10000 0 -0.32 4 4
PDPK1 -0.003 0.043 0.41 6 -10000 0 6
HGF/MET/SHIP -0.025 0.12 -10000 0 -0.34 76 76
S1P5 pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.086 0.46 6 -10000 0 6
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.047 -10000 0 -0.33 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.044 0.16 -10000 0 -0.49 63 63
RhoA/GTP -0.004 0.088 -10000 0 -0.48 6 6
negative regulation of cAMP metabolic process -0.01 0.094 -10000 0 -0.3 27 27
GNAZ -0.012 0.11 -10000 0 -0.54 24 24
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 0.001 0.075 -10000 0 -0.54 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.01 0.095 -10000 0 -0.3 27 27
RhoA/GDP 0.008 0.018 -10000 0 -0.43 1 1
RHOA 0.01 0.025 -10000 0 -0.58 1 1
GNAI1 -0.002 0.088 -10000 0 -0.55 14 14
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.022 0.022 -9999 0 -0.35 2 2
SNTA1 0.006 0.056 -9999 0 -0.54 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.012 0.067 -9999 0 -0.38 16 16
MAPK12 -0.002 0.092 -9999 0 -0.37 22 22
CCND1 0.006 0.042 -9999 0 -0.22 8 8
p38 gamma/SNTA1 0.001 0.093 -9999 0 -0.38 21 21
MAP2K3 0.01 0.025 -9999 0 -0.58 1 1
PKN1 0.008 0.043 -9999 0 -0.58 3 3
G2/M transition checkpoint -0.002 0.091 -9999 0 -0.37 22 22
MAP2K6 0.009 0.06 -9999 0 -0.32 18 18
MAPT -0.023 0.11 -9999 0 -0.33 47 47
MAPK13 0.017 0.026 -9999 0 -0.42 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.009 0.043 -9999 0 -0.35 8 8
S1P3 pathway

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.087 -9999 0 -0.53 15 15
mol:S1P 0 0.005 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.008 0.087 -9999 0 -0.26 46 46
GNAO1 -0.043 0.16 -9999 0 -0.49 63 63
S1P/S1P3/G12/G13 0.018 0.041 -9999 0 -0.3 9 9
AKT1 0.002 0.09 -9999 0 -0.56 10 10
AKT3 -0.011 0.2 -9999 0 -1.2 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.087 -9999 0 -0.53 15 15
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 -0.002 0.088 -9999 0 -0.56 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.005 0.061 -9999 0 -0.54 7 7
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.008 0.11 -9999 0 -0.44 17 17
MAPK3 -0.002 0.11 -9999 0 -0.51 12 12
MAPK1 -0.002 0.11 -9999 0 -0.51 12 12
JAK2 -0.011 0.13 -9999 0 -0.46 24 24
CXCR4 -0.016 0.13 -9999 0 -0.49 25 25
FLT1 0.007 0.057 -9999 0 -0.54 6 6
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC -0.002 0.11 -9999 0 -0.49 12 12
S1P/S1P3/Gi -0.008 0.11 -9999 0 -0.44 17 17
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.003 0.1 -9999 0 -0.48 12 12
VEGFA 0.012 0.02 -9999 0 -0.45 1 1
S1P/S1P2/Gi -0.004 0.09 -9999 0 -0.31 19 19
VEGFR1 homodimer/VEGFA homodimer 0.017 0.046 -9999 0 -0.38 7 7
RHOA 0.01 0.025 -9999 0 -0.58 1 1
S1P/S1P3/Gq 0 0.099 -9999 0 -0.34 36 36
GNAQ 0.005 0.06 -9999 0 -0.58 6 6
GNAZ -0.011 0.11 -9999 0 -0.54 24 24
G12/G13 0.015 0.026 -9999 0 -0.42 2 2
GNA14 -0.008 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 21 21
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.035 -9999 0 -0.58 2 2
GNA11 0.007 0.051 -9999 0 -0.53 5 5
Rac1/GTP -0.002 0.1 -9999 0 -0.5 11 11
Class IB PI3K non-lipid kinase events

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0 0.081 0.58 11 -10000 0 11
PI3K Class IB/PDE3B 0 0.081 -10000 0 -0.58 11 11
PDE3B 0 0.081 -10000 0 -0.58 11 11
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.011 0 -10000 0 -10000 0 0
NFATC1 0.031 0.06 -10000 0 -0.3 14 14
NFATC2 0.015 0.057 -10000 0 -0.24 12 12
NFATC3 0.017 0.02 -10000 0 -0.41 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.054 0.14 -10000 0 -0.46 34 34
Exportin 1/Ran/NUP214 0.015 0.052 -10000 0 -0.35 11 11
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.067 0.13 -10000 0 -0.47 37 37
BCL2/BAX 0.003 0.076 -10000 0 -0.4 20 20
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0.004 -10000 0 -10000 0 0
BAX 0.01 0.025 -10000 0 -0.58 1 1
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0.01 0.031 -10000 0 -0.52 2 2
CABIN1/MEF2D -0.046 0.13 -10000 0 -0.44 35 35
Calcineurin A alpha-beta B1/BCL2 -0.007 0.1 -10000 0 -0.55 19 19
FKBP8 0.009 0.035 -10000 0 -0.58 2 2
activation-induced cell death of T cells 0.045 0.13 0.43 35 -10000 0 35
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
XPO1 0 0.081 -10000 0 -0.58 11 11
SFN 0.005 0.057 -10000 0 -0.47 8 8
MAP3K8 0.009 0.032 -10000 0 -0.52 2 2
NFAT4/CK1 alpha 0.022 0.047 -10000 0 -0.38 6 6
MEF2D/NFAT1/Cbp/p300 0.022 0.097 -10000 0 -0.42 12 12
CABIN1 -0.054 0.14 -10000 0 -0.47 34 34
CALM1 0.011 0.002 -10000 0 -10000 0 0
RAN 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.06 -10000 0 -0.58 6 6
CAMK4 -0.013 0.11 -10000 0 -0.55 25 25
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.01 0.025 -10000 0 -0.58 1 1
YWHAH 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.008 0.094 -10000 0 -0.37 35 35
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.01 0.025 -10000 0 -0.58 1 1
MAPK9 0.011 0 -10000 0 -10000 0 0
YWHAG 0.011 0 -10000 0 -10000 0 0
FKBP1A 0.011 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.04 0.061 -10000 0 -0.34 4 4
PRKCH 0.005 0.06 -10000 0 -0.58 6 6
CABIN1/Cbp/p300 0.013 0.037 -10000 0 -0.42 4 4
CASP3 0.009 0.035 -10000 0 -0.58 2 2
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.002 -10000 0 -10000 0 0
apoptosis -0.005 0.037 0.23 1 -0.65 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.03 -10000 0 -0.38 2 2
PRKCB -0.039 0.16 -10000 0 -0.54 52 52
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.018 -10000 0 -0.37 1 1
BAD/BCL-XL 0.016 0.023 -10000 0 -0.37 2 2
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.032 -10000 0 -0.52 2 2
PRKCA 0.01 0.031 -10000 0 -0.52 2 2
PRKCG -0.14 0.24 -10000 0 -0.51 171 171
PRKCQ -0.044 0.17 -10000 0 -0.58 54 54
FKBP38/BCL2 0.002 0.078 -10000 0 -0.4 21 21
EP300 0.007 0.049 -10000 0 -0.58 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.034 0.06 -10000 0 -0.32 4 4
CaM/Ca2+/FKBP38 0.014 0.023 -10000 0 -0.36 2 2
FKBP12/FK506 0.008 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.023 -10000 0 -0.36 2 2
CaM/Ca2+/CAMK IV 0 0.072 -10000 0 -0.33 25 25
NFATc/ERK1 0.035 0.058 -10000 0 -0.31 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.067 0.13 -10000 0 -0.47 36 36
NR4A1 0.011 0.13 -10000 0 -0.41 45 45
GSK3B 0.009 0.035 -10000 0 -0.58 2 2
positive T cell selection 0.017 0.02 -10000 0 -0.41 1 1
NFAT1/CK1 alpha -0.012 0.045 -10000 0 -0.42 4 4
RCH1/ KPNB1 0.017 0 -10000 0 -10000 0 0
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 -0.021 0.13 -10000 0 -0.52 35 35
MEF2D 0.01 0.025 -10000 0 -0.59 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.008 0.043 -10000 0 -0.58 3 3
NFATc/p38 alpha 0.034 0.058 -10000 0 -0.31 2 2
CREBBP 0.011 0.002 -10000 0 -10000 0 0
BCL2 -0.007 0.1 -10000 0 -0.55 19 19
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.094 -9999 0 -0.5 19 19
MDM2/SUMO1 0.003 0.11 -9999 0 -0.58 19 19
HDAC4 0.011 0.019 -9999 0 -0.46 1 1
Ran/GTP/Exportin 1/HDAC1 -0.018 0.094 -9999 0 -0.5 19 19
SUMO1 -0.008 0.11 -9999 0 -0.58 19 19
NPC/RanGAP1/SUMO1 -0.005 0.097 -9999 0 -0.44 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.001 0.12 -9999 0 -0.54 24 24
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 -0.008 0.1 -9999 0 -0.57 19 19
SUMO1/HDAC4 0.004 0.11 -9999 0 -0.55 19 19
SUMO1/HDAC1 0.005 0.11 -9999 0 -0.55 19 19
RANGAP1 0.01 0.031 -9999 0 -0.52 2 2
MDM2/SUMO1/SUMO1 0.015 0.073 -9999 0 -0.35 19 19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.001 0.097 -9999 0 -0.43 24 24
Ran/GTP 0.005 0.089 -9999 0 -0.53 14 14
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.044 -9999 0 -0.52 4 4
UBE2I 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.005 0.12 -9999 0 -0.68 15 15
NPC -0.004 0.057 -9999 0 -0.31 19 19
PIAS2 0.01 0.027 -9999 0 -0.46 2 2
PIAS1 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.023 0.049 -10000 0 -0.37 6 6
HDAC3 0.011 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.014 0.077 -10000 0 -0.4 19 19
GATA1/HDAC4 0.005 0.054 -10000 0 -0.32 15 15
GATA1/HDAC5 0.004 0.057 -10000 0 -0.33 16 16
GATA2/HDAC5 -0.003 0.092 -10000 0 -0.41 27 27
HDAC5/BCL6/BCoR 0.02 0.031 -10000 0 -0.28 6 6
HDAC9 -0.038 0.16 -10000 0 -0.54 51 51
Glucocorticoid receptor/Hsp90/HDAC6 0.005 0.08 -10000 0 -0.37 19 19
HDAC4/ANKRA2 0.016 0.023 -10000 0 -0.37 2 2
HDAC5/YWHAB 0.016 0.023 -10000 0 -0.37 2 2
NPC/RanGAP1/SUMO1/Ubc9 -0.001 0.097 -10000 0 -0.43 24 24
GATA2 -0.014 0.12 -10000 0 -0.55 26 26
HDAC4/RFXANK 0.014 0.032 -10000 0 -0.37 4 4
BCOR 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.007 0.047 -10000 0 -0.55 4 4
HDAC5 0.01 0.031 -10000 0 -0.52 2 2
GNB1/GNG2 0.011 0.047 -10000 0 -0.38 8 8
Histones 0.011 0.081 -10000 0 -1.2 1 1
ADRBK1 0.009 0.037 -10000 0 -0.5 3 3
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
XPO1 0 0.081 -10000 0 -0.58 11 11
HDAC5/ANKRA2 0.015 0.029 -10000 0 -0.39 3 3
HDAC4/Ubc9 0.016 0.014 -10000 0 -0.32 1 1
HDAC7 0.01 0.025 -10000 0 -0.58 1 1
HDAC5/14-3-3 E 0.016 0.023 -10000 0 -0.37 2 2
TUBA1B 0.011 0 -10000 0 -10000 0 0
HDAC6 0.011 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.014 0.042 -10000 0 -0.46 4 4
CAMK4 -0.013 0.11 -10000 0 -0.55 25 25
Tubulin/HDAC6 0.006 0.072 -10000 0 -0.29 32 32
SUMO1 -0.008 0.11 -10000 0 -0.58 19 19
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.011 0 -10000 0 -10000 0 0
GATA1 -0.004 0.073 -10000 0 -0.46 14 14
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.015 0.12 -10000 0 -0.54 28 28
SUMO1/HDAC4 0.004 0.11 -10000 0 -0.55 19 19
SRF 0.01 0.027 -10000 0 -0.46 2 2
HDAC4/YWHAB 0.016 0.014 -10000 0 -0.32 1 1
Tubulin -0.003 0.085 -10000 0 -0.35 32 32
HDAC4/14-3-3 E 0.016 0.014 -10000 0 -0.32 1 1
GNB1 0.011 0 -10000 0 -10000 0 0
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
BCL6/BCoR 0.015 0.028 -10000 0 -0.32 4 4
HDAC4/HDAC3/SMRT (N-CoR2) 0.02 0.032 -10000 0 -0.32 5 5
HDAC4/SRF 0.006 0.076 -10000 0 -0.33 27 27
HDAC4/ER alpha -0.018 0.11 -10000 0 -0.37 51 51
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.011 0.08 -10000 0 -1.2 1 1
cell motility 0.006 0.072 -10000 0 -0.29 32 32
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.011 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.016 0.018 -10000 0 -0.42 1 1
BCL6 0.008 0.039 -10000 0 -0.46 4 4
HDAC4/CaMK II delta B 0.011 0.019 -10000 0 -0.45 1 1
Hsp90/HDAC6 0.015 0.026 -10000 0 -0.42 2 2
ESR1 -0.036 0.15 -10000 0 -0.52 50 50
HDAC6/HDAC11 0.015 0.026 -10000 0 -0.42 2 2
Ran/GTP/Exportin 1 0.006 0.12 -10000 0 -0.68 15 15
NPC -0.004 0.057 -10000 0 -0.31 19 19
MEF2C 0.001 0.074 -10000 0 -0.52 11 11
RAN 0.011 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.026 0.048 -10000 0 -0.29 9 9
GNG2 0.004 0.064 -10000 0 -0.53 8 8
NCOR2 0.007 0.047 -10000 0 -0.55 4 4
TUBB2A -0.017 0.12 -10000 0 -0.49 32 32
HDAC11 0.009 0.035 -10000 0 -0.58 2 2
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
RANBP2 -0.008 0.1 -10000 0 -0.57 19 19
ANKRA2 0.01 0.025 -10000 0 -0.58 1 1
RFXANK 0.008 0.04 -10000 0 -0.54 3 3
nuclear import -0.023 0.019 0.32 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.001 0.089 -9999 0 -0.34 35 35
forebrain development 0 0.15 -9999 0 -0.57 23 23
GNAO1 -0.043 0.16 -9999 0 -0.49 63 63
SMO/beta Arrestin2 -0.001 0.091 -9999 0 -0.4 28 28
SMO -0.015 0.12 -9999 0 -0.56 28 28
ARRB2 0.012 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.015 0.099 -9999 0 -0.67 5 5
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.009 0.035 -9999 0 -0.58 2 2
GNAI2 0.012 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.026 0.031 -9999 0 -0.32 4 4
GNAI1 -0.002 0.088 -9999 0 -0.55 14 14
XPO1 0.002 0.081 -9999 0 -0.58 11 11
GLI1/Su(fu) -0.037 0.13 -9999 0 -0.64 14 14
SAP30 0.009 0.035 -9999 0 -0.58 2 2
mol:GDP -0.015 0.12 -9999 0 -0.56 28 28
MIM/GLI2A 0.002 0.091 -9999 0 -0.54 15 15
IFT88 0.007 0.049 -9999 0 -0.58 4 4
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GLI2 0.023 0.058 -9999 0 -0.57 2 2
GLI3 0.009 0.1 -9999 0 -0.71 5 5
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
SAP18 0.01 0.019 -9999 0 -0.46 1 1
embryonic digit morphogenesis 0.007 0.049 -9999 0 -0.58 4 4
GNG2 0.004 0.064 -9999 0 -0.53 8 8
Gi family/GTP -0.016 0.11 -9999 0 -0.34 39 39
SIN3B 0.01 0.025 -9999 0 -0.58 1 1
SIN3A 0.01 0.025 -9999 0 -0.58 1 1
GLI3/Su(fu) 0.025 0.081 -9999 0 -0.55 5 5
GLI2/Su(fu) 0.03 0.066 -9999 0 -0.37 6 6
FOXA2 -0.037 0.18 -9999 0 -0.96 21 21
neural tube patterning 0 0.15 -9999 0 -0.57 23 23
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.019 0.043 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CSNK1G2 0.009 0.035 -9999 0 -0.58 2 2
CSNK1G3 0.01 0.025 -9999 0 -0.58 1 1
MTSS1 0.002 0.091 -9999 0 -0.55 15 15
embryonic limb morphogenesis 0 0.15 -9999 0 -0.57 23 23
SUFU 0.014 0.048 -9999 0 -10000 0 0
LGALS3 0.009 0.037 -9999 0 -0.5 3 3
catabolic process 0.028 0.11 -9999 0 -0.42 17 17
GLI3A/CBP 0.008 0.06 -9999 0 -0.35 14 14
KIF3A 0 0.081 -9999 0 -0.58 11 11
GLI1 -0.001 0.15 -9999 0 -0.59 23 23
RAB23 0.006 0.056 -9999 0 -0.54 6 6
CSNK1A1 0.009 0.035 -9999 0 -0.58 2 2
IFT172 0.011 0 -9999 0 -10000 0 0
RBBP7 0.01 0.025 -9999 0 -0.58 1 1
Su(fu)/Galectin3 0.017 0.049 -9999 0 -0.36 2 2
GNAZ -0.012 0.11 -9999 0 -0.54 24 24
RBBP4 0.01 0.025 -9999 0 -0.58 1 1
CSNK1G1 0.01 0.025 -9999 0 -0.58 1 1
PIAS1 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GLI2/SPOP 0.028 0.055 -9999 0 -0.54 2 2
STK36 0.014 0.003 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.008 0.1 -9999 0 -0.45 13 13
PTCH1 0 0.17 -9999 0 -0.97 11 11
MIM/GLI1 0.001 0.17 -9999 0 -0.61 26 26
CREBBP 0.008 0.06 -9999 0 -0.35 14 14
Su(fu)/SIN3/HDAC complex 0.035 0.027 -9999 0 -10000 0 0
Insulin Pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.028 0.084 -9999 0 -0.5 5 5
TC10/GTP -0.022 0.071 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.014 0.06 -9999 0 -0.33 16 16
HRAS 0.008 0.042 -9999 0 -0.49 4 4
APS homodimer -0.015 0.12 -9999 0 -0.52 29 29
GRB14 -0.12 0.24 -9999 0 -0.54 138 138
FOXO3 0.001 0.058 -9999 0 -0.66 3 3
AKT1 -0.031 0.12 -9999 0 -0.38 2 2
INSR 0.01 0.035 -9999 0 -0.58 2 2
Insulin Receptor/Insulin 0.027 0.034 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.007 0.049 -9999 0 -0.58 4 4
SORBS1 -0.013 0.11 -9999 0 -0.51 27 27
CRK 0.011 0.019 -9999 0 -0.46 1 1
PTPN1 0.025 0.033 -9999 0 -0.59 1 1
CAV1 0.008 0.064 -9999 0 -0.32 15 15
CBL/APS/CAP/Crk-II/C3G 0.006 0.088 -9999 0 -0.31 27 27
Insulin Receptor/Insulin/IRS1/NCK2 0.017 0.052 -9999 0 -0.32 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.048 -9999 0 -0.28 16 16
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.045 -9999 0 -0.51 2 2
RPS6KB1 -0.026 0.12 -9999 0 -0.57 2 2
PARD6A 0.007 0.046 -9999 0 -0.48 5 5
CBL 0.011 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.008 -9999 0 -10000 0 0
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.055 0.093 -9999 0 -0.53 2 2
HRAS/GTP -0.018 0.066 -9999 0 -0.47 3 3
Insulin Receptor 0.01 0.035 -9999 0 -0.58 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.023 0.046 -9999 0 -0.3 11 11
PRKCI -0.019 0.055 -9999 0 -0.59 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.064 0.11 -9999 0 -0.42 2 2
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.019 0.028 -9999 0 -0.31 1 1
PI3K -0.009 0.048 -9999 0 -0.29 16 16
NCK2 0.01 0.025 -9999 0 -0.58 1 1
RHOQ 0.011 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
AKT2 -0.032 0.12 -9999 0 -0.4 4 4
PRKCZ -0.017 0.042 -9999 0 -0.78 1 1
SH2B2 -0.015 0.12 -9999 0 -0.52 29 29
SHC/SHIP 0.007 0.08 -9999 0 -0.3 36 36
F2RL2 -0.036 0.16 -9999 0 -0.56 47 47
TRIP10 0.01 0.025 -9999 0 -0.58 1 1
Insulin Receptor/Insulin/Shc 0.015 0.023 -9999 0 -0.31 2 2
TC10/GTP/CIP4/Exocyst 0.015 0.016 -9999 0 -0.36 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.027 0.026 -9999 0 -0.3 1 1
RAPGEF1 0.01 0.025 -9999 0 -0.58 1 1
RASA1 0.009 0.035 -9999 0 -0.58 2 2
NCK1 0.009 0.035 -9999 0 -0.58 2 2
CBL/APS/CAP/Crk-II 0 0.093 -9999 0 -0.33 26 26
TC10/GDP 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.02 0.038 -9999 0 -0.32 6 6
INPP5D 0 0.084 -9999 0 -0.32 36 36
SOS1 0.01 0.025 -9999 0 -0.58 1 1
SGK1 -0.012 0.07 -9999 0 -0.93 3 3
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
IRS1 0.002 0.074 -9999 0 -0.58 9 9
p62DOK/RasGAP 0.02 0.028 -9999 0 -0.31 1 1
INS 0.001 0.027 -9999 0 -0.45 2 2
mol:PI-3-4-P2 0 0.084 -9999 0 -0.32 36 36
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.024 0.11 -9999 0 -0.5 3 3
PTPRA 0.012 0.003 -9999 0 -10000 0 0
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
TC10/GTP/CIP4 0.015 0.016 -9999 0 -0.36 1 1
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.021 0.041 -9999 0 -0.25 12 12
Insulin Receptor/Insulin/IRS1 0.01 0.049 -9999 0 -0.31 13 13
Insulin Receptor/Insulin/IRS3 0.009 0.032 -9999 0 -0.37 4 4
Par3/Par6 -0.001 0.093 -9999 0 -0.31 41 41
Rapid glucocorticoid signaling

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.001 0.078 -10000 0 -0.27 42 42
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.019 -10000 0 -0.32 2 2
GNB1/GNG2 0.011 0.04 -10000 0 -0.32 8 8
GNB1 0.011 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.011 0.071 -10000 0 -0.28 36 36
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.005 0.018 0.074 36 -10000 0 36
GNAL -0.021 0.13 -10000 0 -0.5 36 36
GNG2 0.004 0.064 -10000 0 -0.53 8 8
CRH -0.001 0.027 -10000 0 -0.46 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.015 -10000 0 -0.36 1 1
MAPK11 0 0.04 -10000 0 -0.22 17 17
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.016 0.088 -9999 0 -0.47 15 15
STMN1 0.008 0.072 -9999 0 -0.43 15 15
Aurora B/RasGAP/Survivin 0.025 0.031 -9999 0 -0.48 2 2
Chromosomal passenger complex/Cul3 protein complex -0.012 0.078 -9999 0 -0.39 2 2
BIRC5 0.012 0.02 -9999 0 -0.46 1 1
DES -0.11 0.19 -9999 0 -0.55 90 90
Aurora C/Aurora B/INCENP 0.013 0.063 -9999 0 -0.3 21 21
Aurora B/TACC1 0.012 0.046 -9999 0 -0.35 9 9
Aurora B/PP2A 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.013 0.012 -9999 0 -0.28 1 1
mitotic metaphase/anaphase transition 0 0.001 -9999 0 -10000 0 0
NDC80 0.009 0.069 -9999 0 -0.43 14 14
Cul3 protein complex -0.056 0.14 -9999 0 -0.3 142 142
KIF2C 0.02 0.02 -9999 0 -0.42 1 1
PEBP1 0.012 0.001 -9999 0 -10000 0 0
KIF20A 0.009 0.035 -9999 0 -0.58 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.018 0.027 -9999 0 -0.43 2 2
SEPT1 -0.008 0.1 -9999 0 -0.53 21 21
SMC2 0.002 0.074 -9999 0 -0.58 9 9
SMC4 -0.004 0.094 -9999 0 -0.58 15 15
NSUN2/NPM1/Nucleolin 0.024 0.032 -9999 0 -0.33 1 1
PSMA3 0.011 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.015 0.002 -9999 0 -10000 0 0
AURKB 0.015 0.005 -9999 0 -10000 0 0
AURKC -0.01 0.11 -9999 0 -0.55 21 21
CDCA8 0.012 0.001 -9999 0 -10000 0 0
cytokinesis 0.014 0.04 -9999 0 -0.32 1 1
Aurora B/Septin1 0.005 0.057 -9999 0 -0.32 1 1
AURKA 0.011 0.001 -9999 0 -10000 0 0
INCENP 0.012 0.001 -9999 0 -10000 0 0
KLHL13 -0.11 0.22 -9999 0 -0.5 141 141
BUB1 0.01 0.025 -9999 0 -0.59 1 1
hSgo1/Aurora B/Survivin 0.022 0.035 -9999 0 -0.31 6 6
EVI5 0.004 0.07 -9999 0 -0.58 8 8
RhoA/GTP -0.001 0.019 -9999 0 -0.34 1 1
SGOL1 0.006 0.055 -9999 0 -0.58 5 5
CENPA 0.023 0.021 -9999 0 -0.26 3 3
NCAPG 0.008 0.043 -9999 0 -0.58 3 3
Aurora B/HC8 Proteasome 0.019 0.004 -9999 0 -10000 0 0
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.018 0.019 -9999 0 -0.43 1 1
RHOA 0.01 0.025 -9999 0 -0.58 1 1
NCAPH 0.01 0.025 -9999 0 -0.58 1 1
NPM1 0.011 0.055 -9999 0 -0.48 7 7
RASA1 0.009 0.035 -9999 0 -0.58 2 2
KLHL9 0.01 0.025 -9999 0 -0.58 1 1
mitotic prometaphase 0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.004 -9999 0 -10000 0 0
PPP1CC 0.01 0.025 -9999 0 -0.58 1 1
Centraspindlin 0.027 0.02 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
NSUN2 0.017 0.004 -9999 0 -10000 0 0
MYLK -0.005 0.072 -9999 0 -0.24 47 47
KIF23 0.012 0.001 -9999 0 -10000 0 0
VIM 0.016 0.042 -9999 0 -0.39 6 6
RACGAP1 0.012 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.004 -9999 0 -10000 0 0
Chromosomal passenger complex 0.028 0.017 -9999 0 -0.22 2 2
Chromosomal passenger complex/EVI5 0.02 0.053 -9999 0 -0.3 8 8
TACC1 0.002 0.072 -9999 0 -0.57 9 9
PPP2R5D 0.011 0 -9999 0 -10000 0 0
CUL3 0.009 0.035 -9999 0 -0.58 2 2
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
BARD1 signaling events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.012 0.048 -10000 0 -0.42 7 7
ATM 0.002 0.074 -10000 0 -0.58 9 9
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.008 0.04 -10000 0 -0.54 3 3
ATR 0.009 0.035 -10000 0 -0.58 2 2
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.013 0.066 -10000 0 -0.44 10 10
protein ubiquitination 0.02 0.063 -10000 0 -0.33 16 16
XRCC5 0.01 0.025 -10000 0 -0.58 1 1
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0.007 0.092 -10000 0 -0.46 19 19
MRE11A 0.003 0.069 -10000 0 -0.58 8 8
DNA-PK 0.021 0.035 -10000 0 -0.52 2 2
FA complex/FANCD2/Ubiquitin 0.034 0.059 -10000 0 -0.54 4 4
FANCF 0.005 0.06 -10000 0 -0.58 6 6
BRCA1 0.01 0.025 -10000 0 -0.58 1 1
CCNE1 0.009 0.034 -10000 0 -0.46 3 3
CDK2/Cyclin E1 0.014 0.03 -10000 0 -0.34 4 4
FANCG 0.011 0.019 -10000 0 -0.46 1 1
BRCA1/BACH1/BARD1 0.011 0.051 -10000 0 -0.42 8 8
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN -0.005 0.098 -10000 0 -0.58 16 16
FANCA 0.011 0 -10000 0 -10000 0 0
DNA repair 0.048 0.068 -10000 0 -0.58 4 4
BRCA1/BARD1/ubiquitin 0.011 0.051 -10000 0 -0.42 8 8
BARD1/DNA-PK 0.023 0.05 -10000 0 -0.35 9 9
FANCL 0.008 0.043 -10000 0 -0.58 3 3
mRNA polyadenylation -0.012 0.048 0.42 7 -10000 0 7
BRCA1/BARD1/CTIP/M/R/N Complex 0.004 0.16 -10000 0 -0.74 18 18
BRCA1/BACH1/BARD1/TopBP1 0.017 0.047 -10000 0 -0.35 9 9
BRCA1/BARD1/P53 -0.008 0.11 -10000 0 -0.33 60 60
BARD1/CSTF1/BRCA1 0.018 0.044 -10000 0 -0.35 8 8
BRCA1/BACH1 0.01 0.025 -10000 0 -0.58 1 1
BARD1 0.004 0.065 -10000 0 -0.58 7 7
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.018 0.044 -10000 0 -0.35 8 8
BRCA1/BARD1/UbcH7 0.018 0.044 -10000 0 -0.35 8 8
BRCA1/BARD1/RAD51/PCNA 0.025 0.04 -10000 0 -0.32 8 8
BARD1/DNA-PK/P53 -0.002 0.11 -10000 0 -0.6 3 3
BRCA1/BARD1/Ubiquitin 0.011 0.051 -10000 0 -0.42 8 8
BRCA1/BARD1/CTIP 0.009 0.098 -10000 0 -0.41 25 25
FA complex 0.028 0.053 -10000 0 -1 1 1
BARD1/EWS 0.012 0.048 -10000 0 -0.42 7 7
RBBP8 0 0.1 -10000 0 -0.53 19 19
TP53 -0.043 0.17 -10000 0 -0.58 53 53
TOPBP1 0.01 0.025 -10000 0 -0.58 1 1
G1/S transition of mitotic cell cycle 0.009 0.11 0.33 60 -10000 0 60
BRCA1/BARD1 0.022 0.064 -10000 0 -0.33 16 16
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.048 -10000 0 -0.43 7 7
CDK2 0.01 0.025 -10000 0 -0.58 1 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0 -10000 0 -10000 0 0
RAD50 0.01 0.025 -10000 0 -0.58 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.051 -10000 0 -0.42 8 8
EWSR1 0.011 0 -10000 0 -10000 0 0
TCGA08_rtk_signaling

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.01 0.11 -10000 0 -0.57 21 21
HRAS 0.008 0.042 -10000 0 -0.49 4 4
EGFR 0.004 0.064 -10000 0 -0.53 8 8
AKT 0.017 0.076 -10000 0 -0.34 18 18
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.01 0.025 -10000 0 -0.58 1 1
FOXO1 0.01 0.025 -10000 0 -0.58 1 1
AKT3 -0.011 0.11 -10000 0 -0.51 25 25
FOXO4 0.01 0.025 -10000 0 -0.58 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
PIK3CB 0.007 0.047 -10000 0 -0.55 4 4
NRAS 0.001 0.077 -10000 0 -0.58 10 10
PIK3CG -0.044 0.17 -10000 0 -0.55 57 57
PIK3R3 0.008 0.043 -10000 0 -0.58 3 3
PIK3R2 0.01 0.025 -10000 0 -0.58 1 1
NF1 0.008 0.043 -10000 0 -0.58 3 3
RAS 0.008 0.055 0.21 1 -0.31 8 9
ERBB2 0 0.073 -10000 0 -0.46 14 14
proliferation/survival/translation -0.02 0.045 0.26 7 -0.15 1 8
PI3K 0.009 0.064 0.18 2 -0.26 18 20
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
KRAS 0.005 0.058 -10000 0 -0.56 6 6
FOXO 0.035 0.026 0.16 2 -10000 0 2
AKT2 0.009 0.037 -10000 0 -0.5 3 3
PTEN 0.005 0.06 -10000 0 -0.58 6 6
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.021 0.037 -10000 0 -0.26 10 10
epithelial cell differentiation 0.023 0.023 -10000 0 -0.3 3 3
CYFIP2 0.001 0.077 -10000 0 -0.58 10 10
ENAH 0.037 0.067 -10000 0 -0.42 6 6
EGFR 0.004 0.064 -10000 0 -0.53 8 8
EPHA2 0.006 0.056 -10000 0 -0.54 6 6
MYO6 0.029 0.022 -10000 0 -10000 0 0
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.015 0.059 -10000 0 -0.38 12 12
AQP5 -0.038 0.1 -10000 0 -0.47 24 24
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -10000 0 -0.27 4 4
regulation of calcium-dependent cell-cell adhesion -0.003 0.093 -10000 0 -0.28 43 43
EGF -0.18 0.25 -10000 0 -0.5 209 209
NCKAP1 0.009 0.035 -10000 0 -0.58 2 2
AQP3 -0.023 0.07 -10000 0 -0.47 9 9
cortical microtubule organization 0.023 0.023 -10000 0 -0.3 3 3
GO:0000145 0.026 0.024 -10000 0 -0.26 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.023 -10000 0 -0.3 3 3
MLLT4 0.009 0.035 -10000 0 -0.58 2 2
ARF6/GDP -0.005 0.039 -10000 0 -0.48 2 2
ARF6 0.01 0.025 -10000 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.046 -10000 0 -0.37 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.026 -10000 0 -10000 0 0
PVRL2 0.01 0.031 -10000 0 -0.52 2 2
ZYX 0.028 0.026 -10000 0 -0.28 1 1
ARF6/GTP 0.027 0.048 -10000 0 -0.59 2 2
CDH1 0.01 0.025 -10000 0 -0.58 1 1
EGFR/EGFR/EGF/EGF -0.084 0.11 -10000 0 -0.48 1 1
RhoA/GDP -0.002 0.023 -10000 0 -0.28 1 1
actin cytoskeleton organization 0.032 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.01 0.025 -10000 0 -0.58 1 1
GIT1 0.01 0.025 -10000 0 -0.58 1 1
IGF1R 0.01 0.025 -10000 0 -0.58 1 1
IGF1 -0.071 0.19 -10000 0 -0.52 88 88
DIAPH1 -0.013 0.091 -10000 0 -0.62 12 12
Wnt receptor signaling pathway -0.023 0.023 0.3 3 -10000 0 3
RHOA 0.01 0.025 -10000 0 -0.58 1 1
RhoA/GTP -0.005 0.039 -10000 0 -0.48 2 2
CTNNA1 0.009 0.035 -10000 0 -0.58 2 2
VCL 0.032 0.028 -10000 0 -10000 0 0
EFNA1 0.011 0.019 -10000 0 -0.46 1 1
LPP 0.032 0.028 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.004 0.032 -10000 0 -10000 0 0
SEC6/SEC8 -0.003 0.025 -10000 0 -10000 0 0
MGAT3 -0.003 0.094 -10000 0 -0.29 43 43
HGF/MET -0.023 0.072 -10000 0 -10000 0 0
HGF -0.036 0.16 -10000 0 -0.55 49 49
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.037 -10000 0 -0.26 10 10
actin cable formation 0.051 0.057 -10000 0 -0.4 3 3
KIAA1543 0.031 0.033 -10000 0 -10000 0 0
KIFC3 0.024 0.042 -10000 0 -10000 0 0
NCK1 0.009 0.035 -10000 0 -0.58 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.029 0.022 -10000 0 -10000 0 0
NCK1/GIT1 0.015 0.032 -10000 0 -0.42 3 3
mol:GDP 0.023 0.023 -10000 0 -0.3 3 3
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.029 0.022 -10000 0 -10000 0 0
PIP5K1C 0.028 0.026 -10000 0 -0.28 4 4
LIMA1 0.004 0.065 -10000 0 -0.58 7 7
ABI1 0.01 0.025 -10000 0 -0.58 1 1
ROCK1 0.038 0.06 -10000 0 -0.47 4 4
adherens junction assembly 0.038 0.067 -10000 0 -1.1 1 1
IGF-1R heterotetramer/IGF1 -0.037 0.088 -10000 0 -0.55 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -10000 0 -0.4 4 4
MET 0.01 0.031 -10000 0 -0.52 2 2
PLEKHA7 0.028 0.026 -10000 0 -10000 0 0
mol:GTP 0.023 0.046 -10000 0 -0.37 6 6
establishment of epithelial cell apical/basal polarity 0.045 0.029 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.021 0.037 -10000 0 -0.26 10 10
regulation of cell-cell adhesion 0.032 0.027 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.037 -10000 0 -0.26 10 10
VEGFR1 specific signals

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.015 0.082 -9999 0 -0.46 14 14
VEGFR1 homodimer/NRP1 0.007 0.081 -9999 0 -0.47 14 14
mol:DAG 0.014 0.091 -9999 0 -0.64 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.013 0.076 -9999 0 -0.45 12 12
CaM/Ca2+ 0.019 0.086 -9999 0 -0.6 7 7
HIF1A 0.006 0.083 -9999 0 -0.54 12 12
GAB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.028 0.096 -9999 0 -0.62 10 10
PLCG1 0.014 0.092 -9999 0 -0.65 7 7
NOS3 0.025 0.11 -9999 0 -0.59 11 11
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.025 0.1 -9999 0 -0.56 11 11
FLT1 0.012 0.093 -9999 0 -0.54 14 14
PGF -0.001 0.077 -9999 0 -0.47 15 15
VEGFR1 homodimer/NRP2/VEGFR121 0.008 0.1 -9999 0 -0.73 5 5
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
eNOS/Hsp90 0.03 0.1 -9999 0 -0.59 11 11
endothelial cell proliferation 0.004 0.12 -9999 0 -0.73 7 7
mol:Ca2+ 0.014 0.09 -9999 0 -0.63 7 7
MAPK3 0.022 0.083 -9999 0 -0.56 7 7
MAPK1 0.022 0.083 -9999 0 -0.56 7 7
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
PLGF homodimer -0.001 0.077 -9999 0 -0.47 15 15
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.002 0.08 -9999 0 -0.49 15 15
VEGFA homodimer 0.011 0.019 -9999 0 -0.45 1 1
VEGFR1 homodimer/VEGFA homodimer 0.015 0.082 -9999 0 -0.46 14 14
platelet activating factor biosynthetic process 0.026 0.081 -9999 0 -0.54 7 7
PI3K 0.019 0.1 -9999 0 -0.67 9 9
PRKCA 0.018 0.086 -9999 0 -0.59 7 7
PRKCB -0.008 0.12 -9999 0 -0.6 10 10
VEGFR1 homodimer/PLGF homodimer 0.008 0.096 -9999 0 -0.48 16 16
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.014 0.091 -9999 0 -0.64 7 7
RASA1 0.02 0.08 -9999 0 -0.69 5 5
NRP2 -0.013 0.11 -9999 0 -0.5 27 27
VEGFR1 homodimer 0.012 0.093 -9999 0 -0.54 14 14
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.035 -9999 0 -0.58 2 2
eNOS/Caveolin-1 0.025 0.11 -9999 0 -0.64 9 9
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
mol:PI-3-4-5-P3 0.018 0.098 -9999 0 -0.66 9 9
mol:L-citrulline 0.025 0.1 -9999 0 -0.56 11 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.012 0.12 -9999 0 -0.67 12 12
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.02 0.083 -9999 0 -0.68 6 6
CD2AP -0.018 0.13 -9999 0 -0.58 29 29
PI3K/GAB1 0.023 0.095 -9999 0 -0.64 9 9
PDPK1 0.022 0.093 -9999 0 -0.62 9 9
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.018 0.093 -9999 0 -0.71 7 7
mol:NADP 0.025 0.1 -9999 0 -0.56 11 11
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
ubiquitin-dependent protein catabolic process 0.011 0.12 -9999 0 -0.66 12 12
VEGFR1 homodimer/NRP2 0.001 0.11 -9999 0 -0.45 21 21
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.01 0.027 -10000 0 -0.44 2 2
TRAF2/ASK1 0.014 0.027 -10000 0 -0.36 3 3
ATM 0.002 0.074 -10000 0 -0.58 9 9
MAP2K3 0.013 0.097 -10000 0 -0.58 12 12
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.094 -10000 0 -0.54 12 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.004 0.085 -10000 0 -0.46 19 19
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
GADD45A 0.009 0.035 -10000 0 -0.58 2 2
GADD45B 0.008 0.039 -10000 0 -0.46 4 4
MAP3K1 0.005 0.06 -10000 0 -0.58 6 6
MAP3K6 0.003 0.068 -10000 0 -0.56 8 8
MAP3K7 0.011 0 -10000 0 -10000 0 0
MAP3K4 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.009 0.056 -10000 0 -0.41 10 10
TAK1/TAB family 0.004 0.022 0.18 3 -10000 0 3
RAC1/OSM/MEKK3 0.02 0.031 -10000 0 -0.4 3 3
TRAF2 0.01 0.025 -10000 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 -0.012 0.069 -10000 0 -0.46 12 12
TRAF6 0.006 0.015 -10000 0 -0.36 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.053 0.17 -10000 0 -0.49 72 72
CCM2 0.01 0.031 -10000 0 -0.52 2 2
CaM/Ca2+/CAMKIIB -0.024 0.1 -10000 0 -0.29 72 72
MAPK11 -0.003 0.083 -10000 0 -0.48 17 17
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.015 0.097 -10000 0 -0.26 73 73
OSM/MEKK3 0.014 0.039 -10000 0 -0.51 3 3
TAOK1 0.003 0.079 -10000 0 -0.46 14 14
TAOK2 0.008 0.048 -10000 0 -0.35 10 10
TAOK3 0.008 0.045 -10000 0 -0.35 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.035 -10000 0 -0.58 2 2
MAP3K10 0.007 0.051 -10000 0 -0.53 5 5
MAP3K3 0.009 0.035 -10000 0 -0.58 2 2
TRX/ASK1 0.012 0.022 -10000 0 -0.35 2 2
GADD45/MTK1/MTK1 0.016 0.054 -10000 0 -0.37 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.083 -9999 0 -0.45 3 3
CRKL 0.02 0.068 -9999 0 -0.42 4 4
mol:DAG 0.026 0.061 -9999 0 -0.33 7 7
HRAS 0.036 0.065 -9999 0 -0.41 4 4
MAPK8 0.019 0.047 -9999 0 -0.33 5 5
RAP1A 0.019 0.071 -9999 0 -0.45 5 5
GAB1 0.02 0.068 -9999 0 -0.42 4 4
MAPK14 0.02 0.045 -9999 0 -0.33 4 4
EPO 0.001 0.055 -9999 0 -0.46 8 8
PLCG1 0.026 0.063 -9999 0 -0.34 7 7
EPOR/TRPC2/IP3 Receptors 0.005 0.06 -9999 0 -0.49 8 8
RAPGEF1 0.01 0.025 -9999 0 -0.58 1 1
EPO/EPOR (dimer)/SOCS3 0.006 0.074 -9999 0 -0.34 19 19
GAB1/SHC/GRB2/SOS1 -0.013 0.052 -9999 0 -0.45 3 3
EPO/EPOR (dimer) 0.007 0.061 -9999 0 -0.35 15 15
IRS2 0.016 0.076 -9999 0 -0.41 5 5
STAT1 0.029 0.08 -9999 0 -0.45 6 6
STAT5B 0.029 0.066 -9999 0 -0.36 6 6
cell proliferation 0.024 0.044 -9999 0 -0.32 4 4
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.082 -9999 0 -0.52 8 8
TEC 0.02 0.068 -9999 0 -0.42 4 4
SOCS3 -0.002 0.08 -9999 0 -0.49 15 15
STAT1 (dimer) 0.029 0.079 -9999 0 -0.44 6 6
JAK2 -0.008 0.11 -9999 0 -0.55 21 21
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
EPO/EPOR (dimer)/JAK2 0.026 0.074 -9999 0 -0.31 18 18
EPO/EPOR 0.007 0.061 -9999 0 -0.35 15 15
LYN 0.012 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.014 0.089 -9999 0 -0.4 6 6
elevation of cytosolic calcium ion concentration 0.005 0.06 -9999 0 -0.49 8 8
SHC1 0.011 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.02 0.051 -9999 0 -0.28 15 15
mol:IP3 0.026 0.061 -9999 0 -0.33 7 7
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.011 0.098 -9999 0 -0.48 6 6
SH2B3 0.011 0.007 -9999 0 -10000 0 0
NFKB1 0.019 0.047 -9999 0 -0.34 4 4
EPO/EPOR (dimer)/JAK2/SOCS3 -0.016 0.061 -9999 0 -0.3 20 20
PTPN6 0.014 0.071 -9999 0 -0.31 18 18
TEC/VAV2/GRB2 0.019 0.087 -9999 0 -0.4 5 5
EPOR 0.005 0.06 -9999 0 -0.49 8 8
INPP5D -0.015 0.12 -9999 0 -0.58 26 26
mol:GDP -0.013 0.053 -9999 0 -0.46 3 3
SOS1 0.01 0.025 -9999 0 -0.58 1 1
PLCG2 -0.01 0.11 -9999 0 -0.54 22 22
CRKL/CBL/C3G 0.031 0.066 -9999 0 -0.46 2 2
VAV2 0.007 0.091 -9999 0 -0.41 6 6
CBL 0.02 0.068 -9999 0 -0.42 4 4
SHC/Grb2/SOS1 -0.014 0.056 -9999 0 -0.41 5 5
STAT5A 0.029 0.066 -9999 0 -0.36 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.041 0.082 -9999 0 -0.46 4 4
LYN/PLCgamma2 0.002 0.078 -9999 0 -0.39 22 22
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
BTK 0 0.1 -9999 0 -0.42 11 11
BCL2 0.025 0.16 -9999 0 -0.83 16 16
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.059 -9999 0 -0.34 5 5
ERC1 0.009 0.034 -9999 0 -0.46 3 3
RIP2/NOD2 -0.001 0.085 -9999 0 -0.4 24 24
NFKBIA 0.036 0.014 -9999 0 -10000 0 0
BIRC2 -0.002 0.088 -9999 0 -0.58 13 13
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
RIPK2 0.011 0 -9999 0 -10000 0 0
IKBKG 0.019 0.073 -9999 0 -0.46 5 5
IKK complex/A20 0.02 0.088 -9999 0 -0.45 6 6
NEMO/A20/RIP2 0.011 0 -9999 0 -10000 0 0
XPO1 0 0.081 -9999 0 -0.58 11 11
NEMO/ATM 0.02 0.092 -9999 0 -0.53 11 11
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.008 0.051 -9999 0 -0.36 11 11
IKK complex/ELKS -0.016 0.066 -9999 0 -0.49 6 6
BCL10/MALT1/TRAF6 0.017 0.062 -9999 0 -0.49 7 7
NOD2 -0.013 0.12 -9999 0 -0.56 24 24
NFKB1 0.013 0.025 -9999 0 -0.58 1 1
RELA 0.014 0 -9999 0 -10000 0 0
MALT1 0.006 0.055 -9999 0 -0.58 5 5
cIAP1/UbcH5C 0.007 0.065 -9999 0 -0.42 13 13
ATM 0.002 0.074 -9999 0 -0.58 9 9
TNF/TNFR1A -0.003 0.088 -9999 0 -0.39 28 28
TRAF6 0.01 0.025 -9999 0 -0.58 1 1
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
CHUK 0.007 0.049 -9999 0 -0.58 4 4
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.016 0.12 -9999 0 -0.54 28 28
NF kappa B1 p50/RelA 0.032 0.016 -9999 0 -0.34 1 1
BCL10 0.007 0.049 -9999 0 -0.58 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.014 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.028 0.08 -9999 0 -0.56 5 5
CYLD 0.01 0.025 -9999 0 -0.58 1 1
IKK complex/PKC alpha 0.031 0.078 -9999 0 -0.53 5 5
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.02 0.026 -9999 0 -0.35 2 2
BIRC5 0.011 0.019 -9999 0 -0.46 1 1
NFKBIA 0.023 0.013 -9999 0 -10000 0 0
CPEB1 -0.051 0.17 -9999 0 -0.54 63 63
AKT1 0.022 0.02 -9999 0 -0.35 1 1
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.018 0.023 -9999 0 -0.49 1 1
NDEL1/TACC3 0.025 0.015 -9999 0 -10000 0 0
GADD45A 0.009 0.035 -9999 0 -0.58 2 2
GSK3B 0.008 0.033 -9999 0 -0.55 2 2
PAK1/Aurora A 0.021 0.013 -9999 0 -10000 0 0
MDM2 0.008 0.044 -9999 0 -0.52 4 4
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 0.017 0.026 -9999 0 -0.42 2 2
TP53 -0.01 0.11 -9999 0 -0.33 54 54
DLG7 0.015 0.013 -9999 0 -0.2 2 2
AURKAIP1 0.01 0.031 -9999 0 -0.52 2 2
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 0.026 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.023 -9999 0 -0.49 1 1
AURKA 0.018 0.016 -9999 0 -0.24 2 2
AURKB 0.011 0.019 -9999 0 -0.24 3 3
CDC25B 0.022 0.016 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.011 -9999 0 -10000 0 0
mRNA polyadenylation -0.018 0.097 -9999 0 -0.29 63 63
Aurora A/CPEB -0.018 0.097 -9999 0 -0.29 63 63
Aurora A/TACC1/TRAP/chTOG 0.028 0.043 -9999 0 -0.31 8 8
BRCA1 0.01 0.025 -9999 0 -0.58 1 1
centrosome duplication 0.021 0.013 -9999 0 -10000 0 0
regulation of centrosome cycle 0.024 0.015 -9999 0 -10000 0 0
spindle assembly 0.027 0.042 -9999 0 -0.31 8 8
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.029 0.033 -9999 0 -0.4 3 3
CENPA 0.013 0.033 -9999 0 -0.42 3 3
Aurora A/PP2A 0.021 0.013 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.013 0.049 -9999 0 -0.57 1 1
negative regulation of DNA binding -0.01 0.11 -9999 0 -0.33 54 54
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0.018 -9999 0 -0.42 1 1
RASA1 0.009 0.035 -9999 0 -0.58 2 2
Ajuba/Aurora A 0.019 0.012 -9999 0 -10000 0 0
mitotic prometaphase 0 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.016 -9999 0 -0.24 2 2
TACC1 0.002 0.072 -9999 0 -0.57 9 9
TACC3 0.011 0.019 -9999 0 -0.46 1 1
Aurora A/Antizyme1 0.026 0.021 -9999 0 -0.32 1 1
Aurora A/RasGAP 0.02 0.026 -9999 0 -0.35 2 2
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 0.011 0.004 -9999 0 -10000 0 0
GIT1 0.01 0.025 -9999 0 -0.58 1 1
GIT1/beta-PIX/PAK1 0.023 0.016 -9999 0 -0.35 1 1
Importin alpha/Importin beta/TPX2 0.017 0.026 -9999 0 -0.42 2 2
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.025 0.022 -9999 0 -0.32 1 1
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.026 0.055 -10000 0 -1.1 1 1
regulation of axonogenesis -0.02 0.045 0.6 2 -10000 0 2
myoblast fusion -0.016 0.032 0.4 2 -10000 0 2
mol:GTP 0.007 0.023 -10000 0 -0.33 2 2
regulation of calcium-dependent cell-cell adhesion 0.004 0.098 0.28 61 -10000 0 61
ARF1/GTP -0.002 0.02 -10000 0 -0.31 2 2
mol:GM1 0.007 0.017 -10000 0 -0.34 1 1
mol:Choline 0.02 0.035 -10000 0 -0.43 3 3
lamellipodium assembly 0.006 0.041 -10000 0 -0.46 2 2
MAPK3 0.019 0.029 -10000 0 -0.34 3 3
ARF6/GTP/NME1/Tiam1 -0.004 0.099 -10000 0 -0.28 61 61
ARF1 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP 0.016 0.033 -10000 0 -0.4 2 2
ARF1/GDP 0.025 0.033 -10000 0 -0.36 2 2
ARF6 0.01 0.029 -10000 0 -0.67 1 1
RAB11A 0.011 0 -10000 0 -10000 0 0
TIAM1 -0.041 0.16 -10000 0 -0.51 59 59
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.029 -10000 0 -0.34 3 3
actin filament bundle formation -0.017 0.036 0.52 2 -10000 0 2
KALRN 0.003 0.043 -10000 0 -0.33 7 7
RAB11FIP3/RAB11A 0.016 0.023 -10000 0 -0.37 2 2
RhoA/GDP 0.017 0.036 -10000 0 -0.52 2 2
NME1 0.012 0.019 -10000 0 -0.45 1 1
Rac1/GDP 0.018 0.028 -10000 0 -0.37 2 2
substrate adhesion-dependent cell spreading 0.007 0.022 -10000 0 -0.33 2 2
cortical actin cytoskeleton organization 0.006 0.041 -10000 0 -0.46 2 2
RAC1 0.011 0 -10000 0 -10000 0 0
liver development 0.007 0.022 -10000 0 -0.33 2 2
ARF6/GTP 0.007 0.023 -10000 0 -0.33 2 2
RhoA/GTP -0.002 0.03 -10000 0 -0.68 1 1
mol:GDP 0.005 0.038 -10000 0 -0.4 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.018 0.025 -10000 0 -0.29 3 3
RHOA 0.01 0.025 -10000 0 -0.58 1 1
PLD1 0.014 0.039 -10000 0 -0.49 3 3
RAB11FIP3 0.01 0.031 -10000 0 -0.52 2 2
tube morphogenesis 0.006 0.041 -10000 0 -0.46 2 2
ruffle organization 0.02 0.045 -10000 0 -0.6 2 2
regulation of epithelial cell migration 0.007 0.022 -10000 0 -0.33 2 2
PLD2 0.016 0.018 -10000 0 -0.34 1 1
PIP5K1A 0.02 0.046 -10000 0 -0.6 2 2
mol:Phosphatidic acid 0.02 0.035 -10000 0 -0.43 3 3
Rac1/GTP 0.006 0.041 -10000 0 -0.46 2 2
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.003 0.092 -9999 0 -0.41 27 27
AKT1 0.052 0.087 -9999 0 -0.54 8 8
PTK2B 0.024 0.093 -9999 0 -0.66 5 5
VEGFR2 homodimer/Frs2 0.022 0.073 -9999 0 -0.85 3 3
CAV1 -0.002 0.08 -9999 0 -0.49 15 15
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.03 0.072 -9999 0 -0.81 3 3
endothelial cell proliferation 0.046 0.096 -9999 0 -0.51 7 7
mol:Ca2+ 0.035 0.07 -9999 0 -0.69 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.035 0.069 -9999 0 -0.77 3 3
RP11-342D11.1 0.028 0.068 -9999 0 -0.69 3 3
CDH5 0.006 0.05 -9999 0 -0.48 6 6
VEGFA homodimer 0.023 0.055 -9999 0 -0.38 9 9
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.043 0.16 -9999 0 -0.53 57 57
HRAS/GDP -0.009 0.059 -9999 0 -0.54 5 5
SH2D2A 0.011 0.019 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.016 0.075 -9999 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.03 0.064 -9999 0 -0.71 3 3
VEGFR1 homodimer 0.006 0.056 -9999 0 -0.54 6 6
SHC/GRB2/SOS1 -0.009 0.062 -9999 0 -0.63 4 4
GRB10 0.033 0.086 -9999 0 -0.7 6 6
PTPN11 0.006 0.055 -9999 0 -0.58 5 5
GRB2 0.011 0 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.076 -9999 0 -0.6 6 6
HRAS 0.008 0.042 -9999 0 -0.49 4 4
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.12 -9999 0 -0.79 10 10
HIF1A 0.002 0.074 -9999 0 -0.58 9 9
FRS2 0.009 0.035 -9999 0 -0.58 2 2
oxygen and reactive oxygen species metabolic process 0.034 0.068 -9999 0 -0.76 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.004 0.091 -9999 0 -0.52 17 17
Nck/Pak 0.015 0.026 -9999 0 -0.42 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.027 0.073 -9999 0 -0.65 4 4
mol:GDP -0.009 0.06 -9999 0 -0.6 4 4
mol:NADP 0.042 0.084 -9999 0 -0.41 14 14
eNOS/Hsp90 0.045 0.083 -9999 0 -0.39 15 15
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
mol:IP3 0.035 0.071 -9999 0 -0.7 3 3
HIF1A/ARNT 0.009 0.061 -9999 0 -0.46 9 9
SHB 0.011 0.019 -9999 0 -0.46 1 1
VEGFA 0.012 0.02 -9999 0 -0.45 1 1
VEGFC -0.012 0.11 -9999 0 -0.54 24 24
FAK1/Vinculin 0.036 0.11 -9999 0 -0.68 9 9
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0.025 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.022 0.096 -9999 0 -0.7 5 5
PTPN6 0.011 0 -9999 0 -10000 0 0
EPAS1 0.015 0.04 -9999 0 -0.41 4 4
mol:L-citrulline 0.042 0.084 -9999 0 -0.41 14 14
ITGAV 0 0.081 -9999 0 -0.58 11 11
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.035 0.069 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer 0.032 0.075 -9999 0 -0.76 3 3
VEGFR2/3 heterodimer 0.014 0.093 -9999 0 -0.49 15 15
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 0.033 0.082 -9999 0 -0.61 6 6
VEGFR2 homodimer 0.021 0.072 -9999 0 -0.58 7 7
FLT1 0.006 0.056 -9999 0 -0.54 6 6
NEDD4 0.009 0.049 -9999 0 -0.58 4 4
MAPK3 0.028 0.073 -9999 0 -0.52 5 5
MAPK1 0.028 0.073 -9999 0 -0.52 5 5
VEGFA145/NRP2 0 0.08 -9999 0 -0.35 28 28
VEGFR1/2 heterodimer 0.02 0.075 -9999 0 -0.51 9 9
KDR 0.021 0.073 -9999 0 -0.59 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.091 -9999 0 -0.59 6 6
SRC 0.01 0.025 -9999 0 -0.58 1 1
platelet activating factor biosynthetic process 0.03 0.075 -9999 0 -0.5 6 6
PI3K 0.044 0.096 -9999 0 -0.64 7 7
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.03 0.066 -9999 0 -0.71 3 3
FES 0.029 0.085 -9999 0 -0.68 4 4
GAB1 -0.01 0.067 -9999 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.064 -9999 0 -0.71 3 3
CTNNB1 0.011 0 -9999 0 -10000 0 0
SOS1 0.01 0.025 -9999 0 -0.58 1 1
ARNT 0.01 0.025 -9999 0 -0.58 1 1
eNOS/Caveolin-1 0.04 0.089 -9999 0 -0.38 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes 0.027 0.078 -9999 0 -0.81 3 3
PI3K/GAB1 0.055 0.085 -9999 0 -0.58 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.038 0.071 -9999 0 -0.7 4 4
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.007 0.12 -9999 0 -0.62 12 12
HSP90AA1 0.009 0.035 -9999 0 -0.58 2 2
CDC42 0.033 0.084 -9999 0 -0.75 4 4
actin cytoskeleton reorganization 0.03 0.063 -9999 0 -0.71 3 3
PTK2 0.031 0.12 -9999 0 -0.68 10 10
EDG1 0.028 0.068 -9999 0 -0.69 3 3
mol:DAG 0.035 0.071 -9999 0 -0.7 3 3
CaM/Ca2+ 0.037 0.065 -9999 0 -0.64 3 3
MAP2K3 0.039 0.071 -9999 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.035 0.089 -9999 0 -0.72 6 6
PLCG1 0.035 0.072 -9999 0 -0.71 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.036 0.062 -9999 0 -0.68 3 3
IQGAP1 0.008 0.04 -9999 0 -0.54 3 3
YES1 0.004 0.065 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.076 -9999 0 -0.81 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.031 0.063 -9999 0 -0.71 3 3
cell migration 0.054 0.095 -9999 0 -0.65 6 6
mol:PI-3-4-5-P3 0.043 0.089 -9999 0 -0.58 7 7
FYN 0.005 0.061 -9999 0 -0.55 7 7
VEGFB/NRP1 0.033 0.065 -9999 0 -0.65 3 3
mol:NO 0.042 0.084 -9999 0 -0.41 14 14
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.059 -9999 0 -0.54 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.089 -9999 0 -0.72 6 6
VHL 0.01 0.025 -9999 0 -0.58 1 1
ITGB3 -0.005 0.093 -9999 0 -0.54 17 17
NOS3 0.043 0.094 -9999 0 -0.46 14 14
VEGFR2 homodimer/VEGFA homodimer/Sck 0 0.11 -9999 0 -0.67 4 4
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.068 -9999 0 -0.65 3 3
PRKCB 0.013 0.11 -9999 0 -0.59 6 6
VCL 0.009 0.035 -9999 0 -0.58 2 2
VEGFA165/NRP1 0.029 0.069 -9999 0 -0.69 3 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.028 0.073 -9999 0 -0.62 5 5
VEGFA165/NRP2 0 0.08 -9999 0 -0.35 28 28
MAPKKK cascade 0.049 0.08 -9999 0 -0.54 8 8
NRP2 -0.013 0.11 -9999 0 -0.5 27 27
VEGFC homodimer -0.012 0.11 -9999 0 -0.54 24 24
NCK1 0.009 0.035 -9999 0 -0.58 2 2
ROCK1 0 0.081 -9999 0 -0.58 11 11
FAK1/Paxillin 0.037 0.1 -9999 0 -0.64 9 9
MAP3K13 0.035 0.074 -9999 0 -0.68 4 4
PDPK1 0.047 0.08 -9999 0 -0.51 7 7
Aurora C signaling

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.01 0.061 -9999 0 -0.32 16 16
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.003 0.017 -9999 0 -10000 0 0
AURKB 0.011 0 -9999 0 -10000 0 0
AURKC -0.01 0.11 -9999 0 -0.55 21 21
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.01 0.066 -10000 0 -0.86 1 1
oxygen homeostasis 0.005 0.014 -10000 0 -10000 0 0
TCEB2 0.005 0.057 -10000 0 -0.47 8 8
TCEB1 0.011 0.019 -10000 0 -0.46 1 1
VHL/Elongin B/Elongin C/HIF2A -0.015 0.055 -10000 0 -0.46 4 4
EPO 0.074 0.18 -10000 0 -0.6 8 8
FIH (dimer) 0.017 0.012 -10000 0 -10000 0 0
APEX1 0.017 0.014 -10000 0 -10000 0 0
SERPINE1 0.054 0.23 -10000 0 -0.69 19 19
FLT1 -0.014 0.11 -10000 0 -0.99 6 6
ADORA2A 0.07 0.19 -10000 0 -0.7 8 8
germ cell development 0.065 0.21 -10000 0 -0.69 12 12
SLC11A2 0.075 0.19 -10000 0 -0.67 7 7
BHLHE40 0.075 0.19 -10000 0 -0.69 7 7
HIF1AN 0.017 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.021 0.12 -10000 0 -0.44 6 6
ETS1 0.015 0.064 -10000 0 -0.48 9 9
CITED2 -0.005 0.067 -10000 0 -1.1 2 2
KDR -0.012 0.1 -10000 0 -0.88 6 6
PGK1 0.075 0.19 -10000 0 -0.67 7 7
SIRT1 0.006 0.055 -10000 0 -0.58 5 5
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.082 0.22 -10000 0 -0.77 8 8
EPAS1 0.05 0.091 -10000 0 -0.37 5 5
SP1 0.016 0.025 -10000 0 -0.58 1 1
ABCG2 0.043 0.24 -10000 0 -0.76 13 13
EFNA1 0.075 0.19 -10000 0 -0.67 7 7
FXN 0.072 0.19 -10000 0 -0.65 8 8
POU5F1 0.064 0.22 -10000 0 -0.72 12 12
neuron apoptosis -0.08 0.21 0.74 8 -10000 0 8
EP300 0.007 0.049 -10000 0 -0.58 4 4
EGLN3 0.004 0.085 -10000 0 -0.51 15 15
EGLN2 0.015 0.039 -10000 0 -0.49 3 3
EGLN1 0.017 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.018 0.043 -10000 0 -0.31 9 9
VHL 0.01 0.025 -10000 0 -0.58 1 1
ARNT 0.016 0.029 -10000 0 -0.6 1 1
SLC2A1 0.067 0.2 -10000 0 -0.72 8 8
TWIST1 0.046 0.24 -10000 0 -0.68 21 21
ELK1 0.017 0.025 -10000 0 -0.58 1 1
HIF2A/ARNT/Cbp/p300 0.066 0.12 -10000 0 -0.43 4 4
VEGFA 0.075 0.19 -10000 0 -0.67 7 7
CREBBP 0.011 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.015 0.067 -10000 0 -0.35 20 20
Ran/GTP/Exportin 1/HDAC1 -0.014 0.076 -10000 0 -0.4 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.069 -10000 0 -0.32 20 20
SUMO1 -0.008 0.11 -10000 0 -0.58 19 19
ZFPM1 -0.004 0.086 -10000 0 -0.49 17 17
NPC/RanGAP1/SUMO1/Ubc9 -0.001 0.097 -10000 0 -0.43 24 24
FKBP3 -0.003 0.091 -10000 0 -0.58 14 14
Histones 0.03 0.037 -10000 0 -10000 0 0
YY1/LSF 0.015 0.061 -10000 0 -0.51 3 3
SMG5 0.01 0.025 -10000 0 -0.58 1 1
RAN 0.011 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.016 0.057 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.018 0.041 -10000 0 -10000 0 0
SAP18 0.011 0.019 -10000 0 -0.46 1 1
RELA 0.018 0.056 -10000 0 -10000 0 0
HDAC1/Smad7 0.022 0.022 -10000 0 -0.35 2 2
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
HDAC3/TR2 0.018 0.043 -10000 0 -0.31 1 1
NuRD/MBD3 Complex 0.036 0.033 -10000 0 -0.34 3 3
NF kappa B1 p50/RelA 0.021 0.055 -10000 0 -0.51 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.014 0.12 -10000 0 -0.55 26 26
GATA1 -0.004 0.073 -10000 0 -0.46 14 14
Mad/Max 0.014 0.03 -10000 0 -0.34 4 4
NuRD/MBD3 Complex/GATA1/Fog1 0.036 0.053 -10000 0 -0.44 4 4
RBBP7 0.01 0.025 -10000 0 -0.58 1 1
NPC -0.004 0.057 -10000 0 -0.31 19 19
RBBP4 0.01 0.025 -10000 0 -0.58 1 1
MAX 0.011 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
NFKBIA 0.013 0.045 -10000 0 -10000 0 0
KAT2B -0.006 0.1 -10000 0 -0.58 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.033 0.025 -10000 0 -10000 0 0
SIN3 complex 0.027 0.031 -10000 0 -0.32 4 4
SMURF1 0.011 0 -10000 0 -10000 0 0
CHD3 0.009 0.035 -10000 0 -0.58 2 2
SAP30 0.009 0.035 -10000 0 -0.58 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.01 0.025 -10000 0 -0.58 1 1
YY1/HDAC3 0.019 0.059 -10000 0 -0.54 1 1
YY1/HDAC2 0.016 0.055 -10000 0 -0.26 20 20
YY1/HDAC1 0.016 0.055 -10000 0 -0.61 1 1
NuRD/MBD2 Complex (MeCP1) 0.035 0.03 -10000 0 -0.36 1 1
PPARG 0.011 0.079 -10000 0 -0.32 27 27
HDAC8/hEST1B 0.023 0.016 -10000 0 -0.35 1 1
UBE2I 0.011 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -10000 0 -10000 0 0
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.048 -10000 0 -0.31 3 3
MBD3L2 -0.001 0.019 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.022 0.022 -10000 0 -0.35 2 2
CREBBP 0.011 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.038 0.034 -10000 0 -0.34 3 3
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.013 0.045 -10000 0 -10000 0 0
HDAC2 0.011 0 -10000 0 -10000 0 0
YY1 0.013 0.063 -10000 0 -0.31 20 20
HDAC8 0.011 0 -10000 0 -10000 0 0
SMAD7 0.009 0.035 -10000 0 -0.58 2 2
NCOR2 0.007 0.047 -10000 0 -0.55 4 4
MXD1 0.008 0.042 -10000 0 -0.49 4 4
STAT3 0.019 0.03 -10000 0 -0.34 4 4
NFKB1 0.01 0.025 -10000 0 -0.58 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.008 0.1 -10000 0 -0.57 19 19
YY1/LSF/HDAC1 0.021 0.056 -10000 0 -0.47 3 3
YY1/SAP30/HDAC1 0.021 0.054 -10000 0 -0.39 3 3
EP300 0.007 0.049 -10000 0 -0.58 4 4
STAT3 (dimer non-phopshorylated) 0.019 0.03 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.045 -10000 0 -10000 0 0
histone deacetylation 0.035 0.029 -10000 0 -0.36 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.044 -10000 0 -10000 0 0
nuclear export -0.022 0.016 0.35 1 -10000 0 1
PRKACA 0.011 0 -10000 0 -10000 0 0
GATAD2B 0.011 0 -10000 0 -10000 0 0
GATAD2A 0.01 0.025 -10000 0 -0.58 1 1
GATA2/HDAC3 0.004 0.079 -10000 0 -0.32 21 21
GATA1/HDAC1 0.006 0.052 -10000 0 -0.32 14 14
GATA1/HDAC3 0.003 0.056 -10000 0 -0.33 2 2
CHD4 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.003 0.088 -10000 0 -0.39 28 28
SIN3/HDAC complex/Mad/Max 0.036 0.027 -10000 0 -0.36 1 1
NuRD Complex 0.04 0.042 -10000 0 -0.47 2 2
positive regulation of chromatin silencing 0.029 0.036 -10000 0 -10000 0 0
SIN3B 0.01 0.025 -10000 0 -0.58 1 1
MTA2 0.011 0 -10000 0 -10000 0 0
SIN3A 0.01 0.025 -10000 0 -0.58 1 1
XPO1 0 0.081 -10000 0 -0.58 11 11
SUMO1/HDAC1 0.005 0.11 -10000 0 -0.55 19 19
HDAC complex 0.028 0.02 -10000 0 -0.32 2 2
GATA1/Fog1 -0.005 0.082 -10000 0 -0.35 30 30
FKBP25/HDAC1/HDAC2 0.014 0.058 -10000 0 -0.35 14 14
TNF -0.016 0.12 -10000 0 -0.54 28 28
negative regulation of cell growth 0.036 0.027 -10000 0 -0.36 1 1
NuRD/MBD2/PRMT5 Complex 0.035 0.03 -10000 0 -0.36 1 1
Ran/GTP/Exportin 1 0.006 0.12 -10000 0 -0.68 15 15
NF kappa B/RelA/I kappa B alpha 0.019 0.069 -10000 0 -0.33 19 19
SIN3/HDAC complex/NCoR1 0.034 0.024 -10000 0 -10000 0 0
TFCP2 0.009 0.035 -10000 0 -0.58 2 2
NR2C1 0.01 0.025 -10000 0 -0.58 1 1
MBD3 0.007 0.051 -10000 0 -0.53 5 5
MBD2 0.006 0.055 -10000 0 -0.58 5 5
Atypical NF-kappaB pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.015 0.029 -9999 0 -0.39 3 3
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.033 -9999 0 -0.33 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.049 -9999 0 -10000 0 0
NFKBIA 0.009 0.052 -9999 0 -0.22 21 21
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.02 -9999 0 -0.35 1 1
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.008 0.043 -9999 0 -0.58 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.032 -9999 0 -0.32 5 5
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.02 -9999 0 -0.31 2 2
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
NF kappa B1 p50 dimer 0.015 0.023 -9999 0 -0.37 2 2
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
NFKB1 0.017 0.023 -9999 0 -0.37 2 2
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.014 0.053 -9999 0 -0.22 21 21
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.028 0.047 -9999 0 -10000 0 0
SRC 0.01 0.025 -9999 0 -0.58 1 1
PI3K 0.013 0.041 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA 0.014 0.053 -9999 0 -0.22 21 21
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
SYK 0.011 0.019 -9999 0 -0.46 1 1
I kappa B alpha/PIK3R1 0.013 0.054 -9999 0 -0.28 4 4
cell death 0.027 0.046 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.019 0.033 -9999 0 -0.33 5 5
LCK -0.032 0.14 -9999 0 -0.51 48 48
BCL3 0.008 0.04 -9999 0 -0.54 3 3
E-cadherin signaling in the nascent adherens junction

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.032 0.026 -9999 0 -0.46 1 1
KLHL20 -0.018 0.052 -9999 0 -0.23 25 25
CYFIP2 0.001 0.077 -9999 0 -0.58 10 10
Rac1/GDP 0.044 0.04 -9999 0 -0.49 1 1
ENAH 0.026 0.051 -9999 0 -0.48 2 2
AP1M1 0.01 0.025 -9999 0 -0.58 1 1
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.025 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.004 0.033 -9999 0 -0.41 2 2
ABI1/Sra1/Nap1 -0.014 0.039 -9999 0 -0.21 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.012 0.073 -9999 0 -0.32 20 20
RAPGEF1 0.04 0.033 -9999 0 -0.44 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.027 -9999 0 -0.48 1 1
CRK 0.036 0.029 -9999 0 -0.43 1 1
E-cadherin/gamma catenin/alpha catenin 0.021 0.031 -9999 0 -0.35 4 4
alphaE/beta7 Integrin -0.004 0.091 -9999 0 -0.39 30 30
IQGAP1 0.008 0.04 -9999 0 -0.54 3 3
NCKAP1 0.009 0.035 -9999 0 -0.58 2 2
Rap1/GTP/I-afadin 0.02 0.025 -9999 0 -0.32 3 3
DLG1 0.031 0.034 -9999 0 -0.46 1 1
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.027 -9999 0 -0.26 5 5
MLLT4 0.009 0.035 -9999 0 -0.58 2 2
ARF6/GTP/NME1/Tiam1 -0.009 0.093 -9999 0 -0.28 61 61
PI3K -0.005 0.035 -9999 0 -0.34 5 5
ARF6 0.01 0.025 -9999 0 -0.58 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.015 0.026 -9999 0 -0.42 2 2
TIAM1 -0.043 0.16 -9999 0 -0.52 59 59
E-cadherin(dimer)/Ca2+ 0.026 0.023 -9999 0 -0.3 3 3
AKT1 -0.003 0.023 -9999 0 -0.23 4 4
PIK3R1 0.008 0.043 -9999 0 -0.58 3 3
CDH1 0.01 0.025 -9999 0 -0.58 1 1
RhoA/GDP 0.043 0.041 -9999 0 -0.49 1 1
actin cytoskeleton organization 0.018 0.05 -9999 0 -0.17 25 25
CDC42/GDP 0.041 0.048 -9999 0 -0.42 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.024 -9999 0 -0.26 4 4
ITGB7 -0.017 0.12 -9999 0 -0.53 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.028 0.025 -9999 0 -0.32 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.023 -9999 0 -0.3 3 3
mol:GDP 0.04 0.045 -9999 0 -0.6 1 1
CDC42/GTP/IQGAP1 0.011 0.051 -9999 0 -0.45 6 6
JUP 0.01 0.025 -9999 0 -0.58 1 1
p120 catenin/RhoA/GDP 0.035 0.041 -9999 0 -0.49 1 1
RAC1/GTP/IQGAP1 0.014 0.025 -9999 0 -0.33 3 3
PIP5K1C/AP1M1 0.016 0.033 -9999 0 -0.77 1 1
RHOA 0.01 0.025 -9999 0 -0.58 1 1
CDC42 0.006 0.055 -9999 0 -0.58 5 5
CTNNA1 0.009 0.035 -9999 0 -0.58 2 2
positive regulation of S phase of mitotic cell cycle 0.016 0.034 -9999 0 -0.27 1 1
NME1 0.011 0.019 -9999 0 -0.46 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.029 -9999 0 -0.46 1 1
regulation of cell-cell adhesion -0.004 0.029 -9999 0 -0.35 2 2
WASF2 -0.007 0.02 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.026 -9999 0 -0.44 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.016 0.072 -9999 0 -0.3 23 23
CCND1 0.019 0.041 -9999 0 -0.35 1 1
VAV2 0.01 0.15 -9999 0 -0.68 25 25
RAP1/GDP 0.036 0.036 -9999 0 -0.49 1 1
adherens junction assembly 0.031 0.028 -9999 0 -0.45 1 1
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0.025 -9999 0 -0.58 1 1
PIP5K1C 0.01 0.025 -9999 0 -0.58 1 1
regulation of heterotypic cell-cell adhesion 0.021 0.07 -9999 0 -0.41 1 1
E-cadherin/beta catenin 0 0.022 -9999 0 -0.35 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.029 -9999 0 -0.46 1 1
PIK3CA 0.009 0.035 -9999 0 -0.58 2 2
Rac1/GTP -0.029 0.083 -9999 0 -0.37 24 24
E-cadherin/beta catenin/alpha catenin 0.021 0.027 -9999 0 -0.35 3 3
ITGAE 0.011 0.019 -9999 0 -0.46 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.027 -9999 0 -0.49 1 1
mTOR signaling pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.051 0.28 5 -0.29 13 18
FRAP1 0.012 0.017 -10000 0 -10000 0 0
AKT1 0.017 0.049 0.22 5 -0.26 14 19
INSR 0.009 0.035 -10000 0 -0.58 2 2
Insulin Receptor/Insulin 0.006 0.027 -10000 0 -0.32 4 4
mol:GTP -0.006 0.038 -10000 0 -0.54 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.027 -10000 0 -0.3 3 3
TSC2 0.009 0.031 -10000 0 -0.52 2 2
RHEB/GDP -0.005 0.034 -10000 0 -0.49 1 1
TSC1 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.007 0.049 -10000 0 -0.34 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.03 -10000 0 -0.35 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0.025 -10000 0 -0.58 1 1
RPS6KB1 0.017 0.049 -10000 0 -0.4 5 5
MAP3K5 0.007 0.023 -10000 0 -0.38 2 2
PIK3R1 0.008 0.043 -10000 0 -0.58 3 3
apoptosis 0.007 0.023 -10000 0 -0.38 2 2
mol:LY294002 0 0 0.001 1 -0.002 9 10
EIF4B 0.021 0.043 -10000 0 -0.34 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.044 -10000 0 -0.34 4 4
eIF4E/eIF4G1/eIF4A1 -0.001 0.015 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.013 0.05 -10000 0 -0.3 14 14
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.024 0.16 5 -0.2 1 6
FKBP1A 0.012 0 -10000 0 -10000 0 0
RHEB/GTP -0.005 0.033 -10000 0 -0.48 1 1
mol:Amino Acids 0 0 0.001 1 -0.002 9 10
FKBP12/Rapamycin 0.009 0.001 -10000 0 -10000 0 0
PDPK1 -0.004 0.045 0.23 5 -0.26 13 18
EIF4E 0.009 0.035 -10000 0 -0.58 2 2
ASK1/PP5C 0.017 0.04 -10000 0 -0.62 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.012 0.031 -10000 0 -0.51 2 2
TSC1/TSC2 0.025 0.046 -10000 0 -0.6 1 1
tumor necrosis factor receptor activity 0 0 0.002 9 -0.001 1 10
RPS6 0.007 0.046 -10000 0 -0.48 5 5
PPP5C 0.011 0 -10000 0 -10000 0 0
EIF4G1 0.011 0 -10000 0 -10000 0 0
IRS1 0.001 0.048 -10000 0 -0.38 9 9
INS -0.001 0.027 -10000 0 -0.46 2 2
PTEN 0.005 0.06 -10000 0 -0.58 6 6
PDK2 -0.005 0.048 0.23 5 -0.27 15 20
EIF4EBP1 0.009 0.045 -10000 0 -1 1 1
PIK3CA 0.009 0.035 -10000 0 -0.58 2 2
PPP2R5D 0.017 0.016 -10000 0 -10000 0 0
peptide biosynthetic process 0.01 0.034 -10000 0 -0.27 8 8
RHEB 0.011 0 -10000 0 -10000 0 0
EIF4A1 0.011 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 6 -0.003 1 7
EEF2 0.01 0.034 -10000 0 -0.27 8 8
eIF4E/4E-BP1 0.013 0.046 -10000 0 -0.96 1 1
Class I PI3K signaling events mediated by Akt

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.031 -10000 0 -0.32 4 4
CDKN1B 0.023 0.049 -10000 0 -0.52 4 4
CDKN1A 0.021 0.052 -10000 0 -0.41 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.008 0.04 -10000 0 -0.54 3 3
FOXO3 0.024 0.045 -10000 0 -0.54 3 3
AKT1 -0.006 0.044 -10000 0 -0.57 3 3
BAD 0.01 0.031 -10000 0 -0.52 2 2
AKT3 0.002 0.058 -10000 0 -0.26 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.023 0.047 -10000 0 -0.47 4 4
AKT1/ASK1 0.022 0.054 -10000 0 -0.58 4 4
BAD/YWHAZ 0.02 0.033 -10000 0 -0.34 5 5
RICTOR -0.009 0.11 -10000 0 -0.58 20 20
RAF1 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.021 0.052 0.55 4 -10000 0 4
TSC1 0.024 0.045 -10000 0 -0.54 3 3
YWHAZ 0.008 0.043 -10000 0 -0.58 3 3
AKT1/RAF1 0.024 0.046 -10000 0 -0.54 3 3
EP300 0.007 0.049 -10000 0 -0.58 4 4
mol:GDP 0.019 0.047 -10000 0 -0.56 3 3
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.054 -10000 0 -0.54 4 4
YWHAQ 0.011 0 -10000 0 -10000 0 0
TBC1D4 0.016 0.035 -10000 0 -0.34 5 5
MAP3K5 0.009 0.035 -10000 0 -0.58 2 2
MAPKAP1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.031 0.031 0.3 4 -10000 0 4
YWHAH 0.011 0 -10000 0 -10000 0 0
AKT1S1 0.023 0.053 -10000 0 -0.63 3 3
CASP9 0.023 0.047 -10000 0 -0.54 3 3
YWHAB 0.011 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.059 -10000 0 -0.63 4 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.021 0.027 -10000 0 -0.35 3 3
YWHAE 0.011 0 -10000 0 -10000 0 0
SRC 0.01 0.025 -10000 0 -0.58 1 1
AKT2/p21CIP1 0.025 0.052 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.014 -10000 0 -10000 0 0
CHUK 0.022 0.059 -10000 0 -0.55 5 5
BAD/BCL-XL 0.034 0.051 -10000 0 -0.58 3 3
mTORC2 0.003 0.063 -10000 0 -0.33 20 20
AKT2 0.013 0.019 -10000 0 -0.24 3 3
FOXO1-3a-4/14-3-3 family 0.041 0.048 -10000 0 -0.46 4 4
PDPK1 0.011 0 -10000 0 -10000 0 0
MDM2 0.022 0.053 -10000 0 -0.49 5 5
MAPKKK cascade -0.024 0.045 0.52 3 -10000 0 3
MDM2/Cbp/p300 0.031 0.059 -10000 0 -0.54 4 4
TSC1/TSC2 0.028 0.053 -10000 0 -0.6 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.056 -10000 0 -0.51 4 4
glucose import 0.006 0.07 -10000 0 -0.26 35 35
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.02 0.032 -10000 0 -0.34 3 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.006 0.07 -10000 0 -0.26 35 35
GSK3A 0.024 0.045 -10000 0 -0.54 3 3
FOXO1 0.023 0.047 -10000 0 -0.54 3 3
GSK3B 0.023 0.056 -10000 0 -0.59 4 4
SFN 0.005 0.057 -10000 0 -0.47 8 8
G1/S transition of mitotic cell cycle 0.028 0.054 -10000 0 -0.57 4 4
p27Kip1/14-3-3 family 0.036 0.03 -10000 0 -0.39 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
KPNA1 0.009 0.035 -10000 0 -0.58 2 2
HSP90AA1 0.009 0.035 -10000 0 -0.58 2 2
YWHAG 0.011 0 -10000 0 -10000 0 0
RHEB 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.049 -9999 0 -0.58 4 4
positive regulation of NF-kappaB transcription factor activity 0.011 0.048 -9999 0 -0.36 9 9
MAP2K4 0.033 0.037 -9999 0 -10000 0 0
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
TNFRSF10B 0.01 0.025 -9999 0 -0.58 1 1
TNFRSF10A 0.011 0 -9999 0 -10000 0 0
SMPD1 0.013 0.029 -9999 0 -0.24 7 7
IKBKG 0.01 0.025 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.007 0.043 -9999 0 -0.46 5 5
TRAIL/TRAILR2 0.013 0.041 -9999 0 -0.42 5 5
TRAIL/TRAILR3 -0.006 0.089 -9999 0 -0.35 35 35
TRAIL/TRAILR1 0.014 0.036 -9999 0 -0.42 4 4
TRAIL/TRAILR4 0.011 0.048 -9999 0 -0.36 9 9
TRAIL/TRAILR1/DAP3/GTP 0.02 0.029 -9999 0 -0.32 4 4
IKK complex -0.005 0.039 -9999 0 -0.4 5 5
RIPK1 0.011 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.008 0 -9999 0 -10000 0 0
MAPK3 0.015 0.041 -9999 0 -0.42 5 5
MAP3K1 0.03 0.031 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.007 0.043 -9999 0 -0.45 5 5
TRADD 0.011 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.011 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.026 -9999 0 -10000 0 0
CFLAR 0.011 0 -9999 0 -10000 0 0
MAPK1 0.015 0.041 -9999 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.027 -9999 0 -10000 0 0
mol:ceramide 0.013 0.029 -9999 0 -0.24 7 7
FADD 0.011 0 -9999 0 -10000 0 0
MAPK8 0.037 0.039 -9999 0 -0.39 1 1
TRAF2 0.01 0.025 -9999 0 -0.58 1 1
TRAILR3 (trimer) -0.016 0.11 -9999 0 -0.49 31 31
CHUK 0.007 0.049 -9999 0 -0.58 4 4
TRAIL/TRAILR1/FADD 0.021 0.031 -9999 0 -0.35 4 4
DAP3 0.011 0 -9999 0 -10000 0 0
CASP10 -0.002 0.037 -9999 0 -0.34 5 5
JNK cascade 0.011 0.048 -9999 0 -0.36 9 9
TRAIL (trimer) 0.007 0.049 -9999 0 -0.58 4 4
TNFRSF10C -0.016 0.11 -9999 0 -0.49 31 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.027 -9999 0 -0.3 4 4
TRAIL/TRAILR2/FADD 0.02 0.035 -9999 0 -0.35 5 5
cell death 0.013 0.029 -9999 0 -0.24 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.029 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.01 0.025 -9999 0 -0.58 1 1
CASP8 0 0.036 -9999 0 -0.8 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.03 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.022 0.071 -10000 0 -0.51 2 2
BAG4 0.009 0.035 -10000 0 -0.58 2 2
BAD 0.018 0.036 -10000 0 -0.4 2 2
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.52 29 29
BAX 0.019 0.034 -10000 0 -0.52 1 1
EnzymeConsortium:3.1.4.12 0.008 0.019 -10000 0 -0.097 2 2
IKBKB 0.027 0.068 -10000 0 -0.48 2 2
MAP2K2 0.027 0.036 -10000 0 -0.43 1 1
MAP2K1 0.026 0.037 -10000 0 -0.31 2 2
SMPD1 0.012 0.024 -10000 0 -0.24 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.028 0.067 -10000 0 -0.44 1 1
MAP2K4 0.02 0.048 -10000 0 -0.29 10 10
protein ubiquitination 0.027 0.071 -10000 0 -0.44 4 4
EnzymeConsortium:2.7.1.37 0.029 0.041 -10000 0 -0.3 2 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.023 0.033 -10000 0 -0.24 3 3
CRADD 0.011 0.025 -10000 0 -0.58 1 1
mol:ceramide 0.014 0.029 -10000 0 -0.2 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0.015 0 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.016 0.045 -10000 0 -0.32 7 7
TRADD 0.012 0 -10000 0 -10000 0 0
RELA/p50 0.011 0 -10000 0 -10000 0 0
MAPK3 0.028 0.036 -10000 0 -0.28 2 2
MAPK1 0.028 0.036 -10000 0 -0.28 2 2
p50/RELA/I-kappa-B-alpha 0.017 0 -10000 0 -10000 0 0
FADD 0.023 0.068 -10000 0 -0.46 1 1
KSR1 0.018 0.033 -10000 0 -0.26 3 3
MAPK8 0.024 0.047 -10000 0 -0.28 10 10
TRAF2 0.01 0.025 -10000 0 -0.58 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.025 0.074 -10000 0 -0.51 3 3
TNF R/SODD 0.015 0.026 -10000 0 -0.42 2 2
TNF -0.015 0.12 -10000 0 -0.54 28 28
CYCS 0.018 0.046 0.13 10 -0.25 8 18
IKBKG 0.027 0.071 -10000 0 -0.51 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.018 0.071 -10000 0 -0.38 3 3
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.022 0.037 0.13 10 -0.35 2 12
TNF/TNF R/SODD 0.005 0.078 -10000 0 -0.32 30 30
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.032 -10000 0 -0.58 1 1
NSMAF 0.023 0.067 -10000 0 -0.46 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.007 0.1 -10000 0 -0.55 19 19
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.015 0.072 -9999 0 -10000 0 0
PLK1 0.053 0.13 -9999 0 -1 2 2
CDKN1B 0.094 0.073 -9999 0 -0.43 4 4
FOXO3 0.051 0.13 -9999 0 -0.65 4 4
KAT2B 0.002 0.1 -9999 0 -0.58 17 17
FOXO1/SIRT1 0.002 0.054 -9999 0 -0.45 2 2
CAT 0.055 0.12 -9999 0 -0.73 2 2
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.019 0.027 -9999 0 -0.57 1 1
FOXO1 0.022 0.047 -9999 0 -0.28 2 2
MAPK10 0.009 0.083 -9999 0 -0.29 34 34
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.067 0.066 -9999 0 -0.58 2 2
response to oxidative stress 0.009 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.003 0.089 -9999 0 -0.64 4 4
XPO1 0.001 0.081 -9999 0 -0.58 11 11
EP300 0.008 0.05 -9999 0 -0.58 4 4
BCL2L11 0.026 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.023 0.053 -9999 0 -0.51 2 2
mol:GDP 0.009 0.013 -9999 0 -10000 0 0
RAN 0.013 0.001 -9999 0 -10000 0 0
GADD45A 0.079 0.09 -9999 0 -0.88 3 3
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.053 0.054 -9999 0 -0.59 3 3
MST1 -0.026 0.15 -9999 0 -0.5 50 50
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.044 -9999 0 -0.45 3 3
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.032 0.017 -9999 0 -0.34 1 1
MAPK9 0.032 0.007 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
YWHAZ 0.008 0.043 -9999 0 -0.58 3 3
SIRT1 0.008 0.057 -9999 0 -0.57 5 5
SOD2 0.094 0.088 -9999 0 -0.63 2 2
RBL2 0.063 0.12 -9999 0 -1.4 2 2
RAL/GDP 0.026 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.05 -9999 0 -0.58 4 4
Ran/GTP 0.012 0.002 -9999 0 -10000 0 0
CSNK1G2 0.009 0.035 -9999 0 -0.58 2 2
RAL/GTP 0.032 0.01 -9999 0 -10000 0 0
CSNK1G1 0.01 0.025 -9999 0 -0.58 1 1
FASLG -0.083 0.36 -9999 0 -1.4 40 40
SKP2 0.008 0.043 -9999 0 -0.58 3 3
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.018 0.021 -9999 0 -0.44 1 1
CCNB1 0.055 0.12 -9999 0 -0.73 2 2
FOXO1-3a-4/beta catenin 0.098 0.09 -9999 0 -0.44 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.053 -9999 0 -0.5 2 2
CSNK1A1 0.009 0.035 -9999 0 -0.58 2 2
SGK1 0.007 0.077 -9999 0 -0.48 14 14
CSNK1G3 0.01 0.025 -9999 0 -0.58 1 1
Ran/GTP/Exportin 1 0.014 0.052 -9999 0 -0.36 11 11
ZFAND5 0.068 0.068 -9999 0 -0.72 2 2
SFN 0.005 0.057 -9999 0 -0.47 8 8
CDK2 0.009 0.026 -9999 0 -0.58 1 1
FOXO3A/14-3-3 0.048 0.052 -9999 0 -0.42 4 4
CREBBP 0.01 0.009 -9999 0 -10000 0 0
FBXO32 0.053 0.12 -9999 0 -0.73 2 2
BCL6 0.064 0.1 -9999 0 -0.65 2 2
RALB 0.012 0.001 -9999 0 -10000 0 0
RALA 0.012 0.001 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
Arf6 trafficking events

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.015 0.12 -10000 0 -0.5 30 30
CLTC 0.024 0.033 -10000 0 -0.7 1 1
calcium ion-dependent exocytosis 0.02 0.023 -10000 0 -0.46 1 1
Dynamin 2/GTP 0.019 0.023 -10000 0 -0.29 3 3
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.022 0.031 -10000 0 -0.7 1 1
CPE -0.039 0.12 -10000 0 -0.32 92 92
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.02 0.022 -10000 0 -0.45 1 1
CTNND1 0.024 0.021 -10000 0 -0.3 2 2
DNM2 0.01 0.025 -10000 0 -0.58 1 1
mol:PI-4-5-P2 0.024 0.032 -10000 0 -0.5 2 2
TSHR -0.001 0.065 -10000 0 -0.29 27 27
INS 0.009 0.011 -10000 0 -10000 0 0
BIN1 0.006 0.055 -10000 0 -0.58 5 5
mol:Choline 0.02 0.022 -10000 0 -0.45 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.019 -10000 0 -0.31 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.01 0.025 -10000 0 -0.58 1 1
mol:Ca2+ 0.018 0.023 -10000 0 -0.29 3 3
JUP 0.021 0.032 -10000 0 -0.7 1 1
ASAP2/amphiphysin II 0.017 0.04 -10000 0 -0.32 8 8
ARF6/GTP 0.008 0.018 -10000 0 -0.43 1 1
CDH1 0.021 0.032 -10000 0 -0.7 1 1
clathrin-independent pinocytosis 0.008 0.018 -10000 0 -0.43 1 1
MAPK8IP3 0.005 0.058 -10000 0 -0.51 7 7
positive regulation of endocytosis 0.008 0.018 -10000 0 -0.43 1 1
EXOC2 0.01 0.025 -10000 0 -0.58 1 1
substrate adhesion-dependent cell spreading 0.026 0.066 -10000 0 -0.61 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.01 0.025 -10000 0 -0.58 1 1
regulation of calcium-dependent cell-cell adhesion 0.002 0.029 0.62 1 -10000 0 1
positive regulation of phagocytosis 0.015 0.016 -10000 0 -0.36 1 1
ARF6/GTP/JIP3 0.011 0.039 -10000 0 -0.31 8 8
ACAP1 0.014 0.032 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.008 0.071 -10000 0 -0.7 1 1
clathrin heavy chain/ACAP1 0.027 0.033 -10000 0 -0.66 1 1
JIP4/KLC1 0.021 0.02 -10000 0 -0.32 2 2
EXOC1 0.01 0.025 -10000 0 -0.58 1 1
exocyst 0.026 0.067 -10000 0 -0.62 4 4
RALA/GTP 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.014 0.022 -10000 0 -0.36 2 2
receptor recycling 0.008 0.018 -10000 0 -0.43 1 1
CTNNA1 0.023 0.029 -10000 0 -0.3 4 4
NME1 0.014 0.02 -10000 0 -0.31 2 2
clathrin coat assembly 0.024 0.032 -10000 0 -0.69 1 1
IL2RA 0.001 0.07 -10000 0 -0.5 2 2
VAMP3 0.015 0.016 -10000 0 -0.36 1 1
GLUT4/clathrin heavy chain/ACAP1 -0.013 0.054 -10000 0 -0.45 2 2
EXOC6 0.008 0.043 -10000 0 -0.58 3 3
PLD1 0.016 0.03 -10000 0 -0.37 3 3
PLD2 0.018 0.008 -10000 0 -10000 0 0
EXOC5 -0.006 0.1 -10000 0 -0.58 17 17
PIP5K1C 0.024 0.033 -10000 0 -0.51 2 2
SDC1 0.021 0.032 -10000 0 -0.7 1 1
ARF6/GDP 0.014 0.02 -10000 0 -0.31 2 2
EXOC7 0.011 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.002 0.03 -10000 0 -0.64 1 1
mol:Phosphatidic acid 0.02 0.022 -10000 0 -0.45 1 1
endocytosis -0.016 0.04 0.32 8 -10000 0 8
SCAMP2 0.011 0 -10000 0 -10000 0 0
ADRB2 0.008 0.079 -10000 0 -0.65 1 1
EXOC3 0.011 0 -10000 0 -10000 0 0
ASAP2 0.009 0.035 -10000 0 -0.58 2 2
Dynamin 2/GDP 0.02 0.023 -10000 0 -0.29 3 3
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 0.002 0.084 -10000 0 -0.29 25 25
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.031 -10000 0 -0.59 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.007 0.025 0.26 5 -10000 0 5
BUB1B 0.017 0.029 -10000 0 -0.32 4 4
PLK1 0.015 0.007 -10000 0 -10000 0 0
PLK1S1 0.011 0.019 -10000 0 -0.27 2 2
KIF2A 0.02 0.015 -10000 0 -0.32 1 1
regulation of mitotic centrosome separation 0.015 0.007 -10000 0 -10000 0 0
GOLGA2 0.009 0.035 -10000 0 -0.58 2 2
Hec1/SPC24 0.011 0.068 -10000 0 -0.29 28 28
WEE1 0.017 0.045 -10000 0 -0.51 4 4
cytokinesis 0.021 0.049 -10000 0 -0.51 3 3
PP2A-alpha B56 0.029 0.036 -10000 0 -0.78 1 1
AURKA 0.014 0.004 -10000 0 -10000 0 0
PICH/PLK1 0.021 0.058 -10000 0 -0.3 15 15
CENPE 0.01 0.06 -10000 0 -0.32 18 18
RhoA/GTP 0.008 0.018 -10000 0 -0.43 1 1
positive regulation of microtubule depolymerization 0.02 0.015 -10000 0 -0.31 1 1
PPP2CA 0.011 0 -10000 0 -10000 0 0
FZR1 0.01 0.025 -10000 0 -0.58 1 1
TPX2 0.012 0.017 -10000 0 -0.26 2 2
PAK1 0.011 0 -10000 0 -10000 0 0
SPC24 -0.002 0.088 -10000 0 -0.55 14 14
FBXW11 0.011 0 -10000 0 -10000 0 0
CLSPN 0.013 0.02 -10000 0 -0.32 2 2
GORASP1 0.011 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.016 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 0.011 1 -10000 0 1
STAG2 0.007 0.049 -10000 0 -0.58 4 4
GRASP65/GM130/RAB1/GTP -0.001 0.018 -10000 0 -10000 0 0
spindle elongation 0.015 0.007 -10000 0 -10000 0 0
ODF2 0.011 0.001 -10000 0 -10000 0 0
BUB1 -0.002 0.036 -10000 0 -0.86 1 1
TPT1 0.013 0.005 -10000 0 -10000 0 0
CDC25C 0.015 0.004 -10000 0 -10000 0 0
CDC25B 0.01 0.027 -10000 0 -0.45 2 2
SGOL1 0.007 0.025 -10000 0 -0.26 5 5
RHOA 0.01 0.025 -10000 0 -0.58 1 1
CCNB1/CDK1 -0.003 0.026 -10000 0 -0.27 4 4
CDC14B 0.007 0.032 -10000 0 -0.43 3 3
CDC20 0.011 0 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.047 -10000 0 -0.3 13 13
mitosis 0 0 -10000 0 -10000 0 0
FBXO5 0.016 0.028 -10000 0 -0.31 4 4
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 -0.003 0.091 -10000 0 -0.58 14 14
metaphase plate congression 0.014 0.006 -10000 0 -10000 0 0
ERCC6L 0.019 0.061 -10000 0 -0.32 16 16
NLP/gamma Tubulin 0.012 0.004 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.013 0.005 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0 -10000 0 -10000 0 0
PPP1R12A 0.007 0.05 -10000 0 -0.58 4 4
interphase 0 0 -10000 0 -10000 0 0
PLK1/PRC1-2 0.025 0.02 -10000 0 -0.3 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.024 -10000 0 -0.29 3 3
RAB1A 0.01 0.025 -10000 0 -0.58 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0 0.001 0.012 1 -0.008 1 2
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.026 -10000 0 -0.4 1 1
microtubule-based process 0.019 0.021 -10000 0 -0.32 2 2
Golgi organization 0.015 0.007 -10000 0 -10000 0 0
Cohesin/SA2 0.015 0.028 -10000 0 -0.31 4 4
PPP1CB/MYPT1 0.011 0.052 -10000 0 -0.48 6 6
KIF20A 0.009 0.035 -10000 0 -0.58 2 2
APC/C/CDC20 0.02 0.006 -10000 0 -10000 0 0
PPP2R1A 0.01 0.025 -10000 0 -0.58 1 1
chromosome segregation 0.01 0.046 -10000 0 -0.29 13 13
PRC1 0.011 0 -10000 0 -10000 0 0
ECT2 0.013 0.052 -10000 0 -0.33 13 13
C13orf34 0.017 0.005 -10000 0 -10000 0 0
NUDC 0.014 0.006 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.029 -10000 0 -0.32 4 4
spindle assembly 0.015 0.005 -10000 0 -10000 0 0
spindle stabilization 0.011 0.019 -10000 0 -0.27 2 2
APC/C/HCDH1 0.013 0.031 -10000 0 -0.36 4 4
MKLP2/PLK1 0.019 0.021 -10000 0 -0.32 2 2
CCNB1 0.012 0.001 -10000 0 -10000 0 0
PPP1CB 0.008 0.043 -10000 0 -0.59 3 3
BTRC 0.01 0.025 -10000 0 -0.58 1 1
ROCK2 0.011 0.071 -10000 0 -0.48 11 11
TUBG1 0.013 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.025 -10000 0 -0.27 4 4
MLF1IP -0.001 0.066 -10000 0 -0.44 13 13
INCENP 0.011 0.001 -10000 0 -10000 0 0
Circadian rhythm pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.036 0.058 -10000 0 -1.1 1 1
CLOCK 0.012 0.032 -10000 0 -0.51 2 2
TIMELESS/CRY2 0.032 0.055 -10000 0 -1.2 1 1
DEC1/BMAL1 0.007 0.048 -10000 0 -0.33 11 11
ATR 0.009 0.035 -10000 0 -0.58 2 2
NR1D1 0.03 0.061 -10000 0 -1.3 1 1
ARNTL 0.012 0.035 -10000 0 -0.58 2 2
TIMELESS 0.031 0.059 -10000 0 -1.3 1 1
NPAS2 0.012 0.032 -10000 0 -0.51 2 2
CRY2 0.011 0 -10000 0 -10000 0 0
mol:CO -0.011 0.009 0.12 3 -10000 0 3
CHEK1 0.01 0.025 -10000 0 -0.58 1 1
mol:HEME 0.011 0.009 -10000 0 -0.12 3 3
PER1 0.003 0.064 -10000 0 -0.5 9 9
BMAL/CLOCK/NPAS2 0.033 0.037 -10000 0 -0.34 4 4
BMAL1/CLOCK 0.034 0.068 -10000 0 -0.88 2 2
S phase of mitotic cell cycle 0.036 0.058 -10000 0 -1.1 1 1
TIMELESS/CHEK1/ATR 0.036 0.059 -10000 0 -1.2 1 1
mol:NADPH 0.011 0.009 -10000 0 -0.12 3 3
PER1/TIMELESS 0.028 0.068 -10000 0 -0.93 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.003 0.057 -10000 0 -0.46 9 9
Insulin-mediated glucose transport

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.009 0.059 -10000 0 -0.35 6 6
CaM/Ca2+ 0.008 0 -10000 0 -10000 0 0
AKT1 0.01 0.025 -10000 0 -0.58 1 1
AKT2 0.009 0.037 -10000 0 -0.5 3 3
STXBP4 0.005 0.06 -10000 0 -0.58 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.028 0.057 0.2 6 -0.36 4 10
YWHAZ 0.008 0.043 -10000 0 -0.58 3 3
CALM1 0.011 0 -10000 0 -10000 0 0
YWHAQ 0.011 0 -10000 0 -10000 0 0
TBC1D4 0.015 0.041 -10000 0 -0.42 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.011 0 -10000 0 -10000 0 0
YWHAB 0.011 0 -10000 0 -10000 0 0
SNARE/Synip 0.019 0.038 -10000 0 -0.35 6 6
YWHAG 0.011 0 -10000 0 -10000 0 0
ASIP 0 0.054 -10000 0 -0.46 8 8
PRKCI 0.008 0.043 -10000 0 -0.58 3 3
AS160/CaM/Ca2+ 0.008 0 -10000 0 -10000 0 0
RHOQ 0.011 0 -10000 0 -10000 0 0
GYS1 0.021 0.044 -10000 0 -0.47 4 4
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
TRIP10 0.01 0.025 -10000 0 -0.58 1 1
TC10/GTP/CIP4/Exocyst 0.015 0.016 -10000 0 -0.36 1 1
AS160/14-3-3 0.033 0.033 -10000 0 -0.34 2 2
VAMP2 0.011 0 -10000 0 -10000 0 0
SLC2A4 0.028 0.061 -10000 0 -0.4 4 4
STX4 0.011 0 -10000 0 -10000 0 0
GSK3B 0.018 0.046 -10000 0 -0.58 3 3
SFN 0.005 0.057 -10000 0 -0.47 8 8
LNPEP 0.003 0.069 -10000 0 -0.58 8 8
YWHAE 0.011 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.034 0.052 -10000 0 -0.41 6 6
adherens junction organization 0.032 0.033 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.052 -10000 0 -0.48 3 3
FMN1 0.027 0.049 -10000 0 -0.3 9 9
mol:IP3 0.03 0.038 -10000 0 -0.38 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.031 -10000 0 -0.37 2 2
CTNNB1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.034 0.044 -10000 0 -0.69 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.04 -10000 0 -0.56 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.031 0.037 -10000 0 -0.39 3 3
VASP 0.032 0.029 -10000 0 -0.46 1 1
ZYX 0.032 0.039 -10000 0 -0.74 1 1
JUB 0.032 0.029 -10000 0 -0.46 1 1
EGFR(dimer) 0.029 0.046 -10000 0 -0.33 6 6
E-cadherin/beta catenin-gamma catenin 0.021 0.021 -10000 0 -0.34 2 2
mol:PI-3-4-5-P3 0.03 0.038 -10000 0 -0.3 6 6
PIK3CA 0.01 0.035 -10000 0 -0.58 2 2
PI3K 0.031 0.039 -10000 0 -0.31 6 6
FYN 0.031 0.055 -10000 0 -0.33 7 7
mol:Ca2+ 0.029 0.038 -10000 0 -0.37 2 2
JUP 0.01 0.025 -10000 0 -0.59 1 1
PIK3R1 0.009 0.043 -10000 0 -0.58 3 3
mol:DAG 0.03 0.038 -10000 0 -0.38 2 2
CDH1 0.01 0.025 -10000 0 -0.58 1 1
RhoA/GDP 0.037 0.055 -10000 0 -0.49 4 4
establishment of polarity of embryonic epithelium 0.032 0.029 -10000 0 -0.45 1 1
SRC 0.01 0.025 -10000 0 -0.58 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.01 0.025 -10000 0 -0.58 1 1
EGFR 0.004 0.064 -10000 0 -0.53 8 8
CASR 0.028 0.045 -10000 0 -0.45 1 1
RhoA/GTP 0.032 0.04 -10000 0 -0.47 2 2
AKT2 0.034 0.048 -10000 0 -0.58 2 2
actin cable formation 0.032 0.047 -10000 0 -0.4 2 2
apoptosis -0.032 0.048 0.37 6 -10000 0 6
CTNNA1 0.01 0.035 -10000 0 -0.58 2 2
mol:GDP 0.032 0.055 -10000 0 -0.52 3 3
PIP5K1A 0.031 0.037 -10000 0 -0.4 3 3
PLCG1 0.03 0.039 -10000 0 -0.39 2 2
Rac1/GTP -0.005 0.037 -10000 0 -0.37 3 3
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Arf1 pathway

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.002 0.03 -9999 0 -0.63 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.021 -9999 0 -0.23 3 3
AP2 0.014 0.03 -9999 0 -0.34 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.016 0.002 -9999 0 -10000 0 0
CLTB 0.009 0.037 -9999 0 -0.5 3 3
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.016 -9999 0 -0.26 1 1
CD4 -0.014 0.12 -9999 0 -0.55 26 26
CLTA 0.011 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ARFGAP1 0.007 0.027 -9999 0 -0.36 3 3
mol:PI-4-5-P2 -0.001 0.019 -9999 0 -0.32 2 2
ARF1/GTP -0.001 0.012 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.026 -9999 0 -0.3 3 3
mol:Choline -0.001 0.019 -9999 0 -0.32 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0.019 -9999 0 -0.45 1 1
DDEF1 -0.001 0.02 -9999 0 -0.33 2 2
ARF1/GDP 0.005 0.021 -9999 0 -0.26 3 3
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.013 0.01 -9999 0 -0.22 1 1
Rac/GTP 0.009 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.019 0.022 -9999 0 -0.25 3 3
ARFIP2 0.01 0.003 -9999 0 -10000 0 0
COPA 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.011 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0.011 -9999 0 -0.26 1 1
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.011 -9999 0 -0.2 1 1
AP2A1 0.008 0.042 -9999 0 -0.49 4 4
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.02 0.029 -9999 0 -0.61 1 1
ARF1/GDP/Membrin 0.015 0.011 -9999 0 -0.19 1 1
Arfaptin 2/Rac/GDP 0.015 0.002 -9999 0 -10000 0 0
CYTH2 0.012 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.016 0.011 -9999 0 -0.25 1 1
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.008 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.017 0.051 -9999 0 -0.22 21 21
PLD2 -0.001 0.019 -9999 0 -0.32 2 2
ARF-GAP1/v-SNARE 0.007 0.027 -9999 0 -0.36 3 3
PIP5K1A -0.001 0.02 -9999 0 -0.33 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.002 0.019 -9999 0 -0.28 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.019 -9999 0 -0.32 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.027 -9999 0 -0.36 3 3
GOSR2 -0.001 0.008 -9999 0 -10000 0 0
USO1 -0.005 0.05 -9999 0 -0.48 6 6
GBF1 -0.001 0.019 -9999 0 -0.42 1 1
ARF1/GTP/Arfaptin 2 0.016 0.011 -9999 0 -0.24 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.005 0.078 -9999 0 -0.32 30 30
Alternative NF-kappaB pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.013 0.041 -9999 0 -0.42 5 5
FBXW11 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
CHUK 0.007 0.049 -9999 0 -0.58 4 4
NF kappa B2 p100/RelB 0.029 0.052 -9999 0 -0.66 2 2
NFKB1 0.01 0.025 -9999 0 -0.58 1 1
MAP3K14 0.01 0.025 -9999 0 -0.58 1 1
NF kappa B1 p50/RelB 0.014 0.032 -9999 0 -0.37 4 4
RELB 0.009 0.037 -9999 0 -0.5 3 3
NFKB2 0.01 0.031 -9999 0 -0.52 2 2
NF kappa B2 p52/RelB 0.013 0.038 -9999 0 -0.49 3 3
regulation of B cell activation 0.013 0.038 -9999 0 -0.49 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.005 0.06 -10000 0 -0.58 6 6
SMAD2 0.013 0.024 0.24 1 -0.25 2 3
SMAD3 0.029 0.031 -10000 0 -0.25 1 1
SMAD3/SMAD4 0.034 0.029 -10000 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.019 0.041 -10000 0 -0.35 7 7
SMAD2/SMAD2/SMAD4 0.029 0.033 -10000 0 -10000 0 0
PPM1A 0.011 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.039 0.19 1 -0.31 6 7
MAP3K1 0.005 0.06 -10000 0 -0.58 6 6
TRAP-1/SMAD4 0.011 0.051 -10000 0 -0.42 8 8
MAPK3 0.01 0.025 -10000 0 -0.58 1 1
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
NUP214 0.011 0 -10000 0 -10000 0 0
CTDSP1 0.01 0.025 -10000 0 -0.58 1 1
CTDSP2 0.011 0 -10000 0 -10000 0 0
CTDSPL 0.011 0 -10000 0 -10000 0 0
KPNB1 0.011 0 -10000 0 -10000 0 0
TGFBRAP1 0.009 0.035 -10000 0 -0.58 2 2
UBE2I 0.011 0 -10000 0 -10000 0 0
NUP153 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
PIAS4 0.01 0.025 -10000 0 -0.58 1 1
E-cadherin signaling events

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.022 0.022 -9999 0 -0.35 2 2
E-cadherin/beta catenin 0.016 0.018 -9999 0 -0.42 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.025 -9999 0 -0.58 1 1
CDH1 0.01 0.025 -9999 0 -0.58 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 574 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QG.A5Z2 TCGA.QG.A5Z1 TCGA.QG.A5YX TCGA.QG.A5YW
109_MAP3K5 0.044 0.044 0.044 0.044
47_PPARGC1A 0.011 0.011 0.011 0.011
105_BMP4 0.011 0.011 -0.58 0.011
105_BMP6 0.011 0.011 -0.58 0.011
105_BMP7 0.011 0.011 0.011 0.011
105_BMP2 0.011 0.011 0.011 0.011
131_RELN/VLDLR 0.029 0.029 -0.32 0.029
30_TGFB1/TGF beta receptor Type II 0.011 0.011 -0.58 0.011
84_STAT5B -0.14 -0.0065 -0.18 0.037
84_STAT5A -0.14 -0.0065 -0.18 0.037
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/6044560/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle