PARADIGM pathway analysis of mRNASeq expression data
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1NC5ZP6
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/C1NC5ZP6
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 37 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family 166
Angiopoietin receptor Tie2-mediated signaling 157
Aurora B signaling 127
FOXM1 transcription factor network 104
Aurora C signaling 99
Endothelins 76
Glypican 2 network 61
TCGA08_retinoblastoma 59
amb2 Integrin signaling 58
Fc-epsilon receptor I signaling in mast cells 54
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 482 . 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 ( 482 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 0.3444 166 8659 52 -0.65 0.35 1000 -1000 -0.092 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3257 157 13888 88 -0.78 0.06 1000 -1000 -0.12 -1000
Aurora B signaling 0.2635 127 8534 67 -0.62 0.005 1000 -1000 -0.084 -1000
FOXM1 transcription factor network 0.2158 104 5345 51 -0.71 0.002 1000 -1000 -0.21 -1000
Aurora C signaling 0.2054 99 696 7 -0.41 0 1000 -1000 -0.044 -1000
Endothelins 0.1577 76 7381 96 -0.45 0.038 1000 -1000 -0.097 -1000
Glypican 2 network 0.1266 61 245 4 -0.087 -0.07 1000 -1000 -0.039 -1000
TCGA08_retinoblastoma 0.1224 59 475 8 -0.28 0.084 1000 -1000 -0.026 -1000
amb2 Integrin signaling 0.1203 58 4801 82 -0.69 0 1000 -1000 -0.098 -1000
Fc-epsilon receptor I signaling in mast cells 0.1120 54 5261 97 -0.26 0.033 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 0.1079 52 5485 105 -0.18 0.038 1000 -1000 -0.084 -1000
Visual signal transduction: Cones 0.1037 50 1927 38 -0.28 0.009 1000 -1000 -0.08 -1000
IL4-mediated signaling events 0.1037 50 4583 91 -0.8 0.44 1000 -1000 -0.17 -1000
Signaling events regulated by Ret tyrosine kinase 0.1037 50 4113 82 -0.2 0 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.1017 49 5614 114 -0.56 0.37 1000 -1000 -0.09 -1000
Signaling mediated by p38-alpha and p38-beta 0.0934 45 1995 44 -0.13 0 1000 -1000 -0.056 -1000
Arf6 signaling events 0.0830 40 2497 62 -0.31 0.015 1000 -1000 -0.072 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0830 40 2102 52 -0.38 0.057 1000 -1000 -0.079 -1000
BMP receptor signaling 0.0809 39 3186 81 -0.39 0.033 1000 -1000 -0.12 -1000
PLK1 signaling events 0.0809 39 3373 85 -0.36 0.071 1000 -1000 -0.063 -1000
Nectin adhesion pathway 0.0768 37 2338 63 -0.27 0 1000 -1000 -0.086 -1000
Integrins in angiogenesis 0.0747 36 3079 84 -0.47 0.002 1000 -1000 -0.11 -1000
Glypican 1 network 0.0705 34 1637 48 -0.22 0.03 1000 -1000 -0.058 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0705 34 2694 78 -0.13 0.036 1000 -1000 -0.093 -1000
TCGA08_p53 0.0664 32 229 7 -0.19 0.096 1000 -1000 -0.031 -1000
Nongenotropic Androgen signaling 0.0664 32 1695 52 -0.16 0.046 1000 -1000 -0.069 -1000
FOXA2 and FOXA3 transcription factor networks 0.0643 31 1433 46 -0.79 0.073 1000 -1000 -0.11 -1000
HIF-1-alpha transcription factor network 0.0602 29 2213 76 -0.44 0.016 1000 -1000 -0.22 -1000
Syndecan-3-mediated signaling events 0.0581 28 991 35 -0.34 0 1000 -1000 -0.074 -1000
Calcium signaling in the CD4+ TCR pathway 0.0581 28 881 31 -0.21 0.012 1000 -1000 -0.14 -1000
LPA4-mediated signaling events 0.0539 26 312 12 -0.14 0.017 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0539 26 2021 76 -0.4 0.028 1000 -1000 -0.07 -1000
Canonical Wnt signaling pathway 0.0539 26 1375 51 -0.47 0.16 1000 -1000 -0.069 -1000
IL23-mediated signaling events 0.0539 26 1617 60 -0.24 0.018 1000 -1000 -0.18 -1000
Reelin signaling pathway 0.0519 25 1404 56 -0.13 0.003 1000 -1000 -0.12 -1000
IL6-mediated signaling events 0.0519 25 1936 75 -0.48 0.05 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0519 25 1713 68 -0.23 0.015 1000 -1000 -0.14 -1000
Presenilin action in Notch and Wnt signaling 0.0498 24 1500 61 -0.47 0.013 1000 -1000 -0.089 -1000
Visual signal transduction: Rods 0.0498 24 1253 52 -0.18 0 1000 -1000 -0.1 -1000
ErbB4 signaling events 0.0456 22 1542 69 -0.38 0.2 1000 -1000 -0.11 -1000
Aurora A signaling 0.0436 21 1272 60 -0.49 0.029 1000 -1000 -0.067 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0436 21 2723 125 -0.21 0 1000 -1000 -0.12 -1000
Wnt signaling 0.0436 21 150 7 -0.096 0 1000 -1000 -0.056 -1000
Regulation of Androgen receptor activity 0.0436 21 1532 70 -0.42 0.018 1000 -1000 -0.081 -1000
IL12-mediated signaling events 0.0415 20 1755 87 -0.15 0.018 1000 -1000 -0.15 -1000
Syndecan-1-mediated signaling events 0.0415 20 687 34 -0.35 0 1000 -1000 -0.082 -1000
Osteopontin-mediated events 0.0394 19 758 38 -0.3 0 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0394 19 650 33 -0.27 0 1000 -1000 -0.079 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0394 19 2378 120 -0.27 0.13 1000 -1000 -0.093 -1000
HIF-2-alpha transcription factor network 0.0353 17 756 43 -0.37 0.2 1000 -1000 -0.12 -1000
Plasma membrane estrogen receptor signaling 0.0353 17 1521 86 -0.18 0.033 1000 -1000 -0.097 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0332 16 907 54 -0.15 0.02 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0332 16 1550 93 -0.064 0.036 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0311 15 106 7 -0.023 0.004 1000 -1000 -0.033 -1000
p75(NTR)-mediated signaling 0.0290 14 1781 125 -0.34 0 1000 -1000 -0.14 -1000
PDGFR-alpha signaling pathway 0.0290 14 653 44 -0.21 0.014 1000 -1000 -0.073 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0270 13 1178 85 -0.16 0.009 1000 -1000 -0.091 -1000
Ras signaling in the CD4+ TCR pathway 0.0270 13 230 17 -0.054 0.009 1000 -1000 -0.068 -1000
Caspase cascade in apoptosis 0.0228 11 843 74 -0.069 0.034 1000 -1000 -0.07 -1000
Regulation of nuclear SMAD2/3 signaling 0.0228 11 1521 136 -0.33 0.092 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 0.0228 11 303 26 -0.1 0 1000 -1000 -0.1 -1000
FAS signaling pathway (CD95) 0.0228 11 533 47 -0.2 0.009 1000 -1000 -0.059 -1000
Syndecan-2-mediated signaling events 0.0207 10 692 69 -0.17 0.032 1000 -1000 -0.073 -1000
Effects of Botulinum toxin 0.0207 10 266 26 -0.073 0.005 1000 -1000 -0.087 -1000
EGFR-dependent Endothelin signaling events 0.0207 10 214 21 -0.063 0 1000 -1000 -0.093 -1000
JNK signaling in the CD4+ TCR pathway 0.0187 9 160 17 -0.04 0.022 1000 -1000 -0.079 -1000
S1P1 pathway 0.0187 9 351 36 -0.061 0.01 1000 -1000 -0.088 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0187 9 696 74 -0.17 0.068 1000 -1000 -0.11 -1000
BCR signaling pathway 0.0187 9 970 99 -0.11 0.039 1000 -1000 -0.1 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0166 8 285 34 -0.028 0 1000 -1000 -0.084 -1000
Hedgehog signaling events mediated by Gli proteins 0.0166 8 569 65 -0.61 0.043 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.0166 8 601 67 -0.17 0.009 1000 -1000 -0.1 -1000
S1P4 pathway 0.0166 8 214 25 -0.066 0.002 1000 -1000 -0.066 -1000
Signaling events mediated by HDAC Class III 0.0145 7 289 40 -0.15 0.051 1000 -1000 -0.059 -1000
TRAIL signaling pathway 0.0145 7 343 48 -0.095 0.046 1000 -1000 -0.082 -1000
IL2 signaling events mediated by STAT5 0.0145 7 175 22 -0.15 0.06 1000 -1000 -0.068 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0124 6 182 28 -0.18 0.02 1000 -1000 -0.069 -1000
Cellular roles of Anthrax toxin 0.0124 6 257 39 -0.09 0.017 1000 -1000 -0.032 -1000
Signaling events mediated by PTP1B 0.0124 6 517 76 -0.1 0.033 1000 -1000 -0.092 -1000
Retinoic acid receptors-mediated signaling 0.0124 6 371 58 -0.22 0.034 1000 -1000 -0.075 -1000
IL1-mediated signaling events 0.0104 5 344 62 -0.059 0.042 1000 -1000 -0.12 -1000
IL2 signaling events mediated by PI3K 0.0104 5 296 58 -0.22 0.073 1000 -1000 -0.1 -1000
Regulation of p38-alpha and p38-beta 0.0104 5 315 54 -0.095 0.037 1000 -1000 -0.089 -1000
IL27-mediated signaling events 0.0104 5 305 51 -0.12 0.011 1000 -1000 -0.092 -1000
LPA receptor mediated events 0.0104 5 539 102 -0.1 0.034 1000 -1000 -0.11 -1000
Insulin Pathway 0.0104 5 379 74 -0.12 0.031 1000 -1000 -0.11 -1000
S1P3 pathway 0.0104 5 251 42 -0.18 0.042 1000 -1000 -0.067 -1000
Signaling events mediated by PRL 0.0104 5 190 34 -0.13 0.029 1000 -1000 -0.075 -1000
Signaling events mediated by HDAC Class II 0.0083 4 324 75 -0.08 0 1000 -1000 -0.077 -1000
BARD1 signaling events 0.0083 4 283 57 -0.13 0.022 1000 -1000 -0.083 -1000
Ephrin B reverse signaling 0.0083 4 228 48 -0.07 0.04 1000 -1000 -0.084 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0083 4 354 83 -0.069 0.049 1000 -1000 -0.096 -1000
Signaling events mediated by HDAC Class I 0.0083 4 444 104 -0.08 0.041 1000 -1000 -0.083 -1000
Arf6 trafficking events 0.0083 4 288 71 -0.086 0.032 1000 -1000 -0.093 -1000
IGF1 pathway 0.0083 4 274 57 -0.019 0.041 1000 -1000 -0.11 -1000
p38 MAPK signaling pathway 0.0083 4 212 44 -0.068 0.034 1000 -1000 -0.079 -1000
ErbB2/ErbB3 signaling events 0.0062 3 253 65 -0.078 0.055 1000 -1000 -0.086 -1000
IFN-gamma pathway 0.0062 3 252 68 -0.068 0.065 1000 -1000 -0.11 -1000
Class I PI3K signaling events 0.0062 3 261 73 -0.049 0.027 1000 -1000 -0.084 -1000
Regulation of Telomerase 0.0062 3 381 102 -0.12 0.024 1000 -1000 -0.12 -1000
VEGFR1 specific signals 0.0062 3 209 56 -0.21 0.045 1000 -1000 -0.099 -1000
Circadian rhythm pathway 0.0041 2 56 22 -0.031 0.038 1000 -1000 -0.066 -1000
a4b1 and a4b7 Integrin signaling 0.0041 2 14 5 -0.006 -0.002 1000 -1000 -0.04 -1000
EPO signaling pathway 0.0041 2 111 55 -0.008 0.065 1000 -1000 -0.12 -1000
Ceramide signaling pathway 0.0041 2 171 76 -0.024 0.04 1000 -1000 -0.071 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0041 2 78 37 -0.009 0.028 1000 -1000 -0.09 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0041 2 134 45 -0.028 0.061 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0041 2 249 85 -0.07 0.032 1000 -1000 -0.11 -1000
TCGA08_rtk_signaling 0.0041 2 76 26 -0.065 0.038 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0041 2 212 97 -0.04 0.055 1000 -1000 -0.11 -1000
E-cadherin signaling in keratinocytes 0.0041 2 87 43 -0.022 0.042 1000 -1000 -0.086 -1000
Class IB PI3K non-lipid kinase events 0.0041 2 6 3 -0.003 -1000 1000 -1000 -0.036 -1000
PLK2 and PLK4 events 0.0021 1 4 3 -0.002 0.017 1000 -1000 -0.03 -1000
Insulin-mediated glucose transport 0.0021 1 50 32 -0.057 0.034 1000 -1000 -0.078 -1000
S1P5 pathway 0.0021 1 28 17 -0.009 0.006 1000 -1000 -0.067 -1000
FoxO family signaling 0.0021 1 98 64 -0.089 0.08 1000 -1000 -0.1 -1000
Paxillin-dependent events mediated by a4b1 0.0021 1 54 36 -0.008 0.02 1000 -1000 -0.086 -1000
Rapid glucocorticoid signaling 0.0021 1 35 20 -0.009 0.007 1000 -1000 -0.042 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 0 23 0 0.036 1000 -1000 -0.089 -1000
Canonical NF-kappaB pathway 0.0000 0 33 39 -0.02 0.071 1000 -1000 -0.098 -1000
Arf6 downstream pathway 0.0000 0 15 43 -0.024 0.025 1000 -1000 -0.051 -1000
mTOR signaling pathway 0.0000 0 0 53 -0.003 0.03 1000 -1000 -0.072 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 57 68 -0.057 0.043 1000 -1000 -0.088 -1000
ceramide signaling pathway 0.0000 0 47 49 -0.02 0.043 1000 -1000 -0.071 -1000
Signaling mediated by p38-gamma and p38-delta 0.0000 0 13 15 -0.001 0.027 1000 -1000 -0.07 -1000
Atypical NF-kappaB pathway 0.0000 0 14 31 -0.002 0.03 1000 -1000 -0.076 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 48 76 -0.023 0.053 1000 -1000 -0.099 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 -0.001 0.025 1000 -1000 -0.067 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0 1000 -1000 -0.056 -1000
Arf1 pathway 0.0000 0 44 54 -0.022 0.022 1000 -1000 -0.058 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 -0.001 0 1000 -1000 -0.077 -1000
Total NA 2603 161083 7203 -25 -990 131000 -131000 -12 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.43 0.3 -10000 0 -0.69 225 225
IHH -0.47 0.38 -10000 0 -0.81 269 269
SHH Np/Cholesterol/GAS1 -0.071 0.17 -10000 0 -0.46 71 71
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.071 0.16 0.45 71 -10000 0 71
SMO/beta Arrestin2 -0.36 0.25 -10000 0 -0.59 233 233
SMO -0.38 0.27 -10000 0 -0.6 274 274
AKT1 -0.15 0.11 -10000 0 -0.32 3 3
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.005 0.06 -10000 0 -0.66 4 4
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.38 0.27 -10000 0 -0.59 274 274
STIL -0.33 0.25 -10000 0 -0.53 251 251
DHH N/PTCH2 -0.046 0.16 -10000 0 -0.56 39 39
DHH N/PTCH1 -0.36 0.24 -10000 0 -0.54 294 294
PIK3CA 0 0 -10000 0 -10000 0 0
DHH -0.052 0.19 -10000 0 -0.74 34 34
PTHLH -0.58 0.36 -10000 0 -0.92 225 225
determination of left/right symmetry -0.38 0.27 -10000 0 -0.59 274 274
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.57 0.35 -10000 0 -0.9 225 225
IHH N/Hhip -0.65 0.38 -10000 0 -0.82 383 383
DHH N/Hhip -0.41 0.3 -10000 0 -0.6 330 330
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.38 0.27 -10000 0 -0.59 274 274
pancreas development -0.49 0.35 -10000 0 -0.74 322 322
HHAT 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.012 0.095 -10000 0 -0.74 8 8
somite specification -0.38 0.27 -10000 0 -0.59 274 274
SHH Np/Cholesterol/PTCH1 -0.35 0.25 -10000 0 -0.55 255 255
SHH Np/Cholesterol/PTCH2 -0.069 0.16 -10000 0 -0.43 77 77
SHH Np/Cholesterol/Megalin -0.29 0.27 -10000 0 -0.5 276 276
SHH -0.066 0.2 -10000 0 -0.55 72 72
catabolic process -0.37 0.25 -10000 0 -0.57 282 282
SMO/Vitamin D3 -0.37 0.27 -10000 0 -0.59 248 248
SHH Np/Cholesterol/Hhip -0.36 0.26 -10000 0 -0.5 340 340
LRP2 -0.38 0.37 -10000 0 -0.74 247 247
receptor-mediated endocytosis -0.5 0.31 -10000 0 -0.72 281 281
SHH Np/Cholesterol/BOC -0.067 0.16 -10000 0 -0.44 74 74
SHH Np/Cholesterol/CDO -0.069 0.16 -10000 0 -0.44 70 70
mesenchymal cell differentiation 0.35 0.26 0.5 340 -10000 0 340
mol:Vitamin D3 -0.35 0.26 -10000 0 -0.56 255 255
IHH N/PTCH2 -0.31 0.27 -10000 0 -0.54 269 269
CDON -0.008 0.075 -10000 0 -0.74 5 5
IHH N/PTCH1 -0.38 0.26 -10000 0 -0.58 282 282
Megalin/LRPAP1 -0.29 0.28 -10000 0 -0.56 247 247
PTCH2 -0.009 0.076 -10000 0 -0.68 6 6
SHH Np/Cholesterol -0.065 0.16 -10000 0 -0.44 72 72
PTCH1 -0.37 0.25 -10000 0 -0.57 282 282
HHIP -0.5 0.35 -10000 0 -0.74 322 322
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.53 0.53 -10000 0 -1 264 264
NCK1/PAK1/Dok-R -0.25 0.23 -10000 0 -0.45 264 264
NCK1/Dok-R -0.7 0.66 -10000 0 -1.3 264 264
PIK3CA 0.007 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.06 0.1 0.25 104 -10000 0 104
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.002 0.004 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.053 0.13 0.26 31 -0.57 9 40
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.61 0.58 -10000 0 -1.1 264 264
FN1 -0.017 0.11 -10000 0 -0.74 11 11
PLD2 -0.68 0.71 -10000 0 -1.3 264 264
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.047 0.18 -10000 0 -0.74 31 31
ELK1 -0.58 0.61 -10000 0 -1.1 264 264
GRB7 -0.005 0.052 -10000 0 -0.57 4 4
PAK1 -0.001 0.026 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.66 0.62 -10000 0 -1.2 264 264
CDKN1A -0.36 0.35 -10000 0 -0.68 256 256
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.7 0.66 -10000 0 -1.3 264 264
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.37 0.38 -10000 0 -0.71 264 264
PLG -0.69 0.71 -10000 0 -1.3 264 264
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.51 0.48 -10000 0 -0.95 264 264
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 0.002 0.004 -10000 0 -10000 0 0
ANGPT2 -0.34 0.34 -10000 0 -0.75 167 167
BMX -0.76 0.75 -10000 0 -1.4 264 264
ANGPT1 -0.37 0.61 -10000 0 -1.4 124 124
tube development -0.42 0.4 -10000 0 -0.78 262 262
ANGPT4 -0.33 0.37 -10000 0 -0.74 216 216
response to hypoxia -0.035 0.036 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.76 0.72 -10000 0 -1.4 264 264
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.017 0.13 -10000 0 -0.74 15 15
STAT5A (dimer) -0.49 0.47 -10000 0 -0.91 261 261
mol:L-citrulline -0.37 0.38 -10000 0 -0.71 264 264
AGTR1 -0.3 0.37 -10000 0 -0.74 199 199
MAPK14 -0.7 0.7 -10000 0 -1.3 264 264
Tie2/SHP2 -0.61 0.62 -10000 0 -1.2 231 231
TEK -0.68 0.69 -10000 0 -1.4 231 231
RPS6KB1 -0.5 0.51 -10000 0 -0.96 264 264
Angiotensin II/AT1 -0.23 0.28 -10000 0 -0.57 199 199
Tie2/Ang1/GRB2 -0.74 0.72 -10000 0 -1.3 264 264
MAPK3 -0.6 0.63 -10000 0 -1.2 264 264
MAPK1 -0.6 0.63 -10000 0 -1.2 264 264
Tie2/Ang1/GRB7 -0.74 0.72 -10000 0 -1.3 264 264
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.68 0.71 -10000 0 -1.3 264 264
PI3K -0.64 0.63 -10000 0 -1.2 264 264
FES -0.7 0.7 -10000 0 -1.3 264 264
Crk/Dok-R -0.7 0.66 -10000 0 -1.3 264 264
Tie2/Ang1/ABIN2 -0.74 0.72 -10000 0 -1.3 264 264
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.46 0.46 -10000 0 -0.88 264 264
STAT5A 0 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.5 0.51 -10000 0 -0.96 264 264
Tie2/Ang2 -0.62 0.59 -10000 0 -1.2 262 262
Tie2/Ang1 -0.78 0.82 -10000 0 -1.5 264 264
FOXO1 -0.46 0.47 -10000 0 -0.89 264 264
ELF1 -0.034 0.052 -10000 0 -10000 0 0
ELF2 -0.69 0.72 -10000 0 -1.3 264 264
mol:Choline -0.63 0.65 -10000 0 -1.2 264 264
cell migration -0.14 0.12 -10000 0 -0.25 118 118
FYN -0.49 0.47 -10000 0 -0.91 262 262
DOK2 -0.066 0.21 -10000 0 -0.74 43 43
negative regulation of cell cycle -0.32 0.32 -10000 0 -0.61 261 261
ETS1 -0.062 0.16 -10000 0 -0.66 17 17
PXN -0.4 0.41 -10000 0 -0.77 264 264
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.43 0.44 -10000 0 -0.82 264 264
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.063 0.16 -10000 0 -0.81 13 13
MAPKKK cascade -0.63 0.65 -10000 0 -1.2 264 264
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.73 0.73 -10000 0 -1.4 264 264
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.32 0.34 -10000 0 -0.63 264 264
mol:Phosphatidic acid -0.63 0.65 -10000 0 -1.2 264 264
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.37 0.38 -10000 0 -0.71 264 264
Rac1/GTP -0.48 0.44 -10000 0 -0.88 264 264
MMP2 -0.68 0.71 -10000 0 -1.3 264 264
Aurora B signaling

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
Condensin I complex -0.18 0.14 -9999 0 -0.36 110 110
STMN1 -0.29 0.19 -9999 0 -0.4 347 347
Aurora B/RasGAP/Survivin -0.5 0.22 -9999 0 -0.63 335 335
Chromosomal passenger complex/Cul3 protein complex -0.2 0.1 -9999 0 -0.33 125 125
BIRC5 -0.49 0.21 -9999 0 -0.58 410 410
DES -0.56 0.38 -9999 0 -0.83 311 311
Aurora C/Aurora B/INCENP -0.22 0.15 -9999 0 -0.31 338 338
Aurora B/TACC1 -0.24 0.16 -9999 0 -0.34 347 347
Aurora B/PP2A -0.29 0.19 -9999 0 -0.4 347 347
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.059 0.044 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.003 -9999 0 -10000 0 0
NDC80 -0.41 0.29 -9999 0 -0.55 362 362
Cul3 protein complex -0.012 0.065 -9999 0 -0.37 15 15
KIF2C -0.16 0.085 -9999 0 -0.24 248 248
PEBP1 -0.001 0.034 -9999 0 -0.76 1 1
KIF20A -0.3 0.29 -9999 0 -0.58 249 249
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.29 0.19 -9999 0 -0.4 347 347
SEPT1 -0.001 0.026 -9999 0 -0.57 1 1
SMC2 0 0 -9999 0 -10000 0 0
SMC4 0 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.1 0.065 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.15 0.1 -9999 0 -0.21 49 49
AURKB -0.41 0.26 -9999 0 -0.57 347 347
AURKC -0.003 0.043 -9999 0 -0.66 2 2
CDCA8 -0.16 0.26 -9999 0 -0.58 131 131
cytokinesis -0.32 0.16 -9999 0 -0.49 171 171
Aurora B/Septin1 -0.3 0.16 -9999 0 -0.47 160 160
AURKA -0.015 0.12 -9999 0 -0.57 21 21
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.014 0.089 -9999 0 -0.57 12 12
BUB1 -0.049 0.17 -9999 0 -0.58 45 45
hSgo1/Aurora B/Survivin -0.62 0.31 -9999 0 -0.78 352 352
EVI5 0.005 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.18 -9999 0 -0.52 119 119
SGOL1 -0.3 0.29 -9999 0 -0.57 251 251
CENPA -0.24 0.12 -9999 0 -0.31 338 338
NCAPG -0.1 0.22 -9999 0 -0.57 87 87
Aurora B/HC8 Proteasome -0.29 0.19 -9999 0 -0.4 347 347
NCAPD2 -0.001 0.026 -9999 0 -0.57 1 1
Aurora B/PP1-gamma -0.29 0.19 -9999 0 -0.4 347 347
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.29 0.29 -9999 0 -0.57 245 245
NPM1 -0.13 0.082 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.005 0.058 -9999 0 -0.74 3 3
mitotic prometaphase -0.012 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.29 0.19 -9999 0 -0.4 347 347
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.19 -9999 0 -0.54 149 149
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.13 0.082 -9999 0 -10000 0 0
MYLK -0.15 0.1 -9999 0 -0.61 2 2
KIF23 -0.12 0.23 -9999 0 -0.58 96 96
VIM -0.3 0.21 -9999 0 -0.42 347 347
RACGAP1 0.001 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.13 0.082 -9999 0 -10000 0 0
Chromosomal passenger complex -0.27 0.14 -9999 0 -0.35 331 331
Chromosomal passenger complex/EVI5 -0.49 0.25 -9999 0 -0.63 339 339
TACC1 -0.003 0.048 -9999 0 -0.74 2 2
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.58 0.42 -9999 0 -1 129 129
PLK1 -0.19 0.2 -9999 0 -10000 0 0
BIRC5 -0.32 0.16 -9999 0 -10000 0 0
HSPA1B -0.58 0.42 -9999 0 -1.1 120 120
MAP2K1 -0.012 0.023 -9999 0 -10000 0 0
BRCA2 -0.58 0.42 -9999 0 -1.1 118 118
FOXM1 -0.7 0.54 -9999 0 -1.2 167 167
XRCC1 -0.58 0.42 -9999 0 -1 132 132
FOXM1B/p19 -0.6 0.42 -9999 0 -1 164 164
Cyclin D1/CDK4 -0.54 0.4 -9999 0 -0.99 112 112
CDC2 -0.61 0.45 -9999 0 -1.1 166 166
TGFA -0.52 0.38 -9999 0 -0.95 105 105
SKP2 -0.58 0.42 -9999 0 -1 130 130
CCNE1 -0.13 0.24 -9999 0 -0.58 107 107
CKS1B -0.58 0.42 -9999 0 -1.1 120 120
RB1 -0.26 0.15 -9999 0 -0.49 18 18
FOXM1C/SP1 -0.65 0.45 -9999 0 -1.1 168 168
AURKB -0.28 0.19 -9999 0 -10000 0 0
CENPF -0.64 0.47 -9999 0 -1.1 185 185
CDK4 0.001 0.028 -9999 0 -0.59 1 1
MYC -0.51 0.37 -9999 0 -0.91 120 120
CHEK2 -0.012 0.023 -9999 0 -10000 0 0
ONECUT1 -0.57 0.42 -9999 0 -1 143 143
CDKN2A -0.25 0.29 -9999 0 -0.56 224 224
LAMA4 -0.58 0.43 -9999 0 -1 133 133
FOXM1B/HNF6 -0.65 0.5 -9999 0 -1.2 142 142
FOS -0.63 0.49 -9999 0 -1.2 148 148
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.58 0.42 -9999 0 -1.1 120 120
response to radiation -0.024 0.022 -9999 0 -10000 0 0
CENPB -0.58 0.42 -9999 0 -1 132 132
CENPA -0.71 0.46 -9999 0 -1.1 214 214
NEK2 -0.69 0.47 -9999 0 -1.1 198 198
HIST1H2BA -0.58 0.42 -9999 0 -1.1 118 118
CCNA2 -0.15 0.26 -9999 0 -0.58 125 125
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.66 0.49 -9999 0 -1.2 136 136
CCNB2 -0.66 0.48 -9999 0 -1.1 200 200
CCNB1 -0.62 0.46 -9999 0 -1.1 135 135
ETV5 -0.58 0.43 -9999 0 -1.1 121 121
ESR1 -0.59 0.45 -9999 0 -1.1 116 116
CCND1 -0.55 0.41 -9999 0 -1 115 115
GSK3A -0.004 0.018 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.17 0.24 -9999 0 -0.44 187 187
CDK2 0.002 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.031 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.64 0.41 -9999 0 -1.1 168 168
GAS1 -0.58 0.43 -9999 0 -1.1 135 135
MMP2 -0.58 0.43 -9999 0 -1 133 133
RB1/FOXM1C -0.58 0.44 -9999 0 -1.1 140 140
CREBBP 0 0 -9999 0 -10000 0 0
Aurora C 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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.23 0.14 -9999 0 -0.32 347 347
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.04 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.57 347 347
AURKC -0.003 0.043 -9999 0 -0.66 2 2
Endothelins

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
AKT1 -0.029 0.23 -9999 0 -0.58 51 51
PTK2B 0.002 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.078 0.28 -9999 0 -0.88 35 35
EDN1 -0.041 0.25 -9999 0 -0.78 41 41
EDN3 -0.091 0.24 -9999 0 -0.7 62 62
EDN2 -0.087 0.21 -9999 0 -0.59 71 71
HRAS/GDP -0.18 0.3 -9999 0 -0.63 122 122
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.053 0.2 -9999 0 -0.48 60 60
ADCY4 -0.078 0.22 -9999 0 -0.65 42 42
ADCY5 -0.09 0.23 -9999 0 -0.65 47 47
ADCY6 -0.054 0.19 -9999 0 -0.6 32 32
ADCY7 -0.053 0.18 -9999 0 -0.59 31 31
ADCY1 -0.054 0.19 -9999 0 -0.58 32 32
ADCY2 -0.086 0.21 -9999 0 -0.62 41 41
ADCY3 -0.053 0.18 -9999 0 -0.59 31 31
ADCY8 -0.18 0.25 -9999 0 -0.65 56 56
ADCY9 -0.054 0.19 -9999 0 -0.58 34 34
arachidonic acid secretion -0.15 0.27 -9999 0 -0.54 117 117
ETB receptor/Endothelin-1/Gq/GTP -0.32 0.35 -9999 0 -0.7 173 173
GNAO1 -0.004 0.05 -9999 0 -0.63 3 3
HRAS 0 0.002 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.038 0.26 -9999 0 -0.54 51 51
ETA receptor/Endothelin-1/Gs/GTP 0.03 0.25 -9999 0 -0.55 46 46
mol:GTP 0 0.004 -9999 0 -10000 0 0
COL3A1 -0.045 0.25 -9999 0 -0.7 31 31
EDNRB -0.45 0.36 -9999 0 -0.74 296 296
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.045 0.27 -9999 0 -0.76 40 40
CYSLTR1 -0.092 0.36 -9999 0 -0.87 70 70
SLC9A1 -0.007 0.12 -9999 0 -0.36 19 19
mol:GDP -0.2 0.33 -9999 0 -0.69 126 126
SLC9A3 -0.37 0.38 -9999 0 -0.73 204 204
RAF1 -0.21 0.32 -9999 0 -0.65 137 137
JUN -0.056 0.22 -9999 0 -0.62 33 33
JAK2 -0.029 0.23 -9999 0 -0.58 51 51
mol:IP3 -0.21 0.3 -9999 0 -0.66 127 127
ETA receptor/Endothelin-1 0.018 0.32 -9999 0 -0.67 51 51
PLCB1 0.003 0.005 -9999 0 -10000 0 0
PLCB2 -0.005 0.096 -9999 0 -0.74 8 8
ETA receptor/Endothelin-3 -0.057 0.21 -9999 0 -0.55 67 67
FOS -0.2 0.35 -9999 0 -0.85 85 85
Gai/GDP -0.007 0.067 -9999 0 -0.95 1 1
CRK 0.002 0.004 -9999 0 -10000 0 0
mol:Ca ++ -0.25 0.36 -9999 0 -0.75 137 137
BCAR1 0.005 0.005 -9999 0 -10000 0 0
PRKCB1 -0.2 0.29 -9999 0 -0.63 128 128
GNAQ 0.008 0.035 -9999 0 -0.74 1 1
GNAZ -0.009 0.082 -9999 0 -0.74 6 6
GNAL -0.006 0.067 -9999 0 -0.74 4 4
Gs family/GDP -0.21 0.26 -9999 0 -0.62 122 122
ETA receptor/Endothelin-1/Gq/GTP -0.065 0.23 -9999 0 -0.52 66 66
MAPK14 -0.24 0.28 -9999 0 -0.65 128 128
TRPC6 -0.086 0.3 -9999 0 -0.99 33 33
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.034 -9999 0 -0.74 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.26 0.3 -9999 0 -0.63 153 153
ETB receptor/Endothelin-2 -0.4 0.29 -9999 0 -0.58 327 327
ETB receptor/Endothelin-3 -0.4 0.31 -9999 0 -0.61 321 321
ETB receptor/Endothelin-1 -0.38 0.34 -9999 0 -0.61 309 309
MAPK3 -0.22 0.36 -9999 0 -0.7 141 141
MAPK1 -0.22 0.36 -9999 0 -0.75 120 120
Rac1/GDP -0.18 0.3 -9999 0 -0.63 123 123
cAMP biosynthetic process -0.078 0.21 -9999 0 -0.59 44 44
MAPK8 -0.078 0.26 -9999 0 -0.61 65 65
SRC 0 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.17 -9999 0 -0.51 41 41
p130Cas/CRK/Src/PYK2 -0.19 0.32 -9999 0 -0.66 124 124
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.18 0.3 -9999 0 -0.63 122 122
COL1A2 -0.26 0.31 -9999 0 -0.73 101 101
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.05 0.19 -9999 0 -0.46 74 74
mol:DAG -0.21 0.3 -9999 0 -0.66 127 127
MAP2K2 -0.2 0.32 -9999 0 -0.64 141 141
MAP2K1 -0.2 0.32 -9999 0 -0.64 142 142
EDNRA 0.015 0.14 -9999 0 -0.66 9 9
positive regulation of muscle contraction -0.031 0.2 -9999 0 -0.59 31 31
Gq family/GDP -0.2 0.3 -9999 0 -0.69 115 115
HRAS/GTP -0.22 0.32 -9999 0 -0.68 128 128
PRKCH -0.2 0.29 -9999 0 -0.65 117 117
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.2 0.29 -9999 0 -0.66 118 118
PRKCB -0.22 0.32 -9999 0 -0.7 124 124
PRKCE -0.2 0.29 -9999 0 -0.65 117 117
PRKCD -0.2 0.29 -9999 0 -0.65 117 117
PRKCG -0.22 0.3 -9999 0 -0.66 130 130
regulation of vascular smooth muscle contraction -0.24 0.42 -9999 0 -1 86 86
PRKCQ -0.23 0.34 -9999 0 -0.72 132 132
PLA2G4A -0.16 0.29 -9999 0 -0.59 117 117
GNA14 -0.17 0.32 -9999 0 -0.74 114 114
GNA15 0.008 0.005 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.005 -9999 0 -10000 0 0
Rac1/GTP 0.038 0.26 -9999 0 -0.54 51 51
MMP1 -0.23 0.24 -9999 0 -0.43 250 250
Glypican 2 network

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
MDK -0.012 0.082 -9999 0 -0.57 10 10
GPC2 -0.087 0.2 -9999 0 -0.57 73 73
GPC2/Midkine -0.071 0.16 -9999 0 -0.42 81 81
neuron projection morphogenesis -0.07 0.16 -9999 0 -0.42 81 81
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.061 0.2 -10000 0 -0.71 41 41
CDKN2C 0.03 0.032 -10000 0 -10000 0 0
CDKN2A -0.28 0.3 -10000 0 -0.59 224 224
CCND2 0.073 0.082 0.26 42 -10000 0 42
RB1 -0.079 0.085 -10000 0 -0.27 42 42
CDK4 0.084 0.088 0.26 42 -10000 0 42
CDK6 0.081 0.09 0.29 42 -10000 0 42
G1/S progression 0.072 0.091 0.26 42 -10000 0 42
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.063 0.22 -9999 0 -0.72 42 42
alphaM/beta2 Integrin/GPIbA -0.064 0.21 -9999 0 -0.7 43 43
alphaM/beta2 Integrin/proMMP-9 -0.077 0.21 -9999 0 -0.57 64 64
PLAUR 0 0 -9999 0 -10000 0 0
HMGB1 0 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.059 0.2 -9999 0 -0.69 41 41
AGER -0.69 0.2 -9999 0 -0.75 443 443
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG -0.048 0.18 -9999 0 -0.74 31 31
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.48 0.26 -9999 0 -0.52 443 443
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 25 25
CYR61 -0.04 0.17 -9999 0 -0.74 26 26
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.21 0.29 -9999 0 -0.63 112 112
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.32 -9999 0 -0.74 121 121
MYH2 -0.32 0.35 -9999 0 -0.7 171 171
MST1R -0.048 0.18 -9999 0 -0.74 31 31
leukocyte activation during inflammatory response -0.089 0.22 -9999 0 -0.58 65 65
APOB -0.049 0.18 -9999 0 -0.72 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.006 0.067 -9999 0 -0.74 4 4
JAM3 0 0 -9999 0 -10000 0 0
GP1BA -0.007 0.072 -9999 0 -0.71 5 5
alphaM/beta2 Integrin/CTGF -0.075 0.24 -9999 0 -0.72 50 50
alphaM/beta2 Integrin -0.26 0.37 -9999 0 -0.76 116 116
JAM3 homodimer 0 0 -9999 0 -10000 0 0
ICAM2 -0.048 0.18 -9999 0 -0.74 31 31
ICAM1 -0.065 0.21 -9999 0 -0.74 42 42
phagocytosis triggered by activation of immune response cell surface activating receptor -0.24 0.36 -9999 0 -0.74 116 116
cell adhesion -0.063 0.21 -9999 0 -0.7 43 43
NFKB1 -0.47 0.3 -9999 0 -0.93 110 110
THY1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.045 0.14 -9999 0 -0.45 48 48
alphaM/beta2 Integrin/LRP/tPA -0.058 0.19 -9999 0 -0.64 41 41
IL6 -0.49 0.39 -9999 0 -1.1 112 112
ITGB2 -0.031 0.15 -9999 0 -0.74 20 20
elevation of cytosolic calcium ion concentration -0.073 0.2 -9999 0 -0.64 41 41
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.28 -9999 0 -0.64 90 90
JAM2 -0.11 0.26 -9999 0 -0.74 73 73
alphaM/beta2 Integrin/ICAM1 -0.11 0.28 -9999 0 -0.64 85 85
alphaM/beta2 Integrin/uPA/Plg -0.076 0.2 -9999 0 -0.65 41 41
RhoA/GTP -0.3 0.36 -9999 0 -0.85 114 114
positive regulation of phagocytosis -0.18 0.27 -9999 0 -0.74 69 69
Ron/MSP -0.037 0.14 -9999 0 -0.55 32 32
alphaM/beta2 Integrin/uPAR/uPA -0.074 0.2 -9999 0 -0.65 41 41
alphaM/beta2 Integrin/uPAR -0.059 0.2 -9999 0 -0.69 41 41
PLAU -0.036 0.14 -9999 0 -0.57 30 30
PLAT -0.007 0.063 -9999 0 -0.57 6 6
actin filament polymerization -0.29 0.32 -9999 0 -0.65 171 171
MST1 -0.001 0.026 -9999 0 -0.57 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.091 0.23 -9999 0 -0.59 65 65
TNF -0.42 0.28 -9999 0 -0.85 110 110
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.081 0.22 -9999 0 -0.68 43 43
fibrinolysis -0.076 0.2 -9999 0 -0.65 41 41
HCK -0.008 0.075 -9999 0 -0.74 5 5
dendritic cell antigen processing and presentation -0.24 0.36 -9999 0 -0.74 116 116
VTN -0.29 0.36 -9999 0 -0.74 189 189
alphaM/beta2 Integrin/CYR61 -0.084 0.25 -9999 0 -0.73 55 55
LPA -0.021 0.11 -9999 0 -0.57 18 18
LRP1 0 0 -9999 0 -10000 0 0
cell migration -0.074 0.21 -9999 0 -0.66 42 42
FN1 -0.017 0.11 -9999 0 -0.74 11 11
alphaM/beta2 Integrin/Thy1 -0.059 0.2 -9999 0 -0.69 41 41
MPO -0.031 0.15 -9999 0 -0.74 20 20
KNG1 -0.014 0.089 -9999 0 -0.57 12 12
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.25 0.33 -9999 0 -0.76 113 113
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.045 -9999 0 -0.57 3 3
CTGF -0.026 0.14 -9999 0 -0.74 17 17
alphaM/beta2 Integrin/Hck -0.064 0.22 -9999 0 -0.71 43 43
ITGAM -0.062 0.21 -9999 0 -0.75 40 40
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.36 -9999 0 -0.66 136 136
HP -0.23 0.34 -9999 0 -0.74 151 151
leukocyte adhesion -0.44 0.3 -9999 0 -0.81 145 145
SELP -0.19 0.32 -9999 0 -0.74 121 121
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -9999 0 -10000 0 0
LAT2 -0.16 0.26 -9999 0 -0.53 116 116
AP1 -0.19 0.26 -9999 0 -0.64 103 103
mol:PIP3 -0.16 0.29 -9999 0 -0.66 83 83
IKBKB -0.07 0.16 -9999 0 -0.34 76 76
AKT1 -0.18 0.24 -9999 0 -0.67 67 67
IKBKG -0.07 0.16 -9999 0 -0.34 76 76
MS4A2 -0.17 0.31 -9999 0 -0.75 109 109
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.002 -9999 0 -10000 0 0
MAP3K1 -0.1 0.23 -9999 0 -0.53 81 81
mol:Ca2+ -0.11 0.21 -9999 0 -0.46 83 83
LYN 0.004 0.05 -9999 0 -0.77 2 2
CBLB -0.16 0.24 -9999 0 -0.63 73 73
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.057 0.15 -9999 0 -0.44 62 62
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.002 0.034 -9999 0 -0.74 1 1
PLD2 -0.21 0.29 -9999 0 -0.57 148 148
PTPN13 -0.13 0.24 -9999 0 -0.59 74 74
PTPN11 0.005 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.08 0.19 -9999 0 -0.42 70 70
SYK 0.006 0.036 -9999 0 -0.77 1 1
GRB2 0 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.2 0.27 -9999 0 -0.7 83 83
LAT -0.16 0.24 -9999 0 -0.63 73 73
PAK2 -0.12 0.26 -9999 0 -0.61 82 82
NFATC2 -0.18 0.33 -9999 0 -0.94 66 66
HRAS -0.14 0.29 -9999 0 -0.69 83 83
GAB2 -0.018 0.12 -9999 0 -0.74 12 12
PLA2G1B -0.003 0.037 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.34 -9999 0 -0.64 194 194
Antigen/IgE/Fc epsilon R1 -0.24 0.32 -9999 0 -0.59 194 194
mol:GDP -0.16 0.31 -9999 0 -0.73 88 88
JUN 0 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0 0.002 -9999 0 -10000 0 0
FOS -0.085 0.24 -9999 0 -0.74 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.17 0.26 -9999 0 -0.54 116 116
CHUK -0.07 0.16 -9999 0 -0.34 76 76
KLRG1 -0.16 0.24 -9999 0 -0.63 71 71
VAV1 -0.16 0.25 -9999 0 -0.64 78 78
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.16 0.24 -9999 0 -0.63 73 73
negative regulation of mast cell degranulation -0.14 0.22 -9999 0 -0.58 71 71
BTK -0.2 0.33 -9999 0 -0.8 87 87
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.2 0.32 -9999 0 -0.88 68 68
GAB2/PI3K/SHP2 -0.19 0.27 -9999 0 -0.75 67 67
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.17 0.25 -9999 0 -0.69 72 72
RAF1 0.025 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.23 0.32 -9999 0 -0.61 150 150
FCER1G -0.016 0.13 -9999 0 -0.76 14 14
FCER1A -0.22 0.35 -9999 0 -0.76 143 143
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.31 -9999 0 -0.55 194 194
MAPK3 0.033 0.024 -9999 0 -10000 0 0
MAPK1 0.033 0.024 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.021 0.071 -9999 0 -10000 0 0
DUSP1 -0.095 0.25 -9999 0 -0.74 62 62
NF-kappa-B/RelA -0.059 0.076 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.13 0.25 -9999 0 -0.59 80 80
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.16 0.24 -9999 0 -0.63 77 77
FER -0.16 0.24 -9999 0 -0.63 74 74
RELA 0 0 -9999 0 -10000 0 0
ITK -0.078 0.18 -9999 0 -0.66 37 37
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.16 0.31 -9999 0 -0.74 84 84
cytokine secretion -0.043 0.055 -9999 0 -10000 0 0
SPHK1 -0.16 0.24 -9999 0 -0.51 116 116
PTK2 -0.14 0.26 -9999 0 -0.63 77 77
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.21 0.29 -9999 0 -0.74 83 83
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.15 0.28 -9999 0 -0.64 83 83
MAP2K2 0.03 0.024 -9999 0 -10000 0 0
MAP2K1 0.03 0.024 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.14 0.22 -9999 0 -0.59 71 71
MAP2K4 0.009 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.24 0.34 -9999 0 -0.6 195 195
mol:Choline -0.2 0.28 -9999 0 -0.56 148 148
SHC/Grb2/SOS1 -0.14 0.22 -9999 0 -0.6 69 69
FYN -0.002 0.034 -9999 0 -0.74 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.12 0.24 -9999 0 -0.6 70 70
HCLS1 -0.16 0.24 -9999 0 -0.6 80 80
PRKCB -0.11 0.22 -9999 0 -0.49 83 83
FCGR2B -0.014 0.1 -9999 0 -0.74 9 9
IGHE -0.004 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.14 0.22 -9999 0 -0.6 71 71
LCP2 -0.011 0.089 -9999 0 -0.74 7 7
PLA2G4A -0.16 0.24 -9999 0 -0.65 72 72
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.2 0.28 -9999 0 -0.56 148 148
IKK complex -0.039 0.12 -9999 0 -0.27 29 29
WIPF1 0 0 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.057 0.21 -10000 0 -0.74 41 41
GNB1/GNG2 -0.069 0.089 -10000 0 -0.21 69 69
AKT1 -0.035 0.13 -10000 0 -0.22 40 40
EGF -0.014 0.099 -10000 0 -0.69 10 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.036 0.13 -10000 0 -0.61 15 15
mol:Ca2+ -0.073 0.18 -10000 0 -0.31 170 170
LYN -0.016 0.076 -10000 0 -0.53 7 7
RhoA/GTP -0.046 0.059 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.081 0.2 -10000 0 -0.35 164 164
GNG2 -0.008 0.075 -10000 0 -0.74 5 5
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.017 0.1 -10000 0 -0.57 5 5
G beta5/gamma2 -0.091 0.12 -10000 0 -0.29 69 69
PRKCH -0.088 0.21 -10000 0 -0.36 162 162
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
TXA2/TP beta/beta Arrestin3 -0.002 0.014 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.022 0.12 -10000 0 -0.74 14 14
G12 family/GTP -0.11 0.14 -10000 0 -0.31 164 164
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.002 0.034 -10000 0 -0.74 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.038 0.13 0.41 19 -10000 0 19
mol:NADP -0.005 0.058 -10000 0 -0.74 3 3
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.058 0.2 -10000 0 -0.74 38 38
mol:IP3 -0.099 0.22 -10000 0 -0.39 170 170
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.15 0.3 -10000 0 -0.53 170 170
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.03 0.1 -10000 0 -0.6 7 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.018 0.085 -10000 0 -0.56 8 8
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.018 0.12 -10000 0 -0.74 12 12
PRKCB1 -0.099 0.22 -10000 0 -0.39 165 165
GNAQ -0.002 0.034 -10000 0 -0.74 1 1
mol:L-citrulline -0.005 0.058 -10000 0 -0.74 3 3
TXA2/TXA2-R family -0.15 0.3 -10000 0 -0.55 164 164
LCK -0.015 0.075 -10000 0 -0.53 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.018 0.089 -10000 0 -0.71 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.044 -10000 0 -0.35 4 4
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.018 0.088 -10000 0 -0.71 5 5
MAPK14 -0.043 0.14 -10000 0 -0.24 79 79
TGM2/GTP -0.12 0.26 -10000 0 -0.45 174 174
MAPK11 -0.043 0.14 -10000 0 -0.24 89 89
ARHGEF1 -0.034 0.11 -10000 0 -0.2 37 37
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.098 0.23 -10000 0 -0.4 164 164
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.075 0.19 -10000 0 -0.32 162 162
cAMP biosynthetic process -0.094 0.21 -10000 0 -0.36 174 174
Gq family/GTP/EBP50 -0.035 0.11 -10000 0 -0.54 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.015 0.071 -10000 0 -0.52 6 6
GNB5 0 0 -10000 0 -10000 0 0
GNB1 -0.002 0.034 -10000 0 -0.74 1 1
EGF/EGFR 0.024 0.095 -10000 0 -0.42 10 10
VCAM1 -0.068 0.17 -10000 0 -0.3 163 163
TP beta/Gq family/GDP/G beta5/gamma2 -0.017 0.1 -10000 0 -0.57 5 5
platelet activation -0.059 0.19 -10000 0 -0.3 164 164
PGI2/IP -0.014 0.088 -10000 0 -0.57 12 12
PRKACA -0.021 0.1 -10000 0 -0.45 22 22
Gq family/GDP/G beta5/gamma2 -0.02 0.1 -10000 0 -0.59 5 5
TXA2/TP beta/beta Arrestin2 -0.002 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.11 -10000 0 -0.76 6 6
mol:DAG -0.11 0.25 -10000 0 -0.44 165 165
EGFR -0.022 0.12 -10000 0 -0.63 17 17
TXA2/TP alpha -0.14 0.28 -10000 0 -0.5 174 174
Gq family/GTP -0.066 0.12 -10000 0 -0.28 114 114
YES1 -0.015 0.071 -10000 0 -0.52 6 6
GNAI2/GTP -0.017 0.084 -10000 0 -0.62 6 6
PGD2/DP -0.016 0.095 -10000 0 -0.57 14 14
SLC9A3R1 -0.005 0.052 -10000 0 -0.57 4 4
FYN -0.015 0.076 -10000 0 -0.57 6 6
mol:NO -0.005 0.058 -10000 0 -0.74 3 3
GNA15 0 0 -10000 0 -10000 0 0
PGK/cGMP -0.041 0.14 -10000 0 -0.5 40 40
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.052 0.16 -10000 0 -0.78 16 16
NOS3 -0.005 0.058 -10000 0 -0.74 3 3
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.088 0.21 -10000 0 -0.36 163 163
PRKCB -0.097 0.22 -10000 0 -0.38 165 165
PRKCE -0.087 0.21 -10000 0 -0.37 153 153
PRKCD -0.096 0.22 -10000 0 -0.39 162 162
PRKCG -0.11 0.23 -10000 0 -0.41 163 163
muscle contraction -0.13 0.28 -10000 0 -0.5 166 166
PRKCZ -0.081 0.2 -10000 0 -0.35 163 163
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.019 0.095 -10000 0 -0.72 6 6
PRKCQ -0.11 0.23 -10000 0 -0.4 168 168
MAPKKK cascade -0.13 0.27 -10000 0 -0.48 167 167
SELE -0.11 0.23 -10000 0 -0.42 162 162
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.1 -10000 0 -0.73 7 7
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 114 114
chemotaxis -0.17 0.34 -10000 0 -0.62 163 163
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.02 0.086 -9999 0 -0.42 17 17
RGS9BP -0.015 0.11 -9999 0 -0.74 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.037 -9999 0 -0.57 2 2
mol:Na + -0.18 0.18 -9999 0 -0.35 241 241
mol:ADP -0.008 0.092 -9999 0 -0.42 23 23
GNAT2 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.062 0.17 -9999 0 -0.49 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.025 0.12 -9999 0 -0.57 21 21
CNGB3 -0.28 0.29 -9999 0 -0.57 239 239
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.21 0.2 -9999 0 -0.36 289 289
Cone PDE6 -0.054 0.14 -9999 0 -0.44 41 41
Cone Metarhodopsin II -0.015 0.069 -9999 0 -0.32 23 23
Na + (4 Units) -0.22 0.2 -9999 0 -0.36 289 289
GNAT2/GDP -0.054 0.14 -9999 0 -0.42 61 61
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.005 -9999 0 -10000 0 0
Cone Transducin -0.021 0.091 -9999 0 -0.44 17 17
SLC24A2 -0.11 0.22 -9999 0 -0.57 92 92
GNB3/GNGT2 -0.027 0.12 -9999 0 -0.51 26 26
GNB3 -0.011 0.077 -9999 0 -0.57 9 9
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.002 0.037 -9999 0 -0.57 2 2
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.18 0.18 -9999 0 -0.35 241 241
mol:Pi -0.062 0.16 -9999 0 -0.49 61 61
Cone CNG Channel -0.14 0.14 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.22 -9999 0 -0.57 92 92
RGS9 -0.081 0.23 -9999 0 -0.74 53 53
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.026 0.14 -9999 0 -0.74 17 17
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.39 0.54 -10000 0 -1.2 103 103
STAT6 (cleaved dimer) -0.45 0.48 -10000 0 -1.1 135 135
IGHG1 -0.12 0.19 -10000 0 -0.41 4 4
IGHG3 -0.38 0.51 -10000 0 -1.1 132 132
AKT1 -0.14 0.26 -10000 0 -0.92 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.22 -10000 0 -1.1 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.27 -10000 0 -1 9 9
THY1 -0.39 0.54 -10000 0 -1.2 102 102
MYB -0.021 0.11 -10000 0 -0.59 17 17
HMGA1 -0.004 0.045 -10000 0 -0.57 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.31 -10000 0 -0.67 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.27 -10000 0 -1 9 9
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D -0.002 0.034 -10000 0 -0.74 1 1
SOCS5 0.019 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.44 0.48 -10000 0 -1.1 135 135
SOCS1 -0.23 0.35 -10000 0 -0.74 95 95
SOCS3 -0.16 0.27 -10000 0 -1 8 8
FCER2 -0.34 0.5 -10000 0 -1.2 72 72
PARP14 0.007 0.006 -10000 0 -10000 0 0
CCL17 -0.46 0.62 -10000 0 -1.4 123 123
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.23 -10000 0 -0.9 7 7
T cell proliferation -0.38 0.54 -10000 0 -1.2 105 105
IL4R/JAK1 -0.39 0.53 -10000 0 -1.2 103 103
EGR2 -0.41 0.56 -10000 0 -1.2 108 108
JAK2 -0.003 0.034 -10000 0 -10000 0 0
JAK3 0.012 0.007 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.009 0.014 -10000 0 -10000 0 0
COL1A2 -0.1 0.18 -10000 0 -0.59 3 3
CCL26 -0.42 0.55 -10000 0 -1.2 116 116
IL4R -0.42 0.57 -10000 0 -1.3 103 103
PTPN6 0.019 0.014 -10000 0 -10000 0 0
IL13RA2 -0.42 0.57 -10000 0 -1.3 109 109
IL13RA1 -0.003 0.034 -10000 0 -10000 0 0
IRF4 -0.17 0.36 -10000 0 -0.88 82 82
ARG1 -0.12 0.24 -10000 0 -0.84 25 25
CBL -0.18 0.29 -10000 0 -0.7 33 33
GTF3A 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.05 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.31 -10000 0 -0.84 77 77
CD40LG -0.12 0.29 -10000 0 -0.74 85 85
MAPK14 -0.18 0.3 -10000 0 -0.79 20 20
mitosis -0.14 0.25 -10000 0 -0.84 9 9
STAT6 -0.46 0.63 -10000 0 -1.3 128 128
SPI1 -0.043 0.19 -10000 0 -0.74 34 34
RPS6KB1 -0.13 0.24 -10000 0 -0.88 7 7
STAT6 (dimer) -0.46 0.63 -10000 0 -1.3 128 128
STAT6 (dimer)/PARP14 -0.42 0.58 -10000 0 -1.2 120 120
mast cell activation 0.008 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.3 -10000 0 -0.81 34 34
FRAP1 -0.14 0.26 -10000 0 -0.92 9 9
LTA -0.39 0.54 -10000 0 -1.2 103 103
FES -0.002 0.034 -10000 0 -0.74 1 1
T-helper 1 cell differentiation 0.44 0.61 1.3 128 -10000 0 128
CCL11 -0.38 0.52 -10000 0 -1.2 106 106
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.27 -10000 0 -1.1 9 9
IL2RG 0 0.095 -10000 0 -0.73 8 8
IL10 -0.39 0.54 -10000 0 -1.2 104 104
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.005 0.058 -10000 0 -0.74 3 3
IL4 -0.078 0.14 -10000 0 -10000 0 0
IL5 -0.39 0.54 -10000 0 -1.2 102 102
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.42 -10000 0 -0.9 103 103
COL1A1 -0.14 0.23 -10000 0 -0.64 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.4 0.55 -10000 0 -1.2 102 102
IL2R gamma/JAK3 -0.004 0.072 -10000 0 -0.55 8 8
TFF3 -0.44 0.62 -10000 0 -1.4 110 110
ALOX15 -0.62 0.76 -10000 0 -1.5 178 178
MYBL1 -0.001 0.026 -10000 0 -0.57 1 1
T-helper 2 cell differentiation -0.31 0.43 -10000 0 -0.93 105 105
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.26 -10000 0 -1 9 9
mol:PI-3-4-5-P3 -0.14 0.26 -10000 0 -0.92 9 9
PI3K -0.15 0.28 -10000 0 -1 9 9
DOK2 -0.066 0.21 -10000 0 -0.74 43 43
ETS1 0 0.11 -10000 0 -0.71 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.22 -10000 0 -0.87 7 7
ITGB3 -0.4 0.55 -10000 0 -1.2 104 104
PIGR -0.8 0.83 -10000 0 -1.6 255 255
IGHE 0.028 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.11 0.21 -10000 0 -0.85 7 7
BCL6 0.001 0.004 -10000 0 -10000 0 0
OPRM1 -0.4 0.54 -10000 0 -1.2 103 103
RETNLB -0.4 0.54 -10000 0 -1.2 102 102
SELP -0.56 0.74 -10000 0 -1.6 150 150
AICDA -0.38 0.51 -10000 0 -1.2 104 104
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.043 0.056 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.099 0.14 -9999 0 -0.43 20 20
JUN -0.063 0.14 -9999 0 -0.42 17 17
HRAS 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.22 -9999 0 -0.48 124 124
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.22 -9999 0 -0.48 124 124
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.16 0.22 -9999 0 -0.48 119 119
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.43 124 124
GRB7 -0.005 0.052 -9999 0 -0.57 4 4
RET51/GFRalpha1/GDNF -0.17 0.22 -9999 0 -0.48 124 124
MAPKKK cascade -0.13 0.18 -9999 0 -0.59 19 19
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.42 182 182
lamellipodium assembly -0.095 0.13 -9999 0 -0.4 20 20
RET51/GFRalpha1/GDNF/SHC -0.17 0.22 -9999 0 -0.48 124 124
PIK3CA 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.48 119 119
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.22 -9999 0 -0.43 182 182
MAPK3 -0.14 0.18 -9999 0 -0.62 21 21
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.065 0.21 -9999 0 -0.74 42 42
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.14 0.18 -9999 0 -0.55 39 39
DOK5 -0.007 0.069 -9999 0 -0.67 5 5
GFRA1 -0.18 0.32 -9999 0 -0.74 119 119
MAPK8 -0.096 0.13 -9999 0 -0.44 17 17
HRAS/GTP -0.14 0.2 -9999 0 -0.62 21 21
tube development -0.15 0.21 -9999 0 -0.46 119 119
MAPK1 -0.14 0.18 -9999 0 -0.62 21 21
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.33 119 119
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.19 0.25 -9999 0 -0.51 144 144
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.22 -9999 0 -0.48 124 124
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.23 -9999 0 -0.49 125 125
PRKCA -0.003 0.048 -9999 0 -0.74 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.15 -9999 0 -0.36 119 119
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.37 47 47
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.22 -9999 0 -0.49 125 125
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.021 0.11 -9999 0 -0.58 17 17
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.061 0.14 -9999 0 -0.41 17 17
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.42 182 182
SHANK3 -0.003 0.048 -9999 0 -0.74 2 2
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.34 119 119
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.33 120 120
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.14 -9999 0 -0.47 17 17
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.48 17 17
PI3K -0.14 0.2 -9999 0 -0.48 120 120
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.21 -9999 0 -0.46 119 119
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.1 0.14 -9999 0 -0.47 17 17
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.22 -9999 0 -0.48 124 124
GAB1 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
IRS2 -0.005 0.058 -9999 0 -0.74 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.48 17 17
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.49 125 125
GRB2 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.093 0.21 -9999 0 -0.57 78 78
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.22 -9999 0 -0.48 124 124
Rac1/GTP -0.11 0.16 -9999 0 -0.48 20 20
RET9/GFRalpha1/GDNF -0.18 0.24 -9999 0 -0.47 182 182
GFRalpha1/GDNF -0.2 0.27 -9999 0 -0.54 182 182
Glucocorticoid receptor regulatory network

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.06 0.099 0.35 3 -10000 0 3
SMARCC2 0.011 0 -10000 0 -10000 0 0
SMARCC1 0.011 0 -10000 0 -10000 0 0
TBX21 -0.2 0.35 -10000 0 -1 62 62
SUMO2 0.002 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0 -10000 0 -10000 0 0
FKBP4 -0.001 0.026 -10000 0 -0.57 1 1
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.13 0.1 0.34 42 -10000 0 42
PRL -0.085 0.12 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/TIF2 0.31 0.25 0.6 150 -10000 0 150
RELA -0.046 0.1 -10000 0 -10000 0 0
FGG -0.13 0.47 0.55 51 -0.62 222 273
GR beta/TIF2 0.14 0.12 0.37 49 -0.39 1 50
IFNG -0.34 0.24 -10000 0 -0.68 98 98
apoptosis 0.028 0.12 0.46 2 -0.55 1 3
CREB1 0.001 0.028 -10000 0 -10000 0 0
histone acetylation -0.012 0.15 0.36 2 -0.42 16 18
BGLAP -0.096 0.14 -10000 0 -0.59 5 5
GR/PKAc 0.12 0.1 0.33 32 -10000 0 32
NF kappa B1 p50/RelA -0.083 0.18 -10000 0 -0.48 37 37
SMARCD1 0.011 0 -10000 0 -10000 0 0
MDM2 0.11 0.098 0.29 59 -0.31 1 60
GATA3 -0.014 0.13 -10000 0 -0.71 17 17
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.17 0.42 -10000 0 -1.3 51 51
GSK3B 0.002 0.006 -10000 0 -10000 0 0
NR1I3 0.047 0.11 0.47 1 -10000 0 1
CSN2 0.16 0.16 0.44 42 -10000 0 42
BRG1/BAF155/BAF170/BAF60A 0 0 -10000 0 -10000 0 0
NFATC1 0.001 0.034 -10000 0 -0.74 1 1
POU2F1 0.005 0.014 -10000 0 -10000 0 0
CDKN1A 0.026 0.015 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.57 48 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.14 0.33 38 -10000 0 38
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.034 0.16 0.46 1 -0.9 9 10
JUN -0.29 0.16 -10000 0 -0.51 108 108
IL4 -0.11 0.15 -10000 0 -0.52 16 16
CDK5R1 -0.009 0.078 -10000 0 -0.57 9 9
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.44 0.24 -10000 0 -0.59 276 276
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.099 0.33 37 -10000 0 37
cortisol/GR alpha (monomer) 0.37 0.32 0.72 162 -10000 0 162
NCOA2 -0.002 0.034 -10000 0 -0.74 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.17 0.24 -10000 0 -0.83 55 55
AP-1/NFAT1-c-4 -0.53 0.24 -10000 0 -0.68 271 271
AFP -0.19 0.15 -10000 0 -0.65 16 16
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.18 0.15 0.49 36 -10000 0 36
TP53 0.029 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.54 0.25 -10000 0 -0.69 285 285
KRT14 -0.37 0.22 -10000 0 -0.61 136 136
TBP 0.017 0 -10000 0 -10000 0 0
CREBBP 0.11 0.066 0.34 1 -10000 0 1
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.01 0.03 -10000 0 -10000 0 0
AP-1 -0.53 0.25 -10000 0 -0.68 274 274
MAPK14 0.002 0.005 -10000 0 -10000 0 0
MAPK10 -0.011 0.095 -10000 0 -0.74 8 8
MAPK11 0.002 0.006 -10000 0 -10000 0 0
KRT5 -0.56 0.25 -10000 0 -0.68 322 322
interleukin-1 receptor activity 0.008 0.028 -10000 0 -10000 0 0
NCOA1 0.012 0.002 -10000 0 -10000 0 0
STAT1 0.017 0 -10000 0 -10000 0 0
CGA -0.12 0.17 -10000 0 -0.63 11 11
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.19 0.51 88 -10000 0 88
MAPK3 0.002 0.006 -10000 0 -10000 0 0
MAPK1 0.002 0.005 -10000 0 -10000 0 0
ICAM1 -0.27 0.45 -10000 0 -1.1 75 75
NFKB1 -0.046 0.1 -10000 0 -0.33 1 1
MAPK8 -0.24 0.17 -10000 0 -0.48 109 109
MAPK9 0.002 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.025 0.12 0.46 2 -0.58 1 3
BAX 0.026 0.015 -10000 0 -10000 0 0
POMC -0.21 0.24 -10000 0 -0.7 52 52
EP300 0.11 0.066 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.33 0.25 0.61 159 -10000 0 159
proteasomal ubiquitin-dependent protein catabolic process 0.076 0.074 0.26 14 -0.27 1 15
SGK1 0.17 0.076 -10000 0 -10000 0 0
IL13 -0.27 0.2 -10000 0 -0.87 25 25
IL6 -0.34 0.53 -10000 0 -1.3 102 102
PRKACG -0.001 0.026 -10000 0 -0.57 1 1
IL5 -0.24 0.17 -10000 0 -0.78 21 21
IL2 -0.34 0.21 -10000 0 -0.68 78 78
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.2 0.29 -10000 0 -0.72 73 73
CDK5R1/CDK5 -0.006 0.056 -10000 0 -0.41 9 9
NF kappa B1 p50/RelA/PKAc -0.059 0.12 -10000 0 -0.47 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 148 -10000 0 148
SMARCA4 0.011 0 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.14 0.4 101 -10000 0 101
NF kappa B1 p50/RelA/Cbp 0.036 0.18 0.38 13 -0.53 2 15
JUN (dimer) -0.29 0.16 -10000 0 -0.51 108 108
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.42 0.51 -10000 0 -1 185 185
NR3C1 0.2 0.2 0.52 93 -10000 0 93
NR4A1 -0.1 0.26 -10000 0 -0.72 68 68
TIF2/SUV420H1 -0.001 0.025 -10000 0 -0.56 1 1
MAPKKK cascade 0.028 0.12 0.46 2 -0.55 1 3
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.6 157 -10000 0 157
PBX1 0 0.06 -10000 0 -0.74 3 3
POU1F1 -0.002 0.047 -10000 0 -0.57 3 3
SELE -0.47 0.61 -10000 0 -1.3 155 155
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.14 0.4 101 -10000 0 101
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 148 -10000 0 148
mol:cortisol 0.2 0.2 0.42 164 -0.23 3 167
MMP1 -0.32 0.19 -10000 0 -0.48 274 274
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.39 -9999 0 -1.2 49 49
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.036 0.12 -9999 0 -0.43 8 8
ATF2/c-Jun -0.01 0.098 -9999 0 -0.43 3 3
MAPK11 -0.036 0.12 -9999 0 -0.31 72 72
MITF -0.041 0.16 -9999 0 -0.37 82 82
MAPKAPK5 -0.032 0.15 -9999 0 -0.36 72 72
KRT8 -0.032 0.15 -9999 0 -0.36 72 72
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.054 0.18 -9999 0 -0.46 72 72
CEBPB -0.032 0.15 -9999 0 -0.36 72 72
SLC9A1 -0.032 0.15 -9999 0 -0.36 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.026 0.15 -9999 0 -0.35 72 72
p38alpha-beta/MNK1 -0.065 0.13 -9999 0 -0.58 8 8
JUN -0.009 0.098 -9999 0 -0.42 3 3
PPARGC1A -0.13 0.28 -9999 0 -0.51 142 142
USF1 -0.032 0.15 -9999 0 -0.36 72 72
RAB5/GDP/GDI1 -0.045 0.095 -9999 0 -0.4 8 8
NOS2 -0.098 0.32 -9999 0 -1.2 31 31
DDIT3 -0.032 0.15 -9999 0 -0.36 72 72
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.018 0.12 -9999 0 -0.43 9 9
p38alpha-beta/HBP1 -0.065 0.13 -9999 0 -0.58 8 8
CREB1 -0.03 0.16 -9999 0 -0.38 72 72
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.021 0.13 -9999 0 -0.52 8 8
RPS6KA4 -0.032 0.15 -9999 0 -0.36 72 72
PLA2G4A -0.025 0.14 -9999 0 -0.53 13 13
GDI1 -0.032 0.15 -9999 0 -0.36 72 72
TP53 -0.044 0.18 -9999 0 -0.45 72 72
RPS6KA5 -0.032 0.15 -9999 0 -0.36 72 72
ESR1 -0.053 0.19 -9999 0 -0.42 86 86
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.041 0.17 -9999 0 -0.39 79 79
MEF2A -0.032 0.15 -9999 0 -0.36 72 72
EIF4EBP1 -0.032 0.16 -9999 0 -0.38 72 72
KRT19 -0.039 0.18 -9999 0 -0.4 74 74
ELK4 -0.032 0.15 -9999 0 -0.36 72 72
ATF6 -0.032 0.15 -9999 0 -0.36 72 72
ATF1 -0.03 0.16 -9999 0 -0.38 72 72
p38alpha-beta/MAPKAPK2 -0.065 0.13 -9999 0 -0.58 8 8
p38alpha-beta/MAPKAPK3 -0.065 0.13 -9999 0 -0.58 8 8
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.017 0.094 -9999 0 -0.51 16 16
ARNO/beta Arrestin1-2 -0.17 0.24 -9999 0 -0.45 181 181
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EPHA2 -0.005 0.058 -9999 0 -0.74 3 3
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.027 0.12 -9999 0 -0.5 26 26
ARRB2 0.007 0.011 -9999 0 -10000 0 0
mol:GTP 0.015 0.026 -9999 0 -0.15 8 8
ARRB1 -0.14 0.29 -9999 0 -0.74 91 91
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.019 0.1 -9999 0 -0.57 16 16
EGF -0.014 0.099 -9999 0 -0.69 10 10
somatostatin receptor activity 0 0 -9999 0 -0.001 141 141
ARAP2 -0.002 0.034 -9999 0 -0.74 1 1
mol:GDP -0.12 0.16 -9999 0 -0.33 134 134
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 116 116
ITGA2B -0.023 0.13 -9999 0 -0.74 15 15
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.43 3 3
ADAP1 -0.014 0.1 -9999 0 -0.74 9 9
KIF13B -0.012 0.095 -9999 0 -0.74 8 8
HGF/MET -0.12 0.23 -9999 0 -0.56 104 104
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.11 0.15 -9999 0 -0.31 141 141
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.023 0.1 -9999 0 -0.42 26 26
ADRB2 -0.21 0.33 -9999 0 -0.74 137 137
receptor agonist activity 0 0 -9999 0 0 145 145
actin filament binding 0 0 -9999 0 -0.001 141 141
SRC 0 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.095 -9999 0 -0.74 8 8
GNAQ -0.002 0.034 -9999 0 -0.74 1 1
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 116 116
ARF6/GDP -0.013 0.071 -9999 0 -0.34 4 4
ARF6/GDP/GULP/ACAP1 -0.12 0.14 -9999 0 -0.43 47 47
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.021 0.092 -9999 0 -0.43 23 23
ACAP1 -0.003 0.043 -9999 0 -0.66 2 2
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.014 -9999 0 -0.31 1 1
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 101 101
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 101 101
endosomal lumen acidification 0 0 0 1 -0.001 90 91
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.014 0.1 -9999 0 -0.74 9 9
GNAQ/ARNO 0.004 0.02 -9999 0 -0.41 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 10 10
MET -0.004 0.054 -9999 0 -0.68 3 3
GNA14 -0.18 0.32 -9999 0 -0.74 114 114
GNA15 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 140 140
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.001 0.026 -9999 0 -0.57 1 1
AGTR1 -0.31 0.36 -9999 0 -0.74 199 199
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.014 -9999 0 -0.31 1 1
IPCEF1/ARNO -0.018 0.079 -9999 0 -0.41 12 12
alphaIIb/beta3 Integrin -0.027 0.12 -9999 0 -0.56 23 23
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.032 0.03 -9999 0 -10000 0 0
VDR -0.002 0.034 -9999 0 -0.74 1 1
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.13 0.18 -9999 0 -0.54 10 10
RXRs/LXRs/DNA/Oxysterols -0.098 0.16 -9999 0 -0.64 10 10
MED1 0 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.012 0.06 -9999 0 -10000 0 0
RXRs/NUR77 -0.28 0.27 -9999 0 -0.49 277 277
RXRs/PPAR -0.18 0.2 -9999 0 -0.57 43 43
NCOR2 -0.002 0.034 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.026 -9999 0 -0.57 1 1
RARs/VDR/DNA/Vit D3 -0.003 0.032 -9999 0 -0.41 3 3
RARA 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.034 -9999 0 -0.74 1 1
RARs/RARs/DNA/9cRA -0.002 0.027 -9999 0 -0.42 2 2
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.057 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.013 0.061 -9999 0 -10000 0 0
THRA 0 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.026 -9999 0 -0.57 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.23 0.22 -9999 0 -0.43 253 253
NR1H4 -0.005 0.052 -9999 0 -0.57 4 4
RXRs/LXRs/DNA -0.21 0.2 -9999 0 -0.56 10 10
NR1H2 0.015 0.004 -9999 0 -10000 0 0
NR1H3 0.014 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.21 0.2 -9999 0 -0.4 254 254
NR4A1 -0.1 0.25 -9999 0 -0.74 65 65
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.12 0.14 -9999 0 -0.34 11 11
RXRG -0.38 0.37 -9999 0 -0.74 253 253
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.004 -9999 0 -10000 0 0
RXRB 0.014 0.005 -9999 0 -10000 0 0
THRB -0.026 0.14 -9999 0 -0.74 17 17
PPARG -0.089 0.24 -9999 0 -0.74 58 58
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.1 0.23 -9999 0 -1.2 13 13
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.097 0.16 -9999 0 -0.64 10 10
PPARA 0 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.003 0.048 -9999 0 -0.74 2 2
RXRs/NUR77/BCL2 -0.2 0.2 -9999 0 -0.36 277 277
SREBF1 -0.082 0.15 -9999 0 -0.6 9 9
RXRs/RXRs/DNA/9cRA -0.23 0.22 -9999 0 -0.43 253 253
ABCA1 -0.082 0.15 -9999 0 -0.6 9 9
RARs/THRs -0.016 0.079 -9999 0 -10000 0 0
RXRs/FXR -0.23 0.22 -9999 0 -0.43 253 253
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.21 -9999 0 -0.56 73 73
SMAD6-7/SMURF1 -0.053 0.15 -9999 0 -0.48 53 53
NOG -0.027 0.14 -9999 0 -0.73 18 18
SMAD9 -0.1 0.22 -9999 0 -0.59 72 72
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.023 0.13 -9999 0 -0.47 23 23
BMP7/USAG1 -0.25 0.27 -9999 0 -0.5 238 238
SMAD5/SKI -0.05 0.11 -9999 0 -0.46 19 19
SMAD1 0.033 0.027 -9999 0 -10000 0 0
BMP2 -0.098 0.25 -9999 0 -0.74 64 64
SMAD1/SMAD1/SMAD4 -0.035 0.096 -9999 0 -10000 0 0
BMPR1A 0 0 -9999 0 -10000 0 0
BMPR1B -0.057 0.2 -9999 0 -0.74 37 37
BMPR1A-1B/BAMBI -0.04 0.13 -9999 0 -0.48 39 39
AHSG -0.018 0.099 -9999 0 -0.57 15 15
CER1 -0.002 0.037 -9999 0 -0.57 2 2
BMP2-4/CER1 -0.075 0.18 -9999 0 -0.5 70 70
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.067 0.14 -9999 0 -0.5 29 29
BMP2-4 (homodimer) -0.085 0.21 -9999 0 -0.58 71 71
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.045 0.14 -9999 0 -0.45 48 48
RGMA -0.062 0.18 -9999 0 -0.57 52 52
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.13 -9999 0 -0.45 29 29
BMP2-4/USAG1 -0.16 0.27 -9999 0 -0.55 142 142
SMAD6/SMURF1/SMAD5 -0.05 0.11 -9999 0 -0.46 19 19
SOSTDC1 -0.14 0.29 -9999 0 -0.74 93 93
BMP7/BMPR2/BMPR1A-1B -0.14 0.19 -9999 0 -0.53 43 43
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.02 0.12 -9999 0 -0.74 13 13
HFE2 -0.002 0.037 -9999 0 -0.57 2 2
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.076 0.18 -9999 0 -0.5 71 71
SMAD5/SMAD5/SMAD4 -0.05 0.11 -9999 0 -0.47 18 18
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.05 0.1 -9999 0 -0.45 17 17
BMP7 (homodimer) -0.2 0.28 -9999 0 -0.58 169 169
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.028 0.11 -9999 0 -0.48 28 28
SMAD1/SKI -0.004 0.012 -9999 0 -10000 0 0
SMAD6 -0.08 0.23 -9999 0 -0.74 52 52
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.084 0.19 -9999 0 -0.5 70 70
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.34 0.28 -9999 0 -0.57 288 288
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.043 0.15 -9999 0 -0.56 37 37
CHRDL1 -0.39 0.37 -9999 0 -0.74 251 251
ENDOFIN/SMAD1 -0.004 0.012 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.04 0.11 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.005 0.06 -9999 0 -0.66 4 4
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.3 -9999 0 -0.55 277 277
BMP2-4/GREM1 -0.28 0.22 -9999 0 -0.62 70 70
SMAD7 -0.002 0.034 -9999 0 -0.74 1 1
SMAD8A/SMAD8A/SMAD4 -0.096 0.2 -9999 0 -0.55 72 72
SMAD1/SMAD6 -0.004 0.012 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.2 0.28 -9999 0 -0.58 169 169
BMP6 -0.02 0.12 -9999 0 -0.74 13 13
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.058 0.12 -9999 0 -0.41 30 30
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.004 0.012 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.025 -9999 0 -0.56 1 1
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.084 0.14 -9999 0 -0.46 41 41
CHRD -0.004 0.054 -9999 0 -0.68 3 3
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.14 -9999 0 -0.5 29 29
BMP4 -0.015 0.1 -9999 0 -0.72 10 10
FST -0.092 0.21 -9999 0 -0.57 77 77
BMP2-4/NOG -0.09 0.21 -9999 0 -0.53 81 81
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.13 0.18 -9999 0 -0.5 43 43
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.071 0.074 0.15 169 -10000 0 169
BUB1B -0.13 0.098 -10000 0 -0.22 194 194
PLK1 -0.013 0.036 -10000 0 -0.13 8 8
PLK1S1 -0.003 0.02 -10000 0 -10000 0 0
KIF2A -0.004 0.033 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.013 0.036 -10000 0 -0.13 8 8
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.2 0.23 -10000 0 -0.41 236 236
WEE1 -0.006 0.038 -10000 0 -10000 0 0
cytokinesis -0.11 0.12 -10000 0 -0.27 82 82
PP2A-alpha B56 -0.007 0.022 -10000 0 -10000 0 0
AURKA -0.006 0.029 -10000 0 -0.12 8 8
PICH/PLK1 -0.11 0.17 -10000 0 -0.46 53 53
CENPE -0.041 0.11 -10000 0 -0.35 54 54
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.032 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.06 0.048 -10000 0 -0.12 4 4
PAK1 0.002 0.026 -10000 0 -0.57 1 1
SPC24 -0.17 0.26 -10000 0 -0.57 144 144
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.013 0.039 -10000 0 -0.15 5 5
GORASP1 0 0 -10000 0 -10000 0 0
metaphase 0 0.003 -10000 0 -0.012 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.02 -10000 0 -0.066 4 4
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.001 0.008 -10000 0 -10000 0 0
spindle elongation -0.013 0.036 -10000 0 -0.13 8 8
ODF2 0.004 0.005 -10000 0 -10000 0 0
BUB1 -0.005 0.032 -10000 0 -10000 0 0
TPT1 -0.003 0.02 -10000 0 -10000 0 0
CDC25C -0.077 0.057 -10000 0 -10000 0 0
CDC25B 0.009 0.003 -10000 0 -10000 0 0
SGOL1 -0.071 0.074 -10000 0 -0.15 169 169
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.029 0.079 -10000 0 -10000 0 0
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.36 0.28 -10000 0 -0.57 308 308
PLK1/PBIP1 -0.03 0.063 -10000 0 -0.33 18 18
mitosis -0.001 0.005 0.022 13 -10000 0 13
FBXO5 -0.004 0.031 -10000 0 -10000 0 0
CDC2 -0.001 0.004 -10000 0 -0.013 4 4
NDC80 -0.2 0.27 -10000 0 -0.57 167 167
metaphase plate congression -0.007 0.025 -10000 0 -10000 0 0
ERCC6L -0.11 0.16 -10000 0 -0.49 36 36
NLP/gamma Tubulin -0.005 0.021 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0 0 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.2 0.2 -10000 0 -0.37 256 256
GRASP65/GM130/RAB1/GTP/PLK1 -0.008 0.015 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.043 0.035 -10000 0 -10000 0 0
microtubule-based process -0.18 0.17 -10000 0 -0.34 249 249
Golgi organization -0.013 0.036 -10000 0 -0.13 8 8
Cohesin/SA2 -0.019 0.024 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.3 0.29 -10000 0 -0.57 249 249
APC/C/CDC20 -0.22 0.16 -10000 0 -0.34 308 308
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.029 0.062 -10000 0 -0.32 18 18
PRC1 -0.057 0.17 -10000 0 -0.57 48 48
ECT2 -0.016 0.073 -10000 0 -0.35 18 18
C13orf34 -0.003 0.028 -10000 0 -10000 0 0
NUDC -0.007 0.025 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.13 0.097 -10000 0 -0.22 194 194
spindle assembly -0.008 0.029 -10000 0 -10000 0 0
spindle stabilization -0.003 0.02 -10000 0 -10000 0 0
APC/C/HCDH1 0 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.18 0.17 -10000 0 -0.34 249 249
CCNB1 -0.058 0.19 -10000 0 -0.57 57 57
PPP1CB 0 0 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.001 0.025 -10000 0 -10000 0 0
TUBG1 -0.003 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.076 -10000 0 -10000 0 0
MLF1IP -0.011 0.083 -10000 0 -0.43 18 18
INCENP 0.004 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.002 0.034 -9999 0 -0.74 1 1
alphaV beta3 Integrin -0.009 0.071 -9999 0 -0.56 8 8
PTK2 -0.1 0.16 -9999 0 -0.57 40 40
positive regulation of JNK cascade -0.034 0.09 -9999 0 -0.34 37 37
CDC42/GDP -0.022 0.13 -9999 0 -0.46 37 37
Rac1/GDP -0.02 0.13 -9999 0 -0.46 37 37
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.041 0.11 -9999 0 -0.42 37 37
nectin-3/I-afadin -0.043 0.15 -9999 0 -0.56 37 37
RAPGEF1 -0.033 0.15 -9999 0 -0.53 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.046 0.17 -9999 0 -0.62 37 37
PDGFB-D/PDGFRB -0.002 0.034 -9999 0 -0.74 1 1
TLN1 -0.02 0.15 -9999 0 -0.51 31 31
Rap1/GTP -0.034 0.097 -9999 0 -0.37 37 37
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.043 0.15 -9999 0 -0.56 37 37
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.033 0.16 -9999 0 -0.58 37 37
MLLT4 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K -0.032 0.11 -9999 0 -0.4 38 38
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.41 231 231
positive regulation of lamellipodium assembly -0.037 0.096 -9999 0 -0.35 40 40
PVRL1 -0.27 0.29 -9999 0 -0.57 231 231
PVRL3 -0.057 0.2 -9999 0 -0.74 37 37
PVRL2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
CLDN1 -0.1 0.22 -9999 0 -0.58 87 87
JAM-A/CLDN1 -0.089 0.17 -9999 0 -0.49 38 38
SRC -0.077 0.18 -9999 0 -0.7 37 37
ITGB3 -0.012 0.095 -9999 0 -0.74 8 8
nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.41 231 231
FARP2 -0.037 0.16 -9999 0 -0.57 37 37
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.037 0.13 -9999 0 -0.48 37 37
nectin-1/I-afadin -0.2 0.21 -9999 0 -0.41 231 231
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.39 249 249
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.034 0.09 -9999 0 -0.34 37 37
alphaV/beta3 Integrin/Talin -0.047 0.14 -9999 0 -0.49 35 35
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.05 0.15 -9999 0 -0.54 31 31
VAV2 -0.041 0.17 -9999 0 -0.58 40 40
RAP1/GDP -0.039 0.11 -9999 0 -0.43 37 37
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.037 0.13 -9999 0 -0.48 37 37
nectin-3(dimer)/I-afadin/I-afadin -0.043 0.15 -9999 0 -0.56 37 37
Rac1/GTP -0.045 0.12 -9999 0 -0.43 40 40
PTPRM -0.055 0.16 -9999 0 -0.43 61 61
E-cadherin/beta catenin/alpha catenin -0.13 0.13 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.029 0.12 -9999 0 -0.56 25 25
alphaV beta3 Integrin -0.023 0.11 -9999 0 -0.5 22 22
PTK2 -0.19 0.23 -9999 0 -0.69 39 39
IGF1R 0 0 -9999 0 -10000 0 0
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
CDKN1B -0.23 0.29 -9999 0 -0.58 187 187
VEGFA 0 0 -9999 0 -10000 0 0
ILK -0.23 0.29 -9999 0 -0.58 187 187
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.21 0.27 -9999 0 -0.54 187 187
PTK2B -0.027 0.12 -9999 0 -0.47 28 28
alphaV/beta3 Integrin/JAM-A -0.18 0.22 -9999 0 -0.43 196 196
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.011 0.069 -9999 0 -0.48 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.014 0.076 -9999 0 -0.43 15 15
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.16 -9999 0 -0.65 19 19
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.065 -9999 0 -0.48 9 9
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.038 0.14 -9999 0 -0.78 10 10
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.19 0.18 -9999 0 -0.35 260 260
RPS6KB1 -0.035 0.13 -9999 0 -0.72 10 10
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.1 0.18 -9999 0 -0.77 22 22
GPR124 0 0 -9999 0 -10000 0 0
MAPK1 -0.1 0.18 -9999 0 -0.77 22 22
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.31 0.24 -9999 0 -0.49 305 305
cell adhesion -0.012 0.067 -9999 0 -0.42 11 11
ANGPTL3 -0.005 0.052 -9999 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.025 0.11 -9999 0 -0.48 25 25
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.058 0.2 -9999 0 -0.74 38 38
ITGB3 -0.012 0.095 -9999 0 -0.74 8 8
IGF1 -0.024 0.13 -9999 0 -0.73 16 16
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.008 0.061 -9999 0 -0.48 8 8
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.005 0.058 -9999 0 -0.74 3 3
alphaV/beta3 Integrin/CD47 -0.011 0.072 -9999 0 -0.48 11 11
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.034 0.13 -9999 0 -0.51 32 32
CSF1 -0.006 0.067 -9999 0 -0.74 4 4
PIK3C2A -0.23 0.29 -9999 0 -0.58 187 187
PI4 Kinase/Pyk2 -0.16 0.21 -9999 0 -0.75 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.03 0.12 -9999 0 -0.51 28 28
FAK1/Vinculin -0.15 0.18 -9999 0 -0.51 39 39
alphaV beta3/Integrin/ppsTEM5 -0.008 0.061 -9999 0 -0.48 8 8
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.29 0.36 -9999 0 -0.74 189 189
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.023 0.13 -9999 0 -0.74 15 15
F11R 0.002 0.1 -9999 0 -0.56 15 15
alphaV/beta3 Integrin/Lactadherin -0.008 0.061 -9999 0 -0.48 8 8
alphaV/beta3 Integrin/TGFBR2 -0.045 0.16 -9999 0 -0.54 40 40
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.039 -9999 0 -0.43 4 4
HSP90AA1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.007 0.056 -9999 0 -0.44 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.017 0.11 -9999 0 -0.74 11 11
alphaV/beta3 Integrin/Pyk2 -0.028 0.12 -9999 0 -0.47 28 28
SDC1 -0.002 0.034 -9999 0 -0.74 1 1
VAV3 -0.004 0.041 -9999 0 -0.4 5 5
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.15 0.18 -9999 0 -0.51 39 39
cell migration -0.13 0.16 -9999 0 -0.48 30 30
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.16 0.2 -9999 0 -0.76 13 13
SPP1 -0.3 0.28 -9999 0 -0.57 255 255
KDR -0.038 0.16 -9999 0 -0.74 25 25
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.47 0.36 -9999 0 -0.74 305 305
angiogenesis -0.11 0.22 -9999 0 -0.76 24 24
Rac1/GTP -0.004 0.037 -9999 0 -10000 0 0
EDIL3 -0.04 0.17 -9999 0 -0.74 26 26
cell proliferation -0.045 0.16 -9999 0 -0.54 40 40
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.034 0.11 -10000 0 -0.48 16 16
fibroblast growth factor receptor signaling pathway -0.034 0.11 -10000 0 -0.48 16 16
LAMA1 -0.17 0.26 -10000 0 -0.57 141 141
PRNP 0 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.15 0.25 -10000 0 -0.56 128 128
SMAD2 -0.024 0.14 -10000 0 -0.43 38 38
GPC1/PrPc/Cu2+ -0.018 0.078 -10000 0 -0.35 25 25
GPC1/Laminin alpha1 -0.14 0.22 -10000 0 -0.45 151 151
TDGF1 -0.004 0.045 -10000 0 -0.57 3 3
CRIPTO/GPC1 -0.024 0.097 -10000 0 -0.41 28 28
APP/GPC1 -0.021 0.091 -10000 0 -0.41 25 25
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.001 0.086 -10000 0 -0.35 6 6
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.056 0.14 -10000 0 -0.42 63 63
SERPINC1 -0.007 0.063 -10000 0 -0.57 6 6
FYN 0 0.089 -10000 0 -0.35 29 29
FGR -0.033 0.15 -10000 0 -0.48 32 32
positive regulation of MAPKKK cascade 0.002 0.11 -10000 0 -0.46 13 13
SLIT2 -0.17 0.31 -10000 0 -0.74 110 110
GPC1/NRG -0.036 0.13 -10000 0 -0.46 38 38
NRG1 -0.02 0.12 -10000 0 -0.74 13 13
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.018 0.076 -10000 0 -0.34 25 25
LYN -0.001 0.091 -10000 0 -0.38 8 8
mol:Spermine -0.013 0.095 -10000 0 -0.42 25 25
cell growth -0.034 0.11 -10000 0 -0.48 16 16
BMP signaling pathway 0.03 0.13 0.57 25 -10000 0 25
SRC 0.001 0.086 -10000 0 -0.34 28 28
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.22 0.34 -10000 0 -0.74 143 143
GPC1 -0.03 0.13 -10000 0 -0.57 25 25
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.023 0.13 -10000 0 -0.39 53 53
HCK -0.004 0.099 -10000 0 -0.36 33 33
FGF2 -0.023 0.13 -10000 0 -0.74 15 15
FGFR1 -0.002 0.034 -10000 0 -0.74 1 1
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 -0.058 0.2 -10000 0 -0.74 38 38
cell death -0.021 0.091 -10000 0 -0.41 25 25
ATIII/GPC1 -0.027 0.1 -10000 0 -0.41 31 31
PLA2G2A/GPC1 -0.18 0.27 -10000 0 -0.56 160 160
LCK 0 0.089 -10000 0 -0.35 29 29
neuron differentiation -0.036 0.13 -10000 0 -0.46 38 38
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.058 0.2 -10000 0 -0.74 38 38
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.009 0.14 -10000 0 -10000 0 0
CRKL -0.013 0.15 -10000 0 -0.41 60 60
HRAS -0.058 0.14 -10000 0 -0.62 11 11
mol:PIP3 -0.025 0.14 -10000 0 -0.39 60 60
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.022 0.16 -10000 0 -0.43 60 60
FOXO3 -0.007 0.14 -10000 0 -0.37 60 60
AKT1 -0.016 0.14 -10000 0 -0.4 60 60
BAD -0.007 0.14 -10000 0 -0.37 60 60
megakaryocyte differentiation -0.049 0.2 -10000 0 -0.49 78 78
GSK3B -0.007 0.14 -10000 0 -0.37 60 60
RAF1 0.006 0.13 -10000 0 -0.48 11 11
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.022 0.16 -10000 0 -0.43 60 60
STAT1 -0.074 0.36 -10000 0 -1 60 60
HRAS/SPRED1 -0.047 0.11 -10000 0 -0.48 11 11
cell proliferation -0.021 0.15 -10000 0 -0.42 60 60
PIK3CA 0 0 -10000 0 -10000 0 0
TEC -0.005 0.058 -10000 0 -0.74 3 3
RPS6KB1 -0.022 0.15 -10000 0 -0.43 60 60
HRAS/SPRED2 -0.047 0.11 -10000 0 -0.48 11 11
LYN/TEC/p62DOK -0.053 0.14 -10000 0 -0.42 60 60
MAPK3 0.018 0.099 -10000 0 -0.32 11 11
STAP1 -0.045 0.2 -10000 0 -0.49 74 74
GRAP2 -0.04 0.17 -10000 0 -0.74 26 26
JAK2 -0.11 0.28 -10000 0 -0.85 60 60
STAT1 (dimer) -0.071 0.35 -10000 0 -0.99 60 60
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.054 0.14 -10000 0 -0.4 60 60
actin filament polymerization -0.021 0.15 -10000 0 -0.42 60 60
LYN -0.003 0.048 -10000 0 -0.74 2 2
STAP1/STAT5A (dimer) -0.049 0.25 -10000 0 -0.67 60 60
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.045 0.12 -10000 0 -10000 0 0
PI3K -0.05 0.13 -10000 0 -0.4 60 60
PTEN 0 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.1 0.44 -10000 0 -1.3 60 60
MAPK8 -0.022 0.16 -10000 0 -0.43 60 60
STAT3 (dimer) -0.021 0.15 -10000 0 -0.42 60 60
positive regulation of transcription 0.02 0.084 -10000 0 -0.3 1 1
mol:GDP -0.062 0.15 -10000 0 -0.67 11 11
PIK3C2B -0.021 0.16 -10000 0 -0.43 60 60
CBL/CRKL -0.007 0.14 -10000 0 -10000 0 0
FER -0.022 0.16 -10000 0 -0.43 60 60
SH2B3 -0.023 0.16 -10000 0 -0.43 62 62
PDPK1 -0.016 0.13 -10000 0 -0.36 60 60
SNAI2 -0.022 0.16 -10000 0 -0.43 60 60
positive regulation of cell proliferation -0.044 0.26 -10000 0 -0.74 60 60
KITLG 0.013 0.005 -10000 0 -10000 0 0
cell motility -0.044 0.26 -10000 0 -0.74 60 60
PTPN6 0.004 0.01 -10000 0 -10000 0 0
EPOR 0.01 0.1 -10000 0 -10000 0 0
STAT5A (dimer) -0.032 0.22 -10000 0 -0.61 60 60
SOCS1 -0.002 0.034 -10000 0 -0.74 1 1
cell migration 0.036 0.18 0.45 72 -10000 0 72
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.002 0.064 -10000 0 -0.57 6 6
VAV1 -0.008 0.075 -10000 0 -0.74 5 5
GRB10 -0.022 0.16 -10000 0 -0.43 60 60
PTPN11 0.003 0.008 -10000 0 -10000 0 0
SCF/KIT -0.058 0.15 -10000 0 -0.46 60 60
GO:0007205 0 0.008 -10000 0 -10000 0 0
MAP2K1 0.015 0.11 -10000 0 -0.36 11 11
CBL 0 0 -10000 0 -10000 0 0
KIT -0.13 0.47 -10000 0 -1.4 60 60
MAP2K2 0.015 0.11 -10000 0 -0.36 11 11
SHC/Grb2/SOS1 -0.049 0.13 -10000 0 -0.4 60 60
STAT5A -0.034 0.22 -10000 0 -0.63 60 60
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.021 0.15 -10000 0 -0.42 60 60
SHC/GRAP2 -0.03 0.13 -10000 0 -0.56 26 26
PTPRO -0.05 0.21 -10000 0 -0.5 78 78
SH2B2 -0.022 0.16 -10000 0 -0.43 60 60
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.037 0.18 -10000 0 -0.46 72 72
CREBBP 0.028 0.011 -10000 0 -10000 0 0
BCL2 0.01 0.1 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.19 0.22 -10000 0 -0.42 224 224
TP53 -0.05 0.056 -10000 0 -10000 0 0
Senescence -0.05 0.056 -10000 0 -10000 0 0
Apoptosis -0.05 0.056 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.096 0.11 0.31 4 -0.42 1 5
MDM4 0 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.098 0.18 -10000 0 -0.44 107 107
regulation of S phase of mitotic cell cycle -0.064 0.13 -10000 0 -0.31 101 101
GNAO1 -0.004 0.05 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.051 0.16 -10000 0 -0.46 17 17
T-DHT/AR -0.12 0.23 -10000 0 -0.57 101 101
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 55 55
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.034 -10000 0 -0.74 1 1
mol:GDP -0.12 0.23 -10000 0 -0.56 101 101
cell proliferation -0.057 0.2 -10000 0 -0.65 17 17
PIK3CA 0 0 -10000 0 -10000 0 0
FOS -0.085 0.29 -10000 0 -0.86 55 55
mol:Ca2+ -0.013 0.022 -10000 0 -0.085 8 8
MAPK3 -0.052 0.18 -10000 0 -0.58 17 17
MAPK1 -0.021 0.096 -10000 0 -0.3 17 17
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 55 55
cAMP biosynthetic process 0.011 0.021 -10000 0 -10000 0 0
GNG2 -0.008 0.075 -10000 0 -0.74 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 55 55
HRAS/GTP -0.086 0.16 -10000 0 -0.4 101 101
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 55 55
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.046 0.18 0.45 55 -10000 0 55
T-DHT/AR/PELP1 -0.1 0.2 -10000 0 -0.49 101 101
HRAS/GDP -0.11 0.21 -10000 0 -0.52 101 101
CREB1 -0.051 0.19 -10000 0 -0.49 55 55
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.16 0.3 -10000 0 -0.74 101 101
GNB1 -0.002 0.034 -10000 0 -0.74 1 1
RAF1 -0.058 0.17 -10000 0 -0.46 17 17
RAC1-CDC42/GDP -0.1 0.2 -10000 0 -0.5 101 101
T-DHT/AR/PELP1/Src -0.093 0.18 -10000 0 -0.44 101 101
MAP2K2 -0.051 0.16 -10000 0 -0.46 17 17
T-DHT/AR/PELP1/Src/PI3K -0.064 0.13 -10000 0 -0.31 101 101
GNAZ -0.009 0.082 -10000 0 -0.74 6 6
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.024 0.065 -10000 0 -0.48 6 6
mol:T-DHT 0 0.001 0.001 17 -0.003 38 55
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.007 0.037 -10000 0 -0.57 2 2
Gi family/GTP -0.043 0.085 -10000 0 -0.48 4 4
CDC42 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.27 0.34 -10000 0 -0.83 53 53
PCK1 -0.14 0.21 -10000 0 -0.74 19 19
HNF4A -0.32 0.4 -10000 0 -1 51 51
KCNJ11 -0.28 0.39 -10000 0 -1 39 39
AKT1 -0.002 0.086 -10000 0 -10000 0 0
response to starvation -0.009 0.033 -10000 0 -10000 0 0
DLK1 -0.3 0.38 -10000 0 -0.94 49 49
NKX2-1 -0.79 0.79 -10000 0 -1.5 256 256
ACADM -0.27 0.34 -10000 0 -0.84 50 50
TAT -0.12 0.2 -10000 0 -0.79 8 8
CEBPB 0.003 0.006 -10000 0 -10000 0 0
CEBPA 0.002 0.035 -10000 0 -0.75 1 1
TTR -0.053 0.19 -10000 0 -0.81 14 14
PKLR -0.28 0.34 -10000 0 -0.85 54 54
APOA1 -0.43 0.55 -10000 0 -1.4 79 79
CPT1C -0.27 0.34 -10000 0 -0.83 53 53
ALAS1 -0.12 0.18 -10000 0 -10000 0 0
TFRC -0.17 0.25 -10000 0 -0.92 11 11
FOXF1 0.007 0.24 0.28 6 -0.62 52 58
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.014 0.083 -10000 0 -0.6 8 8
CPT1A -0.27 0.34 -10000 0 -0.83 53 53
HMGCS1 -0.27 0.34 -10000 0 -0.84 50 50
NR3C1 0.017 0.012 -10000 0 -10000 0 0
CPT1B -0.27 0.34 -10000 0 -0.83 54 54
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.007 0.03 -10000 0 -10000 0 0
GCK -0.27 0.34 -10000 0 -0.84 53 53
CREB1 0.007 0.016 -10000 0 -10000 0 0
IGFBP1 -0.12 0.17 -10000 0 -0.69 2 2
PDX1 -0.19 0.24 -10000 0 -0.75 4 4
UCP2 -0.27 0.34 -10000 0 -0.84 47 47
ALDOB -0.27 0.36 -10000 0 -0.9 36 36
AFP 0.018 0.13 -10000 0 -0.76 3 3
BDH1 -0.27 0.34 -10000 0 -0.84 52 52
HADH -0.27 0.36 -10000 0 -0.94 23 23
F2 -0.35 0.42 -10000 0 -1 63 63
HNF1A -0.014 0.083 -10000 0 -0.6 8 8
G6PC 0.009 0.086 -10000 0 -0.73 1 1
SLC2A2 -0.18 0.23 -10000 0 -0.86 2 2
INS -0.009 0.011 -10000 0 -10000 0 0
FOXA1 0.073 0.14 0.3 30 -0.57 11 41
FOXA3 -0.011 0.15 -10000 0 -0.74 17 17
FOXA2 -0.32 0.41 -10000 0 -0.9 75 75
ABCC8 -0.29 0.39 -10000 0 -1 42 42
ALB 0.026 0.12 -10000 0 -0.67 4 4
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.43 -9999 0 -1.2 36 36
HDAC7 -0.007 0.013 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 -9999 0 -0.9 34 34
SMAD4 0 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.43 -9999 0 -1.2 36 36
AP1 -0.066 0.18 -9999 0 -0.56 55 55
ABCG2 -0.24 0.5 -9999 0 -1.3 56 56
HIF1A -0.022 0.07 -9999 0 -10000 0 0
TFF3 -0.23 0.47 -9999 0 -1.3 43 43
GATA2 -0.072 0.23 -9999 0 -0.74 52 52
AKT1 -0.032 0.058 -9999 0 -10000 0 0
response to hypoxia -0.046 0.064 -9999 0 -10000 0 0
MCL1 -0.2 0.43 -9999 0 -1.2 36 36
NDRG1 -0.2 0.43 -9999 0 -1.2 34 34
SERPINE1 -0.2 0.43 -9999 0 -1.2 34 34
FECH -0.2 0.43 -9999 0 -1.2 33 33
FURIN -0.2 0.43 -9999 0 -1.2 36 36
NCOA2 0.007 0.034 -9999 0 -0.74 1 1
EP300 -0.023 0.088 -9999 0 -10000 0 0
HMOX1 -0.2 0.43 -9999 0 -1.2 37 37
BHLHE40 -0.2 0.43 -9999 0 -1.2 36 36
BHLHE41 -0.2 0.44 -9999 0 -1.3 38 38
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.03 0.077 -9999 0 -0.51 4 4
ENG 0.005 0.13 -9999 0 -0.83 6 6
JUN 0.008 0.005 -9999 0 -10000 0 0
RORA -0.2 0.43 -9999 0 -1.2 36 36
ABCB1 -0.2 0.45 -9999 0 -1.4 60 60
TFRC -0.2 0.43 -9999 0 -1.2 36 36
CXCR4 -0.2 0.43 -9999 0 -1.2 36 36
TF -0.22 0.45 -9999 0 -1.2 42 42
CITED2 -0.2 0.44 -9999 0 -1.2 37 37
HIF1A/ARNT -0.24 0.49 -9999 0 -1.4 41 41
LDHA -0.033 0.047 -9999 0 -10000 0 0
ETS1 -0.2 0.45 -9999 0 -1.3 37 37
PGK1 -0.2 0.43 -9999 0 -1.2 37 37
NOS2 -0.24 0.48 -9999 0 -1.2 51 51
ITGB2 -0.21 0.46 -9999 0 -1.3 39 39
ALDOA -0.2 0.43 -9999 0 -1.2 35 35
Cbp/p300/CITED2 -0.24 0.43 -9999 0 -1.2 42 42
FOS -0.077 0.24 -9999 0 -0.74 55 55
HK2 -0.2 0.43 -9999 0 -1.2 37 37
SP1 0.011 0.024 -9999 0 -10000 0 0
GCK -0.029 0.14 -9999 0 -0.73 1 1
HK1 -0.2 0.43 -9999 0 -1.2 34 34
NPM1 -0.2 0.43 -9999 0 -1.2 34 34
EGLN1 -0.2 0.43 -9999 0 -1.2 37 37
CREB1 0.016 0 -9999 0 -10000 0 0
PGM1 -0.2 0.43 -9999 0 -1.2 36 36
SMAD3 0 0.002 -9999 0 -10000 0 0
EDN1 -0.16 0.39 -9999 0 -1.2 47 47
IGFBP1 -0.2 0.44 -9999 0 -1.2 37 37
VEGFA -0.23 0.31 -9999 0 -0.84 31 31
HIF1A/JAB1 -0.017 0.029 -9999 0 -10000 0 0
CP -0.22 0.46 -9999 0 -1.3 37 37
CXCL12 -0.22 0.48 -9999 0 -1.3 44 44
COPS5 0.009 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.004 -9999 0 -10000 0 0
BNIP3 -0.2 0.43 -9999 0 -1.2 33 33
EGLN3 -0.24 0.46 -9999 0 -1.2 47 47
CA9 -0.42 0.47 -9999 0 -1.3 63 63
TERT -0.3 0.48 -9999 0 -1.3 50 50
ENO1 -0.2 0.43 -9999 0 -1.2 34 34
PFKL -0.2 0.43 -9999 0 -1.2 36 36
NCOA1 0 0.001 -9999 0 -10000 0 0
ADM -0.2 0.43 -9999 0 -1.2 38 38
ARNT -0.023 0.069 -9999 0 -10000 0 0
HNF4A 0.002 0.075 -9999 0 -0.57 8 8
ADFP -0.2 0.43 -9999 0 -1.2 40 40
SLC2A1 -0.44 0.35 -9999 0 -0.94 88 88
LEP -0.24 0.47 -9999 0 -1.2 49 49
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -9999 0 -0.92 39 39
EPO -0.08 0.25 -9999 0 -0.83 3 3
CREBBP -0.023 0.088 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.25 0.37 -9999 0 -0.97 47 47
PFKFB3 -0.2 0.43 -9999 0 -1.2 36 36
NT5E -0.2 0.43 -9999 0 -1.2 36 36
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.01 0.058 -9999 0 -0.37 11 11
Syndecan-3/Neurocan -0.02 0.073 -9999 0 -0.28 34 34
POMC -0.054 0.17 -9999 0 -0.58 45 45
EGFR -0.022 0.12 -9999 0 -0.63 17 17
Syndecan-3/EGFR -0.012 0.061 -9999 0 -0.33 17 17
AGRP -0.34 0.37 -9999 0 -0.74 223 223
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.04 0.15 -9999 0 -0.57 34 34
long-term memory -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/IL8 -0.013 0.062 -9999 0 -0.31 20 20
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN -0.002 0.034 -9999 0 -0.74 1 1
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.025 0.12 -9999 0 -0.57 21 21
SRC 0 0 -9999 0 -10000 0 0
PTN -0.02 0.12 -9999 0 -0.7 14 14
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.027 0.081 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.19 0.2 -9999 0 -0.4 223 223
Syndecan-3/AgRP/MC4R -0.19 0.2 -9999 0 -0.4 223 223
Fyn/Cortactin -0.001 0.025 -9999 0 -0.56 1 1
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.013 0.062 -9999 0 -0.3 20 20
IL8 -0.025 0.12 -9999 0 -0.61 20 20
Syndecan-3/Fyn/Cortactin -0.001 0.018 -9999 0 -0.39 1 1
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.057 0.15 -9999 0 -0.42 65 65
Gamma Secretase 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.011 0.037 -9999 0 -0.54 1 1
NFATC2 -0.06 0.18 -9999 0 -0.52 66 66
NFATC3 0.012 0.028 -9999 0 -10000 0 0
CD40LG -0.17 0.38 -9999 0 -0.79 108 108
PTGS2 -0.14 0.34 -9999 0 -0.73 94 94
JUNB -0.002 0.034 -9999 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 -0.001 0.003 -9999 0 -10000 0 0
JUN -0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.002 0.037 -9999 0 -0.57 2 2
CREM 0 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.1 0.18 -9999 0 -0.56 46 46
FOS -0.086 0.24 -9999 0 -0.74 55 55
IFNG -0.11 0.3 -9999 0 -0.64 79 79
AP-1/NFAT1-c-4 -0.21 0.31 -9999 0 -0.76 90 90
FASLG -0.12 0.32 -9999 0 -0.7 77 77
NFAT1-c-4/ICER1 -0.083 0.16 -9999 0 -0.51 46 46
IL2RA -0.11 0.3 -9999 0 -0.77 36 36
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.15 0.34 -9999 0 -0.8 65 65
JunB/Fra1/NFAT1-c-4 -0.08 0.16 -9999 0 -0.49 46 46
IL4 -0.12 0.29 -9999 0 -0.65 69 69
IL2 -0.004 0.014 -9999 0 -10000 0 0
IL3 -0.019 0.023 -9999 0 -10000 0 0
FKBP1A 0 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0 0.003 -9999 0 -10000 0 0
LPA4-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
ADCY4 -0.016 0.13 -9999 0 -0.5 31 31
ADCY5 -0.029 0.15 -9999 0 -0.5 44 44
ADCY6 0.016 0.032 -9999 0 -0.49 2 2
ADCY7 0.017 0.023 -9999 0 -0.49 1 1
ADCY1 0.015 0.04 -9999 0 -0.49 3 3
ADCY2 -0.026 0.13 -9999 0 -0.4 49 49
ADCY3 0.017 0.023 -9999 0 -0.49 1 1
ADCY8 -0.14 0.23 -9999 0 -0.48 153 153
PRKCE 0.009 0.026 -9999 0 -0.57 1 1
ADCY9 0.016 0.032 -9999 0 -0.49 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.069 0.13 -9999 0 -0.44 25 25
Coregulation of Androgen receptor activity

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
NRIP1 0.002 0.004 -9999 0 -10000 0 0
SVIL 0.002 0.004 -9999 0 -10000 0 0
ZNF318 0 0.005 -9999 0 -10000 0 0
JMJD2C -0.004 0.026 -9999 0 -0.082 46 46
T-DHT/AR/Ubc9 -0.13 0.21 -9999 0 -0.53 101 101
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0 0.001 -9999 0 -10000 0 0
PELP1 0 0.001 -9999 0 -10000 0 0
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.001 0.004 -9999 0 -10000 0 0
MED1 0 0.002 -9999 0 -10000 0 0
MAK -0.052 0.19 -9999 0 -0.74 34 34
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.002 0.004 -9999 0 -10000 0 0
GSN 0.002 0.004 -9999 0 -10000 0 0
NCOA2 -0.002 0.034 -9999 0 -0.74 1 1
NCOA6 0.002 0.004 -9999 0 -10000 0 0
DNA-PK 0 0.006 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.093 0.24 -9999 0 -0.94 34 34
XRCC5 0 0.002 -9999 0 -10000 0 0
UBE3A 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.15 0.23 -9999 0 -0.54 111 111
FHL2 -0.055 0.081 -9999 0 -0.55 2 2
RANBP9 0.002 0.004 -9999 0 -10000 0 0
JMJD1A -0.035 0.07 -9999 0 -0.13 157 157
CDK6 -0.002 0.037 -9999 0 -0.57 2 2
TGFB1I1 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.14 0.22 -9999 0 -0.53 106 106
XRCC6 0 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.24 -9999 0 -0.56 102 102
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0.004 -9999 0 -10000 0 0
BRCA1 0.002 0.004 -9999 0 -10000 0 0
TCF4 -0.001 0.034 -9999 0 -0.74 1 1
CDKN2A -0.27 0.29 -9999 0 -0.57 224 224
SRF 0.016 0.007 -9999 0 -10000 0 0
NKX3-1 -0.11 0.14 -9999 0 -0.95 2 2
KLK3 0.028 0.051 -9999 0 -10000 0 0
TMF1 0 0.001 -9999 0 -10000 0 0
HNRNPA1 0 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.13 0.21 -9999 0 -0.53 101 101
AR -0.17 0.31 -9999 0 -0.77 101 101
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0 0.002 -9999 0 -10000 0 0
PAWR 0 0.001 -9999 0 -10000 0 0
PRKDC 0 0.002 -9999 0 -10000 0 0
PA2G4 0 0.003 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.12 0.19 -9999 0 -0.48 101 101
RPS6KA3 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.21 -9999 0 -0.53 101 101
LATS2 -0.001 0.034 -9999 0 -0.74 1 1
T-DHT/AR/PRX1 -0.12 0.19 -9999 0 -0.48 101 101
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0 0.034 -9999 0 -0.74 1 1
KLK2 -0.095 0.14 -9999 0 -0.5 28 28
CASP8 0 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.48 102 102
TMPRSS2 -0.4 0.54 -9999 0 -1.2 156 156
CCND1 -0.01 0.086 -9999 0 -0.72 7 7
PIAS1 0.001 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.019 0.036 -9999 0 -0.078 115 115
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.001 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.52 103 103
CMTM2 -0.097 0.25 -9999 0 -0.74 63 63
SNURF -0.023 0.13 -9999 0 -0.74 15 15
ZMIZ1 -0.008 0.048 -9999 0 -0.8 1 1
CCND3 0 0.001 -9999 0 -10000 0 0
TGIF1 0 0.002 -9999 0 -10000 0 0
FKBP4 0 0.026 -9999 0 -0.57 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.003 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.13 0.28 -10000 0 -0.74 86 86
TLE1 0.002 0.031 -10000 0 -0.61 1 1
MACF1 0.004 0.048 -10000 0 -0.74 2 2
CTNNB1 0.067 0.099 0.29 10 -10000 0 10
WIF1 -0.47 0.36 -10000 0 -0.74 306 306
beta catenin/RanBP3 0.003 0.092 0.4 20 -10000 0 20
KREMEN2 -0.37 0.27 -10000 0 -0.57 314 314
DKK1 -0.039 0.15 -10000 0 -0.62 30 30
beta catenin/beta TrCP1 0.069 0.093 0.28 10 -10000 0 10
FZD1 0.001 0.003 -10000 0 -10000 0 0
AXIN2 -0.038 0.28 -10000 0 -1.5 17 17
AXIN1 0.008 0.005 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.052 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.02 0.063 0.24 29 -10000 0 29
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.041 -10000 0 -10000 0 0
HNF1A -0.006 0.076 -10000 0 -0.58 8 8
CTBP1 0.004 0.018 -10000 0 -10000 0 0
MYC 0.007 0.049 -10000 0 -10000 0 0
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.3 0.25 -10000 0 -0.72 86 86
NKD1 -0.071 0.22 -10000 0 -0.73 47 47
TCF4 0.002 0.038 -10000 0 -0.74 1 1
TCF3 0.004 0.018 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.019 -10000 0 -10000 0 0
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.018 0.097 0.45 22 -10000 0 22
LEF1 0.002 0.031 -10000 0 -0.58 1 1
DVL1 0.08 0.061 -10000 0 -10000 0 0
CSNK2A1 0.001 0.003 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.068 -10000 0 -0.56 1 1
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.67 24 24
LRP6 0.001 0.004 -10000 0 -10000 0 0
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.009 0.18 -10000 0 -1.5 6 6
WNT1 0.004 0.037 -10000 0 -0.57 2 2
GSK3A 0.007 0.005 -10000 0 -10000 0 0
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.001 0.034 -10000 0 -0.74 1 1
PPP2R5D 0.076 0.1 0.37 47 -10000 0 47
APC 0 0.019 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.16 0.12 0.26 304 -10000 0 304
CREBBP 0.004 0.018 -10000 0 -10000 0 0
IL23-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
CCL2 -0.13 0.44 -10000 0 -1.2 44 44
IL23A -0.14 0.43 -10000 0 -1.2 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.36 -10000 0 -1.1 47 47
positive regulation of T cell mediated cytotoxicity -0.14 0.46 -10000 0 -1.2 47 47
ITGA3 -0.13 0.42 -10000 0 -1.2 41 41
IL17F -0.063 0.28 -10000 0 -0.74 29 29
IL12B 0.016 0.025 -10000 0 -10000 0 0
STAT1 (dimer) -0.21 0.38 -10000 0 -1.2 47 47
CD4 -0.13 0.43 -10000 0 -1.2 39 39
IL23 -0.14 0.41 -10000 0 -1.1 38 38
IL23R 0.003 0.085 -10000 0 -10000 0 0
IL1B -0.14 0.44 -10000 0 -1.2 39 39
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.13 0.4 -10000 0 -1.1 35 35
TYK2 0.011 0.019 -10000 0 -10000 0 0
STAT4 -0.012 0.095 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.027 0.16 -10000 0 -0.74 22 22
IL12RB1 -0.038 0.19 -10000 0 -0.77 31 31
PIK3CA 0 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.027 0.15 -10000 0 -0.59 31 31
IL23R/JAK2 0.003 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.14 0.46 -10000 0 -1.2 47 47
natural killer cell activation 0 0.007 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
NFKB1 0.004 0.006 -10000 0 -10000 0 0
RELA 0.004 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.39 -10000 0 -1.1 38 38
ALOX12B -0.17 0.42 -10000 0 -1.2 38 38
CXCL1 -0.14 0.46 -10000 0 -1.3 45 45
T cell proliferation -0.14 0.46 -10000 0 -1.2 47 47
NFKBIA 0.004 0.006 -10000 0 -10000 0 0
IL17A -0.042 0.24 -10000 0 -0.59 21 21
PI3K -0.21 0.36 -10000 0 -1.1 47 47
IFNG -0.001 0.029 0.098 1 -0.13 8 9
STAT3 (dimer) -0.2 0.34 -10000 0 -1 47 47
IL18R1 -0.001 0.076 -10000 0 -0.74 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.061 0.28 -10000 0 -0.83 23 23
IL18/IL18R -0.029 0.13 -10000 0 -0.56 25 25
macrophage activation -0.012 0.017 -10000 0 -0.044 37 37
TNF -0.14 0.45 -10000 0 -1.2 47 47
STAT3/STAT4 -0.21 0.37 -10000 0 -1.1 48 48
STAT4 (dimer) -0.22 0.39 -10000 0 -1.2 48 48
IL18 0.002 0.059 -10000 0 -0.74 3 3
IL19 -0.13 0.4 -10000 0 -1.1 37 37
STAT5A (dimer) -0.21 0.38 -10000 0 -1.2 47 47
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.003 0.048 -10000 0 -0.74 2 2
CXCL9 -0.13 0.43 -10000 0 -1.2 40 40
MPO -0.15 0.45 -10000 0 -1.2 50 50
positive regulation of humoral immune response -0.14 0.46 -10000 0 -1.2 47 47
IL23/IL23R/JAK2/TYK2 -0.16 0.52 -10000 0 -1.4 47 47
IL6 -0.24 0.58 -10000 0 -1.3 95 95
STAT5A 0 0 -10000 0 -10000 0 0
IL2 0.006 0.008 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.007 -10000 0 -10000 0 0
CD3E -0.12 0.42 -10000 0 -1.2 32 32
keratinocyte proliferation -0.14 0.46 -10000 0 -1.2 47 47
NOS2 -0.17 0.48 -10000 0 -1.2 62 62
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.008 0.056 -9999 0 -0.41 9 9
VLDLR -0.003 0.048 -9999 0 -0.74 2 2
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.002 0.034 -9999 0 -0.74 1 1
ITGA3 -0.008 0.075 -9999 0 -0.74 5 5
RELN/VLDLR/Fyn -0.086 0.19 -9999 0 -0.48 86 86
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.001 0.022 -9999 0 -0.4 1 1
AKT1 -0.055 0.12 -9999 0 -0.52 2 2
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.57 30 30
RELN/LRP8/DAB1 -0.099 0.18 -9999 0 -0.41 115 115
LRPAP1/LRP8 -0.003 0.032 -9999 0 -0.41 3 3
RELN/LRP8/DAB1/Fyn -0.093 0.17 -9999 0 -0.43 84 84
DAB1/alpha3/beta1 Integrin -0.087 0.16 -9999 0 -0.69 5 5
long-term memory -0.12 0.19 -9999 0 -0.45 82 82
DAB1/LIS1 -0.086 0.16 -9999 0 -0.63 4 4
DAB1/CRLK/C3G -0.083 0.15 -9999 0 -0.61 4 4
PIK3CA 0 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.087 0.16 -9999 0 -0.64 4 4
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.065 0.2 -9999 0 -0.66 48 48
CDK5R1 -0.011 0.077 -9999 0 -0.57 9 9
RELN -0.13 0.28 -9999 0 -0.74 85 85
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.087 0.18 -9999 0 -0.48 88 88
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.2 -9999 0 -0.46 101 101
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.099 0.18 -9999 0 -0.46 85 85
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.093 0.17 -9999 0 -0.42 86 86
RELN/LRP8 -0.086 0.18 -9999 0 -0.47 88 88
GRIN2B/RELN/LRP8/DAB1/Fyn -0.094 0.17 -9999 0 -0.43 85 85
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.006 0.057 -9999 0 -0.56 5 5
RAP1A -0.077 0.14 -9999 0 -0.57 4 4
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.003 0.043 -9999 0 -0.66 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.005 0.052 -9999 0 -0.57 4 4
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.014 0.096 -9999 0 -0.43 2 2
neuron adhesion -0.075 0.14 -9999 0 -0.64 4 4
LRP8 -0.004 0.045 -9999 0 -0.57 3 3
GSK3B -0.027 0.12 -9999 0 -0.48 2 2
RELN/VLDLR/DAB1/Fyn -0.093 0.17 -9999 0 -0.43 85 85
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.065 0.12 -9999 0 -0.32 85 85
CDK5 0 0 -9999 0 -10000 0 0
MAPT 0.003 0.085 -9999 0 -0.67 7 7
neuron migration -0.031 0.17 -9999 0 -0.56 4 4
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.081 -9999 0 -0.44 2 2
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 83 83
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.25 -10000 0 -0.73 13 13
CRP -0.15 0.25 -10000 0 -0.73 15 15
cell cycle arrest -0.17 0.28 -10000 0 -0.65 54 54
TIMP1 -0.11 0.21 -10000 0 -0.6 10 10
IL6ST -0.016 0.13 -10000 0 -0.74 16 16
Rac1/GDP -0.066 0.19 -10000 0 -0.69 19 19
AP1 -0.003 0.15 -10000 0 -0.5 12 12
GAB2 -0.002 0.12 -10000 0 -0.74 12 12
TNFSF11 -0.16 0.26 -10000 0 -0.67 33 33
HSP90B1 -0.001 0.05 -10000 0 -10000 0 0
GAB1 0.013 0.009 -10000 0 -10000 0 0
MAPK14 -0.03 0.17 -10000 0 -0.73 15 15
AKT1 0.043 0.054 -10000 0 -10000 0 0
FOXO1 0.049 0.05 -10000 0 -10000 0 0
MAP2K6 -0.053 0.18 -10000 0 -0.73 16 16
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.076 0.2 -10000 0 -0.69 18 18
MITF -0.07 0.19 -10000 0 -0.48 62 62
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0 0 -10000 0 -10000 0 0
A2M -0.46 0.69 -10000 0 -1.5 157 157
CEBPB 0.016 0.004 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.03 0.11 0.23 4 -0.53 5 9
STAT3 -0.18 0.29 -10000 0 -0.69 54 54
STAT1 -0.008 0.016 -10000 0 -10000 0 0
CEBPD -0.14 0.25 -10000 0 -0.8 13 13
PIK3CA 0.01 0.003 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
JUN 0 0 -10000 0 -10000 0 0
PIAS3/MITF -0.087 0.17 -10000 0 -0.63 24 24
MAPK11 -0.03 0.17 -10000 0 -0.73 15 15
STAT3 (dimer)/FOXO1 -0.19 0.31 -10000 0 -0.75 56 56
GRB2/SOS1/GAB family -0.031 0.17 -10000 0 -0.64 18 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.052 0.19 -10000 0 -0.45 61 61
GRB2 0.013 0.009 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
LBP -0.11 0.21 -10000 0 -0.64 6 6
PIK3R1 0.008 0.005 -10000 0 -10000 0 0
JAK1 0.01 0.005 -10000 0 -10000 0 0
MYC -0.14 0.25 -10000 0 -0.73 13 13
FGG -0.48 0.57 -10000 0 -1.1 226 226
macrophage differentiation -0.17 0.28 -10000 0 -0.65 54 54
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.2 -10000 0 -0.52 64 64
JUNB -0.14 0.24 -10000 0 -0.72 14 14
FOS -0.084 0.24 -10000 0 -0.74 55 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.19 -10000 0 -0.48 60 60
STAT1/PIAS1 -0.086 0.17 -10000 0 -0.47 54 54
GRB2/SOS1/GAB family/SHP2/PI3K 0.014 0.057 -10000 0 -10000 0 0
STAT3 (dimer) -0.18 0.28 -10000 0 -0.68 54 54
PRKCD -0.091 0.22 -10000 0 -0.76 14 14
IL6R -0.008 0.12 -10000 0 -0.74 12 12
SOCS3 -0.016 0.17 -10000 0 -0.86 9 9
gp130 (dimer)/JAK1/JAK1/LMO4 -0.01 0.089 -10000 0 -0.47 17 17
Rac1/GTP -0.11 0.17 -10000 0 -0.5 51 51
HCK -0.003 0.076 -10000 0 -0.74 5 5
MAPKKK cascade 0.045 0.12 -10000 0 -0.53 12 12
bone resorption -0.15 0.25 -10000 0 -0.63 34 34
IRF1 -0.14 0.25 -10000 0 -0.73 13 13
mol:GDP -0.068 0.19 -10000 0 -0.48 57 57
SOS1 0.01 0.015 -10000 0 -10000 0 0
VAV1 -0.07 0.2 -10000 0 -0.49 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.047 0.19 -10000 0 -0.76 18 18
PTPN11 -0.006 0.013 -10000 0 -10000 0 0
IL6/IL6RA -0.1 0.24 -10000 0 -0.6 87 87
gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.088 -10000 0 -0.47 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.088 -10000 0 -0.47 17 17
IL6 -0.12 0.28 -10000 0 -0.74 82 82
PIAS3 0 0 -10000 0 -10000 0 0
PTPRE 0.01 0.05 -10000 0 -0.74 2 2
PIAS1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.077 0.18 -10000 0 -0.42 75 75
LMO4 0.007 0.029 -10000 0 -0.59 1 1
STAT3 (dimer)/PIAS3 -0.21 0.22 -10000 0 -0.66 54 54
MCL1 0.05 0.048 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.001 0.094 -10000 0 -0.58 12 12
NFATC2 -0.055 0.3 -10000 0 -0.74 68 68
NFATC3 0.013 0.054 -10000 0 -10000 0 0
CD40LG -0.18 0.45 -10000 0 -1.1 70 70
ITCH -0.008 0.11 -10000 0 -10000 0 0
CBLB -0.008 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.28 -10000 0 -1.1 27 27
JUNB -0.002 0.034 -10000 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.053 0.12 -10000 0 -10000 0 0
T cell anergy -0.06 0.18 -10000 0 -0.45 77 77
TLE4 -0.022 0.24 -10000 0 -0.81 22 22
Jun/NFAT1-c-4/p21SNFT -0.12 0.27 -10000 0 -1 26 26
AP-1/NFAT1-c-4 -0.23 0.39 -10000 0 -1.2 43 43
IKZF1 -0.032 0.28 -10000 0 -1 21 21
T-helper 2 cell differentiation -0.045 0.28 -10000 0 -0.81 43 43
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.65 55 55
CALM1 -0.028 0.064 -10000 0 -10000 0 0
EGR2 -0.018 0.31 -10000 0 -1.2 19 19
EGR3 -0.02 0.31 -10000 0 -1.2 21 21
NFAT1/FOXP3 -0.091 0.21 -10000 0 -0.74 24 24
EGR1 -0.006 0.1 -10000 0 -0.74 9 9
JUN 0.002 0.022 -10000 0 -10000 0 0
EGR4 -0.005 0.087 -10000 0 -0.57 11 11
mol:Ca2+ -0.032 0.073 -10000 0 -10000 0 0
GBP3 -0.041 0.28 -10000 0 -0.9 32 32
FOSL1 -0.002 0.037 -10000 0 -0.57 2 2
NFAT1-c-4/MAF/IRF4 -0.098 0.26 -10000 0 -0.97 28 28
DGKA -0.019 0.23 -10000 0 -0.81 18 18
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.15 0.3 -10000 0 -0.96 37 37
CTLA4 -0.018 0.21 -10000 0 -0.79 15 15
NFAT1-c-4 (dimer)/EGR1 -0.11 0.28 -10000 0 -1 28 28
NFAT1-c-4 (dimer)/EGR4 -0.11 0.27 -10000 0 -0.96 29 29
FOS -0.083 0.24 -10000 0 -0.75 55 55
IFNG -0.16 0.35 -10000 0 -1 52 52
T cell activation -0.04 0.24 -10000 0 -0.78 21 21
MAF 0 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.19 0.77 15 -10000 0 15
TNF -0.038 0.3 -10000 0 -0.95 31 31
FASLG -0.087 0.45 -10000 0 -1.5 38 38
TBX21 -0.064 0.23 -10000 0 -0.74 50 50
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.06 0.22 -10000 0 -0.75 45 45
PTPN1 -0.019 0.23 -10000 0 -0.81 18 18
NFAT1-c-4/ICER1 -0.1 0.26 -10000 0 -0.97 28 28
GATA3 -0.024 0.13 -10000 0 -0.71 17 17
T-helper 1 cell differentiation -0.16 0.34 -10000 0 -0.98 53 53
IL2RA -0.15 0.28 -10000 0 -0.9 40 40
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.019 0.23 -10000 0 -0.78 20 20
E2F1 0.015 0.004 -10000 0 -10000 0 0
PPARG -0.089 0.24 -10000 0 -0.74 58 58
SLC3A2 -0.019 0.23 -10000 0 -0.77 21 21
IRF4 -0.009 0.082 -10000 0 -0.74 6 6
PTGS2 -0.15 0.42 -10000 0 -1 60 60
CSF2 -0.15 0.42 -10000 0 -1.1 53 53
JunB/Fra1/NFAT1-c-4 -0.096 0.25 -10000 0 -0.91 29 29
IL4 -0.049 0.3 -10000 0 -0.85 43 43
IL5 -0.12 0.36 -10000 0 -1 41 41
IL2 -0.041 0.24 -10000 0 -0.8 21 21
IL3 -0.037 0.049 -10000 0 -10000 0 0
RNF128 -0.096 0.31 -10000 0 -0.8 77 77
NFATC1 0.003 0.19 -10000 0 -0.78 15 15
CDK4 0.007 0.16 0.62 8 -10000 0 8
PTPRK -0.019 0.23 -10000 0 -0.86 15 15
IL8 -0.12 0.38 -10000 0 -1 45 45
POU2F1 0 0.003 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.005 -10000 0 -10000 0 0
AES 0 0.002 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.002 0.037 -10000 0 -0.57 2 2
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 -0.001 0.033 -10000 0 -0.73 1 1
AP1 -0.076 0.18 -10000 0 -0.42 86 86
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.001 0.042 -10000 0 -0.56 1 1
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.47 0.36 -10000 0 -0.74 306 306
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 -0.37 0.27 -10000 0 -0.57 314 314
DKK1 -0.039 0.15 -10000 0 -0.62 30 30
beta catenin/beta TrCP1 0.007 0.06 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.026 0.3 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES -0.001 0.027 -10000 0 -10000 0 0
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.085 0.24 -10000 0 -0.74 55 55
JUN 0 0 -10000 0 -10000 0 0
MAP3K7 0 0.003 -10000 0 -10000 0 0
CTNNB1 0.01 0.065 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.3 0.25 -10000 0 -0.72 86 86
HNF1A -0.009 0.073 -10000 0 -0.57 8 8
CTBP1 0 0.002 -10000 0 -10000 0 0
MYC 0.002 0.012 -10000 0 -10000 0 0
NKD1 -0.071 0.22 -10000 0 -0.73 47 47
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
apoptosis -0.076 0.18 -10000 0 -0.42 86 86
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.002 0.012 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.026 0.3 1 -10000 0 1
DVL1 -0.045 0.044 -10000 0 -0.67 1 1
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 24 24
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.001 0.006 -10000 0 -10000 0 0
CCND1 -0.016 0.16 -10000 0 -1.4 6 6
WNT1 -0.002 0.037 -10000 0 -0.57 2 2
Axin1/APC/beta catenin 0.01 0.045 0.27 1 -0.36 1 2
DKK2 -0.13 0.28 -10000 0 -0.74 86 86
NOTCH1 precursor/DVL1 -0.022 0.029 -10000 0 -0.55 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.001 0.034 -10000 0 -0.74 1 1
NOTCH/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
PPP2R5D 0.01 0.1 0.31 47 -0.25 1 48
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.28 0.21 -10000 0 -0.44 305 305
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.054 -9999 0 -0.42 8 8
Metarhodopsin II/Arrestin -0.001 0.023 -9999 0 -0.36 2 2
PDE6G/GNAT1/GTP -0.015 0.079 -9999 0 -0.42 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.009 0.073 -9999 0 -0.57 8 8
GRK1 -0.002 0.037 -9999 0 -0.57 2 2
CNG Channel -0.055 0.13 -9999 0 -0.58 6 6
mol:Na + -0.094 0.15 -9999 0 -0.52 22 22
mol:ADP -0.002 0.037 -9999 0 -0.57 2 2
RGS9-1/Gbeta5/R9AP -0.062 0.17 -9999 0 -0.49 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.096 0.15 -9999 0 -0.54 22 22
CNGB1 -0.051 0.16 -9999 0 -0.57 43 43
RDH5 -0.003 0.048 -9999 0 -0.74 2 2
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.089 0.14 -9999 0 -0.5 22 22
Na + (4 Units) -0.087 0.14 -9999 0 -0.49 22 22
RGS9 -0.081 0.23 -9999 0 -0.74 53 53
GNB1/GNGT1 -0.13 0.19 -9999 0 -0.41 150 150
GNAT1/GDP -0.059 0.15 -9999 0 -0.43 61 61
GUCY2D 0 0 -9999 0 -10000 0 0
GNGT1 -0.18 0.26 -9999 0 -0.57 149 149
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.031 0.11 -9999 0 -0.42 30 30
mol:11-cis-retinal -0.003 0.048 -9999 0 -0.74 2 2
mol:cGMP -0.078 0.13 -9999 0 -10000 0 0
GNB1 -0.002 0.034 -9999 0 -0.74 1 1
Rhodopsin -0.004 0.045 -9999 0 -0.49 4 4
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.007 0.063 -9999 0 -0.57 6 6
Metarhodopsin II -0.003 0.029 -9999 0 -0.32 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.084 0.14 -9999 0 -10000 0 0
RGS9BP -0.015 0.11 -9999 0 -0.74 10 10
Metarhodopsin II/Transducin -0.052 0.076 -9999 0 -0.37 2 2
GCAP Family/Ca ++ -0.086 0.14 -9999 0 -0.32 129 129
PDE6A/B -0.026 0.12 -9999 0 -0.54 23 23
mol:Pi -0.062 0.16 -9999 0 -0.49 61 61
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.15 -9999 0 -0.32 156 156
PDE6B -0.013 0.098 -9999 0 -0.72 9 9
PDE6A -0.021 0.12 -9999 0 -0.72 14 14
PDE6G -0.014 0.1 -9999 0 -0.74 9 9
RHO -0.002 0.037 -9999 0 -0.57 2 2
PDE6 -0.075 0.17 -9999 0 -0.8 10 10
GUCA1A -0.15 0.25 -9999 0 -0.57 129 129
GC2/GCAP Family -0.085 0.14 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0 0 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.079 0.11 -10000 0 -0.51 17 17
epithelial cell differentiation -0.035 0.1 -10000 0 -0.54 10 10
ITCH 0.023 0.027 -10000 0 -10000 0 0
WWP1 -0.039 0.088 -10000 0 -10000 0 0
FYN -0.002 0.034 -10000 0 -0.74 1 1
EGFR -0.022 0.12 -10000 0 -0.63 17 17
PRL -0.009 0.073 -10000 0 -0.57 8 8
neuron projection morphogenesis 0.002 0.087 -10000 0 -10000 0 0
PTPRZ1 -0.38 0.27 -10000 0 -0.57 323 323
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.042 0.074 -10000 0 -0.48 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.056 0.094 -10000 0 -0.49 13 13
ADAM17 0.023 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.058 0.11 -10000 0 -0.49 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.18 0.22 -10000 0 -0.54 123 123
NCOR1 0 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.052 0.089 -10000 0 -0.48 14 14
GRIN2B -0.027 0.1 -10000 0 -0.53 7 7
ErbB4/ErbB2/betacellulin -0.073 0.13 -10000 0 -0.51 26 26
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.025 0.13 -10000 0 -0.74 16 16
PRLR -0.039 0.15 -10000 0 -0.63 30 30
E4ICDs/ETO2 -0.072 0.1 -10000 0 -0.6 8 8
axon guidance 0.054 0.072 -10000 0 -10000 0 0
NEDD4 0.021 0.043 -10000 0 -0.71 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.036 0.13 -10000 0 -0.46 37 37
CBFA2T3 -0.012 0.095 -10000 0 -0.74 8 8
ErbB4/ErbB2/HBEGF -0.055 0.09 -10000 0 -0.45 16 16
MAPK3 -0.037 0.069 -10000 0 -10000 0 0
STAT1 (dimer) -0.064 0.079 -10000 0 -0.43 1 1
MAPK1 -0.037 0.069 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.052 0.086 -10000 0 -0.46 13 13
NRG1 0.015 0.097 -10000 0 -0.56 13 13
NRG3 -0.19 0.32 -10000 0 -0.74 122 122
NRG2 -0.078 0.23 -10000 0 -0.74 51 51
NRG4 -0.07 0.19 -10000 0 -0.57 59 59
heart development 0.054 0.072 -10000 0 -10000 0 0
neural crest cell migration -0.052 0.085 -10000 0 -0.46 13 13
ERBB2 0.029 0.032 -10000 0 -0.42 2 2
WWOX/E4ICDs -0.064 0.08 -10000 0 -0.43 1 1
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.1 0.14 -10000 0 -0.47 35 35
apoptosis 0.2 0.26 0.57 123 -10000 0 123
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.17 -10000 0 -0.54 51 51
ErbB4/ErbB2/epiregulin -0.13 0.18 -10000 0 -0.47 96 96
ErbB4/ErbB4/betacellulin/betacellulin -0.099 0.15 -10000 0 -0.55 37 37
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.084 0.13 -10000 0 -0.55 22 22
MDM2 -0.043 0.098 -10000 0 -0.43 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.04 0.079 -10000 0 -0.46 13 13
STAT5A 0.057 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.063 0.12 -10000 0 -0.6 13 13
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.059 0.073 -10000 0 -0.4 1 1
STAT5A (dimer) -0.037 0.11 -10000 0 -0.59 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.045 0.067 -10000 0 -10000 0 0
LRIG1 -0.002 0.034 -10000 0 -0.74 1 1
EREG -0.15 0.29 -10000 0 -0.72 102 102
BTC -0.057 0.2 -10000 0 -0.74 37 37
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.054 0.072 -10000 0 -10000 0 0
ERBB4 -0.078 0.097 -10000 0 -0.49 1 1
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 -0.02 0.025 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.077 0.12 -10000 0 -0.42 29 29
glial cell differentiation 0.058 0.072 0.4 1 -10000 0 1
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.02 0.15 -10000 0 -0.6 12 12
Aurora A signaling

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
Aurora A/GADD45A 0.016 0.039 -9999 0 -10000 0 0
BIRC5 -0.49 0.2 -9999 0 -0.57 410 410
NFKBIA 0.018 0.04 -9999 0 -10000 0 0
CPEB1 -0.048 0.18 -9999 0 -0.74 31 31
AKT1 0.018 0.04 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.014 0.035 -9999 0 -10000 0 0
NDEL1/TACC3 0.018 0.039 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.013 0.006 -9999 0 -10000 0 0
PAK1/Aurora A 0.015 0.043 -9999 0 -0.34 1 1
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.28 0.2 -9999 0 -0.41 337 337
TP53 0.019 0.027 -9999 0 -10000 0 0
DLG7 0.01 0.039 -9999 0 -10000 0 0
AURKAIP1 0 0 -9999 0 -10000 0 0
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.019 0.041 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.035 -9999 0 -10000 0 0
AURKA 0.017 0.049 -9999 0 -10000 0 0
AURKB -0.086 0.049 -9999 0 -0.16 20 20
CDC25B 0.02 0.034 -9999 0 -10000 0 0
G2/M transition checkpoint 0.014 0.035 -9999 0 -10000 0 0
mRNA polyadenylation -0.016 0.12 -9999 0 -0.44 31 31
Aurora A/CPEB -0.016 0.12 -9999 0 -0.44 31 31
Aurora A/TACC1/TRAP/chTOG 0.023 0.044 -9999 0 -0.4 2 2
BRCA1 0 0 -9999 0 -10000 0 0
centrosome duplication 0.015 0.043 -9999 0 -0.34 1 1
regulation of centrosome cycle 0.017 0.038 -9999 0 -10000 0 0
spindle assembly 0.015 0.043 -9999 0 -0.4 2 2
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.24 0.1 -9999 0 -0.41 21 21
CENPA -0.074 0.041 -9999 0 -0.17 20 20
Aurora A/PP2A 0.016 0.039 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.029 0.03 -9999 0 -10000 0 0
negative regulation of DNA binding 0.019 0.027 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.014 0.035 -9999 0 -10000 0 0
mitotic prometaphase 0.025 0.017 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.049 -9999 0 -10000 0 0
TACC1 -0.003 0.048 -9999 0 -0.74 2 2
TACC3 -0.002 0.037 -9999 0 -0.57 2 2
Aurora A/Antizyme1 0.02 0.036 -9999 0 -10000 0 0
Aurora A/RasGAP 0.016 0.039 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.006 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.016 -9999 0 -0.34 1 1
Importin alpha/Importin beta/TPX2 -0.28 0.2 -9999 0 -0.41 337 337
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.21 0.16 -9999 0 -0.46 21 21
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
CKAP5 0 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.009 0.071 -9999 0 -0.56 8 8
AKT1 -0.01 0.2 -9999 0 -0.65 25 25
PTK2B -0.097 0.23 -9999 0 -0.88 27 27
VEGFR2 homodimer/Frs2 -0.11 0.26 -9999 0 -0.6 91 91
CAV1 -0.21 0.33 -9999 0 -0.74 135 135
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.1 0.24 -9999 0 -0.92 25 25
endothelial cell proliferation -0.007 0.2 -9999 0 -0.61 28 28
mol:Ca2+ -0.053 0.24 -9999 0 -0.84 25 25
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.098 0.23 -9999 0 -0.88 25 25
RP11-342D11.1 -0.059 0.24 -9999 0 -0.84 25 25
CDH5 -0.15 0.3 -9999 0 -0.74 95 95
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.003 0.048 -9999 0 -0.74 2 2
HRAS/GDP -0.079 0.18 -9999 0 -0.71 25 25
SH2D2A -0.002 0.034 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.075 0.17 -9999 0 -0.66 26 26
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.1 0.24 -9999 0 -0.9 26 26
VEGFR1 homodimer 0 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.088 0.21 -9999 0 -0.81 25 25
GRB10 -0.052 0.24 -9999 0 -0.83 25 25
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.17 0.31 -9999 0 -0.94 53 53
HRAS 0 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.055 0.12 -9999 0 -0.45 27 27
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.096 0.22 -9999 0 -0.86 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.035 0.16 -9999 0 -0.74 23 23
Nck/Pak -0.001 0.019 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.1 0.24 -9999 0 -0.94 25 25
mol:GDP -0.085 0.2 -9999 0 -0.77 25 25
mol:NADP -0.008 0.17 -9999 0 -0.54 27 27
eNOS/Hsp90 -0.003 0.16 -9999 0 -0.5 26 26
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.054 0.24 -9999 0 -0.85 25 25
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFC -0.003 0.048 -9999 0 -0.74 2 2
FAK1/Vinculin -0.042 0.24 -9999 0 -0.84 27 27
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.1 0.25 -9999 0 -0.94 27 27
PTPN6 0 0 -9999 0 -10000 0 0
EPAS1 -0.13 0.29 -9999 0 -0.71 91 91
mol:L-citrulline -0.008 0.17 -9999 0 -0.54 27 27
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.098 0.23 -9999 0 -0.88 25 25
VEGFR2 homodimer/VEGFA homodimer -0.1 0.24 -9999 0 -0.93 25 25
VEGFR2/3 heterodimer -0.14 0.29 -9999 0 -0.63 103 103
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 -0.051 0.24 -9999 0 -0.87 25 25
VEGFR2 homodimer -0.1 0.3 -9999 0 -0.69 91 91
FLT1 0 0 -9999 0 -10000 0 0
NEDD4 -0.002 0.034 -9999 0 -0.74 1 1
MAPK3 -0.046 0.23 -9999 0 -0.76 28 28
MAPK1 -0.046 0.23 -9999 0 -0.76 28 28
VEGFA145/NRP2 -0.005 0.051 -9999 0 -0.56 4 4
VEGFR1/2 heterodimer -0.11 0.26 -9999 0 -0.6 91 91
KDR -0.1 0.3 -9999 0 -0.69 91 91
VEGFA165/NRP1/VEGFR2 homodimer -0.097 0.23 -9999 0 -0.9 25 25
SRC 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.046 0.23 -9999 0 -0.78 28 28
PI3K -0.088 0.21 -9999 0 -0.82 25 25
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.1 0.24 -9999 0 -0.92 25 25
FES -0.056 0.25 -9999 0 -0.88 25 25
GAB1 -0.092 0.22 -9999 0 -0.84 25 25
VEGFR2 homodimer/VEGFA homodimer/Src -0.1 0.24 -9999 0 -0.92 25 25
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.097 0.23 -9999 0 -0.57 59 59
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.24 -9999 0 -0.92 25 25
PI3K/GAB1 -0.012 0.2 -9999 0 -0.67 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.094 0.22 -9999 0 -0.85 25 25
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.28 -9999 0 -1.1 28 28
HSP90AA1 0 0 -9999 0 -10000 0 0
CDC42 -0.055 0.24 -9999 0 -0.87 25 25
actin cytoskeleton reorganization -0.1 0.24 -9999 0 -0.89 26 26
PTK2 -0.053 0.27 -9999 0 -0.94 27 27
EDG1 -0.059 0.24 -9999 0 -0.84 25 25
mol:DAG -0.054 0.24 -9999 0 -0.85 25 25
CaM/Ca2+ -0.086 0.2 -9999 0 -0.78 25 25
MAP2K3 -0.044 0.23 -9999 0 -0.82 25 25
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.098 0.23 -9999 0 -0.89 25 25
PLCG1 -0.055 0.24 -9999 0 -0.87 25 25
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.098 0.23 -9999 0 -0.88 25 25
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.1 0.24 -9999 0 -0.92 25 25
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.1 0.24 -9999 0 -0.55 91 91
cell migration -0.039 0.23 -9999 0 -0.75 27 27
mol:PI-3-4-5-P3 -0.081 0.19 -9999 0 -0.73 25 25
FYN -0.002 0.034 -9999 0 -0.74 1 1
VEGFB/NRP1 -0.089 0.21 -9999 0 -0.79 25 25
mol:NO -0.008 0.17 -9999 0 -0.54 27 27
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.079 0.18 -9999 0 -0.71 25 25
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.098 0.23 -9999 0 -0.89 25 25
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.095 -9999 0 -0.74 8 8
NOS3 -0.015 0.19 -9999 0 -0.62 27 27
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.24 -9999 0 -0.93 26 26
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.043 0.23 -9999 0 -0.8 26 26
PRKCB -0.062 0.25 -9999 0 -0.88 27 27
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.095 0.22 -9999 0 -0.84 25 25
VEGFR1/2 heterodimer/VEGFA homodimer -0.1 0.24 -9999 0 -0.92 25 25
VEGFA165/NRP2 -0.005 0.051 -9999 0 -0.56 4 4
MAPKKK cascade -0.078 0.18 -9999 0 -0.71 25 25
NRP2 -0.006 0.067 -9999 0 -0.74 4 4
VEGFC homodimer -0.003 0.048 -9999 0 -0.74 2 2
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.042 0.24 -9999 0 -0.84 27 27
MAP3K13 -0.055 0.24 -9999 0 -0.87 25 25
PDPK1 -0.013 0.19 -9999 0 -0.62 25 25
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.044 0.085 -9999 0 -0.31 24 24
FZD6 0 0 -9999 0 -10000 0 0
WNT6 -0.096 0.21 -9999 0 -0.57 81 81
WNT4 -0.011 0.085 -9999 0 -0.66 8 8
FZD3 0 0 -9999 0 -10000 0 0
WNT5A -0.012 0.084 -9999 0 -0.59 10 10
WNT11 -0.038 0.16 -9999 0 -0.68 27 27
Regulation of Androgen receptor activity

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
HDAC1 0.02 0 -9999 0 -10000 0 0
SMARCC1 0.007 0.008 -9999 0 -10000 0 0
REL 0 0.002 -9999 0 -10000 0 0
HDAC7 -0.03 0.12 -9999 0 -10000 0 0
JUN 0.001 0.003 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.003 0.048 -9999 0 -0.74 2 2
KAT5 0 0.001 -9999 0 -10000 0 0
MAPK14 0.011 0.026 -9999 0 -0.44 1 1
FOXO1 0 0 -9999 0 -10000 0 0
T-DHT/AR -0.038 0.13 -9999 0 -0.44 1 1
MAP2K6 0.005 0.028 -9999 0 -0.59 1 1
BRM/BAF57 -0.001 0.025 -9999 0 -0.56 1 1
MAP2K4 0.007 0.007 -9999 0 -10000 0 0
SMARCA2 -0.001 0.034 -9999 0 -0.74 1 1
PDE9A -0.11 0.24 -9999 0 -0.85 28 28
NCOA2 0.002 0.034 -9999 0 -0.74 1 1
CEBPA -0.001 0.034 -9999 0 -0.74 1 1
EHMT2 0.001 0.003 -9999 0 -10000 0 0
cell proliferation -0.048 0.17 -9999 0 -0.52 24 24
NR0B1 -0.18 0.27 -9999 0 -0.57 155 155
EGR1 -0.013 0.1 -9999 0 -0.74 9 9
RXRs/9cRA -0.23 0.22 -9999 0 -0.44 253 253
AR/RACK1/Src -0.016 0.074 -9999 0 -10000 0 0
AR/GR -0.064 0.12 -9999 0 -0.34 40 40
GNB2L1 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.012 0.016 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.015 0.074 -9999 0 -0.45 1 1
SRC 0.018 0.041 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
KLK3 -0.13 0.15 -9999 0 -0.58 17 17
APPBP2 0.007 0.006 -9999 0 -10000 0 0
TRIM24 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.037 0.053 -9999 0 -10000 0 0
TMPRSS2 -0.42 0.57 -9999 0 -1.2 156 156
RXRG -0.39 0.37 -9999 0 -0.74 253 253
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.004 0.005 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.021 0.13 -9999 0 -0.48 3 3
AR -0.054 0.15 -9999 0 -0.33 101 101
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
SRY -0.005 0.052 -9999 0 -0.57 4 4
GATA2 -0.08 0.23 -9999 0 -0.74 52 52
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.34 0.28 -9999 0 -0.57 283 283
T-DHT/AR/RACK1/Src -0.016 0.069 -9999 0 -10000 0 0
positive regulation of transcription -0.08 0.23 -9999 0 -0.74 52 52
DNAJA1 0.007 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -9999 0 -10000 0 0
NCOA1 0.014 0.004 -9999 0 -10000 0 0
SPDEF -0.096 0.25 -9999 0 -0.73 64 64
T-DHT/AR/TIF2 0.012 0.059 -9999 0 -0.37 2 2
T-DHT/AR/Hsp90 -0.037 0.053 -9999 0 -10000 0 0
GSK3B 0.007 0.005 -9999 0 -10000 0 0
NR2C1 0 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.012 0.043 -9999 0 -0.38 1 1
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0 0.002 -9999 0 -10000 0 0
POU2F1 -0.001 0.042 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.13 0.15 -9999 0 -0.46 24 24
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0 0.002 -9999 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.13 -10000 0 -0.4 24 24
TBX21 -0.095 0.5 -10000 0 -1.4 55 55
B2M 0.008 0.049 -10000 0 -0.74 2 2
TYK2 0.016 0.016 -10000 0 -10000 0 0
IL12RB1 -0.033 0.19 -10000 0 -0.77 31 31
GADD45B -0.033 0.37 -10000 0 -1.2 36 36
IL12RB2 -0.045 0.18 -10000 0 -0.57 51 51
GADD45G -0.017 0.33 -10000 0 -1 33 33
natural killer cell activation 0.006 0.019 -10000 0 -10000 0 0
RELB -0.001 0.026 -10000 0 -0.57 1 1
RELA 0 0 -10000 0 -10000 0 0
IL18 0.008 0.06 -10000 0 -0.75 3 3
IL2RA -0.008 0.073 -10000 0 -0.66 6 6
IFNG -0.009 0.076 -10000 0 -0.68 6 6
STAT3 (dimer) -0.005 0.29 -10000 0 -0.79 41 41
HLA-DRB5 -0.064 0.22 -10000 0 -0.74 47 47
FASLG -0.05 0.41 -10000 0 -1.2 42 42
NF kappa B2 p52/RelB -0.13 0.3 -10000 0 -1 39 39
CD4 -0.013 0.13 -10000 0 -0.74 14 14
SOCS1 -0.002 0.034 -10000 0 -0.74 1 1
EntrezGene:6955 -0.001 0.009 -10000 0 -10000 0 0
CD3D -0.007 0.11 -10000 0 -0.74 11 11
CD3E -0.004 0.1 -10000 0 -0.74 9 9
CD3G -0.036 0.18 -10000 0 -0.74 30 30
IL12Rbeta2/JAK2 -0.02 0.14 -10000 0 -0.41 51 51
CCL3 -0.027 0.35 -10000 0 -1.1 30 30
CCL4 -0.03 0.36 -10000 0 -1.1 37 37
HLA-A 0.009 0.034 -10000 0 -0.74 1 1
IL18/IL18R 0.017 0.15 -10000 0 -0.59 25 25
NOS2 -0.079 0.44 -10000 0 -1.2 53 53
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.13 -10000 0 -0.4 21 21
IL1R1 -0.026 0.35 -10000 0 -1 36 36
IL4 -0.004 0.019 -10000 0 -10000 0 0
JAK2 0.016 0.016 -10000 0 -10000 0 0
EntrezGene:6957 0 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.027 0.31 -10000 0 -1.3 22 22
RAB7A 0.007 0.28 -10000 0 -0.82 30 30
lysosomal transport 0.012 0.27 -10000 0 -0.77 30 30
FOS -0.15 0.49 -10000 0 -1.2 76 76
STAT4 (dimer) -0.008 0.34 -10000 0 -0.96 40 40
STAT5A (dimer) -0.13 0.3 -10000 0 -0.96 45 45
GZMA -0.033 0.37 -10000 0 -1.1 38 38
GZMB -0.035 0.38 -10000 0 -1.2 36 36
HLX 0 0 -10000 0 -10000 0 0
LCK -0.037 0.39 -10000 0 -1.1 41 41
TCR/CD3/MHC II/CD4 -0.084 0.33 -10000 0 -0.91 46 46
IL2/IL2R -0.014 0.1 -10000 0 -0.67 9 9
MAPK14 -0.015 0.34 -10000 0 -1 37 37
CCR5 -0.026 0.36 -10000 0 -1.1 32 32
IL1B -0.002 0.12 -10000 0 -0.77 11 11
STAT6 0.018 0.1 -10000 0 -0.26 15 15
STAT4 -0.012 0.095 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.017 0.016 -10000 0 -10000 0 0
CD8A 0 0.09 -10000 0 -0.74 7 7
CD8B -0.011 0.12 -10000 0 -0.7 15 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.13 0.4 24 -10000 0 24
IL2RB -0.005 0.058 -10000 0 -0.74 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.31 -10000 0 -0.84 40 40
IL2RG -0.012 0.095 -10000 0 -0.74 8 8
IL12 0.016 0.081 -10000 0 -0.57 8 8
STAT5A 0 0 -10000 0 -10000 0 0
CD247 -0.007 0.11 -10000 0 -0.75 11 11
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.1 -10000 0 -0.75 8 8
IL12/IL12R/TYK2/JAK2 -0.053 0.45 -10000 0 -1.2 46 46
MAP2K3 -0.019 0.34 -10000 0 -1 38 38
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.019 0.34 -10000 0 -1 38 38
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.053 0.21 -10000 0 -0.74 40 40
IL18RAP -0.021 0.16 -10000 0 -0.75 22 22
IL12Rbeta1/TYK2 -0.016 0.15 -10000 0 -0.6 31 31
EOMES -0.023 0.22 -10000 0 -1.4 11 11
STAT1 (dimer) -0.003 0.29 -10000 0 -0.82 36 36
T cell proliferation 0.006 0.26 -10000 0 -0.69 37 37
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.078 -10000 0 -0.75 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.1 0.23 -10000 0 -0.77 39 39
ATF2 -0.003 0.31 -10000 0 -0.91 36 36
Syndecan-1-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 0 -9999 0 -10000 0 0
CCL5 -0.014 0.1 -9999 0 -0.74 9 9
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.088 0.1 -9999 0 -0.42 4 4
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 -0.091 0.078 -9999 0 -0.4 5 5
Syndecan-1/Syntenin -0.09 0.077 -9999 0 -0.4 4 4
MAPK3 -0.057 0.087 -9999 0 -0.48 1 1
HGF/MET -0.12 0.23 -9999 0 -0.56 104 104
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.09 0.077 -9999 0 -0.39 5 5
Syndecan-1/RANTES -0.098 0.1 -9999 0 -0.55 10 10
Syndecan-1/CD147 -0.083 0.072 -9999 0 -0.51 1 1
Syndecan-1/Syntenin/PIP2 -0.087 0.074 -9999 0 -0.39 4 4
LAMA5 -0.002 0.034 -9999 0 -0.74 1 1
positive regulation of cell-cell adhesion -0.086 0.073 -9999 0 -0.38 4 4
MMP7 -0.038 0.15 -9999 0 -0.62 29 29
HGF -0.16 0.3 -9999 0 -0.74 101 101
Syndecan-1/CASK -0.084 0.094 -9999 0 -0.41 4 4
Syndecan-1/HGF/MET -0.17 0.17 -9999 0 -0.54 57 57
regulation of cell adhesion -0.049 0.085 -9999 0 -0.46 1 1
HPSE 0 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.088 0.1 -9999 0 -0.42 4 4
SDC1 -0.088 0.1 -9999 0 -0.43 4 4
Syndecan-1/Collagen -0.088 0.1 -9999 0 -0.42 4 4
PPIB 0 0 -9999 0 -10000 0 0
MET -0.004 0.054 -9999 0 -0.68 3 3
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 25 25
MAPK1 -0.057 0.087 -9999 0 -0.48 1 1
homophilic cell adhesion -0.087 0.099 -9999 0 -0.42 4 4
MMP1 -0.35 0.28 -9999 0 -0.57 298 298
Osteopontin-mediated events

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
IKK alpha homodimer -0.15 0.14 -9999 0 -0.56 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.11 -9999 0 -0.58 3 3
alphaV/beta3 Integrin/Osteopontin/Src -0.21 0.2 -9999 0 -0.4 255 255
AP1 -0.16 0.16 -9999 0 -0.6 31 31
ILK -0.14 0.17 -9999 0 -0.53 8 8
bone resorption -0.12 0.12 -9999 0 -0.6 4 4
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.14 0.13 -9999 0 -0.65 3 3
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.025 -9999 0 -0.56 1 1
alphaV/beta3 Integrin/Osteopontin -0.18 0.17 -9999 0 -0.44 25 25
MAP3K1 -0.14 0.17 -9999 0 -0.54 8 8
JUN 0 0 -9999 0 -10000 0 0
MAPK3 -0.12 0.16 -9999 0 -0.56 5 5
MAPK1 -0.12 0.16 -9999 0 -0.56 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.16 -9999 0 -0.58 5 5
ITGB3 -0.012 0.094 -9999 0 -0.74 8 8
NFKBIA -0.1 0.16 -9999 0 -0.54 5 5
FOS -0.084 0.24 -9999 0 -0.74 55 55
CD44 -0.002 0.034 -9999 0 -0.74 1 1
CHUK 0 0 -9999 0 -10000 0 0
PLAU -0.1 0.16 -9999 0 -0.58 4 4
NF kappa B1 p50/RelA -0.12 0.11 -9999 0 -0.56 3 3
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.009 0.071 -9999 0 -0.56 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.14 0.17 -9999 0 -0.52 9 9
VAV3 -0.13 0.17 -9999 0 -0.53 9 9
MAP3K14 -0.14 0.17 -9999 0 -0.53 8 8
ROCK2 0 0 -9999 0 -10000 0 0
SPP1 -0.3 0.28 -9999 0 -0.56 255 255
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.13 -9999 0 -0.73 3 3
MMP2 -0.1 0.17 -9999 0 -0.52 32 32
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.25 0.35 -9999 0 -0.74 160 160
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0 0 -9999 0 -10000 0 0
TCEB1 0 0 -9999 0 -10000 0 0
HIF1A/p53 -0.009 0.022 -9999 0 -10000 0 0
HIF1A -0.011 0.025 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.27 0.29 -9999 0 -0.57 224 224
ARNT/IPAS -0.19 0.26 -9999 0 -0.56 160 160
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.009 0.022 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.022 -9999 0 -10000 0 0
PHD1-3/OS9 -0.045 0.11 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.016 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.009 0.022 -9999 0 -10000 0 0
EGLN3 -0.084 0.2 -9999 0 -0.57 71 71
EGLN2 0 0 -9999 0 -10000 0 0
EGLN1 0 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.13 0.14 -9999 0 -0.35 35 35
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.064 0.098 -10000 0 -0.32 4 4
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.57 146 146
NT3 (dimer)/TRKB -0.12 0.19 -10000 0 -0.53 34 34
SHC/Grb2/SOS1/GAB1/PI3K 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.095 0.25 -10000 0 -0.74 62 62
PIK3CA 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.009 0.082 -10000 0 -0.74 6 6
NTRK2 -0.14 0.26 -10000 0 -0.62 105 105
NTRK3 -0.22 0.34 -10000 0 -0.74 143 143
NT-4/5 (dimer)/TRKB -0.12 0.19 -10000 0 -0.39 147 147
neuron apoptosis 0.13 0.19 0.47 86 -10000 0 86
SHC 2-3/Grb2 -0.14 0.21 -10000 0 -0.52 86 86
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.054 0.098 -10000 0 -0.55 8 8
SHC3 -0.16 0.26 -10000 0 -0.69 85 85
STAT3 (dimer) -0.005 0.043 -10000 0 -0.37 6 6
NT3 (dimer)/TRKA -0.041 0.12 -10000 0 -0.48 11 11
RIN/GDP -0.046 0.093 -10000 0 -0.28 2 2
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.023 0.068 -10000 0 -0.46 2 2
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.013 0.11 -10000 0 -0.88 7 7
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.094 -10000 0 -0.74 8 8
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.035 0.12 -10000 0 -0.47 36 36
TRKA/NEDD4-2 -0.007 0.062 -10000 0 -0.56 6 6
ELMO1 -0.017 0.11 -10000 0 -0.74 11 11
RhoG/GTP/ELMO1/DOCK1 -0.011 0.073 -10000 0 -0.49 11 11
NGF -0.017 0.11 -10000 0 -0.7 12 12
HRAS 0 0 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.018 0.12 -10000 0 -0.74 12 12
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.031 0.087 -10000 0 -0.4 13 13
mol:GDP -0.067 0.13 -10000 0 -0.42 2 2
NGF (dimer) -0.017 0.11 -10000 0 -0.7 12 12
RhoG/GDP -0.013 0.085 -10000 0 -0.57 11 11
RIT1/GDP -0.042 0.093 -10000 0 -0.28 1 1
TIAM1 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.23 -10000 0 -0.45 153 153
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.01 0.083 -10000 0 -0.69 7 7
RAP1/GDP -0.047 0.067 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.095 0.25 -10000 0 -0.74 62 62
ubiquitin-dependent protein catabolic process -0.017 0.087 -10000 0 -0.48 15 15
Schwann cell development -0.054 0.036 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.006 0.039 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.22 0.27 -10000 0 -0.72 74 74
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.077 -10000 0 -10000 0 0
STAT3 -0.005 0.043 -10000 0 -0.37 6 6
axon guidance -0.21 0.25 -10000 0 -0.68 74 74
MAPK3 -0.005 0.12 -10000 0 -0.43 33 33
MAPK1 -0.005 0.12 -10000 0 -0.43 33 33
CDC42/GDP -0.042 0.093 -10000 0 -0.28 1 1
NTF3 -0.01 0.083 -10000 0 -0.69 7 7
NTF4 -0.012 0.095 -10000 0 -0.74 8 8
NGF (dimer)/TRKA/FAIM -0.017 0.087 -10000 0 -0.46 18 18
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.27 0.2 -10000 0 -0.42 302 302
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.13 0.24 -10000 0 -0.49 144 144
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.057 0.08 -10000 0 -10000 0 0
Rac1/GDP -0.042 0.093 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.017 0.088 -10000 0 -0.46 18 18
neuron projection morphogenesis 0.004 0.073 -10000 0 -0.42 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.017 0.087 -10000 0 -0.48 15 15
MAP2K1 0 0 -10000 0 -10000 0 0
NGFR -0.047 0.16 -10000 0 -0.57 40 40
NGF (dimer)/TRKA/GIPC/GAIP -0.011 0.055 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.047 0.12 -10000 0 -0.66 15 15
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.062 -10000 0 -0.56 6 6
SQSTM1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.21 -10000 0 -0.5 79 79
NGF (dimer)/TRKA/p62/Atypical PKCs -0.014 0.073 -10000 0 -0.4 15 15
MATK -0.028 0.14 -10000 0 -0.74 18 18
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.043 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.025 0.073 -10000 0 -0.33 15 15
Rac1/GTP -0.18 0.13 -10000 0 -0.32 139 139
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.029 -10000 0 -10000 0 0
oxygen homeostasis -0.01 0.013 -10000 0 -10000 0 0
TCEB2 0 0 -10000 0 -10000 0 0
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.099 0.12 -10000 0 -0.44 9 9
EPO -0.15 0.21 -10000 0 -0.66 13 13
FIH (dimer) 0.003 0.009 -10000 0 -10000 0 0
APEX1 0.003 0.012 -10000 0 -10000 0 0
SERPINE1 -0.2 0.24 -10000 0 -0.78 13 13
FLT1 -0.038 0.16 -10000 0 -0.98 12 12
ADORA2A -0.19 0.23 -10000 0 -0.71 19 19
germ cell development -0.19 0.24 -10000 0 -0.74 17 17
SLC11A2 -0.2 0.24 -10000 0 -0.73 19 19
BHLHE40 -0.2 0.24 -10000 0 -0.74 18 18
HIF1AN 0.003 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.14 0.16 -10000 0 -0.48 38 38
ETS1 0.003 0.12 -10000 0 -0.75 12 12
CITED2 -0.033 0.16 -10000 0 -1.3 8 8
KDR -0.092 0.33 -10000 0 -1.3 32 32
PGK1 -0.2 0.24 -10000 0 -0.73 19 19
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.21 0.29 -10000 0 -0.79 38 38
EPAS1 -0.12 0.16 -10000 0 -0.4 75 75
SP1 0.016 0 -10000 0 -10000 0 0
ABCG2 -0.24 0.32 -10000 0 -0.96 56 56
EFNA1 -0.2 0.24 -10000 0 -0.76 14 14
FXN -0.19 0.23 -10000 0 -0.75 13 13
POU5F1 -0.2 0.24 -10000 0 -0.78 17 17
neuron apoptosis 0.2 0.28 0.76 38 -10000 0 38
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.084 0.21 -10000 0 -0.59 71 71
EGLN2 0.003 0.009 -10000 0 -10000 0 0
EGLN1 0.003 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.003 0.012 -10000 0 -10000 0 0
SLC2A1 -0.37 0.28 -10000 0 -0.74 93 93
TWIST1 -0.27 0.3 -10000 0 -0.76 65 65
ELK1 0.016 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.14 0.15 -10000 0 -0.53 13 13
VEGFA -0.2 0.24 -10000 0 -0.68 34 34
CREBBP 0 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.023 0.1 -10000 0 -0.46 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.11 -10000 0 -0.47 22 22
AKT1 -0.004 0.18 -10000 0 -0.82 21 21
PIK3CA 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.007 0.18 -10000 0 -0.83 21 21
mol:Ca2+ -0.087 0.23 -10000 0 -0.48 115 115
IGF1R 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.021 0.099 -10000 0 -0.49 21 21
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.002 0.17 0.78 21 -10000 0 21
RhoA/GTP -0.016 0.073 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.027 0.11 -10000 0 -0.52 22 22
regulation of stress fiber formation -0.032 0.07 0.58 1 -10000 0 1
E2/ERA-ERB (dimer) -0.021 0.099 -10000 0 -0.49 21 21
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.019 0.091 -10000 0 -0.45 21 21
pseudopodium formation 0.032 0.07 -10000 0 -0.58 1 1
E2/ER alpha (dimer)/PELP1 -0.021 0.099 -10000 0 -0.49 21 21
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.008 0.075 -10000 0 -0.74 5 5
GNAO1 -0.004 0.05 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.016 0.13 -10000 0 -0.54 22 22
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.1 -10000 0 -0.5 21 21
mol:NADP 0.016 0.13 -10000 0 -0.54 22 22
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.093 0.24 -10000 0 -0.5 115 115
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.22 -10000 0 -0.51 114 114
PLCB2 -0.13 0.23 -10000 0 -0.51 119 119
IGF1 -0.024 0.13 -10000 0 -0.73 16 16
mol:L-citrulline 0.016 0.13 -10000 0 -0.54 22 22
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.046 -10000 0 -0.67 1 1
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0 0 -10000 0 -10000 0 0
GNAQ -0.002 0.034 -10000 0 -0.74 1 1
ESR1 -0.032 0.15 -10000 0 -0.74 21 21
Gq family/GDP/Gbeta gamma -0.073 0.14 -10000 0 -0.81 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.071 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.027 0.11 -10000 0 -0.52 22 22
GNAZ -0.009 0.082 -10000 0 -0.74 6 6
E2/ER alpha (dimer) -0.025 0.12 -10000 0 -0.57 21 21
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.006 0.067 -10000 0 -0.74 4 4
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.034 -10000 0 -0.74 1 1
HBEGF 0.015 0.12 -10000 0 -0.72 5 5
cAMP biosynthetic process -0.02 0.091 -10000 0 -0.41 24 24
SRC 0.019 0.11 -10000 0 -0.44 22 22
PI3K 0 0 -10000 0 -10000 0 0
GNB1 -0.002 0.034 -10000 0 -0.74 1 1
G13/GDP/Gbeta gamma -0.023 0.11 -10000 0 -0.49 21 21
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.03 0.11 -10000 0 -0.46 23 23
Gs family/GTP -0.021 0.092 -10000 0 -0.42 24 24
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.017 0.12 -10000 0 -0.51 22 22
mol:DAG -0.093 0.24 -10000 0 -0.5 115 115
Gs family/GDP/Gbeta gamma -0.024 0.1 -10000 0 -0.46 21 21
MSN 0.033 0.076 -10000 0 -0.64 1 1
Gq family/GTP -0.13 0.24 -10000 0 -0.54 114 114
mol:PI-3-4-5-P3 -0.006 0.17 -10000 0 -0.8 21 21
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.017 0.12 0.51 22 -10000 0 22
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.02 0.096 -10000 0 -0.47 21 21
NOS3 0.016 0.13 -10000 0 -0.57 22 22
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.14 -10000 0 -0.64 21 21
E2/ER alpha (dimer)/PELP1/Src -0.028 0.12 -10000 0 -0.55 22 22
ruffle organization 0.032 0.07 -10000 0 -0.58 1 1
ROCK2 -0.014 0.067 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 114 114
GNA15 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MMP9 0.011 0.12 -10000 0 -0.59 5 5
MMP2 0.023 0.12 -10000 0 -0.79 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.003 0.048 -9999 0 -0.74 2 2
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.086 0.18 -9999 0 -0.47 88 88
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.053 0.18 -9999 0 -0.43 82 82
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.57 30 30
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.006 0.067 -9999 0 -0.74 4 4
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.003 0.032 -9999 0 -0.41 3 3
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.011 0.077 -9999 0 -0.57 9 9
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.15 0.25 -9999 0 -0.57 124 124
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.2 -9999 0 -0.5 85 85
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.091 0.14 -9999 0 -0.48 26 26
MAP1B -0.002 0.019 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.072 0.15 -9999 0 -0.6 2 2
RELN -0.13 0.28 -9999 0 -0.74 85 85
PAFAH/LIS1 -0.004 0.043 -9999 0 -0.48 4 4
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.068 0.11 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.062 0.12 -9999 0 -0.56 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.099 0.15 -9999 0 -0.51 26 26
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.02 0 -9999 0 -10000 0 0
PAFAH1B3 -0.005 0.056 -9999 0 -0.61 4 4
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.001 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.086 0.13 -9999 0 -0.46 26 26
LRP8 -0.004 0.045 -9999 0 -0.57 3 3
NDEL1/Katanin 60 -0.091 0.14 -9999 0 -0.48 26 26
P39/CDK5 -0.14 0.19 -9999 0 -0.66 25 25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.042 0.16 -9999 0 -0.4 82 82
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.09 0.17 -9999 0 -0.42 85 85
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 83 83
CDC42 0 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.04 0.14 -10000 0 -0.6 25 25
FYN 0.002 0.23 -10000 0 -0.89 25 25
LAT/GRAP2/SLP76 -0.053 0.18 -10000 0 -0.69 31 31
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
AKT1 0.023 0.14 -10000 0 -0.48 29 29
B2M 0.007 0.049 -10000 0 -0.75 2 2
IKBKG -0.009 0.03 -10000 0 -0.18 1 1
MAP3K8 -0.003 0.048 -10000 0 -0.74 2 2
mol:Ca2+ -0.006 0.022 -10000 0 -0.12 15 15
integrin-mediated signaling pathway -0.001 0.022 -10000 0 -0.48 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.21 -10000 0 -0.75 29 29
TRPV6 -0.019 0.12 -10000 0 -0.69 14 14
CD28 0.001 0.077 -10000 0 -0.75 5 5
SHC1 0.006 0.21 -10000 0 -0.81 25 25
receptor internalization -0.01 0.23 -10000 0 -0.83 30 30
PRF1 -0.037 0.32 -10000 0 -1.3 29 29
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.027 0.11 -10000 0 -0.4 24 24
LAT 0.006 0.21 -10000 0 -0.81 25 25
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D -0.007 0.11 -10000 0 -0.75 11 11
CD3E -0.004 0.1 -10000 0 -0.75 9 9
CD3G -0.037 0.18 -10000 0 -0.75 30 30
RASGRP2 -0.013 0.066 -10000 0 -0.18 65 65
RASGRP1 0.025 0.14 -10000 0 -0.46 31 31
HLA-A 0.009 0.035 -10000 0 -0.75 1 1
RASSF5 -0.002 0.034 -10000 0 -0.74 1 1
RAP1A/GTP/RAPL -0.001 0.022 -10000 0 -0.49 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.049 -10000 0 -0.13 26 26
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.017 0.054 -10000 0 -0.25 15 15
PRKCA -0.023 0.076 -10000 0 -0.3 28 28
GRAP2 -0.04 0.17 -10000 0 -0.74 26 26
mol:IP3 -0.033 0.13 0.25 10 -0.49 27 37
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.24 -10000 0 -0.86 26 26
ORAI1 0.01 0.064 0.35 14 -0.57 1 15
CSK 0.004 0.21 -10000 0 -0.82 25 25
B7 family/CD28 -0.064 0.23 -10000 0 -0.87 30 30
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.009 0.25 -10000 0 -1 25 25
PTPN6 0.001 0.21 -10000 0 -0.86 24 24
VAV1 0.004 0.22 -10000 0 -0.84 25 25
Monovalent TCR/CD3 -0.025 0.21 -10000 0 -0.64 36 36
CBL 0 0 -10000 0 -10000 0 0
LCK -0.001 0.23 -10000 0 -0.91 25 25
PAG1 0.001 0.22 -10000 0 -0.84 25 25
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.01 0.25 -10000 0 -0.97 26 26
CD80 -0.016 0.14 -10000 0 -0.75 16 16
CD86 0 0.084 -10000 0 -0.75 6 6
PDK1/CARD11/BCL10/MALT1 -0.021 0.066 -10000 0 -0.3 16 16
HRAS 0 0 -10000 0 -10000 0 0
GO:0035030 0.006 0.19 -10000 0 -0.68 29 29
CD8A -0.001 0.091 -10000 0 -0.75 7 7
CD8B -0.011 0.12 -10000 0 -0.7 15 15
PTPRC -0.039 0.18 -10000 0 -0.74 31 31
PDK1/PKC theta 0.018 0.18 -10000 0 -0.59 32 32
CSK/PAG1 0.007 0.21 -10000 0 -0.87 21 21
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.054 -10000 0 -0.8 2 2
GRAP2/SLP76 -0.063 0.21 -10000 0 -0.81 31 31
STIM1 0.007 0.031 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.058 -10000 0 -0.18 16 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.26 -10000 0 -0.92 30 30
mol:DAG -0.032 0.11 -10000 0 -0.44 27 27
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.007 0.11 -10000 0 -0.75 11 11
cytotoxic T cell degranulation -0.031 0.3 -10000 0 -1.2 30 30
RAP1A/GTP -0.009 0.022 -10000 0 -0.068 24 24
mol:PI-3-4-5-P3 0.018 0.17 -10000 0 -0.59 29 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.045 0.17 0.26 10 -0.66 27 37
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.012 0.095 -10000 0 -0.74 8 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.05 0.16 -10000 0 -0.66 28 28
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.024 0.13 -10000 0 -0.67 17 17
CARD11 -0.004 0.05 -10000 0 -0.63 3 3
PRKCB -0.033 0.1 -10000 0 -0.36 36 36
PRKCE -0.023 0.074 -10000 0 -0.3 23 23
PRKCQ 0.006 0.21 -10000 0 -0.69 33 33
LCP2 -0.01 0.089 -10000 0 -0.74 7 7
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.026 0.12 -10000 0 -0.4 29 29
IKK complex 0.035 0.046 -10000 0 -0.13 10 10
RAS family/GDP -0.003 0.007 -10000 0 -10000 0 0
MAP3K14 0.032 0.088 -10000 0 -0.31 20 20
PDPK1 0.027 0.13 -10000 0 -0.46 27 27
TCR/CD3/MHC I/CD8/Fyn -0.011 0.25 -10000 0 -1 23 23
Ephrin A reverse 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
MAPKKK cascade -0.016 0.075 -9999 0 -0.36 21 21
EFNA5 -0.003 0.048 -9999 0 -0.74 2 2
FYN 0.004 0.074 -9999 0 -0.33 22 22
neuron projection morphogenesis -0.016 0.075 -9999 0 -0.36 21 21
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.016 0.075 -9999 0 -0.36 21 21
EPHA5 -0.023 0.11 -9999 0 -0.57 19 19
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.007 0.062 -9999 0 -0.56 6 6
Necdin/E2F1 -0.007 0.062 -9999 0 -0.56 6 6
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.038 0.11 -9999 0 -0.44 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.096 0.19 -9999 0 -0.54 54 54
NT-4/5 (dimer)/p75(NTR) -0.043 0.13 -9999 0 -0.44 48 48
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
AKT1 -0.032 0.099 -9999 0 -0.69 2 2
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.095 0.25 -9999 0 -0.74 62 62
MGDIs/NGR/p75(NTR)/LINGO1 -0.061 0.14 -9999 0 -0.68 7 7
FURIN 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.096 0.19 -9999 0 -0.51 67 67
LINGO1 -0.052 0.16 -9999 0 -0.57 44 44
Sortilin/TRAF6/NRIF -0.004 0.039 -9999 0 -10000 0 0
proBDNF (dimer) -0.095 0.25 -9999 0 -0.74 62 62
NTRK1 -0.009 0.082 -9999 0 -0.74 6 6
RTN4R -0.003 0.043 -9999 0 -0.66 2 2
neuron apoptosis -0.031 0.16 -9999 0 -0.6 10 10
IRAK1 0 0 -9999 0 -10000 0 0
SHC1 -0.018 0.13 -9999 0 -0.55 9 9
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.041 0.12 -9999 0 -0.48 15 15
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.046 0.13 -9999 0 -0.48 20 20
Mammalian IAPs/DIABLO -0.005 0.048 -9999 0 -0.43 6 6
proNGF (dimer) -0.017 0.11 -9999 0 -0.7 12 12
MAGED1 0 0 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.094 -9999 0 -0.74 8 8
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.033 0.1 -9999 0 -0.47 9 9
NGF -0.017 0.11 -9999 0 -0.7 12 12
cell cycle arrest -0.021 0.13 -9999 0 -0.51 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.018 0.06 -9999 0 -0.47 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.036 0.11 -9999 0 -0.48 8 8
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.039 0.12 -9999 0 -0.55 9 9
PSENEN 0 0 -9999 0 -10000 0 0
mol:ceramide -0.015 0.12 -9999 0 -0.47 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.013 0.046 -9999 0 -0.37 2 2
p75(NTR)/beta APP -0.034 0.11 -9999 0 -0.41 40 40
BEX1 -0.089 0.23 -9999 0 -0.68 63 63
mol:GDP -0.026 0.13 -9999 0 -0.39 50 50
NGF (dimer) -0.033 0.11 -9999 0 -0.5 17 17
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.055 0.13 -9999 0 -0.63 7 7
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.034 0.1 -9999 0 -0.48 9 9
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.039 0.12 -9999 0 -0.55 9 9
RHOB -0.002 0.034 -9999 0 -0.74 1 1
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.01 0.083 -9999 0 -0.69 7 7
TP53 -0.075 0.15 -9999 0 -0.67 7 7
PRDM4 -0.015 0.12 -9999 0 -0.47 15 15
BDNF (dimer) -0.27 0.24 -9999 0 -0.65 84 84
PIK3CA 0 0 -9999 0 -10000 0 0
SORT1 -0.009 0.082 -9999 0 -0.74 6 6
activation of caspase activity -0.037 0.11 -9999 0 -0.44 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.12 -9999 0 -0.48 15 15
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.14 -9999 0 -0.57 8 8
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.015 0.12 -9999 0 -0.47 15 15
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.045 0.13 -9999 0 -0.52 15 15
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.042 0.13 -9999 0 -0.43 47 47
MAPK8 -0.009 0.14 -9999 0 -0.56 6 6
MAPK9 -0.009 0.14 -9999 0 -0.56 6 6
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.01 0.083 -9999 0 -0.69 7 7
NTF4 -0.012 0.095 -9999 0 -0.74 8 8
NDN -0.009 0.082 -9999 0 -0.74 6 6
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.03 0.093 -9999 0 -0.65 2 2
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.048 -9999 0 -0.43 6 6
RhoA-B-C/GTP -0.039 0.12 -9999 0 -0.54 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.08 0.16 -9999 0 -0.71 7 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.086 0.18 -9999 0 -0.47 67 67
PRKACB 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.072 0.19 -9999 0 -0.56 62 62
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.082 -9999 0 -0.74 6 6
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.013 0.13 -9999 0 -0.45 13 13
BAD -0.003 0.14 -9999 0 -0.55 6 6
RIPK2 0 0 -9999 0 -10000 0 0
NGFR -0.047 0.16 -9999 0 -0.57 40 40
CYCS -0.037 0.11 -9999 0 -0.69 2 2
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.035 0.11 -9999 0 -0.5 9 9
BCL2L11 -0.003 0.14 -9999 0 -0.55 6 6
BDNF (dimer)/p75(NTR) -0.1 0.22 -9999 0 -0.53 96 96
PI3K -0.035 0.11 -9999 0 -0.5 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.041 0.12 -9999 0 -0.48 15 15
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.047 0.14 -9999 0 -0.45 50 50
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.041 0.12 -9999 0 -0.48 15 15
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG -0.004 0.045 -9999 0 -0.57 3 3
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.084 0.17 -9999 0 -0.62 17 17
SQSTM1 0 0 -9999 0 -10000 0 0
NGFRAP1 0 0 -9999 0 -10000 0 0
CASP3 0 0.13 -9999 0 -0.5 6 6
E2F1 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.018 0.072 -9999 0 -0.51 2 2
NGF (dimer)/TRKA -0.02 0.1 -9999 0 -0.53 18 18
MMP7 -0.038 0.15 -9999 0 -0.62 29 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -9999 0 -0.55 4 4
MMP3 -0.34 0.28 -9999 0 -0.57 291 291
APAF-1/Caspase 9 -0.03 0.084 -9999 0 -0.54 3 3
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0 0.074 -9999 0 -0.71 5 5
PDGF/PDGFRA/CRKL -0.006 0.053 -9999 0 -0.52 5 5
positive regulation of JUN kinase activity -0.004 0.04 -9999 0 -0.42 4 4
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.097 0.21 -9999 0 -0.57 81 81
AP1 -0.13 0.34 -9999 0 -1.1 55 55
mol:IP3 0.01 0.06 -9999 0 -0.54 5 5
PLCG1 0.01 0.061 -9999 0 -0.54 5 5
PDGF/PDGFRA/alphaV Integrin -0.006 0.053 -9999 0 -0.52 5 5
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.06 -9999 0 -0.54 5 5
CAV3 -0.12 0.27 -9999 0 -0.74 76 76
CAV1 -0.21 0.33 -9999 0 -0.74 135 135
SHC/Grb2/SOS1 -0.004 0.04 -9999 0 -0.42 4 4
PDGF/PDGFRA/Shf -0.006 0.053 -9999 0 -0.52 5 5
FOS -0.087 0.35 -9999 0 -1.1 55 55
JUN -0.007 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.006 0.053 -9999 0 -0.52 5 5
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0.01 0.06 -9999 0 -0.54 5 5
PDGF/PDGFRA 0 0.074 -9999 0 -0.71 5 5
actin cytoskeleton reorganization -0.006 0.053 -9999 0 -0.52 5 5
SRF 0.005 0.014 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.005 0.045 -9999 0 -0.47 4 4
PDGF/PDGFRA/Crk/C3G -0.005 0.045 -9999 0 -0.47 4 4
JAK1 0.013 0.056 -9999 0 -0.52 5 5
ELK1/SRF -0.006 0.04 -9999 0 -0.42 4 4
SHB 0 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0.018 -9999 0 -10000 0 0
GO:0007205 0.011 0.062 -9999 0 -0.54 5 5
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.004 0.04 -9999 0 -0.42 4 4
PDGF/PDGFRA/SHB -0.006 0.053 -9999 0 -0.52 5 5
PDGF/PDGFRA/Caveolin-1 -0.16 0.26 -9999 0 -0.57 138 138
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 0.014 0.062 -9999 0 -0.52 4 4
PIK3CA 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.006 0.053 -9999 0 -0.52 5 5
JAK-STAT cascade 0.013 0.055 -9999 0 -0.52 5 5
cell proliferation -0.006 0.053 -9999 0 -0.52 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.04 -9999 0 -0.51 3 3
CRKL -0.025 0.12 -9999 0 -0.43 2 2
mol:PIP3 -0.016 0.006 -9999 0 -10000 0 0
AKT1 0.003 0.005 -9999 0 -10000 0 0
PTK2B 0 0 -9999 0 -10000 0 0
RAPGEF1 -0.017 0.11 -9999 0 -0.4 2 2
RANBP10 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.1 0.2 -9999 0 -0.48 103 103
MAP3K5 -0.01 0.11 -9999 0 -0.44 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.095 0.18 -9999 0 -0.44 103 103
AP1 -0.057 0.16 -9999 0 -0.5 55 55
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
apoptosis -0.073 0.24 -9999 0 -0.73 55 55
STAT3 (dimer) -0.033 0.13 -9999 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.045 0.086 -9999 0 -10000 0 0
INPP5D -0.002 0.034 -9999 0 -0.74 1 1
CBL/CRK -0.018 0.11 -9999 0 -0.4 2 2
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
PTEN 0 0 -9999 0 -10000 0 0
ELK1 -0.004 0.022 -9999 0 -0.24 3 3
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.039 0.076 -9999 0 -0.46 2 2
PAK1 0.009 0.014 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.1 0.2 -9999 0 -0.48 103 103
HRAS -0.08 0.15 -9999 0 -0.59 4 4
DOCK1 -0.017 0.11 -9999 0 -0.4 2 2
GAB1 -0.034 0.12 -9999 0 -0.39 4 4
CRK -0.025 0.12 -9999 0 -0.43 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.12 0.22 -9999 0 -0.54 103 103
JUN 0 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.054 0.1 -9999 0 -0.25 103 103
PIK3R1 0 0 -9999 0 -10000 0 0
cell morphogenesis -0.01 0.14 -9999 0 -10000 0 0
GRB2/SHC -0.045 0.088 -9999 0 -0.5 2 2
FOS -0.085 0.24 -9999 0 -0.74 55 55
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.004 0.022 -9999 0 -0.24 3 3
HGF/MET/MUC20 -0.1 0.2 -9999 0 -0.48 104 104
cell migration -0.044 0.087 -9999 0 -0.5 2 2
GRB2 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
MET/RANBP10 -0.003 0.04 -9999 0 -0.51 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.066 0.13 -9999 0 -10000 0 0
MET/MUC20 -0.003 0.041 -9999 0 -0.52 3 3
RAP1B -0.009 0.1 -9999 0 -10000 0 0
RAP1A -0.009 0.1 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.1 0.2 -9999 0 -0.48 103 103
RAF1 -0.044 0.16 -9999 0 -0.55 4 4
STAT3 -0.063 0.12 -9999 0 -10000 0 0
cell proliferation -0.047 0.18 -9999 0 -0.52 4 4
RPS6KB1 -0.019 0.036 -9999 0 -10000 0 0
MAPK3 -0.007 0.019 -9999 0 -10000 0 0
MAPK1 -0.007 0.019 -9999 0 -0.23 2 2
RANBP9 0 0 -9999 0 -10000 0 0
MAPK8 0.008 0.095 -9999 0 -0.39 1 1
SRC -0.061 0.12 -9999 0 -10000 0 0
PI3K -0.045 0.088 -9999 0 -0.5 2 2
MET/Glomulin -0.003 0.037 -9999 0 -0.46 3 3
SOS1 0 0 -9999 0 -10000 0 0
MAP2K1 -0.034 0.15 -9999 0 -0.5 4 4
MET -0.004 0.054 -9999 0 -0.68 3 3
MAP4K1 -0.018 0.12 -9999 0 -0.47 4 4
PTK2 0 0 -9999 0 -10000 0 0
MAP2K2 -0.034 0.15 -9999 0 -0.59 2 2
BAD 0.009 0.005 -9999 0 -10000 0 0
MAP2K4 -0.002 0.1 -9999 0 -0.45 2 2
SHP2/GRB2/SOS1/GAB1 -0.047 0.091 -9999 0 -0.45 2 2
INPPL1 0 0 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
SH3KBP1 -0.003 0.048 -9999 0 -0.74 2 2
HGS -0.048 0.095 -9999 0 -0.42 4 4
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 101 101
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
PTPRJ -0.003 0.048 -9999 0 -0.74 2 2
NCK/PLCgamma1 -0.051 0.098 -9999 0 -0.53 2 2
PDPK1 -0.006 0.006 -9999 0 -10000 0 0
HGF/MET/SHIP -0.1 0.2 -9999 0 -0.48 103 103
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.054 0.13 -9999 0 -0.37 57 57
MAP3K8 0.005 0.048 -9999 0 -0.74 2 2
FOS 0.002 0.1 -9999 0 -0.46 6 6
PRKCA 0.006 0.049 -9999 0 -0.75 2 2
PTPN7 0.007 0.043 -9999 0 -0.66 2 2
HRAS 0 0 -9999 0 -10000 0 0
PRKCB -0.028 0.16 -9999 0 -0.74 24 24
NRAS 0 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.009 0.061 -9999 0 -0.45 1 1
MAP2K1 -0.001 0.13 -9999 0 -0.52 25 25
ELK1 -0.001 0.004 -9999 0 -10000 0 0
BRAF -0.03 0.12 -9999 0 -0.52 25 25
mol:GTP -0.001 0.002 -9999 0 -0.006 55 55
MAPK1 0.009 0.061 -9999 0 -0.28 6 6
RAF1 -0.03 0.12 -9999 0 -0.52 25 25
KRAS 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0 0.12 -10000 0 -0.48 25 25
ACTA1 -0.013 0.16 -10000 0 -0.64 25 25
NUMA1 0 0.12 -10000 0 -0.48 25 25
SPTAN1 -0.011 0.16 -10000 0 -0.64 25 25
LIMK1 -0.011 0.16 -10000 0 -0.64 25 25
BIRC3 -0.009 0.082 -10000 0 -0.74 6 6
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.012 0.16 -10000 0 -0.63 28 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0 0.12 -10000 0 -0.48 25 25
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.01 0.15 -10000 0 -0.62 25 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.011 0.16 -10000 0 -0.64 25 25
MADD 0 0 -10000 0 -10000 0 0
TFAP2A -0.069 0.12 -10000 0 -0.78 12 12
BID 0.004 0.075 -10000 0 -0.3 27 27
MAP3K1 0.003 0.047 -10000 0 -0.23 10 10
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.16 -10000 0 -0.63 26 26
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.034 -10000 0 -0.21 2 2
neuron apoptosis 0.019 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.004 0.15 -10000 0 -0.61 25 25
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.017 0.073 -10000 0 -0.51 2 2
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD -0.004 0.15 -10000 0 -0.61 25 25
CASP7 -0.005 0.043 0.36 6 -10000 0 6
KRT18 0.013 0.02 -10000 0 -10000 0 0
apoptosis -0.003 0.15 -10000 0 -0.57 25 25
DFFA -0.011 0.16 -10000 0 -0.64 25 25
DFFB -0.011 0.16 -10000 0 -0.64 25 25
PARP1 0.002 0.035 0.21 2 -10000 0 2
actin filament polymerization 0.002 0.14 0.58 25 -10000 0 25
TNF -0.02 0.12 -10000 0 -0.73 13 13
CYCS 0.007 0.056 -10000 0 -0.27 11 11
SATB1 0.02 0.079 -10000 0 -0.62 2 2
SLK -0.011 0.16 -10000 0 -0.64 25 25
p15 BID/BAX -0.015 0.062 -10000 0 -0.34 10 10
CASP2 0.034 0.052 -10000 0 -0.44 1 1
JNK cascade -0.003 0.047 0.23 10 -10000 0 10
CASP3 -0.019 0.17 -10000 0 -0.68 25 25
LMNB2 0.032 0.049 -10000 0 -0.48 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.002 0.034 -10000 0 -0.74 1 1
Mammalian IAPs/DIABLO -0.005 0.048 -10000 0 -0.43 6 6
negative regulation of DNA binding -0.068 0.12 -10000 0 -0.77 12 12
stress fiber formation -0.01 0.15 -10000 0 -0.62 25 25
GZMB -0.022 0.18 -10000 0 -0.73 27 27
CASP1 0.011 0.052 -10000 0 -0.73 2 2
LMNB1 0.032 0.049 -10000 0 -0.48 1 1
APP 0.019 0.016 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.008 0.14 -10000 0 -0.56 25 25
LMNA 0.032 0.049 -10000 0 -0.48 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.047 -10000 0 -0.47 1 1
LRDD -0.002 0.034 -10000 0 -0.74 1 1
SREBF1 -0.011 0.16 -10000 0 -0.64 25 25
APAF-1/Caspase 9 -0.003 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0 0.12 -10000 0 -0.47 25 25
CFL2 -0.003 0.15 -10000 0 -0.6 25 25
GAS2 -0.063 0.22 -10000 0 -0.52 71 71
positive regulation of apoptosis 0.034 0.049 -10000 0 -0.47 1 1
PRF1 -0.038 0.16 -10000 0 -0.74 25 25
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.007 0.013 -10000 0 -10000 0 0
HSPA8 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.024 0.11 -10000 0 -0.52 21 21
AKT1 0.006 0.021 -10000 0 -10000 0 0
GSC -0.038 0.13 -10000 0 -0.44 9 9
NKX2-5 -0.29 0.28 -10000 0 -0.57 247 247
muscle cell differentiation 0.092 0.097 0.44 6 -10000 0 6
SMAD2-3/SMAD4/SP1 -0.009 0.034 -10000 0 -10000 0 0
SMAD4 0.017 0.026 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.01 0.035 -10000 0 -0.46 1 1
SMAD3/SMAD4/VDR 0.009 0.033 -10000 0 -10000 0 0
MYC 0.007 0.024 -10000 0 -10000 0 0
CDKN2B -0.093 0.41 -10000 0 -1.4 41 41
AP1 -0.036 0.12 -10000 0 -0.41 11 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.029 0.088 -10000 0 -0.42 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.048 0.17 -10000 0 -0.58 44 44
SMAD3/SMAD4/GR -0.003 0.014 -10000 0 -10000 0 0
GATA3 -0.026 0.13 -10000 0 -0.71 17 17
SKI/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
MEF2C/TIF2 -0.17 0.19 -10000 0 -0.68 31 31
endothelial cell migration -0.013 0.023 -10000 0 -10000 0 0
MAX 0 0 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 0 0 -10000 0 -10000 0 0
RUNX3 0 0 -10000 0 -10000 0 0
RUNX1 0 0 -10000 0 -10000 0 0
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0 0 -10000 0 -10000 0 0
VDR -0.002 0.034 -10000 0 -0.74 1 1
CDKN1A 0.058 0.042 -10000 0 -10000 0 0
KAT2B 0 0.048 -10000 0 -0.74 2 2
SMAD2/SMAD2/SMAD4/FOXH1 -0.046 0.11 -10000 0 -0.47 13 13
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.013 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.001 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.001 0.017 -10000 0 -10000 0 0
SAP30 0 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.031 -10000 0 -10000 0 0
JUN 0.007 0.13 -10000 0 -0.4 10 10
SMAD3/SMAD4/IRF7 -0.004 0.039 -10000 0 -0.54 2 2
TFE3 0.016 0.001 -10000 0 -10000 0 0
COL1A2 0.005 0.051 -10000 0 -0.4 4 4
mesenchymal cell differentiation 0.001 0.017 -10000 0 -10000 0 0
DLX1 -0.33 0.28 -10000 0 -0.57 276 276
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.071 0.24 -10000 0 -0.73 55 55
SMAD3/SMAD4/Max -0.003 0.014 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0.016 -10000 0 -10000 0 0
ZBTB17 0.006 0.019 -10000 0 -10000 0 0
LAMC1 0.048 0.028 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.017 -10000 0 -10000 0 0
IRF7 -0.003 0.048 -10000 0 -0.74 2 2
ESR1 -0.032 0.15 -10000 0 -0.74 21 21
HNF4A -0.009 0.073 -10000 0 -0.57 8 8
MEF2C -0.16 0.22 -10000 0 -0.71 31 31
SMAD2-3/SMAD4 -0.009 0.029 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.011 0.021 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.001 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.005 0.01 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 -0.001 0.026 -10000 0 -0.58 1 1
GCN5L2 0.003 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.004 0.022 -10000 0 -10000 0 0
MSG1/HSC70 -0.002 0.032 -10000 0 -0.49 2 2
SMAD2 0.004 0.027 -10000 0 -10000 0 0
SMAD3 0.019 0.022 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.039 0.027 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.013 0.029 -10000 0 -0.4 2 2
NCOR1 0 0 -10000 0 -10000 0 0
NCOA2 -0.002 0.034 -10000 0 -0.74 1 1
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A -0.059 0.14 -10000 0 -0.41 69 69
SMAD2-3/SMAD4/SP1/MIZ-1 0.016 0.052 -10000 0 -10000 0 0
IFNB1 0.035 0.049 -10000 0 -0.48 3 3
SMAD3/SMAD4/MEF2C -0.17 0.19 -10000 0 -0.69 31 31
CITED1 -0.003 0.043 -10000 0 -0.66 2 2
SMAD2-3/SMAD4/ARC105 -0.007 0.023 -10000 0 -10000 0 0
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.011 0.15 -10000 0 -0.48 41 41
RUNX1-3/PEBPB2 0 0 -10000 0 -10000 0 0
SMAD7 -0.024 0.1 -10000 0 -1.1 1 1
MYC/MIZ-1 0.013 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.072 0.29 6 -10000 0 6
IL10 0.026 0.11 -10000 0 -0.71 5 5
PIASy/HDAC complex 0.005 0.005 -10000 0 -10000 0 0
PIAS3 0.004 0.007 -10000 0 -10000 0 0
CDK2 0.005 0.01 -10000 0 -10000 0 0
IL5 0.023 0.096 -10000 0 -0.5 6 6
CDK4 0.005 0.028 -10000 0 -0.57 1 1
PIAS4 0.006 0.005 -10000 0 -10000 0 0
ATF3 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.002 0.027 -10000 0 -10000 0 0
FOXG1 -0.061 0.18 -10000 0 -0.57 51 51
FOXO3 0.015 0.028 -10000 0 -10000 0 0
FOXO1 0.015 0.028 -10000 0 -10000 0 0
FOXO4 0.015 0.028 -10000 0 -10000 0 0
heart looping -0.16 0.22 -10000 0 -0.7 31 31
CEBPB 0.008 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.2 0.18 -10000 0 -0.4 56 56
MYOD1 -0.082 0.2 -10000 0 -0.57 69 69
SMAD3/SMAD4/HNF4 -0.007 0.048 -10000 0 -0.38 1 1
SMAD3/SMAD4/GATA3 -0.02 0.094 -10000 0 -0.51 15 15
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.004 0.025 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.017 0.011 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.2 0.19 -10000 0 -0.65 33 33
ITGB5 0.056 0.034 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.11 0.2 -10000 0 -0.5 101 101
AR -0.16 0.3 -10000 0 -0.74 101 101
negative regulation of cell growth 0.004 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.052 0.13 -10000 0 -0.41 14 14
E2F5 0 0 -10000 0 -10000 0 0
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.031 0.088 -10000 0 -0.55 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.019 0.095 -10000 0 -0.35 8 8
TFDP1 -0.004 0.045 -10000 0 -0.57 3 3
SMAD3/SMAD4/AP1 -0.035 0.12 -10000 0 -0.41 9 9
SMAD3/SMAD4/RUNX2 -0.001 0.017 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.1 0.26 -9999 0 -0.74 66 66
GNB1/GNG2 -0.042 0.086 -9999 0 -0.47 7 7
mol:DAG -0.002 0.095 -9999 0 -0.48 4 4
PLCG1 -0.038 0.08 -9999 0 -0.5 4 4
YES1 -0.04 0.077 -9999 0 -0.45 1 1
FZD3 0 0 -9999 0 -10000 0 0
FZD6 0 0 -9999 0 -10000 0 0
G protein -0.038 0.081 -9999 0 -0.51 4 4
MAP3K7 -0.015 0.14 -9999 0 -0.54 13 13
mol:Ca2+ -0.002 0.093 -9999 0 -0.47 4 4
mol:IP3 -0.002 0.095 -9999 0 -0.48 4 4
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 -0.002 0.034 -9999 0 -0.74 1 1
CAMK2A -0.025 0.15 -9999 0 -0.58 14 14
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.044 0.085 -9999 0 -0.31 24 24
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.04 0.077 -9999 0 -0.45 1 1
GO:0007205 -0.001 0.094 -9999 0 -0.42 7 7
WNT6 -0.096 0.21 -9999 0 -0.57 81 81
WNT4 -0.011 0.085 -9999 0 -0.66 8 8
NFAT1/CK1 alpha -0.08 0.14 -9999 0 -0.54 17 17
GNG2 -0.008 0.075 -9999 0 -0.74 5 5
WNT5A -0.012 0.084 -9999 0 -0.59 10 10
WNT11 -0.038 0.16 -9999 0 -0.68 27 27
CDC42 -0.004 0.088 -9999 0 -0.43 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.02 -10000 0 -10000 0 0
RFC1 0.002 0.02 -10000 0 -10000 0 0
PRKDC 0.002 0.02 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.012 0.037 0.26 1 -10000 0 1
FASLG/FAS/FADD/FAF1 -0.018 0.075 0.24 5 -0.34 20 25
MAP2K4 -0.012 0.13 -10000 0 -0.5 8 8
mol:ceramide -0.007 0.11 -10000 0 -0.44 21 21
GSN 0.002 0.02 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.09 0.22 3 -0.41 21 24
FAS 0.007 0.035 -10000 0 -0.76 1 1
BID 0.003 0.029 0.31 4 -10000 0 4
MAP3K1 0.003 0.079 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
RB1 0.002 0.02 -10000 0 -10000 0 0
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.2 -10000 0 -0.48 107 107
ARHGDIB 0.001 0.023 -10000 0 -0.32 1 1
FADD 0.009 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.02 -10000 0 -10000 0 0
NFKB1 -0.039 0.08 -10000 0 -0.29 7 7
MAPK8 -0.033 0.19 -10000 0 -0.44 80 80
DFFA 0.002 0.02 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.02 -10000 0 -10000 0 0
FAS/FADD/MET -0.004 0.041 -10000 0 -0.49 3 3
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.005 0.072 -10000 0 -0.7 5 5
FAF1 0.009 0.004 -10000 0 -10000 0 0
PARP1 0.002 0.02 -10000 0 -10000 0 0
DFFB 0.002 0.02 -10000 0 -10000 0 0
CHUK -0.034 0.07 -10000 0 -10000 0 0
FASLG -0.022 0.15 -10000 0 -0.75 20 20
FAS/FADD -0.002 0.027 -10000 0 -0.58 1 1
HGF -0.16 0.3 -10000 0 -0.74 101 101
LMNA 0.002 0.018 -10000 0 -10000 0 0
CASP6 0.002 0.02 -10000 0 -10000 0 0
CASP10 0.007 0.034 -10000 0 -0.74 1 1
CASP3 0.003 0.023 0.23 4 -10000 0 4
PTPN13 -0.006 0.067 -10000 0 -0.74 4 4
CASP8 0.004 0.041 0.43 4 -10000 0 4
IL6 -0.2 0.51 -10000 0 -1.3 82 82
MET -0.004 0.054 -10000 0 -0.68 3 3
ICAD/CAD 0.002 0.019 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.008 0.12 -10000 0 -0.44 21 21
activation of caspase activity by cytochrome c 0.003 0.029 0.31 4 -10000 0 4
PAK2 0.002 0.02 -10000 0 -10000 0 0
BCL2 0.001 0.026 -10000 0 -0.57 1 1
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.014 0.085 -9999 0 -0.51 13 13
EPHB2 -0.009 0.073 -9999 0 -0.57 8 8
Syndecan-2/TACI -0.013 0.072 -9999 0 -0.41 15 15
LAMA1 -0.17 0.26 -9999 0 -0.57 141 141
Syndecan-2/alpha2 ITGB1 -0.013 0.07 -9999 0 -0.4 15 15
HRAS 0 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.038 -9999 0 -0.48 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.032 0.036 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.003 0.034 -9999 0 -0.44 3 3
LAMA3 -0.018 0.12 -9999 0 -0.74 12 12
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.022 0.12 -9999 0 -0.74 14 14
Syndecan-2/MMP2 -0.007 0.064 -9999 0 -0.55 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis -0.009 0.057 -9999 0 -0.38 11 11
Syndecan-2/GM-CSF -0.053 0.15 -9999 0 -0.48 53 53
determination of left/right symmetry 0.014 0.045 -9999 0 -0.56 3 3
Syndecan-2/PKC delta -0.003 0.038 -9999 0 -0.48 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 -0.023 0.14 -9999 0 -0.43 53 53
MAPK1 -0.023 0.14 -9999 0 -0.43 53 53
Syndecan-2/RACK1 -0.003 0.032 -9999 0 -0.41 3 3
NF1 0 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.045 -9999 0 -0.56 3 3
ITGA2 0 0 -9999 0 -10000 0 0
MAPK8 0.027 0.04 -9999 0 -0.47 3 3
Syndecan-2/alpha2/beta1 Integrin -0.085 0.13 -9999 0 -0.5 3 3
Syndecan-2/Kininogen -0.012 0.065 -9999 0 -0.37 15 15
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.03 -9999 0 -0.38 3 3
Syndecan-2/CASK/Protein 4.1 -0.003 0.035 -9999 0 -0.44 3 3
extracellular matrix organization -0.003 0.037 -9999 0 -0.48 3 3
actin cytoskeleton reorganization -0.014 0.085 -9999 0 -0.51 13 13
Syndecan-2/Caveolin-2/Ras -0.015 0.085 -9999 0 -0.46 16 16
Syndecan-2/Laminin alpha3 -0.015 0.083 -9999 0 -0.48 15 15
Syndecan-2/RasGAP -0.002 0.03 -9999 0 -0.39 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.009 0.058 -9999 0 -0.38 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.029 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.016 0.099 -9999 0 -0.63 12 12
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.003 0.038 -9999 0 -0.48 3 3
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.025 0.036 -9999 0 -0.43 3 3
FN1 -0.017 0.11 -9999 0 -0.74 11 11
Syndecan-2/IL8 -0.018 0.087 -9999 0 -0.4 22 22
SDC2 0.014 0.045 -9999 0 -0.56 3 3
KNG1 -0.014 0.089 -9999 0 -0.57 12 12
Syndecan-2/Neurofibromin -0.003 0.038 -9999 0 -0.48 3 3
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.077 0.23 -9999 0 -0.74 50 50
Syndecan-2/TGFB1 -0.003 0.038 -9999 0 -0.48 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.003 0.035 -9999 0 -0.44 3 3
Syndecan-2/Ezrin -0.003 0.034 -9999 0 -0.43 3 3
PRKACA 0.025 0.036 -9999 0 -0.43 3 3
angiogenesis -0.018 0.086 -9999 0 -0.4 22 22
MMP2 -0.006 0.067 -9999 0 -0.74 4 4
IL8 -0.025 0.12 -9999 0 -0.61 20 20
calcineurin-NFAT signaling pathway -0.013 0.072 -9999 0 -0.41 15 15
Effects of Botulinum toxin

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
STX1A 0.006 0.039 -9999 0 -0.42 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.059 0.17 -9999 0 -0.56 50 50
STXBP1 -0.005 0.058 -9999 0 -0.74 3 3
ACh/CHRNA1 -0.015 0.074 -9999 0 -0.42 14 14
RAB3GAP2/RIMS1/UNC13B -0.05 0.15 -9999 0 -0.49 49 49
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 -0.073 0.22 -9999 0 -0.74 48 48
mol:ACh 0.005 0.025 -9999 0 -0.15 11 11
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.043 0.12 -9999 0 -0.65 3 3
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.073 -9999 0 -0.42 14 14
UNC13B -0.005 0.058 -9999 0 -0.74 3 3
CHRNA1 -0.018 0.11 -9999 0 -0.63 14 14
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.015 0.071 -9999 0 -0.39 16 16
SNAP25 -0.007 0.05 -9999 0 -0.32 11 11
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.019 0.1 -9999 0 -0.57 16 16
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.006 0.05 -9999 0 -0.41 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.043 0.12 -9999 0 -0.65 3 3
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0 0 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EGF/EGFR -0.056 0.15 -9999 0 -0.45 52 52
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.084 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.008 0.075 -9999 0 -0.74 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.014 0.099 -9999 0 -0.69 10 10
EGF/EGFR dimer/SHC -0.023 0.099 -9999 0 -0.52 12 12
mol:GDP -0.019 0.083 -9999 0 -0.8 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.063 0.21 -9999 0 -0.74 41 41
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.076 -9999 0 -0.74 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.018 0.077 -9999 0 -0.75 1 1
FRAP1 -0.018 0.08 -9999 0 -0.77 1 1
EGF/EGFR dimer -0.027 0.12 -9999 0 -0.5 26 26
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.053 0.16 -9999 0 -0.56 46 46
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.033 0.12 -9999 0 -0.47 34 34
MAP4K1 -0.006 0.067 -9999 0 -0.74 4 4
MAP3K8 -0.003 0.048 -9999 0 -0.74 2 2
PRKCB -0.037 0.16 -9999 0 -0.74 24 24
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.015 0.097 -9999 0 -0.72 3 3
JUN -0.005 0.16 -9999 0 -0.66 24 24
MAP3K7 0.015 0.097 -9999 0 -0.72 3 3
GRAP2 -0.04 0.17 -9999 0 -0.74 26 26
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.099 -9999 0 -0.77 3 3
LAT 0 0 -9999 0 -10000 0 0
LCP2 -0.011 0.089 -9999 0 -0.74 7 7
MAPK8 -0.012 0.16 -9999 0 -0.7 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.024 0.094 -9999 0 -0.76 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.031 0.12 -9999 0 -0.81 3 3
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.029 0.12 -9999 0 -0.56 25 25
PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.01 0.029 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.001 0.14 -9999 0 -0.59 7 7
GNAO1 0.006 0.051 -9999 0 -0.64 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.1 -9999 0 -0.5 8 8
PLCG1 0.006 0.13 -9999 0 -0.54 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.009 0.004 -9999 0 -10000 0 0
GNAI1 0.008 0.035 -9999 0 -0.75 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.011 0.11 -9999 0 -0.48 25 25
S1P1/S1P -0.031 0.091 -9999 0 -0.38 25 25
negative regulation of cAMP metabolic process 0 0.13 -9999 0 -0.57 7 7
MAPK3 -0.011 0.19 -9999 0 -0.55 49 49
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.038 0.16 -9999 0 -0.74 25 25
PLCB2 0.004 0.11 -9999 0 -0.45 9 9
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.027 0.077 -9999 0 -0.41 7 7
receptor internalization -0.03 0.085 -9999 0 -0.36 25 25
PTGS2 -0.061 0.34 -9999 0 -1.1 49 49
Rac1/GTP -0.027 0.077 -9999 0 -0.41 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA 0 0.001 -9999 0 -10000 0 0
negative regulation of T cell proliferation 0 0.13 -9999 0 -0.57 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0 0.084 -9999 0 -0.74 6 6
MAPK1 -0.011 0.19 -9999 0 -0.55 49 49
S1P1/S1P/PDGFB-D/PDGFRB 0.006 0.11 -9999 0 -0.56 7 7
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 -0.023 0.13 -9999 0 -0.74 15 15
ENAH 0.058 0.023 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EPHA2 -0.005 0.058 -9999 0 -0.74 3 3
MYO6 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.083 -9999 0 -0.48 15 15
AQP5 -0.17 0.25 -9999 0 -0.55 149 149
CTNND1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.17 -9999 0 -0.38 136 136
EGF -0.014 0.099 -9999 0 -0.69 10 10
NCKAP1 0 0 -9999 0 -10000 0 0
AQP3 -0.08 0.19 -9999 0 -0.55 70 70
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.033 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GDP -0.002 0.025 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.43 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.044 0 -9999 0 -10000 0 0
PVRL2 0 0 -9999 0 -10000 0 0
ZYX 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.031 -9999 0 -0.4 3 3
CDH1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.077 -9999 0 -0.76 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
IGF1R 0 0 -9999 0 -10000 0 0
IGF1 -0.024 0.13 -9999 0 -0.73 16 16
DIAPH1 -0.02 0.11 -9999 0 -0.64 15 15
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.025 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
VCL 0.04 0 -9999 0 -10000 0 0
EFNA1 0 0 -9999 0 -10000 0 0
LPP 0.04 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.002 0.029 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.11 0.18 -9999 0 -0.39 136 136
HGF/MET -0.08 0.15 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 101 101
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0 -9999 0 -10000 0 0
actin cable formation 0.068 0.028 -9999 0 -10000 0 0
KIAA1543 0.039 0.019 -9999 0 -10000 0 0
KIFC3 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
EXOC3 0 0 -9999 0 -10000 0 0
ACTN1 0 0 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
STX4 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
LIMA1 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
ROCK1 -0.002 0.022 -9999 0 -10000 0 0
adherens junction assembly 0.052 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.012 0.065 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.004 0.054 -9999 0 -0.68 3 3
PLEKHA7 0 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.034 -9999 0 -0.43 3 3
establishment of epithelial cell apical/basal polarity 0 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0 -9999 0 -10000 0 0
BCR signaling pathway

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
JUN 0.014 0.094 -10000 0 -0.47 10 10
IKBKB 0.015 0.051 -10000 0 -0.27 3 3
AKT1 0.003 0.085 -10000 0 -0.27 17 17
IKBKG 0.017 0.053 -10000 0 -0.28 5 5
CALM1 -0.009 0.097 -10000 0 -0.49 12 12
PIK3CA 0 0 -10000 0 -10000 0 0
MAP3K1 0 0.14 -10000 0 -0.7 11 11
MAP3K7 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.1 0.23 2 -0.53 12 14
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.001 0.08 0.18 3 -0.26 9 12
LYN -0.003 0.048 -10000 0 -0.74 2 2
BLNK -0.002 0.034 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.03 0.12 -10000 0 -0.52 28 28
CD22 -0.076 0.21 -10000 0 -0.62 51 51
CAMK2G -0.002 0.091 -10000 0 -0.64 5 5
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D -0.001 0.034 -10000 0 -0.74 1 1
SHC/GRB2/SOS1 -0.021 0.091 -10000 0 -0.74 3 3
GO:0007205 -0.018 0.1 -10000 0 -0.54 12 12
SYK -0.002 0.034 -10000 0 -0.74 1 1
ELK1 -0.01 0.099 -10000 0 -0.5 12 12
NFATC1 -0.007 0.12 -10000 0 -0.54 14 14
B-cell antigen/BCR complex -0.03 0.12 -10000 0 -0.52 28 28
PAG1/CSK -0.007 0.062 -10000 0 -0.56 6 6
NFKBIB 0.014 0.019 0.078 2 -10000 0 2
HRAS -0.002 0.094 -10000 0 -0.48 12 12
NFKBIA 0.014 0.019 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.018 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.029 0.12 -10000 0 -0.77 6 6
mol:GDP -0.019 0.1 -10000 0 -0.52 12 12
PTEN 0 0 -10000 0 -10000 0 0
CD79B -0.006 0.064 -10000 0 -0.7 4 4
NF-kappa-B/RelA/I kappa B alpha 0.018 0.016 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.015 0.14 -10000 0 -0.56 18 18
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.026 0.1 0.23 4 -0.55 12 16
CSK 0 0 -10000 0 -10000 0 0
FOS -0.047 0.16 -10000 0 -0.41 64 64
CHUK 0.017 0.053 -10000 0 -0.28 5 5
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.022 0.081 -10000 0 -0.61 6 6
PTPN6 -0.07 0.2 -10000 0 -0.78 25 25
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.024 -10000 0 -0.12 11 11
VAV2 -0.059 0.16 -10000 0 -0.83 13 13
ubiquitin-dependent protein catabolic process 0.018 0.019 0.081 2 -10000 0 2
BTK -0.11 0.33 -10000 0 -1.1 45 45
CD19 -0.066 0.17 -10000 0 -0.66 23 23
MAP4K1 -0.006 0.067 -10000 0 -0.74 4 4
CD72 -0.001 0.026 -10000 0 -0.57 1 1
PAG1 -0.009 0.082 -10000 0 -0.74 6 6
MAPK14 0.01 0.12 -10000 0 -0.59 10 10
SH3BP5 -0.011 0.089 -10000 0 -0.74 7 7
PIK3AP1 -0.012 0.13 -10000 0 -0.68 12 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.032 0.13 -10000 0 -0.61 18 18
RAF1 0.005 0.088 -10000 0 -0.62 5 5
RasGAP/p62DOK/SHIP -0.028 0.12 -10000 0 -0.74 7 7
CD79A -0.035 0.15 -10000 0 -0.66 26 26
re-entry into mitotic cell cycle -0.001 0.08 0.18 3 -0.26 9 12
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.018 0.074 -10000 0 -0.49 5 5
MAPK1 0.018 0.074 -10000 0 -0.49 5 5
CD72/SHP1 -0.065 0.18 -10000 0 -0.72 25 25
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.01 0.12 -10000 0 -0.59 10 10
actin cytoskeleton organization -0.014 0.15 -10000 0 -0.67 13 13
NF-kappa-B/RelA 0.039 0.031 0.16 2 -10000 0 2
Calcineurin -0.02 0.073 -10000 0 -0.57 5 5
PI3K -0.064 0.14 -10000 0 -0.6 17 17
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.023 0.1 0.26 4 -0.53 12 16
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.038 0.16 -10000 0 -0.91 12 12
DAPP1 -0.042 0.18 -10000 0 -1.1 11 11
cytokine secretion -0.005 0.11 -10000 0 -0.5 14 14
mol:DAG -0.026 0.1 0.23 4 -0.55 12 16
PLCG2 0 0 -10000 0 -10000 0 0
MAP2K1 0.012 0.082 -10000 0 -0.55 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.14 -10000 0 -0.59 21 21
mol:PI-3-4-5-P3 -0.047 0.099 -10000 0 -0.4 17 17
ETS1 -0.004 0.11 -10000 0 -0.51 16 16
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.025 0.11 -10000 0 -0.48 18 18
B-cell antigen/BCR complex/LYN -0.042 0.16 -10000 0 -0.74 17 17
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0.002 -10000 0 -10000 0 0
RAC1 -0.016 0.16 -10000 0 -0.73 13 13
B-cell antigen/BCR complex/LYN/SYK -0.068 0.19 -10000 0 -0.75 25 25
CARD11 -0.012 0.11 -10000 0 -0.55 12 12
FCGR2B -0.014 0.1 -10000 0 -0.74 9 9
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.016 0.026 -10000 0 -10000 0 0
PTPRC -0.048 0.18 -10000 0 -0.74 31 31
PDPK1 -0.031 0.067 -10000 0 -0.27 14 14
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.018 0.013 -10000 0 -0.1 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.028 0.11 0.45 30 -10000 0 30
KIRREL -0.005 0.091 -10000 0 -0.75 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.028 0.11 -10000 0 -0.45 30 30
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.022 0.084 -10000 0 -0.46 8 8
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.012 0.051 -10000 0 -0.34 7 7
FYN -0.02 0.08 -10000 0 -0.46 8 8
mol:Ca2+ -0.021 0.083 -10000 0 -0.45 8 8
mol:DAG -0.022 0.084 -10000 0 -0.46 8 8
NPHS2 -0.003 0.048 -10000 0 -0.58 3 3
mol:IP3 -0.022 0.084 -10000 0 -0.46 8 8
regulation of endocytosis -0.018 0.074 -10000 0 -0.43 8 8
Nephrin/NEPH1/podocin/Cholesterol -0.022 0.086 -10000 0 -0.46 8 8
establishment of cell polarity -0.028 0.11 -10000 0 -0.45 30 30
Nephrin/NEPH1/podocin/NCK1-2 -0.019 0.075 -10000 0 -0.51 2 2
Nephrin/NEPH1/beta Arrestin2 -0.019 0.075 -10000 0 -0.44 8 8
NPHS1 -0.021 0.12 -10000 0 -0.57 23 23
Nephrin/NEPH1/podocin -0.02 0.081 -10000 0 -0.47 8 8
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.022 0.084 -10000 0 -0.46 8 8
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.022 0.084 -10000 0 -0.46 8 8
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.02 0.13 -10000 0 -0.49 26 26
cytoskeleton organization -0.015 0.064 -10000 0 -0.51 1 1
Nephrin/NEPH1 -0.02 0.079 -10000 0 -0.32 30 30
Nephrin/NEPH1/ZO-1 -0.022 0.087 -10000 0 -0.46 8 8
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.006 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.058 -9999 0 -0.45 8 8
forebrain development -0.089 0.14 -9999 0 -0.49 9 9
GNAO1 0.001 0.051 -9999 0 -0.63 3 3
SMO/beta Arrestin2 -0.002 0.027 -9999 0 -0.42 2 2
SMO 0.003 0.038 -9999 0 -0.58 2 2
ARRB2 0.005 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.043 0.015 -9999 0 -10000 0 0
mol:GTP -0.003 0.004 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.005 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.035 -9999 0 -0.75 1 1
XPO1 0.006 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.11 0.11 -9999 0 -0.58 3 3
SAP30 0.006 0.006 -9999 0 -10000 0 0
mol:GDP 0.003 0.038 -9999 0 -0.58 2 2
MIM/GLI2A -0.033 0.05 -9999 0 -10000 0 0
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.005 0.005 -9999 0 -10000 0 0
GLI2 0.037 0.021 -9999 0 -10000 0 0
GLI3 0.04 0.016 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.006 0.006 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.008 0.075 -9999 0 -0.74 5 5
Gi family/GTP 0.001 0.05 -9999 0 -0.33 5 5
SIN3B 0.006 0.006 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.001 0.009 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.032 -9999 0 -10000 0 0
FOXA2 -0.61 0.6 -9999 0 -1.2 244 244
neural tube patterning -0.089 0.14 -9999 0 -0.49 9 9
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.009 -9999 0 -10000 0 0
GNB1 -0.002 0.034 -9999 0 -0.74 1 1
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 -0.033 0.05 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.089 0.14 -9999 0 -0.49 9 9
SUFU 0.011 0.017 -9999 0 -10000 0 0
LGALS3 0 0 -9999 0 -10000 0 0
catabolic process -0.001 0.012 -9999 0 -10000 0 0
GLI3A/CBP 0.005 0.033 -9999 0 -0.38 1 1
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.091 0.15 -9999 0 -0.55 6 6
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.006 0.006 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.001 0.009 -9999 0 -10000 0 0
GNAZ -0.004 0.083 -9999 0 -0.74 6 6
RBBP4 0.006 0.006 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.002 0.014 -9999 0 -10000 0 0
STK36 0.006 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.056 -9999 0 -0.62 2 2
PTCH1 -0.082 0.17 -9999 0 -1 6 6
MIM/GLI1 -0.23 0.29 -9999 0 -0.52 244 244
CREBBP 0.005 0.033 -9999 0 -0.38 1 1
Su(fu)/SIN3/HDAC complex 0.029 0.029 -9999 0 -10000 0 0
Syndecan-4-mediated 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
PTK2 0.009 0.095 -9999 0 -0.61 11 11
Syndecan-4/Syndesmos -0.019 0.059 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.044 0.11 -9999 0 -0.59 7 7
Syndecan-4/ADAM12 -0.089 0.13 -9999 0 -0.44 16 16
CCL5 -0.014 0.1 -9999 0 -0.74 9 9
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.005 0.045 -9999 0 -0.57 3 3
ADAM12 -0.16 0.25 -9999 0 -0.57 131 131
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.011 0.033 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.094 0.13 -9999 0 -0.45 6 6
Syndecan-4/CXCL12/CXCR4 -0.046 0.12 -9999 0 -0.63 7 7
Syndecan-4/Laminin alpha3 -0.028 0.085 -9999 0 -0.6 2 2
MDK -0.012 0.082 -9999 0 -0.57 10 10
Syndecan-4/FZD7 -0.019 0.06 -9999 0 -10000 0 0
Syndecan-4/Midkine -0.024 0.072 -9999 0 -0.5 2 2
FZD7 -0.001 0.026 -9999 0 -0.57 1 1
Syndecan-4/FGFR1/FGF -0.029 0.089 -9999 0 -0.55 5 5
THBS1 -0.009 0.082 -9999 0 -0.74 6 6
integrin-mediated signaling pathway -0.023 0.066 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.044 0.11 -9999 0 -0.59 7 7
Syndecan-4/TACI -0.025 0.075 -9999 0 -10000 0 0
CXCR4 0 0 -9999 0 -10000 0 0
cell adhesion -0.007 0.059 -9999 0 -0.36 13 13
Syndecan-4/Dynamin -0.019 0.059 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.023 0.086 -9999 0 -0.68 5 5
Syndecan-4/GIPC -0.019 0.059 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.026 0.082 -9999 0 -0.68 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.17 0.26 -9999 0 -0.57 141 141
LAMA3 -0.018 0.12 -9999 0 -0.74 12 12
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.05 -9999 0 -0.69 2 2
Syndecan-4/alpha-Actinin -0.019 0.059 -9999 0 -10000 0 0
TFPI -0.061 0.2 -9999 0 -0.74 40 40
F2 -0.013 0.096 -9999 0 -0.57 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.072 0.16 -9999 0 -0.64 5 5
ACTN1 0 0 -9999 0 -10000 0 0
TNC -0.011 0.08 -9999 0 -0.59 9 9
Syndecan-4/CXCL12 -0.049 0.13 -9999 0 -0.66 7 7
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.06 0.2 -9999 0 -0.74 39 39
TNFRSF13B -0.016 0.099 -9999 0 -0.63 12 12
FGF2 -0.023 0.13 -9999 0 -0.74 15 15
FGFR1 -0.002 0.034 -9999 0 -0.74 1 1
Syndecan-4/PI-4-5-P2 0.007 0.069 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.015 0.11 -9999 0 -0.73 11 11
cell migration -0.004 0.013 -9999 0 -10000 0 0
PRKCD 0.002 0.006 -9999 0 -10000 0 0
vasculogenesis -0.023 0.083 -9999 0 -0.65 5 5
SDC4 0.008 0.073 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.024 0.068 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.009 0.026 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.019 0.059 -9999 0 -10000 0 0
MMP9 -0.02 0.13 -9999 0 -0.57 25 25
Rac1/GTP -0.008 0.061 -9999 0 -0.37 13 13
cytoskeleton organization -0.018 0.058 -9999 0 -10000 0 0
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.05 0.13 -9999 0 -0.66 7 7
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.05 -9999 0 -0.63 3 3
CDC42/GTP -0.029 0.087 -9999 0 -0.47 3 3
PLCG1 0.002 0.1 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.028 0.085 -9999 0 -0.46 3 3
S1PR5 -0.009 0.072 -9999 0 -0.6 7 7
S1PR4 -0.066 0.21 -9999 0 -0.74 43 43
MAPK3 0.002 0.1 -9999 0 -0.48 3 3
MAPK1 0.002 0.1 -9999 0 -0.48 3 3
S1P/S1P5/Gi -0.007 0.04 -9999 0 -0.31 2 2
GNAI1 -0.002 0.034 -9999 0 -0.74 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.045 -9999 0 -0.37 7 7
RHOA -0.036 0.12 -9999 0 -0.41 43 43
S1P/S1P4/Gi -0.033 0.097 -9999 0 -0.32 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.009 0.082 -9999 0 -0.74 6 6
S1P/S1P4/G12/G13 -0.039 0.13 -9999 0 -0.44 43 43
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.048 0.41 6 -10000 0 6
CDKN1A 0 0 -10000 0 -10000 0 0
KAT2B -0.003 0.048 -10000 0 -0.74 2 2
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.002 0.037 -10000 0 -0.57 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.049 0.15 -10000 0 -0.42 71 71
PPARGC1A -0.15 0.3 -10000 0 -0.74 96 96
FHL2 -0.005 0.052 -10000 0 -0.57 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A 0.012 0.048 -10000 0 -0.41 6 6
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.011 0.037 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.097 0.2 -10000 0 -0.49 96 96
p53/SIRT1 0 0 -10000 0 -10000 0 0
SIRT1/FOXO4 0 0 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.028 -10000 0 -10000 0 0
HIST1H1E -0.014 0.046 -10000 0 -10000 0 0
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.051 0.12 0.48 2 -10000 0 2
TP53 0 0 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.027 -10000 0 -0.41 2 2
ACSS2 0.017 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.051 0.12 -10000 0 -0.48 2 2
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0 0 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity -0.028 0.12 -10000 0 -0.56 24 24
MAP2K4 0.04 0.011 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.003 0.048 -10000 0 -0.74 2 2
SMPD1 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.037 0.16 -10000 0 -0.74 24 24
TRAIL/TRAILR2 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.072 0.19 -10000 0 -0.56 62 62
TRAIL/TRAILR1 -0.002 0.036 -10000 0 -0.56 2 2
TRAIL/TRAILR4 -0.028 0.12 -10000 0 -0.56 24 24
TRAIL/TRAILR1/DAP3/GTP -0.002 0.028 -10000 0 -0.44 2 2
IKK complex -0.001 0.01 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.009 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.037 0.16 -10000 0 -0.74 24 24
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.003 0.048 -10000 0 -0.74 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.02 -10000 0 -10000 0 0
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.026 -10000 0 -10000 0 0
mol:ceramide 0 0 -10000 0 -10000 0 0
FADD 0 0 -10000 0 -10000 0 0
MAPK8 0.046 0.01 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.095 0.25 -10000 0 -0.74 62 62
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.031 -10000 0 -0.48 2 2
DAP3 0 0 -10000 0 -10000 0 0
CASP10 0.013 0.066 0.29 23 -0.4 1 24
JNK cascade -0.028 0.12 -10000 0 -0.56 24 24
TRAIL (trimer) 0 0 -10000 0 -10000 0 0
TNFRSF10C -0.095 0.25 -10000 0 -0.74 62 62
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.026 -10000 0 -0.41 2 2
TRAIL/TRAILR2/FADD 0 0 -10000 0 -10000 0 0
cell death 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0 -10000 0 -10000 0 0
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0 0.003 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.008 0.12 -9999 0 -0.74 12 12
ELF1 -0.004 0.034 -9999 0 -0.37 3 3
CCNA2 -0.15 0.25 -9999 0 -0.57 125 125
PIK3CA 0.01 0.001 -9999 0 -10000 0 0
JAK3 0.01 0.001 -9999 0 -10000 0 0
PIK3R1 0.01 0.001 -9999 0 -10000 0 0
JAK1 0.01 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.055 0.074 -9999 0 -0.68 3 3
SHC1 0.01 0.001 -9999 0 -10000 0 0
SP1 -0.002 0.029 -9999 0 -0.37 3 3
IL2RA 0.018 0.085 -9999 0 -0.69 6 6
IL2RB 0.005 0.059 -9999 0 -0.74 3 3
SOS1 0.01 0.001 -9999 0 -10000 0 0
IL2RG -0.002 0.096 -9999 0 -0.74 8 8
G1/S transition of mitotic cell cycle -0.014 0.11 -9999 0 -0.93 3 3
PTPN11 0.01 0.001 -9999 0 -10000 0 0
CCND2 0.02 0.077 -9999 0 -0.96 3 3
LCK 0.009 0.034 -9999 0 -0.74 1 1
GRB2 0.01 0.001 -9999 0 -10000 0 0
IL2 0.005 0.005 -9999 0 -10000 0 0
CDK6 -0.002 0.037 -9999 0 -0.57 2 2
CCND3 0.06 0.064 -9999 0 -0.56 3 3
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0 0.007 -9999 0 -10000 0 0
GNAO1 -0.004 0.05 -9999 0 -0.63 3 3
mol:Sphinganine-1-P 0.02 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.004 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.006 -9999 0 -10000 0 0
S1PR5 -0.009 0.072 -9999 0 -0.6 7 7
S1PR4 -0.066 0.21 -9999 0 -0.74 43 43
GNAI1 -0.002 0.034 -9999 0 -0.74 1 1
S1P/S1P5/G12 -0.005 0.039 -9999 0 -0.43 1 1
S1P/S1P3/Gq -0.067 0.12 -9999 0 -0.64 2 2
S1P/S1P4/Gi -0.031 0.093 -9999 0 -0.5 3 3
GNAQ -0.002 0.034 -9999 0 -0.74 1 1
GNAZ -0.009 0.082 -9999 0 -0.74 6 6
GNA14 -0.18 0.32 -9999 0 -0.74 114 114
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.048 -10000 0 -0.74 2 2
ANTXR2 -0.011 0.089 -10000 0 -0.74 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.1 7 7
monocyte activation -0.002 0.082 -10000 0 -0.45 15 15
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.002 0.018 -10000 0 -0.31 1 1
CYAA 0.006 0.069 -10000 0 -0.54 7 7
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B 0.003 0.074 -10000 0 -0.41 14 14
Channel -0.008 0.072 -10000 0 -0.57 7 7
NLRP1 -0.004 0.038 -10000 0 -0.47 3 3
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.1 7 -10000 0 7
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.09 0.18 -10000 0 -0.44 100 100
PA/Cellular Receptors -0.009 0.077 -10000 0 -0.61 7 7
apoptosis -0.002 0.013 -10000 0 -0.1 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.067 -10000 0 -0.53 7 7
macrophage activation 0.017 0.012 -10000 0 -10000 0 0
TNF -0.02 0.12 -10000 0 -0.73 13 13
VCAM1 -0.015 0.079 -10000 0 -0.46 15 15
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.013 0.12 2 -10000 0 2
IL18 0.01 0.046 -10000 0 -0.45 4 4
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.1 7 7
LEF -0.002 0.013 -10000 0 -0.11 7 7
CASP1 -0.003 0.032 -10000 0 -0.28 4 4
mol:cAMP -0.002 0.016 -10000 0 -10000 0 0
necrosis -0.002 0.013 -10000 0 -0.1 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.068 -10000 0 -0.54 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.034 -10000 0 -0.74 1 1
Jak2/Leptin Receptor -0.026 0.098 -10000 0 -0.38 28 28
PTP1B/AKT1 -0.006 0.024 -10000 0 -10000 0 0
FYN -0.002 0.034 -10000 0 -0.74 1 1
p210 bcr-abl/PTP1B 0.024 0.037 -10000 0 -0.31 1 1
EGFR -0.013 0.12 -10000 0 -0.63 17 17
EGF/EGFR -0.021 0.085 -10000 0 -0.48 12 12
CSF1 -0.006 0.067 -10000 0 -0.74 4 4
AKT1 0.007 0.005 -10000 0 -10000 0 0
INSR 0.007 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.023 0.077 -10000 0 -0.4 9 9
Insulin Receptor/Insulin -0.004 0.019 -10000 0 -10000 0 0
HCK -0.008 0.075 -10000 0 -0.74 5 5
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.035 -10000 0 -0.29 1 1
EGF -0.005 0.1 -10000 0 -0.69 10 10
YES1 0 0 -10000 0 -10000 0 0
CAV1 -0.026 0.11 -10000 0 -0.47 11 11
TXN 0.007 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.005 0.022 -10000 0 -10000 0 0
cell migration -0.024 0.037 0.31 1 -10000 0 1
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.039 0.15 -10000 0 -0.63 30 30
ITGA2B -0.023 0.13 -10000 0 -0.74 15 15
CSF1R -0.014 0.1 -10000 0 -0.74 9 9
Prolactin Receptor/Prolactin -0.035 0.13 -10000 0 -0.47 37 37
FGR -0.049 0.18 -10000 0 -0.74 32 32
PTP1B/p130 Cas -0.006 0.025 -10000 0 -0.29 1 1
Crk/p130 Cas -0.005 0.022 -10000 0 -10000 0 0
DOK1 0.033 0.036 -10000 0 -0.33 1 1
JAK2 0.014 0.048 -10000 0 -0.32 1 1
Jak2/Leptin Receptor/Leptin -0.043 0.082 -10000 0 -0.48 3 3
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 0.024 0.037 -10000 0 -0.31 1 1
LYN -0.003 0.048 -10000 0 -0.74 2 2
CDH2 -0.035 0.14 -10000 0 -0.58 29 29
SRC 0.023 0.016 -10000 0 -10000 0 0
ITGB3 -0.012 0.095 -10000 0 -0.74 8 8
CAT1/PTP1B 0.017 0.12 -10000 0 -0.51 15 15
CAPN1 0.007 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.015 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.039 0.076 -10000 0 -0.54 2 2
negative regulation of transcription 0.014 0.048 -10000 0 -0.32 1 1
FCGR2A -0.017 0.11 -10000 0 -0.74 11 11
FER 0.007 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.027 0.12 -10000 0 -0.56 23 23
BLK -0.036 0.15 -10000 0 -0.66 26 26
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.005 -10000 0 -10000 0 0
LEPR -0.04 0.17 -10000 0 -0.74 28 28
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.001 0.14 -10000 0 -0.61 16 16
PRL -0.01 0.073 -10000 0 -0.57 8 8
SOCS3 0.002 0.093 -10000 0 -1.4 2 2
SPRY2 -0.005 0.059 -10000 0 -0.75 3 3
Insulin Receptor/Insulin/IRS1 0 0 -10000 0 -10000 0 0
CSF1/CSF1R -0.016 0.076 -10000 0 -0.46 11 11
Ras protein signal transduction 0.005 0.012 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.1 0.22 -10000 0 -0.57 84 84
STAT5B 0.022 0.037 -10000 0 -0.25 1 1
STAT5A 0.022 0.037 -10000 0 -0.25 1 1
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.033 -10000 0 -0.38 2 2
CSN2 -0.012 0.04 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
LAT 0.011 0.077 -10000 0 -0.48 11 11
YBX1 0.001 0.003 -10000 0 -10000 0 0
LCK -0.002 0.034 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.001 0.026 -10000 0 -0.57 1 1
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 0 0 -9999 0 -10000 0 0
VDR -0.002 0.034 -9999 0 -0.74 1 1
Cbp/p300/PCAF -0.002 0.031 -9999 0 -0.48 2 2
EP300 0 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.029 -9999 0 -0.31 1 1
KAT2B -0.003 0.048 -9999 0 -0.74 2 2
MAPK14 0 0 -9999 0 -10000 0 0
AKT1 0.02 0.034 -9999 0 -0.31 2 2
RAR alpha/9cRA/Cyclin H -0.007 0.029 -9999 0 -0.35 2 2
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.031 0.033 -9999 0 -0.41 1 1
CDC2 0.001 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.03 -9999 0 -10000 0 0
NCOR2 -0.002 0.034 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.026 -9999 0 -0.57 1 1
RXRs/RARs/NRIP1/9cRA -0.024 0.082 -9999 0 -0.6 2 2
NCOA2 -0.002 0.034 -9999 0 -0.74 1 1
NCOA3 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.034 -9999 0 -0.74 1 1
RARG 0.01 0.001 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.01 0.002 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0.001 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.065 0.072 -9999 0 -0.67 2 2
RARA 0.013 0.043 -9999 0 -0.29 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.036 -9999 0 -0.41 1 1
PRKCA 0.009 0.048 -9999 0 -0.74 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.041 0.09 -9999 0 -0.63 2 2
RXRG -0.22 0.22 -9999 0 -0.42 254 254
RXRA 0.02 0.041 -9999 0 -0.31 2 2
RXRB 0.006 0.065 -9999 0 -0.41 2 2
VDR/Vit D3/DNA -0.001 0.026 -9999 0 -0.57 1 1
RBP1 -0.02 0.1 -9999 0 -0.57 17 17
CRBP1/9-cic-RA -0.015 0.078 -9999 0 -0.42 17 17
RARB 0.008 0.048 -9999 0 -0.74 2 2
PRKCG -0.032 0.15 -9999 0 -0.57 35 35
MNAT1 0 0 -9999 0 -10000 0 0
RAR alpha/RXRs -0.031 0.081 -9999 0 -0.66 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.07 -9999 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.038 -9999 0 -0.4 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.041 0.09 -9999 0 -0.63 2 2
positive regulation of DNA binding -0.006 0.028 -9999 0 -0.33 2 2
NRIP1 -0.037 0.084 -9999 0 -0.69 1 1
RXRs/RARs -0.048 0.091 -9999 0 -0.54 3 3
RXRs/RXRs/DNA/9cRA -0.07 0.076 -9999 0 -0.69 2 2
PRKACA 0 0 -9999 0 -10000 0 0
CDK7 0 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.005 0.018 -9999 0 -10000 0 0
CCNH 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.035 -10000 0 -10000 0 0
IRAK/TOLLIP 0 0 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.059 0.16 -10000 0 -0.47 61 61
IL1A -0.053 0.18 -10000 0 -0.65 39 39
IL1B 0.004 0.094 -10000 0 -0.56 13 13
IRAK/TRAF6/p62/Atypical PKCs 0 0 -10000 0 -10000 0 0
IL1R2 -0.028 0.12 -10000 0 -0.57 24 24
IL1R1 -0.002 0.034 -10000 0 -0.74 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.04 0.22 8 -10000 0 8
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.009 0.082 -10000 0 -0.74 6 6
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.042 0.012 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.011 0.064 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.031 0.11 -10000 0 -0.46 19 19
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.028 0.1 -10000 0 -0.42 19 19
IL1 beta fragment/IL1R1/IL1RAP -0.013 0.073 -10000 0 -0.43 14 14
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.036 0.013 -10000 0 -10000 0 0
IRAK1 0.022 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.007 0.064 -10000 0 -0.54 6 6
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.04 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.013 0.073 -10000 0 -0.43 14 14
IL1 beta/IL1R2 -0.03 0.11 -10000 0 -0.5 13 13
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.057 -10000 0 -10000 0 0
IRAK3 -0.018 0.12 -10000 0 -0.74 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.016 0.08 -10000 0 -0.78 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.069 -10000 0 -0.62 1 1
IL1 alpha/IL1R1/IL1RAP -0.034 0.12 -10000 0 -0.42 39 39
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.013 0.066 -10000 0 -0.64 1 1
CASP1 -0.003 0.048 -10000 0 -0.74 2 2
IL1RN/IL1R2 -0.026 0.1 -10000 0 -0.43 29 29
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.012 0.068 -10000 0 -0.4 14 14
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.054 -10000 0 -0.61 1 1
PIK3CA 0 0 -10000 0 -10000 0 0
IL1RN -0.008 0.07 -10000 0 -0.63 6 6
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.012 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.049 0.058 -10000 0 -0.83 1 1
UGCG -0.002 0.009 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.034 0.066 -10000 0 -0.46 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.024 0.015 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.043 -10000 0 -0.48 3 3
FRAP1 0.071 0.067 -10000 0 -0.56 3 3
FOXO3 0.073 0.064 -10000 0 -0.55 3 3
AKT1 0.068 0.068 -10000 0 -0.6 3 3
GAB2 -0.008 0.12 -10000 0 -0.74 12 12
SMPD1 -0.002 0.009 -10000 0 -10000 0 0
SGMS1 -0.002 0.009 -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 0.02 0.001 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.044 0.029 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.026 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.012 0.001 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
JAK1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.072 0.059 -10000 0 -0.6 1 1
MYB 0.014 0.1 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.059 0.075 -10000 0 -0.68 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.058 0.073 -10000 0 -0.66 3 3
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation 0.064 0.068 -10000 0 -0.6 3 3
SHC1 0.01 0.002 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.008 -10000 0 -0.039 17 17
PRKCZ 0.065 0.07 -10000 0 -0.63 3 3
NF kappa B1 p50/RelA -0.007 0.043 -10000 0 -0.47 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.043 0.064 -10000 0 -0.64 3 3
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA 0.002 0.075 -10000 0 -0.66 6 6
IL2RB 0.008 0.059 -10000 0 -0.74 3 3
TERT -0.22 0.28 -10000 0 -0.57 190 190
E2F1 0.018 0.048 -10000 0 -0.45 2 2
SOS1 0.01 0.002 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.019 17 -10000 0 17
PTPN11 0.01 0.002 -10000 0 -10000 0 0
IL2RG 0 0.096 -10000 0 -0.74 8 8
actin cytoskeleton organization 0.064 0.068 -10000 0 -0.6 3 3
GRB2 0.01 0.002 -10000 0 -10000 0 0
IL2 0.007 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.005 -10000 0 -10000 0 0
LCK 0.011 0.034 -10000 0 -0.74 1 1
BCL2 0.073 0.057 -10000 0 -0.54 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.001 0.026 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.003 0.025 -9999 0 -0.26 4 4
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.002 0.034 -9999 0 -0.74 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.049 0.18 -9999 0 -0.74 32 32
p38 alpha/TAB1 -0.012 0.044 -9999 0 -0.33 2 2
PRKG1 -0.058 0.2 -9999 0 -0.74 38 38
DUSP8 -0.014 0.1 -9999 0 -0.74 9 9
PGK/cGMP/p38 alpha -0.038 0.11 -9999 0 -0.38 38 38
apoptosis -0.012 0.043 -9999 0 -0.32 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN -0.003 0.048 -9999 0 -0.74 2 2
DUSP1 -0.095 0.25 -9999 0 -0.74 62 62
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
SRC 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 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 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.031 0.08 -9999 0 -0.35 11 11
BLK -0.036 0.15 -9999 0 -0.66 26 26
HCK -0.008 0.075 -9999 0 -0.74 5 5
MAP2K3 0 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.002 0.034 -9999 0 -0.74 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.033 0.061 -9999 0 -0.36 2 2
positive regulation of innate immune response 0.037 0.088 -9999 0 -0.38 11 11
LCK -0.002 0.034 -9999 0 -0.74 1 1
p38alpha-beta/MKP7 -0.019 0.065 -9999 0 -0.44 2 2
p38alpha-beta/MKP5 -0.02 0.069 -9999 0 -0.45 4 4
PGK/cGMP -0.045 0.15 -9999 0 -0.57 38 38
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.059 0.13 -9999 0 -0.49 17 17
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.007 0.072 -9999 0 -0.71 5 5
IL27-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
TGFB1 0.003 0.026 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.069 -10000 0 -10000 0 0
IL27/IL27R/JAK1 -0.028 0.094 -10000 0 -0.58 1 1
TBX21 -0.029 0.22 -10000 0 -0.62 43 43
IL12B 0.009 0.004 -10000 0 -10000 0 0
IL12A 0.001 0.074 -10000 0 -0.57 8 8
IL6ST -0.016 0.14 -10000 0 -0.75 16 16
IL27RA/JAK1 -0.003 0.013 -10000 0 -10000 0 0
IL27 0.008 0.007 -10000 0 -10000 0 0
TYK2 0.011 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.062 0.14 -10000 0 -0.69 3 3
T-helper 2 cell differentiation -0.003 0.069 -10000 0 -10000 0 0
T cell proliferation during immune response -0.003 0.069 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.069 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.001 0.003 -10000 0 -10000 0 0
IL12RB1 -0.039 0.18 -10000 0 -0.74 31 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.018 0.19 -10000 0 -0.63 12 12
IL27/IL27R/JAK2/TYK2 0.002 0.069 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.003 0.069 -10000 0 -10000 0 0
STAT1 (dimer) -0.058 0.16 0.51 3 -0.77 6 9
JAK2 0.006 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.012 0.057 -10000 0 -10000 0 0
T cell proliferation -0.052 0.18 -10000 0 -0.51 26 26
IL12/IL12R/TYK2/JAK2 0.007 0.093 -10000 0 -0.59 2 2
IL17A -0.062 0.14 -10000 0 -0.69 3 3
mast cell activation -0.003 0.069 -10000 0 -10000 0 0
IFNG 0.006 0.02 -10000 0 -0.13 4 4
T cell differentiation -0.003 0.005 -10000 0 -0.022 4 4
STAT3 (dimer) -0.012 0.057 -10000 0 -10000 0 0
STAT5A (dimer) -0.012 0.057 -10000 0 -10000 0 0
STAT4 (dimer) -0.018 0.08 -10000 0 -0.48 6 6
STAT4 -0.012 0.095 -10000 0 -0.74 8 8
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.018 0.077 -10000 0 -10000 0 0
GATA3 -0.035 0.24 -10000 0 -1.4 14 14
IL18 0.006 0.045 -10000 0 -0.57 3 3
positive regulation of mast cell cytokine production -0.012 0.056 -10000 0 -10000 0 0
IL27/EBI3 -0.003 0.042 -10000 0 -0.52 3 3
IL27RA 0.007 0.017 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.74 82 82
STAT5A 0 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.006 -10000 0 -10000 0 0
IL1B -0.003 0.086 -10000 0 -0.57 11 11
EBI3 0.001 0.055 -10000 0 -0.69 3 3
TNF -0.005 0.092 -10000 0 -0.56 13 13
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.009 0.081 -9999 0 -0.67 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.047 -9999 0 -10000 0 0
AP1 -0.054 0.13 -9999 0 -0.72 3 3
mol:PIP3 -0.02 0.078 -9999 0 -0.58 3 3
AKT1 -0.006 0.051 -9999 0 -0.57 3 3
PTK2B 0.017 0.038 -9999 0 -0.4 1 1
RHOA 0.028 0.016 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0.082 -9999 0 -0.49 2 2
MAGI3 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.011 0.059 -9999 0 -0.41 6 6
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.061 -9999 0 -0.4 7 7
NF kappa B1 p50/RelA -0.024 0.066 -9999 0 -0.65 1 1
endothelial cell migration 0.015 0.089 -9999 0 -0.82 5 5
ADCY4 0.017 0.098 -9999 0 -0.62 6 6
ADCY5 0.011 0.096 -9999 0 -0.66 4 4
ADCY6 0.031 0.07 -9999 0 -0.59 4 4
ADCY7 0.031 0.069 -9999 0 -0.66 3 3
ADCY1 0.031 0.07 -9999 0 -0.66 3 3
ADCY2 0.018 0.082 -9999 0 -0.68 3 3
ADCY3 0.031 0.069 -9999 0 -0.66 3 3
ADCY8 -0.037 0.12 -9999 0 -0.66 5 5
ADCY9 0.031 0.074 -9999 0 -0.65 4 4
GSK3B 0.023 0.036 -9999 0 -0.38 1 1
arachidonic acid secretion 0.034 0.07 -9999 0 -0.67 3 3
GNG2 -0.008 0.075 -9999 0 -0.74 5 5
TRIP6 0 0.004 -9999 0 -10000 0 0
GNAO1 0.017 0.063 -9999 0 -0.55 5 5
HRAS 0 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.074 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.042 -9999 0 -0.92 1 1
JUN 0 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.004 0.039 -9999 0 -0.48 3 3
TIAM1 -0.002 0.049 -9999 0 -1.1 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0 0.083 -9999 0 -0.5 2 2
PLCB3 0.021 0.037 -9999 0 -0.44 3 3
FOS -0.085 0.24 -9999 0 -0.74 55 55
positive regulation of mitosis 0.034 0.07 -9999 0 -0.67 3 3
LPA/LPA1-2-3 -0.014 0.072 -9999 0 -0.49 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.024 0.048 -9999 0 -0.51 1 1
GNAZ 0.013 0.075 -9999 0 -0.52 8 8
EGFR/PI3K-beta/Gab1 -0.021 0.081 -9999 0 -0.62 3 3
positive regulation of dendritic cell cytokine production -0.014 0.072 -9999 0 -0.48 6 6
LPA/LPA2/MAGI-3 -0.001 0.007 -9999 0 -10000 0 0
ARHGEF1 -0.003 0.041 -9999 0 -0.55 2 2
GNAI2 0.02 0.051 -9999 0 -0.64 2 2
GNAI3 0.02 0.051 -9999 0 -0.64 2 2
GNAI1 0.019 0.066 -9999 0 -0.84 2 2
LPA/LPA3 -0.014 0.078 -9999 0 -0.46 14 14
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.005 0.056 -9999 0 -0.5 5 5
HB-EGF/EGFR -0.047 0.14 -9999 0 -0.51 22 22
HBEGF -0.022 0.14 -9999 0 -0.47 41 41
mol:DAG 0 0.083 -9999 0 -0.5 2 2
cAMP biosynthetic process 0.019 0.076 -9999 0 -0.66 4 4
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
GNB1 -0.002 0.034 -9999 0 -0.74 1 1
LYN 0.015 0.085 -9999 0 -0.64 2 2
GNAQ -0.009 0.05 -9999 0 -0.38 5 5
LPAR2 0 0 -9999 0 -10000 0 0
LPAR3 -0.018 0.1 -9999 0 -0.62 14 14
LPAR1 -0.005 0.056 -9999 0 -0.83 2 2
IL8 0.001 0.13 -9999 0 -0.49 11 11
PTK2 -0.013 0.067 -9999 0 -0.56 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.011 0.059 -9999 0 -0.41 6 6
EGFR -0.022 0.12 -9999 0 -0.63 17 17
PLCG1 -0.016 0.085 -9999 0 -0.36 10 10
PLD2 -0.013 0.067 -9999 0 -0.56 2 2
G12/G13 -0.004 0.044 -9999 0 -0.59 2 2
PI3K-beta -0.007 0.062 -9999 0 -0.69 3 3
cell migration 0.002 0.03 -9999 0 -0.26 1 1
SLC9A3R2 -0.005 0.058 -9999 0 -0.74 3 3
PXN 0.025 0.049 -9999 0 -0.52 1 1
HRAS/GTP -0.009 0.067 -9999 0 -0.61 4 4
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 25 25
PRKCE 0.008 0.034 -9999 0 -0.74 1 1
PRKCD 0.007 0.079 -9999 0 -0.47 2 2
Gi(beta/gamma) -0.011 0.08 -9999 0 -0.65 5 5
mol:LPA -0.001 0.017 -9999 0 -0.21 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.002 0.06 -9999 0 -0.64 1 1
MAPKKK cascade 0.034 0.07 -9999 0 -0.67 3 3
contractile ring contraction involved in cytokinesis 0.027 0.016 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.17 -9999 0 -0.4 118 118
GNA15 -0.008 0.047 -9999 0 -0.38 4 4
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT 0.023 0.063 -9999 0 -0.42 7 7
GNA11 -0.008 0.047 -9999 0 -0.38 4 4
Rac1/GTP -0.002 0.045 -9999 0 -0.98 1 1
MMP2 0.015 0.09 -9999 0 -0.83 5 5
Insulin Pathway

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
CBL/APS/CAP -0.047 0.12 -9999 0 -10000 0 0
TC10/GTP -0.046 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.047 0.18 -9999 0 -0.74 31 31
FOXO3 -0.004 0.014 -9999 0 -10000 0 0
AKT1 -0.021 0.082 -9999 0 -10000 0 0
INSR 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.092 0.24 -9999 0 -0.74 60 60
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.031 0 -9999 0 -10000 0 0
CAV1 -0.12 0.19 -9999 0 -0.42 135 135
CBL/APS/CAP/Crk-II/C3G -0.05 0.13 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.087 -9999 0 -10000 0 0
PARD6A 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.019 0.072 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -10000 0 0
Insulin Receptor 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0 0 -9999 0 -10000 0 0
PRKCI -0.006 0.022 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.088 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.021 0.082 -9999 0 -10000 0 0
PRKCZ -0.006 0.022 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.001 0.018 -9999 0 -10000 0 0
F2RL2 -0.1 0.22 -9999 0 -0.58 88 88
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.054 0.14 -9999 0 -0.43 60 60
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.001 0.019 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.007 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.001 0.019 -9999 0 -0.42 1 1
GRB2 0 0 -9999 0 -10000 0 0
EIF4EBP1 0.013 0.1 -9999 0 -10000 0 0
PTPRA 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.053 0.11 -9999 0 -0.41 3 3
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.034 -9999 0 -0.74 1 1
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.006 0.039 -9999 0 -0.31 7 7
GNAO1 0.007 0.051 -9999 0 -0.63 3 3
S1P/S1P3/G12/G13 0 0.001 -9999 0 -10000 0 0
AKT1 -0.003 0.024 -9999 0 -0.46 1 1
AKT3 0.041 0.063 -9999 0 -1.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.034 -9999 0 -0.74 1 1
GNAI2 0.011 0.001 -9999 0 -10000 0 0
GNAI3 0.011 0.001 -9999 0 -10000 0 0
GNAI1 0.009 0.034 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.011 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.04 -9999 0 -10000 0 0
MAPK3 0.039 0.038 -9999 0 -10000 0 0
MAPK1 0.039 0.038 -9999 0 -10000 0 0
JAK2 0.042 0.038 -9999 0 -10000 0 0
CXCR4 0.039 0.038 -9999 0 -10000 0 0
FLT1 0.012 0.001 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.039 0.038 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.041 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.031 -9999 0 -10000 0 0
VEGFA 0.012 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.03 0.039 -9999 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer 0.022 0.003 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.075 0.14 -9999 0 -0.32 114 114
GNAQ -0.002 0.034 -9999 0 -0.74 1 1
GNAZ 0.002 0.083 -9999 0 -0.74 6 6
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.32 -9999 0 -0.74 114 114
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.005 0.031 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.13 0.24 -9999 0 -0.57 107 107
mol:Halofuginone 0 0 -9999 0 -10000 0 0
ITGA1 -0.008 0.075 -9999 0 -0.74 5 5
CDKN1A -0.003 0.022 -9999 0 -10000 0 0
PRL-3/alpha Tubulin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.03 0.13 -9999 0 -0.56 26 26
AGT -0.04 0.17 -9999 0 -0.73 26 26
CCNA2 -0.053 0.15 -9999 0 -0.69 3 3
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 0.01 0.078 -9999 0 -0.56 9 9
CDK2/Cyclin E1 -0.062 0.11 -9999 0 -0.43 2 2
MAPK3 0.02 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.02 0 -9999 0 -10000 0 0
PTP4A1 0.024 0.062 -9999 0 -10000 0 0
PTP4A3 0 0 -9999 0 -10000 0 0
PTP4A2 0 0 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 -0.003 0.022 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.011 0.062 -9999 0 -10000 0 0
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC -0.003 0.022 -9999 0 -10000 0 0
RHOA -0.003 0.022 -9999 0 -10000 0 0
cell motility 0.029 0.028 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.007 0.053 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.006 0.057 -9999 0 -0.56 5 5
ROCK1 0.029 0.028 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis 0.024 0.061 -9999 0 -10000 0 0
ATF5 -0.008 0.068 -9999 0 -0.57 7 7
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.005 0.048 -9999 0 -0.43 6 6
HDAC3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.05 0.16 -9999 0 -0.56 43 43
GATA1/HDAC5 -0.05 0.16 -9999 0 -0.56 43 43
GATA2/HDAC5 -0.06 0.17 -9999 0 -0.56 52 52
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.005 0.056 -9999 0 -0.61 4 4
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.08 0.23 -9999 0 -0.74 52 52
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.062 -9999 0 -0.56 6 6
Histones -0.001 0.014 -9999 0 -10000 0 0
ADRBK1 0 0 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0 0 -9999 0 -10000 0 0
HDAC6 0 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.005 0.058 -9999 0 -0.74 3 3
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
GATA1 -0.066 0.21 -9999 0 -0.74 43 43
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 -0.002 0.034 -9999 0 -0.74 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.022 -9999 0 -0.48 1 1
HDAC4/SRF -0.003 0.038 -9999 0 -0.48 3 3
HDAC4/ER alpha -0.024 0.11 -9999 0 -0.56 21 21
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.001 0.014 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.032 0.15 -9999 0 -0.74 21 21
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.014 0.1 -9999 0 -0.74 9 9
RAN 0 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.008 0.058 -9999 0 -0.4 10 10
GNG2 -0.008 0.075 -9999 0 -0.74 5 5
NCOR2 -0.002 0.034 -9999 0 -0.74 1 1
TUBB2A 0 0 -9999 0 -10000 0 0
HDAC11 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
ANKRA2 0 0 -9999 0 -10000 0 0
RFXANK 0 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
UBE2L3 0 0 -9999 0 -10000 0 0
FANCD2 0.022 0 -9999 0 -10000 0 0
protein ubiquitination -0.062 0.12 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
M/R/N Complex 0 0 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
DNA-PK 0 0 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -9999 0 -10000 0 0
FANCF 0 0 -9999 0 -10000 0 0
BRCA1 0 0 -9999 0 -10000 0 0
CCNE1 -0.13 0.24 -9999 0 -0.57 107 107
CDK2/Cyclin E1 -0.091 0.17 -9999 0 -0.41 107 107
FANCG -0.002 0.037 -9999 0 -0.57 2 2
BRCA1/BACH1/BARD1 0 0 -9999 0 -10000 0 0
FANCE 0 0 -9999 0 -10000 0 0
FANCC 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
FANCA -0.002 0.037 -9999 0 -0.57 2 2
DNA repair 0.01 0.099 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0 0 -9999 0 -10000 0 0
BARD1/DNA-PK 0 0 -9999 0 -10000 0 0
FANCL -0.001 0.026 -9999 0 -0.57 1 1
mRNA polyadenylation 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0 0 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0 0 -9999 0 -10000 0 0
BRCA1/BACH1 0 0 -9999 0 -10000 0 0
BARD1 0 0 -9999 0 -10000 0 0
PCNA 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.041 0.1 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0 0 -9999 0 -10000 0 0
FA complex -0.001 0.016 -9999 0 -10000 0 0
BARD1/EWS 0 0 -9999 0 -10000 0 0
RBBP8 0.02 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
TOPBP1 0 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0 0 -9999 0 -10000 0 0
BRCA1/BARD1 -0.062 0.12 -9999 0 -10000 0 0
CSTF1 0 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.076 0.19 -9999 0 -0.57 64 64
RAD50 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0 0 -9999 0 -10000 0 0
EWSR1 0 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 -0.002 0.034 -10000 0 -0.74 1 1
EPHB2 -0.009 0.073 -10000 0 -0.57 8 8
EFNB1 0.018 0.028 -10000 0 -0.41 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.037 0.091 -10000 0 -0.53 1 1
Ephrin B2/EPHB1-2 -0.044 0.11 -10000 0 -0.53 2 2
neuron projection morphogenesis -0.035 0.087 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/Tiam1 -0.04 0.099 -10000 0 -0.57 1 1
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.069 -10000 0 -0.73 4 4
YES1 -0.007 0.088 -10000 0 -0.96 4 4
Ephrin B1/EPHB1-2/NCK2 -0.04 0.099 -10000 0 -0.57 1 1
PI3K -0.006 0.068 -10000 0 -0.74 4 4
mol:GDP -0.04 0.098 -10000 0 -0.56 1 1
ITGA2B -0.023 0.13 -10000 0 -0.74 15 15
endothelial cell proliferation -0.001 0.022 -10000 0 -0.48 1 1
FYN -0.008 0.088 -10000 0 -0.96 4 4
MAP3K7 -0.007 0.071 -10000 0 -0.78 4 4
FGR -0.019 0.1 -10000 0 -0.99 4 4
TIAM1 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.024 0.1 -10000 0 -0.42 27 27
LYN -0.008 0.088 -10000 0 -0.96 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.083 -10000 0 -0.91 4 4
Ephrin B1/EPHB1-2 -0.009 0.077 -10000 0 -0.84 4 4
SRC -0.008 0.087 -10000 0 -0.95 4 4
ITGB3 -0.012 0.095 -10000 0 -0.74 8 8
EPHB1 -0.07 0.19 -10000 0 -0.57 59 59
EPHB4 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.49 1 1
alphaIIb/beta3 Integrin -0.027 0.12 -10000 0 -0.56 23 23
BLK -0.014 0.095 -10000 0 -1 4 4
HCK -0.01 0.089 -10000 0 -0.95 4 4
regulation of stress fiber formation 0.04 0.098 0.56 1 -10000 0 1
MAPK8 0.021 0.066 -10000 0 -0.69 4 4
Ephrin B1/EPHB1-2/RGS3 -0.04 0.099 -10000 0 -0.57 1 1
endothelial cell migration -0.006 0.065 -10000 0 -0.62 5 5
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.003 0.078 -10000 0 -0.86 4 4
regulation of focal adhesion formation 0.04 0.098 0.56 1 -10000 0 1
chemotaxis 0.04 0.098 0.56 1 -10000 0 1
PIK3CA 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.089 -10000 0 -0.52 1 1
angiogenesis -0.009 0.076 -10000 0 -0.83 4 4
LCK -0.008 0.09 -10000 0 -0.99 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.046 0.019 -10000 0 -10000 0 0
NFATC2 0.002 0.069 -10000 0 -0.31 1 1
NFATC3 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.013 0.12 -10000 0 -0.51 18 18
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.034 0.1 -10000 0 -0.49 18 18
BCL2/BAX -0.001 0.019 -10000 0 -0.41 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.003 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.037 0.1 -10000 0 -0.51 16 16
Calcineurin A alpha-beta B1/BCL2 -0.001 0.026 -10000 0 -0.57 1 1
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.037 0.1 0.5 16 -10000 0 16
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.57 48 48
MAP3K8 0.006 0.048 -10000 0 -0.74 2 2
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.055 0.12 -10000 0 -0.45 13 13
CABIN1 -0.013 0.12 -10000 0 -0.52 18 18
CALM1 0.001 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.005 0.058 -10000 0 -0.74 3 3
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.036 -10000 0 -0.56 2 2
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.003 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.003 0.017 -10000 0 -10000 0 0
PRKCH 0 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.003 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.007 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.024 -10000 0 -10000 0 0
PRKCB -0.037 0.16 -10000 0 -0.74 24 24
PRKCE -0.002 0.034 -10000 0 -0.74 1 1
JNK2/NFAT4 0 0 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.003 -10000 0 -10000 0 0
PRKCA -0.003 0.048 -10000 0 -0.74 2 2
PRKCG -0.042 0.15 -10000 0 -0.57 35 35
PRKCQ -0.069 0.22 -10000 0 -0.74 45 45
FKBP38/BCL2 -0.001 0.019 -10000 0 -0.41 1 1
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.046 0.025 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.003 0.039 -10000 0 -0.49 3 3
NFATc/ERK1 0.049 0.018 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.034 0.1 -10000 0 -0.48 18 18
NR4A1 -0.053 0.25 -10000 0 -0.68 65 65
GSK3B 0.009 0.003 -10000 0 -10000 0 0
positive T cell selection 0 0 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.021 0.045 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.009 0.003 -10000 0 -10000 0 0
AKAP5 -0.003 0.048 -10000 0 -0.74 2 2
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.025 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.012 0.07 -9999 0 -0.45 12 12
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.06 -9999 0 -0.38 12 12
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.034 -9999 0 -0.74 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.005 0.03 -9999 0 -10000 0 0
YY1/LSF -0.001 0.018 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.009 0.053 -9999 0 -0.34 12 12
I kappa B alpha/HDAC1 -0.006 0.036 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.008 0.047 -9999 0 -0.3 12 12
HDAC1/Smad7 -0.001 0.022 -9999 0 -0.48 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.006 0.036 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.007 0.042 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.08 0.23 -9999 0 -0.74 52 52
GATA1 -0.066 0.21 -9999 0 -0.74 43 43
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.019 0.062 -9999 0 -0.45 1 1
RBBP7 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.007 0.041 -9999 0 -10000 0 0
KAT2B -0.003 0.048 -9999 0 -0.74 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.006 0.035 -9999 0 -10000 0 0
YY1/HDAC2 -0.001 0.018 -9999 0 -10000 0 0
YY1/HDAC1 -0.001 0.018 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0 -9999 0 -10000 0 0
PPARG -0.053 0.13 -9999 0 -0.37 69 69
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.007 0.041 -9999 0 -0.43 1 1
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.022 -9999 0 -0.48 1 1
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.01 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.041 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 -0.001 0.022 -9999 0 -0.34 2 2
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 -0.002 0.034 -9999 0 -0.74 1 1
NCOR2 -0.002 0.034 -9999 0 -0.74 1 1
MXD1 0 0 -9999 0 -10000 0 0
STAT3 0.022 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.016 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.016 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.022 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.041 -9999 0 -10000 0 0
histone deacetylation 0.041 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.032 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.053 0.14 -9999 0 -0.44 52 52
GATA1/HDAC1 -0.05 0.16 -9999 0 -0.56 43 43
GATA1/HDAC3 -0.044 0.13 -9999 0 -0.44 43 43
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.015 0.089 -9999 0 -0.55 13 13
SIN3/HDAC complex/Mad/Max 0 0 -9999 0 -10000 0 0
NuRD Complex 0 0.01 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.03 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.051 0.16 -9999 0 -0.56 44 44
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.02 0.12 -9999 0 -0.73 13 13
negative regulation of cell growth 0.041 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.01 0.063 -9999 0 -0.4 12 12
SIN3/HDAC complex/NCoR1 0 0 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 -0.002 0.034 -9999 0 -0.74 1 1
MBD2 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.006 0.067 -10000 0 -0.74 4 4
CLTC 0.027 0.009 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.023 0.008 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.014 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.024 0.007 -10000 0 -10000 0 0
CPE 0.014 0.028 -10000 0 -0.42 2 2
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.007 -10000 0 -10000 0 0
CTNND1 0.027 0.014 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.006 -10000 0 -10000 0 0
TSHR 0.003 0.066 -10000 0 -0.35 16 16
INS 0.01 0.002 -10000 0 -10000 0 0
BIN1 -0.003 0.048 -10000 0 -0.74 2 2
mol:Choline -0.001 0.007 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.017 -10000 0 -0.35 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.014 -10000 0 -10000 0 0
JUP 0.024 0.007 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.002 0.028 -10000 0 -0.44 2 2
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.024 0.007 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.01 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.12 -10000 0 -0.36 3 3
clathrin heavy chain/ACAP1 0.032 0.01 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.027 0.014 -10000 0 -10000 0 0
NME1 0.015 0.017 -10000 0 -0.35 1 1
clathrin coat assembly 0.027 0.009 -10000 0 -10000 0 0
IL2RA 0.022 0.026 -10000 0 -10000 0 0
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.003 0.033 -10000 0 -0.36 4 4
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.01 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.028 0.007 -10000 0 -10000 0 0
SDC1 0.024 0.014 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.016 -10000 0 -0.35 1 1
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.01 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.007 -10000 0 -10000 0 0
endocytosis 0.002 0.028 0.44 2 -10000 0 2
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.086 0.19 -10000 0 -0.38 137 137
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.001 0.014 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.065 0.18 -10000 0 -0.38 113 113
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.009 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0 0 -9999 0 -10000 0 0
PTK2 0 0 -9999 0 -10000 0 0
CRKL 0.01 0.072 -9999 0 -0.39 15 15
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
IRS1/Crk -0.012 0.068 -9999 0 -0.39 15 15
IGF-1R heterotetramer/IGF1/PTP1B -0.015 0.079 -9999 0 -0.45 15 15
AKT1 0.03 0.063 -9999 0 -10000 0 0
BAD 0.036 0.06 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.072 -9999 0 -0.39 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.013 0.068 -9999 0 -0.39 15 15
RAF1 0.038 0.058 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.012 0.064 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.014 0.074 -9999 0 -0.42 15 15
PIK3CA 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.063 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.033 0.051 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.056 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.011 0.062 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.007 0.016 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.013 0.068 -9999 0 -0.39 15 15
Crk/p130 Cas/Paxillin -0.011 0.06 -9999 0 -10000 0 0
IGF1R 0.007 0.016 -9999 0 -10000 0 0
IGF1 -0.015 0.13 -9999 0 -0.74 16 16
IRS2/Crk -0.014 0.07 -9999 0 -0.4 3 3
PI3K -0.012 0.063 -9999 0 -10000 0 0
apoptosis 0.008 0.045 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.021 0.086 -9999 0 -0.46 15 15
RAF1/14-3-3 E 0.041 0.051 -9999 0 -10000 0 0
BAD/14-3-3 0.04 0.056 -9999 0 -10000 0 0
PRKCZ 0.03 0.063 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.008 0.046 -9999 0 -10000 0 0
PTPN1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.015 0.085 -9999 0 -0.49 15 15
BCAR1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.013 0.069 -9999 0 -0.39 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.012 0.067 -9999 0 -0.38 15 15
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0.072 -9999 0 -0.39 15 15
IRS1 0.003 0.077 -9999 0 -0.42 15 15
IRS2 0.007 0.08 -9999 0 -0.39 18 18
IGF-1R heterotetramer/IGF1 -0.019 0.1 -9999 0 -0.56 16 16
GRB2 0 0 -9999 0 -10000 0 0
PDPK1 -0.011 0.059 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKD1 0.008 0.12 -9999 0 -0.49 26 26
SHC1 0 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
MAP2K3 0.027 0.023 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.034 0.022 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.009 0.082 -9999 0 -0.74 6 6
TXN 0.007 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GADD45B -0.022 0.12 -9999 0 -0.74 14 14
MAP3K1 0 0 -9999 0 -10000 0 0
MAP3K6 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
MAP3K4 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.005 -9999 0 -10000 0 0
TRAF6 0.007 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.068 0.18 -9999 0 -0.57 57 57
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.042 0.11 -9999 0 -0.35 57 57
MAPK11 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.037 0.1 -9999 0 -0.31 57 57
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.014 0.02 -9999 0 -0.42 1 1
TAOK2 0.014 0 -9999 0 -10000 0 0
TAOK3 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAP3K10 -0.001 0.026 -9999 0 -0.57 1 1
MAP3K3 0 0 -9999 0 -10000 0 0
TRX/ASK1 0 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.017 0.086 -9999 0 -0.43 19 19
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.018 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.008 0.044 -9999 0 -10000 0 0
NFATC4 0.032 0.054 -9999 0 -10000 0 0
ERBB2IP 0.001 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.01 0.059 -9999 0 -10000 0 0
JUN 0.044 0.058 -9999 0 -0.49 1 1
HRAS 0 0 -9999 0 -10000 0 0
DOCK7 0.029 0.064 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.012 0.07 -9999 0 -0.42 13 13
AKT1 0.01 0.002 -9999 0 -10000 0 0
BAD 0.018 0.001 -9999 0 -10000 0 0
MAPK10 -0.009 0.045 -9999 0 -0.33 4 4
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.011 0.063 -9999 0 -10000 0 0
RAF1 0.048 0.057 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.048 0.14 -9999 0 -0.44 52 52
STAT3 0 0 -9999 0 -10000 0 0
cell migration 0.04 0.045 -9999 0 -0.3 2 2
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.039 0.15 -9999 0 -0.56 8 8
FOS 0.01 0.2 -9999 0 -0.5 60 60
NRAS 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.059 -9999 0 -10000 0 0
MAPK3 0.046 0.11 -9999 0 -0.47 5 5
MAPK1 0.046 0.11 -9999 0 -0.64 1 1
JAK2 0.029 0.064 -9999 0 -10000 0 0
NF2 -0.001 0.019 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.009 0.054 -9999 0 -0.33 13 13
NRG1 -0.011 0.12 -9999 0 -0.74 13 13
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.032 0.06 -9999 0 -10000 0 0
MAPK9 -0.005 0.028 -9999 0 -10000 0 0
ERBB2 -0.002 0.027 -9999 0 -0.42 2 2
ERBB3 0.009 0.004 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.003 0.008 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
RNF41 0.025 0.004 -9999 0 -10000 0 0
FRAP1 0.009 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.007 0.04 -9999 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.001 0.023 -9999 0 -0.35 2 2
CHRNA1 0.043 0.12 -9999 0 -0.63 6 6
myelination 0.037 0.052 -9999 0 -10000 0 0
PPP3CB -0.009 0.052 -9999 0 -10000 0 0
KRAS 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.008 0.046 -9999 0 -10000 0 0
NRG2 -0.078 0.23 -9999 0 -0.74 51 51
mol:GDP 0.015 0.059 -9999 0 -0.33 13 13
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 0.055 0.058 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 -0.01 0.055 -9999 0 -10000 0 0
MAP2K1 0.036 0.11 -9999 0 -0.48 5 5
heart morphogenesis -0.01 0.059 -9999 0 -10000 0 0
RAS family/GDP -0.008 0.044 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PRKACA -0.001 0.004 -9999 0 -10000 0 0
CHRNE 0.02 0.017 -9999 0 -0.24 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.002 -9999 0 -10000 0 0
nervous system development -0.01 0.059 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.042 -9999 0 -0.39 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.004 0.034 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.002 0.023 -9999 0 -0.49 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.013 0.045 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.039 -9999 0 -0.38 1 1
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.004 0.039 -9999 0 -0.38 2 2
AKT1 -0.004 0.034 -9999 0 -10000 0 0
MAP2K1 0.042 0.045 -9999 0 -0.39 1 1
MAP3K11 0.033 0.045 -9999 0 -0.39 2 2
IFNGR1 0.009 0.035 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.05 0.13 -9999 0 -0.48 37 37
Rap1/GTP -0.003 0.029 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.005 0.044 -9999 0 -0.4 5 5
CEBPB 0.042 0.13 -9999 0 -0.72 2 2
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.007 0.067 -9999 0 -1.2 1 1
STAT1 -0.004 0.039 -9999 0 -0.38 2 2
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0.001 0.077 -9999 0 -0.68 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.004 0.037 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.019 0.065 -9999 0 -0.41 2 2
mol:Ca2+ -0.005 0.041 -9999 0 -0.38 5 5
MAPK3 0.043 0.062 -9999 0 -10000 0 0
STAT1 (dimer) -0.017 0.059 -9999 0 -10000 0 0
MAPK1 0.043 0.062 -9999 0 -0.44 1 1
JAK2 0.01 0.005 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0.01 0.005 -9999 0 -10000 0 0
CAMK2D 0 0 -9999 0 -10000 0 0
DAPK1 0.02 0.18 -9999 0 -0.64 33 33
SMAD7 0.038 0.045 -9999 0 -0.33 1 1
CBL/CRKL/C3G -0.004 0.035 -9999 0 -10000 0 0
PI3K -0.004 0.037 -9999 0 -10000 0 0
IFNG 0.001 0.077 -9999 0 -0.68 6 6
apoptosis 0.018 0.13 -9999 0 -0.44 33 33
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.057 0.2 -9999 0 -0.74 37 37
CAMK2B -0.068 0.18 -9999 0 -0.57 57 57
FRAP1 0.044 0.039 -9999 0 -10000 0 0
PRKCD -0.004 0.035 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.013 0.045 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.065 0.038 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.004 0.038 -9999 0 -10000 0 0
SOCS1 -0.003 0.066 -9999 0 -1.5 1 1
mol:GDP -0.004 0.034 -9999 0 -10000 0 0
CASP1 0.037 0.047 -9999 0 -0.33 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.044 0.041 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.036 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.029 -9999 0 -10000 0 0
CBL -0.003 0.04 -9999 0 -0.38 1 1
MAP3K1 0.034 0.046 -9999 0 -0.39 2 2
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.013 0.045 -9999 0 -10000 0 0
PTPN11 -0.005 0.042 -9999 0 -0.38 5 5
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.026 -9999 0 -10000 0 0
DAPP1 0.009 0.12 -9999 0 -0.56 14 14
Src family/SYK family/BLNK-LAT/BTK-ITK 0.005 0.17 -9999 0 -0.65 22 22
mol:DAG 0.026 0.087 -9999 0 -0.28 22 22
HRAS 0 0.001 -9999 0 -10000 0 0
RAP1A 0 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.026 0.055 -9999 0 -0.32 7 7
PLCG2 0 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
ARF5 0 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.028 -9999 0 -10000 0 0
ARF1/GTP -0.002 0.027 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.028 -9999 0 -10000 0 0
ADAP1 -0.009 0.057 -9999 0 -10000 0 0
ARAP3 -0.002 0.028 -9999 0 -10000 0 0
INPPL1 0 0 -9999 0 -10000 0 0
PREX1 -0.011 0.089 -9999 0 -0.74 7 7
ARHGEF6 -0.028 0.14 -9999 0 -0.74 18 18
ARHGEF7 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
NRAS 0 0.001 -9999 0 -10000 0 0
FYN -0.002 0.034 -9999 0 -0.74 1 1
ARF6 0 0 -9999 0 -10000 0 0
FGR -0.049 0.18 -9999 0 -0.74 32 32
mol:Ca2+ 0.024 0.047 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0 0 -9999 0 -10000 0 0
ZAP70 -0.012 0.095 -9999 0 -0.74 8 8
mol:IP3 0.027 0.064 -9999 0 -10000 0 0
LYN -0.003 0.048 -9999 0 -0.74 2 2
ARF1/GDP 0.026 0.055 -9999 0 -0.32 7 7
RhoA/GDP -0.006 0.034 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK -0.002 0.034 -9999 0 -0.74 1 1
actin cytoskeleton reorganization 0.045 0.066 -9999 0 -0.49 3 3
SRC 0 0 -9999 0 -10000 0 0
PLEKHA2 0.025 0.023 -9999 0 -0.48 1 1
RAC1 0 0 -9999 0 -10000 0 0
PTEN 0 0.003 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.026 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.026 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.033 0.11 -9999 0 -0.51 17 17
BLK -0.036 0.15 -9999 0 -0.66 26 26
PDPK1 0 0 -9999 0 -10000 0 0
CYTH1 -0.002 0.026 -9999 0 -10000 0 0
HCK -0.008 0.075 -9999 0 -0.74 5 5
CYTH3 -0.002 0.026 -9999 0 -10000 0 0
CYTH2 -0.002 0.026 -9999 0 -10000 0 0
KRAS 0 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.013 -9999 0 -10000 0 0
SGK1 -0.001 0.014 -9999 0 -10000 0 0
INPP5D -0.002 0.034 -9999 0 -0.74 1 1
mol:GDP 0.022 0.058 -9999 0 -0.34 7 7
SOS1 0 0 -9999 0 -10000 0 0
SYK -0.002 0.034 -9999 0 -0.74 1 1
ARF6/GDP -0.006 0.034 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.028 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.028 -9999 0 -10000 0 0
VAV1 -0.008 0.075 -9999 0 -0.74 5 5
mol:PI-3-4-P2 0.018 0.026 -9999 0 -0.56 1 1
RAS family/GTP/PI3K Class I -0.002 0.028 -9999 0 -0.36 3 3
PLEKHA1 0.025 0.023 -9999 0 -0.48 1 1
Rac1/GDP 0.026 0.055 -9999 0 -0.32 7 7
LAT 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.019 0.099 -9999 0 -0.46 19 19
ITK -0.031 0.1 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.024 0.12 -9999 0 -0.4 22 22
LCK -0.002 0.034 -9999 0 -0.74 1 1
BTK -0.037 0.11 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.09 0.19 -9999 0 -0.77 5 5
RAD9A 0 0 -9999 0 -10000 0 0
AP1 -0.064 0.18 -9999 0 -0.56 55 55
IFNAR2 0.007 0.006 -9999 0 -10000 0 0
AKT1 -0.004 0.062 -9999 0 -0.3 10 10
ER alpha/Oestrogen -0.025 0.12 -9999 0 -0.57 21 21
NFX1/SIN3/HDAC complex 0.024 0.021 -9999 0 -10000 0 0
EGF -0.008 0.1 -9999 0 -0.69 10 10
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0.001 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.15 -9999 0 -0.72 5 5
SAP18 0.005 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.025 0.13 -9999 0 -0.58 26 26
WRN -0.002 0.034 -9999 0 -0.74 1 1
SP1 0.008 0.006 -9999 0 -10000 0 0
SP3 0.006 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.13 -9999 0 -0.64 5 5
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.092 0.19 -9999 0 -0.79 5 5
CCND1 -0.084 0.21 -9999 0 -1.2 7 7
MAX 0.006 0.005 -9999 0 -10000 0 0
RBBP7 0.005 0.005 -9999 0 -10000 0 0
RBBP4 0.005 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.005 0.005 -9999 0 -10000 0 0
Telomerase/911 0.016 0.032 -9999 0 -10000 0 0
CDKN1B 0.015 0.052 -9999 0 -0.46 4 4
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 0.005 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.006 0.005 -9999 0 -10000 0 0
JUN 0.006 0.005 -9999 0 -10000 0 0
E6 -0.003 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0.001 -9999 0 -10000 0 0
FOS -0.079 0.24 -9999 0 -0.74 55 55
IFN-gamma/IRF1 -0.006 0.056 -9999 0 -0.5 6 6
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.012 0.082 -9999 0 -0.57 10 10
Telomerase -0.026 0.052 -9999 0 -10000 0 0
IRF1 0.009 0.007 -9999 0 -10000 0 0
ESR1 -0.028 0.15 -9999 0 -0.74 21 21
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
HDAC1 0.005 0.005 -9999 0 -10000 0 0
HDAC2 0.007 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.022 0.005 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.006 0.005 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 0 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.14 -9999 0 -0.71 5 5
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.01 0.009 -9999 0 -10000 0 0
MAPK1 0.01 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.007 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.017 0.12 -9999 0 -0.64 17 17
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.027 0.12 -9999 0 -0.5 26 26
MYC 0.007 0.005 -9999 0 -10000 0 0
IL2 0 0.012 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
TGFB1 0.005 0.007 -9999 0 -10000 0 0
TRF2/BLM -0.008 0.054 -9999 0 -0.38 10 10
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.15 -9999 0 -0.71 5 5
SP1/HDAC2 0 0.002 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.13 -9999 0 -0.64 5 5
Smad3/Myc 0.011 0.014 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG 0 0.077 -9999 0 -0.68 6 6
Telomerase/PinX1 -0.1 0.13 -9999 0 -0.64 5 5
Telomerase/AKT1/mTOR/p70S6K -0.003 0.062 -9999 0 -10000 0 0
SIN3B 0.005 0.005 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.13 -9999 0 -0.64 5 5
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.001 0.024 -9999 0 -0.52 1 1
Telomerase/hnRNP C1/C2 -0.1 0.13 -9999 0 -0.64 5 5
E2F1 0.007 0.006 -9999 0 -10000 0 0
ZNFX1 0.005 0.005 -9999 0 -10000 0 0
PIF1 -0.053 0.17 -9999 0 -0.57 45 45
NCL 0 0 -9999 0 -10000 0 0
DKC1 0 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.018 0.074 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.061 -9999 0 -10000 0 0
HIF1A 0 0 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.011 0.046 -9999 0 -10000 0 0
PLCG1 0.018 0.074 -9999 0 -10000 0 0
NOS3 0.041 0.067 -9999 0 -0.58 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.041 0.065 -9999 0 -0.55 1 1
FLT1 0.026 0 -9999 0 -10000 0 0
PGF -0.03 0.13 -9999 0 -0.57 25 25
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.039 -9999 0 -0.43 4 4
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.045 0.063 -9999 0 -0.53 1 1
endothelial cell proliferation 0.018 0.093 -9999 0 -0.62 1 1
mol:Ca2+ 0.018 0.073 -9999 0 -10000 0 0
MAPK3 0.029 0.071 -9999 0 -10000 0 0
MAPK1 0.029 0.071 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.03 0.13 -9999 0 -0.57 25 25
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.21 0.33 -9999 0 -0.74 135 135
VEGFA homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.035 0.069 -9999 0 -10000 0 0
PI3K -0.014 0.061 -9999 0 -10000 0 0
PRKCA 0.023 0.074 -9999 0 -10000 0 0
PRKCB 0.003 0.12 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.018 0.075 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.074 -9999 0 -10000 0 0
RASA1 0.035 0 -9999 0 -10000 0 0
NRP2 -0.006 0.067 -9999 0 -0.74 4 4
VEGFR1 homodimer 0.026 0 -9999 0 -10000 0 0
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.066 0.18 -9999 0 -0.58 6 6
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.06 -9999 0 -10000 0 0
mol:L-citrulline 0.041 0.065 -9999 0 -0.55 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.013 0.056 -9999 0 -10000 0 0
PDPK1 -0.013 0.056 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.041 0.065 -9999 0 -0.55 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.004 0.043 -9999 0 -0.47 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.001 0.012 -9999 0 -10000 0 0
CLOCK 0.013 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0 0 -9999 0 -10000 0 0
DEC1/BMAL1 -0.022 0.093 -9999 0 -0.41 26 26
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.038 0 -9999 0 -10000 0 0
ARNTL 0.013 0 -9999 0 -10000 0 0
TIMELESS 0.038 0 -9999 0 -10000 0 0
NPAS2 0.013 0 -9999 0 -10000 0 0
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 -0.001 0.026 -9999 0 -0.57 1 1
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 -0.005 0.058 -9999 0 -0.74 3 3
BMAL/CLOCK/NPAS2 0.035 0 -9999 0 -10000 0 0
BMAL1/CLOCK 0.037 0.037 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.012 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.012 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS -0.003 0.033 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.031 0.13 -9999 0 -0.57 26 26
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.002 0.034 -9999 0 -0.74 1 1
ITGA4 -0.006 0.067 -9999 0 -0.74 4 4
alpha4/beta7 Integrin -0.006 0.057 -9999 0 -0.56 5 5
alpha4/beta1 Integrin -0.005 0.051 -9999 0 -0.56 4 4
EPO signaling pathway

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
BCL2L1 0.066 0.037 -10000 0 -10000 0 0
CRKL 0.039 0.038 -10000 0 -10000 0 0
mol:DAG -0.005 0.034 -10000 0 -0.39 2 2
HRAS -0.003 0.025 -10000 0 -10000 0 0
MAPK8 0.027 0.046 -10000 0 -0.44 2 2
RAP1A 0.039 0.038 -10000 0 -10000 0 0
GAB1 0.039 0.038 -10000 0 -10000 0 0
MAPK14 0.027 0.046 -10000 0 -0.44 2 2
EPO 0.004 0.064 -10000 0 -0.56 6 6
PLCG1 -0.005 0.035 -10000 0 -0.4 2 2
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.006 0.048 -10000 0 -0.5 2 2
GAB1/SHC/GRB2/SOS1 -0.003 0.027 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.005 0.045 -10000 0 -0.4 6 6
IRS2 0.036 0.05 -10000 0 -10000 0 0
STAT1 0.051 0.042 -10000 0 -0.39 2 2
STAT5B -0.005 0.034 -10000 0 -0.4 2 2
cell proliferation 0.034 0.043 -10000 0 -0.4 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.004 0.029 -10000 0 -10000 0 0
TEC 0.036 0.05 -10000 0 -10000 0 0
SOCS3 -0.003 0.048 -10000 0 -0.74 2 2
STAT1 (dimer) 0.051 0.041 -10000 0 -0.38 2 2
JAK2 0.011 0.004 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.041 0.041 -10000 0 -0.37 2 2
EPO/EPOR -0.005 0.045 -10000 0 -0.4 6 6
LYN 0.008 0.048 -10000 0 -0.74 2 2
TEC/VAV2 0.039 0.068 -10000 0 -0.73 2 2
elevation of cytosolic calcium ion concentration 0.012 0.004 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.001 0.049 -10000 0 -0.49 2 2
mol:IP3 -0.005 0.034 -10000 0 -0.39 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.042 -10000 0 -10000 0 0
SH2B3 0.008 0.048 -10000 0 -0.74 2 2
NFKB1 0.027 0.046 -10000 0 -0.44 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.002 0.031 0.3 2 -10000 0 2
PTPN6 0.033 0.04 -10000 0 -0.37 2 2
TEC/VAV2/GRB2 -0.008 0.058 -10000 0 -0.7 2 2
EPOR 0.012 0.004 -10000 0 -10000 0 0
INPP5D -0.002 0.034 -10000 0 -0.74 1 1
mol:GDP -0.003 0.028 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.004 0.029 -10000 0 -10000 0 0
VAV2 0.036 0.056 -10000 0 -0.5 3 3
CBL 0.039 0.038 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.004 0.029 -10000 0 -10000 0 0
STAT5A -0.005 0.034 -10000 0 -0.4 2 2
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.062 0.043 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.002 0.036 -10000 0 -0.56 2 2
PTPN11 0 0 -10000 0 -10000 0 0
BTK 0 0.13 -10000 0 -0.39 45 45
BCL2 0.065 0.04 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.017 0.037 -10000 0 -0.56 2 2
MAP4K4 0.032 0.057 -10000 0 -0.64 1 1
BAG4 -0.001 0.026 -10000 0 -0.57 1 1
PKC zeta/ceramide -0.002 0.018 0.18 2 -10000 0 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.082 -10000 0 -0.74 6 6
BAX 0.001 0.01 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.017 0.003 -10000 0 -10000 0 0
BAD -0.001 0.019 0.19 2 -10000 0 2
SMPD1 0.019 0.042 -10000 0 -0.24 12 12
RB1 -0.001 0.019 0.19 2 -10000 0 2
FADD/Caspase 8 0.04 0.055 -10000 0 -0.61 1 1
MAP2K4 0.005 0.018 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.005 0.018 -10000 0 -10000 0 0
EGF -0.014 0.099 -10000 0 -0.69 10 10
mol:ceramide -0.01 0.02 0.2 2 -10000 0 2
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.037 -10000 0 -0.56 2 2
ASAH1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.019 0.19 2 -10000 0 2
cell proliferation -0.012 0.058 -10000 0 -0.33 15 15
BID 0.024 0.039 -10000 0 -0.38 1 1
MAP3K1 -0.001 0.019 0.19 2 -10000 0 2
EIF2A 0.012 0.017 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.017 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.017 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.002 0.018 0.18 2 -10000 0 2
FADD 0.032 0.057 -10000 0 -0.64 1 1
KSR1 -0.001 0.019 0.19 2 -10000 0 2
MAPK8 0.009 0.017 0.19 2 -10000 0 2
PRKRA -0.001 0.019 0.19 2 -10000 0 2
PDGFA -0.003 0.048 -10000 0 -0.74 2 2
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.024 0.13 -10000 0 -0.73 16 16
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.01 0.02 0.2 2 -10000 0 2
CTSD 0 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.062 -10000 0 -0.35 15 15
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.037 -10000 0 -0.56 2 2
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.054 -10000 0 -0.68 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.078 -10000 0 -0.46 14 14
mol:Sphingosine-1-phosphate 0.017 0.037 -10000 0 -0.56 2 2
MAP2K1 0.012 0.017 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0.001 0.014 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -10000 0 -0.41 1 1
EIF2AK2 0.005 0.018 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.013 0.076 -10000 0 -0.48 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.027 -10000 0 -0.32 1 1
MAP2K2 0.012 0.017 -10000 0 -10000 0 0
SMPD3 0.017 0.064 -10000 0 -0.42 6 6
TNF -0.02 0.12 -10000 0 -0.73 13 13
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.005 0.039 0.23 11 -10000 0 11
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.001 0.014 -10000 0 -10000 0 0
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.005 0.05 -9999 0 -0.49 5 5
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.006 0.067 -9999 0 -0.74 4 4
alpha4/beta7 Integrin/MAdCAM1 -0.006 0.05 -9999 0 -0.43 5 5
EPO -0.007 0.063 -9999 0 -0.57 6 6
alpha4/beta7 Integrin -0.006 0.057 -9999 0 -0.56 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.051 -9999 0 -0.56 4 4
EPO/EPOR (dimer) -0.005 0.046 -9999 0 -0.41 6 6
lamellipodium assembly 0 0.004 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.005 0.036 -9999 0 -0.34 4 4
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.004 0.045 -9999 0 -0.57 3 3
cell adhesion -0.006 0.05 -9999 0 -0.43 5 5
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.021 0.072 -9999 0 -0.6 5 5
ITGB7 -0.002 0.034 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.009 0.074 -9999 0 -0.54 8 8
p130Cas/Crk/Dock1 -0.007 0.057 -9999 0 -0.72 2 2
VCAM1 -0.008 0.073 -9999 0 -0.66 6 6
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.039 -9999 0 -0.43 4 4
BCAR1 0.028 0.068 -9999 0 -0.56 5 5
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.004 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
Caspase 8 (4 units) -0.011 0.047 -9999 0 -10000 0 0
NEF -0.007 0.037 -9999 0 -10000 0 0
NFKBIA -0.001 0.012 -9999 0 -10000 0 0
BIRC3 0.029 0.088 -9999 0 -0.75 6 6
CYCS 0.032 0.064 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.13 -9999 0 -0.83 11 11
MAP2K7 0.034 0.051 -9999 0 -10000 0 0
protein ubiquitination 0.056 0.038 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.002 0.034 -9999 0 -0.74 1 1
BID 0.026 0.067 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.004 0.036 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
CFLAR 0 0 -9999 0 -10000 0 0
FADD 0 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.036 -9999 0 -10000 0 0
MAPK8 0.04 0.048 -9999 0 -10000 0 0
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.015 0.062 -9999 0 -0.3 16 16
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.006 0.034 -9999 0 -10000 0 0
CHUK 0.057 0.04 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.018 -9999 0 -0.4 1 1
TCRz/NEF -0.028 0.13 -9999 0 -0.51 26 26
TNF -0.02 0.12 -9999 0 -0.73 13 13
FASLG -0.021 0.2 -9999 0 -0.82 26 26
NFKB1 -0.001 0.012 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.078 -9999 0 -0.46 14 14
CASP6 -0.007 0.028 -9999 0 -10000 0 0
CASP7 0.061 0.085 -9999 0 -0.6 6 6
RELA -0.001 0.012 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.061 0.085 -9999 0 -0.6 6 6
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -9999 0 -0.41 1 1
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.043 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.013 0.062 -9999 0 -0.49 6 6
BCL2 0.044 0.048 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.008 0.054 -10000 0 -0.38 10 10
cell-cell adhesion 0.032 0.079 0.46 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.007 0.044 -10000 0 -0.4 1 1
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.013 0.067 -10000 0 -0.35 18 18
Ephrin B1/EPHB1 -0.043 0.12 -10000 0 -0.35 59 59
HRAS/GDP -0.031 0.08 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.039 0.097 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.006 0.041 -10000 0 -0.38 1 1
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.036 0.095 -10000 0 -10000 0 0
endothelial cell migration -0.001 0.018 -10000 0 -0.4 1 1
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.005 0.052 -10000 0 -0.57 4 4
PAK1 -0.009 0.051 -10000 0 -10000 0 0
HRAS 0 0 -10000 0 -10000 0 0
RRAS -0.006 0.042 -10000 0 -0.38 1 1
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.035 0.09 -10000 0 -10000 0 0
lamellipodium assembly -0.032 0.079 -10000 0 -0.46 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.018 0.047 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.009 0.073 -10000 0 -0.57 8 8
EPHB3 -0.021 0.11 -10000 0 -0.57 18 18
EPHB1 -0.07 0.19 -10000 0 -0.57 59 59
EPHB4 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.08 -10000 0 -0.43 1 1
Ephrin B/EPHB2 -0.007 0.045 -10000 0 -0.41 1 1
Ephrin B/EPHB3 -0.013 0.06 -10000 0 -0.41 1 1
JNK cascade -0.038 0.097 -10000 0 -0.57 1 1
Ephrin B/EPHB1 -0.037 0.097 -10000 0 -0.41 1 1
RAP1/GDP -0.018 0.069 -10000 0 -10000 0 0
EFNB2 -0.002 0.034 -10000 0 -0.74 1 1
EFNB3 -0.002 0.037 -10000 0 -0.57 2 2
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.044 0.11 -10000 0 -0.53 2 2
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.032 0.079 -10000 0 -0.46 1 1
Rap1/GTP -0.032 0.078 -10000 0 -0.47 1 1
axon guidance -0.008 0.054 -10000 0 -0.38 10 10
MAPK3 0.026 0.053 -10000 0 -10000 0 0
MAPK1 0.026 0.053 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.074 -10000 0 -0.39 1 1
actin cytoskeleton reorganization -0.027 0.066 -10000 0 -10000 0 0
CDC42/GDP -0.02 0.074 -10000 0 -0.39 1 1
PI3K -0.001 0.019 -10000 0 -0.41 1 1
EFNA5 -0.003 0.048 -10000 0 -0.74 2 2
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.49 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.004 0.024 -10000 0 -0.31 1 1
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.031 0.076 -10000 0 -10000 0 0
PTK2 0.01 0.026 -10000 0 -10000 0 0
MAP4K4 -0.039 0.098 -10000 0 -0.57 1 1
SRC 0 0 -10000 0 -10000 0 0
KALRN -0.005 0.058 -10000 0 -0.74 3 3
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.059 -10000 0 -10000 0 0
MAP2K1 0.019 0.055 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.042 0.11 -10000 0 -0.61 1 1
cell migration 0.027 0.056 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.006 0.042 -10000 0 -0.38 1 1
PXN 0 0 -10000 0 -10000 0 0
TF 0.011 0.091 -10000 0 -10000 0 0
HRAS/GTP -0.034 0.085 -10000 0 -0.5 1 1
Ephrin B1/EPHB1-2 -0.043 0.11 -10000 0 -0.62 1 1
cell adhesion mediated by integrin -0.002 0.041 0.41 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.037 0.092 -10000 0 -0.54 1 1
RAC1-CDC42/GTP -0.039 0.086 -10000 0 -0.47 2 2
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.018 0.069 -10000 0 -10000 0 0
ruffle organization -0.032 0.078 -10000 0 -0.47 1 1
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.032 0.049 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.009 0.054 -10000 0 -0.4 4 4
ROCK1 0.009 0.063 -10000 0 -0.31 18 18
RAS family/GDP -0.023 0.058 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.083 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src/Paxillin -0.018 0.048 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.007 0.072 -10000 0 -0.71 5 5
HRAS 0 0 -10000 0 -10000 0 0
EGFR -0.022 0.12 -10000 0 -0.63 17 17
AKT 0.032 0.023 -10000 0 -0.38 1 1
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.002 0.034 -10000 0 -0.74 1 1
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.004 0.054 -10000 0 -0.68 3 3
PIK3CA 0 0 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.065 0.21 -10000 0 -0.74 42 42
PIK3R3 0 0 -10000 0 -10000 0 0
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 0 0 -10000 0 -10000 0 0
RAS 0.016 0.034 -10000 0 -10000 0 0
ERBB2 -0.002 0.037 -10000 0 -0.57 2 2
proliferation/survival/translation -0.018 0.034 0.21 2 -10000 0 2
PI3K 0.014 0.051 -10000 0 -0.26 3 3
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.038 0.015 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.032 -9999 0 -0.62 1 1
PDGFB-D/PDGFRB/SLAP -0.031 0.13 -9999 0 -0.58 26 26
PDGFB-D/PDGFRB/APS/CBL -0.001 0.022 -9999 0 -0.48 1 1
AKT1 -0.004 0.038 -9999 0 -0.53 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.04 -9999 0 -0.66 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
FGR -0.04 0.15 -9999 0 -0.6 32 32
mol:Ca2+ 0.027 0.041 -9999 0 -0.7 1 1
MYC 0.044 0.051 -9999 0 -0.46 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.018 -9999 0 -0.39 1 1
LRP1/PDGFRB/PDGFB -0.001 0.022 -9999 0 -0.48 1 1
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.027 0.042 -9999 0 -0.71 1 1
PTEN 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
GRB7 -0.005 0.052 -9999 0 -0.57 4 4
PDGFB-D/PDGFRB/SHP2 -0.001 0.025 -9999 0 -0.56 1 1
PDGFB-D/PDGFRB/GRB10 -0.001 0.025 -9999 0 -0.56 1 1
cell cycle arrest -0.031 0.13 -9999 0 -0.58 26 26
HRAS 0 0 -9999 0 -10000 0 0
HIF1A 0.055 0.04 -9999 0 -0.46 1 1
GAB1 0.028 0.054 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.033 0.05 -9999 0 -0.66 1 1
PDGFB-D/PDGFRB 0.001 0.024 -9999 0 -0.49 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.025 -9999 0 -0.56 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.035 -9999 0 -0.63 1 1
positive regulation of MAPKKK cascade -0.001 0.025 -9999 0 -0.56 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.027 0.042 -9999 0 -0.72 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.005 0.045 -9999 0 -0.44 5 5
SHB 0 0 -9999 0 -10000 0 0
BLK -0.02 0.1 -9999 0 -0.59 15 15
PTPN2 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.025 -9999 0 -0.56 1 1
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.029 0.068 -9999 0 -0.57 2 2
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.004 0.044 -9999 0 -0.56 3 3
LCK -0.002 0.036 -9999 0 -0.55 2 2
PDGFRB 0.009 0.035 -9999 0 -0.75 1 1
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.006 0.066 -9999 0 -0.59 6 6
ABL1 0.024 0.053 -9999 0 -0.66 1 1
PDGFB-D/PDGFRB/CBL 0.026 0.059 -9999 0 -0.77 1 1
PTPN1 0.001 0.003 -9999 0 -10000 0 0
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 0 0 -9999 0 -10000 0 0
cell proliferation 0.043 0.048 -9999 0 -0.43 1 1
SLA -0.04 0.17 -9999 0 -0.74 26 26
actin cytoskeleton reorganization 0.002 0.02 -9999 0 -10000 0 0
SRC 0 0.023 -9999 0 -0.49 1 1
PI3K -0.005 0.042 -9999 0 -0.6 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.004 0.038 -9999 0 -0.48 1 1
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.031 0.041 -9999 0 -0.69 1 1
LYN -0.002 0.045 -9999 0 -0.56 3 3
LRP1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0 0 -9999 0 -10000 0 0
STAT5A 0 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.019 -9999 0 -10000 0 0
SPHK1 0.01 0.003 -9999 0 -10000 0 0
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.027 0.042 -9999 0 -0.72 1 1
PLCG1 0.027 0.043 -9999 0 -0.74 1 1
NHERF/PDGFRB -0.007 0.059 -9999 0 -0.56 4 4
YES1 0 0.022 -9999 0 -0.48 1 1
cell migration -0.007 0.058 -9999 0 -0.56 4 4
SHC/Grb2/SOS1 0 0.019 -9999 0 -10000 0 0
SLC9A3R2 -0.005 0.058 -9999 0 -0.74 3 3
SLC9A3R1 -0.005 0.052 -9999 0 -0.57 4 4
NHERF1-2/PDGFRB/PTEN -0.006 0.053 -9999 0 -0.51 4 4
FYN -0.001 0.035 -9999 0 -0.53 2 2
DOK1 0.029 0.021 -9999 0 -0.44 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.04 0.063 -9999 0 -0.67 1 1
PRKCD 0.029 0.022 -9999 0 -0.44 1 1
FER 0.029 0.022 -9999 0 -0.44 1 1
MAPKKK cascade -0.001 0.017 -9999 0 -10000 0 0
RASA1 0.029 0.022 -9999 0 -0.44 1 1
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk 0.001 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.025 -9999 0 -0.56 1 1
chemotaxis 0.024 0.051 -9999 0 -0.63 1 1
STAT1-3-5/STAT1-3-5 -0.001 0.017 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.001 0.026 -9999 0 -0.57 1 1
PTPRJ -0.003 0.048 -9999 0 -0.74 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0 -9999 0 -10000 0 0
adherens junction organization 0.033 0.032 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.009 0.049 -9999 0 -10000 0 0
FMN1 0.014 0.099 -9999 0 -0.38 29 29
mol:IP3 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNND1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.038 0 -9999 0 -10000 0 0
VASP 0.039 0 -9999 0 -10000 0 0
ZYX 0.039 0 -9999 0 -10000 0 0
JUB 0.039 0 -9999 0 -10000 0 0
EGFR(dimer) -0.011 0.057 -9999 0 -0.38 6 6
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
FYN 0.042 0.036 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP -0.009 0.049 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
CASR 0.036 0.039 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
actin cable formation 0.02 0.097 -9999 0 -0.36 29 29
apoptosis 0 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
mol:GDP -0.01 0.053 -9999 0 -10000 0 0
PIP5K1A 0.039 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.01 0.052 -9999 0 -0.34 6 6
homophilic cell adhesion 0.001 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.003 0.047 0.74 2 -10000 0 2
PI3K Class IB/PDE3B -0.003 0.048 -10000 0 -0.74 2 2
PDE3B -0.003 0.048 -10000 0 -0.74 2 2
PLK2 and PLK4 events

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
PLK2 -0.002 0.034 -9999 0 -0.74 1 1
PLK4 -0.001 0.026 -9999 0 -0.57 1 1
regulation of centriole replication 0.017 0.033 -9999 0 -0.48 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.001 0.022 -9999 0 -10000 0 0
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.033 0.033 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.02 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.002 0.037 -9999 0 -0.57 2 2
PRKCI 0 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.028 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.009 0.029 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 0.034 0.035 -9999 0 -10000 0 0
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.022 0 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.57 48 48
LNPEP 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.006 0.035 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.045 -9999 0 -0.37 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.05 -9999 0 -0.63 3 3
RhoA/GTP -0.006 0.035 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.007 0.04 -9999 0 -0.3 2 2
GNAZ -0.009 0.082 -9999 0 -0.74 6 6
GNAI3 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
S1PR5 -0.009 0.072 -9999 0 -0.6 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.007 0.04 -9999 0 -0.31 2 2
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.034 -9999 0 -0.74 1 1
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.024 0.033 -9999 0 -10000 0 0
PLK1 -0.089 0.21 -9999 0 -0.73 3 3
CDKN1B 0.05 0.085 -9999 0 -10000 0 0
FOXO3 -0.023 0.16 -9999 0 -0.63 3 3
KAT2B 0.005 0.05 -9999 0 -0.74 2 2
FOXO1/SIRT1 0.018 0.025 -9999 0 -10000 0 0
CAT -0.017 0.16 -9999 0 -1.4 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.009 0.016 -9999 0 -10000 0 0
FOXO1 0.027 0.021 -9999 0 -10000 0 0
MAPK10 0.022 0.057 -9999 0 -0.41 8 8
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.079 0.032 -9999 0 -10000 0 0
response to oxidative stress -0.003 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.063 0.099 -9999 0 -0.61 2 2
XPO1 0.01 0 -9999 0 -10000 0 0
EP300 0.006 0.006 -9999 0 -10000 0 0
BCL2L11 0.015 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.027 -9999 0 -10000 0 0
mol:GDP -0.003 0.02 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
GADD45A 0.046 0.073 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.053 0.03 -9999 0 -10000 0 0
MST1 0.007 0.03 -9999 0 -0.56 1 1
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.038 0.038 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.03 0.008 -9999 0 -10000 0 0
MAPK9 0.029 0.008 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
SIRT1 0.008 0.013 -9999 0 -10000 0 0
SOD2 0.054 0.096 -9999 0 -10000 0 0
RBL2 0.018 0.11 -9999 0 -10000 0 0
RAL/GDP 0.014 0.014 -9999 0 -10000 0 0
CHUK 0.008 0.015 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.017 0.017 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG -0.044 0.3 -9999 0 -1.5 20 20
SKP2 -0.004 0.045 -9999 0 -0.57 3 3
USP7 0.011 0 -9999 0 -10000 0 0
IKBKB 0.007 0.03 -9999 0 -0.56 1 1
CCNB1 -0.033 0.18 -9999 0 -0.73 3 3
FOXO1-3a-4/beta catenin -0.015 0.039 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.027 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.008 0.014 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.08 0.029 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.57 48 48
CDK2 0.006 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.052 -9999 0 -10000 0 0
CREBBP 0.006 0.006 -9999 0 -10000 0 0
FBXO32 -0.018 0.15 -9999 0 -0.66 2 2
BCL6 0.018 0.11 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.006 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
ITGA4 -0.006 0.067 -10000 0 -0.74 4 4
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.006 0.057 -10000 0 -0.56 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.004 0.043 -10000 0 -0.48 4 4
alpha4/beta7 Integrin/Paxillin -0.004 0.044 -10000 0 -0.43 5 5
lamellipodium assembly 0 0.005 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
TLN1 0 0 -10000 0 -10000 0 0
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.003 0.033 -10000 0 -10000 0 0
cell adhesion -0.003 0.036 -10000 0 -0.4 4 4
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.039 -10000 0 -0.43 4 4
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.002 0.034 -10000 0 -0.74 1 1
ARF6/GDP 0.001 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.008 0.065 -10000 0 -0.57 5 5
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 -0.008 0.073 -10000 0 -0.66 6 6
alpha4/beta1 Integrin/Paxillin/Talin -0.003 0.037 -10000 0 -0.4 4 4
alpha4/beta1 Integrin/Paxillin/GIT1 -0.003 0.037 -10000 0 -0.4 4 4
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.036 0.4 4 -10000 0 4
CBL 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.003 0.037 -10000 0 -0.4 4 4
Rac1/GTP 0 0.005 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.009 0.065 -10000 0 -0.46 9 9
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.02 -10000 0 -0.42 1 1
GNB1/GNG2 -0.006 0.054 -10000 0 -0.49 6 6
GNB1 -0.002 0.034 -10000 0 -0.74 1 1
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 -0.004 0.041 -10000 0 -0.46 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.01 0.11 4 -10000 0 4
GNAL -0.006 0.067 -10000 0 -0.74 4 4
GNG2 -0.008 0.075 -10000 0 -0.74 5 5
CRH -0.001 0.026 -10000 0 -0.57 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.007 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0 0 -9999 0 -9999 0 0
SMAD2 0.012 0 -9999 0 -9999 0 0
SMAD3 0.036 0 -9999 0 -9999 0 0
SMAD3/SMAD4 0 0 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
PPM1A 0 0 -9999 0 -9999 0 0
CALM1 0 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
MAP3K1 0 0 -9999 0 -9999 0 0
TRAP-1/SMAD4 0 0 -9999 0 -9999 0 0
MAPK3 0 0 -9999 0 -9999 0 0
MAPK1 0 0 -9999 0 -9999 0 0
NUP214 0 0 -9999 0 -9999 0 0
CTDSP1 0 0 -9999 0 -9999 0 0
CTDSP2 0 0 -9999 0 -9999 0 0
CTDSPL 0 0 -9999 0 -9999 0 0
KPNB1 0 0 -9999 0 -9999 0 0
TGFBRAP1 0 0 -9999 0 -9999 0 0
UBE2I 0 0 -9999 0 -9999 0 0
NUP153 0 0 -9999 0 -9999 0 0
KPNA2 0 0 -9999 0 -9999 0 0
PIAS4 0 0 -9999 0 -9999 0 0
Canonical NF-kappaB 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
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.071 0.019 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.002 0.036 -9999 0 -0.56 2 2
NFKBIA 0.041 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
RIPK2 0 0 -9999 0 -10000 0 0
IKBKG -0.001 0.016 -9999 0 -10000 0 0
IKK complex/A20 -0.01 0.056 -9999 0 -10000 0 0
NEMO/A20/RIP2 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM -0.001 0.015 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.001 0.016 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.003 0.048 -9999 0 -0.74 2 2
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.015 0.089 -9999 0 -0.55 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.003 0.048 -9999 0 -0.74 2 2
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.02 0.12 -9999 0 -0.73 13 13
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex -0.001 0.018 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.027 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.038 0.002 -10000 0 -10000 0 0
regulation of axonogenesis -0.024 0.019 -10000 0 -10000 0 0
myoblast fusion 0.001 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.001 0.015 0.32 1 -10000 0 1
ARF1/GTP 0 0.002 -10000 0 -10000 0 0
mol:GM1 0.009 0.004 -10000 0 -10000 0 0
mol:Choline 0.023 0.028 -10000 0 -0.33 3 3
lamellipodium assembly -0.001 0.013 -10000 0 -10000 0 0
MAPK3 0.025 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.015 -10000 0 -0.32 1 1
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.011 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.01 -10000 0 -10000 0 0
ARF6 0.008 0.002 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 0.011 0.001 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.003 -10000 0 -10000 0 0
actin filament bundle formation 0.001 0.009 -10000 0 -10000 0 0
KALRN -0.003 0.035 -10000 0 -0.44 3 3
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.009 -10000 0 -10000 0 0
NME1 0.01 0.026 -10000 0 -0.57 1 1
Rac1/GDP -0.001 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.004 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.013 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development 0 0.004 -10000 0 -10000 0 0
ARF6/GTP 0 0.004 -10000 0 -10000 0 0
RhoA/GTP 0 0.002 -10000 0 -10000 0 0
mol:GDP -0.001 0.012 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.001 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.015 0.032 -10000 0 -0.38 3 3
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.013 -10000 0 -10000 0 0
ruffle organization 0.024 0.019 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.004 -10000 0 -10000 0 0
PLD2 0.018 0.004 -10000 0 -10000 0 0
PIP5K1A -0.001 0.016 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.028 -10000 0 -0.33 3 3
Rac1/GTP -0.001 0.013 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -9999 0 -9999 0 0
MKNK1 0 0 -9999 0 -9999 0 0
mol:PIP3 0 0 -9999 0 -9999 0 0
FRAP1 0.013 0 -9999 0 -9999 0 0
AKT1 0 0 -9999 0 -9999 0 0
INSR 0 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -9999 0 -9999 0 0
TSC2 0 0 -9999 0 -9999 0 0
RHEB/GDP 0 0 -9999 0 -9999 0 0
TSC1 0 0 -9999 0 -9999 0 0
Insulin Receptor/IRS1 0 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0 0 -9999 0 -9999 0 0
RPS6KB1 0.025 0 -9999 0 -9999 0 0
MAP3K5 0.009 0 -9999 0 -9999 0 0
PIK3R1 0 0 -9999 0 -9999 0 0
apoptosis 0.009 0 -9999 0 -9999 0 0
mol:LY294002 0 0 -9999 0 -9999 0 0
EIF4B 0.03 0 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -9999 0 -9999 0 0
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.028 0 -9999 0 -9999 0 0
FKBP1A 0 0 -9999 0 -9999 0 0
RHEB/GTP 0 0 -9999 0 -9999 0 0
mol:Amino Acids 0 0 -9999 0 -9999 0 0
FKBP12/Rapamycin 0 0 -9999 0 -9999 0 0
PDPK1 0 0 -9999 0 -9999 0 0
EIF4E 0 0 -9999 0 -9999 0 0
ASK1/PP5C 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0 -9999 0 -9999 0 0
TSC1/TSC2 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RPS6 0 0 -9999 0 -9999 0 0
PPP5C 0 0 -9999 0 -9999 0 0
EIF4G1 0 0 -9999 0 -9999 0 0
IRS1 0.007 0 -9999 0 -9999 0 0
INS 0 0 -9999 0 -9999 0 0
PTEN 0 0 -9999 0 -9999 0 0
PDK2 0 0 -9999 0 -9999 0 0
EIF4EBP1 0.004 0.02 -9999 0 -9999 0 0
PIK3CA 0 0 -9999 0 -9999 0 0
PPP2R5D 0.019 0 -9999 0 -9999 0 0
peptide biosynthetic process 0.014 0 -9999 0 -9999 0 0
RHEB 0 0 -9999 0 -9999 0 0
EIF4A1 0 0 -9999 0 -9999 0 0
mol:Rapamycin 0 0 -9999 0 -9999 0 0
EEF2 0.015 0 -9999 0 -9999 0 0
eIF4E/4E-BP1 -0.003 0.014 -9999 0 -9999 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.02 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.033 0 -9999 0 -10000 0 0
CDKN1A 0.033 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
FOXO3 0.033 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0 0 -9999 0 -10000 0 0
AKT3 0.014 0.02 -9999 0 -0.42 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0 0 -9999 0 -10000 0 0
RAF1 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.033 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.033 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.021 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAPKAP1 0 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.03 0.025 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
AKT1S1 0.033 0 -9999 0 -10000 0 0
CASP9 0.033 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0 -9999 0 -10000 0 0
CHUK 0.033 0 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.014 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 0.027 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
MDM2 0.032 0.014 -9999 0 -10000 0 0
MAPKKK cascade 0 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0 0.011 -9999 0 -10000 0 0
TSC1/TSC2 0.038 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.01 -9999 0 -10000 0 0
glucose import 0.023 0.041 -9999 0 -0.43 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.023 0.042 -9999 0 -0.43 4 4
GSK3A 0.033 0 -9999 0 -10000 0 0
FOXO1 0.033 0 -9999 0 -10000 0 0
GSK3B 0.033 0 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.57 48 48
G1/S transition of mitotic cell cycle 0.038 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.029 0.039 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
KPNA1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
RHEB 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.036 0.057 -9999 0 -0.53 1 1
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
BAD 0.027 0.021 -9999 0 -10000 0 0
NFKBIA 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.082 -9999 0 -0.74 6 6
BAX 0.027 0.021 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.016 -9999 0 -0.12 1 1
IKBKB 0.041 0.056 -9999 0 -0.5 1 1
MAP2K2 0.038 0.023 -9999 0 -10000 0 0
MAP2K1 0.038 0.023 -9999 0 -10000 0 0
SMPD1 0.017 0.016 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.042 0.056 -9999 0 -0.51 1 1
MAP2K4 0.033 0.021 -9999 0 -10000 0 0
protein ubiquitination 0.043 0.055 -9999 0 -0.5 1 1
EnzymeConsortium:2.7.1.37 0.042 0.025 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.033 0.023 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
mol:ceramide 0.021 0.022 -9999 0 -0.16 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0 0 -9999 0 -10000 0 0
MAP3K1 0.027 0.021 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
RELA/p50 0 0 -9999 0 -10000 0 0
MAPK3 0.04 0.023 -9999 0 -10000 0 0
MAPK1 0.04 0.023 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.036 0.057 -9999 0 -0.53 1 1
KSR1 0.027 0.022 -9999 0 -10000 0 0
MAPK8 0.038 0.02 -9999 0 -10000 0 0
TRAF2 0 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.042 0.054 -9999 0 -0.5 1 1
TNF R/SODD -0.001 0.019 -9999 0 -0.41 1 1
TNF -0.02 0.12 -9999 0 -0.73 13 13
CYCS 0.028 0.021 -9999 0 -10000 0 0
IKBKG 0.042 0.054 -9999 0 -0.5 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.03 0.06 -9999 0 -0.56 1 1
RELA 0 0 -9999 0 -10000 0 0
RIPK1 0 0.001 -9999 0 -10000 0 0
AIFM1 0.028 0.021 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.013 0.078 -9999 0 -0.46 14 14
TNFRSF1A 0 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.023 0.016 -9999 0 -10000 0 0
NSMAF 0.036 0.057 -9999 0 -0.52 1 1
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.027 0 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.025 0.024 -9999 0 -10000 0 0
MAPK12 0.027 0.015 -9999 0 -10000 0 0
CCND1 0.013 0.052 -9999 0 -0.44 6 6
p38 gamma/SNTA1 -0.001 0.013 -9999 0 -10000 0 0
MAP2K3 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.027 0.015 -9999 0 -10000 0 0
MAP2K6 0.021 0.016 -9999 0 -0.34 1 1
MAPT 0.023 0.046 -9999 0 -0.37 6 6
MAPK13 0.02 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.016 -9999 0 -0.34 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.018 -9999 0 -10000 0 0
NFKBIA 0.025 0.018 -9999 0 -0.26 2 2
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.016 -9999 0 -0.34 1 1
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.016 -9999 0 -0.34 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.016 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer -0.001 0.019 -9999 0 -0.41 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.019 0.02 -9999 0 -0.41 1 1
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.019 -9999 0 -0.25 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.001 0.017 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.017 -9999 0 -0.26 1 1
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK -0.002 0.034 -9999 0 -0.74 1 1
I kappa B alpha/PIK3R1 -0.001 0.015 -9999 0 -10000 0 0
cell death -0.001 0.016 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.016 -9999 0 -0.34 1 1
LCK -0.002 0.034 -9999 0 -0.74 1 1
BCL3 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0 0 -9999 0 -10000 0 0
KLHL20 -0.004 0.03 -9999 0 -0.38 1 1
CYFIP2 -0.023 0.13 -9999 0 -0.74 15 15
Rac1/GDP 0.053 0.011 -9999 0 -10000 0 0
ENAH 0 0 -9999 0 -10000 0 0
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.034 -9999 0 -0.25 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.02 -9999 0 -0.43 1 1
RAPGEF1 0.048 0.002 -9999 0 -10000 0 0
CTNND1 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.042 0.005 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.001 0.025 -9999 0 -0.56 1 1
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.014 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 0 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0.052 0.011 -9999 0 -10000 0 0
actin cytoskeleton organization -0.003 0.022 -9999 0 -0.26 1 1
CDC42/GDP 0.052 0.011 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
ITGB7 -0.002 0.034 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.051 0.012 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.006 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.004 0.031 -9999 0 -0.25 7 7
NME1 -0.001 0.026 -9999 0 -0.57 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
WASF2 -0.003 0.017 -9999 0 -0.14 1 1
Rap1/GTP 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.018 -9999 0 -0.4 1 1
CCND1 -0.005 0.039 -9999 0 -0.32 7 7
VAV2 0.04 0.062 -9999 0 -0.74 3 3
RAP1/GDP 0 0.001 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.001 0.017 -9999 0 -10000 0 0
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.053 -9999 0 -0.49 3 3
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 -0.001 0.013 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.025 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.014 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0 0 -9999 0 -9999 0 0
JUP 0 0 -9999 0 -9999 0 0
CDH1 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0 -9999 0 -10000 0 0
AP2 -0.001 0.019 -9999 0 -0.41 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.022 0.12 -9999 0 -0.74 14 14
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 -0.001 0.026 -9999 0 -0.57 1 1
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.022 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.008 0.043 -9999 0 -0.26 14 14
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.015 0.082 -9999 0 -0.48 14 14
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 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 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.013 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.019 -9999 0 -0.41 1 1
RELB -0.001 0.026 -9999 0 -0.57 1 1
NFKB2 0 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.016 -9999 0 -0.35 1 1
regulation of B cell activation -0.001 0.016 -9999 0 -0.35 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 482 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V TCGA.O2.A52S
109_MAP3K5 0.047 0.047 0.047 -0.2
47_PPARGC1A 0 0 0 -0.74
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 -0.57 -0.57 0
105_BMP2 -0.74 0 0 0
131_RELN/VLDLR 0 0 0 -0.43
30_TGFB1/TGF beta receptor Type II 0.016 0.014 0.014 0.013
84_STAT5B -0.0052 0.038 0.038 -0.07
84_STAT5A -0.0052 0.038 0.038 -0.07
Methods & Data
Input

  • Expression Data Normalization = Normal controls 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/LUSC-TP/6044648/LUSC-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)
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